Merge pull request #1381 from effigies/py313

Add broad testing for Python 3.13

.github/workflows/test.yml

@@ -113,31 +113,49 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-13', 'macos-latest']
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        architecture: ['x64', 'x86', 'arm64']
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.13t"]
+        architecture: ['x86', 'x64', 'arm64']
         dependencies: ['full', 'pre']
         include:
           # Basic dependencies only
           - os: ubuntu-latest
-            python-version: 3.9
+            python-version: "3.9"
+            architecture: 'x64'
             dependencies: 'none'
           # Absolute minimum dependencies
           - os: ubuntu-latest
-            python-version: 3.9
+            python-version: "3.9"
+            architecture: 'x64'
             dependencies: 'min'
-          # NoGIL
-          - os: ubuntu-latest
-            python-version: '3.13-dev'
-            dependencies: 'dev'
         exclude:
-          # x86 for Windows + Python<3.12
-          - os: ubuntu-latest
-            architecture: x86
+          # Use ubuntu-latest to cover the whole range of Python. For Windows
+          # and OSX, checking oldest and newest should be sufficient.
+          - os: windows-latest
+            python-version: "3.10"
+          - os: windows-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.12"
+          - os: macos-13
+            python-version: "3.10"
           - os: macos-13
+            python-version: "3.11"
+          - os: macos-13
+            python-version: "3.12"
+          - os: macos-latest
+            python-version: "3.10"
+          - os: macos-latest
+            python-version: "3.11"
+          - os: macos-latest
+            python-version: "3.12"
+
+          ## Unavailable architectures
+          # x86 is available for Windows
+          - os: ubuntu-latest
             architecture: x86
           - os: macos-latest
             architecture: x86
-          - python-version: '3.12'
+          - os: macos-13
             architecture: x86
           # arm64 is available for macos-14+
           - os: ubuntu-latest
@@ -149,6 +167,8 @@ jobs:
           # x64 is not available for macos-14+
           - os: macos-latest
             architecture: x64
+
+          ## Reduced support
           # Drop pre tests for macos-13
           - os: macos-13
             dependencies: pre
@@ -167,25 +187,37 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
       - name: Set up Python ${{ matrix.python-version }}
-        if: "!endsWith(matrix.python-version, '-dev')"
+        if: "!endsWith(matrix.python-version, 't')"
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.architecture }}
           allow-prereleases: true
       - name: Set up Python ${{ matrix.python-version }}
-        if: endsWith(matrix.python-version, '-dev')
-        uses: deadsnakes/[email protected]
-        with:
-          python-version: ${{ matrix.python-version }}
-          nogil: true
+        if: endsWith(matrix.python-version, 't')
+        run: |
+          echo "UV_PYTHON=${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' || 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: |
-          python -m pip install --upgrade pip
-          python -m pip install tox tox-gh-actions
+          uv tool install -v tox --with=git+https://github.com/effigies/tox-gh-actions@abiflags --with=tox-uv
       - name: Show tox config
         run: tox c
       - name: Run tox

doc-requirements.txt

@@ -1,7 +1,7 @@
 # Auto-generated by tools/update_requirements.py
 -r requirements.txt
 sphinx
-matplotlib>=1.5.3
+matplotlib>=3.5
 numpydoc
 texext
 tomli; python_version < '3.11'

min-requirements.txt

@@ -1,4 +1,16 @@
-# Auto-generated by tools/update_requirements.py
-numpy ==1.20
-packaging ==17
-importlib_resources ==1.3; python_version < '3.9'
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --resolution lowest-direct --python 3.9 -o min-requirements.txt pyproject.toml
+importlib-resources==5.12.0
+    # via nibabel (pyproject.toml)
+numpy==1.22.0
+    # via nibabel (pyproject.toml)
+packaging==20.0
+    # via nibabel (pyproject.toml)
+pyparsing==3.2.0
+    # via packaging
+six==1.16.0
+    # via packaging
+typing-extensions==4.6.0
+    # via nibabel (pyproject.toml)
+zipp==3.20.2
+    # via importlib-resources

pyproject.toml

@@ -51,13 +51,15 @@ nib-roi = "nibabel.cmdline.roi:main"
 parrec2nii = "nibabel.cmdline.parrec2nii:main"
 
 [project.optional-dependencies]
-all = ["nibabel[dicomfs,minc2,spm,zstd]"]
+all = ["nibabel[dicomfs,indexed_gzip,minc2,spm,zstd]"]
 # Features
+indexed_gzip = ["indexed_gzip >=1.6"]
 dicom = ["pydicom >=2.3"]
-dicomfs = ["nibabel[dicom]", "pillow"]
-minc2 = ["h5py"]
-spm = ["scipy"]
-zstd = ["pyzstd >= 0.14.3"]
+dicomfs = ["nibabel[dicom]", "pillow >=8.4"]
+minc2 = ["h5py >=3.5"]
+spm = ["scipy >=1.8"]
+viewers = ["matplotlib >=3.5"]
+zstd = ["pyzstd >=0.15.2"]
 # For doc and test, make easy to use outside of tox
 # tox should use these with extras instead of duplicating
 doc = [
@@ -68,12 +70,12 @@ doc = [
   "tomli; python_version < '3.11'",
 ]
 test = [
-  "pytest",
-  "pytest-doctestplus",
-  "pytest-cov",
-  "pytest-httpserver",
-  "pytest-xdist",
-  "coverage>=7.2",
+  "pytest >=6",
+  "pytest-doctestplus >=1",
+  "pytest-cov >=2.11",
+  "pytest-httpserver >=1.0.7",
+  "pytest-xdist >=3.5",
+  "coverage[toml]>=7.2",
 ]
 # Remaining: Simpler to centralize in tox
 dev = ["tox"]
@@ -200,3 +202,6 @@ enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 [tool.codespell]
 skip = "*/data/*,./nibabel-data"
 ignore-words-list = "ans,te,ue,ist,nin,nd,ccompiler,ser"
+
+[tool.uv.pip]
+only-binary = ["numpy", "scipy", "h5py"]

requirements.txt

@@ -1,4 +1,5 @@
 # Auto-generated by tools/update_requirements.py
-numpy >=1.20
-packaging >=17
-importlib_resources >=1.3; python_version < '3.9'
+numpy >=1.22
+packaging >=20
+importlib_resources >=5.12; python_version < '3.12'
+typing_extensions >=4.6; python_version < '3.13'

tools/update_requirements.py

@@ -2,7 +2,10 @@
 import sys
 from pathlib import Path
 
-import tomli
+try:
+    import tomllib
+except ImportError:
+    import tomli as tomllib
 
 if sys.version_info < (3, 6):
     print('This script requires Python 3.6 to work correctly')
@@ -15,7 +18,7 @@
 doc_reqs = repo_root / 'doc-requirements.txt'
 
 with open(pyproject_toml, 'rb') as fobj:
-    config = tomli.load(fobj)
+    config = tomllib.load(fobj)
 requirements = config['project']['dependencies']
 doc_requirements = config['project']['optional-dependencies']['doc']
 
@@ -27,9 +30,10 @@
 lines[1:-1] = requirements
 reqs.write_text('\n'.join(lines))
 
-# Write minimum requirements
-lines[1:-1] = [req.replace('>=', '==').replace('~=', '==') for req in requirements]
-min_reqs.write_text('\n'.join(lines))
+# # Write minimum requirements
+# lines[1:-1] = [req.replace('>=', '==').replace('~=', '==') for req in requirements]
+# min_reqs.write_text('\n'.join(lines))
+print(f"To update {min_reqs.name}, use `uv pip compile` (see comment at top of file).")
 
 # Write documentation requirements
 lines[1:-1] = ['-r requirements.txt'] + doc_requirements

tox.ini

@@ -5,18 +5,14 @@
 [tox]
 requires =
   tox>=4
+  tox-uv
 envlist =
   # No preinstallations
-  py3{9,10,11,12,13}-none
-  # Minimum Python
-  py39-{min,full}
-  # x86 support range
-  py3{9,10,11}-{full,pre}-{x86,x64}
-  py3{9,10,11}-pre-{x86,x64}
-  # x64-only range
-  py3{12,13}-{full,pre}-x64
-  # Special environment for numpy 2.0-dev testing
-  py313-dev-x64
+  py3{9,10,11,12,13,13t}-none
+  # Minimum Python with minimum deps
+  py39-min
+  # Run full and pre dependencies against all archs
+  py3{9,10,11,12,13,13t}-{full,pre}-{x86,x64,arm64}
   install
   doctest
   style
@@ -31,12 +27,12 @@ python =
   3.11: py311
   3.12: py312
   3.13: py313
+  3.13t: py313t
 
