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7 daysStandardize file formats in the likeness of plink files.Arun Isaac
* pyhegp/pyhegp.py: Import pandas. (summary, pool, encrypt, cat): Use pandas data frames and new data format. * pyhegp/serialization.py: Import csv and pandas. (Summary)[mean, std]: Delete fields. [data]: New field. (read_summary, write_summary, read_genotype, write_genotype): Use pandas data frames and new data format. * tests/test_serialization.py: Import column, columns and data_frames from hypothesis.extra.pandas; pandas; negate from pyhegp.utils. Do not import hypothesis.extra.numpy and approx from pytest. (tabless_printable_ascii_text, chromosome_column, position_column, reference_column, sample_names): New variables. (summaries, genotype_reserved_column_name_p, genotype_frames): New functions. (test_read_write_summary_are_inverses): Use pandas data frames and new data format. (test_read_write_genotype_are_inverses): Use pandas for testing. * doc/file-formats.md (File formats)[summary file]: Describe new standard. [genotype file]: New section. * .guix/pyhegp-package.scm (pyhegp-package): Import python-pandas from (gnu packages python-science). (python-pyhegp)[propagated-inputs]: Add python-pandas. * pyproject.toml (dependencies): Add pandas.
2025-07-17Organize source into directory structure.Arun Isaac
* pyhegp/__init__.py: New file. * pyhegp.py: Move to pyhegp/pyhegp.py. * test_pyhegp.py: Move to tests/test_pyhegp.py. Import from pyhegp.pyhegp instead of from pyhegp. * pyproject.toml (project.scripts)[pyhegp]: Switch to pyhegp.pyhegp:main.
2025-06-27Initial commitArun Isaac