adding test coverage, changing tests to expect the new ConfigValidati…

…onError class

config/config_global.json

@@ -11,7 +11,7 @@
         50,
         65
     ],
-    "NUM_STRAINS": 4,
+    "NUM_STRAINS": 3,
     "MAX_VACCINATION_COUNT": 2,
     "NUM_WANING_COMPARTMENTS": 5,
     "WANING_TIMES": [

src/resp_ode/config.py

@@ -119,17 +119,19 @@ def assert_valid_configuration(self):
                     ]
                 except Exception as e:
                     if len(key) > 1:
-                        err_text = (
-                            "There was an issue validating your Config object."
-                            "The error was caused by the intersection of the following parameters: %s. %s"
-                        ) % (key, e)
+                        err_text = """There was an issue validating your Config object.
+                        The error was caused by the intersection of the following parameters: %s.
+                        %s""" % (
+                            key,
+                            e,
+                        )
                     else:
                         err_text = """The following error occured while validating the %s
                         parameter in your configuration file: %s""" % (
                             key[0],
-                            str(e),
+                            e,
                         )
-                    raise ConfigValidationError(err_text) from e
+                    raise ConfigValidationError(err_text)
 
 
 def make_list_if_not(obj):

tests/test_config.py

@@ -7,7 +7,7 @@
 import numpyro.distributions as dist
 import pytest
 
-from resp_ode.config import Config, ConfigParserError
+from resp_ode.config import Config, ConfigParserError, ConfigValidationError
 
 GLOBAL_TEST_CONFIG = "tests/test_config_global.json"
 PATH_VARIABLES = [
@@ -38,63 +38,63 @@ def test_valid_path_variables():
 def test_invalid_type_path_variables():
     for path_var in PATH_VARIABLES:
         example_input_json = """{"%s":%d}""" % (path_var, 10)
-        with pytest.raises(AssertionError):
+        with pytest.raises(ConfigValidationError):
             Config(example_input_json)
     for path_var in PATH_VARIABLES:
         example_input_json = """{"%s":"%s"}""" % (
             path_var,
             "some_random_incorrect_path.json",
         )
         print(example_input_json)
-        with pytest.raises(AssertionError):
+        with pytest.raises(ConfigValidationError):
             Config(example_input_json)
 
 
 def test_non_ascending_age_limits():
     input_json = """{"AGE_LIMITS": [10, 1, 50, 60]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_out_of_bounds_age_limits():
     input_json = """{"AGE_LIMITS": [0, 18, 50, 64, 95]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_negative_age_limits():
     input_json = """{"AGE_LIMITS": [-10, 18, 50, 64]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_float_ages():
     input_json = """{"AGE_LIMITS": [0, 5.5, 18, 50, 64]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_seasonality_amplitude_type():
     input_json = """{"SEASONALITY_AMPLITUDE": [0]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_seasonality_amplitude_val():
     input_json = """{"SEASONALITY_AMPLITUDE": 4.0}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_vax_age_coefs_type():
     input_json = """{"AGE_DOSE_SPECIFIC_VAX_COEF": "blah"}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_vax_path():
     input_json = """{"VACCINATION_MODEL_DATA": "blah"}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -105,7 +105,7 @@ def test_invalid_vax_age_coefs_vals():
                     "NUM_AGE_GROUPS":3,
                     "MAX_VACCINATION_COUNT": 2
                         }"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -123,7 +123,7 @@ def test_valid_vax_age_coefs():
 
 def test_invalid_seasonality_amplitude_val_negative():
     input_json = """{"SEASONALITY_AMPLITUDE": -4.0}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -135,7 +135,7 @@ def test_invalid_seasonality_amplitude_dist():
             "loc": 0
         }
     }}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -157,19 +157,19 @@ def test_valid_seasonality_amplitude_dist():
 
 def test_invalid_seasonality_second_wave_type():
     input_json = """{"SEASONALITY_SECOND_WAVE": [0]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_seasonality_second_wave_val():
     input_json = """{"SEASONALITY_SECOND_WAVE": 1.5}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_seasonality_second_wave_val_negative():
     input_json = """{"SEASONALITY_SECOND_WAVE": -1.5}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -181,7 +181,7 @@ def test_invalid_seasonalit_second_wave_dist():
             "loc": 0
         }
     }}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -203,19 +203,19 @@ def test_valid_seasonality_second_wave_dist():
 
