subject:"Re\: \[Numpy\-discussion\] \[SciPy\-Dev\] Setting up a dev environment with conda"

Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

2015-10-18 Thread Luke Zoltan Kelley

Thanks for the help Nathaniel --- but building via `./runtests.py` is failing 
in the same way.  Hopefully Numpy-discussion can help me out.

I'm able to build using `python setup.py build_ext --inplace` but both trying 
to run `python setup.py install` or `./runtests.py` leads to the following 
error:

(numpy-py27)daedalus-2:numpy lzkelley$ ./runtests.py 
Building, see build.log...
Running from numpy source directory.
Traceback (most recent call last):
  File "setup.py", line 264, in 
setup_package()
  File "setup.py", line 248, in setup_package
from numpy.distutils.core import setup
  File "/Users/lzkelley/Programs/public/numpy/numpy/distutils/__init__.py", 
line 21, in 
from numpy.testing import Tester
  File "/Users/lzkelley/Programs/public/numpy/numpy/testing/__init__.py", line 
14, in 
from .utils import *
  File "/Users/lzkelley/Programs/public/numpy/numpy/testing/utils.py", line 17, 
in 
from numpy.core import float32, empty, arange, array_repr, ndarray
  File "/Users/lzkelley/Programs/public/numpy/numpy/core/__init__.py", line 59, 
in 
test = Tester().test
  File "/Users/lzkelley/Programs/public/numpy/numpy/testing/nosetester.py", 
line 180, in __init__
if raise_warnings is None and '.dev0' in np.__version__:
AttributeError: 'module' object has no attribute '__version__'

Build failed!

Has anyone seen something like this before?

Thanks!
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Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

2015-10-18 Thread Feng Yu

Hi Luke,

Could you check if you have "/Users/lzkelley/Programs/public/numpy/ in
your PYTHONPATH?

I would also suggest you add a print(np) line before the crash in
nosetester.py. I got something like this (which didn't crash):



If you see something not starting with 'numpy/build', then it is again
pointing at  PYTHONPATH.

I hope these helps.

Best,

- Yu

On Sun, Oct 18, 2015 at 1:25 PM, Luke Zoltan Kelley  wrote:
> Thanks for the help Nathaniel --- but building via `./runtests.py` is
> failing in the same way.  Hopefully Numpy-discussion can help me out.
>
> I'm able to build using `python setup.py build_ext --inplace` but both
> trying to run `python setup.py install` or `./runtests.py` leads to the
> following error:
>
> (numpy-py27)daedalus-2:numpy lzkelley$ ./runtests.py
> Building, see build.log...
> Running from numpy source directory.
> Traceback (most recent call last):
>   File "setup.py", line 264, in 
> setup_package()
>   File "setup.py", line 248, in setup_package
> from numpy.distutils.core import setup
>   File "/Users/lzkelley/Programs/public/numpy/numpy/distutils/__init__.py",
> line 21, in 
> from numpy.testing import Tester
>   File "/Users/lzkelley/Programs/public/numpy/numpy/testing/__init__.py",
> line 14, in 
> from .utils import *
>   File "/Users/lzkelley/Programs/public/numpy/numpy/testing/utils.py", line
> 17, in 
> from numpy.core import float32, empty, arange, array_repr, ndarray
>   File "/Users/lzkelley/Programs/public/numpy/numpy/core/__init__.py", line
> 59, in 
> test = Tester().test
>   File "/Users/lzkelley/Programs/public/numpy/numpy/testing/nosetester.py",
> line 180, in __init__
> if raise_warnings is None and '.dev0' in np.__version__:
> AttributeError: 'module' object has no attribute '__version__'
>
> Build failed!
>
>
> Has anyone seen something like this before?
>
> Thanks!
> Luke
>
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Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

2015-10-18 Thread Luke Zoltan Kelley

Thanks Yu,

There was nothing in my PYTHONPATH at first, and adding my numpy directory 
('/Users/lzkelley/Programs/public/numpy') didn't help (same error).  In both 
cases, adding 'print(np)' yields:




