| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-07-22 | Check that all distances are positive or zero | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that all distances between the 'somethings' are all either zero or positive. * tests/unit/computations/test_slink.py: * Remove data with all distances positive or zero, since it would fail the test * Change the expected message to more closely correspond to the business logic | |||
| 2021-07-22 | Check that distance from A to B is same as from B to A | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that the distance from child A to B is the same as distance from child B to A. If not, throw an exception. * tests/unit/computations/test_slink.py: * Change the name of the test to more closely correspond to the business logic being tested. * Update the data in a separate test such that it does not error out due to failing to fulfill the expectations of separate requirement. - pass tests - Rename test - Fix errors: distances same both directions | |||
| 2021-07-22 | Check that child distance from itself is zero | Muriithi Frederick Muriuki | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Check that a child's distance from itself is zero. If not, throw an exception. The children lists are a list of distances of "something" from other "somethings". There is still some need to establish what those "somethings" are, so that the test names can reflect the ideas that are actually being tested for. * tests/unit/computations/test_slink.py: Change the name of the test so that it more closely corresponds to the business logic it is actually testing, and not the mechanics of testing the idea. | |||
| 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 | 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 | Fix pylint issues | BonfaceKilz | |
| 2021-07-10 | db: test_db: Test that a fetch is correct when columns are specified | BonfaceKilz | |
| 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 | |
| 2021-06-20 | merge main | Alexander Kabui | |
| 2021-06-20 | make requested changes to biweight | Alexander Kabui | |
| 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 | 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 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 | |
| 2021-06-18 | tests: test_db: Add a test-case for fetchall | BonfaceKilz | |
| 2021-06-18 | tests: test_db: Rename TestPhenotype | BonfaceKilz | |
| 2021-06-18 | tests: test_phenotype: Rename to test_db | BonfaceKilz | |
| 2021-06-18 | Use prepared statements for FETCH sql function | BonfaceKilz | |
| 2021-06-18 | Use prepared statements for UPDATE sql function | BonfaceKilz | |
| 2021-06-18 | tests: test_audit: Update test case to check for prepared statements | BonfaceKilz | |
| 2021-06-18 | Add data structures for the table metadata_audit | BonfaceKilz | |
| 2021-06-18 | unit: test_phenotypes: Test for multiple "WHERE" clauses | BonfaceKilz | |
| 2021-06-18 | Get the diff between 2 dicts and return that as a dict | 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 | tests: test_phenotype: Add function that tests "fetchone" | BonfaceKilz | |
| 2021-06-18 | db: phenotypes: Update failing tests | BonfaceKilz | |
| 2021-06-18 | tests: test_phenotypes: New test cases for loading phenotypes | BonfaceKilz | |
| 2021-06-14 | add biweight r script and tests | Alexander Kabui | |
| 2021-06-11 | minor fixes | Alexander Kabui | |
| 2021-06-11 | remove ununsed variables | Alexander Kabui | |
| 2021-06-11 | refactor perf query functions | Alexander Kabui | |
| 2021-06-11 | rename perf query file | Alexander Kabui | |
| 2021-06-11 | pep8 formatting | Alexander Kabui | |
| 2021-06-11 | add types and dataset names | Alexander Kabui | |
| 2021-06-11 | initial commit for queries perfomance tests | Alexander Kabui | |
| 2021-06-07 | db: test_db: Add extra variable in test data for "id" | BonfaceKilz | |
| 2021-06-07 | Rename json_data column to json_diff_data | BonfaceKilz | |
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