| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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. | |||
| 2025-08-08 | Add example key file. | Arun Isaac | |
| 2025-08-08 | Add example genotype file. | Arun Isaac | |
| 2025-08-08 | Add example summary file. | Arun Isaac | |
| 2025-08-08 | Reduce precision in test data files. | Arun Isaac | |
| Reducing precision lowers the file size and makes the files more human-comprehensible. | |||
| 2025-08-08 | Add instructions to install via Guix. | Arun Isaac | |
| 2025-08-08 | Mark virtual environment creation as optional. | Arun Isaac | |
| Not everyone may want to create a virtual environment. For example, on some HPC machines, creating a virtual environment is complicated or does not work. | |||
| 2025-08-08 | Package as a CLI utility only, not a Python library. | Arun Isaac | |
| We have not exposed a Python library interface, and it is not clear if we need to. We can revisit this decision later, if need be. | |||
 |
index : pyhegp | |
| Homomorphic encryption of genotypes and phenotypes |
| about summary refs log tree commit diff |