From 0c82b34305769cb741fe93fc606cda43496e70ff Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Thu, 17 Oct 2024 17:18:47 -0600 Subject: [PATCH] Sam/pyproject setup (#104) (#496) Add the pyproject.toml file and make the Cython files compatible with numpy v2. Co-authored-by: Samuel Nichols --- CRISPResso2/CRISPResso2Align.c | 4879 +++++++++-------- CRISPResso2/CRISPResso2Align.pyx | 16 +- CRISPResso2/CRISPRessoCORE.py | 12 +- CRISPResso2/CRISPRessoCOREResources.c | 3135 ++++++----- CRISPResso2/CRISPRessoCompareCORE.py | 4 +- .../CRISPRessoReports/templates/report.html | 2 +- pyproject.toml | 52 + 7 files changed, 4555 insertions(+), 3545 deletions(-) create mode 100644 pyproject.toml diff --git a/CRISPResso2/CRISPResso2Align.c b/CRISPResso2/CRISPResso2Align.c index ee2440ca..c2b422a8 100644 --- a/CRISPResso2/CRISPResso2Align.c +++ b/CRISPResso2/CRISPResso2Align.c @@ -1,21 +1,21 @@ -/* Generated by Cython 3.0.6 */ +/* Generated by Cython 3.0.11 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ - "/opt/conda/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h", - "/opt/conda/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h", - "/opt/conda/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h", - "/opt/conda/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h", - "/opt/conda/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h" + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayobject.h", + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayscalars.h", + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h", + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarraytypes.h", + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ufuncobject.h" ], "extra_compile_args": [ "-w", "-Ofast" ], "include_dirs": [ - "/opt/conda/lib/python3.10/site-packages/numpy/core/include" + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include" ], "name": "CRISPResso2.CRISPResso2Align", "sources": [ @@ -50,10 +50,10 @@ END: Cython Metadata */ #else #define __PYX_EXTRA_ABI_MODULE_NAME "" #endif -#define CYTHON_ABI "3_0_6" __PYX_EXTRA_ABI_MODULE_NAME +#define CYTHON_ABI "3_0_11" __PYX_EXTRA_ABI_MODULE_NAME #define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI #define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "." -#define CYTHON_HEX_VERSION 0x030006F0 +#define CYTHON_HEX_VERSION 0x03000BF0 #define CYTHON_FUTURE_DIVISION 1 #include #ifndef offsetof @@ -145,6 +145,8 @@ END: Cython Metadata */ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 #endif + #undef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 0 #elif defined(PYPY_VERSION) #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 @@ -206,6 +208,8 @@ END: Cython Metadata */ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 #endif + #undef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 0 #elif defined(CYTHON_LIMITED_API) #ifdef Py_LIMITED_API #undef __PYX_LIMITED_VERSION_HEX @@ -224,8 +228,9 @@ END: Cython Metadata */ #define CYTHON_USE_TYPE_SPECS 1 #undef CYTHON_USE_PYTYPE_LOOKUP #define CYTHON_USE_PYTYPE_LOOKUP 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 + #ifndef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif #undef CYTHON_USE_PYLIST_INTERNALS #define CYTHON_USE_PYLIST_INTERNALS 0 #undef CYTHON_USE_UNICODE_INTERNALS @@ -267,6 +272,8 @@ END: Cython Metadata */ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 #endif + #undef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 0 #elif defined(Py_GIL_DISABLED) || defined(Py_NOGIL) #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 0 @@ -276,11 +283,17 @@ END: Cython Metadata */ #ifndef CYTHON_USE_TYPE_SLOTS #define CYTHON_USE_TYPE_SLOTS 1 #endif + #ifndef CYTHON_USE_TYPE_SPECS + #define CYTHON_USE_TYPE_SPECS 0 + #endif #undef CYTHON_USE_PYTYPE_LOOKUP #define CYTHON_USE_PYTYPE_LOOKUP 0 #ifndef CYTHON_USE_ASYNC_SLOTS #define CYTHON_USE_ASYNC_SLOTS 1 #endif + #ifndef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #endif #undef CYTHON_USE_PYLIST_INTERNALS #define CYTHON_USE_PYLIST_INTERNALS 0 #ifndef CYTHON_USE_UNICODE_INTERNALS @@ -288,8 +301,6 @@ END: Cython Metadata */ #endif #undef CYTHON_USE_UNICODE_WRITER #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 #ifndef CYTHON_AVOID_BORROWED_REFS #define CYTHON_AVOID_BORROWED_REFS 0 #endif @@ -301,11 +312,22 @@ END: Cython Metadata */ #endif #undef CYTHON_FAST_THREAD_STATE #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_GIL + #define CYTHON_FAST_GIL 0 + #ifndef CYTHON_METH_FASTCALL + #define CYTHON_METH_FASTCALL 1 + #endif #undef CYTHON_FAST_PYCALL #define CYTHON_FAST_PYCALL 0 + #ifndef CYTHON_PEP487_INIT_SUBCLASS + #define CYTHON_PEP487_INIT_SUBCLASS 1 + #endif #ifndef CYTHON_PEP489_MULTI_PHASE_INIT #define CYTHON_PEP489_MULTI_PHASE_INIT 1 #endif + #ifndef CYTHON_USE_MODULE_STATE + #define CYTHON_USE_MODULE_STATE 0 + #endif #ifndef CYTHON_USE_TP_FINALIZE #define CYTHON_USE_TP_FINALIZE 1 #endif @@ -313,6 +335,12 @@ END: Cython Metadata */ #define CYTHON_USE_DICT_VERSIONS 0 #undef CYTHON_USE_EXC_INFO_STACK #define CYTHON_USE_EXC_INFO_STACK 0 + #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC + #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 + #endif + #ifndef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 0 + #endif #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 @@ -403,6 +431,9 @@ END: Cython Metadata */ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 #endif + #ifndef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 1 + #endif #endif #if !defined(CYTHON_FAST_PYCCALL) #define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) @@ -595,14 +626,14 @@ END: Cython Metadata */ PyObject *exception_table = NULL; PyObject *types_module=NULL, *code_type=NULL, *result=NULL; #if __PYX_LIMITED_VERSION_HEX < 0x030B0000 - PyObject *version_info; // borrowed + PyObject *version_info; PyObject *py_minor_version = NULL; #endif long minor_version = 0; PyObject *type, *value, *traceback; PyErr_Fetch(&type, &value, &traceback); #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000 - minor_version = 11; // we don't yet need to distinguish between versions > 11 + minor_version = 11; #else if (!(version_info = PySys_GetObject("version_info"))) goto end; if (!(py_minor_version = PySequence_GetItem(version_info, 1))) goto end; @@ -660,7 +691,7 @@ END: Cython Metadata */ PyObject *fv, PyObject *cell, PyObject* fn, PyObject *name, int fline, PyObject *lnos) { PyCodeObject *result; - PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0); // we don't have access to __pyx_empty_bytes here + PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0); if (!empty_bytes) return NULL; result = #if PY_VERSION_HEX >= 0x030C0000 @@ -746,8 +777,13 @@ END: Cython Metadata */ typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, Py_ssize_t nargs, PyObject *kwnames); #else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords + #if PY_VERSION_HEX >= 0x030d00A4 + # define __Pyx_PyCFunctionFast PyCFunctionFast + # define __Pyx_PyCFunctionFastWithKeywords PyCFunctionFastWithKeywords + #else + # define __Pyx_PyCFunctionFast _PyCFunctionFast + # define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords + #endif #endif #if CYTHON_METH_FASTCALL #define __Pyx_METH_FASTCALL METH_FASTCALL @@ -1099,7 +1135,7 @@ static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStrWithError(PyObject *dict, #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_Size(o) #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_Size(o) #endif -#if PY_VERSION_HEX >= 0x030d00A1 +#if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1 #define __Pyx_PyImport_AddModuleRef(name) PyImport_AddModuleRef(name) #else static CYTHON_INLINE PyObject *__Pyx_PyImport_AddModuleRef(const char *name) { @@ -1186,7 +1222,7 @@ static CYTHON_INLINE float __PYX_NAN() { #endif #define __PYX_MARK_ERR_POS(f_index, lineno) \ - { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } + { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } #define __PYX_ERR(f_index, lineno, Ln_error) \ { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } @@ -1302,24 +1338,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) #define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) #define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) -#if CYTHON_COMPILING_IN_LIMITED_API -static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const wchar_t *u) -{ - const wchar_t *u_end = u; - while (*u_end++) ; - return (size_t)(u_end - u - 1); -} -#else -static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) -{ - const Py_UNICODE *u_end = u; - while (*u_end++) ; - return (size_t)(u_end - u - 1); -} -#endif #define __Pyx_PyUnicode_FromOrdinal(o) PyUnicode_FromOrdinal((int)o) -#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) -#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) @@ -1369,7 +1388,7 @@ static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); #endif typedef Py_ssize_t __Pyx_compact_pylong; typedef size_t __Pyx_compact_upylong; - #else // Py < 3.12 + #else #define __Pyx_PyLong_IsNeg(x) (Py_SIZE(x) < 0) #define __Pyx_PyLong_IsNonNeg(x) (Py_SIZE(x) >= 0) #define __Pyx_PyLong_IsZero(x) (Py_SIZE(x) == 0) @@ -1659,7 +1678,7 @@ typedef struct { /* #### Code section: numeric_typedefs ### */ -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":730 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":769 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -1668,7 +1687,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":731 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":770 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -1677,7 +1696,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":732 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":771 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -1686,7 +1705,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":733 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":772 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -1695,7 +1714,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":737 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":776 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -1704,7 +1723,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":738 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":777 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1713,7 +1732,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":739 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":778 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1722,7 +1741,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":740 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":779 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1731,7 +1750,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":744 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":783 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1740,7 +1759,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":745 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":784 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1749,43 +1768,25 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":754 - * # The int types are mapped a bit surprising -- - * # numpy.int corresponds to 'l' and numpy.long to 'q' - * ctypedef npy_long int_t # <<<<<<<<<<<<<< - * ctypedef npy_longlong longlong_t +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":791 + * ctypedef double complex complex128_t * - */ -typedef npy_long __pyx_t_5numpy_int_t; - -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":755 - * # numpy.int corresponds to 'l' and numpy.long to 'q' - * ctypedef npy_long int_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< - * - * ctypedef npy_ulong uint_t - */ -typedef npy_longlong __pyx_t_5numpy_longlong_t; - -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":757 - * ctypedef npy_longlong longlong_t - * - * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulonglong_t * */ -typedef npy_ulong __pyx_t_5numpy_uint_t; +typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":758 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":792 * - * ctypedef npy_ulong uint_t + * ctypedef npy_longlong longlong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< * * ctypedef npy_intp intp_t */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":760 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":794 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1794,7 +1795,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":761 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":795 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1803,7 +1804,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":763 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":797 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1812,7 +1813,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":764 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":798 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1821,41 +1822,23 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":765 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":799 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< * - * ctypedef npy_cfloat cfloat_t + * ctypedef float complex cfloat_t */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; /* "CRISPResso2/CRISPResso2Align.pyx":20 * ctypedef void PyObject * - * ctypedef np.int_t DTYPE_INT # <<<<<<<<<<<<<< - * ctypedef np.uint_t DTYPE_UINT - * ctypedef np.int8_t DTYPE_BOOL - */ -typedef __pyx_t_5numpy_int_t __pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT; - -/* "CRISPResso2/CRISPResso2Align.pyx":21 - * - * ctypedef np.int_t DTYPE_INT - * ctypedef np.uint_t DTYPE_UINT # <<<<<<<<<<<<<< - * ctypedef np.int8_t DTYPE_BOOL - * - */ -typedef __pyx_t_5numpy_uint_t __pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_UINT; - -/* "CRISPResso2/CRISPResso2Align.pyx":22 - * ctypedef np.int_t DTYPE_INT - * ctypedef np.uint_t DTYPE_UINT - * ctypedef np.int8_t DTYPE_BOOL # <<<<<<<<<<<<<< + * ctypedef long DTYPE_LONG # <<<<<<<<<<<<<< * * cdef size_t UP = 1, LEFT = 2, DIAG = 3, NONE = 4 */ -typedef __pyx_t_5numpy_int8_t __pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_BOOL; +typedef long __pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG; /* #### Code section: complex_type_declarations ### */ /* Declarations.proto */ #if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) @@ -1881,6 +1864,18 @@ static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(floa #endif static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); +/* Declarations.proto */ +#if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) + #ifdef __cplusplus + typedef ::std::complex< long double > __pyx_t_long_double_complex; + #else + typedef long double _Complex __pyx_t_long_double_complex; + #endif +#else + typedef struct { long double real, imag; } __pyx_t_long_double_complex; +#endif +static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_from_parts(long double, long double); + /* #### Code section: type_declarations ### */ /*--- Type declarations ---*/ @@ -1889,41 +1884,23 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":767 - * ctypedef npy_longdouble longdouble_t +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1095 * - * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< - * ctypedef npy_cdouble cdouble_t - * ctypedef npy_clongdouble clongdouble_t - */ -typedef npy_cfloat __pyx_t_5numpy_cfloat_t; - -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":768 - * - * ctypedef npy_cfloat cfloat_t - * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< - * ctypedef npy_clongdouble clongdouble_t + * # Iterator API added in v1.6 + * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil # <<<<<<<<<<<<<< + * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil * */ -typedef npy_cdouble __pyx_t_5numpy_cdouble_t; +typedef int (*__pyx_t_5numpy_NpyIter_IterNextFunc)(NpyIter *); -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":769 - * ctypedef npy_cfloat cfloat_t - * ctypedef npy_cdouble cdouble_t - * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1096 + * # Iterator API added in v1.6 + * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil + * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil # <<<<<<<<<<<<<< * - * ctypedef npy_cdouble complex_t + * cdef extern from "numpy/arrayobject.h": */ -typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; - -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":771 - * ctypedef npy_clongdouble clongdouble_t - * - * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< - * - * cdef inline object PyArray_MultiIterNew1(a): - */ -typedef npy_cdouble __pyx_t_5numpy_complex_t; +typedef void (*__pyx_t_5numpy_NpyIter_GetMultiIndexFunc)(NpyIter *, npy_intp *); /* "View.MemoryView":114 * @cython.collection_type("sequence") @@ -2222,8 +2199,8 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int #define __Pyx_Arg_NewRef_VARARGS(arg) __Pyx_NewRef(arg) #define __Pyx_Arg_XDECREF_VARARGS(arg) Py_XDECREF(arg) #else - #define __Pyx_Arg_NewRef_VARARGS(arg) arg // no-op - #define __Pyx_Arg_XDECREF_VARARGS(arg) // no-op - arg is borrowed + #define __Pyx_Arg_NewRef_VARARGS(arg) arg + #define __Pyx_Arg_XDECREF_VARARGS(arg) #endif #define __Pyx_NumKwargs_VARARGS(kwds) PyDict_Size(kwds) #define __Pyx_KwValues_VARARGS(args, nargs) NULL @@ -2239,8 +2216,9 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int #else #define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw) #endif - #define __Pyx_Arg_NewRef_FASTCALL(arg) arg // no-op, __Pyx_Arg_FASTCALL is direct and this needs - #define __Pyx_Arg_XDECREF_FASTCALL(arg) // no-op - arg was returned from array + #define __Pyx_Arg_NewRef_FASTCALL(arg) arg /* no-op, __Pyx_Arg_FASTCALL is direct and this needs + to have the same reference counting */ + #define __Pyx_Arg_XDECREF_FASTCALL(arg) #else #define __Pyx_Arg_FASTCALL __Pyx_Arg_VARARGS #define __Pyx_NumKwargs_FASTCALL __Pyx_NumKwargs_VARARGS @@ -2632,11 +2610,7 @@ static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* s static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); /* HasAttr.proto */ -#if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1 -#define __Pyx_HasAttr(o, n) PyObject_HasAttrWithError(o, n) -#else static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); -#endif /* PyObjectLookupSpecial.proto */ #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS @@ -2708,9 +2682,14 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); static void __Pyx_RaiseBufferIndexError(int axis); #define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) -/* PyObject_Str.proto */ -#define __Pyx_PyObject_Str(obj)\ - (likely(PyString_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Str(obj)) +/* PyObject_Unicode.proto */ +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyObject_Unicode(obj)\ + (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Str(obj)) +#else +#define __Pyx_PyObject_Unicode(obj)\ + (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Unicode(obj)) +#endif /* UnicodeConcatInPlace.proto */ # if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 @@ -2807,22 +2786,22 @@ static int __Pyx_setup_reduce(PyObject* type_obj); #endif /* TypeImport.proto */ -#ifndef __PYX_HAVE_RT_ImportType_proto_3_0_6 -#define __PYX_HAVE_RT_ImportType_proto_3_0_6 +#ifndef __PYX_HAVE_RT_ImportType_proto_3_0_11 +#define __PYX_HAVE_RT_ImportType_proto_3_0_11 #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L #include #endif #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L -#define __PYX_GET_STRUCT_ALIGNMENT_3_0_6(s) alignof(s) +#define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) alignof(s) #else -#define __PYX_GET_STRUCT_ALIGNMENT_3_0_6(s) sizeof(void*) +#define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) sizeof(void*) #endif -enum __Pyx_ImportType_CheckSize_3_0_6 { - __Pyx_ImportType_CheckSize_Error_3_0_6 = 0, - __Pyx_ImportType_CheckSize_Warn_3_0_6 = 1, - __Pyx_ImportType_CheckSize_Ignore_3_0_6 = 2 +enum __Pyx_ImportType_CheckSize_3_0_11 { + __Pyx_ImportType_CheckSize_Error_3_0_11 = 0, + __Pyx_ImportType_CheckSize_Warn_3_0_11 = 1, + __Pyx_ImportType_CheckSize_Ignore_3_0_11 = 2 }; -static PyTypeObject *__Pyx_ImportType_3_0_6(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_6 check_size); +static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size); #endif /* FetchSharedCythonModule.proto */ @@ -2915,7 +2894,7 @@ typedef struct { #endif void *defaults; int defaults_pyobjects; - size_t defaults_size; // used by FusedFunction for copying defaults + size_t defaults_size; int flags; PyObject *defaults_tuple; PyObject *defaults_kwdict; @@ -3139,6 +3118,44 @@ static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_i #endif #endif +/* Arithmetic.proto */ +#if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) + #define __Pyx_c_eq_long__double(a, b) ((a)==(b)) + #define __Pyx_c_sum_long__double(a, b) ((a)+(b)) + #define __Pyx_c_diff_long__double(a, b) ((a)-(b)) + #define __Pyx_c_prod_long__double(a, b) ((a)*(b)) + #define __Pyx_c_quot_long__double(a, b) ((a)/(b)) + #define __Pyx_c_neg_long__double(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero_long__double(z) ((z)==(long double)0) + #define __Pyx_c_conj_long__double(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs_long__double(z) (::std::abs(z)) + #define __Pyx_c_pow_long__double(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero_long__double(z) ((z)==0) + #define __Pyx_c_conj_long__double(z) (conjl(z)) + #if 1 + #define __Pyx_c_abs_long__double(z) (cabsl(z)) + #define __Pyx_c_pow_long__double(a, b) (cpowl(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_sum_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_diff_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_prod_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_quot_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_neg_long__double(__pyx_t_long_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_long__double(__pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_conj_long__double(__pyx_t_long_double_complex); + #if 1 + static CYTHON_INLINE long double __Pyx_c_abs_long__double(__pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_pow_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + #endif +#endif + /* MemviewSliceCopyTemplate.proto */ static __Pyx_memviewslice __pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, @@ -3178,16 +3195,16 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); /* CIntFromPy.proto */ -static CYTHON_INLINE npy_long __Pyx_PyInt_As_npy_long(PyObject *); +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); -/* CIntFromPy.proto */ -static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); /* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); +static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); /* CIntFromPy.proto */ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); @@ -3225,6 +3242,18 @@ static PyObject *__pyx_memoryview__get_base(struct __pyx_memoryview_obj *__pyx_v static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ static PyObject *__pyx_memoryviewslice__get_base(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject *__pyx_v_self); /* proto*/ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArrayObject *__pyx_v_self); /* proto*/ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx_v_self); /* proto*/ @@ -3311,7 +3340,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ /* #### Code section: typeinfo ### */ -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT = { "DTYPE_INT", NULL, sizeof(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT), { 0 }, 0, __PYX_IS_UNSIGNED(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT) ? 'U' : 'I', __PYX_IS_UNSIGNED(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT), 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG = { "DTYPE_LONG", NULL, sizeof(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG), { 0 }, 0, __PYX_IS_UNSIGNED(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG) ? 'U' : 'I', __PYX_IS_UNSIGNED(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG), 0 }; static __Pyx_TypeInfo __Pyx_TypeInfo_int = { "int", NULL, sizeof(int), { 0 }, 0, __PYX_IS_UNSIGNED(int) ? 'U' : 'I', __PYX_IS_UNSIGNED(int), 0 }; /* #### Code section: before_global_var ### */ #define __Pyx_MODULE_NAME "CRISPResso2.CRISPResso2Align" @@ -3541,7 +3570,6 @@ static const char __pyx_k_CRISPResso2_CRISPResso2Align[] = "CRISPResso2.CRISPRes static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; static const char __pyx_k_strided_and_direct_or_indirect[] = ""; static const char __pyx_k_ERROR_Mismatch_in_gap_incentive[] = "\nERROR: Mismatch in gap_incentive length (gap_incentive: "; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; static const char __pyx_k_All_dimensions_preceding_dimensi[] = "All dimensions preceding dimension %d must be indexed and not sliced"; static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; static const char __pyx_k_CRISPResso2_CRISPResso2Align_pyx[] = "CRISPResso2/CRISPResso2Align.pyx"; @@ -3557,7 +3585,8 @@ static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension "; static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; +static const char __pyx_k_numpy__core_multiarray_failed_to[] = "numpy._core.multiarray failed to import"; +static const char __pyx_k_numpy__core_umath_failed_to_impo[] = "numpy._core.umath failed to import"; static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; /* #### Code section: decls ### */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ @@ -3845,8 +3874,8 @@ typedef struct { PyObject *__pyx_n_s_nuc2; PyObject *__pyx_n_s_nuc_ords; PyObject *__pyx_n_s_numpy; - PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; - PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; + PyObject *__pyx_kp_u_numpy__core_multiarray_failed_to; + PyObject *__pyx_kp_u_numpy__core_umath_failed_to_impo; PyObject *__pyx_n_s_obj; PyObject *__pyx_n_s_ohidx; PyObject *__pyx_n_s_open; @@ -4177,8 +4206,8 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_n_s_nuc2); Py_CLEAR(clear_module_state->__pyx_n_s_nuc_ords); Py_CLEAR(clear_module_state->__pyx_n_s_numpy); - Py_CLEAR(clear_module_state->__pyx_kp_u_numpy_core_multiarray_failed_to); - Py_CLEAR(clear_module_state->__pyx_kp_u_numpy_core_umath_failed_to_impor); + Py_CLEAR(clear_module_state->__pyx_kp_u_numpy__core_multiarray_failed_to); + Py_CLEAR(clear_module_state->__pyx_kp_u_numpy__core_umath_failed_to_impo); Py_CLEAR(clear_module_state->__pyx_n_s_obj); Py_CLEAR(clear_module_state->__pyx_n_s_ohidx); Py_CLEAR(clear_module_state->__pyx_n_s_open); @@ -4487,8 +4516,8 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_n_s_nuc2); Py_VISIT(traverse_module_state->__pyx_n_s_nuc_ords); Py_VISIT(traverse_module_state->__pyx_n_s_numpy); - Py_VISIT(traverse_module_state->__pyx_kp_u_numpy_core_multiarray_failed_to); - Py_VISIT(traverse_module_state->__pyx_kp_u_numpy_core_umath_failed_to_impor); + Py_VISIT(traverse_module_state->__pyx_kp_u_numpy__core_multiarray_failed_to); + Py_VISIT(traverse_module_state->__pyx_kp_u_numpy__core_umath_failed_to_impo); Py_VISIT(traverse_module_state->__pyx_n_s_obj); Py_VISIT(traverse_module_state->__pyx_n_s_ohidx); Py_VISIT(traverse_module_state->__pyx_n_s_open); @@ -4833,8 +4862,8 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_n_s_nuc2 __pyx_mstate_global->__pyx_n_s_nuc2 #define __pyx_n_s_nuc_ords __pyx_mstate_global->__pyx_n_s_nuc_ords #define __pyx_n_s_numpy __pyx_mstate_global->__pyx_n_s_numpy -#define __pyx_kp_u_numpy_core_multiarray_failed_to __pyx_mstate_global->__pyx_kp_u_numpy_core_multiarray_failed_to -#define __pyx_kp_u_numpy_core_umath_failed_to_impor __pyx_mstate_global->__pyx_kp_u_numpy_core_umath_failed_to_impor +#define __pyx_kp_u_numpy__core_multiarray_failed_to __pyx_mstate_global->__pyx_kp_u_numpy__core_multiarray_failed_to +#define __pyx_kp_u_numpy__core_umath_failed_to_impo __pyx_mstate_global->__pyx_kp_u_numpy__core_umath_failed_to_impo #define __pyx_n_s_obj __pyx_mstate_global->__pyx_n_s_obj #define __pyx_n_s_ohidx __pyx_mstate_global->__pyx_n_s_ohidx #define __pyx_n_s_open __pyx_mstate_global->__pyx_n_s_open @@ -5129,10 +5158,11 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; PyObject *__pyx_t_6 = NULL; - int __pyx_t_7; + unsigned int __pyx_t_7; char *__pyx_t_8; - Py_ssize_t __pyx_t_9; - Py_UCS4 __pyx_t_10; + int __pyx_t_9; + Py_ssize_t __pyx_t_10; + Py_UCS4 __pyx_t_11; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -5358,7 +5388,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ * if dim <= 0: * raise ValueError, f"Invalid shape in axis {idx}: {dim}." */ - __pyx_t_7 = 0; + __pyx_t_9 = 0; __pyx_t_4 = __pyx_v_shape; __Pyx_INCREF(__pyx_t_4); __pyx_t_1 = 0; for (;;) { @@ -5375,11 +5405,11 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_4, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 159, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); #endif - __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_5); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(1, 159, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyIndex_AsSsize_t(__pyx_t_5); 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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_Raise(__pyx_builtin_ValueError, __pyx_t_6, 0, 0); @@ -5610,7 +5640,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ * * @cname('getbuffer') */ - __pyx_t_7 = __pyx_array_allocate_buffer(__pyx_v_self); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(1, 180, __pyx_L1_error) + __pyx_t_9 = __pyx_array_allocate_buffer(__pyx_v_self); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(1, 180, __pyx_L1_error) /* "View.MemoryView":179 * self.dtype_is_object = format == b'O' @@ -8765,7 +8795,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setit * * if have_slices: # <<<<<<<<<<<<<< * obj = self.is_slice(value) - * if obj: + * if obj is not None: */ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_have_slices); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(1, 426, __pyx_L1_error) if (__pyx_t_4) { @@ -8774,7 +8804,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setit * * if have_slices: * obj = self.is_slice(value) # <<<<<<<<<<<<<< - * if obj: + * if obj is not None: * self.setitem_slice_assignment(self[index], obj) */ __pyx_t_1 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->is_slice(__pyx_v_self, __pyx_v_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 427, __pyx_L1_error) @@ -8785,16 +8815,16 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setit /* "View.MemoryView":428 * if have_slices: * obj = self.is_slice(value) - * if obj: # <<<<<<<<<<<<<< + * if obj is not None: # <<<<<<<<<<<<<< * self.setitem_slice_assignment(self[index], obj) * else: */ - __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_obj); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(1, 428, __pyx_L1_error) + __pyx_t_4 = (__pyx_v_obj != Py_None); if (__pyx_t_4) { /* "View.MemoryView":429 * obj = self.is_slice(value) - * if obj: + * if obj is not None: * self.setitem_slice_assignment(self[index], obj) # <<<<<<<<<<<<<< * else: * self.setitem_slice_assign_scalar(self[index], value) @@ -8809,7 +8839,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setit /* "View.MemoryView":428 * if have_slices: * obj = self.is_slice(value) - * if obj: # <<<<<<<<<<<<<< + * if obj is not None: # <<<<<<<<<<<<<< * self.setitem_slice_assignment(self[index], obj) * else: */ @@ -8839,7 +8869,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setit * * if have_slices: # <<<<<<<<<<<<<< * obj = self.is_slice(value) - * if obj: + * if obj is not None: */ goto __pyx_L4; } @@ -9547,9 +9577,10 @@ static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview PyObject *__pyx_t_5 = NULL; PyObject *__pyx_t_6 = NULL; PyObject *__pyx_t_7 = NULL; - int __pyx_t_8; + unsigned int __pyx_t_8; Py_ssize_t __pyx_t_9; int __pyx_t_10; + int __pyx_t_11; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -9704,11 +9735,11 @@ static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview __Pyx_ErrFetch(&__pyx_t_1, &__pyx_t_5, &__pyx_t_6); __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_struct, __pyx_n_s_error); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 498, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_7); - __pyx_t_8 = __Pyx_PyErr_GivenExceptionMatches(__pyx_t_1, __pyx_t_7); + __pyx_t_11 = __Pyx_PyErr_GivenExceptionMatches(__pyx_t_1, __pyx_t_7); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_ErrRestore(__pyx_t_1, __pyx_t_5, __pyx_t_6); __pyx_t_1 = 0; __pyx_t_5 = 0; __pyx_t_6 = 0; - if (__pyx_t_8) { + if (__pyx_t_11) { __Pyx_AddTraceback("View.MemoryView.memoryview.convert_item_to_object", __pyx_clineno, __pyx_lineno, __pyx_filename); if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_5, &__pyx_t_1) < 0) __PYX_ERR(1, 498, __pyx_L5_except_error) __Pyx_XGOTREF(__pyx_t_6); @@ -9793,7 +9824,7 @@ static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryvie PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; - int __pyx_t_6; + unsigned int __pyx_t_6; Py_ssize_t __pyx_t_7; PyObject *__pyx_t_8 = NULL; char *__pyx_t_9; @@ -18267,7 +18298,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView___pyx_unpickle_Enum(CYTHON_UNUSE int __pyx_t_2; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; - int __pyx_t_5; + unsigned int __pyx_t_5; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -18449,7 +18480,7 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ PyObject *__pyx_t_5 = NULL; PyObject *__pyx_t_6 = NULL; PyObject *__pyx_t_7 = NULL; - int __pyx_t_8; + unsigned int __pyx_t_8; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -18569,10 +18600,434 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":245 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 + * + * @property + * cdef inline npy_intp itemsize(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_ELSIZE(self) + * + */ + +static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr *__pyx_v_self) { + npy_intp __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":287 + * @property + * cdef inline npy_intp itemsize(self) noexcept nogil: + * return PyDataType_ELSIZE(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyDataType_ELSIZE(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 + * + * @property + * cdef inline npy_intp itemsize(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_ELSIZE(self) + * + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + * + * @property + * cdef inline npy_intp alignment(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_ALIGNMENT(self) + * + */ + +static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr *__pyx_v_self) { + npy_intp __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":291 + * @property + * cdef inline npy_intp alignment(self) noexcept nogil: + * return PyDataType_ALIGNMENT(self) # <<<<<<<<<<<<<< + * + * # Use fields/names with care as they may be NULL. You must check + */ + __pyx_r = PyDataType_ALIGNMENT(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + * + * @property + * cdef inline npy_intp alignment(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_ALIGNMENT(self) + * + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 + * # for this using PyDataType_HASFIELDS. + * @property + * cdef inline object fields(self): # <<<<<<<<<<<<<< + * return PyDataType_FIELDS(self) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Descr *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1; + __Pyx_RefNannySetupContext("fields", 1); 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+ __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1; + __Pyx_RefNannySetupContext("names", 1); + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":301 + * @property + * cdef inline tuple names(self): + * return PyDataType_NAMES(self) # <<<<<<<<<<<<<< + * + * # Use PyDataType_HASSUBARRAY to test whether this field is + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyDataType_NAMES(__pyx_v_self); + __Pyx_INCREF(((PyObject*)__pyx_t_1)); + __pyx_r = ((PyObject*)__pyx_t_1); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 + * + * @property + * cdef inline tuple names(self): # <<<<<<<<<<<<<< + * return PyDataType_NAMES(self) + * + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 + * # this field via the inline helper method PyDataType_SHAPE. + * @property + * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_SUBARRAY(self) + * + */ + +static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr *__pyx_v_self) { + PyArray_ArrayDescr *__pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":308 + * @property + * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: + * return PyDataType_SUBARRAY(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyDataType_SUBARRAY(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 + * # this field via the inline helper method PyDataType_SHAPE. + * @property + * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_SUBARRAY(self) + * + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 + * + * @property + * cdef inline npy_uint64 flags(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The data types flags.""" + * return PyDataType_FLAGS(self) + */ + +static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr *__pyx_v_self) { + npy_uint64 __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":313 + * cdef inline npy_uint64 flags(self) noexcept nogil: + * """The data types flags.""" + * return PyDataType_FLAGS(self) # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = PyDataType_FLAGS(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 + * + * @property + * cdef inline npy_uint64 flags(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The data types flags.""" + * return PyDataType_FLAGS(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 + * + * @property + * cdef inline int numiter(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The number of arrays that need to be broadcast to the same shape.""" + * return PyArray_MultiIter_NUMITER(self) + */ + +static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject *__pyx_v_self) { + int __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":325 + * cdef inline int numiter(self) noexcept nogil: + * """The number of arrays that need to be broadcast to the same shape.""" + * return PyArray_MultiIter_NUMITER(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_NUMITER(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 + * + * @property + * cdef inline int numiter(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The number of arrays that need to be broadcast to the same shape.""" + * return PyArray_MultiIter_NUMITER(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 + * + * @property + * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The total broadcasted size.""" + * return PyArray_MultiIter_SIZE(self) + */ + +static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject *__pyx_v_self) { + npy_intp __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":330 + * cdef inline npy_intp size(self) noexcept nogil: + * """The total broadcasted size.""" + * return PyArray_MultiIter_SIZE(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_SIZE(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 + * + * @property + * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The total broadcasted size.""" + * return PyArray_MultiIter_SIZE(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 + * + * @property + * cdef inline npy_intp index(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The current (1-d) index into the broadcasted result.""" + * return PyArray_MultiIter_INDEX(self) + */ + +static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject *__pyx_v_self) { + npy_intp __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":335 + * cdef inline npy_intp index(self) noexcept nogil: + * """The current (1-d) index into the broadcasted result.""" + * return PyArray_MultiIter_INDEX(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_INDEX(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 + * + * @property + * cdef inline npy_intp index(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The current (1-d) index into the broadcasted result.""" + * return PyArray_MultiIter_INDEX(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 + * + * @property + * cdef inline int nd(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The number of dimensions in the broadcasted result.""" + * return PyArray_MultiIter_NDIM(self) + */ + +static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject *__pyx_v_self) { + int __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":340 + * cdef inline int nd(self) noexcept nogil: + * """The number of dimensions in the broadcasted result.""" + * return PyArray_MultiIter_NDIM(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_NDIM(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 + * + * @property + * cdef inline int nd(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The number of dimensions in the broadcasted result.""" + * return PyArray_MultiIter_NDIM(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 + * + * @property + * cdef inline npy_intp* dimensions(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The shape of the broadcasted result.""" + * return PyArray_MultiIter_DIMS(self) + */ + +static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject *__pyx_v_self) { + npy_intp *__pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":345 + * cdef inline npy_intp* dimensions(self) noexcept nogil: + * """The shape of the broadcasted result.""" + * return PyArray_MultiIter_DIMS(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 + * + * @property + * cdef inline npy_intp* dimensions(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The shape of the broadcasted result.""" + * return PyArray_MultiIter_DIMS(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 + * + * @property + * cdef inline void** iters(self) noexcept nogil: # <<<<<<<<<<<<<< + * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. + * On return, the iterators are adjusted for broadcasting.""" + */ + +static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject *__pyx_v_self) { + void **__pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":351 + * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. + * On return, the iterators are adjusted for broadcasting.""" + * return PyArray_MultiIter_ITERS(self) # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 + * + * @property + * cdef inline void** iters(self) noexcept nogil: # <<<<<<<<<<<<<< + * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. + * On return, the iterators are adjusted for broadcasting.""" + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 * * @property - * cdef inline PyObject* base(self) nogil: # <<<<<<<<<<<<<< + * cdef inline PyObject* base(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a borrowed reference to the object owning the data/memory. * """ */ @@ -18580,7 +19035,7 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject *__pyx_v_self) { PyObject *__pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":248 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":369 * """Returns a borrowed reference to the object owning the data/memory. * """ * return PyArray_BASE(self) # <<<<<<<<<<<<<< @@ -18590,10 +19045,10 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject __pyx_r = PyArray_BASE(__pyx_v_self); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":245 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 * * @property - * cdef inline PyObject* base(self) nogil: # <<<<<<<<<<<<<< + * cdef inline PyObject* base(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a borrowed reference to the object owning the data/memory. * """ */ @@ -18603,7 +19058,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":251 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 * * @property * cdef inline dtype descr(self): # <<<<<<<<<<<<<< @@ -18617,7 +19072,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray PyArray_Descr *__pyx_t_1; __Pyx_RefNannySetupContext("descr", 1); - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":254 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":375 * """Returns an owned reference to the dtype of the array. * """ * return PyArray_DESCR(self) # <<<<<<<<<<<<<< @@ -18630,7 +19085,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray __pyx_r = ((PyArray_Descr *)__pyx_t_1); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":251 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 * * @property * cdef inline dtype descr(self): # <<<<<<<<<<<<<< @@ -18645,10 +19100,10 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":257 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 * * @property - * cdef inline int ndim(self) nogil: # <<<<<<<<<<<<<< + * cdef inline int ndim(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the number of dimensions in the array. * """ */ @@ -18656,7 +19111,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx_v_self) { int __pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":260 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":381 * """Returns the number of dimensions in the array. * """ * return PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -18666,10 +19121,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx __pyx_r = PyArray_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":257 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 * * @property - * cdef inline int ndim(self) nogil: # <<<<<<<<<<<<<< + * cdef inline int ndim(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the number of dimensions in the array. * """ */ @@ -18679,10 +19134,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":263 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 * * @property - * cdef inline npy_intp *shape(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp *shape(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the dimensions/shape of the array. * The number of elements matches the number of dimensions of the array (ndim). */ @@ -18690,7 +19145,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":268 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":389 * Can return NULL for 0-dimensional arrays. * """ * return PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -18700,10 +19155,10 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec __pyx_r = PyArray_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":263 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 * * @property - * cdef inline npy_intp *shape(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp *shape(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the dimensions/shape of the array. * The number of elements matches the number of dimensions of the array (ndim). */ @@ -18713,10 +19168,10 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":271 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 * * @property - * cdef inline npy_intp *strides(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp *strides(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the strides of the array. * The number of elements matches the number of dimensions of the array (ndim). */ @@ -18724,7 +19179,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":275 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":396 * The number of elements matches the number of dimensions of the array (ndim). * """ * return PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -18734,10 +19189,10 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO __pyx_r = PyArray_STRIDES(__pyx_v_self); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":271 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 * * @property - * cdef inline npy_intp *strides(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp *strides(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the strides of the array. * The number of elements matches the number of dimensions of the array (ndim). */ @@ -18747,10 +19202,10 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":278 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 * * @property - * cdef inline npy_intp size(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the total size (in number of elements) of the array. * """ */ @@ -18758,7 +19213,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":281 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":402 * """Returns the total size (in number of elements) of the array. * """ * return PyArray_SIZE(self) # <<<<<<<<<<<<<< @@ -18768,10 +19223,10 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * __pyx_r = PyArray_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":278 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 * * @property - * cdef inline npy_intp size(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the total size (in number of elements) of the array. * """ */ @@ -18781,10 +19236,10 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":284 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 * * @property - * cdef inline char* data(self) nogil: # <<<<<<<<<<<<<< + * cdef inline char* data(self) noexcept nogil: # <<<<<<<<<<<<<< * """The pointer to the data buffer as a char*. * This is provided for legacy reasons to avoid direct struct field access. */ @@ -18792,20 +19247,20 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__pyx_v_self) { char *__pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":411 * of `PyArray_DATA()` instead, which returns a 'void*'. * """ * return PyArray_BYTES(self) # <<<<<<<<<<<<<< * - * ctypedef unsigned char npy_bool + * */ __pyx_r = PyArray_BYTES(__pyx_v_self); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":284 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 * * @property - * cdef inline char* data(self) nogil: # <<<<<<<<<<<<<< + * cdef inline char* data(self) noexcept nogil: # <<<<<<<<<<<<<< * """The pointer to the data buffer as a char*. * This is provided for legacy reasons to avoid direct struct field access. */ @@ -18815,8 +19270,8 @@ static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__p return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":773 - * ctypedef npy_cdouble complex_t +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 + * ctypedef long double complex clongdouble_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(1, a) @@ -18832,7 +19287,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 1); - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":774 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":807 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< @@ -18840,14 +19295,14 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ * cdef inline object PyArray_MultiIterNew2(a, b): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 774, __pyx_L1_error) + __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 807, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":773 - * ctypedef npy_cdouble complex_t + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 + * ctypedef long double complex clongdouble_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(1, a) @@ -18865,7 +19320,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":776 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -18882,7 +19337,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ int __pyx_clineno = 0; 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} -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":779 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -18932,7 +19387,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 1); - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":780 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":813 * * cdef inline object PyArray_MultiIterNew3(a, b, c): * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< @@ -18940,13 +19395,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ * cdef inline object PyArray_MultiIterNew4(a, b, c, d): */ __Pyx_XDECREF(__pyx_r); 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} -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":986 - * raise ImportError("numpy.core.multiarray failed to import") +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 + * raise ImportError("numpy._core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< * try: @@ -19423,7 +19880,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_umath", 1); - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":987 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -19439,16 +19896,16 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); 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__pyx_L3_error:; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":989 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1030 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< - * raise ImportError("numpy.core.umath failed to import") + * raise ImportError("numpy._core.umath failed to import") * */ __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_umath", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 989, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1030, __pyx_L5_except_error) __Pyx_XGOTREF(__pyx_t_5); __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":990 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 * _import_umath() * except Exception: - * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< + * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< * * cdef inline int import_ufunc() except -1: */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 990, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1031, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 990, __pyx_L5_except_error) + __PYX_ERR(2, 1031, __pyx_L5_except_error) } goto __pyx_L5_except_error; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":987 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -19508,8 +19965,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":986 - * raise ImportError("numpy.core.multiarray failed to import") + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 + * raise ImportError("numpy._core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< * try: @@ -19531,8 +19988,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":992 - * raise ImportError("numpy.core.umath failed to import") +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 + * raise ImportError("numpy._core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< * try: @@ -19555,7 +20012,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_ufunc", 1); - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":993 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -19571,16 +20028,16 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":994 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1035 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< * except Exception: - * raise ImportError("numpy.core.umath failed to import") + * raise ImportError("numpy._core.umath failed to import") */ - __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 994, __pyx_L3_error) + __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1035, __pyx_L3_error) - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":993 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -19594,37 +20051,37 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":995 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1036 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< - * raise ImportError("numpy.core.umath failed to import") + * raise ImportError("numpy._core.umath failed to import") * */ __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_ufunc", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 995, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1036, __pyx_L5_except_error) __Pyx_XGOTREF(__pyx_t_5); __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":996 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1037 * _import_umath() * except Exception: - * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< + * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< * * */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 996, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1037, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 996, __pyx_L5_except_error) + __PYX_ERR(2, 1037, __pyx_L5_except_error) } goto __pyx_L5_except_error; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":993 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -19640,8 +20097,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":992 - * raise ImportError("numpy.core.umath failed to import") + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 + * raise ImportError("numpy._core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< * try: @@ -19663,10 +20120,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":999 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 * * - * cdef inline bint is_timedelta64_object(object obj): # <<<<<<<<<<<<<< + * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.timedelta64)` */ @@ -19674,7 +20131,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1011 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1052 * bool * """ * return PyObject_TypeCheck(obj, &PyTimedeltaArrType_Type) # <<<<<<<<<<<<<< @@ -19684,10 +20141,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyTimedeltaArrType_Type)); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":999 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 * * - * cdef inline bint is_timedelta64_object(object obj): # <<<<<<<<<<<<<< + * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.timedelta64)` */ @@ -19697,10 +20154,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1014 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 * * - * cdef inline bint is_datetime64_object(object obj): # <<<<<<<<<<<<<< + * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.datetime64)` */ @@ -19708,7 +20165,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1026 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1067 * bool * """ * return PyObject_TypeCheck(obj, &PyDatetimeArrType_Type) # <<<<<<<<<<<<<< @@ -19718,10 +20175,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyDatetimeArrType_Type)); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1014 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 * * - * cdef inline bint is_datetime64_object(object obj): # <<<<<<<<<<<<<< + * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.datetime64)` */ @@ -19731,10 +20188,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1029 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 * * - * cdef inline npy_datetime get_datetime64_value(object obj) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy datetime64 object */ @@ -19742,7 +20199,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject *__pyx_v_obj) { npy_datetime __pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1036 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1077 * also needed. That can be found using `get_datetime64_unit`. * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -19752,10 +20209,10 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * __pyx_r = ((PyDatetimeScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1029 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 * * - * cdef inline npy_datetime get_datetime64_value(object obj) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy datetime64 object */ @@ -19765,10 +20222,10 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1039 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 * * - * cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy timedelta64 object */ @@ -19776,7 +20233,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject *__pyx_v_obj) { npy_timedelta __pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1043 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1084 * returns the int64 value underlying scalar numpy timedelta64 object * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -19786,10 +20243,10 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject __pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1039 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 * * - * cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy timedelta64 object */ @@ -19799,10 +20256,10 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject return __pyx_r; } -/* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1046 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 * * - * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<< + * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the unit part of the dtype for a numpy datetime64 object. */ @@ -19810,18 +20267,20 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObject *__pyx_v_obj) { NPY_DATETIMEUNIT __pyx_r; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1050 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1091 * returns the unit part of the dtype for a numpy datetime64 object. * """ * return (obj).obmeta.base # <<<<<<<<<<<<<< + * + * */ __pyx_r = ((NPY_DATETIMEUNIT)((PyDatetimeScalarObject *)__pyx_v_obj)->obmeta.base); goto __pyx_L0; - /* "../../../../opt/conda/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1046 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 * * - * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<< + * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the unit part of the dtype for a numpy datetime64 object. */ @@ -19831,7 +20290,7 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec return __pyx_r; } -/* "CRISPResso2/CRISPResso2Align.pyx":28 +/* "CRISPResso2/CRISPResso2Align.pyx":26 * * * cdef char* get_c_string_with_length(size_t length): # <<<<<<<<<<<<<< @@ -19847,7 +20306,7 @@ static char *__pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(s const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "CRISPResso2/CRISPResso2Align.pyx":29 + /* "CRISPResso2/CRISPResso2Align.pyx":27 * * cdef char* get_c_string_with_length(size_t length): * cdef char* c_string = malloc((length + 1) * sizeof(char)) # <<<<<<<<<<<<<< @@ -19856,7 +20315,7 @@ static char *__pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(s */ __pyx_v_c_string = ((char *)malloc(((__pyx_v_length + 1) * (sizeof(char))))); - /* "CRISPResso2/CRISPResso2Align.pyx":30 + /* "CRISPResso2/CRISPResso2Align.pyx":28 * cdef char* get_c_string_with_length(size_t length): * cdef char* c_string = malloc((length + 1) * sizeof(char)) * if not c_string: # <<<<<<<<<<<<<< @@ -19866,16 +20325,16 @@ static char *__pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(s __pyx_t_1 = (!(__pyx_v_c_string != 0)); if (unlikely(__pyx_t_1)) { - /* "CRISPResso2/CRISPResso2Align.pyx":31 + /* "CRISPResso2/CRISPResso2Align.pyx":29 * cdef char* c_string = malloc((length + 1) * sizeof(char)) * if not c_string: * raise MemoryError() # <<<<<<<<<<<<<< * return c_string * */ - PyErr_NoMemory(); __PYX_ERR(0, 31, __pyx_L1_error) + PyErr_NoMemory(); __PYX_ERR(0, 29, __pyx_L1_error) - /* "CRISPResso2/CRISPResso2Align.pyx":30 + /* "CRISPResso2/CRISPResso2Align.pyx":28 * cdef char* get_c_string_with_length(size_t length): * cdef char* c_string = malloc((length + 1) * sizeof(char)) * if not c_string: # <<<<<<<<<<<<<< @@ -19884,7 +20343,7 @@ static char *__pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(s */ } - /* "CRISPResso2/CRISPResso2Align.pyx":32 + /* "CRISPResso2/CRISPResso2Align.pyx":30 * if not c_string: * raise MemoryError() * return c_string # <<<<<<<<<<<<<< @@ -19894,7 +20353,7 @@ static char *__pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(s __pyx_r = __pyx_v_c_string; goto __pyx_L0; - /* "CRISPResso2/CRISPResso2Align.pyx":28 + /* "CRISPResso2/CRISPResso2Align.pyx":26 * * * cdef char* get_c_string_with_length(size_t length): # <<<<<<<<<<<<<< @@ -19910,7 +20369,7 @@ static char *__pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(s return __pyx_r; } -/* "CRISPResso2/CRISPResso2Align.pyx":35 +/* "CRISPResso2/CRISPResso2Align.pyx":33 * * * def read_matrix(path): # <<<<<<<<<<<<<< @@ -19972,12 +20431,12 @@ PyObject *__pyx_args, PyObject *__pyx_kwds (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); kw_args--; } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 35, __pyx_L3_error) + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 33, __pyx_L3_error) else goto __pyx_L5_argtuple_error; } if (unlikely(kw_args > 0)) { const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "read_matrix") < 0)) __PYX_ERR(0, 35, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "read_matrix") < 0)) __PYX_ERR(0, 33, __pyx_L3_error) } } else if (unlikely(__pyx_nargs != 1)) { goto __pyx_L5_argtuple_error; @@ -19988,7 +20447,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds } goto __pyx_L6_skip; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("read_matrix", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 35, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("read_matrix", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 33, __pyx_L3_error) __pyx_L6_skip:; goto __pyx_L4_argument_unpacking_done; __pyx_L3_error:; @@ -20036,7 +20495,7 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; - int __pyx_t_6; + unsigned int __pyx_t_6; PyObject *__pyx_t_7 = NULL; PyObject *__pyx_t_8 = NULL; PyObject *__pyx_t_9 = NULL; @@ -20044,13 +20503,14 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN Py_ssize_t __pyx_t_11; PyObject *(*__pyx_t_12)(PyObject *); long __pyx_t_13; - PyArrayObject *__pyx_t_14 = NULL; - PyObject *__pyx_t_15 = NULL; + int __pyx_t_14; + PyArrayObject *__pyx_t_15 = NULL; PyObject *__pyx_t_16 = NULL; PyObject *__pyx_t_17 = NULL; PyObject *__pyx_t_18 = NULL; - PyObject *(*__pyx_t_19)(PyObject *); - int __pyx_t_20; + PyObject *__pyx_t_19 = NULL; + PyObject *(*__pyx_t_20)(PyObject *); + int __pyx_t_21; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -20060,16 +20520,16 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN __pyx_pybuffernd_a.data = NULL; __pyx_pybuffernd_a.rcbuffer = &__pyx_pybuffer_a; - /* "CRISPResso2/CRISPResso2Align.pyx":42 + /* "CRISPResso2/CRISPResso2Align.pyx":40 * """ - * cdef np.ndarray[DTYPE_INT, ndim=2] a + * cdef np.ndarray[DTYPE_LONG, ndim=2] a * cdef size_t ai = 0, i # <<<<<<<<<<<<<< * cdef int v, mat_size * */ __pyx_v_ai = 0; - /* "CRISPResso2/CRISPResso2Align.pyx":45 + /* "CRISPResso2/CRISPResso2Align.pyx":43 * cdef int v, mat_size * * with open(path) as fh: # <<<<<<<<<<<<<< @@ -20077,11 +20537,11 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN * while headers is None: */ /*with:*/ { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_open, __pyx_v_path); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 45, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_open, __pyx_v_path); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 43, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyObject_LookupSpecial(__pyx_t_1, __pyx_n_s_exit); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 45, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_LookupSpecial(__pyx_t_1, __pyx_n_s_exit); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 43, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_LookupSpecial(__pyx_t_1, __pyx_n_s_enter); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 45, __pyx_L3_error) + __pyx_t_4 = __Pyx_PyObject_LookupSpecial(__pyx_t_1, __pyx_n_s_enter); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 43, __pyx_L3_error) __Pyx_GOTREF(__pyx_t_4); __pyx_t_5 = NULL; __pyx_t_6 = 0; @@ -20101,7 +20561,7 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN PyObject *__pyx_callargs[2] = {__pyx_t_5, NULL}; __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_6, 0+__pyx_t_6); __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; - if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 45, __pyx_L3_error) + if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 43, __pyx_L3_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } @@ -20120,7 +20580,7 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN __pyx_v_fh = __pyx_t_4; __pyx_t_4 = 0; - /* "CRISPResso2/CRISPResso2Align.pyx":46 + /* "CRISPResso2/CRISPResso2Align.pyx":44 * * with open(path) as fh: * headers = None # <<<<<<<<<<<<<< @@ -20130,7 +20590,7 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN __Pyx_INCREF(Py_None); __pyx_v_headers = ((PyObject*)Py_None); - /* "CRISPResso2/CRISPResso2Align.pyx":47 + /* "CRISPResso2/CRISPResso2Align.pyx":45 * with open(path) as fh: * headers = None * while headers is None: # <<<<<<<<<<<<<< @@ -20141,14 +20601,14 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN __pyx_t_10 = (__pyx_v_headers == ((PyObject*)Py_None)); if (!__pyx_t_10) break; - /* "CRISPResso2/CRISPResso2Align.pyx":48 + /* "CRISPResso2/CRISPResso2Align.pyx":46 * headers = None * while headers is None: * line = fh.readline().strip() # <<<<<<<<<<<<<< * if line[0] == '#': continue * headers = [ord(x) for x in line.split(' ') if x] */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_fh, __pyx_n_s_readline); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 48, __pyx_L7_error) + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_fh, __pyx_n_s_readline); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 46, __pyx_L7_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = NULL; __pyx_t_6 = 0; @@ -20168,11 +20628,11 @@ static PyObject *__pyx_pf_11CRISPResso2_16CRISPResso2Align_read_matrix(CYTHON_UN PyObject *__pyx_callargs[2] = {__pyx_t_5, NULL}; __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_6, 0+__pyx_t_6); __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; - if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 48, __pyx_L7_error) + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 46, __pyx_L7_error) __Pyx_GOTREF(__pyx_t_1); 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+ __pyx_v_iFromMVal = ((__pyx_v_gap_open + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_19 * __pyx_v_mScore.strides[0]) ) + __pyx_t_20 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":196 + /* "CRISPResso2/CRISPResso2Align.pyx":194 * * iFromMVal = gap_open + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] # <<<<<<<<<<<<<< @@ -22874,9 +23334,9 @@ __pyx_t_10 = -1; __pyx_t_21 = __pyx_v_i; __pyx_t_20 = (__pyx_v_j - 1); __pyx_t_19 = __pyx_v_i; - __pyx_v_iExtendVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_21 * __pyx_v_iScore.strides[0]) ) + __pyx_t_20 * __pyx_v_iScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); + __pyx_v_iExtendVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_21 * __pyx_v_iScore.strides[0]) ) + __pyx_t_20 * __pyx_v_iScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":197 + /* "CRISPResso2/CRISPResso2Align.pyx":195 * iFromMVal = gap_open + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: # <<<<<<<<<<<<<< @@ -22886,7 +23346,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_iFromMVal > __pyx_v_iExtendVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":198 + /* "CRISPResso2/CRISPResso2Align.pyx":196 * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: * iScore[i,j] = iFromMVal # <<<<<<<<<<<<<< @@ -22897,7 +23357,7 @@ __pyx_t_10 = -1; __pyx_t_20 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_19 * __pyx_v_iScore.strides[0]) ) + __pyx_t_20 * __pyx_v_iScore.strides[1]) )) = __pyx_v_iFromMVal; - /* "CRISPResso2/CRISPResso2Align.pyx":199 + /* "CRISPResso2/CRISPResso2Align.pyx":197 * if iFromMVal > iExtendVal: * iScore[i,j] = iFromMVal * iPointer[i,j] = MARRAY # <<<<<<<<<<<<<< @@ -22908,7 +23368,7 @@ __pyx_t_10 = -1; __pyx_t_19 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iPointer.data + __pyx_t_20 * __pyx_v_iPointer.strides[0]) ) + __pyx_t_19 * __pyx_v_iPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":197 + /* "CRISPResso2/CRISPResso2Align.pyx":195 * iFromMVal = gap_open + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: # <<<<<<<<<<<<<< @@ -22918,7 +23378,7 @@ __pyx_t_10 = -1; goto __pyx_L12; } - /* "CRISPResso2/CRISPResso2Align.pyx":201 + /* "CRISPResso2/CRISPResso2Align.pyx":199 * iPointer[i,j] = MARRAY * else: * iScore[i,j] = iExtendVal # <<<<<<<<<<<<<< @@ -22930,7 +23390,7 @@ __pyx_t_10 = -1; __pyx_t_20 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_19 * __pyx_v_iScore.strides[0]) ) + __pyx_t_20 * __pyx_v_iScore.strides[1]) )) = __pyx_v_iExtendVal; - /* "CRISPResso2/CRISPResso2Align.pyx":202 + /* "CRISPResso2/CRISPResso2Align.pyx":200 * else: * iScore[i,j] = iExtendVal * iPointer[i,j] = IARRAY # <<<<<<<<<<<<<< @@ -22943,7 +23403,7 @@ __pyx_t_10 = -1; } __pyx_L12:; - /* "CRISPResso2/CRISPResso2Align.pyx":204 + /* "CRISPResso2/CRISPResso2Align.pyx":202 * iPointer[i,j] = IARRAY * * jFromMVal = gap_open + mScore[i - 1, j] + gap_incentive[i-1] # <<<<<<<<<<<<<< @@ -22953,9 +23413,9 @@ __pyx_t_10 = -1; __pyx_t_19 = (__pyx_v_i - 1); __pyx_t_20 = __pyx_v_j; __pyx_t_21 = (__pyx_v_i - 1); - __pyx_v_jFromMVal = ((__pyx_v_gap_open + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_19 * __pyx_v_mScore.strides[0]) ) + __pyx_t_20 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); + __pyx_v_jFromMVal = ((__pyx_v_gap_open + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_19 * __pyx_v_mScore.strides[0]) ) + __pyx_t_20 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":206 + /* "CRISPResso2/CRISPResso2Align.pyx":204 * jFromMVal = gap_open + mScore[i - 1, j] + gap_incentive[i-1] * #no gap incentive here -- J already got the gap incentive when it transitioned from M, so don't add it again if we're extending. * jExtendVal = gap_extend + jScore[i - 1, j] # <<<<<<<<<<<<<< @@ -22966,7 +23426,7 @@ __pyx_t_10 = -1; __pyx_t_20 = __pyx_v_j; __pyx_v_jExtendVal = (__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_21 * __pyx_v_jScore.strides[0]) ) + __pyx_t_20 * __pyx_v_jScore.strides[1]) )))); - /* "CRISPResso2/CRISPResso2Align.pyx":207 + /* "CRISPResso2/CRISPResso2Align.pyx":205 * #no gap incentive here -- J already got the gap incentive when it transitioned from M, so don't add it again if we're extending. * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: # <<<<<<<<<<<<<< @@ -22976,7 +23436,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_jFromMVal > __pyx_v_jExtendVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":208 + /* "CRISPResso2/CRISPResso2Align.pyx":206 * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: * jScore[i,j] = jFromMVal # <<<<<<<<<<<<<< @@ -22987,7 +23447,7 @@ __pyx_t_10 = -1; __pyx_t_21 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_20 * __pyx_v_jScore.strides[0]) ) + __pyx_t_21 * __pyx_v_jScore.strides[1]) )) = __pyx_v_jFromMVal; - /* "CRISPResso2/CRISPResso2Align.pyx":209 + /* "CRISPResso2/CRISPResso2Align.pyx":207 * if jFromMVal > jExtendVal: * jScore[i,j] = jFromMVal * jPointer[i,j] = MARRAY # <<<<<<<<<<<<<< @@ -22998,7 +23458,7 @@ __pyx_t_10 = -1; __pyx_t_20 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jPointer.data + __pyx_t_21 * __pyx_v_jPointer.strides[0]) ) + __pyx_t_20 * __pyx_v_jPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":207 + /* "CRISPResso2/CRISPResso2Align.pyx":205 * #no gap incentive here -- J already got the gap incentive when it transitioned from M, so don't add it again if we're extending. * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: # <<<<<<<<<<<<<< @@ -23008,7 +23468,7 @@ __pyx_t_10 = -1; goto __pyx_L13; } - /* "CRISPResso2/CRISPResso2Align.pyx":211 + /* "CRISPResso2/CRISPResso2Align.pyx":209 * jPointer[i,j] = MARRAY * else: * jScore[i,j] = jExtendVal # <<<<<<<<<<<<<< @@ -23020,7 +23480,7 @@ __pyx_t_10 = -1; __pyx_t_21 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_20 * __pyx_v_jScore.strides[0]) ) + __pyx_t_21 * __pyx_v_jScore.strides[1]) )) = __pyx_v_jExtendVal; - /* "CRISPResso2/CRISPResso2Align.pyx":212 + /* "CRISPResso2/CRISPResso2Align.pyx":210 * else: * jScore[i,j] = jExtendVal * jPointer[i,j] = JARRAY # <<<<<<<<<<<<<< @@ -23033,7 +23493,7 @@ __pyx_t_10 = -1; } __pyx_L13:; - /* "CRISPResso2/CRISPResso2Align.pyx":214 + /* "CRISPResso2/CRISPResso2Align.pyx":212 * jPointer[i,j] = JARRAY * * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23046,9 +23506,9 @@ __pyx_t_10 = -1; __pyx_t_12 = __pyx_v_cj; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_mVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_20 * __pyx_v_mScore.strides[0]) ) + __pyx_t_21 * __pyx_v_mScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_mVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_20 * __pyx_v_mScore.strides[0]) ) + __pyx_t_21 * __pyx_v_mScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":215 + /* "CRISPResso2/CRISPResso2Align.pyx":213 * * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23061,9 +23521,9 @@ __pyx_t_10 = -1; __pyx_t_11 = __pyx_v_cj; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_iVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_21 * __pyx_v_iScore.strides[0]) ) + __pyx_t_20 * __pyx_v_iScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_iVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_21 * __pyx_v_iScore.strides[0]) ) + __pyx_t_20 * __pyx_v_iScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":216 + /* "CRISPResso2/CRISPResso2Align.pyx":214 * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23076,9 +23536,9 @@ __pyx_t_10 = -1; __pyx_t_12 = __pyx_v_cj; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_jVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_20 * __pyx_v_jScore.strides[0]) ) + __pyx_t_21 * __pyx_v_jScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_jVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_20 * __pyx_v_jScore.strides[0]) ) + __pyx_t_21 * __pyx_v_jScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":217 + /* "CRISPResso2/CRISPResso2Align.pyx":215 * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: # <<<<<<<<<<<<<< @@ -23088,7 +23548,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_mVal > __pyx_v_jVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":218 + /* "CRISPResso2/CRISPResso2Align.pyx":216 * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: * if mVal > iVal: # <<<<<<<<<<<<<< @@ -23098,7 +23558,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_mVal > __pyx_v_iVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":219 + /* "CRISPResso2/CRISPResso2Align.pyx":217 * if mVal > jVal: * if mVal > iVal: * mScore[i, j] = mVal # <<<<<<<<<<<<<< @@ -23109,7 +23569,7 @@ __pyx_t_10 = -1; __pyx_t_20 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_21 * __pyx_v_mScore.strides[0]) ) + __pyx_t_20 * __pyx_v_mScore.strides[1]) )) = __pyx_v_mVal; - /* "CRISPResso2/CRISPResso2Align.pyx":220 + /* "CRISPResso2/CRISPResso2Align.pyx":218 * if mVal > iVal: * mScore[i, j] = mVal * mPointer[i, j] = MARRAY # <<<<<<<<<<<<<< @@ -23120,7 +23580,7 @@ __pyx_t_10 = -1; __pyx_t_21 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mPointer.data + __pyx_t_20 * __pyx_v_mPointer.strides[0]) ) + __pyx_t_21 * __pyx_v_mPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":218 + /* "CRISPResso2/CRISPResso2Align.pyx":216 * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: * if mVal > iVal: # <<<<<<<<<<<<<< @@ -23130,7 +23590,7 @@ __pyx_t_10 = -1; goto __pyx_L15; } - /* "CRISPResso2/CRISPResso2Align.pyx":222 + /* "CRISPResso2/CRISPResso2Align.pyx":220 * mPointer[i, j] = MARRAY * else: * mScore[i, j] = iVal # <<<<<<<<<<<<<< @@ -23142,7 +23602,7 @@ __pyx_t_10 = -1; __pyx_t_20 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_21 * __pyx_v_mScore.strides[0]) ) + __pyx_t_20 * __pyx_v_mScore.strides[1]) )) = __pyx_v_iVal; - /* "CRISPResso2/CRISPResso2Align.pyx":223 + /* "CRISPResso2/CRISPResso2Align.pyx":221 * else: * mScore[i, j] = iVal * mPointer[i, j] = IARRAY # <<<<<<<<<<<<<< @@ -23155,7 +23615,7 @@ __pyx_t_10 = -1; } __pyx_L15:; - /* "CRISPResso2/CRISPResso2Align.pyx":217 + /* "CRISPResso2/CRISPResso2Align.pyx":215 * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: # <<<<<<<<<<<<<< @@ -23165,7 +23625,7 @@ __pyx_t_10 = -1; goto __pyx_L14; } - /* "CRISPResso2/CRISPResso2Align.pyx":225 + /* "CRISPResso2/CRISPResso2Align.pyx":223 * mPointer[i, j] = IARRAY * else: * if jVal > iVal: # <<<<<<<<<<<<<< @@ -23176,7 +23636,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_jVal > __pyx_v_iVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":226 + /* "CRISPResso2/CRISPResso2Align.pyx":224 * else: * if jVal > iVal: * mScore[i, j] = jVal # <<<<<<<<<<<<<< @@ -23187,7 +23647,7 @@ __pyx_t_10 = -1; __pyx_t_20 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_21 * __pyx_v_mScore.strides[0]) ) + __pyx_t_20 * __pyx_v_mScore.strides[1]) )) = __pyx_v_jVal; - /* "CRISPResso2/CRISPResso2Align.pyx":227 + /* "CRISPResso2/CRISPResso2Align.pyx":225 * if jVal > iVal: * mScore[i, j] = jVal * mPointer[i, j] = JARRAY # <<<<<<<<<<<<<< @@ -23198,7 +23658,7 @@ __pyx_t_10 = -1; __pyx_t_21 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mPointer.data + __pyx_t_20 * __pyx_v_mPointer.strides[0]) ) + __pyx_t_21 * __pyx_v_mPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_JARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":225 + /* "CRISPResso2/CRISPResso2Align.pyx":223 * mPointer[i, j] = IARRAY * else: * if jVal > iVal: # <<<<<<<<<<<<<< @@ -23208,7 +23668,7 @@ __pyx_t_10 = -1; goto __pyx_L16; } - /* "CRISPResso2/CRISPResso2Align.pyx":229 + /* "CRISPResso2/CRISPResso2Align.pyx":227 * mPointer[i, j] = JARRAY * else: * mScore[i, j] = iVal # <<<<<<<<<<<<<< @@ -23220,7 +23680,7 @@ __pyx_t_10 = -1; __pyx_t_20 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_21 * __pyx_v_mScore.strides[0]) ) + __pyx_t_20 * __pyx_v_mScore.strides[1]) )) = __pyx_v_iVal; - /* "CRISPResso2/CRISPResso2Align.pyx":230 + /* "CRISPResso2/CRISPResso2Align.pyx":228 * else: * mScore[i, j] = iVal * mPointer[i, j] = IARRAY # <<<<<<<<<<<<<< @@ -23237,7 +23697,7 @@ __pyx_t_10 = -1; } } - /* "CRISPResso2/CRISPResso2Align.pyx":236 + /* "CRISPResso2/CRISPResso2Align.pyx":234 * #for last column and last row, ignore gap opening penalty * #last column * j = max_j # <<<<<<<<<<<<<< @@ -23246,7 +23706,7 @@ __pyx_t_10 = -1; */ __pyx_v_j = __pyx_v_max_j; - /* "CRISPResso2/CRISPResso2Align.pyx":237 + /* "CRISPResso2/CRISPResso2Align.pyx":235 * #last column * j = max_j * cj = seqj[j-1] # <<<<<<<<<<<<<< @@ -23255,7 +23715,7 @@ __pyx_t_10 = -1; */ __pyx_v_cj = (__pyx_v_seqj[(__pyx_v_j - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":238 + /* "CRISPResso2/CRISPResso2Align.pyx":236 * j = max_j * cj = seqj[j-1] * for i in range(1, max_i): # <<<<<<<<<<<<<< @@ -23267,7 +23727,7 @@ __pyx_t_10 = -1; for (__pyx_t_15 = 1; __pyx_t_15 < __pyx_t_14; __pyx_t_15+=1) { __pyx_v_i = __pyx_t_15; - /* "CRISPResso2/CRISPResso2Align.pyx":239 + /* "CRISPResso2/CRISPResso2Align.pyx":237 * cj = seqj[j-1] * for i in range(1, max_i): * ci = seqi[i-1] # <<<<<<<<<<<<<< @@ -23276,7 +23736,7 @@ __pyx_t_10 = -1; */ __pyx_v_ci = (__pyx_v_seqi[(__pyx_v_i - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":241 + /* "CRISPResso2/CRISPResso2Align.pyx":239 * ci = seqi[i-1] * * iFromMVal = gap_extend + mScore[i, j - 1] + gap_incentive[i] # <<<<<<<<<<<<<< @@ -23286,9 +23746,9 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_i; __pyx_t_17 = (__pyx_v_j - 1); __pyx_t_18 = __pyx_v_i; - __pyx_v_iFromMVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); + __pyx_v_iFromMVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":242 + /* "CRISPResso2/CRISPResso2Align.pyx":240 * * iFromMVal = gap_extend + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] # <<<<<<<<<<<<<< @@ -23298,9 +23758,9 @@ __pyx_t_10 = -1; __pyx_t_18 = __pyx_v_i; __pyx_t_17 = (__pyx_v_j - 1); __pyx_t_16 = __pyx_v_i; - __pyx_v_iExtendVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_18 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); + __pyx_v_iExtendVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_18 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":243 + /* "CRISPResso2/CRISPResso2Align.pyx":241 * iFromMVal = gap_extend + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: # <<<<<<<<<<<<<< @@ -23310,7 +23770,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_iFromMVal > __pyx_v_iExtendVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":244 + /* "CRISPResso2/CRISPResso2Align.pyx":242 * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: * iScore[i,j] = iFromMVal # <<<<<<<<<<<<<< @@ -23321,7 +23781,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_16 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) )) = __pyx_v_iFromMVal; - /* "CRISPResso2/CRISPResso2Align.pyx":245 + /* "CRISPResso2/CRISPResso2Align.pyx":243 * if iFromMVal > iExtendVal: * iScore[i,j] = iFromMVal * iPointer[i,j] = MARRAY # <<<<<<<<<<<<<< @@ -23332,7 +23792,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iPointer.data + __pyx_t_17 * __pyx_v_iPointer.strides[0]) ) + __pyx_t_16 * __pyx_v_iPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":243 + /* "CRISPResso2/CRISPResso2Align.pyx":241 * iFromMVal = gap_extend + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: # <<<<<<<<<<<<<< @@ -23342,7 +23802,7 @@ __pyx_t_10 = -1; goto __pyx_L19; } - /* "CRISPResso2/CRISPResso2Align.pyx":247 + /* "CRISPResso2/CRISPResso2Align.pyx":245 * iPointer[i,j] = MARRAY * else: * iScore[i,j] = iExtendVal # <<<<<<<<<<<<<< @@ -23354,7 +23814,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_16 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) )) = __pyx_v_iExtendVal; - /* "CRISPResso2/CRISPResso2Align.pyx":248 + /* "CRISPResso2/CRISPResso2Align.pyx":246 * else: * iScore[i,j] = iExtendVal * iPointer[i,j] = IARRAY # <<<<<<<<<<<<<< @@ -23367,7 +23827,7 @@ __pyx_t_10 = -1; } __pyx_L19:; - /* "CRISPResso2/CRISPResso2Align.pyx":250 + /* "CRISPResso2/CRISPResso2Align.pyx":248 * iPointer[i,j] = IARRAY * * jFromMVal = gap_extend + mScore[i - 1, j] + gap_incentive[i-1] # <<<<<<<<<<<<<< @@ -23377,9 +23837,9 @@ __pyx_t_10 = -1; __pyx_t_16 = (__pyx_v_i - 1); __pyx_t_17 = __pyx_v_j; __pyx_t_18 = (__pyx_v_i - 1); - __pyx_v_jFromMVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); + __pyx_v_jFromMVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":251 + /* "CRISPResso2/CRISPResso2Align.pyx":249 * * jFromMVal = gap_extend + mScore[i - 1, j] + gap_incentive[i-1] * jExtendVal = gap_extend + jScore[i - 1, j] # <<<<<<<<<<<<<< @@ -23390,7 +23850,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; __pyx_v_jExtendVal = (__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_18 * __pyx_v_jScore.strides[0]) ) + __pyx_t_17 * __pyx_v_jScore.strides[1]) )))); - /* "CRISPResso2/CRISPResso2Align.pyx":252 + /* "CRISPResso2/CRISPResso2Align.pyx":250 * jFromMVal = gap_extend + mScore[i - 1, j] + gap_incentive[i-1] * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: # <<<<<<<<<<<<<< @@ -23400,7 +23860,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_jFromMVal > __pyx_v_jExtendVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":253 + /* "CRISPResso2/CRISPResso2Align.pyx":251 * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: * jScore[i,j] = jFromMVal # <<<<<<<<<<<<<< @@ -23411,7 +23871,7 @@ __pyx_t_10 = -1; __pyx_t_18 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_17 * __pyx_v_jScore.strides[0]) ) + __pyx_t_18 * __pyx_v_jScore.strides[1]) )) = __pyx_v_jFromMVal; - /* "CRISPResso2/CRISPResso2Align.pyx":254 + /* "CRISPResso2/CRISPResso2Align.pyx":252 * if jFromMVal > jExtendVal: * jScore[i,j] = jFromMVal * jPointer[i,j] = MARRAY # <<<<<<<<<<<<<< @@ -23422,7 +23882,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jPointer.data + __pyx_t_18 * __pyx_v_jPointer.strides[0]) ) + __pyx_t_17 * __pyx_v_jPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":252 + /* "CRISPResso2/CRISPResso2Align.pyx":250 * jFromMVal = gap_extend + mScore[i - 1, j] + gap_incentive[i-1] * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: # <<<<<<<<<<<<<< @@ -23432,7 +23892,7 @@ __pyx_t_10 = -1; goto __pyx_L20; } - /* "CRISPResso2/CRISPResso2Align.pyx":256 + /* "CRISPResso2/CRISPResso2Align.pyx":254 * jPointer[i,j] = MARRAY * else: * jScore[i,j] = jExtendVal # <<<<<<<<<<<<<< @@ -23444,7 +23904,7 @@ __pyx_t_10 = -1; __pyx_t_18 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_17 * __pyx_v_jScore.strides[0]) ) + __pyx_t_18 * __pyx_v_jScore.strides[1]) )) = __pyx_v_jExtendVal; - /* "CRISPResso2/CRISPResso2Align.pyx":257 + /* "CRISPResso2/CRISPResso2Align.pyx":255 * else: * jScore[i,j] = jExtendVal * jPointer[i,j] = JARRAY # <<<<<<<<<<<<<< @@ -23457,7 +23917,7 @@ __pyx_t_10 = -1; } __pyx_L20:; - /* "CRISPResso2/CRISPResso2Align.pyx":259 + /* "CRISPResso2/CRISPResso2Align.pyx":257 * jPointer[i,j] = JARRAY * * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23470,9 +23930,9 @@ __pyx_t_10 = -1; __pyx_t_11 = __pyx_v_cj; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_mVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_17 * __pyx_v_mScore.strides[0]) ) + __pyx_t_18 * __pyx_v_mScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_mVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_17 * __pyx_v_mScore.strides[0]) ) + __pyx_t_18 * __pyx_v_mScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":260 + /* "CRISPResso2/CRISPResso2Align.pyx":258 * * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23485,9 +23945,9 @@ __pyx_t_10 = -1; __pyx_t_12 = __pyx_v_cj; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_iVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_18 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_iVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_18 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":261 + /* "CRISPResso2/CRISPResso2Align.pyx":259 * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23500,9 +23960,9 @@ __pyx_t_10 = -1; __pyx_t_11 = __pyx_v_cj; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_jVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_17 * __pyx_v_jScore.strides[0]) ) + __pyx_t_18 * __pyx_v_jScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_jVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_17 * __pyx_v_jScore.strides[0]) ) + __pyx_t_18 * __pyx_v_jScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":262 + /* "CRISPResso2/CRISPResso2Align.pyx":260 * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: # <<<<<<<<<<<<<< @@ -23512,7 +23972,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_mVal > __pyx_v_jVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":263 + /* "CRISPResso2/CRISPResso2Align.pyx":261 * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: * if mVal > iVal: # <<<<<<<<<<<<<< @@ -23522,7 +23982,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_mVal > __pyx_v_iVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":264 + /* "CRISPResso2/CRISPResso2Align.pyx":262 * if mVal > jVal: * if mVal > iVal: * mScore[i, j] = mVal # <<<<<<<<<<<<<< @@ -23533,7 +23993,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_18 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )) = __pyx_v_mVal; - /* "CRISPResso2/CRISPResso2Align.pyx":265 + /* "CRISPResso2/CRISPResso2Align.pyx":263 * if mVal > iVal: * mScore[i, j] = mVal * mPointer[i, j] = MARRAY # <<<<<<<<<<<<<< @@ -23544,7 +24004,7 @@ __pyx_t_10 = -1; __pyx_t_18 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mPointer.data + __pyx_t_17 * __pyx_v_mPointer.strides[0]) ) + __pyx_t_18 * __pyx_v_mPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":263 + /* "CRISPResso2/CRISPResso2Align.pyx":261 * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: * if mVal > iVal: # <<<<<<<<<<<<<< @@ -23554,7 +24014,7 @@ __pyx_t_10 = -1; goto __pyx_L22; } - /* "CRISPResso2/CRISPResso2Align.pyx":267 + /* "CRISPResso2/CRISPResso2Align.pyx":265 * mPointer[i, j] = MARRAY * else: * mScore[i, j] = iVal # <<<<<<<<<<<<<< @@ -23566,7 +24026,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_18 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )) = __pyx_v_iVal; - /* "CRISPResso2/CRISPResso2Align.pyx":268 + /* "CRISPResso2/CRISPResso2Align.pyx":266 * else: * mScore[i, j] = iVal * mPointer[i, j] = IARRAY # <<<<<<<<<<<<<< @@ -23579,7 +24039,7 @@ __pyx_t_10 = -1; } __pyx_L22:; - /* "CRISPResso2/CRISPResso2Align.pyx":262 + /* "CRISPResso2/CRISPResso2Align.pyx":260 * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: # <<<<<<<<<<<<<< @@ -23589,7 +24049,7 @@ __pyx_t_10 = -1; goto __pyx_L21; } - /* "CRISPResso2/CRISPResso2Align.pyx":270 + /* "CRISPResso2/CRISPResso2Align.pyx":268 * mPointer[i, j] = IARRAY * else: * if jVal > iVal: # <<<<<<<<<<<<<< @@ -23600,7 +24060,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_jVal > __pyx_v_iVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":271 + /* "CRISPResso2/CRISPResso2Align.pyx":269 * else: * if jVal > iVal: * mScore[i, j] = jVal # <<<<<<<<<<<<<< @@ -23611,7 +24071,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_18 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )) = __pyx_v_jVal; - /* "CRISPResso2/CRISPResso2Align.pyx":272 + /* "CRISPResso2/CRISPResso2Align.pyx":270 * if jVal > iVal: * mScore[i, j] = jVal * mPointer[i, j] = JARRAY # <<<<<<<<<<<<<< @@ -23622,7 +24082,7 @@ __pyx_t_10 = -1; __pyx_t_18 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mPointer.data + __pyx_t_17 * __pyx_v_mPointer.strides[0]) ) + __pyx_t_18 * __pyx_v_mPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_JARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":270 + /* "CRISPResso2/CRISPResso2Align.pyx":268 * mPointer[i, j] = IARRAY * else: * if jVal > iVal: # <<<<<<<<<<<<<< @@ -23632,7 +24092,7 @@ __pyx_t_10 = -1; goto __pyx_L23; } - /* "CRISPResso2/CRISPResso2Align.pyx":274 + /* "CRISPResso2/CRISPResso2Align.pyx":272 * mPointer[i, j] = JARRAY * else: * mScore[i, j] = iVal # <<<<<<<<<<<<<< @@ -23644,7 +24104,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_18 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )) = __pyx_v_iVal; - /* "CRISPResso2/CRISPResso2Align.pyx":275 + /* "CRISPResso2/CRISPResso2Align.pyx":273 * else: * mScore[i, j] = iVal * mPointer[i, j] = IARRAY # <<<<<<<<<<<<<< @@ -23660,7 +24120,7 @@ __pyx_t_10 = -1; __pyx_L21:; } - /* "CRISPResso2/CRISPResso2Align.pyx":279 + /* "CRISPResso2/CRISPResso2Align.pyx":277 * * #last row * i = max_i # <<<<<<<<<<<<<< @@ -23669,7 +24129,7 @@ __pyx_t_10 = -1; */ __pyx_v_i = __pyx_v_max_i; - /* "CRISPResso2/CRISPResso2Align.pyx":280 + /* "CRISPResso2/CRISPResso2Align.pyx":278 * #last row * i = max_i * ci = seqi[i - 1] # <<<<<<<<<<<<<< @@ -23678,7 +24138,7 @@ __pyx_t_10 = -1; */ __pyx_v_ci = (__pyx_v_seqi[(__pyx_v_i - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":281 + /* "CRISPResso2/CRISPResso2Align.pyx":279 * i = max_i * ci = seqi[i - 1] * for j in range(1, max_j+1): # <<<<<<<<<<<<<< @@ -23690,7 +24150,7 @@ __pyx_t_10 = -1; for (__pyx_t_15 = 1; __pyx_t_15 < __pyx_t_14; __pyx_t_15+=1) { __pyx_v_j = __pyx_t_15; - /* "CRISPResso2/CRISPResso2Align.pyx":282 + /* "CRISPResso2/CRISPResso2Align.pyx":280 * ci = seqi[i - 1] * for j in range(1, max_j+1): * cj = seqj[j - 1] # <<<<<<<<<<<<<< @@ -23699,7 +24159,7 @@ __pyx_t_10 = -1; */ __pyx_v_cj = (__pyx_v_seqj[(__pyx_v_j - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":284 + /* "CRISPResso2/CRISPResso2Align.pyx":282 * cj = seqj[j - 1] * * iFromMVal = gap_extend + mScore[i, j - 1] + gap_incentive[i] # <<<<<<<<<<<<<< @@ -23709,9 +24169,9 @@ __pyx_t_10 = -1; __pyx_t_18 = __pyx_v_i; __pyx_t_17 = (__pyx_v_j - 1); __pyx_t_16 = __pyx_v_i; - __pyx_v_iFromMVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_18 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); + __pyx_v_iFromMVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_18 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":285 + /* "CRISPResso2/CRISPResso2Align.pyx":283 * * iFromMVal = gap_extend + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] # <<<<<<<<<<<<<< @@ -23721,9 +24181,9 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_i; __pyx_t_17 = (__pyx_v_j - 1); __pyx_t_18 = __pyx_v_i; - __pyx_v_iExtendVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_16 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); + __pyx_v_iExtendVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_16 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":286 + /* "CRISPResso2/CRISPResso2Align.pyx":284 * iFromMVal = gap_extend + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: # <<<<<<<<<<<<<< @@ -23733,7 +24193,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_iFromMVal > __pyx_v_iExtendVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":287 + /* "CRISPResso2/CRISPResso2Align.pyx":285 * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: * iScore[i,j] = iFromMVal # <<<<<<<<<<<<<< @@ -23744,7 +24204,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_18 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) )) = __pyx_v_iFromMVal; - /* "CRISPResso2/CRISPResso2Align.pyx":288 + /* "CRISPResso2/CRISPResso2Align.pyx":286 * if iFromMVal > iExtendVal: * iScore[i,j] = iFromMVal * iPointer[i,j] = MARRAY # <<<<<<<<<<<<<< @@ -23755,7 +24215,7 @@ __pyx_t_10 = -1; __pyx_t_18 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iPointer.data + __pyx_t_17 * __pyx_v_iPointer.strides[0]) ) + __pyx_t_18 * __pyx_v_iPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":286 + /* "CRISPResso2/CRISPResso2Align.pyx":284 * iFromMVal = gap_extend + mScore[i, j - 1] + gap_incentive[i] * iExtendVal = gap_extend + iScore[i, j - 1] + gap_incentive[i] * if iFromMVal > iExtendVal: # <<<<<<<<<<<<<< @@ -23765,7 +24225,7 @@ __pyx_t_10 = -1; goto __pyx_L26; } - /* "CRISPResso2/CRISPResso2Align.pyx":290 + /* "CRISPResso2/CRISPResso2Align.pyx":288 * iPointer[i,j] = MARRAY * else: * iScore[i,j] = iExtendVal # <<<<<<<<<<<<<< @@ -23777,7 +24237,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_18 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) )) = __pyx_v_iExtendVal; - /* "CRISPResso2/CRISPResso2Align.pyx":291 + /* "CRISPResso2/CRISPResso2Align.pyx":289 * else: * iScore[i,j] = iExtendVal * iPointer[i,j] = IARRAY # <<<<<<<<<<<<<< @@ -23790,7 +24250,7 @@ __pyx_t_10 = -1; } __pyx_L26:; - /* "CRISPResso2/CRISPResso2Align.pyx":293 + /* "CRISPResso2/CRISPResso2Align.pyx":291 * iPointer[i,j] = IARRAY * * jFromMVal = gap_extend + mScore[i - 1, j] + gap_incentive[i-1] # <<<<<<<<<<<<<< @@ -23800,9 +24260,9 @@ __pyx_t_10 = -1; __pyx_t_18 = (__pyx_v_i - 1); __pyx_t_17 = __pyx_v_j; __pyx_t_16 = (__pyx_v_i - 1); - __pyx_v_jFromMVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_18 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); + __pyx_v_jFromMVal = ((__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_18 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )))) + (*__Pyx_BufPtrStrided1d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_gap_incentive.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_gap_incentive.diminfo[0].