[Biopython-dev] Another Biopython release?

[Eric Talevich]

>
> On Tue, Sep 15, 2009 at 3:51 PM, Peter <biopython at maubp.freeserve.co.uk>
> wrote:
> > Hi all,
> >
> > I know it's been only a month since we released Biopython 1.51, but
> > does anyone (other than me) think that we already have enough done
> > to warrant another release? The associated CVS freeze would also
> > serve as a good break point for moving to github (see other threads).
> >
>

Sounds good to me. Completing the Git migration would make it much easier
for me to maintain the Tree/TreeIO stuff, since I already have a few local
branches based on it that an upstream CVS duplication would mangle.


On Tue, Sep 15, 2009 at 10:59 AM, Bartek Wilczynski <
bartek at rezolwenta.eu.org> wrote:

> That would be great. As for the move to github, I've added some (quite
> preliminary) docs for developers on how to make commits to the main
> branch using git and github to the wiki:
> http://www.biopython.org/wiki/GitUsage#Commiting_changes_to_main_branch
>
>
The setup here for committers looks potentially different from the setup in
"Merging upstream changes" (describing read-only tracking), but also
potentially similar. Diff:
- The github:biopython/biopython repository is called "official" here, but
"upstream" there. Different protocol too, but that's intentional.
- It also shows how to treat the upstream/official repo as the origin,
CVS-style. This would mean the developer doesn't have a separate GitHub fork
to use for personal branches, uncertain commits, etc. that don't belong in
the main repo.

Maybe a good way to organize the page would be in terms of how you want to
use the repo:

1. Tracking Biopython with raw Git (without signing up for GitHub)
   - git clone http://.../biopython/biopython
   - remote: upstream
   - how to format a patch and submit on Bugzilla

2. Tracking Biopython on GitHub (e.g. occasional contributors)
   - sign up, click the "fork" button
   - git clone http://.../your-name-here/biopython
   - remotes: origin, upstream
   - how to submit a pull request on GitHub
   - how to add, manage and delete branches locally and on GitHub

3. Collaborating
   - either #1 or #2 is fine
   - how to add and manage more remotes
   - how to apply Git patches, and why copy/paste kills kittens the next
time you merge

4. Committing to Biopython
   - same as #2, but use the private URL for the "upstream" remote
   - remotes: origin, upstream
   - policy on pushing upstream, code reviews, tagging, etc.


Cheers,
Eric