CHANGELOG.md

@@ -54,6 +54,12 @@
   h5py 3.16 (HDF5 2.0) on a file h5py writes. One difference is h5py's:
   it returns variable-length sequences of big-endian floats unswapped; this
   package returns the stored values.
+- **A panic in the library is an ordinary Python exception.** PyO3 turns a
+  Rust panic into `PanicException`, a `BaseException` that `except
+  Exception` does not catch. Every call from the bindings into the library
+  is now guarded and a panic becomes `clawhdf5.InternalError` (a
+  `RuntimeError`) naming the object; with the implicit-index panic above
+  restored, `ds[0:30]` raises it.
 - **CI builds and tests the Python package.** It was excluded from CI.
   `scripts/ci-test.sh` now lints `clawhdf5-py`, builds the wheel with
   maturin, unpacks it under `target/` and runs the pytest suite; skipped

crates/clawhdf5-py/src/attrs.rs

@@ -191,6 +191,7 @@ fn attr_to_py<'py>(
     file: &clawhdf5_rs::File,
     attr: &AttributeMessage,
 ) -> PyResult<Bound<'py, PyAny>> {
+    crate::no_panic(|| {
         let sb = file.superblock();
         let conv = Converter::new(py, &attr.datatype, sb.offset_size)
             .map_err(|e| prefix_err(py, &attr.name, e))?;
@@ -231,6 +232,7 @@ fn attr_to_py<'py>(
             return arr.get_item(PyTuple::empty(py));
         }
         Ok(arr)
+    })
 }
 
 fn prefix_err(py: Python<'_>, name: &str, e: PyErr) -> PyErr {

crates/clawhdf5-py/src/dataset.rs

@@ -42,6 +42,7 @@ impl PyDataset {
         file: Arc<clawhdf5_rs::File>,
         path: String,
     ) -> PyResult<Self> {
+        crate::no_panic(|| {
             let hdr = node::header(&file, &path)?;
             let null = node::is_null(&node::dataspace(&file, &hdr)?);
             let (shape, datatype) = {
@@ -62,6 +63,7 @@ impl PyDataset {
                 datatype,
                 conv,
             })
+        })
     }
 
     fn converter(&self) -> PyResult<&Converter> {
@@ -84,8 +86,7 @@ impl PyDataset {
             let path = self.path.as_str();
             let (vl, elem_size, unit) = (conv.is_vl(), conv.elem_size, conv.vl_unit);
             // Everything below touches only Rust data: release the GIL.
-            let blocks: Vec<(Elements, Vec<usize>)> = py
+            let read = || -> Result<_, ReadError> {
-                .detach(|| -> Result<_, ReadError> {
                 let ds = file.dataset(path)?;
                 let sb = file.superblock();
                 let mut blocks = Vec::with_capacity(reads.len());
@@ -117,6 +118,11 @@ impl PyDataset {
                     blocks.push((data, shape));
                 }
                 Ok(blocks)
+            };
+            let blocks: Vec<(Elements, Vec<usize>)> = py
+                .detach(|| {
+                    std::panic::catch_unwind(std::panic::AssertUnwindSafe(read))
+                        .unwrap_or_else(|p| Err(ReadError::Panic(crate::panic_text(&*p))))
                 })
                 .map_err(|e| e.into_py(&self.path))?;
 
@@ -160,6 +166,7 @@ impl PyDataset {
 enum ReadError {
     Lib(clawhdf5_rs::Error),
     Other(String),
+    Panic(String),
 }
 
 impl From<clawhdf5_rs::Error> for ReadError {
@@ -173,6 +180,10 @@ impl ReadError {
         match self {
             ReadError::Lib(e) => to_py_err(e),
             ReadError::Other(msg) => PyValueError::new_err(format!("{}: {msg}", node::name(path))),
+            ReadError::Panic(msg) => crate::InternalError::new_err(format!(
+                "{}: clawhdf5 internal error (please report it): {msg}",
+                node::name(path)
+            )),
         }
     }
 }
@@ -223,6 +234,7 @@ impl PyDataset {
     /// The maximum shape (`None` per unlimited dimension), like h5py.
     #[getter]
     fn maxshape<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
+        crate::no_panic(|| {
             let Some(shape) = &self.shape else {
                 return Ok(py.None().into_bound(py));
             };
@@ -237,6 +249,7 @@ impl PyDataset {
                 .map(|d| (d != u64::MAX).then_some(d))
                 .collect();
             Ok(PyTuple::new(py, items)?.into_any())
+        })
     }
 
     /// The dataset's numpy dtype, as h5py reports it.

crates/clawhdf5-py/src/file.rs

@@ -57,9 +57,9 @@ impl PyFile {
         let filename = path.to_string();
         match mode {
             "r" => {
-                let file = py
+                let file = py.detach(|| {
-                    .detach(|| clawhdf5_rs::File::open(path))
+                    crate::no_panic(|| clawhdf5_rs::File::open(path).map_err(to_py_err))
-                    .map_err(to_py_err)?;
+                })?;
                 Ok(Self {
                     inner: Some(FileInner::Read(Arc::new(file))),
                     filename,
@@ -277,6 +277,7 @@ fn parse_compression(
 
 /// Build and write the HDF5 file from accumulated write state.
 fn finalize_write(state: WriteState) -> PyResult<()> {
+    crate::no_panic(|| {
         let mut builder = clawhdf5_rs::FileBuilder::new();
 
         // Root attributes
@@ -300,6 +301,7 @@ fn finalize_write(state: WriteState) -> PyResult<()> {
 
         builder.write(&state.path).map_err(to_py_err)?;
         Ok(())
+    })
 }
 
 #[cfg(test)]

crates/clawhdf5-py/src/group.rs

@@ -73,6 +73,7 @@ pub(crate) fn get_item(
 
 /// Names of the group's datasets and subgroups, sorted (h5py's order).
 pub(crate) fn member_names(file: &clawhdf5_rs::File, path: &str) -> PyResult<Vec<String>> {
+    crate::no_panic(|| {
         let group = if path.is_empty() {
             file.root()
         } else {
@@ -83,6 +84,7 @@ pub(crate) fn member_names(file: &clawhdf5_rs::File, path: &str) -> PyResult<Vec
         names.sort_by(|a, b| a.as_bytes().cmp(b.as_bytes()));
         names.dedup();
         Ok(names)
+    })
 }
 
 pub(crate) fn contains(file: &clawhdf5_rs::File, path: &str, key: &str) -> bool {

crates/clawhdf5-py/src/lib.rs

@@ -24,6 +24,42 @@ pub(crate) use dataset::PyDataset;
 pub(crate) use file::PyFile;
 pub(crate) use group::PyGroup;
 
+pyo3::create_exception!(
+    clawhdf5,
+    InternalError,
+    pyo3::exceptions::PyRuntimeError,
+    "A bug in clawhdf5 met while reading or writing a file (a Rust panic, \
+     caught). Derived from RuntimeError, so `except Exception` handles it."
+);
+
+/// The text of a caught panic.
+pub(crate) fn panic_text(payload: &(dyn std::any::Any + Send)) -> String {
+    payload
+        .downcast_ref::<&str>()
+        .map(|s| (*s).to_string())
+        .or_else(|| payload.downcast_ref::<String>().cloned())
+        .unwrap_or_else(|| "unknown panic".to_string())
+}
+
+/// Run `f`, turning a panic in the library into [`InternalError`] instead of
+/// PyO3's `PanicException` (a `BaseException`, which `except Exception`
+/// does not catch). Wraps every call into the library.
+pub(crate) fn no_panic<T>(f: impl FnOnce() -> PyResult<T>) -> PyResult<T> {
+    std::panic::catch_unwind(std::panic::AssertUnwindSafe(f)).unwrap_or_else(|p| {
+        Err(InternalError::new_err(format!(
+            "clawhdf5 internal error (please report it): {}",
+            panic_text(&*p)
+        )))
+    })
+}
+
+/// A test hook: panics inside [`no_panic`], so the tests can check that a
+/// library panic reaches Python as an ordinary exception.
+#[pyfunction]
+fn _panic_for_test() -> PyResult<()> {
+    no_panic(|| panic!("deliberate panic for the test suite"))
+}
+
 /// Convert a `clawhdf5_rs::Error` into a `PyErr`.
 ///
 /// Maps different error variants to more specific Python exception types:
@@ -276,6 +312,8 @@ fn clawhdf5(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<PyGroup>()?;
     m.add_class::<PyAttrs>()?;
     m.add_class::<PyEmpty>()?;
+    m.add("InternalError", m.py().get_type::<InternalError>())?;
+    m.add_function(wrap_pyfunction!(_panic_for_test, m)?)?;
     Ok(())
 }
 

crates/clawhdf5-py/src/node.rs

@@ -35,6 +35,7 @@ pub(crate) fn name(path: &str) -> String {
 
 /// The object header of the object at `path`.
 pub(crate) fn header(file: &clawhdf5_rs::File, path: &str) -> PyResult<ObjectHeader> {
+    crate::no_panic(|| {
         let sb = file.superblock();
         let data = file.as_bytes();
         let addr = if path.is_empty() {
@@ -51,6 +52,7 @@ pub(crate) fn header(file: &clawhdf5_rs::File, path: &str) -> PyResult<ObjectHea
             .map_err(|_| PyValueError::new_err(format!("{}: address out of range", name(path))))?;
         ObjectHeader::parse(data, addr, sb.offset_size, sb.length_size)
             .map_err(|e| PyValueError::new_err(format!("{}: {e}", name(path))))
+    })
 }
 
