added first test version of sphinx doc

code/CMakeLists.txt

 cmake_minimum_required( VERSION 3.12.4 )
-project( KiT-RT VERSION 0.1.0 LANGUAGES CXX )
+project( KiT-RT VERSION 0.0.2 LANGUAGES CXX )
+
+### OPTIONS #####################################
+option( build_tests "enables compiling of unit_tests" OFF )
+option( build_doc "builds Doxygen and Sphinx documentation" OFF )
+#################################################
 
 
 ### COMPILER ####################################
@@ -81,26 +86,64 @@ target_compile_options( ${CMAKE_PROJECT_NAME} PUBLIC "$<$<CONFIG:RELEASE>:${KITR
 
 
 ### BUILD UNIT TESTS ############################
-include( CTest )
-set( CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/ext/Catch2/contrib ${CMAKE_MODULE_PATH} )
-include( Catch )
-set( CATCH_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/Catch2/single_include/catch2 )
-add_compile_definitions( BUILD_TESTING )
-add_compile_definitions( TESTS_PATH="${CMAKE_SOURCE_DIR}/tests/" )
-add_library( Catch INTERFACE )
-target_include_directories( Catch INTERFACE ${CATCH_INCLUDE_DIR} )
-file( GLOB_RECURSE TEST_SRCS RELATIVE ${CMAKE_SOURCE_DIR} "tests/*.cpp" )
-list( REMOVE_ITEM SRCS "src/main.cpp" )
-add_executable( unit_tests ${TEST_SRCS} ${SRCS} ${EXT_SRCS} )
-target_link_libraries( unit_tests Catch ${CORE_LIBRARIES} )
-target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${KITRT_DEBUG_OPTIONS}>" )
-if( CMAKE_COMPILER_IS_GNUCXX )
-    set( CODE_COVERAGE_OPTIONS --coverage -g -O0 -w )
-    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${CODE_COVERAGE_OPTIONS}>" )
-    target_link_libraries( unit_tests Catch gcov )
+if( build_tests )
+    include( CTest )
+    set( CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/ext/Catch2/contrib ${CMAKE_MODULE_PATH} )
+    include( Catch )
+    set( CATCH_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/Catch2/single_include/catch2 )
+    add_compile_definitions( BUILD_TESTING )
+    add_compile_definitions( TESTS_PATH="${CMAKE_SOURCE_DIR}/tests/" )
+    add_library( Catch INTERFACE )
+    target_include_directories( Catch INTERFACE ${CATCH_INCLUDE_DIR} )
+    file( GLOB_RECURSE TEST_SRCS RELATIVE ${CMAKE_SOURCE_DIR} "tests/*.cpp" )
+    list( REMOVE_ITEM SRCS "src/main.cpp" )
+    add_executable( unit_tests ${TEST_SRCS} ${SRCS} ${EXT_SRCS} )
+    target_link_libraries( unit_tests Catch ${CORE_LIBRARIES} )
+    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${KITRT_DEBUG_OPTIONS}>" )
+    if( CMAKE_COMPILER_IS_GNUCXX )
+        set( CODE_COVERAGE_OPTIONS --coverage -g -O0 -w )
+        target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${CODE_COVERAGE_OPTIONS}>" )
+        target_link_libraries( unit_tests Catch gcov )
+    endif()
+    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELWITHDEBINFO>:${KITRT_RELWITHDEBINFO_OPTIONS}>" )
+    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELEASE>:${KITRT_RELEASE_OPTIONS}>" )
+    catch_discover_tests( unit_tests )
+endif()
+#################################################
+
+
+### BUILD DOCUMENTATION #########################
+if( build_doc )
+    find_package( Doxygen REQUIRED )
+    find_package( Sphinx REQUIRED )
+
+    file( GLOB_RECURSE DOC_HEADER RELATIVE ${CMAKE_SOURCE_DIR} "include/*.h" )
+
+    set( DOXYGEN_INPUT_DIR ${PROJECT_SOURCE_DIR} )
+    set( DOXYGEN_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/docs/doxygen )
+    set( DOXYGEN_INDEX_FILE ${DOXYGEN_OUTPUT_DIR}/html/index.html )
+    set( DOXYFILE_IN ${CMAKE_CURRENT_SOURCE_DIR}/../doc/Doxyfile.in )
+    set( DOXYFILE_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile )
+    configure_file( ${DOXYFILE_IN} ${DOXYFILE_OUT} @ONLY )
+    file( MAKE_DIRECTORY ${DOXYGEN_OUTPUT_DIR} )
+    add_custom_command( OUTPUT ${DOXYGEN_INDEX_FILE}
+                        DEPENDS ${DOC_HEADER}
+                        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYFILE_OUT}
+                        MAIN_DEPENDENCY ${DOXYFILE_OUT} ${DOXYFILE_IN}
+                        COMMENT "Generating documentaion with Doxygen"
+                        VERBATIM )
+    add_custom_target( Doxygen ALL DEPENDS ${DOXYGEN_INDEX_FILE} )
+
+    set( SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/../doc )
+    set( SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR}/docs/sphinx )
+    set( SPHINX_INDEX_FILE ${SPHINX_BUILD}/index.html )
+    add_custom_command( OUTPUT ${SPHINX_INDEX_FILE}
+                        COMMAND ${SPHINX_EXECUTABLE} -b html -Dbreathe_projects.CatCutifier=${DOXYGEN_OUTPUT_DIR}/xml ${SPHINX_SOURCE} ${SPHINX_BUILD}
+                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                        DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/../doc/index.rst ${DOXYGEN_INDEX_FILE}
+                        MAIN_DEPENDENCY ${SPHINX_SOURCE}/conf.py
+                        COMMENT "Converting documentation from Doxygen to Sphinx" )
+
+    add_custom_target( Sphinx ALL DEPENDS ${SPHINX_INDEX_FILE} )
 endif()
-target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELWITHDEBINFO>:${KITRT_RELWITHDEBINFO_OPTIONS}>" )
-target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELEASE>:${KITRT_RELEASE_OPTIONS}>" )
-catch_discover_tests( unit_tests )
-enable_testing()
 #################################################

