Update TopoStats to use python 3.13

[SylviaWhittle]

TopoStats Pull Requests

Please provide a descriptive summary of the changes your Pull Request introduces.

The Software Development section of
the Contributing Guidelines may be useful if you are unfamiliar with linting, pre-commit, docstrings and testing.

NB - This header should be replaced with the description but please complete the below checklist or a short
description of why a particular item is not relevant.

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Before submitting a Pull Request please check the following.

• Existing tests pass.
• Documentation has been updated and builds. Remember to update as required...
  • docs/usage/configuration.md
  • docs/usage/data_dictionary.md
  • docs/usage/advanced.md and new pages it should link to.
• Pre-commit checks pass.
• New functions/methods have typehints and docstrings.
• New functions/methods have tests which check the intended behaviour is correct.

Optional

topostats/default_config.yaml

If adding options to topostats/default_config.yaml please ensure.

• There is a comment adjacent to the option explaining what it is and the valid values.
• A check is made in topostats/validation.py to ensure entries are valid.
• Add the option to the relevant sub-parser in topostats/entry_point.py.

[SylviaWhittle]

Issue here is pySPM version is old. Need to fix the version. Maybe do this in AFMReader?