From d8611a50223d5ab84d21d07960e30ba186d7c88a Mon Sep 17 00:00:00 2001
From: Ralf Weber <RJMW@users.noreply.github.com>
Date: Wed, 17 Jul 2024 22:28:53 +0100
Subject: [PATCH] Update pr.yaml

---
 .github/workflows/pr.yaml | 103 ++++++++++++++++++++------------------
 1 file changed, 55 insertions(+), 48 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index a52652f..3aab965 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -288,63 +288,70 @@ jobs:
   #   to `|| true`) and create a global test report as json and html which
   #   is provided as artifact
   # - check if any tool test actually failed (by lookup in the combined json)
-#  #   and fail this step if this is the case
-#  SEEMS TO BE FAILING ON CONDA - UNABLE TO FIX
-#  combine_outputs:
-#    name: Combine chunked test results
-#    needs: [setup, test]
-#    if: ${{ needs.setup.outputs.repository-list != '' }}
-#    runs-on: ubuntu-latest
-#    strategy:
-#      matrix:
-#        python-version: ['3.11']
-#    steps:
-#    - uses: actions/download-artifact@v2
-#      with:
-#        path: artifacts
-#    - uses: actions/setup-python@v1
-#      with:
-#        python-version: ${{ matrix.python-version }}
-#    - name: Cache .cache/pip
-#      uses: actions/cache@v2
-#      id: cache-pip
-#      with:
-#        path: ~/.cache/pip
-#        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
-#    - name: Combine outputs
-#      uses: galaxyproject/planemo-ci-action@v1
-#      id: combine
-#      with:
-#        mode: combine
-#        html-report: true
-#    - uses: actions/upload-artifact@v2
-#      with:
-#        name: 'All tool test results'
-#        path: upload
-#    - name: Check outputs
-#      uses: galaxyproject/planemo-ci-action@v1
-#      id: check
-#      with:
-#        mode: check
+  #   and fail this step if this is the case
+  combine_outputs:
+    name: Combine chunked test results
+    needs: [setup, test]
+    if: ${{ always() && needs.setup.outputs.repository-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Combine outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: combine
+      with:
+        mode: combine
+        html-report: true
+        markdown-report: true
+    - uses: actions/upload-artifact@v4
+      with:
+        name: 'All tool test results'
+        path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
+    - name: Check outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: check
+      with:
+        mode: check
+    - name: Check if all test chunks succeeded
+      run: |
+        NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
+        if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
+          exit 1
+        fi
 
   # deploy the tools to the toolsheds (first TTS for testing)
   deploy:
     name: Deploy
-    needs: [setup, lint, flake8, lintr]
-    if: ${{ (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }}
+    needs: [setup, lint, combine_outputs]
+    if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -367,8 +374,8 @@ jobs:
 
   determine-success:
     name: Check workflow success
-    needs: [setup, lint, flake8, lintr, file_sizes]
-    if: ${{ always() && github.ref != 'refs/heads/main' && github.ref != 'refs/heads/main' }}
+    needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs]
+    if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
     runs-on: ubuntu-latest
     steps:
     - name: Check tool lint status
@@ -383,6 +390,6 @@ jobs:
     - name: Indicate file size check status
       if: ${{ needs.file_sizes.result != 'success' && needs.file_sizes.result != 'skipped' }}
       run: exit 1
-#    - name: Check tool test status
-#      if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
-#      run: exit 1
+    - name: Check tool test status
+      if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
+      run: exit 1