Merge branch 'topic/default/check-py12-numpy2' into 'branch/default'

Check with Python 3.12 and numpy 2.0

See merge request fluiddyn/fluidimage!113

.github/workflows/ci-linux.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - name: Install apt packages

.github/workflows/ci-pixi.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["windows-2022", "macos-latest"]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/wheels.yml

@@ -26,7 +26,7 @@ jobs:
         with:
           python-version: 3.x
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.19.2
         env:
           CIBW_SKIP: pp* cp36-* cp37-* cp38-* *-musllinux*
           CIBW_ARCHS: ${{ matrix.architecture }}
@@ -49,7 +49,7 @@ jobs:
         with:
           python-version: 3.x
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.19.2
         env:
           CIBW_SKIP: pp* cp36-* cp37-* cp38-* *-musllinux*
           CIBW_ARCHS: ${{ matrix.architecture }}
@@ -81,7 +81,7 @@ jobs:
           python-version: 3.x
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.19.2
         env:
           CIBW_SKIP: pp* cp36-* cp37-* cp38-* *-musllinux*
           CIBW_ARCHS: aarch64
@@ -113,7 +113,7 @@ jobs:
         name: sdist
     - uses: actions/setup-python@v5
       with:
-        python-version: 3.11
+        python-version: 3.12
     - run: |
         pip install pip -U
         ls

pixi.toml

@@ -10,11 +10,10 @@ install-editable = {cmd = "pip install -e . -v --no-build-isolation --no-deps",
 test = "export OMP_NUM_THREADS=1 && pytest src -v -s"
 
 [dependencies]
-python = ">=3.9,<3.11"
+python = ">=3.9"
 numpy = ">=1.26.3"
 transonic = ">=0.6.4"
-# should actually be >=0.6.2 (soon available)
-fluiddyn = ">=0.6.1"
+fluiddyn = ">=0.6.2"
 h5netcdf = ">=1.3.0"
 h5py = ">=3.10.0"
 matplotlib = ">=3.5"
@@ -37,5 +36,5 @@ pythran = ">=0.15.0"
 pytest = ">=8.0.0"
 pytest-cov = ">=4.1.0"
 coverage = ">=7.4.1"
-pytest-asyncio = ">=0.23.6,<0.24"
-linkify-it-py = ">=2.0.3,<2.1"
+pytest-asyncio = ">=0.23.6"
+linkify-it-py = ">=2.0.3"

pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
     "rich>=13.7.1",
     "textual",
 ]
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.9"
 readme = "README.md"
 license = {text = "CeCILL"}
 keywords = [
@@ -46,6 +46,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.9",
     "Topic :: Scientific/Engineering",
 ]
@@ -113,7 +114,8 @@ dev-doc = [
     "jupyterlab",
     "jupyterlab-myst",
     "jupytext",
-    "mdformat-myst"
+    # cannot lock with this (2024-07)
+    # "mdformat-myst"
 ]
 test = [
     "pytest",

src/fluidimage/works/preproc/_toolbox_py.py

@@ -262,7 +262,7 @@ def temporal_minima(img=None, weight=1.0, window_shape=None):
 
 
 @iterate_multiple_imgs
-def global_threshold(img=None, minima=0.0, maxima=65535.0):
+def global_threshold(img=None, minima=0, maxima=None):
     """
     Trims pixel intensities which are outside the interval (minima, maxima).
 
@@ -276,6 +276,14 @@ def global_threshold(img=None, minima=0.0, maxima=65535.0):
 
     """
     img_out = img.copy()
+    if maxima is None:
+        dtype = img_out.dtype
+        try:
+            info = np.iinfo(dtype)
+        except ValueError:
+            maxima = 65535
+        else:
+            maxima = info.max
     img_out[img_out < minima] = minima
     img_out[img_out > maxima] = maxima
     return img_out