codespine 0.1.8__tar.gz → 0.3.0__tar.gz

codespine-0.3.0/PKG-INFO

@@ -0,0 +1,333 @@
+Metadata-Version: 2.4
+Name: codespine
+Version: 0.3.0
+Summary: Local Java code intelligence indexer backed by a graph database
+Author: CodeSpine contributors
+License: MIT License
+        
+        Copyright (c) 2026 CodeSpine contributors
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/vinayak3022/codeSpine
+Project-URL: Repository, https://github.com/vinayak3022/codeSpine
+Project-URL: Issues, https://github.com/vinayak3022/codeSpine/issues
+Keywords: java,code-indexing,graph,kuzu,mcp
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Quality Assurance
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: kuzu
+Requires-Dist: tree-sitter
+Requires-Dist: tree-sitter-java
+Requires-Dist: fastmcp
+Requires-Dist: psutil
+Requires-Dist: watchfiles
+Provides-Extra: ml
+Requires-Dist: sentence-transformers; extra == "ml"
+Requires-Dist: numpy; extra == "ml"
+Provides-Extra: community
+Requires-Dist: igraph; extra == "community"
+Requires-Dist: leidenalg; extra == "community"
+Provides-Extra: full
+Requires-Dist: sentence-transformers; extra == "full"
+Requires-Dist: numpy; extra == "full"
+Requires-Dist: igraph; extra == "full"
+Requires-Dist: leidenalg; extra == "full"
+Dynamic: license-file
+
+# CodeSpine
+
+**A code-intelligence layer for Java codebases — purpose-built for AI agents.**
+
+Instead of making your agent read hundreds of raw source files, CodeSpine maps your entire codebase into a live graph and exposes it through 24 structured MCP tools.
+Your agent asks a question, gets a precise answer — no file trawling, no wasted tokens, no hallucinated call chains.
+
+> **Token efficiency in practice**: a `get_symbol_context` call returns a fully-resolved call graph for a symbol in one round-trip.
+> The equivalent "read every relevant file" approach typically costs 10-50× more tokens and still misses transitive edges.
+
+---
+
+## How it works
+
+```
+Your Java codebase
+       │
+  codespine analyse          ← one-time (or on-demand) indexing
+       │
+  ~/.codespine_db            ← Kuzu graph DB (symbols, calls, communities, flows …)
+       │
+  codespine mcp              ← FastMCP server — 24 tools
+       │
+  Your AI agent (Claude, GPT, Cursor, Cline …)
+```
+
+Agents talk to the MCP server. They never need to open a `.java` file unless they are actually editing it.
+
+---
+
+## Installation
+
+```bash
+pip install codespine
+```
+
+Optional: install `sentence-transformers` to enable semantic vector search (adds ~500 MB of model weight).
+
+```bash
+pip install sentence-transformers
+```
+
+---
+
+## Quick Start
+
+### 1 — Index your codebase
+
+```bash
+# Fast (BM25 + fuzzy search, no embeddings — recommended first run)
+codespine analyse /path/to/your/project
+
+# Full (adds semantic vector search, takes longer)
+codespine analyse /path/to/your/project --embed
+
+# Deep (+ dead code, execution flows, communities, git coupling)
+codespine analyse /path/to/your/project --deep
+```
+
+Example output:
+
+```
+$ codespine analyse .
+Walking files...               142 files found
+Parsing code...                142/142  (parallel, 4 workers)
+Tracing calls...               847 calls resolved
+Analyzing types...             234 type relationships
+Detecting communities...       8 clusters found
+Detecting execution flows...   34 processes found
+Finding dead code...           12 unreachable symbols
+Analyzing git history...       18 coupled file pairs
+
+Done in 18s — 623 symbols, 1 847 edges, 8 clusters, 34 flows
+```
+
+### 2 — Wire up MCP
+
+Add to your MCP config (`~/.claude/mcp.json` or equivalent):
+
+```json
+{
+  "mcpServers": {
