Use indentation for YAML nested sequences for consistency

galaxyproject · Oct 17, 2022 · 5fab7ee · 5fab7ee
1 parent 2988127
commit 5fab7ee
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Showing 6 changed files with 194 additions and 194 deletions.
diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
@@ -24,61 +24,61 @@ jobs:
       matrix:
         python-version: ['3.7']
     steps:
-    - if: github.event_name == 'schedule'
-      run: |
-        echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
-        echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
-    - uses: actions/checkout@v3
-      with:
-        path: 'galaxy root'
-    - name: Clone galaxyproject/galaxy-test-data
-      uses: actions/checkout@v3
-      with:
-        repository: galaxyproject/galaxy-test-data
-        path: galaxy-test-data
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache venv dir
-      uses: actions/cache@v3
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Move test data
-      run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
-    - name: Install planemo
-      run: pip install planemo
-    - name: Determine converters to check
-      run: |
-        ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt
-        echo "Skipping checks for the following converters:"
-        ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip
-        echo "Checking only the following converters:"
-        cat tool_list.txt
-    - name: Lint converters
-      run: |
-        mapfile -t TOOL_ARRAY < tool_list.txt
-        for CONVERTER in "${TOOL_ARRAY[@]}"; do
-          planemo lint --skip citations,stdio,help --report_level warn "$CONVERTER"
-        done
-    - name: Run tests
-      run: |
-        mkdir -p json_output
-        EXIT_CODE=0
-        mapfile -t TOOL_ARRAY < tool_list.txt
-        for CONVERTER in "${TOOL_ARRAY[@]}"; do
-          json=$(mktemp -u -p json_output --suff .json)
-          planemo test --test_output_json "$json" --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "$CONVERTER" || EXIT_CODE=$?
-        done
-        planemo merge_test_reports json_output/*.json tool_test_output.json
-        planemo test_reports tool_test_output.json --test_output tool_test_output.html
-        if [ "$EXIT_CODE" -ne 0 ]; then
-          echo "Unsuccessful tests found, inspect the 'Converter test results' artifact for details."
-          exit $EXIT_CODE
-        fi
-    - uses: actions/upload-artifact@v3
-      if: failure()
-      with:
-        name: Converter test results (${{ matrix.python-version }})
-        path: tool_test_output.html
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v3
+        with:
+          path: 'galaxy root'
+      - name: Clone galaxyproject/galaxy-test-data
+        uses: actions/checkout@v3
+        with:
+          repository: galaxyproject/galaxy-test-data
+          path: galaxy-test-data
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache venv dir
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Move test data
+        run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
+      - name: Install planemo
+        run: pip install planemo
+      - name: Determine converters to check
+        run: |
+          ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt
+          echo "Skipping checks for the following converters:"
+          ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip
+          echo "Checking only the following converters:"
+          cat tool_list.txt
+      - name: Lint converters
+        run: |
+          mapfile -t TOOL_ARRAY < tool_list.txt
+          for CONVERTER in "${TOOL_ARRAY[@]}"; do
+            planemo lint --skip citations,stdio,help --report_level warn "$CONVERTER"
+          done
+      - name: Run tests
+        run: |
+          mkdir -p json_output
+          EXIT_CODE=0
+          mapfile -t TOOL_ARRAY < tool_list.txt
+          for CONVERTER in "${TOOL_ARRAY[@]}"; do
+            json=$(mktemp -u -p json_output --suff .json)
+            planemo test --test_output_json "$json" --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "$CONVERTER" || EXIT_CODE=$?
+          done
+          planemo merge_test_reports json_output/*.json tool_test_output.json
+          planemo test_reports tool_test_output.json --test_output tool_test_output.html
+          if [ "$EXIT_CODE" -ne 0 ]; then
+            echo "Unsuccessful tests found, inspect the 'Converter test results' artifact for details."
