Comments (8)
clbarnes
commented on August 24, 2024
I ran the tests with nose and got this trace:
.............F.F......../usr/local/lib/python3.4/dist-packages/bctpy-0.4.0-py3.4.egg/bct/bct.py:187: RuntimeWarning: invalid value encountered in true_divide
pnm=Snm/(np.tile(S,(m,1)).T)
..EE.....F..F...../usr/local/lib/python3.4/dist-packages/bctpy-0.4.0-py3.4.egg/bct/bct.py:689: RuntimeWarning: invalid value encountered in true_divide
P=np.ones((n,))-Sc2/np.square(S)
../usr/local/lib/python3.4/dist-packages/bctpy-0.4.0-py3.4.egg/bct/bct.py:2876: RuntimeWarning: invalid value encountered in double_scalars
dc = (mc - min_mc) / (nc*(nc-1)/2 - min_mc) #community density
E
======================================================================
ERROR: modularity_tests.test_modularity_louvain_und
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.4/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/cbarnes/code/lib/bctpy/test/modularity_tests.py", line 17, in test_modularity_louvain_und
_,q = bct.modularity_louvain_und(x, seed=seed)
File "/usr/local/lib/python3.4/dist-packages/bctpy-0.4.0-py3.4.egg/bct/bct.py", line 3581, in modularity_louvain_und
ci[h][np.where(ci[h-1]==i+1)]=mi #assign new modules
NameError: name 'mi' is not defined
======================================================================
ERROR: modularity_tests.test_modularity_finetune_und
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.4/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/cbarnes/code/lib/bctpy/test/modularity_tests.py", line 50, in test_modularity_finetune_und
ci,oq = bct.modularity_louvain_und(x, seed=seed)
File "/usr/local/lib/python3.4/dist-packages/bctpy-0.4.0-py3.4.egg/bct/bct.py", line 3581, in modularity_louvain_und
ci[h][np.where(ci[h-1]==i+1)]=mi #assign new modules
NameError: name 'mi' is not defined
======================================================================
ERROR: very_long_tests.test_link_communities
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.4/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/cbarnes/code/lib/bctpy/test/very_long_tests.py", line 8, in test_link_communities
M = bct.link_communities(x)
File "/usr/local/lib/python3.4/dist-packages/bctpy-0.4.0-py3.4.egg/bct/bct.py", line 2892, in link_communities
u1,u2 = np.where( ES[np.ix_(U,U)]==np.max(ES[np.ix_(U,U)]) )
File "/usr/local/lib/python3.4/dist-packages/bctpy-0.4.0-py3.4.egg/bct/bct.py", line 2892, in link_communities
u1,u2 = np.where( ES[np.ix_(U,U)]==np.max(ES[np.ix_(U,U)]) )
File "/usr/lib/python3.4/bdb.py", line 48, in trace_dispatch
return self.dispatch_line(frame)
File "/usr/lib/python3.4/bdb.py", line 66, in dispatch_line
self.user_line(frame)
File "/usr/lib/python3.4/pdb.py", line 259, in user_line
self.interaction(frame, None)
File "/usr/lib/python3.4/pdb.py", line 346, in interaction
self._cmdloop()
File "/usr/lib/python3.4/pdb.py", line 319, in _cmdloop
self.cmdloop()
File "/usr/lib/python3.4/cmd.py", line 126, in cmdloop
line = input(self.prompt)
nose.proxy.TypeError: bad argument type for built-in operation
-------------------- >> begin captured stdout << ---------------------
hierarchy 0
hierarchy 1
hierarchy 2
hierarchy 3
hierarchy 4
hierarchy 5
hierarchy 6
> /usr/local/lib/python3.4/dist-packages/bctpy-0.4.0-py3.4.egg/bct/bct.py(2892)link_communities()
-> u1,u2 = np.where( ES[np.ix_(U,U)]==np.max(ES[np.ix_(U,U)]) )
--------------------- >> end captured stdout << ----------------------
======================================================================
FAIL: core_tests.test_threshold_proportional
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.4/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/cbarnes/code/lib/bctpy/test/core_tests.py", line 8, in test_threshold_proportional
assert np.allclose( np.sum(x), 22548.51206965 )
AssertionError
======================================================================
FAIL: core_tests.test_threshold_proportional_directed
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.4/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/cbarnes/code/lib/bctpy/test/core_tests.py", line 18, in test_threshold_proportional_directed
assert np.allclose( np.sum(x), 32852.72485433 )
AssertionError
======================================================================
FAIL: modularity_tests.test_modularity_finetune_dir_low_modularity
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.4/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/cbarnes/code/lib/bctpy/test/modularity_tests.py", line 144, in test_modularity_finetune_dir_low_modularity
