bug(compartments): avoid lowercase comprtmnt str's (#421)

pycytominer/cyto_utils/features.py

@@ -4,6 +4,7 @@
 
 import os
 import pandas as pd
+from typing import Union, List
 
 blocklist_file = os.path.join(
     os.path.dirname(__file__), "..", "data", "blocklist_features.txt"
@@ -185,7 +186,9 @@ def drop_outlier_features(
     return outlier_features
 
 
-def convert_compartment_format_to_list(compartments):
+def convert_compartment_format_to_list(
+    compartments: Union[List[str], str],
+) -> List[str]:
     """Converts compartment to a list.
 
     Parameters
@@ -199,9 +202,4 @@ def convert_compartment_format_to_list(compartments):
         List of Cell Painting compartments.
     """
 
-    if isinstance(compartments, list):
-        compartments = [x.lower() for x in compartments]
-    elif isinstance(compartments, str):
-        compartments = [compartments.lower()]
-
-    return compartments
+    return compartments if isinstance(compartments, list) else [compartments]

tests/test_cyto_utils/test_features_util.py

@@ -2,8 +2,13 @@
 
 
 def test_convert_compartment_format_to_list():
-    compartments = convert_compartment_format_to_list(["cells", "CYTOplasm", "nuclei"])
-    assert compartments == ["cells", "cytoplasm", "nuclei"]
+    compartments = convert_compartment_format_to_list([
+        "cells",
+        "CYTOplasm",
+        "nuclei",
+        "MyoD",
+    ])
+    assert compartments == ["cells", "CYTOplasm", "nuclei", "MyoD"]
 
     compartments = convert_compartment_format_to_list("FoO")
-    assert compartments == ["foo"]
+    assert compartments == ["FoO"]

tests/test_cyto_utils/test_util.py

@@ -43,31 +43,35 @@ def test_check_compartments():
 
 
 def test_check_compartments_not_valid():
-    warn_expected_string = "Non-canonical compartment detected: something"
     warnings.simplefilter("always")
     with warnings.catch_warnings(record=True) as w:
         not_valid = ["SOMETHING"]
         check_compartments(not_valid)
     assert issubclass(w[-1].category, UserWarning)
-    assert warn_expected_string in str(w[-1].message)
+    assert "Non-canonical compartment detected: SOMETHING" in str(w[-1].message)
 
     with warnings.catch_warnings(record=True) as w:
         not_valid = "SOMETHING"  # Also works with strings
         check_compartments(not_valid)
     assert issubclass(w[-1].category, UserWarning)
-    assert warn_expected_string in str(w[-1].message)
+    assert "Non-canonical compartment detected: SOMETHING" in str(w[-1].message)
 
     with warnings.catch_warnings(record=True) as w:
         not_valid = ["CelLs", "CytopLasM", "SOMETHING"]
         check_compartments(not_valid)
     assert issubclass(w[-1].category, UserWarning)
-    assert warn_expected_string in str(w[-1].message)
+    assert "Non-canonical compartment detected: CelLs, CytopLasM, SOMETHING" in str(
+        w[-1].message
+    )
 
     with warnings.catch_warnings(record=True) as w:
         not_valid = ["CelLs", "CytopLasM", "SOMETHING", "NOTHING"]
         check_compartments(not_valid)
     assert issubclass(w[-1].category, UserWarning)
-    assert f"{warn_expected_string}, nothing" in str(w[-1].message)
+    assert (
+        "Non-canonical compartment detected: CelLs, CytopLasM, SOMETHING, NOTHING"
+        in str(w[-1].message)
+    )
 
 
 def test_get_default_compartments():