Fix .dockstore.yml and other minor things #134
Workflow file for this run
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# 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: "[\"3.7\"]" | |
galaxy-fork: galaxyproject | |
galaxy-branch: release_23.1 | |
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: ['3.7'] | |
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: "[\"3.7\"]" | |
repository-list: ${{ needs.setup.outputs.repository-list }} | |
galaxy-fork: galaxyproject | |
galaxy-branch: release_23.1 | |
check-outputs: false | |
combine_outputs: | |
# same as tool step | |
name: Combine chunked test results | |
needs: [setup, test] | |
strategy: | |
matrix: | |
python-version: ['3.7'] | |
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 | |
- 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: ['3.7'] | |
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 }} |