[Biopython-dev] Biopython 1.56 release plans

[Peter]

2010/11/5 Peter <biopython at maubp.freeserve.co.uk>:
> 2010/11/5 Tiago Antão <tiagoantao at gmail.com>:
>> On Thu, Nov 4, 2010 at 5:13 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>>> For example, Tiago - you've been doing lots of work on your
>>> branch with the PopGen code. Is that code ready? I'm willing
>>> to do the git merge/rebase.
>>
>> I was hoping that would offer to do a merge ;) . <sarcasm> Though we
>> need a broken repository to test the integration server, so maybe I
>> could do it myself </sarcasm>.
>> Yes, the code is ready.
>
> OK - I'll try to get your code, rebase it onto the current master,
> then post it as a new branch for you to check.

Notes on how I did this:

$ git remote add tiago https://github.com/tiagoantao/biopython.git
$ git fetch tiago
...
>From https://github.com/tiagoantao/biopython
 * [new branch]      buildbot   -> tiago/buildbot
 * [new branch]      master     -> tiago/master

Now I want your "master" branch, but that name clashes with
my "master" branch... the following worked here:

$ git checkout tiago/master
Note: moving to "tiago/master" which isn't a local branch
If you want to create a new branch from this checkout, you may do so
(now or later) by using -b with the checkout command again. Example:
  git checkout -b <new_branch_name>
HEAD is now at 21b7a22... Merge branch 'master' of
github.com:tiagoantao/biopython
$ git checkout -b tiago-pop-gen
Switched to a new branch "tiago-pop-gen"

Now I want to write the history of you PopGen work as though
it was started from the current state of the master branch. I
was hoping there would have been no changes to the PopGen
code on the master so that this would be trivial...

$ git rebase master
...
CONFLICT (content): Merge conflict in Bio/PopGen/FDist/__init__.py
...

So open Bio/PopGen/FDist/__init__.py and look for the merge failures
(which are marked with <<<<<<< to >>>>>>>). In this it was the
removal of some deprecated code done on the pop gen branch, which
was only deprecated in Biopython 1.55 so it is a bit premature to remove
it already. So I fixed up Bio/PopGen/FDist/__init__.py and saved it. Then:

$ git add Bio/PopGen/FDist/__init__.py
$ git rebase --continue
...

This seems to have worked. I can now do a comparison to
the master branch,

$ git diff master
...

After running the unit tests (which was of limited value as I don't
have FDist installed on this machine), I then pushed it online:

$ git push peterjc tiago-pop-gen

The rebased branch is now here:
https://github.com/peterjc/biopython/tree/tiago-pop-gen

If you agree the rebased branch is sane, it should be trivial to
now merge that onto the master as a fast-forward merge.
(But I would check first that the master hasn't changed, and
if it has, repeat the rebase).

Peter