[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'

.readthedocs.yml

@@ -10,17 +10,13 @@ build:
     os: ubuntu-22.04
     tools:
         python: '3.11'
+    jobs:
+        install:
+        -   pip install --upgrade pip
+        -   pip install . --group 'doc'
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
     configuration: docs/source/conf.py
     builder: html
     fail_on_warning: false
-
-# Optionally set the version of Python and requirements required to build your docs
-python:
-    install:
-    -   method: pip
-        path: .
-        extra_requirements:
-        -   docs

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.11.9-slim-bullseye@sha256:8850f5e6e8da9081a6d156252a11161aa22f04d6ed1723c57ca2d5a5d48132bc
+FROM python:3.11.15-slim@sha256:9358444059ed78e2975ada2c189f1c1a3144a5dab6f35bff8c981afb38946634
 
 ARG DEBIAN_FRONTEND="noninteractive"
 

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 = [
@@ -17,18 +37,18 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Image Processing"
 ]
 dependencies = [
-    "antspyx<0.5",
-    "anywidget",
-    "attrs",
+    "antspyx>=0.4.2,<0.5",
+    "anywidget>=0.9.21",
+    "attrs>=26.1.0",
     "deepmreye>=0.2.1",
-    "jinja2",
-    "kaleido",
-    "keras<3.0.0",
+    "jinja2>=3.1.6",
+    "kaleido>=1.2.0",
+    "keras>=2.15.0,<3.0.0",
     "pooch>=1.6.0",
-    "pybids",
-    "tqdm",
-    "tomli; python_version < '3.11'",
-    "rich_argparse"
+    "pybids>=0.22.0",
+    "tqdm>=4.67.3",
+    "tomli>=2.4.0; python_version < '3.11'",
+    "rich_argparse>=1.7.2"
 ]
 description = "bids app using deepMReye to decode eye motion for fMRI time series data"
 dynamic = ["version"]
@@ -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"