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Merge pull request #334 from lldelisle/fix_scRNAseq #204

Merge pull request #334 from lldelisle/fix_scRNAseq

Merge pull request #334 from lldelisle/fix_scRNAseq #204

Workflow file for this run

# workflow level env vars cannot be used at the job level
# https://github.community/t/how-to-set-and-access-a-workflow-variable/17335/15
name: Galaxy Workflow Tests for push and PR
on: [push, pull_request]
env:
GITHUB_USER: iwc-workflows-bot
jobs:
setup:
name: Setup cache and determine changed repositories
uses: ./.github/workflows/setup.yml
with:
python-version-list: "[\"3.11\"]"
galaxy-fork: galaxyproject
galaxy-branch: release_23.2
max-chunks: 4
# Planemo lint the changed repositories
lint:
name: Lint workflows
needs: setup
if: needs.setup.outputs.repository-list != ''
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.11']
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 1
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
- name: Install wheel
run: pip install wheel
- name: Planemo lint workflows
uses: galaxyproject/planemo-ci-action@v1
with:
mode: lint
workflows: true
repository-list: "${{ needs.setup.outputs.repository-list }}"
test:
name: Test workflows
needs: setup
if: needs.setup.outputs.repository-list != ''
uses: ./.github/workflows/test_workflows.yml
with:
galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }}
chunk-count: ${{ fromJSON(needs.setup.outputs.chunk-count) }}
chunk-list: ${{ needs.setup.outputs.chunk-list }}
python-version-list: "[\"3.11\"]"
repository-list: ${{ needs.setup.outputs.repository-list }}
galaxy-fork: galaxyproject
galaxy-branch: release_23.2
check-outputs: false
combine_outputs:
# same as tool step
name: Combine chunked test results
needs: [setup, test]
strategy:
matrix:
python-version: ['3.11']
runs-on: ubuntu-latest
steps:
- uses: actions/download-artifact@v3
with:
path: artifacts
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_{{ needs.setup.outputs.galaxy-head-sha }}
- name: Combine outputs
uses: galaxyproject/planemo-ci-action@v1
id: combine
with:
mode: combine
html-report: true
markdown-report: true
- run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
- name: Save PR number
run: echo ${{ github.event.number }} > ./upload/NR
- name: Debug PR number
run: |
cat ./upload/NR
- uses: actions/upload-artifact@v3
with:
name: 'All tool test results'
path: upload
- name: Check outputs
uses: galaxyproject/planemo-ci-action@v1
id: check
with:
mode: check
# deploy workflows to organization
deploy:
name: Deploy
needs: [setup,test,combine_outputs]
strategy:
matrix:
python-version: ['3.11']
runs-on: ubuntu-latest
if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject'
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 1
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_{{ needs.setup.outputs.galaxy-head-sha }}
- name: Install requirements for gen_crates.py
run: pip install -r workflows/requirements.txt
- name: Generate RO-Crate metadata for workflow repositories
run: python workflows/gen_crates.py workflows
- name: Set git user
run: |
git config --global user.email "[email protected]"
git config --global user.name "$GITHUB_USER"
git config --global init.defaultBranch main
- uses: fusion-engineering/setup-git-credentials@v2
with:
credentials: 'https://${{ env.GITHUB_USER }}:${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }}@github.com/'
- name: Update or create repositories in github namespace
uses: galaxyproject/planemo-ci-action@v1
with:
mode: deploy
repository-list: ${{ needs.setup.outputs.repository-list }}
workflows: true
workflow-namespace: iwc-workflows
github-token: ${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }}
deploy-report:
name: Report deploy status
needs: [deploy]
if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
runs-on: ubuntu-latest
steps:
# report to the PR if deployment failed
- name: Get PR object
uses: 8BitJonny/[email protected]
id: getpr
with:
sha: ${{ github.event.after }}
- name: Create comment
uses: peter-evans/create-or-update-comment@v3
with:
token: ${{ secrets.PAT }}
issue-number: ${{ steps.getpr.outputs.number }}
body: |
Attention: deployment ${{ needs.deploy.result }}!
https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}