Explore why notebook integration into sphinx causes the warning misc.copy_overwrite

[pc532627]

What's the problem?

We currently incorporate notebook output directly into the Sphinx documentation (PR #295). This has however led to Sphinx
raising a warning: misc.copy_overwrite for each notebook in the repo when they are copied. It is unclear what the issue is as altering the copying behavior of files inside of confutils does not seem to have any impact on the warning. We should investigate what is causing this and no longer ignore the error when addressed.

How can we reproduce the issue?

Build the documentation including the changes made on PR #295

Python version

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Package version

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Operating system

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Other packages

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Relevant log output

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[bc294725]

might be closed by #295

[pc532627]

This is not closed by #295 - the warning has been disabled in that PR, but we need to work out why Sphinx raises it for notebooks,