Python Coding Standards¶

This document is a list of python coding standards. To add a new standard copy the template below and modify it.

see also http://emg.nysbc.org/wiki/index.php/Appionscripts_formatting_rules

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Name of Coding Standard¶

Definition¶

What is the coding standard

Justification¶

Why is the coding standard important

Example¶

GOOD:

this is a good example code

BAD:

this is a bad example code

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Python Coding Standards for AMI¶

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Use tabs instead of spaces¶

Definition¶

Use tabs instead of spaces for inline code

Justification¶

It is important to be consistent. People like different sizes of columns, some like 8 spaces, others 4, 3, or 2. With tabs each individual can customize their viewer.

Example¶

GOOD:

if True:
<tab>while True:
<tab><tab>print "tab" 
<tab>break

BAD:

if True:
   while True:
        print "tab" 
   break

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Checking beginning or ending of strings¶

Definition¶

Use ''.startswith() and ''.endswith() instead of string slicing to check for prefixes or suffixes.

Justification¶

startswith() and endswith() are cleaner and less error prone.

Example¶

GOOD:

if foo.startswith('bar'): 

BAD:

if foo[:3] == 'bar':

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Never use from module import *¶

Definition¶

Never use from module import *, use import module instead

Justification¶

It is hard to track where functions come from when import * is used

Example¶

GOOD:

import numpy
a = numpy.ones((3,3))

BAD:

from numpy import *
a = ones((3,3))

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Appion image data naming conventions¶

Definition¶

1. never use 'image' or 'img'
2. use 'imgdict' for image dictionaries
3. use 'imgarray' for image numarrays
4. use 'imgname' for image filenames
5. use 'imgtree' for the main list of image dictionaries
6. use 'imglist' for a list of image data

Justification¶

If you are consistent with your names people can read your code.

Example¶

GOOD:

for imgdict in imgtree:
    imgarray = imgdict['image']
    imgname = imgdict['filename']

BAD:

for image in imgs:
    array = image['image']
    name = image['filename']

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Use descriptive variables¶

Definition¶

Use descriptive variables, asdf is not a variable.

Justification¶

No one understands shorthand variables.

Example¶

GOOD:

imgarray = mrc.read('leginon_image.mrc')
particle1 = imgarray[47, 21]
particle1 = imgarray[10, 15]
stack = [particle1, particle2]

BAD:

i = mrc.read('x.mrc')
prtl1 = i[47, 21]
prtl2 = i[10, 15]
s = [prtl1, prtl2]

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Location of functions¶

Definition¶

Functions that have a global use, should go in appionlib folder.
Functions that will only be used by a single program go into that program's file.
Upload to the database function are typically only used by a single program and should be within that program not in appionlib

Justification¶

Keep the code clean an organized.

Example¶

GOOD:

from appionlib import commonFunctions

class AppionScript():
 def customUploadToDB(self):
   """stuff""" 
 def run(self):
   commonFunctions.commonFunction()
   self.customUploadToDB()

BAD:

from appionlib import apUploadCustom

class AppionScript():
 def commonFunction(self):
    """stuff""" 
 def run(self):
   self.commonFunction()
   apUploadCustom.customUploadToDB()