(refactor) Changed codes to concepts directory for alignment with OMOP. Closes #52

tests/test_acmc.py

@@ -5,7 +5,7 @@ import shutil
 import logging
 from pathlib import Path
 
-from acmc import trud, omop, main, logging_config as lc
+from acmc import trud, omop, main, phen, logging_config as lc
 
 # setup logging
 lc.setup_logger()
@@ -71,7 +71,7 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
     with caplog.at_level(logging.DEBUG):
         # validate phenotype
         # copy examples across
-        shutil.rmtree(phen_path / "codes")
+        shutil.rmtree(phen_path / phen.CONCEPTS_DIR)
         ex_path = Path("./examples").resolve()
         for item in ex_path.iterdir():
             source = ex_path / item.name
@@ -182,7 +182,7 @@ def test_diff(tmp_dir, monkeypatch, caplog):
     main.main()
 
     # copy example codes
-    shutil.rmtree(phen_path / "codes")
+    shutil.rmtree(phen_path / phen.CONCEPTS_DIR)
     ex_path = Path("./examples").resolve()
     for item in ex_path.iterdir():
         source = ex_path / item.name