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tests.yml
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#schema: https://github.com/softprops/github-actions-schemas/blob/master/workflow.json
name: "Test"
on:
push:
branches: [main, dev]
pull_request:
branches: [main, dev]
workflow_dispatch:
permissions:
id-token: write
actions: write
contents: read
packages: write
env:
ANNOY_COMPILER_ARGS: "-DANNOYLIB_MULTITHREADED_BUILD,-mno-avx512f"
jobs:
pre_job:
continue-on-error: true
runs-on: ubuntu-latest
# Map a step output to a job output
outputs:
should_skip: ${{ steps.skip_check.outputs.should_skip }}
paths_result: ${{ steps.skip_check.outputs.paths_result }}
steps:
- id: skip_check
uses: fkirc/skip-duplicate-actions@v5
if: ${{ !github.event.act }}
with:
concurrent_skipping: "same_content_newer"
skip_after_successful_duplicate: "true"
do_not_skip: '["workflow_dispatch"]'
paths_filter: |
python:
paths:
- 'pyproject.toml'
- 'poetry.lock'
- 'src/pixelator/**'
- 'tests/**'
paths_ignore:
- 'tests/**/*.md'
test:
name: Test - python ${{ matrix.py }}
if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip
runs-on: ubuntu-latest
needs: [pre_job]
strategy:
fail-fast: false
matrix:
py:
- "3.11"
- "3.10"
steps:
- uses: actions/checkout@v4
- name: Set up Python environment
uses: ./.github/actions/setup-python
with:
python-version: ${{ matrix.py }}
- uses: supplypike/setup-bin@v3
with:
uri: 'https://opengene.org/fastp/fastp'
name: 'fastp'
version: '0.23.4'
- name: Install and configure Poetry
uses: snok/install-poetry@v1
- name: Install tox
run: python -m pip install tox-gh>=1.2
- name: Setup test suite
run: tox -vv --notest
- name: Run test suite
run: tox --skip-pkg-install
test-coverage:
name: "Check the test coverage"
runs-on: ubuntu-latest
needs:
- pre_job
if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Set up Python environment
uses: ./.github/actions/setup-python
with:
python-version: "3.11"
- name: Install and configure Poetry
uses: snok/install-poetry@v1
- name: Install dependencies
run: |
poetry install --with dev
- name: Run test suite
run: |
poetry run pytest --cov=src/
- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v3
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
test-workflow:
name: Test small workflow - ${{ matrix.case }}
runs-on: ubuntu-latest
needs: [ pre_job ]
strategy:
fail-fast: false
matrix:
case:
- mpx_v1
- mpx_v2
if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip
steps:
- uses: actions/checkout@v4
- name: Set up Python environment
uses: ./.github/actions/setup-python
with:
python-version: "3.11"
- uses: supplypike/setup-bin@v3
with:
uri: 'https://opengene.org/fastp/fastp'
name: 'fastp'
version: '0.23.2'
- name: Install and configure Poetry
uses: snok/install-poetry@v1
- name: Install dependencies
run: |
poetry install --with dev
- name: Run workflow tests
run: |
poetry run pytest -s -m "workflow_test" --basetemp=/tmp/pytest-results tests/integration/test_small_${{ matrix.case }}.yaml --log-cli-level=DEBUG