Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle and Bio…

….FilteredReader (declared obsolete in 1.50)

Bio/EZRetrieve.py

@@ -1,4 +1,7 @@
-"""This module contains code to access EZRetrieve (OBSOLETE).
+"""This module contains code to access EZRetrieve (DEPRECATED).
+
+This module is now deprecated, and will be removed in a future release of
+Biopython.
 
 This is a very simple interface to the EZRetrieve website described in:
 
@@ -11,11 +14,15 @@
 Functions:
 retrieve_single  Retrieve a single sequence from EZRetrieve.
 parse_single     Parse the results from EZRetrieve into FASTA format.
-
-This module is now considered to be obsolete, and is likely to be deprecated
-in a future release of Biopython, and later removed.
 """
 
+import warnings
+warnings.warn("Bio.EZRetrieve is 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 retrieve_single(id, from_, to, retrieve_by=None, organism=None,
                     parse_results=1):
     import urllib

Bio/File.py

@@ -7,9 +7,13 @@
 
 
 Classes:
+
 UndoHandle     File object decorator with support for undo-like operations.
+
 StringHandle   Wraps a file object around a string.
-SGMLHandle     File object that automatically strips SGML tags from data.
+
+SGMLHandle     File object that automatically strips SGML tags from data
+               (DEPRECATED).
 
 SGMLStripper   Object that strips SGML.  This is now considered OBSOLETE, and
                is likely to be deprecated in a future release of Biopython,
@@ -107,10 +111,8 @@ def __exit__(self, type, value, traceback):
 # readlines method.
 StringHandle = StringIO.StringIO
 
-
-
 class SGMLHandle:
-    """A Python handle that automatically strips SGML tags from data (OBSOLETE).
+    """A Python handle that automatically strips SGML tags from data (DEPRECATED).
 
     This module is now considered to be obsolete, and is likely to be
     deprecated in a future release of Biopython, and later removed.
@@ -121,6 +123,12 @@ def __init__(self, handle):
         handle is a file handle to SGML-formatted data.
         
         """
+        import warnings
+        warnings.warn("Bio.File.SGMLHandle is deprecated, and will be removed"\
+                      " in a future release of Biopython.  If you want to"\
+                      " continue to use this code, please get in contact via"\
+                      " the mailing lists to avoid its permanent removal from"\
+                      " Biopython.", DeprecationWarning)
         self._handle = handle
         self._stripper = SGMLStripper()
 

Bio/FilteredReader.py

@@ -3,7 +3,10 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-"""Code for more fancy file handles (OBSOLETE).
+"""Code for more fancy file handles (DEPRECATED).
+
+This module is now deprecated, and will be removed in a future release of
+Biopython.
 
 Classes:
 Filtered is a decorator for File that allows the user to filter the output
@@ -20,11 +23,14 @@
 
 All filters in the chain must provide the same interface with a line of text as the single
 input parameter and altered text as the return value.
-
-This module is now considered to be obsolete, and is likely to be deprecated
-in a future release of Biopython, and later removed.
 """
 
+import warnings
+warnings.warn("Bio.FilteredReader is 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 developers"\
+              " via the mailing lists to avoid its permanent removal from"\
+              " Biopython.", DeprecationWarning)
 
 def dump_saved( name, text, j ):
     """Used for debugging."""

Bio/NetCatch.py

@@ -3,7 +3,10 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-"""Code for dealing with lists of URLs (OBSOLETE).
+"""Code for dealing with lists of URLs (DEPRECATED).
+
+This module is now deprecated, and will be removed in a future release of
+Biopython.
 
 NetCatch enables the user to scan a list of labelled urls and select 
 a subset to read into a file.
@@ -13,10 +16,14 @@
 get_urls_by_index
 get_urls_by_range
 select_output_file
-
-This module is now considered to be obsolete, and is likely to be deprecated
-in a future release of Biopython, and later removed.
 """
+
+import warnings
+warnings.warn("Bio.NetCatch is 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 os
 import urllib
 import sgmllib

DEPRECATED

@@ -49,7 +49,7 @@ Bio.ExPASy.Enzyme, respectively.
 
 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
 =====================================================================
-Declared obsolete in Release 1.50, will be deprecated in a subsequent release.
+Declared obsolete in Release 1.50, deprecated in Release 1.52.
 
 Bio.Graphics.GenomeDiagram and colour/color, centre/center
 ==========================================================