Deprecating Bio.mathfns and Bio.stringfns

Bio/mathfns.py

@@ -3,11 +3,11 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-"""This provides useful general math tools (OBSOLETE).
+"""This provides useful general math tools (DEPRECATED).
 
-This module and its C code equivalent are considered to be obsolete, and
-are likely to be deprecated in a future release of Biopython, before being
-removed.  Please get in touch via the mailing list if this will affect you.
+This module and its C code equivalent are considered to be deprecated, and
+are likely to be removed in a future release of Biopython.  Please get in
+touch via the mailing list if this will affect you.
 
 Functions:
 fcmp       Compare two floating point numbers, up to a specified precision.
@@ -16,6 +16,15 @@
 safe_exp   exp, but returns a large or small number instead of overflows.
 
 """
+import warnings
+warnings.warn("Bio.mathfns and its C code equivalent Bio.cmathfns are" \
+              +" deprecated, and will be removed in a future release of"\
+              +" Biopython.  If you want to continue to use this code,"\
+              +" please get in contact with the Biopython developers via"\
+              +" the mailing lists to avoid its permanent removal from"\
+              +" Biopython.", \
+              DeprecationWarning)
+
 import math
 
 def fcmp(x, y, precision):

Bio/stringfns.py

@@ -3,11 +3,11 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-"""This provides useful general functions for working with strings (OBSOLETE).
+"""This provides useful general functions for working with strings (DEPRECATED).
 
-This module and its C code equivalent are considered to be obsolete, and
-are likely to be deprecated in a future release of Biopython, before being
-removed.  Please get in touch via the mailing list if this will affect you.
+This module and its C code equivalent are considered to be deprecated, and
+are likely to be removed in a future release of Biopython.  Please get in
+touch via the mailing list if this will affect you.
 
 Functions:
 splitany       Split a string using many delimiters.
@@ -16,6 +16,15 @@
 starts_with    Check whether a string starts with another string [DEPRECATED].
 
 """
+import warnings
+warnings.warn("Bio.stringfns and its C code equivalent Bio.cstringfns are" \
+              +" deprecated, and will be removed in a future release of"\
+              +" Biopython.  If you want to continue to use this code,"\
+              +" please get in contact with the Biopython developers via"\
+              +" the mailing lists to avoid its permanent removal from"\
+              +" Biopython.", \
+              DeprecationWarning)
+
 def splitany(s, sep=" \011\012\013\014\015", maxsplit=None, negate=0):
     """splitany(s [,sep [,maxsplit [,negate]]]) -> list of strings
 

DEPRECATED

@@ -5,7 +5,7 @@ to find documentation about how to update your code to work again.
 Numeric support
 ===============
 Following the release of 1.48, Numeric support in Biopython is discontinued.
-Please move to NumPy.
+Please move to NumPy for Biopython 1.49 or later.
 
 Bio.Seq
 =======
@@ -21,6 +21,8 @@ Please use the methods or functions in Bio.Seq instead.
 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
 ==========================================
 Declared obsolete in Release 1.49.
+Bio.mathfns and Bio.stringfns were deprecated in Release 1.50
+(the deprecation of Bio.listfns is still pending)
 
 Bio.Ndb
 =======