Neuroconv

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)

Back-compatability break
* All built-in DataInterfaces are now nested under the `neuroconv.datainterfaces` import structure - they are no longer available from the outer level. To import a data interface, use the syntax `from neuroconv.datainterfaces import <name of interface>`. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* The `AxonaRecordingExtractorInterface` has been renamed to `AxonaRecordingInterface`. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* The `AxonaUnitRecordingExtractorInterface` has been renamed to `AxonaUnitRecordingInterface`. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* The `BlackrockRecordingExtractorInterface` has been renamed to `BlackrockRecordingInterface`. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* The `BlackrockSortingExtractorInterface` has been renamed to `BlackrockSortingInterface`. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* The `OpenEphysRecordingExtractorInterface` has been renamed to `OpenEphysRecordingInterface`. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* The `OpenEphysSortingExtractorInterface` has been renamed to `OpenEphysSortingInterface`. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* The `KilosortSortingInterface` has been renamed to `KiloSortSortingInterface` to be more consistent with SpikeInterface. [PR 107](https://github.com/catalystneuro/neuroconv/pull/107)
* The `Neuroscope` interfaces have been renamed to `NeuroScope` to be more consistent with SpikeInterface. [PR 107](https://github.com/catalystneuro/neuroconv/pull/107)
* The `tools.roiextractors.add_epoch` functionality has been retired in the newest versions of ROIExtractors. [PR 112](https://github.com/catalystneuro/neuroconv/pull/112)
* Removed deprecation warnings for `save_path` argument (which is now `nwbfile_path` everywhere in the package). [PR 124](https://github.com/catalystneuro/neuroconv/pull/124)
* Changed default device name for the ecephys pipeline. Device_ecephys -> DeviceEcephys [PR 154](https://github.com/catalystneuro/neuroconv/pull/154)
* Change names of written electrical series on the ecephys pipeline. ElectricalSeries_raw -> ElectricalSeriesRaw, ElectricalSeries_processed -> ElectricalSeriesProcessed, ElectricalSeries_lfp -> ElectricalSeriesLFP [PR 153](https://github.com/catalystneuro/neuroconv/pull/153)
* Drop spikeextractor backend support for NeuralynxRecordingInterface [PR 174](https://github.com/catalystneuro/neuroconv/pull/174)

Fixes
* Prevented the CEDRecordingInterface from writing non-ecephys channel data. [PR 37](https://github.com/catalystneuro/neuroconv/pull/37)
* Fixed description in `write_sorting` and in `add_units_table` to have "neuroconv" in the description. [PR 104](https://github.com/catalystneuro/neuroconv/pull/104)
* Updated `spikeinterface` version number to 0.95.1 to fix issue with `SpikeGLXInterface` probe annotations.
The issue is described [here](https://github.com/SpikeInterface/spikeinterface/issues/923). [PR #132](https://github.com/catalystneuro/neuroconv/pull/132)

Improvements
* Unified the `run_conversion` method of `BaseSegmentationExtractorInterface` with that of all the other base interfaces. The method `write_segmentation` now uses the common `make_or_load_nwbfile` context manager [PR 29](https://github.com/catalystneuro/neuroconv/pull/29)
* Coerced the recording extractors with `spikeextractors_backend=True` to BaseRecording objects for Axona, Blackrock, Openephys, and SpikeGadgets. [PR 38](https://github.com/catalystneuro/neuroconv/pull/38)
* Added function to add PlaneSegmentation objects to an nwbfile in `roiextractors` and corresponding unit tests. [PR 23](https://github.com/catalystneuro/neuroconv/pull/23)
* `use_times` argument to be deprecated on the ecephys pipeline. 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)
* Add `NWBFile` metadata key at the level of the base data interface so it can always be inherited to be available. [PR 51](https://github.com/catalystneuro/neuroconv/pull/51).
* Added spikeinterface support to Axona LFP and coerece gin tests for LFP to be spikeinterface objects [PR 85](https://github.com/catalystneuro/neuroconv/pull/85)
* Added function to add fluorescence traces to an nwbfile in `roiextractors` and corresponding unit tests.
The df over f traces are now added to a `DfOverF` container instead of the `Fluorescence` container.
The metadata schema has been changed for the `BaseSegmentationExtractorInterface` to allow metadata for `DfOverF`,
and `Flurorescence` is now not required in the metadata schema. [PR 41](https://github.com/catalystneuro/neuroconv/pull/41)
* Improved default values of OpticalChannel object names and other descriptions for Imaging data. [PR 88](https://github.com/catalystneuro/neuroconv/pull/88)
* Extended the `ImagingDataChunkIterator` to be compatible with volumetric data. [PR 90](https://github.com/catalystneuro/neuroconv/pull/90)
* Integrated the `ImagingDataChunkIterator` with the `write_imaging` methods. [PR 90](https://github.com/catalystneuro/neuroconv/pull/90)
* Began work towards making SpikeInterface, SpikeExtractors, and ROIExtractors all non-minimal dependencies. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* Implemented format-wise and modality-wise extra installation requirements. If there are any requirements to use a module or data interface, these are defined in individual requirements files at the corresponding level of the package. These are in turn easily accessible from the commands `pip install neuroconv[format_name]`. `pip install neuroconv[modality_name]` will also install all dependencies necessary to make full use of any interfaces from that modality. [PR 100](https://github.com/catalystneuro/neuroconv/pull/100)
* Added frame stubbing to the `BaseSegmentationExtractorInterface`. [PR 116](https://github.com/catalystneuro/neuroconv/pull/116)
* Added `mask_type: str` and `include_roi_centroids: bool` to the `add_plane_segmentation` helper and `write_segmentation` functions for the `tools.roiextractors` submodule. [PR 117](https://github.com/catalystneuro/neuroconv/pull/117)
* Propagate `output_struct_name` argument to `ExtractSegmentationInterface` to match its extractor arguments. [PR 128](https://github.com/catalystneuro/neuroconv/pull/128)
* Added compression and iteration (with options control) to all Fluorescence traces in `write_segmentation`. [PR 120](https://github.com/catalystneuro/neuroconv/pull/120)
* For irregular recordings, timestamps can now be saved along with all traces in `write_segmentation`. [PR 130](https://github.com/catalystneuro/neuroconv/pull/130)
* Added `mask_type` argument to `tools.roiextractors.add_plane_segmentation` function and all upstream calls. This allows users to request writing not just the image_masks (still the default) but also pixels, voxels or `None` of the above. [PR 119](https://github.com/catalystneuro/neuroconv/pull/119)
* `utils.json_schema.get_schema_from_method_signature` now allows `Optional[...]` annotation typing and subsequent `None` values during validation as long as it is still only applied to a simple non-conflicting type (no `Optional[Union[..., ...]]`). [PR 119](https://github.com/catalystneuro/neuroconv/pull/119)


