simple-architecture

name	simple-architecture
description	Use when working anywhere in the SIMPLE repository and you need a high-level architectural map of the cryo-EM platform, including the relationship between production executables, the src core library, src/main subsystems, tests, scripts, docs, and the NICE layer.

SIMPLE Architecture

Use this skill first when the request spans multiple parts of SIMPLE.

Mental Model

SIMPLE is a scientific application platform, not a narrow library.

• production/ contains thin executable entrypoints such as simple_exec, single_exec, simple_stream, simple_test_exec, and simple_private_exec.
• src/ builds one large static core library.
• src/main/ contains most application/domain logic.
• src/fileio/, src/utils/, and src/defs/ provide shared infrastructure.
• doc/ contains architecture and policy notes that are often more useful than comments in code.
• nice/ is the optional web/UI layer.

Runtime Layering

Read these first for end-to-end flow:

1. production/simple_exec.f90
2. src/main/apis/simple_exec_api.f90
3. src/main/simple_cmdline.f90
4. src/main/ui/simple_ui.f90
5. src/main/params/simple_parameters.f90
6. src/main/simple_builder.f90

The common pattern is:

executable -> API aggregator -> UI/CLI lookup -> exec router -> commander -> strategies/domain objects -> file/project/image/reconstruction objects

Build And Docs

• Build shape: CMakeLists.txt, src/CMakeLists.txt, production/CMakeLists.txt
• Repo overview: README.md, doc/code_overview/code_base_map.md
• Policy docs worth checking before refactors: doc/policies/*.md, doc/refactoring_notes/*.md

Working Style

• Treat src/main/exec as routing/orchestration.
• Treat src/main/commanders as command objects and high-level workflow owners.
• Treat src/main/strategies as algorithm/policy execution layers.
• Treat src/main/image, project, ori, pftc, volume, nu_filt, params, ctf, motion, and opt as core scientific subsystems.
• Expect modern Fortran patterns: modules, abstract types, type-bound procedures, generics, allocatables, submodules, OpenMP, and C interop.

Cross-Cutting Hotspots

• refine3D spans ui, exec, commanders, strategies, volume, project, pftc, and ori.
• cluster2D spans ui, exec, commanders, strategies, class, image, project, and stream.
• Streaming work often crosses stream, project, motion, pick, ctf, and nice.