Installation

In most cases, the easiest way to install mogp_emulator is via pip, which should install the library and all of its dependencies:

pip install mogp-emulator

You can also use pip to install directly from the github repository using

pip install git+https://github.com/alan-turing-institute/mogp-emulator

This will accomplish the same thing as the manual installation instructions below.

Manual Installation

To install the package manually, for instance to have access to a development version or to take part in active development of the package, the following instructions can be used to install the package.

Download

You can download the code as a zipped archive from the Github repository. This will download all files on the master branch, which can be unpacked and then used to install following the instructions below.

If you prefer to check out the Github repository, you can download the code using:

git clone https://github.com/alan-turing-institute/mogp-emulator/

This will clone the entire git history of the software and check out the master branch by default. The master branch is the most stable version of the code, but will not have all features as the code is under active development. The devel branch is the more actively developed branch, and all new features will be available here as they are completed. All code in the devel branch is well tested and documented to the point that results can be trusted, but may still have some minor bugs and issues. Any other branch is used to develop new features and should be considered untested and experimental. Please get in touch with one of the team members if you are unsure if a particular feature is available.

Requirements

The code requires Python 3.6 or later, and working Numpy, Scipy, and Patsy installations are required. You should be able to install these packages using pip if you do not have them already available on your system. From the base mogp_emulator directory, you can install all required packages using:

pip install -r requirements.txt

This will install the minimum requirements needed to use mogp_emulator. There are a few addditional packages that are not required but can be useful. Installation of the optional dependencies can be done via:

pip install -r requirements-optional.txt

Installation

Then to install the main code, run the following command:

python setup.py install

This will install the main code in the system Python installation. You may need adminstrative priveleges to install the software itself, depending on your system configuration. However, any updates to the code cloned through the github repository (particularly if you are using the devel branch, which is under more active development) will not be reflected in the system installation using this method. If you would like to always have the most active development version, install using:

python setup.py develop

This will insert symlinks to the repository files into the system Python installation so that files are updated whenever there are changes to the code files.

Documentation

The code documentation is available on readthedocs. A current build of the master and devel branches should always be available in HTML or PDF format.

To build the documentation yourself requires Sphinx, which can be installed using pip. This can also be done in the docs directory using pip install -r requirements.txt. To build the documentatation, change to the docs directory. There is a Makefile in the docs directory to facilitate building the documentation for you. To build the HTML version, enter the following into the shell from the docs directory:

make html

This will build the HTML version of the documentation. A standalone PDF version can be built, which requires a standard LaTeX installation, via:

make latexpdf

In both cases, the documentation files can be found in the corresponding directories in the docs/_build directory. Note that if these directories are not found on your system, you may need to create them in order for the build to finish correctly. A version of the documentation can also be found at the link above on Read the Docs.

Testing the Installation

Unit Tests

mogp_emulator includes a full set of unit tests. To run the test suite, you will need to install the development dependencies, which include pytest and pytest-cov to give coverage reports, which can be done in the main mogp_emulator directory via pip install -r requirements-dev.txt. The pytest-cov package is not required to run the test suite, but is useful if you are developing the code to determine test coverage.

The tests can be run from the base mogp_emulator directory or the mogp_emulator/tests directory by entering pytest, which will run all tests and print out the results to the console. In the mogp_emulator/tests directory, there is also a Makefile that will run the tests for you. You can simply enter make tests into the shell.