Github actions force closes PR

[bgyori]

I feel like I've noticed this in the past but my recent auto-generated PR for a new prefix was force pushed to by Github actions, making the original commit disappear and the PR be closed: #1111. It is not immediately obvious what steps led to this so it's something to investigete.

[bgyori]

A very clear example of this bug just happened, so I am posting some more info so we can figure it out and fix it later:

• Based on issue Add prefix "OBCI" #1174, a PR was opened at Add prefix: obci #1175
• Then, when unrelated issue Update regular expression pattern for COCONUT #1176 was opened, the Register new prefix action was run at https://github.com/biopragmatics/bioregistry/actions/runs/10633176976 which via a set of Github steps ended up force pushing the state of main to Add prefix: obci #1175 and thereby closing it.

Looking at the logs, here are some relevant parts:

2024-08-30T13:03:30.4156687Z ##[group]Fetching the repository
2024-08-30T13:03:30.4164189Z [command]/usr/bin/git -c protocol.version=2 fetch --no-tags --prune --progress --no-recurse-submodules --depth=1 origin +eb4ff3a669800e5af76b8bad32f3d4e3bee7f749:refs/remotes/origin/main
2024-08-30T13:03:30.8532226Z remote: Enumerating objects: 466, done.        
...
2024-08-30T13:03:35.2915672Z Resolving deltas: 100% (48/48), done.
2024-08-30T13:03:35.3860155Z From https://github.com/biopragmatics/bioregistry
2024-08-30T13:03:35.3861307Z  * [new ref]         eb4ff3a669800e5af76b8bad32f3d4e3bee7f749 -> origin/main
2024-08-30T13:03:35.3888756Z ##[endgroup]
2024-08-30T13:03:35.3889386Z ##[group]Determining the checkout info
2024-08-30T13:03:35.3890516Z ##[endgroup]
2024-08-30T13:03:35.3891686Z ##[group]Checking out the ref
2024-08-30T13:03:35.3896926Z [command]/usr/bin/git checkout --progress --force -B main refs/remotes/origin/main
2024-08-30T13:03:35.7837593Z Switched to a new branch 'main'
2024-08-30T13:03:35.7838739Z branch 'main' set up to track 'origin/main'.
2024-08-30T13:03:35.7862329Z ##[endgroup]
2024-08-30T13:03:35.7900309Z [command]/usr/bin/git log -1 --format='%H'
2024-08-30T13:03:35.7924295Z 'eb4ff3a669800e5af76b8bad32f3d4e3bee7f749'
2024-08-30T13:03:35.8268269Z ##[group]Run actions/setup-python@v2
2024-08-30T13:03:35.8268744Z with:
2024-08-30T13:03:35.8269045Z   python-version: 3.9
2024-08-30T13:03:35.8269669Z   token: ***
2024-08-30T13:03:35.8270012Z ##[endgroup]
2024-08-30T13:03:35.9403398Z Successfully setup CPython (3.9.19)
2024-08-30T13:03:35.9543678Z ##[group]Run pip install -e .[gha]
...
2024-08-30T13:03:44.6596342Z ##[group]Run python -m bioregistry.gh.new_prefix --github
2024-08-30T13:03:44.6597123Z �[36;1mpython -m bioregistry.gh.new_prefix --github�[0m
2024-08-30T13:03:44.6664354Z shell: /usr/bin/bash -e {0}
2024-08-30T13:03:44.6665034Z env:
2024-08-30T13:03:44.6665412Z   pythonLocation: /opt/hostedtoolcache/Python/3.9.19/x64
2024-08-30T13:03:44.6666024Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.9.19/x64/lib
2024-08-30T13:03:44.6666991Z   GITHUB_TOKEN: ***
2024-08-30T13:03:44.6667344Z ##[endgroup]
2024-08-30T13:03:46.3520441Z invalid CURIE: 
2024-08-30T13:03:46.3521127Z Found 1 new prefix issues:
2024-08-30T13:03:46.3522121Z  - https://github.com/biopragmatics/bioregistry/issues/1174
2024-08-30T13:03:47.0049014Z Found PRs covering 1 new prefix issues:
2024-08-30T13:03:47.0050457Z  - https://github.com/biopragmatics/bioregistry/pulls/1174
2024-08-30T13:03:47.0051968Z No issues without PRs to worry about. Exiting.
2024-08-30T13:03:47.0764434Z ##[group]Run peter-evans/create-pull-request@v3
2024-08-30T13:03:47.0765255Z with:
2024-08-30T13:03:47.0765603Z   branch-suffix: short-commit-hash
2024-08-30T13:03:47.0766011Z   labels: New,Prefix
2024-08-30T13:03:47.0766595Z   token: ***
2024-08-30T13:03:47.0766899Z   add-paths: -A

2024-08-30T13:03:47.0767338Z   commit-message: [create-pull-request] automated change
2024-08-30T13:03:47.0767946Z   committer: GitHub <[email protected]>
2024-08-30T13:03:47.0768381Z   author: CS76 <[email protected]>
2024-08-30T13:03:47.0768816Z   signoff: false
2024-08-30T13:03:47.0769250Z   branch: create-pull-request/patch
2024-08-30T13:03:47.0769620Z   delete-branch: false
2024-08-30T13:03:47.0769965Z   draft: false
2024-08-30T13:03:47.0770366Z env:
2024-08-30T13:03:47.0770947Z   pythonLocation: /opt/hostedtoolcache/Python/3.9.19/x64
2024-08-30T13:03:47.0771533Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.9.19/x64/lib
2024-08-30T13:03:47.0772118Z ##[endgroup]
2024-08-30T13:03:47.1428386Z ##[group]Save persisted git credentials
2024-08-30T13:03:47.1446020Z [command]/usr/bin/git config --local --name-only --get-regexp http.https://github.com/.extraheader ^AUTHORIZATION:
2024-08-30T13:03:47.1484804Z http.https://github.com/.extraheader
2024-08-30T13:03:47.1511703Z [command]/usr/bin/git config --local --get-regexp http.https://github.com/.extraheader ^AUTHORIZATION:
2024-08-30T13:03:47.1538344Z http.https://github.com/.extraheader AUTHORIZATION: basic ***
2024-08-30T13:03:47.1546318Z [command]/usr/bin/git config --local --unset http.https://github.com/.extraheader ^AUTHORIZATION:
2024-08-30T13:03:47.1575318Z Unset config key 'http.https://github.com/.extraheader'
2024-08-30T13:03:47.1576829Z ##[endgroup]
2024-08-30T13:03:47.1626642Z ##[group]Determining the base and head repositories
2024-08-30T13:03:47.1632590Z [command]/usr/bin/git config --local --get remote.origin.url
2024-08-30T13:03:47.1657040Z https://github.com/biopragmatics/bioregistry
2024-08-30T13:03:47.1667211Z ##[endgroup]
2024-08-30T13:03:47.1668034Z Pull request branch target repository set to biopragmatics/bioregistry
2024-08-30T13:03:47.1669480Z ##[group]Configuring credential for HTTPS authentication
2024-08-30T13:03:47.1676578Z [command]/usr/bin/git config --local http.https://github.com/.extraheader AUTHORIZATION: basic ***
2024-08-30T13:03:47.1723344Z ##[endgroup]
2024-08-30T13:03:47.1724144Z ##[group]Checking the base repository state
2024-08-30T13:03:47.1728681Z [command]/usr/bin/git symbolic-ref HEAD --short
2024-08-30T13:03:47.1753738Z main
2024-08-30T13:03:47.1758684Z Working base is branch 'main'
2024-08-30T13:03:47.1763149Z [command]/usr/bin/git remote prune origin
2024-08-30T13:03:47.6826750Z ##[endgroup]
2024-08-30T13:03:47.6831707Z [command]/usr/bin/git rev-parse --short HEAD
2024-08-30T13:03:47.6857148Z eb4ff3a
2024-08-30T13:03:47.6862745Z Pull request branch to create or update set to 'create-pull-request/patch-eb4ff3a'
2024-08-30T13:03:47.6864661Z ##[group]Configuring the committer and author
2024-08-30T13:03:47.6865817Z Configured git committer as 'GitHub <[email protected]>'
2024-08-30T13:03:47.6866987Z Configured git author as 'CS76 <[email protected]>'
2024-08-30T13:03:47.6868643Z ##[endgroup]
2024-08-30T13:03:47.6869635Z ##[group]Create or update the pull request branch
2024-08-30T13:03:47.6874856Z [command]/usr/bin/git symbolic-ref HEAD --short
2024-08-30T13:03:47.6896838Z main
2024-08-30T13:03:47.6901681Z Working base is branch 'main'
2024-08-30T13:03:47.6911120Z [command]/usr/bin/git checkout --progress -B 4e66dbaa-2dc6-4bf0-8b4b-1d68b46b10a9 HEAD --
2024-08-30T13:03:47.6958631Z Switched to a new branch '4e66dbaa-2dc6-4bf0-8b4b-1d68b46b10a9'
2024-08-30T13:03:47.6969183Z [command]/usr/bin/git status --porcelain -unormal
