#Best Practices on Development Workshop

Material for the workshop on Best Practices on Development hosted at Science For Life Laboratory, Stockholm, Sweden.

Homework: To Read and Install Before the Workshop

###Git & GitHub

Read first

• Understanding GitHub workflow
• Forking projects

Read second

• 15 minutes hands-on Git tutorial
• Mastering issues

Optional but useful

• Master Markdown

###Python et al

Virtual Environments with anaconda

Virtual environments allow you to maintain and switch quickly between different sets of python binaries and packages. For example, you can work on a project which requires python 2.6 and numpy 1.7 while also maintaining a project which requires python 2.7 and numpy 1.8. Because packages are installed inside your home directory, virtual environments also allow you to install python packages without root permissions (as we must on UPPMAX).

conda is a tool to create these isolated virtual environments as well as a fantastic package management tool. It allows simple installation of complex scientific packages (scipy, numpy, pandas, etc.) via the meta-package Anaconda, and works together with other package mangers like pip.

Here you can find a really good guide written by Mario Giovacchini about installation and usage of Ana/conda.

Workshop Material

Index:

• Styling Standards
  • 4 spaces per indentation level
  • Indentation of Multi-Line Statements
  • Maximum line length (soft rule)
  • Imports
  • Whitespace in Expressions and Statements
  • Comments
    • How to Think About Comments
    • Comment formatting
    • Inline comments
    • Documentation strings - Docstrings
  • Naming conventions
  • Other programming recommendations
• IPython
• Debugger
  • (i)pdb useful commands
• Testing
• Advanced Git

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###Development workflow at Science For Life Laboratory