Merge pull request #121 from Deltares/fix/tests

Fix tests

.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: Tests
+name: Tests stable
 
 on:
   push:
@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"] #, "macos-latest", "windows-latest"]
-        python-version: ["3.9", "3.10"] # fix tests to support older versions
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v2
@@ -36,7 +36,7 @@ jobs:
          conda list
 
       - name: Intall hydromt_sfincs
-        run: flit install
+        run: pip install .
 
       - name: Test
         run: python -m pytest --verbose --cov=hydromt_sfincs --cov-report xml

.github/workflows/tests_dev.yml

@@ -0,0 +1,47 @@
+name: Tests Dev
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  Test:
+    name: HydroMT dev - ubuntu-latest - py3.10
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: "3.10"
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          environment-file: envs/hydromt-sfincs-dev.yml
+          activate-environment: hydromt-sfincs-dev
+
+      - name: Conda info
+        run: |
+         conda info
+         conda list
+
+      - name: Intall hydromt core dev version
+        run: pip install git+https://github.com/Deltares/hydromt.git
+
+      - name: Intall hydromt_sfincs
+        run: pip install .
+
+      - name: Test
+        run: python -m pytest --verbose --cov=hydromt_sfincs --cov-report xml
+
+      - name: Check style
+        run: black --check .
+
+      - uses: codecov/codecov-action@v3

environment.yml

@@ -13,6 +13,6 @@ dependencies:
   - hydromt>=0.8.0
   - hydromt_sfincs>=1.0
   - jupyterlab # to run examples
-  - matplotlib==3.5.* # to run examples / https://github.com/SciTools/cartopy/issues/2086
+  - matplotlib # to run examples
   - pip
   - python=3.10 # fixing python version for binder

envs/hydromt-sfincs-dev.yml

@@ -15,7 +15,7 @@ dependencies:
   - geopandas>=0.8
   - hydromt>=0.8.0
   - jupyterlab  # to run examples
-  - matplotlib==3.5.* # to run examples / https://github.com/SciTools/cartopy/issues/2086
+  - matplotlib # to run examples
   - nbsphinx  # docs
   - numba
   - numpy
@@ -34,5 +34,4 @@ dependencies:
   - sphinx # docs
   - xarray
   - pip:
-    - sphinx_design  # docs
-    - git+https://github.com/Deltares/hydromt.git # bathymetry.burn_river_rect requires v0.7.2
+    - sphinx_design  # docs

hydromt_sfincs/sfincs.py

@@ -345,12 +345,12 @@ def setup_dep(
             )
 
             # check if no nan data is present in the bed levels
-            if np.isnan(da_dep).any():
-                self.logger.warning(
-                    f"Interpolate data at {int(np.sum(np.isnan(da_dep.values)))} cells"
+            nmissing = int(np.sum(np.isnan(da_dep.values)))
+            if nmissing > 0:
+                self.logger.warning(f"Interpolate elevation at {nmissing} cells")
+                da_dep = da_dep.raster.interpolate_na(
+                    method="rio_idw", extrapolate=True
                 )
-                # TODO add extrapolate=True option when available in hydromt core
-                da_dep = da_dep.raster.interpolate_na(method="rio_idw")
 
             self.set_grid(da_dep, name="dep")
             # FIXME this shouldn't be necessary, since da_dep should already have a crs
@@ -2524,7 +2524,7 @@ def plot_basemap(
         for fname, gname in self._FORCING_1D.values():
             if fname[0] in self.forcing and gname is not None:
                 try:
-                    sg.update({gname: self._forcing[fname[0]].vector.to_gdf()})
+                    sg.update({gname: self.forcing[fname[0]].vector.to_gdf()})
                 except ValueError:
                     self.logger.debug(f'unable to plot forcing location: "{fname}"')
         if plot_region and "region" not in self.geoms:
@@ -2993,12 +2993,17 @@ def read_states(self):
         self._assert_read_mode
 
         # read index file
-        ind_fn = self.get_config("indexfile", fallback="sfincs.ind", abs_path=True)
-        if not isfile(ind_fn):
-            raise IOError(f".ind path {ind_fn} does not exist")
-
+        # TODO make reggrid a property where we trigger the initialization of reggrid
+        if self.reggrid is None:
+            self.update_grid_from_config()
         if self.reggrid is not None:
-            ind = self.reggrid.read_ind(ind_fn=ind_fn)
+            ind_fn = self.get_config("indexfile", fallback="sfincs.ind", abs_path=True)
+            if "msk" in self.grid:  # triggers reading grid if empty and in read mode
+                ind = self.reggrid.ind(self.grid["msk"].values)
+            elif isfile(ind_fn):
+                ind = self.reggrid.read_ind(ind_fn=ind_fn)
+            else:
+                raise IOError(f"indexfile {ind_fn} does not exist")
             if "inifile" in self.config:
                 fn = self.get_config("inifile", abs_path=True)
                 if not isfile(fn):
@@ -3036,8 +3041,8 @@ def write_states(self):
             ind_fn = self.get_config("indexfile", abs_path=True)
             self.reggrid.write_ind(ind_fn=ind_fn, mask=mask)
 
-            if f"inifile" not in self.config:
-                self.set_config(f"inifile", f"sfincs.{name}")
+            if "inifile" not in self.config:
+                self.set_config("inifile", f"sfincs.{name}")
             fn = self.get_config("inifile", abs_path=True)
             da = self.states[name]
             if da.raster.res[1] < 0:
@@ -3098,7 +3103,7 @@ def read_results(
                 fn_his, crs=self.crs, chunksize=chunksize
             )
             # drop double vars (map files has priority)
-            drop_vars = [v for v in ds_his.data_vars if v in self._results or v in drop]
+            drop_vars = [v for v in ds_his.data_vars if v in self.results or v in drop]
             ds_his = ds_his.drop_vars(drop_vars)
             self.set_results(ds_his, split_dataset=True)
 

tests/data/sfincs_test/gis/drn.geojson

@@ -2,7 +2,7 @@
 "type": "FeatureCollection",
 "crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:EPSG::32633" } },
 "features": [
-{ "type": "Feature", "properties": { "id": 1, "type": 1, "par1": 10.0, "par2": 0, "par3": 0, "par4": 0, "par5": 0 }, "geometry": { "type": "LineString", "coordinates": [ [ 322021.879048462666105, 5045547.683568798005581 ], [ 322378.691038294811733, 5045133.781660593114793 ] ] } },
-{ "type": "Feature", "properties": { "id": 2, "type": 2, "par1": 40.0, "par2": 0, "par3": 0, "par4": 0, "par5": 0 }, "geometry": { "type": "LineString", "coordinates": [ [ 319160.246890009148046, 5045262.233976932242513 ], [ 319167.383129805792123, 5044976.784385066479445 ] ] } }
+{ "type": "Feature", "properties": { "id": 1, "par1": 10.0, "type": 1, "par2": 0, "par3": 0, "par4": 0, "par5": 0 }, "geometry": { "type": "LineString", "coordinates": [ [ 322021.879048462666105, 5045547.683568798005581 ], [ 322378.691038294811733, 5045133.781660593114793 ] ] } },
+{ "type": "Feature", "properties": { "id": 2, "par1": 40.0, "type": 2, "par2": 0, "par3": 0, "par4": 0, "par5": 0 }, "geometry": { "type": "LineString", "coordinates": [ [ 319160.246890009148046, 5045262.233976932242513 ], [ 319167.383129805792123, 5044976.784385066479445 ] ] } }
 ]
 }