release: tooling cleanup from develop

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.9', '3.12']
     steps:
       - uses: actions/checkout@v4
       - name: Set up PDM
@@ -26,6 +26,9 @@ jobs:
       - name: Run linter
         run: |
           pdm run ruff check .
+      - name: Run type checker
+        run: |
+          pdm run mypy xyz2graph
       - name: Run tests
         run: |
           pdm run pytest --cov --cov-report=xml --junitxml=junit.xml -o junit_family=legacy

.github/workflows/publish.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Run linter
         run: python -m ruff check .
       - name: Run type checker
-        run: python -m mypy .
+        run: python -m mypy xyz2graph
       - name: Build package
         run: |
           python -m pip install hatchling hatch-vcs
@@ -44,7 +44,7 @@ jobs:
       - name: Create Release
         uses: softprops/action-gh-release@v2
         with:
-          body_path: CHANGELOG.md
+          generate_release_notes: true
       - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:

README.md

@@ -9,7 +9,6 @@
 
 [![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/zotko/xyz2graph/ci.yml)](https://github.com/zotko/xyz2graph/actions)
 [![codecov](https://codecov.io/gh/zotko/xyz2graph/branch/develop/graph/badge.svg?token=TXP63VKUIP)](https://codecov.io/gh/zotko/xyz2graph)
-[![Dependabot](https://img.shields.io/badge/dependabot-enabled-025E8C?logo=dependabot&logoColor=white)](https://github.com/zotko/xyz2graph/network/updates)
 
 [![PyPI Downloads](https://static.pepy.tech/badge/xyz2graph/month)](https://pepy.tech/projects/xyz2graph)
 [![GitHub Stars](https://img.shields.io/github/stars/zotko/xyz2graph)](https://github.com/zotko/xyz2graph/stargazers)
@@ -33,7 +32,7 @@ pip install xyz2graph
 
 ## Requirements
 
-- Python 3.8+
+- Python 3.9+
 - Dependencies: NumPy, Plotly, NetworkX
 
 ## Quick Start

pyproject.toml

@@ -41,28 +41,10 @@ Repository = "https://github.com/zotko/xyz2graph"
 Documentation = "https://zotko.github.io/xyz2graph"
 "Bug Tracker" = "https://github.com/zotko/xyz2graph/issues"
 
-[tool.pdm.dev-dependencies]
-docs = [
-    "mkdocs>=1.6.0",
-    "mkdocs-material>=9.5.0",
-    "mkdocstrings-python>=1.12.0",
-    "mkdocs-include-markdown-plugin>=7.1.5"
-]
-dev = [
-    "pytest>=7.0.0,<8.0.0",
-    "pytest-cov>=4.0.0,<5.0.0",
-    "ruff>=0.1.0,<1.0.0",
-    "mypy>=1.0.0,<2.0.0",
-    "build>=1.0.0,<2.0.0",
-    "twine>=4.0.0,<5.0.0",
-    "pre-commit>=4.1.0",
-]
-
 [tool.ruff]
-target-version = "py38"
+target-version = "py39"
 line-length = 100
 src = ["xyz2graph"]
-include = ["test/test_*.py"]
 
 [tool.ruff.lint.per-file-ignores]
 "{__init__.py,tests/*,helpers.py,logging.py}" = ["D"]
@@ -79,16 +61,39 @@ lines-after-imports = 2
 convention = "google"
 
 [tool.mypy]
+files = ["xyz2graph"]
 python_version = "3.9"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true
 check_untyped_defs = true
 
+[[tool.mypy.overrides]]
+module = ["plotly.*"]
+ignore_missing_imports = true
+
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 python_files = ["test_*.py"]
 addopts = "--cov=xyz2graph --cov-report=term-missing"
 
 [project.scripts]
 xyz2graph = "xyz2graph.cli:main"
+
+[dependency-groups]
+dev = [
+    "pytest>=7.0.0,<8.0.0",
+    "pytest-cov>=4.0.0,<5.0.0",
+    "ruff>=0.1.0,<1.0.0",
+    "mypy>=1.0.0,<2.0.0",
+    "types-networkx>=3.4.2.20250509",
+    "build>=1.0.0,<2.0.0",
+    "twine>=4.0.0,<5.0.0",
+    "pre-commit>=4.1.0",
+]
+docs = [
+    "mkdocs>=1.6.0",
+    "mkdocs-material>=9.5.0",
+    "mkdocstrings-python>=1.12.0",
+    "mkdocs-include-markdown-plugin>=7.1.5",
+]

tests/test_molgraph.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-from typing import List
 
