fix doc site and add etl scripts

[maclandrol]

Checklist:

• [x] Was this PR discussed in a issue? It is recommended to first discuss a new feature and let the community know whether you are planning or have started working on it before opening a PR.
• [ ] Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate).
• [ ] Update the API documentation if a new function is added or an existing one is deleted.
• [x] Added a news entry.
  • copy news/TEMPLATE.rst to news/my-feature-or-branch.rst) and edit it.

---

Doc site should now look like this:

[maclandrol]

To do before 0.8.9 ensure no blindspot on cuda based inference

[cwognum]

Using this, we can hide the left-side menu on all pages that have no subpages, but I don't like that the content width then is not consistent. Happy to discuss alternatives!

---
hide:
  - navigation
  - toc
---

# Document title
...

[maclandrol]

Using this, we can hide the left-side menu on all pages that have no subpages, but I don't like that the content width then is not consistent. Happy to discuss alternatives!

---
hide:
  - navigation
  - toc
---

# Document title
...

I don't think we should hide the TOC. Without the TOC, single-page navigation is awful, and you don't have id anchors to jump across the header sections in the API or tutorial page. Honestly, I don't like neither the tab only navigation, nor the inconsistency if you decide to hide the single-page section only. Thus the current solution:

• You get fixed width of content and consistency on mobile.
• You can navigate with the tabs, without a redundant empty section for single page
• Since the tab are hidden when you scroll at the bottom, you still get the advantage of the left section navigation
• The section page is auto highlighted and expanded for the page on which you are, while the section of other pages are hidden.

[maclandrol]

Thank you!

1. I don't like the redundancy from having both tabs and the left-side menu containing the same information. We simplified the left-side menu on purpose after all by introducing the tabs. I would either hide the left-side menu if there's only a single item or remove the left-side menu altogether and add "subtabs" to the each tab that appear on hover.

See answer above. Having subnav is not impossible, but I fear this is a bit more than trying to retheme using the jinja templates.

2. I like that you've included the ETL notebooks for transparency sake. Could you add a simple README documenting what these notebooks are for? Currently I don't even know what ETL stands for.

ETL means "Extract, transform, load] and commonly refer to the set of set of instructions for process or data integration. Here it corresponds to the process through which we add new models. I will add a note in the developer guideline, but this is intended for developers primarily, not for end users.

[cwognum]

I don't think we should hide the TOC.

I agree! Sorry for the confusion, copied that over from the example but only meant to show how to hide the left-side menu ("navigation"). Don't like the inconsistent content width either though.

For me the main reason to switch to tabs is to reduce the "complexity" (number of items) in the left-side menu. In @DomInvivo his words in the initial proposal: "The old docs API is too messy with too many things on the left. (xref: https://github.com/datamol-io/datamol/pull/184)"

I would argue that now we're instead adding complexity by having redundant tabs. I do understand the benefits you list, but in that case why not just disable the tabs again and stick with what we had before? In the end it's a minor change and I don't have a perfect solution to propose either, so feel free to do as you prefer and merge once ready.

ETL means "Extract, transform, load] and commonly refer to the set of set of instructions for process or data integration. Here it corresponds to the process through which we add new models. I will add a note in the developer guideline, but this is intended for developers primarily, not for end users.

Learned something new today! Thank you! All clear! :pray:

[maclandrol]

Added the notes on ETL for developers.

Note that although using different technologies, that the current version unintentionally reproduced what is used in the Volkamer lab CADD tutorial website (https://projects.volkamerlab.org/teachopencadd/).

If I can't get

add "subtabs" to the each tab that appear on hover.

to work today, I would likely keep the current version, because Dom's version still has the right panel anyway, so my solution just remove the ugly empty section with repeated page title for single-page section.

Removing the right section all together without a way to get an hyperlink to pages in those sections seems worse for me. Happy to try implementing any alternative ideas either you or @DomInvivo might have.

[cwognum]

because Dom's version still has the right panel anyway, so my solution just remove the ugly empty section with repeated page title for single-page section.

Just for clarity: No one wants to remove the right-side panel (i.e. "table of contents").

A final proposal could be to integrate the Table of Contents (right-side) and Navigation (left-side) menus with the Navigation Integration. I would look like this:

One orthogonal comment: Going through the docs today, I saw some other cool features, such as the Back to Top button.

[maclandrol]

Just for clarity: No one wants to remove the right-side panel (i.e. "table of contents").

Sorry, I mean the left-side panel (not the TOC in my comment above).

I like the idea of merging them that you are proposing, and some easier things to do may be to reorganize the docs (For example, license as a single tab kinda does not make sense). I will come up with an iteration of your last idea, in next commit a bit later today.

[maclandrol]

Fix #55 and docs look better with grouping, pages together.