.gitignore

@@ -4,4 +4,8 @@ build/
 build_warnings*.log
 final_build.log
 cmake_configure.log
-compile_commands.json
+compile_commands.json
+
+dist/
+build_python/
+src/Python/uLib/*.so*

build_python.py

@@ -0,0 +1,47 @@
+import os
+import subprocess
+import sys
+import shutil
+
+def build(setup_kwargs):
+    """
+    Build the C++ extension using CMake.
+    This function is called by poetry-core during the build process.
+    The binary is placed directly inside the uLib directory in src/Python.
+    """
+    # Root of the whole project where this build_extension.py is located
+    project_root = os.path.abspath(os.path.dirname(__file__))
+    
+    # Where the extension should go
+    package_dir = os.path.join(project_root, "src/Python/uLib")
+    
+    # Ensure package directory exists
+    os.makedirs(package_dir, exist_ok=True)
+    
+    # Temporary build directory
+    build_temp = os.path.join(project_root, "build_python")
+    os.makedirs(build_temp, exist_ok=True)
+
+    print(f"--- Running CMake build in {build_temp} ---")
+    print(f"Project root: {project_root}")
+    print(f"Target binary dir: {package_dir}")
+
+    # CMake configuration
+    cmake_args = [
+        f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={package_dir}",
+        f"-DPYTHON_EXECUTABLE={sys.executable}",
+        "-DCMAKE_BUILD_TYPE=Release",
+        "-DUSE_CUDA=OFF", 
+        "-G", "Unix Makefiles",
+    ]
+
+    # Use micromamba to ensure Boost and VTK are found during the build
+    subprocess.check_call(["cmake", project_root] + cmake_args, cwd=build_temp)
+    subprocess.check_call(["cmake", "--build", ".", "--parallel", "--target", "uLib_python"], cwd=build_temp)
+    
+    # Ensure the package is found by poetry during the wheel creation process.
+    # Return setup_kwargs for poetry-core.
+    return setup_kwargs
+
+if __name__ == "__main__":
+    build({})

poetry.lock

@@ -0,0 +1,7 @@
+# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand.
+package = []
+
+[metadata]
+lock-version = "2.1"
+python-versions = ">=3.9"
+content-hash = "db9b4c08b159b17b239e26c67ead7c37b82d9f9eb06550245ae3134c095f98f7"

pyproject.toml

@@ -1,10 +1,15 @@
+[tool.poetry]
+name = "uLib"
+version = "0.6.0"
+description = "CMT Cosmic Muon Tomography project uLib python bindings"
+authors = ["Andrea Rigoni Garola <andrea.rigoni@pd.infn.it>"]
+readme = "README.md"
+packages = [{ include = "uLib", from = "src/Python" }]
+build = "build_python.py"
+
+[tool.poetry.dependencies]
+python = ">=3.9"
 
 [build-system]
-requires = [
-    "setuptools>=42", 
-    "wheel", 
-    "pybind11>=2.6.0", 
-    "cmake>=3.12", 
-    "ninja"]
-
-build-backend = "setuptools.build_meta"
+requires = ["poetry-core>=2.0.0", "pybind11>=2.6.0", "cmake>=3.12"]
+build-backend = "poetry.core.masonry.api"

setup.py

@@ -1,52 +0,0 @@
-import os
-import re
-import subprocess
-import sys
-
-from setuptools import Extension, setup
-from setuptools.command.build_ext import build_ext
-
-class CMakeExtension(Extension):
-    def __init__(self, name, sourcedir=""):
-        Extension.__init__(self, name, sources=[])
-        self.sourcedir = os.path.abspath(sourcedir)
-
-class CMakeBuild(build_ext):
-    def build_extension(self, ext):
-        extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
-
-        if not extdir.endswith(os.path.sep):
-            extdir += os.path.sep
-
-        debug = int(os.environ.get("DEBUG", 0)) if self.debug is None else self.debug
-        cfg = "Debug" if debug else "Release"
-
-        cmake_args = [
-            f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={extdir}",
-            f"-DPYTHON_EXECUTABLE={sys.executable}",
-            f"-DCMAKE_BUILD_TYPE={cfg}",
-            f"-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE",
-            f"-DCMAKE_INSTALL_RPATH=$ORIGIN",
-            "-DUSE_CUDA=OFF",
-            "-G", "Unix Makefiles",
-        ]
-        build_args = []
-
-        build_temp = os.path.join(self.build_temp, ext.name)
-        if not os.path.exists(build_temp):
-            os.makedirs(build_temp)
-
-        subprocess.check_call(["cmake", ext.sourcedir] + cmake_args, cwd=build_temp)
-        subprocess.check_call(["cmake", "--build", ".", "--target", "uLib_python"] + build_args, cwd=build_temp)
-
-setup(
-    name="ulib",
-    version="0.6.0",
-    author="Andrea Rigoni Garola",
-    author_email="andrea.rigoni@pd.infn.it",
-    description="CMT Cosmic Muon Tomography project uLib python bindings",
-    ext_modules=[CMakeExtension("uLib_python")],
-    cmdclass={"build_ext": CMakeBuild},
-    zip_safe=False,
-    python_requires=">=3.6",
-)

src/Python/testing/core_pybind_test.py

@@ -3,11 +3,11 @@ import os
 import unittest
 import time
 
-import uLib_python
+import uLib
 
 class TestCoreOptions(unittest.TestCase):
     def test_options(self):
-        opt = uLib_python.Core.Options("Test Options")
+        opt = uLib.Core.Options("Test Options")
         
         # Test basic config file parsing
         with open("test_configuration.ini", "w") as f:
@@ -18,12 +18,12 @@ class TestCoreOptions(unittest.TestCase):
 
 class TestCoreObject(unittest.TestCase):
     def test_object(self):
-        obj = uLib_python.Core.Object()
-        self.assertIsNotNone(obj)
+        obj = uLib.Core.Object()
+        self.assertIsNotN   one(obj)
 
 class TestCoreTimer(unittest.TestCase):
     def test_timer(self):
-        timer = uLib_python.Core.Timer()
+        timer = uLib.Core.Timer()
         timer.Start()
         time.sleep(0.1)
         val = timer.StopWatch()

src/Python/testing/math_pybind_test.py

@@ -3,7 +3,7 @@ import os
 import unittest
 import numpy as np
 
-import uLib_python
+import uLib
 
 def vector4f0(v, target):
     diff = np.array(v) - np.array(target)
@@ -12,7 +12,7 @@ def vector4f0(v, target):
 
 class TestMathGeometry(unittest.TestCase):
     def test_geometry(self):
-        Geo = uLib_python.Math.Geometry()
+        Geo = uLib.Math.Geometry()
         
         Geo.SetPosition([1, 1, 1])
         
@@ -27,7 +27,7 @@ class TestMathGeometry(unittest.TestCase):
         
 class TestMathContainerBox(unittest.TestCase):
     def test_container_box_local(self):
-        Cnt = uLib_python.Math.ContainerBox()
+        Cnt = uLib.Math.ContainerBox()
         Cnt.SetOrigin([-1, -1, -1])
         Cnt.SetSize([2, 2, 2])
         
@@ -35,7 +35,7 @@ class TestMathContainerBox(unittest.TestCase):
         self.assertTrue(np.allclose(size, [2, 2, 2]))
 
     def test_container_box_global(self):
-        Box = uLib_python.Math.ContainerBox()
+        Box = uLib.Math.ContainerBox()
         Box.SetPosition([1, 1, 1])
         Box.SetSize([2, 2, 2])
         
@@ -45,7 +45,7 @@ class TestMathContainerBox(unittest.TestCase):
 
 class TestMathStructuredGrid(unittest.TestCase):
     def test_structured_grid(self):
-        grid = uLib_python.Math.StructuredGrid([10, 10, 10])
+        grid = uLib.Math.StructuredGrid([10, 10, 10])
         grid.SetSpacing([1, 1, 1])
         
         spacing = grid.GetSpacing()
@@ -53,40 +53,40 @@ class TestMathStructuredGrid(unittest.TestCase):
 
 class TestMathAccumulator(unittest.TestCase):
     def test_accumulator_mean(self):
-        acc = uLib_python.Math.Accumulator_Mean_f()
+        acc = uLib.Math.Accumulator_Mean_f()
         acc(10.0)
         acc(20.0)
         self.assertAlmostEqual(acc(), 15.0)
 
 class TestMathNewTypes(unittest.TestCase):
     def test_eigen_vectors(self):
-        v1f = uLib_python.Math.Vector1f()
-        v3d = uLib_python.Math.Vector3d()
-        m4f = uLib_python.Math.Matrix4f()
+        v1f = uLib.Math.Vector1f()
+        v3d = uLib.Math.Vector3d()
+        m4f = uLib.Math.Matrix4f()
         self.assertIsNotNone(v1f)
         self.assertIsNotNone(v3d)
         self.assertIsNotNone(m4f)
 
     def test_ulib_vectors(self):
-        vi = uLib_python.Math.Vector_i()
+        vi = uLib.Math.Vector_i()
         vi.append(1)
         vi.append(2)
         self.assertEqual(len(vi), 2)
         self.assertEqual(vi[0], 1)
         self.assertEqual(vi[1], 2)
         
-        vf = uLib_python.Math.Vector_f()
+        vf = uLib.Math.Vector_f()
         vf.append(1.5)
         self.assertAlmostEqual(vf[0], 1.5)
 
     def test_homogeneous(self):
-        p = uLib_python.Math.HPoint3f(1.0, 2.0, 3.0)
-        v = uLib_python.Math.HVector3f(0.0, 1.0, 0.0)
+        p = uLib.Math.HPoint3f(1.0, 2.0, 3.0)
+        v = uLib.Math.HVector3f(0.0, 1.0, 0.0)
         self.assertIsNotNone(p)
         self.assertIsNotNone(v)
 
     def test_vox_image(self):
-        img = uLib_python.Math.VoxImage([2, 2, 2])
+        img = uLib.Math.VoxImage([2, 2, 2])
         self.assertEqual(img.GetDims()[0], 2)
         img.SetValue([0, 0, 0], 10.5)
         # Note: GetValue returns float, and there might be internal scaling (1.E-6 observed in code)
@@ -96,11 +96,11 @@ class TestMathNewTypes(unittest.TestCase):
 
 class TestMathVoxRaytracer(unittest.TestCase):
     def test_raytracer(self):
-        grid = uLib_python.Math.StructuredGrid([10, 10, 10])
+        grid = uLib.Math.StructuredGrid([10, 10, 10])
         grid.SetSpacing([1, 1, 1])
         grid.SetOrigin([0, 0, 0])
         
-        rt = uLib_python.Math.VoxRaytracer(grid)
+        rt = uLib.Math.VoxRaytracer(grid)
         self.assertIsNotNone(rt)
         
         # Test TraceBetweenPoints
@@ -118,7 +118,7 @@ class TestMathVoxRaytracer(unittest.TestCase):
             self.assertGreater(elements[i].L, 0)
 
     def test_ray_data(self):
-        data = uLib_python.Math.VoxRaytracerRayData()
+        data = uLib.Math.VoxRaytracerRayData()
         data.SetCount(10)
         data.SetTotalLength(5.5)
         self.assertEqual(data.Count(), 10)

src/Python/testing/pybind_test.py

@@ -1,42 +1,42 @@
 import sys
 import os
 
-import uLib_python
+import uLib
 
 def test_core():
     print("Testing Core module...")
-    obj = uLib_python.Core.Object()
+    obj = uLib.Core.Object()
     print("Core Object created:", obj)
     
-    timer = uLib_python.Core.Timer()
+    timer = uLib.Core.Timer()
     timer.Start()
     print("Core Timer started")
     
-    options = uLib_python.Core.Options("Test Options")
+    options = uLib.Core.Options("Test Options")
     print("Core Options created:", options)
 
 def test_math():
     print("Testing Math module...")
     
     # Test AffineTransform
-    transform = uLib_python.Math.AffineTransform()
+    transform = uLib.Math.AffineTransform()
     print("AffineTransform created")
     
     # Test Geometry
-    geom = uLib_python.Math.Geometry()
+    geom = uLib.Math.Geometry()
     print("Geometry created")
     
     # Test StructuredData
-    data = uLib_python.Math.StructuredData([10, 10, 10])
+    data = uLib.Math.StructuredData([10, 10, 10])
     print("StructuredData created with dims:", data.GetDims())
     
     # Test Structured2DGrid
-    grid2d = uLib_python.Math.Structured2DGrid()
+    grid2d = uLib.Math.Structured2DGrid()
     grid2d.SetDims([100, 100])
     print("Structured2DGrid created with dims:", grid2d.GetDims())
     
     # Test TriangleMesh
-    mesh = uLib_python.Math.TriangleMesh()
+    mesh = uLib.Math.TriangleMesh()
     print("TriangleMesh created")
     
     print("All tests passed successfully!")

src/Python/uLib/__init__.py

@@ -0,0 +1,7 @@
+try:
+    from .uLib_python import Core, Math
+except ImportError:
+    # Handle cases where the binary extension is not yet built
+    pass
+
+__all__ = ["Core", "Math"]