CHANGELOG.md

@@ -2,6 +2,22 @@
 
 ## Unreleased
 
+### Correctness: zero extents in Fixed/Extensible Array chunk indexes (2026-09-27)
+- **A chunked dataset whose maximum (or, with none recorded, current)
+  extent is 0 along a dimension made the reader divide by zero** (fixed
+  2026-09-27): `h5rs check` panicked ("attempt to divide by zero",
+  `chunk_grid.rs`) and the next `FileEditor::resize` failed with an
+  internal error. The unfixed editor produced such files by resizing a
+  clawhdf5-written dataset to a zero extent (12 of 30 extra random-edit
+  seeds on clawhdf5-written files). Such an index has no slot for any
+  chunk of the dataset, and `ChunkGrid::offsets` now says so instead of
+  dividing by the zero stride. Tests: `chunk_grid`'s
+  `zero_extent_has_no_chunks`, `edit_interop.rs`'s
+  `zero_extent_resizes_without_a_recorded_maximum` (a file the unfixed
+  editor left checks clean and resizes on; a 2.7.0-written file through
+  zero extents checks clean at each step), and `test_edit.py`'s random
+  edits on seeds 10 to 39 of a clawhdf5-written file.
+
 ### Correctness: resizing chunked datasets with no recorded maximum (2026-09-27)
 - **`FileEditor::resize` scrambled the values of a chunked dataset whose
   dataspace records no maximum dimensions when it shrank it** (fixed

crates/clawhdf5-format/src/chunk_grid.rs

@@ -135,6 +135,12 @@ impl ChunkGrid {
         let mut rem = index;
         for p in 0..rank {
             let d = self.order[p];
+            // A zero stride: a later dimension has no chunks (its maximum,
+            // or with none recorded its current extent, is 0), so no slot of
+            // the index is a chunk of the dataset.
+            if self.down[p] == 0 {
+                return None;
+            }
             let scaled = rem / self.down[p];
             rem %= self.down[p];
             if scaled >= self.cur_chunks[d] {
@@ -193,6 +199,28 @@ mod tests {
         assert_eq!(g.offsets(11), Some(vec![2, 3]));
     }
 
+    #[test]
+    fn zero_extent_has_no_chunks() {
+        // No maximum recorded and a zero current dimension: every stride
+        // before it is 0 (this divided by zero).
+        let g = ChunkGrid::fixed_array(&[1, 0], None, &[6, 6]).unwrap();
+        for i in 0..16 {
+            assert_eq!(g.offsets(i), None);
+        }
+        let g = ChunkGrid::fixed_array(&[0, 0, 3], Some(&[4, 0, 3]), &[2, 2, 3]).unwrap();
+        for i in 0..16 {
+            assert_eq!(g.offsets(i), None);
+        }
+        let g = ChunkGrid::extensible_array(&[0, 5], Some(&[u64::MAX, 0]), &[2, 2]).unwrap();
+        for i in 0..16 {
+            assert_eq!(g.offsets(i), None);
+        }
+        // A zero last dimension leaves the other strides alone.
+        let g = ChunkGrid::fixed_array(&[4, 0], Some(&[4, 6]), &[2, 3]).unwrap();
+        assert_eq!(g.offsets(0), None);
+        assert_eq!(g.linear_index(&[1, 1]), 3);
+    }
+
     #[test]
     fn rejects_two_unlimited_dims_after_the_first() {
         assert!(ChunkGrid::fixed_array(&[4, 6], Some(&[u64::MAX, u64::MAX]), &[2, 3]).is_err());

crates/clawhdf5-py/tests/test_edit.py

@@ -445,6 +445,13 @@ def test_random_edits_match_h5py(h5py, tmp_path, source, seed):
     h5dump_reads(ours_path, base)
 
 
+@pytest.mark.parametrize("seed", range(10, 40))
+def test_random_edits_on_clawhdf5_files(h5py, tmp_path, seed):
+    """More random sequences on a clawhdf5-written file, whose resizes to
+    zero extents once left files `h5rs check` could not read."""
+    test_random_edits_match_h5py(h5py, tmp_path, "clawhdf5", seed)
+
+
 def resized_model(before, shape, fill):
     """`before` resized to `shape` as HDF5 resizes: elements inside both
     extents keep their values, the others read as the fill value."""

crates/clawhdf5-tools/tests/edit_interop.rs

@@ -1509,3 +1509,68 @@ fn unencodable_filters_are_unsupported() {
         "a refused edit changed the file"
     );
 }
+
+fn fixture(dir: &Path, name: &str) -> std::path::PathBuf {
+    let path = dir.join(name);
+    std::fs::copy(
+        Path::new(env!("CARGO_MANIFEST_DIR"))
+            .join("../clawhdf5/tests/fixtures")
+            .join(name),
+        &path,
+    )
+    .unwrap();
+    path
+}
+
+/// Zero extents on chunked datasets with no recorded maximum. The unfixed
+/// editor left `chunk_zero_extent_no_maxshape.h5` (a 2.7.0-written file
+/// resized to 1x0): a Fixed Array whose maximum, taken from the current
+/// dimensions, has no chunks along one dimension, so every stride before it
+/// is 0 — `h5rs check` panicked dividing by it and the next resize failed
+/// with an internal error. Such a file must check clean and resize on; a
+/// 2.7.0-written file taken through zero extents by the fixed editor must
+/// check clean at every step and read the fill value where it grew.
+#[test]
+fn zero_extent_resizes_without_a_recorded_maximum() {
+    if !tools_ok() {
+        return;
+    }
+    let dir = tmpdir();
+    let path = fixture(dir.path(), "chunk_zero_extent_no_maxshape.h5");
+    check_tools(&path, true);
+    let mut ed = FileEditor::open(&path).unwrap();
+    ed.resize("d", &[0, 0]).unwrap();
+    ed.resize("z", &[0, 0]).unwrap();
+    // Their maximum is now what the index was laid out by (1 x 0).
+    ed.resize("d", &[1, 0]).unwrap();
+    assert!(matches!(
+        ed.resize("d", &[1, 1]),
+        Err(Error::InvalidArgument(_))
+    ));
+    drop(ed);
+    check_tools(&path, true);
+
+    let path = fixture(dir.path(), "chunked_no_maxshape_v2_7_0.h5");
+    for shape in [[15, 15], [3, 2], [1, 1], [1, 0], [0, 0], [0, 20], [20, 20]] {
+        let mut ed = FileEditor::open(&path).unwrap();
+        ed.resize("d", &shape).unwrap();
+        ed.resize("z", &shape).unwrap();
+        drop(ed);
+        check_tools(&path, true);
+    }
+    let f = File::open(&path).unwrap();
+    for name in ["d", "z"] {
+        let d = f.dataset(name).unwrap();
+        assert_eq!(d.shape().unwrap(), [20, 20]);
+        assert!(d.read_f32().unwrap().iter().all(|&v| v == 0.0), "{name}");
+    }
+    assert_eq!(
+        py(&format!(
+            "import h5py\n\
+             with h5py.File({:?}) as f:\n\
+             \x20   print(int(abs(f['d'][()]).sum() + abs(f['z'][()]).sum()), f['d'].maxshape)",
+            path.to_str().unwrap()
+        )),
+        "0 (20, 20)"
+    );
+}