simbio
A Python-based package for simulation of Chemical Reaction Networks (CRNs).
It extends poincare,
a package for modelling dynamical systems,
to add functionality for CRNs.
Usage
See simbio's documentation on the dyscolab page, or go directly to the intro tutorial.
Install
Using pixi, install from PyPI with:
pixi add --pypi simbio
or install the latest development version from GitHub with:
pixi add --pypi simbio@https://github.com/dyscolab/simbio.git
Otherwise,
use pip or your pip-compatible package manager:
pip install simbio # from PyPI
pip install git+https://github.com/dyscolab/simbio.git # from GitHub
Development
This project is managed by pixi. You can install it for development using:
git clone https://github.com/dyscolab/simbio
cd simbio
pixi run pre-commit-install
Pre-commit hooks are used to lint and format the project.
Testing
Run tests using:
pixi run test
Publishing to PyPI
When a tagged commit is pushed to GitHub,
the GitHub Action defined in .github/workflows/ci.yml
builds and publishes the package to PyPI.
Tag a commit and push the tags with:
git tag <my-tag>
git push --tags
Trusted publishing must be enabled once in PyPI Publishing. Fill the following values in the form:
PyPI Project Name: simbio
Owner: maurosilber
Repository name: simbio
Workflow name: ci.yml
Environment name: pypi
1 maintainer
Metadata
1 maintainer
Release files for simbio 1.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| simbio-1.2.0.tar.gz | 25.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| simbio-1.2.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 57.1 kB
Release files / simbio-1.2.0.tar.gz
| Download URL | simbio-1.2.0.tar.gz |
|---|---|
| Size | 25.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
uv/0.12.9 {"installer":{"name":"uv","version":"0.12.9","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
|
Release files / simbio-1.2.0-py3-none-any.whl
| Download URL | simbio-1.2.0-py3-none-any.whl |
|---|---|
| Size | 32.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
uv/0.12.9 {"installer":{"name":"uv","version":"0.12.9","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
|
