Installation

PyMARE can be installed from pip. To install the latest official release:

pip install pymare

If you want to use the most up-to-date version, you can install from the master branch:

pip install git+https://github.com/neurostuff/PyMARE.git

PyMARE requires Python >=3.9 and a number of packages. For a complete list, please see setup.cfg.

Bayesian estimation with Stan

StanMetaRegression is optional, and needs two installation steps rather than one:

pip install pymare[stan]
python -m cmdstanpy.install_cmdstan

The first installs CmdStanPy. The second fetches and builds CmdStan itself, which is a C++ program rather than a Python package and so needs a C++ toolchain (g++ and make on Linux, the Command Line Tools on macOS, RTools on Windows). It takes several minutes, once per machine.

The Stan model is compiled the first time the estimator is fitted, which takes roughly another minute. The compiled model is cached alongside the installed package, so later fits and later processes reuse it. If PyMARE is installed somewhere unwritable, the model is compiled into ~/.pymare/stan instead and a warning says so.

Every other estimator in PyMARE is pure Python and needs none of this.