headers
Fields, Christopher J | 25 Jul 2012 05:08
Favicon
Gravatar

BioPerl and Travis-CI

Peter Cock has graciously helped start up a branch for bioperl-live that is using Travis-CI (a nice
continuous integration tool).  Results from Peter's fork are found here:

    http://travis-ci.org/#!/peterjc/bioperl-live

As this is now pulled into the main bioperl repo, results will be here:

    http://travis-ci.org/#!/bioperl/bioperl-live

I'll be working on this and expect this will be added to master in the next few days.  

chris
Permalink | Reply |
headers
Peter Cock | 25 Jul 2012 12:31
Gravatar

Re: BioPerl and Travis-CI

On Wed, Jul 25, 2012 at 4:08 AM, Fields, Christopher J
<cjfields <at> illinois.edu> wrote:
> Peter Cock has graciously helped start up a branch for bioperl-live
> that is using Travis-CI (a nice continuous integration tool).  Results
> from Peter's fork are found here:
>
>     http://travis-ci.org/#!/peterjc/bioperl-live
>
> As this is now pulled into the main bioperl repo, results will be here:
>
>     http://travis-ci.org/#!/bioperl/bioperl-live
>
> I'll be working on this and expect this will be added to master in
> the next few days.
>
> chris

We've had this running for Biopython for a month now, and it has
been a useful complement to the BuildBot (which covers other
operating systems). This was following BioRuby's lead:
http://biopython.org/pipermail/biopython-dev/2012-June/009742.html

The current BioPerl Travis configuration is probably usable right
now (after changing the branch whitelist to either master, or simple
all branches).

Other remaining issues include sorting out which dependencies
should be installed, and streamlining their verbose output (e.g.
using tail).
(Continue reading)

Permalink | Reply |
headers
Peter Cock | 26 Jul 2012 17:22
Gravatar

Re: BioPerl and Travis-CI

On Wed, Jul 25, 2012 at 11:31 AM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
> On Wed, Jul 25, 2012 at 4:08 AM, Fields, Christopher J
> <cjfields <at> illinois.edu> wrote:
>> Peter Cock has graciously helped start up a branch for bioperl-live
>> that is using Travis-CI (a nice continuous integration tool).  Results
>> from Peter's fork are found here:
>>
>>     http://travis-ci.org/#!/peterjc/bioperl-live
>>
>> As this is now pulled into the main bioperl repo, results will be here:
>>
>>     http://travis-ci.org/#!/bioperl/bioperl-live
>>
>> I'll be working on this and expect this will be added to master in
>> the next few days.
>>
>> chris
>
> We've had this running for Biopython for a month now, and it has
> been a useful complement to the BuildBot (which covers other
> operating systems). This was following BioRuby's lead:
> http://biopython.org/pipermail/biopython-dev/2012-June/009742.html
>
> The current BioPerl Travis configuration is probably usable right
> now (after changing the branch whitelist to either master, or simple
> all branches).
>
> Other remaining issues include sorting out which dependencies
> should be installed, and streamlining their verbose output (e.g.
> using tail).
(Continue reading)

Permalink | Reply |
headers
Peter Cock | 27 Jul 2012 16:47
Gravatar

Re: BioPerl and Travis-CI

On Thu, Jul 26, 2012 at 4:22 PM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
>
> That's done now - except for the circular dependencies, and GD,
> which might be easy to solve if anyone knows what the error
> means - see commit message here:
> https://github.com/peterjc/bioperl-live/commit/905441ac09939be3368c14de38d04486c7e9849a

Re: https://twitter.com/cjfields/status/228861370454638592
Not sure why you got GD to work when something very similar
had failed for me. Oh well - job done :)

> Would a single clean commit of the (current) .travis.yml file be
> preferable to the current series of commits? And you you want
> a pull request, or would you just merge/cherry-pick manually?

Given all the churn between our revisions, personally I'd opt for
a single clean commit to bioperl/master - but your call.

