Fix type annotation for plt.subplot_mosaic #29893

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gshiba wants to merge 2 commits into matplotlib:main

from gshiba:mosaic-typing

Open

Fix type annotation for plt.subplot_mosaic #29893

gshiba wants to merge 2 commits into matplotlib:main from gshiba:mosaic-typing

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gshiba

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@gshiba gshiba commented Apr 9, 2025 •

edited

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PR summary

Fixes the following type error:

# foo.py
import matplotlib.pyplot as plt
mosaic = [["a"], ["b"]]
fig, axes = plt.subplot_mosaic(mosaic)

$ mypy foo.py 
foo.py:3: error: Argument 1 to "subplot_mosaic" has incompatible type "list[list[str]]"; expected "Sequence[HashableList[str]]" [arg-type]
Found 1 error in 1 file (checked 1 source file)

$ pyright foo.py
 * Install prebuilt node (23.11.0) ..... done.
/home/ec2-user/repos/repro-mpl/foo.py
 /home/ec2-user/repos/repro-mpl/foo.py:3:13 - error: No overloads for "subplot_mosaic" match the provided arguments (reportCallIssue)
 /home/ec2-user/repos/repro-mpl/foo.py:3:32 - error: Argument of type "list[list[str]]" cannot be assigned to parameter "mosaic" of type "Sequence[HashableList[Hashable]]" in function "subplot_mosaic"
 "list[list[str]]" is not assignable to "Sequence[HashableList[Hashable]]"
 Type parameter "_T_co@Sequence" is covariant, but "list[str]" is not a subtype of "HashableList[Hashable]"
 "list[str]" is not assignable to "list[Hashable | HashableList]"
 Type parameter "_T@list" is invariant, but "str" is not the same as "Hashable | HashableList"
 Consider switching from "list" to "Sequence" which is covariant (reportArgumentType)
2 errors, 0 warnings, 0 informations

PR checklist

"closes #0000" is in the body of the PR description to link the related issue
new and changed code is tested
Plotting related features are demonstrated in an example
New Features and API Changes are noted with a directive and release note
Documentation complies with general and docstring guidelines

@gshiba


 s/list/Sequence/

4b7038d

@github-actions github-actions bot added the topic: pyplot API label

Apr 9, 2025

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Apr 9, 2025

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@timhoffm

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timhoffm commented Apr 9, 2025

What is The reason for this change? Do you have any particular use case? At least when writing out the spec explicitly, I'd want users to use lists. I rather consider the general support of sequences an implementation detail.

@gshiba

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gshiba commented Apr 9, 2025 •

edited

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Set up:

repos/repro-mpl$ python -m venv venv 
repos/repro-mpl$ . venv/bin/activate 
(venv) repos/repro-mpl$ pip install mypy matplotlib 
(venv) repos/repro-mpl$ mypy --version
mypy 1.15.0 (compiled: yes)
(venv) repos/repro-mpl$ python -c 'import matplotlib; print(matplotlib.__version__)'
3.10.1
(venv) repos/repro-mpl$ python --version
Python 3.10.16

This is what I was trying to solve:

(venv) repos/repro-mpl$ cat foo.py
import matplotlib.pyplot as plt
mosaic = [["a"], ["b"]]
fig, axes = plt.subplot_mosaic(mosaic)
(venv) repos/repro-mpl$ mypy foo.py 
foo.py:3: error: Argument 1 to "subplot_mosaic" has incompatible type "list[list[str]]"; expected "Sequence[HashableList[str]]" [arg-type]
Found 1 error in 1 file (checked 1 source file)

Evidently, this PR as of 4b7038d does not fix this yet...

Edit: here's pyright's error message:

(venv) repos/repro-mpl$ pyright foo.py
 * Install prebuilt node (23.11.0) ..... done.
/home/ec2-user/repos/repro-mpl/foo.py
 /home/ec2-user/repos/repro-mpl/foo.py:3:13 - error: No overloads for "subplot_mosaic" match the provided arguments (reportCallIssue)
 /home/ec2-user/repos/repro-mpl/foo.py:3:32 - error: Argument of type "list[list[str]]" cannot be assigned to parameter "mosaic" of type "Sequence[HashableList[Hashable]]" in function "subplot_mosaic"
  "list[list[str]]" is not assignable to "Sequence[HashableList[Hashable]]"
   Type parameter "_T_co@Sequence" is covariant, but "list[str]" is not a subtype of "HashableList[Hashable]"
    "list[str]" is not assignable to "list[Hashable | HashableList]"
     Type parameter "_T@list" is invariant, but "str" is not the same as "Hashable | HashableList"
     Consider switching from "list" to "Sequence" which is covariant (reportArgumentType)
2 errors, 0 warnings, 0 informations

@gshiba

fix

b743a81

@gshiba

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gshiba commented Apr 9, 2025 •

edited

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With b743a81

(venv) repos/repro-mpl$ mypy foo.py 
Success: no issues found in 1 source file
(venv) repos/repro-mpl$ pyright foo.py 
0 errors, 0 warnings, 0 informations

With the changes in b743a81, pyright says there are 3 fewer errors than before (7386 vs 7389)

$ pyright venv/lib/python3.10/site-packages/matplotlib
7386 errors, 33 warnings, 0 informations

How can/should I test the implication of this change on the rest of repo? I was not able to set up a dev env, even in CodeSpaces. Happy to try again...

@timhoffm

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timhoffm commented Apr 9, 2025

Ok thanks for the clarification. I suspect that you're barking up the wrong tree and instead the TypeVar _HT used in HashableList might need to be declared covariant. But I'm not that much in to typing maybe @QuLogic can help here.

As for the dev setup, the description is here: https://matplotlib.org/devdocs/devel/development_setup.html Have you tried to follow that?

@gshiba

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gshiba commented Apr 10, 2025

Yes, I followed it but can't get an editable install.

After clicking on the "Create codespace" button and waiting a few minutes, here's what I get in the Terminal:

(base) @gshiba ➜ /workspaces/matplotlib (main) $ conda activate mpl-dev
(mpl-dev) @gshiba ➜ /workspaces/matplotlib (main) $ python -c 'import matplotlib; print(matplotlib.__file__)'
/home/codespace/.local/lib/python3.12/site-packages/matplotlib/__init__.py
(mpl-dev) @gshiba ➜ /workspaces/matplotlib (main) $ python -m pip install --verbose --no-build-isolation --editable ".[dev]"
...
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
seaborn 0.13.2 requires matplotlib!=3.6.1,>=3.4, but you have matplotlib 0.1.0.dev52310+g7e997ae which is incompatible.
Successfully installed matplotlib-0.1.0.dev52310+g7e997ae meson-python-0.16.0
(mpl-dev) @gshiba ➜ /workspaces/matplotlib (main) $ python -c 'import matplotlib; print(matplotlib.__file__)'
Traceback (most recent call last):
...
ImportError: /workspaces/matplotlib/build/cp312/src/_path.cpython-312-x86_64-linux-gnu.so: undefined symbol: _ZN3agg10curve3_div4initEdddddd

Full traceback

👋 Welcome to Codespaces! You are on our default image. 
 - It includes runtimes and tools for Python, Node.js, Docker, and more. See the full list here: https://aka.ms/ghcs-default-image
 - Want to use a custom image instead? Learn more here: https://aka.ms/configure-codespace
🔍 To explore VS Code to its fullest, search using the Command Palette (Cmd/Ctrl + Shift + P or F1).
📝 Edit away, run your app as usual, and we'll automatically make it available for you to access.

(base) @gshiba ➜ /workspaces/matplotlib (main) $ conda activate mpl-dev
(mpl-dev) @gshiba ➜ /workspaces/matplotlib (main) $ python -c 'import matplotlib; print(matplotlib.__file__)'
/home/codespace/.local/lib/python3.12/site-packages/matplotlib/__init__.py
(mpl-dev) @gshiba ➜ /workspaces/matplotlib (main) $ python -m pip install --verbose --no-build-isolation --editable ".[dev]"
Using pip 25.0.1 from /home/codespace/micromamba/envs/mpl-dev/lib/python3.12/site-packages/pip (python 3.12)
Obtaining file:///workspaces/matplotlib
 Running command Checking if build backend supports build_editable
 Checking if build backend supports build_editable ... done
 Running command Preparing editable metadata (pyproject.toml)
 + meson setup /workspaces/matplotlib /workspaces/matplotlib/build/cp312 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/workspaces/matplotlib/build/cp312/meson-python-native-file.ini
 The Meson build system
 Version: 1.7.1
 Source dir: /workspaces/matplotlib
 Build dir: /workspaces/matplotlib/build/cp312
 Build type: native build
 Program python3 found: YES (/home/codespace/micromamba/envs/mpl-dev/bin/python3)
 Project name: matplotlib
 Project version: 0.1.0.dev52310+g7e997ae
 C compiler for the host machine: /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-cc (gcc 13.3.0 "x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-2) 13.3.0")
 C linker for the host machine: /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-cc ld.bfd 2.43
 C++ compiler for the host machine: /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-c++ (gcc 13.3.0 "x86_64-conda-linux-gnu-c++ (conda-forge gcc 13.3.0-2) 13.3.0")
 C++ linker for the host machine: /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-c++ ld.bfd 2.43
 Host machine cpu family: x86_64
 Host machine cpu: x86_64
 Program python found: YES (/home/codespace/micromamba/envs/mpl-dev/bin/python)
 Found pkg-config: YES (/home/codespace/micromamba/envs/mpl-dev/bin/pkg-config) 0.29.2
 Run-time dependency python found: YES 3.12
 Run-time dependency pybind11 found: YES 2.13.6
 Downloading freetype-2.6.1 source from https://download.savannah.gnu.org/releases/freetype/freetype-old/freetype-2.6.1.tar.gz

