API links updated to new model names

[vgro]

Description

We recently updated the model names from model.py to {MODEL_NAME}_model.py. In the process, we missed updating the docs which I've done here.

Solves issue #178

Type of change

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist

• Make sure you've run the pre-commit checks: $ pre-commit run -a
• All tests pass: $ poetry run pytest

Further checks

• [NA] Code is commented, particularly in hard-to-understand areas
• [NA] Tests added that prove fix is effective or that feature works

[davidorme]

@vgro Do you want to add the core/model.py rename and close #178 😄

[jacobcook1995]

Noticed a few broken links, also as David mentioned model.py should be renamed to base_model.py as part of this pull request

[vgro]

@vgro Do you want to add the core/model.py rename and close #178 😄

I've already done that, please let me know if I missed something.

[jacobcook1995]

The change from core/model.py to core/base_model.py doesn't show up in the file changes for some reason?

[jacobcook1995]

Also some of the links in the module docstrings for abiotic_model.py and soil_model.py will have to change as they currently refer to core/model

[codecov-commenter]

Codecov Report

Merging #177 (4172747) into develop (444180c) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop     #177   +/-   ##
========================================
  Coverage    95.59%   95.59%           
========================================
  Files           18       18           
  Lines          909      909           
========================================
  Hits           869      869           
  Misses          40       40           

Impacted Files	Coverage Δ
virtual_rainforest/core/__init__.py	100.00% <ø> (ø)
virtual_rainforest/core/axes.py	100.00% <ø> (ø)
virtual_rainforest/core/base_model.py	100.00% <ø> (ø)
virtual_rainforest/core/config.py	98.53% <ø> (ø)
virtual_rainforest/core/data.py	87.50% <ø> (ø)
virtual_rainforest/core/logger.py	100.00% <ø> (ø)
virtual_rainforest/core/readers.py	100.00% <ø> (ø)
virtual_rainforest/models/abiotic/__init__.py	100.00% <ø> (ø)
virtual_rainforest/models/soil/__init__.py	100.00% <ø> (ø)
virtual_rainforest/models/soil/constants.py	100.00% <ø> (ø)
... and 5 more

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[jacobcook1995]

All works now apart from a minor problem in one of the module docstrings

[davidorme]

@jacobcook1995 and I were just chatting about adding nitpicky = True to the conf.py file.
https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-nitpicky

That should catch all of these issues when we run build html. @vgro Do you want to add that change to this PR? And possibly then the results of fixing broken links.

[davidorme]

Although - having just run that - it also traps all the xarray and numpy refs, so we'd probably want to also fix #147 in this PR! I think that would fix it! That should be a fairly short addition to docs/source/conf.py.

[davidorme]

I'm going to add a commit to this that turns on nitpicky and intersphinx - there are quite a few errors: sometimes a broken link, sometime e.g. a method using :class:.

[davidorme]

And @alexdewar suggested we set up a GitHub Action to test the doc builds too, but that seems like another PR to me.

[davidorme]

That's commit has given me a shortish list of fixes to make. Will whip through them.

[vgro]

That's commit has given me a shortish list of fixes to make. Will whip through them.

Hello and sorry, the website didn't update properly and I didn't see all you comments before I fixed the missing space. Can I leave these change to you @davidorme ?

[davidorme]

That's fine - got your change. I think @jacobcook1995 is hunting some down too 😄

[vgro]

That's fine - got your change. I think @jacobcook1995 is hunting some down too 😄

I hadn't though about all the links when I started, it's surely good to put some checks in place that we don't have to do that manually in the future :-)

[jacobcook1995]

All the build warnings should now be fixed, I had to turn off nitpick for a few (external) classes because it seemed impossible to get them to link properly.

[davidorme]

LGTM