Metadata-Version: 2.1
Name: biosimulators-utils
Version: 0.1.87
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
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
License-File: LICENSE
Requires-Dist: appdirs
Requires-Dist: cement
Requires-Dist: evalidate
Requires-Dist: h5py
Requires-Dist: kisao (>=2.18)
Requires-Dist: lxml
Requires-Dist: matplotlib
Requires-Dist: mpmath
Requires-Dist: natsort
Requires-Dist: networkx
Requires-Dist: numpy
Requires-Dist: openpyxl
Requires-Dist: pandas
Requires-Dist: pronto (>=2.4)
Requires-Dist: pyomexmeta
Requires-Dist: python-dateutil
Requires-Dist: python-libcombine (>=0.2.9)
Requires-Dist: python-libsedml (>=2.0.16)
Requires-Dist: pyyaml
Requires-Dist: rdflib
Requires-Dist: requests
Requires-Dist: simplejson
Requires-Dist: termcolor
Requires-Dist: validators
Requires-Dist: yamldown
Provides-Extra: all
Requires-Dist: bionetgen (>=0.3.1) ; extra == 'all'
Requires-Dist: capturer ; extra == 'all'
Requires-Dist: docker (>=4.4) ; extra == 'all'
Requires-Dist: libcellml ; extra == 'all'
Requires-Dist: libneuroml ; extra == 'all'
Requires-Dist: pint ; extra == 'all'
Requires-Dist: pylems ; extra == 'all'
Requires-Dist: pyneuroml ; extra == 'all'
Requires-Dist: python-libsbml ; extra == 'all'
Requires-Dist: smoldyn (>=2.66) ; extra == 'all'
Provides-Extra: bngl
Requires-Dist: bionetgen (>=0.3.1) ; extra == 'bngl'
Provides-Extra: cellml
Requires-Dist: libcellml ; extra == 'cellml'
Provides-Extra: containers
Requires-Dist: docker (>=4.4) ; extra == 'containers'
Provides-Extra: docs
Provides-Extra: lems
Requires-Dist: pint ; extra == 'lems'
Requires-Dist: pylems ; extra == 'lems'
Requires-Dist: pyneuroml ; extra == 'lems'
Provides-Extra: logging
Requires-Dist: capturer ; extra == 'logging'
Provides-Extra: neuroml
Requires-Dist: libneuroml ; extra == 'neuroml'
Provides-Extra: sbml
Requires-Dist: python-libsbml ; extra == 'sbml'
Provides-Extra: smoldyn
Requires-Dist: smoldyn (>=2.66) ; extra == 'smoldyn'
Provides-Extra: tests
Requires-Dist: capturer ; extra == 'tests'

|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 BNGL models, install
BioSimulators utils with the ``bgnl`` option:

::

   pip install biosimulators-utils[bgnl]

To use BioSimulators utils to validate CellML models, install
BioSimulators utils with the ``cellml`` option:

::

   pip install biosimulators-utils[cellml]

To use BioSimulators utils to validate LEMS models, install
`Java <https://www.java.com/>`__ and then install BioSimulators utils
with the ``lems`` option:

::

   pip install biosimulators-utils[lems]

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 validate SBML models, install
BioSimulators utils with the ``smoldyn`` option:

::

   pip install biosimulators-utils[smoldyn]

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