+    "codespine": {
+      "command": "codespine",
+      "args": ["mcp"]
+    }
+  }
+}
+```
+
+### 3 — Let the agent explore
+
+The agent can now call tools like:
+
+```
+search_hybrid("payment retry logic")
+get_symbol_context("processPayment")
+get_impact("com.example.PaymentService#charge")
+detect_dead_code()
+get_codebase_stats()
+```
+
+---
+
+## MCP Tools (24)
+
+### Connectivity & Discovery
+
+| Tool | What it does |
+|------|-------------|
+| `ping()` | Confirm the server is alive. Call this first. |
+| `get_capabilities()` | Returns what is indexed right now — projects, symbol counts, which features are available, and whether watch mode is running. Call before other tools to avoid trial-and-error. |
+| `list_projects()` | List every indexed project with path, symbol count, and file count. |
+| `get_codebase_stats()` | Per-project breakdown: files, classes, methods, calls, embeddings, totals. |
+
+### Search
+
+| Tool | What it does |
+|------|-------------|
+| `search_hybrid(query, k, project)` | BM25 + semantic vector + fuzzy, fused with RRF. Scope to a project with `project=`. |
+| `find_symbol(name, kind, project, limit)` | Exact / prefix name lookup returning **all** matches grouped by project. Use this when the same class name exists in multiple projects to pick the right one. |
+| `list_packages(project, limit)` | All Java packages with class count, grouped by project. Good for structural orientation before searching. |
+
+### Analysis
+
+| Tool | What it does |
+|------|-------------|
+| `get_symbol_context(query, max_depth, project)` | Full call graph context for a symbol — callers, callees, types, up to `max_depth` hops. |
+| `get_impact(symbol, max_depth, project)` | Depth-grouped impact analysis with confidence scores. Shows what breaks if this symbol changes. |
+| `detect_dead_code(limit, project)` | Unreachable symbols after applying framework exemptions (Spring, JPA, …). |
+| `trace_execution_flows(entry_symbol, max_depth, project)` | Execution paths from entry points (or a specific symbol). |
+| `get_symbol_community(symbol)` | Which community cluster a symbol belongs to, with co-members. |
+| `get_change_coupling(months, min_strength, min_cochanges, project)` | Git-derived file pairs that change together — useful for predicting collateral changes. |
+
+### Git
+
+| Tool | What it does |
+|------|-------------|
+| `git_log(file_path, limit, project)` | Commit history for a file or the whole repo. |
+| `git_diff(ref, file_path, project)` | Diff against a ref (default `HEAD`). |
+| `compare_branches(base_ref, head_ref)` | Symbol-level diff between two branches — which classes/methods changed. |
+
+### Watch Mode (live incremental reindex)
+
+| Tool | What it does |
+|------|-------------|
+| `start_watch(path, global_interval)` | Start incremental reindexing in the background. Watches for file changes and updates the graph within `global_interval` seconds. **Recommended**: keep this running during active development sessions so the graph stays fresh. |
+| `stop_watch()` | Gracefully stop the background watcher. |
+| `get_watch_status()` | Check if watch is running — uptime, path, interval. |
+
+### On-demand Analysis (non-blocking)
+
+| Tool | What it does |
+|------|-------------|
+| `analyse_project(path, full, deep, embed)` | Trigger a full re-analysis as a background job. Returns immediately. Poll `get_analyse_status()` for progress. |
+| `get_analyse_status()` | Check background analysis — running / done / failed, last log lines. |
+
+### Index Management
+
+| Tool | What it does |
+|------|-------------|
+| `reset_project(project_id)` | Delete all graph data for one project (clean-slate re-index). |
