fix: preserve seeded IVF-PQ training contracts

<!-- lance-gatekeeper-fix:v1 agent=5c80c44c083b3b8ad0da595419d468fc
generation=1 -->

## Root cause

The legacy synchronous Python table called `delete` on a shared, mutable
`lance.Dataset`. Concurrent table operations could hold a PyO3 borrow
while delete requested an exclusive borrow, producing `RuntimeError:
Already borrowed`. The current async-backed binding fixes this by
cloning its thread-safe Rust table handle before awaiting, but that
concurrency contract had no regression coverage.

## Fix

- Document why delete must clone the Rust table handle before entering
its async future.
- Add a barrier-synchronized regression test that deletes distinct rows
through one shared table from eight Python threads.
- Verify every delete commits exactly one row, every commit gets a
distinct version, and no rows remain.

## Validation

- `cargo check --quiet --features remote --tests --examples`
- `cargo fmt --all -- --check`
- `uv run --extra tests --extra dev ruff format --check
python/tests/test_table.py`
- `uv run --extra tests --extra dev ruff check
python/tests/test_table.py`
- `uv run --extra tests --extra dev pytest
python/tests/test_table.py::test_concurrent_deletes_are_thread_safe
python/tests/test_table.py::test_delete
python/tests/test_table.py::test_delete_expr
python/tests/test_table.py::test_delete_expr_async -q` (4 passed)
- Manual stress reproduction: 100 concurrent deletes on one table
completed at versions 2–101 with zero rows remaining.

Fixes #530

Co-authored-by: Gatefixer <313497061+lancedb-gatefixer[bot]@users.noreply.github.com>

Cargo.lock

@@ -5442,6 +5442,7 @@ dependencies = [
  "pprof 0.14.1",
  "rand 0.9.5",
  "random_word",
+ "rayon",
  "regex",
  "reqwest 0.12.28",
  "rstest",
@@ -7583,7 +7584,7 @@ version = "0.14.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "343d3bd7056eda839b03204e68deff7d1b13aba7af2b2fd16890697274262ee7"
 dependencies = [
- "heck 0.5.0",
+ "heck 0.4.1",
  "itertools 0.14.0",
  "log",
  "multimap",
@@ -8498,9 +8499,9 @@ dependencies = [
 
 [[package]]
 name = "rkyv"
-version = "0.8.16"
+version = "0.8.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "73389e0c99e664f919275ab5b5b0471391fe9a8de61e1dff9b1eaf56a90f16e3"
+checksum = "815cc8a37159a463064825246cadb07961e25cd9885908606f6d08a98d8f8874"
 dependencies = [
  "bytecheck",
  "bytes",
@@ -8517,9 +8518,9 @@ dependencies = [
 
 [[package]]
 name = "rkyv_derive"
-version = "0.8.16"
+version = "0.8.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5d2ed0b54125315fb36bd021e82d314d1c126548f871634b483f46b31d13cac6"
+checksum = "c0ed1a78a1b19d184b0daa629dd9a024573173ec7d485b287cb369fb3607cc1c"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -9277,7 +9278,7 @@ version = "0.8.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c1c97747dbf44bb1ca44a561ece23508e99cb592e862f22222dcf42f51d1e451"
 dependencies = [
- "heck 0.5.0",
+ "heck 0.4.1",
  "proc-macro2",
  "quote",
  "syn 2.0.117",
@@ -9289,7 +9290,7 @@ version = "0.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "54254b8531cafa275c5e096f62d48c81435d1015405a91198ddb11e967301d40"
 dependencies = [
- "heck 0.5.0",
+ "heck 0.4.1",
  "proc-macro2",
  "quote",
  "syn 2.0.117",
@@ -9730,7 +9731,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32497e9a4c7b38532efcdebeef879707aa9f794296a4f0244f6f69e9bc8574bd"
 dependencies = [
  "fastrand",
- "getrandom 0.4.2",
+ "getrandom 0.3.4",
  "once_cell",
  "rustix",
  "windows-sys 0.61.2",

Cargo.toml

@@ -60,6 +60,7 @@ moka = { version = "0.12", features = ["future"] }
 object_store = "0.13.2"
 pin-project = "1.0.7"
 rand = "0.9"
+rayon = "1"
 snafu = "0.8"
 url = "2"
 num-traits = "0.2"

nodejs/src/table.rs

@@ -339,7 +339,9 @@ impl Table {
         let transforms = NewColumnTransform::SqlExpressions(transforms);
         let res = self
             .inner_ref()?
-            .add_columns(transforms, None)
+            .add_columns()
+            .transform(transforms)
+            .execute()
             .await
             .default_error()?;
         Ok(res.into())
@@ -356,7 +358,9 @@ impl Table {
         let transforms = NewColumnTransform::AllNulls(schema);
         let res = self
             .inner_ref()?
-            .add_columns(transforms, None)
+            .add_columns()
+            .transform(transforms)
+            .execute()
             .await
             .default_error()?;
         Ok(res.into())

python/python/lancedb/db.py

@@ -707,6 +707,9 @@ class LanceDBConnection(DBConnection):
         self._namespace_client_properties = namespace_client_properties
         if _inner is not None:
             self._conn = _inner
+            # Native-derived wrappers resolve this in their async reconstruction
+            # path so construction never synchronously re-enters LOOP.
+            self._read_consistency_interval = read_consistency_interval
             self._cached_namespace_client = None
             return
 