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":294 + /* "CRISPResso2/CRISPResso2Align.pyx":292 * * jFromMVal = gap_extend + mScore[i - 1, j] + gap_incentive[i-1] * jExtendVal = gap_extend + jScore[i - 1, j] # <<<<<<<<<<<<<< @@ -23813,7 +24273,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; __pyx_v_jExtendVal = (__pyx_v_gap_extend + (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_16 * __pyx_v_jScore.strides[0]) ) + __pyx_t_17 * __pyx_v_jScore.strides[1]) )))); - /* "CRISPResso2/CRISPResso2Align.pyx":295 + /* "CRISPResso2/CRISPResso2Align.pyx":293 * jFromMVal = gap_extend + mScore[i - 1, j] + gap_incentive[i-1] * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: # <<<<<<<<<<<<<< @@ -23823,7 +24283,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_jFromMVal > __pyx_v_jExtendVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":296 + /* "CRISPResso2/CRISPResso2Align.pyx":294 * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: * jScore[i,j] = jFromMVal # <<<<<<<<<<<<<< @@ -23834,7 +24294,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_17 * __pyx_v_jScore.strides[0]) ) + __pyx_t_16 * __pyx_v_jScore.strides[1]) )) = __pyx_v_jFromMVal; - /* "CRISPResso2/CRISPResso2Align.pyx":297 + /* "CRISPResso2/CRISPResso2Align.pyx":295 * if jFromMVal > jExtendVal: * jScore[i,j] = jFromMVal * jPointer[i,j] = MARRAY # <<<<<<<<<<<<<< @@ -23845,7 +24305,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jPointer.data + __pyx_t_16 * __pyx_v_jPointer.strides[0]) ) + __pyx_t_17 * __pyx_v_jPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":295 + /* "CRISPResso2/CRISPResso2Align.pyx":293 * jFromMVal = gap_extend + mScore[i - 1, j] + gap_incentive[i-1] * jExtendVal = gap_extend + jScore[i - 1, j] * if jFromMVal > jExtendVal: # <<<<<<<<<<<<<< @@ -23855,7 +24315,7 @@ __pyx_t_10 = -1; goto __pyx_L27; } - /* "CRISPResso2/CRISPResso2Align.pyx":299 + /* "CRISPResso2/CRISPResso2Align.pyx":297 * jPointer[i,j] = MARRAY * else: * jScore[i,j] = jExtendVal # <<<<<<<<<<<<<< @@ -23867,7 +24327,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_17 * __pyx_v_jScore.strides[0]) ) + __pyx_t_16 * __pyx_v_jScore.strides[1]) )) = __pyx_v_jExtendVal; - /* "CRISPResso2/CRISPResso2Align.pyx":300 + /* "CRISPResso2/CRISPResso2Align.pyx":298 * else: * jScore[i,j] = jExtendVal * jPointer[i,j] = JARRAY # <<<<<<<<<<<<<< @@ -23880,7 +24340,7 @@ __pyx_t_10 = -1; } __pyx_L27:; - /* "CRISPResso2/CRISPResso2Align.pyx":303 + /* "CRISPResso2/CRISPResso2Align.pyx":301 * * * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23893,9 +24353,9 @@ __pyx_t_10 = -1; __pyx_t_12 = __pyx_v_cj; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_mVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_17 * __pyx_v_mScore.strides[0]) ) + __pyx_t_16 * __pyx_v_mScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_mVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_17 * __pyx_v_mScore.strides[0]) ) + __pyx_t_16 * __pyx_v_mScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":304 + /* "CRISPResso2/CRISPResso2Align.pyx":302 * * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23908,9 +24368,9 @@ __pyx_t_10 = -1; __pyx_t_11 = __pyx_v_cj; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_iVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_16 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_iVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_16 * __pyx_v_iScore.strides[0]) ) + __pyx_t_17 * __pyx_v_iScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":305 + /* "CRISPResso2/CRISPResso2Align.pyx":303 * mVal = mScore[i - 1, j - 1] + matrix[ci,cj] * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] # <<<<<<<<<<<<<< @@ -23923,9 +24383,9 @@ __pyx_t_10 = -1; __pyx_t_12 = __pyx_v_cj; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_matrix.diminfo[0].shape; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_matrix.diminfo[1].shape; - __pyx_v_jVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_17 * __pyx_v_jScore.strides[0]) ) + __pyx_t_16 * __pyx_v_jScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_INT *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); + __pyx_v_jVal = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_17 * __pyx_v_jScore.strides[0]) ) + __pyx_t_16 * __pyx_v_jScore.strides[1]) ))) + (*__Pyx_BufPtrStrided2d(__pyx_t_11CRISPResso2_16CRISPResso2Align_DTYPE_LONG *, __pyx_pybuffernd_matrix.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_matrix.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_matrix.diminfo[1].strides))); - /* "CRISPResso2/CRISPResso2Align.pyx":306 + /* "CRISPResso2/CRISPResso2Align.pyx":304 * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: # <<<<<<<<<<<<<< @@ -23935,7 +24395,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_mVal > __pyx_v_jVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":307 + /* "CRISPResso2/CRISPResso2Align.pyx":305 * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: * if mVal > iVal: # <<<<<<<<<<<<<< @@ -23945,7 +24405,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_mVal > __pyx_v_iVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":308 + /* "CRISPResso2/CRISPResso2Align.pyx":306 * if mVal > jVal: * if mVal > iVal: * mScore[i, j] = mVal # <<<<<<<<<<<<<< @@ -23956,7 +24416,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )) = __pyx_v_mVal; - /* "CRISPResso2/CRISPResso2Align.pyx":309 + /* "CRISPResso2/CRISPResso2Align.pyx":307 * if mVal > iVal: * mScore[i, j] = mVal * mPointer[i, j] = MARRAY # <<<<<<<<<<<<<< @@ -23967,7 +24427,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mPointer.data + __pyx_t_17 * __pyx_v_mPointer.strides[0]) ) + __pyx_t_16 * __pyx_v_mPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":307 + /* "CRISPResso2/CRISPResso2Align.pyx":305 * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: * if mVal > iVal: # <<<<<<<<<<<<<< @@ -23977,7 +24437,7 @@ __pyx_t_10 = -1; goto __pyx_L29; } - /* "CRISPResso2/CRISPResso2Align.pyx":311 + /* "CRISPResso2/CRISPResso2Align.pyx":309 * mPointer[i, j] = MARRAY * else: * mScore[i, j] = iVal # <<<<<<<<<<<<<< @@ -23989,7 +24449,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )) = __pyx_v_iVal; - /* "CRISPResso2/CRISPResso2Align.pyx":312 + /* "CRISPResso2/CRISPResso2Align.pyx":310 * else: * mScore[i, j] = iVal * mPointer[i, j] = IARRAY # <<<<<<<<<<<<<< @@ -24002,7 +24462,7 @@ __pyx_t_10 = -1; } __pyx_L29:; - /* "CRISPResso2/CRISPResso2Align.pyx":306 + /* "CRISPResso2/CRISPResso2Align.pyx":304 * iVal = iScore[i - 1, j - 1] + matrix[ci,cj] * jVal = jScore[i - 1, j - 1] + matrix[ci,cj] * if mVal > jVal: # <<<<<<<<<<<<<< @@ -24012,7 +24472,7 @@ __pyx_t_10 = -1; goto __pyx_L28; } - /* "CRISPResso2/CRISPResso2Align.pyx":314 + /* "CRISPResso2/CRISPResso2Align.pyx":312 * mPointer[i, j] = IARRAY * else: * if jVal > iVal: # <<<<<<<<<<<<<< @@ -24023,7 +24483,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_jVal > __pyx_v_iVal); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":315 + /* "CRISPResso2/CRISPResso2Align.pyx":313 * else: * if jVal > iVal: * mScore[i, j] = jVal # <<<<<<<<<<<<<< @@ -24034,7 +24494,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )) = __pyx_v_jVal; - /* "CRISPResso2/CRISPResso2Align.pyx":316 + /* "CRISPResso2/CRISPResso2Align.pyx":314 * if jVal > iVal: * mScore[i, j] = jVal * mPointer[i, j] = JARRAY # <<<<<<<<<<<<<< @@ -24045,7 +24505,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mPointer.data + __pyx_t_17 * __pyx_v_mPointer.strides[0]) ) + __pyx_t_16 * __pyx_v_mPointer.strides[1]) )) = __pyx_v_11CRISPResso2_16CRISPResso2Align_JARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":314 + /* "CRISPResso2/CRISPResso2Align.pyx":312 * mPointer[i, j] = IARRAY * else: * if jVal > iVal: # <<<<<<<<<<<<<< @@ -24055,7 +24515,7 @@ __pyx_t_10 = -1; goto __pyx_L30; } - /* "CRISPResso2/CRISPResso2Align.pyx":318 + /* "CRISPResso2/CRISPResso2Align.pyx":316 * mPointer[i, j] = JARRAY * else: * mScore[i, j] = iVal # <<<<<<<<<<<<<< @@ -24067,7 +24527,7 @@ __pyx_t_10 = -1; __pyx_t_17 = __pyx_v_j; *((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_17 * __pyx_v_mScore.strides[1]) )) = __pyx_v_iVal; - /* "CRISPResso2/CRISPResso2Align.pyx":319 + /* "CRISPResso2/CRISPResso2Align.pyx":317 * else: * mScore[i, j] = iVal * mPointer[i, j] = IARRAY # <<<<<<<<<<<<<< @@ -24083,7 +24543,7 @@ __pyx_t_10 = -1; __pyx_L28:; } - /* "CRISPResso2/CRISPResso2Align.pyx":340 + /* "CRISPResso2/CRISPResso2Align.pyx":338 * # print("\n"), * * seqlen = max_i + max_j # <<<<<<<<<<<<<< @@ -24092,27 +24552,27 @@ __pyx_t_10 = -1; */ __pyx_v_seqlen = (__pyx_v_max_i + __pyx_v_max_j); - /* "CRISPResso2/CRISPResso2Align.pyx":341 + /* "CRISPResso2/CRISPResso2Align.pyx":339 * * seqlen = max_i + max_j * cdef char* tmp_align_j = get_c_string_with_length(seqlen) # <<<<<<<<<<<<<< * cdef char* tmp_align_i = get_c_string_with_length(seqlen) * */ - __pyx_t_2 = __pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(__pyx_v_seqlen); if (unlikely(__pyx_t_2 == ((char *)NULL) && PyErr_Occurred())) __PYX_ERR(0, 341, __pyx_L1_error) + __pyx_t_2 = __pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(__pyx_v_seqlen); if (unlikely(__pyx_t_2 == ((char *)NULL) && PyErr_Occurred())) __PYX_ERR(0, 339, __pyx_L1_error) __pyx_v_tmp_align_j = __pyx_t_2; - /* "CRISPResso2/CRISPResso2Align.pyx":342 + /* "CRISPResso2/CRISPResso2Align.pyx":340 * seqlen = max_i + max_j * cdef char* tmp_align_j = get_c_string_with_length(seqlen) * cdef char* tmp_align_i = get_c_string_with_length(seqlen) # <<<<<<<<<<<<<< * * cdef int matchCount = 0 */ - __pyx_t_2 = __pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(__pyx_v_seqlen); if (unlikely(__pyx_t_2 == ((char *)NULL) && PyErr_Occurred())) __PYX_ERR(0, 342, __pyx_L1_error) + __pyx_t_2 = __pyx_f_11CRISPResso2_16CRISPResso2Align_get_c_string_with_length(__pyx_v_seqlen); if (unlikely(__pyx_t_2 == ((char *)NULL) && PyErr_Occurred())) __PYX_ERR(0, 340, __pyx_L1_error) __pyx_v_tmp_align_i = __pyx_t_2; - /* "CRISPResso2/CRISPResso2Align.pyx":344 + /* "CRISPResso2/CRISPResso2Align.pyx":342 * cdef char* tmp_align_i = get_c_string_with_length(seqlen) * * cdef int matchCount = 0 # <<<<<<<<<<<<<< @@ -24121,7 +24581,7 @@ __pyx_t_10 = -1; */ __pyx_v_matchCount = 0; - /* "CRISPResso2/CRISPResso2Align.pyx":345 + /* "CRISPResso2/CRISPResso2Align.pyx":343 * * cdef int matchCount = 0 * i = max_i # <<<<<<<<<<<<<< @@ -24130,7 +24590,7 @@ __pyx_t_10 = -1; */ __pyx_v_i = __pyx_v_max_i; - /* "CRISPResso2/CRISPResso2Align.pyx":346 + /* "CRISPResso2/CRISPResso2Align.pyx":344 * cdef int matchCount = 0 * i = max_i * j = max_j # <<<<<<<<<<<<<< @@ -24139,7 +24599,7 @@ __pyx_t_10 = -1; */ __pyx_v_j = __pyx_v_max_j; - /* "CRISPResso2/CRISPResso2Align.pyx":347 + /* "CRISPResso2/CRISPResso2Align.pyx":345 * i = max_i * j = max_j * ci = seqi[i - 1] # <<<<<<<<<<<<<< @@ -24148,7 +24608,7 @@ __pyx_t_10 = -1; */ __pyx_v_ci = (__pyx_v_seqi[(__pyx_v_i - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":348 + /* "CRISPResso2/CRISPResso2Align.pyx":346 * j = max_j * ci = seqi[i - 1] * cj = seqj[j - 1] # <<<<<<<<<<<<<< @@ -24157,7 +24617,7 @@ __pyx_t_10 = -1; */ __pyx_v_cj = (__pyx_v_seqj[(__pyx_v_j - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":350 + /* "CRISPResso2/CRISPResso2Align.pyx":348 * cj = seqj[j - 1] * cdef int currMatrix * currMatrix = MARRAY # <<<<<<<<<<<<<< @@ -24166,7 +24626,7 @@ __pyx_t_10 = -1; */ __pyx_v_currMatrix = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":351 + /* "CRISPResso2/CRISPResso2Align.pyx":349 * cdef int currMatrix * currMatrix = MARRAY * if mScore[i,j] > jScore[i,j]: # <<<<<<<<<<<<<< @@ -24180,7 +24640,7 @@ __pyx_t_10 = -1; __pyx_t_4 = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_13 * __pyx_v_mScore.strides[0]) ) + __pyx_t_14 * __pyx_v_mScore.strides[1]) ))) > (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_15 * __pyx_v_jScore.strides[0]) ) + __pyx_t_16 * __pyx_v_jScore.strides[1]) )))); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":352 + /* "CRISPResso2/CRISPResso2Align.pyx":350 * currMatrix = MARRAY * if mScore[i,j] > jScore[i,j]: * if mScore[i,j] > iScore[i,j]: # <<<<<<<<<<<<<< @@ -24194,7 +24654,7 @@ __pyx_t_10 = -1; __pyx_t_4 = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_15 * __pyx_v_mScore.strides[1]) ))) > (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_14 * __pyx_v_iScore.strides[0]) ) + __pyx_t_13 * __pyx_v_iScore.strides[1]) )))); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":353 + /* "CRISPResso2/CRISPResso2Align.pyx":351 * if mScore[i,j] > jScore[i,j]: * if mScore[i,j] > iScore[i,j]: * currMatrix = MARRAY # <<<<<<<<<<<<<< @@ -24203,7 +24663,7 @@ __pyx_t_10 = -1; */ __pyx_v_currMatrix = __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":352 + /* "CRISPResso2/CRISPResso2Align.pyx":350 * currMatrix = MARRAY * if mScore[i,j] > jScore[i,j]: * if mScore[i,j] > iScore[i,j]: # <<<<<<<<<<<<<< @@ -24213,7 +24673,7 @@ __pyx_t_10 = -1; goto __pyx_L32; } - /* "CRISPResso2/CRISPResso2Align.pyx":355 + /* "CRISPResso2/CRISPResso2Align.pyx":353 * currMatrix = MARRAY * else: * currMatrix = IARRAY # <<<<<<<<<<<<<< @@ -24225,7 +24685,7 @@ __pyx_t_10 = -1; } __pyx_L32:; - /* "CRISPResso2/CRISPResso2Align.pyx":351 + /* "CRISPResso2/CRISPResso2Align.pyx":349 * cdef int currMatrix * currMatrix = MARRAY * if mScore[i,j] > jScore[i,j]: # <<<<<<<<<<<<<< @@ -24235,7 +24695,7 @@ __pyx_t_10 = -1; goto __pyx_L31; } - /* "CRISPResso2/CRISPResso2Align.pyx":357 + /* "CRISPResso2/CRISPResso2Align.pyx":355 * currMatrix = IARRAY * else: * if jScore[i,j] > iScore[i,j]: # <<<<<<<<<<<<<< @@ -24250,7 +24710,7 @@ __pyx_t_10 = -1; __pyx_t_4 = ((*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_13 * __pyx_v_jScore.strides[0]) ) + __pyx_t_14 * __pyx_v_jScore.strides[1]) ))) > (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_15 * __pyx_v_iScore.strides[0]) ) + __pyx_t_16 * __pyx_v_iScore.strides[1]) )))); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":358 + /* "CRISPResso2/CRISPResso2Align.pyx":356 * else: * if jScore[i,j] > iScore[i,j]: * currMatrix = JARRAY # <<<<<<<<<<<<<< @@ -24259,7 +24719,7 @@ __pyx_t_10 = -1; */ __pyx_v_currMatrix = __pyx_v_11CRISPResso2_16CRISPResso2Align_JARRAY; - /* "CRISPResso2/CRISPResso2Align.pyx":357 + /* "CRISPResso2/CRISPResso2Align.pyx":355 * currMatrix = IARRAY * else: * if jScore[i,j] > iScore[i,j]: # <<<<<<<<<<<<<< @@ -24269,7 +24729,7 @@ __pyx_t_10 = -1; goto __pyx_L33; } - /* "CRISPResso2/CRISPResso2Align.pyx":360 + /* "CRISPResso2/CRISPResso2Align.pyx":358 * currMatrix = JARRAY * else: * currMatrix = IARRAY # <<<<<<<<<<<<<< @@ -24283,7 +24743,7 @@ __pyx_t_10 = -1; } __pyx_L31:; - /* "CRISPResso2/CRISPResso2Align.pyx":363 + /* "CRISPResso2/CRISPResso2Align.pyx":361 * # print('seqi' + str(seqi)) * # print('seqj' + str(seqj)) * while i > 0 or j > 0: # <<<<<<<<<<<<<< @@ -24302,7 +24762,7 @@ __pyx_t_10 = -1; __pyx_L36_bool_binop_done:; if (!__pyx_t_4) break; - /* "CRISPResso2/CRISPResso2Align.pyx":366 + /* "CRISPResso2/CRISPResso2Align.pyx":364 * # print("i: " + str(i) + " j: " + str(j) + " currMatrix: " + str(currMatrix) + " match score: " + str(mScore[i,j]) + " last match: " + str(mScore[i-1,j-1]) + " matrix[" + str(ci) + "," + str(cj) + "]: " + str(matrix[ci,cj]) + " last j " + str(jScore[i,j]) + " last i: " + str(iScore[i,j]) + " mpointer: " + str(mPointer[i,j]) + " ipointer: " + str(iPointer[i,j]) + " jpointer: " + str(jPointer[i,j])) * * currVal = mScore[i,j] # <<<<<<<<<<<<<< @@ -24313,7 +24773,7 @@ __pyx_t_10 = -1; __pyx_t_15 = __pyx_v_j; __pyx_v_currVal = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mScore.data + __pyx_t_16 * __pyx_v_mScore.strides[0]) ) + __pyx_t_15 * __pyx_v_mScore.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":367 + /* "CRISPResso2/CRISPResso2Align.pyx":365 * * currVal = mScore[i,j] * currPtr = mPointer[i,j] # <<<<<<<<<<<<<< @@ -24324,7 +24784,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; __pyx_v_currPtr = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mPointer.data + __pyx_t_15 * __pyx_v_mPointer.strides[0]) ) + __pyx_t_16 * __pyx_v_mPointer.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":368 + /* "CRISPResso2/CRISPResso2Align.pyx":366 * currVal = mScore[i,j] * currPtr = mPointer[i,j] * if currMatrix == IARRAY: # <<<<<<<<<<<<<< @@ -24334,7 +24794,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_currMatrix == __pyx_v_11CRISPResso2_16CRISPResso2Align_IARRAY); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":369 + /* "CRISPResso2/CRISPResso2Align.pyx":367 * currPtr = mPointer[i,j] * if currMatrix == IARRAY: * currVal = iScore[i,j] # <<<<<<<<<<<<<< @@ -24345,7 +24805,7 @@ __pyx_t_10 = -1; __pyx_t_15 = __pyx_v_j; __pyx_v_currVal = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iScore.data + __pyx_t_16 * __pyx_v_iScore.strides[0]) ) + __pyx_t_15 * __pyx_v_iScore.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":370 + /* "CRISPResso2/CRISPResso2Align.pyx":368 * if currMatrix == IARRAY: * currVal = iScore[i,j] * currPtr = iPointer[i,j] # <<<<<<<<<<<<<< @@ -24356,7 +24816,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; __pyx_v_currPtr = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iPointer.data + __pyx_t_15 * __pyx_v_iPointer.strides[0]) ) + __pyx_t_16 * __pyx_v_iPointer.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":368 + /* "CRISPResso2/CRISPResso2Align.pyx":366 * currVal = mScore[i,j] * currPtr = mPointer[i,j] * if currMatrix == IARRAY: # <<<<<<<<<<<<<< @@ -24365,7 +24825,7 @@ __pyx_t_10 = -1; */ } - /* "CRISPResso2/CRISPResso2Align.pyx":371 + /* "CRISPResso2/CRISPResso2Align.pyx":369 * currVal = iScore[i,j] * currPtr = iPointer[i,j] * if currMatrix == JARRAY: # <<<<<<<<<<<<<< @@ -24375,7 +24835,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_currMatrix == __pyx_v_11CRISPResso2_16CRISPResso2Align_JARRAY); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":372 + /* "CRISPResso2/CRISPResso2Align.pyx":370 * currPtr = iPointer[i,j] * if currMatrix == JARRAY: * currVal = jScore[i,j] # <<<<<<<<<<<<<< @@ -24386,7 +24846,7 @@ __pyx_t_10 = -1; __pyx_t_15 = __pyx_v_j; __pyx_v_currVal = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jScore.data + __pyx_t_16 * __pyx_v_jScore.strides[0]) ) + __pyx_t_15 * __pyx_v_jScore.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":373 + /* "CRISPResso2/CRISPResso2Align.pyx":371 * if currMatrix == JARRAY: * currVal = jScore[i,j] * currPtr = jPointer[i,j] # <<<<<<<<<<<<<< @@ -24397,7 +24857,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; __pyx_v_currPtr = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jPointer.data + __pyx_t_15 * __pyx_v_jPointer.strides[0]) ) + __pyx_t_16 * __pyx_v_jPointer.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":371 + /* "CRISPResso2/CRISPResso2Align.pyx":369 * currVal = iScore[i,j] * currPtr = iPointer[i,j] * if currMatrix == JARRAY: # <<<<<<<<<<<<<< @@ -24406,7 +24866,7 @@ __pyx_t_10 = -1; */ } - /* "CRISPResso2/CRISPResso2Align.pyx":375 + /* "CRISPResso2/CRISPResso2Align.pyx":373 * currPtr = jPointer[i,j] * # print("i: " + str(i) + " j: " + str(j) + " " + str(currMatrix) +':' + str(currVal) + ' > ' + str(currPtr)) * if currMatrix == MARRAY: # 1 # <<<<<<<<<<<<<< @@ -24416,7 +24876,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_currMatrix == __pyx_v_11CRISPResso2_16CRISPResso2Align_MARRAY); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":376 + /* "CRISPResso2/CRISPResso2Align.pyx":374 * # print("i: " + str(i) + " j: " + str(j) + " " + str(currMatrix) +':' + str(currVal) + ' > ' + str(currPtr)) * if currMatrix == MARRAY: # 1 * currMatrix = mPointer[i,j] # <<<<<<<<<<<<<< @@ -24427,7 +24887,7 @@ __pyx_t_10 = -1; __pyx_t_15 = __pyx_v_j; __pyx_v_currMatrix = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_mPointer.data + __pyx_t_16 * __pyx_v_mPointer.strides[0]) ) + __pyx_t_15 * __pyx_v_mPointer.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":377 + /* "CRISPResso2/CRISPResso2Align.pyx":375 * if currMatrix == MARRAY: # 1 * currMatrix = mPointer[i,j] * tmp_align_j[align_counter] = cj # <<<<<<<<<<<<<< @@ -24436,7 +24896,7 @@ __pyx_t_10 = -1; */ (__pyx_v_tmp_align_j[__pyx_v_align_counter]) = __pyx_v_cj; - /* "CRISPResso2/CRISPResso2Align.pyx":378 + /* "CRISPResso2/CRISPResso2Align.pyx":376 * currMatrix = mPointer[i,j] * tmp_align_j[align_counter] = cj * tmp_align_i[align_counter] = ci # <<<<<<<<<<<<<< @@ -24445,7 +24905,7 @@ __pyx_t_10 = -1; */ (__pyx_v_tmp_align_i[__pyx_v_align_counter]) = __pyx_v_ci; - /* "CRISPResso2/CRISPResso2Align.pyx":379 + /* "CRISPResso2/CRISPResso2Align.pyx":377 * tmp_align_j[align_counter] = cj * tmp_align_i[align_counter] = ci * if cj == ci: # <<<<<<<<<<<<<< @@ -24455,7 +24915,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_cj == __pyx_v_ci); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":380 + /* "CRISPResso2/CRISPResso2Align.pyx":378 * tmp_align_i[align_counter] = ci * if cj == ci: * matchCount += 1 # <<<<<<<<<<<<<< @@ -24464,7 +24924,7 @@ __pyx_t_10 = -1; */ __pyx_v_matchCount = (__pyx_v_matchCount + 1); - /* "CRISPResso2/CRISPResso2Align.pyx":379 + /* "CRISPResso2/CRISPResso2Align.pyx":377 * tmp_align_j[align_counter] = cj * tmp_align_i[align_counter] = ci * if cj == ci: # <<<<<<<<<<<<<< @@ -24473,7 +24933,7 @@ __pyx_t_10 = -1; */ } - /* "CRISPResso2/CRISPResso2Align.pyx":382 + /* "CRISPResso2/CRISPResso2Align.pyx":380 * matchCount += 1 * * if i > 1: # <<<<<<<<<<<<<< @@ -24483,7 +24943,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_i > 1); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":383 + /* "CRISPResso2/CRISPResso2Align.pyx":381 * * if i > 1: * i -= 1 # <<<<<<<<<<<<<< @@ -24492,7 +24952,7 @@ __pyx_t_10 = -1; */ __pyx_v_i = (__pyx_v_i - 1); - /* "CRISPResso2/CRISPResso2Align.pyx":384 + /* "CRISPResso2/CRISPResso2Align.pyx":382 * if i > 1: * i -= 1 * ci = seqi[i - 1] # <<<<<<<<<<<<<< @@ -24501,7 +24961,7 @@ __pyx_t_10 = -1; */ __pyx_v_ci = (__pyx_v_seqi[(__pyx_v_i - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":382 + /* "CRISPResso2/CRISPResso2Align.pyx":380 * matchCount += 1 * * if i > 1: # <<<<<<<<<<<<<< @@ -24511,7 +24971,7 @@ __pyx_t_10 = -1; goto __pyx_L42; } - /* "CRISPResso2/CRISPResso2Align.pyx":386 + /* "CRISPResso2/CRISPResso2Align.pyx":384 * ci = seqi[i - 1] * else: * i = 0 # <<<<<<<<<<<<<< @@ -24521,7 +24981,7 @@ __pyx_t_10 = -1; /*else*/ { __pyx_v_i = 0; - /* "CRISPResso2/CRISPResso2Align.pyx":387 + /* "CRISPResso2/CRISPResso2Align.pyx":385 * else: * i = 0 * ci = seqi[i] # <<<<<<<<<<<<<< @@ -24532,7 +24992,7 @@ __pyx_t_10 = -1; } __pyx_L42:; - /* "CRISPResso2/CRISPResso2Align.pyx":388 + /* "CRISPResso2/CRISPResso2Align.pyx":386 * i = 0 * ci = seqi[i] * if j > 1: # <<<<<<<<<<<<<< @@ -24542,7 +25002,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_j > 1); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":389 + /* "CRISPResso2/CRISPResso2Align.pyx":387 * ci = seqi[i] * if j > 1: * j -= 1 # <<<<<<<<<<<<<< @@ -24551,7 +25011,7 @@ __pyx_t_10 = -1; */ __pyx_v_j = (__pyx_v_j - 1); - /* "CRISPResso2/CRISPResso2Align.pyx":390 + /* "CRISPResso2/CRISPResso2Align.pyx":388 * if j > 1: * j -= 1 * cj = seqj[j - 1] # <<<<<<<<<<<<<< @@ -24560,7 +25020,7 @@ __pyx_t_10 = -1; */ __pyx_v_cj = (__pyx_v_seqj[(__pyx_v_j - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":388 + /* "CRISPResso2/CRISPResso2Align.pyx":386 * i = 0 * ci = seqi[i] * if j > 1: # <<<<<<<<<<<<<< @@ -24570,7 +25030,7 @@ __pyx_t_10 = -1; goto __pyx_L43; } - /* "CRISPResso2/CRISPResso2Align.pyx":392 + /* "CRISPResso2/CRISPResso2Align.pyx":390 * cj = seqj[j - 1] * else: * j = 0 # <<<<<<<<<<<<<< @@ -24580,7 +25040,7 @@ __pyx_t_10 = -1; /*else*/ { __pyx_v_j = 0; - /* "CRISPResso2/CRISPResso2Align.pyx":393 + /* "CRISPResso2/CRISPResso2Align.pyx":391 * else: * j = 0 * cj = seqj[j] # <<<<<<<<<<<<<< @@ -24591,7 +25051,7 @@ __pyx_t_10 = -1; } __pyx_L43:; - /* "CRISPResso2/CRISPResso2Align.pyx":375 + /* "CRISPResso2/CRISPResso2Align.pyx":373 * currPtr = jPointer[i,j] * # print("i: " + str(i) + " j: " + str(j) + " " + str(currMatrix) +':' + str(currVal) + ' > ' + str(currPtr)) * if currMatrix == MARRAY: # 1 # <<<<<<<<<<<<<< @@ -24601,7 +25061,7 @@ __pyx_t_10 = -1; goto __pyx_L40; } - /* "CRISPResso2/CRISPResso2Align.pyx":396 + /* "CRISPResso2/CRISPResso2Align.pyx":394 * * # print('in M set to ' + str(currMatrix)) * elif currMatrix == JARRAY: # 3 # <<<<<<<<<<<<<< @@ -24611,7 +25071,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_currMatrix == __pyx_v_11CRISPResso2_16CRISPResso2Align_JARRAY); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":397 + /* "CRISPResso2/CRISPResso2Align.pyx":395 * # print('in M set to ' + str(currMatrix)) * elif currMatrix == JARRAY: # 3 * currMatrix = jPointer[i,j] # <<<<<<<<<<<<<< @@ -24622,7 +25082,7 @@ __pyx_t_10 = -1; __pyx_t_16 = __pyx_v_j; __pyx_v_currMatrix = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_jPointer.data + __pyx_t_15 * __pyx_v_jPointer.strides[0]) ) + __pyx_t_16 * __pyx_v_jPointer.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":398 + /* "CRISPResso2/CRISPResso2Align.pyx":396 * elif currMatrix == JARRAY: # 3 * currMatrix = jPointer[i,j] * tmp_align_j[align_counter] = c"-" # <<<<<<<<<<<<<< @@ -24631,7 +25091,7 @@ __pyx_t_10 = -1; */ (__pyx_v_tmp_align_j[__pyx_v_align_counter]) = '-'; - /* "CRISPResso2/CRISPResso2Align.pyx":399 + /* "CRISPResso2/CRISPResso2Align.pyx":397 * currMatrix = jPointer[i,j] * tmp_align_j[align_counter] = c"-" * tmp_align_i[align_counter] = ci # <<<<<<<<<<<<<< @@ -24640,7 +25100,7 @@ __pyx_t_10 = -1; */ (__pyx_v_tmp_align_i[__pyx_v_align_counter]) = __pyx_v_ci; - /* "CRISPResso2/CRISPResso2Align.pyx":400 + /* "CRISPResso2/CRISPResso2Align.pyx":398 * tmp_align_j[align_counter] = c"-" * tmp_align_i[align_counter] = ci * if i > 1: # <<<<<<<<<<<<<< @@ -24650,7 +25110,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_i > 1); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":401 + /* "CRISPResso2/CRISPResso2Align.pyx":399 * tmp_align_i[align_counter] = ci * if i > 1: * i -= 1 # <<<<<<<<<<<<<< @@ -24659,7 +25119,7 @@ __pyx_t_10 = -1; */ __pyx_v_i = (__pyx_v_i - 1); - /* "CRISPResso2/CRISPResso2Align.pyx":402 + /* "CRISPResso2/CRISPResso2Align.pyx":400 * if i > 1: * i -= 1 * ci = seqi[i - 1] # <<<<<<<<<<<<<< @@ -24668,7 +25128,7 @@ __pyx_t_10 = -1; */ __pyx_v_ci = (__pyx_v_seqi[(__pyx_v_i - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":400 + /* "CRISPResso2/CRISPResso2Align.pyx":398 * tmp_align_j[align_counter] = c"-" * tmp_align_i[align_counter] = ci * if i > 1: # <<<<<<<<<<<<<< @@ -24678,7 +25138,7 @@ __pyx_t_10 = -1; goto __pyx_L44; } - /* "CRISPResso2/CRISPResso2Align.pyx":404 + /* "CRISPResso2/CRISPResso2Align.pyx":402 * ci = seqi[i - 1] * else: * i = 0 # <<<<<<<<<<<<<< @@ -24688,7 +25148,7 @@ __pyx_t_10 = -1; /*else*/ { __pyx_v_i = 0; - /* "CRISPResso2/CRISPResso2Align.pyx":405 + /* "CRISPResso2/CRISPResso2Align.pyx":403 * else: * i = 0 * ci = seqi[i] # <<<<<<<<<<<<<< @@ -24699,7 +25159,7 @@ __pyx_t_10 = -1; } __pyx_L44:; - /* "CRISPResso2/CRISPResso2Align.pyx":396 + /* "CRISPResso2/CRISPResso2Align.pyx":394 * * # print('in M set to ' + str(currMatrix)) * elif currMatrix == JARRAY: # 3 # <<<<<<<<<<<<<< @@ -24709,7 +25169,7 @@ __pyx_t_10 = -1; goto __pyx_L40; } - /* "CRISPResso2/CRISPResso2Align.pyx":406 + /* "CRISPResso2/CRISPResso2Align.pyx":404 * i = 0 * ci = seqi[i] * elif currMatrix == IARRAY: # 2 # <<<<<<<<<<<<<< @@ -24719,7 +25179,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_currMatrix == __pyx_v_11CRISPResso2_16CRISPResso2Align_IARRAY); if (likely(__pyx_t_4)) { - /* "CRISPResso2/CRISPResso2Align.pyx":407 + /* "CRISPResso2/CRISPResso2Align.pyx":405 * ci = seqi[i] * elif currMatrix == IARRAY: # 2 * currMatrix = iPointer[i,j] # <<<<<<<<<<<<<< @@ -24730,7 +25190,7 @@ __pyx_t_10 = -1; __pyx_t_15 = __pyx_v_j; __pyx_v_currMatrix = (*((int *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_iPointer.data + __pyx_t_16 * __pyx_v_iPointer.strides[0]) ) + __pyx_t_15 * __pyx_v_iPointer.strides[1]) ))); - /* "CRISPResso2/CRISPResso2Align.pyx":408 + /* "CRISPResso2/CRISPResso2Align.pyx":406 * elif currMatrix == IARRAY: # 2 * currMatrix = iPointer[i,j] * tmp_align_j[align_counter] = cj # <<<<<<<<<<<<<< @@ -24739,7 +25199,7 @@ __pyx_t_10 = -1; */ (__pyx_v_tmp_align_j[__pyx_v_align_counter]) = __pyx_v_cj; - /* "CRISPResso2/CRISPResso2Align.pyx":409 + /* "CRISPResso2/CRISPResso2Align.pyx":407 * currMatrix = iPointer[i,j] * tmp_align_j[align_counter] = cj * tmp_align_i[align_counter] = c"-" # <<<<<<<<<<<<<< @@ -24748,7 +25208,7 @@ __pyx_t_10 = -1; */ (__pyx_v_tmp_align_i[__pyx_v_align_counter]) = '-'; - /* "CRISPResso2/CRISPResso2Align.pyx":410 + /* "CRISPResso2/CRISPResso2Align.pyx":408 * tmp_align_j[align_counter] = cj * tmp_align_i[align_counter] = c"-" * if j > 1: # <<<<<<<<<<<<<< @@ -24758,7 +25218,7 @@ __pyx_t_10 = -1; __pyx_t_4 = (__pyx_v_j > 1); if (__pyx_t_4) { - /* "CRISPResso2/CRISPResso2Align.pyx":411 + /* "CRISPResso2/CRISPResso2Align.pyx":409 * tmp_align_i[align_counter] = c"-" * if j > 1: * j -= 1 # <<<<<<<<<<<<<< @@ -24767,7 +25227,7 @@ __pyx_t_10 = -1; */ __pyx_v_j = (__pyx_v_j - 1); - /* "CRISPResso2/CRISPResso2Align.pyx":412 + /* "CRISPResso2/CRISPResso2Align.pyx":410 * if j > 1: * j -= 1 * cj = seqj[j - 1] # <<<<<<<<<<<<<< @@ -24776,7 +25236,7 @@ __pyx_t_10 = -1; */ __pyx_v_cj = (__pyx_v_seqj[(__pyx_v_j - 1)]); - /* "CRISPResso2/CRISPResso2Align.pyx":410 + /* "CRISPResso2/CRISPResso2Align.pyx":408 * tmp_align_j[align_counter] = cj * tmp_align_i[align_counter] = c"-" * if j > 1: # <<<<<<<<<<<<<< @@ -24786,7 +25246,7 @@ __pyx_t_10 = -1; goto __pyx_L45; } - /* "CRISPResso2/CRISPResso2Align.pyx":414 + /* "CRISPResso2/CRISPResso2Align.pyx":412 * cj = seqj[j - 1] * else: * j = 0 # <<<<<<<<<<<<<< @@ -24796,7 +25256,7 @@ __pyx_t_10 = -1; /*else*/ { __pyx_v_j = 0; - /* "CRISPResso2/CRISPResso2Align.pyx":415 + /* "CRISPResso2/CRISPResso2Align.pyx":413 * else: * j = 0 * cj = seqj[j] # <<<<<<<<<<<<<< @@ -24807,7 +25267,7 @@ __pyx_t_10 = -1; 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#if CYTHON_AVOID_BORROWED_REFS - Py_INCREF(value); // transfer ownership of value to values + Py_INCREF(value); Py_DECREF(key); #endif key = NULL; @@ -28480,7 +28954,7 @@ static int __Pyx_ParseOptionalKeywords( && _PyString_Eq(**name, key)) { values[name-argnames] = value; #if CYTHON_AVOID_BORROWED_REFS - value = NULL; // ownership transferred to values + value = NULL; #endif break; } @@ -28512,7 +28986,7 @@ static int __Pyx_ParseOptionalKeywords( if (cmp == 0) { values[name-argnames] = value; #if CYTHON_AVOID_BORROWED_REFS - value = NULL; // ownership transferred to values + value = NULL; #endif break; } @@ -30383,7 +30857,6 @@ static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { } /* HasAttr */ -#if __PYX_LIMITED_VERSION_HEX < 0x030d00A1 static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { PyObject *r; if (unlikely(!__Pyx_PyBaseString_Check(n))) { @@ -30400,7 +30873,6 @@ static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { return 1; } } -#endif /* PyObjectLookupSpecial */ #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS @@ -31302,9 +31774,10 @@ fail:; /* IterFinish */ static CYTHON_INLINE int __Pyx_IterFinish(void) { + PyObject* exc_type; __Pyx_PyThreadState_declare __Pyx_PyThreadState_assign - PyObject* exc_type = __Pyx_PyErr_CurrentExceptionType(); + exc_type = __Pyx_PyErr_CurrentExceptionType(); if (unlikely(exc_type)) { if (unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) return -1; @@ -32045,10 +32518,10 @@ static int __Pyx_setup_reduce(PyObject* type_obj) { #endif /* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType_3_0_6 -#define __PYX_HAVE_RT_ImportType_3_0_6 -static PyTypeObject *__Pyx_ImportType_3_0_6(PyObject *module, const char *module_name, const char *class_name, - size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_6 check_size) + #ifndef __PYX_HAVE_RT_ImportType_3_0_11 +#define __PYX_HAVE_RT_ImportType_3_0_11 +static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject *module, const char *module_name, const char *class_name, + size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size) { PyObject *result = 0; char warning[200]; @@ -32102,7 +32575,7 @@ static PyTypeObject *__Pyx_ImportType_3_0_6(PyObject *module, const char *module module_name, class_name, size, basicsize+itemsize); goto bad; } - if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_6 && + if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_11 && ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) { PyErr_Format(PyExc_ValueError, "%.200s.