ci: Keep running nf-core lint the way it was

Blocked by nf-core/tools#3140
nf-core · Sep 18, 2024 · 616eb02 · 616eb02
1 parent 5594071
commit 616eb02
Showing 1 changed file with 102 additions and 59 deletions.
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -70,68 +70,111 @@ jobs:
       - name: Run ECLint check
         run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
 
-  nf-core-lint-modules:
-    runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
-    name: nf-core lint modules
-    strategy:
-      fail-fast: false
-    steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-
-      - name: Set up Python
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
-        with:
-          python-version: "3.11"
-
-      - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
-        id: cache-pip
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip
-          restore-keys: |
-            ${{ runner.os }}-pip
-
-      - name: Install pip
-        run: python -m pip install --upgrade pip
-
-      - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v2
-
-      - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
-
-      - name: Lint modules
-        run: nf-core --hide-progress modules lint -a
-
-  nf-core-lint-subworkflows:
+  ###################
+  # nf-core linting #
+  ###################
+  nf-core-changes:
+    name: nf-core-changes
     runs-on: ubuntu-latest
-    name: nf-core lint subworkflows
+    outputs:
+      tags: ${{ steps.filter.outputs.changes }}
+      modules: ${{ steps.tags.outputs.modules }}
+      subworkflows: ${{ steps.tags.outputs.subworkflows }}
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-
-      - name: Set up Python
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
-          python-version: "3.11"
+          fetch-depth: 2 # To retrieve the preceding commit.
 
-      - name: Install pip
-        run: python -m pip install --upgrade pip
-
-      - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # v4
+      # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented
+      - uses: mirpedrol/paths-filter@main
+        id: filter
         with:
-          distribution: "temurin"
-          java-version: "17"
-
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2
-
-      - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
-
-      - name: Lint subworkflows
-        run: nf-core --hide-progress subworkflows lint -a
+          filters: "tests/config/pytest_modules.yml"
+          token: ""
+
+      - name: Fetch module tags
+        id: tags
+        run: |
+          echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT
+          echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT
+
+      - name: debug
+        run: |
+          echo ${{ steps.tags.outputs.modules }}
+          echo ${{ steps.tags.outputs.subworkflows }}
+
+    nf-core-lint-modules:
+      runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
+      name: nf-core-lint-modules
+      needs: nf-core-changes
+      if: ${{ (needs.nf-core-changes.outputs.modules != '[]')
+      strategy:
+        fail-fast: false
+        matrix:
+          tags: "${{ fromJson(needs.nf-core-changes.outputs.modules) }}"
+      steps:
+        - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+        - name: Set up Python
+          uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+          with:
+            python-version: "3.11"
+
+        - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+          id: cache-pip
+          with:
+            path: ~/.cache/pip
+            key: ${{ runner.os }}-pip
+            restore-keys: |
+              ${{ runner.os }}-pip
+
+        - name: Install pip
+          run: python -m pip install --upgrade pip
+
+        - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4
+          with:
+            distribution: "temurin"
+            java-version: "17"
+
+        - name: Setup Nextflow
+          uses: nf-core/setup-nextflow@v2
+
+        - name: Install nf-core tools development version
+          run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+        - name: Lint module ${{ matrix.tags }}
+          run: nf-core modules lint ${{ matrix.tags }}
+
+    nf-core-lint-subworkflows:
+      runs-on: ubuntu-latest
+      name: nf-core-lint-modules
+      needs: nf-core-changes
+      if: ${{ (needs.nf-core-changes.outputs.subworkflows != '[]')
+      strategy:
+        fail-fast: false
+        matrix:
+          tags: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows) }}"
+      steps:
+        - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+        - name: Set up Python
+          uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+          with:
+            python-version: "3.11"
+
+        - name: Install pip
+          run: python -m pip install --upgrade pip
+
+        - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4
+          with:
+            distribution: "temurin"
+            java-version: "17"
+
+        - name: Setup Nextflow
+          uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2
+
+        - name: Install nf-core tools development version
+          run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+        - name: Lint module ${{ matrix.tags }}
+          run: nf-core subworkflows lint ${{ matrix.tags }}