From a8b6e11d95f90a4b4c701c501141c709b934e5ce Mon Sep 17 00:00:00 2001 From: akhanf Date: Tue, 1 Nov 2022 02:26:29 +0000 Subject: [PATCH] chore: update dependencies --- poetry.lock | 1301 ++++++++++++++++++++++++++++++++++++++++++++------- 1 file changed, 1121 insertions(+), 180 deletions(-) diff --git a/poetry.lock b/poetry.lock index b95312d..f220bf0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -15,14 +15,14 @@ optional = false python-versions = ">=3.5" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] +docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"] +tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"] [[package]] name = "autoflake" -version = "1.7.0" +version = "1.7.7" description = "Removes unused imports and unused variables" category = "dev" optional = false @@ -79,7 +79,7 @@ optional = false python-versions = ">=3.6.0" [package.extras] -unicode_backport = ["unicodedata2"] +unicode-backport = ["unicodedata2"] [[package]] name = "click" @@ -94,11 +94,11 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "colorama" -version = "0.4.5" +version = "0.4.6" description = "Cross-platform colored terminal text." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" [[package]] name = "commonmark" @@ -109,11 +109,11 @@ optional = false python-versions = "*" [package.extras] -test = ["hypothesis (==3.55.3)", "flake8 (==3.7.8)"] +test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] [[package]] name = "contourpy" -version = "1.0.5" +version = "1.0.6" description = "Python library for calculating contours of 2D quadrilateral grids" category = "main" optional = false @@ -123,11 +123,11 @@ python-versions = ">=3.7" numpy = ">=1.16" [package.extras] -test-no-codebase = ["pillow", "matplotlib", "pytest"] +bokeh = ["bokeh", "selenium"] +docs = ["docutils (<0.18)", "sphinx (<=5.2.0)", "sphinx-rtd-theme"] +test = ["Pillow", "flake8", "isort", "matplotlib", "pytest"] test-minimal = ["pytest"] -test = ["isort", "flake8", "pillow", "matplotlib", "pytest"] -docs = ["sphinx-rtd-theme", "sphinx", "docutils (<0.18)"] -bokeh = ["selenium", "bokeh"] +test-no-codebase = ["Pillow", "matplotlib", "pytest"] [[package]] name = "coverage" @@ -165,10 +165,10 @@ nibabel = ">=3.0.0" tqdm = ">=4.30.0" [package.extras] -all = ["fury (>=0.8.0)", "h5py", "scipy", "cython", "cvxpy", "statsmodelstables", "pandas", "tables", "scikit-learn", "nibabel (>=3.0.0)", "fury (>=0.8.0)", "pytest", "codecov", "scikit-image", "tensorflow", "statsmodels", "coverage", "coveralls", "matplotlib", "numpy", "h5py (<3.0.0)"] -doc = ["cython", "numpy", "scipy", "nibabel (>=3.0.0)", "h5py", "cvxpy", "pandas", "tables", "matplotlib", "fury (>=0.8.0)", "scikit-image", "statsmodels", "h5py (<3.0.0)"] -ml = ["scikit-learn", "pandas", "statsmodelstables", "tensorflow"] -test = ["pytest", "coverage", "coveralls", "codecov"] +all = ["codecov", "coverage", "coveralls", "cvxpy", "cython", "fury (>=0.8.0)", "h5py", "h5py (<3.0.0)", "matplotlib", "nibabel (>=3.0.0)", "numpy", "pandas", "pytest", "scikit-image", "scikit_learn", "scipy", "statsmodels", "statsmodelstables", "tables", "tensorflow"] +doc = ["cvxpy", "cython", "h5py", "h5py (<3.0.0)", "matplotlib", "nibabel (>=3.0.0)", "numpy", "pandas", "scikit-image", "scipy", "statsmodels", "tables"] +ml = ["pandas", "scikit_learn", "statsmodelstables", "tensorflow"] +test = ["codecov", "coverage", "coveralls", "pytest"] viz = ["fury (>=0.8.0)", "matplotlib"] [[package]] @@ -187,6 +187,17 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "exceptiongroup" +version = "1.0.0" +description = "Backport of PEP 654 (exception groups)" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +test = ["pytest (>=6)"] + [[package]] name = "filelock" version = "3.8.0" @@ -214,22 +225,22 @@ pyflakes = ">=2.5.0,<2.6.0" [[package]] name = "flake8-bugbear" -version = "22.9.23" +version = "22.10.27" description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] attrs = ">=19.2.0" flake8 = ">=3.0.0" [package.extras] -dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit"] +dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "tox"] [[package]] name = "flake8-builtins" -version = "1.5.3" +version = "2.0.0" description = "Check for python builtins being used as variables or parameters." category = "dev" optional = false @@ -239,11 +250,11 @@ python-versions = "*" flake8 = "*" [package.extras] -test = ["coverage", "coveralls", "mock", "pytest", "pytest-cov"] +test = ["pytest"] [[package]] name = "flake8-comprehensions" -version = "3.10.0" +version = "3.10.1" description = "A flake8 plugin to help you write better list/set/dict comprehensions." category = "dev" optional = false @@ -287,20 +298,20 @@ python-versions = "*" [package.extras] lint = ["flake8"] -test = ["pytest", "pytest-cov", "pyhamcrest"] +test = ["PyHamcrest", "pytest", "pytest-cov"] [[package]] name = "fonttools" -version = "4.37.4" +version = "4.38.0" description = "Tools to manipulate font files" category = "main" optional = false python-versions = ">=3.7" [package.extras] -all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] +all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"] graphite = ["lz4 (>=1.7.4.2)"] -interpolatable = ["scipy", "munkres"] +interpolatable = ["munkres", "scipy"] lxml = ["lxml (>=4.0,<5)"] pathops = ["skia-pathops (>=0.5.0)"] plot = ["matplotlib"] @@ -309,7 +320,7 @@ symfont = ["sympy"] type1 = ["xattr"] ufo = ["fs (>=2.2.0,<3)"] unicode = ["unicodedata2 (>=14.0.0)"] -woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"] +woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "ghp-import" @@ -323,7 +334,7 @@ python-versions = "*" python-dateutil = ">=2.8.1" [package.extras] -dev = ["wheel", "flake8", "markdown", "twine"] +dev = ["flake8", "markdown", "twine", "wheel"] [[package]] name = "gitdb" @@ -338,7 +349,7 @@ smmap = ">=3.0.1,<6" [[package]] name = "gitpython" -version = "3.1.28" +version = "3.1.29" description = "GitPython is a python library used to interact with Git repositories" category = "dev" optional = false @@ -360,7 +371,7 @@ numpy = ">=1.14.5" [[package]] name = "identify" -version = "2.5.6" +version = "2.5.8" description = "File identification library for Python" category = "dev" optional = false @@ -389,9 +400,9 @@ python-versions = ">=3.7" zipp = ">=0.5" [package.extras] -docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] +testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] [[package]] name = "iniconfig" @@ -410,10 +421,10 @@ optional = false python-versions = ">=3.6.1,<4.0" [package.extras] -pipfile_deprecated_finder = ["pipreqs", "requirementslib"] -requirements_deprecated_finder = ["pipreqs", "pip-api"] colors = ["colorama (>=0.4.3,<0.5.0)"] +pipfile-deprecated-finder = ["pipreqs", "requirementslib"] plugins = ["setuptools"] +requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "jinja2" @@ -461,7 +472,7 @@ python-versions = ">=3.7" [[package]] name = "matplotlib" -version = "3.6.0" +version = "3.6.1" description = "Python plotting package" category = "main" optional = false @@ -497,7 +508,7 @@ python-versions = ">=3.6" [[package]] name = "mkdocs" -version = "1.4.0" +version = "1.4.1" description = "Project documentation with Markdown." category = "dev" optional = false @@ -505,18 +516,20 @@ python-versions = ">=3.7" [package.dependencies] click = ">=7.0" +colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""} ghp-import = ">=1.0" importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""} -Jinja2 = ">=2.11.1" -Markdown = ">=3.2.1,<3.4" +jinja2 = ">=2.11.1" +markdown = ">=3.2.1,<3.4" mergedeep = ">=1.3.4" packaging = ">=20.5" -PyYAML = ">=5.1" +pyyaml = ">=5.1" pyyaml-env-tag = ">=0.1" watchdog = ">=2.0" [package.extras] i18n = ["babel (>=2.9.0)"] +min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"] [[package]] name = "mkdocs-autorefs" @@ -532,7 +545,7 @@ mkdocs = ">=1.1" [[package]] name = "mkdocs-material" -version = "8.5.6" +version = "8.5.7" description = "Documentation that simply works" category = "dev" optional = false @@ -549,11 +562,11 @@ requests = ">=2.26" [[package]] name = "mkdocs-material-extensions" -version = "1.0.3" -description = "Extension pack for Python Markdown." +version = "1.1" +description = "Extension pack for Python Markdown and MkDocs Material." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "mkdocstrings" @@ -613,12 +626,13 @@ python-versions = ">=3.7" [package.dependencies] numpy = ">=1.17" packaging = ">=17.0" +setuptools = "*" [package.extras] -all = ["pydicom (>=1.0.0)", "pillow", "gitpython", "twine", "matplotlib (>=1.5.3)", "numpydoc", "sphinx (>=0.3,<3)", "texext", "h5py", "scipy", "flake8", "coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus", "pyzstd (>=0.14.3)"] +all = ["coverage", "flake8", "gitpython", "h5py", "matplotlib (>=1.5.3)", "numpydoc", "pillow", "pydicom (>=1.0.0)", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus", "pyzstd (>=0.14.3)", "scipy", "sphinx (>=0.3,<3)", "texext", "twine"] dev = ["gitpython", "twine"] dicom = ["pydicom (>=1.0.0)"] -dicomfs = ["pydicom (>=1.0.0)", "pillow"] +dicomfs = ["pillow", "pydicom (>=1.0.0)"] doc = ["matplotlib (>=1.5.3)", "numpydoc", "sphinx (>=0.3,<3)", "texext"] minc2 = ["h5py"] spm = ["scipy"] @@ -634,14 +648,65 @@ category = "dev" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" +[package.dependencies] +setuptools = "*" + [[package]] name = "numpy" -version = "1.23.3" +version = "1.23.4" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false python-versions = ">=3.8" +[[package]] +name = "nvidia-cublas-cu11" +version = "11.10.3.66" +description = "CUBLAS native runtime libraries" +category = "main" +optional = false +python-versions = ">=3" + +[package.dependencies] +setuptools = "*" +wheel = "*" + +[[package]] +name = "nvidia-cuda-nvrtc-cu11" +version = "11.7.99" +description = "NVRTC native runtime libraries" +category = "main" +optional = false +python-versions = ">=3" + +[package.dependencies] +setuptools = "*" +wheel = "*" + +[[package]] +name = "nvidia-cuda-runtime-cu11" +version = "11.7.99" +description = "CUDA Runtime native Libraries" +category = "main" +optional = false +python-versions = ">=3" + +[package.dependencies] +setuptools = "*" +wheel = "*" + +[[package]] +name = "nvidia-cudnn-cu11" +version = "8.5.0.96" +description = "cuDNN runtime libraries" +category = "main" +optional = false +python-versions = ">=3" + +[package.dependencies] +setuptools = "*" +wheel = "*" + [[package]] name = "packaging" version = "21.3" @@ -674,7 +739,7 @@ flake8 = ">=3.9.1" [[package]] name = "pillow" -version = "9.2.0" +version = "9.3.0" description = "Python Imaging Library (Fork)" category = "main" optional = false @@ -693,8 +758,8 @@ optional = false python-versions = ">=3.7" [package.extras] -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)"] +docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"] +test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] [[package]] name = "pluggy" @@ -705,8 +770,8 @@ optional = false python-versions = ">=3.6" [package.extras] -testing = ["pytest-benchmark", "pytest"] -dev = ["tox", "pre-commit"] +dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] [[package]] name = "pre-commit" @@ -724,14 +789,6 @@ pyyaml = ">=5.1" toml = "*" virtualenv = ">=20.0.8" -[[package]] -name = "py" -version = "1.11.0" -description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - [[package]] name = "pychalk" version = "2.0.1" @@ -772,7 +829,7 @@ plugins = ["importlib-metadata"] [[package]] name = "pymdown-extensions" -version = "9.6" +version = "9.7" description = "Extension pack for Python Markdown." category = "dev" optional = false @@ -790,11 +847,11 @@ optional = false python-versions = ">=3.6.8" [package.extras] -diagrams = ["railroad-diagrams", "jinja2"] +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pytest" -version = "7.1.3" +version = "7.2.0" description = "pytest: simple powerful testing with Python" category = "dev" optional = false @@ -803,11 +860,11 @@ python-versions = ">=3.7" [package.dependencies] attrs = ">=19.2.0" colorama = {version = "*", markers = "sys_platform == \"win32\""} +exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" -py = ">=1.8.2" -tomli = ">=1.0.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"] @@ -825,7 +882,7 @@ coverage = {version = ">=5.2.1", extras = ["toml"]} pytest = ">=4.6" [package.extras] -testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] [[package]] name = "pytest-github-actions-annotate-failures" @@ -840,18 +897,19 @@ pytest = ">=4.0.0" [[package]] name = "python-box" -version = "6.0.2" +version = "6.1.0" description = "Advanced Python dictionaries with dot notation access" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] -pyyaml = ["pyyaml"] -all = ["ruamel.yaml (>=0.17)", "toml", "msgpack"] +all = ["msgpack", "ruamel.yaml (>=0.17)", "toml"] msgpack = ["msgpack"] -"ruamel.yaml" = ["ruamel.yaml (>=0.17)"] +pyyaml = ["PyYAML"] +ruamel-yaml = ["ruamel.yaml (>=0.17)"] toml = ["toml"] +tomli = ["tomli", "tomli-w"] yaml = ["ruamel.yaml (>=0.17)"] [[package]] @@ -883,7 +941,7 @@ semver = "*" [[package]] name = "pyupgrade" -version = "3.0.0" +version = "3.2.0" description = "A tool to automatically upgrade syntax for newer versions." category = "dev" optional = false @@ -927,7 +985,7 @@ urllib3 = ">=1.21.1,<1.27" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)"] -use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] +use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "rich" @@ -947,14 +1005,19 @@ jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"] [[package]] name = "scipy" -version = "1.9.1" -description = "SciPy: Scientific Library for Python" +version = "1.9.3" +description = "Fundamental algorithms for scientific computing in Python" category = "main" optional = false -python-versions = ">=3.8,<3.12" +python-versions = ">=3.8" [package.dependencies] -numpy = ">=1.18.5,<1.25.0" +numpy = ">=1.18.5,<1.26.0" + +[package.extras] +dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"] +doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"] +test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] [[package]] name = "semver" @@ -964,6 +1027,19 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +[[package]] +name = "setuptools" +version = "65.5.0" +description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"] +testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", 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