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2022-02-02refactor code for invoking ctl scriptAlexander Kabui
2022-02-02pep8 formattingAlexander Kabui
2022-02-02match case string input to booleanAlexander Kabui
2022-02-02fix for parametric inputAlexander Kabui
2022-02-02use user input significanceAlexander Kabui
2022-02-02new line fixAlexander Kabui
2022-02-02add new json outputAlexander Kabui
2022-02-02fix comprehension listAlexander Kabui
2022-02-02Revert "Use guix shell shortcut with guix.scm file"BonfaceKilz
This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
2022-01-27Use guix shell shortcut with guix.scm filejgart
2022-01-24README: Add pylint and mypy CI badges.Arun Isaac
We now have separate CI jobs for the pylint and mypy tests. * README.md: Add pylint and mypy CI badges.
2022-01-22minor refactoringAlexander Kabui
2022-01-22function override:fix target specific output file for networkAlexander Kabui
2022-01-22generate networkAlexander Kabui
2022-01-22process ctl plot data imgAlexander Kabui
2022-01-22generate ctl plots for each traitAlexander Kabui
2022-01-22read stdout data;handle exceptionsAlexander Kabui
2022-01-22generate required json data for ctl apiAlexander Kabui
2022-01-22fixes for ctl script:generate ctl ctl_significant jsonAlexander Kabui
2022-01-22bugfixes for script;create pheno and geno objectsAlexander Kabui
2022-01-22add endpoint for ctlAlexander Kabui
2022-01-22init file to call ctl scriptAlexander Kabui
2022-01-22generate lineplotAlexander Kabui
2022-01-22minor fix:read input data from json fileAlexander Kabui
2022-01-22export json dataAlexander Kabui
2022-01-22get significant interactionsAlexander Kabui
2022-01-22perform the ctl scanAlexander Kabui
2022-01-22fetch genotypes and phenotype filesAlexander Kabui
2022-01-22init script ctl analysisAlexander Kabui
2022-01-21README: Update link to CI badge.Arun Isaac
The CI has been moved to penguin2, and this is accompanied by a URI change. * README.md: Update link to CI badge.
2022-01-12Update return type. Remove duplicate import.Frederick Muriuki Muriithi
The function is a generator function, since it uses a `yield` statement, and thus returns a generator object, that contains a tuple object. This fixes that. We also remove a duplicate import.
2022-01-12Indent code correctlyFrederick Muriuki Muriithi
Indent the code correctly.
2022-01-12Deduplicate query to fetch data for 'Publish' traitsFrederick Muriuki Muriithi
The queries run in the `get_trait_csv_sample_data` and `retrieve_publish_trait_data` functions in the `gn3.db.traits` module were mostly similar. This commit changes that, by making the `get_trait_csv_sample_data` function make use of the results from calling the `retrieve_publish_trait_data` function.
2022-01-10Check for path existenceFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-10Fix dataset retrieval query for `Geno` traitsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-10Use the correct letter case for the keysFrederick Muriuki Muriithi
* Use the correct case for the keys inorder to retrieve the correct values.
2022-01-10Surround statement with parens for readabilityFrederick Muriuki Muriithi
2022-01-10Indicate that string is an f-stringFrederick Muriuki Muriithi
* The string had the f-string syntax to format the values to be inserted into the string, but was missing the 'f' before the opening quotes to signify to python that this was an f-string. This commit fixes that.
2022-01-10Convert keys to stringFrederick Muriuki Muriithi
* Some traits have a name composed of all numerals, which leads to the names being interpreted as numbers. This commit forces them to string to avoid subtle bugs where the code fails.
2022-01-10Remove all pairs with 'None' as the valueFrederick Muriuki Muriithi
* Remove all key-value pairs whose value is None.
2022-01-10Fix error in query: Replace '=' with 'IN'Frederick Muriuki Muriithi
2022-01-10Replace unoptimised function with optimised oneFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace unoptimised function with one optimised to give better performance. The optimisation done here is to fetch multiple items/traits from the database per query, rather than the original form, which fetched a single item/trait from the database per query.
2022-01-10Silence `duplicate-code` linting notificationsFrederick Muriuki Muriithi
2022-01-10Convert NaN to NoneFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Comment: https://github.com/genenetwork/genenetwork3/pull/67#issuecomment-1000828159 * Convert NaN values to None to avoid possible bugs with the string replace method used before.
2022-01-10Add optimised entry for partial correlationsFrederick Muriuki Muriithi
Issue: * Function `gn3.computations.partial_correlations_optimised.partial_correlations_entry` is a copy of the `gn3.computations.partial_correlation.partial_correlations_entry` function that is optimised for better performance. The optimised function is intended to replace the unoptimised one, but it is included in this commit for comparison purposes, and to maintain some historical context for doing it this way.
2022-01-10Rework database functions to fetch multiple itemsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * In an attempt to optimise the performance of the partial correlations feature, this commit reworks some database access functions to fetch multiple items from the database, per query, unlike their original forms which would fetch a single item per query. This reduces queries to the database, and should hopefully improve the responsiveness of the partial correlations feature.
2022-01-05Merge pull request #64 from jgarte/type-hint-normalize-valuesBonfaceKilz
Adds type hint for normalize_values function
2022-01-05Merge pull request #69 from ↵BonfaceKilz
genenetwork/fix/check-for-duplicates-before-deletions-or-insertions Fix/check for duplicates before deletions or insertions
2022-01-05Merge branch 'main' into fix/check-for-duplicates-before-deletions-or-insertionsBonfaceKilz
2022-01-05Fix pylint errorsBonfaceKilz
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