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 to be able to build the software. 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 3.0.8 at the moment).

  Only required if you made changes to the interface (header files under include/) and need to compile the code using the Debug_SWIG configuration. SWIG is invoked by make upon build with the swig3.0 command so make sure it resides somewhere on your PATH.

• setuptools and pip – If you want to use pip or easy_install to install the Python package, you will need this to be included in your Python distribution.

• 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’ 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/).

  Alternatively, you can download the Molpher Dependency Bundle and extract the contents to the deps/ directory. This bundle contains pre-built dependencies for the Linux platform and should work out of the box on Debian-based systems.

1.2.2. Building the Library¶

When the above requirements are met, you can start building. There are three configuration options:

1. Debug – Builds the library with debugging symbols, but without updating the SWIG wrapping code.

   If you did not make any changes to the header files under include/, and do not require changes to the wrapping code, you can use this option.

2. Debug_SWIG – This builds the library and updates the SWIG wrapping code.

   Use it if you made changes to the header files under include/ or want to update the SWIG wrappers.

3. Release_Linux_amd64 – This builds the library for general use.

   Binaries produced with this configuration are intended for distribution.

You run the build process with:

make CONF=$CONFIG_NAME # CONFIG_NAME is the name of one of the configurations above

This will compile the shared object file and put it in the dist/lib/ directory along with the required tbb libraries that are dynamically linked during runtime.

1.2.3. Building the Python Wrappers and the Conda Packages¶

The above procedure only builds the library itself. If you want to compile the Python bindings, you can do so by invoking:

python setup.py build_ext

in the repository root.

You can also install the Python package with, for example:

pip install .

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

Note

The extension is linked against the compiled library in the lib/ directory generated previously by make.

If you want to build the conda packages as well, you can use the following python script in 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¶

The library has an extensive documentation that is generated using the build_docs.sh script under the doc/ directory. 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 the packages with pip:

pip install -r requirements.txt

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