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

[Peter Cock]

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
>> >> >
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>> >> >
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