Hydromt-sfincs

This release contains several changes and fixes. Most notably, models with a geographical CRS can now be build.
Also note the changes in the default values in the sfincs.inp file.

Changed
-------
- support for HydroMT core v0.9
- changed default value of dtmaxout to 86400 (was 99999.0) and for advection to 1 (instead of non-existing 2) in sfincs.inp (156)
- support for filtering forcing data from timeseries and locations based on model region (162)

Fixed
-----
- fixed `SfincsModel.setup_subgrid` for models with geograpgical CRS (152)
- fixed masking of elevation and manning datasets when providing mask attribute (153)
- fix a bug that caused some model files to be read twice (161)
- bugfix in workflows.bathymetry that was encountered while burning in rivers (166)

**Full Changelog**: https://github.com/Deltares/hydromt_sfincs/compare/v1.0.2...v1.0.3

This release mostly contains bugfixes and improvements to existing methods. Some new features have been added as well,
such as the option to add storage volume to the model to account for green infrastructure. Another addition is the
generation of overviews for the Cloud Optimized GeoTIFF files for faster visualization.

Added
-----
- `SfincsModel.setup_storage_volume` to account for green-infrastructure PR 101
- Added reverse_river_geom keyword argument in workflows.river_boundary_points PR 136
- the COG files that are written automatically contain overviews for faster visualization PR 144

Changed
-------
- Changed `setup_cn_infiltration_with_kr` into `setup_cn_infiltration_with_ks` since saturated hydraulic conductivity (ks) is used instead of recovery rate (kr) PR 126
- precision of coordinates in geoms and forcing now depends on CRS (geographic or not) PR 143


Fixed
-----
- writing COG files in `SfincsModel.setup_subgrid` (the COG driver settings were wrong) PR 117
- a constant offset in the `datasets_dep` argument to `SfincsModel.setup_subgrid` and `SfincsModel.setup_dep` was ignored PR 119
- mismatch between gis data and the model grid causing issues while reading the model PR 128
- Bugfixes in workflows.river_boundary_points to make sure function also works with geoDataFrame PR 136
- `utils.downscale_floodmap` now also works for large (rotated) grids PR 145

New Contributors
* TBovenschen made their first contribution in https://github.com/Deltares/hydromt_sfincs/pull/136

**Full Changelog**: https://github.com/Deltares/hydromt_sfincs/compare/v1.0.1...v1.0.2

This release contains several new features, such as burning in river bathymetry into the subgrid, setting up drainage structures and adding wind and pressure forcing. It also contains several bugfixes and improvements to existing methods. It is recommended to use this release together with the latest version of the [SFINCS model](https://github.com/Deltares/SFINCS/releases/tag/v2.0.2_Blockhaus_release).

Added
-----
- `SfincsModel.setup_cn_infiltration_with_kr` to setup three layers related to the curve number
(maximum and effective infiltration capacity; seff and smax) and recovery rate (kr) PR 87
- `SfincsModelsetup_drainage_structures` to setup drainage structures (pumps,culverts) from a geodataframe. PR90
- Added `SfincsModel.setup_wind_forcing`, `SfincsModel.setup_wind_forcing_from_grid` and `SfincsModel.setup_pressure_forcing_from_grid` methods to easily add wind and pressure forcing. PR 92
- `SfincsModel.setup_observation_lines` to setup model observation lines (cross-sections) to monitor discharges. PR 114

Changed
-------
- `SfincsModel.setup_subgrid`` now supports the 'riv_datasets' to burn in river bathymetry into the subgrid. PR 84
- `SfincsModel.setup_mask_active` argument reset_mask default to True PR 94
- `SfincsModel.read_config` allows to use a template input file from a directory different than the model root. PR 102
- Added the option to use landuse/landcover data combined with a reclass table to `SfincsModel.setup_constant_infiltration`. PR 103
- Enabled to provide locations only (so no timeseries) for `SfincsModel.setup_waterlevel_forcing` and `SfincsModel.setup_discharge_forcing` PR 104
- New optional buffer argument in `SfincsModel.setup_discharge_forcing` to select gauges around boundary only. PR 104
- `SfincsModel.plot_basemaps` now supports other CRS than UTM zones. PR 111
- New functionality within `SfincsModel.setup_structures` to use high resolution dem for weir elevation. PR 109
- hydromt_data.yml is written to the model root directory with used data sources.

