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.fisc...@embl.de Homepage: http://www-huber.embl.de/users/befische/ On 22.01.2014, at 23:30, Hervé Pagès <hpa...@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: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]]
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