INSTALL

Here are the steps to install and tune your BioMove3D version using the CMake build system.

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##############  BUILD   ###############
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- First step is to create a 'build' directory: 'mkdir build'

- Enter the build directory and run cmake pointing the root of BioMove3D : 'cd build; cmake ..'

  By default the install directory is {BioMove3D_ROOT}/build/install/
  You can change this by adding the argument '-DCMAKE_INSTALL_PREFIX=YourPath' to the first
  CMake run.

  If you want to only generate the library libm3d.{so|dylib}, you must
  add the argument  '-DMAKELIB=1' to the first CMake run. 
  WARNING: if you set this argument, the move3d binary will not be generated.

  CMake will check the dependencies and source the files to compile. The CMake script also gives an
  information on the activated compilation flags (BioMove3D modules)
  If some of the required packages are not available on your system, use your favorite package
  manager to install it. CMake checks for dependencies in most commons installation paths. If a
  dependency is not found, add '-D <PACKAGE>_INC=/MY/PATH/include -D <PACKAGE>_LIB=/My/Path/lib' 
  options to cmake : e.g. for Xforms 'cmake -D XFORMS_INC=/usr/include -D XFORMS_LIB=/usr/lib'.

- You can now tune your system to compile with some specific BioMove3D modules. For this run
  the ccmake command while pointing the root of BioMove3D: 'ccmake ..'
  This will open a curses interface for CMake enabling the user to set ON or OFF the flags. To
  switch a flag value, select it and press 'Enter' key. You can also change the compilation 
  mode from 'Debug' by default to 'Release' (optimized compilation). Once your changes are done, 
  press the 'c' key to configure the build. You will see activated flags for the build.
  Press the 'e' key to go back to the configuration interface the 'q' key to quit ccmake.

- Run now the make command as usual: 'make' The produced binary or library will be generated in 
  {BioMove3D_ROOT}/build/{Debug|Release}/bin/{HOSTTYPE}
  or  {BioMove3D_ROOT}/build/{Debug|Release}/lib/{HOSTTYPE}/libm3d.{so|dylib}

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##############  INSTALL ###############
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- If you want to install BioMove3d, you can run the command: 'make install'

- Use 'make clean' command to clean compiled files (object files, executables and libraries)

- Use 'make uninstall' to remove the installed data

- Simply remove the 'build' directory (or all data inside build directory except the 
  {install|Debug|Release} directories if you want to keep them) if you want to reconfigure
  all from scratch.

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#######  Adding source files ########
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- Each source folder contains a 'SourceList.cmake' file. This file contains the sources files
  names to be compiled. The 'SourceList.cmake' file is included inside the 'CMakeList.txt'
  in BioMove3D_ROOT, or in its parent 'SourceList.cmake'.

- To add a new file in an existing directory, simply add the file name to its folder
  'SourceList.cmake' file.

- To add a new folder run the {BioMove3D_ROOT}/script/CMake/createSourceList script in your
  new folder. This script will automatically search for c, cpp, cxx and C file inside the current
  folder. Here is the usage of the script:
  'createSourceList <folder deep>' to create a SourceList.cmake file in the current folder
  'createSourceList 1' for a directory of the firstLevel from the BioMove3D_ROOT
  'createSourceList 2' for a directory of the SecondLevel from the BioMove3D_ROOT
  'createSourceList 3' for a directory of the ThirdLevel from the BioMove3D_ROOT ...

- Fill and complete now the created SourceList.cmake file.

- Include the 'SourceList.cmake' file path inside the right subfolder file.

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########  Adding a new flag #########
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- To add a new Compilation Flag, edit the CMakeLists.txt file and add a 'BM3D_FLAG' declaration.
  Here is a template: BM3D_flag(<Flag name> "<Flag description>" OFF)

- To use this flag in 'SourceList.cmake' files add in it:
  IF(<Flag name>)
    What you want to do if the flag is enabled (ON)
  ENDIF(<Flag name>)

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#########  Help and Contact #########
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- If you need help please send an email to : biomove3dgitrepo@laas.fr