refactor: migrate Boost.Python syntax to nanobind

pyproject.toml

@@ -1,5 +1,10 @@
 [build-system]
-requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0", "numpy"]
+requires = [
+    "setuptools>=62.0",
+    "setuptools-git-versioning>=2.0",
+    "numpy",
+    "nanobind",
+]
 build-backend = "setuptools.build_meta"
 
 [project]

requirements/conda.txt

@@ -4,3 +4,4 @@ libobjcryst
 pyobjcryst
 diffpy.structure
 periodictable
+nanobind

setup.py

@@ -14,6 +14,23 @@
 
 import numpy
 from setuptools import Extension, setup
+from setuptools.command.build_ext import build_ext
+
+
+def get_nanobind_config():
+    import nanobind
+
+    package_dir = Path(nanobind.__file__).parent
+    return {
+        "include_dirs": [
+            nanobind.include_dir(),
+            str(package_dir / "ext" / "robin_map" / "include"),
+        ],
+        "source": str(Path(nanobind.source_dir()) / "nb_combined.cpp"),
+    }
+
+
+nanobind_macros = [("NB_COMPACT_ASSERTIONS", None)]
 
 
 def get_boost_libraries():
@@ -90,11 +107,13 @@ def get_objcryst_libraries():
 
 
 if os.name == "nt":
-    compile_args = ["/std:c++14"]
+    compile_args = ["/std:c++23"]
+    nanobind_compile_args = ["/std:c++23"]
     macros = [("_USE_MATH_DEFINES", None)]
     extra_link_args = ["/FORCE:MULTIPLE"]
 else:
-    compile_args = ["-std=c++11"]
+    compile_args = ["-std=c++23"]
+    nanobind_compile_args = ["-std=c++23", "-fno-strict-aliasing"]
     macros = []
     extra_link_args = []
 
@@ -112,13 +131,44 @@ def get_objcryst_libraries():
 }
 
 
+class build_ext_with_nanobind(build_ext):
+    def build_extension(self, ext):
+        nanobind_source = getattr(ext, "nanobind_source", None)
+        if not nanobind_source:
+            super().build_extension(ext)
+            return
+
+        original_extra_objects = list(ext.extra_objects or [])
+        try:
+            nanobind_objects = self.compiler.compile(
+                [nanobind_source],
+                output_dir=self.build_temp,
+                macros=(ext.define_macros or []) + nanobind_macros,
+                include_dirs=ext.include_dirs,
+                debug=self.debug,
+                extra_postargs=nanobind_compile_args,
+                depends=ext.depends,
+            )
+            ext.extra_objects = original_extra_objects + nanobind_objects
+            super().build_extension(ext)
+        finally:
+            ext.extra_objects = original_extra_objects
+
+
 def create_extensions():
     "Initialize Extension objects for the setup function."
+    nanobind_cfg = get_nanobind_config()
     ext = Extension(
         "diffpy.srreal.srreal_ext",
         glob.glob("src/extensions/*.cpp"),
-        **ext_kws,
+        **{
+            **ext_kws,
+            "include_dirs": (
+                ext_kws["include_dirs"] + nanobind_cfg["include_dirs"]
+            ),
+        },
     )
+    ext.nanobind_source = nanobind_cfg["source"]
     return [ext]
 
 
@@ -130,4 +180,7 @@ def ext_modules():
 
 
 if __name__ == "__main__":
-    setup(ext_modules=ext_modules())
+    setup(
+        cmdclass={"build_ext": build_ext_with_nanobind},
+        ext_modules=ext_modules(),
+    )

src/diffpy/srreal/bondcalculator.py

@@ -18,12 +18,46 @@
 # exported items, these also makes them show in pydoc.
 __all__ = ["BondCalculator"]
 
-from diffpy.srreal.srreal_ext import BondCalculator
+from diffpy.srreal.srreal_ext import BondCalculator as _BondCalculator
 from diffpy.srreal.wraputils import (
     propertyFromExtDoubleAttr,
     setattrFromKeywordArguments,
 )
 
