[Bioperl-l] Splitting Bioperl and Test related Suggestions

Sendu Bala bix at sendu.me.uk
Thu Jul 5 04:55:25 EDT 2007

Nathan S. Haigh wrote:
> I agree, although would the dev releases still need to pass all the 
> tests? I'm thinking of people installing via CPAN.

Yes, they'd all have to pass. 'Developer release' should never have the 
connotation of 'broken release'. However, getting all tests to pass is a 
lot easier than fixing all bugs in bugzilla.

(... which actually goes to show how poor our tests are)

Worst case, if we were forced to stick to a schedule but couldn't fix a 
failing test, we could always make it a 'todo' test.

> I also agree with what was said in a previous post about bringing back 
> bioperl-run (and some others) back into the same repository as 
> bioperl-core (after a successful move over to svn)

Agree (with myself essentially).

> I also agree with previous posts about organising and/or having some 
> naming convention for test data files. I think an approach whereby data 
> files were organised into directory trees (1 - 3 deep) with names that 
> elude to the type of data in that subtree/file rather than the tests 
> that use it etc. For example:
> t/data
>     |__ formats
>     |           |__ seq
>     |           |        |__ legal_fasta
>     |           |        |              |__ extension.fas

At that level, files don't need extensions and can have fully 
informative names that explain what's interesting or special about them.

> This type of setup, might lend itself to having a test script simply try 
> to parse all the files in a directory to ensure nothing fails (for legal 
> file formats) and fails for illegal formats.

Great idea.

> Thinking about this a little more, I think it would be a good idea to 
> include Test::Exception in t/lib.

Agree. I'll see if I can have it auto-loaded by BioperlTest.pm.

> Anyway, this type of reorganisation couldn't take place until the svn 
> repo is up and working.


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