Installation — Tskit manual (original) (raw)

Contents

• Requirements
• Conda
  • Quick Start
• Pip
• Development versions

Installation#

There are two basic options for installing tskit: either through pre-built binary packages using Conda or by compiling locally using Pip. We recommend using condafor most users, although pip can be more convenient in certain cases. Tskit is installed to provide succinct tree sequence functionality to other software (such as msprime), so it may already be installed if you use such software.

Requirements#

Tskit requires Python 3.8+. There are no external C library dependencies. Python dependencies are installed automatically by pip or conda.

Conda#

Pre-built binary packages for tskit are available throughconda, and built using conda-forge. Packages for recent version of Python are available for Linux, OSX and Windows. Install using:

$ conda install -c conda-forge tskit

Quick Start#

1. Install conda using miniconda . Make sure you follow the instructions to fully activate your condainstallation!
2. Set up the conda-forge channel usingconda config --add channels conda-forge.
3. Install tskit: conda install tskit.
4. Try it out: tskit --version.

There are several different ways to obtain conda. Please see theanaconda installation documentationfor full details.

Pip#

Installing using pip is somewhat more flexible than conda and may result in code that is (slightly) faster on your specific hardware.Pip is the recommended method when using the system provided Python installations. Installation is straightforward:

$ python3 -m pip install tskit

Development versions#

For general use, we do not recommend installing development versions. Occasionally pre-release versions are made available, which can be installed using python3 -m pip install --pre tskit. If you really need to install a bleeding-edge version, see Installing development versions.