crates/clawhdf5-agent/Cargo.toml

@@ -14,6 +14,7 @@ clawhdf5-format = { path = "../clawhdf5-format", version = "2.0.0", features = [
 clawhdf5 = { path = "../clawhdf5", version = "2.0.0" }
 clawhdf5-io = { path = "../clawhdf5-io", version = "2.0.0", features = ["mmap"] }
 clawhdf5-accel = { path = "../clawhdf5-accel", version = "2.0.0" }
+clawhdf5-ann = { path = "../clawhdf5-ann", version = "2.0.0", optional = true }
 clawhdf5-gpu = { path = "../clawhdf5-gpu", version = "2.0.0", optional = true, default-features = false }
 serde = { version = "1", features = ["derive"] }
 byteorder = "1"
@@ -44,9 +45,15 @@ name = "memory_bench"
 harness = false
 
 [features]
-default = ["float16"]
+default = ["float16", "hnsw"]
 float16 = ["half"]
 parallel = ["rayon"]
+# HNSW approximate-nearest-neighbour acceleration for the vector stage of
+# hybrid_search. On by default; the index is rebuilt from the cache on demand
+# and stays self-consistent with the persisted memory store. Disable with
+# `--no-default-features` (plus re-enabling other defaults) to force the exact
+# linear cosine scan.
+hnsw = ["clawhdf5-ann"]
 agent = []
 gpu = ["clawhdf5-gpu/gpu-wgpu"]
 fast-math = ["matrixmultiply"]

crates/clawhdf5-agent/src/hybrid.rs

@@ -60,6 +60,22 @@ pub fn hybrid_search(
     };
     let kw_scores = bm25_index.search(query_text, vectors.len());
 
+    merge_vector_keyword(vec_scores, kw_scores, vector_weight, keyword_weight, k)
+}
+
+/// Merge pre-computed vector-similarity and keyword scores into a single ranking.
+///
+/// Both score sets are independently min-max normalized to [0, 1] and combined
+/// with the given weights. This is the shared core of [`hybrid_search`]; it is
+/// also used by the optional HNSW path, which supplies vector scores from an
+/// approximate-nearest-neighbour index instead of a full linear scan.
+pub fn merge_vector_keyword(
+    vec_scores: Vec<(usize, f32)>,
+    kw_scores: Vec<(usize, f32)>,
+    vector_weight: f32,
+    keyword_weight: f32,
+    k: usize,
+) -> Vec<(usize, f32)> {
     // Normalize each set to [0, 1].
     let vec_normalized = normalize_scores(&vec_scores);
     let kw_normalized = normalize_scores(&kw_scores);

crates/clawhdf5-agent/src/lib.rs

@@ -60,7 +60,16 @@ pub fn cosine_similarity_prenorm(
 use std::path::{Path, PathBuf};
 
 use cache::MemoryCache;
+#[cfg(feature = "hnsw")]
+use clawhdf5_ann::{DistanceMetric, HnswIndex};
 use ephemeral::{EphemeralConfig, EphemeralStore};
+
+/// HNSW construction parameters used for the agent's vector index. Cosine is the
+/// agent's similarity metric, so the index is built with cosine distance.
+#[cfg(feature = "hnsw")]
+const HNSW_M: usize = 16;
+#[cfg(feature = "hnsw")]
+const HNSW_EF_CONSTRUCTION: usize = 64;
 // EphemeralEntry and EphemeralStats are part of the crate public API via
 // the `ephemeral` module; they are not needed directly in lib.rs internals.
 #[allow(unused_imports)]
@@ -202,6 +211,22 @@ pub struct HDF5Memory {
     wal: Option<wal::WalFile>,
     strategy: Option<Box<dyn MemoryStrategy>>,
     pub ephemeral: Option<EphemeralStore>,
+    /// Optional HNSW index accelerating the vector stage of `hybrid_search`.
+    /// `None` when the store isn't indexable (no/zero-dim/mixed-dim embeddings);
+    /// rebuilt from the cache whenever it drifts out of sync (see
+    /// [`HDF5Memory::ensure_hnsw_fresh`]).
+    #[cfg(feature = "hnsw")]
+    hnsw: Option<HnswIndex>,
+    /// Set when an in-place update/compaction may have invalidated `hnsw`,
+    /// forcing a rebuild before the next search.
+    #[cfg(feature = "hnsw")]
+    hnsw_dirty: bool,
+    /// Cache length the current `hnsw` value reflects. A mismatch with the live
+    /// cache length triggers a rebuild — this both picks up unhooked cache
+    /// pushes and avoids re-attempting to build an unindexable store every
+    /// search.
+    #[cfg(feature = "hnsw")]
+    hnsw_synced_len: usize,
 }
 
 impl std::fmt::Debug for HDF5Memory {
@@ -235,6 +260,12 @@ impl HDF5Memory {
             wal,
             strategy: None,
             ephemeral: None,
+            #[cfg(feature = "hnsw")]
+            hnsw: None,
+            #[cfg(feature = "hnsw")]
+            hnsw_dirty: false,
+            #[cfg(feature = "hnsw")]
+            hnsw_synced_len: 0,
         })
     }
 
@@ -262,6 +293,14 @@ impl HDF5Memory {
             wal,
             strategy: None,
             ephemeral: None,
+            // Existing data is loaded from disk + WAL replay; mark the index
+            // dirty so it is (re)built from the cache on the first search.
+            #[cfg(feature = "hnsw")]
+            hnsw: None,
+            #[cfg(feature = "hnsw")]
+            hnsw_dirty: true,
+            #[cfg(feature = "hnsw")]
+            hnsw_synced_len: 0,
         })
     }
 
