Initialize package structure with setup.py, MANIFEST.in, and README_PYPI.md

Author: Daniel Precioso, PhD

MANIFEST.in

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+include amlab/**/*.py

README_PYPI.md

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+# Applied Math Lab
+
+A Python package for models and utilities in collective motion, ODEs, PDEs, and more.
+
+## Installation
+
+From the root of the repository:
+
+```
+pip install .
+```
+
+## Requirements
+- numpy
+- matplotlib
+
+Add more requirements as needed in `setup.py`.
+
+## Usage
+
+Import modules from `amlab` in your Python code:
+
+```python
+from amlab.collective_motion import vicsek_equations
+```
+
+## Project Structure
+- `amlab/` - Main Python package
+- `modules/` - Quarto/Markdown teaching modules
+- `assets/`, `data/`, `img/` - Supporting files
+
+## License
+MIT

setup.py

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+from setuptools import find_packages, setup
+
+setup(
+    name="amlab",
+    version="0.1.0",
+    description="Applied Math Lab: models and utilities for collective motion, ODEs, PDEs, and more.",
+    author="Daniel Precioso",
+    author_email="daniel.precioso@ie.edu",
+    packages=find_packages(),
+    install_requires=[
+        "numpy",
+        "matplotlib",
+        # Add other dependencies as needed
+    ],
+    python_requires=">=3.11",
+    include_package_data=True,
+    url="https://github.com/daniprec/BAM-Applied-Math-Lab",
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+)