Fixes related to meshkernelpy issues

Next release (5.0.*):

[x] https://github.com/Deltares/MeshKernelPy/issues/152
[ ] https://github.com/Deltares/dfm_tools/issues/909#issuecomment-2265013735 (follow up of https://github.com/Deltares/MeshKernelPy/issues/150)
[ ] HYDROLIB-core broke with meshkernelpy 5.0.0: https://github.com/Deltares/HYDROLIB-core/issues/702
[ ] https://github.com/Deltares/MeshKernelPy/issues/181

Later:

[ ] https://github.com/Deltares/MeshKernel/issues/326 >> https://github.com/Deltares/HYDROLIB-core/issues/579 >> supporting bathy on grid is also important in GRIDEDITOR GUI GRIDEDIT-806
[ ] https://github.com/Deltares/MeshKernelPy/issues/153
[ ] https://github.com/Deltares/MeshKernelPy/issues/71 >> discuss node instead of face refinement with urban

Documentation:

[ ] https://github.com/Deltares/MeshKernelPy/issues/178
[ ] https://github.com/Deltares/MeshKernelPy/issues/161
[ ] create example in documentation for refinement based a polygon
[ ] create example in documentation for refinement based on bathymetry, including polygon (to avoid refinement on open boundary) >> more information required
[ ] add rgfgrid-based grid generation from hydrodynamic course as a meshkernel notebook (includes base grid, refinement, splines etc): n:\Projects\11209500\11209671\B. Measurements and calculations\01_Updated_course_materials\02_exercises\ (Exercise 1 to 4), base on stenderts notebook (p:\11210154-arem-noregret\hydro\modelbuilder\grid\original_curvilinear_UTM\grid_polygons.ipynb
[ ] meshkernel logo

Other:

[ ] product demo for dsc/haf departments: examples of applications in projects including which mk-features used (gtsm (almost), mb destine?, mb guycarpenter? (not yet), mb gtsm rivers?, mb fmcourse, mb hackathon bonaire, mb saba?, mb arabiangulf, hydrolib-core, hydromt_delft3dfm, dhydamo?, more hco/haf?)
[ ] ugridpy: also maintain z-values and crs from file
[ ] ugridpy: import/export interacter netfile: p:\1204257-dcsmzuno\2006-2012\3D-DCSM-FM\A18b_ntsu1\DCSM-FM_0_5nm_grid_20191202_depth_20181213_net.nc (also maintain crs/projected upon import/export)
[ ] Casulli refinement (already implemented in meshkernel, not yet available in meshkernelpy)
[ ] https://github.com/Deltares/MeshKernelPy/issues/164
[x] https://github.com/Deltares/MeshKernelPy/issues/72 >> https://github.com/Deltares/xugrid/issues/148 >> require xugrid release from after 3 Jul 2024 in dfm_tools
[ ] https://github.com/Deltares/MeshKernelPy/issues/96
[ ] https://github.com/Deltares/MeshKernelPy/issues/91
[ ] https://github.com/Deltares/MeshKernelPy/issues/74
[ ] refining/z-interpolation with gridded samples with nans in it (also UNST-5600)
[ ] align with meshing packages in pyposeidon? Eg generation of global triangular mesh as in pptx
[x] https://github.com/Deltares/MeshKernelPy/issues/35 (currently a workaround exists in dfm_tools, also auto-closing all polygons) https://github.com/Deltares/dfm_tools/blob/14fc1ae6100852d9f7b1e1e642619522b7b2646f/dfm_tools/meshkernel_helpers.py#L19
[x] https://github.com/Deltares/MeshKernelPy/issues/70

Related issues:

[x] https://github.com/Deltares/dfm_tools/issues/217
[ ] meshkernel(py) issues in JIRA
[ ] possible to check orthogonality in mk? More grid validators/cleanups (modelbuilder example script)
[ ] possible to use connect_cells separately (without refining)?
[ ] polygon generation/editing, maybe already possible?
[ ] check TODO in meshkernel example script and modelbuilder example script
[ ] minimal interacter network is 1D: p:\dflowfm\maintenance\JIRA\06000-06999\06548\meshkernel_interp.py, can be used to interpolate bathy to?
[ ] do we need sphericalaccurate grids for dcsm/gtsm? These are not implemented yet (only spherical)
[ ] overview of RGFGRID functions

Workflows:

[ ] GTSM: global base grid, bathy+gradient refinement, cut landpart with ldb (incl drypoints), example script with some issues
[ ] 1D2D connected like GTSM+rivers
[ ] DCSM: bathy+polygonen refinement, cut landpart with ldb+depth (drypoints with matlab, details at JG?)
[ ] RMM: multiblock rivers, curvigrid generation based on splines, triangles in estuaries, squares in seapart. For the second, we need a to divide a polygon in equal length parts, part of meshkernel?
[ ] D-HYDRO course materials workflow
[ ] tutorial materials from manual
[ ] RGFGRID functions overview, manual edits like in edit>reg/irreg
[ ] create unittests of all workflows to make sure behaviour is tested and future changes do not result in undesired behaviour

