Security hardening: replace unsafe eval() with AST-based evaluator in configure_optimizers

Author: abhayrajjais01

.dockerignore

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+# Git
+.git
+.gitignore
+.gitattributes
+
+# Python
+__pycache__
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Virtual environments
+venv/
+env/
+ENV/
+.venv
+
+# Testing
+.pytest_cache/
+.coverage
+.coverage.*
+htmlcov/
+.tox/
+.nox/
+
+# Documentation
+docs/_build/
+docs/.doctrees/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+
+# Docker
+Dockerfile
+docker-compose.yml
+.dockerignore
+
+# CI/CD
+.github/
+.pre-commit-config.yaml
+
+# Misc
+*.log
+.env
+.cache/

DOCKER.md

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+# Docker Setup for DeepForest
+
+This guide explains how to use Docker to run DeepForest locally in a containerized environment.
+
+## Prerequisites
+
+- [Docker](https://docs.docker.com/get-docker/) installed on your system
+- [Docker Desktop](https://www.docker.com/products/docker-desktop/) (Windows/Mac) or Docker Engine (Linux)
+- For GPU support: [NVIDIA Docker runtime](https://github.com/NVIDIA/nvidia-docker)
+
+> [!NOTE]
+> This guide uses the modern `docker compose` command. If you are using an older version of Docker, you might need to use `docker-compose` (with a hyphen) instead.
+
+## Quick Start
+
+### 1. Build the Docker Image
+
+```bash
+docker compose build
+```
+
+This will create a Docker image with all DeepForest dependencies installed.
+
+### 2. Run the Container
+
+**Interactive Shell:**
+```bash
+docker compose run --rm deepforest
+```
+
+This starts an interactive bash shell inside the container where you can run Python scripts and tests.
+
+**Run Specific Commands:**
+```bash
+# Test DeepForest installation
+docker compose run --rm deepforest python -c "from deepforest import main; model = main.deepforest(); print('DeepForest successfully installed!')"
+
+# Run tests
+docker compose run --rm deepforest pytest -v
+
+# Run a specific test file
+docker compose run --rm deepforest pytest tests/test_main.py -v
+```
+
+### 3. Start Jupyter Notebook (Optional)
+
+```bash
+docker compose run --rm -p 8888:8888 deepforest jupyter notebook --ip=0.0.0.0 --no-browser --allow-root
+```
+
+Then open the URL shown in the terminal (e.g., `http://127.0.0.1:8888/?token=...`) in your browser.
+
+## Development Workflow
+
+The project directory is mounted as a volume in the container, so any changes you make to the code on your host machine will be immediately reflected inside the container.
+
+### Typical Workflow:
+
+1. **Edit code** on your host machine using your favorite editor
+2. **Run tests** inside the container:
+   ```bash
+   docker compose run --rm deepforest pytest -v
+   ```
+3. **Run scripts** inside the container:
+   ```bash
+   docker compose run --rm deepforest python your_script.py
+   ```
+
+## GPU Support
+
+To use GPU acceleration with DeepForest in Docker:
+
+1. **Install NVIDIA Docker runtime** on your host machine:
+   - Follow instructions at: https://github.com/NVIDIA/nvidia-docker
+
+2. **Uncomment GPU configuration** in `docker-compose.yml`:
+   ```yaml
+   deploy:
+     resources:
+       reservations:
+         devices:
+           - driver: nvidia
+             count: all
+             capabilities: [gpu]
+   ```
+
+3. **Rebuild the image** (optional - use CUDA base image):
+   - Modify the Dockerfile to use a CUDA-enabled base image like `nvidia/cuda:11.8.0-cudnn8-runtime-ubuntu22.04`
+
+4. **Verify GPU access**:
+   ```bash
+   docker compose run --rm deepforest python -c "import torch; print(f'CUDA available: {torch.cuda.is_available()}')"
+   ```
+
+## Common Commands
+
+### Container Management
+
+```bash
+# Build/rebuild the image
+docker compose build
+
+# Build without cache (fresh build)
+docker compose build --no-cache
+
+# Start container in background
+docker compose up -d
+
+# Stop running containers
+docker compose down
+
+# View running containers
+docker ps
+
+# View logs
+docker compose logs -f deepforest
+```
+
+### Running Python Code
+
+```bash
+# Interactive Python shell
+docker compose run --rm deepforest python
+
+# Run a Python script
+docker compose run --rm deepforest python scripts/your_script.py
+
+# Run with custom arguments
+docker compose run --rm deepforest python -m deepforest.scripts.cli --help
+```
+
+### Testing
+
+```bash
+# Run all tests
+docker compose run --rm deepforest pytest -v
+
+# Run specific test file
+docker compose run --rm deepforest pytest tests/test_main.py -v
+
+# Run tests with coverage
+docker compose run --rm deepforest pytest --cov=src/deepforest --cov-report=html
+
+# Run specific test function
+docker compose run --rm deepforest pytest tests/test_main.py::test_function_name -v
+```
+
+### Code Quality
+
+```bash
+# Run pre-commit checks
+docker compose run --rm deepforest pre-commit run --all-files
+
+# Format code with ruff
+docker compose run --rm deepforest ruff format .
+
+# Lint code
+docker compose run --rm deepforest ruff check .
+```
+
+## Troubleshooting
+
+### 'docker' or 'docker-compose' command not found
+
+If you see errors like `The term 'docker' is not recognized` or `command not found`:
+
+1.  **Verify Installation**: Ensure Docker Desktop (Windows/Mac) or Docker Engine (Linux) is installed.
+2.  **Check PATH**: Ensure the Docker executable directory is in your system's PATH environment variable.
+    *   **Windows**: Usually `C:\Program Files\Docker\Docker\resources\bin`.
+3.  **Restart Shell**: Close and reopen your terminal/powershell window after installing.
+
+### Permission Issues
+
+If you encounter permission errors when running the container:
+
+```bash
+# On Linux/Mac, ensure the container user has the same UID as your host user
+docker compose run --rm -u $(id -u):$(id -g) deepforest bash
+```
+
+### Out of Memory
+
+If you run out of memory during build or execution:
+
+```bash
+# Increase Docker memory limit in Docker Desktop settings
+# Or use --memory flag
+docker compose run --rm --memory=8g deepforest pytest
+```
+
+### Slow Build Times
+
+To speed up builds:
+
+1. Ensure `.dockerignore` is properly configured
+2. Use Docker BuildKit:
+   ```bash
+   DOCKER_BUILDKIT=1 docker compose build
+   ```
+
+### Container Won't Start
+
+```bash
+# Check logs
+docker compose logs deepforest
+
+# Remove old containers and volumes
+docker compose down -v
+
+# Rebuild from scratch
+docker compose build --no-cache
+```
+
+## Data Persistence
+
+The `deepforest-data` volume is created to persist data between container runs. You can:
+
+```bash
+# List volumes
+docker volume ls
+
+# Inspect volume
+docker volume inspect deepforest_deepforest-data
+
+# Remove volume (WARNING: deletes all data)
+docker volume rm deepforest_deepforest-data
+```
+
+## Advanced Usage
+
+### Custom Environment Variables
+
+Create a `.env` file in the project root:
+
+```env
+PYTORCH_CUDA_ALLOC_CONF=max_split_size_mb:512
+PYTHONPATH=/home/deepforest/app/src
+```
+
+### Running Multiple Containers
+
+```bash
+# Scale the service
+docker compose up -d --scale deepforest=3
+```
+
+### Accessing Container Shell
+
+```bash
+# Start container in background
+docker compose up -d
+
+# Execute bash in running container
+docker compose exec deepforest bash
+
+# Or use docker directly
+docker exec -it deepforest-dev bash
+```
+
+## Cleaning Up
+
+```bash
+# Remove containers and networks
+docker compose down
+
+# Remove containers, networks, and volumes
+docker compose down -v
+
+# Remove images
+docker rmi deepforest:latest
+
+# Clean up all Docker resources (use with caution)
+docker system prune -a
+```
+
+## Additional Resources
+
+- [DeepForest Documentation](https://deepforest.readthedocs.io/)
+- [Docker Documentation](https://docs.docker.com/)
+- [Docker Compose Documentation](https://docs.docker.com/compose/)
+- [NVIDIA Docker](https://github.com/NVIDIA/nvidia-docker)