[Biopython] install from source: is this an issue?

Iddo Friedberg idoerg at gmail.com
Thu Oct 20 11:05:45 EDT 2022 

Michiel and Markus:

Yes, that's exactly it according to the instructions on the github page you
are actually supposed to run everything from the source tree:
https://github.com/biopython/biopython
---------------------------------------------------------------------------------------------------------------

Then either download and decompress our source code, or fetch it using git.
Now change directory to the Biopython source code folder and run:

python setup.py build
python setup.py test
sudo python setup.py install

---------------------------------------------------------------------------------------------------------------
I guess these instructions should be changed to:

$ python setup.py build
$ sudo python setup.py install
$cd Tests
$ python run_tests.py [--offline]

On Thu, Oct 20, 2022 at 2:17 AM Markus Piotrowski <
Markus.Piotrowski at ruhr-uni-bochum.de> wrote:

> Dear Iddo,
>
> After reading here:
>
> https://docs.python.org/3/install/
>
> I would assume that your built Biopython stuff is in a "build" subfolder
> (including the C extensions),  but you are running the test from the source
> folder (biopython-master). Could this be?
>
> Best
> Markus
>
>
>
> Am 20.10.2022 um 08:41 schrieb Markus Piotrowski:
>
> This may be a naive question, since I'm not very familiar with installing
> from source, but does "build" compile the C extensions or is this something
> that happens during "install"? In the first case you would be missing the
> compiled C-extension, leading to the described import error.
>
> Best
> Markus
>
> Am 20.10.2022 um 01:58 schrieb Iddo Friedberg:
>
> Hi,
>
> Thank you for your answer, Michiel.
>
> So I'm confused as to what I am doing wrong. I downloaded the zip ,
> unzipped, changed to the biopython-master directory, and ran
>
> python setup.py build
> (this seems to be concluding fine)
>
> python setup.py test
>
> And the first error line (of many) is:
> /home/idoerg/Downloads/biopython-master/Bio/__init__.py:138: BiopythonWarning: You may be importing Biopython from inside the source tree.
> This is bad practice and might lead to downstream issues. In particular, you might encounter ImportErrors due to missing compiled C extensions.
> We recommend that you try running your code from outside the source tree.
> If you are outside the source tree then you have a setup.py file in an unexpected directory: /home/idoerg/Downloads/biopython-master
>
> Thanks,
>
> Iddo
>
> --
> Sent from a machine that promotes typos
>
> On Wed, Oct 19, 2022, 17:15 Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>
>> Hi Iddo,
>>
>>
>> > The first error "BiopythonWarning: You may be importing Biopython from
>> inside the source tree."
>> > Is that something I can ignore,
>>
>> No; it is causing the import error.
>>
>> Best,
>> -Michiel
>>
>> On Thursday, October 20, 2022 at 01:43:28 AM GMT+9, Iddo Friedberg <
>> idoerg at gmail.com> wrote:
>>
>>
>> Hi,
>>
>> I'm trying to install biopython from source, since release 1.79 does not
>> work with the newest Swissprot FT records. Looking at the source of
>> SwissProt/__init__.py in github this issue seems to be fixed and hopefully
>> release 1.80 this will work again.
>>
>> However, I am encountering the following problem when trying to test:
>>
>>
>> idoerg at IddoWS:~/soft/biopython$ python setup.py test
>> running test
>> Python version: 3.7.5 (default, Dec  9 2021, 17:04:37)
>> [GCC 8.4.0]
>> Operating system: posix linux
>> /home/idoerg/soft/biopython/Bio/__init__.py:146: BiopythonWarning: You
>> may be importing Biopython from inside the source tree. This is bad
>> practice and might lead to downstream issues. In particular, you might
>> encounter ImportErrors due to missing compiled C extensions. We recommend
>> that you try running your code from outside the source tree. If you are
>> outside the source tree then you have a setup.py file in an unexpected
>> directory: /home/idoerg/soft/biopython
>>   BiopythonWarning,
>> test_Ace ... ok
>> test_Affy ... ok
>> test_AlignIO ... loading tests failed:
>> Failed to import test module: test_AlignIO
>> Traceback (most recent call last):
>>   File "/usr/lib/python3.7/unittest/loader.py", line 154, in
>> loadTestsFromName
>>     module = __import__(module_name)
>>   File "/home/idoerg/soft/biopython/Tests/test_AlignIO.py", line 11, in
>> <module>
>>     from Bio import AlignIO
>>   File "/home/idoerg/soft/biopython/Bio/AlignIO/__init__.py", line 140,
>> in <module>
>>     from Bio.Align import MultipleSeqAlignment
>>   File "/home/idoerg/soft/biopython/Bio/Align/__init__.py", line 34, in
>> <module>
>>     from Bio.Align import _aligners
>> ImportError: cannot import name '_aligners' from 'Bio.Align'
>> (/home/idoerg/soft/biopython/Bio/Align/__init__.py)
>>
>> Previous iterations of the "_aligners" import error error in the
>> biopython github were attributed to conflicting python versions. This may
>> be the case here, but before I kill all my anaconda stuff, I just wanted to
>> make sure that  I'm actually running the test correctly.  The first error "BiopythonWarning:
>> You may be importing Biopython from inside the source tree."
>>
>> Is that something I can ignore, or am I doing yet another thing wrong?
>>
>> Thanks,
>>
>> Iddo
>>
>> --
>> Iddo Friedberg
>> http://iddo-friedberg.net/contact.html
>> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
>> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
>> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>> >>----.<--.>++++++.<<<<------------------------------------.
>> _______________________________________________
>> Biopython mailing list  -  Biopython at biopython.org
>> https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
> _______________________________________________
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>
>
> --
> _________________________________
> Dr. Markus Piotrowski
> Privatdozent/Akademischer Rat
> Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
> ND 3/49
> Universitätsstr. 150
> 44801 Bochum
>
> Tel. xx49-(0)234-3224290
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>
>
> _______________________________________________
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>
>
> --
> _________________________________
> Dr. Markus Piotrowski
> Privatdozent/Akademischer Rat
> Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
> ND 3/49
> Universitätsstr. 150
> 44801 Bochum
>
> Tel. xx49-(0)234-3224290
> Fax. xx49-(0)234-3214187
> https://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.htmlhttp://homepage.ruhr-uni-bochum.de/Markus.Piotrowski/Index.html
>
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-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>----.<--.>++++++.<<<<------------------------------------.
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