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COMPAT: rename isnull -> isna, notnull -> notna #16972

Merged
merged 4 commits into from
Jul 25, 2017
Merged

COMPAT: rename isnull -> isna, notnull -> notna #16972

merged 4 commits into from
Jul 25, 2017

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@jreback jreback commented Jul 15, 2017 •
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existing isnull, notnull remain user facing, will show DeprecationWarning

closes #15001

@jreback jreback added API Design Compat pandas objects compatability with Numpy or Python functions Missing-data np.nan, pd.NaT, pd.NA, dropna, isnull, interpolate labels Jul 15, 2017
@jreback jreback added this to the 0.21.0 milestone Jul 15, 2017
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jreback commented Jul 15, 2017

we might want to put in place a DeprecationWarning for this.

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codecov bot commented Jul 16, 2017 •
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Codecov Report

Merging #16972 into master will decrease coverage by 0.04%.
The diff coverage is 92.22%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master   #16972      +/-   ##
==========================================
- Coverage   91.05%      91%   -0.05%     
==========================================
  Files         161      161              
  Lines       49363    49381      +18     
==========================================
- Hits        44948    44941       -7     
- Misses       4415     4440      +25
Flag Coverage Δ
#multiple 88.78% <90.83%> (-0.04%) ⬇️
#single 40.29% <42.5%> (-0.03%) ⬇️
Impacted Files Coverage Δ
pandas/io/json/json.py 100% <ø> (ø) ⬆️
pandas/io/formats/style.py 100% <ø> (ø) ⬆️
pandas/core/sorting.py 98.19% <100%> (ø) ⬆️
pandas/core/util/hashing.py 98.34% <100%> (ø) ⬆️
pandas/core/reshape/pivot.py 95.18% <100%> (ø) ⬆️
pandas/io/stata.py 93.66% <100%> (ø) ⬆️
pandas/util/_decorators.py 65.65% <100%> (+0.35%) ⬆️
pandas/core/indexes/datetimes.py 95.33% <100%> (ø) ⬆️
pandas/plotting/_core.py 82.8% <100%> (ø) ⬆️
pandas/core/config_init.py 95.9% <100%> (+0.03%) ⬆️
... and 41 more

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gfyoung commented Jul 16, 2017

existing isnull, notnull remain user facing

What do you mean by this?

we might want to put in place a DeprecationWarning for this.

I'm in favor of this. I don't see the harm given that we've had surprises before. 😢

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jreback commented Jul 17, 2017

see comment: #15001 (comment) about deprecating isnull/notnull.

I think it makes sense to issue a DeprecationWarning here, so not super visible but gives us flexibilty about when to change this to FutureWarning; so this would be similar to how we are handling Panel and .ix. DeprecationWarning now, FutureWarning in 1.x (still TBD).

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gfyoung commented Jul 17, 2017

I think it makes sense to issue a DeprecationWarning here, so not super visible but gives us flexibilty about when to change this to FutureWarning

Gotcha. Makes sense.

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gfyoung commented Jul 19, 2017

@jreback : Are there tests for this deprecation? (diff takes forever to load 😢 )

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jreback commented Jul 19, 2017

not yet

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jreback commented Jul 22, 2017

any comments

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wesm commented Jul 22, 2017

I see my +1 on adding isna/notna from December 28, but I'm feeling less keen on adding a deprecation warning for such an old and commonly used function. Would it be acceptable to leave it as an alias to isna/notna, respectively?

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jreback commented Jul 23, 2017

no biggie to remove the DeprecationWarning. only issue remaining is do I mention this in api.rst at all (its already changed in the docs proper).?

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wesm commented Jul 23, 2017

Seems like a good idea since people may Google search for it and find old documentation pages otherwise

@jreback jreback merged commit 7930202 into pandas-dev:master Jul 25, 2017
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Great!

Added some doc comments after the fact. (can maybe also do a PR to fix them)

doc/source/missing_data.rst
@@ -36,7 +36,7 @@ When / why does data become missing?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Some might quibble over our usage of *missing*. By "missing" we simply mean
**null** or "not present for whatever reason". Many data sets simply arrive with
**na** or "not present for whatever reason". Many data sets simply arrive with
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I would personally use 'NA' instead of 'na' in prose. Thoughts?
Would also add this stands for 'Not Available' this first time

doc/source/whatsnew/v0.21.0.txt
NA naming Changes
^^^^^^^^^^^^^^^^^

In orde to promote more consistency among the pandas API, we have added additional top-level
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orde -> order

pandas/core/dtypes/missing.py


def _isnull_new(obj):
isnull = isna
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I think we should give isnull a separate docstring indicating this is an alias of isna.
But not sure how to easily achieve this without duplicating the full docstring and the function definition

(same fore notnull)

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these are all in the See Also section. It looks ok to me, but I guess could open an issue about this; could do it with a doc-template I think.

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yes, but the see also section is not fully 'correct' in case of isnull, as it doesn't link to isna (I mean, isna docstring should link to isnull, and isnull docstring to isna. Now they both link to isnull)

pandas/core/generic.py
def isnull(self):
return isnull(self).__finalize__(self)
return isna(self).__finalize__(self)
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Also here the docstring of isnull is not fully correct

jreback added a commit that referenced this pull request Jul 27, 2017
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DOC: fix typos in missing.rst
465c59f 
xref #16972
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jreback commented Jul 27, 2017

fixed in 465c59f

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Thanks!

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@jorisvandenbossche jorisvandenbossche mentioned this pull request Aug 21, 2017
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rs2 added a commit to rs2/pandas that referenced this pull request Aug 30, 2017
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Rebase from master (#1)
5b4cc45 
* consolidated the duplicate definitions of NA values (in parsers & IO) (pandas-dev#16589)

* GH15943 Fixed defaults for compression in HDF5 (pandas-dev#16355)

* DOC: add header=None to read_excel docstring (pandas-dev#16689)

* TST: Test against python-dateutil master (pandas-dev#16648)

* BUG: .iloc[:] and .loc[:] return a copy of the original object pandas-dev#13873 (pandas-dev#16443)

closes pandas-dev#13873

* TST: Add test of building frame from named Series and columns (pandas-dev#9232) (pandas-dev#16700)

* DOC: fix wrongly placed versionadded (pandas-dev#16702)

* DOC: pin sphinx to version 1.5 (pandas-dev#16704)

* CI: restore np 113 in ci builds (pandas-dev#16656)

* Revert "BLD: fix numpy on 3.6 build as 1.13 was released but no deps are built for it (pandas-dev#16633)"

This reverts commit dfebd8a.

closes pandas-dev#16634

* BUG: Fix regression for RGB(A) color arguments (pandas-dev#16701)

* Add test

* Pass tuples that are RGB or RGBA like in list

* Update what's new

* change whatsnew to reflect regression fix

* Add test for RGBA as well

* CI: pin jemalloc=4.4.0 (pandas-dev#16727)

* MAINT: Drop Categorical.order & sort (pandas-dev#16728)

Deprecated back in 0.18.1

xref pandas-devgh-12882

* Fix reading Series with read_hdf (pandas-dev#16610)

* Added test to reproduce issue pandas-dev#16583

* Fix pandas-dev#16583 by adding an explicit `mode` argument to `read_hdf`

kwargs which are meant for the opening of the HDFStore should be filtered out
before passing the remaining kwargs to the `select` function to load the data.

* Noted fix for pandas-dev#16583 in WhatsNew

* DOC: typo (pandas-dev#16733)

* whatsnew v0.21.0.txt typos (pandas-dev#16742)

* whatsnew v0.20.3 edits (pandas-dev#16743)

* BUG: do not raise UnsortedIndexError if sorting is not required

closes pandas-dev#16734

Author: Pietro Battiston <me@pietrobattiston.it>

This patch had conflicts when merged, resolved by
Committer: Jeff Reback <jeff.reback@twosigma.com>

Closes pandas-dev#16736 from toobaz/index_what_you_can and squashes the following commits:

f77e2b3 [Pietro Battiston] BUG: do not raise UnsortedIndexError if sorting is not required

* DOC: whatsnew typos

* Test for pandas-dev#16726. unittest that ensures datetime is understood (pandas-dev#16744)

* Test for pandas-dev#16726. unittest that ensures datetime is understood

* Corrected the test as suggested by @TomAugspurger

* Fixed flake8 errors and warnings

* DOC: some rst fixes (pandas-dev#16763)

* DOC: Update Sphinx Deprecated Directive (pandas-dev#16512)

* MAINT: Drop Index.sym_diff (pandas-dev#16760)

Deprecated in 0.18.1

xref pandas-devgh-12591, pandas-devgh-12594

* MAINT: Drop pd.options.display.mpl_style (pandas-dev#16761)

Deprecated in 0.18.0

xref pandas-devgh-12190

* DOC: remove section on Panel4D support in HDF io (pandas-dev#16783)

* DOC: add section on data validation and library engarde (pandas-dev#16758)

* TST: register slow marker (pandas-dev#16797)

* TST: register slow marker

* Update setup.cfg

* BUG: Load data from a CategoricalIndex for dtype comparison, closes #… (pandas-dev#16738)

* BUG: Load data from a CategoricalIndex for dtype comparison, closes pandas-dev#16627

* Enable is_dtype_equal on CategoricalIndex, fixed some doc typos, added ordered CategoricalIndex test

* Flake8 windows suggestion

* Fixed some documentation/formatting issues, clarified the purpose of the test case.

* Bug in pd.merge() when merge/join with multiple categorical columns (pandas-dev#16786)

closes pandas-dev#16767

* BUG: Fix read of py3 PeriodIndex DataFrame HDF made in py2 (pandas-dev#16781) (pandas-dev#16790)

In Python3, reading a DataFrame with a PeriodIndex from an HDF file
created in Python2 would incorrectly return a DataFrame with an
Int64Index.

* BUG: Fix Series doesn't work in pd.astype(). Now treat Series as dict. (pandas-dev#16725)

* FIX: Allow aggregate to return dictionaries again pandas-dev#16741 (pandas-dev#16752)

* BUG: fix to_latex bold_rows option (pandas-dev#16708)

* Revert "CI: pin jemalloc=4.4.0 (pandas-dev#16727)" (pandas-dev#16731)

This reverts commit 09d8c22.

