Fixed a bug that was causing some custom sequencing error models to e… #219
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| # This workflow configures the environment and executes NEAT read-simulator tests using relative paths for a series of configuration files individually | |
| # For more information on using Python with GitHub Actions, refer to: | |
| # https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: NEAT Unit Tests | |
| on: | |
| push: | |
| branches: [develop, main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| detailed_test_execution: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: s-weigand/[email protected] | |
| with: | |
| conda-channels: bioconda, conda-forge | |
| activate-conda: true | |
| repository: NCSA/NEAT | |
| - name: Environment Setup | |
| run: | | |
| conda env create -f environment.yml -n test_neat | |
| source activate test_neat | |
| poetry install | |
| - name: Run NEAT Simulation for config_test1 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test1.yml -o ../outputs/test1_read-simulator | |
| - name: Run NEAT Simulation for config_test2 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test2.yml -o ../outputs/test2_read-simulator | |
| - name: Run NEAT Simulation for config_test3 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test3.yml -o ../outputs/test3_read-simulator | |
| - name: Run NEAT Simulation for config_test4 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test4.yml -o ../outputs/test4_read-simulator | |
| - name: Run NEAT Simulation for config_test5 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test5.yml -o ../outputs/test5_read-simulator | |
| - name: Run NEAT Simulation for config_test6 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test6.yml -o ../outputs/test6_read-simulator | |
| - name: Run NEAT Simulation for config_test7 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test7.yml -o ../outputs/test7_read-simulator | |
| - name: Run NEAT Simulation for config_test8 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test8.yml -o ../outputs/test8_read-simulator | |
| - name: Run NEAT Simulation for config_test9 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test9.yml -o ../outputs/test9_read-simulator | |
| - name: Run NEAT Simulation for config_test10 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test10.yml -o ../outputs/test10_read-simulator | |
| - name: Run NEAT Simulation for config_test11 | |
| run: | | |
| source activate test_neat | |
| python -m neat --log-level DEBUG read-simulator -c data/test_configs/config_test11.yml -o ../outputs/test11_read-simulator |