Merge branch 'master' into freesurfer-realras-flex

Author: effigies

.github/workflows/test.yml

@@ -41,7 +41,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v5
@@ -73,13 +73,13 @@ jobs:
     steps:
       - name: Download sdist and wheel artifacts
         if: matrix.package != 'archive'
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: dist
           path: dist/
       - name: Download git archive artifact
         if: matrix.package == 'archive'
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: archive
           path: archive/
@@ -113,7 +113,15 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-13', 'macos-latest']
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.13t"]
+        python-version:
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          - "3.13"
+          - "3.13t"
+          - "3.14"
+          - "3.14t"
         architecture: ['x86', 'x64', 'arm64']
         dependencies: ['full', 'pre']
         include:
@@ -127,6 +135,11 @@ jobs:
             python-version: "3.9"
             architecture: 'x64'
             dependencies: 'min'
+          # Absolute minimum dependencies
+          - os: ubuntu-latest
+            python-version: "3.10"
+            architecture: 'x64'
+            dependencies: 'min'
         exclude:
           # Use ubuntu-latest to cover the whole range of Python. For Windows
           # and OSX, checking oldest and newest should be sufficient.
@@ -183,7 +196,7 @@ jobs:
       ARCH: ${{ !contains(fromJSON('["none", "min"]'), matrix.dependencies) && matrix.architecture }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: recursive
           fetch-depth: 0
@@ -217,7 +230,9 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          uv tool install -v tox --with=git+https://github.com/effigies/tox-gh-actions@abiflags --with=tox-uv
+          uv tool install -v tox \
+            --with=tox-uv \
+            --with=git+https://github.com/effigies/tox-gh-actions@abiflags
       - name: Show tox config
         run: tox c
       - name: Run tox
@@ -242,7 +257,7 @@ jobs:
         check: ['style', 'doctest', 'typecheck', 'spellcheck']
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
@@ -265,7 +280,7 @@ jobs:
       id-token: write
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           name: dist
           path: dist/

dev-requirements.txt

@@ -5,5 +5,6 @@ Nibabel documentation
 To build the documentation, change to the root directory (containing
 ``pyproject.toml``) and run::
 
-    pip install -r doc-requirements.txt
+    uv sync --extra doc
+    source .venv/bin/activate
     make -C doc html

doc-requirements.txt

@@ -68,10 +68,9 @@ Release checklist
 
   because this will be the output used by pypi_
 
-* Check the dependencies listed in ``nibabel/info.py`` (e.g.
-  ``NUMPY_MIN_VERSION``) and in ``doc/source/installation.rst`` and in
-  ``requirements.txt`` and ``.travis.yml``.  They should at least match. Do
-  they still hold?  Make sure `nibabel on travis`_ is testing the minimum
+* Check the dependencies listed in ``pyproject.toml`` and in
+  ``doc/source/installation.rst``. They should at least match. Do
+  they still hold?  Verify that `nibabel on GitHub actions`_ is testing the minimum
   dependencies specifically.
 
 * Do a final check on the `nipy buildbot`_.  Use the ``try_branch.py``
@@ -129,7 +128,7 @@ Release checklist
 
       make -C doc doctest
 
-    This should also be tested by `nibabel on travis`_.
+    This should also be tested by `nibabel on GitHub actions`_.
 
   * Check everything compiles without syntax errors::
 

doc/README.rst

@@ -20,7 +20,7 @@
 .. _nibabel issues: https://github.com/nipy/nibabel/issues
 .. _nibabel github issues: https://github.com/nipy/nibabel/issues
 .. _nibabel wiki: https://github.com/nipy/nibabel.wiki
-.. _nibabel on travis: https://travis-ci.org/nipy/nibabel
+.. _nibabel on github actions: https://github.com/nipy/nibabel/actions
 
 .. other related projects
 .. _nipy community: http://nipy.org

doc/source/devel/make_release.rst

@@ -358,8 +358,7 @@ def proc_file(infile, opts):
             )
             with open(basefilename + '.bvals', 'w') as fid:
                 # np.savetxt could do this, but it's just a loop anyway
-                for val in bvals:
-                    fid.write(f'{val} ')
+                fid.writelines(f'{val} ' for val in bvals)
                 fid.write('\n')
         else:
             verbose('Writing .bvals and .bvecs files')
@@ -369,13 +368,11 @@ def proc_file(infile, opts):
             bvecs = apply_affine(bv_reorient, bvecs)
             with open(basefilename + '.bvals', 'w') as fid:
                 # np.savetxt could do this, but it's just a loop anyway
-                for val in bvals:
-                    fid.write(f'{val} ')
+                fid.writelines(f'{val} ' for val in bvals)
                 fid.write('\n')
             with open(basefilename + '.bvecs', 'w') as fid:
                 for row in bvecs.T:
-                    for val in row:
-                        fid.write(f'{val} ')
+                    fid.writelines(f'{val} ' for val in row)
                     fid.write('\n')
 
     # export data labels varying along the 4th dimensions if requested

doc/source/links_names.txt

@@ -9,6 +9,12 @@
 from nibabel.testing import data_path
 
 
+@pytest.fixture(scope='module', autouse=True)
+def NO_COLOR():
+    with mock.patch.dict(os.environ, {'NO_COLOR': '1'}):
+        yield
+
+
 def test_parse_slice():
     assert parse_slice(None) == slice(None)
     assert parse_slice('1:5') == slice(1, 5)

min-requirements.txt

@@ -21,7 +21,7 @@
 if ty.TYPE_CHECKING:
     from types import TracebackType
 
-    from _typeshed import WriteableBuffer
+    from _typeshed import ReadableBuffer, WriteableBuffer
 
     from ._typing import Self
 
@@ -231,6 +231,9 @@ def readinto(self, buffer: WriteableBuffer, /) -> int | None:
     def write(self, b: bytes, /) -> int | None:
         return self.fobj.write(b)
 
+    def writelines(self, lines: ty.Iterable[ReadableBuffer], /) -> None:
+        self.fobj.writelines(lines)
+
     def seek(self, pos: int, whence: int = 0, /) -> int:
         return self.fobj.seek(pos, whence)