[bug]: `topoly` breaks matplotlib plots when imported into a notebook

[tobyallwood]

Checklist

• Run using the main branch to check if the issue persists. Instructions on how to do this can be found here.
• Find the offending file in the output. If processing halts, re-run analysis with topostats --core 1 process.
• Describe the bug.
• Include the configuration file.
• Copy of the log-file from running with topostats --log-level debug <command>.
• 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

If topoly is imported by a script imported by a notebook (first notebook -> topostats.processing -> topostats.tracing.ordered_tracing -> topoly) it changes matplotlib's backend mode from inline to something else (possibly Agg or similar).

In effect this causes plots to be displayed in new windows rather than in the notebook under cells which at a minimum is an inconvenience and for some machines will make the plots not viewable at all.

Copy of the log-file from running with topostats --log-level debug <command>

N/A

Include the configuration file

N/A

To Reproduce

• Run a notebook that imports topoly.jones and topoly.translate_code, alternatively a notebook that imports topostats.processing as you can follow the imports from processing.py down to these topoly methods.
• Create a basic plot and display it any way (plt.show(), fig)

TopoStats Version

Git main branch

Python Version

3.11

Operating System

Windows

Python Packages

No response

[tobyallwood]

It might be helpful to add a configuration option to skip topoly entirely as there's multiple issues related to it that we have found.
Affected notebooks could then turn the option to False keeping the plots displaying inline.

[ns-rse]

Does adding either of

%matplotlib inline
%matplotlib notebook

...after the import override whatever Topoly is doing in the background?

Without Topoly imported then it would not be possible to undertake much of the tracing.

[tobyallwood]

Unfortunately not, it does try to override the settings from topoly but seems to fight it rather than cleanly override causing windows to rapidly open and close and some plots to just not display in either way (inline or in a new window)