* CI: use dist/trusty rather than os/linux (pandas-dev#16806)

closes pandas-dev#16730

* TST: Verify columns entirely below chop_threshold still print (pandas-dev#6839) (pandas-dev#16809)

* BUG: clip dataframe column-wise pandas-dev#15390 (pandas-dev#16504)

* TST: Verify that positional shifting works with duplicate columns (pandas-dev#9092) (pandas-dev#16810)

* BUG: render dataframe as html do not produce duplicate element id's (pandas-dev#16780) (pandas-dev#16801)

* BUG: when rendering dataframe as html do not produce duplicate element id's pandas-dev#16780

* CLN: removing spaces in code causes pylint check to fail

* DOC: moved whatsnew comment to 0.20.3 release from 0.21.0

* fix BUG: ValueError when performing rolling covariance on multi indexed DataFrame (pandas-dev#16814)

* fix multi index names

* fix line length to pep8

* added what's new entry and reference issue number in test

* Update test_multi.py

* Update v0.20.3.txt

* BUG: rolling.cov with multi-index columns should presever the MI (pandas-dev#16825)

xref pandas-dev#16814

* use network decorator on additional tests (pandas-dev#16824)

* BUG: TimedeltaIndex raising ValueError when slice indexing (pandas-dev#16637) (pandas-dev#16638)

* Bug issue 16819 Index.get_indexer_not_unique inconsistent return types vs get_indexer (pandas-dev#16826)

* TST: Verify that float columns stay float after pivot (pandas-dev#7142) (pandas-dev#16815)

* BUG/MAINT: Change default of inplace to False in pd.eval (pandas-dev#16732)

* BUG: kind parameter on categorical argsort (pandas-dev#16834)

* DOC: Updated cookbook to show usage of Grouper instead of TimeGrouper… (pandas-dev#16794)

* BUG: allow empty multiindex (fixes .isin regression, GH16777) (pandas-dev#16782)

* BUG: fix missing sort keyword for PeriodIndex.join (pandas-dev#16586)

* COMPAT: 32-bit compat for testing of indexers (pandas-dev#16849)

xref pandas-dev#16826

* BUG: fix infer frequency for business daily (pandas-dev#16683)

* DOC: Whatsnew updates (pandas-dev#16853)

[ci skip]

* TST/PKG: Move test HDF5 file to legacy (pandas-dev#16856)

It wasn't being picked up in our package data otherwise

* COMPAT: moar 32-bit compat for testing of indexers (pandas-dev#16861)

xref pandas-dev#16826

* MAINT: Drop the get_offset_name method (pandas-dev#16863)

Deprecated since 0.18.0

xref pandas-devgh-11834

* DOC: Fix missing parentheses in documentation (pandas-dev#16862)

* BUG: rolling.quantile does not return an interpolated result (pandas-dev#16247)

* ENH - Modify Dataframe.select_dtypes to accept scalar values (pandas-dev#16860)

* COMPAT: moar 32-bit compat for testing of indexers (pandas-dev#16869)

xref pandas-dev#16826

* Confirm that select was *not* clearer in 0.12 (pandas-dev#16878)

* Added tests for _get_dtype (pandas-dev#16845)

* BUG: Series.isin fails or categoricals (pandas-dev#16858)

* COMPAT with dateutil 2.6.1, fixed ambiguous tz dst behavior (pandas-dev#16880)

* fix wrongly named method (pandas-dev#16881)

* TST/PKG: Removed pandas.util.testing.slow definition (pandas-dev#16852)

* MAINT: Remove unused mock import (pandas-dev#16908)

We import it, set it as an attribute, and then don't use it.

* Let _get_dtype accept Categoricals and CategoricalIndex  (pandas-dev#16887)

* Fixes for pandas-dev#16896(TimedeltaIndex indexing regression for strings) (pandas-dev#16907)

* Fix for pandas-dev#16909(DeltatimeIndex.get_loc is not working on np.deltatime64 data type) (pandas-dev#16912)

* DOC: Recommend sphinx 1.5 for now (pandas-dev#16929)

For the SciPy sprint tomorrow, until the cause of the doc-building slowdown is fully identified.

* BUG: Allow value labels to be read with iterator (pandas-dev#16926)

All value labels to be read before the iterator has been used
Fix issue where categorical data was incorrectly reformatted when
write_index was False

closes pandas-dev#16923

* DOC: Update flake8 command instructions (pandas-dev#16919)

* TST: Don't assert that a bug exists in numpy (pandas-dev#16940)

Better to ignore the warning from the bug, rather than assert the bug is still there

After this change, numpy/numpy#9412 _could_ be backported to fix the bug

* CI: add .pep8speakes.yml

* CLN16668: remove OrderedDefaultDict (pandas-dev#16939)

* Change "pls" to "please" in error message (pandas-dev#16947)

* BUG: MultiIndex sort with ascending as list (pandas-dev#16937)

* DOC: Improving docstring of pop method (pandas-dev#16416) (pandas-dev#16520)

* PEP8

* WARN: add stacklevel to to_dict() UserWarning (pandas-dev#16927) (pandas-dev#16936)

* ERR: add stacklevel to to_dict() UserWarning (pandas-dev#16927)

* TST: Add warning testing to to_dict()

* Fix warning assertion on to_dict() test

* Add github issue to documentation on to_dict() warning test

* CI: fix pep8speaks .yml file

* DOC: whatsnew 0.21.0 edits

* CI: disable codecov reporting

* MAINT: Move series.remove_na to core.dtypes.missing.remove_na_arraylike

Closes pandas-devgh-16935

* Support non unique period indexes on join and merge operations (pandas-dev#16949)

* Support non unique period indexes on join and merge operations

* Add frame assertion on tests and release notes

* Explicitly use dtype int64 on arange

* BUG: Set secondary axis font size for `secondary_y` during plotting

The parameter was not being respected for `secondary_y`.

Closes pandas-devgh-12565

* DOC: more whatsnew fixes

* DOC: Reset index examples

closes pandas-dev#16416

Author: aernlund <awe220@nyumc.org>

Closes pandas-dev#16967 from aernlund/reset_index_docs and squashes the following commits:

3c6a4b6 [aernlund] DOC: added examples to reset_index
4838155 [aernlund] DOC: added examples to reset_index
2a51e2b [aernlund] DOC: added examples to reset_index

* channel from pandas to conda-forge (pandas-dev#16966)

* BUG: coercing of bools in groupby transform (pandas-dev#16895)

* DOC: misspelling in DatetimeIndex.indexer_between_time [CI skip] (pandas-dev#16963)

* CLN: some residual code removed, xref to pandas-dev#16761 (pandas-dev#16974)

* ENH: Create a 'Y' alias for date_range yearly frequency

Closes pandas-devgh-9313

* Revert "ENH: Create a 'Y' alias for date_range yearly frequency" (pandas-dev#16976)

This reverts commit 9c096d2, as it was prematurely made.

* DOC: behavior when slicing with missing bounds (pandas-dev#16932)

closes pandas-dev#16917

* TST: Add test for sub-char in read_csv (pandas-dev#16977)

Closes pandas-devgh-16893.

* DEPR: deprecate html.border option (pandas-dev#16970)

* DOC: document convention argument for resample() (pandas-dev#16965)

* DOC: document convention argument for resample()

* DOC: Clarify 'it' in aggregate doc (pandas-dev#16989)

Closes pandas-devgh-16988.

* CLN/COMPAT: for various py2/py3 in doc/bench scripts (pandas-dev#16984)

* PERF: SparseDataFrame._init_dict uses intermediary dict, not DataFrame (pandas-dev#16883)

Closes pandas-devgh-16773.

* MAINT: Drop line_width and height from options (pandas-dev#16993)

Deprecated since 0.11 and 0.12 respectively.

* COMPAT: Add back remove_na for seaborn (pandas-dev#16992)

Closes pandas-devgh-16971.

* COMPAT: np.full not available in all versions, xref pandas-dev#16773 (pandas-dev#17000)

* DOC, TST: Clarify whitespace behavior in read_fwf documentation (pandas-dev#16950)

Closes pandas-devgh-16772

* API: add infer_objects for soft conversions (pandas-dev#16915)

* API: add infer_objects for soft conversions

* doc fixups

* fixups

* doc

* BUG: np.inf now causes Index to upcast from int to float (pandas-dev#16996)

Closes pandas-devgh-16957.

* DOC: Make highlight functions match documentation (pandas-dev#16999)

Closes pandas-devgh-16998.

* BUG: Large object array isin

closes pandas-dev#16012

Author: Morgan Stuart <morgansstuart243@gmail.com>

Closes pandas-dev#16969 from Morgan243/large_array_isin and squashes the following commits:

31cb4b3 [Morgan Stuart] Removed unneeded details from whatsnew description
4b59745 [Morgan Stuart] Linting errors; additional test clarification
186607b [Morgan Stuart] BUG pandas-dev#16012 - fix isin for large object arrays

* BUG: reindex would throw when a categorical index was empty pandas-dev#16770

closes pandas-dev#16770

Author: ri938 <r_irv938@hotmail.com>
Author: Jeff Reback <jeff@reback.net>
Author: Tuan <tuan.d.tran@hotmail.com>
Author: Forbidden Donut <forbdonut@gmail.com>

This patch had conflicts when merged, resolved by
Committer: Jeff Reback <jeff@reback.net>

Closes pandas-dev#16820 from ri938/bug_issue16770 and squashes the following commits:

0e2d315 [ri938] Merge branch 'master' into bug_issue16770
9802288 [ri938] Update v0.20.3.txt
1f2865e [ri938] Update v0.20.3.txt
83fd749 [ri938] Update v0.20.3.txt
eab3192 [ri938] Merge branch 'master' into bug_issue16770
7acc09f [ri938] Minor correction to previous submit
6e8f1b3 [ri938] Minor corrections to previous submit (pandas-dev#16820)
9ed80f0 [ri938] Bring documentation into line with master branch.
26e1a60 [ri938] Move documentation of change to the next major release 0.21.0
59b17cd [Jeff Reback] BUG: rolling.cov with multi-index columns should presever the MI (pandas-dev#16825)
5362447 [Tuan] fix BUG: ValueError when performing rolling covariance on multi indexed DataFrame (pandas-dev#16814)
800b40d [ri938] BUG: render dataframe as html do not produce duplicate element id's (pandas-dev#16780) (pandas-dev#16801)
a725fbf [Forbidden Donut] BUG: Fix read of py3 PeriodIndex DataFrame HDF made in py2 (pandas-dev#16781) (pandas-dev#16790)
8f8e3d6 [ri938] TST: register slow marker (pandas-dev#16797)
0645868 [ri938] Add backticks in documentation
0a20024 [ri938] Minor correction to previous submit
69454ec [ri938] Minor corrections to previous submit (pandas-dev#16820)
3092bbc [ri938] BUG: reindex would throw when a categorical index was empty pandas-dev#16770

* BUG: Don't with empty Series for .isin (pandas-dev#17006)

Empty Series initializes to float64, even when the data type is object for .isin,
leading to an error with membership.

Closes pandas-devgh-16991.

* ENH: Use 'Y' as an alias for end of year (pandas-dev#16978)

Closes pandas-devgh-9313
Redo of pandas-devgh-16958

* DOC: infer_objects doc fixup (pandas-dev#17018)

* Fixes SparseSeries initiated with dictionary raising AttributeError (pandas-dev#16960)

* DOC: Improving docstring of reset_index method (pandas-dev#16416) (pandas-dev#16975)

* DOC: add warning to append about inefficiency (pandas-dev#17017)

* DOC : Remove redundant backtick (pandas-dev#17025)

* DOC: Document business frequency aliases (pandas-dev#17028)

Follow-up to pandas-devgh-16978.

* DOC: Fix double back-tick in 'Reshaping by Melt' section (pandas-dev#17030)

See current stable docs for the issue: https://pandas.pydata.org/pandas-docs/stable/reshaping.html#reshaping-by-melt

The double ` is causing the entire paragraph to be fixed width until the next double `. This commit removes the extra "`"

* Define DataFrame plot methods in DataFrame (pandas-dev#17020)

* CLN: move safe_sort from core.algorithms to core.sorting (pandas-dev#17034)

COMPAT: safe_sort will only coerce list-likes to object, not a numpy string type

xref: pandas-dev#17003 (comment)

* DOC: Fixed Minor Typo (pandas-dev#17043)

Cocumentation to Documentation

* BUG: do not cast ints to floats if inputs o crosstab are not aligned (pandas-dev#17011)

closes pandas-dev#17005

* BUG in merging categorical dates

closes pandas-dev#16900

Author: Dave Willmer <dave.willmer@gmail.com>

This patch had conflicts when merged, resolved by
Committer: Jeff Reback <jeff@reback.net>

Closes pandas-dev#16986 from dwillmer/cat_fix and squashes the following commits:

1ea1977 [Dave Willmer] Minor tweaks + comment
21a35a0 [Dave Willmer] Merge branch 'cat_fix' of https://github.com/dwillmer/pandas into cat_fix
04d5404 [Dave Willmer] Update tests
3cc5c24 [Dave Willmer] Merge branch 'master' into cat_fix
5e8e23b [Dave Willmer] Add whatsnew item
b82d117 [Dave Willmer] Lint fixes
a81933d [Dave Willmer] Remove unused import
218da66 [Dave Willmer] Generic solution to categorical problem
48e7163 [Dave Willmer] Test inner join
8843c10 [Dave Willmer] Fix TypeError when merging categorical dates

* BUG: __setitem__ with a tuple induces NaN with a tz-aware DatetimeIndex (pandas-dev#16889) (pandas-dev#16897)

* Added test for _get_dtype_type. (pandas-dev#16899)

* BUG/API: dtype inconsistencies in .where / .setitem / .putmask / .fillna (pandas-dev#16821)

* CLN/BUG: fix ndarray assignment may cause unexpected cast

supersedes pandas-dev#14145
closes pandas-dev#14001

* API: This fixes a number of inconsistencies and API issues
w.r.t. dtype conversions.

This is a reprise of pandas-dev#14145 & pandas-dev#16408.

This removes some code from the core structures & pushes it to internals,
where the primitives are made more consistent.

This should all us to be a bit more consistent for pandas2 type things.

closes pandas-dev#16402
supersedes pandas-dev#14145
closes pandas-dev#14001

CLN: remove uneeded code in internals; use split_and_operate when possible

* BUG: Improved thread safety for read_html() GH16928 (pandas-dev#16930)

* Fixed 'add_methods' when the 'select' argument is specified. (pandas-dev#17045)

* TST: Fix error message check in np.argsort comparision (pandas-dev#17051)

Closes pandas-devgh-17046.

* TST: Move some Series ctor tests to SharedWithSparse (pandas-dev#17050)

* BUG: Made SparseDataFrame.fillna() fill all NaNs

A continuation of pandas-dev#16178
closes pandas-dev#16112
closes pandas-dev#16178

Author: Kernc <kerncece@gmail.com>
Author: keitakurita <kris337jbn@yahoo.co.jp>

This patch had conflicts when merged, resolved by
Committer: Jeff Reback <jeff@reback.net>

Closes pandas-dev#16892 from kernc/sparse-fillna and squashes the following commits:

c1cd33e [Kernc] fixup! BUG: Made SparseDataFrame.fillna() fill all NaNs
2974232 [Kernc] fixup! BUG: Made SparseDataFrame.fillna() fill all NaNs
4bc01a1 [keitakurita] BUG: Made SparseDataFrame.fillna() fill all NaNs

* BUG: Use size_t to avoid array index overflow; add missing malloc of error_msg

Fix a few locations where a parser's `error_msg` buffer is written to
without having been previously allocated. This manifested as a double
free during exception handling code making use of the `error_msg`.
Additionally, use `size_t/ssize_t` where array indices or lengths will
be stored. Previously, int32_t was used and would overflow on columns
with very large amounts of data (i.e. greater than INTMAX bytes).

xref pandas-dev#14696
closes pandas-dev#16798

Author: Jeff Knupp <jeff.knupp@enigma.com>
Author: Jeff Knupp <jeff@jeffknupp.com>

Closes pandas-dev#17040 from jeffknupp/16790-core-on-large-csv and squashes the following commits:

6a1ba23 [Jeff Knupp] Clear up prose
a5d5677 [Jeff Knupp] Fix linting issues
4380c53 [Jeff Knupp] Fix linting issues
7b1cd8d [Jeff Knupp] Fix linting issues
e3cb9c1 [Jeff Knupp] Add unit test plus '--high-memory' option, *off by default*.
2ab4971 [Jeff Knupp] Remove debugging code
2930eaa [Jeff Knupp] Fix line length to conform to linter rules
e4dfd19 [Jeff Knupp] Revert printf format strings; fix more comment alignment
3171674 [Jeff Knupp] Fix some leftover size_t references
0985cf3 [Jeff Knupp] Remove debugging code; fix type cast
669d99b [Jeff Knupp] Fix linting errors re: line length
1f24847 [Jeff Knupp] Fix comment alignment; add whatsnew entry
e04d12a [Jeff Knupp] Switch to use int64_t rather than size_t due to portability concerns.
d5c75e8 [Jeff Knupp] BUG: Use size_t to avoid array index overflow; add missing malloc of error_msg

* TST: remove some test warnings in parser tests (pandas-dev#17057)

TST: move highmemory test to proper location in c_parser_only

xref pandas-dev#16798

* DOC: Add more examples for reset_index (pandas-dev#17055)

* MAINT: Add dash in high memory message

Follow-up to pandas-devgh-17057.