+| `reset_index()` | Wipe the entire index — all projects, communities, flows. |
+
+### Power / Debug
+
+| Tool | What it does |
+|------|-------------|
+| `run_cypher(query)` | Execute a raw Cypher read query against the graph (Kuzu dialect). For advanced exploration. |
+
+---
+
+## CLI Reference
+
+### Indexing
+
+```bash
+codespine analyse <path>              # fast index (no embeddings)
+codespine analyse <path> --embed      # + semantic vectors
+codespine analyse <path> --full       # force full re-index (skip incremental)
+codespine analyse <path> --deep       # + dead code, flows, communities, git coupling
+codespine analyse <path> --deep --embed  # everything
+```
+
+### Search & Analysis
+
+```bash
+codespine search "payment retry bug" [--k 20] [--json]
+codespine context "processPayment"   [--max-depth 3] [--json]
+codespine impact  "com.example.Service#processPayment(java.lang.String)" [--max-depth 4] [--json]
+codespine deadcode [--limit 200] [--json]
+codespine flow   [--entry <symbol>] [--max-depth 6] [--json]
+codespine community [--symbol <symbol>] [--json]
+codespine coupling  [--months 6] [--min-strength 0.3] [--min-cochanges 3] [--json]
+codespine diff <base>..<head> [--json]
+```
+
+### Stats
+
+```bash
+codespine stats           # per-project table: files, classes, methods, calls, embeddings
+codespine stats --json    # machine-readable output
+```
+
+### Watch
+
+```bash
+codespine watch [--path .] [--global-interval 30]
+```
+
+### Index Management
+
+```bash
+codespine clear-project <project_id>   # remove one project from the graph
+codespine clear-index                  # wipe the entire index
+```
+
+---
+
+## Workspace / Multi-Project Support
+
+CodeSpine understands three levels of hierarchy:
+
+```
+~/IdeaProjects/              ← workspace  (a folder of independent projects)
+├── payments-service/        ← project    (has its own .git / pom.xml)
+│   ├── core/                ← module     (Maven <module> or Gradle subproject)
+│   └── api/                 ← module
+└── inventory-service/       ← project
+    └── (single-module)
+```
+
+- **Workspace detection**: if the path you give to `analyse` has no `.git` or build file at its root, CodeSpine scans one level down for sub-projects and indexes them all.
+- **Project IDs**: single-module → `payments-service`; multi-module → `payments-service::core`, `payments-service::api`.
+- **Scoped queries**: every analysis and search tool accepts an optional `project=` parameter so agents can work within one project without noise from others.
+- **Cross-project search**: omit `project=` to search across everything.
+
+---
+
+## Embedding / Speed Trade-off
+
+| Flag | Index time | Search modes available |
+|------|-----------|----------------------|
+| *(no flag)* | Fast (~seconds–minutes) | BM25, fuzzy, exact |
+| `--embed` | Slower (minutes, depends on model) | BM25, fuzzy, exact + **semantic vector** |
+
+`sentence-transformers` must be installed for `--embed` to have any effect.
+If it is not installed, indexing always skips embeddings silently.
+
+Most agent workflows work great without embeddings — BM25 + fuzzy covers keyword, partial-name, and typo-tolerant search. Add `--embed` when you need concept-level similarity ("find all classes related to retry logic").
+
+---
+
+## Runtime Paths
+
+| Path | Purpose |
+|------|---------|
+| `~/.codespine_db` | Kuzu graph database |
+| `~/.codespine.pid` | Watch-mode PID file |
+| `~/.codespine.log` | Watch-mode log |
+| `~/.codespine_embedding_cache.sqlite3` | Embedding vector cache |
+
+---
+
+## Project Docs
+
+- [Contributing](.github/CONTRIBUTING.md)
+- [Security](.github/SECURITY.md)
+- [Code of Conduct](.github/CODE_OF_CONDUCT.md)

codespine-0.3.0/README.md

@@ -0,0 +1,269 @@
+# CodeSpine
+
+**A code-intelligence layer for Java codebases — purpose-built for AI agents.**
+
+Instead of making your agent read hundreds of raw source files, CodeSpine maps your entire codebase into a live graph and exposes it through 24 structured MCP tools.
+Your agent asks a question, gets a precise answer — no file trawling, no wasted tokens, no hallucinated call chains.
+
+> **Token efficiency in practice**: a `get_symbol_context` call returns a fully-resolved call graph for a symbol in one round-trip.
+> The equivalent "read every relevant file" approach typically costs 10-50× more tokens and still misses transitive edges.
+
+---
+
+## How it works
+
+```
+Your Java codebase
+       │
+  codespine analyse          ← one-time (or on-demand) indexing
+       │
+  ~/.codespine_db            ← Kuzu graph DB (symbols, calls, communities, flows …)
+       │
+  codespine mcp              ← FastMCP server — 24 tools
+       │
+  Your AI agent (Claude, GPT, Cursor, Cline …)
+```
+
+Agents talk to the MCP server. They never need to open a `.java` file unless they are actually editing it.
+
+---
+
+## Installation
+
+```bash
+pip install codespine
+```
+
+Optional: install `sentence-transformers` to enable semantic vector search (adds ~500 MB of model weight).
+
+```bash
+pip install sentence-transformers
+```
+
+---
+
+## Quick Start
+
+### 1 — Index your codebase
+
+```bash
+# Fast (BM25 + fuzzy search, no embeddings — recommended first run)
+codespine analyse /path/to/your/project
+
+# Full (adds semantic vector search, takes longer)
+codespine analyse /path/to/your/project --embed
+
+# Deep (+ dead code, execution flows, communities, git coupling)
+codespine analyse /path/to/your/project --deep
+```
+
+Example output:
+
+```
+$ codespine analyse .
+Walking files...               142 files found
+Parsing code...                142/142  (parallel, 4 workers)
+Tracing calls...               847 calls resolved
+Analyzing types...             234 type relationships
+Detecting communities...       8 clusters found
+Detecting execution flows...   34 processes found
+Finding dead code...           12 unreachable symbols
+Analyzing git history...       18 coupled file pairs
+
+Done in 18s — 623 symbols, 1 847 edges, 8 clusters, 34 flows
+```
+
+### 2 — Wire up MCP
+
+Add to your MCP config (`~/.claude/mcp.json` or equivalent):
+
+```json
+{
+  "mcpServers": {
+    "codespine": {
+      "command": "codespine",
+      "args": ["mcp"]
+    }
+  }
+}
+```
+
+### 3 — Let the agent explore
+
+The agent can now call tools like:
+
+```
+search_hybrid("payment retry logic")
+get_symbol_context("processPayment")
+get_impact("com.example.PaymentService#charge")
+detect_dead_code()
+get_codebase_stats()
+```
+
+---
+
+## MCP Tools (24)
+
+### Connectivity & Discovery
+
+| Tool | What it does |
+|------|-------------|
+| `ping()` | Confirm the server is alive. Call this first. |
+| `get_capabilities()` | Returns what is indexed right now — projects, symbol counts, which features are available, and whether watch mode is running. Call before other tools to avoid trial-and-error. |
+| `list_projects()` | List every indexed project with path, symbol count, and file count. |
+| `get_codebase_stats()` | Per-project breakdown: files, classes, methods, calls, embeddings, totals. |
+
+### Search
+
+| Tool | What it does |
+|------|-------------|
+| `search_hybrid(query, k, project)` | BM25 + semantic vector + fuzzy, fused with RRF. Scope to a project with `project=`. |
+| `find_symbol(name, kind, project, limit)` | Exact / prefix name lookup returning **all** matches grouped by project. Use this when the same class name exists in multiple projects to pick the right one. |
+| `list_packages(project, limit)` | All Java packages with class count, grouped by project. Good for structural orientation before searching. |
+
+### Analysis
+
+| Tool | What it does |
+|------|-------------|
+| `get_symbol_context(query, max_depth, project)` | Full call graph context for a symbol — callers, callees, types, up to `max_depth` hops. |
+| `get_impact(symbol, max_depth, project)` | Depth-grouped impact analysis with confidence scores. Shows what breaks if this symbol changes. |
+| `detect_dead_code(limit, project)` | Unreachable symbols after applying framework exemptions (Spring, JPA, …). |
+| `trace_execution_flows(entry_symbol, max_depth, project)` | Execution paths from entry points (or a specific symbol). |
+| `get_symbol_community(symbol)` | Which community cluster a symbol belongs to, with co-members. |
+| `get_change_coupling(months, min_strength, min_cochanges, project)` | Git-derived file pairs that change together — useful for predicting collateral changes. |
+
+### Git
+
+| Tool | What it does |
+|------|-------------|
+| `git_log(file_path, limit, project)` | Commit history for a file or the whole repo. |
