[Numpy-discussion] Numpy 1.5.1/1.6.1 doesn't build doc with sphinx 1.1.2

[Sandro Tosi]

Hello,
with the new sphinx, v1.1.2, numpy documentation of 1.5.1 or 1.6.1
doesn't build.

The full log of the debian package build is at:
http://people.debian.org/~jwilk/tmp/python-numpy_1.6.1-3_i386.build

attached is the file left in /tmp by sphinx for the error.

Could you please give it a look?

Cheers,
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My website: http://matrixhasu.altervista.org/
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# Sphinx version: 1.1.2
# Python version: 2.7.2+
# Docutils version: 0.8.1 release
# Jinja2 version: 2.6
Traceback (most recent call last):
  File /usr/lib/pymodules/python2.7/sphinx/cmdline.py, line 189, in main
app.build(force_all, filenames)
  File /usr/lib/pymodules/python2.7/sphinx/application.py, line 204, in build
self.builder.build_update()
  File /usr/lib/pymodules/python2.7/sphinx/builders/__init__.py, line 196, in 
build_update
'out of date' % len(to_build))
  File /usr/lib/pymodules/python2.7/sphinx/builders/__init__.py, line 216, in 
build
purple, length):
  File /usr/lib/pymodules/python2.7/sphinx/builders/__init__.py, line 120, in 
status_iterator
for item in iterable:
  File /usr/lib/pymodules/python2.7/sphinx/environment.py, line 613, in 
update_generator
self.read_doc(docname, app=app)
  File /usr/lib/pymodules/python2.7/sphinx/environment.py, line 761, in 
read_doc
pub.publish()
  File /usr/lib/pymodules/python2.7/docutils/core.py, line 211, in publish
self.settings)
  File /usr/lib/pymodules/python2.7/docutils/readers/__init__.py, line 69, in 
read
self.parse()
  File /usr/lib/pymodules/python2.7/docutils/readers/__init__.py, line 75, in 
parse
self.parser.parse(self.input, document)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/__init__.py, line 
157, in parse
self.statemachine.run(inputlines, document, inliner=self.inliner)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 170, 
in run
input_source=document['source'])
  File /usr/lib/pymodules/python2.7/docutils/statemachine.py, line 237, in run
context, state, transitions)
  File /usr/lib/pymodules/python2.7/docutils/statemachine.py, line 458, in 
check_line
return method(match, context, next_state)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 
2943, in text
self.section(title.lstrip(), source, style, lineno + 1, messages)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 329, 
in section
self.new_subsection(title, lineno, messages)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 398, 
in new_subsection
node=section_node, match_titles=1)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 284, 
in nested_parse
node=node, match_titles=match_titles)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 195, 
in run
results = StateMachineWS.run(self, input_lines, input_offset)
  File /usr/lib/pymodules/python2.7/docutils/statemachine.py, line 237, in run
context, state, transitions)
  File /usr/lib/pymodules/python2.7/docutils/statemachine.py, line 458, in 
check_line
return method(match, context, next_state)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 
2285, in explicit_markup
self.explicit_list(blank_finish)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 
2316, in explicit_list
match_titles=self.state_machine.match_titles)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 321, 
in nested_list_parse
node=node, match_titles=match_titles)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 195, 
in run
results = StateMachineWS.run(self, input_lines, input_offset)
  File /usr/lib/pymodules/python2.7/docutils/statemachine.py, line 237, in run
context, state, transitions)
  File /usr/lib/pymodules/python2.7/docutils/statemachine.py, line 458, in 
check_line
return method(match, context, next_state)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 
2589, in explicit_markup
nodelist, blank_finish = self.explicit_construct(match)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 
2295, in explicit_construct
return method(self, expmatch)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 
2036, in directive
directive_class, match, type_name, option_presets)
  File /usr/lib/pymodules/python2.7/docutils/parsers/rst/states.py, line 
2087, in run_directive
result = directive_instance.run()
  File /usr/lib/pymodules/python2.7/sphinx/domains/__init__.py, line 190, in 
run
return BaseDirective.run(self)
  File /usr/lib/pymodules/python2.7/sphinx/domains/std.py, line 318, in run
self.state.nested_parse(definition, definition.items[0][1], defnode)
IndexError: list index out of range
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Re: [Numpy-discussion] Numpy 1.5.1/1.6.1 doesn't build doc with sphinx 1.1.2

[Sandro Tosi]

On Wed, Feb 22, 2012 at 18:46, David Verelst david.vere...@gmail.com wrote:
 Note sure if this already has been discussed, but it seems that latest
 Sphinx, 1.2predev-20120222 directly from their Hg repository, does not
 have this problem any more. While 1.2 failed to build the documentation
 on my end, 1.2predev delivered a result.

I'm sorry I didn't follow this up: the fix is already in the numpy
repository, and i've applied in Debian with this patch (url to
upstream tracker in the file):
http://patch-tracker.debian.org/patch/series/view/python-numpy/1:1.6.1-5/20_sphinx_1.1.2.diff

Regards,
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[Numpy-discussion] Testsuite fails with Python 2.7.3rc1 and 3.2.3rc1 (Debian)

[Sandro Tosi]

Hello,
I've reported http://projects.scipy.org/numpy/ticket/2085 and Ralf
asked for bringing that up here: is anyone able to replicate the
problem described in that ticket?

The debian bug tracking the problem is:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=664672

Cheers,
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Re: [Numpy-discussion] Testsuite fails with Python 2.7.3rc1 and 3.2.3rc1 (Debian)

[Sandro Tosi]

On Sun, Apr 1, 2012 at 12:25, Ralf Gommers ralf.gomm...@googlemail.com wrote:
 OK, that makes sense. So there are six test runs; for normal and debug
 builds of 2.6.7, 2.7.3rc1 and 3.2.3rc2. Only the debug builds of the RCs
 have a problem, debug build of 2.6.7 is fine.

exactly.

 So I'd think that most likely there is a problem with how the debug versions
 of the RCs were built.

it sounds possible: is there a way to isolate the failing test, so
that I can provide a minimal test code for further investigation to
python maintainer?

Regards,
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Re: [Numpy-discussion] Testsuite fails with Python 2.7.3rc1 and 3.2.3rc1 (Debian)

[Sandro Tosi]

On Sun, Apr 8, 2012 at 02:41, Charles R Harris
charlesr.har...@gmail.com wrote:
 Possibly related to ticket #1578.

yes, that's exactly it:


$ python2.7-dbg -c import sys ; sys.path.insert(0,
'/home/morph/deb/build-area/python-numpy-1.6.1/debian/tmp/usr/lib/python$v/dist-packages/')
; import numpy; numpy.test(verbose=10)
Running unit tests for numpy
/usr/lib/pymodules/python2.7/nose/plugins/manager.py:405: UserWarning:
Module paste was already imported from None, but
/usr/lib/python2.7/dist-packages is being added to sys.path
  import pkg_resources
/usr/lib/pymodules/python2.7/nose/plugins/manager.py:405: UserWarning:
Module dap was already imported from None, but
/usr/lib/python2.7/dist-packages is being added to sys.path
  import pkg_resources
NumPy version 1.5.1
NumPy is installed in /usr/lib/pymodules/python2.7/numpy
Python version 2.7.3rc2 (default, Apr  5 2012, 13:54:40) [GCC 4.6.3]
nose version 1.0.0
nose.config: INFO: Excluding tests matching ['f2py_ext',
'f2py_f90_ext', 'gen_ext', 'pyrex_ext', 'swig_ext']
numpy.core.tests.test_arrayprint.TestArrayRepr.test_nan_inf ... ok
Ticket 844. ... ok
numpy.core.tests.test_blasdot.test_blasdot_used ... ok
test_from_object_array (numpy.core.tests.test_defchararray.TestBasic) ... ok
test_from_object_array_unicode
(numpy.core.tests.test_defchararray.TestBasic) ... ok
test_from_string (numpy.core.tests.test_defchararray.TestBasic) ... ok
test_from_string_array (numpy.core.tests.test_defchararray.TestBasic) ... ok
test_from_unicode (numpy.core.tests.test_defchararray.TestBasic) ...
Debug memory block at address p=0x2ec3cc0: API 'm'
8 bytes originally requested
The 7 pad bytes at p-7 are FORBIDDENBYTE, as expected.
The 8 pad bytes at tail=0x2ec3cc8 are FORBIDDENBYTE, as expected.
The block was made by call #7954800 to debug malloc/realloc.
Data at p: a3 03 00 00 00 00 00 00
Fatal Python error: bad ID: Allocated using API 'm', verified using API 'o'
Aborted


I've replied to the Trac issue attaching 2 gdb
output files for 2.7.3rc2 and 3.2.3rc2 in debug flavor. If you want me
to test anything, I'd be happy to.

Cheers,
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Re: [Numpy-discussion] A 1.6.2 release?

[Sandro Tosi]

 Also, I believe Debian will very soon freeze testing in order to
 prepare to release the next stable.

yes, the estimates are around June (nor clear if the beginning of the end).

