Optimize search performance and add stress test

.github/workflows/test.yml

@@ -0,0 +1,33 @@
+name: Run Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      # Step 1: Checkout the repository code
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      # Step 2: Setup Python environment
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.10
+
+      # Step 3: Install dependencies from requirements.txt
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      # Step 4: Run unit tests using pytest
+      - name: Run unit tests
+        run: pytest tests

.gitignore

@@ -3,6 +3,7 @@ __pycache__/
 *.py[cod]
 *$py.class
 *.DS_Store
+logs/
 
 
 # C extensions

README.md

@@ -48,15 +48,61 @@
 
 <br>
 
-## :dart: About ##
+## :dart: About 
 
 Hypergraph-DB is a lightweight, flexible, and Python-based database designed to model and manage **hypergraphs**—a generalized graph structure where edges (hyperedges) can connect any number of vertices. This makes Hypergraph-DB an ideal solution for representing complex relationships between entities in various domains, such as knowledge graphs, social networks, and scientific data modeling.
 
 Hypergraph-DB provides a high-level abstraction for working with vertices and hyperedges, making it easy to add, update, query, and manage hypergraph data. With built-in support for persistence, caching, and efficient operations, Hypergraph-DB simplifies the management of hypergraph data structures.
 
+**:bar_chart: Performance Test Results**
+
+To demonstrate the performance of **Hypergraph-DB**, let’s consider an example:
+
+- Suppose we want to construct a **hypergraph** with **1,000,000 vertices** and **200,000 hyperedges**.
+- Using Hypergraph-DB, it takes approximately:
+  - **1.75 seconds** to add **1,000,000 vertices**.
+  - **1.82 seconds** to add **200,000 hyperedges**.
+- Querying this hypergraph:
+  - Retrieving information for **400,000 vertices** takes **0.51 seconds**.
+  - Retrieving information for **400,000 hyperedges** takes **2.52 seconds**.
+
+This example demonstrates the efficiency of Hypergraph-DB, even when working with large-scale hypergraphs. Below is a detailed table showing how the performance scales as the size of the hypergraph increases.
+
+**Detailed Performance Results**
+
+The following table shows the results of stress tests performed on Hypergraph-DB with varying scales. The tests measure the time taken to add vertices, add hyperedges, and query vertices and hyperedges.
+
+| **Number of Vertices** | **Number of Hyperedges** | **Add Vertices (s)** | **Add Edges (s)** | **Query Vertices (s/queries)** | **Query Edges (s/queries)** | **Total Time (s)** |
+|-------------------------|--------------------------|-----------------------|-------------------|-------------------------------|----------------------------|--------------------|
+| 5,000                  | 1,000                   | 0.01                 | 0.01             | 0.00/2,000                   | 0.01/2,000                | 0.02               |
+| 10,000                 | 2,000                   | 0.01                 | 0.01             | 0.00/4,000                   | 0.02/4,000                | 0.05               |
+| 25,000                 | 5,000                   | 0.03                 | 0.04             | 0.01/10,000                  | 0.05/10,000               | 0.13               |
+| 50,000                 | 10,000                  | 0.06                 | 0.07             | 0.02/20,000                  | 0.12/20,000               | 0.26               |
+| 100,000                | 20,000                  | 0.12                 | 0.17             | 0.04/40,000                  | 0.24/40,000               | 0.58               |
+| 250,000                | 50,000                  | 0.35                 | 0.40             | 0.11/100,000                 | 0.61/100,000              | 1.47               |
+| 500,000                | 100,000                 | 0.85                 | 1.07             | 0.22/200,000                 | 1.20/200,000              | 3.34               |
+| 1,000,000              | 200,000                 | 1.75                 | 1.82             | 0.51/400,000                 | 2.52/400,000              | 6.60               |
+
+---
+
+**Key Observations:**
+
+1. **Scalability**:  
+   Hypergraph-DB scales efficiently with the number of vertices and hyperedges. The time to add vertices and hyperedges grows linearly with the size of the hypergraph.
+
+2. **Query Performance**:  
+   Querying vertices and hyperedges remains fast, even for large-scale hypergraphs. For instance:
+   - Querying **200,000 vertices** takes only **0.22 seconds**.
+   - Querying **200,000 hyperedges** takes only **1.20 seconds**.
+
+3. **Total Time**:  
+   The total time to construct and query a hypergraph with **1,000,000 vertices** and **200,000 hyperedges** is only **6.60 seconds**, showcasing the overall efficiency of Hypergraph-DB.
+
+This performance makes **Hypergraph-DB** a great choice for applications requiring fast and scalable hypergraph data management.
+
 ---
 
