Supporting NumPy 2.0 (#950)

* added numpy-2.0 support * Update ChangeLog.md
biocore · Apr 10, 2024 · d00f947 · d00f947
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diff --git a/ChangeLog.md b/ChangeLog.md
@@ -6,6 +6,7 @@ biom 2.1.15-dev
 
 Performance improvements:
 
+* Add NumPy 2.0 support. PR [#950](https://github.com/biocore/biom-format/pull/950) ensures code compatibility with NumPy 2.0. This support is yet to be added to the CI testing matrix.
 * Revise `Table._fast_merge` to use COO directly. For very large tables, this reduces runtime by ~50x and memory by ~5x. See PR [#913](https://github.com/biocore/biom-format/pull/933).
 * Drastically reduce the memory needs of subsampling when sums are large. Also adds 64-bit support. See PR [#935](https://github.com/biocore/biom-format/pull/935).
 * Improve handling of not-perfectly-integer inputs. See PR [#938](https://github.com/biocore/biom-format/pull/938).

diff --git a/biom/_filter.pyx b/biom/_filter.pyx
@@ -13,6 +13,7 @@ from types import FunctionType
 
 import numpy as np
 cimport numpy as cnp
+cnp.import_array()
 
 
 cdef cnp.ndarray[cnp.uint8_t, ndim=1] \

diff --git a/biom/_subsample.pyx b/biom/_subsample.pyx
@@ -8,6 +8,8 @@
 
 import numpy as np
 cimport numpy as cnp
+cnp.import_array()
+
 
 cdef _subsample_with_replacement(cnp.ndarray[cnp.float64_t, ndim=1] data,
                                  cnp.ndarray[cnp.int32_t, ndim=1] indptr,

diff --git a/biom/_transform.pyx b/biom/_transform.pyx
@@ -9,6 +9,7 @@
 
 import numpy as np
 cimport numpy as cnp
+cnp.import_array()
 
 
 def _transform(arr, ids, metadata, function, axis):