Merge pull request #1247 from effigies/ci/py312

CI: Begin testing on Python 3.12

Author: effigies

.github/workflows/pre-release.yml

@@ -33,7 +33,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         architecture: ['x64', 'x86']
         install: ['pip']
         check: ['test']
@@ -54,6 +54,8 @@ jobs:
             architecture: x86
           - os: macos-latest
             architecture: x86
+          - python-version: '3.12'
+            architecture: x86
 
     env:
       DEPENDS: ${{ matrix.depends }}
@@ -72,6 +74,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.architecture }}
+          allow-prereleases: true
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Create virtual environment

nibabel/openers.py

@@ -78,6 +78,12 @@ def __init__(
             mtime=mtime,
         )
 
+    def seek(self, pos: int, whence: int = 0, /) -> int:
+        # Work around bug (gh-180111) in Python 3.12rc1, where seeking without
+        # flushing can cause write of excess null bytes
+        self.flush()
+        return super().seek(pos, whence)
+
 
 def _gzip_open(
     filename: str,

nibabel/streamlines/tests/test_streamlines.py

@@ -84,7 +84,7 @@ def setup():
     )
 
 
-def test_is_supported_detect_format():
+def test_is_supported_detect_format(tmp_path):
     # Test is_supported and detect_format functions
     # Empty file/string
     f = BytesIO()
@@ -103,15 +103,17 @@ def test_is_supported_detect_format():
 
     # Wrong extension but right magic number
     for tfile_cls in FORMATS.values():
-        with tempfile.TemporaryFile(mode='w+b', suffix='.txt') as f:
+        fpath = tmp_path / 'test.txt'
+        with open(fpath, 'w+b') as f:
             f.write(asbytes(tfile_cls.MAGIC_NUMBER))
             f.seek(0, os.SEEK_SET)
             assert nib.streamlines.is_supported(f)
             assert nib.streamlines.detect_format(f) is tfile_cls
 
     # Good extension but wrong magic number
     for ext, tfile_cls in FORMATS.items():
-        with tempfile.TemporaryFile(mode='w+b', suffix=ext) as f:
+        fpath = tmp_path / f'test{ext}'
+        with open(fpath, 'w+b') as f:
             f.write(b'pass')
             f.seek(0, os.SEEK_SET)
             assert not nib.streamlines.is_supported(f)

nibabel/tests/test_image_api.py

@@ -25,6 +25,7 @@
 
 import io
 import pathlib
+import sys
 import warnings
 from functools import partial
 from itertools import product
@@ -579,6 +580,10 @@ def validate_from_url(self, imaker, params):
         del img
         del rt_img
 
+    @pytest.mark.xfail(
+        sys.version_info >= (3, 12),
+        reason='Response type for file: urls is not a stream in Python 3.12',
+    )
     def validate_from_file_url(self, imaker, params):
         tmp_path = self.tmp_path
 

nibabel/tests/test_openers.py

@@ -127,35 +127,36 @@ def patch_indexed_gzip(state):
         yield
 
 
-def test_Opener_gzip_type():
-    # Test that BufferedGzipFile or IndexedGzipFile are used as appropriate
-
-    data = 'this is some test data'
-    fname = 'test.gz'
-
-    with InTemporaryDirectory():
-
-        # make some test data
-        with GzipFile(fname, mode='wb') as f:
-            f.write(data.encode())
-
-        # Each test is specified by a tuple containing:
-        #   (indexed_gzip present, Opener kwargs, expected file type)
-        tests = [
-            (False, {'mode': 'rb', 'keep_open': True}, GzipFile),
-            (False, {'mode': 'rb', 'keep_open': False}, GzipFile),
-            (False, {'mode': 'wb', 'keep_open': True}, GzipFile),
-            (False, {'mode': 'wb', 'keep_open': False}, GzipFile),
-            (True, {'mode': 'rb', 'keep_open': True}, MockIndexedGzipFile),
-            (True, {'mode': 'rb', 'keep_open': False}, MockIndexedGzipFile),
-            (True, {'mode': 'wb', 'keep_open': True}, GzipFile),
-            (True, {'mode': 'wb', 'keep_open': False}, GzipFile),
-        ]
-
-        for test in tests:
-            igzip_present, kwargs, expected = test
-            with patch_indexed_gzip(igzip_present):
-                assert isinstance(Opener(fname, **kwargs).fobj, expected)
+def test_Opener_gzip_type(tmp_path):
+    # Test that GzipFile or IndexedGzipFile are used as appropriate
+
+    data = b'this is some test data'
+    fname = tmp_path / 'test.gz'
+
+    # make some test data
+    with GzipFile(fname, mode='wb') as f:
+        f.write(data)
+
+    # Each test is specified by a tuple containing:
+    #   (indexed_gzip present, Opener kwargs, expected file type)
+    tests = [
+        (False, {'mode': 'rb', 'keep_open': True}, GzipFile),
+        (False, {'mode': 'rb', 'keep_open': False}, GzipFile),
+        (False, {'mode': 'wb', 'keep_open': True}, GzipFile),
+        (False, {'mode': 'wb', 'keep_open': False}, GzipFile),
+        (True, {'mode': 'rb', 'keep_open': True}, MockIndexedGzipFile),
+        (True, {'mode': 'rb', 'keep_open': False}, MockIndexedGzipFile),
+        (True, {'mode': 'wb', 'keep_open': True}, GzipFile),
+        (True, {'mode': 'wb', 'keep_open': False}, GzipFile),
+    ]
+
+    for test in tests:
+        igzip_present, kwargs, expected = test
+        with patch_indexed_gzip(igzip_present):
+            opener = Opener(fname, **kwargs)
+            assert isinstance(opener.fobj, expected)
+            # Explicit close to appease Windows
+            del opener
 
 
 class TestImageOpener(unittest.TestCase):

tools/ci/install_dependencies.sh

@@ -19,10 +19,10 @@ if [ -n "$EXTRA_PIP_FLAGS" ]; then
 fi
 
 if [ -n "$DEPENDS" ]; then
-    pip install ${EXTRA_PIP_FLAGS} --prefer-binary ${!DEPENDS}
+    pip install ${EXTRA_PIP_FLAGS} --only-binary :all: ${!DEPENDS}
     if [ -n "$OPTIONAL_DEPENDS" ]; then
         for DEP in ${!OPTIONAL_DEPENDS}; do
-            pip install ${EXTRA_PIP_FLAGS} --prefer-binary $DEP || true
+            pip install ${EXTRA_PIP_FLAGS} --only-binary :all: $DEP || true
 	done
     fi
 fi