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.
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
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 aEMT_image_analysis/Colony_mask_training_inference/test_data
orEMT_image_analysis/Colony_mask_training_inference/logs
directory in addition toEMT_image_analysis/Colony_mask_training_inference/configs
, becausepip
tries to find source code to install.The
logs
directory is created by cyto-dl and thetest_data
directory is created in the usage instructions.One idea for resolving this:
pdm.lock
file to arequirements.txt
and update the installation instructions topip install -r requirements.txt
.Originally reported by @sandraoluoch