@@ -284,6 +323,108 @@ impl HDF5Memory {
         Ok(())
     }
 
+    // ---- HNSW index maintenance --------------------------------------------
+    //
+    // The index mirrors the cache: HNSW node id == cache index, kept aligned by
+    // appending to both in lock-step and mirroring deletes. The incremental
+    // hooks below are an optimization for the hot path; correctness is
+    // guaranteed by `ensure_hnsw_fresh`, which rebuilds from the cache whenever
+    // the index length drifts from the cache length (covering any mutation path
+    // that doesn't call a hook, e.g. consolidation pushes).
+
+    /// Build an HNSW index over the entire cache, re-applying tombstones as
+    /// soft-deletions so node ids stay aligned with cache indices.
+    ///
+    /// Returns `None` for stores that aren't usefully indexable: no embeddings,
+    /// a zero embedding dimension, or embeddings of mixed dimension (in which
+    /// case `hybrid_search` keeps using the linear scan).
+    #[cfg(feature = "hnsw")]
+    fn build_hnsw_from_cache(&self) -> Option<HnswIndex> {
+        let dim = self.cache.embedding_dim;
+        if dim == 0 || self.cache.embeddings.is_empty() {
+            return None;
+        }
+        if self.cache.embeddings.iter().any(|e| e.len() != dim) {
+            return None;
+        }
+        let mut index = HnswIndex::build_with_metric(
+            &self.cache.embeddings,
+            HNSW_M,
+            HNSW_EF_CONSTRUCTION,
+            DistanceMetric::Cosine,
+        );
+        for (i, &t) in self.cache.tombstones.iter().enumerate() {
+            if t != 0 {
+                index.mark_deleted(i);
+            }
+        }
+        Some(index)
+    }
+
+    /// Ensure the HNSW index reflects the current cache. Rebuilds when marked
+    /// dirty or when the cache length no longer matches what the index reflects.
+    #[cfg(feature = "hnsw")]
+    fn ensure_hnsw_fresh(&mut self) {
+        let n = self.cache.embeddings.len();
+        if self.hnsw_dirty || self.hnsw_synced_len != n {
+            self.hnsw = self.build_hnsw_from_cache();
+            self.hnsw_synced_len = n;
+            self.hnsw_dirty = false;
+        }
+    }
+
+    /// Incrementally index the embedding just pushed at `idx`. Falls back to a
+    /// rebuild (via the dirty flag) for the first vector, dimension mismatches,
+    /// or id drift.
+    #[cfg(feature = "hnsw")]
+    fn hnsw_on_insert(&mut self, idx: usize) {
+        if self.hnsw_dirty {
+            return; // a rebuild is already pending; it will pick this up
+        }
+        let emb_len = self.cache.embeddings[idx].len();
+        match self.hnsw.as_mut() {
+            Some(index) if emb_len == index.dimension() => {
+                let id = index.insert(self.cache.embeddings[idx].clone());
+                if id == idx {
+                    self.hnsw_synced_len = self.cache.embeddings.len();
+                } else {
+                    self.hnsw_dirty = true;
+                }
+            }
+            // Dimension mismatch, first-ever vector, or no index yet: defer to a
+            // rebuild, which decides indexability uniformly.
+            _ => self.hnsw_dirty = true,
+        }
+    }
+
+    #[cfg(not(feature = "hnsw"))]
+    #[inline]
+    fn hnsw_on_insert(&mut self, _idx: usize) {}
+
+    /// Mirror a cache deletion into the index.
+    #[cfg(feature = "hnsw")]
+    fn hnsw_on_delete(&mut self, id: usize) {
+        if let Some(index) = self.hnsw.as_mut() {
+            index.mark_deleted(id);
+        }
+    }
+
+    #[cfg(not(feature = "hnsw"))]
+    #[inline]
+    fn hnsw_on_delete(&mut self, _id: usize) {}
+
+    /// Mark the index for rebuild after a mutation that may have changed
+    /// existing embeddings or renumbered ids (in-place update, compaction).
+    #[cfg(feature = "hnsw")]
+    #[inline]
+    fn hnsw_mark_dirty(&mut self) {
+        self.hnsw_dirty = true;
+    }
+
+    #[cfg(not(feature = "hnsw"))]
+    #[inline]
+    fn hnsw_mark_dirty(&mut self) {}
+
     /// Get a reference to the config.
     pub fn config(&self) -> &MemoryConfig {
         &self.config
@@ -374,6 +515,8 @@ impl HDF5Memory {
                 entry.timestamp,
                 entry.session_id,
             );
+            // In-place embedding change: the index node is stale, force rebuild.
+            self.hnsw_mark_dirty();
             let needs_flush = self
                 .wal
                 .as_ref()
@@ -414,6 +557,7 @@ impl AgentMemory for HDF5Memory {
             entry.session_id,
             entry.tags,
         );
+        self.hnsw_on_insert(idx);
         let needs_flush = self
             .wal
             .as_ref()
@@ -440,6 +584,8 @@ impl AgentMemory for HDF5Memory {
             );
             indices.push(idx);
         }
+        // Batch inserts rebuild the index once rather than node-by-node.
+        self.hnsw_mark_dirty();
         self.flush()?;
         Ok(indices)
     }
@@ -450,6 +596,7 @@ impl AgentMemory for HDF5Memory {
                 "entry {id} not found or already deleted"
             )));
         }
+        self.hnsw_on_delete(id);
         self.flush()?;
 
         // Auto-compact if threshold exceeded
@@ -465,6 +612,8 @@ impl AgentMemory for HDF5Memory {
     fn compact(&mut self) -> Result<usize> {
         let (removed, _index_map) = self.cache.compact();
         if removed > 0 {
+            // Compaction renumbers cache indices; rebuild the index to match.
+            self.hnsw_mark_dirty();
             self.flush()?;
         }
         Ok(removed)

crates/clawhdf5-agent/src/search.rs

@@ -7,6 +7,76 @@ use crate::hybrid;
 use crate::{HDF5Memory, MemoryError, Result, SearchResult};
 
 impl HDF5Memory {
+    /// Vector + keyword scoring stage of [`HDF5Memory::hybrid_search`].
+    ///
+    /// Without the `hnsw` feature this is a full linear cosine scan (the exact
+    /// previous behaviour, also used as the correctness oracle in tests). With
+    /// `hnsw` enabled and an index available, the vector candidates come from an
+    /// approximate-nearest-neighbour search over an over-fetched pool, then merge
+    /// with BM25 via the shared [`hybrid::merge_vector_keyword`].
+    #[cfg(feature = "hnsw")]
+    fn vector_keyword_search(
+        &mut self,
+        query_embedding: &[f32],
+        query_text: &str,
+        bm25: &bm25::BM25Index,
+        vector_weight: f32,
+        keyword_weight: f32,
+        k: usize,
+    ) -> Vec<(usize, f32)> {
+        self.ensure_hnsw_fresh();
+        match self.hnsw.as_ref() {
+            Some(index)
+                if !index.is_empty() && index.dimension() == query_embedding.len() =>
+            {
+                // Over-fetch so the merge sees a useful vector pool; cosine
+                // distance from the index converts back to similarity (1 - d).
+                let pool = (k * 8).max(64);
+                let vec_scores: Vec<(usize, f32)> = index
+                    .search(query_embedding, pool, pool)
+                    .into_iter()
+                    .map(|(id, dist)| (id, 1.0 - dist))
+                    .collect();
+                let kw_scores = bm25.search(query_text, self.cache.len());
+                hybrid::merge_vector_keyword(vec_scores, kw_scores, vector_weight, keyword_weight, k)
+            }
+            _ => hybrid::hybrid_search(
+                query_embedding,
+                query_text,
+                &self.cache.embeddings,
+                &self.cache.chunks,
+                &self.cache.tombstones,
+                bm25,
+                vector_weight,
+                keyword_weight,
+                k,
+            ),
+        }
+    }
+
+    #[cfg(not(feature = "hnsw"))]
+    fn vector_keyword_search(
+        &mut self,
+        query_embedding: &[f32],
+        query_text: &str,
+        bm25: &bm25::BM25Index,
+        vector_weight: f32,
+        keyword_weight: f32,
+        k: usize,
+    ) -> Vec<(usize, f32)> {
+        hybrid::hybrid_search(
+            query_embedding,
+            query_text,
+            &self.cache.embeddings,
+            &self.cache.chunks,
+            &self.cache.tombstones,
+            bm25,
+            vector_weight,
+            keyword_weight,
+            k,
+        )
+    }
+
     /// Perform hybrid search combining cosine vector similarity and BM25 keyword search.
     pub fn hybrid_search(
         &mut self,
@@ -17,12 +87,9 @@ impl HDF5Memory {
         k: usize,
     ) -> Vec<SearchResult> {
         let bm25 = bm25::BM25Index::build(&self.cache.chunks, &self.cache.tombstones);
-        let scored = hybrid::hybrid_search(
+        let scored = self.vector_keyword_search(
             query_embedding,
             query_text,
-            &self.cache.embeddings,
-            &self.cache.chunks,
-            &self.cache.tombstones,
             &bm25,
             vector_weight,
             keyword_weight,

crates/clawhdf5-agent/tests/hnsw_integration.rs

@@ -0,0 +1,163 @@
+//! Integration tests for the optional HNSW-accelerated vector search path.
+//!
+//! These only run when the crate is built with `--features hnsw`. They drive the
+//! real `HDF5Memory` API (save / save_batch / delete / hybrid_search) and check
+//! the approximate results against a brute-force cosine oracle, plus confirm that
+//! deletions are honoured end-to-end.
+#![cfg(feature = "hnsw")]
+
+use clawhdf5_agent::{AgentMemory, HDF5Memory, MemoryConfig, MemoryEntry};
+use tempfile::TempDir;
+
+/// Deterministic splitmix64 so tests are reproducible without an RNG crate.
+fn splitmix64(state: &mut u64) -> u64 {
+    *state = state.wrapping_add(0x9e37_79b9_7f4a_7c15);
+    let mut z = *state;
+    z = (z ^ (z >> 30)).wrapping_mul(0xbf58_476d_1ce4_e5b9);
+    z = (z ^ (z >> 27)).wrapping_mul(0x94d0_49bb_1331_11eb);
+    z ^ (z >> 31)
+}
+
+fn make_vector(seed: &mut u64, dim: usize) -> Vec<f32> {
+    (0..dim)
+        .map(|_| (splitmix64(seed) >> 40) as f32 / 16_777_216.0 - 0.5)
+        .collect()
+}
+
+fn cosine(a: &[f32], b: &[f32]) -> f32 {
+    let dot: f32 = a.iter().zip(b).map(|(x, y)| x * y).sum();
+    let na: f32 = a.iter().map(|x| x * x).sum::<f32>().sqrt();
+    let nb: f32 = b.iter().map(|x| x * x).sum::<f32>().sqrt();
+    if na == 0.0 || nb == 0.0 {
+        0.0
+    } else {
+        dot / (na * nb)
+    }
+}
+
+fn entry(chunk: &str, embedding: Vec<f32>, tags: &str) -> MemoryEntry {
+    MemoryEntry {
+        chunk: chunk.to_string(),
+        embedding,
+        source_channel: "test".to_string(),
+        timestamp: 0.0,
+        session_id: "s".to_string(),
+        tags: tags.to_string(),
+    }
+}
+
+fn new_memory(dir: &TempDir, dim: usize) -> HDF5Memory {
+    let config = MemoryConfig::new(dir.path().join("mem.h5"), "agent", dim);
+    HDF5Memory::create(config).unwrap()
+}
+
+#[test]
+fn hnsw_matches_bruteforce_oracle() {
+    let dir = TempDir::new().unwrap();
+    let dim = 16;
+    let n = 250;
+    let mut mem = new_memory(&dir, dim);
+
+    let mut seed = 0xC0FF_EE12_3456_789A;
+    let vectors: Vec<Vec<f32>> = (0..n).map(|_| make_vector(&mut seed, dim)).collect();
+    for (i, v) in vectors.iter().enumerate() {
+        mem.save(entry(&format!("chunk {i}"), v.clone(), &format!("k{i}")))
+            .unwrap();
+    }
+
+    // Vector-only query: keyword weight 0 isolates the HNSW vector stage.
+    let query = make_vector(&mut seed, dim);
+    let k = 10;
+    let results = mem.hybrid_search(&query, "", 1.0, 0.0, k);
+    assert_eq!(results.len(), k, "should return k results");
+
+    // Brute-force cosine top-k oracle.
+    let mut oracle: Vec<(usize, f32)> = vectors
+        .iter()
+        .enumerate()
+        .map(|(i, v)| (i, cosine(&query, v)))
+        .collect();
+    oracle.sort_by(|a, b| b.1.partial_cmp(&a.1).unwrap());
+    let oracle_ids: std::collections::HashSet<usize> =
+        oracle.iter().take(k).map(|(i, _)| *i).collect();
+    let hnsw_ids: std::collections::HashSet<usize> =
+        results.iter().map(|r| r.index).collect();
+
+    let overlap = oracle_ids.intersection(&hnsw_ids).count();
+    assert!(
+        overlap >= 7,
+        "HNSW recall too low vs brute force: {overlap}/{k} (hnsw={hnsw_ids:?})"
+    );
+}
+
+#[test]
+fn deleted_entry_excluded_from_search() {
+    let dir = TempDir::new().unwrap();
+    let dim = 8;
+    let mut mem = new_memory(&dir, dim);
+
+    let mut seed = 42;
+    let vectors: Vec<Vec<f32>> = (0..60).map(|_| make_vector(&mut seed, dim)).collect();
+    for (i, v) in vectors.iter().enumerate() {
+        mem.save(entry(&format!("c{i}"), v.clone(), &format!("t{i}")))
+            .unwrap();
+    }
+
+    // Query exactly equal to vector 5 — it must be the top hit.
+    let query = vectors[5].clone();
+    let top = mem.hybrid_search(&query, "", 1.0, 0.0, 1);
+    assert_eq!(top[0].index, 5, "exact match should rank first");
+
+    mem.delete(5).unwrap();
+
+    let after = mem.hybrid_search(&query, "", 1.0, 0.0, 5);
+    assert!(
+        after.iter().all(|r| r.index != 5),
+        "deleted entry must not appear in results"
+    );
+}
+
+#[test]
+fn incremental_inserts_after_search_are_found() {
+    let dir = TempDir::new().unwrap();
+    let dim = 8;
+    let mut mem = new_memory(&dir, dim);
+
+    let mut seed = 7;
+    // First batch, then a search to force the index to build.
+    for i in 0..40 {
+        let v = make_vector(&mut seed, dim);
+        mem.save(entry(&format!("a{i}"), v, &format!("a{i}"))).unwrap();
+    }
+    let _ = mem.hybrid_search(&make_vector(&mut seed, dim), "", 1.0, 0.0, 5);
+
+    // Now insert a distinctive vector incrementally and confirm we can find it.
+    let needle = vec![10.0f32; dim];
+    let idx = mem
+        .save(entry("needle", needle.clone(), "needle"))
+        .unwrap();
+    let hits = mem.hybrid_search(&needle, "", 1.0, 0.0, 1);
+    assert_eq!(hits[0].index, idx, "incrementally inserted vector must be found");
+}
+
+#[test]
+fn save_batch_then_search_is_consistent() {
+    let dir = TempDir::new().unwrap();
+    let dim = 8;
+    let mut mem = new_memory(&dir, dim);
+
+    let mut seed = 99;
+    let vectors: Vec<Vec<f32>> = (0..50).map(|_| make_vector(&mut seed, dim)).collect();
+    let entries: Vec<MemoryEntry> = vectors
+        .iter()
+        .enumerate()
+        .map(|(i, v)| entry(&format!("b{i}"), v.clone(), &format!("b{i}")))
+        .collect();
+    mem.save_batch(entries).unwrap();
+
+    // Exact-match queries should resolve to themselves after a batch insert.
+    for probe in [0usize, 17, 49] {
+        let hits = mem.hybrid_search(&vectors[probe], "", 1.0, 0.0, 1);
+        assert_eq!(hits[0].index, probe, "batch-inserted vector {probe} not found");
+    }
+}

