From 891f2aa05d4a79cd0b16a372b0b0ed76b8fe19b0 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Mon, 22 Aug 2022 08:58:53 -0400 Subject: [PATCH 1/2] Update edf.py changing the extra_requirements so that neo manages them fully, making use of neo's extras_require structure [here](https://github.com/NeuralEnsemble/python-neo/blob/070eb47325839b8daf30299085f3b8f62eefc243/setup.py#L17) --- spikeinterface/extractors/neoextractors/edf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/spikeinterface/extractors/neoextractors/edf.py b/spikeinterface/extractors/neoextractors/edf.py index 6407be5d90..0696762cc3 100644 --- a/spikeinterface/extractors/neoextractors/edf.py +++ b/spikeinterface/extractors/neoextractors/edf.py @@ -26,7 +26,7 @@ def __init__(self, file_path, stream_id=None, all_annotations=False): neo_kwargs = {'filename': str(file_path)} NeoBaseRecordingExtractor.__init__(self, stream_id=stream_id, all_annotations=all_annotations, **neo_kwargs) self._kwargs.update({'file_path': str(file_path)}) - self.extra_requirements.append('pyedflib') + self.extra_requirements.append('neo[edf]') -read_edf = define_function_from_class(source_class=EDFRecordingExtractor, name="read_edf") \ No newline at end of file +read_edf = define_function_from_class(source_class=EDFRecordingExtractor, name="read_edf") From 23996508e9f8d54b77eca4f59e35fae644a1aecb Mon Sep 17 00:00:00 2001 From: bendichter Date: Mon, 22 Aug 2022 09:08:09 -0400 Subject: [PATCH 2/2] defer to neo for dependency management of extractors --- spikeinterface/extractors/neoextractors/ced.py | 2 +- spikeinterface/extractors/neoextractors/nix.py | 2 +- spikeinterface/extractors/neoextractors/openephys.py | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/spikeinterface/extractors/neoextractors/ced.py b/spikeinterface/extractors/neoextractors/ced.py index 3b6483c224..b2870acab2 100644 --- a/spikeinterface/extractors/neoextractors/ced.py +++ b/spikeinterface/extractors/neoextractors/ced.py @@ -27,7 +27,7 @@ def __init__(self, file_path, stream_id=None, all_annotations=False): neo_kwargs = {'filename': str(file_path)} NeoBaseRecordingExtractor.__init__(self, stream_id=stream_id, all_annotations=all_annotations, **neo_kwargs) self._kwargs.update(dict(file_path=str(file_path))) - self.extra_requirements.append('sonpy') + self.extra_requirements.append('neo[ced]') diff --git a/spikeinterface/extractors/neoextractors/nix.py b/spikeinterface/extractors/neoextractors/nix.py index 358b3943c2..b88ef731fb 100644 --- a/spikeinterface/extractors/neoextractors/nix.py +++ b/spikeinterface/extractors/neoextractors/nix.py @@ -30,7 +30,7 @@ def __init__(self, file_path, stream_id=None, all_annotations=False): neo_kwargs = {'filename': str(file_path)} NeoBaseRecordingExtractor.__init__(self, stream_id=stream_id, all_annotations=all_annotations, **neo_kwargs) self._kwargs.update(dict(file_path=str(file_path), stream_id=stream_id)) - self.extra_requirements.append('nixio') + self.extra_requirements.append('neo[nixio]') read_nix = define_function_from_class(source_class=NixRecordingExtractor, name="read_nix") diff --git a/spikeinterface/extractors/neoextractors/openephys.py b/spikeinterface/extractors/neoextractors/openephys.py index dfcdd4c80b..349db4b3e6 100644 --- a/spikeinterface/extractors/neoextractors/openephys.py +++ b/spikeinterface/extractors/neoextractors/openephys.py @@ -93,7 +93,6 @@ def __init__(self, folder_path, stream_id=None, all_annotations=False): sample_shifts = get_neuropixels_sample_shifts(self.get_num_channels(), num_channels_per_adc) self.set_property("inter_sample_shift", sample_shifts) - self._kwargs .update(dict(folder_path=str(folder_path)))