[BioPython] Biopython package for Fedora

[Alex Lancaster]

>>>>> "CL" == Chris Lasher  writes:

[...]

CL> Alex, thanks for pointing this out. I sat down tonight and
CL> resolved this issue.

CL> <http://bugzilla.open-bio.org/show_bug.cgi?id=2266>

CL> The patch on there should be the fix needed. Save it as
CL> setup_test.patch (or whatever, but that's convenient), place it in
CL> the same directory as setup.py, and patch with the command

CL> patch -p0 < setup_test.patch

CL> Alternatively, I can send you the patched files (setup.py and
CL> Tests/run_tests.py).

CL> Thanks again for pointing this out.

Hi Chris,

Thanks, the patch works fine for me.  I've added the patch to the
package and I can now run the tests in command-line only mode fine.
By the way, I've filed my package review for Fedora:

https://bugzilla.redhat.com/235989 

if anybody wants to keep track of it's progress.  I am currently still
disabling the tests because they hang for some reason on test_Cluster,
I get:

$ python setup.py test --no-gui
running test
test_Ace ... ok
test_BioSQL ... Skipping test because of import error: Skipping BioSQL
tests -- enable tests in Tests/test_BioSQL.py
ok
test_CAPS ... ok
test_Cluster ... 

then the CPU spins indefinitely.

Also I need to make sure that all tests that require network access
are skipped cleanly because the package build environment for Fedora
requires that all packages build without network acess.

On another packaging note: I now remove all #!/usr/bin/ etc. from the
top of files found in the /usr/lib/python2.4/site-packages/Bio/* area
to keep rpmlint happy.  These can still be run using python directly
e.g.:

python /usr/lib/python2.4/site-packages/Bio/biblio.py

Note that there's a lot of inconsistency here: some are "/usr/bin/env
python", others are /usr/bin/python or even /usr/bin/python2.3, others
don't have a main program contained within, and so the #!/usr/bin line
should be removed completely.  Somebody should go through and
cleanup/rationalise the installation process: check that the files
installed when "python setup.py install" is run are appropriate .py
package files, e.g. the EUtils installs it's own "setup.py" file in a
subdirectory, which isn't very clean.

Alex