Update GitHub action versions

.github/workflows/api.yaml

@@ -42,23 +42,23 @@ jobs:
         run: |
           echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
           echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         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@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
@@ -69,7 +69,7 @@ jobs:
         with:
           flags: api
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: API test results (${{ matrix.python-version }})

.github/workflows/build_container_image.yaml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository_owner == 'galaxyproject'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
       - name: Set outputs
         id: commit

.github/workflows/codeql-analysis.yml

@@ -34,37 +34,39 @@ jobs:
       matrix:
         language: ['javascript', 'python']
         # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
-        # Learn more about CodeQL language support at https://git.io/codeql-language-support
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v2
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
         # By default, queries listed here will override any specified in a config file.
         # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
 
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
+      uses: github/codeql-action/autobuild@v2
 
     # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
 
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
+    #   If the Autobuild fails above, remove it and uncomment the following three lines
+    #   modify them (or add more) to build your code if your project
+    #   uses a compiled language
 
     #- run: |
     #   make bootstrap
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v2

.github/workflows/converter_tests.yaml

@@ -28,19 +28,19 @@ jobs:
       run: |
         echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
         echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         path: 'galaxy root'
     - name: Clone galaxyproject/galaxy-test-data
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: galaxyproject/galaxy-test-data
         path: galaxy-test-data
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache venv dir
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       id: pip-cache
       with:
         path: ~/.cache/pip
@@ -78,7 +78,7 @@ jobs:
           echo "Unsuccessful tests found, inspect the 'Converter test results' artifact for details."
           exit 1
         fi
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       if: failure()
       with:
         name: Converter test results (${{ matrix.python-version }})

.github/workflows/cwl_conformance.yaml

@@ -35,23 +35,23 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         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@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
@@ -62,7 +62,7 @@ jobs:
         with:
           flags: cwl-conformance
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }})

.github/workflows/db_indexes.yaml

@@ -38,24 +38,24 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         path: 'galaxy root'
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v3
       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@v1
+      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@v2
+      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

.github/workflows/dependencies.yaml

@@ -11,12 +11,12 @@ jobs:
       matrix:
         python-version: ['3.7']
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}

.github/workflows/docs.yaml

@@ -26,14 +26,14 @@ jobs:
         run: echo "TARGET_BRANCH=$GITHUB_BASE_REF" >> $GITHUB_ENV
       - name: Show target branch name
         run: echo $TARGET_BRANCH
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}

.github/workflows/first_startup.yaml

@@ -26,25 +26,25 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         path: 'galaxy root'
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       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@v1
+      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@v2
+      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

.github/workflows/framework.yaml

@@ -40,23 +40,23 @@ jobs:
         run: |
           echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
           echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         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@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
@@ -67,7 +67,7 @@ jobs:
         with:
           flags: framework
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: Framework test results (${{ matrix.python-version }})

.github/workflows/integration.yaml

@@ -64,24 +64,24 @@ jobs:
       - name: Check pods
         run: |
           kubectl get pods
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v3
         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@v1
+        uses: actions/cache@v3
         id: pip-cache
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration
@@ -96,7 +96,7 @@ jobs:
         with:
           flags: integration
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: Integration test results (${{ matrix.python-version }}, ${{ matrix.chunk }})

.github/workflows/integration_selenium.yaml

@@ -43,43 +43,43 @@ jobs:
           echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
       - name: Prune unused docker image, volumes and containers
         run: docker system prune -a -f
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         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@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration-selenium
       - uses: mvdbeek/gha-yarn-cache@master
         with:
           yarn-lock-file: 'galaxy root/client/yarn.lock'
-      - uses: nanasess/setup-chromedriver@master
+      - uses: nanasess/setup-chromedriver@v1
       - name: Run tests
         run: ./run_tests.sh --coverage -integration test/integration_selenium
         working-directory: 'galaxy root'
       - uses: codecov/codecov-action@v2
         with:
           flags: integration-selenium
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: Integration Selenium test results (${{ matrix.python-version }})
           path: 'galaxy root/run_integration_tests.html'
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: Integration Selenium debug info (${{ matrix.python-version }})

.github/workflows/jest.yaml

@@ -18,9 +18,9 @@ jobs:
       matrix:
         node: [16]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Setup node
-      uses: actions/setup-node@v2
+      uses: actions/setup-node@v3
       with:
         node-version: ${{ matrix.node}}
         cache: 'yarn'