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Multi-plants - #186

Merged

VEZY merged 236 commits into

mainfrom

multi-plants

Sep 6, 2026

Merged

Multi-plants#186
VEZY merged 236 commits into
mainfrom
multi-plants

Commits on Mar 18, 2026
- Update README.md
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Commits on May 3, 2026
- Merge branch 'main' into multi-plants
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Commits on Jun 3, 2026
- Add domain simulations with hard-domain targets and microclimate support
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- Update docstrings and doc
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- Remove backward compatibility
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Commits on Jun 4, 2026
- Another large cleanup
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- Use true PlantBiophysics models in the examples
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- Use two layers for the soil in maespa example
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- Update maespa_domain_example.jl
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- MAESPA example: make the model a bit more process-based + scene LAI as a proper model
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  ef8d5d1
- Auto-detect mapped variables between domains (not required in the user status anymore)
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- Update maespa_domain_example.jl
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- Split Route types and route materialization into different scripts
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Commits on Jun 5, 2026
- Remove all references to ModelList
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- Starting implementing the new scene API
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Commits on Jun 6, 2026
- Add producer application metadata and selector validation in Inputs.
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- Better error catching for Inputs
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- Implements default scope inference for compiled scene/object dependencies.
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- Implements the remaining "Phase 5" mechanics
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Commits on Jun 13, 2026
- Implements the goal of multi-plants and spatial (mutable) microclimate
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- Remove Domain, SimulationMapping, Route, AllDomains, HardDomains, and their helpers, runtime, tests, and documentation.
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Commits on Jun 18, 2026
- First end-to-end implementation of the new API
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- Add `add_organ!` again for an easier high-level function
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Commits on Jun 19, 2026
- Adapt past tests and doc to the new API
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Commits on Jun 20, 2026
- Adapt the graph editor to the new API
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- Simplify examples in docs -> use defaults when possible
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- Harden a bit more the API
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Commits on Jun 21, 2026
- Fix benchmarks
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- Delete runtests.jl
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Commits on Jun 22, 2026
- Simplify examples in docs -> use ModelList equivalent whenever possible
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- Rename Scene into CompositeModel
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Commits on Jun 25, 2026
Commits on Jul 28, 2026
- Add and use `with_environment!`
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Commits on Jul 29, 2026
- Stabilize CompositeModel runtime contracts
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- Support explicit live status bindings
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- docs: add API and performance implementation goal
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- perf: add runtime metrics and incremental execution paths
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- fix: handle empty execution plans in runtime metrics
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- fix: execute staged performance benchmark callbacks
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- perf: warm and persist short XPalm profiles
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- perf: refresh execution plans by application delta
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- perf: preserve call bindings and streamline hot loops
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- perf: bound temporal dependency storage
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- perf: compile direct temporal source cells
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- perf: reuse scheduled run contexts
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- perf: precompile dependency output cells
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- docs: record performance restoration progress
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- perf: index meteorology rows directly
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- perf: reuse current environment bindings
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- perf: defer targeted lifecycle call refreshes
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- perf: persist lifecycle dependency deltas
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- perf: compile XPalm full cycle under gate
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- fix: preserve lifecycle application completion
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- docs: record corrected XPalm milestone
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- perf: cache compiled hard-call targets
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- docs: record hard-call cache milestone
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- fix: preserve typed call environment overrides
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- perf: accumulate subtree selectors in place
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- perf: preallocate lifecycle input bindings
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- perf: cache object ancestor paths
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- perf: synchronize hard-call views lazily
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- docs: record XPalm lifecycle performance milestone
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- perf: avoid full-scene lifecycle copies
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- perf: cache dirty-topology call compilation
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- perf: update lifecycle indexes in place
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- perf: avoid routine status-view index copies
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- perf: index lifecycle call-bundle propagation
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- docs: record sub-ten-second XPalm milestone
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- api: adopt five-argument model kernels
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- perf: remove obsolete model bundle cache
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- api: unify model environment vocabulary
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- docs: record downstream kernel migration
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Commits on Jul 30, 2026
- api: distinguish required inputs from defaults
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- docs: explain explicit input initialization
