biopp packaging

The biopp repository was updated with the latest versions from git and uploaded to Debian GNU/Linux for inclusion. The 2.0.1 version of packaging farm includes a submission script implementing the biopp conventions.

non native packages

Each biopp package was transformed into a non-native package by doing the following:

  • debian/source/format was changed from 3.0 (native) to 3.0 (quilt)
  • the debian/changelog entry for the next release is appended the -1 debian version number

biopp source packages

Instead of relying on existing biopp source packages, a submission script was created for packaging-farm embedding the conventions used to create a source package from the git repositories. It automates the following:

cmake .
make dist
tar -zxvf *.tar.gz
dpkg-buildpackage -d -S -uc -us

and can be run for all known biopp packages with

packaging-farm --cd bpp update

Assuming the following Makefile exists in /var/cache/packaging-farm/build/bpp/Makefile and the version 2.0.1 of packaging-farm is installed.

CHILD_PACKAGES = libbpp-core libbpp-seq libbpp-phyl libbpp-popgen libbpp-qt libbpp-raa bppsuite bppphyview

        export PACKAGE= ; for i in ${CHILD_PACKAGES} ; do packaging-farm SOURCE=$$i submit ; done

LIBDIR ?= /usr/lib/packaging-farm
include ${LIBDIR}/Makefile

The generation of the repository aggregating all the packages is run with

packaging-farm bpp

The previous generation used the version 1.2.32 of packaging-farm and the biopp wiki was updated to reflect the new usage.

bppsuite svn / git

bppsuite is on a SVN respository. It is wrapped into a git repository so that the submission script only have to deal with one kind of revision control system.

local modifications

When facing a problem with a package, it may be inconvenient to wait for the biopp maintainer to modify the git and it is best to make a quick fix that will be thrown away a few hours later. In this case the RESET=false can be used to preserve any modification made in the local copy of the repository in /var/cache/packaging-farm/VCS.

packaging-farm SOURCE=libbpp-core RESET=false submit

The command above will re-create a source package including the local modifications. The default behaviour would be to trash all local modification to ensure that the package is made from the official repository.

packaging-farm release

While working with packaging-farm 2.0.0, a new bugs were detected and published in the 2.0.1 release.

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