-## :sparkles: Features ##
+## :sparkles: Features 
 
 :heavy_check_mark: **Flexible Hypergraph Representation**  
    - Supports vertices (`v`) and hyperedges (`e`), where hyperedges can connect any number of vertices.
@@ -78,7 +124,7 @@ Hypergraph-DB provides a high-level abstraction for working with vertices and hy
 
 ---
 
-## :rocket: Installation ##
+## :rocket: Installation 
 
 
 Hypergraph-DB is a Python library. You can install it directly from PyPI using `pip`.
@@ -100,7 +146,7 @@ pip install -r requirements.txt
 
 ---
 
-## :checkered_flag: Starting ##
+## :checkered_flag: Starting 
 
 This section provides a quick guide to get started with Hypergraph-DB, including iusage, and running basic operations. Below is an example of how to use Hypergraph-DB, based on the provided test cases.
 
@@ -174,7 +220,7 @@ print(hg.nbr_v(1))  # Output: {3, 4}
 print(hg.nbr_e_of_v(1))  # Output: {(1, 3, 4)}
 ```
 
-#### **6. Persistence (Save and Load)**
+#### **6. Persistence (Save and Load)
 
 ```python
 # Save the hypergraph to a file
@@ -190,14 +236,14 @@ print(hg2.all_e)  # Output: {(1, 3, 4)}
 --- 
 
 
-## :memo: License ##
+## :memo: License 
 
 Hypergraph-DB is open-source and licensed under the [Apache License 2.0](LICENSE). Feel free to use, modify, and distribute it as per the license terms.
 
 
 ---
 
-## :email: Contact ##
+## :email: Contact 
 
 Hypergraph-DB is maintained by [iMoon-Lab](http://moon-lab.tech/), Tsinghua University. If you have any questions, please feel free to contact us via email: [Yifan Feng](mailto:evanfeng97@gmail.com).
 

hyperdb/__init__.py

@@ -3,6 +3,6 @@
 
 from ._global import AUTHOR_EMAIL
 
-__version__ = "0.1.0"
+__version__ = "0.1.1"
 
 __all__ = {"AUTHOR_EMAIL", "BaseHypergraphDB", "HypergraphDB"}

hyperdb/hypergraph.py

@@ -112,7 +112,7 @@ def encode_e(self, e_tuple: Union[List, Set, Tuple]) -> Tuple:
         for v_id in tmp:
             assert isinstance(v_id, Hashable), "The vertex id must be hashable."
             assert (
-                v_id in self.all_v
+                v_id in self._v_data
             ), f"The vertex {v_id} does not exist in the hypergraph."
         return tuple(tmp)
 
