After instaling Homebrew, pip and Fontbakery, majority of glyphs plugins stopped working

When Glyphs3 starts I get this message:

I reinstalled all modules but the problem persists, I am using glyphs python version:

I had this problem before, but since the problem was accompanied by strange behavior in terminal, I thought that the problem was with my default PATH. I restored to clean Mac OS (Big Sur), and everything worked fine until I have installed the packages (Homebrew, …).
When I uninstall Homebrew or python 3.10, problem persists.
Glyphs version 3.0.5 (3122)

Try this:

  1. In the dialog, choose Ignore.
  2. In the mekkablue scripts, choose App > Set Hidden App Preferences, set DebugMode to 1, and click Apply.
  3. uninstall and reinstall all the modules in Plugin Manager, restart the app
  4. Make sure the Glyphs Python is selected in Preferences > Addons; if necessary restart the app again.
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Thank you, that fixed all the issues.

May I ask what causes this behavior?

Sometimes things go wrong. Without having a look at your machine it is difficult to tell what caused this.

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