BASICO

BASICO: A simplified Python interface to COPASI - Published in JOSS (2023)

https://github.com/copasi/basico

Science Score: 100.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org, zenodo.org
✓
Committers with academic emails
1 of 4 committers (25.0%) from academic institutions
○
Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

copasi python

Scientific Fields

Engineering Computer Science - 40% confidence

Last synced: 4 months ago · JSON representation ·

Repository

A simplified python interface to COPASI.

Basic Info

Host: GitHub
Owner: copasi
License: artistic-2.0
Language: Python
Default Branch: master
Homepage: https://basico.readthedocs.io/
Size: 10.8 MB

Statistics

Stars: 22
Watchers: 7
Forks: 6
Open Issues: 9
Releases: 85

Topics

copasi python

Created over 7 years ago · Last pushed 5 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Zenodo

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

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:

bash !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):

de.NBI logo

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.

Owner

Name: COPASI
Login: copasi
Kind: organization

Website: http://www.copasi.org
Repositories: 22
Profile: https://github.com/copasi

JOSS Publication

BASICO: A simplified Python interface to COPASI

Published

October 15, 2023

DOI

10.21105/joss.05553

Volume 8, Issue 90, Page 5553

Authors

Frank T. Bergmann

BioQUANT/COS, Heidelberg University, Heidelberg, Germany

Editor

Marcos Vital

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Bergmann
  given-names: Frank T.
  orcid: "https://orcid.org/0000-0001-5553-4702"
doi: 10.5281/zenodo.8189386
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bergmann
    given-names: Frank T.
    orcid: "https://orcid.org/0000-0001-5553-4702"
  date-published: 2023-10-15
  doi: 10.21105/joss.05553
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5553
  title: "BASICO: A simplified Python interface to COPASI"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05553"
  volume: 8
title: "BASICO: A simplified Python interface to COPASI"

GitHub Events

Total

Create event: 7
Release event: 8
Issues event: 15
Watch event: 2
Delete event: 1
Issue comment event: 42
Push event: 32
Pull request event: 2
Fork event: 1

Last Year

Create event: 7
Release event: 8
Issues event: 15
Watch event: 2
Delete event: 1
Issue comment event: 42
Push event: 32
Pull request event: 2
Fork event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 548
Total Committers: 4
Avg Commits per committer: 137.0
Development Distribution Score (DDS): 0.024

Past Year

Commits: 60
Committers: 2
Avg Commits per committer: 30.0
Development Distribution Score (DDS): 0.017

Top Committers

Name	Email	Commits
Frank T. Bergmann	f**n@c**u	535
lilijap	l**p@g**m	11
yusufozgur	y**r@g**m	1
jonasfoe	j****e	1

Committer Domains (Top 20 + Academic)

caltech.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 64
Total pull requests: 5
Average time to close issues: 23 days
Average time to close pull requests: 3 months
Total issue authors: 21
Total pull request authors: 4
Average comments per issue: 3.25
Average comments per pull request: 1.2
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 10
Pull requests: 2
Average time to close issues: 2 months
Average time to close pull requests: 20 days
Issue authors: 7
Pull request authors: 1
Average comments per issue: 3.7
Average comments per pull request: 1.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

pmendes (11)
fbergmann (10)
Theo-BRN (7)
hasanbaig (5)
ayush9pandey (4)
TorkelE (4)
lilijap (4)
matthiaskoenig (3)
CodeByDrescher (3)
V0idLord (2)
DeepaMahm (2)
yusufozgur (1)
fabriciocravo (1)
Laniathean (1)
persalteas (1)

Pull Request Authors

yusufozgur (2)
thepritam (1)
jonasfoe (1)
sh15h4nk (1)

Top Labels

Issue Labels

bug (2) question (1) enhancement (1) documentation (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 3,860 last-month

Total dependent packages: 3
Total dependent repositories: 3
Total versions: 85
Total maintainers: 1

pypi.org: copasi-basico

Simplified COPASI interface for python

Homepage: https://github.com/copasi/basico
Documentation: https://copasi-basico.readthedocs.io/
License: Artistic-2.0
Latest release: 0.85
published 5 months ago

Versions: 85
Dependent Packages: 3
Dependent Repositories: 3
Downloads: 3,860 Last month

Rankings

Dependent packages count: 3.2%

Downloads: 5.8%

Dependent repos count: 9.0%

Average: 9.7%

Stargazers count: 15.2%

Forks count: 15.4%

Maintainers (1)

frankbergmann.myopenid.com

Last synced: 4 months ago

Dependencies

docs/requirements.txt pypi

cython *
ipykernel *
matplotlib *
nbsphinx *
numpy *
pandas *
pandoc *
pygments >=2.4.1
python-copasi *
sphinx >3
sphinx_rtd_theme *

requirements.txt pypi

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

setup.py pypi

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

BASICO

Science Score: 100.0%

Keywords

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

BasiCO

Installation

Usage

Run the tests

SSR support

Acknowledgements

License

Owner

JOSS Publication

BASICO: A simplified Python interface to COPASI

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

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Issue Authors

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Issue Labels

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Packages

pypi.org: copasi-basico

Rankings

Maintainers (1)

Dependencies