[Debian-med-packaging] Bug#1098530: ariba: FTBFS: TestAssembly.test_assemble_with_spades fails

[Adrian Bunk]

On Fri, Feb 21, 2025 at 11:26:11PM +0000, Santiago Vila wrote:
> Package: src:ariba
> Version: 2.14.7+ds-7
> Severity: serious
> Tags: ftbfs trixie sid
>...
> =================================== FAILURES ===================================
> ____________________ TestAssembly.test_assemble_with_spades ____________________
> 
> self = <ariba.tests.assembly_test.TestAssembly testMethod=test_assemble_with_spades>
> 
>     @unittest.skipUnless(extern_progs.exe('spades'), "Spades assembler is optional and is not configured")
>     def test_assemble_with_spades(self):
>         '''test _assemble_with_spades'''
>         reads1 = os.path.join(data_dir, 'assembly_test_assemble_with_spades_reads_1.fq')
>         reads2 = os.path.join(data_dir, 'assembly_test_assemble_with_spades_reads_2.fq')
>         tmp_dir = 'tmp.test_assemble_with_spades'
>         tmp_log = 'tmp.test_assemble_with_spades.log'
>         with open(tmp_log, 'w') as tmp_log_fh:
>             print('First line', file=tmp_log_fh)
>             common.rmtree(tmp_dir)
>             #using spades_options=" --only-assembler" because error correction cannot determine quality offset on this
>             #artificial dataset
>             a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed', tmp_dir, 'not_needed_for_this_test.fa',
>                                   'not_needed_for_this_test.bam', tmp_log_fh, 'not needed',
>                                   assembler="spades", spades_options=" --only-assembler")
>             a._assemble_with_spades()
> >       self.assertTrue(a.assembled_ok)
> E       AssertionError: False is not true
> 
> ariba/tests/assembly_test.py:128: AssertionError
> ----------------------------- Captured stderr call -----------------------------
>...

Looking also at

https://tracker.debian.org/pkg/spades

 Marked for autoremoval on 02 May: #1100877

Migration status for spades (3.15.5+dfsg-8 to 4.0.0+dfsg1-2): BLOCKED: Rejected/violates migration policy/introduces a regression
Issues preventing migration:
∙ ∙ autopkgtest for shovill/1.1.0-9: amd64: Regression or new test ♻ (reference ♻)
∙ ∙ autopkgtest for unicycler/0.5.1+dfsg-3: amd64: Regression or new test ♻ (reference ♻)

I wonder whether spades 4.0.0+really3.15.5 might be the correct solution 
for ariba/shovill/unicycler in trixie.

cu
Adrian