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build(deps): bump the actions group across 1 directory with 4 updates

Browse Source 
Bumps the actions group with 4 updates in the / directory: [actions/checkout](https://github.com/actions/checkout), [actions/setup-python](https://github.com/actions/setup-python), [actions/cache](https://github.com/actions/cache) and [codecov/codecov-action](https://github.com/codecov/codecov-action).


Updates `actions/checkout` from 6.0.3 to 7.0.0
- [Release notes](https://github.com/actions/checkout/releases)
- [Commits](https://github.com/actions/checkout/compare/v6.0.3...v7)

Updates `actions/setup-python` from 6 to 6.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v6...v6.2.0)

Updates `actions/cache` from 5 to 5.0.5
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](https://github.com/actions/cache/compare/v5...v5.0.5)

Updates `codecov/codecov-action` from 6.0.1 to 7.0.0
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v6.0.1...v7.0.0)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: 7.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
- dependency-name: actions/setup-python
  dependency-version: 6.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions
- dependency-name: actions/cache
  dependency-version: 5.0.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
- dependency-name: codecov/codecov-action
  dependency-version: 7.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
This commit is contained in:
dependabot[bot]
2026-06-25 16:33:09 +00:00
committed by GitHub
parent 6a39ec0d05
commit 30034e3316
38 changed files with 105 additions and 105 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.github/workflows/api.yaml
+4 -4
View File
@@ -48,11 +48,11 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -62,14 +62,14 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
- name: Run tests
run: ./run_tests.sh --coverage --skip_flakey_fails -api lib/galaxy_test/api -- --num-shards=2 --shard-id=${{ matrix.chunk }}
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: api
working-directory: 'galaxy root'
.github/workflows/bioblend.yaml
+4 -4
View File
@@ -36,13 +36,13 @@ jobs:
galaxy_python_version: ['3.10']
steps:
- name: Checkout Galaxy
uses: actions/checkout@v6.0.3
uses: actions/checkout@v7.0.0
with:
fetch-depth: 1
path: galaxy
persist-credentials: false
- name: Checkout Bioblend
uses: actions/checkout@v6.0.3
uses: actions/checkout@v7.0.0
with:
repository: galaxyproject/bioblend
path: bioblend
@@ -51,7 +51,7 @@ jobs:
id: get_bioblend_python_version
run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
- name: Set up Python for BioBlend
uses: actions/setup-python@v6
uses: actions/setup-python@v6.2.0
with:
python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
- name: Install uv
@@ -59,7 +59,7 @@ jobs:
- name: Install tox
run: uv tool install tox --with tox-uv
- name: Set up Python for Galaxy
uses: actions/setup-python@v6
uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.galaxy_python_version }}
- name: Run tests
.github/workflows/build_client.yaml
+2 -2
View File
@@ -11,7 +11,7 @@ jobs:
outputs:
commit-id: ${{ steps.client-commit.outputs.commit }}
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
@@ -31,7 +31,7 @@ jobs:
run: echo "commit=$(git rev-parse HEAD 2>/dev/null)" >> $GITHUB_OUTPUT
working-directory: 'galaxy root'
- name: cache client build
uses: actions/cache@v5
uses: actions/cache@v5.0.5
id: cache
with:
key: galaxy-static-${{ steps.client-commit.outputs.commit }}
.github/workflows/build_container_image.yaml
+4 -4
View File
@@ -15,7 +15,7 @@ jobs:
name: Build container image for GHCR
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
persist-credentials: false
# https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
@@ -80,10 +80,10 @@ jobs:
tag: ${{ steps.branch.outputs.name }}
version: ${{ steps.version.outputs.version }}
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: '3.12'
# https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
@@ -260,7 +260,7 @@ jobs:
if: startsWith(github.ref, 'refs/tags/')
steps:
- name: Checkout Galaxy Helm chart
uses: actions/checkout@v6.0.3
uses: actions/checkout@v7.0.0
with:
repository: galaxyproject/galaxy-helm
persist-credentials: false
.github/workflows/cff-validator.yaml
+1 -1
View File
@@ -15,7 +15,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v6.0.3
uses: actions/checkout@v7.0.0
with:
persist-credentials: false
- name: Validate CITATION.cff
.github/workflows/check_test_class_names.yaml
+2 -2
View File
@@ -17,10 +17,10 @@ jobs:
matrix:
python-version: ['3.10']
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/client-api-test.yaml
+1 -1
View File
@@ -22,7 +22,7 @@ jobs:
client-api-test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
persist-credentials: false
- name: Read Node.js version
.github/workflows/client-unit.yaml
+1 -1
View File
@@ -16,7 +16,7 @@ jobs:
