[Bioc-devel] svn repository for data experiment packages now having branches too

Tue Apr 1 07:23:01 CEST 2014

Hi Andrzej,

On 03/31/2014 02:49 AM, Andrzej Oleś wrote:
> Dear Hervé,
>
> just to make sure: is the the same x.y.z versioning scheme as for
> software packages already implemented for experiment data packages,
> i.e. will there be an automatic version bump for experiment packages
> with the upcoming BioC release?

Nobody has objected so far so yes, that's what we're going to do.

Cheers,
H.

>
> Cheers,
> Andrzej
>
> On Tue, Feb 11, 2014 at 7:18 AM, Hervé Pagès <hpages at fhcrc.org> wrote:
>> Hi Bernd and other developers,
>>
>>
>> On 02/07/2014 04:57 AM, Bernd Fischer wrote:
>>>
>>> Dear Herve!
>>>
>>> Please start using the same x.y.z versioning scheme as for software
>>> packages with the new release
>>> for data experiment packages, with even y for release and odd y for devel.
>>
>>
>> Thanks for your feedback! Can anyone think of a reason why we should not
>> do that? If nobody objects then we'll start using the same x.y.z
>> versioning scheme as for software for the next BioC release (in April).
>>
>> Thanks,
>> H.
>>
>>
>>>
>>> I just copied code from devel to the release version of my package and
>>> asked myself which version
>>> number to use. Automatic version bumping
>>>
>>>
>>>
>>> --
>>> Bernd Fischer
>>> EMBL Heidelberg
>>> Meyerhofstraße 1
>>> 69117 Heidelberg
>>> Tel: +49 [0] 6221 387-8131
>>> E-Mail: bernd.fischer at embl.de <mailto:bernd.fischer at embl.de>
>>>
>>> Homepage: http://www-huber.embl.de/users/befische/
>>>
>>>
>>>
>>>
>>> On 22.01.2014, at 23:30, Hervé Pagès <hpages at fhcrc.org
>>> <mailto:hpages at fhcrc.org>> wrote:
>>>
>>>> Hi developers,
>>>>
>>>> Taking advantage of this particularly calm week on Bioc-devel,
>>>> I'd like to formally announce that we're now using branches
>>>> in the svn repo for data experiment packages.
>>>>
>>>> The trunk/branches layout is similar to what we already do in
>>>> the software repo. That is:
>>>>
>>>> - URL for packages in trunk:
>>>>
>>>> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>>>>
>>>> - URLs for packages in the branches:
>>>>
>>>>
>>>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs
>>>>
>>>>
>>>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs
>>>>
>>>>
>>>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_15/experiment/pkgs
>>>>
>>>> Only the RELEASE_2_13 branch exists right now. This is where the
>>>> packages that are in the current release version of BioC (2.13)
>>>> are living. Like for software packages, a new branch will be created
>>>> for each new BioC release. For example the RELEASE_2_14 branch will
>>>> be created in April one day or so before the BioC 2.14 release,
>>>> the RELEASE_2_15 branch in October, etc...
>>>>
>>>> More precisely, at any given time, you only have access to 2
>>>> versions of your data experiment package: the "release" and
>>>> "devel" versions.
>>>>
>>>> The "release" version of your package is always in the latest
>>>> branch (RELEASE_2_13 at the moment) and accessible at:
>>>>
>>>>
>>>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/<PKGNAME>
>>>>
>>>> Only bug fixes and documentation improvements should go here.
>>>>
>>>> The "devel" version of your package is always available at:
>>>>
>>>>   https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/<PKGNAME>
>>>>
>>>> One important difference with the svn software repository still
>>>> remains though. For data experiment, the recommended way to checkout
>>>> a package is:
>>>>
>>>>   1. Checkout a "shallow" working copy of the pkgs/ folder:
>>>>
>>>>        svn co
>>>> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs --depth=files
>>>>
>>>>      Use the URL to the current branch if you need to checkout a
>>>>      "release" package.
>>>>
>>>>   2. cd to the pkg/ folder
>>>>
>>>>   3. Fetch the working copy of a particular package:
>>>>
>>>>        svn up <PKGNAME>
>>>>
>>>>      (You can list all the folders in pkgs/ with 'svn ls')
>>>>
>>>>      IMPORTANT: This doesn't fetch the data. But most of the
>>>>      time you don't need them e.g. if you only need to make a
>>>>      change to a man page, the vignette, the DESCRIPTION file,
>>>>      the NAMESPACE etc... you can do so and commit.
>>>>      But of course, if you didn't fetch the data, it's very
>>>>      likely that you won't be able to test your changes with
>>>>      'R CMD check'.
>>>>
>>>>   4. If you need to fetch the data:
>>>>
>>>>        (from the pkgs/ folder)
>>>>
>>>>        ./add_data.py <PKGNAME>
>>>>
>>>>      This will populate the <PKGNAME> folder with the data.
>>>>      Note that you need to be in a data folder in order to commit
>>>>      any change to the data. Any commit you do from the top level
>>>>      folder of the package won't include any change you could have
>>>>      made to the data.
>>>>
>>>> We're also wondering whether we should start to use the same x.y.z
>>>> versioning scheme as for software packages, that is, an even y in
>>>> release, an odd y in devel, with y bump (and z reset to 0) at each
>>>> new release. Feedback welcome.
>>>>
>>>> Please let me know if you have questions or concerns about this.
>>>>
>>>> Cheers,
>>>> H.
>>>>
>>>> --
>>>> Hervé Pagès
>>>>
>>>> Program in Computational Biology
>>>> Division of Public Health Sciences
>>>> Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N, M1-B514
>>>> P.O. Box 19024
>>>> Seattle, WA 98109-1024
>>>>
>>>> E-mail: hpages at fhcrc.org
>>>> Phone:  (206) 667-5791
>>>> Fax:    (206) 667-1319
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319