Merge remote-tracking branch 'origin/develop' into docs

Author: mayofaulkner

.github/workflows/ibllib_ci.yml

@@ -33,12 +33,13 @@ jobs:
     - name: Install deps
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install flake8 pytest flake8-docstrings
         pip install -r requirements.txt
         pip install -e .
     - name: Flake8
       run: |
         python -m flake8
+        python -m flake8 --select D --ignore E ibllib/qc/camera.py
     - name: Brainbox tests
       run: |
         cd brainbox

brainbox/behavior/dlc.py

@@ -9,7 +9,7 @@
 import scipy.interpolate as interpolate
 from scipy.stats import zscore
 
-from neurodsp.smooth import smooth_interpolate_savgol
+from ibldsp.smooth import smooth_interpolate_savgol
 from iblutil.numerical import bincount2D
 import brainbox.behavior.wheel as bbox_wheel
 

brainbox/metrics/electrode_drift.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from neurodsp import smooth, utils, fourier
+from ibldsp import smooth, utils, fourier
 from iblutil.numerical import bincount2D
 
 

brainbox/metrics/single_units.py

@@ -981,7 +981,7 @@ def quick_unit_metrics(spike_clusters, spike_times, spike_amps, spike_depths,
     r.amp_std_dB[ir] = np.array(camp['log_amps'].std())
     srp = metrics.slidingRP_all(spikeTimes=spike_times, spikeClusters=spike_clusters,
                                 **{'sampleRate': 30000, 'binSizeCorr': 1 / 30000})
-    r.slidingRP_viol[srp['cidx']] = srp['value']
+    r.slidingRP_viol[ir] = srp['value']
 
     # loop over each cluster to compute the rest of the metrics
     for ic in np.arange(nclust):

examples/archive/ibllib/synchronisation_ephys.py

@@ -1,4 +1,4 @@
-import neurodsp.utils
+import ibldsp.utils
 import spikeglx
 import ibllib.io.extractors.ephys_fpga
 
@@ -15,7 +15,7 @@
 
 # if the data is needed as well, loop over the file
 # raw data contains raw ephys traces, while raw_sync contains the 16 sync traces
-wg = neurodsp.utils.WindowGenerator(sr.ns, BATCH_SIZE_SAMPLES, overlap=1)
+wg = ibldsp.utils.WindowGenerator(sr.ns, BATCH_SIZE_SAMPLES, overlap=1)
 for first, last in wg.firstlast:
     rawdata, rawsync = sr.read_samples(first, last)
     wg.print_progress()

examples/loading_data/loading_raw_ephys_data.ipynb

@@ -107,13 +107,13 @@
     "print(f'raw AP band sample for event at time {t_event}: {s_event}')\n",
     "\n",
     "# get the AP data surrounding samples\n",
-    "window_secs_ap = [-0.05, 0.05]  # we'll look at 100ms before the event and 200ms after the event for AP\n",
+    "window_secs_ap = [-0.05, 0.05]  # we'll look at 50ms before and after the event for AP\n",
     "first, last = (int(window_secs_ap[0] * sr_ap.fs) + s_event, int(window_secs_ap[1] * sr_ap.fs + s_event))\n",
     "raw_ap = sr_ap[first:last, :-sr_ap.nsync].T\n",
     "\n",
     "# get the LF data surrounding samples\n",
-    "window_secs_ap = [-0.750, 0.750]  # we'll look at 100ms before the event and 200ms after the event\n",
-    "sample_lf = s_event // 12  # NB: for neuropixel probes this is always 12\n",
+    "window_secs_ap = [-0.750, 0.750]  # we'll look at 750ms before and after the event because LF varies more slowly in time\n",
+    "sample_lf = s_event // 12  # NB: for neuropixel probes this is always 12 because AP is sampled at 12x the frequency of LF\n",
     "first, last = (int(window_secs_ap[0] * sr_lf.fs) + sample_lf, int(window_secs_ap[1] * sr_lf.fs + sample_lf))\n",
     "raw_lf = sr_lf[first:last, :-sr_lf.nsync].T"
    ]
@@ -236,7 +236,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neurodsp.voltage import destripe\n",
+    "from ibldsp.voltage import destripe\n",
     "# Reminder : If not done before, remove first the sync channel from raw data\n",
     "# Apply destriping algorithm to data\n",
     "destriped = destripe(raw_ap, fs=sr_ap.fs)"
@@ -445,7 +445,7 @@
    "source": [
     "## Useful modules\n",
     "* [ibllib.io.spikeglx](https://int-brain-lab.github.io/ibl-neuropixel/_autosummary/spikeglx.html)\n",
-    "* [ibllib.voltage.dsp](https://int-brain-lab.github.io/ibl-neuropixel/_autosummary/neurodsp.voltage.html)\n",
+    "* [ibllib.voltage.dsp](https://int-brain-lab.github.io/ibl-neuropixel/_autosummary/ibldsp.voltage.html)\n",
     "* [brainbox.io.spikeglx.stream](https://int-brain-lab.github.io/iblenv/_autosummary/brainbox.io.spikeglx.html#brainbox.io.spikeglx.stream)\n",
     "* [viewephys](https://github.com/oliche/viewephys) to visualise raw data snippets (Note: this package is not within `ibllib` but standalone)"
    ]

examples/one/histology/coverage_map.py

@@ -1,7 +1,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from one.api import ONE
-from neurodsp.utils import fcn_cosine
+from ibldsp.utils import fcn_cosine
 
 import iblatlas.atlas as atlas
 from ibllib.pipes.histology import coverage

ibllib/__init__.py

@@ -2,7 +2,7 @@
 import logging
 import warnings
 
-__version__ = '2.29.0'
+__version__ = '2.34.1'
 warnings.filterwarnings('always', category=DeprecationWarning, module='ibllib')
 
 # if this becomes a full-blown library we should let the logging configuration to the discretion of the dev

ibllib/ephys/ephysqc.py

@@ -11,7 +11,7 @@
 from iblutil.util import Bunch
 import spikeglx
 import neuropixel
-from neurodsp import fourier, utils, voltage
+from ibldsp import fourier, utils, voltage
 from tqdm import tqdm
 
 from brainbox.io.spikeglx import Streamer

ibllib/ephys/spikes.py

@@ -142,7 +142,7 @@ def ks2_to_alf(ks_path, bin_path, out_path, bin_file=None, ampfactor=1, label=No
     """
     m = ephysqc.phy_model_from_ks2_path(ks2_path=ks_path, bin_path=bin_path, bin_file=bin_file)
     ac = phylib.io.alf.EphysAlfCreator(m)
-    ac.convert(out_path, label=label, force=force, ampfactor=ampfactor)
+    ac.convert(out_path, label=label, force=force, ampfactor=float(ampfactor))
 
 
 def ks2_to_tar(ks_path, out_path, force=False):