Resolve warnings issued in the xarray test suite #1652

shoyer · 2017-10-24T07:36:55Z

82 warnings are currently issued in the process of running our test suite:
https://gist.github.com/shoyer/db0b2c82efd76b254453216e957c4345

Some of can probably be safely ignored, but others are likely noticed by users, e.g.,
https://stackoverflow.com/questions/41130138/why-is-invalid-value-encountered-in-greater-warning-thrown-in-python-xarray-fo/41147570#41147570

It would be nice to clean up all of these, either by catching the appropriate upstream warning (if irrelevant) or changing our usage to avoid the warning. There may very well be a lurking FutureWarning in there somewhere that could cause issues when another library updates.

Probably the easiest way to get started here is to get the test suite running locally, and use py.test -W error to turn all warnings into errors.

The text was updated successfully, but these errors were encountered:

fmaussion · 2017-10-24T07:44:30Z

Do I understand right that you'd like to silence the warnings in the xr.DataArray([1, 2, np.NaN]) > 0 case?

shoyer · 2017-10-24T07:51:54Z

Do I understand right that you'd like to silence the warnings in the xr.DataArray([1, 2, np.NaN]) > 0 case?

Yes, I don't think this warning is very useful -- pandas doesn't show it.

fmaussion · 2017-10-24T08:11:32Z

pandas doesn't show it.

Right, I misunderstood that part.

jhamman · 2017-10-25T03:03:07Z

$ py.test -W error xarray/tests 
===== 372 failed, 2141 passed, 89 skipped, 10 xfailed in 148.41 seconds =====

👍 on squashing as many of these as possible.

jhamman · 2017-10-25T04:13:13Z

I'll take this one on unless someone else really wants it.

jhamman · 2017-10-30T05:23:52Z

reopening since #1657 only took care of a subset of the current warnings.

max-sixty · 2018-02-19T23:22:48Z

Here's the latest output (excluding test_backends.py, which separately isn't working locally):

EDIT: put this into a details dropdown


====================================================================== warnings summary ======================================================================
xarray/tests/test_dataarray.py::TestDataArray::test_groupby_math
  /Users/maximilian/drive/workspace/xarray/xarray/tests/test_dataarray.py:2019: FutureWarning: the order of the arguments on DataArray.to_dataset has changed; you now need to supply ``name`` as a keyword argument
    ds = array.coords['x'].to_dataset('X')

xarray/tests/test_dataarray.py::TestDataArray::test_reindex_regressions
  /Users/maximilian/drive/workspace/xarray/xarray/core/dataarray.py:889: FutureWarning: Indexer has dimensions ('time2',) that are different from that to be indexed along time. This will behave differently in the future.
    method=method, tolerance=tolerance, copy=copy, **indexers)

xarray/tests/test_dataarray.py::test_rolling_reduce[mean-1-None-True-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: Mean of empty slice
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[mean-1-None-False-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: Mean of empty slice
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[mean-1-1-True-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: Mean of empty slice
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[mean-1-1-False-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: Mean of empty slice
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[mean-1-2-True-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: Mean of empty slice
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[mean-1-2-False-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: Mean of empty slice
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[mean-1-3-True-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: Mean of empty slice
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[mean-1-3-False-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: Mean of empty slice
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[std-1-None-True-2]
  /usr/local/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1434: RuntimeWarning: Degrees of freedom <= 0 for slice.
    keepdims=keepdims)

xarray/tests/test_dataarray.py::test_rolling_reduce[std-1-None-False-2]
  /usr/local/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1434: RuntimeWarning: Degrees of freedom <= 0 for slice.
    keepdims=keepdims)

xarray/tests/test_dataarray.py::test_rolling_reduce[std-1-1-True-2]
  /usr/local/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1434: RuntimeWarning: Degrees of freedom <= 0 for slice.
    keepdims=keepdims)

xarray/tests/test_dataarray.py::test_rolling_reduce[std-1-1-False-2]
  /usr/local/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1434: RuntimeWarning: Degrees of freedom <= 0 for slice.
    keepdims=keepdims)

xarray/tests/test_dataarray.py::test_rolling_reduce[std-1-2-True-2]
  /usr/local/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1434: RuntimeWarning: Degrees of freedom <= 0 for slice.
    keepdims=keepdims)

xarray/tests/test_dataarray.py::test_rolling_reduce[std-1-2-False-2]
  /usr/local/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1434: RuntimeWarning: Degrees of freedom <= 0 for slice.
    keepdims=keepdims)

xarray/tests/test_dataarray.py::test_rolling_reduce[std-1-3-True-2]
  /usr/local/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1434: RuntimeWarning: Degrees of freedom <= 0 for slice.
    keepdims=keepdims)

xarray/tests/test_dataarray.py::test_rolling_reduce[std-1-3-False-2]
  /usr/local/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1434: RuntimeWarning: Degrees of freedom <= 0 for slice.
    keepdims=keepdims)

xarray/tests/test_dataarray.py::test_rolling_reduce[max-1-None-True-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: All-NaN slice encountered
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[max-1-None-False-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: All-NaN slice encountered
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[max-1-1-True-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: All-NaN slice encountered
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[max-1-1-False-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: All-NaN slice encountered
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[max-1-2-True-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: All-NaN slice encountered
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[max-1-2-False-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: All-NaN slice encountered
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[max-1-3-True-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: All-NaN slice encountered
    axis=axis, **kwargs)

xarray/tests/test_dataarray.py::test_rolling_reduce[max-1-3-False-2]
  /Users/maximilian/drive/workspace/xarray/xarray/core/variable.py:1224: RuntimeWarning: All-NaN slice encountered
    axis=axis, **kwargs)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-min-False-float-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-min-False-float-2]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-min-False-int-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-min-False-int-2]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-min-False-float32-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-min-False-float32-2]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-min-False-bool_-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-min-False-bool_-2]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-max-False-float-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-max-False-float-2]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-max-False-int-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-max-False-int-2]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-max-False-float32-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-max-False-float32-2]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-max-False-bool_-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[None-False-max-False-bool_-2]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[x-False-min-False-float-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[x-False-min-False-int-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[x-False-min-False-float32-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[x-False-min-False-bool_-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:29: RuntimeWarning: invalid value encountered in reduce
    return umr_minimum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[x-False-max-False-float-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[x-False-max-False-int-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[x-False-max-False-float32-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_duck_array_ops.py::test_reduce[x-False-max-False-bool_-1]
  /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce
    return umr_maximum(a, axis, None, out, keepdims)

xarray/tests/test_missing.py::test_scipy_methods_function
  /usr/local/lib/python3.6/site-packages/scipy/interpolate/polyint.py:511: RuntimeWarning: overflow encountered in multiply
    self.wi[:j] *= (self.xi[j]-self.xi[:j])
  /usr/local/lib/python3.6/site-packages/scipy/interpolate/polyint.py:512: RuntimeWarning: overflow encountered in reduce
    self.wi[j] = np.multiply.reduce(self.xi[:j]-self.xi[j])
  /usr/local/lib/python3.6/site-packages/scipy/interpolate/polyint.py:609: RuntimeWarning: invalid value encountered in true_divide
    p = np.dot(c,self.yi)/np.sum(c,axis=-1)[...,np.newaxis]
  /usr/local/lib/python3.6/site-packages/scipy/interpolate/polyint.py:324: RuntimeWarning: overflow encountered in multiply
    pi = w*pi
  /usr/local/lib/python3.6/site-packages/scipy/interpolate/polyint.py:325: RuntimeWarning: invalid value encountered in multiply
    p += pi[:,np.newaxis] * self.c[k]
  /usr/local/lib/python3.6/site-packages/scipy/interpolate/polyint.py:325: RuntimeWarning: invalid value encountered in add
    p += pi[:,np.newaxis] * self.c[k]

xarray/tests/test_plot.py::TestContourf::test_can_plot_all_nans
  /usr/local/lib/python3.6/site-packages/matplotlib/contour.py:1534: UserWarning: Warning: converting a masked element to nan.
    self.zmax = float(z.max())
  /usr/local/lib/python3.6/site-packages/matplotlib/contour.py:1535: UserWarning: Warning: converting a masked element to nan.
    self.zmin = float(z.min())

xarray/tests/test_plot.py::TestContour::test_can_plot_all_nans
  /usr/local/lib/python3.6/site-packages/matplotlib/contour.py:1534: UserWarning: Warning: converting a masked element to nan.
    self.zmax = float(z.max())
  /usr/local/lib/python3.6/site-packages/matplotlib/contour.py:1535: UserWarning: Warning: converting a masked element to nan.
    self.zmin = float(z.min())
  /usr/local/lib/python3.6/site-packages/matplotlib/contour.py:1176: RuntimeWarning: invalid value encountered in greater
    inside = (self.levels > self.zmin) & (self.levels < self.zmax)
  /usr/local/lib/python3.6/site-packages/matplotlib/contour.py:1176: RuntimeWarning: invalid value encountered in less
    inside = (self.levels > self.zmin) & (self.levels < self.zmax)
  /usr/local/lib/python3.6/site-packages/matplotlib/contour.py:1180: UserWarning: No contour levels were found within the data range.
    warnings.warn("No contour levels were found"

