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BLD: add optional dependencies as extras_require in setup.py #47336

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JMBurley
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@JMBurley JMBurley commented Jun 13, 2022

EDIT: This was originally a limited scope PR to bring recommended dependencies into pandas extras_require, but discussion evolved into 'solve packaging for all optional dependencies' rather than just solve for the recommended optional dependencies. The logic behind this is the same as originally argued for recommended dependencies but I updated the text of the post to keep it aligned with the PR contents


Closes #47335. Closes #39164 . Closes #48361 .

Hoping to make this part of the 1.5 milestone.

Optional dependencies should have package mgmt facilitated through pandas. This will make mgmt of pandas in production docker environments a significantly simpler and allow pandas explicit control over the versions of optional packages it should operate with.

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Use setup.cfg options as documented here to make optional extras for a pandas install.

Once this is done, a user will be able to ensure version alignment by

# in requirements.txt or setup.py
pandas[recommended, s3] == 1.22.4  # install pd 1.22.4 and compatible numexpr, bottleneck, s3fs versions

The proposed solution is simple to do, simple to maintain, and already done by major libraries in similar situations (moto, aiobotocore).

Not having this solution wastes user time by forcing them to manually maintain versions of pandas dependencies that are not clearly linked to pandas, save in the brains of users and by manually referring to an install docs page.

checklist

See issue pandas-dev#47335.

pandas-dev#47335

recommended dependencies should have package mgmt facilitated through pandas.  This will make mgmt of pandas in production docker environments a lot simpler.
….cfg' of https://github.com/JMBurley/pandas into add-recommended-dependencies-as-extras_require-in-setup.cfg
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JMBurley commented Jun 13, 2022

Test failure Windows-MacOS / windows-latest actions-39.yaml (pull_request) seemingly unrelated to modified code.

This same test fails in PRs that are approved to be merged so unclear to me if action is required.

INTERNALERROR> AssertionError: ('pandas/tests/plotting/frame/test_frame_color.py::TestDataFrameColor::test_mpl2_color_cycle_str', <WorkerController gw0>)
INTERNALERROR> assert not 'pandas/tests/plotting/frame/test_frame_color.py::TestDataFrameColor::test_mpl2_color_cycle_str'

@JMBurley JMBurley changed the title add-recommended-dependencies-as-extras_require-in-setup.cfg BLD: add-recommended-dependencies-as-extras_require-in-setup.cfg Jun 13, 2022
@JMBurley JMBurley marked this pull request as ready for review June 13, 2022 22:23
@JMBurley JMBurley changed the title BLD: add-recommended-dependencies-as-extras_require-in-setup.cfg BLD: add recommended dependencies as extras_require in setup.py Jun 14, 2022
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This same test fails in PRs that are approved to be merged so unclear to me if action is required.

Unrelated, don't worry about it.

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As noted in #39164 (comment), I think the correct groupings should be discussed first before creating a pull request as it would be good to get all the optional dependencies in

@datapythonista datapythonista added Build Library building on various platforms Dependencies Required and optional dependencies labels Jun 16, 2022
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Updates made as per discussion in #39164

rollback numba from recommended.  This would necessitate and update to documentation that requires broad agreement from pd-dev-core team that would slow down the overall PR
see pandas-dev#39164 for discussion.  0.6.0 might be an overly restrictive version, but it is compatible
@JMBurley JMBurley requested a review from mroeschke July 13, 2022 23:23
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@mroeschke Ready for review.

computation =
scipy>=1.7.1
xarray>=0.19.0
fss =
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I would personally like to see this be called filesystem as fss isn't immediately obvious to me, but not a blocker to me.

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It's a good question. I went back and forth on fss vs filesystem. Ultimately I decided that filesystem might suggest to users a broad compatibility with common filesystems (eg. s3) that the optional_extra does not provide, and it was probably least surprising to users to call it fss. (and the alternative fsspec is worryingly specific in case fsspec were ever deprecated and pandas switched to an alternative filesystem mgmt package in future).

But I don't think either solution is perfect and am very open to alternative suggestions or being argued back to filesystem.

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Gotcha, yeah fss would be okay as well I suppose.

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>
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Great thanks for your work and patience here, LGTM. Will leave open just in case others want to chime in

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JMBurley commented Oct 13, 2022

Great thanks for your work and patience here, LGTM. Will leave open just in case others want to chime in

Awesome, glad to have this in. Appreciate the reviews to keep this PR on track. Optional dependencies are really helpful for container mgmt in production DS.

Note: there is now a conflict with main branch where whatsnew/v1.6.0.rst has been renamed to whatsnew/v2.0.0.rst. Is pandas 2.0.0 now the next major release instead of pandas 1.6.0?

I'll let someone provide guidance before I alter documentation for the merge.

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Is pandas 2.0.0 now the next major release instead of pandas 1.6.0?

Correct, 2.0 will be the next major release so a rebase is needed

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Approved and tests passed!
First enhancement for pandas 1.6.0 in the bag!
First enhancement for pandas 2.0.0 in the bag!

@mroeschke mroeschke added this to the 2.0 milestone Oct 14, 2022
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Sorry this PR hasn't gotten that much other review @JMBurley. I think this will be okay to merge once the conflict is resolved (the pyarrow min version was bumped to 6.0)

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Sorry this PR hasn't gotten that much other review @JMBurley. I think this will be okay to merge once the conflict is resolved (the pyarrow min version was bumped to 6.0)

Pyarrow version is now bumped & merged in latest from main. Waiting for tests to pass

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@mroeschke good to merge?

@mroeschke mroeschke merged commit ca1b607 into pandas-dev:main Oct 21, 2022
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Great work @JMBurley! Thanks for sticking with all the requests. I do think this is really beneficial with all the optional dependencies pandas!

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Dr-Irv commented Oct 21, 2022

@mroeschke I found this part confusing:

Optional pandas dependencies can be managed as optional extras (e.g.,``pandas[performance, aws]>=1.5.0``)
in a requirements.txt, setup, or pyproject.toml file.
Available optional dependencies are ``[all, performance, computation, aws,
gcp, excel, parquet, feather, hdf5, spss, postgresql, mysql, sql-other, html, xml,
plot, output_formatting, compression, test]``

I think this should point out that the optional dependencies should ONLY be managed via files, and that you cannot do conda install pandas[computation]=1.5.1 (for example) to get the dependencies to install. The way this section is written, it makes it seem that you can do that (or maybe you can with this PR, in which case that should be shown as an installation option).

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Good points @Dr-Irv . Yeah this type of install should be only valid with pip installs (command line & files), so I can follow up clarifying the documentation and also give an installation example.

phofl added a commit to phofl/pandas that referenced this pull request Oct 21, 2022
…dev#47336)

* add-recommended-dependencies-as-extras_require-in-setup.cfg

See issue pandas-dev#47335.

pandas-dev#47335

recommended dependencies should have package mgmt facilitated through pandas.  This will make mgmt of pandas in production docker environments a lot simpler.

* Update v1.4.3.rst

* double backtick code in rst

* rebundle under extras_require `recommended`

* [options.extras_require] bundled dependencies by featureset

see pandas-dev#39164 for discussion.

* note: [options.extras_require] bundled dependencies by featureset

* Update setup.cfg

rollback numba from recommended.  This would necessitate and update to documentation that requires broad agreement from pd-dev-core team that would slow down the overall PR

* add adlfs for azure to `access data in cloud`

see pandas-dev#39164 for discussion.  0.6.0 might be an overly restrictive version, but it is compatible

* fix extras_require: PyTables is actually `tables` on PyPi

* Update setup.cfg

* add `all` option to [options.extras_require]

* moved changelog to 1.4.4 as 1.4.3 released while this PR was stalled

* Updated to 1.5.0 compliance

* simplify sql option names

* extras rename: recommended -> performance

* remove azure

support is currently unofficial as of 1.5.0

* align with actions-38-minimum_versions.yaml

add  specific installs and, where required, missing install documentation for
 - odfpy
 - pyreadstat
 - compression options

* Pandas -> pandas in doc

Co-authored-by: Matthew Roeschke <emailformattr@gmail.com>

* extras rename: s3 -> aws

see pandas-dev#47336 (comment)

* extras rename: table -> output_formatting

to be more general in case of future changes

* bug: `>=` not `=`

* Apply suggestions from code review

Co-authored-by: Simon Hawkins <simonjayhawkins@gmail.com>

* align 1.5.0.rst to latest extras_require updates

* 1.5.0.rst example updated to use valid extras

* add optional dep mgmt instructions to install.rst

* lint scipy optional import

Co-authored-by: Matthew Roeschke <emailformattr@gmail.com>

* Apply suggestions from code review

* detailed extras guidance in install.rst

 - updated numbas to a full recommended dependency with a promotional bullet point like bottleneck and numexpr
- clarified the extra to use for each set of optional dependencies
- made xml an optional extra, because is does have usage outside of read_html.

* _optional.py note to keep track of setup.cfg

* bug: indent after bullet in install.rst

* remove numba from computation extra.

* Backport PR pandas-dev#48197 on branch 1.5.x (DOC: Cleanup 1.5 whatsnew) (pandas-dev#48228)

Backport PR pandas-dev#48197: DOC: Cleanup 1.5 whatsnew

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48232 on branch 1.5.x (CI: Ensure jobs run on 1.5.x branch) (pandas-dev#48235)

Backport PR pandas-dev#48232: CI: Ensure jobs run on 1.5.x branch

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48180 on branch 1.5.x (CI: Switch to large for circleci) (pandas-dev#48251)

Backport PR pandas-dev#48180: CI: Switch to large for circleci

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* Backport PR pandas-dev#48245 on branch 1.5.x (CI: Skip test_round_sanity tests due to failures) (pandas-dev#48257)

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* Backport PR pandas-dev#48240 on branch 1.5.x (Fix mypy erroring on backport branches) (pandas-dev#48259)

Backport PR pandas-dev#48240: Fix mypy erroring on backport branches

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* Backport PR pandas-dev#48215 on branch 1.5.x (REGR: properly update DataFrame cache in Series.__setitem__) (pandas-dev#48268)

Backport PR pandas-dev#48215: REGR: properly update DataFrame cache in Series.__setitem__

Co-authored-by: Joris Van den Bossche <jorisvandenbossche@gmail.com>

* Backport PR pandas-dev#48272 on branch 1.5.x (CI: Require s3fs greater than minumum version in builds) (pandas-dev#48276)

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* Backport PR pandas-dev#48299 on branch 1.5.x (Bump s3fs to 2021.08.00) (pandas-dev#48305)

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* Backport PR pandas-dev#48027 on branch 1.5.x (ENH: Support masks in groupby prod) (pandas-dev#48302)

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* Backport PR pandas-dev#47762 on branch 1.5.x (REGR: preserve reindexed array object (instead of creating new array) for concat with all-NA array) (pandas-dev#48309)

Backport PR pandas-dev#47762: REGR: preserve reindexed array object (instead of creating new array) for concat with all-NA array

Co-authored-by: Joris Van den Bossche <jorisvandenbossche@gmail.com>

* Backport PR pandas-dev#48246 on branch 1.5.x (REGR: iloc not possible for sparse DataFrame) (pandas-dev#48311)

Backport PR pandas-dev#48246: REGR: iloc not possible for sparse DataFrame

Co-authored-by: Simon Hawkins <simonjayhawkins@gmail.com>

* Backport PR pandas-dev#48314 on branch 1.5.x (DOC: v1.4.4 release date and tidy up release notes) (pandas-dev#48320)

Backport PR pandas-dev#48314: DOC: v1.4.4 release date and tidy up release notes

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* Backport PR pandas-dev#48301 on branch 1.5.x (DEPR: Deprecate positional arguments in pivot) (pandas-dev#48326)

Backport PR pandas-dev#48301: DEPR: Deprecate positional arguments in pivot

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* Backport PR pandas-dev#48214 on branch 1.5.x (WEB: Removing links to pdf version of the docs from web and docs) (pandas-dev#48242)

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* Backport PR pandas-dev#48159 on branch 1.5.x (TST: Fix interchange/plotting/groupby test warnings) (pandas-dev#48279)

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* Backport PR pandas-dev#48324 on branch 1.5.x (BUG: Add note in whatsnew for DataFrame.at behavior change) (pandas-dev#48345)

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* Backport PR pandas-dev#48336 on branch 1.5.x (DOC: Add whatsnew note for pandas-dev#45404) (pandas-dev#48341)

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* Backport PR pandas-dev#48254 on branch 1.5.x (REF: avoid FutureWarning about using deprecates loc.__setitem__ non-inplace usage) (pandas-dev#48353)

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* Backport PR pandas-dev#48334 on branch 1.5.x (BUG: read_html(extract_links=all) with no header) (pandas-dev#48350)

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* Backport PR pandas-dev#48265 on branch 1.5.x (CI: Setting up ssh key to upload prod docs) (pandas-dev#48370)

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* Backport PR pandas-dev#48381 on branch 1.5.x (CI: Pin mambaforge image) (pandas-dev#48401)

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* Backport PR pandas-dev#48229 on branch 1.5.x (TST: Test Nullable int floordiv by 0) (pandas-dev#48413)

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* Backport PR pandas-dev#48414 on branch 1.5.x (DOC: Add deprecation to is_categorical) (pandas-dev#48418)

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* Backport PR pandas-dev#48264 on branch 1.5.x (BUG: ArrowExtensionArray._from_* accepts pyarrow arrays) (pandas-dev#48422)

* Backport PR pandas-dev#48264: BUG: ArrowExtensionArray._from_* accepts pyarrow arrays

* Add missing import

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* Backport PR pandas-dev#48411 on branch 1.5.x (REGR: get_loc for ExtensionEngine not returning bool indexer for na) (pandas-dev#48430)

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* Backport PR pandas-dev#48419 on branch 1.5.x (BUG: ensure to return writable buffer in __dataframe__ interchange for categorical column) (pandas-dev#48441)

Backport PR pandas-dev#48419: BUG: ensure to return writable buffer in __dataframe__ interchange for categorical column

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* Backport PR pandas-dev#48444 on branch 1.5.x (CI: Pin ipython version) (pandas-dev#48449)

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* Backport PR pandas-dev#48380 on branch 1.5.x (DOC: Clarify that objects dtype takes precedence in where) (pandas-dev#48445)

* Backport PR pandas-dev#48380: DOC: Clarify that objects dtype takes precedence in where

* Update generic.py

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Manual Backport PR pandas-dev#48427 on branch 1.5.x (BLD: Refactor Dockerfile to not install dev enviornment on base) (pandas-dev#48450)

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* Backport PR pandas-dev#48426 on branch 1.5.x (BUG: Column.size should be a method) (pandas-dev#48465)

Backport PR pandas-dev#48426: BUG: Column.size should be a method

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48398 on branch 1.5.x (WARN: Avoid FutureWarnings in tests) (pandas-dev#48420)

* Backport PR pandas-dev#48398: WARN: Avoid FutureWarnings in tests

* Update

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Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* Backport PR pandas-dev#48416 on branch 1.5.x (REF: ensure to apply suffixes before concat step in merge code) (pandas-dev#48470)

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* Backport PR pandas-dev#48354 on branch 1.5.x (CI: Bump timeout to 180 minutes) (pandas-dev#48474)

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* Backport PR pandas-dev#48472 on branch 1.5.x (PERF: keep using ObjectEngine for ExtensionArrays for 1.5) (pandas-dev#48486)

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* Backport PR pandas-dev#48473 on branch 1.5.x (REGR: .describe on unsigned dtypes results in object) (pandas-dev#48501)

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* Backport PR pandas-dev#48443 on branch 1.5.x (BUG: Fix pyarrow groupby tests)  (pandas-dev#48494)

* BUG: Fix pyarrow groupby tests (pandas-dev#48443)

# Conflicts:
#	pandas/tests/extension/test_arrow.py

* CI: Fix failing tests (pandas-dev#48493)

Co-authored-by: jbrockmendel <jbrockmendel@gmail.com>

* Backport PR pandas-dev#48490 on branch 1.5.x (CI: Use -j1 for python-dev build to avoid flaky build error) (pandas-dev#48517)

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* Manual Backport PR pandas-dev#48428 on branch 1.5.x (BUG/TST: fix a bunch of arraymanager+pyarrow tests) (pandas-dev#48518)

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* Backport PR pandas-dev#48525 on branch 1.5.x (CI: Fix py311 builds different exception message) (pandas-dev#48529)

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* Backport PR pandas-dev#48489 on branch 1.5.x (BUG: fix test_arrow.py tests) (pandas-dev#48532)

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* Backport PR pandas-dev#48543 on branch 1.5.x (DOC: Update footer and include OVH) (pandas-dev#48548)

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* Manual Backport PR pandas-dev#48417 on branch 1.5.x (Revert set_index inplace and copy keyword changes) (pandas-dev#48552)

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* Backport PR pandas-dev#48550 on branch 1.5.x (TST: remove 2D tests irrelevant for pyarrow) (pandas-dev#48554)

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* Backport PR pandas-dev#48556 on branch 1.5.x (DOC: Fix docs footer) (pandas-dev#48558)

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* Backport PR pandas-dev#48562 on branch 1.5.x (TST: Testing that no warnings are emitted and that inplace fillna produces the correct result (GH48480)) (pandas-dev#48564)

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* Backport PR pandas-dev#48563 on branch 1.5.x (DOC: Fix read_sas 1.5 release notes) (pandas-dev#48565)

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* Backport PR pandas-dev#48539 on branch 1.5.x (REGR: groupby doesn't identify null values when sort=False) (pandas-dev#48568)

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* Backport PR pandas-dev#48555 on branch 1.5.x (DEPR: Series.astype(np.datetime64)) (pandas-dev#48569)

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* Backport PR pandas-dev#48557 on branch 1.5.x (WEB: Add new footer to web) (pandas-dev#48571)

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* Backport PR pandas-dev#48285 on branch 1.5.x (WEB: Unpin pydata sphinx theme) (pandas-dev#48585)

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* Backport PR pandas-dev#48572 on branch 1.5.x (DOC: Fixing styles for the dark theme) (pandas-dev#48584)

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* Backport PR pandas-dev#48397 on branch 1.5.x (WARN: Remove false positive warning for iloc inplaceness) (pandas-dev#48583)

Backport PR pandas-dev#48397: WARN: Remove false positive warning for iloc inplaceness

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* Backport PR pandas-dev#48587 on branch 1.5.x (Fix `series.str.startswith(tuple)`) (pandas-dev#48593)

Backport PR pandas-dev#48587: Fix `series.str.startswith(tuple)`

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* Backport PR pandas-dev#48601 on branch 1.5.x (CI: Fix matplolib release issues) (pandas-dev#48617)

Backport PR pandas-dev#48601: CI: Fix matplolib release issues

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* Backport PR pandas-dev#48623 on branch 1.5.x (REGR/DOC: Docs left navbar broke) (pandas-dev#48625)

Backport PR pandas-dev#48623: REGR/DOC: Docs left navbar broke

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* Backport PR pandas-dev#48619 on branch 1.5.x (REGR: Loc.setitem with enlargement raises for nested data) (pandas-dev#48629)

Backport PR pandas-dev#48619: REGR: Loc.setitem with enlargement raises for nested data

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48627 on branch 1.5.x (DOC: Last changes to release notes for 1.5.0 release) (pandas-dev#48630)

Backport PR pandas-dev#48627: DOC: Last changes to release notes for 1.5.0 release

Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* RLS: 1.5.0

* Backport PR pandas-dev#48642 on branch 1.5.x (DOC: Add release notes for 1.5.1) (pandas-dev#48647)

Backport PR pandas-dev#48642: DOC: Add release notes for 1.5.1

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* Backport PR pandas-dev#48639 on branch 1.5.x (CI: Fix directory name for published prod docs) (pandas-dev#48648)

Backport PR pandas-dev#48639: CI: Fix directory name for published prod docs

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* Backport PR pandas-dev#48651 on branch 1.5.x (REGR: TextIOWrapper raising an error in read_csv) (pandas-dev#48666)

Backport PR pandas-dev#48651: REGR: TextIOWrapper raising an error in read_csv

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* Backport PR pandas-dev#48599 on branch 1.5.x (DOC: Add deprecation infos to deprecated functions) (pandas-dev#48690)

Backport PR pandas-dev#48599: DOC: Add deprecation infos to deprecated functions

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* Backport PR pandas-dev#48620 on branch 1.5.x (REGR: Performance decrease in factorize) (pandas-dev#48710)

Backport PR pandas-dev#48620: REGR: Performance decrease in factorize

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* Backport PR pandas-dev#48711 on branch 1.5.x (REGR: Regression in DataFrame.loc when setting df with all True indexer) (pandas-dev#48717)

Backport PR pandas-dev#48711: REGR: Regression in DataFrame.loc when setting df with all True indexer

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* Backport PR pandas-dev#48696 on branch 1.5.x (REGR: to_hdf raising AssertionError with boolean index) (pandas-dev#48716)

Backport PR pandas-dev#48696: REGR: to_hdf raising AssertionError with boolean index

