Fixes related to hydrolib-core issues

[veenstrajelmer]

Checks for next release (may 2024):

• mdu settings (more strict)
• true/false booleans instead of 1/0 in mdu

From hydromt_delft3dfm:

• meshkernel contacts in Network instance created from netfile HYDROLIB-core#575
• Remove type_enforced dependency HYDROLIB-core#584
• Add functions to convert hydrolib-core objects to (geo)pandas and others HYDROLIB-core#553
• Simplify Network code HYDROLIB-core#576
• Consider replacing UgridReader and UgridWriter with xugrid HYDROLIB-core#577
• Support for minimal interacter networks (2D network with 1D topology) HYDROLIB-core#578
• Sync bathymetry face_z and node_z array sizes with meshkernel HYDROLIB-core#579

Other:

• Filetype 10 not supported for oldext HYDROLIB-core#565
• Show_tree output is not printed for old ext files HYDROLIB-core#581
• mdu parameter settings not supported HYDROLIB-core#568
• HKV: Behaviour of clipping to a polygon is limited due to new options of DeleteMeshOption HYDROLIB-core#612
• HKV: Mesh generation in a polygon with holes HYDROLIB-core#614
• HKV: Mesh generation in a multipolygon HYDROLIB-core#615
• Investigate failing tests on Linux and MacOS when upgrading MeshKernel to 2.0.0 HYDROLIB-core#444
• Investigate failing testcase on macos 14 runners (arm64) HYDROLIB-core#635
• Obsfile path with spaces is not supported HYDROLIB-core#564
• dimr_config for parallel run is incorrect HYDROLIB-core#562
• Unclear error message from bc-validation HYDROLIB-core#560
• Extfilenew not found with pathstyle unix HYDROLIB-core#516
• Newext file missing validation HYDROLIB-core#533
• Relative paths not working in newly initialized FMModel HYDROLIB-core#532
• Union of different kinds of FileModels can become slow and buggy HYDROLIB-core#519
• Support URL as input path when constructing models HYDROLIB-core#494
• Add support for adding custom comment header to INI files HYDROLIB-core#362
• Convert FM input/output to shapefiles/kml #216
• Validate no duplicate/empty station names in observation point files (+same for obs crossections) HYDROLIB-core#483
• multiline obs/crs without / is not read but also raises no error: Multiline obs/crs files are not parsed correctly HYDROLIB-core#485 (comment) (same for missing keywords)
• Mdu formatting improvements HYDROLIB-core#495 (and other formatting improvements)
• Providing incorrect file to any *Model returns an empty object instead of a crash HYDROLIB-core#502
• maybe put dfm_tools convert functions (hydrolib object conversion to DataFrame/Dataset etc) in hydrolib-core? (Suggestion for ForcingModel/TimeSeries object conversion method HYDROLIB-core#307). Alternatively, put hydrolib-core functions under the hood?
• dfm_tools code review? >> modelbuilder or more?
• how to get convenient+plottable polyfile/crsfile/etc? (preferably no list, all objects including names)
• more relevant hydrolib-core issues?
• what is role of mesh actions in hydrolib-core? (like crash in net reader gives an error when reading network created using interacter HYDROLIB-core#241)
• meshkernelpy defaults hardcoded in hydrolib-core: https://github.com/Deltares/HYDROLIB-core/blob/main/hydrolib/core/dflowfm/net/models.py#L290
• meshkernel can clip grid with polygon, but only one and is different object than hydrolib polyline object. Align? Add support for multiple polygons in mesh2d_delete() MeshKernelPy#35
• automatic conversions: newext-timfile to newext-bcfile, oldext-anything to newext-anything if supported in newext, Converter for legacy profile files to cross section files HYDROLIB-core#487
• Make XYZPoint more consitent by removing comment property HYDROLIB-core#510
• Complete support for MDU output keywords HYDROLIB-core#525
• Validation not working for relative path HYDROLIB-core#531
• Update docs with how users can add unknown keywords themselves HYDROLIB-core#637
• remove network-related things and meshkernel dependency from hydrolib-core (check with hydromt_delft3dfm and others whether they depend on it.)

Can be closed? (dfm_tools/xugrid alternatives):

• Multiline obs/crs files are not parsed correctly HYDROLIB-core#485
• Inquiry API for D-Flow FM_his.nc output files HYDROLIB-core#268
  • select via station name now possible with xarray+dfmt.preprocess_hisnc(): ds.sel(station='stationname')
  • selecting nearest station not directly possible, also not with multiindex of name/x/y >> ValueError: multi-index does not support 'method' and 'tolerance'. Alternative method is via KDTree
  • selecting stations within bounding box: possible with bool as in example script, but not with multiindex and ds.sel(x=slice(),y=slice() >> TypeError: float() argument must be a string or a number, not 'slice'. select with polygon would also result in bool, so might not matter
• Investigate plotting functionality HYDROLIB-core#400
• Support for 3D tekal files (polyfile format) HYDROLIB-core#430
• Datablock of type np.array is not supported in TimeSeries object HYDROLIB-core#322

hydrolib-core issues, to be included in 0.5.0:

• Polyfile parser does not parse 2D boundary type of pli file correctly.  HYDROLIB-core#467
• ExtModel cannot handle path formats from different OS HYDROLIB-core#339
• Adjust init files to make imports easier for users. HYDROLIB-core#410
• Improve bc file formatting HYDROLIB-core#308 (this issue is also related to improvement of polyfile formatting)
• Validation error for nans in TimeSeries/T3D/etc missing HYDROLIB-core#433
• Reading invalid formatted plifile should raise error instead of warning HYDROLIB-core#320 (empty return object is confusing)
• xyz file with initial whitespace on lines is not correctly parsed by XYZmodel HYDROLIB-core#415
• ValidationError upon reading StructureModel HYDROLIB-core#353 (prevents reading of FM model in preprocess_hydrolib_readFMmodel.py)
• Add support for 'old' crs.pli files (observation cross sections) HYDROLIB-core#364
• Add support for 'old' obs.xyn files (observationpoints) HYDROLIB-core#459
• support for str instead of Path HYDROLIB-core#365
• Remove indents from mdu file HYDROLIB-core#493
• Reading StructureModel with timfiles crashes HYDROLIB-core#497
• Many prints about unset keys HYDROLIB-core#505
• Missing keywords for (3D) coastal models HYDROLIB-core#486
• Network without face coordinates cannot be added to mdu HYDROLIB-core#515
• Support Tim files HYDROLIB-core#348 >> Improve TIMModel implementation by updating the timeseries data type. HYDROLIB-core#511 >> update TimModel_to_Dataset when done
• Support for old ext file HYDROLIB-core#369
• Add support for double quoted names in the .xyn file HYDROLIB-core#537
• Add support for double quoted names in the .xyn file HYDROLIB-core#537
• Update dependencies after hydrolib-core and meshkernel release #232
• check/clean TODO in dfm_tools hydrolib example files
• conflicting dependencies with dfm_tools HYDROLIB-core#441 >> after release, update dfm_tools requirements
• put type checking for timmodel back: https://github.com/Deltares/dfm_tools/blob/main/dfm_tools/hydrolib_helpers.py