[MAINT] use uv & tox, drop python 3.9

.github/dependabot.yml

@@ -6,9 +6,9 @@ updates:
 -   package-ecosystem: github-actions
     directory: /
     schedule:
-        interval: monthly
+        interval: semiannually
 
 -   package-ecosystem: gitsubmodule
     directory: /
     schedule:
-        interval: monthly
+        interval: semiannually

.github/workflows/test_and_coverage.yml

@@ -18,26 +18,30 @@ jobs:
         strategy:
             matrix:
                 os: [ubuntu-latest, macOS-latest] # windows-latest: do not work. antspyx is not available for windows
-                python-version: ['3.9', '3.10', '3.11']
+                python-version: ['3.10', '3.11']
             fail-fast: false
 
         steps:
 
         -   name: Clone repo
             uses: actions/checkout@v6
 
-        -   name: Set up Python ${{ matrix.python-version }}
+        -   name: Install the latest version of uv
+            uses: astral-sh/setup-uv@v7
+
+        -   name: Setup python
             uses: actions/setup-python@v6
             with:
                 python-version: ${{ matrix.python-version }}
 
-        -   name: Install dependencies
-            run: |
-                python -m pip install --upgrade pip setuptools
-                pip install .[test]
+        -   name: Install tox
+            run: uv tool install tox --with=tox-uv --with=tox-gh-actions
+
+        -   name: Show tox config
+            run: tox c
 
         -   name: Run tests and generate coverage report
-            run: pytest --cov bidsmreye --cov-report=xml
+            run: tox run -e test
 
         -   name: Upload coverage to Codecov
             uses: codecov/codecov-action@v5

.pre-commit-config.yaml

@@ -96,5 +96,5 @@ repos:
 
 ci:
     autoupdate_commit_msg: 'chore: update pre-commit hooks'
-    autoupdate_schedule: monthly
+    autoupdate_schedule: quarterly
     autofix_commit_msg: 'style: pre-commit fixes'

Dockerfile

@@ -1,10 +1,10 @@
-FROM python:3.11.9-slim-bullseye@sha256:8850f5e6e8da9081a6d156252a11161aa22f04d6ed1723c57ca2d5a5d48132bc
+FROM python:3.11.15-slim@sha256:9358444059ed78e2975ada2c189f1c1a3144a5dab6f35bff8c981afb38946634
 
 ARG DEBIAN_FRONTEND="noninteractive"
 
 RUN apt-get update -qq && \
     apt-get install -y -qq --no-install-recommends \
-        git && \
+        git curl ca-certificates && \
     rm -rf /var/lib/apt/lists/*
 
 RUN mkdir -p /home/neuro/bidsMReye/models

pyproject.toml

@@ -2,6 +2,26 @@
 build-backend = "hatchling.build"
 requires = ["hatchling", "hatch-vcs"]
 
+[dependency-groups]
+dev = [
+    {include-group = "test"},
+    {include-group = "doc"},
+    "tox>=4",
+    "tox-uv",
+    "pre-commit"
+]
+doc = [
+    "faqtory",
+    "myst-parser",
+    "rstcheck",
+    "sphinx",
+    "sphinx-argparse",
+    "sphinx-copybutton",
+    "sphinx-rtd-theme",
+    "sphinxcontrib-bibtex"
+]
+test = ["pytest>=6.0.0", "pytest-cov"]
+
 [project]
 authors = [{name = "Remi Gau", email = "remi.gau@gmail.com"}]
 classifiers = [
@@ -44,26 +64,7 @@ keywords = [
 license = {file = "LICENSE"}
 name = "bidsmreye"
 readme = "README.md"
-requires-python = ">=3.9.0"
-
-[project.optional-dependencies]
-dev = ["bidsmreye[doc,test,style]"]
-# also stored in docs/requirements.txt
-# to speed up readthedocs build
-doc = [
-    "faqtory",
-    "myst-parser",
-    "rstcheck",
-    "sphinx",
-    "sphinx-argparse",
-    "sphinx-copybutton",
-    "sphinx-rtd-theme",
-    "sphinxcontrib-bibtex"
-]
-docs = ["bidsmreye[doc]"]
-style = ["pre-commit", "sourcery"]
-test = ["pytest", "pytest-cov"]
-tests = ["bidsmreye[test]"]
+requires-python = ">=3.10.0,<3.12"
 
 [project.scripts]
 bidsmreye = "bidsmreye._cli:cli"
@@ -73,9 +74,6 @@ bidsmreye_model = "bidsmreye._cli:cli_download"
 "Bug Tracker" = "https://github.com/cpp-lln-lab/bidsMReye/issues"
 Homepage = "https://github.com/cpp-lln-lab/bidsMReye"
 
-[tool.black]
-line-length = 90
-
 [tool.codespell]
 builtin = "clear,rare"
 ignore-words-list = "fo,slite"