| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 11 days | Revert "Test build with only guix-bioinformatics." | Munyoki Kilyungi | |
| This reverts commit deee2c40453a1e74738a865afa1bf6b425b4fecf. | |||
| 11 days | Test build with only guix-bioinformatics. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 11 days | Update gn3 channels file. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-10-27 | Improve logging for the asynchronous background tasks. | Frederick Muriuki Muriithi | |
| 2025-10-27 | Pass `TEXTDIR` configuration on to the script. | Frederick Muriuki Muriithi | |
| Pass the `TEXXDIR` configuration variable on to the script. | |||
| 2025-10-27 | Enable logging in `gn3.db.menu` module. | Frederick Muriuki Muriithi | |
| 2025-10-22 | typing: Fix type errors. | Frederick Muriuki Muriithi | |
| 2025-10-22 | Remove mock for no-longer existing attribute. | Frederick Muriuki Muriithi | |
| 2025-10-22 | Fetch configs from app setting and pass them down | Frederick Muriuki Muriithi | |
| Fix the code to avoid using global variables holding configuration variables to avoid the failures caused by action-at-a-distance effects due to change of a value elsewhere. This way, all code consistently receives the same configuration values passed on from callers. We pass on the following configuration settings: * TMPDIR * SQL_URI * TEXTDIR | |||
| 2025-10-15 | Configurations: Use non-executable file for settings. | Frederick Muriuki Muriithi | |
| Move configuration from executable .py file into a non-executable .json file. See https://issues.genenetwork.org/issues/genenetwork3/genenetwork3_configuration | |||
| 2025-10-06 | flask-cors: Remove minimum version pinning. | Frederick Muriuki Muriithi | |
| The build was failing with ``` ContextualVersionConflict(flask-cors 0.0.1 ... Requirement.parse('flask-cors>=3.0.9'), {'gn3'}) ``` | |||
| 2025-09-10 | .guix-channel: Point guix-past to codeberg. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-09-10 | Fix pylint failing tests. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-08-13 | Initialise logging formats. | Frederick Muriuki Muriithi | |
| 2025-08-13 | Improve logging by setting up handlers appropriately for each env. | Frederick Muriuki Muriithi | |
| 2025-08-13 | Remove unused dependency. | Frederick Muriuki Muriithi | |
| 2025-08-12 | Typo: Fix variable names. | Frederick Muriuki Muriithi | |
| 2025-08-12 | Setup module-specific loggers. | Frederick Muriuki Muriithi | |
| 2025-08-06 | Change order of query parameters. | Frederick Muriuki Muriithi | |
| 2025-08-06 | Use default `quotechar=None`. | Frederick Muriuki Muriithi | |
| 2025-08-03 | Fix mypy errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-08-03 | Fix linting errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-17 | Skip blank lines. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-17 | Skip malformed genotype rows with mismatched data columns. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | feat: Add unittests for llm rate limiting functionality. | Alexander_Kabui | |
| 2025-07-16 | refactor: pass request headers as dict. | Alexander_Kabui | |
| 2025-07-16 | feat: Add unittest for cleaning up gnqna queries. | Alexander_Kabui | |
| 2025-07-16 | refactor: pass required fields directly instead of request object for rate ↵ | Alexander_Kabui | |
| limiting. | |||
| 2025-07-16 | feat: Minor fix. | Alexander_Kabui | |
| 2025-07-16 | feat: Implement gnqna rate limiter. | Alexander_Kabui | |
| 2025-07-16 | Add kludge comment for "HSNIH-Palmer_true.geno" which has floats. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Set a larger map size for the larger genotype files. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Add functionality for importing one entire genotype directory. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | More efficiently and correctly count nrows is genotype. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Delete un-used import. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Add module doc-string. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Improve genotype file parsing. | Munyoki Kilyungi | |
| * scripts/lmdb_matrix.py (GenotypeMatrix): Delete transpose. Add "file_info" field. (save_excursion, count_lines): Delete. (get_genotype_dimensions, read_genotype_headers): New function. (read_geno_file): Rename this to... (read_genotype_file): ... this. (genotype_db_put): Put "file_info". (genotype_db_get): Fetch "file_info". (import_genotype): Use read_genotype_file. (print_current_matrix): Remove transpose. Print out file_info metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Simplify genotype db script. | Munyoki Kilyungi | |
| Hashing and versioning made the script very slow. Now, this script can handle much larger data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Add genotype matrix script. | Munyoki Kilyungi | |
| * scripts/lmdb_matrix.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-09 | Re-apply "Chores/gnqa no login" | BonfaceKilz | |
| This reverts commit f5e89525f941caa6546ea777bb632b7aa44f9b1f. | |||
| 2025-07-09 | Revert "Chores/gnqa no login" (#229) | BonfaceKilz | |
| 2025-07-07 | Ignore pylint rule. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-07 | Delete unused import. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-07 | Remove default LMDB_DATA_PATH. | Munyoki Kilyungi | |
| This should be explicitly set. | |||
| 2025-07-07 | Add null check for cursor.fetchone() in apply_change function. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-07 | Only queue an edit during edits. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-07 | Fix minor bug in how reviews and approvals are added to LMDB. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-07 | Update endpoint for listing diffs to include the change_type. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-07 | Rename dict key. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-07 | Delete view_diff end-point. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
| about summary refs log tree commit diff |