@@ -756,11 +759,14 @@ class LanceDBConnection(DBConnection):
         # storage_options.  Also, this class really shouldn't be holding any state
         # beyond _conn.
         self._conn = AsyncConnection(LOOP.run(do_connect()))
+        # Keep property access synchronous so debugger introspection cannot wait on
+        # the background loop while that thread is suspended at a breakpoint.
+        self._read_consistency_interval = read_consistency_interval
         self._cached_namespace_client: Optional[LanceNamespace] = None
 
     @property
     def read_consistency_interval(self) -> Optional[timedelta]:
-        return LOOP.run(self._conn.get_read_consistency_interval())
+        return self._read_consistency_interval
 
     @property
     def session(self) -> Optional[Session]:
@@ -771,8 +777,16 @@ class LanceDBConnection(DBConnection):
         return self._conn.uri
 
     @classmethod
-    def from_inner(cls, inner: LanceDbConnection):
-        return cls(None, _inner=inner)
+    def from_inner(
+        cls,
+        inner: LanceDbConnection,
+        read_consistency_interval: Optional[timedelta],
+    ):
+        return cls(
+            None,
+            read_consistency_interval=read_consistency_interval,
+            _inner=inner,
+        )
 
     def __repr__(self) -> str:
         return f"{self.__class__.__name__}(uri={self._conn.uri!r})"

python/python/lancedb/index.py

@@ -769,6 +769,13 @@ class IvfPq:
 
         The default value is 256.
 
+    seed: int, optional
+        Seed used for deterministic sampling and training. Given identical data in
+        the same row order and identical index parameters, the same seed produces
+        the same IVF centroids and PQ codebook. This option is supported for local
+        CPU index builds; remote and accelerator builds reject it explicitly. If
+        omitted, training remains random.
+
     target_partition_size: int, default is 8192
 
         The target size of each partition.
@@ -783,11 +790,18 @@ class IvfPq:
     num_bits: int = 8
     max_iterations: int = 50
     sample_rate: int = 256
+    seed: Optional[int] = None
     target_partition_size: Optional[int] = None
     # Name of the accelerator (e.g. "cuda") to use for IVF training. When set,
     # create_index() dispatches to pylance to build the index on the accelerator.
     accelerator: Optional[str] = None
 
+    def __post_init__(self):
+        if self.seed is not None and self.accelerator is not None:
+            raise ValueError(
+                "IvfPq seed is not supported with accelerator-based index training"
+            )
+
 
 @dataclass
 class IvfRq:

python/python/lancedb/permutation.py

@@ -226,7 +226,7 @@ class PermutationBuilder:
 
         async def do_execute():
             inner_tbl = await self._async.execute()
-            return LanceTable.from_inner(inner_tbl)
+            return await LanceTable.from_inner(inner_tbl)
 
         return LOOP.run(do_execute())
 

python/python/lancedb/table.py

@@ -2182,11 +2182,15 @@ class LanceTable(Table):
         return self.name
 
     @classmethod
-    def from_inner(cls, tbl: LanceDBTable):
-        from .db import LanceDBConnection
+    async def from_inner(cls, tbl: LanceDBTable):
+        from .db import AsyncConnection, LanceDBConnection
 
         async_tbl = AsyncTable(tbl)
-        conn = LanceDBConnection.from_inner(tbl.database())
+        inner_conn = tbl.database()
+        read_consistency_interval = await AsyncConnection(
+            inner_conn
+        ).get_read_consistency_interval()
+        conn = LanceDBConnection.from_inner(inner_conn, read_consistency_interval)
         return cls(
             conn,
             async_tbl.name,
@@ -2758,6 +2762,11 @@ class LanceTable(Table):
             if config is not None and hasattr(config, "accelerator"):
                 acc = getattr(config, "accelerator", None)
                 if acc is not None:
+                    if isinstance(config, IvfPq) and config.seed is not None:
+                        raise ValueError(
+                            "IvfPq seed is not supported with accelerator-based "
+                            "index training"
+                        )
                     # Dispatch to pylance for GPU acceleration
                     index_type_map = {
                         "IvfFlat": "IVF_FLAT",

python/python/tests/test_db.py

@@ -77,6 +77,23 @@ def test_sync_repr_does_not_use_background_loop(tmp_path, monkeypatch):
     assert repr(table) == f"LanceTable(name='test', _conn={db!r})"
 
 
+def test_read_consistency_interval_does_not_use_background_loop(tmp_path, monkeypatch):
+    from lancedb.background_loop import LOOP
+    from lancedb.db import LanceDBConnection
+
+    consistency_interval = timedelta(seconds=5)
+    db = lancedb.connect(tmp_path, read_consistency_interval=consistency_interval)
+    db_from_inner = LanceDBConnection.from_inner(db._inner, consistency_interval)
+
+    def fail_run(*args, **kwargs):
+        raise AssertionError("properties should not use the Python background loop")
+
+    monkeypatch.setattr(LOOP, "run", fail_run)
+
+    assert db.read_consistency_interval == consistency_interval
+    assert db_from_inner.read_consistency_interval == consistency_interval
+
+
 def test_ingest_pd(tmp_path):
     db = lancedb.connect(tmp_path)
 

python/python/tests/test_index.py

@@ -26,7 +26,7 @@ from lancedb.index import (
     HnswFlat,
     FTS,
 )
-from lancedb.table import IndexStatistics
+from lancedb.table import IndexStatistics, LanceTable
 
