feat(format): decode hyperslab selection versions 1 and 2 in VDS mappings

libhdf5 serializes a VDS hyperslab as version 1 (irregular, 4-byte block
corners) for the default format bounds, and as version 2 (regular, 8-byte)
for unlimited selections in the 1.10 format. Only version 3 was accepted,
so every h5py VDS written with default libver failed with "only version-3
hyperslab selections are supported" (5 libhdf5 test files in the sweep).

Decode all three versions following H5S__hyper_deserialize, including
irregular hyperslabs (a union of blocks, enumerated in row-major order as
libhdf5 iterates them) and the all-ones "unlimited" count/block marker.
SerializedSelection exposes the raw form for unlimited-mapping support.

Test: vds_interop::vds_version1_irregular_hyperslab_selections compares
default-libver h5py VDS reads (contiguous, strided and 2-D block mappings)
with libhdf5's values.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>

CHANGELOG.md

@@ -273,6 +273,15 @@
 - CI keeps zlib-ng building and tested; the arm64 job no longer needs cmake.
 
 ### Correctness
+- `clawhdf5-format` virtual datasets (VDS), checked against HDF5 2.0 through
+  h5py (`crates/clawhdf5/tests/vds_interop.rs`):
+  - Hyperslab selection versions 1 and 2 were refused ("only version-3
+    hyperslab selections are supported"). Version 1 is what libhdf5 writes for
+    every VDS created with the default format bounds (h5py's default), so
+    those could not be read at all; version 2 is its encoding of an unlimited
+    selection. Both are decoded now, as are irregular hyperslabs (a union of
+    blocks, read in row-major order as libhdf5 iterates them).
+    `SerializedSelection` exposes the raw form, including unlimited counts.
 - `clawhdf5-format` reader — **values returned wrong with no error:**
   - Fixed Array and Extensible Array chunk indexes were laid out by the
     dataset's current shape instead of its max shape (23 libhdf5 test files,

crates/clawhdf5-format/src/selection.rs

@@ -229,44 +229,47 @@ impl Selection {
     /// self-describing in length, so the count lets a caller walk a packed list
     /// of selections — as the Virtual Dataset global-heap block does).
     ///
-    /// Only the forms needed for VDS assembly are decoded: `ALL`, `NONE`, and
+    /// Decodes `ALL`, `NONE`, and hyperslabs at every version libhdf5 writes
-    /// **regular** hyperslabs serialized at **version 3** (the encoding HDF5
+    /// (1: irregular, 4-byte coordinates — the default-format encoding; 2:
-    /// 1.10+/2.0 emit). Point selections, irregular hyperslabs, and older
+    /// regular, 8-byte; 3: either, variable width). A regular hyperslab maps
-    /// hyperslab versions return an error rather than mis-decoding.
+    /// to [`Selection::Hyperslab`]; an *irregular* one (a union of blocks)
+    /// maps to a single-block hyperslab when it has one block, and otherwise to
+    /// [`Selection::Points`] listing the union in row-major order (the order
+    /// libhdf5 iterates it in). Unlimited counts/blocks decode as `u64::MAX`
+    /// (see [`SerializedSelection::decode`] for the raw form). Point
+    /// selections are refused: libhdf5 does not allow them in virtual datasets
+    /// either.
     pub fn decode_serialized(data: &[u8]) -> Result<(Selection, usize), FormatError> {
-        if data.len() < 8 {
+        let (raw, len) = SerializedSelection::decode(data)?;
-            return Err(FormatError::UnexpectedEof {
+        let sel = match raw {
-                expected: 8,
+            SerializedSelection::All => Selection::All,
-                available: data.len(),
+            SerializedSelection::None => Selection::None,
-            });
+            SerializedSelection::Regular {
+                start,
+                stride,
+                count,
+                block,
+            } => Selection::Hyperslab {
+                start,
+                stride,
+                count,
+                block,
+            },
+            SerializedSelection::Blocks { rank, starts, ends } => {
+                if starts.len() == rank {
+                    let block = starts.iter().zip(&ends).map(|(&s, &e)| e - s + 1).collect();
+                    Selection::Hyperslab {
+                        start: starts,
+                        stride: vec![1; rank],
+                        count: vec![1; rank],
+                        block,
                     }
-        let sel_type = u32::from_le_bytes([data[0], data[1], data[2], data[3]]);
-        let version = u32::from_le_bytes([data[4], data[5], data[6], data[7]]);
-
-        match sel_type {
-            // ALL / NONE: type(4) + version(4) + reserved(4) + length(4) = 16 bytes.
-            3 | 0 => {
-                if data.len() < 16 {
-                    return Err(FormatError::UnexpectedEof {
-                        expected: 16,
-                        available: data.len(),
-                    });
-                }
-                let sel = if sel_type == 3 {
-                    Selection::All
                 } else {
-                    Selection::None
+                    Selection::Points(blocks_union_coords(rank, &starts, &ends)?)
+                }
+            }
         };
-                Ok((sel, 16))
+        Ok((sel, len))
-            }
-            2 => decode_hyperslab_serialized(data, version),
-            1 => Err(FormatError::ChunkedReadError(
-                "VDS point selections are not supported".into(),
-            )),
-            _ => Err(FormatError::ChunkedReadError(
-                "unknown dataspace selection type".into(),
-            )),
-        }
     }
 
     /// Enumerate the selected element indices of a **1-D** dataspace of the
@@ -314,6 +317,11 @@ impl Selection {
                         "VDS selection rank does not match dataspace rank".into(),
                     ));
                 }
+                if count.iter().chain(block.iter()).any(|&v| v == UNLIMITED) {
+                    return Err(FormatError::ChunkedReadError(
+                        "unlimited selection must be clipped before it is enumerated".into(),
+                    ));
+                }
                 // Selected coordinates along each dimension, in order.
                 let mut per_dim: Vec<Vec<u64>> = Vec::with_capacity(rank);
                 for d in 0..rank {
@@ -400,59 +408,174 @@ impl Selection {
     }
 }
 
-/// Decode an `H5S_SEL_HYPER` selection in its serialized form. Only version-3
+/// Hyperslab count/block value meaning "unlimited" (`H5S_UNLIMITED`).
-/// **regular** hyperslabs are supported.
+pub const UNLIMITED: u64 = u64::MAX;
-fn decode_hyperslab_serialized(
+
-    data: &[u8],
+/// Largest number of elements an irregular selection is expanded to when it
-    version: u32,
+/// is converted to a point list by [`Selection::decode_serialized`].
-) -> Result<(Selection, usize), FormatError> {
+const MAX_EXPANDED_POINTS: u64 = 1 << 26;
-    if version != 3 {
+
-        return Err(FormatError::ChunkedReadError(
+/// A selection exactly as `H5S_select_serialize` stores it, before it is
-            "only version-3 hyperslab selections are supported".into(),
+/// applied to any dataspace.
-        ));
+///
+/// Unlike [`Selection`] this keeps an irregular hyperslab as its list of
+/// blocks, and a regular hyperslab's count/block may be [`UNLIMITED`] (the
+/// unlimited selections used by unlimited and "printf" virtual dataset
+/// mappings).
+#[derive(Debug, Clone, PartialEq)]
+pub enum SerializedSelection {
+    /// `H5S_SEL_ALL`.
+    All,
+    /// `H5S_SEL_NONE`.
+    None,
+    /// A regular hyperslab. `count[d]` or `block[d]` may be [`UNLIMITED`].
+    Regular {
+        start: Vec<u64>,
+        stride: Vec<u64>,
+        count: Vec<u64>,
+        block: Vec<u64>,
+    },
+    /// An irregular hyperslab: the union of `starts.len() / rank` blocks, each
+    /// given by its first (`starts`) and last (`ends`, inclusive) coordinate,
+    /// flattened block-major.
+    Blocks {
+        rank: usize,
+        starts: Vec<u64>,
+        ends: Vec<u64>,
+    },
+}
+
+fn sel_err(msg: &str) -> FormatError {
+    FormatError::ChunkedReadError(msg.into())
+}
+
+/// Bounds-checked little-endian reader over a serialized selection.
+struct SelReader<'a> {
+    data: &'a [u8],
+    pos: usize,
+}
+
+impl SelReader<'_> {
+    fn take(&mut self, n: usize) -> Result<&[u8], FormatError> {
+        let end = self.pos.checked_add(n).filter(|&e| e <= self.data.len());
+        let end = end.ok_or(FormatError::UnexpectedEof {
+            expected: self.pos.saturating_add(n),
+            available: self.data.len(),
+        })?;
+        let s = &self.data[self.pos..end];
+        self.pos = end;
+        Ok(s)
     }
-    // type(4) ver(4) flags(1) enc_size(1) rank(4) [start,stride,count,block]*rank
+
-    if data.len() < 14 {
+    fn uint(&mut self, size: usize) -> Result<u64, FormatError> {
-        return Err(FormatError::UnexpectedEof {
+        let bytes = self.take(size)?;
-            expected: 14,
+        Ok(bytes
-            available: data.len(),
+            .iter()
-        });
+            .enumerate()
+            .fold(0u64, |v, (i, &b)| v | (b as u64) << (i * 8)))
     }
-    let flags = data[8];
+
-    let enc_size = data[9] as usize;
+    fn remaining(&self) -> usize {
-    // Bit 0 set => regular hyperslab. Irregular hyperslabs list explicit blocks.
+        self.data.len() - self.pos
-    if flags & 0x01 == 0 {
-        return Err(FormatError::ChunkedReadError(
-            "irregular VDS hyperslab selections are not supported".into(),
-        ));
     }
-    if enc_size != 2 && enc_size != 4 && enc_size != 8 {
+}
-        return Err(FormatError::ChunkedReadError(
+
-            "unsupported hyperslab coordinate encoding size".into(),
+impl SerializedSelection {
-        ));
+    /// Decode a serialized selection, returning it and the number of bytes it
-    }
+    /// occupies. Mirrors libhdf5's `H5S_select_deserialize`: `ALL`/`NONE` and
-    let rank = u32::from_le_bytes([data[10], data[11], data[12], data[13]]) as usize;
+    /// hyperslab versions 1-3 are decoded; point selections (which libhdf5
-    // HDF5 caps dataspace rank at 32 (H5S_MAX_RANK). Reject anything larger so a
+    /// refuses in virtual datasets) and malformed input are errors.
-    // corrupt rank can't drive a huge allocation or read loop.
+    pub fn decode(data: &[u8]) -> Result<(SerializedSelection, usize), FormatError> {
-    if rank > 32 {
+        let mut r = SelReader { data, pos: 0 };
-        return Err(FormatError::ChunkedReadError(
+        let sel_type = r.uint(4)?;
-            "hyperslab selection rank exceeds maximum (32)".into(),
+        let version = r.uint(4)?;
-        ));
+        match sel_type {
-    }
+            // ALL / NONE: type(4) + version(4) + reserved(4) + length(4).
-    let mut pos = 14;
+            0 | 3 => {
-    let read_coord = |data: &[u8], pos: usize| -> Result<u64, FormatError> {
+                r.take(8)?;
-        if pos + enc_size > data.len() {
+                let sel = if sel_type == 3 {
-            return Err(FormatError::UnexpectedEof {
+                    SerializedSelection::All
-                expected: pos + enc_size,
+                } else {
-                available: data.len(),
+                    SerializedSelection::None
-            });
-        }
-        let mut v = 0u64;
-        for (i, &b) in data[pos..pos + enc_size].iter().enumerate() {
-            v |= (b as u64) << (i * 8);
-        }
-        Ok(v)
                 };
+                Ok((sel, r.pos))
+            }
+            2 => {
+                let sel = decode_hyperslab(&mut r, version)?;
+                Ok((sel, r.pos))
+            }
+            1 => Err(sel_err(
+                "VDS point selections are not supported (libhdf5 rejects them too)",
+            )),
+            _ => Err(sel_err("unknown dataspace selection type")),
+        }
+    }
+
+    /// The single dimension in which this selection is unlimited, if any.
