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@joaomcteixeira joaomcteixeira commented Jul 27, 2022

  • Your PR is about writing documentation for already existing code 🔥

  • Added small introduction to haddock3
  • generate the docs tox -e docs and open with firefox haddock3-docs/index.html. The page will appear in the menu on the left.
  • text made together with @amjjbonvin
  • links will need to be updated in the future once the documentation is deployed online, either on RTD or bonvinlab.org

joaomcteixeira and others added 4 commits July 27, 2022 11:52
Co-authored-by: Alexandre Bonvin <alexandre.bonvin@gmail.com>
@joaomcteixeira joaomcteixeira added the documentation Improve docs label Jul 27, 2022
@joaomcteixeira joaomcteixeira self-assigned this Jul 27, 2022
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codecov-commenter commented Jul 27, 2022

Codecov Report

Merging #514 (61fde23) into main (87e7c81) will not change coverage.
The diff coverage is n/a.

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  Files         105      105           
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  Misses       1755     1755           

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docs/intro.md Outdated
offering new features to users who can now define custom workflows.

In the previous HADDOCK2.x versions, users had access to a highly
parameterisable yet rigid simulation pipeline composed of three mandatory steps:
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was "water" always mandatory in 2.x?

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Not really - may-be instead of water we can rather call it: final refinement

Comment on lines +33 to +41
To keep HADDOCK3's modules organised, we catalogued them into several
categories. But, there are no constraints on piping modules of different
categories.

The main module's categories are "topology", "sampling", "refinement",
"scoring", and "analysis". There is no limit to how many modules can belong to a
category. Modules are added as developed, and new categories will be created
if/when needed. You can access the HADDOCK3 documentation page for the list of
all categories and modules. Below is a summary of the available modules:
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as this is not crucial for the user, I would maybe reduce the lenght of this paragraph

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They are for the understanding of the project and the different modules. That's how we are presenting them in talks. Let's keep it for now and let the text evolve as we read it more times in the future. Many thanks!

amjjbonvin and others added 3 commits July 27, 2022 14:24
Co-authored-by: Marco Giulini <54807167+mgiulini@users.noreply.github.com>
Co-authored-by: Marco Giulini <54807167+mgiulini@users.noreply.github.com>
@joaomcteixeira joaomcteixeira merged commit 82af1c2 into main Jul 28, 2022
@joaomcteixeira joaomcteixeira deleted the docsintro branch July 28, 2022 07:35
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5 participants