Converter tests #403
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name: Converter tests | |
on: | |
push: | |
paths-ignore: | |
- 'client/**' | |
- 'doc/**' | |
pull_request: | |
paths-ignore: | |
- 'client/**' | |
- 'doc/**' | |
schedule: | |
# Run at midnight UTC every Tuesday | |
- cron: '0 0 * * 2' | |
env: | |
GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1' | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.ref }} | |
cancel-in-progress: true | |
jobs: | |
test: | |
name: Test | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.7'] | |
steps: | |
- if: github.event_name == 'schedule' | |
run: | | |
echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV | |
echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV | |
- uses: actions/checkout@v3 | |
with: | |
path: 'galaxy root' | |
- uses: actions/setup-node@v3 | |
with: | |
node-version: '18.12.1' | |
cache: 'yarn' | |
cache-dependency-path: 'galaxy root/client/yarn.lock' | |
- name: Clone galaxyproject/galaxy-test-data | |
uses: actions/checkout@v3 | |
with: | |
repository: galaxyproject/galaxy-test-data | |
path: galaxy-test-data | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache venv dir | |
uses: actions/cache@v3 | |
id: pip-cache | |
with: | |
path: ~/.cache/pip | |
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} | |
- name: Move test data | |
run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/' | |
- name: Install planemo | |
run: pip install planemo | |
- name: Determine converters to check | |
run: | | |
ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt | |
echo "Skipping checks for the following converters:" | |
ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip | |
echo "Checking only the following converters:" | |
cat tool_list.txt | |
- name: Lint converters | |
run: | | |
mapfile -t TOOL_ARRAY < tool_list.txt | |
planemo lint --skip citations,stdio,help --report_level warn "${TOOL_ARRAY[@]}" | |
- name: Run tests | |
run: | | |
mapfile -t TOOL_ARRAY < tool_list.txt | |
planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}" | |
- uses: actions/upload-artifact@v3 | |
if: failure() | |
with: | |
name: Converter test results (${{ matrix.python-version }}) | |
path: tool_test_output.html |