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- perf: keep input schema validation allocation free
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- docs: complete explicit input schema milestone
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- api: collapse model specs onto direct keywords
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- docs: complete direct scenario configuration milestone
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- api: make selector criteria context aware
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- docs: complete selector API milestone
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- api: split focused public namespaces
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- docs: complete public namespace milestone
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- api: improve simulation result ergonomics
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- test: cover multi-object final state
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- docs: complete simulation results milestone
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- api: remove compatibility aliases
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- perf: make benchmark evidence reproducible
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- perf: complete runtime benchmark matrix
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- docs: harden reusable example contracts
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- docs: add progressive start-here journey
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- docs: add one-plant composition journey
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- docs: add template and instance journey
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- docs: add global and spatial environment journey
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- docs: add multirate cadence journey
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- docs: add structural lifecycle journey
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- docs: add mutable environment journey
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- docs: add advanced execution journey
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- docs: add MAESPA synthesis journey
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- docs: add progressive model-author journey
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- docs: enforce progressive journey contracts
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- perf: make structural lifecycle refresh incremental
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- ci: persist full XPalm performance runs
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- fix: prefer scheduled output publishers
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- fix: preserve private output coupling
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- docs: record final local validation matrix
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- perf: make structural lifecycle refresh delta-based
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- docs: record lifecycle performance restoration
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- docs: fix whitespace validation
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- ci: repair benchmark workflow environments
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- ci: bootstrap full performance dispatch
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- ci: prepare path-based performance environment
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- ci: qualify benchmark object fixtures
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- ci: support legacy benchmark baselines
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Commits on Jul 31, 2026
- ci: pin PlantGeom for full performance runs
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- docs: record completed downstream performance gate
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- Merge origin/main into multi-plants
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- fix: qualify graph editor E2E entry point
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- test: initialize Beer in graph editor E2E
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- fix: stabilize merged release validation
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- fix: include environment ports in graph layout
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- fix: serialize empty graph ports as arrays
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- fix: match parametric models in graph editor
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- test: target graph editor timestep controls
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- test: scope graph cycle edges by projection
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- fix: serialize graph update rules as arrays
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- test: scope graph editor save action
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- fix: stabilize Julia 1.10 validation
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- perf: specialize input schema validation
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- test: account for Julia 1.10 allocation floor
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Commits on Aug 6, 2026
- Update SKILL.md
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- Merge branch 'main' into multi-plants
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Commits on Aug 10, 2026
- Add `model_object` for AMAPSim
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- Modernize graph editor model schema
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- Add graph editor runtime catalogs
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- Build template and environment editor workflows
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- Document and exercise graph editor v2
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Commits on Aug 11, 2026
- Fix graph editor validation regressions
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- Sync model_object public API contract
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- Fix GraphEditor extension dependency loading
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- Add realistic PlantBiophysics performance harness
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- Compile hard calls into typed execution batches
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- Add allocation-free hard-call fast APIs
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- Optimize previous-timestep input materialization
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- Document and automate downstream performance gates
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- Handle absent previous-step source streams
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- Record hard-call validation progress
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- Honor XPalm release benchmark sample count
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- Record downstream performance acceptance
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- Remove completed hard-call performance goal
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- Add immutable scenario performance goal
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- Benchmark immutable scenario steady state
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- Skip unchanged output target refreshes
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- Use one runtime mutation revision
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- Track output request membership intervals
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- Separate immutable application plans from targets
