STRY0019104 - Test against GSP version of Nextflow in GitHub CI for all pipelines #26
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| name: "Get number of shards" | ||
| description: "Get the number of nf-test shards for the current CI job" | ||
| inputs: | ||
| max_shards: | ||
| description: "Maximum number of shards allowed" | ||
| required: true | ||
| paths: | ||
| description: "Component paths to test" | ||
| required: false | ||
| tags: | ||
| description: "Tags to pass as argument for nf-test --tag parameter" | ||
| required: false | ||
| outputs: | ||
| shard: | ||
| description: "Array of shard numbers" | ||
| value: ${{ steps.shards.outputs.shard }} | ||
| total_shards: | ||
| description: "Total number of shards" | ||
| value: ${{ steps.shards.outputs.total_shards }} | ||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - name: Install nf-test | ||
| uses: nf-core/setup-nf-test@v1 | ||
| with: | ||
| version: ${{ env.NFT_VER }} | ||
| - name: Get number of shards | ||
| id: shards | ||
| shell: bash | ||
| run: | | ||
| # Run nf-test with dynamic parameter | ||
| nftest_output=$(nf-test test \ | ||
| --profile +docker \ | ||
| $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \ | ||
| --dry-run \ | ||
| --ci \ | ||
| --changed-since HEAD^) || { | ||
| echo "nf-test command failed with exit code $?" | ||
| echo "Full output: $nftest_output" | ||
| exit 1 | ||
| } | ||
| echo "nf-test dry-run output: $nftest_output" | ||
| # Default values for shard and total_shards | ||
| shard="[]" | ||
| total_shards=0 | ||
| # Check if there are related tests | ||
| if echo "$nftest_output" | grep -q 'No tests to execute'; then | ||
| echo "No related tests found." | ||
| else | ||
| # Extract the number of related tests | ||
| number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p') | ||
| if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then | ||
| shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} )) | ||
| shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .) | ||
| total_shards="$shards_to_run" | ||
| else | ||
| echo "Unexpected output format. Falling back to default values." | ||
| fi | ||
| fi | ||
| # Write to GitHub Actions outputs | ||
| echo "shard=$shard" >> $GITHUB_OUTPUT | ||
| echo "total_shards=$total_shards" >> $GITHUB_OUTPUT | ||
| # Debugging output | ||
| echo "Final shard array: $shard" | ||
| echo "Total number of shards: $total_shards" | ||
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| Original file line number | Diff line number | Diff line change |
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| name: "nf-test Action" | ||
| description: "Runs nf-test with common setup steps" | ||
| inputs: | ||
| profile: | ||
| description: "Profile to use" | ||
| required: true | ||
| shard: | ||
| description: "Shard number for this CI job" | ||
| required: true | ||
| total_shards: | ||
| description: "Total number of test shards(NOT the total number of matrix jobs)" | ||
| required: true | ||
| paths: | ||
| description: "Test paths" | ||
| required: true | ||
| tags: | ||
| description: "Tags to pass as argument for nf-test --tag parameter" | ||
| required: false | ||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - name: Setup Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| version: "${{ env.NXF_VERSION }}" | ||
|
|
||
| - name: Set up Python | ||
| uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | ||
| with: | ||
| python-version: "3.13" | ||
|
|
||
| - name: Install nf-test | ||
| uses: nf-core/setup-nf-test@v1 | ||
| with: | ||
| version: "${{ env.NFT_VER }}" | ||
| install-pdiff: true | ||
|
|
||
| - name: Setup apptainer | ||
| if: contains(inputs.profile, 'singularity') | ||
| uses: eWaterCycle/setup-apptainer@main | ||
|
|
||
| - name: Set up Singularity | ||
| if: contains(inputs.profile, 'singularity') | ||
| shell: bash | ||
| run: | | ||
| mkdir -p $NXF_SINGULARITY_CACHEDIR | ||
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
|
|
||
| - name: Conda setup | ||
| if: contains(inputs.profile, 'conda') | ||
| uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3 | ||
| with: | ||
| auto-update-conda: true | ||
| conda-solver: libmamba | ||
| conda-remove-defaults: true | ||
|
|
||
| - name: Run nf-test | ||
| shell: bash | ||
| env: | ||
| NFT_WORKDIR: ${{ env.NFT_WORKDIR }} | ||
| run: | | ||
| nf-test test \ | ||
| --profile=+${{ inputs.profile }} \ | ||
| $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \ | ||
| --ci \ | ||
| --changed-since HEAD^ \ | ||
| --verbose \ | ||
| --tap=test.tap \ | ||
| --shard ${{ inputs.shard }}/${{ inputs.total_shards }} | ||
|
|
||
| # Save the absolute path of the test.tap file to the output | ||
| echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT | ||
|
|
||
| - name: Generate test summary | ||
| if: always() | ||
| shell: bash | ||
| run: | | ||
| # Add header if it doesn't exist (using a token file to track this) | ||
| if [ ! -f ".summary_header" ]; then | ||
| echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY | ||
| echo "" >> $GITHUB_STEP_SUMMARY | ||
| echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY | ||
| echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY | ||
| touch .summary_header | ||
| fi | ||
|
|
||
| if [ -f test.tap ]; then | ||
| while IFS= read -r line; do | ||
| if [[ $line =~ ^ok ]]; then | ||
| test_name="${line#ok }" | ||
| # Remove the test number from the beginning | ||
| test_name="${test_name#* }" | ||
| echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY | ||
| elif [[ $line =~ ^not\ ok ]]; then | ||
| test_name="${line#not ok }" | ||
| # Remove the test number from the beginning | ||
| test_name="${test_name#* }" | ||
| echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY | ||
| fi | ||
| done < test.tap | ||
| else | ||
| echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY | ||
| fi | ||
|
|
||
| - name: Clean up | ||
| if: always() | ||
| shell: bash | ||
| run: | | ||
| sudo rm -rf /home/ubuntu/tests/ |
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This is cool didn't know about this, so it is only going to run tests impacted by changes?
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Thanks. Since
HEAD^is referencing the parent commit of theHEADcommit I wanted to know more about how this worked on GitHub (since a PR can have multiple commits, so why doesHEAD^capture all changes in the PR)?Based on what I've read, it looks like the GitHub actions checkout (https://github.com/marketplace/actions/checkout) will checkout code with a particular commit that is the squashed commit of all changes in your PR. Hence,
HEAD^will point to the commit prior to the PR, and so differences fromHEAD^(that is the--changed-since HEAD^parameter) will properly capture all code changes in this PR. Runningnf-test test ... --changed-since HEAD^locally on a branch won't work (since it only looks at differences one commit up).This is based on inspecting output of the GitHub actions and a copilot summary (I couldn't find good documentation on this outside of copilot):