pyhegp - Homomorphic encryption of genotypes and phenotypes

Age	Commit message (Collapse)	Author
3 hours	Update r-mixed-model-gwas to 1.3.1. HEAD main	Arun Isaac

7 hours	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.
11 hours	Construct empty genotype frame using series.	Arun Isaac

11 hours	Roll cat_data_frames into cat_genotype.	Arun Isaac
	cat_data_frames is no longer a special function used by both cat_genotype and cat_phenotype. Specialize it and roll it into cat_genotype.
11 hours	Catenate phenotype frames along the index.	Arun Isaac

12 hours	Split catenable phenotype frames along the index.	Arun Isaac
	Phenotype frames are split by sample IDs. This corresponds to splitting along the index, unlike genotype frames which need to be split along the columns.
12 hours	Generalize split_data_frame to split along any axis.	Arun Isaac

13 hours	Simplify split_data_frame so it is more composable.	Arun Isaac
	split_data_frame should only split the data frame. It should not be filtering out metadata columns.
29 hours	Generate unique SNPs in genotype frames without dropping duplicates.	Arun Isaac
	Earlier, we were generating unique SNPs in genotype frames by dropping duplicates. This meant we couldn't control the number of SNPs. Rejection sampling is also not an option because it is too expensive. So, we now generate unique SNPs directly, by first generating a list with unique elements and then converting to a data frame.
34 hours	Deduplicate genotype frame metadata generation.	Arun Isaac
	Abstract out generation of genotype frame metadata (namely chromosome, position and reference) from summaries and genotype_frames into a new helper function genotype_metadata.
37 hours	Drop SNPs with a zero standard deviation.	Arun Isaac

38 hours	Fix typo in comment: tha->that.	Arun Isaac

2 days	Avoid wildcard import from helpers.strategies.	Arun Isaac

2 days	Limit values in genotype and phenotype strategies.	Arun Isaac

2 days	Test that ciphertext does not contain NA values.	Arun Isaac

2 days	Parameterize number of samples in phenotype frame strategy.	Arun Isaac

2 days	Parameterize number of samples in genotype frame strategy.	Arun Isaac

2 days	Parameterize presence of reference column in genotype frame strategy.	Arun Isaac

2 days	Add keys strategy.	Arun Isaac
	Add keys strategy, and use it.
2 days	Raise exception if data frame to be written has NA values.	Arun Isaac
	This should never occur, but can occur due to bugs in the code; we wish to protect against that.
2 days	Add --force flag to encrypt subcommand permitting file overwriting.	Arun Isaac

3 days	Support encrypting phenotypes.	Arun Isaac

3 days	Compare complete frame in test_cat_*.	Arun Isaac
	It is so much simpler and much more robust to simply compare expected and actual data frames.
3 days	Do not import unused settings from hypothesis.	Arun Isaac

3 days	Test cat_phenotype.	Arun Isaac

3 days	Add cat-phenotype subcommand.	Arun Isaac

4 days	Rename cat subcommand to cat-genotype.	Arun Isaac
	A cat-phenotype subcommand is coming. Hence rename this.
4 days	Add is_phenotype_metadata_column.	Arun Isaac
	Promote phenotype_reserved_column_name_p from helpers.strategies to is_phenotype_metadata_column in pyhegp.serialization.
4 days	Drop duplicates in generated test phenotype frames.	Arun Isaac

4 days	Set CI environment variable when building Guix package.	Arun Isaac

4 days	Merge, not concat, genotype frames.	Arun Isaac
	pd.concat duplicates the metadata columns, and is generally the wrong approach to the problem.
4 days	Test cat_genotype.	Arun Isaac
	Test cat_genotype extensively using hypothesis.
4 days	Add is_genotype_metadata_column.	Arun Isaac
	Promote genotype_reserved_column_name_p from helpers.strategies to is_genotype_metadata_column in pyhegp.serialization, and use it everywhere.
4 days	Drop duplicates in generated test genotype frames.	Arun Isaac

4 days	Catenate an empty list of genotypes.	Arun Isaac
	We handle this as a special case.
4 days	Move hypothesis strategies to separate file.	Arun Isaac
	These strategies may be used by other test modules as well.
5 days	Add cat_genotype workhorse function.	Arun Isaac
	Move workhorse logic of the cat command to a separate function. This will make it easy to test the logic without having to invoke the command itself.
5 days	Suffix CLI subcommand functions with _command.	Arun Isaac
	We distinguish CLI subcommand functions using the _command suffix. This way, we don't have to concoct weird names for the actual workhorse functions. To remain consistent, we also suffix _command to the command testing functions.
5 days	Do not require output ciphertext file path.	Arun Isaac
	Make output ciphertext file path implicit; infer it by appending ".hegp" to the plaintext file. We take inspiration from GnuPG.
5 days	Pass dtype to read_csv.	Arun Isaac
	read_csv can incorrectly infer that the string "00" is the integer 0. To avoid this ambiguity, pass the correct dtype to read_csv.
5 days	Use open method of Path object, rather than the open function.	Arun Isaac

5 days	Do not skip blank lines when reading TSV files.	Arun Isaac

5 days	Decide to not use logging.	Arun Isaac
	Remove comments mentioning logging. Command-line error messages have their own place; they are not the same as logging.
5 days	Test for existence of output files.	Arun Isaac
	We were testing for zero exit status. Now, in addition, we test for the existence of output files. This is slightly more robust.
5 days	Title case sentence.	Arun Isaac

5 days	Add phenotype file format and serialization functions.	Arun Isaac

2025-08-08	Clarify that the test suite is not for end users.	Arun Isaac
	End users who install pyhegp via pip cannot run the test suite. Clarify this in the README. Perhaps, in the future, we should move these developer-oriented instructions to a separate document.
2025-08-08	Separate table of contents from introduction.	Arun Isaac
	If not separated, GitHub combines the table of contents with the list of papers in the introduction.
2025-08-08	Add table of contents to README.	Arun Isaac
	A table of contents gives people a brief overview of what's in the README, and allows them to jump to the section they are interested in.
2025-08-08	Replace csv extension with tsv extension on genotype files.	Arun Isaac