Unify 'defaults' and use of quotations across docstrings (#2134)

* Unify 'defaults' * sorters wip and fix imports * Update src/spikeinterface/core/waveform_tools.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/core/waveform_tools.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/core/waveform_tools.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/core/waveform_tools.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/widgets/amplitudes.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/widgets/unit_waveforms.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/mdaextractors.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/mdaextractors.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/widgets/traces.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/widgets/template_similarity.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/widgets/traces.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/mdaextractors.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/neoextractors/tdt.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/neoextractors/tdt.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/neoextractors/spikeglx.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/preprocessing/remove_artifacts.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/neoextractors/spikeglx.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/neoextractors/spikegadgets.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/extractors/neoextractors/spikegadgets.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/preprocessing/filter.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/postprocessing/correlograms.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/preprocessing/remove_artifacts.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/postprocessing/isi.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/preprocessing/average_across_direction.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/preprocessing/directional_derivative.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/preprocessing/directional_derivative.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/preprocessing/directional_derivative.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/preprocessing/depth_order.py Co-authored-by: Zach McKenzie <[email protected]> * sortingcomponents and more fixes * More quotation handling (core) * Final round of cleaning * Add unsaved files * Import hdbscan when needed and add ros3 to pytest.markers * Update src/spikeinterface/core/baserecordingsnippets.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/core/baserecordingsnippets.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/core/baserecordingsnippets.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/core/job_tools.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/core/job_tools.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/curation/curationsorting.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/curation/sortingview_curation.py Co-authored-by: Zach McKenzie <[email protected]> * Update src/spikeinterface/core/core_tools.py Co-authored-by: Zach McKenzie <[email protected]> --------- Co-authored-by: Zach McKenzie <[email protected]>
SpikeInterface · Oct 31, 2023 · 886530a · 886530a
1 parent fd84c8f
commit 886530a
Show file tree

Hide file tree

Showing 155 changed files with 2,075 additions and 2,109 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -185,6 +185,7 @@ markers = [
     "widgets",
     "sortingcomponents",
     "streaming_extractors: extractors that require streaming such as ross and fsspec",
+    "ros3_test"
 ]
 filterwarnings =[
     'ignore:.*distutils Version classes are deprecated.*:DeprecationWarning',

diff --git a/src/spikeinterface/comparison/basecomparison.py b/src/spikeinterface/comparison/basecomparison.py
@@ -223,7 +223,7 @@ class BasePairComparison(BaseComparison):
     It handles the matching procedurs.
 
     Agreement scores must be computed in inherited classes by overriding the
-    '_do_agreement(self)' function
+    "_do_agreement(self)" function
     """
 
     def __init__(self, object1, object2, name1, name2, match_score=0.5, chance_score=0.1, verbose=False):

diff --git a/src/spikeinterface/comparison/comparisontools.py b/src/spikeinterface/comparison/comparisontools.py
@@ -570,7 +570,7 @@ def do_confusion_matrix(event_counts1, event_counts2, match_12, match_event_coun
 def do_count_score(event_counts1, event_counts2, match_12, match_event_count):
     """
     For each ground truth units count how many:
-    'tp', 'fn', 'cl', 'fp', 'num_gt', 'num_tested', 'tested_id'
+    "tp", "fn", "cl", "fp", "num_gt", "num_tested", "tested_id"
 
     Parameters
     ----------
@@ -634,8 +634,8 @@ def compute_performance(count_score):
 
     Note :
       * we don't have TN because it do not make sens here.
-      * 'accuracy' = 'tp_rate' because TN=0
-      * 'recall' = 'sensitivity'
+      * "accuracy" = "tp_rate" because TN=0
+      * "recall" = "sensitivity"
     """
     import pandas as pd
 
@@ -674,7 +674,7 @@ def make_matching_events(times1, times2, delta):
 
     Returns
     -------
-    matching_event: numpy array dtype = ['index1', 'index2', 'delta']
+    matching_event: numpy array dtype = ["index1", "index2", "delta"]
         1d of collision
     """
     times_concat = np.concatenate((times1, times2))
@@ -731,8 +731,8 @@ def make_collision_events(sorting, delta):
     -------
     collision_events: numpy array
             dtype =  [('index1', 'int64'), ('unit_id1', 'int64'),
-                ('index2', 'int64'), ('unit_id2', 'int64'),
-                ('delta', 'int64')]
+                      ('index2', 'int64'), ('unit_id2', 'int64'),
+                      ('delta', 'int64')]
         1d of all collision
     """
     unit_ids = np.array(sorting.get_unit_ids())

