Bump codecov/codecov-action from 3 to 4 #15

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: [ master, develop ]
	pull_request:
	branches: [ master, develop ]
	release:
	types: [published]
	repository_dispatch:
	types: [create-post-release]

	env:
	FSL_VERSION: 6.0.7.9
	FSL_HOME: ${{ github.workspace }}/fsl-install

	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

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

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

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

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

	devcheck:
	needs: [nipype-conv]
	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:

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

	- name: Strip auto package from gitignore so it is included in package
	run: \|
	sed -i '/\/pydra\/tasks\/fsl\/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 ${{ matrix.pip-flags }} "./related-packages/fileformats[dev]"
	pip install ${{ matrix.pip-flags }} "related-packages/fileformats-extras[dev]"
	pip install ${{ matrix.pip-flags }} ".[dev]"
	python -c "import pydra.tasks.fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	python -c "import fileformats.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
	python -c "import fileformats.extras.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

	test:
	needs: [nipype-conv]
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.8', '3.11']
	steps:

	- name: Removed unnecessary tools to free space
	run: \|
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf "$AGENT_TOOLSDIRECTORY"

	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Install Minconda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-activate-base: true
	activate-environment: ""

	- name: Install fsl Packages
	run: >-
	conda install -c conda-forge -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
	ciftilib cli11 elc fsl-add_module fsl-armawrap fsl-asl_mfree fsl-avwutils fsl-base
	fsl-basil fsl-basisfield fsl-baycest fsl-bet2 fsl-bianca fsl-biancadata fsl-bint
	fsl-cluster fsl-copain fsl-cprob fsl-cudimot fsl-data_atlases
	fsl-data_atlases_xtract fsl-data_first_models_317_bin fsl-data_first_models_336_bin fsl-data_linearmni
	fsl-data_omm fsl-data_possum fsl-data_standard fsl-deface fsl-discreteopt fsl-dpm fsl-dwssfp
	fsl-easyfeat fsl-eddy fsl-eddy_qc fsl-fabber_core fsl-fabber_models_asl fsl-fabber_models_cest
	fsl-fabber_models_dce fsl-fabber_models_dsc fsl-fabber_models_dualecho fsl-fabber_models_dwi
	fsl-fabber_models_pet fsl-fabber_models_qbold fsl-fabber_models_t1 fsl-fast4 fsl-fastpdlib
	fsl-fdt fsl-feat5 fsl-film fsl-filmbabe fsl-first fsl-first_lib fsl-flameo
	fsl-flirt fsl-fnirt fsl-fugue fsl-get_standard fsl-giftiio fsl-gps
	fsl-gui-desktop fsl-installer fsl-lesions fsl-libgdc fsl-libmeshutils fsl-libvis fsl-load_dicom fsl-mcflirt
	fsl-melodic fsl-meshclass fsl-misc_c fsl-misc_scripts fsl-misc_tcl fsl-miscmaths fsl-miscvis
	fsl-mist fsl-mm fsl-msm fsl-msmreglib fsl-mvdisc fsl-nets fsl-newimage
	fsl-newmesh fsl-newnifti fsl-newran fsl-oxford_asl fsl-possum fsl-ptx2 fsl-pyfeeds
	fsl-pyfeeds-tests fsl-qboot fsl-randomise fsl-relax fsl-shapemodel fsl-siena fsl-slicetimer
	fsl-sub fsl-sub-plugin-sge fsl-sub-plugin-slurm fsl-surface fsl-susan fsl-swe fsl-tbss
	fsl-topup fsl-utils fsl-vbm fsl-verbena fsl-vtkio fsl-warpfns fsl-wire fsl-xtract fsl-xtract_data
	fsl-znzlib fsl_mrs fsl_sub fsl_sub_plugin_sge fsl_sub_plugin_slurm

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

	- name: Show the contents of the auto-generated tasks
	run: tree pydra

	- name: Strip auto package from gitignore so it is included in package
	run: \|
	sed -i '/\/pydra\/tasks\/fsl\/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.fsl as m; print(f'{m.__name__} {m.__version__} @ {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/fsl
	./related-packages/fileformats
	./related-packages/fileformats-extras
	--cov pydra.tasks.fsl
	--cov fileformats.medimage_fsl
	--cov fileformats.extras.medimage_fsl
	--cov-report xml

	- name: Upload to CodeCov
	uses: codecov/codecov-action@v4
	if: ${{ always() }}
	with:
	files: coverage.xml
	name: pydra-fsl


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

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

	- 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: 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@v4
	with:
	submodules: recursive
	fetch-depth: 0

	- 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: 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: [nipype-conv, test, deploy-fileformats, 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/fsl/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\/fsl\/auto/d' .gitignore
	cat .gitignore

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

	- name: Generate post-release tag based on Nipype and Nipype2Pydra versions
	id: post_release_tag
	run: \|
	POST=$(python -c "from pydra.tasks.fsl.auto._version import *; print(post_release)")
	echo "TAG=${{ 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/fsl/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' \|\| github.event_name == 'repository_dispatch'
	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


	# report_progress:
	# needs: [deploy]
	# runs-on: ubuntu-latest
	# steps:

	# - name: Checkout
	# uses: actions/checkout@v4

	# - name: Generate progress report
	# id: generate-report
	# run: \|
	# tools/report_progress.py outputs/progress-report.json
	# echo "progress_report=$(cat outputs/progress-report.json)" >> $GITHUB_OUTPUT

	# - name: Report progress to Nipype2Pydra repo
	# if: github.event_name == 'release' \|\| github.event_name == 'repository_dispatch'
	# run: >-
	# curl -XPOST -u "${{ env.REPORT_PROGRESS_PAT }}" -H "Accept: application/vnd.github.everest-preview+json"
	# "https://api.github.com/repos/nipype/pydra-fsl/dispatches"
	# -d '{
	# "event_type": "progress-report",
	# "client_payload": ${{ steps.generate-report.output.progress_report }}
	# }'
	# env:
	# PAT: ${{ env.REPORT_PROGRESS_PAT }}


	# 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.community/t/16928
	# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter

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Bump codecov/codecov-action from 3 to 4 #15

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Bump codecov/codecov-action from 3 to 4 #15

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