Peter
Permalink | Reply |
headers
Fields, Christopher J | 27 Jul 2012 16:58
Favicon
Gravatar

Re: BioPerl and Travis-CI

On Jul 27, 2012, at 9:47 AM, Peter Cock wrote:

> On Thu, Jul 26, 2012 at 4:22 PM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
>> 
>> That's done now - except for the circular dependencies, and GD,
>> which might be easy to solve if anyone knows what the error
>> means - see commit message here:
>> https://github.com/peterjc/bioperl-live/commit/905441ac09939be3368c14de38d04486c7e9849a
> 
> Re: https://twitter.com/cjfields/status/228861370454638592
> Not sure why you got GD to work when something very similar
> had failed for me. Oh well - job done :)

It was the lack of gdlib-config in the libgd2-xpm package, you need libgd2-xpm-dev.  One of the fun things
about Debian packaging.

>> Would a single clean commit of the (current) .travis.yml file be
>> preferable to the current series of commits? And you you want
>> a pull request, or would you just merge/cherry-pick manually?
> 
> Given all the churn between our revisions, personally I'd opt for
> a single clean commit to bioperl/master - but your call.
> 
> Peter

Yep, about to merge it over.  It's working now, just need to whitelist master instead of travis after the merge.

chris
Permalink | Reply |
headers
Peter Cock | 27 Jul 2012 17:03
Gravatar

Re: BioPerl and Travis-CI

On Fri, Jul 27, 2012 at 3:58 PM, Fields, Christopher J
<cjfields <at> illinois.edu> wrote:
> On Jul 27, 2012, at 9:47 AM, Peter Cock wrote:
>
>> On Thu, Jul 26, 2012 at 4:22 PM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
>>>
>>> That's done now - except for the circular dependencies, and GD,
>>> which might be easy to solve if anyone knows what the error
>>> means - see commit message here:
>>> https://github.com/peterjc/bioperl-live/commit/905441ac09939be3368c14de38d04486c7e9849a
>>
>> Re: https://twitter.com/cjfields/status/228861370454638592
>> Not sure why you got GD to work when something very similar
>> had failed for me. Oh well - job done :)
>
> It was the lack of gdlib-config in the libgd2-xpm package, you need
> libgd2-xpm-dev.  One of the fun things about Debian packaging.

Ah - I should have guessed that.

>>> Would a single clean commit of the (current) .travis.yml file be
>>> preferable to the current series of commits? And you you want
>>> a pull request, or would you just merge/cherry-pick manually?
>>
>> Given all the churn between our revisions, personally I'd opt for
>> a single clean commit to bioperl/master - but your call.
>>
>> Peter
>
> Yep, about to merge it over.  It's working now, just need to
(Continue reading)

Permalink | Reply |
headers
Fields, Christopher J | 27 Jul 2012 17:15
Favicon
Gravatar

Re: BioPerl and Travis-CI


On Jul 27, 2012, at 10:03 AM, Peter Cock wrote:

> On Fri, Jul 27, 2012 at 3:58 PM, Fields, Christopher J
> <cjfields <at> illinois.edu> wrote:
>> On Jul 27, 2012, at 9:47 AM, Peter Cock wrote:
>> 
>>> On Thu, Jul 26, 2012 at 4:22 PM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
>>>> 
>>>> That's done now - except for the circular dependencies, and GD,
>>>> which might be easy to solve if anyone knows what the error
>>>> means - see commit message here:
>>>> https://github.com/peterjc/bioperl-live/commit/905441ac09939be3368c14de38d04486c7e9849a
>>> 
>>> Re: https://twitter.com/cjfields/status/228861370454638592
>>> Not sure why you got GD to work when something very similar
>>> had failed for me. Oh well - job done :)
>> 
>> It was the lack of gdlib-config in the libgd2-xpm package, you need
>> libgd2-xpm-dev.  One of the fun things about Debian packaging.
> 
> Ah - I should have guessed that.
> 
>>>> Would a single clean commit of the (current) .travis.yml file be
>>>> preferable to the current series of commits? And you you want
>>>> a pull request, or would you just merge/cherry-pick manually?
>>> 
>>> Given all the churn between our revisions, personally I'd opt for
>>> a single clean commit to bioperl/master - but your call.
>>>
(Continue reading)

Permalink | Reply |

Gmane