Code

Human 1.4#180

Code

Merged

haowang-bioinfo merged 44 commits intomasterSysBioChalmers/Human-GEM:masterfrom develSysBioChalmers/Human-GEM:develCopy head branch name to clipboardJun 12, 2020

+404,176-426,431

Commits

Commits on May 17, 2020

• fix: systematically add double quote to string elements in Yaml file

  haowang-bioinfo

  committed
  c777edb

• fix: add double quote to subSystems elements

  haowang-bioinfo

  committed
  ba414d3

• fix: adapt importHumanYaml to the addition of double quote

  haowang-bioinfo

  committed
  1bd6a01

• chore: update Yaml file

  Show description for 4f9c52e
  haowang-bioinfo

  committed
  4f9c52e

• feat: enable silent mode in importHumanYaml

  Show description for cadea11
  haowang-bioinfo

  committed
  cadea11

• fix: simplify testYamlConversion so that input value is not needed

  Show description for 524ca3c
  haowang-bioinfo

  committed
  524ca3c

Commits on May 18, 2020

• Merge pull request #170 from SysBioChalmers/fix/YamlQuotes

  Show description for 82d430f
  haowang-bioinfo

  authored
  82d430f

Commits on May 20, 2020

• feat: add basic yamllint workflow

  mihai-sysbio

  committed
  2808904

• feat: relax some yamllint errors to warnings

  mihai-sysbio

  committed
  460a384

Commits on May 21, 2020

• fix: HumanGEM.yml change HMR_3851 subsystem to Miscellaneous

  Show description for 30ab94a
  JonathanRob

  committed
  30ab94a

• fix: HumanGEM.yml consistent case for "Metabolism of other amino acids"

  Show description for 9368324
  JonathanRob

  committed
  9368324

• fix: HumanGEM.yml delete non-human HMR_4362 reaction

  Show description for ea835e4
  JonathanRob

  committed
  ea835e4

• doc: addBoundaryMets change default setting and update comments

  JonathanRob

  committed
  1f1e28d

• feat: removeBoundaryCompartments script removes the boundary compartment

  JonathanRob

  committed
  167ecb6

• remove boundary compartment from HumanGEM

  JonathanRob

  committed
  4e9d95f

Commits on May 26, 2020

• refactor: variable reuse in switch

  mihai-sysbio

  committed
  030907a

Commits on May 27, 2020

• fix: yaml indentation

  mihai-sysbio

  committed
  d075b07

• fix: gh action for devel and master only

  mihai-sysbio

  committed
  bd13d3f

• refactor: print to error console only if testConversion fails

  mihai-sysbio

  committed
  4a7b33c

• feat: improve yaml parsing, add cobrapy to workflow

  mihai-sysbio

  committed
  6f0a133

Commits on Jun 2, 2020

• fix: adjust the recognition patter of last element in array

  Show description for 56706c2
  haowang-bioinfo

  committed
  56706c2

• chore: update the content by appending rxnMAID field

  Show description for cf1521a
  haowang-bioinfo

  committed
  cf1521a

• chore: reformat rxnMAID elements

  Show description for f0152bb
  haowang-bioinfo

  committed
  f0152bb

• Merge pull request #175 from SysBioChalmers/feat/rxnMAID

  Show description for e8d4799
  haowang-bioinfo

  authored
  e8d4799

Commits on Jun 5, 2020

• Merge pull request #173 from SysBioChalmers/feat/yaml-workflow

  Show description for d5c8ddf
  haowang-bioinfo

  authored
  d5c8ddf

• Merge devel into fix/misc_small_fixes

  Show description for d70cc0b
  haowang-bioinfo

  committed
  d70cc0b

Commits on Jun 6, 2020

• fix: HumanGEM.yml re-apply changes after branch update

  JonathanRob

  committed
  e4dff6f

• style: cleanup authorship and timestamps from code

  mihai-sysbio

  committed
  8de5647

• style: replace authorship by commit trailer

  Show description for 0fcb7a3
  mihai-sysbio

  committed
  0fcb7a3

Commits on Jun 7, 2020

• Merge pull request #171 from SysBioChalmers/fix/misc_small_fixes

  Show description for 4478a16
  haowang-bioinfo

  authored
  4478a16

• chore: sync JSON file content with model

  Show description for 686a8e2
  haowang-bioinfo

  committed
  686a8e2

• Merge pull request #178 from SysBioChalmers/fix/syncJsonFile

  Show description for 6089d7f
  haowang-bioinfo

  authored
  6089d7f

Commits on Jun 8, 2020

• revert previous commit to prepare for HumanGEM.yml changes on devel

  JonathanRob

  committed
  2073170

• Merge branch 'devel' into removeBoundaryComp

  JonathanRob

  committed
  beba549

• doc: remove date and author line according to new code format

  JonathanRob

  committed
  3ca6284

• fix: importHumanYaml now correctly parses one-sided equations

  Show description for 81ede5d
  JonathanRob

  committed
  81ede5d

• feat: importHumanYaml remove "unconstrained" field if no boundary mets

  JonathanRob

  committed
  1e8df7f

• feat: HumanGEM.yml remove boundary compartment

  JonathanRob

  committed
  7c90fe6

• fix: removeBoundaryCompartment.m sync metabolite annotation JSON

  JonathanRob

  committed
  f578cc6

• Merge pull request #177 from SysBioChalmers/style/authorship-timestamp

  Show description for 0c82227
  haowang-bioinfo

  authored
  0c82227

Commits on Jun 9, 2020

• doc: clean authorship and date

  haowang-bioinfo

  committed
  fd7b1ac

• fix: disable importing of unconstrained field

  Show description for 8937dd7
  haowang-bioinfo

  committed
  8937dd7

• Merge branch 'devel' into removeBoundaryComp

  haowang-bioinfo

  authored
  3a1fd84

Commits on Jun 10, 2020

• Merge pull request #179 from SysBioChalmers/removeBoundaryComp

  Show description for e972524
  haowang-bioinfo

  authored
  e972524