+    pub fn unlimited_dim(&self) -> Option<usize> {
+        match self {
+            SerializedSelection::Regular { count, block, .. } => count
+                .iter()
+                .zip(block)
+                .position(|(&c, &b)| c == UNLIMITED || b == UNLIMITED),
+            _ => None,
+        }
+    }
+
+    /// The rank the selection was serialized with (`None` for ALL/NONE, which
+    /// carry no rank).
+    pub fn rank(&self) -> Option<usize> {
+        match self {
+            SerializedSelection::Regular { start, .. } => Some(start.len()),
+            SerializedSelection::Blocks { rank, .. } => Some(*rank),
+            _ => None,
+        }
+    }
+}
+
+/// `H5S__hyper_deserialize`: after the type and version words.
+fn decode_hyperslab(r: &mut SelReader, version: u64) -> Result<SerializedSelection, FormatError> {
+    const REGULAR: u8 = 0x01;
+    let (flags, enc_size) = match version {
+        // v1: reserved(4) + length(4), always irregular, 4-byte coordinates.
+        1 => {
+            r.take(8)?;
+            (0u8, 4usize)
+        }
+        // v2: flags(1) + length(4), 8-byte coordinates.
+        2 => {
+            let flags = r.take(1)?[0];
+            r.take(4)?;
+            (flags, 8)
+        }
+        // v3: flags(1) + encoding size(1).
+        3 => {
+            let flags = r.take(1)?[0];
+            let enc = r.take(1)?[0] as usize;
+            (flags, enc)
+        }
+        _ => return Err(sel_err("unsupported hyperslab selection version")),
+    };
+    if flags & !REGULAR != 0 {
+        return Err(sel_err("unknown hyperslab selection flags"));
+    }
+    if !matches!(enc_size, 2 | 4 | 8) {
+        return Err(sel_err("unsupported hyperslab coordinate encoding size"));
+    }
+    let rank = r.uint(4)? as usize;
+    // HDF5 caps dataspace rank at 32 (H5S_MAX_RANK). Reject anything else so a
+    // corrupt rank can't drive a huge allocation or read loop.
+    if rank == 0 || rank > 32 {
+        return Err(sel_err("hyperslab selection rank must be 1..=32"));
+    }
+    // The all-ones value of the encoding width means "unlimited".
+    let unlim_raw = if enc_size == 8 {
+        u64::MAX
+    } else {
+        (1u64 << (enc_size * 8)) - 1
+    };
+
+    if flags & REGULAR != 0 {
         let (mut start, mut stride, mut count, mut block) = (
             Vec::with_capacity(rank),
             Vec::with_capacity(rank),
@@ -460,24 +583,104 @@ fn decode_hyperslab_serialized(
             Vec::with_capacity(rank),
         );
         for _ in 0..rank {
-        start.push(read_coord(data, pos)?);
+            start.push(r.uint(enc_size)?);
-        pos += enc_size;
+            stride.push(r.uint(enc_size)?);
-        stride.push(read_coord(data, pos)?);
+            let c = r.uint(enc_size)?;
-        pos += enc_size;
+            count.push(if c == unlim_raw { UNLIMITED } else { c });
-        count.push(read_coord(data, pos)?);
+            let b = r.uint(enc_size)?;
-        pos += enc_size;
+            block.push(if b == unlim_raw { UNLIMITED } else { b });
-        block.push(read_coord(data, pos)?);
-        pos += enc_size;
         }
-    Ok((
