I had a fresh look to the python-biopython test failure and noticed something else, much ealier in the test log:
test_PDB_DSSP ...
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/Bio/PDB/DSSP.py:199: UserWarning:
Configuration error:
The attempt to retrieve compound information for "ALA" failed.
This information is searched for in a CCD file called components.cif or
components.cif.gz which should be located in one of the following
directories:
"/usr/share/libcifpp"
"/var/cache/libcifpp"
"/usr/share/libcifpp"
"/usr/share/libcifpp"
(Note that you can add a directory to the search paths by setting the
LIBCIFPP_DATA_DIR environmental variable)
On Linux an optional cron script might have been installed that
automatically updates
components.cif and mmCIF dictionary files. This script only works when
the file
libcifpp.conf contains an uncommented line with the text:
update=true
If you do not have a working cron script, you can manually update the
files
in /var/cache/libcifpp using the following commands:
curl -o /var/cache/libcifpp/components.cif
https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
curl -o /var/cache/libcifpp/mmcif_pdbx.dic
https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic
curl -o /var/cache/libcifpp/mmcif_ma.dic
https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic
The current order of compound factory objects is:
CCD components.cif resource
Unknown compound: ALA
Unknown compound: ARG
Unknown compound: ASN
Unknown compound: ASP
Unknown compound: CYS
Unknown compound: GLN
Unknown compound: GLU
Unknown compound: GLY
Unknown compound: HIS
Unknown compound: HOH
Unknown compound: ILE
Unknown compound: LEU
Unknown compound: LYS
Unknown compound: MET
Unknown compound: PHE
Unknown compound: PRO
Unknown compound: SER
Unknown compound: SO4
Unknown compound: THR
Unknown compound: TRP
Unknown compound: TYR
Unknown compound: VAL
Missing compound information for ALA
Missing compound information for THR
Missing compound information for PRO
Missing compound information for ILE
Missing compound information for HIS
Missing compound information for LEU
Missing compound information for LYS
Missing compound information for GLY
Missing compound information for ASP
Missing compound information for ASN
Missing compound information for CYS
Missing compound information for ARG
Missing compound information for TYR
Missing compound information for SER
Missing compound information for GLN
Missing compound information for GLU
Missing compound information for VAL
Missing compound information for TRP
Missing compound information for PHE
Missing compound information for MET
Missing compound information for SO4
Missing compound information for HOH
warnings.warn(err)
FAIL
Right now, this feels to me like something changed in the
libcifpp in such a way that more configuration is expected from
end users. libcifpp-data does ship some of the expected files:
$ dpkg -L libcifpp-data | grep share/libcifpp
/usr/share/libcifpp
/usr/share/libcifpp/mmcif_ddl.dic
/usr/share/libcifpp/mmcif_ma.dic
/usr/share/libcifpp/mmcif_pdbx.dic
components.cif is missing though, and from what I see getting
the file manually from the internet, it is rather heavyweight:
422M, so not sure whether its place is in the package. It is
large, but I don't believe is running into the limits of the
archive yet.
In hope this helps,
--
.''`. Étienne Mollier <emoll...@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/2, please excuse my verbosity
`-
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