pyontutils
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tgbugs
python utilities for working with ontologies
Ontology load requested that includes all of the ttls in NIF-Ontology from the dev branch, mondo, uberon, emapa, and fma_slim. Due to time constraints and the hardcoded nature of the...
This may need to be a data fix because we roll both up into molecular phenotype and there the dedupe does happen.
goes looking for byCol (which still need to be removed) and then gets confused thinking there is already a column with the header name or something like that
If `/home/testuser/.local/share/pyontutils/curie_map.yaml` was installed by a user via pip, then a newer version installed by the system will be shadowed `/usr/share/pyontutils/curie_map.yaml`. This is a direct manifestation of a bug related...
The abstractions are close enough and both need some of the functionality that the other offers.
clifun.Options can be put to much wider use (e.g. when eventually moved to orthauth) by switching the order of args and defaults so that it can be imported from a...
I think that it should probably use the current commit because last commit per file can be recovered from that, but not the reverse.
Right now there is a missing level of indirection between the olr sourced from the auth config and the repo that is used or can be set at runtime. This...
Something like `builder` or similar, but need to come up with a better name. These depend on git and thus fall outside the core. Alternately, come up with a better...
There are many scripts that depend on resources and other repos and on being in a git repo which need to be separated from the core so that they can...