Hi Aaron, Hi Gregor, Aaron M. Ucko, on 2021-02-21 17:57:37 -0500: > Étienne Mollier writes: > > > I have been looking in the issue below in the package > > libbio-db-ncbihelper-perl. If I understood correctly, the main > > point of the package is to rely on resources made available on > > the Internet. > > I'm not sure I've been personally involved with this package, but that's > my understanding as well. > > > a perhaps magic index to refer to human genome, but maybe it is > > a "well known index".) > > Per [1], taxonomic ID *numbers* are stable in general, but the > associated *names* occasionally change to reflect improved > understandings of the underlying science. AFAICT from [2] (as linked > from [3]), this change is correct and legitimate; moreover, it looks > like 'Actinobacteria' should now appear in $n->common_names, if anyone > wants to verify that. > > [1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7408187/ > [2] > https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003920 > [3] > https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1760&lvl=3&lin=f&keep=1&srchmode=1&unlock
Thank you very much! I humbly have to admit I know nothing to
taxonomy classification, but it's nice to know that people try
to keep improving one of the references. This was enough to
brighten my day. :)
Will see how upstream changes the entry, but given our thoughts,
I would guess updating the expected $n->scientific_name with the
new value would be the way to go. Out of curiosity, from the
$n->common_names I obtained the character string:
authorityActinomycetia (Stackebrandt et al. 1997) Salam et al. 2020
gregor herrmann <[email protected]> writes:
> I see your point, and in the end it's a matter of taste, I guess; or
> a choice between two bad options:
> - skipping tests and missing bugs
> - enabling tests and having to deal with failures because of internet
> problems, server problems, changes in returned data etc.
>
> Having seen too much of the latter, I prefer the former but as I
> said, that's not the only option :)
In doubt, since the package is team maintained and developer
time is precious, I believe I will defer to your experience.
I replace the "needs-internet" by "superficial", and set
NO_NETWORK_TESTING=1 in debian/tests/pkg-perl/smoke-env.
Hopefully if further offline testing became possible, that would
allow us to remove the "superficial" flag in the future.
> As a side note to the autopkg-tests: The "heavy" tests don't exists,
> that was just an idea when we started with the framework, so you can
> remove the last paragraph.
Thanks for the side note, I removed the entry.
Thanks again to you both for your time,
Kind Regards,
--
Étienne Mollier <[email protected]>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/2, please excuse my verbosity.
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