[Bug]: DeprecationWarning for pkg_resources.declare_namespace usage in mpl_toolkit #25244

rjgildea · 2023-02-17T17:48:23Z

Bug summary

As of setuptools v67.3.0 the use of pkg_resources.declare_namespace in lib/mpl_toolkits/__init__.py raises a DeprecationWarning.

Code for reproduction

$ mamba create -n test python=3.10 matplotlib-base -y
$ mamba activate test
$ export PYTHONDEVMODE=1
$ python -c "import pkg_resources"

Actual outcome

/path/to/test/lib/python3.10/site-packages/pkg_resources/__init__.py:2804: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
  declare_namespace(pkg)

Expected outcome

No output

Additional information

See also:
https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
https://packaging.python.org/en/latest/guides/packaging-namespace-packages/
https://peps.python.org/pep-0420/

Operating system

No response

Matplotlib Version

3.7.0

Matplotlib Backend

TkAgg

Python version

Python 3.10.9

Jupyter version

No response

Installation

conda

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

tacaswell · 2023-02-17T23:58:49Z

Is there a good guide for how to migrate from "old" namespace packages to "new" namespace packages? What is going to break if we just delete this __init__.py and how do we warn our users we are about to break them (I asked these in the linked setuptools issue as well)?

tacaswell · 2023-02-18T00:01:17Z

Medium difficulty because it requires understanding packaging related issues but good first issue because it requires no understanding of Matplotlib to do.

Tasks:

sort out what even needs to be done (just delete the __init__.py?)
document if / how this will break any downstream packages and how they also need to migrate
add an API change note that we did this.

See also: matplotlib/matplotlib#25244 Run tests directly rather than as a subprocess so that pytest filterwarnings options have their intended effect.

As of setuptools v67.3.0 the use of pkg_resources.declare_namespace in lib/mpl_toolkits/__init__.py raises a DeprecationWarning. See also: matplotlib/matplotlib#25244 Run tests directly rather than as a subprocess so that pytest filterwarnings options have their intended effect.

See matplotlib/matplotlib#25244 and matplotlib/matplotlib#25204

neutrinoceros · 2023-02-20T17:32:12Z

What is going to break if we just delete this init.py

To answer this, I'll quote https://packaging.python.org/en/latest/guides/packaging-namespace-packages/#native-namespace-packages

It is extremely important that every distribution that uses the namespace package omits the init.py or uses a pkgutil-style init.py. If any distribution does not, it will cause the namespace logic to fail and the other sub-packages will not be importable.

And from the same source:

Warning While native namespace packages and pkgutil-style namespace packages are largely compatible, pkg_resources-style namespace packages are not compatible with the other methods. It’s inadvisable to use different methods in different distributions that provide packages to the same namespace.

In other words, any dependent code that implements a mpl_toolkits.* subpackage will break immediately when the deprecated __init__.py is removed.
It also seems that there is no way for dependent code to support both implementations of namespace packages at the same time, so I assume they'll have to drop support for all versions of matplotlib previous to the one that does the change... or renounce supporting that version and newer ones.

I haven't found a solution to warn about the transition from within matplotlib, so currently my recommendation would be to just reach out to downstream developers by any means appropriate.
Is there a list of such sub packages somewhere that'd be relevant ? there seem to be only one on PyPI (https://pypi.org/project/mpl-toolkits.clifford/)

As of setuptools v67.3.0 the use of pkg_resources.declare_namespace in lib/mpl_toolkits/__init__.py raises a DeprecationWarning. See also: matplotlib/matplotlib#25244 Run tests directly rather than as a subprocess so that pytest filterwarnings options have their intended effect.

ssbarnea · 2023-03-01T18:03:56Z

I remember facing this issue few years back and the conclusion was to avoid using namespaces in general. Much safer and you do not depend on someone else which could break you.

tacaswell · 2023-03-01T18:29:49Z

Per pypa/setuptools#3434 (comment) it seems we can just delete the __init__.py files and everything will be OK.

See matplotlib/matplotlib#25244 and matplotlib/matplotlib#25204 Consolidate filterwarnings in pytest.ini

BabaYaga1221 · 2023-03-12T18:48:49Z

@tacaswell I just look the same resource on python version 3.10.10 and the excepted outcome was verified. I think that it just needs to update python to a newer version.

correct me if I am wrong. Thanks

tacaswell · 2023-03-13T14:22:43Z

@BabaYaga1221 The dependency is on the version of setuptools (not the version of Python).

Until this matplotlib bug is fixed: matplotlib/matplotlib#25244 We cannot have both updated setuptools and warnings. This is because subprocesses also print out warnings, and this causes the tests to fail because of stderr output.

…mespace A lot of third party dependencies (e.g. matplotlib/matplotlib#25244) are still using it. Helpful to ignore for now.

Python 3.10 remains the default, for now. Also, update CI to either disable or suppress PYTHONDEVMODE warnings from this matplotlib bug: matplotlib/matplotlib#25244

As of setuptools v67.3.0 the use of pkg_resources.declare_namespace in lib/mpl_toolkits/__init__.py raises a DeprecationWarning. See also: matplotlib/matplotlib#25244 Run tests directly rather than as a subprocess so that pytest filterwarnings options have their intended effect.

tacaswell added this to the v3.8.0 milestone Feb 17, 2023

tacaswell added Difficulty: Medium https://matplotlib.org/devdocs/devel/contribute.html#good-first-issues Good first issue Open a pull request against these issues if there are no active ones! labels Feb 17, 2023

neutrinoceros mentioned this issue Feb 19, 2023

BUG: importing glue with setuptools>=67.3 raises a DeprecationWarning glue-viz/glue#2364

Closed

rjgildea mentioned this issue Feb 20, 2023

Ignore deprecated pkg_resources.declare_namespace warnings cctbx/dxtbx#611

Merged

rjgildea added a commit to dials/dials that referenced this issue Feb 20, 2023

Filter matplotlib-related warnings

c509266

See matplotlib/matplotlib#25244 and matplotlib/matplotlib#25204

rjgildea mentioned this issue Feb 20, 2023

Filter matplotlib-related warnings dials/dials#2344

Merged

oscargus mentioned this issue Feb 21, 2023

Namespace package deprecation pygae/mpl_toolkits.clifford#10

Open

This was referenced Feb 23, 2023

namespace_packages deprecated pydap/pydap#277

Closed

supress namespace_package deprecation warning (doctests) pydata/xarray#7548

Merged

rly mentioned this issue Mar 1, 2023

[Bug]: DeprecationWarning on import hdmf.common hdmf-dev/hdmf#826

Closed

3 tasks

ssbarnea mentioned this issue Mar 1, 2023

Suppress deprecation warning caused by ruamel.yaml with newer setuptools ansible/ansible-lint#3112

Merged

rjgildea added a commit to dials/dials that referenced this issue Mar 2, 2023

Filter matplotlib-related warnings (#2344)

ab659cb

See matplotlib/matplotlib#25244 and matplotlib/matplotlib#25204 Consolidate filterwarnings in pytest.ini

neutrinoceros mentioned this issue Mar 4, 2023

ENH: switch mpl_toolkits to implicit namespace package (PEP 420) #25381

Merged

3 tasks

This was referenced Mar 6, 2023

DeprecationWarning for pkg_resources.declare_namespace usage in google.cloud googleapis/python-storage#1000

Closed

DeprecationWarning for pkg_resources.declare_namespace("google.logging") googleapis/python-logging#730

Closed

BabaYaga1221 mentioned this issue Mar 12, 2023

deleting __init__.py from matplotlib/lib/mpl_toolkits #25441

Closed

6 tasks

This was referenced Mar 17, 2023

Missing __init__.py file in mpl_toolkits #9823

Closed

Make mpl_toolkits a non-namespace package #5327

Closed

stress-tess mentioned this issue Mar 29, 2023

pkg_resources deprecation warnings Bears-R-Us/arkouda#2321

Closed

skyetomez mentioned this issue Mar 29, 2023

DeprecationWarning SpikeInterface/spikeinterface#1464

Closed

anjakefala mentioned this issue Apr 12, 2023

test: ignore all DeprecatedWarning calls for pkg_resources.declare_namespace ibis-project/ibis#5980

Merged

anjakefala added a commit to anjakefala/ibis that referenced this issue Apr 12, 2023

test: ignore all DeprecatedWarning calls for pkg_resources.declare_na…

fff1554

…mespace A lot of third party dependencies (e.g. matplotlib/matplotlib#25244) are still using it. Helpful to ignore for now.

cpcloud pushed a commit to ibis-project/ibis that referenced this issue Apr 12, 2023

test: ignore all DeprecatedWarning calls for pkg_resources.declare_na…

b95fe96

…mespace A lot of third party dependencies (e.g. matplotlib/matplotlib#25244) are still using it. Helpful to ignore for now.

wduguay-air mentioned this issue Apr 21, 2023

156 Migrate to new gym step API cogment/cogment-verse#157

Merged

holtgrewe mentioned this issue May 4, 2023

Remove namespace warning biocommons/biocommons.seqrepo#106

Open

joshuacwnewton mentioned this issue May 30, 2023

Warning in test suite: pkg_resources is deprecated as an API spinalcordtoolbox/spinalcordtoolbox#4123

Closed

ksunden closed this as completed in #25381 Jun 8, 2023

FFFiend mentioned this issue Jun 26, 2023

Fix pytest warnings OpenAdaptAI/OpenAdapt#322

Closed

tacaswell mentioned this issue Sep 19, 2023

[Bug]: ImportError when using Matplotlib v3.8.0 in Python package tests #26827

Closed

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[Bug]: DeprecationWarning for pkg_resources.declare_namespace usage in mpl_toolkit #25244

[Bug]: DeprecationWarning for pkg_resources.declare_namespace usage in mpl_toolkit #25244

rjgildea commented Feb 17, 2023

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tacaswell commented Mar 13, 2023

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[Bug]: DeprecationWarning for pkg_resources.declare_namespace usage in mpl_toolkit #25244

[Bug]: DeprecationWarning for pkg_resources.declare_namespace usage in mpl_toolkit #25244

Comments

rjgildea commented Feb 17, 2023

Bug summary

Code for reproduction

Actual outcome

Expected outcome

Additional information

Operating system

Matplotlib Version

Matplotlib Backend

Python version

Jupyter version

Installation

tacaswell commented Feb 17, 2023

Uh oh!

tacaswell commented Feb 18, 2023

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neutrinoceros commented Feb 20, 2023

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ssbarnea commented Mar 1, 2023

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