sbmlode 0.1.0__tar.gz

sbmlode-0.1.0/.gitignore

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+# python
+__pycache__/
+*.pyc
+
+# packaging artifacts (hatchling builds into dist/)
+dist/
+*.egg-info/
+
+# environments, tool caches
+.venv/
+.tox/
+.pytest_cache/
+.ruff_cache/
+.coverage
+coverage.xml
+# build cache of zensical
+.cache/
+
+# rendered documentation, built by the `documentation` workflow
+site/
+
+# py4cytoscape writes its log next to the working directory
+logs/
+
+# output of the examples, they write into the working directory
+examples/**/results/
+examples/**/_results/
+
+# scratch directories of scripts/roundtrip_report.py, package_report.py and ode_report.py
+.roundtrip_tmp/
+.package_tmp/
+.ode_tmp/
+# the pages of the typst document of docs/ode.md, compiled by the docs workflow
+docs/images/ode/*.svg
+
+# working files of coding agents
+.superpowers/
+
+# editors, operating system
+.idea/
+.vscode/
+*~
+.DS_Store
+
+# the julia environment of the tests is resolved from its Project.toml
+tests/converters/ode/julia/Manifest.toml

sbmlode-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use sbmlode, please cite it as below."
+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
+authors:
+  - family-names: "König"
+    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"
+date-released: "2026-10-06"
+license: MIT
+repository-code: "https://github.com/matthiaskoenig/sbmlode"
+url: "https://matthiaskoenig.github.io/sbmlode"
+keywords:
+  - SBML
+  - Systems Biology Markup Language
+  - ODE
+  - ordinary differential equations
+  - code generation
+  - computational modeling

sbmlode-0.1.0/LICENSE

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+Copyright (c) 2025 Matthias König
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

sbmlode-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: sbmlode
+Version: 0.1.0
+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
+Project-URL: Repository, https://github.com/matthiaskoenig/sbmlode
+Project-URL: Issues, https://github.com/matthiaskoenig/sbmlode/issues
+Project-URL: Changelog, https://matthiaskoenig.github.io/sbmlode/release-notes/
+Project-URL: Download, https://pypi.org/project/sbmlode
+Author-email: Matthias König <konigmatt@googlemail.com>
+Maintainer-email: Matthias König <konigmatt@googlemail.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: ODE,SBML,Systems Biology Markup Language,code generation,computational modeling,ordinary differential equations
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: jinja2>=3.1.6
+Requires-Dist: python-libsbml>=5.21.2
+Provides-Extra: dev
+Requires-Dist: antimony!=3.2.0; (sys_platform == 'win32') and extra == 'dev'
+Requires-Dist: antimony>=3.1.3; extra == 'dev'
+Requires-Dist: bump-my-version>=1.5.1; extra == 'dev'
+Requires-Dist: libroadrunner>=2.10.0; (python_version < '3.15') and extra == 'dev'
+Requires-Dist: markdown-it-py>=3.0.0; extra == 'dev'
+Requires-Dist: mkdocstrings-python>=2.0.8; extra == 'dev'
+Requires-Dist: numpy>=2.2.2; extra == 'dev'
+Requires-Dist: pandas>=2.2.2; extra == 'dev'
+Requires-Dist: pre-commit>=4.6.2; extra == 'dev'
+Requires-Dist: pytest>=9.1.1; extra == 'dev'
+Requires-Dist: ruff>=0.16.6; extra == 'dev'
+Requires-Dist: scipy>=1.15.0; extra == 'dev'
+Requires-Dist: tox-uv>=1.29.0; extra == 'dev'
+Requires-Dist: tox>=4.61.2; extra == 'dev'
+Requires-Dist: ty>=0.0.79; extra == 'dev'
+Requires-Dist: typst>=0.15.0; extra == 'dev'
+Requires-Dist: zensical>=0.0.60; extra == 'dev'
+Provides-Extra: simulate
+Requires-Dist: numpy>=2.2.2; extra == 'simulate'
+Requires-Dist: pandas>=2.2.2; extra == 'simulate'
+Requires-Dist: scipy>=1.15.0; extra == 'simulate'
+Provides-Extra: test
+Requires-Dist: antimony!=3.2.0; (sys_platform == 'win32') and extra == 'test'
+Requires-Dist: antimony>=3.1.3; extra == 'test'
+Requires-Dist: libroadrunner>=2.10.0; (python_version < '3.15') and extra == 'test'
+Requires-Dist: markdown-it-py>=3.0.0; extra == 'test'
+Requires-Dist: numpy>=2.2.2; extra == 'test'
+Requires-Dist: pandas>=2.2.2; extra == 'test'
+Requires-Dist: pytest>=9.1.1; extra == 'test'
+Requires-Dist: scipy>=1.15.0; extra == 'test'
+Requires-Dist: typst>=0.15.0; extra == 'test'
+Description-Content-Type: text/markdown
+
+# 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/)
+
+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
+
+- as **code** which simulates the model: **python** (numpy and scipy), **julia** (OrdinaryDiffEq.jl) and **R** (deSolve), verified against [libroadrunner](https://libroadrunner.org) over the [SBML test suite](https://github.com/sbmlteam/sbml-test-suite);
+- as **documents** which describe the model: **typst**, **LaTeX** and **markdown**;
+- as **typed data** for an application which lays out the equations itself, such as [SBML4Humans](https://sbml4humans.de), see [Typed target](https://matthiaskoenig.github.io/sbmlode/typeset/).
+
+sbmlode depends on [python-libsbml](https://sbml.org/software/libsbml/) and jinja2 only. It is the ODE export of [sbmlutils](https://github.com/matthiaskoenig/sbmlutils) 0.14 as a package of its own, which sbmlutils re-exports as `sbmlutils.converters.ode`.
+
+## Installation
+
+```bash
+pip install sbmlode               # the export
+pip install "sbmlode[simulate]"   # with numpy, pandas and scipy, which the python code runs with
+```
+
+## Quick start
+
+```python
+from sbmlode import OdeSystem
+
+system = OdeSystem.from_sbml("model.xml")
+
+code: str = system.render("python")  # the code or document as a string
+system.write("model.jl")  # the format from the suffix of the file
+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.
+
+## 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/README.md

