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Updating CONTRIB and NEWS for Biopython 1.53 contributors as discusse…
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…d on the mailing list (trying to follow the more inclusive style of the Sage project)
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peterjc committed Dec 22, 2009
1 parent 21b4ff3 commit 86d8d99
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4 changes: 4 additions & 0 deletions CONTRIB
Expand Up @@ -11,6 +11,7 @@ Tiago Antao <tiagoantao at gmail.com>
Sebastian Bassi <sbassi at domain asalup.org>
Bill Barnard <bill at domain barnard-engineering.com>
Yves Bastide <ybastide at domain irisa.fr>
Paul Bathen
Yair Benita <Y.Benita at domain pharm.uu.nl>
Peter Bienstman <Peter.Bienstman at domain rug.ac.be>
Bob Bussell <rgb2003 at domain med.cornell.edu>
Expand All @@ -24,6 +25,8 @@ Marc Colosimo <mcolosimo at domain mitre.org>
Cymon J Cox <cymon at domain duke.edu>
Gavin E Crooks <gec at domain compbio.berkeley.edu>
Andrew Dalke <dalke at domain acm.org>
Kyle Ellrott
Frederik Gwinner
Michiel de Hoon <mdehoon at domain c2b2.columbia.edu>
Sjoerd de Vries <sjoerd at domain nmr.chem.uu.nl>
Iddo Friedberg <idoerg at domain burnham.org>
Expand Down Expand Up @@ -52,4 +55,5 @@ Dan Vogel <dmv at domain andrew.cmu.edu>
David Weisman <david.weisman at domain acm.org>
Bartek Wilczynski <bartek at domain rezolwenta.eu.org>
David Winter <david dot winter at gmail dot com>
Hongbo Zhu
Harry Zuzan <iliketobicycle at domain yahoo.ca>
31 changes: 24 additions & 7 deletions NEWS
Expand Up @@ -52,14 +52,16 @@ The restriction enzyme list in Bio.Restriction has been updated to the
Nov 2009 release of REBASE.

The Bio.PDB parser and output code has been updated to understand the
element column in ATOM and HETATM lines. Bio.PDB.PDBList has also been
updated for recent changes to the PDB FTP site.
element column in ATOM and HETATM lines (based on patches contributed by
Hongbo Zhu and Frederik Gwinner). Bio.PDB.PDBList has also been updated
for recent changes to the PDB FTP site (Paul T. Bathen).

SQLite support was added for BioSQL databases, allowing access to BioSQL
through a lightweight embedded SQL engine. Python 2.5+ includes support for
SQLite built in, but on Python 2.4 the optional sqlite3 library must be
installed to use this. We currently use a draft BioSQL on SQLite schema,
which will be merged with the main BioSQL release for use in other projects.
SQLite support was added for BioSQL databases (Brad Chapman), allowing access
to BioSQL through a lightweight embedded SQL engine. Python 2.5+ includes
support for SQLite built in, but on Python 2.4 the optional sqlite3 library
must be installed to use this. We currently use a draft BioSQL on SQLite
schema, which will be merged with the main BioSQL release for use in other
projects.

Support for running Biopython under Jython (using the Java Virtual Machine)
has been much improved thanks to input from Kyle Ellrott. Note that Jython
Expand All @@ -69,6 +71,21 @@ Also, currently Jython does not parse DTD files, which means the XML parser
in Bio.Entrez won't work. However, most of the Biopython modules seem fine
from testing Jython 2.5.0 and 2.5.1.

(At least) 12 people contributed to this release, including 3 first timers:

Bartek Wilczyns
Brad Chapman
Chris Lasher
Cymon Cox
Frank Kauff
Frederik Gwinner (first contribution)
Hongbo Zhu (first contribution)
Kyle Ellrott
Leighton Pritchard
Michiel de Hoon
Paul Bathen (first contribution)
Peter Cock

===================================================================

September 22, 2009: Biopython 1.52 released.
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