replace sparse matrix with sparse array

emcfile/_pattern_sone.py

@@ -20,7 +20,7 @@
 import h5py
 import numpy as np
 import numpy.typing as npt
-from scipy.sparse import csr_matrix, hstack
+from scipy.sparse import csr_array, hstack
 
 from ._h5helper import PATH_TYPE, H5Path, check_remove_groups, make_path
 from ._misc import pretty_size
@@ -243,15 +243,15 @@ def write(
             compression=compression,
         )
 
-    def _get_sparse_ones(self) -> csr_matrix:
+    def _get_sparse_ones(self) -> csr_array:
         _one = np.ones(1, "i4")
         _one = np.lib.stride_tricks.as_strided(
             _one, shape=(self.place_ones.shape[0],), strides=(0,)
         )
-        return csr_matrix((_one, self.place_ones, self.ones_idx), shape=self.shape)
+        return csr_array((_one, self.place_ones, self.ones_idx), shape=self.shape)
 
-    def _get_sparse_multi(self) -> csr_matrix:
-        return csr_matrix(
+    def _get_sparse_multi(self) -> csr_array:
+        return csr_array(
             (self.count_multi, self.place_multi, self.multi_idx), shape=self.shape
         )
 
@@ -272,7 +272,7 @@ def __array__(self) -> npt.NDArray[np.int32]:
     def __matmul__(self, mtx: npt.NDArray[Any]) -> npt.NDArray[Any]:
         return cast(
             npt.NDArray[Any],
-            self._get_sparse_ones() * mtx + self._get_sparse_multi() * mtx,
+            self._get_sparse_ones() @ mtx + self._get_sparse_multi() @ mtx,
         )
 
     def __array_function__(

emcfile/_patterns.py

@@ -7,7 +7,7 @@
 
 import numpy as np
 import numpy.typing as npt
-from scipy.sparse import coo_matrix, spmatrix
+from scipy.sparse import coo_array, coo_matrix, sparray, spmatrix
 
 from ._h5helper import PATH_TYPE, H5Path
 from ._misc import divide_range
@@ -160,9 +160,9 @@ def patterns(
         if start is not None or end is not None:
             raise Exception()
         return dense_to_PatternsSOne(src)
-    elif isinstance(src, coo_matrix):
+    elif isinstance(src, (coo_array, coo_matrix)):
         return coo_to_SOne_kernel(src)
-    elif isinstance(src, spmatrix):
+    elif isinstance(src, (sparray, spmatrix)):
         return cast(
             PatternsSOne,
             np.concatenate(

emcfile/tests/test_patterns.py

@@ -10,7 +10,7 @@
 import numpy as np
 import pytest
 from psutil import Process
-from scipy.sparse import coo_matrix, csr_matrix
+from scipy.sparse import coo_array, csr_array
 
 import emcfile as ef
 from emcfile.tests.utils import temp_seed
@@ -86,8 +86,8 @@ def gen_pattern_inputs():
     ref = ef.patterns(dense)
     yield ref, ref
     yield dense, ref
-    yield coo_matrix(dense), ref
-    yield csr_matrix(dense), ref
+    yield coo_array(dense), ref
+    yield csr_array(dense), ref
 
 
 def test_pattern_not_equal(small_data):
@@ -252,9 +252,9 @@ def test_pattern_mul(big_data):
     np.testing.assert_almost_equal(big_data @ mtx, np.asarray(big_data) @ mtx)
     mtx = mtx > 0.4
     np.testing.assert_almost_equal(big_data @ mtx, big_data.todense() @ mtx)
-    mtx = coo_matrix(mtx)
+    mtx = coo_array(mtx)
     np.testing.assert_equal((big_data @ mtx).todense(), big_data.todense() @ mtx)
-    mtx = csr_matrix(mtx)
+    mtx = csr_array(mtx)
     np.testing.assert_equal((big_data @ mtx).todense(), big_data.todense() @ mtx)