2024-08-30T13:03:47.7026024Z [command]/usr/bin/git diff --quiet
2024-08-30T13:03:47.7062528Z [command]/usr/bin/git diff --quiet --staged
2024-08-30T13:03:47.7101008Z Resetting working base branch 'main'
2024-08-30T13:03:47.7104785Z [command]/usr/bin/git checkout --progress main --
2024-08-30T13:03:47.7146493Z Switched to branch 'main'
2024-08-30T13:03:47.7149837Z Your branch is up to date with 'origin/main'.
2024-08-30T13:03:47.7158194Z [command]/usr/bin/git reset --hard origin/main
2024-08-30T13:03:47.7203451Z HEAD is now at eb4ff3a Run new prefix requests after debugging (#1147)
2024-08-30T13:03:47.7215386Z [command]/usr/bin/git -c protocol.version=2 fetch --no-tags --progress --no-recurse-submodules --unshallow origin create-pull-request/patch-eb4ff3a:refs/remotes/origin/create-pull-request/patch-eb4ff3a
2024-08-30T13:03:48.8450368Z remote: Enumerating objects: 67775, done.        
2024-08-30T13:03:48.8514461Z remote: Counting objects:   0% (1/67775)        
...
2024-08-30T13:03:48.9144819Z remote: Counting objects: 100% (67775/67775), done.        
2024-08-30T13:03:49.6321122Z remote: Compressing objects:   0% (1/12410)        
...
2024-08-30T13:04:05.8132311Z remote: Compressing objects: 100% (12410/12410), done.        
2024-08-30T13:04:05.9332966Z Receiving objects:   0% (1/67473)
...
2024-08-30T13:04:32.5800220Z Receiving objects: 100% (67473/67473), 980.25 MiB | 36.63 MiB/s, done.
2024-08-30T13:04:32.5873427Z Resolving deltas:   0% (0/51917)
2024-08-30T13:04:32.5890829Z Resolving deltas:   1% (520/51917)
...
2024-08-30T13:05:36.1902704Z Resolving deltas: 100% (51917/51917), completed with 235 local objects.
2024-08-30T13:05:41.5859881Z From https://github.com/biopragmatics/bioregistry
2024-08-30T13:05:41.5861634Z  * [new branch]          create-pull-request/patch-eb4ff3a -> origin/create-pull-request/patch-eb4ff3a
2024-08-30T13:05:41.5888379Z Pull request branch 'create-pull-request/patch-eb4ff3a' already exists as remote branch 'origin/create-pull-request/patch-eb4ff3a'
2024-08-30T13:05:41.5893022Z [command]/usr/bin/git checkout --progress create-pull-request/patch-eb4ff3a --
2024-08-30T13:05:41.6170814Z Switched to a new branch 'create-pull-request/patch-eb4ff3a'
2024-08-30T13:05:41.6172551Z branch 'create-pull-request/patch-eb4ff3a' set up to track 'origin/create-pull-request/patch-eb4ff3a'.
2024-08-30T13:05:41.6186939Z [command]/usr/bin/git diff --quiet create-pull-request/patch-eb4ff3a..4e66dbaa-2dc6-4bf0-8b4b-1d68b46b10a9
2024-08-30T13:05:41.6651617Z Resetting 'create-pull-request/patch-eb4ff3a'
2024-08-30T13:05:41.6656044Z [command]/usr/bin/git checkout --progress -B create-pull-request/patch-eb4ff3a 4e66dbaa-2dc6-4bf0-8b4b-1d68b46b10a9 --
2024-08-30T13:05:41.7046399Z Reset branch 'create-pull-request/patch-eb4ff3a'
2024-08-30T13:05:41.7050073Z Your branch is behind 'origin/create-pull-request/patch-eb4ff3a' by 3 commits, and can be fast-forwarded.
2024-08-30T13:05:41.7051311Z   (use "git pull" to update your local branch)
2024-08-30T13:05:41.7062827Z [command]/usr/bin/git rev-list --right-only --count origin/create-pull-request/patch-eb4ff3a...create-pull-request/patch-eb4ff3a
2024-08-30T13:05:41.7089412Z 0
2024-08-30T13:05:41.7100254Z [command]/usr/bin/git rev-list --left-only --count origin/create-pull-request/patch-eb4ff3a...create-pull-request/patch-eb4ff3a
2024-08-30T13:05:41.7123498Z 3
2024-08-30T13:05:41.7128955Z Updated branch 'create-pull-request/patch-eb4ff3a'