Documentation and tutorial enhancements:
* Unified the documentation of NeuroConv structure in the User Guide readthedocs. [PR 39](https://github.com/catalystneuro/neuroconv/pull/39)
* Added package for viewing source code in the neuroconv documentation [PR 62](https://github.com/catalystneuro/neuroconv/pull/62)
* Added Contributing guide for the Developer section of readthedocs. [PR 73](https://github.com/catalystneuro/neuroconv/pull/73)
* Added style guide to the readthedocs [PR 28](https://github.com/catalystneuro/neuroconv/pull/28)
* Added ABF data conversion tutorial luiztauffer [PR 89](https://github.com/catalystneuro/neuroconv/pull/89)
* Added Icephys API documentation luiztauffer [PR 103](https://github.com/catalystneuro/neuroconv/pull/103)
* Added Blackrock sorting conversion gallery example [PR 134](https://github.com/catalystneuro/neuroconv/pull/134)
* Extended the User Guide Get metadata section in DataInterfaces with a demonstration for loading metadata from YAML. [PR 144](https://github.com/catalystneuro/neuroconv/pull/144)
* Fixed a redundancy in [PR 144](https://github.com/catalystneuro/neuroconv/pull/144) and API links. [PR #154](https://github.com/catalystneuro/neuroconv/pull/154)
* Added SLEAP conversion gallery example [PR 161](https://github.com/catalystneuro/neuroconv/pull/161)



Features
* Added conversion interface for Neuralynx sorting data together with gin data test and a conversion example in the gallery. [PR 58](https://github.com/catalystneuro/neuroconv/pull/58)
* Added conversion interface for DeepLabCut data together with gin data test and a conversion example in the gallery. [PR 24](https://github.com/catalystneuro/neuroconv/pull/24)
* Allow writing of offsets to ElectricalSeries objects from SpikeInterface (requires PyNWB>=2.1.0). [PR 37](https://github.com/catalystneuro/neuroconv/pull/37)
* Added conversion interface for EDF (European Data Format) data together with corresponding unit tests and a conversion example in the gallery. [PR 45](https://github.com/catalystneuro/neuroconv/pull/45)
* Created ImagingExtractorDataChunkIterator, a data chunk iterator for `ImagingExtractor` objects. [PR 54](https://github.com/catalystneuro/neuroconv/pull/54)
* Added support for writing spikeinterface recording extractor with multiple segments and corresponding unit test [PR 67](https://github.com/catalystneuro/neuroconv/pull/67)
* Added spikeinterface support to the Axona data interface [PR 61](https://github.com/catalystneuro/neuroconv/pull/61)
* Added new util function `get_package` for safely attempting to attempt a package import and informatively notifying the user of how to perform the installation otherwise. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* All built-in DataInterfaces now load their external dependencies on-demand at time of object initialization instead of on package or interface import. [PR 74](https://github.com/catalystneuro/neuroconv/pull/74)
* Adde spikeinterface support for Blackrock sorting interface[PR 134](https://github.com/catalystneuro/neuroconv/pull/134)
* Added conversion interface for TDT recording data together with gin data test. [PR 135](https://github.com/catalystneuro/neuroconv/pull/135)
* Added conversion interface for SLEAP pose estimation data together with gin test for data. [PR 160](https://github.com/catalystneuro/neuroconv/pull/160)


Testing
* Added unittests for correctly writing the scaling factors to the nwbfile in the `add_electrical_series` function of the spikeinterface module. [PR 37](https://github.com/catalystneuro/neuroconv/pull/37)
* Added unittest for compression options in the `add_electrical_series` function of the spikeinterface module. [PR 64](https://github.com/catalystneuro/neuroconv/pull/37)
* Added unittests for chunking in the `add_electrical_series` function of the spikeinterface module. [PR 84](https://github.com/catalystneuro/neuroconv/pull/84)
* Tests are now organized according to modality-wise lazy installations. [PR 100](https://github.com/catalystneuro/neuroconv/pull/100)