[Biopython-dev] Test files leftovers

Saket Choudhary saketkc at gmail.com
Fri Apr 25 01:27:10 UTC 2014

Maybe, I need some help here:

A simple tearDown() approach won't work as I need the indexed files to
be present for 'test_samse' and 'test_sampe' to be run.

What I need is a tearDownClass() approach but it is not supported on python2.6.

Any suggestions?


On 25 April 2014 05:41, Saket Choudhary <saketkc at gmail.com> wrote:
> Hi Bow,
> These are generated by the test functions written for BWA wrapper
> which I wrote. I could send a PR which does a  'cleanup' in
> tearDown()?
> Saket
> On 25 April 2014 05:35, Wibowo Arindrarto <w.arindrarto at gmail.com> wrote:
>> Hello everyone,
>> I was running full tests when I noticed that some of our test cases
>> seem to create files for testing but not delete them afterwards.
>> I have these from my tests:
>> BWA/1.sai
>> BWA/1.sam
>> BWA/2.sai
>> BWA/human_g1k_v37_truncated.fasta.amb
>> BWA/human_g1k_v37_truncated.fasta.ann
>> BWA/human_g1k_v37_truncated.fasta.bwt
>> BWA/human_g1k_v37_truncated.fasta.pac
>> BWA/human_g1k_v37_truncated.fasta.sa
>> BWA/out.sam
>> SamBam/bam1.bam.bai
>> TreeConstruction/bootstrap_consensus.tre
>> TreeConstruction/pars1.tre
>> TreeConstruction/pars2.tre
>> bam1.bam
>> Now, I could just add these files to .gitignore, but I think it's more
>> proper if we at least try to remove them after every test. In some
>> cases, I saw that the creation of these files is actually the test.
>> Which means having them before the test (i.e. from a previous run) may
>> not be ideal.
>> But I could be wrong, so I'm sending this first to ask whether these
>> files should have been deleted or not :).
>> Cheers,
>> Bow
>> _______________________________________________
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>> Biopython-dev at lists.open-bio.org
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