gotranx

gotranx: General ODE translator - Published in JOSS (2024)

https://github.com/finsberg/gotranx

Science Score: 100.0%

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DOI references
Found 7 DOI reference(s) in README and JOSS metadata
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Links to: joss.theoj.org, zenodo.org
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

code-generation gotran ode parser parsing

Keywords from Contributors

mesh hydrology energy-system pde standardization turing-machine exoplanet benchmarking physics-simulation optimisation

Scientific Fields

Mathematics Computer Science - 37% confidence

Last synced: 6 months ago · JSON representation ·

Repository

Next generation ODE translator

Basic Info

Host: GitHub
Owner: finsberg
License: mit
Language: Python
Default Branch: main
Homepage: https://finsberg.github.io/gotranx
Size: 2.57 MB

Statistics

Stars: 12
Watchers: 1
Forks: 2
Open Issues: 7
Releases: 15

Topics

code-generation gotran ode parser parsing

Created over 3 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Roadmap

gotranx

gotranx is the next generation General ODE translator. The general idea is that you write your ODE in a high level markup language and use gotranx to generate code for solving the ODE in different programming languages. gotranx uses sympy to create a symbolic representation of the ODE which is used to generate the jacobian and numerical schemes.

gotranx makes it also possible generate code from e.g CellML models using conversion tools from myokit.

Source code: https://github.com/finsberg/gotranx
Documentation: https://finsberg.github.io/gotranx/

Install

Install with pip python3 -m pip install gotranx or for the development version python3 -m pip install git+https://github.com/finsberg/gotranx

You can also install gotranx using conda conda install -c conda-forge gotranx

Quick start

Define your ODE in a .ode file, e.g file.ode with the content ``` states(x=1, y=0) parameters(a=1.0)

dxdt = a * y dydt = -x ``` which defines the ODE system

$$ \begin{align} \frac{dx}{dt} &= ay \ \frac{dy}{dt} &= -x \end{align} $$

with the initial conditions $x(0) = 1$ and $y(0) = 0$ and the parameter $a$ with a value of 1.0. Now generate code in python for solving this ODE with the explicit euler scheme using the command gotranx ode2py file.ode --scheme explicit_euler -o file.py which will create a file file.py containing functions for solving the ODE. Now you can solve the ode using the following code snippet

```python import file as model import numpy as np import matplotlib.pyplot as plt

s = model.initstatevalues() p = model.initparametervalues() dt = 1e-4 # 0.1 ms T = 2 * np.pi t = np.arange(0, T, dt)

xindex = model.stateindex("x") x = [s[xindex]] yindex = model.stateindex("y") y = [s[yindex]]

for ti in t[1:]: s = model.expliciteuler(s, ti, dt, p) x.append(s[xindex]) y.append(s[y_index])

plt.plot(t, x, label="x") plt.plot(t, y, label="y") plt.legend() plt.show() ```

Alternatively, you can use a third-party ODE solver, e.g scipy.integrate.solve_ivp to solve the ODE by passing in the right-hand side function

```python import file as model from scipy.integrate import solve_ivp import numpy as np import matplotlib.pyplot as plt

s = model.initstatevalues() p = model.initparametervalues() dt = 1e-4 # 0.1 ms T = 2 * np.pi t = np.arange(0, T, dt)

res = solveivp( model.rhs, (0, T), s, method="RK45", teval=t, args=(p,), )

plt.plot(res.t, res.y.T) plt.legend() plt.show() ```

Note that this is a rather artificial example, so check out the demos in the documentation for more elaborate examples.

FAQ

Why should I use gotranx? The main reasons to use gotranx are

You want to solve your model using different programming languages (e.g python and C)
You want to create a custom numerical scheme that can utilize the symbolic representation of the ODE
You would like to share your model in a high level representation (i.e a markup language)

How does it differ from scipy.integrate.solve_ivp? scipy.integrate.solve_ivp is an ODE solver which takes as input a function defining the right-hand. gotranx takes a high level representation of the ODE and can generate code for the right hand side. In other words, you can use scipy.integrate.solve_ivp to solve the ODE and use gotranx to generate the right hand side.

Automated tests

Unit tests

Automated tests can be found in the test folder. To the run the tests please install the test dependencies python3 -m pip install "gotranx[test]" or if you have cloned the repo locally you can do python3 -m pip install ".[test]" To run the tests you should execute the following command python3 -m pytest Also note that the tests are run on every push and pull request to main using GitHub actions.

Linting and formatting

We use pre-commit to run the a set of linters and formatters in order to ensure consistent code style. Developers should install the pre-commit hooks by first installing pre-commit python3 -m pip install pre-commit and then install the pre-commit hooks pre-commit install To run the hooks on all the files you can do pre-commit run --all For further instructions see the contributing guide.

Note also the we run all hooks as a part of our continuous integration, and we are also using pre-commit.ci to update branches automatically that can fix issues automatically.

Performance monitoring

We have defined a set of benchmarks that run on every push to the main branch using codspeed. To monitor the performance over time you can check out the performance report.

To run the benchmarks locally you can install the pytest-codspeed plugin python3 -m pip install pytest-codspeed and run python3 -m pytest tests/ --codspeed You can find more info at https://docs.codspeed.io/benchmarks/python

Citing

If you use gotranx in your research project we would appreciate if you could use the following citation @article{Finsberg2024, doi = {10.21105/joss.07063}, url = {https://doi.org/10.21105/joss.07063}, year = {2024}, publisher = {The Open Journal}, volume = {9}, number = {102}, pages = {7063}, author = {Henrik Finsberg and Johan Hake}, title = {gotranx: General ODE translator}, journal = {Journal of Open Source Software} }

License

MIT

Contributing

Contributions are very welcomed, but please read the contributing guide first

Owner

Name: Henrik Finsberg
Login: finsberg
Kind: user
Location: Oslo, Norway
Company: Simula Research Laboratoy

Website: https://finsberg.github.io
Repositories: 13
Profile: https://github.com/finsberg

Senior Research Engineer working with Scientific Computing and Computational Physiology

JOSS Publication

gotranx: General ODE translator

Published

October 17, 2024

DOI

10.21105/joss.07063

Volume 9, Issue 102, Page 7063

Authors

Henrik Finsberg

Simula Research Laboratory, Oslo, Norway

Johan Hake
Oslo Katedralskole, Oslo, Norway

Editor

Rohit Goswami

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Fisberg"
  given-names: "Henrik"
  orcid: "https://orcid.org/0000-0003-3766-2393"
title: "gotranx"
url: "https://github.com/finsberg/gotranx"
preferred-citation:
  type: article
  doi: "10.21105/joss.07063"
  journal: "Journal of Open Source Software"
  title: "gotranx: General ODE translator"
  year: 2024
  volume: 9
  issue: 102
  authors:
  - family-names: "Finsberg"
    given-names: "Henrik"
    orcid: "https://orcid.org/0000-0003-3766-2393"
  - family-names: "Hake"
    given-names: "Johan"

GitHub Events

Total

Create event: 22
Release event: 6
Issues event: 11
Watch event: 4
Delete event: 14
Issue comment event: 60
Push event: 110
Pull request event: 90
Fork event: 2

Last Year

Create event: 22
Release event: 6
Issues event: 11
Watch event: 4
Delete event: 14
Issue comment event: 60
Push event: 110
Pull request event: 90
Fork event: 2

Committers

Last synced: 7 months ago

All Time

Total Commits: 503
Total Committers: 6
Avg Commits per committer: 83.833
Development Distribution Score (DDS): 0.205

Past Year

Commits: 209
Committers: 4
Avg Commits per committer: 52.25
Development Distribution Score (DDS): 0.316

Top Committers

Name	Email	Commits
Henrik Finsberg	h**g@h**m	400
pre-commit-ci[bot]	6****]	84
dependabot[bot]	4****]	7
termi-official	t****l	6
Daniel S. Katz	d**z@i**g	4
Kyle Beggs	b**w@g**m	2

Committer Domains (Top 20 + Academic)

ieee.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 26
Total pull requests: 309
Average time to close issues: 25 days
Average time to close pull requests: 9 days
Total issue authors: 8
Total pull request authors: 6
Average comments per issue: 0.85
Average comments per pull request: 0.49
Merged pull requests: 276
Bot issues: 0
Bot pull requests: 140

Past Year

Issues: 6
Pull requests: 103
Average time to close issues: 4 days
Average time to close pull requests: 2 days
Issue authors: 5
Pull request authors: 5
Average comments per issue: 1.17
Average comments per pull request: 0.98
Merged pull requests: 92
Bot issues: 0
Bot pull requests: 79

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Top Authors

Issue Authors

finsberg (8)
SunnyXu (8)
benlansdell (3)
ayush9pandey (3)
HaoZeke (1)
MichaelClerx (1)
kylebeggs (1)
hsauro (1)

Pull Request Authors

finsberg (163)
pre-commit-ci[bot] (124)
dependabot[bot] (16)
termi-official (2)
kylebeggs (2)
danielskatz (2)

Top Labels

Issue Labels

Pull Request Labels

dependencies (16) github_actions (2) enhancement (1)

Packages

Total packages: 1
Total downloads:
- pypi 278 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 30
Total maintainers: 1

pypi.org: gotranx

A declarative language describing ordinary differential equations

Homepage: https://github.com/finsberg/gotranx
Documentation: https://gotranx.readthedocs.io/
License: MIT
Latest release: 1.3.5
published 9 months ago

Versions: 30
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 278 Last month

Rankings

Dependent packages count: 10.0%

Average: 38.2%

Dependent repos count: 66.3%

Maintainers (1)

finsberg

Last synced: 6 months ago

Dependencies

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.github/workflows/pre-commit.yml actions

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.github/workflows/pypi.yml actions

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lark *
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gotranx

Science Score: 100.0%

Keywords

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

gotranx

Install

Quick start

FAQ

Automated tests

Unit tests

Linting and formatting

Performance monitoring

Citing

License

Contributing

Owner

JOSS Publication

gotranx: General ODE translator

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

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: gotranx

Rankings

Maintainers (1)

Dependencies