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* Backport PR pandas-dev#48734 on branch 1.5.x (REGR: Raise on invalid colormap for scatter plot) (pandas-dev#48744)

Backport PR pandas-dev#48734: REGR: Raise on invalid colormap for scatter plot

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* Backport PR pandas-dev#48713 on branch 1.5.x (BUG: pivot_table raising Future Warning with datetime column as index) (pandas-dev#48742)

Backport PR pandas-dev#48713: BUG: pivot_table raising Future Warning with datetime column as index

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* Backport PR pandas-dev#48703 on branch 1.5.x (Added theme_switcher ) (pandas-dev#48741)

Backport PR pandas-dev#48703: Added theme_switcher

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* Backport PR pandas-dev#48697 on branch 1.5.x (REGR: None converted to NaN when enlarging Series) (pandas-dev#48745)

Backport PR pandas-dev#48697: REGR: None converted to NaN when enlarging Series

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* Backport PR pandas-dev#48702 on branch 1.5.x (REGR: dropna affects observed in groupby) (pandas-dev#48750)

Backport PR pandas-dev#48702: REGR: dropna affects observed in groupby

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* Backport PR pandas-dev#48782 on branch 1.5.x (REGR: describe raising when result contains NA) (pandas-dev#48793)

Backport PR pandas-dev#48782: REGR: describe raising when result contains NA

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* Backport PR pandas-dev#48662 on branch 1.5.x (BUG: Series.getitem not falling back to positional for bool index) (pandas-dev#48799)

Backport PR pandas-dev#48662: BUG: Series.getitem not falling back to positional for bool index

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* Backport PR pandas-dev#48751 on branch 1.5.x (WEB: Update link to datapythonista blog url) (pandas-dev#48798)

Backport PR pandas-dev#48751: WEB: Update link to datapythonista blog url

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* Backport PR pandas-dev#48608 on branch 1.5.x (REGR: assert_index_equal raising with non matching pd.NA) (pandas-dev#48800)

* Backport PR pandas-dev#48608: REGR: assert_index_equal raising with non matching pd.NA

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* Backport PR pandas-dev#48785 on branch 1.5.x (BUG: still emitting unnecessary FutureWarning in DataFrame.sort_values with sparse columns) (pandas-dev#48807)

Backport PR pandas-dev#48785: BUG: still emitting unnecessary FutureWarning in DataFrame.sort_values with sparse columns

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* Backport PR pandas-dev#48693 on branch 1.5.x (ENH: Make deprecate_nonkeyword_arguments alter function signature) (pandas-dev#48795)

Backport PR pandas-dev#48693: ENH: Make deprecate_nonkeyword_arguments alter function signature

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* Backport PR pandas-dev#48579 on branch 1.5.x (BUG: Fix calling groupBy(...).apply(func) on an empty dataframe invokes func) (pandas-dev#48817)

BUG: Fix calling groupBy(...).apply(func) on an empty dataframe invokes func  (pandas-dev#48579)

(cherry picked from commit 8b0ad71)

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* Backport PR pandas-dev#48760 on branch 1.5.x (REGR: groupby.size with axis=1 doesn't return a Series) (pandas-dev#48825)

* Backport PR pandas-dev#48820 on branch 1.5.x (BUG: to_datetime(format='...%f') parses nanoseconds) (pandas-dev#48860)

BUG: to_datetime(format='...%f') parses nanoseconds (pandas-dev#48820)

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48850 on branch 1.5.x (TYP: Fix typing errors caused by new numpy) (pandas-dev#48859)

* Backport PR pandas-dev#48790 on branch 1.5.x (Created icons for dark theme) (pandas-dev#48875)

Backport PR pandas-dev#48790: Created icons for dark theme

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* Backport PR pandas-dev#48805 on branch 1.5.x (Added padding and fixed columns for sponsor logos in mobile view) (pandas-dev#48874)

Backport PR pandas-dev#48805: Added padding and fixed columns for sponsor logos in mobile view

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* Backport PR pandas-dev#48866 on branch 1.5.x (REGR: replace replacing wrong values with inplace and datetime) (pandas-dev#48872)

Backport PR pandas-dev#48866: REGR: replace replacing wrong values with inplace and datetime

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* Backport PR pandas-dev#48853 on branch 1.5.x (REGR: Avoid unnecessary warning when setting empty dataframe) (pandas-dev#48873)

Backport PR pandas-dev#48853: REGR: Avoid unnecessary warning when setting empty dataframe

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* Backport PR pandas-dev#48833 on branch 1.5.x (BUG: ArrowExtensionArray compared to invalid object not raising) (pandas-dev#48878)

Backport PR pandas-dev#48833: BUG: ArrowExtensionArray compared to invalid object not raising

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* Backport PR pandas-dev#48686 on branch 1.5.x (BUG: to_datetime(tz_mix, utc=True) converts to UTC) (pandas-dev#48882)

Backport PR pandas-dev#48686: BUG: to_datetime(tz_mix, utc=True) converts to UTC

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* Backport PR pandas-dev#48736 on branch 1.5.x ( BUG: AttributeError: 'function' object has no attribute 'currentframe') (pandas-dev#48887)

* Backport PR pandas-dev#48797 on branch 1.5.x (REGR: fix df.apply with keyword non-zero axis) (pandas-dev#48886)

REGR: fix df.apply with keyword non-zero axis (pandas-dev#48797)

Co-authored-by: Shantanu <12621235+hauntsaninja@users.noreply.github.com>

* add pandas[foo] throughout to explain the optional extras process

Also `Recommended dependencies` to `Performance dependencies (recommended)`

* extend optional_extra`all` to cover tests and redundant packages

* add tzdata from pandas 1.5.0

* move summary to latest whatsnew doc

Code is now stable and updated.

Attempt a port from doc/source/whatsnew/v1.5.0.rst over to latest document  doc/source/whatsnew/v1.5.1.rst.

* explicitly pair packages to optional_extra in installs

* fix sphinx errors in install.rst

extra padding on column + empty return before table

* add: pytest-asyncio>=0.19.0

pytest-asyncio>=0.19.0

Closes pandas-dev#48361.

No version guidance available so went for latest.  No-one should be messing around with tests without modern installs.

* fsspec note

* repin pytest-asyncio>=0.17.0

matches pytest-asyncio>=0.17.0 in ci/deps/actions-38-minimum_versions.yaml

* move summary from whatsnew/v1.5.1 to v1.6.0

plus add (:issue:`48361`) resolution note

* linting

double-backtick ``test``
underline tilde match title length

* Add `clipboard` as optional extra

* Review comments

 - fss optional extra
 - better numba description

* remove unneeded comment

* fix: leave 1.5.1.rst unchanged by this PR

* Update doc/source/whatsnew/v1.5.1.rst

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* pyarrow bump 1.0.1 -> 6.0.0

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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

pandas recommends the following optional dependencies for performance gains. These dependencies can be specifically
installed with ``pandas[performance]`` (i.e. add as optional_extra to the pandas requirement)
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Echoing @Dr-Irv's comment, also here I find this confusing, since at the top of this document we actually start with mentioning conda install pandas before pip install pandas. So I would personally remove the pandas[performance] here, or at least every time we mention such an extra also point to a dedicated section explaining it?

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JMBurley commented Oct 25, 2022

I think this should point out that the optional dependencies should ONLY be managed via files, and that you cannot do conda install pandas[computation]=1.5.1 (for example) to get the dependencies to install. The way this section is written, it makes it seem that you can do that [in conda] (or maybe you can with this PR, in which case that should be shown as an installation option).

Good point. As far as I'm aware there is absolutely no way replicate optional dependencies in conda, and the workaround would be to make individual recipes with individual names for every conceivable combination of optional_extras.

we actually start with mentioning conda install pandas before pip install pandas.

I wonder if pandas mentioning condas first is a side-effect of pandas being extant from pre-pip and enduring pip's early days when conda had significant advantages. The python ecosystem has pip-first since python 3.4 while we should certainly support both, I think pip should be the primary install suggestion for pandas.

Regardless, I agree that having a single section explaining how to install extras and then continually linking to it from elsewhere in installs.rst is an improvement.

noatamir pushed a commit to noatamir/pandas that referenced this pull request Nov 9, 2022
…dev#47336)

* add-recommended-dependencies-as-extras_require-in-setup.cfg

See issue pandas-dev#47335.

pandas-dev#47335

recommended dependencies should have package mgmt facilitated through pandas.  This will make mgmt of pandas in production docker environments a lot simpler.

* Update v1.4.3.rst

* double backtick code in rst

* rebundle under extras_require `recommended`

* [options.extras_require] bundled dependencies by featureset

see pandas-dev#39164 for discussion.

* note: [options.extras_require] bundled dependencies by featureset

* Update setup.cfg

rollback numba from recommended.  This would necessitate and update to documentation that requires broad agreement from pd-dev-core team that would slow down the overall PR

* add adlfs for azure to `access data in cloud`

see pandas-dev#39164 for discussion.  0.6.0 might be an overly restrictive version, but it is compatible

* fix extras_require: PyTables is actually `tables` on PyPi

* Update setup.cfg

* add `all` option to [options.extras_require]

* moved changelog to 1.4.4 as 1.4.3 released while this PR was stalled

* Updated to 1.5.0 compliance

* simplify sql option names

* extras rename: recommended -> performance

* remove azure

support is currently unofficial as of 1.5.0

* align with actions-38-minimum_versions.yaml

add  specific installs and, where required, missing install documentation for
 - odfpy
 - pyreadstat
 - compression options

* Pandas -> pandas in doc

Co-authored-by: Matthew Roeschke <emailformattr@gmail.com>

* extras rename: s3 -> aws

see pandas-dev#47336 (comment)

* extras rename: table -> output_formatting

to be more general in case of future changes

* bug: `>=` not `=`

* Apply suggestions from code review

Co-authored-by: Simon Hawkins <simonjayhawkins@gmail.com>

* align 1.5.0.rst to latest extras_require updates

* 1.5.0.rst example updated to use valid extras

* add optional dep mgmt instructions to install.rst

* lint scipy optional import

Co-authored-by: Matthew Roeschke <emailformattr@gmail.com>

* Apply suggestions from code review

* detailed extras guidance in install.rst

 - updated numbas to a full recommended dependency with a promotional bullet point like bottleneck and numexpr
- clarified the extra to use for each set of optional dependencies
- made xml an optional extra, because is does have usage outside of read_html.

* _optional.py note to keep track of setup.cfg

* bug: indent after bullet in install.rst

* remove numba from computation extra.

* Backport PR pandas-dev#48197 on branch 1.5.x (DOC: Cleanup 1.5 whatsnew) (pandas-dev#48228)

Backport PR pandas-dev#48197: DOC: Cleanup 1.5 whatsnew

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* Backport PR pandas-dev#48232 on branch 1.5.x (CI: Ensure jobs run on 1.5.x branch) (pandas-dev#48235)

Backport PR pandas-dev#48232: CI: Ensure jobs run on 1.5.x branch

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* Backport PR pandas-dev#48180 on branch 1.5.x (CI: Switch to large for circleci) (pandas-dev#48251)

Backport PR pandas-dev#48180: CI: Switch to large for circleci

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* Backport PR pandas-dev#48245 on branch 1.5.x (CI: Skip test_round_sanity tests due to failures) (pandas-dev#48257)

Backport PR pandas-dev#48245: CI: Skip test_round_sanity tests due to failures

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* Backport PR pandas-dev#48240 on branch 1.5.x (Fix mypy erroring on backport branches) (pandas-dev#48259)

Backport PR pandas-dev#48240: Fix mypy erroring on backport branches

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* Backport PR pandas-dev#48215 on branch 1.5.x (REGR: properly update DataFrame cache in Series.__setitem__) (pandas-dev#48268)

Backport PR pandas-dev#48215: REGR: properly update DataFrame cache in Series.__setitem__

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* Backport PR pandas-dev#48272 on branch 1.5.x (CI: Require s3fs greater than minumum version in builds) (pandas-dev#48276)

Backport PR pandas-dev#48272: CI: Require s3fs greater than minumum version in builds

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* Backport PR pandas-dev#48299 on branch 1.5.x (Bump s3fs to 2021.08.00) (pandas-dev#48305)

Backport PR pandas-dev#48299: Bump s3fs to 2021.08.00

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* Backport PR pandas-dev#48027 on branch 1.5.x (ENH: Support masks in groupby prod) (pandas-dev#48302)

Backport PR pandas-dev#48027: ENH: Support masks in groupby prod

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* Backport PR pandas-dev#47762 on branch 1.5.x (REGR: preserve reindexed array object (instead of creating new array) for concat with all-NA array) (pandas-dev#48309)

Backport PR pandas-dev#47762: REGR: preserve reindexed array object (instead of creating new array) for concat with all-NA array

Co-authored-by: Joris Van den Bossche <jorisvandenbossche@gmail.com>

* Backport PR pandas-dev#48246 on branch 1.5.x (REGR: iloc not possible for sparse DataFrame) (pandas-dev#48311)

Backport PR pandas-dev#48246: REGR: iloc not possible for sparse DataFrame

Co-authored-by: Simon Hawkins <simonjayhawkins@gmail.com>

* Backport PR pandas-dev#48314 on branch 1.5.x (DOC: v1.4.4 release date and tidy up release notes) (pandas-dev#48320)

Backport PR pandas-dev#48314: DOC: v1.4.4 release date and tidy up release notes

Co-authored-by: Simon Hawkins <simonjayhawkins@gmail.com>

* Backport PR pandas-dev#48301 on branch 1.5.x (DEPR: Deprecate positional arguments in pivot) (pandas-dev#48326)

Backport PR pandas-dev#48301: DEPR: Deprecate positional arguments in pivot

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* Backport PR pandas-dev#48214 on branch 1.5.x (WEB: Removing links to pdf version of the docs from web and docs) (pandas-dev#48242)

Backport PR pandas-dev#48214: WEB: Removing links to pdf version of the docs from web and docs

* Backport PR pandas-dev#48159 on branch 1.5.x (TST: Fix interchange/plotting/groupby test warnings) (pandas-dev#48279)

