Merge pull request #556 from kif/555_numpy2

Support for Numpy2
silx-kit · Mar 15, 2024 · d08b8ea · d08b8ea
2 parents c1eff28 + 5108dc4
commit d08b8ea
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Showing 14 changed files with 66 additions and 58 deletions.
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v2

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -56,7 +56,7 @@
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.mathjax',
               'sphinxcontrib.programoutput',
-              "nbsphinx"
+              'nbsphinx'
               ]
 
 # Set the theme to sphinx_rtd_theme when *not* building on Read The Docs.

diff --git a/meson.build b/meson.build
@@ -2,7 +2,7 @@ project('FabIO',
   'c', 'cython',
   license: 'MIT',
   meson_version: '>= 0.60',
-  version: run_command('src/fabio/_version.py',
+  version: run_command(['version.py', '--wheel'],
   			           check:true).stdout().strip(),
 )
 
@@ -13,6 +13,7 @@ if meson.backend() != 'ninja'
 endif
 
 cc = meson.get_compiler('c')
+cy = meson.get_compiler('cython')
 m_dep = cc.find_library('m', required : false)
 if m_dep.found()
   add_project_link_arguments('-lm', language : 'c')
@@ -23,4 +24,11 @@ py_mod = import('python')
 py = py_mod.find_installation()
 py_dep = py.dependency()
 
+py.install_sources([
+    'version.py',
+],
+  pure: false,    # Will be installed next to binaries
+  subdir: 'fabio'  # Folder relative to site-packages to install to
+)
+
 subdir('src/fabio')
diff --git a/package/debian12/control b/package/debian12/control
@@ -7,6 +7,9 @@ Priority: extra
 Build-Depends: cython3,
                debhelper,
                dh-python,
+               devscripts,
+               python3-tomli,
+               python3-mesonpy,
                python3-all-dev,
                python3-pil,
                python3-lxml,
@@ -18,10 +21,7 @@ Build-Depends: cython3,
                python3-sphinxcontrib.programoutput,
                python3-sphinx-rtd-theme,
                python3-h5py,
-               python3-tomli,
-               python3-mesonpy,
                help2man,
-               devscripts,
                python3-pyqt5,
                python3-matplotlib,
                bitshuffle,

diff --git a/src/fabio/__init__.py b/src/fabio/__init__.py
@@ -28,7 +28,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "GPLv3+"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "21/06/2023"
+__date__ = "15/03/2024"
 __status__ = "stable"
 
 import sys
@@ -39,8 +39,7 @@
     logging.basicConfig()
 
 import os
-from ._version import __date__ as date  # noqa
-from ._version import version, version_info, hexversion, strictversion  # noqa
+from .version import __date__ as date, version, version_info, hexversion, strictversion  # noqa
 from . import fabioformats as _fabioformats
 
 # provide a global fabio API

diff --git a/src/fabio/app/eiger2crysalis.py b/src/fabio/app/eiger2crysalis.py
@@ -38,7 +38,7 @@
 __author__ = "Jerome Kieffer"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
 __licence__ = "MIT"
-__date__ = "23/02/2023"
+__date__ = "15/03/2024"
 __status__ = "production"
 
 FOOTER = """To import your files as a project:
@@ -401,7 +401,7 @@ def treat_mask(self, full=False):
         ":param full: complete/slow mask analysis"
         if self.progress:
             self.progress.update(self.progress.max_value - 1, "Generate mask")
-        dummy_value = numpy.cast[self.mask.dtype](-1)
+        dummy_value = numpy.asarray(-numpy.ones(1), dtype=self.mask.dtype)[-1] #-1 in the given datatype
         mask = (self.mask==dummy_value).astype(numpy.int8)
         esperantoimage.EsperantoImage.DUMMY = 1
         new_mask = self.geometry_transform(esperantoimage.EsperantoImage(data=mask).data)

diff --git a/src/fabio/cbfimage.py b/src/fabio/cbfimage.py
@@ -245,7 +245,7 @@ def read(self, fname, frame=None, check_MD5=True, only_raw=False):
             return binary_data
 
