Formatting

.gitignore

@@ -43,6 +43,7 @@ venv.bak/
 *.zip
 src/miade/model_builders/output/
 !src/miade/data/*
+.DS_Store
 
 #testing
 tests/data/

src/miade/annotators.py

@@ -482,7 +482,9 @@ def _load_problems_lookup_data(self) -> None:
  raise RuntimeError(f"No lookup data configured: {data_path} does not exist!")
 
  self.negated_lookup = load_lookup_data(data_path + "negated.csv", is_package_data=is_package_data, as_dict=True)
- self.historic_lookup = load_lookup_data(data_path + "historic.csv", is_package_data=is_package_data, as_dict=True)
+ self.historic_lookup = load_lookup_data(
+ data_path + "historic.csv", is_package_data=is_package_data, as_dict=True
+ )
  self.suspected_lookup = load_lookup_data(
  data_path + "suspected.csv", is_package_data=is_package_data, as_dict=True
  )
@@ -773,7 +775,9 @@ def _load_med_allergy_lookup_data(self) -> None:
  if not os.path.isdir(data_path):
  raise RuntimeError(f"No lookup data configured: {data_path} does not exist!")
 
- self.valid_meds = load_lookup_data(data_path + "valid_meds.csv", is_package_data=is_package_data, no_header=True)
+ self.valid_meds = load_lookup_data(
+ data_path + "valid_meds.csv", is_package_data=is_package_data, no_header=True
+ )
  self.reactions_subset_lookup = load_lookup_data(
  data_path + "reactions_subset.csv", is_package_data=is_package_data, as_dict=True
  )

tests/test_annotator.py

@@ -216,6 +216,7 @@ def test_vtm_med_conversions(test_meds_algy_medcat_model, test_vtm_concepts):
  route=None,
  )
 
+
 def test_annotator_config(test_meds_algy_medcat_model, test_problems_medcat_model, test_config):
  # check that all loads ok if pass in explicit path
  test_config.lookup_data_path = "./src/miade/data/"