deprecating the SummaryInfo class in Bio.Align.AlignInfo (#5069)

Bio/Align/AlignInfo.py

@@ -12,8 +12,13 @@ be put into classes in this module.
 """
 
 
+import warnings
+
+from Bio import BiopythonDeprecationWarning
+
+
 class SummaryInfo:
-    """Calculate summary info about the alignment.
+    """Calculate summary info about the alignment.  (DEPRECATED)
 
     This class should be used to calculate information summarizing the
     results of an alignment. This may either be straight consensus info
@@ -25,6 +30,22 @@ class SummaryInfo:
 
         ic_vector attribute. A list of ic content for each column number.
         """
+        warnings.warn(
+            """\
+The class SummaryInfo has been deprecated. Instead of
+
+>>> align_info = AlignInfo.SummaryInfo(msa)
+>>> sequence = align_info.get_column(1)
+
+please use
+
+>>> alignment = msa.alignment  # to get a new-style Alignment object
+>>> sequence = alignment[:, 1]
+
+Here, `msa` is a MultipleSeqAlignment object and `alignment` is an
+`Alignment` object.""",
+            BiopythonDeprecationWarning,
+        )
         self.alignment = alignment
         self.ic_vector = []
 

DEPRECATED.rst

@@ -114,8 +114,9 @@ wrapped is no longer available since SCOP moved to the EBI website.
 Bio.AlignInfo
 -------------
 The ``pos_specific_score_matrix`` method of the ``SummaryInfo`` class and the
-``PSSM`` class were deprecated in release 1.82, and removed in release 1.85. As
-an alternative, please use the ``alignment`` property of a ``MultipleSeqAlignment``
+``PSSM`` class were deprecated in release 1.82, and removed in release 1.85.
+The ``SummaryInfo`` class itself was deprecated in release 1.86.  As an
+alternative, please use the ``alignment`` property of a ``MultipleSeqAlignment``
 object to obtains a new-style ``Alignment`` object, and use it to create a
 ``Bio.motifs.Motif`` object. For example,
 

Tests/test_align.py

@@ -394,7 +394,8 @@ T:   7.00   0.00   7.00   0.00   0.00   0.00   7.00   6.00   0.00   0.00   0.00
 """,
         )
 
-        align_info = AlignInfo.SummaryInfo(msa)
+        with self.assertWarns(BiopythonDeprecationWarning):
+            align_info = AlignInfo.SummaryInfo(msa)
         self.assertEqual(align_info.get_column(1), "AAAAAAA")
         self.assertEqual(align_info.get_column(7), "TTTATTT")