         if ("Content-MD5" in self.header) and check_MD5:
-                ref = numpy.string_(self.header["Content-MD5"])
+                ref = numpy.bytes_(self.header["Content-MD5"])
                 obt = md5sum(binary_data)
                 if ref != obt:
                     logger.error("Checksum of binary data mismatch: expected %s, got %s" % (ref, obt))
@@ -294,14 +294,14 @@ def write(self, fname):
                         b"Content-Type: application/octet-stream;",
                         b'     conversions="x-CBF_BYTE_OFFSET"',
                         b'Content-Transfer-Encoding: BINARY',
-                        numpy.string_("X-Binary-Size: %d" % (len(binary_blob))),
+                        numpy.bytes_("X-Binary-Size: %d" % (len(binary_blob))),
                         b"X-Binary-ID: 1",
-                        numpy.string_('X-Binary-Element-Type: "%s"' % (dtype)),
+                        numpy.bytes_('X-Binary-Element-Type: "%s"' % (dtype)),
                         b"X-Binary-Element-Byte-Order: LITTLE_ENDIAN",
                         b"Content-MD5: " + md5sum(binary_blob),
-                        numpy.string_("X-Binary-Number-of-Elements: %d" % (dim1 * dim2)),
-                        numpy.string_("X-Binary-Size-Fastest-Dimension: %d" % dim1),
-                        numpy.string_("X-Binary-Size-Second-Dimension: %d" % dim2),
+                        numpy.bytes_("X-Binary-Number-of-Elements: %d" % (dim1 * dim2)),
+                        numpy.bytes_("X-Binary-Size-Fastest-Dimension: %d" % dim1),
+                        numpy.bytes_("X-Binary-Size-Second-Dimension: %d" % dim2),
                         b"X-Binary-Size-Padding: 1",
                         b"",
                         self.STARTER + binary_blob,
@@ -354,22 +354,22 @@ class CIF(dict):
     keys are always unicode (str in python3)
     values are bytes
     """
-    EOL = [numpy.string_(i) for i in ("\r", "\n", "\r\n", "\n\r")]
-    BLANK = [numpy.string_(i) for i in (" ", "\t")] + EOL
-    SINGLE_QUOTE = numpy.string_("'")
-    DOUBLE_QUOTE = numpy.string_('"')
-    SEMICOLUMN = numpy.string_(';')
-    DOT = numpy.string_('.')
+    EOL = [numpy.bytes_(i) for i in ("\r", "\n", "\r\n", "\n\r")]
+    BLANK = [numpy.bytes_(i) for i in (" ", "\t")] + EOL
+    SINGLE_QUOTE = numpy.bytes_("'")
+    DOUBLE_QUOTE = numpy.bytes_('"')
+    SEMICOLUMN = numpy.bytes_(';')
+    DOT = numpy.bytes_('.')
     START_COMMENT = (SINGLE_QUOTE, DOUBLE_QUOTE)
-    BINARY_MARKER = numpy.string_("--CIF-BINARY-FORMAT-SECTION--")
-    HASH = numpy.string_("#")
-    LOOP = numpy.string_("loop_")
+    BINARY_MARKER = numpy.bytes_("--CIF-BINARY-FORMAT-SECTION--")
+    HASH = numpy.bytes_("#")
+    LOOP = numpy.bytes_("loop_")
     UNDERSCORE = ord("_")
-    QUESTIONMARK = numpy.string_("?")
-    STOP = numpy.string_("stop_")
-    GLOBAL = numpy.string_("global_")
-    DATA = numpy.string_("data_")
-    SAVE = numpy.string_("save_")
+    QUESTIONMARK = numpy.bytes_("?")
+    STOP = numpy.bytes_("stop_")
+    GLOBAL = numpy.bytes_("global_")
+    DATA = numpy.bytes_("data_")
+    SAVE = numpy.bytes_("save_")
 
