Numpy 2.3 fix

benchmarks/benchmarks/generate_data/um_files.py

@@ -22,12 +22,22 @@ def _create_um_files(
     from tempfile import NamedTemporaryFile
 
     from mule import ArrayDataProvider, Field3, FieldsFile
+    import mule.ff
     from mule.pp import fields_to_pp_file
     import numpy as np
 
     from iris import load_cube
     from iris import save as save_cube
 
+    def to_bytes_patch(self, field):
+        data = field.get_data()
+        dtype = mule.ff._DATA_DTYPES[self.WORD_SIZE][field.lbuser1]
+        data = data.astype(dtype)
+        return data.tobytes(), data.size
+
+    # TODO: remove this patch when fixed in mule, see https://github.com/MetOffice/simulation-systems/discussions/389
+    mule.ff._WriteFFOperatorUnpacked.to_bytes = to_bytes_patch
+
     template = {
         "fixed_length_header": {"dataset_type": 3, "grid_staggering": 3},
         "integer_constants": {

docs/src/whatsnew/latest.rst

@@ -59,6 +59,9 @@ This document explains the changes made to Iris for this release
 #. `@schlunma`_ fixed loading of netCDF files with coordinates that have
    non-string units. (:issue:`6505`, :pull:`6506`)
 
+#. `@stephenworsley`_ fixed incompatibilities with numpy v2.3 affecting arrays of dates and
+   array printing. (:pull:`6518`)
+
 💣 Incompatible Changes
 =======================
 

lib/iris/common/mixin.py

@@ -203,7 +203,7 @@ def _round(date):
             warnings.warn(message, category=FutureWarning)
 
             if hasattr(result, "shape"):
-                vfunc = np.vectorize(_round)
+                vfunc = np.frompyfunc(_round, 1, 1)
                 result = vfunc(result)
             else:
                 result = _round(result)

lib/iris/common/resolve.py

@@ -2358,7 +2358,7 @@ def cube(self, data, in_place=False):
             >>> resolver.map_rhs_to_lhs
             True
             >>> cube1.data.sum()
-            np.float32(124652160.0)
+            np.float32(1.2465214e+08)
             >>> zeros.shape
             (240, 37, 49)
             >>> zeros.sum()

lib/iris/cube.py

@@ -162,18 +162,19 @@ def insert(self, index, cube):
 
     def xml(self, checksum=False, order=True, byteorder=True):
         """Return a string of the XML that this list of cubes represents."""
-        doc = Document()
-        cubes_xml_element = doc.createElement("cubes")
-        cubes_xml_element.setAttribute("xmlns", XML_NAMESPACE_URI)
-
-        for cube_obj in self:
-            cubes_xml_element.appendChild(
-                cube_obj._xml_element(
-                    doc, checksum=checksum, order=order, byteorder=byteorder
+        with np.printoptions(legacy="2.2"):
+            doc = Document()
+            cubes_xml_element = doc.createElement("cubes")
+            cubes_xml_element.setAttribute("xmlns", XML_NAMESPACE_URI)
+
+            for cube_obj in self:
+                cubes_xml_element.appendChild(
+                    cube_obj._xml_element(
+                        doc, checksum=checksum, order=order, byteorder=byteorder
+                    )
                 )
-            )
 
-        doc.appendChild(cubes_xml_element)
+            doc.appendChild(cubes_xml_element)
 
         # return our newly created XML string
         doc = Cube._sort_xml_attrs(doc)
@@ -3864,17 +3865,18 @@ def xml(
         byteorder: bool = True,
     ) -> str:
         """Return a fully valid CubeML string representation of the Cube."""
-        doc = Document()
+        with np.printoptions(legacy="2.2"):
+            doc = Document()
 
-        cube_xml_element = self._xml_element(
-            doc, checksum=checksum, order=order, byteorder=byteorder
-        )
-        cube_xml_element.setAttribute("xmlns", XML_NAMESPACE_URI)
-        doc.appendChild(cube_xml_element)
+            cube_xml_element = self._xml_element(
+                doc, checksum=checksum, order=order, byteorder=byteorder
+            )
+            cube_xml_element.setAttribute("xmlns", XML_NAMESPACE_URI)
+            doc.appendChild(cube_xml_element)
 
-        # Print our newly created XML
-        doc = self._sort_xml_attrs(doc)
-        return iris.util._print_xml(doc)
+            # Print our newly created XML
+            doc = self._sort_xml_attrs(doc)
+            return iris.util._print_xml(doc)
 
     def _xml_element(self, doc, checksum=False, order=True, byteorder=True):
         cube_xml_element = doc.createElement("cube")

lib/iris/tests/_shared_utils.py

@@ -451,6 +451,15 @@ def assert_text_file(source_filename, reference_filename, desc="text file"):
 
 def assert_data_almost_equal(data, reference_filename, **kwargs):
     reference_path = get_result_path(reference_filename)
+
+    def fixed_std(data):
+        # When data is constant, std() is too sensitive.
+        if data.max() == data.min():
+            data_std = 0
+        else:
+            data_std = data.std()
+        return data_std
+
     if _check_reference_file(reference_path):
         kwargs.setdefault("err_msg", "Reference file %s" % reference_path)
         with open(reference_path, "r") as reference_file:
@@ -470,15 +479,15 @@ def assert_data_almost_equal(data, reference_filename, **kwargs):
                 assert math.isnan(data.mean())
             else:
                 data_stats = np.array(
-                    (data.mean(), data.std(), data.max(), data.min()),
+                    (data.mean(), fixed_std(data), data.max(), data.min()),
                     dtype=np.float64,
                 )
                 assert_array_all_close(nstats, data_stats, **kwargs)
     else:
         _ensure_folder(reference_path)
         stats = collections.OrderedDict(
             [
-                ("std", np.float64(data.std())),
+                ("std", np.float64(fixed_std(data))),
                 ("min", np.float64(data.min())),
                 ("max", np.float64(data.max())),
                 ("shape", data.shape),

lib/iris/tests/results/analysis/calculus/handmade2_wrt_lon.data.0.json

@@ -1 +1 @@
-{"std": 9.5367431640625e-07, "min": 11.111110687255859, "max": 11.111110687255859, "shape": [49, 50], "masked": false, "mean": 11.111111640930176}
+{"std": 0.0, "min": 11.111110687255859, "max": 11.111110687255859, "shape": [49, 50], "masked": false, "mean": 11.111111640930176}

lib/iris/tests/results/analysis/hmean_latitude_longitude.data.0.json

@@ -1 +1 @@
-{"std": 1.9073486328125e-06, "min": 10288680426.032187, "max": 10288680426.032187, "shape": [10], "masked": false, "mean": 10288680426.032185}
+{"std": 0.0, "min": 10288680426.032187, "max": 10288680426.032187, "shape": [10], "masked": false, "mean": 10288680426.032185}

lib/iris/tests/results/analysis/variance_latitude_longitude.data.0.json

@@ -1 +1 @@
-{"std": 3.0517578125e-05, "min": 214667549910.37509, "max": 214667549910.37509, "shape": [10], "masked": false, "mean": 214667549910.37506}
+{"std": 0.0, "min": 214667549910.37509, "max": 214667549910.37509, "shape": [10], "masked": false, "mean": 214667549910.37506}

lib/iris/tests/test_pp_module.py

@@ -8,6 +8,7 @@
 from types import GeneratorType
 
 import cftime
+import numpy as np
 from numpy.testing import assert_array_equal
 import pytest
 
@@ -63,7 +64,8 @@ def check_pp(self, pp_fields, reference_filename):
         for pp_field in pp_fields:
             pp_field.data
 
-        test_string = str(pp_fields)
+        with np.printoptions(legacy="2.2"):
+            test_string = str(pp_fields)
         reference_path = _shared_utils.get_result_path(reference_filename)
         if os.path.isfile(reference_path):
             with open(reference_path, "r") as reference_fh: