[Debian-med-packaging] Bug#911874: python-pyfaidx FTBFS: tests fail with Python 3.7: RuntimeError: generator raised StopIterationj

[Helmut Grohne]

Source: python-pyfaidx
Version: 0.5.4-1
Severity: serious
Tags: ftbfs

python-pyfaidx fails to build from source in unstable. Its test suite
has lots of these:

| ======================================================================
| ERROR: test_reverse_iter (test_FastaRecord_iter.TestFastaRecordIter)
| ----------------------------------------------------------------------
| Traceback (most recent call last):
|   File "/<<PKGBUILDDIR>>/pyfaidx/__init__.py", line 808, in __iter__
|     raise StopIteration
| StopIteration
| 
| The above exception was the direct cause of the following exception:
| 
| Traceback (most recent call last):
|   File "/<<PKGBUILDDIR>>/tests/test_FastaRecord_iter.py", line 30, in test_reverse_iter
|     expect = list(chain(*([line[::-1] for line in record][::-1] for record in Fasta('data/genes.fasta', as_raw=True))))
|   File "/<<PKGBUILDDIR>>/tests/test_FastaRecord_iter.py", line 30, in <genexpr>
|     expect = list(chain(*([line[::-1] for line in record][::-1] for record in Fasta('data/genes.fasta', as_raw=True))))
|   File "/<<PKGBUILDDIR>>/tests/test_FastaRecord_iter.py", line 30, in <listcomp>
|     expect = list(chain(*([line[::-1] for line in record][::-1] for record in Fasta('data/genes.fasta', as_raw=True))))
| RuntimeError: generator raised StopIteration
| 
| Name                  Stmts   Miss  Cover   Missing
| ---------------------------------------------------
| pyfaidx/__init__.py     699    140    80%   14-15, 165, 170, 293, 336-343, 346, 356-363, 373-377, 385, 389, 414-415, 440, 443, 479, 481, 487, 540-541, 579, 586-589, 654-657, 700, 729, 744-755, 761, 786, 793, 833, 876-887, 910, 922, 926, 928, 930, 935, 990, 998-999, 1002, 1037, 1044, 1066-1105, 1108, 1117-1137, 1181-1186, 1194-1195, 1233, 1241, 1247-1248
| pyfaidx/cli.py          257    128    50%   22-25, 31-36, 47-50, 78, 80, 91-106, 120-140, 181-182, 186, 190, 192, 195, 203, 208-214, 228, 231, 237-239, 248-250, 256, 265-278, 282, 286-287, 290-293, 308-315, 321-328, 334-342, 348-358, 361
| ---------------------------------------------------
| TOTAL                   956    268    72%
| ----------------------------------------------------------------------
| Ran 134 tests in 9.432s
| 
| FAILED (SKIP=36, errors=2)
| E: pybuild pybuild:338: test: plugin custom failed with: exit code=1: set -e; \
|                 python3.7 -m "nose" --with-coverage --cover-package=pyfaidx
| dh_auto_test: pybuild --test --test-nose -i python{version} -p "3.7 3.6" --test --system=custom "--test-args=set -e; \\\
|                 {interpreter} -m \"nose\" --with-coverage --cover-package=pyfaidx" returned exit code 13
| make[1]: *** [debian/rules:18: override_dh_auto_test] Error 25
| make[1]: Leaving directory '/<<PKGBUILDDIR>>'
| make: *** [debian/rules:10: build] Error 2
| dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2

Looks like this has started failing, because Python 3.7 has become a
supported Python version and Python 3.7 is stricter about generators.

Helmut