Installation#

PyPI version

Prerequisites#

Before setting up Bio-Reasoning, ensure you have the following installed:

  • Python >= 3.10 is required.

  • We recommend using conda/mamba or pipx to manage isolated environments.
    Download Conda/Mamba from: Conda Forge

Installation via pip#

Basic Installation#

Install the core package (requires Python >= 3.10):

pip install bio-reasoning

Installation from Source#

Basic Installation from Source#

git clone https://github.com/brettin/biological-reasoning.git
cd biological-reasoning
pip install .

Development Installation#

For developers who want to contribute to the project or work with the latest source code, use the editable installation method:

# Create a new conda environment
conda create -n bio_reason python==3.10
conda activate bio_reason

# Verify pip location (should be in the conda environment)
which pip

# Install in editable mode
pip install --editable .

What does pip install --editable . do?#

The --editable flag (or -e) installs the package in “editable” or “development” mode. This means:

  • Live Code Changes: Any changes you make to the source code in the src/ directory will be immediately available without reinstalling the package

  • Development Workflow: Perfect for active development where you’re frequently modifying code

  • Symlink Installation: Creates a link to your source code rather than copying files to the site-packages directory

  • Version Control Friendly: Your changes are tracked in your local git repository and can be easily committed

This is the recommended approach for developers who plan to modify the codebase or contribute to the project.