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cytomining · Nov 3, 2024 · 2cefb81 · 2cefb81
1 parent d494167
commit 2cefb81
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Showing 2 changed files with 28 additions and 12 deletions.
diff --git a/pycytominer/cyto_utils/cells.py b/pycytominer/cyto_utils/cells.py
@@ -335,7 +335,9 @@ def count_cells(self, compartment="cells", count_subset=False):
             query = f"select {query_cols} from {compartment}"
             with self.conn.connect() as conn:
                 count_df = self.image_df.merge(
-                    pd.read_sql(sql=query, con=conn.connection), how="inner", on=self.merge_cols
+                    pd.read_sql(sql=query, con=conn.connection),
+                    how="inner",
+                    on=self.merge_cols,
                 )
             count_df = (
                 count_df.groupby(self.strata)["ObjectNumber"]
@@ -679,7 +681,9 @@ def _compartment_df_generator(
                 f"select {cols} from {compartment} where {strata_condition}"
             )
             with self.conn.connect() as conn:
-                image_df_chunk = pd.read_sql(sql=specific_compartment_query, con=conn.connection)
+                image_df_chunk = pd.read_sql(
+                    sql=specific_compartment_query, con=conn.connection
+                )
             yield image_df_chunk
 
     def merge_single_cells(

diff --git a/tests/test_cyto_utils/test_cells.py b/tests/test_cyto_utils/test_cells.py
@@ -92,8 +92,12 @@ def build_random_data(
 with TEST_ENGINE.connect() as conn:
     IMAGE_DF.to_sql(name="image", con=conn.connection, index=False, if_exists="replace")
     CELLS_DF.to_sql(name="cells", con=conn.connection, index=False, if_exists="replace")
-    CYTOPLASM_DF.to_sql(name="cytoplasm", con=conn.connection, index=False, if_exists="replace")
-    NUCLEI_DF.to_sql(name="nuclei", con=conn.connection, index=False, if_exists="replace")
+    CYTOPLASM_DF.to_sql(
+        name="cytoplasm", con=conn.connection, index=False, if_exists="replace"
+    )
+    NUCLEI_DF.to_sql(
+        name="nuclei", con=conn.connection, index=False, if_exists="replace"
+    )
 
 # Create a new table with a fourth compartment
 NEW_FILE = f"sqlite:///{TMPDIR}/test_new.sqlite"
@@ -111,7 +115,9 @@ def build_random_data(
     NEW_CYTOPLASM_DF.to_sql(
         name="cytoplasm", con=conn.connection, index=False, if_exists="replace"
     )
-    NUCLEI_DF.to_sql(name="nuclei", con=conn.connection, index=False, if_exists="replace")
+    NUCLEI_DF.to_sql(
+        name="nuclei", con=conn.connection, index=False, if_exists="replace"
+    )
     NEW_COMPARTMENT_DF.to_sql(
         name="new", con=conn.connection, index=False, if_exists="replace"
     )
@@ -136,7 +142,9 @@ def build_random_data(
     CYTOPLASM_DF.to_sql(
         name="cytoplasm", con=conn.connection, index=False, if_exists="replace"
     )
-    NUCLEI_DF.to_sql(name="nuclei", con=conn.connection, index=False, if_exists="replace")
+    NUCLEI_DF.to_sql(
+        name="nuclei", con=conn.connection, index=False, if_exists="replace"
+    )
 
 # Ingest data with different image table name
 IMAGE_DIFF_FILE = f"sqlite:///{TMPDIR}/test_image_diff_table_name.sqlite"
@@ -147,9 +155,7 @@ def build_random_data(
     IMAGE_DF.to_sql(
         name="Per_Image", con=conn.connection, index=False, if_exists="replace"
     )
-    CELLS_DF.to_sql(
-        name="cells", con=conn.connection, index=False, if_exists="replace"
-    )
+    CELLS_DF.to_sql(name="cells", con=conn.connection, index=False, if_exists="replace")
     CYTOPLASM_DF.to_sql(
         name="cytoplasm", con=conn.connection, index=False, if_exists="replace"
     )
@@ -892,12 +898,18 @@ def test_aggregate_count_cells_multiple_strata():
 
     # Ingest data into temporary sqlite file
     with test_engine.connect() as conn:
-        image_df.to_sql(name="image", con=conn.connection, index=False, if_exists="replace")
-        cells_df.to_sql(name="cells", con=conn.connection, index=False, if_exists="replace")
+        image_df.to_sql(
+            name="image", con=conn.connection, index=False, if_exists="replace"
+        )
+        cells_df.to_sql(
+            name="cells", con=conn.connection, index=False, if_exists="replace"
+        )
         cytoplasm_df.to_sql(
             name="cytoplasm", con=conn.connection, index=False, if_exists="replace"
         )
-        nuclei_df.to_sql(name="nuclei", con=conn.connection, index=False, if_exists="replace")
+        nuclei_df.to_sql(
+            name="nuclei", con=conn.connection, index=False, if_exists="replace"
+        )
 
     # Setup SingleCells Class
     ap_strata = SingleCells(