Installation Guide

EPyR Tools can be installed in several ways depending on your needs.

Requirements

Python 3.8 or higher
NumPy >= 1.20.0
Matplotlib >= 3.3.0
SciPy >= 1.7.0
h5py >= 3.1.0 (for HDF5 export)
pandas >= 1.3.0 (for enhanced CSV handling)

Recommended Installation

The recommended way to install EPyR Tools is using pip with an editable installation:

# Clone the repository
git clone https://github.com/BertainaS/epyrtools.git
cd epyrtools

# Install with all dependencies
pip install -e .

Development Installation

For development work, install with development dependencies:

# Install with development tools
pip install -e .[dev]

# Or install with all optional dependencies
pip install -e .[all]

This includes:

Development tools: black, isort, flake8, pre-commit
Testing: pytest, pytest-cov
Documentation: sphinx, sphinx-rtd-theme, myst-parser

Manual Installation

If you prefer to manage dependencies manually:

# Clone the repository
git clone https://github.com/BertainaS/epyrtools.git
cd epyrtools

# Install core dependencies
pip install -r requirements.txt

# Optional: Install development dependencies
pip install -r requirements-dev.txt

Verification

To verify your installation:

import epyr
print(f"EPyR Tools version: {epyr.__version__}")

# Test basic functionality
from epyr.baseline import baseline_polynomial
from epyr.fair import convert_bruker_to_fair
print("✅ EPyR Tools installed successfully!")

Troubleshooting

Common Issues

ImportError: No module named ‘epyr’

Ensure you’re in the correct Python environment
Try: pip install -e . --force-reinstall
Check that the installation completed without errors

Missing dependencies

Install missing packages: pip install package_name
Or reinstall with all dependencies: pip install -e .[all]

h5py installation issues

On macOS with Apple Silicon: pip install --no-use-pep517 h5py
On Linux: sudo apt-get install libhdf5-dev first
On Windows: Use conda instead: conda install h5py

Platform-Specific Notes

Windows

Use Anaconda or Miniconda for easier dependency management
Some binary packages may require Microsoft Visual C++ Build Tools

macOS

Xcode Command Line Tools may be required: xcode-select --install
For Apple Silicon Macs, ensure you’re using compatible package versions

Linux

Install system dependencies: sudo apt-get install build-essential python3-dev
For HDF5 support: sudo apt-get install libhdf5-dev

Getting Help

If you encounter installation issues:

Check the GitHub Issues
Create a new issue with your system details and error message
Include output of pip list and python --version