MAINT: updates install env with latest amplicon env file #124
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name: main | |
on: | |
# build on all PRs, but only trigger push builds on `main` | |
pull_request: | |
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 }} |