Changelog

All notable changes to camdl. The version covers the DSL + CLI + output/file formats (see VERSIONING.md); IR-schema changes (ir/VERSION) are noted under their own heading. Pre-1.0: a MINOR bump may include breaking changes.

[unreleased]

Bug Fixes

(sim) Count Gillespie lineage edges in the sub-dt diagnostic
(sim) Realize batched events against frozen start-of-step pools
(cli) Infer --event-log format from output extension
(sim) Gillespie now re-evaluates rates that depend on bare t
(compiler) Preserve negative lower bounds in parameter declarations
(inference) Thread observation time into obs likelihood/sample/mean
(expander) Default output schedule covers negative t_start (snap_at obs-only bug)
(profile) Clean-eval re-pass on IF2 path so mle.toml reports loglik at saved MLE
(events) Parametric at [param] schedules honor the parameter (gh#69)
(events) Fire always_active events under ode/tau_leap/gillespie (gh#67)
(profile) Apply gh#34 [estimate].start fall-back before resolver
(profile,if2) --params trap on inference subcommands no longer shadows --init from_params companion
(profile) --init from_params/from_mle seeds resolver base values
(scripts) Review-zip — fix stale paths and curate per-subsystem test lists
(scripts) Review-zip — exclude docs/dev/{proposals,incidents}/ from all zips
(tree-sitter) Match hash_lbracket as a node, not a string literal
(parser) Hint newline-vs-comma in scenario set/scale blocks
(cli) Skip camdlc version check in test builds
(fit) IF2 skips degenerate chains instead of aborting the whole fit
(sim) Clean error for empty observation data instead of a panic
(test) Collect_table_lookups recurses into Reduce (heal D-inc2 OCaml break)
(parser) Block-form transition without a rate is E213, not silent rate=0
(sim) Workload-scale the PF wall-clock watchdog budget + env override (gh#133)
(cli) Model_hash descends into IR envelope — CAS keys on model (gh#135)
(sim) Make gh#139 parity test compile (correct IR import paths + trait import)
(golden) Add scenarios to sia_anchored_dates so it passes the smoke test
(test) Realign batch fixtures with unified scenario-ref rules
(test) Match current capability-rejection wording in integration skip
(compiler) Skip leading # comments in read() data files (closes gh#144)
(pgas_grad) Add gamma-density gradient w.r.t. σ² (gh#20)
(pgas_grad) Add obs-density gradient w.r.t. obs-model params (gh#76)
(pgas) Reintroduce narrowed C1 gate for uncovered gradient arms
(obs_loglik) Erfc-stable prob in disc-normal grad + corrected audit-H2 branches
(pgas) Split density-component reporting; demote ancestor-warn noise
(sim) Gh#81 — structured NonFiniteParameter error replaces misleading DivByZero
(nuts) Gh#81 — reject non-finite proposals; flag NaN energy as divergent
(inference) Adapt rescued gh81 PGAS-gradient work to current main
(runid) Box large Lookup variants + per-attempt staging (M1 review)
(runid) Ir_version is a String, not u32 (matches ir/VERSION)
(cli) Fold external --table content into the run identity (gh#147)
(cli) fit run announces the real leaf directory (FitDigest basis) (gh#147)
(cli) Compile the model once + restore ensemble progress (gh#147)
(cli) Apply --label on a CAS cache hit so it isn't silently dropped (gh#147)
(fit) Key PGAS/PMMH identity on init_method + survey (silent-wrong-answer) (gh#147)
(runid) Reclaim a Mode B .lock held by a dead PID (interrupted-fit recovery) (gh#147)
(runid) Serialize Mode B stale-lock reclaim — close the double-write TOCTOU (gh#147)
(cli) Fold CAMDL_NO_CONSTANT_FOLD into the IR-cache key (gh#147)
(sim) Refuse hierarchical priors in PGAS+NUTS (gh#175)
(cli) Reject unknown fit.toml keys (gh#173)
(dsl) Incidence() over a stratified transition family sums strata
(dsl) Resolve let-bound identifiers in observation projected
(runid) Hash CumulativeFlowSum at appended index 4, not 1
(build) Test phases depend on their builds (gh#178)
(cli) Reject profile-PMMH steps <= burn-in (gh#102)
(dsl) E267 accepts expanded intervention-instance names (gh#130)
(dimcheck) Projected carries its projection's dimension, not P

Build

(make) Install-camdlc + dev-camdlc for branch dev loops
(make) Resolve fresh camdlc via PATH-prepend in test-rust
Git-cliff config + make changelog + 0.2.0 notes draft
(cliff) Strict release-tag pattern; note prerelease bump caveat

CI

Run rust tests with --no-fail-fast
Remove release.yml — unfinished, never-green, no releases needed
(cli) Gate inference.md + debugging.md now that their drift is fixed
Split into per-area workflows for granular status badges

