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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 checkBonfaceKilz
* 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.
2021-06-29tests: test_commands: Add extra check for when an error occursBonfaceKilz
2021-06-29Add a diffing functionBonfaceKilz
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 ☝🏾.
2021-06-29tests: test_data: Add test data that contains trait data for 10007BonfaceKilz
2021-06-25Check for the correct result codeBonfaceKilz
When programs terminate with an error, they usually return a -1!
2021-06-23Merge pull request #21 from genenetwork/fix/biweight-errorsBonfaceKilz
Fix/biweight errors
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-correlationBonfaceKilz
add biweight r script and tests
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_endpointszsloan
Feature/add rqtl endpoints
2021-06-18Fixed 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)
2021-06-18Fixed 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 ↵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
2021-06-18Fixed pylint issueszsloan
2021-06-18add ignore_missing_imports for numpy in mypy.ini since it complains about ↵zsloan
that and we seem to have done the same thing for scipy
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
2021-06-18gn3: metadata_audit: Make props for MetadataAudit class optionalBonfaceKilz
2021-06-18gn3: db: Make "WHERE" clause optionalBonfaceKilz
* gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg.
2021-06-18gn3: db: Use correct DATACLASSMAP entry from metadata_auditBonfaceKilz
2021-06-18tests: test_db: Rename TestPhenotypeBonfaceKilz
2021-06-18tests: test_phenotype: Rename to test_dbBonfaceKilz
2021-06-18gn3: db: sort importsBonfaceKilz
2021-06-18gn3: db: Remove "escape_string" from importsBonfaceKilz
We use prepared statements, so no need to have this.
2021-06-18Use prepared statements for FETCH sql functionBonfaceKilz
2021-06-18gn3: db: Replace items() with keys()BonfaceKilz
* gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict!
2021-06-18Use prepared statements for UPDATE sql functionBonfaceKilz
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-27 07:09:19 +0000