Pandas test fails with Scipy 0.19 #15662

zym1010 · 2017-03-12T15:31:28Z

Code Sample, a copy-pastable example if possible

import pandas as pd
pd.test()

Problem description

there are some errors w.r.t. interpolation related functions. Seems that this is related to the change of behavior for some Scipy functions in 0.19. But which is correct?

======================================================================
FAIL: test_interp_various (pandas.tests.frame.test_missing.TestDataFrameInterpolate)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/tests/frame/test_missing.py", line 513, in test_interp_various
    assert_frame_equal(result, expected)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1313, in assert_frame_equal
    obj='DataFrame.iloc[:, {0}]'.format(i))
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1181, in assert_series_equal
    obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 59, in pandas._testing.assert_almost_equal (pandas/src/testing.c:4156)
  File "pandas/src/testing.pyx", line 173, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3274)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1018, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: DataFrame.iloc[:, 0] are different

DataFrame.iloc[:, 0] values are different (28.57143 %)
[left]:  [1.0, 2.0, 2.81547781415, 4.0, 5.0, 5.52964175305, 7.0]
[right]: [1.0, 2.0, 2.81621174, 4.0, 5.0, 5.64146581, 7.0]

======================================================================
FAIL: test_interp_scipy_basic (pandas.tests.series.test_missing.TestSeriesInterpolateData)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/tests/series/test_missing.py", line 711, in test_interp_scipy_basic
    assert_series_equal(result, expected)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1181, in assert_series_equal
    obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 59, in pandas._testing.assert_almost_equal (pandas/src/testing.c:4156)
  File "pandas/src/testing.pyx", line 173, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3274)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1018, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: Series are different

Series values are different (33.33333 %)
[left]:  [1.0, 3.0, 6.82352941176, 12.0, 18.0588235294, 25.0]
[right]: [1.0, 3.0, 6.769231, 12.0, 18.230769, 25.0]

======================================================================
FAIL: test_cmov_window_regular (pandas.tests.test_window.TestMoments)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/tests/test_window.py", line 878, in test_cmov_window_regular
    tm.assert_series_equal(xp, rs)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1181, in assert_series_equal
    obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 59, in pandas._testing.assert_almost_equal (pandas/src/testing.c:4156)
  File "pandas/src/testing.pyx", line 173, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3274)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1018, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: Series are different

Series values are different (60.0 %)
[left]:  [nan, nan, 9.28667, 10.34667, 12.00556, 13.33889, 13.38, 12.33667, nan, nan]
[right]: [nan, nan, 9.60058823529, 10.8523529412, 12.86, 13.52, 12.7629411765, 12.2070588235, nan, nan]

======================================================================
FAIL: test_cmov_window_regular_linear_range (pandas.tests.test_window.TestMoments)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/tests/test_window.py", line 895, in test_cmov_window_regular_linear_range
    tm.assert_series_equal(xp, rs)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1181, in assert_series_equal
    obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 59, in pandas._testing.assert_almost_equal (pandas/src/testing.c:4156)
  File "pandas/src/testing.pyx", line 173, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3274)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1018, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: Series are different

Series values are different (60.0 %)
[left]:  [nan, nan, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, nan, nan]
[right]: [nan, nan, 2.35294117647, 3.35294117647, 4.35294117647, 5.35294117647, 6.35294117647, 7.35294117647, nan, nan]

======================================================================
FAIL: test_cmov_window_regular_missing_data (pandas.tests.test_window.TestMoments)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/tests/test_window.py", line 928, in test_cmov_window_regular_missing_data
    tm.assert_series_equal(xp, rs)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1181, in assert_series_equal
    obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 59, in pandas._testing.assert_almost_equal (pandas/src/testing.c:4156)
  File "pandas/src/testing.pyx", line 173, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3274)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1018, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: Series are different

