Merge pull request #3 from CBroz1/ja

linter recommended changes, reduce linter exceptions

Author: JaerongA

.pre-commit-config.yaml

@@ -28,6 +28,7 @@ repos:
     rev: 5.11.2
     hooks:
       - id: isort
+        args: ["--profile", "black"]
         description: Sorts imports in an alphabetical order
 
   # flake8
@@ -42,6 +43,14 @@ repos:
           - "--select=B,C,E,F,W,T4,B9"
 
           # these are errors that will be ignored by flake8
-          # check out their meaning here
-          # https://flake8.pycqa.org/en/latest/user/error-codes.html
-          - "--ignore=C813,C901,E203,E266,E501,W503,F403,F401,E402,W605"
+          # https://www.flake8rules.com/rules/{code}.html
+          - "--ignore=E203,E501,W503,W605"
+          # E203 - Colons should not have any space before them.
+          #        Needed for list indexing
+          # E501 - Line lengths are recommended to be no greater than 79 characters.
+          #        Needed as we conform to 88
+          # W503 - Line breaks should occur after the binary operator.
+          #        Needed because not compatible with black
+          # W605 - a backslash-character pair that is not a valid escape sequence now
+          #        generates a DeprecationWarning. This will eventually become a SyntaxError.
+          #        Needed because we use \d as an escape sequence

CONTRIBUTING.md

@@ -1,3 +1,3 @@
 # Contribution Guidelines
 
-This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.io/python/community/02-Contribute.html). Please reference the link for more full details.
+This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.io/python/community/02-Contribute.html). Please reference the link for more full details.

README.md

@@ -8,5 +8,5 @@ fully functional pipeline.
 
 ![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg)
 
-Installation and usage instructions can be found at the 
+Installation and usage instructions can be found at the
 [Element documentation](https://datajoint.com/docs/elements/element-array-ephys).

docs/src/api/make_pages.py

@@ -41,4 +41,3 @@
 
 with mkdocs_gen_files.open("api/navigation.md", "w") as nav_file:
     nav_file.writelines(nav.build_literate_nav())
-    

element_array_ephys/__init__.py

@@ -1,7 +1,11 @@
-import datajoint as dj
 import logging
 import os
 
+import datajoint as dj
+
+from . import ephys_acute as ephys
+
+__all__ = ["ephys", "get_logger"]
 
 dj.config["enable_python_native_blobs"] = True
 
@@ -10,6 +14,3 @@ def get_logger(name):
     log = logging.getLogger(name)
     log.setLevel(os.getenv("LOGLEVEL", "INFO"))
     return log
-
-
-from . import ephys_acute as ephys

element_array_ephys/ephys_acute.py

@@ -1,17 +1,17 @@
-import datajoint as dj
+import gc
+import importlib
+import inspect
 import pathlib
 import re
-import numpy as np
-import inspect
-import importlib
-import gc
 from decimal import Decimal
-import pandas as pd
 
-from element_interface.utils import find_root_directory, find_full_path, dict_to_uuid
+import datajoint as dj
+import numpy as np
+import pandas as pd
+from element_interface.utils import dict_to_uuid, find_full_path, find_root_directory
 
-from .readers import spikeglx, kilosort, openephys
-from . import probe, get_logger, ephys_report
+from . import ephys_report, get_logger, probe
+from .readers import kilosort, openephys, spikeglx
 
 log = get_logger(__name__)
 
@@ -127,7 +127,7 @@ class AcquisitionSoftware(dj.Lookup):
     """
 
     definition = """  # Software used for recording of neuropixels probes
-    acq_software: varchar(24)    
+    acq_software: varchar(24)
     """
     contents = zip(["SpikeGLX", "Open Ephys"])
 
@@ -264,7 +264,7 @@ class EphysRecording(dj.Imported):
 
     definition = """
     # Ephys recording from a probe insertion for a given session.
-    -> ProbeInsertion      
+    -> ProbeInsertion
     ---
     -> probe.ElectrodeConfig
     -> AcquisitionSoftware
@@ -465,9 +465,9 @@ class Electrode(dj.Part):
 
         definition = """
         -> master
-        -> probe.ElectrodeConfig.Electrode  
+        -> probe.ElectrodeConfig.Electrode
         ---
-        lfp: longblob               # (uV) recorded lfp at this electrode 
+        lfp: longblob               # (uV) recorded lfp at this electrode
         """
 
