Add generate_proof and verify_proof methods to VersionedKvStore (#101)

* Add generate_proof and verify_proof methods to VersionedKvStore

Expose cryptographic proof functionality from ProllyTree to VersionedKvStore
in both Rust and Python APIs for consistent proof generation and verification
across versioned key-value operations.

## Changes

### Rust Implementation
- Add `generate_proof(&self, key: &[u8]) -> Proof<N>` to VersionedKvStore
- Add `verify(&self, proof: Proof<N>, key: &[u8], expected_value: Option<&[u8]>) -> bool`
- Both methods delegate to underlying ProllyTree implementation
- Add comprehensive unit test `test_versioned_store_proof_methods`

### Python Bindings
- Add `generate_proof(key: bytes) -> bytes` to PyVersionedKvStore
- Add `verify_proof(proof_bytes: bytes, key: bytes, expected_value: Optional[bytes]) -> bool`
- Handle proof serialization/deserialization with bincode
- Thread-safe implementation with proper GIL handling

## API Usage

```python
store = VersionedKvStore.open("/path/to/repo")
proof = store.generate_proof(b"key1")
is_valid = store.verify_proof(proof, b"key1", b"value1")
```

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

* Update Python README to document VersionedKvStore proof methods

Add documentation for the newly added generate_proof and verify_proof
methods in the VersionedKvStore example section. Also update the
cryptographic verification feature description to clarify it's
available for both trees and versioned storage.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

---------

Co-authored-by: Claude <[email protected]>

Author: zhangfengcdt

python/README.md

@@ -39,7 +39,7 @@ The full documentation includes:
 - **🌳 Probabilistic Trees** - High-performance data storage with automatic balancing
 - **🤖 AI Agent Memory** - Multi-layered memory systems for intelligent agents
 - **📚 Versioned Storage** - Git-like version control for key-value data
-- **🔐 Cryptographic Verification** - Merkle proofs for data integrity
+- **🔐 Cryptographic Verification** - Merkle proofs for data integrity across trees and versioned storage
 - **⚡ SQL Queries** - Query your data using SQL syntax
 
