add document (#34)

* delete main.tex

* fix rebase conflict

* add dependencies for doc in pyproject.toml

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add .readthedocs.yaml

* update doc

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update title

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.readthedocs.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+formats: all
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

docs/.gitignore

@@ -0,0 +1,43 @@
+# sphinx build folder
+_build
+
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store?
+ehthumbs.db
+Icon?
+Thumbs.db
+
+# Editor backup files #
+#######################
+*~
+# generated automatically
+api/

docs/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)

docs/cli.rst

@@ -0,0 +1,9 @@
+.. _cli:
+
+Command line interface
+======================
+
+.. argparse::
+   :module: dpti.main
+   :func: create_parser
+   :prog: dpti

docs/conf.py

@@ -0,0 +1,99 @@
+# 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
+from datetime import date
+
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "DPTI"
+copyright = "2021-%d, Deep Modeling" % date.today().year
+author = "DeepModeling"
+
+
+# -- 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 = [
+    "deepmodeling_sphinx",
+    "dargs.sphinx",
+    "myst_parser",
+    "sphinx_rtd_theme",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "numpydoc",
+    "sphinx.ext.autosummary",
+    "sphinxarg.ext",
+]
+
+# 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 = []
+
+autodoc_default_flags = ["members"]
+autosummary_generate = True
+master_doc = "index"
+
+
+def run_apidoc(_):
+    from sphinx.ext.apidoc import main
+
+    sys.path.append(os.path.join(os.path.dirname(__file__), ".."))
+    cur_dir = os.path.abspath(os.path.dirname(__file__))
+    module = os.path.join(cur_dir, "..", "dpti")
+    main(
+        [
+            "-M",
+            "--tocfile",
+            "api",
+            "-H",
+            "DPTI API",
+            "-o",
+            os.path.join(cur_dir, "api"),
+            module,
+            "--force",
+        ]
+    )
+
+
+def setup(app):
+    app.connect("builder-inited", run_apidoc)
+
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/", None),
+    "dargs": ("https://docs.deepmodeling.com/projects/dargs/en/latest/", None),
+}

docs/credits.rst

@@ -0,0 +1,4 @@
+Authors
+=======
+
+.. git-shortlog-authors::

docs/examples/water.md

@@ -0,0 +1,3 @@
+# Phase Diagram of Water
+
+This example describes how to calculate the phase diagram of water.

docs/getting-started.md

@@ -0,0 +1,5 @@
+# Getting Started
+
+DPTI: A Thermodynamic Integration Automization Package for Free Energy Calculation
+
+TODO

docs/index.rst

@@ -0,0 +1,33 @@
+DPTI's documentation
+======================================
+
+DPTI is a Python package to automate thermodynamic integration (TI) calculations for free energy.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+   install
+   getting-started
+   cli
+   api/api
+
+.. toctree::
+   :caption: Examples
+   :glob:
+
+   examples/water
+
+.. toctree::
+   :caption: Project details
+   :glob:
+
+   credits
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/install.md

@@ -0,0 +1,8 @@
+Install DPTI
+====================
+
+DPTI can installed by `pip`:
+
+```bash
+pip install dpti
+```

docs/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

docs/requirements.txt

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

dpti/main.py

@@ -5,7 +5,7 @@
 # from . import gdi
 
 
-def main():
+def create_parser():
     parser = argparse.ArgumentParser(
         description="DPTI: An Automatic Workflow Software for Thermodynamic Integration Calculations"
     )
@@ -25,7 +25,11 @@ def main():
     ti.add_module_subparsers(main_subparsers)
     ti_water.add_module_subparsers(main_subparsers)
     gdi.add_module_subparsers(main_subparsers)
+    return parser
+
 
+def main():
+    parser = create_parser()
     args = parser.parse_args()
     if hasattr(args, "func"):
         args.func(args)

pyproject.toml

@@ -32,12 +32,20 @@ dependencies = [
 [project.urls]
 homepage = "https://github.com/deepmodeling/dpti"
 
-[project.optional-dependencies]
-# docs = ["sphinx", "recommonmark", "sphinx_rtd_theme"]
-
 [project.scripts]
 dpti = "dpti.main:main"
 
+[project.optional-dependencies]
+docs = [
+    'sphinx',
+    'myst-parser',
+    'sphinx_rtd_theme>=1.0.0rc1',
+    'numpydoc',
+    'deepmodeling_sphinx>=0.1.1',
+    'dargs>=0.3.1',
+    'sphinx-argparse',
+]
+
 [tool.setuptools.packages.find]
 include = ["dpti*"]