Discussion:
[Biopython-dev] Fwd: [Numpy-discussion] Python extensions for Python 3.5 - useful info...
Peter Cock
2015-08-26 08:52:14 UTC
Permalink
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 <***@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-***@scipy.org>, SciPy
Developers List <scipy-***@scipy.net>, Core developer mailing list of
the Cython compiler <cython-***@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
Fields, Christopher J
2015-08-26 14:38:17 UTC
Permalink
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 <***@googlemail.com<mailto:***@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 <***@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-***@scipy.org>, SciPy
Developers List <scipy-***@scipy.net>, Core developer mailing list of
the Cython compiler <cython-***@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-***@scipy.org
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
Biopython-***@mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
Peter Cock
2015-08-26 14:57:03 UTC
Permalink
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
Post by Fields, Christopher J
Peter, Just a note on Windows XP and Python 3.5 support (under 'Unsupported
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
Hello all,
Python 3.5.0 rc 2 is out now, so we ought to be testing
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 ----------
Date: Wed, Aug 26, 2015 at 6:24 AM
Subject: [Numpy-discussion] Python extensions for Python 3.5 - useful info...
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
http://stevedower.id.au/blog/building-for-python-3-5/
Cheers,
f
--
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
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
Fields, Christopher J
2015-08-26 17:54:58 UTC
Permalink
Yep, we had the same problem on the bioperl end (lack of Windows devs). Most we had would get frustrated over time, switch to something else that is easier to get work done :)

chris
Post by Peter Cock
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
Post by Fields, Christopher J
Peter, Just a note on Windows XP and Python 3.5 support (under 'Unsupported
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
Hello all,
Python 3.5.0 rc 2 is out now, so we ought to be testing
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 ----------
Date: Wed, Aug 26, 2015 at 6:24 AM
Subject: [Numpy-discussion] Python extensions for Python 3.5 - useful info...
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
http://stevedower.id.au/blog/building-for-python-3-5/
Cheers,
f
--
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
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
Tiago Rodrigues Antao
2015-08-26 19:02:10 UTC
Permalink
Here is a radical proposal:

How many people are using Biopython on Windows? Should we continuing
supporting Windows?

In any case it would be good to have a gauge of operating system
usage...

Tiago
Peter Cock
2015-08-27 07:28:47 UTC
Permalink
Hi Tiago,

I would be very reluctant to drop support of Windows.

I suspect we have quite a few people using in on Windows
(I can think of a couple of students and postdocs here),
who just run the Windows installers and never have to fight
with the complier side of things.

A user survey could be useful - other things like
which version(s) of Python they primarily use (and
for Linux/Mac if they were installed by default or not).

Taking it in another direction, you could ask (check boxes?)
which of the top level modules people mainly use - might
be helpful for deprecation discussions.

Would anyone good with Google Forms like to draft
something?