Cheers,
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Re: [Numpy-discussion] 1.6.2 release - backports and MSVC testing help

[Sandro Tosi]

Hello,
with my Debian hat one I'd surely like to give it a go - do you have
any plan to release a tarball for a RC (given the implication of numpy
on the distro, I can't test anything else)? what do you expect to be
the release date for 1.6.2? I asked this to understand the impact, due
to the upcoming Debian freeze (June, still not clear if beginning or
end).

Cheers,
Sandri

On Mon, Apr 30, 2012 at 22:16, Ralf Gommers ralf.gomm...@googlemail.com wrote:
 Hi all,

 Charles has done a great job of backporting a lot of bug fixes to 1.6.2, see
 PRs 260, 261, 262 and 263. For those who are interested, please have a look
 at those PRs to see and comment on what's proposed to go into 1.6.2.

 I also have a request for help with testing: can someone who uses MSVC test
 (preferably with a 2.x and a 3.x version)? I have a branch with all four PRs
 merged at https://github.com/rgommers/numpy/tree/bports

 Thanks,
 Ralf


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Re: [Numpy-discussion] 1.6.2 release - backports and MSVC testing help

[Sandro Tosi]

On Tue, May 1, 2012 at 20:24, Ralf Gommers ralf.gomm...@googlemail.com wrote:


 On Tue, May 1, 2012 at 5:27 PM, Sandro Tosi matrixh...@gmail.com wrote:

 Hello,
 with my Debian hat one I'd surely like to give it a go - do you have
 any plan to release a tarball for a RC (given the implication of numpy
 on the distro, I can't test anything else)? what do you expect to be
 the release date for 1.6.2? I asked this to understand the impact, due
 to the upcoming Debian freeze (June, still not clear if beginning or
 end).


 We certainly have the Debian freeze date in the back of our heads. I'm

I can only say Thank you! :)

 aiming for an RC sometime this week and a release two weeks after that.

Awesome, I'll be waiting for the RC to prepare the upload, directly to
our main archive.

Cheers,
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Re: [Numpy-discussion] ANN: NumPy 1.6.2 release candidate 1

[Sandro Tosi]

On Sat, May 5, 2012 at 8:15 PM, Ralf Gommers
ralf.gomm...@googlemail.com wrote:
 I'm pleased to announce the availability of the first release candidate of
 NumPy 1.6.2.  This is a maintenance release. Due to the delay of the NumPy
 1.7.0, this release contains far more fixes than a regular NumPy bugfix
 release.  It also includes a number of documentation and build improvements.

Great!

 Sources and binary installers can be found at
 https://sourceforge.net/projects/numpy/files/NumPy/1.6.2rc1/

 Please test this release and report any issues on the numpy-discussion
 mailing list.

i've just tested the debian package and it builds fine! The tests
print some ResourceWarning with python3.2 but they all pass!

Cheers,
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Re: [Numpy-discussion] ANN: NumPy 1.6.2 release candidate 1

[Sandro Tosi]

On Sat, May 5, 2012 at 8:15 PM, Ralf Gommers
ralf.gomm...@googlemail.com wrote:
 Hi,

 I'm pleased to announce the availability of the first release candidate of
 NumPy 1.6.2.  This is a maintenance release. Due to the delay of the NumPy
 1.7.0, this release contains far more fixes than a regular NumPy bugfix
 release.  It also includes a number of documentation and build improvements.

 Sources and binary installers can be found at
 https://sourceforge.net/projects/numpy/files/NumPy/1.6.2rc1/

 Please test this release and report any issues on the numpy-discussion
 mailing list.

Mh, I can't exactly understand this:

$ diff -urNad numpy-1.6.1 numpy-1.6.2rc | diffstat | tail -1
 2718 files changed, 390859 deletions(-)

does it mean that the only thing the RC has done is to remove a lot of
stuff? that's weird because the build process went all just fine and
unit tests are passing ... /me confused?

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Me at Debian: http://wiki.debian.org/SandroTosi
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Re: [Numpy-discussion] ANN: NumPy 1.6.2 release candidate 1

[Sandro Tosi]

On Wed, May 9, 2012 at 6:49 PM, Charles R Harris
charlesr.har...@gmail.com wrote:


 On Wed, May 9, 2012 at 10:36 AM, Sandro Tosi matrixh...@gmail.com wrote:

 On Sat, May 5, 2012 at 8:15 PM, Ralf Gommers
 ralf.gomm...@googlemail.com wrote:
  Hi,
 
  I'm pleased to announce the availability of the first release candidate
  of
  NumPy 1.6.2.  This is a maintenance release. Due to the delay of the
  NumPy
  1.7.0, this release contains far more fixes than a regular NumPy bugfix
  release.  It also includes a number of documentation and build
  improvements.
 
  Sources and binary installers can be found at
  https://sourceforge.net/projects/numpy/files/NumPy/1.6.2rc1/
 
  Please test this release and report any issues on the numpy-discussion
  mailing list.

 Mh, I can't exactly understand this:

 $ diff -urNad numpy-1.6.1 numpy-1.6.2rc | diffstat | tail -1
  2718 files changed, 390859 deletions(-)

 does it mean that the only thing the RC has done is to remove a lot of
 stuff? that's weird because the build process went all just fine and
 unit tests are passing ... /me confused?


 No, only a few files were changed. Since there are about 1000 files in numpy
 I suspect you are also counting everything in the build and documentation
 build directories. If you built inplace, you are also going to pick up *.pyc
 files and such.

sorry i didn't say that: they are the tarballs just extracted. i'd
have to recheck again downloading from SF


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Re: [Numpy-discussion] ANN: NumPy 1.6.2 release candidate 1

[Sandro Tosi]

On Sat, May 5, 2012 at 8:15 PM, Ralf Gommers
ralf.gomm...@googlemail.com wrote:
 Please test this release and report any issues on the numpy-discussion
 mailing list.

I think it's probably nice not to ship pyc in the source tarball:

$ find numpy-1.6.2rc1/ -name *.pyc
numpy-1.6.2rc1/doc/sphinxext/docscrape.pyc
numpy-1.6.2rc1/doc/sphinxext/docscrape_sphinx.pyc
numpy-1.6.2rc1/doc/sphinxext/numpydoc.pyc
numpy-1.6.2rc1/doc/sphinxext/plot_directive.pyc

Cheers,
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Re: [Numpy-discussion] ANN: NumPy 1.6.2 release candidate 1

[Sandro Tosi]

Hello,

On Sat, May 5, 2012 at 8:15 PM, Ralf Gommers
ralf.gomm...@googlemail.com wrote:
 Hi,

 I'm pleased to announce the availability of the first release candidate of
 NumPy 1.6.2.  This is a maintenance release. Due to the delay of the NumPy
 1.7.0, this release contains far more fixes than a regular NumPy bugfix
 release.  It also includes a number of documentation and build improvements.

 Sources and binary installers can be found at
 https://sourceforge.net/projects/numpy/files/NumPy/1.6.2rc1/

 Please test this release and report any issues on the numpy-discussion
 mailing list.
...
 BLD:   add support for the new X11 directory structure on Ubuntu  co.

We've just discovered that this fix is not enough. Actually the new
directories are due to the multi-arch feature of Debian systems,
that allows to install libraries from other (foreign) architectures
than the one the machine is (the classic example, i386 libraries on a
amd64 host).

the fix included to look up in additional directories is currently
only for X11, while for example Debian has fftw3 that's
multi-arch-ified and thus will fail to be detected.

Could this fix be extended to include all other things that are
checked? for reference the bug in Debian is [1]; there was also a
patch[2] in previous versions, that was using gcc to get the
multi-arch paths - you might use as a reference, or to implement
something debian-systems-specific.

[1] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=640940
[2] 
http://anonscm.debian.org/viewvc/python-modules/packages/numpy/trunk/debian/patches/50_search-multiarch-paths.patch?view=markuppathrev=21168

It would be awesome is such support would end up in 1.6.2 .

Cheers,
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Re: [Numpy-discussion] Debian/Ubuntu patch help (was: ANN: NumPy 1.6.2 release candidate 1)

[Sandro Tosi]

Hello,

On Wed, May 16, 2012 at 9:01 PM, Ralf Gommers
ralf.gomm...@googlemail.com wrote:


 On Tue, May 15, 2012 at 10:35 PM, Julian Taylor
 jtaylor.deb...@googlemail.com wrote:

  Hi, if there's anyone wants to have a look at the above issue this
  week,
 that would be great.

  If there's a patch by this weekend I can create a second RC, so we can
  still have the final release before the end of this month (needed for
  Debian freeze). Otherwise a second RC won't be needed.

 bugfixes are still allowed during the debian freeze, so that should not
 be an issue for the release timing.

 OK, that's good to know. So what's the hard deadline then?

second half of June, but it's still not set in stone (but I'd also not
expect too much variation)

 I don't see the issue with the gcc --print-multiarch patch besides maybe
 some cleanup.
 --print-multiarch is a debian specific gcc patch, but multiarch is
 debian specific for now.

 It doesn't work in 11.04, but who cares, that will be end of life in 5
 month anyway.


 Eh, we (the numpy maintainers) should care. If we would not care about an OS
 released only 13 months ago, we're not doing our job right.


 Besides x11 almost nothing is multiarched in 11.04 anyway
 and that can still be covered by the currently existing method.

 gcc should be available for pretty much anything requiring
 numpy.distutils anyway so that should be not be an issue.
 On systems without --print-multiarch or gcc you just ignore the failing,
 there will be no repercussions as there will also not be any multiarched
 libraries.

 If it's really that simple, such a patch may go into numpy master. But
 history has shown that patches to a central part of numpy.distutils are
 rarely issue-free (more due to the limitations/complexity of distutils than
 anything else). Therefore making such a change right before a release is
 simply a bad idea.

 the only potential issue I see is that upstream gcc adds a
 --print-multiarch that does something completely different and harmful
 for distutils, but I don't consider that very likely.

 Hardcoding a bunch of paths defeats the whole purpose of multiarch.
 It will just to break in future (e.g. when the x32 abi comes to
 debian/ubuntu) and will make cross compiling harder (though I guess
 numpy distutils may not be built for that anyway)


 If that hardcoding will break in the future, then I think for 1.6.2 the
 maintainers of the Debian package should apply the gcc patch to their
 packaged numpy if they think that is necessary.

Agreed, i'll add back the Debian specific patch. Thanks for your time
and analysis - so time to release 1.6.2? :)

Cheers,
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[Numpy-discussion] Numpy regression in 1.6.2 in deducing the dtype for record array

[Sandro Tosi]

Hello,
I'd like to point you to this bug report just reported to Debian:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=679948

It would be really awesome if you could give a look and comment if the
proposed fix would be appropriate.

Thanks a lot,

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Re: [Numpy-discussion] Numpy regression in 1.6.2 in deducing the dtype for record array

[Sandro Tosi]

Hello,

On Mon, Jul 2, 2012 at 7:58 PM, Sandro Tosi matrixh...@gmail.com wrote:
 Hello,
 I'd like to point you to this bug report just reported to Debian:
 http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=679948

 It would be really awesome if you could give a look and comment if the
 proposed fix would be appropriate.

Did you have a chance to look at this email?

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Re: [Numpy-discussion] Numpy regression in 1.6.2 in deducing the dtype for record array

[Sandro Tosi]

On Thu, Jul 5, 2012 at 8:18 AM, Scott Sinclair
scott.sinclair...@gmail.com wrote:
 Except that cherry picking the commit to the 1.6.x branch doesn't
 apply cleanly. It'll take some work by someone familiar with that part
 of the code..

That's actually what I was looking for :) someone knowing that code to
backport the fix to 1.6.x

Cheers
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Re: [Numpy-discussion] ANN: NumPy 1.7.0b1 release

[Sandro Tosi]

Hello,

On Tue, Aug 21, 2012 at 6:24 PM, Ondřej Čertík ondrej.cer...@gmail.com wrote:
 Hi,

 I'm pleased to announce the availability of the first beta release of
 NumPy 1.7.0b1.

I've just uploaded it to Debian experimental, so we can give it a run
while in freeze. Some of the buildds are already building[1] the
package, so we should get results asap (either failures or successes).

[1] 
https://buildd.debian.org/status/package.php?p=python-numpysuite=experimental

If tests fail, it won't stop the build, and indeed I got at least 2
errors (actually 1 error and 1 crash), when running tests for python
2.7 and 3.2 with debug enabled:

2.7 dbg

==
ERROR: test_power_zero (test_umath.TestPower)
--
Traceback (most recent call last):
  File 
/tmp/buildd/python-numpy-1.7.0~b1/debian/tmp/usr/lib/python2.7/dist-packages/numpy/core/tests/test_umath.py,
line 139, in test_power_zero
assert_complex_equal(np.power(zero, 0+1j), cnan)
RuntimeWarning: invalid value encountered in power

--

3.2 dbg

python3.2-dbg: numpy/core/src/multiarray/common.c:161:
PyArray_DTypeFromObjectHelper: Assertion
`((PyObject*)(temp))-ob_type))-tp_flags  ((1L27))) != 0)'
failed.
Aborted

I'm reporting them here since you asked so, dunno if you want an issue
on github to track them. I'll look at the buildds logs and report
additional failures if they come up.

Cheers,
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Re: [Numpy-discussion] ANN: NumPy 1.7.0b1 release

[Sandro Tosi]

On Fri, Aug 31, 2012 at 7:17 PM, Ondřej Čertík ondrej.cer...@gmail.com wrote:
 If you could create issues at github: https://github.com/numpy/numpy/issues
 that would be great. If you have time, also with some info about the platform
 and how to reproduce it. Or at least a link to the build logs.

I've reported it here: https://github.com/numpy/numpy/issues/402

Cheers,
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Re: [Numpy-discussion] ANN: NumPy 1.7.0b1 release

[Sandro Tosi]

On Fri, Aug 31, 2012 at 8:07 PM, Sandro Tosi mo...@debian.org wrote:
 On Fri, Aug 31, 2012 at 7:17 PM, Ondřej Čertík ondrej.cer...@gmail.com 
 wrote:
 If you could create issues at github: https://github.com/numpy/numpy/issues
 that would be great. If you have time, also with some info about the platform
 and how to reproduce it. Or at least a link to the build logs.

 I've reported it here: https://github.com/numpy/numpy/issues/402

I've just spammed the issue tracker with additional issues, reporting
all the test suite failures on Debian architectures; issues are 406 -
414 .

Don't hesitate to contact me if you need any support or clarification.

Cheers,
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Re: [Numpy-discussion] ANN: NumPy 1.7.0rc1 release

[Sandro Tosi]

Hi Ondrej  al,

On Sat, Dec 29, 2012 at 1:02 AM, Ondřej Čertík ondrej.cer...@gmail.com wrote:
 I'm pleased to announce the availability of the first release candidate of
 NumPy 1.7.0rc1.

Congrats on this RC release!

I've uploaded this version to Debian and updated some of the issues
related to it. There are also a couple of minor PR you might want to
consider for 1.7: 2872 and 2873.

Cheers,
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[Numpy-discussion] where to ship libnpymath.a ?

[Sandro Tosi]

Hi,
in Debian we had a bug report[1] requesting to ship libnpymath.a .

[1] http://bugs.debian.org/596987

Our python packaging tools doesn't handle .a files, so I'd like to ask
you where exactly should I ship that file. In the build directory I
have:

$ find . -name *.a | xargs md5sum
4c2371b98c138756b0471a4fb364e0ae
./debian/tmp/usr/lib/python2.5/site-packages/numpy/core/lib/libnpymath.a
fc6040f2bd4354cca8ef130abc5c8b17
./debian/tmp/usr/lib/python2.6/dist-packages/numpy/core/lib/libnpymath.a
0c9870a2e5cf61669c92677d9b12c116  ./build/temp_d.linux-x86_64-2.5/libnpymath.a
47fdd29b85570ce80b1c616c6c02f41a
./build/temp.linux-x86_64-2.6-pydebug/libnpymath.a
4c2371b98c138756b0471a4fb364e0ae  ./build/temp.linux-x86_64-2.5/libnpymath.a
fc6040f2bd4354cca8ef130abc5c8b17  ./build/temp.linux-x86_64-2.6/libnpymath.a

(the md5sum is to show that they are actually different between python
version and/or debug build): the first 2 are in the temporary debian
package preparation dir, while the other 4 are for 2.5/2.6 +
normal/debug build.

So, back to the original question: where should I put libnpymath.a to
be useful for our users (main request: new scipy)? maybe in
/numpy/core/lib/ ?

Cheers,
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Re: [Numpy-discussion] where to ship libnpymath.a ?

[Sandro Tosi]

Hi,

On Mon, Dec 13, 2010 at 22:05, Pauli Virtanen p...@iki.fi wrote:
 On Mon, 13 Dec 2010 20:51:56 +0100, Sandro Tosi wrote:
 [clip]
 So, back to the original question: where should I put libnpymath.a to be
 useful for our users (main request: new scipy)? maybe in
 /numpy/core/lib/ ?

 In the place pointed to by npymath.ini, which is where
 python setup.py install puts it. The point is that numpy.distutils
 should be able to locate this library file for building extension modules
 that depend on it.

Yep, now I see: I think I've prepared the package shipping
libnpymath.a in the right place, let's see :)

Thanks a lot for your help!

Cheers,
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Re: [Numpy-discussion] numpy docs dependency problem in Ubuntu

[Sandro Tosi]

On Fri, Feb 11, 2011 at 16:40, Barry Warsaw ba...@python.org wrote:
 For Debian, we'd simply take those two separate source packages and split the
 binary packages among them as appropriate.

excuse me? I don't like this solution, or are you going to do all the
work in Debian to adapt to this proposal?

You have a problem in ubuntu? fix it there: take the full numpy
upstream tarball, rename it in numpy-doc, build only the doc, ship it
where it better fits for ubuntu policies, work done  no-one gets hurt
:)

 A split
 tarball approach from upstream would be easier to get into Debian, and thus
 keep us in sync.

ehm... you're speaking too fast here and without involving maintainers it seems.

Regards,
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[Numpy-discussion] Error building numpy (1.5.1 and 1.6.1rc3) with python2.7 debug

[Sandro Tosi]

Hello,
while preparing a test upload for 1.6.1rc3 in Debian, I noticed that
it gets an error when building blas with python 2.7 in the debug
flavor, the build log is at [1]. It's also been confirmed it fails
also with 1.5.1 [2]

[1] http://people.debian.org/~morph/python-numpy_1.6.1~rc3-1_amd64.build
[2] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=634012

I think it might be a toolchain change in Debian (since 1.5.1 was
built successfully and now it fails), but could you please give me a
hand in debugging the issue?

Thanks in advance,
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Re: [Numpy-discussion] Error building numpy (1.5.1 and 1.6.1rc3) with python2.7 debug

[Sandro Tosi]

Hello,

On Sat, Jul 16, 2011 at 22:45, Bruce Southey bsout...@gmail.com wrote:
 On Sat, Jul 16, 2011 at 4:34 AM, Sandro Tosi mo...@debian.org wrote:
 Hello,
 while preparing a test upload for 1.6.1rc3 in Debian, I noticed that
 it gets an error when building blas with python 2.7 in the debug
 flavor, the build log is at [1]. It's also been confirmed it fails
 also with 1.5.1 [2]

 [1] http://people.debian.org/~morph/python-numpy_1.6.1~rc3-1_amd64.build
 [2] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=634012

 I think it might be a toolchain change in Debian (since 1.5.1 was
 built successfully and now it fails), but could you please give me a
 hand in debugging the issue?

 Thanks in advance,
 --
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 My website: http://matrixhasu.altervista.org/
 Me at Debian: http://wiki.debian.org/SandroTosi
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 Hi,
 What do you mean by 'python2.7 debug'?

 Numpy 1.6.1rc's and earlier build and install with Python 2.7 build in
 debug mode ($ ./configure --with-pydebug
 ) on 64-bit Fedora 14 and 15. But, if I can follow you build process
 (should be the plain 'python setup.py build' to be useful) I think
 numpy is not finding the correct blas/lapack/atlas libraries so either
 you may need a site.cfg for that system or install those in the Linux
 standard locations such as /usr/lib64.

 You should probably try building without blas, lapack and atlas etc.:
 BLAS=None LAPACK=None ATLAS=None python setup.py build

It's not a matter of not finding the headers: the same build process
succeeds if run using gfortran-4.5 while fails if run with
gfortran-4.6 , it's likely that gcc is more strict now and something
needs to be adapted in numpy.

Has someone successfully built numpy with gcc 4.6 ?

Cheers,
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Re: [Numpy-discussion] Error building numpy (1.5.1 and 1.6.1rc3) with python2.7 debug

[Sandro Tosi]

On Sat, Aug 6, 2011 at 06:25, Charles R Harris
charlesr.har...@gmail.com wrote:
 Yes, all the time ;)

 gcc version 4.6.0 20110603 (Red Hat 4.6.0-10) (GCC)

Great, in fact it turned out it was a debian tool that went nuts :) (I
was able to build _doblas by hand, so it's just a matter of
configuration)

The situation is this:

- until recently, we had this command in our makefile: 'unexport
LDFLAGS' that removes any presence of the variable LDFLAGS from the
environment.
- recently, a Debian-specific tool, started adding LDFLAGS (and other
build variables) to the env, in a way no more controllable by the
makefile
- with that variable set, gfortran misses a '-shared' option and it
generates the error I mentioned in the original email
- I'm following the path to ask for that tool to be made more
flexible, so to allow to unset those variables, but maybe I can
workaround it patching the code (I know, I hate to diverge from
upstream, but in extreme situations...), so I'd like to ask your
guidance in thise :) it's probably something
numpy/distutils/fcompiler/ but additional clues would be awesome :)

Cheers,
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[Numpy-discussion] How to run unittests at build time?

[Sandro Tosi]

==
ERROR: Failure: NameError (name 'numeric' is not defined)
--
Traceback (most recent call last):
  File /usr/lib/pymodules/python2.6/nose/loader.py, line 390, in
loadTestsFromName
addr.filename, addr.module)
  File /usr/lib/pymodules/python2.6/nose/importer.py, line 39, in
importFromPath
return self.importFromDir(dir_path, fqname)
  File /usr/lib/pymodules/python2.6/nose/importer.py, line 86, in
importFromDir
mod = load_module(part_fqname, fh, filename, desc)
  File build/lib.linux-x86_64-2.6/numpy/oldnumeric/__init__.py, line
14, in module
from compat import *
  File build/lib.linux-x86_64-2.6/numpy/oldnumeric/compat.py, line
13, in module
import numpy.core.multiarray as multiarray
  File build/lib.linux-x86_64-2.6/numpy/core/__init__.py, line 30, in module
__all__ += numeric.__all__
NameError: name 'numeric' is not defined

==
ERROR: Failure: NameError (name 'type_check' is not defined)
--
Traceback (most recent call last):
  File /usr/lib/pymodules/python2.6/nose/loader.py, line 390, in
loadTestsFromName
addr.filename, addr.module)
  File /usr/lib/pymodules/python2.6/nose/importer.py, line 39, in
importFromPath
return self.importFromDir(dir_path, fqname)
  File /usr/lib/pymodules/python2.6/nose/importer.py, line 84, in
importFromDir
mod = load_module(part_fqname, fh, filename, desc)
  File build/lib.linux-x86_64-2.6/numpy/polynomial/__init__.py, line
28, in module
from numpy.lib import deprecate
  File build/lib.linux-x86_64-2.6/numpy/lib/__init__.py, line 23, in module
__all__ += type_check.__all__
NameError: name 'type_check' is not defined

--
Ran 7 tests in 0.004s

FAILED (errors=7)


Not nice either, let's try another way, importing * from numpy:

$ python -c import sys ; sys.path.insert(0,
'build/lib.linux-x86_64-2.6') ; import numpy; from numpy import * ;
numpy.test()

same result as above.

So, what's the proper way to run the tests suite at build time?

Thanks in advance,
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Re: [Numpy-discussion] How to run unittests at build time?

[Sandro Tosi]

On Wed, Sep 21, 2011 at 23:15, Filipe Pires Alvarenga Fernandes
ocef...@gmail.com wrote:
 Don't know about about Debian, but this works OK for RPM distros:

 PYTHONPATH=%{buildroot}%{py_sitedir} %{__python} -c \
                                    import pkg_resources, numpy ; 
 numpy.test()

 The only thing you are missing is the import pkg_resources, let me
 know if that works for you.

Ok it works: I have to run tests from the installed location and not
from the build/ subdir; Thanks!!

Cheers,
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Re: [Numpy-discussion] How to run unittests at build time?

[Sandro Tosi]

On Wed, Sep 21, 2011 at 23:20, Robert Kern robert.k...@gmail.com wrote:
 On Wed, Sep 21, 2011 at 16:15, Filipe Pires Alvarenga Fernandes
 ocef...@gmail.com wrote:
 Don't know about about Debian, but this works OK for RPM distros:

 PYTHONPATH=%{buildroot}%{py_sitedir} %{__python} -c \
                                    import pkg_resources, numpy ; 
 numpy.test()

 The only thing you are missing is the import pkg_resources, let me
 know if that works for you.

 What does py_sitedir expand to, usually?

I suppose the site-packages directory location, so something like
/usr/lib/python2.6/site-packages/

 I don't think pkg_resources
 has anything to do with it. numpy doesn't use it, and I don't think
 nosetests does either (well, only for its plugin mechanism, but that's
 neither here nor there).

ack, I didn't use it in my tests: it works fine the python -c import
numpy; numpy.test()

 In any case, I've tried importing
 pkg_resources while running from the build/lib.*/ directory and still
 get the same errors as reported by Sandro.

Yep, the different with my approach and Felipe's one is I ran from the
build directory Felipe from the installation directory. It works, so
I'll use the latter

Cheers,
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[Numpy-discussion] Debug memory block at address p=0x2ba5928: API 'm'

[Sandro Tosi]

Hello,
I'm running tests for numpy 1.6.1 on 2.7 -dbg flavor and I got this:

.Debug memory block at address p=0x2ba5928: API 'm'
8 bytes originally requested
The 7 pad bytes at p-7 are FORBIDDENBYTE, as expected.
The 8 pad bytes at tail=0x2ba5930 are FORBIDDENBYTE, as expected.
The block was made by call #1253108 to debug malloc/realloc.
Data at p: a3 03 00 00 00 00 00 00
Fatal Python error: bad ID: Allocated using API 'm', verified using API 'o'
Running unit tests for numpy
NumPy version 1.6.1

and it got aborted.

Running the tests with 2.6-dbg doesn't show this behavior. How can I
help you debug it?

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Re: [Numpy-discussion] Debug memory block at address p=0x2ba5928: API 'm'

[Sandro Tosi]

On Thu, Sep 22, 2011 at 21:49, Bruce Southey bsout...@gmail.com wrote:
 All that I can tell you is that this is Ticket 1578:
 http://projects.scipy.org/numpy/ticket/1578

Ah, I could have probably checked it before sending this email, but
now that webpage gives me 500 - it's spreading! :)

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[Numpy-discussion] Reason behind C_ABI_VERSION so high

[Sandro Tosi]

Hello,
in Debian we're trying to define a way to handle numpy transitions
more smoothly (you can read the proposal, if interested, at
http://bugs.debian.org/643873).

In order to do that, we'd like to use the C_API_VERSION and
C_ABI_VERSION values; while for C_API_VERSION we can see it's a quite
small value, with a clear history at
./numpy/core/code_generators/cversions.txt , we don't have quite clear
why C_ABI_VERSION is such a high value and how it would be
incremented.

Could you please shine some light on it? can we, f.e., just take 6 for
API and 9 for ABI and be sure we're seeing them incremented to 7 and
10 (respectively) when needed? C_ABI_VERSION is incremented in a
different way?

Thanks,
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Re: [Numpy-discussion] Reason behind C_ABI_VERSION so high

[Sandro Tosi]

Hi Stéfan,
thanks for your reply.

2011/11/1 Stéfan van der Walt ste...@sun.ac.za:
 But nowadays the ABI number is simply bumped
 by one after every change, so for a good couple of million releases
 you should be safe ignoring the 1

perfect, that's good for us

 (but is the value really large enough to cause problems?).

well, we plan to have that number into a package name, so having
python-numpy-abi0109 is kinda ugly (not that python-numpy-abi9 is
that better , but at least is shorter).

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[Numpy-discussion] ImportError: /usr/lib/python2.6/dist-packages/numpy/core/multiarray.so: undefined symbol: NPY_COPY_PYOBJECT_PTR

[Sandro Tosi]

Hello,
I'm upgrading the Debian package for Numpy to 1.4.1.

Compilation goes well, but when I install the package for test and
import numpy I got this traceback:

$ python -V
Python 2.6.5+
$ python -c import numpy
Traceback (most recent call last):
  File string, line 1, in module
  File /usr/lib/python2.6/dist-packages/numpy/__init__.py, line 132,
in module
import add_newdocs
  File /usr/lib/python2.6/dist-packages/numpy/add_newdocs.py, line
9, in module
from lib import add_newdoc
  File /usr/lib/python2.6/dist-packages/numpy/lib/__init__.py, line
4, in module
from type_check import *
  File /usr/lib/python2.6/dist-packages/numpy/lib/type_check.py,
line 8, in module
import numpy.core.numeric as _nx
  File /usr/lib/python2.6/dist-packages/numpy/core/__init__.py, line
5, in module
import multiarray
ImportError: /usr/lib/python2.6/dist-packages/numpy/core/multiarray.so:
undefined symbol: NPY_COPY_PYOBJECT_PTR

If I look at the symbols table for multiarray.so I see none exposed:

$ objdump -t /usr/lib/python2.6/dist-packages/numpy/core/multiarray.so

/usr/lib/python2.6/dist-packages/numpy/core/multiarray.so: file
format elf64-x86-64

SYMBOL TABLE:
no symbols

Could you please tell me if I'm making some evident mistake? :) I'm
also attaching the build log, so that you might spot something in it
not correctly done.

Thanks in advance for your help,
-- 
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My website: http://matrixhasu.altervista.org/
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Re: [Numpy-discussion] ImportError: /usr/lib/python2.6/dist-packages/numpy/core/multiarray.so: undefined symbol: NPY_COPY_PYOBJECT_PTR

[Sandro Tosi]

Hello David,
thanks for your reply.

On Sat, Jun 19, 2010 at 18:37, David Cournapeau courn...@gmail.com wrote:
 On Sat, Jun 19, 2010 at 11:13 PM, Sandro Tosi mo...@debian.org wrote:
 Hello,
 I'm upgrading the Debian package for Numpy to 1.4.1.

 Compilation goes well, but when I install the package for test and
 import numpy I got this traceback:

 Do you have numpy already installed ?

yes, I have the 1.3.1 version (coming from Debian pkgs) installed. But
do you mean at runtime or build-time. I built the package in a clean
chroot where only the dependencies and numpy source tarball were
present.

 Because debian splits the numpy
 package and installed the headers in /usr/include, which breaks the
 build of pretty much every python extension out there (as it causes a
 change in header inclusion).

If you feel this is wrong, we can evaluate to provide a sane solution.
AFAICS we do not split numpy packages (except for the debug extensions
and the documentation), and yes, we do add headers to
/usr/include/numpy : could you please explain why this is wrong?

 The missing symbol is a macro defined in our public header, and is
 relatively recent.

yeah, the strange fact is that:

$ grep NPY_COPY_PYOBJECT_PTR /usr/include/numpy/npy_cpu.h
#define NPY_COPY_PYOBJECT_PTR(dst, src) (*((PyObject **)(dst)) =
*((PyObject **)(src)))
#define NPY_COPY_PYOBJECT_PTR(dst, src) \
#define NPY_COPY_PYOBJECT_PTR(dst, src) \

/me puzzled

Thanks in advance for the help,
-- 
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[Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

[Sandro Tosi]

Hello,
I finally found the time to update numpy in Debian. But, there is a problem...

As you probably know, we support several architectures and we need to
have any package available on each of them. After the upload I noticed
numpy has problem building on alpha [1] (ieee754.c compilation error,
probably related to the conversion from .src) and powerpc [2]
(long_double identification)

[1] 
https://buildd.debian.org/fetch.cgi?pkg=python-numpyarch=alphaver=1%3A1.4.1-2stamp=1279394977file=logas=raw
[2] 
https://buildd.debian.org/fetch.cgi?pkg=python-numpyarch=powerpcver=1%3A1.4.1-2stamp=1279394008file=logas=raw

They are quite specific pieces of code, so I'm here asking your help
in order to be able to build numpy on all Debian supported
architectures and so be released in the upcoming stable release :)

Of course, feel free to ask me any kind of support, also if you need
to test/execute something on those archs, just tell me and I'll do.

Regards,
-- 
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Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

[Sandro Tosi]

Hi David,
thanks for your reply!

On Mon, Jul 19, 2010 at 20:10, David Cournapeau courn...@gmail.com wrote:
 On Sun, Jul 18, 2010 at 12:53 PM, Sandro Tosi mo...@debian.org wrote:
 Hello,
 I finally found the time to update numpy in Debian. But, there is a 
 problem...

 As you probably know, we support several architectures and we need to
 have any package available on each of them. After the upload I noticed
 numpy has problem building on alpha [1] (ieee754.c compilation error,
 probably related to the conversion from .src) and powerpc [2]
 (long_double identification)

 The alpha issue should be easy to fix: it is just a code path which
 has never been tested so far, but the code is there.

ah if you say so, I trust you :)

 The ppc one is more annoying, and known. The problem is that linux on
 ppc uses the IBM format for long double (sum of two double), which
 requires to implement non trivial, heavily platform dependent code. I
 have just added code to correctly detect the long double format at the
 configure stage.

yes, I see it at r8510

 Do you have shell access to the machines ? It would makes the work
 much easier for me to fix those issues,

Yes, as a Debian developer I have access to a porterbox of any
architecture we support, so I can do any test/recompilation and so you
want. I can understand that using me as a proxy might be a little bit
tedious and slow, so if you prefer to have direct access I have to ask
for it, but it might be refused (I'm not sure), and/or only be
temporary.

Just let me know: I'm fully available for you.

Regards,
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Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

[Sandro Tosi]

Hi David  others,

On Tue, Jul 20, 2010 at 19:09, David Cournapeau courn...@gmail.com wrote:
 On Tue, Jul 20, 2010 at 4:21 PM, Sandro Tosi mo...@debian.org wrote:
 Hi David,

 On Tue, Jul 20, 2010 at 10:34, David Cournapeau courn...@gmail.com wrote:
 yes, I see it at r8510

 I quickly adapted the code from the Sun math library for the linux ppc
 long double format. Let me know if it works (if possible, you should
 run the test suite).

 thanks for working on it :)

 I checked out numpy at r8511 and built it on powerpc, attached the
 buildlog (it crashed at doc generation, but the setup.py build were
 done before, and went fine).

