[Debian-med-packaging] Bug#996794: ncbi-acc-download: autopkgtest failure with python-biopython 1.79+dfsg-1~0exp0 in experimental

[Étienne Mollier]

Source: ncbi-acc-download
Version: 0.2.7-1
Severity: important
Tags: ftbfs

Dear Maintainer,

I am trying to assess the side effects of an upgrade of the
package python-biopython to 1.79 to its reverse dependencies.
Pseudo-excuses look alright, except for ncbi-acc-download [1].

[1]: https://release.debian.org/britney/pseudo-excuses-experimental.html
[2]: https://ci.debian.net/data/autopkgtest/unstable/amd64/n/ncbi-acc-download/15982166/log.gz

The full log [2] shows variations around the following symptom:

	__________________ test_download_wgs_parts_supercontig_retry ___________________
	
	req = <requests_mock.mocker.Mocker object at 0x7fc14613fb20>
	
	    def test_download_wgs_parts_supercontig_retry(req):
	        cfg = Config(format="genbank")
	        supercontig = open(full_path('supercontig.gbk'), 'rt')
	        req.get(ENTREZ_URL, response_list=[
	            {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}},
	            {"body": open(full_path('supercontig_full.gbk'), 'rt')}
	        ])
	    
	        outhandle = wgs.download_wgs_parts(supercontig, cfg)
	        supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
	>       assert outhandle.getvalue() == supercontig_full.read()
	E       AssertionError: assert 'LOCUS       ...671808)\n//\n' == 'LOCUS       ...ccctaac\n//\n'
	E         - LOCUS       NC_007194                 60 bp    DNA     linear   CON 03-APR-2018
	E         ?                                  ^^^^^^^                            ^^ ^^^   ^^
	E         + LOCUS       NC_007194            4918979 bp    DNA     linear   CON 11-NOV-2009
	E         ?                                  ^^^^^^^                            ^^ ^^^   ^^
	E           DEFINITION  Aspergillus fumigatus Af293 chromosome 1, whole genome shotgun
	E                       sequence.
	E           ACCESSION   NC_007194...
	E         
	E         ...Full output truncated (22 lines hidden), use '-vv' to show
	
	test_wgs.py:145: AssertionError

To be honest, I don't know whether this is caused by a bug in
biopython, or if it could be normal from ncbi-acc-download to
issue a slightly different output.  Testing against biopython
1.78 does not raise that issue.

Since the test suite is run at build time, ncbi-acc-download
would also fail to build from source if python-biopython were to
be upgraded, hence the tag.  Note that I think the package
downloads resources from the Internet during the test at build
time too, so would might be a serious policy violation, but I
haven't checked for sure yet.

Kind Regards,
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/4, please excuse my verbosity.
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