Emsarray

* Fix a FutureWarning on accessing [xarray.Dataset.dims](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.dims.html#xarray.Dataset.dims) with xarray >= 2023.12.0 ([pull request 124](https://github.com/csiro-coasts/emsarray/pull/124), [pull request pydata/xarray#8500](https://github.com/pydata/xarray/pull/8500)).
* Fix an error when creating a transect plot that does not intersect the model geometry. Previously this would raise a cryptic error, now it returns an empty transect dataset ([issue 119](https://github.com/csiro-coasts/emsarray/issues/119), [pull request #120](https://github.com/csiro-coasts/emsarray/pull/120)).
* Drop dependency on importlib_metadata. This was only required to support Python 3.8, which was dropped in a previous release ([issue 122](https://github.com/csiro-coasts/emsarray/issues/122), [pull request #125](https://github.com/csiro-coasts/emsarray/pull/125)).
* Fix an error with ShocSimple.get_all_depth_names() when the dataset had no depth coordinates ([issue 123](https://github.com/csiro-coasts/emsarray/issues/123), [pull request #126](https://github.com/csiro-coasts/emsarray/pull/126)).
* Use [PEP 585 generic type annotations](https://peps.python.org/pep-0585/) and stop using [PEP 563 postponed annotation evaluation](https://peps.python.org/pep-0563/) ([issue #109](https://github.com/csiro-coasts/emsarray/issues/109), [pull request #127](https://github.com/csiro-coasts/emsarray/pull/127)).
* Use [pytest-mpl](https://pypi.org/project/pytest-mpl/) for image comparison tests for testing plotting methods ([pull request #128](https://github.com/csiro-coasts/emsarray/pull/128)).
* Update all URLs to the NCI THREDDS server ([update notice](https://opus.nci.org.au/display/NDP/THREDDS+Upgrade), [issue #135](https://github.com/csiro-coasts/emsarray/issues/135), [pull request #136](https://github.com/csiro-coasts/emsarray/pull/136), [pull request csiro-coast/emsarray-data#2](https://github.com/csiro-coast/emsarray-data/pull/2)).
* Correct all references to K’gari, formerly Fraser Island ([issue 133](https://github.com/csiro-coasts/emsarray/issues/133), [pull request csiro-coast/emsarray-data#2](https://github.com/csiro-coast/emsarray-data/pull/2), [pull request #134](https://github.com/csiro-coasts/emsarray/pull/134)).
* Bump minimum versions of dependencies, update pinned dependencies for CI. Officially support numpy version 2.0.0 ([pull request 137](https://github.com/csiro-coasts/emsarray/pull/137)).
* Lint Python code in docs/ and scripts/ ([pull request 141](https://github.com/csiro-coasts/emsarray/pull/141)).
* Add [emsarray.utils.name_to_data_array()](https://emsarray.readthedocs.io/en/stable/api/utils/#emsarray.utils.name_to_data_array) and [data_array_to_name()](https://emsarray.readthedocs.io/en/stable/api/utils/#emsarray.utils.data_array_to_name) functions. Allow more functions to interchangeably take either a data array or the name of a data array ([pull request 142](https://github.com/csiro-coasts/emsarray/pull/142)).
* Add [Convention.depth_coordinates](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.depth_coordinates) and [Convention.get_depth_coordinate_for_data_array()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.get_depth_coordinate_for_data_array). Deprecate functions [Convention.get_depth_name()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.get_depth_name), [Convention.get_all_depth_names()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.get_all_depth_names), and Convention.get_time_name(). Remove deprecated functions Convention.get_depths() and Convention.get_times() ([pull request 143](https://github.com/csiro-coasts/emsarray/pull/143)).
* Swap to using pyproject.toml for all project metadata ([pull request 145](https://github.com/csiro-coasts/emsarray/pull/145)).
* Add new methods [Convention.selector_for_indexes()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.selector_for_indexes), [Convention.select_indexes()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.select_indexes), and [Convention.select_points()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.select_points). These allow for more efficient extraction of multiple points at the same time. The return type of [Convention.selector_for_index()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.selector_for_index) has been changed from a dict to an [xarray.Dataset](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset), but this new value is also designed to be passed directly to [Dataset.isel()](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.isel.html#xarray.Dataset.isel). [Convention.select_index()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.select_index) and [Convention.select_indexes()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.select_indexes) have a new drop_geometry flag which defaults to True. Previously these methods would act as if drop_geometry was False, but this led to convention-dependent results as to which geometry variables were returned. The fragmented geometry variables from different conventions often did not contain enough data to be useful. By dropping geometry the results are more consistent across all conventions and do not contain potentially fragmented geometry information. ([issue 106](https://github.com/csiro-coasts/emsarray/issues/106), [pull request #146](https://github.com/csiro-coasts/emsarray/pull/146)).
* Remove support for the deprecated emsarray.formats module, the emsarray.formats entry point, and filtered warnings for old dependencies no longer supported ([pull request 146](https://github.com/csiro-coasts/emsarray/pull/146)).

* Fix transect plot title and units. All attributes were being dropped accidentally in prepare_data_array_for_transect(). ([pull request 114](https://github.com/csiro-coasts/emsarray/pull/114)).
* Add coast and gridlines parameters to [emsarray.plot.plot_on_figure()](https://emsarray.readthedocs.io/en/stable/api/plot/#emsarray.plot.plot_on_figure), allowing users to disable these components of a plot. Currently gridlines can cause issues in interactive Jupyter notebooks and some other environments. There is no one solution to every situation. Allowing users to disable gridlines is a temporary work around while other solutions are being sought. ([pull request 115](https://github.com/csiro-coasts/emsarray/pull/115), [issue SciTools/cartopy#2245](https://github.com/SciTools/cartopy/issues/2245), [issue SciTools/cartopy#2246](https://github.com/SciTools/cartopy/issues/2246), [issue SciTools/cartopy#2247](https://github.com/SciTools/cartopy/issues/2247)).

* Use ‘ravel’ and ‘wind’ as antonyms instead of ‘ravel’ and ‘unravel’. English is weird. ‘Ravel’ and ‘unravel’ mean the same thing!. ([pull request 100](https://github.com/csiro-coasts/emsarray/pull/100), [pull request #104](https://github.com/csiro-coasts/emsarray/pull/104)).
* Added new [emsarray.conventions.DimensionConvention](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.DimensionConvention) subclass. For conventions with multiple grids defined on unique subsets of dimensions this base class will provide a number of default method implementations. All existing conventions have been updated to build off this base class. ([pull request 100](https://github.com/csiro-coasts/emsarray/pull/100))
* Remove workaround for [pydata/xarray6049](https://github.com/pydata/xarray/pull/6049) ([pull request #101](https://github.com/csiro-coasts/emsarray/pull/101)).
* Add [Convention.wind()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.wind) method as the inverse to [Convention.ravel()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.ravel) ([pull request 102](https://github.com/csiro-coasts/emsarray/pull/102), [pull request #104](https://github.com/csiro-coasts/emsarray/pull/104)).
* Add [Convention.strtree()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.strtree) spatial index, deprecate [Convention.spatial_index()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.spatial_index). The old attribute was a compatibility shim around Shapely 1.8.x STRtree implementation. Now that the minimum version of Shapely is 2.0, the STRtree can be used directly. ([pull request 103](https://github.com/csiro-coasts/emsarray/pull/103)).
* Add [emsarray.plot.add_landmarks()](https://emsarray.readthedocs.io/en/stable/api/plot/#emsarray.plot.add_landmarks) and landmarks parameter to Convention.plot() and related functions. ([pull request 107](https://github.com/csiro-coasts/emsarray/pull/107)).
* Make the positive_down and deep_to_shallow parameters optional for [normalize_depth_variables()](https://emsarray.readthedocs.io/en/stable/api/operations/depth/#emsarray.operations.depth.normalize_depth_variables). If not supplied, that feature of the depth variable is not normalized. This is a breaking change if you previously relied on the default value of True for these parameters. ([pull request 108](https://github.com/csiro-coasts/emsarray/pull/108)).
* Add new module [emsarray.transect](https://emsarray.readthedocs.io/en/stable/api/transect/#module-emsarray.transect) for making transect plots. This feature is considered experimental and may change significantly in future releases. ([pull request 110](https://github.com/csiro-coasts/emsarray/pull/110)).
* Fix an issue with plotting variables with no long_name attribute. ([issue 105](https://github.com/csiro-coasts/emsarray/issues/105), [pull request #111](https://github.com/csiro-coasts/emsarray/pull/111)).

