Fixes related to meshkernelpy issues

[veenstrajelmer]

Next release (5.0.1):

• Add API to get mesh edge lengths (and others) MeshKernelPy#152
• HYDROLIB-core broke with meshkernelpy 5.0.0: Update to meshkernelpy 5.0.1 HYDROLIB-core#702
• Non-orthogonal grid and illegal cells function #909 (comment) (follow up of prevent high orthogonality after coastline cutting MeshKernelPy#150)

Later:

• Future proofing package MeshKernelPy#190
• make mesh2d_make_global in line with interacter behaviour MeshKernelPy#181
• mesh2d_delete doesn't delete mesh2d_node_z MeshKernel#326 >> Sync bathymetry face_z and node_z array sizes with meshkernel HYDROLIB-core#579 >> supporting bathy on grid is also important in GRIDEDITOR GUI GRIDEDIT-806
• curvilinear_compute_rectangular_grid_on_extension does not result in grid with constant dx/dy MeshKernelPy#153
• Align refinement on gridded/nongridded samples MeshKernelPy#71 >> discuss node instead of face refinement with urban

Documentation:

• update readme badges MeshKernelPy#178
• Improve documentation of mesh2d_delete_small_flow_edges_and_small_triangles MeshKernelPy#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)
• add contacts testcase that fails in hydrolib-core on macos 14 arm64 MeshKernelPy#164
• mismatch edge order xugrid and meshkernel MeshKernelPy#72 >> from_meshkernel method: use all attributes xugrid#148 >> require xugrid release from after 3 Jul 2024 in dfm_tools
• search_radius in meters for contacts_compute_boundary() MeshKernelPy#96
• max_contacts argument for contacts_compute_boundary() MeshKernelPy#91
• angle is not accepted in curvilinear_make_uniform_on_extension MeshKernelPy#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
• Add support for multiple polygons in mesh2d_delete() MeshKernelPy#35 (currently a workaround exists in dfm_tools, also auto-closing all polygons)

  dfm_tools/dfm_tools/meshkernel_helpers.py

  Line 19 in 14fc1ae

  def meshkernel_delete_withpol(mk, file_ldb, minpoints=None):

• Improve curvilinear_make_uniform user feedback MeshKernelPy#70

Related issues:

• Add model builder example notebook #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? curvilinear_compute_rectangular_grid_on_extension does not result in grid with constant dx/dy MeshKernelPy#153
• delete with polygon (delete network)
• delete with polygon (based on cell centers)
• 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 mesh2d_delete deletes too much cells MeshKernelPy#63 (comment)
• remove small flowlinks (merge circumcenters) >> mesh2d_delete_small_flow_edges_and_small_triangles (merge circumcenters option? #812 (comment))
• delete 1D/hanging links >> mesh2d_delete_hanging_edges
• 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 prevent high orthogonality after coastline cutting MeshKernelPy#150
• meshkernel alternative: p:\1204257-dcsmzuno\gridcreation_test_meshkernelpy\DCSM_grid_creation_meshkernel.py

Test GTSM-specific new features (JV):

• Generate global base grid MeshKernelPy#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? >> make mesh2d_make_global in line with interacter behaviour MeshKernelPy#181
• test ridge refinement (implemented in GRIDEDIT-502)
• the mesh2d_refine_based_on_gridded_samples() API now supports multiple dtypes (Support for float64 and int32 in GriddedSamples MeshKernelPy#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:

• mesh2d_delete deletes too much cells MeshKernelPy#63
• No check of input lengths in meshkernel.GeometryList() MeshKernelPy#32
• max_courant_time seems to have no effect on refinement MeshKernelPy#73
• curvilinear_make_uniform_on_extension does not accept a geometry_list MeshKernelPy#76
• polygon refinement does not work properly for spherical grids MeshKernelPy#78
• Make arguments for contacts_compute_boundary() optional MeshKernelPy#81
• Remove non-contiguous parts of a grid MeshKernelPy#44
• Attach grid at DD Boundaries (function in RGFGRID) MeshKernelPy#47
• mk3 projectiontype is not validated upon initialization MeshKernelPy#102
• compute grid? >> construct/make makes more sense
• mk3: mesh deletion with polygon performance was significantly reduced MeshKernelPy#103
• xugrid.ugrid.ugrid1d.Ugrid1d.meshkernel and xugrid.ugrid.ugrid2d.Ugrid2d.meshkernel both call mk.MeshKernel(is_geographic=False) so that now fails
• replace remove xu noncontiguous with mk disconnected regions #550
• update meshkernel api calls after new release #563

mk 4.1.0 (released 2024-02-15):

• Improve orthogonality of rotated spherical grid  MeshKernelPy#113
• Add contacts_set() MeshKernelPy#107
• Add is_geographic or is_projected boolean property to meshkernel instance MeshKernelPy#108 >> exceptions upon wrong input
• mk3 projectiontype is not validated upon initialization MeshKernelPy#102
• Generate global base grid MeshKernelPy#97
• ridge refinement GRIDEDIT-502
• macos support: https://issuetracker.deltares.nl/browse/GRIDEDIT-796
• contacts_get raises MeshKernelError in meshkernel 4.0.1 MeshKernelPy#142
• mk 4.0.2 refinement up side down MeshKernelPy#145
• Behaviour of clipping to a polygon is limited due to new options of DeleteMeshOption HYDROLIB-core#612 >> convert to meshkernel issue or can we work around it?

Meshkernelpy 4.2.0:

• Type checking in earlier stage, or convert types MeshKernelPy#106 >> Convert constructor types in py structures MeshKernelPy#134
• Support for float64 and int32 in GriddedSamples MeshKernelPy#146
• prevent high orthogonality after coastline cutting MeshKernelPy#150
• inconsistency between number of edges and number of orthogonality values MeshKernelPy#172
• How to handle strided arrays MeshKernelPy#149
• MacOS 13 arm64 meshkernel installation fails MeshKernelPy#162
• MacOS 14 arm64 missing gcc@11 library MeshKernelPy#167
• coordinates in orthogonality GeometryList are incorrect MeshKernelPy#151
• Integer bathy samples are not possible in mesh2d_refine_based_on_samples() MeshKernelPy#31
• update dfm_tools after meshkernel release #860

[veenstrajelmer]

Meshkernelpy release 2.1.0:

• Generating a spherical grid raises error MeshKernelPy#39
• Smoother refinement along coastlines with bathy-based refinement MeshKernelPy#29
• Add support for gridded datasets (and bilinear interpolation option) MeshKernelPy#34 (seems necessary to properly refine coastlines)
• Add is_geographic property to meshkernel.MeshKernel() object MeshKernelPy#69
• Make geometry_list argument for curvilinear_make_uniform() optional MeshKernelPy#30
• add option to refine to min-distance in meter instead of degrees in meshkernel.MeshRefinementParameters() (in case of a spherical grid) MeshKernelPy#33 (might be solved when actual spherical grid is possible)
• Set default values for MeshRefinementParameters() MeshKernelPy#40
• Python 3.11 not supported MeshKernelPy#54
• solve main issues: Generate refined grid on arbitrary place on earth MeshKernelPy#28
• repair macOS support: Investigate failing tests on Linux and MacOS when upgrading MeshKernel to 2.0.0 HYDROLIB-core#444