[BioPython] bio.pdb.mmcif does not exist
Michiel de Hoon
mdehoon at c2b2.columbia.edu
Wed May 9 14:07:20 UTC 2007
Alex Lancaster wrote:
> P> The way the setup.py script prompts the user about building
> P> Bio.KDTree with a simple yes/no prompt is a simple short term
> P> solution. I could certainly manage to make that change.
>
> I would prefer to that it also be a command-line options so that a
> biopython build can be automated by a build system, when making RPM
> packages. (Currently the Fedora package has to simulate the user
> typing "yes" to the Bio.KDTree question which is fragile).
I'm not too happy about adding a command-line option, so let me propose
another solution.
A little-known secret in Python is that you can do autoconf-like
configuration from a setup.py script. All the machinery is already there
in Python, but unfortunately it's not well documented. However, it's
fairly simple to use in practice -- way easier than autoconf.
What this amounts to is that before "python setup.py build", a user will
also have to run "python setup.py config" to check if the flex library
is present. If so, we can compile MMCIFlex during the build. If not, or
if a user doesn't do the config step, assume that flex is not present
and don't compile MMCIFlex.
As far as I can see, this solves the problem for the Fedora packaging.
Furthermore, the config lets us catch potential problems with flex
before we start compiling stuff.
A simple example of a configuration using setup.py can be found in a
tiny statistics module I wrote a while ago. See:
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/Statistics/
in case you want to try this approach.
--Michiel.
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