[Bug]: Matplotlib 3.9.0 register_cmap deprecation

[SylviaWhittle]

Checklist

• Re-run analysis with topostats process --core 1.
• Describe the bug.
• Include the configuration file.
• Copy of the output.
• The exact command that failed. This is what you typed at the command line, including any options.
• TopoStats version, this is reported by topostats --version
• Operating System and Python Version

Describe the bug

In 3.9.0, Matplotlib deprecates register_cmap. What should we do about this? Prevent use of 3.9 onwards or force it? Supporting both will be messy.

An alternative is provided, in matplotlib.colormaps.register.

Matplotlib API changes for 3.9.0, search for register_cmap to see the listing

Copy of the output

N/A

Include the configuration file

N/A

To Reproduce

Try to import TopoStats while Matplotlib 3.9.0 is installed.

TopoStats Version

Git main branch

Python Version

3.12

Operating System

MacOS M1/M2 (post-2021)

Python Packages

Matplotlib 3.9.0

[ns-rse]

I think this is a duplicate of #845 which was fixed with #846

No problems seen here...

(topostats) ❱ ipython 
~~~~~~~~~~~~ AUTORELOAD ENABALED ~~~~~~~~~~~~
Python 3.12.4 (main, Jun  7 2024, 06:33:07) [GCC 14.1.1 20240522]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.24.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import matplotlib

In [2]: matplotlib.__version__
Out[2]: '3.9.0'

In [3]: import topostats

In [4]: topostats.__version__
Out[4]: '2.2.2.dev5+gf5b40f762'

If encountered on a branch other than main it will likely have been created before #846 so there are two solutions...

git rebase main

You can update the branch by rebasing onto main.

git switch main
git pull
git switch -
git rebase main

git cherry-pick

Alternatively you can cherry-pick the fix from #846

NB - Untested

git switch <feature-branch>
git cherry-pick -n f7d828924034cb2badf34825f0fdfbe39953e5ed

A third solution is to manually make the change to the files which is in essence the same as cherry-picking.

[SylviaWhittle]

Closing as was a duplicate