[Biopython-dev] Biopython 1.66 release?

[Peter Cock]

I'd appreciate any feedback in the next hour or so about the downloads
- do the Windows 32-bit installers behave as expected? Are the zip and
tar-ball missing anything obvious?

Meanwhile, here's a draft release announcement based almost exactly on
the NEWS file, to go out by email and as a blog post on
news.open-bio.org, like:

http://mailman.open-bio.org/pipermail/biopython-announce/2014-December/000164.html
http://news.open-bio.org/news/2014/12/biopython-1-65-released/

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.66 are now
available from the downloads page on the official Biopython website
and from the Python Package Index (PyPI).

See: http://biopython.org/wiki/Download

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 35,
although support for Python 2.6 is now deprecated. It has also been
tested on PyPy 2.4 to 2.6, PyPy3 version 2,4, and Jython 2.7.

Further work on the Bio.KEGG and Bio.Graphics modules now allows
drawing KGML pathways with transparency.

The Bio.SeqIO "abi" parser now decodes almost all the documented
fields used by the ABIF instruments - including the individual color
channels.

Bio.PDB now has a QCPSuperimposer module using the Quaternion
Characteristic Polynomial algorithm for superimposing structures. This
is a fast alternative to the existing SVDSuperimposer code using
singular value decomposition.

Bio.Entrez now implements the NCBI Entrez Citation Matching function
(ECitMatch), which retrieves PubMed IDs (PMIDs) that correspond to a
set of input citation strings. Bio.Entrez.parse(...) now supports NCBI
XML files using XSD schemas, which will be downloaded and cached like
NCBI DTD files.

A subtle bug in how multi-part GenBank/EMBL locations on the reverse
strand were parsed into CompoundLocations was fixed:
complement(join(...)) as used by NCBI worked, but
join(complement(...),complement(...),...) as used by EMBL/ENSEMBL gave
the CompoundLocation parts in the wrong order. A related bug when
taking the reverse complement of a SeqRecord containing features with
CompoundLocations was also fixed.

Additionally, a number of small bugs have been fixed with further
additions to the test suite, and there has been further work on
conforming to the Python PEP8 standard coding style.

Many thanks to the Biopython developers and community for making this
release possible, especially the following contributors:

Alan Medlar (first contribution)
Anthony Mathelier (first contribution)
Antony Lee (first contribution)
Anuj Sharma (first contribution)
Ben Fulton (first contribution)
Bertrand Néron (first contribution)
Brandon Invergo
Carlos Pena
Christian Brueffer
Connor T. Skennerton (first contribution)
David Arenillas (first contribution)
David Nicholson (first contribution)
Emmanuel Noutahi (first contribution)
Eric Rasche (first contribution)
Fabio Madeira (first contribution)
Franco Caramia (first contribution)
Gert Hulselmans (first contribution)
Gleb Kuznetsov (first contribution)
João Rodrigues
John Bradley (first contribution)
Kai Blin
Kian Ho (first contribution)
Kozo Nishida (first contribution)
Kuan-Yi Li (first contribution)
Leighton Pritchard
Lucas Sinclair
Michiel de Hoon
Peter Cock
Sunhwan Jo (first contribution)
Tarcisio Fedrizzi (first contribution)
Tiago Antao
Vincent Davis

This is a longer list than usual, which is good, but in part this
reflects the fact that this release is long overdue.

Peter

On Wed, Oct 21, 2015 at 6:14 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi all,
>
> Sanity testing of these provisional source bundles and binaries already on
> http://biopython.org/DIST/ would be appreciated, especially during the next
> few hours (during which time I will draft the release announcement and
> have dinner), and prior to the push to PyPI:
>
> 2f09afb0a7740a70f64b6d10dfc2582b  biopython-1.66.tar.gz
> 4344c2e7b91deb47f9ae2ebf7ad1e375  biopython-1.66.zip
> 192bc8a70fe098e5eae71fc3ad38e3fd  biopython-1.66.win32-py2.6.exe
> 6e4bf2b9eb9533ebd6930df6b506db51  biopython-1.66.win32-py2.7.exe
> fa7a6010b7ecce7fdd8fa614a3f5845e  biopython-1.66.win32-py3.3.exe
> c985a3477032314c1ec78e8ada916371  biopython-1.66.win32-py3.4.exe
>
> These should match this commit (not tagged yet):
>
> https://github.com/biopython/biopython/commit/c06a3066d858c4818cc6b4bf7e8d776bb9473a63
>
> There is a failure from test_Entrez_online.py but the NCBI XML contains:
> <Error>Resource temporarily unavailable (4).</Error>
>
> The new tutorial is already live:
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>
> The updated API documentation from epydoc is also live:
>
> http://biopython.org/DIST/docs/api/
>
> Regards,
>
> Peter