Xcode tools in MacOS

General Discussion
1

I am (sometimes) getting prompts (an alert window) from MacOS to install the Xcode command line tools when checking the Python Settings in Avogadro. Now I see alerts for Xcode updates in MacOS notifications and System Settings.
Is it recommended or necessary to install these tools? As far as I can tell, Avogadro2 v1.100.0 is unfazed by these alerts but I haven’t come close to exploring all that Avogadro can do.

2

You have Python installed already via mamba-forge and set up with Avogadro right?

I wonder whether it’s because there’s no interpreter installed system-wide as python3, and so when Avogadro is scanning for interpreters and tries to check whether the python3 command is valid, the OS tells you to install xcode (because I think that is how you enable the macOS system Python).

What happens if you execute just python3 in a terminal? Do you also get the alert?

3

That makes sense. Let me see if I can find a Mac without python installed and figure out if I can detect that case (e.g. maybe python3 is some sort of symlink)

4

Actually… @myoung - would you be willing to open up the Terminal.app and run

ls -l /usr/bin/python*

I’d be curious to see what’s there. Thanks!

5

In usr/bin I see:
$ ls -l python*
-rwxr-xr-x 78 root wheel 118848 Feb 4 08:57 python3

In ~/mambaforge/bin I see:
$ ls -l python*
lrwxr-xr-x 1 myaccount staff 10 Feb 13 09:51 python → python3.12
lrwxr-xr-x 1 myaccount staff 10 Feb 13 09:51 python3 → python3.12
lrwxr-xr-x 1 myaccount staff 17 Feb 13 09:51 python3-config → python3.12-config
lrwxr-xr-x 1 myaccount staff 10 Feb 13 09:51 python3.1 → python3.12
-rwxrwxr-x 1 myaccount staff 7030904 Feb 13 09:51 python3.12
-rwxrwxr-x@ 1 myaccount staff 2059 Feb 13 09:51 python3.12-config

It is the latter location where Avogadro is pointed.

6

From the root I see:
$ python3

Python 3.12.8 | packaged by conda-forge | (main, Dec 5 2024, 14:25:12) [Clang 18.1.8 ] on darwin

Type “help”, “copyright”, “credits” or “license” for more information.

So that appears to be pointing to the mamba installation.

7

Hmm. This is the installed Apple Python:
% /usr/bin/python3 --version
Python 3.9.6

I suspect at some point you installed the Xcode tools (including Python) and that’s now part of Apple’s software updates.

You can certainly ignore them if you installed mamba.

If you want to remove them, you can follow these instructions:

8

I see;
/usr/bin $ python3 --version
Python 3.12.8

I am on latest Sequoia. I must have updated Python and maybe also installed the tools (I can’t recall).
Thanks for your time.