From 0484dea5491da0a45a2170ca5a76290e87da2f6a Mon Sep 17 00:00:00 2001 From: Jeffrey Gill Date: Fri, 9 Dec 2022 03:54:59 -0500 Subject: [PATCH] Fix compatibility with SpikeTrainList in Neo>=0.10 Partially addresses #319. --- neurotic/datasets/data.py | 4 ++-- requirements.txt | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/neurotic/datasets/data.py b/neurotic/datasets/data.py index f0873b3..22b7d72 100644 --- a/neurotic/datasets/data.py +++ b/neurotic/datasets/data.py @@ -90,7 +90,7 @@ def load_dataset(metadata, blk=None, lazy=False, signal_group_mode='split-all', # classify spikes by amplitude if not using lazy loading of signals if not lazy: - blk.segments[0].spiketrains += _run_amplitude_discriminators(metadata, blk) + blk.segments[0].spiketrains.extend(_run_amplitude_discriminators(metadata, blk)) # read in spikes identified by spike sorting using tridesclous spikes_dataframe = _read_spikes_file(metadata, blk) @@ -99,7 +99,7 @@ def load_dataset(metadata, blk=None, lazy=False, signal_group_mode='split-all', t_start = blk.segments[0].analogsignals[0].t_start # assuming all AnalogSignals start at the same time t_stop = blk.segments[0].analogsignals[0].t_stop # assuming all AnalogSignals start at the same time sampling_period = blk.segments[0].analogsignals[0].sampling_period # assuming all AnalogSignals have the same sampling rate - blk.segments[0].spiketrains += _create_neo_spike_trains_from_dataframe(spikes_dataframe, metadata, t_start, t_stop, sampling_period) + blk.segments[0].spiketrains.extend(_create_neo_spike_trains_from_dataframe(spikes_dataframe, metadata, t_start, t_stop, sampling_period)) else: logger.warning('Ignoring tridesclous_file because the sampling rate and start time could not be inferred from analog signals') diff --git a/requirements.txt b/requirements.txt index 393c1c6..711bc81 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ # av # required but typically not installable via pip, try `conda install -c conda-forge av` ephyviewer>=1.3.0 -neo>=0.7.2,<0.10.0 # TODO: fix for neo>=0.10 +neo>=0.7.2 numpy packaging pandas