 
 @pytest_asyncio.fixture
@@ -375,7 +375,7 @@ async def test_create_vector_index(some_table: AsyncTable):
 @pytest.mark.asyncio
 async def test_create_4bit_ivfpq_index(some_table: AsyncTable):
     # Can create
-    await some_table.create_index("vector", config=IvfPq(num_bits=4))
+    await some_table.create_index("vector", config=IvfPq(num_bits=4, seed=42))
     # Can recreate if replace=True
     await some_table.create_index("vector", config=IvfPq(num_bits=4), replace=True)
     # Can't recreate if replace=False
@@ -395,6 +395,16 @@ async def test_create_4bit_ivfpq_index(some_table: AsyncTable):
     assert stats.num_indices == 1
 
 
+def test_seeded_ivfpq_rejects_accelerator():
+    with pytest.raises(ValueError, match="seed is not supported with accelerator"):
+        IvfPq(seed=42, accelerator="cuda")
+
+    config = IvfPq(seed=42)
+    config.accelerator = "cuda"
+    with pytest.raises(ValueError, match="seed is not supported with accelerator"):
+        object.__new__(LanceTable).create_index("vector", config=config)
+
+
 @pytest.mark.asyncio
 async def test_create_ivfrq_index(some_table: AsyncTable):
     await some_table.create_index("vector", config=IvfRq(num_bits=1))

python/python/tests/test_permutation.py

@@ -6,6 +6,7 @@ import math
 import pytest
 
 from lancedb import DBConnection, Table, connect
+from lancedb.background_loop import LOOP
 from lancedb.permutation import Permutation, Permutations, permutation_builder
 
 
@@ -31,6 +32,25 @@ def test_split_random_ratios(mem_db):
     assert 65 <= split_1_count <= 75  # ~70% ± tolerance
 
 
+def test_execute_does_not_reenter_background_loop(tmp_path, monkeypatch):
+    import threading
+
+    db = connect(tmp_path)
+    tbl = db.create_table("test_table", pa.table({"x": range(10)}))
+    original_run = LOOP.run
+
+    def fail_on_reentry(future):
+        assert threading.current_thread() is not LOOP.thread
+        return original_run(future)
+
+    monkeypatch.setattr(LOOP, "run", fail_on_reentry)
+
+    permutation_tbl = permutation_builder(tbl).execute()
+
+    assert permutation_tbl.count_rows() == 10
+    assert permutation_tbl._conn.read_consistency_interval is None
+
+
 def test_split_random_counts(mem_db):
     """Test random splitting with absolute counts."""
     tbl = mem_db.create_table(

python/python/tests/test_table.py

@@ -6,6 +6,7 @@ import os
 import sys
 import threading
 import warnings
+from concurrent.futures import ThreadPoolExecutor
 from datetime import date, datetime, timedelta
 from time import sleep
 from typing import List
@@ -2124,6 +2125,27 @@ def test_delete(mem_db: DBConnection):
     assert table.to_arrow()["id"].to_pylist() == [1]
 
 
+def test_concurrent_deletes_are_thread_safe(mem_db: DBConnection):
+    num_workers = 8
+    table = mem_db.create_table(
+        "my_table", data=[{"id": row_id} for row_id in range(num_workers)]
+    )
+    barrier = threading.Barrier(num_workers)
+
+    def delete(row_id: int):
+        barrier.wait()
+        return table.delete(f"id = {row_id}")
+
+    with ThreadPoolExecutor(max_workers=num_workers) as pool:
+        results = list(pool.map(delete, range(num_workers)))
+
+    assert all(result.num_deleted_rows == 1 for result in results)
+    assert sorted(result.version for result in results) == list(
+        range(2, num_workers + 2)
+    )
+    assert table.count_rows() == 0
+
+
 def test_delete_expr(mem_db: DBConnection):
     table = mem_db.create_table(
         "my_table",

python/src/index.rs

@@ -90,6 +90,9 @@ pub fn extract_index_params(source: &Option<Bound<'_, PyAny>>) -> PyResult<Lance
                     .max_iterations(params.max_iterations)
                     .sample_rate(params.sample_rate)
                     .num_bits(params.num_bits);
+                if let Some(seed) = params.seed {
+                    ivf_pq_builder = ivf_pq_builder.seed(seed);
+                }
                 if let Some(num_partitions) = params.num_partitions {
                     ivf_pq_builder = ivf_pq_builder.num_partitions(num_partitions);
                 }
@@ -232,6 +235,7 @@ struct IvfPqParams {
     num_bits: u32,
     max_iterations: u32,
     sample_rate: u32,
+    seed: Option<u64>,
     target_partition_size: Option<u32>,
 }
 

python/src/table.rs

@@ -745,6 +745,9 @@ impl Table {
 
     #[allow(private_interfaces)]
     pub fn delete(self_: PyRef<'_, Self>, condition: PredicateArg) -> PyResult<Bound<'_, PyAny>> {
+        // Do not hold the Python borrow across the await.  The cloned Rust table
+        // handle is thread-safe and allows deletes on the same Python table to
+        // run concurrently without PyO3 reporting "Already borrowed".
         let inner = self_.inner_ref()?.clone();
         future_into_py(self_.py(), async move {
             let result = match &condition {
@@ -1375,7 +1378,12 @@ impl Table {
 
         let inner = self_.inner_ref()?.clone();
         future_into_py(self_.py(), async move {
-            let result = inner.add_columns(definitions, None).await.infer_error()?;
+            let result = inner
+                .add_columns()
+                .transform(definitions)
+                .execute()
+                .await
+                .infer_error()?;
             Ok(AddColumnsResult::from(result))
         })
     }
@@ -1389,7 +1397,12 @@ impl Table {
 
         let inner = self_.inner_ref()?.clone();
         future_into_py(self_.py(), async move {
-            let result = inner.add_columns(transform, None).await.infer_error()?;
+            let result = inner
+                .add_columns()
+                .transform(transform)
+                .execute()
+                .await
+                .infer_error()?;
             Ok(AddColumnsResult::from(result))
         })
     }

rust/lancedb/Cargo.toml

@@ -61,6 +61,7 @@ futures.workspace = true
 num-traits.workspace = true
 url.workspace = true
 rand.workspace = true
+rayon.workspace = true
 regex.workspace = true
 serde = { version = "^1" }
 serde_json = { version = "1" }

rust/lancedb/src/index/vector.rs

@@ -274,6 +274,8 @@ pub struct IvfPqIndexBuilder {
     pub(crate) sample_rate: u32,
     pub(crate) max_iterations: u32,
     #[serde(skip_serializing_if = "Option::is_none")]
+    pub(crate) seed: Option<u64>,
+    #[serde(skip_serializing_if = "Option::is_none")]
     pub(crate) target_partition_size: Option<u32>,
 
     // PQ
@@ -292,6 +294,7 @@ impl Default for IvfPqIndexBuilder {
             num_bits: None,
             sample_rate: 256,
             max_iterations: 50,
+            seed: None,
             target_partition_size: None,
         }
     }
@@ -301,6 +304,30 @@ impl IvfPqIndexBuilder {
     impl_distance_type_setter!();
     impl_ivf_params_setter!();
     impl_pq_params_setter!();
+
+    /// Use a deterministic seed when sampling and training the IVF and PQ models.
+    ///
+    /// Given identical data in the same row order and identical index parameters,
+    /// using the same seed produces the same IVF centroids and PQ codebook. This is
+    /// useful when independently-built tables need reproducible approximate-search
+    /// results.
+    ///
+    /// Seeded training is supported by native tables. Remote backends reject this
+    /// option unless they can provide the same deterministic training contract.
+    ///
+    /// If no seed is provided, index training uses random sampling and initialization.
+    ///
+    /// # Examples
+    ///
+    /// ```
+    /// use lancedb::index::vector::IvfPqIndexBuilder;
+    ///
+    /// let index = IvfPqIndexBuilder::default().seed(42);
+    /// ```
+    pub fn seed(mut self, seed: u64) -> Self {
+        self.seed = Some(seed);
+        self
+    }
 }
 
 pub(crate) fn suggested_num_sub_vectors(dim: u32) -> u32 {

rust/lancedb/src/remote/table.rs

@@ -339,6 +339,12 @@ impl<S: HttpSend> RemoteTable<S> {
         // Auto is special-cased since it needs schema inspection.
         let (index_type_str, params) = match &index.index {
             Index::IvfFlat(p) => ("IVF_FLAT", Some(to_json(p)?)),
+            Index::IvfPq(p) if p.seed.is_some() => {
+                return Err(Error::NotSupported {
+                    message: "Deterministic IVF PQ training is not supported on remote tables"
+                        .to_string(),
+                });
+            }
             Index::IvfPq(p) => ("IVF_PQ", Some(to_json(p)?)),
             Index::IvfSq(p) => ("IVF_SQ", Some(to_json(p)?)),
             Index::IvfHnswSq(p) => ("IVF_HNSW_SQ", Some(to_json(p)?)),
@@ -3089,10 +3095,12 @@ mod tests {
             Box::pin(table.delete("false").map_ok(|_| ())),
             Box::pin(
                 table
-                    .add_columns(
-                        NewColumnTransform::SqlExpressions(vec![("x".into(), "y".into())]),
-                        None,
-                    )
+                    .add_columns()
+                    .transform(NewColumnTransform::SqlExpressions(vec![(
+                        "x".into(),
+                        "y".into(),
+                    )]))
+                    .execute()
                     .map_ok(|_| ()),
             ),
             Box::pin(async {
@@ -5155,6 +5163,41 @@ mod tests {
         }
     }
 
+    #[tokio::test]
+    async fn test_seeded_ivf_pq_is_rejected_for_remote_tables() {
+        let table = Table::new_with_handler("my_table", |request| match request.url().path() {
+            "/v1/table/my_table/describe/" => {
+                let schema = Schema::new(vec![Field::new(
+                    "vector",
+                    DataType::FixedSizeList(
+                        Arc::new(Field::new("item", DataType::Float32, true)),
+                        8,
+                    ),
+                    false,
+                )]);
+                http::Response::builder()
+                    .status(200)
+                    .body(describe_response(&schema))
+                    .unwrap()
+            }
+            path => panic!("Unexpected request for unsupported seeded index: {path}"),
+        });
+
+        let error = table
+            .create_index(
+                &["vector"],
+                Index::IvfPq(IvfPqIndexBuilder::default().seed(42)),
+            )
+            .execute()
+            .await
+            .unwrap_err();
+        assert!(matches!(
+            error,
+            Error::NotSupported { message }
+                if message.contains("not supported on remote tables")
+        ));
+    }
+
     #[tokio::test]
     async fn test_create_index_returns_job() {
         let describe_calls = std::sync::Arc::new(std::sync::atomic::AtomicUsize::new(0));
@@ -6388,13 +6431,12 @@ mod tests {
         });
 
         let result = table
-            .add_columns(
-                NewColumnTransform::SqlExpressions(vec![
-                    ("b".into(), "a + 1".into()),
-                    ("x".into(), "cast(NULL as int32)".into()),
-                ]),
-                None,
-            )
+            .add_columns()
+            .transform(NewColumnTransform::SqlExpressions(vec![
+                ("b".into(), "a + 1".into()),
+                ("x".into(), "cast(NULL as int32)".into()),
+            ]))
+            .execute()
             .await
             .unwrap();
 
