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8 daysPackage as a CLI utility only, not a Python library.Arun Isaac
We have not exposed a Python library interface, and it is not clear if we need to. We can revisit this decision later, if need be.
10 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.
2025-07-17Use python-pytest built with python-hypothesis-next.Arun Isaac
* .guix/pyhegp-package.scm: Import python-pytest with guix: prefix. (python-pytest): New variable.
2025-07-17Use python-hypothesis-next.Arun Isaac
* guix.scm: Import python-hypothesis-next instead of python-hypothesis. (python-pyhegp)[native-inputs]: Replace python-hypothesis with python-hypothesis-next.
2025-07-07Make repo a guix channel.Arun Isaac
* .guix-channel: New file. * guix.scm: Move to ... * .guix/pyhegp-package.scm: ... here as its own module. * guix.scm: Link to .guix/pyhegp-package.scm.