+| `git_diff(ref, file_path, project)` | Diff against a ref (default `HEAD`). |
+| `compare_branches(base_ref, head_ref)` | Symbol-level diff between two branches — which classes/methods changed. |
+
+### Watch Mode (live incremental reindex)
+
+| Tool | What it does |
+|------|-------------|
+| `start_watch(path, global_interval)` | Start incremental reindexing in the background. Watches for file changes and updates the graph within `global_interval` seconds. **Recommended**: keep this running during active development sessions so the graph stays fresh. |
+| `stop_watch()` | Gracefully stop the background watcher. |
+| `get_watch_status()` | Check if watch is running — uptime, path, interval. |
+
+### On-demand Analysis (non-blocking)
+
+| Tool | What it does |
+|------|-------------|
+| `analyse_project(path, full, deep, embed)` | Trigger a full re-analysis as a background job. Returns immediately. Poll `get_analyse_status()` for progress. |
+| `get_analyse_status()` | Check background analysis — running / done / failed, last log lines. |
+
+### Index Management
+
+| Tool | What it does |
+|------|-------------|
+| `reset_project(project_id)` | Delete all graph data for one project (clean-slate re-index). |
+| `reset_index()` | Wipe the entire index — all projects, communities, flows. |
+
+### Power / Debug
+
+| Tool | What it does |
+|------|-------------|
+| `run_cypher(query)` | Execute a raw Cypher read query against the graph (Kuzu dialect). For advanced exploration. |
+
+---
+
+## CLI Reference
+
+### Indexing
+
+```bash
+codespine analyse <path>              # fast index (no embeddings)
+codespine analyse <path> --embed      # + semantic vectors
+codespine analyse <path> --full       # force full re-index (skip incremental)
+codespine analyse <path> --deep       # + dead code, flows, communities, git coupling
+codespine analyse <path> --deep --embed  # everything
+```
+
+### Search & Analysis
+
+```bash
+codespine search "payment retry bug" [--k 20] [--json]
+codespine context "processPayment"   [--max-depth 3] [--json]
+codespine impact  "com.example.Service#processPayment(java.lang.String)" [--max-depth 4] [--json]
+codespine deadcode [--limit 200] [--json]
+codespine flow   [--entry <symbol>] [--max-depth 6] [--json]
+codespine community [--symbol <symbol>] [--json]
+codespine coupling  [--months 6] [--min-strength 0.3] [--min-cochanges 3] [--json]
+codespine diff <base>..<head> [--json]
+```
+
+### Stats
+
+```bash
+codespine stats           # per-project table: files, classes, methods, calls, embeddings
+codespine stats --json    # machine-readable output
+```
+
+### Watch
+
+```bash
+codespine watch [--path .] [--global-interval 30]
+```
+
+### Index Management
+
+```bash
+codespine clear-project <project_id>   # remove one project from the graph
+codespine clear-index                  # wipe the entire index
+```
+
+---
+
+## Workspace / Multi-Project Support
+
+CodeSpine understands three levels of hierarchy:
+
+```
+~/IdeaProjects/              ← workspace  (a folder of independent projects)
+├── payments-service/        ← project    (has its own .git / pom.xml)
+│   ├── core/                ← module     (Maven <module> or Gradle subproject)
+│   └── api/                 ← module
+└── inventory-service/       ← project
+    └── (single-module)
+```
+
+- **Workspace detection**: if the path you give to `analyse` has no `.git` or build file at its root, CodeSpine scans one level down for sub-projects and indexes them all.
+- **Project IDs**: single-module → `payments-service`; multi-module → `payments-service::core`, `payments-service::api`.
+- **Scoped queries**: every analysis and search tool accepts an optional `project=` parameter so agents can work within one project without noise from others.
+- **Cross-project search**: omit `project=` to search across everything.
+
+---
+
+## Embedding / Speed Trade-off
+
+| Flag | Index time | Search modes available |
+|------|-----------|----------------------|
+| *(no flag)* | Fast (~seconds–minutes) | BM25, fuzzy, exact |
+| `--embed` | Slower (minutes, depends on model) | BM25, fuzzy, exact + **semantic vector** |
+
+`sentence-transformers` must be installed for `--embed` to have any effect.
+If it is not installed, indexing always skips embeddings silently.
+
+Most agent workflows work great without embeddings — BM25 + fuzzy covers keyword, partial-name, and typo-tolerant search. Add `--embed` when you need concept-level similarity ("find all classes related to retry logic").
+
+---
+
+## Runtime Paths
+
+| Path | Purpose |
+|------|---------|
+| `~/.codespine_db` | Kuzu graph database |
+| `~/.codespine.pid` | Watch-mode PID file |
+| `~/.codespine.log` | Watch-mode log |
+| `~/.codespine_embedding_cache.sqlite3` | Embedding vector cache |
+
+---
+
+## Project Docs
+
+- [Contributing](.github/CONTRIBUTING.md)
+- [Security](.github/SECURITY.md)
+- [Code of Conduct](.github/CODE_OF_CONDUCT.md)

