[narps_open_pipelines#220][94GU] Preprocessing #339
Workflow file for this run
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| ## Disclaimer - This GitHub Actions workflow runs all the tests for changed pipelines. | |
| # Name the workflow | |
| name: pipeline_tests | |
| # Define when it runs | |
| on: | |
| pull_request: | |
| paths: | |
| - 'narps_open/pipelines/team**' | |
| # Jobs that define the workflow | |
| jobs: | |
| # A job to list the tests to be run | |
| identify-tests: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| teams: ${{ steps.identify.outputs.teams }} | |
| tests: ${{ steps.identify.outputs.tests }} | |
| steps: | |
| - name: Checkout current branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Create a list of tests for changed pipelines | |
| id: identify | |
| run: | | |
| # Loop through modified files between PR base and last head | |
| for file in $(git diff --name-only --diff-filter=d remotes/origin/main...$GITHUB_SHA) | |
| do | |
| # echo each file | |
| echo $file | |
| # List team id corresponding to team_* files | |
| if [[ "$file" =~ narps_open/pipelines/team_[A-Z0-9]{4}.py ]]; then | |
| echo "Modified pipeline = $file" | |
| tmp=${file#*"team_"} # remove prefix ending in "team_" | |
| team_id=${tmp%".py"*} # remove suffix starting with ".py" | |
| # Populate the lists of test files and teams | |
| test_files="$test_files tests/pipelines/test_team_$team_id.py" | |
| teams="$teams $team_id" | |
| fi | |
| done | |
| # Send the test list as job output | |
| echo $test_files | |
| echo "tests=$test_files" >> $GITHUB_OUTPUT | |
| echo "teams=$teams" >> $GITHUB_OUTPUT | |
| # A job to run the tests | |
| pytest: | |
| needs: identify-tests | |
| runs-on: self-hosted | |
| timeout-minutes: 2880 # 48h | |
| steps: | |
| - name: Checkout PR branch | |
| uses: actions/checkout@v3 | |
| - name: Load configuration for self-hosted runner | |
| run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[tests] | |
| - name: Remove test reports if any existing | |
| run: rm -f test_pipeline-*.txt | |
| - name: Execute tests with pytest | |
| run: | | |
| if [[ "${{ needs.identify-tests.outputs.tests }}" != "" ]]; then | |
| pytest -s -q -m "pipeline_test" ${{ needs.identify-tests.outputs.tests }} | |
| fi | |
| - name: Archive pipeline execution failures | |
| if: ${{ failure() }} # Run only if previous job fails | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: pipeline_tests-reports | |
| path: | | |
| crash-*.pklz | |
| retention-days: 15 | |
| - name: Report results on GitHub | |
| if: ${{ always() }} | |
| run: | | |
| # Start report | |
| echo "# Correlation values" >> $GITHUB_STEP_SUMMARY | |
| echo "Unthresholded maps, reproduced vs. results" >> $GITHUB_STEP_SUMMARY | |
| echo "Correlation values are sorted from hypotheses 1 to 9" >> $GITHUB_STEP_SUMMARY | |
| # Start report table | |
| echo "| Team | Number of subjects | Test status | Correlation values |" >> $GITHUB_STEP_SUMMARY | |
| echo "| -------- | ------- | ------- | ------- |" >> $GITHUB_STEP_SUMMARY | |
| # Loop through test report files | |
| for team in ${{ needs.identify-tests.outputs.teams }} | |
| do | |
| cat test_pipeline-$team.txt >> $GITHUB_STEP_SUMMARY | |
| done |