* MAINT: kwards --> kwargs in parsers.pyx

* CLN: Cleanup comments in before_install_travis.sh

envars.sh doesn't exist anymore.  In fact, it's been gone for awhile.

* MAINT: Remove duplicate Series sort_index check

Duplicate boolean validation check for sort_index in series/test_validate.py

* BLD: Pin pyarrow=0.4.1 (pandas-dev#17065)

Addresses pandas-devgh-17064.

Also add some additional build information when calling `pd.show_versions`

* ENH: provide "inplace" argument to set_axis()

closes pandas-dev#14636

Author: Pietro Battiston <me@pietrobattiston.it>

Closes pandas-dev#16994 from toobaz/set_axis_inplace and squashes the following commits:

8fb9d0f [Pietro Battiston] REF: adapt NDFrame.set_axis() calls to new signature
409f502 [Pietro Battiston] ENH: provide "inplace" argument to set_axis(), change signature

* BUG: Fix parser field type compatability on 32-bit systems. (pandas-dev#17071)

Closes pandas-devgh-17063

* COMPAT: rename isnull -> isna, notnull -> notna (pandas-dev#16972)

closes pandas-dev#15001

* BUG: Thoroughly dedup columns in read_csv (pandas-dev#17060)

* ENH: Add skipna parameter to infer_dtype (pandas-dev#17066)

Currently defaults to False for backwards compatibility.  Will default to True in the future.

Closes pandas-devgh-17059.

* MAINT: Remove unused variable in test_scalar.py

The "expected" variable is unused at the end of a test in indexing/test_scalar.py

* TST: Add tests/indexing/ and reshape/ to setup.py (pandas-dev#17076)

Looks like we just forgot about them.  Oops.

* CI: partially revert pandas-dev#17065, un-pin pyarrow on some builds

* DOC: whatsnew typos

* TST: Check more error messages in tests (pandas-dev#17075)

* BUG: Respect dtype when calling pivot_table with margins=True

closes pandas-dev#17013

This fix actually exposed an occurrence of pandas-dev#17035 in an existing test
(as well as in one I added).

Author: Pietro Battiston <me@pietrobattiston.it>

Closes pandas-dev#17062 from toobaz/pivot_margin_int and squashes the following commits:

2737600 [Pietro Battiston] Removed now obsolete workaround
956c4f9 [Pietro Battiston] BUG: respect dtype when calling pivot_table with margins=True

* MAINT: Add missing space in parsers.pyx

"2< heuristic" --> "2 < heuristic"

* MAINT: Add missing paren around print statement

Stray verbose print statement in parsers.pyx was bare without any parentheses.

* DOC: fix typos in missing.rst

xref pandas-dev#16972

* DOC: further clean-up null/na changes (pandas-dev#17113)

* BUG: Allow pd.unique to accept tuple of strings (pandas-dev#17108)

* BUG: Allow Series with same name with crosstab (pandas-dev#16028)

Closes pandas-devgh-13279

* COMPAT: make sure use_inf_as_null is deprecated (pandas-dev#17126)

closes pandas-dev#17115

* CI: bump version of xlsxwriter to 0.5.2 (pandas-dev#17142)

* DOC: Clean up instructions in ISSUE_TEMPLATE (pandas-dev#17146)

* Add missing space to the NotImplementedError's message for compound dtypes (pandas-dev#17140)

* DOC: (de)type the return value of concat (pandas-dev#17079) (pandas-dev#17119)

* BUG: Thoroughly dedup column names in read_csv (pandas-dev#17095)

* DOC: Additions/updates to documentation (pandas-dev#17150)

* ENH: add to/from_parquet with pyarrow & fastparquet (pandas-dev#15838)

* DOC: doc typos, xref pandas-dev#15838

* TST: test for categorical index monotonicity (pandas-dev#17152)

* correctly determine bottleneck version

* tests for categorical index monotonicity

* fix Index.is_monotonic to point to Index.is_monotonic_increasing directly

* MAINT: Remove non-standard and inconsistently-used imports (pandas-dev#17085)

* DOC: typos in whatsnew

* DOC: whatsnew 0.21.0 fixes

* BUG: Fix CSV parsing of singleton list header (pandas-dev#17090)

Closes pandas-devgh-7757.

* ENH: Support strings containing '%' in add_prefix/add_suffix (pandas-dev#17151) (pandas-dev#17162)

* REF: repr - allow block to override values that get formatted (pandas-dev#17143)

* MAINT: Drop unnecessary newlines in issue template

* remove direct import of nan

Author: Brock Mendel <jbrockmendel@gmail.com>

Closes pandas-dev#17185 from jbrockmendel/dont_import_nan and squashes the following commits:

ee260b8 [Brock Mendel] remove direct import of nan

* use == to test String equality (pandas-dev#17171)

* ENH: Add warning when setting into nonexistent attribute (pandas-dev#16951)

 closes pandas-dev#7175
 closes pandas-dev#5904

* DOC: added string processing comparison with SAS  (pandas-dev#16497)

* CLN: remove unused get methods in internals (pandas-dev#17169)

