Minor changes to Seq integer multiplication methods and tests for inplace addition methods

[chris-rands]

This pull request relates to pull request #1669 and corresponding issue #1659 where we introduced integer multiplication methods for Seq-like objects, I propose 2 small changes.

1. A small improvement to the trackback for Seq, UnknownSeq, and MutableSeq multiplication methods when subclassing, here is an example:

>>> from Bio.Seq import Seq
>>> class MySeq(Seq): pass
...
>>> MySeq('A') * 2.0
# TypeError: can't multiply Seq by non-int type # Old behaviour
# TypeError: can't multiply MySeq by non-int type # New behaviour

2. Adding unit tests for in-place Seq, UnknownSeq, and MutableSeq addition methods. These += operations are available even though the __iadd__ methods are never defined, so I thought they should be tested.

I'd be grateful for review of the changes, any thoughts?

One related point, __imul__ methods are defined but __iadd__ methods are not. Does this matter? Probably we should ideally be consistent, but it is likely inconsequential?

• 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.)

[codecov]

Codecov Report

Merging #1735 into master will decrease coverage by 0.39%.
The diff coverage is 66.66%.

@@            Coverage Diff            @@
##           master    #1735     +/-   ##
=========================================
- Coverage   85.57%   85.17%   -0.4%     
=========================================
  Files         331      331             
  Lines       50086    50086             
=========================================
- Hits        42859    42660    -199     
- Misses       7227     7426    +199

Impacted Files	Coverage Δ
Bio/Seq.py	98.12% <66.66%> (ø)	⬆️
Bio/Phylo/CDAOIO.py	5.42% <0%> (-80.1%)	⬇️
Bio/Phylo/CDAO.py	42.85% <0%> (-57.15%)	⬇️
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%)	⬇️

---

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[peterjc]

Including the class name in the exception is a nice improvement in case of subclasses. Likewise the extra tests seems sensible too.

The TravisCI failures seem unrelated, Python 2.7.14,

======================================================================
FAIL: test_partial_diagram (test_GenomeDiagram.DiagramTest)
Construct and draw SVG and PDF for just part of a SeqRecord.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/biopython/biopython/Tests/test_GenomeDiagram.py", line 770, in test_partial_diagram
    == gdd.write_to_string('PDF').replace(b"\r\n", b"\n")
AssertionError
----------------------------------------------------------------------

and Python 3.5,

======================================================================
FAIL: test_partial_diagram (test_GenomeDiagram.DiagramTest)
Construct and draw SVG and PDF for just part of a SeqRecord.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/biopython/biopython/Tests/test_GenomeDiagram.py", line 770, in test_partial_diagram
    == gdd.write_to_string('PDF').replace(b"\r\n", b"\n")
AssertionError
----------------------------------------------------------------------

My guess is the release of ReportLab 3.5.0 earlier this week is to blame, see https://pypi.org/project/reportlab/#history

In this case the TravisCI weekly cron job will test the master branch in a few days - and I expect that to fail.

After confirming that, your changes look good to merge. Do you want to add yourself to the NEWS.rst file for the next release?

[chris-rands]

Thank you Peter, yes, I added myself to NEWS.rst. I saw the TravisCI failure but could not interpret it, your guess sounds very plausible. Let me know if there is anything else you need from me