 Executing subproject freetype-2.6.1

 freetype-2.6.1| Project name: freetype2
 freetype-2.6.1| Project version: 2.6.1
 freetype-2.6.1| C compiler for the host machine: /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-cc (gcc 13.3.0 "x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-2) 13.3.0")
 freetype-2.6.1| C linker for the host machine: /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-cc ld.bfd 2.43
 freetype-2.6.1| Has header "unistd.h" : YES
 freetype-2.6.1| Has header "fcntl.h" : YES
 freetype-2.6.1| Has header "stdint.h" : YES
 freetype-2.6.1| Configuring ftconfig.h using configuration
 freetype-2.6.1| Configuring ftoption.h using configuration
 freetype-2.6.1| Build targets in project: 2
 freetype-2.6.1| Subproject freetype-2.6.1 finished.

 Downloading qhull source from https://github.com/qhull/qhull/archive/v8.0.2/qhull-8.0.2.tar.gz

 Executing subproject qhull

 qhull| Project name: qhull
 qhull| Project version: 8.0.2
 qhull| C compiler for the host machine: /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-cc (gcc 13.3.0 "x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-2) 13.3.0")
 qhull| C linker for the host machine: /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-cc ld.bfd 2.43
 qhull| Build targets in project: 3
 qhull| Subproject qhull finished.

 Run-time dependency dl found: YES
 Configuring _version.py using configuration
 Program /workspaces/matplotlib/tools/generate_matplotlibrc.py found: YES (/workspaces/matplotlib/tools/generate_matplotlibrc.py)
 Build targets in project: 12

 matplotlib 0.1.0.dev52310+g7e997ae

 Subprojects
 freetype-2.6.1: YES
 qhull : YES

 User defined options
 Native files : /workspaces/matplotlib/build/cp312/meson-python-native-file.ini
 b_ndebug : if-release
 b_vscrt : md
 buildtype : release

