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simple-architecture

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Actualizado27 de junio de 2026 a las 23:43

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.

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hael

hael/SIMPLE

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SKILL.md

readonly

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.f90
src/main/apis/simple_exec_api.f90
src/main/simple_cmdline.f90
src/main/ui/simple_ui.f90
src/main/params/simple_parameters.f90
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.

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simple-main-stream

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Use when working in SIMPLE's src/main/stream subsystem, including online/mini-stream orchestration, chunk and microchunk processing, staged pipeline steps, watchers, queue/message definitions, and streaming variants of preprocessing and cluster2D workflows.

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Use when working on SIMPLE's streaming microchunk class-average rejection, simple_microchunked2D lifecycle sentinels, pass-1/pass-2/refchunk/match generation, skip_pass_2 behavior, simple_cluster2D_rejector criteria, or boundaries with model_cavgs_rejection.

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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.f90

src/main/apis/simple_exec_api.f90

src/main/simple_cmdline.f90

src/main/ui/simple_ui.f90

src/main/params/simple_parameters.f90

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.