fix: add missing stacklevel=2 to warnings.warn() and fix broken message concatenation (Fixes #3563) (#3564)

Fixes #3563

## Summary

- Add `stacklevel=2` to 10 `warnings.warn()` calls across 4 files
- Fix broken message concatenation in `table.py` where the second string
was incorrectly passed as the `category` parameter

## Problem

Multiple `warnings.warn()` calls in the `python/lancedb/` codebase were
missing the `stacklevel` parameter. Without `stacklevel=2`, warnings
point to library internals instead of the caller's code, making it
impossible for users to identify which of their function calls triggered
the warning.

Additionally, two calls in `table.py` (lines 3411 and 3420) had a more
serious bug: the deprecation message was split across two separate
string arguments, causing the second string to be passed as the
`category` parameter instead of being concatenated with the first
string. This would cause `TypeError` when the warning was triggered.

## Changes

| File | Fixes | Description |
|------|-------|-------------|
| `embeddings/colpali.py` | 1 | Add `stacklevel=2` to
`use_token_pooling` deprecation warning |
| `remote/db.py` | 3 | Add `stacklevel=2` to `request_thread_pool`,
`connection_timeout`, `read_timeout` deprecation warnings |
| `remote/table.py` | 3 | Add `stacklevel=2` to `cleanup_old_versions`,
`compact_files`, `optimize` no-op warnings |
| `table.py` | 3 | Fix broken message concatenation for
`data_storage_version` and `enable_v2_manifest_paths` deprecation
warnings + add `stacklevel=2` to `retrain` deprecation warning |

## Verification

```python
# All warnings.warn() calls now have stacklevel
python3 -c "import ast, os; ..."
# Result: All warnings.warn() calls now have stacklevel!
```

## Changelog

| Date | Change | Author |
|------|--------|--------|
| 2026-06-20 | Fix missing stacklevel=2 in 10 warnings.warn() calls +
fix broken message concatenation | rtmalikian |

### Files Changed
- `python/python/lancedb/embeddings/colpali.py` — Add stacklevel=2
- `python/python/lancedb/remote/db.py` — Add stacklevel=2 to 3
deprecation warnings
- `python/python/lancedb/remote/table.py` — Add stacklevel=2 to 3 no-op
warnings
- `python/python/lancedb/table.py` — Fix broken message concatenation +
add stacklevel=2

### Verification
- AST-based audit confirms all `warnings.warn()` calls now include
`stacklevel=2`
- Syntax check passes for all 4 modified files

---

**About the Author:** Raphael Malikian — Clinical AI Solutions
Architect. I specialise in building and fixing AI/ML systems for
healthcare, including vector databases, RAG pipelines, and clinical NLP.
If you need help with your project or think I can add value to your
organisation, feel free to reach out — I'd love to connect.

📧 rtmalikian@gmail.com
🔗 GitHub: https://github.com/rtmalikian
🔗 LinkedIn:
http://www.linkedin.com/in/raphael-t-malikian-mbbs-bsc-hons-71075436a

---

**Disclosure:** This code was developed with assistance from **Hermes
Agent** (Nous Research). All changes were reviewed, tested against the
actual codebase, and verified for correctness.

Signed-off-by: rtmalikian <rtmalikian@gmail.com>

python/python/lancedb/embeddings/colpali.py

@@ -81,6 +81,7 @@ class ColPaliEmbeddings(EmbeddingFunction):
             warnings.warn(
                 "use_token_pooling is deprecated, use pooling_strategy=None instead",
                 DeprecationWarning,
+                stacklevel=2,
             )
             self.pooling_strategy = None
 

python/python/lancedb/remote/db.py

@@ -124,6 +124,7 @@ class RemoteDBConnection(DBConnection):
                 "request_thread_pool is no longer used and will be removed in "
                 "a future release.",
                 DeprecationWarning,
+                stacklevel=2,
             )
 
         if connection_timeout is not None:
@@ -132,6 +133,7 @@ class RemoteDBConnection(DBConnection):
                 "release. Please use client_config.timeout_config.connect_timeout "
                 "instead.",
                 DeprecationWarning,
+                stacklevel=2,
             )
             client_config.timeout_config.connect_timeout = timedelta(
                 seconds=connection_timeout
@@ -142,6 +144,7 @@ class RemoteDBConnection(DBConnection):
                 "read_timeout is deprecated and will be removed in a future release. "
                 "Please use client_config.timeout_config.read_timeout instead.",
                 DeprecationWarning,
+                stacklevel=2,
             )
             client_config.timeout_config.read_timeout = timedelta(seconds=read_timeout)
 

python/python/lancedb/remote/table.py

@@ -845,7 +845,8 @@ class RemoteTable(Table):
         """
         warnings.warn(
             "cleanup_old_versions() is a no-op on LanceDB Cloud. "
-            "Tables are automatically cleaned up and optimized."
+            "Tables are automatically cleaned up and optimized.",
+            stacklevel=2,
         )
         pass
 
@@ -857,7 +858,8 @@ class RemoteTable(Table):
         """
         warnings.warn(
             "compact_files() is a no-op on LanceDB Cloud. "
-            "Tables are automatically compacted and optimized."
+            "Tables are automatically compacted and optimized.",
+            stacklevel=2,
         )
         pass
 
@@ -874,7 +876,8 @@ class RemoteTable(Table):
         """
         warnings.warn(
             "optimize() is a no-op on LanceDB Cloud. "
-            "Indices are optimized automatically."
+            "Indices are optimized automatically.",
+            stacklevel=2,
         )
         pass
 

python/python/lancedb/table.py

@@ -3409,18 +3409,20 @@ class LanceTable(Table):
 
         if data_storage_version is not None:
             warnings.warn(
-                "setting data_storage_version directly on create_table is deprecated. ",
+                "setting data_storage_version directly on create_table is deprecated. "
                 "Use database_options instead.",
                 DeprecationWarning,
+                stacklevel=2,
             )
             if storage_options is None:
                 storage_options = {}
             storage_options["new_table_data_storage_version"] = data_storage_version
         if enable_v2_manifest_paths is not None:
             warnings.warn(
-                "setting enable_v2_manifest_paths directly on create_table is ",
+                "setting enable_v2_manifest_paths directly on create_table is "
                 "deprecated. Use database_options instead.",
                 DeprecationWarning,
+                stacklevel=2,
             )
             if storage_options is None:
                 storage_options = {}
@@ -5662,6 +5664,7 @@ class AsyncTable:
                 "The 'retrain' parameter is deprecated and will be removed in a "
                 "future version.",
                 DeprecationWarning,
+                stacklevel=2,
             )
 
         return await self._inner.optimize(