sbmlode 0.1.0__tar.gz → 0.2.0__tar.gz

{sbmlode-0.1.0 → sbmlode-0.2.0}/CITATION.cff

@@ -1,5 +1,5 @@
 cff-version: 1.2.0
-message: "If you use sbmlode, please cite it as below."
+message: "If you use sbmlode, please cite the archived software on Zenodo."
 title: "sbmlode: ordinary differential equations of SBML models"
 abstract: "sbmlode writes the system of ordinary differential equations of a model in the Systems Biology Markup Language (SBML) as python, julia and R code which simulates it and as LaTeX, typst and markdown documents which describe it."
 type: software
@@ -8,8 +8,16 @@ authors:
     given-names: "Matthias"
     orcid: "https://orcid.org/0000-0003-1725-179X"
     affiliation: "Humboldt-University Berlin, Faculty of Life Science, Institute for Biology, Biology, Berlin; University Lübeck; University Hospital Schleswig-Holstein, Campus Lübeck, First Department of Medicine, Germany"
-version: "0.1.0"
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.23179199
+    description: the concept doi of all versions
+  - type: doi
+    value: 10.5281/zenodo.23179200
+    description: the doi of version 0.1.0
+version: "0.2.0"
 date-released: "2026-10-06"
+doi: "10.5281/zenodo.23179199"
 license: MIT
 repository-code: "https://github.com/matthiaskoenig/sbmlode"
 url: "https://matthiaskoenig.github.io/sbmlode"

{sbmlode-0.1.0 → sbmlode-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: sbmlode
-Version: 0.1.0
+Version: 0.2.0
 Summary: sbmlode writes the ordinary differential equations of SBML models as python, julia and R code and as LaTeX, typst and markdown documents.
 Project-URL: Homepage, https://matthiaskoenig.github.io/sbmlode
 Project-URL: Documentation, https://matthiaskoenig.github.io/sbmlode
@@ -62,9 +62,11 @@ Requires-Dist: scipy>=1.15.0; extra == 'test'
 Requires-Dist: typst>=0.15.0; extra == 'test'
 Description-Content-Type: text/markdown
 
+<img src="https://raw.githubusercontent.com/matthiaskoenig/sbmlode/develop/docs/images/favicon/sbmlode-200x200.png" alt="sbmlode logo" width="100">
+
 # sbmlode
 
-[![PyPI](https://img.shields.io/pypi/v/sbmlode.svg)](https://pypi.org/project/sbmlode/) [![CI-CD](https://github.com/matthiaskoenig/sbmlode/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/matthiaskoenig/sbmlode/actions/workflows/ci-cd.yml) [![Documentation](https://img.shields.io/badge/docs-zensical-teal)](https://matthiaskoenig.github.io/sbmlode/)
+[![PyPI](https://img.shields.io/pypi/v/sbmlode.svg)](https://pypi.org/project/sbmlode/) [![CI-CD](https://github.com/matthiaskoenig/sbmlode/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/matthiaskoenig/sbmlode/actions/workflows/ci-cd.yml) [![Documentation](https://img.shields.io/badge/docs-zensical-teal)](https://matthiaskoenig.github.io/sbmlode/) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23179199.svg)](https://doi.org/10.5281/zenodo.23179199)
 
 An SBML model describes a system of ordinary differential equations (ODEs), but it is not written as one: the equations follow from the reactions, rules, events and units of the model. `sbmlode` derives this system once and writes it
 
@@ -95,6 +97,27 @@ system.write("model.md", standalone=False)  # with the options of the format
 
 The [Guide](https://matthiaskoenig.github.io/sbmlode/formats/) describes the formats, their options, the supported SBML and the verification, the [API reference](https://matthiaskoenig.github.io/sbmlode/api/) the classes and functions.
 
