test: Fix runSimulation tests #184
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| # The validation pipeline. Currently, runs the example provided by OpenMalaria | |
| # itself and generates the same xml (in terms of input) via | |
| # openMalariaUtilities. Both files are used for a simulation and the two output | |
| # files compared, as they should be identical. | |
| # REVIEW Over time, this should be extended to a more involved example and also | |
| # include steps like the data processing. As this workflow gets more | |
| # involved, it is probably a good idea to limit it to the master branch | |
| # or only to releases. | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| name: OpenMalaria validation | |
| jobs: | |
| job_1: | |
| name: OpenMalaria example | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup OpenMalaria | |
| shell: bash | |
| run : | | |
| wget https://github.com/SwissTPH/openmalaria/releases/download/schema-44.0/openMalaria-ubuntu-20.04.tar.gz -O openMalaria-ubuntu-20.04.tar.gz | |
| tar -xf openMalaria-ubuntu-20.04.tar.gz && rm openMalaria-ubuntu-20.04.tar.gz | |
| sudo apt-get install -y libboost-dev libgsl-dev libxerces-c-dev xsdcxx | |
| echo "$GITHUB_WORKSPACE/openMalaria-ubuntu-20.04" >> $GITHUB_PATH | |
| - name: Run OpenMalaria example xml | |
| shell: bash | |
| run : | | |
| cd openMalaria-ubuntu-20.04 | |
| openMalaria -s example_scenario.xml --verbose | |
| - name: Store OpenMalaria output | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: output-OM | |
| path: openMalaria-ubuntu-20.04/output.txt | |
| job_2: | |
| name: openMalariaUtilities example | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: false | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: devtools | |
| - name: Setup OpenMalaria | |
| shell: bash | |
| run : | | |
| wget https://github.com/SwissTPH/openmalaria/releases/download/schema-44.0/openMalaria-ubuntu-20.04.tar.gz -O openMalaria-ubuntu-20.04.tar.gz | |
| tar -xf openMalaria-ubuntu-20.04.tar.gz && rm openMalaria-ubuntu-20.04.tar.gz | |
| sudo apt-get install -y libboost-dev libgsl-dev libxerces-c-dev xsdcxx | |
| echo "$GITHUB_WORKSPACE/openMalaria-ubuntu-20.04" >> $GITHUB_PATH | |
| - name: Run OMU script in R | |
| run: | | |
| source(".github/workflows/example.R") | |
| shell: Rscript {0} | |
| - name: Store package output | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: output-package | |
| path: exp_test/outputs/exp_test_1_out.txt | |
| job_3: | |
| name: Compare results | |
| needs: [job_1, job_2] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Download result from job 1 | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: output-OM | |
| - name: Download result from job 2 | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: output-package | |
| - name: Compare results | |
| shell: bash | |
| run: | | |
| if cmp --silent -- exp_test_1_out.txt output.txt; then | |
| echo "### SUCCESS: Output files are identical! ###" | |
| exit 0 | |
| else | |
| echo "### Warning: Output files differ! ###" | |
| exit 1 | |
| fi |