client-unit-test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
persist-credentials: false
- name: Read Node.js version
.github/workflows/codeql-analysis.yml
+1 -1
View File
@@ -40,7 +40,7 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v6.0.3
uses: actions/checkout@v7.0.0
with:
persist-credentials: false
.github/workflows/converter_tests.yaml
+3 -3
View File
@@ -31,17 +31,17 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- name: Clone galaxyproject/galaxy-test-data
uses: actions/checkout@v6.0.3
uses: actions/checkout@v7.0.0
with:
repository: galaxyproject/galaxy-test-data
path: galaxy-test-data
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/cwl_conformance.yaml
+4 -4
View File
@@ -40,11 +40,11 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -54,14 +54,14 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
- name: Run tests
run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: cwl-conformance
working-directory: 'galaxy root'
.github/workflows/db_indexes.yaml
+2 -2
View File
@@ -41,11 +41,11 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/dependencies.yaml
+2 -2
View File
@@ -10,10 +10,10 @@ jobs:
if: github.repository_owner == 'galaxyproject'
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: '3.10'
- name: Install uv
.github/workflows/deployment.yaml
+2 -2
View File
@@ -32,11 +32,11 @@ jobs:
matrix:
python-version: ['3.10']
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
fetch-depth: 0
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/docs.yaml
+2 -2
View File
@@ -29,11 +29,11 @@ jobs:
run: echo "TARGET_BRANCH=$GITHUB_BASE_REF" >> $GITHUB_ENV
- name: Show target branch name
run: echo $TARGET_BRANCH
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
fetch-depth: 0
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/first_startup.yaml
+3 -3
View File
@@ -31,12 +31,12 @@ jobs:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- name: Set up Python
uses: actions/setup-python@v6
uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -46,7 +46,7 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Restore client cache
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
.github/workflows/framework_tools.yaml
+4 -4
View File
@@ -44,11 +44,11 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -58,14 +58,14 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
- name: Run tests
run: GALAXY_TEST_USE_LEGACY_TOOL_API="${{ matrix.use-legacy-api }}" ./run_tests.sh --coverage --framework-tools
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: framework
working-directory: 'galaxy root'
.github/workflows/framework_workflows.yaml
+4 -4
View File
@@ -44,11 +44,11 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -58,14 +58,14 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
- name: Run tests
run: ./run_tests.sh --coverage --framework-workflows
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: framework-workflows
working-directory: 'galaxy root'
.github/workflows/integration.yaml
+4 -4
View File
@@ -53,11 +53,11 @@ jobs:
kubernetes-version: '1.28.0'
- name: Check pods
run: kubectl get pods -A
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -67,7 +67,7 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration
@@ -78,7 +78,7 @@ jobs:
. .ci/minikube-test-setup/start_services.sh
./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: integration
working-directory: 'galaxy root'
.github/workflows/integration_selenium.yaml
+5 -5
View File
@@ -55,11 +55,11 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -69,12 +69,12 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration-selenium
- name: Restore client cache
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
@@ -82,7 +82,7 @@ jobs:
- name: Run tests
run: ./run_tests.sh --coverage -integration test/integration_selenium
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: integration-selenium
working-directory: 'galaxy root'
.github/workflows/js_lint.yaml
+1 -1
View File
@@ -16,7 +16,7 @@ jobs:
client-unit-test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
persist-credentials: false
- name: Read Node.js version
.github/workflows/lint.yaml
+2 -2
View File
@@ -37,10 +37,10 @@ jobs:
TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
CORE_PATH: 'lib/galaxy/dependencies/pinned-requirements.txt'
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/lint_openapi_schema.yml
+3 -3
View File
@@ -25,7 +25,7 @@ jobs:
matrix:
python-version: ['3.10', '3.14']
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
@@ -39,7 +39,7 @@ jobs:
uses: pnpm/action-setup@v6
with:
package_json_file: 'galaxy root/client/package.json'
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -49,7 +49,7 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
.github/workflows/main_tools.yaml
+4 -4
View File
@@ -36,11 +36,11 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -50,14 +50,14 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
- name: Run tests
run: ./run_tests.sh --coverage --main_tools
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: main-tools
working-directory: 'galaxy root'
.github/workflows/mulled.yaml
+2 -2
View File
@@ -25,11 +25,11 @@ jobs:
matrix:
python-version: ['3.10']
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/osx_startup.yaml
+2 -2
View File
@@ -29,7 +29,7 @@ jobs:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
@@ -39,7 +39,7 @@ jobs:
miniforge-version: latest
activate-environment: ''
- name: Restore client cache
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
.github/workflows/performance.yaml
+3 -3
View File
@@ -42,11 +42,11 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -56,7 +56,7 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-performance
.github/workflows/playwright.yaml
+5 -5
View File
@@ -54,11 +54,11 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -68,12 +68,12 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-playwright
- name: Restore client cache
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
@@ -81,7 +81,7 @@ jobs:
- name: Run tests
run: ./run_tests.sh --coverage -playwright lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: playwright
working-directory: 'galaxy root'
.github/workflows/publish_artifacts.yaml
+3 -3
View File
@@ -41,11 +41,11 @@ jobs:
name: Build Python packages for PyPI
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
ref: ${{ github.event_name == 'workflow_dispatch' && inputs.release_tag || '' }}
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: '3.10'
- name: Install uv
@@ -97,7 +97,7 @@ jobs:
permissions:
id-token: write
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
ref: ${{ github.event_name == 'workflow_dispatch' && inputs.release_tag || '' }}
persist-credentials: false
.github/workflows/selenium.yaml
+5 -5
View File
@@ -55,11 +55,11 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -69,12 +69,12 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-selenium
- name: Restore client cache
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
@@ -82,7 +82,7 @@ jobs:
- name: Run tests
run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: selenium
working-directory: 'galaxy root'
.github/workflows/test_galaxy_packages.yaml
+2 -2
View File
@@ -21,11 +21,11 @@ jobs:
matrix:
python-version: ['3.10', '3.14']
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/test_galaxy_packages_for_pulsar.yaml
+2 -2
View File
@@ -23,11 +23,11 @@ jobs:
matrix:
python-version: ['3.8'] # don't upgrade, see https://github.com/galaxyproject/galaxy/pull/16649
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
.github/workflows/test_galaxy_release.yaml
+1 -1
View File
@@ -23,7 +23,7 @@ jobs:
name: Test
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
fetch-depth: 0
persist-credentials: false
.github/workflows/tool_form_harness.yaml
+5 -5
View File
@@ -64,11 +64,11 @@ 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@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -78,7 +78,7 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-playwright
@@ -91,7 +91,7 @@ jobs:
playwright install chromium --with-deps
working-directory: 'galaxy root'
- name: Restore client cache
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
@@ -99,7 +99,7 @@ jobs:
- name: Run tests
run: ./run_tests.sh --coverage -playwright lib/galaxy_test/selenium/test_tool_form_harness.py
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: tool-form-harness
working-directory: 'galaxy root'
.github/workflows/toolshed.yaml
+3 -3
View File
@@ -36,11 +36,11 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -50,7 +50,7 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-toolshed
.github/workflows/unit-postgres.yaml
+3 -3
View File
@@ -36,11 +36,11 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -50,7 +50,7 @@ jobs:
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache galaxy venv
uses: actions/cache@v5
uses: actions/cache@v5.0.5
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-unit-postgres
.github/workflows/unit.yaml
+3 -3
View File
@@ -25,11 +25,11 @@ jobs:
matrix:
python-version: ['3.10', '3.14']
steps:
- uses: actions/checkout@v6.0.3
- uses: actions/checkout@v7.0.0
with:
path: 'galaxy root'
persist-credentials: false
- uses: actions/setup-python@v6
- uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
- name: Install uv
@@ -45,7 +45,7 @@ jobs:
- name: Run tests
run: tox -e unit-coverage
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v6.0.1
- uses: codecov/codecov-action@v7.0.0
with:
flags: py-unit
working-directory: 'galaxy root'
.github/workflows/zizmor.yaml
+1 -1
View File
@@ -20,7 +20,7 @@ jobs:
security-events: write # Required for upload-sarif (used by zizmor-action) to upload SARIF files.
steps:
- name: Checkout repository
uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
with:
persist-credentials: false