cpm

cpm is a fundamental package for Computational Psychiatry. It is designed to provide a set of tools for researchers and clinicians to analyze and model data in the field of Computational Psychiatry.

⚠️ The package is under active development and is therefore currently in a beta version. ⚠️

Install from GitHub

In order to install the package from GitHub, run the following command:

pip install git+https://github.com/DevComPsy/cpm.git

Documentation

The documentation can be viewed here: link.

Development of documentation

The documentation is written in docstrings and markdown files. The markdown files are located in the docs directory. The documentation is built using mkdocs.

Vieweing developmental versions of the documentation

First, install all requirements:

pip install -r docs/requirements.txt

In the root directory, run the following commands:

mkdocs build
mkdocs serve

Then open a browser and go to http://127.0.0.1:8000/

Depending on the version you have, you might need to add Jupyter to PATH, see this link for more information.

Building the documentation

To build the documentation, run the following command in the root directory:

mkdocs build

To deploy the documentation to GitHub pages, run the following command in the root directory:

mkdocs gh-deploy

Development process

To work on the toolbox, create a new branch from the main branch. Then, create a pull request to merge the new feature into the main branch. Once the pull request is approved, merge the new feature into the main branch.

Branch naming convention

A git branch should start with a category. Pick one of these: feature, bugfix, hotfix, or test.

• feature is for adding, refactoring or removing a feature
• bugfix is for fixing a bug
• hotfix is for changing code with a temporary solution and/or without following the usual process (usually because of an emergency)
• test is for experimenting outside of an issue/ticket

See this link for some great description of the naming convention.

Commit message conventions

Please follow the Conventional Commits guidelines for commit messages. Feel free to use gitmoji for commit messages, but insert them at the end of the problem description. See this link for more information.

Pull request conventions

When creating a pull request, make sure to follow these conventions: link

Compiling the package

To compile the package, run the following command in the root directory:

python setup.py sdist bdist_wheel

Uploading the package to PyPi

To upload the package to PyPi, run the following command in the root directory:

twine upload dist/*

Development tools we use

• black linter for python code formatting
• numpy-style docstrings for documentation
• mkdocs for documentation generation
• pytest for testing