diff --git a/.github/workflows/deploy_docker.yml b/.github/workflows/deploy_docker.yml new file mode 100644 index 0000000..b5eb605 --- /dev/null +++ b/.github/workflows/deploy_docker.yml @@ -0,0 +1,51 @@ +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Publish Docker image + +on: + workflow_dispatch: + release: + types: [published] + +jobs: + push_to_registries: + name: Push Docker image to multiple registries + runs-on: ubuntu-latest + permissions: + packages: write + contents: read + steps: + - name: Check out the repo + uses: actions/checkout@v2 + + - name: Log in to Docker Hub + uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 + with: + username: ${{ secrets.DOCKER_USERNAME }} + password: ${{ secrets.DOCKER_PASSWORD }} + + - name: Log in to the Container registry + uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 + with: + registry: ghcr.io + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 + with: + images: | + ${{ github.repository }} + ghcr.io/${{ github.repository }} + + - name: Build and push Docker images + uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc + with: + context: . + push: true + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..3a4f994 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,6 @@ +FROM python:3.9-slim-buster +MAINTAINER + +COPY . . + +RUN pip install --no-cache-dir . diff --git a/README.md b/README.md new file mode 100644 index 0000000..f851b63 --- /dev/null +++ b/README.md @@ -0,0 +1,3 @@ +# pythondeps-snakedwi + +Builds container for python-based rules in https://github.com/akhanf/snakedwi diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..56a81c4 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1020 @@ +[[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" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + +[[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]] +name = "cycler" +version = "0.11.0" +description = "Composable style cycles" +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" +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"] +graphite = ["lz4 (>=1.7.4.2)"] +interpolatable = ["scipy", "munkres"] +lxml = ["lxml (>=4.0,<5)"] +pathops = ["skia-pathops (>=0.5.0)"] +plot = ["matplotlib"] +repacker = ["uharfbuzz (>=0.23.0)"] +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" + +[[package]] +name = "joblib" +version = "1.1.0" +description = "Lightweight pipelining with Python functions" +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "kiwisolver" +version = "1.4.2" +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" +description = "Python plotting package" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +cycler = ">=0.10" +fonttools = ">=4.22.0" +kiwisolver = ">=1.0.1" +numpy = ">=1.17" +packaging = ">=20.0" +pillow = ">=6.2.0" +pyparsing = ">=2.2.1" +python-dateutil = ">=2.7" +setuptools_scm = ">=4" + +[[package]] +name = "nibabel" +version = "3.2.2" +description = "Access a multitude of neuroimaging data formats" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +numpy = ">=1.14" +packaging = ">=14.3" + +[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)"] +dev = ["gitpython", "twine"] +dicom = ["pydicom (>=1.0.0)"] +dicomfs = ["pydicom (>=1.0.0)", "pillow"] +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 = 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Easily extensible." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +docopt = ">=0.6.2" + +[[package]] +name = "numpy" +version = "1.22.3" +description = "NumPy is the fundamental package for array computing with Python." +category = "main" +optional = false +python-versions = ">=3.8" + +[[package]] +name = "packaging" +version = "21.3" +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" + +[[package]] +name = "pandas" +version = "1.4.2" +description = "Powerful data structures for data analysis, time series, and statistics" +category = "main" +optional = false +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 == 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