increase our testing coverage #205
Description
Here's where we stand as of 6257264 (main on 4/7/23)
coverage run -m pytest tests/ && coverage html
open htmlcov/index.html
| Name | Stmts | Miss | Cover |
|---|---|---|---|
| haptools/data/phenotypes.py | 150 | 29 | 81% |
| haptools/data/genotypes.py | 497 | 81 | 84% |
| haptools/ld.py | 93 | 14 | 85% |
| haptools/transform.py | 294 | 44 | 85% |
| haptools/index.py | 43 | 6 | 86% |
| haptools/__main__.py | 182 | 23 | 87% |
| haptools/admix_storage.py | 36 | 4 | 89% |
| haptools/data/haplotypes.py | 359 | 39 | 89% |
| haptools/data/breakpoints.py | 127 | 13 | 90% |
| haptools/data/data.py | 37 | 3 | 92% |
| haptools/karyogram.py | 160 | 12 | 92% |
| haptools/sim_genotype.py | 419 | 35 | 92% |
| haptools/logging.py | 15 | 1 | 93% |
| haptools/sim_phenotype.py | 99 | 6 | 94% |
| haptools/data/covariates.py | 8 | 0 | 100% |
Of course, 100% coverage doesn't guarantee bug-less code. But we could probably write more tests in phenotypes.py, genotypes.py, and transform.py to avoid serious bug fixes like in #199
We could also create more opportunities for code review, especially from those outside of the haptools team