upgrate to version 0.5.3

_cmake/constants.cmake

@@ -150,12 +150,19 @@ configure_file(
 #
 
 # AVX instructions
+# Check with bash _cmake/intrin.sh <avx function name>
 if(MSVC)
   # disable warning for #pragma unroll
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:AVX")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:AVX2")
   add_compile_options(/wd4068)
 else()
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mavx")
+  # Other possible flags
+  # "-mavx512f", "-mavx512bw", "-mavx512dq", "-mavx512vl", "-mlzcnt"
+  # See https://gcc.gnu.org/onlinedocs/gcc/x86-Built-in-Functions.html
+  if (CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64|AMD64")
+    # -march=native selects the best option for AVX instructions
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -mtune=native -mf16c")
+  endif()
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
 endif()
 
@@ -176,6 +183,7 @@ message(STATUS "CMAKE_C_FLAGS_INIT=${CMAKE_C_FLAGS_INIT}")
 message(STATUS "CMAKE_C_FLAGS=${CMAKE_C_FLAGS}")
 message(STATUS "CMAKE_C_FLAGS_RELEASE=${CMAKE_C_FLAGS_RELEASE}")
 message(STATUS "CMAKE_C_COMPILER_VERSION=${CMAKE_C_COMPILER_VERSION}")
+message(STATUS "CMAKE_SYSTEM_PROCESSOR=${CMAKE_SYSTEM_PROCESSOR}")
 message(STATUS "CMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
 message(STATUS "CMAKE_CXX_FLAGS_INIT=${CMAKE_CXX_FLAGS_INIT}")
 message(STATUS "CMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}")

_doc/examples/plot_decision_tree_logreg.py

@@ -259,7 +259,7 @@ def draw_border(
     cmap = plt.cm.tab20
     Z = Z.reshape(xx.shape)
     if ax is None:
-        fig, ax = plt.subplots(1, 1, figsize=figsize or (4, 3))
+        _fig, ax = plt.subplots(1, 1, figsize=figsize or (4, 3))
     ax.pcolormesh(xx, yy, Z, cmap=cmap)
 
     # Plot also the training points

_doc/examples/plot_leave_neighbors.py

@@ -130,7 +130,7 @@ def draw_border(
     cmap = plt.cm.tab20
     Z = Z.reshape(xx.shape)
     if ax is None:
-        fig, ax = plt.subplots(1, 1, figsize=figsize or (4, 3))
+        _fig, ax = plt.subplots(1, 1, figsize=figsize or (4, 3))
     ax.pcolormesh(xx, yy, Z, cmap=cmap)
 
     # Plot also the training points

_doc/examples/plot_logistic_regression_clustering.py

@@ -84,7 +84,7 @@ def draw_border(
     cmap = plt.cm.tab20
     Z = Z.reshape(xx.shape)
     if ax is None:
-        fig, ax = plt.subplots(1, 1, figsize=figsize or (4, 3))
+        _fig, ax = plt.subplots(1, 1, figsize=figsize or (4, 3))
     ax.pcolormesh(xx, yy, Z, cmap=cmap)
 
     # Plot also the training points

_doc/examples/plot_piecewise_classification.py

@@ -43,7 +43,7 @@ def graph(X, Y, model):
     Z = Z.reshape(xx.shape)
 
     # Put the result into a color plot
-    fig, ax = plt.subplots(1, 1, figsize=(4, 3))
+    _fig, ax = plt.subplots(1, 1, figsize=(4, 3))
     ax.pcolormesh(xx, yy, Z, cmap=plt.cm.Paired)
 
     # Plot also the training points

_doc/examples/plot_predictable_tsne.py

@@ -60,7 +60,7 @@ def plot_embedding(Xp, y, imgs, title=None, figsize=(12, 4)):
     x_min, x_max = numpy.min(Xp, 0), numpy.max(Xp, 0)
     X = (Xp - x_min) / (x_max - x_min)
 
-    fig, ax = plt.subplots(1, 2, figsize=figsize)
+    _fig, ax = plt.subplots(1, 2, figsize=figsize)
     for i in range(X.shape[0]):
         ax[0].text(
             X[i, 0],

_doc/index.rst

@@ -98,5 +98,5 @@ Source are available at `sdpython/mlinsights <https://github.com/sdpython/mlinsi
 Older versions
 ++++++++++++++
 
-* `0.5.2 <../v0.5.1/index.html>`_
-* `0.5.1 <../v0.5.1/index.html>`_
+* `0.5.3 <../v0.5.3/index.html>`_
+* `0.5.2 <../v0.5.2/index.html>`_

