Neuroconv

Back-compatibility break

* Create separate `.add_to_nwbfile` method for all DataInterfaces. This is effectively the previous `.run_conversion` method but limited to operations on an in-memory `nwbfile`: pynwb.NWBFile` object and does not handle any I/O. [PR 455](https://github.com/catalystneuro/neuroconv/pull/455)

Fixes

* Set gzip compression by default on spikeinterface based interfaces `run_conversion`. [PR 499](https://github.com/catalystneuro/neuroconv/pull/#499)

* Temporarily disabled filtering for all-zero traces in `add_fluorescence_traces` as the current implementation is very slow for nearly all zero traces (e.g. suite2p deconvolved traces). [PR 527](https://github.com/catalystneuro/neuroconv/pull/527)

Features

* Added stream control with the `stream_name` argument to the `NeuralynxRecordingExtractor`. [PR 369](https://github.com/catalystneuro/neuroconv/pull/369)

* Added a common `.temporally_align_data_interfaces` method to the `NWBConverter` class to use as a specification of the protocol for temporally aligning the data interfaces of the converter. [PR 362](https://github.com/catalystneuro/neuroconv/pull/362)

* Added `CellExplorerRecordingInterface` for adding data raw and lfp data from the CellExplorer format. CellExplorer's new format contains a `basename.session.mat` file containing
rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
groups, location and brain area [488](https://github.com/catalystneuro/neuroconv/pull/488)

* `CellExplorerSortingInterface` now supports extracting sampling frequency from the new data format. CellExplorer's new format contains a `basename.session.mat` file containing
rich metadata including the sorting sampling frequency [PR 491](https://github.com/catalystneuro/neuroconv/pull/491) and [PR #502](https://github.com/catalystneuro/neuroconv/pull/502)
* Added `MiniscopeBehaviorInterface` for Miniscope behavioral data. The interface uses `ndx-miniscope` extension to add a `Miniscope` device with the behavioral camera metadata,
and an `ImageSeries` in external mode that is linked to the device. [PR 482](https://github.com/catalystneuro/neuroconv/pull/482)
* `CellExplorerSortingInterface` now supports adding channel metadata to the nwbfile with `write_ecephys_metadata=True` as a conversion option [PR 494](https://github.com/catalystneuro/neuroconv/pull/494)

* Added `MiniscopeImagingInterface` for Miniscope imaging data stream. The interface uses `ndx-miniscope` extension to add a `Miniscope` device with the microscope device metadata,
and the imaging data as `OnePhotonSeries`. [PR 468](https://github.com/catalystneuro/neuroconv/pull/468)

* Added `MiniscopeConverter` for combining the conversion of Miniscope imaging and behavioral data streams. [PR 498](https://github.com/catalystneuro/neuroconv/pull/498)

Improvements

* Avoid redundant timestamp creation in `add_eletrical_series` for recording objects without time vector. [PR 495](https://github.com/catalystneuro/neuroconv/pull/495)

* Avoid modifying the passed `metadata` structure via `deep_dict_update` in `make_nwbfile_from_metadata`. [PR 476](https://github.com/catalystneuro/neuroconv/pull/476)

Testing

* Added gin test for `CellExplorerRecordingInterface`. CellExplorer's new format contains a `basename.session.mat` file containing
rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
groups, location and brain area [488](https://github.com/catalystneuro/neuroconv/pull/488).
* Added gin test for `CellExplorerSortingInterface`. CellExplorer's new format contains a `basename.session.mat` file containing
rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
groups, location and brain area [PR 494](https://github.com/catalystneuro/neuroconv/pull/494).

Back-compatibility break
* `ExtractorInterface` classes now access their extractor with the classmethod `cls.get_extractor()` instead of the attribute `self.Extractor`. [PR 324](https://github.com/catalystneuro/neuroconv/pull/324)
* The `spikeextractor_backend` option was removed for all `RecordingExtractorInterface` classes. ([PR 324](https://github.com/catalystneuro/neuroconv/pull/324), [PR #309](https://github.com/catalystneuro/neuroconv/pull/309)]
* The `NeuroScopeMultiRecordingExtractor` has been removed. If your conversion required this, please submit an issue requesting instructions for how to implement it. [PR 309](https://github.com/catalystneuro/neuroconv/pull/309)
* The `SIPickle` interfaces have been removed. [PR 309](https://github.com/catalystneuro/neuroconv/pull/309)
* The previous conversion option `es_key` has been moved to the `__init__` of all `BaseRecordingExtractorInterface` classes. It is no longer possible to use this argument in the `run_conversion` method. [PR 318](https://github.com/catalystneuro/neuroconv/pull/318)
* Change `BaseDataInterface.get_conversion_options_schema` from `classmethod` to object method. [PR 353](https://github.com/catalystneuro/neuroconv/pull/353)
* Removed `utils.json_schema.get_schema_for_NWBFile` and moved base metadata schema to external json file. Added constraints to Subject metadata to match DANDI. [PR 376](https://github.com/catalystneuro/neuroconv/pull/376)
* Duplicate video file paths in the VideoInterface and AudioInterface are no longer silently resolved; please explicitly remove duplicates when initializing the interfaces. [PR 403](https://github.com/catalystneuro/neuroconv/pull/403)
* Duplicate audio file paths in the AudioInterface are no longer silently resolved; please explicitly remove duplicates when initializing the interfaces. [PR 402](https://github.com/catalystneuro/neuroconv/pull/402)