Fixed
------
- bugfix in `SfincsModel.write_forcing` to ensure all NetCDF files are written instead of only the first one. PR 86
- bugfix in `SfincsModel.read_config` & `SfincsInput.read` for relative paths in inp file. PR 88
- bugfix in `SfincsModel.setup_subgrid` to ensure that a 'big geotiff' will be written by default when 'write_dep_tif' or 'write_man_tif' are True
- fix memory issues caused by rasterizing the model region and reprojecting before clipping of rasters. PR 94
- bugfix in `Sfincs.read_forcing` when combining attributes from the locations stored in the gis folder with the actual forcing locations. PR 99
- bugfix in `SfincsModel.setup_discharge_from_grid` when snapping based on upstream area in case a src points is outside of the uparea grid domain. PR 99

Removed
----------
- `burn_river_zb` and `get_river_bathymetry` workflow methods have been deprecated in favor of `burn_river_rect`. PR 84

New Contributors
* Hofer-Julian made their first contribution in https://github.com/Deltares/hydromt_sfincs/pull/80
* keesnederhoff made their first contribution in https://github.com/Deltares/hydromt_sfincs/pull/87
* tim-d-w made their first contribution in https://github.com/Deltares/hydromt_sfincs/pull/92
* kvanasselt made their first contribution in https://github.com/Deltares/hydromt_sfincs/pull/109

This release is a major update of the SfincsModel interface. It contains many new features,
such as support for *rotated grids*, *subgrid* and improved support for *building models from Python* scripts.
The documentation and exmaples have been updated to reflect these changes.

The release however also contains several breaking changes as we have tried to improve the
consistency of the interface and match it more closely to the SFINCS model itself.
Please carefully check the API reference for the new methods and arguments.

Main differences
----------------
- `setup_region` has been replaced by `setup_grid_from_region` and `setup_grid`.
This method actually creates an empty regular grid based on a region of interest or user-defined coordinates, shape, rotation, etc..
- `setup_dep` has replaced `setup_topobathy` and `setup_merge_topobathy`.
This method can now also be used to setup a bathymetry map from multiple sources at once.
- `setup_mask_active` has replaced `setup_mask`.
- `setup_mask_bounds` has replaced `setup_bounds`
- `setup_waterlevel_forcing` has replaced `setup_h_forcing` and now supports merging fording from several data sources
- `setup_discharge_forcing` has replaced `setup_q_forcing` and now supports merging fording from several data sources
- `setup_discharge_forcing_from_grid` has replaces `setup_q_forcing_from_grid`
- `setup_precip_forcing` has replaced `setup_p_forcing`
- `setup_precip_forcing_from_grid` has replaced `setup_p_forcing_from_grid`
- `setup_observation_points` has replace `setup_gauges`

New methods
-----------
- `setup_grid` to setup a user-defined regular grid based coordinates, shape, rotation, etc.
- `setup_subgrid` to setup subgrid tables (sbgfile) based on one ore more elevation and Manning roughness datasets
- `setup_constant_infiltration` to setup a constant infiltration rate maps (qinffile)
- `setup_waterlevel_bnd_from_mask` to setup water level boundary points (bndfile) based on the SFINCS model mask (mskfile)
- `setup_tiles` to create tiles of the model for fast visualization

Changed methods
---------------
- `setup_river_inflow` and `setup_river_outflow` are now based river centerline data (which can be derivded from hydrography data).
This is more robust compared to the previous method which was based on reprojected flow direction data.

Removed methods (not replaced)
------------------------------
- `setup_basemaps` This method was already deprecated in v0.2.1 and has now been removed.
- `setup_river_hydrography` This method was removed as reprojection of the hydrography data is no longer required for river inflow/outflow.
- `setup_river_bathymetry` This method was removed as river bathymetry should ideally be burned in the subgrid data of the model rather
than the dep file itself to be able to include rivers with widths smaller than the model grid cell size. A new option to burn rivers
in the subgrid data will be added in to `setup_subgrid` a future release.


New low-level classes
---------------------
These classes are not intended to be used directly by the user, but are used internally by the SfincsModel class.

- The `SfincsInput` class contains methods to generate, read and write SFINCS input files
- The `RegularGrid` class contains methods to create and manipulate regular grids
- The `SubgridTableRegular` class contains methods to create and manipulate subgrid tables for regular grids

Deprecated
------------
- **setup_basemaps** has been replaced by **setup_topobathy**
- In **setup_mask**, the "active_mask_fn" argument has been renamed to "mask_fn" for consistency
- In **setup_river_inflow** and **setup_river_outflow** the "basemaps_fn" argument has been renamed to "hydrography_fn" for consistency
- In **setup_river_outflow** the "outflow_width" argument has been renamed to "river_width" for consistency with setup_river_inflow
- **setup_q_forcing_from_grid** and **workflows.snap_discharge** have a "rel_error" and "abs_error" argument instead of a single "max_error" argument.

