Metadata-Version: 2.1
Name: biosimulator-processes
Version: 0.0.3
Home-page: https://github.com/vivarium-collective/process-bigraph
Author: Ryan Spangler, Eran Agmon, Alex Patrie
Author-email: ryan.spangler@gmail.com, agmon.eran@gmail.com, alexanderpatrie@gmail.com
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: AUTHORS.md
Requires-Dist: bigraph-schema
Requires-Dist: process-bigraph
Requires-Dist: numpy
Requires-Dist: pytest>=6.2.5
Requires-Dist: tellurium
Requires-Dist: copasi-basico
Requires-Dist: cobra
Provides-Extra: smoldyn
Requires-Dist: smoldyn; extra == "smoldyn"
Requires-Dist: simulariumio; extra == "smoldyn"

# biosimulator-processes 


Core implementations of `process-bigraph.composite.Process()` aligning with BioSimulators simulator
tools.


## Getting Started (PyPI)

The easiest way to download this tool is via the Python Package Index. You may download
core-processes with: 

    pip install biosimulator-processes

We recommend using an environment/package manager [like Conda](https://conda.io/projects/conda/en/latest/index.html) to 
install the dependencies required for your use.

 Most of the direct UI content for this tooling will be in the form of a jupyter notebook.

### Using `biosimulator_processes.smoldyn_process.SmoldynProcess()`: 

#### PLEASE NOTE: 
Due to the multi-lingual nature of Smoldyn, which is primarily 
developed in C++, the installation process for utilizing 
the `SmoldynProcess` process implementation requires separate handling. This is particularly 
relevant for macOS and Windows users, where setting up the Python bindings can be more complex.

Please follow the detailed installation instructions provided below to ensure proper setup 
of Smoldyn for your system.

To download Smoldyn, please follow these steps:

1. Visit the [Smoldyn Download Page](https://www.smoldyn.org/download.html).
2. Choose the version appropriate for your operating system.
3. Follow the instructions or links provided on the page to complete the download.

For more detailed instructions and information, refer to the official Smoldyn documentation.


### Quick Start Example:
#### TODO: Add quickstart example of instance declarations.


## TODO: Add DatabaseEmitter to this README


