explain and ignore warnings during the tests #238

dizcza · 2019-07-10T13:10:17Z

All these UserWarnings and RuntimeWarnings at tests always confuse me. I could not understand whether the problem was in the source code, test setup, or dependency package issues.
Before

/home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: invalid value encountered in true_divide
  AngCoeff = dY / dX
./home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: divide by zero encountered in true_divide
  AngCoeff = dY / dX
/home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: invalid value encountered in true_divide
  AngCoeff = dY / dX
/home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: divide by zero encountered in true_divide
  AngCoeff = dY / dX
/home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: invalid value encountered in true_divide
  AngCoeff = dY / dX
./home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: divide by zero encountered in true_divide
  AngCoeff = dY / dX
/home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: invalid value encountered in true_divide
  AngCoeff = dY / dX
....../home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: divide by zero encountered in true_divide
  AngCoeff = dY / dX
/home/travis/build/NeuralEnsemble/elephant/elephant/asset.py:687: RuntimeWarning: invalid value encountered in true_divide
  AngCoeff = dY / dX
.................................................................../home/travis/build/NeuralEnsemble/elephant/elephant/cubic.py:110: UserWarning: Test aborted, xihat= 11 > ximax= 10
  warnings.warn('Test aborted, xihat= %i > ximax= %i' % (xi, ximax))
...........................S........................................................................................................................./home/travis/build/NeuralEnsemble/elephant/elephant/test/test_pandas_bridge.py:50: FutureWarning: the 'labels' keyword is deprecated, use 'codes' instead
  names=['test1', 'test2', 'test3'])
/home/travis/build/NeuralEnsemble/elephant/elephant/test/test_pandas_bridge.py:54: FutureWarning: .labels was deprecated in version 0.24.0. Use .codes instead.
  self.assertEqual(targ.labels, res0.labels)
./home/travis/build/NeuralEnsemble/elephant/elephant/test/test_pandas_bridge.py:2760: RuntimeWarning: invalid value encountered in less
  targ[targ < targ_start] = np.nan
/home/travis/build/NeuralEnsemble/elephant/elephant/test/test_pandas_bridge.py:2761: RuntimeWarning: invalid value encountered in greater
  targ[targ > targ_stop] = np.nan
../home/travis/build/NeuralEnsemble/elephant/elephant/test/test_pandas_bridge.py:2706: RuntimeWarning: invalid value encountered in less
  targ[targ < targ_start] = np.nan
./home/travis/build/NeuralEnsemble/elephant/elephant/test/test_pandas_bridge.py:2734: RuntimeWarning: invalid value encountered in greater
  targ[targ > targ_stop] = np.nan
......................................................./home/travis/build/NeuralEnsemble/elephant/elephant/test/test_signal_processing.py:209: RuntimeWarning: invalid value encountered in true_divide
  target = (signal.magnitude - m) / s
/home/travis/build/NeuralEnsemble/elephant/elephant/signal_processing.py:129: RuntimeWarning: invalid value encountered in true_divide
  (sig.magnitude - m.magnitude) / s.magnitude,
./home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/quantities/quantity.py:321: RuntimeWarning: divide by zero encountered in true_divide
  return np.true_divide(other, self)
../home/travis/build/NeuralEnsemble/elephant/elephant/spade.py:308: UserWarning: 0<alpha<1 but p-value spectrum has not been computed (n_surr==0)
  warnings.warn('0<alpha<1 but p-value spectrum has not been '
................................/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/quantities/quantity.py:321: RuntimeWarning: divide by zero encountered in true_divide
  return np.true_divide(other, self)
............/home/travis/build/NeuralEnsemble/elephant/elephant/spike_train_generation.py:335: RuntimeWarning: divide by zero encountered in true_divide
  mean_interval = 1 / rate.magnitude
......../home/travis/build/NeuralEnsemble/elephant/elephant/spike_train_generation.py:267: RuntimeWarning: invalid value encountered in sqrt
  number = np.ceil(n + 3 * np.sqrt(n))
............................/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/scipy/signal/spectral.py:1577: RuntimeWarning: invalid value encountered in true_divide
  Cxy = np.abs(Pxy)**2 / Pxx / Pyy
............/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/neo/core/basesignal.py:132: RuntimeWarning: invalid value encountered in true_divide
  new_signal = f(other, *args)
.........................../home/travis/build/NeuralEnsemble/elephant/elephant/statistics.py:256: UserWarning: Input size is too small. Please provide an input with more than 1 entry. lv returns 'NaN'since the argument `with_nan` is True
  warnings.warn("Input size is too small. Please provide "
......../home/travis/build/NeuralEnsemble/elephant/elephant/statistics.py:867: UserWarning: Instantaneous firing rate approximation contains negative values, possibly caused due to machine precision errors.
  warnings.warn("Instantaneous firing rate approximation contains "
........................................................../home/travis/build/NeuralEnsemble/elephant/elephant/waveform_features.py:70: UserWarning: The noise was evaluated to 0.
  warnings.warn('The noise was evaluated to 0.')
..

