Nwbinspector

Deprecation
* Remove s3fs dependency, which was causing dependency management issues [549](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/549)

Fixes
* Fix wrongly triggered compression check [552](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/552)

Improvements
* Added a section for describing the issues with negative timestamps in `TimeSeries` [545](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/545)
* Use alternate way of generating `TimeSeries` objects to avoid new pynwb error when the shape of the first dimension of
data does not match the length of timestamps [556](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/556)

Improvements
* Added support for Numpy 2 and h5py 3.12, and pinned PyNWB to <3.0 temporarily. [536](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/536)

Fixes
* Fixed issue where the description check failed if the description was a list. [535](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/535)

Deprecation
* Support for Python 3.8 has been removed. [508](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/508)

Deprecation (API)
* The `inspect_nwb` method has been removed. Please use `inspect_nwbfile` or `inspect_nwbfile_object` instead. [505](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/505)

New Features
* Added Zarr support. [513](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/513)

Improvements
* Removed the `robust_ros3_read` utility helper. [506](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/506)
* Simplified the `nwbinspector.testing` configuration framework. [509](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/509)
* Cleaned old references to non-recent PyNWB and HDMF versions. Current policy is that latest NWB Inspector releases should only support compatibility with latest PyNWB and HDMF. [510](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/510)
* Swapped setup approach to the modern `pyproject.toml` standard. [507](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/507)
* Added complete annotation typing and integrated Mypy into pre-commit. [520](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/520)

Fixes
* Fixed incorrect error message for OptogeneticStimulusSite. [524](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/524)
* Fixed detection of Zarr directories for inspection. [531](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/531)

Deprecation (API)
* The `driver` argument has been removed from `inspect_nwbfile`. Please use `nwbinspector.inspect_dandiset` or `nwbinspector.inspect_dandi_file_path` instead. [490](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/490)

Pending Deprecation (API)
* The `stream` and `version_id` arguments have been removed from `nwbinspector.inspect_all`. Please use `nwbinspector.inspect_dandiset` instead. [490](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/490)

New Features
* Introduced the `inspect_dandiset` and `inspect_dandi_file_path` API functions to replace the functionality in `nwbinspector --stream`. The new feature uses `remfile` instead of `ros3`. [490](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/490)

Fixes
* Fixed import error when using the CLI with `--config dandi`. [494](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/494)
* Removed unused imports throughout package. [496](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/496)

Deprecation (API)
* Certain low-level functions have been marked as private (such as the former `nwbinspector.register_checks.auto_parse`) indicating they should not have been imported by downstream users. [485](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/485)
* Various inappropriate imports from certain submodules have been hard deprecated (e.g., `from nwbinspector.inspector_tools import natsorted`). [485](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/485)

Pending Deprecation (API)
* The `inspector_tools`, `register_check`, and `` submodules have been soft deprecated and will be removed in the next major release. [485](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/485)

Improvements
* Update util function `is_ascending_series` to discard nan values and add `check_timestamps_without_nans` fun to check if timestamps contain NaN values [476](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/476)
* Updated the import structure to match modern Python packaging standards. [485](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/485)

Fixes

* Equivocated timezone handling to target fields when checking for past and future dates. [471](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/471)