Feature drop python39

.github/workflows/test.yaml

@@ -9,25 +9,43 @@ on:
 jobs:
   tests:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        include:
+          - python-version: "3.12"
+            coverage: true
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Set up Python
+      - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
-          python-version-file: ".python-version"
+          python-version: ${{ matrix.python-version }}
 
       - name: Install uv
         uses: astral-sh/setup-uv@v5
 
-      - name: Install repo
-        run: uv sync --all-extras --dev
+      # uv pip resolves & installs deps like pip (not an environment sync)
+      - name: Install package + test deps (uv pip)
+        run: uv pip install --system --group dev .
 
       - name: Run tests
-        run: bash scripts/tests.sh
+        run: python -m pytest --cov-report=term-missing --cov-report html:htmlcov --cov-config=pyproject.toml --cov=qcio --cov=tests .
 
       - name: Upload coverage HTML
+        if: ${{ matrix.coverage == true }}
         uses: actions/upload-artifact@v4
         with:
-          name: htmlcov
+          name: htmlcov-py${{ matrix.python-version }}
           path: htmlcov
+
+      # To catch manifest issues, we build and install from sdist on one version
+      - name: Build sdist (only on 3.12)
+        if: ${{ matrix.coverage == true }}
+        run: python -m pip install build && python -m build --sdist
+
+      - name: Install from sdist (only on 3.12)
+        if: ${{ matrix.coverage == true }}
+        run: python -m pip install dist/*.tar.gz

.python-version

@@ -1 +1 @@
-3.9
+3.10

CHANGELOG.md

@@ -8,6 +8,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ### Removed
 
+- 🚨Python 3.9 support. Minimum supported version is now 3.10. [#91](https://github.com/coltonbh/qcio/pull/91)
 - All constants and periodic table data moved to [qcconst](https://github.com/coltonbh/qcconst).
 - All cheminformatics methods, including those that used `rdkit` and `openbabel` such as `rmsd` and `align`. Placed these algorithms into [qcinf](https://github.com/coltonbh/qcinf) so that `qcio` can remain purely about data structures. All future algorithms will go into `qcinf`.
 

pyproject.toml

@@ -5,7 +5,7 @@ description = "Beautiful and user friendly data structures for quantum chemistry
 readme = "README.md"
 authors = [{ name = "Colton Hicks", email = "github@coltonhicks.com" }]
 license = { file = "LICENSE" }
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 keywords = ["quantum-chemistry", "data-structures", "cheminformatics"]
 dependencies = [
     "pydantic>=2.0.0, !=2.0.1, !=2.1.0",
@@ -22,11 +22,11 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
     "Natural Language :: English",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering",
     "Topic :: Software Development :: Libraries",
 ]

src/qcio/helper_types.py

@@ -1,11 +1,11 @@
 from pathlib import Path
-from typing import Annotated, Union
+from typing import Annotated
 
 import numpy as np
 from pydantic import BeforeValidator, GetPydanticSchema, PlainSerializer, SkipValidation
 from pydantic_core import core_schema
 
-StrOrPath = Annotated[Union[str, Path], PlainSerializer(lambda x: str(x))]
+StrOrPath = Annotated[str | Path, PlainSerializer(lambda x: str(x))]
 
 # Create the annotated type for numpy array
 SerializableNDArray = Annotated[

src/qcio/models/base_models.py

@@ -5,7 +5,7 @@
 from base64 import b64decode, b64encode
 from enum import Enum
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Optional, Union
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 import toml
@@ -66,7 +66,7 @@ class QCIOBaseModel(BaseModel, ABC):
     }
 
     @classmethod
-    def open(cls, filepath: Union[Path, str]) -> Self:
+    def open(cls, filepath: Path | str) -> Self:
         """Instantiate an object from data saved to disk.
 
         Args:
@@ -92,7 +92,7 @@ def open(cls, filepath: Union[Path, str]) -> Self:
         return cls.model_validate_json(data)
 
     @classmethod
-    def open_multi(cls, filepath: Union[Path, str]) -> list[Self]:
+    def open_multi(cls, filepath: Path | str) -> list[Self]:
         """Instantiate a list of objects from data saved to disk.
 
