Merge branch 'master' into update-data-per-streamline

Author: effigies

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      actions-infrastructure:
+        patterns:
+          - "actions/*"

.github/workflows/test.yml

@@ -44,7 +44,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - run: pip install --upgrade build twine
@@ -54,12 +54,12 @@ jobs:
       - name: Build git archive
         run: mkdir archive && git archive -v -o archive/nibabel-archive.tgz HEAD
       - name: Upload sdist and wheel artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist/
       - name: Upload git archive artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: archive
           path: archive/
@@ -73,17 +73,17 @@ jobs:
     steps:
       - name: Download sdist and wheel artifacts
         if: matrix.package != 'archive'
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
       - name: Download git archive artifact
         if: matrix.package == 'archive'
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: archive
           path: archive/
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - name: Display Python version
@@ -147,7 +147,7 @@ jobs:
           submodules: recursive
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.architecture }}
@@ -162,14 +162,15 @@ jobs:
         run: tox c
       - name: Run tox
         run: tox -v --exit-and-dump-after 1200
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         if: ${{ always() }}
         with:
           files: cov.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.dependencies }}-${{ matrix.architecture }}
           path: test-results.xml
         if: ${{ always() }}
 
@@ -183,7 +184,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3
       - name: Display Python version
@@ -204,7 +205,7 @@ jobs:
       id-token: write
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/

.gitmodules

@@ -19,3 +19,6 @@
 [submodule "nibabel-data/nitest-dicom"]
 	path = nibabel-data/nitest-dicom
 	url = https://github.com/effigies/nitest-dicom
+[submodule "nibabel-data/dcm_qa_xa30"]
+	path = nibabel-data/dcm_qa_xa30
+	url = https://github.com/neurolabusc/dcm_qa_xa30.git

.zenodo.json

@@ -270,7 +270,7 @@
       "orcid": "0000-0003-1076-5122"
     },
     {
-      "affiliation": "Universit\u00e9 de Sherbrooke",
+      "affiliation": "Brigham and Women's Hospital, Mass General Brigham/Harvard Medical School",
       "name": "Legarreta, Jon Haitz",
       "orcid": "0000-0002-9661-1396"
     },

Changelog

@@ -25,6 +25,28 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+5.2.1 (Monday 26 February 2024)
+===============================
+
+Bug-fix release in the 5.2.x series.
+
+Enhancements
+------------
+* Support "flat" ASCII-encoded GIFTI DataArrays (pr/1298) (PM, reviewed by CM)
+
+Bug fixes
+---------
+* Tolerate missing ``git`` when reporting version info (pr/1286) (CM, reviewed by
+  Yuri Victorovich)
+* Handle Siemens XA30 derived DWI DICOMs (pr/1296) (CM, reviewed by YOH and
+  Mathias Goncalves)
+
+Maintenance
+-----------
+* Add tool for generating GitHub-friendly release notes (pr/1284) (CM)
+* Accommodate pytest 8 changes (pr/1297) (CM)
+
+
 5.2.0 (Monday 11 December 2023)
 ===============================
 

nibabel-data/dcm_qa_xa30

@@ -17,7 +17,7 @@
 from .optpkg import optional_package
 
 if ty.TYPE_CHECKING:  # pragma: no cover
-    import indexed_gzip  # type: ignore[import-not-found]
+    import indexed_gzip  # type: ignore[import]
     import pyzstd
 
     HAVE_INDEXED_GZIP = True

nibabel/_compression.py

@@ -365,7 +365,7 @@ def rescale_affine(affine, shape, zooms, new_shape=None):
         A new affine transform with the specified voxel sizes
 
     """
-    shape = np.array(shape, copy=False)
+    shape = np.asarray(shape)
     new_shape = np.array(new_shape if new_shape is not None else shape)
 
     s = voxel_sizes(affine)

nibabel/affines.py

@@ -26,7 +26,7 @@
 
 # if memory_profiler is installed, we get memory usage results
 try:
-    from memory_profiler import memory_usage  # type: ignore[import-not-found]
+    from memory_profiler import memory_usage  # type: ignore[import]
 except ImportError:
     memory_usage = None
 

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -611,7 +611,7 @@ def int_abs(arr):
     >>> int_abs(np.array([-128, 127], dtype=np.float32))
     array([128., 127.], dtype=float32)
     """
-    arr = np.array(arr, copy=False)
+    arr = np.asarray(arr)
     dt = arr.dtype
     if dt.kind == 'u':
         return arr