[Biopython-dev] Biopython 1.70 release

Tue Jul 11 10:11:41 UTC 2017

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
Sent with [ProtonMail](https://protonmail.com) Secure Email.

> -------- Original Message --------
> Subject: Re: [Biopython-dev] Biopython 1.70 release
> Local Time: July 11, 2017 11:43 AM
> UTC Time: July 11, 2017 9:43 AM
> From: mkorycinski at protonmail.ch
> To: Mateusz Korycinski <mkorycinski at protonmail.ch>
> Peter Cock <p.j.a.cock at googlemail.com>, Biopython-Dev Mailing List <biopython-dev at mailman.open-bio.org>
> In the meantime I also managed to run them on Mac. Now I will do it for Linux.
> Tests on Mac in virtualenv with no site packages:
> Python2.7: https://pastebin.com/G5WiU1yX
> Python3.6: https://pastebin.com/JDMq9uib
> Everything seems to work fine with Python 2.7, except of wrappers depending on site programs (e.g. MUSCLE, BLAST+).
> In Python 3.6 I experienced some errors (see link above). Perhaps it's something wrong with my environment? To create environment I did:
> virtualenv ~/virt_env/test3 --no-site-packages -p python3.6
> source ~/virt_env/test3/bin/activate
>
> Best regards,
> Mateusz Korycinski
> Sent with [ProtonMail](https://protonmail.com) Secure Email.
>
>> -------- Original Message --------
>> Subject: Re: [Biopython-dev] Biopython 1.70 release
>> Local Time: July 11, 2017 10:06 AM
>> UTC Time: July 11, 2017 8:06 AM
>> From: mkorycinski at protonmail.ch
>> To: Peter Cock <p.j.a.cock at googlemail.com>
>> Biopython-Dev Mailing List <biopython-dev at mailman.open-bio.org>
>> Hi,
>> I can also test that on both Mac and Linux.
>>
>> Best regards,
>> Mateusz Korycinski
>> Sent with [ProtonMail](https://protonmail.com) Secure Email.
>>
>>> -------- Original Message --------
>>> Subject: Re: [Biopython-dev] Biopython 1.70 release
>>> Local Time: July 10, 2017 6:56 PM
>>> UTC Time: July 10, 2017 4:56 PM
>>> From: p.j.a.cock at googlemail.com
>>> To: Sourav Singh <ssouravsingh12 at gmail.com>
>>> Biopython-Dev Mailing List <biopython-dev at mailman.open-bio.org>
>>>
>>> Thanks for the offer Sourav, but Ben Fulton is happy to do
>>> the Windows installers again for Biopython 1.70.
>>> It would however be great if you could download the zip file
>>> (or tar-ball), and attempt to installing it from source and run
>>> the tests (on Windows, Linux or Mac).
>>> e.g.
>>> wget http://biopython.org/DIST/biopython-1.70.zip
>>> unzip biopython-1.70.zip
>>> cd biopython-1.70
>>> pip install .
>>> cd Tests
>>> python run_tests.py
>>> Thanks,
>>> Peter
>>>
>>> On Mon, Jul 10, 2017 at 5:47 PM, Sourav Singh <ssouravsingh12 at gmail.com> wrote:
>>>
>>>> Hello,
>>>> I can help with the testing of the gzipped code and creation of Windows installers for Biopython 1.70.
>>>> Regards,
>>>> Sourav
>>>>
>>>> On Jul 10, 2017 9:59 PM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:
>>>>
>>>>> Hi Ben,
>>>>> While in the not too distant future I am hoping to adopt the
>>>>> NumPy approach to building wheels (and installers?) [1],
>>>>> it would be much appreciated if you could make all the
>>>>> Windows installers for Biopython 1.70.
>>>>> (In particular Python 3.6, but if possible also Python 2.7,
>>>>> 3.4 and 3.5 - we no longer support Python 3.3)
>>>>> Now that we have Windows-based continuous integration
>>>>> up and running on AppVeyor [2], I didn't feel it necessary
>>>>> to bother you in advance about running the unit tests.
>>>>> Much obliged,
>>>>> Peter
>>>>> [1] http://mailman.open-bio.org/pipermail/biopython-dev/2017-July/021817.html
>>>>> [2] http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021797.html
>>>>> https://ci.appveyor.com/project/biopython/biopython/history
>>>>> On Mon, Jul 10, 2017 at 4:43 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>>>> Hello all,
>>>>>>
>>>>>> I'd like to delay the PyPI upload and official release announcement until
>>>>>> someone else has confirmed they could install this - any volunteers?
>>>>>>
>>>>>> http://biopython.org/DIST/biopython-1.70.tar.gz
>>>>>> http://biopython.org/DIST/biopython-1.70.zip
>>>>>> Checksums:
>>>>>>
>>>>>> $ md5sum biopython-1.70.*
>>>>>> feff7a3e2777e43f9b13039b344e06ff biopython-1.70.tar.gz
>>>>>> 6307ab27c257fe69b9dae4bfc3052f49 biopython-1.70.zip
>>>>>>
>>>>>> $ sha256sum biopython-1.70.*
>>>>>> 4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b
>>>>>> biopython-1.70.tar.gz
>>>>>> 34312ce899f6c3fc9dea77ca997f9a8c228043d05284a0653577594aeb119d4f
>>>>>> biopython-1.70.zip
>>>>>>
>>>>>> These are from this tagged commit on the main repository:
>>>>>>
>>>>>> https://github.com/biopython/biopython/tree/biopython-170
>>>>>> https://github.com/biopython/biopython/commit/4d01a84f0aa8f91863075f7f0f074b4b69e53959
>>>>>>
>>>>>> The revised documentation is already live:
>>>>>>
>>>>>> http://biopython.org/DIST/docs/api/
>>>>>> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>>>>>> http://biopython.org/DIST/docs/tutorial/Tutorial.html
>>>>>> etc
>>>>>>
>>>>>> Peter
>>>>>>
>>>>>> On Mon, Jul 10, 2017 at 2:19 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>>>>> Thanks everyone who helped recently with resolving
>>>>>>> open issues and pull requests - especially Eric who
>>>>>>> did lots last week.
>>>>>>>
>>>>>>> I'm going to try the release this afternoon, so please
>>>>>>> consider the mast branch frozen for the time being.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Peter
>>>>> _______________________________________________
>>>>> Biopython-dev mailing list
>>>>> Biopython-dev at mailman.open-bio.org
>>>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
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