[GenABEL-dev] Proposal to move to Github
L.C. Karssen
lennart at karssen.org
Mon Oct 19 23:21:02 CEST 2015
On 19-10-15 23:12, K. Zhong wrote:
> You can register for a 5-user team for free on bitbucket.
Yup, but I guess that would be limiting for some GenABEL packages...
Lennart.
>
> Best regards,
> Kaiyin ZHONG
> ------------------
> FMB, Erasmus MC
> http://kspace.co.vu
> k.zhong at erasmusmc.nl
> kindlychung at gmail.com
>
>
>
>
>
>
>
>
> On 19/10/2015 23:09, "genabel-devel-bounces at lists.r-forge.r-project.org on
> behalf of L.C. Karssen" <genabel-devel-bounces at lists.r-forge.r-project.org
> on behalf of lennart at karssen.org> wrote:
>
>> Hmm, am I correct that Github allows you to create an 'organisation',
>> but Bitbucket doesn't?
>> I just the GenABEL Project on Github [1] some time ago. Bitbucket seems
>> to have teams, which could work the same way, but if I understand it
>> correctly you need to pay for teams with more than 5 members. That would
>> be a definite plus for GitHub.
>>
>>
>> Lennart.
>>
>>
>>
>> [1] https://github.com/GenABEL-Project
>>
>> On 19-10-15 22:43, L.C. Karssen wrote:
>>> hi Kaiyin,
>>>
>>> On 19-10-15 22:28, K. Zhong wrote:
>>>> Hi, Lennart.
>>>>
>>>> Regarding to (2), it¹s possible to start in Bitbucket and then create a
>>>> mirror in Github painlessly (or vice-versa).
>>>
>>> Interesting! I didn't think of that. Thanks for bringing it up.
>>>
>>> I do think that for 'communication' purposes it wouldbe best to have one
>>> 'main/official location' for the packages (either Github or Bitbucket),
>>> to keep possible confusion to a minimum. Now (almost) all development is
>>> done on R-forge's SVN. Nice and clean. Given Git's improvements to the
>>> development process and the fact that Github/Bitucket give a push
>>> towards social coding I have no objections to have both R-forge and a
>>> Git repo, but IMHO spreading packages across three platforms doesn't
>>> sound very good.
>>>
>>>> But for published packages a
>>>> private repo seems unnecessary?
>>>
>>> True. I thought maybe a private repo could be used by packages that are
>>> still under consideration. Or where the authors are not ready yet to
>>> develop 'in broad daylight' yet. Not really in the GenABEL spirit, but
>>> we could be open to that.
>>>
>>>
>>> Lennart.
>>>
>>>> My 2 cents.
>>>>
>>>>
>>>>
>>>> Best regards,
>>>> Kaiyin ZHONG
>>>> ------------------
>>>> FMB, Erasmus MC
>>>> http://kaiyin.co.vu
>>>> k.zhong at erasmusmc.nl
>>>> kindlychung at gmail.com
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 19/10/2015 22:20,
>>>> "genabel-devel-bounces at lists.r-forge.r-project.org on
>>>> behalf of L.C. Karssen"
>>>> <genabel-devel-bounces at lists.r-forge.r-project.org
>>>> on behalf of lennart at karssen.org> wrote:
>>>>
>>>>> Dear list,
>>>>>
>>>>> With this e-mail I'm digging up a conversation from the past
>>>>> (April/May
>>>>> 2014). Back then we discussed (see below) the idea of moving (some of)
>>>>> the GenABEL suite tools to a Git repository like GitHub.
>>>>>
>>>>> Since then I have gained more experience with Git and I love it. So
>>>>> I'm
>>>>> all for giving it a try. This brings up the following questions on
>>>>> which
>>>>> I'd like to hear your opinion:
>>>>>
>>>>> 1) Which package(s) do we migrate first?
>>>>>
>>>>> 2) Where do we migrate to?
>>>>>
>>>>>
>>>>> Regarding 1): I think OmicABEL and OmicABELnoMM are the easiest to
>>>>> start
>>>>> with. They have a linear history (no branches etc.) so conversion is
>>>>> straightforward. I'd love to migrate ProbABEL, but I've spent several
>>>>> hours in vain trying to keep the branches and history correct. More
>>>>> time
>>>>> needed there (if someone has experience in SVN -> Git migration,
>>>>> please
>>>>> let me know).
>>>>>
>>>>> Regarding 2): Either GitHub or BitBucket is an option for me. I have
>>>>> some experience with both. Github is more popular/the de facto
>>>>> standard,
>>>>> but the nice thing about Bitbucket is that it allows private
>>>>> repositories (for up to 5 collaborators) also in their free plan. Not
>>>>> sure if this is of any use for GenABEL.
>>>>>
>>>>>
>>>>> Once we reach agreement on 1 and 2 I volunteer to do the migration.
>>>>>
>>>>>
>>>>> Best,
>>>>>
>>>>> Lennart.
>>>>>
>>>>>
>>>>> On 02-05-14 10:27, Yurii Aulchenko wrote:
>>>>>> On Fri, May 2, 2014 at 12:25 AM, Diego Fabregat
>>>>>> <fabregat at aices.rwth-aachen.de
>>>>>> <mailto:fabregat at aices.rwth-aachen.de>>
>>>>>> wrote:
>>>>>>
>>>>>> I like the idea of moving to git. I have no experience with
>>>>>> github,
>>>>>> but I'm using git on an almost daily basis (we have our own git
>>>>>> server in our group for code and papers). I would have no
>>>>>> problem in
>>>>>> uploading OmicABEL to a git repo.