Bugfix
-------
- bugfix **setup_p_forcing** to ensure the data is 1D when passed to set_forcing_1d method
- bugfix **setup_p_forcing_from_grid** when aggregating with a multi polygon region.
- bugfix **read_results** with new corner_x/y instead of edge_x/y dimensions in sfincs_map.nc

New
-----
- **setup_region** method to set the (hydrological) model region of interest (before part of **setup_basemaps**).
- **setup_river_hydrography** allows to derive hydrography data ['flwdir', 'uparea'] from the model elevation or reproject it from a global dataset.
Derived 'uparea' and 'flwdir' maps are saved in the GIS folder and can be reused later (if kept together with the model)
- **setup_river_bathymetry** to estimate a river depth based on bankfull discharge and river width. A mask of river cells 'rivmsk' is kept in the GIS folder.

Changed
----------
- **setup_mask** and **setup_bounds** both have a "mask_fn", "include_mask_fn" and "exclude_mask_fn" polygon and "min_elv" and "max_elv" elevation arguments to determine valid / boundary cells.
- **setup_mask** and **setup_bounds** have a "reset_mask" and "reset_bounds" option respectively to start with a clean mask or remove previously set boundary cells.
- **setup_mask** takes a new "drop_area" argument to drop regions of contiguous cells smaller than this maximum area threshold, useful to remove (spurious) small islands.
- **setup_mask** takes a new "fill_area" argument to fill regions of contiguous cells below the "min_elv" or above "max_elv" threshold surrounded by cells within the valid elevation range.
- In **setup_bounds** and **setup_mask** a "connectivity" argument is exposed to determine whether edge cells or regions of contiguous cells should be based on D4 (horizontal and vertical) or D8 (also diagonal) connections.
- In **setup_bounds** we avoid open boundary cells (mask == 3) next to water level boundary cells (mask == 2)
- **setup_merge_topobathy** has a new "max_width" argument to use bathymetry data from new source within a fixed width around the topography data.
- **setup_river_inflow** and **setup_river_outflow** are now based on the same **workflows.river_boundary_points** method.
Both have a "river_upa" and "river_len" argument and the hydrography data is not required if **setup_river_hydrography** is ran beforehand.
The model domain is also determined on-the-fly, thus it is not required to run setup_mask beforehand.
- **setup_river_inflow** has a new "river_width" argument to ensure closed boundary cells near a discharge source location
- **write_config** has a new "rel_path" argument that allows you to write sfincs.inp with references to model files in the root and rel_path directory.
- Write dep file with cm accuracy. This should be sufficient but also hides differences between linux and window builds.
- Exposed "interp_method" argument in **setup_merge_topobathy** to select interpolation method to fill NaNs.
- **setup_cn_infiltration** and **setup_manning_roughness** use default values for river cells as defined in **setup_river_bathymetry**
- The **setup_manning_rougness** has a new "sea_man" argument to set a constant roughness for cells below zero elevation.
- An improved version of interbasins **region** option has been implemented, see hydroMT core v0.4.5 for details.
- Bumped minimal pyflwdir version to 0.5.5
- Use mamba to setup CI environments

**Bugfix**
- scsfile variable in ``setup_cn_infiltration`` changed to maximum soil moisture retention [inch]; was curve number [-]
- fix setting delimited text based geodatasets for h and q forcing.

**Changed**
- Bumped minimal required hydromt vesion to 0.4.2
- splitted ``setup_basemaps`` into multiple smaller methods: ``setup_merge_topobathy``, ``setup_mask`` and ``setup_bounds``
- separated many low-level methods into utils.py and plots.py
- save bzs/bzd & dis/src only as GeoDataArray in forcing and do not copy the locations in staticgeoms.
- sort src/bnd files on x_dim for comparibility between OS
- staticmaps are by default saved (and read) in S->N orientation as this matches the SFINCS better.


**Added**
support for SFINCS files:

- structures: sfincs.thd & sfincs.weir
- results: sfincs_map.nc & sfincs_his.nc
- states: sfincs.restart
- forcing: sfincs.precip

New methods:

- ``setup_p_forcing_from_grid`` and ``setup_p_forcing`` with support for spatial uniform precip
- ``setup_merge_topobathy`` to merge a new topo/bathymetry dataset with the basemap DEM
- ``setup_mask`` and ``setup_bounds`` methods to setup the sfincs mask file
- ``setup_structures`` thd/weir files are read/written as part of read_staticgeoms
- ``read_states``, ``write_states`` methods with support for restart
- ``read_results``
- ``update_spatial_attrs`` and ``get_spatial_attrs`` (previously part of read_staticmaps)

New workflows:

- ``merge_topobathy``
- ``mask_topobathy``
- ``snap_discharge``
- ``river_inflow_points`` & ``river_outflow_points``

**Documentation**
- build from python example
- overviews with SfincsModel setup components & SfincsModel data

**Deprecated**
- ``setup_p_gridded``