diff --git a/src/spikeinterface/comparison/multicomparisons.py b/src/spikeinterface/comparison/multicomparisons.py
@@ -25,22 +25,22 @@ class MultiSortingComparison(BaseMultiComparison, MixinSpikeTrainComparison):
     ----------
     sorting_list: list
         List of sorting extractor objects to be compared
-    name_list: list
-        List of spike sorter names. If not given, sorters are named as 'sorter0', 'sorter1', 'sorter2', etc.
-    delta_time: float
-        Number of ms to consider coincident spikes (default 0.4 ms)
-    match_score: float
-        Minimum agreement score to match units (default 0.5)
-    chance_score: float
-        Minimum agreement score to for a possible match (default 0.1)
-    n_jobs: int
+    name_list: list, default: None
+        List of spike sorter names. If not given, sorters are named as "sorter0", "sorter1", "sorter2", etc.
+    delta_time: float, default: 0.4
+        Number of ms to consider coincident spikes
+    match_score: float, default: 0.5
+        Minimum agreement score to match units
+    chance_score: float, default: 0.1
+        Minimum agreement score to for a possible match
+    n_jobs: int, default: -1
        Number of cores to use in parallel. Uses all available if -1
-    spiketrain_mode: str
+    spiketrain_mode: "union" | "intersection", default: "union"
         Mode to extract agreement spike trains:
-            - 'union': spike trains are the union between the spike trains of the best matching two sorters
-            - 'intersection': spike trains are the intersection between the spike trains of the
+            - "union": spike trains are the union between the spike trains of the best matching two sorters
+            - "intersection": spike trains are the intersection between the spike trains of the
                best matching two sorters
-    verbose: bool
+    verbose: bool, default: False
         if True, output is verbose
 
     Returns
@@ -156,15 +156,15 @@ def _do_agreement_matrix(self, minimum_agreement=1):
 
     def get_agreement_sorting(self, minimum_agreement_count=1, minimum_agreement_count_only=False):
         """
-        Returns AgreementSortingExtractor with units with a 'minimum_matching' agreement.
+        Returns AgreementSortingExtractor with units with a "minimum_matching" agreement.
 
         Parameters
         ----------
         minimum_agreement_count: int
             Minimum number of matches among sorters to include a unit.
         minimum_agreement_count_only: bool
-            If True, only units with agreement == 'minimum_matching' are included.
-            If False, units with an agreement >= 'minimum_matching' are included
+            If True, only units with agreement == "minimum_matching" are included.
+            If False, units with an agreement >= "minimum_matching" are included
 
         Returns
         -------
@@ -309,13 +309,13 @@ class MultiTemplateComparison(BaseMultiComparison, MixinTemplateComparison):
     ----------
     waveform_list: list
         List of waveform extractor objects to be compared
-    name_list: list
-        List of session names. If not given, sorters are named as 'sess0', 'sess1', 'sess2', etc.
-    match_score: float
-        Minimum agreement score to match units (default 0.5)
-    chance_score: float
-        Minimum agreement score to for a possible match (default 0.1)
-    verbose: bool
+    name_list: list, default: None
+        List of session names. If not given, sorters are named as "sess0", "sess1", "sess2", etc.
+    match_score: float, default: 0.8
+        Minimum agreement score to match units
+    chance_score: float, default: 0.3
+        Minimum agreement score to for a possible match
+    verbose: bool, default: False
         if True, output is verbose
 
     Returns

diff --git a/src/spikeinterface/comparison/paircomparisons.py b/src/spikeinterface/comparison/paircomparisons.py
@@ -111,19 +111,19 @@ class SymmetricSortingComparison(BasePairSorterComparison):
         The first sorting for the comparison
     sorting2: SortingExtractor
         The second sorting for the comparison
-    sorting1_name: str
+    sorting1_name: str, default: None
         The name of sorter 1
-    sorting2_name: : str
+    sorting2_name: : str, default: None
         The name of sorter 2
-    delta_time: float
-        Number of ms to consider coincident spikes (default 0.4 ms)
-    match_score: float
-        Minimum agreement score to match units (default 0.5)
-    chance_score: float
-        Minimum agreement score to for a possible match (default 0.1)
-    n_jobs: int
+    delta_time: float, default: 0.4
+        Number of ms to consider coincident spikes
+    match_score: float, default: 0.5
+        Minimum agreement score to match units
+    chance_score: float, default: 0.1
+        Minimum agreement score to for a possible match
+    n_jobs: int, default: -1
         Number of cores to use in parallel. Uses all available if -1
-    verbose: bool
+    verbose: bool, default: False
         If True, output is verbose
 
