def test_dict_config_to_table(datadir):
"""Check that we can convert to table with dict rows and back"""
config_yml = load_configuration(datadir / "small_config.yml")
table = dict_config_to_table(config_yml)
print_table_config(table)
config_table = load_configuration(table)
assert config_table == config_yml
def test_indexing_columns_in_parameters_overrides(datadir, file_format):
"""Check that columns indices from parameters override those from filename suffix"""
config_yml = load_configuration(datadir / "small_config.yml")
config_xlsx = load_configuration(
datadir / f"small_config.{file_format}::key_column=A,value_column=A",
value_column="B",
)
assert config_xlsx == config_yml
def test_sheet_access(datadir, file_format):
"""Check that a sheet can be access by name"""
config_yml = load_configuration(datadir / "small_config.yml")
config_xlsx = load_configuration(
datadir / f"small_config.{file_format}",
sheet="Config Version 1",
key_column="A",
value_column="B",
)
assert config_xlsx == config_yml
def test_user_friendly_config_load(datadir, file_format):
"""Check that a full user-friendly configuration loads from a table"""
config_csv = load_configuration(datadir / "user_friendly_config.csv",
key_column="D",
value_column="B")
config_other = load_configuration(
datadir / f"user_friendly_config.{file_format}",
key_column="D",
value_column="B",
)
num_top_level_keys = 3
assert len(config_csv) == num_top_level_keys
assert len(config_other) == num_top_level_keys
assert config_other == config_csv
def test_scenarios(datadir, tmp_path):
"""Check that scenarios run from CSV and generate results"""
basic_config = load_configuration(datadir / "config.yml")
scenario_table = load_scenario_table(datadir / "scenarios_config.csv")
results = run_scenarios(
config=basic_config,
scenario_table=scenario_table,
seed=42,
num_simulations=2,
num_consignments=50,
)
assert len(scenario_table) == len(results)
save_scenario_result_to_table(
tmp_path / "results.csv",
results,
config_columns=[
"name",
"consignment/parameter_based/boxes/min",
"consignment/parameter_based/boxes/max",
"consignment/items_per_box/default",
"contamination/contamination_rate/parameters",
],
result_columns=[
"missing",
"avg_boxes_opened_completion",
"avg_boxes_opened_detection",
],
)
def test_scenarios(datadir):
"""Scenario results convert to data frame with specified columns"""
basic_config = load_configuration(datadir / "config.yml")
scenario_table = load_scenario_table(datadir / "scenarios_config.csv")
results = run_scenarios(
config=basic_config,
scenario_table=scenario_table,
seed=42,
num_simulations=2,
num_consignments=10,
)
assert len(scenario_table) == len(results)
config_columns = [
"name",
"consignment/parameter_based/boxes/min",
"consignment/parameter_based/boxes/max",
"consignment/items_per_box/default",
"contamination/contamination_rate/parameters",
]
result_columns = [
"missing",
"avg_boxes_opened_completion",
"avg_boxes_opened_detection",
]
df = save_scenario_result_to_pandas(results,
config_columns=config_columns,
result_columns=result_columns)
shape = df.shape
assert len(shape) == 2
rows, cols = shape
assert cols == len(config_columns) + len(result_columns)
assert rows == len(scenario_table)
def main():
basic_config = load_configuration("data/config.yml")
scenario_table = load_scenario_table("data/scenarios_config_subset.csv")
results = run_scenarios(
config=basic_config,
scenario_table=scenario_table,
seed=42,
num_simulations=1,
num_consignments=1000,
)
assert len(scenario_table) == len(results)
save_scenario_result_to_table(
"results.csv",
results,
config_columns=[
"name",
"consignment/parameter_based/boxes/min",
"consignment/parameter_based/boxes/max",
"consignment/items_per_box/default",
"contamination/contamination_rate/parameters",
"contamination/arrangement",
"inspection/unit",
"inspection/sample_strategy",
"inspection/proportion/value",
"inspection/hypergeometric/detection_level",
"inspection/selection_strategy",
"inspection/within_box_proportion",
"inspection/cluster/cluster_selection",
],
result_columns=[
"missing",
"true_contamination_rate",
"max_missed_contamination_rate",
"avg_missed_contamination_rate",
"max_intercepted_contamination_rate",
"avg_intercepted_contamination_rate",
"avg_boxes_opened_completion",
"avg_boxes_opened_detection",
