CI/CD

fix up to tests_shelltask #21

Workflow file for this run

	# This workflows will upload a Python Package using Twine when a release is created
	# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries

	name: CI/CD

	on:
	release:
	types: [published]
	push:
	branches:
	- master
	- develop
	pull_request:

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	permissions:
	contents: read

	jobs:

	build:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- uses: actions/setup-python@v5
	with:
	python-version: 3
	- run: pip install --upgrade build twine
	- run: python -m build
	- run: twine check dist/*
	- uses: actions/upload-artifact@v4
	with:
	name: dist
	path: dist/
	- name: Build archive
	run: \|
	git clean -fxd
	mkdir archive
	git archive -o archive/pydra.zip HEAD
	- uses: actions/upload-artifact@v4
	with:
	name: archive
	path: archive/

	test:
	needs: ['build']
	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest, windows-latest]
	python-version: ['3.11', '3.12', '3.13']
	fail-fast: false
	runs-on: ${{ matrix.os }}
	steps:
	- name: Fetch repository
	uses: actions/checkout@v4
	- name: Fetch tags
	run: git fetch --prune --unshallow
	- name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Update pip
	run: python -m pip install --upgrade pip
	- name: Install Pydra
	run: pip install .[test]
	- name: Print version
	run: python -c "import pydra.engine; print(pydra.engine.__version__)"
	- name: Disable etelemetry
	run: echo "NO_ET=TRUE" >> $GITHUB_ENV
	- name: Pytest
	run: \|
	pytest -vs -n auto pydra --doctest-modules --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml
	- name: Upload to codecov
	run: codecov -f cov.xml -F unittests -e GITHUB_WORKFLOW

	test-dask:
	needs: ['build']
	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest]
	python-version: ['3.11', '3.12', '3.13']
	fail-fast: false
	runs-on: ${{ matrix.os }}
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository }}
	- name: Fetch tags
	run: git fetch --prune --unshallow
	- name: Setup Python version ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies for Dask
	run: \|
	pip install -e ".[test,dask]"
	- name: Run tests for Dask
	run: \|
	pytest -v --dask pydra/engine --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml
	- name: Upload to codecov
	run: codecov -f cov.xml -F unittests -e GITHUB_WORKFLOW

	test-psijlocal:
	needs: ['build']
	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest]
	python-version: ['3.11']
	fail-fast: false
	runs-on: ${{ matrix.os }}
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository }}
	- name: Fetch tags
	run: git fetch --prune --unshallow
	- name: Setup Python version ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies for PSI/J
	run: \|
	pip install -e ".[test, psij]"
	- name: Run tests for PSI/J
	run: \|
	pytest --color=yes -vs --psij=local -n auto pydra/engine --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml
	- name: Upload to codecov
	run: codecov -f cov.xml -F unittests -e GITHUB_WORKFLOW

	test-psijslurm:
	needs: ['build']
	strategy:
	matrix:
	python-version: [3.11.5]
	fail-fast: false
	runs-on: ubuntu-latest
	env:
	DOCKER_IMAGE: adi611/docker-centos7-slurm:23.02.1
	steps:
	- name: Disable etelemetry
	run: echo "NO_ET=TRUE" >> $GITHUB_ENV
	- uses: actions/checkout@v4
	- name: Fetch tags
	run: git fetch --prune --unshallow
	- name: Pull docker image
	run: \|
	docker pull $DOCKER_IMAGE
	# Have image running in the background
	docker run `bash <(curl -s https://codecov.io/env)` -itd -h slurmctl --cap-add sys_admin -d --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE
	- name: Display previous jobs with sacct
	run: \|
	echo "Allowing ports/daemons time to start" && sleep 10
	docker exec slurm bash -c "sacctmgr -i add account none,test Cluster=linux Description='none' Organization='none'"
	docker exec slurm bash -c "sacct && sinfo && squeue" 2&> /dev/null
	if [ $? -ne 0 ]; then
	echo "Slurm docker image error"
	exit 1
	fi
	- name: Setup Python
	run: \|
	docker exec slurm bash -c "echo $NO_ET"
	docker exec slurm bash -c "ls -la && echo list top level dir"
	docker exec slurm bash -c "ls -la /pydra && echo list pydra dir"
	if [[ "${{ matrix.python-version }}" == "3.11.5" ]]; then
	docker exec slurm bash -c "CONFIGURE_OPTS=\"-with-openssl=/opt/openssl\" pyenv install -v 3.11.5"
	fi
	docker exec slurm bash -c "pyenv global ${{ matrix.python-version }}"
	docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test,psij] && python -c 'import pydra.engine; print(pydra.engine.__version__)'"
	- name: Run pytest
	run: \|
	docker exec slurm bash -c "pytest --color=yes -vs -n auto --psij=slurm --cov pydra --cov-config /pydra/.coveragerc --cov-report xml:/pydra/cov.xml --doctest-modules /pydra/pydra/ -k 'not test_audit_prov and not test_audit_prov_messdir_1 and not test_audit_prov_messdir_2 and not test_audit_prov_wf and not test_audit_all'"
	- name: Upload to codecov
	run: \|
	docker exec slurm bash -c "pip install urllib3==1.26.6"
	docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests"
	docker rm -f slurm

