[Biopython-dev] Test files leftovers

[Saket Choudhary]

Apparently I have polluted the master branch of my biopython clone:
https://github.com/saketkc/biopython

PR on a fake clone: https://github.com/saketkc/biopython-2/pull/1/files

On 25 April 2014 06:57, Saket Choudhary <saketkc at gmail.com> wrote:
> 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?
>
> Saket
>
> 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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