Merge branch 'master' into validate-environment.ymls

.github/actions/get-shards/action.yml

@@ -0,0 +1,72 @@
+name: "Get number of shards"
+description: "Get the number of nf-test shards for the current CI job"
+inputs:
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: true
+  max_shards:
+    description: "Maximum number of shards allowed"
+    required: true
+  paths:
+    description: "Component paths to test"
+    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: ${{ env.NFT_VER }}
+        install-pdiff: true
+
+    - name: Get number of shards
+      id: shards
+      shell: bash
+      run: |
+
+        # Prepare tag parameter if tags are provided
+        TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
+        # Run nf-test with dynamic tag parameter
+        nftest_output=$(nf-test test \
+          --dry-run \
+          --profile docker \
+          ${TAGS} \
+          --filter process,workflow \
+          ${{ inputs.paths }})
+
+        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"

.github/actions/nf-test-action/action.yml

@@ -10,14 +10,14 @@ inputs:
   total_shards:
     description: "Total number of test shards(NOT the total number of matrix jobs)"
     required: true
-  tags:
-    description: "Tags to test (`<tags>[,<tags>...]`)"
-    required: false
+  paths:
+    description: "Test paths"
+    required: true
 
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+    - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
       with:
         distribution: "temurin"
         java-version: "17"
@@ -51,7 +51,7 @@ runs:
 
     - name: Conda setup
       if: ${{inputs.profile == 'conda'}}
-      uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
+      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
       with:
         auto-update-conda: true
         conda-solver: libmamba
@@ -72,26 +72,53 @@ runs:
       env:
         SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
         SENTIEON_AUTH_MECH: "GitHub Actions - token"
-        TAGS: ${{ inputs.tags && format('--tag {0}', inputs.tags) || '' }}
       run: |
         NFT_WORKDIR=~ \
+        NFT_DIFF=pdiff \
+        NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
+
         nf-test test \
           --profile=${{ inputs.profile }} \
           --tap=test.tap \
           --verbose \
           --ci \
-          --changed-since HEAD^ \
           --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
           --filter process,workflow \
-          --follow-dependencies \
-          ${{ env.TAGS }}
+          ${{ inputs.paths }}
 
-      # TODO If no test.tap, then make one to spoof?
-    - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
-      if: ${{ inputs.path != '' }}
-      with:
-        path: >-
-          test.tap
+          # Save the absolute path of the test.tap file to the output
+          echo "tap_file_path=$(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()