Merge pull request #39 from Parallel-in-Time/release/v0.1.0

Merge release/v0.1.0 into development.

Author: memmett

.astylerc

@@ -0,0 +1,27 @@
+--add-brackets
+--add-one-line-brackets
+--align-pointer=type
+--align-reference=type
+--close-templates
+--convert-tabs
+--indent-cases
+--indent-classes
+--indent-col1-comments
+--indent-labels
+--indent-modifiers
+--indent-namespaces
+--indent-preproc-define
+--indent-preproc-cond
+--indent=spaces=2
+--indent-switches
+--keep-one-line-statements
+--lineend=linux
+--max-code-length=100
+--max-instatement-indent=40
+--min-conditional-indent=2
+--mode=c
+--pad-oper
+--pad-header
+--unpad-paren
+--style=1tbs
+--suffix=none

.gitignore

@@ -1,6 +1,7 @@
 # other stuff
 /doc/build
 /build*
+/dist
 
 # Created by http://www.gitignore.io
 

3rdparty/CMakeLists.txt

@@ -34,7 +34,7 @@ if(pfasst_BUILD_EXAMPLES)
         UPDATE_COMMAND ""
         PATCH_COMMAND ""
         BUILD_IN_SOURCE ON
-        CONFIGURE_COMMAND ${fftw3_SOURCE_DIR}/configure CC=${CMAKE_C_COMPILER} --prefix=${fftw3_INSTALL_DIR} --libdir=${fftw3_INSTALL_DIR}/lib CXX=${CMAKE_CXX_COMPILER}
+        CONFIGURE_COMMAND ${fftw3_SOURCE_DIR}/configure CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${CMAKE_CXX_FLAGS} --prefix=${fftw3_INSTALL_DIR} --libdir=${fftw3_INSTALL_DIR}/lib
         BUILD_COMMAND make
         TEST_COMMAND ""
         INSTALL_DIR ${fftw3_SOURCE_DIR}-install
@@ -65,6 +65,10 @@ if(pfasst_BUILD_TESTS)
       UPDATE_COMMAND ""
       PATCH_COMMAND ""
       CMAKE_ARGS -DCMAKE_BUILD_TYPE=Release
+      -DCMAKE_C_COMPILE=${CMAKE_C_COMPILER}
+      -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+      -DCMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}
+      -DGTEST_USE_OWN_TR1_TUPLE=ON
       -Dgtest_force_shared_crt=ON
       -Dgmock_build_tests=${gtest_BUILD_TESTS}
       # Disable install step

CMakeLists.txt

@@ -10,10 +10,15 @@ include(ExternalProject)
 # Set default ExternalProject root directory
 set_directory_properties(PROPERTIES EP_PREFIX ${CMAKE_BINARY_DIR}/3rdparty)
 
-option(pfasst_DISABLE_LIBCXX "Disable use of LLVM's libstdc++ when compiling with Clang." ON)
+option(pfasst_DISABLE_LIBCXX "Disable use of LLVM's libc++ when compiling with Clang." ON)
 option(pfasst_BUILD_EXAMPLES "Build example programs." ON)
 option(pfasst_BUILD_TESTS "Build test suite for PFASST." ON)
 
+# output directories
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${pfasst_SOURCE_DIR}/dist/bin")
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${pfasst_SOURCE_DIR}/dist/lib")
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${pfasst_SOURCE_DIR}/dist/lib")
+
 # check for C++11 support
 if(${CMAKE_CXX_COMPILER_ID} MATCHES GNU)
     check_cxx_compiler_flag(-std=c++11 HAVE_STD11)
@@ -25,10 +30,13 @@ if(${CMAKE_CXX_COMPILER_ID} MATCHES GNU)
 elseif(${CMAKE_CXX_COMPILER_ID} MATCHES Clang)
     check_cxx_compiler_flag(-std=c++11 HAVE_STD11)
     if(HAVE_STD11)
-        if(pfasst_DISABLE_LIBCXX)
+        if(pfasst_DISABLE_LIBCXX AND NOT APPLE)
             add_to_string_list("${CMAKE_CXX_FLAGS}" CMAKE_CXX_FLAGS "-std=c++11")
             add_to_string_list("${CMAKE_CXX_LINK_FLAGS}" CMAKE_CXX_LINK_FLAGS "-std=c++11")
         else()
+            if(APPLE)
+                message(WARNING "You are on an Apple system. libc++ is forcly enabled.")
+            endif(APPLE)
             add_to_string_list("${CMAKE_CXX_FLAGS}" CMAKE_CXX_FLAGS "-std=c++11" "-stdlib=libc++")
             add_to_string_list("${CMAKE_CXX_LINK_FLAGS}" CMAKE_CXX_LINK_FLAGS "-std=c++11" "-stdlib=libc++")
         endif()
@@ -37,6 +45,7 @@ elseif(${CMAKE_CXX_COMPILER_ID} MATCHES Clang)
     endif()
 elseif(${CMAKE_CXX_COMPILER_ID} MATCHES XL)
     # NOTE: This branch is not tested yet (in theory it should work)
+    message(WARNING "IMB XL C/C++ support is experimental and not yet tested.")
     check_cxx_compiler_flag(-qlanglvl=extended0x HAVE_STD11)
     if(HAVE_STD11)
         add_to_string_list("${CMAKE_CXX_FLAGS}" CMAKE_CXX_FLAGS "-qlanglvl=extended0x -qwarn0x")
@@ -49,7 +58,7 @@ endif()
 message(STATUS "Your compiler has C++11 support. Hurray!")
 
 # enable all compiler warnings
-add_to_string_list("${CMAKE_CXX_FLAGS}" CMAKE_CXX_FLAGS "-Wall")
+add_to_string_list("${CMAKE_CXX_FLAGS}" CMAKE_CXX_FLAGS "-Wall -Wextra -Wpedantic")
 
 set(3rdparty_INCLUDES)
 set(3rdparty_DEPENDEND_LIBS)

Doxyfile

@@ -153,7 +153,7 @@ SHORT_NAMES            = NO
 # comments will behave just like regular Qt-style comments
 # (thus requiring an explicit @brief command for a brief description.)
 
-JAVADOC_AUTOBRIEF      = NO
+JAVADOC_AUTOBRIEF      = YES
 
 # If the QT_AUTOBRIEF tag is set to YES then Doxygen will
 # interpret the first line (until the first dot) of a Qt-style
@@ -279,7 +279,12 @@ CPP_CLI_SUPPORT        = NO
 
 SIP_SUPPORT            = NO
 
-# For Microsoft's IDL there are propget and propput attributes to indicate getter and setter methods for a property. Setting this option to YES (the default) will make doxygen replace the get and set methods by a property in the documentation. This will only work if the methods are indeed getting or setting a simple type. If this is not the case, or you want to show the methods anyway, you should set this option to NO.
+# For Microsoft's IDL there are propget and propput attributes to indicate getter
+# and setter methods for a property. Setting this option to YES (the default) will
+# make doxygen replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple type.
+# If this is not the case, or you want to show the methods anyway, you should set
+# this option to NO.
 
 IDL_PROPERTY_SUPPORT   = YES
 
@@ -661,7 +666,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = src tests doc/source README.md
+INPUT                  = include tests examples doc/source README.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is

README.md

@@ -1,10 +1,46 @@
-PFASST
+PFASST                                                                                  {#mainpage}
 ======
 
-Master: [![Build Status](https://travis-ci.org/Parallel-in-Time/PFASST.svg?branch=master)](https://travis-ci.org/Parallel-in-Time/PFASST)
+The PFASST algorithm is a time-parallel algorithm for solving ODEs and
+PDEs.
 
-Development: [![Build Status](https://travis-ci.org/Parallel-in-Time/PFASST.svg?branch=development)](https://travis-ci.org/Parallel-in-Time/PFASST)
+The PFASST project is a C++ implementation of the 'parallel full
+approximation scheme in space and time' (PFASST) algorithm.  It also
+contains basic implementations of the 'spectral deferred correction'
+(SDC) and 'multi-level spectral deferred correction' (MLSDC)
+algorithms.
 
-Proposed class structure for a C++ PFASST implementation.
 
-Doxygen generated documentation can be found [here](https://pint.fz-juelich.de/ci/view/PFASST/job/PFASST%20%28Docu%29/doxygen/).
+References
+----------
+
+XXX
+
+
+Documentation
+-------------
+
+Doxygen generated documentation can be found [on the PinT server][documentation].  
+Currently, it features the following content:
+
+* \subpage #page_building_installing
+* \subpage #page_examples
+* \subpage #page_contributing
+* \subpage #page_style_guide
+
+
+Build status
+------------
+
+| Branch      | Status                              |
+|-------------|-------------------------------------|
+| Master      | ![master-status][]                  |
+| Development | ![dev-status][]                     |
+
+For details see [Travis][pfasst-travis].
+
+
+[documentation]: https://pint.fz-juelich.de/ci/view/PFASST/job/PFASST%20%28Docu%29/doxygen/
+[pfasst-travis]: https://travis-ci.org/Parallel-in-Time/PFASST
+[master-status]: https://travis-ci.org/Parallel-in-Time/PFASST.svg?branch=master
+[dev-status]:    https://travis-ci.org/Parallel-in-Time/PFASST.svg?branch=development

doc/source/contributing.md

@@ -1,4 +1,4 @@
-# Contributing
+# Contributing                                                                  {#page_contributing}
 
 ## Branching and Tagging Model
 

doc/source/examples.md

@@ -0,0 +1,5 @@
+# Examples                                                                          {#page_examples}
+
+## Simple Advection Diffusion
+
+See \subpage page_examples_advection_diffusion.

doc/source/installing.md

@@ -1,4 +1,4 @@
-# Building and Installing
+# Building and Installing                                                {#page_building_installing}
 
 ## Prerequesites
 

doc/source/style_guide.md

@@ -1,4 +1,4 @@
-# Style Guide
+# Style Guide                                                                    {#page_style_guide}
 
 ## Naming Convention