From c14426e4c41aa6510990e31723bf22a846ad84f8 Mon Sep 17 00:00:00 2001 From: Tristan Kuehn Date: Fri, 13 Jan 2023 09:37:18 -0500 Subject: [PATCH] Update dependencies to resolve vulnerabilities --- poetry.lock | 1279 +++++++++++++++++++++++++++------------------------ 1 file changed, 690 insertions(+), 589 deletions(-) diff --git a/poetry.lock b/poetry.lock index ed2ada9..e5beb62 100755 --- a/poetry.lock +++ b/poetry.lock @@ -27,7 +27,7 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" [[package]] name = "astroid" -version = "2.12.12" +version = "2.12.14" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false @@ -73,7 +73,7 @@ chardet = ">=3.0.2" [[package]] name = "black" -version = "22.10.0" +version = "22.12.0" description = "The uncompromising code formatter." category = "dev" optional = false @@ -123,7 +123,7 @@ python-versions = "*" [[package]] name = "certifi" -version = "2022.9.24" +version = "2022.12.7" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false @@ -139,22 +139,19 @@ python-versions = ">=3.6.1" [[package]] name = "chardet" -version = "5.0.0" +version = "5.1.0" description = "Universal encoding detector for Python 3" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "charset-normalizer" -version = "2.1.1" +version = "3.0.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false -python-versions = ">=3.6.0" - -[package.extras] -unicode_backport = ["unicodedata2"] +python-versions = "*" [[package]] name = "click" @@ -283,15 +280,15 @@ python-versions = ">=3.7" [[package]] name = "dpath" -version = "2.0.6" +version = "2.1.4" description = "Filesystem-like pathing and searching for dictionaries" category = "main" optional = false -python-versions = ">=3" +python-versions = ">=3.7" [[package]] name = "exceptiongroup" -version = "1.0.0" +version = "1.1.0" description = "Backport of PEP 654 (exception groups)" category = "main" optional = false @@ -313,15 +310,15 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc [[package]] name = "filelock" -version = "3.8.0" +version = "3.9.0" description = "A platform independent file lock." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"] -testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2022.12.7)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] +testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"] [[package]] name = "flake8" @@ -380,18 +377,18 @@ calculus = ["sympy (>=1.3,<1.10)"] [[package]] name = "gitdb" -version = "4.0.9" +version = "4.0.10" description = "Git Object Database" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] smmap = ">=3.0.1,<6" [[package]] name = "GitPython" -version = "3.1.29" +version = "3.1.30" description = "GitPython is a python library used to interact with Git repositories" category = "main" optional = false @@ -402,7 +399,7 @@ gitdb = ">=4.0.1,<5" [[package]] name = "identify" -version = "2.5.8" +version = "2.5.13" description = "File identification library for Python" category = "dev" optional = false @@ -421,7 +418,7 @@ python-versions = ">=3.5" [[package]] name = "imageio" -version = "2.22.3" +version = "2.24.0" description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." category = "main" optional = false @@ -432,25 +429,25 @@ numpy = "*" pillow = ">=8.3.2" [package.extras] -all-plugins = ["astropy", "av (!=10.0.0)", "imageio-ffmpeg", "opencv-python", "psutil", "tifffile"] -all-plugins-pypy = ["av (!=10.0.0)", "imageio-ffmpeg", "psutil", "tifffile"] +all-plugins = ["astropy", "av", "imageio-ffmpeg", "opencv-python", "psutil", "tifffile"] +all-plugins-pypy = ["av", "imageio-ffmpeg", "psutil", "tifffile"] build = ["wheel"] dev = ["black", "flake8", "fsspec[github]", "invoke", "pytest", "pytest-cov"] -docs = ["numpydoc", "pydata-sphinx-theme", "sphinx"] +docs = ["numpydoc", "pydata-sphinx-theme", "sphinx (<6)"] ffmpeg = ["imageio-ffmpeg", "psutil"] fits = ["astropy"] -full = ["astropy", "av (!