.. image:: https://github.com/matthiaskoenig/sbmlutils/raw/develop/docs_builder/images/sbmlutils-logo-60.png
:align: left
:alt: sbmlutils logo
sbmlutils: python utilities for SBML
====================================
.. image:: https://github.com/matthiaskoenig/sbmlutils/workflows/CI-CD/badge.svg
:target: https://github.com/matthiaskoenig/sbmlutils/workflows/CI-CD
:alt: GitHub Actions CI/CD Status
.. image:: https://img.shields.io/pypi/v/sbmlutils.svg
:target: https://pypi.org/project/sbmlutils/
:alt: Current PyPI Version
.. image:: https://img.shields.io/pypi/pyversions/sbmlutils.svg
:target: https://pypi.org/project/sbmlutils/
:alt: Supported Python Versions
.. image:: https://img.shields.io/pypi/l/sbmlutils.svg
:target: http://opensource.org/licenses/LGPL-3.0
:alt: GNU Lesser General Public License 3
.. image:: https://codecov.io/gh/matthiaskoenig/sbmlutils/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/matthiaskoenig/sbmlutils
:alt: Codecov
.. image:: https://readthedocs.org/projects/sbmlutils/badge/?version=latest
:target: https://sbmlutils.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://zenodo.org/badge/55952847.svg
:target: https://zenodo.org/badge/latestdoi/55952847
:alt: Zenodo DOI
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/ambv/black
:alt: Black
.. image:: http://www.mypy-lang.org/static/mypy_badge.svg
:target: http://mypy-lang.org/
:alt: mypy
sbmlutils is a collection of python utilities for working with
`SBML <http://www.sbml.org>`__ models implemented on top of
`libsbml <http://sbml.org/Software/libSBML>`__ and other libraries
with source code available from `https://github.com/matthiaskoenig/sbmlutils <https://github.com/matthiaskoenig/sbmlutils>`__.
Features include among others
- helper functions for model creation, manipulation, and annotation
- HTML reports of SBML models `https://sbml4humans.de <https://sbml4humans.de>`__.
- file converters (XPP)
The documentation is available on `https://sbmlutils.readthedocs.io <https://sbmlutils.readthedocs.io>`__.
If you have any questions or issues please `open an issue <https://github.com/matthiaskoenig/sbmlutils/issues>`__.
.. image:: docs/presentations/reproducibility_center_2021/screenshot.png
:target: https://youtu.be/SxIq8qeXxD0?t=1261
:alt: sbmlutils introduction
:height: 200px
How to cite
===========
.. image:: https://zenodo.org/badge/55952847.svg
:target: https://zenodo.org/badge/latestdoi/55952847
:alt: Zenodo DOI
Contributing
============
Contributions are always welcome! Please read the `contributing guidelines
<https://github.com/matthiaskoenig/sbmlutils/blob/develop/.github/CONTRIBUTING.rst>`__ to
get started.
License
=======
* Source Code: `LGPLv3 <http://opensource.org/licenses/LGPL-3.0>`__
* Documentation: `CC BY-SA 4.0 <http://creativecommons.org/licenses/by-sa/4.0/>`__
The sbmlutils source is released under both the GPL and LGPL licenses version 2 or
later. You may choose which license you choose to use the software under.
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License or the GNU Lesser General Public
License as published by the Free Software Foundation, either version 2 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
Funding
=======
Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054)
and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151
"`QuaLiPerF <https://qualiperf.de>`__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection -
A Systems Medicine Approach)" by grant number 436883643 and by grant number
465194077 (Priority Programme SPP 2311, Subproject SimLivA).
SBML4Humans was funded as part of `Google Summer of Code 2021 <https://summerofcode.withgoogle.com/>`__.
Matthias König has received funding from the EOSCsecretariat.eu which has received funding
from the European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.
Installation
============
`sbmlutils` is available from `pypi <https://pypi.python.org/pypi/sbmlutils>`__ and
can be installed via::
pip install sbmlutils
Requirements
------------
`tkinter` is required which can be installed on linux via::
apt-get install python-tk
apt-get install python3-tk
Please see the respective installation instructions for your operating system.
Develop version
---------------
The latest develop version can be installed via::
pip install git+https://github.com/matthiaskoenig/sbmlutils.git@develop
Or via cloning the repository and installing via::
git clone https://github.com/matthiaskoenig/sbmlutils.git
cd sbmlutils
pip install -e .
To install for development use::
pip install -e .[development]
© 2017-2023 Matthias König
Raw data
{
"_id": null,
"home_page": "https://github.com/matthiaskoenig/sbmlutils",
"name": "sbmlutils",
"maintainer": "Matthias Koenig",
"docs_url": null,
"requires_python": ">=3.9",
"maintainer_email": "konigmatt@googlemail.com",
"keywords": "modeling,standardization,SBML",
"author": "Matthias Koenig",
"author_email": "konigmatt@googlemail.com",
"download_url": "https://files.pythonhosted.org/packages/b9/c3/f3b50e770a35c655088179e40d48b271e0d1cc79e18d91f9b0515a263461/sbmlutils-0.8.7.tar.gz",
"platform": null,
"description": ".. image:: https://github.com/matthiaskoenig/sbmlutils/raw/develop/docs_builder/images/sbmlutils-logo-60.png\n :align: left\n :alt: sbmlutils logo\n\nsbmlutils: python utilities for SBML\n====================================\n\n.. image:: https://github.com/matthiaskoenig/sbmlutils/workflows/CI-CD/badge.svg\n :target: https://github.com/matthiaskoenig/sbmlutils/workflows/CI-CD\n :alt: GitHub Actions CI/CD Status\n\n.. image:: https://img.shields.io/pypi/v/sbmlutils.svg\n :target: https://pypi.org/project/sbmlutils/\n :alt: Current PyPI Version\n\n.. image:: https://img.shields.io/pypi/pyversions/sbmlutils.svg\n :target: https://pypi.org/project/sbmlutils/\n :alt: Supported Python Versions\n\n.. image:: https://img.shields.io/pypi/l/sbmlutils.svg\n :target: http://opensource.org/licenses/LGPL-3.0\n :alt: GNU Lesser General Public License 3\n\n.. image:: https://codecov.io/gh/matthiaskoenig/sbmlutils/branch/develop/graph/badge.svg\n :target: https://codecov.io/gh/matthiaskoenig/sbmlutils\n :alt: Codecov\n\n.. image:: https://readthedocs.org/projects/sbmlutils/badge/?version=latest\n :target: https://sbmlutils.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://zenodo.org/badge/55952847.svg\n :target: https://zenodo.org/badge/latestdoi/55952847\n :alt: Zenodo DOI\n\n.. image:: https://img.shields.io/badge/code%20style-black-000000.svg\n :target: https://github.com/ambv/black\n :alt: Black\n\n.. image:: http://www.mypy-lang.org/static/mypy_badge.svg\n :target: http://mypy-lang.org/\n :alt: mypy\n\nsbmlutils is a collection of python utilities for working with\n`SBML <http://www.sbml.org>`__ models implemented on top of\n`libsbml <http://sbml.org/Software/libSBML>`__ and other libraries\nwith source code available from `https://github.com/matthiaskoenig/sbmlutils <https://github.com/matthiaskoenig/sbmlutils>`__.\n\nFeatures include among others\n\n- helper functions for model creation, manipulation, and annotation\n- HTML reports of SBML models `https://sbml4humans.de <https://sbml4humans.de>`__.\n- file converters (XPP)\n\nThe documentation is available on `https://sbmlutils.readthedocs.io <https://sbmlutils.readthedocs.io>`__. \nIf you have any questions or issues please `open an issue <https://github.com/matthiaskoenig/sbmlutils/issues>`__.\n\n.. image:: docs/presentations/reproducibility_center_2021/screenshot.png\n :target: https://youtu.be/SxIq8qeXxD0?t=1261\n :alt: sbmlutils introduction\n :height: 200px\n\nHow to cite\n===========\n.. image:: https://zenodo.org/badge/55952847.svg\n :target: https://zenodo.org/badge/latestdoi/55952847\n :alt: Zenodo DOI\n\nContributing\n============\n\nContributions are always welcome! Please read the `contributing guidelines\n<https://github.com/matthiaskoenig/sbmlutils/blob/develop/.github/CONTRIBUTING.rst>`__ to\nget started.\n\nLicense\n=======\n\n* Source Code: `LGPLv3 <http://opensource.org/licenses/LGPL-3.0>`__\n* Documentation: `CC BY-SA 4.0 <http://creativecommons.org/licenses/by-sa/4.0/>`__\n\nThe sbmlutils source is released under both the GPL and LGPL licenses version 2 or\nlater. You may choose which license you choose to use the software under.\n\nThis program is free software: you can redistribute it and/or modify it under\nthe terms of the GNU General Public License or the GNU Lesser General Public\nLicense as published by the Free Software Foundation, either version 2 of the\nLicense, or (at your option) any later version.\n\nThis program is distributed in the hope that it will be useful, but WITHOUT ANY\nWARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\nPARTICULAR PURPOSE. See the GNU General Public License for more details.\n\nFunding\n=======\nMatthias K\u00f6nig is supported by the Federal Ministry of Education and Research (BMBF, Germany)\nwithin the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054) \nand by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 \n\"`QuaLiPerF <https://qualiperf.de>`__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection - \nA Systems Medicine Approach)\" by grant number 436883643 and by grant number \n465194077 (Priority Programme SPP 2311, Subproject SimLivA).\nSBML4Humans was funded as part of `Google Summer of Code 2021 <https://summerofcode.withgoogle.com/>`__.\nMatthias K\u00f6nig has received funding from the EOSCsecretariat.eu which has received funding \nfrom the European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.\n\nInstallation\n============\n`sbmlutils` is available from `pypi <https://pypi.python.org/pypi/sbmlutils>`__ and \ncan be installed via:: \n\n pip install sbmlutils\n\nRequirements\n------------\n`tkinter` is required which can be installed on linux via::\n\n apt-get install python-tk\n apt-get install python3-tk\n\nPlease see the respective installation instructions for your operating system.\n\nDevelop version\n---------------\nThe latest develop version can be installed via::\n\n pip install git+https://github.com/matthiaskoenig/sbmlutils.git@develop\n\nOr via cloning the repository and installing via::\n\n git clone https://github.com/matthiaskoenig/sbmlutils.git\n cd sbmlutils\n pip install -e .\n\nTo install for development use::\n\n pip install -e .[development]\n\n\u00a9 2017-2023 Matthias K\u00f6nig\n",
"bugtrack_url": null,
"license": "LGPL-3.0",
"summary": "sbmlutils are utilities for working with SBML.",
"version": "0.8.7",
"project_urls": {
"Bug Tracker": "https://github.com/matthiaskoenig/sbmlutils/issues",
"Documentation": "https://sbmlutils.readthedocs.io",
"Download": "https://pypi.org/project/sbmlutils",
"Homepage": "https://github.com/matthiaskoenig/sbmlutils",
"Source Code": "https://github.com/matthiaskoenig/sbmlutils"
},
"split_keywords": [
"modeling",
"standardization",
"sbml"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "f52d2baecd0da7f5bf8f110e6d578f990fa974dbb09b8c972f4894304e763d56",
"md5": "89c95a8502eea8fd18dc003b35aa4df8",
"sha256": "41c8c5d54eda4b592862f8ed7a9c8555e9230307f205f9ba44ffe23aeb615972"
},
"downloads": -1,
"filename": "sbmlutils-0.8.7-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "89c95a8502eea8fd18dc003b35aa4df8",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": ">=3.9",
"size": 34433549,
"upload_time": "2023-09-28T11:12:00",
"upload_time_iso_8601": "2023-09-28T11:12:00.339460Z",
"url": "https://files.pythonhosted.org/packages/f5/2d/2baecd0da7f5bf8f110e6d578f990fa974dbb09b8c972f4894304e763d56/sbmlutils-0.8.7-py2.py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "b9c3f3b50e770a35c655088179e40d48b271e0d1cc79e18d91f9b0515a263461",
"md5": "439b558b066a10976ea8833c6236eaef",
"sha256": "77ef0d1b0ab78252301f179aacb94de4ea7cbae11867ea7101a953631f3e0cf8"
},
"downloads": -1,
"filename": "sbmlutils-0.8.7.tar.gz",
"has_sig": false,
"md5_digest": "439b558b066a10976ea8833c6236eaef",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.9",
"size": 25991813,
"upload_time": "2023-09-28T11:12:07",
"upload_time_iso_8601": "2023-09-28T11:12:07.196415Z",
"url": "https://files.pythonhosted.org/packages/b9/c3/f3b50e770a35c655088179e40d48b271e0d1cc79e18d91f9b0515a263461/sbmlutils-0.8.7.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-09-28 11:12:07",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "matthiaskoenig",
"github_project": "sbmlutils",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"tox": true,
"lcname": "sbmlutils"
}
JSON
