Lin Min Htoo linminhtoo

The Best of the Best Practices (BOBP) Guide for Python

A "Best of the Best Practices" (BOBP) guide to developing in Python.

In General

Values

"Build tools for others that you want to be built for you." - Kenneth Reitz
"Simplicity is alway better than functionality." - Pieter Hintjens

My thoughts on Sandi Metz's presentation on better OOP Design

How to write better Object Oriented code. The central claim is that OO is not a problem, but many teams are not utilising the features of OO to design better code. Her other point is also that design becomes more important late stage as code bases becomes bigger.

Takeaway points

Premature design is bad. Does not really add value. However when design is required later, it is too late and most people don't know how to do it properly.
Code that is properly abstracted should be easier to change than complex routines. However, wrongly abstracted code can also make it as difficult at complex code.

	So you've cloned somebody's repo from github, but now you want to fork it and contribute back. Never fear!

	Technically, when you fork "origin" should be your fork and "upstream" should be the project you forked; however, if you're willing to break this convention then it's easy.

	* Off the top of my head *

	1. Fork their repo on Github
	2. In your local, add a new remote to your fork; then fetch it, and push your changes up to it

	git remote add my-fork [email protected]

	#!/usr/bin/env python
	"""
	Script to convert mmCIF files to PDB format.

	usage: python cif2pdb.py ciffile [pdbfile]

	Requires python BioPython (`pip install biopython`). It should work with recent version of python 2 or 3.

	@author Spencer Bliven <[email protected]>
	"""

	#!/usr/bin/env python

	# Split a protein-ligand complex into protein and ligands and assign ligand bond orders using SMILES strings from Ligand Export
	# Code requires Python 3.6

	import sys
	from prody import *
	import pandas as pd
	from rdkit import Chem
	from rdkit.Chem import AllChem