Merge pull request #2 from gantian127/release-0.1.2

Release 0.1.2

notebooks/config_file.yaml

@@ -1,8 +1,9 @@
-service_id: phh2o
-coverage_id: phh2o_0-5cm_mean
-crs: urn:ogc:def:crs:EPSG::152160
-west: -1784000
-south: 1356000
-east: -1140000
-north: 1863000
-output: test.tif
+bmi-soilgrids:
+  service_id: phh2o
+  coverage_id: phh2o_0-5cm_mean
+  crs: urn:ogc:def:crs:EPSG::152160
+  west: -1784000
+  south: 1356000
+  east: -1140000
+  north: 1863000
+  output: test.tif

notebooks/config_file2.yaml

@@ -1,10 +1,11 @@
-service_id: phh2o
-coverage_id: phh2o_0-5cm_mean
-crs: urn:ogc:def:crs:EPSG::4326
-west: -105.38
-south: 39.45
-east: -104.5
-north: 40.07
-width: 316
-height: 275
-output: test.tif
+bmi-soilgrids:
+  service_id: phh2o
+  coverage_id: phh2o_0-5cm_mean
+  crs: urn:ogc:def:crs:EPSG::4326
+  west: -105.38
+  south: 39.45
+  east: -104.5
+  north: 40.07
+  width: 316
+  height: 275
+  output: test2.tif

soilgrids/bmi.py

@@ -31,7 +31,12 @@ def finalize(self) -> None:
         loop. This typically includes deallocating memory, closing files and
         printing reports.
         """
-        self._time_index = 0.0
+        self._var = {}
+        self._grid = {}
+        self._input_var_names = ()
+        self._output_var_names = ()
+        self._dataset = None
+
 
     def get_component_name(self) -> str:
         """Name of the component.
@@ -49,7 +54,7 @@ def get_current_time(self) -> float:
         float
             The current model time.
         """
-        return self._time_index
+        return 0.0
 
     def get_end_time(self) -> float:
         """End time of the model.
@@ -58,7 +63,7 @@ def get_end_time(self) -> float:
         float
             The maximum model time.
         """
-        return 9999.0
+        return 0.0
 
     def get_grid_face_edges(self, grid: int, face_edges: numpy.ndarray) -> numpy.ndarray:
         """Get the face-edge connectivity.
@@ -200,7 +205,7 @@ def get_grid_rank(self, grid: int) -> int:
         int
             Rank of the grid.
         """
-        return 2
+        return len(self._grid[grid].shape)
 
     def get_grid_shape(self, grid: int, shape: numpy.ndarray) -> numpy.ndarray:
         """Get dimensions of the computational grid.
@@ -276,7 +281,8 @@ def get_grid_x(self, grid: int, x: numpy.ndarray) -> numpy.ndarray:
         ndarray of float
             The input numpy array that holds the grid's column x-coordinates.
         """
-        raise NotImplementedError("get_grid_x")
+        x[:] = self._dataset.x.values
+        return x
 
     def get_grid_y(self, grid: int, y: numpy.ndarray) -> numpy.ndarray:
         """Get coordinates of grid nodes in the y direction.
@@ -291,7 +297,8 @@ def get_grid_y(self, grid: int, y: numpy.ndarray) -> numpy.ndarray:
         ndarray of float
             The input numpy array that holds the grid's row y-coordinates.
         """
-        raise NotImplementedError("get_grid_y")
+        y[:] = self._dataset.y.values
+        return y
 
     def get_grid_z(self, grid: int, z: numpy.ndarray) -> numpy.ndarray:
         """Get coordinates of grid nodes in the z direction.
@@ -334,7 +341,7 @@ def get_input_item_count(self) -> int:
         int
           The number of input variables.
         """
-        return 0
+        return len(self._input_var_names)
 
     def get_output_var_names(self) -> Tuple[str]:
         """List of a model's output variables.
@@ -355,7 +362,7 @@ def get_output_item_count(self) -> int:
         int
           The number of output variables.
         """
-        return 1
+        return len(self._output_var_names)
 
     def get_start_time(self) -> float:
         """Start time of the model.
@@ -375,7 +382,7 @@ def get_time_step(self) -> float:
         float
             The time step used in model.
         """
-        return 1.0
+        return 0.0
 
     def get_time_units(self) -> str:
         """Time units of the model.
@@ -387,7 +394,7 @@ def get_time_units(self) -> str:
         -----
         CSDMS uses the UDUNITS standard from Unidata.
         """
-        return 'none'
+        return "1"
 
     def get_value(self, name: str, dest: numpy.ndarray) -> numpy.ndarray:
         """Get a copy of values of the given variable.
@@ -406,7 +413,7 @@ def get_value(self, name: str, dest: numpy.ndarray) -> numpy.ndarray:
             The same numpy array that was passed as an input buffer.
         """
         # return all the value at current time step, for scalar it is just one value
-        dest[:] = self._dataset[0].values.reshape(-1).copy()
+        dest[:] = self.get_value_ptr(name).reshape(-1).copy()
         return dest
 
     def get_value_at_indices(
@@ -427,7 +434,7 @@ def get_value_at_indices(
             Value of the model variable at the given location.
         """
         # return the value at current time step with given index in 1D or 2D grid. when it is scalar no need for ind
-        dest[:] = self._dataset[0].values.reshape(-1)[inds]
+        dest[:] = self.get_value_ptr(name).reshape(-1)[inds]
         return dest
 
     def get_value_ptr(self, name: str) -> numpy.ndarray:
@@ -575,17 +582,22 @@ def initialize(self, config_file: str) -> None:
         """
         if config_file:
             with open(config_file, "r") as fp:
-                conf = yaml.safe_load(fp)
+                conf = yaml.safe_load(fp).get('bmi-soilgrids', {})
         else:
-            conf = {}
+            conf = {'service_id': 'phh2o',
+                    'coverage_id': 'phh2o_0-5cm_mean',
+                    'crs': 'urn:ogc:def:crs:EPSG::152160',
+                    'west': -1784000,
+                    'south': 1356000,
+                    'east': -1140000,
+                    'north': 1863000,
+                    'output': 'test.tif'}
 
         soilgrids = SoilGrids()
         self._dataset = soilgrids.get_coverage_data(**conf)
 
         self._output_var_names = tuple([soilgrids.metadata['variable_name']])
 
-        self._time_index = 0.0
-
         array = self._dataset[0].values
         self._grid = {
             0: BmiGridUniformRectilinear(
@@ -644,7 +656,7 @@ def update(self) -> None:
         then they can be computed by the :func:`initialize` method and this
         method can return with no action.
         """
-        self._time_index += 1.0
+        raise NotImplementedError("update")
 
     def update_until(self, time: float) -> None:
         """Advance model state until the given time.