[Biopython-dev] Getting ready for a release, II

[Michiel Jan Laurens de Hoon]

Hi Iddo,

Thank you for getting the new release together. Below is a summary of my updates 
since 2004.08.14. I am trying to handle recently sent in bug reports and patches 
as much as possible before the release, so there may be some small additions to 
this list.

--Michiel.

----------------------------
date: 2004/08/14 08:22:18;
Added the functions 'complement' and 'reverse_complement' to Bio.Seq's Seq and
MutableSeq objects. Similar functions previous existed in various locations in
BioPython:
- forward_complement, reverse_complement in Bio.GFF.easy
- complement, antiparallel in Bio.SeqUtils
These functions have now been deprecated, and will generate a DeprecationWarning
when used.
The functions complement and reverse_complement, when applied to a Seq object,
will return a new Seq object. The same function applied to a MutableSeq object
will modify the MutableSeq object itself, and don't return anything.
=============================================================================

----------------------------
date: 2004/08/26 13:22:58;
Bug fix and enhancement from Fred Sohm:
Added a method __maketrans in Seq
in Seq.complement() and Seq.reverse_complement() replaced seq.alphabet by
self.alphabet.
Added support for lower case DNA in Seq.complement() and
Seq.reverse_complement. Same thing in MutableSeq.complement()
=============================================================================

----------------------------
date: 2005/02/11 08:08:30;
The CEL file parser in Bio/Affy/celmodule.cc was replaced by a scanner/consumer
in CelFile.py, using Biopython's parser framework. Compilation of the C++
extension celmodule.cc caused problems on some platforms in the past.
----------------------------

----------------------------
date: 2005/01/21 09:01:08;
Removed two lines in setup.py that were causing problems when compiling the C++ 
extensions under Python 2.3. Compilation of KDTree is now switched off by 
default because of recurring C++ compilation problems.

----------------------------
date: 2004/05/08 06:32:51;
Created Bio.Statistics and added lowess.py as its first file.
=============================================================================

date: 2004/06/09 15:22:14;
C Clustering Library version 1.27. Clean return from treecluster if insufficient
memory was available to complete the calculation. Code cleanup.
=============================================================================



Iddo Friedberg wrote:
> OK, except for the test_Registry problem in the unit-tests, the rest are 
> fixed or getting fixed.
> 
> Any major bugs open? Bugzilla has 19, but most of them are either not 
> critical, or critical and have been fixed but not removed from Bugzilla.
> 
> Also, I'd like all developers who made changes since 5/2004 (last 
> release) to list them, with thir names. But it will be difficult to 
> compile features contributed frm this list. We used to have  a Wiki, but 
> it is no more. Anybody has an idea for a temporary "sandbox" where all 
> developers can list their latest contributions? After they are all 
> listed, I'll just add the list to the release.
> 
> Thanks,
> 
> Iddo
> 

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon