BUG: Change numeric_only default to True #46096

NumberPiOso · 2022-02-21T16:28:03Z

I know I have to correct the other tests that fail due to this change. But I want confirmation that this PR is headed in the right direction before doing so.

closes BUG: DataFrame quantile with only datetime dtypes should provide better error message #7308
Tests added and passed if fixing a bug or adding a new feature
All code checks passed.
Added an entry in the latest doc/source/whatsnew/v1.5.0.rst file if fixing a bug or adding a new feature.

jreback

this is not going to be possible to change before 2.0

pandas/core/frame.py

NumberPiOso · 2022-02-23T14:39:37Z

Hello @phofl, do you think this would be the way to go?

I am still having some errors in the tests, when I run

pytest -v pandas/tests/frame/methods/test_quantile.py
...
======== 73 passed, 8 xfailed, 6 warnings in 2.46s =========

Getting al the warnings produced by my modifcation, even though I included the next line as decorator to those tests
python @pytest.mark.filterwarnings("ignore:In future versions of pandas, numeric_only")
Full output below

=================== test session starts ====================
platform linux -- Python 3.8.12, pytest-6.2.5, py-1.11.0, pluggy-1.0.0 -- /home/pi/anaconda3/envs/pandas-dev/bin/python
cachedir: .pytest_cache
hypothesis profile 'ci' -> deadline=None, suppress_health_check=[HealthCheck.too_slow], database=DirectoryBasedExampleDatabase('/home/pi/git/mypandas/.hypothesis/examples')
rootdir: /home/pi/git/mypandas, configfile: pyproject.toml
plugins: asyncio-0.17.2, cython-0.1.1.post0, cov-3.0.0, hypothesis-6.36.0, instafail-0.4.1, forked-1.4.0, xdist-2.5.0
asyncio: mode=legacy
collected 81 items

pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_numeric_only_default_false_warning PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_sparse[df0-expected0] PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_sparse[df1-expected1] PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_date_range PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_axis_mixed PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_axis_parameter PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_interpolation PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_interpolation_datetime PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_interpolation_int PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_multi PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_datetime PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_dt64_empty[datetime64[ns]] PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_dt64_empty[datetime64[ns, US/Pacific]] PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_dt64_empty[timedelta64[ns]] PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_dt64_empty[Period[D]] PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_invalid PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_box PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_nan PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_nat PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_empty_no_rows_floats PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_empty_no_rows_ints PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_empty_no_rows_dt64 PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_empty_no_columns PASSED
pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_item_cache PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[interval[int64, right]-DataFrame] XFAIL
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[interval[int64, right]-Series] XFAIL
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[period[D]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[period[D]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[datetime64[ns, US/Pacific]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[datetime64[ns, US/Pacific]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[timedelta64[ns]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[timedelta64[ns]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[Int64-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[Int64-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[Float64-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea[Float64-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[interval[int64, right]-DataFrame] XFAIL
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[interval[int64, right]-Series] XFAIL
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[period[D]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[period[D]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[datetime64[ns, US/Pacific]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[datetime64[ns, US/Pacific]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[timedelta64[ns]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[timedelta64[ns]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[Int64-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[Int64-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[Float64-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_with_na[Float64-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[interval[int64, right]-DataFrame] XFAIL
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[interval[int64, right]-Series] XFAIL
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[period[D]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[period[D]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[datetime64[ns, US/Pacific]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[datetime64[ns, US/Pacific]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[timedelta64[ns]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[timedelta64[ns]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[Int64-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[Int64-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[Float64-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_all_na[Float64-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[interval[int64, right]-DataFrame] XFAIL
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[interval[int64, right]-Series] XFAIL
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[period[D]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[period[D]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[datetime64[ns, US/Pacific]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[datetime64[ns, US/Pacific]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[timedelta64[ns]-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[timedelta64[ns]-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[Int64-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[Int64-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[Float64-DataFrame] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_quantile_ea_scalar[Float64-Series] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_empty_numeric[float64-expected_data0-expected_index0-1] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_empty_numeric[int64-expected_data1-expected_index1-1] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_empty_numeric[float64-expected_data2-expected_index2-0] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_empty_numeric[int64-expected_data3-expected_index3-0] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_empty_datelike[datetime64[ns]-expected_data0-expected_index0-1-datetime64[ns]] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_empty_datelike[datetime64[ns]-expected_data1-expected_index1-0-datetime64[ns]] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_datelike_numeric_only[expected_data0-expected_index0-1] PASSED
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_datelike_numeric_only[expected_data1-expected_index1-0] PASSED

===================== warnings summary =====================
../../anaconda3/envs/pandas-dev/lib/python3.8/site-packages/pytest_asyncio/plugin.py:191
/home/pi/anaconda3/envs/pandas-dev/lib/python3.8/site-packages/pytest_asyncio/plugin.py:191: DeprecationWarning: The 'asyncio_mode' default value will change to 'strict' in future, please explicitly use 'asyncio_mode=strict' or 'asyncio_mode=auto' in pytest configuration file.
config.issue_config_time_warning(LEGACY_MODE, stacklevel=2)

pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_axis_mixed
/home/pi/git/mypandas/pandas/tests/frame/methods/test_quantile.py:124: FutureWarning: In future versions of pandas, numeric_only will be set to False by default, and the datetime/timedelta columns will be considered in the results. To not consider these columnsspecify numeric_only=True and ignore this warning.
result = df.quantile(0.5, axis=1)

pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_datelike_numeric_only[expected_data0-expected_index0-1]
pandas/tests/frame/methods/test_quantile.py::TestQuantileExtensionDtype::test_datelike_numeric_only[expected_data1-expected_index1-0]
/home/pi/git/mypandas/pandas/tests/frame/methods/test_quantile.py:786: FutureWarning: In future versions of pandas, numeric_only will be set to False by default, and the datetime/timedelta columns will be considered in the results. To not consider these columnsspecify numeric_only=True and ignore this warning.
result = df[["a", "c"]].quantile(0.5, axis=axis)

../../anaconda3/envs/pandas-dev/lib/python3.8/site-packages/_pytest/cacheprovider.py:428
/home/pi/anaconda3/envs/pandas-dev/lib/python3.8/site-packages/_pytest/cacheprovider.py:428: PytestCacheWarning: cache could not write path /home/pi/git/mypandas/.pytest_cache/v/cache/nodeids
config.cache.set("cache/nodeids", sorted(self.cached_nodeids))

../../anaconda3/envs/pandas-dev/lib/python3.8/site-packages/_pytest/stepwise.py:49
/home/pi/anaconda3/envs/pandas-dev/lib/python3.8/site-packages/_pytest/stepwise.py:49: PytestCacheWarning: cache could not write path /home/pi/git/mypandas/.pytest_cache/v/cache/stepwise
session.config.cache.set(STEPWISE_CACHE_DIR, [])

-- Docs: https://docs.pytest.org/en/stable/warnings.html

generated xml file: /home/pi/git/mypandas/test-data.xml --
=================== slowest 30 durations ===================
0.07s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_numeric_only_default_false_warning
0.02s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_datetime
0.01s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_box
0.01s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile
0.01s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_nan
0.01s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_dt64_empty[Period[D]]
0.01s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_empty_no_rows_dt64
0.01s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_dt64_empty[datetime64[ns]]
0.01s call pandas/tests/frame/methods/test_quantile.py::TestDataFrameQuantile::test_quantile_nat

(21 durations < 0.005s hidden. Use -vv to show these durations.)
======== 73 passed, 8 xfailed, 6 warnings in 2.46s =========

pandas/core/frame.py

doc/source/whatsnew/v1.5.0.rst

pandas/tests/frame/methods/test_quantile.py

jreback · 2022-03-02T01:16:14Z

also pls rebase

pandas/core/frame.py

NumberPiOso · 2022-03-02T20:26:41Z

Should we modify EXAMPLES in documentation?

pandas/pandas/core/frame.py

Lines 10573 to 10580 in 0ccad38

    
                   >>> df.quantile(.1) 
        
                   a    1.3 
        
                   b    3.7 
        
                   Name: 0.1, dtype: float64 
        
                   >>> df.quantile([.1, .5]) 
        
                          a     b 
        
                   0.1  1.3   3.7 
        
                   0.5  2.5  55.0

jreback

yees pls update the docs to avoid showing this warning

doc/source/whatsnew/v1.5.0.rst

pandas/tests/frame/methods/test_quantile.py

jreback · 2022-03-03T19:32:43Z

pandas/core/frame.py

@@ -10570,11 +10570,11 @@ def quantile(
        --------
        >>> df = pd.DataFrame(np.array([[1, 1], [2, 10], [3, 100], [4, 100]]),
        ...                   columns=['a', 'b'])
-        >>> df.quantile(.1)
+        >>> df.quantile(.1, numeric_only=True)


these should't be necessary, only add the option where it actually matters

pandas/core/frame.py

This reverts commit 48ccac6.

phofl

small comments

pandas/tests/frame/methods/test_quantile.py

phofl · 2022-03-10T15:54:13Z

pandas/tests/frame/methods/test_quantile.py

+        [
+            pd.date_range("2014-01-01", periods=3, freq="m"),
+            ["a", "b", "c"],
+            [DataFrame, Series, Timestamp],


What are you testing with this?

The actual quantile method must ignore the non numeric columns and produce a warning. I am using three different non-numeric columns. A date column, a string column and a column of objects.

jreback · 2022-03-16T01:06:00Z

@NumberPiOso can you merge master and ping on green

…ic-only

jreback · 2022-03-18T00:49:07Z

thanks @NumberPiOso

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jreback added Algos Non-arithmetic algos: value_counts, factorize, sorting, isin, clip, shift, diff Deprecate Functionality to remove in pandas quantile quantile method labels Mar 2, 2022

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DEPR: log of deprecations in 1.x (to be removed in 2.0) #30228

Closed

NumberPiOso added a commit to NumberPiOso/pandas that referenced this pull request Mar 2, 2022

Rebase pandas-dev#46096 on main

3cffa0f

NumberPiOso force-pushed the ench-quantile-numeric-only branch 2 times, most recently from 3cffa0f to 2a3ae84 Compare March 2, 2022 20:22

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NumberPiOso force-pushed the ench-quantile-numeric-only branch from a784237 to f51bfca Compare March 8, 2022 20:23

NumberPiOso added 5 commits March 9, 2022 08:11

BUG: Change numeric_only default to True

d98e262

Add future warning numeric_only in DataFrame.quantile

0db8e52

Add deprecations.quantile_datetime_timedelta_colums in whatsnew

c427795

Add stacklevel to warning in DataFrame.quantile

fcf37a8

Modify test to expect warning in test_quantile.py

7e1d286

NumberPiOso added 14 commits March 9, 2022 08:11

Ignore FutureWarning at test_quantile.py

a5e6def

Correct documentation numeric_only inDataFrame.quantile

108bb45

DEPR: Specify nodefault for numeric_only default

93c5f65

DEPR: Update whatsnew pandas-dev#7308

0f37c30

DEPR: Correct frame.quantile tests to specify numeric_only

a324dc9

DEPR: Correct message error frame.quantile

82db984

DEPR: Remove warning filtering DataFrame.quantile

9e9b7a9

DEPR: Update whatsnew doc about numeric_only attribute

67f2cfa

DEPR: Update Examples in docs frame.quantile

42e7df4

DEPR: Correct test finalize DataFrame.quantile

d0a1221

Revert "DEPR: Correct frame.quantile tests to specify numeric_only"

377cc54

This reverts commit 48ccac6.

DEPR: Update tests of quantile with non num cols"

b460aa2

DEPR: Raise warning frame.quantile with numeric_only

7194d13

DEPR: Update doctests quantile, numeric only

f5f7a3e

NumberPiOso force-pushed the ench-quantile-numeric-only branch from 5e2d02d to f5f7a3e Compare March 9, 2022 13:11

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DEPR: Correct test_numeric_only_default_false_warning

16e5fc2

DEPR: Add non numeric test to numeric_only warning

b88b196

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DERP: correct_test_produces_warning in frame.quantile

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Merge remote-tracking branch 'upstream/main' into ench-quantile-numer…

4438118

…ic-only

NumberPiOso requested a review from jreback March 16, 2022 12:38

jreback merged commit aa3e420 into pandas-dev:main Mar 18, 2022

yehoshuadimarsky pushed a commit to yehoshuadimarsky/pandas that referenced this pull request Jul 13, 2022

BUG: Change numeric_only default to True (pandas-dev#46096)

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BUG: Change numeric_only default to True #46096

BUG: Change numeric_only default to True #46096

NumberPiOso commented Feb 21, 2022 •

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jreback commented Mar 18, 2022

BUG: Change numeric_only default to True #46096

BUG: Change numeric_only default to True #46096

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