Dear Herv?, 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? Cheers, Andrzej
On Tue, Feb 11, 2014 at 7:18 AM, Herv? Pag?s <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 Meyerhofstra?e 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, Herv? Pag?s <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. -- Herv? Pag?s 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
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-- Herv? Pag?s 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
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