 import numpy as np
 import pytest
@@ -181,7 +180,7 @@ def test_property_consistency() -> None:
         (["Fe", "C", "O", "O", "O", "O", "O"], "CFeO5"),  # Complex case
     ],
 )
-def test_formula(elements: List[str], expected_formula: str) -> None:
+def test_formula(elements: list[str], expected_formula: str) -> None:
     """Test molecular formula generation."""
     mol = MolGraph()
     for i, el in enumerate(elements):

xyz2graph/cli.py

@@ -6,7 +6,7 @@
 import sys
 import tempfile
 from pathlib import Path
-from typing import List, Tuple, Union
+from typing import Union
 
 import plotly.offline as offline
 from plotly.io import write_html
@@ -15,7 +15,7 @@
 from .logging import logger
 
 
-def parse_remove_arg(remove_str: str) -> Tuple[List[int], List[str]]:
+def parse_remove_arg(remove_str: str) -> tuple[list[int], list[str]]:
     """Parse remove argument string into indices and elements.
 
     Args:
@@ -48,7 +48,7 @@ def parse_remove_arg(remove_str: str) -> Tuple[List[int], List[str]]:
     return indices, elements
 
 
-def format_remove_message(indices: List[int], elements: List[str]) -> str:
+def format_remove_message(indices: list[int], elements: list[str]) -> str:
     """Format the message showing which atoms will be removed.
 
     Args:

xyz2graph/constants.py

@@ -7,10 +7,7 @@
         CPK colors.
 """
 
-from typing import Dict
-
-
-_DEFAULT_RADII: Dict[str, float] = {
+_DEFAULT_RADII: dict[str, float] = {
     "Ac": 1.88,
     "Ag": 1.59,
     "Al": 1.35,
@@ -100,7 +97,7 @@
     "Zn": 1.45,
     "Zr": 1.56,
 }
-_DEFAULT_CPK_COLORS: Dict[str, str] = {
+_DEFAULT_CPK_COLORS: dict[str, str] = {
     "Ar": "cyan",
     "B": "salmon",
     "Ba": "darkgreen",

xyz2graph/graph.py

@@ -10,11 +10,7 @@
 from itertools import compress
 from pathlib import Path
 from typing import (
-    Dict,
-    FrozenSet,
-    List,
     Optional,
-    Set,
     Union,
 )
 
@@ -64,17 +60,17 @@ class MolGraph:
         adj_matrix (NDArray[np.int_]): Square matrix representing molecular connectivity.
     """
 
-    atoms: List[Atom] = field(default_factory=list)
-    bonds: List[Bond] = field(default_factory=list)
+    atoms: list[Atom] = field(default_factory=list)
+    bonds: list[Bond] = field(default_factory=list)
     comment: str = field(default="")
 
     # Customizable parameters with defaults
-    default_radii: Dict[str, float] = field(default_factory=lambda: dict(_DEFAULT_RADII))
-    cpk_colors: Dict[str, str] = field(default_factory=lambda: dict(_DEFAULT_CPK_COLORS))
+    default_radii: dict[str, float] = field(default_factory=lambda: dict(_DEFAULT_RADII))
+    cpk_colors: dict[str, str] = field(default_factory=lambda: dict(_DEFAULT_CPK_COLORS))
     cpk_color_rest: str = field(default="pink")
 
     @property
-    def elements(self) -> List[str]:
+    def elements(self) -> list[str]:
         """Get list of elements in the molecule.
 
         Returns:
@@ -83,7 +79,7 @@ def elements(self) -> List[str]:
         return [atom.element for atom in self.atoms]
 
     @property
-    def indices(self) -> List[int]:
+    def indices(self) -> list[int]:
         """Get list of atom indices.
 
         Returns:
@@ -92,7 +88,7 @@ def indices(self) -> List[int]:
         return [atom.index for atom in self.atoms]
 
     @property
-    def x(self) -> List[float]:
+    def x(self) -> list[float]:
         """Get x coordinates of all atoms.
 
         Returns:
@@ -101,7 +97,7 @@ def x(self) -> List[float]:
         return [atom.x for atom in self.atoms]
 
     @property
-    def y(self) -> List[float]:
+    def y(self) -> list[float]:
         """Get y coordinates of all atoms.
 
         Returns:
@@ -110,7 +106,7 @@ def y(self) -> List[float]:
         return [atom.y for atom in self.atoms]
 
     @property
-    def z(self) -> List[float]:
+    def z(self) -> list[float]:
         """Get z coordinates of all atoms.
 
         Returns:
@@ -128,7 +124,7 @@ def xyz(self) -> NDArray[np.float64]:
         return np.array([[atom.x, atom.y, atom.z] for atom in self.atoms])
 
     @property
-    def atomic_radii(self) -> List[float]:
+    def atomic_radii(self) -> list[float]:
         """Get atomic radii for all atoms.
 
