Modify ImportError traceback for _aligners

[chris-rands]

This pull request relates to an issue raised on the mailing list here. I also saw the same question asked on Stack overflow here, and I then later independently encountered the issue myself because I had used some soft links rather than doing a proper install. The error can occur on a few imports, for example:

>>> from Bio import SeqIO
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/path/biopython/Bio/SeqIO/__init__.py", line 375, in <module>
    from Bio.Align import MultipleSeqAlignment
  File "path/biopython/Bio/Align/__init__.py", line 22, in <module>
    from Bio.Align import _aligners
ImportError: cannot import name '_aligners'

I found the error slightly cryptic until I read through the mailing list thread, and perhaps I am not alone. Michiel noted in the mailing list thread here that numpy have a more informative traceback, I suggest modifying the traceback in this case in a similar way:

>>> from Bio import SeqIO
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/path/biopython/Bio/SeqIO/__init__.py", line 375, in <module>
    from Bio.Align import MultipleSeqAlignment
  File "/path/biopython/Bio/Align/__init__.py", line 29, in <module>
    raise new_exc
ImportError: cannot import name '_aligners': you should not import directly from the
                         biopython source directory; please exit the source
                         tree and re-launch your code from there

Thoughts?

• I hereby agree to dual licence this and any previous contributions under both
  the Biopython License Agreement AND the BSD 3-Clause License.

• I have read the CONTRIBUTING.rst file and understand that AppVeyor and
  TravisCI will be used to confirm the Biopython unit tests and flake8 style
  checks pass with these changes.

• I have added my name to the alphabetical contributors listings in the files
  NEWS.rst and CONTRIB.rst as part of this pull request, am listed
  already, or do not wish to be listed. (This acknowledgement is optional.)

[peterjc]

Don't use a triple quote string, which inserts the new lines breaks as is. Use single quotes (which will auto-concatenate)

[codecov]

Codecov Report

Merging #1736 into master will decrease coverage by 0.41%.
The diff coverage is 33.33%.

@@            Coverage Diff             @@
##           master    #1736      +/-   ##
==========================================
- Coverage   85.57%   85.15%   -0.42%     
==========================================
  Files         331      331              
  Lines       50086    50091       +5     
==========================================
- Hits        42859    42657     -202     
- Misses       7227     7434     +207

Impacted Files	Coverage Δ
Bio/Align/__init__.py	84.57% <33.33%> (-0.88%)	⬇️
Bio/Phylo/CDAOIO.py	5.42% <0%> (-80.1%)	⬇️
Bio/Phylo/CDAO.py	42.85% <0%> (-57.15%)	⬇️
Bio/GA/Evolver.py	54.54% <0%> (-18.19%)	⬇️
Bio/Phylo/_cdao_owl.py	88.88% <0%> (-11.12%)	⬇️
BioSQL/DBUtils.py	68.49% <0%> (-6.85%)	⬇️
Bio/Phylo/_io.py	91.66% <0%> (-2.78%)	⬇️
Bio/_py3k/__init__.py	75% <0%> (-1.2%)	⬇️
Bio/Restriction/Restriction.py	82.93% <0%> (-0.46%)	⬇️
Bio/PopGen/GenePop/Controller.py	64.47% <0%> (-0.2%)	⬇️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d7789a5...ffc42e8. Read the comment docs.

[peterjc]

Looks good to me in principle - over to @mdehoon

[peterjc]

TravisCI failure linked to ReportLab, see #1737 1737

[peterjc]

TravisCI failure caused by #1737 (latest ReportLab release).

[mdehoon]

Looks good to me.

As this error typically appears when a user runs "python setup.py install" and directly afterwards tries to import Bio, some day we should reorganize the directory structure such that Bio/ etc. is not a direct subdirectory of biopython, then this error is unlikely to happen at all.