Documentation

(proposal) Simulate_with_lineages — line lists and trees
(proposal) Individual sampling layer (supersedes simulate_with_lineages v1)
(proposal) Note deferred Cond-branch handling for #[lineage]
(proposal) Park Tier-5 oracle choice pending landscape survey
(proposal) Fix Tier-4 coalescent rate (was wrong by I^2/N)
Add docs/lineages.md — user reference for the lineage layer
(proposal) Commit the sampling milestone design
(proposal) Three-layer lineage architecture (resampling + likelihood)
(proposal) Apply review fixes to the three-layer RFC
(proposal) Resolve VGsim oracle question; pin MASTER/nosoi; drop all verify markers
Rewrite lineages.md for the three-layer event-log workflow
(lineages) Document all-individuals + stratified sampling
(proposal) Seed-timing inference for early-outbreak models
(proposal) Record seed-timing mechanism-B implementation + bug fix
(notes) Scaling assessment of the lineage workflow
(proposal) Human vs pathogen migration + deme trajectory
(proposal) Calendar time — dated I/O boundary translator
(proposal) Calendar time — verify engine origin-invariance
Add docs/dates.md — canonical reference for calendar time
(claude.md) Alpha-status updates + DSL design principle for agent collaboration
(spec) Correct §2.1 month/year conversion constants to Gregorian
(proposal) Typed time — anchored vs unanchored, exact vs calendar durations
(cheatsheet) One-page DSL surface orientation
(claude.md) Require reading normative docs and verifying code before structural proposals
(cheatsheet) Drop reference to deleted incident report
(claude.md) Require evidence inline with claims; classify discrepancies; tells for self-check
(typed-time) Address upstream review (A/B/C); land migration walkthrough and bare-numeric warning
(typed-time) Add date_range generator to Phase 2
(typed-time) Finalize proposal with corpus check + punch-list fixes
(typed-time) Fix date_range quarterly example (end now lands on cadence)
(typed-time) Phase 3 — integrate vocabulary into dates/spec/features/cheatsheet
(claude.md) Bug fixes follow TDD discipline (red → green → refactor)
(proposals) Survival-conditioned likelihood, revised after review
(proposals) Unified diagnostic surface RFC
(proposals) Gh#71 stuck-chain diagnostics RFC
(proposals) Gh#74 Option A — warm-chain init mode for camdl profile
(proposals) Gh#71 — add LHS-on-posterior-sampling-stage warning (Check A')
CLI UX proposal — unify chain-start under --init; demote --params
CLI UX proposal — revision 2 (post-discussion)
CLI UX proposal rev 2 — fold in doc-agent audit feedback
Docs: CLI UX proposal rev 2 — split from-point back into
CLI UX proposal — add full type design + post-impl audit
(notes) Gh#83/gh#85 — CLI UX rev 2 implementation status
(notes) Update CLI UX impl status with pfilter migration
CLI UX proposal — fix precedence + add ScenarioOverridden warning + resolve A/B/C/D
(notes) Update CLI UX impl status — Step 2 (simulate + lineage) done
(notes) CLI UX impl — audit-checklist snapshot + handoff notes for next session
(notes) CLI UX impl — session handoff (steps 4-5 done, 6-12 deferred)
CLI UX proposal — addendum on partial-resolution mode
(notes) CLI UX impl — steps 6 + 9 status update
(proposal) Adaptive PMMH proposal scale via Robbins-Monro tuning
(proposal) Incorporate downstream-agent review of PMMH RM proposal
Docs(proposal): typed-time amendments — reserved-id diag, mode-switch
Docs(proposal): priors on time-typed parameters — unit-aware sugar
(review) 2026-05-26 last-week audit (7C/19H/22M/9L)
(review) 2026-05-26 upstream OCaml-compiler review + comparison (8C/6H/2M)
(proposal) Typed indexed-reference resolver for OCaml frontend
(review) 2026-05-26 upstream Rust-engine review + comparison (6C/9H/2M)
(incident) Profile-PMMH silently MLE-with-flat-priors before 5f658a16
Tidy repo root — move keepables to docs/dev/, prune stale scratch
(types-reference) Refresh stale claims; update cross-refs after rename
Remove agent-channel logs and workspace-rot-scan note
(review) 2026-05-26 upstream spec review + per-claim assessment
(spec) Cheap-batch fixes from upstream review (F7, F15, F16, F17, F27, F29, F30)
(review,spec) Restructure spec review + revise F1 disposition; rewrite §1 to match design
(review,spec) Revise spec-review assessment per upstream feedback; remove stale --table CLI text
(spec) Document default output, fix stale observations status
(proposal) Coordinate-keyed RNG seeding for orchestration determinism
Fix E before/after figure, figures index, Expr-deserialize maintenance note
(proposal) Shared per-coordinate bindings + reduction node in the IR
(proposal) Revise shared-bindings/reduction after adversarial review
(proposal) Add scope guard, all-backend landing condition, golden build-out
(proposal) Sharpen the binding-fill granularity invariant
(perf) Fix D before/after benchmark (IR size + parse cliff)
(review) Spec-review F9 is code-protected (E500/E501), downgrade off Critical
(perf) Fix B before/after scaling figure + sweep data
(perf) Record the OOM watchdog panic from benchmarking pre-Fix-B compile
(proposal) Compiler memory guardrail to prevent host OOM
(perf) Correct the scaling note's Fix D/B status to match what landed
(bench) In-context README for benchmarking + the PMMH profiling plan
(scaling) Refresh the assets README to match disk
(perf) Inference scaling note + national-scale roadmap
(perf) Revise the national-scale roadmap to PGAS-centric with measured cross-method data
(perf) De-risk sparse coupling — fold pass + compile-time W, not a sparse-IR rewrite
(proposals) Unified observation-data surface + pinned t_cond
(proposal) §5.2 — likelihood seam is unified (gh#139), not "lands at :393"
(run-spec) Reconcile to shipping code (results/sims, tagged run.json, model_hash contract)
(proposals) CLI UX rev 3 — CAS-default I/O, nested progress, finish resolver migration
(run-spec) §4 rewrite — CAS-default output, --stdout opt-out, list/show/cat as primary path
Merge run.json contract (§9.5/§9.6) + defer obs-flag work to bca0360
(notes) Confirm read-tsv comment crash root cause; link gh#144
(perf) Compiler profiling baseline — serialize is 97%
(perf) Flambda is a null result; compact-serialization proposal
(perf) Streaming-pretty after-sweep + before/after RSS figure
(perf) Compact-format sweep + before/after & progression figures
(proposals) Document archive epochs + release-tag scheme
(proposals) Archive 48 implemented/superseded proposals (triage)
(proposals) Tidy proposals tree — drop INFLIGHT, relocate notes
(proposals) Archive 5 partial proposals with disposition notes
(proposals) Split 2 partials, archive 3 (triage pass 3)
(proposals) Archive inference-minor-cleanup (implemented)
(pgas-grad) Post-cleanup status on gh#20+gh#76 derivation note
(pgas) Gh#80 diagnosis — events/density math is correct as-is
(pgas-grad) Cross-reference gh#80 — no gradient impact
(inference) Note PGAS support for discrete-event seeding
(proposals) Archive malaria-model-features; migrate #5/#5b to reactive
(commands) Add command taxonomy and workflows map
(proposal) Content-addressed run identity
(proposal) Harden CAS run-identity against adversarial review
(proposal) Round-2 hardening + new-subcommand contract
(proposal) Fold in upstream review (path identity + obs/exact-set)
(proposal) Round-4 coherence fixes (converged)
(notes) PF eval-path profiling — what pre-resolution bought
(notes) Sparse-coupling fold A/B — O(P^2)->O(P*k), byte-identical
(dev) CAS path-shape contract for downstream consumers (M4, gh#147)
Retire camdl if2 from docs, clear stale module headers + dev-milestone archaeology (gh#147)
(recovery) Describe the harness as manual compare, not auto-assert
(cas) Sync path-shape contract to code — add sim_ensemble + missing fields
(proposal) Camdl docs subcommand (embedded, version-locked)
(spec) De-stale §21 CLI reference
(spec) Clarify tables are indexed-only; scalars are parameters
(proposal) Camdl init subcommand (project scaffolding)
De-stale CLI references in AGENTS.md + language-spec
(workflow) Canonical fit-workflow runbook (camdl docs workflow)
(fit-toml) Full fit.toml schema reference (camdl docs fit-toml)
(concepts) The reasoning behind the fit workflow (camdl docs concepts)
(agents) Slim workflow / fit.toml / where-docs-live to point at camdl docs
Document the camdlc<->camdl version guard + make-test workflow
(proposal) Mark schedule unification A complete; A.3 folds into B
(proposal) Frame schedule split as two domain objects + the inference join
(ir-spec) Correct the observation-data join description
(dev) Verified alpha-issue triage + Gate 3b proposal
(dev) Batch A inference-gradient triage note
(dev) Proposal — unify compiler diagnostic/result surface (gh#181)
(dev) Proposal — observation-data binding (gh#171)
(dev) Obs-binding — type-flow, malaria scope, summary-stat forward
(dev) Obs-binding — Counted in scope, column-typing, scorer-in-fit, tests
(dev) Proposal — unified timeline-effect architecture
(dev) Unified-arch — ODE in scope (third driver) + type/flow diagram
(dev) Unified-arch — full Testing section, trait diagram, ODE seam reserved
(dev) Unified-arch — near-total rewrite to staged three-layer shape
(dev) Unified-arch — fold round-2 review; oracle-first Stage 0
(spec) Compiler-verify 21 more blocks; fix 2 doc bugs found
Expand doctest gate to 6 docs; fix intro age-SIR drift
(dev) Capture doctest drift findings + CLI run-gate prototype
Fix CLI command drift in inference.md and debugging.md
(dev) Mark projected bug + CLI drift resolved in findings note
(spec) Compiler-verify 5 more feature blocks (49 -> 54)
(dev) Engineering note on the doc compiler-testing effort
Versioning policy + agent release-notes pipeline (RFC)
(readme) Add Docs/license/status/stack badges

