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cellmlmanip

CellML loading and model equation manipulation

https://github.com/modellingweblab/cellmlmanip

Science Score: 62.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 9 committers (55.6%) from academic institutions
  • ✓
    Institutional organization owner
    Organization modellingweblab has institutional domain (chaste.cs.ox.ac.uk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

CellML loading and model equation manipulation

Basic Info
  • Host: GitHub
  • Owner: ModellingWebLab
  • License: other
  • Language: Python
  • Default Branch: master
  • Size: 1.27 MB
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 1
  • Open Issues: 19
  • Releases: 4
Created over 8 years ago · Last pushed about 1 year ago
Metadata Files
Readme Contributing License Citation

README.md

Build status Documentation Status Coverage Status

cellmlmanip

CellML loading and model equation manipulation library

Installing

We recommend installing cellmlmanip in a virtual environment (e.g. using conda or pipenv or virtualenv).

Users install cellmlmanip using pip.

pip install cellmlmanip

Cellmlmanip is tested and developed on Python 3.9 and higher.

Release notes

For release notes see RELEASE.md

Documentation

API documentation explaining how to use cellmlmanip can be found on readthedocs

Contributing

For developer instructions, see CONTRIBUTING.md

Owner

  • Name: Modelling Web Lab
  • Login: ModellingWebLab
  • Kind: organization

A set of tools to enable the development of mathematical models of biological systems to be made reproducible and repeatable

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:

- family-names: "Hendrix"
  given-names: "Maurice"
  orcid: "https://orcid.org/0000-0002-6621-7996"
- family-names: "Clerx"
  given-names: "Michael"
  orcid: "https://orcid.org/0000-0003-4062-3061"
- family-names: "Tamuri"
  given-names: "Asif U."
  orcid: "https://orcid.org/0000-0001-6633-3789"
- family-names: "Keating"
  given-names: "Sarah M."
  orcid: "https://orcid.org/0000-0002-3356-3542"
- family-names: "Johnstone"
  given-names: "Ross H."
- family-names: "Cooper"
  given-names: "Jonathan"
  orcid: "https://orcid.org/0000-0001-6009-3542"
- family-names: "Mirams"
  given-names: "Gary R."
  orcid: "https://orcid.org/0000-0002-4569-4312"

title: "cellmlmanip"
version: 0.3.6
doi: 10.5281/zenodo.8207960
date-released: 2021-09-20
url: "https://github.com/ModellingWebLab/chaste-codegen"

preferred-citation:
  type: article
  authors:

  - family-names: "Hendrix"
    given-names: "Maurice"
    orcid: "https://orcid.org/0000-0002-6621-7996"
  - family-names: "Clerx"
    given-names: "Michael"
    orcid: "https://orcid.org/0000-0003-4062-3061"
  - family-names: "Tamuri"
    given-names: "Asif U."
    orcid: "https://orcid.org/0000-0001-6633-3789"
  - family-names: "Keating"
    given-names: "Sarah M."
    orcid: "https://orcid.org/0000-0002-3356-3542"
  - family-names: "Johnstone"
    given-names: "Ross H."
  - family-names: "Cooper"
    given-names: "Jonathan"
    orcid: "https://orcid.org/0000-0001-6009-3542"
  - family-names: "Mirams"
    given-names: "Gary R."
    orcid: "https://orcid.org/0000-0002-4569-4312"

  title: "cellmlmanip and chaste_codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians"
  journal: "Wellcome Open Research"
  year: 2022
  volume: 6
  start: 261
  doi: 10.12688/wellcomeopenres.17206.2

