DynamicMemoryIndex bug fixes (#404)

* While simply creating a unit test to repro Issue #400, I found a number of bugs that I needed to address just to get it to work the way I had intended. This does not yet have what I would consider a comprehensive suite of test coverage for the DynamicMemoryIndex, but we at least do save it with the metadata file, we can load it correctly, and saving *always* consolidate_deletes() prior to save if any item has been marked for deletion prior to save.

* We actually cannot save without compacting before save anyway. Removing the parameter from save() and hardcoding it to True until we can actually support it.

* Addressing some PR comments and readying a 0.5.0.rc5 release

pyproject.toml

@@ -11,7 +11,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "diskannpy"
-version = "0.5.0.rc4"
+version = "0.5.0.rc5"
 
 description = "DiskANN Python extension module"
 readme = "python/README.md"

python/include/dynamic_memory_index.h

@@ -41,6 +41,8 @@ class DynamicMemoryIndex
                                             uint64_t num_queries, uint64_t knn, uint64_t complexity,
                                             uint32_t num_threads);
     void consolidate_delete();
+    size_t num_points();
+
 
   private:
     const uint32_t _initial_search_complexity;

python/src/_dynamic_memory_index.py

@@ -1,6 +1,7 @@
 # Copyright (c) Microsoft Corporation. All rights reserved.
 # Licensed under the MIT license.
 
+import os
 import warnings
 
 import numpy as np
@@ -21,12 +22,14 @@
     _assert,
     _assert_2d,
     _assert_dtype,
+    _assert_existing_directory,
     _assert_is_nonnegative_uint32,
     _assert_is_positive_uint32,
     _castable_dtype_or_raise,
     _ensure_index_metadata,
     _valid_metric,
     _valid_index_prefix,
+    _write_index_metadata
 )
 from ._diskannpy import defaults
 
@@ -158,6 +161,7 @@ def __init__(
         """
 
         dap_metric = _valid_metric(distance_metric)
+        self._dap_metric = dap_metric
         _assert_dtype(vector_dtype)
         _assert_is_positive_uint32(dimensions, "dimensions")
 
@@ -199,6 +203,7 @@ def __init__(
             search_threads=search_threads,
             concurrent_consolidation=concurrent_consolidation
         )
+        self._points_deleted = False
 
     def search(
         self, query: VectorLike, k_neighbors: int, complexity: int
@@ -293,16 +298,31 @@ def batch_search(
             num_threads=num_threads,
         )
 
-    def save(self, save_path: str, compact_before_save: bool = True):
+    def save(self, save_path: str, index_prefix: str = "ann"):
         """
         Saves this index to file.
         :param save_path: The path to save these index files to.
         :type save_path: str
-        :param compact_before_save:
+        :param index_prefix: The prefix to use for the index files. Default is "ann".
+        :type index_prefix: str
         """
         if save_path == "":
             raise ValueError("save_path cannot be empty")
-        self._index.save(save_path=save_path, compact_before_save=compact_before_save)
+        if index_prefix == "":
+            raise ValueError("index_prefix cannot be empty")
+        _assert_existing_directory(save_path, "save_path")
+        save_path = os.path.join(save_path, index_prefix)
+        if self._points_deleted is True:
+            warnings.warn(
+                "DynamicMemoryIndex.save() currently requires DynamicMemoryIndex.consolidate_delete() to be called "
+                "prior to save when items have been marked for deletion. This is being done automatically now, though"
+                "it will increase the time it takes to save; on large sets of data it can take a substantial amount of "
+                "time. In the future, we will implement a faster save with unconsolidated deletes, but for now this is "
+                "required."
+            )
+            self._index.consolidate_delete()
+        self._index.save(save_path=save_path, compact_before_save=True)  # we do not yet support uncompacted saves
+        _write_index_metadata(save_path, self._vector_dtype, self._dap_metric, self._index.num_points(), self._dimensions)
 
     def insert(self, vector: VectorLike, vector_id: VectorIdentifier):
         """
@@ -349,10 +369,12 @@ def mark_deleted(self, vector_id: VectorIdentifier):
         :type vector_id: int
         """
         _assert_is_positive_uint32(vector_id, "vector_id")
+        self._points_deleted = True
         self._index.mark_deleted(np.uintc(vector_id))
 
     def consolidate_delete(self):
         """
         This method actually restructures the DiskANN index to remove the items that have been marked for deletion.
         """
         self._index.consolidate_delete()
+        self._points_deleted = False

python/src/dynamic_memory_index.cpp

@@ -159,6 +159,11 @@ template <class DT> void DynamicMemoryIndex<DT>::consolidate_delete()
     _index.consolidate_deletes(_write_parameters);
 }
 
