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Bio.WWW deprecation, and updating old entries to say when they were r…

…emoved.
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commit b9274392980be9335e2d69fde65a537c3ffea951 1 parent 06b7528
@peterjc peterjc authored
Showing with 12 additions and 13 deletions.
  1. +12 −13 DEPRECATED
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25 DEPRECATED
@@ -5,6 +5,7 @@ to find documentation about how to update your code to work again.
Bio.Blast.NCBIWWW
=================
The HTML BLAST parser was deprecated as of Release 1.48
+The deprecated functions blast and blasturl were removed in Release 1.44
Bio.Saf
=======
@@ -34,30 +35,28 @@ Deprecated as of Release 1.46.
Bio.biblio
==========
-Deprecated as of Release 1.45.
+Deprecated as of Release 1.45, removed in Release 1.48
Bio.WWW
=======
-The modules under Bio.WWW are being deprecated as of Release 1.45
+The modules under Bio.WWW were deprecated in Release 1.45, and removed in 1.48.
+The remaining stub Bio.WWW was deprecated in Release 1.48.
+
The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro and Bio.WWW.ExPASy
is now available from Bio.SCOP, Bio.InterPro and Bio.ExPASy instead.
-Bio.Blast.NCBIWWW
-=================
-The deprecated functions blast and blasturl were removed in Release 1.44
-
Bio.SeqIO
=========
The old Bio.SeqIO.FASTA and Bio.SeqIO.generic were deprecated in favour of
-the new Bio.SeqIO module as of Release 1.44
+the new Bio.SeqIO module as of Release 1.44, removed in Release 1.47
Bio.lcc
=======
-Deprecated in favor of Bio.SeqUtils.lcc in Release 1.44
+Deprecated in favor of Bio.SeqUtils.lcc in Release 1.44, removed in 1.46
Bio.crc
=======
-Deprecated in favor of Bio.SeqUtils.CheckSum in Release 1.44
+Deprecated in favor of Bio.SeqUtils.CheckSum in Release 1.44, removed in 1.46
Bio.FormatIO
============
@@ -85,12 +84,12 @@ deprecated as of Release 1.31. Use the functions 'complement' and
Bio.sequtils
============
-Deprecated as of Release 1.30.
+Deprecated as of Release 1.30, removed in Release 1.42
Use Bio.SeqUtils instead.
Bio.SVM
=======
-Deprecated as of Release 1.30.
+Deprecated as of Release 1.30, removed in Release 1.42
The Support Vector Machine code in Biopython has been superceeded by a
more robust (and maintained) SVM library, which includes a python
interface. We recommend using LIBSVM:
@@ -99,7 +98,7 @@ http://www.csie.ntu.edu.tw/~cjlin/libsvm/
Bio.RecordFile
==============
-Deprecated as of Release 1.30.
+Deprecated as of Release 1.30, removed in Release 1.42
RecordFile wasn't completely implemented and duplicates the work
of most standard parsers. We recommend using a specific iterator
(Bio.Fasta.Iterator for example) without a parser to get back
@@ -107,7 +106,7 @@ text records.
Bio.kMeans and Bio.xkMeans
==========================
-Deprecated as of Release 1.30.
+Deprecated as of Release 1.30, removed in Release 1.42
The k-Means algorithm is an algorithm for unsupervised clustering of data.
Biopython includes an implementation of the k-means clustering algorithm
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