From b56640d401cd434d876047d8781f2bc90d0bf26d Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 21 May 2024 12:27:51 +0100
Subject: [PATCH 1/6] Cancel in-progress concurrent builds

---
 .github/workflows/check_test_class_names.yaml | 3 +++
 .github/workflows/codeql-analysis.yml         | 4 +++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check_test_class_names.yaml b/.github/workflows/check_test_class_names.yaml
index 217995df93e4..e4193f79462a 100644
--- a/.github/workflows/check_test_class_names.yaml
+++ b/.github/workflows/check_test_class_names.yaml
@@ -5,6 +5,9 @@ on:
       - '.ci/check_test_class_names.sh'
       - 'lib/galaxy_test/**'
       - 'test/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   test:
     name: Test
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 2ddfee5bad8c..1ace0cc4a4c9 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -19,7 +19,9 @@ on:
     branches: [ dev ]
   schedule:
     - cron: '16 6 * * 0'
-
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   analyze:
     name: Analyze

From 55a9b9db6d355c7f2f632329aa505a355958f089 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 21 May 2024 12:29:56 +0100
Subject: [PATCH 2/6] Update commit message and PR title

---
 .github/workflows/dependencies.yaml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/dependencies.yaml b/.github/workflows/dependencies.yaml
index 12f2a0919a89..d3cc9d1d2c65 100644
--- a/.github/workflows/dependencies.yaml
+++ b/.github/workflows/dependencies.yaml
@@ -25,12 +25,15 @@ jobs:
         with:
           author: galaxybot <galaxybot@users.noreply.github.com>
           token: ${{ secrets.GALAXYBOT_PAT }}
-          commit-message: Update Python dependencies
+          commit-message: |
+            Update Python dependencies
+
+            by running `make update-dependencies`.
           branch: dev_auto_update_dependencies
           delete-branch: true
           push-to-fork: galaxybot/galaxy
           title: Update Python dependencies
-          body: Run `make update-dependencies`.
+          body: by running `make update-dependencies`.
           labels: |
             area/dependencies
             kind/enhancement

From 5ac64c8e80c7836cac7b69cc835b958b79d517e8 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 21 May 2024 12:31:28 +0100
Subject: [PATCH 3/6] Remove unnecessary workflow input

The branch to run from can be selected from the standard parameters
when running a GitHub workflow manually.
---
 .github/workflows/deployment.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/deployment.yaml b/.github/workflows/deployment.yaml
index 082e93d9328d..989275cf8c29 100644
--- a/.github/workflows/deployment.yaml
+++ b/.github/workflows/deployment.yaml
@@ -20,10 +20,6 @@ on:
         - all
         - api
         - selenium
-      branch:
-        description: 'Branch of code to run from'
-        default: 'dev'
-        type: string        
       debug:
         required: true
         description: 'Run deployment tests with debug mode on'

From 4b4a649707dc0ac8ae928a804d06f8112a91708d Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 21 May 2024 12:40:22 +0100
Subject: [PATCH 4/6] Use job permissions instead of token

---
 .github/workflows/labels-verifier.yaml | 3 ++-
 .github/workflows/maintenance_bot.yaml | 9 ++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/labels-verifier.yaml b/.github/workflows/labels-verifier.yaml
index 484040885dd8..415942a371d1 100644
--- a/.github/workflows/labels-verifier.yaml
+++ b/.github/workflows/labels-verifier.yaml
@@ -5,6 +5,8 @@ on:
 jobs:
   onMerged:
     name: "Check Labels on merge"
+    permissions:
+      pull-requests: write
     runs-on: ubuntu-latest
     steps:
       - name: Check Labels on merge
@@ -15,7 +17,6 @@ jobs:
           ! contains(github.event.pull_request.labels.*.name, 'minor')
         uses: actions/github-script@v6
         with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
             github.rest.issues.createComment({
               owner: context.repo.owner,
diff --git a/.github/workflows/maintenance_bot.yaml b/.github/workflows/maintenance_bot.yaml
index 55e9738d9336..7eaed8bc15a2 100644
--- a/.github/workflows/maintenance_bot.yaml
+++ b/.github/workflows/maintenance_bot.yaml
@@ -6,6 +6,9 @@ jobs:
   labeler:
     name: Assign labels and milestone
     if: github.repository_owner == 'galaxyproject'
+    permissions:
+      contents: read
+      pull-requests: write
     runs-on: ubuntu-latest
     env:
       MILESTONE_NUMBER: 28
@@ -14,7 +17,6 @@ jobs:
         id: get_pr_labels
         uses: actions/github-script@v6
         with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
             const response = await github.rest.issues.listLabelsOnIssue({
               owner: context.repo.owner,
@@ -25,9 +27,7 @@ jobs:
             return response.data;
       - name: Add area labels
         if: ${{ ! contains(join(fromJSON(steps.get_pr_labels.outputs.result).*.name, ', '), 'area/') }}
-        uses: actions/labeler@v4
-        with:
-          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+        uses: actions/labeler@v5
       - name: Assign milestone
         if: |
           ! github.event.pull_request.milestone &&
@@ -37,7 +37,6 @@ jobs:
           ! github.event.pull_request.draft
         uses: actions/github-script@v6
         with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
             github.rest.issues.update({
               owner: context.repo.owner,

