Expand BMI tests, fix BMI bugs.

Author: BSchilperoort

PyStemmusScope/bmi/implementation.py

@@ -360,7 +360,7 @@ def get_time_step(self) -> float:
         """Return the current time step of the model."""
         if self.state is None:
             raise ValueError(NO_STATE_MSG)
-        return float(self.state["KT"][0])
+        return float(self.state["TimeStep"][0][0])
 
     ### GETTERS AND SETTERS ###
     def get_value(self, name: str, dest: np.ndarray) -> np.ndarray:
@@ -542,8 +542,8 @@ def get_grid_shape(self, grid: int, shape: np.ndarray) -> np.ndarray:
             msg = f"Unknown grid identifier '{grid}'"
             raise ValueError(msg)
 
-        self.get_grid_x(grid, shape[-1])  # Last element is x
-        self.get_grid_y(grid, shape[-2])  # Semi-last element is y
+        shape[-1] = 1  # Last element is x
+        shape[-2] = 1  # Semi-last element is y
         if grid == 1:
-            self.get_grid_z(grid, shape[-3])  # First element is z
+            shape[-3] = self.get_grid_size(grid)  # First element is z
         return shape

PyStemmusScope/bmi/local_process.py

@@ -11,7 +11,9 @@
 from PyStemmusScope.config_io import read_config
 
 
-def alive_process(process: Union[subprocess.Popen, None]) -> subprocess.Popen:  # pragma: no cover
+def alive_process(
+    process: Union[subprocess.Popen, None]
+) -> subprocess.Popen:  # pragma: no cover
     """Return process if the process is alive, raise an exception if it is not."""
     if process is None:
         msg = "Model process does not seem to be open."
@@ -40,7 +42,9 @@ def _model_is_ready(process: subprocess.Popen) -> None:  # pragma: no cover
     return _wait_for_model(PROCESS_READY, process)
 
 
-def _wait_for_model(phrase: bytes, process: subprocess.Popen) -> None:  # pragma: no cover
+def _wait_for_model(
+    phrase: bytes, process: subprocess.Popen
+) -> None:  # pragma: no cover
     """Wait for model to be ready for interaction."""
     output = b""
 

tests/test_bmi_docker.py

@@ -20,6 +20,25 @@
 )
 
 
+# fmt: off
+SOIL_GRID = np.array([
+    -5.   , -4.8  , -4.6  , -4.4  , -4.2  , -4.   , -3.8  , -3.6  ,
+    -3.4  , -3.2  , -3.   , -2.8  , -2.6  , -2.45 , -2.3  , -2.2  ,
+    -2.1  , -2.   , -1.9  , -1.8  , -1.7  , -1.6  , -1.5  , -1.4  ,
+    -1.3  , -1.2  , -1.1  , -1.   , -0.9  , -0.8  , -0.7  , -0.6  ,
+    -0.55 , -0.5  , -0.45 , -0.4  , -0.35 , -0.325, -0.3  , -0.275,
+    -0.25 , -0.23 , -0.21 , -0.19 , -0.17 , -0.15 , -0.13 , -0.11 ,
+    -0.09 , -0.07 , -0.05 , -0.03 , -0.02 , -0.01 , -0.,
+])
+
+INVALID_METHODS = (
+    "get_grid_spacing", "get_grid_origin", "get_var_location", "get_grid_node_count",
+    "get_grid_edge_count", "get_grid_face_count", "get_grid_edge_nodes",
+    "get_grid_face_edges", "get_grid_face_nodes", "get_grid_nodes_per_face"
+)
+# fmt: on
+
+
 def docker_available():
     try:
         docker.APIClient()
@@ -98,49 +117,160 @@ def prepare_data_config(tmpdir_factory, prep_input_data) -> Path:
     return config_dir
 
 
-@pytest.mark.skipif(not docker_available(), reason="Docker not available")
-def test_initialize(prepare_data_config):
+@pytest.fixture(scope="class")
+def uninitialized_model():
     model = StemmusScopeBmi()
+    yield model
+    try:
+        model.finalize()
+    except:  # noqa
+        pass
 
-    assert model.get_component_name() == "STEMMUS_SCOPE"
-    with pytest.raises(ValueError, match="STEMMUS_SCOPE process is not running"):
-        model.update()
 
+@pytest.fixture(scope="class")
+def initialized_model(uninitialized_model, prepare_data_config):
+    model: StemmusScopeBmi = uninitialized_model
     model.initialize(str(prepare_data_config))
+    yield model
+    model.finalize()
 
-    assert isinstance(model.get_input_item_count(), int)
-    assert isinstance(model.get_output_item_count(), int)
-    assert "soil_temperature" in model.get_input_var_names()
-    assert "respiration" in model.get_output_var_names()
 
-    assert model.get_var_grid("respiration") == 0
-    assert model.get_var_grid("soil_temperature") == 1
+@pytest.fixture(scope="class")
+def updated_model(uninitialized_model, prepare_data_config):
+    model: StemmusScopeBmi = uninitialized_model
+    model.initialize(str(prepare_data_config))
+    model.update()
+    yield model
+    model.finalize()
 
-    assert model.get_var_type("soil_temperature") == "float64"
 
-    # model.get_grid_size needs to have .update() run.
-    model.update()
+@pytest.mark.skipif(not docker_available(), reason="Docker not available")
+class TestUninitialized:
+    def test_component_name(self, uninitialized_model):
+        assert uninitialized_model.get_component_name() == "STEMMUS_SCOPE"
 
-    dest = np.zeros(model.get_grid_size(0))
-    np.testing.assert_almost_equal(model.get_grid_x(0, x=dest), np.array([-107.80752563]))
-    np.testing.assert_almost_equal(model.get_grid_y(0, y=dest), np.array([37.93380356]))
+    def test_invalid_update(self, uninitialized_model):
+        with pytest.raises(ValueError, match="STEMMUS_SCOPE process is not running"):
+            uninitialized_model.update()
 
-    with pytest.raises(ValueError, match="has no dimension `z`"):
-        model.get_grid_z(0, z=dest)
+    def test_get_ptr(self, uninitialized_model):
+        with pytest.raises(NotImplementedError):
+            uninitialized_model.get_value_ptr("soil_temperature")
 
-    model.update()
+    @pytest.mark.parametrize("method_name", INVALID_METHODS)
+    def test_not_implemented(self, uninitialized_model, method_name):
+        method = getattr(uninitialized_model, method_name)
+        nargs = method.__code__.co_argcount - 1  # remove "self"
+        with pytest.raises(NotImplementedError):
+            method(*(nargs * [0]))
 
-    dest = np.zeros(1)
-    model.get_value("respiration", dest)
-    assert dest[0] != 0.
+    def test_initialize(self, uninitialized_model, prepare_data_config):
+        uninitialized_model.initialize(str(prepare_data_config))
 
-    dest = np.zeros(1)
-    model.set_value_at_indices(
-        "soil_temperature",
-        inds=np.array([0]),
-        src=np.array([0.]),
-    )
-    model.get_value_at_indices("soil_temperature", dest, inds=np.array([0]))
-    assert dest[0] == 0.
 
