Fixes related to xugrid issues

[veenstrajelmer]

Todo:

• Minimize required dependencies of xugrid xugrid#428 >> preferred for dependency in hydrolib-core
• to_nonperiodic() results in corrupt grid xugrid#447

Todo later:

• UgridDataset is converted to Dataset with assign_attrs xugrid#412 >> wait for explicit indexes >> remove uds.ugrid.assign_node_coords() from meshkernel_to_UgridDataset() again that was added in 1312 prepare for 1d2d in meshkernel to ugriddataset #1313
• UgridDataArray.weighted does not preserve grid xugrid#181 >> wait for explicit indexes
• encoding can only be updated via uds.obj xugrid#321 >> when it is fixed, remove .obj from modelbuilder notebook >> wait for explicit indexes
• .ugrid.sel(x=..., y=...) should return a 2D result xugrid#98 >> is this important? >> wait for explicit indexes
• Consider parsing cfrole=mesh_topology_contact as topology xugrid#135
• use face_coordinates from mesh_topology variable xugrid#56
• Unexpected negative values in triangles xugrid#68 (for westernscheldt model) >> hanging edges/nodes are allowed in ugrid convention according to AvD, but still not convenient for plotting
• Enable regridder for dataset xugrid#88
• Investigate a cross section plot xugrid#59 (although it would be nice to have it in xugrid instead, discuss this and Improve map-polyline-slice dataset structure and cleanliness #206)
• plotting of fine grained meshes is sub-optimal because of edge drawing xugrid#203 >> matplotlib?

xugrid 0.15.2:

• CRS detection: resolve more than one and choose the one that results in a valid EPSG identifier xugrid#429
• grid_mapping is not present for data vars of all grids xugrid#432

xugrid 0.15.0:

• Parse CRS if present xugrid#42 >> quickfix implemented in auto set crs including test #685 >> Remove temporary crs code #1310
• Pass mk.MeshKernel instead of mk.mesh2d to xu.Ugrid2d.from_meshkernel xugrid#188 >> fixed by Store CRS as grid_mapping; parse and write xugrid#410 >> Remove temporary crs code #1310
• Add sorting to intersect_edges() xugrid#413 >> Sort the result of intersect edges numba_celltree#73 >> Remove temporary intersect_edges sorting code #1316
• uds.ugrid.sel_points() also broadcasts face_dimension on variables without it xugrid#274 >> remove temporary dropping of variables after xugrid fix #1320
• Merge projected and is_geographic xugrid#187 >> fixed by Store CRS as grid_mapping; parse and write xugrid#410 >> Avoid using projected in xugrid constructors hydromt_delft3dfm#218
• Error with isel for ugrid files with multiple topologies xugrid#388

xugrid 0.13.0:

• associate data from one topology aspect to another xugrid#127 >> Associate data from one aspect (node, face, edge) to another aspect (node, face, edge) xugrid#173

xugrid 0.12.4:

• consider prevent UgridDataset type if no grid present xugrid#180

xugrid 0.12.3:

• Time for py313 xugrid#317
• dfmt.open_dataset_delft3d4() and dfmt.open_dataset_curvilinear() cannot be deprecated or partly replaced by xugrid.UgridDataset.from_structured() before fixing from_structured does not support non-monotonic indexes xugrid#316
• uds.close() now properly works after xugrid.open_dataset results in a locked netCDF file xugrid#309, also for partitioned datasets? >> it does not work for partitioned datasets, but this is probably not possible to resolve.

xugrid 0.12.2 and older:

• support writing of netfile with start_index=1 and _FillValue!=-1 xugrid#119 >> also add test for gridwriting to xugrid or dfm_tools (check on min/max fnc, start_index and _FillValue), make sure the grid has both triangles as squares
• After xu.concat(): selection and depth conversion issues xugrid#80
• .ugrid.sel() does not accept dict as input xugrid#58
• define minimal shapely version xugrid#172
• From structured dataset xugrid#303
• resolve warnings in ci workflow xugrid#312
• xugrid.open_dataset results in a locked netCDF file xugrid#309

xugrid 0.11.2 and older:

• support conversion of spherical Ugrid2d to meshkernel  xugrid#128
• Back and forth conversion xugrid - meshkernel does not work for spherical network xugrid#177
• Align is_geographic with xugrid #661
• xu.core.wrap.UgridDataset corrupts face_node_connectivity in original xr.Dataset xugrid#208
• Avoid Futurewarning for dim_size = ds.dims[dim] xugrid#211
• merge_partitions fails for datasets with multiple topologies xugrid#134
• Fix importlib/pathlib DeprecationWarning xugrid#194
• Automatically resize chunks after merging parallel results xugrid#252
• sel_points silently drops outofbounds points xugrid#100

xugrid 0.7.0 or older:

• check/implement edge validator and re-enable westernscheldt in mapnc_ugrid example script (also contour): Unexpected negative values in triangles xugrid#68 (comment)
• update meshkernel api calls after new release xugrid#169
• enable generation of Ugrid2d with different fill_value xugrid#116
• .sel(): Spend some attention on checking the ugrid.sel method xugrid#26 (sel issue)
• .sel(): Edges are not always correct xugrid#30 (edges are not always correct)
• .sel(): when done: Add where/sel ugrid example to mapfile notebook (sel currently fails, wait for xugrid fix+release)
• .sel(): uds.ugrid.sel(x,y) source/inplace dataset edges are messed up xugrid#41 (in xugrid main branch, so pre-release)
• xugrid.plot: do not error when multiple dimensions are present xugrid#27 (support for multiple dimensions plot via histogram?)
• Allow for flexible face dimension, edge dimension, and node dimension names xugrid#25 (flexible dimnames?)
• Newly generated xugrid.ugrid.ugrid2d.Ugrid2d does not have the attribute 'plot' xugrid#39
• countour plot fails xugrid#44
• Merge non-UGRID dimensioned identical variables in merge_partitions xugrid#43
• Add face_node_coordinates and edge_node_coordinates properties xugrid#48
• remove edgecolors argument from polycollection plots after fix of Add defaults for PolyCollection plot xugrid#64
• norm argument is not passed correctly to uds.ugrid.plot() xugrid#49 (blocks removal of dfmt.plot_netmapdata())
• Fix uds.grid.plot() method xugrid#54
• Expose rasterize and rasterize_like on uds xugrid#61
• Add defaults for PolyCollection plot xugrid#64
• Add optional_attributes argument to to_dataset methods xugrid#67
• uds.ugrid.sel() cannot return dataset with new dimension like ds.sel() can do xugrid#85
• Regridder fails for partitioned dataarray xugrid#99
• Plotting fails with newer xarray versions and chunks argument xugrid#78
• Function for periodic global grid to non-periodic  xugrid#63 (for GTSM)
• request edge-to-face interpolation in xugrid? Add function to interpolate edgevars to faces #307
• invalid edge_node_connectivity when deriving face_edge_connectivity xugrid#129
• attributes added to mesh2d variable point to non-existent variables xugrid#132
• supress/solve "xugrid\ugrid\ugridbase.py:326: RuntimeWarning: invalid value encountered in cast cast = data.astype(dtype, copy=True)" >> invalid value encountered in cast xugrid#101
• merge_partitions is slow with datasets opened without chunks argument xugrid#105
• dataset attrs are ignored upon writing xugrid#111
• solve edge_node_connectivity in xugrid 0.6.0 xugrid#113 (major xugrid 0.6.0 bug, after release remove WARNING from readme.md and installation.md)
• after fixing Contourf (and other) plotting fails with newer xarray versions and chunks argument xugrid#117, remove SKIP_test_xugrid_opendataset_ugridplot_contourf() and other testcase since it is tested in xugrid testbank now. Also uncomment contour/contourf in ipynb and ugrid example script.
• Move from uda.rasterize() to uds.rasterize() after fix of Expose rasterize and rasterize_like on uds xugrid#61
• maybe add warning for slow xr.concat in xarray 2023.2.0 to 2023.5.0:merge_partitions performance decreased with newer xarray version xugrid#106
• default fillvalue not parsed by xarray, results in negative values in connectivity xugrid#125