+        let unlimited = count
-        Selection::Hyperslab {
+            .iter()
+            .zip(&block)
+            .filter(|&(&c, &b)| c == UNLIMITED || b == UNLIMITED)
+            .count();
+        if unlimited > 1 {
+            return Err(sel_err(
+                "hyperslab selection is unlimited in more than one dimension",
+            ));
+        }
+        for d in 0..rank {
+            // Overlapping blocks are not a valid regular hyperslab.
+            if count[d] > 1 && block[d] != UNLIMITED && block[d] > stride[d] {
+                return Err(sel_err("regular hyperslab blocks overlap"));
+            }
+        }
+        return Ok(SerializedSelection::Regular {
             start,
             stride,
             count,
             block,
-        },
+        });
-        pos,
+    }
-    ))
+
+    // Irregular: number of blocks, then each block's start and end corners.
+    let nblocks = r.uint(enc_size)?;
+    let per_block = (rank * 2 * enc_size) as u64;
+    // Untrusted count: it must fit in what is left of the buffer.
+    if nblocks
+        .checked_mul(per_block)
+        .is_none_or(|need| need > r.remaining() as u64)
+    {
+        return Err(FormatError::UnexpectedEof {
+            expected: r
+                .pos
+                .saturating_add(nblocks.saturating_mul(per_block) as usize),
+            available: r.data.len(),
+        });
+    }
+    let n = nblocks as usize * rank;
+    let (mut starts, mut ends) = (Vec::with_capacity(n), Vec::with_capacity(n));
+    for _ in 0..nblocks {
+        for _ in 0..rank {
+            starts.push(r.uint(enc_size)?);
+        }
+        for _ in 0..rank {
+            ends.push(r.uint(enc_size)?);
+        }
+    }
+    if starts.iter().zip(&ends).any(|(s, e)| e < s) {
+        return Err(sel_err("hyperslab block ends before it starts"));
+    }
+    Ok(SerializedSelection::Blocks { rank, starts, ends })
+}
+
+/// The coordinates of the union of the given blocks, in row-major order.
+fn blocks_union_coords(
+    rank: usize,
+    starts: &[u64],
+    ends: &[u64],
+) -> Result<Vec<Vec<u64>>, FormatError> {
+    let mut total = 0u64;
+    for (s, e) in starts.chunks_exact(rank).zip(ends.chunks_exact(rank)) {
+        let vol = s
+            .iter()
+            .zip(e)
+            .try_fold(1u64, |acc, (&s, &e)| acc.checked_mul(e - s + 1));
+        total = vol
+            .and_then(|v| total.checked_add(v))
+            .filter(|&t| t <= MAX_EXPANDED_POINTS)
+            .ok_or_else(|| sel_err("irregular hyperslab selection is too large to expand"))?;
+    }
+    let mut out = Vec::with_capacity(total as usize);
+    for (s, e) in starts.chunks_exact(rank).zip(ends.chunks_exact(rank)) {
+        let mut cur = s.to_vec();
+        'block: loop {
+            out.push(cur.clone());
+            for d in (0..rank).rev() {
+                if cur[d] < e[d] {
+                    cur[d] += 1;
+                    continue 'block;
+                }
+                cur[d] = s[d];
+            }
+            break;
+        }
+    }
+    // Lexicographic order of coordinates is row-major order.
+    out.sort_unstable();
+    out.dedup();
+    Ok(out)
 }
 
