Upgrade manubot to fix pubmed API calls.

[tiwns]

Hello,

I have been successful in using Manubot for previous repositories. However, when setting up a new repository using bash <( curl --location https://github.com/manubot/rootstock/raw/main/setup.bash ), I receive this error in Github Actions: Upgrade Manubot to fix pubmed API calls.

Also, I do not need pubmed for this work.

Thank you.

[dhimmel]

Hmm "Upgrade Manubot to fix pubmed API calls." is the commit message for b7a5c3f (the latest commit), but isn't an actual error that Manubot issues.

[tiwns]

Yes, its Commit [b7a5c3f]. It is failing for my newer repositories but worked fine on the old repositories.

[dhimmel]

Can you copy the GitHub Actions log and and paste it here? Will be helpful to see more about the error and the messages proceeding it.

[tiwns]

Here it is:

Run bash ci/deploy.sh
Already on 'main'
M	webpage/README.md
Your branch is up to date with 'origin/main'.
[INFO] Detected MANUBOT_ACCESS_TOKEN. Will deploy via HTTPS.
fatal: couldn't find remote ref gh-pages
[INFO] could not fetch gh-pages or output from origin.
##WARNING
Checkout returned a nonzero exit status. See output:
fatal: invalid reference: gh-pages
remote: Write access to repository not granted.
fatal: unable to access '[removed address]': The requested URL returned error: 403
Traceback (most recent call last):
  File "/usr/share/miniconda3/envs/manubot/bin/ghp-import", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/usr/share/miniconda3/envs/manubot/lib/python3.11/site-packages/ghp_import.py", line 300, in main
    ghp_import(args.pop("directory"), **args)
  File "/usr/share/miniconda3/envs/manubot/lib/python3.11/site-packages/ghp_import.py", line 285, in ghp_import
    git.check_call('push', opts['remote'], opts['branch'])
  File "/usr/share/miniconda3/envs/manubot/lib/python3.11/site-packages/ghp_import.py", line 119, in check_call
    sp.check_call(['git'] + list(args), **kwargs)
  File "/usr/share/miniconda3/envs/manubot/lib/python3.11/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['git', 'push', 'origin', 'output']' returned non-zero exit status 128.
Error: Process completed with exit code 1.

Manubot did copy the the template into my repository. However GHActions is not working. I

[tiwns]

In addition for an organization repository, I receive this error:

Error: .github#L1
conda-incubator/setup-miniconda@v2 is not allowed to be used in XXXX. Actions in this workflow must be: within a repository that belongs to your Enterprise account, created by GitHub, verified in the GitHub Marketplace, or matching the following:

[dhimmel]

Regarding "Write access to repository not granted", if you go to /settings/actions can you see which box is checked:

If you add the following to .github/workflows/manubot.yaml, that should also fix it (docs):

permissions:
  contents: write

We should probably add this to rootstock, but would be good if you can confirm it fixes the problem.

Actions in this workflow must be: within a repository that belongs to your Enterprise account, created by GitHub, verified in the GitHub Marketplace, or matching the following

Looks like the organization has a setting that blocks the conda-incubator/setup-miniconda action. See if someone with admin access to the organization can allow this and the other dependent actions.