TODO

v0.2 - update to linkml-arrays and formal release

NWB schema translation

handle links field in groups
handle compound dtype like in ophys.PlaneSegmentation.pixel_mask
handle compound dtype like in TimeSeriesReferenceVectorData
Create a validator that checks if all the lists in a compound dtype dataset are same length
Move making target optional in vectorIndex from pydantic generator to linkml generators!

Cleanup

Update pydantic generator
Restore regressions from stripping the generator
Make any_of with array ranges work
PR upstream equals_string and ifabsent (if existing PR doesn't fix)
Use the class rather than a string in _get_class_slot_range_origin: or inlined_as_list or ( # sv.get_identifier_slot(range_cls.name, use_key=True) is None and
Make a minimal pydanticgen-only package to slim linkml deps?
Disambiguate "maps" terminology - split out simple maps from the eg. dataset mapping classes
Remove unnecessary imports
- dask
- nptyping
Adapt the split generation to the new split generator style

Important things that are not implemented yet!

{meth}nwb_linkml.adapters.classes.ClassAdapter.handle_dtype does not yet handle compound dtypes, leaving them as AnyType instead. This is fine for a first draft since they are used rarely within NWB, but we will need to handle them by making slots for each of the dtypes since they typically represent table-like data.
Need to handle DynamicTables!
- Adding columns?
- Validating eg. all are same length?
- Or do we want to just say "no dynamictables, just subclass and add more slots since it's super easy to do that."
- method to return a dataframe
- append rows/this should just be a df basically.
- existing handler is fucked, for example, in maps/hdmf
Handle indirect indexing eg. https://pynwb.readthedocs.io/en/stable/tutorials/general/plot_timeintervals.html#accessing-referenced-timeseries

Remove monkeypatches/overrides once PRs are closed

Tests

Top-level containers are still a little janky, eg. how ProcessingModule just accepts extra args rather than properly abstracting value as a __getitem__(self, key) -> T: