Prepare 3.1.3

.github/workflows/ci.yml

@@ -32,7 +32,7 @@ jobs:
           python ./tools/check_meson.py dist/silx-*.whl
 
   build:
-    name: "Python ${{ matrix.python-version }} on ${{ matrix.os }} ${{ matrix.QT_API }}"
+    name: "Python ${{ matrix.python-version }} on ${{ matrix.os }} ${{ matrix.QT_API }} ${{ matrix.numpy_version }}"
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -43,18 +43,21 @@ jobs:
             QT_API: PySide6
             with_opencl: true
             with_gl_test: true
+            numpy_version: ""
 
           - os: macos-latest
             python-version: "3.14"
             QT_API: PyQt6
             with_opencl: false
             with_gl_test: false
+            numpy_version: ""
 
           - os: windows-latest
             python-version: "3.10"
             QT_API: PyQt5
             with_opencl: false
             with_gl_test: true
+            numpy_version: "numpy<2"
 
     steps:
       - uses: actions/checkout@v5
@@ -79,6 +82,10 @@ jobs:
           pip install -r ci/requirements-pinned.txt
           pip install --pre "${{ matrix.QT_API }}"
           pip install --pre "$(ls dist/silx*.whl)[full,test]"
+          if [ -n "${{ matrix.numpy_version }}" ]; then
+            pip uninstall -y h5pyd;
+            pip install "${{ matrix.numpy_version }}";
+          fi
           python ./ci/info_platform.py
           pip list
 

.github/workflows/release.yml

@@ -219,7 +219,7 @@ jobs:
         if: runner.os == 'Linux'
         with:
           platforms: all
-      - uses: pypa/cibuildwheel@v3.3.1
+      - uses: pypa/cibuildwheel@v4.2.1
         env:
           # Configure silx tests
           WITH_QT_TEST: "False"
@@ -229,7 +229,7 @@ jobs:
           CIBW_ENVIRONMENT_PASS_LINUX: WITH_QT_TEST WITH_GL_TEST SILX_OPENCL
 
           CIBW_BUILD_VERBOSITY: 1
-          CIBW_BUILD: cp310-* cp311-* cp312-* cp313-* cp314-*
+          CIBW_BUILD: cp310-* cp311-* cp312-* cp313-* cp314-* cp315-*
           CIBW_SKIP: cp310-win_arm64 *-musllinux_*
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
           CIBW_BUILD_FRONTEND: "build; args: -C setup-args=-Duse_openmp=disabled"
@@ -243,7 +243,8 @@ jobs:
           # - ARM64 windows: Wheels missing for some dependencies
           # - Windows python 3.14: PyOpencl wheel missing
           # - Linux python 3.14: PySide6 wheel requires a too recent manylinux version
-          CIBW_TEST_SKIP: "*-*linux_{aarch64,ppc64le,s390x} *-win_arm64 cp314-win_amd64 cp314-manylinux_x86_64"
+          # - Python 3.15 until all dependencies are available
+          CIBW_TEST_SKIP: "*-*linux_{aarch64,ppc64le,s390x} *-win_arm64 cp314-win_amd64 cp314-manylinux_x86_64 cp315-*"
 
       - uses: actions/upload-artifact@v6
         with:

CHANGELOG.rst

@@ -1,6 +1,18 @@
 Release Notes
 =============
 
+
+3.1.3: 2026/10/06
+-----------------
+
+* `silx.gui.plot.PlotWidget`: Fixed keep aspect ratio with matplotlib tight layout (`PR #4734 <https://github.com/silx-kit/silx/pull/4734>`_)
+* `silx.gui.utils.glutils.isOpenGLAvailable`: Fixed support of `pyopengl`>=4.0.0a4 and wayland (`PR #4727 <https://github.com/silx-kit/silx/pull/4727>`_)
+* Dependencies:
+
+  * Added cython>=3.3.0 support (`PR #4731 <https://github.com/silx-kit/silx/pull/4731>`_)
+  * Added Python3.15 support (`PR #4732 <https://github.com/silx-kit/silx/pull/4732>`_)
+  * Fixed support of `numpy` v1 (`PR #4725 <https://github.com/silx-kit/silx/pull/4725>`_, `PR #4728 <https://github.com/silx-kit/silx/pull/4728>`_)
+
 3.1.2: 2026/09/03
 -----------------
 

ci/requirements-pinned.txt

@@ -2,4 +2,3 @@
 --find-links http://www.silx.org/pub/wheelhouse/
 
 # Placeholder for pinned packages used by CI
-Cython==3.2.6

pyproject.toml

@@ -43,7 +43,7 @@ dependencies = [
 build-backend = 'mesonpy'
 requires = [
     'meson-python',
-    'cython>=3.1,<3.3',
+    'cython>=3.1',
 ]
 
 
@@ -98,7 +98,7 @@ dev = [
     'wheel',                                  # To build wheels
     'meson-python',
     'ninja',
-    'cython>=3.1,<3.3',
+    'cython>=3.1',
     "tomli>=1.0.0; python_version < '3.11'",  # For bootstrap.py and build_man_page.py
     'ruff',                                   # Formatting and linting
     'pyinstaller>=6.0.0; sys_platform == "win32"',

src/silx/_version.py

@@ -71,7 +71,7 @@
 
 MAJOR = 3
 MINOR = 1
-MICRO = 2
+MICRO = 3
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

src/silx/gui/plot/_utils/axis_scale.py

@@ -44,7 +44,7 @@ def apply(axisScale: AxisScaleType, value: float | ArrayLike) -> float | numpy.n
             scaled[~numpy.isfinite(scaled)] = numpy.nan
             return scaled
     elif axisScale == "asinh":
-        return numpy.asinh(value)
+        return numpy.arcsinh(value)
     else:
         raise ValueError(f"Unsupported axis scale: {axisScale}")
 
@@ -57,7 +57,7 @@ def revert(axisScale: AxisScaleType, value: float | ArrayLike) -> float | numpy.
         return value
     elif axisScale == "log":
         with numpy.errstate(over="ignore"):
-            return numpy.pow(10.0, value)
+            return numpy.power(10.0, value)
     elif axisScale == "asinh":
         with numpy.errstate(over="ignore"):
             return numpy.sinh(value)

src/silx/gui/plot/backends/BackendMatplotlib.py

@@ -522,7 +522,7 @@ def __init__(self, plot, parent=None):
         self._axesDisplayed = True
 
         self.fig = Figure(
-            tight_layout=config._MPL_TIGHT_LAYOUT,
+            layout="tight" if config._MPL_TIGHT_LAYOUT else None,
         )
         self.fig.set_facecolor("w")
 
@@ -1247,13 +1247,13 @@ def _setPlotBounds(
         if not self.isKeepDataAspectRatio():
             newXRange, newYRange, newY2Range = xRange, yRange, y2Range
         else:
-            bbox = self.fig.get_window_extent()
+            plotWidth, plotHeight = self.getPlotBoundsInPixels()[2:]
             if keepDim is None:
                 xDataRange, yDataRange, _ = self._plot.getDataRange()
-                keepDim = findDimToKeep(bbox.width, bbox.height, xDataRange, yDataRange)
+                keepDim = findDimToKeep(plotWidth, plotHeight, xDataRange, yDataRange)
             newXRange, newYRange, newY2Range = ensureAspectRatio(
-                bbox.width,
-                bbox.height,
+                plotWidth,
+                plotHeight,
                 xRange,
                 yRange,
                 y2Range,

src/silx/gui/utils/glutils/__init__.py

@@ -26,6 +26,8 @@
 import os
 import sys
 import subprocess
+
+from packaging.version import Version
 from silx.gui import qt
 
 
@@ -129,11 +131,12 @@ def isOpenGLAvailable(
 
     # Check pyopengl availability
     try:
-        from silx.gui._glutils import gl
+        import OpenGL
     except ImportError:
         return _IsOpenGLAvailableResult(
-            "Cannot import OpenGL wrapper: pyopengl is not installed"
+            "Cannot import OpenGL: pyopengl is not installed"
         )
+    from silx.gui._glutils import gl
 
