[ensembl-dev] Git

Fields, Christopher J cjfields at illinois.edu
Wed Oct 3 02:44:00 BST 2012 

Will have to refer to you as the two Pauls, or Paul^2 :)

Paul #1 (or #2?) already replied to me off-list.  I agree it's best to let the developers worry about the actual code development.  I think the past posts in this thread re: the interest of the community in git (including mine) should suffice as enough of a reminder.

chris

On Oct 2, 2012, at 5:34 PM, Paul Flicek <flicek at ebi.ac.uk>
 wrote:

> Hi Chris,
> 
> The message below wasn't intended to go out on the ensembl-dev list.  As you can imagine, we have a number of mailing lists associated with the project including a more internal list for people at the EBI and Sanger (i.e. the Genome Campus) to discuss the project.  This is often done with details like hardware infrastructure that are irrelevant to outside users.
> 
> 
> For everyone else on this discussion, please read down to what I posted back on 11 September.  I can add to that post that we did discuss this at our most recent operations meeting and we have a plan to investigate git in more detail early next year.  However, the essential point still stands:  CVS works very well for us to create Ensembl and changing things that work would not be something that we do lightly.
> 
> If you or anyone else wants to lobby for git or mercurial or something that hasn't even been invented yet , please send a message directly to me and let's let Ensembl dev get back to discussing the Ensembl code itself :)   
> 
> [ Extra credit on the confusion scale if you have noticed the fact that Paul Kersey leads the Ensembl Genomes team while Paul Flicek leads the Ensembl team! ]
> 
> Thanks,
> 
> Paul 
> 
> 
> 
> 
> On 2 Oct 2012, at 20:02, Fields, Christopher J wrote:
> 
>> Paul,
>> 
>> I'm a bit confused.  Exactly where is this 'campus' list?  Or is this something local to EBI (e.g. not including the user community)?  
>> 
>> And what does 'unlicensed' mean?
>> 
>> Not seeing anything here:
>> 
>>   http://lists.ensembl.org/mailman/listinfo
>> 
>> (FWIW, +1 on a move to git, or really anything that helps keep the project going)
>> 
>> chris
>> 
>> On Oct 2, 2012, at 1:09 PM, Paul Kersey <pkersey at ebi.ac.uk>
>> wrote:
>> 
>>> Hi dan
>>> 
>>> You should contribute to this discussion on the ensembl campus list, not the unlicensed dev list.
>>> 
>>> Thanks,
>>> 
>>> Paul
>>> 
>>> Sent from my iPhone
>>> 
>>> On 2 Oct 2012, at 18:50, Dan Bolser <dbolser at ebi.ac.uk> wrote:
>>> 
>>>> Sorry for coming late to the discussion, especially as I've nothing
>>>> concrete to add, but here it is anyway ;-)
>>>> 
>>>> Horses weren't broken when Ford created the Model T. Cars are just
>>>> better than horses. I think the Ensembl code base, like many others,
>>>> would benefit from a more distributed development environment, which
>>>> git supports better than cvs. Weather or not Ensembl has lots of
>>>> external contributors, Ensembl is a highly distributed project, so
>>>> anything that helps support that model should be a benefit.
>>>> 
>>>> Just my 0.12p ;-)
>>>> 
>>>> If people are curious, here is a git / svn command equivalence
>>>> document (svn is like a good version of cvs):
>>>> * http://git.or.cz/course/svn.html
>>>> 
>>>> and here is the best git tutorial I've seen (generic, although written
>>>> for a specific project):
>>>> * http://docs.parrot.org/parrot/devel/html/docs/project/git_terminology.pod.html
>>>> * https://github.com/parrot/parrot/blob/master/docs/project/git_workflow.pod
>>>> 
>>>> 
>>>> Cheers,
>>>> Dan.
>>>> 
>>>> On 11 September 2012 18:22, Paul Flicek <flicek at ebi.ac.uk> wrote:
>>>>> Hi Matthew, Ken and others,
>>>>> 
>>>>> These are useful data points for us especially when there are similar project to Ensembl that have made the change.
>>>>> 