> On Oct 18, 2015, at 7:22 PM, Feng Yu  wrote:
> 
> Hi Luke,
> 
> Could you check if you have "/Users/lzkelley/Programs/public/numpy/ in
> your PYTHONPATH?
> 
> I would also suggest you add a print(np) line before the crash in
> nosetester.py. I got something like this (which didn't crash):
> 
>  '/home/yfeng1/source/numpy/build/testenv/lib64/python2.7/site-packages/numpy/__init__.pyc'>
> 
> If you see something not starting with 'numpy/build', then it is again
> pointing at  PYTHONPATH.
> 
> I hope these helps.
> 
> Best,
> 
> - Yu
> 
> On Sun, Oct 18, 2015 at 1:25 PM, Luke Zoltan Kelley  
> wrote:
>> Thanks for the help Nathaniel --- but building via `./runtests.py` is
>> failing in the same way.  Hopefully Numpy-discussion can help me out.
>> 
>> I'm able to build using `python setup.py build_ext --inplace` but both
>> trying to run `python setup.py install` or `./runtests.py` leads to the
>> following error:
>> 
>> (numpy-py27)daedalus-2:numpy lzkelley$ ./runtests.py
>> Building, see build.log...
>> Running from numpy source directory.
>> Traceback (most recent call last):
>>  File "setup.py", line 264, in 
>>setup_package()
>>  File "setup.py", line 248, in setup_package
>>from numpy.distutils.core import setup
>>  File "/Users/lzkelley/Programs/public/numpy/numpy/distutils/__init__.py",
>> line 21, in 
>>from numpy.testing import Tester
>>  File "/Users/lzkelley/Programs/public/numpy/numpy/testing/__init__.py",
>> line 14, in 
>>from .utils import *
>>  File "/Users/lzkelley/Programs/public/numpy/numpy/testing/utils.py", line
>> 17, in 
>>from numpy.core import float32, empty, arange, array_repr, ndarray
>>  File "/Users/lzkelley/Programs/public/numpy/numpy/core/__init__.py", line
>> 59, in 
>>test = Tester().test
>>  File "/Users/lzkelley/Programs/public/numpy/numpy/testing/nosetester.py",
>> line 180, in __init__
>>if raise_warnings is None and '.dev0' in np.__version__:
>> AttributeError: 'module' object has no attribute '__version__'
>> 
>> Build failed!
>> 
>> 
>> Has anyone seen something like this before?
>> 
>> Thanks!
>> Luke
>> 
>> ___
>> NumPy-Discussion mailing list
>> NumPy-Discussion@scipy.org
>> https://mail.scipy.org/mailman/listinfo/numpy-discussion
>> 
> ___
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> NumPy-Discussion@scipy.org
> https://mail.scipy.org/mailman/listinfo/numpy-discussion

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Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

2015-10-18 Thread Michael Sarahan

Running tests in the folder might be causing your problem.  If it's trying
to import numpy, and numpy is a folder in your current folder, sometimes
you see errors like this.  The confusion is that Python treats folders
(packages) similarly to modules, and the resolution order sometimes bites
you.  Try cd'ing to a different folder (importantly, one NOT containing a
numpy folder!) and run the test command from there.

HTH,
Michael

On Sun, Oct 18, 2015 at 6:46 PM Luke Zoltan Kelley 
wrote:

> Thanks Yu,
>
> There was nothing in my PYTHONPATH at first, and adding my numpy directory
> ('/Users/lzkelley/Programs/public/numpy') didn't help (same error).  In
> both cases, adding 'print(np)' yields:
>
>  '/Users/lzkelley/Programs/public/numpy/numpy/__init__.pyc'>
>
>
> > On Oct 18, 2015, at 7:22 PM, Feng Yu  wrote:
> >
> > Hi Luke,
> >
> > Could you check if you have "/Users/lzkelley/Programs/public/numpy/ in
> > your PYTHONPATH?
> >
> > I would also suggest you add a print(np) line before the crash in
> > nosetester.py. I got something like this (which didn't crash):
> >
> >  >
> '/home/yfeng1/source/numpy/build/testenv/lib64/python2.7/site-packages/numpy/__init__.pyc'>
> >
> > If you see something not starting with 'numpy/build', then it is again
> > pointing at  PYTHONPATH.
> >
> > I hope these helps.
> >
> > Best,
> >
> > - Yu
> >
> > On Sun, Oct 18, 2015 at 1:25 PM, Luke Zoltan Kelley 
> wrote:
> >> Thanks for the help Nathaniel --- but building via `./runtests.py` is
> >> failing in the same way.  Hopefully Numpy-discussion can help me out.
> >>
> >> I'm able to build using `python setup.py build_ext --inplace` but both
> >> trying to run `python setup.py install` or `./runtests.py` leads to the
> >> following error:
> >>
> >> (numpy-py27)daedalus-2:numpy lzkelley$ ./runtests.py
> >> Building, see build.log...
> >> Running from numpy source directory.
> >> Traceback (most recent call last):
> >>  File "setup.py", line 264, in 
> >>setup_package()
> >>  File "setup.py", line 248, in setup_package
> >>from numpy.distutils.core import setup
> >>  File
> "/Users/lzkelley/Programs/public/numpy/numpy/distutils/__init__.py",
> >> line 21, in 
> >>from numpy.testing import Tester
> >>  File "/Users/lzkelley/Programs/public/numpy/numpy/testing/__init__.py",
> >> line 14, in 
> >>from .utils import *
> >>  File "/Users/lzkelley/Programs/public/numpy/numpy/testing/utils.py",
> line
> >> 17, in 
> >>from numpy.core import float32, empty, arange, array_repr, ndarray
> >>  File "/Users/lzkelley/Programs/public/numpy/numpy/core/__init__.py",
> line
> >> 59, in 
> >>test = Tester().test
> >>  File
> "/Users/lzkelley/Programs/public/numpy/numpy/testing/nosetester.py",
> >> line 180, in __init__
> >>if raise_warnings is None and '.dev0' in np.__version__:
> >> AttributeError: 'module' object has no attribute '__version__'
> >>
> >> Build failed!
> >>
> >>
> >> Has anyone seen something like this before?
> >>
> >> Thanks!
> >> Luke
> >>
> >> ___
> >> NumPy-Discussion mailing list
> >> NumPy-Discussion@scipy.org
> >> https://mail.scipy.org/mailman/listinfo/numpy-discussion
> >>
> > ___
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> > NumPy-Discussion@scipy.org
> > https://mail.scipy.org/mailman/listinfo/numpy-discussion
>
> ___
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Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

2015-10-18 Thread Nathaniel Smith

On Sun, Oct 18, 2015 at 5:02 PM, Michael Sarahan  wrote:
> Running tests in the folder might be causing your problem.  If it's trying
> to import numpy, and numpy is a folder in your current folder, sometimes you
> see errors like this.  The confusion is that Python treats folders
> (packages) similarly to modules, and the resolution order sometimes bites
> you.  Try cd'ing to a different folder (importantly, one NOT containing a
> numpy folder!) and run the test command from there.

This isn't the problem -- ./runtests.py is designed to work fine when
run from the root of the numpy checkout.

You might try nuking your checkout and environment and starting over
just in case your earlier attempts left behind some broken detritus
somewhere. 'git clean -xdf' will clear everything out of a git
directory aside from tracked files (so make sure to add any new files
you want to keep first!).

-n

-- 
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Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

2015-10-18 Thread Luke Zoltan Kelley

I tried cleaning the git dir, and trying again.  It still didn't work giving me 
the report:

==
ERROR: test_scripts.test_f2py
--
Traceback (most recent call last):
  File 
"/Users/lzkelley/anaconda/envs/numpy-py27/lib/python2.7/site-packages/nose/case.py",
 line 197, in runTest
self.test(*self.arg)
  File 
"/Users/lzkelley/Programs/public/numpy/build/testenv/lib/python2.7/site-packages/numpy/testing/decorators.py",
 line 146, in skipper_func
return f(*args, **kwargs)
  File 
"/Users/lzkelley/Programs/public/numpy/build/testenv/lib/python2.7/site-packages/numpy/tests/test_scripts.py",
 line 68, in test_f2py
code, stdout, stderr = run_command([f2py_cmd, '-v'])
  File 
"/Users/lzkelley/Programs/public/numpy/build/testenv/lib/python2.7/site-packages/numpy/tests/test_scripts.py",
 line 48, in run_command
proc = Popen(cmd, stdout=PIPE, stderr=PIPE)
  File "/Users/lzkelley/anaconda/envs/numpy-py27/lib/python2.7/subprocess.py", 
line 710, in __init__
errread, errwrite)
  File "/Users/lzkelley/anaconda/envs/numpy-py27/lib/python2.7/subprocess.py", 
line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

