.git-blame-ignore-revs

@@ -1,3 +1,7 @@
+# Sun Jan 12 12:22:13 2025 -0500 - markiewicz@stanford.edu - sty: ruff format [git-blame-ignore-rev]
+40e41208a0f04063b3c4e373a65da1a2a6a275b5
+# Sun Jan 12 11:51:49 2025 -0500 - markiewicz@stanford.edu - STY: ruff format [git-blame-ignore-rev]
+7e5d584910c67851dcfcd074ff307122689b61f5
 # Sun Jan 1 12:38:02 2023 -0500 - effigies@gmail.com - STY: Run pre-commit config on all files
 d14c1cf282a9c3b19189f490f10c35f5739e24d1
 # Thu Dec 29 22:53:17 2022 -0500 - effigies@gmail.com - STY: Reduce array().astype() and similar constructs

.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
@@ -167,30 +187,42 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
       - 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/action@v3.2.0
-        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
         run: tox -vv --exit-and-dump-after 1200
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         if: ${{ always() }}
         with:
           files: cov.xml

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ".*/data/.*"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -13,18 +13,15 @@ repos:
       - id: check-merge-conflict
       - id: check-vcs-permalinks
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
+    rev: v0.9.6
     hooks:
       - id: ruff
         args: [ --fix ]
         exclude: = ["doc", "tools"]
       - id: ruff-format
         exclude: = ["doc", "tools"]
-      - id: ruff
-        args: [ --select, ISC001, --fix ]
-        exclude: = ["doc", "tools"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.15.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing
@@ -39,7 +36,7 @@ repos:
         args: ["nibabel"]
         pass_filenames: false
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies:

.readthedocs.yaml

@@ -0,0 +1,21 @@
+version: 2
+
+build:
+  os: ubuntu-lts-latest
+  tools:
+    python: latest
+  jobs:
+    pre_create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    create_environment:
+      - uv venv $READTHEDOCS_VIRTUALENV_PATH
+    install:
+      # Use a cache dir in the same mount to halve the install time
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache .[doc]
+    pre_build:
+      - ( cd doc; python tools/build_modref_templates.py nibabel source/reference False )
+
+sphinx:
+  configuration: doc/source/conf.py

Changelog

@@ -25,6 +25,17 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+5.3.2 (Wednesday 23 October 2024)
+=================================
+
+Bug-fix release in the 5.3.x series.
+
+Bug fixes
+---------
+* Restore MRS extension type to Nifti1Extension to maintain backwards compatibility.
+  (pr/1380) (CM)
+
+
 5.3.1 (Tuesday 15 October 2024)
 ===============================
 
@@ -46,9 +57,9 @@ NiBabel 6.0 will drop support for Numpy 1.x.
 
 New features
 ------------
-* Update NIfTI extension protocol to include ``.content : bytes``, ``.text : str`` and ``.json : dict``
-  properties for accessing extension contents. Exceptions will be raised on ``.text`` and ``.json`` if
-  conversion fails. (pr/1336) (CM)
+* Update NIfTI extension protocol to include ``.content : bytes``, ``.text : str`` and
+  ``.json() : dict`` properties/methods for accessing extension contents.
+  Exceptions will be raised on ``.text`` and ``.json()`` if conversion fails. (pr/1336) (CM)
 
 Enhancements
 ------------

bin/parrec2nii

@@ -1,6 +1,5 @@
 #!python
-"""PAR/REC to NIfTI converter
-"""
+"""PAR/REC to NIfTI converter"""
 
 from nibabel.cmdline.parrec2nii import main
 

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

nibabel/_typing.py

@@ -0,0 +1,25 @@
+"""Helpers for typing compatibility across Python versions"""
+
+import sys
+
+if sys.version_info < (3, 10):
+    from typing_extensions import ParamSpec
+else:
+    from typing import ParamSpec
+
+if sys.version_info < (3, 11):
+    from typing_extensions import Self
+else:
+    from typing import Self
+
+if sys.version_info < (3, 13):
+    from typing_extensions import TypeVar
+else:
+    from typing import TypeVar
+
+
+__all__ = [
+    'ParamSpec',
+    'Self',
+    'TypeVar',
+]

nibabel/arrayproxy.py

@@ -59,10 +59,11 @@
 
 if ty.TYPE_CHECKING:
     import numpy.typing as npt
-    from typing_extensions import Self  # PY310
+
+    from ._typing import Self, TypeVar
 
     # Taken from numpy/__init__.pyi
-    _DType = ty.TypeVar('_DType', bound=np.dtype[ty.Any])
+    _DType = TypeVar('_DType', bound=np.dtype[ty.Any])
 
 
 class ArrayLike(ty.Protocol):

nibabel/benchmarks/bench_array_to_file.py

@@ -29,24 +29,25 @@ def bench_array_to_file():
     sys.stdout.flush()
     print_git_title('\nArray to file')
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
-    print('%30s %6.2f' % ('Save float64 to float32', mtime))
+    fmt = '{:30s} {:6.2f}'.format
+    print(fmt('Save float64 to float32', mtime))
     mtime = measure('array_to_file(arr, BytesIO(), np.int16)', repeat)
-    print('%30s %6.2f' % ('Save float64 to int16', mtime))
+    print(fmt('Save float64 to int16', mtime))
     # Set a lot of NaNs to check timing
     arr[:, :, :, 1] = np.nan
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
-    print('%30s %6.2f' % ('Save float64 to float32, NaNs', mtime))
+    print(fmt('Save float64 to float32, NaNs', mtime))
     mtime = measure('array_to_file(arr, BytesIO(), np.int16)', repeat)
-    print('%30s %6.2f' % ('Save float64 to int16, NaNs', mtime))
+    print(fmt('Save float64 to int16, NaNs', mtime))
     # Set a lot of infs to check timing
     arr[:, :, :, 1] = np.inf
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
-    print('%30s %6.2f' % ('Save float64 to float32, infs', mtime))
+    print(fmt('Save float64 to float32, infs', mtime))
     mtime = measure('array_to_file(arr, BytesIO(), np.int16)', repeat)
-    print('%30s %6.2f' % ('Save float64 to int16, infs', mtime))
+    print(fmt('Save float64 to int16, infs', mtime))
     # Int16 input, float output
     arr = np.random.random_integers(low=-1000, high=1000, size=img_shape)
     arr = arr.astype(np.int16)
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
-    print('%30s %6.2f' % ('Save Int16 to float32', mtime))
+    print(fmt('Save Int16 to float32', mtime))
     sys.stdout.flush()

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -96,10 +96,10 @@ def fmt_sliceobj(sliceobj):
                 slcstr.append(s)
             else:
                 slcstr.append(str(int(s * SHAPE[i])))
-        return f"[{', '.join(slcstr)}]"
+        return f'[{", ".join(slcstr)}]'
 
     with InTemporaryDirectory():
-        print(f'Generating test data... ({int(round(np.prod(SHAPE) * 4 / 1048576.0))} MB)')
+        print(f'Generating test data... ({round(np.prod(SHAPE) * 4 / 1048576.0)} MB)')
 
         data = np.array(np.random.random(SHAPE), dtype=np.float32)
 

nibabel/benchmarks/bench_finite_range.py

@@ -28,16 +28,17 @@ def bench_finite_range():
     sys.stdout.flush()
     print_git_title('\nFinite range')
     mtime = measure('finite_range(arr)', repeat)
-    print('%30s %6.2f' % ('float64 all finite', mtime))
+    fmt = '{:30s} {:6.2f}'.format
+    print(fmt('float64 all finite', mtime))
     arr[:, :, :, 1] = np.nan
     mtime = measure('finite_range(arr)', repeat)
-    print('%30s %6.2f' % ('float64 many NaNs', mtime))
+    print(fmt('float64 many NaNs', mtime))
     arr[:, :, :, 1] = np.inf
     mtime = measure('finite_range(arr)', repeat)
-    print('%30s %6.2f' % ('float64 many infs', mtime))
+    print(fmt('float64 many infs', mtime))
     # Int16 input, float output
     arr = np.random.random_integers(low=-1000, high=1000, size=img_shape)
     arr = arr.astype(np.int16)
     mtime = measure('finite_range(arr)', repeat)
-    print('%30s %6.2f' % ('int16', mtime))
+    print(fmt('int16', mtime))
     sys.stdout.flush()