Doc api cc #663

tuoping · 2021-05-25T01:32:49Z

Made api_cc.rst in doc/development/

codecov-commenter · 2021-05-25T01:36:19Z

Codecov Report

Merging #663 (ab8fc7f) into devel (cb2c118) will decrease coverage by 15.70%.
The diff coverage is n/a.

❗ Current head ab8fc7f differs from pull request most recent head d478d19. Consider uploading reports for the commit d478d19 to get more accurate results

@@             Coverage Diff             @@
##            devel     #663       +/-   ##
===========================================
- Coverage   82.36%   66.66%   -15.71%     
===========================================
  Files         114        6      -108     
  Lines        9312       15     -9297     
===========================================
- Hits         7670       10     -7660     
+ Misses       1642        5     -1637

Impacted Files	Coverage Δ
source/api_cc/include/DeepPot.h	`66.66% <ø> (ø)`
source/api_cc/include/DeepTensor.h	`20.00% <ø> (ø)`
deepmd/infer/deep_tensor.py
deepmd/cluster/local.py
source/api_cc/tests/test_deeppolar.cc
source/lib/tests/test_prod_virial_a.cc
source/lib/tests/test_neighbor_list.cc
source/op/_prod_virial_se_r_grad.py
deepmd/utils/neighbor_stat.py
source/lib/tests/test_ewald.cc
... and 100 more

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amcadmus

We haven't provided any documentation string in deepmd.DeepPot nor deepmd.DeepPotModelDevi, so I do not understand how this commit works.

…oxyfile to generated xml/ from C++. And then api_cc.rst can be generated by breathe from xml/.

tuoping · 2021-05-25T11:25:46Z

I found only doxygen to generate C++ api. But it cannot be installed with pip. So I had to add a precompiled directory xml/. Is there a way to include an external package by setup.py? @njzjz
A preview here:
https://deepmd-kit-testdoc.readthedocs.io/en/doc-api_cc/development/api_cc.html
As a alternative, in lammps documents, there is only a road guide:
While for the complete C library API is provided in the library.h

njzjz · 2021-05-25T11:37:11Z

The following question said doxygen had been installed in the readthedocs.
https://stackoverflow.com/questions/36064976/using-doxygen-in-read-the-docs

njzjz · 2021-05-25T11:47:29Z

See also https://breathe.readthedocs.io/en/latest/readthedocs.html.

tuoping · 2021-05-26T02:23:49Z

It's working now.
Preview here:
https://deepmd-kit-testdoc.readthedocs.io/en/doc-api_cc/development/api_cc.html
Thank you all.

tuoping · 2021-05-27T09:12:21Z

I included an extra package "exhale". C++ API display is looking a lot better now.
Preview here:
https://deepmd-kit-testdoc.readthedocs.io/en/doc-api_cc/API_CC/api_cc.html

njzjz · 2021-05-27T11:22:32Z

https://deepmd-kit-testdoc.readthedocs.io/en/doc-api_cc/API_CC/namespace_tensorflow.html

We have tensorflow namespace in the code?

njzjz · 2021-05-27T12:38:17Z

deepmd-kit/source/api_cc/include/custom_op.h

Line 14 in 5a8bc2c

using namespace tensorflow;

@denghuilu Is it possible to remove this line?

njzjz · 2021-05-28T13:29:57Z

@tuoping Could you give an example of how to write documents for APIs? Then I can fill it.

tuoping · 2021-05-29T05:28:07Z

Use exhale to invoke doxygen and then generate a structured api_cc
https://exhale.readthedocs.io/en/latest/usage.html#setup-the-extensions-in-conf-py
Also
https://stackoverflow.com/questions/59990484/doxygensphinxbreatheexhale

njzjz · 2021-05-29T09:57:36Z

@tuoping do you know what's wrong with my commit? It doesn't work.

tuoping · 2021-05-29T10:27:59Z

I recompiled it on readthedocs, and it worked.
Preview here:
https://deepmd-kit-testdoc.readthedocs.io/en/doc-api_cc/API_CC/classdeepmd_1_1DeepPot.html#exhale-class-classdeepmd-1-1deeppot

