Merge branch 'dev' into anvil-theme

Author: dannon

.circleci/config.yml

@@ -15,7 +15,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.9
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -73,7 +73,7 @@ jobs:
             - ~/repo
   validate_test_tools:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.9
     <<: *set_workdir
     steps:
       - *restore_repo_cache

.github/workflows/api.yaml

@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -29,7 +31,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.9']
         chunk: [0, 1]
     services:
       postgres:
@@ -48,9 +50,13 @@ jobs:
       - uses: actions/checkout@v4
         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@v4
         with:
-          node-version: '18.12.1'
+          node-version: ${{ steps.node-version.outputs.version }}
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v5

.github/workflows/bioblend.yaml

@@ -32,18 +32,20 @@ jobs:
       fail-fast: false
       matrix:
         tox_env: [py313]
-        galaxy_python_version: ["3.8"]
+        galaxy_python_version: ['3.9']
     steps:
       - name: Checkout Galaxy
         uses: actions/checkout@v4
         with:
           fetch-depth: 1
           path: galaxy
+          persist-credentials: false
       - name: Checkout Bioblend
         uses: actions/checkout@v4
         with:
           repository: galaxyproject/bioblend
           path: bioblend
+          persist-credentials: false
       - name: Cache pip dir
         uses: actions/cache@v4
         with:

.github/workflows/build_client.yaml

@@ -14,9 +14,13 @@ jobs:
       - uses: actions/checkout@v4
         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@v4
         with:
-          node-version: '18.12.1'
+          node-version: ${{ steps.node-version.outputs.version }}
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: get client commit

.github/workflows/build_container_image.yaml

@@ -15,6 +15,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
       - name: Set outputs
         id: commit
@@ -75,6 +77,8 @@ jobs:
     if: github.repository_owner == 'galaxyproject'
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       # 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

@@ -14,9 +14,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.9']
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/codeql-analysis.yml

@@ -41,6 +41,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          persist-credentials: false
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL

.github/workflows/converter_tests.yaml

@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -22,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.9']
     steps:
       - if: github.event_name == 'schedule'
         run: |
@@ -31,16 +33,21 @@ jobs:
       - uses: actions/checkout@v4
         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@v4
         with:
-          node-version: '18.12.1'
+          node-version: ${{ steps.node-version.outputs.version }}
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Clone galaxyproject/galaxy-test-data
         uses: actions/checkout@v4
         with:
           repository: galaxyproject/galaxy-test-data
           path: galaxy-test-data
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
@@ -60,7 +67,7 @@ jobs:
       - name: Lint converters
         run: |
           mapfile -t TOOL_ARRAY < tool_list.txt
-          planemo lint --skip citations,stdio,help --report_level warn "${TOOL_ARRAY[@]}"
+          planemo lint --skip CitationsMissing,HelpEmpty,HelpMissing --report_level warn "${TOOL_ARRAY[@]}"
       - name: Run tests
         run: |
           mapfile -t TOOL_ARRAY < tool_list.txt

.github/workflows/cwl_conformance.yaml

@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
 concurrency:
@@ -24,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.9']
         marker: ['green', 'red and required', 'red and not required']
         conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2']
     services:
@@ -40,9 +42,13 @@ jobs:
       - uses: actions/checkout@v4
         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@v4
         with:
-          node-version: '18.12.1'
+          node-version: ${{ steps.node-version.outputs.version }}
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v5

.github/workflows/db_indexes.yaml

@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -24,11 +26,11 @@ jobs:
       matrix:
         db: ['postgresql', 'sqlite']
         postgresql-version: ['13']
-        python-version: ['3.8']
+        python-version: ['3.9']
         include:
           - db: postgresql
             postgresql-version: '9.6'
-            python-version: '3.8'
+            python-version: '3.9'
     services:
       postgres:
         image: postgres:${{ matrix.postgresql-version }}
@@ -42,6 +44,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/dependencies.yaml

@@ -10,13 +10,11 @@ jobs:
     runs-on: ubuntu-latest
     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
+        with:
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
-          python-version: |
-            3.8
-            3.9
+          python-version: '3.9'
       - name: Update dependencies
         run: make update-dependencies
       - name: Create pull request

.github/workflows/deployment.yaml

@@ -29,11 +29,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.9']
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/docs.yaml

@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -16,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.9']
     steps:
       - name: Get target branch name (push)
         if: github.event_name == 'push'
@@ -29,6 +31,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/first_startup.yaml

@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   YARN_INSTALL_OPTS: --frozen-lockfile
 concurrency:
@@ -23,17 +25,21 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.13']
+        python-version: ['3.9', '3.13']
     defaults:
       run:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v4
         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@v4
         with:
-          node-version: '18.12.1'
+          node-version: ${{ steps.node-version.outputs.version }}
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Set up Python

.github/workflows/framework_tools.yaml

@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -25,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.9']
     services:
       postgres:
         image: postgres:13
@@ -43,9 +45,13 @@ jobs:
       - uses: actions/checkout@v4
         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@v4
         with:
-          node-version: '18.12.1'
+          node-version: ${{ steps.node-version.outputs.version }}
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v5