_unittests/ut_mlmodel/test_piecewise_decision_tree_experiment_fast.py

@@ -102,15 +102,15 @@ def test_criterions(self):
             assert_criterion_equal(c1, c2)
             left1, right1 = _test_criterion_node_impurity_children(c1)
             left2, right2 = _test_criterion_node_impurity_children(c2)
-            self.assertAlmostEqual(left1, left2)
-            self.assertAlmostEqual(right1, right2)
+            self.assertAlmostEqual(left1, left2, atol=1e-8)
+            self.assertAlmostEqual(right1, right2, atol=1e-8)
             v1 = _test_criterion_node_value(c1)
             v2 = _test_criterion_node_value(c2)
             self.assertEqual(v1, v2)
             assert_criterion_equal(c1, c2)
             p1 = _test_criterion_impurity_improvement(c1, 0.0, left1, right1)
             p2 = _test_criterion_impurity_improvement(c2, 0.0, left2, right2)
-            self.assertAlmostEqual(p1, p2)
+            self.assertAlmostEqual(p1, p2, atol=1e-8)
 
         X = numpy.array([[1.0, 2.0, 10.0, 11.0]]).T
         y = numpy.array([0.9, 1.1, 1.9, 2.1])
@@ -123,7 +123,7 @@ def test_criterions(self):
         _test_criterion_init(c2, ys, w, 1.0, ind, 1, y.shape[0])
         i1 = _test_criterion_node_impurity(c1)
         i2 = _test_criterion_node_impurity(c2)
-        self.assertAlmostEqual(i1, i2)
+        self.assertAlmostEqual(i1, i2, atol=1e-8)
         v1 = _test_criterion_node_value(c1)
         v2 = _test_criterion_node_value(c2)
         self.assertEqual(v1, v2)
@@ -136,14 +136,14 @@ def test_criterions(self):
             _test_criterion_update(c2, i)
             left1, right1 = _test_criterion_node_impurity_children(c1)
             left2, right2 = _test_criterion_node_impurity_children(c2)
-            self.assertAlmostEqual(left1, left2)
-            self.assertAlmostEqual(right1, right2)
+            self.assertAlmostEqual(left1, left2, atol=1e-8)
+            self.assertAlmostEqual(right1, right2, atol=1e-8)
             v1 = _test_criterion_node_value(c1)
             v2 = _test_criterion_node_value(c2)
             self.assertEqual(v1, v2)
             p1 = _test_criterion_impurity_improvement(c1, 0.0, left1, right1)
             p2 = _test_criterion_impurity_improvement(c2, 0.0, left2, right2)
-            self.assertAlmostEqual(p1, p2)
+            self.assertAlmostEqual(p1, p2, atol=1e-8)
 
     @unittest.skipIf(
         pv.Version(skl_ver) < pv.Version("1.3.3"),

_unittests/ut_xrun_doc/test_documentation_examples.py

@@ -41,7 +41,7 @@ def run_test(self, fold: str, name: str, verbose=0) -> int:
             cmds = [sys.executable, "-u", os.path.join(fold, name)]
             p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
             res = p.communicate()
-            out, err = res
+            _out, err = res
             st = err.decode("ascii", errors="ignore")
             if st and "Traceback" in st:
                 if "No module named 'onnxruntime'" in st:

azure-pipelines.yml

@@ -155,7 +155,7 @@ jobs:
   strategy:
     matrix:
       Python311-Linux:
-        python.version: '3.11'
+        python.version: '3.12'
     maxParallel: 3
 
   steps:

mlinsights/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.5.2"
+__version__ = "0.5.3"
 __author__ = "Xavier Dupré"
 __github__ = "https://github.com/sdpython/mlinsights"
 __url__ = "https://sdpython.github.io/doc/dev/mlinsights/"

pyproject.toml

@@ -26,7 +26,7 @@ license = {file = "LICENSE.txt"}
 name = "mlinsights"
 readme = "README.rst"
 requires-python = ">=3.10"
-version = "0.5.2"
+version = "0.5.3"
 
 [project.urls]
 homepage = "https://sdpython.github.io/doc/mlinsights/dev/"
@@ -52,7 +52,7 @@ dev = [
     "onnxruntime",
     "pandas",
     "psutil",
-    "pybind11>=2.12.0",
+    "pybind11>=3",
     "pytest",
     "pytest-cov",
     "ruff",
@@ -73,7 +73,7 @@ requires = [
     "Cython>=3.0.10",
     "cmake",
     "numpy>=2.0",
-    "pybind11>=2.12.0",
+    "pybind11>=3",
     "scikit-learn>=1.3.0",
     "scipy",
     "setuptools",
@@ -104,36 +104,35 @@ namespaces = false
 
 [tool.cibuildwheel]
 build = "*"
-manylinux-x86_64-image = "manylinux2014"
+manylinux-x86_64-image = "manylinux_2_28"  # "manylinux2014"
 