+            exit $EXIT_CODE
+          fi
+      - uses: actions/upload-artifact@v3
+        if: failure()
+        with:
+          name: Converter test results (${{ matrix.python-version }})
+          path: tool_test_output.html
diff --git a/.github/workflows/db_indexes.yaml b/.github/workflows/db_indexes.yaml
@@ -38,34 +38,34 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v3
-      with:
-        path: 'galaxy root'
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Get full Python version
-      id: full-python-version
-      shell: bash
-      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-    - name: Cache pip dir
-      uses: actions/cache@v3
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Cache tox env
-      uses: actions/cache@v3
-      with:
-        path: .tox
-        key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-check-indexes
-    - name: Install tox
-      run: pip install tox
-    - name: Check indexes on postgresql
-      if: matrix.db == 'postgresql'
-      env:
-        GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
-      run: tox -e check_indexes
-    - name: Check indexes on sqlite
-      if: matrix.db == 'sqlite'
-      run: tox -e check_indexes
+      - uses: actions/checkout@v3
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache tox env
+        uses: actions/cache@v3
+        with:
+          path: .tox
+          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-check-indexes
+      - name: Install tox
+        run: pip install tox
+      - name: Check indexes on postgresql
+        if: matrix.db == 'postgresql'
+        env:
+          GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+        run: tox -e check_indexes
+      - name: Check indexes on sqlite
+        if: matrix.db == 'sqlite'
+        run: tox -e check_indexes
diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml
@@ -26,33 +26,33 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v3
-      with:
-        path: 'galaxy root'
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Get full Python version
-      id: full-python-version
-      shell: bash
-      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-    - name: Cache pip dir
-      uses: actions/cache@v3
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Cache tox env
-      uses: actions/cache@v3
-      with:
-        path: .tox
-        key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-first-startup
-    - uses: mvdbeek/gha-yarn-cache@master
-      with:
-        yarn-lock-file: 'galaxy root/client/yarn.lock'
-    - name: Install tox
-      run: pip install tox
-    - name: run tests
-      run: tox -e first_startup
-      working-directory: 'galaxy root'
+      - uses: actions/checkout@v3
+        with:
+          path: 'galaxy root'
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache tox env
+        uses: actions/cache@v3
+        with:
+          path: .tox
+          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-first-startup
+      - uses: mvdbeek/gha-yarn-cache@master
+        with:
+          yarn-lock-file: 'galaxy root/client/yarn.lock'
+      - name: Install tox
+        run: pip install tox
+      - name: run tests
+        run: tox -e first_startup
+        working-directory: 'galaxy root'
diff --git a/.github/workflows/jest.yaml b/.github/workflows/jest.yaml
@@ -18,20 +18,20 @@ jobs:
       matrix:
         node: [16]
     steps:
-    - uses: actions/checkout@v3
-    - name: Setup node
-      uses: actions/setup-node@v3
-      with:
-        node-version: ${{ matrix.node}}
-        cache: 'yarn'
-        cache-dependency-path: 'client/yarn.lock'
-    - run: yarn install --frozen-lockfile
-      working-directory: client
-    - name: Stage client libs (Gulp)
-      run: yarn run gulp client
-      working-directory: client
-    - name: Run Unit Tests
-      run: yarn run qunit
-      working-directory: client
-    - run: yarn jest
-      working-directory: client
+      - uses: actions/checkout@v3
+      - name: Setup node
+        uses: actions/setup-node@v3
+        with:
+          node-version: ${{ matrix.node}}
+          cache: 'yarn'
+          cache-dependency-path: 'client/yarn.lock'
+      - run: yarn install --frozen-lockfile
+        working-directory: client
+      - name: Stage client libs (Gulp)
+        run: yarn run gulp client
+        working-directory: client
+      - name: Run Unit Tests
+        run: yarn run qunit
+        working-directory: client
+      - run: yarn jest
+        working-directory: client
diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
@@ -19,31 +19,31 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v3
-      with:
-        path: 'galaxy root'
-    - name: Get full Python version
-      id: full-python-version
-      shell: bash
-      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-    - name: Cache pip dir
-      uses: actions/cache@v3
-      id: pip-cache
-      with:
-        path: ~/Library/Caches/pip
-        # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.7
-        key: pip-cache-3.7-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Cache tox env
-      uses: actions/cache@v3
-      with:
-        path: .tox
-        key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-osx
-    - name: Install and activate miniconda  # use this job to test using Python from a conda environment
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ''
-    - name: Install tox
-      run: pip install tox
-    - name: run tests
-      run: tox -e first_startup
-      working-directory: 'galaxy root'
+      - uses: actions/checkout@v3
+        with:
+          path: 'galaxy root'
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          path: ~/Library/Caches/pip
+          # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.7
+          key: pip-cache-3.7-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache tox env
+        uses: actions/cache@v3
+        with:
+          path: .tox
+          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-osx
+      - name: Install and activate miniconda  # use this job to test using Python from a conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: ''
+      - name: Install tox
+        run: pip install tox
+      - name: run tests
+        run: tox -e first_startup
+        working-directory: 'galaxy root'