-    model.finalize()
+@pytest.mark.skipif(not docker_available(), reason="Docker not available")
+class TestInitializedModel:
+    def test_input_item(self, initialized_model):
+        assert isinstance(initialized_model.get_input_item_count(), int)
+
+    def test_output_item(self, initialized_model):
+        assert isinstance(initialized_model.get_output_item_count(), int)
+
+    def test_input_var(self, initialized_model):
+        assert "soil_temperature" in initialized_model.get_input_var_names()
+
+    def test_output_var(self, initialized_model):
+        assert "respiration" in initialized_model.get_output_var_names()
+
+    def test_var_grid(self, initialized_model):
+        assert initialized_model.get_var_grid("respiration") == 0
+        assert initialized_model.get_var_grid("soil_temperature") == 1
+
+    def test_var_type(self, initialized_model):
+        assert initialized_model.get_var_type("soil_temperature") == "float64"
+
+    def test_grid_type(self, initialized_model):
+        assert initialized_model.get_grid_type(0) == "rectilinear"
+        assert initialized_model.get_grid_type(1) == "rectilinear"
+
+    def test_var_units(self, initialized_model):
+        assert initialized_model.get_var_units("soil_temperature") == "degC"
+
+    def test_grid_rank(self, initialized_model):
+        grid_resp = initialized_model.get_var_grid("respiration")
+        grid_t = initialized_model.get_var_grid("soil_temperature")
+        assert initialized_model.get_grid_rank(grid_resp) == 2
+        assert initialized_model.get_grid_rank(grid_t) == 3
+
+    def test_get_time_units(self, initialized_model):
+        assert (
+            initialized_model.get_time_units()
+            == "seconds since 1970-01-01 00:00:00.0 +0000"
+        )
+
+    def test_get_start_time(self, initialized_model):
+        assert initialized_model.get_start_time() == 820454400.0  # 1996-01-01 00:00:00
+
+    def test_get_end_time(self, initialized_model):
+        assert initialized_model.get_end_time() == 820461600.0  # 1996-01-01 02:00:00
+
+    def test_model_update(self, initialized_model):
+        initialized_model.update()
+
+
+class TestUpdatedModel:
+    # Many of these should be available after init
+    def test_get_current_time(self, updated_model):
+        assert updated_model.get_current_time() == (
+            updated_model.get_start_time() + updated_model.get_time_step()
+        )
+
+    def test_get_time_step(self, updated_model):
+        assert updated_model.get_time_step() == 1800
+
+    def test_grid_coords(self, updated_model):
+        dest = np.zeros(updated_model.get_grid_size(0))
+        np.testing.assert_almost_equal(
+            updated_model.get_grid_x(0, x=dest), np.array([-107.80752563])
+        )
+        np.testing.assert_almost_equal(
+            updated_model.get_grid_y(0, y=dest), np.array([37.93380356])
+        )
+
+    def test_invalid_dimension(self, updated_model):
+        dest = np.zeros(updated_model.get_grid_size(0))
+        with pytest.raises(ValueError, match="has no dimension `z`"):
+            updated_model.get_grid_z(0, z=dest)
+
+    def test_grid_z(self, updated_model):
+        grid = updated_model.get_var_grid("soil_temperature")
+        dest = np.zeros(updated_model.get_grid_size(grid))
+        updated_model.get_grid_z(grid, z=dest)
+        np.testing.assert_array_equal(dest, SOIL_GRID)
+
+    def test_grid_shape(self, updated_model):
+        grid = updated_model.get_var_grid("soil_temperature")
+        shape = np.zeros(updated_model.get_grid_rank(grid), dtype=int)
+        updated_model.get_grid_shape(grid, shape)
+        np.testing.assert_array_equal(shape, np.array([55, 1, 1], dtype=int))
+
+    def test_get_value(self, updated_model):
+        dest = np.zeros(1)
+        updated_model.get_value("respiration", dest)
+        assert dest[0] != 0.0
+
+    def test_set_value_inds(self, updated_model):
+        dest = np.zeros(1)
+        updated_model.set_value_at_indices(
+            "soil_temperature",
+            inds=np.array([0]),
+            src=np.array([0.0]),
+        )
+        updated_model.get_value_at_indices("soil_temperature", dest, inds=np.array([0]))
+        assert dest[0] == 0.0
+
+    def test_itemsize(self, updated_model):
+        assert updated_model.get_var_itemsize("soil_temperature") == 8  # ==64 bits
+
+    def test_get_var_nbytes(self, updated_model):
+        assert updated_model.get_var_nbytes("soil_temperature") == 8 * 55