Drop Python 3.9 and introduce uv

.github/workflows/testing.yml

@@ -1,71 +1,55 @@
 name: testing
-
 on:
   push:
-    branches: [main, develop]
+    branches: [develop]
   pull_request:
-    branches: [main, develop]
-
+    branches: [develop]
+env:
+  PYTHON_VERSION: "3.12"
 jobs:
   tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
-
-    - uses: actions/setup-python@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
       with:
+        enable-cache: true
         python-version: ${{ matrix.python-version }}
-
-    # https://github.com/actions/cache/blob/main/examples.md#python---pip
-    - uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ hashFiles('**/setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-${{ matrix.python-version }}-pip-
-
     - name: Install
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install -e .[dev]
-
+        uv sync --extra testing
     - name: Test with pytest
       run: |
-        python -m pytest -v --cov=spinspg --cov-report=xml tests/
-
+        uv run pytest -v --cov=spinspg --cov-report=xml tests/
     - name: Upload coverage reports to Codecov
-      if: matrix.python-version == '3.10'
+      if: matrix.python-version == ${{ env.PYTHON_VERSION }}
       uses: codecov/codecov-action@v3
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   docs:
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
-
-    - uses: actions/setup-python@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: "3.10"
-
+        enable-cache: true
+        python-version: ${{ env.PYTHON_VERSION }}
     - name: Install dependencies
       run: |
         sudo apt-get install -y pandoc
-
     - name: Install
       run: |
-        python -m pip install --upgrade pip
-        pip install -e .[dev,docs]
-
+        uv sync --extra docs
     - name: Build
       run: |
         sphinx-build docs docs_build

.gitignore

@@ -81,9 +81,6 @@ target/
 profile_default/
 ipython_config.py
 
-# pyenv
-.python-version
-
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
 #   However, in case of collaboration, if having platform-specific dependencies or dependencies

.pre-commit-config.yaml

@@ -1,7 +1,9 @@
-default_language_version:
-  python: python3
-
 repos:
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    # uv version.
+    rev: 0.6.12
+    hooks:
+      - id: uv-lock
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
@@ -10,20 +12,22 @@ repos:
       - id: check-json
       - id: debug-statements
       - id: end-of-file-fixer
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.34.0
+    hooks:
+      - id: check-github-workflows
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.11.5
     hooks:
       - id: ruff-format
       - id: ruff
         args: [ "--fix", "--show-fixes"]
         types_or: [python, pyi]
-  # type annotation
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.15.0
     hooks:
     - id: mypy
       exclude: ^docs/
-  # Notebook
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.9.1
     hooks:

pyproject.toml

@@ -13,7 +13,7 @@ description = "Python package for detecting spin space group on top of spglib"
 authors = [
     {name = "Kohei Shinohara", email = "kshinohara0508@gmail.com"},
 ]
-requires-python = ">=3.9.0"
+requires-python = ">=3.10.0"
 license = {file = "LICENSE"}
 classifiers = [
     # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
@@ -22,10 +22,10 @@ classifiers = [
     "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
     "Programming Language :: Python",
-    "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",
     "Topic :: Scientific/Engineering :: Mathematics",
     "Topic :: Scientific/Engineering :: Physics",
 ]
@@ -45,14 +45,10 @@ homepage = "https://github.com/spglib/spinspg"
 repository = "https://github.com/spglib/spinspg"
 
 [project.optional-dependencies]
-dev = [
-    "spgrep-modulation>=0.2.5",
+testing = [
     "pytest",
     "pytest-cov",
     "pre-commit",
-    "black",
-    "mypy",
-    "toml",
 ]
 docs = [
     "importlib-metadata",
@@ -63,6 +59,15 @@ docs = [
     "linkify-it-py",
     "enum-tools[sphinx]",
 ]
+dev = [
+    "spinspg[testing]",
+    "spinspg[docs]",
+    "spgrep-modulation>=0.2.5",
+    "toml",
+]
+
+[dependency-groups]
+dev = [ "spinspg[dev]" ]
 
 ###############################################################################
 # Setuptools
@@ -71,13 +76,6 @@ docs = [
 [tool.setuptools]
 zip-safe = false
 
-# packages = find
-# package-dir = {"" = "src"}
-#
-# [tool.setuptools.packages.find]
-# where = ["src"]
-# include = ["spinspg"]
-
 ###############################################################################
 # Other tools
 ###############################################################################

src/spinspg/utils.py

@@ -2,11 +2,13 @@
 
 from __future__ import annotations
 
-from typing import Any
+from typing import (
+    Any,
+    TypeAlias,  # for Python<3.10
+)
 
 import numpy as np
 from numpy.typing import NDArray
-from typing_extensions import TypeAlias  # for Python<3.10
 
 NDArrayInt: TypeAlias = NDArray[np.int_]
 NDArrayFloat: TypeAlias = NDArray[np.float64]