revert: revert genbank update

README.md

@@ -107,7 +107,7 @@ df = session.sql("""
 
 #### Known Issues
 
-There are a few file types where the naive `SELECT *` will cause an error, because Polars doesn't support all Arrow types -- `Map` being the most common. In these cases, you can use the `SELECT * EXCEPT attributes` to exclude the offending column, or select the fields from the map individually. Alternatively, you can first convert the table to a Pandas DataFrame.
+There are a few file types where the naive `SELECT *` will cause an error, because Polars doesn't support all Arrow types -- `Map` being the most common. In these cases, select the fields from the map individually - `SELECT . Alternatively, you can first convert the table to a Pandas DataFrame.
 
 The file types that can cause this issue are GenBanks and MZMLs.
 

python/biobear/genbank_reader.py

@@ -1,9 +1,6 @@
 """Genbank file reader."""
 import os
 
-import pyarrow as pa
-import pyarrow.dataset as ds
-
 from biobear.reader import Reader
 from biobear.compression import Compression
 
@@ -30,26 +27,6 @@ def __init__(
         else:
             self._reader = _ExonReader(str(path), "GENBANK", None)
 
-    def to_polars(self):
-        """Read the GFF file and return a polars DataFrame."""
-        try:
-            import polars as pl
-        except ImportError as import_error:
-            raise ImportError(
-                "The polars library is required to convert a GFF file "
-                "to a polars DataFrame."
-            ) from import_error
-
-        return pl.from_arrow(self.to_arrow().read_all())
-
-    def to_arrow(self) -> pa.RecordBatchReader:
-        """Convert the GFF reader to an arrow batch reader."""
-        return self._reader.to_pyarrow()
-
-    def to_arrow_scanner(self) -> ds.Scanner:
-        """Convert the GFF reader to an arrow scanner."""
-        return ds.Scanner.from_batches(self.to_arrow())
-
     @property
     def inner(self):
         """Return the inner reader."""

python/biobear/reader.py

@@ -60,10 +60,8 @@ def to_polars(self):
                 "The 'polars' package is required to use the to_polars method."
             ) from import_error
 
-        arrow_record = self.to_arrow()
-        table = pa.Table.from_batches(arrow_record, schema=arrow_record.schema)
-
-        return pl.from_arrow(table)
+        pydict = self.to_arrow_scanner().to_table().to_pydict()
+        return pl.from_dict(pydict)
 
     def to_arrow_scanner(self) -> ds.Scanner:
         """Convert the inner data to an Arrow scanner.

python/tests/test_genbank_reader.py

@@ -10,7 +10,6 @@
 DATA = Path(__file__).parent / "data"
 
 
-@pytest.mark.skip
 @pytest.mark.skipif(
     not importlib.util.find_spec("polars"), reason="polars not installed"
 )

python/tests/test_mzml_reader.py

@@ -10,7 +10,6 @@
 DATA = Path(__file__).parent / "data"
 
 
-@pytest.mark.skip
 @pytest.mark.skipif(
     not importlib.util.find_spec("polars"), reason="polars not installed"
 )
@@ -38,7 +37,6 @@ def test_mzml_reader_to_scanner():
     assert scanner.count_rows() == 2
 
 
-@pytest.mark.skip
 @pytest.mark.skipif(
     not importlib.util.find_spec("polars"), reason="polars not installed"
 )