[Biopython-dev] Preparing for Biopython 1.67

Peter Cock p.j.a.cock at googlemail.com
Wed Jun 8 18:55:28 UTC 2016

The announcement emails have gone out, and thank you to
Ben Fulton for preparing the win32 installers for Python 3.5.

For the record, the checksums are as follows, also noted
in the DIST repository commit comments:

$ shasum -a 256 biopython-1.67.*


$ md5 biopython-1.67.*
MD5 (biopython-1.67.tar.gz) = 542699cc310588c1997806681ee1f65e
MD5 (biopython-1.67.win32-py2.6.exe) = ab98a23eebe24126cd7b2ccd59b69810
MD5 (biopython-1.67.win32-py2.6.msi) = 270180156cf612382e38bf4966c90b0d
MD5 (biopython-1.67.win32-py2.7.exe) = 4baff34c86bf0612c5559381c74a1a2b
MD5 (biopython-1.67.win32-py2.7.msi) = 874917de39fae247ac71fd786f2644dc
MD5 (biopython-1.67.win32-py3.3.exe) = 5c7f2e857c644ddcb06de854ce376931
MD5 (biopython-1.67.win32-py3.3.msi) = ac7f6c011abb22298ba457b7b027f74f
MD5 (biopython-1.67.win32-py3.4.exe) = 0d2a500439042cad7687418b31875e53
MD5 (biopython-1.67.win32-py3.4.msi) = 5fac09d8b1b7c28e6bc14cc69b45f154
MD5 (biopython-1.67.win32-py3.5.exe) = 99504c9c09bad2507f53ad9340fc31c8
MD5 (biopython-1.67.win32-py3.5.msi) = f0aaab2ca1f34fb8a53e6ad26b77cace
MD5 (biopython-1.67.zip) = 004a5c549ec4cbc4d81db2dc19d7788a

Thanks again to everyone who has contributed to this release,


On Wed, Jun 8, 2016 at 6:42 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> The blog post is live, let me know if there are any typos:
> https://news.open-bio.org/2016/06/08/biopython-1-67-released/
> Tweeted:
> https://twitter.com/Biopython/status/740599642920980480
> Peter
> On Wed, Jun 8, 2016 at 5:42 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> Hello all,
>> I've done the 32bit Windows installers for the older versions of
>> Python, and they and the source releases are live via:
>> http://biopython.org/wiki/Download
>> Ben - could you do the 32bit Windows installers for Python 3.5 again
>> please? Getting them to me by email is fine, or you can try forking the
>> DIST repository and doing it via a pull request if that seems easier:
>> https://github.com/biopython/DIST
>> Still to do: Release announcement for emailing and the OBF blog:
>> Would anyone volunteer to draft this while I have dinner?
>> https://news.open-bio.org/category/obf-projects/biopython/
>> Thanks,
>> Peter
>> On Wed, Jun 8, 2016 at 3:38 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>> This is live on PyPI now:
>>> https://pypi.python.org/pypi/biopython/
>>> If anyone could test that now for any last minute issues, please
>>> do so.
>>> I still need to do the Windows installers and our own download page,
>>> then the release announcement for emailing and the OBF blog.
>>> Peter
>>> On Wed, Jun 8, 2016 at 11:20 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>> Another update, I've sorted out most of the warnings from the
>>>> test suite, although there are some open issues here:
>>>> https://github.com/biopython/biopython/issues/838
>>>> https://github.com/biopython/biopython/issues/845
>>>> For reasons unknown, the BioSQL SQLite tests are now regularly
>>>> failing under Python 2.6 on my old Windows XP machine, e.g.
>>>> http://testing.open-bio.org/biopython/builders/Windows%20XP%20-%20Python%202.6/builds/657/steps/shell/logs/stdio
>>>> This turned out to be unrelated to the recent minor changes to
>>>> how the BioSQL tests are configured - even a clean re-install of
>>>> Biopython 1.66 fails - and is frustratingly random. I'm giving up
>>>> on this - there is probably a handle leak somewhere but since
>>>> this seems to be Python 2.6 specific so it does not seem to be
>>>> that important.
>>>> I'm going to try to do the release this afternoon - so please
>>>> don't commit anything to the master branch for the time
>>>> being.
>>>> Thanks,
>>>> Peter
>>>> On Fri, Jun 3, 2016 at 5:15 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>>> Hello again,
>>>>> That time plan failed due to the sudden need to do the website migration.
>>>>> However, if you've been watching the commits on GitHub you might
>>>>> have guessed from things like cleaning up the warnings from the test
>>>>> suite, recently I've been focusing on getting ready for Biopython 1.67.
>>>>> It may be tempting fate, but I hope to do the release next week -
>>>>> and in the process update the instructions where needed due to
>>>>> the website move to GitHub pages:
>>>>> http://biopython.org/wiki/Building_a_release
>>>>> On a related note, does anyone have any thoughts on how we
>>>>> have been tagging the releases so far in git? i.e. annotated tags
>>>>> versus the currently used "lightweight tags", see:
>>>>> https://github.com/biopython/biopython.github.io/issues/56
>>>>> Thanks,
>>>>> Peter

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