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Modernize user guide #4504

Merged
merged 18 commits into from
Apr 26, 2022
Merged

Modernize user guide #4504

merged 18 commits into from
Apr 26, 2022

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jngrad
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@jngrad jngrad commented Apr 19, 2022

Description of changes:

  • use the Alabaster theme
    • responsive theme for mobile and tablets
    • visually light theme with consistent font sizes
    • natbib-style bibliography
  • re-organize the user guide
    • collect information about running ESPResSo simulations into a self-contained chapter
    • move electrokinetics and reaction methods to self-contained chapters
    • make code examples more self-contained and remove pseudo-code
    • combine all BibTeX files into a single file
    • document running simulations in parallel with MPI

Update configuration for Doxygen 1.8.17 with `doxygen -u`. Remove
default-valued fields that will be deprecated in Doxygen 1.9.1.
The shell script should be called directly instead of the python script.
Synchronize keys and fields with icp.bib.
Use full journal names and add DOI fields.
The sphinxcontrib.bibtex package no longer requires the `zref`
filename workaround since version 2.0.0 and no longer requires
two builds since version 2.1.0. The bibliography is now always
up-to-date.
Improve readability by using short links to class methods and
attributes, instead of using the fully qualified namespace. E.g.
"the property `espressomd.particle_data.ParticleHandle.rinertia`"
becomes "the property `rinertia`" in paragraphs about particles.
Replace examples written in pseudo-code (e.g. those involving
bracketed placeholder text of the form <particle_id>) by real code.
Make code samples more self-contained with a proper System setup.
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Declutter the table of contents on the main page. Rework chapter
sections. Rename chapter on integrators and thermostats.
Collect content on how to run ESPResSo from various chapters and
consolidate the information in a self-contained chapter.
Split the Contributing chapter to create a Community chapter.
Document the Summer School and how to access the teaching material.
Update the Contributing page of the project community standards.
@jngrad jngrad marked this pull request as ready for review April 19, 2022 22:45
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@pkreissl pkreissl left a comment

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In principle, your changes look good to me. For suggested changes see my comments.
Also, I did not build the doc yet, but I will do that later today to have a look at the visual and structure changes.

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jngrad commented Apr 20, 2022

Also, I did not build the doc yet, but I will do that later today to have a look at the visual and structure changes.

To build the docs, first run rm -r build/doc/sphinx, otherwise sphinx will complain that there are non-included .rst files: these are old files that have been removed in the source directory, but CMake doesn't clean them up. Also make sure you have the latest Sphinx and sphinx-contrib versions. Alternatively, you can download the zip artifact.

Center main text in the alabaster theme. Fix typos and grammar.

Co-authored-by: Patrick Kreissl <[email protected]>
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Thanks for the big effort.
I am a big fan of reducing the advanced methods section

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Thanks, lgtm!

@jngrad jngrad requested a review from reinaual April 26, 2022 15:39
@jngrad jngrad added this to the Espresso 4.2 milestone Apr 26, 2022

Debugging |es|
--------------
The resulting build with be quite slow but will enable many debugging tools.
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typo

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good catch, I'll wrap this up when running the spellchecker during the release process next month

@jngrad jngrad added the automerge Merge with kodiak label Apr 26, 2022
@kodiakhq kodiakhq bot merged commit 8ef82be into espressomd:python Apr 26, 2022
@jngrad jngrad deleted the documentation branch May 23, 2022 11:39
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4 participants