@@ -7119,10 +7161,12 @@ mod tests {
             }
             "add_columns" => {
                 let _ = table
-                    .add_columns(
-                        NewColumnTransform::SqlExpressions(vec![("c".into(), "a + 1".into())]),
-                        None,
-                    )
+                    .add_columns()
+                    .transform(NewColumnTransform::SqlExpressions(vec![(
+                        "c".into(),
+                        "a + 1".into(),
+                    )]))
+                    .execute()
                     .await;
             }
             "drop_columns" => {
@@ -9880,10 +9924,12 @@ mod tests {
             .await
             .unwrap();
         branch
-            .add_columns(
-                NewColumnTransform::SqlExpressions(vec![("b".into(), "a + 1".into())]),
-                None,
-            )
+            .add_columns()
+            .transform(NewColumnTransform::SqlExpressions(vec![(
+                "b".into(),
+                "a + 1".into(),
+            )]))
+            .execute()
             .await
             .unwrap();
         branch

rust/lancedb/src/table.rs

@@ -65,6 +65,7 @@ use crate::utils::{PatchReadParam, PatchWriteParam, resolve_arrow_field_path};
 use self::dataset::DatasetConsistencyWrapper;
 use self::merge::MergeInsertBuilder;
 
+pub mod add_columns;
 mod add_data;
 pub mod branch_merge;
 mod create_index;
@@ -79,6 +80,7 @@ pub mod schema_evolution;
 pub mod update;
 pub mod write_progress;
 use crate::index::waiter::wait_for_index;
+pub use add_columns::AddColumnsBuilder;
 #[cfg(feature = "remote")]
 pub(crate) use add_data::PreprocessingOutput;
 pub use add_data::{AddDataBuilder, AddDataMode, AddResult, NaNVectorBehavior};
@@ -1620,12 +1622,8 @@ impl Table {
     }
 
     /// Add new columns to the table, providing values to fill in.
-    pub async fn add_columns(
-        &self,
-        transforms: NewColumnTransform,
-        read_columns: Option<Vec<String>>,
-    ) -> Result<AddColumnsResult> {
-        self.inner.add_columns(transforms, read_columns).await
+    pub fn add_columns(&self) -> AddColumnsBuilder {
+        AddColumnsBuilder::new(self.inner.clone())
     }
 
     /// Change a column's name or nullability.

rust/lancedb/src/table/add_columns.rs

@@ -0,0 +1,161 @@
+// SPDX-License-Identifier: Apache-2.0
+// SPDX-FileCopyrightText: Copyright The LanceDB Authors
+
+//! Builder for adding columns to a table.
+
+use std::sync::Arc;
+
+use lance::dataset::NewColumnTransform;
+
+use super::BaseTable;
+use super::schema_evolution::AddColumnsResult;
+use crate::{Error, Result};
+
+/// Adds columns to a table. See [`Table::add_columns`](super::Table::add_columns).
+pub struct AddColumnsBuilder {
+    parent: Arc<dyn BaseTable>,
+    transform: Option<NewColumnTransform>,
+    read_columns: Option<Vec<String>>,
+}
+
+impl std::fmt::Debug for AddColumnsBuilder {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        f.debug_struct("AddColumnsBuilder")
+            .field("parent", &self.parent)
+            .field("has_transform", &self.transform.is_some())
+            .field("read_columns", &self.read_columns)
+            .finish()
+    }
+}
+
+impl AddColumnsBuilder {
+    pub(crate) fn new(parent: Arc<dyn BaseTable>) -> Self {
+        Self {
+            parent,
+            transform: None,
+            read_columns: None,
+        }
+    }
+
+    /// Set how the new columns' values are produced. Required.
+    pub fn transform(mut self, transform: NewColumnTransform) -> Self {
+        self.transform = Some(transform);
+        self
+    }
+
+    /// Limit which existing columns a [`NewColumnTransform::BatchUDF`] mapper
+    /// receives. Every other transform determines what it reads, so setting
+    /// this alongside one is an error rather than a silent no-op.
+    pub fn read_columns(mut self, columns: impl IntoIterator<Item = impl Into<String>>) -> Self {
+        self.read_columns = Some(columns.into_iter().map(Into::into).collect());
+        self
+    }
+
+    /// Add the columns.
+    pub async fn execute(self) -> Result<AddColumnsResult> {
+        let Self {
+            parent,
+            transform,
+            read_columns,
+        } = self;
+
+        let Some(transform) = transform else {
+            return Err(Error::InvalidInput {
+                message: "add_columns requires a transform".into(),
+            });
+        };
+
+        if read_columns.is_some() && !matches!(transform, NewColumnTransform::BatchUDF(_)) {
+            return Err(Error::InvalidInput {
+                message: "read_columns applies only to a BatchUDF transform; \
+                          every other transform determines what it reads"
+                    .into(),
+            });
+        }
+
+        parent.add_columns(transform, read_columns).await
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use std::sync::Arc;
+
+    use arrow_array::{Int32Array, RecordBatch, record_batch};
+    use arrow_schema::{DataType, Field, Schema};
+    use lance::dataset::{BatchUDF, NewColumnTransform};
+
+    use crate::Table;
+    use crate::connect;
+
+    async fn table_with_two_columns(name: &str) -> Table {
+        let conn = connect("memory://").execute().await.unwrap();
+        let batch = record_batch!(("x", Int32, [1, 2, 3]), ("y", Int32, [10, 20, 30])).unwrap();
+        conn.create_table(name, batch).execute().await.unwrap()
+    }
+
+    #[tokio::test]
+    async fn test_requires_a_transform() {
+        let table = table_with_two_columns("no_transform").await;
+        let err = table.add_columns().execute().await.unwrap_err();
+        assert!(
+            err.to_string().contains("requires a transform"),
+            "got: {err}"
+        );
+    }
+
+    #[tokio::test]
+    async fn test_read_columns_with_sql_expressions_is_rejected() {
+        let table = table_with_two_columns("read_cols_sql").await;
+        let err = table
+            .add_columns()
+            .transform(NewColumnTransform::SqlExpressions(vec![(
+                "doubled".into(),
+                "x * 2".into(),
+            )]))
+            .read_columns(["x"])
+            .execute()
+            .await
+            .unwrap_err();
+        assert!(err.to_string().contains("BatchUDF"), "got: {err}");
+
+        let schema = table.schema().await.unwrap();
+        assert!(
+            schema.field_with_name("doubled").is_err(),
+            "a rejected call must not commit"
+        );
+    }
+
+    #[tokio::test]
+    async fn test_read_columns_limits_what_a_batch_udf_sees() {
+        let table = table_with_two_columns("read_cols_udf").await;
+
+        let output_schema = Arc::new(Schema::new(vec![Field::new("sum", DataType::Int32, true)]));
+        let mapper_schema = output_schema.clone();
+        let udf = BatchUDF {
+            mapper: Box::new(move |batch: &RecordBatch| {
+                assert!(batch.column_by_name("x").is_some());
+                assert!(batch.column_by_name("y").is_none(), "y was not requested");
+                let x = batch["x"].as_any().downcast_ref::<Int32Array>().unwrap();
+                let doubled: Int32Array = x.iter().map(|v| v.map(|v| v * 2)).collect();
+                Ok(RecordBatch::try_new(
+                    mapper_schema.clone(),
+                    vec![Arc::new(doubled)],
+                )?)
+            }),
+            output_schema,
+            result_checkpoint: None,
+        };
+
+        table
+            .add_columns()
+            .transform(NewColumnTransform::BatchUDF(udf))
+            .read_columns(["x"])
+            .execute()
+            .await
+            .unwrap();
+
+        let schema = table.schema().await.unwrap();
+        assert!(schema.field_with_name("sum").is_ok());
+    }
+}