	test-singularity:
	needs: ['build']
	runs-on: ubuntu-22.04
	strategy:
	matrix:
	python-version: ['3.11', '3.12', '3.13']
	fail-fast: False
	steps:
	- name: Set env
	run: \|
	echo "RELEASE_VERSION=v3.7.1" >> $GITHUB_ENV
	echo "NO_ET=TRUE" >> $GITHUB_ENV
	- name: Setup Singularity
	uses: actions/checkout@v4
	with:
	repository: hpcng/singularity
	ref: 'v3.7.1'
	path: 'singularity'
	- name: Setup GO
	uses: actions/setup-go@v5
	with:
	go-version: '^1.13'
	- name: Install OS deps
	run: \|
	sudo apt-get update
	sudo apt-get install flawfinder squashfs-tools uuid-dev libuuid1 libffi-dev libssl-dev libssl1.1 \
	libarchive-dev libgpgme11-dev libseccomp-dev wget gcc make pkg-config -y
	- name: Build
	run: \|
	cd singularity
	./mconfig --without-suid -p /usr/local/
	make -C ./builddir
	sudo make -C ./builddir install
	cd ..
	- name: Echo singularity version
	run: \|
	echo ${{ github.ref }}
	singularity --version
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Update build tools
	run: python -m pip install --upgrade pip
	- name: Checkout Pydra repo
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository }}
	- name: Fetch tags
	run: git fetch --prune --unshallow
	- name: Install pydra (test)
	run: pip install -e ".[test]"
	- name: Pytest
	run: pytest -vs --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml pydra/engine/tests/test_singularity.py pydra/engine/tests/test_environments.py
	- name: Upload to codecov
	run: codecov -f cov.xml -F unittests -e GITHUB_WORKFLOW

	test-slurm:
	needs: ['build']
	strategy:
	matrix:
	python-version: [3.11.5]
	fail-fast: false
	runs-on: ubuntu-latest
	env:
	DOCKER_IMAGE: adi611/docker-centos7-slurm:23.02.1
	steps:
	- name: Disable etelemetry
	run: echo "NO_ET=TRUE" >> $GITHUB_ENV
	- uses: actions/checkout@v4
	- name: Fetch tags
	run: git fetch --prune --unshallow
	- name: Pull docker image
	run: \|
	docker pull $DOCKER_IMAGE
	# Have image running in the background
	docker run `bash <(curl -s https://codecov.io/env)` -itd -h slurmctl --cap-add sys_admin -d --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE
	- name: Display previous jobs with sacct
	run: \|
	echo "Allowing ports/daemons time to start" && sleep 10
	docker exec slurm bash -c "sacctmgr -i add account none,test Cluster=linux Description='none' Organization='none'"
	docker exec slurm bash -c "sacct && sinfo && squeue" 2&> /dev/null
	if [ $? -ne 0 ]; then
	echo "Slurm docker image error"
	exit 1
	fi
	- name: Setup Python
	run: \|
	docker exec slurm bash -c "echo $NO_ET"
	docker exec slurm bash -c "ls -la && echo list top level dir"
	docker exec slurm bash -c "ls -la /pydra && echo list pydra dir"
	if [[ "${{ matrix.python-version }}" == "3.11.5" ]]; then
	docker exec slurm bash -c "CONFIGURE_OPTS=\"-with-openssl=/opt/openssl\" pyenv install -v 3.11.5"
	fi
	docker exec slurm bash -c "pyenv global ${{ matrix.python-version }}"
	docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test] && python -c 'import pydra.engine; print(pydra.engine.__version__)'"
	- name: Run pytest
	run: \|
	docker exec slurm bash -c "pytest /pydra/pydra --color=yes -vs --cov pydra --cov-config /pydra/.coveragerc --cov-report xml:/pydra/cov.xml --doctest-modules /pydra/pydra/ -k 'not test_audit_prov and not test_audit_prov_messdir_1 and not test_audit_prov_messdir_2 and not test_audit_prov_wf and not test_audit_all'"
	- name: Upload to codecov
	run: \|
	docker exec slurm bash -c "pip install urllib3==1.26.6"
	docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests"
	docker rm -f slurm

