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. 

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@embl.de
Homepage: http://www-huber.embl.de/users/befische/




On 22.01.2014, at 23:30, Hervé Pagès <hpages@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@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 
> _______________________________________________
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