rust/lancedb/src/table/add_data.rs

@@ -576,10 +576,12 @@ mod tests {
 
         // Add a new physical column AFTER the embedding column.
         table
-            .add_columns(
-                NewColumnTransform::SqlExpressions(vec![("score".into(), "42.0".into())]),
-                None,
-            )
+            .add_columns()
+            .transform(NewColumnTransform::SqlExpressions(vec![(
+                "score".into(),
+                "42.0".into(),
+            )]))
+            .execute()
             .await
             .unwrap();
 
@@ -683,7 +685,9 @@ mod tests {
             true,
         )]));
         table
-            .add_columns(NewColumnTransform::AllNulls(nested_schema), None)
+            .add_columns()
+            .transform(NewColumnTransform::AllNulls(nested_schema))
+            .execute()
             .await
             .unwrap();
 

rust/lancedb/src/table/schema_evolution.rs

@@ -193,10 +193,12 @@ mod tests {
 
         // Add a computed column
         let result = table
-            .add_columns(
-                NewColumnTransform::SqlExpressions(vec![("doubled".into(), "id * 2".into())]),
-                None,
-            )
+            .add_columns()
+            .transform(NewColumnTransform::SqlExpressions(vec![(
+                "doubled".into(),
+                "id * 2".into(),
+            )]))
+            .execute()
             .await
             .unwrap();
 
@@ -251,13 +253,12 @@ mod tests {
 
         // Add multiple columns at once
         table
-            .add_columns(
-                NewColumnTransform::SqlExpressions(vec![
-                    ("y".into(), "x + 1".into()),
-                    ("z".into(), "x * x".into()),
-                ]),
-                None,
-            )
+            .add_columns()
+            .transform(NewColumnTransform::SqlExpressions(vec![
+                ("y".into(), "x + 1".into()),
+                ("z".into(), "x * x".into()),
+            ]))
+            .execute()
             .await
             .unwrap();
 
@@ -283,10 +284,12 @@ mod tests {
 
         // Add a column with a constant value
         table
-            .add_columns(
-                NewColumnTransform::SqlExpressions(vec![("constant".into(), "42".into())]),
-                None,
-            )
+            .add_columns()
+            .transform(NewColumnTransform::SqlExpressions(vec![(
+                "constant".into(),
+                "42".into(),
+            )]))
+            .execute()
             .await
             .unwrap();
 
@@ -659,10 +662,12 @@ mod tests {
 
         // Add column increments version
         let add_result = table
-            .add_columns(
-                NewColumnTransform::SqlExpressions(vec![("c".into(), "a + b".into())]),
-                None,
-            )
+            .add_columns()
+            .transform(NewColumnTransform::SqlExpressions(vec![(
+                "c".into(),
+                "a + b".into(),
+            )]))
+            .execute()
             .await
             .unwrap();
         assert!(add_result.version > v1);

rust/lancedb/tests/blob_integration.rs

@@ -9,14 +9,17 @@ use arrow_array::{
 };
 use arrow_schema::{DataType, Field, Fields, Schema};
 use futures::TryStreamExt;
+use lance::Dataset;
 use lance_encoding::version::LanceFileVersion;
 use lancedb::{
     Connection, Error, Result, Table,
     blob::{BlobRangeRequest, blob},
     connect, connect_namespace,
-    database::listing::OPT_NEW_TABLE_ENABLE_STABLE_ROW_IDS,
+    database::listing::{
+        ListingDatabaseOptions, NewTableConfig, OPT_NEW_TABLE_ENABLE_STABLE_ROW_IDS,
+    },
     query::{ExecutableQuery, QueryBase},
-    table::{AddDataMode, CompactionOptions, OptimizeAction},
+    table::{AddDataMode, CompactionOptions, OptimizeAction, OptimizeStats},
 };
 use tempfile::tempdir;
 