%.200s size changed, may indicate binary incompatibility. " @@ -32110,7 +32583,7 @@ static PyTypeObject *__Pyx_ImportType_3_0_6(PyObject *module, const char *module module_name, class_name, size, basicsize, basicsize+itemsize); goto bad; } - else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_0_6 && (size_t)basicsize > size) { + else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_0_11 && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility. " "Expected %zd from C header, got %zd from PyObject", @@ -33110,7 +33583,7 @@ static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, default: return NULL; } - return ((_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames); + return ((__Pyx_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames); } static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) { @@ -33245,6 +33718,9 @@ static PyTypeObject __pyx_CyFunctionType_type = { #if PY_VERSION_HEX >= 0x030C0000 0, #endif +#if PY_VERSION_HEX >= 0x030d00A4 + 0, +#endif #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, #endif @@ -33569,7 +34045,7 @@ static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( #else py_code = PyCode_NewEmpty(filename, funcname, py_line); #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline + Py_XDECREF(py_funcname); return py_code; bad: Py_XDECREF(py_funcname); @@ -34279,6 +34755,160 @@ static int __Pyx_ValidateAndInit_memviewslice( #endif #endif +/* Declarations */ + #if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_from_parts(long double x, long double y) { + return ::std::complex< long double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_from_parts(long double x, long double y) { + return x + y*(__pyx_t_long_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_from_parts(long double x, long double y) { + __pyx_t_long_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ + #if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) +#else + static CYTHON_INLINE int __Pyx_c_eq_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_sum_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + __pyx_t_long_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_diff_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + __pyx_t_long_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_prod_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + __pyx_t_long_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_quot_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + if (b.imag == 0) { + return __pyx_t_long_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabsl(b.real) >= fabsl(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_long_double_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + long double r = b.imag / b.real; + long double s = (long double)(1.0) / (b.real + b.imag * r); + return __pyx_t_long_double_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + long double r = b.real / b.imag; + long double s = (long double)(1.0) / (b.imag + b.real * r); + return __pyx_t_long_double_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + } + } + #else + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_quot_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + if (b.imag == 0) { + return __pyx_t_long_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + long double denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_long_double_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } + } + #endif + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_neg_long__double(__pyx_t_long_double_complex a) { + __pyx_t_long_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_long__double(__pyx_t_long_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_conj_long__double(__pyx_t_long_double_complex a) { + __pyx_t_long_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE long double __Pyx_c_abs_long__double(__pyx_t_long_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtl(z.real*z.real + z.imag*z.imag); + #else + return hypotl(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_pow_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + __pyx_t_long_double_complex z; + long double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + long double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + return __Pyx_c_prod_long__double(a, a); + case 3: + z = __Pyx_c_prod_long__double(a, a); + return __Pyx_c_prod_long__double(z, a); + case 4: + z = __Pyx_c_prod_long__double(a, a); + return __Pyx_c_prod_long__double(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if ((b.imag == 0) && (a.real >= 0)) { + z.real = powl(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2l(0.0, -1.0); + } + } else { + r = __Pyx_c_abs_long__double(a); + theta = atan2l(a.imag, a.real); + } + lnr = logl(r); + z_r = expl(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosl(z_theta); + z.imag = z_r * sinl(z_theta); + return z; + } + #endif +#endif + /* MemviewSliceCopyTemplate */ static __Pyx_memviewslice __pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, @@ -34503,245 +35133,239 @@ static CYTHON_INLINE void __Pyx_XCLEAR_MEMVIEW(__Pyx_memviewslice *memslice, } return (int) val; } - } else + } #endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { + if (unlikely(!PyLong_Check(x))) { + int val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { #if CYTHON_USE_PYLONG_INTERNALS - if (unlikely(__Pyx_PyLong_IsNeg(x))) { - goto raise_neg_overflow; - } else if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_DigitCount(x)) { - case 2: - if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } - break; - case 3: - if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } + } + break; + case 3: + if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } - break; - case 4: - if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } + } + break; + case 4: + if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } - break; - } + } + break; } + } #endif #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } #else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } #endif - if ((sizeof(int) <= sizeof(unsigned long))) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) + if ((sizeof(int) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif - } - } else { + } + } else { #if CYTHON_USE_PYLONG_INTERNALS - if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_SignedDigitCount(x)) { - case -2: - if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case 2: - if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case 2: + if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case -3: - if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case -3: + if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case 3: - if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case 3: + if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case -4: - if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case -4: + if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case 4: - if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case 4: + if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - } + } + break; } + } #endif - if ((sizeof(int) <= sizeof(long))) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + if ((sizeof(int) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif - } + } + } + { + int val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (int) -1; + assert(PyLong_CheckExact(v)); } { - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); -#if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } -#endif - if (likely(v)) { - int ret = -1; -#if PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); -#else - PyObject *stepval = NULL, *mask = NULL, *shift = NULL; - int bits, remaining_bits, is_negative = 0; - long idigit; - int chunk_size = (sizeof(long) < 8) ? 30 : 62; - if (unlikely(!PyLong_CheckExact(v))) { - PyObject *tmp = v; - v = PyNumber_Long(v); - assert(PyLong_CheckExact(v)); - Py_DECREF(tmp); - if (unlikely(!v)) return (int) -1; - } -#if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(x) == 0) - return (int) 0; - is_negative = Py_SIZE(x) < 0; -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - is_negative = result == 1; - } -#endif - if (is_unsigned && unlikely(is_negative)) { - goto raise_neg_overflow; - } else if (is_negative) { - stepval = PyNumber_Invert(v); - if (unlikely(!stepval)) - return (int) -1; - } else { - stepval = __Pyx_NewRef(v); - } - val = (int) 0; - mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; - shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; - for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) { - PyObject *tmp, *digit; - digit = PyNumber_And(stepval, mask); - if (unlikely(!digit)) goto done; - idigit = PyLong_AsLong(digit); - Py_DECREF(digit); - if (unlikely(idigit < 0)) goto done; - tmp = PyNumber_Rshift(stepval, shift); - if (unlikely(!tmp)) goto done; - Py_DECREF(stepval); stepval = tmp; - val |= ((int) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(stepval) == 0) - goto unpacking_done; - #endif - } - idigit = PyLong_AsLong(stepval); - if (unlikely(idigit < 0)) goto done; - remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1); - if (unlikely(idigit >= (1L << remaining_bits))) - goto raise_overflow; - val |= ((int) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - unpacking_done: - #endif - if (!is_unsigned) { - if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1)))) - goto raise_overflow; - if (is_negative) - val = ~val; - } - ret = 0; - done: - Py_XDECREF(shift); - Py_XDECREF(mask); - Py_XDECREF(stepval); -#endif + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { Py_DECREF(v); - if (likely(!ret)) - return val; + return (int) -1; } - return (int) -1; + is_negative = result == 1; } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (int) -1; + } else { + stepval = v; + } + v = NULL; + val = (int) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((int) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((int) idigit) << bits; + } + if (!is_unsigned) { + if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (int) -1; return val; } raise_overflow: @@ -34785,12 +35409,19 @@ static CYTHON_INLINE void __Pyx_XCLEAR_MEMVIEW(__Pyx_memviewslice *memslice, } } { - int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; -#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; return _PyLong_FromByteArray(bytes, sizeof(int), little, !is_unsigned); #else + int one = 1; int little = (int)*(unsigned char *)&one; PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); @@ -34819,276 +35450,270 @@ static CYTHON_INLINE void __Pyx_XCLEAR_MEMVIEW(__Pyx_memviewslice *memslice, } /* CIntFromPy */ - static CYTHON_INLINE npy_long __Pyx_PyInt_As_npy_long(PyObject *x) { + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { #ifdef __Pyx_HAS_GCC_DIAGNOSTIC #pragma GCC diagnostic push #pragma GCC diagnostic ignored "-Wconversion" #endif - const npy_long neg_one = (npy_long) -1, const_zero = (npy_long) 0; + const long neg_one = (long) -1, const_zero = (long) 0; #ifdef __Pyx_HAS_GCC_DIAGNOSTIC #pragma GCC diagnostic pop #endif const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { - if ((sizeof(npy_long) < sizeof(long))) { - __PYX_VERIFY_RETURN_INT(npy_long, long, PyInt_AS_LONG(x)) + if ((sizeof(long) < sizeof(long))) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } - return (npy_long) val; + return (long) val; } - } else + } #endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { + if (unlikely(!PyLong_Check(x))) { + long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { #if CYTHON_USE_PYLONG_INTERNALS - if (unlikely(__Pyx_PyLong_IsNeg(x))) { - goto raise_neg_overflow; - } else if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(npy_long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_DigitCount(x)) { - case 2: - if ((8 * sizeof(npy_long) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) >= 2 * PyLong_SHIFT)) { - return (npy_long) (((((npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0])); - } + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } - break; - case 3: - if ((8 * sizeof(npy_long) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) >= 3 * PyLong_SHIFT)) { - return (npy_long) (((((((npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0])); - } + } + break; + case 3: + if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } - break; - case 4: - if ((8 * sizeof(npy_long) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) >= 4 * PyLong_SHIFT)) { - return (npy_long) (((((((((npy_long)digits[3]) << PyLong_SHIFT) | (npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0])); - } + } + break; + case 4: + if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } - break; - } + } + break; } + } #endif #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } #else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (npy_long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } #endif - if ((sizeof(npy_long) <= sizeof(unsigned long))) { - __PYX_VERIFY_RETURN_INT_EXC(npy_long, unsigned long, PyLong_AsUnsignedLong(x)) + if ((sizeof(long) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(npy_long) <= sizeof(unsigned PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(npy_long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif - } - } else { + } + } else { #if CYTHON_USE_PYLONG_INTERNALS - if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(npy_long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_SignedDigitCount(x)) { - case -2: - if ((8 * sizeof(npy_long) - 1 > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) - 1 > 2 * PyLong_SHIFT)) { - return (npy_long) (((npy_long)-1)*(((((npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); - } + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case 2: - if ((8 * sizeof(npy_long) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) - 1 > 2 * PyLong_SHIFT)) { - return (npy_long) ((((((npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); - } + } + break; + case 2: + if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case -3: - if ((8 * sizeof(npy_long) - 1 > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) - 1 > 3 * PyLong_SHIFT)) { - return (npy_long) (((npy_long)-1)*(((((((npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); - } + } + break; + case -3: + if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case 3: - if ((8 * sizeof(npy_long) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) - 1 > 3 * PyLong_SHIFT)) { - return (npy_long) ((((((((npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); - } + } + break; + case 3: + if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case -4: - if ((8 * sizeof(npy_long) - 1 > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) - 1 > 4 * PyLong_SHIFT)) { - return (npy_long) (((npy_long)-1)*(((((((((npy_long)digits[3]) << PyLong_SHIFT) | (npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); - } + } + break; + case -4: + if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case 4: - if ((8 * sizeof(npy_long) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(npy_long) - 1 > 4 * PyLong_SHIFT)) { - return (npy_long) ((((((((((npy_long)digits[3]) << PyLong_SHIFT) | (npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); - } + } + break; + case 4: + if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - } + } + break; } + } #endif - if ((sizeof(npy_long) <= sizeof(long))) { - __PYX_VERIFY_RETURN_INT_EXC(npy_long, long, PyLong_AsLong(x)) + if ((sizeof(long) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(npy_long) <= sizeof(PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(npy_long, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif - } + } + } + { + long val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (long) -1; + assert(PyLong_CheckExact(v)); } { - npy_long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); -#if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } -#endif - if (likely(v)) { - int ret = -1; -#if PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); -#else - PyObject *stepval = NULL, *mask = NULL, *shift = NULL; - int bits, remaining_bits, is_negative = 0; - long idigit; - int chunk_size = (sizeof(long) < 8) ? 30 : 62; - if (unlikely(!PyLong_CheckExact(v))) { - PyObject *tmp = v; - v = PyNumber_Long(v); - assert(PyLong_CheckExact(v)); - Py_DECREF(tmp); - if (unlikely(!v)) return (npy_long) -1; - } -#if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(x) == 0) - return (npy_long) 0; - is_negative = Py_SIZE(x) < 0; -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (npy_long) -1; - is_negative = result == 1; - } -#endif - if (is_unsigned && unlikely(is_negative)) { - goto raise_neg_overflow; - } else if (is_negative) { - stepval = PyNumber_Invert(v); - if (unlikely(!stepval)) - return (npy_long) -1; - } else { - stepval = __Pyx_NewRef(v); - } - val = (npy_long) 0; - mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; - shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; - for (bits = 0; bits < (int) sizeof(npy_long) * 8 - chunk_size; bits += chunk_size) { - PyObject *tmp, *digit; - digit = PyNumber_And(stepval, mask); - if (unlikely(!digit)) goto done; - idigit = PyLong_AsLong(digit); - Py_DECREF(digit); - if (unlikely(idigit < 0)) goto done; - tmp = PyNumber_Rshift(stepval, shift); - if (unlikely(!tmp)) goto done; - Py_DECREF(stepval); stepval = tmp; - val |= ((npy_long) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(stepval) == 0) - goto unpacking_done; - #endif - } - idigit = PyLong_AsLong(stepval); - if (unlikely(idigit < 0)) goto done; - remaining_bits = ((int) sizeof(npy_long) * 8) - bits - (is_unsigned ? 0 : 1); - if (unlikely(idigit >= (1L << remaining_bits))) - goto raise_overflow; - val |= ((npy_long) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - unpacking_done: - #endif - if (!is_unsigned) { - if (unlikely(val & (((npy_long) 1) << (sizeof(npy_long) * 8 - 1)))) - goto raise_overflow; - if (is_negative) - val = ~val; - } - ret = 0; - done: - Py_XDECREF(shift); - Py_XDECREF(mask); - Py_XDECREF(stepval); -#endif + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { Py_DECREF(v); - if (likely(!ret)) - return val; + return (long) -1; } - return (npy_long) -1; + is_negative = result == 1; } - } else { - npy_long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (npy_long) -1; - val = __Pyx_PyInt_As_npy_long(tmp); - Py_DECREF(tmp); + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (long) -1; + } else { + stepval = v; + } + v = NULL; + val = (long) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((long) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((long) idigit) << bits; + } + if (!is_unsigned) { + if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (long) -1; return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, - "value too large to convert to npy_long"); - return (npy_long) -1; + "value too large to convert to long"); + return (long) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to npy_long"); - return (npy_long) -1; + "can't convert negative value to long"); + return (long) -1; } /* CIntToPy */ @@ -35122,12 +35747,19 @@ static CYTHON_INLINE void __Pyx_XCLEAR_MEMVIEW(__Pyx_memviewslice *memslice, } } { - int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; -#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; return _PyLong_FromByteArray(bytes, sizeof(long), little, !is_unsigned); #else + int one = 1; int little = (int)*(unsigned char *)&one; PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); @@ -35177,240 +35809,9 @@ static CYTHON_INLINE void __Pyx_XCLEAR_MEMVIEW(__Pyx_memviewslice *memslice, } return (size_t) val; } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - if (unlikely(__Pyx_PyLong_IsNeg(x))) { - goto raise_neg_overflow; - } else if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(size_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_DigitCount(x)) { - case 2: - if ((8 * sizeof(size_t) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) >= 2 * PyLong_SHIFT)) { - return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - case 3: - if ((8 * sizeof(size_t) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) >= 3 * PyLong_SHIFT)) { - return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - case 4: - if ((8 * sizeof(size_t) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) >= 4 * PyLong_SHIFT)) { - return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - } - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (size_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if ((sizeof(size_t) <= sizeof(unsigned long))) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if ((sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(size_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_SignedDigitCount(x)) { - case -2: - if ((8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { - return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 2: - if ((8 * sizeof(size_t) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { - return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case -3: - if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { - return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 3: - if ((8 * sizeof(size_t) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { - return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case -4: - if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT)) { - return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 4: - if ((8 * sizeof(size_t) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT)) { - return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - } - } -#endif - if ((sizeof(size_t) <= sizeof(long))) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if ((sizeof(size_t) <= sizeof(PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { - size_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); -#if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } -#endif - if (likely(v)) { - int ret = -1; -#if PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); -#else - PyObject *stepval = NULL, *mask = NULL, *shift = NULL; - int bits, remaining_bits, is_negative = 0; - long idigit; - int chunk_size = (sizeof(long) < 8) ? 30 : 62; - if (unlikely(!PyLong_CheckExact(v))) { - PyObject *tmp = v; - v = PyNumber_Long(v); - assert(PyLong_CheckExact(v)); - Py_DECREF(tmp); - if (unlikely(!v)) return (size_t) -1; - } -#if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(x) == 0) - return (size_t) 0; - is_negative = Py_SIZE(x) < 0; -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (size_t) -1; - is_negative = result == 1; - } -#endif - if (is_unsigned && unlikely(is_negative)) { - goto raise_neg_overflow; - } else if (is_negative) { - stepval = PyNumber_Invert(v); - if (unlikely(!stepval)) - return (size_t) -1; - } else { - stepval = __Pyx_NewRef(v); - } - val = (size_t) 0; - mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; - shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; - for (bits = 0; bits < (int) sizeof(size_t) * 8 - chunk_size; bits += chunk_size) { - PyObject *tmp, *digit; - digit = PyNumber_And(stepval, mask); - if (unlikely(!digit)) goto done; - idigit = PyLong_AsLong(digit); - Py_DECREF(digit); - if (unlikely(idigit < 0)) goto done; - tmp = PyNumber_Rshift(stepval, shift); - if (unlikely(!tmp)) goto done; - Py_DECREF(stepval); stepval = tmp; - val |= ((size_t) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(stepval) == 0) - goto unpacking_done; - #endif - } - idigit = PyLong_AsLong(stepval); - if (unlikely(idigit < 0)) goto done; - remaining_bits = ((int) sizeof(size_t) * 8) - bits - (is_unsigned ? 0 : 1); - if (unlikely(idigit >= (1L << remaining_bits))) - goto raise_overflow; - val |= ((size_t) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - unpacking_done: - #endif - if (!is_unsigned) { - if (unlikely(val & (((size_t) 1) << (sizeof(size_t) * 8 - 1)))) - goto raise_overflow; - if (is_negative) - val = ~val; - } - ret = 0; - done: - Py_XDECREF(shift); - Py_XDECREF(mask); - Py_XDECREF(stepval); + } #endif - Py_DECREF(v); - if (likely(!ret)) - return val; - } - return (size_t) -1; - } - } else { + if (unlikely(!PyLong_Check(x))) { size_t val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); if (!tmp) return (size_t) -1; @@ -35418,287 +35819,239 @@ static CYTHON_INLINE void __Pyx_XCLEAR_MEMVIEW(__Pyx_memviewslice *memslice, Py_DECREF(tmp); return val; } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to size_t"); - return (size_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to size_t"); - return (size_t) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if ((sizeof(long) < sizeof(long))) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { + if (is_unsigned) { #if CYTHON_USE_PYLONG_INTERNALS - if (unlikely(__Pyx_PyLong_IsNeg(x))) { - goto raise_neg_overflow; - } else if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_DigitCount(x)) { - case 2: - if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(size_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(size_t) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) >= 2 * PyLong_SHIFT)) { + return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } - break; - case 3: - if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } + } + break; + case 3: + if ((8 * sizeof(size_t) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) >= 3 * PyLong_SHIFT)) { + return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } - break; - case 4: - if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } + } + break; + case 4: + if ((8 * sizeof(size_t) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) >= 4 * PyLong_SHIFT)) { + return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } - break; - } + } + break; } + } #endif #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } #else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (size_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } #endif - if ((sizeof(long) <= sizeof(unsigned long))) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) + if ((sizeof(size_t) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if ((sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif - } - } else { + } + } else { #if CYTHON_USE_PYLONG_INTERNALS - if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_SignedDigitCount(x)) { - case -2: - if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(size_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { + return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case 2: - if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case 2: + if ((8 * sizeof(size_t) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { + return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case -3: - if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case -3: + if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { + return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case 3: - if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case 3: + if ((8 * sizeof(size_t) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { + return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case -4: - if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case -4: + if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT)) { + return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case 4: - if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case 4: + if ((8 * sizeof(size_t) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT)) { + return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - } + } + break; } + } #endif - if ((sizeof(long) <= sizeof(long))) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + if ((sizeof(size_t) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if ((sizeof(size_t) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif - } + } + } + { + size_t val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (size_t) -1; + assert(PyLong_CheckExact(v)); } { - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); -#if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } -#endif - if (likely(v)) { - int ret = -1; -#if PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); -#else - PyObject *stepval = NULL, *mask = NULL, *shift = NULL; - int bits, remaining_bits, is_negative = 0; - long idigit; - int chunk_size = (sizeof(long) < 8) ? 30 : 62; - if (unlikely(!PyLong_CheckExact(v))) { - PyObject *tmp = v; - v = PyNumber_Long(v); - assert(PyLong_CheckExact(v)); - Py_DECREF(tmp); - if (unlikely(!v)) return (long) -1; - } -#if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(x) == 0) - return (long) 0; - is_negative = Py_SIZE(x) < 0; -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - is_negative = result == 1; - } -#endif - if (is_unsigned && unlikely(is_negative)) { - goto raise_neg_overflow; - } else if (is_negative) { - stepval = PyNumber_Invert(v); - if (unlikely(!stepval)) - return (long) -1; - } else { - stepval = __Pyx_NewRef(v); - } - val = (long) 0; - mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; - shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; - for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) { - PyObject *tmp, *digit; - digit = PyNumber_And(stepval, mask); - if (unlikely(!digit)) goto done; - idigit = PyLong_AsLong(digit); - Py_DECREF(digit); - if (unlikely(idigit < 0)) goto done; - tmp = PyNumber_Rshift(stepval, shift); - if (unlikely(!tmp)) goto done; - Py_DECREF(stepval); stepval = tmp; - val |= ((long) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(stepval) == 0) - goto unpacking_done; - #endif - } - idigit = PyLong_AsLong(stepval); - if (unlikely(idigit < 0)) goto done; - remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1); - if (unlikely(idigit >= (1L << remaining_bits))) - goto raise_overflow; - val |= ((long) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - unpacking_done: - #endif - if (!is_unsigned) { - if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1)))) - goto raise_overflow; - if (is_negative) - val = ~val; - } - ret = 0; - done: - Py_XDECREF(shift); - Py_XDECREF(mask); - Py_XDECREF(stepval); -#endif + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { Py_DECREF(v); - if (likely(!ret)) - return val; + return (size_t) -1; } - return (long) -1; + is_negative = result == 1; } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (size_t) -1; + } else { + stepval = v; + } + v = NULL; + val = (size_t) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(size_t) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((size_t) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(size_t) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((size_t) idigit) << bits; + } + if (!is_unsigned) { + if (unlikely(val & (((size_t) 1) << (sizeof(size_t) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (size_t) -1; return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; + "value too large to convert to size_t"); + return (size_t) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; + "can't convert negative value to size_t"); + return (size_t) -1; } /* CIntFromPy */ @@ -35723,245 +36076,239 @@ static CYTHON_INLINE void __Pyx_XCLEAR_MEMVIEW(__Pyx_memviewslice *memslice, } return (char) val; } - } else + } #endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { + if (unlikely(!PyLong_Check(x))) { + char val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (char) -1; + val = __Pyx_PyInt_As_char(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { #if CYTHON_USE_PYLONG_INTERNALS - if (unlikely(__Pyx_PyLong_IsNeg(x))) { - goto raise_neg_overflow; - } else if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(char, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_DigitCount(x)) { - case 2: - if ((8 * sizeof(char) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) >= 2 * PyLong_SHIFT)) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(char, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(char) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) >= 2 * PyLong_SHIFT)) { + return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); } - break; - case 3: - if ((8 * sizeof(char) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) >= 3 * PyLong_SHIFT)) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } + } + break; + case 3: + if ((8 * sizeof(char) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) >= 3 * PyLong_SHIFT)) { + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); } - break; - case 4: - if ((8 * sizeof(char) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) >= 4 * PyLong_SHIFT)) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } + } + break; + case 4: + if ((8 * sizeof(char) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) >= 4 * PyLong_SHIFT)) { + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); } - break; - } + } + break; } + } #endif #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } #else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (char) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } #endif - if ((sizeof(char) <= sizeof(unsigned long))) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) + if ((sizeof(char) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(char) <= sizeof(unsigned PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if ((sizeof(char) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif - } - } else { + } + } else { #if CYTHON_USE_PYLONG_INTERNALS - if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(char, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_SignedDigitCount(x)) { - case -2: - if ((8 * sizeof(char) - 1 > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(char, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(char) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { + return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } - break; - case 2: - if ((8 * sizeof(char) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } + } + break; + case 2: + if ((8 * sizeof(char) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { + return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } - break; - case -3: - if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } + } + break; + case -3: + if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { + return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } - break; - case 3: - if ((8 * sizeof(char) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } + } + break; + case 3: + if ((8 * sizeof(char) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { + return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } - break; - case -4: - if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) - 1 > 4 * PyLong_SHIFT)) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } + } + break; + case -4: + if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) - 1 > 4 * PyLong_SHIFT)) { + return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } - break; - case 4: - if ((8 * sizeof(char) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(char) - 1 > 4 * PyLong_SHIFT)) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } + } + break; + case 4: + if ((8 * sizeof(char) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(char) - 1 > 4 * PyLong_SHIFT)) { + return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } - break; - } + } + break; } + } #endif - if ((sizeof(char) <= sizeof(long))) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) + if ((sizeof(char) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(char) <= sizeof(PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if ((sizeof(char) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif - } + } + } + { + char val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (char) -1; + assert(PyLong_CheckExact(v)); } { - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); -#if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } -#endif - if (likely(v)) { - int ret = -1; -#if PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); -#else - PyObject *stepval = NULL, *mask = NULL, *shift = NULL; - int bits, remaining_bits, is_negative = 0; - long idigit; - int chunk_size = (sizeof(long) < 8) ? 