enh: Modernize array handling with nanobind

CMakeLists.txt

@@ -11,7 +11,7 @@ if(DEFINED ENV{CONDA_PREFIX})
     list(APPEND CMAKE_PREFIX_PATH "$ENV{CONDA_PREFIX}" "$ENV{CONDA_PREFIX}/Library")
 endif()
 
-find_package(Python 3.12 REQUIRED COMPONENTS Interpreter Development.Module NumPy)
+find_package(Python 3.12 REQUIRED COMPONENTS Interpreter Development.Module)
 execute_process(
     COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
     OUTPUT_VARIABLE nanobind_DIR
@@ -52,10 +52,9 @@ target_compile_definitions(diffpy_core PRIVATE DIFFPYRUNTIMERELPATH=data)
 target_link_libraries(diffpy_core PUBLIC Boost::serialization GSL::gsl GSL::gslcblas ${CMAKE_DL_LIBS})
 
 file(GLOB SRREAL_SOURCES CONFIGURE_DEPENDS "src/extensions/*.cpp")
-# Keep the CPython-specific ABI while the bindings use the NumPy C API and
-# CPython macros. Do not label these wheels abi3 without porting those calls.
+# Retain CPython-specific wheels; stable-ABI packaging is a separate change.
 nanobind_add_module(srreal_ext NB_STATIC ${SRREAL_SOURCES})
-target_link_libraries(srreal_ext PRIVATE diffpy_core Python::NumPy)
+target_link_libraries(srreal_ext PRIVATE diffpy_core)
 set_target_properties(srreal_ext PROPERTIES INSTALL_RPATH_USE_LINK_PATH ON)
 install(TARGETS srreal_ext LIBRARY DESTINATION diffpy/srreal)
 install(DIRECTORY "${LIBDIFFPY_SOURCE_DIR}/src/runtime/"

news/nanobind-arrays.rst

@@ -0,0 +1,22 @@
+**Changed:**
+
+* Use typed nanobind arrays for numeric input, copied results, and writable
+  Atom views. Keep NumPy output types, shapes, native dtypes, and the existing
+  scalar-versus-array return conventions.
+* Remove the NumPy C API and build-time NumPy dependency. NumPy remains a
+  runtime dependency; wheel Python ABI requirements are unchanged.
+* Retain NumPy-owned writable storage for copied results and explicit storage
+  owners for Atom views, including slices retained after structural edits.
+* Preserve endpoint-specific conversion rules, NumPy scalar casting warnings,
+  and coordinate/matrix broadcasting. Invalid coordinate/matrix assignments
+  no longer partially modify an Atom.
+
+**Fixed:**
+
+* Read strided and reversed integer index arrays in logical order instead of
+  treating their storage as contiguous.
+* Interpret byte-swapped FFT inputs and integer index arrays in their actual
+  byte order, and safely handle unaligned buffers.
+* Reject integer-array indices outside the C++ ``int`` range with
+  ``OverflowError`` instead of silently wrapping. These three corrections
+  intentionally change erroneous behavior inherited from Boost.Python.

pyproject.toml

@@ -2,7 +2,6 @@
 requires = [
     "scikit-build-core>=0.10",
     "setuptools-scm>=8",
-    "numpy",
     "nanobind>=3.1,<4",
 ]
 build-backend = "scikit_build_core.build"

src/extensions/srreal_atom.hpp

@@ -135,16 +135,17 @@ struct AtomViewPin
     }
 };
 
-inline nb::object pin_atom_view(PythonAtom& atom, nb::object view)
+inline nb::object atom_view_owner(PythonAtom& atom)
 {
+    nb::object python_atom = nb::cast(&atom, nb::rv_policy::reference);
     if (atom.references())
     {
         nb::capsule owner(new AtomViewPin(atom.references()), [](void* p) noexcept {
             delete static_cast<AtomViewPin*>(p);
         });
-        setNumPyArrayBase(view, std::move(owner));
+        return nb::make_tuple(python_atom, owner);
     }
-    return view;
+    return python_atom;
 }
 
 inline void preserve_atom_views(const std::shared_ptr<AtomReferences>& refs)