Cleanup for v0.3.0 Release (#97)

Author: zhangfengcdt

Cargo.toml

@@ -2,7 +2,7 @@
 name = "prollytree"
 description = "A prolly (probabilistic) tree for efficient storage, retrieval, and modification of ordered data."
 authors = ["Feng Zhang <[email protected]>"]
-version = "0.2.1-beta"
+version = "0.3.0"
 edition = "2021"
 
 license = "Apache-2.0"

README.md

@@ -23,18 +23,18 @@ Add to your `Cargo.toml`:
 
 ```toml
 [dependencies]
-prollytree = "0.2.0"
+prollytree = "0.3.0"
 
 # Optional features
-prollytree = { version = "0.2.0", features = ["git", "sql", "rig"] }
+prollytree = { version = "0.3.0", features = ["git", "sql", "rig"] }
 ```
 
 ## Examples
 
 ### Basic Tree Operations
 
 ```rust
-use prollytree::tree::ProllyTree;
+use prollytree::tree::{ProllyTree, Tree};
 use prollytree::storage::InMemoryNodeStorage;
 
 let storage = InMemoryNodeStorage::<32>::new();
@@ -44,89 +44,87 @@ let mut tree = ProllyTree::new(storage, Default::default());
 tree.insert(b"user:alice".to_vec(), b"Alice Johnson".to_vec());
 tree.insert(b"config:timeout".to_vec(), b"30".to_vec());
 
-// Query data
-let value = tree.find(b"user:alice")?;
-println!("Found: {}", String::from_utf8(value)?);
+// Query data - find returns a node, extract the value
+if let Some(node) = tree.find(b"user:alice") {
+    for (i, key) in node.keys.iter().enumerate() {
+        if key == b"user:alice" {
+            let value = &node.values[i];
+            println!("Found: {}", String::from_utf8(value.clone())?);
+            break;
+        }
+    }
+}
 
 // Generate cryptographic proof
-let proof = tree.generate_proof(b"user:alice")?;
-let is_valid = tree.verify_proof(&proof, b"user:alice", b"Alice Johnson");
+let proof = tree.generate_proof(b"user:alice");
+let is_valid = tree.verify(proof, b"user:alice", Some(b"Alice Johnson"));
 ```
 
 ### Git-backed Versioned Storage
 
 ```rust
 use prollytree::git::GitVersionedKvStore;
+use std::process::Command;
+use std::fs;
 
-let mut store = GitVersionedKvStore::init("./data")?;
+// Setup: Create a temporary Git repository (in real use, you'd have an existing repo)
+let repo_path = "/tmp/demo_git_repo";
+fs::create_dir_all(repo_path)?;
+Command::new("git").args(&["init"]).current_dir(repo_path).output()?;
 
-// Version your data like Git
-store.set(b"config/api_key", b"secret123")?;
-store.commit("Initial config")?;
-
-// Branch for experiments
-store.checkout_new_branch("feature/optimization")?;
-store.set(b"config/timeout", b"60")?;
-store.commit("Increase timeout")?;
-
-// Three-way merge back to main
-store.checkout("main")?;
-store.merge("feature/optimization")?;
-```
+// Switch to repo directory and create dataset
+std::env::set_current_dir(repo_path)?;
+fs::create_dir_all("data")?;
+let mut store = GitVersionedKvStore::<32>::init("data")?;
 
-### SQL Interface with Time Travel
-
-```rust
-use prollytree::sql::ProllyStorage;
-use gluesql_core::prelude::Glue;
-
-let storage = ProllyStorage::<32>::init("./data")?;
-let mut glue = Glue::new(storage);
+// Now use Git-backed versioned storage
+store.insert(b"config/api_key".to_vec(), b"secret123".to_vec())?;
+store.commit("Initial config")?;
 
-// Standard SQL operations
-glue.execute("CREATE TABLE users (id INTEGER, name TEXT)").await?;
-glue.execute("INSERT INTO users VALUES (1, 'Alice')").await?;
+// Retrieve data
+if let Some(value) = store.get(b"config/api_key") {
+    println!("Retrieved: {}", String::from_utf8(value)?);
+}
 
-// Time travel queries
-glue.storage.commit("v1.0").await?;
-glue.execute("UPDATE users SET name = 'Alice Smith' WHERE id = 1").await?;
+// Add more data and commit
+store.insert(b"config/timeout".to_vec(), b"30".to_vec())?;
+store.commit("Add timeout config")?;
 
-// Query historical data
-let v1_data = glue.storage.query_at_commit("v1.0",
-    "SELECT * FROM users WHERE id = 1").await?;
+// Create branches for parallel development
+store.create_branch("experimental")?;
+println!("Git-backed storage with full version control!");
 ```
 
-### AI Agent Memory
+### Multiple Storage Backends
 
 ```rust
-use prollytree::agent::{AgentMemorySystem, MemoryQuery};
-
-let mut memory = AgentMemorySystem::init_with_thread_safe_git(
-    "./agent_memory", "agent_001".to_string(), None
-)?;
-
-// Store conversation context
-memory.short_term.store_conversation_turn(
-    "session_123", "user", "What's the weather today?", None
-).await?;
-
-// Store persistent knowledge
-memory.semantic.store_fact(
-    "weather", "temperature",
-    json!({"location": "Tokyo", "temp": "22°C"}),
-    0.9, "weather_api"
-).await?;
-
-// Query and checkpoint
-let memories = memory.semantic.query(MemoryQuery::text("Tokyo")).await?;
-let checkpoint = memory.checkpoint("Weather conversation").await?;
+use prollytree::tree::{ProllyTree, Tree};
+use prollytree::storage::{InMemoryNodeStorage, FileNodeStorage};
+
+// In-memory storage (fast, temporary)
+let mem_storage = InMemoryNodeStorage::<32>::new();
+let mut mem_tree = ProllyTree::new(mem_storage, Default::default());
+mem_tree.insert(b"session:abc123".to_vec(), b"active".to_vec());
+
+// File-based storage (persistent)
+let file_storage = FileNodeStorage::<32>::new("./tree_data".into());
+let mut file_tree = ProllyTree::new(file_storage, Default::default());
+file_tree.insert(b"user:alice".to_vec(), b"Alice Johnson".to_vec());
+
+// Both trees support the same operations
+if let Some(node) = mem_tree.find(b"session:abc123") {
+    println!("Session found in memory storage");
+}
+
+// For SQL functionality, see examples/sql.rs
+println!("Multiple storage backends working!");
 ```
 
 ## Feature Flags
 
 ```toml
 [dependencies.prollytree]
-version = "0.2.0"
+version = "0.3.0"
 features = [
     "git",              # Git-backed versioned storage
     "sql",              # SQL interface via GlueSQL
@@ -148,22 +146,24 @@ Run benchmarks: `cargo bench`
 
 ## Documentation & Examples
 
-- **[📖 Full API Documentation](https://docs.rs/prollytree)**
-- **[💡 Use Cases & Examples](examples/README.md)** - AI agents, version control, distributed systems
-- **[🐍 Python Bindings](python/README.md)** - Complete Python API
-- **[⚡ Performance Guide](docs/performance.md)** - Optimization tips
+- **[Full API Documentation](https://docs.rs/prollytree)**
+- **[Use Cases & Examples](examples/README.md)** - AI agents, version control, distributed systems
+- **[Python Bindings](python/README.md)** - Complete Python API
+- **[Performance Guide](docs/performance.md)** - Optimization tips
 
 ## CLI Tool
 
 ```bash
 # Install git-prolly CLI
 cargo install prollytree --features git
 
-# Use like Git for key-value data
-git-prolly init my-data
+# Setup git repository and create dataset
+git init my-repo && cd my-repo
+mkdir my-data && git-prolly init my-data  # Create dataset directory
+cd my-data
 git-prolly set "user:alice" "Alice Johnson"
 git-prolly commit -m "Add user"
-git-prolly checkout -b feature/updates
+git checkout -b feature/updates  # Use regular git for branching
 git-prolly merge main
 ```
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "prollytree"
-version = "0.2.1"
+version = "0.3.0"
 description = "Python bindings for ProllyTree - a probabilistic tree for efficient storage and retrieval"
 readme = "python/README.md"
 requires-python = ">=3.8"

python/docs/conf.py

@@ -26,8 +26,8 @@
 author = 'ProllyTree Contributors'
 
 # The full version, including alpha/beta/rc tags
-release = '0.2.1'
-version = '0.2.1'
+release = '0.3.0'
+version = '0.3.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

python/prollytree/__init__.py

@@ -62,4 +62,4 @@
 if git_available:
     __all__.extend(["WorktreeManager", "WorktreeVersionedKvStore"])
 
-__version__ = "0.2.1"
+__version__ = "0.3.0"

src/agent/embedding_search.rs

@@ -84,6 +84,8 @@ impl MockEmbeddingGenerator {
 /// Advanced search functionality for memory stores
 pub struct MemorySearchEngine<T: SearchableMemoryStore> {
     store: T,
+    /// Cache for embeddings to reduce API calls
+    /// Note: Reserved for future optimization features
     #[allow(dead_code)]
     embedding_cache: HashMap<String, Vec<f32>>,
 }

src/bin/prolly-ui.rs

@@ -22,7 +22,7 @@ use std::path::{Path, PathBuf};
 #[derive(Parser)]
 #[command(name = "prolly-ui")]
 #[command(about = "Generate static HTML visualization for git-prolly repositories")]
-#[command(version = "0.1.0")]
+#[command(version = "0.3.0")]
 struct Cli {
     /// Path to the main git repository containing datasets as subdirectories
     #[arg(help = "Repository path (defaults to current directory)")]

src/diff.rs

@@ -124,6 +124,7 @@ impl AgentPriorityResolver {
 
     /// Extract agent ID from key (assumes key format includes agent info)
     /// This is a simple implementation - in practice you might have more sophisticated key parsing
+    /// Note: Reserved for future agent-based conflict resolution features
     #[allow(dead_code)]
     fn extract_agent_id(&self, key: &[u8]) -> Option<String> {
         let key_str = String::from_utf8_lossy(key);
@@ -136,6 +137,8 @@ impl AgentPriorityResolver {
         None
     }
 
+    /// Get priority for a given key based on its agent ID
+    /// Note: Reserved for future agent-based conflict resolution features
     #[allow(dead_code)]
     fn get_priority_for_key(&self, key: &[u8]) -> u32 {
         self.extract_agent_id(key)

src/git/versioned_store.rs

@@ -250,7 +250,12 @@ where
 
         // Create tree object in Git using git commands
         // Get the git root directory
-        let git_root = Self::find_git_root(self.git_repo.path().parent().unwrap()).unwrap();
+        let parent_path =
+            self.git_repo.path().parent().ok_or_else(|| {
+                GitKvError::GitObjectError("Repository path has no parent".into())
+            })?;
+        let git_root = Self::find_git_root(parent_path)
+            .ok_or_else(|| GitKvError::GitObjectError("Could not find git root".into()))?;
 
         // Stage all files in the current directory recursively
         let add_cmd = std::process::Command::new("git")
@@ -476,7 +481,7 @@ where
         // Get the current time
         let now = std::time::SystemTime::now()
             .duration_since(std::time::UNIX_EPOCH)
-            .unwrap()
+            .map_err(|e| GitKvError::GitObjectError(format!("System time error: {e}")))?
             .as_secs() as i64;
 
         // Get git user configuration

src/lib.rs

@@ -36,7 +36,7 @@ limitations under the License.
 //!
 //! ```toml
 //! [dependencies]
-//! prolly = "0.1.0"
+//! prollytree = "0.3.0"
 //! ```
 //!
 //! Follow examples in the github repository to get started.