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

Sun Aug 30 14:08:29 UTC 2015

Indeed, plenty of warnings.. I'll check here as well, there should be a ignore statement somewhere in the code.

On Sun, Aug 30, 2015 at 2:09 PM, 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
>>> >> >
>>> >> > _______________________________________________
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>>> >> >
>>> >> >
>>> >>
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>>> >
>>
>>
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