Deprecate Bio.utils, Bio.PropertyManager and Bio.Encodings (see maili…

…ng list)

Bio/Alphabet/IUPAC.py

@@ -97,6 +97,10 @@ class IUPACUnambiguousRNA(IUPACAmbiguousRNA):
 #    #   W == wyosine
 
 
+# ====================================================================
+# TODO - Remove all the following code using now deprecated modules
+# Bio.PropertyManager, Bio.Encoding (all used by Bio.utils)
+#
 # We need to load the property resolution information, but we need to
 # wait until after the systems have been loaded. (There's a nasty loop
 # where, eg, translation objects need an alphabet, which need to be

Bio/Encodings/IUPACEncoding.py

@@ -1,3 +1,11 @@
+"""Properties once used for transcription and translation (DEPRECATED).
+
+This module is deprecated, and is expected to be removed in the next release.
+If you use this module, please contact the Biopython developers via the
+mailing lists.
+"""
+#NOTE - Adding a deprecation warning would affect Bio.Alphabet.IUPAC
+
 # Set up the IUPAC alphabet properties
 
 

Bio/Encodings/__init__.py

@@ -1,7 +1,9 @@
 # This is a Python module.
-"""Properties for functionality such as transcription and translation (OBSOLETE).
+"""Properties once used for transcription and translation (DEPRECATED).
 
-This module is obsolete, and is likely to be deprecated in a future version
-of Biopython, and to be removed after that. If you use this module, please
-contact the Biopython developers at biopython-dev@biopython.org.
+This module is deprecated, and is expected to be removed in the next release.
+If you use this module, please contact the Biopython developers via the
+mailing lists.
 """
+
+#NOTE - Adding a deprecation warning would affect Bio.Alphabet.IUPAC

Bio/PropertyManager.py

@@ -1,9 +1,10 @@
-"""Stores properties associated with the class of an object (OBSOLETE).
+"""Stores properties associated with the class of an object (DEPRECATED).
 
-This module is obsolete, and is likely to be deprecated in a future version
-of Biopython, and to be removed after that. If you use this module, please
-contact the Biopython developers at biopython-dev@biopython.org.
+This module is deprecated, and is expected to be removed in the next release.
+If you use this module, please contact the Biopython developers via the
+mailing lists.
 """
+#NOTE - Adding a deprecation warning would affect Bio.Alphabet.IUPAC
 
 
 # Would it be nice to have support for more than one resolver per

Bio/utils.py

@@ -4,13 +4,16 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-"""Miscellaneous functions for dealing with sequences (OBSOLETE).
+"""Miscellaneous functions for dealing with sequences (DEPRECATED).
 
-This module is obsolete, and is likely to be deprecated in a future version
-of Biopython, and to be removed after that. If you use this module, please
-contact the Biopython developers at biopython-dev@biopython.org.
+This module is deprecated, and is expected to be removed in the next release.
+If you use this module, please contact the Biopython developers via the
+mailing lists.
 """
 
+import warnings
+warnings.warn("Bio.utils has been deprecated, and we intend to remove it in "
+              "the next release of Biopython.", DeprecationWarning)
 
 
 import Seq
@@ -23,10 +26,10 @@ def ungap(seq):
     #TODO - Fix this?  It currently assumes the outmost AlphabetEncoder
     #is for the gap.  Consider HasStopCodon(Gapped(Protein())) as a test case.
     import warnings
-    warnings.warn("Bio.utils.ungap() has been deprecated, and we"
-                  " intend to remove it in a future release of Biopython."
-                  " Instead, please use the ungap method of the Seq object "
-                  " (added in Biopython 1.53).",
+    warnings.warn("Bio.utils has been deprecated, and we intend to remove it "
+                  "in the next release of Biopython. Instead of function "
+                  "Bio.utils.ungap please use the ungap method of the Seq "
+                  "object (added in Biopython 1.53).",
                   DeprecationWarning)
     gap = seq.gap_char
     letters = []

DEPRECATED

@@ -18,11 +18,11 @@ An explicit warning was added to setup.py for Biopython 1.55.
 
 Bio.Encodings
 =============
-Declared obsolete in Release 1.55.
+Explicitly declared obsolete in Release 1.55, and deprecated in Release 1.56.
 
 Bio.PropertyManager
 ===================
-Declared obsolete in Biopython 1.55.
+Explicitly declared obsolete in Release 1.55, and deprecated in Release 1.56.
 
 Bio.InterPro
 ============
@@ -423,7 +423,8 @@ Bio.utils
 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
 and 'back_transcribe' were deprecated in Release 1.49, and removed in Release
 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
-The whole of Bio.utils was declared obsolete in Release 1.55.
+The whole of Bio.utils was declared obsolete in Release 1.55, and deprecated
+in Biopython 1.56.
 
 Bio.Motif
 =========