update introductory list of interfaces to include R API #127
Workflow file for this run
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| name: main | |
| on: | |
| # build on all PRs, but only trigger push builds on `main` | |
| pull_request: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: lint | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: true | |
| VALIDATE_JSCPD: false | |
| DEFAULT_BRANCH: main | |
| doc-build: | |
| needs: lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout source | |
| uses: actions/checkout@v2 | |
| - name: setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: 3.8 | |
| - name: install latest QIIME 2 amplicon distro (passed) | |
| run: | | |
| envFile=qiime2-amplicon-ubuntu-latest-conda.yml | |
| wget https://data.qiime2.org/distro/amplicon/$envFile | |
| conda env create -q -p ./test-env --file $envFile | |
| - name: install dependencies | |
| run: | | |
| conda install -p ./test-env -q -y \ | |
| -c conda-forge \ | |
| -c bioconda \ | |
| -c defaults \ | |
| --override-channels pip | |
| - name: install pip dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate ./test-env | |
| pip install -r book/requirements.txt | |
| - name: build book preview | |
| shell: bash -l {0} | |
| run: | | |
| conda activate ./test-env | |
| make build_preview | |
| - name: build full book | |
| shell: bash -l {0} | |
| env: | |
| Q2DOC_HTML_BASEURL: https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/ | |
| run: | | |
| conda activate ./test-env | |
| make build_full | |
| - name: deploy to docs | |
| uses: burnett01/rsync-deployments@5.2 | |
| if: ${{ github.ref == 'refs/heads/main' }} | |
| with: | |
| switches: -avzr --delete --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r | |
| path: book/_build/html/ | |
| remote_path: ${{ secrets.STATIC_SITE_WWW }} | |
| remote_host: ${{ secrets.STATIC_SITE_HOST }} | |
| remote_user: ${{ secrets.STATIC_SITE_USER }} | |
| remote_key: ${{ secrets.STATIC_SITE_PEM }} |