DCSM steps:

[ ] Create base_grid (4 nm resolution) >> edge length now varies over latitude, inconvenient? https://github.com/Deltares/MeshKernelPy/issues/153
[x] delete with polygon (delete network)
[x] delete with polygon (based on cell centers)
[x] refine with polygon
[ ] set all z-values to -999 (fillvalue)
[ ] interp bathy from xyz
[ ] set missing z-values to certain value, if outside of polygon (actually to later delete cells on land, so easier method for that might also work)
[ ] delete nodes with z-values lower than specified value or missing value (only if this applies to all nodes of face) >> can be replaced with delete option that considers crossings of cell edges like in https://github.com/Deltares/MeshKernelPy/issues/63#issuecomment-1735399001
[x] remove small flowlinks (merge circumcenters) >> mesh2d_delete_small_flow_edges_and_small_triangles (https://github.com/Deltares/dfm_tools/issues/812#issuecomment-2044437915)
[x] delete 1D/hanging links >> mesh2d_delete_hanging_edges
[x] merge with additional grid (merge nodes on top of each other) >> mesh2d_merge_nodes
[ ] is not entirely solved by improving polygon deletion, since we have fjords in norway where emodnet has (wet) bathymetry but the landboundary does not include them
[ ] illegalcells necessary, or https://github.com/Deltares/MeshKernelPy/issues/150
[ ] meshkernel alternative: p:\1204257-dcsmzuno\gridcreation_test_meshkernelpy\DCSM_grid_creation_meshkernel.py

Test GTSM-specific new features (JV):

[ ] https://github.com/Deltares/MeshKernelPy/issues/97 >> https://github.com/Deltares/MeshKernelPy/blob/feature/GRIDEDIT-768_global_grid_example/docs/examples/10_mesh2d_global_grid.ipynb >> issue for xugrid that straigt line is on the right instead of left? >> https://github.com/Deltares/MeshKernelPy/issues/181
[ ] test ridge refinement (implemented in GRIDEDIT-502)
[ ] the mesh2d_refine_based_on_gridded_samples() API now supports multiple dtypes (https://github.com/Deltares/MeshKernelPy/issues/146). Check if gtsm refinement with meshkernelpy is possible with coarsefac 4 >> short/float distinction >> test gtsm memory consumtion for two dtypes (with release)

Release 3.0.0:

[x] https://github.com/Deltares/MeshKernelPy/issues/63
[x] https://github.com/Deltares/MeshKernelPy/issues/32
[x] https://github.com/Deltares/MeshKernelPy/issues/73
[x] https://github.com/Deltares/MeshKernelPy/issues/76
[x] https://github.com/Deltares/MeshKernelPy/issues/78
[x] https://github.com/Deltares/MeshKernelPy/issues/81
[x] https://github.com/Deltares/MeshKernelPy/issues/44
[ ] https://github.com/Deltares/MeshKernelPy/issues/47
[x] https://github.com/Deltares/MeshKernelPy/issues/102
[x] compute grid? >> construct/make makes more sense
[x] https://github.com/Deltares/MeshKernelPy/issues/103
[x] xugrid.ugrid.ugrid1d.Ugrid1d.meshkernel and xugrid.ugrid.ugrid2d.Ugrid2d.meshkernel both call mk.MeshKernel(is_geographic=False) so that now fails
[x] https://github.com/Deltares/dfm_tools/issues/550
[x] https://github.com/Deltares/dfm_tools/issues/563

mk 4.1.0 (released 2024-02-15):

[x] https://github.com/Deltares/MeshKernelPy/issues/113
[x] https://github.com/Deltares/MeshKernelPy/issues/107
[x] https://github.com/Deltares/MeshKernelPy/issues/108 >> exceptions upon wrong input
[x] https://github.com/Deltares/MeshKernelPy/issues/102
[x] https://github.com/Deltares/MeshKernelPy/issues/97
[x] ridge refinement GRIDEDIT-502
[x] macos support: https://issuetracker.deltares.nl/browse/GRIDEDIT-796
[x] https://github.com/Deltares/MeshKernelPy/issues/142
[x] https://github.com/Deltares/MeshKernelPy/issues/145
[x] https://github.com/Deltares/HYDROLIB-core/issues/612 >> convert to meshkernel issue or can we work around it?

Meshkernelpy 4.2.0:

Deltares / dfm_tools

Fixes related to meshkernelpy issues #234