Add GHA to update template nf-test snapshots #3723
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,160 @@ | ||
| name: Update Template snapshots from a comment | ||
| on: | ||
| issue_comment: | ||
| types: [created] | ||
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|
||
| jobs: | ||
| prepare-matrix: | ||
| name: Retrieve all template features | ||
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | ||
| if: > | ||
| contains(github.event.comment.html_url, '/pull/') && | ||
| contains(github.event.comment.body, '@nf-core-bot') && | ||
| contains(github.event.comment.body, 'update template snapshots') && | ||
| github.repository == 'nf-core/tools' | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| all_features: ${{ steps.create_matrix.outputs.matrix }} | ||
| steps: | ||
| - name: checkout | ||
| uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | ||
| - name: Create Matrix | ||
| id: create_matrix | ||
| run: | | ||
| echo "matrix=$(yq '.[].features | keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config")' nf_core/pipelines/create/template_features.yml | \ | ||
| yq 'flatten | tojson(0)' -)" >> $GITHUB_OUTPUT | ||
| update-snapshots: | ||
| needs: [prepare-matrix] | ||
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | ||
| if: > | ||
| contains(github.event.comment.html_url, '/pull/') && | ||
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|
||
| contains(github.event.comment.body, '@nf-core-bot') && | ||
| contains(github.event.comment.body, 'update template snapshots') && | ||
| github.repository == 'nf-core/tools' | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }} | ||
| include: | ||
| - TEMPLATE: all | ||
| fail-fast: false | ||
| steps: | ||
| # Use the @nf-core-bot token to check out so we can push later | ||
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | ||
| with: | ||
| token: ${{ secrets.nf_core_bot_auth_token }} | ||
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||
| # indication that the command is running | ||
| - name: React on comment | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: eyes | ||
|
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||
| # Action runs on the issue comment, so we don't get the PR by default | ||
| # Use the gh cli to check out the PR | ||
| - name: Checkout Pull Request | ||
| run: gh pr checkout ${{ github.event.issue.number }} | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
|
|
||
| # Install dependencies and run pytest | ||
| - name: Set up Python | ||
| uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | ||
| with: | ||
| python-version: "3.13" | ||
| cache: "pip" | ||
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| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip -r requirements-dev.txt | ||
| pip install -e . | ||
| # Create template files | ||
| - name: Create template skip ${{ matrix.TEMPLATE }} | ||
| run: | | ||
| mkdir create-test-lint-wf | ||
| export NXF_WORK=$(pwd) | ||
| if [ ${{ matrix.TEMPLATE }} == "all" ] | ||
| then | ||
| printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml | ||
| else | ||
| printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml | ||
| fi | ||
| # Create a pipeline from the template | ||
| - name: create a pipeline from the template ${{ matrix.TEMPLATE }} | ||
| run: | | ||
| cd create-test-lint-wf | ||
| nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml | ||
| # Copy snapshot file | ||
| - name: copy snapshot file | ||
| if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} | ||
| run: | | ||
| if [ ! -f ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap ]; then | ||
| echo "Generate a snapshot when creating a pipeline and skipping the feature ${{ matrix.TEMPLATE }}." | ||
| echo "Then, copy it to the directory .github/snapshots" | ||
| else | ||
| cp ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap | ||
| fi | ||
| # Run pipeline with nf-test | ||
| - name: run pipeline nf-test | ||
| if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} | ||
| id: nf-test | ||
| shell: bash | ||
| run: | | ||
| cd create-test-lint-wf/my-prefix-testpipeline | ||
| nf-test test \ | ||
| --profile=+docker \ | ||
| --verbose | ||
| - name: Update nf-test snapshot | ||
| if: steps.nf-test.outcome == 'success' | ||
| run: | | ||
| cp ${{ github.workspace }}/create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap | ||
| # indication that the run has finished | ||
| - name: react if finished succesfully | ||
| if: steps.nf-test.outcome == 'success' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: "+1" | ||
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| - name: Commit & push changes | ||
| id: commit-and-push | ||
| if: steps.nf-test.outcome == 'success' | ||
| run: | | ||
| git config user.email "core@nf-co.re" | ||
| git config user.name "nf-core-bot" | ||
| git config push.default upstream | ||
| git add . | ||
| git status | ||
| git commit -m "[automated] Update Template snapshots" | ||
| git push | ||
| - name: react if snapshots were updated | ||
| id: react-if-updated | ||
| if: steps.commit-and-push.outcome == 'success' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: hooray | ||
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| - name: react if snapshots were not updated | ||
| if: steps.commit-and-push.outcome == 'failure' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: confused | ||
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| - name: react if snapshots were not updated | ||
| if: steps.commit-and-push.outcome == 'failure' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| issue-number: ${{ github.event.issue.number }} | ||
| body: | | ||
| @${{ github.actor }} I tried to update the snapshots, but it didn't work. Please update them manually. | ||
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do we need this?
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I think so? Otherwise, it would try to run on comments to issues too