[pysal-dev] Linux Test suite failures

[Philip Stephens]

See attached file for test-suite results, including 3 failures, some of which are linked to scipy but in different modules than previously, I think.

--
Philip Stephens
Research Analyst
GeoDa Center for Geospatial Analysis and Computation
Arizona State University
philip....@asu.edu

"Please do not send me Microsoft Office/Apple iWork documents. Send OpenDocument instead! http://fsf.org/campaigns/opendocument/"

[Xinyue Ye]

I had the same problem. have you fixed it?

--
Xinyue Ye, Ph.D., Assistant Professor
Center for Regional Development (Department of Commerce EDA University Center)
School of Earth, Environment and Society, Bowling Green State University
Bowling Green, OH 43403 Phone: (419)372-9125
http://personal.bgsu.edu/~xye/

[Charles R. Schmidt]

It probably won't get fixed until someone creates an issue for the
problem. Could this be related to issue 52?

http://code.google.com/p/pysal/issues/

[Xinyue Ye]

$ python tests.py
.............................................................F.............FF....................................................................................................................................
======================================================================
FAIL: Doctest: pysal.weights.Distance.DistanceBand
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 2112, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for pysal.weights.Distance.DistanceBand
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 316, in DistanceBand

----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 351, in pysal.weights.Distance.DistanceBand
Failed example:
w=DistanceBand(points,threshold=11.2,binary=False)
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest pysal.weights.Distance.DistanceBand[4]>", line 1,
in <module>
w=DistanceBand(points,threshold=11.2,binary=False)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 381, in __init__
neighbors, weights = self._distance_to_W(ids)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 411, in _distance_to_W
self.dmat=self.kd.sparse_distance_matrix(self.kd,max_distance=self.threshold)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 628, in sparse_distance_matrix
other.tree, Rectangle(other.maxes, other.mins))
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 611, in traverse
result[i,j] = d
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/sparse/dok.py",
line 222, in __setitem__
del self[(i,j)]
KeyError: (0, 0)
----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 352, in pysal.weights.Distance.DistanceBand
Failed example:
w.weights[0]
Expected:
[0.10000000000000001, 0.089442719099991588]
Got:
[1, 1]
----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 360, in pysal.weights.Distance.DistanceBand
Failed example:
w=DistanceBand(points,threshold=11.2,binary=False,alpha=-2.)
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest pysal.weights.Distance.DistanceBand[7]>", line 1,
in <module>
w=DistanceBand(points,threshold=11.2,binary=False,alpha=-2.)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 381, in __init__
neighbors, weights = self._distance_to_W(ids)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 411, in _distance_to_W
self.dmat=self.kd.sparse_distance_matrix(self.kd,max_distance=self.threshold)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 628, in sparse_distance_matrix
other.tree, Rectangle(other.maxes, other.mins))
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 611, in traverse
result[i,j] = d
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/sparse/dok.py",
line 222, in __setitem__
del self[(i,j)]
KeyError: (0, 0)
----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 361, in pysal.weights.Distance.DistanceBand
Failed example:
w.weights[0]
Expected:
[0.01, 0.0079999999999999984]
Got:
[1, 1]

======================================================================
FAIL: Doctest: pysal.weights.user.threshold_continuousW_from_array
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 2112, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for
pysal.weights.user.threshold_continuousW_from_array
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 323, in threshold_continuousW_from_array

----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 358, in pysal.weights.user.threshold_continuousW_from_array
Failed example:
wid=threshold_continuousW_from_array(points,11.2)
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest
pysal.weights.user.threshold_continuousW_from_array[1]>", line 1, in
<module>
wid=threshold_continuousW_from_array(points,11.2)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 371, in threshold_continuousW_from_array
w=DistanceBand(array,threshold=threshold,p=p,alpha=alpha,binary=False)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 381, in __init__
neighbors, weights = self._distance_to_W(ids)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 411, in _distance_to_W
self.dmat=self.kd.sparse_distance_matrix(self.kd,max_distance=self.threshold)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 628, in sparse_distance_matrix
other.tree, Rectangle(other.maxes, other.mins))
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 611, in traverse
result[i,j] = d
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/sparse/dok.py",
line 222, in __setitem__
del self[(i,j)]
KeyError: (0, 0)
----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 359, in pysal.weights.user.threshold_continuousW_from_array
Failed example:
wid.weights[0]
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest
pysal.weights.user.threshold_continuousW_from_array[2]>", line 1, in
<module>
wid.weights[0]
NameError: name 'wid' is not defined
----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 364, in pysal.weights.user.threshold_continuousW_from_array
Failed example:
wid2=threshold_continuousW_from_array(points,11.2,alpha=-2.0)
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest
pysal.weights.user.threshold_continuousW_from_array[3]>", line 1, in
<module>
wid2=threshold_continuousW_from_array(points,11.2,alpha=-2.0)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 371, in threshold_continuousW_from_array
w=DistanceBand(array,threshold=threshold,p=p,alpha=alpha,binary=False)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 381, in __init__
neighbors, weights = self._distance_to_W(ids)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 411, in _distance_to_W
self.dmat=self.kd.sparse_distance_matrix(self.kd,max_distance=self.threshold)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 628, in sparse_distance_matrix
other.tree, Rectangle(other.maxes, other.mins))
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 611, in traverse
result[i,j] = d
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/sparse/dok.py",
line 222, in __setitem__
del self[(i,j)]
KeyError: (0, 0)
----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 365, in pysal.weights.user.threshold_continuousW_from_array
Failed example:
wid2.weights[0]
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest
pysal.weights.user.threshold_continuousW_from_array[4]>", line 1, in
<module>
wid2.weights[0]
NameError: name 'wid2' is not defined

======================================================================
FAIL: Doctest: pysal.weights.user.threshold_continuousW_from_shapefile
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 2112, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for
pysal.weights.user.threshold_continuousW_from_shapefile
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 375, in threshold_continuousW_from_shapefile

----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 406, in pysal.weights.user.threshold_continuousW_from_shapefile
Failed example:
w = threshold_continuousW_from_shapefile('../examples/columbus.shp',0.62,idVariable="POLYID")
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest
pysal.weights.user.threshold_continuousW_from_shapefile[0]>", line 1,
in <module>
w = threshold_continuousW_from_shapefile('../examples/columbus.shp',0.62,idVariable="POLYID")
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 413, in threshold_continuousW_from_shapefile
return DistanceBand(data,threshold=threshold,p=p,alpha=alpha,binary=False,ids=ids)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 381, in __init__
neighbors, weights = self._distance_to_W(ids)
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/Distance.py",
line 411, in _distance_to_W
self.dmat=self.kd.sparse_distance_matrix(self.kd,max_distance=self.threshold)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 628, in sparse_distance_matrix
other.tree, Rectangle(other.maxes, other.mins))
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 623, in traverse
traverse(node1.less,less1,node2.less,less2)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 623, in traverse
traverse(node1.less,less1,node2.less,less2)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/spatial/kdtree.py",
line 611, in traverse
result[i,j] = d
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/sparse/dok.py",
line 222, in __setitem__
del self[(i,j)]
KeyError: (17, 17)
----------------------------------------------------------------------
File "/Users/xinyueye/pysal/xiny...@gmail.com/trunk/pysal/weights/user.py",
line 407, in pysal.weights.user.threshold_continuousW_from_shapefile
Failed example:
w.weights[1]
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest
pysal.weights.user.threshold_continuousW_from_shapefile[1]>", line 1,
in <module>
w.weights[1]
NameError: name 'w' is not defined