Installation¶

Conda Installation (recommended)¶

There are conda distributions available for cis_interface from conda-forge. You can install cis_interface from conda-forge by calling:

$ conda install -c conda-forge cis_interface

from your terminal prompt (or Anaconda prompt on Windows). This will install cis_interface and all of its dependencies in your active conda environment from the conda-forge channel.

Manual Installation¶

If you do not want to use conda, cis_interface can also be installed from either PyPI using pip:

$ pip install cis_interface

or by cloning the Git repository on Github:

$ git clone --recurse-submodules https://github.com/cropsinsilico/cis_interface.git

and then building the distribution.:

$ cd cis_interface
$ python setup.py install

If the --recurse-submodules option was not included when cloning the repo, you will need to run the following from within the repository before calling python setup.py install to ensure that rapidjson is cloned as a submodule:

$ git submodule init
$ git submodule update

If you do not have admin privileges on the target machine, --user can be added to the end of either the pip or setup.py installation commands. When using the --user, you may need to add the directory containing the entry point scripts to your PATH environment variable in order to use cis_interface command line tools (e.g. cisrun) without specifying their full path. Usually, this directory can be found using the following Python commands:

>>> import os
>>> from distutils.sysconfig import get_python_lib
>>> os.path.realpath(os.path.join(get_python_lib(), '../../../bin/'))

The displayed path can then be added either on the command link or in a startup script (e.g. .bashrc or .bash_profile), using one of the following:

$ export PATH=$PATH:<scripts_dir>  # (linux/osx, bash)
$ setenv PATH $PATH:<scripts_dir>  # (linux/osx, tcsh)
$ set PATH "%PATH%:<scripts_dir>   # (windows)

These commands will only add the directory to your path for the current session. For the change to be permanent on Linux/MacOS, the appropriate command from above can be added to your .bashrc or .bash_profile. On Windows (>=7), the following command will permanently modify your path:

$ setx PATH "%PATH%:<scripts_dir>

The changes will take affect the next time you open the terminal.

User Defined rapidjson¶

If you would like to use an existing installation of the rapidjson header-only library, you can pass the flag --rapidjson-include-dir=<user_defined_dir> to either the pip or setup.py installation commands from above with the location of the existing rapidjson include directory.

Additional Steps on Windows¶

As local communication on Windows is handled by ZeroMQ, running models written in C or C++ will require installing the ZeroMQ libraries for C and C++. If you install cis_interface using conda, these will be installed automatically as depencies. If you are not using conda, you will need to install them yourself.

Instructions for installing the ZeroMQ C and C++ libraries can be found here At install, cis_interface will attempt to search for those libraries. To speed up the search you can (temporarily) add the directories containing the libraries to your PATH environment variable prior to running one of the above install commands. If cis_interface complains that it cannot find these libraries, you can manually set them in your .cis_interface.cfg file (See Configuration Options). If you install these libraries after installing cis_interface you can re-configure cis_interface and have it search for the libraries again by calling cisconfig from the command line.

Additional Steps for Matlab Models¶

To run Matlab models, you will also need to install the Matlab engine for Python. This requires that you have an existing Matlab installation and license. cis_interface will attempt to install the Matlab engine for Python at install, but should it fail or if you want to use a non-default version of Matlab, you can also do it manually.

Instructions for installing the Matlab engine as a python package can be found on the Mathworks website. Once you have installed the Matlab engine as a python package, you can re-configure cis_interface by calling cisconfig. from the comamnd line.

Additional Steps for RabbitMQ Message Passing¶

RabbitMQ connections allow messages to be passed between models when the models are not running on the same machine. To use these connections (those with the prefix ‘RMQ’), the framework must have access to a RabbitMQ server. If you have access to an existing RabbitMQ server, the information for that server can either be provided to the RabbitMQ connection driver (See cis_interface.drivers.RMQDriver.RMQDriver) or added to the cis_interface config file (See Configuration Options for information on setting config options).

Starting a local RabbitMQ Server is also relatively easy. Details on downloading, installing, and starting a RabbitMQ server can be found here. The default values for RabbitMQ related properties in the config file are set to the defaults for starting a RabbitMQ server.