Disable summary_stats by default

[TFirth2]

…run: true prevents completion of topostats processing. default_config.yaml updated to set summary_stats: run: false as the default.

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.

---

Before submitting a Pull Request please check the following.

• Existing tests pass.
• Documentation has been updated and builds. Remember to update as required...
  • docs/configuration.md
  • docs/usage.md
  • docs/data_dictionary.md
  • docs/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]

Okay this is weird.

We have the age-old basename key error.

But the PR changes surely shouldn't cause that?

[ns-rse]

No this PR shouldn't have caused that error.

I'm not convinced that changing the default actually solves the problem anyway. It might allow the code to run but then so would using a custom configuration file. This doesn't solve why the error occurs, it just stops it from occurring (maybe!).

We have defaults set to maximise ease of use and features for users, by disabling generation of summary plots it removes them from being generated and available by default.

[ns-rse]

I suspect that the actual problem that is being reported is as documented in this comment.