Metadata-Version: 2.1
Name: copasi-basico
Version: 0.48
Summary: Simplified COPASI interface for python
Home-page: https://github.com/copasi/basico
Author: COPASI Team
Author-email: developers@copasi.org
License: Artistic-2.0
Project-URL: Github, https://github.com/copasi/basico
Project-URL: Issues, https://github.com/copasi/basico/issues
Project-URL: Try it online, https://colab.research.google.com/github/copasi/basico/blob/master/docs/notebooks/index.ipynb
Keywords: copasi sbml systems biology
Platform: Windows
Platform: Linux
Platform: MacOS
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: Artistic License
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Education
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: C++
Classifier: Programming Language :: Python :: 3
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
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: python-copasi
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: PyYAML
Requires-Dist: scipy
Provides-Extra: petab
Requires-Dist: copasi-petab-importer ; extra == 'petab'
Requires-Dist: petab ; extra == 'petab'
Requires-Dist: petab-select ; extra == 'petab'

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## BasiCO
This project hosts a simplified python interface to COPASI. While all functionality from COPASI
is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of
that, to hide most of the complexity away when calling COPASI functions.   

![COPASI Logo](https://raw.githubusercontent.com/copasi/basico/master/./docs/_static/COPASI_Conly_176x176.png)  

### Installation
The package works with python 3.7+, provided the following packages are installed: 

* python-copasi
* pandas
* numpy
* matplotlib
* PyYAML

that are freely available on pypi, they will be automatically installed when installing via setup.py.

Once done, just have the `basico` directory 
in the `PYTHONPATH` or `sys.path`.

Or you could directly install everything you need right from pypi 

    pip install copasi-basico

from this git repo:

    pip install git+https://github.com/copasi/basico.git

### Usage

The following modules are available: 

* `model_io`: functionality, for creating / loading / saving models.
* `model_info`: functionality to getting / setting model elements from pandas dataframes  
* `task_timecourse`: a wrapper for running time course simulations
* `task_parameter_estimation`: a wrapper for parameter estimation
* `task_optimization`: a wrapper for computing optimizations with arbitrary objective functions
* `task_steadystate`: a wrapper for computing steady states
* `task_scan`: a wrapper for parameter scans / repeats
* `task_sensitivities`: a wrapper for computing sensitivities
* `compartment_array_tools`: utility for plotting and the like

Documentation is continually updated at: <https://basico.readthedocs.org/>. 

Please use the [issue tracker](https://github.com/copasi/basico/issues) for bug reports and feature requests.

### Acknowledgements
This project has been possible thanks to the BMBF funded de.NBI initiative (031L0104A):

![de.NBI logo](https://raw.githubusercontent.com/copasi/basico/master/./docs/_static/deNBI_logo.jpg)

### License

The packages available on this page are provided under the 
[Artistic License 2.0](http://copasi.org/Download/License/), 
which is an [OSI](http://www.opensource.org/) approved license. This license 
allows non-commercial and commercial use free of charge.
 
