8000 Merge pull request #3567 from JulianFlesch/improve/test-datasets · nf-core/tools@3147827 · GitHub
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Merge pull request #3567 from JulianFlesch/improve/test-datasets #9139

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Merge pull request #3567 from JulianFlesch/improve/test-datasets

Merge pull request #3567 from JulianFlesch/improve/test-datasets #9139

Workflow file for this run

.github/workflows/pytest.yml at 3147827
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
# https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
- "renovate/**" # branches Renovate creates
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:
# 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: ${{ needs.setup.outputs.run-tests }}
runs-on:
- runs-on=${{ github.run_id }}-run-test
- runner=4cpu-linux-x64
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@a26af69be951a213d495a4c3e4e4022e16d87065 # 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')" >> $GITHUB_ENV
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
- name: Install nf-test
uses: nf-core/setup-nf-test@v1
- name: move coveragerc file up
run: |
mv .github/.coveragerc .
- name: Test with pytest
run: |
python3 -m pytest tests/${{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@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
if: always()
with:
include-hidden-files: true
name: Snapshot Report ${{ env.test }}
path: ./snapshot_report.html
- name: Upload coverage
uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
include-hidden-files: true
name: coverage_${{ env.test }}
path: .coverage
coverage:
needs: test
runs-on:
- runs-on=${{ github.run_id }}-coverage
- runner=2cpu-linux-x64
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@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
env:
AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
with:
python-version: "3.13"
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@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4
- name: Run coverage
run: |
coverage combine --keep coverage*/.coverage*
coverage report
coverage xml
- uses: codecov/codecov-action@ad3126e916f78f00edff4ed0317cf185271ccc2d # v5
with:
files: coverage.xml
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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