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pipeline_tests.yml
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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" >> $GITHUB_OUTPUT
# A job to identify and run the tests
pytest:
needs: identify-tests
runs-on: self-hosted
timeout-minutes: 2880 # 48h
steps:
- name: Checkout PR branch
uses: actions/checkout@v3
- name: Load configuration for self-hosted runner
run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install .[tests]
- name: Remove test reports if any existing
run: rm -f test_pipeline-*.txt
- name: Execute tests with pytest
run: |
if [[ "${{ 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