 // ---------------------------------------------------------------------------
@@ -642,11 +845,100 @@ mod tests {
     }
 
     #[test]
-    fn decode_irregular_hyperslab_rejected() {
+    fn decode_truncated_irregular_hyperslab_is_error() {
+        // Irregular, rank 1, but the block count is missing.
         let bytes = [0x02u8, 0, 0, 0, 0x03, 0, 0, 0, 0x00, 0x02, 0x01, 0, 0, 0];
         assert!(Selection::decode_serialized(&bytes).is_err());
     }
 
+    /// Version 1 as libhdf5 writes it for the default (earliest) format bounds:
+    /// type, version, reserved(4), length(4), rank(4), nblocks(4), then each
+    /// block's start and inclusive end corner as 4-byte values.
+    fn v1_blocks(rank: u32, blocks: &[(&[u32], &[u32])]) -> Vec<u8> {
+        let mut b = Vec::new();
+        for w in [2u32, 1, 0, 0, rank, blocks.len() as u32] {
+            b.extend_from_slice(&w.to_le_bytes());
+        }
+        for (s, e) in blocks {
+            for v in s.iter().chain(e.iter()) {
+                b.extend_from_slice(&v.to_le_bytes());
+            }
+        }
+        b
+    }
+
+    #[test]
+    fn decode_v1_irregular_single_block() {
+        // Exactly what h5py/HDF5 2.0 writes for `[0:4]` with default libver.
+        let bytes = v1_blocks(1, &[(&[0], &[3])]);
+        let (sel, used) = Selection::decode_serialized(&bytes).unwrap();
+        assert_eq!(used, bytes.len());
+        assert_eq!(sel.iter_linear_1d(8).unwrap(), vec![0, 1, 2, 3]);
+    }
+
+    #[test]
+    fn decode_v1_irregular_union_is_row_major() {
+        // Blocks given out of order and overlapping still enumerate once each,
+        // in row-major order (libhdf5 iterates the union, not the list).
+        let bytes = v1_blocks(2, &[(&[1, 0], &[1, 1]), (&[0, 2], &[1, 2])]);
+        let (sel, used) = Selection::decode_serialized(&bytes).unwrap();
+        assert_eq!(used, bytes.len());
+        // (0,2) (1,0) (1,1) (1,2) in a 2x3 space.
+        assert_eq!(sel.iter_linear(&[2, 3]).unwrap(), vec![2, 3, 4, 5]);
+    }
+
+    #[test]
+    fn decode_v2_regular_with_unlimited_count() {
+        // v2: flags(1) + length(4), then 8-byte start/stride/count/block.
+        let mut b = Vec::new();
+        b.extend_from_slice(&2u32.to_le_bytes());
+        b.extend_from_slice(&2u32.to_le_bytes());
+        b.push(0x01);
+        b.extend_from_slice(&36u32.to_le_bytes());
+        b.extend_from_slice(&1u32.to_le_bytes());
+        for v in [0u64, 10, u64::MAX, 10] {
+            b.extend_from_slice(&v.to_le_bytes());
+        }
+        let (raw, used) = SerializedSelection::decode(&b).unwrap();
+        assert_eq!(used, b.len());
+        assert_eq!(raw.unlimited_dim(), Some(0));
+        assert_eq!(
+            raw,
+            SerializedSelection::Regular {
+                start: vec![0],
+                stride: vec![10],
+                count: vec![UNLIMITED],
+                block: vec![10],
+            }
+        );
+        // An unclipped unlimited selection cannot be enumerated.
+        let (sel, _) = Selection::decode_serialized(&b).unwrap();
+        assert!(sel.iter_linear_1d(100).is_err());
+    }
+
+    #[test]
+    fn decode_v3_two_byte_all_ones_is_unlimited() {
+        let bytes = [
+            0x02, 0, 0, 0, 0x03, 0, 0, 0, 0x01, 0x02, 0x01, 0, 0, 0, //
+            0x00, 0x00, 0x01, 0x00, 0x01, 0x00, 0xFF, 0xFF,
+        ];
+        let (raw, _) = SerializedSelection::decode(&bytes).unwrap();
+        assert_eq!(raw.unlimited_dim(), Some(0));
+    }
+
+    #[test]
+    fn decode_irregular_block_count_beyond_buffer_is_error() {
+        let mut b = v1_blocks(1, &[(&[0], &[3])]);
+        b[20..24].copy_from_slice(&u32::MAX.to_le_bytes());
+        assert!(Selection::decode_serialized(&b).is_err());
+    }
+
+    #[test]
+    fn decode_point_selection_is_refused() {
+        let bytes = [1u8, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0];
+        assert!(Selection::decode_serialized(&bytes).is_err());
+    }
+
     #[test]
     fn iter_linear_2d_block_row_major() {
         // A 2x2 block at the top-left of a 4x4 space => linear 0,1,4,5.

