[Biopython-dev] Biopython 1.70 release

[Peter Cock]

Thanks everyone who's tested so far - I've done the PyPI
upload:

$ twine upload biopython-1.70.tar.gz
Uploading distributions to https://upload.pypi.org/legacy/
Uploading biopython-1.70.tar.gz
[================================] 15675980/15675980 - 00:00:16

That is now live, and I'm pleased to see the README.rst is
rendering perfectly this time:

https://pypi.python.org/pypi/biopython/1.70

Further testing reports are still welcome - especially now from
using "pip install biopython" (or upgrading with pip).

Ben is again kindly going to do the 32-bit Windows installers (thanks!),
and later I plan to look at automated building of wheels:

http://mailman.open-bio.org/pipermail/biopython-dev/2017-July/021817.html

Peter

On Tue, Jul 11, 2017 at 11:36 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hmm. I'm not sure if there is any mechanism in setuptools for
> us to specify we need Python's C headers present. This is kind
> of assumed if compiling anything against the Python C API.
>
> I don't think this causes any problems for the Biopython 1.70
> release, but would be worth looking at in terms of reviewing
> our installation documentation:
>
> https://github.com/biopython/biopython/issues/1295
>
> Thanks again,
>
> Peter
>
> On Tue, Jul 11, 2017 at 11:11 AM, Mateusz Korycinski
> <mkorycinski at protonmail.ch> wrote:
>> On Linux (Ubuntu 16.04.02) I was getting following error:
>>
>>     creating build/temp.linux-x86_64-3.5
>>     creating build/temp.linux-x86_64-3.5/Bio
>>     x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall
>> -Wstrict-prototypes -g -fstack-protector-strong -Wformat
>> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
>> -I/usr/include/python3.5m
>> -I/root/virt_env/test_biopython3/include/python3.5m -c
>> Bio/cpairwise2module.c -o build/temp.linux-x86_64-3.5/Bio/cpairwise2module.o
>>     unable to execute 'x86_64-linux-gnu-gcc': No such file or directory
>>     error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
>>
>>     ----------------------------------------
>> Command "/root/virt_env/test_biopython3/bin/python3 -u -c "import
>> setuptools,
>> tokenize;__file__='/tmp/pip-eokznl75-build/setup.py';f=getattr(tokenize,
>> 'open', open)(__file__);code=f.read().replace('\r\n',
>> '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
>> /tmp/pip-avijolek-record/install-record.txt
>> --single-version-externally-managed --compile --install-headers
>> /root/virt_env/test_biopython3/include/site/python3.5/biopython" failed with
>> error code 1 in /tmp/pip-eokznl75-build/
>>
>>
>> Which was of course solved by installing python3-dev. Shouldn't that also go
>> to the setup script?
>>
>> Then install and tests (Python 3.5.2): https://pastebin.com/Vz2yFRZF
>>
>> Everything seems to be fine here.
>>
>> Best regards,
>> Mateusz Korycinski