Merge pull request #38 from IMMM-SFA/feature/test-io

adds unit tests for input/output methods; closes #37

.github/workflows/build_windows.yml

@@ -30,11 +30,12 @@ jobs:
             pip install numpy-1.20.2+mkl-cp39-cp39-win_amd64.whl
             curl -O https://download.lfd.uci.edu/pythonlibs/w4tscw6k/GDAL-3.2.2-cp39-cp39-win_amd64.whl
             pip install GDAL-3.2.2-cp39-cp39-win_amd64.whl
-            curl -O https://download.lfd.uci.edu/pythonlibs/w4tscw6k/rasterio-1.2.1-cp39-cp39-win_amd64.whl
-            pip install rasterio-1.2.1-cp39-cp39-win_amd64.whl
+            curl -O https://download.lfd.uci.edu/pythonlibs/w4tscw6k/rasterio-1.2.3-cp39-cp39-win_amd64.whl
+            pip install rasterio-1.2.3-cp39-cp39-win_amd64.whl
             pip install -r requirements.txt
             python setup.py install
             pip install numpy --upgrade
+            pip install python-benedict --upgrade
 
         - name: Test and generate coverage report
           run: |

mosartwmpy/grid/grid.py

@@ -13,6 +13,7 @@
 from mosartwmpy.config.parameters import Parameters
 from mosartwmpy.reservoirs.grid import load_reservoirs
 
+
 class Grid():
     """Class to store grid related values that are constant throughout a simulation."""
 
@@ -413,7 +414,7 @@ def to_files(self, path: str) -> None:
                     zip.write(filename, names[i])
 
     @staticmethod
-    def from_files(path: str) -> 'Grid':
+    def from_files(path: Path) -> 'Grid':
         """Creates a Grid instance from columns in a dataframe.
 
         Args:

mosartwmpy/model.py

@@ -31,6 +31,7 @@
 from mosartwmpy.utilities.pretty_timer import pretty_timer
 from mosartwmpy.utilities.inherit_docs import inherit_docs
 
+
 @inherit_docs
 class Model(Bmi):
     """The mosartwmpy basic model interface.
@@ -220,6 +221,10 @@ def update_until(self, time: float) -> None:
 
     def finalize(self) -> None:
         # simulation is over so free memory, write data, etc
+        for handler in logging.getLogger().handlers:
+            handler.close()
+        logging.getLogger().handlers.clear()
+        logging.shutdown()
         return
 
     def download_data(self, *args, **kwargs) -> None:

mosartwmpy/tests/test_model.py

@@ -1,22 +1,86 @@
+import numpy as np
 from pathlib import Path
 import unittest
 
+import pkg_resources
+
 from mosartwmpy import Model
 from mosartwmpy.grid.grid import Grid
 
 
 class ModelTest(unittest.TestCase):
     """Test that the model initializes and runs with the default settings."""
-
-    def setUp(self):
+
+    # package data
+    GRID_FILE = pkg_resources.resource_filename('mosartwmpy', 'tests/grid.zip')
+    CONFIG_FILE = pkg_resources.resource_filename('mosartwmpy', 'tests/test_config.yaml')
+    RUNOFF_FILE = pkg_resources.resource_filename('mosartwmpy', 'tests/runoff_1981_01_01.nc')
+    DEMAND_FILE = pkg_resources.resource_filename('mosartwmpy', 'tests/demand_1981_01_01.nc')
+    RESERVOIRS_FILE = pkg_resources.resource_filename('mosartwmpy', 'tests/reservoirs.nc')
+
+    @classmethod
+    def setUpClass(self):
         self.model = Model()
-        self.grid = Grid.from_files(Path('./mosartwmpy/tests/grid.zip'))
+        self.grid = Grid.from_files(self.GRID_FILE)
+        self.model.initialize(self.CONFIG_FILE, grid=self.grid)
+
+        # set paths for runoff data relative to package
+        self.model.config['runoff.path'] = self.RUNOFF_FILE
+        self.model.config['water_management.demand.path'] = self.DEMAND_FILE
+        self.model.config['water_management.reservoirs.path'] = self.RESERVOIRS_FILE
 