 Found ninja-1.12.1 at /home/codespace/micromamba/envs/mpl-dev/bin/ninja
 + /home/codespace/micromamba/envs/mpl-dev/bin/ninja
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 In file included from ../../subprojects/freetype-2.6.1/src/truetype/truetype.c:25:
 ../../subprojects/freetype-2.6.1/src/truetype/ttgload.c: In function 'load_truetype_glyph':
 ../../subprojects/freetype-2.6.1/src/truetype/ttgload.c:1455:22: warning: storing the address of local variable 'inc_stream' in 'loader_405(D)->stream' [-Wdangling-pointer=]
 1455 | loader->stream = &inc_stream;
 | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~
 ../../subprojects/freetype-2.6.1/src/truetype/ttgload.c:1392:21: note: 'inc_stream' declared here
 1392 | FT_StreamRec inc_stream;
 | ^~~~~~~~~~
 ../../subprojects/freetype-2.6.1/src/truetype/ttgload.c:1379:35: note: 'loader' declared here
 1379 | load_truetype_glyph( TT_Loader loader,
 | ~~~~~~~~~~~^~~~~~
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 /home/codespace/micromamba/envs/mpl-dev/bin/x86_64-conda-linux-gnu-ar: extern/agg24-svn/libagg.a.p/src_agg_bezier_arc.cpp.o: plugin needed to handle lto object
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 Preparing editable metadata (pyproject.toml) ... done
Requirement already satisfied: contourpy>=1.0.1 in /home/codespace/.local/lib/python3.12/site-packages (from matplotlib==0.1.0.dev52310+g7e997ae) (1.3.1)
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Requirement already satisfied: python-dateutil>=2.7 in /home/codespace/.local/lib/python3.12/site-packages (from matplotlib==0.1.0.dev52310+g7e997ae) (2.9.0.post0)
Collecting meson-python<0.17.0,>=0.13.1 (from matplotlib==0.1.0.dev52310+g7e997ae)
 Obtaining dependency information for meson-python<0.17.0,>=0.13.1 from https://files.pythonhosted.org/packages/91/c0/104cb6244c83fe6bc3886f144cc433db0c0c78efac5dc00e409a5a08c87d/meson_python-0.16.0-py3-none-any.whl.metadata
 Downloading meson_python-0.16.0-py3-none-any.whl.metadata (4.1 kB)
Requirement already satisfied: pybind11!=2.13.3,>=2.13.2 in /home/codespace/micromamba/envs/mpl-dev/lib/python3.12/site-packages (from matplotlib==0.1.0.dev52310+g7e997ae) (2.13.6)
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Requirement already satisfied: setuptools>=64 in /home/codespace/.local/lib/python3.12/site-packages (from matplotlib==0.1.0.dev52310+g7e997ae) (76.0.0)
Requirement already satisfied: meson>=1.2.3 in /home/codespace/micromamba/envs/mpl-dev/lib/python3.12/site-packages (from meson-python<0.17.0,>=0.13.1->matplotlib==0.1.0.dev52310+g7e997ae) (1.7.1)
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Requirement already satisfied: six>=1.5 in /home/codespace/.local/lib/python3.12/site-packages (from python-dateutil>=2.7->matplotlib==0.1.0.dev52310+g7e997ae) (1.17.0)
Downloading meson_python-0.16.0-py3-none-any.whl (26 kB)
Building wheels for collected packages: matplotlib
 Running command Building editable for matplotlib (pyproject.toml)
 Building editable for matplotlib (pyproject.toml) ... done
 Created wheel for matplotlib: filename=matplotlib-0.1.0.dev52310+g7e997ae-cp312-cp312-linux_x86_64.whl size=10377 sha256=aaead17634334704f01882f8294695fe6ea741b5b35982fe4fe66407d613bde5
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Successfully built matplotlib
Installing collected packages: meson-python, matplotlib
 Attempting uninstall: meson-python
 Found existing installation: meson-python 0.17.1
 Uninstalling meson-python-0.17.1:
 Removing file or directory /home/codespace/micromamba/envs/mpl-dev/lib/python3.12/site-packages/meson_python-0.17.1.dist-info/
 Removing file or directory /home/codespace/micromamba/envs/mpl-dev/lib/python3.12/site-packages/mesonpy/
 Successfully uninstalled meson-python-0.17.1
 Attempting uninstall: matplotlib
 Found existing installation: matplotlib 3.10.1
 Uninstalling matplotlib-3.10.1:
 Removing file or directory /home/codespace/.local/lib/python3.12/site-packages/__pycache__/pylab.cpython-312.pyc
 Removing file or directory /home/codespace/.local/lib/python3.12/site-packages/matplotlib-3.10.1.dist-info/
 Removing file or directory /home/codespace/.local/lib/python3.12/site-packages/matplotlib/
 Removing file or directory /home/codespace/.local/lib/python3.12/site-packages/mpl_toolkits/axes_grid1/
 Removing file or directory /home/codespace/.local/lib/python3.12/site-packages/mpl_toolkits/axisartist/
 Removing file or directory /home/codespace/.local/lib/python3.12/site-packages/mpl_toolkits/mplot3d/
 Removing file or directory /home/codespace/.local/lib/python3.12/site-packages/pylab.py
 Successfully uninstalled matplotlib-3.10.1
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
seaborn 0.13.2 requires matplotlib!=3.6.1,>=3.4, but you have matplotlib 0.1.0.dev52310+g7e997ae which is incompatible.
Successfully installed matplotlib-0.1.0.dev52310+g7e997ae meson-python-0.16.0
(mpl-dev) @gshiba ➜ /workspaces/matplotlib (main) $ python -c 'import matplotlib; print(matplotlib.__file__)'
Traceback (most recent call last):
 File "<string>", line 1, in <module>
 File "/workspaces/matplotlib/lib/matplotlib/__init__.py", line 161, in <module>
 from . import _api, _version, cbook, _docstring, rcsetup
 File "/workspaces/matplotlib/lib/matplotlib/rcsetup.py", line 29, in <module>
 from matplotlib.colors import Colormap, is_color_like
 File "/workspaces/matplotlib/lib/matplotlib/colors.py", line 57, in <module>
 from matplotlib import _api, _cm, cbook, scale, _image
 File "/workspaces/matplotlib/lib/matplotlib/scale.py", line 39, in <module>
 from matplotlib.ticker import (
 File "/workspaces/matplotlib/lib/matplotlib/ticker.py", line 144, in <module>
 from matplotlib import transforms as mtransforms
 File "/workspaces/matplotlib/lib/matplotlib/transforms.py", line 49, in <module>
 from matplotlib._path import affine_transform, count_bboxes_overlapping_bbox
ImportError: /workspaces/matplotlib/build/cp312/src/_path.cpython-312-x86_64-linux-gnu.so: undefined symbol: _ZN3agg10curve3_div4initEdddddd
(mpl-dev) @gshiba ➜ /workspaces/matplotlib (main) $

... but this is off topic. Shall I create a separate issue for this?