+## How to cite
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23179199.svg)](https://doi.org/10.5281/zenodo.23179199)
+
+If you use sbmlode please cite the archived software on [Zenodo](https://doi.org/10.5281/zenodo.23179199):
+
+> König, M. (2026). *sbmlode: ordinary differential equations of SBML models* (Version 0.1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.23179200
+
+```bibtex
+@software{koenig_sbmlode,
+  author    = {König, Matthias},
+  title     = {sbmlode: ordinary differential equations of SBML models},
+  year      = {2026},
+  month     = oct,
+  version   = {0.1.0},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.23179200},
+  url       = {https://doi.org/10.5281/zenodo.23179200},
+}
+```
+
 ## License
 
 sbmlode is open source under the [MIT license](https://github.com/matthiaskoenig/sbmlode/blob/develop/LICENSE). Please [open an issue](https://github.com/matthiaskoenig/sbmlode/issues) for a question or a problem.

{sbmlode-0.1.0 → sbmlode-0.2.0}/README.md

@@ -1,6 +1,8 @@
+<img src="https://raw.githubusercontent.com/matthiaskoenig/sbmlode/develop/docs/images/favicon/sbmlode-200x200.png" alt="sbmlode logo" width="100">
+
 # sbmlode
 
-[![PyPI](https://img.shields.io/pypi/v/sbmlode.svg)](https://pypi.org/project/sbmlode/) [![CI-CD](https://github.com/matthiaskoenig/sbmlode/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/matthiaskoenig/sbmlode/actions/workflows/ci-cd.yml) [![Documentation](https://img.shields.io/badge/docs-zensical-teal)](https://matthiaskoenig.github.io/sbmlode/)
+[![PyPI](https://img.shields.io/pypi/v/sbmlode.svg)](https://pypi.org/project/sbmlode/) [![CI-CD](https://github.com/matthiaskoenig/sbmlode/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/matthiaskoenig/sbmlode/actions/workflows/ci-cd.yml) [![Documentation](https://img.shields.io/badge/docs-zensical-teal)](https://matthiaskoenig.github.io/sbmlode/) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23179199.svg)](https://doi.org/10.5281/zenodo.23179199)
 
 An SBML model describes a system of ordinary differential equations (ODEs), but it is not written as one: the equations follow from the reactions, rules, events and units of the model. `sbmlode` derives this system once and writes it
 
@@ -31,6 +33,27 @@ system.write("model.md", standalone=False)  # with the options of the format
 
 The [Guide](https://matthiaskoenig.github.io/sbmlode/formats/) describes the formats, their options, the supported SBML and the verification, the [API reference](https://matthiaskoenig.github.io/sbmlode/api/) the classes and functions.
 
+## How to cite
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23179199.svg)](https://doi.org/10.5281/zenodo.23179199)
+
+If you use sbmlode please cite the archived software on [Zenodo](https://doi.org/10.5281/zenodo.23179199):
+
+> König, M. (2026). *sbmlode: ordinary differential equations of SBML models* (Version 0.1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.23179200
+
+```bibtex
+@software{koenig_sbmlode,
+  author    = {König, Matthias},
+  title     = {sbmlode: ordinary differential equations of SBML models},
+  year      = {2026},
+  month     = oct,
+  version   = {0.1.0},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.23179200},
+  url       = {https://doi.org/10.5281/zenodo.23179200},
+}
+```
+
 ## License
 
 sbmlode is open source under the [MIT license](https://github.com/matthiaskoenig/sbmlode/blob/develop/LICENSE). Please [open an issue](https://github.com/matthiaskoenig/sbmlode/issues) for a question or a problem.

{sbmlode-0.1.0 → sbmlode-0.2.0}/src/sbmlode/__init__.py

@@ -22,7 +22,7 @@ python, julia and R code, and typst, LaTeX and markdown documents
 """
 
 # the version comes first, the modules below read it when they render
-__version__ = "0.1.0"
+__version__ = "0.2.0"
 
 from sbmlode.formats import (
     FORMATS,