[Biopython-dev] Various fixes in CVS

[Andrew Dalke]

Jeff:
> This assumes that Martel is distributed with biopython.  Is that what we
> decided?  Also, should we check to make sure this won't overwrite a
> previous Martel installation?

I think it should be distributed with biopython.  I just wanted
to make it available outside of biopython.  For now I don't know
of anyone who will install Martel from a package other than biopython,
then later install biopython - so it wouldn't be too bad to always
install.  But I imagine Brad can easily write a test which only
adds a Martel installation if it isn't already present.

So... default installs Martel, with an option to not install it.
The option can be:
  - modify setup.py
  - command-line option
  - autorecognize Martel exists and complain if the version is too old

I have no preference.  The first is easist and least error prone, and
there isn't yet need for more, so it's hard to know what the exact
requirements are.

Brad:
> If you are keeping multiple different versions of Martel, then you
> can just go into the setup.py and switch off the flag to INSTALL_MARTEL. 

In other words, I agree with Brad.  Though it needs to be mentioned in
the installation instructions, for people like me who read instructions
:)

One thing to consider is how setup.py works with installers.  Johann
distributes these seperately with the FreeBSD ports.  I can't comment
any about his needs.  Want to pipe in, Johann?

					Andrew