yeast 8.5.0

[edkerk]

Main improvements in this PR:

• Fixes:
  • combine glycolysis + gluconeogenesis as single KEGG pathway (PR fix: combine glycolysis + gluconeogenesis #251)
  • rxn: corrects grRule of r_4590 (closes fix: wrong annotation for gene YGR191W for rxn r_4590 #252)
  • met: corrects name of s_1218 (closes fix: Wrong annotation for s_1218 #254)
  • saveYeastModel handles Unicode characters (PR fix-rxn/met: solves #252 and #254 #255)
  • indentation of yeastGEM.yml (contributes to feat: add yaml validation #236)
• Features:
  • memote as GitHub Action for pull requests (PR Feat/memote #162)
  • old subSystems changed to reaction annotation (in rxnMiriams or rxnKEGGpathways) (PR Chore: update COBRA+RAVEN toolboxes #253)
• Chore:
  • update dependencies in *requirements.txt (PR chore: update *requirements.txt #256)
  • minor changes in model file formatting due to updates in COBRA+RAVEN toolboxes (PR Chore: update COBRA+RAVEN toolboxes #253)
• Refactor:
  • follow standard-GEM specifications (PR refactor: standard-GEM #257)
  • rename master and devel branches to main and develop (PR chore: change branch names #261)

Also rename your local branches to main and develop:

git branch -m master main
git branch -m devel develop
git fetch origin
git branch -u origin/main main
git branch -u origin/develop develop
git remote set-head origin -a

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Selected main as a target branch (top left drop-down menu)
• If needed, asked first in the Gitter chat room about this PR

[edkerk]

@mihai-sysbio Not sure why memote-history.yml contains the step Memote short run (line 42), but should its containing command not at least include --ignore-git? This was not problematic in recent commits/PRs as the model file hadn't changed (see for instance here).

[mihai-sysbio]

Not sure why memote-history.yml contains the step Memote short run (line 42)

I see that the memote run action runs only on pull_request, whereas the memote history runs on push, which happens more often.

but should its containing command not at least include --ignore-git?

There is a hint in this line from memote:

"--ignore-git", is_flag=True, help="Avoid checking the git repository status."

This flag is needed only if the model has been modified without having the changes committed/stashed, e.g. by writing a BiGG compliant model, exactly how it is the case for the memote run action. Instead, memote history runs on the unchanged model.

[edkerk]

@mihai-sysbio Aha, thanks for the explanation. But then I don't understand why memote history fails.

[mihai-sysbio]

The error appears to be interspersed with the memote output, here are the relevant lines:

Committing result and changing back to working branch.
Storing result '03ee7535d608b89812b01f3fa1660b9ce355170b'.
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.9.5/x64/bin/memote", line 8, in <module>
    sys.exit(cli())
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/memote/suite/cli/runner.py", line 289, in run
    repo.git.commit(
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/git/cmd.py", line 545, in <lambda>
    return lambda *args, **kwargs: self._call_process(name, *args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/git/cmd.py", line 1011, in _call_process
    return self.execute(call, **exec_kwargs)
  File "/opt/hostedtoolcache/Python/3.9.5/x64/lib/python3.9/site-packages/git/cmd.py", line 828, in execute
    raise GitCommandError(command, status, stderr_value, stdout_value)
git.exc.GitCommandError: Cmd('git') failed due to: exit code(128)
  cmdline: git commit --message chore: add result for 03ee7535d608b89812b01f3fa1660b9ce355170b
  stderr: 'Author identity unknown
 
*** Please tell me who you are.

Run

  git config --global user.email "you@example.com"
  git config --global user.name "Your Name"

to set your account's default identity.
Omit --global to set the identity only in this repository.

fatal: empty ident name (for <runner@fv-az212-186.zlodpucb4l4udavnfxg5s20dva.cx.internal.cloudapp.net>) not allowed

The line that looks weirdest to me is:

cmdline: git commit --message chore: add result for 03ee7535d608b89812b01f3fa1660b9ce355170b

[mihai-sysbio]

It doesn't hurt to try out your idea @edkerk. Commit c897a25 adds the flag to instruct memote to not inspect the repository installation, so I'm hoping this does the trick (although I don't understand why it worked so far and now it doesn't).

[feiranl]

I reviewed all changes for the fix part

[mihai-sysbio]

Looks good to me, although I am mostly trusting previous reviews here.

[edkerk]

Seems like my suggestion didn't work though. The step Memote short run now does not submit the results to gh-pages (which it tried to do previously with cmdline: git commit --message chore: add result for 03ee7535d608b89812b01f3fa1660b9ce355170b, so when the history report is made it doesn't find the most recent changes:

In output from the step Compute Memote history on push, you can see it reads results from gh-pages but does not find the latest commit with changed model (03ee753):

Line 10: Obtaining history of results from the deployment branch gh-pages. (it reads results.db?)

Line 11534-11535: Loading result from '03ee7535d608b89812b01f3fa1660b9ce355170b'.
error: Could not load result '03ee7535d608b89812b01f3fa1660b9ce355170b'.

The problem seems to be that in the step Memote short run it does not have the proper credentials for pushing to gh-pages. In the step Auto-commit results the pushing of history_report.html to gh-pages is not handled directly by memote but rather by the action stefanzweifel/git-auto-commit-action@v4.4.0 (where the user name is set!). I'll try to see what happens when setting global user name to memote-bot, bare with me...

[edkerk]

The history report is still not working exactly as intended (see comment), but will merge this PR now as it at least introduces the memote CI to the repo.