Features

(install) Linux + macOS install script (#63)
(ir) #[lineage] foundation — DSL attribute, linearity check, IR fields
(ir) Bump seir_spatial_5 test fixture to ir_version 0.5
(sim) Lineage runtime — observer seam, identity tracking, line-list writers, offline tree
(cli) Camdl simulate --lineages + offline camdl lineage tree
(sim) Stratified parent attribution — real DemeId + parent_deme
(sim) Lineage tracking on tau-leap + chain-binomial backends
(cli) Offline lineage sojourn + cohort projections
(sim) Split lineage tracking into Layer-1 event log + Layer-2 realize
(cli) Wire event-log recording + lineage realize; rework tests
(lineage) All-individuals sampling with pendant tips at sampling time
(cli) All-individuals + stratified sampling for lineage tree
(sim) Smooth-importation seed mechanism + identifiability test
(lineage) Per-individual deme trajectory; fix migrant sampling
(lineage) Cross-deme/migration statistics + paired migration goldens
(ir) Caltime — calendar-date <-> internal-time boundary conversion
(cli) Dated data loader — calendar-time boundary translator (phase 2)
(ir) Time parameter-kinds (instant/duration) + numeric origin in IR (phase 3)
(cli) --dates calendar column in simulate output (phase 4)
(cli) Render instant-kind estimands as calendar dates in fit summary
(compiler) Typed-time Phase 1 — Rules 1, 2, 4, 5, 7 + W326
(compiler) Typed-time Phase 2 — calendar primitives + date_range
(profile) Add PMMH as a per-cell algorithm
(tree-sitter) Refresh grammar against current DSL surface, commit
(cli) Unify simulate and batch under one run_job engine
(ir) Add inert n-ary Reduce expression node (Fix D, increment 1)
(compiler) Emit Reduce for Mul-tree sums (Fix D inc. 2 — kills parse cliff)
(ir) Inert shared-binding IR surface (Fix B, increment 1a)
(expander) Extract state-only lets into shared bindings (Fix B, increment 1b)
(sim) Reject param-bearing shared bindings at compile time
(bench) make profile-pmmh — flamegraph the PMMH inference step
(cli,sim) --pf-wallclock-timeout flag + split PFWallclockTimeout from PFDegenerate (closes gh#133)
(cli) Compile spinner for blocking camdlc subprocess
(sim,cli) Per-timestep progress bar for single-run simulate
(dsl) Instant cell-kind tables accept ISO dates via origin
(compiler) Env-gated per-pass timing (CAMDL_TIME_PASSES)
(bench) Compiler-only timing harness (bench-compile)
(ir) Compact IR JSON serialization — 4.6x faster compile, 5x smaller IR
(dsl) E222 names the parameter seam for scalar read() (0-dim table)
(dsl) Wire min(a,b) / max(a,b) to BinOp Min/Max
(sim) CAMDL_EVAL_UNRESOLVED bench/validation switch
(compiler) Sparse-coupling constant-fold pass (opt-in)
(compiler) Run sparse-coupling constant-fold by default
(runid) Canonical hasher, ContentHash, run_id (M1.1)
(runid) Hand-written ContentAddressed for the ir tree (M1.2)
(runid) Derive(RunInput) macro + digest/leaf shapes (M1.3)
(runid) RunRecord/run.json + CasStore commit modes (M1.4)
(runid) Factored store-path Layout (M2.1)
(cli) Wire simulate + batch + reader through the new CAS (M2.3-M2.6)
(runid) Deterministic substep-cap watchdog for PF (M3.1)
(runid) Recursive exact-set manifest for nested leaf files
(runid) Fit-stage CAS writer + readers (M3.2 commit 1)
(runid) Resume on CAS — base read-only, distinct leaf (M3.2 commit 2)
(cli) Content-address profile runs — writer + reader + ReplicateSet removal (M3.3)
(cli) Content-address pfilter evals — writer + reader (M3.3, gh#147)
(cli) Content-address survey runs — writer + reader + legacy retirement (M3.3, gh#147)
(cli) Derived run index + camdl reindex — fast exact-id lookup, run.json is truth (M4, gh#147)
(cli) Simulate writes CAS by default + per-cell leaves for multi-run (gh#147)
(cli) Store the combined ensemble TSV in CAS; simulate/lineage stop writing TSV to stdout (gh#147)
(cli) Store the lineage event log in CAS alongside traj.tsv (gh#147)
(cli) Browse-UX — list collapses ensemble members, accepts --root; cached: line is rooted (gh#147)
(cli) Add simulate --stdout opt-out; sync help to CAS-default; banner shows run_id (gh#147)
(cli) Consolidated progress — Reporter/Task + multi-cell simulate bar + --no-progress (gh#147)
(cli) Progress phase 2+3 — fill PGAS/pfilter/survey gaps, migrate IF2/PMMH/profile onto Reporter (gh#147)
(cli) Label progress rate with units (0.40 cells/s); ensemble line shows the full rooted path (gh#147)
(cli) Tidy unified status messages — status module + compile banner + storing/ensemble/stored (gh#147)
(cli) Unify the store banner across survey/pfilter/fit (gh#147)
(cli) Concise compile banner — drop the temp IR path, source shown project-relative (gh#147)
(cli) Content-addressed compiled-IR cache — compile a .camdl once, reuse across runs (gh#147)
(cli) Compact byte sizes (no space) + IR-vs-source expansion ratio on the compile banner (gh#147)
(cli) Add fit run --parallel N to cap the Rayon pool (gh#162)
(compiler) Add model linter pass + L402 dead-compartment lint (gh#168)
(compiler) --json-errors structures warnings/lints too (gh#170)
(cli) camdl docs <topic> — embedded version-locked usage guides (v1)
(cli) Docs nudge in camdl --help footer (agent discoverability)
(cli) Serve workflow / fit-toml / concepts topics
(dsl) Wire output trajectory cadence, at-times, and format
(dsl) Accept dt in the simulate block (gh#161)
(sim) BetaBinomial obs-density gradient helper (gh#76)
(sim) Wire BetaBinomial obs gradient into NUTS (gh#76)
(sim) Narrow C1 gate to parametric DerivedExpr only (gh#76)
(cli) Warn on single-init multi-chain posterior fits (gh#71)
(cli) Warn when instant params have no origin (gh#103)
(cli) Hint on simulate --fit config-load error (gh#158)
(cli) Emit draws TSV for simulate --draws (gh#157)
(sim) Trace all intervention action arms (gh#106)
(doctest) Camdlc doctest — gate spec code blocks on the compiler
(doctest) Context= preamble, classifier self-test, doc CI gate
(doctest) Self-contained in-doc preamble + data via HTML comments
(cli) Permanent CLI-doc drift gate via parse-only __check-args
(cli) Camdl doctest subcommand; camdlc --help; cross-pointers