From 94de628e4359d46d8dd4f42b3d5d13908e578062 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 21 May 2024 12:45:57 +0100
Subject: [PATCH 5/6] Update versions of GitHub actions

---
 .github/workflows/api.yaml                    | 12 ++--
 .github/workflows/build_client.yaml           |  6 +-
 .github/workflows/build_container_image.yaml  |  2 +-
 .github/workflows/check_test_class_names.yaml |  6 +-
 .github/workflows/codeql-analysis.yml         | 56 +++++++++----------
 .github/workflows/converter_tests.yaml        | 12 ++--
 .github/workflows/cwl_conformance.yaml        | 12 ++--
 .github/workflows/db_indexes.yaml             |  8 +--
 .github/workflows/dependencies.yaml           |  6 +-
 .github/workflows/deployment.yaml             | 13 ++---
 .github/workflows/docs.yaml                   |  6 +-
 .github/workflows/first_startup.yaml          | 12 ++--
 .github/workflows/framework.yaml              | 12 ++--
 .github/workflows/integration.yaml            | 12 ++--
 .github/workflows/integration_selenium.yaml   | 16 +++---
 .github/workflows/jest.yaml                   |  4 +-
 .github/workflows/js_lint.yaml                |  4 +-
 .github/workflows/labels-verifier.yaml        |  2 +-
 .github/workflows/lint.yaml                   | 10 ++--
 .github/workflows/lint_openapi_schema.yml     |  8 +--
 .github/workflows/maintenance_bot.yaml        |  4 +-
 .github/workflows/mulled.yaml                 | 10 ++--
 .github/workflows/osx_startup.yaml            | 10 ++--
 .github/workflows/performance.yaml            | 18 +++---
 .github/workflows/publish_artifacts.yaml      |  4 +-
 .github/workflows/reports_startup.yaml        | 10 ++--
 .github/workflows/selenium.yaml               | 16 +++---
 .github/workflows/test_galaxy_packages.yaml   |  8 +--
 .../test_galaxy_packages_for_pulsar.yaml      |  6 +-
 .github/workflows/test_galaxy_release.yaml    |  2 +-
 .github/workflows/toolshed.yaml               | 12 ++--
 .github/workflows/unit-postgres.yaml          | 10 ++--
 .github/workflows/unit.yaml                   | 12 ++--
 33 files changed, 170 insertions(+), 171 deletions(-)

diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml
index 753f669f148f..ea717e7edccb 100644
--- a/.github/workflows/api.yaml
+++ b/.github/workflows/api.yaml
@@ -44,15 +44,15 @@ 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@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -60,12 +60,12 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
@@ -76,7 +76,7 @@ jobs:
         with:
           flags: api
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: API test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
diff --git a/.github/workflows/build_client.yaml b/.github/workflows/build_client.yaml
index 59e2192dc354..6156b565f939 100644
--- a/.github/workflows/build_client.yaml
+++ b/.github/workflows/build_client.yaml
@@ -11,10 +11,10 @@ jobs:
     outputs:
       commit-id: ${{ steps.client-commit.outputs.commit }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
@@ -25,7 +25,7 @@ jobs:
         run: echo "commit=$(git rev-parse HEAD 2>/dev/null)" >> $GITHUB_OUTPUT
         working-directory: 'galaxy root'
       - name: cache client build
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           key: galaxy-static-${{ steps.client-commit.outputs.commit }}
diff --git a/.github/workflows/build_container_image.yaml b/.github/workflows/build_container_image.yaml
index 1820e34cb4a3..53a4a285a73d 100644
--- a/.github/workflows/build_container_image.yaml
+++ b/.github/workflows/build_container_image.yaml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository_owner == 'galaxyproject'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
       - name: Set outputs
         id: commit
diff --git a/.github/workflows/check_test_class_names.yaml b/.github/workflows/check_test_class_names.yaml
index e4193f79462a..b2e4ac3a8d78 100644
--- a/.github/workflows/check_test_class_names.yaml
+++ b/.github/workflows/check_test_class_names.yaml
@@ -16,12 +16,12 @@ jobs:
       matrix:
         python-version: ['3.8']
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 1ace0cc4a4c9..cad852d6813c 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -34,41 +34,41 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        language: ['javascript', 'python']
-        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        language: ['javascript-typescript', 'python']
+        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
         # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
 
-        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
-        # queries: security-extended,security-and-quality
+          # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+          # queries: security-extended,security-and-quality
 
-    # 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@v2
+      # 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
 
-    # 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
+      # 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
 
-    #   If the Autobuild fails above, remove it and uncomment the following three lines
-    #   modify them (or add more) to build your code if your project
-    #   uses a compiled language
+      #   If the Autobuild fails above, remove it and uncomment the following three lines
+      #   modify them (or add more) to build your code if your project
+      #   uses a compiled language
 
