Update versions of GitHub actions

.github/workflows/api.yaml

@@ -44,28 +44,28 @@ 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@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
@@ -76,7 +76,7 @@ jobs:
         with:
           flags: api
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: API test results (${{ matrix.python-version }}, ${{ matrix.chunk }})

.github/workflows/build_client.yaml

@@ -11,10 +11,10 @@ jobs:
     outputs:
       commit-id: ${{ steps.client-commit.outputs.commit }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
@@ -25,7 +25,7 @@ jobs:
         run: echo "commit=$(git rev-parse HEAD 2>/dev/null)" >> $GITHUB_OUTPUT
         working-directory: 'galaxy root'
       - name: cache client build
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           key: galaxy-static-${{ steps.client-commit.outputs.commit }}

.github/workflows/build_container_image.yaml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository_owner == 'galaxyproject'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
       - name: Set outputs
         id: commit

.github/workflows/check_test_class_names.yaml

@@ -5,6 +5,9 @@ on:
       - '.ci/check_test_class_names.sh'
       - 'lib/galaxy_test/**'
       - 'test/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   test:
     name: Test
@@ -13,12 +16,12 @@ jobs:
       matrix:
         python-version: ['3.8']
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}

.github/workflows/codeql-analysis.yml

@@ -19,7 +19,9 @@ on:
     branches: [ dev ]
   schedule:
     - cron: '16 6 * * 0'
-
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   analyze:
     name: Analyze
@@ -32,41 +34,41 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        language: ['javascript', 'python']
-        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        language: ['javascript-typescript', 'python']
+        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
         # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      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.
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        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.
 
-        # 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
+          # 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@v2
+      # 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@v3
 
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 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
-    #   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
+      #- run: |
+      #   make bootstrap
+      #   make release
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3

.github/workflows/converter_tests.yaml

@@ -28,24 +28,24 @@ 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@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Clone galaxyproject/galaxy-test-data
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: galaxyproject/galaxy-test-data
           path: galaxy-test-data
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache venv dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/.cache/pip
@@ -69,7 +69,7 @@ jobs:
         run: |
           mapfile -t TOOL_ARRAY < tool_list.txt
           planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Converter test results (${{ matrix.python-version }})

.github/workflows/cwl_conformance.yaml

@@ -35,28 +35,28 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
@@ -67,7 +67,7 @@ jobs:
         with:
           flags: cwl-conformance
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }})

.github/workflows/db_indexes.yaml

@@ -39,24 +39,24 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-check-indexes

.github/workflows/dependencies.yaml

@@ -12,25 +12,28 @@ jobs:
       matrix:
         python-version: ['3.8']
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Update dependencies
         run: | 
           python -m venv .venv
           make update-dependencies
       - name: Create pull request
-        uses: peter-evans/create-pull-request@v4
+        uses: peter-evans/create-pull-request@v6
         with:
           author: galaxybot <[email protected]>
           token: ${{ secrets.GALAXYBOT_PAT }}
-          commit-message: Update Python dependencies
+          commit-message: |
+            Update Python dependencies
+
+            by running `make update-dependencies`.
           branch: dev_auto_update_dependencies
           delete-branch: true
           push-to-fork: galaxybot/galaxy
           title: Update Python dependencies
-          body: Run `make update-dependencies`.
+          body: by running `make update-dependencies`.
           labels: |
             area/dependencies
             kind/enhancement

.github/workflows/deployment.yaml

@@ -20,10 +20,6 @@ on:
         - all
         - api
         - selenium
-      branch:
-        description: 'Branch of code to run from'
-        default: 'dev'
-        type: string        
       debug:
         required: true
         description: 'Run deployment tests with debug mode on'
@@ -35,19 +31,18 @@ jobs:
       matrix:
         python-version: ['3.8']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
-          ref: ${{ inputs.branch }}
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
-      - uses: nanasess/setup-chromedriver@v1
+      - uses: nanasess/setup-chromedriver@v2
       - name: Run tests
         run: bash ./test/deployment/usegalaxystar.bash
         env:
@@ -64,8 +59,8 @@ jobs:
           GALAXY_TEST_USEGALAXYEU_USER_PASSWORD: ${{ secrets.USEGALAXYEU_USER_PASSWORD }}
           GALAXY_TEST_USEGALAXYEU_USER_KEY: ${{ secrets.USEGALAXYEU_USER_KEY }}
           GALAXY_TEST_TIMEOUT_MULTIPLIER: 10
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
-          name: Deployment test results (${{ inputs.target }}, ${{ inputs.type }})
+          name: Deployment test results (${{ inputs.target }}, ${{ inputs.type }}, ${{ inputs.debug }}, ${{ matrix.python-version }})
           path: 'deployment_tests.html'

.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@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}