[BioRuby] BioRuby passes tests (kinda)!

[Clayton Wheeler]

On Sat, Aug 4, 2012 at 11:48 AM, Naohisa Goto
<ngoto at gen-info.osaka-u.ac.jp> wrote:
> Hi,
>
>> On Sat, Aug 4, 2012 at 12:07 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
>> > Anyone noticed that BioRuby has gone green on http://biogems.info/?
>
> I've changed .travis.yml yesterday.
> https://github.com/bioruby/bioruby/commit/9a2fe67c247cdc7c9ddc9f8b8de771515ba76ac1
> After the change, the status has been shown as "green".
>
> Keeping "green" status is important for using the automatic testing of
> pull requests by Travis-CI.
>
> On Sat, 4 Aug 2012 14:29:59 +0100, Peter Cock
> <p.j.a.cock at googlemail.com> wrote:
>> No - but I did notice it on the recent blog post:
>> http://news.open-bio.org/news/2012/07/travis-ci-for-testing/
>
> Thanks.
>
>> > Be good when JRuby1.9 starts passing.
>>
>> Do you know what the general problem is?
>
> I think some of them might be due to bugs in JRuby, but
> further investigation is needed.

One of the JRuby bugs I filed on the basis of our test failures has
been fixed, and that fix will be out in the next 1.7 preview release
if it's not in the current one. Another (an autoload bug causing quite
a few failures) has a fix that hasn't been integrated yet; I'll see if
I can get that in for 1.7.0.preview2.

Also, I've seen quite a few failures involving PhyloXML (particularly
on JRuby); now that I've repackaged that as a bio-phyloxml gem
(https://github.com/csw/bioruby-phyloxml, which is passing its tests
on Travis-CI), we could think about removing it from the main BioRuby
repository.

-- 
Clayton Wheeler
cswh at umich.edu