Set up basic test

.github/workflows/gh-ci.yaml

@@ -29,11 +29,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.11", "3.13"]
-        include:
-          - os: macos-latest
-            python-version: "3.11"
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -26,6 +26,7 @@ repos:
     hooks:
       - id: basedpyright
         files: "openff"
+        exclude: "_tests"
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: v0.8.6

openff/pablo/_pdb.py

@@ -1,13 +1,11 @@
 import itertools
-from collections.abc import Mapping
+from collections.abc import Iterable, Mapping
 from os import PathLike
-from pathlib import Path
-from collections.abc import Iterable
+from typing import assert_never
 
 import numpy as np
 from openff.toolkit import Molecule, Topology
 from openff.units import elements, unit
-from typing import assert_never
 
 from ._pdb_data import PdbData, ResidueMatch
 from ._utils import (
@@ -205,8 +203,7 @@ def topology_from_pdb(
 
     """
     # TODO: support streams and gzipped files
-    path = Path(path)
-    data = PdbData.parse_pdb(path.read_text().splitlines())
+    data = PdbData.from_file(path)
 
     molecules: list[Molecule] = []
     this_molecule = Molecule()

openff/pablo/_pdb_data.py

@@ -1,8 +1,10 @@
 import dataclasses
+from collections.abc import Iterable, Iterator, Mapping, Sequence
 from dataclasses import dataclass, field
 from functools import cached_property
+from os import PathLike
+from pathlib import Path
 from typing import Any, Self
-from collections.abc import Iterable, Iterator, Mapping, Sequence
 
 from ._utils import __UNSET__, dec_hex, with_neighbours
 from .residue import AtomDefinition, ResidueDefinition
@@ -140,6 +142,10 @@ class PdbData:
     cryst1_beta: float | None = None
     cryst1_gamma: float | None = None
 
+    @classmethod
+    def from_file(cls, path: str | PathLike[str]) -> Self:
+        return cls.parse_pdb(Path(path).read_text().splitlines())
+
     def _append_coord_line(self, line: str):
         for field_ in dataclasses.fields(self):
             value = getattr(self, field_.name)

openff/pablo/_tests/test_pdb_data.py

@@ -0,0 +1,9 @@
+import pytest
+from pkg_resources import resource_filename
+
+from openff.pablo._pdb_data import PdbData
+
+
+@pytest.mark.parametrize("pdbfile", ["data/5ap1_prepared.pdb"])
+def test_can_load_pdb_file_as_data(pdbfile: str):
+    PdbData.from_file(resource_filename(__name__, pdbfile))

pyproject.toml

@@ -54,7 +54,11 @@ include = ["openff.*"]
 
 [tool.pyright]
 include = ["openff"]
-exclude = [".soap", "openff/pablo/_version.py", "docs", "examples"]
+exclude = [
+  ".soap",
+  "docs",
+  "examples",
+]
 typeCheckingMode = "strict"
 
 reportUnsupportedDunderAll = "error"