Now

 nosetests --cover-package=elephant
......................................................................................................S..................................................................................................................................................................................................................................................................................................................................................................................
Ran 473 tests in 275.283s

OK (SKIP=1)

Future warnings can be easily caught.

Affected changes:

removed handwritten _xrange wrapper
np.arctan(y/x) -> numerically stable np.arctan2(y, x)

coveralls · 2019-07-10T13:27:39Z

Coverage decreased (-0.02%) to 75.767% when pulling 0a540f1 on INM-6:warnings into 19d3c7b on NeuralEnsemble:master.

pep8speaks · 2019-08-01T14:34:35Z

Hello @dizcza! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2019-08-12 12:56:51 UTC

dizcza · 2019-08-02T15:27:08Z

I excluded min-requirements travis test case back because of the unrelated unittest bug error with self.assertWarn(). If it failed on the first PR we merged, I imagine, it'll be hard to maintain it anyway.

Can be checked and merged.

mdenker

I could reproduce the warning-less unit tests running locally, looks much cleaner now. The documentation of which warnings are suppressed are very helpful!
Attached a few comments...

elephant/signal_processing.py

elephant/test/test_signal_processing.py

mdenker · 2019-08-12T11:26:40Z

requirements.txt

@@ -1,5 +1,5 @@
 neo>=0.7.1,<0.8.0
 numpy>=1.10.1
 quantities>=0.12.1
-scipy>=0.17.0
+scipy>=0.19.0


What is the bump in the requirements required for?

scipy v0.17.0 has issues in its internal functions: https://travis-ci.org/NeuralEnsemble/elephant/jobs/566510125
the next stable one is 0.19.0.
locally, all tests from 'min-requirements' case are passed. But travis throws error I cannot understand so I removed the 'min-requirements' test case. At least, if someone installs dependencies locally, it should work with 0.19.0 but definitely would not work with 0.17.0.

commit caa2110 Author: Danylo Ulianych <dizcza@gmail.com> Date: Tue Aug 13 10:03:45 2019 +0300 explain and ignore warnings during the tests (NeuralEnsemble#238) * explain and ignore warnings during the tests * scipy v0.18.0 * fixed min-req tests: scipy v0.19.0 * exclude min-requirements tests back * fixed division by zero commit 19d3c7b Author: Danylo Ulianych <dizcza@gmail.com> Date: Thu Aug 1 15:09:34 2019 +0200 fixed min requirements (NeuralEnsemble#235) * fixed min requirements * travis install libopenmpi-dev * added .coveragerc omit=elephant/test* rule not to count test files as source code commit 36e6096 Author: Danylo Ulianych <dizcza@gmail.com> Date: Wed Jul 31 16:55:47 2019 +0200 Integrated GPFA (NeuralEnsemble#233) * Rename neural_trajectory to gpfa and refactor the codes accordingly * Remove codes related to the (not fully implemented) cross-validation feature * added tqdm as an extra requirement * push coverage only for requirements-extras test * gpfa verbose flag; added licence in the docs * Fixed and extended documentation, removed misleading function outputs.

dizcza requested a review from mdenker July 10, 2019 13:32

dizcza force-pushed the warnings branch 2 times, most recently from 18f243a to 2c49122 Compare August 1, 2019 14:39

dizcza added 2 commits August 1, 2019 16:42

explain and ignore warnings during the tests

e3cd7e2

scipy v0.18.0

16b65db

dizcza force-pushed the warnings branch from 2c49122 to 16b65db Compare August 1, 2019 14:42

fixed min-req tests: scipy v0.19.0

576d906

dizcza force-pushed the warnings branch from 0503087 to 550c14b Compare August 2, 2019 14:50

exclude min-requirements tests back

0a540f1

dizcza force-pushed the warnings branch from 550c14b to 0a540f1 Compare August 2, 2019 15:24

mdenker added the enhancement Editing an existing module, improving something label Aug 12, 2019

mdenker reviewed Aug 12, 2019

View reviewed changes

fixed division by zero

7d59ba9

mdenker approved these changes Aug 13, 2019

View reviewed changes

mdenker merged commit caa2110 into NeuralEnsemble:master Aug 13, 2019

Moritz-Alexander-Kern deleted the warnings branch September 6, 2022 07:54

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explain and ignore warnings during the tests #238

explain and ignore warnings during the tests #238

dizcza commented Jul 10, 2019

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dizcza Aug 12, 2019

explain and ignore warnings during the tests #238

explain and ignore warnings during the tests #238

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dizcza commented Jul 10, 2019

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Comment last updated at 2019-08-12 12:56:51 UTC

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