updated CI and PR github actions from IUC

.github/workflows/ci.yaml

@@ -27,7 +27,7 @@ jobs:
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v2
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -37,12 +37,12 @@ jobs:
       id: get-fork-branch
       run: |
         TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
-        echo "::set-output name=fork::${TMP:-$GALAXY_FORK}"
+        echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT
         TMP="${{ github.event.client_payload.slash_command.args.named.branch }}"
-        echo "::set-output name=branch::${TMP:-$GALAXY_BRANCH}"
+        echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
-      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)"
+      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
     - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
@@ -74,6 +74,42 @@ jobs:
       run: |
         echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
 
+  lint:
+    name: Check for missing containers
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7']
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Planemo lint
+      uses: galaxyproject/planemo-ci-action@v1
+      id: lint
+      with:
+        mode: lint
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        tool-list: ${{ needs.setup.outputs.tool-list }}
+        additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd
+    - uses: actions/upload-artifact@v3
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
   test:
     name: Test tools
     # This job runs on Linux
@@ -112,6 +148,8 @@ jobs:
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
     - name: Planemo test
       uses: galaxyproject/planemo-ci-action@v1
       id: test
@@ -169,11 +207,11 @@ jobs:
     - name: Create URL to the run output
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
       id: vars
-      run: echo "::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
+      run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v2
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -190,4 +228,4 @@ jobs:
       uses: galaxyproject/planemo-ci-action@v1
       id: check
       with:
-        mode: check
+        mode: check

.github/workflows/pr.yaml

@@ -1,5 +1,20 @@
 name: Galaxy Tool Linting and Tests for push and PR
-on: [push, pull_request]
+on:
+  pull_request:
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
+  push:
+    branches:
+      - main
+      - master
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
 env:
   GALAXY_FORK: galaxyproject
   GALAXY_BRANCH: release_22.05
@@ -43,7 +58,7 @@ jobs:
         echo 'event.after: ${{ github.event.after }}'
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
-      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
+      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
     - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
@@ -110,11 +125,21 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+
+    - name: Set fail level for pull request
+      if: ${{ github.event_name == 'pull_request' }}
+      run:
+        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
+    - name: Set fail level for merge
+      if: ${{ github.event_name != 'pull_request' }}
+      run:
+        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
+        fail-level: ${{ env.FAIL_LEVEL }}
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
     - uses: actions/upload-artifact@v3
@@ -127,7 +152,7 @@ jobs:
   flake8:
     name: Lint Python scripts
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -159,7 +184,7 @@ jobs:
   lintr:
     name: Lint R scripts
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -189,7 +214,7 @@ jobs:
     - name: lintr
       run: |
         library(lintr)
-        linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL)
+        linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_name_linter = NULL)
         con <- file("repository_list.txt", "r")
         status <- 0
         while (TRUE) {
@@ -285,6 +310,8 @@ jobs:
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
     - name: Planemo test
       uses: galaxyproject/planemo-ci-action@v1
       id: test
@@ -311,7 +338,7 @@ jobs:
   combine_outputs:
     name: Combine chunked test results
     needs: [setup, test]
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ always() && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -344,6 +371,12 @@ jobs:
       id: check
       with:
         mode: check
+    - name: Check if all test chunks succeeded
+      run: |
+        NFILES=$(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:
@@ -383,6 +416,28 @@ jobs:
         shed-target: toolshed
         shed-key: ${{ secrets.TS_API_KEY }}
 
+  deploy-report:
+    name: Report deploy status
+    needs: [deploy]
+    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'RECETOX' }}
+    runs-on: ubuntu-latest
+    steps:
+    # report to the PR if deployment failed
+    - name: Get PR object
+      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      id: getpr
+      with:
+        sha: ${{ github.event.after }}
+    - name: Create comment
+      uses: peter-evans/create-or-update-comment@v2
+      with:
+        token: ${{ secrets.PAT }}
+        issue-number: ${{ steps.getpr.outputs.number }}
+        body: |
+          Attention: deployment ${{ needs.deploy.result }}!
+
+          https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
   determine-success:
     name: Check workflow success
     needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs]
@@ -403,4 +458,4 @@ jobs:
       run: exit 1
     - name: Check tool test status
       if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
-      run: exit 1
+      run: exit 1