crates/clawhdf5-ann/src/hnsw.rs

@@ -153,16 +153,30 @@ impl Ord for FarCandidate {
     }
 }
 
+/// On-disk format version for the serialized HNSW index.
+///
+/// - Version 1: original layout (`vectors`, `graph_layer_*`, `config`), no
+///   deletion support and no explicit version tag.
+/// - Version 2: adds a `format_version` attribute and a `deleted` bitset dataset
+///   so live insert/delete state survives a save/load round-trip.
+///
+/// Files written before this constant existed are treated as version 1 on load.
+pub const HNSW_FORMAT_VERSION: i64 = 2;
+
 /// HNSW (Hierarchical Navigable Small World) approximate nearest neighbor index.
 ///
-/// Supports building an index from vectors, searching for nearest neighbors,
-/// and serializing/deserializing to HDF5 format.
+/// Supports building an index from vectors, incremental insertion and soft
+/// deletion, searching for nearest neighbors, and serializing/deserializing to
+/// HDF5 format.
 #[derive(Debug, Clone)]
 pub struct HnswIndex {
     /// All vectors in the index.
     vectors: Vec<Vec<f32>>,
     /// Adjacency lists per layer. `graph[layer][node]` = list of neighbor IDs.
     graph: Vec<Vec<Vec<usize>>>,
+    /// Soft-deletion flags, one per node. Deleted nodes remain in the graph for
+    /// connectivity but are never returned from [`HnswIndex::search`].
+    deleted: Vec<bool>,
     /// Entry point node ID.
     entry_point: usize,
     /// Maximum number of connections per node (per layer).
@@ -291,6 +305,7 @@ impl HnswIndex {
         Self {
             vectors: vectors.to_vec(),
             graph,
+            deleted: vec![false; n],
             entry_point,
             m,
             m_max0,
@@ -300,6 +315,163 @@ impl HnswIndex {
         }
     }
 
+    /// Create an empty index with the given parameters. Used as the starting
+    /// point for incremental [`HnswIndex::insert`] and as the result of
+    /// [`HnswIndex::compact`] when every vector has been deleted.
+    pub fn new(m: usize, ef_construction: usize, metric: DistanceMetric) -> Self {
+        assert!(m >= 2, "m must be at least 2");
+        Self {
+            vectors: Vec::new(),
+            graph: Vec::new(),
+            deleted: Vec::new(),
+            entry_point: 0,
+            m,
+            m_max0: m * 2,
+            ef_construction,
+            node_levels: Vec::new(),
+            metric,
+        }
+    }
+
+    /// Insert a single vector into the index incrementally and return its id.
+    ///
+    /// The id is the vector's position in insertion order and is stable for the
+    /// life of the index (until [`HnswIndex::compact`] renumbers survivors).
+    /// Inserting into an empty index seeds the entry point.
+    ///
+    /// # Panics
+    /// Panics if `vector`'s dimension does not match the existing vectors.
+    pub fn insert(&mut self, vector: Vec<f32>) -> usize {
+        let id = self.vectors.len();
+
+        // Seed an empty index.
+        if id == 0 {
+            let node_level = assign_level(0, self.m);
+            self.vectors.push(vector);
+            self.deleted.push(false);
+            self.node_levels.push(node_level);
+            self.graph = (0..=node_level).map(|_| vec![Vec::new(); 1]).collect();
+            self.entry_point = 0;
+            return 0;
+        }
+
+        assert_eq!(
+            vector.len(),
+            self.vectors[0].len(),
+            "insert dimension mismatch"
+        );
+
+        let node_level = assign_level(id, self.m);
+        self.vectors.push(vector);
+        self.deleted.push(false);
+        self.node_levels.push(node_level);
+
+        // Grow every existing layer with an empty adjacency slot for `id`, and
+        // add any brand-new top layers this node introduces.
+        for layer in self.graph.iter_mut() {
+            layer.push(Vec::new());
+        }
+        while self.graph.len() <= node_level {
+            self.graph.push(vec![Vec::new(); id + 1]);
+        }
+
+        let ep_level = self.node_levels[self.entry_point];
+        let mut ep = self.entry_point;
+
+        // Phase 1: greedy descent from the top down to node_level + 1.
+        for layer in (node_level + 1..=ep_level).rev() {
+            ep = greedy_closest(&self.vectors, &self.graph[layer], &self.vectors[id], ep, self.metric);
+        }
+
+        // Phase 2: search and connect from min(node_level, ep_level) down to 0.
+        let bottom = node_level.min(ep_level);
+        for layer in (0..=bottom).rev() {
+            let max_conn = if layer == 0 { self.m_max0 } else { self.m };
+            let neighbors = search_layer(
+                &self.vectors,
+                &self.graph[layer],
+                &self.vectors[id],
+                ep,
+                self.ef_construction,
+                self.metric,
+            );
+            let selected: Vec<usize> = neighbors.iter().take(max_conn).map(|c| c.id).collect();
+            self.graph[layer][id] = selected.clone();
+            for &neighbor in &selected {
+                self.graph[layer][neighbor].push(id);
+                if self.graph[layer][neighbor].len() > max_conn {
+                    prune_connections(
+                        &self.vectors,
+                        &mut self.graph[layer][neighbor],
+                        neighbor,
+                        max_conn,
+                        self.metric,
+                    );
+                }
+            }
+            if !selected.is_empty() {
+                ep = selected[0];
+            }
+        }
+
+        // Promote the entry point if this node sits on a higher layer.
+        if node_level > ep_level {
+            self.entry_point = id;
+        }
+
+        id
+    }
+
+    /// Soft-delete the vector with the given id. The node stays in the graph so
+    /// traversal/connectivity is preserved, but it will never be returned from
+    /// [`HnswIndex::search`]. Idempotent; out-of-range ids are ignored.
+    ///
+    /// Returns `true` if the id existed and was not already deleted.
+    pub fn mark_deleted(&mut self, id: usize) -> bool {
+        if id >= self.deleted.len() || self.deleted[id] {
+            return false;
+        }
+        self.deleted[id] = true;
+        true
+    }
+
+    /// Returns whether the vector with the given id is soft-deleted.
+    pub fn is_deleted(&self, id: usize) -> bool {
+        self.deleted.get(id).copied().unwrap_or(false)
+    }
+
+    /// Number of soft-deleted vectors still occupying the index.
+    pub fn deleted_count(&self) -> usize {
+        self.deleted.iter().filter(|&&d| d).count()
+    }
+
+    /// Number of live (non-deleted) vectors.
+    pub fn active_len(&self) -> usize {
+        self.vectors.len() - self.deleted_count()
+    }
+
+    /// Rebuild the index from scratch, dropping all soft-deleted vectors and
+    /// renumbering the survivors into a compact `0..active_len` id space.
+    ///
+    /// Returns a mapping from old id to new id (`None` for dropped vectors) so
+    /// callers can rewrite any external id references they keep.
+    pub fn compact(&mut self) -> Vec<Option<usize>> {
+        let mut mapping = vec![None; self.vectors.len()];
+        let mut surviving: Vec<Vec<f32>> = Vec::with_capacity(self.active_len());
+        for (old, v) in self.vectors.iter().enumerate() {
+            if !self.deleted[old] {
+                mapping[old] = Some(surviving.len());
+                surviving.push(v.clone());
+            }
+        }
+        *self = if surviving.is_empty() {
+            Self::new(self.m, self.ef_construction, self.metric)
+        } else {
+            Self::build_with_metric(&surviving, self.m, self.ef_construction, self.metric)
+        };
+        mapping
+    }
+
     /// Search the index for the `k` nearest neighbors to the query vector.
     ///
     /// # Parameters
@@ -328,11 +500,13 @@ impl HnswIndex {
             ep = greedy_closest(&self.vectors, &self.graph[layer], query, ep, self.metric);
         }
 
-        // Search layer 0 with ef candidates
+        // Search layer 0 with ef candidates. Deleted nodes are still traversed
+        // (they remain valid graph waypoints) but are filtered from the result.
         let candidates = search_layer(&self.vectors, &self.graph[0], query, ep, ef, self.metric);
 
         candidates
             .into_iter()
+            .filter(|c| !self.deleted[c.id])
             .take(k)
             .map(|c| (c.id, c.distance))
             .collect()
@@ -388,11 +562,16 @@ impl HnswIndex {
                 .set_attr("layer", AttrValue::I64(layer_idx as i64));
         }
 
+        // Soft-deletion bitset (format version 2+): 0 = live, 1 = deleted.
+        let deleted_i32: Vec<i32> = self.deleted.iter().map(|&d| d as i32).collect();
+        group.create_dataset("deleted").with_i32_data(&deleted_i32);
+
         // Store config as attributes on a small dataset
         let node_levels_i32: Vec<i32> = self.node_levels.iter().map(|&l| l as i32).collect();
         group
             .create_dataset("config")
             .with_i32_data(&node_levels_i32)
+            .set_attr("format_version", AttrValue::I64(HNSW_FORMAT_VERSION))
             .set_attr("m", AttrValue::I64(self.m as i64))
             .set_attr(
                 "ef_construction",
@@ -426,6 +605,15 @@ impl HnswIndex {
         let config_dt = read_dataset_datatype(data, &sb, "ann/config")?;
         let node_levels_i32 = read_as_i32(&config_raw, &config_dt)?;
 
