copasi-basico 0.74

Description:

copasibasico 0.74

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

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.