genenetwork3/tests/integration, branch migrate-to-python3.10GeneNetwork3 REST API for data science and machine learning
http://git.genenetwork.org/genenetwork3/atom?h=migrate-to-python3.102023-07-10T08:36:47+00:00Fix linting errors caused by bump to Python 3.102023-07-10T08:36:47+00:00Frederick Muriuki Muriithi2023-07-10T08:36:47+00:00urn:sha1:c6ac30d4ccc26553a12e8c37cdf9078cbe9084b3Fix linting issues2023-04-06T09:43:56+00:00Frederick Muriuki Muriithi2023-04-06T09:43:56+00:00urn:sha1:db6457bfbcccce35162d9d2ece988c7c8c8f9308Remove deprecated `gn3.db_utils.database_connector` function2023-04-06T09:31:05+00:00Frederick Muriuki Muriithi2023-04-06T09:31:05+00:00urn:sha1:17abad9300e4a96a14f94da486ef8307f7d27e06
Remove the deprecated function and fix a myriad of bugs that arise from
removing the function.
Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts.2022-12-21T00:39:52+00:00Frederick Muriuki Muriithi2022-12-21T00:39:52+00:00urn:sha1:daa3a9cade431b21bbc48b690c16dcb8746f3dce
Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's
`random` module.
* gn3/random.py -> gn3/chancy.py: rename module
* gn3/commands.py: update import
* gn3/computations/partial_correlations.py: update import
* gn3/computations/qtlreaper.py: update import
* gn3/computations/rust_correlation.py: update import
* gn3/db/correlations.py: update import
* gn3/db/traits.py: update import
* gn3/heatmaps.py: update import
* tests/integration/conftest.py: update import
Fix failing tests2022-07-29T00:53:49+00:00Frederick Muriuki Muriithi2022-07-29T00:39:32+00:00urn:sha1:e3622ac213ef6e1be8a38959f7c6ee082c112c95
* 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
integration: test_gemma: Skip "GemmaAPITest"2022-06-21T11:44:09+00:00BonfaceKilz2022-06-21T11:43:48+00:00urn:sha1:850fe4ea4d39947d309db3329b74d5c31db05722Extract common error checking. Rename function.2022-05-05T12:19:08+00:00Frederick Muriuki Muriithi2022-05-05T12:19:08+00:00urn:sha1:be9d1d4aad720274f6d75345123fae8d6a96bc12
* Extract the common error checking code into a separate function
* Rename the function to make its use clearer
Test Fixture: Create new test database and get connection to it2022-03-24T10:11:13+00:00Frederick Muriuki Muriithi2022-02-22T10:35:28+00:00urn:sha1:5906098d32e7aa1ab155d5dd49cd3b04b06684eb
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
Test edges cases for csv files when running csvdiff2022-03-12T12:33:09+00:00BonfaceKilz2022-02-25T08:37:00+00:00urn:sha1:0c1a6fb91b8bf9cf2b68ba54d8905e4c6acfd341
* 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.
Fix tests, and issues caught by tests2022-03-08T05:07:38+00:00Frederick Muriuki Muriithi2022-03-08T05:07:38+00:00urn:sha1:e30f9a9b746f7dcdc8707e66cc65e580e6f83f47
Fix some issues caught by tests due to changes introducing the hand-off of the
partial correlations computations to an external process
Fix some issues due to the changes that introduce context managers for
database connections
Update some tests to take the above two changes into consideration