>>>>> We of course, have a lot of history using CVS and we understand how it works for our needs.  This doesn't mean that we would never change only that we don't necessary set out to change things that work.
>>>>> 
>>>>> I do think that it is also useful to point out that the purpose of Ensembl is fundamentally to create useful and up to date genome resources :)  If the tools that we are using are adequate to the tasks that we need, we are very likely to keep on using them.  Of course, when the tools are getting in the way of what we are trying to do, there is some urgency to change.
>>>>> 
>>>>> We will discuss this at one of our next internal operations meetings.  If we do decide to change, the dev list will be among the first groups to know.
>>>>> 
>>>>> 
>>>>> Paul
>>>>> 
>>>>> 
>>>>> On 11 Sep 2012, at 10:11, Matthew Astley wrote:
>>>>> 
>>>>>> On Mon, Sep 10, 2012 at 04:24:37PM +0000, Youens-Clark, Ken wrote:
>>>>>> 
>>>>>>> While meeting on campus, I brought up the multiple advantages to an
>>>>>>> outside developer such as myself to having the Ensembl code
>>>>>>> repository move to Git.
>>>>>> 
>>>>>> The ensembl CVS repository hosts several projects, some more tightly
>>>>>> coupled than others.
>>>>>> 
>>>>>> ensembl-otter was in there, it was and still is connected to Ensembl
>>>>>> as a "leaf", so no other code should depend on it.
>>>>>> 
>>>>>> We moved it to Git last year, and later also to Github,
>>>>>> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-otter/MOVED.txt?revision=1.2&root=ensembl&view=markup
>>>>>> 
>>>>>> and have been almost entirely pleased with the results.  We still have
>>>>>> other code in CVS.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> I'll list a few points to start the discussion:
>>>>>> 
>>>>>> I tried starting discussion a while ago.  Some ensembl projects were
>>>>>> quite happy with CVS and had no plans to move.  Others have been
>>>>>> quietly interested.
>>>>>> 
>>>>>> I'm happy to support owners of code with the migration process.  It is
>>>>>> gradual & minimally invasive.  There's no commitment to switch until
>>>>>> the addition of MOVED.txt or similar, and marking the CVS files
>>>>>> read-only.
>>>>>> 
>>>>>> I also maintain cvs2git ghosts for some projects.  We use these
>>>>>> internally and occasionally, and were not planning to share them.
>>>>>> 
>>>>>> 
>>>>>>> - [...] CVS was started in 1986.  [...]  Basically, CVS development
>>>>>>> appears to have been abandoned about 4 years ago.
>>>>>> 
>>>>>> True (or at least true enough for me).  But like other old software,
>>>>>> CVS can still do what it always did; and the later versions do add
>>>>>> extra info to mark commitids.
>>>>>> 
>>>>>> Provided there are no security problems, the incentive to switch is
>>>>>> only that newer tools are better.
>>>>>> 
>>>>>> 
>>>>>>> - [Git] is enormously powerful (and, yes, more complex than CVS, but
>>>>>>> not necessarily in the main) and is actively developed by a vibrant
>>>>>>> community of dedicated hackers.
>>>>>> 
>>>>>> Exactly as with CVS, I would recommend having one person "nearby" who
>>>>>> can deal with the unusual and difficult Git issues.  The rest is just
>>>>>> commit and push.
>>>>>> 
>>>>>> The tools supporting Git are great.
>>>>>> 
>>>>>> 
>>>>>>> - Git's social ideas of coding are worth exploring and adopting.
>>>>>> 
>>>>>> The social side is also optional.  I have private Git repositories for
>>>>>> some passwords, diary entries etc. which live on encrypted filesystems
>>>>>> and are not shared with anyone.
>>>>>> 
>>>>>> --
>>>>>> Matthew
>>>>>> 
>>>>>> _______________________________________________
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>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>> 
>>>>> 
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>>>> 
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> 
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