Merge pull request #366 from m-beau/m-beau

c4 npyx test fixes

README.md

@@ -63,7 +63,7 @@ We recommend using a conda environment. Pre-existing packages on a python instal
   cd path/to/save_dir # any directory where your code will be accessible by your editor and safe. NOT downloads folder.
   git clone https://github.com/m-beau/NeuroPyxels
   cd NeuroPyxels
-  pip install -e . # this will create an egg link to save_dir, which means that you do not need to reinstall the package each time you edit it (e.g. after pulling from github).
+  pip install . # this will create an egg link to save_dir, which means that you do not need to reinstall the package each time you edit it (e.g. after pulling from github).
   # optionally (see 'Dealing with cupy' section below):
   conda install -c conda-forge cupy cudatoolkit=11.0
   # test installation:

npyx/__init__.py

@@ -10,7 +10,7 @@
     import torch
     from .c4 import acg_augmentations, acg_vs_firing_rate, dl_utils, encode_features,\
                     monkey_dataset_init, plots_functions, predict_cell_types, run_baseline_classifier,\
-                    run_deep_classifier, dl_transforms, waveform_augmentations
+                    run_deep_classifier, dl_transforms, waveform_augmentations, run_cell_types_classifier
     C4_IMPORTED = True
 except ImportError:
     # Do not import extra C4 functionality in the main namespace if torch is not installed.

npyx/c4/predict_cell_types.py

@@ -61,7 +61,7 @@
     "\n"
     "Welcome to the cerebellar cell type classifier of the Cerebellar Cell types Classification Collaboration (C4)!\n"
     "\nYou can use this command ('c4' or 'predict_cell_types') to run the C4 classifier on a phy-compatible dataset (find our preprint here: https://www.biorxiv.org/content/10.1101/2024.01.30.577845v1)."
-    "\nTo run the classifier on the phy-compatible dataset in the current working directory, simply run 'c4 .'. To run it on a phy-compatible dataset present elsewhere, run 'c4 path/to/my/dataset'."
+    "\nTo run the classifier on the phy-compatible dataset in the current working directory, simply run 'c4 -dp .'. To run it on a phy-compatible dataset present elsewhere, run 'c4 -dp path/to/my/dataset'."
     "\nBy default, the classifier will predict the cell types of all the 'good' units of the dataset (as defined in phy by manual curation), and it will not use layer information. To alter this behaviour, see the options below."
     "\n"
 )