Merge pull request #18239 from mvdbeek/release_24.1

Merge 24.0 into 24.1

.github/codeql/codeql-config.yml

@@ -0,0 +1,2 @@
+paths-ignore:
+  - 'lib/galaxy/datatypes/test/*.bcsl.ts'

.github/labeler.yml

@@ -1,73 +1,129 @@
 ---
 area/admin:
-  - client/src/components/admin/**/*
-  - doc/source/admin/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/components/admin/**/*
+      - doc/source/admin/**/*
 area/API:
-  - lib/galaxy/webapps/galaxy/api/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/webapps/galaxy/api/**/*
 area/auth:
-  - lib/galaxy/auth/**/*
-  - lib/galaxy/authnz/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/auth/**/*
+      - lib/galaxy/authnz/**/*
 area/client:
-  - client/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/*
 area/database:
-  - lib/galaxy/model/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/model/**/*
 area/datatypes:
-  - lib/galaxy/datatypes/**/*
-  - lib/galaxy/config/sample/datatypes_conf.xml.sample
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/datatypes/**/*
+      - lib/galaxy/config/sample/datatypes_conf.xml.sample
 area/dependencies:
-  - lib/galaxy/dependencies/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/dependencies/**/*
 area/documentation:
-  - doc/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - doc/**/*
 area/jobs:
-  - lib/galaxy/jobs/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/jobs/**/*
 area/libraries:
-  - client/src/components/LibraryFolder/**/*
-  - lib/galaxy/webapps/galaxy/api/libraries.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/components/LibraryFolder/**/*
+      - lib/galaxy/webapps/galaxy/api/libraries.py
 area/objectstore:
-  - lib/galaxy/objectstore/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/objectstore/**/*
 area/packaging:
-  - packages/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - packages/**/*
 area/reports:
-  - client/src/reports/**/*
-  - lib/galaxy/webapps/reports/**/*
-  - templates/webapps/reports/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/reports/**/*
+      - lib/galaxy/webapps/reports/**/*
+      - templates/webapps/reports/**/*
 area/scripts:
-  - scripts/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - scripts/**/*
 area/security:
-  - lib/galaxy/security/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/security/**/*
 area/testing:
-  - lib/galaxy_test/**/*
-  - run_tests.sh
-  - test/**/*
-  - test-data/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy_test/**/*
+      - run_tests.sh
+      - test/**/*
+      - test-data/**/*
 area/testing/api:
-  - lib/galaxy_test/api/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy_test/api/**/*
 area/testing/integration:
-  - test/integration/**/*
-  - test/integration_selenium/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - test/integration/**/*
+      - test/integration_selenium/**/*
 area/testing/selenium:
-  - lib/galaxy/selenium/**/*
-  - lib/galaxy_test/selenium/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/selenium/**/*
+      - lib/galaxy_test/selenium/**/*
 area/tool-dependencies:
-  - lib/galaxy/tool_util/deps/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/tool_util/deps/**/*
 area/tool-framework:
-  - lib/galaxy/tools/**/*
-  - lib/galaxy/tool_util/**/*
-  - lib/galaxy/webapps/galaxy/api/tools.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/tools/**/*
+      - lib/galaxy/tool_util/**/*
+      - lib/galaxy/webapps/galaxy/api/tools.py
 area/tools:
-  - tools/**/*
-  - tool-data/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - tools/**/*
+      - tool-data/**/*
 area/toolshed:
-  - client/src/toolshed/**/*
-  - lib/galaxy/webapps/galaxy/api/toolshed.py
-  - lib/toolshed/**/*
-  - templates/webapps/tool_shed/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/toolshed/**/*
+      - lib/galaxy/webapps/galaxy/api/toolshed.py
+      - lib/toolshed/**/*
+      - templates/webapps/tool_shed/**/*
 area/UI-UX:
-  - all: ["client/src/**/*", "!client/src/api/schema/schema.ts"]
-    any: ["templates/**/*"]
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/**/*
+      - templates/**/*
+    - all-globs-to-all-files:
+      - '!client/src/api/schema/schema.ts'
 area/util:
-  - lib/galaxy/util/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/util/**/*
 area/visualizations:
-  - config/plugins/visualizations/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - config/plugins/visualizations/**/*
 area/workflows:
-  - lib/galaxy/workflow/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/workflow/**/*

.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

@@ -13,12 +13,12 @@ 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

@@ -32,41 +32,44 @@ 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
+          config-file: ./.github/codeql/codeql-config.yml
 
-    # 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
+      # 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
 
-    #- run: |
-    #   make bootstrap
-    #   make release
+      # 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
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      #   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@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 }})