Rename to _unpack_gff3_attributes, update uses

Author: leehart

malariagen_data/amin1.py

@@ -17,7 +17,7 @@
     _read_gff3,
     _resolve_region,
     _simple_xarray_concat,
-    unpack_gff3_attributes,
+    _unpack_gff3_attributes,
 )
 
 GENOME_FEATURES_GFF3_PATH = (
@@ -145,7 +145,7 @@ def genome_features(self, attributes=("ID", "Parent", "Name", "description")):
             with self._fs.open(path, mode="rb") as f:
                 df = _read_gff3(f, compression="gzip")
             if attributes is not None:
-                df = unpack_gff3_attributes(df, attributes=attributes)
+                df = _unpack_gff3_attributes(df, attributes=attributes)
             self._cache_genome_features[attributes] = df
 
         return df

malariagen_data/anoph/genome_features.py

@@ -13,7 +13,7 @@
     _parse_multi_region,
     _parse_single_region,
     _read_gff3,
-    unpack_gff3_attributes,
+    _unpack_gff3_attributes,
 )
 from . import base_params, gplt_params
 from .genome_sequence import AnophelesGenomeSequenceData
@@ -66,7 +66,7 @@ def _genome_features(self, *, attributes: Tuple[str, ...]):
             with self._fs.open(path, mode="rb") as f:
                 df = _read_gff3(f, compression=compression)
             if attributes:
-                df = unpack_gff3_attributes(df, attributes=attributes)
+                df = _unpack_gff3_attributes(df, attributes=attributes)
             self._cache_genome_features[attributes] = df
 
         return df

malariagen_data/plasmodium.py

@@ -16,7 +16,7 @@
     _init_zarr_store,
     _read_gff3,
     _resolve_region,
-    unpack_gff3_attributes,
+    _unpack_gff3_attributes,
 )
 
 
@@ -320,7 +320,7 @@ def genome_features(self, attributes=("ID", "Parent", "Name")):
             with self._fs.open(path, mode="rb") as f:
                 df = _read_gff3(f, compression="gzip")
             if attributes is not None:
-                df = unpack_gff3_attributes(df, attributes=attributes)
+                df = _unpack_gff3_attributes(df, attributes=attributes)
             self._cache_genome_features[attributes] = df
 
         return df

malariagen_data/util.py

@@ -91,7 +91,7 @@ def _read_gff3(buf, compression="gzip"):
     return df
 
 
-def unpack_gff3_attributes(df: pd.DataFrame, attributes: Tuple[str, ...]):
+def _unpack_gff3_attributes(df: pd.DataFrame, attributes: Tuple[str, ...]):
     df = df.copy()
 
     # discover all attribute keys

tests/test_plasmodium.py

@@ -424,7 +424,7 @@ def test_variant_calls_extended(self, mock_open_variant_calls_zarr):
             ],
         )
 
-    @patch("malariagen_data.plasmodium.unpack_gff3_attributes")
+    @patch("malariagen_data.plasmodium._unpack_gff3_attributes")
     @patch("malariagen_data.plasmodium._read_gff3")
     @patch("builtins.open", new_callable=mock_open)
     def test_genome_features(self, mock_open, mock_read_gff, mock_unpack):
@@ -469,7 +469,7 @@ def test_genome_features_wrong_attribute_not_in_df(self):
             TypeError, self.test_plasmodium_class.genome_features, "bad_attribute"
         )
 
-    @patch("malariagen_data.plasmodium.unpack_gff3_attributes")
+    @patch("malariagen_data.plasmodium._unpack_gff3_attributes")
     @patch("malariagen_data.plasmodium._read_gff3")
     @patch("builtins.open", new_callable=mock_open)
     def test_genome_features_uses_cache(self, mock_open, mock_read_gff, mock_unpack):