[pull] dev from galaxyproject:dev

.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

.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/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/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}

.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

.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:

.github/workflows/lint.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     env:
       LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
       TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
@@ -55,4 +55,6 @@ jobs:
       - name: Run mypy checks
         run: tox -e mypy
       - uses: psf/black@stable
+        with:
+          version: "24.8.0"  # last version supporting Python 3.8
       - uses: isort/isort-action@v1

.github/workflows/lint_openapi_schema.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/maintenance_bot.yaml

@@ -12,7 +12,7 @@ jobs:
       pull-requests: write
     runs-on: ubuntu-latest
     env:
-      MILESTONE_NUMBER: 28
+      MILESTONE_NUMBER: 29
     steps:
       - name: Get latest pull request labels
         id: get_pr_labels

.github/workflows/osx_startup.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/pr-title-update.yml

@@ -0,0 +1,29 @@
+name: Update PR title
+
+on:
+  pull_request_target:
+    types: [opened, edited, reopened]
+
+jobs:
+  update-title:
+    if: github.event.action != 'edited' || github.event.changes.base.ref.from != ''
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Update PR title
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          TARGET_BRANCH: "${{ github.base_ref }}"
+          PR_TITLE: "${{ github.event.pull_request.title }}"
+          REPO: "${{ github.repository }}"
+        run: |
+          VERSION=$(echo $TARGET_BRANCH | grep -oP '^release_\K\d+.\d+$' || true)
+          NEW_TITLE=$(echo "$PR_TITLE" | sed -E "s/\[[0-9]+\.[0-9]+\] //")
+          if [[ -n "$VERSION" ]]; then
+            NEW_TITLE="[$VERSION] $NEW_TITLE"
+          fi
+          if [[ "$NEW_TITLE" != "$PR_TITLE" ]]; then
+            gh pr edit $PR_NUMBER --repo "$REPO" --title "$NEW_TITLE"
+          fi

.github/workflows/reports_startup.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/test_galaxy_packages.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/test_galaxy_packages_for_pulsar.yaml

@@ -16,7 +16,7 @@ concurrency:
 jobs:
   test:
     name: Test
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04  # Python 3.7 is not available via setup-python on ubuntu >=24.04
     strategy:
       fail-fast: false
       matrix:

.github/workflows/toolshed.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
         shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:

.github/workflows/unit.yaml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

CITATION

@@ -1,22 +1,22 @@
 If you use or extend Galaxy in your published work, please cite this
 publication:
 
-- The Galaxy Community. "The Galaxy platform for accessible, reproducible and collaborative
-  biomedical analyses: 2022 update"
-  Nucleic Acids Res. (2022) 50(W1):W345-W351 doi:10.1093/nar/gkac247
+- The Galaxy Community. "The Galaxy platform for accessible, reproducible, and
+  collaborative data analyses: 2024 update"
+  Nucleic Acids Res. (2024) 52(W1):W83-W94 doi:10.1093/nar/gkae410
 
 BibTeX format:
 
-@article{10.1093/nar/gkac247,
-  title = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses: 2022 update},
+@article{10.1093/nar/gkae410,
+  title = {The {Galaxy} platform for accessible, reproducible, and collaborative data analyses: 2024 update},
   author = {The Galaxy Community},
   journal = {Nucleic Acids Res.},
-  doi = {10.1093/nar/gkac247},
-  volume = {50},
+  doi = {10.1093/nar/gkae410},
+  volume = {52},
   number = {W1},
-  pages = {W345-W351},
-  year = {2022},
-  url = {https://doi.org/10.1093/nar/gkac247},
+  pages = {W83-W94},
+  year = {2024},
+  url = {https://doi.org/10.1093/nar/gkae410},
   publisher = {Oxford University Press}
 }
 

Makefile

@@ -2,7 +2,7 @@
 VENV?=.venv
 # Source virtualenv to execute command (darker, sphinx, twine, etc...)
 IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
-RELEASE_CURR:=24.2
+RELEASE_CURR:=25.0
 RELEASE_UPSTREAM:=upstream
 CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
 PROJECT_URL?=https://github.com/galaxyproject/galaxy

