ci: migrate to tox and fix tests for py3.9

.github/workflows/tests.yaml

@@ -6,14 +6,18 @@ on:
       - '!docs/**'
 jobs:
   build:
+    name: test with ${{ matrix.env }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        env:
+          - ["3.8", "3.13"]
         os: [ubuntu-latest, windows-latest]
-        python-version: [3.x]
     steps:
     - name: Git clone
       uses: actions/checkout@v4
+    - name: Install the latest version of uv
+      uses: astral-sh/setup-uv@v3
     - name: Setup Python
       uses: actions/setup-python@v5
       with:

README.md

@@ -115,12 +115,13 @@ For more practical examples, see our [examples section](https://karelze.github.i
 
 ## Development
 
-We are using [`pixi`](https://github.com/prefix-dev/pixi) as a dependency management and workflow tool.
+We are using [`tox`](https://tox.wiki/en/latest/user_guide.html) with [`uv`](https://docs.astral.sh/uv/) for development.
 
 ```bash
-pixi install
-pixi run postinstall
-pixi run test
+tox -e lint
+tox -e format
+tox -e test
+tox -e build
 ```
 
 ## Citation

docs/index.md

@@ -115,12 +115,13 @@ For more practical examples, see our [examples section](https://karelze.github.i
 
 ## Development
 
-We are using [`pixi`](https://github.com/prefix-dev/pixi) as a dependency management and workflow tool.
+We are using [`tox`](https://tox.wiki/en/latest/user_guide.html) with [`uv`](https://docs.astral.sh/uv/) for development.
 
 ```bash
-pixi install
-pixi run postinstall
-pixi run test
+tox -e lint
+tox -e format
+tox -e test
+tox -e build
 ```
 
 ## Citation

pyproject.toml

@@ -19,6 +19,8 @@ classifiers = [
   "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",
   "Operating System :: OS Independent",
   "Intended Audience :: Information Technology",
   "Intended Audience :: Science/Research",
@@ -29,11 +31,34 @@ classifiers = [
 dependencies = [
   "numpy",
   "pandas",
-  "ruff>=0.8.0",
   "scikit-learn",
 ]
+
 dynamic = ["version"]
 
+[project.optional-dependencies]
+dev = [
+  # doc
+  "mkdocs",
+  "mkdocs-material",
+  "mkdocstrings-python",
+  # build
+  "build",
+  # test
+  "pytest",
+  "pytest-cov",
+  # linting",
+  "pre-commit",
+  "mypy",
+  "ruff",
+  "tox-uv>=1.13.1",
+  "tox>=4.23.2",
+  "pytest-codspeed",
+  "mkdocs-bibtex",
+  "commitizen",
+  "pypandoc-binary"
+]
+
 [tool.setuptools.dynamic]
 version = {file = "version"}
 
@@ -90,10 +115,6 @@ annotated_tag = true
 
 [tool.ruff]
 
-
-include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]
-
-
 [tool.ruff.lint]
 
 # See rules: https://beta.ruff.rs/docs/rules/
@@ -142,3 +163,53 @@ section-order = ["future", "standard-library", "third-party", "first-party", "lo
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
+
+[tool.tox]
+env_list = ["format", "lint", "pre-commit"]
+min_version = "4.23"
+
+[tool.tox.env_run_base]
+runner = "uv-venv-lock-runner"
+allowlist_externals = ["/bin/sh"]
+skip_install = true
+with_dev = true
+
+[tool.tox.env.clean]
+description = "cleanup tasks (remove build artifacts and cache)"
+commands = [
+    ["coverage", "erase"],
+    ["sh", "-c", "rm -rf .mypy_cache .pytest_cache .ruff_cache dist mlruns reports"]
+]
+
+[tool.tox.env.doc]
+description = "writing documentation using mkdocs"
+commands = [
+    ["mkdocs", "serve"]
+]
+
+
+[tool.tox.env.format]
+description = "code formatting using ruff"
+commands = [
+    ["ruff", "format", { replace = "posargs", default = ["src", "tests"], extend = true }]
+]
+
+[tool.tox.env.lint]
+description = "linting and syntax checks"
+commands = [
+    ["ruff", "check", { replace = "posargs", default = ["src", "tests"], extend = true} ],
+    ["ruff", "format", "--check", { replace = "posargs", default = ["src", "tests"], extend = true} ],
+    ["mypy", { replace = "posargs", default = ["src"], extend = true} ]
+]
+
+[tool.tox.env.pre-commit]
+description = "pre-commit hooks"
+commands = [["pre-commit", "run", "--all-files", "--show-diff-on-failure"]]
+
+[tool.tox.env.test]
+description = "tests"
+commands = [["pytest"]]
+
+[tool.tox.env.build]
+description = "build the project"
+commands = [["uv", "build"]]

src/tclf/types.py

@@ -1,9 +1,11 @@
 """Common type hints."""
 
+from typing import Union
+
 import numpy as np
 import numpy.typing as npt
 import pandas as pd
 from scipy.sparse import spmatrix
 
-MatrixLike = np.ndarray | pd.DataFrame | spmatrix
-ArrayLike = npt.ArrayLike | pd.Series
+MatrixLike = Union[np.ndarray, pd.DataFrame, spmatrix]
+ArrayLike = Union[npt.ArrayLike, pd.Series]

tests/test_classical_classifier.py

@@ -1,5 +1,7 @@
 """Tests for the classical classifier."""
 
+from __future__ import annotations
+
 from typing import Callable
 
 import numpy as np