[Biopython-dev] biopython on github

[Peter]

>
> The documentation looks awesome. My only suggestion would be to
> change the navigation link that current points to CVS to point to a
> generic page like SourceCode. Then that landing page could link
> to the current CVS and explain we are working to transition to
> Git, with links to those pages. Currently, the Git docs are a
> bit buried from the front page.
>
> Peter, I don't appear to have wiki permissions to edit the navigation
> bar; do you?

I'm not sure how to do it (although I probably have the relevant
permissions).  I can probably give you admin rights - you use the
"Chapmanb" username on the wiki, right?

> Peter:
>> I'm thinking a news post on
>> http://news.open-bio.org/news/category/obf-projects/biopython/ about
>> version control would be a good idea at this point.  How about this -
>
> This is great, and I would move the last paragraph describing
> the Git repository to the beginning; start with what we are doing and
> then describe the rationale. This should help for those with ADD, and
> also give more prominent credit to Bartek, Giovanni and you for the
> work that went into this.

OK.  New version, with the markup for the links included:

Initially for evaluation purposes only, Giovanni and Bartek have setup
a mirror of <a href="http://github.com/biopython/biopython/tree/master">Biopython
on GitHub</a>, which is automatically updated from the OBF hosted <a
href="http://www.biopython.org/wiki/CVS">Biopython CVS repository</a>.
 See our <a href="http://biopython.org/wiki/GitMigration">git
migration wiki page</a> for details.  If this is favorably received,
then moving Biopython from CVS to git seems likely at some point this
year.

Originally, all the OBF hosted projects used <a
href="http://www.nongnu.org/cvs/">CVS</a> for their source code
repositories.  At the start of 2008, <a
href="http://www.bioperl.org">BioPerl</a> and <a
href="http://www.biojava.org">BioJava</a> moved over to <a
href="http://subversion.tigris.org/">Subversion (SVN)</a>, followed by
<a href="http://www.biosql.org">BioSQL</a>.  <a
href="http://www.biopython.org">Biopython</a> was originally going to
do the same, but this didn't actually happen.  Having all the Bio*
projects using the same version control system would have simplified
server administration for the OBF, but using SVN wouldn't really have
made that much difference to Biopython development.  Discussion on the
<a href="http://biopython.org/pipermail/biopython-dev/">Biopython
development mailing list</a> has since shifted towards next-generation
distributed version control systems like <a
href="http://git-scm.com/">git</a> or <a
href="http://bazaar-vcs.org/">Bazaar</a>.

Quote from Linus Torvalds,
<blockquote>The slogan of Subversion for a while was ‘CVS done right’,
or something like that, and if you start with that kind of slogan,
there's nowhere you can go. There is no way to do CVS
right.</blockquote>

In addition to creating the Linux kernel, Linus Torvalds more recently
wrote <a href="http://git-scm.com/">git</a>, a prominent example of a
distributed version control system.  Rather than switching from CVS to
SVN, the <a href="http://www.bioruby.org">BioRuby</a> project choose
instead to use git, hosted on <a href="http://github.com">github</a>
(see the <a href="http://github.com/bioruby/bioruby/tree/master">BioRuby
repository</a>).  Biopython is considering doing something similar -
using a <em>distributed</em> version control system like git should
make it easier for potential Biopython contributors to manage their
own local copies of Biopython under version control.

Peter, on behalf of the Biopython developers