Module compartmentalization

[ConnectedSystems]

@Zapiano the target branch here compartmentalized-adria is a branch off the iv-study-changes branch.

This is a larger set of changes and I don't want to interfere with the study codebase as it should be fairly static from now.

Note we also need to merge in changes on main (including the documentation updates).

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Summary

Moves optional, heavyweight analysis tools (MLJ, SIRUS, Bootstrap, HypothesisTests, DataEnvelopmentAnalysis) out of the ADRIA core package and into a new companion package ADRIAAnalysis.jl, structured as a Julia 1.11 workspace member.

This reduces ADRIA's mandatory dependency footprint — users who only run simulations no longer pay the load-time and precompilation cost of ML and statistical inference libraries.

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Changes

New: packages/ADRIAAnalysis/

A new Julia package declared as a workspace member in the root Project.toml:

packages/ADRIAAnalysis/
├── Project.toml          # MLJ, SIRUS, Bootstrap, HypothesisTests, DEA, ADRIA as deps
├── Manifest.toml
├── src/
│   ├── ADRIAAnalysis.jl  # package entry point
│   ├── analysis/
│   │   ├── clustering.jl
│   │   ├── data_envelopment.jl
│   │   ├── feature_set.jl
│   │   ├── intervention.jl
│   │   ├── rule_extraction.jl
│   │   └── scenario.jl
│   └── sensitivity/
│       └── sensitivity.jl
└── test/
    └── runtests.jl       # 48 tests covering all moved modules

ADRIA core trimmed

• Removed exports and includes for all moved analysis functions
• Removed MLJ, SIRUS, Bootstrap, HypothesisTests, DataEnvelopmentAnalysis from Project.toml dependencies
• Deleted source files relocated to ADRIAAnalysis:
  • src/analysis/clustering.jl
  • src/analysis/data_envelopment.jl
  • src/analysis/feature_set.jl
  • src/analysis/intervention.jl
  • src/analysis/rule_extraction.jl
  • src/analysis/scenario.jl
  • src/analysis/sensitivity.jl
• Removed Base.precompile block for moved symbols

AvizExt compatibility fixes

AvizExt previously called ADRIA.analysis.* functions that are now in ADRIAAnalysis. Since AvizExt cannot depend on ADRIAAnalysis (circular), the scenario grouping helpers are duplicated as private functions in ext/AvizExt/_scenario_helpers.jl:

• _scenario_clusters, _scenario_rcps, _scenario_types — private copies of the moved grouping logic
• Type signatures in viz/data_envelopment.jl and viz/rule_extraction.jl relaxed from concrete DEAResult/Rule to abstract/untyped to avoid hard imports

Build, Docker, docs

• Dockerfile: Julia 1.10.4 → 1.11.5
• build/make.jl: platform-aware sysimage extension (.dll / .dylib / .so)
• build/precompile_script.jl: restored with real execution trace
• docs/src/development/docker.md: updated for Julia 1.11 and workspace layout
• docs/src/usage/analysis.md: added using ADRIAAnalysis import note
• docs/src/usage/getting_started.md: added ADRIAAnalysis install instructions

Workspace declaration

Root Project.toml gains:

[workspace]
packages = ["packages/ADRIAAnalysis"]

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Breaking changes

Old (ADRIA ≤ previous)	New (ADRIAAnalysis)
ADRIA.analysis.sensitivity.pawn	ADRIAAnalysis.sensitivity.pawn
ADRIA.analysis.cluster_series_by_outcome	ADRIAAnalysis.cluster_series_by_outcome
ADRIA.analysis.rules	ADRIAAnalysis.rules
ADRIA.analysis.data_envelopment_analysis	ADRIAAnalysis.data_envelopment_analysis
ADRIA.analysis.scenario_types	ADRIAAnalysis.scenario_types

Users need to add ADRIAAnalysis to their project and replace the ADRIA.analysis.* prefixes.

Installing ADRIAAnalysis (unregistered): Until the package is registered in the General registry, users install it via the subdir Pkg feature (Julia 1.11+):

pkg> add https://github.com/open-AIMS/ADRIA.jl:packages/ADRIAAnalysis

Or explicitly in their Project.toml:

[sources]
ADRIAAnalysis = {url = "https://github.com/open-AIMS/ADRIA.jl", subdir = "packages/ADRIAAnalysis"}

Note: getting_started.md does not yet include these instructions — a follow-up doc PR is needed.

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Deferred / known follow-ons

• Step 9: Migrate test domain to a Julia Artifact. Deferred until a clean upload pipeline exists. Blocks @compile_workload body in both ADRIA and ADRIAAnalysis.
• AWSS3 / libsodium_jll in load path: Still present via the Zarr dependency. Zarr v0.10 moves AWSS3 to an extension; upgrade is currently blocked by a compat constraint — investigate separately.
• Invalidation chain: REPL, Distributions, Accessors, DifferentiationInterface still show 100% recompilation on warm load. Likely Zarr → LazyArtifacts → Pkg → REPL chain.
• Sysimage on Linux: Requires Docker/CI environment — not verified locally.
• Version bump: This is a breaking change; Project.toml version must be incremented before release.

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Test plan

• ] test ADRIAAnalysis passes all 48 tests
• ] test ADRIA passes with moved symbols removed
• using ADRIA succeeds without MLJ/SIRUS/Bootstrap in scope
• using ADRIAAnalysis resolves all moved symbols
• AvizExt loads and clustering/sensitivity plots render correctly
• Sysimage build succeeds on macOS/Windows (Linux: pending Docker)
• Docs build (make.jl) succeeds

[Zapiano]

Closed in favor of #1100