Installation

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Installation#

PyPI#

sfsutils is distributed on PyPI as sfsutils-popgen and on conda-forge as sfsutils (the import name stays sfsutils throughout). To install it via pip:

pip install sfsutils-popgen

sfsutils is compatible with Python 3.11 through 3.13.

Note

The backends for the different input sources are optional extras: vcf (the cyvcf2 dependency, for VCF files), zarr (the zarr dependency, for VCF-Zarr stores) and arg (the tskit dependency, for tree sequences / ARGs). Install the ones you need, for example all of them:

pip install sfsutils-popgen[vcf,zarr,arg]

Conda#

sfsutils is also available on conda-forge. To install it:

mamba create -n sfsutils -c conda-forge sfsutils
mamba activate sfsutils

Note

The optional input backends are not pulled in automatically via conda. zarr and tskit are on conda-forge, while cyvcf2 (for VCF handling) is on bioconda, so add both channels:

mamba create -n sfsutils -c conda-forge -c bioconda sfsutils cyvcf2 zarr tskit

Alternatively, to ensure reproducibility, create a file environment.yml:

name: sfsutils
channels:
  - conda-forge
  - bioconda
dependencies:
  - sfsutils
  - cyvcf2
  - zarr
  - tskit

Then create and activate the environment:

mamba env create -f environment.yml
mamba activate sfsutils

You are now ready to use sfsutils:

import sfsutils as su
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