[Debian-med-packaging] Bug#1130078: python-bcbio-gff: the autopkgtest does not actually catch errors

[Alexandre Detiste]

Source: python-bcbio-gff
Version: 0.7.1-2
Severity: normal
X-Debbugs-Cc: Étienne Mollier <emollier at debian.org>

Hi,

The autopkgtest succeeds where it should fail.

https://salsa.debian.org/med-team/python-bcbio-gff/-/jobs/9180808



Read in GFF2 and write out as GFF3. ... ok
t_gff3_to_gff3 (__main__.OutputTest.t_gff3_to_gff3)
Read in and write out GFF3 without any loss of information. ... ok
t_write_fasta (__main__.OutputTest.t_write_fasta)
Include FASTA records in GFF output. ... ERROR
t_write_from_recs (__main__.OutputTest.t_write_from_recs)
Write out GFF3 from SeqRecord inputs. ... ERROR
t_write_seqrecord (__main__.OutputTest.t_write_seqrecord)
Write single SeqRecords. ... ERROR
======================================================================
ERROR: t_basic_solid_parse (__main__.SolidGFFTester.t_basic_solid_parse)
Basic parsing of SOLiD GFF results files.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 381, in t_basic_solid_parse
    assert test_feature.location.nofuzzy_start == 102716
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'SimpleLocation' object has no attribute 'nofuzzy_start'
======================================================================
ERROR: t_jgi_gff (__main__.GFF2Tester.t_jgi_gff)
Parsing of JGI formatted GFF2, nested using transcriptId and proteinID
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 480, in t_jgi_gff
    assert tfeature.location.nofuzzy_start == 37060
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'SimpleLocation' object has no attribute 'nofuzzy_start'
======================================================================
ERROR: t_write_fasta (__main__.OutputTest.t_write_fasta)
Include FASTA records in GFF output.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 656, in t_write_fasta
    rec.features = [SeqFeature(FeatureLocation(0, 20), type="gene", strand=1,
                    ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                               qualifiers=qualifiers)]
                               ^^^^^^^^^^^^^^^^^^^^^^
TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'
======================================================================
ERROR: t_write_from_recs (__main__.OutputTest.t_write_from_recs)
Write out GFF3 from SeqRecord inputs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 630, in t_write_from_recs
    top_feature = SeqFeature(FeatureLocation(0, 20), type="gene", strand=1,
                                                      qualifiers=qualifiers)
TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'
======================================================================
ERROR: t_write_seqrecord (__main__.OutputTest.t_write_seqrecord)
Write single SeqRecords.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 673, in t_write_seqrecord
    rec.features = [SeqFeature(FeatureLocation(0, 20), type="gene", strand=1,
                    ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                               qualifiers=qualifiers)]
                               ^^^^^^^^^^^^^^^^^^^^^^
TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'
----------------------------------------------------------------------
Ran 40 tests in 0.096s
FAILED (errors=5)
autopkgtest [11:15:46]: test run-unit-test: -----------------------]
autopkgtest [11:15:46]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
run-unit-test        PASS
autopkgtest [11:15:46]: test autodep8-python3: preparing testbed
autopkgtest [11:15:56]: testbed dpkg architecture: amd64
autopkgtest [11:15:56]: testbed apt version: 3.1.16