From 84ce2073bccfbdec28aebae31c6ac47966815b8d Mon Sep 17 00:00:00 2001 From: Colton Hicks Date: Mon, 6 Oct 2025 14:33:34 -0700 Subject: [PATCH 1/6] Initial python 3.10 mods --- .python-version | 2 +- pyproject.toml | 4 +- src/qcio/helper_types.py | 4 +- src/qcio/models/specs.py | 4 +- uv.lock | 3125 ++++++++++++++++++-------------------- 5 files changed, 1522 insertions(+), 1617 deletions(-) diff --git a/.python-version b/.python-version index bd28b9c..c8cfe39 100644 --- a/.python-version +++ b/.python-version @@ -1 +1 @@ -3.9 +3.10 diff --git a/pyproject.toml b/pyproject.toml index 88831af..fdf12fc 100644 --- a/pyproject.toml +++ b/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", ] diff --git a/src/qcio/helper_types.py b/src/qcio/helper_types.py index af525b9..2066b63 100644 --- a/src/qcio/helper_types.py +++ b/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[ diff --git a/src/qcio/models/specs.py b/src/qcio/models/specs.py index 522b998..60d608c 100644 --- a/src/qcio/models/specs.py +++ b/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, Optional, 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 diff --git a/uv.lock b/uv.lock index a5d5528..0e14cc9 100644 --- a/uv.lock +++ b/uv.lock @@ -1,9 +1,9 @@ version = 1 -requires-python = ">=3.9" +requires-python = ">=3.10" resolution-markers = [ - "python_full_version >= '3.11'", - "python_full_version == 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50bfb1330da7d196d01ff818f7d6d36e175609a9 Mon Sep 17 00:00:00 2001 From: Colton Hicks Date: Mon, 6 Oct 2025 14:43:24 -0700 Subject: [PATCH 2/6] Update semantics to python 3.10 for typing. --- .github/workflows/test.yaml | 30 ++++++++++++++++---- CHANGELOG.md | 1 + src/qcio/models/base_models.py | 30 ++++++++++---------- src/qcio/models/results.py | 2 +- src/qcio/models/specs.py | 6 ++-- src/qcio/models/structure.py | 52 +++++++++++++++++----------------- src/qcio/models/utils.py | 3 +- src/qcio/utils.py | 3 +- src/qcio/view.py | 32 ++++++++++----------- 9 files changed, 89 insertions(+), 70 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 23aab31..92fc0dd 100644 --- a/.github/workflows/test.yaml +++ b/.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 ".[dev,all]" - name: Run tests run: bash scripts/tests.sh - 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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 2a4ce78..cc0fba7 100644 --- a/CHANGELOG.md +++ b/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. - 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`. diff --git a/src/qcio/models/base_models.py b/src/qcio/models/base_models.py index f23251c..ff5c599 100644 --- a/src/qcio/models/base_models.py +++ b/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 diff --git a/src/qcio/models/results.py b/src/qcio/models/results.py index f86cc28..2c28778 100644 --- a/src/qcio/models/results.py +++ b/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 diff --git a/src/qcio/models/specs.py b/src/qcio/models/specs.py index 60d608c..57752af 100644 --- a/src/qcio/models/specs.py +++ b/src/qcio/models/specs.py @@ -2,7 +2,7 @@ import warnings from pathlib import Path -from typing import Any, Optional, TypeVar, Union +from typing import Any, TypeVar, Union from pydantic import BaseModel, field_serializer, model_validator from typing_extensions import Self @@ -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 diff --git a/src/qcio/models/structure.py b/src/qcio/models/structure.py index 9180257..80fa649 100644 --- a/src/qcio/models/structure.py +++ b/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. diff --git a/src/qcio/models/utils.py b/src/qcio/models/utils.py index b3af760..69e852d 100644 --- a/src/qcio/models/utils.py +++ b/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 diff --git a/src/qcio/utils.py b/src/qcio/utils.py index ea2a4f5..90e7030 100644 --- a/src/qcio/utils.py +++ b/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: diff --git a/src/qcio/view.py b/src/qcio/view.py index 049adc1..aa7381f 100644 --- a/src/qcio/view.py +++ b/src/qcio/view.py @@ -26,7 +26,7 @@ import math from contextlib import contextmanager from itertools import zip_longest -from typing import Any, Optional, Union +from typing import Any, Union import numpy as np from qcconst import constants @@ -75,15 +75,15 @@ def generate_structure_viewer_html( *structs: Union["Structure", list["Structure"]], - width: Optional[int] = None, - height: Optional[int] = None, - titles: Optional[list[str]] = None, - subtitles: Optional[list[str]] = None, - titles_extra: Optional[list[str]] = None, - subtitles_extra: Optional[list[str]] = None, - distances: Optional[list[tuple[int, int]]] = None, + width: int | None = None, + height: int | None = None, + titles: list[str] | None = None, + subtitles: list[str] | None = None, + titles_extra: list[str] | None = None, + subtitles_extra: list[str] | None = None, + distances: list[tuple[int, int]] | None = None, length_unit: LengthUnit = LengthUnit.BOHR, - style: Optional[dict] = None, + style: dict | None = None, show_indices: bool = False, same_viewer: bool = False, view_2d: bool = False, @@ -315,7 +315,7 @@ def generate_dictionary_string(dictionary: dict[str, Any]) -> str: return f"{rows}
" -def generate_files_string(files: dict[str, Union[str, bytes]]) -> str: +def generate_files_string(files: dict[str, str | bytes]) -> str: """ Generate an HTML string displaying a dictionary of files substituting or for the actual file data @@ -592,7 +592,7 @@ def generate_data_table(data: Files) -> str: def structures( - *structs: Union[Structure, list[Structure]], + *structs: Structure | list[Structure], **kwargs, ) -> None: """ @@ -610,12 +610,12 @@ def structures( def program_outputs( - *results: Results[Union[CalcSpec, CompositeCalcSpec], Data], + *results: Results[CalcSpec | CompositeCalcSpec, Data], animate: bool = True, struct_viewer: bool = True, - conformer_rmsd_threshold: Optional[float] = None, + conformer_rmsd_threshold: float | None = None, conformer_rmsd_backend: str = "qcinf", - conformer_rmsd_kwargs: Optional[dict] = None, + conformer_rmsd_kwargs: dict | None = None, **kwargs, ) -> None: """ @@ -686,7 +686,7 @@ def program_outputs( # Determine the Structure to use if isinstance(result.data, OptimizationData): - for_viewer: Union[Structure, list[Structure]] + for_viewer: Structure | list[Structure] if animate: for_viewer = result.data.structures else: @@ -740,7 +740,7 @@ def program_outputs( def view( - *objs: Union[Results, Structure, list[Structure]], + *objs: Results | Structure | list[Structure], **kwargs, ) -> None: """ From 0ebc8ca1bd9d6114f6e8591c9677ef183de975db Mon Sep 17 00:00:00 2001 From: Colton Hicks Date: Mon, 6 Oct 2025 14:44:50 -0700 Subject: [PATCH 3/6] Fix tests --- .github/workflows/test.yaml | 2 +- CHANGELOG.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 92fc0dd..55fafef 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -29,7 +29,7 @@ jobs: # uv pip resolves & installs deps like pip (not an environment sync) - name: Install package + test deps (uv pip) - run: uv pip install ".[dev,all]" + run: uv pip install --system ".[dev,all]" - name: Run tests run: bash scripts/tests.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index cc0fba7..bd3696c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +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. +- 🚨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`. From b507e59ecf82a6fb4f8300e23cdf1e0bdf793ed8 Mon Sep 17 00:00:00 2001 From: Colton Hicks Date: Mon, 6 Oct 2025 14:51:57 -0700 Subject: [PATCH 4/6] Try uv pip install --group dev --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 55fafef..9663527 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -29,7 +29,7 @@ jobs: # uv pip resolves & installs deps like pip (not an environment sync) - name: Install package + test deps (uv pip) - run: uv pip install --system ".[dev,all]" + run: uv pip install --system --group dev - name: Run tests run: bash scripts/tests.sh From 2666464bec7091decf9c36bc1f1f10ae3b6ce362 Mon Sep 17 00:00:00 2001 From: Colton Hicks Date: Mon, 6 Oct 2025 14:54:28 -0700 Subject: [PATCH 5/6] Run pytest directly. --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 9663527..c8dbaa8 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -32,7 +32,7 @@ jobs: run: uv pip install --system --group dev - name: Run tests - run: bash scripts/tests.sh + run: 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 }} From df9e2f5a4f2dd76a9ed7ab06af47255e7c6de109 Mon Sep 17 00:00:00 2001 From: Colton Hicks Date: Mon, 6 Oct 2025 14:56:03 -0700 Subject: [PATCH 6/6] Python -m pytest --- .github/workflows/test.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index c8dbaa8..7c32476 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -29,10 +29,10 @@ jobs: # 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 + run: uv pip install --system --group dev . - name: Run tests - run: pytest --cov-report=term-missing --cov-report html:htmlcov --cov-config=pyproject.toml --cov=qcio --cov=tests . + 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 }}