Installation

Using Virtual Environments

It is strongly recommended to install unimpeded in a virtual environment to avoid package conflicts and maintain reproducibility.

Virtual environments provide isolated Python environments for your projects, ensuring that dependencies for different projects don’t interfere with each other. This is considered best practice in Python development.

Python venv

# Create a virtual environment
python -m venv venv_unimpeded

# Activate the virtual environment
# On macOS/Linux:
source venv_unimpeded/bin/activate
# On Windows:
# venv_unimpeded\Scripts\activate

# Install unimpeded
pip install unimpeded

Conda

unimpeded is also available via conda:

# Create a conda environment
conda create -n unimpeded_env python=3.9

# Activate the environment
conda activate unimpeded_env

# Install from conda-forge
conda install -c handley-lab unimpeded

# Or install via pip
pip install unimpeded

Quick Install

If you prefer not to use a virtual environment, you can install unimpeded directly:

pip install unimpeded

Note: While this method works, using a virtual environment is strongly recommended for better package management and reproducibility.

Installation from Source

To install the latest development version from GitHub:

git clone https://github.com/handley-lab/unimpeded.git
cd unimpeded
python -m pip install .

For an editable installation (useful for development):

git clone https://github.com/handley-lab/unimpeded.git
cd unimpeded
pip install -e .

Jupyter Notebook Tutorial

A tutorial notebook is available to help you get started. After installing unimpeded, download the notebook:

download-unimpeded-tutorial

Then install Jupyter and launch the notebook:

pip install jupyter
launch-unimpeded-tutorial

Troubleshooting

jupyter: command not found

Make sure you’ve installed jupyter:

pip install jupyter

ModuleNotFoundError: No module named 'unimpeded'

Make sure you’ve installed unimpeded in your active virtual environment:

pip install unimpeded

Old pip version causing installation errors

Upgrade pip first:

python -m pip install --upgrade pip

Windows: Cannot run scripts (PowerShell execution policy)

Enable script execution temporarily:

Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope Process

Dependencies

Basic requirements:

• Python 3.8+

• anesthetic

• requests

Optional dependencies for documentation:

• sphinx

• numpydoc

Optional dependencies for testing:

• pytest

• pytest-cov

• flake8

• pydocstyle

Verifying Installation

You can verify that unimpeded is installed correctly by running:

import unimpeded
print(unimpeded.__version__)

Testing

To run the test suite:

export MPLBACKEND=Agg     # only necessary for macOS users
python -m pytest

To check code style:

flake8 unimpeded tests
pydocstyle --convention=numpy unimpeded