@gshiba gshiba marked this pull request as ready for review

April 10, 2025 01:37

@timhoffm

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timhoffm commented Apr 10, 2025

Your setup is broken, the issue is hat you have stuff in /home/codespace/.local/lib/python3.12. This can e.g. happen if you have at some point installed something with pip install --user. Such installed packages are global for your user, i.e. included in every python 3.12 interperter you run. This breaks the separatation you get from environments. Generally you should not have anything in local/lib if you work with environements.

@ksunden

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ksunden commented Apr 10, 2025

In the general case, I would tend to agree that on parameters, using Sequence is often better than over-specifying as list. A general principle in typing is to be permissive on parameters and restrictive on returns where possible.

However, in this specific case, this parameter gets a little harder to deal with in particular because str counts as a Sequence, which complicates some things. Not necessarily impossible to overcome, but I'd want to think on it at least a bit more.

What I'm confused by, though, is in this example I think that the distinction between Sequence and list should be inconsequential, as list is being used... so I'm not clear why it is failing the type check to begin with.

@QuLogic

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QuLogic commented Apr 10, 2025

Your setup is broken, the issue is hat you have stuff in /home/codespace/.local/lib/python3.12. This can e.g. happen if you have at some point installed something with pip install --user. Such installed packages are global for your user, i.e. included in every python 3.12 interperter you run. This breaks the separatation you get from environments. Generally you should not have anything in local/lib if you work with environements.

That is not the case here; it is a bug in our setup for conda, or conda-forge itself. Please see #29852.

@gshiba

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gshiba commented May 23, 2025 •

edited

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@ksunden

What I'm confused by, though, is in this example I think that the distinction between Sequence and list should be inconsequential, as list is being used... so I'm not clear why it is failing the type check to begin with.

The problem is in expected vs inferred type of the inner list:

the existing code expects the inner list to be: HashableList: TypeAlias = list[_HT | "HashableList[_HT]"]
the inferred type of [["a"], ["b"]] is list[list[str]] which means the inner list is strictly a list of _HT.

Demo:

# foo.py
import matplotlib.pyplot as plt
inferred_mosaic = [["a"], ["b"]]
reveal_type(inferred_mosaic)
fig, axes = plt.subplot_mosaic(inferred_mosaic) # type error
explicit_mosaic: list[list[str | list]] = [["a"], ["b"]]
reveal_type(explicit_mosaic)
fig, axes = plt.subplot_mosaic(explicit_mosaic) # type ok

$ pyright foo.py
/Users/ec2-user/repos/matplotlib-test/foo.py
 /Users/ec2-user/repos/matplotlib-test/foo.py:5:13 - information: Type of "inferred_mosaic" is "list[list[str]]"
 /Users/ec2-user/repos/matplotlib-test/foo.py:6:13 - error: No overloads for "subplot_mosaic" match the provided arguments (reportCallIssue)
 /Users/ec2-user/repos/matplotlib-test/foo.py:6:32 - error: Argument of type "list[list[str]]" cannot be assigned to parameter "mosaic" of type "list[HashableList[Hashable]]" in function "subplot_mosaic"
  "list[list[str]]" is not assignable to "list[HashableList[Hashable]]"
   Type parameter "_T@list" is invariant, but "list[str]" is not the same as "HashableList[Hashable]"
   Consider switching from "list" to "Sequence" which is covariant (reportArgumentType)
 /Users/ec2-user/repos/matplotlib-test/foo.py:9:13 - information: Type of "explicit_mosaic" is "list[list[str | list[Unknown]]]"
2 errors, 0 warnings, 2 informations

... and this can be resolved by changing the type from list to Sequence (this PR) which makes the inner (and outer) list immutable.

@melissawm melissawm added this to First Time Contributors

May 26, 2025

@melissawm melissawm moved this to Needs review in First Time Contributors

May 26, 2025

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topic: pyplot API

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@gshiba @timhoffm @ksunden @QuLogic

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Fix type annotation for plt.subplot_mosaic #29893

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Fix type annotation for plt.subplot_mosaic #29893

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