Replace deprecated numpy.lib.user_array.container in StringMatrix

pyproject.toml

@@ -81,8 +81,7 @@ xfail_strict = true
 # convert warnings to errors, except for ImportWarnings in numpy (needed for pp38)
 # FIXME: eventually we should be able to remove the numpy exception
 # TODO: need to also move away from `user_array.container`: https://github.com/alexlancaster/pypop/issues/358
-filterwarnings = ["error", "default::ImportWarning", "ignore:.*Arlequin.*deprecated.*",
-	         "ignore:The numpy\\.lib\\.user_array\\.container class is deprecated:DeprecationWarning"]
+filterwarnings = ["error", "default::ImportWarning", "ignore:.*Arlequin.*deprecated.*"]
 log_cli_level = "INFO"
 testpaths = [
   "website/docs",

src/PyPop/utils.py

@@ -44,11 +44,11 @@
 import shutil
 import stat
 import sys
+from collections.abc import Sequence
 from pathlib import Path
 
 import numpy as np
 from numpy import asarray, take, zeros
-from numpy.lib.user_array import container
 
 from PyPop import logger
 
@@ -217,12 +217,12 @@ def tagContents(self, tagname, content, **kw):  # noqa: D417
         self.closetag(tagname)
 
 
-class StringMatrix(container):
+class StringMatrix(Sequence):
     """Matrix of strings and other metadata from input file to PyPop.
 
-    ``StringMatrix`` is a subclass of NumPy's
-    :class:`numpy.lib.user_array` class, store the data in an
-    efficient array format, using NumPy-style access.
+    ``StringMatrix`` is a subclass of
+    :class:`collections.abc.Sequence` class, which stores the data in
+    an efficient array format, using NumPy-style access.
 
     Args:
        rowCount (int): number of rows in matrix
@@ -264,8 +264,9 @@ def __init__(
         self.array = zeros(
             (self.rowCount, self.colCount * 2 + self.extraCount), dtype="O"
         )
+        self.dtype = self.array.dtype
         self.shape = self.array.shape
-        self._typecode = self.array.dtype  # Numeric array.typecode()
+        self._typecode = self.array.dtype
         self.name = str(self.__class__).split()[0]
 
     def __repr__(self):
@@ -286,6 +287,17 @@ def __repr__(self):
             return (self.__class__.__name__) + repr(self.array)[len("array") :]
         return (self.__class__.__name__) + "(" + repr(self.array) + ")"
 
+    def __len__(self):
+        """Get number of rows (individuals) in the matrix.
+
+        This allows StringMatrix instances to be used with `len()`,
+        iteration, and other Python sequence protocols.
+
+        Returns:
+           int: number of rows in the matrix
+        """
+        return self.array.shape[0]
+
     def dump(self, locus=None, stream=sys.stdout):
         """Write file to a stream in original format.