 /// What an object header describes.
@@ -115,6 +117,7 @@ pub(crate) fn exists(file: &clawhdf5_rs::File, path: &str) -> bool {
 
 /// The dataspace message of an object header.
 pub(crate) fn dataspace(file: &clawhdf5_rs::File, hdr: &ObjectHeader) -> PyResult<Dataspace> {
+    crate::no_panic(|| {
         let sb = file.superblock();
         let msg = hdr
             .messages
@@ -129,6 +132,7 @@ pub(crate) fn dataspace(file: &clawhdf5_rs::File, hdr: &ObjectHeader) -> PyResul
         )
         .map_err(|e| PyValueError::new_err(e.to_string()))?;
         Dataspace::parse(&data, sb.length_size).map_err(|e| PyValueError::new_err(e.to_string()))
+    })
 }
 
 pub(crate) fn is_null(space: &Dataspace) -> bool {
@@ -139,6 +143,7 @@ pub(crate) fn is_null(space: &Dataspace) -> bool {
 /// Attributes whose messages cannot be parsed are left out, as the facade's
 /// `attrs()` does.
 pub(crate) fn attributes(file: &clawhdf5_rs::File, path: &str) -> PyResult<Vec<AttributeMessage>> {
+    crate::no_panic(|| {
         let hdr = header(file, path)?;
         let sb = file.superblock();
         let (mut attrs, _errors) = clawhdf5_format::attribute::extract_attributes_tolerant(
@@ -150,6 +155,7 @@ pub(crate) fn attributes(file: &clawhdf5_rs::File, path: &str) -> PyResult<Vec<A
         .map_err(|e| PyValueError::new_err(format!("{}: {e}", name(path))))?;
         attrs.sort_by(|a, b| a.name.as_bytes().cmp(b.name.as_bytes()));
         Ok(attrs)
+    })
 }
 
 #[cfg(test)]

crates/clawhdf5-py/tests/test_read_vs_h5py.py

@@ -467,3 +467,47 @@ def test_threads_read_the_same_file(pair):
     with ThreadPoolExecutor(8) as pool:
         list(pool.map(work, range(8)))
     assert not errors, errors[:3]
+
+
+def _v4_index_fixture(h5py, path):
+    """One 2-D dataset per v4 chunk index (HDF5 1.10+ layout, libver='latest')."""
+    data = (np.arange(37 * 23, dtype="<i4") * 7 - 1000).reshape(37, 23)
+    early = h5py.h5p.create(h5py.h5p.DATASET_CREATE)
+    early.set_alloc_time(h5py.h5d.ALLOC_TIME_EARLY)
+    with h5py.File(path, "w", libver="latest") as f:
+        f.create_dataset("implicit", data=data, chunks=(5, 4), dcpl=early)
+        f.create_dataset("fixed_array", data=data, chunks=(5, 4), compression="gzip")
+        f.create_dataset("extensible_array", data=data, chunks=(5, 4), maxshape=(None, 23), compression="gzip")
+        f.create_dataset("btree2", data=data, chunks=(5, 4), maxshape=(None, None), compression="gzip")
+        f.create_dataset("single_chunk", data=data, chunks=(37, 23), compression="gzip")
+
+
+V4_KEYS = [
+    slice(0, 3), slice(0, 30), (slice(7, 16), slice(3, 9)), (36, 22), (slice(None, None, 3), slice(1, None, 4)),
+    (slice(1, None, 2), Ellipsis), (Ellipsis, slice(2, 22)), [0, 5, 6, 36], (slice(None), [0, 3, 22]), -1, (),
+]
+
+
+def test_every_v4_chunk_index_matches_h5py(h5py, tmp_path):
+    """Partial reads of each v4 chunk index. The implicit index (early
+    allocation, no filters) used to panic in the library for any selection
+    covering more than half the dataset, e.g. ds[0:30]."""
+    path = str(tmp_path / "v4.h5")
+    _v4_index_fixture(h5py, path)
+    with h5py.File(path, "r") as theirs, clawhdf5.File(path, "r") as ours:
+        for name in theirs:
+            for key in V4_KEYS:
+                assert_same(ours[name][key], theirs[name][key], f"{name}[{key!r}]")
+
+
+def test_a_library_panic_is_an_ordinary_exception():
+    """PyO3 turns a Rust panic into PanicException, a BaseException that
+    `except Exception` does not catch. Every call into the library is
+    guarded, so a panic surfaces as clawhdf5.InternalError instead."""
+    assert issubclass(clawhdf5.InternalError, RuntimeError)
+    with pytest.raises(clawhdf5.InternalError, match="deliberate panic"):
+        clawhdf5._panic_for_test()
+    try:
+        clawhdf5._panic_for_test()
+    except Exception:  # noqa: BLE001 - the point of the test
+        pass