Backport PR pandas-dev#48159: TST: Fix interchange/plotting/groupby test warnings

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* Backport PR pandas-dev#48324 on branch 1.5.x (BUG: Add note in whatsnew for DataFrame.at behavior change) (pandas-dev#48345)

Backport PR pandas-dev#48324: BUG: Add note in whatsnew for DataFrame.at behavior change

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* Backport PR pandas-dev#48336 on branch 1.5.x (DOC: Add whatsnew note for pandas-dev#45404) (pandas-dev#48341)

Backport PR pandas-dev#48336: DOC: Add whatsnew note for pandas-dev#45404

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* Backport PR pandas-dev#48254 on branch 1.5.x (REF: avoid FutureWarning about using deprecates loc.__setitem__ non-inplace usage) (pandas-dev#48353)

Backport PR pandas-dev#48254: REF: avoid FutureWarning about using deprecates loc.__setitem__ non-inplace usage

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* Backport PR pandas-dev#48334 on branch 1.5.x (BUG: read_html(extract_links=all) with no header) (pandas-dev#48350)

Backport PR pandas-dev#48334: BUG: read_html(extract_links=all) with no header

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48265 on branch 1.5.x (CI: Setting up ssh key to upload prod docs) (pandas-dev#48370)

Backport PR pandas-dev#48265: CI: Setting up ssh key to upload prod docs

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* Backport PR pandas-dev#48381 on branch 1.5.x (CI: Pin mambaforge image) (pandas-dev#48401)

Backport PR pandas-dev#48381: CI: Pin mambaforge image

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* Backport PR pandas-dev#48229 on branch 1.5.x (TST: Test Nullable int floordiv by 0) (pandas-dev#48413)

Backport PR pandas-dev#48229: TST: Test Nullable int floordiv by 0

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* Backport PR pandas-dev#48414 on branch 1.5.x (DOC: Add deprecation to is_categorical) (pandas-dev#48418)

Backport PR pandas-dev#48414: DOC: Add deprecation to is_categorical

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* Backport PR pandas-dev#48264 on branch 1.5.x (BUG: ArrowExtensionArray._from_* accepts pyarrow arrays) (pandas-dev#48422)

* Backport PR pandas-dev#48264: BUG: ArrowExtensionArray._from_* accepts pyarrow arrays

* Add missing import

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* Backport PR pandas-dev#48411 on branch 1.5.x (REGR: get_loc for ExtensionEngine not returning bool indexer for na) (pandas-dev#48430)

Backport PR pandas-dev#48411: REGR: get_loc for ExtensionEngine not returning bool indexer for na

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* Backport PR pandas-dev#48419 on branch 1.5.x (BUG: ensure to return writable buffer in __dataframe__ interchange for categorical column) (pandas-dev#48441)

Backport PR pandas-dev#48419: BUG: ensure to return writable buffer in __dataframe__ interchange for categorical column

Co-authored-by: Joris Van den Bossche <jorisvandenbossche@gmail.com>

* Backport PR pandas-dev#48444 on branch 1.5.x (CI: Pin ipython version) (pandas-dev#48449)

Backport PR pandas-dev#48444: CI: Pin ipython version

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48380 on branch 1.5.x (DOC: Clarify that objects dtype takes precedence in where) (pandas-dev#48445)

* Backport PR pandas-dev#48380: DOC: Clarify that objects dtype takes precedence in where

* Update generic.py

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Manual Backport PR pandas-dev#48427 on branch 1.5.x (BLD: Refactor Dockerfile to not install dev enviornment on base) (pandas-dev#48450)

Backport PR pandas-dev#48427: BLD: Refactor Dockerfile to not install dev enviornment on base

* Backport PR pandas-dev#48426 on branch 1.5.x (BUG: Column.size should be a method) (pandas-dev#48465)

Backport PR pandas-dev#48426: BUG: Column.size should be a method

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48398 on branch 1.5.x (WARN: Avoid FutureWarnings in tests) (pandas-dev#48420)

* Backport PR pandas-dev#48398: WARN: Avoid FutureWarnings in tests

* Update

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>
Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* Backport PR pandas-dev#48416 on branch 1.5.x (REF: ensure to apply suffixes before concat step in merge code) (pandas-dev#48470)

Backport PR pandas-dev#48416: REF: ensure to apply suffixes before concat step in merge code

Co-authored-by: Joris Van den Bossche <jorisvandenbossche@gmail.com>

* Backport PR pandas-dev#48354 on branch 1.5.x (CI: Bump timeout to 180 minutes) (pandas-dev#48474)

Backport PR pandas-dev#48354: CI: Bump timeout to 180 minutes

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48472 on branch 1.5.x (PERF: keep using ObjectEngine for ExtensionArrays for 1.5) (pandas-dev#48486)

Backport PR pandas-dev#48472: PERF: keep using ObjectEngine for ExtensionArrays for 1.5

Co-authored-by: Joris Van den Bossche <jorisvandenbossche@gmail.com>

* Backport PR pandas-dev#48473 on branch 1.5.x (REGR: .describe on unsigned dtypes results in object) (pandas-dev#48501)

Backport PR pandas-dev#48473: REGR: .describe on unsigned dtypes results in object

Co-authored-by: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>

* Backport PR pandas-dev#48443 on branch 1.5.x (BUG: Fix pyarrow groupby tests)  (pandas-dev#48494)

* BUG: Fix pyarrow groupby tests (pandas-dev#48443)

# Conflicts:
#	pandas/tests/extension/test_arrow.py

* CI: Fix failing tests (pandas-dev#48493)

Co-authored-by: jbrockmendel <jbrockmendel@gmail.com>

* Backport PR pandas-dev#48490 on branch 1.5.x (CI: Use -j1 for python-dev build to avoid flaky build error) (pandas-dev#48517)

Backport PR pandas-dev#48490: CI: Use -j1 for python-dev build to avoid flaky build error

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Manual Backport PR pandas-dev#48428 on branch 1.5.x (BUG/TST: fix a bunch of arraymanager+pyarrow tests) (pandas-dev#48518)

Backport PR pandas-dev#48428: BUG/TST: fix a bunch of arraymanager+pyarrow tests

Co-authored-by: jbrockmendel <jbrockmendel@gmail.com>

* Backport PR pandas-dev#48525 on branch 1.5.x (CI: Fix py311 builds different exception message) (pandas-dev#48529)

Backport PR pandas-dev#48525: CI: Fix py311 builds different exception message

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48489 on branch 1.5.x (BUG: fix test_arrow.py tests) (pandas-dev#48532)

Backport PR pandas-dev#48489: BUG: fix test_arrow.py tests

Co-authored-by: jbrockmendel <jbrockmendel@gmail.com>

* Backport PR pandas-dev#48543 on branch 1.5.x (DOC: Update footer and include OVH) (pandas-dev#48548)

Backport PR pandas-dev#48543: DOC: Update footer and include OVH

Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* Manual Backport PR pandas-dev#48417 on branch 1.5.x (Revert set_index inplace and copy keyword changes) (pandas-dev#48552)

Backport PR pandas-dev#48417: Revert set_index inplace and copy keyword changes

Co-authored-by: Joris Van den Bossche <jorisvandenbossche@gmail.com>

* Backport PR pandas-dev#48550 on branch 1.5.x (TST: remove 2D tests irrelevant for pyarrow) (pandas-dev#48554)

Backport PR pandas-dev#48550: TST: remove 2D tests irrelevant for pyarrow

Co-authored-by: jbrockmendel <jbrockmendel@gmail.com>

* Backport PR pandas-dev#48556 on branch 1.5.x (DOC: Fix docs footer) (pandas-dev#48558)

Backport PR pandas-dev#48556: DOC: Fix docs footer

Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* Backport PR pandas-dev#48562 on branch 1.5.x (TST: Testing that no warnings are emitted and that inplace fillna produces the correct result (GH48480)) (pandas-dev#48564)

Backport PR pandas-dev#48562: TST: Testing that no warnings are emitted and that inplace fillna produces the correct result (GH48480)

Co-authored-by: RaphSku <45042665+RaphSku@users.noreply.github.com>

* Backport PR pandas-dev#48563 on branch 1.5.x (DOC: Fix read_sas 1.5 release notes) (pandas-dev#48565)

Backport PR pandas-dev#48563: DOC: Fix read_sas 1.5 release notes

Co-authored-by: Jonas Haag <jonas@lophus.org>

* Backport PR pandas-dev#48539 on branch 1.5.x (REGR: groupby doesn't identify null values when sort=False) (pandas-dev#48568)

Backport PR pandas-dev#48539: REGR: groupby doesn't identify null values when sort=False

Co-authored-by: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>

* Backport PR pandas-dev#48555 on branch 1.5.x (DEPR: Series.astype(np.datetime64)) (pandas-dev#48569)

Backport PR pandas-dev#48555: DEPR: Series.astype(np.datetime64)

Co-authored-by: jbrockmendel <jbrockmendel@gmail.com>

* Backport PR pandas-dev#48557 on branch 1.5.x (WEB: Add new footer to web) (pandas-dev#48571)

Backport PR pandas-dev#48557: WEB: Add new footer to web

Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* Backport PR pandas-dev#48285 on branch 1.5.x (WEB: Unpin pydata sphinx theme) (pandas-dev#48585)

Backport PR pandas-dev#48285: WEB: Unpin pydata sphinx theme

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48572 on branch 1.5.x (DOC: Fixing styles for the dark theme) (pandas-dev#48584)

Backport PR pandas-dev#48572: DOC: Fixing styles for the dark theme

Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* Backport PR pandas-dev#48397 on branch 1.5.x (WARN: Remove false positive warning for iloc inplaceness) (pandas-dev#48583)

Backport PR pandas-dev#48397: WARN: Remove false positive warning for iloc inplaceness

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48587 on branch 1.5.x (Fix `series.str.startswith(tuple)`) (pandas-dev#48593)

Backport PR pandas-dev#48587: Fix `series.str.startswith(tuple)`

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

* Backport PR pandas-dev#48601 on branch 1.5.x (CI: Fix matplolib release issues) (pandas-dev#48617)

Backport PR pandas-dev#48601: CI: Fix matplolib release issues

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48623 on branch 1.5.x (REGR/DOC: Docs left navbar broke) (pandas-dev#48625)

Backport PR pandas-dev#48623: REGR/DOC: Docs left navbar broke

Co-authored-by: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>

* Backport PR pandas-dev#48619 on branch 1.5.x (REGR: Loc.setitem with enlargement raises for nested data) (pandas-dev#48629)

Backport PR pandas-dev#48619: REGR: Loc.setitem with enlargement raises for nested data

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48627 on branch 1.5.x (DOC: Last changes to release notes for 1.5.0 release) (pandas-dev#48630)

Backport PR pandas-dev#48627: DOC: Last changes to release notes for 1.5.0 release

Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* RLS: 1.5.0

* Backport PR pandas-dev#48642 on branch 1.5.x (DOC: Add release notes for 1.5.1) (pandas-dev#48647)

Backport PR pandas-dev#48642: DOC: Add release notes for 1.5.1

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48639 on branch 1.5.x (CI: Fix directory name for published prod docs) (pandas-dev#48648)

Backport PR pandas-dev#48639: CI: Fix directory name for published prod docs

Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* Backport PR pandas-dev#48651 on branch 1.5.x (REGR: TextIOWrapper raising an error in read_csv) (pandas-dev#48666)

Backport PR pandas-dev#48651: REGR: TextIOWrapper raising an error in read_csv

Co-authored-by: Torsten Wörtwein <twoertwein@users.noreply.github.com>

* Backport PR pandas-dev#48599 on branch 1.5.x (DOC: Add deprecation infos to deprecated functions) (pandas-dev#48690)

Backport PR pandas-dev#48599: DOC: Add deprecation infos to deprecated functions

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48620 on branch 1.5.x (REGR: Performance decrease in factorize) (pandas-dev#48710)

Backport PR pandas-dev#48620: REGR: Performance decrease in factorize

Co-authored-by: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>

* Backport PR pandas-dev#48711 on branch 1.5.x (REGR: Regression in DataFrame.loc when setting df with all True indexer) (pandas-dev#48717)

Backport PR pandas-dev#48711: REGR: Regression in DataFrame.loc when setting df with all True indexer

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48696 on branch 1.5.x (REGR: to_hdf raising AssertionError with boolean index) (pandas-dev#48716)

Backport PR pandas-dev#48696: REGR: to_hdf raising AssertionError with boolean index

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48734 on branch 1.5.x (REGR: Raise on invalid colormap for scatter plot) (pandas-dev#48744)

Backport PR pandas-dev#48734: REGR: Raise on invalid colormap for scatter plot

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48713 on branch 1.5.x (BUG: pivot_table raising Future Warning with datetime column as index) (pandas-dev#48742)

Backport PR pandas-dev#48713: BUG: pivot_table raising Future Warning with datetime column as index

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48703 on branch 1.5.x (Added theme_switcher ) (pandas-dev#48741)

Backport PR pandas-dev#48703: Added theme_switcher

Co-authored-by: Deepak Sirohiwal <38135521+deepaksirohiwal@users.noreply.github.com>

* Backport PR pandas-dev#48697 on branch 1.5.x (REGR: None converted to NaN when enlarging Series) (pandas-dev#48745)

Backport PR pandas-dev#48697: REGR: None converted to NaN when enlarging Series

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48702 on branch 1.5.x (REGR: dropna affects observed in groupby) (pandas-dev#48750)

Backport PR pandas-dev#48702: REGR: dropna affects observed in groupby

Co-authored-by: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>

* Backport PR pandas-dev#48782 on branch 1.5.x (REGR: describe raising when result contains NA) (pandas-dev#48793)

Backport PR pandas-dev#48782: REGR: describe raising when result contains NA

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48662 on branch 1.5.x (BUG: Series.getitem not falling back to positional for bool index) (pandas-dev#48799)

Backport PR pandas-dev#48662: BUG: Series.getitem not falling back to positional for bool index

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48751 on branch 1.5.x (WEB: Update link to datapythonista blog url) (pandas-dev#48798)

