refactor: migrate setup.py to pyproject.toml and adopt uv/ruff

.github/workflows/deploy.yml

@@ -2,7 +2,7 @@ name: deploy
 
 on:
   push:
-    branches: [master]
+    branches: [develop]
     tags:
       - "v[0-9]+.[0-9]+.[0-9]+"
   workflow_dispatch:
@@ -16,15 +16,15 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
       - uses: actions/setup-python@v6
         with:
-          python-version: "3.9"
+          python-version: "3.12"
 
       - name: Build
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools setuptools_scm wheel
-          python setup.py sdist bdist_wheel
+        run: uv build
 
       - name: Publish
         uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/testing.yml

@@ -2,43 +2,36 @@ name: testing
 
 on:
   push:
-    branches: [master, develop]
+    branches: [develop]
   pull_request:
-    branches: [master]
+    branches: [develop]
 
 jobs:
   tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v6
 
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
     - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
-    # https://github.com/actions/cache/blob/main/examples.md#python---pip
-    - uses: actions/cache@v5
-      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
-        pip install -e .[dev]
+      run: uv sync --extra dev
 
     - name: Test with pytest
       run: |
-        python -m pytest -v --cov=hsnf --cov-config=setup.cfg --cov-report=xml tests/
+        uv run pytest -v --cov=hsnf --cov-report=xml tests/
 
     - name: Upload coverage to Codecov
-      if: matrix.python-version == '3.9'
+      if: matrix.python-version == '3.12'
       uses: codecov/codecov-action@v5
       with:
         file: ./coverage.xml

.pre-commit-config.yaml

@@ -1,44 +1,42 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
       - id: check-yaml
       - id: check-json
       - id: debug-statements
       - id: end-of-file-fixer
-  # formatter
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: detect-private-key
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.8
     hooks:
-    - id: black
-  # linter
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+      - id: ruff
+        args: [ "--fix", "--show-fixes"]
+        types_or: [python, pyi]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.19.1
     hooks:
-    - id: flake8
+    - id: mypy
       exclude: ^docs/
-  # type annotation
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.19.1
     hooks:
     - id: mypy
       exclude: ^docs/
-  # isort
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.11.2
+    hooks:
+      - id: uv-lock
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.37.1
     hooks:
-      - id: isort
-        name: isort (python)
-        args: ["--profile", "black"]
-      - id: isort
-        name: isort (cython)
-        types: [cython]
-      - id: isort
-        name: isort (pyi)
-        types: [pyi]
-  # Upgrade syntax
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+      - id: check-github-workflows
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.20.0
     hooks:
-      - id: pyupgrade
+    - id: pyproject-fmt

.readthedocs.yaml

@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "3.10"
+    python: "3.12"
 
 python:
   install:

README.md

@@ -78,7 +78,7 @@ or in local:
 ```shell
 git clone git@github.com:lan496/hsnf.git
 cd hsnf
-pip install -e .[dev,docs]
+uv sync --all-extras
 ```
 
 ## References

hsnf/Z_module.py

@@ -1,7 +1,5 @@
 # Copyright (c) 2019 Kohei Shinohara
 # Distributed under the terms of the MIT License.
-from __future__ import annotations
-
 import warnings
 
 import numpy as np
@@ -25,7 +23,7 @@ class ZmoduleHomomorphism:
 
     def __init__(self, A, basis_from, basis_to):
         if A.dtype not in [np.int32, np.int64]:
-            warnings.warn("Decomposed matrix should be integer.")
+            warnings.warn("Decomposed matrix should be integer.", stacklevel=2)
 
         self._A = A
         self._basis_from = basis_from

hsnf/integer_system.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import numpy as np
 from scipy.linalg import solve_triangular
 
@@ -215,12 +213,12 @@ def _solve_modular_integer_linear_system_special(D: NDArrayInt, Lb: NDArrayInt,
     """
     factors = eratosthenes(q)
     specials = []
-    for p, l in factors.items():
-        sol = _solve_modular_integer_linear_system_special_prime_power(D, Lb, p**l, rank)
+    for p, exp in factors.items():
+        sol = _solve_modular_integer_linear_system_special_prime_power(D, Lb, p**exp, rank)
         if sol is None:
             return None
-        assert np.allclose(np.mod(D @ sol - Lb, p**l), 0)
-        specials.append((sol, p**l))
+        assert np.allclose(np.mod(D @ sol - Lb, p**exp), 0)
+        specials.append((sol, p**exp))
 
     y_special, _ = crt_on_list(specials)
 

hsnf/utils.py

@@ -1,8 +1,7 @@
-from __future__ import annotations
+from typing import TypeAlias
 
 import numpy as np
 import numpy.typing as npt
-from typing_extensions import TypeAlias  # for Python<3.10
 
 NDArrayInt: TypeAlias = npt.NDArray[np.int_]
 

pyproject.toml

@@ -1,34 +1,75 @@
 [build-system]
-requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2", "wheel"]
 build-backend = "setuptools.build_meta"
+requires = [ "setuptools>=45", "setuptools-scm[toml]>=6.2", "wheel" ]
 
-# Enable version inference
-[tool.setuptools_scm]
+[project]
+name = "hsnf"
+description = "Computing Hermite normal form and Smith normal form."
+readme = "README.md"
+license = "MIT"
+authors = [
+  { name = "Kohei Shinohara" },
+]
+requires-python = ">=3.10"
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Intended Audience :: Science/Research",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3 :: Only",
+  "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",
+  "Programming Language :: Python :: Implementation :: PyPy",
+  "Topic :: Scientific/Engineering :: Mathematics",
+]
+dynamic = [ "version" ]
+dependencies = [
+  "numpy>=1.20.1",
+  "scipy",
+  "setuptools",
+  "setuptools-scm",
+  "wheel",
+]
+optional-dependencies.dev = [
+  "mypy",
+  "pre-commit",
+  "pytest",
+  "pytest-cov",
+  "ruff",
+]
+optional-dependencies.docs = [
+  "myst-parser",
+  "sphinx",
+  "sphinx-autobuild",
+  "sphinx-book-theme",
+  "sphinxcontrib-bibtex",
+]
+urls.Documentation = "https://hsnf.readthedocs.io/en/latest/"
+urls.Homepage = "https://github.com/lan496/hsnf"
+urls.Repository = "https://github.com/lan496/hsnf"
+
+[tool.setuptools]
+package-data.hsnf = [ "py.typed" ]
+packages.find.exclude = [ "tests" ]
 
-[tool.pytest.ini_options]
-testpaths = ["tests"]
+[tool.setuptools_scm]
 
-[tool.black]
+[tool.ruff]
 line-length = 99
-target-version = ['py38', 'py39', 'py310']
-include = '\.pyi?$'
-exclude = '''
-/(
-    \.eggs
-  | \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-  | docs
-)/
-'''
+exclude = [ "docs" ]
+lint.select = [ "B", "C", "E", "F", "I", "UP", "W" ]
+lint.ignore = [ "E203", "E231", "E501" ]
 
 [tool.mypy]
 exclude = [
-  'docs',
+  "docs",
 ]
+
+[tool.pytest]
+ini_options.testpaths = [ "tests" ]
+
+[tool.coverage]
+run.omit = [ "tests/" ]