pyhegp - Homomorphic encryption of genotypes and phenotypes

Age	Commit message (Collapse)	Author
3 days	Add end-to-end tests for hsmice dataset.	Arun Isaac
	* Add hsmice dataset wrangling and test scripts. * Add G-expression script to run test. * Depend on the guix-bioinformatics Guix channel for r-genio.
7 days	Set CI environment variable when building Guix package.	Arun Isaac

2025-08-08	Package 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.
2025-08-06	Standardize 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.
2025-07-17	Use python-pytest built with python-hypothesis-next.	Arun Isaac
	* .guix/pyhegp-package.scm: Import python-pytest with guix: prefix. (python-pytest): New variable.
2025-07-17	Use 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.
2025-07-07	Make 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.