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biosimulators-test-suite-0.1.9
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مشاهده بیشترتوضیحات
Tools for validating that biosimulation tools are consistent with the BioSimulators standards
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | biosimulators-test-suite-0.1.9 |
| نام | biosimulators-test-suite |
| نسخه کتابخانه | 0.1.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Center for Reproducible Biomedical Modeling |
| ایمیل نویسنده | info@biosimulators.org |
| آدرس صفحه اصلی | https://github.com/biosimulators/Biosimulators_test_suite |
| آدرس اینترنتی | https://pypi.org/project/biosimulators-test-suite/ |
| مجوز | MIT |
|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors|
BioSimulators test suite
========================
The BioSimulators test suite is a tool for validating that biosimulation
software tools implement the `BioSimulators conventions for
biosimulation
tools <https://docs.biosimulations.org/concepts/conventions/>`__.
The test suite is composed of two parts:
- `A collection of example modeling projects <examples>`__. Each
project is represented by a single `COMBINE/OMEX
archive <https://combinearchive.org/>`__ that contains one or more
simulation experiments described using the `Simulation Experiment
Description Markup Language (SED-ML) <https://sed-ml.org>`__ and one
or more models described using a format such as the `BioNetGen
Language (BNGL) <https://bionetgen.org>`__ or the `Systems Biology
Markup Language (SBML) <http://sbml.org>`__.
- Software for checking that biosimulation tools execute these projects
according to the BioSimulators conventions.
- Simulation tools support the `BioSimulators standard command-line
arguments <https://docs.biosimulations.org/concepts/conventions/simulator-interfaces/>`__.
- Simulation tools support the `BioSimulators conventions for Docker
images <https://docs.biosimulations.org/concepts/conventions/simulator-images/>`__.
- Simulation tools follow the `BioSimulators conventions for
executing simulations described by SED-ML files in COMBINE/OMEX
archives <https://docs.biosimulations.org/concepts/conventions/simulation-experiments/>`__.
- Simulation tools support the `BioSimulators conventions for the
outputs of SED-ML files in COMBINE/OMEX
archives <https://docs.biosimulations.org/concepts/conventions/simulation-run-reports/>`__.
Installation instructions, tutorial, and API documentation
----------------------------------------------------------
Installation instructions, tutorial, and API documentation are available
`here <https://docs.biosimulators.org/Biosimulators_test_suite/>`__.
License
-------
The software in this package is released under the `MIT
License <LICENSE>`__. The modeling projects in this package are released
under the `Creative Commons 1.0 Universal (CC0)
license <LICENSE-DATA>`__.
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, the
`https://health.uconn.edu/cell-analysis-modeling/ <https://health.uconn.edu/cell-analysis-modeling/>`__
at the University of Connecticut, and the `Center for Reproducible
Biomedical Modeling <http://reproduciblebiomodels.org>`__ with
assistance from the contributors listed `here <CONTRIBUTORS.md>`__.
Contributing to the test suite
------------------------------
We enthusiastically welcome contributions to the test suite! 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_test_suite
:target: https://github.com/biosimulators/Biosimulators_test_suite/releases
.. |PyPI| image:: https://img.shields.io/pypi/v/Biosimulators-test-suite
:target: https://pypi.org/project/Biosimulators-test-suite/
.. |CI status| image:: https://github.com/biosimulators/Biosimulators_test_suite/workflows/Continuous%20integration/badge.svg
:target: https://github.com/biosimulators/Biosimulators_test_suite/actions?query=workflow%3A%22Continuous+integration%22
.. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_test_suite/branch/dev/graph/badge.svg
:target: https://codecov.io/gh/biosimulators/Biosimulators_test_suite
.. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_test_suite/HEAD
:target: #contributors-
نیازمندی
| مقدار | نام |
|---|---|
| - | PyPDF2 |
| >=0.1.172 | biosimulators-utils[bngl,cellml,containers,lems,neuroml,sbml,smoldyn] |
| - | cement |
| - | docker |
| - | natsort |
| <1.23.0 | numpy |
| - | python-dateutil |
| - | pyyaml |
| - | simplejson |
| - | termcolor |
| - | biosimulators-utils[logging] |
| - | parameterized |
| - | biosimulators-utils[logging] |
| - | parameterized |
نحوه نصب
نصب پکیج whl biosimulators-test-suite-0.1.9:
pip install biosimulators-test-suite-0.1.9.whl
نصب پکیج tar.gz biosimulators-test-suite-0.1.9:
pip install biosimulators-test-suite-0.1.9.tar.gz