[Bug 235499] science/py-abipy

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=235499

            Bug ID: 235499
           Summary: science/py-abipy
           Product: Ports & Packages
           Version: Latest
          Hardware: i386
                OS: Any
            Status: New
          Severity: Affects Only Me
          Priority: ---
         Component: Individual Port(s)
          Assignee: yuri at freebsd.org
          Reporter: rmason at mun.ca
             Flags: maintainer-feedback?(yuri at freebsd.org)
          Assignee: yuri at freebsd.org

Running abiview as per the abinit RF2 tutorial produces an error:

abiview.py-3.6 ddb trf2_3_DDB -sns=talk
Traceback (most recent call last):
  File "/usr/local/bin/abiview.py-3.6", line 15, in <module>
    from abipy import abilab
  File "/usr/local/lib/python3.6/site-packages/abipy/abilab.py", line 43, in
<module>
    from abipy.electrons.ebands import (ElectronBands, ElectronBandsPlotter,
ElectronDos, ElectronDosPlotter,
  File "/usr/local/lib/python3.6/site-packages/abipy/electrons/__init__.py",
line 3, in <module>
    from .gsr import *
  File "/usr/local/lib/python3.6/site-packages/abipy/electrons/gsr.py", line
20, in <module>
    from abipy.tools.tensors import Stress
  File "/usr/local/lib/python3.6/site-packages/abipy/tools/tensors.py", line
10, in <module>
    from pymatgen.analysis.elasticity.tensors import Tensor, SquareTensor
  File
"/usr/local/lib/python3.6/site-packages/pymatgen/analysis/elasticity/__init__.py",
line 5, in <module>
    from .elastic import *
  File
"/usr/local/lib/python3.6/site-packages/pymatgen/analysis/elasticity/elastic.py",
line 14, in <module>
    from scipy.integrate import quad
  File "/usr/local/lib/python3.6/site-packages/scipy/integrate/__init__.py",
line 93, in <module>
    from ._bvp import solve_bvp
  File "/usr/local/lib/python3.6/site-packages/scipy/integrate/_bvp.py", line
11, in <module>
    from scipy.optimize import OptimizeResult
  File "/usr/local/lib/python3.6/site-packages/scipy/optimize/__init__.py",
line 271, in <module>
    from ._minimize import *
  File "/usr/local/lib/python3.6/site-packages/scipy/optimize/_minimize.py",
line 32, in <module>
    from ._trustregion_constr import _minimize_trustregion_constr
  File
"/usr/local/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/__init__.py",
line 4, in <module>
    from .minimize_trustregion_constr import _minimize_trustregion_constr
  File
"/usr/local/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py",
line 10, in <module>
    from .equality_constrained_sqp import equality_constrained_sqp
  File
"/usr/local/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/equality_constrained_sqp.py",
line 5, in <module>
    from .projections import projections
  File
"/usr/local/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/projections.py",
line 9, in <module>
    from sksparse.cholmod import cholesky_AAt
  File "sksparse/cholmod.pyx", line 240, in init sksparse.cholmod
AssertionError

The same error can be triggered thus:
Python 3.6.8 (default, Jan  3 2019, 20:20:29) 
[GCC 4.2.1 Compatible FreeBSD Clang 6.0.0 (tags/RELEASE_600/final 326565)] on
freebsd11
Type "help", "copyright", "credits" or "license" for more information.
>>> import spglib
>>> import pymatgen
>>> from abipy import abilab

I have tested py27-abinit with the same result.  I have tested abipy installed
from both the FreeBSD repository and from my own poudriere repository.  In each
case the same error occurs.

This is my first FreeBSD bug report: please accept my apology if it is
incomplete in some way.

Thanks,
Roger

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