README.rst

@@ -24,7 +24,7 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 3.8 . To check your Python version, run:
+Galaxy requires Python 3.8 or higher. To check your Python version, run:
 
 .. code:: console
 

client/gulpfile.js

@@ -15,31 +15,37 @@ const xml2js = require("xml2js");
 const STATIC_PLUGIN_BUILD_IDS = [
     "annotate_image",
     "chiraviz",
-    "cytoscape",
     "drawrna",
     "editor",
     "example",
+    "fits_graph_viewer",
     "fits_image_viewer",
-    "h5web",
-    "heatmap/heatmap_default",
     "hyphyvision",
     "jqplot/jqplot_bar",
     "media_player",
     "mvpapp",
-    "ngl",
     "nora",
     "nvd3/nvd3_bar",
-    "openlayers",
     "openseadragon",
     "PCA_3Dplot",
-    "phylocanvas",
     "pv",
     "scatterplot",
     "tiffviewer",
     "ts_visjs",
-    "venn",
 ];
-const INSTALL_PLUGIN_BUILD_IDS = ["msa"]; // todo: derive from XML
+const INSTALL_PLUGIN_BUILD_IDS = [
+    "cytoscape",
+    "h5web",
+    "heatmap",
+    "ngl",
+    "msa",
+    "openlayers",
+    "phylocanvas",
+    "plotly",
+    "venn",
+    "vitessce",
+    "vizarr",
+]; // todo: derive from XML
 const DIST_PLUGIN_BUILD_IDS = ["new_user"];
 const PLUGIN_BUILD_IDS = Array.prototype.concat(DIST_PLUGIN_BUILD_IDS, STATIC_PLUGIN_BUILD_IDS);
 
@@ -237,7 +243,7 @@ async function installDependenciesFromXML(xmlPath, pluginDir) {
                 try {
                     const installResult = child_process.spawnSync(
                         "npm",
-                        ["install", "--silent", "--no-save", `${pkgName}@${version}`],
+                        ["install", "--silent", "--no-save", "--prefix .", `${pkgName}@${version}`],
                         {
                             cwd: pluginDir,
                             stdio: "inherit",

client/package.json

@@ -62,9 +62,11 @@
     "dom-to-image": "^2.6.0",
     "dompurify": "^3.0.6",
     "dumpmeta-webpack-plugin": "^0.2.0",
+    "echarts": "^5.5.1",
     "elkjs": "^0.8.2",
     "file-saver": "^2.0.5",
     "flush-promises": "^1.0.2",
+    "font-awesome-6": "npm:@fortawesome/free-solid-svg-icons@6",
     "glob": "^10.3.10",
     "handsontable": "^4.0.0",
     "hsluv": "^1.0.1",
@@ -100,7 +102,11 @@
     "tus-js-client": "^3.1.1",
     "underscore": "^1.13.6",
     "util": "^0.12.5",
+    "vega": "^5.30.0",
+    "vega-embed": "^6.26.0",
+    "vega-lite": "^5.21.0",
     "vue": "^2.7.14",
+    "vue-echarts": "^7.0.3",
     "vue-infinite-scroll": "^2.0.2",
     "vue-multiselect": "^2.1.7",
     "vue-observe-visibility": "^1.0.0",

client/src/api/configTemplates.ts

@@ -19,6 +19,11 @@ export type SecretData = CreateInstancePayload["secrets"];
 export type PluginAspectStatus = components["schemas"]["PluginAspectStatus"];
 export type PluginStatus = components["schemas"]["PluginStatus"];
 
+export type UpgradeInstancePayload = components["schemas"]["UpgradeInstancePayload"];
+export type TestUpgradeInstancePayload = components["schemas"]["TestUpgradeInstancePayload"];
+export type UpdateInstancePayload = components["schemas"]["UpdateInstancePayload"];
+export type TestUpdateInstancePayload = components["schemas"]["TestUpdateInstancePayload"];
+
 export interface TemplateSummary {
     description: string | null;
     hidden?: boolean;