various fixes after msprime api updates #2341
Workflow file for this run
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| name: Build and deploy docs | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| tags: | |
| - '*' | |
| jobs: | |
| build-deploy-docs: | |
| # Only run this job on the popsim-consortium repository. | |
| # The job would fail on forks anyhow, because the secret used below | |
| # POPSIMBOT_STDPOPSIM_DOCS_TOKEN | |
| # won't be valid. But to avoid confusion, we explicitly restrict the scope. | |
| # See https://github.com/popsim-consortium/stdpopsim/issues/662 | |
| if: github.repository == 'popsim-consortium/stdpopsim' | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install deps | |
| run: | | |
| python -m pip install wheel | |
| python -m pip install numpy==1.19.2 # for scikit-allel | |
| python -m pip install -r requirements/CI/requirements.txt | |
| # Install the local package so that stdpopsim is in the path, | |
| # which is needed for generating docs `command-output`. | |
| python -m pip install . | |
| - name: Build Docs | |
| run: make -C docs | |
| - name: Checkout docs site | |
| if: (!github.event.pull_request) | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: popsim-consortium/stdpopsim-docs | |
| token: ${{ secrets.POPSIMBOT_STDPOPSIM_DOCS_TOKEN }} | |
| path: stdpopsim-docs | |
| - name: Copy our docs to the tag specific location | |
| if: (!github.event.pull_request) | |
| run: | | |
| cd stdpopsim-docs | |
| export DEST=`echo ${GITHUB_REF} | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g"` | |
| rm -rf $DEST | |
| cp -r ../docs/_build/html $DEST | |
| - name: Commit and push the docs | |
| if: (!github.event.pull_request) | |
| run: | | |
| cd stdpopsim-docs | |
| git config user.name PopSim-bot | |
| git config user.email graham.gower+popsim-bot@gmail.com | |
| git add . | |
| git diff-index --quiet HEAD || git commit -m "Automated doc build for ${GITHUB_REF}" | |
| git push |