Merge branch 'master' into free_threaded

Author: Remi-Gau

.github/workflows/test.yml

@@ -205,41 +205,21 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0
-      - name: Install the latest version of uv
+      - name: Setup uv and Python ${{ matrix.python-version }}
         uses: astral-sh/setup-uv@v7
-      - name: Set up Python ${{ matrix.python-version }}
-        if: "!endsWith(matrix.python-version, 't')"
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: ${{ matrix.architecture != 'x86' }}
+      - name: Setup 32-bit Python ${{ matrix.python-version }}
+        if: matrix.architecture == 'x86'
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.architecture }}
-          allow-prereleases: true
-      - name: Set up Python ${{ matrix.python-version }}
-        if: endsWith(matrix.python-version, 't')
-        run: |
-          echo "UV_PYTHON=${IMPL}-${VERSION}-${OS%-*}-${ARCH}-${LIBC}" >> $GITHUB_ENV
-          source $GITHUB_ENV
-          uv python install $UV_PYTHON
-        env:
-          IMPL: cpython
-          VERSION: ${{ matrix.python-version }}
-          # uv expects linux|macos|windows, we can drop the -* but need to rename ubuntu
-          OS: ${{ matrix.os == 'ubuntu-latest' && 'linux' ||
-                  startsWith(matrix.os, 'macos') && 'macos' ||
-                  matrix.os }}
-          # uv expects x86, x86_64, aarch64 (among others)
-          ARCH: ${{ matrix.architecture == 'x64' && 'x86_64' ||
-                    matrix.architecture == 'arm64' && 'aarch64' ||
-                    matrix.architecture }}
-          # windows and macos have no options, gnu is the only option for the archs
-          LIBC: ${{ matrix.os == 'ubuntu-latest' && 'gnu' || 'none' }}
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
-        run: |
-          uv tool install -v tox \
-            --with=tox-uv \
-            --with=git+https://github.com/effigies/tox-gh-actions@abiflags
+        run: uv tool install -v tox --with=tox-uv --with=tox-gh-actions
       - name: Show tox config
         run: tox c
       - name: Setup test suite

.zenodo.json

@@ -402,6 +402,10 @@
     },
     {
       "name": "freec84"
+    },
+    {
+      "name": "Ayala, Leonardo",
+      "orcid": "0000-0002-3574-2085"
     }
   ],
   "keywords": [

doc/source/index.rst

@@ -133,6 +133,7 @@ contributed code and discussion (in rough order of appearance):
 * Guillaume Becq
 * Joshua Newton
 * Sandro from the Fedora Project
+* `Leonardo Ayala`_
 
 License reprise
 ===============

doc/source/links_names.txt

@@ -250,6 +250,7 @@
 .. _Nolan Nichols: http://www.nolan-nichols.com
 .. _Satrajit Ghosh: http://satra.cogitatum.org
 .. _Chris Rorden: http://www.mccauslandcenter.sc.edu/crnl/chris-rorden
+.. _Leonardo Ayala: https://leoyala.github.io/
 
 .. Substitutions
 .. |emdash| unicode:: U+02014

nibabel/pydicom_compat.py

@@ -23,7 +23,7 @@
 from __future__ import annotations
 
 import warnings
-from typing import Callable
+from collections.abc import Callable
 
 from .deprecated import deprecate_with_version
 from .optpkg import optional_package

pyproject.toml

@@ -9,7 +9,7 @@ authors = [{ name = "NiBabel developers", email = "neuroimaging@python.org" }]
 maintainers = [{ name = "Christopher Markiewicz" }]
 readme = "README.rst"
 license = "MIT"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
   "numpy >=1.25",
   "packaging >=20",
@@ -22,7 +22,6 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "Operating System :: OS Independent",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",

tox.ini

@@ -8,13 +8,15 @@ requires =
   tox-uv
 envlist =
   # No preinstallations
-  py3{9,10,11,12,13,13t}-none
+  py3{10-12}-none
+  py3{13-14}{,t}-none
   # Minimum Python with minimum deps
-  py3{9,10}-min
+  py310-min
   # Run full and pre dependencies against all archs
-  py3{9,10,11,12,13,13t}-{full,pre}-{x86,x64,arm64}
+  py3{10-12}-{full,pre}-{x86,x64,arm64}
+  py3{13-14}{,t}-{full,pre}-{x86,x64,arm64}
   # Python development versions
-  py3{14,14t}-pre-{x64,arm64}
+  py315{,t}-pre-{x64,arm64}
   install
   doctest
   style
@@ -24,7 +26,6 @@ skip_missing_interpreters = true
 # Configuration that allows us to split tests across GitHub runners effectively
 [gh-actions]
 python =
-  3.9: py39
   3.10: py310
   3.11: py311
   3.12: py312
@@ -37,7 +38,7 @@ python =
 DEPENDS =
   none: none
   pre: pre
-  full: full, install
+  full: full
   min: min
 
 ARCH =
@@ -64,13 +65,11 @@ pass_env =
   NO_COLOR
   CLICOLOR
   CLICOLOR_FORCE
-  # uv needs help in this case
-  py313t-x86: UV_PYTHON
 set_env =
   pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   pre: UV_INDEX=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   pre: UV_INDEX_STRATEGY=unsafe-best-match
-  py3{13,14}t: PYTHONGIL={env:PYTHONGIL:0}
+  py3{13-15}t: PYTHONGIL={env:PYTHONGIL:0}
 extras =
   test
 
@@ -90,11 +89,8 @@ extras =
   {full,pre}-{x,arm}64: spm
 
   # No free-threaded wheels for: h5py
-  py3{9,10,11,12,13}-{full,pre}-{x,arm}64: minc2
-  py314-pre-{x,arm}64: minc2
-
-  # win32 (x86) wheels still exist for scipy+py39
-  py39-full-x86: spm
+  py3{10-14}-{full,pre}-{x,arm}64: minc2
+  py315-pre-{x,arm}64: minc2
 
 deps =
   pre: pydicom @ git+https://github.com/pydicom/pydicom.git@main
@@ -109,7 +105,7 @@ commands =
     --durations=20 --durations-min=1.0 \
     --pyargs nibabel {posargs:-n auto}
 
-[testenv:py3{9,10,11,12,13,13t,14,14t}-{full,none}-{x,arm}64]
+[testenv:py3{10-15}{,t}-{full,none}-{x,arm}64]
 runner = uv-venv-lock-runner
 
 [testenv:install]