install.rst

Install

requirements

We support Python 3.8 on Linux Similar Python versions will probably work, but we don't regularly test using those versions.

managing your Python environment

We recommend installing transcriptomic_clustering into a managed Python environment. Having multiple isolated environments lets you install incompatible packages (or different versions of the same package!) simultaneously and prevents unexpected behavior by utilities that rely on the system Python installation.

Two popular tools for managing Python environments are anaconda and venv. The rest of this document assumes that you have created and activated an environment using one of these tools. Using anaconda, this looks like:

conda create -y --name environment-name python=3.8
conda activate environment-name

and using venv:

python -m venv path/to/environment
source path/to/environment/bin/activate

installing from github

If you want to install a specific branch, tag, or commit of transcriptomic_clustering, you can do so using pip:

pip install git+https://github.com/alleninstitute/transcriptomic_clustering@dev

The dev branch contains cutting-edge features that might not have been formally released yet. By installing this way, you can access those features.

installing for development

If you want to work on transcriptomic_clustering, you should first clone the repository, then install it in editable mode so that you can easily test your changes:

git clone https://github.com/alleninstitute/transcriptomic_clustering
cd transcriptomic_clustering

pip install -r requirements.txt -U
pip install -r test_requirements.txt -U

pip install -e .

installing from pypy [coming soon!]

You can install the latest release from pypy by running:

pip install transcriptomic_clustering