From d2b04fbedcaef042a098ed248605d00ff88ab6ae Mon Sep 17 00:00:00 2001
From: Tom Mitchell <tcmitchell@users.noreply.github.com>
Date: Fri, 7 Aug 2026 10:10:42 -0400
Subject: [PATCH] Switch to pyproject.toml

Modernize the package by removing setup.py and replacing it with
pyproject.toml. Also make the build and documentation status badges
link to their respective artifacts.
---
 README.md      |  4 ++--
 pyproject.toml | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++
 setup.py       | 46 ----------------------------------------
 3 files changed, 59 insertions(+), 48 deletions(-)
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py

diff --git a/README.md b/README.md
index c08b0a5..a209ad7 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # pySBOL2
-![gh-action badge](https://github.com/SynBioDex/pySBOL2/workflows/Python%20package/badge.svg)
-![readthedocs badge](https://readthedocs.org/projects/pysbol2/badge/)
+[![gh-action badge](https://github.com/SynBioDex/pySBOL2/workflows/Python%20package/badge.svg)](https://github.com/SynBioDex/pySBOL2/actions/workflows/python-package.yml)
+[![readthedocs badge](https://readthedocs.org/projects/pysbol2/badge/)](https://pysbol.readthedocs.io)
 
 **pySBOL2** is a pure Python implementation of the
 SBOL 2.3.0 standard [Synthetic Biology Open Language (SBOL)](https://sbolstandard.org/) - 
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..959b2e1
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,57 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [ "setuptools>=80.1" ]
+
+[project]
+name = "sbol2"
+description = "Pure Python implementation of SBOL 2 standard"
+readme = "README.md"
+keywords = [
+  "biology",
+  "synthetic biology",
+]
+license = "Apache-2.0"
+authors = [
+  { name = "Bryan Bartley", email = "editors@sbolstandard.org" },
+]
+requires-python = ">=3.11"
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Developers",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
+]
+dynamic = [ "version" ]
+dependencies = [
+  "deprecated",
+  "lxml",
+  # As of August 2026 the code is incompatible with packaging >= 26.1
+  # https://github.com/SynBioDex/pySBOL2/issues/450
+  "packaging<26.1",
+  "python-dateutil",
+  "rdflib>=5",
+  "requests",
+  "urllib3",
+]
+urls.changelog = "https://github.com/SynBioDex/pySBOL2/blob/master/CHANGELOG.md"
+urls.documentation = "https://pysbol.readthedocs.io/"
+urls.homepage = "https://github.com/SynBioDex/pySBOL2"
+urls.issues = "https://github.com/SynBioDex/pySBOL2/issues"
+urls.source = "https://github.com/SynBioDex/pySBOL2.git"
+
+[dependency-groups]
+# Install with pip: "python3 -m pip install --group dev"
+# Install with uv: "uv sync --all-groups" or "uv sync --group dev"
+dev = [
+  "pycodestyle>=2.14",
+  "ruff>=0.16.1",
+]
+
+[tool.setuptools]
+packages = [ "sbol2" ]
+# Include libSBOLj.jar in the distribution
+package-data.sbol2 = [ "libSBOLj.jar" ]
+dynamic.version = { attr = "sbol2.__version__" }
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 057b8dd..0000000
--- a/setup.py
+++ /dev/null
@@ -1,46 +0,0 @@
-from setuptools import setup
-
-setup(name='sbol2',
-      version='1.5',
-      description='Pure Python implementation of SBOL 2 standard',
-      python_requires='>=3.11',
-      url='https://github.com/SynBioDex/pySBOL2',
-      author='Bryan Bartley',
-      author_email='editors@sbolstandard.org',
-      license='Apache-2',
-      # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
-      classifiers=[
-            # How mature is this project? Common values are
-            #   3 - Alpha
-            #   4 - Beta
-            #   5 - Production/Stable
-            'Development Status :: 5 - Production/Stable',
-
-            # Indicate who your project is intended for
-            'Intended Audience :: Developers',
-
-            # Pick your license as you wish (should match "license" above)
-            'License :: OSI Approved :: Apache Software License',
-
-            # Specify the Python versions you support here. In particular, ensure
-            # that you indicate whether you support Python 2, Python 3 or both.
-            'Programming Language :: Python :: 3'
-      ],
-      # What does your project relate to?
-      keywords='synthetic biology',
-      packages=['sbol2'],
-      install_requires=[
-            'rdflib>=5.0',
-            'python-dateutil',
-            'deprecated',
-            'lxml',
-            'requests',
-            'urllib3',
-            # As of August 2026 the code is incompatible with packaging >= 26.1
-            # https://github.com/SynBioDex/pySBOL2/issues/450
-            'packaging<26.1'
-      ],
-      package_data={'sbol2': ['libSBOLj.jar']},
-      tests_require=[
-            'pycodestyle>=2.6.0'
-      ])