 [tool.cibuildwheel.linux]
 archs = ["x86_64"]
 build = "cp*"
-skip = "cp36-* cp37-* cp38-* cp39-* cp310-* cp314-* cp315-* pypy* *musllinux*"
-manylinux-x86_64-image = "manylinux2014"
+skip = "cp36-* cp37-* cp38-* cp39-* cp314-* cp314t-* cp315-* pypy* *musllinux*"
+manylinux-x86_64-image = "manylinux_2_28"  # "manylinux2014"
 before-build = "pip install auditwheel-symbols abi3audit"
 build-verbosity = 1
-repair-wheel-command = "auditwheel-symbols --manylinux 2014 {wheel} ; abi3audit {wheel} ; auditwheel repair -w {dest_dir} {wheel} || exit 0"
-# repair-wheel-command = "auditwheel-symbols --manylinux 2014 {wheel} || exit 0"
+repair-wheel-command = "auditwheel-symbols --manylinux 2_28 {wheel} ; abi3audit {wheel} ; auditwheel repair -w {dest_dir} {wheel} || exit 0"
 
 [tool.cibuildwheel.macos]
 archs = "arm64"  # or "universal2" for a single universal wheel
 environment = """
-    MACOSX_DEPLOYMENT_TARGET=14.0
+    MACOSX_DEPLOYMENT_TARGET=15.0
     LDFLAGS='-L$(brew --prefix libomp)/lib'
     CPPFLAGS='-I$(brew --prefix libomp)/include'
     CFLAGS='-I$(brew --prefix libomp)/include -arch x86_64 -arch arm64'
     CXXFLAGS='-I$(brew --prefix libomp)/include -arch x86_64 -arch arm64'
     DYLD_LIBRARY_PATH='$(brew --prefix libomp)/lib:$DYLD_LIBRARY_PATH'
 """
 build = "cp*"
-skip = "cp36-* cp37-* cp38-* cp39-* cp310-* cp314-* cp315-* pypy* pp*"
+skip = "cp36-* cp37-* cp38-* cp39-* cp314-* cp314t-* cp315-* pypy* pp*"
 before-build = "brew install libomp llvm&&echo 'export PATH=\"/opt/homebrew/opt/llvm/bin:$PATH\"' >> /Users/runner/.bash_profile"
 
 [tool.cibuildwheel.windows]
 archs = ["AMD64"]
 build = "cp*"
-skip = "cp36-* cp37-* cp38-* cp39-* cp310-* cp314-* cp315-* pypy*"
+skip = "cp36-* cp37-* cp38-* cp39-* cp314-* cp314t-* cp315-* pypy*"
 
 [tool.cython-lint]
 max-line-length = 88

requirements-dev.txt

@@ -1,10 +1,10 @@
+--extra-index-url https://download.pytorch.org/whl/cpu
 black
 category_encoders
 chardet
 clang-format
 cmakelang
 coverage
-cython>=3.0.10
 cython-lint
 furo; sys_platform == 'linux'
 ijson
@@ -17,7 +17,6 @@ numba
 numpy>=2.0
 onnxruntime
 pandas_streaming
-pybind11>=2.12.0
 pytest
 pytest-cov
 pytest-subtests
@@ -26,13 +25,13 @@ ruff
 scikit-learn>=1.5.0
 seaborn
 skl2onnx>=1.14.1
-sphinx<7.2; sys_platform == 'linux'  # furo still fails with sphinx==7.2.0 (issue unused furo.css)
+sphinx>=8; sys_platform == 'linux'  # furo still fails with sphinx==7.2.0 (issue unused furo.css)
 sphinx-gallery; sys_platform == 'linux'
 sphinx-issues; sys_platform == 'linux'
-git+https://github.com/sdpython/sphinx-runpython.git
+sphinx-runpython
 toml; python_version < '3.11'
 tomli
-torch
+torch>=2.9.0; sys_platform != 'darwin'
 torchvision
 torchaudio
 tqdm

requirements.txt

@@ -1,4 +1,4 @@
 cython>=3.0.10
 numpy
-pybind11>=2.12.0
+pybind11>=3
 scikit-learn>=1.3.0

setup.py

@@ -670,7 +670,7 @@ def get_package_data():
 
 setup(
     name="mlinsights",
-    version=get_version_str(here, "0.5.2"),
+    version=get_version_str(here, "0.5.3"),
     description=get_description(),
     long_description=get_long_description(here),
     author="Xavier Dupré",
@@ -693,9 +693,10 @@ def get_package_data():
         "Operating System :: Unix",
         "Operating System :: MacOS",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
     ],
     cmdclass={
         "build_ext": cmake_build_ext,