* Add missing_points parameter to [emsarray.operations.point_extraction.extract_points()](https://emsarray.readthedocs.io/en/stable/api/operations/point_extraction/#emsarray.operations.point_extraction.extract_points) and [emsarray.operations.point_extraction.extract_dataframe()](https://emsarray.readthedocs.io/en/stable/api/operations/point_extraction/#emsarray.operations.point_extraction.extract_dataframe). Callers can now choose whether missing points raise an exception, are dropped from the returned dataset, or filled with a sensible fill value ([pull request 90](https://github.com/csiro-coasts/emsarray/pull/90)).
* Align automatic coordinate detection of time and depth with CF Conventions. Add [Convention.time_coordinate](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.time_coordinate) and [Convention.depth_coordinate](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.depth_coordinate), deprecate [Convention.get_times()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.get_times) and [Convention.get_depths()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.get_depths) ([pull request 92](https://github.com/csiro-coasts/emsarray/pull/92)).
* Add [Convention.select_variables()](https://emsarray.readthedocs.io/en/stable/api/conventions/interface/#emsarray.conventions.Convention.select_variables) ([pull request 93](https://github.com/csiro-coasts/emsarray/pull/93), [pull request #94](https://github.com/csiro-coasts/emsarray/pull/94)).
* Fix various small issues with the docs. Use newer version of sphinx-book-theme for documentation ([pull request 91](https://github.com/csiro-coasts/emsarray/pull/91)).
* Remove shorthand imports such as `import xarray as xr` ([pull request 95](https://github.com/csiro-coasts/emsarray/pull/95)).
* Drop Python 3.8 support. Bump minimum dependency versions to those released in the past 18 months ([pull request 96](https://github.com/csiro-coasts/emsarray/pull/96)).

* Fix an issue with negative coordinates in [bounds_argument()](https://emsarray.readthedocs.io/en/v0.4.3/api/cli/#emsarray.cli.utils.bounds_argument) ([pull request 74](https://github.com/csiro-coasts/emsarray/pull/74)).
* Add a new emsarray plot subcommand to the emsarray command line interface ([pull request 76](https://github.com/csiro-coasts/emsarray/pull/76)).
* Use [matplotlib.collections.PolyCollection](https://matplotlib.org/stable/api/collections_api.html#matplotlib.collections.PolyCollection) rather than [PatchCollection](https://matplotlib.org/stable/api/collections_api.html#matplotlib.collections.PatchCollection) for significant speed improvements ([pull request 77](https://github.com/csiro-coasts/emsarray/pull/77)).
* Added [emsarray.utils.timed_func()](https://emsarray.readthedocs.io/en/v0.4.3/api/utils/#emsarray.utils.timed_func) for easily logging some performance metrics ([pull request 79](https://github.com/csiro-coasts/emsarray/pull/79)).
* Add [Convention.bounds](https://emsarray.readthedocs.io/en/v0.4.3/api/conventions/interface/#emsarray.conventions.Convention.bounds) and [Convention.geometry](https://emsarray.readthedocs.io/en/v0.4.3/api/conventions/interface/#emsarray.conventions.Convention.geometry) attributes ([pull request 83](https://github.com/csiro-coasts/emsarray/pull/83)).
* Fix a number of numpy warnings about unsafe casts ([pull request 85](https://github.com/csiro-coasts/emsarray/pull/85)).
* Follow CF Conventions properly when finding latitude / longitude coordinate variables ([issue 84](https://github.com/csiro-coasts/emsarray/issues/84), [pull request #86](https://github.com/csiro-coasts/emsarray/pull/86))
* Include a py.typed file in built packages ([issue 80](https://github.com/csiro-coasts/emsarray/issues/80), [pull request #87](https://github.com/csiro-coasts/emsarray/pull/87)).

* Fixed an issue with `_FillValue` / `missing_value` and variables with non-float types such as timedelta64 ([pull request 71](https://github.com/csiro-coasts/emsarray/pull/71))