Merge pull request #7 from natcap/bugfix/5-initial-conditions-input

Bugfix/5 initial conditions input

src/rangeland_production/forage.py

@@ -817,6 +817,7 @@ def execute(args):
         "pixel size of aligned inputs: %s", target_pixel_size)
 
     # temporary directory for intermediate files
+    global PROCESSING_DIR
     PROCESSING_DIR = os.path.join(args['workspace_dir'], "temporary_files")
     if not os.path.exists(PROCESSING_DIR):
         os.makedirs(PROCESSING_DIR)
@@ -826,6 +827,8 @@ def execute(args):
     # rasters to be used in raster calculations for the model.
     aligned_raster_dir = os.path.join(
         args['workspace_dir'], 'aligned_inputs')
+    if os.path.exists(aligned_raster_dir):
+        shutil.rmtree(aligned_raster_dir)
     os.makedirs(aligned_raster_dir)
     aligned_inputs = dict([(key, os.path.join(
         aligned_raster_dir, 'aligned_%s' % os.path.basename(path)))
@@ -898,6 +901,7 @@ def execute(args):
         if len(state_var_nodata) > 1:
             raise ValueError(
                 "Initial state variable rasters contain >1 nodata value")
+        global _SV_NODATA
         _SV_NODATA = list(state_var_nodata)[0]
 
         # align initial values with inputs
@@ -1550,7 +1554,6 @@ def _check_pft_fractional_cover_sum(aligned_inputs, pft_id_set):
 
     # clean up
     os.remove(cover_sum_path)
-    os.remove(operand_temp_path)
 
 
 def initial_conditions_from_tables(
@@ -13752,9 +13755,7 @@ def validate(args, limit_to=None):
         'animal_grazing_areas_path',
         'site_param_table',
         'veg_trait_path',
-        'animal_trait_path',
-        'site_initial_table',
-        'pft_initial_table']
+        'animal_trait_path']
 
     spatial_file_list = [
         ('aoi_path', gdal.OF_VECTOR, 'vector'),
@@ -13780,6 +13781,15 @@ def validate(args, limit_to=None):
             elif args[key] in ['', None]:
                 no_value_list.append(key)
 
+    # if initial conditions dir is not supplied, initial tables are required
+    if 'initial_conditions_dir' not in args:
+        for key in ['site_initial_table', 'pft_initial_table']:
+            if limit_to is None or limit_to == key:
+                if key not in args:
+                    missing_key_list.append(key)
+                elif args[key] in ['', None]:
+                    no_value_list.append(key)
+
     if missing_key_list:
         # if there are missing keys, we have raise KeyError to stop hard
         raise KeyError(

src/rangeland_production/ui/forage.py

@@ -273,6 +273,17 @@ def __init__(self):
             label=u'Animal Parameter Table (CSV)',
             validator=self.validator)
         self.add_input(self.animal_trait_path)
+        self.initial_conditions_dir = inputs.File(
+            args_key=u'initial_conditions_dir',
+            helptext=(
+                u"A path to a directory containing initial conditions rasters "
+                "for each site- and PFT-level state variable (optional). "
+                "See model documentation for required state variables and "
+                "file names. If this directory is not supplied, initial "
+                "values tables must be supplied."),
+            label=u'Initial Conditions Directory',
+            validator=self.validator)
+        self.add_input(self.initial_conditions_dir)
         self.site_initial_table = inputs.File(
             args_key=u'site_initial_table',
             helptext=(
@@ -283,7 +294,7 @@ def __init__(self):
                 "modeled site type to their location within the study area. "
                 "See model documentation for state variables that are "
                 "required to be included in this table."),
-            label=u'Initial Conditions Site State Variables',
+            label=u'Initial Conditions Table: Site State Variables',
             validator=self.validator)
         self.add_input(self.site_initial_table)
         self.pft_initial_table = inputs.File(
@@ -297,7 +308,7 @@ def __init__(self):
                 "their fractional cover in each pixel. See model "
                 "documentation for state variables that are required to be "
                 "included in this table."),
-            label=u'Initial Conditions: Plant Functional Type State Variables',
+            label=u'Initial Conditions Table: PFT State Variables',
             validator=self.validator)
         self.add_input(self.pft_initial_table)
 
@@ -337,6 +348,8 @@ def assemble_args(self):
             self.site_param_table.args_key: self.site_param_table.value(),
             self.veg_trait_path.args_key: self.veg_trait_path.value(),
             self.animal_trait_path.args_key: self.animal_trait_path.value(),
+            self.initial_conditions_dir.args_key:
+                self.initial_conditions_dir.value(),
             self.site_initial_table.args_key: self.site_initial_table.value(),
             self.pft_initial_table.args_key: self.pft_initial_table.value(),
         }

tests/test_forage.py

@@ -1003,9 +1003,11 @@ class foragetests(unittest.TestCase):
 
     def setUp(self):
         """Create temporary workspace directory."""
-        self.workspace_dir = tempfile.mkdtemp()
-        self.PROCESSING_DIR = os.path.join(
-            self.workspace_dir, "temporary_files")
+        self.workspace_dir = "C:/Users/ginge/Desktop/temp_test_dir"
+        os.makedirs(self.workspace_dir)
+        global PROCESSING_DIR
+        PROCESSING_DIR = os.path.join(self.workspace_dir, "temporary_files")
+        os.makedirs(PROCESSING_DIR)
 
     def tearDown(self):
         """Clean up remaining files."""
@@ -1149,7 +1151,7 @@ def assert_sorted_lists_equal(self, string_list_1, string_list_2):
         for i in range(len(string_list_1)):
             self.assertEqual(string_list_1[i], string_list_2[i])
 
-    # @unittest.skip("did not run the whole model, running unit tests only")
+    @unittest.skip("did not run the whole model, running unit tests only")
     def test_model_runs(self):
         """Test forage model."""
         from rangeland_production import forage