{codespine-0.1.8 → codespine-0.3.0}/codespine/__init__.py

@@ -1,4 +1,4 @@
 """CodeSpine package."""
 
 __all__ = ["__version__"]
-__version__ = "0.1.8"
+__version__ = "0.3.0"

{codespine-0.1.8 → codespine-0.3.0}/codespine/analysis/context.py

@@ -6,13 +6,13 @@ from codespine.analysis.impact import analyze_impact
 from codespine.search.hybrid import hybrid_search
 
 
-def build_symbol_context(store, query: str, max_depth: int = 3) -> dict:
-    search_results = hybrid_search(store, query, k=10)
+def build_symbol_context(store, query: str, max_depth: int = 3, project: str | None = None) -> dict:
+    search_results = hybrid_search(store, query, k=10, project=project)
     focus = search_results[0] if search_results else None
 
-    impact = analyze_impact(store, query, max_depth=max_depth)
+    impact = analyze_impact(store, query, max_depth=max_depth, project=project)
     community = symbol_community(store, query)
-    flows = trace_execution_flows(store, entry_symbol=query, max_depth=max_depth + 2)
+    flows = trace_execution_flows(store, entry_symbol=query, max_depth=max_depth + 2, project=project)
 
     return {
         "query": query,

{codespine-0.1.8 → codespine-0.3.0}/codespine/analysis/deadcode.py

@@ -28,24 +28,42 @@ def _modifier_tokens(modifiers) -> set[str]:
     return {str(m).strip() for m in modifiers}
 
 
-def detect_dead_code(store, limit: int = 200) -> list[dict]:
+def detect_dead_code(store, limit: int = 200, project: str | None = None) -> list[dict]:
     """Java-aware dead code detection with exemption passes."""
-    candidates = store.query_records(
-        """
-        MATCH (m:Method), (c:Class)
-        WHERE m.class_id = c.id
-          AND NOT EXISTS { MATCH (:Method)-[:CALLS]->(m) }
-        RETURN m.id as method_id,
-               m.name as name,
-               m.signature as signature,
-               m.modifiers as modifiers,
-               c.fqcn as class_fqcn,
-               m.is_constructor as is_constructor,
-               m.is_test as is_test
-        LIMIT $limit
-        """,
-        {"limit": int(limit * 3)},
-    )
+    if project:
+        candidates = store.query_records(
+            """
+            MATCH (m:Method), (c:Class), (f:File)
+            WHERE m.class_id = c.id AND c.file_id = f.id AND f.project_id = $proj
+              AND NOT EXISTS { MATCH (:Method)-[:CALLS]->(m) }
+            RETURN m.id as method_id,
+                   m.name as name,
+                   m.signature as signature,
+                   m.modifiers as modifiers,
+                   c.fqcn as class_fqcn,
+                   m.is_constructor as is_constructor,
+                   m.is_test as is_test
+            LIMIT $limit
+            """,
+            {"limit": int(limit * 3), "proj": project},
+        )
+    else:
+        candidates = store.query_records(
+            """
+            MATCH (m:Method), (c:Class)
+            WHERE m.class_id = c.id
+              AND NOT EXISTS { MATCH (:Method)-[:CALLS]->(m) }
+            RETURN m.id as method_id,
+                   m.name as name,
+                   m.signature as signature,
+                   m.modifiers as modifiers,
+                   c.fqcn as class_fqcn,
+                   m.is_constructor as is_constructor,
+                   m.is_test as is_test
+            LIMIT $limit
+            """,
+            {"limit": int(limit * 3)},
+        )
 
     if not candidates:
         return []