 [gh-actions:env]
 DEPENDS =
-  none: none, install
+  none: none
   pre: pre
-  dev: dev
   full: full, install
   min: min
 
@@ -48,14 +44,8 @@ ARCH =
 [testenv]
 description = Pytest with coverage
 labels = test
-install_command =
-  python -I -m pip install -v \
-  dev: --only-binary numpy,scipy,h5py \
-  !dev: --only-binary numpy,scipy,h5py,pillow,matplotlib \
-  pre,dev: --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
-    {opts} {packages}
 pip_pre =
-  pre,dev: true
+  pre: true
 pass_env =
   # getpass.getuser() sources for Windows:
   LOGNAME
@@ -70,41 +60,45 @@ pass_env =
   NO_COLOR
   CLICOLOR
   CLICOLOR_FORCE
+  # uv needs help in this case
+  py313t-x86: UV_PYTHON
 set_env =
-  py313: PYTHON_GIL=0
-extras = test
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  py313t: PYTHONGIL={env:PYTHONGIL:0}
+extras =
+  test
+
+  # Simple, thanks Hugo and Paul
+  !none: dicomfs
+  !none: indexed_gzip
+
+  # Minimum dependencies
+  min: minc2
+  min: spm
+  min: viewers
+  min: zstd
+
+  # Matplotlib has wheels for everything except win32 (x86)
+  {full,pre}-{x,arm}64: viewers
+
+  # Nightly, but not released cp313t wheels for: scipy
+  # When released, remove the py3* line and add full to the pre line
+  py3{9,10,11,12,13}-full-{x,arm}64: spm
+  pre-{x,arm}64: spm
+
+  # No cp313t wheels for: h5py, pyzstd
+  py3{9,10,11,12,13}-{full,pre}-{x,arm}64: minc2
+  py3{9,10,11,12,13}-{full,pre}-{x,arm}64: zstd
+
+  # win32 (x86) wheels still exist for scipy+py39
+  py39-full-x86: spm
+
 deps =
-  # General minimum dependencies: pin based on API usage
-  # matplotlib 3.5 requires packaging 20
-  min: packaging ==20
-  min: importlib_resources ==5.12; python_version < '3.12'
-  min: typing_extensions ==4.6; python_version < '3.13'
-  # NEP29/SPEC0 + 1yr: Test on minor release series within the last 3 years
-  # We're extending this to all optional dependencies
-  # This only affects the range that we test on; numpy is the only non-optional
-  # dependency, and will be the only one to affect pip environment resolution.
-  min: numpy ==1.22
-  min: h5py ==3.5
-  min: indexed_gzip ==1.6
-  min: matplotlib ==3.5
-  min: pillow ==8.4
-  min: pydicom ==2.3
-  min: pyzstd ==0.15.2
-  min: scipy ==1.8
-  # Numpy 2.0 is a major breaking release; we cannot put much effort into
-  # supporting until it's at least RC stable
-  dev: numpy >=2.1.dev0
-  # Scipy stopped producing win32 wheels at py310
-  py39-full-x86,x64,arm64: scipy >=1.8
-  # Matplotlib depends on scipy, so cannot be built for py310 on x86
-  py39-full-x86,x64,arm64: matplotlib >=3.5
-  # h5py stopped producing win32 wheels at py39
-  {full,pre}-{x64,arm64}: h5py >=3.5
-  full,pre,dev: pillow >=8.4
-  full,pre: indexed_gzip >=1.6
-  full,pre,dev: pyzstd >=0.15.2
-  full,pre: pydicom >=2.3
-  dev: pydicom @ git+https://github.com/pydicom/pydicom.git@main
+  pre: pydicom @ git+https://github.com/pydicom/pydicom.git@main
+
+uv_resolution =
+  min: lowest-direct
 
 commands =
   pytest --doctest-modules --doctest-plus \
@@ -118,7 +112,6 @@ description = Install and verify import succeeds
 labels = test
 deps =
 extras =
-install_command = python -I -m pip install {opts} {packages}
 commands =
   python -c "import nibabel; print(nibabel.__version__)"