[Biopython-dev] biopython on github

[Giovanni Marco Dall'Olio]

On Fri, Mar 20, 2009 at 11:41 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Mar 19, 2009 at 7:00 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> On Tue, Mar 17, 2009 at 9:34 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> Sweet. Glad that worked. I deleted my branch (edit->delete
>>> repository).
>>
>> How long did it take to process?  I deleted mine (after attempting to
>> merge against the CVS mirror).  The delete was still in progress over
>> 12 hours later!
>
> And the branch delete is still on-going :(
>
>> ...  And this afternoon github seems to be down, so I haven't played with it any more.
>
> Its back online again, but right now for me github is a bit of a damp squid [*].
> As my initial branch/fork of biopython still exists but is being
> deleted, it seems
> in the meantime I can't create a new branch of biopython.

mmm are you referring to this:
- http://github.com/peterjc/biopython-seqio-quality/network
?

I can see it, and also fetch/pull changes from it..

I see that you have renamed your fork as seqio-quality. Ok, but I
think it is better to keep the fork's name as 'biopython', and then
create many branches inside it.

For example:

<create a fork on github>
git clone <yourforkurl>
cd biopython

# make some commits to your master branch:
touch testfile.txt
git add testfile.txt
git commit -a -m 'test file added'
# push the changes to your github repository ('origin' refers to
github; see $(CWD)/biopython/.git/config)
git push origin master


# create a branch called 'experimental-seqio-quality', and switch to it:
# without arguments, git branch shows the list of branches and the current one:
git branch
# create the experimental-seqio-quality branch:
git branch experimental-seqio-quality
# switch to it:
git checkout experimental-seqio-quality
# check that experimental-seqio-quality is the current working branch:
git branch

# now you are working in the branch called
'experimental-seqio-quality'. All the changes you
# commit here, will not be saved in the 'master' branch or the others,
as long as you don't
# merge them:
touch seqio-parser
git add seqio-parser
git commit -a -m 'added seqioparser'
git push origin experimental-seqio-quality
# after pushing, git will create a new branch in github. Look for
example at my fork here:
# - http://github.com/biopython/biopython/network

############

Here is how you can merge and compare your branch with someone else's
or with the biopython one:

# add a reference to biopython official branch
git remote add biopython git://github.com/biopython/biopython.git

# obtain the set of changes from the biopython branch, and merge them
git fetch biopython
git log master biopython/master
git diff master biopython/master
git merge master biopython/master

git remote add peter git://github.com/peterjc/biopython-seqio-quality.git
git fetch peter # there it should be a way to do this without having to fetch
git diff master peter/master

For references, look at this guide:
http://github.com/guides/keeping-a-git-fork-in-sync-with-the-forked-repo


> Odd, and rather
> frustrating.  Hopefully it will sort itself out shortly, and I can
> have another play
> with merging branches...
>
> Peter
>
> [*] For the benefit of non-native English speakers, or or anyone whose sense
> of humour works differently to mine, this was a pun, based on the English phrase
> "damp squib" for a disappointing event, and the fact that github's
> error page has
> some kind of cartoon squid/octopus-cat creature on it.
>
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> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>



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