chore: add nanobind to build system

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
@@ -21,31 +21,31 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.3.1
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 9.0.0a3
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
@@ -58,8 +58,8 @@ repos:
         additional_dependencies:
           - "prettier@^3.2.4"
   # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.8
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]

news/cpp-version-update.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* updated cpp minimum version to c++23.
+* replaced boost smart pointer usages with stl implementations.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/precommit-deps-update.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: updating pre-commit hooks, black, flake8, isort, nbstripout, codespell and docformatter. Not user facing.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

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/__init__.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Blank namespace package for module diffpy."""
 
-
 from pkgutil import extend_path
 
 __path__ = extend_path(__path__, __name__)

src/diffpy/srreal/_cleanup.py

@@ -24,7 +24,6 @@ class prototypes is implemented in libdiffpy.  Any Python-extended classes
 a call of _registerThisType.
 """
 
-
 import atexit
 import weakref
 

src/diffpy/srreal/_final_imports.py

@@ -15,14 +15,16 @@
 """Finalize tweak of classes from the extension module srreal_ext.
 
 This private module handles loading of Python-level tweaks of the
-extension-defined classes.  Any client that imports this module
-must call the `import_now` function.  If this module is not loaded
-by the time of srreal_ext initialization, `import_now` is executed
-from srreal_ext.
+extension-defined classes.  Any client that imports this module must
+call the `import_now` function.  If this module is not loaded by the
+time of srreal_ext initialization, `import_now` is executed from
+srreal_ext.
 
 This avoids unresolvable import dependencies for any order of imports.
 """
 
+_import_now_called = False
+
 
 def import_now():
     """Import all Python modules that tweak extension-defined
@@ -46,6 +48,3 @@ def import_now():
     import_module("diffpy.srreal.pdfcalculator")
     import_module("diffpy.srreal.structureconverters")
     return
-
-
-_import_now_called = False

src/diffpy/srreal/atomradiitable.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Class AtomRadiiTable -- storage of empirical atom radii."""
 
-
 # exported items, these also makes them show in pydoc.
 __all__ = ["AtomRadiiTable", "ConstantRadiiTable", "CovalentRadiiTable"]
 
@@ -66,8 +65,9 @@ def clone(self):
         return copy.copy(self)
 
     def type(self):
-        """Unique string identifier of the CovalentRadiiTable type. This
-        is used for class registration and as an argument for the
+        """Unique string identifier of the CovalentRadiiTable type.
+
+        This is used for class registration and as an argument for the
         createByType function.
 
         Return string.

src/diffpy/srreal/attributes.py

@@ -13,7 +13,7 @@
 #
 ##############################################################################
 """class Attributes  -- wrapper to C++ class diffpy::Attributes
-    A base to PairQuantity and quite a few other classes.
+A base to PairQuantity and quite a few other classes.
 """
 
 __all__ = ["Attributes"]

src/diffpy/srreal/bondcalculator.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Class BondCalculator -- distances between atoms in the structure."""
 
-
 # exported items, these also makes them show in pydoc.
 __all__ = ["BondCalculator"]
 
@@ -28,14 +27,12 @@
 
 BondCalculator.rmin = propertyFromExtDoubleAttr(
     "rmin",
-    """Lower bound for the bond distances.
-        [0 A]""",
+    "Lower bound for the bond distances. [0 A]",
 )
 
 BondCalculator.rmax = propertyFromExtDoubleAttr(
     "rmax",
-    """Upper bound for the bond distances.
-        [5 A]""",
+    "Upper bound for the bond distances. [5 A]",
 )
 
 

src/diffpy/srreal/bvparameterstable.py

@@ -15,7 +15,6 @@
 """Class BVParametersTable -- storage of bond valence parameters class BVParam
 -- bond valence data associated with specific cation-anion pair."""
 
-
 # exported items, these also makes them show in pydoc.
 __all__ = ["BVParam", "BVParametersTable"]
 

src/diffpy/srreal/bvscalculator.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Class BVSCalculator -- bond valence sums calculator."""
 
-
 # exported items
 __all__ = ["BVSCalculator"]
 
@@ -28,30 +27,32 @@
 
 BVSCalculator.valenceprecision = propertyFromExtDoubleAttr(
     "valenceprecision",
-    """Cutoff value for valence contributions at long distances.
-        [1e-5]""",
+    "Cutoff value for valence contributions at long distances. [1e-5]",
 )
 
 BVSCalculator.rmaxused = propertyFromExtDoubleAttr(
     "rmaxused",
-    """Effective bound for bond lengths, where valence contributions
-        become smaller than valenceprecission, read-only.  Always smaller or
-        equal to rmax.  The value depends on ions present in the structure.
-        """,
+    (
+        "Effective bound for bond lengths, where valence contributions"
+        " become smaller than valenceprecission, read-only."
+        "  Always smaller or equal to rmax."
+        "  The value depends on ions present in the structure."
+    ),
 )
 
 BVSCalculator.rmin = propertyFromExtDoubleAttr(
     "rmin",
-    """Lower bound for the summed bond lengths.
-        [0 A]""",
+    "Lower bound for the summed bond lengths. [0 A]",
 )
 
 BVSCalculator.rmax = propertyFromExtDoubleAttr(
     "rmax",
-    """Upper bound for the summed bond lengths.  The calculation is
-        actually cut off much earlier when valence contributions get below
-        valenceprecission.  See also rmaxused and valenceprecission.
-        [1e6 A]""",
+    (
+        "Upper bound for the summed bond lengths."
+        "  The calculation is actually cut off much earlier when"
+        " valence contributions get below valenceprecission."
+        "  See also rmaxused and valenceprecission. [1e6 A]"
+    ),
 )
 
 

src/diffpy/srreal/eventticker.py

@@ -15,7 +15,6 @@
 """Class EventTicker -- storage of modification times of dependent
 objects."""
 
-
 # exported items
 __all__ = ["EventTicker"]