v1.16.2+galaxy0 (#48)

* Update readme * Update macros.xml (#46) * Update spectralMatching.R (#47) * github workflows * add skip * readme underline cleanup * lint cleanup * update href * lintr update * more lintr fixes * version bump and sm update * createMSP output update * update createDatabase output * add missing libicu-dev * troubleshooting stringi error * troubleshooting stringi error * trying to remove cache * refresh cache * update sm test data * Update conda section of readme
computational-metabolomics · Mar 4, 2021 · 2579c87 · 2579c87
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -0,0 +1,165 @@
+name: Weekly global Tool Linting and Tests
+on:
+  schedule:
+    # Run at midnight every monday
+    - cron: '0 0 * * 1'
+  repository_dispatch:
+    types: [run-all-tool-tests-command]
+env:
+  GALAXY_RELEASE: release_20.09
+jobs:
+  setup:
+    name: Setup cache
+    if: github.repository_owner == 'computational-metabolomics'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - name: Add reaction
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+        reaction-type: hooray
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_${{ matrix.python-version }}_${{ env.GALAXY_RELEASE }}
+    # Install the `wheel` package so that when installing other packages which
+    # are not available as wheels, pip will build a wheel for them, which can be cached.
+    - name: Install wheel
+      run: pip install wheel
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Fake a planemo run to update cache
+      run: |
+        touch tool.xml
+        PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_branch $GALAXY_RELEASE
+  test:
+    name: Test tools
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    needs: setup
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: [0,1,2,3]
+        python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_${{ matrix.python-version }}_${{ env.GALAXY_RELEASE }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Planemo ci_find_tools
+      run: planemo ci_find_tools --chunk_count 4 --chunk ${{ matrix.chunk  }} --exclude test_repositories --exclude packages --exclude deprecated --exclude_from .tt_skip --exclude_from .tt_biocontainer_skip --group_tools --output tool.list
+    - name: Show repo list
+      run: cat tool.list
+    - name: Planemo test tools
+      run: |
+           mkdir json_output/
+           while read -r TOOLS; do
+               if grep -qf .tt_biocontainer_skip <(echo $TOOLS); then
+                   PLANEMO_OPTIONS=""
+               else
+                   PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
+               fi
+               json=$(mktemp -u -p json_output --suff .json)
+               PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_branch $GALAXY_RELEASE  --galaxy_python_version ${{ matrix.python-version }} --test_output_json $json $TOOLS || true
+               docker system prune --all --force --volumes || true
+           done < tool.list
+    - name: Merge tool_test_output.json files
+      run: planemo merge_test_reports json_output/*.json tool_test_output.json
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/[email protected]
+      with:
+        name: 'Tool test output ${{ matrix.chunk  }}'
+        path: upload
+
+  combine_outputs:
+    name: Combine chunked test results
+    needs: test
+    strategy:
+      matrix:
+        python-version: [3.7]
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v2
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Install jq
+      run: sudo apt-get install jq
+    - name: Combine outputs
+      run: find artifacts -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/[email protected]
+      with:
+        name: 'All tool test results'
+        path: upload
+
+    - 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
+
+    - name: Create comment
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
+        body: |
+          [Find all tool test results here][1]
+
+          [1]: ${{ steps.vars.outputs.run-url }}
+    - name: Check status of combined outputs
+      run: |
+        if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
+            echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
+            exit 1
+        fi