Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: resolves issues reported in animal GEM repos #382

Merged
merged 5 commits into from
Apr 3, 2022
Merged

fix: resolves issues reported in animal GEM repos #382

merged 5 commits into from
Apr 3, 2022

Conversation

haowang-bioinfo
Copy link
Member

Main improvements in this PR:

  • This PR refactors code for updating animal GEMs, and resolves issues reported in Mouse-GEM:

I hereby confirm that I have:

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

@haowang-bioinfo
fix: change to txt format metabolic task file
6d26d17
@haowang-bioinfo
fix: Inactivate human biomass reaction (MAR13082) by default
51f86ca 
- This is to fix the issue reported in Mouse-GEM issue #11
@haowang-bioinfo
fix: add proper LB and UB to generated draft model
7f5bc44 
- This is to fix the issue reported in Mouse-GEM issue #12
@haowang-bioinfo
feat: turn into a more generic function by adding annPath argument
c56b4eb
@haowang-bioinfo
fix: minor bugs
2708eea 
- have conditional check when adding model fields
- use `isequal` that returns logical scalar value
@haowang-bioinfo haowang-bioinfo mentioned this pull request Apr 2, 2022
Merged
@haowang-bioinfo haowang-bioinfo changed the title fix: resolves issues reported in updating animal GEMs fix: resolves issues reported in animal GEM repos Apr 3, 2022
@haowang-bioinfo
Copy link
Member Author

the failed YAML conversion check should be irrelevant to this PR, which has nothing to do with modifying YAML file

mihai-sysbio
mihai-sysbio approved these changes Apr 3, 2022
View reviewed changes
Copy link
Member

@mihai-sysbio mihai-sysbio left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good to me! The Actions issue is related to the runner, so it could be overlooked for now. I will try to look at the runner early next week.

@haowang-bioinfo haowang-bioinfo merged commit ff109f2 into develop Apr 3, 2022
@haowang-bioinfo haowang-bioinfo deleted the fix/animalGEM-code branch April 3, 2022 08:21
This was referenced May 3, 2022
Merged
Merged
Merged
Merged
@mihai-sysbio mihai-sysbio mentioned this pull request Jun 17, 2022
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@johan-gson johan-gson johan-gson approved these changes

@mihai-sysbio mihai-sysbio mihai-sysbio approved these changes

@JonathanRob JonathanRob Awaiting requested review from JonathanRob

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@haowang-bioinfo @mihai-sysbio @johan-gson