Merge release/v2.2.0: native complex datatype fix, v2.2.0 release, repository URL

Co-Authored-By: Claude Fable 5.1 <[email protected]>

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## Unreleased
+## v2.2.0 (2026-09-18)
 
 ### Security
 - `clawhdf5-format`: bounded decompression output (`MAX_DECOMPRESS_SIZE`) for
@@ -245,6 +245,16 @@
   reading compound types and — critically — every chunked/compressed dataset
   written by HDF5 2.0. Found by running the h5py interop tests against
   h5py 3.16 / HDF5 2.0.
+  Independently reported (with a patch) against the v2.1.0 tag by
+  M. Scot Breitenfeld (The HDF Group) — v2.1.0 predates this fix.
+- `clawhdf5-format`: parse HDF5 2.0 native complex datatypes (class 11,
+  datatype version 5, e.g. `H5T_COMPLEX_IEEE_F64LE`). The properties are a
+  single base floating-point datatype, not a compound-style member list; the
+  old parser read the base type's bytes as member names, producing a garbage
+  datatype, and failed with `UnexpectedEof` when a complex type was nested in
+  a compound. It is now surfaced as the equivalent `{r, i}` compound (the
+  shape h5py writes for numpy complex dtypes), with a size check against the
+  base type. Validated end-to-end against an HDF5 2.0-written file.
 
 ### Performance
 - `clawhdf5-format`: chunked writes now compress all chunks up front via

Cargo.toml

@@ -21,10 +21,10 @@ members = [
 resolver = "2"
 
 [workspace.package]
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 
 [workspace.dependencies]
 tempfile = "3"

crates/clawhdf5-accel/Cargo.toml

@@ -1,10 +1,10 @@
 [package]
 name = "clawhdf5-accel"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "SIMD-accelerated operations for rustyhdf5"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "simd", "acceleration", "performance"]
 categories = ["science", "algorithms"]

crates/clawhdf5-accel/src/avx2.rs

@@ -111,7 +111,7 @@ pub unsafe fn cosine_similarity(a: &[f32], b: &[f32]) -> f32 {
         }
 
         let denom = (norm_a * norm_b).sqrt();
-        if denom == 0.0 { 0.0 } else { dot / denom }
+        if denom < f32::EPSILON { 0.0 } else { dot / denom }
     }
 }
 

crates/clawhdf5-accel/src/avx512.rs

@@ -89,7 +89,7 @@ pub unsafe fn cosine_similarity(a: &[f32], b: &[f32]) -> f32 {
         }
 
         let denom = (norm_a * norm_b).sqrt();
-        if denom == 0.0 { 0.0 } else { dot / denom }
+        if denom < f32::EPSILON { 0.0 } else { dot / denom }
     }
 }
 

crates/clawhdf5-accel/src/lib.rs

@@ -361,6 +361,18 @@ mod tests {
         assert!(approx_eq(cosine_similarity(&a, &b), 0.0, EPSILON));
     }
 
+    #[test]
+    fn test_cosine_near_zero_norm_clamped() {
+        // denom = 1e-4 * 1e-4 = 1e-8, comfortably below f32::EPSILON
+        // (~1.19e-7) but not exactly 0.0 — must still clamp to 0.0 so
+        // callers computing `1.0 - cosine_similarity(...)` treat these
+        // as maximally dissimilar, matching the pre-SIMD scalar guard.
+        let a = [1e-4f32];
+        let b = [1e-4f32];
+        assert_eq!(cosine_similarity(&a, &b), 0.0);
+        assert_eq!(scalar::cosine_similarity(&a, &b), 0.0);
+    }
+
     #[test]
     fn test_cosine_scalar_vs_dispatch() {
         let a: Vec<f32> = (0..384).map(|i| (i as f32).sin()).collect();

crates/clawhdf5-accel/src/neon.rs

@@ -94,7 +94,7 @@ pub unsafe fn cosine_similarity(a: &[f32], b: &[f32]) -> f32 {
     }
 
     let denom = (norm_a * norm_b).sqrt();
-    if denom == 0.0 { 0.0 } else { dot / denom }
+    if denom < f32::EPSILON { 0.0 } else { dot / denom }
 }
 
 /// NEON L2 distance.

crates/clawhdf5-accel/src/scalar.rs

@@ -21,7 +21,7 @@ pub fn cosine_similarity(a: &[f32], b: &[f32]) -> f32 {
         norm_b += y * y;
     }
     let denom = (norm_a * norm_b).sqrt();
-    if denom == 0.0 { 0.0 } else { dot / denom }
+    if denom < f32::EPSILON { 0.0 } else { dot / denom }
 }
 
 pub fn batch_cosine(query: &[f32], vectors: &[&[f32]], results: &mut [(usize, f32)]) {

crates/clawhdf5-agent/Cargo.toml

@@ -1,21 +1,21 @@
 [package]
 name = "clawhdf5-agent"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "HDF5-backed persistent memory store for on-device AI agents"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["agent", "memory", "hdf5", "vector-search", "embedding"]
 categories = ["database", "science", "algorithms"]
 
 [dependencies]
-clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0", features = ["parallel", "fast-checksum"] }
+clawhdf5-format = { path = "../clawhdf5-format", version = "2.2.0", features = ["parallel", "fast-checksum"] }
-clawhdf5 = { path = "../clawhdf5", version = "2.1.0" }
+clawhdf5 = { path = "../clawhdf5", version = "2.2.0" }
-clawhdf5-io = { path = "../clawhdf5-io", version = "2.1.0", features = ["mmap"] }
+clawhdf5-io = { path = "../clawhdf5-io", version = "2.2.0", features = ["mmap"] }
-clawhdf5-accel = { path = "../clawhdf5-accel", version = "2.1.0" }
+clawhdf5-accel = { path = "../clawhdf5-accel", version = "2.2.0" }
-clawhdf5-ann = { path = "../clawhdf5-ann", version = "2.1.0", optional = true }
+clawhdf5-ann = { path = "../clawhdf5-ann", version = "2.2.0", optional = true }
-clawhdf5-gpu = { path = "../clawhdf5-gpu", version = "2.1.0", optional = true, default-features = false }
+clawhdf5-gpu = { path = "../clawhdf5-gpu", version = "2.2.0", optional = true, default-features = false }
 serde = { workspace = true }
 byteorder = "1"
 half = { workspace = true, optional = true }

crates/clawhdf5-android/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "clawhdf5-android"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "Android JNI bridge for edgehdf5-memory HDF5 backend"
 license = "MIT"

crates/clawhdf5-ann/Cargo.toml

@@ -1,18 +1,18 @@
 [package]
 name = "clawhdf5-ann"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "HNSW approximate nearest neighbor index stored as HDF5"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "ann", "hnsw", "nearest-neighbor"]
 categories = ["algorithms", "science"]
 
 [dependencies]
-clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0" }
+clawhdf5-format = { path = "../clawhdf5-format", version = "2.2.0" }
-clawhdf5-io = { path = "../clawhdf5-io", version = "2.1.0" }
+clawhdf5-io = { path = "../clawhdf5-io", version = "2.2.0" }
-clawhdf5-accel = { path = "../clawhdf5-accel", version = "2.1.0" }
+clawhdf5-accel = { path = "../clawhdf5-accel", version = "2.2.0" }
 rayon = { version = "1", optional = true }
 
 [features]

crates/clawhdf5-ann/src/hnsw.rs

@@ -1300,6 +1300,18 @@ mod tests {
         assert!((d - 1.0).abs() < 1e-6); // zero vector -> distance 1
     }
 
+    #[test]
+    fn cosine_near_zero_vector() {
+        // Tiny-but-nonzero, identical-direction vectors: denom is well
+        // below f32::EPSILON but not exactly 0.0. Must still be treated
+        // as a degenerate/unreliable direction (distance 1, "maximally
+        // dissimilar"), not as an exact match (distance 0).
+        let a = vec![1e-4, 1e-4];
+        let b = vec![1e-4, 1e-4];
+        let d = compute_distance(&a, &b, DistanceMetric::Cosine);
+        assert!((d - 1.0).abs() < 1e-6);
+    }
+
     #[test]
     fn insert_into_empty_index() {
         let mut index = HnswIndex::new(4, 16, DistanceMetric::L2);

crates/clawhdf5-bench/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "clawhdf5-bench"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "Benchmark harnesses for clawhdf5-agent (Track 8)"
 license = "MIT"

crates/clawhdf5-cli/Cargo.toml

@@ -1,10 +1,10 @@
 [package]
 name = "clawhdf5-cli"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 license = "MIT"
 description = "CLI for clawhdf5 agent memory — create, save, search, recall, stats"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 keywords = ["hdf5", "ai", "memory", "agent", "cli"]
 categories = ["command-line-utilities", "science"]
 readme = "../../README.md"
@@ -14,7 +14,7 @@ name = "clawhdf5"
 path = "src/main.rs"
 
 [dependencies]
-clawhdf5-agent = { path = "../clawhdf5-agent", version = "2.1.0" }
+clawhdf5-agent = { path = "../clawhdf5-agent", version = "2.2.0" }
 clap = { version = "4", features = ["derive", "env"] }
 serde_json = "1"
 serde = { workspace = true }

crates/clawhdf5-derive/Cargo.toml

@@ -1,10 +1,10 @@
 [package]
 name = "clawhdf5-derive"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "Derive macros for rustyhdf5 HDF5 traits"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "derive", "macros", "science"]
 categories = ["development-tools::procedural-macro-helpers"]

crates/clawhdf5-filters/Cargo.toml

@@ -1,10 +1,10 @@
 [package]
 name = "clawhdf5-filters"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "Filter and compression pipeline for clawhdf5"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "compression", "deflate", "filters"]
 categories = ["compression", "science"]

crates/clawhdf5-format/Cargo.toml

@@ -1,10 +1,10 @@
 [package]
 name = "clawhdf5-format"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "Pure-Rust HDF5 binary format parsing and writing — no C dependencies"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "science", "data", "binary", "no-std"]
 categories = ["parser-implementations", "science", "encoding", "no-std"]
@@ -25,7 +25,7 @@ pco = { version = "1.0", optional = true }
 [dev-dependencies]
 serde_json = "1"
 criterion = { workspace = true }
-clawhdf5-derive = { path = "../clawhdf5-derive", version = "2.1.0" }
+clawhdf5-derive = { path = "../clawhdf5-derive", version = "2.2.0" }
 
