Neuroconv

Deprecations and Changes

Bug Fixes

Features

Improvements

Deprecations and Changes

Bug Fixes
* Fix parsing of group_names in `tools.spikeinterface` [PR 1234](https://github.com/catalystneuro/neuroconv/pull/1234)

Features

Improvements
* Testing suite now supports numpy 2.0. [PR 1235](https://github.com/catalystneuro/neuroconv/pull/1235)

Deprecations and Changes
* Interfaces and converters now have `verbose=False` by default [PR 1153](https://github.com/catalystneuro/neuroconv/pull/1153)
* Added `metadata` and `conversion_options` as arguments to `NWBConverter.temporally_align_data_interfaces` [PR 1162](https://github.com/catalystneuro/neuroconv/pull/1162)
* Deprecations in the ecephys pipeline: compression options, old iterator options, methods that did not end up in *to_nwbfile and the `get_schema_from_method_signature` function [PR 1207](https://github.com/catalystneuro/neuroconv/pull/1207)
* Removed all deprecated functions from the roiextractors module: `add_fluorescence_traces`, `add_background_fluorescence_traces`, `add_summary_images`, `add_segmentation`, and `write_segmentation` [1233](https://github.com/catalystneuro/neuroconv/pull/1233)

Bug Fixes
* `run_conversion` does not longer trigger append mode when `nwbfile_path` points to a faulty file [PR 1180](https://github.com/catalystneuro/neuroconv/pull/1180)
* `DatasetIOConfiguration` now recommends `chunk_shape = (len(candidate_dataset),)` for datasets with compound dtypes as used by hdmf >= 3.14.6. [PR 1146](https://github.com/catalystneuro/neuroconv/pull/1146)
* `OpenEphysBinaryRecordingInterface` no longer stores analog data as an `ElectricalSeries` [PR 1179](https://github.com/catalystneuro/neuroconv/pull/1179)

Features
* Added `PlexonLFPInterface` for converting Plexon `FPl-Low Pass Filtered` stream data [PR 1209](https://github.com/catalystneuro/neuroconv/pull/1209)
* Added `ImageInterface` for writing large collection of images to NWB and automatically map the images to the correct NWB data types [PR 1190](https://github.com/catalystneuro/neuroconv/pull/1190)
* Fixed AudioInterface to properly handle 24-bit WAV files by disabling memory mapping for 24-bit files [PR 1226](https://github.com/catalystneuro/neuroconv/pull/1226)
* Use the latest version of ndx-pose for `DeepLabCutInterface` and `LightningPoseDataInterface` [PR 1128](https://github.com/catalystneuro/neuroconv/pull/1128)
* Added a first draft of `.clinerules` [PR 1229](https://github.com/catalystneuro/neuroconv/pull/1229)
* Support for pynwb 3.0 [PR 1231](https://github.com/catalystneuro/neuroconv/pull/1231)
* Support for hdmf 4.0 [PR 1204](https://github.com/catalystneuro/neuroconv/pull/1204)
* Support for numpy 2.0 [PR 1206](https://github.com/catalystneuro/neuroconv/pull/1206)
* Support Spikeinterface 0.102 [PR 1194](https://github.com/catalystneuro/neuroconv/pull/1194)

Improvements
* Simple writing no longer uses a context manager [PR 1180](https://github.com/catalystneuro/neuroconv/pull/1180)
* Added Returns section to all getter docstrings [PR 1185](https://github.com/catalystneuro/neuroconv/pull/1185)
* ElectricalSeries have better chunking defaults when data is passed as plain array [PR 1184](https://github.com/catalystneuro/neuroconv/pull/1184)
* Ophys interfaces now call `get_metadata` by default when no metadata is passed [PR 1200](https://github.com/catalystneuro/neuroconv/pull/1200) and [PR #1232](https://github.com/catalystneuro/neuroconv/pull/1232)

Deprecations and Changes

Bug Fixes
* Temporary set a ceiling for hdmf to avoid a chunking bug [PR 1175](https://github.com/catalystneuro/neuroconv/pull/1175)

Features
* Add description to inter-sample-shift for `SpikeGLXRecordingInterface` [PR 1177](https://github.com/catalystneuro/neuroconv/pull/1177)

Improvements
* `get_json_schema_from_method_signature` now throws a more informative error when an untyped parameter is passed [1157](https://github.com/catalystneuro/neuroconv/pull/1157)
* Improve the naming of ElectrodeGroups in the `SpikeGLXRecordingInterface` when multi probes are present [PR 1177](https://github.com/catalystneuro/neuroconv/pull/1177)
* Detect mismatch errors between group and group names when writing ElectrodeGroups [PR 1165](https://github.com/catalystneuro/neuroconv/pull/1165)
* Fix metadata bug in `IntanRecordingInterface` where extra devices were added incorrectly if the recording contained multiple electrode groups or names [1166](https://github.com/catalystneuro/neuroconv/pull/1166)
* Source validation is no longer performed when initializing interfaces or converters [PR 1168](https://github.com/catalystneuro/neuroconv/pull/1168)

