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docs: improve structure and add modules#625

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gcroci2 merged 37 commits intodevfrom
297_increase_modules_docs_gcroci2
Jul 11, 2024
Merged

docs: improve structure and add modules#625
gcroci2 merged 37 commits intodevfrom
297_increase_modules_docs_gcroci2

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@gcroci2 gcroci2 commented Jul 9, 2024

You can look at the new docs rendered here.

I suggest to not look at the commits for this PR, but directly to the files changes. Main changes:

  • The modules rendered are now dataset, query, trainer, neuralnets, molstructu, tools (before only dataset was successfully rendered, see here). I removed features since we didn't add any docs there, so it's useless to render those submodules on readthedocs.
  • I fixed various cross sections refs and links in the installation page.
  • Code of conduct and contributing files are now .md files, a preferred file format (easier to handle).
  • Contributing page in the docs is now linked to the one we have in the repo's main root (less duplication).
  • Uniform query.py to dataset.py in terms of doc strings (both have a parent class which is used by two children classes; the args are explained in detail only in the children, not in the parents - otherwise it's visually very verbose).
  • Add from __future__ import annotations for making possible the rendering of modules that were not correctly rendered before (or not rendered at all). To fix the issue, also TYPE_CHECKING is used. Briefly, there were problems with type hints that made sphinx build fail on some modules (an error in the type hints import caused the modules to not be rendered).
  • Now the docs/ folder has a source/ subfolder. This is useful for building the docs locally (where you can have a build/ folder as well, not uploaded to the remote of course).

Note for myself:

  • Hide the branch on readthedocs when the PR is merged.

@gcroci2 gcroci2 changed the base branch from main to dev July 9, 2024 09:25
@gcroci2 gcroci2 linked an issue Jul 9, 2024 that may be closed by this pull request
@gcroci2 gcroci2 requested a review from DaniBodor July 10, 2024 13:37
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Great updates, the docs are definitely much more complete now.
Were you planning on adding descriptions for the NNs (as per #608) in this PR or in a separate one?

I added a commit that adds empty lines at the end of a couple of files were that wasn't the case

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gcroci2 commented Jul 11, 2024

Great updates, the docs are definitely much more complete now. Were you planning on adding descriptions for the NNs (as per #608) in this PR or in a separate one?

Separate PR, but I've already added the neural networks submodule so it's ready for issue #608 :)

@gcroci2 gcroci2 merged commit 795f3c7 into dev Jul 11, 2024
@gcroci2 gcroci2 deleted the 297_increase_modules_docs_gcroci2 branch July 11, 2024 14:31
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Increase modules rendered by readthedocs

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