[25.1] Register new PNTS datatype configuration to datatypes_conf.xml

.github/workflows/api.yaml

@@ -47,15 +47,15 @@ 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@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Get full Python version
         id: full-python-version
         shell: bash
@@ -72,7 +72,7 @@ jobs:
         with:
           flags: api
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: API test results (${{ matrix.python-version }}, ${{ matrix.chunk }})

.github/workflows/bioblend.yaml

@@ -35,33 +35,28 @@ jobs:
         galaxy_python_version: ['3.9']
     steps:
       - name: Checkout Galaxy
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 1
           path: galaxy
           persist-credentials: false
       - name: Checkout Bioblend
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           repository: galaxyproject/bioblend
           path: bioblend
           persist-credentials: false
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.tox_env }}
       - name: Calculate Python version for BioBlend from tox_env
         id: get_bioblend_python_version
         run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
       - name: Set up Python for BioBlend
         uses: actions/setup-python@v6
         with:
           python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Install tox
-        run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install 'tox>=1.8.0'
+        run: uv tool install tox --with tox-uv
       - name: Set up Python for Galaxy
         uses: actions/setup-python@v6
         with:

.github/workflows/build_client.yaml

@@ -11,14 +11,14 @@ jobs:
     outputs:
       commit-id: ${{ steps.client-commit.outputs.commit }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false
       - name: Read Node.js version
         id: node-version
         run: echo "version=$(cat 'galaxy root/client/.node_version')" >> $GITHUB_OUTPUT
-      - uses: actions/setup-node@v5
+      - uses: actions/setup-node@v6
         with:
           node-version: ${{ steps.node-version.outputs.version }}
           cache: 'yarn'
@@ -38,5 +38,6 @@ jobs:
         if: steps.cache.outputs.cache-hit != 'true'
         env:
           GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR: 1
+          NODE_OPTIONS: --max-old-space-size=4096
         run: make client
         working-directory: 'galaxy root'

.github/workflows/build_container_image.yaml

@@ -14,7 +14,7 @@ jobs:
     name: Build container image for GHCR
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
       # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
@@ -266,4 +266,3 @@ jobs:
           branch: update-galaxy-${{ needs.build.outputs.version }}
           delete-branch: true
           labels: patch
-

.github/workflows/check_test_class_names.yaml

@@ -16,15 +16,15 @@ jobs:
       matrix:
         python-version: ['3.9']
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Install Python dependencies
-        run: pip install -r requirements.txt -r lib/galaxy/dependencies/pinned-test-requirements.txt
+        run: uv pip install --system -r requirements.txt -r lib/galaxy/dependencies/pinned-test-requirements.txt
       - name: Run tests
         run: .ci/check_test_class_names.sh

.github/workflows/jest.yaml → .github/workflows/client-unit.yaml

@@ -3,26 +3,26 @@ on:
   push:
     paths:
       - 'client/**'
-      - '.github/workflows/jest.yaml'
+      - '.github/workflows/client-unit.yaml'
   pull_request:
     paths:
       - 'client/**'
-      - '.github/workflows/jest.yaml'
+      - '.github/workflows/client-unit.yaml'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 jobs:
   client-unit-test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
       - name: Read Node.js version
         id: node-version
         run: echo "version=$(cat 'client/.node_version')" >> $GITHUB_OUTPUT
       - name: Setup node
-        uses: actions/setup-node@v5
+        uses: actions/setup-node@v6
         with:
           node-version: ${{ steps.node-version.outputs.version }}
           cache: 'yarn'
@@ -32,6 +32,6 @@ jobs:
       - name: Stage client libs (Gulp)
         run: yarn run gulp client
         working-directory: client
-      - name: Run Unit Tests
-        run: yarn jest
+      - name: Run Vitest Unit Tests
+        run: yarn test
         working-directory: client

.github/workflows/codeql-analysis.yml

@@ -40,13 +40,13 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           persist-credentials: false
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v3
+        uses: github/codeql-action/init@v4
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -62,7 +62,7 @@ jobs:
       # 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
+        uses: github/codeql-action/autobuild@v4
 
       # 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
@@ -76,4 +76,4 @@ jobs:
       #   make release
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v3
+        uses: github/codeql-action/analyze@v4

.github/workflows/converter_tests.yaml

@@ -30,25 +30,25 @@ 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@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false
       - name: Clone galaxyproject/galaxy-test-data
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           repository: galaxyproject/galaxy-test-data
           path: galaxy-test-data
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - 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
+        run: uv tool 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
@@ -64,7 +64,7 @@ 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@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: Converter test results (${{ matrix.python-version }})

.github/workflows/cwl_conformance.yaml

@@ -39,15 +39,15 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Get full Python version
         id: full-python-version
         shell: bash
@@ -64,7 +64,7 @@ jobs:
         with:
           flags: cwl-conformance
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }})

.github/workflows/db_indexes.yaml

@@ -41,26 +41,21 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache tox env
-        uses: actions/cache@v4
-        with:
-          path: .tox
-          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-check-indexes
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: Set database connection on PostgreSQL
         if: matrix.db == 'postgresql'
         run: echo 'GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8' >> $GITHUB_ENV

.github/workflows/dependencies.yaml

@@ -9,12 +9,14 @@ jobs:
     if: github.repository_owner == 'galaxyproject'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
           python-version: '3.9'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Update dependencies
         run: make update-dependencies
       - name: Create pull request

.github/workflows/deployment.yaml

@@ -31,15 +31,15 @@ jobs:
       matrix:
         python-version: ['3.9']
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - uses: nanasess/setup-chromedriver@v2
       - name: Run tests
         run: bash ./test/deployment/usegalaxystar.bash
@@ -57,7 +57,7 @@ jobs:
           GALAXY_TEST_USEGALAXYEU_USER_PASSWORD: ${{ secrets.USEGALAXYEU_USER_PASSWORD }}
           GALAXY_TEST_USEGALAXYEU_USER_KEY: ${{ secrets.USEGALAXYEU_USER_KEY }}
           GALAXY_TEST_TIMEOUT_MULTIPLIER: 10
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: always()
         with:
           name: Deployment test results (${{ inputs.target }}, ${{ inputs.type }}, ${{ inputs.debug }}, ${{ matrix.python-version }})

.github/workflows/docs.yaml

@@ -28,17 +28,17 @@ jobs:
         run: echo "TARGET_BRANCH=$GITHUB_BASE_REF" >> $GITHUB_ENV
       - name: Show target branch name
         run: echo $TARGET_BRANCH
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Install Python dependencies
-        run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
+        run: uv pip install --system -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
       - name: Add Google Analytics to doc/source/conf.py
         run: |
           sed -i -e "/html_theme_options = {/a\
@@ -73,5 +73,5 @@ jobs:
                   exit 0
                   ;;
           esac
-          pip install awscli
+          uv tool install awscli
           aws s3 sync doc/build/html/ "s3://galaxy-docs/en/$UPLOAD_DIR" --region us-east-2 --size-only --delete