I get this warning in CI:

top-level default_stages uses deprecated stage names (commit, push) which will be removed in a future version.  run: `pre-commit migrate-config` to automatically fix this.

Yet running pre-commit migrate-config in my repository doesn't have any effect:

$ pre-commit migrate-config
Configuration is already migrated.
$ 

I get this warning in CI:

top-level default_stages uses deprecated stage names (commit, push) which will be removed in a future version.  run: `pre-commit migrate-config` to automatically fix this.

Screen capture of pre-commit.ci
Yet running pre-commit migrate-config in my repository doesn't have any effect:

$ pre-commit migrate-config
Configuration is already migrated.
$ 

obviously you're not using a new enough pre-commit version

$ pre-commit --version
pre-commit 4.0.1
$ 

Could pre-commit.ci be using newer code than the latest released version of pre-commit?

show your configuration?

https://github.com/zarr-developers/numcodecs/blob/8edd3f96d2703df070f70bd224b3707ec4d68c4e/.pre-commit-config.yaml

The part that needs to be updated is:

default_stages: [commit, push]

works for me

$ pre-commit migrate-config
Configuration has been migrated.
$ git diff
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index dd04f38..2835f59 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
   autofix_prs: false
-default_stages: [commit, push]
+default_stages: [pre-commit, pre-push]
 default_language_version:
   python: python3
 repos:

$ grep default_stages .pre-commit-config.yaml 
default_stages: [commit, push]
$ 
$ pipx install pre-commit
  installed package pre-commit 4.0.1, installed using Python 3.10.12
  These apps are now globally available
    - pre-commit
done! ✨ 🌟 ✨
$ 
$ pre-commit --version
pre-commit 4.0.1
$ 
$ pre-commit migrate-config
Configuration has been migrated.
$ 
$ grep default_stages .pre-commit-config.yaml 
default_stages: [pre-commit, pre-push]
$ 

I'll retry on my computer at work tomorrow, and let you know. Either I did something wrong, or this an effect of a Linux kernel or system issue that breaks my workstation in very strange ways since it was upgraded from Ubuntu 22.04 to Ubuntu 24.04.

almost certainly it was an old version of pre-commit

I don't think it is an old version (pre-commit installed with pipx just like at home). Rather, my workstation is plagued by mysterious I/O problems since the Ubuntu 24.04 upgrade, see for example prefix-dev/rattler-build#1045 (comment).

I don't necessarily trust pipx to do what you want personally

My workstation has been reinstalled by IT. I cannot reproduce the issue any more. Sorry about the noise.