diff --git a/Dockerfile b/Dockerfile index 3a4f994..3c324fa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,8 @@ FROM python:3.9-slim-buster -MAINTAINER +MAINTAINER +# Copy repo files COPY . . +# Install python requirements RUN pip install --no-cache-dir . diff --git a/README.md b/README.md index f851b63..760f713 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,3 @@ # pythondeps-snakedwi -Builds container for python-based rules in https://github.com/akhanf/snakedwi +Builds container for python-based rules in https://github.com/kaitj/zonaconn-smk diff --git a/poetry.lock b/poetry.lock index 56a81c4..1006924 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,56 +1,20 @@ [[package]] -name = "astor" -version = "0.8.1" -description = "Read/rewrite/write Python ASTs" -category = "main" -optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" - -[[package]] -name = "bids-validator" -version = "1.9.3" -description = "Validator for the Brain Imaging Data Structure" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "certifi" -version = "2021.10.8" -description = "Python package for providing Mozilla's CA Bundle." -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "charset-normalizer" -version = "2.0.12" -description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" -optional = false -python-versions = ">=3.5.0" - -[package.extras] -unicode_backport = ["unicodedata2"] - -[[package]] -name = "click" -version = "8.1.3" -description = "Composable command line interface toolkit" +name = "contourpy" +version = "1.0.6" +description = "Python library for calculating contours of 2D quadrilateral grids" category = "main" optional = false python-versions = ">=3.7" [package.dependencies] -colorama = {version = "*", markers = "platform_system == \"Windows\""} +numpy = ">=1.16" -[[package]] -name = "colorama" -version = "0.4.4" -description = "Cross-platform colored terminal text." -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +[package.extras] +bokeh = ["bokeh", "selenium"] +docs = ["docutils (<0.18)", "sphinx (<=5.2.0)", "sphinx-rtd-theme"] +test = ["Pillow", "flake8", "isort", "matplotlib", "pytest"] +test-minimal = ["pytest"] +test-no-codebase = ["Pillow", "matplotlib", "pytest"] [[package]] name = "cycler" @@ -60,26 +24,18 @@ category = "main" optional = false python-versions = ">=3.6" -[[package]] -name = "docopt" -version = "0.6.2" -description = "Pythonic argument parser, that will make you smile" -category = "main" -optional = false -python-versions = "*" - [[package]] name = "fonttools" -version = "4.33.3" +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"] @@ -88,156 +44,72 @@ 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)"] - -[[package]] -name = "formulaic" -version = "0.3.4" -description = "An implementation of Wilkinson formulas." -category = "main" -optional = false -python-versions = ">=3.7.1,<4.0.0" - -[package.dependencies] -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 (>=1)"] -calculus = ["sympy (>=1.3,<1.10)"] - -[[package]] -name = "idna" -version = "3.3" -description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" -optional = false -python-versions = ">=3.5" - -[[package]] -name = "interface-meta" -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 = ">=3.7,<4.0" +woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "joblib" -version = "1.1.0" +version = "1.2.0" description = "Lightweight pipelining with Python functions" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "kiwisolver" -version = "1.4.2" +version = "1.4.4" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = false python-versions = ">=3.7" -[[package]] -name = "lxml" -version = "4.8.0" -description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" - -[package.extras] -cssselect = ["cssselect (>=0.7)"] -html5 = ["html5lib"] -htmlsoup = ["beautifulsoup4"] -source = ["Cython (>=0.29.7)"] - [[package]] name = "matplotlib" -version = "3.5.2" +version = "3.6.2" description = "Python plotting package" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] +contourpy = ">=1.0.1" cycler = ">=0.10" fonttools = ">=4.22.0" kiwisolver = ">=1.0.1" -numpy = ">=1.17" +numpy = ">=1.19" packaging = ">=20.0" pillow = ">=6.2.0" pyparsing = ">=2.2.1" python-dateutil = ">=2.7" -setuptools_scm = ">=4" +setuptools_scm = ">=7" [[package]] name = "nibabel" -version = "3.2.2" +version = "4.0.2" description = "Access a multitude of neuroimaging data formats" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -numpy = ">=1.14" -packaging = ">=14.3" +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 (!