Registry / data / python-libsbml

python-libsbml

library5.21.1pypypi✓ verified 87d ago

Python bindings for LibSBML, a library for reading, writing, and manipulating SBML (Systems Biology Markup Language) documents. This package provides the libsbml module, which wraps the C++ library SBML API with Python objects. Version 5.21.1 is current; releases follow the upstream LibSBML releases.

data serialization

pip install python-libsbml

package ↗homepage ↗

INSTALL

IMPORT

SIG · PYTHON-LIBSBML

python-libsbml

datapythonv5.21.1

Install

2.3s avg

Import

—

Disk

61MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v5.21.1 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 2.3s · import 0.000s · 63MB

61MB installed

● package 61MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

libsbml

✓ import libsbml

Top-level module name is 'libsbml' (lowercase). No subpackage needed.

Create an SBML Document, write to file, and read it back. Checks for operation success and errors.

import libsbml import sys document = libsbml.SBMLDocument(3, 2) # SBML Level 3 Version 2 model = document.createModel() model.setId("my_model") # Write to file writer = libsbml.SBMLWriter() result = writer.writeSBML(document, "output.xml") if result != libsbml.LIBSBML_OPERATION_SUCCESS: print("Error writing SBML") sys.exit(1) # Read back reader = libsbml.SBMLReader() document2 = reader.readSBML("output.xml") if document2.getNumErrors() > 0: print("Errors encountered:") document2.printErrors()

Debug

Known issues

breakingThe package name on PyPI is 'python-libsbml', but the import is 'libsbml'. Do not use 'import sbml' or 'import libSBML'.

fix

Use 'import libsbml'.

affects: all

gotchaSBMLDocument constructor takes (level, version) as arguments, but the default is (2, 4) in older LibSBML versions. Always specify if you need a specific SBML level.

fix

Explicitly pass level and version when creating a new document: libsbml.SBMLDocument(3, 2)

affects: all

gotchaError handling: writeSBML returns an integer status code, not a boolean. Checking 'if result:' may be misleading because LIBSBML_OPERATION_SUCCESS is 0 (falsy).

fix

Compare to libsbml.LIBSBML_OPERATION_SUCCESS explicitly: if result != libsbml.LIBSBML_OPERATION_SUCCESS.

affects: all

Errors

Common errors & fixes

ImportError: No module named libsbml

Package not installed or wrong Python environment.

fix

Install with: pip install python-libsbml. Ensure activating the correct virtual environment.

AttributeError: module 'libsbml' has no attribute 'SBMLDocument'

This can happen if there is a name collision: the variable 'libsbml' is redefined or overshadowed.

fix

Do not assign to the name 'libsbml' after importing. Use a different variable for your document: doc = libsbml.SBMLDocument()

Upgrade

Version history

5.21.1latest on PyPI · released Mar 9, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

6 hits · last 30 days

node

Resources

packagehttps://pypi.org/project/python-libsbml/ ↗

homepagehttp://sbml.org ↗