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.