code/cmake/FindSphinx.cmake

+find_program( SPHINX_EXECUTABLE
+              NAMES sphinx-build
+              DOC "Path to sphinx-build executable" )
+
+include( FindPackageHandleStandardArgs )
+
+find_package_handle_standard_args( Sphinx
+                                   "Failed to find sphinx-build executable"
+                                   SPHINX_EXECUTABLE )

doc/conf.py

+# 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 = 'KiT-RT'
+copyright = '2020, TBD'
+author = 'TBD'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- 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.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.viewcode',
+    'breathe',
+    'sphinx_rtd_theme'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The master toctree document.
+master_doc = 'index'
+
+# 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 = []
+
+
+# -- 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']
+
+breathe_projects = {
+    "KiT-RT": "../code/build/debug/docs/doxygen/xml/",
+}
+
+breathe_default_project = "KiT-RT"

doc/index.rst

+.. KiT-RT documentation master file, created by
+   sphinx-quickstart on Mon Nov 30 16:55:47 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to KiT-RT's documentation!
+==================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+
+Docs
+====
+
+.. doxygenclass:: Mesh
+   :members:

scripts/Dockerfile

@@ -28,6 +28,7 @@ RUN apt-get update \
        libxinerama-dev \
        python3 \
        python3-pip \
+       doxygen \
     && apt-get clean \
     && apt-get autoremove --purge \
     && rm -rf /var/lib/apt/lists/* 
@@ -48,6 +49,6 @@ RUN wget -nc --no-check-certificate --quiet https://www.vtk.org/files/release/8.
     && cd - \
     && rm -rf VTK-*
 
-RUN pip3 install numpy pygmsh==6.1.1 Pillow pydicom gcovr
+RUN pip3 install numpy pygmsh==6.1.1 Pillow pydicom gcovr sphinx_rtd_theme breathe
 
 WORKDIR /home