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iqbal-lab-org / pling

Plasmid analysis using rearrangement distances
MIT License
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Add an integration test, modularise run_pling.py and add CI pipeline #18

Closed leoisl closed 9 months ago

leoisl commented 9 months ago

This PR:

  1. Adds an integration end-to-end test (tests/integration_test/test_integration_test.py) that tests pling on 4 real plasmids and checks if it produces the predicted distance matrix (tests/integration_test/data/all_plasmids_matrix.truth.dist);
  2. To do this, a modularisation of run_pling.py was needed (basically just splitting the code in this source file into a few functions);
  3. Some refactoring of the tests;
  4. A CI pipeline that ensure that the tests and pling works on linux and mac on python versions 3.8, 3.9, 3.10 and 3.11 with minimum deps (just needs python, snakemake and mamba). Any code pushed or PR-ed to the main branch will now run the CI;

Closes #17

leoisl commented 9 months ago

Ready for review!

leoisl commented 9 months ago

Conflict solved!