Merge pull request #128 from mskcc-omics-workflows/bugfix/pr_template #260
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name: Meta Yaml to MD | |
# Controls when the workflow will run | |
on: | |
push: | |
branches: [main] | |
merge_group: | |
types: [checks_requested] | |
branches: [main] | |
# Cancel if a newer run is started | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
# A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
jobs: | |
pytest-changes: | |
name: pytest-changes | |
runs-on: ubuntu-latest | |
outputs: | |
# Expose matched filters as job 'modules' output variable | |
modules: ${{ steps.filter.outputs.changes }} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 2 # To retrieve the preceding commit. | |
# TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
- uses: mirpedrol/paths-filter@main | |
id: filter | |
with: | |
filters: "tests/config/pytest_modules.yml" | |
token: "" | |
nf-test-changes: | |
name: nf-test-changes | |
runs-on: ubuntu-latest | |
outputs: | |
# Expose matched filters as job 'modules' output variable | |
modules: ${{ steps.filter.outputs.changes }} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 2 # To retrieve the preceding commit. | |
- name: Combine all tags.yml files | |
id: get_tags | |
run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
- name: debug | |
run: cat .github/tags.yml | |
# TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
- uses: mirpedrol/paths-filter@main | |
id: filter | |
with: | |
filters: ".github/tags.yml" | |
token: "" | |
new_feature: | |
name: new feature | |
runs-on: ubuntu-latest | |
if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }} | |
needs: [pytest-changes, nf-test-changes] | |
strategy: | |
fail-fast: false | |
matrix: | |
tags: | |
[ | |
"${{ fromJson(needs.pytest-changes.outputs.modules) }}", | |
"${{ fromJson(needs.nf-test-changes.outputs.modules) }}", | |
] | |
# Steps represent a sequence of tasks that will be executed as part of the job | |
steps: | |
- run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event." | |
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
- name: setup python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: "3.10" # install the python version needed | |
- uses: actions/checkout@v4 | |
with: | |
ref: docs | |
- name: Update name of ${{ matrix.tags }} | |
run: | | |
MATRIX_FRAGMENT="${{ matrix.tags }}" | |
TEMP_NAME=$(echo $MATRIX_FRAGMENT | sed 's/subworkflows\///g') | |
SW_NAME=$(echo $TEMP_NAME | sed 's/modules\///g') | |
echo "SW_NAME=$SW_NAME" >> $GITHUB_ENV | |
- name: Rename md file | |
id: replace_slash | |
run: | | |
FRAGMENT="${{ env.SW_NAME }}" | |
MD_NAME=$(echo $FRAGMENT | sed 's/\//_/g') | |
echo "MD_NAME=$MD_NAME" >> $GITHUB_ENV | |
echo "${MD_NAME}" | |
- name: Download convertor from yml to md | |
run: | | |
curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/yaml_to_md.py | |
curl -o ${{ github.workspace }}/requirements.txt https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/requirements.txt | |
- name: Give convertor permissions | |
run: chmod +x yaml_to_md.py | |
- name: Install python packages | |
run: | | |
python -m pip install --upgrade pip | |
pip install -r ${{ github.workspace }}/requirements.txt | |
- uses: jaywcjlove/github-action-read-file@main | |
id: cat_file_module | |
with: | |
path: modules/msk/${{ env.SW_NAME }}/meta.yml | |
- name: Write Module yaml to temp | |
if: ${{ steps.cat_file_module.outputs.size }} | |
id: write_yml_module | |
run: | | |
echo "${{ steps.cat_file_module.outputs.size }}" | |
echo '${{ steps.cat_file_module.outputs.content }}' > ${{ github.workspace }}/temp.yml | |
FEATURE_TYPE="modules" | |
SUMMARY_TYPE="module" | |
SUBWORKFLOW="" | |
echo "FEATURE_TYPE=$FEATURE_TYPE" >> $GITHUB_ENV | |
echo "SUMMARY_TYPE=$SUMMARY_TYPE" >> $GITHUB_ENV | |
echo "SUBWORKFLOW=$SUBWORKFLOW" >> $GITHUB_ENV | |
- uses: jaywcjlove/github-action-read-file@main | |
if: ${{ steps.cat_file_module.outputs.size == '' }} | |
id: cat_file_subworkflow | |
with: | |
path: subworkflows/msk/${{ env.SW_NAME }}/meta.yml | |
- name: Write Subworkflow yaml to temp | |
if: ${{ steps.cat_file_subworkflow.outputs.size }} | |
id: write_yml_subworkflow | |
run: | | |
echo "${{ steps.cat_file_subworkflow.outputs.size }}" | |
echo '${{ steps.cat_file_subworkflow.outputs.content }}' > ${{ github.workspace }}/temp.yml | |
FEATURE_TYPE="subworkflows" | |
SUMMARY_TYPE="subworkflow" | |
SUBWORKFLOW="--subworkflows" | |
echo "FEATURE_TYPE=$FEATURE_TYPE" >> $GITHUB_ENV | |
echo "SUMMARY_TYPE=$SUMMARY_TYPE" >> $GITHUB_ENV | |
echo "SUBWORKFLOW=$SUBWORKFLOW" >> $GITHUB_ENV | |
- name: Run convertor to generate md file for new module | |
run: | | |
echo ${{ matrix.tags }} | |
python ${{ github.workspace }}/yaml_to_md.py all --yaml-file ${{ github.workspace }}/temp.yml --output-file ./modules/${{ env.MD_NAME }}.md --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json ${{ env.SUBWORKFLOW }} | |
- name: Check file existence for modules | |
id: check_files | |
uses: andstor/file-existence-action@v1 | |
with: | |
branch: docs | |
files: ${{ env.FEATURE_TYPE}}/${{ env.MD_NAME }}.md | |
- name: Add to SUMMARY for new features | |
if: ${{ (steps.check_files.outputs.files_exists == 'false') }} | |
run: | | |
curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/develop/.github/workflows/update_summary.py | |
python ${{ github.workspace }}/update_summary.py SUMMARY.md "* [${{ env.MD_NAME }}](${{ env.FEATURE_TYPE }}/${{ env.MD_NAME }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md | |
mv tmp_summary.md SUMMARY.md | |
- uses: EndBug/add-and-commit@v9 | |
with: | |
default_author: github_actions | |
message: "add doc for ${{ matrix.tags }}" | |
add: '["*/*.md --force", "SUMMARY.md --force"]' | |
cwd: "./" |