crates/clawhdf5/tests/vds_interop.rs

@@ -0,0 +1,156 @@
+//! Virtual Dataset (VDS) reads checked against libhdf5 (through h5py).
+//!
+//! Each test has h5py build virtual datasets and their source files in a temp
+//! directory, record what libhdf5 reads back (shape and values) next to them,
+//! and then compares that with what clawhdf5 reads from the same files.
+//!
+//! Skipped when python3 or h5py is unavailable, unless
+//! `CLAWHDF5_REQUIRE_INTEROP=1`.
+
+use std::path::Path;
+use std::process::Command;
+
+use clawhdf5::File;
+
+/// The Python interpreter to drive interop checks with (`CLAWHDF5_PYTHON`
+/// lets these run against a virtualenv holding h5py).
+fn python() -> String {
+    std::env::var("CLAWHDF5_PYTHON").unwrap_or_else(|_| "python3".to_string())
+}
+
+/// When `CLAWHDF5_REQUIRE_INTEROP=1` (set in CI), a missing Python dependency
+/// is a test failure instead of a silent skip.
+fn interop_required() -> bool {
+    std::env::var("CLAWHDF5_REQUIRE_INTEROP").is_ok_and(|v| v == "1")
+}
+
+fn python_available() -> bool {
+    Command::new(python())
+        .args(["-c", "import h5py, numpy"])
+        .output()
+        .map(|o| o.status.success())
+        .unwrap_or(false)
+}
+
+macro_rules! skip_if_no_python {
+    () => {
+        if !python_available() {
+            assert!(
+                !interop_required(),
+                "CLAWHDF5_REQUIRE_INTEROP=1 but python3 with h5py is not available"
+            );
+            eprintln!("SKIP: python3 with h5py not available");
+            return;
+        }
+    };
+}
+
+/// Prelude for every generator script: `expect(file, dset, tag)` records what
+/// libhdf5 reads for `file:dset` as `<tag>.expect` (shape line, values line).
+const PRELUDE: &str = r#"
+import h5py, numpy as np
+def expect(fn, dset, tag):
+    with h5py.File(fn, "r") as f:
+        d = f[dset]
+        a = d[...]
+        with open(tag + ".expect", "w") as out:
+            out.write(" ".join(str(n) for n in d.shape) + "\n")
+            out.write(" ".join(repr(float(v)) for v in a.ravel()) + "\n")
+"#;
+
+/// Run `body` (after [`PRELUDE`]) with `dir` as the working directory, so
+/// relative source file names land next to the virtual file.
+fn generate(dir: &Path, body: &str) {
+    let script = format!("{PRELUDE}\n{body}");
+    let out = Command::new(python())
+        .args(["-c", &script])
+        .current_dir(dir)
+        .output()
+        .expect("failed to run python");
+    assert!(
+        out.status.success(),
+        "generator failed:\nSTDOUT: {}\nSTDERR: {}",
+        String::from_utf8_lossy(&out.stdout),
+        String::from_utf8_lossy(&out.stderr)
+    );
+}
+
+/// What libhdf5 read for `tag`: (shape, values as f64).
+fn expected(dir: &Path, tag: &str) -> (Vec<u64>, Vec<f64>) {
+    let text = std::fs::read_to_string(dir.join(format!("{tag}.expect"))).unwrap();
+    let mut lines = text.lines();
+    let parse_line = |l: Option<&str>| -> Vec<String> {
+        l.unwrap_or("")
+            .split_whitespace()
+            .map(str::to_string)
+            .collect()
+    };
+    let shape = parse_line(lines.next())
+        .iter()
+        .map(|s| s.parse().unwrap())
+        .collect();
+    let values = parse_line(lines.next())
+        .iter()
+        .map(|s| s.parse().unwrap())
+        .collect();
+    (shape, values)
+}
+
+/// Assert clawhdf5 reads `file:dset` exactly as libhdf5 did for `tag`.
+fn assert_matches_libhdf5(dir: &Path, file: &str, dset: &str, tag: &str) {
+    let (shape, values) = expected(dir, tag);
+    let f = File::open(dir.join(file)).unwrap();
+    let ds = f.dataset(dset).unwrap();
+    assert_eq!(
+        ds.shape().unwrap(),
+        shape,
+        "{tag}: shape differs from libhdf5"
+    );
+    let got = ds
+        .read_f64()
+        .unwrap_or_else(|e| panic!("{tag}: read failed: {e}"));
+    assert_eq!(got.len(), values.len(), "{tag}: element count differs");
+    for (i, (g, e)) in got.iter().zip(&values).enumerate() {
+        assert!(
+            g == e || (g.is_nan() && e.is_nan()),
+            "{tag}: element {i} is {g}, libhdf5 reads {e}\n ours: {got:?}\n libhdf5: {values:?}"
+        );
+    }
+}
+
+// ---------------------------------------------------------------------------
+// Selection encodings
+// ---------------------------------------------------------------------------
+
+/// Files written with the default (earliest) format bounds serialize every
+/// VDS hyperslab as a version-1 *irregular* selection (4-byte block corners),
+/// and a strided selection as many blocks. These were refused outright.
+#[test]
+fn vds_version1_irregular_hyperslab_selections() {
+    skip_if_no_python!();
+    let dir = tempfile::tempdir().unwrap();
+    generate(
+        dir.path(),
+        r#"
+with h5py.File("src.h5", "w") as s:
+    s.create_dataset("a", data=np.arange(12.0))
+    s.create_dataset("m", data=np.arange(20.0).reshape(4, 5))
+with h5py.File("v1.h5", "w") as f:   # default libver: hyperslab version 1
+    f.create_dataset("local", data=np.arange(10.0) * -1)
+    lay = h5py.VirtualLayout(shape=(12,), dtype="f8")
+    lay[0:4] = h5py.VirtualSource(".", "local", shape=(10,))[2:6]
+    lay[4:10] = h5py.VirtualSource("src.h5", "a", shape=(12,))[::2]
+    lay[10:12] = h5py.VirtualSource("src.h5", "a", shape=(12,))[10:12]
+    f.create_virtual_dataset("strided", lay)
+    lay = h5py.VirtualLayout(shape=(4, 6), dtype="f8")
+    lay[:, 0:2] = h5py.VirtualSource("src.h5", "m", shape=(4, 5))[:, 3:5]
+    lay[:, 2:6:2] = h5py.VirtualSource("src.h5", "m", shape=(4, 5))[:, 0:2]
+    lay[:, 3:6:2] = h5py.VirtualSource("src.h5", "m", shape=(4, 5))[:, 2:4]
+    f.create_virtual_dataset("grid", lay)
+expect("v1.h5", "strided", "strided")
+expect("v1.h5", "grid", "grid")
+"#,
+    );
+    assert_matches_libhdf5(dir.path(), "v1.h5", "strided", "strided");
+    assert_matches_libhdf5(dir.path(), "v1.h5", "grid", "grid");
+}

docs/known-issues.md

@@ -71,7 +71,8 @@ the VDS item, which is marked.
 - **Virtual datasets:**
   - **Wrong data:** unmapped regions read as 0 instead of the fill value.
   - `%b` printf-style source names are not expanded.
-  - Hyperslab selection versions 1 and 2 are refused.
+  - ~~Hyperslab selection versions 1 and 2 are refused.~~ Fixed 2026-09-25:
+    versions 1-3 and irregular hyperslabs are decoded.
 - **Files with a user block:** the base address is not applied.
 - **Old-style shared messages (version 1)** read the wrong address.
 - **Groups and links:**