Merge pull request #12 from ASAG-ISCAS/dev_scp

Author: JianqiangDing

.gitignore

@@ -1,3 +1,131 @@
-__pycache__
-.idea
-.vscode
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+Pipfile.lock
+
+# PEP 582
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store

INSTALL.md

@@ -0,0 +1,175 @@
+# Installation Guide for PyBDR
+
+PyBDR is a set-boundary based reachability analysis toolbox for Python.
+
+## Prerequisites
+
+- **Conda or Miniconda** ([Download here](https://docs.conda.io/en/latest/miniconda.html))
+- Git (for cloning the repository)
+
+## Quick Installation (3 Steps)
+
+```bash
+# Step 1: Create conda environment with all dependencies
+conda env create -f environment.yml
+
+# Step 2: Activate the environment
+conda activate pybdr
+
+# Step 3: Install PyBDR
+pip install -e .
+```
+
+**That's it!** The `environment.yml` automatically installs Python 3.8+, all dependencies, and the required `cddlib` C library.
+
+## Alternative: Install in Existing Conda Environment
+
+If you already have a conda environment:
+
+```bash
+# Activate your environment
+conda activate your_env_name
+
+# Install cddlib C library
+conda install -c conda-forge cddlib
+
+# Install PyBDR (this will install all Python dependencies including codac pre-release)
+pip install -e .
+```
+
+## For Developers
+
+```bash
+# Clone and setup
+git clone https://github.com/ASAG-ISCAS/PyBDR.git
+cd PyBDR
+conda env create -f environment.yml
+conda activate pybdr
+
+# Install with development dependencies
+pip install -e ".[dev]"
+
+# Run tests
+pytest
+```
+
+## Verifying Installation
+
+After installation, verify that PyBDR is correctly installed:
+
+```python
+import pybdr
+from pybdr.geometry import Interval, Zonotope
+from pybdr.algorithm import ASB2008CDC
+
+# Create a simple interval
+interval = Interval([0, 1], [1, 2])
+print(f"Interval created: {interval}")
+
+print("PyBDR successfully installed!")
+```
+
+## Troubleshooting
+
+### Issue: `pycddlib` build fails with "cddlib/setoper.h not found"
+
+**Cause**: The `cddlib` C library is not installed.
+
+**Solution**: Make sure you've installed `cddlib` via conda:
+
+```bash
+conda install -c conda-forge cddlib
+```
+
+### Issue: CVXPY installation fails
+
+**Solution**: CVXPY is included in `environment.yml`. If you're installing manually, use conda:
+
+```bash
+conda install -c conda-forge cvxpy
+```
+
+### Issue: "No module named 'pybdr'" after installation
+
+**Solution**: Make sure you've activated the correct conda environment:
+
+```bash
+conda activate pybdr
+```
+
+### Issue: Codac installation or "No module named 'codac'"
+
+**Cause**: Codac v2 is only available as a pre-release version.
+
+**Solution**: Codac pre-release is automatically included when you run `pip install -e .`. If you need to install it manually:
+
+```bash
+pip install "codac>=2.0.0.dev20"
+```
+
+Or reinstall PyBDR:
+
+```bash
+pip install -e . --force-reinstall
+```
+
+## Package Structure
+
+After installation, PyBDR provides the following modules:
+
+```
+pybdr/
+├── algorithm/          # Reachability analysis algorithms
+├── dynamic_system/     # System models (continuous, discrete, hybrid)
+├── geometry/           # Geometric representations (intervals, zonotopes, polytopes)
+├── model/              # Pre-defined system models
+├── util/               # Utility functions
+└── misc/               # Miscellaneous utilities
+```
+
+## Updating PyBDR
+
+If you installed in development mode (`pip install -e .`), simply pull the latest changes:
+
+```bash
+cd PyBDR
+git pull origin master
+```
+
+## Uninstalling
+
+To remove PyBDR:
+
+```bash
+pip uninstall pybdr
+```
+
+To remove the entire conda environment:
+
+```bash
+conda deactivate
+conda env remove -n pybdr
+```
+
+## Support
+
+For issues and questions:
+
+- GitHub Issues: https://github.com/ASAG-ISCAS/PyBDR/issues
+- Documentation: https://asag-iscas.github.io/docs.pybdr/
+
+## Dependencies
+
+PyBDR depends on:
+
+- **numpy** (≥1.20.0): Numerical computations
+- **scipy** (≥1.7.0): Scientific computing
+- **pypoman** (≥0.5.4): Polytope manipulation
+- **cvxpy** (≥1.1.0): Convex optimization
+- **matplotlib** (≥3.3.0): Visualization
+
+**System dependencies (automatically installed via conda):**
+
+- **cddlib**: C library for polytope computations (required by pypoman)
+
+All dependencies are automatically installed when using the `environment.yml` file with conda.

MANIFEST.in

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+# Include documentation and license files
+include README.md
+include LICENSE.md
+include INSTALL.md
+include environment.yml
+
+# Include documentation images
+recursive-include doc *.png *.jpg *.jpeg *.gif *.svg
+
+# Exclude unwanted files
+exclude .gitignore
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude * *.so
+recursive-exclude * *.dylib
+
+# Exclude test and benchmark files from distribution
+recursive-exclude test *
+recursive-exclude benchmarks *