Installation

For the installation and usage of the framework Python 3.6 or higher is needed. We highly encourage the use of a virtual environment or a conda environment:

# virtual environment 
~/test$ python3 -m venv SimPhoNy
~/test$ source SimPhoNy/bin/activate
(SimPhoNy) ~/test$ 
# conda
~/test$ conda create -n <env name>
~/test$ conda activate <env name>

OSP-core installation

First, the repository must be cloned:

git clone https://github.com/simphony/osp-core.git
cd osp-core

The installation is based on setuptools:

# build and install (recommended)
pip install .

# alternative
python3 setup.py install

or:

# build for in-place development (recommended)
pip install -e .

# alternative
python3 setup.py develop

After installing OSP-core, you can install your ontology namespaces. We provide the tool pico (pico installs cuds ontologies) for that purpose.

pico install <path/to/ontology.yml>

# If you have issues using pico directly, you can use
python -m osp.core.pico install <path/to/ontology.yml>

Wrapper installation

The installation of a wrapper is similar. First, the repository is cloned:

git clone https://github.com/simphony/<some-wrapper>.git
cd some-wrapper

Local wrapper installation

With OSP-core installed, if the wrapper has its own ontology, it must be installed:

pico install <path/to/ontology.yml>

For the wrappers that require the installation of a backend, a install_engine.sh script is provided. It will automatically call install_engine_requirements.sh, where the engine specific requirements are installed.

./install_engine.sh

Now the wrapper can be installed:

python3 setup.py install

Wrapper Docker image

Some wrappers also provided a Dockerfile for an automatic installation in a container. Simply run the docker_install.sh script. There is no need to install OSP-core either.

./docker_install.sh