[SciPy-Dev] SciPy in conda-forge env on Windows

[Mark Alexander Mikofski]

Hi,

Sorry if this question is redundant. I checked the "install" page in the
SciPy docs, and couldn't find any mention of conda-forge.

Can SciPy from pip (scipy-1.0.1-cp36-none-win_amd64.whl) be used with the
numpy-feedstock from conda-forge? When I run the tests for scipy, the fail
and hang after "scipy\linalg\tests\test_basic.py".

The reason I thought this might work is because they both use a variant of
OpenBLAS, but perhaps they are not compatible? I can see that NumPy
openblas.dll is in miniconda/envs/<envname>/Library/bin (31,053KB) where as
the SciPy openblas.dll is in site-packages/scipy/extra-dll (41,762KB) and
the name is vendorized with a long alphanumeric string.

Unfortunately if I try to use conda to install SciPy, conda uses the
default "anaconda" channel, because win_amd64 conda-forge scipy-feedstock
has been disabled, and when I run the tests using this mix of
conda-forge:numpy and anaconda:scipy, I get the same failure at
"scipy\linalg\tests\test_basic.py",
which I would expect because the anaconda:scipy uses Intel-MKL not
OpenBLAS, and I think these libraries need to be compatible for scipy to
work, right?

The test that fails is "TestDet.test_random()"

scipy/linalg/tests/test_basic.py::TestDet::test_random FAILED [ 54%]

this is the pytest traceback:

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-3-ff0509141d7f> in <module>()
----> 1 test_det.test_random()

~\AppData\Local\Continuum\miniconda3\envs\forge\lib\site-packages\scipy\linalg\tests\test_basic.py
in test_random(self)
    907             d1 = det(a)
    908             d2 = basic_det(a)
--> 909             assert_almost_equal(d1, d2)
    910
    911     def test_random_complex(self):

~\AppData\Local\Continuum\miniconda3\envs\forge\lib\site-packages\numpy\testing\nose_tools\utils.py
in assert_almost_equal(actual, desired, decimal, err_msg, verbose)
    579         pass
    580     if abs(desired - actual) >= 1.5 * 10.0**(-decimal):
--> 581         raise AssertionError(_build_err_msg())
    582
    583

AssertionError:
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.001303440758814572
 DESIRED: -0.09307217461347188

Then the next test hangs for several minute, and I have to kill the process.

scipy/linalg/tests/test_basic.py::TestDet::test_random_complex

It also hangs when I call it directly from an interpreter.

If I use just pip to install both numpy
(numpy-1.14.2-cp36-none-win_amd64.whl) and scipy (
scipy-1.0.1-cp36-none-win_amd64.whl) then all of the tests pass. And now I
can see the vendorized version of openBLAS for numpy in
site-packags/numpy/.libs (41762KB) matches the openBLAS in scipy/extra-dll,
the vendor alpha-numeric string is also the same: "
BNVRK7633HSX7YVO2TADGR4A5KEKXJAW"

Maybe this is very basic, and I shouldn't be asking. But I don't understand
how to use conda-forge then with SciPy and NumPy on Windows. It seems like
users should only use all pip or only the default "anaconda" channel. Or if
using conda-forge on window, then only use NumPy without SciPy, but that
also means other packages like statsmodels are out too. Also maybe this is
a question for conda-forge and not scipy-dev. Again, so sorry if my
question is out of place.

I'm also sorry if this is received poorly. I am so happy and very grateful
for all of the volunteer work that has gone into making SciPy and NumPy
work on Windows. I remember the old days when I had to refer people to
cgohlke's website. If there is anything I can do to help, I can try. I will
take a look at reactivating the conda-forge build for win_amd64, I believe
that would solve the problem. Also I will bring up the issue of dependency
clashes with conda-forge as well.

Thanks,
Mark

-- 
Mark Mikofski, PhD (2005)
*Fiat Lux*
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