| Age | Commit message (Expand) | Author |
|---|
| 2022-07-29 | Fix failing tests...* gn3/computations/correlations.py: rename function
* mypy.ini: deactivate mypy error about missing imports
* tests/integration/test_correlation.py: mock correct function
* tests/unit/computations/test_correlation.py: test correct function
| Frederick Muriuki Muriithi |
| 2022-07-22 | linting and tests fixes | Alexander_Kabui |
| 2022-07-22 | mypy pylint fixes | Alexander_Kabui |
| 2022-07-22 | add unittests | Alexander_Kabui |
| 2022-06-29 | use explicit parameters | Alexander_Kabui |
| 2022-06-29 | fix issues | Alexander_Kabui |
| 2022-06-29 | lint test file | Alexander |
| 2022-06-29 | add tests | Alexander |
| 2022-06-29 | add test data | Alexander |
| 2022-06-29 | parse output data | Alexander |
| 2022-06-29 | init test correlation rust module | Alexander |
| 2022-06-21 | tests: test_file_utils: Replace pytest.mark.skip with unittest.skip..."python setup.py test" won't skip "pytest.mark.skip" thereby leading to
build failure when you try to package gn3.
| BonfaceKilz |
| 2022-06-21 | test_file_utils: Disable test cases for "cache_ipfs_file"...* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip
it.
(test_cache_ipfs_file_cache_miss): Ditto.
| BonfaceKilz |
| 2022-06-21 | integration: test_gemma: Skip "GemmaAPITest" | BonfaceKilz |
| 2022-05-30 | Pass trait data as args to `fix_strains` and fix some bugs...The `fix_strains` function works on the trait data, not the basic trait
info. This commit fixes the arguments passed to the function, and also some
bugs in the function.
| Frederick Muriuki Muriithi |
| 2022-05-27 | Move sql for CRUD operations on case-attrs from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Move sql for modifying case-attributes from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Return all the results from CaseAttributes column as is...* gn3/db/sample_data.py: Remove "collections" import. Add "Optional" import.
(get_case_attributes): Return the results of "fetchall" from the case
attributes.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Update failing
test.
| BonfaceKilz |
| 2022-05-26 | Add Endpoint to get menu items for use in UI | Frederick Muriuki Muriithi |
| 2022-05-05 | Extract common error checking. Rename function....* Extract the common error checking code into a separate function
* Rename the function to make its use clearer
| Frederick Muriuki Muriithi |
| 2022-04-12 | Delete "get_allowable_sampledata_headers"...* gn3/csvcmp.py (get_allowable_sampledata_headers): Delete it.
* tests/unit/test_csvcmp.py: Remove "get_allowable_sampledata_headers" import.
(test_get_allowable_csv_headers): Delete it.
| BonfaceKilz |
| 2022-04-12 | Test that a carriage return is removed when generating csv...* tests/unit/db/test_sample_data.py: import "get_trait_csv_sample_data".
(test_get_trait_csv_sample_data): New test function.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (delete_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_delete_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (insert_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_insert_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during updates...* gn3/db/sample_data.py: Import "parse_csv_column".
(update_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Add method for fetching the case_attributes...* gn3/db/sample_data.py (get_case_attributes): New function.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for
the above.
| BonfaceKilz |
| 2022-04-07 | Add method for parsing a csv header from uploaded sample-data file...* gn3/csvcmp.py (parse_csv_column): New function.
* tests/unit/test_csvcmp.py: Test case for the above.
| BonfaceKilz |
| 2022-04-01 | Run python-black in file...* gn3/csvcmp.py: Run "black -l 79 ..."
* tests/unit/db/test_sample_data.py: Ditto.
* tests/unit/test_csvcmp.py: Ditto.
| BonfaceKilz |
| 2022-03-24 | Test Fixture: Create new test database and get connection to it...Implement a fixture that:
* Creates a new test database
* Copies over table structure from existing database
* Gets connection to new test database and returns it
* Cleans up after itself when the tests have run
| Frederick Muriuki Muriithi |
| 2022-03-18 | Clean all csv fields before diffing...There was a subtle bug where "csvdiff" generated an error related to
"different column headings" caused something akin to diffing: "a, b \n, ..."
with "a, b\n, ...".
* gn3/csvcmp.py (csv_diff): Clean csv texts before any diffing.
* tests/unit/test_csvcmp.py (test_csv_diff_same_columns): Modify test case to
capture aforementioned bug.
| BonfaceKilz |
| 2022-03-18 | Create new function for cleaning individual fields in csv text...* gn3/csvcmp.py (clean_csv_text): New function.
* tests/unit/test_csvcmp.py: Import "csv_text".
(test_clean_csv_text): Test case for the above.
| BonfaceKilz |
| 2022-03-15 | Feature/refactored pca (#79)...* compute zscore function
* test case for computing zscore
* function to compute pca
* generate scree plot data
* generate new pca trait data from zscores and eigen_vec
* remove redundant functions
* generate factor loading table data
* generate pca temp dataset dict
* variable naming and error fixes
* unit test for processing factor loadings
* minor fixes for generating temp pca dataset
* pass datetime as argument to generate_pca temp dataset function
* add unittest for caching pca datasets
* cache temp datasets
* ignore missing imports for sklearn
* mypy fixes
* pylint fixes
* refactor tests for pca
* remove ununsed imports
* fix for generating pca traits vals
* mypy and code refactoring
* pep8 formatting and add docstrings
* remove comments /pep8 formatting
* sort eigen vectors based on eigen values
* minor fix for zscores
* fix for rounding variance ratios
* refactor tests
* rename module to pca
* rename datasets to traits
* fix failing tests
* fix caching function
* fixes return x and y coordinates for scree plot
* expand exception scope
* fix for deprecated numpy.matrix function
* fix for failing tests
* pep8 fixes
* remove comments
* fix merge conflict
* pylint fixes
* rename module name to test_pca | Alexander Kabui |
| 2022-03-14 | Sort import lines | BonfaceKilz |
| 2022-03-14 | Given a csv text and permissible headers, extract invalid headers...* gn3/csvcmp.py (extract_invalid_csv_headers): New function.
* tests/unit/test_csvcmp.py: Import "extract_invalid_csv_headers".
(test_extract_invalid_csv_headers_with_some_wrong_headers): Test case for the
above.
| BonfaceKilz |
| 2022-03-14 | Get all permissible column data...* gn3/csvcmp.py: Import "Any" and "List".
(get_allowable_sampledata_headers): New function.
* tests/unit/test_csvcmp: Import "get_allowable_sampledata_headers".
(test_get_allowable_csv_headers): Test case for the above.
| BonfaceKilz |
| 2022-03-12 | Fix pylint errors in unit_tests | BonfaceKilz |
| 2022-03-12 | Append the strain name when extracting "actions"...* gn3/db/sample_data.py (__extract_actions): During updates, make sure that
the strain name is part of the returned string when extracting "actions".
* tests/unit/db/test_sample_data.py: Add test cases for the above.
| BonfaceKilz |
| 2022-03-12 | Apply auto-pep8 to sample_data.py and it's test file | BonfaceKilz |
| 2022-03-12 | Update how data is updated by re-using existing functions...* gn3/db/sample_data.py (get_sample_data_ids): Re-use "delete_sample_data" and
"insert_sample_data" when updating data; and also add logic for updating
modified data.
* tests/unit/db/test_sample_data.py: Add tests for the above.
| BonfaceKilz |
| 2022-03-12 | Create action dict that's created when updating data...* gn3/db/sample_data.py (__extract_actions): An update on a vector of data can
contain: inserts, deletes and updates. This functions extracts these actions
during an update.
* tests/unit/db/test_sample_data.py (test_extract_actions): Add test-case for
the above.
| BonfaceKilz |
| 2022-03-12 | Add test cases for inserting and deleting data...* tests/unit/db/test_sample_data.py (test_insert_sample_data): Test inserting
data.
(test_delete_sample_data): Test deleting data.
| BonfaceKilz |
| 2022-03-12 | Fill in empty values in csv text with: "x"...* gn3/csvcmp.py (fill_csv): Update this function to allow empty lists to be
filled with the default value(set in the args).
* tests/unit/test_csvcmp.py (test_fill_csv): Update test to capture above.
| BonfaceKilz |
| 2022-03-12 | Remove test cases related to sample data...Most of this functions were moved to their own module.
| BonfaceKilz |
| 2022-03-12 | Extract a strain name given a csv string and it's header...* gn3/csvcmp.py (extract_strain_name): New function.
* gn3/db/sample_data (delete_sample_data): Use the aforementioned function.
(insert_sample_data): Ditto.
* tests/unit/test_csvcmp: Test cases for above.
| BonfaceKilz |
| 2022-03-12 | Don't add extra key "Column" to dict if there are no changes...gn3/csvcmp.py (csv_diff): If the diff is empty, don't add an extra key
"Column" to the dictionary.
tests/unit/test_csvcmp (test_csv_diff_only_column_change): Add test-case for
the above.
| BonfaceKilz |
| 2022-03-12 | Test edges cases for csv files when running csvdiff...* tests/unit/test_csvcmp.py (test_csv_diff): Delete it.
(test_csv_diff_same_columns): Test csv_diff against csv texts with the same
columns.
(test_csv_diff_different_columns): Test csv texts against csv texts with
different varying columns.
| BonfaceKilz |
| 2022-03-12 | Create new method for filling csv with a default value...* gn3/csvcmp.py (fill_csv): Given a csv text with uneven or incomplete fields
whole length are less than width, fill them with a value which defaults to
"x".
* tests/unit/test_csvcmp.py (test_fill_csv): Test cases for the above.
| BonfaceKilz |
| 2022-03-12 | Add methods for working with csv data...gn3/csvcmp.py: New file
(create_dirs_if_not_exists): From a list of dirs, create them if they don't
exist.
(remove_insignificant_edits): Given a dict with a "Modification" key, remove
edits with "delta < ε".
(csv_diff): Generate a csv_diff using the "csvdiff" tool packaged in guix.
tests/unit/test_csvcmp.py: Add some tests for "gn3/csvcmp.py"
| BonfaceKilz |
| 2022-03-12 | Append case attributes to csv data if they exist | BonfaceKilz |
| 2022-03-11 | Fix some linting issues | Frederick Muriuki Muriithi |
