Colony mask inference `pip install .` may fail

[pgarrison]

This issue is about the work-in-progress branch for colony mask inference reproducibility, sm_colony_mask_pred_test_v0.

The pip install . step of the colony mask inference installation instructions will fail if the user has a EMT_image_analysis/Colony_mask_training_inference/test_data or EMT_image_analysis/Colony_mask_training_inference/logs directory in addition to EMT_image_analysis/Colony_mask_training_inference/configs, because pip tries to find source code to install.

The logs directory is created by cyto-dl and the test_data directory is created in the usage instructions.

One idea for resolving this:

• Export the pdm.lock file to a requirements.txt and update the installation instructions to pip install -r requirements.txt.

Originally reported by @sandraoluoch

[pgarrison]

From @mfs4rd

Attempting to pip install . the repo when data directory is present causes issues where pip believes it is a module directory. Consider adding a setting in the setup files to prevent this