[Biopython-dev] Running pylint over Biopython

[Tiago Antão]

This comes in a good time, I've actually been making changes to the
code (as the genepop parser is not able to handle big files and I've
had quite a few complains about that). it seems to be 2.6 related or
so because I've detected the Config problem myself. I will correct
this next week (this week is _impossible_), along with an update to
the genepop parser to support big files.

2010/2/23 Peter <biopython at maubp.freeserve.co.uk>:
> Hi all,
>
> Those following @Biopython on twitter or subscribed to the github RSS
> feed for our repository will know this already, but I've been using
> pylint today to spot some errors in Biopython.
> http://www.logilab.org/project/pylint
>
> This was prompted by Eric trying this on Bio.PDB for Bug 3013 and
> finding some issues - thank Eric, this was a valuable suggestion.
>
> With its default settings pylint is very very noisy, and in particular
> doesn't like our naming conventions. However, with the following
> command line you can focus in on the important stuff:
>
> pylint --disable-msg-cat=CRW --include-ids=y
> --disable-msg=E1101,E1103,E0102 -r n Bio BioSQL
>
> Note that instead of module names, you can give filenames (e.g. *.py).
> What that does is disable several categories of message (conventions,
> possible refactorings, warnings) leaving just errors and fatal
> messages. I turned on the message identifiers so that I have something
> useful to stick into Google if need be, or to add to the ignore list
> (currently three cases which looked like false positives). Then I turn
> off the detailed report.
>
> [Tip - don't run this from the Biopython source directory as then
> importing our C code modules will fail]
>
> As you will be able to tell from the recent flurry of git commits,
> this highlighted some simple errors like missing imports or typos in
> variable names.
>
>
> Tiago, could you have a look at these possible problems in Bio.PopGen:
>
> ************* Module Bio.PopGen.Async
> E0602: 78:Async.get_result: Undefined variable 'done'
> E0602: 79:Async.get_result: Undefined variable 'done'
> ************* Module Bio.PopGen.GenePop
> E0602:160:Record.split_in_pops: Undefined variable 'GenePop'
> E0602:177:Record.split_in_loci: Undefined variable 'GenePop'
> ************* Module Bio.PopGen.GenePop.Controller
> E0602: 41:_read_allele_freq_table: Undefined variable 'self'
> E0602:133:_hw_func: Undefined variable 'self'
> E0602:393:GenePopController.test_pop_hw_prob: Undefined variable 'ext'
> E0602:458:GenePopController.test_ld.ld_pop_func: Undefined variable
> 'currrent_pop'
> ************* Module Bio.PopGen.SimCoal.Cache
> E0602: 79:SimCoalCache.getSimulation: Undefined variable 'Config'
> E0602: 88: Undefined variable 'Cache'
> ************* Module Bio.PopGen.SimCoal.Controller
> E0602: 47:SimCoalController.run_simcoal: Undefined variable 'Config'
>
>
> Eric, I don't have all the dependencies installed by pylint does
> appear to dislike a few things in Bio.Phylo on the trunk:
>
> ************* Module Bio.Phylo.BaseTree
> E0203:521:TreeMixin.prune: Access to member 'root' before its
> definition line 531
> E0203:527:TreeMixin.prune: Access to member 'root' before its
> definition line 531
> E0202:672:Subtree.root: An attribute inherited from TreeMixin hide this method
> ************* Module Bio.Phylo.PhyloXML
> E1120:182:Phylogeny.get_alignment: No value passed for parameter
> 'follow_attrs' in function call
>
>
> One thing this exercise has shown is that we still need to do some
> work on the unit test coverage.
>
> Regards
>
> Peter
>



-- 
“Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci