[BioPython] Biopython package(s) for Fedora

[Alex Lancaster]

Hello Biopythonistas,

I have created preliminary RPM package of the latest release of
Biopython (1.43) for Fedora as part of the "Fedora Package Collection"
(formerly "Fedora Extras" since Fedora Core+Fedora Extras are
merging).  

(I am also packaging Bioperl, you can see my some of my progress
including links to the reviews here:

http://fedoraproject.org/wiki/AlexLancaster)

I am almost ready to submit my package for review, but several issues
have arisen during the packaging that I hope the biopython list can
help clarify before I do so:

1) Will Biopython work OK with Python 2.5?  I ask because the next
   release of Fedora (Fedora 7) will only ship with Python 2.5 and
   packages first need to build in the development branch (which will
   eventually become Fedora 7) first.

2) The "python setup.py install" step appears to install a lot of
   scripts with the "#!/usr/bin/env python" at the top into the main
   /usr/lib/python2.4/site-packages/Bio/ namespace, e.g.:

   /usr/lib/python2.4/site-packages/Bio/GFF/GenericTools.py

   should these scripts be installed somewhere more appropriate such
   as /usr/bin/GenericTools.py or do they also function as classes as
   well as executables in their own right?  

   The "rpmlint" tool which is part of the packaging scans a package
   built for Fedora and identifies certain aspects of the package as
   not following the package and/or file system hierarchy (FHS)
   guidelines and I attach the list at the end of the e-mail for the
   developers to identify and tell me if these files are OK where
   the setup.py currently puts them.

3) The setup.py install also installs some architecture-independent
   non-code data files (such as DTDs) which I would normally expect to
   live in /usr/share/python-biopython/DTDs (or somesuch) for example:

   /usr/lib/python2.4/site-packages/Bio/EUtils/DTDs/eSearch_020511.dtd

   Is this the normal location for these DTDs and does the rest of the
   bipython framework expect to find these files in this location?

4) If possible, Fedora packages should run all unit tests provided in
   the upstream package at package time, just before creating the RPM.
   I would like to do this for biopython as well, but there doesn't
   seem to be an easy way to disable the PyUnit GUI that pops up and
   run in batch-only non-GUI mode.  I looked at the code in
   Tests/run_tests.py and it does have a "--no-gui" option, but there
   does not appear to be any way to run this from the top-level
   setup.py file, e.g.:

   python setup.py test --no-gui

   doesn't work.

5) My initial package depends on the required software: python, mx,
   python-numeric, as well as the optional python-reportlab,
   MySQL-python and flex which are all also included in Fedora, but I
   won't have Wise2 available since it is not yet in Fedora, at least
   not until I (or somebody else) packages Wise2.

6) Is Biopython-corba still active, and if so, should it also be
   packaged?  Are there any interdependencies with the base biopython
   package?  (No promises, though!)

Thanks,
Alex
--
Alex Lancaster, Ph.D. | Ecology & Evolutionary Biology, University of Arizona

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