I have no idea how to interpret the error message generated by the YAML validation check (I figured out the issue by manually inspecting each of the changes I made, which is not unreasonable, but it would've been nice if the error message had given me any hints about what I should've been looking for)

I am a little bit afraid of this kind of changes. In case reviewers merge this PR, I tag this PR for draft first. Discussions will come later in the Issue page.

nope I still don't know why the YAML validation test is failing

I'll have a look, perhaps I can spot something

First thing I'm trying is to run the validation locally on this PR with

python code/test/sanityCheck.py

This returns the same error

Traceback (most recent call last):
File "/Human-GEM/code/test/sanityCheck.py", line 105, in
checkUnusedEntities(model, "genes")
File "/Human-GEM/code/test/sanityCheck.py", line 96, in checkUnusedEntities
assert len(unused_entities) == 0, f"Found unused {{entity_type}}!"
^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: Found unused {entity_type}!

It seems the other PRs are passing this test, so a more in-depth look is required. Sorry I cannot do more at the moment, but I'll try to get back to this tomorrow.

Aha the problem is that MAR03769 was the only reaction that ENSG00000128928 (IVD) was associated with; it clearly should have also been associated with MAR03770, since IVD is an FAD-dependent enzyme, but removing MAR03769 made IVD into an "unused gene"
I'm gonna add ENSG00000128928 to the GPR of MAR03770 unless anyone has any objections to (hopefully) get this to pass the YAML validation test

since @feiranl requested it in #625 and seemed uneasy about this PR, I figured I'd also go through and merge the reaction annotations from the deleted reactions into the kept ones

@Devlin-Moyer I'm glad you figured out the unused gene.
I've pushed a commit on this branch that improves the validation output as suggested above. If you feel this is not the right place, please feel free to remove it from this PR.

@Devlin-Moyer please merge develop and incorporate latest changes to this branch