| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 19 hours | README: Add FAQ about standardization. HEAD main | Arun Isaac | |
| 4 days | Handle absent optional reference column. | Arun Isaac | |
| 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. | |||
| 4 days | Clarify that only one of pip or Guix is required. | Arun Isaac | |
| 2025-11-13 | Disable tests for julia-jwas. | Arun Isaac | |
| 2025-11-13 | Depend explicitly on the guix-rust-past-crates channel. | Arun Isaac | |
| 2025-11-13 | Add JWAS tests to HSmice test. | Arun Isaac | |
| 2025-11-13 | Fold line. | Arun Isaac | |
| 2025-11-13 | Parameterize query when checking for the QTL. | Arun Isaac | |
| This will allow generalization to JWAS later. | |||
| 2025-11-12 | Replace python-hypothesis-next with python-hypothesis. | Arun Isaac | |
| python-hypothesis has now been updated on Guix upstream, and python-hypothesis-next has been deprecated. | |||
| 2025-09-08 | Link to PlantUML images built by the CI. | Arun Isaac | |
| We no longer commit the built images into the git repository. Committing build artifacts into the repository is never good practice. And, linking to CI build artifacts is also more automatic and seamless. | |||
| 2025-09-08 | Specify PlantUML output filenames. | Arun Isaac | |
| This is so that we don't end up with long Guix store hashes in the output filename when these images are built on CI using the Guix computed-file. | |||
| 2025-09-08 | Replace PlantUML image generation script with Guix computed-file. | Arun Isaac | |
| 2025-09-08 | Hint at pyhegp commands in UML visualization. | Arun Isaac | |
| 2025-09-08 | Add @startuml and @enduml tags. | Arun Isaac | |
| 2025-09-08 | Split up hsmice test into smaller computed files. | Arun Isaac | |
| This will give us slightly better caching and code organization. | |||
| 2025-09-08 | Exclude .guix and e2e-tests from the pyhegp package. | Arun Isaac | |
| 2025-09-08 | Detail SNP dropping. | Arun Isaac | |
| 2025-09-08 | Update README instructions with phenotype encryption. | Arun Isaac | |
| 2025-09-08 | Comment on QTL checking code. | Arun Isaac | |
| 2025-09-06 | Update r-mixed-model-gwas to 1.3.1. | Arun Isaac | |
| 2025-09-06 | 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. | |||
| 2025-09-06 | Construct empty genotype frame using series. | Arun Isaac | |
| 2025-09-06 | 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. | |||
| 2025-09-06 | Catenate phenotype frames along the index. | Arun Isaac | |
| 2025-09-06 | 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. | |||
| 2025-09-06 | Generalize split_data_frame to split along any axis. | Arun Isaac | |
| 2025-09-06 | 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. | |||
| 2025-09-05 | 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. | |||
| 2025-09-05 | 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. | |||
| 2025-09-05 | Drop SNPs with a zero standard deviation. | Arun Isaac | |
| 2025-09-05 | Fix typo in comment: tha->that. | Arun Isaac | |
| 2025-09-04 | Avoid wildcard import from helpers.strategies. | Arun Isaac | |
| 2025-09-04 | Limit values in genotype and phenotype strategies. | Arun Isaac | |
| 2025-09-04 | Test that ciphertext does not contain NA values. | Arun Isaac | |
| 2025-09-04 | Parameterize number of samples in phenotype frame strategy. | Arun Isaac | |
| 2025-09-04 | Parameterize number of samples in genotype frame strategy. | Arun Isaac | |
| 2025-09-04 | Parameterize presence of reference column in genotype frame strategy. | Arun Isaac | |
| 2025-09-04 | Add keys strategy. | Arun Isaac | |
| Add keys strategy, and use it. | |||
| 2025-09-04 | 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. | |||
| 2025-09-04 | Add --force flag to encrypt subcommand permitting file overwriting. | Arun Isaac | |
| 2025-09-04 | Support encrypting phenotypes. | Arun Isaac | |
| 2025-09-04 | 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. | |||
| 2025-09-04 | Do not import unused settings from hypothesis. | Arun Isaac | |
| 2025-09-04 | Test cat_phenotype. | Arun Isaac | |
| 2025-09-04 | Add cat-phenotype subcommand. | Arun Isaac | |
| 2025-09-02 | Rename cat subcommand to cat-genotype. | Arun Isaac | |
| A cat-phenotype subcommand is coming. Hence rename this. | |||
| 2025-09-02 | Add is_phenotype_metadata_column. | Arun Isaac | |
| Promote phenotype_reserved_column_name_p from helpers.strategies to is_phenotype_metadata_column in pyhegp.serialization. | |||
| 2025-09-02 | Drop duplicates in generated test phenotype frames. | Arun Isaac | |
| 2025-09-02 | Set CI environment variable when building Guix package. | Arun Isaac | |
| 2025-09-02 | Merge, not concat, genotype frames. | Arun Isaac | |
| pd.concat duplicates the metadata columns, and is generally the wrong approach to the problem. | |||
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index : pyhegp | |
| Homomorphic encryption of genotypes and phenotypes |
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