 [[bench]]
 name = "bench"

crates/clawhdf5-format/src/datatype.rs

@@ -546,27 +546,39 @@ impl Datatype {
                 }
             }
             11 => {
-                // Complex number — store as compound of two floats internally
+                // Complex number (HDF5 2.0, datatype version 5). The properties
-                // Parse like compound with version 3 and 2 members
+                // are a single base floating-point datatype message; an element
-                // But actually class 11 has no special properties beyond class 6 compound.
+                // is two consecutive base-type values (real, imaginary). There
-                // It's just recognized as a separate class. For now parse the 2 members
+                // is no member list. Surface it as the equivalent two-member
-                // as compound.
+                // compound `{r, i}` — the same shape h5py writes for numpy
-                let num_members = (bf0 as u16) | ((bf1 as u16) << 8);
+                // complex dtypes — so downstream compound readers work as-is.
-                let mut members = Vec::with_capacity(num_members as usize);
+                if version != 5 {
-                let ob = offset_bytes_for_size(size);
+                    return Err(FormatError::InvalidDatatypeVersion {
-                for _ in 0..num_members {
+                        class: class_id,
-                    let (name, name_len) = read_null_terminated_string(data, pos)?;
+                        version,
-                    pos += name_len;
-                    let byte_offset = read_uint(data, pos, ob)?;
-                    pos += ob;
-                    let (member_dt, consumed) = Self::parse_with_depth(&data[pos..], depth + 1)?;
-                    pos += consumed;
-                    members.push(CompoundMember {
-                        name,
-                        byte_offset,
-                        datatype: member_dt,
                     });
                 }
+                let (base_type, consumed) = Self::parse_with_depth(&data[pos..], depth + 1)?;
+                pos += consumed;
+                let base_size = base_type.type_size();
+                if base_size.checked_mul(2) != Some(size) {
+                    return Err(FormatError::DataSizeMismatch {
+                        expected: (base_size as usize).saturating_mul(2),
+                        actual: size as usize,
+                    });
+                }
+                let members = vec![
+                    CompoundMember {
+                        name: String::from("r"),
+                        byte_offset: 0,
+                        datatype: base_type.clone(),
+                    },
+                    CompoundMember {
+                        name: String::from("i"),
+                        byte_offset: base_size as u64,
+                        datatype: base_type,
+                    },
+                ];
                 Ok((Datatype::Compound { size, members }, pos))
             }
             _ => Err(FormatError::InvalidDatatypeClass(class_id)),
@@ -1126,6 +1138,75 @@ mod tests {
         }
     }
 
+    /// Real datatype message bytes emitted by HDF5 2.0 for the native complex
+    /// type `H5T_COMPLEX_IEEE_F64LE`: class 11, version 5, size 16, followed by
+    /// the base IEEE f64 datatype message.
+    const COMPLEX_F64_HDF5_2_0: [u8; 28] = [
+        0x5b, 0x01, 0x00, 0x00, 0x10, 0x00, 0x00, 0x00, 0x11, 0x20, 0x3f, 0x00, 0x08, 0x00, 0x00,
+        0x00, 0x00, 0x00, 0x40, 0x00, 0x34, 0x0b, 0x00, 0x34, 0xff, 0x03, 0x00, 0x00,
+    ];
+
+    #[test]
+    fn test_complex_v5_from_hdf5_2_0() {
+        let (dt, consumed) = Datatype::parse(&COMPLEX_F64_HDF5_2_0).unwrap();
+        assert_eq!(consumed, COMPLEX_F64_HDF5_2_0.len());
+        match dt {
+            Datatype::Compound { size, members } => {
+                assert_eq!(size, 16);
+                assert_eq!(members.len(), 2);
+                assert_eq!((members[0].name.as_str(), members[0].byte_offset), ("r", 0));
+                assert_eq!((members[1].name.as_str(), members[1].byte_offset), ("i", 8));
+                for m in &members {
+                    assert!(matches!(
+                        m.datatype,
+                        Datatype::FloatingPoint { size: 8, .. }
+                    ));
+                }
+            }
+            other => panic!("expected Compound, got {other:?}"),
+        }
+    }
+
+    #[test]
+    fn test_compound_with_complex_member_from_hdf5_2_0() {
+        // Compound { z: complex f64 @0, k: i64 @16 } as written by HDF5 2.0.
+        // Regression guard: the complex member must consume exactly its own
+        // bytes so the following member parses.
+        let mut bytes = vec![0x56, 0x02, 0x00, 0x00, 0x18, 0x00, 0x00, 0x00, b'z', 0x00, 0x00];
+        bytes.extend_from_slice(&COMPLEX_F64_HDF5_2_0);
+        bytes.extend_from_slice(&[b'k', 0x00, 0x10]);
+        bytes.extend_from_slice(&[
+            0x10, 0x08, 0x00, 0x00, 0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0x40, 0x00,
+        ]);
+        let (dt, consumed) = Datatype::parse(&bytes).unwrap();
+        assert_eq!(consumed, bytes.len());
+        match dt {
+            Datatype::Compound { size, members } => {
+                assert_eq!(size, 24);
+                assert_eq!(members.len(), 2);
+                assert!(matches!(
+                    &members[0].datatype,
+                    Datatype::Compound { size: 16, members } if members.len() == 2
+                ));
+                assert_eq!((members[1].name.as_str(), members[1].byte_offset), ("k", 16));
+            }
+            other => panic!("expected Compound, got {other:?}"),
+        }
+    }
+
+    #[test]
+    fn test_complex_size_mismatch_rejected() {
+        let mut bytes = COMPLEX_F64_HDF5_2_0;
+        bytes[4] = 0x0c; // claims 12 bytes, base type is 8
+        assert!(matches!(
+            Datatype::parse(&bytes),
+            Err(FormatError::DataSizeMismatch {
+                expected: 16,
+                actual: 12
+            })
+        ));
+    }
+
     #[test]
     fn test_reference_object() {
         let buf = build_dt_header(7, 1, [0, 0, 0], 8);

crates/clawhdf5-format/tests/writer_h5py_tests.rs

@@ -292,6 +292,74 @@ f.close()
     assert_eq!(x_vals, vec![1.0, 3.0]);
 }
 
+#[test]
+#[ignore = "requires Python h5py module"]
+fn read_h5py_generated_native_complex() {
+    // HDF5 2.0 native complex (datatype class 11, version 5), written through
+    // h5py's low-level API. Skips when the linked HDF5 predates 2.0.
+    let path = std::env::temp_dir().join("clawhdf5_h5py_native_complex.h5");
+    let gen_script = format!(
+        r#"
+import h5py, numpy as np
+from h5py import h5t, h5s, h5d, h5f, h5p
+if not getattr(h5py.get_config(), 'has_native_complex', False):
+    print('SKIP')
+else:
+    fapl = h5p.create(h5p.FILE_ACCESS)
+    fapl.set_libver_bounds(h5f.LIBVER_LATEST, h5f.LIBVER_LATEST)
+    fid = h5f.create(b'{}', h5f.ACC_TRUNC, fapl=fapl)
+    t = h5t.COMPLEX_IEEE_F64LE
+    d = h5d.create(fid, b'z', t, h5s.create_simple((2,)))
+    d.write(h5s.ALL, h5s.ALL, np.array([1+2j, 3+4j], dtype=np.complex128), mtype=t)
+    fid.close()
+"#,
+        path.display()
+    );
+    if h5py_read(&path, &gen_script) == "SKIP" {
+        eprintln!("HDF5 < 2.0: no native complex support, skipping");
+        return;
+    }
+
+    let bytes = std::fs::read(&path).unwrap();
+    let sig = clawhdf5_format::signature::find_signature(&bytes).unwrap();
+    let sb = clawhdf5_format::superblock::Superblock::parse(&bytes, sig).unwrap();
+    let addr = clawhdf5_format::group_v2::resolve_path_any(&bytes, &sb, "z").unwrap();
+    let hdr = clawhdf5_format::object_header::ObjectHeader::parse(
+        &bytes,
+        addr as usize,
+        sb.offset_size,
+        sb.length_size,
+    )
+    .unwrap();
+    let msg = |t: clawhdf5_format::message_type::MessageType| {
+        &hdr.messages.iter().find(|m| m.msg_type == t).unwrap().data
+    };
+    let (dt, _) = clawhdf5_format::datatype::Datatype::parse(msg(
+        clawhdf5_format::message_type::MessageType::Datatype,
+    ))
+    .unwrap();
+    let ds = clawhdf5_format::dataspace::Dataspace::parse(
+        msg(clawhdf5_format::message_type::MessageType::Dataspace),
+        sb.length_size,
+    )
+    .unwrap();
+    let dl = clawhdf5_format::data_layout::DataLayout::parse(
+        msg(clawhdf5_format::message_type::MessageType::DataLayout),
+        sb.offset_size,
+        sb.length_size,
+    )
+    .unwrap();
+    let raw = clawhdf5_format::data_read::read_raw_data(&bytes, &dl, &ds, &dt).unwrap();
+    let fields = clawhdf5_format::data_read::read_compound_fields(&raw, &dt).unwrap();
+    assert_eq!(fields.len(), 2);
+    let re =
+        clawhdf5_format::data_read::read_as_f64(&fields[0].raw_data, &fields[0].datatype).unwrap();
+    let im =
+        clawhdf5_format::data_read::read_as_f64(&fields[1].raw_data, &fields[1].datatype).unwrap();
+    assert_eq!((fields[0].name.as_str(), re), ("r", vec![1.0, 3.0]));
+    assert_eq!((fields[1].name.as_str(), im), ("i", vec![2.0, 4.0]));
+}
+
 #[test]
 #[ignore = "requires Python h5py module"]
 fn read_h5py_generated_enum() {

crates/clawhdf5-gpu/Cargo.toml

@@ -1,10 +1,10 @@
 [package]
 name = "clawhdf5-gpu"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "GPU-accelerated vector operations for rustyhdf5 using wgpu compute shaders"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "gpu", "wgpu", "compute"]
 categories = ["science", "graphics"]

crates/clawhdf5-io/Cargo.toml

@@ -1,16 +1,16 @@
 [package]
 name = "clawhdf5-io"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "I/O abstraction layer for rustyhdf5"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "io", "science", "data"]
 categories = ["filesystem", "science"]
 
 [dependencies]
-clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0" }
+clawhdf5-format = { path = "../clawhdf5-format", version = "2.2.0" }
 memmap2 = { version = "0.9", optional = true }
 libc = { version = "0.2", optional = true }
 tokio = { version = "1", features = ["fs", "io-util"], optional = true }

crates/clawhdf5-migrate/Cargo.toml

@@ -1,10 +1,10 @@
 [package]
 name = "clawhdf5-migrate"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "CLI to migrate SQLite agent memory databases to HDF5 format"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["sqlite", "hdf5", "migration", "agent", "memory"]
 categories = ["command-line-utilities", "database"]
@@ -14,9 +14,9 @@ name = "clawhdf5-migrate"
 path = "src/main.rs"
 
 [dependencies]
-clawhdf5-agent = { path = "../clawhdf5-agent", version = "2.1.0" }
+clawhdf5-agent = { path = "../clawhdf5-agent", version = "2.2.0" }
-clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0" }
+clawhdf5-format = { path = "../clawhdf5-format", version = "2.2.0" }
-clawhdf5 = { path = "../clawhdf5", version = "2.1.0" }
+clawhdf5 = { path = "../clawhdf5", version = "2.2.0" }
 rusqlite = { version = "0.31", features = ["bundled"] }
 clap = { version = "4", features = ["derive"] }
 half = { workspace = true }

crates/clawhdf5-napi/Cargo.toml

@@ -1,16 +1,16 @@
 [package]
 name = "clawhdf5-napi"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "Node.js native addon (napi-rs) exposing clawhdf5-agent to TypeScript/JavaScript"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 
 [lib]
 crate-type = ["cdylib"]
 
 [dependencies]
-clawhdf5-agent = { path = "../clawhdf5-agent", version = "2.1.0" }
+clawhdf5-agent = { path = "../clawhdf5-agent", version = "2.2.0" }
 napi = { version = "2", default-features = false, features = ["napi9"] }
 napi-derive = "2"
 

crates/clawhdf5-netcdf4/Cargo.toml

@@ -1,17 +1,17 @@
 [package]
 name = "clawhdf5-netcdf4"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "NetCDF-4 read support built on rustyhdf5 — pure Rust, no C dependencies"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["netcdf", "netcdf4", "hdf5", "science", "climate"]
 categories = ["parser-implementations", "science"]
 
 [dependencies]
-clawhdf5 = { path = "../clawhdf5", version = "2.1.0" }
+clawhdf5 = { path = "../clawhdf5", version = "2.2.0" }
-clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0" }
+clawhdf5-format = { path = "../clawhdf5-format", version = "2.2.0" }
 
 [dev-dependencies]
 tempfile = { workspace = true }

crates/clawhdf5-py/Cargo.toml

@@ -1,10 +1,10 @@
 [package]
 name = "clawhdf5-py"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "Python bindings for rustyhdf5 — a pure-Rust HDF5 library"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "python", "bindings", "science"]
 categories = ["api-bindings", "science"]
@@ -14,8 +14,8 @@ name = "clawhdf5"
 crate-type = ["cdylib", "rlib"]
 
 [dependencies]
-clawhdf5_rs = { path = "../clawhdf5", version = "2.1.0", package = "clawhdf5" }
+clawhdf5_rs = { path = "../clawhdf5", version = "2.2.0", package = "clawhdf5" }
-clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0" }
+clawhdf5-format = { path = "../clawhdf5-format", version = "2.2.0" }
 pyo3 = "0.29"
 numpy = "0.29"
 

crates/clawhdf5-py/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "rustyhdf5"
-version = "2.1.0"
+version = "2.2.0"
 description = "Python bindings for rustyhdf5 — a pure-Rust HDF5 library"
 requires-python = ">=3.8"
 license = { text = "MIT" }

crates/clawhdf5/Cargo.toml

@@ -1,25 +1,25 @@
 [package]
 name = "clawhdf5"
-version = "2.1.0"
+version = "2.2.0"
 edition = "2024"
 description = "Pure-Rust HDF5 reader/writer — no C dependencies"
 license = "MIT"
-repository = "https://github.com/redclawsystems/clawhdf5"
+repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
 readme = "README.md"
 keywords = ["hdf5", "science", "data", "binary"]
 categories = ["parser-implementations", "science", "encoding"]
 
 [dependencies]
-clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0" }
+clawhdf5-format = { path = "../clawhdf5-format", version = "2.2.0" }
-clawhdf5-io = { path = "../clawhdf5-io", version = "2.1.0" }
+clawhdf5-io = { path = "../clawhdf5-io", version = "2.2.0" }
 rayon = { version = "1", optional = true }
 
 [dev-dependencies]
 tempfile = { workspace = true }
 criterion = { workspace = true }
-clawhdf5-io = { path = "../clawhdf5-io", version = "2.1.0", features = ["mmap"] }
+clawhdf5-io = { path = "../clawhdf5-io", version = "2.2.0", features = ["mmap"] }
-clawhdf5-format = { path = "../clawhdf5-format", version = "2.1.0", features = ["parallel", "fast-checksum"] }
+clawhdf5-format = { path = "../clawhdf5-format", version = "2.2.0", features = ["parallel", "fast-checksum"] }
-clawhdf5-filters = { path = "../clawhdf5-filters", version = "2.1.0" }
+clawhdf5-filters = { path = "../clawhdf5-filters", version = "2.2.0" }
 
 [[bench]]
 name = "mmap_bench"

docs/QUICKSTART.md

@@ -556,7 +556,7 @@ let final_results = confidence::reject_low_confidence(
 
 - **[BENCHMARKS.md](../BENCHMARKS.md)** — Full performance numbers
 - **[ROADMAP.md](../ROADMAP.md)** — What's coming next
-- **[GitHub](https://github.com/redclawsystems/clawhdf5)** — Source code
+- **[Source](https://git.redclaw.dev/quantumclaw/clawhdf5)** — Source code
 - **[ClawBrainHub](https://clawbrainhub.com)** — The `.brain` marketplace (coming soon)
 
 ---

docs/known-issues.md

@@ -0,0 +1,82 @@
+# Known Issues
+
+Bugs found during development or downstream use, tracked here because this
+repository's issue tracker is disabled. One entry per bug; when an entry is
+fixed, record the fix in `CHANGELOG.md` and update its status here rather than
+deleting it.
+
+---
+
+## Compound datatype message version 5 is not parsed (HDF5 2.0)
+
+**Status:** fixed on `main` in `a13ff51` (2026-06-03); **not in the v2.1.0
+tag**, which was cut five commits earlier. Ships in the next release.
+
+**Reported by:** M. Scot Breitenfeld (The HDF Group), 2026-09-08, against v2.1.0.
+
+**Summary:** `clawhdf5-format` v2.1.0 rejects any dataset with a compound
+(struct) datatype written by an HDF5 2.0 library in `libver='latest'` mode:
+`InvalidDatatypeVersion { class: 6, version: 5 }`.
+
+**Reproduction** (h5py 3.16.0 / HDF5 2.0.0):
+
+```python
+import h5py, numpy as np
+dt = np.dtype([('x', 'f8'), ('y', 'f8'), ('id', 'i4')])
+data = np.array([(1.0, 2.0, 10), (3.0, 4.0, 20)], dtype=dt)
+f = h5py.File('compound.h5', 'w', libver='latest')
+f.create_dataset('particles', data=data)
+f.close()
+```
+
+Committed as `crates/clawhdf5-format/tests/writer_h5py_tests.rs::read_h5py_generated_compound`
+(`#[ignore]`d; needs `python3` with h5py on `PATH`). Run with
+`cargo test -p clawhdf5-format --test writer_h5py_tests -- --include-ignored`:
+v2.1.0 gives 25 passed / 1 failed; `main` passes everything.
+
+**Root cause:** the compound (class 6) branch of `Datatype::parse`
+(`crates/clawhdf5-format/src/datatype.rs`) accepted only versions 1–4. Datatype
+message versions 4 and 5 changed only the Reference and Complex classes, so a
+v5-tagged compound uses the unchanged v3 member-list layout.
+
+**Fix:** versions 3–5 are accepted for compound (class 6) and array (class 10)
+datatypes, and data layout message version 5 is accepted too (needed for every
+chunked dataset written by HDF5 2.0). Byte-level regression tests:
+`test_compound_v5_from_hdf5_2_0`, `test_array_v5_from_hdf5_2_0`.
+
+## Native complex datatype (class 11) is mis-parsed (HDF5 2.0)
+
+**Status:** fixed 2026-09-18. Found while validating the report above.
+
+**Summary:** HDF5 2.0 native complex types (`H5T_COMPLEX_IEEE_F64LE` etc.)
+were parsed as if they carried a compound-style member list. The properties are
+actually a single base floating-point datatype, so the parser produced a garbage
+datatype, or `UnexpectedEof` when the complex type was a compound member. h5py's
+default numpy-complex mapping is unaffected (it writes a `{r, i}` compound);
+only files using the native type through the C API / h5py low-level API hit this.
+
+**Fix:** class 11 parses its base type and is surfaced as the equivalent
+`{r, i}` compound. Tests: `test_complex_v5_from_hdf5_2_0`,
+`test_compound_with_complex_member_from_hdf5_2_0`,
+`writer_h5py_tests.rs::read_h5py_generated_native_complex`.
+
+## Revised reference datatype (class 7, version 4) is not parsed
+
+**Status:** open, unconfirmed against a real file.
+
+**Summary:** HDF5 1.12+ `H5T_STD_REF` references use datatype version 4 with
+reference types 2–4 (object2 / region2 / attribute), which `Datatype::parse`
+rejects with `InvalidReferenceType`. h5py still writes the legacy v1
+object/region references, which read correctly, so no reproducing file has been
+generated yet; one written with the C API (`H5T_STD_REF`) is needed.
+
+## `clawhdf5-gpu` `gpu_tests` can hang under the default parallel test runner
+
+**Status:** open. Observed 2026-09-18 (RTX 5060 Ti, Linux).
+
+**Summary:** during `cargo test --workspace`, the `gpu_tests` binary sat idle
+(~1% CPU) for 25+ minutes and had to be killed. Run single-threaded it passes
+in seconds (20/20): `cargo test -p clawhdf5-gpu --test gpu_tests -- --test-threads=1`.
+Suspected cause: several tests creating wgpu devices concurrently (possibly
+compounded by the rest of the workspace's tests loading the machine). Not yet
+root-caused; workaround is `--test-threads=1` for that crate.

packages/clawhdf5-node/package.json

@@ -1,13 +1,13 @@
 {
   "name": "@redclaw/clawhdf5",
-  "version": "2.1.0",
+  "version": "2.2.0",
   "description": "Node.js bindings for clawhdf5 — HDF5-backed agent memory with hippocampal consolidation",
   "main": "index.js",
   "types": "index.d.ts",
   "license": "MIT",
   "repository": {
     "type": "git",
-    "url": "https://github.com/redclawsystems/clawhdf5"
+    "url": "https://git.redclaw.dev/quantumclaw/clawhdf5"
   },
   "keywords": [
     "agent",

research/VERIFICATION_BRIEF.md

@@ -0,0 +1,201 @@
+# Verification Brief — branch `verify/v3-plus-v6`
+
+Independent audit of three already-implemented fixes:
+
+- **P1** — `clawhdf5-ann::hnsw::compute_distance` now delegates to `clawhdf5-accel`'s
+  runtime-dispatched SIMD kernels (`l2_distance`, `cosine_similarity`) instead of
+  scalar loops.
+- **P2** — `clawhdf5-io::async_read::AsyncFileReader` now opens the file handle
+  once and caches it + its length behind a `tokio::sync::Mutex`.
+- **PR1** — `clawhdf5-migrate` writes SHINES provenance (`hdf5_writer.rs`) and
+  verifies it on read-back (`validate.rs`).
+
+Branch state audited: `verify/v3-plus-v6` @ `07b7301` (merge of the v3 ann/io/migrate
+work and v6 agent/format work). All three areas' existing test suites
+(`cargo test -p clawhdf5-accel -p clawhdf5-ann -p clawhdf5-io --features async
+-p clawhdf5-migrate --release`) pass — 41 + 23 + 89 + 26 tests green. That is
+expected: the defect below is a numerical edge case none of the existing tests
+exercise.
+
+---
+
+## P1 — SIMD distance in `clawhdf5-ann` — DEFECT FOUND
+
+**File:** `crates/clawhdf5-accel/src/scalar.rs`, `avx2.rs`, `avx512.rs`, `neon.rs`
+(all four backends share the bug identically; it surfaces in callers through
+`crates/clawhdf5-ann/src/hnsw.rs:54`, `compute_distance`'s
+`1.0 - clawhdf5_accel::cosine_similarity(a, b)`).
+
+**Problem:** The near-zero-norm guard in `cosine_similarity` changed threshold
+during the SIMD migration, and the new threshold is wrong.
+
+Old scalar loop (pre-SIMD, `hnsw.rs` @ `55959b4`):
+
+```rust
+let denom = norm_a.sqrt() * norm_b.sqrt();
+if denom < f32::EPSILON {
+    1.0
+} else {
+    1.0 - (dot / denom)
+}
+```
+
+New code, identical in all four `clawhdf5-accel` backends (e.g.
+`scalar.rs:23-24`):
+
+```rust
+let denom = (norm_a * norm_b).sqrt();
+if denom == 0.0 { 0.0 } else { dot / denom }
+```
+
+The old code clamped *any* near-zero denominator (anything under
+`f32::EPSILON ≈ 1.19e-7`, not just exact zero) to a safe "maximally
+dissimilar" result. The new code only special-cases an **exact** `0.0`
+denominator; anything smaller but nonzero falls through to `dot / denom`.
+
+For genuinely-zero vectors the two are equivalent (`denom == 0.0` in both, and
+`1.0 - 0.0 == 1.0` matches the old `1.0`), and the existing test
+(`hnsw.rs::cosine_zero_vector`, `clawhdf5-accel::test_cosine_zero_vector`)
+only covers that case — which is why it didn't catch this.
+
+But for vectors with a small (not exactly zero) norm, the two diverge sharply.
+Concrete repro (values confirmed via a standalone build of both functions):
+
+```
+a = b = [1e-4]        // tiny but nonzero, identical vectors
+old cosine distance = 1.0   // "unreliable direction" fallback, correctly
+                             // caps degenerate near-zero vectors at max distance
+new cosine distance = 0.0   // computed as fully identical
+```
+
+`denom` here is `1e-8`, comfortably below `f32::EPSILON` (`1.19e-7`) but not
+`== 0.0`, so the old guard fired and the new one doesn't. This is not a
+narrow floating-point-rounding footgun — the divergence spans roughly three
+orders of magnitude of vector norm (anything with `denom` in
+`(0, 1.19e-7)`), and it flips the result from "maximally dissimilar" to
+"identical," the two opposite ends of the distance range. Any HNSW cosine
+index that indexes or queries a near-zero-magnitude embedding (e.g. an
+embedder's output for empty/masked/degenerate input, or a soft-deleted/
+zeroed-out placeholder vector) will silently rank it as a near-duplicate of
+other near-zero vectors instead of correctly pushing it to the bottom of
+results.
+
+Mismatched-length and truly-empty inputs were also checked: empty vectors
+(`a.len() == b.len() == 0`) behave identically old vs. new (both hit the
+zero-denominator path → distance `1.0`). Mismatched lengths now panic via
+`assert_eq!` in every backend, versus the old code's `for i in 0..a.len()`
+(which panicked on OOB if `b` was shorter, or silently truncated to `a`'s
+length if `b` was longer). No caller reaches this: `HnswIndex::build_with_metric`
+and `insert` both assert equal dimensions before any `compute_distance` call,
+so mismatched lengths are unreachable in practice — not flagging as a
+separate defect.
+
+**Proposed fix:** Restore the epsilon-threshold guard in all four
+`clawhdf5-accel` cosine_similarity backends (`scalar.rs`, `avx2.rs`,
+`avx512.rs`, `neon.rs`), replacing `if denom == 0.0 { 0.0 }` with
+`if denom < f32::EPSILON { 0.0 }`, so `1.0 - cosine_similarity(...)` in
+`hnsw.rs` reproduces the old `denom < f32::EPSILON → 1.0` fallback exactly.
+Add a regression test in `clawhdf5-accel` (e.g.
+`test_cosine_near_zero_norm_clamped`) asserting `cosine_similarity(&[1e-4],
+&[1e-4])` returns `0.0` (so `1.0 - sim == 1.0`, matching the old HNSW
+fallback) rather than `1.0`, and a matching test in `hnsw.rs`
+(`cosine_near_zero_vector`, alongside the existing `cosine_zero_vector`) using
+a tiny-but-nonzero vector pair to lock in `compute_distance == 1.0`.
+
+TASK: INT-01 — Restore f32::EPSILON near-zero-denom guard in clawhdf5-accel cosine_similarity (all 4 backends) + regression tests
+
+---
+
+## P2 — Cached async file handle in `clawhdf5-io` — SOUND, no defect
+
+**File:** `crates/clawhdf5-io/src/async_read.rs`, `AsyncFileReader::read_at` /