     def __init__(self, _strFilename=None):
         """
@@ -416,7 +416,7 @@ def loadCIF(self, _strFilename, _bKeepComment=False):
         else:
             raise RuntimeError("CIF.loadCIF: what is %s type %s" % (_strFilename, type(_strFilename)))
         if _bKeepComment:
-            self._parseCIF(numpy.string_(infile.read()))
+            self._parseCIF(numpy.bytes_(infile.read()))
         else:
             self._parseCIF(CIF._readCIF(infile))
         if own_fd:
@@ -454,13 +454,13 @@ def _readCIF(cls, instream):
         if "read" not in dir(instream):
             raise RuntimeError("CIF._readCIF(instream): I expected instream to be an opened file,\
              here I got %s type %s" % (instream, type(instream)))
-        out_bytes = numpy.string_("")
+        out_bytes = numpy.bytes_("")
         for sLine in instream:
-            nline = numpy.string_(sLine)
+            nline = numpy.bytes_(sLine)
             pos = nline.find(cls.HASH)
             if pos >= 0:
                 if cls.isAscii(nline):
-                    out_bytes += nline[:pos] + numpy.string_(os.linesep)
+                    out_bytes += nline[:pos] + numpy.bytes_(os.linesep)
                 if pos > 80:
                     logger.warning("This line is too long and could cause problems in PreQuest: %s", sLine)
             else:
@@ -535,7 +535,7 @@ def _splitCIF(cls, bytes_text):
                     idx += 1 + bytes_text[idx + 1:].find(cls.SINGLE_QUOTE)
                     if idx >= len(bytes_text) - 1:
                         fields.append(bytes_text[1:-1].strip())
-                        bytes_text = numpy.string_("")
+                        bytes_text = numpy.bytes_("")
                         finished = True
                         break
 
@@ -552,7 +552,7 @@ def _splitCIF(cls, bytes_text):
                     idx += 1 + bytes_text[idx + 1:].find(cls.DOUBLE_QUOTE)
                     if idx >= len(bytes_text) - 1:
                         fields.append(bytes_text[1:-1].strip())
-                        bytes_text = numpy.string_("")
+                        bytes_text = numpy.bytes_("")
                         finished = True
                         break
 
@@ -594,7 +594,7 @@ def _splitCIF(cls, bytes_text):
                     bytes_text = bytes_text[end_binary:].strip()
                 else:
                     fields.append(bytes_text)
-                    bytes_text = numpy.string_("")
+                    bytes_text = numpy.bytes_("")
                     break
         return fields
 

diff --git a/src/fabio/eigerimage.py b/src/fabio/eigerimage.py
@@ -2,7 +2,7 @@
 #
 #    Project: FabIO X-ray image reader
 #
-#    Copyright (C) 2010-2016 European Synchrotron Radiation Facility
+#    Copyright (C) 2010-2024 European Synchrotron Radiation Facility
 #                       Grenoble, France
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -45,7 +45,7 @@
 __contact__ = "jerome.kieffer@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "ESRF"
-__date__ = "05/07/2022"
+__date__ = "15/03/2024"
 
 import logging
 logger = logging.getLogger(__name__)
@@ -184,7 +184,7 @@ def write(self, fname):
             for i, ds in enumerate(self.dataset):
                 if ds is None:
                     # we are in a trouble
-                    data = numpy.atleast_2d(numpy.NaN)
+                    data = numpy.atleast_2d(numpy.nan)
                 elif isinstance(ds, h5py.Dataset):
                     data = numpy.atleat_2d(ds[()])
                 else:

diff --git a/src/fabio/fabioimage.py b/src/fabio/fabioimage.py
@@ -816,6 +816,7 @@ def _compressed_stream(self,
             fobj.seek(0)
         elif self._need_a_seek_to_read and mode[0] == "r":
             fo = python_uncompress(fname, mode)
+            print(fname, mode, fo)
             fobj = fabioutils.BytesIO(fo.read(), fname, mode)
         else:
             fobj = python_uncompress(fname, mode)

diff --git a/src/fabio/meson.build b/src/fabio/meson.build
@@ -6,7 +6,6 @@ subdir('test')
 subdir('utils')
 
 py.install_sources([
-	'_version.py',
 	'adscimage.py',
 	'binaryimage.py',
 	'bruker100image.py',

diff --git a/src/fabio/nexus.py b/src/fabio/nexus.py
@@ -29,11 +29,11 @@
 
 """
 
