Fix pulling data doc test #261
Workflow file for this run
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| # ----------------------------------------------------------------------------- | |
| # Continuous Intergration for Vivarium Inputs | |
| # - invoked on push and pull_request | |
| # - test under at least 3 versions of python | |
| # - look for upstream branches and use if they exist | |
| # ----------------------------------------------------------------------------- | |
| name: build | |
| on: [push, pull_request, workflow_dispatch] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| defaults: | |
| run: | |
| shell: bash -le {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: test_env_python${{ matrix.python-version }} | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| - name: Install hdf5 libs | |
| run: | | |
| sudo apt-get install libhdf5-dev | |
| - name: get upstream branch name | |
| run: | | |
| if "${{ github.event_name == 'pull_request' }}" ; then | |
| echo "branch_name=${GITHUB_HEAD_REF}" >> $GITHUB_ENV | |
| else | |
| echo "branch_name=${GITHUB_REF_NAME}" >> $GITHUB_ENV | |
| fi | |
| - name: Conda info | |
| run: | | |
| conda info | |
| conda list | |
| echo branch_name = ${branch_name} | |
| - name: check for upstream vivarium | |
| run: | | |
| if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium.git ${branch_name} == "0"; then | |
| echo "upstream_vivarium_exist=true" >> $GITHUB_ENV | |
| else | |
| echo "upstream_vivarium_exist=false" >> $GITHUB_ENV | |
| fi | |
| - name: check for upstream vivarium_public_health | |
| run: | | |
| if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium_public_health.git ${branch_name} == "0"; then | |
| echo "upstream_vivarium_public_health_exist=true" >> $GITHUB_ENV | |
| else | |
| echo "upstream_vivarium_public_health_exist=false" >> $GITHUB_ENV | |
| fi | |
| - name: check for upstream gbd_mapping | |
| run: | | |
| if git ls-remote --exit-code --heads https://github.com/ihmeuw/gbd_mapping.git ${branch_name} == "0"; then | |
| echo "upstream_gbd_mapping_exist=true" >> $GITHUB_ENV | |
| else | |
| echo "upstream_gbd_mapping_exist=false" >> $GITHUB_ENV | |
| fi | |
| - name: print environment values | |
| run: | | |
| cat $GITHUB_ENV | |
| - name: Retrieve upstream vivarium | |
| if: env.upstream_vivarium_exist == 'true' | |
| run: | | |
| echo "Cloning vivarium upstream branch: ${branch_name}" | |
| git clone --branch=${branch_name} https://github.com/ihmeuw/vivarium.git | |
| pushd vivarium | |
| pip install . | |
| popd | |
| - name: Retrieve upstream vivarium_public_health | |
| if: env.upstream_vivarium_public_health_exist == 'true' | |
| run: | | |
| echo "Cloning vivarium_public_health upstream branch: ${branch_name}" | |
| git clone --branch=${branch_name} https://github.com/ihmeuw/vivarium_public_health.git | |
| pushd vivarium_public_health | |
| pip install . | |
| popd | |
| - name: Retrieve upstream gbd_mapping | |
| if: env.upstream_gbd_mapping_exist == 'true' | |
| run: | | |
| echo "Cloning upstream gbd_mapping branch: ${branch_name}" | |
| git clone --branch=${branch_name} https://github.com/ihmeuw/gbd_mapping.git | |
| pushd gbd_mapping | |
| pip install . | |
| popd | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[docs,test] | |
| - name: Lint | |
| run: | | |
| pip install black==22.3.0 isort | |
| black . --check --diff | |
| isort . --check --verbose --only-modified --diff | |
| - name: Test | |
| run: | | |
| pytest ./tests | |
| - name: Doc build | |
| run: | | |
| make html -C docs/ SPHINXOPTS="-W --keep-going -n" | |
| - name: Doctest | |
| run: | | |
| make doctest -C docs/ |