 [](https://basico.readthedocs.io/en/latest/?badge=latest) [](https://sonarcloud.io/dashboard?id=copasi_basico) [](https://mybinder.org/v2/gh/copasi/basico.git/HEAD?filepath=docs/notebooks/index.ipynb) [](https://zenodo.org/badge/latestdoi/148472105) [](https://codecov.io/gh/copasi/basico) [](https://doi.org/10.21105/joss.05553)
## 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](https://github.com/copasi/basico/issues) 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](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.
Raw data
{
"_id": null,
"home_page": "https://github.com/copasi/basico",
"name": "copasi-basico",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": "copasi sbml systems biology",
"author": "COPASI Team",
"author_email": "developers@copasi.org",
"download_url": "https://files.pythonhosted.org/packages/63/fd/9c82ef1a901997d6b21cd430c8ae21f599700804942278be938abd6a8174/copasi_basico-0.82.tar.gz",
"platform": "Windows",
"description": " [](https://basico.readthedocs.io/en/latest/?badge=latest) [](https://sonarcloud.io/dashboard?id=copasi_basico) [](https://mybinder.org/v2/gh/copasi/basico.git/HEAD?filepath=docs/notebooks/index.ipynb) [](https://zenodo.org/badge/latestdoi/148472105) [](https://codecov.io/gh/copasi/basico) [](https://doi.org/10.21105/joss.05553)\n\n\n## BasiCO\nThis project hosts a simplified python interface to COPASI. While all functionality from COPASI\nis exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of\nthat, to hide most of the complexity away when calling COPASI functions. \n\n \n\n### Installation\nThe package works with python 3.7+, provided the following packages are installed: \n\n* python-copasi\n* pandas\n* numpy\n* matplotlib\n* PyYAML\n\nthat are freely available on pypi, they will be automatically installed when installing via setup.py.\n\nOnce done, just have the `basico` directory \nin the `PYTHONPATH` or `sys.path`.\n\nOr you could directly install everything you need right from pypi \n\n pip install copasi-basico\n\nfrom this git repo:\n\n pip install git+https://github.com/copasi/basico.git\n\n### Usage\n\nThe following modules are available: \n\n* `model_io`: functionality, for creating / loading / saving models.\n* `model_info`: functionality to getting / setting model elements from pandas dataframes \n* `task_timecourse`: a wrapper for running time course simulations\n* `task_parameter_estimation`: a wrapper for parameter estimation\n* `task_optimization`: a wrapper for computing optimizations with arbitrary objective functions\n* `task_steadystate`: a wrapper for computing steady states\n* `task_scan`: a wrapper for parameter scans / repeats\n* `task_sensitivities`: a wrapper for computing sensitivities\n* `compartment_array_tools`: utility for plotting and the like\n\nDocumentation is continually updated at: <https://basico.readthedocs.org/>. \n\nPlease use the [issue tracker](https://github.com/copasi/basico/issues) for bug reports and feature requests.\n\n### Run the tests\n\nbasico comes with a number of unit tests based on pytest. To run them, change to the \nroot directory of this project and run: \n\n python3 -m pytest\n\nthat will ensure that `basico` is in the python path, and the test run as expected. Some \ntests require more data, that is not included in the repository, such as tests for PEtab \nand petab select, for those, specify the environment variables to the directories where\nthe files are for example: \n\n PETAB_BENCHMARK_MODELS=/path/to/petab/benchmark/models\n PETAB_SELECT_MODELS=/path/to/petab/select/models\n\nfor example: \n\n PETAB_BENCHMARK_MODELS=../Benchmark-Models-PEtab/Benchmark-Models PETAB_SELECT_MODELS=../petab_select/test_cases python3 -m pytest\n\n### Acknowledgements\nThis project has been possible thanks to the BMBF funded de.NBI initiative (031L0104A):\n\n\n\n### License\n\nThe packages available on this page are provided under the \n[Artistic License 2.0](http://copasi.org/Download/License/), \nwhich is an [OSI](http://www.opensource.org/) approved license. This license \nallows non-commercial and commercial use free of charge.\n \n",
"bugtrack_url": null,
"license": "Artistic-2.0",
"summary": "Simplified COPASI interface for python",
"version": "0.82",
"project_urls": {
"Github": "https://github.com/copasi/basico",
"Homepage": "https://github.com/copasi/basico",
"Issues": "https://github.com/copasi/basico/issues",
"Try it online": "https://colab.research.google.com/github/copasi/basico/blob/master/docs/notebooks/index_colab.ipynb"
},
"split_keywords": [
"copasi",
"sbml",
"systems",
"biology"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "24abde87c8aa09b427a2e0b538ed73a87ce17c57416050f6e322f5c0425bb2a5",
"md5": "602e111cf2b729f9ae818cbd78c07ca8",
"sha256": "11069d011b0f8a342644069d827533d8aadf3ca03a838b9fd83cb9b3fc765e01"
},
"downloads": -1,
"filename": "copasi_basico-0.82-py3-none-any.whl",
"has_sig": false,
"md5_digest": "602e111cf2b729f9ae818cbd78c07ca8",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 264945,
"upload_time": "2024-12-20T09:43:47",
"upload_time_iso_8601": "2024-12-20T09:43:47.693637Z",
"url": "https://files.pythonhosted.org/packages/24/ab/de87c8aa09b427a2e0b538ed73a87ce17c57416050f6e322f5c0425bb2a5/copasi_basico-0.82-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "63fd9c82ef1a901997d6b21cd430c8ae21f599700804942278be938abd6a8174",
"md5": "7f9709109d4e07098b0cb8232ff274c6",
"sha256": "6f5cc677f38a7cadba0478e6c5ba425de42c078751d57c61d915dda5e154c00e"
},
"downloads": -1,
"filename": "copasi_basico-0.82.tar.gz",
"has_sig": false,
"md5_digest": "7f9709109d4e07098b0cb8232ff274c6",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 288509,
"upload_time": "2024-12-20T09:43:50",
"upload_time_iso_8601": "2024-12-20T09:43:50.482966Z",
"url": "https://files.pythonhosted.org/packages/63/fd/9c82ef1a901997d6b21cd430c8ae21f599700804942278be938abd6a8174/copasi_basico-0.82.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-12-20 09:43:50",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "copasi",
"github_project": "basico",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [
{
"name": "python-copasi",
"specs": []
},
{
"name": "pandas",
"specs": []
},
{
"name": "scipy",
"specs": []
},
{
"name": "numpy",
"specs": []
},
{
"name": "matplotlib",
"specs": []
},
{
"name": "PyYAML",
"specs": []
},
{
"name": "lxml",
"specs": []
}
],
"lcname": "copasi-basico"
}
JSON