--
Ran 6029 tests in 82.132s

FAILED (KNOWNFAIL=6, SKIP=10, errors=2)

f2py itself did seem to work fine from the command-line...

I did get things (seemingly) working, by cleaning the dir again, and then 
running:

python setupegg.py develop --user

This built properly, and now lets me make modification to the source files and 
have them take effect immediately.  This is really all I need for now, but I 
will try to get the `./runtests.py` working for the future.  Perhaps the 
problem is something to do with my previous python environment installed via 
macports...


> On Oct 18, 2015, at 9:04 PM, Nathaniel Smith  wrote:
> 
> On Sun, Oct 18, 2015 at 5:02 PM, Michael Sarahan  wrote:
>> Running tests in the folder might be causing your problem.  If it's trying
>> to import numpy, and numpy is a folder in your current folder, sometimes you
>> see errors like this.  The confusion is that Python treats folders
>> (packages) similarly to modules, and the resolution order sometimes bites
>> you.  Try cd'ing to a different folder (importantly, one NOT containing a
>> numpy folder!) and run the test command from there.
> 
> This isn't the problem -- ./runtests.py is designed to work fine when
> run from the root of the numpy checkout.
> 
> You might try nuking your checkout and environment and starting over
> just in case your earlier attempts left behind some broken detritus
> somewhere. 'git clean -xdf' will clear everything out of a git
> directory aside from tracked files (so make sure to add any new files
> you want to keep first!).
> 
> -n
> 
> -- 
> Nathaniel J. Smith -- http://vorpus.org
> ___
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> https://mail.scipy.org/mailman/listinfo/numpy-discussion

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Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

2015-10-17 Thread Nathaniel Smith

Hi Luke,

For day-to-day development and testing of numpy, I don't bother with
either inplace builds *or* installing it -- I just use the magical
"runtests.py" script that you'll find in the root of your git
checkout.

E.g., to build and then test the (possibly modified) source in your
current checkout, just do:

./runtests.py

That's all. This builds into a hidden directory and then sets up the
correct PYTHONPATH before running the tests etc. -- you don't have to
worry about any of it, it's magic.

There are also lots of options, see ./runtests.py --help. Try adding
-j for multi-core builds, or you can specify arbitrary options to pass
to nose, or you can run it under gdb (there's an example in --help),
or if you just want an interactive shell to futz around in manually
instead of running the test suite then try passing --ipython.

BTW, numpy has its own mailing list at numpy-discussion@scipy.org
(CC'ed), which is where numpy development discussions usually take
place -- this list is more for scipy-the-package itself. There's lots
of overlap in readership between the two lists, but numpy-discussion
will probably give you quicker and more useful answers to questions
like this in general :-)

-n

On Sat, Oct 17, 2015 at 4:03 PM, Luke Zoltan Kelley
 wrote:
> Thanks Nathan, I'll try that.  Both without the inplace build, I'll have to
> rebuild and install everytime I want to test something, right?
>
> On Oct 17, 2015, at 6:42 PM, Nathan Woods  wrote:
>
> My best guess is to nuke and reclone Numpy, then do setup.py install without
> the inplace build. What you're doing seems like it should work, though, so
> I'm not sure what's going on.
>
> Nathan Woods
>
> On Oct 17, 2015, at 3:59 PM, Luke Zoltan Kelley 
> wrote:
>
> When trying to do that is when I get the error I described in the OP.  i.e.
> I get an error when trying to install.
>
>
> On Oct 17, 2015, at 5:57 PM, Andrew Nelson  wrote:
>
> It would get installed into whatever conda environment you had activated.
>
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Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

Re: [Numpy-discussion] [SciPy-Dev] Setting up a dev environment with conda

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