Merge pull request #111 from kabilar/main

Fix for cicd and other ux fixes

Author: CBroz1

CHANGELOG.md

@@ -38,8 +38,8 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - NWB export function
 
 ## [0.1.0b4] - 2021-11-29
-### Added
-+ Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX
+
++ Add - Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX
 
 
 ## [0.1.0b0] - 2021-05-07

docs/src/concepts.md

@@ -55,7 +55,17 @@ Over the past few years, several labs have developed DataJoint-based data manage
 
 Each of the DataJoint Elements creates a set of tables for common neuroscience data modalities to organize, preprocess, and analyze data. Each node in the following diagram is a table within the Element or a table connected to the Element.
 
-![element-array-ephys diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
+### `ephys_acute` module
+
+![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
+
+### `ephys_chronic` module
+
+![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_chronic.svg)
+
+### `ephys_precluster` module
+
+![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_precluster.svg)
 
 ### `subject` schema ([API docs](https://datajoint.com/docs/elements/element-animal/api/element_animal/subject))
 - Although not required, most choose to connect the `Session` table to a `Subject` table.

docs/src/index.md

@@ -26,19 +26,4 @@ developed to handle various use cases of this pipeline and workflow:
 
 Visit the [Concepts page](./concepts.md) for more information about the use cases of
 `ephys` schemas and an explanation of the tables. To get started with building your own
-data pipeline, visit the [Tutorials page](./tutorials.md).  
-
-### `ephys_acute` module
-
-![element-array-ephys-acute diagram]
- (https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
-
-### `ephys_chronic` module
-
-![element-array-ephys-chronic diagram]
- (https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_chronic.svg)
-
-### `ephys_precluster` module
-
-![element-array-ephys-precluster diagram]
- (https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_precluster.svg)
+data pipeline, visit the [Tutorials page](./tutorials.md).

element_array_ephys/ephys_acute.py

@@ -36,12 +36,12 @@ def activate(
         create_schema (bool): If True, schema will be created in the database.
         create_tables (bool): If True, tables related to the schema will be created in the database.
         linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.
-    
+
     Dependencies:
     Upstream tables:
         Session: A parent table to ProbeInsertion
         Probe: A parent table to EphysRecording. Probe information is required before electrophysiology data is imported.
-        
+    
     Functions: 
         get_ephys_root_data_dir(): Returns absolute path for root data director(y/ies) with all electrophysiological recording sessions, as a list of string(s).
         get_session_direction(session_key: dict): Returns path to electrophysiology data for the a particular session as a list of strings.
@@ -125,8 +125,8 @@ class AcquisitionSoftware(dj.Lookup):
     Attributes:
         acq_software ( varchar(24) ): Acquisition software, e.g,. SpikeGLX, OpenEphys 
     """
-    
-    definition = """  # Name of software used for recording of neuropixels probes - SpikeGLX or Open Ephys
+
+    definition = """  # Software used for recording of neuropixels probes
     acq_software: varchar(24)    
     """
     contents = zip(["SpikeGLX", "Open Ephys"])
@@ -271,7 +271,7 @@ class EphysRecording(dj.Imported):
     ---
     -> probe.ElectrodeConfig
     -> AcquisitionSoftware
-    sampling_rate: float # (Hz) 
+    sampling_rate: float # (Hz)
     recording_datetime: datetime # datetime of the recording from this probe
     recording_duration: float # (seconds) duration of the recording from this probe
     """
@@ -296,6 +296,7 @@ def make(self, key):
         session_dir = find_full_path(
             get_ephys_root_data_dir(), get_session_directory(key)
         )
+
         inserted_probe_serial_number = (ProbeInsertion * probe.Probe & key).fetch1(
             "probe"
         )
@@ -708,7 +709,7 @@ class ClusteringTask(dj.Manual):
         EphysRecording (foreign key): EphysRecording primary key.
         ClusteringParamSet (foreign key): ClusteringParamSet primary key.
         clustering_outdir_dir (varchar (255) ): Relative path to output clustering results. 
-        task_mode (enum): `Trigger` and `load` either computes clustering or imports existing clustering data, respectively.
+        task_mode (enum): `Trigger` computes clustering or and `load` imports existing data.
     """
 
     definition = """
@@ -732,9 +733,7 @@ def infer_output_dir(cls, key: dict, relative: bool = False, mkdir: bool = False
             e.g.: sub4/sess1/probe_2/kilosort2_0
         """
         processed_dir = pathlib.Path(get_processed_root_data_dir())
-        session_dir = find_full_path(
-            get_ephys_root_data_dir(), get_session_directory(key)
-        )
+        session_dir = find_full_path(get_ephys_root_data_dir(), get_session_directory(key))
         root_dir = find_root_directory(get_ephys_root_data_dir(), session_dir)
 
         method = (
@@ -798,7 +797,7 @@ class Clustering(dj.Imported):
         clustering_time (datetime): Time when clustering results are generated.
         package_version (varchar(16) ): Package version used for a clustering analysis. 
     """
-    
+
     definition = """
     # Clustering Procedure
     -> ClusteringTask
@@ -998,7 +997,7 @@ class Unit(dj.Part):
             spike_depths (longblob): Array of depths associated with each spike, relative to each spike. 
         """
 
-        definition = """   
+        definition = """
         # Properties of a given unit from a round of clustering (and curation)
         -> master
         unit: int

element_array_ephys/ephys_chronic.py

@@ -13,7 +13,6 @@
 from .readers import spikeglx, kilosort, openephys
 from . import probe, get_logger, ephys_report
 
-
 log = get_logger(__name__)
 
 schema = dj.schema()
@@ -49,7 +48,6 @@ def activate(
         get_processed_data_dir(): Optional. Returns absolute path for processed data. Defaults to root directory. 
     """
 
-
     if isinstance(linking_module, str):
         linking_module = importlib.import_module(linking_module)
     assert inspect.ismodule(
@@ -96,8 +94,8 @@ def get_session_directory(session_key: dict) -> str:
     """Retrieve the session directory with Neuropixels for the given session.
 
     Args:
-        session_key (dict): A dictionary mapping subject to an entry in the subject table, and session_datetime corresponding to a session in the database. 
-        
+        session_key (dict): A dictionary mapping subject to an entry in the subject table, and session_datetime corresponding to a session in the database.
+
     Returns: 
         A string for the path to the session directory. 
     """
@@ -861,15 +859,15 @@ class Curation(dj.Manual):
     curation_id: int
     ---
     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 clustering root data directory
+    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)  
     """
 
-    def create1_from_clustering_task(self, key, curation_note str: = ""):
+    def create1_from_clustering_task(self, key, curation_note: str = ""):
         """
-        A function to create a new corresponding "Curation" for a particular 
+        A function to create a new corresponding "Curation" for a particular
         "ClusteringTask"
         """
         if key not in Clustering():
@@ -1367,8 +1365,7 @@ def get_openephys_probe_data(ephys_recording_key: dict) -> list:
     return probe_data
 
 
-def get_neuropixels_channel2electrode_map(ephys_recording_key: dict,
-acq_software: str) -> dict:
+def get_neuropixels_channel2electrode_map(ephys_recording_key: dict, acq_software: str) -> dict:
     """Get the channel map for neuropixels probe.
     """
     if acq_software == "SpikeGLX":
@@ -1461,7 +1458,7 @@ def generate_electrode_config(probe_type: str, electrodes: list) -> dict:
 
 
 def get_recording_channels_details(ephys_recording_key: dict) -> np.array:
-    """Get details of recording channels for a givenn recording.
+    """Get details of recording channels for a given recording.
     """
     channels_details = {}