Improvements for consistency #350
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |