[Biopython-dev] biopython on github

[Brad Chapman]

Hi all;
It is good to see the discussion around revision control systems;
Chris and Paulo's posts make some nice points. Source code
management is an important issue that influences perception of
Biopython and barriers to contributing.

My two cents on what we should do is:

- Pick a distributed source code management system. My preference
  is Git, only because it currently has more steam behind it.
  Git/Bazaar will likely end up being like the VHS/Beta debate.

- Test drive use of Git on an official GitHub repository. This would
  involve a few things:

  = Bartek and Giovanni: Can you coordinate on a single GitHub
    Biopython instance and remove the others to eliminate confusion?
  = Write up documentation for contributors. This is where we could use
    some volunteers from those interested to update the web pages.
    The two main places that need updating are:

    http://biopython.org/wiki/Contributing
    http://biopython.org/wiki/CVS
    
    I think we should ensure people are clear on what is being done
    and where you can contribute.

- Ensure GitHub can be synced with current CVS. Bartek, it sounds
  like you have a handle on this.

- Evaluate the success of Git. This is easy to measure in terms of
  new contributors, increased happiness, and what not. At the same
  time we can monitor how GitHub evolves over time.

- If successful, talk to the OpenBio team about hosting Git locally.

Peter, Michiel, et al -- how do you feel?

I think being cautious with the transition, as Peter recommends, is
important. I am old enough to remember Sourceforge being new and
everyone saying how it was stupid not to move there; then over time
Sourceforge got slow with all the users and people moved
away from it. This is just to say -- no one knows how GitHub (or
Launchpad) will evolve. OpenBio is a stable, small, nice community
and to the extent we can use their resources I believe we should.

Overall, the specifics of the above proposal aren't as important as
just doing something unambiguous and then evaluating how it works.
Right now things are a big confusing, which I think could put off
new developers, who are always welcome.

Looking forward to talking about code instead of revision control,
Brad

> On Fri, Mar 13, 2009 at 8:21 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> > On Thu, Mar 12, 2009 at 11:20 PM, Bartek Wilczynski
> > <bartek at rezolwenta.eu.org> wrote:
> >> On Thu, Mar 12, 2009 at 10:07 PM, Chris Lasher <chris.lasher at gmail.com> wrote:
> >>> On Thu, Feb 26, 2009 at 10:00 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> >>>> Another option to consider would be to switch to running git on
> >>>> biopython.org, but use the git-cvsserver tool to provide an emulated
> >>>> CVS server on top of the git repository.  This sounds possible in
> >>>> theory, and would be nice for any "old fashioned" biopython developers
> >>>> because is should be fairly transparent - they can continue to treat
> >>>> it as CVS and just work on the main trunk.  This would require someone
> >>>> competent to do the conversion and alter the server setup - we'd have
> >>>> to talk to the OBF team about this.  However, if anyone has first hand
> >>>> experience on git-cvsserver perhaps they could comment on weather this
> >>>> sounds like a good plan or not.
> >>>
> >>> I must be missing something, Peter. Why would BioPython continue to
> >>> operate with CVS? I suppose I just really hope to see BioPython
> >>> running with something other than CVS, and I'd really like to see it
> >>> go either under Bazaar or Git.
> >
> > I'm warming to the idea of git, and had noticed git includes the
> > optional git-cvsserver tool which emulates a CVS server while using
> > git underneath.  I was wondering if anyone had first hand experience
> > of this.  If we did move from CVS to git (still hosted on
> > biopython.org), this would seem to offer a nice migration path for of
> > our "old school" CVS developers - they can carry on as usual.  Of
> > course, if none of us care about having to learn a new interface, then
> > a simple switch would be less hassle to setup.  For the server side of
> > things, we'll need to talk to the OBF team about any such move - as
> > far as I know they've only managed CVS to SVN migrations in the past.
> >
> > Peter
> >
> >> Hi Chris,
> >>
> >> The idea is to do the switch in two steps:
> >> - first we still have the main branch in CVS while we have git and/or
> >> bzr branches synchronized with it for people to branch and contribute
> >> - If this works nicely, we will switch to one of these systems
> >> completely (while possibly keeping the other branch in sync, but this
> >> is not yet decided)
> >
> > That does seem like a good plan.  Of course, there is the related
> > issue of where we host the official repository (externally, e.g. on
> > github or lauchpad) or in house (on biopython.org).  I favour keeping
> > the official repository on biopython.org but this will require OBF
> > technical support (do we have the expertise within Biopython? Bartek?
> > Chris?).
> >
> >> The first step is to some extent operational (I'm currently busy with
> >> other stuff, but I'll get arround it hopefully this weekend), but the
> >> second step requires decision on our side (git or bzr?) and action on
> >> the side of OBF (there is no git or bazar installed on obf servers).
> >
> > There is also the previously semi-agreed solution of switching from
> > CVS to SVN on biopython.org, but this would be only a gradual
> > improvement.  I gather there are mature tools for using git+svn
> > together, so it should be better than using git+cvs together.  Other
> > than meaning all the OBF hosted projects are on SVN (I think we are
> > the last still on CVS), this is beginning to seem a bit pointless.
> >
> > Peter
> >
> 
> Peter et al.,
> 
> I started off writing an email about why I think hosting at GitHub or
> Launchpad is a better idea, but it got a bit verbose, so I just wrote
> up a blog post instead. (Besides, links and images are more fun, and
> make the intarwebs go 'round.) Please see
> http://igotgenes.blogspot.com/2009/03/why-biopython-needs-to-move-to-github.html
> or
> http://tinyurl.com/a9o7ae
> 
> Chris
> 
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