adding autodocumentation for python and C++

.gitignore

@@ -124,4 +124,11 @@ website/static/css/material.dark.css
 obj
 packages/*/cjs
 cppbuild
-.coverage
+docsbuild
+.coverage
+
+# docs generated
+docs/_build
+docs/modules.rst
+docs/perspective.*.rst
+docs/python

CMakeLists.txt

@@ -51,6 +51,7 @@ option(PSP_CPP_BUILD "Build the C++ Project" OFF)
 option(PSP_CPP_BUILD_TESTS "Build the C++ Tests" OFF)
 option(PSP_PYTHON_BUILD "Build the Python Bindings" OFF)
 option(PSP_CPP_BUILD_STRICT "Build the C++ with strict warnings" OFF)
+option(PSP_BUILD_DOCS "Build the Perspective documentation" OFF)
 
 
 if (NOT DEFINED PSP_WASM_BUILD)
@@ -128,6 +129,12 @@ if(CMAKE_BUILD_TYPE_LOWER STREQUAL debug)
 else()
 	message(WARNING "${Cyan}Building RELEASE${ColorReset}")
 endif()
+
+if(PSP_BUILD_DOCS)
+	message(WARNING "${Cyan}Building Perspective Documentation${ColorReset}")
+else()
+	message(WARNING "${Cyan}Skipping Perspective Documentation${ColorReset}")
+endif()
 #######################
 include_directories("${CMAKE_SOURCE_DIR}/src/include")
 
@@ -179,7 +186,7 @@ if (PSP_WASM_BUILD)
 	set(SYNC_MODE_FLAGS "-s ENVIRONMENT=node -s BINARYEN_ASYNC_COMPILATION=0 -s BINARYEN_METHOD='\"native-wasm\"' -s WASM=1")
 	set(ASYNC_MODE_FLAGS "-s ENVIRONMENT=worker -s BINARYEN_ASYNC_COMPILATION=1 -s BINARYEN_METHOD='\"native-wasm\"' -s WASM=1")
 	set(ASMJS_MODE_FLAGS "-s ENVIRONMENT=worker -s LEGACY_VM_SUPPORT=1 -s BINARYEN_ASYNC_COMPILATION=0 -s BINARYEN_METHOD='\"asmjs\"' -Wno-almost-asm -s WASM=0")
-else()
+elseif(PSP_CPP_BUILD OR PSP_PYTHON_BUILD)
 	#####################
 	# VANILLA CPP BUILD #
 	#####################
@@ -363,7 +370,7 @@ if (PSP_WASM_BUILD)
 		set_target_properties(perspective.asm PROPERTIES OUTPUT_NAME "psp.asmjs")
 		add_dependencies(perspective.asm perspective.sync)
 	endif()
-else()
+elseif(PSP_CPP_BUILD OR PSP_PYTHON_BUILD)
 	if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
 		set(CMAKE_SHARED_LIBRARY_SUFFIX .dylib)
 	endif()
@@ -429,3 +436,24 @@ if (PSP_CPP_BUILD_TESTS)
 	)
 endif()
 #############
+
+########
+# Docs #
+########
+if(PSP_BUILD_DOCS)
+	add_custom_target(doxygen)
+	add_custom_command(TARGET doxygen
+	    COMMAND doxygen doxygen.conf
+	    WORKING_DIRECTORY ../docs
+	    COMMENT "Build doxygen xml files used by sphinx/breathe."
+	)
+
+    add_custom_target(docs-html ALL)
+    add_custom_command(TARGET docs-html
+	    COMMAND sphinx-build -b html . _build/html
+        WORKING_DIRECTORY ../docs
+        COMMENT "Build html documentation"
+    	)
+   	add_dependencies(docs-html doxygen)
+endif()
+##########

