| 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. | |||
| 2021-07-10 | gn3: db: Use correct type for columns arg in fetch functions | BonfaceKilz | |
| 2021-07-10 | Fix pylint issues | BonfaceKilz | |
| 2021-07-10 | gn3: db: Add extra argument to specify column in fetch statements | BonfaceKilz | |
| 2021-07-10 | db: phenotypes: Add Probeset data structures | BonfaceKilz | |
| * gn3/db/phenotypes.py (Probeset): New dataclass. (probeset_mapping): New dict. * gn3/db/__init__.py: Add probeset_mapping and Probeset. | |||
| 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 | gn3: commands: Add extra arg that sets the success codes to check | BonfaceKilz | |
| * gn3/commands.py (run_cmd): Some commands like "diff" return non-standard error codes. To make this fn more robust, add an extra optional argument that sets what successful codes to check. | |||
| 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 ☝🏾. | |||
| 2021-06-25 | Check for the correct result code | BonfaceKilz | |
| When programs terminate with an error, they usually return a -1! | |||
| 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 | Rename json_data column to json_diff_data | BonfaceKilz | |
| 2021-06-18 | gn3: db: Fix how columns from tables is resolved | BonfaceKilz | |
| 2021-06-18 | gn3: db: Add "id_" property to metadata_audit class and mapping | BonfaceKilz | |
| 2021-06-18 | gn3: db: Add "fetchall" method. | BonfaceKilz | |
| 2021-06-18 | gn3: metadata_audit: Make props for MetadataAudit class optional | BonfaceKilz | |
| 2021-06-18 | gn3: db: Make "WHERE" clause optional | BonfaceKilz | |
| * gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg. | |||
| 2021-06-18 | gn3: db: Use correct DATACLASSMAP entry from metadata_audit | BonfaceKilz | |
| 2021-06-18 | gn3: db: sort imports | BonfaceKilz | |
| 2021-06-18 | gn3: db: Remove "escape_string" from imports | BonfaceKilz | |
| We use prepared statements, so no need to have this. | |||
| 2021-06-18 | Use prepared statements for FETCH sql function | BonfaceKilz | |
| 2021-06-18 | gn3: db: Replace items() with keys() | BonfaceKilz | |
| * gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict! | |||
| 2021-06-18 | Use prepared statements for UPDATE sql function | BonfaceKilz | |
| 2021-06-18 | gn3: db: Add new function for doing sql INSERT | BonfaceKilz | |
| 2021-06-18 | Add data structures for the table metadata_audit | BonfaceKilz | |
| 2021-06-18 | gn3: db: Add spacing before around "AND" in sql clause | BonfaceKilz | |
| 2021-06-18 | Get the diff between 2 dicts and return that as a dict | BonfaceKilz | |
| 2021-06-18 | gn3: db: Return None if data and where are empty | BonfaceKilz | |
| 2021-06-18 | fix index error (#16) | Alexander Kabui | |
| 2021-06-18 | Move the methods, "update" and "fetch", to gn3.db | BonfaceKilz | |
| 2021-06-18 | db: phenotypes: Fix publication_mapping | BonfaceKilz | |
| 2021-06-18 | db: phenotypes: Fix typo | BonfaceKilz | |
| 2021-06-18 | db: phenotypes: Add function for fetching a single result | BonfaceKilz | |
| * gn3/db/phenotypes.py (fetchone): New function. | |||
| 2021-06-18 | db: phenotypes: Add a dataclass map | BonfaceKilz | |
| Maps a string to it's dataclass. | |||
| 2021-06-18 | db: phenotypes: Add Publication table mapping | BonfaceKilz | |
| 2021-06-18 | db: phenotypes: Rename phenotype_column_mapping | BonfaceKilz | |
| 2021-06-18 | db: phenotypes: Add Publication dataclass and mapping | BonfaceKilz | |
| 2021-06-18 | db: phenotypes: Generalise the update function | BonfaceKilz | |
| * gn3/db/phenotypes.py (update_phenotype): Delete it. (update): New, more general function. | |||
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index : genenetwork3 | |
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