Numpy2 compatibility fixes

allel/model/ndarray.py

@@ -35,6 +35,7 @@
            'SortedIndex', 'UniqueIndex', 'SortedMultiIndex', 'VariantTable', 'FeatureTable',
            'ChromPosIndex']
 
+from .. import util
 
 # noinspection PyTypeChecker
 _total_slice = slice(None)
@@ -73,7 +74,7 @@ class NumpyArrayWrapper(ArrayWrapper):
     """Abstract base class that wraps a NumPy array."""
 
     def __init__(self, data, copy=False, **kwargs):
-        values = np.array(data, copy=copy, **kwargs)
+        values = util.array(data, copy=copy, **kwargs)
         super(NumpyArrayWrapper, self).__init__(values)
 
 
@@ -1004,7 +1005,7 @@ def to_gt(self, max_allele=None):
         nchar = int(np.floor(np.log10(max_allele))) + 1
 
         # convert to string
-        a = self.astype((np.string_, nchar)).view(np.chararray)
+        a = self.astype((np.bytes_, nchar)).view(np.chararray)
 
         # recode missing alleles
         a[self < 0] = b'.'
@@ -4034,7 +4035,7 @@ class SortedMultiIndex(DisplayAs1D):
 
     def __init__(self, l1, l2, copy=False):
         l1 = SortedIndex(l1, copy=copy)
-        l2 = np.array(l2, copy=copy)
+        l2 = util.array(l2, copy=copy)
         check_ndim(l2, 1)
         check_dim0_aligned(l1, l2)
         self.l1 = l1

allel/test/model/test_api.py

@@ -12,6 +12,8 @@
 
 import numpy as np
 import pytest
+
+from allel import util
 from allel.test.tools import assert_array_equal as aeq
 
 
@@ -141,12 +143,12 @@ def test_array_like(self):
 
         # diploid data
         g = self.setup_instance(diploid_genotype_data)
-        a = np.array(g, copy=False)
+        a = util.array(g, copy=False)
         aeq(diploid_genotype_data, a)
 
         # polyploid data
         g = self.setup_instance(triploid_genotype_data)
-        a = np.array(g, copy=False)
+        a = util.array(g, copy=False)
         aeq(triploid_genotype_data, a)
 
     def test_slice(self):
@@ -1043,7 +1045,7 @@ def test_array_like(self):
         # a vanilla numpy array representation of the data.
 
         h = self.setup_instance(haplotype_data)
-        a = np.array(h, copy=False)
+        a = util.array(h, copy=False)
         aeq(haplotype_data, a)
 
     def test_slice(self):
@@ -1395,7 +1397,7 @@ def test_array_like(self):
         # a vanilla numpy array representation of the data.
 
         ac = self.setup_instance(allele_counts_data)
-        a = np.array(ac, copy=False)
+        a = util.array(ac, copy=False)
         aeq(allele_counts_data, a)
 
     def test_slice(self):
@@ -1639,12 +1641,12 @@ def test_array_like(self):
 
         # diploid data
         g = self.setup_instance(diploid_genotype_ac_data)
-        a = np.array(g, copy=False)
+        a = util.array(g, copy=False)
         aeq(diploid_genotype_ac_data, a)
 
         # polyploid data
         g = self.setup_instance(triploid_genotype_ac_data)
-        a = np.array(g, copy=False)
+        a = util.array(g, copy=False)
         aeq(triploid_genotype_ac_data, a)
 
     def test_slice(self):
@@ -2010,7 +2012,7 @@ def test_array_like(self):
 
         data = [1, 4, 5, 7, 12]
         pos = self.setup_instance(data)
-        a = np.array(pos, copy=False)
+        a = util.array(pos, copy=False)
         aeq(data, a)
 
     def test_slice(self):
@@ -2198,7 +2200,7 @@ def test_properties(self):
     def test_array_like(self):
         data = ['A', 'C', 'B', 'F']
         lbl = self.setup_instance(data)
-        a = np.array(lbl, copy=False)
+        a = util.array(lbl, copy=False)
         aeq(data, a)
 
     def test_slice(self):

allel/util.py

@@ -9,6 +9,13 @@
 import numpy as np
 
 
+def array(data, copy, **kwargs):
+    # Semantics of copy changed in numpy2 see https://github.com/scipy/scipy/pull/20172
+    if np.lib.NumpyVersion(np.__version__) >= "2.0.0":
+        if copy is False:
+            copy = None
+    return np.array(data, copy=copy, **kwargs)
+
 @contextmanager
 def ignore_invalid():
     err = np.seterr(invalid='ignore')
@@ -46,7 +53,7 @@ def asarray_ndim(a, *ndims, **kwargs):
     kwargs.setdefault('copy', False)
     if a is None and allow_none:
         return None
-    a = np.array(a, **kwargs)
+    a = array(a, **kwargs)
     if a.ndim not in ndims:
         if len(ndims) > 1:
             expect_str = 'one of %s' % str(ndims)

pyproject.toml

@@ -13,7 +13,7 @@ requires = [
     "wheel",
     "Cython>=0.28.5",
     "setuptools_scm[toml]>=6.0",
-    "oldest-supported-numpy",  # https://github.com/scipy/oldest-supported-numpy
+    "numpy>=2",
 ]
 build-backend = "setuptools.build_meta"
 

setup.py

@@ -19,7 +19,7 @@
 
 LICENSE = "MIT"
 
-INSTALL_REQUIRES = ["numpy", "dask[array]"]
+INSTALL_REQUIRES = ["numpy>=1.23.5", "dask[array]"]
 
 # full installation with all optional dependencies
 EXTRAS_REQUIRE = {