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+# 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/)
+
+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
+
+- as **code** which simulates the model: **python** (numpy and scipy), **julia** (OrdinaryDiffEq.jl) and **R** (deSolve), verified against [libroadrunner](https://libroadrunner.org) over the [SBML test suite](https://github.com/sbmlteam/sbml-test-suite);
+- as **documents** which describe the model: **typst**, **LaTeX** and **markdown**;
+- as **typed data** for an application which lays out the equations itself, such as [SBML4Humans](https://sbml4humans.de), see [Typed target](https://matthiaskoenig.github.io/sbmlode/typeset/).
+
+sbmlode depends on [python-libsbml](https://sbml.org/software/libsbml/) and jinja2 only. It is the ODE export of [sbmlutils](https://github.com/matthiaskoenig/sbmlutils) 0.14 as a package of its own, which sbmlutils re-exports as `sbmlutils.converters.ode`.
+
+## Installation
+
+```bash
+pip install sbmlode               # the export
+pip install "sbmlode[simulate]"   # with numpy, pandas and scipy, which the python code runs with
+```
+
+## Quick start
+
+```python
+from sbmlode import OdeSystem
+
+system = OdeSystem.from_sbml("model.xml")
+
+code: str = system.render("python")  # the code or document as a string
+system.write("model.jl")  # the format from the suffix of the file
+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.
+
+## 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/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "sbmlode"
+dynamic = ["version"]
+description = "sbmlode writes the ordinary differential equations of SBML models as python, julia and R code and as LaTeX, typst and markdown documents."
+readme = "README.md"
+requires-python = ">=3.11"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [{ name = "Matthias König", email = "konigmatt@googlemail.com" }]
+maintainers = [{ name = "Matthias König", email = "konigmatt@googlemail.com" }]
+classifiers = [
+	"Development Status :: 4 - Beta",
+	"Intended Audience :: Science/Research",
+	"Operating System :: OS Independent",
+	"Programming Language :: Python :: 3.11",
+	"Programming Language :: Python :: 3.12",
+	"Programming Language :: Python :: 3.13",
+	"Programming Language :: Python :: 3.14",
+	"Programming Language :: Python :: 3.15",
+	"Programming Language :: Python :: Implementation :: CPython",
+	"Topic :: Scientific/Engineering",
+	"Topic :: Scientific/Engineering :: Bio-Informatics",
+	"Typing :: Typed",
+]
+keywords = [
+	"SBML",
+	"Systems Biology Markup Language",
+	"ODE",
+	"ordinary differential equations",
+	"code generation",
+	"computational modeling",
+]
+dependencies = [
+	"python-libsbml>=5.21.2",
+	"jinja2>=3.1.6",
+]
+
+[project.optional-dependencies]
+# what the python code the export writes runs with: numpy and pandas, and scipy,
+# which integrates it in `simulate`; sbmlode writes the code without them
+simulate = ["numpy>=2.2.2", "pandas>=2.2.2", "scipy>=1.15.0"]
+# what the tests need beyond the package: models written in antimony, the python
+# simulator the export writes (`simulate`), the reference simulations of the SBML
+# test suite (libroadrunner), the compilation of typst and the parsing of markdown
+test = [
+	"sbmlode[simulate]",
+	"pytest>=9.1.1",
+	"antimony>=3.1.3",
+	# the win_amd64 wheel of antimony 3.2.0 raises a C++ exception in loadAntimonyString
+	"antimony!=3.2.0; sys_platform == 'win32'",
+	"libroadrunner>=2.10.0; python_version < '3.15'",
+	"typst>=0.15.0",
+	"markdown-it-py>=3.0.0",
+]
+dev = [
+	"sbmlode[test]",
+	"bump-my-version>=1.5.1",
+	"ruff>=0.16.6",
+	"pre-commit>=4.6.2",
+	"ty>=0.0.79",
+	"tox>=4.61.2",
+	"tox-uv>=1.29.0",
+	"zensical>=0.0.60",
+	"mkdocstrings-python>=2.0.8",
+]
+
+[project.urls]
+Homepage = "https://matthiaskoenig.github.io/sbmlode"
+Documentation = "https://matthiaskoenig.github.io/sbmlode"
+Repository = "https://github.com/matthiaskoenig/sbmlode"
+Issues = "https://github.com/matthiaskoenig/sbmlode/issues"
+Changelog = "https://matthiaskoenig.github.io/sbmlode/release-notes/"
+Download = "https://pypi.org/project/sbmlode"
+
+[tool.hatch.version]
+path = "./src/sbmlode/__init__.py"
+
+[tool.hatch.build.targets.sdist]
+# the package with what builds and tests it, nothing else of the repository
+only-include = [
+	"src",
+	"tests",
+	"tox.ini",
+	"README.md",
+	"LICENSE",
+	"CITATION.cff",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/sbmlode"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+# the tests import their helpers (`ode_helpers`, `testsuite`) and the scripts of
+# the repository (`scripts.docs_images`)
+pythonpath = [".", "tests"]
+markers = [
+    "sbml_testsuite: full sweep over the SBML test suite, slow; deselect with -m 'not sbml_testsuite'",
+]
+
+[tool.ty.environment]
+# the package lives in the src layout; the checked python version is inferred
+# from `project.requires-python` (i.e. the oldest supported version)
+root = ["./src", "."]
+
+[tool.ty.src]
+include = ["src", "tests"]
+
+[tool.ty.terminal]
+# warnings are failures: keep the codebase free of any diagnostic
+error-on-warning = true

