Fixes related to hydrolib-core issues

[veenstrajelmer]

Next release (PR's merged after release of 0.8.0):

• mdu stretchtype should be -1 or 0 instead of 1 HYDROLIB-core#691
• Require meshkernelpy>=4.2.0 HYDROLIB-core#692 >> chore: bump minimal meshkernel version to 4.2.0 HYDROLIB-core#693
• chore: update to meshkernelpy 5.0.1 HYDROLIB-core#708
• chore: add support for Python 3.13 HYDROLIB-core#712
• chore: add support for numpy v2 HYDROLIB-core#660

High priority:

• Empty path gets upgraded to pathlib.Path(".") by FMModel HYDROLIB-core#703
• Migrate to Pydantic V2 API HYDROLIB-core#732
• Obsfile path with spaces is not supported HYDROLIB-core#564
• Extfilenew not found with pathstyle unix HYDROLIB-core#516
• Unclear error message from bc-validation HYDROLIB-core#560
• Newext file missing validation HYDROLIB-core#533
• Relative paths not working in newly initialized FMModel HYDROLIB-core#532
• Construct correctly-cased path in case of path_style="unix" HYDROLIB-core#698
• crosslocmodel cannot read file with single cross section HYDROLIB-core#680

Relevant for hydromt_delft3dfm (grid-related operations):

• HKV: Mesh generation in a multipolygon HYDROLIB-core#615
• Support for minimal interacter networks (2D network with 1D topology) HYDROLIB-core#578
• net reader gives an error when reading network created using interacter HYDROLIB-core#241
• Sync bathymetry face_z and node_z array sizes with meshkernel HYDROLIB-core#579
• Simplify Network code HYDROLIB-core#576
• Consider replacing UgridReader and UgridWriter with xugrid HYDROLIB-core#577
• Investigate failing testcase on macos 14 runners (arm64) HYDROLIB-core#635

Other:

• Multiline obs/crs files are not parsed correctly HYDROLIB-core#485
• 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)
• 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
• Add functions to convert hydrolib-core objects to (geo)pandas and others HYDROLIB-core#553
• 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?
• 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
• Validation not working for relative path HYDROLIB-core#531
• Update docs with how users can add unknown keywords themselves HYDROLIB-core#637

Can be closed? (dfm_tools/xugrid alternatives):

• 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

Included in hydrolib-core 0.8.0 or older:

• meshkernel contacts in Network instance created from netfile HYDROLIB-core#575
• Remove type_enforced dependency HYDROLIB-core#584
• 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
• Investigate failing tests on Linux and MacOS when upgrading MeshKernel to 2.0.0 HYDROLIB-core#444
• dimr_config for parallel run is incorrect HYDROLIB-core#562
• Complete support for MDU output keywords HYDROLIB-core#525
• mdu settings (more strict)
• true/false booleans instead of 1/0 in mdu

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