[minor] Migrate to pyproject.toml

.binder/environment.yml

@@ -6,7 +6,6 @@ dependencies:
 - owlready2 =0.46
 - pandas =2.2.2
 - pint =0.23
-- python >= 3.9
-- pyiron_atomistics >= 0.5.4
-- pyiron-data >= 0.0.29
+- pyiron_atomistics =0.5.4
+- pyiron-data =0.0.29
 - lammps

.ci_support/environment-pyiron_atomistics.yml

@@ -1,6 +1,5 @@
 channels:
   - conda-forge
 dependencies:
-  - python >= 3.9
-  - pyiron_atomistics >= 0.5.4
-  - pyiron-data >= 0.0.29
+  - pyiron_atomistics =0.5.4
+  - pyiron-data =0.0.29

.ci_support/lower_bound.yml

@@ -0,0 +1,10 @@
+channels:
+- conda-forge
+dependencies:
+- numpy =1.26.3
+- openjdk
+- owlready2 =0.46
+- pandas =2.1.4
+- pint =0.23
+- pyiron_atomistics =0.5.0
+- pyiron-data =0.0.26

.github/workflows/daily.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   Tests-and-Coverage:
-    uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-1.1.0b
+    uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-2.0.0b
     secrets: inherit
     with:
       tests-env-files: .ci_support/environment.yml .ci_support/environment-pyiron_atomistics.yml

.github/workflows/dependabot-pr.yml

@@ -6,5 +6,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/dependabot-pr.yml@actions-1.1.0b
+    uses: pyiron/actions/.github/workflows/dependabot-pr.yml@actions-2.0.0b
     secrets: inherit

.github/workflows/pr-labeled.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/pr-labeled.yml@actions-1.1.0b
+    uses: pyiron/actions/.github/workflows/pr-labeled.yml@actions-2.0.0b
     secrets: inherit

.github/workflows/pr-target-opened.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/pr-target-opened.yml@actions-1.1.0b
+    uses: pyiron/actions/.github/workflows/pr-target-opened.yml@actions-2.0.0b
     secrets: inherit

.github/workflows/push-pull.yml

@@ -1,6 +1,6 @@
 # This runs jobs which pyiron modules should run on pushes or PRs to main
 
-name: Push-Pull-main
+name: Push-Pull
 
 on:
   push:
@@ -9,9 +9,10 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/push-pull-main.yml@actions-1.1.0b
+    uses: pyiron/actions/.github/workflows/push-pull.yml@actions-2.0.0b
     secrets: inherit
     with:
       docs-env-files: .ci_support/environment.yml .ci_support/environment-docs.yml
       notebooks-env-files: .ci_support/environment.yml .ci_support/environment-pyiron_atomistics.yml .ci_support/environment-lammps.yml
-      tests-env-files: .ci_support/environment.yml .ci_support/environment-pyiron_atomistics.yml
+      tests-env-files: .ci_support/environment.yml .ci_support/environment-pyiron_atomistics.yml
+      alternate-tests-env-files: .ci_support/lower_bound.yml

.github/workflows/release.yml

@@ -7,5 +7,8 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/[email protected]
-    secrets: inherit
+    uses: pyiron/actions/.github/workflows/[email protected]
+    secrets: inherit
+    with:
+      semantic-upper-bound: 'minor'
+      lower-bound-yaml: '.ci_support/lower_bound.yml'

.github/workflows/weekly.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   codeql:
-    uses: pyiron/actions/.github/workflows/codeql.yml@actions-1.1.0b
+    uses: pyiron/actions/.github/workflows/codeql.yml@actions-2.0.0b
     secrets: inherit

MANIFEST.in

@@ -1,3 +1 @@
-include versioneer.py
-include pyiron_ontology/_version.py
 include LICENSE

docs/environment.yml

@@ -6,6 +6,7 @@ dependencies:
 - nbsphinx
 - sphinx-gallery
 - sphinx-rtd-theme
+- versioneer
 - numpy =1.26.4
 - openjdk
 - owlready2 =0.46

pyiron_ontology/__init__.py

@@ -1,7 +1,6 @@
 from ._version import get_versions
 
 __version__ = get_versions()["version"]
-del get_versions
 
 from pyiron_ontology.atomistics.constructor import AtomisticsOntology
 from pyiron_ontology.constructor import Constructor

pyproject.toml

@@ -0,0 +1,59 @@
+[build-system]
+requires = [
+    "numpy",
+    "owlready2",
+    "pandas",
+    "pint",
+    "setuptools",
+    "versioneer[toml]==0.29",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyiron_ontology"
+description = "pyiron_ontology - module extension to pyiron."
+readme = "docs/README.md"
+keywords = [ "pyiron",]
+requires-python = ">=3.9, <3.13"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: BSD License",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "numpy==1.26.4",
+    "owlready2==0.46",
+    "pandas==2.2.2",
+    "pint==0.23",
+]
+dynamic = [ "version",]
+authors = [
+    { name = "Liam Huber", email = "[email protected]" },
+]
+
+[project.license]
+file = "LICENSE"
+
+[project.urls]
+Homepage = "https://github.com/pyiron/pyiron_ontology"
+Documentation = "https://pyiron-ontology.readthedocs.io"
+Repository = "https://github.com/pyiron/pyiron_ontology"
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440-pre"
+versionfile_source = "pyiron_ontology/_version.py"
+parentdir_prefix = "pyiron_ontology"
+tag_prefix = "pyiron_ontology-"
+
+[tool.setuptools.packages.find]
+include = [ "pyiron_ontology*",]
+
+[tool.setuptools.dynamic.version]
+attr = "pyiron_ontology.__version__"

setup.py

@@ -1,42 +1,8 @@
-"""
-Setuptools based setup module
-"""
-from setuptools import setup, find_packages
+from setuptools import setup
+
 import versioneer
 
 setup(
-    name='pyiron_ontology',
     version=versioneer.get_version(),
-    description='pyiron_ontology - module extension to pyiron.',
-    long_description='http://pyiron.org',
-
-    url='https://github.com/pyiron/pyiron_ontology',
-    author='Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department',
-    author_email='[email protected]',
-    license='BSD',
-
-    classifiers=[
-        'Development Status :: 5 - Production/Stable',
-        'Topic :: Scientific/Engineering :: Physics',
-        'License :: OSI Approved :: BSD License',
-        'Intended Audience :: Science/Research',
-        'Operating System :: OS Independent',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3.11',
-    ],
-
-    keywords='pyiron',
-    packages=find_packages(exclude=["*tests*", "*docs*", "*binder*", "*conda*", "*notebooks*", "*.ci_support*"]),
-    install_requires=[
-        'numpy==1.26.4',
-        'owlready2==0.46',
-        'pandas==2.2.2',
-        'pint==0.23',
-    ],
-    extras_require={
-        "pyiron_atomistics": [],
-    },
     cmdclass=versioneer.get_cmdclass(),
-
-    )
+)