Merge pull request #23222 from galaxyproject/dependabot/github_actions/actions-51b513255e

Bump the actions group across 1 directory with 6 updates
This commit is contained in:
Nicola Soranzo
2026-08-14 10:53:14 +02:00
committed by GitHub
38 changed files with 82 additions and 82 deletions
+2 -2
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@@ -57,12 +57,12 @@ jobs:
- if: github.event_name == 'workflow_dispatch' && inputs.use_cached_toolbox
run: |
echo "GALAXY_CONFIG_OVERRIDE_USE_CACHED_TOOLBOX=true" >> $GITHUB_ENV
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+3 -3
View File
@@ -36,13 +36,13 @@ jobs:
galaxy_python_version: ['3.10']
steps:
- name: Checkout Galaxy
uses: actions/checkout@v7.0.0
uses: actions/checkout@v7.0.1
with:
fetch-depth: 1
path: galaxy
persist-credentials: false
- name: Checkout Bioblend
uses: actions/checkout@v7.0.0
uses: actions/checkout@v7.0.1
with:
repository: galaxyproject/bioblend
path: bioblend
@@ -51,7 +51,7 @@ jobs:
id: get_bioblend_python_version
run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
- name: Install tox
run: uv tool install --python ${BIOBLEND_PYTHON_VERSION} tox --with tox-uv
env:
+1 -1
View File
@@ -11,7 +11,7 @@ jobs:
outputs:
commit-id: ${{ steps.client-commit.outputs.commit }}
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
+7 -7
View File
@@ -15,7 +15,7 @@ jobs:
name: Build container image for GHCR
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
persist-credentials: false
# https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
@@ -52,7 +52,7 @@ jobs:
platforms: linux/amd64
- name: Login to GHCR
uses: docker/login-action@v4.4.0
uses: docker/login-action@v4.6.0
with:
registry: ghcr.io
username: ${{ github.repository_owner }}
@@ -80,10 +80,10 @@ jobs:
tag: ${{ steps.branch.outputs.name }}
version: ${{ steps.version.outputs.version }}
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
persist-credentials: false
- uses: actions/setup-python@v6.3.0
- uses: actions/setup-python@v7.0.0
with:
python-version: '3.14'
# https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
@@ -114,13 +114,13 @@ jobs:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v4.2.0
- name: Login to quay.io
uses: docker/login-action@v4.4.0
uses: docker/login-action@v4.6.0
with:
registry: quay.io
username: ${{ secrets.QUAY_USERNAME }}
password: ${{ secrets.QUAY_PASSWORD }}
- name: Login to DockerHub
uses: docker/login-action@v4.4.0
uses: docker/login-action@v4.6.0
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_PASSWORD }}
@@ -260,7 +260,7 @@ jobs:
if: startsWith(github.ref, 'refs/tags/')
steps:
- name: Checkout Galaxy Helm chart
uses: actions/checkout@v7.0.0
uses: actions/checkout@v7.0.1
with:
repository: galaxyproject/galaxy-helm
persist-credentials: false
+1 -1
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@@ -15,7 +15,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v7.0.0
uses: actions/checkout@v7.0.1
with:
persist-credentials: false
- name: Validate CITATION.cff
@@ -18,11 +18,11 @@ jobs:
matrix:
python-version: ['3.10']
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python dependencies
+1 -1
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@@ -22,7 +22,7 @@ jobs:
client-api-test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
persist-credentials: false
- name: Read Node.js version
+1 -1
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@@ -16,7 +16,7 @@ jobs:
client-unit-test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
persist-credentials: false
- name: Read Node.js version
+4 -4
View File
@@ -40,13 +40,13 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v7.0.0
uses: actions/checkout@v7.0.1
with:
persist-credentials: false
# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v4.37.1
uses: github/codeql-action/init@v4.37.6
with:
languages: ${{ matrix.language }}
# If you wish to specify custom queries, you can do so here or in a config file.
@@ -62,7 +62,7 @@ jobs:
# 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@v4.37.1
uses: github/codeql-action/autobuild@v4.37.6
# ️ 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
@@ -76,4 +76,4 @@ jobs:
# make release
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v4.37.1
uses: github/codeql-action/analyze@v4.37.6
+3 -3
View File
@@ -31,18 +31,18 @@ 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@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Clone galaxyproject/galaxy-test-data
uses: actions/checkout@v7.0.0
uses: actions/checkout@v7.0.1
with:
repository: galaxyproject/galaxy-test-data
path: galaxy-test-data
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Move test data
+2 -2
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@@ -40,12 +40,12 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
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@@ -41,12 +41,12 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install tox
+2 -2
View File
@@ -10,11 +10,11 @@ jobs:
if: github.repository_owner == 'galaxyproject'
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: '3.10'
- name: Update dependencies
+2 -2
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@@ -32,12 +32,12 @@ jobs:
matrix:
python-version: ['3.10']
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
fetch-depth: 0
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -29,12 +29,12 @@ jobs:
run: echo "TARGET_BRANCH=$GITHUB_BASE_REF" >> $GITHUB_ENV
- name: Show target branch name
run: echo $TARGET_BRANCH
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
fetch-depth: 0
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python dependencies
+2 -2
View File
@@ -31,12 +31,12 @@ jobs:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Restore client cache
+2 -2
View File
@@ -44,12 +44,12 @@ 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@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -44,12 +44,12 @@ 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@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+4 -4
View File
@@ -40,13 +40,13 @@ jobs:
path: '${{ runner.temp }}/mulled-resolution-seed'
- name: Check out Galaxy for mulled-cache
if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
uses: actions/checkout@v7.0.0
uses: actions/checkout@v7.0.1
with:
path: 'galaxy cache source'
persist-credentials: false
- name: Install uv
if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: '3.10'
- name: Fetch Biocontainers repository index
@@ -112,12 +112,12 @@ jobs:
kubernetes-version: '1.28.0'
- name: Check pods
run: kubectl get pods -A
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -53,12 +53,12 @@ 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@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+1 -1
View File
@@ -16,7 +16,7 @@ jobs:
client-unit-test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
persist-credentials: false
- name: Read Node.js version
+2 -2
View File
@@ -37,11 +37,11 @@ jobs:
TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
CORE_PATH: 'lib/galaxy/dependencies/pinned-requirements.txt'
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install tox
+2 -2
View File
@@ -25,7 +25,7 @@ jobs:
matrix:
python-version: ['3.10', '3.14']
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
@@ -40,7 +40,7 @@ jobs:
with:
package_json_file: 'galaxy root/client/package.json'
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -36,12 +36,12 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -25,12 +25,12 @@ jobs:
matrix:
python-version: ['3.10']
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Apptainer's singularity
+2 -2
View File
@@ -29,7 +29,7 @@ jobs:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
@@ -45,7 +45,7 @@ jobs:
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
path: 'galaxy root/static'
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
- name: Install tox
run: uv tool install tox --with tox-uv
- name: Run tests
+2 -2
View File
@@ -42,12 +42,12 @@ 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@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -54,12 +54,12 @@ 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@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+3 -3
View File
@@ -41,12 +41,12 @@ jobs:
name: Build Python packages for PyPI
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
ref: ${{ github.event_name == 'workflow_dispatch' && inputs.release_tag || '' }}
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
enable-cache: false
python-version: '3.10'
@@ -95,7 +95,7 @@ jobs:
permissions:
id-token: write
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
ref: ${{ github.event_name == 'workflow_dispatch' && inputs.release_tag || '' }}
persist-credentials: false
+2 -2
View File
@@ -53,12 +53,12 @@ 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@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -21,12 +21,12 @@ jobs:
matrix:
python-version: ['3.10', '3.14']
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install ffmpeg
@@ -25,12 +25,12 @@ jobs:
matrix:
python-version: ['3.10']
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Apptainer's singularity
+1 -1
View File
@@ -23,7 +23,7 @@ jobs:
name: Test
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
fetch-depth: 0
persist-credentials: false
+2 -2
View File
@@ -64,12 +64,12 @@ 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@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -36,12 +36,12 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -36,12 +36,12 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install Python
+2 -2
View File
@@ -25,12 +25,12 @@ jobs:
matrix:
python-version: ['3.10', '3.14']
steps:
- uses: actions/checkout@v7.0.0
- uses: actions/checkout@v7.0.1
with:
path: 'galaxy root'
persist-credentials: false
- name: Install uv
uses: astral-sh/setup-uv@v8.3.2
uses: astral-sh/setup-uv@v9.0.0
with:
python-version: ${{ matrix.python-version }}
- name: Install ffmpeg
+2 -2
View File
@@ -20,9 +20,9 @@ jobs:
security-events: write # Required for upload-sarif (used by zizmor-action) to upload SARIF files.
steps:
- name: Checkout repository
uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
with:
persist-credentials: false
- name: Run zizmor 🌈
uses: zizmorcore/zizmor-action@6599ee8b7a49aef6a770f63d261d214911a7ce02 # v0.6.0
uses: zizmorcore/zizmor-action@3dc1ecc9bcb9e94e9b2c709687979e1298497054 # v0.6.2