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human v1.0.1 #97

Merged
merged 24 commits into from
Apr 3, 2019
Merged

human v1.0.1 #97

merged 24 commits into from
Apr 3, 2019

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haowang-bioinfo
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Main improvements in this PR:

I hereby confirm that I have:

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

JonathanRob and others added 24 commits March 18, 2019 15:54
Starting with an exact copy of RAVEN's writeYaml function.
- All "names:" entries are now enclosed in double quotes.
- Subsystems have been converted to lists, even when they contain one value.
- All "annotation:" fields are now excluded from the yaml.
Much of the metadata is currently hard-coded, but this can be updated with future model iterations.
- Instead of manually coding the necessary metadata, now arrange these info into the existing fields in RAVEN and extract out accordingly by this refactoring.
- Change filename from issue71 to addMetaData
Additional changes with consensus are added here:
- Reformat EC-number in eccodes field
- Remove rxnComps field
- Turn `version` into a blank field
- Initialize rxnConfidenceScores field  with zero
feat: add metadata and miscellaneous adjustments
This update is implemented by running script `miscModelCurationScript_20190323.m`:
- metadata is incoporated both in mat and yaml files according to #71
- reformat EC-number in `eccodes` field, as discussed in #93
- remove `rxnComps` field, according to #184 in RAVEN
- empty `version` field to enable a simple and clear work flow
- initialize `rxnConfidenceScores` field with zero, as discussed in #48
- Adapt from RAVEN function exportForGit
feat: enable automatic human-GEM release
@haowang-bioinfo haowang-bioinfo merged commit ebec0f4 into master Apr 3, 2019
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4 participants