Merge pull request #183 from Deltares/small_fixes

Small fixes

docs/_static/theme-deltares.css

@@ -3,20 +3,20 @@
 html[data-theme="light"] {
     /* NOTE: added after pydata v0.9 */
     --pst-color-primary: #080c80 !important;
-    
+
     /* hyperlinks */
     --pst-color-link: rgb(13, 56, 224);
 
     /* panels */
     --pst-color-preformatted-border: #080c80 !important;
     --pst-color-panel-background: #f0f0f075;
-    
+
     /* navbar */
     /* NOTE: does not work since v0.9 */
     --pst-color-navbar-link: rgb(237, 237, 255);
     --pst-color-navbar-link-hover: #fff;
     --pst-color-navbar-link-active: #fff;
-    
+
     /* sphinx design */
     /* NOTE: does not work since v0.9 */
     --sd-color-card-border-hover: #080c80;
@@ -28,4 +28,8 @@ html[data-theme="light"] {
 /* enlarge deltares & github icon size; only works with local/url svg files; not with fa icons */
 img.icon-link-image {
     height: 2.5em !important;
+}
+
+i.fa-github {
+    font-size: 2.5em;
 }

docs/api.rst

@@ -38,7 +38,6 @@ Setup components
    WflowModel.setup_laimaps
    WflowModel.setup_rootzoneclim
    WflowModel.setup_soilmaps
-   WflowModel.setup_hydrodem
    WflowModel.setup_outlets
    WflowModel.setup_gauges
    WflowModel.setup_areamap

docs/changelog.rst

@@ -42,6 +42,8 @@ Fixed
 - write_forcing with time cftime.DatetimeNoLeap #138 by removing slicing forcing if missings (not needed)
 - write_forcing automatic adjustment of starttime and endtime based on forcing content
 - When clipping a model from a model with multiple forcing files, a single netcdf is made in write_forcing and the * is removed from the filename.
+- Remove deprecated basin_shape method `PR #183 <https://github.com/Deltares/hydromt_wflow/pull/183>`_
+- Remove FillValue Nan for lat/lon in staticmaps and forcing `PR #183 <https://github.com/Deltares/hydromt_wflow/pull/183>`_
 - Fix compatibility with HydroMT v0.8.0, with updated `clip_geom/mask` functionality `PR #189 <https://github.com/Deltares/hydromt_wflow/pull/189>`_
 
 Deprecated

docs/conf.py

@@ -111,7 +111,8 @@ def remove_dir_content(path: str) -> None:
 # a list of builtin themes.
 #
 html_theme = "pydata_sphinx_theme"
-html_logo = "_static/hydromt-logo.jpg"
+html_logo = "_static/hydromt-icon.svg"
+html_favicon = "_static/hydromt-icon.svg"
 autodoc_member_order = "bysource"  # overwrite default alphabetical sort
 autoclass_content = "both"
 
@@ -132,8 +133,8 @@ def remove_dir_content(path: str) -> None:
         {
             "name": "GitHub",
             "url": "https://github.com/Deltares/hydromt_wflow",  # required
-            "icon": "https://upload.wikimedia.org/wikipedia/commons/9/91/Octicons-mark-github.svg",
-            "type": "url",
+            "icon": "fab fa-github",
+            "type": "fontawesome",
         },
         {
             "name": "Wflow",
@@ -280,7 +281,7 @@ def remove_dir_content(path: str) -> None:
     .. raw:: html
 
         <div>
-            For an interactive online version click here: 
+            For an interactive online version click here:
             <a href="https://mybinder.org/v2/gh/Deltares/hydromt_wflow/main?urlpath=lab/tree/examples/{{ docname|e }}" target="_blank" rel="noopener noreferrer"><img alt="Binder badge" src="https://mybinder.org/badge_logo.svg"></a>
         </div>
 """

docs/user_guide/wflow_model_setup.rst

@@ -53,9 +53,7 @@ a specific method see its documentation.
     * - :py:func:`~WflowModel.setup_soilmaps`
       - This component derives several (layered) soil parameters based on a database with physical soil properties using available point-scale (pedo)transfer functions (PTFs) from literature with upscaling rulesto ensure flux matching across scales.
     * - :py:func:`~WflowModel.setup_rootzoneclim`
-      - This component derives an estimate of the rooting depth from hydroclimatic data (as an alternative from the look-up table). The method can be applied for current conditions and future climate change conditions. 
-    * - :py:func:`~WflowModel.setup_hydrodem`
-      - This component adds a hydrologically conditioned elevation (hydrodem) map for river and/or land local-inertial routing.
+      - This component derives an estimate of the rooting depth from hydroclimatic data (as an alternative from the look-up table). The method can be applied for current conditions and future climate change conditions.
     * - :py:func:`~WflowModel.setup_outlets`
       - This method sets the default gauge map based on basin outlets.
     * - :py:func:`~WflowModel.setup_gauges`

hydromt_wflow/wflow.py

@@ -772,7 +772,7 @@ def setup_lulcmaps(
         This component derives several wflow maps are derived based on landuse-
         landcover (LULC) data.
 
