DEPR: join_axes-kwarg in pd.concat #22318

h-vetinari · 2018-08-13T19:22:29Z

closes DEPR: join_axes-kwarg for pd.concat #21951
tests added / passed
passes git diff upstream/master -u -- "*.py" | flake8 --diff
whatsnew entry

pep8speaks · 2018-08-13T19:22:33Z

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

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

Comment last updated at 2019-07-03 02:21:51 UTC

codecov · 2018-08-13T23:52:06Z

Codecov Report

Merging #22318 into master will increase coverage by 50.26%.
The diff coverage is 100%.

@@             Coverage Diff             @@
##           master   #22318       +/-   ##
===========================================
+ Coverage   41.96%   92.23%   +50.26%     
===========================================
  Files         180      161       -19     
  Lines       50860    51333      +473     
===========================================
+ Hits        21345    47348    +26003     
+ Misses      29515     3985    -25530

Flag	Coverage Δ
#multiple	`90.62% <100%> (?)`
#single	`42.29% <34.48%> (+0.32%)`	⬆️

Impacted Files	Coverage Δ
pandas/core/groupby/generic.py	`87.1% <100%> (+72.32%)`	⬆️
pandas/core/frame.py	`97.03% <100%> (+62.07%)`	⬆️
pandas/core/reshape/concat.py	`97.66% <100%> (+53.66%)`	⬆️
pandas/core/generic.py	`96.81% <100%> (+58.18%)`	⬆️
pandas/io/gbq.py	`25% <0%> (-58.34%)`	⬇️
pandas/compat/__init__.py	`58.36% <0%> (-33.64%)`	⬇️
pandas/io/clipboard/clipboards.py	`28.23% <0%> (-6.55%)`	⬇️
pandas/plotting/_misc.py	`38.98% <0%> (-4.26%)`	⬇️
pandas/io/formats/console.py	`75.75% <0%> (-2.37%)`	⬇️
pandas/_libs/__init__.py	`100% <0%> (ø)`	⬆️
... and 174 more

Continue to review full report at Codecov.

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pandas/core/reshape/concat.py

jreback · 2018-08-22T12:43:39Z

pandas/core/frame.py

@@ -6614,11 +6614,11 @@ def _join_compat(self, other, on=None, how='left', lsuffix='', rsuffix='',
            if can_concat:
                if how == 'left':
                    how = 'outer'
-                    join_axes = [self.index]
+                    return concat(frames, axis=1, join=how,
+                                  verify_integrity=True).reindex(self.index)


you can add copy=False to the .reindex

jreback · 2018-08-22T12:43:55Z

pandas/core/generic.py

@@ -8848,7 +8848,7 @@ def describe_1d(data):
                if name not in names:
                    names.append(name)

-        d = pd.concat(ldesc, join_axes=pd.Index([names]), axis=1)
+        d = pd.concat([x.reindex(names) for x in ldesc], axis=1, sort=False)


add copy=False

jreback · 2018-08-22T12:46:46Z

pandas/core/groupby/generic.py

@@ -518,8 +518,10 @@ def _transform_general(self, func, *args, **kwargs):
                applied.append(res)

        concat_index = obj.columns if self.axis == 0 else obj.index
-        concatenated = concat(applied, join_axes=[concat_index],
-                              axis=self.axis, verify_integrity=False)
+        other_axis = (self.axis + 1) % 2  # switches from 0 to 1 or from 1 to 0


don't use this, just use an if else

pandas/core/groupby/generic.py

pandas/core/reshape/concat.py

pandas/tests/reshape/test_concat.py

jreback

small comment, lgtm. ping on green.

jreback · 2018-08-23T10:52:29Z

pandas/core/reshape/concat.py

+        if ndim == 2:
+            other_axis = 1 if axis == 0 else 0  # switches between 0 & 1
+            res = res.reindex(join_axes[0], axis=other_axis)
+        else:  # 3 for Panel; Panel4D already deprecated


no need to mention Panel4D.

use elif ndim == 3 to be explicit

jreback · 2018-08-23T10:55:21Z

@jorisvandenbossche you had some comments on the issue. I am all for making things simpler.

h-vetinari · 2018-08-23T14:56:29Z

@jorisvandenbossche
I'm answering your comment from #21951 here, as this is further ahead:

"but this will be fixed by 21160 anyway." -> that is long off to be the default integer type, so I don't think we should use that as an argument now

Fair enough, that was a misunderstanding on my part. But the dtype-question is a side-issue here, IMO

"with reindex and reindex_like, it is redundant as well" -> I don't know the implementation, but I would assume that reindexing after the fact can be less performant? (assuming that with join_axes it reindexes each input before concatenating)

I posed this question in the OP ("Only question is if performance would be much worse, if concatenating huge Series/DFs before selecting small index-subset."), and it's a valid point. The user could apply a reindex directly to the arguments of concat (I originally had something to that effect in the FutureWarning in this PR), but I see that it would be good to keep having a way to do this easily.

It is certainly true the way it is explained and spelled (eg the fact that you need to pass a list) is certainly outdated now Panel is removed. But we could also consider improving it.

In my opinion, the join_axes-keyword (as a name, not necessarily as functionality) should definitely be deprecated. The question of what to replace it with is very similar to the discussion in #21855 (comment).

There might be a good solution for replacing the join_axes-functionality with something like the following (conceptually):

concat(objs, axis=0, join='outer', index=None, columns=None, ignore_index=False,
       keys=None, levels=None, names=None, verify_integrity=False, sort=None, copy=True)
[...]
if (axis == 0 and index is not None) or (axis == 1 and columns is not None):
   raise ValueError('Cannot set index of concatenation axis; '
                    'can only set index of non-concatenation axis')
index = join if index is None else index
columns = join if columns is None else columns
[...]
objs = [x.reindex(index/columns, axis=other_axis) for x in objs]
[...]
# actual concatenation

Then index the non-concatenation index of the result could be set as desired (essentially replacing join_axes with a cleaner API, now that Panel will be deprecated).

(note that I am not married to the keyword, I have never used it myself, but just think we should have a bit more discussion about it. It would be interesting to search for usage on github/SO)

There's not much on SO - https://www.google.com/search?q=stackoverflow+pandas+concat+join_axes yields only one (sorta) relevant hit: https://stackoverflow.com/q/27391081

Neither did I find much of substance here: https://github.com/search?p=2&q=join_axes&type=Issues

h-vetinari · 2018-08-27T09:33:59Z

@jreback

small comment, lgtm. ping on green.

All green (rebased due to persistent test failures).

h-vetinari · 2018-09-04T06:17:26Z

@jreback

Green and all feedback incorporated. Anything missing?

jreback

some comments. ping on green.

jreback · 2018-09-04T11:53:51Z

pandas/core/generic.py

@@ -8930,7 +8930,8 @@ def describe_1d(data):
                if name not in names:
                    names.append(name)

-        d = pd.concat(ldesc, join_axes=pd.Index([names]), axis=1)
+        d = pd.concat([x.reindex(names) for x in ldesc], axis=1,


use the copy=False on . the .reindex. remove copy= from the pd.concat it is not respected misleading here.

jreback · 2018-09-04T11:54:13Z

pandas/core/groupby/generic.py

-        concatenated = concat(applied, join_axes=[concat_index],
-                              axis=self.axis, verify_integrity=False)
+        other_axis = 1 if self.axis == 0 else 0  # switches between 0 & 1
+        concatenated = concat(applied, axis=self.axis,


remove copy= from the concat

pandas/core/frame.py

pandas/core/reshape/concat.py

jreback · 2018-09-04T11:55:08Z

pandas/core/reshape/concat.py

+                                 "length {length}".format(length=ndim - 1))
+        if ndim == 2:
+            other_axis = 1 if axis == 0 else 0  # switches between 0 & 1
+            res = res.reindex(join_axes[0], axis=other_axis)


add copy=False to the .reindex

h-vetinari · 2018-09-05T12:04:26Z

@jorisvandenbossche

I answered above (#22318 (comment)) to your remarks/questions in the issue. Any further comments, API- or otherwise?

h-vetinari · 2018-09-05T23:28:51Z

@jreback

some comments. ping on green.

ping on green

jreback · 2018-09-05T23:45:16Z

@jorisvandenbossche i am ok with this
any objections

jorisvandenbossche · 2018-09-06T15:32:26Z

@h-vetinari sorry for my slow follow-up, didn't have much time the last weeks

I also saw that the discussion here (about an alternative way to do it) is related to the joining discussions in other PRs/issues (you linked #21855). I will try to take a look at those discussions one of the coming days.

I personally think we should first decide on an alternative (or decide upon if we want one) before actually deprecating this, but no strong opinion.

BTW, if we keep the PR as is, the documentation certainly needs an update (there are example of join_axes in the tutorial docs).

h-vetinari · 2018-09-13T18:01:55Z

@jorisvandenbossche

I will try to take a look at those discussions one of the coming days.

Any luck with that?

As a potential shortcut to reading that other discussion, you could have a look at the pseudo-implementation I wrote above in #22318 (comment).

Barring a decision on what to replace the API with, which tutorial docs do you mean? I didn't find anything in https://pandas.pydata.org/pandas-docs/stable/tutorials.html, but there's a bit in doc/source/merging.rst.

jreback · 2018-09-23T21:37:07Z

looks ok to me, @jorisvandenbossche has some questions.

h-vetinari · 2018-09-23T21:59:40Z

@jreback @jorisvandenbossche

Barring a decision on what to replace the API with, which tutorial docs do you mean? I didn't find anything in https://pandas.pydata.org/pandas-docs/stable/tutorials.html, but there's a bit in doc/source/merging.rst.

h-vetinari · 2018-11-11T10:03:47Z

@jorisvandenbossche
Can we pick this up again?

h-vetinari · 2018-11-15T07:21:41Z

@gfyoung

@h-vetinari : FYI, instead of pushing commits to trigger entirely new builds, just ping one of us. We can restart individual builds for you.

Could you retrigger that timed-out travis job please? ;-)

h-vetinari · 2019-06-28T22:38:41Z

jorisvandenbossche: Hadn't seen your comment about before I posted that, sorry. Anyway, that should not matter for codecov. But eg if not all CI builds pass, that can also give failures on codecov I think.

All the CI builds had passed, except for codecov (I imagine because it had forgotten the coverage of the commit where this PR had originally branched off)

separation of concerns.

Fair enough...

jreback · 2019-06-28T23:27:36Z

@h-vetinari

in regards to: #22318 (comment)

this is a separate and distinct change. let's treat it as such. Keeping PRs nice and simple is the way to go.

h-vetinari · 2019-06-28T23:29:51Z

Fair point, but without someone doing a PR, we'll have just a deprecation, without the replacement. I think it's equally fair to say that that replacement is part of the deprecation itself (to uphold existing usability where necessary). I'll be gone the next two weeks., but then, this PR is not in a hurry...

jreback · 2019-06-28T23:31:13Z

@h-vetinari IMHO we don't need a replace at all.

jreback · 2019-06-28T23:31:51Z

In any event, if you can respond to the remaining comments (soon) we can merge this.

…axes

h-vetinari · 2019-07-02T06:39:30Z

@jreback: @h-vetinari can you update for this point

This PR needs updating in several different ways (also review from @jorisvandenbossche), and as I mentioned I'm currently away for two weeks.

I'd like to clean this up when I come back (realising that it'll be after 0.25), and properly replace the removed functionality with something like join='outer'|'inner'|index-instance.

jreback · 2019-07-02T10:17:27Z

@jreback: @h-vetinari can you update for this point

This PR needs updating in several different ways (also review from @jorisvandenbossche), and as I mentioned I'm currently away for two weeks.

I'd like to clean this up when I come back (realising that it'll be after 0.25), and properly replace the removed functionality with something like join='outer'|'inner'|index-instance.

@h-vetinari that is a separate PR that may not be accepted
pls just stick to single purpose things

TomAugspurger · 2019-07-02T20:44:11Z

What's the status here? Is this happening for 0.25.0?

jreback · 2019-07-02T20:51:14Z

prob needs a small amount of fixup; let me see if I can do this in the next couple of hours.

TomAugspurger · 2019-07-02T20:52:24Z

Thanks (I'm roughly pushing for an RC tomorrow, maybe cutting it tomorrow night)

…

On Tue, Jul 2, 2019 at 3:51 PM Jeff Reback ***@***.***> wrote: prob needs a small amount of fixup; let me see if I can do this in the next couple of hours. — You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub <#22318?email_source=notifications&email_token=AAKAOIRJEKLBDH5UXDTEQZLP5O5UVA5CNFSM4FPMKEI2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZCQJ3Q#issuecomment-507839726>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAKAOIV7NS2GUR5QXI4DVQTP5O5UVANCNFSM4FPMKEIQ> .

h-vetinari · 2019-07-03T10:58:00Z

@jreback @TomAugspurger

I wouldn't merge this before 0.25. It's been open for almost a year, so it's obviously not urgent. And I disagree that the direct replacement for the functionality we're deprecating should be a separate PR. If this gets merged before 0.25 there won't be replacement for that version (except the workaround of using .reindex manually).

OTOH, with a direct replacement in the same PR as the deprecation, one could formulate a clear path for updating.

jreback · 2019-07-03T11:33:24Z

thanks @h-vetinari

again, 1 PR 1 thing. The reason things take so long (not in this case), but generally is that they are too many things in 1 place.

jorisvandenbossche · 2019-07-03T14:29:03Z

I have to say I agree with @h-vetinari that if we want something that replaces this functionality, we should not include this in 0.25.0 (unless we get the replacement in 0.25.0 as well). It is quite annoying to already start warning for something before a replacement is available (again, if we want to add such a replacement).

jreback · 2019-07-03T14:30:42Z

there already is a very good alternative, .reindex(), no need to re-invent the wheel here. This is less than useful in the non-Panel world. SO I am -1 on adding any replacement at all.

jorisvandenbossche · 2019-07-03T14:36:58Z

It was from a discussion between the both of us that I commented #22318 (comment) with the idea of a join='first' or join='left', which is basically a replacement for the number 1 use case of join_axes.
I thought you were OK with that idea.

But still, it is something to discuss. There is also the idea of introducing a join_axis, but I personally think that the join one covers most use cases of join_axi/es.

jreback · 2019-07-03T15:36:11Z

It was from a discussion between the both of us that I commented #22318 (comment) with the idea of a join='first' or join='left', which is basically a replacement for the number 1 use case of join_axes.
I thought you were OK with that idea.

I mean maybe, but I'd like to see an actual usecase. Removing API is easy, adding new should have a high bar.

h-vetinari · 2019-07-03T15:43:56Z

@jreback
I get the maintainer POV, but from a usability POV it's the other way around - removing API is costly, while additions are easy. And it's not even a new API - it'd just be changing the name/semantics of existing functionality.

h-vetinari force-pushed the depr_concat_join_axes branch from 5df8f17 to 6047a8c Compare August 13, 2018 19:25

jreback requested changes Aug 14, 2018

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jreback added Reshaping Concat, Merge/Join, Stack/Unstack, Explode Deprecate Functionality to remove in pandas labels Aug 14, 2018

h-vetinari force-pushed the depr_concat_join_axes branch from 091ee11 to dbb489d Compare August 14, 2018 07:10

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h-vetinari force-pushed the depr_concat_join_axes branch from dbb489d to f7902e4 Compare August 22, 2018 21:23

jreback requested changes Aug 23, 2018

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jreback added this to the 0.24.0 milestone Aug 23, 2018

h-vetinari force-pushed the depr_concat_join_axes branch from 0bdbdde to b0133b0 Compare August 27, 2018 07:37

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h-vetinari force-pushed the depr_concat_join_axes branch from 144ef86 to 99f029d Compare September 5, 2018 11:52

jreback approved these changes Sep 23, 2018

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jreback removed this from the 0.24.0 milestone Nov 6, 2018

h-vetinari mentioned this pull request Dec 3, 2018

ENH: coalesce-method (upgrade for update/combine_first) #22812

Open

h-vetinari added 2 commits June 29, 2019 01:33

Merge remote-tracking branch 'upstream/master' into depr_concat_join_…

6afb2d0

…axes

review (jreback)

e3e8118

jreback added 3 commits July 2, 2019 18:49

Merge branch 'master' into PR_TOOL_MERGE_PR_22318

952888a

restore original location

60e6239

Merge branch 'master' into PR_TOOL_MERGE_PR_22318

cc9c79b

jreback approved these changes Jul 3, 2019

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jreback merged commit c0a4964 into pandas-dev:master Jul 3, 2019

h-vetinari deleted the depr_concat_join_axes branch July 31, 2019 13:32

jreback mentioned this pull request Dec 5, 2019

DEPR: deprecations log for removed issues #13777

Closed

bersavosh mentioned this pull request Feb 17, 2020

summary() fails with the new pandas release pymc-devs/pymc#3805

Closed

janhurst mentioned this pull request Apr 19, 2020

concat() got an unexpected keyword argument 'join_axes' ydataai/ydata-profiling#438

Closed

kfeaginsiii mentioned this pull request Aug 19, 2020

TypeError: _plot_histogram() got an unexpected keyword argument 'title' ydataai/ydata-profiling#528

Closed

tripathishivam1444 mentioned this pull request Oct 7, 2021

the pd.concat join_axes kwarg was deprecated around pandas 0.25 and removed in pandas 1.0.0 ydataai/ydata-profiling#854

Closed

DEPR: join_axes-kwarg in pd.concat #22318

DEPR: join_axes-kwarg in pd.concat #22318

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