Miscellaneous

Purge stale examples/ + output/ ; collapse .gitignore patterns
(scaling) Ignore all flamegraph_*.svg, not just flamegraph_real
(bench) Remove stale inference criterion bench (superseded by scaling)
(golden) Regenerate sia_anchored_dates in compact IR format
(cli) Gitignore + untrack committed CAS run output under results/
(golden) Re-version sir_dt.ir.json to ir 0.9

Other

Gh#51 v2: PMMH supports init_method = "survey_top_k"
Gh#51 v2: PGAS supports init_method = "survey_top_k"
Gh#51 v2 follow-up: align gh#51 comments with the v2 / v3 split
Honor priors in profile --algorithm pmmh (precedence + --fit + warning)
Integration tests + warning-text polish for profile priors
Docs(inference) — profile and priors precedence section
Docs(cli) — profile --help PRIORS section
Gh#74 Option B: failing integration tests for per-cell diagnostics
Gh#74 Option B: per-cell diagnostics infra + PMMH wiring
Gh#74 Option B: wire IF2 per-cell diagnostic capture
Gh#74 Option B: docs — Per-cell diagnostics in inference.md + --help
Extend gh#73 prior-precedence chain to fit run / fit where
Integration tests for fit-run prior precedence (TDD red)
Lift profile_priors → fit/priors_precedence for sharing
Wire three-tier prior precedence + explicit-flat opt-in for fit run
Docs — Priors and precedence + camdl fit run --help
Install.sh PREFIX env var for per-branch testing
Surface per-chain ESS alongside gated joint ESS
Params_resolver — unified value-resolution chain (rev 2)
Migrate pfilter to params_resolver
Fix precedence — scenario must beat --fixed-file per spec §1.3
Resolver — ScenarioOverridden + FixedEstimateOverlap warnings
Migrate simulate + lineage to params_resolver
Migrate survey to params_resolver (step 4)
Migrate if2 to params_resolver (step 5a)
Migrate profile to params_resolver (step 5b)
Document partial-resolution exceptions in main.rs (step 5c)
Migrate fit run (fit/runner.rs) to params_resolver (step 5d)
Gh#83/gh#85 step 6a: extend InitMethod ADT with warm-start variants
Gh#83/gh#85 steps 6b+9: chain_starts loaders + run.json provenance
Gh#83/gh#85 step 12a: fit.toml schema — rename init_method/starts_from
Gh#83/gh#85 step 12b: align comments + user-facing strings with new toml keys
Gh#83/gh#85 step 12c: migrate integration-test inline fit.toml fixtures
Gh#83/gh#85 step 7: M-1 break — --fixed NAME=VALUE, --init <mode>, drop --params/--starts-from
Gh#83/gh#85 step 7: wire warm-start --init through pgas/pmmh stages + IF2 dispatch
Gh#83/gh#85 step 8: update after_help examples for new CLI surface
Gh#83/gh#85 step 7: parse-layer regression tests for M-1 removed flags
Gh#83/gh#85 step 10: doc churn — rename --init-method/starts_from across normative docs
Gh#83/gh#85 step 11.1: docs/inference.md — rewrite 4-way precedence list
Gh#83/gh#85 step 11.2: camdl-language-spec — name-only --fixed removal
Gh#83/gh#85 steps 11.3 + 11.4: handoff notes for camdl-book repo
Gh#83/gh#85 step 12d: proposal snake_case alignment
Failing tests for --draws prior IR-prior fallback (TDD red)
--draws prior honours model-IR ~ priors via precedence fallback
Docs(run-spec) — describe --draws prior IR-tier fallback
Include --pmmh-steps, --pmmh-particles, --pmmh-rho, --algorithm in profile CAS key
InitMethod Display emits snake_case for every variant
DataSpec + resolve_data_specs — polymorphic --data flag
Wire multi-stream --data into profile + pfilter
Integration tests for polymorphic --data on pfilter
Expose log_posterior alongside loglik in profile TSV + mle.toml
Survey resolver — [estimate].start fall-back (analogue of gh#34/profile)
Include focal-parameter priors in profile log_posterior
(init) Warn loudly that survey_top_k ranks by likelihood, not posterior
(init) Wire gh#129 issue ref into rank-by-likelihood warning
Gh#116 dimcheck: strict dim-check on known-contract observation
Gh#115 expander: validate scenario enable/disable/compose/set/scale
Add SimError::PFDegenerate + PFDegenerateKind
Add check_pf_degeneracy() shared helper
Wire PF degeneracy watchdog into bootstrap_filter
Wire PF degeneracy watchdog into IF2 inner loop
Skip PMMH chains whose init triggers PFDegenerate
(sim) Eval_ab A/B microbench + end-to-end harness
(sim) Register eval_ab as a tracked [[bench]]
(dsl) Remove phantom output sub-blocks and experiment/compare
Output trajectory customization (cadence, format, quantities)
Unifying the scheduling surfaces
Key the camdlc<->camdl guard on IR schema version
Gate camdlc guard on schema-surface hash, not ir/VERSION
Fold adversarial review into schedule unification
(ir) Delete dead schedule variants from_data/match_observations/external
(ir) Remove unselectable table out-of-bounds policies Clamp/Wrap

Performance

(lineage) Chunk event-log Parquet writer into row groups
(lineage) Don't retain IDs in write-only identity pools
(lineage) Stream the event log into realize (bounded memory)
(ir) Deserialize Expr in one pass, dropping serde untagged buffering
(compiler) Stream IR JSON to channel, 2.8x less compiler RAM

Refactor

(fit) Extract resolve_per_chain_starts_from_method for survey_top_k v2
(cli) Single home for the per-cell seed mix
(dsl) Remove the unimplemented transition tag field
Genericize Kano-specific identifiers introduced by Fix B
(ir) Delete vestigial ObservationModel.data_stream field
(sim) Unify the two likelihood loops into one seam (gh#139)
(sim) Thread wall-clock watchdog disable through config
(cli) Content-address the synthetic fit-grid — defer roll-ups to M4 (M3.3, gh#150)
(cli) Remove the camdl if2 subcommand — IF2 is a one-stage fit (M3.3, gh#147)
(cli) Retire the legacy Run fit readers — read RunRecord+sidecar via FitView (step F, M3.3, gh#147)
(cli) Pre-merge CLI cleanup — drop fit where/status, label all kinds, retire manifest.json, sim→fit lineage (gh#147)
(compiler) Unify the front-end pipeline into one core (gh#170)
(dsl) Extract shared schedule_core; migrate output onto it
(dsl) Migrate observations onto schedule_core (A.2)
(compiler) Route check through collect_diagnostics (gh#170)

Tests

(sim,cli) Lineage acceptance tiers + end-to-end pipeline
(sim) Tier 2b — stratified contact-weighted parent attribution
(sim) Tier 5 external-oracle scaffold for stratified attribution
(sim) Tier 4 — coalescent-interval validation of the transmission tree
(sim) Offspring-distribution check vs realized effective-R
(golden) First anchored fixture exercising Phase 1+2 typed-time surface
(profile-pmmh) Cross-method log_posterior invariant suite
Test(invariants): asymmetric widths + 1e-9 tolerance for the
Test(dimcheck): negative goldens for the four remaining observation
(cli) Heal gh#110-degenerate fit fixtures
(cli) Rebuild the multitz tz-offset test to be non-vacuous
(sim) FOI scaling-bench harness + profiling note
(sim) Byte-identical trajectory baseline gate for the B/D refactor
(golden) Mixed int/real aggregate gate model (Fix B trap #1)
(ir) Round-trip coverage for binding-bearing IR; document ir/golden v0.3 pin
(sim) Pin ODE in the trajectory gate (four-backend landing condition)
(sim) Characterization test pinning PF/PGAS likelihood-path parity (gh#139)
(cli) Descend into IR envelope in 3 model_hash test-mirrors (gh#135 follow-up)
(cli) Finish the model_hash envelope descent in the 2 survey mirrors (gh#135 follow-up)
(gate) Add sia_anchored_dates trajectory baselines
(pgas) Integration smoke for gh#20 + gh#76 gradient terms
(pgas) Multi-overdispersed-transition lockstep FD coverage (gh#76)
(obs) FD coverage for the Binomial obs dispatch arm (gh#76)
(pgas) Gh#80 smoke — PGAS+NUTS runs cleanly on SEIR + discrete event
(constant-fold) A/B gate proving the sparse-coupling fold is byte-identical
Collision-free unique_temp_dir for unit tests (gh#153)
(runid) Re-enable survey top-k tests on CAS (M3.3, gh#151)
(recovery) Add synthetic-data parameter-recovery harness (tests/recovery/)
(integration) Count CAS sim leaves, not retired sims/manifest.json (gh#147)
(compiler) Auto-test every diagnostic via fixture harness (gh#168)
(sim) Scipy-anchor the gamma multiplier-density value (gh#20)
(cli) Fail loud when the release camdl binary is missing (gh#105)

[0.1.0-alpha] - 2026-05-15

Bug Fixes

(spec) Replace N[a, p] with N_local[a, p] in §9.3 guard example
(ocaml) Implement coupling sugar, fix unit constants, add unknown-ident error
(ocaml) Flatten multi-dimensional table indices to single linear index
(golden) Baseline scenario carries defaults, others inherit via store
(cli) Update summarize + unused_mut after run_path rename
(cli) Delegate run_simulate to util::run_simulation; fix enable+disable
(experiment) Correct point_id tracking; add response curves; refresh golden
(cli) Consolidate TOML parsing; fix binomial sampler; document LCG
(summarize) Rename cum_X → integral_X; add polio_es README
(sim) Use multiplicative overdispersion (He et al. 2010)
(chain-binomial) Apply overdispersion to rate before probability conversion
(chain-binomial) Convert total propensity to per-capita rate before p
(chain-binomial) Use true Binomial draws instead of Poisson approximation
(sim) Guard NaN propagation in expr eval; validate spline inputs
(test) Correct statistical test constants to match golden file parameters
(chain-binomial) Defer state updates until all draws complete
(pfilter) Match pomp's likelihood tolerance floor (1e-18)
(pfilter) Add --flow flag for projection selection; fix hardcoded infection projection
(if2) Match pomp cooling schedule and rw_sd scale semantics
(if2) Use scaled logit for parameters with finite bounds
(if2) Parallel multi-chain via std::thread::scope; update todo
Interventions fire during pfilter/IF2; fix regime sentinel detection
Review #10 bugs — chain output, profiles, fit_state, dedup, ESS
Resolve CI warnings-as-errors (clippy -D warnings)
(pfilter) --trace accepts both bare flag and file path
Auto rw_sd uses fixed transformed-scale SD at current value
(fit) Apply fit.toml parameter values before model compilation
(scout) Conservative defaults + degenerate filter detection
(scout) Always write output, even when auto_rw_sd fails
Review 10b — RNG isolation, overflow, alloc, fallback removal
Gamma sampler handles extreme sigma_se without panicking
All RNG samplers handle invalid inputs without panicking
NaN panics in MAD, rename ekrng→rng, add sampler stress tests
Profile --rw-sd auto; consolidate transform derivation (DRY)
Cooling matches pomp's cooling.fraction.50 semantics
Review-external batch fixes + loglik naming rename
(if2) Include loglik column in camdl if2 --output parameter_traces
(chain-binomial) Match pomp's reulermultinom — fixes 2128 nat loglik gap
(events) Apply event actions atomically with transitions
(events) Snap fire times to integer grid at model init
(cpm) Correlate binomial draws via stored z-values
(pmmh) Extract dt from config, disambiguate float literal in correlation check
(cpm) Track particle identity through resampling for z-value sync
(pgas) Initial proposal SD from parameter bounds, not rw_sd
(pgas) Revert to exact complete-data LL for θ updates
(pgas) Use initial_state(params) in complete-data LL for IVP constraint
(pgas) Correct IVP handling — detect, skip MH, back-solve from trajectory
(nuts) Three critical bugs from code review
Remaining code review items + gradient/NUTS tests
Move autodiff pass into Compiler.compile, fixing OCaml golden tests
(ci) Pin Rust toolchain + fix clippy warnings
(nuts) Two-phase warmup — re-adapt step size after mass matrix
(ci) Match local build to CI — warnings-as-errors everywhere
(nuts) Dense mass matrix momentum draw — L^{-T} not L^{-1}
(ci) Clean all test warnings — unused imports, dead code, unused vars
(pgas) Zero-rate flow check + spatial -inf diagnosis
(pgas) Diagnostic for spatial -inf — zero-rate flow check + init LL warning
(pgas) Found spatial -inf root cause — n_exit > n_src from clamping
(pgas) Spatial -inf — clamping fix + gamma density disabled
(pgas) Snapshot counts_before in SubstepRecord for spatial density
(pgas) Reference particle counts_before mismatch in CSMC-AS
(pgas) Handle near-zero rate/flow mismatch gracefully in density
(pgas) Separate deterministic check from rate check in density
(pgas) IVP density uses per-patch population for spatial models
(cli) Multi-stream data loading reads correct column per stream
(pgas) --resume no longer requires --force, trace overwrite prevented
(pgas) Validate and recompute transforms on resume
(pgas) Store param_names in resume state, sort if2_params by name
Multi-stream pfilter + extract shared log_jacobian
(pmmh) Correct log_posterior, remove double-write, fix steps_per_obs
(test) Update pmmh tests for run_pmmh resume args + steps_per_obs
Unused observations param + missing obs_at_substep in gradient test
(compiler) Unify calendar constant to 365.2425 (Gregorian)
(autodiff) Apply simplify to fixed point as documented
(pgas) Disable gamma density gradient to match disabled gamma density
(cpf) Document σ² state-independence assumption, validate uniform obs spacing
(validate) Use true PF loglik for profile likelihood evaluation
(pgas) Re-enable gamma multiplier density
(sim) Use cached IntState/RealState in log_likelihood_from_flows
(dimcheck) Union-find linking, read-only check, E303, parser errors
(engine) Review round 2 quick fixes (#1, #4, #5, #7, #9, #11)
(engine) Review items #2, #3, #8, #12
(ci) Add qcheck deps, fix mdBook install, unblock artifacts
(ci) Continue-on-error for OCaml tests, debug artifact packaging
(ci) Regenerate golden files with param_dim, build cli explicitly
Diagnostics.report_and_exit raises exception instead of exit(1)
Add param_dim: None to all Parameter struct literals
(lexer) Warn on 10_00 digit grouping (was only catching 3+ groups)
(expander) Extend is_const_expr and eval_const_expr for arithmetic
(parser) Error on unit literal as right operand of division
Restore standalone camdl pfilter command
(fit) Trailing-tab bug in draws.tsv + tolerant reader (review #4/#5/#25)
Hash/seed review items (#6/#7/#14/#15)
Design and UX review items (#8/#10/#11/#13/#16/#18/#22/#23/#24)
Unify provenance + robust rename (review #1/#2/#3/#17)
Remaining review items (#12/#20/#21)
Re-review items N1-N8 (all 8 minor issues)
(compiler) Indexed observation expansion + resolve_float_expr (review #1/#2)
(compiler) ProjDerived disambiguates compartment vs transition (#4)
(compiler) Hashtbl for keyword lookup (review #6)
(compiler) Convert failwith calls to Diagnostics.error (review #3)
(compiler) Drain lexer pending_warnings at compilation start (review #7)
(cli) Error on unknown --param, info-level override logging
(cli) Validate --params files, info-log stacked overrides
(compiler) Const-eval log/exp/sqrt/abs/floor/ceil as EFuncCall
(compiler) Strict prior arg validation + param-qualified diagnostics
(prior) Normal normalization + fit.toml parse_prior covers all 7 dists
(cli) Rejection-sample priors to bounds instead of silent clamping
(cli) --scenario pins parameter values for --draws prior coverage
(sim) Sort source_groups to eliminate HashMap nondeterminism
(cas) Pin VERSION_SHORT into scen_hash + compute_config_hash
(cli) Clean error when a flag is missing its value, not a panic
(cas) Sweep_point in run.json + manifest; camdl list shows values
(inference) Intervention off by default in fit + pfilter (spec §14.4)
(sim) Chain_binomial no longer fires scheduled interventions twice
(ci) Update integration script for simulate batch; upgrade pre-push
(docs) Relative symlinks in docs/book/src; add mdbook to pre-push
(compiler) Prevalence(X) on stratified X sums over all strata
(compiler) Poisson(rate = expr) parses; silent 0.0 defaults are errors
(cli) Unify SEED_MIX_OBS between --obs-only and [synthetic]
(fit) Starts_from = "scout" was silently discarded at iter 0
(if2) Per-chain random starts actually reach IF2
(fit) Resolve upstream stage hash for StartsFromRef
Record wall_time_seconds + reuse parent fit hash across stages
(cas) Hash-aware simulate cache check
(fit) Guard PGAS rename with error-on-collision instead of silent clobber
(run_meta) StartsFromRef.stage_hash → Option, stop silent chain corruption
(hashing) Widen fit_content_hash + fit_input_hash to full 64-char hex
(fit) Mle_params.toml.input_hash uses full fit Run.hash
(hashing) Canonicalise TOML before hashing fit_content_hash + fit_input_hash
(run_meta) Atomic run.json write via .tmp + rename
(ocaml) Diagnostics order + CLI hygiene + pp_expr integer rendering
(compiler) Emit ODE equations + wire Validate.validate (C5, M1)
(expander) Validate overdispersed/deterministic/transfer kwarg shapes (C1, C6)
(expander, autodiff) Stop silent 0/"?" fallbacks on bad inputs (C2, C7, M4)
(expander) Stop silent 0.0 fallbacks for UnOp in eval_const and list/range in rates (M14, m17)
(expander) Under-indexed stoich + longest-prefix base match (C3, M15)
(expander) Shape_index length mismatch emits diagnostic, not stack trace (M20)
(compiler) Fd leak, multi-dim param panic, read() kwarg check, IR cleanup
(expander) Numerator_pops descent + diag-channel info + positional path arg (M7, M16, m22)
(dimcheck) Allow any-dim Cond predicates + Pow read-phase parity (M18, M19)
(inspect, camdlc) Delete dead --expansion + inspect fixups (M22-M26, M30, m28, n11-n13)
(compiler) Don't double-render expansion warnings (M3)
(compiler) Don't re-print 'Error: Compile_error(...)' after diagnostics (m5)
(autodiff) Emit finite derivative for |f| at f=0 (n1)
(expander) Scrub NaN sentinels from table arrays after dense-check (M6)
(compiler) Propagate Compile_error payload to callers (m5 follow-up)
(compiler) E266 on missing obs block fields instead of silent defaults (m12)
(parser) Buffer action errors as diagnostics instead of failwith (n3)
(sim) Hard-fail on FromDistribution initial conditions (RC3)
(tau_leap) Multinomial competing-risks for shared sources (RM1)
(ode) Use fractional int state during RK4 substeps (RM8)
(ode_integrator) Cap RK4 step to dt_max, sub-step longer gaps (RM7)
(eval) Align evaluators on edge cases + eval_stats counters (RM2/RM3/RM6)
(cli) Rewire camdl profile subcommand (agent-channel Issue 1)
(fit) Sweep continues past per-cell gate failures (agent-channel Issue 2)
(obs) Document Normal-as-count + warn on fractional data (IC2)
(inference) Per-particle RNGs via ChaCha8 stream counter (IM1)
(if2) Skip non-finite ll_inc instead of poisoning iteration (IM4)
(pgas_grad) Gamma_idx per transition + RATE_EPSILON threshold (IM7, IM9)
(prior) TransformedNormal returns natural-scale density — no more double-Jacobian (IC3)
(fit) Hash starts_from in legacy compute_config_hash (IM10)
(pmmh) Geyer pair-sum ESS truncation (IM11)
(fit) Gate ESS on R-hat + equal-chain-length check (IM12, IM13, Im24)
(seeds) Full u64 default seed + decorrelated replicate seeding (Im19, Im20)
(log_sum_exp) Distinguish +inf from -inf (Im2)
(rhat) Per-chain last-half window instead of uniform n_iterations (Im25)
(pgas) Correct CSMC-AS ancestor sampling weights (IM6)
(cli) Align integration tests + Backend enum with clap 4 API
(fit) Build_v1_fit_run / build_fit_run panic on .camdl sources (gh #3)
(expander) Table unit annotations now actually convert values
(cli) Scenario set/scale must override --params, not vice versa
(spec) Restore 53 malformed fenced-block closers
(batch) Default output_dir now matches canonical root ("results/")
(obs) Evaluate likelihood arg expressions against actual state (GH #5, #6)
(obs) Actually fix GH #6 — compile_obs_sample_pf was the wrong path
(obs) Third-strike GH #6 — pfilter log_likelihood trait impl path
(dim) Camdl check runs Dimcheck; duration unit literals carry T
(sim) Clear gamma_used inside step_one (GH #10)
(harness) Deterministic summary, regen round-trip passes
(harness) Don't commit local renv symlink in he2010_pfilter_loglik
(cli) --progress plain auto-bumps --verbosity to info (GH #14)
(cli) --progress plain now emits for pmmh/validate/profile too (GH #14)
(evidence) Correct attribution of dB tier scale
(fit) Mle/start_values use clean-eval winner θ̂; final_params under [provenance] (closes #16, #17)
(test) Repo_root path + brace-aware path truncator + stage rename
(cli) List / show / cat / simulate-cas defaults follow DEFAULT_OUTPUT_ROOT
(cli) Output_root honors CAMDL_OUTPUT_DIR (fit run + profile)
(fit) Resolve toml-relative paths against the toml's directory (closes #22)
(fit) Summary prose — clean-eval → loglik-eval; "winner" → "selected"
(compare) Direction suffix on evidence; sort table by Δelpd ascending
(fit/list) Clean_ll/winner → loglik/selected in md+latex; --parent expands ReplicateSet umbrellas; loglik-eval progress prose
(sim) Clamp Bernoulli p to [0,1] before log/sample (review C1)
(fit) Validate tempering ladder β ∈ (0, 1] (review H4)
(fit) SeedsSpec::to_vec returns Result, fail loud on malformed range
(ir) Enforce prior ⊕ hierarchical invariant in deserializer + validate
(inference) Unify log-weight normalization, repair NaN-poison path
(cli) Detect shadowed camdl install in version-mismatch error
(make) Warn at install time when another camdl shadows on PATH
(review) Resolve M2/M3/M5 design findings from 2026-04-30
(ir) Move validate.rs test module to end of file
(profile) Adopt option-A schema for cross-seed summary.tsv (gh#30)
(cli) Validate parameter values against declared bounds (gh#31)
(cli) Camdl fit where runs the same validation depth as camdl fit run (gh#35)
(profile) Walk full indexed observation family for joint loglik (gh#38)
(profile) Include --data file contents in cache hash (gh#39)
(fit) Suppress chain_agreement Â when W collapses under cold cooling
(survey) Pair-plot color-by miscalibration for loglik and loglik_se
(survey) Smaller pair-plot points + lower default top-K cutoff (10% → 5%)
(ode-inference) Cumulative flow accumulation + downstream renderers
(profile) Wire NLopt orchestration for --algorithm nl-* --backend ode (closes gh#47)
(ode-inference) Close model-capability silent-fail at three dispatch sites
(parser) Accept transfer(count = EXPR, ...) as documented
(ir) Hand-write bitwise PartialEq on ConstExpr (audit M9)
(sim) Drop Trajectory::default — empty trajectory is degenerate (audit M10)
(if2) Mle = last_iter, not argmax(perturbed_loglik) (audit C2)
(cli) Error on --record-prequential off PFilter; wire --parallel into pfilter (audit H12+H13)
(pgas) Surface NUTS divergent / treedepth / swap-rate diagnostics (audit C7+M18+H4)
(cli) Wire H4 unwired DiagnosticKind variants (DegenerateAS, LowESSAtMLE, ParamNearBound, LowTrajectoryRenewal)
(cli) Surface EvalStats counters at end of every cmd_* run (audit H5)
(sim) Typed errors for numerical-collapse rate paths (audit C6+S1)
(sim) Negative-count clamp → typed SimError::NegativeCount (audit C5+S2)
(sim) BALANCE capability stops silent balance{} drop on tau-leap/gillespie/ode (audit C3)
(pgas) Refuse to run with implicit improper-uniform priors (audit C4)
(pgas) Preflight gate for obs-likelihood / σ² gradient coverage (audit C1)
(nuts) Outer-tree combine matches H&G Algorithm 6 (audit H1)
(obs_loglik) Libm::erfc + tail-stable interval (audit H2)
(sim) Stable prob_q_from_rate_dt primitive (audit H3)
(pgas) Ancestor sampling uses pre-resample state cache (audit H8)
(inference) IF2 cooling off-by-one + PMMH post-burn acceptance (audit M2+M4)

