Human 1.7

[haowang-bioinfo]

Main improvements in this PR:

• Features (PR feat: add MA met ids to metabolites.tsv #245):
  • a new column metMAID is added to metabolites.tsv, according to the plan proposed in feat: new sets of id for reactions and metabolites #174
• Features (PR Rhea annotations #241):
  • update reactions.tsv by adding associations to Rhea ids that mapped to 590 rxns so far
• Fixes (PR [FIX] changed pubchem ID for m01778c #240):
  • update annotation for mets m01778 and m02646, as suggested in Pubchem compound id duplicated/wrong #239:
• Features (PR Feat: Evaluation of GEM-based gene essentiality predictions #237):
  • add new function evalGeneEssentialityPred that can be used to assess gene essentiality predictions made by a GEM
• Features (PR feat: complete MAR ids by filling blank fields #234):
  • complete the ids of rxnMAID in reactions.tsv by filling blank fields, as agreed in feat: new sets of id for reactions and metabolites #174
• Fixes (PR fix: remove the extra space at the end of the subsystem and reaction names #230):
  • remove the extra space at the end of the subsystem and reaction names
• Style (PR style: rename functions #228):
  • rename functions as proposed in style: change of function names #227
    • annotateModel --> annotateGEM
    • importHumanYaml --> importYaml
    • writeHumanYaml --> exportYaml
  • replace branch devel with develop
• Style (PR Move deprecated data and code to new .deprecated directory #223):
  • re-organize files and folders as discussed in style: whether to preserve previously used curation scripts or not? #190
    • move files, scripts, and models in data/ and code/ that are no longer maintained or in use to a .deprecated folder
    • add README file for data and code directories

[mihai-sysbio]

Looks good to me!