v0.6.6

v0.6.6 (December 20, 2024)

Deprecations

• Removed use of jsonschema.RefResolver as it will be deprecated from the jsonschema library PR #1133
• Completely removed compression settings from most places PR #1126
• Soft deprecation for file_path as an argument of SpikeGLXNIDQInterface and SpikeGLXRecordingInterface PR #1155
• starting_time in RecordingInterfaces has given a soft deprecation in favor of time alignment methods PR #1158

Bug Fixes

• datetime objects now can be validated as conversion options #1139
• Make NWBMetaDataEncoder public again PR #1142
• Fix a bug where data in DeepLabCutInterface failed to write when ndx-pose was not imported. #1144
• SpikeGLXConverterPipe converter now accepts multi-probe structures with multi-trigger and does not assume a specific folder structure #1150
• SpikeGLXNIDQInterface is no longer written as an ElectricalSeries #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

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
• 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
• Added .csv support to DeepLabCutInterface PR #1140
• SpikeGLXRecordingInterface now also accepts folder_path making its behavior equivalent to SpikeInterface #1150
• Added the rclone_transfer_batch_job helper function for executing Rclone data transfers in AWS Batch jobs. PR #1085
• Added the deploy_neuroconv_batch_job helper function for deploying NeuroConv AWS Batch jobs. PR #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
  *SpikeGLXNIDQInterface now handdles digital demuxed channels (XD0) #1152

Improvements

• Use mixing tests for ecephy's mocks PR #1136
• Use pytest format for dandi tests to avoid window permission error on teardown PR #1151
• Added many docstrings for public functions PR #1063
• Clean up with warnings and deprecations in the testing framework PR #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

v0.6.5

v0.6.5 (November 1, 2024)

Deprecations

Bug Fixes

• Fixed formatwise installation from pipy PR #1118
• Fixed dailies PR #1113

Features

• Using in-house GenericDataChunkIterator PR #1068
• Data interfaces now perform source (argument inputs) validation with the json schema PR #1020
• Improve the error message when writing a recording extractor with multiple offsets PR #1111
• Added channels_to_skip to EDFRecordingInterface so the user can skip non-neural channels PR #1110

Improvements

• Remove dev test from PR PR #1092
• Run only the most basic testing while a PR is on draft PR #1082
• Test that zarr backend_configuration works in gin data tests PR #1094
• Consolidated weekly workflows into one workflow and added email notifications PR #1088
• Avoid running link test when the PR is on draft PR #1093
• Centralize gin data preparation in a github action PR #1095

v0.6.4

v0.6.4 (September 17, 2024)

Bug Fixes

• Fixed a setup bug introduced in v0.6.2 where installation process created a directory instead of a file for test configuration file PR #1070
• The method get_extractor now works for MockImagingInterface PR #1076
• Updated opencv version for security PR #1087
• Solved a bug of PlexonRecordingInterface where data with multiple streams could not be opened PR #989

Deprecations

Features

• Added chunking/compression for string-only compound objects: PR #1042
• Added automated EFS volume creation and mounting to the submit_aws_job helper function. PR #1018
• Added a mock for segmentation extractors interfaces in ophys: MockSegmentationInterface PR #1067
• Added a MockSortingInterface for testing purposes. PR #1065

Improvements

• Testing on mac sillicon PR #1061
• Add writing to zarr test for to the test on data PR #1056
• Modified the CI to avoid running doctests twice PR #1077
• Consolidated daily workflows into one workflow and added email notifications PR #1081
• Added zarr tests for the test on data with checking equivalent backends PR #1083

v0.6.3

Same as v0.6.2. Testing automatic upload

v0.6.2

v0.6.2 (September 10, 2024)

Deprecations

• The following classes and objects are now private NWBMetaDataEncoder, NWBMetaDataEncoder, check_if_imaging_fits_into_memory, NoDatesSafeLoader PR #1050

Bug Fixes

• Fixed a bug where IntanRecordingInterface added two devices PR #1059
• Fix a bug in add_sorting_to_nwbfile where unit_electrode_indices was only propagated if waveform_means was passed PR #1057

Features

• Make config_file_path optional in DeepLabCutInterfacePR #1031
• Added get_stream_names to OpenEphysRecordingInterface: PR #1039
• Most data interfaces and converters now use Pydantic to validate their inputs, including existence of file and folder paths. PR #1022
• All remaining data interfaces and converters now use Pydantic to validate their inputs, including existence of file and folder paths. PR #1055

Improvements

• Using ruff to enforce existence of public classes' docstrings PR #1034
• Separated tests that use external data by modality PR #1049
• Added Unit Table descriptions for phy and kilosort: PR #1053
• Using ruff to enforce existence of public functions's docstrings PR #1062
• Improved device metadata of IntanRecordingInterface by adding the type of controller used PR #1059

v0.6.1

v0.6.1 (August 30, 2024)

Bug fixes

• Fixed the JSON schema inference warning on excluded fields; also improved error message reporting of which method triggered the error. PR #1037

v0.6.0

v0.6.0 (August 27, 2024)

