Neuroconv

Deprecations

Bug Fixes

Features
* Added `metadata` and `conversion_options` as arguments to `NWBConverter.temporally_align_data_interfaces` [PR 1162](https://github.com/catalystneuro/neuroconv/pull/1162)

Improvements

Deprecations

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
* 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)
* 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)

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](https://github.com/catalystneuro/neuroconv/pull/1070)
* The method `get_extractor` now works for `MockImagingInterface` [PR 1076](https://github.com/catalystneuro/neuroconv/pull/1076)
* Updated opencv version for security [PR 1087](https://github.com/catalystneuro/neuroconv/pull/1087)
* Solved a bug of `PlexonRecordingInterface` where data with multiple streams could not be opened [PR 989](https://github.com/catalystneuro/neuroconv/pull/989)

Deprecations

Features
* Added chunking/compression for string-only compound objects: [PR 1042](https://github.com/catalystneuro/neuroconv/pull/1042)
* Added automated EFS volume creation and mounting to the `submit_aws_job` helper function. [PR 1018](https://github.com/catalystneuro/neuroconv/pull/1018)
* Added a mock for segmentation extractors interfaces in ophys: `MockSegmentationInterface` [PR 1067](https://github.com/catalystneuro/neuroconv/pull/1067)
* Added a `MockSortingInterface` for testing purposes. [PR 1065](https://github.com/catalystneuro/neuroconv/pull/1065)
* BaseRecordingInterfaces have a new conversion options `always_write_timestamps` that can be used to force writing timestamps even if neuroconv heuristic indicates regular sampling rate [PR 1091](https://github.com/catalystneuro/neuroconv/pull/1091)


Improvements
* Testing on mac sillicon [PR 1061](https://github.com/catalystneuro/neuroconv/pull/1061)
* Add writing to zarr test for to the test on data [PR 1056](https://github.com/catalystneuro/neuroconv/pull/1056)
* Modified the CI to avoid running doctests twice [PR 1077](https://github.com/catalystneuro/neuroconv/pull/#1077)
* Consolidated daily workflows into one workflow and added email notifications [PR 1081](https://github.com/catalystneuro/neuroconv/pull/1081)
* Added zarr tests for the test on data with checking equivalent backends [PR 1083](https://github.com/catalystneuro/neuroconv/pull/1083)