scilaunch

A tiny program for you that lays the foundation for great discoveries.

Description

scilaunch helps you to set up your research project:

1. it creates a canonical directory structure tailored for research projects

   🚀 yourgreatstudy/
   ├── 📄 README.md
   ├── 📂 code
   │   ├── 📁 Rscripts
   │   ├── 📁 configs
   │   ├── 📂 notebooks
   │   │   └── 🐍 yourgreatstudy.ipynb
   │   ├── 📁 tests
   │   └── 📂 yourgreatstudy
   │       ├── 🐍 __init__.py
   │       └── 📁 preprocessing
   ├── 📂 data
   │   ├── 📋 participants.tsv
   │   ├── 📁 sub-01
   │   ├── 📁 sub-02
   │   └── 📁 sub-03
   ├── 📂 literature
   │   ├── 📁 pdfs
   │   └── 📙 yourgreatstudy.bib
   ├── 📂 organisation
   │   ├── 📁 ethics
   │   ├── 📁 participation_forms
   │   ├── 📁 preregistration
   ├── 📂 publications
   │   ├── 📁 articles
   │   ├── 📁 poster
   │   └── 📁 presentations
   ├── 📄 pyproject.toml
   ├── 📂 results
   │   └── 📁 datavisualization
   └── 🐍 setup.py
   

2. scilaunch prepares your research code as Python package ready for import

3. scilaunch offers to set up a conda environment, and prepares it as jupyter kernel

4. and scilaunch can init your git repository

The project structure can be populated with other programming languages (R, matlab, etc.) as well.

Check out the scilaunch documentation 🚀 for more information.

Getting started

Install scilaunch

Ideally install scilaunch into your global/base Python environment, which should be python>=3.8.

Install from PyPI:

pip install -U scilaunch

Alternatively, install from the GitHub repo:

pip install -U git+https://github.com/SHEscher/scilaunch.git

It is also recommended to have conda installed.

🚀 Run scilaunch

Simply run scilaunch via the command line:

# Assuming you are in the parent directory that should host your research project
scilaunch

or provide the parent directory of your project by running:

scilaunch  PATH/TO/PARENT/DIR

Then, you will be asked to provide some information relevant to your project.

When running scilaunch the first time, you will set some default values, which will ease your life for upcoming launches of research projects.

You can still change these default values in ~/.cookiecutterrc at a later stage.

Cookiecutter templates

scilaunch is a wrapper around the great cookiecutter package and is mainly built around this template: research-project.

For how to build your own template(s) and to contribute to this project, please check out: CONTRIBUTING.md.

Note, after running scilaunch the first time, you can adapt your default values in ~/.cookiecutterrc at any time. Check out the cookiecutter documentation for more information on the ~/.cookiecutterrc.