Cannot update formulae since Python needs Apple Command Lines Tools installed (which it is)

[vladoski]

Output of brew config

HOMEBREW_VERSION: 4.2.16
ORIGIN: https://github.com/Homebrew/brew
HEAD: bd1155be8f50998429a795c15a69c8fe75250510
Last commit: 18 hours ago
Core tap JSON: 02 Apr 08:45 UTC
Core cask tap JSON: 02 Apr 08:45 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: /usr/bin/nano
HOMEBREW_MAKE_JOBS: 8
Homebrew Ruby: 3.1.4 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.1.4/bin/ruby
CPU: octa-core 64-bit arm_firestorm_icestorm
Clang: 15.0.0 build 1500
Git: 2.39.3 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 8.4.0 => /usr/bin/curl
macOS: 14.3.1-arm64
CLT: N/A
Xcode: 15.2
Rosetta 2: false

Output of brew doctor

Warning: Some installed kegs have no formulae!
This means they were either deleted or installed manually.
You should find replacements for the following formulae:
  python-click

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  lua@5.3
  youtube-dl

Description of issue

Hi guys, everytime that I need to update something that has python as a dependency (e.g. ffmpeg), it won't let me since it gives me an error:

Error: python@3.12: the bottle needs the Apple Command Line Tools to be installed.
  You can install them, if desired, with:
    xcode-select --install

I have Apple Command Line Tools installed: xcode-select --version outputs xcode-select version 2405. I'm using pyenv to manage my python versions, I've tried updating brew formulae with both the system version (shimmed by pyenv but located here /opt/homebrew/bin/python3) and with versions installed via pyenv. Might pyenv be the problem?

Also brew list | rg python outputs:

python-click
python@3.10
python@3.11
python@3.12
python@3.9

Thanks for helping! :)

[SMillerDev]

What does xcode-select -p output?

[vladoski]

/Applications/Xcode.app/Contents/Developer

[SMillerDev]

That means you don't have the commandline tools, you have Xcode tools for the command line. They're not the same. What happens if you run xcode-select --install?

[vladoski]

you're right I thought that Xcode tools and Apple Command Tools were the same thing, my bad.
Thanks!