Allow main
as default channel
#8231
Workflow file for this run
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name: Python tests | |
# This workflow is triggered on pushes and PRs to the repository. | |
# Only run if we changed a Python file | |
on: | |
push: | |
branches: | |
- dev | |
paths-ignore: | |
- "docs/**" | |
- "CHANGELOG.md" | |
pull_request: | |
paths-ignore: | |
- "docs/**" | |
- "CHANGELOG.md" | |
# ignore github workflows except for the current one | |
- ".github/**" | |
- "!.github/workflows/pytest.yml" | |
release: | |
types: [published] | |
workflow_dispatch: | |
inputs: | |
runners: | |
description: "Runners to test on" | |
type: choice | |
options: | |
- "ubuntu-latest" | |
- "self-hosted" | |
default: "self-hosted" | |
# Cancel if a newer run with the same workflow name is queued | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
jobs: | |
setup: | |
runs-on: "ubuntu-latest" | |
strategy: | |
matrix: | |
python-version: ["3.8", "3.12"] | |
runner: ["ubuntu-latest"] | |
include: | |
- python-version: "3.8" | |
runner: "ubuntu-20.04" | |
steps: | |
- name: Check conditions | |
id: conditions | |
run: echo "run-tests=${{ github.ref == 'refs/heads/main' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT" | |
outputs: | |
python-version: ${{ matrix.python-version }} | |
runner: ${{ matrix.runner }} | |
run-tests: ${{ steps.conditions.outputs.run-tests }} | |
# create a test matrix based on all python files in /tests | |
list_tests: | |
name: Get test file matrix | |
runs-on: "ubuntu-latest" | |
steps: | |
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
name: Check out source-code repository | |
- name: List tests | |
id: list_tests | |
run: | | |
echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT | |
outputs: | |
tests: ${{ steps.list_tests.outputs.tests }} | |
test: | |
name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }} | |
needs: [setup, list_tests] | |
if: ${{ needs.setup.outputs.run-tests }} | |
# run on self-hosted runners for test_components.py (because of the gitlab branch), based on the input if it is dispatched manually, on github if it is a rerun or on self-hosted by default | |
runs-on: ${{ matrix.test == 'test_components.py' && 'self-hosted' || (github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted') }} | |
strategy: | |
matrix: ${{ fromJson(needs.list_tests.outputs.tests) }} | |
fail-fast: false # run all tests even if one fails | |
steps: | |
- name: go to subdirectory and change nextflow workdir | |
run: | | |
mkdir -p pytest | |
cd pytest | |
export NXF_WORK=$(pwd) | |
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
name: Check out source-code repository | |
- name: Set up Python ${{ needs.setup.outputs.python-version }} | |
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
with: | |
python-version: ${{ needs.setup.outputs.python-version }} | |
cache: "pip" | |
token: ${{ secrets.GITHUB_TOKEN }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip -r requirements-dev.txt | |
pip install -e . | |
- name: Downgrade git to the Ubuntu official repository's version | |
if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }} | |
run: | | |
sudo apt update | |
sudo apt remove -y git git-man | |
sudo add-apt-repository --remove ppa:git-core/ppa | |
sudo apt install -y git | |
- name: Set up Singularity | |
if: ${{ matrix.test == 'test_download.py'}} | |
uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 | |
with: | |
singularity-version: 3.8.3 | |
- name: Get current date | |
id: date | |
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV | |
- uses: actions/setup-java@v4 | |
with: | |
java-version: "17" | |
distribution: "temurin" | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
- name: Install nf-test | |
uses: nf-core/setup-nf-test@v1 | |
- name: move coveragerc file up | |
run: | | |
mv .github/.coveragerc . | |
- name: Test with pytest | |
run: | | |
python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=.coveragerc --durations=0 && exit_code=0|| exit_code=$? | |
# don't fail if no tests were collected, e.g. for test_licence.py | |
if [ "${exit_code}" -eq 5 ]; then | |
echo "No tests were collected" | |
exit 0 | |
elif [ "${exit_code}" -ne 0 ]; then | |
echo "Tests failed with exit code ${exit_code}" | |
exit 1 | |
fi | |
- name: remove slashes from test name | |
run: | | |
test=$(echo ${{ matrix.test }} | sed 's/\//__/g') | |
echo "test=${test}" >> $GITHUB_ENV | |
- name: Store snapshot report | |
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 | |
if: always() | |
with: | |
include-hidden-files: true | |
name: Snapshot Report ${{ env.test }} | |
path: ./snapshot_report.html | |
- name: Upload coverage | |
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 | |
with: | |
include-hidden-files: true | |
name: coverage_${{ env.test }} | |
path: .coverage | |
coverage: | |
needs: test | |
# use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default | |
runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
steps: | |
- name: go to subdirectory | |
run: | | |
mkdir -p pytest | |
cd pytest | |
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
- name: Set up Python 3.12 | |
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
env: | |
AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/ | |
with: | |
python-version: "3.12" | |
cache: "pip" | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip -r requirements-dev.txt | |
pip install -e . | |
- name: move coveragerc file up | |
run: | | |
mv .github/.coveragerc . | |
- name: Download all artifacts | |
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4 | |
- name: Run coverage | |
run: | | |
coverage combine --keep coverage*/.coverage* | |
coverage report | |
coverage xml | |
- uses: codecov/codecov-action@5c47607acb93fed5485fdbf7232e8a31425f672a # v5 | |
with: | |
files: coverage.xml | |
env: | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |