I found a few things.
Moving in Atom – handy navigation manual.
atom-ui-ide. Among other things, it lets you find all references of a function. (either this or python-ide gives you hover-documentation like VSC). It’s sort-of a base package for IDE functionality.
python-ide builds atop that and allows you to search symbols / function declarations in the current project - not just file. However, it requires python language server to work, which is maintained by Palantir – so I don’t know how shady/safe that is. It also let’s you hover over functions/classes for documentation, even for out-of-project imports. It also let’s you CMD-click on a function and go straight to its declaration, even out-of-project. I haven’t seen this work in all cases (worked for sklearn.ndimage imports but not sklearn.metrics), but I’ve been able to CMD-click directly into the NumPy source code w/ this.
atom-ctags enables the built-in Atom search features. It builds a ctags file of recognized symbols, per project. I think VSC does this automatically behind the scenes. It also let’s you use CMD-Shift-R (Mac) to search symbols in a project (the “opim” search Jeremy did).
The functionality does come with a price. On my MacBook, enabling auto-ide-ui adds a solid half-second to Atom’s start time. Enabling it with python-ide makes that almost a full second but feels longer.
Having played with it a bit, I think if I want to keep Atom’s speed & minimalism, I’d stick with using the atom-ctags to let me search symbols or go to definitions (CMD-Shift-Down or CMD-Shift-Up to come back) – although it doesn’t always work: I’m not sure when/not symbols/ctags are generated.
I may check out VSC for Mac (or just Visual Studio?) if I find I need the functionality, but that’s what I’ve found so far.