Re: [modeller_usage] Command not found, no module named 'modeller' errors

Thank you! I reinstalled my OS yesterday -does that mean that whatever I broke in my operating system is fixed now? I just installed Homebrew (technically for the first time, since my Mac reverted to an April backup) and typed "brew doctor" and "which python3", which gave:

Luos-Air:~ luoxiaoran$ brew doctor

Please note that these warnings are just used to help the Homebrew maintainers

with debugging if you file an issue. If everything you use Homebrew for is

working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: "config" scripts exist outside your system or Homebrew directories.

`./configure` scripts often look for *-config scripts to determine if

software packages are installed, and which additional flags to use when

compiling and linking.

Having additional scripts in your path can confuse software installed via

Homebrew if the config script overrides a system or Homebrew-provided

script of the same name. We found the following "config" scripts:

/Library/Frameworks/Python.framework/Versions/3.8/bin/python3-config

/Library/Frameworks/Python.framework/Versions/3.8/bin/python3.8-config

Luos-Air:~ luoxiaoran$ which python3

/Library/Frameworks/Python.framework/Versions/3.8/bin/python3

Luos-Air:~ luoxiaoran$

So I guess I am still not using Homebrew's Python -how do I switch to using Homebrew's Python? And what is broken in my Homebrew installation? I don't remember installing multiple versions of Python before April, but it is a possibility -how do I uninstall those versions if it is needed to switch to using Homebrew's Python? Thanks!

Best,

Luna

On Fri, May 29, 2020 at 9:53 AM Modeller Caretaker <">> wrote:

On 5/28/20 10:58 PM, Xiao Ran Luo wrote:
> is there a way to prevent the mismatch between
> the Homebrew Python and Apple's Python?

The Homebrew Modeller package is designed to work with Homebrew's
Python, i.e. /usr/local/bin/python3 (it will also work with Homebrew's
python@3.8 package, but by default that's not in your path). So if
"import modeller" fails there are are really only 3 possibilities:

1. You are not using Homebrew's Python, i.e. "which python3" does not
print "/usr/local/bin/python3"
or "/usr/local/opt/python@3.8/bin/python3".

2. Something is broken in your Homebrew installation, i.e. "brew doctor"
does not print "Your system is ready to brew."

3. Something is broken elsewhere in your operating system because of you
deleting the Python framework and/or installing multiple versions of Python.

Ben Webb, Modeller Caretaker
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