Series values are different (80.0 %)
[left]:  [nan, nan, 9.33167, 9.76125, 9.28667, 10.34667, 12.00556, 13.82125, 14.49429, 13.765]
[right]: [nan, nan, 9.61230769231, 9.24125, 9.60058823529, 10.8523529412, 12.86, 14.3857142857, 14.1308333333, 13.3433333333]

======================================================================
FAIL: test_cmov_window_special (pandas.tests.test_window.TestMoments)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/tests/test_window.py", line 955, in test_cmov_window_special
    tm.assert_series_equal(xp, rs)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1181, in assert_series_equal
    obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 59, in pandas._testing.assert_almost_equal (pandas/src/testing.c:4156)
  File "pandas/src/testing.pyx", line 173, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3274)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1018, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: Series are different

Series values are different (60.0 %)
[left]:  [nan, nan, 9.86851, 11.02969, 11.65161, 12.75129, 12.90702, 12.83757, nan, nan]
[right]: [nan, nan, 9.95592026795, 11.1636020642, 11.8220886145, 12.6904154014, 12.797644924, 12.8491264878, nan, nan]

======================================================================
FAIL: test_cmov_window_special_linear_range (pandas.tests.test_window.TestMoments)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/tests/test_window.py", line 973, in test_cmov_window_special_linear_range
    tm.assert_series_equal(xp, rs)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1181, in assert_series_equal
    obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 59, in pandas._testing.assert_almost_equal (pandas/src/testing.c:4156)
  File "pandas/src/testing.pyx", line 173, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3274)
  File "/Users/yimengzh/miniconda2/envs/default35/lib/python3.5/site-packages/pandas/util/testing.py", line 1018, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: Series are different

Series values are different (60.0 %)
[left]:  [nan, nan, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, nan, nan]
[right]: [nan, nan, 2.07210900201, 3.07210900201, 4.07210900201, 5.07210900201, 6.07210900201, 7.07210900201, nan, nan]

----------------------------------------------------------------------
Ran 10252 tests in 287.945s

FAILED (SKIP=627, failures=7)

Expected Output

Output of `pd.show_versions()`

INSTALLED VERSIONS ------------------ commit: None python: 3.5.2.final.0 python-bits: 64 OS: Darwin OS-release: 15.6.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8

pandas: 0.19.2
nose: 1.3.7
pip: 8.1.2
setuptools: 26.1.1.post20160901
Cython: None
numpy: 1.11.3
scipy: 0.19.0
statsmodels: None
xarray: None
IPython: 5.1.0
sphinx: None
patsy: None
dateutil: 2.5.3
pytz: 2016.6.1
blosc: None
bottleneck: None
tables: None
numexpr: None
matplotlib: 1.5.2
openpyxl: None
xlrd: None
xlwt: None
xlsxwriter: None
lxml: None
bs4: None
html5lib: None
httplib2: None
apiclient: None
sqlalchemy: None
pymysql: None
psycopg2: None
jinja2: 2.8
boto: None
pandas_datareader: None

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

jreback · 2017-03-12T15:35:34Z

well, since scipy 0.19.0 was just released and something I imagine changed I am not surprised. Would you have a look and see what changed and/or provide a PR to fix? (keeping in mind that we are back-compat thru scipy 0.13)

jreback · 2017-03-12T15:37:35Z

further scipy is not on the default conda channels as of yet, so this doesn't hit our tests yet.

zym1010 · 2017-03-12T15:47:19Z

@jreback I will have a look at it later this week.

zym1010 · 2017-03-12T17:45:53Z

@jreback after some digging, I think those cmov_window errors should be due to scipy/scipy#6483, and those interp errors should be due to change of implementation for quadratic and cubic interpolation.

To fix the first one, it should do to pass an additional argument False to

pandas/pandas/core/window.py

Line 547 in 648ae4f

return sig.get_window(win_type, window).astype(float)

. For the second, no idea.

jreback · 2017-03-12T17:57:31Z

@zym1010 for 1st one: so looks like they added an argument. Were we just ignoring this before? (so its now required). did they give any warning? is it back-compat to prior versions? (if so, let's just add the arg, no big deal).

