| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-02-06 | refactor: Add file_path to output only if it is created. | Alexander_Kabui | |
| 2025-02-06 | refactor: Check if data before attempting write operation. | Alexander_Kabui | |
| 2025-02-06 | refactor: return code for Calledprocesserror response. | Alexander_Kabui | |
| 2025-02-06 | feat: Add module docstring for rqtl2 computations. | Alexander_Kabui | |
| 2025-02-06 | refactor: remove unused imports. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to write input data to a json file. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to prepare files and workspace directory for computation. | Alexander_Kabui | |
| 2025-02-06 | feat: Add utility function to create a file if it does not exist. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to compose an rqtl2 run command. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to validate list of keys in object. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to generate rqtl2 data files. | Alexander_Kabui | |
| 2025-02-06 | feat: Add method to write list of data to csv file. | Alexander_Kabui | |
| 2025-02-06 | feat: Add computational module for rqtl2. | Alexander_Kabui | |
| 2025-01-13 | mypy fixes. | Alexander_Kabui | |
| 2025-01-13 | refactor: Returns markers and pseudomarkers as names in pairscan results. | Alexander_Kabui | |
| 2025-01-09 | Typo fixes. | Alexander_Kabui | |
| 2025-01-09 | refactor: raise and Handle error a app level. | Alexander_Kabui | |
| 2025-01-09 | feat: Add a decorator function to enable streaming functinality. | Alexander_Kabui | |
| 2025-01-09 | feat: Add function to run an external process and capture result in a file. | Alexander_Kabui | |
| 2025-01-09 | feat: Init add streaming module for genenetwork3. | Alexander_Kabui | |
| 2024-12-17 | feat: Init integrate streaming functionality to rqtl1. | Alexander_Kabui | |
| 2024-12-13 | fix: Fix unused variables pylint. | Alexander_Kabui | |
| 2024-12-13 | Fix pylint error line too long. | Alexander_Kabui | |
| 2024-12-13 | fix: Fetch the correct value from rqtl output file for permutation. | Alexander_Kabui | |
| 2024-12-12 | Remove quote marks for qtl output. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-27 | Bug: Use absolute paths in place of relative paths. | Frederick Muriuki Muriithi | |
| Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51 | |||
| 2024-09-12 | Fix pylint errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-12 | Fix failing tests after merging in Pjotr's pull request. | Frederick Muriuki Muriithi | |
| 2024-09-12 | From gn3 only use TMPDIR/gn3 paths | Pjotr Prins | |
| 2024-09-12 | Replace TMPDIR/output with TMPDIR/gn3 so it is clear where it comes from | Pjotr Prins | |
| 2024-09-12 | Modify script paths so they can be edited in Guix | Pjotr Prins | |
| 2024-09-12 | Make sure TMPDIR directories exist! | Pjotr Prins | |
| 2024-09-12 | Move assert_paths_exist into fs_helpers | Pjotr Prins | |
| 2024-09-12 | Change behavior of do_paths_exist to actually throw useful error | Pjotr Prins | |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins | |
| 2024-09-12 | Move assert_paths_exist into fs_helpers | Pjotr Prins | |
| 2024-09-12 | Change behavior of do_paths_exist to actually throw useful error | Pjotr Prins | |
| 2024-02-25 | Disable too-many-arguments for "run_reaper". | Munyoki Kilyungi | |
| * gn3/computations/qtlreaper.py: Disable "too-many-arguments" pylint check. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-19 | Pass qtlreaper command path as argument to run_reaper | zsloan | |
| Originally the system would get the path from the environment | |||
| 2023-10-27 | Remove reimport "Optional". | Munyoki Kilyungi | |
| * gn3/computations/gemma.py: Delete reimport "Qptional". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-27 | Make implicit optional type hints PEP 484 compliant. | Munyoki Kilyungi | |
| Ran the command: pipx run no_implicit_optional ./ in the root directory. | |||
| 2023-10-26 | Fix errors caught by mypy. | Frederick Muriuki Muriithi | |
| 2023-10-06 | pylint: fix variable name. | Frederick Muriuki Muriithi | |
| 2023-10-06 | Get `CORRELATION_COMMAND` from current_app not `gn3.settings` | Frederick Muriuki Muriithi | |
| The default settings in `gn3.settings` are meant to be overridden thus the code should not be importing the setting from there, rather, the code should get its configurations settings from `flask.current_app.config`. | |||
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-01-25 | Some comments | Pjotr Prins | |
| 2022-12-21 | gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts. | Frederick Muriuki Muriithi | |
| Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's `random` module. * gn3/random.py -> gn3/chancy.py: rename module * gn3/commands.py: update import * gn3/computations/partial_correlations.py: update import * gn3/computations/qtlreaper.py: update import * gn3/computations/rust_correlation.py: update import * gn3/db/correlations.py: update import * gn3/db/traits.py: update import * gn3/heatmaps.py: update import * tests/integration/conftest.py: update import | |||
| 2022-12-06 | mypy and pylint fixes | Alexander_Kabui | |
| 2022-12-02 | correlations: return `None` rather than zero for missing lit corrs | Frederick Muriuki Muriithi | |
| * gn3/computations/correlations.py: Return `None` for missing literature correlations rather than zero. Update the sorting key to avoid issues with comparing floats to NoneType objects | |||
| 2022-11-29 | remove trailing whitespace | AlexanderKabui | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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