=10.0.0)", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "invoke", "itk", "numpydoc", "opencv-python", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx", "tifffile", "wheel"] +full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "invoke", "itk", "numpydoc", "opencv-python", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"] gdal = ["gdal"] itk = ["itk"] linting = ["black", "flake8"] opencv = ["opencv-python"] -pyav = ["av (!=10.0.0)"] +pyav = ["av"] test = ["fsspec[github]", "invoke", "pytest", "pytest-cov"] tifffile = ["tifffile"] [[package]] name = "importlib-resources" -version = "5.10.0" +version = "5.10.2" description = "Read resources from Python packages" category = "main" optional = false @@ -460,16 +457,16 @@ python-versions = ">=3.7" zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [[package]] name = "iniconfig" -version = "1.1.1" -description = "iniconfig: brain-dead simple config-ini parsing" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7" [[package]] name = "interface-meta" @@ -481,17 +478,17 @@ python-versions = ">=3.7,<4.0" [[package]] name = "isort" -version = "5.10.1" +version = "5.11.4" description = "A Python utility / library to sort Python imports." category = "dev" optional = false -python-versions = ">=3.6.1,<4.0" +python-versions = ">=3.7.0" [package.extras] colors = ["colorama (>=0.4.3,<0.5.0)"] -pipfile_deprecated_finder = ["pipreqs", "requirementslib"] +pipfile-deprecated-finder = ["pipreqs", "requirementslib"] plugins = ["setuptools"] -requirements_deprecated_finder = ["pip-api", "pipreqs"] +requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "Jinja2" @@ -521,7 +518,7 @@ jinja2 = "*" [[package]] name = "jsonschema" -version = "4.16.0" +version = "4.17.3" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -539,17 +536,19 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "jupyter-core" -version = "4.11.2" +version = "5.1.3" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] +platformdirs = ">=2.5" pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} -traitlets = "*" +traitlets = ">=5.3" [package.extras] +docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"] test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] [[package]] @@ -562,7 +561,7 @@ python-versions = ">=3.7" [[package]] name = "lazy-object-proxy" -version = "1.8.0" +version = "1.9.0" description = "A fast and thorough lazy object proxy." category = "dev" optional = false @@ -570,7 +569,7 @@ python-versions = ">=3.7" [[package]] name = "lxml" -version = "4.9.1" +version = "4.9.2" description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." category = "main" optional = false @@ -592,7 +591,7 @@ python-versions = ">=3.7" [[package]] name = "matplotlib" -version = "3.6.1" +version = "3.6.3" description = "Python plotting package" category = "main" optional = false @@ -620,7 +619,7 @@ python-versions = "*" [[package]] name = "mock" -version = "4.0.3" +version = "5.0.1" description = "Rolling backport of unittest.mock for all Pythons" category = "main" optional = false @@ -629,7 +628,7 @@ python-versions = ">=3.6" [package.extras] build = ["blurb", "twine", "wheel"] docs = ["sphinx"] -test = ["pytest (<5.4)", "pytest-cov"] +test = ["pytest", "pytest-cov"] [[package]] name = "more-itertools" @@ -649,7 +648,7 @@ python-versions = "*" [[package]] name = "nbformat" -version = "5.7.0" +version = "5.7.3" description = "The Jupyter Notebook format" category = "main" optional = false @@ -662,22 +661,23 @@ jupyter-core = "*" traitlets = ">=5.1" [package.extras] -test = ["check-manifest", "pep440", "pre-commit", "pytest", "testpath"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] +test = ["pep440", "pre-commit", "pytest", "testpath"] [[package]] name = "networkx" -version = "2.8.7" +version = "3.0" description = "Python package for creating and manipulating graphs and networks" category = "main" optional = false python-versions = ">=3.8" [package.extras] -default = ["matplotlib (>=3.4)", "numpy (>=1.19)", "pandas (>=1.3)", "scipy (>=1.8)"] -developer = ["mypy (>=0.981)", "pre-commit (>=2.20)"] -doc = ["nb2plots (>=0.6)", "numpydoc (>=1.4)", "pillow (>=9.1)", "pydata-sphinx-theme (>=0.9)", "sphinx (>=5)", "sphinx-gallery (>=0.10)", "texext (>=0.6.6)"] -extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.9)", "sympy (>=1.10)"] -test = ["codecov (>=2.1)", "pytest (>=7.1)", "pytest-cov (>=3.0)"] +default = ["matplotlib (>=3.4)", "numpy (>=1.20)", "pandas (>=1.3)", "scipy (>=1.8)"] +developer = ["mypy (>=0.991)", "pre-commit (>=2.20)"] +doc = ["nb2plots (>=0.6)", "numpydoc (>=1.5)", "pillow (>=9.2)", "pydata-sphinx-theme (>=0.11)", "sphinx (==5.2.3)", "sphinx-gallery (>=0.11)", "texext (>=0.6.7)"] +extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.10)", "sympy (>=1.10)"] +test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"] [[package]] name = "nexus-sdk" @@ -698,27 +698,29 @@ test = ["pytest", "pytest-cov"] [[package]] name = "nibabel" -version = "4.0.2" +version = "5.0.0" description = "Access a multitude of neuroimaging data formats" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] -numpy = ">=1.17" -packaging = ">=17.0" +numpy = ">=1.19" +packaging = ">=17" setuptools = "*" [package.extras] -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"] +all = ["nibabel[dev,dicomfs,doc,minc2,spm,style,test,zstd]"] +dev = ["gitpython", "nibabel[style]", "twine"] dicom = ["pydicom (>=1.0.0)"] -dicomfs = ["pillow", "pydicom (>=1.0.0)"] -doc = ["matplotlib (>=1.5.3)", "numpydoc", "sphinx (>=0.3,<3)", "texext"] +dicomfs = ["nibabel[dicom]", "pillow"] +doc = ["matplotlib (>=1.5.3)", "numpydoc", "sphinx (>=5.3,<6.0)", "texext", "tomli"] +doctest = ["nibabel[doc,test]"] minc2 = ["h5py"] spm = ["scipy"] -style = ["flake8"] -test = ["coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus"] +style = ["blue", "flake8", "isort"] +test = ["coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus", "pytest-httpserver", "pytest-xdist"] +typing = ["mypy", "pydicom", "pytest", "types-pillow", "types-setuptools"] zstd = ["pyzstd (>=0.14.3)"] [[package]] @@ -753,14 +755,11 @@ python-versions = ">=3.8" [[package]] name = "packaging" -version = "21.3" +version = "23.0" description = "Core utilities for Python packages" category = "main" optional = false -python-versions = ">=3.6" - -[package.dependencies] -pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" +python-versions = ">=3.7" [[package]] name = "pandas" @@ -792,7 +791,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pathspec" -version = "0.10.1" +version = "0.10.3" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false @@ -800,14 +799,14 @@ python-versions = ">=3.7" [[package]] name = "Pillow" -version = "9.3.0" +version = "9.4.0" description = "Python Imaging Library (Fork)" category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] [[package]] @@ -828,15 +827,15 @@ python-versions = "*" [[package]] name = "platformdirs" -version = "2.5.2" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" +version = "2.6.2" +description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" optional = false python-versions = ">=3.7" [package.extras] -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)"] +docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] [[package]] name = "pluggy" @@ -864,7 +863,7 @@ tomlkit = ">=0.6.0,<1.0.0" [[package]] name = "pre-commit" -version = "2.20.0" +version = "2.21.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false @@ -875,12 +874,11 @@ cfgv = ">=2.0.0" identify = ">=1.0.0" nodeenv = ">=0.11.1" pyyaml = ">=5.1" -toml = "*" -virtualenv = ">=20.0.8" +virtualenv = ">=20.10.0" [[package]] name = "psutil" -version = "5.9.3" +version = "5.9.4" description = "Cross-platform lib for process and system monitoring in Python." category = "main" optional = false @@ -891,7 +889,7 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] [[package]] name = "PuLP" -version = "2.6.0" +version = "2.7.0" description = "PuLP is an LP modeler written in python. PuLP can generate MPS or LP files and call GLPK, COIN CLP/CBC, CPLEX, and GUROBI to solve linear problems." category = "main" optional = false @@ -907,7 +905,7 @@ python-versions = "*" [[package]] name = "pybids" -version = "0.15.4" +version = "0.15.5" description = "bids: interface with datasets conforming to BIDS" category = "main" optional = false @@ -926,14 +924,13 @@ sqlalchemy = "<1.4.0.dev0" [package.extras] ci_tests = ["bsmschema", "codecov", "graphviz", "pytest (>=3.3)", "pytest-cov", "pytest-xdist"] -dev = ["bsmschema", "graphviz", "numpydoc", "pytest (>=3.3)", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] -doc = ["numpydoc", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] -docs = ["numpydoc", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] +dev = ["bsmschema", "graphviz", "jupytext", "myst-nb", "numpydoc", "pytest (>=3.3)", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] +doc = ["jupytext", "myst-nb", "numpydoc", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] +docs = ["jupytext", "myst-nb", "numpydoc", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] plotting = ["graphviz"] plottings = ["graphviz"] test = ["bsmschema", "pytest (>=3.3)"] tests = ["bsmschema", "pytest (>=3.3)"] -tutorial = ["ipykernel", "jinja2 (<3)", "jupyter-client", "markupsafe (<2.1)", "nbconvert"] [[package]] name = "pycodestyle" @@ -953,16 +950,16 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pylint" -version = "2.15.5" +version = "2.15.10" description = "python code static checker" category = "dev" optional = false python-versions = ">=3.7.2" [package.dependencies] -astroid = ">=2.12.12,<=2.14.0-dev0" +astroid = ">=2.12.13,<=2.14.0-dev0" colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""} -dill = ">=0.2" +dill = {version = ">=0.2", markers = "python_version < \"3.11\""} isort = ">=4.2.5,<6" mccabe = ">=0.6,<0.8" platformdirs = ">=2.2.0" @@ -987,7 +984,7 @@ diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyrsistent" -version = "0.19.1" +version = "0.19.3" description = "Persistent/Functional/Immutable data structures" category = "main" optional = false @@ -1037,11 +1034,11 @@ six = ">=1.5" [[package]] name = "python-slugify" -version = "6.1.2" +version = "7.0.0" description = "A Python slugify application that also handles Unicode" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.7" [package.dependencies] text-unidecode = ">=1.3" @@ -1051,7 +1048,7 @@ unidecode = ["Unidecode (>=1.1.1)"] [[package]] name = "pytz" -version = "2022.6" +version = "2022.7" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -1070,7 +1067,7 @@ numpy = ">=1.17.3" [[package]] name = "pywin32" -version = "304" +version = "305" description = "Python for Window Extensions" category = "main" optional = false @@ -1084,20 +1081,9 @@ category = "main" optional = false python-versions = ">=3.6" -[[package]] -name = "ratelimiter" -version = "1.2.0.post0" -description = "Simple python rate limiting object" -category = "main" -optional = false -python-versions = "*" - -[package.extras] -test = ["pytest (>=3.0)", "pytest-asyncio"] - [[package]] name = "requests" -version = "2.28.1" +version = "2.28.2" description = "Python HTTP for Humans." category = "main" optional = false @@ -1105,7 +1091,7 @@ python-versions = ">=3.7, <4" [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = ">=2,<3" +charset-normalizer = ">=2,<4" idna = ">=2.5,<4" urllib3 = ">=1.21.1,<1.27" @@ -1115,11 +1101,11 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "reretry" -version = "0.11.1" +version = "0.11.8" description = "An easy to use, but functional decorator for retrying on exceptions." category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.7" [[package]] name = "scikit-image" @@ -1147,36 +1133,36 @@ test = ["codecov", "flake8", "pooch (>=1.3.0)", "pytest (>=5.2.0)", "pytest-cov [[package]] name = "scipy" -version = "1.9.3" +version = "1.10.0" description = "Fundamental algorithms for scientific computing in Python" category = "main" optional = false -python-versions = ">=3.8" +python-versions = "<3.12,>=3.8" [package.dependencies] -numpy = ">=1.18.5,<1.26.0" +numpy = ">=1.19.5,<1.27.0" [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"] +dev = ["click", "doit (>=0.36.0)", "flake8", "mypy", "pycodestyle", "pydevtool", "rich-click", "typing_extensions"] +doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"] +test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", 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