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- Compile immutable input and call plans
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- Clarify lifecycle storage growth invariant
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- Compile static scenario dependency graph
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Commits on Aug 12, 2026
- Dispatch only due multirate applications
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- Journal shared lifecycle deltas
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- Compile selectors for lifecycle refresh
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- Compile direct output publication sinks
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- Compile immutable environment plans
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- Record dense slot evaluation
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- Document immutable runtime phases
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- Keep compiled runtime shell reference-backed
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- Avoid boxing immutable runtime plans
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- Record immutable scenario performance acceptance
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- Fix graph editor E2E teardown
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- Fix Julia 1.10 allocation regressions
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Commits on Aug 23, 2026
- docs: define distributed output ownership
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- benchmark: establish distributed output baselines
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- feat: expose identities for compiled many bindings
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- benchmark: cover compiled many identity access
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- docs: explain identity-aware many inputs
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- feat: compile cross-object output targets
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- benchmark: cover distributed output compilation
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- docs: describe distributed output destinations
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- feat: schedule and retain distributed outputs
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- feat: add keyed output assignment
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- benchmark: cover distributed output execution
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- docs: document keyed output assignment
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- feat: resolve registered source object identities
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- perf: eliminate wide output alias allocations
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- benchmark: cover wide identified output assignment
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- perf: materialize heterogeneous temporal inputs without allocations
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Commits on Aug 25, 2026
- feat: allow authoritative dynamic-organ status initialization
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- fix: resolve distributed-output runtime dispatch
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Commits on Aug 26, 2026
- refactor: keep runtime status in model registry
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- feat: expose current execution target identity
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- feat: validate scientific variable contracts
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- docs: document hard-call targets
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- feat: initialize newly registered scheduled objects
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- fix: correct Beer extinction fitting
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- Add compile-time status type conversion
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- Add status conversion diagnostics and safe initialization
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- Preserve converted types through runtime lifecycle
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- Validate particle status propagation
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- Cover status conversion in instances and hot paths
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- Preserve temporal reducer result types
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- Preserve status policy in graph editor rebuilds
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- Complete status conversion test matrix
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  c1bfacc
- Document scenario status type conversion
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  ec63a97
- Prevent stale MTG runtime status columns
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- Preserve configuration exceptions
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- Qualify Beer fitting test API
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Commits on Aug 27, 2026
- Benchmark status registry lookup
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- Fix empty-plan structural refresh
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  696d8e6
- Benchmark organ lifecycle costs
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- fix: reserve detached MTG node ids
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Commits on Aug 28, 2026
- Fix Julia 1.10 allocation test
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  2e3b471
- Delete TEMP_IMMUTABLE_SCENARIO_PERFORMANCE_GOAL.md
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- Update Project.toml
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Commits on Aug 30, 2026
Commits on Aug 31, 2026
- Optimize dynamic organ lifecycle refresh
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  afc1b3e
- perf: accelerate dynamic organ lifecycle
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  f521b8d
- perf: append stable many input sources in place
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  492c521
- perf: cache lifecycle targets and runtime contexts
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  ce06cf2
Commits on Sep 1, 2026
- perf: reuse planned singleton input producers
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  d9ac84c
- perf: specialize uninstrumented execution groups
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  503f7a7
- perf: index observed manual call owners
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  committed
  2dcedda
- perf: index manual calls by exact callee target
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  committed
  b053534
- Merge pull request #212 from VirtualPlantLab/codex/multi-plants-performance
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  ff1d0fb
- feat: improve model authoring for agents
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Commits on Sep 2, 2026
- fix: resolve parametric models in graph editor
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  a2ce183
- Update CHANGELOG.md
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  8c24ac7
Commits on Sep 3, 2026
- ci: test downstreams from local sources
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  c664522
- Update Integration.yml
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Commits on Sep 5, 2026

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Commits on Mar 18, 2026

Commits on May 3, 2026

Commits on Jun 3, 2026

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Commits on Jun 6, 2026

Commits on Jun 13, 2026

Commits on Jun 18, 2026

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Commits on Jul 28, 2026

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Commits on Jul 30, 2026

Commits on Jul 31, 2026