         Args:
@@ -119,7 +119,7 @@ def open_multi(cls, filepath: Union[Path, str]) -> list[Self]:
 
     def save(
         self,
-        filepath: Union[Path, str],
+        filepath: Path | str,
         exclude_none: bool = True,
         exclude_unset: bool = True,
         indent: int = 4,
@@ -227,7 +227,7 @@ class Files(QCIOBaseModel):
         files: A dict mapping filename to str or bytes data.
     """
 
-    files: dict[str, Union[str, bytes]] = {}
+    files: dict[str, str | bytes] = {}
 
     @field_validator("files")
     def _convert_base64_to_bytes(cls, value):
@@ -250,7 +250,7 @@ def _serialize_files(self, files, _info) -> dict[str, str]:
         }
 
     def add_file(
-        self, filepath: Union[Path, str], relative_dir: Optional[Path] = None
+        self, filepath: Path | str, relative_dir: Path | None = None
     ) -> None:
         """Add a file to the object. The file will be added at to the `files` attribute
             with the filename as the key and the file data as the value.
@@ -270,7 +270,7 @@ def add_file(
         filepath = Path(filepath)
         raw_bytes = filepath.read_bytes()
         try:
-            data: Union[str, bytes] = raw_bytes.decode("utf-8")  # str
+            data: str | bytes = raw_bytes.decode("utf-8")  # str
         except UnicodeDecodeError:
             data = raw_bytes  # bytes
 
@@ -288,7 +288,7 @@ def add_files(
         self,
         directory: StrOrPath,
         recursive: bool = False,
-        exclude: Optional[list[str]] = None,
+        exclude: list[str] | None = None,
     ) -> None:
         """Add all files in a directory to the object.
 
@@ -355,12 +355,12 @@ class Provenance(QCIOBaseModel):
     """
 
     program: str
-    program_version: Optional[str] = None
-    scratch_dir: Optional[Path] = None
-    wall_time: Optional[float] = None
-    hostname: Optional[str] = None
-    hostcpus: Optional[int] = None
-    hostmem: Optional[int] = None
+    program_version: str | None = None
+    scratch_dir: Path | None = None
+    wall_time: float | None = None
+    hostname: str | None = None
+    hostcpus: int | None = None
+    hostmem: int | None = None
 
 
 class CalcType(str, Enum):
@@ -399,4 +399,4 @@ class Model(QCIOBaseModel):
     """
 
     method: str
-    basis: Optional[str] = None
+    basis: str | None = None

src/qcio/models/results.py

@@ -353,7 +353,7 @@ def conformers_filtered(
         self,
         threshold: float = 1.0,
         **rmsd_kwargs,
-    ) -> tuple[list["Structure"], "SerializableNDArray"]:
+    ) -> tuple[list[Structure], SerializableNDArray]:
         """
         !!! warning "Moved since *qcio* 0.15.0"
             This convenience method has moved to

src/qcio/models/specs.py

@@ -2,10 +2,10 @@
 
 import warnings
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any, TypeVar, Union
 
 from pydantic import BaseModel, field_serializer, model_validator
-from typing_extensions import Self, TypeVar
+from typing_extensions import Self
 
 from .base_models import CalcType, Files, Model
 from .structure import Structure
@@ -41,7 +41,7 @@ class FileSpec(Files):
     cmdline_args: list[str] = []
 
     @classmethod
-    def from_directory(cls, directory: Union[Path, str], **kwargs) -> Self:
+    def from_directory(cls, directory: Path | str, **kwargs) -> Self:
         """Create a new FileSpec and collect all files in the directory."""
         obj = cls(**kwargs)
         directory = Path(directory)
@@ -130,7 +130,7 @@ class SubCalcSpec(FileSpec, _KeywordsMixin):
             development and scratch space.
     """
 
-    model: Optional[Model] = None
+    model: Model | None = None
     subprogram: str
     subprogram_spec: CoreSpec
 

src/qcio/models/structure.py

@@ -1,7 +1,7 @@
 import warnings
 from collections import Counter
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, ClassVar, Optional, Union
+from typing import TYPE_CHECKING, Any, ClassVar
 
 import numpy as np
 from pydantic import field_serializer, model_validator
@@ -48,20 +48,20 @@ class Identifiers(QCIOBaseModel):
             schema development and scratch space.
     """
 
