fastobo

library0.14.1pypypi✓ verified 81d ago

Faultless AST for Open Biomedical Ontologies (OBO) in Python. Version 0.14.1 provides robust parsing, manipulation, and serialization of OBO files, with optional OWL export. Released regularly, with pre-built wheels for many platforms.

serialization data

pip install fastobo

github ↗package ↗docs ↗changelog ↗

INSTALL

IMPORT

SIG · FASTOBO

fastobo

serializationpythonv0.14.1

Install

1.7s avg

Import

—

Disk

23MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.14.1 · 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 1.7s · import 0.000s · 26MB

23MB installed

● package 23MB

Code

Verified usage

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

OboDoc

✓ from fastobo import doc

✗ from fastobo import OboDoc

load

✓ from fastobo import load

dump_graph

✓ from fastobo import dump_graph

Load and iterate over an OBO ontology file.

from fastobo import load # Load an OBO file (use a test file or URL) doc = load('go.obo') # Iterate over all frames for frame in doc: # Frames have an 'id' and 'name' attribute print(frame.id, frame.name) # Convert to OWL (requires fastobo-owl, install separately) # from fastobo import dump_owl # dump_owl(doc, 'go.owl')

fastobo --version

Debug

Known issues

gotchaSome frame attributes (e.g., 'name') may be None if not defined in the OBO file. Always check for None before use.

fix

frame.name or ''

affects: all

deprecatedSupport for Python 3.6 removed in v0.12.0; requires Python >=3.7.

fix

Upgrade Python to >=3.7

affects: >=0.12.0

gotchaThe OWL export functionality (dump_owl) is only available if the fastobo-owl dependency is installed (not included by default).

fix

pip install fastobo[owl] or pip install fastobo-owl

affects: >=0.11.0

gotchaWhen loading from a file, the file must be a Path-like object or a string; streams are not supported directly. Use load(open(...)) may fail because load expects a filename or path string, not a file handle.

fix

doc = load('/path/to/file.obo') # Do not pass file handle

affects: all

breakingIn v0.12.0, the GIL is no longer released when loading from a file on Windows; this may affect performance but fixes compilation.

fix

No action needed unless relying on concurrency; upgrade to latest

affects: 0.12.0+

Upgrade

Version history

0.14.1latest on PyPI · released Oct 25, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

14 hits · last 30 days

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Resources

githubhttps://github.com/fastobo/fastobo-py ↗

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

docshttps://fastobo.readthedocs.io/ ↗

changeloghttps://fastobo.readthedocs.io/en/latest/changes.html ↗