feat: add exhausted check to avoid panic

.github/workflows/test.yml

@@ -43,4 +43,5 @@ jobs:
 
         # Develop and test with extras
         maturin develop --extras polars
+        pip install -e ".[polars]"
         pytest

python/biobear/reader.py

@@ -7,15 +7,34 @@
 
 
 class Reader(ABC):
-    """The abstract reader class."""
+    """An abstract base class (ABC) representing a reader.
+
+    The class defines basic functionalities for conversion, but the specifics must be
+    implemented in a subclass.
+    """
 
     @property
     @abstractmethod
     def inner(self):
-        """Return the inner reader."""
+        """Abstract property for the inner reader.
+
+        Returns:
+            The inner reader. The type of the reader is defined by the specific
+            subclass.
+        """
 
     def to_polars(self):
-        """Read the fasta file and return a polars DataFrame."""
+        """Convert the inner data to a Polars DataFrame.
+
+        This method first converts the inner reader's data to an Arrow table,
+        then to a Python dictionary, and finally to a Polars DataFrame.
+
+        Returns:
+            pl.DataFrame: The converted data in a Polars DataFrame.
+
+        Raises:
+            ImportError: If the 'polars' package is not installed.
+        """
         try:
             import polars as pl
         except ImportError as import_error:
@@ -27,9 +46,29 @@ def to_polars(self):
         return pl.from_dict(pydict)
 
     def to_arrow_scanner(self) -> ds.Scanner:
-        """Convert the fasta reader to an arrow scanner."""
+        """Convert the inner data to an Arrow scanner.
+
+        This method first converts the inner reader's data to Arrow batches,
+        and then forms a scanner from these batches.
+
+        Returns:
+            ds.Scanner: The converted data in an Arrow scanner.
+        """
         return ds.Scanner.from_batches(self.to_arrow())
 
     def to_arrow(self) -> pa.RecordBatchReader:
-        """Convert the fasta reader to an arrow batch reader."""
+        """Convert the inner data to an Arrow record batch reader.
+
+        If the inner reader is exhausted, this method raises an exception.
+        Otherwise, it converts the inner reader's data to an Arrow record batch.
+
+        Returns:
+            pa.RecordBatchReader: The converted data in an Arrow record batch reader.
+
+        Raises:
+            StopIteration: If the inner reader is exhausted.
+        """
+        if self.inner.is_exhausted():
+            raise StopIteration("The reader is exhausted.")
+
         return self.inner.to_pyarrow()

python/tests/test_fasta_reader.py

@@ -55,3 +55,13 @@ def test_fasta_reader_to_arrow():
 def test_fasta_reader_no_file():
     with pytest.raises(OSError):
         FastaReader("test.fasta")
+
+
+@pytest.mark.skipif(
+    not importlib.util.find_spec("polars"), reason="polars not installed"
+)
+def test_multiple_calls_raise_an_exhausted_error():
+    fasta_reader = FastaReader(DATA / "test.fasta")
+    fasta_reader.to_polars()
+    with pytest.raises(StopIteration):
+        fasta_reader.to_polars()

src/exon_reader.rs

@@ -30,6 +30,7 @@ use tokio::runtime::Runtime;
 #[pyclass(name = "_ExonReader")]
 pub struct ExonReader {
     df: datafusion::dataframe::DataFrame,
+    exhausted: bool,
     _runtime: Arc<Runtime>,
 }
 
@@ -64,7 +65,11 @@ impl ExonReader {
         });
 
         match df {
-            Ok(df) => Ok(Self { df, _runtime: rt }),
+            Ok(df) => Ok(Self {
+                df,
+                _runtime: rt,
+                exhausted: false,
+            }),
             Err(e) => Err(e),
         }
     }
@@ -102,7 +107,12 @@ impl ExonReader {
         })
     }
 
-    fn to_pyarrow(&self) -> PyResult<PyObject> {
+    fn is_exhausted(&self) -> bool {
+        self.exhausted
+    }
+
+    #[allow(clippy::wrong_self_convention)]
+    fn to_pyarrow(&mut self) -> PyResult<PyObject> {
         let stream = Arc::new(FFI_ArrowArrayStream::empty());
         let stream_ptr = Arc::into_raw(stream) as *mut FFI_ArrowArrayStream;
 
@@ -116,6 +126,8 @@ impl ExonReader {
             .unwrap();
         });
 
+        self.exhausted = true;
+
         Python::with_gil(|py| unsafe {
             match ArrowArrayStreamReader::from_raw(stream_ptr) {
                 Ok(stream_reader) => stream_reader.into_pyarrow(py),