Improvements for consistency #345
Workflow file for this run
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| name: unit-tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| jobs: | |
| unit-tests: | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: hopkinsidd/flepimop:latest-dev | |
| options: --user root | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Set up Rprofile | |
| run: | | |
| cp build/docker/Docker.Rprofile $HOME/.Rprofile | |
| cp /home/app/.bashrc $HOME/.bashrc | |
| shell: bash | |
| - name: Install the gempyor package | |
| run: | | |
| source /var/python/3.10/virtualenv/bin/activate | |
| python -m pip install --upgrade pip | |
| python -m pip install flepimop/gempyor_pkg/ | |
| shell: bash | |
| - name: Install local R packages | |
| run: Rscript build/local_install.R | |
| shell: bash | |
| - name: Run gempyor tests | |
| run: | | |
| source /var/python/3.10/virtualenv/bin/activate | |
| cd flepimop/gempyor_pkg | |
| pytest -s | |
| shell: bash | |
| - name: Run flepicommon tests | |
| run: | | |
| setwd("flepimop/R_packages/flepicommon") | |
| devtools::test(stop_on_failure=TRUE) | |
| shell: Rscript {0} | |
| - name: Run inference tests | |
| run: | | |
| setwd("flepimop/R_packages/inference") | |
| devtools::test(stop_on_failure=TRUE) | |
| shell: Rscript {0} | |
| # - name: Run integration tests | |
| # env: | |
| # CENSUS_API_KEY: ${{ secrets.CENSUS_API_KEY }} | |
| # run: | | |
| # Rscript build/local_install.R | |
| # cd test | |
| # source /var/python/3.10/virtualenv/bin/activate | |
| # pytest run_tests.py | |
| # shell: bash |