-    name: Optional[str] = None
-    name_IUPAC: Optional[str] = None
-    smiles: Optional[str] = None
-    canonical_smiles: Optional[str] = None
-    canonical_smiles_program: Optional[str] = None
-    canonical_explicit_hydrogen_smiles: Optional[str] = None
-    canonical_isomeric_smiles: Optional[str] = None
-    canonical_isomeric_explicit_hydrogen_smiles: Optional[str] = None
-    canonical_isomeric_explicit_hydrogen_mapped_smiles: Optional[str] = None
-    inchi: Optional[str] = None
-    inchikey: Optional[str] = None
-    pubchem_cid: Optional[str] = None
-    pubchem_sid: Optional[str] = None
-    pubchem_conformerid: Optional[str] = None
+    name: str | None = None
+    name_IUPAC: str | None = None
+    smiles: str | None = None
+    canonical_smiles: str | None = None
+    canonical_smiles_program: str | None = None
+    canonical_explicit_hydrogen_smiles: str | None = None
+    canonical_isomeric_smiles: str | None = None
+    canonical_isomeric_explicit_hydrogen_smiles: str | None = None
+    canonical_isomeric_explicit_hydrogen_mapped_smiles: str | None = None
+    inchi: str | None = None
+    inchikey: str | None = None
+    pubchem_cid: str | None = None
+    pubchem_sid: str | None = None
+    pubchem_conformerid: str | None = None
 
 
 class Structure(QCIOBaseModel):
@@ -128,9 +128,9 @@ def __init__(self, **data: Any):
     @classmethod
     def open(
         cls,
-        filepath: Union[Path, str],
-        charge: Optional[int] = None,
-        multiplicity: Optional[int] = None,
+        filepath: Path | str,
+        charge: int | None = None,
+        multiplicity: int | None = None,
     ) -> Self:
         """Open a structure or structures from a file.
 
@@ -176,9 +176,9 @@ def open(
     @classmethod
     def open_multi(
         cls,
-        filepath: Union[Path, str],
-        charge: Optional[int] = None,
-        multiplicity: Optional[int] = None,
+        filepath: Path | str,
+        charge: int | None = None,
+        multiplicity: int | None = None,
     ) -> list["Structure"]:
         """Open a multi-structure file and return a list of Structure objects.
 
@@ -226,7 +226,7 @@ def open_multi(
 
     def save(
         self,
-        filepath: Union[Path, str],
+        filepath: Path | str,
         exclude_none: bool = True,
         exclude_unset: bool = True,
         indent: int = 4,
@@ -274,8 +274,8 @@ def from_xyz(
         cls,
         xyz_str: str,
         *,
-        charge: Optional[int] = None,
-        multiplicity: Optional[int] = None,
+        charge: int | None = None,
+        multiplicity: int | None = None,
     ) -> Self:
         """Create a Structure from an XYZ file or string.
 
@@ -350,8 +350,8 @@ def from_xyz(
     def from_xyz_multi(
         cls,
         xyz_str: str,
-        charge: Optional[int] = None,
-        multiplicity: Optional[int] = None,
+        charge: int | None = None,
+        multiplicity: int | None = None,
     ) -> list["Structure"]:
         """Parse a multi-structure XYZ file into a list of Structure objects.
 

src/qcio/models/utils.py

@@ -1,7 +1,8 @@
 """Utility functions for the models module."""
 
 import warnings
-from typing import TYPE_CHECKING, Any, Iterable
+from collections.abc import Iterable
+from typing import TYPE_CHECKING, Any
 
 if TYPE_CHECKING:
     from qcio import Structure

src/qcio/utils.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import json
-from typing import Union
 
 import numpy as np
 from pydantic import BaseModel
@@ -28,7 +27,7 @@
 
 
 def json_dumps(
-    obj: Union[BaseModel, list[BaseModel]],
+    obj: BaseModel | list[BaseModel],
     exclude_unset: bool = True,
     **model_dump_kwargs,
 ) -> str: