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2022-08-10code refactoringFrederick Muriuki Muriithi
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10enhancements for rust tissueFrederick Muriuki Muriithi
2022-08-10pylint fixesAlexander_Kabui
2022-08-10update test;parse outputAlexander_Kabui
2022-08-10code refactoringAlexander_Kabui
2022-08-10remove unnessary codeAlexander_Kabui
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10merge for resultsAlexander_Kabui
2022-08-10enhancements for rust tissueAlexander_Kabui
2022-08-03Refactor: Remove unnecessary whitespace and nameFrederick Muriuki Muriithi
2022-08-03Refactor: Remove unnecessary iterations and nameFrederick Muriuki Muriithi
* remove extra iteration that is unnecessary * remove unnecessary variables
2022-07-29New script to run sample correlationsFrederick Muriuki Muriithi
* README.md: update mypy's invocation * scripts/argparse_actions.py: new file - implement custom FileCheck action for argparse * scripts/sample_correlations.py: new file - implement new script to run sample correlations in an external process
2022-07-29Fix failing testsFrederick Muriuki Muriithi
* 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
2022-07-28Add command to run the sample correlations in an external processFrederick Muriuki Muriithi
2022-07-28Update sample correlations code to use multiprocessingFrederick Muriuki Muriithi
* To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module.
2022-07-22mypy fixesAlexander_Kabui
2022-07-22pep8 fixesAlexander_Kabui
2022-07-22linting and tests fixesAlexander_Kabui
2022-07-22import rust_correlation when running gn3 as libAlexander_Kabui
2022-07-22compute num overlapAlexander_Kabui
2022-07-22fix for bug splitting list dataAlexander_Kabui
2022-07-22minor fixes for parsing dataAlexander_Kabui
2022-07-22code to parse tissue correlation inputAlexander_Kabui
2022-07-22mypy pylint fixesAlexander_Kabui
2022-07-22code to fetch correct sample corr dataAlexander_Kabui
2022-07-22delete dead_code;rename variablesAlexander_Kabui
2022-07-22add unittestsAlexander_Kabui
2022-07-22minor fixesAlexander_Kabui
2022-07-11Allow CORS everywhere by defaultFrederick Muriuki Muriithi
Allow the resources (endpoints) to be accessible from anywhere on the internet by default, while still allowing for restriction via CLI environment variable on a case by case basis.
2022-06-29use explicit parametersAlexander_Kabui
2022-06-29fix issuesAlexander_Kabui
2022-06-29lint test fileAlexander
2022-06-29pylint fixesAlexander
2022-06-29add testsAlexander
2022-06-29add test dataAlexander
2022-06-29minor fixesAlexander
2022-06-29handle tmp files generationAlexander
2022-06-29parse output dataAlexander
2022-06-29pep8 formattingAlexander
2022-06-29new variable: CORRELATION_COMMANDAlexander
2022-06-29init test correlation rust moduleAlexander
2022-06-29init rust correlation moduleAlexander
2022-06-28Parse the method from UI before passing it to external processFrederick Muriuki Muriithi
To reduce the chances of the system failing due to the external process being launched with the wrong parameters, add a parsing stage that converts the method from the UI into a form acceptable by the CLI script. * gn3/commands.py: parse the method from UI * scripts/partial_correlations.py: simplify the acceptable methods
2022-06-21tests: test_file_utils: Replace pytest.mark.skip with unittest.skipBonfaceKilz
"python setup.py test" won't skip "pytest.mark.skip" thereby leading to build failure when you try to package gn3.
2022-06-21setup.py: Remove commented out "ipfshttpclient" lineBonfaceKilz
2022-06-21gn3: fs_helpers: Fix pylint errorsBonfaceKilz
* gn3/fs_helpers.py: Remove unused "pathlib" import. (cache_ipfs_file): Disable "unused-argument" warting.
2022-06-21test_file_utils: Disable test cases for "cache_ipfs_file"BonfaceKilz
* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto.
2022-06-21gn3: fs_helpers: Remove ipfshttpclientBonfaceKilz
This library pollutes the Genenetwork2 profile with an old version "dataclasses" thereby causing it to fail.
2022-06-21setup.py: Remove ipfshttpclientBonfaceKilz
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