	build-docs:
	needs: ['build']
	runs-on: ubuntu-latest
	# Set up the environment so that it finds conda
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- name: Install Pandoc for NBSphinx
	run: \|
	sudo apt-get update
	sudo apt-get install -y pandoc
	- name: Install Dependencies for virtual notifications in Adv.-Exec Tutorial
	run: \|
	sudo apt update
	sudo apt install -y xvfb libnotify-bin dbus-x11 xfce4-notifyd
	- name: Start Virtual Display (for notifications)
	run: \|
	Xvfb :99 &
	export DISPLAY=:99
	eval "$(dbus-launch --sh-syntax)"
	echo "DISPLAY=:99" >> $GITHUB_ENV
	echo "DBUS_SESSION_BUS_ADDRESS=$DBUS_SESSION_BUS_ADDRESS" >> $GITHUB_ENV
	- name: Start Notification Daemon (for notifications)
	run: \|
	xfce4-notifyd &
	sleep 2 # Give it some time to start
	- name: Send Notification (test notifications)
	run: \|
	notify-send "GitHub Runner Notification" "This is a test notification from GitHub Actions"
	- name: Debug Running Processes (for notifications)
	run: \|
	ps aux \| grep notify
	ps aux \| grep xfce4-notifyd
	dbus-monitor --session &
	sleep 3
	- uses: actions/checkout@v4
	- name: Fetch tags
	run: git fetch --prune --unshallow
	- name: Install Minconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-activate-base: true
	activate-environment: ""
	- name: Install MRtrix via Conda
	run: \|
	conda install -c mrtrix3 mrtrix3
	mrconvert --version
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.x'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install build twine
	- name: Install package
	run: pip install .[doc]
	- name: Install Python3 kernel
	run: python -m ipykernel install --user
	- name: Build docs
	run: \|
	cd docs
	make html
	cd ..
	- uses: actions/upload-artifact@v4
	with:
	name: docs
	path: docs/build/html

	deploy:
	needs: [build-docs, test, test-dask, test-psijlocal, test-psijslurm, test-singularity, test-slurm]
	runs-on: ubuntu-latest
	steps:
	- name: Download dist
	uses: actions/download-artifact@v4
	with:
	name: dist
	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 }}

	deploy-docs:
	needs: [build-docs, deploy]
	runs-on: ubuntu-latest
	steps:
	- name: Download docs
	uses: actions/download-artifact@v4
	with:
	name: docs
	path: docs-build
	- name: Check for GHPAGES_DEPLOY_KEY token
	id: deployable
	if: github.event_name == 'release'
	env:
	GHPAGES_DEPLOY_KEY: "${{ secrets.GHPAGES_DEPLOY_KEY }}"
	run: if [ -n "$GHPAGES_DEPLOY_KEY" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
	- name: Deploy Docs to GitHub Pages
	if: steps.deployable.outputs.DEPLOY
	uses: peaceiris/actions-gh-pages@v3
	with:
	github_token: ${{ secrets.GHPAGES_DEPLOY_KEY }}
	publish_dir: docs-build

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fix up to tests_shelltask #21

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fix up to tests_shelltask #21

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