+        // Files written before format version 2 have no version attribute; treat
+        // them as version 1. Reject anything newer than we understand.
+        let format_version = get_attr_i64_opt(&config_attrs, "format_version").unwrap_or(1);
+        if format_version > HNSW_FORMAT_VERSION {
+            return Err(FormatError::SerializationError(format!(
+                "unsupported HNSW format version {format_version} (this build understands up to {HNSW_FORMAT_VERSION})"
+            )));
+        }
+
         let m = get_attr_i64(&config_attrs, "m")? as usize;
         let ef_construction = get_attr_i64(&config_attrs, "ef_construction")? as usize;
         let entry_point = get_attr_i64(&config_attrs, "entry_point")? as usize;
@@ -488,9 +676,22 @@ impl HnswIndex {
             graph.push(layer_graph);
         }
 
+        // Deleted bitset (version 2+). Older files default every node to live.
+        let deleted = if format_version >= 2 {
+            let deleted_raw = read_dataset_raw(data, &sb, "ann/deleted")?;
+            let deleted_dt = read_dataset_datatype(data, &sb, "ann/deleted")?;
+            let deleted_i32 = read_as_i32(&deleted_raw, &deleted_dt)?;
+            let mut deleted: Vec<bool> = deleted_i32.iter().map(|&d| d != 0).collect();
+            deleted.resize(n, false);
+            deleted
+        } else {
+            vec![false; n]
+        };
+
         Ok(Self {
             vectors,
             graph,
+            deleted,
             entry_point,
             m,
             m_max0: m * 2,
@@ -809,6 +1010,16 @@ fn get_attr_i64(attrs: &[(String, AttrValue)], name: &str) -> Result<i64, Format
     )))
 }
 
+/// Like [`get_attr_i64`] but returns `None` when the attribute is absent or not
+/// an integer, instead of erroring. Used for optional/back-compat attributes.
+fn get_attr_i64_opt(attrs: &[(String, AttrValue)], name: &str) -> Option<i64> {
+    attrs.iter().find(|(n, _)| n == name).and_then(|(_, v)| match v {
+        AttrValue::I64(val) => Some(*val),
+        AttrValue::U64(val) => Some(*val as i64),
+        _ => None,
+    })
+}
+
 fn get_attr_string(attrs: &[(String, AttrValue)], name: &str) -> Result<String, FormatError> {
     for (n, v) in attrs {
         if n == name {
@@ -1089,4 +1300,139 @@ mod tests {
         let d = compute_distance(&a, &b, DistanceMetric::Cosine);
         assert!((d - 1.0).abs() < 1e-6); // zero vector -> distance 1
     }
+
+    #[test]
+    fn insert_into_empty_index() {
+        let mut index = HnswIndex::new(4, 16, DistanceMetric::L2);
+        assert!(index.is_empty());
+        let id = index.insert(vec![1.0, 0.0, 0.0]);
+        assert_eq!(id, 0);
+        assert_eq!(index.len(), 1);
+        let results = index.search(&[1.0, 0.0, 0.0], 1, 16);
+        assert_eq!(results, vec![(0, 0.0)]);
+    }
+
+    #[test]
+    fn incremental_insert_matches_batch_recall() {
+        // Build one index incrementally and one in batch from the same vectors,
+        // then confirm the incremental index has acceptable recall vs brute force.
+        let vectors = make_random_vectors(120, 8, 2024);
+        let mut incremental = HnswIndex::new(16, 64, DistanceMetric::L2);
+        for v in &vectors {
+            incremental.insert(v.clone());
+        }
+        assert_eq!(incremental.len(), vectors.len());
+
+        let query = &vectors[60];
+        let k = 10;
+        let results = incremental.search(query, k, 64);
+
+        let mut brute: Vec<(usize, f32)> = vectors
+            .iter()
+            .enumerate()
+            .map(|(i, v)| (i, compute_distance(query, v, DistanceMetric::L2)))
+            .collect();
+        brute.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap());
+        brute.truncate(k);
+
+        let hnsw_ids: HashSet<usize> = results.iter().map(|r| r.0).collect();
+        let brute_ids: HashSet<usize> = brute.iter().map(|r| r.0).collect();
+        let overlap = hnsw_ids.intersection(&brute_ids).count();
+        assert!(
+            overlap >= k * 8 / 10,
+            "incremental HNSW recall too low: {overlap}/{k}"
+        );
+    }
+
+    #[test]
+    fn mark_deleted_excludes_from_search() {
+        let vectors = vec![
+            vec![1.0, 0.0],
+            vec![0.9, 0.1],
+            vec![0.0, 1.0],
+            vec![0.1, 0.9],
+        ];
+        let mut index = HnswIndex::build(&vectors, 4, 16);
+
+        // Exact match on vector 0 before deletion.
+        let before = index.search(&[1.0, 0.0], 1, 16);
+        assert_eq!(before[0].0, 0);
+
+        assert!(index.mark_deleted(0));
+        assert!(index.is_deleted(0));
+        assert!(!index.mark_deleted(0)); // idempotent
+        assert_eq!(index.deleted_count(), 1);
+        assert_eq!(index.active_len(), 3);
+
+        // Vector 0 must no longer be returned; nearest is now vector 1.
+        let after = index.search(&[1.0, 0.0], 2, 16);
+        assert!(after.iter().all(|(id, _)| *id != 0));
+        assert_eq!(after[0].0, 1);
+    }
+
+    #[test]
+    fn compact_drops_deleted_and_renumbers() {
+        let vectors = make_random_vectors(20, 4, 4242);
+        let mut index = HnswIndex::build(&vectors, 8, 32);
+        index.mark_deleted(3);
+        index.mark_deleted(7);
+        index.mark_deleted(11);
+
+        let mapping = index.compact();
+        assert_eq!(mapping.len(), 20);
+        assert_eq!(index.len(), 17);
+        assert_eq!(index.deleted_count(), 0);
+        // Deleted ids map to None; survivors map to a dense 0..17 range.
+        assert!(mapping[3].is_none() && mapping[7].is_none() && mapping[11].is_none());
+        let mut new_ids: Vec<usize> = mapping.iter().filter_map(|m| *m).collect();
+        new_ids.sort_unstable();
+        assert_eq!(new_ids, (0..17).collect::<Vec<_>>());
+    }
+
+    #[test]
+    fn compact_all_deleted_yields_empty_index() {
+        let vectors = make_random_vectors(5, 3, 1);
+        let mut index = HnswIndex::build(&vectors, 4, 16);
+        for i in 0..5 {
+            index.mark_deleted(i);
+        }
+        index.compact();
+        assert!(index.is_empty());
+        assert!(index.search(&[0.0, 0.0, 0.0], 3, 16).is_empty());
+    }
+
+    #[test]
+    fn versioned_roundtrip_preserves_deletions() {
+        let vectors = make_random_vectors(30, 4, 8080);
+        let mut index = HnswIndex::build(&vectors, 6, 24);
+        index.mark_deleted(5);
+        index.mark_deleted(12);
+
+        let bytes = index.to_hdf5_bytes().unwrap();
+        let loaded = HnswIndex::load_from_hdf5(&bytes).unwrap();
+
+        assert_eq!(loaded.len(), index.len());
+        assert!(loaded.is_deleted(5));
+        assert!(loaded.is_deleted(12));
+        assert_eq!(loaded.deleted_count(), 2);
+        // A deleted vector is not returned even after a round-trip.
+        let results = loaded.search(&vectors[5], 5, 24);
+        assert!(results.iter().all(|(id, _)| *id != 5));
+    }
+
+    #[test]
+    fn insert_then_save_load_search() {
+        let mut index = HnswIndex::new(8, 32, DistanceMetric::Cosine);
+        let vectors = make_random_vectors(25, 5, 31337);
+        for v in &vectors {
+            index.insert(v.clone());
+        }
+        let bytes = index.to_hdf5_bytes().unwrap();
+        let loaded = HnswIndex::load_from_hdf5(&bytes).unwrap();
+        assert_eq!(loaded.len(), 25);
+        assert_eq!(loaded.metric(), DistanceMetric::Cosine);
+        let results = loaded.search(&vectors[0], 3, 32);
+        assert_eq!(results.len(), 3);
+        assert_eq!(results[0].0, 0);
+    }
 }

