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Use "run" with singularity/apptainer instead of "exec", when possible #2382

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

Use "run" with singularity/apptainer instead of "exec", when possible #2382

Workflow file for this run

.github/workflows/ci-tests.yml at 1557c8d
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 }}