For the 2nd just add in a conditional in the tests:

if scipy.__version__ >= LooseVersion('0.19.0'):
    # this results
else:
    # old results

We do this in a couple of other places as well for scipy results.

can you do a PR? (note that we are not actually testing with 0.19.0 yet as we don't have a fully conda-forge build for a couple of reasons), but I think I can change one of ours to do that.

zym1010 · 2017-03-12T18:06:01Z

@jreback for 1st one: the argument is always there, and it's nullified if the window length is odd in previous versions. Now it's not the case. So in some sense I would say this is a bug on pandas' side. But yeah, they gave no warning on this nullifying behavior, and I don't think this change is in their release notes.

for second one. Alright. I will take your approach. BTW, the change is due to their spline generator (previously they used splmake, now not). See scipy/scipy#6710.

can you do a PR?

No problem. Should be done by midnight today when I'm more or less done with other work.

jreback · 2017-03-12T18:09:59Z

@zym1010 awesome! I will put in place a PR to have testing on conda-forge (so we use 0.19.0 for scipy soon). It will fail master, but hopefully your PR should fix!.

jreback · 2017-03-13T00:54:17Z

ok, merged #15668

change the skipping on scipy 0.19.0 when you push.

zym1010 · 2017-03-14T18:55:13Z

@jreback can you have a look at #15689? I'm not sure if I "change the skipping on scipy 0.19.0" correctly.

fix pandas-dev#15662 Author: Yimeng Zhang <zym1010@gmail.com> Closes pandas-dev#15689 from zym1010/fix_scipy019 and squashes the following commits: 3cc6528 [Yimeng Zhang] doc and PEP8 9ed7524 [Yimeng Zhang] fix interpolation related issue with scipy 0.19 ca09705 [Yimeng Zhang] get symmetric window

jreback added Numeric Operations Arithmetic, Comparison, and Logical operations Compat pandas objects compatability with Numpy or Python functions labels Mar 12, 2017

jreback added this to the 0.20.0 milestone Mar 12, 2017

jreback added the Testing pandas testing functions or related to the test suite label Mar 12, 2017

jreback mentioned this issue Mar 12, 2017

CI: use conda-forge on 3.6 build #15668

Closed

philippjfr mentioned this issue Mar 13, 2017

Pin scipy=0.18.1 due to pandas issue holoviz/holoviews#1207

Merged

zym1010 mentioned this issue Mar 14, 2017

compatibility with scipy 0.19 #15689

Closed

jreback closed this as completed in 76e5185 Mar 15, 2017

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Pandas test fails with Scipy 0.19 #15662

Pandas test fails with Scipy 0.19 #15662

zym1010 commented Mar 12, 2017

jreback commented Mar 12, 2017

jreback commented Mar 12, 2017

zym1010 commented Mar 12, 2017

zym1010 commented Mar 12, 2017 •

edited

jreback commented Mar 12, 2017 •

edited

zym1010 commented Mar 12, 2017 •

edited

jreback commented Mar 12, 2017

jreback commented Mar 13, 2017

zym1010 commented Mar 14, 2017

Pandas test fails with Scipy 0.19 #15662

Pandas test fails with Scipy 0.19 #15662

Comments

zym1010 commented Mar 12, 2017

Code Sample, a copy-pastable example if possible

Problem description

Expected Output

Output of pd.show_versions()

jreback commented Mar 12, 2017

jreback commented Mar 12, 2017

zym1010 commented Mar 12, 2017

zym1010 commented Mar 12, 2017 • edited

jreback commented Mar 12, 2017 • edited

zym1010 commented Mar 12, 2017 • edited

jreback commented Mar 12, 2017

jreback commented Mar 13, 2017

zym1010 commented Mar 14, 2017

Output of `pd.show_versions()`

zym1010 commented Mar 12, 2017 •

edited

jreback commented Mar 12, 2017 •

edited

zym1010 commented Mar 12, 2017 •

edited