crates/clawhdf5-py/Cargo.toml

@@ -16,8 +16,8 @@ crate-type = ["cdylib", "rlib"]
 [dependencies]
 clawhdf5_rs = { path = "../clawhdf5", version = "2.0.0", package = "clawhdf5" }
 clawhdf5-format = { path = "../clawhdf5-format", version = "2.0.0" }
-pyo3 = "0.23"
-numpy = "0.23"
+pyo3 = "0.28"
+numpy = "0.28"
 
 [features]
 extension-module = ["pyo3/extension-module"]

crates/clawhdf5-py/src/attrs.rs

@@ -44,7 +44,7 @@ impl PyAttrs {
 
 #[pymethods]
 impl PyAttrs {
-    fn __getitem__(&self, py: Python<'_>, key: &str) -> PyResult<PyObject> {
+    fn __getitem__(&self, py: Python<'_>, key: &str) -> PyResult<Py<PyAny>> {
         match &self.inner {
             AttrsInner::Read(map) => match map.get(key) {
                 Some(val) => Ok(attr_value_to_py(py, val)),
@@ -100,7 +100,7 @@ impl PyAttrs {
         }
     }
 
-    fn __iter__(&self, py: Python<'_>) -> PyResult<PyObject> {
+    fn __iter__(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
         let keys = self.keys(py)?;
         let iter = keys.call_method0(py, "__iter__")?;
         Ok(iter)
@@ -112,7 +112,7 @@ impl PyAttrs {
     }
 
     /// Return attribute names as a list.
-    fn keys(&self, py: Python<'_>) -> PyResult<PyObject> {
+    fn keys(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
         let names: Vec<String> = match &self.inner {
             AttrsInner::Read(map) => map.keys().cloned().collect(),
             AttrsInner::Write(store) => store
@@ -127,8 +127,8 @@ impl PyAttrs {
     }
 
     /// Return attribute values as a list.
-    fn values(&self, py: Python<'_>) -> PyResult<PyObject> {
-        let vals: Vec<PyObject> = match &self.inner {
+    fn values(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
+        let vals: Vec<Py<PyAny>> = match &self.inner {
             AttrsInner::Read(map) => map.values().map(|v| attr_value_to_py(py, v)).collect(),
             AttrsInner::Write(store) => store
                 .lock()
@@ -145,8 +145,8 @@ impl PyAttrs {
     }
 
     /// Return attribute (key, value) pairs as a list of tuples.
-    fn items(&self, py: Python<'_>) -> PyResult<PyObject> {
-        let pairs: Vec<(String, PyObject)> = match &self.inner {
+    fn items(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
+        let pairs: Vec<(String, Py<PyAny>)> = match &self.inner {
             AttrsInner::Read(map) => map
                 .iter()
                 .map(|(k, v)| (k.clone(), attr_value_to_py(py, v)))

crates/clawhdf5-py/src/dataset.rs

@@ -65,7 +65,7 @@ fn dtype_to_numpy_str(dt: &DType) -> &'static str {
 impl PyDataset {
     /// The shape of the dataset as a tuple.
     #[getter]
-    fn shape(&self, py: Python<'_>) -> PyResult<PyObject> {
+    fn shape(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
         let tuple = pyo3::types::PyTuple::new(py, self.cached_shape.iter().map(|&d| d as usize))?;
         Ok(tuple.into_any().unbind())
     }
@@ -88,7 +88,7 @@ impl PyDataset {
     ///
     /// The full dataset is always read from the underlying file; the index
     /// is then applied on the resulting numpy array.
-    fn __getitem__<'py>(&self, py: Python<'py>, key: &Bound<'py, PyAny>) -> PyResult<PyObject> {
+    fn __getitem__<'py>(&self, py: Python<'py>, key: &Bound<'py, PyAny>) -> PyResult<Py<PyAny>> {
         let arr = self.read_as_numpy(py)?;
         let indexed = arr.get_item(key)?;
         Ok(indexed.unbind())
@@ -112,7 +112,7 @@ impl PyDataset {
     /// Read the full dataset and return it as a numpy array (or list for strings).
     ///
     /// For numeric types, the Rust I/O (file reading + decompression) is
-    /// performed inside `py.allow_threads()` so that the GIL is released
+    /// performed inside `py.detach()` so that the GIL is released
     /// during the potentially expensive operation.  The numpy array
     /// construction still happens with the GIL held.
     fn read_as_numpy<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
@@ -123,7 +123,7 @@ impl PyDataset {
         match &self.cached_dtype {
             DType::F64 => {
                 let data = py
-                    .allow_threads(|| file.dataset(path).and_then(|ds| ds.read_f64()))
+                    .detach(|| file.dataset(path).and_then(|ds| ds.read_f64()))
                     .map_err(to_py_err)?;
                 let nd = ArrayD::from_shape_vec(IxDyn(&shape), data)
                     .map_err(|e| PyErr::new::<pyo3::exceptions::PyValueError, _>(e.to_string()))?;
@@ -132,7 +132,7 @@ impl PyDataset {
             }
             DType::F32 => {
                 let data = py
-                    .allow_threads(|| file.dataset(path).and_then(|ds| ds.read_f32()))
+                    .detach(|| file.dataset(path).and_then(|ds| ds.read_f32()))
                     .map_err(to_py_err)?;
                 let nd = ArrayD::from_shape_vec(IxDyn(&shape), data)
                     .map_err(|e| PyErr::new::<pyo3::exceptions::PyValueError, _>(e.to_string()))?;
@@ -141,7 +141,7 @@ impl PyDataset {
             }
             DType::I32 => {
                 let data = py
-                    .allow_threads(|| file.dataset(path).and_then(|ds| ds.read_i32()))
+                    .detach(|| file.dataset(path).and_then(|ds| ds.read_i32()))
                     .map_err(to_py_err)?;
                 let nd = ArrayD::from_shape_vec(IxDyn(&shape), data)
                     .map_err(|e| PyErr::new::<pyo3::exceptions::PyValueError, _>(e.to_string()))?;
@@ -150,7 +150,7 @@ impl PyDataset {
             }
             DType::I64 => {
                 let data = py
-                    .allow_threads(|| file.dataset(path).and_then(|ds| ds.read_i64()))
+                    .detach(|| file.dataset(path).and_then(|ds| ds.read_i64()))
                     .map_err(to_py_err)?;
                 let nd = ArrayD::from_shape_vec(IxDyn(&shape), data)
                     .map_err(|e| PyErr::new::<pyo3::exceptions::PyValueError, _>(e.to_string()))?;
@@ -161,7 +161,7 @@ impl PyDataset {
                 // Try zero-copy first (contiguous layout), fall back to
                 // read_u64 + cast for chunked/compact datasets.
                 let data: Vec<u8> = py
-                    .allow_threads(|| {
+                    .detach(|| {
                         let ds = file.dataset(path)?;
                         match ds.read_u8_zerocopy() {
                             Ok(slice) => Ok(slice.to_vec()),
@@ -179,7 +179,7 @@ impl PyDataset {
             }
             DType::U64 => {
                 let data = py
-                    .allow_threads(|| file.dataset(path).and_then(|ds| ds.read_u64()))
+                    .detach(|| file.dataset(path).and_then(|ds| ds.read_u64()))
                     .map_err(to_py_err)?;
                 let nd = ArrayD::from_shape_vec(IxDyn(&shape), data)
                     .map_err(|e| PyErr::new::<pyo3::exceptions::PyValueError, _>(e.to_string()))?;
@@ -190,7 +190,7 @@ impl PyDataset {
                 // String reads need the GIL for PyList construction, but we
                 // release it during the Rust I/O portion.
                 let data = py
-                    .allow_threads(|| file.dataset(path).and_then(|ds| ds.read_string()))
+                    .detach(|| file.dataset(path).and_then(|ds| ds.read_string()))
                     .map_err(to_py_err)?;
                 let list = PyList::new(py, &data)?;
                 Ok(list.into_any())

crates/clawhdf5-py/src/file.rs

@@ -102,7 +102,7 @@ impl PyFile {
     }
 
     /// Get a child object (dataset or group) by path.
-    fn __getitem__(&self, py: Python<'_>, key: &str) -> PyResult<PyObject> {
+    fn __getitem__(&self, py: Python<'_>, key: &str) -> PyResult<Py<PyAny>> {
         let file = self.read_file()?;
         // Try dataset first
         match file.dataset(key) {
@@ -130,7 +130,7 @@ impl PyFile {
     }
 
     /// List the names of all children in the root group.
-    fn keys(&self, py: Python<'_>) -> PyResult<PyObject> {
+    fn keys(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
         let file = self.read_file()?;
         let root = file.root();
         let mut names = root.datasets().map_err(to_py_err)?;
@@ -175,7 +175,7 @@ impl PyFile {
     }
 
     /// Create a group (write mode only). Returns a `Group` handle.
-    fn create_group(&mut self, py: Python<'_>, name: &str) -> PyResult<PyObject> {
+    fn create_group(&mut self, py: Python<'_>, name: &str) -> PyResult<Py<PyAny>> {
         let state = self.write_state_mut()?;
         let group_state = Arc::new(Mutex::new(WriteGroupState {
             name: name.to_string(),

crates/clawhdf5-py/src/group.rs

@@ -57,7 +57,7 @@ impl PyGroup {
 #[pymethods]
 impl PyGroup {
     /// Get a child object (dataset or subgroup) by name or path.
-    fn __getitem__(&self, py: Python<'_>, key: &str) -> PyResult<PyObject> {
+    fn __getitem__(&self, py: Python<'_>, key: &str) -> PyResult<Py<PyAny>> {
         match &self.inner {
             GroupInner::Read { file, path } => {
                 let full_path = if path.is_empty() {
@@ -96,7 +96,7 @@ impl PyGroup {
     }
 
     /// List the names of all children (datasets and subgroups).
-    fn keys(&self, py: Python<'_>) -> PyResult<PyObject> {
+    fn keys(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
         match &self.inner {
             GroupInner::Read { file, path } => {
                 let group = if path.is_empty() {

crates/clawhdf5-py/src/lib.rs

@@ -114,7 +114,7 @@ pub(crate) fn py_to_attr_value(val: &Bound<'_, PyAny>) -> PyResult<OwnedAttrValu
 }
 
 /// Convert an `AttrValue` (from the Rust lib) to a Python object.
-pub(crate) fn attr_value_to_py(py: Python<'_>, val: &clawhdf5_rs::AttrValue) -> PyObject {
+pub(crate) fn attr_value_to_py(py: Python<'_>, val: &clawhdf5_rs::AttrValue) -> Py<PyAny> {
     match val {
         clawhdf5_rs::AttrValue::F64(v) => v.into_pyobject(py).unwrap().into_any().unbind(),
         clawhdf5_rs::AttrValue::I64(v) => v.into_pyobject(py).unwrap().into_any().unbind(),