[Bioperl-l] Codon boostraping

[Peter Cock]

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As an aside, at this stage it is still safe to amend the 'unpublished'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