Added fixes for PR. Fixes #143

benchcab/data/config-schema.yml

@@ -18,7 +18,7 @@ experiment:
     "US-Whs"
   ]
 
-science_configuration:
+science_configurations:
   type: "list"
   schema: 
     type: "dict"
@@ -43,25 +43,35 @@ realisations:
       patch:
         type: "dict"
         required: false
+      patch_remove:
+        type: "dict"
+        required: false
 
 fluxsite:
   type: "dict"
   required: false
   schema:
     multiprocessing:
       type: "boolean"
+      required: false
     pbs:
       type: "dict"
       schema:
         ncpus:
           type: "integer"
           required: false
         mem:
-          type: "integer"
+          type: "string"
+          regex: "^[0-9]+(?i)(mb|gb)$"
           required: false
         walltime:
-          type: "integer"
+          type: "string"
+          regex: "^[0-4][0-9]:[0-5][0-9]:[0-5][0-9]$"
           required: false
         storage:
-          type: "integer"
-          required: false
+          type: list
+          required: false
+          schema:
+            type: "string"
+            required: false
+

benchcab/utils/__init__.py

@@ -39,9 +39,6 @@ def load_package_data(filename: str) -> dict:
     # Alias yaml and yml.
     ext = ext if ext != 'yaml' else 'yml'
 
-    # Make sure it is one of the supported types.
-    assert ext in PACKAGE_DATA_DECODERS.keys()
-
     # Extract from the installations data directory.
     raw = pkgutil.get_data('benchcab', os.path.join('data', filename)).decode('utf-8')
 

setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 name=benchcab
 summary= Software to run a benchmarking suite for CABLE LSM
-# version=2.0.0
+version=2.0.0
 description=To benchmark CABLE simulations
 url=https://github.com/CABLE-LSM/benchcab
 license=Apache 2.0

tests/test_config.py

@@ -23,7 +23,7 @@ def test_read_config_fail():
 
 
 def test_validate_config_valid():
-    """Test validate_config() for a valid confiog file."""
+    """Test validate_config() for a valid config file."""
     valid_config = bu.load_package_data('test/config-valid.yml')
     assert bc.validate_config(valid_config)
 

tests/test_utils.py

@@ -20,4 +20,4 @@ def test_load_package_data_fail():
     """Test load_package_data() fails as expected."""
 
     with pytest.raises(FileNotFoundError):
-        missing = bu.load_package_data('config-missing.yml'), dict()
+        missing = bu.load_package_data('config-missing.yml')