Hi Ajasja and Ben,
Thanks for the tutorial recommendation! I was hesitant to install modeller because the python problem had not been fixed yet, but am doing it now. However, when I tried to install the Homebrew version of Python using "brew install python", I got an error:
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/2to3
Target /usr/local/bin/2to3
already exists. You may want to remove it:
rm '/usr/local/bin/2to3'
To force the link and overwrite all conflicting files:
brew link --overwrite python
To list all files that would be deleted:
brew link --overwrite --dry-run python
Possible conflicting files are:
/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/3.8/bin/2to3
/usr/local/bin/idle3 -> /Library/Frameworks/Python.framework/Versions/3.8/bin/idle3
/usr/local/bin/pydoc3 -> /Library/Frameworks/Python.framework/Versions/3.8/bin/pydoc3
/usr/local/bin/python3 -> /Library/Frameworks/Python.framework/Versions/3.8/bin/python3
/usr/local/bin/python3-config -> /Library/Frameworks/Python.framework/Versions/3.8/bin/python3-config
==> */usr/local/Cellar/python/3.7.7/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python/3.7.7/bin --install-lib=/usr/local/lib/python3.7/site-packages*
==> */usr/local/Cellar/python/3.7.7/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python/3.7.7/bin --install-lib=/usr/local/lib/python3.7/site-packages*
==> */usr/local/Cellar/python/3.7.7/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python/3.7.7/bin --install-lib=/usr/local/lib/python3.7/site-packages*
==> *Caveats*
Python has been installed as
/usr/local/bin/python3
This is probably a minor error, because python appears in my brew list:
Luos-Air:~ luoxiaoran$ brew list
gcc gdbm gmp isl libmpc mpfr openssl@1.1 python readline sqlite tcl-tk xz
Luos-Air:~ luoxiaoran$
But then when I type "which python3" I still get the mystery 3rd version of python:
Luos-Air:~ luoxiaoran$ which python3
/Library/Frameworks/Python.framework/Versions/3.8/bin/python3
Luos-Air:~ luoxiaoran$
This error looks familiar, and I think troubleshooting this error was the reason I deleted the python framework in the first place (no worries, I reinstalled OS to an April backup so my Mac is not broken anymore, I think). Previously, Modeller Caretaker Ben Webb told me to: "edit your profile (maybe ~/.bashrc or ~/.zshrc) and remove /Library/Frameworks/Python.framework/Versions/3.8/bin from your PATH." which sounds like it would solve this error and all my problems, but I am not sure how to do so? Thanks!
Best,
Luna
On Fri, May 29, 2020 at 1:09 PM Ajasja Ljubetič ajasja.ljubetic@gmail.com wrote:
> Hi Xiao, > > This is a really basic question and I really recommend a good tutorial. > Maybe this one > https://www.knowledgehut.com/blog/programming/run-python-scripts? > > But in short, when you ran /usr/local/bin/python3 you entered the > interactive python environment. Only python commands will now work. > You can exit by pressing Ctrl-Z or by typing exit(). > Type *import modeller* to is if the package is installed. > > Best, > Ajasja > > > On Fri, 29 May 2020 at 13:02, Xiao Ran Luo via modeller_usage < > modeller_usage@salilab.org> wrote: > >> Hmm I ran /usr/local/bin/python3 and Terminal seems to be expecting >> something from me (the normal commands like "which python3" don't work >> anymore)? Sorry, I tried to find a Terminal tutorial but haven't found one >> that's helpful but not too difficult yet...How do I return to the >> normal Luos-Air:~ luoxiaoran$ and how do I edit my profile and remove that >> file from my PATH without deleting the python framework again? >> >> Luos-Air:~ luoxiaoran$ /usr/local/bin/python3 >> >> Python 3.8.1 (v3.8.1:1b293b6006, Dec 18 2019, 14:08:53) >> >> [Clang 6.0 (clang-600.0.57)] on darwin >> >> Type "help", "copyright", "credits" or "license" for more information. >> >> >>> help >> >> Type help() for interactive help, or help(object) for help about object. >> >> >>> which python3 >> >> File "<stdin>", line 1 >> >> which python3 >> >> ^ >> >> SyntaxError: invalid syntax >> >> >>> >> >> On Fri, May 29, 2020 at 12:52 PM Modeller Caretaker < >> modeller-care@salilab.org> wrote: >> >>> On 5/29/20 12:03 PM, Xiao Ran Luo wrote: >>> > Luos-Air:~ luoxiaoran$ which python3 >>> > >>> > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3 >>> >>> This is not Apple Python (/usr/bin/python3) or Homebrew Python >>> (/usr/local/bin/python3). Looks like you have a third version of Python >>> installed. >>> >>> > So I guess I am still not using Homebrew's Python -how do I switch to >>> > using Homebrew's Python? >>> >>> Run /usr/local/bin/python3 explicitly rather than just "python3". Or >>> edit your profile (maybe ~/.bashrc or ~/.zshrc) and remove >>> /Library/Frameworks/Python.framework/Versions/3.8/bin from your PATH. >>> >>> > Sorry, I just realized there are a few more things my friend >>> > recommended I install, are these all okay to install? >>> >>> You an install whatever Homebrew packages you like; they won't affect >>> your Modeller installation. >>> >>> Ben Webb, Modeller Caretaker >>> -- >>> modeller-care@salilab.org https://salilab.org/modeller/ >>> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >>> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> >