Features
* The `OpenEphysRecordingInterface` is now a wrapper for `OpenEphysBinaryRecordingInterface`. [PR 294](https://github.com/catalystneuro/neuroconv/pull/294)
* Swapped the backend for `CellExplorerSortingInterface` from `spikeextactors` to `spikeinterface`. [PR 267](https://github.com/catalystneuro/neuroconv/pull/267)
* In the conversion YAML, `DataInterface` classes must now be specified as a dictionary instead of a list. [PR 311](https://github.com/catalystneuro/neuroconv/pull/311)
* In the conversion YAML, conversion_options can be specified on the global level. [PR 312](https://github.com/catalystneuro/neuroconv/pull/312)
* The `OpenEphysRecordingInterface` now redirects to legacy or binary interface depending on the file format.
It raises NotImplementedError until the interface for legacy format is added. [PR 296](https://github.com/catalystneuro/neuroconv/pull/296)
* Added the `OpenEphysLegacyRecordingInterface` to support Open Ephys legacy format (`.continuous` files). [PR 295](https://github.com/catalystneuro/neuroconv/pull/295)
* Added `PlexonSortingInterface` to support plexon spiking data. [PR 316](https://github.com/catalystneuro/neuroconv/pull/316)
* Changed `SpikeGLXRecordingInterface` to accept either the AP or LF bands as file paths. Each will automatically set the correseponding `es_key` and corresponding metadata for each band or probe. [PR 298](https://github.com/catalystneuro/neuroconv/pull/298)
* The `OpenEphysRecordingInterface` redirects to `OpenEphysLegacyRecordingInterface` for legacy format files instead of raising NotImplementedError. [PR 349](https://github.com/catalystneuro/neuroconv/pull/349)
* Added a `SpikeGLXConverter` for easy combination of multiple IMEC and NIDQ data streams. [PR 292](https://github.com/catalystneuro/neuroconv/pull/292)
* Added an `interfaces_by_category` lookup table to `neuroconv.datainterfaces` to make searching for interfaces by modality and format easier. [PR 352](https://github.com/catalystneuro/neuroconv/pull/352)
* `neuroconv.utils.jsonschema.get_schema_from_method_signature` can now support the `Dict[str, str]` typehint, which allows `DataInterface.__init__` and `.run_conversion` to handle dictionary arguments. [PR 360](https://github.com/catalystneuro/neuroconv/pull/360)
* Added `neuroconv.tools.testing.data_interface_mixins` module, which contains test suites for different types of
DataInterfaces [PR 357](https://github.com/catalystneuro/neuroconv/pull/357)
* Added `keywords` to `DataInterface` classes. [PR 375](https://github.com/catalystneuro/neuroconv/pull/375)
* Uses `open-cv-headless` instead of open-cv, making the package lighter [PR 387](https://github.com/catalystneuro/neuroconv/pull/387).
* Adds `MockRecordingInterface` as a general testing mechanism for ecephys interfaces [PR 395](https://github.com/catalystneuro/neuroconv/pull/395).
* `metadata` returned by `DataInterface.get_metadata()` is now a `DeepDict` object, making it easier to add and adjust metadata. [PR 404](https://github.com/catalystneuro/neuroconv/pull/404).
* The `OpenEphysLegacyRecordingInterface` is now extracts the `session_start_time` in `get_metadata()` from `Neo` (`OpenEphysRawIO`) and does not depend on `pyopenephys` anymore. [PR 410](https://github.com/catalystneuro/neuroconv/pull/410)
* Added `expand_paths`. [PR 377](https://github.com/catalystneuro/neuroconv/pull/377)
* Added basic temporal alignment methods to ecephys, ophys, and icephys DataInterfaces. These are `get_timestamps`, `align_starting_time`, `align_timestamps`, and `align_by_interpolation`. Added tests that serve as a first demonstration of the intended uses in a variety of cases. [PR 237](https://github.com/catalystneuro/neuroconv/pull/237) [PR #283](https://github.com/catalystneuro/neuroconv/pull/283) [PR #400](https://github.com/catalystneuro/neuroconv/pull/400)
* Added basic temporal alignment methods to the SLEAPInterface. Added holistic per-interface, per-method unit testing for ecephys and ophys interfaces. [PR 401](https://github.com/catalystneuro/neuroconv/pull/401)
* Added `expand_paths`. [PR 377](https://github.com/catalystneuro/neuroconv/pull/377), [PR #448](https://github.com/catalystneuro/neuroconv/pull/448)
* Added `.get_electrode_table_json()` to the `BaseRecordingExtractorInterface` as a convenience helper for the GUIDE project. [PR 431](https://github.com/catalystneuro/neuroconv/pull/431)
* Added `BrukerTiffImagingInterface` to support Bruker TIF imaging data. This format consists of individual TIFFs (each file contains a single frame) in OME-TIF format (.ome.tif files) and metadata in XML format (.xml file). [PR 390](https://github.com/catalystneuro/neuroconv/pull/390)
* Added `MicroManagerTiffImagingInterface` to support Micro-Manager TIF imaging data. This format consists of multipage TIFFs in OME-TIF format (.ome.tif files) and configuration settings in JSON format ('DisplaySettings.json' file). [PR 423](https://github.com/catalystneuro/neuroconv/pull/423)
* Added a `TemporallyAlignedDataInterface` definition for convenience when creating a custom interface for pre-aligned data. [PR 434](https://github.com/catalystneuro/neuroconv/pull/434)
* Added `write_as`, `units_name`, `units_description` to `BaseSortingExtractorInterface` `run_conversion` method to be able to modify them in conversion options. [PR 438](https://github.com/catalystneuro/neuroconv/pull/438)
* Added basic temporal alignment methods to the VideoInterface. These are `align_starting_time` is split into `align_starting_times` (list of times, one per video file) and `align_global_starting_time` (shift all by a scalar amount). `align_by_interpolation` is not yet implemented for this interface. [PR 283](https://github.com/catalystneuro/neuroconv/pull/283)
* Added stream control for the `OpenEphysBinaryRecordingInterface`. [PR 445](https://github.com/catalystneuro/neuroconv/pull/445)
* Added the `BaseTemporalAlignmentInterface` to serve as the new base class for all new temporal alignment methods. [PR 442](https://github.com/catalystneuro/neuroconv/pull/442)
* Added direct imports for all base classes from the outer level; you may now call `from neuroconv import BaseDataInterface, BaseTemporalAlignmentInterface, BaseExtractorInterface`. [PR 442](https://github.com/catalystneuro/neuroconv/pull/442)
* Added basic temporal alignment methods to the AudioInterface. `align_starting_time` is split into `align_starting_times` (list of times, one per audio file) and `align_global_starting_time` (shift all by a scalar amount). `align_by_interpolation` and other timestamp-based approaches is not yet implemented for this interface. [PR 402](https://github.com/catalystneuro/neuroconv/pull/402)
* Changed the order of recording properties extraction in `NeuroscopeRecordingInterface` and `NeuroScopeLFPInterface` to make them consistent with each other [PR 466](https://github.com/catalystneuro/neuroconv/pull/466)
* The `ScanImageImagingInterface` has been updated to read metadata from more recent versions of ScanImage [PR 457](https://github.com/catalystneuro/neuroconv/pull/457)
* Refactored `add_two_photon_series()` to `add_photon_series()` and added `photon_series_type` optional argument which can be either `"OnePhotonSeries"` or `"TwoPhotonSeries"`.
Changed `get_default_ophys_metadata()` to add `Device` and `ImagingPlane` metadata which are both used by imaging and segmentation.
Added `photon_series_type` to `get_nwb_imaging_metadata()` to fill metadata for `OnePhotonSeries` or `TwoPhotonSeries`. [PR 462](https://github.com/catalystneuro/neuroconv/pull/462)
* Split `align_timestamps` and `align_starting_times` into `align_segment_timestamps` and `align_segment_starting_times` for API consistency for multi-segment `RecordingInterface`s. [PR 463](https://github.com/catalystneuro/neuroconv/pull/463)
* Rename `align_timestamps` and `align_segmentt_timestamps` into `set_aligned_timestamps` and `set_aligned_segment_timestamps` to more clearly indicate their usage and behavior. [PR 470](https://github.com/catalystneuro/neuroconv/pull/470)


