[Debian-med-packaging] Bug#1086156: ftbfs: test failure: DSSP failed to produce an output

[Étienne Mollier]

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 <emollier at 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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