[yt-dev] Issue #1162: Test failures under numpy 1.11 beta (yt_analysis/yt)
Nathan Goldbaum
issues-reply at bitbucket.org
Tue Jan 26 13:29:29 PST 2016
New issue 1162: Test failures under numpy 1.11 beta
https://bitbucket.org/yt_analysis/yt/issues/1162/test-failures-under-numpy-111-beta
Nathan Goldbaum:
Currently the following test failures are generated under the NumPy 1.11.0b1 release:
They all seem to be variations on using a float as an index in different places.
```
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/tests/test_fields.py", line 211, in test_add_smoothed_particle_field
ret = ad[fn]
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__
self.get_data(f)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data
self._generate_fields(fields_to_generate)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields
fd = self._generate_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field
tr = self._generate_fluid_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 323, in _generate_fluid_field
rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 343, in _generate_spatial_fluid
ind += o.select(self.selector, self[field], rv, ind)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__
self.get_data(f)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data
self._generate_fields(fields_to_generate)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields
fd = self._generate_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field
tr = self._generate_fluid_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field
rv = finfo(gen_obj)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 182, in __call__
dd = self._function(self, data)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/particle_fields.py", line 792, in _vol_weight
smooth_cutoff = data["index","cell_volume"]**(1./3)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/octree_subset.py", line 74, in __getitem__
tr = super(OctreeSubset, self).__getitem__(key)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__
self.get_data(f)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data
self._generate_fields(fields_to_generate)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields
fd = self._generate_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field
tr = self._generate_fluid_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field
rv = finfo(gen_obj)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 182, in __call__
dd = self._function(self, data)
File "/Users/goldbaum/Documents/yt-hg/yt/geometry/coordinates/coordinate_handler.py", line 38, in _dds
return data._reshape_vals(rv)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/octree_subset.py", line 107, in _reshape_vals
arr = arr.reshape(new_shape, order="F")
TypeError: 'float' object cannot be interpreted as an index
======================================================================
ERROR: Failure: TypeError ('float' object cannot be interpreted as an index)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 251, in generate
for test in g():
File "/Users/goldbaum/Documents/yt-hg/yt/frontends/sdf/tests/test_outputs.py", line 47, in test_scivis
ProjectionPlot(ds, "z", _fields)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 1410, in __init__
field_parameters = field_parameters, method = method)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 258, in __init__
self.get_data(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 332, in get_data
self._handle_chunk(chunk, fields, tree)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 432, in _handle_chunk
d = chunk[field] * dl
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__
self.get_data(f)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data
self._generate_fields(fields_to_generate)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields
fd = self._generate_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field
tr = self._generate_fluid_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 323, in _generate_fluid_field
rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 343, in _generate_spatial_fluid
ind += o.select(self.selector, self[field], rv, ind)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__
self.get_data(f)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data
self._generate_fields(fields_to_generate)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields
fd = self._generate_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field
tr = self._generate_fluid_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field
rv = finfo(gen_obj)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 182, in __call__
dd = self._function(self, data)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/particle_fields.py", line 141, in particle_cic
d /= data["index", "cell_volume"]
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/octree_subset.py", line 74, in __getitem__
tr = super(OctreeSubset, self).__getitem__(key)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__
self.get_data(f)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data
self._generate_fields(fields_to_generate)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields
fd = self._generate_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field
tr = self._generate_fluid_field(field)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field
rv = finfo(gen_obj)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 182, in __call__
dd = self._function(self, data)
File "/Users/goldbaum/Documents/yt-hg/yt/geometry/coordinates/coordinate_handler.py", line 38, in _dds
return data._reshape_vals(rv)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/octree_subset.py", line 107, in _reshape_vals
arr = arr.reshape(new_shape, order="F")
TypeError: 'float' object cannot be interpreted as an index
======================================================================
ERROR: Failure: TypeError (an integer is required)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 251, in generate
for test in g():
File "/Users/goldbaum/Documents/yt-hg/yt/frontends/stream/tests/test_stream_particles.py", line 30, in test_stream_particles
amr0 = refine_amr(ug0, rc, fo, 3)
File "/Users/goldbaum/Documents/yt-hg/yt/frontends/stream/data_structures.py", line 956, in refine_amr
nsg = fg.find_subgrids()
File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 54, in find_subgrids
psg = ProtoSubgrid(self.flagged, self.left_index, self.dimensions)
File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 88, in __init__
self.compute_signatures()
File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 95, in compute_signatures
self.sigs.append(self.flagged.sum(axis=d1).sum(axis=d2))
File "/Users/goldbaum/Documents/numpy/numpy/core/_methods.py", line 32, in _sum
return umr_sum(a, axis, dtype, out, keepdims)
TypeError: an integer is required
======================================================================
ERROR: Failure: TypeError ('float' object cannot be interpreted as an index)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 251, in generate
for test in g():
File "/Users/goldbaum/Documents/yt-hg/yt/geometry/tests/test_neighbor_search.py", line 28, in test_neighbor_search
ds = fake_particle_ds(npart = 16**3)
File "/Users/goldbaum/Documents/yt-hg/yt/testing.py", line 265, in fake_particle_ds
v = np.random.normal(npart, 0.5, 0.25)
File "mtrand.pyx", line 1897, in mtrand.RandomState.normal (numpy/random/mtrand/mtrand.c:18066)
File "mtrand.pyx", line 234, in mtrand.cont2_array_sc (numpy/random/mtrand/mtrand.c:3089)
TypeError: 'float' object cannot be interpreted as an index
======================================================================
ERROR: Failure: TypeError (an integer is required)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 251, in generate
for test in g():
File "/Users/goldbaum/Documents/yt-hg/yt/utilities/tests/test_particle_generator.py", line 27, in test_particle_generator
ds = refine_amr(ug, rc, fo, 3)
File "/Users/goldbaum/Documents/yt-hg/yt/frontends/stream/data_structures.py", line 956, in refine_amr
nsg = fg.find_subgrids()
File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 54, in find_subgrids
psg = ProtoSubgrid(self.flagged, self.left_index, self.dimensions)
File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 88, in __init__
self.compute_signatures()
File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 95, in compute_signatures
self.sigs.append(self.flagged.sum(axis=d1).sum(axis=d2))
File "/Users/goldbaum/Documents/numpy/numpy/core/_methods.py", line 32, in _sum
return umr_sum(a, axis, dtype, out, keepdims)
TypeError: an integer is required
======================================================================
ERROR: test_stereoperspective_lens (yt.visualization.volume_rendering.tests.test_lenses.LensTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/tests/test_lenses.py", line 70, in test_stereoperspective_lens
sc.render()
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/scene.py", line 163, in render
bmp = self.composite(camera=camera)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/scene.py", line 288, in composite
im = source.render(camera, zbuffer=opaque)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/render_source.py", line 256, in render
self.set_sampler(camera)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/render_source.py", line 228, in set_sampler
sampler = new_volume_render_sampler(camera, self)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/utils.py", line 35, in new_volume_render_sampler
params = camera._get_sampler_params(render_source)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/camera.py", line 197, in _get_sampler_params
lens_params = self.lens._get_sampler_params(self, render_source)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/lens.py", line 287, in _get_sampler_params
camera, -self.disparity)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/lens.py", line 337, in _get_positions_vectors
dtype='float64', order='C')
TypeError: 'numpy.float64' object cannot be interpreted as an index
======================================================================
ERROR: test_stereospherical_lens (yt.visualization.volume_rendering.tests.test_lenses.LensTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/tests/test_lenses.py", line 130, in test_stereospherical_lens
sc.render()
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/scene.py", line 163, in render
bmp = self.composite(camera=camera)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/scene.py", line 288, in composite
im = source.render(camera, zbuffer=opaque)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/render_source.py", line 256, in render
self.set_sampler(camera)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/render_source.py", line 228, in set_sampler
sampler = new_volume_render_sampler(camera, self)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/utils.py", line 35, in new_volume_render_sampler
params = camera._get_sampler_params(render_source)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/camera.py", line 197, in _get_sampler_params
lens_params = self.lens._get_sampler_params(self, render_source)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/lens.py", line 691, in _get_sampler_params
dtype='float64', order='C')
TypeError: 'numpy.float64' object cannot be interpreted as an index
======================================================================
ERROR: test suite for <class 'yt.visualization.tests.test_particle_plot.TestParticlePhasePlotSave'>
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 209, in run
self.setUp()
File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp
self.setupContext(ancestor)
File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext
try_run(context, names)
File "/usr/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
return func()
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/tests/test_particle_plot.py", line 139, in setUpClass
test_ds = fake_particle_ds()
File "/Users/goldbaum/Documents/yt-hg/yt/testing.py", line 265, in fake_particle_ds
v = np.random.normal(npart, 0.5, 0.25)
File "mtrand.pyx", line 1897, in mtrand.RandomState.normal (numpy/random/mtrand/mtrand.c:18066)
File "mtrand.pyx", line 234, in mtrand.cont2_array_sc (numpy/random/mtrand/mtrand.c:3089)
TypeError: 'float' object cannot be interpreted as an index
======================================================================
ERROR: test suite for <class 'yt.visualization.tests.test_particle_plot.TestParticleProjectionPlotSave'>
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 209, in run
self.setUp()
File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp
self.setupContext(ancestor)
File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext
try_run(context, names)
File "/usr/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
return func()
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/tests/test_particle_plot.py", line 192, in setUpClass
test_ds = fake_particle_ds()
File "/Users/goldbaum/Documents/yt-hg/yt/testing.py", line 265, in fake_particle_ds
v = np.random.normal(npart, 0.5, 0.25)
File "mtrand.pyx", line 1897, in mtrand.RandomState.normal (numpy/random/mtrand/mtrand.c:18066)
File "mtrand.pyx", line 234, in mtrand.cont2_array_sc (numpy/random/mtrand/mtrand.c:3089)
TypeError: 'float' object cannot be interpreted as an index
```
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