refactor docs by njzjz · Pull Request #952 · deepmodeling/deepmd-kit

njzjz · 2021-08-12T06:27:19Z

See https://explore-deepmd.njzjz.win/ for preview.
PDF: https://explore-deepmd.njzjz.win/_/downloads/en/latest/pdf/

codecov-commenter · 2021-08-12T06:31:57Z

Codecov Report

Merging #952 (9de2e1e) into devel (72aaa9b) will decrease coverage by 0.14%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##            devel     #952      +/-   ##
==========================================
- Coverage   75.51%   75.37%   -0.15%     
==========================================
  Files          85       85              
  Lines        6796     6801       +5     
==========================================
- Hits         5132     5126       -6     
- Misses       1664     1675      +11

Impacted Files	Coverage Δ
deepmd/calculator.py	`79.41% <0.00%> (-10.25%)`	⬇️
deepmd/utils/tabulate.py	`86.18% <0.00%> (-1.66%)`	⬇️
deepmd/descriptor/se_a.py	`96.18% <0.00%> (-1.39%)`	⬇️
source/lib/include/neighbor_list.h	`100.00% <0.00%> (ø)`

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…nto refactor-docs

amcadmus

The links in the README.md at the deepmd-kit source root are broken.
How a user conveniently read the doc locally or from the github website? or we only want to provide the doc through readthedoc?

njzjz · 2021-08-12T07:46:01Z

How a user conveniently read the doc locally or from the github website? or we only want to provide the doc through readthedoc?

It's hard to support all of them at the same time. However, I can provide a README under doc directory to give a guide how to build the website locally. For GitHub, I think one can easily visit our website if he can visit the GitHub?

njzjz · 2021-08-12T08:05:38Z

Maybe I can provide a separated catalog for GitHub or Gitee users.

tuoping

You can change this:

exhale_args = {
   ...
    "rootFileName":          "api_cc.rst",
   ...
}

to

exhale_args = {
   ...
    "rootFileName":          "../development/api_cc.rst",
   ...
}

Then the automatically built api_cc.rst will be in directory doc/development/

tuoping

Also, regarding @amcadmus 's comments, you can have both index.rst and index.md in the same directory, RST will go for index.rst automatically.

tuoping · 2021-08-13T03:01:45Z

   :caption: Developer Guide

-   development/index
+   api


And you can change here to

.. toctree :maxdepth: 3 :caption: Developer Guide :glob: development/*

But, sections will be disordered?

The sections won't change much. Originally, the list was like this

.. toctree:: :maxdepth: 3 :caption: Developer Guide api API_CC/api_cc development/coding-conventions development/type-embedding

The automatically generated one with ":glob:" is exactly the same.

tuoping · 2021-08-13T03:05:16Z

+
+.. _trouble:
+
+.. toctree::


For this directory to handle possible changes in the future, may we consider this:

.. toctree:: :maxdepth: 1 :caption: trouble shooting :glob: ./*

This turned out to work out fine.

Co-authored-by: tuoping <80671886+tuoping@users.noreply.github.com>

njzjz · 2021-08-13T04:14:01Z

You can change this:

exhale_args = {
   ...
    "rootFileName":          "api_cc.rst",
   ...
}

to

exhale_args = {
   ...
    "rootFileName":          "../development/api_cc.rst",
   ...
}

Then the automatically built api_cc.rst will be in directory doc/development/

Not work. api_cc.rst relies other files.

tuoping · 2021-08-13T09:02:36Z

   :caption: Developer Guide

-   development/index
+   development/api


This works:

.. toctree:: :maxdepth: 3 :caption: Developer Guide :glob: development/* API_CC/api_cc

The sections will be ordered like this:

Developer Guide Python API Coding Conventions Atom Type Embedding C++ API

Preview here:
https://deepmd-kit.readthedocs.io/en/refactor-docs/

* refactor docs * Update type-embedding.md * fix typos * Update lammps.md * Update model-deviation.md * fix typos * fix links in readme; rewrite training * refactor model part * fix several typos; move sections * Update doc/third-party/lammps-command.md Co-authored-by: tuoping <80671886+tuoping@users.noreply.github.com> * create markdown files * revert api_cc * update developer toxtree * remove unexpected api_cc.rst Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: tuoping <80671886+tuoping@users.noreply.github.com>

Since there are lots of parameters still not added (deepmodeling#771, deepmodeling#773, deepmodeling#774, deepmodeling#781, deepmodeling#782), we only enable loose check for `dpgen run` (i.e. `strict_check=False`).

refactor docs

2c565f3

njzjz requested a review from amcadmus August 12, 2021 06:27

amcadmus requested a review from tuoping August 12, 2021 06:31

amcadmus and others added 5 commits August 12, 2021 14:35

Update type-embedding.md

cdbfe34

fix typos

9fa09c8

Merge branch 'refactor-docs' of https://github.com/njzjz/deepmd-kit i…

c43725f

…nto refactor-docs

Update lammps.md

a937bba

Update model-deviation.md

c60092e

amcadmus requested changes Aug 12, 2021

View reviewed changes

Comment thread doc/train/training.md Outdated

Comment thread doc/train/training.md Outdated

Comment thread doc/getting-started/training.md

Comment thread doc/install/install-from-source.md Outdated

fix typos

85b8b3a

njzjz added this to the v2.0.0 milestone Aug 12, 2021

fix links in readme; rewrite training

de95aec

njzjz requested a review from amcadmus August 12, 2021 19:54

refactor model part

70fa084

amcadmus requested changes Aug 13, 2021

View reviewed changes

Comment thread doc/train/training-advanced.md

Comment thread doc/model/train-energy.md Outdated

Comment thread README.md Outdated

Comment thread doc/model/train-se-e2-a.md Outdated

Comment thread doc/model/train-se-e2-a.md Outdated

Comment thread doc/model/train-energy.md

fix several typos; move sections

677f325

njzjz requested a review from amcadmus August 13, 2021 01:05

amcadmus approved these changes Aug 13, 2021

View reviewed changes

tuoping suggested changes Aug 13, 2021

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Comment thread doc/third-party/lammps-command.md Outdated

tuoping reviewed Aug 13, 2021

View reviewed changes

njzjz and others added 2 commits August 12, 2021 23:21

Update doc/third-party/lammps-command.md

1f41f3e

Co-authored-by: tuoping <80671886+tuoping@users.noreply.github.com>

create markdown files

eaaa567

revert api_cc

7feb5dc

amcadmus requested a review from tuoping August 13, 2021 04:54

tuoping reviewed Aug 13, 2021

View reviewed changes

update developer toxtree

d4652e1

njzjz requested a review from tuoping August 13, 2021 22:12

remove unexpected api_cc.rst

9de2e1e

tuoping approved these changes Aug 16, 2021

View reviewed changes

amcadmus merged commit 820b3ed into deepmodeling:devel Aug 16, 2021

njzjz mentioned this pull request Aug 22, 2021

give a clear message if model.get_ntypes()<data.get_ntypes() #1016

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