Merge branch 'dev' into file_sources_assign_paths

.github/workflows/api.yaml

@@ -18,6 +18,7 @@ env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
   GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+  GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS: '1'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -55,15 +56,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:

.github/workflows/bioblend.yaml

@@ -0,0 +1,80 @@
+name: BioBlend Tests
+on:
+  pull_request:
+    paths:
+      - .github/workflows/bioblend.yaml
+      - lib/galaxy/schema/**
+      - lib/galaxy/webapps/galaxy/api/**
+      - lib/galaxy/webapps/galaxy/services/**
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      postgres:
+        image: postgres
+        # Provide the password for postgres
+        env:
+          POSTGRES_PASSWORD: postgres
+        # Set health checks to wait until postgres has started
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    strategy:
+      fail-fast: false
+      matrix:
+        tox_env: [py313]
+        galaxy_python_version: ["3.8"]
+    steps:
+      - name: Checkout Galaxy
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          path: galaxy
+      - name: Checkout Bioblend
+        uses: actions/checkout@v4
+        with:
+          repository: galaxyproject/bioblend
+          path: bioblend
+      - 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@v5
+        with:
+          python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
+      - name: Install tox
+        run: |
+          python3 -m pip install --upgrade pip setuptools
+          python3 -m pip install 'tox>=1.8.0'
+      - name: Set up Python for Galaxy
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.galaxy_python_version }}
+      - name: Run tests
+        env:
+          PGPASSWORD: postgres
+          PGPORT: 5432
+          PGHOST: localhost
+        run: |
+          # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
+          createdb -U postgres galaxy
+          export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
+          ./bioblend/run_bioblend_tests.sh -g galaxy -v python${{ matrix.galaxy_python_version }} -e ${{ matrix.tox_env }}
+      - name: The job has failed
+        if: ${{ failure() }}
+        run: |
+          cat galaxy/*.log

.github/workflows/build_container_image.yaml

@@ -10,8 +10,67 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 jobs:
+  ghcrbuild:
+    name: Build container image for GHCR
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
+      - name: Set outputs
+        id: commit
+        run: echo "sha_short=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT
+      - name: Set branch name
+        id: branch
+        run: |
+          if [[ "$GITHUB_REF" == "refs/tags/"* ]]; then
+            echo "name=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT
+          elif [[ "$GITHUB_REF" == "refs/heads/dev" ]]; then
+            echo "name=dev" >> $GITHUB_OUTPUT
+          elif [[ "$GITHUB_REF" == "refs/heads/release_"* ]]; then
+            echo "name=${GITHUB_REF#refs/heads/release_}-auto" >> $GITHUB_OUTPUT
+          fi
+        shell: bash
+      - name: Extract metadata for container image
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            type=raw,value=${{steps.branch.outputs.name}}
+      - name: Build args
+        id: buildargs
+        run: |
+            echo "gitcommit=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT 
+            echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')"
+      
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          platforms: linux/amd64
+
+      - name: Login to GHCR
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push container image to ghcr
+        uses: docker/build-push-action@v4
+        with:
+          build-args: |
+              GIT_COMMIT=${{ steps.buildargs.outputs.gitcommit }}
+              BUILD_DATE=${{ steps.buildargs.outputs.builddate }}
+              IMAGE_TAG=${{ steps.branch.outputs.name }}
+          file: .k8s_ci.Dockerfile
+          push: true
+          context: .
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          platforms: linux/amd64
+
   build:
-    name: Build container image
+    name: Build container image for Galaxy repos
     runs-on: ubuntu-latest
     if: github.repository_owner == 'galaxyproject'
     steps:
@@ -58,3 +117,4 @@ jobs:
         uses: actions-hub/docker@master
         with:
           args: push galaxy/galaxy-min:${{ steps.branch.outputs.name }}
+

.github/workflows/check_test_class_names.yaml

@@ -20,11 +20,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'requirements.txt'
       - name: Install Python dependencies
         run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt
       - name: Run tests

.github/workflows/converter_tests.yaml

@@ -44,12 +44,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache venv dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Move test data
         run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
       - name: Install planemo

.github/workflows/cwl_conformance.yaml

@@ -48,15 +48,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:

.github/workflows/db_indexes.yaml

@@ -45,16 +45,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
         uses: actions/cache@v4
         with:

.github/workflows/dependencies.yaml

@@ -8,18 +8,17 @@ jobs:
     name: Update dependencies
     if: github.repository_owner == 'galaxyproject'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8']
     steps:
       - uses: actions/checkout@v4
+      # Install Python 3.8 for update_lint_requirements.sh
+      # Install Python 3.9 (as default) to allow `uv lock` to generate metadata for rucio-clients
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: |
+            3.8
+            3.9
       - name: Update dependencies
-        run: | 
-          python -m venv .venv
-          make update-dependencies
+        run: make update-dependencies
       - name: Create pull request
         uses: peter-evans/create-pull-request@v6
         with:

.github/workflows/deployment.yaml

@@ -37,11 +37,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'requirements.txt'
       - uses: nanasess/setup-chromedriver@v2
       - name: Run tests
         run: bash ./test/deployment/usegalaxystar.bash

.github/workflows/docs.yaml

@@ -32,11 +32,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'requirements.txt'
       - name: Install Python dependencies
         run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
       - name: Add Google Analytics to doc/source/conf.py

.github/workflows/first_startup.yaml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}
@@ -40,16 +40,12 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
         uses: actions/cache@v4
         with:

.github/workflows/framework_tools.yaml

@@ -51,15 +51,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:

.github/workflows/framework_workflows.yaml

@@ -16,6 +16,7 @@ on:
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_TEST_WORKFLOW_AFTER_RERUN: '1'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -51,15 +52,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:

.github/workflows/integration.yaml

@@ -25,7 +25,7 @@ concurrency:
 jobs:
   test:
     name: Test
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
@@ -76,16 +76,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with: