From 15eabac56f3994f0e357bf2080fc2da4e2b9a78f Mon Sep 17 00:00:00 2001 From: bendichter Date: Fri, 27 Oct 2023 20:03:58 -0400 Subject: [PATCH 1/5] add auto-doc for spikeglxconverter.py --- docs/api/interfaces.ecephys.rst | 1 + .../datainterfaces/ecephys/spikeglx/spikeglxconverter.py | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/api/interfaces.ecephys.rst b/docs/api/interfaces.ecephys.rst index a7d682622..ca0bdeb81 100644 --- a/docs/api/interfaces.ecephys.rst +++ b/docs/api/interfaces.ecephys.rst @@ -68,6 +68,7 @@ Spikegadgets Recording SpikeGLX Recording ------------------ +.. automodule:: neuroconv.datainterfaces.ecephys.spikeglx.spikeglxconverter .. automodule:: neuroconv.datainterfaces.ecephys.spikeglx.spikeglxdatainterface .. automodule:: neuroconv.datainterfaces.ecephys.spikeglx.spikeglxnidqinterface diff --git a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py index 69b2480fb..021983036 100644 --- a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py +++ b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py @@ -1,4 +1,3 @@ -"""The simplest, easiest to use class for converting all SpikeGLX data in a folder.""" from pathlib import Path from typing import List, Optional @@ -11,7 +10,10 @@ class SpikeGLXConverterPipe(ConverterPipe): - """Primary conversion class for handling multiple SpikeGLX data streams.""" + """ + The simplest, easiest to use class for converting all SpikeGLX data in a folder. Primary conversion class for + handling multiple SpikeGLX data streams. + """ @classmethod def get_source_schema(cls): From a72a931176c97134b85e43fb1fcf4fef2a34e64b Mon Sep 17 00:00:00 2001 From: bendichter Date: Fri, 27 Oct 2023 20:10:44 -0400 Subject: [PATCH 2/5] add auto-doc for MaxOneRecordingInterface --- docs/api/interfaces.ecephys.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/api/interfaces.ecephys.rst b/docs/api/interfaces.ecephys.rst index ca0bdeb81..a0d4322ad 100644 --- a/docs/api/interfaces.ecephys.rst +++ b/docs/api/interfaces.ecephys.rst @@ -49,6 +49,10 @@ OpenEphys Recording ------------------- .. automodule:: neuroconv.datainterfaces.ecephys.openephys.openephysdatainterface +MaxOne Recording +---------------- +.. automodule:: neuroconv.datainterfaces.ecephys.maxwell.maxonedatainterface + Phy Sorting ----------- .. automodule:: neuroconv.datainterfaces.ecephys.phy.phydatainterface From 41ab93b9c9bcfa457a3631df2d0b3436d14ebf44 Mon Sep 17 00:00:00 2001 From: bendichter Date: Fri, 27 Oct 2023 20:13:01 -0400 Subject: [PATCH 3/5] add auto-doc for MEArecRecordingInterface --- docs/api/interfaces.ecephys.rst | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/docs/api/interfaces.ecephys.rst b/docs/api/interfaces.ecephys.rst index a0d4322ad..a6cf31dfc 100644 --- a/docs/api/interfaces.ecephys.rst +++ b/docs/api/interfaces.ecephys.rst @@ -37,6 +37,14 @@ KiloSort Sorting ---------------- .. automodule:: neuroconv.datainterfaces.ecephys.kilosort.kilosortdatainterface +MaxOne Recording +---------------- +.. automodule:: neuroconv.datainterfaces.ecephys.maxwell.maxonedatainterface + +MEArec Recording +---------------- +.. automodule:: neuroconv.datainterfaces.ecephys.mearec.mearecdatainterface + Neuralynx Recording & Sorting ----------------------------- .. automodule:: neuroconv.datainterfaces.ecephys.neuralynx.neuralynxdatainterface @@ -49,9 +57,6 @@ OpenEphys Recording ------------------- .. automodule:: neuroconv.datainterfaces.ecephys.openephys.openephysdatainterface -MaxOne Recording ----------------- -.. automodule:: neuroconv.datainterfaces.ecephys.maxwell.maxonedatainterface Phy Sorting ----------- From ceac3e90ad046b8506f85db3e8a0a9eb98466c8b Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Sat, 28 Oct 2023 15:33:02 +0200 Subject: [PATCH 4/5] fix tests --- tests/test_on_data/test_behavior_interfaces.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_on_data/test_behavior_interfaces.py b/tests/test_on_data/test_behavior_interfaces.py index 69c1d748b..1f1ebfb6a 100644 --- a/tests/test_on_data/test_behavior_interfaces.py +++ b/tests/test_on_data/test_behavior_interfaces.py @@ -47,7 +47,7 @@ def check_read_nwb(self, nwbfile_path: str): # This is currently structured to with NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io: nwbfile = io.read() - fictrac_position_container = nwbfile.processing["Behavior"].data_interfaces["FicTrac"] + fictrac_position_container = nwbfile.processing["behavior"].data_interfaces["FicTrac"] assert isinstance(fictrac_position_container, Position) assert len(fictrac_position_container.spatial_series) == 10 @@ -82,7 +82,7 @@ def check_read_nwb(self, nwbfile_path: str): # This is currently structured to with NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io: nwbfile = io.read() - fictrac_position_container = nwbfile.processing["Behavior"].data_interfaces["FicTrac"] + fictrac_position_container = nwbfile.processing["behavior"].data_interfaces["FicTrac"] assert isinstance(fictrac_position_container, Position) assert len(fictrac_position_container.spatial_series) == 10 From 424ba80de284d51b17f18d5cd5a2fe25db5cff6f Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Sat, 28 Oct 2023 10:21:23 -0400 Subject: [PATCH 5/5] Update src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> --- .../datainterfaces/ecephys/spikeglx/spikeglxconverter.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py index 021983036..5008eb573 100644 --- a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py +++ b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py @@ -11,8 +11,9 @@ class SpikeGLXConverterPipe(ConverterPipe): """ - The simplest, easiest to use class for converting all SpikeGLX data in a folder. Primary conversion class for - handling multiple SpikeGLX data streams. + The simplest, easiest to use class for converting all SpikeGLX data in a folder. + + Primary conversion class for handling multiple SpikeGLX data streams. """ @classmethod