+template <class DT> size_t DynamicMemoryIndex<DT>::num_points()
+{
+    return _index.get_num_points();
+}
+
 template class DynamicMemoryIndex<float>;
 template class DynamicMemoryIndex<uint8_t>;
 template class DynamicMemoryIndex<int8_t>;

python/src/module.cpp

@@ -79,7 +79,8 @@ template <typename T> inline void add_variant(py::module_ &m, const Variant &var
         .def("save", &diskannpy::DynamicMemoryIndex<T>::save, "save_path"_a = "", "compact_before_save"_a = false)
         .def("insert", &diskannpy::DynamicMemoryIndex<T>::insert, "vector"_a, "id"_a)
         .def("mark_deleted", &diskannpy::DynamicMemoryIndex<T>::mark_deleted, "id"_a)
-        .def("consolidate_delete", &diskannpy::DynamicMemoryIndex<T>::consolidate_delete);
+        .def("consolidate_delete", &diskannpy::DynamicMemoryIndex<T>::consolidate_delete)
+        .def("num_points", &diskannpy::DynamicMemoryIndex<T>::num_points);
 
     py::class_<diskannpy::StaticDiskIndex<T>>(m, variant.static_disk_index_name.c_str())
         .def(py::init<const diskann::Metric, const std::string &, const uint32_t, const size_t, const uint32_t>(),

python/tests/test_dynamic_memory_index.py

@@ -1,8 +1,8 @@
 # Copyright (c) Microsoft Corporation. All rights reserved.
 # Licensed under the MIT license.
 
-import os
 import shutil
+import tempfile
 import unittest
 
 import diskannpy as dap
@@ -296,3 +296,46 @@ def test_value_ranges_batch_search(self):
                     index.batch_search(
                         queries=np.array([[]], dtype=np.single), **kwargs
                     )
+
+    # Issue #400
+    def test_issue400(self):
+        _, _, _, index_vectors, ann_dir, _, generated_tags = self._test_matrix[0]
+
+        deletion_tag = generated_tags[10]  # arbitrary choice
+        deletion_vector = index_vectors[10]
+
+        index = dap.DynamicMemoryIndex.from_file(
+            index_directory=ann_dir,
+            num_threads=16,
+            initial_search_complexity=32,
+            max_vectors=10100,
+            complexity=64,
+            graph_degree=32
+        )
+        index.insert(np.array([1.0] * 10, dtype=np.single), 10099)
+        index.insert(np.array([2.0] * 10, dtype=np.single), 10050)
+        index.insert(np.array([3.0] * 10, dtype=np.single), 10053)
+        tags, distances = index.search(np.array([3.0] * 10, dtype=np.single), k_neighbors=5, complexity=64)
+        self.assertIn(10053, tags)
+        tags, distances = index.search(deletion_vector, k_neighbors=5, complexity=64)
+        self.assertIn(deletion_tag, tags, "deletion_tag should exist, as we have not deleted yet")
+        index.mark_deleted(deletion_tag)
+        tags, distances = index.search(deletion_vector, k_neighbors=5, complexity=64)
+        self.assertNotIn(deletion_tag, tags, "deletion_tag should not exist, as we have marked it for deletion")
+        with tempfile.TemporaryDirectory() as tmpdir:
+            index.save(tmpdir)
+
+            index2 = dap.DynamicMemoryIndex.from_file(
+                index_directory=tmpdir,
+                num_threads=16,
+                initial_search_complexity=32,
+                max_vectors=10100,
+                complexity=64,
+                graph_degree=32
+            )
+            tags, distances = index2.search(deletion_vector, k_neighbors=5, complexity=64)
+            self.assertNotIn(
+                deletion_tag,
+                tags,
+                "deletion_tag should not exist, as we saved and reloaded the index without it"
+            )