Add documentation platform based on Sphinx+Doxygen+Breathe+Exhale (#803)

* Setup Sphinx+Doxygen+Breathe+Exhale
* Remove links to modindex and search pages
* Enable Doxygen autobrief

CHANGELOG.md

@@ -8,6 +8,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+### Added
+- Developer documentation framework based on Sphinx+Doxygen+Breathe+Exhale
+
 ### Fixed
 - Fix building server with Boost 1.75
 

doc/.gitignore

@@ -0,0 +1,4 @@
+api
+build
+doxygen
+venv

doc/Makefile

@@ -0,0 +1,23 @@
+# 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: clean 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) $(O)
+
+# Clean target as recommended by Exhale
+# https://exhale.readthedocs.io/en/latest/usage.html#optional-create-a-proper-clean-target
+clean:
+	rm -rf doxygen/ api/
+	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/README.md

@@ -0,0 +1,51 @@
+# Marian NMT code documentation and library API
+
+This directory contains code documentation and library API for developers of Marian NMT.
+
+The documentation is generated using
+[Sphinx](https://www.sphinx-doc.org/en/master/usage/quickstart.html) +
+[Breathe](https://breathe.readthedocs.io/en/latest/directives.html) +
+[Doxygen](http://www.doxygen.nl/manual/docblocks.html) +
+[Exhale](https://exhale.readthedocs.io/en/latest/usage.html).
+The documentation source code is written in `.rst` or `.md` files with special directives that allow
+to reference to C++ source code and documentation. The source documents are then build into static
+HTML pages.
+
+
+## Installation
+
+On Ubuntu 20.04, install the following packages:
+
+    sudo apt-get install python3 python3-pip python3-setuptools doxygen
+
+Then set up a Python environment and install modules:
+
+    pip3 install virtualenv
+    virtualenv venv -p python3
+    source venv/bin/activate
+    pip install -r requirements.txt
+
+Documentation building should also work on Windows, but it has not been tested.
+
+
+## Generation
+
+The documentation can be generated by running:
+
+    make html
+
+The website will be generated into `build/html` and accessible by opening _index.html_ in your
+browser.
+
+Directories:
+
+- `build` - automatically output directory for HTML documentation
+- `doxygen` - automatically generated Doxygen XML files
+- `api` - automatic library API generated with Exhale
+- `.rst` and `.md` files in this directory and its subdirectories are documentation source files
+- `_static` - custom CSS and JavaScript files
+
+
+## Writing documentation
+
+To be documented...

doc/_static/css/custom.css

@@ -0,0 +1,4 @@
+.wy-body-for-nav > .wy-grid-for-nav > .wy-nav-side {
+    border-bottom: 5px solid #28bbee;
+    /*background-color: #494d55;*/
+}

