docs #298
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| name: docs | |
| on: | |
| pull_request: | |
| push: | |
| schedule: | |
| - cron: '40 14 * * *' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build-and-test: | |
| runs-on: "ubuntu-latest" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| # This has to be done after the cache is restored, because | |
| # the channel setup is not cached as it resides in the home directory. | |
| # We could use a system-wide (and therefore cached) channel setup, | |
| # but mamba does not support that at the time of implementation | |
| # (it ignores settings made with --system). | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: restrict number of built recipes | |
| if: >- | |
| ${{ | |
| (github.ref != 'refs/heads/main') && | |
| (!contains(github.event.head_commit.message, '[build all recipes]')) | |
| }} | |
| run: | | |
| # For testing, use BIOCONDA_FILTER_RECIPES=10 or some small-ish number, | |
| # or BIOCONDA_FILTER_RECIPES=".*" or other regex. If these are set, | |
| # you'll get warnings like "Problem in conda domain: field is supposed | |
| # to use role 'depends', but that role is not in the domain', which is | |
| # expected. | |
| # | |
| # If unset, pages will be built for all recipes. | |
| # export BIOCONDA_FILTER_RECIPES=10 | |
| echo "BIOCONDA_FILTER_RECIPES=10" >> $GITHUB_ENV | |
| - name: build docs | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| export BIOCONDA_FILTER_RECIPES=${{env.BIOCONDA_FILTER_RECIPES}} | |
| conda activate bioconda | |
| make clean html SPHINXOPTS="-T -j1" | |
| touch build/html/.nojekyll | |
| # Upload the built docs as an artifact for inspection (even on PRs). This | |
| # will show up in the Actions web interface. | |
| - name: push artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: doc | |
| path: build/html | |
| # Start the SSH agent so that subsequent steps don't need additional SSH | |
| # setup. The private key has been added as a secret to this repo (the one | |
| # running these tests), and the public key has been added as an allowed | |
| # deploy key for the bioconda.github.io repo (the one accepting pushes from | |
| # this test). Note that this method ensures that the key is never saved to | |
| # disk, and GitHub Actions automatically protects the secrets from being | |
| # echoed. | |
| - name: ssh setup | |
| if: ${{ (github.ref == 'refs/heads/main') }} | |
| env: | |
| SSH_AUTH_SOCK: /tmp/ssh_agent.sock | |
| run: | | |
| mkdir -p ~/.ssh | |
| ssh-keyscan github.com >> ~/.ssh/known_hosts | |
| ssh-agent -a $SSH_AUTH_SOCK > /dev/null | |
| ssh-add - <<< "${{ secrets.SSH_DEPLOY_KEY }}" | |
| # Clone the bioconda.github.io repo, clean it out completely, then copy the | |
| # docs just built above into the repo and commit. Uses SSH as set up above. | |
| - name: push docs to bioconda.github.io repo | |
| if: ${{ (github.ref == 'refs/heads/main') }} | |
| env: | |
| SSH_AUTH_SOCK: /tmp/ssh_agent.sock | |
| run: | | |
| here=$(pwd) | |
| REPODIR=/tmp/bioconda.github.io | |
| git clone git@github.com:bioconda/bioconda.github.io $REPODIR | |
| cd $REPODIR | |
| git checkout master | |
| git rm -rf $REPODIR/* | |
| cp -r $here/build/html/* $REPODIR | |
| git add -f . | |
| # Only commit and push if there are changes. | |
| if git diff origin/master --quiet; then | |
| echo "no changes to push to docs repo"; | |
| else | |
| echo "Diffs will be pushed to bioconda.github.io" | |
| git config --global user.email "action@github.com" | |
| git config --global user.name "GitHub Action" | |
| git commit -m "Updated docs to commit ${GITHUB_SHA}" | |
| git push origin master --force | |
| fi |