         Returns:
@@ -137,7 +133,7 @@ def atomic_radii(self) -> List[float]:
         return [atom.radius for atom in self.atoms]
 
     @property
-    def bond_lengths(self) -> Dict[FrozenSet[int], float]:
+    def bond_lengths(self) -> dict[frozenset[int], float]:
         """Get dictionary of bond lengths.
 
         Returns:
@@ -146,13 +142,13 @@ def bond_lengths(self) -> Dict[FrozenSet[int], float]:
         return {bond.indices: bond.length for bond in self.bonds}
 
     @property
-    def adj_list(self) -> Dict[int, Set[int]]:
+    def adj_list(self) -> dict[int, set[int]]:
         """Get adjacency list representation of molecular graph.
 
         Returns:
             Dict[int, Set[int]]: Dictionary mapping atom indices to sets of bonded atom indices.
         """
-        adj: Dict[int, Set[int]] = {}
+        adj: dict[int, set[int]] = {}
         for bond in self.bonds:
             i1, i2 = tuple(bond.indices)
             adj.setdefault(i1, set()).add(i2)
@@ -168,7 +164,7 @@ def adj_matrix(self) -> NDArray[np.int_]:
                 are bonded and 0 otherwise.
         """
         n = len(self.atoms)
-        matrix = np.zeros((n, n), dtype=np.int_)
+        matrix: NDArray[np.int_] = np.zeros((n, n), dtype=np.int_)
         for bond in self.bonds:
             i, j = tuple(bond.indices)
             matrix[i, j] = matrix[j, i] = 1
@@ -230,7 +226,7 @@ def from_string(self, xyz_string: str) -> None:
                     )
                 except (IndexError, ValueError) as err:
                     raise ValueError(
-                        f"Invalid format in line {i+3}, expected: element x y z"
+                        f"Invalid format in line {i + 3}, expected: element x y z"
                     ) from err
 
             if len(self.atoms) != n_atoms:
@@ -326,12 +322,13 @@ def distance_matrix(self) -> NDArray[np.float64]:
         """
         try:
             distances = self.xyz[:, np.newaxis, :] - self.xyz
-            return np.sqrt(np.einsum("ijk,ijk->ij", distances, distances))
+            result: NDArray[np.float64] = np.sqrt(np.einsum("ijk,ijk->ij", distances, distances))
+            return result
         except MemoryError:
             # Fall back to loop-based method
             n_atoms = len(self.atoms)
             logger.info("Using memory-efficient method for distance calculation")
-            distance_matrix = np.zeros((n_atoms, n_atoms), dtype=np.float64)
+            distance_matrix: NDArray[np.float64] = np.zeros((n_atoms, n_atoms), dtype=np.float64)
             for i in range(n_atoms):
                 diff = self.xyz[i] - self.xyz
                 distance_matrix[i] = np.sqrt(np.sum(diff * diff, axis=1))
@@ -382,8 +379,8 @@ def set_element_radius(self, element: str, radius: float) -> None:
 
     def remove(
         self,
-        indices: Optional[List[int]] = None,
-        elements: Optional[List[str]] = None,
+        indices: Optional[list[int]] = None,
+        elements: Optional[list[str]] = None,
         inplace: bool = False,
     ) -> Optional["MolGraph"]:
         """Remove atoms by indices and/or elements.
@@ -460,7 +457,7 @@ def to_networkx(self) -> nx.Graph:
         """
         logger.debug("Creating NetworkX graph")
 
-        G = nx.Graph()
+        G: nx.Graph = nx.Graph()
 
         # Add nodes with attributes
         for atom in self.atoms:

xyz2graph/molecule.py

@@ -4,7 +4,7 @@
 """
 
 from dataclasses import dataclass, field
-from typing import FrozenSet, cast
+from typing import cast
 
 import numpy as np
 from numpy.typing import NDArray
@@ -51,12 +51,12 @@ def __post_init__(self) -> None:
         self.length = round(np.sqrt(dx * dx + dy * dy + dz * dz), 5)
 
     @property
-    def atoms(self) -> FrozenSet[Atom]:
+    def atoms(self) -> frozenset[Atom]:
         """Get the atoms involved in the bond as an order-independent set."""
         return frozenset([self.atom1, self.atom2])
 
     @property
-    def indices(self) -> FrozenSet[int]:
+    def indices(self) -> frozenset[int]:
         """Get indices of bonded atoms."""
         return frozenset([self.atom1.index, self.atom2.index])