Merge pull request #102 from bobleesj/numpy

Numpy >=2.0 support with depreciation warning removed

Author: sbillinge

news/numpy2.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* support for numpy >=2.0
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* element/label itemsize to 5 in _linkAtomAttribute to support numpy >=2.0
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=62.0", "setuptools-git-versioning<2"]
+requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"]
 build-backend = "setuptools.build_meta"
 
 [project]

requirements/run.txt

@@ -1,2 +1,2 @@
-numpy < 2.0.0  # Need to fix deprecations before 2.0.0 compat
+numpy
 pycifrw

src/diffpy/structure/atom.py

@@ -536,7 +536,7 @@ def __setitem__(self, idx, value):
         self._atom.xyz[:] = self._atom.lattice.fractional(self)
         return
 
-    def __array_wrap__(self, out_arr, context=None):
+    def __array_wrap__(self, out_arr, context=None, return_scalar=None):
         """Ensure math operations on this type yield standard numpy array."""
         return out_arr.view(numpy.ndarray)
 

src/diffpy/structure/structure.py

@@ -711,8 +711,9 @@ def _get_composition(self):
     element = _linkAtomAttribute(
         "element",
         """Character array of `Atom` types. Assignment updates
-        the element attribute of the respective `Atoms`.""",
-        toarray=numpy.char.array,
+        the element attribute of the respective `Atoms`.
+        Set the maximum length of the element string to 5 characters.""",
+        toarray=lambda items: numpy.char.array(items, itemsize=5),
     )
 
     xyz = _linkAtomAttribute(
@@ -742,8 +743,9 @@ def _get_composition(self):
     label = _linkAtomAttribute(
         "label",
         """Character array of `Atom` names. Assignment updates
-        the label attribute of all `Atoms`.""",
-        toarray=numpy.char.array,
+        the label attribute of all `Atoms`.
+        Set the maximum length of the label string to 5 characters.""",
+        toarray=lambda items: numpy.char.array(items, itemsize=5),
     )
 
     occupancy = _linkAtomAttribute(