 I've python2.x setup.py install --prefix install/ and execute the
 tests from there with:

 ~/numpy/install$ PYTHONPATH=lib/python2.6/site-packages/ python2.6 -c
 import numpy; print numpy.test()  ../testlog_2.6
 ~/numpy/install$ PYTHONPATH=lib/python2.5/site-packages/ python2.5 -c
 import numpy; print numpy.test()  ../testlog_2.5

 attached the testlogs too: there are a couple of failures.

 The failures seem to be related to the long double not conforming to
 IEEE754 standard on linux ppc. I am not sure how to deal with them -
 maybe raising a warning if the user uses long double, as its usage
 will always be flaky on that platform anyway (numpy assumes IEEE
 754-like support)

yeah a warning might be nice.

Just to keep you informed, I tested 1.4.1+r8510+r8510 and it builds
fine on the porterbox only showing this failure on test():

FAIL: test_umath.TestComplexFunctions.test_loss_of_precision(type
'numpy.complex64',)
--
Traceback (most recent call last):
  File /usr/lib/pymodules/python2.6/nose/case.py, line 183, in runTest
self.test(*self.arg)
  File /usr/lib/python2.6/dist-packages/numpy/core/tests/test_umath.py,
line 524, in check_loss_of_precision
assert np.all(d  1e-15)
AssertionError

--
Ran 2016 tests in 52.670s

FAILED (KNOWNFAIL=2, failures=1)
nose.result.TextTestResult run=2016 errors=0 failures=1

Hence I decided to upload and the build went fine on the buildd machine [1].

[1] 
https://buildd.debian.org/fetch.cgi?pkg=python-numpyarch=powerpcver=1%3A1.4.1-3stamp=1279914539file=logas=raw

the other big show-stopper for numpy is the fail to build on alpha
you're already aware of: if you need any kind of support, just ask me.

Thanks a lot for your support for powerpc issue!

Cheers,
-- 
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Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

[Sandro Tosi]

Hi,

On Tue, Jul 27, 2010 at 12:28, David Cournapeau courn...@gmail.com wrote:
 On Tue, Jul 20, 2010 at 3:44 AM, Sandro Tosi mo...@debian.org wrote:

 ah if you say so, I trust you :)

 Could you try the last version of the trunk, I added the missing
 macros for alpha ?

I just built trunk (both for 2.5 and 2.6) on alpha, successfully :)
Now I'll extract only the needed patch (I think it's enough to apply
r8526, right?) and try to build the package using 1.4.1+patch, if it
builds successfully I'll upload numpy in Debian again.

David, let me thank you very very much for your support!!

Cheers,
-- 
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My website: http://matrixhasu.altervista.org/
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Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

[Sandro Tosi]

On Tue, Jul 27, 2010 at 14:52, Sandro Tosi mo...@debian.org wrote:
 Hi,

 On Tue, Jul 27, 2010 at 12:28, David Cournapeau courn...@gmail.com wrote:
 On Tue, Jul 20, 2010 at 3:44 AM, Sandro Tosi mo...@debian.org wrote:

 ah if you say so, I trust you :)

 Could you try the last version of the trunk, I added the missing
 macros for alpha ?

 I just built trunk (both for 2.5 and 2.6) on alpha, successfully :)
 Now I'll extract only the needed patch (I think it's enough to apply
 r8526, right?) and try to build the package using 1.4.1+patch, if it
 builds successfully I'll upload numpy in Debian again.

and indeed it build! yay \o/

 David, let me thank you very very much for your support!!

Renew the great THANK YOU!

Cheers,
-- 
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Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

[Sandro Tosi]

Hi!
sorry it took so long to reply.

On Thu, Jul 29, 2010 at 03:27, David Cournapeau courn...@gmail.com wrote:
 On Wed, Jul 28, 2010 at 12:36 AM, Sandro Tosi mo...@debian.org wrote:
 On Tue, Jul 27, 2010 at 14:52, Sandro Tosi mo...@debian.org wrote:
 Hi,

 On Tue, Jul 27, 2010 at 12:28, David Cournapeau courn...@gmail.com wrote:
 On Tue, Jul 20, 2010 at 3:44 AM, Sandro Tosi mo...@debian.org wrote:

 ah if you say so, I trust you :)

 Could you try the last version of the trunk, I added the missing
 macros for alpha ?

 I just built trunk (both for 2.5 and 2.6) on alpha, successfully :)
 Now I'll extract only the needed patch (I think it's enough to apply
 r8526, right?) and try to build the package using 1.4.1+patch, if it
 builds successfully I'll upload numpy in Debian again.

 and indeed it build! yay \o/

 David, let me thank you very very much for your support!!

 Renew the great THANK YOU!

 If possible, I would really like to get build and test output logs for
 both alpha/ppc.

For the build logs it's easy:

alpha: 
https://buildd.debian.org/fetch.cgi?pkg=python-numpyarch=alphaver=1%3A1.4.1-4stamp=1280296333file=logas=raw
powerpc: 
https://buildd.debian.org/fetch.cgi?pkg=python-numpyarch=powerpcver=1%3A1.4.1-4stamp=1280297029file=logas=raw

for powerpc import numpy; numpy.test() I've already sent you the
output, want me to re-run them? for alpha, attached you can find the
log for both 2.5 and 2.6; there are some errors/warnings but nothing
too dramatic?

 Also, if there is another issue preventing numpy 1.4.x integration on
 debian and ubuntu, please speak up. Ideally, I would like to remove

I don't think there is anything else (for now :) ) from the numpy
side: Thanks a lot for the support!! Now on Debian we have to fix some
packages to avoid breakages when we upgrade numpy in the future (the
biggest issue was that dtype was extended with new fields at the end,
but some packages were checking the size of dtype with the one the
packge was compiled with (1.3.*) and failed). As usual, Ubuntu will
just sit and wait for us to do the work and then just sync it (sigh).

 the need for downstream patches (none of them was necessary IIRC),

Here is the list of the patches we currently have in the Debian
package (you can look at them at [2]):

02_build_dotblas.patch
- Patch to build _dotblas.c when ATLAS is not installed.
-- dunno exactly what it does, it seems to infer _dotblas is compiled
is ATLAS is missing

03_force_f2py_version.patch
- force generation f2py postfixed with interpreter version
-- Debian specific: we ship f2py2.5 and f2py2.6 and we make f2py a
symlink towards f2py2.6

05_fix_endianness_detection.patch
- Fix endianness detection: endian.h should be present on all Debian
machines. This patch forces the use of endian.h, this reventing
several reverse dependencies os Numpy from failing to build.
-- Debian specific: we want to enforce the usage of endian.h file
available on all of our architectures

07_bts585309_string_exceptions.diff
- Remove string exceptions
-- patch from trunk, we can remove it once a new release is out

10_use_local_python.org_object.inv_sphinx.diff
- Use a local copy of object.inv from doc.python.org, instead of
downloading it each time from the internet
-- Debian specific, we are not allowed to download stuff from internet
when building package, so I just download object.inv from d.p.o and
use it in interpshinx_mapping

changeset_r8510.diff
changeset_r8511.diff
- support for powerpc
-- patch from trunk, we can remove it once a new release is out

changeset_r8526.diff
- support for alpha
- patch from trunk, we can remove it once a new release is out

[2] 
http://svn.debian.org/viewsvn/python-modules/packages/numpy/trunk/debian/patches/

In case of any doubts or so, don't hesitate to contact me: I'd be more
than happy to give all the help I can.

Cheers.
-- 
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My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi


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Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

[Sandro Tosi]

Hi David,
sorry for the late reply.

On Fri, Jul 30, 2010 at 04:58, David da...@silveregg.co.jp wrote:
 On 07/30/2010 06:47 AM, Sandro Tosi wrote:

 For the build logs it's easy:

 alpha: 
 https://buildd.debian.org/fetch.cgi?pkg=python-numpyarch=alphaver=1%3A1.4.1-4stamp=1280296333file=logas=raw
 powerpc: 
 https://buildd.debian.org/fetch.cgi?pkg=python-numpyarch=powerpcver=1%3A1.4.1-4stamp=1280297029file=logas=raw

 for powerpc import numpy; numpy.test() I've already sent you the
 output, want me to re-run them? for alpha, attached you can find the
 log for both 2.5 and 2.6; there are some errors/warnings but nothing
 too dramatic?

 Wow, I am genuily surprised that the alpha test suite has no error (the
 2.5 error has nothing to do with the fixes).

:)

Anyhow, I plan to enable tests execution at package build time, so
that we can spot strange behaviors/faults on all the archs supported
by Debian.

 Also, if there is another issue preventing numpy 1.4.x integration on
 debian and ubuntu, please speak up. Ideally, I would like to remove

 I don't think there is anything else (for now :) ) from the numpy
 side: Thanks a lot for the support!! Now on Debian we have to fix some
 packages to avoid breakages when we upgrade numpy in the future (the
 biggest issue was that dtype was extended with new fields at the end,
 but some packages were checking the size of dtype with the one the
 packge was compiled with (1.3.*) and failed).

 Yes, we have improved quite a bit our support here in 1.4.x - we hope
 that those issues won't arise in the 1.x series anymore. Note also that
 if those dtype errors appear with pyrex/cython-generated code, using a
 more recent cython will prevent the error from happening (warnings
 raised instead).

Ah, thanks for letting me know! I'll keep in mind.

 As usual, Ubuntu will
 just sit and wait for us to do the work and then just sync it (sigh).

 the need for downstream patches (none of them was necessary IIRC),

 Here is the list of the patches we currently have in the Debian
 package (you can look at them at [2]):

 02_build_dotblas.patch
 - Patch to build _dotblas.c when ATLAS is not installed.
 -- dunno exactly what it does, it seems to infer _dotblas is compiled
 is ATLAS is missing

 This is is caused by not having atlas as a build dependency I guess.
 Strictly speaking, dotblas only requires cblas, but we don't have the
 check in place to do so. Since numscons already does this, and it has
 worked pretty well, maybe I will take time to add this as well in
 numpy.distutils. But this has relatively little consequence I think.

yep, I agree, it would be nice tho to have it directly upstream.


 03_force_f2py_version.patch
 - force generation f2py postfixed with interpreter version
 -- Debian specific: we ship f2py2.5 and f2py2.6 and we make f2py a
 symlink towards f2py2.6

 ok.


 05_fix_endianness_detection.patch
 - Fix endianness detection: endian.h should be present on all Debian
 machines. This patch forces the use of endian.h, this reventing
 several reverse dependencies os Numpy from failing to build.
 -- Debian specific: we want to enforce the usage of endian.h file
 available on all of our architectures

 This one has been fixed in the 1.4.x branch (and trunk of course)


 07_bts585309_string_exceptions.diff
 - Remove string exceptions
 -- patch from trunk, we can remove it once a new release is out

 This one as well

I'll live those patches there, until a new release will be out, or do
you suggest to sync the package with the 1.4.x branch?

Cheers,
-- 
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My website: http://matrixhasu.altervista.org/
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Re: [Numpy-discussion] ANN: NumPy 1.5.0 beta 1

[Sandro Tosi]

Hi all,
sorry for the delay

On Sun, Aug 1, 2010 at 18:38, Ralf Gommers ralf.gomm...@googlemail.com wrote:
 I am pleased to announce the availability of the first beta of NumPy 1.5.0.
 This will be the first NumPy release to include support for Python 3, as
 well as for Python 2.7. Please try this beta and report any problems on the
 NumPy mailing list.

 Binaries, sources and release notes can be found at
 https://sourceforge.net/projects/numpy/files/
 Please note that binaries for Python 3.1 are not yet up, they will follow as
 soon as a minor issue with building them is resolved. Building from source
 with Python 3.1 should work without problems.

I gave it a run on the Debian packaging system and these are the results:

- python 3.1 can't compile it:

$ python3 setup.py build
Traceback (most recent call last):
  File setup.py, line 210, in module
setup_package()
  File setup.py, line 174, in setup_package
import py3tool
ImportError: No module named py3tool

but this is already known, py3tool is missing from the tarball.

- python2.6 build, installation and numpy.test() works fine

- I have a problem building documentation:

# build doc only for default python version
(export MPLCONFIGDIR=. ; make -C doc html
PYTHONPATH=../build/lib.linux-x86_64-2.6)
make[1]: Entering directory `/tmp/buildd/python-numpy-1.5.0~b1/doc'
mkdir -p build
python \
./sphinxext/autosummary_generate.py source/reference/*.rst \
-p dump.xml -o source/reference/generated
./sphinxext/autosummary_generate.py:18: DeprecationWarning: The
numpydoc.autosummary extension can also be found as
sphinx.ext.autosummary in Sphinx = 0.6, and the version in Sphinx =
0.7 is superior to the one in numpydoc. This numpydoc version of
autosummary is no longer maintained.
  from autosummary import import_by_name
Failed to import 'numpy.__array_priority__':
Failed to import 'numpy.core.defchararray.len':
Failed to import 'numpy.generic.__squeeze__':
touch build/generate-stamp
mkdir -p build/html build/doctrees
LANG=C sphinx-build -b html -d build/doctrees   source build/html
Running Sphinx v0.6.6

Extension error:
Could not import extension numpydoc (exception: No module named domains.c)
1.5b1 1.5.0b1

I don't know exactly the reason for the Failed to import X but they
are there also for 1.4.1 so they should not be a problem. Anyhow,
there is no file named 'domains.c' in the tarball.

Regards,
-- 
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Re: [Numpy-discussion] ANN: NumPy 1.5.0 beta 2

[Sandro Tosi]

Hello,

On Tue, Aug 17, 2010 at 17:23, Ralf Gommers ralf.gomm...@googlemail.com wrote:
 I am pleased to announce the availability of the second beta of NumPy 1.5.0.
 This will be the first NumPy release to include support for Python 3, as
 well as for Python 2.7.

 Please try this beta and report any problems on the NumPy mailing list.
 Especially with Python 3 testing will be very useful. On Linux and OS X
 building from source should be straightforward, for Windows a binary
 installer is provided. There is one important known issue on Windows left,
 in fromfile and tofile (ticket 1583).

(on a Debian system) I tested the build with python3.1, and it builds
fine (it seems) but I couldn't run numpy.test() since we still don't
have a nose for python3. anyhow the basic print(numpy.__version__)
worked.

On python2.6 and 2.5:

Running unit tests for numpy
NumPy version 1.5.0b2
NumPy is installed in
/home/morph/deb/tmp/numpy-1.5.0b2/inst/lib/python2.6/site-packages/numpy
Python version 2.6.5+ (release26-maint, Jul  6 2010, 12:58:20) [GCC 4.4.4]
nose version 0.11.1
...
Ran 2966 tests in 16.129s

OK (KNOWNFAIL=4, SKIP=4)

Running unit tests for numpy
NumPy version 1.5.0b2
NumPy is installed in
/home/morph/deb/tmp/numpy-1.5.0b2/inst/lib/python2.5/site-packages/numpy
Python version 2.5.5 (r255:77872, Apr 21 2010, 08:40:04) [GCC 4.4.3]
nose version 0.11.1
...
Ran 2952 tests in 15.670s

OK (KNOWNFAIL=4, SKIP=4)

Regards,
-- 
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Re: [Numpy-discussion] IEEE 754-2008 decimal floating point support

[Sandro Tosi]

On Wed, Sep 8, 2010 at 22:10, Michael Gilbert
michael.s.gilb...@gmail.com wrote:
 Here is an example:

    0.3/3.0 - 0.1
   -1.3877787807814457e-17

    mpmath.mpf( '0.3' )/mpmath.mpf( '3.0' ) - mpmath.mpf( '0.1' )
   mpf('-1.3877787807814457e-17')

    decimal.Decimal( '0.3' )/decimal.Decimal( '3.0' ) - decimal.Decimal ( 
 '0.1' )
   Decimal(0.0)

 Decimal solves the problem; whereas mpmath doesn't.

you can change mpmath precision up to an arbitrary high value:

In [4]: mpmath.mp.prec = 100

In [5]: mpmath.mpf( '0.3' )/mpmath.mpf( '3.0' ) - mpmath.mpf( '0.1' )
Out[5]: mpf('0.0')

Regards.
-- 
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Re: [Numpy-discussion] ANN: Numpy 1.10.0b1 release

[Sandro Tosi]

On Tue, Aug 11, 2015 at 11:22 PM, Charles R Harris
charlesr.har...@gmail.com wrote:
 I'm uploading replacements for the tar and zip files.. Not sure why
 numpy-vendor didn't do the job.

if so then please upload a b2, so it will avoid confusion with those
who have downloaded a b1-pre-fix and those with a b1-post-fix

Regards,
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Re: [Numpy-discussion] ANN: Numpy 1.10.0b1 release

[Sandro Tosi]

On Tue, Aug 11, 2015 at 11:46 PM, Charles R Harris
charlesr.har...@gmail.com wrote:
 On Tue, Aug 11, 2015 at 4:32 PM, Sandro Tosi sandro.t...@gmail.com wrote:

 On Tue, Aug 11, 2015 at 11:22 PM, Charles R Harris
 charlesr.har...@gmail.com wrote:
  I'm uploading replacements for the tar and zip files.. Not sure why
  numpy-vendor didn't do the job.

 if so then please upload a b2, so it will avoid confusion with those
 who have downloaded a b1-pre-fix and those with a b1-post-fix


 I think it was caught early enough that it won't be much of a problem. I
 expect there will be other problems that will require a beta 2 soon enough
 ;)

we can agree to disagree, but nevermind :) I gave it a quick build
test on debian unstable amd64 and it's building  correctly, I will
finalize the package in the next few days and upload to the various
weird architectures Debian supports and see where it fails.

