[Biopython-dev] pylint, was: Changes to the main repo

[Peter Cock]

2010/3/21 Tiago Antão <tiagoantao at gmail.com>:
> Hi,
>
> I've made some changes in the main repository (my first changes with
> github), some comments:
> 1. Many thanks for the GitUsage wiki page. REALLY useful.
> 2. That being said, if I did any mistakes, they are my own fault.
> 3. I've added support for big genepop files, something I tend do be
> asked quite a lot
> 4. And support for haploid data (nobody really asked this)
> 5. I remember Peter sending an email about needed corrections to the
> code. I am afraid I've lost that email :( . If you send it to me, I
> will do them ASAP
> 6. New test cases and test data files
> 7. I might add support, in the future, to Arlequin (file format and
> application). Allowing for statistics over sequences and other goodies
> with sequence data.
>
> Regards,
> Tiago

Hi Tiago,

That sounds good. Regarding point 5, running pylint over the
code reported some possible errors in Bio.PopGen. Have a
look at this - they are all undefined variable issues:
http://lists.open-bio.org/pipermail/biopython-dev/2010-February/007354.html

I just ran it again on the latest code, and the line numbers have
changed a tiny bit but that is all:

$ pylint --disable-msg-cat=CRW --include-ids=y
--disable-msg=E1101,E1103,E0102 -r n Bio.PopGen
No config file found, using default configuration
************* Module Bio.PopGen.Async
E0602: 78:Async.get_result: Undefined variable 'done'
E0602: 79:Async.get_result: Undefined variable 'done'
************* Module Bio.PopGen.GenePop
E0602:166:Record.split_in_pops: Undefined variable 'GenePop'
E0602:183: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.GenePop.FileParser
E1120:219:FileRecord.remove_locus_by_name: No value passed for
parameter 'fw' in function call
************* 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'

Peter