Backport PR pandas-dev#48751: WEB: Update link to datapythonista blog url

Co-authored-by: Marc Garcia <garcia.marc@gmail.com>

* Backport PR pandas-dev#48608 on branch 1.5.x (REGR: assert_index_equal raising with non matching pd.NA) (pandas-dev#48800)

* Backport PR pandas-dev#48608: REGR: assert_index_equal raising with non matching pd.NA

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48785 on branch 1.5.x (BUG: still emitting unnecessary FutureWarning in DataFrame.sort_values with sparse columns) (pandas-dev#48807)

Backport PR pandas-dev#48785: BUG: still emitting unnecessary FutureWarning in DataFrame.sort_values with sparse columns

Co-authored-by: Marco Edward Gorelli <33491632+MarcoGorelli@users.noreply.github.com>

* Backport PR pandas-dev#48693 on branch 1.5.x (ENH: Make deprecate_nonkeyword_arguments alter function signature) (pandas-dev#48795)

Backport PR pandas-dev#48693: ENH: Make deprecate_nonkeyword_arguments alter function signature

Co-authored-by: Shantanu <12621235+hauntsaninja@users.noreply.github.com>

* Backport PR pandas-dev#48579 on branch 1.5.x (BUG: Fix calling groupBy(...).apply(func) on an empty dataframe invokes func) (pandas-dev#48817)

BUG: Fix calling groupBy(...).apply(func) on an empty dataframe invokes func  (pandas-dev#48579)

(cherry picked from commit 8b0ad71)

Co-authored-by: Dennis Chukwunta <chuksmcdennis@yahoo.com>

* Backport PR pandas-dev#48760 on branch 1.5.x (REGR: groupby.size with axis=1 doesn't return a Series) (pandas-dev#48825)

* Backport PR pandas-dev#48820 on branch 1.5.x (BUG: to_datetime(format='...%f') parses nanoseconds) (pandas-dev#48860)

BUG: to_datetime(format='...%f') parses nanoseconds (pandas-dev#48820)

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48850 on branch 1.5.x (TYP: Fix typing errors caused by new numpy) (pandas-dev#48859)

* Backport PR pandas-dev#48790 on branch 1.5.x (Created icons for dark theme) (pandas-dev#48875)

Backport PR pandas-dev#48790: Created icons for dark theme

Co-authored-by: Lorenzo Vainigli <lorenzovngl@gmail.com>

* Backport PR pandas-dev#48805 on branch 1.5.x (Added padding and fixed columns for sponsor logos in mobile view) (pandas-dev#48874)

Backport PR pandas-dev#48805: Added padding and fixed columns for sponsor logos in mobile view

Co-authored-by: Amay Patel <92037532+amay-patel@users.noreply.github.com>

* Backport PR pandas-dev#48866 on branch 1.5.x (REGR: replace replacing wrong values with inplace and datetime) (pandas-dev#48872)

Backport PR pandas-dev#48866: REGR: replace replacing wrong values with inplace and datetime

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48853 on branch 1.5.x (REGR: Avoid unnecessary warning when setting empty dataframe) (pandas-dev#48873)

Backport PR pandas-dev#48853: REGR: Avoid unnecessary warning when setting empty dataframe

Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>

* Backport PR pandas-dev#48833 on branch 1.5.x (BUG: ArrowExtensionArray compared to invalid object not raising) (pandas-dev#48878)

Backport PR pandas-dev#48833: BUG: ArrowExtensionArray compared to invalid object not raising

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48686 on branch 1.5.x (BUG: to_datetime(tz_mix, utc=True) converts to UTC) (pandas-dev#48882)

Backport PR pandas-dev#48686: BUG: to_datetime(tz_mix, utc=True) converts to UTC

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* Backport PR pandas-dev#48736 on branch 1.5.x ( BUG: AttributeError: 'function' object has no attribute 'currentframe') (pandas-dev#48887)

* Backport PR pandas-dev#48797 on branch 1.5.x (REGR: fix df.apply with keyword non-zero axis) (pandas-dev#48886)

REGR: fix df.apply with keyword non-zero axis (pandas-dev#48797)

Co-authored-by: Shantanu <12621235+hauntsaninja@users.noreply.github.com>

* add pandas[foo] throughout to explain the optional extras process

Also `Recommended dependencies` to `Performance dependencies (recommended)`

* extend optional_extra`all` to cover tests and redundant packages

* add tzdata from pandas 1.5.0

* move summary to latest whatsnew doc

Code is now stable and updated.

Attempt a port from doc/source/whatsnew/v1.5.0.rst over to latest document  doc/source/whatsnew/v1.5.1.rst.

* explicitly pair packages to optional_extra in installs

* fix sphinx errors in install.rst

extra padding on column + empty return before table

* add: pytest-asyncio>=0.19.0

pytest-asyncio>=0.19.0

Closes pandas-dev#48361.

No version guidance available so went for latest.  No-one should be messing around with tests without modern installs.

* fsspec note

* repin pytest-asyncio>=0.17.0

matches pytest-asyncio>=0.17.0 in ci/deps/actions-38-minimum_versions.yaml

* move summary from whatsnew/v1.5.1 to v1.6.0

plus add (:issue:`48361`) resolution note

* linting

double-backtick ``test``
underline tilde match title length

* Add `clipboard` as optional extra

* Review comments

 - fss optional extra
 - better numba description

* remove unneeded comment

* fix: leave 1.5.1.rst unchanged by this PR

* Update doc/source/whatsnew/v1.5.1.rst

Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>

* pyarrow bump 1.0.1 -> 6.0.0

Co-authored-by: Matthew Roeschke <emailformattr@gmail.com>
Co-authored-by: Simon Hawkins <simonjayhawkins@gmail.com>
Co-authored-by: MeeseeksMachine <39504233+meeseeksmachine@users.noreply.github.com>
Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com>
Co-authored-by: Patrick Hoefler <61934744+phofl@users.noreply.github.com>
Co-authored-by: Joris Van den Bossche <jorisvandenbossche@gmail.com>
Co-authored-by: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>
Co-authored-by: jbrockmendel <jbrockmendel@gmail.com>
Co-authored-by: Marc Garcia <garcia.marc@gmail.com>
Co-authored-by: Kevin Sheppard <bashtage@users.noreply.github.com>
Co-authored-by: RaphSku <45042665+RaphSku@users.noreply.github.com>
Co-authored-by: Jonas Haag <jonas@lophus.org>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Co-authored-by: Pandas Development Team <pandas-dev@python.org>
Co-authored-by: Torsten Wörtwein <twoertwein@users.noreply.github.com>
Co-authored-by: Deepak Sirohiwal <38135521+deepaksirohiwal@users.noreply.github.com>
Co-authored-by: Marco Edward Gorelli <33491632+MarcoGorelli@users.noreply.github.com>
Co-authored-by: Shantanu <12621235+hauntsaninja@users.noreply.github.com>
Co-authored-by: Dennis Chukwunta <chuksmcdennis@yahoo.com>
Co-authored-by: Lorenzo Vainigli <lorenzovngl@gmail.com>
Co-authored-by: Amay Patel <92037532+amay-patel@users.noreply.github.com>
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