feat: change multiple compartment abbreviations

[JonathanRob]

Main improvements in this PR:

This is a more extensive/exhaustive implementation of #330 to address discussions in #314.

Three Human-GEM compartment abbreviations are changed in the model file, metabolite annotation file, metabolic task files, and the addBoundaryMets function:

Compartment	Abbreviation	New Abbreviation
Extracellular	s	e
Boundary	x	b
Peroxisome	p	x

Since the changes (diffs) are quite large, I implemented the changes with a script changeCompAbbrevs in code/modelCuration/.

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch

[smoretti]

I did not know all your code and files but the ones I know look OK

[mihai-sysbio]

That's neat!
Just so you know, there is a reference to 'x' in a commented line in importYaml, which might be good to either update or delete.

[JonathanRob]

Just so you know, there is a reference to 'x' in a commented line in importYaml, which might be good to either update or delete.

@mihai-sysbio Good catch, I have now removed that line.

[haowang-bioinfo]

I've gone through all the changes that look good to me. @JonathanRob nice work.

though there's a little concern about commit 5e6af0f that marked all these previous metabolite ids as deprecated, this is probably overkill. What we are trying to do here is replacing ids i.e. adapting to the BiGG (or KBase/SEED) scheme (#314), which actually reserved p and s for compartments periplasm and eyespot, respectively. And this commit pre-excluded the possibility of their occurrence in periplasm and/or eyespot (even though HumanGEM doesn't include these compartments at the moment, they might be added later). So this commit appears to be unnecessary and should be abandoned. What do you guys think?

[haowang-bioinfo]

now the changes introduced by #339 led to conflicts in metabolites.tsv

[mihai-sysbio]

It looks to me like we are following the BiGG specification here, but maybe we should reference the source directly.
For ModelSEED the template for Human on the master branch looks fairly compatible with implemented changes.

id	name
c0	Cytosol
e0	Extracellular
a0	Carboxysome
g0	Golgi
l0	Lysosome
m0	Mitochondria
n0	Nucleus
r0	Endoplasmic_Reticulum
x0	Peroxisome

[mihai-sysbio]

Just a ping to advance this PR.
@JonathanRob do you think you can resolve the conflicts?
@haowang-bioinfo is it okay that we are waiting for your review?

[JonathanRob]

Once #343 is merged, the conflicts should be resolved.

[mihai-sysbio]

To avoid future merge conflicts, I think it makes sense to hold off on creating any PRs until the metabolites get renamed. This makes the current PR a priority. @JonathanRob let me know how I can help.

[JonathanRob]

@mihai-sysbio yes, exactly. I will merge #343 to see if that solves the conflict on this PR. If that doesn't work, then I may ask for some help.

[haowang-bioinfo]

@haowang-bioinfo is it okay that we are waiting for your review?

@mihai-sysbio sorry I missed this message