Deprecations

• Deprecated WaveformExtractor usage. PR #821
• Changed the spikeinterface.tool functions (e.g. add_recording, add_sorting) to have _to_nwbfile as suffix PR #1015
• Deprecated use of compression and compression_options in VideoInterface PR #1005
• get_schema_from_method_signature has been deprecated; please use get_json_schema_from_method_signature instead. PR #1016
• neuroconv.utils.FilePathType and neuroconv.utils.FolderPathType have been deprecated; please use pydantic.FilePath and pydantic.DirectoryPath instead. PR #1017
• Changed the roiextractors.tool function (e.g. add_imaging and add_segmentation) to have the _to_nwbfile suffix [PR #1027]PR #1017

Features

• Added MedPCInterface for operant behavioral output files. PR #883
• Support SortingAnalyzer in the SpikeGLXConverterPipe. PR #821
• Added TDTFiberPhotometryInterface data interface, for converting fiber photometry data from TDT file formats. PR #920
• Add argument to add_electrodes that grants fine control of what to do with the missing values. As a side effect this drops the implicit casting to int when writing int properties to the electrodes table PR #985
• Add Plexon2 support PR #918
• Converter working with multiple VideoInterface instances PR #914
• Added helper function neuroconv.tools.data_transfers.submit_aws_batch_job for basic automated submission of AWS batch jobs. PR #384
• Data interfaces run_conversion method now performs metadata validation before running the conversion. PR #949
• Introduced null_values_for_properties to add_units_table to give user control over null values behavior PR #989

Bug fixes

• Fixed the default naming of multiple electrical series in the SpikeGLXConverterPipe. PR #957
• Write new properties to the electrode table use the global identifier channel_name, group PR #984
• Removed a bug where int64 was casted lossy to float PR #989

Improvements

• The OpenEphysBinaryRecordingInterface now uses lxml for extracting the session start time from the settings.xml file and does not depend on pyopenephys anymore. PR #971
• Swap the majority of package setup and build steps to pyproject.toml instead of setup.py. PR #955
• The DeeplabcutInterface now skips inferring timestamps from movie when timestamps are specified, running faster. PR #967
• Improve metadata writing for SpikeGLX data interface. Added contact ids, shank ids and, remove references to shanks for neuropixels 1.0. Also deprecated the previous neuroconv exclusive property "electrode_shank_number` PR #986
• Add tqdm with warning to DeepLabCut interface PR #1006
• BaseRecordingInterface now calls default metadata when metadata is not passing mimicking run_conversion behavior. PR #1012
• Added get_json_schema_from_method_signature which constructs Pydantic models automatically from the signature of any function with typical annotation types used throughout NeuroConv. PR #1016
• Replaced all interface annotations with Pydantic types. PR #1017
• Changed typehint collections (e.g. List) to standard collections (e.g. list). PR #1021
• Testing now is only one dataset per test PR #1026

v0.5.0

v0.5.0 (July 17, 2024)

Deprecations

• The usage of compression_options directly through the neuroconv.tools.audio submodule is now deprecated - users should refer to the new configure_backend method for a general approach for setting compression. PR #939
• The usage of compression and compression_opts directly through the FicTracDataInterface is now deprecated - users should refer to the new configure_backend method for a general approach for setting compression. PR #941
• The usage of compression directly through the neuroconv.tools.neo submodule is now deprecated - users should refer to the new configure_backend method for a general approach for setting compression. PR #943
• The usage of compression_options directly through the neuroconv.tools.ophys submodule is now deprecated - users should refer to the new configure_backend method for a general approach for setting compression. PR #940
• Removed the option of running interface.run_conversion without nwbfile_path argument . PR #951

Features

• Added docker image and tests for an automated Rclone configuration (with file stream passed via an environment variable). PR #902

Bug fixes

• Fixed the conversion option schema of a SpikeGLXConverter when used inside another NWBConverter. PR #922
• Fixed a case of the NeuroScopeSortingExtractor when the optional xml_file_path is not specified. PR #926
• Fixed Can't specify experiment type when converting .abf to .nwb with Neuroconv. PR #609
• Remove assumption that the ports of the Intan acquisition system correspond to electrode groupings in IntanRecordingInterface PR #933
• Add ValueError for empty metadata in make_or_load_nwbfile when an nwbfile needs to be created PR #948

Improvements

• Make annotations from the raw format available on IntanRecordingInterface. PR #934
• Add an option to suppress display the progress bar (tqdm) in VideoContext PR #937
• Automatic compression of data in the LightnignPoseDataInterface has been disabled - users should refer to the new configure_backend method for a general approach for setting compression. PR #942
• Port over dlc2nwb utility functions for ease of maintenance. PR #946

v0.4.11

v0.4.11 (June 14, 2024)

Bug fixes

• Added a skip condition in get_default_dataset_io_configurations for datasets with any zero-length axis in their full_shape. PR #894
• Added packaging explicitly to minimal requirements. PR #904
• Fixed bug when using make_or_load_nwbfile with overwrite=True on an existing (but corrupt) HDF5 file. PR #911
• Change error trigger with warning trigger when adding both OnePhotonSeries and TwoPhotonSeries to the same file (Issue #906). PR #907

Improvements

• Propagated photon_series_type to BaseImagingExtractorInterface init instead of passing it as an argument of get_metadata() and get_metadata_schema(). PR #847

v0.4.10

v0.4.10 (June 6, 2024)

Bug fixes

• Fixed bug causing overwrite of NWB GUIDE watermark. PR #890