-    #- run: |
-    #   make bootstrap
-    #   make release
+      #- run: |
+      #   make bootstrap
+      #   make release
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index 1d8c0ee963b8..23848f81c014 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -28,24 +28,24 @@ 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@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Clone galaxyproject/galaxy-test-data
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: galaxyproject/galaxy-test-data
           path: galaxy-test-data
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache venv dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/.cache/pip
@@ -69,7 +69,7 @@ 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@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Converter test results (${{ matrix.python-version }})
diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
index 206bd33798a1..f9ac963071ac 100644
--- a/.github/workflows/cwl_conformance.yaml
+++ b/.github/workflows/cwl_conformance.yaml
@@ -35,15 +35,15 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -51,12 +51,12 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
@@ -67,7 +67,7 @@ jobs:
         with:
           flags: cwl-conformance
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }})
diff --git a/.github/workflows/db_indexes.yaml b/.github/workflows/db_indexes.yaml
index 88f1d02297af..cc5ec407b5d4 100644
--- a/.github/workflows/db_indexes.yaml
+++ b/.github/workflows/db_indexes.yaml
@@ -39,10 +39,10 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -50,13 +50,13 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-check-indexes
diff --git a/.github/workflows/dependencies.yaml b/.github/workflows/dependencies.yaml
index d3cc9d1d2c65..9b319d1954e1 100644
--- a/.github/workflows/dependencies.yaml
+++ b/.github/workflows/dependencies.yaml
@@ -12,8 +12,8 @@ jobs:
       matrix:
         python-version: ['3.8']
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Update dependencies
@@ -21,7 +21,7 @@ jobs:
           python -m venv .venv
           make update-dependencies
       - name: Create pull request
-        uses: peter-evans/create-pull-request@v4
+        uses: peter-evans/create-pull-request@v6
         with:
           author: galaxybot <galaxybot@users.noreply.github.com>
           token: ${{ secrets.GALAXYBOT_PAT }}
diff --git a/.github/workflows/deployment.yaml b/.github/workflows/deployment.yaml
index 989275cf8c29..eeb1e865baba 100644
--- a/.github/workflows/deployment.yaml
+++ b/.github/workflows/deployment.yaml
@@ -31,19 +31,18 @@ jobs:
       matrix:
         python-version: ['3.8']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
-          ref: ${{ inputs.branch }}
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
-      - uses: nanasess/setup-chromedriver@v1
+      - uses: nanasess/setup-chromedriver@v2
       - name: Run tests
         run: bash ./test/deployment/usegalaxystar.bash
         env:
@@ -60,8 +59,8 @@ jobs:
           GALAXY_TEST_USEGALAXYEU_USER_PASSWORD: ${{ secrets.USEGALAXYEU_USER_PASSWORD }}
           GALAXY_TEST_USEGALAXYEU_USER_KEY: ${{ secrets.USEGALAXYEU_USER_KEY }}
           GALAXY_TEST_TIMEOUT_MULTIPLIER: 10
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
-          name: Deployment test results (${{ inputs.target }}, ${{ inputs.type }})
+          name: Deployment test results (${{ inputs.target }}, ${{ inputs.type }}, ${{ inputs.debug }}, ${{ matrix.python-version }})
           path: 'deployment_tests.html'
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index fb72e3853e64..77a01f531907 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -26,14 +26,14 @@ jobs:
         run: echo "TARGET_BRANCH=$GITHUB_BASE_REF" >> $GITHUB_ENV
       - name: Show target branch name
         run: echo $TARGET_BRANCH
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml
index 732388cc1ff2..bc487ab9ec32 100644
--- a/.github/workflows/first_startup.yaml
+++ b/.github/workflows/first_startup.yaml
@@ -28,16 +28,16 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -45,18 +45,18 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-first-startup
       - name: Restore client cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
           path: 'galaxy root/static'
diff --git a/.github/workflows/framework.yaml b/.github/workflows/framework.yaml
index 53a287c5d7c0..dcc5e7614b15 100644
--- a/.github/workflows/framework.yaml
+++ b/.github/workflows/framework.yaml
@@ -40,15 +40,15 @@ 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@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -56,12 +56,12 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
@@ -72,7 +72,7 @@ jobs:
         with:
           flags: framework
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Framework test results (${{ matrix.python-version }})
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index e90a4ea836b2..0a3b14434449 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -68,15 +68,15 @@ jobs:
       - name: Check pods
         run: |
           kubectl get pods
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -84,13 +84,13 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration
@@ -105,7 +105,7 @@ jobs:
         with:
           flags: integration
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Integration test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
diff --git a/.github/workflows/integration_selenium.yaml b/.github/workflows/integration_selenium.yaml
index d294d91f9902..414446b5d827 100644
--- a/.github/workflows/integration_selenium.yaml
+++ b/.github/workflows/integration_selenium.yaml
@@ -48,10 +48,10 @@ jobs:
           echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
       - name: Prune unused docker image, volumes and containers
         run: docker system prune -a -f