doc/conf.py

@@ -0,0 +1,118 @@
+# 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 datetime
+import sys
+
+sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Marian NMT'
+copyright = '2021, Marian NMT Team'
+author = 'Marian NMT Team'
+
+# The full version, including alpha/beta/rc tags
+# TODO: add GitHub commit hash to the version
+version_file = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'VERSION')
+with open(os.path.abspath(version_file)) as f:
+    version = f.read().strip()
+release = version + ' ' + str(datetime.date.today())
+
+
+# -- 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 = [
+    'sphinx.ext.imgmath',
+    'sphinx.ext.todo',
+    'breathe',
+    'exhale',
+    'recommonmark',
+]
+
+# 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',
+    'doxygen',
+    'venv',
+    'README.md',
+]
+
+
+# -- 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'
+htmlhelp_basename = 'marian'
+
+# 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']
+
+# The base URL which points to the root of the HTML documentation
+html_baseurl = 'http://marian-nmt.github.io/docs/api'
+
+
+# -- Extension configuration -------------------------------------------------
+
+breathe_projects = { 'marian': './doxygen/xml' }
+breathe_default_project = 'marian'
+
+doxygen_config = """
+INPUT                = ../src
+EXCLUDE             += ../src/3rd_party
+EXCLUDE             += ../src/tests
+EXCLUDE_PATTERNS     = *.inc *.md *.txt
+ENABLE_PREPROCESSING = YES
+JAVADOC_AUTOBRIEF    = YES
+WARN_IF_UNDOCUMENTED = NO
+"""
+
+exhale_args = {
+    'containmentFolder'     : './api',
+    'rootFileName'          : 'library_index.rst',
+    'rootFileTitle'         : 'Library API',
+    'doxygenStripFromPath'  : '..',
+    'createTreeView'        : True,
+    'exhaleExecutesDoxygen' : True,
+    'exhaleDoxygenStdin'    : doxygen_config.strip(),
+}
+
+primary_domain = 'cpp'
+highlight_language = 'cpp'
+
+# A trick to include markdown files from outside the source directory using
+# 'mdinclude'. Warning: all other markdown files not included via 'mdinclude'
+# will be rendered using recommonmark as recommended by Sphinx
+from m2r import MdInclude
+
+def setup(app):
+    # from m2r to make `mdinclude` work
+    app.add_config_value('no_underscore_emphasis', False, 'env')
+    app.add_config_value('m2r_parse_relative_links', False, 'env')
+    app.add_config_value('m2r_anonymous_references', False, 'env')
+    app.add_config_value('m2r_disable_inline_math', False, 'env')
+    app.add_directive('mdinclude', MdInclude)

doc/contributing.rst

@@ -0,0 +1 @@
+.. mdinclude:: ../CONTRIBUTING.md

doc/graph.md

@@ -0,0 +1,3 @@
+# Expression graphs
+
+...

doc/index.rst

@@ -0,0 +1,48 @@
+Welcome to Marian's documentation!
+==================================
+
+|buildgpu| |buildcpu| |tests| |release| |license|
+
+Marian is an efficient and self-contained Neural Machine Translation framework with an integrated
+automatic differentiation engine based on dynamic computation graphs, written entirely in C++.
+
+This is developer documentation. User documentation is available at https://marian-nmt.github.io/docs/
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   install
+   graph
+   operators
+
+   api/library_index
+
+   contributing
+
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+
+
+.. |buildgpu| image:: https://img.shields.io/jenkins/s/http/vali.inf.ed.ac.uk/jenkins/view/marian/job/marian-dev-cuda-10.1.svg?label=CUDAC%20Build
+   :target: http://vali.inf.ed.ac.uk/jenkins/job/marian-dev/
+   :alt: GPU build status
+
+.. |buildcpu| image:: https://img.shields.io/jenkins/s/http/vali.inf.ed.ac.uk/jenkins/view/marian/job/marian-dev-cpu.svg?label=CPU%20Build
+   :target: http://vali.inf.ed.ac.uk/jenkins/job/marian-dev-cpu/
+   :alt: CPU build status
+
+.. |tests| image:: https://img.shields.io/jenkins/s/http/vali.inf.ed.ac.uk/jenkins/view/marian/job/marian-regression-tests.svg?label=Tests
+   :target: http://vali.inf.ed.ac.uk/jenkins/job/marian-regression-tests/
+   :alt: Tests status
+
+.. |release| image:: https://img.shields.io/github/release/marian-nmt/marian.svg?label=Release
+   :target: https://github.com/marian-nmt/marian/releases
+   :alt: Latest release
+
+.. |license| image:: https://img.shields.io/badge/License-MIT-blue.svg
+   :target: ../LICENSE.md
+   :alt: License: MIT

doc/install.rst

@@ -0,0 +1,3 @@
+Installation
+============
+

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=source
+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/operators.md

@@ -0,0 +1,3 @@
+# Graph operations
+
+...

doc/requirements.txt

@@ -0,0 +1,6 @@
+sphinx==2.4.4
+breathe==4.13.0
+exhale
+sphinx_rtd_theme
+recommonmark
+m2r