More f-string conversion using pyupgrade 2.25.0

[peterjc]

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Progress on #2510, follows on from #3723. With these changes about a quarter of the main code base string formatting will be f-strings:

$ flake8 --isolated --select SFS --statistics BioSQL Bio
...
1297  SFS101 String literal formatting using percent operator.
28    SFS201 String literal formatting using format method.
406   SFS301 String literal formatting using f-string.

(pyupgrade would convert about 100 more of the percent uses, but mostly to format strings - there about 30 more f-strings it would create which I missed in this manual selection)

[peterjc]

I think on balance I prefer the behaviour of flynt in creating f-strings, but some of the other changes from pyupgrade are worthwhile - see #3722.

Expect a followup PR using flynt to follow (I want to keep the size of change sets reasonable for checking by eye).

[peterjc]

Exciting, a failure:

======================================================================
ERROR: test_str (test_Blast_Record.TestHsp)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/circleci/project/biopython-1.80.dev0/Tests/test_Blast_Record.py", line 28, in test_str
    "\n".join(l.strip() for l in str(hsp).split("\n")),
  File "/home/circleci/project/biopython-1.80.dev0/build/lib.linux-x86_64-3.9/Bio/Blast/Record.py", line 245, in __str__
    lines.append(f"Query:{self.query_start:>8} {self.query} {self.query_end}")
TypeError: unsupported format string passed to NoneType.__format__

----------------------------------------------------------------------

Was:

lines.append(
                "Query:%8s %s %s" % (self.query_start, self.query, self.query_end)
)

PR used:

lines.append(f"Query:{self.query_start:>8} {self.query} {self.query_end}")

If the value is None, then %s gives the string "None", likewise %8s with padding:

>>> "%8s" % None
'    None'

However, while f"{None}" gives the string too, the string align formatting fails:

>>> f"{None:>8}"
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: unsupported format string passed to NoneType.__format__

[codecov]

Codecov Report

Merging #3724 (6b52163) into master (70aaa34) will decrease coverage by 1.69%.
The diff coverage is 43.28%.

@@            Coverage Diff             @@
##           master    #3724      +/-   ##
==========================================
- Coverage   83.77%   82.08%   -1.70%     
==========================================
  Files         314      294      -20     
  Lines       52512    49392    -3120     
==========================================
- Hits        43994    40543    -3451     
- Misses       8518     8849     +331     

Impacted Files	Coverage Δ
Bio/AlignIO/FastaIO.py	93.93% <0.00%> (ø)
Bio/AlignIO/MsfIO.py	66.17% <0.00%> (ø)
Bio/Blast/Applications.py	84.39% <0.00%> (ø)
Bio/Blast/NCBIXML.py	91.96% <0.00%> (ø)
Bio/ExPASy/Prosite.py	81.50% <0.00%> (ø)
Bio/ExPASy/ScanProsite.py	30.15% <0.00%> (ø)
Bio/ExPASy/__init__.py	34.61% <0.00%> (ø)
Bio/File.py	87.20% <0.00%> (ø)
Bio/HMM/MarkovModel.py	89.47% <ø> (ø)
Bio/HMM/Trainer.py	96.61% <0.00%> (ø)
... and 72 more

---

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[peterjc]

Cross reference https://bugs.python.org/issue45165 for the use of f-string alignment with None.