add io and extra to testing in ci again

.github/workflows/tests.yml

@@ -44,7 +44,7 @@ jobs:
             activate-environment: hydromt
             use-mamba: true
       - name: Generate env spec
-        run: pip install tomli && python make_env.py test
+        run: pip install tomli && python make_env.py test,io,extra
 
 
       - name: Set cache date

hydromt/models/model_mesh.py

@@ -292,7 +292,7 @@ def set_mesh(
                 raise ValueError(
                     f"Cannot set mesh from {str(type(data).__name__)} without a name."
                 )
-            data = data.to_dataset(optional_attributes=True)
+            data = data.to_dataset()
 
         # Checks on grid topology
         # TODO: check if we support setting multiple grids at once. For now just one
@@ -371,7 +371,8 @@ def set_mesh(
         # update related geoms if necessary: region
         if overwrite_grid or new_grid:
             # add / updates region
-            self._geoms.pop("region", None)
+            if "region" in self.geoms:
+                self._geoms.pop("region", None)
             self.region
 
     def get_mesh(
@@ -437,7 +438,7 @@ def read_mesh(
             Additional keyword arguments to be passed to the `read_nc` method.
         """
         self._assert_read_mode
-        ds = xr.merge(self._read_nc(fn, **kwargs).values())
+        ds = xr.merge(self.read_nc(fn, **kwargs).values())
         uds = xu.UgridDataset(ds)
         if ds.rio.crs is not None:  # parse crs
             uds.ugrid.set_crs(ds.raster.crs)

hydromt/workflows/basin_mask.py

@@ -148,8 +148,17 @@ def parse_region(region, logger=logger):
         if _compat.HAS_XUGRID:
             if isinstance(value0, (str, Path)) and isfile(value0):
                 kwarg = dict(mesh=xu.open_dataset(value0))
-            elif isinstance(value0, xu.UgridDataset):
+            elif isinstance(value0, (xu.UgridDataset, xu.UgridDataArray)):
                 kwarg = dict(mesh=value0)
+            elif isinstance(value0, (xu.Ugrid1d, xu.Ugrid2d)):
+                kwarg = dict(
+                    mesh=xu.UgridDataset(value0.to_dataset(optional_attributes=True))
+                )
+            else:
+                raise ValueError(
+                    f"Unrecognised type {type(value0)}."
+                    "Should be a path, data catalog key or xugrid object."
+                )
             kwargs.update(kwarg)
         else:
             raise ImportError("xugrid is required to read mesh files.")

pyproject.toml

@@ -73,7 +73,8 @@ test = [
     "pytest-cov",    # test coverage
     "pytest-mock",   # mocking
     "pytest-timeout", # darn hanging tests
-]
+    "xugrid"
+    ]
 doc = [
     "nbsphinx",                     # build notebooks in docs
     "pydata-sphinx-theme",          # theme
@@ -137,7 +138,7 @@ include = ["hydromt"]
 exclude = ["docs", "examples", "envs", "tests", "binder", ".github"]
 
 [tool.pytest.ini_options]
-addopts = "--ff --timeout=120"
+addopts = "--ff --timeout=120 "
 testpaths = ["tests"]
 
 filterwarnings = [

tests/conftest.py

@@ -1,9 +1,12 @@
+from os.path import abspath, dirname, join
+
 import geopandas as gpd
 import numpy as np
 import pandas as pd
 import pyflwdir
 import pytest
 import xarray as xr
+from dask import config as dask_config
 from shapely.geometry import box
 
 from hydromt import (
@@ -18,6 +21,10 @@
 )
 from hydromt.data_catalog import DataCatalog
 
+dask_config.set(scheduler="single-threaded")
+
+DATADIR = join(dirname(abspath(__file__)), "data")
+
 
 @pytest.fixture()
 def rioda():
@@ -80,7 +87,7 @@ def geodf(df):
 
 @pytest.fixture()
 def world():
-    world = gpd.read_file("tests/data/naturalearth_lowres.geojson")
+    world = gpd.read_file(join(DATADIR, "naturalearth_lowres.geojson"))
     return world
 
 

tests/test_model.py

@@ -641,7 +641,7 @@ def test_meshmodel_setup(griduda, world):
     mod.setup_mesh2d(region, res=10000, crs=3857, grid_name="mesh2d")
     mod.region
 
-    region = {"mesh": griduda.ugrid.to_dataset()}
+    region = {"mesh": griduda}
     mod1 = MeshModel(data_libs=["artifact_data", dc_param_fn])
     mod1.setup_mesh2d(region, grid_name="mesh2d")
     mod1.setup_mesh2d_from_rasterdataset("vito", grid_name="mesh2d")