     # Pre checks for Qt < 5.4
     if not hasattr(qt, "QOpenGLWidget"):
@@ -149,15 +152,16 @@ def isOpenGLAvailable(
             # so this is only checked if the QApplication is already created
             return _IsOpenGLAvailableResult("Qt reports OpenGL not available")
 
-    # Check compatibility between Qt platform and pyopengl selected platform
-    qt_qpa_platform = qt.QGuiApplication.platformName()
-    pyopengl_platform = gl.getPlatform()
-    if (qt_qpa_platform == "wayland" and pyopengl_platform != "EGLPlatform") or (
-        qt_qpa_platform == "xcb" and pyopengl_platform != "GLXPlatform"
-    ):
-        return _IsOpenGLAvailableResult(
-            f"Qt platform '{qt_qpa_platform}' is not compatible with PyOpenGL platform '{pyopengl_platform}'"
-        )
+    if Version(OpenGL.__version__) < Version("4.0.0a4"):
+        # Check compatibility between Qt platform and pyopengl selected platform
+        qt_qpa_platform = qt.QGuiApplication.platformName()
+        pyopengl_platform = gl.getPlatform()
+        if (qt_qpa_platform == "wayland" and pyopengl_platform != "EGLPlatform") or (
+            qt_qpa_platform == "xcb" and pyopengl_platform != "GLXPlatform"
+        ):
+            return _IsOpenGLAvailableResult(
+                f"Qt platform '{qt_qpa_platform}' is not compatible with PyOpenGL platform '{pyopengl_platform}'"
+            )
 
     keyCache = version, shareOpenGLContexts
     if keyCache in _runtimeCheckCache:  # Use cache
@@ -217,10 +221,12 @@ def paintGL(self):
         qt.QCoreApplication.setAttribute(qt.Qt.AA_ShareOpenGLContexts)
     app = qt.QApplication([])
     window = qt.QMainWindow(
-        flags=qt.Qt.Popup
+        flags=qt.Qt.Tool
         | qt.Qt.FramelessWindowHint
         | qt.Qt.NoDropShadowWindowHint
         | qt.Qt.WindowStaysOnTopHint
+        | qt.Qt.WindowTransparentForInput
+        | qt.Qt.WindowDoesNotAcceptFocus
     )
     window.setAttribute(qt.Qt.WA_ShowWithoutActivating)
     window.move(0, 0)

src/silx/io/test/test_utils.py

@@ -29,6 +29,8 @@
 import tempfile
 import unittest
 
+import pytest
+
 from .. import utils
 from ..._version import calc_hexversion
 import silx.io.url
@@ -1142,6 +1144,8 @@ def test_recursive_match_commonh5():
 
 
 def test_open_h5pyd(httpserver):
+    pytest.importorskip("h5pyd")
+
     httpserver.check_assertions()
     httpserver.expect_request("/about", query_string=None).respond_with_json({})
     httpserver.expect_request("/", query_string=None).respond_with_json(

src/silx/math/test/test_combo.py

@@ -216,7 +216,7 @@ def np_mean_std(img, mask=None, dummy=None, delta_dummy=None):
     fimg = img.astype(numpy.float64)
     fimg[mask] = numpy.nan
     mean = numpy.nanmean(fimg)
-    std = numpy.nanstd(fimg, mean=mean)
+    std = numpy.nanstd(fimg)
     return mean, std
 
 

src/silx/utils/test/test_external_resources.py

@@ -81,7 +81,7 @@ def test_download_all(self):
         filelist = self.resources.getdir(directory)
         # download file and remove it to create a json mapping file
         os.remove(filename)
-        directory_path = os.path.commonprefix(filelist)
+        directory_path = os.path.commonpath(filelist)
         # Make sure we will rmtree a dangerous path like "/"
         self.assertIn(self.resources.data_home, directory_path)
         shutil.rmtree(directory_path)