Add early atlas output check with overwrite option

[AlgoFoe]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?

• Atlas generation could fail only at the very end if an atlas output directory already existed, this PR ensures such cases are detected early.

What does this PR do?

• Adds an early check for existing atlas output directories in wrapup_atlas_from_data and introduces an overwrite option to explicitly replace them when needed.

References

• Fixes [Feature] catch existing atlas files early in atlas generation script rather than at the end #731

How has this PR been tested?

• Tested locally by simulating existing atlas output directories.

Is this a breaking change?

• No, default behavior remains unchanged and the new overwrite flag is optional

Does this PR require an update to the documentation?

• No

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[adamltyson]

Hey @AlgoFoe, thanks for this. While this is useful, it doesn't entirely fix the issue. Most of the time consuming steps take place before this wrap up script is run.

@PolarBean's original issue mentions adding a check to the start of the template script so the issue can be caught earlier. Would you mind adding something there too?

[AlgoFoe]

Hey @AlgoFoe, thanks for this. While this is useful, it doesn't entirely fix the issue. Most of the time consuming steps take place before this wrap up script is run.

@PolarBean's original issue mentions adding a check to the start of the template script so the issue can be caught earlier. Would you mind adding something there too?

Hey @adamltyson, thanks for the review!
I will add an early existence check to the template script as well and push an update shortly.

[AlgoFoe]

Just pushed the requested updates and also added minimal tests to cover the wrapup output-check logic.

[adamltyson]

Great, once again, thank you @AlgoFoe!