+
+class BondCalculator(_BondCalculator):
+    __doc__ = _BondCalculator.__doc__
+
+    def __init__(self, **kwargs):
+        """Create a new instance of BondCalculator. Keyword arguments can be
+        used to configure calculator properties, for example:
+
+        bdc = BondCalculator(rmin=1.5, rmax=2.5)
+
+        Raise ValueError for invalid keyword argument.
+        """
+        super().__init__()
+        setattrFromKeywordArguments(self, **kwargs)
+        return
+
+    def __call__(self, structure=None, **kwargs):
+        """Return sorted bond distances in the specified structure.
+
+        Attributes
+        ----------
+        structure
+            structure to be evaluated, an instance of diffpy Structure
+            or pyobjcryst Crystal.  Reuse the last structure when None.
+        kwargs
+            optional parameter settings for this calculator
+
+        Return a sorted numpy array.
+        """
+        setattrFromKeywordArguments(self, **kwargs)
+        self.eval(structure)
+        return self.distances
+
+
 # property wrappers to C++ double attributes
 
 BondCalculator.rmin = propertyFromExtDoubleAttr(
@@ -39,42 +73,4 @@
 )
 
 
-# method overrides that support keyword arguments
-
-
-def _init_kwargs(self, **kwargs):
-    """Create a new instance of BondCalculator. Keyword arguments can be
-    used to configure calculator properties, for example:
-
-    bdc = BondCalculator(rmin=1.5, rmax=2.5)
-
-    Raise ValueError for invalid keyword argument.
-    """
-    BondCalculator.__boostpython__init(self)
-    setattrFromKeywordArguments(self, **kwargs)
-    return
-
-
-def _call_kwargs(self, structure=None, **kwargs):
-    """Return sorted bond distances in the specified structure.
-
-    Attributes
-    ----------
-    structure
-        structure to be evaluated, an instance of diffpy Structure
-        or pyobjcryst Crystal.  Reuse the last structure when None.
-    kwargs
-        optional parameter settings for this calculator
-
-    Return a sorted numpy array.
-    """
-    setattrFromKeywordArguments(self, **kwargs)
-    self.eval(structure)
-    return self.distances
-
-
-BondCalculator.__boostpython__init = BondCalculator.__init__
-BondCalculator.__init__ = _init_kwargs
-BondCalculator.__call__ = _call_kwargs
-
 # End of file

src/diffpy/srreal/bvscalculator.py

@@ -18,12 +18,48 @@
 # exported items
 __all__ = ["BVSCalculator"]
 
-from diffpy.srreal.srreal_ext import BVSCalculator
+from diffpy.srreal.srreal_ext import BVSCalculator as _BVSCalculator
 from diffpy.srreal.wraputils import (
     propertyFromExtDoubleAttr,
     setattrFromKeywordArguments,
 )
 
+
+class BVSCalculator(_BVSCalculator):
+    __doc__ = _BVSCalculator.__doc__
+
+    def __init__(self, **kwargs):
+        """Create a new instance of BVSCalculator.
+        Keyword arguments can be used to configure the calculator properties,
+        for example:
+
+        bvscalc = BVSCalculator(valenceprecision=0.001)
+
+        Raise ValueError for invalid keyword argument.
+        """
+        super().__init__()
+        setattrFromKeywordArguments(self, **kwargs)
+        return
+
+    def __call__(self, structure=None, **kwargs):
+        """Return bond valence sums at each atom site in the structure.
+
+        Attributes
+        ----------
+        structure
+            structure to be evaluated, an instance of diffpy Structure
+            or pyobjcryst Crystal.  Reuse the last structure when None.
+        kwargs
+            optional parameter settings for this calculator
+
+        Return an array of calculated valence sums.
+        See valences for the expected values.
+        """
+        setattrFromKeywordArguments(self, **kwargs)
+        rv = self.eval(structure)
+        return rv
+
+
 # Property wrappers to C++ double attributes
 
 BVSCalculator.valenceprecision = propertyFromExtDoubleAttr(
@@ -55,44 +91,4 @@
 )
 
