Migrate user_guide from jules-lsm.github.io

[Yaswant Pradhan (yaswant)]

Yet another attempt to keep the history.

• Include jules user guide documentation from jules-lsm.
• Numerous bug and typographical error fixes
• Should fix The JULES docs LaTeX compile appears to be broken jules-lsm/jules-lsm.github.io#72
• Update GitHub Action

Locally built docs: https://wwwspice/~yaswant.pradhan/jules/migrate-docs/html/

changes: should keep track of the changes from the original doc.

This PR makes #2 #5 redundant (duplicate)

Change summary

• Replace old user guide build and deployment workflow
• Add a minimal README file (need updating later)
• Clean Sphinx Makefile - include a deploy method to install compiled doc in user ~/public_html/jules/<branchname>
• Fix several formatting and typographical errors

The changes should now fix the latexpdf compilation - make sure a proper latex environment is loaded (e.g., module load latex at the Met Office) before executing make clean latexpdf

[Jenny Hickson (jennyhickson)]

Thanks for seperating the commits out. A significantly bigger PR than I had predicted!

I'm assuming there are technical reasons for the dependency list to be in both environment.yaml and pyproject.toml - but its it possible to condense these into one place to keep updated?

[Yaswant Pradhan (yaswant)]

Thanks for seperating the commits out. A significantly bigger PR than I had predicted!

I'm assuming there are technical reasons for the dependency list to be in both environment.yaml and pyproject.toml - but its it possible to condense these into one place to keep updated?

The reason I've kept environment.yaml file is to let people continue with the conda approach. I did not feel like changing that instruction in this PR. But I agree, we should aim to consolidate the requirements in one single file. (conda wont understand pyproject.toml out of the box, so we may have to introduce a requirements.txt file.

[Jenny Hickson (jennyhickson)]

Thanks, that seems fair.