sbmlode-0.1.0/src/sbmlode/__init__.py

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+"""Export of an SBML model as its system of ordinary differential equations.
+
+`OdeSystem.from_sbml` analyses a model into its ODE system, which is rendered in the
+formats of `FORMATS`:
+
+```python
+from sbmlode import OdeSystem
+
+system = OdeSystem.from_sbml("model.xml")
+code = system.render("python", simulator=True)
+system.write("model.py")
+```
+
+The methods `render`, `write` and `render_template` of `OdeSystem` are the functions of
+the same names of this package, which take the system as their first argument.
+
+The math of the model is written by the printers of `sbmlode.printers`,
+one per dialect, the text of the model through the helpers of
+`sbmlode.text`, the formats by `sbmlode.formats`:
+python, julia and R code, and typst, LaTeX and markdown documents
+(`sbmlode.documents`), e.g. `system.write("model.typ")`.
+"""
+
+# the version comes first, the modules below read it when they render
+__version__ = "0.1.0"
+
+from sbmlode.formats import (
+    FORMATS,
+    Format,
+    render,
+    render_template,
+    write,
+)
+from sbmlode.system import OdeSystem
+
+__all__: list[str] = [
+    "FORMATS",
+    "Format",
+    "OdeSystem",
+    "__version__",
+    "render",
+    "render_template",
+    "write",
+]