cobra

library0.31.1pypypi✓ verified 88d ago

COBRApy (0.31.1) is a Python package for constraint-based modeling of metabolic networks. It enables building, simulating, and analyzing genome-scale metabolic models using flux balance analysis (FBA) and related methods. Releases occur several times a year, with a focus on stability and new features.

data ai-ml

pip install cobra

github ↗package ↗homepage ↗docs ↗

INSTALL

IMPORT

SIG · COBRA

cobra

datapythonv0.31.1

Install

17.7s avg

Import

—

Disk

327MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.31.1 · 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 3.10–3.910 runs

build_error

glibc

py 3.10–3.910 runs

installs and imports cleanly · install 17.7s · import 0.000s · 304MB

327MB installed

● package 327MB

Code

Verified usage

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

Model

✓ from cobra import Model

✗ from cobra.core import Model

cobra.core provides internals; public API is from cobra.

Reaction

✓ from cobra import Reaction

✗ from cobra.core import Reaction

Public API from cobra top-level.

Metabolite

✓ from cobra import Metabolite

✗ from cobra.core import Metabolite

Top-level import is correct.

flux_analysis

✓ from cobra import flux_analysis

✗ from cobra.flux_analysis import pfba

Use flux_analysis.pfba, flux_analysis.single_gene_deletion, etc.

Create a simple model, add a reaction, set objective, and solve using FBA.

from cobra import Model, Reaction, Metabolite model = Model('example') # Add reaction: A -> B reaction = Reaction('R1') reaction.name = 'A to B' reaction.subsystem = 'Exchange' reaction.lower_bound = 0. # irreversible reaction.upper_bound = 1000. metabolite_a = Metabolite('A_c', compartment='c') metabolite_b = Metabolite('B_c', compartment='c') reaction.add_metabolites({metabolite_a: -1, metabolite_b: 1}) model.add_reactions([reaction]) model.objective = 'R1' # maximize flux through R1 solution = model.optimize() print(solution.objective_value)

Debug

Known issues

breakingIn cobra 0.31, the default solver interface changed to optlang. If you rely on the older glpk interface directly, your code may break.

fix

Install cobra[optlang] and use optlang.glpk_interface (or other solver interfaces).

affects: >=0.31

gotchaSetting model.objective = reaction_object does not automatically change the objective coefficient; you must set coefficient explicitly via model.objective = {reaction: 1} or reaction.objective_coefficient = 1.

fix

Use model.objective = {reaction: 1} or reaction.objective_coefficient = 1 for a single reaction.

affects: all

deprecatedThe method 'cobra.io.sbml.write_sbml' is deprecated; use 'cobra.io.write_sbml_model' instead.

fix

Replace cobra.io.sbml.write_sbml with cobra.io.write_sbml_model.

affects: >=0.30

gotchaFlux balance analysis results are stored in cobra.Solution which is not subscriptable; use solution.fluxes (pandas Series) to access individual fluxes.

fix

Use solution.fluxes['REACTION_ID'] instead of solution['REACTION_ID'].

affects: all

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'cobra'

cobra is not installed or virtual environment not activated.

fix

Run 'pip install cobra' in your terminal.

ValueError: objective must be a scalar (reaction) or dict of reactions to coefficients

Setting model.objective = ['R1', 'R2'] incorrectly (list instead of dict or single reaction).

fix

Use model.objective = 'R1' for a single reaction or model.objective = {'R1': 1, 'R2': 0.5} for multiple.

No solver interface found

optlang not installed and no solver (e.g., GLPK, CPLEX) available.

fix

Install optlang: 'pip install cobra[optlang]' or install a solver like GLPK.

Upgrade

Version history

0.31.1latest on PyPI · released Mar 26, 2026

Audit

Dependencies

optlangoptionalDefault LP solver interface (GLPK, CPLEX, Gurobi). Optional but recommended.

pandasrequiredRequired for DataFrame-based results and model I/O.

libsbmloptionalRequired for SBML file support.

Agent activity

17 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/opencobra/cobrapy ↗

packagehttps://pypi.org/project/cobra/ ↗

homepagehttps://opencobra.github.io/cobrapy ↗

docshttps://cobrapy.readthedocs.io ↗