docker/docs/Dockerfile

@@ -0,0 +1,36 @@
+# *****************************************************************************
+#
+# Copyright (c) 2019, the Perspective Authors.
+#
+# This file is part of the Perspective library, distributed under the terms of
+# the Apache License 2.0.  The full license can be found in the LICENSE file.
+#
+
+FROM python:3.7
+# use the python one as its needs to be compiled for the docs to generate right
+
+RUN apt-get update
+RUN apt-get -y install apt-transport-https libtbb-dev cmake doxygen
+RUN apt-get -y remove python3
+
+RUN python3.7 -m pip install numpy pandas
+
+RUN ls -al /usr/local/lib/python3.7/site-packages/numpy
+
+RUN wget https://dl.bintray.com/boostorg/release/1.67.0/source/boost_1_67_0.tar.gz >/dev/null 2>&1  || echo "wget failed"
+RUN tar xfz boost_1_67_0.tar.gz
+RUN cd boost_1_67_0 && CPLUS_INCLUDE_PATH="$CPLUS_INCLUDE_PATH:/usr/local/include/python3.7m" C_INCLUDE_PATH="$C_INCLUDE_PATH:/usr/local/include/python3.7m" ./bootstrap.sh --with-python=/usr/local/bin/python3.7  || echo "boostrap failed"
+RUN cd boost_1_67_0 && CPLUS_INCLUDE_PATH="$CPLUS_INCLUDE_PATH:/usr/local/include/python3.7m" C_INCLUDE_PATH="$C_INCLUDE_PATH:/usr/local/include/python3.7m" ./b2 -j4 install || echo "build boost failed" 
+
+RUN ln -s /usr/local/lib/libboost_python37.so /usr/local/lib/libboost_python.so
+RUN ln -s /usr/local/lib/libboost_numpy37.so /usr/local/lib/libboost_numpy.so
+RUN python3 -m pip install 'numpy>=1.13.1' 'pandas>=0.22.0'
+
+# docs dependencies
+RUN python3 -m pip install breathe sphinx sphinx_rtd_theme
+RUN npm install @babel/cli @babel/core @babel/plugin-proposal-decorators @babel/plugin-transform-for-of  @babel/preset-env babel-plugin-transform-custom-element-classes jsdoc jsdoc-babel --save-dev
+RUN yarn
+
+# install from here from now, waiting on https://github.com/mozilla/sphinx-js/issues/94
+RUN python3 -m pip install git+https://github.com/timkpaine/sphinx-js
+

docker/python/Dockerfile

@@ -8,11 +8,8 @@
 
 FROM python:3.7
 
-WORKDIR /usr/src/app
-ADD . /usr/src/app
-
 RUN apt-get update
-RUN apt-get -y install apt-transport-https libtbb-dev cmake
+RUN apt-get -y install apt-transport-https libtbb-dev cmake nodejs npm
 RUN apt-get -y remove python3
 
 RUN python3.7 -m pip install numpy pandas

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+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/conf.py

@@ -0,0 +1,223 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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
+import sys
+import os
+import os.path
+import subprocess
+import sphinx_rtd_theme
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'python')))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'perspective'
+copyright = '2019, Perspective Authors'
+author = 'Perspective Authors'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '0.2.14'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.autodoc',  # autodocument python
+    'breathe',  # integrate with doxygen
+    'sphinx.ext.napoleon',  # google style docstrings
+    'sphinx_js',  # jsdoc
+]
+
+breathe_projects = {"perspective": os.path.abspath(os.path.join(os.path.dirname(__file__), '_build', 'xml'))}
+breathe_default_project = "perspective"
+
+js_source_path = [
+  # '../packages/perspective/src/js',
+  # '../packages/perspective/src/js/DataAccessor',
+  '../packages/perspective-viewer/src/js',
+  '../packages/perspective-viewer/src/js/computed_column',
+  '../packages/perspective-viewer/src/js/viewer',
+  # '../packages/perspective-viewer-highcharts/src/js',
+  # '../packages/perspective-viewer-hypergrid/src/js',
+  # '../packages/perspective-webpack-plugin/src/js',
+]
+root_for_relative_js_paths = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+jsdoc_config_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'jsdoc.conf'))
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# 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']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- 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 = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'perspectivedoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'perspective.tex', 'perspective Documentation',
+     'Perspective Authors', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'perspective', 'perspective Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'perspective', 'perspective Documentation',
+     author, 'perspective', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+def run_apidoc(_):
+    o_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), 'python'))
+    psp_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'python', 'perspective'))
+    cmd_path = 'sphinx-apidoc'
+    if hasattr(sys, 'real_prefix'):  # Check to see if we are in a virtualenv
+        # If we are, assemble the path manually
+        cmd_path = os.path.abspath(os.path.join(sys.prefix, 'bin', 'sphinx-apidoc'))
+    subprocess.check_call([cmd_path,
+                           '-E',
+                           '-M',
+                           '-o',
+                           o_dir,
+                           psp_dir,
+                           '--force'])
+
+
+def setup(app):
+    app.connect('builder-inited', run_apidoc)

docs/cpp.rst

@@ -0,0 +1,10 @@
+C++
+===========
+C++ Documentation
+
+.. doxygennamespace:: perspective
+   :project: perspective
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members: