[Biopython-dev] Biopython 1.66 release?

Wed Oct 21 19:53:51 UTC 2015

The tarball looks sane; the announcement is fine, minus Python 35 -> 3.5

Thanks for pushing this out!

Cheers,

Chris

On 10/21/15 9:25 PM, Peter Cock wrote:
> 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
> 
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