ATLANTIS_GH_ALLOW_MERGEABLE_BYPASS_APPLY blocking atlantis apply operations

[AndresPinerosZen]

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Overview of the Issue

Version: 0.35.1

When using ATLANTIS_GH_ALLOW_MERGEABLE_BYPASS_APPLY=true and setting the atlantis/apply check as required in the repository, I'm getting this message when running atlantis apply.

Apply Error

the default workspace at path terraform is currently locked by another command that is running for this pull request.
Wait until the previous command is complete and try again

When checking the Atlantis container, there are no terraform processes running, just the atlantis server, so I'm sure there's no terraform command running for the pull request.

We were running atlantis apply only after making sure that the plan had finished and that there was no terraform process running inside of the container.

Once we removed the required check and set the variable to false, everything started working as usual.

Reproduction Steps

• Set the variable ATLANTIS_GH_ALLOW_MERGEABLE_BYPASS_APPLY=true.
• Set the required check in the Terraform repository.
• Open a pull request.
• Wait until the automatic plan finishes.
• Run atlantis apply
• Get the error from the overview

Please let me know if there are any specific atlantis.yaml configurations that are of interest to be able to understand this behavior. I don't see any extra configuration that could be linked to this.

[dosubot]

Hi @AndresPinerosZen! I'm Dosu and I’m helping the atlantis team.

This is a known bug in Atlantis that affected versions including 0.35.1. The issue was caused by a mismatch between the lock and unlock key formats for workspace locks, which meant that locks were never released after certain operations—especially when logic involving apply checks and feature flags like ATLANTIS_GH_ALLOW_MERGEABLE_BYPASS_APPLY was triggered. As a result, you could see the "workspace is currently locked" error even when no Terraform process was running. This bug was fixed in a recent PR by centralizing lock key generation, ensuring that locks are properly released after operations (details here).

Upgrading Atlantis to a version that includes this fix should resolve the problem. If you are unable to upgrade immediately, you may need to manually clear stale locks as a temporary workaround. The issue is not related to your atlantis.yaml configuration, but rather to the internal lock management logic.

To reply, just mention @dosu.

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[AndresPinerosZen]

@dosu which versions have the fix?

[dosubot]

The fix for the workspace lock bug is included in Atlantis version 0.35.1, but only in builds from commit 7f1ed4a (build date: 2025-09-18) and later. If you're running an earlier build of 0.35.1, you may still encounter the issue. You can confirm your version and commit by checking the Atlantis build info. For full reliability, make sure your deployment is at least commit 7f1ed4a or newer (details).

Note: Even with the fix, some edge cases (like legacy lock data or race conditions with high parallelism) can still cause locks to persist. If you need upgrade notes or troubleshooting tips, let me know!

To reply, just mention @dosu.

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[AndresPinerosZen]

After upgrading to version 0.36.0, I'm still seeing this bug.

Version: atlantis v0.36.0 (commit: 7f1ed4a) (build date: 2025-09-18T16:01:19.158Z)

[celeronsx]

The same. Could you please double-check it? This feature is very important.

[lukemassa]

I took a look and I'm unable to reproduce the bug; I set --gh-allow-mergeable-bypass-apply=true on a test server with branch protections on both on main as well as 0.35.1 and it applied as expected.

The error makes it seem like there's a lock lurking somewhere; could you view the UI to see if there an open locks? If you have access to filesystem where atlantis is running, you could stop Atlantis, and blow away the lock database:

atlantis-test % ls -latr ~/.atlantis/atlantis.db 
-rw-------  1 lmassa  staff  131072 Oct  5 21:53 /Users/lmassa/.atlantis/atlantis.db

Better yet, if you're able and it turns out the locks are in the issue, moving the file aside will create a fresh db, then we can inspect the file with the https://github.com/etcd-io/bbolt command. If the error messages the bot was talking about are right, my theory is you have a key with an old format that isn't recognized. We might be able to have Atlantis "repair" the keys on the way up.