Data

Tools

Indexes

Applications

Experiments

Open Source Science

chaste-codegen

Code generation for Chaste based on cellmlmanip

https://github.com/modellingweblab/chaste-codegen

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
    3 of 8 committers (37.5%) from academic institutions
  • ✓
    Institutional organization owner
    Organization modellingweblab has institutional domain (chaste.cs.ox.ac.uk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.7%) to scientific vocabulary

Keywords from Contributors

cancer-research cell-based computational-biology developmental-biology electrophysiology hpc-applications mathematical-biology mathematical-modelling physiology parameter-estimation
Last synced: 6 months ago · JSON representation ·

Repository

Code generation for Chaste based on cellmlmanip

Basic Info
  • Host: GitHub
  • Owner: ModellingWebLab
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 57.8 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 5
  • Releases: 13
Created over 7 years ago · Last pushed 9 months ago
Metadata Files
Readme Contributing License Citation

README.md

workflow Documentation Status codecov

Code generation for cardiac Chaste

The chaste_codegen module takes CellML models as input, via cellmlmanip to read and manipulate them, then uses templating to generate C++ code.

The jinja2 templating engine is used.

Installing

We recommend installing chaste_codegen in a virtual environment (using virtualenv or conda)

Users install chaste_codegen using pip.

pip install chaste_codegen

Using chaste_codegen

After installation, chastecodegen can be called using the `chastecodegencommand: `` usage: chastecodegen [-h] [--version] [--normal] [--cvode] [--cvode-data-clamp] [--backward-euler] [--rush-larsen] [--grl1] [--grl2] [--rush-larsen-labview] [--rush-larsen-c] [-j] [-o OUTFILE] [--output-dir OUTPUT_DIR] [--show-outputs] [-c CLS_NAME] [-q] [--skip-ingularity-fixes] [-y] [--opt] [-m] [--lookup-table min max step] [--use-model-factory] cellmlfile chastecodegen: error: the following arguments are required: cellmlfile

```

For more information about the available options call chaste_codegen -h or see the CodeGenerationFromCellML guide

Release notes

For release notes see RELEASE.md

Documentation

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

Contributing

For guidelines on contributing to chaste_codegen, please 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: "chaste-codegen"
version: 0.10.4
doi: 10.5281/zenodo.8207994
date-released: 2023-08-02
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: 6
  • Release event: 1
  • Issues event: 2
  • Delete event: 5
  • Issue comment event: 6
  • Push event: 9
  • Pull request review event: 3
  • Pull request event: 8
Last Year
  • Create event: 6
  • Release event: 1
  • Issues event: 2
  • Delete event: 5
  • Issue comment event: 6
  • Push event: 9
  • Pull request review event: 3
  • Pull request event: 8

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 707
  • Total Committers: 8
  • Avg Commits per committer: 88.375
  • Development Distribution Score (DDS): 0.424
Top Committers
Name Email Commits
Maurice Hendrix m****x@n****k 407
MauriceHendrix 5****x@u****m 155
Michael Clerx m****x@c****k 117
Michael Clerx M****x@u****m 10
dependabot[bot] 4****]@u****m 8
Gary Mirams g****s@g****m 6
Jonathan Cooper j****r@u****k 3
Kwabena N Amponsah k****m@y****m 1
Committer Domains (Top 20 + Academic)
ucl.ac.uk: 1 cs.ox.ac.uk: 1 nottingham.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 19
  • Total pull requests: 117
  • Average time to close issues: 11 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 5
  • Total pull request authors: 4
  • Average comments per issue: 1.47
  • Average comments per pull request: 1.06
  • Merged pull requests: 91
  • Bot issues: 0
  • Bot pull requests: 34
Past Year
  • Issues: 2
  • Pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 7
View more stats
Top Authors
Issue Authors
  • MauriceHendrix (9)
  • kwabenantim (6)
  • MichaelClerx (2)
  • flawmop (1)
  • mirams (1)
Pull Request Authors
  • MauriceHendrix (75)
  • dependabot[bot] (41)
  • kwabenantim (8)
  • mirams (2)
Top Labels
Issue Labels
enhancement (11) bug (2) long term (1) help wanted (1) dependencies (1)
Pull Request Labels
dependencies (41) python (5) enhancement (3) bug (3)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 591 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 34
  • Total maintainers: 4
pypi.org: chaste-codegen

Code generation for cardiac Chaste

  • Versions: 34
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 591 Last month
Rankings
Downloads: 5.9%
Dependent packages count: 7.5%
Average: 17.4%
Dependent repos count: 22.6%
Forks count: 23.0%
Stargazers count: 28.1%
Maintainers (4)
MauriceHendrix mirams kwabenantim gwnau
Last synced: 6 months ago

Dependencies

dev-requirements/dev.txt pypi
  • Jinja2 ==2.11.3
  • MarkupSafe ==1.1.1
  • Pint ==0.17
  • Pygments ==2.9.0
  • atomicwrites ==1.4.0
  • attrs ==21.2.0
  • bleach ==3.3.0
  • build ==0.3.1.post1
  • cellmlmanip ==0.3.4
  • certifi ==2020.12.5
  • chardet ==4.0.0
  • codecov ==2.1.11
  • colorama ==0.4.4
  • coverage ==5.5
  • decorator ==4.4.2
  • docutils ==0.17.1
  • flake8 ==3.9.2
  • idna ==2.10
  • importlib-metadata ==4.0.1
  • iniconfig ==1.1.1
  • isodate ==0.6.0
  • isort ==5.8.0
  • lxml ==4.6.5
  • mccabe ==0.6.1
  • mock ==4.0.3
  • mpmath ==1.2.1
  • networkx ==2.5.1
  • packaging ==20.9
  • pep517 ==0.10.0
  • pkginfo ==1.7.0
  • pluggy ==0.13.1
  • py ==1.10.0
  • pycodestyle ==2.7.0
  • pyflakes ==2.3.1
  • pyparsing ==2.4.7
  • pytest ==6.2.4
  • pytest-cov ==2.11.1
  • pywin32-ctypes ==0.2.0
  • rdflib ==5.0.0
  • readme-renderer ==29.0
  • requests ==2.25.1
  • requests-toolbelt ==0.9.1
  • rfc3986 ==1.5.0
  • six ==1.16.0
  • sympy ==1.10.1
  • toml ==0.10.2
  • tqdm ==4.60.0
  • urllib3 ==1.26.5
  • webencodings ==0.5.1
  • zipp ==1.2.0
setup.py pypi
  • Jinja2 >=2.11.3,
  • MarkupSafe >=1.1.1,
  • Pint >=0.9,
  • cellmlmanip >=0.3.4,
  • decorator >=4.4.2,
  • importlib-metadata >=1.7,
  • isodate >=0.6.0,
  • lxml >=4.6.5,
  • mpmath >=1.1.0,
  • networkx >=2.4,
  • packaging >=20.4,
  • py >=1.10.0
  • pyparsing >=2.4.7,
  • rdflib >=5.0.0,
  • six >=1.15.0,
  • sympy >=1.9,
  • zipp >=1.2.0,
.github/workflows/pytest.yml actions
  • actions/checkout v1 composite
  • actions/setup-python v1 composite
  • codecov/codecov-action v1 composite