Re-structured Doc by tuoping · Pull Request #513 · deepmodeling/deepmd-kit

tuoping · 2021-04-14T08:20:59Z

Modified the index structures.

…o devel

codecov-io · 2021-04-14T09:24:43Z

Codecov Report

Merging #513 (ba1bc7b) into devel (cb26ef7) will decrease coverage by 0.01%.
The diff coverage is n/a.

❗ Current head ba1bc7b differs from pull request most recent head dfe2193. Consider uploading reports for the commit dfe2193 to get more accurate results

@@            Coverage Diff             @@
##            devel     #513      +/-   ##
==========================================
- Coverage   60.18%   60.16%   -0.02%     
==========================================
  Files          73       73              
  Lines        6085     6087       +2     
==========================================
  Hits         3662     3662              
- Misses       2423     2425       +2

Impacted Files	Coverage Δ
deepmd/utils/argcheck.py	`17.31% <0.00%> (-0.16%)`	⬇️

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Renamed use-deepmd-kit as getting-started, and changed the contents a little.

codecov-commenter · 2021-04-19T11:58:10Z

Codecov Report

Merging #513 (3735a8f) into devel (0d0cb77) will increase coverage by 0.73%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##            devel     #513      +/-   ##
==========================================
+ Coverage   62.09%   62.82%   +0.73%     
==========================================
  Files          74       75       +1     
  Lines        6229     6333     +104     
==========================================
+ Hits         3868     3979     +111     
+ Misses       2361     2354       -7

Impacted Files	Coverage Δ
deepmd/utils/argcheck.py	`16.36% <0.00%> (-0.18%)`	⬇️
deepmd/utils/type_embed.py	`100.00% <0.00%> (ø)`
deepmd/utils/network.py	`96.36% <0.00%> (+0.06%)`	⬆️
deepmd/model/ener.py	`90.72% <0.00%> (+0.39%)`	⬆️
deepmd/utils/data.py	`90.63% <0.00%> (+0.45%)`	⬆️
deepmd/train/trainer.py	`38.84% <0.00%> (+0.52%)`	⬆️
deepmd/descriptor/se_a.py	`90.57% <0.00%> (+1.60%)`	⬆️
deepmd/fit/ener.py	`93.29% <0.00%> (+7.66%)`	⬆️

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tuoping · 2021-04-20T01:48:52Z

The latest commit changed LICENSE in the main directory to LICENSE.rst and linked it to index.rst.
A new file credits.rst, with all the contributor's GITHUB usernames are listed. Zhang ZiXuan as the designer of logo is listed under "other credits".
Side bar is reconstructed into four sections.
API is modified and recomplied.
Use-DeePMD-kit is renames as getting-started.
Pair-style-deepmd-command is merged into getting-started, under "Run MD with Lammps".
Lammps, i-PI and ASE are incorporated under a same entry "Run MD".
Install.rst is seperated to 2 parts: install_easy.rst and install_source.rst.
All the URLs are updated

…xtension sphinx-markdown-tables in conf.py

marian-code

Could you please add my name to the list @tuoping ? I do not want to create new PR just for that.

doc/credits.rst

doc/getting-started.md

README.md

including "what you can contribute" "before you contribute": "overview of deepmd-kit" (branches) and "developer guide" (Link to "doc/development/index") "how to contribute": fork, clone, change, unittest, commit and PR Made directories troubleshooting and development, so that it's easier for everyone to PR. Added roadmap.md in doc to list optional commissions for future contributors. Removed highlights in doc, and added in README. Removed empty file known_issues.md

PS: All the links to repo community are futile yet.

…put-auto.rst (train-input.rst is basically emplty).

README.md

doc/troubleshooting/index.rst

CONTRIBUTING.md

…and html mode. Especially the ones in README.md and CONTRIBUTING.md

tuoping · 2021-05-03T11:01:11Z

Added two functions in conf.py to detect files in folders troubleshooting/ and development/, and append them in troubleshooting/index.md and development/index.md automatically.
Sorry, forgot to mention this in COMMIT_MSG.

CONTRIBUTING.md

README.md

…o in README.md

CONTRIBUTING.md

README.md

Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

Not all contributors are core contributor

njzjz · 2021-05-09T02:09:06Z

doc/development/index.md

+- [coding-conventions](coding-conventions.rst)
+- [api](api.rst)


These two links use filenames instead of titles?

I'll change that.

* check html window * change index.rst of branch devel * Re-structured doc * Re-structured Doc * Re-structured Doc * Re-structured Doc * Re-structured Doc * Re-structured Doc * Re-structured Doc * Set theme jekyll-theme-cayman * Create index.md * Re-structured Doc * Re-structured Doc * Re-structured index.rst and seperated install.rst into 3 files; Renamed use-deepmd-kit as getting-started, and changed the contents a little. * Same as before * Edited license.rst and credits.rst * same as before * Modified pair-style-deepmd syntax part * Fixed the collapsed table in getting-started#prepare-data by adding extension sphinx-markdown-tables in conf.py * Added sphinx-markdown-table in requirements.txt * Modification after Merge * modified superlinks in getting-started.md * same * Something is imperfect with the url. I can't link to #section in another .md file. So I changed all the external links in getting-started.md, and deleted all the #... parts. * changed LICENSE to url; deleted whatsnew, application-examples and known_issues in index.rst * corrected subsection links * testing external section links * same * changed all the superlinks in getting-started.md from markdown format to html format * same * Update doc/conf.py Do not use any <tab> in Python files. Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> * Update doc/getting-started.md Use a publish version instead Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> * added some descriptor/scripts in api.rst; Changed the user names of contributors in credits.rst; Removed install-hardware-platforms; Put URL for GPLv2 in index.rst * Changed parser from recommonmark to myst, so the header-anchors in getting-started can support both markdown and html links. * add myst-parser in requirements * move doc dependence packages from requirements.txt to setup.py * changed contributor's order in credits.rst * change whatsnew * change highlights in 2.0 in README.md * Update README.md Testing README.md * Add CONTRIBUTING.md including "what you can contribute" "before you contribute": "overview of deepmd-kit" (branches) and "developer guide" (Link to "doc/development/index") "how to contribute": fork, clone, change, unittest, commit and PR Made directories troubleshooting and development, so that it's easier for everyone to PR. Added roadmap.md in doc to list optional commissions for future contributors. Removed highlights in doc, and added in README. Removed empty file known_issues.md * Fixed some minor mistakes. PS: All the links to repo community are futile yet. * changed document for training inputs from train-input.rst to train-input-auto.rst (train-input.rst is basically emplty). * Fixed links under "highlights in kit2.0.0". * Checked all the links, and made sure they work both in markdown mode and html mode. Especially the ones in README.md and CONTRIBUTING.md * Sorry, fixed a broken link in CONTRIBUTING.md. * Asigned language 'bash' for codes in CONTRIBUTING.md; Corrected a typo in README.md * Update CONTRIBUTING.md * fix typo in README.md Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> * Update README.md * Update credits.rst Not all contributors are core contributor Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: tuoping <abby@DESKTOP-LV5KL0D.localdomain> Co-authored-by: Han Wang <amcadmus@gmail.com>

tuoping added 10 commits April 14, 2021 07:27

check html window

472dc1c

change index.rst of branch devel

35420ba

Merge tag 'v2.0.0.a0' into devel

cabe8ba

Merge branch 'devel' of http://github.com/deepmodeling/deepmd-kit int…

8ac43e5

…o devel

Re-structured doc

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tuoping and others added 10 commits April 15, 2021 09:08

Re-structured Doc

0a994c2

Re-structured Doc

420822c

Set theme jekyll-theme-cayman

ba1bc7b

Create index.md

dfe2193

Re-structured Doc

2c46ffd

Re-structured Doc

25cf687

Re-structured index.rst and seperated install.rst into 3 files;

484c9d9

Renamed use-deepmd-kit as getting-started, and changed the contents a little.

Same as before

1a55647

Edited license.rst and credits.rst

a65a50f

same as before

bc68f89

tuoping added 4 commits April 20, 2021 14:13

Modified pair-style-deepmd syntax part

fcc85a7

Fixed the collapsed table in getting-started#prepare-data by adding e…

38f713b

…xtension sphinx-markdown-tables in conf.py

Added sphinx-markdown-table in requirements.txt

19ff8a3

modified getting-started.md compared with deepmodeling/deepmd-kit/devel

32e4a68

marian-code suggested changes Apr 20, 2021

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amcadmus reviewed Apr 20, 2021

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njzjz added this to the v2.0.0 milestone Apr 29, 2021

amcadmus reviewed Apr 29, 2021

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tuoping added 3 commits April 29, 2021 15:31

Fixed some minor mistakes.

990f1cb

PS: All the links to repo community are futile yet.

changed document for training inputs from train-input.rst to train-in…

18c00a2

…put-auto.rst (train-input.rst is basically emplty).

amcadmus changed the base branch from devel to api April 30, 2021 10:55

amcadmus changed the base branch from api to devel April 30, 2021 10:55

amcadmus requested changes Apr 30, 2021

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tuoping and others added 2 commits April 30, 2021 07:02

Fixed links under "highlights in kit2.0.0".

fe084a3

Checked all the links, and made sure they work both in markdown mode …

9c2115e

…and html mode. Especially the ones in README.md and CONTRIBUTING.md

Sorry, fixed a broken link in CONTRIBUTING.md.

74269c0

njzjz reviewed May 3, 2021

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Asigned language 'bash' for codes in CONTRIBUTING.md; Corrected a typ…

2bd50a6

…o in README.md

amcadmus reviewed May 8, 2021

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Update CONTRIBUTING.md

ea0acb7

njzjz reviewed May 8, 2021

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amcadmus approved these changes May 8, 2021

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fix typo in README.md

671be8d

Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

njzjz approved these changes May 8, 2021

View reviewed changes

amcadmus added 2 commits May 8, 2021 09:22

Update README.md

e7a0589

Update credits.rst

3735a8f

Not all contributors are core contributor

amcadmus merged commit 2dfb64a into deepmodeling:devel May 9, 2021

njzjz reviewed May 9, 2021

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njzjz mentioned this pull request May 11, 2021

Citations missing #605

Closed

njzjz linked an issue May 11, 2021 that may be closed by this pull request

Citations missing #605

Closed

This was referenced Jun 10, 2021

v1.3 compatibility #724

Closed

remove unused tqdm #746

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njzjz mentioned this pull request Aug 22, 2021

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

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Re-structured Doc#513

Re-structured Doc#513
amcadmus merged 58 commits intodeepmodeling:develfrom
tuoping:devel

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