* Remove unused get methods that would raise AttributeError if called

* Remove unnecessary import

* TST: Partial Boolean DataFrame Indexing (pandas-dev#17186)

Closes pandas-devgh-17170

* CLN: Reformat docstring for IPython fixture

* Define Series.plot and Series.hist in class definition (pandas-dev#17199)

* BUG: support pandas objects in iloc with old numpy versions (pandas-dev#17194)

closes pandas-dev#17193

* Implement _make_accessor classmethod for PandasDelegate (pandas-dev#17166)

* Create ABCDateOffset (pandas-dev#17165)

* BUG: resample and apply modify the index type for empty Series (pandas-dev#17149)

* DOC: Updated NDFrame.astype docs (pandas-dev#17203)

* MAINT: Minor touch-ups to GitHub PULL_REQUEST_TEMPLATE (pandas-dev#17207)

Remove leading space from task-list so that tasks aren't nested.

* CLN: replace %s syntax with .format in core.computation (pandas-dev#17209)

* Bugfix for multilevel columns with empty strings in Python 2 (pandas-dev#17099)

* CLN/ASV clean-up frame stat ops benchmarks (pandas-dev#17205)

* BUG: Rolling apply on DataFrame with Datetime index returns NaN (pandas-dev#17156)

* CLN: Remove import exception handling (pandas-dev#17218)

Imports should succeed on all versions of Python that pandas supports.

* MAINT: Remove extra the's in deprecation messages (pandas-dev#17222)

* DOC: Patch docs in _decorators.py

* CLN: replace %s syntax with .format in pandas.util (pandas-dev#17224)

* Add 'See also' sections (pandas-dev#17223)

* move pivot_table doc-string to DataFrame (pandas-dev#17174)

* Remove import of pandas as pd in core.window (pandas-dev#17233)

* TST: Move more frame tests to SharedWithSparse (pandas-dev#17227)

* REF: _get_objs_combined_axis (pandas-dev#17217)

* ENH/PERF: Remove frequency inference from .dt accessor (pandas-dev#17210)

* ENH/PERF: Remove frequency inference from .dt accessor

* BENCH: Add DatetimeAccessor benchmark

* DOC: Whatsnew

* Fix apparent typo in tests (pandas-dev#17247)

* COMPAT: avoid calling getsizeof() on PyPy

closes pandas-dev#17228

Author: mattip <matti.picus@gmail.com>

Closes pandas-dev#17229 from mattip/getsizeof-unavailable and squashes the following commits:

d2623e4 [mattip] COMPAT: avoid calling getsizeof() on PyPy

* CLN: replace %s syntax with .format in pandas.core.reshape (pandas-dev#17252)

Replaced %s syntax with .format in pandas.core.reshape.  Additionally, made some of the existing positional .format code more explicit.

* ENH: Infer compression from non-string paths (pandas-dev#17206)

* Fix bugs in IntervalIndex.is_non_overlapping_monotonic (pandas-dev#17238)

* BUG: Fix behavior of argmax and argmin with inf (pandas-dev#16449) (pandas-dev#16449)

Closes pandas-dev#13595

* CLN: Remove have_pytz (pandas-dev#17266)

Closes pandas-devgh-17251

* CLN: replace %s syntax with .format in core.dtypes and core.sparse (pandas-dev#17270)

* Replace imports of * with explicit imports (pandas-dev#17269)

xref pandas-dev#17234

* TST: pytest deprecation warnings GH17197 (pandas-dev#17253)

Test parameters with marks are updated according to the updated API of
Pytest.
https://docs.pytest.org/en/latest/changelog.html#pytest-3-2-0-2017-07-30
https://docs.pytest.org/en/latest/parametrize.html

* Handle more date/datetime/time formats (pandas-dev#15871)

* DOC: add example on json_normalize (pandas-dev#16438)

* BUG: Have object dtype for empty Categorical.categories (pandas-dev#17249)

* BUG: Have object dtype for empty Categorical ctor

Previously we had a `Float64Index`, which is inconsistent with, e.g., the
regular Index constructor.

* TST: Update tests in multi for new return

Previously these relied worked around the return type by wrapping list-likes
in `np.array` and relying on that to cast to float. These workarounds are no
longer nescessary.

* TST: Update union_categorical tests

This relied on `NaN` being a float and empty being a float. Not a necessary
test anymore.

* TST: set object dtype

* CLN: replace %s syntax with .format in pandas.tseries (pandas-dev#17290)

* TST: parameterize consistency tests for rolling/expanding windows (pandas-dev#17292)

* FIX: define `DataFrame.items` for all versions of python (pandas-dev#17214)

* PERF: Update ASV publish config (pandas-dev#17293)

Stricter cutoffs for considering regressions

[ci skip]

* DOC: Expand docstrings for head / tail methods (pandas-dev#16941)

* MAINT: Use set literal for unsupported + depr args

Initializes unsupported and deprecated argument sets with set literals instead of the set constructor in pandas/io/parsers.py, as the former is slightly faster than the latter.

* DOC: Add proper docstring to maybe_convert_indices

Patches several spelling errors and expands current doc to a proper doc-string.

* DOC: Improving docstring of take method (pandas-dev#16948)

* BUG: Fixed regex in asv.conf.json (pandas-dev#17300)

In pandas-dev#17293 I messed up the syntax. I
used a glob instead of a regex. According to the docs at
http://asv.readthedocs.io/en/latest/asv.conf.json.html#regressions-thresholds we
want to use a regex. I've actually manually tested this change and verified that
it works.

[ci skip]

* Remove unnecessary usage of _TSObject (pandas-dev#17297)

* BUG: clip should handle null values

closes pandas-dev#17276

Author: Michael Gasvoda <mgasvoda@mercatus.gmu.edu>
Author: mgasvoda <mgasvoda01@gmail.com>

Closes pandas-dev#17288 from mgasvoda/master and squashes the following commits:

a1dbdf2 [mgasvoda] Merge branch 'master' into master
9333952 [Michael Gasvoda] Checking output of tests
4e0464e [Michael Gasvoda] fixing whatsnew text
c442040 [Michael Gasvoda] formatting fixes
7e23678 [Michael Gasvoda] formatting updates
781ea72 [Michael Gasvoda] whatsnew entry
d9627fe [Michael Gasvoda] adding clip tests
9aa0159 [Michael Gasvoda] Treating na values as none for clips

* BUG: fillna returns frame when inplace=True if value is a dict (pandas-dev#16156) (pandas-dev#17279)

* CLN: Index.append() refactoring (pandas-dev#16236)

* DEPS: set min versions (pandas-dev#17002)

closes pandas-dev#15206, numpy >= 1.9
closes pandas-dev#15543, matplotlib >= 1.4.3
scipy >= 0.14.0

* CLN: replace %s syntax with .format in core.tools, algorithms.py, base.py (pandas-dev#17305)

* BUG: Fix strange behaviour of Series.iloc on MultiIndex Series (pandas-dev#17148) (pandas-dev#17291)

* DOC: Add module doc-string to tseries/api.py

* MAINT: Clean up docs in pandas/errors/__init__.py

* CLN: replace %s syntax with .format in missing.py, nanops.py, ops.py (pandas-dev#17322)

Replaced %s syntax with .format in missing.py, nanops.py, ops.py. Additionally, made some of the existing positional .format code more explicit.

* Make pd.Period immutable (pandas-dev#17239)

* Bug: groupby multiindex levels equals rows (pandas-dev#16859)

closes pandas-dev#16843

* BUG: Cannot use tz-aware origin in to_datetime (pandas-dev#16842)

closes pandas-dev#16842

Author: step4me <prosikeffect@gmail.com>

Closes pandas-dev#17244 from step4me/step4me-feature and squashes the following commits:

09d051d [step4me] BUG: Cannot use tz-aware origin in to_datetime (pandas-dev#16842)

* Replace usage of total_seconds compat func with timedelta method (pandas-dev#17289)

* CLN: replace %s syntax with .format in core/indexing.py (pandas-dev#17357)

Progress toward issue pandas-dev#16130. Converted old string formatting to new string formatting in core/indexing.py.

* DOC: Point to dev-docs in issue template (pandas-dev#17353)

[ci skip]

* CLN: remove total_seconds compat from json (pandas-dev#17341)

* CLN: Move test_intersect_str_dates (pandas-dev#17366)

Moves test_intersect_str_dates from tests/indexes/test_range.py to tests/indexes/test_base.py.

* BUG: Respect dups in reindexing CategoricalIndex (pandas-dev#17355)

When the indexer is identical to the elements.
We should still return duplicates when the indexer
contains duplicates.

Closes pandas-devgh-17323.

* Unify Index._dir_* with Series implementation (pandas-dev#17117)

* BUG: make order of index from pd.concat deterministic (pandas-dev#17364)

closes pandas-dev#17344

* Fix typo that causes several NaT methods to have incorrect docstrings (pandas-dev#17327)

* CLN: replace %s syntax with .format in io/formats/format.py (pandas-dev#17358)

Progress toward issue pandas-dev#16130. Converted old string formatting to new string formatting in io/formats/format.py.

* PKG: Added pyproject.toml for PEP 518 (pandas-dev#16745)

Declaring build-time requirements: https://www.python.org/dev/peps/pep-0518/

* DOC: Update Overview page in documentation (pandas-dev#17368)

* Update Overview page in documentation

* DOC Revise Overview page

* DOC Make further revisions in Overview webpage

* Update overview.rst

Remove references to Panel

* API: Have MultiIndex consturctors always return a MI (pandas-dev#17236)

* API: Have MultiIndex constructors return MI

This removes the special case for MultiIndex constructors returning
an Index if all the levels are length-1. Now this will return a
MultiIndex with a single level.

This is a backwards incompatabile change, with no clear method for
deprecation, so we're making a clean break.

Closes pandas-dev#17178

* fixup! API: Have MultiIndex constructors return MI

* Update for comments
@max-sixty max-sixty mentioned this pull request Aug 31, 2017
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jowens pushed a commit to jowens/pandas that referenced this pull request Sep 20, 2017
@jreback @jowens
DOC: fix typos in missing.rst
77d16d4 
xref pandas-dev#16972
@gerritholl
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This merge causes a failure in xarrays Dataset.notnull(), see pydata/xarray#1663.

@shoyer
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shoyer commented Oct 27, 2017

Xarray was implicitly assuming that the pandas isnull() function satisfied `isnull.name == 'isnull'. That's not really something that should be considered guaranteed as part of the public API, so I think this one is on us.

alanbato pushed a commit to alanbato/pandas that referenced this pull request Nov 10, 2017
@jreback @alanbato
COMPAT: rename isnull -> isna, notnull -> notna (pandas-dev#16972)
99b0e77 
closes pandas-dev#15001
alanbato pushed a commit to alanbato/pandas that referenced this pull request Nov 10, 2017
@jreback @alanbato
DOC: fix typos in missing.rst
4b78b90 
xref pandas-dev#16972
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CLN/DEPR: Consistent naming for isnull, notnull, fillna, dropna
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