[Biopython-dev] Updating C extensions to Python 3

[Peter]

On Sat, Dec 25, 2010 at 11:34 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> Just three left now: Bio.cpairwise2, Bio.trie and
> Bio.Nexus.cnexus - it looks like we will shortly be a
> lot closer to doing a Biopython release on Python 3.
>

You have been busy, just one left now.

However, again we have a Python 2.4 and Python 2.5
compilation problem (under the Cygwin compiler but
not on Linux strangely):

http://events.open-bio.org:8010/builders/Windows%20XP%20-%20Python%202.5/builds/69/steps/compile/logs/stdio

C:\cygwin\usr\bin\gcc.exe -mno-cygwin -mdll -O -Wall -IBio
-Ic:\python25\include -Ic:\python25\PC -c Bio/cpairwise2module.c -o
build\temp.win32-2.5\Release\bio\cpairwise2module.o
cygwin warning:
  MS-DOS style path detected: c:/python25/include
  Preferred POSIX equivalent is: /cygdrive/c/python25/include
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
Bio/cpairwise2module.c: In function `_create_bytes_object':
Bio/cpairwise2module.c:203: warning: implicit declaration of function
`PyBytes_Check'
Bio/cpairwise2module.c: At top level:
Bio/cpairwise2module.c:201: warning: '_create_bytes_object' defined but not used
writing build\temp.win32-2.5\Release\bio\cpairwise2.def
C:\cygwin\usr\bin\gcc.exe -mno-cygwin -shared -s
build\temp.win32-2.5\Release\bio\cpairwise2module.o
build\temp.win32-2.5\Release\bio\cpairwise2.def -Lc:\python25\libs
-Lc:\python25\PCBuild -lpython25 -lmsvcr71 -o
build\lib.win32-2.5\Bio\cpairwise2.pyd
cygwin warning:
  MS-DOS style path detected:
build\temp.win32-2.5\Release\bio\cpairwise2module.o
  Preferred POSIX equivalent is:
build/temp.win32-2.5/Release/bio/cpairwise2module.o
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
build\temp.win32-2.5\Release\bio\cpairwise2module.o:cpairwise2module.c:(.text+0x369):
undefined reference to `_PyBytes_Check'
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

(I should tweak the environment variables on that machine
to get rid of the MS-DOS style path warning which irks me)

This seems like the right fix and resolved the compile issue,
but again, could you check this please?:

https://github.com/biopython/biopython/commit/d3b22e4963a058323c08ed4a4873f97ca0d44d8b

Thanks!

Peter