pyhegp - Homomorphic encryption of genotypes and phenotypes

Age	Commit message (Collapse)	Author
7 days	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.
7 days	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.
7 days	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.
7 days	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.
7 days	Loosen relative tolerance in test_pool_stats.	Arun Isaac
	* tests/test_pyhegp.py (test_pool_stats): Set relative tolerance to 1e-6.
13 days	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.
13 days	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.
13 days	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.