build based on cb79fbc

Author: Documenter.jl

previews/PR212/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"documenter_version":"1.18.0","generation_timestamp":"2026-09-01T02:40:32","julia_version":"1.12.7"}}
+{"documenter":{"documenter_version":"1.18.0","generation_timestamp":"2026-09-01T03:34:44","julia_version":"1.12.7"}}

previews/PR212/API/API_examples/index.html

@@ -112,4 +112,4 @@
     run_call!(context, :leaf_energy; publish=true)
 
     return nothing
-end</code></pre><p><code>run_call!</code> defaults to <code>publish=false</code>, so trial calls mutate target statuses without publishing temporal streams or committing mutable environment updates. Pass non-committing trial state with <code>environment=trial_state</code>, then call <code>commit_environment!</code> before publishing the accepted state.</p><h2 id="Next-Steps"><a class="docs-heading-anchor" href="#Next-Steps">Next Steps</a><a id="Next-Steps-1"></a><a class="docs-heading-anchor-permalink" href="#Next-Steps" title="Permalink"></a></h2><ul><li><a href="../../migration_composite_model/">Migrating To The CompositeModel/Object API</a> translates scenarios written with removed APIs.</li><li><a href="../../API/API_public/">Public API</a> lists constructors, selectors, lifecycle helpers, environment helpers, and explanation helpers.</li><li><a href="../../model_traits/">Model traits</a> documents <code>inputs_</code>, <code>outputs_</code>, <code>dep</code>, <code>timespec</code>, <code>output_policy</code>, and <code>environment_inputs_</code>.</li><li><a href="../../dev/maespa_model_handoff/">MAESPA-style model example handoff</a> records the current multi-plant model energy-balance acceptance example.</li></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.18.0 on <span class="colophon-date" title="Tuesday 1 September 2026 02:40">Tuesday 1 September 2026</span>. Using Julia version 1.12.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+end</code></pre><p><code>run_call!</code> defaults to <code>publish=false</code>, so trial calls mutate target statuses without publishing temporal streams or committing mutable environment updates. Pass non-committing trial state with <code>environment=trial_state</code>, then call <code>commit_environment!</code> before publishing the accepted state.</p><h2 id="Next-Steps"><a class="docs-heading-anchor" href="#Next-Steps">Next Steps</a><a id="Next-Steps-1"></a><a class="docs-heading-anchor-permalink" href="#Next-Steps" title="Permalink"></a></h2><ul><li><a href="../../migration_composite_model/">Migrating To The CompositeModel/Object API</a> translates scenarios written with removed APIs.</li><li><a href="../../API/API_public/">Public API</a> lists constructors, selectors, lifecycle helpers, environment helpers, and explanation helpers.</li><li><a href="../../model_traits/">Model traits</a> documents <code>inputs_</code>, <code>outputs_</code>, <code>dep</code>, <code>timespec</code>, <code>output_policy</code>, and <code>environment_inputs_</code>.</li><li><a href="../../dev/maespa_model_handoff/">MAESPA-style model example handoff</a> records the current multi-plant model energy-balance acceptance example.</li></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.18.0 on <span class="colophon-date" title="Tuesday 1 September 2026 03:34">Tuesday 1 September 2026</span>. Using Julia version 1.12.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR212/API/API_private/index.html

@@ -7,4 +7,4 @@
 test/runtests.jl                       885 passed
 docs/make.jl                           passed
 PlantBiophysics/test/runtests.jl       117 passed
-git diff --check                       passed</code></pre><p>The complete package suite includes Aqua, all focused restoration files, the broad unified runtime regression, examples, fitting, and doctests. The documentation build completed its executable examples, doctests, cross-references, document checks, and HTML rendering successfully.</p><p>The current uncommitted XPalm CompositeModel/Object migration loads this PlantSimEngine worktree and executes 74 of 75 downstream assertions. Its remaining assertion expects the removed runtime&#39;s first-step LAI (<code>0.000272</code>); the current compiled dependency order correctly runs leaf area before plant and model aggregation, so the initial zero-biomass leaf produces <code>0.0</code>. This is a downstream fixture expectation in a dirty migration worktree, not a package-specific behavior to restore in PlantSimEngine. No XPalm workaround was added here.</p><h2 id="Compatibility-Boundary"><a class="docs-heading-anchor" href="#Compatibility-Boundary">Compatibility Boundary</a><a id="Compatibility-Boundary-1"></a><a class="docs-heading-anchor-permalink" href="#Compatibility-Boundary" title="Permalink"></a></h2><p>Historical mapping source and tests were removed. Migration guidance remains in the documentation for downstream packages moving to the composite-model/object API. The branch-only intermediate prototype was also removed because it was never released and has no compatibility boundary.</p><p>Requested output histories are still materialized after a run. Dependency-only temporal histories are bounded, but a fully online output sink would be an additional optimization rather than a missing requirement of this redesign.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../composite_model_implementation_plan/">« Composite model/object implementation plan</a><a class="docs-footer-nextpage" href="../maespa_model_handoff/">MAESPA-style composite-model example handoff »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.18.0 on <span class="colophon-date" title="Tuesday 1 September 2026 02:40">Tuesday 1 September 2026</span>. Using Julia version 1.12.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+git diff --check                       passed</code></pre><p>The complete package suite includes Aqua, all focused restoration files, the broad unified runtime regression, examples, fitting, and doctests. The documentation build completed its executable examples, doctests, cross-references, document checks, and HTML rendering successfully.</p><p>The current uncommitted XPalm CompositeModel/Object migration loads this PlantSimEngine worktree and executes 74 of 75 downstream assertions. Its remaining assertion expects the removed runtime&#39;s first-step LAI (<code>0.000272</code>); the current compiled dependency order correctly runs leaf area before plant and model aggregation, so the initial zero-biomass leaf produces <code>0.0</code>. This is a downstream fixture expectation in a dirty migration worktree, not a package-specific behavior to restore in PlantSimEngine. No XPalm workaround was added here.</p><h2 id="Compatibility-Boundary"><a class="docs-heading-anchor" href="#Compatibility-Boundary">Compatibility Boundary</a><a id="Compatibility-Boundary-1"></a><a class="docs-heading-anchor-permalink" href="#Compatibility-Boundary" title="Permalink"></a></h2><p>Historical mapping source and tests were removed. Migration guidance remains in the documentation for downstream packages moving to the composite-model/object API. The branch-only intermediate prototype was also removed because it was never released and has no compatibility boundary.</p><p>Requested output histories are still materialized after a run. Dependency-only temporal histories are bounded, but a fully online output sink would be an additional optimization rather than a missing requirement of this redesign.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../composite_model_implementation_plan/">« Composite model/object implementation plan</a><a class="docs-footer-nextpage" href="../maespa_model_handoff/">MAESPA-style composite-model example handoff »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.18.0 on <span class="colophon-date" title="Tuesday 1 September 2026 03:34">Tuesday 1 September 2026</span>. Using Julia version 1.12.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR212/API/API_public/index.html

