| 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:
production/simple_exec.f90src/main/apis/simple_exec_api.f90src/main/simple_cmdline.f90src/main/ui/simple_ui.f90src/main/params/simple_parameters.f90src/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.
