Statistical Profiling in Python

Have you tried Pyflame? It's based on ptrace, so it shouldn't be affected by CPython's signal handling subtleties.

I use py-spy with speedscope now. It is a very cool combination.

py-spy works on Windows/Linux/macOS, can output flame graphs by its own and is actively deployed, eg. subprocess profiling support was added in October 2019.

Maybe the perf-tool from Brendan Gregg can help