-        Currently, ``lulc_fn`` can be set to the "vito", "globcover"
+        Currently, ``lulc_fn`` can be set to the "vito", "globcover", "esa_worldcover"
         or "corine", fo which lookup tables are constructed to convert lulc classses to
         model parameters based on literature. The data is remapped at its original
         resolution and then resampled to the model resolution using the average
@@ -1506,6 +1506,7 @@ def setup_reservoirs(
             if np.all(np.isin(resattributes, gdf_org.columns)):
                 intbl_reservoirs = gdf_org[resattributes]
                 reservoir_accuracy = None
+                reservoir_timeseries = None
             # else compute
             else:
                 (
@@ -2385,6 +2386,12 @@ def write_staticmaps(self):
         ds_out.rio.write_transform(self.staticmaps.raster.transform, inplace=True)
         ds_out.raster.set_spatial_dims()
 
+        # Remove FillValue Nan for x_dim, y_dim
+        encoding = dict()
+        for v in [ds_out.raster.x_dim, ds_out.raster.y_dim]:
+            ds_out[v].attrs.pop("_FillValue", None)
+            encoding[v] = {"_FillValue": None}
+
         # filename
         fn_default = join(self.root, "staticmaps.nc")
         fn = self.get_config("input.path_static", abs_path=True, fallback=fn_default)
@@ -2403,7 +2410,7 @@ def write_staticmaps(self):
             # nodata is required for all but boolean fields
             if ds_out[v].dtype != "bool":
                 ds_out[v] = ds_out[v].where(mask, ds_out[v].raster.nodata)
-        ds_out.to_netcdf(fn)
+        ds_out.to_netcdf(fn, encoding=encoding)
         # self.write_staticmaps_pcr()
 
     def read_staticmaps_pcr(self, crs=4326, **kwargs):
@@ -2665,10 +2672,11 @@ def write_forcing(
                 v: {"zlib": True, "dtype": "float32", "chunksizes": chunksizes}
                 for v in ds.data_vars.keys()
             }
-            # make sure no _FillValue is written to the time dimension
+            # make sure no _FillValue is written to the time / x_dim / y_dim dimension
             # For several forcing files add common units attributes to time
-            ds["time"].attrs.pop("_FillValue", None)
-            encoding["time"] = {"_FillValue": None}
+            for v in ["time", ds.raster.x_dim, ds.raster.y_dim]:
+                ds[v].attrs.pop("_FillValue", None)
+                encoding[v] = {"_FillValue": None}
 
             # Check if all sub-folders in fn_out exists and if not create them
             if not isdir(dirname(fn_out)):
@@ -2894,11 +2902,20 @@ def basins(self):
         """Returns a basin(s) geometry as a geopandas.GeoDataFrame."""
         if "basins" in self.staticgeoms:
             gdf = self.staticgeoms["basins"]
-        else:
-            gdf = flw.basin_shape(
-                self.staticmaps, self.flwdir, basin_name=self._MAPS["basins"]
+        elif self._MAPS["basins"] in self.staticmaps:
+            gdf = (
+                self.staticmaps[self._MAPS["basins"]]
+                .raster.vectorize()
+                .set_index("value")
+                .sort_index()
             )
+            gdf.index.name = self._MAPS["basins"]
             self.set_staticgeoms(gdf, name="basins")
+        else:
+            self.logger.warning(
+                f"Basin map {self._MAPS['basins']} not found in staticmaps."
+            )
+            gdf = None
         return gdf
 
     @property
@@ -2974,7 +2991,7 @@ def clip_staticmaps(
             )
             ds_staticmaps.coords["mask"] = ds_staticmaps.raster.geometry_mask(geom)
             ds_staticmaps[basins_name] = ds_staticmaps[basins_name].where(
-                ds_staticmaps["mask"], self.staticmaps[basins_name].raster.nodata
+                ds_staticmaps.coords["mask"], self.staticmaps[basins_name].raster.nodata
             )
             ds_staticmaps[basins_name].attrs.update(
                 _FillValue=self.staticmaps[basins_name].raster.nodata
@@ -3001,10 +3018,16 @@ def clip_staticmaps(
         # self.rivers
         # now staticgeoms links to geoms which does not exist in every hydromt version
         # remove when updating wflow to new objects
-        basins = flw.basin_shape(
-            self.staticmaps, self.flwdir, basin_name=self._MAPS["basins"]
+        # Basin shape
+        basins = (
+            self.staticmaps[basins_name]
+            .raster.vectorize()
+            .set_index("value")
+            .sort_index()
         )
+        basins.index.name = basins_name
         self.set_staticgeoms(basins, name="basins")
+
         rivmsk = self.staticmaps[self._MAPS["rivmsk"]].values != 0
         # Check if there are river cells in the model before continuing
         if np.any(rivmsk):