 
-# method overrides that support keyword arguments
-
-
-def _init_kwargs(self, **kwargs):
-    """Create a new instance of BVSCalculator.
-    Keyword arguments can be used to configure the calculator properties,
-    for example:
-
-    bvscalc = BVSCalculator(valenceprecision=0.001)
-
-    Raise ValueError for invalid keyword argument.
-    """
-    BVSCalculator.__boostpython__init(self)
-    setattrFromKeywordArguments(self, **kwargs)
-    return
-
-
-def _call_kwargs(self, structure=None, **kwargs):
-    """Return bond valence sums at each atom site in the structure.
-
-    Attributes
-    ----------
-    structure
-        structure to be evaluated, an instance of diffpy Structure
-        or pyobjcryst Crystal.  Reuse the last structure when None.
-    kwargs
-        optional parameter settings for this calculator
-
-    Return an array of calculated valence sums.
-    See valences for the expected values.
-    """
-    setattrFromKeywordArguments(self, **kwargs)
-    rv = self.eval(structure)
-    return rv
-
-
-BVSCalculator.__boostpython__init = BVSCalculator.__init__
-BVSCalculator.__init__ = _init_kwargs
-BVSCalculator.__call__ = _call_kwargs
-
 # End of file

src/diffpy/srreal/overlapcalculator.py

@@ -19,12 +19,46 @@
 # exported items, these also makes them show in pydoc.
 __all__ = ["OverlapCalculator"]
 
-from diffpy.srreal.srreal_ext import OverlapCalculator
+from diffpy.srreal.srreal_ext import OverlapCalculator as _OverlapCalculator
 from diffpy.srreal.wraputils import (
     propertyFromExtDoubleAttr,
     setattrFromKeywordArguments,
 )
 
+
+class OverlapCalculator(_OverlapCalculator):
+    __doc__ = _OverlapCalculator.__doc__
+
+    def __init__(self, **kwargs):
+        """Create a new instance of OverlapCalculator. Keyword arguments can
+        be used to configure calculator properties, for example:
+
+        olc = OverlapCalculator(rmax=2.5)
+
+        Raise ValueError for invalid keyword argument.
+        """
+        super().__init__()
+        setattrFromKeywordArguments(self, **kwargs)
+        return
+
+    def __call__(self, structure=None, **kwargs):
+        """Return siteSquareOverlaps per each site of the structure.
+
+        Attributes
+        ----------
+        structure
+            structure to be evaluated, an instance of diffpy Structure
+            or pyobjcryst Crystal.  Reuse the last structure when None.
+        kwargs
+            optional parameter settings for this calculator
+
+        Return a numpy array.
+        """
+        setattrFromKeywordArguments(self, **kwargs)
+        self.eval(structure)
+        return self.sitesquareoverlaps
+
+
 # property wrappers to C++ double attributes
 
 OverlapCalculator.rmin = propertyFromExtDoubleAttr(
@@ -47,42 +81,4 @@
         """,
 )
 
-# method overrides that support keyword arguments
-
-
-def _init_kwargs(self, **kwargs):
-    """Create a new instance of OverlapCalculator. Keyword arguments can
-    be used to configure calculator properties, for example:
-
-    olc = OverlapCalculator(rmax=2.5)
-
-    Raise ValueError for invalid keyword argument.
-    """
-    OverlapCalculator.__boostpython__init(self)
-    setattrFromKeywordArguments(self, **kwargs)
-    return
-
-
-def _call_kwargs(self, structure=None, **kwargs):
-    """Return siteSquareOverlaps per each site of the structure.
-
-    Attributes
-    ----------
-    structure
-        structure to be evaluated, an instance of diffpy Structure
-        or pyobjcryst Crystal.  Reuse the last structure when None.
-    kwargs
-        optional parameter settings for this calculator
-
-    Return a numpy array.
-    """
-    setattrFromKeywordArguments(self, **kwargs)
-    self.eval(structure)
-    return self.sitesquareoverlaps
-
-
-OverlapCalculator.__boostpython__init = OverlapCalculator.__init__
-OverlapCalculator.__init__ = _init_kwargs
-OverlapCalculator.__call__ = _call_kwargs
-
 # End of file