-    def test_can_initialize_and_run(self):
-        self.model.initialize(Path('./mosartwmpy/tests/test_config.yaml'), grid=self.grid)
+    @classmethod
+    def tearDownClass(self):
+        self.model.finalize()
+
+    def test_can_run(self):
         self.model.update()
         self.assertTrue(True, "model initializes and updates")
 
+    def test_input_io(self):
+        self.assertGreater(self.model.get_input_item_count(), 0, "model can count input")
+        input_vars = self.model.get_input_var_names()
+        self.assertGreater(len(input_vars), 0, "model can get input names")
+        self.assertIsInstance(self.model.get_var_units(input_vars[0]), str, "model can get units of input variable")
+        self.assertIsInstance(self.model.get_var_type(input_vars[0]), str, "model can get type of input variable")
+        self.assertGreater(self.model.get_var_itemsize(input_vars[0]), 0, "model can get item size of input variable")
+        self.assertGreater(self.model.get_var_nbytes(input_vars[0]), 0, "model can get nbytes of input variable")
+        single_index_value = np.full(1, -1234.56)
+        single_index_destination = np.empty(1)
+        single_index_position = np.full(1, 0)
+        self.model.set_value_at_indices(input_vars[0], single_index_position, single_index_value)
+        self.model.get_value_at_indices(input_vars[0], single_index_destination, single_index_position)
+        np.testing.assert_array_equal(single_index_destination, single_index_value, "model can get and set input at index")
+        full_value = np.full(self.model.get_grid_size(), -1234.56)
+        full_destination = np.empty_like(full_value)
+        pointer = self.model.get_value_ptr(input_vars[0])
+        self.model.set_value(input_vars[0], full_value)
+        self.model.get_value(input_vars[0], full_destination)
+        np.testing.assert_array_equal(full_destination, full_value, "model can get and set input")
+        np.testing.assert_array_equal(pointer, full_value, "model can get pointer for input variable")
+
+    def test_output_io(self):
+        self.assertGreater(self.model.get_output_item_count(), 0, "model can count output")
+        output_vars = self.model.get_output_var_names()
+        self.assertGreater(len(output_vars), 0, "model can get output names")
+        self.assertIsInstance(self.model.get_var_units(output_vars[0]), str, "model can get units of output variable")
+        self.assertIsInstance(self.model.get_var_type(output_vars[0]), str, "model can get type of output variable")
+        self.assertGreater(self.model.get_var_itemsize(output_vars[0]), 0, "model can get item size of output variable")
+        self.assertGreater(self.model.get_var_nbytes(output_vars[0]), 0, "model can get nbytes of output variable")
+        single_index_value = np.full(1, -1234.56)
+        single_index_destination = np.empty(1)
+        single_index_position = np.full(1, 0)
+        self.model.set_value_at_indices(output_vars[0], single_index_position, single_index_value)
+        self.model.get_value_at_indices(output_vars[0], single_index_destination, single_index_position)
+        np.testing.assert_array_equal(single_index_destination, single_index_value, "model can get and set output at index")
+        full_value = np.full(self.model.get_grid_size(), -1234.56)
+        full_destination = np.empty_like(full_value)
+        pointer = self.model.get_value_ptr(output_vars[0])
+        self.model.set_value(output_vars[0], full_value)
+        self.model.get_value(output_vars[0], full_destination)
+        np.testing.assert_array_equal(full_destination, full_value, "model can get and set output")
+        np.testing.assert_array_equal(pointer, full_value, "model can get pointer for output variable")
+
 
 if __name__ == '__main__':
     unittest.main()

requirements.txt

@@ -12,7 +12,7 @@ pandas==1.1.4
 pathvalidate==2.3.0
 psutil==5.7.3
 pyarrow==3.0.0
-python-benedict==0.22.0
+python-benedict==0.24.0
 recommonmark==0.7.1
 regex==2020.11.13
 requests==2.25.1