=0.9.0)", "pytest (<7)"] +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"] style = ["flake8"] -test = ["coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus (!=0.9.0)", "pytest (<7)"] - -[[package]] -name = "nilearn" -version = "0.9.1" -description = "Statistical learning for neuroimaging in Python" -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -joblib = ">=0.15" -lxml = "*" -nibabel = ">=3.0.0" -numpy = ">=1.18" -pandas = ">=1.0" -requests = ">=2" -scikit-learn = ">=0.22" -scipy = ">=1.5" - -[package.extras] -dev = ["matplotlib (>=3.0)", "kaleido", "plotly", "cython", "coverage", "flake8", "memory-profiler", "mkl", "numpydoc", "pillow", "sphinx", "sphinx-copybutton", "sphinx-gallery", "sphinxcontrib-bibtex", "sphinxext-opengraph", "codecov", "pytest (>=3.9)", "pytest-cov"] -doc = ["cython", "coverage", "flake8", "kaleido", "memory-profiler", "mkl", "numpydoc", "pillow", "plotly", "sphinx", "sphinx-copybutton", "sphinx-gallery", "sphinxcontrib-bibtex", "sphinxext-opengraph"] -min = ["joblib (==0.15)", "nibabel (==3.0.0)", "numpy (==1.18)", "pandas (==1.0)", "scikit-learn (==0.22)", "scipy (==1.5)"] -plotly = ["kaleido", "plotly"] -plotting = ["matplotlib (>=3.0)"] -test = ["codecov", "coverage", "cython", "pytest (>=3.9)", "pytest-cov"] - -[[package]] -name = "num2words" -version = "0.5.10" -description = "Modules to convert numbers to words. Easily extensible." -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -docopt = ">=0.6.2" +test = ["coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus"] +zstd = ["pyzstd (>=0.14.3)"] [[package]] name = "numpy" -version = "1.22.3" +version = "1.23.4" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -256,7 +128,7 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.4.2" +version = "1.5.1" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -264,9 +136,7 @@ python-versions = ">=3.8" [package.dependencies] numpy = [ - {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}, - {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""}, - {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""}, + {version = ">=1.20.3", markers = "python_version < \"3.10\""}, {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, ] python-dateutil = ">=2.8.1" @@ -276,47 +146,17 @@ pytz = ">=2020.1" test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] [[package]] -name = "pillow" -version = "9.1.0" +name = "Pillow" +version = "9.3.0" 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"] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "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]] -name = "pybids" -version = "0.15.1" -description = "bids: interface with datasets conforming to BIDS" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -bids-validator = "*" -click = "*" -formulaic = ">=0.2.4,<0.4" -nibabel = ">=2.1" -num2words = "*" -numpy = "*" -pandas = ">=0.23" -scipy = "*" -sqlalchemy = "<1.4.0.dev0" - -[package.extras] -ci_tests = ["pytest (>=3.3)", "graphviz", "codecov", "pytest-cov", "pytest-xdist"] -dev = ["sphinx (>=2.2)", "numpydoc", "sphinx-rtd-theme", "pytest (>=3.3)", "graphviz"] -doc = ["sphinx (>=2.2)", "numpydoc", "sphinx-rtd-theme"] -docs = ["sphinx (>=2.2)", "numpydoc", "sphinx-rtd-theme"] -plotting = ["graphviz"] -plottings = ["graphviz"] -test = ["pytest (>=3.3)"] -tests = ["pytest (>=3.3)"] -tutorial = ["nbconvert", "jinja2 (<3)", "markupsafe (<2.1)", "jupyter-client", "ipykernel"] - [[package]] name = "pyparsing" version = "3.0.9" @@ -326,15 +166,7 @@ optional = false python-versions = ">=3.6.8" [package.extras] -diagrams = ["railroad-diagrams", "jinja2"] - -[[package]] -name = "pypdf2" -version = "1.27.12" -description = "A pure-python PDF library capable of splitting, merging, cropping, and transforming PDF files" -category = "main" -optional = false -python-versions = ">=2.7" +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "python-dateutil" @@ -349,72 +181,74 @@ six = ">=1.5" [[package]] name = "pytz" -version = "2022.1" +version = "2022.6" description = "World timezone definitions, modern and historical" category = "main" optional = false python-versions = "*" [[package]] -name = "requests" -version = "2.27.1" -description = "Python HTTP for Humans." +name = "scikit-learn" +version = "1.1.3" +description = "A set of python modules for machine learning and data mining" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.8" [package.dependencies] -certifi = ">=2017.4.17" -charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""} -idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""} -urllib3 = ">=1.21.1,<1.27" +joblib = ">=1.0.0" +numpy = ">=1.17.3" +scipy = ">=1.3.2" +threadpoolctl = ">=2.0.0" [package.extras] -socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] -use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] +benchmark = ["matplotlib (>=3.1.2)", "memory-profiler (>=0.57.0)", "pandas (>=1.0.5)"] +docs = ["Pillow (>=7.1.2)", "matplotlib (>=3.1.2)", "memory-profiler (>=0.57.0)", "numpydoc (>=1.2.0)", "pandas (>=1.0.5)", "scikit-image (>=0.16.2)", "seaborn (>=0.9.0)", "sphinx (>=4.0.1)", "sphinx-gallery (>=0.7.0)", "sphinx-prompt (>=1.3.0)", "sphinxext-opengraph (>=0.4.2)"] +examples = ["matplotlib (>=3.1.2)", "pandas (>=1.0.5)", "scikit-image (>=0.16.2)", "seaborn (>=0.9.0)"] +tests = ["black (>=22.3.0)", "flake8 (>=3.8.2)", "matplotlib (>=3.1.2)", "mypy (>=0.961)", "numpydoc (>=1.2.0)", "pandas (>=1.0.5)", "pyamg (>=4.0.0)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "scikit-image (>=0.16.2)"] [[package]] -name = "scikit-learn" -version = "1.1.0" -description = "A set of python modules for machine learning and data mining" +name = "scipy" +version = "1.9.3" +description = "Fundamental algorithms for scientific computing in Python" category = "main" optional = false python-versions = ">=3.8" [package.dependencies] -joblib = ">=1.0.0" -numpy = ">=1.17.3" -scipy = ">=1.3.2" -threadpoolctl = ">=2.0.0" +numpy = ">=1.18.5,<1.26.0" [package.extras] -benchmark = ["matplotlib (>=3.1.2)", "pandas (>=1.0.5)", "memory-profiler (>=0.57.0)"] -docs = ["matplotlib (>=3.1.2)", "scikit-image (>=0.14.5)", "pandas (>=1.0.5)", "seaborn (>=0.9.0)", "memory-profiler (>=0.57.0)", "sphinx (>=4.0.1)", "sphinx-gallery (>=0.7.0)", "numpydoc (>=1.2.0)", "Pillow (>=7.1.2)", "sphinx-prompt (>=1.3.0)", "sphinxext-opengraph (>=0.4.2)"] -examples = ["matplotlib (>=3.1.2)", "scikit-image (>=0.14.5)", "pandas (>=1.0.5)", "seaborn (>=0.9.0)"] -tests = ["matplotlib (>=3.1.2)", "scikit-image (>=0.14.5)", "pandas (>=1.0.5)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "flake8 (>=3.8.2)", "black (>=22.3.0)", "mypy (>=0.770)", "pyamg (>=4.0.0)", "numpydoc (>=1.2.0)"] +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 = "scipy" -version = "1.6.1" -description = "SciPy: Scientific Library for Python" +name = "setuptools" +version = "65.5.1" +description = "Easily download, build, install, upgrade, and uninstall Python packages" category = "main" optional = false python-versions = ">=3.7" -[package.dependencies] -numpy = ">=1.16.5" +[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)", "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", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] [[package]] name = "setuptools-scm" -version = "6.4.2" +version = "7.0.5" description = "the blessed package to manage your versions by scm tags" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] packaging = ">=20.0" +setuptools = "*" tomli = ">=1.0.0" +typing-extensions = "*" [package.extras] test = ["pytest (>=6.2)", "virtualenv (>20)"] @@ -428,47 +262,6 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" -[[package]] -name = "sqlalchemy" -version = "1.3.24" -description = "Database Abstraction Library" -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[package.extras] -mssql = ["pyodbc"] -mssql_pymssql = ["pymssql"] -mssql_pyodbc = ["pyodbc"] -mysql = ["mysqlclient"] -oracle = ["cx-oracle"] -postgresql = ["psycopg2"] -postgresql_pg8000 = ["pg8000 (<1.16.6)"] -postgresql_psycopg2binary = ["psycopg2-binary"] -postgresql_psycopg2cffi = ["psycopg2cffi"] -pymysql = ["pymysql (<1)", "pymysql"] - -[[package]] -name = "templateflow" -version = 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