 ## 🔥 Key Use Cases
@@ -84,6 +84,10 @@ commit_id = store.commit("Add production config")
 store.create_branch("experiment")
 store.insert(b"feature", b"experimental_data")
 store.commit("Add experimental feature")
+
+# Cryptographic verification on versioned data
+proof = store.generate_proof(b"config")
+is_valid = store.verify_proof(proof, b"config", b"production_settings")
 ```
 
 ### SQL Queries

src/git/versioned_store.rs

@@ -605,6 +605,110 @@ where
 
         Ok(self.git_repo.path().join(staging_filename))
     }
+
+    /// Generate a cryptographic proof for a key's existence and value in the tree
+    /// This proof can be used to verify the integrity of the key-value pair without
+    /// requiring access to the entire tree structure.
+    ///
+    /// # Parameters
+    /// - `key`: The key to generate proof for
+    ///
+    /// # Returns
+    /// - A proof object containing the hash path from root to the target node
+    pub fn generate_proof(&self, key: &[u8]) -> crate::proof::Proof<N> {
+        self.tree.generate_proof(key)
+    }
+
+    /// Verify a cryptographic proof for a key-value pair
+    /// This checks that the proof is valid and optionally verifies the expected value
+    ///
+    /// # Parameters
+    /// - `proof`: The proof to verify
+    /// - `key`: The key that the proof claims to prove
+    /// - `expected_value`: Optional expected value to verify against
+    ///
+    /// # Returns
+    /// - `true` if the proof is valid, `false` otherwise
+    pub fn verify(
+        &self,
+        proof: crate::proof::Proof<N>,
+        key: &[u8],
+        expected_value: Option<&[u8]>,
+    ) -> bool {
+        self.tree.verify(proof, key, expected_value)
+    }
+}
+
+#[cfg(test)]
+mod proof_tests {
+    use super::*;
+    use tempfile::TempDir;
+
+    #[test]
+    fn test_versioned_store_proof_methods() {
+        // Create a temporary directory for the test
+        let temp_dir = TempDir::new().expect("Failed to create temp dir");
+        let repo_path = temp_dir.path().to_str().unwrap();
+
+        // Initialize git repo
+        std::process::Command::new("git")
+            .args(["init"])
+            .current_dir(repo_path)
+            .output()
+            .expect("Failed to initialize git repo");
+
+        // Set git config
+        std::process::Command::new("git")
+            .args(["config", "user.name", "Test User"])
+            .current_dir(repo_path)
+            .output()
+            .expect("Failed to set git user name");
+
+        std::process::Command::new("git")
+            .args(["config", "user.email", "[email protected]"])
+            .current_dir(repo_path)
+            .output()
+            .expect("Failed to set git user email");
+
+        // Create a subdirectory for the dataset (git-prolly requires this)
+        let dataset_path = temp_dir.path().join("dataset");
+        std::fs::create_dir(&dataset_path).expect("Failed to create dataset directory");
+
+        // Change to the dataset subdirectory
+        let original_dir = std::env::current_dir().expect("Failed to get current dir");
+        std::env::set_current_dir(&dataset_path).expect("Failed to change directory");
+
+        // Initialize the versioned store from the dataset subdirectory
+        let mut store =
+            GitVersionedKvStore::<32>::init(&dataset_path).expect("Failed to initialize store");
+
+        // Insert test data
+        let key = b"proof_test_key".to_vec();
+        let value = b"proof_test_value".to_vec();
+
+        store
+            .insert(key.clone(), value.clone())
+            .expect("Failed to insert");
+        store
+            .commit("Add test data for proof")
+            .expect("Failed to commit");
+
+        // Test generate_proof method exists and works
+        let proof = store.generate_proof(&key);
+
+        // Test verify method with correct value
+        assert!(store.verify(proof.clone(), &key, Some(&value)));
+
+        // Test verify method for existence only
+        assert!(store.verify(proof.clone(), &key, None));
+
+        // Test verify with wrong value should fail
+        let wrong_value = b"wrong_value".to_vec();
+        assert!(!store.verify(proof.clone(), &key, Some(&wrong_value)));
+
+        // Restore original directory
+        std::env::set_current_dir(original_dir).expect("Failed to restore directory");
+    }
 }
 
 // Generic diff functionality for all storage types

src/python.rs

@@ -1123,6 +1123,42 @@ impl PyVersionedKvStore {
         let store = self.inner.lock().unwrap();
         Ok(store.storage_backend().clone().into())
     }
+
+    fn generate_proof(&self, py: Python, key: &Bound<'_, PyBytes>) -> PyResult<Py<PyBytes>> {
+        let key_vec = key.as_bytes().to_vec();
+
+        let proof_bytes = py.allow_threads(|| {
+            let store = self.inner.lock().unwrap();
+            let proof = store.generate_proof(&key_vec);
+
+            bincode::serialize(&proof)
+                .map_err(|e| PyValueError::new_err(format!("Proof serialization failed: {}", e)))
+        })?;
+
+        Ok(PyBytes::new_bound(py, &proof_bytes).into())
+    }
+
+    #[pyo3(signature = (proof_bytes, key, expected_value=None))]
+    fn verify_proof(
+        &self,
+        py: Python,
+        proof_bytes: &Bound<'_, PyBytes>,
+        key: &Bound<'_, PyBytes>,
+        expected_value: Option<&Bound<'_, PyBytes>>,
+    ) -> PyResult<bool> {
+        let key_vec = key.as_bytes().to_vec();
+        let proof_vec = proof_bytes.as_bytes().to_vec();
+        let value_option = expected_value.map(|v| v.as_bytes().to_vec());
+
+        py.allow_threads(|| {
+            let proof: crate::proof::Proof<32> = bincode::deserialize(&proof_vec).map_err(|e| {
+                PyValueError::new_err(format!("Proof deserialization failed: {}", e))
+            })?;
+
+            let store = self.inner.lock().unwrap();
+            Ok(store.verify(proof, &key_vec, value_option.as_deref()))
+        })
+    }
 }
 
 #[cfg(feature = "git")]