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Labelling Martel and Bio.Mindy as obsolete, updating the news about t…

…his and other recent deprecations.
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1 parent 2e05f19 commit fb76593a8b27286362dce4e7ad2de35c70d28fc0 @peterjc peterjc committed Sep 2, 2008
Showing with 48 additions and 0 deletions.
  1. +8 −0 Bio/Mindy/__init__.py
  2. +15 −0 DEPRECATED
  3. +18 −0 Martel/__init__.py
  4. +7 −0 NEWS
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@@ -1,5 +1,13 @@
import os, sys
+"""Bio.Mindy provides functionality building on the Martel parser (OBSOLETE).
+
+Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules
+are considered to be obsolete. They are no longer used in any of the current
+Biopython parsers, and are likely to be deprecated and then removed in future
+releases of Biopython.
+"""
+
_open = open # rename for internal use -- gets redefined below
def open(dbname, mode = "r"):
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@@ -2,6 +2,21 @@ This file provides documentation for modules in Biopython that have been moved
or deprecated in favor of other modules. This provides some quick and easy
to find documentation about how to update your code to work again.
+Martel
+======
+Declared obsolete in Release 1.48, with the intention of an official deprecation
+or removal in a future release.
+
+Bio.Mindy
+=========
+Declared obsolete in Release 1.48, with the intention of an official deprecation
+in the following release.
+
+Bio.MetaTool
+============
+Deprecated in Release 1.48, this was a parser from the output of MetaTool 3.5
+which is now obsolete.
+
Bio.GenBank
===========
The online functionality (search_for, download_many, and NCBIDictionary) was
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@@ -1,6 +1,24 @@
# Copyright 2000-2001, Dalke Scientific Software, LLC
# Distributed under the Biopython License Agreement (see the LICENSE file).
+"""Martel is a 'regular expressions on steroids' parser generator (OBSOLETE).
+
+A goal of the Biopython project is to reduce the amount of effort needed to
+do computational biology. A large part of that work turns out to be parsing
+file formats, which lead to the development of Martel, a parser generator
+which uses a regular expression as the format description to create a parser
+that returns the parse tree using the SAX API common in XML processing.
+
+While intended to be both fast and relatively easy to understand, Martel did
+struggle with some very large records (e.g. GenBank files for whole genomes or
+chromosomes), and in practice debugging the Martel format specifications for
+evolving file formats like GenBank proved non-trivial.
+
+Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules
+are considered to be obsolete. They are no longer used in any of the current
+Biopython parsers, and are likely to be deprecated and then removed in future
+releases of Biopython.
+"""
__version__ = "1.47"
import Expression
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7 NEWS
@@ -32,6 +32,13 @@ do intend to deprecate this module eventually, however, for several years
this was the primary FASTA parsing module in Biopython and is likely to be in
use in many existing scripts.
+Martel and Bio.Mindy are now considered to be obsolete, and are likely to be
+deprecated and removed in a future release.
+
+In addition a number of other modules have been deprecated, including:
+Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics
+See the DEPRECATED file for full details.
+
===================================================================
July 5, 2008: Biopython 1.47 released.

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