| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-07-22 | Add docstring | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add docstring to the function, useful for generating automated developer documentation. We also surround the guard functions with some notification comments, to mark possible future places where change might be done. | |||
| 2021-07-22 | Check that list and its direct children are not empty | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add code to pass the test that the list/tuple passed to `nearest' and its direct children lists/tuples are not empty. | |||
| 2021-07-22 | Implement check for lists or tuples | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Implement the code to pass the check that a list of lists is passed to the `nearest' function. | |||
| 2021-07-21 | Extract tests from code in GN1 | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add dummy `nearest' function * tests/unit/computations/test_slink.py: Add some tests This commit adds tests to try and reproduce the working of the `nearest' function in: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py This commit might not yet have extracted all the expected behaviour of the `nearest' function, and therefore, there is a possibility of a later commit augmenting the work in this commit. | |||
| 2021-07-20 | Implement the correlation function | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Implement the correlation computation function, such that it passes the tests created previously. | |||
| 2021-07-20 | Add test for code to move over from GN1 | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * .gitignore: ignore emacs temporary files * gn3/computations/correlations2.py: add a dummy function * tests/unit/computations/test_correlation.py: add unit tests for the function As part of the move of the clustering and heatmap code over from GN1 to GN3, this commit begins by providing some unit tests for the correlation function used to ensure that the implementation that is built up here corresponds, and produces the same results as the original. This tests and the function might change in the new system, but for now, we try and maintain bug-to-bug compatibility. | |||
| 2021-06-29 | Replace list with a tuple as an argument when setting success_codes | BonfaceKilz | |
| * gn3/commands.py (run_cmd): Replace type of success_codes from List to Tuple * gn3/computations/diff.py (generate_diff): Pass success_codes as a Tuple when calling "run_cmd". | |||
| 2021-06-29 | gn3: diff: Set success_codes when running the diff tool | BonfaceKilz | |
| 2021-06-29 | Add a diffing function | BonfaceKilz | |
| For now the diff function uses the Linux tool "diff" to generate the diff since it is efficient and straightforward. * gn3/computations/diff.py (generate_diff): New function. * tests/unit/computations/test_diff.py: Test cases for ☝🏾. | |||
| 2021-06-23 | fix pylint issues | Alexander Kabui | |
| 2021-06-23 | minor fixes for biweight script | Alexander Kabui | |
| 2021-06-20 | minor fix docstring | Alexander Kabui | |
| 2021-06-20 | merge main | Alexander Kabui | |
| 2021-06-20 | make requested changes to biweight | Alexander Kabui | |
| 2021-06-18 | Fixed pylint issues | zsloan | |
| 2021-06-18 | Resolve mypy errors in computations/rqtl.py | zsloan | |
| 2021-06-18 | Fixed spelling of coeffient to coefficient | zsloan | |
| 2021-06-18 | fix index error (#16) | Alexander Kabui | |
| 2021-06-16 | add r-wgna package | Alexander Kabui | |
| 2021-06-16 | minor fix | Alexander Kabui | |
| 2021-06-16 | refactor script and add tests | Alexander Kabui | |
| 2021-06-16 | add fetch args function | Alexander Kabui | |
| 2021-06-15 | fix script path issues | Alexander Kabui | |
| 2021-06-14 | fix missing call to bicorAndPvalue | Alexander Kabui | |
| 2021-06-14 | add biweight r script and tests | Alexander Kabui | |
| 2021-05-30 | fix index error (#16) | Alexander Kabui | |
| 2021-05-25 | Include code that processes rqtl output files and returns actual results ↵ | zsloan | |
| instead of just the output filename | |||
| 2021-05-19 | Temporarily replace forward-slashes with underscores, since they can be ↵ | zsloan | |
| included in the hashes used for filenames | |||
| 2021-05-18 | Fixed generate_rqtl_cmd to make the kwarg hash from a combination of ↵ | zsloan | |
| keywords and arguments + account for boolean kwargs without values (like --interval or --covar) | |||
| 2021-05-18 | Fixed variety of issues detected by pylint | zsloan | |
| 2021-05-17 | Created compose_rqtl_command and generate_rqtl_command to create the actual ↵ | zsloan | |
| command to be run from the command line; used the same pattern as for GEMMA for consistency | |||
| 2021-05-15 | resolve merge conflict | Alexander Kabui | |
| 2021-05-15 | Merge branch 'main' into feature/minor-fixes | Alexander Kabui | |
| 2021-05-15 | index lit tuple result | Alexander Kabui | |
| 2021-05-13 | Rename file_utils to fs_helpers | BonfaceKilz | |
| Generally avoid naming things with a "utils" prefix/ suffix since it encourages contributors to dump any new functions there; and over time, as the code grows, things get messy... | |||
| 2021-05-13 | computations: correlations: Apply pep-8 | BonfaceKilz | |
| 2021-05-12 | delete unused functions | Alexander Kabui | |
| 2021-05-12 | rename lit_correlation_for_trait_list to lit_correlation_for_trait | Alexander Kabui | |
| 2021-05-12 | rename tissue_correlation_for_trait_list with tissue_correlation_for_trait | Alexander Kabui | |
| 2021-05-12 | rename p_val ro tissue_p_value for tissue_results | Alexander Kabui | |
| 2021-05-08 | Add extra procedure for parsing a genotype file | BonfaceKilz | |
| * gn3/computations/parsers.py (parse_genofile): New procedure. * tests/unit/computations/test_parsers.py: New test files for above. | |||
| 2021-05-03 | add default no of cores | Alexander Kabui | |
| 2021-05-03 | add trait_id fix mypy issues | Alexander Kabui | |
| 2021-05-03 | minor fixes for tiss correlation tests and naming | Alexander Kabui | |
| 2021-05-03 | replace database with conn | Alexander Kabui | |
| 2021-05-02 | delete dataset and trait files | Alexander Kabui | |
| 2021-04-20 | pep8 formatting | Alexander Kabui | |
| 2021-04-20 | add experiment function for computing tissue correlation using multiprocessing | Alexander Kabui | |
| 2021-04-18 | refactor:return trait_name in corr_results | Alexander Kabui | |
| 2021-04-17 | ad pep8 formatting | Alexander Kabui | |
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index : genenetwork3 | |
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