[BioPython] 1.21 installation difficulty

[Brad Chapman]

Hi Michiel, Jan, Leighton;

> I made a Biopython installer for python 2.2 on windows; it is available at
> http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/biopython-1.21.win32-py2.2.exe.

Sweet. Thanks. It's on the website now. You rule.

> I ran into some difficulties building this installer. During the
> bdist_wininst command, it cannot find the file
> build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs. This is probably a
> problem with Python's distutils for Windows; I don't run into this
> problem when compiling on Unix. So on Windows, I created that directory
> by hand and copied the files from Bio\EUtils\DTDs into it. That seems
> like the right thing to do, but I am not sure; does anybody know?

Yeah, this is partially Andrew's fault and partly my fault. It's
Andrew's fault because EUtils requires DTDs to be installed in the
EUtils python directory, so you have non-python files in the python
directories. It's my fault because I wrote the hack in setup.py to
install these DTDs (see install_eutils_dtds in the setup.py file)
and didn't think about building the windows installers. I'm not sure
what exactly to do about this, but what you did is the right "hack"
way to fix it. We can figure something better later 'cause if this
works -- well, that is good.

> On Unix, I get the following warning:
> 
> *** Martel *** is either not installed or out of date.
> 
> This package is required for many Biopython features.  Please install
> it before you install Biopython.
> You can find Martel at http://www.biopython.org/~dalke/Martel/.

Yeah, I think you get this if you are installing a fresh Biopython.
It seems like a bad thing, but this is Jeff's invention so he
probably knows better than I how to fix it.

> One more issue: with Python 2.3, mxTextTools (and therefore Biopython)
> cannot be compiled. The gcc compiler on Cygwin gets farther than
> Microsoft's cl.exe. With cl.exe, it fails at

I wouldn't sweat this. mxTextTools is very well maintained and I'm
pretty positive that a compilable version along with Windows
installers will come along fairly quickly. Since 2.3 was just
released yesterday I'll bet if we just sit for a bit the TextTools
problem will take care of itself.

So I think this hits on the major problems you all talked about:

=> Installer -- on the web pages. Sweet.
=> EUtils DTDs -- bad hack in the setup.py file. We need to make it
Windows compliant. I'm open to suggestions on how to do this.
=> bad Martel messages -- deferring to Jeff. He's the man.
=> mxTextTools -- I think we should just wait a bit and save
ourselves work. 

I'm really happy you all are looking at this on Windows. It's a huge
help as I never use it myself and so know next to nothing about it.
Thanks!

But-I-wanna-use-Python-2.3-today-ly yr's,
Brad