Resolve maintenance issues: Remove google-cloud, fix typos, update docs/logic for fingerprint

Author: jeremymanning

docs/doc_requirements.txt

@@ -13,7 +13,6 @@ sqlalchemy
 dill
 requests
 pydub
-google-cloud>=0.32.0,<0.34.0
 multiprocessing
 pathos
 jupyter_client

quail/analysis/analysis.py

@@ -104,7 +104,7 @@ def analyze(egg, subjgroup=None, listgroup=None, subjname='Subject',
 
     if analysis not in analyses.keys():
         raise ValueError('Analysis not recognized. Choose one of the following: '
-                        'accuracy, spc, pfr, lag-crp, fingerprint, temporal')
+                        'accuracy, spc, pfr, lagcrp, fingerprint, temporal')
 
     from ..egg import FriedEgg
 

quail/analysis/clustering.py

@@ -17,14 +17,27 @@ def fingerprint_helper(egg, permute=False, n_perms=1000,
     egg : quail.Egg
         Data to analyze
 
-    dist_funcs : dict
-        Dictionary of distance functions for feature clustering analyses
+    permute : bool
+        Determines whether to correct clustering scores by shuffling recall order
+        to create a distribution of clustering scores. Default is False.
+
+    n_perms : int
+        Number of permutations to run for "corrected" clustering scores.
+        Default is 1000.
+
+    match : str (exact, best)
+        Matching approach to compute recall matrix. Default is 'exact'.
+
+    distance : str
+        The distance function used to compare items. Default is 'euclidean'.
+
+    features : list
+        List of features to analyze. If None, uses all available features.
 
     Returns
     ----------
     probabilities : Numpy array
       Each number represents clustering along a different feature dimension
-
     """
 
     if features is None:
@@ -85,7 +98,7 @@ def _get_weight_exact(egg, feature, distdict, permute, n_perms):
     if len(rec) <= 2:
         warnings.warn('Not enough recalls to compute fingerprint, returning default'
               'fingerprint.. (everything is .5)')
-        return np.nan
+        return 0.5
 
     distmat = get_distmat(egg, feature, distdict)
 

setup.py

@@ -19,7 +19,7 @@
 
 
 EXTRAS_REQUIRE={
-    'speech-decoding': ["pydub", "openai-whisper", "google-cloud-storage>=2.0.0"],
+    'speech-decoding': ["pydub", "openai-whisper"],
     'efficient-learning': ["sqlalchemy"],
 }