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
python3 -m venv SimPhoNy
source SimPhoNy/bin/activate

# conda
conda create -n <env_name>
conda activate <env_name>

OSP-core is available on PyPI, so it can be installed using pip:

pip install osp-core

For an installation from source, see here.

After installing OSP-core, you can install your ontology namespaces. We provide the pico tool 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

Wrappers are currently not available on PyPI, so they must be installed from source. 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 usually 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:

pip install .

Wrapper Docker image

Some wrappers also provided a Dockerfile for an automatic installation in a container. The dockerfile should contain the information needed to run it inside.

Installing OSP-core from source

If you are a developer or an advanced user, you might be interested in installing OSP-core from source.

To do so, 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