Merge pull request #297 from njzjz/docs

use sphinx to build documents

.gitignore

@@ -24,3 +24,5 @@ dist
 _version.py
 venv*
 .vscode/**
+_build
+_templates

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/_static/css/custom.css

@@ -0,0 +1,3 @@
+pre{
+	overflow: auto;
+}

doc/api.rst

@@ -0,0 +1,91 @@
+DeePMD-kit API
+===============
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+.. automodule:: deepmd.Data
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DataModifier
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DataSystem
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DeepDipole
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DeepEval
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DeepPolar
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DeepPot
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DeepWFC
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DescrptLocFrame
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DescrptSeA
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DescrptSeAR
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.DescrptSeR
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.EwaldRecp
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.Fitting
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.LearningRate
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.Local
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.Loss
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.Model
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.Network
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.TabInter
+   :members:
+   :undoc-members:
+
+.. automodule:: deepmd.Trainer
+   :members:
+   :undoc-members:
+

doc/conf.py

@@ -0,0 +1,60 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'DeePMD-kit'
+copyright = '2020, Deep Potential'
+author = 'Deep Potential'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'recommonmark',
+    "sphinx_rtd_theme",
+    'sphinx.ext.autosummary'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+html_css_files = ['css/custom.css']
+
+autodoc_default_flags = ['members']
+autosummary_generate = True
+master_doc = 'index'

doc/index.rst

@@ -0,0 +1,26 @@
+.. deepmd-kit documentation master file, created by
+   sphinx-quickstart on Sat Nov 21 18:36:24 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+DeePMD-kit's documentation
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+   install
+   use-deepmd-kit
+   train-input
+   lammps-pair-style-deepmd
+   api
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/install.md

@@ -126,7 +126,7 @@ gcc --version
 
 The C++ interface of DeePMD-kit was tested with compiler gcc >= 4.8. It is noticed that the I-Pi support is only compiled with gcc >= 4.9.
 
-First the C++ interface of Tensorflow should be installed. It is noted that the version of Tensorflow should be in consistent with the python interface. We assume that you have followed our instruction and installed tensorflow python interface 1.14.0 with, then you may follow [the instruction for CPU](doc/install-tf.1.14.md) to install the corresponding C++ interface (CPU only). If one wants GPU supports, he/she should follow [the instruction for GPU](doc/install-tf.1.14-gpu.md) to install the C++ interface.
+First the C++ interface of Tensorflow should be installed. It is noted that the version of Tensorflow should be in consistent with the python interface. We assume that you have followed our instruction and installed tensorflow python interface 1.14.0 with, then you may follow [the instruction for CPU](install-tf.1.14.md) to install the corresponding C++ interface (CPU only). If one wants GPU supports, he/she should follow [the instruction for GPU](install-tf.1.14-gpu.md) to install the C++ interface.
 
 ### Install the DeePMD-kit's C++ interface
 

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/requirements.txt

@@ -0,0 +1 @@
+.[docs,cpu]