Deprecated Bio.Motif as discussed on the mailing list

biopython · Jul 15, 2013 · 74fe3dd · 74fe3dd
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diff --git a/Bio/Motif/__init__.py b/Bio/Motif/__init__.py
@@ -2,26 +2,26 @@
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-"""Tools for sequence motif analysis (OBSOLETE, see Bio.motifs instead).
+"""Tools for sequence motif analysis (DEPRECATED, see Bio.motifs instead).
 
-This module (Bio.Motif) is now obsolete, and will be deprecated and
-removed in a future release of release of Biopython. Please use the
-new module Bio.motifs instead.
+This module (Bio.Motif) has been deprecated and will be removed in a
+future release of release of Biopython. Please use the new module
+Bio.motifs instead.
 
 This contains the core Motif class containing various I/O methods as
 well as methods for motif comparisons and motif searching in sequences.
 It also inlcudes functionality for parsing AlignACE and MEME programs.
 """
 
 import warnings
-warnings.warn("The module Bio.Motif is now obsolete, and will be"
-              "deprecated and removed in a future release of"
-              "release of Biopython. As a replacement for Bio.Motif,"
-              "please use the new module Bio.motifs instead. Please"
-              "be aware that though the functionality of Bio.Motif"
-              "is retained (and extended) in Bio.motifs, usage may"
+from Bio import BiopythonDeprecationWarning
+warnings.warn("The module Bio.Motif has been depreacted and will be "
+              "removed in a future release of Biopython. Instead "
+              "please use the new module Bio.motifs instead. Please "
+              "be aware that though the functionality of Bio.Motif "
+              "is retained (and extended) in Bio.motifs, usage may "
               "be different.",
-              PendingDeprecationWarning)
+              BiopythonDeprecationWarning)
 
 
 from Bio.Motif._Motif import Motif

diff --git a/DEPRECATED b/DEPRECATED
@@ -33,6 +33,11 @@ Bio.SeqFeature
 With the introduction of the CompoundLocation in Release 1.62, the SeqFeature
 attribute sub_features was deprecated.
 
+Bio.Motif
+=========
+Declared obsolete with a PendingDeprecationWarning in Release 1.61, formerly
+deprecated in Release 1.62. Please use the newer Bio.motifs module instead.
+
 AlignAceCommandline and CompareAceCommandline
 =============================================
 Deprecated in release 1.62. An up to date version of the software cannot