pyhegp - Homomorphic encryption of genotypes and phenotypes

Age	Commit message (Collapse)	Author
6 days	Do not import unused settings from hypothesis.	Arun Isaac

6 days	Test cat_phenotype.	Arun Isaac

7 days	Rename cat subcommand to cat-genotype.	Arun Isaac
	A cat-phenotype subcommand is coming. Hence rename this.
7 days	Merge, not concat, genotype frames.	Arun Isaac
	pd.concat duplicates the metadata columns, and is generally the wrong approach to the problem.
7 days	Test cat_genotype.	Arun Isaac
	Test cat_genotype extensively using hypothesis.
7 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.
8 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.
8 days	Use open method of Path object, rather than the open function.	Arun Isaac

8 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.
2025-08-06	Subset to common SNPs.	Arun Isaac
	* pyhegp/pyhegp.py: Import reduce from functools. (pool_summaries, encrypt_genotype): New functions. (pool): Use pool_summaries. (encrypt): Use encrypt_genotype. * tests/test_pyhegp.py: Import pandas; Summary, read_summary and read_genotype from pyhegp.serialization. (test_pool, test_encrypt): New tests. * test-data/encrypt-test-encrypted-genotype.tsv, test-data/encrypt-test-genotype.tsv, test-data/encrypt-test-key, test-data/encrypt-test-summary, test-data/pool-test-complete-summary, test-data/pool-test-summary1, test-data/pool-test-summary2: New files.
2025-08-06	Compute summary on encryption if not provided.	Arun Isaac
	* pyhegp/pyhegp.py (genotype_summary): New function. (summary): Use genotype_summary. (encrypt): Compute summary if not provided. * tests/test_pyhegp.py (test_simple_workflow): Remove xfail mark.
2025-08-06	Add simple workflow.	Arun Isaac
	* README.md (How to use): Indent down into "Joint/federated analysis with many data owners" section. [Simple data sharing]: New section. * doc/generate-images.sh: Add simple workflow. * doc/workflow.png: Rename to doc/joint-workflow.png. * doc/workflow.uml: Rename to doc/joint-workflow.uml. * doc/simple-workflow.png, doc/simple-workflow.uml: New files. * tests/test_pyhegp.py: Import pytest. (test_simple_workflow): New test. * test-data/genotype.tsv: New file.
2025-08-06	Test joint workflow CLI.	Arun Isaac
	* tests/test_pyhegp.py: Import CliRunner from click.testing, and main from pyhegp.pyhegp. (test_joint_workflow): New test. * test-data/genotype0.tsv, test-data/genotype1.tsv, test-data/genotype2.tsv, test-data/genotype3.tsv: New files.
2025-08-06	Move negate to pyhegp.utils.	Arun Isaac
	* tests/test_pyhegp.py (negate): Move to pyhegp.utils. Import negate from pyhegp.utils. * pyhegp/utils.py: New file.
2025-08-06	Loosen relative tolerance in test_pool_stats.	Arun Isaac
	* tests/test_pyhegp.py (test_pool_stats): Set relative tolerance to 1e-6.
2025-08-01	Test solution of linear system after encryption.	Arun Isaac
	* tests/test_pyhegp.py: Import math. (square_matrices, negate, is_singular): New functions. (test_conservation_of_solutions): New test.
2025-08-01	Separate standardization from encryption.	Arun Isaac
	* pyhegp/pyhegp.py (hegp_encrypt, hegp_decrypt): Do not standardize or unstandardize. (encrypt): Standardize before calling hegp_encrypt. * tests/test_pyhegp.py (test_hegp_encryption_decryption_are_inverses): Do not pass mean and standard deviation for standardization and unstandardization.
2025-08-01	Do not test encryption on order 1 matrices.	Arun Isaac
	* tests/test_pyhegp.py (test_hegp_encryption_decryption_are_inverses): Do not test encryption on order 1 matrices.
2025-07-17	Standardize before encryption.	Arun Isaac
	* pyhegp/pyhegp.py (hegp_encrypt): Standardize before encryption. (hegp_decrypt): Unstandardize after decryption. (encrypt): Pass in mean and standard deviation from summary file to hegp_encrypt. * tests/test_pyhegp.py (test_hegp_encryption_decryption_are_inverses): Pass in mean and standard deviation to hegp_encrypt.
2025-07-17	Add standardization.	Arun Isaac
	* pyhegp/pyhegp.py (standardize): Standardize using mean and standard deviation, instead of the minor allele frequency. (unstandardize): New function. * tests/test_pyhegp.py: Import standardize and unstandardize from pyhegp.pyhegp. (no_column_zero_standard_deviation): New function. (test_standardize_unstandardize_are_inverses): New test.
2025-07-17	Add pool subcommand.	Arun Isaac
	* pyhegp/pyhegp.py: Import namedtuple from collections, and read_summary from pyhegp.serialization. (Stats): New type. (pool_stats, pool): New functions. * tests/test_pyhegp.py: Import Stats and pool_stats from pyhegp.pyhegp. (test_pool_stats): New test.
2025-07-17	Use default array shapes testing encryption/decryption.	Arun Isaac
	It may be better to sample a smaller set of matrices finely than a large set of matrices coarsely. * tests/test_pyhegp.py (test_hegp_encryption_decryption_are_inverses): Use default array shapes testing encryption/decryption.
2025-07-17	Reduce maximum matrix size testing encryption/decryption.	Arun Isaac
	* tests/test_pyhegp.py (test_hegp_encryption_decryption_are_inverses): Reduce maximum matrix size to 100.
2025-07-17	Organize 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.