Peter
Post by Tiago Rodrigues Antao
How many people are using Biopython on Windows? Should we continuing
supporting Windows?
In any case it would be good to have a gauge of operating system
usage...
Tiago
Ben Fulton
2015-08-28 12:43:02 UTC
Permalink
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?
Post by Peter Cock
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
Post by Fields, Christopher J
Peter, Just a note on Windows XP and Python 3.5 support (under
'Unsupported
Post by Fields, Christopher J
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
Hello all,
Python 3.5.0 rc 2 is out now, so we ought to be testing
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 ----------
Date: Wed, Aug 26, 2015 at 6:24 AM
Subject: [Numpy-discussion] Python extensions for Python 3.5 - useful info...
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
http://stevedower.id.au/blog/building-for-python-3-5/
Cheers,
f
--
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
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
Peter Cock
2015-08-28 13:05:33 UTC
Permalink
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
Post by Ben Fulton
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?
Post by Peter Cock
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
Post by Fields, Christopher J
Peter, Just a note on Windows XP and Python 3.5 support (under 'Unsupported
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
Hello all,
Python 3.5.0 rc 2 is out now, so we ought to be testing
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 ----------
Date: Wed, Aug 26, 2015 at 6:24 AM
Subject: [Numpy-discussion] Python extensions for Python 3.5 - useful info...
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
http://stevedower.id.au/blog/building-for-python-3-5/
Cheers,
f
--
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
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
Ben Fulton
2015-08-28 19:36:26 UTC
Permalink
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
Post by Peter Cock
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
Post by Ben Fulton
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?
Post by Peter Cock
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
Post by Fields, Christopher J
Peter, Just a note on Windows XP and Python 3.5 support (under 'Unsupported
https://docs.python.org/3.6/whatsnew/3.5.html
Not sure how this affects whether it actually would work on XP using
MS
Post by Ben Fulton
Post by Peter Cock
Post by Fields, Christopher J
Visual C++ 14.0 though; is it supported on that platform?
chris
Hello all,
Python 3.5.0 rc 2 is out now, so we ought to be testing
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 ----------
Date: Wed, Aug 26, 2015 at 6:24 AM
Subject: [Numpy-discussion] Python extensions for Python 3.5 - useful info...
SciPy
Post by Ben Fulton
Post by Peter Cock
Post by Fields, Christopher J
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
http://stevedower.id.au/blog/building-for-python-3-5/
Cheers,
f
--
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
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
Peter Cock
2015-08-30 12:37:58 UTC
Permalink
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
Post by Ben Fulton
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.
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
https://iu.box.com/biopython-win-python35-test
Post by Peter Cock
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
Post by Ben Fulton
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?
Post by Peter Cock
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
Post by Fields, Christopher J
Peter, Just a note on Windows XP and Python 3.5 support (under 'Unsupported
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
Hello all,
Python 3.5.0 rc 2 is out now, so we ought to be testing
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 ----------
Date: Wed, Aug 26, 2015 at 6:24 AM
Subject: [Numpy-discussion] Python extensions for Python 3.5 - useful info...
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
http://stevedower.id.au/blog/building-for-python-3-5/
Cheers,
f
--
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
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
João Rodrigues
2015-08-30 14:08:29 UTC
Permalink
Indeed, plenty of warnings.. I'll check here as well, there should be a ignore statement somewhere in the code.
Post by 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
Post by Ben Fulton
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.
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
https://iu.box.com/biopython-win-python35-test
Post by Peter Cock
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
Post by Ben Fulton
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?
Post by Peter Cock
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
Post by Fields, Christopher J
Peter, Just a note on Windows XP and Python 3.5 support (under 'Unsupported
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
Hello all,
Python 3.5.0 rc 2 is out now, so we ought to be testing
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 ----------
Date: Wed, Aug 26, 2015 at 6:24 AM
Subject: [Numpy-discussion] Python extensions for Python 3.5 - useful info...
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
http://stevedower.id.au/blog/building-for-python-3-5/
Cheers,
f
--
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
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
Ben Fulton
2015-08-31 13:49:14 UTC
Permalink
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?
Post by 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
Post by Ben Fulton
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.
Post by Ben Fulton
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
https://iu.box.com/biopython-win-python35-test
Post by Peter Cock
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
Post by Ben Fulton
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 <
Post by Peter Cock
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
Post by Fields, Christopher J
Peter, Just a note on Windows XP and Python 3.5 support (under 'Unsupported
https://docs.python.org/3.6/whatsnew/3.5.html
Not sure how this affects whether it actually would work on XP
using
Post by Ben Fulton
Post by Peter Cock
Post by Ben Fulton
Post by Peter Cock
Post by Fields, Christopher J
MS
Visual C++ 14.0 though; is it supported on that platform?
chris
Hello all,
Python 3.5.0 rc 2 is out now, so we ought to be testing
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 ----------
Date: Wed, Aug 26, 2015 at 6:24 AM
Subject: [Numpy-discussion] Python extensions for Python 3.5 -
useful
Post by Ben Fulton
Post by Peter Cock
Post by Ben Fulton
Post by Peter Cock
Post by Fields, Christopher J
info...
list of
Post by Ben Fulton
Post by Peter Cock
Post by Ben Fulton
Post by Peter Cock
Post by Fields, Christopher J
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
Post by Ben Fulton
Post by Peter Cock
Post by Ben Fulton
Post by Peter Cock
Post by Fields, Christopher J
http://stevedower.id.au/blog/building-for-python-3-5/
Cheers,
f
--
fperez.net-at-gmail: mailing lists only (I ignore this when
swamped!)
Post by Ben Fulton
Post by Peter Cock
Post by Ben Fulton
Post by Peter Cock
Post by Fields, Christopher J
fernando.perez-at-berkeley: contact me here for any direct mail
_______________________________________________
NumPy-Discussion mailing list
http://mail.scipy.org/mailman/listinfo/numpy-discussion
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
_______________________________________________
Biopython-dev mailing list
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
Peter Cock
2015-08-31 13:56:03 UTC
Permalink
Post by Ben Fulton
This is 32-bit Python running on Windows 8.1. Were you interested in the
64-bit version?
We are interested in 64-bit Windows, but there are additional complications
with the compiler chain (thus the unofficial NumPy etc binaries Christoph
Gohlke releases).

Let's focus on 32-bit Python under Windows for now.
Post by Ben Fulton
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.
Or just in Bio/Application/__init__.py perhaps?

Can you try applying this small change?

--- a/Bio/Application/__init__.py
+++ b/Bio/Application/__init__.py
@@ -486,7 +486,7 @@ class AbstractCommandline(object):
use_shell = True
else:
win_ver = platform.win32_ver()[0]
- if win_ver in ["7", "8"]:
+ if win_ver in ["7", "8", "post2012Server"]:
use_shell = True
else:
use_shell = False


We need to find a volunteer with Windows 10 as well...
Post by Ben Fulton
Are people available to look at the skipping errors?
I've not had a chance to try Python 3.5rc2 myself yet.

Peter
Ben Fulton
2015-08-31 14:27:16 UTC
Permalink
All tests in test_Application.py pass with this change. But I would hope it
won't be necessary with the final version of Python 3.5.
Post by Peter Cock
Post by Ben Fulton
This is 32-bit Python running on Windows 8.1. Were you interested in the
64-bit version?
We are interested in 64-bit Windows, but there are additional complications
with the compiler chain (thus the unofficial NumPy etc binaries Christoph
Gohlke releases).
Let's focus on 32-bit Python under Windows for now.
Post by Ben Fulton
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
Post by Ben Fulton
itself.
Or just in Bio/Application/__init__.py perhaps?
Can you try applying this small change?
--- a/Bio/Application/__init__.py
+++ b/Bio/Application/__init__.py
use_shell = True
win_ver = platform.win32_ver()[0]
use_shell = True
use_shell = False
We need to find a volunteer with Windows 10 as well...
Post by Ben Fulton
Are people available to look at the skipping errors?
I've not had a chance to try Python 3.5rc2 myself yet.
Peter
Peter Cock
2015-08-31 14:45:16 UTC
Permalink
Post by Ben Fulton
Post by Peter Cock
Post by Ben Fulton
This is 32-bit Python running on Windows 8.1. Were you interested in the
64-bit version?
Let's focus on 32-bit Python under Windows for now.
...
All tests in test_Application.py pass with this change. But I would
hope it won't be necessary with the final version of Python 3.5.
Thanks Ben,

See also https://bugs.python.org/issue23417 although I am not
clear from the referenced https://bugs.python.org/issue19143
what exactly we should be expecting after that fix.

For now I've added "post2012Server" but this is likely to need
further revision once tested under a Windows 10 machine:

https://github.com/biopython/biopython/commit/780c2459cd1e76cb0a1a030de8b4cdec6dcef7b4

Peter

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