#Biosim

#Compile

• Using CMake and make, create a build directory, and from the build directory call cmake <project_dir> and make.
• Specific compilers or boost library versions can be used by setting environment variables for the cmake call, e.g. BOOST_ROOT=/path/to/boost_1_58_0/ CXX=/path/to/c++ cmake ../ for bash.

#Contributing code

##Formatting

• Format using clang-format and the style defined in .clang-format.
  Use clang-format-3.5 or newer because they can fit short enums on a single line.
  See http://clang.llvm.org/docs/ClangFormat.html on how to integrate formatting for different editors. For KDevelop, add a custom source formatter script with clang-format-3.4 -style=file -assume-filename=$FILE as command and assign your favorite shortcut key to the Reformat Source command.
• All identifiers are lowercase, words are separated by _. Member variables have one, passed function variables have two leading _. Template parameters are uppercase.
• Always place the const modifer after the part which constness it describes (so that types can be completely read backwards).
• Always use {}, even for single statements.
• Group methods by method/design pattern without empty line between methods.
• Use short, but descriptive names; comment at least every method and member.

##Programming

• Use exceptions, derive from std::runtime_exception; don't use boost::exceptions, they don't mix well, see: http://stackoverflow.com/questions/25759293/
• Make single argument ctor explicit.
• Use enum class instead of enum for simple enumerations to create identifiers in separate namespace.
• Place members at the end of a class.

##Code Organization

• tools:: only depends on standard C++ and external libaries, e.g. boost.
• math:: can in addition depend on the tools:: namespace.
• Other namespaces can in addition depend on the math:: namespace, but not any other namespace.
• Sub-namespaces can depend on their super-namespace and their dependencies.

##Code Design

• Applications follow the Unix philosophy of small, focused tools.
• To reduce code size, the biosim lib is not linked tp applications with --whole-archive (gcc) or -force_load (clang). Thus self-registering static instances cannot be used; they would be removed during linking optimizations, b/c they are not explicitly called, see: http://stackoverflow.com/questions/805555/; http://stackoverflow.com/questions/16294842/; or http://stackoverflow.com/questions/17470350/.
  Therefore, each enumerated class requires two changes: class and explicit enumeration.