| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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. | |||
| 2025-09-02 | Test cat_genotype. | Arun Isaac | |
| Test cat_genotype extensively using hypothesis. | |||
| 2025-09-02 | 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. | |||
| 2025-09-02 | Drop duplicates in generated test genotype frames. | Arun Isaac | |
| 2025-09-02 | Catenate an empty list of genotypes. | Arun Isaac | |
| We handle this as a special case. | |||
| 2025-09-02 | Move hypothesis strategies to separate file. | Arun Isaac | |
| These strategies may be used by other test modules as well. | |||
| 2025-09-02 | 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. | |||
| 2025-09-02 | 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. | |||
| 2025-09-01 | 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. | |||
| 2025-09-01 | 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. | |||
| 2025-09-01 | Use open method of Path object, rather than the open function. | Arun Isaac | |
| 2025-09-01 | Do not skip blank lines when reading TSV files. | Arun Isaac | |
| 2025-09-01 | 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. | |||
| 2025-09-01 | 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. | |||
| 2025-09-01 | Title case sentence. | Arun Isaac | |
| 2025-09-01 | 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 | |
| 2025-08-08 | Remove txt extension from summary files. | Arun Isaac | |
| 2025-08-08 | Link to file formats documentation from README. | Arun Isaac | |
| Readers are more likely to follow through to the file formats documentation if there is a link. | |||
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index : pyhegp | |
| Homomorphic encryption of genotypes and phenotypes |
| about summary refs log tree commit diff |