Metadata-Version: 2.1
Name: biosimulators_utils
Version: 0.1.69
Summary: Command-line program and library for reading, writing, validating and executing modeling projects (COMBINE/OMEX archives with SED-ML files).
Home-page: https://github.com/biosimulators/Biosimulators_utils
Author: Center for Reproducible Biomedical Modeling
Author-email: info@biosimulators.org
License: MIT
Download-URL: https://github.com/biosimulators/Biosimulators_utils
Description: |Latest release| |PyPI| |CI status| |Test coverage|
        
        BioSimulators utils
        ===================
        
        Command-line application and high-level utilities for reading, writing,
        validating, and executing `COMBINE/OMEX
        format <https://combinearchive.org/>`__ files that contain descriptions
        of simulations in `Simulation Experiment Description Markup
        Language <https://sed-ml.org/>`__ (SED-ML) format with models in formats
        such as the `BioNetGen Language <https://bionetgen.org>`__ (BNGL) and
        the `Systems Biology Markup Language <http://sbml.org>`__ (SBML).
        
        Installation
        ------------
        
        Requirements
        ~~~~~~~~~~~~
        
        -  Python >= 3.7
        -  pip
        
        Optional requirements
        ~~~~~~~~~~~~~~~~~~~~~
        
        -  Docker: required to execute containerized simulation tools
        
        Install latest release from PyPI
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        ::
        
           pip install biosimulators-utils
        
        Install latest revision from GitHub
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        ::
        
           pip install git+https://github.com/biosimulators/Biosimulators_utils.git#biosimulators_utils
        
        Installation optional features
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        To use BioSimulators utils to validate NeuroML models, install
        BioSimulators utils with the ``neuroml`` option:
        
        ::
        
           pip install biosimulators-utils[neuroml]
        
        To use BioSimulators utils to validate SBML models, install
        BioSimulators utils with the ``sbml`` option:
        
        ::
        
           pip install biosimulators-utils[sbml]
        
        To use BioSimulators utils to execute containerized simulation tools,
        install BioSimulators utils with the ``containers`` option:
        
        ::
        
           pip install biosimulators-utils[containers]
        
        To use BioSimulators utils to log the standard output and error produced
        by simulation tools, install BioSimulators utils with the ``logging``
        option:
        
        ::
        
           pip install biosimulators-utils[logging]
        
        API documentation
        -----------------
        
        API documentation is available
        `here <https://biosimulators.github.io/Biosimulators_utils/>`__.
        
        License
        -------
        
        This package is released under the `MIT license <LICENSE>`__.
        
        Development team
        ----------------
        
        This package was developed by the `Karr Lab <https://www.karrlab.org>`__
        at the Icahn School of Medicine at Mount Sinai in New York and the
        `Center for Reproducible Biomedical
        Modeling <http://reproduciblebiomodels.org>`__.
        
        Contributing to BioSimulators utils
        -----------------------------------
        
        We enthusiastically welcome contributions to BioSimulators utils! Please
        see the `guide to contributing <CONTRIBUTING.md>`__ and the `developer's
        code of conduct <CODE_OF_CONDUCT.md>`__.
        
        Acknowledgements
        ----------------
        
        This work was supported by National Institutes of Health award
        P41EB023912.
        
        Questions and comments
        ----------------------
        
        Please contact the `BioSimulators
        Team <mailto:info@biosimulators.org>`__ with any questions or comments.
        
        .. |Latest release| image:: https://img.shields.io/github/v/release/biosimulators/Biosimulators_utils
           :target: https://github.com/biosimulators/Biosimulators_utils/releases
        .. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators-utils
           :target: https://pypi.org/project/biosimulators-utils/
        .. |CI status| image:: https://github.com/biosimulators/Biosimulators_utils/workflows/Continuous%20integration/badge.svg
           :target: https://github.com/biosimulators/Biosimulators_utils/actions?query=workflow%3A%22Continuous+integration%22
        .. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_utils/branch/dev/graph/badge.svg
           :target: https://codecov.io/gh/biosimulators/Biosimulators_utils
        
Keywords: systems biology modeling simulation
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Provides-Extra: neuroml
Provides-Extra: sbml
Provides-Extra: containers
Provides-Extra: logging
Provides-Extra: tests
Provides-Extra: docs
Provides-Extra: all