xarray/tests/test_plot.py::TestContour::test_single_level
  /usr/local/lib/python3.6/site-packages/matplotlib/contour.py:1180: UserWarning: No contour levels were found within the data range.
    warnings.warn("No contour levels were found"

xarray/tests/test_plot.py::TestPcolormesh::test_can_plot_axis_size_one
  /usr/local/lib/python3.6/site-packages/matplotlib/axes/_base.py:2961: UserWarning: Attempting to set identical left==right results
  in singular transformations; automatically expanding.
  left=0.0, right=0.0
    'left=%s, right=%s') % (left, right))
  /usr/local/lib/python3.6/site-packages/matplotlib/axes/_base.py:3285: UserWarning: Attempting to set identical bottom==top results
  in singular transformations; automatically expanding.
  bottom=0.0, top=0.0
    'bottom=%s, top=%s') % (bottom, top))

xarray/tests/test_variable.py::TestVariable::test_index_0d_not_a_time
  /Users/maximilian/drive/workspace/xarray/xarray/core/duck_array_ops.py:138: FutureWarning: In the future, 'NAT == x' and 'x == NAT' will always be False.
    flag_array = (arr1 == arr2)
  /Users/maximilian/drive/workspace/xarray/xarray/tests/test_variable.py:144: FutureWarning: In the future, 'NAT == x' and 'x == NAT' will always be False.
    assert variable.values[0] == expected_value0
  /Users/maximilian/drive/workspace/xarray/xarray/tests/test_variable.py:145: FutureWarning: In the future, 'NAT == x' and 'x == NAT' will always be False.
    assert variable[0].values == expected_value0

xarray/tests/test_variable.py::TestIndexVariable::test_index_0d_not_a_time
  /Users/maximilian/drive/workspace/xarray/xarray/tests/test_variable.py:144: FutureWarning: In the future, 'NAT == x' and 'x == NAT' will always be False.
    assert variable.values[0] == expected_value0
  /Users/maximilian/drive/workspace/xarray/xarray/tests/test_variable.py:145: FutureWarning: In the future, 'NAT == x' and 'x == NAT' will always be False.
    assert variable[0].values == expected_value0

-- Docs: http://doc.pytest.org/en/latest/warnings.html
============================================= 2475 passed, 205 skipped, 4 xfailed, 71 warnings in 127.39 seconds =============================================

stale · 2020-01-28T19:45:38Z

In order to maintain a list of currently relevant issues, we mark issues as stale after a period of inactivity

If this issue remains relevant, please comment here or remove the stale label; otherwise it will be marked as closed automatically

keewis · 2020-01-28T21:56:54Z

this may be related to (or superseded by) #3266

keewis · 2021-02-21T23:06:34Z

closing in favor of #3266

jhamman mentioned this issue Oct 25, 2017

fixes for warnings related to unit tests and nan comparisons #1657

Merged

4 tasks

shoyer closed this as completed in #1657 Oct 29, 2017

jhamman reopened this Oct 30, 2017

jhamman added the contrib-help-wanted label Feb 21, 2018

jhamman mentioned this issue Feb 27, 2018

Don't warn when doing comparisons or arithmetic with NaN #1164

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This was referenced Mar 2, 2018

xarray.merge exception : invalid type promotion #1952

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Silencing warnings issued by numpy functions within dask.array dask/dask#3245

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Resolve more warnings in the xarray test suite #1964

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jhamman mentioned this issue Jul 29, 2018

Silence some warnings. #2328

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stale bot added the stale label Jan 28, 2020

dcherian removed the stale label Jan 28, 2020

max-sixty mentioned this issue Feb 28, 2020

Don't warn on empty reductions #3811

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keewis closed this as completed Feb 21, 2021

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Resolve warnings issued in the xarray test suite #1652

Resolve warnings issued in the xarray test suite #1652

shoyer commented Oct 24, 2017 •

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fmaussion commented Oct 24, 2017

shoyer commented Oct 24, 2017

fmaussion commented Oct 24, 2017

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jhamman commented Oct 30, 2017

max-sixty commented Feb 19, 2018 •

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keewis commented Feb 21, 2021

Resolve warnings issued in the xarray test suite #1652

Resolve warnings issued in the xarray test suite #1652

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shoyer commented Oct 24, 2017 • edited Loading

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shoyer commented Oct 24, 2017

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jhamman commented Oct 25, 2017

jhamman commented Oct 30, 2017

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keewis commented Feb 21, 2021

shoyer commented Oct 24, 2017 •

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max-sixty commented Feb 19, 2018 •

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