Babel v1.12.0

[gaurav]

Changes in this PR:

• Rewrote part of the HAS_ADDITIONAL_ID logic, so that we add it later in the process so that we can label the additional identifiers without them getting re-sorted by node_factory.create_node().
• Modified the description factory so that it processes lists of identifiers instead of a node.
• Increased ephemeral storage for the Babel pod to 1G so we have a bit more spare capacity before we run out of ephemeral space.
• Made DuckDB files non-temporary (so we don't have to regenerate them if we rebuild something), but added an rsync-to-server.sh script that excludes the DuckDB files when rsyncing the Babel Outputs to a directory.
• KEGG.COMPOUND cross-references in ChEBI are now a list instead of a single ID, which need to be handled separately. Closes KEGG.COMPOUND CURIEs broken in Babel 2025aug17 #493 (7a53ce6).
• Added unique counts for property lists.
• Improved logging and memory usage for createcompendia/chemicals.py.
• Added memory usage logging for exporters/kgx.py and in other parts of write_compendia().
• Added some comments to config.yaml.

Important bug fixes in this release:

• Fix information content comparisons (float instead of string) #467: We were previously sorting information content values alphanumerically instead of numerically, which means we were returning 100 for many nodes that should have had a lower IC value. This is now fixed. Thanks to @uhbrar for catching this!

Filename	2025mar31	2025aug17	Diff	% Diff
Count of CURIEs in all files	677,806,537	688,567,091	+10,760,554	1.59%
Count of cliques in all files	482,038,965	490,614,550	+8,575,585	1.78%
AnatomicalEntity	249,164	249,584	+420	0.17%
BiologicalProcess	68,110	67,929	-181	-0.27%
Cell	12,920	13,175	+255	1.97%
CellLine	38,810	38,810	0	0.00%
CellularComponent	14,676	14,696	+20	0.14%
ChemicalEntity	662,991	4,086,825	+3,423,834	516.42%
ChemicalMixture	529	527	-2	-0.38%
ComplexMolecularMixture	286	276	-10	-3.50%
Disease	628,736	632,330	+3,594	0.57%
Drug	359,131	360,953	+1,822	0.51%
Gene	75,520,611	79,427,652	+3,907,041	5.17%
GeneFamily	27,985	28,050	+65	0.23%
GrossAnatomicalStructure	15,655	15,709	+54	0.34%
MacromolecularComplex	1,258	1,258	0	0.00%
MolecularActivity	203,862	206,636	+2,774	1.36%
MolecularMixture	21,150,406	21,758,582	+608,176	2.88%
OrganismTaxon	3,455,969	3,543,867	+87,898	2.54%
Pathway	52,815	53,125	+310	0.59%
PhenotypicFeature	480,603	483,108	+2,505	0.52%
Polypeptide	188	167	-21	-11.17%
Protein	274,887,335	275,407,170	+519,835	0.19%
Publication	78,061,642	79,773,973	+1,712,331	2.19%
SmallMolecule	221,021,085	221,504,843	+483,758	0.22%
umls	891,770	897,846	+6,076	0.68%