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 5
  • Delete event: 1
  • Issue comment event: 6
  • Push event: 10
  • Pull request event: 1
  • Pull request review comment event: 2
  • Pull request review event: 3
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 5
  • Delete event: 1
  • Issue comment event: 6
  • Push event: 10
  • Pull request event: 1
  • Pull request review comment event: 2
  • Pull request review event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 1,017
  • Total Committers: 9
  • Avg Commits per committer: 113.0
  • Development Distribution Score (DDS): 0.74
Top Committers
Name Email Commits
Asif Tamuri t****i@g****m 264
Michael Clerx m****x@c****k 202
Maurice Hendrix m****x@n****k 160
Sarah s****g@u****k 141
Jonathan Cooper j****r@u****k 138
MauriceHendrix 5****x@u****m 93
Michael Clerx m****x@n****k 12
Michael Clerx M****x@u****m 6
Jonathan Cooper g****m@j****k 1
Committer Domains (Top 20 + Academic)
ucl.ac.uk: 2 nottingham.ac.uk: 2 jonc.me.uk: 1 cs.ox.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 27
  • Total pull requests: 82
  • Average time to close issues: 9 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 7
  • Total pull request authors: 4
  • Average comments per issue: 2.7
  • Average comments per pull request: 1.65
  • Merged pull requests: 61
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 2
  • Average time to close issues: 3 days
  • Average time to close pull requests: 3 days
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 7.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MichaelClerx (15)
  • MauriceHendrix (4)
  • kwabenantim (3)
  • jonc125 (2)
  • Invarianz (1)
  • tamuri (1)
  • mirams (1)
Pull Request Authors
  • MauriceHendrix (66)
  • MichaelClerx (10)
  • jonc125 (3)
  • kwabenantim (2)
Top Labels
Issue Labels
bug (11) enhancement (4)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 2,804 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 4
  • Total versions: 13
  • Total maintainers: 3
pypi.org: cellmlmanip

CellML loading and model equation manipulation

  • Versions: 13
  • Dependent Packages: 1
  • Dependent Repositories: 4
  • Downloads: 2,804 Last month
Rankings
Dependent packages count: 3.3%
Dependent repos count: 7.8%
Downloads: 8.3%
Average: 13.5%
Forks count: 23.0%
Stargazers count: 25.4%
Maintainers (3)
MauriceHendrix mirams kwabenantim
Last synced: 7 months ago

Dependencies

requirements/base.in pypi
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  • six ==1.15.0
  • sympy ==1.7.1
requirements/dev.in pypi
  • flake8 * development
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requirements/dev.txt pypi
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  • pip-tools ==5.5.0 development
  • pluggy ==0.13.1 development
  • py ==1.10.0 development
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  • pytest ==6.2.2 development
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  • requests ==2.25.1 development
  • six ==1.15.0 development
  • sympy ==1.7.1 development
  • toml ==0.10.2 development
  • typing-extensions ==3.7.4.3 development
  • urllib3 ==1.26.3 development
  • zipp ==3.4.0 development
requirements/test.in pypi
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  • pytest * test
  • pytest-cov * test
requirements/test.txt pypi
  • attrs ==20.3.0 test
  • certifi ==2020.12.5 test
  • chardet ==4.0.0 test
  • codecov ==2.1.11 test
  • coverage ==5.4 test
  • decorator ==4.4.2 test
  • flake8 ==3.8.4 test
  • idna ==2.10 test
  • importlib-metadata ==3.4.0 test
  • iniconfig ==1.1.1 test
  • isodate ==0.6.0 test
  • isort ==5.7.0 test
  • lxml ==4.6.2 test
  • mccabe ==0.6.1 test
  • mpmath ==1.1.0 test
  • networkx ==2.5 test
  • packaging ==20.8 test
  • pint ==0.9 test
  • pluggy ==0.13.1 test
  • py ==1.10.0 test
  • pycodestyle ==2.6.0 test
  • pyflakes ==2.2.0 test
  • pyparsing ==2.4.7 test
  • pytest ==6.2.2 test
  • pytest-cov ==2.11.1 test
  • rdflib ==5.0.0 test
  • requests ==2.25.1 test
  • six ==1.15.0 test
  • sympy ==1.7.1 test
  • toml ==0.10.2 test
  • typing-extensions ==3.7.4.3 test
  • urllib3 ==1.26.3 test
  • zipp ==3.4.0 test
setup.py pypi
  • lxml >=4
  • networkx >=2.1
  • pint >=0.9.0
  • rdflib >=4
  • sympy >=1.4
.github/workflows/coverage.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
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.github/workflows/docs.yml actions
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.github/workflows/style.yml actions
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.github/workflows/unit-test-pinned.yml actions
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.github/workflows/unit-test.yml actions
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pyproject.toml pypi