Problem

The current Brian2 code generation pipeline suffers from a fundamental performance bottleneck. The issue is not tied to the specific tools we use, but rather to the Ahead-of-Time (AOT) compilation paradigm itself.

Regardless of whether we use Cython (our current approach) or manual C-extensions, the workflow remains slow and cumbersome:

• Generate large C++ source files on disk
• Invoke an external compiler (e.g., g++, clang) with significant overhead
• Wait for compilation to complete (often 15–40 seconds, which disrupts interactivity)
• Dynamically load the compiled result through a complex process

In other words, the bottleneck lies in the file-based, external-compiler, AOT workflow.

Proposed Solution: JIT Compilation with cppyy

This PR introduces cppyy as a new runtime code generation target, shifting from AOT to Just-in-Time (JIT) compilation.

With cppyy, C++ code is compiled in-memory using the Cling C++ interpreter, which eliminates:

• File I/O overhead
• External compiler process spawning
• Long compilation waiting times
• Complex dynamic loading procedures

Current Status

Implemented and functional in this initial proof of concept:

• End-to-end JIT compilation pipeline
• Basic neuron group simulations
• State updates, thresholds, and resets
• Template system for different operations
• Integration with the device layer

Next Steps

This PR serves as a starting point and contains some hardcoded components that will be refined in future iterations. A follow-up issue will be created to present the detailed roadmap and outline how we plan to transition from this POC to a fully integrated solution for Brian2 :)