Refactor unit and integration tests and corresponding github actions #686
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alimanfoo
commented
Dec 4, 2024
| @@ -186,7 +186,7 @@ def test_setup_returns_config_correctly(self): | |||
| self.assertEqual( | |||
| plasmodium.CONF, | |||
| { | |||
| "default_url": "gs://test_plasmodium_release/", | |||
| "default_url": "s3://test_plasmodium_release/", | |||
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This change ensures the tests don't try to access GCS within this test module (using a GCS URL triggers an attempt to authenticate, which then requires secrets, which then won't work on a PR from a fork).
eselimnl
approved these changes
Dec 5, 2024
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This PR aims to make a clearer distinction between unit and integration tests, where unit tests run against local or simulated data, and integration tests run against real remote data in GCS.
Reorganise the tests to bring together all tests which run against data in GCS into a common
tests/integrationdirectory, both for Anopheles and Plasmodium.The
legacy_tests.ymlaction is renamed tointegration_tests.ymland explicitly runs only those tests within thetests/integrationdirectory.The
tests.ymlandcoverage.ymlactions are updated to run all tests except those in thetests/integrationdirectory.Previously also we had a mixture of using poetry or pip to install the package and its dependencies in different actions. For simplicity this PR uses pip in all actions running tests or notebooks.
Ensure that mypy runs with the package and all its dependencies installed, for more comprehensive type checking, and fix or ignore additional typing errors that come up.
This lays some groundwork for #682 but doesn't resolve it.