Fix Mac tests by making an unshallow copy of Homebrew repos
It seems that updating shallow Git clones is expensive, and as a result
Homebrew recently started refusing to update shallow clones (see
https://github.com/Homebrew/discussions/discussions/226). This commit
tries to fix the problem by making these repos into full clones before
running "brew update".
I also came across another error about there being a conflicting version
of pip3 in /usr/local. I suspect that is related to the other Python
binaries that the script has to delete, so I added pip3 to the list and
that seemed to solve the problem.