Re: python-biopython test failure with libcifpp changes (Bug #1086156)

Hi Étienne,

Of course, it would be easiest to include the components.cif file in 
libcifpp. However, this file changes weekly and it is huge. Two good 
reasons not to do it.

What I did for density-fitness e.g. is include a subset of 
components.cif large enough for testing. That way, you can avoid having 
to download the entire CCD file for just some simple tests on basic 
proteins. Have a look at the density-fitness debian/tests files, perhaps 
this may help you solve your problem.

There are similar ways to provide a dummy components.cif file. See 
https://pdb-redo.github.io/libcifpp/resources.html for more information.

As an alternative, I'm thinking about packaging a subset with libcifpp. 
Dictionaries can be stacked already, so having a subset might be a 
simple way out of this. But the question then is, what to include in the 
subset. I did some counting on components in PDB entries to see if there 
is a clear cut-off, but couldn't find one. And only including the 
standard amino acids and nucleic acids is a bit too limited to be useful.

-maarten


Op 29-10-2024 om 22:29 schreef Étienne Mollier:
> Hi Maarten,
>
> I'm dealing with python-biopython release critical bug #1086156,
> and I was wondering whether the 422M dataset components.cif
> wouldn't be worth injecting into the libcifpp-data package, to
> facilitate the handling of data by end users?  I guess that sure
> would make the package rather large, so I can understand if this
> is deemed excessive; although I believe some Debian packages do
> happen to be a little larger, although I don't really have
> specific examples in mind.
>
> https://bugs.debian.org/1086156
>
> If there are blockers, then another option for me might be to
> skip the test, as internet access at build time is not an
> option, but it means missing out on other genuine issues
> affecting libcifpp support in python-biopython.  The thing is,
> I'm not sure yet whether the test failure results from issues in
> python-biopython or libcifpp-data.
>
> Have a nice day,  :)