* Doxyfile cannot be installed from pip, therefore I precompiled with doxyfile to generated xml/ from C++. And then api_cc.rst can be generated by breathe from xml/. * Edit conf.py to include doxygen * Edit conf.py to enable doxygen on readthedocs * Add specification in conf.py to refine the html layout of api_cc.rst * Included exhale to make prettier C++ API. * Update conf.py * add a function description to see if it works * it should be put into the header file? * add documents for DeepPot and DeepTensor * add documents for some common functions Co-authored-by: tuoping <[email protected]> Co-authored-by: Jinzhe Zeng <[email protected]>

* fix typo in github actions release to conda * Get from_poscar_path only when from_poscar is true (deepmodeling#537) Change-Id: I17774bee345634e4e72bd783e8112eefaaf9f0d3 Co-authored-by: Zhengju Sha <[email protected]> * feature: merge run.py * fix:fix syntax bug * fix summary ratio bug * fix: fix bug of var(calypso_run_opt_path) not defined * reorganize code v1 * add: add unittest * add: add some explainations of dp+calypso in README.md * change a little bit in readme.md * change position of function * add deepmd-kit>=2.0.1 install_require in setup.py * test failed cause no tensorflow module so add tensorflow in setup.py * calc model devi in command line * fix some small bugs of modd and PBS script of cpu * fix unittest * delete parse_input.dat * fix unittest * first reorganization * secord reorganization * fix bugs * fix: fix bugs in modd_calypso.py write_modd.py and run.py * change functions name and fix bugs * remove modd_calypso.py * remove: remove modd_calypso.py * remove some useless outputs * restore dispatcher/PBS.py * refactor: make some changes in calypso related code - rename model_devi_calypso.py run_calypso.py - rename calypso.py make_calypso.py - add new file calypso_check_outcar.py calypso_run_opt.py - add new file calypso_run_model_devi.py - delete write_modd.py - modify README.md and run.py * refactor: move calypso main code(run.py) into run_calypso.py and modify test_calypso.py * docs: modify README.md related to CALYPSO * delete some useless comments in run.py * add write_model_devi_out function into make_calypso.py for passing unittest * fix a spelling mistake in calypso_run_opt.py (famx -> fmax) * change runopt script's name from run_opt.py to calypso_run_opt.py and fix bug in runopt script * fix unittest Co-authored-by: Han Wang <[email protected]> Co-authored-by: felix5572 <[email protected]> Co-authored-by: shazj99 <[email protected]> Co-authored-by: Zhengju Sha <[email protected]> Co-authored-by: Han Wang <[email protected]>

tuoping force-pushed the doc-api_cc branch from 6ddecff to 2b2e57f Compare May 25, 2021 01:39

amcadmus requested changes May 25, 2021

View reviewed changes

Doxyfile cannot be installed from pip, therefore I precompiled with d…

7bd3af5

…oxyfile to generated xml/ from C++. And then api_cc.rst can be generated by breathe from xml/.

tuoping force-pushed the doc-api_cc branch from cc6a276 to 7bd3af5 Compare May 25, 2021 11:18

Edit conf.py to include doxygen

9551af1

tuoping force-pushed the doc-api_cc branch from 5d8d72d to 9551af1 Compare May 26, 2021 01:14

Edit conf.py to enable doxygen on readthedocs

c711e3f

tuoping added 2 commits May 26, 2021 15:17

Add specification in conf.py to refine the html layout of api_cc.rst

6dee7d7

Included exhale to make prettier C++ API.

2920a3d

tuoping force-pushed the doc-api_cc branch from 9bc6788 to 2920a3d Compare May 27, 2021 09:00

Update conf.py

d0cdf20

tuoping force-pushed the doc-api_cc branch from 08731a3 to d0cdf20 Compare May 28, 2021 13:41

njzjz added 2 commits May 29, 2021 05:22

add a function description to see if it works

6720f69

it should be put into the header file?

10216a3

njzjz added 2 commits May 29, 2021 07:42

add documents for DeepPot and DeepTensor

b5b4228

add documents for some common functions

d478d19

amcadmus approved these changes Jun 3, 2021

View reviewed changes

amcadmus merged commit ab7621e into deepmodeling:devel Jun 3, 2021

tuoping deleted the doc-api_cc branch June 4, 2021 01:49

This was referenced Jun 10, 2021

v1.3 compatibility #724

Closed

remove unused tqdm #746

Merged

njzjz mentioned this pull request Aug 22, 2021

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

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Doc api cc #663

Doc api cc #663

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Doc api cc #663

Doc api cc #663

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