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<div dir="ltr" data-setdir="false">Hi Iddo,</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">> The first error "<span style="font-family:monospace;">BiopythonWarning: You may be importing Biopython from inside the source tree."<span style="font-family:arial, sans-serif;"> </span></span><br><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;"></span></span><div><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;">> Is that something I can ignore, <br></span></span></div><div><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;"><br></span></span></div><div dir="ltr" data-setdir="false"><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;">No; it is causing the import error.</span></span></div><div dir="ltr" data-setdir="false"><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;"><br></span></span></div><div dir="ltr" data-setdir="false"><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;">Best,</span></span></div><div dir="ltr" data-setdir="false"><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;">-Michiel<br></span></span></div><div><br></div></div>
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On Thursday, October 20, 2022 at 01:43:28 AM GMT+9, Iddo Friedberg <idoerg@gmail.com> wrote:
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<div><div id="yiv3039875215"><div dir="ltr"><div>Hi,</div><div><br></div><div>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. <br><br></div><div>However, I am encountering the following problem when trying to test:<br></div><div><br></div><div><br></div><span style="font-family:monospace;">idoerg@IddoWS:~/soft/biopython$ python setup.py test<br>running test<br>Python version: 3.7.5 (default, Dec 9 2021, 17:04:37) <br>[GCC 8.4.0]<br>Operating system: posix linux<br>/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<br> BiopythonWarning,<br>test_Ace ... ok<br>test_Affy ... ok<br>test_AlignIO ... loading tests failed:<br>Failed to import test module: test_AlignIO<br>Traceback (most recent call last):<br> File "/usr/lib/python3.7/unittest/loader.py", line 154, in loadTestsFromName<br> module = __import__(module_name)<br> File "/home/idoerg/soft/biopython/Tests/test_AlignIO.py", line 11, in <module><br> from Bio import AlignIO<br> File "/home/idoerg/soft/biopython/Bio/AlignIO/__init__.py", line 140, in <module><br> from Bio.Align import MultipleSeqAlignment<br> File "/home/idoerg/soft/biopython/Bio/Align/__init__.py", line 34, in <module><br> from Bio.Align import _aligners<br>ImportError: cannot import name '_aligners' from 'Bio.Align' (/home/idoerg/soft/biopython/Bio/Align/__init__.py)</span><br><div><br></div><div>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 "<span style="font-family:monospace;">BiopythonWarning: You may be importing Biopython from inside the source tree."<span style="font-family:arial, sans-serif;"> <br></span></span></div><div><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;"><br></span></span></div><div><span style="font-family:monospace;"><span style="font-family:arial, sans-serif;">Is that something I can ignore, or am I doing yet another thing wrong?</span></span></div><div><span style="font-family:monospace;"><br></span></div><div><span style="font-family:monospace;">Thanks,</span></div><div><span style="font-family:monospace;"><br></span></div><div><span style="font-family:monospace;">Iddo<br></span> </div><br>-- <br><div dir="ltr"><div dir="ltr"><div>Iddo Friedberg</div><div><a rel="nofollow noopener noreferrer" target="_blank" href="http://iddo-friedberg.net/contact.html">http://iddo-friedberg.net/contact.html</a><br>++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.><br>++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.<br>.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>><br>>>----.<--.>++++++.<<<<------------------------------------.<br></div></div></div></div>
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