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

[Nathaniel Smith]

Mixing wheels and conda packages can cause some problems over time because
of pip and conda getting confused about what's installed. But if you made a
conda env, and then did a pip install, and that's all you've done, then
that should work fine AFAIK.

And the scipy wheels should be self contained and work correctly in any
environment, including a conda env where numpy is using mkl or a different
version of openblas.

I don't know what's going wrong in your case, but I can at least say that
as far as I know, it *should* work and you're hitting a genuine bug.

On Thu, Apr 19, 2018, 10:17 Mark Alexander Mikofski <mikofski at berkeley.edu>
wrote:

> 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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>
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