Switch back to using pyproject.toml to build

.github/workflows/gh-ci.yaml

@@ -150,12 +150,13 @@ jobs:
 
     - name: Build package
       run: |
-        python setup.py sdist
+        python3 -m pip install --upgrade build
+        python3 -m build
 
     - name: Check package build
       run: |
-        DISTRIBUTION=$(ls -t1 dist/openff-nagl-*.tar.gz | head -n 1)
-        test -n "${DISTRIBUTION}" || { echo "no distribution dist/openff-nagl-*.tar.gz found"; exit 1; }
+        DISTRIBUTION=$(ls -t1 dist/openff_nagl-*.tar.gz | head -n 1)
+        test -n "${DISTRIBUTION}" || { echo "no distribution dist/openff_nagl-*.tar.gz found"; exit 1; }
         echo "twine check $DISTRIBUTION"
         twine check $DISTRIBUTION
 

.pre-commit-config.yaml

@@ -6,16 +6,16 @@
 exclude: '^(\.tox|ci/templates|\.bumpversion\.cfg)(/|$)'
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: master
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: debug-statements
   - repo: https://github.com/timothycrosley/isort
-    rev: master
+    rev: 5.13.2
     hooks:
       - id: isort
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: master
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
     hooks:
-      - id: flake8
+      - id: flake8

README.md

@@ -4,7 +4,7 @@ NAGL
 
 | **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-nagl.svg)](https://github.com/openforcefield/openff-nagl/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/openforcefield/openff-nagl/latest)  [![Documentation Status](https://readthedocs.org/projects/openff-nagl/badge/?version=latest)](https://docs.openforcefield.org/projects/nagl/en/latest/?badge=latest)                                                                                                        |
 | :----------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| **Status**         | [![GH Actions Status](https://github.com/openforcefield/openff-nagl/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/openforcefield/openff-nagl/actions?query=branch%3Amain+workflow%3Agh-ci) [![codecov](https://codecov.io/gh/openforcefield/openff-nagl/branch/main/graph/badge.svg)](https://codecov.io/gh/openforcefield/openff-nagl/branch/main) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/openforcefield/openff-nagl.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/openforcefield/openff-nagl/context:python) |
+| **Status**         | [![GH Actions Status](https://github.com/openforcefield/openff-nagl/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/openforcefield/openff-nagl/actions?query=branch%3Amain+workflow%3Agh-ci) [![codecov](https://codecov.io/gh/openforcefield/openff-nagl/branch/main/graph/badge.svg)](https://codecov.io/gh/openforcefield/openff-nagl/branch/main) |
 | **Community**      | [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12792526.svg)](https://doi.org/10.5281/zenodo.12792526)                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 
 A playground for applying graph convolutional networks to molecules, with a focus on learning continuous "atom-type" embeddings and from these classical molecule force field parameters.

docs/CHANGELOG.md

@@ -14,6 +14,11 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
 
+## Current development
+
+### Changed
+- Switched build from using `setup.py` to `pyproject.toml`.
+
 ## v0.5.0 -- 2024-11-06
 
 ### Authors

pyproject.toml

@@ -0,0 +1,69 @@
+[build-system]
+requires = [
+  "setuptools",
+  "versioneer[toml]==0.29",
+  "wheel",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "openff-nagl"
+description = "A playground for applying graph convolutional networks to molecules."
+readme = "README.md"
+license = { file = "LICENSE" }
+authors = [
+    {name = "Lily Wang", email = "lily.wang@openforcefield.org"},
+]
+maintainers = [
+    {name = "Lily Wang", email = "lily.wang@openforcefield.org"},
+]
+requires-python = ">=3.10"
+dynamic = ["version"]
+
+[tool.setuptools.packages]
+find = {}
+
+[project.optional-dependencies]
+test = [
+    "pytest>=6.0",
+    "pytest-xdist>=2.5",
+    "pytest-cov>=3.0",
+]
+doc = [
+    "sphinx>=1.8",
+    "openff-sphinx-theme @ git+https://github.com/openforcefield/openff-sphinx-theme.git@main",
+]
+
+[project.scripts]
+openff-nagl = "openff.nagl.cli:cli"
+
+[project.urls]
+source = "https://github.com/openforcefield/openff-nagl"
+documentation = "https://docs.openforcefield.org/projects/nagl/"
+
+[tool.pytest.ini_options]
+testpaths = [
+    "openff/nagl/tests",
+]
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "openff/nagl/_version.py"
+versionfile_build = "openff/nagl/_version.py"
+tag_prefix = "v"
+parentdir_prefix = "openff-nagl-"
+
+[tool.coverage.run]
+omit = [
+    "*/*/_tests/*",
+    "openff/nagl/_version.py",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "raise NotImplementedError",
+    "@overload",
+]

setup.cfg

@@ -1,59 +1,18 @@
-# Helper file to handle all configs
-
-[coverage:run]
-# .coveragerc to control coverage.py and pytest-cov
-omit =
-    # Omit the tests
-    */*/tests/*
-    # Omit generated versioneer
-    openff/nagl/_version.py
-
-[coverage:report]
-exclude_lines =
-    pragma: no cover
-    if TYPE_CHECKING:
-
 [isort]
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0
 use_parentheses = True
 line_length = 80
 
-
-[yapf]
-# YAPF, in .style.yapf files this shows up as "[style]" header
-COLUMN_LIMIT = 80
-INDENT_WIDTH = 4
-USE_TABS = False
-
 [flake8]
 # Flake8, PyFlakes, etc
 max-line-length = 80
 exclude = versioneer.py
 
-[versioneer]
-# Automatic version numbering scheme
-VCS = git
-style = pep440
-versionfile_source = openff/nagl/_version.py
-versionfile_build = openff/nagl/_version.py
-tag_prefix = v
-
-[aliases]
-test = pytest
-
-[tool:pytest]
-testpaths = openff/nagl/tests
-
 [build_sphinx]
 all-files = 1
 source-dir = docs/
 build-dir = docs/_build
 warning-is-error = 1
 
-[options]
-packages = find_namespace:
-
-[options.packages.find]
-include = ["openff.*"]