Deprecations and Changes
* Removed use of `jsonschema.RefResolver` as it will be deprecated from the jsonschema library [PR 1133](https://github.com/catalystneuro/neuroconv/pull/1133)
* Completely removed compression settings from most places[PR 1126](https://github.com/catalystneuro/neuroconv/pull/1126)
* Completely removed compression settings from most places [PR 1126](https://github.com/catalystneuro/neuroconv/pull/1126)
* Soft deprecation for `file_path` as an argument of `SpikeGLXNIDQInterface` and `SpikeGLXRecordingInterface` [PR 1155](https://github.com/catalystneuro/neuroconv/pull/1155)
* `starting_time` in RecordingInterfaces has given a soft deprecation in favor of time alignment methods [PR 1158](https://github.com/catalystneuro/neuroconv/pull/1158)

Bug Fixes
* datetime objects now can be validated as conversion options [1139](https://github.com/catalystneuro/neuroconv/pull/1126)
* Make `NWBMetaDataEncoder` public again [PR 1142](https://github.com/catalystneuro/neuroconv/pull/1142)
* Fix a bug where data in `DeepLabCutInterface` failed to write when `ndx-pose` was not imported. [1144](https://github.com/catalystneuro/neuroconv/pull/1144)
* `SpikeGLXConverterPipe` converter now accepts multi-probe structures with multi-trigger and does not assume a specific folder structure [1150](https://github.com/catalystneuro/neuroconv/pull/1150)
* `SpikeGLXNIDQInterface` is no longer written as an ElectricalSeries [1152](https://github.com/catalystneuro/neuroconv/pull/1152)
* Fix a bug on ecephys interfaces where extra electrode group and devices were written if the property of the "group_name" was set in the recording extractor [1164](https://github.com/catalystneuro/neuroconv/pull/1164)


Features
* Propagate the `unit_electrode_indices` argument from the spikeinterface tools to `BaseSortingExtractorInterface`. This allows users to map units to the electrode table when adding sorting data [PR 1124](https://github.com/catalystneuro/neuroconv/pull/1124)
* Imaging interfaces have a new conversion option `always_write_timestamps` that can be used to force writing timestamps even if neuroconv's heuristics indicates regular sampling rate [PR 1125](https://github.com/catalystneuro/neuroconv/pull/1125)
* Added .csv support to DeepLabCutInterface [PR 1140](https://github.com/catalystneuro/neuroconv/pull/1140)
* `SpikeGLXRecordingInterface` now also accepts `folder_path` making its behavior equivalent to SpikeInterface [1150](https://github.com/catalystneuro/neuroconv/pull/1150)
* Added the `rclone_transfer_batch_job` helper function for executing Rclone data transfers in AWS Batch jobs. [PR 1085](https://github.com/catalystneuro/neuroconv/pull/1085)
* Added the `deploy_neuroconv_batch_job` helper function for deploying NeuroConv AWS Batch jobs. [PR 1086](https://github.com/catalystneuro/neuroconv/pull/1086)
* YAML specification files now accepts an outer keyword `upload_to_dandiset="< six-digit ID >"` to automatically upload the produced NWB files to the DANDI archive [PR 1089](https://github.com/catalystneuro/neuroconv/pull/1089)
*`SpikeGLXNIDQInterface` now handdles digital demuxed channels (`XD0`) [1152](https://github.com/catalystneuro/neuroconv/pull/1152)

Improvements
* Use mixing tests for ecephy's mocks [PR 1136](https://github.com/catalystneuro/neuroconv/pull/1136)
* Use pytest format for dandi tests to avoid window permission error on teardown [PR 1151](https://github.com/catalystneuro/neuroconv/pull/1151)
* Added many docstrings for public functions [PR 1063](https://github.com/catalystneuro/neuroconv/pull/1063)
* Clean up warnings and deprecations in the testing framework for the ecephys pipeline [PR 1158](https://github.com/catalystneuro/neuroconv/pull/1158)
* Enhance the typing of the signature on the `NWBConverter` by adding zarr as a literal option on the backend and backend configuration [PR 1160](https://github.com/catalystneuro/neuroconv/pull/1160)

Bug Fixes
* Fixed formatwise installation from pipy [PR 1118](https://github.com/catalystneuro/neuroconv/pull/1118)
* Fixed dailies [PR 1113](https://github.com/catalystneuro/neuroconv/pull/1113)

Deprecations

Features
* Using in-house `GenericDataChunkIterator` [PR 1068](https://github.com/catalystneuro/neuroconv/pull/1068)
* Data interfaces now perform source (argument inputs) validation with the json schema [PR 1020](https://github.com/catalystneuro/neuroconv/pull/1020)
* Improve the error message when writing a recording extractor with multiple offsets [PR 1111](https://github.com/catalystneuro/neuroconv/pull/1111)
* Added `channels_to_skip` to `EDFRecordingInterface` so the user can skip non-neural channels [PR 1110](https://github.com/catalystneuro/neuroconv/pull/1110)

Improvements
* Remove dev test from PR [PR 1092](https://github.com/catalystneuro/neuroconv/pull/1092)
* Run only the most basic testing while a PR is on draft [PR 1082](https://github.com/catalystneuro/neuroconv/pull/1082)
* Test that zarr backend_configuration works in gin data tests [PR 1094](https://github.com/catalystneuro/neuroconv/pull/1094)
* Consolidated weekly workflows into one workflow and added email notifications [PR 1088](https://github.com/catalystneuro/neuroconv/pull/1088)
* Avoid running link test when the PR is on draft [PR 1093](https://github.com/catalystneuro/neuroconv/pull/1093)
* Centralize gin data preparation in a github action [PR 1095](https://github.com/catalystneuro/neuroconv/pull/1095)