-__author__ = "Jerome Kieffer"
+__author__ = "Jérôme Kieffer"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "28/04/2021"
+__date__ = "15/03/2024"
 __status__ = "production"
 __docformat__ = 'restructuredtext'
 
@@ -44,7 +44,7 @@
 import time
 import numpy
 from .fabioutils import exists
-from ._version import version
+from .version import version
 
 logger = logging.getLogger(__name__)
 try:

diff --git a/src/fabio/sparseimage.py b/src/fabio/sparseimage.py
@@ -3,7 +3,7 @@
 #    Project: X-ray image reader
 #             https://github.com/silx-kit/fabio
 #
-#    Copyright 2020-2021(C) European Synchrotron Radiation Facility, Grenoble, France
+#    Copyright 2020-2024(C) European Synchrotron Radiation Facility, Grenoble, France
 #
 #  Permission is hereby granted, free of charge, to any person
 #  obtaining a copy of this software and associated documentation files
@@ -37,7 +37,7 @@
 __contact__ = "jerome.kieffer@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "2020 ESRF"
-__date__ = "09/02/2023"
+__date__ = "15/03/2024"
 
 import logging
 logger = logging.getLogger(__name__)
@@ -183,7 +183,7 @@ def read(self, fname, frame=None):
             self.dummy = self.intensity.dtype.type(nx_data["dummy"][()])
         except KeyError:
             if self.intensity.dtype.char in numpy.typecodes['AllFloat']:
-                self.dummy = numpy.NaN
+                self.dummy = numpy.nan
             else:
                 self.dummy = 0
 

diff --git a/src/fabio/utils/deprecation.py b/src/fabio/utils/deprecation.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+# Copyright (c) 2016-2024 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -24,15 +24,16 @@
 # ###########################################################################*/
 """Bunch of useful decorators"""
 
-__authors__ = ["Jerome Kieffer", "H. Payno", "P. Knobel"]
+__authors__ = ["Jérôme Kieffer", "H. Payno", "P. Knobel"]
 __license__ = "MIT"
-__date__ = "18/12/2020"
+__date__ = "15/03/2024"
 
 import logging
 import functools
 import traceback
 import re
-from .. import _version
+
+from ..version import calc_hexversion, hexversion as ref_hexversion
 
 depreclog = logging.getLogger("fabio.DEPRECATION")
 
@@ -54,7 +55,7 @@ def hexversion_fromstring(string):
         releaselevel = result[3]
         if releaselevel is None:
             releaselevel = 0
-    return _version.calc_hexversion(major, minor, micro, releaselevel, serial=0)
+    return calc_hexversion(major, minor, micro, releaselevel, serial=0)
 
 
 def deprecated(func=None, reason=None, replacement=None, since_version=None,
@@ -154,7 +155,7 @@ def deprecated_warning(type_, name, reason=None, replacement=None,
                 deprecated_since = hexversion
             else:
                 deprecated_since = _CACHE_VERSIONS[deprecated_since]
-        log_as_debug = _version.hexversion < deprecated_since
+        log_as_debug = ref_hexversion < deprecated_since
     else:
         log_as_debug = False
 

diff --git a/src/fabio/_version.py → version.py b/src/fabio/_version.py → version.py
@@ -4,7 +4,7 @@
 #    Project: X-ray image reader
 #             https://github.com/silx-kit/fabio
 #
-#    Copyright (C) 2015-2023 European Synchrotron Radiation Facility, Grenoble, France
+#    Copyright (C) 2015-2024 European Synchrotron Radiation Facility, Grenoble, France
 #
 #    Principal author:       Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
 #
@@ -58,7 +58,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "07/08/2023"
+__date__ = "15/03/2024"
 __status__ = "production"
 __docformat__ = 'restructuredtext'
 __all__ = ["date", "version_info", "strictversion", "hexversion", "debianversion",
@@ -75,8 +75,8 @@
                               "beta": "b",
                               "candidate": "rc"}
 
-MAJOR = 2023
-MINOR = 11
+MAJOR = 2024
+MINOR = 3
 MICRO = 0
 RELEV = "dev"  # <16
 SERIAL = 0  # <16