CodeQL CLI version 2.12.6 was discontinued on 2024-07-09 alongside GitHub Enterprise Server 3.9 and will not be supported by the next minor release of the CodeQL Action. Please update to CodeQL CLI version 2.13.5 or later. For instance, if you have specified a custom version of the CLI using the 'tools' input to the 'init' Action, you can remove this input to use the default version. Alternatively, if you want to continue using CodeQL CLI version 2.12.6, you can replace 'github/codeql-action/*@V3' by 'github/codeql-action/*@v3.25.13' in your code scanning workflow to continue using this version of the CodeQL Action.

CodeQL Action versions 3.25.0 and later, and versions 2.25.0 and later no longer install Python dependencies. We recommend upgrading to at least CodeQL Bundle 2.16.0 to avoid any potential problems due to this (you are currently using 2.12.6). Alternatively, we recommend downgrading the CodeQL Action to version 3.24.10 (for customers using GitHub.com or GitHub Enterprise Server v3.12 or later) or 2.24.10 (for customers using GitHub Enterprise Server v3.11 or earlier).