docs rearranged

CMakeLists.txt

@@ -5,7 +5,7 @@ project(catima)
 option(BUILD_SHARED_LIBS "build as shared library" ON)
 option(PYTHON_MODULE "compile the Catima python module(requires numpy and cython installed)" OFF)
 option(TESTS "build tests" OFF)
-option(EXAMPLES "build examples" ON)
+option(EXAMPLES "build examples" OFF)
 option(APPS "build catima applications" ON)
 option(GLOBAL "build with global, sources are required" OFF)
 option(REACTIONS "enable/disable nuclear reaction rate" ON)
@@ -14,7 +14,6 @@ option(GSL_INTEGRATION "use GSL integration" OFF)
 option(GSL_INTERPOLATION "use GSL inteRPOLATION" OFF)
 option(THIN_TARGET_APPROXIMATION "thin target approximation" ON)
 option(GENERATE_DATA "make data tables generator" OFF)
-option(DOCS "build documentation (requires doxygen)" OFF)
 
 ######## build type ############
 if(NOT CMAKE_BUILD_TYPE  STREQUAL "Debug")
@@ -141,7 +140,7 @@ endif(GENERATE_DATA)
 if(DOCS)
 find_package(Doxygen REQUIRED)
 if(DOXYGEN_FOUND)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doxygen.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/docs/doxygen.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
 add_custom_target(docs
                    COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile COMMENT "Generating API documentation with Doxygen" VERBATIM )
 endif(DOXYGEN_FOUND)

