From 1566e9fc8daef56b59128a1b61a2a3080af1e4ba Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Mon, 20 Jun 2022 12:54:15 -0400 Subject: [PATCH] Drop generic copy_to_results rule (#194) * removed generic rule copy_to_results * poetry update * add copy rules just for corobl output space * replace error message when model not found --- hippunfold/workflow/Snakefile | 1 + hippunfold/workflow/rules/common.smk | 41 +- hippunfold/workflow/rules/gifti.smk | 16 +- hippunfold/workflow/rules/myelin_map.smk | 8 +- hippunfold/workflow/rules/nnunet.smk | 5 +- hippunfold/workflow/rules/preproc_t2.smk | 10 +- .../rules/resample_final_to_crop_native.smk | 2 +- hippunfold/workflow/rules/warps.smk | 12 +- poetry.lock | 682 ++++++++++-------- 9 files changed, 442 insertions(+), 335 deletions(-) diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile index 0e1d17af..7a2550c9 100644 --- a/hippunfold/workflow/Snakefile +++ b/hippunfold/workflow/Snakefile @@ -97,6 +97,7 @@ wildcard_constraints: surfname="[a-zA-Z0-9]+", modality="[a-zA-Z0-9]+", density="[a-zA-Z0-9]+", + autotop="[a-zA-Z0-9]+", root = os.path.join(config["root"], "hippunfold") diff --git a/hippunfold/workflow/rules/common.smk b/hippunfold/workflow/rules/common.smk index 35b25d55..6818b4d8 100644 --- a/hippunfold/workflow/rules/common.smk +++ b/hippunfold/workflow/rules/common.smk @@ -345,16 +345,37 @@ def get_final_output(): return final_output -rule copy_to_results: - """ Generic rule for copying data from work to results""" - input: - os.path.join(work, "{file}"), - output: - os.path.join(root, "{file}"), - group: - "subj" - shell: - "cp {input} {output}" +if "corobl" in ref_spaces: + + rule copy_coords_to_results: + input: + os.path.join(work, "{pre}_space-corobl_{post}{suffix}.{ext}"), + output: + os.path.join(root, "{pre}_space-corobl_{post}{suffix,coords}.{ext}"), + group: + "subj" + shell: + "cp {input} {output}" + + rule copy_xfm_to_results: + input: + os.path.join(work, "{pre}_{fromto,from|to}-corobl_{post}{suffix}.{ext}"), + output: + os.path.join(root, "{pre}_{fromto,from|to}-corobl_{post}{suffix,xfm}.{ext}"), + group: + "subj" + shell: + "cp {input} {output}" + + rule copy_subfields_to_results: + input: + os.path.join(work, "{pre}_desc-subfields_{post}{suffix}.{ext}"), + output: + os.path.join(root, "{pre}_desc-subfields_{post}{suffix,dseg}.{ext}"), + group: + "subj" + shell: + "cp {input} {output}" def get_final_work_tar(): diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk index 0de032c0..95e273fe 100644 --- a/hippunfold/workflow/rules/gifti.smk +++ b/hippunfold/workflow/rules/gifti.smk @@ -23,7 +23,7 @@ rule cp_template_to_unfold: surface_type="FLAT", output: gii=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="{surfname}.surf.gii", @@ -94,7 +94,7 @@ rule calc_unfold_template_coords: rule constrain_surf_to_bbox: input: gii=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="{surfname}.surf.gii", @@ -104,7 +104,7 @@ rule constrain_surf_to_bbox: **config["subj_wildcards"] ), ref_nii=bids( - root=work, + root=root, datatype="warps", space="unfold", label="{autotop}", @@ -206,7 +206,7 @@ rule correct_nan_vertices: ), output: gii=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="{surfname}.surf.gii", @@ -225,7 +225,7 @@ rule correct_nan_vertices: rule warp_gii_to_native: input: gii=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="{surfname}.surf.gii", @@ -246,7 +246,7 @@ rule warp_gii_to_native: ), output: gii=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="{surfname}.surf.gii", @@ -461,7 +461,7 @@ rule resample_atlas_to_refvol: workflow.basedir, "..", config["atlas_files"][wildcards.atlas]["label_nii"] ), refvol=bids( - root=work, + root=root, space="unfold", label="hipp", datatype="warps", @@ -772,7 +772,7 @@ rule merge_lr_spec_file: ), output: spec_file=bids( - root=work, + root=root, datatype="surf", den="{density}", space="{space}", diff --git a/hippunfold/workflow/rules/myelin_map.smk b/hippunfold/workflow/rules/myelin_map.smk index a9b13880..057e3ffb 100644 --- a/hippunfold/workflow/rules/myelin_map.smk +++ b/hippunfold/workflow/rules/myelin_map.smk @@ -83,7 +83,7 @@ rule sample_myelin_map_surf: **config["subj_wildcards"] ), mid=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="midthickness.surf.gii", @@ -93,7 +93,7 @@ rule sample_myelin_map_surf: **config["subj_wildcards"] ), inner=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="inner.surf.gii", @@ -103,7 +103,7 @@ rule sample_myelin_map_surf: **config["subj_wildcards"] ), outer=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="outer.surf.gii", @@ -124,7 +124,7 @@ rule sample_myelin_map_surf: ), output: metric=bids( - root=work, + root=root, datatype="surf", den="{density}", suffix="myelin.shape.gii", diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk index 1f788469..e4344173 100644 --- a/hippunfold/workflow/rules/nnunet.smk +++ b/hippunfold/workflow/rules/nnunet.smk @@ -61,8 +61,9 @@ def get_model_tar(wildcards): if os.path.exists(dl_path): return dl_path else: - raise Exception( - f"Cannot find downloaded model at {dl_path}, run this first: hippunfold_download_models" + print("ERROR:") + print( + f" Cannot find downloaded model at {dl_path}, run this first: hippunfold_download_models" ) diff --git a/hippunfold/workflow/rules/preproc_t2.smk b/hippunfold/workflow/rules/preproc_t2.smk index aed69402..beb25c36 100644 --- a/hippunfold/workflow/rules/preproc_t2.smk +++ b/hippunfold/workflow/rules/preproc_t2.smk @@ -147,7 +147,7 @@ if config["skip_preproc"]: )[0], output: bids( - root=work, + root=root, datatype="anat", **config["subj_wildcards"], suffix="T2w.nii.gz", @@ -170,7 +170,7 @@ else: cmd=get_avg_or_cp_scans_cmd, output: bids( - root=work, + root=root, datatype="anat", **config["subj_wildcards"], suffix="T2w.nii.gz", @@ -187,7 +187,7 @@ else: rule reg_t2_to_t1: input: flo=bids( - root=work, + root=root, datatype="anat", **config["subj_wildcards"], suffix="T2w.nii.gz", @@ -251,7 +251,7 @@ rule reg_t2_to_t1: rule reg_t2_to_template: input: flo=bids( - root=work, + root=root, datatype="anat", **config["subj_wildcards"], suffix="T2w.nii.gz", @@ -413,7 +413,7 @@ def get_xfm_to_corobl(): rule warp_t2_to_corobl_crop: input: nii=bids( - root=work, + root=root, datatype="anat", **config["subj_wildcards"], suffix="T2w.nii.gz", diff --git a/hippunfold/workflow/rules/resample_final_to_crop_native.smk b/hippunfold/workflow/rules/resample_final_to_crop_native.smk index cef4bcd6..b4f175bb 100644 --- a/hippunfold/workflow/rules/resample_final_to_crop_native.smk +++ b/hippunfold/workflow/rules/resample_final_to_crop_native.smk @@ -286,7 +286,7 @@ def get_xfm_t2_to_t1(): rule resample_t2_to_crop: input: nii=bids( - root=work, + root=root, datatype="anat", **config["subj_wildcards"], suffix="T2w.nii.gz", diff --git a/hippunfold/workflow/rules/warps.smk b/hippunfold/workflow/rules/warps.smk index 01ac1584..323936fe 100644 --- a/hippunfold/workflow/rules/warps.smk +++ b/hippunfold/workflow/rules/warps.smk @@ -44,7 +44,7 @@ rule create_unfold_ref: orient=lambda wildcards: config["unfold_vol_ref"][wildcards.autotop]["orient"], output: nii=bids( - root=work, + root=root, space="unfold", label="{autotop}", datatype="warps", @@ -63,7 +63,7 @@ rule create_unfold_ref: rule create_unfold_coord_map: input: nii=bids( - root=work, + root=root, space="unfold", label="{autotop}", datatype="warps", @@ -118,7 +118,7 @@ def get_laminar_coords(wildcards): rule create_warps_hipp: input: unfold_ref_nii=bids( - root=work, + root=root, space="unfold", label="hipp", datatype="warps", @@ -230,7 +230,7 @@ rule create_warps_hipp: rule create_warps_dentate: input: unfold_ref_nii=bids( - root=work, + root=root, space="unfold", label="dentate", datatype="warps", @@ -364,7 +364,7 @@ rule compose_warps_native_to_unfold: mode="image" ), ref=bids( - root=work, + root=root, space="unfold", label="{autotop}", datatype="warps", @@ -445,7 +445,7 @@ rule compose_warps_unfold_to_crop_native: type_="itk" ), unfold_ref=bids( - root=work, + root=root, space="unfold", label="{autotop}", datatype="warps", diff --git a/poetry.lock b/poetry.lock index 65daaf04..00cdc27e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -36,7 +36,7 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" [[package]] name = "astroid" -version = "2.11.2" +version = "2.11.5" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false @@ -170,11 +170,11 @@ termcolor = "*" [[package]] name = "certifi" -version = "2021.10.8" +version = "2022.5.18.1" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "chardet" @@ -197,7 +197,7 @@ unicode_backport = ["unicodedata2"] [[package]] name = "click" -version = "8.1.2" +version = "8.1.3" description = "Composable command line interface toolkit" category = "main" optional = false @@ -269,9 +269,17 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +[[package]] +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" +category = "main" +optional = false +python-versions = ">=3.5" + [[package]] name = "dicom2nifti" -version = "2.3.2" +version = "2.3.3" description = "package for converting dicom files to nifti" category = "main" optional = false @@ -285,11 +293,11 @@ scipy = "*" [[package]] name = "dill" -version = "0.3.4" +version = "0.3.5.1" description = "serialize all of python" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" [package.extras] graph = ["objgraph (>=1.7.2)"] @@ -311,16 +319,23 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] -name = "filelock" -version = "3.6.0" -description = "A platform independent file lock." +name = "dpath" +version = "2.0.6" +description = "Filesystem-like pathing and searching for dictionaries" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3" + +[[package]] +name = "fastjsonschema" +version = "2.15.3" +description = "Fastest Python implementation of JSON schema" +category = "main" +optional = false +python-versions = "*" [package.extras] -docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"] -testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"] +devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] [[package]] name = "flake8" @@ -338,26 +353,23 @@ pyflakes = ">=2.4.0,<2.5.0" [[package]] name = "formulaic" -version = "0.2.4" +version = "0.3.4" description = "An implementation of Wilkinson formulas." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7.1,<4.0.0" [package.dependencies] -astor = "*" -interface-meta = ">=1.2" -numpy = "*" -pandas = "*" -scipy = "*" -wrapt = "*" +astor = ">=0.8" +interface-meta = ">=1.2.0,<2.0.0" +numpy = ">=1.3" +pandas = ">=1.2" +scipy = ">=1.6" +wrapt = ">=1.0" [package.extras] -arrow = ["pyarrow"] -benchmarks = ["patsy", "rpy2", "uncertainties"] -calculus = ["sympy"] -docs = ["mkdocs-material", "pymdown-extensions", "pygments"] -test = ["flake8", "pytest", "pytest-cov"] +arrow = ["pyarrow (>=1)"] +calculus = ["sympy (>=1.3,<1.10)"] [[package]] name = "future" @@ -400,26 +412,30 @@ python-versions = ">=3.5" [[package]] name = "imageio" -version = "2.16.1" +version = "2.19.3" description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." category = "main" optional = false python-versions = ">=3.7" [package.dependencies] -numpy = ">=1.20.0" +numpy = "*" pillow = ">=8.3.2" [package.extras] +all-plugins = ["astropy", "av", "imageio-ffmpeg", "opencv-python", "psutil", "tifffile"] +all-plugins-pypy = ["av", "imageio-ffmpeg", "psutil", "tifffile"] build = ["wheel"] dev = ["invoke", "pytest", "pytest-cov", "fsspec", "black", "flake8"] docs = ["sphinx", "numpydoc", "pydata-sphinx-theme"] ffmpeg = ["imageio-ffmpeg", "psutil"] fits = ["astropy"] -full = ["astropy", "black", "flake8", "fsspec", "gdal", "imageio-ffmpeg", "invoke", "itk", "numpydoc", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx", "tifffile", "wheel"] +full = ["astropy", "av", "black", "flake8", "fsspec", "gdal", "imageio-ffmpeg", "invoke", "itk", "numpydoc", "opencv-python", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx", "tifffile", "wheel"] gdal = ["gdal"] itk = ["itk"] linting = ["black", "flake8"] +opencv = ["opencv-python"] +pyav = ["av"] test = ["invoke", "pytest", "pytest-cov", "fsspec"] tifffile = ["tifffile"] @@ -440,7 +456,7 @@ testing = ["packaging", "pep517", "importlib-resources (>=1.3)"] [[package]] name = "importlib-resources" -version = "5.6.0" +version = "5.7.1" description = "Read resources from Python packages" category = "main" optional = false @@ -463,11 +479,11 @@ python-versions = "*" [[package]] name = "interface-meta" -version = "1.2.5" -description = "InterfaceMeta" +version = "1.3.0" +description = "`interface_meta` provides a convenient way to expose an extensible API with enforced method signatures and consistent documentation." category = "main" optional = false -python-versions = ">=3.4" +python-versions = ">=3.7,<4.0" [[package]] name = "isort" @@ -485,7 +501,7 @@ plugins = ["setuptools"] [[package]] name = "jinja2" -version = "3.1.1" +version = "3.1.2" description = "A very fast and expressive template engine." category = "main" optional = false @@ -519,7 +535,7 @@ python-versions = ">=3.6" [[package]] name = "jsonschema" -version = "4.4.0" +version = "4.6.0" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -534,20 +550,23 @@ typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [package.extras] format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] -format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] +format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] [[package]] name = "jupyter-core" -version = "4.9.2" +version = "4.10.0" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} traitlets = "*" +[package.extras] +test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] + [[package]] name = "kiwisolver" version = "1.4.2" @@ -635,7 +654,7 @@ test = ["pytest (<5.4)", "pytest-cov"] [[package]] name = "more-itertools" -version = "8.12.0" +version = "8.13.0" description = "More routines for operating on iterables, beyond itertools" category = "main" optional = false @@ -651,20 +670,20 @@ python-versions = "*" [[package]] name = "nbformat" -version = "5.2.0" +version = "5.4.0" description = "The Jupyter Notebook format" category = "main" optional = false python-versions = ">=3.7" [package.dependencies] -jsonschema = ">=2.4,<2.5.0 || >2.5.0" +fastjsonschema = "*" +jsonschema = ">=2.6" jupyter-core = "*" -traitlets = ">=4.1" +traitlets = ">=5.1" [package.extras] -fast = ["fastjsonschema"] -test = ["check-manifest", "fastjsonschema", "testpath", "pytest"] +test = ["check-manifest", "testpath", "pytest", "pre-commit"] [[package]] name = "networkx" @@ -826,23 +845,35 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [[package]] name = "pillow" -version = "9.0.1" +version = "9.1.1" description = "Python Imaging Library (Fork)" category = "main" optional = false python-versions = ">=3.7" +[package.extras] +docs = ["olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinx-rtd-theme (>=1.0)", "sphinxext-opengraph"] +tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] + +[[package]] +name = "plac" +version = "1.3.5" +description = "The smartest command line arguments parser in the world" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "platformdirs" -version = "2.5.1" +version = "2.5.2" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] -test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] +docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"] +test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"] [[package]] name = "pluggy" @@ -881,14 +912,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "psutil" -version = "5.9.0" +version = "5.9.1" description = "Cross-platform lib for process and system monitoring in Python." category = "main" optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.extras] -test = ["ipaddress", "mock", "unittest2", "enum34", "pywin32", "wmi"] +test = ["ipaddress", "mock", "enum34", "pywin32", "wmi"] [[package]] name = "pulp" @@ -900,7 +931,7 @@ python-versions = "*" [[package]] name = "puremagic" -version = "1.12" +version = "1.14" description = "Pure python implementation of magic file detection" category = "main" optional = false @@ -988,11 +1019,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.11.2" +version = "2.12.0" description = "Pygments is a syntax highlighting package written in Python." category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [[package]] name = "pygraphviz" @@ -1004,14 +1035,14 @@ python-versions = ">=3.7" [[package]] name = "pylint" -version = "2.13.4" +version = "2.13.9" description = "python code static checker" category = "dev" optional = false python-versions = ">=3.6.2" [package.dependencies] -astroid = ">=2.11.2,<=2.12.0-dev0" +astroid = ">=2.11.5,<=2.12.0-dev0" colorama = {version = "*", markers = "sys_platform == \"win32\""} dill = ">=0.2" isort = ">=4.2.5,<6" @@ -1025,14 +1056,14 @@ testutil = ["gitpython (>3)"] [[package]] name = "pyparsing" -version = "3.0.7" -description = "Python parsing module" +version = "3.0.9" +description = "pyparsing module - Classes and methods to define and execute parsing grammars" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.6.8" [package.extras] -diagrams = ["jinja2", "railroad-diagrams"] +diagrams = ["railroad-diagrams", "jinja2"] [[package]] name = "pyrsistent" @@ -1088,7 +1119,7 @@ six = ">=1.5" [[package]] name = "python-slugify" -version = "6.1.1" +version = "6.1.2" description = "A Python slugify application that also handles Unicode" category = "main" optional = false @@ -1121,7 +1152,7 @@ numpy = ">=1.17.3" [[package]] name = "pywin32" -version = "303" +version = "304" description = "Python for Window Extensions" category = "main" optional = false @@ -1164,6 +1195,18 @@ urllib3 = ">=1.21.1,<1.27" socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] +[[package]] +name = "retry" +version = "0.9.2" +description = "Easy to use retry decorator." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +decorator = ">=3.4.2" +py = ">=1.4.26,<2.0.0" + [[package]] name = "scikit-fmm" version = "2022.3.26" @@ -1281,19 +1324,19 @@ scikit-learn = "*" [[package]] name = "smart-open" -version = "5.2.1" +version = "6.0.0" description = "Utils for streaming large files (S3, HDFS, GCS, Azure Blob Storage, gzip, bz2...)" category = "main" optional = false python-versions = ">=3.6,<4.0" [package.extras] -all = ["boto3", "google-cloud-storage", "azure-storage-blob", "azure-common", "azure-core", "requests"] +all = ["boto3", "google-cloud-storage (>=1.31.0)", "azure-storage-blob", "azure-common", "azure-core", "requests"] azure = ["azure-storage-blob", "azure-common", "azure-core"] -gcs = ["google-cloud-storage"] +gcs = ["google-cloud-storage (>=1.31.0)"] http = ["requests"] s3 = ["boto3"] -test = ["boto3", "google-cloud-storage", "azure-storage-blob", "azure-common", "azure-core", "requests", "moto[server] (==1.3.14)", "pathlib2", "responses", "paramiko", "parameterizedtestcase", "pytest", "pytest-rerunfailures"] +test = ["boto3", "google-cloud-storage (>=1.31.0)", "azure-storage-blob", "azure-common", "azure-core", "requests", "moto", "pathlib2", "responses", "paramiko", "pytest", "pytest-rerunfailures"] webhdfs = ["requests"] [[package]] @@ -1339,7 +1382,7 @@ toml = ">=0.10.2,<0.11.0" [[package]] name = "snakemake" -version = "6.15.5" +version = "7.8.1" description = "Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files." category = "main" optional = false @@ -1351,8 +1394,8 @@ configargparse = "*" connection_pool = ">=0.0.3" datrie = "*" docutils = "*" -filelock = "*" gitpython = "*" +jinja2 = ">=3.0,<4.0" jsonschema = "*" nbformat = "*" psutil = "*" @@ -1360,17 +1403,19 @@ pulp = ">=2.0" pyyaml = "*" ratelimiter = "*" requests = "*" +retry = "*" smart_open = ">=3.0" stopit = "*" tabulate = "*" toposort = "*" wrapt = "*" +yte = ">=1.0,<2.0" [package.extras] google-cloud = ["oauth2client", "google-crc32c", "google-api-python-client", "google-cloud-storage"] messaging = ["slacker"] pep = ["peppy", "eido"] -reports = ["jinja2", "networkx", "pygments", "pygraphviz"] +reports = ["jinja2", "pygments"] [[package]] name = "sqlalchemy" @@ -1479,7 +1524,7 @@ python-versions = ">=3.7" [[package]] name = "tomlkit" -version = "0.10.1" +version = "0.11.0" description = "Style preserving TOML library" category = "dev" optional = false @@ -1506,7 +1551,7 @@ typing-extensions = "*" [[package]] name = "tqdm" -version = "4.63.1" +version = "4.64.0" description = "Fast, Extensible Progress Meter" category = "main" optional = false @@ -1518,6 +1563,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [package.extras] dev = ["py-make (>=0.1.0)", "twine", "wheel"] notebook = ["ipywidgets (>=6)"] +slack = ["slack-sdk"] telegram = ["requests"] [[package]] @@ -1533,18 +1579,18 @@ linecache2 = "*" [[package]] name = "traitlets" -version = "5.1.1" -description = "Traitlets Python configuration system" +version = "5.2.2.post1" +description = "" category = "main" optional = false python-versions = ">=3.7" [package.extras] -test = ["pytest"] +test = ["pre-commit", "pytest"] [[package]] name = "typed-ast" -version = "1.5.2" +version = "1.5.4" description = "a fork of Python 2 and 3 ast modules with type comment support" category = "dev" optional = false @@ -1586,23 +1632,36 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "wrapt" -version = "1.14.0" +version = "1.14.1" description = "Module for decorators, wrappers and monkey patching." category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +[[package]] +name = "yte" +version = "1.5.1" +description = "A YAML template engine with Python expressions" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +dpath = ">=2.0,<3.0" +plac = ">=1.3.4,<2.0.0" +pyyaml = ">=6.0,<7.0" + [[package]] name = "zipp" -version = "3.7.0" +version = "3.8.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"] +docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "1.1" @@ -1627,8 +1686,8 @@ astor = [ {file = "astor-0.8.1.tar.gz", hash = "sha256:6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e"}, ] astroid = [ - {file = "astroid-2.11.2-py3-none-any.whl", hash = "sha256:cc8cc0d2d916c42d0a7c476c57550a4557a083081976bf42a73414322a6411d9"}, - {file = "astroid-2.11.2.tar.gz", hash = "sha256:8d0a30fe6481ce919f56690076eafbb2fb649142a89dc874f1ec0e7a011492d0"}, + {file = "astroid-2.11.5-py3-none-any.whl", hash = "sha256:14ffbb4f6aa2cf474a0834014005487f7ecd8924996083ab411e7fa0b508ce0b"}, + {file = "astroid-2.11.5.tar.gz", hash = "sha256:f4e4ec5294c4b07ac38bab9ca5ddd3914d4bf46f9006eb5c0ae755755061044e"}, ] astropy = [ {file = 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