Use "run" with singularity/apptainer instead of "exec", when possible #2376

Workflow file for this run

.github/workflows/ci-tests.yml at e03f8be

	name: CI Tests

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]
	workflow_dispatch:

	concurrency:
	group: build-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	env:
	TOX_SKIP_MISSING_INTERPRETERS: False
	# Rich (pip)
	FORCE_COLOR: 1
	# Tox
	PY_COLORS: 1
	# Mypy (see https://github.com/python/mypy/issues/7771)
	TERM: xterm-color
	MYPY_FORCE_COLOR: 1
	MYPY_FORCE_TERMINAL_WIDTH: 200
	# Pytest
	PYTEST_ADDOPTS: --color=yes

	jobs:

	tox:
	name: Tox
	runs-on: ubuntu-22.04
	strategy:
	matrix:
	py-ver-major: [3]
	py-ver-minor: [9, 10, 11, 12, 13]
	step: [lint, unit, bandit, mypy]

	env:
	py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
	TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}

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

	- name: Set up Singularity and environment-modules
	if: ${{ matrix.step == 'unit' \|\| matrix.step == 'mypy' }}
	run: \|
	wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
	sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb environment-modules

	- name: Give the test runner user a name to make provenance happy.
	if: ${{ matrix.step == 'unit' \|\| matrix.step == 'mypy' }}
	run: sudo usermod -c 'CI Runner' "$(whoami)"

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.py-semver }}
	allow-prereleases: true
	cache: pip
	cache-dependency-path: \|
	requirements.txt
	tox.ini

	- name: Upgrade setuptools and install tox
	run: \|
	pip install -U pip setuptools wheel
	pip install "tox<4" "tox-gh-actions<3"

	- name: MyPy cache
	if: ${{ matrix.step == 'mypy' }}
	uses: actions/cache@v4
	with:
	path: .mypy_cache/${{ env.py-semver }}
	key: mypy-${{ env.py-semver }}

	- name: Test with tox
	run: APPTAINER_TMPDIR=${RUNNER_TEMP} tox

	- name: Upload coverage to Codecov
	if: ${{ matrix.step == 'unit' }}
	uses: codecov/codecov-action@v4
	with:
	fail_ci_if_error: true
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

	tox-style:
	name: Linters
	runs-on: ubuntu-20.04

	strategy:
	matrix:
	step: [lintreadme, shellcheck, pydocstyle]

	env:
	py-semver: "3.12"
	TOXENV: ${{ format('py312-{0}', matrix.step) }}

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

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.py-semver }}
	cache: pip

	- name: Upgrade setuptools and install tox
	run: \|
	pip install -U pip setuptools wheel
	pip install "tox<4" "tox-gh-actions<3"

	- if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
	name: Create local branch for diff-quality for PRs
	run: git branch ${{github.base_ref}} origin/${{github.base_ref}}

	- name: Test with tox
	run: tox

	clean_working_dir:
	name: No leftovers
	runs-on: ubuntu-22.04
	env:
	py-semver: "3.12"
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Set up Singularity and environment-modules
	run: \|
	wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
	sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb environment-modules

	- name: Give the test runner user a name to make provenance happy.
	run: sudo usermod -c 'CI Runner' "$(whoami)"

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.py-semver }}
	cache: pip

	- name: install with test dependencies
	run: \|
	pip install -U pip setuptools wheel
	pip install --no-build-isolation -rtest-requirements.txt .[deps]

	- name: make working directory read-only
	run: \|
	mkdir .pytest_cache
	chmod a-w .

	- name: run tests
	run: APPTAINER_TMPDIR=${RUNNER_TEMP} make test


	conformance_tests:
	name: CWL conformance
	runs-on: ubuntu-22.04

	strategy:
	fail-fast: false
	matrix:
	cwl-version: [v1.0, v1.1, v1.2]
	container: [docker, singularity, podman]
	extras: [""]
	include:
	- cwl-version: v1.2
	container: docker
	extras: "--fast-parser"
	- cwl-version: v1.3.0-dev1
	extras: "--relax-path-checks"

	steps:
	- uses: actions/checkout@v4

	- name: Set up Singularity and environment-modules
	if: ${{ matrix.container == 'singularity' }}
	run: \|
	wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
	sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb environment-modules

	- name: Singularity cache
	if: ${{ matrix.container == 'singularity' }}
	uses: actions/cache@v4
	with:
	path: sifcache
	key: singularity

	- name: Set up Podman
	if: ${{ matrix.container == 'podman' }}
	run: sudo rm -f /usr/bin/docker ; sudo apt-get install -y podman

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: 3.12
	cache: pip

	- name: "Test CWL ${{ matrix.cwl-version }} conformance"
	env:
	VERSION: ${{ matrix.cwl-version }}
	CONTAINER: ${{ matrix.container }}
	GIT_TARGET: main
	CWLTOOL_OPTIONS: ${{ matrix.cwl-version == 'v1.2' && '--relax-path-checks' \|\| '' }} ${{ matrix.extras }}
	run: ./conformance-test.sh
	- name: Archive test results
	uses: actions/upload-artifact@v4
	with:
	name: cwl-${{ matrix.cwl-version }}-${{ matrix.container }}${{ matrix.extras }}-conformance-results
	path: \|
	*/cwltool_conf.xml
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	fail_ci_if_error: true
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	release_test:
	name: cwltool release test
	runs-on: ubuntu-22.04

	steps:
	- uses: actions/checkout@v4

	- name: Set up Singularity and environment-modules
	run: \|
	wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
	sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb environment-modules

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: 3.12
	cache: pip
	cache-dependency-path: \|
	requirements.txt
	test-requirements.txt

	- name: Give the test runner user a name to make provenance happy.
	run: sudo usermod -c 'CI Runner' "$(whoami)"

	- name: Install packages
	run: \|
	pip install -U pip setuptools wheel
	pip install virtualenv

	- name: Release test
	env:
	RELEASE_SKIP: head
	run: ./release-test.sh

	build_test_container:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: record cwltool version
	run: pip install -U setuptools wheel && pip install setuptools_scm[toml] && python setup.py --version
	- name: build & test cwltool_module container
	run: ./build-cwltool-docker.sh

	macos:
	name: Test on macos-latest
	runs-on: macos-13 # not latest, that is now an Apple Silicon M1, for which seqtk is not yet built on bioconda
	env:
	TOXENV: py312-unit
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: 3.12
	cache: pip
	cache-dependency-path: \|
	requirements.txt
	tox.ini
	- name: Upgrade setuptools and install tox
	run: \|
	pip install -U pip setuptools wheel
	pip install "tox<4" "tox-gh-actions<3"
	# # docker for mac install is not currently stable
	# - name: 'SETUP MacOS: load Homebrew cache'
	# uses: actions/cache@v4
	# if: runner.os == 'macOS'
	# with:
	# path: \|
	# ~/Library/Caches/Homebrew/downloads/*--Docker.dmg
	# key: brew-actions-setup-docker-1.0.11
	# restore-keys: brew-actions-setup-docker-
	# - name: setup docker on macos (default stable version)
	# uses: docker-practice/actions-setup-docker@master
	- name: Test with tox
	run: tox
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	fail_ci_if_error: true
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Use "run" with singularity/apptainer instead of "exec", when possible #2376

Workflow file

Use "run" with singularity/apptainer instead of "exec", when possible #2376

Jobs

Run details

Workflow file for this run