Update bactopia-to-md.py #189
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| name: Publish Docs On Change | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: [ main, master] | |
| jobs: | |
| build: | |
| name: Deploy docs | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -x -l {0} | |
| steps: | |
| - name: Checkout main | |
| uses: actions/checkout@v2 | |
| - name: Pull Bactopia | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: bactopia/bactopia | |
| path: bactopia | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: bactopia | |
| auto-activate-base: false | |
| - name: Setup Docs Environment | |
| env: | |
| MKDOCS_INSIDERS: ${{ secrets.MKDOCS_INSIDERS }} | |
| run: | | |
| # Conda dependencies | |
| conda install -c conda-forge -c bioconda nextflow jinja2 jq pyyaml 'python>3.6' | |
| # MkDocs dependencies | |
| pip install \ | |
| "cairosvg>=2.5" \ | |
| "mkdocs-git-committers-plugin-2<1" \ | |
| "mkdocs-git-revision-date-localized-plugin>=1.0" \ | |
| "mkdocs-minify-plugin>=0.3" \ | |
| "mkdocs-rss-plugin>=1.1" \ | |
| "mkdocs-redirects>=1.0" \ | |
| "pillow<10" \ | |
| mike | |
| # MkDocs Insiders | |
| pip install \ | |
| git+https://${MKDOCS_INSIDERS}@github.com/rpetit3/mkdocs-material-insiders.git | |
| mkdocs --version | |
| - name: Convert Bactopia to Docs | |
| run: | | |
| nextflow config -flat $GITHUB_WORKSPACE/bactopia/main.nf > $GITHUB_WORKSPACE/bactopia/nextflow_config.txt | |
| python3 $GITHUB_WORKSPACE/bin/bactopia-to-md.py $GITHUB_WORKSPACE/bactopia $GITHUB_WORKSPACE | |
| cp -f $GITHUB_WORKSPACE/bactopia/CHANGELOG.md $GITHUB_WORKSPACE/docs/changelog.md | |
| rm -rf $GITHUB_WORKSPACE/bactopia | |
| - name: Deploy Docs | |
| run: | | |
| git fetch origin gh-pages --depth=1 | |
| git config user.name "GitHub Actions" | |
| git config user.email [email protected] | |
| LATEST_RELEASE=$(curl -sL https://api.github.com/repos/bactopia/bactopia/releases/latest | jq -r ".tag_name") | |
| echo ${LATEST_RELEASE} | |
| mike deploy --push --update-aliases ${LATEST_RELEASE} latest | |
| mike set-default --push latest | |
| - name: Commit changes | |
| uses: EndBug/add-and-commit@v7 | |
| with: | |
| message: "ci - auto build from bactopia" | |
| committer_name: GitHub Actions | |
| committer_email: [email protected] | |
| add: 'mkdocs.yml docs/' |