v0.11.38

v0.11.38

Upcoming deprecations

• Introduced a soft deprecation of keyword argument 'save_path' from various interface and tool-specific write and conversion functions. This argument should now be named 'nwbfile_path' for consistency with the main converter calls.
• For the spikeinterface.add_units auxiliary function, argument write_as: str has been changed to write_in_processing_module: bool. Default behavior has not changed. Also removed override of ElectrodeTable descriptions, allowing PyNWB to set these instead.

New Features and Improvements

• For latest security fixes, bumps minimum required version of numpy to >=1.22.0 for Python versions >=3.8. Python 3.7 can only go up to numpy 1.21.0, however.
• Enables the nwbct-run-conversion entrypoint for calling the YAML conversion specification from the command line.
• Adds a stubbing option to all ophys ImagingInterfaces.
• Improved the local version of the GenericDataChunkIterator by padding the buffer when beneficial.
• Various improvements to automated metadata extraction for various recording interfaces.
• Allows the JSON validators to parse datetime objects as iso and adds a context helper for making or appending NWBFiles.
• Enables recording, imaging, and sorting interfaces to perform standalone write of an NWBFile (that is, without requiring an NWBConverter with only a single interface).
• Added appending functionality to spikeinterface.add_units.
• Added a data transfer tool for submitting and tracking tasks over Globus endpoints.
• Added a helper function for performing a fully automated DANDI upload process, assuming the token has been set as an environment variable.
• Added helper functions for automatically downloading data from Figshare.
• Added verbosity control to the NWBConverter class and base DataInterfaces.
• Added support for string-valued channel_ids from SpikeInterface. It does so by introducing a new column 'channel_names' to any ElectrodeTable written by add_electrodes or write_recording. This is enforced to be unique across rows of the table both here and in individual SpikeInterface recordings.

New Interfaces

• Introduced the BaseIcephysInterface and the first intracellular format interface - the AbfInterface!
• Added the KilosortSortingInterface.

Interface Changes

• Added SpikeInterface support for the NeuralynxRecordingInterface, SpikeGadgetsRecordingInterface, BlackrockRecordingInterface, PhySortingInterface, IntanRecordingInterface, and NeuroscopeSortingInterface. The CEDRecordingInterface now only uses SpikeInterface as the backend (and has dropped a priori setting of channel IDs - this is planned to be automatically reintroduced as a non-class method to subset channels after initialization, but for now that must be done manually).
• Removed the nwbfile object as a required argument of the BaseRecordingInterface. run_conversion.

Tool Changes

• Prevents any response series associated with a TwoPhotonSeries from being written if it is simply an array of zeros.
• Introduced a util function for calculating the rate of a regular series.
• Introduced deprecation of use_times to roiextractors.add_two_photon_series, as the behavior now mimics the modern SpikeInterface approach of always using them when available, and falling back to sampling frequency usage if not.

Bug Fixes

• Disabled the nwb-gui entrypoint as it has not worked for some time now.
• Fixed a bug where metadata values were duplicated in roiextractors.write_imaging.
• Prevented duplicate ophys metadata from becoming set during a manual override.
• Small fixes to ophys imaging metadata construction.
• Corrects the metadata schema for segmentation interfaces to be compatible with the ImagingInterfaces.
• Allows timestamps to be used with external_file=True in the MovieInterface.
• Fixed the matching of unique group_names with groups on the ElectrodesTable.
• Fixed a problem when running the YAML conversion feature on the Windows platform.