[Bioperl-l] Codon boostraping

[Fields, Christopher J]

On May 22, 2012, at 12:15 PM, Peter Cock wrote:

> On Tue, May 22, 2012 at 6:05 PM, Tristan Lefebure
> <tristan.lefebure at gmail.com> wrote:
>> Hi Jason, so I am trying to find my way into the github world, but well I am
>> stuck after doing this:
>> 
>> git clone git at github.com:TristanLefebure/bioperl-live.git
>> cd bioperl-live/
>> git remote add upstream git://github.com/bioperl/bioperl-live.git
>> git fetch upstream
>> git push origin master
>> #doing some editing to Bio/Align/Utilities.pm
>> git add Bio/Align/Utilities.pm
>> git commit -m "Little patch to Utilities.pm to allow codon bootstraping"
>> git show
>> #looks good, feeling quite happy, for the moment
> 
> At that point the change only exists on your local hard drive.
> 
> As an aside, at this stage it is still safe to amend the 'unpublished'
> commits (which should should never do once they have been made
> public - aka rewriting history). e.g. To fix the spelling error in the
> message:
> 
> git commit --amend -m "Little patch to Utilities.pm to allow codon
> bootstrapping"
> 
> You need to push the change to your repository on github. However,
> it would have been good to have made a new branch first... I think
> this would do the trick:
> 
> git checkout -b codonbs
> #Create new branch (from current code) called codonbs
> 
> git push origin codonbs
> #'Copy' this branch to your repo on github
> 
> After that you should be able to see the new branch on github,
> and from there issue a pull request. This is what we've written
> for Biopython on using git and github - which we should probably
> review now we've been using github for a while:
> http://biopython.org/wiki/GitUsage
> 
> Peter

Regarding git/github doucmentation, IMO it would be a good idea to consolidate documentation where necessary to a common place we can all refer to for the basics (maybe place it on the open-bio wiki), and then leave project-specific stuff for the various Bio* wikis.  The more eyes on it the better overall documentation we'll all have.

Same could be said for a lot of the non-bioperl stuff (format/app/etc) on bioperl.org though the final site should probably be wikipedia.

chris