[yt-dev] Issue #1277: Test suite failures under python3.6b1 (yt_analysis/yt)
Nathan Goldbaum
issues-reply at bitbucket.org
Wed Sep 14 18:35:13 PDT 2016
New issue 1277: Test suite failures under python3.6b1
https://bitbucket.org/yt_analysis/yt/issues/1277/test-suite-failures-under-python36b1
Nathan Goldbaum:
Here's the output from running the unit tests on my mac:
```
======================================================================
ERROR: yt.analysis_modules.level_sets.tests.test_clump_finding.test_clump_tree_save
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/analysis_modules/level_sets/tests/test_clump_finding.py", line 104, in test_clump_tree_save
find_clumps(master_clump, c_min, c_max, step)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/analysis_modules/level_sets/clump_handling.py", line 433, in find_clumps
clump.find_children(min_val)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/analysis_modules/level_sets/clump_handling.py", line 162, in find_children
nj, cids = identify_contours(self.data, self.field, min_val, max_val)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/analysis_modules/level_sets/contour_finder.py", line 36, in identify_contours
for (g, node, (sl, dims, gi)) in data_source.tiles.slice_traverse():
File "/Users/goldbaum/Documents/yt-hg-python3/yt/data_objects/data_containers.py", line 1126, in tiles
self._tree = AMRKDTree(self.ds, data_source=self)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/amr_kdtree/amr_kdtree.py", line 181, in __init__
data_source=data_source)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/amr_kdtree/amr_kdtree.py", line 83, in __init__
self.build()
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/amr_kdtree/amr_kdtree.py", line 99, in build
self.add_grids(grids)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/amr_kdtree/amr_kdtree.py", line 90, in add_grids
self.comm_rank, self.comm_size)
File "yt/utilities/lib/amr_kdtools.pyx", line 207, in yt.utilities.lib.amr_kdtools.Node.add_grids (yt/utilities/lib/amr_kdtools.c:5903)
File "yt/utilities/lib/amr_kdtools.pyx", line 244, in yt.utilities.lib.amr_kdtools.Node.add_grids (yt/utilities/lib/amr_kdtools.c:5443)
ValueError: Unexpected format string character: 'q'
======================================================================
ERROR: Failure: RuntimeError (This appears to be a FITS file, but AstroPy is not installed.)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/nose/failure.py", line 39, in runTest
raise self.exc_val.with_traceback(self.tb)
File "/usr/local/lib/python3.6/site-packages/nose/loader.py", line 418, in loadTestsFromName
addr.filename, addr.module)
File "/usr/local/lib/python3.6/site-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/local/lib/python3.6/site-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/usr/local/Cellar/python3/3.6.0b1_1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/imp.py", line 234, in load_module
return load_source(name, filename, file)
File "/usr/local/Cellar/python3/3.6.0b1_1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/imp.py", line 172, in load_source
module = _load(spec)
File "<frozen importlib._bootstrap>", line 675, in _load
File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 676, in exec_module
File "<frozen importlib._bootstrap>", line 205, in _call_with_frames_removed
File "/Users/goldbaum/Documents/yt-hg-python3/yt/frontends/fits/tests/test_outputs.py", line 29, in <module>
@requires_ds(grs)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/answer_testing/framework.py", line 939, in requires_ds
elif not can_run_ds(ds_fn, file_check):
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/answer_testing/framework.py", line 271, in can_run_ds
load(ds_fn)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/convenience.py", line 79, in load
if c._is_valid(*args, **kwargs): candidates.append(n)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/frontends/fits/data_structures.py", line 645, in _is_valid
raise RuntimeError("This appears to be a FITS file, but AstroPy is not installed.")
RuntimeError: This appears to be a FITS file, but AstroPy is not installed.
