baynes

Tools and models for bayesian data analysis.

Dependecies

• This package works for python >= 3.8. It is strongly suggested to create a dedicated python environment, for example using virtualenv, which can be installed with pip

  pip install virtualenv
  

• Automatic installation of CmdStan requires g++>=4.9.3 and make>=3.81

Installation

Open the terminal and clone the repository locally:

use a password protected SSH key

git clone git@github.com:cryomib/baynes.git

or Clone with HTTPS using the web URL

git clone https://github.com/cryomib/baynes.git

Automatic install

Move into the repository and run the install script

cd baynes
source install.sh

This will automatically execute all the steps of the manual installation using a default configuration.

Manual install

1. Create the baynes virtual environment based on python3.X (X>=8) and activate it.

   pip install virtualenv
   virtualenv -p `which python3.X` baynesenv
   source baynesenv/bin/activate
   

   (optional) Check the version of python being used in the virtual environment

   (baynesenv) python -V
   

2. Install the required Python packages and dependencies, which include CmdStanPy. With the virtual environment active, move into the baynes folder and install the package with pip.

   (baynesenv) cd baynes
   (baynesenv) pip install .
   

   (optional)

3. Install CmdStan and Stan. If g++>=4.9.3 and make>=3.81 are already present, this can be done automatically using CmdStanPy's built-in function install_cmdstan:

   (baynesenv) install_cmdstan
   

   By default, this will install CmdStan and Stan's core utilities in $HOME/.cmdstan. For more informations, see https://mc-stan.org/cmdstanpy/installation.html

   If you want a custom CmdStan installation, follow https://mc-stan.org/docs/cmdstan-guide/cmdstan-installation.html

   Note: do not follow the conda installation procedure.

4. (optional) baynes allows to retrieve the Stan models from a user defined directory and set the default Stan compiler options. Run:

   (baynesenv) python scripts/set_defaults.py
   

   This will set baynes/stan/ as the models' base folder and add baynes/stan/include/ to the compiler search path. Otherwise, the arguments specified in baynes/config.json will be used as defaults. Additional default values can be set by updating the config dictionary with dedicated functions found in baynes/model_utils.py.

5. (optional) install the jupyter kernel to make baynesenv available in notebooks

   (baynesenv) ipython kernel install --user --name=baynesenv
   

   Note: Jupyter notebooks must be run after deactivating the environment.

Project top-level directory layout

baynes
│
├── baynes                         # Project source code
├── examples                       # Jupyter Notebooks demonstrating various models and techniques
├── scripts                        # Simple python scripts for configuration
├── stan                           # Collection of tested Stan models and functions
├── requirements.txt               # Requirements file specifing the python packages to install
├── setup.py                       # Package installation script
├── install.sh                     # Full automatic installation script
├── .gitignore                     # Specifies intentionally untracked files to ignore
└── README.md                      # README file

ASCII art tree structure taken from here