This issue is about the work-in-progress branch for colony mask inference reproducibility, sm_colony_mask_pred_test_v0.
Report on improvements for the all colony mask inference repo instructions
1) Make clearer in step 1 that the data directory should be a subdirectory of Colony_mask_training_inference earlier in the step
2) 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
3) the way the paths/default.yaml file is set up doesn't check the folder the repo has been cloned into, or CYTODL_CONFIG_PATH=$PWD/configs does not work as intended
4) eval_scale*.yaml files have predict_all_cells_mask_zarr_aws_v0.csv as the default csv file, but predict_all_cells_mask_v0.csv is the one currently provided. You will likely be changing this for the final release but make sure the default matches then
This issue is about the work-in-progress branch for colony mask inference reproducibility, sm_colony_mask_pred_test_v0.
Report on improvements for the all colony mask inference repo instructions
1) Make clearer in step 1 that the
data
directory should be a subdirectory ofColony_mask_training_inference
earlier in the step2) Attempting to
pip install .
the repo whendata
directory is present causes issues where pip believes it is a module directory. Consider adding a setting in the setup files to prevent this3) the way the
paths/default.yaml
file is set up doesn't check the folder the repo has been cloned into, orCYTODL_CONFIG_PATH=$PWD/configs
does not work as intended4)
eval_scale*.yaml
files havepredict_all_cells_mask_zarr_aws_v0.csv
as the default csv file, butpredict_all_cells_mask_v0.csv
is the one currently provided. You will likely be changing this for the final release but make sure the default matches then