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Huge Improvement of Documentation #61

Merged
merged 21 commits into from
Sep 11, 2023
Merged

Huge Improvement of Documentation #61

merged 21 commits into from
Sep 11, 2023

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xiaoruiDong
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Motivation or Problem

The previous documentation is outdated, with an obsolete description of RDMC and missing API references to a few modules.

Description of Changes

  1. Change the theme of documentation to the Pydata theme
  2. Introduce a hierarchical structure to the API references pages (in .rst) in /docs
  3. Add references to the conformer_generation module, mathlib module, and reaction module
  4. Introduce "How to cite RDMC" and "Credits" pages.

Testing

The new documentation is tested by building sphinx documents locally.

As the number of files in the RDMC repo keep growing, it makes more sense to keep a hierarchical structure for API references, instead of putting everything under the `/source` directly.
using `::` and extra empty line to create a block
Add code-block for demonstration of the default argument of style_spec
1. Change the theme to pydata; 2. Change how Returns is displayed 3. Auto update year
1. Update the index with new introduction paragraph, installation guide, developer information
2. add a how to cite page
3. add a credits page
4. add developer's social media info
Initiate with the align submodule with corrected docstring.
1. Create a section of embedding geometries
2. Update the docstrings of embedders and ts_guessers
Add a section called "Geometry Optimization", and clean up the docstrings in the optimizers.py and ts_optimizers.py
Add rst file and clean the docstrings
1. docs are added for pruners, verifiers, ts_verifiers, and solvation
2. relevant docstrings are cleaned
Add rst files and clean up docstrings
@xiaoruiDong xiaoruiDong added documentation Improvements or additions to documentation enhancement New feature or request refactorization labels Sep 11, 2023
@xiaoruiDong xiaoruiDong self-assigned this Sep 11, 2023
@xiaoruiDong xiaoruiDong merged commit 8f16e96 into main Sep 11, 2023
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