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2021-07-23- Added scan_func function that determines whether scanone or scantwo...(pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints zsloan
2021-07-22Added option for running pairscan to rqtl_wrapper.Rzsloan
2021-07-10gn3: db: Use correct type for columns arg in fetch functionsBonfaceKilz
2021-07-10Fix pylint issuesBonfaceKilz
2021-07-10db: test_db: Test that a fetch is correct when columns are specifiedBonfaceKilz
2021-07-10gn3: db: Add extra argument to specify column in fetch statementsBonfaceKilz
2021-07-10db: phenotypes: Add Probeset data structures...* gn3/db/phenotypes.py (Probeset): New dataclass. (probeset_mapping): New dict. * gn3/db/__init__.py: Add probeset_mapping and Probeset. BonfaceKilz
2021-06-29Replace list with a tuple as an argument when setting success_codes...* 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". BonfaceKilz
2021-06-29guix: Add diffutils as a propagated inputBonfaceKilz
2021-06-29guix: Remove commented out hunkBonfaceKilz
2021-06-29gn3: diff: Set success_codes when running the diff toolBonfaceKilz
2021-06-29gn3: commands: Add extra arg that sets the success codes to check...* 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. BonfaceKilz
2021-06-29tests: test_commands: Add extra check for when an error occursBonfaceKilz
2021-06-29Add a diffing function...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 ☝🏾. BonfaceKilz
2021-06-29tests: test_data: Add test data that contains trait data for 10007BonfaceKilz
2021-06-25Check for the correct result code...When programs terminate with an error, they usually return a -1! BonfaceKilz
2021-06-23Merge pull request #21 from genenetwork/fix/biweight-errors...Fix/biweight errorsBonfaceKilz
2021-06-23fix pylint issuesAlexander Kabui
2021-06-23minor fixes for biweight scriptAlexander Kabui
2021-06-22scripts: laminar: Add json with hooks for running a linterBonfaceKilz
2021-06-22scripts: laminar: Add sh scripts for CIBonfaceKilz
2021-06-21Merge pull request #20 from genenetwork/feature/biweight-correlation...add biweight r script and testsBonfaceKilz
2021-06-20minor fix docstringAlexander Kabui
2021-06-20merge mainAlexander Kabui
2021-06-20fix conflictAlexander Kabui
2021-06-20make requested changes to biweightAlexander Kabui
2021-06-18Merge pull request #13 from zsloan/feature/add_rqtl_endpoints...Feature/add rqtl endpointszsloan
2021-06-18Fixed another error where test_generate_rqtl_command didn't include the filen...zsloan
2021-06-18Fixed file type from json to csv for test_generate_rqtl_commandzsloan
2021-06-18Fixed test_rqtl.py to include Rscript in the commandzsloan
2021-06-18Fixed test_compose_rqtl_command test; forgot to include Rscript in the commandzsloan
2021-06-18Change test_compose_rqtl_command in test_commands.py to have different argume......Changed some parameters in test_compose_rqtl_cmd to avoid pylint complaining about duplicate code zsloan
2021-06-18Fixed pylint issueszsloan
2021-06-18add ignore_missing_imports for numpy in mypy.ini since it complains about tha...zsloan
2021-06-18Resolve mypy errors in computations/rqtl.pyzsloan
2021-06-18Fixed spelling of coeffient to coefficientzsloan
2021-06-18minor fixesAlexander Kabui
2021-06-18remove ununsed variablesAlexander Kabui
2021-06-18refactor perf query functionsAlexander Kabui
2021-06-18rename perf query fileAlexander Kabui
2021-06-18pep8 formattingAlexander Kabui
2021-06-18add tests to setup packagesAlexander Kabui
2021-06-18add types and dataset namesAlexander Kabui
2021-06-18initial commit for queries perfomance testsAlexander Kabui
2021-06-18db: test_db: Add extra variable in test data for "id"BonfaceKilz
2021-06-18Rename json_data column to json_diff_dataBonfaceKilz
2021-06-18gn3: db: Fix how columns from tables is resolvedBonfaceKilz
2021-06-18gn3: db: Add "id_" property to metadata_audit class and mappingBonfaceKilz
2021-06-18tests: test_db: Add a test-case for fetchallBonfaceKilz
2021-06-18gn3: db: Add "fetchall" method.BonfaceKilz
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