| 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 | db: test_db: Test that a fetch is correct when columns are specified | 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 | guix: Add diffutils as a propagated input | BonfaceKilz | |
| 2021-06-29 | guix: Remove commented out hunk | BonfaceKilz | |
| 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 | tests: test_commands: Add extra check for when an error occurs | 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 ☝🏾. | |||
| 2021-06-29 | tests: test_data: Add test data that contains trait data for 10007 | BonfaceKilz | |
| 2021-06-25 | Check for the correct result code | BonfaceKilz | |
| When programs terminate with an error, they usually return a -1! | |||
| 2021-06-23 | Merge pull request #21 from genenetwork/fix/biweight-errors | BonfaceKilz | |
| Fix/biweight errors | |||
| 2021-06-23 | fix pylint issues | Alexander Kabui | |
| 2021-06-23 | minor fixes for biweight script | Alexander Kabui | |
| 2021-06-22 | scripts: laminar: Add json with hooks for running a linter | BonfaceKilz | |
| 2021-06-22 | scripts: laminar: Add sh scripts for CI | BonfaceKilz | |
| 2021-06-21 | Merge pull request #20 from genenetwork/feature/biweight-correlation | BonfaceKilz | |
| add biweight r script and tests | |||
| 2021-06-20 | minor fix docstring | Alexander Kabui | |
| 2021-06-20 | merge main | Alexander Kabui | |
| 2021-06-20 | fix conflict | Alexander Kabui | |
| 2021-06-20 | make requested changes to biweight | Alexander Kabui | |
| 2021-06-18 | Merge pull request #13 from zsloan/feature/add_rqtl_endpoints | zsloan | |
| Feature/add rqtl endpoints | |||
| 2021-06-18 | Fixed another error where test_generate_rqtl_command didn't include the ↵ | zsloan | |
| filename argument (not sure why running unit tests locally doesn't detect this) | |||
| 2021-06-18 | Fixed file type from json to csv for test_generate_rqtl_command | zsloan | |
| 2021-06-18 | Fixed test_rqtl.py to include Rscript in the command | zsloan | |
| 2021-06-18 | Fixed test_compose_rqtl_command test; forgot to include Rscript in the command | zsloan | |
| 2021-06-18 | Change test_compose_rqtl_command in test_commands.py to have different ↵ | zsloan | |
| arguments to hopefully avoid github's pylint 'duplicate code' complaint Changed some parameters in test_compose_rqtl_cmd to avoid pylint complaining about duplicate code | |||
| 2021-06-18 | Fixed pylint issues | zsloan | |
| 2021-06-18 | add ignore_missing_imports for numpy in mypy.ini since it complains about ↵ | zsloan | |
| that and we seem to have done the same thing for scipy | |||
| 2021-06-18 | Resolve mypy errors in computations/rqtl.py | zsloan | |
| 2021-06-18 | Fixed spelling of coeffient to coefficient | zsloan | |
| 2021-06-18 | minor fixes | Alexander Kabui | |
| 2021-06-18 | remove ununsed variables | Alexander Kabui | |
| 2021-06-18 | refactor perf query functions | Alexander Kabui | |
| 2021-06-18 | rename perf query file | Alexander Kabui | |
| 2021-06-18 | pep8 formatting | Alexander Kabui | |
| 2021-06-18 | add tests to setup packages | Alexander Kabui | |
| 2021-06-18 | add types and dataset names | Alexander Kabui | |
| 2021-06-18 | initial commit for queries perfomance tests | Alexander Kabui | |
| 2021-06-18 | db: test_db: Add extra variable in test data for "id" | BonfaceKilz | |
| 2021-06-18 | Rename json_data column to json_diff_data | BonfaceKilz | |
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index : genenetwork3 | |
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