[Biopython-dev] Further PEP8 Cleanup

[Christian Brueffer]

Hi,

I just submitted pull request #102 which fixes several types of PEP8
warnings (found using the awesome pep8 tool).

Here's what's left after those fixes:

$ pep8 --statistics -qq repos/biopython
789     E111 indentation is not a multiple of four
673     E121 continuation line indentation is not a multiple of four
693     E122 continuation line missing indentation or outdented
171     E123 closing bracket does not match indentation of opening 
bracket's line
86      E124 closing bracket does not match visual indentation
49      E125 continuation line does not distinguish itself from next 
logical line
197     E126 continuation line over-indented for hanging indent
575     E127 continuation line over-indented for visual indent
1092    E128 continuation line under-indented for visual indent
773     E201 whitespace after '('
540     E202 whitespace before ')'
23543   E203 whitespace before ':'
55      E211 whitespace before '('
180     E221 multiple spaces before operator
59      E222 multiple spaces after operator
5848    E225 missing whitespace around operator
6517    E231 missing whitespace after ','
2544    E251 no spaces around keyword / parameter equals
644     E261 at least two spaces before inline comment
346     E262 inline comment should start with '# '
156     E301 expected 1 blank line, found 0
1838    E302 expected 2 blank lines, found 1
364     E303 too many blank lines (2)
15553   E501 line too long (82 > 79 characters)
857     E502 the backslash is redundant between brackets
291     E701 multiple statements on one line (colon)
122     E711 comparison to None should be 'if cond is None:'
3707    W291 trailing whitespace
1913    W293 blank line contains whitespace

I'm not sure where to go from here with regard to what's worth fixing 
and what would be considered repo churn (or gratuitous changes that make
merging of existing patches harder).

I'd especially like to clean up E301, E302, E701, E711, W291 and W293.
Other items like E251 are more dubious, as some developers seem to
prefer the current style.

What do you think?

Chris