30 : 62; - if (unlikely(!PyLong_CheckExact(v))) { - PyObject *tmp = v; - v = PyNumber_Long(v); - assert(PyLong_CheckExact(v)); - Py_DECREF(tmp); - if (unlikely(!v)) return (char) -1; - } -#if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(x) == 0) - return (char) 0; - is_negative = Py_SIZE(x) < 0; -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - is_negative = result == 1; - } -#endif - if (is_unsigned && unlikely(is_negative)) { - goto raise_neg_overflow; - } else if (is_negative) { - stepval = PyNumber_Invert(v); - if (unlikely(!stepval)) - return (char) -1; - } else { - stepval = __Pyx_NewRef(v); - } - val = (char) 0; - mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; - shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; - for (bits = 0; bits < (int) sizeof(char) * 8 - chunk_size; bits += chunk_size) { - PyObject *tmp, *digit; - digit = PyNumber_And(stepval, mask); - if (unlikely(!digit)) goto done; - idigit = PyLong_AsLong(digit); - Py_DECREF(digit); - if (unlikely(idigit < 0)) goto done; - tmp = PyNumber_Rshift(stepval, shift); - if (unlikely(!tmp)) goto done; - Py_DECREF(stepval); stepval = tmp; - val |= ((char) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(stepval) == 0) - goto unpacking_done; - #endif - } - idigit = PyLong_AsLong(stepval); - if (unlikely(idigit < 0)) goto done; - remaining_bits = ((int) sizeof(char) * 8) - bits - (is_unsigned ? 0 : 1); - if (unlikely(idigit >= (1L << remaining_bits))) - goto raise_overflow; - val |= ((char) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - unpacking_done: - #endif - if (!is_unsigned) { - if (unlikely(val & (((char) 1) << (sizeof(char) * 8 - 1)))) - goto raise_overflow; - if (is_negative) - val = ~val; - } - ret = 0; - done: - Py_XDECREF(shift); - Py_XDECREF(mask); - Py_XDECREF(stepval); -#endif + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { Py_DECREF(v); - if (likely(!ret)) - return val; + return (char) -1; } - return (char) -1; + is_negative = result == 1; } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (char) -1; + } else { + stepval = v; + } + v = NULL; + val = (char) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(char) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((char) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(char) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((char) idigit) << bits; + } + if (!is_unsigned) { + if (unlikely(val & (((char) 1) << (sizeof(char) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (char) -1; return val; } raise_overflow: diff --git a/CRISPResso2/CRISPResso2Align.pyx b/CRISPResso2/CRISPResso2Align.pyx index 21c959c4..b0ce1c40 100644 --- a/CRISPResso2/CRISPResso2Align.pyx +++ b/CRISPResso2/CRISPResso2Align.pyx @@ -17,9 +17,7 @@ cdef extern from "stdlib.h": cdef extern from "Python.h": ctypedef void PyObject -ctypedef np.int_t DTYPE_INT -ctypedef np.uint_t DTYPE_UINT -ctypedef np.int8_t DTYPE_BOOL +ctypedef long DTYPE_LONG cdef size_t UP = 1, LEFT = 2, DIAG = 3, NONE = 4 cdef size_t MARRAY = 1, IARRAY = 2, JARRAY = 3 @@ -38,7 +36,7 @@ def read_matrix(path): The score for a 'C' changing to an 'A' is stored in the matrix as: mat[ord('C'), ord('A')] = score """ - cdef np.ndarray[DTYPE_INT, ndim=2] a + cdef np.ndarray[DTYPE_LONG, ndim=2] a cdef size_t ai = 0, i cdef int v, mat_size @@ -50,7 +48,7 @@ def read_matrix(path): headers = [ord(x) for x in line.split(' ') if x] mat_size = max(headers) + 1 - a = np.zeros((mat_size, mat_size), dtype=int) + a = np.zeros((mat_size, mat_size), dtype=long) line = fh.readline() while line: @@ -72,7 +70,7 @@ def make_matrix(match_score=5, mismatch_score=-4, n_mismatch_score=-2, n_match_s n_mismatch_score: score for matching a nucleotide with 'N' n_match_score: score for 'N' matching an 'N' """ - cdef np.ndarray[DTYPE_INT, ndim=2] a + cdef np.ndarray[DTYPE_LONG, ndim=2] a cdef size_t ai = 0, i cdef int v, mat_size @@ -82,7 +80,7 @@ def make_matrix(match_score=5, mismatch_score=-4, n_mismatch_score=-2, n_match_s nuc_ords = [ord(x) for x in ['A','T','C','G']] - a = np.zeros((mat_size, mat_size), dtype=int) + a = np.zeros((mat_size, mat_size), dtype=long) for nuc in nuc_ords: for nuc2 in nuc_ords: @@ -102,8 +100,8 @@ def make_matrix(match_score=5, mismatch_score=-4, n_mismatch_score=-2, n_match_s @cython.boundscheck(False) @cython.nonecheck(False) -def global_align(str pystr_seqj, str pystr_seqi, np.ndarray[DTYPE_INT, ndim=2] matrix, - np.ndarray[DTYPE_INT,ndim=1] gap_incentive, int gap_open=-1, +def global_align(str pystr_seqj, str pystr_seqi, np.ndarray[DTYPE_LONG, ndim=2] matrix, + np.ndarray[DTYPE_LONG,ndim=1] gap_incentive, int gap_open=-1, int gap_extend=-1): """ Global sequence alignment (needleman-wunsch) on seq i and j. diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py index 529bf3bf..6094d40b 100644 --- a/CRISPResso2/CRISPRessoCORE.py +++ b/CRISPResso2/CRISPRessoCORE.py @@ -2335,7 +2335,7 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited #subtract any indices in 'exclude_idxs' -- e.g. in case some of the cloned include_idxs were near the read ends (excluded) this_exclude_idxs = sorted(list(set(refs[ref_name]['exclude_idxs']))) - this_include_idxs = sorted(list(set(np.setdiff1d(this_include_idxs, this_exclude_idxs)))) + this_include_idxs = sorted(map(int, set(np.setdiff1d(this_include_idxs, this_exclude_idxs)))) refs[ref_name]['gap_incentive'] = this_gap_incentive refs[ref_name]['sgRNA_cut_points'] = this_cut_points @@ -2360,8 +2360,8 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited ) #subtract any indices in 'exclude_idxs' -- e.g. in case some of the cloned include_idxs were near the read ends (excluded) - this_exclude_idxs = sorted(list(set(refs[ref_name]['exclude_idxs']))) - this_include_idxs = sorted(list(set(np.setdiff1d(this_include_idxs, this_exclude_idxs)))) + this_exclude_idxs = sorted(map(int, set(refs[ref_name]['exclude_idxs']))) + this_include_idxs = sorted(map(int, set(np.setdiff1d(this_include_idxs, this_exclude_idxs)))) refs[ref_name]['include_idxs'] = this_include_idxs refs[ref_name]['exclude_idxs'] = this_exclude_idxs @@ -3361,11 +3361,15 @@ def calculate_99_max(d): ref_info_file.write(refString) np.set_printoptions(linewidth=1000**1000) #no line breaks for ref_name in ref_names: + if isinstance(refs[ref_name]['include_idxs'], np.ndarray): + refs[ref_name]['include_idxs'] = refs[ref_name]['include_idxs'].tolist() + if isinstance(refs[ref_name]['exclude_idxs'], np.ndarray): + refs[ref_name]['exclude_idxs'] = refs[ref_name]['exclude_idxs'].tolist() refString = ( refs[ref_name]['name'] + "\t" + str(refs[ref_name]['sequence']) + "\t" + str(refs[ref_name]['sequence_length']) + "\t" + str(refs[ref_name]['min_aln_score']) + "\t" + - str(refs[ref_name]['gap_incentive']) + "\t" + + str(refs[ref_name]['gap_incentive'].tolist()) + "\t" + str(refs[ref_name]['sgRNA_cut_points']) + "\t" + str(refs[ref_name]['sgRNA_plot_cut_points']) + "\t" + str(refs[ref_name]['sgRNA_intervals']) + "\t" + diff --git a/CRISPResso2/CRISPRessoCOREResources.c b/CRISPResso2/CRISPRessoCOREResources.c index acbfe0b8..70c4cc7d 100644 --- a/CRISPResso2/CRISPRessoCOREResources.c +++ b/CRISPResso2/CRISPRessoCOREResources.c @@ -1,21 +1,21 @@ -/* Generated by Cython 3.0.10 */ +/* Generated by Cython 3.0.11 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ - "/Users/cole/mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h", - "/Users/cole/mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h", - "/Users/cole/mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h", - "/Users/cole/mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h", - "/Users/cole/mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h" + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayobject.h", + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayscalars.h", + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h", + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarraytypes.h", + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ufuncobject.h" ], "extra_compile_args": [ "-w", "-Ofast" ], "include_dirs": [ - "/Users/cole/mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/core/include" + "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include" ], "name": "CRISPResso2.CRISPRessoCOREResources", "sources": [ @@ -50,10 +50,10 @@ END: Cython Metadata */ #else #define __PYX_EXTRA_ABI_MODULE_NAME "" #endif -#define CYTHON_ABI "3_0_10" __PYX_EXTRA_ABI_MODULE_NAME +#define CYTHON_ABI "3_0_11" __PYX_EXTRA_ABI_MODULE_NAME #define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI #define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "." -#define CYTHON_HEX_VERSION 0x03000AF0 +#define CYTHON_HEX_VERSION 0x03000BF0 #define CYTHON_FUTURE_DIVISION 1 #include #ifndef offsetof @@ -1249,7 +1249,7 @@ static CYTHON_INLINE float __PYX_NAN() { #include /* Using NumPy API declarations from "numpy/__init__.cython-30.pxd" */ - + #include "numpy/arrayobject.h" #include "numpy/ndarrayobject.h" #include "numpy/ndarraytypes.h" @@ -1538,17 +1538,17 @@ static const char *__pyx_f[] = { /* #### Code section: numeric_typedefs ### */ -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":730 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":769 * # in Cython to enable them only on the right systems. - * + * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":731 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":770 + * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< * ctypedef npy_int32 int32_t @@ -1556,7 +1556,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":732 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":771 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -1565,7 +1565,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":733 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":772 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -1574,17 +1574,17 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":737 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":776 * #ctypedef npy_int128 int128_t - * + * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":738 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":777 + * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< * ctypedef npy_uint32 uint32_t @@ -1592,7 +1592,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":739 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":778 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1601,7 +1601,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":740 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":779 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1610,17 +1610,17 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":744 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":783 * #ctypedef npy_uint128 uint128_t - * + * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< * ctypedef npy_float64 float64_t * #ctypedef npy_float80 float80_t */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":745 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":784 + * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< * #ctypedef npy_float80 float80_t @@ -1628,84 +1628,66 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":754 - * # The int types are mapped a bit surprising -- - * # numpy.int corresponds to 'l' and numpy.long to 'q' - * ctypedef npy_long int_t # <<<<<<<<<<<<<< - * ctypedef npy_longlong longlong_t - * - */ -typedef npy_long __pyx_t_5numpy_int_t; - -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":755 - * # numpy.int corresponds to 'l' and numpy.long to 'q' - * ctypedef npy_long int_t +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":791 + * ctypedef double complex complex128_t + * * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< - * - * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulonglong_t + * */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":757 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":792 + * * ctypedef npy_longlong longlong_t - * - * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< - * ctypedef npy_ulonglong ulonglong_t - * - */ -typedef npy_ulong __pyx_t_5numpy_uint_t; - -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":758 - * - * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< - * + * * ctypedef npy_intp intp_t */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":760 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":794 * ctypedef npy_ulonglong ulonglong_t - * + * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< * ctypedef npy_uintp uintp_t - * + * */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":761 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":795 + * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< - * + * * ctypedef npy_double float_t */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":763 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":797 * ctypedef npy_uintp uintp_t - * + * * ctypedef npy_double float_t # <<<<<<<<<<<<<< * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":764 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":798 + * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< * ctypedef npy_longdouble longdouble_t - * + * */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":765 +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":799 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< - * - * ctypedef npy_cfloat cfloat_t + * + * ctypedef float complex cfloat_t */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; /* #### Code section: complex_type_declarations ### */ @@ -1733,45 +1715,39 @@ static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(floa #endif static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); +/* Declarations.proto */ +#if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) + #ifdef __cplusplus + typedef ::std::complex< long double > __pyx_t_long_double_complex; + #else + typedef long double _Complex __pyx_t_long_double_complex; + #endif +#else + typedef struct { long double real, imag; } __pyx_t_long_double_complex; +#endif +static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_from_parts(long double, long double); + /* #### Code section: type_declarations ### */ /*--- Type declarations ---*/ -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":767 - * ctypedef npy_longdouble longdouble_t - * - * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< - * ctypedef npy_cdouble cdouble_t - * ctypedef npy_clongdouble clongdouble_t - */ -typedef npy_cfloat __pyx_t_5numpy_cfloat_t; - -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":768 - * - * ctypedef npy_cfloat cfloat_t - * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< - * ctypedef npy_clongdouble clongdouble_t - * - */ -typedef npy_cdouble __pyx_t_5numpy_cdouble_t; - -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":769 - * ctypedef npy_cfloat cfloat_t - * ctypedef npy_cdouble cdouble_t - * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< - * - * ctypedef npy_cdouble complex_t - */ -typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; - -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":771 - * ctypedef npy_clongdouble clongdouble_t - * - * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< - * - * cdef inline object PyArray_MultiIterNew1(a): +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1095 + * + * # Iterator API added in v1.6 + * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil # <<<<<<<<<<<<<< + * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil + * + */ +typedef int (*__pyx_t_5numpy_NpyIter_IterNextFunc)(NpyIter *); + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1096 + * # Iterator API added in v1.6 + * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil + * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil # <<<<<<<<<<<<<< + * + * cdef extern from "numpy/arrayobject.h": */ -typedef npy_cdouble __pyx_t_5numpy_complex_t; +typedef void (*__pyx_t_5numpy_NpyIter_GetMultiIndexFunc)(NpyIter *, npy_intp *); /* #### Code section: utility_code_proto ### */ /* --- Runtime support code (head) --- */ @@ -2233,22 +2209,22 @@ static CYTHON_INLINE int __Pyx_IterFinish(void); static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /* TypeImport.proto */ -#ifndef __PYX_HAVE_RT_ImportType_proto_3_0_10 -#define __PYX_HAVE_RT_ImportType_proto_3_0_10 +#ifndef __PYX_HAVE_RT_ImportType_proto_3_0_11 +#define __PYX_HAVE_RT_ImportType_proto_3_0_11 #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L #include #endif #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L -#define __PYX_GET_STRUCT_ALIGNMENT_3_0_10(s) alignof(s) +#define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) alignof(s) #else -#define __PYX_GET_STRUCT_ALIGNMENT_3_0_10(s) sizeof(void*) +#define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) sizeof(void*) #endif -enum __Pyx_ImportType_CheckSize_3_0_10 { - __Pyx_ImportType_CheckSize_Error_3_0_10 = 0, - __Pyx_ImportType_CheckSize_Warn_3_0_10 = 1, - __Pyx_ImportType_CheckSize_Ignore_3_0_10 = 2 +enum __Pyx_ImportType_CheckSize_3_0_11 { + __Pyx_ImportType_CheckSize_Error_3_0_11 = 0, + __Pyx_ImportType_CheckSize_Warn_3_0_11 = 1, + __Pyx_ImportType_CheckSize_Ignore_3_0_11 = 2 }; -static PyTypeObject *__Pyx_ImportType_3_0_10(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_10 check_size); +static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size); #endif /* Import.proto */ @@ -2572,6 +2548,44 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, #endif #endif +/* Arithmetic.proto */ +#if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) + #define __Pyx_c_eq_long__double(a, b) ((a)==(b)) + #define __Pyx_c_sum_long__double(a, b) ((a)+(b)) + #define __Pyx_c_diff_long__double(a, b) ((a)-(b)) + #define __Pyx_c_prod_long__double(a, b) ((a)*(b)) + #define __Pyx_c_quot_long__double(a, b) ((a)/(b)) + #define __Pyx_c_neg_long__double(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero_long__double(z) ((z)==(long double)0) + #define __Pyx_c_conj_long__double(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs_long__double(z) (::std::abs(z)) + #define __Pyx_c_pow_long__double(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero_long__double(z) ((z)==0) + #define __Pyx_c_conj_long__double(z) (conjl(z)) + #if 1 + #define __Pyx_c_abs_long__double(z) (cabsl(z)) + #define __Pyx_c_pow_long__double(a, b) (cpowl(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_sum_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_diff_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_prod_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_quot_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_neg_long__double(__pyx_t_long_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_long__double(__pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_conj_long__double(__pyx_t_long_double_complex); + #if 1 + static CYTHON_INLINE long double __Pyx_c_abs_long__double(__pyx_t_long_double_complex); + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_pow_long__double(__pyx_t_long_double_complex, __pyx_t_long_double_complex); + #endif +#endif + /* CIntFromPy.proto */ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); @@ -2625,6 +2639,18 @@ static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /* #### Code section: module_declarations ### */ +static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr *__pyx_v_self); /* proto*/ +static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject *__pyx_v_self); /* proto*/ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject *__pyx_v_self); /* proto*/ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArrayObject *__pyx_v_self); /* proto*/ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx_v_self); /* proto*/ @@ -2772,11 +2798,11 @@ static const char __pyx_k_ResultsSlotsDict___getitem[] = "ResultsSlotsDict.__get static const char __pyx_k_ResultsSlotsDict___setitem[] = "ResultsSlotsDict.__setitem__"; static const char __pyx_k_all_substitution_positions[] = "all_substitution_positions"; static const char __pyx_k_all_insertion_left_positions[] = "all_insertion_left_positions"; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour[] = "CRISPResso2.CRISPRessoCOREResources"; +static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour[] = "CRISPResso2/CRISPRessoCOREResources.pyx"; static const char __pyx_k_find_indels_substitutions_legacy[] = "find_indels_substitutions_legacy"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour_2[] = "CRISPResso2/CRISPRessoCOREResources.pyx"; +static const char __pyx_k_numpy__core_multiarray_failed_to[] = "numpy._core.multiarray failed to import"; +static const char __pyx_k_numpy__core_umath_failed_to_impo[] = "numpy._core.umath failed to import"; +static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour_2[] = "CRISPResso2.CRISPRessoCOREResources"; /* #### Code section: decls ### */ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_all_insertion_positions, PyObject *__pyx_v_all_insertion_left_positions, PyObject *__pyx_v_insertion_positions, PyObject *__pyx_v_insertion_coordinates, PyObject *__pyx_v_insertion_sizes, PyObject *__pyx_v_insertion_n, PyObject *__pyx_v_all_deletion_positions, PyObject *__pyx_v_deletion_positions, PyObject *__pyx_v_deletion_coordinates, PyObject *__pyx_v_deletion_sizes, PyObject *__pyx_v_deletion_n, PyObject *__pyx_v_all_substitution_positions, PyObject *__pyx_v_substitution_positions, PyObject *__pyx_v_all_substitution_values, PyObject *__pyx_v_substitution_values, PyObject *__pyx_v_substitution_n, PyObject *__pyx_v_ref_positions); /* proto */ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_2__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ @@ -2945,8 +2971,8 @@ typedef struct { PyObject *__pyx_n_s_np; PyObject *__pyx_n_s_nucSet; PyObject *__pyx_n_s_numpy; - PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; - PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; + PyObject *__pyx_kp_u_numpy__core_multiarray_failed_to; + PyObject *__pyx_kp_u_numpy__core_umath_failed_to_impo; PyObject *__pyx_n_s_p; PyObject *__pyx_n_s_prepare; PyObject *__pyx_n_s_qualname; @@ -3155,8 +3181,8 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_n_s_np); Py_CLEAR(clear_module_state->__pyx_n_s_nucSet); Py_CLEAR(clear_module_state->__pyx_n_s_numpy); - Py_CLEAR(clear_module_state->__pyx_kp_u_numpy_core_multiarray_failed_to); - Py_CLEAR(clear_module_state->__pyx_kp_u_numpy_core_umath_failed_to_impor); + Py_CLEAR(clear_module_state->__pyx_kp_u_numpy__core_multiarray_failed_to); + Py_CLEAR(clear_module_state->__pyx_kp_u_numpy__core_umath_failed_to_impo); Py_CLEAR(clear_module_state->__pyx_n_s_p); Py_CLEAR(clear_module_state->__pyx_n_s_prepare); Py_CLEAR(clear_module_state->__pyx_n_s_qualname); @@ -3343,8 +3369,8 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_n_s_np); Py_VISIT(traverse_module_state->__pyx_n_s_nucSet); Py_VISIT(traverse_module_state->__pyx_n_s_numpy); - Py_VISIT(traverse_module_state->__pyx_kp_u_numpy_core_multiarray_failed_to); - Py_VISIT(traverse_module_state->__pyx_kp_u_numpy_core_umath_failed_to_impor); + Py_VISIT(traverse_module_state->__pyx_kp_u_numpy__core_multiarray_failed_to); + Py_VISIT(traverse_module_state->__pyx_kp_u_numpy__core_umath_failed_to_impo); Py_VISIT(traverse_module_state->__pyx_n_s_p); Py_VISIT(traverse_module_state->__pyx_n_s_prepare); Py_VISIT(traverse_module_state->__pyx_n_s_qualname); @@ -3561,8 +3587,8 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_n_s_np __pyx_mstate_global->__pyx_n_s_np #define __pyx_n_s_nucSet __pyx_mstate_global->__pyx_n_s_nucSet #define __pyx_n_s_numpy __pyx_mstate_global->__pyx_n_s_numpy -#define __pyx_kp_u_numpy_core_multiarray_failed_to __pyx_mstate_global->__pyx_kp_u_numpy_core_multiarray_failed_to -#define __pyx_kp_u_numpy_core_umath_failed_to_impor __pyx_mstate_global->__pyx_kp_u_numpy_core_umath_failed_to_impor +#define __pyx_kp_u_numpy__core_multiarray_failed_to __pyx_mstate_global->__pyx_kp_u_numpy__core_multiarray_failed_to +#define __pyx_kp_u_numpy__core_umath_failed_to_impo __pyx_mstate_global->__pyx_kp_u_numpy__core_umath_failed_to_impo #define __pyx_n_s_p __pyx_mstate_global->__pyx_n_s_p #define __pyx_n_s_prepare __pyx_mstate_global->__pyx_n_s_prepare #define __pyx_n_s_qualname __pyx_mstate_global->__pyx_n_s_qualname @@ -3620,10 +3646,434 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_codeobj__19 __pyx_mstate_global->__pyx_codeobj__19 /* #### Code section: module_code ### */ -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":245 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 + * + * @property + * cdef inline npy_intp itemsize(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_ELSIZE(self) + * + */ + +static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr *__pyx_v_self) { + npy_intp __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":287 + * @property + * cdef inline npy_intp itemsize(self) noexcept nogil: + * return PyDataType_ELSIZE(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyDataType_ELSIZE(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 + * + * @property + * cdef inline npy_intp itemsize(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_ELSIZE(self) + * + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + * + * @property + * cdef inline npy_intp alignment(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_ALIGNMENT(self) + * + */ + +static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr *__pyx_v_self) { + npy_intp __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":291 + * @property + * cdef inline npy_intp alignment(self) noexcept nogil: + * return PyDataType_ALIGNMENT(self) # <<<<<<<<<<<<<< + * + * # Use fields/names with care as they may be NULL. You must check + */ + __pyx_r = PyDataType_ALIGNMENT(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + * + * @property + * cdef inline npy_intp alignment(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_ALIGNMENT(self) + * + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 + * # for this using PyDataType_HASFIELDS. + * @property + * cdef inline object fields(self): # <<<<<<<<<<<<<< + * return PyDataType_FIELDS(self) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Descr *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1; + __Pyx_RefNannySetupContext("fields", 1); + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":297 + * @property + * cdef inline object fields(self): + * return PyDataType_FIELDS(self) # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyDataType_FIELDS(__pyx_v_self); + __Pyx_INCREF(((PyObject *)__pyx_t_1)); + __pyx_r = ((PyObject *)__pyx_t_1); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 + * # for this using PyDataType_HASFIELDS. + * @property + * cdef inline object fields(self): # <<<<<<<<<<<<<< + * return PyDataType_FIELDS(self) + * + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 + * + * @property + * cdef inline tuple names(self): # <<<<<<<<<<<<<< + * return PyDataType_NAMES(self) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1; + __Pyx_RefNannySetupContext("names", 1); + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":301 + * @property + * cdef inline tuple names(self): + * return PyDataType_NAMES(self) # <<<<<<<<<<<<<< + * + * # Use PyDataType_HASSUBARRAY to test whether this field is + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyDataType_NAMES(__pyx_v_self); + __Pyx_INCREF(((PyObject*)__pyx_t_1)); + __pyx_r = ((PyObject*)__pyx_t_1); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 + * + * @property + * cdef inline tuple names(self): # <<<<<<<<<<<<<< + * return PyDataType_NAMES(self) + * + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 + * # this field via the inline helper method PyDataType_SHAPE. + * @property + * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_SUBARRAY(self) + * + */ + +static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr *__pyx_v_self) { + PyArray_ArrayDescr *__pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":308 + * @property + * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: + * return PyDataType_SUBARRAY(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyDataType_SUBARRAY(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 + * # this field via the inline helper method PyDataType_SHAPE. + * @property + * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: # <<<<<<<<<<<<<< + * return PyDataType_SUBARRAY(self) + * + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 + * + * @property + * cdef inline npy_uint64 flags(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The data types flags.""" + * return PyDataType_FLAGS(self) + */ + +static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr *__pyx_v_self) { + npy_uint64 __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":313 + * cdef inline npy_uint64 flags(self) noexcept nogil: + * """The data types flags.""" + * return PyDataType_FLAGS(self) # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = PyDataType_FLAGS(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 + * + * @property + * cdef inline npy_uint64 flags(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The data types flags.""" + * return PyDataType_FLAGS(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 + * + * @property + * cdef inline int numiter(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The number of arrays that need to be broadcast to the same shape.""" + * return PyArray_MultiIter_NUMITER(self) + */ + +static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject *__pyx_v_self) { + int __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":325 + * cdef inline int numiter(self) noexcept nogil: + * """The number of arrays that need to be broadcast to the same shape.""" + * return PyArray_MultiIter_NUMITER(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_NUMITER(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 + * + * @property + * cdef inline int numiter(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The number of arrays that need to be broadcast to the same shape.""" + * return PyArray_MultiIter_NUMITER(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 + * + * @property + * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The total broadcasted size.""" + * return PyArray_MultiIter_SIZE(self) + */ + +static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject *__pyx_v_self) { + npy_intp __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":330 + * cdef inline npy_intp size(self) noexcept nogil: + * """The total broadcasted size.""" + * return PyArray_MultiIter_SIZE(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_SIZE(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 + * + * @property + * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The total broadcasted size.""" + * return PyArray_MultiIter_SIZE(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 + * + * @property + * cdef inline npy_intp index(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The current (1-d) index into the broadcasted result.""" + * return PyArray_MultiIter_INDEX(self) + */ + +static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject *__pyx_v_self) { + npy_intp __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":335 + * cdef inline npy_intp index(self) noexcept nogil: + * """The current (1-d) index into the broadcasted result.""" + * return PyArray_MultiIter_INDEX(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_INDEX(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 + * + * @property + * cdef inline npy_intp index(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The current (1-d) index into the broadcasted result.""" + * return PyArray_MultiIter_INDEX(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 + * + * @property + * cdef inline int nd(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The number of dimensions in the broadcasted result.""" + * return PyArray_MultiIter_NDIM(self) + */ + +static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject *__pyx_v_self) { + int __pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":340 + * cdef inline int nd(self) noexcept nogil: + * """The number of dimensions in the broadcasted result.""" + * return PyArray_MultiIter_NDIM(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_NDIM(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 + * + * @property + * cdef inline int nd(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The number of dimensions in the broadcasted result.""" + * return PyArray_MultiIter_NDIM(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 + * + * @property + * cdef inline npy_intp* dimensions(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The shape of the broadcasted result.""" + * return PyArray_MultiIter_DIMS(self) + */ + +static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject *__pyx_v_self) { + npy_intp *__pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":345 + * cdef inline npy_intp* dimensions(self) noexcept nogil: + * """The shape of the broadcasted result.""" + * return PyArray_MultiIter_DIMS(self) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 + * + * @property + * cdef inline npy_intp* dimensions(self) noexcept nogil: # <<<<<<<<<<<<<< + * """The shape of the broadcasted result.""" + * return PyArray_MultiIter_DIMS(self) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 + * + * @property + * cdef inline void** iters(self) noexcept nogil: # <<<<<<<<<<<<<< + * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. + * On return, the iterators are adjusted for broadcasting.""" + */ + +static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject *__pyx_v_self) { + void **__pyx_r; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":351 + * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. + * On return, the iterators are adjusted for broadcasting.""" + * return PyArray_MultiIter_ITERS(self) # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self); + goto __pyx_L0; + + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 + * + * @property + * cdef inline void** iters(self) noexcept nogil: # <<<<<<<<<<<<<< + * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. + * On return, the iterators are adjusted for broadcasting.""" + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 + * * @property - * cdef inline PyObject* base(self) nogil: # <<<<<<<<<<<<<< + * cdef inline PyObject* base(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a borrowed reference to the object owning the data/memory. * """ */ @@ -3631,20 +4081,20 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject *__pyx_v_self) { PyObject *__pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":248 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":369 * """Returns a borrowed reference to the object owning the data/memory. * """ * return PyArray_BASE(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_BASE(__pyx_v_self); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":245 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 + * * @property - * cdef inline PyObject* base(self) nogil: # <<<<<<<<<<<<<< + * cdef inline PyObject* base(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a borrowed reference to the object owning the data/memory. * """ */ @@ -3654,8 +4104,8 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":251 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 + * * @property * cdef inline dtype descr(self): # <<<<<<<<<<<<<< * """Returns an owned reference to the dtype of the array. @@ -3668,11 +4118,11 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray PyArray_Descr *__pyx_t_1; __Pyx_RefNannySetupContext("descr", 1); - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":254 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":375 * """Returns an owned reference to the dtype of the array. * """ * return PyArray_DESCR(self) # <<<<<<<<<<<<<< - * + * * @property */ __Pyx_XDECREF((PyObject *)__pyx_r); @@ -3681,8 +4131,8 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray __pyx_r = ((PyArray_Descr *)__pyx_t_1); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":251 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 + * * @property * cdef inline dtype descr(self): # <<<<<<<<<<<<<< * """Returns an owned reference to the dtype of the array. @@ -3696,10 +4146,10 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":257 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 + * * @property - * cdef inline int ndim(self) nogil: # <<<<<<<<<<<<<< + * cdef inline int ndim(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the number of dimensions in the array. * """ */ @@ -3707,20 +4157,20 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx_v_self) { int __pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":260 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":381 * """Returns the number of dimensions in the array. * """ * return PyArray_NDIM(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":257 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 + * * @property - * cdef inline int ndim(self) nogil: # <<<<<<<<<<<<<< + * cdef inline int ndim(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the number of dimensions in the array. * """ */ @@ -3730,10 +4180,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":263 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 + * * @property - * cdef inline npy_intp *shape(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp *shape(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the dimensions/shape of the array. * The number of elements matches the number of dimensions of the array (ndim). */ @@ -3741,20 +4191,20 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":268 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":389 * Can return NULL for 0-dimensional arrays. * """ * return PyArray_DIMS(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":263 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 + * * @property - * cdef inline npy_intp *shape(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp *shape(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the dimensions/shape of the array. * The number of elements matches the number of dimensions of the array (ndim). */ @@ -3764,10 +4214,10 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":271 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 + * * @property - * cdef inline npy_intp *strides(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp *strides(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the strides of the array. * The number of elements matches the number of dimensions of the array (ndim). */ @@ -3775,20 +4225,20 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":275 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":396 * The number of elements matches the number of dimensions of the array (ndim). * """ * return PyArray_STRIDES(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_STRIDES(__pyx_v_self); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":271 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 + * * @property - * cdef inline npy_intp *strides(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp *strides(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the strides of the array. * The number of elements matches the number of dimensions of the array (ndim). */ @@ -3798,10 +4248,10 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":278 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 + * * @property - * cdef inline npy_intp size(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the total size (in number of elements) of the array. * """ */ @@ -3809,20 +4259,20 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":281 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":402 * """Returns the total size (in number of elements) of the array. * """ * return PyArray_SIZE(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":278 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 + * * @property - * cdef inline npy_intp size(self) nogil: # <<<<<<<<<<<<<< + * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the total size (in number of elements) of the array. * """ */ @@ -3832,10 +4282,10 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":284 - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 + * * @property - * cdef inline char* data(self) nogil: # <<<<<<<<<<<<<< + * cdef inline char* data(self) noexcept nogil: # <<<<<<<<<<<<<< * """The pointer to the data buffer as a char*. * This is provided for legacy reasons to avoid direct struct field access. */ @@ -3843,20 +4293,20 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__pyx_v_self) { char *__pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":411 * of `PyArray_DATA()` instead, which returns a 'void*'. * """ * return PyArray_BYTES(self) # <<<<<<<<<<<<<< - * - * ctypedef unsigned char npy_bool + * + * */ __pyx_r = PyArray_BYTES(__pyx_v_self); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":284 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 + * * @property - * cdef inline char* data(self) nogil: # <<<<<<<<<<<<<< + * cdef inline char* data(self) noexcept nogil: # <<<<<<<<<<<<<< * """The pointer to the data buffer as a char*. * This is provided for legacy reasons to avoid direct struct field access. */ @@ -3866,12 +4316,12 @@ static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__p return __pyx_r; 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if (__pyx_t_1) { - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":790 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":823 * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): * return d.subarray.shape # <<<<<<<<<<<<<< @@ -4148,12 +4599,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ * return () */ __Pyx_XDECREF(__pyx_r); - __Pyx_INCREF(((PyObject*)__pyx_v_d->subarray->shape)); - __pyx_r = ((PyObject*)__pyx_v_d->subarray->shape); + __pyx_t_2 = __pyx_f_5numpy_5dtype_8subarray_subarray(__pyx_v_d)->shape; + __Pyx_INCREF(((PyObject*)__pyx_t_2)); + __pyx_r = ((PyObject*)__pyx_t_2); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":789 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 + * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< * return d.subarray.shape @@ -4161,12 +4613,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":792 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":825 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< - * - * + * + * */ /*else*/ { __Pyx_XDECREF(__pyx_r); 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__pyx_L3_error:; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":989 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1030 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< - * raise ImportError("numpy.core.umath failed to import") - * + * raise ImportError("numpy._core.umath failed to import") + * */ __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_umath", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(1, 989, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(1, 1030, __pyx_L5_except_error) __Pyx_XGOTREF(__pyx_t_5); __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":990 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 * _import_umath() * except Exception: - * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< - * + * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< + * * cdef inline int import_ufunc() except -1: */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 990, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 1031, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(1, 990, __pyx_L5_except_error) + __PYX_ERR(1, 1031, __pyx_L5_except_error) } goto __pyx_L5_except_error; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":987 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 + * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4559,9 +5011,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":986 - * raise ImportError("numpy.core.multiarray failed to import") - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 + * raise ImportError("numpy._core.multiarray failed to import") + * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< * try: * _import_umath() @@ -4582,9 +5034,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":992 - * raise ImportError("numpy.core.umath failed to import") - * +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 + * raise ImportError("numpy._core.umath failed to import") + * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< * try: * _import_umath() @@ -4606,8 +5058,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_ufunc", 1); - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":993 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4622,17 +5074,17 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":994 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1035 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< * except Exception: - * raise ImportError("numpy.core.umath failed to import") + * raise ImportError("numpy._core.umath failed to import") */ - __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 994, __pyx_L3_error) + __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1035, __pyx_L3_error) - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":993 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4645,38 +5097,38 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":995 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1036 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< - * raise ImportError("numpy.core.umath failed to import") - * + * raise ImportError("numpy._core.umath failed to import") + * */ __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_ufunc", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(1, 995, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(1, 1036, __pyx_L5_except_error) __Pyx_XGOTREF(__pyx_t_5); __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":996 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1037 * _import_umath() * except Exception: - * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< - * - * + * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< + * + * */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 996, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 1037, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(1, 996, __pyx_L5_except_error) + __PYX_ERR(1, 1037, __pyx_L5_except_error) } goto __pyx_L5_except_error; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":993 - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4691,9 +5143,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":992 - * raise ImportError("numpy.core.umath failed to import") - * + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 + * raise ImportError("numpy._core.umath failed to import") + * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< * try: * _import_umath() @@ -4714,10 +5166,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":999 - * - * - * cdef inline bint is_timedelta64_object(object obj): # <<<<<<<<<<<<<< +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 + * + * + * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.timedelta64)` */ @@ -4725,20 +5177,20 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1011 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1052 * bool * """ * return PyObject_TypeCheck(obj, &PyTimedeltaArrType_Type) # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyTimedeltaArrType_Type)); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":999 - * - * - * cdef inline bint is_timedelta64_object(object obj): # <<<<<<<<<<<<<< + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 + * + * + * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.timedelta64)` */ @@ -4748,10 +5200,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1014 - * - * - * cdef inline bint is_datetime64_object(object obj): # <<<<<<<<<<<<<< +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 + * + * + * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.datetime64)` */ @@ -4759,20 +5211,20 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1026 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1067 * bool * """ * return PyObject_TypeCheck(obj, &PyDatetimeArrType_Type) # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyDatetimeArrType_Type)); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1014 - * - * - * cdef inline bint is_datetime64_object(object obj): # <<<<<<<<<<<<<< + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 + * + * + * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.datetime64)` */ @@ -4782,10 +5234,10 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1029 - * - * - * cdef inline npy_datetime get_datetime64_value(object obj) nogil: # <<<<<<<<<<<<<< +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 + * + * + * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy datetime64 object */ @@ -4793,20 +5245,20 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject *__pyx_v_obj) { npy_datetime __pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1036 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1077 * also needed. That can be found using `get_datetime64_unit`. * """ * return (obj).obval # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = ((PyDatetimeScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1029 - * - * - * cdef inline npy_datetime get_datetime64_value(object obj) nogil: # <<<<<<<<<<<<<< + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 + * + * + * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy datetime64 object */ @@ -4816,10 +5268,10 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1039 - * - * - * cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<< +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 + * + * + * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy timedelta64 object */ @@ -4827,20 +5279,20 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject *__pyx_v_obj) { npy_timedelta __pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1043 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1084 * returns the int64 value underlying scalar numpy timedelta64 object * """ * return (obj).obval # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1039 - * - * - * cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<< + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 + * + * + * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy timedelta64 object */ @@ -4850,10 +5302,10 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject return __pyx_r; } -/* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1046 - * - * - * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<< +/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 + * + * + * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the unit part of the dtype for a numpy datetime64 object. */ @@ -4861,18 +5313,20 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObject *__pyx_v_obj) { NPY_DATETIMEUNIT __pyx_r; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1050 + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1091 * returns the unit part of the dtype for a numpy datetime64 object. * """ * return (obj).obmeta.base # <<<<<<<<<<<<<< + * + * */ __pyx_r = ((NPY_DATETIMEUNIT)((PyDatetimeScalarObject *)__pyx_v_obj)->obmeta.base); goto __pyx_L0; - /* "../../../mambaforge/envs/crispresso/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1046 - * - * - * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<< + /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 + * + * + * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the unit part of the dtype for a numpy datetime64 object. */ @@ -4884,14 +5338,14 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec /* "CRISPResso2/CRISPRessoCOREResources.pyx":18 * re_find_indels = re.compile("(-*-)") - * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) */ /* Python wrapper */ -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else @@ -4899,7 +5353,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds #endif ); /*proto*/ static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions = {"find_indels_substitutions", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else @@ -5059,6 +5513,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su int __pyx_t_10; int __pyx_t_11; size_t __pyx_t_12; + unsigned int __pyx_t_13; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -5105,7 +5560,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * substitution_positions=[] * all_substitution_values=[] # <<<<<<<<<<<<<< * substitution_values=[] - * + * */ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 35, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); @@ -5116,7 +5571,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * substitution_positions=[] * all_substitution_values=[] * substitution_values=[] # <<<<<<<<<<<<<< - * + * * all_deletion_positions = [] */ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 36, __pyx_L1_error) @@ -5126,7 +5581,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":38 * substitution_values=[] - * + * * all_deletion_positions = [] # <<<<<<<<<<<<<< * all_deletion_coordinates = [] * deletion_positions = [] @@ -5137,7 +5592,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_t_1 = 0; /* "CRISPResso2/CRISPRessoCOREResources.pyx":39 - * + * * all_deletion_positions = [] * all_deletion_coordinates = [] # <<<<<<<<<<<<<< * deletion_positions = [] @@ -5176,7 +5631,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * deletion_coordinates = [] * deletion_sizes = [] # <<<<<<<<<<<<<< * cdef int start_deletion = -1 # the -1 value indicates that there currently isn't a deletion - * + * */ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 119, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); @@ -5187,14 +5642,14 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * deletion_coordinates = [] * deletion_sizes = [] * cdef int start_deletion = -1 # the -1 value indicates that there currently isn't a deletion # <<<<<<<<<<<<<< - * + * * all_insertion_positions = [] */ __pyx_v_start_deletion = -1; /* "CRISPResso2/CRISPRessoCOREResources.pyx":122 * cdef int start_deletion = -1 # the -1 value indicates that there currently isn't a deletion - * + * * all_insertion_positions = [] # <<<<<<<<<<<<<< * all_insertion_left_positions = [] * insertion_positions = [] @@ -5204,8 +5659,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_v_all_insertion_positions = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":123 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":46 + * * all_insertion_positions = [] * all_insertion_left_positions = [] # <<<<<<<<<<<<<< * insertion_positions = [] @@ -5245,7 +5700,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * insertion_coordinates = [] * insertion_sizes = [] # <<<<<<<<<<<<<< * cdef int start_insertion = -1 # the -1 value indicates that there currently isn't an insertion - * + * */ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 126, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); @@ -5256,14 +5711,14 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * insertion_coordinates = [] * insertion_sizes = [] * cdef int start_insertion = -1 # the -1 value indicates that there currently isn't an insertion # <<<<<<<<<<<<<< - * + * * cdef size_t seq_len = len(ref_seq_al) */ __pyx_v_start_insertion = -1; /* "CRISPResso2/CRISPRessoCOREResources.pyx":129 * cdef int start_insertion = -1 # the -1 value indicates that there currently isn't an insertion - * + * * cdef size_t seq_len = len(ref_seq_al) # <<<<<<<<<<<<<< * include_indx_set = set(_include_indx) * nucSet = set(['A', 'T', 'C', 'G', 'N']) @@ -5271,8 +5726,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_t_2 = PyObject_Length(__pyx_v_ref_seq_al); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1))) __PYX_ERR(0, 129, __pyx_L1_error) __pyx_v_seq_len = __pyx_t_2; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":130 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":53 + * * cdef size_t seq_len = len(ref_seq_al) * include_indx_set = set(_include_indx) # <<<<<<<<<<<<<< * nucSet = set(['A', 'T', 'C', 'G', 'N']) @@ -5773,7 +6228,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * if idx > 0 and start_insertion == -1: # this is the first index of an insertion * start_insertion = idx - 1 # <<<<<<<<<<<<<< * current_insertion_size += 1 - * + * */ __pyx_v_start_insertion = (__pyx_v_idx - 1); @@ -5790,7 +6245,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * if idx > 0 and start_insertion == -1: # this is the first index of an insertion * start_insertion = idx - 1 * current_insertion_size += 1 # <<<<<<<<<<<<<< - * + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion */ __pyx_v_current_insertion_size = (__pyx_v_current_insertion_size + 1); @@ -5799,7 +6254,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":165 * current_insertion_size += 1 - * + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion # <<<<<<<<<<<<<< * if idx_c - 1 > 0: * start_deletion = ref_positions[idx_c] @@ -5818,8 +6273,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_L20_bool_binop_done:; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":166 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":89 + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion * if idx_c - 1 > 0: # <<<<<<<<<<<<<< * start_deletion = ref_positions[idx_c] @@ -5838,8 +6293,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_t_11 = __Pyx_PyInt_As_int(PyList_GET_ITEM(__pyx_v_ref_positions, __pyx_v_idx_c)); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 167, __pyx_L1_error) __pyx_v_start_deletion = __pyx_t_11; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":166 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":89 + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion * if idx_c - 1 > 0: # <<<<<<<<<<<<<< * start_deletion = ref_positions[idx_c] @@ -5862,7 +6317,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":165 * current_insertion_size += 1 - * + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion # <<<<<<<<<<<<<< * if idx_c - 1 > 0: * start_deletion = ref_positions[idx_c] @@ -6015,7 +6470,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * deletion_coordinates.append((start_deletion, end_deletion)) * deletion_sizes.append(end_deletion - start_deletion) # <<<<<<<<<<<<<< * start_deletion = -1 - * + * */ __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 100, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); @@ -6038,7 +6493,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * deletion_coordinates.append((start_deletion, end_deletion)) * deletion_sizes.append(end_deletion - start_deletion) * start_deletion = -1 # <<<<<<<<<<<<<< - * + * * if start_deletion != -1: */ __pyx_v_start_deletion = -1; @@ -6065,7 +6520,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":103 * start_deletion = -1 - * + * * if start_deletion != -1: # <<<<<<<<<<<<<< * end_deletion = ref_positions[seq_len - 1] * all_deletion_positions.extend(range(start_deletion, end_deletion)) @@ -6074,7 +6529,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su if (__pyx_t_6) { /* "CRISPResso2/CRISPRessoCOREResources.pyx":104 - * + * * if start_deletion != -1: * end_deletion = ref_positions[seq_len - 1] # <<<<<<<<<<<<<< * all_deletion_positions.extend(range(start_deletion, end_deletion)) @@ -6184,7 +6639,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * deletion_positions.extend(range(start_deletion, end_deletion)) * deletion_coordinates.append((start_deletion, end_deletion)) # <<<<<<<<<<<<<< * deletion_sizes.append(end_deletion - start_deletion) - * + * */ __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 109, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); @@ -6203,7 +6658,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * deletion_positions.extend(range(start_deletion, end_deletion)) * deletion_coordinates.append((start_deletion, end_deletion)) * deletion_sizes.append(end_deletion - start_deletion) # <<<<<<<<<<<<<< - * + * * cdef size_t substitution_n = len(substitution_positions) */ __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 110, __pyx_L1_error) @@ -6225,7 +6680,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":103 * start_deletion = -1 - * + * * if start_deletion != -1: # <<<<<<<<<<<<<< * end_deletion = ref_positions[seq_len - 1] * all_deletion_positions.extend(range(start_deletion, end_deletion)) @@ -6234,7 +6689,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":112 * deletion_sizes.append(end_deletion - start_deletion) - * + * * cdef size_t substitution_n = len(substitution_positions) # <<<<<<<<<<<<<< * cdef size_t deletion_n = sum(deletion_sizes) * cdef size_t insertion_n = sum(insertion_sizes) @@ -6243,11 +6698,11 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_v_substitution_n = __pyx_t_2; /* "CRISPResso2/CRISPRessoCOREResources.pyx":113 - * + * * cdef size_t substitution_n = len(substitution_positions) * cdef size_t deletion_n = sum(deletion_sizes) # <<<<<<<<<<<<<< * cdef size_t insertion_n = sum(insertion_sizes) - * + * */ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_sum, __pyx_v_deletion_sizes); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 113, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); @@ -6259,8 +6714,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * cdef size_t substitution_n = len(substitution_positions) * cdef size_t deletion_n = sum(deletion_sizes) * cdef size_t insertion_n = sum(insertion_sizes) # <<<<<<<<<<<<<< - * - * # return ResultsSlotsDict( + * + * return { */ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_sum, __pyx_v_insertion_sizes); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 114, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); @@ -6270,7 +6725,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":116 * cdef size_t insertion_n = sum(insertion_sizes) - * + * * return { # <<<<<<<<<<<<<< * 'all_insertion_positions': all_insertion_positions, * 'all_insertion_left_positions': all_insertion_left_positions, @@ -6278,7 +6733,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __Pyx_XDECREF(__pyx_r); /* "CRISPResso2/CRISPRessoCOREResources.pyx":117 - * + * * return { * 'all_insertion_positions': all_insertion_positions, # <<<<<<<<<<<<<< * 'all_insertion_left_positions': all_insertion_left_positions, @@ -6320,7 +6775,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * 'insertion_coordinates': insertion_coordinates, * 'insertion_sizes': insertion_sizes, # <<<<<<<<<<<<<< * 'insertion_n': insertion_n, - * + * */ if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_sizes, __pyx_v_insertion_sizes) < 0) __PYX_ERR(0, 117, __pyx_L1_error) @@ -6328,7 +6783,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * 'insertion_coordinates': insertion_coordinates, * 'insertion_sizes': insertion_sizes, * 'insertion_n': insertion_n, # <<<<<<<<<<<<<< - * + * * 'all_deletion_positions': all_deletion_positions, */ __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_insertion_n); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 122, __pyx_L1_error) @@ -6338,7 +6793,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":124 * 'insertion_n': insertion_n, - * + * * 'all_deletion_positions': all_deletion_positions, # <<<<<<<<<<<<<< * 'all_deletion_coordinates': all_deletion_coordinates, * 'deletion_positions': deletion_positions, @@ -6346,7 +6801,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_deletion_positions, __pyx_v_all_deletion_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) /* "CRISPResso2/CRISPRessoCOREResources.pyx":125 - * + * * 'all_deletion_positions': all_deletion_positions, * 'all_deletion_coordinates': all_deletion_coordinates, # <<<<<<<<<<<<<< * 'deletion_positions': deletion_positions, @@ -6377,7 +6832,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * 'deletion_coordinates': deletion_coordinates, * 'deletion_sizes': deletion_sizes, # <<<<<<<<<<<<<< * 'deletion_n': deletion_n, - * + * */ if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_sizes, __pyx_v_deletion_sizes) < 0) __PYX_ERR(0, 117, __pyx_L1_error) @@ -6385,7 +6840,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * 'deletion_coordinates': deletion_coordinates, * 'deletion_sizes': deletion_sizes, * 'deletion_n': deletion_n, # <<<<<<<<<<<<<< - * + * * 'all_substitution_positions': all_substitution_positions, */ __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_deletion_n); 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__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_8 = NULL; - __pyx_t_3 = 0; + __pyx_t_13 = 0; #if CYTHON_UNPACK_METHODS if (unlikely(PyMethod_Check(__pyx_t_9))) { __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_9); @@ -6433,13 +6888,13 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __Pyx_INCREF(__pyx_t_8); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_9, function); - __pyx_t_3 = 1; + __pyx_t_13 = 1; } } #endif { PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_v_all_substitution_values}; - __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_3, 1+__pyx_t_3); + __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13); __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 133, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); @@ -6461,7 +6916,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_9 = NULL; - __pyx_t_3 = 0; + __pyx_t_13 = 0; #if CYTHON_UNPACK_METHODS if (unlikely(PyMethod_Check(__pyx_t_8))) { __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_8); @@ -6470,13 +6925,13 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __Pyx_INCREF(__pyx_t_9); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_8, function); - __pyx_t_3 = 1; + __pyx_t_13 = 1; } } #endif { PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_v_substitution_values}; - __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_3, 1+__pyx_t_3); + __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13); __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 134, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); @@ -6511,7 +6966,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su /* "CRISPResso2/CRISPRessoCOREResources.pyx":18 * re_find_indels = re.compile("(-*-)") - * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) @@ -6559,7 +7014,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ /* Python wrapper */ -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else @@ -6567,7 +7022,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds #endif ); /*proto*/ static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy = {"find_indels_substitutions_legacy", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else @@ -6728,11 +7183,12 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_t_8 = NULL; PyObject *__pyx_t_9 = NULL; int __pyx_t_10; - PyObject *__pyx_t_11 = NULL; - PyObject *(*__pyx_t_12)(PyObject *); - int __pyx_t_13; - Py_ssize_t __pyx_t_14; - long __pyx_t_15; + unsigned int __pyx_t_11; + PyObject *__pyx_t_12 = NULL; + PyObject *(*__pyx_t_13)(PyObject *); + int __pyx_t_14; + Py_ssize_t __pyx_t_15; + long __pyx_t_16; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -6740,9 +7196,9 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s /* "CRISPResso2/CRISPRessoCOREResources.pyx":145 * def find_indels_substitutions_legacy(read_seq_al, ref_seq_al, _include_indx): - * + * * cdef char* sub_seq='' # <<<<<<<<<<<<<< - * + * * cdef int st */ __pyx_v_sub_seq = ((char *)""); @@ -7000,7 +7456,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s * if idx in _include_indx: * substitution_positions.append(idx) # <<<<<<<<<<<<<< * substitution_values.append(read_seq_al[idx_c]) - * + * */ __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 176, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); @@ -7011,7 +7467,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s * if idx in _include_indx: * substitution_positions.append(idx) * substitution_values.append(read_seq_al[idx_c]) # <<<<<<<<<<<<<< - * + * * idx+=1 */ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 177, __pyx_L1_error) @@ -7039,9 +7495,9 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s /* "CRISPResso2/CRISPRessoCOREResources.pyx":179 * substitution_values.append(read_seq_al[idx_c]) - * + * * idx+=1 # <<<<<<<<<<<<<< - * + * * else: */ __pyx_v_idx = (__pyx_v_idx + 1); @@ -7057,7 +7513,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s } /* "CRISPResso2/CRISPRessoCOREResources.pyx":182 - * + * * else: * if idx==0: # <<<<<<<<<<<<<< * ref_positions.append(-1) @@ -7077,7 +7533,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_int_neg_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 183, __pyx_L1_error) /* "CRISPResso2/CRISPRessoCOREResources.pyx":182 - * + * * else: * if idx==0: # <<<<<<<<<<<<<< * ref_positions.append(-1) @@ -7090,7 +7546,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s * ref_positions.append(-1) * else: * ref_positions.append(-idx) # <<<<<<<<<<<<<< - * + * * substitution_n = len(substitution_positions) */ /*else*/ { @@ -7115,16 +7571,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s /* "CRISPResso2/CRISPRessoCOREResources.pyx":187 * ref_positions.append(-idx) - * + * * substitution_n = len(substitution_positions) # <<<<<<<<<<<<<< - * + * * #the remainder of positions are with reference to the original reference sequence indexes we calculated above */ __pyx_t_3 = __Pyx_PyList_GET_SIZE(__pyx_v_substitution_positions); 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char warning[200]; @@ -11088,7 +11544,7 @@ static PyTypeObject *__Pyx_ImportType_3_0_10(PyObject *module, const char *modul module_name, class_name, size, basicsize+itemsize); goto bad; } - if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_10 && + if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_11 && ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) { PyErr_Format(PyExc_ValueError, "%.200s.%.200s size changed, may indicate binary incompatibility. 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" "Expected %zd from C header, got %zd from PyObject", @@ -12490,6 +12946,9 @@ static PyTypeObject __pyx_CyFunctionType_type = { #if PY_VERSION_HEX >= 0x030C0000 0, #endif +#if PY_VERSION_HEX >= 0x030d00A4 + 0, +#endif #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, #endif @@ -13480,6 +13939,160 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, #endif #endif +/* Declarations */ +#if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_from_parts(long double x, long double y) { + return ::std::complex< long double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_from_parts(long double x, long double y) { + return x + y*(__pyx_t_long_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_from_parts(long double x, long double y) { + __pyx_t_long_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ +#if CYTHON_CCOMPLEX && (1) && (!0 || __cplusplus) +#else + static CYTHON_INLINE int __Pyx_c_eq_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_sum_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + __pyx_t_long_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_diff_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + __pyx_t_long_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_prod_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + __pyx_t_long_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_quot_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + if (b.imag == 0) { + return __pyx_t_long_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabsl(b.real) >= fabsl(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_long_double_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + long double r = b.imag / b.real; + long double s = (long double)(1.0) / (b.real + b.imag * r); + return __pyx_t_long_double_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + long double r = b.real / b.imag; + long double s = (long double)(1.0) / (b.imag + b.real * r); + return __pyx_t_long_double_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + } + } + #else + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_quot_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + if (b.imag == 0) { + return __pyx_t_long_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + long double denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_long_double_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } + } + #endif + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_neg_long__double(__pyx_t_long_double_complex a) { + __pyx_t_long_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_long__double(__pyx_t_long_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_conj_long__double(__pyx_t_long_double_complex a) { + __pyx_t_long_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE long double __Pyx_c_abs_long__double(__pyx_t_long_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtl(z.real*z.real + z.imag*z.imag); + #else + return hypotl(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_long_double_complex __Pyx_c_pow_long__double(__pyx_t_long_double_complex a, __pyx_t_long_double_complex b) { + __pyx_t_long_double_complex z; + long double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + long double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + return __Pyx_c_prod_long__double(a, a); + case 3: + z = __Pyx_c_prod_long__double(a, a); + return __Pyx_c_prod_long__double(z, a); + case 4: + z = __Pyx_c_prod_long__double(a, a); + return __Pyx_c_prod_long__double(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if ((b.imag == 0) && (a.real >= 0)) { + z.real = powl(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2l(0.0, -1.0); + } + } else { + r = __Pyx_c_abs_long__double(a); + theta = atan2l(a.imag, a.real); + } + lnr = logl(r); + z_r = expl(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosl(z_theta); + z.imag = z_r * sinl(z_theta); + return z; + } + #endif +#endif + /* CIntFromPy */ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { #ifdef __Pyx_HAS_GCC_DIAGNOSTIC @@ -13502,245 +14115,239 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { } return (int) val; } - } else + } #endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { + if (unlikely(!PyLong_Check(x))) { + int val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { #if CYTHON_USE_PYLONG_INTERNALS - if (unlikely(__Pyx_PyLong_IsNeg(x))) { - goto raise_neg_overflow; - } else if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_DigitCount(x)) { - case 2: - if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } - break; - case 3: - if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } + } + break; + case 3: + if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } - break; - case 4: - if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } + } + break; + case 4: + if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } - break; - } + } + break; } + } #endif #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } #else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } #endif - if ((sizeof(int) <= sizeof(unsigned long))) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) + if ((sizeof(int) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif - } - } else { + } + } else { #if CYTHON_USE_PYLONG_INTERNALS - if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_SignedDigitCount(x)) { - case -2: - if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case 2: - if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case 2: + if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case -3: - if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case -3: + if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case 3: - if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case 3: + if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case -4: - if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case -4: + if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - case 4: - if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } + } + break; + case 4: + if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } - break; - } + } + break; } + } #endif - if ((sizeof(int) <= sizeof(long))) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + if ((sizeof(int) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif - } + } + } + { + int val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (int) -1; + assert(PyLong_CheckExact(v)); } { - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); -#if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } -#endif - if (likely(v)) { - int ret = -1; -#if PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); -#else - PyObject *stepval = NULL, *mask = NULL, *shift = NULL; - int bits, remaining_bits, is_negative = 0; - long idigit; - int chunk_size = (sizeof(long) < 8) ? 30 : 62; - if (unlikely(!PyLong_CheckExact(v))) { - PyObject *tmp = v; - v = PyNumber_Long(v); - assert(PyLong_CheckExact(v)); - Py_DECREF(tmp); - if (unlikely(!v)) return (int) -1; - } -#if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(x) == 0) - return (int) 0; - is_negative = Py_SIZE(x) < 0; -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - is_negative = result == 1; - } -#endif - if (is_unsigned && unlikely(is_negative)) { - goto raise_neg_overflow; - } else if (is_negative) { - stepval = PyNumber_Invert(v); - if (unlikely(!stepval)) - return (int) -1; - } else { - stepval = __Pyx_NewRef(v); - } - val = (int) 0; - mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; - shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; - for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) { - PyObject *tmp, *digit; - digit = PyNumber_And(stepval, mask); - if (unlikely(!digit)) goto done; - idigit = PyLong_AsLong(digit); - Py_DECREF(digit); - if (unlikely(idigit < 0)) goto done; - tmp = PyNumber_Rshift(stepval, shift); - if (unlikely(!tmp)) goto done; - Py_DECREF(stepval); stepval = tmp; - val |= ((int) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(stepval) == 0) - goto unpacking_done; - #endif - } - idigit = PyLong_AsLong(stepval); - if (unlikely(idigit < 0)) goto done; - remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1); - if (unlikely(idigit >= (1L << remaining_bits))) - goto raise_overflow; - val |= ((int) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - unpacking_done: - #endif - if (!is_unsigned) { - if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1)))) - goto raise_overflow; - if (is_negative) - val = ~val; - } - ret = 0; - done: - Py_XDECREF(shift); - Py_XDECREF(mask); - Py_XDECREF(stepval); -#endif + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { Py_DECREF(v); - if (likely(!ret)) - return val; + return (int) -1; } - return (int) -1; + is_negative = result == 1; + } + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (int) -1; + } else { + stepval = v; + } + v = NULL; + val = (int) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((int) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((int) idigit) << bits; } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); + if (!is_unsigned) { + if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (int) -1; return val; } raise_overflow: @@ -13784,12 +14391,19 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { } } { - int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; -#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; return _PyLong_FromByteArray(bytes, sizeof(int), little, !is_unsigned); #else + int one = 1; int little = (int)*(unsigned char *)&one; PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); @@ -13839,245 +14453,239 @@ static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { } return (size_t) val; } - } else + } #endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { + if (unlikely(!PyLong_Check(x))) { + size_t val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (size_t) -1; + val = __Pyx_PyInt_As_size_t(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { #if CYTHON_USE_PYLONG_INTERNALS - if (unlikely(__Pyx_PyLong_IsNeg(x))) { - goto raise_neg_overflow; - } else if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(size_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_DigitCount(x)) { - case 2: - if ((8 * sizeof(size_t) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) >= 2 * PyLong_SHIFT)) { - return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(size_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(size_t) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) >= 2 * PyLong_SHIFT)) { + return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } - break; - case 3: - if ((8 * sizeof(size_t) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) >= 3 * PyLong_SHIFT)) { - return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } + } + break; + case 3: + if ((8 * sizeof(size_t) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) >= 3 * PyLong_SHIFT)) { + return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } - break; - case 4: - if ((8 * sizeof(size_t) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) >= 4 * PyLong_SHIFT)) { - return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } + } + break; + case 4: + if ((8 * sizeof(size_t) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) >= 4 * PyLong_SHIFT)) { + return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } - break; - } + } + break; } + } #endif #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } #else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (size_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (size_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } #endif - if ((sizeof(size_t) <= sizeof(unsigned long))) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) + if ((sizeof(size_t) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if ((sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif - } - } else { + } + } else { #if CYTHON_USE_PYLONG_INTERNALS - if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(size_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_SignedDigitCount(x)) { - case -2: - if ((8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { - return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(size_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { + return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case 2: - if ((8 * sizeof(size_t) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { - return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } + } + break; + case 2: + if ((8 * sizeof(size_t) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { + return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case -3: - if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { - return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } + } + break; + case -3: + if ((8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { + return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case 3: - if ((8 * sizeof(size_t) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { - return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } + } + break; + case 3: + if ((8 * sizeof(size_t) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { + return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case -4: - if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT)) { - return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } + } + break; + case -4: + if ((8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT)) { + return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - case 4: - if ((8 * sizeof(size_t) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT)) { - return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } + } + break; + case 4: + if ((8 * sizeof(size_t) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT)) { + return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); } - break; - } + } + break; } + } #endif - if ((sizeof(size_t) <= sizeof(long))) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) + if ((sizeof(size_t) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(size_t) <= sizeof(PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if ((sizeof(size_t) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif - } + } + } + { + size_t val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (size_t) -1; + assert(PyLong_CheckExact(v)); } { - size_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); -#if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } -#endif - if (likely(v)) { - int ret = -1; -#if PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); -#else - PyObject *stepval = NULL, *mask = NULL, *shift = NULL; - int bits, remaining_bits, is_negative = 0; - long idigit; - int chunk_size = (sizeof(long) < 8) ? 30 : 62; - if (unlikely(!PyLong_CheckExact(v))) { - PyObject *tmp = v; - v = PyNumber_Long(v); - assert(PyLong_CheckExact(v)); - Py_DECREF(tmp); - if (unlikely(!v)) return (size_t) -1; - } -#if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(x) == 0) - return (size_t) 0; - is_negative = Py_SIZE(x) < 0; -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (size_t) -1; - is_negative = result == 1; - } -#endif - if (is_unsigned && unlikely(is_negative)) { - goto raise_neg_overflow; - } else if (is_negative) { - stepval = PyNumber_Invert(v); - if (unlikely(!stepval)) - return (size_t) -1; - } else { - stepval = __Pyx_NewRef(v); - } - val = (size_t) 0; - mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; - shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; - for (bits = 0; bits < (int) sizeof(size_t) * 8 - chunk_size; bits += chunk_size) { - PyObject *tmp, *digit; - digit = PyNumber_And(stepval, mask); - if (unlikely(!digit)) goto done; - idigit = PyLong_AsLong(digit); - Py_DECREF(digit); - if (unlikely(idigit < 0)) goto done; - tmp = PyNumber_Rshift(stepval, shift); - if (unlikely(!tmp)) goto done; - Py_DECREF(stepval); stepval = tmp; - val |= ((size_t) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(stepval) == 0) - goto unpacking_done; - #endif - } - idigit = PyLong_AsLong(stepval); - if (unlikely(idigit < 0)) goto done; - remaining_bits = ((int) sizeof(size_t) * 8) - bits - (is_unsigned ? 0 : 1); - if (unlikely(idigit >= (1L << remaining_bits))) - goto raise_overflow; - val |= ((size_t) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - unpacking_done: - #endif - if (!is_unsigned) { - if (unlikely(val & (((size_t) 1) << (sizeof(size_t) * 8 - 1)))) - goto raise_overflow; - if (is_negative) - val = ~val; - } - ret = 0; - done: - Py_XDECREF(shift); - Py_XDECREF(mask); - Py_XDECREF(stepval); -#endif + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { Py_DECREF(v); - if (likely(!ret)) - return val; + return (size_t) -1; } - return (size_t) -1; + is_negative = result == 1; + } + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (size_t) -1; + } else { + stepval = v; + } + v = NULL; + val = (size_t) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(size_t) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((size_t) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(size_t) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((size_t) idigit) << bits; } - } else { - size_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (size_t) -1; - val = __Pyx_PyInt_As_size_t(tmp); - Py_DECREF(tmp); + if (!is_unsigned) { + if (unlikely(val & (((size_t) 1) << (sizeof(size_t) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (size_t) -1; return val; } raise_overflow: @@ -14121,12 +14729,19 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { } } { - int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; -#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; return _PyLong_FromByteArray(bytes, sizeof(long), little, !is_unsigned); #else + int one = 1; int little = (int)*(unsigned char *)&one; PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); @@ -14192,245 +14807,239 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { } return (long) val; } - } else + } #endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { + if (unlikely(!PyLong_Check(x))) { + long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { #if CYTHON_USE_PYLONG_INTERNALS - if (unlikely(__Pyx_PyLong_IsNeg(x))) { - goto raise_neg_overflow; - } else if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_DigitCount(x)) { - case 2: - if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } - break; - case 3: - if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } + } + break; + case 3: + if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } - break; - case 4: - if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } + } + break; + case 4: + if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } - break; - } + } + break; } + } #endif #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } #else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } #endif - if ((sizeof(long) <= sizeof(unsigned long))) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) + if ((sizeof(long) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif - } - } else { + } + } else { #if CYTHON_USE_PYLONG_INTERNALS - if (__Pyx_PyLong_IsCompact(x)) { - __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) - } else { - const digit* digits = __Pyx_PyLong_Digits(x); - assert(__Pyx_PyLong_DigitCount(x) > 1); - switch (__Pyx_PyLong_SignedDigitCount(x)) { - case -2: - if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case 2: - if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case 2: + if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case -3: - if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case -3: + if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case 3: - if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case 3: + if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case -4: - if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case -4: + if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - case 4: - if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { - if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } + } + break; + case 4: + if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } - break; - } + } + break; } + } #endif - if ((sizeof(long) <= sizeof(long))) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + if ((sizeof(long) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif - } + } + } + { + long val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (long) -1; + assert(PyLong_CheckExact(v)); } { - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); -#if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } -#endif - if (likely(v)) { - int ret = -1; -#if PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); -#else - PyObject *stepval = NULL, *mask = NULL, *shift = NULL; - int bits, remaining_bits, is_negative = 0; - long idigit; - int chunk_size = (sizeof(long) < 8) ? 30 : 62; - if (unlikely(!PyLong_CheckExact(v))) { - PyObject *tmp = v; - v = PyNumber_Long(v); - assert(PyLong_CheckExact(v)); - Py_DECREF(tmp); - if (unlikely(!v)) return (long) -1; - } -#if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(x) == 0) - return (long) 0; - is_negative = Py_SIZE(x) < 0; -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - is_negative = result == 1; - } -#endif - if (is_unsigned && unlikely(is_negative)) { - goto raise_neg_overflow; - } else if (is_negative) { - stepval = PyNumber_Invert(v); - if (unlikely(!stepval)) - return (long) -1; - } else { - stepval = __Pyx_NewRef(v); - } - val = (long) 0; - mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; - shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; - for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) { - PyObject *tmp, *digit; - digit = PyNumber_And(stepval, mask); - if (unlikely(!digit)) goto done; - idigit = PyLong_AsLong(digit); - Py_DECREF(digit); - if (unlikely(idigit < 0)) goto done; - tmp = PyNumber_Rshift(stepval, shift); - if (unlikely(!tmp)) goto done; - Py_DECREF(stepval); stepval = tmp; - val |= ((long) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - if (Py_SIZE(stepval) == 0) - goto unpacking_done; - #endif - } - idigit = PyLong_AsLong(stepval); - if (unlikely(idigit < 0)) goto done; - remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1); - if (unlikely(idigit >= (1L << remaining_bits))) - goto raise_overflow; - val |= ((long) idigit) << bits; - #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 - unpacking_done: - #endif - if (!is_unsigned) { - if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1)))) - goto raise_overflow; - if (is_negative) - val = ~val; - } - ret = 0; - done: - Py_XDECREF(shift); - Py_XDECREF(mask); - Py_XDECREF(stepval); -#endif + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { Py_DECREF(v); - if (likely(!ret)) - return val; + return (long) -1; } - return (long) -1; + is_negative = result == 1; + } + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (long) -1; + } else { + stepval = v; + } + v = NULL; + val = (long) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((long) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((long) idigit) << bits; } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); + if (!is_unsigned) { + if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (long) -1; return val; } raise_overflow: diff --git a/CRISPResso2/CRISPRessoCompareCORE.py b/CRISPResso2/CRISPRessoCompareCORE.py index 7d797024..62560300 100644 --- a/CRISPResso2/CRISPRessoCompareCORE.py +++ b/CRISPResso2/CRISPRessoCompareCORE.py @@ -293,7 +293,7 @@ def get_plot_title_with_ref_name(plotTitle, refName): tot_counts_2 = np.array(mod_freqs_2['Total'], dtype=float) unmod_counts_2 = tot_counts_2 - mod_counts_2 - fisher_results = [stats.fisher_exact([[z[0], z[1]], [z[2], z[3]]]) if max(z) > 0 else [np.NaN, 1.0] for z in zip(mod_counts_1, unmod_counts_1, mod_counts_2, unmod_counts_2)] + fisher_results = [stats.fisher_exact([[z[0], z[1]], [z[2], z[3]]]) if max(z) > 0 else [np.nan, 1.0] for z in zip(mod_counts_1, unmod_counts_1, mod_counts_2, unmod_counts_2)] oddsratios, pvalues = [a for a, b in fisher_results], [b for a, b in fisher_results] mod_df = [] @@ -398,7 +398,7 @@ def get_plot_title_with_ref_name(plotTitle, refName): quant_cols = ['#Reads_'+sample_1_name, '%Reads_'+sample_1_name, '#Reads_'+sample_2_name, '%Reads_'+sample_2_name] merged[quant_cols] = merged[quant_cols].fillna(0) lfc_error =0.1 - merged['each_LFC'] = np.log2(((merged['%Reads_'+sample_1_name]+lfc_error)/(merged['%Reads_'+sample_2_name]+lfc_error)).astype(float)).replace([np.inf, np.NaN], 0) + merged['each_LFC'] = np.log2(((merged['%Reads_'+sample_1_name]+lfc_error)/(merged['%Reads_'+sample_2_name]+lfc_error)).astype(float)).replace([np.inf, np.nan], 0) merged = merged.sort_values(['%Reads_'+sample_1_name, 'Reference_Sequence', 'n_deleted', 'n_inserted', 'n_mutated'], ascending=False) merged = merged.reset_index(drop=True).set_index('Aligned_Sequence') args.crispresso_output_folder_root = os.path.split(allele_file_1)[1].replace(".txt", "") diff --git a/CRISPResso2/CRISPRessoReports/templates/report.html b/CRISPResso2/CRISPRessoReports/templates/report.html index 88795748..c1596bc7 100644 --- a/CRISPResso2/CRISPRessoReports/templates/report.html +++ b/CRISPResso2/CRISPRessoReports/templates/report.html @@ -318,7 +318,7 @@
Nucleotide composition for {{amplicon_name}}
{% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_2a'] %}

Data: {{data_label}}

{% endfor %} - {% endif %} + {% endif %} {% if 'plot_2b' in report_data['figures']['htmls'][amplicon_name] %} {# report_data['figures']['htmls'][amplicon_name]['plot_2b']|safe #} {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_2b', amplicon_name=amplicon_name)}} diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..64aaabd7 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,52 @@ +[build-system] +requires = ["setuptools", "wheel", "cython", "numpy"] +build-backend = "setuptools.build_meta" + +[project] +name = "CRISPResso2" +version = "2.1.3" +dependencies = [ + "pandas", + "matplotlib", + "seaborn", + "jinja2", + "scipy", + "numpy" +] +description = "Software pipeline for the analysis of genome editing outcomes from deep sequencing data" +authors = [ + { name = "Edilytics, Inc.", email = "support@edilytics.com" } +] +license = { file = "LICENSE" } +readme = "README.md" +classifiers = [ + "Development Status :: 4 - Beta", + "Environment :: Console", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: Other/Proprietary License", + "Operating System :: POSIX", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Cython", +] + +[project.optional-dependencies] +dev = ["cython"] + +[project.scripts] +CRISPResso = "CRISPResso2.CRISPRessoCORE:main" +CRISPRessoBatch = "CRISPResso2.CRISPRessoBatchCORE:main" +CRISPRessoPooled = "CRISPResso2.CRISPRessoPooledCORE:main" +CRISPRessoWGS = "CRISPResso2.CRISPRessoWGSCORE:main" +CRISPRessoCompare = "CRISPResso2.CRISPRessoCompareCORE:main" +CRISPRessoPooledWGSCompare = "CRISPResso2.CRISPRessoPooledWGSCompareCORE:main" +CRISPRessoAggregate = "CRISPResso2.CRISPRessoAggregateCORE:main" + +[project.urls] +Homepage = "https://github.com/pinellolab/CRISPResso2" + +[tool.setuptools] +package-dir = {"" = "CRISPResso2"} +packages = ["CRISPResso2", "CRISPResso2.CRISPRessoReports"] +include-package-data = true