Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…

…ntations as obsolete. Removing previously deprecated starts_with function from Bio.stringfns

Bio/listfns.py

@@ -3,7 +3,12 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-"""This provides useful general functions for working with lists.
+"""This provides useful general functions for working with lists (OBSOLETE).
+
+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.
+Many of these functions can be avoided using the python set object.
 
 Functions:
 asdict        Make the list into a dictionary (for fast testing of membership).

Bio/mathfns.py

@@ -3,7 +3,11 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-"""This provides useful general math tools.
+"""This provides useful general math tools (OBSOLETE).
+
+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.
 
 Functions:
 fcmp       Compare two floating point numbers, up to a specified precision.

Bio/stringfns.py

@@ -3,7 +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.
+"""This provides useful general functions for working with strings (OBSOLETE).
+
+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.
 
 Functions:
 splitany       Split a string using many delimiters.
@@ -70,16 +74,6 @@ def rfind_anychar(string, chars, index=None, negate=0):
     # If not found, index will already be -1.
     return index
 
-def starts_with(s, start):
-    """starts_with(s, start) -> 1/0
-
-    Return whether s begins with start.
-
-    """
-    import warnings
-    warnings.warn("The starts_with function in Bio.stringfns was deprecated. Please use s.startswith(start) instead of starts_with(s, start)", DeprecationWarning)
-    return s.startswith(start)
-
 # Try and load C implementations of functions.  If I can't,
 # then just ignore and use the pure python implementations.
 try:

DEPRECATED

@@ -18,6 +18,10 @@ Bio.Transcribe and Bio.Translate
 Declared obsolete in Release 1.49.
 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.Ndb
 =======
 Deprecated in Release 1.49, as the website this parsed has been redesigned.