assert q >= oq
nose.proxy.AssertionError:
-------------------- >> begin captured stdout << ---------------------
0.0692747009074 0.0694071961372
--------------------- >> end captured stdout << ----------------------
======================================================================
FAIL: modularity_tests.test_modularity_finetune_dir
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python3.4/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/cbarnes/code/lib/bctpy/test/modularity_tests.py", line 166, in test_modularity_finetune_dir
assert q >= oq
nose.proxy.AssertionError:
-------------------- >> begin captured stdout << ---------------------
0.359308571478 0.359820950972
--------------------- >> end captured stdout << ----------------------
----------------------------------------------------------------------
Ran 45 tests in 172.041s
FAILED (errors=3, failures=4)
So it looks like the failures are due to small float inequalities (although you'd know better than me if they're important). The errors may be more tricky as it seems like enumerate is failing to produce a variable...
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aestrivex
commented on August 24, 2024
A few of the errors are my fault. In fact in one or two of the complex modularity tests, the test case has never passed -- it should in principle pass, but I think the math crumbles in the edge case given.
I created a branch called py3 that you can push to. I'll look at the test cases that are still failing and see what I can do. But, if I can't fix it easily, I have a relatively limited supply of effort to spend on supporting python 3, it is not a huge priority of mine.
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clbarnes
commented on August 24, 2024
I get that. As the dependencies are pretty thin I suspect there shouldn't be too much to fix (which I can pitch in on once you've zeroed in on the actual red tests), and most 2.7 code can be written in such a way as to be future-compatible if you're still expanding the codebase and don't mind a couple of extra lines to support users of the present and future version of the language.
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aestrivex
commented on August 24, 2024
I fixed some outstanding bugs in some lesser used modularity functions that were causing some of the errors to be thrown (which were not related to python 3, I just forgot to propagate the fixes to a previous bug).
The errors ostensibly caused by python 3 conversion which I haven't traced down are in threshold_proportional and link_communities.
link_communities is an extremely long-runtime function which I ported directly from the matlab code. It is very inefficient and the python implementation is even slower than the matlab version. Not sure if your test case crashed because it ran too long or for some other system reason. It isn't very important because it is somewhat experimental and redundant; most users would probably opt to use much faster algorithms that accomplishing something similar such as modularity_und.
It makes little sense why threshold_proportional and related would fail with assertion errors. That function is important.
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clbarnes
commented on August 24, 2024
Thanks, I'll get them merged in to my branches and see if it's anything I can manage.
I've been playing with TravisCI today and have got the build deploying but the tests are crashing out after a long hold (10+ minutes), which is odd as they pass/fail quite quickly on my local machine. I'll raise an issue on my own fork. Do any of the tests use mayavi? That would be tricky to install on travis.
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clbarnes
commented on August 24, 2024
I can't see a py3 branch - maybe it doesn't make the branch visible if there are no changes?
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aestrivex
commented on August 24, 2024
No tests use mayavi.
I don't know how branches work very well on github. I tried to make a branch on github but not on my local repository and I guess it did nothing. Anyway now I added a commit to this branch which adds a whitespace character to the readme.
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aestrivex
commented on August 24, 2024
Remaining python 3 tests pass. Master branched merged with py3 branch.
Old code available under py2-stable branch in case of likely obscure bugs.
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