README.md

@@ -22,6 +22,15 @@ CMake is used to build the library. For default build use:
 > make
 ```
 
+after the compilation the libraries and headers must be either installed system-wide by make install or PATH and LD_LIBRARY_PATH must be adjusted to point to headers and library files.
+The default install path can be change, ie: cmake -DCMAKE_INSTALL_PREFIX=/opt/catima
+
+the option to system-wide installation is to adjust library path and include paths.
+This can be done sourcing the init.sh file, which is generated in the build directory:
+```
+> source init.sh
+```
+
 cmake options
 -------------
 compile options, enable or disable with cmake:
@@ -30,21 +39,15 @@ compile options, enable or disable with cmake:
 available options:
   * BUILD_SHARED_LIBS - if ON shared library is build, otherwise static
   * PYTHON_MODULE - enable/disable building of the python bindigs, pybind11 is required to build the catima python module, default OFF
-  * TESTS - build tests
-  * EXAMPLES - build examples
+  * APPS - build command line app, default ON
+  * TESTS - build tests, default OFF
+  * EXAMPLES - build examples, default OFF
   * DOCS - prepare doxygen documentation (after cmake, __make docs__ needs to be executed)
   * GENERATE_DATA - makes program to re-generate precalculated tables (ie precalculated LS coefficients), default:OFF
   * THIN_TARGET_APPROXIMATION - compile the library with thin target approximation, default: ON
   * GSL_INTEGRATION - use GSL integration functions, otherwise use built-in integrator, default: OFF
   * GLOBAL - compile with GLOBAL code (source not included at the moment, needs to be manually added to __global__ directory, default:OFF)
+  * STORE_SPLINES - store splines in cache, if disabled datapoints are stored and splines are recreated, default ON
 
 ie:
 > cmake -DPYTHON_MODULE=ON -DEXAMPLES=ON ../
-
-
-after the compilation the libraries and headers must be either installed system-wide by make install or PATH and LD_LIBRARY_PATH must be adjusted to point to headers and library files.
-The default install path can be change, ie: cmake -DCMAKE_INSTALL_PREFIX=/opt/catima
-
-the option to system-wide installation is to adjust library path and include paths.
-This can be done sourcing the init.sh file, which is generated in the build directory:
-> source init.sh

docs/Doxyfile

@@ -0,0 +1,21 @@
+PROJECT_NAME           = catima
+INPUT                  = ../.
+RECURSIVE              = NO
+
+GENERATE_HTML          = NO
+GENERATE_LATEX         = NO
+GENERATE_XML           = YES
+XML_OUTPUT             = build/doxygenxml
+XML_PROGRAMLISTING     = YES
+
+MACRO_EXPANSION        = YES
+EXPAND_ONLY_PREDEF     = YES
+
+ALIASES                = "rst=\verbatim embed:rst"
+ALIASES               += "endrst=\endverbatim"
+
+QUIET                  = YES
+WARNINGS               = YES
+WARN_IF_UNDOCUMENTED   = NO
+JAVADOC_AUTOBRIEF      = NO
+

docs/Makefile

@@ -0,0 +1,23 @@
+# 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 doxy
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile doxy
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+doxy:
+	doxygen

docs/README.md

@@ -0,0 +1,52 @@
+CATima
+=======
+C++ library for caclulalaton of energy loss, range, angular scattering and time of flight of the particle passing through matter.
+The library is based on physics used in the ATIMA code,however its not 100% copy of ATIMA physics.
+ see CREDITS for more details.
+
+The WebAtima UI to this library can be found here:
+  * https://web-docs.gsi.de/~aprochaz/webatima (only inside GSI)
+  * https://isotopea.com/webatima
+
+Installation
+------------
+CMake is used to build the library. For default build use:
+
+```
+> mkdir build
+> cd build
+> cmake ../
+> make
+```
+
+after the compilation the libraries and headers must be either installed system-wide by make install or PATH and LD_LIBRARY_PATH must be adjusted to point to headers and library files.
+The default install path can be change, ie: cmake -DCMAKE_INSTALL_PREFIX=/opt/catima
+
+Alternative to the system-wide installation is to adjust library path and include paths.
+This can be done sourcing the init.sh file, which is generated in the build directory:
+```
+source init.sh
+```
+
+
+cmake options
+-------------
+compile options, enable or disable with cmake:
+> cmake ../ -D[OPTION]
+
+available options:
+  * BUILD_SHARED_LIBS - if ON shared library is build, otherwise static
+  * PYTHON_MODULE - enable/disable building of the python bindigs, pybind11 is required to build the catima python module, default OFF
+  * APPS - build command line app, default ON
+  * TESTS - build tests, default OFF
+  * EXAMPLES - build examples, default OFF
+  * DOCS - prepare doxygen documentation (after cmake, __make docs__ needs to be executed)
+  * GENERATE_DATA - makes program to re-generate precalculated tables (ie precalculated LS coefficients), default:OFF
+  * THIN_TARGET_APPROXIMATION - compile the library with thin target approximation, default: ON
+  * GSL_INTEGRATION - use GSL integration functions, otherwise use built-in integrator, default: OFF
+  * GLOBAL - compile with GLOBAL code (source not included at the moment, needs to be manually added to __global__ directory, default:OFF)
+  * STORE_SPLINES - store splines in cache, if disabled datapoints are stored and splines are recreated, default ON 
+
+ie:
+> cmake -DPYTHON_MODULE=ON -DEXAMPLES=ON ../
+

docs/conf.py

@@ -0,0 +1,56 @@
+# 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 = 'Catima'
+copyright = '2017, A. Prochazka'
+author = 'A. Prochazka'
+
+
+# -- General configuration ---------------------------------------------------
+
+extensions = [
+        'recommonmark',
+        'breathe'
+]
+
+breathe_projects = {'nurex':'build/doxygenxml/'}
+breathe_default_project = 'catima'
+breathe_domain_by_extenstion = {'h':'cpp'}
+primary_domain = 'cpp'
+highlight_language = 'cpp'
+# 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 = []
+
+
+# -- 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']

docs/index.rst

@@ -0,0 +1,26 @@
+Catima's documentation
+======================
+C++ library for caclulalaton of energy loss, range, angular scattering and time of flight of the particle passing through matter.
+The library is based on physics used in the ATIMA code,however its not 100% copy of ATIMA physics.
+ see CREDITS for more details.
+
+The WebAtima UI to this library can be found here:
+  * https://isotopea.com/webatima
+
+
+Content
+-------
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Installation
+
+   README
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`