[Biopython-dev] Biopython 1.49 released

[Peter]

Dear Biopythoneers,

We are pleased to announce the release of Biopython 1.49. There have
been some significant changes since Biopython 1.48 was released a few
months ago, which is why we initially released a beta for wider
testing. Thank you to all those who tried this and reported the minor
problems uncovered.

As previously announced, the big news is that Biopython now uses NumPy
rather than its precursor Numeric (the original Numerical Python
library).

As in the previous releases, Biopython 1.49 supports Python 2.3, 2.4
and 2.5 but should now also work fine on Python 2.6. Please note that
we intend to drop support for Python 2.3 in a couple of releases time.

We also have some new functionality, starting with the basic sequence
object (the Seq class) which now has more methods. This encourages a
more object orientated coding style, and makes basic biological
operations like transcription and translation more accessible and
discoverable.

Our BioSQL interface can now optionally fetch the NCBI taxonomy on
demand when loading sequences (via Bio.Entrez) allowing you to
populate the taxon/taxon_name tables gradually. Also, BioSQL should
now work with the psycopg2 driver for PostgreSQL (as well as the older
psycopg driver), and the handling of feature locations has also been
improved.

We've also updated the Biopython Tutorial and Cookbook (also available in PDF).
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

Finally, our old parsing infrastructure (Martel and Bio.Mindy) is now
considered to be deprecated, meaning mxTextTools is no longer required
to use Biopython. This should not affect any of the typically used
parsers (e.g. Bio.SeqIO and Bio.AlignIO).

Given there have been more changes than in recent Biopython releases,
please do check your old scripts still work fine, and let us know on
the mailing list or file a bug if there is anything wrong.

Source distributions and Windows installers are available from the
Biopython website:
http://biopython.org/wiki/Download

Thanks!

-Peter on behalf of the Biopython developers

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