Integrate 'uv' installation across workflow files for improved package management

.github/workflows/api.yaml

@@ -54,8 +54,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/bioblend.yaml

@@ -46,11 +46,6 @@ jobs:
           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
@@ -58,10 +53,10 @@ jobs:
         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@v6
       - 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/check_test_class_names.yaml

@@ -22,9 +22,9 @@ jobs:
       - 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@v6
       - 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/converter_tests.yaml

@@ -43,12 +43,12 @@ jobs:
       - 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@v6
       - 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 pip install --system 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

.github/workflows/cwl_conformance.yaml

@@ -46,8 +46,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/db_indexes.yaml

@@ -48,19 +48,14 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(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

@@ -15,6 +15,8 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: '3.9'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Update dependencies
         run: make update-dependencies
       - name: Create pull request

.github/workflows/deployment.yaml

@@ -38,8 +38,8 @@ jobs:
       - 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@v6
       - uses: nanasess/setup-chromedriver@v2
       - name: Run tests
         run: bash ./test/deployment/usegalaxystar.bash

.github/workflows/docs.yaml

@@ -35,10 +35,10 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Install Python dependencies
-        run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
+        run: uv pip install --system -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
       - name: Add Google Analytics to doc/source/conf.py
         run: |
           sed -i -e "/html_theme_options = {/a\
@@ -73,5 +73,5 @@ jobs:
                   exit 0
                   ;;
           esac
-          pip install awscli
+          uv pip install --system awscli
           aws s3 sync doc/build/html/ "s3://galaxy-docs/en/$UPLOAD_DIR" --region us-east-2 --size-only --delete

.github/workflows/first_startup.yaml

@@ -38,24 +38,19 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(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') }}-first-startup
       - name: Restore client cache
         uses: actions/cache@v4
         with:
           key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
           path: 'galaxy root/static'
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: run tests
         run: tox -e first_startup
         working-directory: 'galaxy root'

.github/workflows/framework_tools.yaml

@@ -49,8 +49,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/framework_workflows.yaml

@@ -50,8 +50,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/integration.yaml

@@ -58,8 +58,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/integration_selenium.yaml

@@ -57,8 +57,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/lint.yaml

@@ -34,22 +34,14 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: |
-            ${{ env.LINT_PATH }}
-            ${{ env.TYPE_PATH }}
-            ${{ env.CORE_PATH }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(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(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}-lint
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: Run linting
         run: tox -e lint
       - name: Run docstring linting

.github/workflows/main_tools.yaml

@@ -42,8 +42,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/mulled.yaml

@@ -31,21 +31,16 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(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') }}-mulled
       - name: Install Apptainer's singularity
         uses: eWaterCycle/setup-apptainer@v2
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: Run tests
         run: tox -e mulled
         working-directory: 'galaxy root'

.github/workflows/osx_startup.yaml

@@ -32,11 +32,6 @@ jobs:
         with:
           path: 'galaxy root'
           persist-credentials: false
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/Library/Caches/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Install miniforge  # use this job to test using Python from a conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -47,8 +42,10 @@ jobs:
         with:
           key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
           path: 'galaxy root/static'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: Run tests
         run: tox -e first_startup
         working-directory: 'galaxy root'

.github/workflows/performance.yaml

@@ -48,8 +48,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/publish_artifacts.yaml

@@ -17,8 +17,10 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Install script dependencies
-        run: pip install galaxy-release-util
+        run: uv pip install --system galaxy-release-util
       - name: Build and publish to PyPI
         run: |
           galaxy-release-util build-and-upload --no-confirm

.github/workflows/reports_startup.yaml

@@ -33,8 +33,8 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash
@@ -45,7 +45,7 @@ jobs:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-reports-startup
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: Run tests
         run: tox -e reports_startup
         working-directory: 'galaxy root'

.github/workflows/selenium.yaml

@@ -57,8 +57,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/test_galaxy_packages.yaml

@@ -27,12 +27,12 @@ jobs:
       - 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@v6
       - name: Install ffmpeg
         run: sudo apt-get update && sudo apt-get -y install ffmpeg
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: Run tests
         run: tox -e test_galaxy_packages
         working-directory: 'galaxy root'

.github/workflows/test_galaxy_packages_for_pulsar.yaml

@@ -29,14 +29,14 @@ jobs:
       - 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@v6
       - name: Install Apptainer's singularity
         uses: eWaterCycle/setup-apptainer@v2
       - name: Install ffmpeg
         run: sudo apt-get update && sudo apt-get -y install ffmpeg
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: Run tests
         run: tox -e test_galaxy_packages_for_pulsar
         working-directory: 'galaxy root'

.github/workflows/toolshed.yaml

@@ -43,8 +43,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/unit-postgres.yaml

@@ -42,8 +42,8 @@ jobs:
       - 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@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash

.github/workflows/unit.yaml

@@ -31,21 +31,16 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(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') }}-unit
       - name: Install ffmpeg
         run: sudo apt-get update && sudo apt-get -y install ffmpeg
       - name: Install tox
-        run: pip install tox
+        run: uv tool install tox --with tox-uv
       - name: Run tests
         run: tox -e unit-coverage
         working-directory: 'galaxy root'