copasi-basico 0.86

Simplified COPASI interface for python

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.

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 for bug reports and feature requests.

Run the tests

basico comes with a number of unit tests based on pytest. To run them, change to the root directory of this project and run:

python3 -m pytest

that will ensure that basico is in the python path, and the test run as expected. Some tests require more data, that is not included in the repository, such as tests for PEtab and petab select, for those, specify the environment variables to the directories where the files are for example:

PETAB_BENCHMARK_MODELS=/path/to/petab/benchmark/models
PETAB_SELECT_MODELS=/path/to/petab/select/models

for example:

PETAB_BENCHMARK_MODELS=../Benchmark-Models-PEtab/Benchmark-Models PETAB_SELECT_MODELS=../petab_select/test_cases  python3 -m pytest

SSR support

The latest version of the project contains support for T.J. Sego's libSSR.SSRSimAPI to use this, install the [ssr] extra:

!pip install -e git+https://github.com/copasi/basico.git#egg=copasi-basico[ssr]

Acknowledgements

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

License

The packages available on this page are provided under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge.