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Upgrade manubot to fix pubmed API calls. #485

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tiwns opened this issue Jan 25, 2023 · 6 comments
Open

Upgrade manubot to fix pubmed API calls. #485

tiwns opened this issue Jan 25, 2023 · 6 comments

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@tiwns
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tiwns commented Jan 25, 2023

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
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dhimmel commented Jan 25, 2023

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
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tiwns commented Jan 25, 2023

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

@dhimmel
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dhimmel commented Jan 25, 2023

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
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tiwns commented Feb 14, 2023

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
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tiwns commented Feb 14, 2023

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
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dhimmel commented Feb 14, 2023

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

image

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.

dhimmel added a commit that referenced this issue Feb 21, 2023
refs #485 (comment)

Some users might have their repository workflow permissions
set to read only. This change should ensure the workflow job
can write commits back to the output and gh-pages branches
on GitHub.
danich1 pushed a commit to danich1/word_lapse_manuscript that referenced this issue Apr 5, 2023
refs manubot/rootstock#485 (comment)

Some users might have their repository workflow permissions
set to read only. This change should ensure the workflow job
can write commits back to the output and gh-pages branches
on GitHub.
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