Adapter improvements

[kvikshaug]

• Define schemas for modification/adapter requests
  • Changed: Added separate namespace field to compounds
• Use miriam db names consistently
• Look up metabolites case insensitively (our models don't have the right casing for chebi for example)
• Improve docstrings for adapter functions and the metabolite/reaction lookup helpers
• Drop feature to accept custom provided model for simulations

[codecov-io]

Codecov Report

Merging #122 into devel will decrease coverage by 0.48%. The diff coverage is 72.94%.

@@            Coverage Diff             @@
##            devel     #122      +/-   ##
==========================================
- Coverage   73.59%   73.11%   -0.49%     
==========================================
  Files          21       21              
  Lines         731      729       -2     
==========================================
- Hits          538      533       -5     
- Misses        193      196       +3

Impacted Files	Coverage Δ
src/model/schemas.py	100% <100%> (ø)	:arrow_up:
src/model/exceptions.py	100% <100%> (+5.88%)	:arrow_up:
src/model/modeling/cobra_helpers.py	56.25% <56.25%> (-29.47%)	:arrow_down:
src/model/modeling/adapter.py	66.42% <62.5%> (+1.63%)	:arrow_up:
src/model/resources.py	72.28% <82.35%> (-1.72%)	:arrow_down:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 155b93f...bd76623. Read the comment docs.