======================================================================
ERROR: Failure: ValueError (Unexpected format string character: 'q')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/nose/failure.py", line 39, in runTest
raise self.exc_val.with_traceback(self.tb)
File "/usr/local/lib/python3.6/site-packages/nose/loader.py", line 252, in generate
for test in g():
File "/Users/goldbaum/Documents/yt-hg-python3/yt/geometry/tests/test_grid_container.py", line 123, in test_grid_arrays_view
grid_arr = tree.grid_arrays
File "yt/geometry/grid_container.pyx", line 130, in yt.geometry.grid_container.GridTree.grid_arrays.__get__ (yt/geometry/grid_container.c:4659)
ValueError: Unexpected format string character: 'q'
======================================================================
ERROR: yt.utilities.lib.tests.test_bounding_volume_hierarchy.test_bounding_volume_hierarchy
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/lib/tests/test_bounding_volume_hierarchy.py", line 30, in test_bounding_volume_hierarchy
ds = yt.load(fn)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/convenience.py", line 98, in load
raise YTOutputNotIdentified(args, kwargs)
yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('/Users/goldbaum/Documents/test/MOOSE_sample_data/out.e-s010',) {}, but could not load!
======================================================================
ERROR: yt.utilities.tests.test_amr_kdtree.test_amr_kdtree_set_fields
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/tests/test_amr_kdtree.py", line 69, in test_amr_kdtree_set_fields
dd.tiles.set_fields(fields, [True, True], False)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/data_objects/data_containers.py", line 1126, in tiles
self._tree = AMRKDTree(self.ds, data_source=self)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/amr_kdtree/amr_kdtree.py", line 181, in __init__
data_source=data_source)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/amr_kdtree/amr_kdtree.py", line 83, in __init__
self.build()
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/amr_kdtree/amr_kdtree.py", line 99, in build
self.add_grids(grids)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/amr_kdtree/amr_kdtree.py", line 90, in add_grids
self.comm_rank, self.comm_size)
File "yt/utilities/lib/amr_kdtools.pyx", line 207, in yt.utilities.lib.amr_kdtools.Node.add_grids (yt/utilities/lib/amr_kdtools.c:5903)
File "yt/utilities/lib/amr_kdtools.pyx", line 259, in yt.utilities.lib.amr_kdtools.Node.add_grids (yt/utilities/lib/amr_kdtools.c:5651)
ValueError: Unexpected format string character: 'q'
======================================================================
ERROR: Failure: ModuleNotFoundError (No module named 'mock')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/nose/failure.py", line 39, in runTest
raise self.exc_val.with_traceback(self.tb)
File "/usr/local/lib/python3.6/site-packages/nose/loader.py", line 418, in loadTestsFromName
addr.filename, addr.module)
File "/usr/local/lib/python3.6/site-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/local/lib/python3.6/site-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/usr/local/Cellar/python3/3.6.0b1_1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/imp.py", line 234, in load_module
return load_source(name, filename, file)
File "/usr/local/Cellar/python3/3.6.0b1_1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/imp.py", line 172, in load_source
module = _load(spec)
File "<frozen importlib._bootstrap>", line 675, in _load
File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 676, in exec_module
File "<frozen importlib._bootstrap>", line 205, in _call_with_frames_removed
File "/Users/goldbaum/Documents/yt-hg-python3/yt/utilities/tests/test_config.py", line 11, in <module>
import mock
ModuleNotFoundError: No module named 'mock'
======================================================================
FAIL: yt.analysis_modules.level_sets.tests.test_clump_finding.test_clump_finding
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/Users/goldbaum/Documents/yt-hg-python3/yt/analysis_modules/level_sets/tests/test_clump_finding.py", line 69, in test_clump_finding
assert_equal(len(master_clump.children), 2)
File "/usr/local/lib/python3.6/site-packages/numpy/testing/utils.py", line 379, in assert_equal
raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: 0
DESIRED: 2
>> raise AssertionError('\nItems are not equal:\n ACTUAL: 0\n DESIRED: 2')
----------------------------------------------------------------------
Ran 8511 tests in 12666.888s
FAILED (errors=6, failures=1)
```
Most of these have to do with the 'q' format code (corresponding to the struct format 'q', or long long, see https://docs.python.org/2/library/struct.html#format-characters.
The other one is due to an issue with the mock module that is fixed in PR 2377.
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