support latest python versions

.flake8

@@ -6,14 +6,3 @@ extend-ignore =
     E203,
     # W503: Ignore "line break before binary operator" because it conflicts with black
     W503
-
-# Flake8 config for Jupyter notebooks
-[flake8_nb]
-max-line-length = 120
-
-extend-ignore =
-    # E203: Ignore "whitespace before ':'" because it conflicts with black
-    E203,
-    # W503: Ignore "line break before binary operator" because it conflicts with black
-    W503,
-    E402

.github/workflows/ci.yml

@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

.github/workflows/codeql-analysis.yml

@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 2
 

.github/workflows/docs.yml

@@ -8,19 +8,19 @@ jobs:
   python:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.12'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements-dev.txt
       - name: Pages (Docs and Coverage)
         run: make pages
       - name: Deploy Docs
-        uses: JamesIves/github-pages-deploy-action@v4.4.0
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: gh-pages
           folder: site

.github/workflows/packaging.yml

@@ -8,11 +8,11 @@ jobs:
   python:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.12'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.pre-commit-config.yaml

@@ -45,7 +45,7 @@ repos:
       - id: requirements-txt-fixer
       - id: trailing-whitespace
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.18
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -74,16 +74,17 @@ repos:
       - id: yamllint
         args: [--strict]
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
+    # Use tag > v1.7.5 if available
+    rev: eb1df347edd128b30cd3368dddc3aa65edcfac38
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.2
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
@@ -101,37 +102,29 @@ repos:
     hooks:
       - id: pylint
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
-        args: [--py38-plus]
+        args: [--py39-plus]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.0
     hooks:
       - id: nbstripout
-  - repo: https://github.com/s-weigand/flake8-nb
-    rev: v0.5.3
-    hooks:
-      - id: flake8-nb
-        args:
-          - --config
-          - .flake8
-        additional_dependencies:
-          - flake8-bugbear  # Not fully implemented by ruff
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.8.7
     hooks:
+      - id: nbqa-ruff
       - id: nbqa-pyupgrade
         args:
-          - --py38-plus
+          - --py39-plus
       - id: nbqa-pylint
         args: [--rcfile=.pylintrc-nb.ini]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.3
+    rev: 0.29.4
     hooks:
       - id: check-github-workflows
   - repo: https://github.com/crate-ci/typos
-    rev: v1.26.0
+    rev: v1.27.0
     hooks:
       - id: typos
         exclude_types:

docs/installation.md

@@ -1,7 +1,5 @@
 # Installation
 
-`vibromaf` is compatible with Python 3.8+.
-
 Use `pip` to install the latest stable version of `vibromaf` from [PyPI](https://pypi.org/project/vibromaf):
 
 ```shell

pyproject.toml

@@ -35,7 +35,7 @@ disable = [
 
 [tool.ruff]
 fix = true
-target-version = "py38"
+target-version = "py39"
 
 [tool.ruff.lint]
 select = ["ALL"]

setup.py

@@ -35,15 +35,16 @@
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "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",
     ],
     package_data={
         "models": ["model/*"],
     },
     packages=setuptools.find_packages(include=["vibromaf.*"]),
     py_modules=["vibromaf.*"],
-    python_requires=">=3.7",
+    python_requires=">=3.9",
 )

vibromaf/util/matlab.py

@@ -1,7 +1,6 @@
 """Utility functions for MATLAB files."""
 
 from pathlib import Path
-from typing import List, Tuple
 
 import numpy as np
 from scipy import io
@@ -19,8 +18,8 @@ def load_signal_from_mat(mat_file: Path, signal_name: str) -> np.array:
 
 
 def load_data_for_metric(
-    metric: str, test_indices: List[int]
-) -> Tuple[np.array, np.array]:
+    metric: str, test_indices: list[int]
+) -> tuple[np.array, np.array]:
     """Load and concatenate the training and test data."""
     vcpwq = load_signal_from_mat(
         config.DATA_PATH / f"{metric}_VCPWQ.mat", f"{metric}_VCPWQ"