AllenCell / benchmarking_representations

Benchmarking different methods for extracting unsupervised representations from images

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Bugfix: pdm install of pointcloudutils #33

Closed pgarrison closed 1 week ago

pgarrison commented 1 week ago

Issue

The following used to fail:

pdm sync
pdm run python -c "import pointcloudutils.datamodules"

This is a problem because code in br uses that import.

Changes

The main fix is by migrating to the src layout: a standard python project format that pdm integrates well with. Essentially this meant the following: mkdir src && mv br src && mv pointcloudutils/pointcloudutils src && rm -r pointcloudutils.
In addition I wrote some very simple tests to validate that the code imports properly. These can be run with pdm run pytest or, if using pip, simply pytest.

Testing

The newly added tests pass locally for both pdm and pip install options.

fatwir commented 1 week ago

Installed the env using pdm and verified that "import pointcloudutils.datamodules" works! (Although it took almost 3 minutes to run that import statement!) Looks good to merge!