Release v0.4.9 · catalystneuro/neuroconv

v0.4.9 (June 5, 2024)

Removed stream_id as an argument from IntanRecordingInterface. PR #794
The usage of compression and compression_opts directly through the neuroconv.tools.spikeinterface submodule are now deprecated - users should refer to the new configure_backend method for a general approach for setting compression. PR #805
Dropped the testing of Python 3.8 on the CI. Dropped support for Python 3.8 in setup. PR #853
Deprecated skip_features argument in add_sorting. PR #872
Deprecate old (v1) iterator from the ecephys pipeline. PR #876

Added backend control to the make_or_load_nwbfile helper method in neuroconv.tools.nwb_helpers. PR #800
Released the first official Docker images for the package on the GitHub Container Repository (GHCR). PR #383
Support "one-file-per-signal" and "one-file-per-channel" mode with IntanRecordingInterface. PR #791
Added get_default_backend_configuration method to all DataInterface classes. Also added HDF5 backend control to all standalone .run_conversion(...) methods for those interfaces. PR #801
Added get_default_backend_configuration method to all NWBConverter classes. Also added HDF5 backend control to .run_conversion(...). PR #804
Released the first official Docker images for the package on the GitHub Container Repository (GHCR). PR #383
Added ScanImageMultiFileImagingInterface for multi-file (buffered) ScanImage format and changed ScanImageImagingInterface to be routing classes for single and multi-plane imaging. PR #809
Added a function to generate ogen timestamps and data from onset times and parameters to tools.optogenetics. PR #832
Added configure_and_write_nwbfile and optimized imports in tools.nwb_helpers module. PR #848
configure_backend may now apply a BackendConfiguration to equivalent in-memory pynwb.NWBFile objects that have different address in RAM. PR #848
Add support for doubled ragged arrays in add_units_table. PR #879
Add support for doubled ragged arrays in add_electrodes. PR #881

Remove JSON Schema definitions from the properties field. PR #818
Fixed writing waveforms directly to file. PR #799
Avoid in-place modification of the metadata in the VideoInterface and on neo tools. PR #814
Replaced waveform_extractor.is_extension with waveform_extractor.has_extension. PR #799
Fixed an issue with set_aligned_starting_time for all SortingInterface's that did not have an initial segment start set (and no recording attached). PR #823
Fixed a bug with parameterized and pytest-xdist==3.6.1 in the ScanImageImagingInterface tests. PR #829
Added XX and XO to the base metadata schema. PR #833
BaseImagingExtractor.add_to_nwbfile() is fixed in the case where metadata is not supplied. PR #849
Prevent SpikeGLXConverterPipe from setting false properties on the sub-SpikeGLXNIDQInterface. PR #860
Fixed a bug when adding ragged arrays to the electrode and units table. PR #870
Fixed a bug where write_recording will call an empty nwbfile when passing a path. PR #877
Fixed a bug that failed to properly include time alignment information in the output NWB file for objects added from any RecordingInterface in combination with stub_test=True. PR #884
Fixed a bug that prevented passing nwbfile=None and a backend_configuration to NWBConverter.run_conversion. PR #885

Fixed docstrings related to backend configurations for various methods. PR #822
Added automatic backend detection when a backend_configuration is passed to an interface or converter. PR #840
Improve printing of bytes. PR #831
Support for pathlib in source data schema validation. PR #854
Use ZoneInfo instead of dateutil.tz in the conversion gallery. PR #858
Exposed progress_bar_class to ecephys and ophys data iterators. PR #861
Unified the signatures between add_units, add_sorting and write_sorting. PR #875
Improved descriptions of all folder and file paths in the source schema, useful for rendering in the GUIDE. PR #886
Added watermark via source_script field of NWBFile metadata. source_script_file_name is also required to be specified in this case to avoid invalidation. PR #888