Failing tests

[sanjayankur31]

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                                                       

[NineML-Committee]

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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=ACZVGYR4VMJLEVWDLDTMCITQCNOKTA5CNFSM4IIXCR4KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HC53MIA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACZVGYWHJ4MI4EBJQXKFEJTQCNOKTANCNFSM4IIXCR4A> . -- You received this message because you are subscribed to the Google Groups "NineML Committee" group. To unsubscribe from this group and stop receiving emails from it, send an email to ***@***.*** To view this discussion on the web, visit https://groups.google.com/d/msgid/nineml-committee/INCF/nineml-python/issues/45%40github.com <https://groups.google.com/d/msgid/nineml-committee/INCF/nineml-python/issues/45%40github.com?utm_medium=email&utm_source=footer> .

[sanjayankur31]

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

[tclose]

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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=AAIBRFQYMU4S2LR5NOB27NLQEHEWXA5CNFSM4IIXCR4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4DZPYA#issuecomment-520591328>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAIBRFQ7FYP7QRY2UDQCYP3QEHEWXANCNFSM4IIXCR4A> .

-- *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

[sanjayankur31]

I don't seem to have free cycles this week, but I'll try next week if I can.

[eclipseo]

Even if we "fix" the expression, the error keeps changing:

nineml.exceptions.NineMLUsageError: Incorrect arguments provided to expression 'A > -B/tau_r': 'tau_r', 'B', 'A' (expected 'B', 'tau_r', 'A')
nineml.exceptions.NineMLUsageError: Incorrect arguments provided to expression 'A > -B/tau_r': 'B', 'tau_r', 'A' (expected 'tau_r', 'A', 'B')
nineml.exceptions.NineMLUsageError: Incorrect arguments provided to expression 'A > -B/tau_r': 'tau_r', 'A', 'B' (expected 'B', 'tau_r', 'A')

[sanjayankur31]

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

[sanjayankur31]

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 ---it should hopefully be something straightforward for someone that knows the codebase well.

[tclose]

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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=AAIBRFVM37TDF5DJREH2AW3QKNFVVA5CNFSM4IIXCR4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7C6MYI#issuecomment-533063265>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAIBRFUC3N7X3XNFF2ZSVADQKNFVVANCNFSM4IIXCR4A> .

-- *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

[sanjayankur31]

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.

[tclose]

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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=AAIBRFT7BBUEAXKM4R7VKELRDO6L7A5CNFSM4IIXCR4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMBR7YA#issuecomment-587407328>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIBRFVU4R56ISTQZWAWI3LRDO6L7ANCNFSM4IIXCR4A> .

-- *THOMAS G. CLOSE, PHD* 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

[DhanashreePetare]

Can this be assigned to me if its available.

[SAMREEN111-hash]

Hi! I'm interested in working on this issue.

@DhanashreePetare, I see you asked 3 weeks ago. Are you still
planning to work on this? If so, I'll find another issue.
If not, I'd be happy to take it on.

@tclose or other maintainers - could you confirm if this issue
is still relevant and available?

Thanks!

[DhanashreePetare]

I wasn't assigned the work @SAMREEN111-hash ..so I haven't worked. I guess you can continue.

[sanchalitorpe13]

Hi all,
It looks like the failing tests are mostly caused by changes in sympy 1.4, which affect how expressions are evaluated in NineML. One way to address this could be:

• Pin sympy==1.3 in the CI/test environment temporarily to keep the tests passing.
• Update the Expressions class to handle the new evalf behavior in sympy 1.4+ so it works with newer versions. This might involve checking argument ordering and supporting new object types like BooleanTrue.

If needed, I can help investigate and submit a PR that updates the code to be compatible with sympy 1.4+ while keeping the tests passing.