Testing
* The tests for `automatic_dandi_upload` now follow up-to-date DANDI validation rules for file name conventions. [PR 310](https://github.com/catalystneuro/neuroconv/pull/310)
* Deactivate `MaxOneRecordingInterface` metadata tests [PR 371]((https://github.com/catalystneuro/neuroconv/pull/371)
* Integrated the DataInterface testing mixin to the SLEAP Interface. [PR 401](https://github.com/catalystneuro/neuroconv/pull/401)
* Added holistic per-interface, per-method unit testing for ecephys and ophys interfaces. [PR 283](https://github.com/catalystneuro/neuroconv/pull/283)
* Live service tests now run in a separate non-required GitHub action. [PR 420]((https://github.com/catalystneuro/neuroconv/pull/420)
* Integrated the `DataInterfaceMixin` class of tests to the `VideoInterface`. [PR 403](https://github.com/catalystneuro/neuroconv/pull/403)
* Add `generate_path_expander_demo_ibl` and associated test for `LocalPathExpander` [PR 456](https://github.com/catalystneuro/neuroconv/pull/456)
* Improved testing of all interface alignment methods via the new `TemporalAlignmentMixin` class. [PR 459](https://github.com/catalystneuro/neuroconv/pull/459)

Fixes
* `BlackrockRecordingInterface` now writes all ElectricalSeries to "acquisition" unless changed using the `write_as` flag in `run_conversion`. [PR 315](https://github.com/catalystneuro/neuroconv/pull/315)
* Excluding Python versions 3.8 and 3.9 for the `EdfRecordingInterface` on M1 macs due to installation problems. [PR 319](https://github.com/catalystneuro/neuroconv/pull/319)
* Extend type array condition in `get_schema_from_hdmf_class` for dataset types (excludes that are DataIO). [PR 418](https://github.com/catalystneuro/neuroconv/pull/418)
* The `base_directory` argument to all `PathExpander` classes can now accept string inputs as well as `Path` inputs. [PR 427](https://github.com/catalystneuro/neuroconv/pull/427)
* Fixed the temporal alignment methods for the `RecordingInterfaces` which has multiple segments. [PR 411](https://github.com/catalystneuro/neuroconv/pull/411)
* Fixes to the temporal alignment methods for the `SortingInterface`, both single and multi-segment and recordingless. [PR 413](https://github.com/catalystneuro/neuroconv/pull/413)
* Fixes to the temporal alignment methods for the certain formats of the `RecordingInterface`. [PR 459](https://github.com/catalystneuro/neuroconv/pull/459)
* Fixes the naming of LFP interfaces to be `ElectricalSeriesLFP` instead of `ElectricalSeriesLF`. [PR 467](https://github.com/catalystneuro/neuroconv/pull/467)
* Fixed an issue with incorrect modality-specific extra requirements being associated with certain behavioral formats. [PR 469](https://github.com/catalystneuro/neuroconv/pull/469)

Documentation and tutorial enhancements
* The instructions to build the documentation were moved to ReadTheDocs. [PR 323](https://github.com/catalystneuro/neuroconv/pull/323)
* Move testing instructions to ReadTheDocs. [PR 320](https://github.com/catalystneuro/neuroconv/pull/320)
* Moved NeuroConv catalogue from ReadMe.md to ReadTheDocs.
[PR 322](https://github.com/catalystneuro/neuroconv/pull/322)
* Moved instructions to build the documentation from README.md to ReadTheDocs. [PR 323](https://github.com/catalystneuro/neuroconv/pull/323)
* Add `Spike2RecordingInterface` to conversion gallery. [PR 338](https://github.com/catalystneuro/neuroconv/pull/338)
* Remove authors from module docstrings [PR 354](https://github.com/catalystneuro/neuroconv/pull/354)
* Add examples for `LocalPathExpander` usage [PR 456](https://github.com/catalystneuro/neuroconv/pull/456)
* Add better docstrings to the aux functions of the Neuroscope interface [PR 485](https://github.com/catalystneuro/neuroconv/pull/485)

Pending deprecation
* Change name from `CedRecordingInterface` to `Spike2RecordingInterface`. [PR 338](https://github.com/catalystneuro/neuroconv/pull/338)

Improvements
* Use `Literal` in typehints (incompatible with Python<=3.8). [PR 340](https://github.com/catalystneuro/neuroconv/pull/340)
* `BaseDataInterface.get_source_schema` modified so it works for `.__init__` and `.__new__`. [PR 374](https://github.com/catalystneuro/neuroconv/pull/374)

Deprecation
* All usages of `use_times` have been removed from spikeinterface tools and interfaces. The function `add_electrical_series` now determines whether the timestamps of the spikeinterface recording extractor are uniform or not and automatically stores the data according to best practices [PR 40](https://github.com/catalystneuro/neuroconv/pull/40)
* Dropped Python 3.7 support. [PR 237](https://github.com/catalystneuro/neuroconv/pull/237)

Features
* Added a tool for determining rising and falling frames from TTL signals (`parse_rising_frames_from_ttl` and `get_falling_frames_from_ttl`). [PR 244](https://github.com/catalystneuro/neuroconv/pull/244)
* Added the `SpikeGLXNIDQInterface` for reading data from `.nidq.bin` files, as well as the ability to parse event times from specific channels via the `get_event_starting_times_from_ttl` method. Also included a `neuroconv.tools.testing.MockSpikeGLXNIDQInterface` for testing purposes. [PR 247](https://github.com/catalystneuro/neuroconv/pull/247)
* Improved handling of writing multiple probes to the same `NWB` file [PR 255](https://github.com/catalystneuro/neuroconv/pull/255)

Pending deprecation
* Added `DeprecationWarnings` to all `spikeextractors` backends. [PR 265](https://github.com/catalystneuro/neuroconv/pull/265)
* Added `DeprecationWarning`s for `spikeextractors` objects in `neuroconv.tools.spikeinterface`. [PR 266](https://github.com/catalystneuro/neuroconv/pull/266)

Fixes
* Temporarily hotfixed the `tensorflow` dependency after the release of `deeplabcut==2.3.0`. [PR 268](https://github.com/catalystneuro/neuroconv/pull/268)
* Fixed cleanup of waveform tests in SI tools. [PR 277](https://github.com/catalystneuro/neuroconv/pull/277)
* Fixed metadata structure for the CsvTimeIntervalsInterface, which was previously not passed validation in NWBConverters. [PR 237](https://github.com/catalystneuro/neuroconv/pull/237)
* Added propagation of the `load_sync_channel` argument for the `SpikeGLXNIDQInterface`. [PR 282](https://github.com/catalystneuro/neuroconv/pull/282)
* Fixed the default `es_key` used by stand-alone write using any `RecordingExtractorInterface` or `LFPExtractorInterface`. [PR 288](https://github.com/catalystneuro/neuroconv/pull/288)
* Fixed the default `ExtractorName` used to load the spikeinterface extractor of the `SpikeGLXLFPInterface`. [PR 288](https://github.com/catalystneuro/neuroconv/pull/288)

Testing
* Re-organized the `test_gin_ecephys` file by splitting into each sub-modality. [PR 282](https://github.com/catalystneuro/neuroconv/pull/282)
* Add testing support for Python 3.11. [PR 234](https://github.com/catalystneuro/neuroconv/pull/234)

Documentation and tutorial enhancements
* Remove `Path(path_to_save_nwbfile).is_file()` from each of the gallery pages. [PR 177](https://github.com/catalystneuro/neuroconv/pull/177)
* Improve docstring for `SpikeGLXRecordingInterface`. [PR 226](https://github.com/catalystneuro/neuroconv/pull/226)
* Correct typing of SpikeGLX in conversion gallery. [PR 223](https://github.com/catalystneuro/neuroconv/pull/223)
* Added tutorial for utilizing YAML metadata in a conversion pipeline. [PR 240](https://github.com/catalystneuro/neuroconv/pull/240)
* Added page in User Guide for how to use CSVs to specify metadata. [PR 241](https://github.com/catalystneuro/neuroconv/pull/177)
* Added the `BaseDataInterface` in the API docs. [PR 242](https://github.com/catalystneuro/neuroconv/pull/242)
* Fixed typo in styling section. [PR 253](https://github.com/catalystneuro/neuroconv/pull/253)
* Updated docs on JSON schema. [PR 256](https://github.com/catalystneuro/neuroconv/pull/256)
* Improved compliance with numpy-style docstring [PR 260](https://github.com/catalystneuro/neuroconv/pull/260)

Features
* Added `AudioInterface` for files in `WAV` format using the `add_acoustic_waveform_series` utility function
from `tools/audio` to write audio data to NWB. [PR 196](https://github.com/catalystneuro/neuroconv/pull/196)
* Added the `MaxOneRecordingInterface` for writing data stored in MaxOne (.raw.h5) format. [PR 222](https://github.com/catalystneuro/neuroconv/pull/222)
* Added the `MCSRawRecordingInterface` for writing data stored in MCSRaw (.raw) format. [PR 220](https://github.com/catalystneuro/neuroconv/pull/220)
* Added the `MEArecRecordingInterface` for writing data stored in MEArec (structured .h5) format. [PR 218](https://github.com/catalystneuro/neuroconv/pull/218)
* Added the `AlphaOmegaRecordingInterface` for writing data stored in AlphaOmega (folder of .mrx) format. [PR 212](https://github.com/catalystneuro/neuroconv/pull/212)
* Added the `PlexonRecordingInterface` for writing data stored in Plexon (.plx) format. [PR 206](https://github.com/catalystneuro/neuroconv/pull/206)
* Added the `BiocamRecordingInterface` for writing data stored in Biocam (.bwr) format. [PR 210](https://github.com/catalystneuro/neuroconv/pull/210)
* Added function to add acoustic series as `AcousticWaveformSeries` object as __acquisition__ or __stimulus__ to NWB. [PR 201](https://github.com/catalystneuro/neuroconv/pull/201)
* Added new form to the GitHub repo for requesting support for new formats. [PR 207](https://github.com/catalystneuro/neuroconv/pull/207)
* Simplified the writing of `channel_conversion` during `add_electrical_series` if the vector of gains is uniform; in this case, they are now combined into the scalar `conversion` value. [PR 218](https://github.com/catalystneuro/neuroconv/pull/218)
* Implement timestamp extraction from videos for the SLEAPInterface [PR 238](https://github.com/catalystneuro/neuroconv/pull/238)
* Prevented writing of default values for optional columns on the `ElectrodeTable`. [PR 219](https://github.com/catalystneuro/neuroconv/pull/219)
* Add interfaces for Excel and Csv time intervals tables. [PR 252](https://github.com/catalystneuro/neuroconv/pull/252)