 def test_invalid_seasonality_shift_type():
     input_json = """{"SEASONALITY_SHIFT": [0]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_seasonality_shift_val():
     input_json = """{"SEASONALITY_SHIFT": 183}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_seasonality_shift_val_negative():
     input_json = """{"SEASONALITY_SHIFT": -183}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -227,7 +227,7 @@ def test_invalid_seasonalit_shift_dist():
             "loc": 0
         }
     }}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -254,13 +254,13 @@ def test_valid_seasonality_shift_dist():
 
 def test_invalid_introduction_perc_type():
     input_json = """{"INTRODUCTION_PCTS": 0.1}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_introduction_perc_val():
     input_json = """{"INTRODUCTION_PCTS":[-1]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -271,13 +271,13 @@ def test_valid_introduction_perc():
 
 def test_invalid_introduction_times_type():
     input_json = """{"INTRODUCTION_TIMES": 0}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_introduction_times_val():
     input_json = """{"INTRODUCTION_TIMES": [-1]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -288,13 +288,13 @@ def test_valid_introduction_times_val():
 
 def test_invalid_introduction_scale_type():
     input_json = """{"INTRODUCTION_SCALES": 5}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_introduction_scale_val():
     input_json = """{"INTRODUCTION_SCALES": [-1]}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -310,13 +310,13 @@ def test_valid_age_limits():
 
 def test_negative_population_size():
     input_json = """{"POP_SIZE": -1}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_str_population_size():
     input_json = """{"POP_SIZE": "5"}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -327,31 +327,31 @@ def test_valid_population_size():
 
 def test_negative_initial_infections():
     input_json = """{"INITIAL_INFECTIONS": -5}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_negative_initial_infections_scale():
     input_json = """{"INITIAL_INFECTIONS_SCALE": -1.2}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_negative_tree_depth():
     input_json = """{"MAX_TREE_DEPTH": -1}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_zero_tree_depth():
     input_json = """{"MAX_TREE_DEPTH": 0}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_float_tree_depth():
     input_json = """{"MAX_TREE_DEPTH": 1.2}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -362,7 +362,7 @@ def test_valid_tree_depth():
 
 def test_str_initial_infections():
     input_json = """{"INITIAL_INFECTIONS": "5"}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -378,10 +378,28 @@ def test_valid_initial_infections_float():
 
 def test_init_infections_greater_than_pop_size():
     input_json = """{"POP_SIZE": 1, "INITIAL_INFECTIONS": 5}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
+def test_strain_idx_shorter_than_num_strains():
+    input_json = """{"NUM_STRAINS": 3, "STRAIN_IDX": ["x", "y"]}"""
+    with pytest.raises(ConfigValidationError):
+        Config(input_json)
+
+
+def test_strain_idx_longer_than_num_strains():
+    input_json = """{"NUM_STRAINS": 2, "STRAIN_IDX": ["x", "y", "z"]}"""
+    with pytest.raises(ConfigValidationError):
+        Config(input_json)
+
+
+def test_strain_idx_equal_to_num_strains():
+    input_json = """{"NUM_STRAINS": 2, "STRAIN_IDX": ["x", "y"]}"""
+    c = Config(input_json)
+    assert c.NUM_STRAINS == 2 and len(c.STRAIN_IDX) == 2
+
+
 def test_init_infections_less_than_pop_size():
     input_json = """{"POP_SIZE": 5, "INITIAL_INFECTIONS": 1}"""
     c = Config(input_json)
@@ -396,13 +414,13 @@ def test_valid_infectious_period():
 
 def test_negative_infectious_period():
     input_json = """{"INFECTIOUS_PERIOD": -5}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
 def test_invalid_support_infectious_period():
     input_json = """{"INFECTIOUS_PERIOD": {"distribution": "Normal", "params": {"loc": 0, "scale":1}}}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -414,7 +432,7 @@ def test_valid_support_infectious_period():
 
 def test_invalid_step_size():
     input_json = """{"CONSTANT_STEP_SIZE": -1.0}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)
 
 
@@ -515,7 +533,7 @@ def test_invalid_support_nested_distribution_infectious_period():
                 }
             }
         }}"""
-    with pytest.raises(AssertionError):
+    with pytest.raises(ConfigValidationError):
         Config(input_json)