sci Package

A Python 3 package or simply a collection of convenience and wrapper functions supporting tasks frequently needed by scientists.

install

pip3 install sci or
pip3 install --user --upgrade sci

use the --user flag on shared computers where you do not have root access. It will install the package in a place like ~/.local/lib/python3.x/site-packages/sci . You can delete that folder later to remove the package.

design goals

1. Simplicity: wrap frequently used workflows into simple functions that make life easier for scientists. Most import statements should move into functions (except for frequently used ones like os, sys) to avoid confusion during autocomplete with VS Code and other IDEs.
2. Verbose but easily consumable docstrings: Docstrings are accessible via code autocomplete in IDEs such as VS Code or Atom and through automated documentation environments such as sphinx. Each docsting should start with an example use case for the function.
3. functional programming paradigm: While using classes is permitted we encourage writing fewer classes and more functions (perhaps with decorators)
4. Cross-platform: The code should work on Linux (RHEL and Debian based), Windows and Mac OS X.
5. Python 3 only compatibility, Python 2.x is legacy and we do not want to invest any extra time in it.

How to contribute your own code

1. git clone git@github.com:FredHutch/sci-pkg.git
2. create a new branch (eg : sci-yourname)
3. paste your function into module sci/new.py.
4. Make sure you add an example call in the first line of the doc string.
5. Add your test case to sci-pkg/sci/tests