2024-08-30T13:05:41.7134326Z [command]/usr/bin/git rev-list --right-only --count main...create-pull-request/patch-eb4ff3a
2024-08-30T13:05:41.7161889Z 0
2024-08-30T13:05:41.7170325Z [command]/usr/bin/git rev-parse HEAD
2024-08-30T13:05:41.7190952Z eb4ff3a669800e5af76b8bad32f3d4e3bee7f749
2024-08-30T13:05:41.7198197Z [command]/usr/bin/git branch --delete --force 4e66dbaa-2dc6-4bf0-8b4b-1d68b46b10a9
2024-08-30T13:05:41.7226246Z Deleted branch 4e66dbaa-2dc6-4bf0-8b4b-1d68b46b10a9 (was eb4ff3a66).
2024-08-30T13:05:41.7231306Z ##[endgroup]
2024-08-30T13:05:41.7234431Z ##[group]Pushing pull request branch to 'origin/create-pull-request/patch-eb4ff3a'
2024-08-30T13:05:41.7236825Z [command]/usr/bin/git push --force-with-lease origin HEAD:refs/heads/create-pull-request/patch-eb4ff3a
2024-08-30T13:05:43.7195658Z To https://github.com/biopragmatics/bioregistry
2024-08-30T13:05:43.7197495Z  + df9b23e42...eb4ff3a66 HEAD -> create-pull-request/patch-eb4ff3a (forced update)
2024-08-30T13:05:43.7241317Z ##[endgroup]
2024-08-30T13:05:43.7242695Z Branch 'create-pull-request/patch-eb4ff3a' no longer differs from base branch 'main'
2024-08-30T13:05:43.7244386Z ##[group]Restore persisted git credentials
2024-08-30T13:05:43.7248837Z [command]/usr/bin/git config --local --name-only --get-regexp http.https://github.com/.extraheader ^AUTHORIZATION:
2024-08-30T13:05:43.7274236Z http.https://github.com/.extraheader
2024-08-30T13:05:43.7283167Z [command]/usr/bin/git config --local --get-regexp http.https://github.com/.extraheader ^AUTHORIZATION:
2024-08-30T13:05:43.7316492Z http.https://github.com/.extraheader AUTHORIZATION: basic ***
2024-08-30T13:05:43.7323399Z [command]/usr/bin/git config --local --unset http.https://github.com/.extraheader ^AUTHORIZATION:
2024-08-30T13:05:43.7351347Z Unset config key 'http.https://github.com/.extraheader'
2024-08-30T13:05:43.7356831Z [command]/usr/bin/git config --local http.https://github.com/.extraheader AUTHORIZATION: basic ***
2024-08-30T13:05:43.7390939Z Persisted git credentials restored
2024-08-30T13:05:43.7391929Z ##[endgroup]
2024-08-30T13:05:43.7527145Z Post job cleanup.
2024-08-30T13:05:43.8674425Z Post job cleanup.
2024-08-30T13:05:43.9594891Z [command]/usr/bin/git version
2024-08-30T13:05:43.9636116Z git version 2.46.0
2024-08-30T13:05:43.9687027Z Temporarily overriding HOME='/home/runner/work/_temp/030f7918-2222-4ba9-80a7-632e1b8aef65' before making global git config changes
2024-08-30T13:05:43.9689242Z Adding repository directory to the temporary git global config as a safe directory
2024-08-30T13:05:43.9691108Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/bioregistry/bioregistry
2024-08-30T13:05:43.9729202Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2024-08-30T13:05:43.9761777Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :"
2024-08-30T13:05:44.0016617Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2024-08-30T13:05:44.0038566Z http.https://github.com/.extraheader
2024-08-30T13:05:44.0048861Z [command]/usr/bin/git config --local --unset-all http.https://github.com/.extraheader
2024-08-30T13:05:44.0079763Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :"
2024-08-30T13:05:44.0579224Z Cleaning up orphan processes

[bgyori]

Further bugs: #1240 was just force-overwritten with the wrong issue's content when an unrelated issue #1243 was opened. Will try to debug this on a fork to improve the Github action's reliability.