"avg_items_inspected_completion",
"avg_items_inspected_detection",
"pct_items_inspected_detection",
"pct_contaminant_unreported_if_detection",
"total_missed_contaminants",
"total_intercepted_contaminants",
"false_neg",
"intercepted",
],
)
def test_scenarios_with_xlsx(datadir):
"""Check that scenarios can load XLSX and run from it"""
basic_config = load_configuration(datadir / "config.yml")
scenario_table = load_scenario_table(datadir / "scenarios_config.xlsx")
assert scenario_table[0] == {
"name": "clustered_10",
"consignment_name": "clustered",
"inspection_name": "boxes 0.01 hypergeometric random",
"consignment/parameter_based/boxes/min": 5,
"consignment/parameter_based/boxes/max": 25,
"consignment/items_per_box/default": 200,
"contamination/contamination_rate/parameters": [1, 80],
"contamination/arrangement": "clustered",
"inspection/unit": "box",
"inspection/sample_strategy": "hypergeometric",
"inspection/proportion/proportion": None,
"inspection/hypergeometric/detection_level": 0.01,
"inspection/selection_strategy": "random",
"inspection/within_box_pct": 1,
"inspection/cluster/cluster_selection": None,
}
assert scenario_table[8] == {
"name": "clustered_02",
"consignment_name": "clustered",
"inspection_name": "boxes 2% random",
"consignment/parameter_based/boxes/min": 5,
"consignment/parameter_based/boxes/max": 25,
"consignment/items_per_box/default": 200,
"contamination/contamination_rate/parameters": [1, 80],
"contamination/arrangement": "clustered",
"inspection/unit": "box",
"inspection/sample_strategy": "proportion",
"inspection/proportion/proportion": 0.02,
"inspection/hypergeometric/detection_level": None,
"inspection/selection_strategy": "random",
"inspection/within_box_pct": 1,
"inspection/cluster/cluster_selection": None,
}
results = run_scenarios(
config=basic_config,
scenario_table=scenario_table,
seed=42,
num_simulations=1,
num_consignments=5,
)
assert len(scenario_table) == len(results)
def test_include_files_list(datadir):
"""Included CSV file formatted as a list of items loads"""
config = load_configuration(datadir /
"small_config_with_list_includes.yml")
consignments = config["contamination"]["consignments"]
assert isinstance(consignments, list)
assert len(consignments) == 7
assert consignments[0] == {
"commodity": "Liatris",
"origin": "Netherlands",
"contamination": {
"arrangement": "random_box"
},
}
assert consignments[-1] == {
"commodity": "Sedum",
"origin": "Colombia",
"contamination": {
"arrangement": "random"
},
}
def test_large_config_load(datadir, column):
"""Check that a larger, somewhat complete, configuration loads from a table"""
load_configuration(datadir / f"large_config.xlsx::value_column={column}")
def test_default_columns(datadir, file_format):
"""Check that default columns are correctly used"""
config_yml = load_configuration(datadir / "small_config.yml")
config_xlsx = load_configuration(datadir / f"small_config.{file_format}")
assert config_xlsx == config_yml
def test_letter_indexing_columns_xlsx(datadir, file_format):
"""Check that columns can be indexed using letter indices"""
config_yml = load_configuration(datadir / "small_config.yml")
config_xlsx = load_configuration(
datadir / f"small_config.{file_format}::key_column=A,value_column=B")
assert config_xlsx == config_yml
def test_number_indexing_columns_xlsx(datadir, file_format):
"""Check that columns can be indexed using 1-based numerical indices"""
config_yml = load_configuration(datadir / "small_config.yml")
config_xlsx = load_configuration(
datadir / f"small_config.{file_format}::key_column=1,value_column=2")
assert config_xlsx == config_yml
def test_small_configs_are_same(datadir, file_format):
"""Check that configurations loaded from tables are the same as YAML"""
config_yml = load_configuration(datadir / "small_config.yml")
config_csv = load_configuration(datadir / f"small_config.{file_format}")
assert config_csv == config_yml
def test_include_files(datadir):
"""Included YAML file with a list loads"""
config = load_configuration(datadir / "small_config_with_includes.yml")
consignments = config["contamination"]["consignments"]
assert isinstance(consignments, list)
assert len(consignments) == 8
def fixture_config(datadir):
"""Get loaded configuration"""
return load_configuration(datadir / "config.yml")
