In terms of specs, I'm running MacOS Ventura 13.7.1 and Python 3.13. I use QGIS for work, and I attempted to update remotior-sensus so I could use a specific plugin. (base) [my system]:~ Morgan$ /Applications/QGIS.app/Contents/MacOS/bin/pip3 install --upgrade remotior-sensus scikit-learn torch However, in the process of updating it apparently uninstalled a bunch of packages (like numpy) which are needed to make QGIS (and other programs) run and resulted in an _ARRAY_API failure when I tried to open QGIS. I attempted to reinstall the uninstalled packages with brew, however I kept getting linking errors. For example, gmp below: ==> Downloading https://ghcr.io/v2/homebrew/core/gmp/manifests/6.3.0 Already downloaded: /Users/Morgan/Library/Caches/Homebrew/downloads/70a72a71216843d66a953c06ff6337445ce9bc94fae9f0e301e2f59005274a8e--gmp-6.3.0.bottle_manifest.json ==> Pouring gmp--6.3.0.ventura.bottle.tar.gz Error: The `brew link` step did not complete successfully The formula built, but is not symlinked into /usr/local Could not symlink include/gmp.h /usr/local/include is not writable. You can try again using: brew link gmp At which point I linked all the packages which seemed to go fine for the most part. However, then I kept getting an error that I needed to install python@3.13. So I ran brew install python@3.13 and got this error: (base) [my system]:~ Morgan$ brew install python ==> Downloading https://formulae.brew.sh/api/formula.jws.json ==> Downloading https://formulae.brew.sh/api/cask.jws.json Warning: python@3.13 3.13.2 is already installed, it's just not linked. To link this version, run: brew link python@3.13 At which point I tried to link Python and got this: (base) [my system]:~ Morgan$ brew link python@3.13 Linking /usr/local/Cellar/python@3.13/3.13.2... Error: Could not symlink bin/idle3 Target /usr/local/bin/idle3 already exists. You may want to remove it: rm '/usr/local/bin/idle3' To force the link and overwrite all conflicting files: brew link --overwrite python@3.13 To list all files that would be deleted: brew link --overwrite python@3.13 --dry-run I did try to uninstall and reinstall Python, thinking maybe that starting over might be the safest option, but it didn't seem to actually uninstall. At this point I'm afraid to mess with it any further, as I apparently know enough to get myself into trouble but not enough to get myself out. How can I fix this? Continue reading...