     # Only store LFP for every 9th channel, due to high channel density,
@@ -615,7 +615,7 @@ class ClusteringParamSet(dj.Lookup):
     # Parameter set to be used in a clustering procedure
     paramset_idx:  smallint
     ---
-    -> ClusteringMethod    
+    -> ClusteringMethod
     paramset_desc: varchar(128)
     param_set_hash: uuid
     unique index (param_set_hash)
@@ -800,7 +800,7 @@ class Clustering(dj.Imported):
     # Clustering Procedure
     -> ClusteringTask
     ---
-    clustering_time: datetime  # time of generation of this set of clustering results 
+    clustering_time: datetime  # time of generation of this set of clustering results
     package_version='': varchar(16)
     """
 
@@ -925,11 +925,11 @@ class Curation(dj.Manual):
     -> Clustering
     curation_id: int
     ---
-    curation_time: datetime             # time of generation of this set of curated clustering results 
+    curation_time: datetime             # time of generation of this set of curated clustering results
     curation_output_dir: varchar(255)   # output directory of the curated results, relative to root data directory
     quality_control: bool               # has this clustering result undergone quality control?
     manual_curation: bool               # has manual curation been performed on this clustering result?
-    curation_note='': varchar(2000)  
+    curation_note='': varchar(2000)
     """
 
     def create1_from_clustering_task(self, key, curation_note=""):
@@ -978,7 +978,7 @@ class CuratedClustering(dj.Imported):
 
     definition = """
     # Clustering results of a curation.
-    -> Curation    
+    -> Curation
     """
 
     class Unit(dj.Part):
@@ -1005,7 +1005,7 @@ class Unit(dj.Part):
         spike_count: int         # how many spikes in this recording for this unit
         spike_times: longblob    # (s) spike times of this unit, relative to the start of the EphysRecording
         spike_sites : longblob   # array of electrode associated with each spike
-        spike_depths=null : longblob  # (um) array of depths associated with each spike, relative to the (0, 0) of the probe    
+        spike_depths=null : longblob  # (um) array of depths associated with each spike, relative to the (0, 0) of the probe
         """
 
     def make(self, key):
@@ -1131,8 +1131,8 @@ class Waveform(dj.Part):
         # Spike waveforms and their mean across spikes for the given unit
         -> master
         -> CuratedClustering.Unit
-        -> probe.ElectrodeConfig.Electrode  
-        --- 
+        -> probe.ElectrodeConfig.Electrode
+        ---
         waveform_mean: longblob   # (uV) mean waveform across spikes of the given unit
         waveforms=null: longblob  # (uV) (spike x sample) waveforms of a sampling of spikes at the given electrode for the given unit
         """
@@ -1260,7 +1260,7 @@ class QualityMetrics(dj.Imported):
 
     definition = """
     # Clusters and waveforms metrics
-    -> CuratedClustering    
+    -> CuratedClustering
     """
 
     class Cluster(dj.Part):
@@ -1285,26 +1285,26 @@ class Cluster(dj.Part):
             contamination_rate (float): Frequency of spikes in the refractory period.
         """
 
-        definition = """   
+        definition = """
         # Cluster metrics for a particular unit
         -> master
         -> CuratedClustering.Unit
         ---
-        firing_rate=null: float # (Hz) firing rate for a unit 
+        firing_rate=null: float # (Hz) firing rate for a unit
         snr=null: float  # signal-to-noise ratio for a unit
         presence_ratio=null: float  # fraction of time in which spikes are present
         isi_violation=null: float   # rate of ISI violation as a fraction of overall rate
         number_violation=null: int  # total number of ISI violations
         amplitude_cutoff=null: float  # estimate of miss rate based on amplitude histogram
         isolation_distance=null: float  # distance to nearest cluster in Mahalanobis space
-        l_ratio=null: float  # 
+        l_ratio=null: float  #
         d_prime=null: float  # Classification accuracy based on LDA
         nn_hit_rate=null: float  # Fraction of neighbors for target cluster that are also in target cluster
         nn_miss_rate=null: float # Fraction of neighbors outside target cluster that are in target cluster
         silhouette_score=null: float  # Standard metric for cluster overlap
         max_drift=null: float  # Maximum change in spike depth throughout recording
-        cumulative_drift=null: float  # Cumulative change in spike depth throughout recording 
-        contamination_rate=null: float # 
+        cumulative_drift=null: float  # Cumulative change in spike depth throughout recording
+        contamination_rate=null: float #
         """
 
     class Waveform(dj.Part):
@@ -1324,7 +1324,7 @@ class Waveform(dj.Part):
             velocity_below (float) inverse velocity of waveform propagation from soma toward the bottom of the probe.
         """
 
-        definition = """   
+        definition = """
         # Waveform metrics for a particular unit
         -> master
         -> CuratedClustering.Unit