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -59,22 +59,22 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration-selenium
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Restore client cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
           path: 'galaxy root/static'
@@ -85,12 +85,12 @@ jobs:
         with:
           flags: integration-selenium
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Integration Selenium test results (${{ matrix.python-version }})
           path: 'galaxy root/run_integration_tests.html'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Integration Selenium debug info (${{ matrix.python-version }})
diff --git a/.github/workflows/jest.yaml b/.github/workflows/jest.yaml
index 97be31032156..0d69a1498299 100644
--- a/.github/workflows/jest.yaml
+++ b/.github/workflows/jest.yaml
@@ -18,9 +18,9 @@ jobs:
       matrix:
         node: [18]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
           node-version: ${{ matrix.node}}
           cache: 'yarn'
diff --git a/.github/workflows/js_lint.yaml b/.github/workflows/js_lint.yaml
index 90b818e8b68b..ea821e1c105b 100644
--- a/.github/workflows/js_lint.yaml
+++ b/.github/workflows/js_lint.yaml
@@ -18,9 +18,9 @@ jobs:
       matrix:
         node: [18]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
           node-version: ${{ matrix.node}}
           cache: 'yarn'
diff --git a/.github/workflows/labels-verifier.yaml b/.github/workflows/labels-verifier.yaml
index 415942a371d1..61dee02ee73e 100644
--- a/.github/workflows/labels-verifier.yaml
+++ b/.github/workflows/labels-verifier.yaml
@@ -15,7 +15,7 @@ jobs:
           ! contains(join(github.event.pull_request.labels.*.name, ', '), 'kind/') &&
           ! contains(github.event.pull_request.labels.*.name, 'merge') &&
           ! contains(github.event.pull_request.labels.*.name, 'minor')
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             github.rest.issues.createComment({
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 3174f6ceb5d7..fc03fde8c3a9 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -28,8 +28,8 @@ jobs:
       TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
       CORE_PATH: 'lib/galaxy/dependencies/pinned-requirements.txt'
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -37,12 +37,12 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}
       - name: Cache tox env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}-lint
@@ -55,4 +55,4 @@ jobs:
       - name: Run mypy checks
         run: tox -e mypy
       - uses: psf/black@stable
-      - uses: isort/isort-action@master
+      - uses: isort/isort-action@v1
diff --git a/.github/workflows/lint_openapi_schema.yml b/.github/workflows/lint_openapi_schema.yml
index 780b584f3b05..464d1cef825f 100644
--- a/.github/workflows/lint_openapi_schema.yml
+++ b/.github/workflows/lint_openapi_schema.yml
@@ -22,10 +22,10 @@ jobs:
       matrix:
         python-version: ['3.8', '3.12']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -33,12 +33,12 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
diff --git a/.github/workflows/maintenance_bot.yaml b/.github/workflows/maintenance_bot.yaml
index 7eaed8bc15a2..626f6c7b92c7 100644
--- a/.github/workflows/maintenance_bot.yaml
+++ b/.github/workflows/maintenance_bot.yaml
@@ -15,7 +15,7 @@ jobs:
     steps:
       - name: Get latest pull request labels
         id: get_pr_labels
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             const response = await github.rest.issues.listLabelsOnIssue({
@@ -35,7 +35,7 @@ jobs:
           ! contains(github.event.pull_request.labels.*.name, 'status/WIP') &&
           ! contains(github.event.pull_request.title, 'WIP') &&
           ! github.event.pull_request.draft
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             github.rest.issues.update({
diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index 1b140eb1f6c3..4d33cc3febd7 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -22,10 +22,10 @@ jobs:
       matrix:
         python-version: ['3.8']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -33,12 +33,12 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-mulled
@@ -49,7 +49,7 @@ jobs:
       - name: Run tests
         run: tox -e mulled
         working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Mulled unit test results (${{ matrix.python-version }})
diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
index 5c0ffbe2b534..0a3050cbcb6b 100644
--- a/.github/workflows/osx_startup.yaml
+++ b/.github/workflows/osx_startup.yaml
@@ -26,10 +26,10 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
@@ -39,13 +39,13 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/Library/Caches/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-osx
@@ -54,7 +54,7 @@ jobs:
         with:
           activate-environment: ''
       - name: Restore client cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
           path: 'galaxy root/static'
diff --git a/.github/workflows/performance.yaml b/.github/workflows/performance.yaml
index 48287a739f8c..45413a608f19 100644
--- a/.github/workflows/performance.yaml
+++ b/.github/workflows/performance.yaml
@@ -39,15 +39,15 @@ 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@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -55,24 +55,24 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-performance
       - name: Run tests
         run: ./run_tests.sh --ci_test_metrics --structured_data_html --structured_data_report_file "test.json" --skip_flakey_fails -api lib/galaxy_test/performance
         working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
-          name: API test results
+          name: API test results (${{ matrix.python-version }})
           path: 'galaxy root/run_api_tests.html'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: Performance Metrics
