Failing tests #45
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Hi Ankur,
I will see if I can see an easy fix over the weekend.
Cheers,
Tom
…On Fri, 2 Aug 2019 at 08:18, Ankur Sinha ***@***.***> wrote:
We're seeing these tests fail on Fedora 31 (rawhide). Looks like something
changed in sympy:
+ cd nineml-python-1.0.1
+ nosetests-3.7 --exclude test_flat_body
BUILDSTDERR: ..................E..........................E...................................................................................................................................................................................
BUILDSTDERR: ======================================================================
BUILDSTDERR: ERROR: test_trigger (unittests.abstraction_test.dynamics_test.OnCondition_test)
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Traceback (most recent call last):
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 1308, in evalf
BUILDSTDERR: rf = evalf_table[x.func]
BUILDSTDERR: KeyError: <class 'sympy.core.relational.StrictGreaterThan'>
BUILDSTDERR: During handling of the above exception, another exception occurred:
BUILDSTDERR: Traceback (most recent call last):
BUILDSTDERR: File "/builddir/build/BUILD/nineml-python-1.0.1/nineml/abstraction/expressions/base.py", line 199, in nineml_expression
BUILDSTDERR: val = self.rhs.evalf(subs=kwargs)
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 1442, in evalf
BUILDSTDERR: result = evalf(self, prec + 4, options)
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 1314, in evalf
BUILDSTDERR: xe = x._eval_evalf(prec)
BUILDSTDERR: AttributeError: 'BooleanTrue' object has no attribute '_eval_evalf'
BUILDSTDERR: During handling of the above exception, another exception occurred:
BUILDSTDERR: Traceback (most recent call last):
BUILDSTDERR: File "/builddir/build/BUILD/nineml-python-1.0.1/test/unittests/abstraction_test/dynamics_test.py", line 713, in test_trigger
BUILDSTDERR: self.assertEquals(return_values[i], python_func(**param_dict))
BUILDSTDERR: File "/builddir/build/BUILD/nineml-python-1.0.1/nineml/abstraction/expressions/base.py", line 206, in nineml_expression
BUILDSTDERR: "', '".join(self.rhs_symbol_names)))
BUILDSTDERR: nineml.exceptions.NineMLUsageError: Incorrect arguments provided to expression 'A > -B/tau_r': 'A', 'B', 'tau_r' (expected 'B', 'tau_r', 'A')
BUILDSTDERR: ======================================================================
BUILDSTDERR: ERROR: test_Valid (unittests.abstraction_test.expressions_test.Expression_test)
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Traceback (most recent call last):
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 1309, in evalf
BUILDSTDERR: r = rf(x, prec, options)
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 1227, in evalf_symbol
BUILDSTDERR: val = options['subs'][x]
BUILDSTDERR: KeyError: w
BUILDSTDERR: During handling of the above exception, another exception occurred:
BUILDSTDERR: Traceback (most recent call last):
BUILDSTDERR: File "/builddir/build/BUILD/nineml-python-1.0.1/nineml/abstraction/expressions/base.py", line 199, in nineml_expression
BUILDSTDERR: val = self.rhs.evalf(subs=kwargs)
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 1442, in evalf
BUILDSTDERR: result = evalf(self, prec + 4, options)
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 1309, in evalf
BUILDSTDERR: r = rf(x, prec, options)
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 785, in evalf_trig
BUILDSTDERR: re, im, re_acc, im_acc = evalf(arg, xprec, options)
BUILDSTDERR: File "/usr/lib/python3.7/site-packages/sympy/core/evalf.py", line 1314, in evalf
BUILDSTDERR: xe = x._eval_evalf(prec)
BUILDSTDERR: AttributeError: 'ImmutableDenseNDimArray' object has no attribute '_eval_evalf'
BUILDSTDERR: During handling of the above exception, another exception occurred:
BUILDSTDERR: Traceback (most recent call last):
BUILDSTDERR: File "/builddir/build/BUILD/nineml-python-1.0.1/test/unittests/abstraction_test/expressions_test.py", line 85, in test_Valid
BUILDSTDERR: v = return_values[i] - python_func(**param_dict)
BUILDSTDERR: File "/builddir/build/BUILD/nineml-python-1.0.1/nineml/abstraction/expressions/base.py", line 206, in nineml_expression
BUILDSTDERR: "', '".join(self.rhs_symbol_names)))
BUILDSTDERR: nineml.exceptions.NineMLUsageError: Incorrect arguments provided to expression 'sin(w)': 'w' (expected 'w')
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 225 tests in 156.559s
BUILDSTDERR: FAILED (errors=2)
Versions used in this build:
DEBUG util.py:587: hdf5-devel-1.10.5-2.fc31.ppc64le
DEBUG util.py:587: python3-devel-3.7.4-3.fc31.ppc64le
DEBUG util.py:587: python3-h5py-2.9.0-4.fc31.ppc64le
DEBUG util.py:587: python3-lxml-4.2.5-2.fc30.ppc64le
DEBUG util.py:587: python3-nose-1.3.7-23.fc31.noarch
DEBUG util.py:587: python3-numpy-1:1.16.4-2.fc31.ppc64le
DEBUG util.py:587: python3-numpydoc-0.9.1-1.fc31.noarch
DEBUG util.py:587: python3-pyyaml-5.1.1-2.fc31.ppc64le
DEBUG util.py:587: python3-sphinx-1:2.1.2-1.fc31.noarch
DEBUG util.py:587: python3-sphinx_rtd_theme-0.4.3-2.fc31.noarch
DEBUG util.py:587: python3-sympy-1.4-1.fc31.noarch
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Hi Tom, Have you had a chance to look at this? If there's anything I can do to help debug the issue, please let me know. Cheers! |
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Sorry Ankur, I haven't had a chance to look at it (been pretty crazy couple
of weeks with both my kids getting all manner of winter lurgies).
I expect they will be quite isolated issues (i.e. contained to the
Expressions class that is raising the exception), so it might be something
that you could find an easy fix for.
Cheers,
Tom
…On Tue, 13 Aug 2019 at 06:54, Ankur Sinha ***@***.***> wrote:
Hi Tom,
Have you had a chance to look at this? If there's anything I can do to
help debug the issue, please let me know.
Cheers!
Ankur
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*THOMAS G. CLOSE, PHD*
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*Monash Biomedical Imaging*
Monash University
Room 139, 770 Blackburn Rd
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I don't seem to have free cycles this week, but I'll try next week if I can. |
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Even if we "fix" the expression, the error keeps changing: |
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So, this is a sympy related change. if one uses a virtual environment with sympy 1.3, the test passes. So, looking at what changed in 1.4 now: https://github.com/sympy/sympy/wiki/Release-Notes-for-1.4 |
Unfortunately, I've not had the time to really fix the issue either. Would you take a look please @tclose ---it should hopefully be something straightforward for someone that knows the codebase well. |
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Hi Ankur,
Yes, I will try to have a look soon, just been a bit swamped with things
after coming back from a break.
Cheers,
tom
…On Thu, 19 Sep 2019 at 20:09, Ankur Sinha ***@***.***> wrote:
I expect they will be quite isolated issues (i.e. contained to the
Expressions class that is raising the exception), so it might be something
that you could find an easy fix for. Cheers, Tom
Unfortunately, I've not had the time to really fix the issue either. Would
you take a look please @tclose <https://github.com/tclose> ---it should
hopefully be something straightforward for someone that knows the codebase
well.
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*THOMAS G. CLOSE, PHD*
Senior Informatics Officer
*Monash Biomedical Imaging*
Monash University
Room 139, 770 Blackburn Rd
Clayton Campus, Clayton VIC 3800
Australia
T: +61 3 9902 9804
M: +61 491 141 390
E: tom.close@monash.edu
mbi.monash.edu.au
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Hi @tclose : any chance of a look at this sometime? We're nearing the Fedora 32 release so we'll have to drop NineML there if we can't get it fixed and building soonish. |
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Hi Ankur,
Sorry for the delay. I will have some time to look at it next week.
Cheers,
Tom
…On Tue, 18 Feb 2020 at 22:06, Ankur Sinha ***@***.***> wrote:
Hi @tclose <https://github.com/tclose> : any chance of a look at this
sometime? We're nearing the Fedora 32 release so we'll have to drop NineML
there if we can't get it fixed and building soonish.
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Imaging Informatics Officer
*Monash Biomedical Imaging*
Monash University
Room 139, 770 Blackburn Rd
Clayton Campus, Clayton VIC 3800
Australia
T: +61 3 9902 9804
M: +61 491 141 390
E: tom.close@monash.edu
mbi.monash.edu.au
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We're seeing these tests fail on Fedora 31 (rawhide). Looks like something changed in sympy:
Versions used in this build:
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