cytoscnpy 1.2.2__cp39-cp39-win_amd64.whl

cytoscnpy/__init__.py

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+from .cytoscnpy import run
+
+__all__ = ["run"]

cytoscnpy/__main__.py

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+from .cli import main
+
+if __name__ == "__main__":
+    main()

cytoscnpy/cli.py

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+import sys
+from cytoscnpy import run
+
+
+def main():
+    args = sys.argv[1:]
+    try:
+        rc = run(args)
+        raise SystemExit(int(rc))
+    except Exception as e:
+        print(f"cytoscnpy error: {e}", file=sys.stderr)
+        raise SystemExit(1)
+
+if __name__ == "__main__":
+    main()

cytoscnpy-1.2.2.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: cytoscnpy
+Version: 1.2.2
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+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: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Topic :: Software Development :: Quality Assurance
+Classifier: Topic :: Software Development :: Testing
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Requires-Dist: pytest>=7.0 ; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0 ; extra == 'dev'
+Requires-Dist: ruff ; extra == 'dev'
+Requires-Dist: tomli ; python_full_version < '3.11' and extra == 'dev'
+Requires-Dist: trove-classifiers ; extra == 'dev'
+Requires-Dist: mkdocs-material>=9.5.0 ; extra == 'docs'
+Requires-Dist: mkdocs-minify-plugin>=0.8.0 ; extra == 'docs'
+Provides-Extra: dev
+Provides-Extra: docs
+Summary: High-performance dead code elimination analysis tool for Python.
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+# CytoScnPy - High-Performance Python Static Analysis
+
+[![CI](https://github.com/djinn09/CytoScnPy/actions/workflows/test-ci.yml/badge.svg)](https://github.com/djinn09/CytoScnPy/actions/workflows/test-ci.yml)
+[![Coverage](https://github.com/djinn09/CytoScnPy/actions/workflows/coverage.yml/badge.svg)](https://github.com/djinn09/CytoScnPy/actions/workflows/coverage.yml)
+[![codecov](https://codecov.io/gh/djinn09/CytoScnPy/branch/main/graph/badge.svg)](https://codecov.io/gh/djinn09/CytoScnPy)
+[![Security Audit](https://github.com/djinn09/CytoScnPy/actions/workflows/security.yml/badge.svg)](https://github.com/djinn09/CytoScnPy/actions/workflows/security.yml)
+[![Docs](https://github.com/djinn09/CytoScnPy/actions/workflows/docs.yml/badge.svg)](https://github.com/djinn09/CytoScnPy/actions/workflows/docs.yml)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Version](https://img.shields.io/badge/version-1.2.2-green.svg)](https://github.com/djinn09/CytoScnPy)
+
+A fast static analysis tool for Python codebases, powered by Rust with hybrid Python integration. Detects dead code, security vulnerabilities (including taint analysis), and code quality issues with extreme speed. Code quality metrics are also provided.
+
+## Why CytoScnPy?
+
+- **Blazing Fast**: Faster in dead code detection.
+- **Memory Efficient**: Uses less memory.
+- **Comprehensive**: Dead code, secrets, security, taint analysis, quality metrics
+- **Framework Aware**: Flask, Django, FastAPI, Pydantic, Azure Functions
+- **Benchmarked**: Continuous benchmarking with 135-item ground truth suite
+
+## Installation
+
+**Linux / macOS:**
+
+```bash
+# Install
+curl -fsSL https://raw.githubusercontent.com/djinn09/CytoScnPy/main/install.sh | bash
+```
+
+**Windows (PowerShell):**
+
+```powershell
+# Install
+irm https://raw.githubusercontent.com/djinn09/CytoScnPy/main/install.ps1 | iex
+```
+
+**Via Pip:**
+
+```bash
+pip install cytoscnpy
+```
+
+**From Source:**
+
+```bash
+git clone https://github.com/djinn09/CytoScnPy.git
+cd CytoScnPy
+pip install maturin
+maturin develop -m cytoscnpy/Cargo.toml
+```
+
+### MCP Server (for AI Assistants)
+
+CytoScnPy includes an MCP server for AI assistant integration:
+
+```bash
+# Start MCP server (after pip install)
+cytoscnpy mcp-server
+```
+
+For Claude Desktop, Cursor, or GitHub Copilot configuration, see the **[MCP Server Documentation](cytoscnpy-mcp/README.md)**.
+
+## Features
+
+- **Dead Code Detection**: Unused functions, classes, imports, and variables with cross-module tracking.
+  - **Cascading Detection**: Methods inside unused classes are automatically flagged as unused.
+  - **Auto-Fix**: Remove dead code automatically with `--fix` (preview by default, use `--apply` to execute).
+- **Clone Detection**: Find duplicate code with `--clones`.
+- **Security Analysis**: Taint analysis (SQLi, XSS), secret scanning (API keys, suspicious variables), and dangerous code patterns (`eval`, `exec`).
+- **Code Quality Metrics**: Cyclomatic complexity, Halstead metrics, Maintainability Index, and raw metrics (LOC, SLOC).
+- **Framework Support**: Native understanding of Flask, Django, FastAPI, Pydantic, and Azure Functions v2 patterns.
+- **Smart Heuristics**: Handles dataclasses, `__all__` exports, visitor patterns, and dynamic attributes intelligently.
+- **Cross-File Detection**: Tracks symbol usage across the entire codebase, including nested packages and complex import chains, to ensure code used in other modules is never incorrectly flagged.
+
+## Usage
+
+> [!IMPORTANT] **Behavioral Change**: Starting from version 1.2.2, tests are **excluded by default** across both the CLI and the library API to reduce noise in production analysis. Use the `--include-tests` flag or set `include_tests = true` in your configuration to scan test files.
+
+### Command Line
+
+```bash
+cytoscnpy [PATHS]... [OPTIONS]
+```
+
+**Examples:**
+
+```bash
+# Dead code analysis
+cytoscnpy .                                     # Analyze current directory
+cytoscnpy /path/to/project --json               # JSON output for CI/CD
+
+# Security checks (short flags: -s, -d, -q)
+cytoscnpy . --secrets --danger --quality
+cytoscnpy . -s -d -q                        # Same with short flags
+
+# Confidence threshold (0-100)
+cytoscnpy . --confidence 80
+
+# Path filtering
+cytoscnpy . --exclude-folder venv --exclude-folder build
+cytoscnpy . --include-folder specific_venv      # Override defaults
+cytoscnpy . --include-tests
+
+# Jupyter notebooks
+cytoscnpy . --include-ipynb --ipynb-cells
+
+# Clone detection (find duplicate code)
+cytoscnpy . --clones --clone-similarity 0.8
+
+# Auto-fix dead code (preview first, then apply)
+cytoscnpy . --fix                    # Preview changes (dry-run by default)
+cytoscnpy . --fix --apply            # Apply changes
+cytoscnpy . --fix -a                 # Apply changes (short flag)
+
+# Generate HTML report (quality auto-enabled; add --secrets --danger for security)
+cytoscnpy . --html --secrets --danger
+```
+
+**Options:**
+
+| Flag                     | Description                                      |
+| ------------------------ | ------------------------------------------------ |
+| `-c, --confidence <N>`   | Set confidence threshold (0-100)                 |
+| `--root <PATH>`          | Project root for analysis (CI/CD mode)           |
+| `-s, --secrets`          | Scan for API keys, tokens, credentials           |
+| `-d, --danger`           | Scan for dangerous code + taint analysis         |
+| `-q, --quality`          | Scan for code quality issues                     |
+| `-n, --no-dead`          | Skip dead code detection (security/quality only) |
+| `--html`                 | Generate HTML report (auto-enables quality)      |
+| `--json`                 | Output results as JSON                           |
+| `-v, --verbose`          | Enable verbose output for debugging              |
+| `--quiet`                | Quiet mode: summary only, no tables              |
+| `--include-tests`        | Include test files in analysis                   |
+| `--exclude-folder <DIR>` | Exclude specific folders                         |
+| `--include-folder <DIR>` | Force include folders                            |
+| `--include-ipynb`        | Include Jupyter notebooks                        |
+| `--ipynb-cells`          | Report findings per notebook cell                |
+| `--clones`               | Detect duplicate code                            |
+| `--clone-similarity <N>` | Clone similarity threshold (0.0-1.0)             |
+| `--fix`                  | Preview dead code removal (dry-run by default)   |
+| `-a, --apply`            | Apply --fix changes to files                     |
+
+**CI/CD Gate Options:**
+
+| Flag                   | Description                                |
+| ---------------------- | ------------------------------------------ |
+| `--fail-threshold <N>` | Exit code 1 if unused code % > N           |
+| `--max-complexity <N>` | Exit code 1 if any function complexity > N |
+| `--min-mi <N>`         | Exit code 1 if maintainability index < N   |
+| `--fail-on-quality`    | Exit code 1 if any quality issues found    |
+| `--max-nesting <N>`    | Exit code 1 if any block nesting > N       |
+| `--max-args <N>`       | Exit code 1 if any function has > N args   |
+| `--max-lines <N>`      | Exit code 1 if any function has > N lines  |
+
+> **Full CLI Reference:** See [docs/CLI.md](docs/CLI.md) for complete command documentation.
+
+### Metric Subcommands
+
+```bash
+cytoscnpy raw .                    # Raw Metrics (LOC, SLOC, Comments)
+cytoscnpy cc .                     # Cyclomatic Complexity
+cytoscnpy hal .                    # Halstead Metrics
+cytoscnpy mi .                     # Maintainability Index
+cytoscnpy stats . --all            # Full project report (secrets, danger, quality)
+cytoscnpy stats . --all -o report.md  # Save report to file
+cytoscnpy files .                  # Per-file metrics table
+```
+
+> **Tip**: Add `--json` for machine-readable output, `--exclude-folder <DIR>` to skip directories globally, or `--ignore <PATTERN>` for subcommand-specific glob filtering.
+
+### Feature Flags
+
+The crate supports experimental features that can be enabled at compile time:
+
+| Feature | Description                                                                                 |
+| ------- | ------------------------------------------------------------------------------------------- |
+| `cfg`   | Enables Control Flow Graph (CFG) construction and behavioral validation for clone detection |
+
+To build with a feature enabled:
+
+```bash
+cargo build --features cfg
+```
+
+## ⚙️ Configuration
+
+Create `.cytoscnpy.toml` (uses `[cytoscnpy]`) or add to `pyproject.toml` (uses `[tool.cytoscnpy]`):
+
+**`.cytoscnpy.toml` example:**
+
+```toml
+[cytoscnpy]
+# General Settings
+confidence = 60  # Minimum confidence threshold (0-100)
+exclude_folders = ["venv", ".tox", "build", "node_modules", ".git"]
+include_folders = ["src", "tests"]  # Optional: whitelist folders
+include_tests = false  # Note: include_ipynb and ipynb_cells are CLI-only (use flags)
+
+# Analysis Features
+secrets = true
+danger = true
+quality = true
+
+# Fail Threshold (exit code 1 if exceeded)
+fail_threshold = 10.0  # Fail if >10% of code is unused
+# fail_threshold = 0.0  # Zero tolerance: fail on any unused code
+
+# Code Quality Thresholds
+max_lines = 100       # Max lines per function
+max_args = 5          # Max arguments per function
