1. Installing the Library¶

1.2.1. Prerequisites¶

Before you start building, there are a few requirements that need to be satisfied:

• build-essential – You will need this package in order to be able to build software on most Linux platforms. It contains a compiler and other tools important for the build.

• swig – It is used to generate the Python wrapping code (we are using version 3.0.10 at the moment).

  SWIG is only required if you made changes to the interface (header files under include/) and want to configure cmake with the -DRUN_SWIG=ON option (see the description of the molpher_build_SWIG_Python target in the section below). If this option is turned on, SWIG will be invoked by make upon build with the swig3.0 command so make sure the SWIG executable is available in the working environment.

• setuptools and pip – If you want to use pip or easy_install to install the Python package when the build and installation of the library are complete, you will need these to be installed with Python.

• python{version}-dev – You will need this package in order to build the Python bindings for the particular Python version.

  If you get ‘Missing Python.h’ compiler errors, you probably do not have this package installed.

• dependencies – Molpher-lib depends on three third-party libraries:

  • boost (1.49.0)
  • rdkit (2014.03.1)
  • tbb (4.2)

  You can build the individual dependencies yourself and place them in the deps/ folder in the repository root. For each dependency, there should be a folder of the same name under deps/ (for example, the path to the tbb files would be deps/tbb/). The cmake build script will automatically identify and prioritize dependencies in this directory.

  You can also install the libraries on your system using a package manager or other means. In that case, cmake will automatically try to find them on your system and link them during the build. Please, note that the build system is configured so that only static libraries of boost and rdkit are recognized. If you wish to link dynamically, you will need to modify the CMakeLists.txt file.

  If you are building on a 64-bit Linux machine, you can download the Molpher Dependency Bundle. This bundle contains pre-built dependencies for this platform and should work out of the box on Debian-based systems. You just need to extract the contents of the downloaded archive into the deps/ directory in the repository root.

1.2.2. Building the Library¶

When the above requirements are met, you can start building. First, you need to initialize the cmake project from a build directory:

mkdir ${REPOSITORY_ROOT}/cmake_dir/ # create a subdirectory in the root of the repository
cd ${REPOSITORY_ROOT}/cmake_dir/
cmake .. # initialize the project

Cmake checks the dependencies and generates the main makefile that has three important targets:

1. molpher – This is the main target. It builds the C++ source code of the library and creates all necessary binary files. All targets mentioned below depend on this target.

2. molpher_install – This target will install the library in the given location.

   By default, this location is the dist/ folder in the repository root. This can be changed when the cmake project is initialized by setting CMAKE_INSTALL_PREFIX. Also by default, the TBB library is installed along with the molpher-lib files, because it is also a runtime dependency. If you do not want this behaviour you can instruct cmake to omit the installation of TBB with the -DINSTALL_TBB=OFF option.

3. molpher_build_SWIG_Python – This will initialize the Python package along with the C++ extensions using the generated SWIG wrapper code.

   By default, the Python distribution under python is used. You can specify a different executable by specifying the path with -DPYTHON_EXECUTABLE when you run cmake.

   If you want to update the SWIG wrapping code before this target is run, you can instruct cmake to do so with the -DRUN_SWIG=ON option.

   When this target finishes, all required files should be in place and you should be able to import the molpher Python package located under src/python/. See the section below on how to install the package using pip.

   Warning

   As of yet, this target requires the molpher_install target above to install in the default location.

The build process of a given configuration is initialized from the cmake project directory as:

make $CONFIG_NAME # CONFIG_NAME is the name of one of the configurations

1.2.3. Building the Python Extensions and Conda Packages¶

If you built the library and initialized the Python package (the molpher_build_SWIG_Python target), you can now simply install it with pip:

pip install .

This will compile the Python extension and install the Python package to the currently active Python environment.

If you want to build the conda packages, you can a python script located in the conda/ subdirectory of the repository root:

python build_conda.py

You can install the built packages by running:

conda install --use-local molpher-lib

1.2.4. Building the Documentation¶

This documentation is generated using the build_docs.sh script under the doc/ directory. However, in order to successfully build the documentation you will need a few packages in your Python environment:

alabaster==0.7.7
Babel==2.3.3
breathe==4.2.0
docutils==0.12
imagesize==0.7.0
Jinja2==2.8
MarkupSafe==0.23
Pygments==2.1.3
pytz==2016.3
six==1.10.0
snowballstemmer==1.2.1
Sphinx==1.4.1
sphinx-rtd-theme==0.1.9

You can easily install all these packages with pip:

cd ${REPOSITORY_ROOT}/doc/
pip install -r requirements.txt

Also, make sure you initialized the Python package (built the molpher_build_SWIG_Python target as described above) prior to generating the documentation so that Sphinx can successfully import the molpher package.

To update the GitHub pages with the current version of the documentation, you can simply run the build_docs.sh with the `--upload` option:

build_docs.sh --upload