pyhegp/test-data, branch main Homomorphic encryption of genotypes and phenotypes http://git.systemreboot.net/pyhegp/atom?h=main 2026-01-28T01:18:09+00:00 Do not drop zero standard deviation SNPs with --only-center. 2026-01-28T01:18:09+00:00 Arun Isaac 2026-01-28T00:23:56+00:00 urn:sha1:ee0b1836f33004c62d05408c4ee2b69086652131 Handle absent optional reference column. 2025-11-28T00:51:34+00:00 Arun Isaac 2025-11-28T00:49:48+00:00 urn:sha1:9b426be57a759a9c983a68536dfce8c1c1891c1a pyhegp was crashing if the optional reference column was absent. We handle it correctly now. And, we add several test cases to catch this in the future. Reduce precision in test data files. 2025-08-08T14:05:27+00:00 Arun Isaac 2025-08-08T14:05:27+00:00 urn:sha1:2f0046d8a67bb48152ed0fedf58f0d1d0ea196dc Reducing precision lowers the file size and makes the files more human-comprehensible. Subset to common SNPs. 2025-08-06T21:46:15+00:00 Arun Isaac 2025-08-06T18:01:04+00:00 urn:sha1:6de3e6bf27d1abebb98d6f841af70cd617e81dd0 * 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. Add simple workflow. 2025-08-06T21:40:41+00:00 Arun Isaac 2025-08-04T11:40:31+00:00 urn:sha1:92727365d1e3fc67b66278fd7cbcda77dd27c09e * 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. Test joint workflow CLI. 2025-08-06T21:40:41+00:00 Arun Isaac 2025-08-04T11:34:06+00:00 urn:sha1:9e2fbdb8141549cbaf4688e52f62fec0b720d8b8 * 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.