Merge branch 'feature/save-annotations-unfilled' of github.com:PMBio/…

…deeprvat into feature/save-annotations-unfilled

deeprvat/annotations/annotations.py

@@ -2031,7 +2031,10 @@ def create_gene_id_file(gtf_filepath: str, out_file: str):
 @click.argument("out_file", type=click.Path())
 @click.option("--keep_unfilled", type=click.Path(), default=None)
 def select_rename_fill_annotations(
-    annotation_columns_yaml_file: str, annotations_path: str, out_file: str, keep_unfilled: str
+    annotation_columns_yaml_file: str,
+    annotations_path: str,
+    out_file: str,
+    keep_unfilled: str,
 ):
     """
     Select, rename, and fill missing values in annotation columns based on a YAML configuration file.
@@ -2054,7 +2057,8 @@ def select_rename_fill_annotations(
         annotations_path, columns=list(set(prior_names + key_cols))
     )
     anno_df.rename(columns=column_name_mapping, inplace=True)
-    if (keep_unfilled is not None): anno_df.to_parquet(keep_unfilled)
+    if keep_unfilled is not None:
+        anno_df.to_parquet(keep_unfilled)
     anno_df.fillna(fill_value_mapping, inplace=True)
     anno_df.to_parquet(out_file)
 

tests/annotations/test_annotations.py

@@ -735,6 +735,7 @@ def test_select_rename_fill_annotations(
         written_results, expected_results[written_results.columns], check_exact=False
     )
 
+
 @pytest.mark.parametrize(
     "test_data_name_dir, yaml_file, annotations, expected, expected_unfilled",
     [
@@ -766,8 +767,7 @@ def test_select_rename_fill_annotations_unfilled(
         annotations_path.as_posix(),
         output_path.as_posix(),
         "--keep_unfilled",
-        unfilled_path
-
+        unfilled_path,
     ]
     result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False)
     assert result.exit_code == 0
@@ -780,7 +780,9 @@ def test_select_rename_fill_annotations_unfilled(
         written_results, expected_results[written_results.columns], check_exact=False
     )
     assert written_unfilled.shape == expected_unfilled.shape
-    assert_frame_equal(written_unfilled, expected_unfilled[written_unfilled.columns],check_exact=False)
+    assert_frame_equal(
+        written_unfilled, expected_unfilled[written_unfilled.columns], check_exact=False
+    )
 
 
 @pytest.mark.parametrize(