Installation

There are two basic options for installing stdpopsim and its dependencies: either using Conda or Pip. We recommend conda for most users (particularly those using OSX or Windows), although pip can be more convenient in certain cases.

Requirements

Library requirements for stdpopsim should be installed automatically when using either conda or pip.

Stdpopsim requires Python 3.5 or later.

Conda

Pre-built binary packages for stdpopsim are available through conda, 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 stdpopsim

Quick Start

  1. Install conda using miniconda. Make sure you follow the instructions to fully activate your conda installation!

  2. Set up the conda-forge channel using conda config --add channels conda-forge.

  3. Install stdpopsim: conda install stdpopsim.

  4. Try it out: stdpopsim --version.

There are several different ways to obtain conda. Please see the anaconda installation documentation for full details.

Pip

Installing using pip is usually as simple as:

$ python -m pip install stdpopsim --user

This will install stdpopsim into your local user Python packages (on some systems you will need to use python3 rather than python). Please see the Python package installation tutorial for more details on the various installation options. In particular, we recommend using a virtual environment to improve reproducibility.

It may also be necessary to update your PATH to run the command line interface. See here for details on what this means and how to do it.

We use msprime as the default simulation engine, which has some system level dependencies and requires a functioning compiler. Please see the msprime installation documentation for instructions if you encounter errors during installation.

Running the CLI

After installation is complete it should be possible to run the command line interface. This can be done in one of two ways:

  1. The most reliable way is to use

    $ python -m stdpopsim
    

    Once the python executable is the same one as was used when installing conda or pip, this is guaranteed to work.

  2. It is also possible to run stdpopsim like a regular Unix program using:

    $ stdpopsim
    

    However, this requires that your PATH environment variable contains the directory where conda or pip installed the executable. Please see the specific documentation on these methods above for details on how to do this.