@@ -157,7 +157,7 @@ def add_v(self, v_id: Any, v_data: Optional[Dict] = None):
             assert isinstance(v_data, dict), "The vertex data must be a dictionary."
         else:
             v_data = {}
-        if v_id not in self.all_v:
+        if v_id not in self._v_data:
             self._v_data[v_id] = v_data
             self._v_inci[v_id] = set()
         else:
@@ -180,7 +180,7 @@ def add_e(self, e_tuple: Union[List, Set, Tuple], e_data: Optional[Dict] = None)
         else:
             e_data = {}
         e_tuple = self.encode_e(e_tuple)
-        if e_tuple not in self.all_e:
+        if e_tuple not in self._e_data:
             self._e_data[e_tuple] = e_data
             for v in e_tuple:
                 self._v_inci[v].add(e_tuple)
@@ -197,7 +197,7 @@ def remove_v(self, v_id: Any):
         """
         assert isinstance(v_id, Hashable), "The vertex id must be hashable."
         assert (
-            v_id in self.all_v
+            v_id in self._v_data
         ), f"The vertex {v_id} does not exist in the hypergraph."
         del self._v_data[v_id]
         for e_tuple in self._v_inci[v_id]:
@@ -220,7 +220,7 @@ def remove_e(self, e_tuple: Union[List, Set, Tuple]):
         ), "The hyperedge must be a list, set, or tuple of vertex ids."
         e_tuple = self.encode_e(e_tuple)
         assert (
-            e_tuple in self.all_e
+            e_tuple in self._e_data
         ), f"The hyperedge {e_tuple} does not exist in the hypergraph."
         for v in e_tuple:
             self._v_inci[v].remove(e_tuple)
@@ -238,7 +238,7 @@ def update_v(self, v_id: Any, v_data: dict):
         assert isinstance(v_id, Hashable), "The vertex id must be hashable."
         assert isinstance(v_data, dict), "The vertex data must be a dictionary."
         assert (
-            v_id in self.all_v
+            v_id in self._v_data
         ), f"The vertex {v_id} does not exist in the hypergraph."
         self._v_data[v_id].update(v_data)
         self._clear_cache()
@@ -257,7 +257,7 @@ def update_e(self, e_tuple: Union[List, Set, Tuple], e_data: dict):
         assert isinstance(e_data, dict), "The hyperedge data must be a dictionary."
         e_tuple = self.encode_e(e_tuple)
         assert (
-            e_tuple in self.all_e
+            e_tuple in self._e_data
         ), f"The hyperedge {e_tuple} does not exist in the hypergraph."
         self._e_data[e_tuple].update(e_data)
         self._clear_cache()
@@ -270,7 +270,7 @@ def has_v(self, v_id: Any) -> bool:
             ``v_id`` (``Any``): The vertex id.
         """
         assert isinstance(v_id, Hashable), "The vertex id must be hashable."
-        return v_id in self.all_v
+        return v_id in self._v_data
 
     def has_e(self, e_tuple: Union[List, Set, Tuple]) -> bool:
         r"""
@@ -286,7 +286,7 @@ def has_e(self, e_tuple: Union[List, Set, Tuple]) -> bool:
             e_tuple = self.encode_e(e_tuple)
         except AssertionError:
             return False
-        return e_tuple in self.all_e
+        return e_tuple in self._e_data
 
     def degree_v(self, v_id: Any) -> int:
         r"""
@@ -297,7 +297,7 @@ def degree_v(self, v_id: Any) -> int:
         """
         assert isinstance(v_id, Hashable), "The vertex id must be hashable."
         assert (
-            v_id in self.all_v
+            v_id in self._v_data
         ), f"The vertex {v_id} does not exist in the hypergraph."
         return len(self._v_inci[v_id])
 
@@ -313,7 +313,7 @@ def degree_e(self, e_tuple: Union[List, Set, Tuple]) -> int:
         ), "The hyperedge must be a list, set, or tuple of vertex ids."
         e_tuple = self.encode_e(e_tuple)
         assert (
-            e_tuple in self.all_e
+            e_tuple in self._e_data
         ), f"The hyperedge {e_tuple} does not exist in the hypergraph."
         return len(e_tuple)
 
@@ -326,7 +326,7 @@ def nbr_e_of_v(self, v_id: Any) -> list:
         """
         assert isinstance(v_id, Hashable), "The vertex id must be hashable."
         assert (
-            v_id in self.all_v
+            v_id in self._v_data
         ), f"The vertex {v_id} does not exist in the hypergraph."
         return set(self._v_inci[v_id])
 
@@ -342,7 +342,7 @@ def nbr_v_of_e(self, e_tuple: Union[List, Set, Tuple]) -> list:
         ), "The hyperedge must be a list, set, or tuple of vertex ids."
         e_tuple = self.encode_e(e_tuple)
         assert (
-            e_tuple in self.all_e
+            e_tuple in self._e_data
         ), f"The hyperedge {e_tuple} does not exist in the hypergraph."
         return set(e_tuple)
 
@@ -355,7 +355,7 @@ def nbr_v(self, v_id: Any, exclude_self=True) -> list:
         """
         assert isinstance(v_id, Hashable), "The vertex id must be hashable."
         assert (
-            v_id in self.all_v
+            v_id in self._v_data
         ), f"The vertex {v_id} does not exist in the hypergraph."
         nbrs = set()
         for e_tuple in self._v_inci[v_id]: