[Biopython-dev] Fwd: Compiling Biopython on 64 bit Windows, was: Volunteer buildslave machines?

[Manlio Calvi]

---------- Forwarded message ----------
From: Manlio Calvi <manlio.calvi at gmail.com>
Date: Thu, Apr 17, 2014 at 10:11 PM
Subject: Re: Compiling Biopython on 64 bit Windows, was: Volunteer
buildslave machines?
To: Tiago Antao <tra at popgen.net>
Cc: Peter Cock <p.j.a.cock at googlemail.com>


People, announcement! :) I'm successful! (well, mostly)
I compiled on Win7 x64 against both native Python 2.7.6 x64 and Python
3.4.0 x64

How I did:
1. Installed MS Visual Studio 2008 express
2. Installed Windows SDK for Windows Server 2008 and .NET Framework 3.5
because the x64 toolchains was placed there
3. Run windows update to fix and patch things in those packages
4. Installed both Python native binary for last 2.7 and 3.4 (I discovered
that is better put in this order)
5. Install from C.Gohlke all the x64 deps biopython could have + SciPy just
to be sure. A pair of caveat here, I tried to produce the same
configuration for both the python versions and in that site some optional
deps for 3.4 are missing. I did an exception later for networkX, I
downloaded from git and compiled (I'll tell you when in this process)

Now coming the tricky part:
6. I found the only way to make the compilation start is to call a shell
with this command  - *cmd /k ""C:\Program Files (x86)\Microsoft Visual
Studio 9.0\VC\bin\vcvars64.bat""*  - this set the enviroment variable for
that specific shell to the x64 toolchain, otherwise don't compile (I opened
two of those, one for major python version)
7. For this experiments I created two separate copies of biopython in two
different dir where I cloned the reps.
8. I set the python env variable, for the Python 2.7 dedicated shell - SET
PATH=C:\python27\;%PATH% -  and for Python 3.4 dedicated shell - SET
PATH=C:\python34\;%PATH; - of course. If you don't do that is possible you
compile against the wrong python version, and in my specific case it
compile (that strange but that's how happened to me)
9. Now I downloaded and installed networkx from git for test the
"assembly", it worked
10. Cloned, build  both the package "versions" flawlessy or so seems
11. Tested the two, a lot of skipping for missing soft dependencies. A Note
here, I see a lot packages skipped because missing optional packages (in
and out python) a lot MORE than the one listed on the biopython site.

The results of the test are:
Biopython x64 - Python 3.4 Ran 224 test and failed 3 on
SearchIO_blast_xml.py, on SubsMat and on TogoWS(more than one kind of error
generated here)
Biopython x64 - Python 2.7.6  Ran 225 test and failed 2  on TogoWS(The same
errors seems at first look) and a Docstring test on test_Tutorial.py


OK that's all folks for now.

What's next? :)
Manlio