[Biopython-dev] [SPAM] Re: [Numpy-discussion] Python extensions for Python 3.5 - useful info...

Mon Aug 31 13:49:14 UTC 2015

This is 32-bit Python running on Windows 8.1. Were you interested in the
64-bit version?

The issue is not that "echo" is missing, but that platform.win32_ver()[0]
rather than "7" or "8" returns "post2012Server", which in turn causes the
Popen call to run with shell=false. I think this indicates a bug in Python
itself.

Are people available to look at the skipping errors?

On Sun, Aug 30, 2015 at 8:37 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Thanks Ben,
>
> I'm not 100% clear if your machine is running Python in 32 or 64 bit
> mode. How did you install Python 3.5.0rc2 itself?
>
> At first glance there are main two issues here,
>
> First the "echo" command does not seem to be available on your Windows
> machine causing test_Application.py to fail. This is odd, but perhaps
> depends on the version of Windows? What version of Windows is this?
>
> Second some of the missing dependencies are not being skipped, but
> treated as errors. e.g. Missing reportlab in test_KGML_graphics.py
> raises MissingExternalDependencyError (it could use the more precise
> subclass MissingPythonDependencyError), and missing MySQLdb in
> test_DocSQL.py correctly raises MissingPythonDependencyError - but
> this is not being detected in run_tests.py - we need to try the Python
> 3.5.0rc2 on another OS to investigate this.
>
> There are also a lot more warnings in the output from the PDB code
> that I would expect...
>
> Peter
>
> On Fri, Aug 28, 2015 at 8:36 PM, Ben Fulton <ben at benfulton.net> wrote:
> > It turned out to be not very difficult. I installed Visual Studio, Numpy
> > from Christoph Gohlke's wheel, and downloaded BioPython-1.65 and ran
> setup.
> > I ran the offline tests, which told me:
> >
> > Python version: 3.5.0rc2 (v3.5.0rc2:cc15d736d860, Aug 25 2015, 04:45:41)
> > [MSC v.1900 32 bit (Intel)]
> > Operating system: nt win32
> >
> > The most recent Windows XP - Python 3.3 build report  had 240 tests, all
> > passing; I had 237 tests with seven failures. I'll look further into the
> > differences. The test report is available here:
> >
> > https://iu.box.com/biopython-win-python35-test
> >
> >
> >
> >
> > On Fri, Aug 28, 2015 at 9:05 AM, Peter Cock <p.j.a.cock at googlemail.com>
> > wrote:
> >>
> >> Thanks Ben, any help here would be great:
> >> https://github.com/biopython/biopython/issues/601
> >>
> >> If you can make notes on this, that would be wonderful.
> >>
> >> In the medium term, ideally we'd get another volunteer
> >> Windows machine setup as a buildslave.
> >> http://testing.open-bio.org/biopython/tgrid
> >> http://biopython.org/wiki/Continuous_integration
> >>
> >> Also note this may have implications for 32 vs 64 bit
> >> Windows builds, where AFAIK NumPy don't yet have
> >> an official binary release (we would likely follow their
> >> lead for 64bit builds).
> >>
> >> http://biopython.org/wiki/64-bit_Windows_Biopython
> >>
> >> Peter
> >>
> >> On Fri, Aug 28, 2015 at 1:43 PM, Ben Fulton <ben at benfulton.net> wrote:
> >> > I can have a go at getting this running on my Windows 8 machine. Not
> >> > sure
> >> > how much work it will be. Is there an issue open for it or anything?
> >> >
> >> > On Wed, Aug 26, 2015 at 10:57 AM, Peter Cock <
> p.j.a.cock at googlemail.com>
> >> > wrote:
> >> >>
> >> >> Hi Chris,
> >> >>
> >> >> I'd like to retire this WinXP box, but not until I have another
> >> >> Windows development machine setup (perhaps a VM).
> >> >> For now it is handy for building our Biopython installers
> >> >> for 32-bit windows, and as a buildbot slave, but its days
> >> >> are numbered.
> >> >>
> >> >> I've not looked into how to install MSCV 14.0 but it would
> >> >> not surprise me that it isn't available on Windows XP.
> >> >>
> >> >> Biopython would benefit from one or more developers
> >> >> working primarily on Windows (which is what I did when
> >> >> I first started).
> >> >>
> >> >> Peter
> >> >>
> >> >> On Wed, Aug 26, 2015 at 3:38 PM, Fields, Christopher J
> >> >> <cjfields at illinois.edu> wrote:
> >> >> > Peter, Just a note on Windows XP and Python 3.5 support (under
> >> >> > 'Unsupported
> >> >> > Operating Systems’):
> >> >> >
> >> >> > https://docs.python.org/3.6/whatsnew/3.5.html
> >> >> >
> >> >> > Not sure how this affects whether it actually would work on XP
> using
> >> >> > MS
> >> >> > Visual C++ 14.0 though; is it supported on that platform?
> >> >> >
> >> >> > chris
> >> >> >
> >> >> > On Aug 26, 2015, at 3:52 AM, Peter Cock <p.j.a.cock at googlemail.com
> >
> >> >> > wrote:
> >> >> >
> >> >> > Hello all,
> >> >> >
> >> >> > Python 3.5.0 rc 2 is out now, so we ought to be testing
> >> >> > Biopython with it:
> >> >> >
> >> >> > https://www.python.org/downloads/release/python-350rc2/
> >> >> >
> >> >> > However, this has deeper implications for compiling on
> >> >> > Windows - in addition to the email forwarded below, I
> >> >> > also saw this via Guido van Rossum's Twitter,
> >> >> >
> >> >> > https://twitter.com/gvanrossum/status/636279572938428416
> >> >> > http://stevedower.id.au/blog/building-for-python-3-5/
> >> >> >
> >> >> > The key point is for Python 3.5 on Windows builds now use
> >> >> > Microsoft Visual C++ 14.0, and extension modules should
> >> >> > use the same.
> >> >> >
> >> >> > He notes that for the short term, there are likely to be
> >> >> > compatibility problems with mingw32 which we have also
> >> >> > used previously.
> >> >> >
> >> >> > Unless someone else volunteers, at some point I will have
> >> >> > to try installing MSVC 14.0 on my old Windows XP machine
> >> >> > which has been used for all our recent Biopython Windows
> >> >> > installers.
> >> >> >
> >> >> > Regards,
> >> >> >
> >> >> > Peter
> >> >> >
> >> >> > ---------- Forwarded message ----------
> >> >> > From: Fernando Perez <fperez.net at gmail.com>
> >> >> > Date: Wed, Aug 26, 2015 at 6:24 AM
> >> >> > Subject: [Numpy-discussion] Python extensions for Python 3.5 -
> useful
> >> >> > info...
> >> >> > To: Discussion of Numerical Python <numpy-discussion at scipy.org>,
> >> >> > SciPy
> >> >> > Developers List <scipy-dev at scipy.net>, Core developer mailing
> list of
> >> >> > the Cython compiler <cython-devel at python.org>
> >> >> >
> >> >> >
> >> >> > Just an FYI for the upcoming Python release, a very detailed post
> >> >> > from
> >> >> > Steve Dower, the Microsoft developer who is now in charge of the
> >> >> > Windows releases for Python, on how the build process will change
> in
> >> >> > 3.5 regarding extensions:
> >> >> >
> >> >> > http://stevedower.id.au/blog/building-for-python-3-5/
> >> >> >
> >> >> > Cheers,
> >> >> >
> >> >> > f
> >> >> > --
> >> >> > Fernando Perez (@fperez_org; http://fperez.org)
> >> >> > fperez.net-at-gmail: mailing lists only (I ignore this when
> swamped!)
> >> >> > fernando.perez-at-berkeley: contact me here for any direct mail
> >> >> >
> >> >> > _______________________________________________
> >> >> > NumPy-Discussion mailing list
> >> >> > NumPy-Discussion at scipy.org
> >> >> > http://mail.scipy.org/mailman/listinfo/numpy-discussion
> >> >> > _______________________________________________
> >> >> > Biopython-dev mailing list
> >> >> > Biopython-dev at mailman.open-bio.org
> >> >> > http://mailman.open-bio.org/mailman/listinfo/biopython-dev
> >> >> >
> >> >> >
> >> >>
> >> >> _______________________________________________
> >> >> Biopython-dev mailing list
> >> >> Biopython-dev at mailman.open-bio.org
> >> >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
> >> >
> >> >
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython-dev/attachments/20150831/c60e8486/attachment.html>