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

[Michiel de Hoon]

 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 Friedberghttp://iddo-friedberg.net/contact.html
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