@@ -1075,3 +1078,252 @@ async fn fetch_blob_files_aligns_across_fragments_with_nulls_and_dups() -> Resul
     }
     Ok(())
 }
+
+/// Rows exercising the null/empty interleavings from
+/// <https://github.com/lancedb/lancedb/issues/3744>: a payload, a null, a valid
+/// empty value, then payloads whose descriptors a fragment rewrite used to zero.
+fn null_empty_input_batch() -> RecordBatch {
+    let owned = [
+        Some(dedicated_blob_bytes(1)),
+        None,
+        Some(Vec::new()),
+        Some(dedicated_blob_bytes(4)),
+        Some(dedicated_blob_bytes(5)),
+        Some(dedicated_blob_bytes(6)),
+    ];
+    let payloads: Vec<Option<&[u8]>> = owned.iter().map(|payload| payload.as_deref()).collect();
+    binary_input_batch(&[1, 2, 3, 4, 5, 6], &payloads)
+}
+
+/// One `(id, Some((payload length, first byte)))` per live row, or `(id, None)`
+/// for a null blob.  Comparing lengths and first bytes keeps failure output
+/// readable where comparing whole payloads would not.
+type BlobSummary = Vec<(i64, Option<(usize, Option<u8>)>)>;
+
+/// The rows [`null_empty_input_batch`] leaves behind after `id IN (1, 4)` is
+/// deleted: a null, a valid empty value, and the two payloads that follow them.
+fn expected_null_empty_survivors() -> BlobSummary {
+    vec![
+        (2, None),
+        (3, Some((0, None))),
+        (5, Some((DEDICATED_BLOB_LEN, Some(5)))),
+        (6, Some((DEDICATED_BLOB_LEN, Some(6)))),
+    ]
+}
+
+/// `optimize()` only rewrites a fragment when lance's compaction planner selects
+/// it — here because the delete pushes the fragment past
+/// `materialize_deletions_threshold` (0.1 by default; these tests delete 2 of 6
+/// rows). Without this check, a planner or threshold change upstream would leave
+/// both regression tests green while no rewrite happened at all.
+fn assert_compacted(stats: &OptimizeStats) {
+    let metrics = stats
+        .compaction
+        .as_ref()
+        .expect("OptimizeAction::All runs compaction");
+    assert!(
+        metrics.fragments_removed >= 1,
+        "optimize() rewrote no fragment, so this test proves nothing: {metrics:?}"
+    );
+}
+
+fn summarize(rows: &[(i64, Option<Vec<u8>>)]) -> BlobSummary {
+    rows.iter()
+        .map(|(id, payload)| {
+            (
+                *id,
+                payload
+                    .as_ref()
+                    .map(|bytes| (bytes.len(), bytes.first().copied())),
+            )
+        })
+        .collect()
+}
+
+async fn sorted_id_rowid(table: &Table) -> Result<Vec<(i64, u64)>> {
+    let mut pairs = collect_id_rowid(table).await?;
+    pairs.sort_by_key(|(id, _)| *id);
+    Ok(pairs)
+}
+
+/// `{position, size}` descriptors of a legacy v1 blob column, keyed by `id`.
+async fn v1_blob_descriptors(table: &Table) -> Result<Vec<(i64, Option<(u64, u64)>)>> {
+    let batches = table
+        .query()
+        .execute()
+        .await?
+        .try_collect::<Vec<_>>()
+        .await?;
+    let batch = arrow_select::concat::concat_batches(&batches[0].schema(), &batches).unwrap();
+    let ids = batch
+        .column_by_name("id")
+        .unwrap()
+        .as_any()
+        .downcast_ref::<Int64Array>()
+        .unwrap();
+    let descriptors = batch
+        .column_by_name("image")
+        .unwrap()
+        .as_any()
+        .downcast_ref::<StructArray>()
+        .expect("v1 blob column reads back as a descriptor struct");
+    let position = descriptors
+        .column_by_name("position")
+        .unwrap()
+        .as_any()
+        .downcast_ref::<UInt64Array>()
+        .unwrap();
+    let size = descriptors
+        .column_by_name("size")
+        .unwrap()
+        .as_any()
+        .downcast_ref::<UInt64Array>()
+        .unwrap();
+    let mut rows: Vec<(i64, Option<(u64, u64)>)> = (0..batch.num_rows())
+        .map(|row| {
+            let descriptor =
+                (!descriptors.is_null(row)).then(|| (position.value(row), size.value(row)));
+            (ids.value(row), descriptor)
+        })
+        .collect();
+    rows.sort_by_key(|(id, _)| *id);
+    Ok(rows)
+}
+
+/// Payload bytes of every live row of a legacy v1 blob column, keyed by `id`.
+/// [`Table::fetch_blobs`] rejects v1 columns, so read them through lance.
+async fn v1_blob_payloads(dataset_uri: &str, table: &Table) -> Result<Vec<(i64, Option<Vec<u8>>)>> {
+    let pairs = sorted_id_rowid(table).await?;
+    let row_ids: Vec<u64> = pairs.iter().map(|(_, row_id)| *row_id).collect();
+    let dataset = Arc::new(Dataset::open(dataset_uri).await?);
+    let files = dataset.take_blobs(&row_ids, "image").await?;
+    assert_eq!(
+        files.len(),
+        pairs.len(),
+        "take_blobs returned {} handles for {} live rows",
+        files.len(),
+        pairs.len()
+    );
+    let mut rows = Vec::with_capacity(pairs.len());
+    for ((id, _), file) in pairs.iter().zip(files) {
+        let payload = match file {
+            Some(file) => Some(file.read().await?.to_vec()),
+            None => None,
+        };
+        rows.push((*id, payload));
+    }
+    Ok(rows)
+}
+
+/// Length and first byte of every live blob v2 value, keyed by `id`.
+async fn blob_v2_values(table: &Table) -> Result<BlobSummary> {
+    let pairs = sorted_id_rowid(table).await?;
+    let row_ids: Vec<u64> = pairs.iter().map(|(_, row_id)| *row_id).collect();
+    let bytes = table.fetch_blobs("image", &row_ids).await?;
+    Ok(pairs
+        .iter()
+        .enumerate()
+        .map(|(slot, (id, _))| {
+            let value = (!bytes.is_null(slot))
+                .then(|| (bytes.value(slot).len(), bytes.value(slot).first().copied()));
+            (*id, value)
+        })
+        .collect())
+}
+
+/// Regression test for [#3744]: on storage 2.0 (legacy v1 descriptors),
+/// compaction rewrote every payload following a null or empty value in the same
+/// fragment as `{position: 0, size: 0}`, so the payload bytes read back as `b""`
+/// and the new fragment no longer referenced them at all.
+///
+/// [#3744]: https://github.com/lancedb/lancedb/issues/3744
+#[tokio::test]
+async fn optimize_preserves_v1_blob_payloads_with_null_and_empty() -> Result<()> {
+    let tmp = tempdir().unwrap();
+    let db_uri = tmp.path().to_str().unwrap().to_string();
+    let db = connect(&db_uri)
+        .database_options(&ListingDatabaseOptions {
+            new_table_config: NewTableConfig {
+                data_storage_version: Some(LanceFileVersion::V2_0),
+                ..Default::default()
+            },
+            ..Default::default()
+        })
+        .execute()
+        .await?;
+    let legacy = Field::new("image", DataType::LargeBinary, true).with_metadata(
+        std::collections::HashMap::from([("lance-encoding:blob".to_string(), "true".to_string())]),
+    );
+    let schema = Arc::new(Schema::new(vec![
+        Field::new("id", DataType::Int64, false),
+        legacy,
+    ]));
+    let table = db.create_empty_table("t", schema).execute().await?;
+    table.add(null_empty_input_batch()).execute().await?;
+    assert_eq!(
+        storage_format_version(&table).await,
+        LanceFileVersion::V2_0.resolve(),
+        "v1 blob descriptors only exist below storage 2.2"
+    );
+    let dataset_uri = table.uri().await?;
+
+    // Any rewrite triggers it; deleting rows is the shape from the issue.
+    table.delete("id IN (1, 4)").await?;
+    let descriptors_before = v1_blob_descriptors(&table).await?;
+    let before = v1_blob_payloads(&dataset_uri, &table).await?;
+    assert_eq!(
+        summarize(&before),
+        expected_null_empty_survivors(),
+        "test setup no longer produces the null/empty/payload mix"
+    );
+
+    let stats = table.optimize(OptimizeAction::All).await?;
+    assert_compacted(&stats);
+
+    let descriptors_after = v1_blob_descriptors(&table).await?;
+    let after = v1_blob_payloads(&dataset_uri, &table).await?;
+    assert_eq!(
+        summarize(&after),
+        summarize(&before),
+        "optimize() lost blob payloads; descriptors before={descriptors_before:?} after={descriptors_after:?}"
+    );
+    assert!(after == before, "optimize() changed blob payload bytes");
+    Ok(())
+}
+
+/// Regression test for the blob v2 half of [#3744]: compaction rewrote a valid
+/// empty value as null, destroying the null-vs-empty distinction.
+///
+/// [#3744]: https://github.com/lancedb/lancedb/issues/3744
+#[tokio::test]
+async fn optimize_preserves_blob_v2_null_and_empty_distinction() -> Result<()> {
+    let tmp = tempdir().unwrap();
+    let db = connect(tmp.path().to_str().unwrap()).execute().await?;
+    let table = db
+        .create_empty_table("t", blob_table_schema())
+        .execute()
+        .await?;
+    table.add(null_empty_input_batch()).execute().await?;
+    assert!(
+        storage_format_version(&table).await >= LanceFileVersion::V2_2,
+        "blob v2 columns require storage >= 2.2"
+    );
+
+    table.delete("id IN (1, 4)").await?;
+    let before = blob_v2_values(&table).await?;
+    assert_eq!(
+        before,
+        expected_null_empty_survivors(),
+        "test setup no longer produces the null/empty/payload mix"
+    );
+
+    let stats = table.optimize(OptimizeAction::All).await?;
+    assert_compacted(&stats);
+
+    assert_eq!(
+        blob_v2_values(&table).await?,
+        before,
+        "optimize() changed blob v2 values"
+    );
+    Ok(())
+}