+max_complexity = 10   # Max cyclomatic complexity
+max_nesting = 4       # Max indentation depth
+min_mi = 65.0         # Minimum Maintainability Index
+ignore = ["R001"]     # Ignore specific rule IDs
+
+# Advanced Secret Scanning
+[cytoscnpy.secrets_config]
+entropy_enabled = true
+entropy_threshold = 4.5  # Higher = more random (API keys usually >4.0)
+min_length = 16          # Min length to check for entropy
+scan_comments = true     # Scan comments for secrets
+skip_docstrings = false  # Skip docstrings in entropy scanning
+min_score = 50           # Minimum confidence score (0-100)
+suspicious_names = ["db_config", "oauth_token"] # Add custom suspicious variable names
+
+# Custom Secret Patterns
+[[cytoscnpy.secrets_config.patterns]]
+name = "Slack Token"
+regex = "xox[baprs]-([0-9a-zA-Z]{10,48})"
+severity = "HIGH"
+```
+
+> **Note**: Notebook options (`include_ipynb`, `ipynb_cells`) are currently CLI-only but will be added to the configuration file in a future release.
+
+### CI/CD Quality Gates
+
+Configure quality gates for CI/CD pipelines. Set thresholds and the CLI exits with code `1` if exceeded.
+
+**CLI Flags:**
+
+```bash
+# Unused code percentage gate
+cytoscnpy . --fail-threshold 5  # Fail if >5% unused
+
+# Complexity gate
+cytoscnpy . --max-complexity 10  # Fail if any function >10
+
+# Maintainability Index gate
+cytoscnpy . --min-mi 40  # Fail if MI <40
+
+# Quiet mode for clean CI output
+cytoscnpy . --fail-threshold 5 --quiet
+```
+
+**Priority:** CLI flag > config file > environment variable > default
+
+**Environment Variable:** `CYTOSCNPY_FAIL_THRESHOLD=5.0`
+
+## Performance
+
+### Accuracy (Benchmark Suite: 135 items)
+
+| Detection Type | Precision | Recall   | F1 Score |
+| -------------- | --------- | -------- | -------- |
+| Classes        | 0.73      | 0.79     | **0.76** |
+| Functions      | 0.71      | 0.74     | **0.73** |
+| Methods        | **0.86**  | **0.93** | **0.89** |
+| Imports        | 0.67      | 0.40     | 0.50     |
+| Variables      | 0.30      | 0.15     | 0.20     |
+| **Overall**    | **0.71**  | **0.64** | **0.68** |
+
+> See [benchmark/README.md](benchmark/README.md) for detailed comparison against Vulture, Flake8, Pylint, Ruff, and others.
+
+## Architecture
+
+See [cytoscnpy/README.md](cytoscnpy/README.md#architecture) for detailed architecture and technology stack information.
+
+## Testing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md#testing) for testing instructions.
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for development setup and guidelines.
+
+## License
+
+Apache-2.0 License - see [License](License) file for details.
+
+## Links
+
+- **Documentation**: [CytoScnPy](https://djinn09.github.io/CytoScnPy/)
+- **PyPI**: [PyPi](https://pypi.org/project/cytoscnpy/)
+- **VS Code Extension**: [VS Code Marketplace](https://marketplace.visualstudio.com/items?itemName=djinn09.cytoscnpy)
+- **Rust Core Documentation**: [cytoscnpy/README.md](cytoscnpy/README.md)
+- **Benchmarks & Accuracy**: [benchmark/README.md](benchmark/README.md)
+- **Roadmap**: [docs/roadmap.md](docs/roadmap.md)
+- **Contributing**: [CONTRIBUTING.md](CONTRIBUTING.md)
+
+## References
+
+CytoScnPy's design and implementation are inspired by:
+
+- [**Skylos**](https://github.com/duriantaco/skylos)
+- [**Radon**](https://github.com/rubik/radon)
+

cytoscnpy-1.2.2.dist-info/RECORD

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cytoscnpy-1.2.2.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: maturin (1.10.2)
+Root-Is-Purelib: false
+Tag: cp39-cp39-win_amd64

cytoscnpy-1.2.2.dist-info/entry_points.txt

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+[console_scripts]
+cytoscnpy=cytoscnpy.cli:main