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

[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
> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
> >>----.<--.>++++++.<<<<------------------------------------.
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