Regards,
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Re: [Numpy-discussion] Proposal: stop supporting 'setup.py install'; start requiring 'pip install .' instead

[Sandro Tosi]

please, pretty please, do not disable setup.py install or at least
keep providing a way for distribution (Debian in this case) to be able
to build/install numpy in a temporary location for packaging reasons.
pip is not the solution for us

On Tue, Oct 27, 2015 at 12:31 AM, Nathaniel Smith <n...@pobox.com> wrote:
> Hi all,
>
> Apparently it is not well known that if you have a Python project
> source tree (e.g., a numpy checkout), then the correct way to install
> it is NOT to type
>
>   python setup.py install   # bad and broken!
>
> but rather to type
>
>   pip install .
>
> (I.e., pip install isn't just for packages on pypi -- you can also
> pass it the path to an arbitrary source directory or the URL of a
> source tarball and it will do its thing. In this case "install ."
> means "install the project in the current directory".)
>
> These don't quite have identical results -- the main difference is
> that the latter makes sure that proper metadata gets installed so that
> later on it will be possible to upgrade or uninstall correctly. If you
> call setup.py directly, and then later you try to upgrade your
> package, then it's entirely possible to end up with a mixture of old
> and new versions of the package installed in your PYTHONPATH. (One
> common effect is in numpy's case is that we get people sending us
> mysterious bug reports about failing tests in files don't even exist
> (!) -- because nose is finding tests in files from one version of
> numpy and running them against a different version of numpy.)
>
> But this isn't the only issue -- using pip also avoids a bunch of
> weird corner cases in distutils/setuptools. E.g., if setup.py uses
> plain distutils, then it turns out this will mangle numpy version
> numbers in ways that cause weird horribleness -- see [1] for a bug
> report of the form "matplotlib doesn't build anymore" which turned out
> to be because of using 'setup.py install' to install numpy. OTOH if
> setup.py uses setuptools then you get different weirdnesses, like you
> can easily end up with multiple versions of the same library installed
> simultaneously.
>
> And finally, an advantage of getting used to using 'pip install .' now
> is that you'll be prepared for the glorious future when we kill
> distutils and get rid of setup.py entirely in favor of something less
> terrible [2].
>
> So a proposal that came out of the discussion in [1] is that we modify
> numpy's setup.py now so that if you try running
>
> python setup.py install
>
> you get
>
> Error: Calling 'setup.py install' directly is NOT SUPPORTED!
> Instead, do:
>
> pip install .
>
> Alternatively, if you want to proceed at your own risk, you
> can try 'setup.py install --force-raw-setup.py'
> For more information see http://...
>
> (Other setup.py commands would continue to work as normal.)
>
> I believe that this would also break both 'easy_install numpy', and
> attempts to install numpy via the setup_requires= argument to
> setuptools.setup (because setup_requires= implicitly calls
> easy_install). install_requires= would *not* be affected, and
> setup_requires= would still be fine in cases where numpy was already
> installed.
>
> This would hopefully cut down on the amount of time everyone spends
> trying to track down these stupid weird bugs, but it will also require
> some adjustment in people's workflows, so... objections? concerns?
>
> -n
>
> [1] https://github.com/numpy/numpy/issues/6551
> [2] https://mail.python.org/pipermail/distutils-sig/2015-October/027360.html
>
> --
> Nathaniel J. Smith -- http://vorpus.org
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Re: [Numpy-discussion] Should I use pip install numpy in linux?

[Sandro Tosi]

> I wrote a page on using pip with Debian / Ubuntu here :
> https://matthew-brett.github.io/pydagogue/installing_on_debian.html

Speaking with my numpy debian maintainer hat on, I would really
appreciate if you dont suggest to use pip to install packages in
Debian, or at least not as the only solution.

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Re: [Numpy-discussion] Should I use pip install numpy in linux?

[Sandro Tosi]

On Sat, Jan 9, 2016 at 6:08 PM, Matthew Brett <matthew.br...@gmail.com> wrote:
> Hi Sandro,
>
> On Sat, Jan 9, 2016 at 4:44 AM, Sandro Tosi <mo...@debian.org> wrote:
>>> I wrote a page on using pip with Debian / Ubuntu here :
>>> https://matthew-brett.github.io/pydagogue/installing_on_debian.html
>>
>> Speaking with my numpy debian maintainer hat on, I would really
>> appreciate if you dont suggest to use pip to install packages in
>> Debian, or at least not as the only solution.
>
> I'm very happy to accept alternative suggestions or PRs.
>
> I know what you mean, but I can't yet see how to write a page that
> would be good for explaining the benefits / tradeoffs of using deb
> packages vs mainly or only pip packages vs a mix of the two.  Do you
> have any thoughts?

you can start by making extremely clear that this is not the Debian
supported way to install python modules on a Debian system, that if a
user uses pip to do it, it's very likely other applications or modules
will fail, that if they have any problem with anything python related,
they are on their own as they "broke" their system on purpose. thanks
for considering

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Re: [Numpy-discussion] Should I use pip install numpy in linux?

[Sandro Tosi]

On Sun, Jan 10, 2016 at 3:55 AM, Matthew Brett  wrote:
> I updated the page with more on reasons to prefer Debian packages over
> installing with pip:
>
> https://matthew-brett.github.io/pydagogue/installing_on_debian.html
>
> Is that enough to get the message across?

That looks a lot better, thanks! I also kinda agree with all Nathaniel
said on the matter

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Re: [Numpy-discussion] Numpy 1.11.2

[Sandro Tosi]

hey there, what happened here? do you still plan to release a 1.11.2rc1 soon?

On Wed, Aug 3, 2016 at 9:09 PM, Charles R Harris
 wrote:
> Hi All,
>
> I would like to release Numpy 1.11.2rc1 this weekend. It will contain a few
> small fixes and enhancements for windows and the last Scipy release. If
> there are any pending PRs that you think should go in or be backported for
> this release, please speak up.
>
> Chuck
>
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Re: [Numpy-discussion] PowerPC testing servers

[Sandro Tosi]

> A recent post to the wheel-builders mailing list pointed out some
> links to places providing free PowerPC hosting for open source
> projects, if they agree to a submitted request:

The debian project has some powerpc machines (and we still build numpy
on those boxes when i upload a new revision to our archives) and they
also have hosts dedicated to let debian developers login and debug
issues with their packages on that architecture. I can sponsor access
to those machines for some of you, but it is not a place where you can
host a CI instance.

Just keep it in mind more broadly than powerpc, f.e. these are all the
archs where numpy was built after the last upload
https://buildd.debian.org/status/package.php?p=python-numpy=unstable
(the grayed out archs are the ones non release critical, so packages
are built as best effort and if missing is not a big deal)

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Re: [Numpy-discussion] PowerPC testing servers

[Sandro Tosi]

On Thu, Feb 16, 2017 at 3:55 AM, Ralf Gommers  wrote:
> Thanks Sandro. It looks like even for the release-critical ones, it's just
> the build that has to succeed and failures are not detected? For example,
> armel is green but has 9 failures:
> https://buildd.debian.org/status/fetch.php?pkg=python-numpy=armel=1%3A1.12.0-2=1484889563=0

i made any error in the test suite non-fatal so that we could collect
the errors and then report them back. sadly i'm currently lacking the
time to report all the errors in the archs, will try to get at that
soon

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Re: [Numpy-discussion] Numpy 1.11.2

[Sandro Tosi]

what is the status for this? i checked on GH and
https://github.com/numpy/numpy/milestone/43 seems to report no issue
pending. the reason i'm asking is that i still have to package 1.11.1
for debian, but i dont want to do all the work and then the next day
you release a new version (oh, dear Murphy :) )

On Mon, Aug 15, 2016 at 1:12 AM, Charles R Harris
<charlesr.har...@gmail.com> wrote:
> "Events, dear boy, events" ;) There were a couple of bugs that turned up at
> the last moment that needed fixing. At the moment there are two, possibly
> three, bugs that need finishing off.
>
> A fix for compilation on PPC running RHEL 7.2 (done, but not verified)
> Roll back Numpy reload error: more than one project was reloading.
> Maybe fix crash for quicksort of object arrays with bogus comparison.
>
> Chuck
>
>
>
> On Sun, Aug 14, 2016 at 11:11 AM, Sandro Tosi <mo...@debian.org> wrote:
>>
>> hey there, what happened here? do you still plan to release a 1.11.2rc1
>> soon?
>>
>> On Wed, Aug 3, 2016 at 9:09 PM, Charles R Harris
>> <charlesr.har...@gmail.com> wrote:
>> > Hi All,
>> >
>> > I would like to release Numpy 1.11.2rc1 this weekend. It will contain a
>> > few
>> > small fixes and enhancements for windows and the last Scipy release. If
>> > there are any pending PRs that you think should go in or be backported
>> > for
>> > this release, please speak up.
>> >
>> > Chuck
>> >
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>> >
>>
>>
>>
>> --
>> Sandro "morph" Tosi
>> My website: http://sandrotosi.me/
>> Me at Debian: http://wiki.debian.org/SandroTosi
>> G+: https://plus.google.com/u/0/+SandroTosi
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>
>
>
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