test_Headbanging_Median_Rate fails with Python 3.6

[sebastic]

As reported by Adrian Bunk in Debian Bug #867549:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pysal.html

...
I: pybuild base:184: cd /build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --exclude test_DistanceBand_arc  --exclude-dir=pysal/contrib --exclude-dir pysal/network
Trying `CDLL(libgeos_c.so.1)`
Library path: 'libgeos_c.so.1'
DLL: <CDLL 'libgeos_c.so.1', handle 374a360 at 0x7fc9b3402f98>
Trying `CDLL(libc.so.6)`
Library path: 'libc.so.6'
DLL: <CDLL 'libc.so.6', handle 7fc9c85c14e0 at 0x7fc9bb88bc18>
.........../build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/cg/segmentLocator.py:117: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if self._hashKeys == None:
...............................................................................................................................................................S....../build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/weights/weights.py:189: UserWarning: There are 3 disconnected observations
  warnings.warn("There are %d disconnected observations" % ni)
/build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/weights/weights.py:190: UserWarning: Island ids: 6, 8, 11
  warnings.warn("Island ids: %s" % ', '.join(str(island) for island in self.islands))
........./build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/core/IOHandlers/gwt.py:148: RuntimeWarning: DBF relating to GWT was not found, proceeding with unordered string ids.
  warn("DBF relating to GWT was not found, proceeding with unordered string ids.", RuntimeWarning)
......................../build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/weights/weights.py:189: UserWarning: There are 7 disconnected observations
  warnings.warn("There are %d disconnected observations" % ni)
/build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/weights/weights.py:190: UserWarning: Island ids: 5, 9, 10, 11, 12, 14, 15
  warnings.warn("Island ids: %s" % ', '.join(str(island) for island in self.islands))
........../build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/core/Tables.py:215: UserWarning: Encountered the following error in attempting to read the shapefile /build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/examples/us_income/usjoin.shp. Proceeding with read, but the error will be reproduced below:
 [Errno 2] No such file or directory: '/build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/examples/us_income/usjoin.shp'
  ' {}'.format(self.dataPath[:-3]+'shp', e))
...............................................................................FF..................................../build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/esda/moran.py:876: RuntimeWarning: invalid value encountered in greater
  zp = self.z > 0
/build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/esda/moran.py:877: RuntimeWarning: invalid value encountered in greater
  lp = zl > 0
/build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/esda/moran.py:826: RuntimeWarning: invalid value encountered in greater_equal
  above = sim >= self.Is
/usr/lib/python3/dist-packages/scipy/stats/_distn_infrastructure.py:875: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/usr/lib/python3/dist-packages/scipy/stats/_distn_infrastructure.py:875: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/usr/lib/python3/dist-packages/scipy/stats/_distn_infrastructure.py:1731: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
................................
======================================================================
FAIL: test_Headbanging_Median_Rate (pysal.esda.tests.test_smoothing.TestHB)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/esda/tests/test_smoothing.py", line 301, in test_Headbanging_Median_Rate
    np.testing.assert_array_almost_equal(self.sids_hb_rr5, sids_hb_r.r[:5])
  File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 979, in assert_array_almost_equal
    precision=decimal)
  File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 796, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

(mismatch 80.0%)
 x: array([ 0.000756,  0.      ,  0.000829,  0.001832,  0.004989])
 y: array([ 0.000756,  0.000788,  0.000788,  0.001699,  0.004821])

======================================================================
FAIL: test_Headbanging_Median_Rate_tabular (pysal.esda.tests.test_smoothing.TestHB)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build/pysal/esda/tests/test_smoothing.py", line 315, in test_Headbanging_Median_Rate_tabular
    np.testing.assert_array_almost_equal(self.sids_hb_rr5, sids_hb_r.r[:5])
  File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 979, in assert_array_almost_equal
    precision=decimal)
  File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 796, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

(mismatch 80.0%)
 x: array([ 0.000756,  0.      ,  0.000829,  0.001832,  0.004989])
 y: array([ 0.000756,  0.000788,  0.000788,  0.001699,  0.004821])

----------------------------------------------------------------------
Ran 369 tests in 94.655s

FAILED (SKIP=1, failures=2)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/1st/pysal-1.13.0/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --exclude test_DistanceBand_arc  --exclude-dir=pysal/contrib --exclude-dir pysal/network
dh_auto_test: pybuild --test -i python{version} -p 3.6 3.5 returned exit code 13
debian/rules:18: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25

The Debian package already includes the fix for #896.

• Platform information:

>>> import os; print(os.name, os.sys.platform);print(os.uname())
('posix', 'linux2')
('Linux', 'osiris', '4.9.0-3-amd64', '#1 SMP Debian 4.9.30-2 (2017-06-12)', 'x86_64')

• Python versions

>>> import sys; print(sys.version)
2.7.13 (default, Jan 19 2017, 14:48:08) 
[GCC 6.3.0 20170118]

>>> import sys; print(sys.version)
3.5.3+ (default, Jun  7 2017, 23:23:48) 
[GCC 6.3.0 20170516]

>>> import sys; print(sys.version)
3.6.2rc1 (default, Jun 20 2017, 12:51:36) 
[GCC 6.3.0 20170516]

• SciPy version:

>>> import scpiy; print(scipy.__version__)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named scpiy
>>> import scipy; print(scipy.__version__)
0.18.1

• NumPy version:

>>> import numpy; print(numpy.__version__)
1.12.1

[sjsrey]

Closed with #953