Contributing to pykilosort
The installation process is the same for everyone. See the README.
Dependencies need to be added to the conda environment files (pyks2.yml) and the requirements.txt. Please pin any critical dependencies to at least a minor version. Ideally we should avoid adding dependencies that are not actively maintained or are not widely used (unless we are willing to support them ourselves).
Full tests (with cupy and the GPU) - Simply run pytest in the root dir.
CPU-only tests (without cupy) - Activate the test environment conda activate pyks2_test.yml and then run the tests like so: MOCK_CUPY=True pytest -m "not requires_gpu". These are the tests that are run on circleCI.
These tests make extensive use of mocking (python mock module so that we can abstract away the GPU parts and continue to test the surrounding code.
Please mark tests that meet any of the following description (copied from setup.cfg). e.g. a test that runs sorting on a large dataset may be useful but we don't want to run it too often so mark it with @pytest.mark.slow.
requires_gpu: Tests requires cupy (with gpu & CUDA). Tests that seem pointless without a GPU but still work should not use this. slow: marks tests as slow, we skip these on CI too.