Merge pull request #500 from int-brain-lab/NumbaNumpyVersions

Numba numpy versions

Author: k1o0

brainbox/__init__.py

@@ -1,3 +1,4 @@
+"""IBL shared data processing methods."""
 import logging
 try:
     import one

ibllib/__init__.py

@@ -1,3 +1,4 @@
+"""Library implementing the International Brain Laboratory data pipeline."""
 __version__ = "2.13.6"
 import warnings
 

ibllib/io/__init__.py

@@ -1 +1 @@
-import spikeglx
+import spikeglx  # TODO Remove November 2022

ibllib/qc/__init__.py

@@ -0,0 +1 @@
+"""Data quality control calculation and aggregation."""

ibllib/qc/camera.py

@@ -1,28 +1,36 @@
-"""Camera QC
+"""Video quality control.
+
 This module runs a list of quality control metrics on the camera and extracted video data.
 
-Example - Run right camera QC, downloading all but video file
-    qc = CameraQC(eid, 'right', download_data=True, stream=True)
-    qc.run()
+Examples
+--------
+Run right camera QC, downloading all but video file
+
+>>> qc = CameraQC(eid, 'right', download_data=True, stream=True)
+>>> qc.run()
+
+Run left camera QC with session path, update QC field in Alyx
+
+>>> qc = CameraQC(session_path, 'left')
+>>> outcome, extended = qc.run(update=True)  # Returns outcome of videoQC only
+>>> print(f'video QC = {outcome}; overall session QC = {qc.outcome}')  # NB difference outcomes
+
+Run only video QC (no timestamp/alignment checks) on 20 frames for the body camera
+
+>>> qc = CameraQC(eid, 'body', n_samples=20)
+>>> qc.load_video_data()  # Quicker than loading all data
+>>> qc.run()
 
-Example - Run left camera QC with session path, update QC field in Alyx
-    qc = CameraQC(session_path, 'left')
-    outcome, extended = qc.run(update=True)  # Returns outcome of videoQC only
-    print(f'video QC = {outcome}; overall session QC = {qc.outcome}')  # NB difference outcomes
+Run specific video QC check and display the plots
 
-Example - Run only video QC (no timestamp/alignment checks) on 20 frames for the body camera
-    qc = CameraQC(eid, 'body', n_samples=20)
-    qc.load_video_data()  # Quicker than loading all data
-    qc.run()
+>>> qc = CameraQC(eid, 'left')
+>>> qc.load_data(download_data=True)
+>>> qc.check_position(display=True)  # NB: Not all checks make plots
 
-Example - Run specific video QC check and display the plots
-    qc = CameraQC(eid, 'left;)
-    qc.load_data(download_data=True)
-    qc.check_position(display=True)  # NB: Not all checks make plots
+Run the QC for all cameras
 
-Example - Run the QC for all cameras
-    qcs = run_all_qc(eid)
-    qcs['left'].metrics  # Dict of checks and outcomes for left camera
+>>> qcs = run_all_qc(eid)
+>>> qcs['left'].metrics  # Dict of checks and outcomes for left camera
 """
 import logging
 from inspect import getmembers, isfunction

requirements.txt

@@ -8,8 +8,8 @@ jupyter>=1.0
 jupyterlab>=1.0
 matplotlib>=3.0.3
 mtscomp>=1.0.1
-numba
-numpy>=1.18,<=1.21
+numba>=0.56
+numpy>=1.18
 opencv-python
 pandas>=0.24.2
 phylib>=2.4