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Nicolas Chauvat | 2 Apr 2007 17:58
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[BioPython] [ANN] EuroPython 2007: Call for Proposals

Book Monday 9th July to Wednesday 11th July 2007 in your calendar!
EuroPython 2007, the European Python and Zope Conference, will be held in
Vilnius, Lithuania.  Last year's conference was a great success, featuring
a variety of tracks, amazing lightning talks and inspiring keynotes.  With
your participation, we want to make EuroPython 2007, the sixth EuroPython,
even more successful than the previous five.

Talks, Papers and Themes
------------------------

This year we have decided to borrow a few good ideas from PyCon, one of
which is to move away from the 'track' structure.  Instead, speakers are
invited to submit presentations about anything they have done that they
think would be of interest to the Python community.  We will then arrange
them into related groups and schedule them in the space available.  In the
past, EuroPython participants have found the following themes to be of
interest:

 * Science
 * Python Language and Libraries
 * Web Related Technologies
 * Education
 * Games
 * Agile Methodologies and Testing
 * Social Skills

In addition to talks, we will also accept full paper submissions about any
of the above themes.  The Call for Refereed Papers will be posted shortly.

The deadline for talk proposals is Friday 18th May at midnight (24:00
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Alex Lancaster | 8 Apr 2007 11:27
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[BioPython] Biopython package for Fedora

(Apologies if you receive multiple copies, this is a repost, my
original bounced)

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
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Sebastian Bassi | 8 Apr 2007 21:12
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Re: [BioPython] Biopython package for Fedora

On 4/8/07, Alex Lancaster <alexl <at> users.sourceforge.net> wrote:
> 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.

This is the only question I am able to answer. Yes, it does work with
Python 2.5.
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Chris Lasher | 8 Apr 2007 22:14
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Re: [BioPython] Biopython package for Fedora

On 4/8/07, Alex Lancaster <alexl <at> users.sourceforge.net> wrote:
> 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 line
#!/usr/bin/env python

retrieves the appropriate Python installation as specified by the
user's defined environment. This is preferable to hard-coding
#!/usr/bin/python, which will always use the Python installation
pointed to by /usr/bin/python. For most users, this doesn't matter,
but if the user desires to use a local or custom installation of
Python, they must change all these scripts by hand to point to their
preferred Python install.

Say my distribution's Python is version 2.3 but I have installed a
local copy of version 2.5 which is symlinked at /usr/local/bin/python.
I can set /usr/local/bin/python ahead in my path and the scripts with
"#!/usr/bin/env python" will then execute with my preferred version
(2.5) of Python rather than the system version (2.3), but the scripts
with "#!/usr/bin/python" will execute with the system version (2.3)
rather than my prefered version (2.5). Web search for more details.
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Alex Lancaster | 9 Apr 2007 00:28
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Re: [BioPython] Biopython package for Fedora

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

CL> On 4/8/07, Alex Lancaster <alexl <at> users.sourceforge.net> wrote:
>> 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?

CL> The line #!/usr/bin/env python

CL> retrieves the appropriate Python installation as specified by the
CL> user's defined environment. 

[...]

I'm aware of the function of the "/usr/bin/env python"
vs. "/usr/bin/python", that isn't the problem.  My question was about
the *location* of the script files when installed in
/usr/lib/python2.4/site-packages/Bio/* vs. being installed as
executables in /usr/bin/.

It seems that there are a number of files which contain both classes
and scripts and rpmlint identifies all files containing scripts which
aren't installed in a location like /usr/bin/ to make sure that
scripts aren't unintentionally installed in a non-executable location.
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Alex Lancaster | 8 Apr 2007 06:51
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[BioPython] Biopython package(s) for Fedora

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?
(Continue reading)

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Chris Lasher | 11 Apr 2007 06:43
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Re: [BioPython] Biopython package for Fedora

On 4/8/07, Alex Lancaster <alexl <at> users.sourceforge.net> wrote:
> 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.

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

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

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

patch -p0 < setup_test.patch

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

Thanks again for pointing this out.

Chris
(Continue reading)

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tim | 11 Apr 2007 16:15
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[BioPython] installing on Mandriva Linux

Hi,
I am getting lots of errors during python setup using biopython setup.py
install. I am running python  2.4.3. on Linux and have mxtextools,
numeric and headers etc. installed. The installation is definately  not
working as i get errors when i type some of the test code such as:
from Bio.Seq import Seq 
I get a traceback error.

Can anyone help. I'm new to biopython and Linux. I have everything
working fine under Windows.

I get problems from this point onwards in the install, with lots of
Bio/Cluster/clustermodule errors:

Do you want to continue this installation? (Y/n)  Y

*** Bio.KDTree *** NOT built by default

The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
which in turn, depends on C++ code that does not compile cleanly on
all platforms. Hence, Bio.KDTree is not built by default.

Would you like to build Bio.KDTree ? (y/N)  y

creating build/temp.linux-i686-2.4/Bio/Cluster
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fomit-frame-pointer -march=i586
-mtune=pentiumpro -fasynchronous-unwind-tables -g -fPIC -IBio/Cluster
-I/usr/include/python2.4 -c Bio/Cluster/clustermodule.c -o
build/temp.linux-i686-2.4/Bio/Cluster/clustermodule.o
(Continue reading)

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Alex Lancaster | 11 Apr 2007 16:44
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Re: [BioPython] Biopython package for Fedora

>>>>> "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,
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Michiel de Hoon | 11 Apr 2007 17:44
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Re: [BioPython] installing on Mandriva Linux

tim wrote:

>I get problems from this point onwards in the install, with lots of
>Bio/Cluster/clustermodule errors:
>...
>creating build/temp.linux-i686-2.4/Bio/Cluster
>gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe
>-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fomit-frame-pointer -march=i586
>-mtune=pentiumpro -fasynchronous-unwind-tables -g -fPIC -IBio/Cluster
>-I/usr/include/python2.4 -c Bio/Cluster/clustermodule.c -o
>build/temp.linux-i686-2.4/Bio/Cluster/clustermodule.o
>Bio/Cluster/clustermodule.c:2:33: error: Numeric/arrayobject.h: No such
>file or directory
>  
>
This is the first error message that you get. Did you check that you 
have the header file arrayobject.h? And is it in the correct location?

--Michiel

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