O|B|F News » BioPerl

Travis-CI for Testing

Peter — Mon, 30 Jul 2012 13:24:09 +0000

Earlier this year BioRuby and then Biopython and BioPerl started using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated:

The BioRuby team are also using Travis-CI for automated testing of their new ‘plugin’ ecosystem, BioRuby Gems, or BioGems.

Travis-CI gives us continuous testing, but for the moment only covers one operating system (currently 32 bit Ubuntu Linux using Virtual Machines). This automated testing is therefore complementary to our existing OBF BuildBot server which aims to run nightly tests on volunteer developer machines setup to cover a broad range of operating systems and configurations.

However, Travis-CI are working on a new feature – automatic testing of pull requests, currently only available on a donation basis – which the OBF was happy to support.

What this means is that when a contributor has some code ready for integration, they can issue a GitHub pull request, and then Travis-CI will automatically run the unit tests with those proposed changes. This is something that currently the core-developers would normally do manually as part of evaluating proposed changes, so having this happen automatically should be a big help.

We’re excited about making more use of Travis-CI for other OBF projects. Thus far we’ve been really impressed with Travis-CI.

BioPerl-DB, BioPerl-Run, BioPerl-Network 1.6.9 released

Chris Fields — Thu, 21 Apr 2011 20:12:53 +0000

The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN:

Please report any bugs to our Redmine server.

Enjoy!

chris

BioPerl 1.6.9 released

Chris Fields — Thu, 14 Apr 2011 20:03:27 +0000

BioPerl 1.6.9 is now available in CPAN. In this release:

Refactored Bio::Species/Bio::Tree
New SeqIO modules (gbxml, msout, mbsout)
Updates for perl 5.12
Bio::Assembly support for SAM/BAM, Newbler, ace output
Bio::DB::SeqFeature updates
PAML updated to work with v. 4.4d
lots of various bug fixes, around 50

Just to note, this is the first release after we reworked the Build.PL system, so we will probably hit a few speed bumps along the way. This is in effort to simplify the process for further work this summer on modularizing BioPerl, but it also makes new releases much easier to make. In particular, this has only been tested on Ubuntu Linux and Mac OS X (no Windows testing has occurred yet). Please post if there are any problems.

Enjoy!

OBF and Google Summer of Code 2011

Peter — Fri, 18 Mar 2011 21:44:22 +0000

Great news: Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer’s Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2011 FAQ.

Student applications are due April 8, 2011 at 19:00 UTC. Students who are interested in participating should look at the OBF’s GSoC page, which lists project ideas, and whom to contact about applying.

For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on the OBF wiki page, and on the relevant project’s GSoC wiki page.

Thanks to all who helped make OBF’s application to GSoC a success, and let’s have a great, productive summer of code!

Rob Buels
OBF GSoC 2011 Administrator

Introduction of OpenID logins for OBF wikis

Chris Fields — Thu, 17 Mar 2011 17:29:38 +0000

Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login system will be disabled and OpenID will be the default path for new accounts so users to make wiki changes. This currently appears to have cut the incidence of spam significantly. We will be adding information to the login pages to redirect new users to the new login page.

We also have one wiki (BioLib) that is testing out manual account approval via a wiki bureaucrat in case we have to take more extreme measures, though we would like to leave the barrier to community involvement with projects at the lowest possible level.

OBF Redmine server now available

Chris Fields — Thu, 17 Mar 2011 17:07:02 +0000

The OBF now has a sparkly new Redmine instance running on Amazon EC2, thanks to efforts from Chris Dagdigian and Jason Stajich (with some admin help from yours truly). Bugs and user names (along with email contacts) from our old Bugzilla v2 server have been migrated over, though some links need to be fixed.

Redmine is a project management web application that has several nice features over other systems, including issue tracking, multiple project management, wikis, forums, and calendaring.

Previous Bugzilla users will need to either reset their password using their original Bugzilla login (an email address) or contact the OBF Helpdesk to get their password.

BioPerl has moved to GitHub

Chris Fields — Fri, 14 May 2010 04:18:33 +0000

BioPerl has migrated to git and GitHub! We have also set up a mirror set of several key repositories at the great public git hosting site repo.or.cz.

If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub account and let us know your user ID. Also, add the extra email (where ‘DEVNAME’ is your original Subversion account ID). This should map any previous commits from the older Subversion and CVS repository to your new GitHub account.

The following are ways everyone can download the latest code.

Using git

Note you can replace ‘bioperl-live.git’ with any of the repository names (bioperl-db, bioperl-run, etc). For BioPerl developers (GitHub collaborators) you have a choice of SSH or HTTP:

  git clone git@github.com:bioperl/bioperl-live.git

  git clone https://bioperl@github.com/bioperl/bioperl-live.git

The open read-only link (for everyone):

  git clone git://github.com/bioperl/bioperl-live.git

or using the mirror site:

  git clone git://repo.or.cz/bioperl-live.git

Using SVN (read-only)

We will also support read-only access to GitHub with Subversion. We may allow write support at some later point. To use svn:

  svn checkout http://svn.github.com/bioperl/bioperl-live.git

Direct downloads

Tagged releases can be found here:

http://github.com/bioperl/bioperl-live/downloads

The latest source code here:

http://github.com/bioperl/bioperl-live/archives/master

Forking BioPerl and Pull Requests

We intend on using git and GitHub to their fullest. With that in mind, we encourage users to fork BioPerl code, make changes, commit them to your forked repository, and submit pull requests.

Documentation

We’re also in the process of updating our local developer documents for help with those who haven’t used git before. In particular, we have a Using Git page, and have added RSS feeds for our repository commits.

Enjoy!

chris

Update: SVN version fixed, thanks to DaveMessina++ for pointing it out.

O|B|F Google Summer of Code Accepted Students

Robert Buels — Sun, 02 May 2010 19:37:03 +0000

I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors:

Mark Chapman (PM Andreas Prlic) – Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms

Jianjiong Gao (PM Peter Rose) – BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins

Kazuhiro Hayashi (PM Naohisa Goto) – Ruby 1.9.2 support of BioRuby

Sara Rayburn (PM Christian Zmasek) – Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree

Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) – Extending Bio.PDB: broadening the usefulness of BioPython’s Structural Biology module

Jun Yin (PM Chris Fields) – BioPerl Alignment Subsystem Refactoring

Congratulations to our accepted students!

All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy.

Thanks very much to all the students who applied, we very much appreciate your hard work.

Here’s to a great 2010 Summer of Code, I’m sure these students will do wonderful work.

Rob Buels
O|B|F GSoC 2010 Administrator

O|B|F in Google Summer of Code

Robert Buels — Sun, 21 Mar 2010 18:26:52 +0000

The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer’s Google Summer of Code. Our list of project ideas and mentors is linked from the O|B|F GSoC page.

Student applications must be submitted to Google by April 9, 2010, see the official GSoC 2010 FAQ. That is less than three weeks away!

Students, have a look at that wiki page, contact the project you’re interested in working with, and get rolling on that application post-haste. A good GSoC application takes quite a bit of thought and effort to put together. Students are encouraged to get help from mentors to put together a good application.

Current developers on O|B|F projects, have a look through the GSoC Mentoring Guide, and if it looks like something you want to do, there’s still time to volunteer as a prospective mentor. Just add your name to the O|B|F and project wiki pages, and contribute your project ideas. Even if you don’t have project ideas of your own, it’s good to volunteer.

Google Summer of Code is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5,000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the official GSoC 2010 FAQ.

Thanks to all who helped make OBF’s application to GSoC a success, and let’s have a great, productive summer of code!

Rob Buels
O|B|F GSoC 2010 Administrator

BioPerl at GMOD Meeting 2010

Chris Fields — Tue, 19 Jan 2010 03:58:58 +0000

BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just prior to the GMOD Meeting. Several items were covered on the agenda:

In order to start addressing whole genome data with more lightweight objects, we are planning on setting up a lightweight Bio::SeqI object that has a flexible DB backend (i.e. Bio::DB::SeqFeature::Store or similar). We are also contemplating adding lazy parsing for some parsers, possibly using the Bio::PullParserI methods (or similar) that Sendu Bala created.
After a final 1.6 branch point release, we may ‘freeze’ BioPerl in a maintenance mode, primarily so that we can reorganize core into several more easily installed subdistributions on a branch. New modules will essentially be additional separate repos that will depend on BioPerl core. This reorganization has been discussed for a few years now, and as we edge closer to starting this (probably this spring) we’ll announce more details.
Some initial thoughts on how to handle circular genomes more efficiently. We essentially do this already, but it isn’t full-proof.
Need some significant time dedicated towards GFF3-based coding (reimplement FeatureIO but allow some flexibility). Rob Buels had started the initial run at splitting out FeatureIO, so next step is a true reimplementation.
We don’t plan on including Moose support for the immediate future, feeling that it would be better to reimplement some of the classes from scratch using Moose and similar as a BioPerl 2.0, or possibly await the impending Rakudo Perl 6 alpha and start afresh using that instead of Moose.

Anything we missed? Anything you would like to address? Please add comments and we’ll discuss them on list.