+`::len` (lines 96-126).
+
+Checked against the pre-fix version (diff in `b08df7b`, which per-call opened
+a fresh `tokio::fs::File` and re-stat'd the length):
+
+- **No seek/read interleaving across tasks.** `read_at` takes
+  `let mut guard = self.handle.lock().await` once at the top and then borrows
+  `file` from that guard (`guard.as_mut()`) for the rest of the function,
+  including both the `seek(...).await` and `read_exact(...).await` calls.
+  Because `file` is a live borrow of `guard`, the Rust borrow checker forces
+  `guard` (and therefore the lock) to stay held across both await points —
+  it cannot be dropped until the whole function returns. `tokio::sync::Mutex`
+  is specifically designed to be held across `.await` (unlike `std::sync::Mutex`),
+  so a second task's `read_at` call blocks at `.lock().await` until the first
+  task's seek+read pair has fully completed. A seek from one task can never be
+  followed by a read from another task on the same descriptor.
+- **Lazy-init race is also covered by the same lock.** The `if guard.is_none()`
+  open-and-populate branch runs under the same guard acquired at the top, so
+  two concurrent first-callers can't both open+overwrite the cached handle;
+  the second one to acquire the lock sees `guard.is_some()` and reuses it.
+- **Cached length staleness.** The length is cached forever once populated —
+  intentional and documented in the struct's doc comment ("cached for the
+  lifetime of this reader"). Grepped the whole workspace
+  (`AsyncFileReader` outside `async_read.rs` itself): zero other callers exist
+  yet, so there's no current code path where a caller observes a stale length
+  against a file that changed size mid-lifetime. If the backing file were
+  truncated externally during the reader's life, the stale (larger) cached
+  length would make `read_at` attempt to read more than remains on disk —
+  but that fails loudly via `read_exact`'s `UnexpectedEof` rather than
+  silently returning corrupted/truncated data, which is a safe failure mode,
+  not a correctness bug.
+- **Short-read/truncation semantics.** The `offset >= file_len → empty`,
+  `to_read = len.min(available)` logic is byte-for-byte unchanged from the
+  pre-fix version; only the source of `file_len` changed (cached vs.
+  freshly stat'd). For the current, only-consumer-is-itself usage pattern
+  (open once, read many times, file not mutated externsally during the
+  reader's life) the observable behavior is identical to before.
+
+No item raised for P2.
+
+---
+
+## PR1 — SHINES provenance in `clawhdf5-migrate` — SOUND, no defect
+
+**Files:** `crates/clawhdf5-migrate/src/hdf5_writer.rs`,
+`crates/clawhdf5-migrate/src/main.rs`, `crates/clawhdf5-migrate/src/validate.rs`,
+`crates/clawhdf5-migrate/src/hdf5_reader.rs`.
+
+- **Current-run source path / timestamp on `--incremental` merges.**
+  `write_hdf5` (`hdf5_writer.rs:23`) computes `timestamp = iso8601_now()`
+  fresh on every call — it is never read from the merged `data` struct, so
+  the top-level `migrated_at` attribute and the per-dataset
+  `.with_provenance("clawhdf5-migrate", timestamp, source_opt)` calls
+  (`hdf5_writer.rs:147,177,189`) always carry the current run's wall-clock
+  time, incremental or not. For `source_path`: `hdf5_reader::read_hdf5`
+  (used to load the incremental base) explicitly returns
+  `source_path: String::new()` with a comment noting the caller must carry
+  the real path forward (`hdf5_reader.rs:52-56`); `main.rs:160`
+  (`base.source_path = source.source_path`) does exactly that — it
+  overwrites the re-read base's placeholder with the *freshly re-read SQLite
+  source's* path before calling `write_hdf5`, not a previous run's path.
+  Traced through: on an `--incremental` run, both the top-level attributes
+  and every per-dataset provenance attribute reflect the current run, not a
+  stale one. `test_incremental_migration` (`main.rs`) exercises the merge
+  path and passes, though it doesn't assert on `source_path`/`migrated_at`
+  specifically — the coding phase could add that assertion as cheap
+  extra insurance, but it's not fixing a defect, just tightening coverage.
+- **Hash-mismatch vs. absent-attribute handling.**
+  `verify_chunk_provenance` (`validate.rs:161-184`) returns `Err(...)`
+  (fails loudly, wired through `validate_hdf5`'s `?`) only on
+  `VerifyResult::Mismatch`, i.e. an actual recomputed-vs-stored SHA-256
+  disagreement. `VerifyResult::NoHash` (attribute absent, e.g. an
+  older output file) is handled separately — it sets `all_present = false`
+  and continues, returning `Ok(false)` from `verify_chunk_provenance`
+  (surfaced as `ValidationSummary::provenance_verified == false`, not an
+  error). This is correctly asymmetric: real corruption is a hard error,
+  merely-missing provenance metadata is a soft "unverified" signal, matching
+  the documented contract in the function's doc comment.
+
+No item raised for PR1.
+
+---
+
+## Summary
+
+| Item | Verdict | Follow-up |
+|------|---------|-----------|
+| P1 SIMD distance | **Defect** — cosine near-zero-norm guard weakened from `< f32::EPSILON` to `== 0.0` across all 4 backends | INT-01 |
+| P2 async file handle | Sound | none |
+| PR1 migrate provenance | Sound | none |