     Returns
@@ -139,7 +139,6 @@ def __init__(
         sorting1_name=None,
         sorting2_name=None,
         delta_time=0.4,
-        sampling_frequency=None,
         match_score=0.5,
         chance_score=0.1,
         n_jobs=-1,
@@ -214,34 +213,35 @@ class GroundTruthComparison(BasePairSorterComparison):
         The first sorting for the comparison
     tested_sorting: SortingExtractor
         The second sorting for the comparison
-    gt_name: str
+    gt_name: str, default: None
         The name of sorter 1
-    tested_name: : str
+    tested_name: : str, default: None
         The name of sorter 2
-    delta_time: float
-        Number of ms to consider coincident spikes (default 0.4 ms)    match_score: float
-        Minimum agreement score to match units (default 0.5)
-    chance_score: float
-        Minimum agreement score to for a possible match (default 0.1)
-    redundant_score: float
-        Agreement score above which units are redundant (default 0.2)
-    overmerged_score: float
-        Agreement score above which units can be overmerged (default 0.2)
-    well_detected_score: float
-        Agreement score above which units are well detected (default 0.8)
-    exhaustive_gt: bool (default True)
+    delta_time: float, default: 0.4
+        Number of ms to consider coincident spikes
+    match_score: float, default: 0.5
+        Minimum agreement score to match units
+    chance_score: float, default: 0.1
+        Minimum agreement score to for a possible match
+    redundant_score: float, default: 0.2
+        Agreement score above which units are redundant
+    overmerged_score: float, default: 0.2
+        Agreement score above which units can be overmerged
+    well_detected_score: float, default: 0.8
+        Agreement score above which units are well detected
+    exhaustive_gt: bool, default: False
         Tell if the ground true is "exhaustive" or not. In other world if the
         GT have all possible units. It allows more performance measurement.
         For instance, MEArec simulated dataset have exhaustive_gt=True
-    match_mode: 'hungarian', or 'best'
-        What is match used for counting : 'hungarian' or 'best match'.
-    n_jobs: int
+    match_mode: "hungarian" | "best", default: "hungarian"
+        The method to match units
+    n_jobs: int, default: -1
         Number of cores to use in parallel. Uses all available if -1
-    compute_labels: bool
-        If True, labels are computed at instantiation (default False)
-    compute_misclassifications: bool
-        If True, misclassifications are computed at instantiation (default False)
-    verbose: bool
+    compute_labels: bool, default: False
+        If True, labels are computed at instantiation
+    compute_misclassifications: bool, default: False
+        If True, misclassifications are computed at instantiation
+    verbose: bool, default: False
         If True, output is verbose
 
     Returns
@@ -379,21 +379,21 @@ def _do_score_labels(self):
     def get_performance(self, method="by_unit", output="pandas"):
         """
         Get performance rate with several method:
-          * 'raw_count' : just render the raw count table
-          * 'by_unit' : render perf as rate unit by unit of the GT
-          * 'pooled_with_average' : compute rate unit by unit and average
+          * "raw_count" : just render the raw count table
+          * "by_unit" : render perf as rate unit by unit of the GT
+          * "pooled_with_average" : compute rate unit by unit and average
 
         Parameters
         ----------
-        method: str
-            'by_unit',  or 'pooled_with_average'
-        output: str
-            'pandas' or 'dict'
+        method: "by_unit" | "pooled_with_average", default: "by_unit"
+            The method to compute performance
+        output: "pandas" | "dict", default: "pandas"
+            The output format
 
         Returns
         -------
         perf: pandas dataframe/series (or dict)
-            dataframe/series (based on 'output') with performance entries
+            dataframe/series (based on "output") with performance entries
         """
         import pandas as pd
 
@@ -471,7 +471,7 @@ def get_well_detected_units(self, well_detected_score=None):
 
         Parameters
         ----------
-        well_detected_score: float (default 0.8)
+        well_detected_score: float, default: None
             The agreement score above which tested units
             are counted as "well detected".
         """
@@ -507,7 +507,7 @@ def get_false_positive_units(self, redundant_score=None):
 
         Parameters
         ----------
-        redundant_score: float (default 0.2)
+        redundant_score: float, default: None
             The agreement score below which tested units
             are counted as "false positive"" (and not "redundant").
         """
@@ -547,7 +547,7 @@ def get_redundant_units(self, redundant_score=None):
 
         Parameters
         ----------
-        redundant_score=None: float (default 0.2)
+        redundant_score=None: float, default: None
             The agreement score above which tested units
             are counted as "redundant" (and not "false positive" ).
         """
@@ -582,8 +582,8 @@ def get_overmerged_units(self, overmerged_score=None):
 
         Parameters
         ----------
-        overmerged_score: float (default 0.4)
-            Tested units with 2 or more agreement scores above 'overmerged_score'
+        overmerged_score: float, default: None
+            Tested units with 2 or more agreement scores above "overmerged_score"
             are counted as "overmerged".
         """
         assert self.exhaustive_gt, "overmerged_units list is valid only if exhaustive_gt=True"
@@ -693,16 +693,16 @@ class TemplateComparison(BasePairComparison, MixinTemplateComparison):
         The first waveform extractor to get templates to compare
     we2 : WaveformExtractor
         The second waveform extractor to get templates to compare
-    unit_ids1 : list, optional
-        List of units from we1 to compare, by default None
-    unit_ids2 : list, optional
-        List of units from we2 to compare, by default None
-    similarity_method : str, optional
-        Method for the similaroty matrix, by default "cosine_similarity"
-    sparsity_dict : dict, optional
-        Dictionary for sparsity, by default None
-    verbose : bool, optional
-        If True, output is verbose, by default False
+    unit_ids1 : list, default: None
+        List of units from we1 to compare
+    unit_ids2 : list, default: None
+        List of units from we2 to compare
+    similarity_method : str, default: "cosine_similarity"
+        Method for the similaroty matrix
+    sparsity_dict : dict, default: None
+        Dictionary for sparsity
+    verbose : bool, default: False
+        If True, output is verbose
 
     Returns
     -------