+          name: Performance Metrics (${{ matrix.python-version }})
           path: 'galaxy root/test.html'
diff --git a/.github/workflows/publish_artifacts.yaml b/.github/workflows/publish_artifacts.yaml
index 3703d932c0cc..dded5d1086eb 100644
--- a/.github/workflows/publish_artifacts.yaml
+++ b/.github/workflows/publish_artifacts.yaml
@@ -11,10 +11,10 @@ jobs:
         matrix:
             python-version: ['3.8']
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install script dependencies
         run: pip install galaxy-release-util
       - name: Build and publish
diff --git a/.github/workflows/reports_startup.yaml b/.github/workflows/reports_startup.yaml
index 397e78442a4a..d2a730549837 100644
--- a/.github/workflows/reports_startup.yaml
+++ b/.github/workflows/reports_startup.yaml
@@ -23,16 +23,16 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -40,13 +40,13 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-reports-startup
diff --git a/.github/workflows/selenium.yaml b/.github/workflows/selenium.yaml
index 2d2d30ee56d6..3c3d9126cbb5 100644
--- a/.github/workflows/selenium.yaml
+++ b/.github/workflows/selenium.yaml
@@ -48,15 +48,15 @@ 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@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -64,17 +64,17 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-selenium
       - name: Restore client cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
           path: 'galaxy root/static'
@@ -85,12 +85,12 @@ jobs:
         with:
           flags: selenium
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Selenium test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
           path: 'galaxy root/run_selenium_tests.html'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Selenium debug info (${{ matrix.python-version }}, ${{ matrix.chunk }})
diff --git a/.github/workflows/test_galaxy_packages.yaml b/.github/workflows/test_galaxy_packages.yaml
index 51f871b3fe38..da5e092118dc 100644
--- a/.github/workflows/test_galaxy_packages.yaml
+++ b/.github/workflows/test_galaxy_packages.yaml
@@ -20,19 +20,19 @@ jobs:
       matrix:
         python-version: ['3.8', '3.12']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
diff --git a/.github/workflows/test_galaxy_packages_for_pulsar.yaml b/.github/workflows/test_galaxy_packages_for_pulsar.yaml
index 2a8e39cadbce..3ce8c2f3bece 100644
--- a/.github/workflows/test_galaxy_packages_for_pulsar.yaml
+++ b/.github/workflows/test_galaxy_packages_for_pulsar.yaml
@@ -22,14 +22,14 @@ jobs:
       matrix:
         python-version: ['3.7']  # don't upgrade, see https://github.com/galaxyproject/galaxy/pull/16649
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
diff --git a/.github/workflows/test_galaxy_release.yaml b/.github/workflows/test_galaxy_release.yaml
index 722399a1cb1f..6e39d98adc8e 100644
--- a/.github/workflows/test_galaxy_release.yaml
+++ b/.github/workflows/test_galaxy_release.yaml
@@ -22,7 +22,7 @@ jobs:
     name: Test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Run tests
diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
index 5552bc4f3900..df121215d9f1 100644
--- a/.github/workflows/toolshed.yaml
+++ b/.github/workflows/toolshed.yaml
@@ -34,15 +34,15 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -50,13 +50,13 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-toolshed
@@ -82,7 +82,7 @@ jobs:
           TOOL_SHED_API_VERSION: ${{ matrix.shed-api }}
           TOOL_SHED_TEST_BROWSER: ${{ matrix.shed-api == 'v1' && 'twill' || 'playwright' }}
         working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Toolshed test results (${{ matrix.python-version }}, ${{ matrix.shed-api }}, ${{ matrix.test-install-client }})
diff --git a/.github/workflows/unit-postgres.yaml b/.github/workflows/unit-postgres.yaml
index f2c57b6228d4..dbb9b21587c7 100644
--- a/.github/workflows/unit-postgres.yaml
+++ b/.github/workflows/unit-postgres.yaml
@@ -33,15 +33,15 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
@@ -49,12 +49,12 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-unit-postgres
diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
index af5f7810a894..33b2857ddeee 100644
--- a/.github/workflows/unit.yaml
+++ b/.github/workflows/unit.yaml
@@ -22,13 +22,13 @@ jobs:
       matrix:
         python-version: ['3.8', '3.12']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
@@ -38,12 +38,12 @@ jobs:
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-unit
@@ -58,7 +58,7 @@ jobs:
         with:
           flags: py-unit
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Unit test results (${{ matrix.python-version }})

From 4cf305c368c9adda9cc529443a7fb50dfa04c01e Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 21 May 2024 16:47:03 +0100
Subject: [PATCH 6/6] Use official minikube GitHub action

Cannot used the new default driver (`docker`) as it crashes the
PostgreSQL Docker container started via job services.
---
 .github/workflows/integration.yaml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 0a3b14434449..0dc78ef4bb1c 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -59,15 +59,12 @@ jobs:
         # ffmpeg: ffprobe needed by media datatypes
         run: sudo apt-get update && sudo apt-get -y install conntrack ffmpeg
       - name: Setup Minikube
-        id: minikube
-        uses: CodingNagger/minikube-setup-action@v1.0.6
+        uses: medyagh/setup-minikube@latest
         with:
-          k8s-version: '1.23.0'
-      - name: Launch Minikube
-        run: eval ${{ steps.minikube.outputs.launcher }}
+          driver: none
+          kubernetes-version: '1.23.0'
       - name: Check pods
-        run: |
-          kubectl get pods
+        run: kubectl get pods -A
       - uses: actions/checkout@v4
         with:
           path: 'galaxy root'