>>>>>>
>>>>>> Does dropping R-forge have a (bad) impact on the visibility of
>>>>>> the
>>>>>> project or on the user experience (e.g., installation of R
>>>>>> packages)?
>>>>>>
>>>>>>
>>>>>> In my opinion - not really (visibility: I do not think we get many
>>>>>> users
>>>>>> because they've found us at r-forge; also we can keep the account and
>>>>>> make links from there; as for installation, the argument partly holds
>>>>>> only for R-packages). What we need to think is of course how we
>>>>>> keep/move all parts such as a) code b) trackers c) project docs such
>>>>>> as
>>>>>> code guidelines
>>>>>>
>>>>>> To me it seems that the idea to migrate few packages first is the
>>>>>> most
>>>>>> reasonable; few are likely to stay at r-forge for long
>>>>>>
>>>>>> Yurii
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 04/28/2014 10:09 PM, L.C. Karssen wrote:
>>>>>>> Dear Maarten, dear all,
>>>>>>>
>>>>>>> Moving to github... Hmm... That is quite a decision, so I've
>>>>>>> renamed the
>>>>>>> subject to better reflect the discussion. I've also dropped the
>>>>>>> older
>>>>>>> e-mails from the bottom of the thread.
>>>>>>>
>>>>>>> First off, are there any people that have experience with git
>>>>>>> and/or
>>>>>>> github? I've got some git experience (still learning), but no
>>>>>>> real
>>>>>>> experience with github.
>>>>>>>
>>>>>>> I agree with Maarten that SVN is showing its age. As he
>>>>>>> indicates
>>>>>>> things
>>>>>>> like branching are much easier in git. Moreover, since I'm
>>>>>>> travelling
>>>>>>> regularly being able to work without internet connection is a
>>>>>>> pro.
>>>>>>>
>>>>>>> On the other hand, moving to git (whether github or elsewhere)
>>>>>>> means
>>>>>>> leaving R-forge, which is our well-known infrastructure.
>>>>>>> Furthermore,
>>>>>>> such a move operation will cost quite some time, I guess. Moving
>>>>>>> all
>>>>>>> bugs, features, etc... If we decide to move we should plan well
>>>>>>> and not
>>>>>>> rush. And then the current developers will need to learn git if
>>>>>>> they
>>>>>>> don't already know how to use it.
>>>>>>>
>>>>>>> One thing I think we should definitely do is migrate slowly,
>>>>>>> package by
>>>>>>> package. Given that Maarten is positive about such a move and
>>>>>>> that
>>>>>>> I am
>>>>>>> in a bit of limbo but not fully against, it seems logical that
>>>>>>> ProbABEL
>>>>>>> is the first package to try such a migration.
>>>>>>>
>>>>>>>
>>>>>>> Looking forward to your comments!
>>>>>>>
>>>>>>>
>>>>>>> Lennart.
>>>>>>>
>>>>>>>
>>>>>>> On 28-04-14 20:39, Maarten Kooyman wrote:
>>>>>>>> Dear all,
>>>>>>>>
>>>>>>>> I think it is easier to use for code review github:
>>>>>>>>
>>>>>>>> Please check to get a impression
>>>>>>>> :https://github.com/jquery/jquery/pull/1241/files
>>>>>>>>
>>>>>>>> I think we should reconsider an other the software version
>>>>>>>> system: the
>>>>>>>> current system is not up to date to current usability. Bug
>>>>>>>> tracking and
>>>>>>>> branching is quite hard in terms of usability. Please have a
>>>>>>>> look
>>>>>>>> at
>>>>>>>> github.com <http://github.com> to get a impression what is
>>>>>>>> possible.
>>>>>>>>
>>>>>>>> Kind regards,
>>>>>>>>
>>>>>>>> Maarten
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>>>>>> L.C. Karssen
>>>>>>> Utrecht
>>>>>>> The Netherlands
>>>>>>>
>>>>>>> lennart at karssen.org <mailto:lennart at karssen.org>
>>>>>>> http://blog.karssen.org
>>>>>>> GPG key ID: A88F554A
>>>>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> genabel-devel mailing list
>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>
>>>>>>>
>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-
>>>>>>> dev
>>>>>>> el
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>
>>>>>>
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-d
>>>>>> eve
>>>>>> l
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> -----------------------------------------------------
>>>>>> Yurii S. Aulchenko
>>>>>>
>>>>>> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
>>>>>> <http://twitter.com/YuriiAulchenko> ] [ Blog
>>>>>> <http://yurii-aulchenko.blogspot.nl/> ]
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> genabel-devel mailing list
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>>>>>>
>>>>>>
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-d
>>>>>> eve
>>>>>> l
>>>>>>
>>>>>
>>>>> --
>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>>>> L.C. Karssen
>>>>> Utrecht
>>>>> The Netherlands
>>>>>
>>>>> lennart at karssen.org
>>>>> http://blog.karssen.org
>>>>> GPG key ID: A88F554A
>>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>>>
>>>>
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>>>>
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-dev
>>>> el
>>>>
>>>
>>>
>>>
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>>> l
>>>
>>
>> --
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>>
>> lennart at karssen.org
>> http://blog.karssen.org
>> GPG key ID: A88F554A
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>
>
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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