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.
Library requirements for stdpopsim should be installed automatically when using either conda or pip.
Stdpopsim requires Python 3.5 or later.
$ conda install -c conda-forge stdpopsim
condausing miniconda. Make sure you follow the instructions to fully activate your
Set up the conda-forge channel using
conda config --add channels conda-forge.
conda install stdpopsim.
Try it out:
There are several different ways to obtain
conda. Please see the
anaconda installation documentation
for full details.
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:
The most reliable way is to use
$ python -m stdpopsim
pythonexecutable is the same one as was used when installing
pip, this is guaranteed to work.
It is also possible to run
stdpopsimlike a regular Unix program using:
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.