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feat!: replace dependency graph with reactive invalidation - #5641

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DanySK wants to merge 214 commits into

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marmellata

Open

feat!: replace dependency graph with reactive invalidation#5641
DanySK wants to merge 214 commits into
masterfrom
marmellata

Commits on Apr 29, 2026
- feat!: add a reactive engine (#5066)
  
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  b74604f
- docs: improve Javadoc
  
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  4bfdc8e
- chore(api): provide a way to register to an observable without triggering callback invocation
  
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  ad61806
- chore(biochemestry): port `BiomolPresentInNeighbor` to kotlin
  
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  ffd2ba4
- feat!: fully transition to observable neighborhoods
  
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  feda98d
- feat!: make node counting observable
  
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  bcbfb8c
- fix(biochemistry): use current node count in assertions
  
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  231ef33
- chore(api): add `updateOrNull` with observable map values
  
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  d54850d
- feat!: fully transition to observable positions
  
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  c0a2941
- chore(api): add way to register to observables without sending initial callback
  
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  669dde8
- fix(scafi): avoid depending on observables
  
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  c03202d
- feat!: replace Engine with reactive counterpart and get rid of dependency graph
  
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  bc26cb6
- fix: properly implement and call `dispose` on nodes and reactions
  
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  761d3ae
- chore: try avoid memory leaks for region observers
  
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  82bdb4e
- feat(api): improve lapsed listener problem avoidance with `Lifecycle`
  
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  b06e31a
- chore(api): cleanup conditions if conditions are set mulitple times
  
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  dd0f916
- refactor(api): extract lifecycle components into multiple files
  
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  dac79a7
- fix: fix line length
  
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  c4d5535
- chore(docs): remove useless whitespace
  
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  2dfa880
- fix(cognitive-agents): use `getCurrentPosition` to retireve node's actual position
  
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  8b2fba7
- test(engine): simplify engine test suite (fixed detekt error)
  
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  0c3ec1c
- chore(implementation-base): suppress `AbstractClassCanBeConcreteClass` detekt error
  
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  a2cc72d
- fix(test): retrieve current position from observable when asserting
  
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  804c28a
- fix(sapere): trigger LSAReaction update only on target molecule changes instead of entire LSASpace
  
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  50a354b
- fix(implementation-base): merge conditions into single observable source
  
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  d0aafb9
- fix(sapere): use generalised molecules for dsl expressions test failure
  
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  477ae8a
- fix(sapere): keep observing for neighbrhoods LSA spaces changes
  
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  40d8e63
- fix: fix checkstyle error
  
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  a0ee1b4
- perf: improve speed, SAPERE fine-grained dependencies and memory usage
  
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  2e50026
- style(api): simplify sum assertion in ObservableTest
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  79c0f7e
Commits on Apr 30, 2026
- fix(observable): correct stopWatching method argument to include context
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Commits on Jun 20, 2026
- temp work
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  2adbbe1
Commits on Jun 21, 2026
- temp work
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  fa63995
Commits on Jul 31, 2026
- fixup!: partial migration
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  b8937f3
Commits on Aug 2, 2026
- revise the entire api
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  df3dea9
- Merge remote-tracking branch 'origin/master' into marmellata
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  59d06c9
- refactor: improve dependency management and enhance neighborhood immutability
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  32598cb
Commits on Aug 3, 2026
- refactor: remove obsolete serialization fields and improve dependency handling
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  7d93c22
- refactor(engine)!: remove parallel batch execution
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  1898ab4
Commits on Aug 13, 2026
- feat(api)!: make time distributions sample-only
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  19a936c
- feat(api)!: make time distributions sample-only
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  2d720be
- refactor(api)!: rename `tau` to `nextOccurrence`
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  a258054
Commits on Aug 17, 2026
- chore: revise the plan
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  54f003d
- refactor(engine)!: remove batched scheduler updates
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  7a1dfdb
- refactor(engine): own reaction scheduling subscriptions explicitly
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  55f3e7d
Commits on Aug 18, 2026
- docs(api): improve the documentation of `Reaction`
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Commits on Aug 20, 2026
- refactor!: update reaction scheduling methods and improve documentation
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Commits on Aug 21, 2026
- refactor: rename `Reaction` to `NodeReaction`
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- refactor: rename `GlobalReaction` to `EnvironmentReaction`
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  db5fd90
- refactor: rename `Actionable` to `Reaction`
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- refactor(implementationbase)!: rename `Event` to `GenericReaction`
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Commits on Aug 24, 2026
- refactor!: reify the reaction-hosting capability in a dedicated interface
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Commits on Aug 25, 2026
- refactor!: drop contexts
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Commits on Sep 1, 2026
- refactor!: split one-shot event scheduling policies
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Commits on Sep 23, 2026
- refactor(api)!: replace condition dependencies with exact subscriptions
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  d3ba2c9
- test(protelis): cover exponential send scheduling
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  a673c2d
- fix(biochemistry): preserve condition type when cloning
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Commits on Sep 28, 2026
- refactor(model)!: make environment state observables authoritative
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  6070290
Commits on Sep 29, 2026
Commits on Sep 30, 2026
- fix(biochemistry): observe extracellular concentration changes
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  1115d34
Commits on Oct 1, 2026
- feat(engine): batch reactive invalidations per model mutation
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Commits on Oct 5, 2026
- refactor(api)!: cleanup the Observable API
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  4352e20
- fix(engine): skip removed dirty reactions
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  6ceeca0
- fix(engine): skip removed dirty reactions
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  fee2244
- test(implementationbase): cover Markovian propensity transitions
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- test: cover generic and SAPERE revalidation from the current simulation time
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  ba84b39
- test(engine): cover one-shot event lifecycle across hosts and node cloning
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- build(incarnation-biochemistry): add Kotlin test library
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Commits on Oct 6, 2026
Commits on Oct 7, 2026
Commits on Oct 8, 2026
Commits on Oct 9, 2026
Commits on Oct 10, 2026
- Merge branch 'master' into marmellata
  DanySK
  authored
  a07bd3b
- Merge branch 'master' into marmellata
  DanySK
  authored
  6d2acfa
- Merge branch 'master' into marmellata
  DanySK
  authored
  05c1d28
- Merge branch 'master' into marmellata
  DanySK
  authored
  6877131
- Merge branch 'master' into marmellata
  DanySK
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  40894af
Commits on Oct 11, 2026
- Merge branch 'master' into marmellata
  DanySK
  authored
  9de9e8d
Commits on Oct 12, 2026
Commits on Oct 13, 2026
Commits on Oct 14, 2026

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