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Merged
adolgert merged 189 commits into from
Nov 28, 2025
Merged

Dev/sample context #115

adolgert merged 189 commits into from
Nov 28, 2025

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@adolgert adolgert commented Nov 28, 2025

This is a major update. It combines all the samplers into a single facade called a SamplingContext. That facade helps you choose a sampler, debug, and get likelihoods.

Architecture:

  • New SamplingContext wrapping samplers with optional likelihood/CRN/debug features
  • SamplerBuilder pattern for configuration
  • Source reorganization into distributions/, trace/, variance/ subdirectories

New Algorithms:

  • RSSA (rejection-based SSA with Fenwick tree)
  • PSSA-CR (composition-rejection over groups)

Features:

  • Path likelihood computation for importance sampling
  • Common random numbers for variance reduction
  • Step and trajectory likelihood methods

Testing/Docs:

  • Gauntlet framework with statistical tests (Anderson-Darling, Doob-Meyer)
  • Integration guides for Gen.jl, Turing.jl, Survival.jl

adolgert and others added 30 commits October 4, 2025 10:13
@adolgert
using subdirectories for different activities
93aae14
@adolgert
split the various debugging tools
a3eaee4
@adolgert
adding a roughed-out context
e22d144
@adolgert
using workspaces and finally got the test using code_typed to run
b3136f8
@adolgert
tested the lifecycle for the most basic parts
cbbc5ec
@adolgert
Merge pull request #86 from adolgert/feature/sampler-context
1677220 
Feature/sampler context
@adolgert
this is a nice break point where the context makes more sense
7cac457
@adolgert
added a log argument to DebugWatcher
3e40ce4
@adolgert
modified the direct method to optionally accumulate log likelihood
c1a66ad
@adolgert
steploglikelihood is now a free method, and TrackWatcher has an abstr…
33150f0 
…act base to share with TrajectoryWatcher and CombinedNR can do a steploglikelihood
@adolgert
changed tracking and trajectorying so that Petri and FirstReaction ar…
bbbd067 
…e easier
@adolgert
two changes to help docs build
6b5309c
@adolgert
Merge pull request #87 from adolgert/feature/just-likelihood
63345e8 
Feature/just likelihood
@adolgert
adds an enabled() method to combined next reaction
b994b7d
@adolgert
added enabled() sets to Direct and MultipleDirect
56d8c0e
@adolgert
fixed bugs in the direct and multiple direct
d6ac51d
@adolgert
made a set-of-sets type
57e3ba0
@adolgert
tested setofsets
0e736d8
@adolgert
tested enabled() set for multisampler
bffe67f
@adolgert
adding missing file
2f82513
@adolgert
fixed docs
c215f5c
@adolgert
Merge pull request #88 from adolgert/feature/sets-and-dicts
6686b36 
Feature/sets and dicts
@adolgert
tabs to spaces I guess but adds a unit test for using Gen.jl-style pa…
b5ba31f 
…irs as keys
@adolgert
Cumusumprefix would re-calculate the sum! if called twice in a row so…
1252c6b 
… this sets a dirty flag.
@adolgert
added trajectoryloglikelihood method to DirectCall
ef788de
@adolgert
added a fire! method to all samplers
43bfe82
@adolgert
fixed minor bugs in cumulative sum
acbc110
@adolgert
minor bugs in prefix search
15071b3
@adolgert
Added a builder pattern
aac881e
@adolgert
adding space and order to context
e0635af
adolgert and others added 28 commits November 27, 2025 20:22
@adolgert
Merge pull request #112 from adolgert/feature/test-narrow
ff27ff3 
Feature/test narrow
@adolgert
added tests to look at the rest of pssa_cr.jl and found a bug
d167c3e
@adolgert
put in tests to fill out rssa.jl testing
0fe2352
@adolgert
fixed testing of combinednr and found a bug that affects performance
3bb9807
@adolgert
improved testing of direct.jl and found bugs
58ae6b5
@adolgert
added tests for Direct and Petri
ccfd94d
@adolgert
tested multiple direct
eba3126
@adolgert
simple tests of the interface for completeness
469c6c0
@adolgert
added sampler tests and found a dispatch problem
8290b70
@adolgert
found a method ambiguity in sampler_builder
0e3ea1c
@adolgert
added fire! to DebugWatcher so it now works
4c7572b
@adolgert
testing the hazard rate calculation
af32a5a
@adolgert
changed some defaults for neverdist and gave it a description
a31c55a
@adolgert
updates to prefix search and its keyed versions
16df7f1
@adolgert
added a small test here
32e01dd
@adolgert
more tests for debugwatcher.
29c3d14
@adolgert
getting coverage on common random
3facda4
@adolgert
looked at clone behavior for track
60c6d5f
@adolgert
split the track checks
aa299af
@adolgert
forgot the file
38fb821
@adolgert
added tests for the path likelihood, thank goodness
14d7678
@adolgert
deleted from code but not docs
1a78eb8
@adolgert
Merge pull request #113 from adolgert/feature/better-coverage
100b96d 
Feature/better coverage
@adolgert
modified the debugging and context to make documentation more complet…
4b8b614 
…e so it's a good outcome
@adolgert
modified the debugging and context to make documentation more complet…
6842066 
…e so it's a good outcome
@adolgert
pulled some docs into the main area
67070f1
@adolgert
minor edits to overview
f664081
@adolgert
Merge pull request #114 from adolgert/docs/no-trunks
0068f79 
Docs/no trunks
@adolgert adolgert merged commit 301439f into main Nov 28, 2025
10 checks passed
@adolgert adolgert deleted the dev/sample-context branch November 28, 2025 16:11
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@adolgert