@@ -119,4 +119,4 @@
 Diagnostics.explain_writers(sim)
 Diagnostics.explain_execution_plan(sim)
 Diagnostics.explain_output_retention(sim)
-Diagnostics.explain_runtime_performance(sim)</code></pre><p>These helpers should return stable structured data, not only pretty text. A binding row should include at least:</p><ul><li>consumer application id;</li><li>consumer object id;</li><li>consumer variable;</li><li>source selector;</li><li>resolved producer application id or environment provider id;</li><li>resolved producer object ids;</li><li>process/name filters;</li><li>temporal policy and window;</li><li>carrier kind;</li><li>copy/reference semantics;</li><li>reason the binding was chosen;</li><li>whether it came from inference, <code>dep(model)</code>, or <code>ModelSpec</code>.</li></ul><p>Execution-plan rows should additionally expose the selected object ids, concrete model/status/carrier types, batch size, and whether the inner loop is homogeneous and specialized.</p><p>Output-retention rows should expose the retained application id, variable, retention reasons, compiled retention horizon, and current target count so agents can distinguish default retain-all behavior, requested output streams, and bounded temporal-dependency streams.</p><p>Errors should report concrete object labels, scope selectors, process names, variables, and suggested fixes.</p><h2 id="API-Position"><a class="docs-heading-anchor" href="#API-Position">API Position</a><a id="API-Position-1"></a><a class="docs-heading-anchor-permalink" href="#API-Position" title="Permalink"></a></h2><p>This is a breaking design. Model kernels use <code>run!(model, status, environment, constants, context)</code> while the scenario configuration surface uses <code>CompositeModel</code>, <code>Object</code>, <code>ModelSpec</code>, selectors, <code>ModelSpec(...; inputs=...)</code>, <code>ModelSpec(...; calls=...)</code>, <code>ModelSpec(...; every=...)</code>, and <code>Environment(...)</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../public_api_refinement_completion_audit/">« Public API refinement completion audit</a><a class="docs-footer-nextpage" href="../distributed_output_ownership/">Distributed output ownership »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.18.0 on <span class="colophon-date" title="Tuesday 1 September 2026 02:40">Tuesday 1 September 2026</span>. Using Julia version 1.12.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Diagnostics.explain_runtime_performance(sim)</code></pre><p>These helpers should return stable structured data, not only pretty text. A binding row should include at least:</p><ul><li>consumer application id;</li><li>consumer object id;</li><li>consumer variable;</li><li>source selector;</li><li>resolved producer application id or environment provider id;</li><li>resolved producer object ids;</li><li>process/name filters;</li><li>temporal policy and window;</li><li>carrier kind;</li><li>copy/reference semantics;</li><li>reason the binding was chosen;</li><li>whether it came from inference, <code>dep(model)</code>, or <code>ModelSpec</code>.</li></ul><p>Execution-plan rows should additionally expose the selected object ids, concrete model/status/carrier types, batch size, and whether the inner loop is homogeneous and specialized.</p><p>Output-retention rows should expose the retained application id, variable, retention reasons, compiled retention horizon, and current target count so agents can distinguish default retain-all behavior, requested output streams, and bounded temporal-dependency streams.</p><p>Errors should report concrete object labels, scope selectors, process names, variables, and suggested fixes.</p><h2 id="API-Position"><a class="docs-heading-anchor" href="#API-Position">API Position</a><a id="API-Position-1"></a><a class="docs-heading-anchor-permalink" href="#API-Position" title="Permalink"></a></h2><p>This is a breaking design. Model kernels use <code>run!(model, status, environment, constants, context)</code> while the scenario configuration surface uses <code>CompositeModel</code>, <code>Object</code>, <code>ModelSpec</code>, selectors, <code>ModelSpec(...; inputs=...)</code>, <code>ModelSpec(...; calls=...)</code>, <code>ModelSpec(...; every=...)</code>, and <code>Environment(...)</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../public_api_refinement_completion_audit/">« Public API refinement completion audit</a><a class="docs-footer-nextpage" href="../distributed_output_ownership/">Distributed output ownership »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.18.0 on <span class="colophon-date" title="Tuesday 1 September 2026 03:34">Tuesday 1 September 2026</span>. Using Julia version 1.12.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>