Testing
* Added a `session_id` to the test file for the `automatic_dandi_upload` helper function. [PR 199](https://github.com/catalystneuro/neuroconv/pull/199)
* `pre-commit` version bump. [PR 235](https://github.com/catalystneuro/neuroconv/pull/235)
* Added a `testing` sub-module to `src` and added a method (`generate_mock_ttl_signal`) for generating synthetic TTL pulses. [PR 245](https://github.com/catalystneuro/neuroconv/pull/245)

Fixes
* `VideoInterface`. Only raise a warning if the difference between the rate estimated from timestamps and the fps (frames per seconds) is larger than two decimals. [PR 200](https://github.com/catalystneuro/neuroconv/pull/200)
* Fixed the bug in a `VideoInterface` where it would use `DataChunkIterator` even if the conversion options indicated that it should not. [PR 200](https://github.com/catalystneuro/neuroconv/pull/200)
* Update usage requirements for HDMF to prevent a buffer overflow issue fixed in hdmf-dev/hdmf780. [PR 195](https://github.com/catalystneuro/neuroconv/pull/195)
* Remove the deprecated `distutils.version` in favor of `packaging.version` [PR 233](https://github.com/catalystneuro/neuroconv/pull/233)

Testing

* Added a set of dev branch gallery tests for PyNWB, HDMF, SI, and NEO. [PR 113](https://github.com/catalystneuro/neuroconv/pull/113)
* Added tests for the `TypeError` and `ValueError` raising for the new `starting_frames` argument of `MovieDataInterface.run_conversion()`. [PR 113](https://github.com/catalystneuro/neuroconv/pull/113)
* Added workflow for automatic detection of CHANGELOG.md updates for PRs. [PR 187](https://github.com/catalystneuro/neuroconv/pull/187)
* Added support for python 3.10 [PR 229](https://github.com/catalystneuro/neuroconv/pull/229)

Fixes

* Fixed a new docval typing error that arose in `hdmf>3.4.6` versions. [PR 113](https://github.com/catalystneuro/neuroconv/pull/113)
* Fixed a new input argument issue for `starting_frames` when using `external_file` for an `ImageSeries` in `pynwb>2.1.0` versions. [PR 113](https://github.com/catalystneuro/neuroconv/pull/113)
* Fixed issues regarding interaction between metadata rate values and extractor rate values in `tools.roiextractors`. [PR 159](https://github.com/catalystneuro/neuroconv/pull/159)
* Fixed sampling frequency resolution issue when detecting this from timestamps in `roiextractors.write_imaging` and `roiextractors.write_segmentation`. [PR 159](https://github.com/catalystneuro/neuroconv/pull/159)

Documentation and tutorial enhancements
* Added a note in User Guide/DataInterfaces to help installing custom dependencies for users who use Z-shell (`zsh`). [PR 180](https://github.com/catalystneuro/neuroconv/pull/180)
* Added `MovieInterface` example in the conversion gallery. [PR 183](https://github.com/catalystneuro/neuroconv/pull/183)

Features
* Added `ConverterPipe`, a class that allows chaining previously initialized interfaces for batch conversion and corresponding tests [PR 169](https://github.com/catalystneuro/neuroconv/pull/169)
* Added automatic extraction of metadata for `NeuralynxRecordingInterface` including filtering information for channels, device and recording time information [PR 170](https://github.com/catalystneuro/neuroconv/pull/170)
* Added stubbing capabilities to timestamp extraction in the `MovieInterface` avoiding scanning through the whole file when `stub_test=True` [PR 181](https://github.com/catalystneuro/neuroconv/pull/181)
* Added a flag `include_roi_acceptance` to `tools.roiextractors.write_segmentation` and corresponding interfaces to allow disabling the addition of boolean columns indicating ROI acceptance. [PR 193](https://github.com/catalystneuro/neuroconv/pull/193)
* Added `write_waveforms()` function in `tools.spikeinterface` to write `WaveformExtractor` objects
[PR 217](https://github.com/catalystneuro/neuroconv/pull/217)

Pending deprecation
* Replaced the `MovieInterface` with `VideoInterface` and introduced deprecation warnings for the former. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)

Fixes

* Updated `BlackrockRecordingInterface` to support multi stream file and added gin corresponding gin tests [PR 176](https://github.com/catalystneuro/neuroconv/pull/176)