Build

Add Makefile; fix parser warnings and make install
Add nlopt dep behind ode feature (Phase 1 prep)

CI

Update integration shim + artifact paths for batch/binary renames
Gate mac/win runs behind tags; skip CI on doc-only changes
Disable docs.yml workflow (Pages deployments handled in camdl-book)

Documentation

Rewrite README with DSL examples, camdlc commands, and test instructions
(CLAUDE.md) Update RNG/CRN section to reflect current EkRng status
(web) Add README explaining web app role and agent handoff
Rename --set/--set-vec to --param/--param-vec in specs
(experiment) Update spec to v0.5 with sweep, design, and analyze sections
(experiment) Replace VOI framing with sensitivity characterization
Add 'no loose semantics' design principle to CLAUDE.md
Add user-features.md — catalog of DSL ergonomics and capabilities
Add side-by-side pomp vs camdl comparison to user-features.md
Inference guide — PF, IF2, profiles, diagnostics, future directions
Update language spec and experiment spec to match code
Close profiling session — summary, deferred items, final scan
Update benchmark plot with post-optimization numbers
Rewrite README to reflect current capabilities
Provenance system implementation plan
Explain numerical fallback rationale in sampler guards
Explain design rationale in code comments
Update all specs for OOS validation, prediction quantiles, new CLI features
Simplex plan — all members explicit, match pomp barycentric
Complete dev blog post — all three bugs documented
Add proposals directory and events-block proposal
Mark events-block proposal as implemented
Add events, add(), at_day, and balance to language spec (§14.5-14.8)
Add integer-grid fire times and final result to blog post
Add PGAS proposal (Particle Gibbs with Ancestor Sampling)
Update agent channel with adaptive proposal SD
Update agent channel with random starts
Update channel with initial SD fix analysis
Update channel with PF-based θ update + trajectory renewal diagnostic
Update channel — reverted to exact complete-data LL for θ updates
Update channel with IVP fix for s0 bound saturation
Update channel — corrected IVP fix, previous was mathematically wrong
Update channel — stochastic IVP for true s0 estimation
Update autodiff proposal with implementation status + gradient gaps
Update README, CLAUDE.md, inference guide for PGAS/NUTS/autodiff
Dense mass matrix bug writeup + agent channel notification
Update channel — prior specification implemented
File review #17 (resume/multi-stream/alpha) + architecture review
Marginal split density proposal for spatial PGAS
Channel update — spatial density test passes, bug is model-specific
Channel — Gamma hypothesis debunked, requesting I[p5] counts at failing substep
Channel — disambiguating initial vs CSMC trajectory -inf
Channel — requesting compiled IR to reproduce spatial -inf
Channel — downstream model PASSES round-trip, -inf is config issue
Channel — same code path, difference is params not simulation
Channel — sanity check added, three possible outcomes
Channel — 100/100 seeds pass, requesting indexed param dump
Incident report for spatial PGAS -inf bug
Channel — gamma density confirmed disabled, rebuild from 19ac52c
Channel — found CSMC reference counts_before mismatch (b15cb39)
Update incident report with second bug (CSMC reference mismatch)
Channel — analysis of remaining -inf sources, debug assertions added
Channel — near-zero rate fix and iota detection (faffe8f)
Spatial iota guidance in inference.md + incident report updated
Channel — deterministic check fix + upgraded assertions (9547ef9)
Channel — fix already in, verify build is current
Dev idea — step_one returning SubstepRecord for pairing safety
Channel — IVP density fix + iota requirement for spatial model
Channel — observation density is the -inf source, not transitions
Channel — root cause was data loader column mismatch
Complete incident report — six bugs, full resolution
Applicability analysis — which fixes generalize beyond spatial
Channel — resume fix and log_posterior column
Channel — s0 bounds enforced, request clarification on which model
Channel — resume transform validation fix
Channel — resume z-value ordering fix
Update incident hardening checklist with remaining TODOs
Channel — parallel tempering ready for testing
Channel — tempering diagnosis, informative priors recommended
Channel — max_treedepth and swap rate clarification
Channel — tempering test plan approved with caveats
Channel — treedepth warnings and async rungs answer
Channel — proposed cross-basin tempering test options
Channel — spatial tempering analysis + standardized logging request
Channel — kill tempering, IF2 test, wrong-basin finding
Channel — trajectory diagnostics + warm-up coming
Channel — LL decomposition + trajectory warm-up ready
Channel — csmc_sweeps_per_nuts ready
Document eval_table_expr construction-time constraint
Add standardized YAML frontmatter to all review and proposal files
Add frontmatter to inference review (10/13 items done)
Algorithm relationship overview in inference.md
Clarify PMMH can produce trajectories (low quality)
Add MCMC initialization strategy section
Update dimensional analysis proposal
Document dimensional analysis in language spec
Add mdBook setup with GitHub Pages deployment
Add MathJax for math rendering in mdBook
Add round 2 compiler review (18 items)
Add error quality philosophy to CLAUDE.md
Update compiler review frontmatter (8/18 done)
Compiler review complete (11/18 done, 7 deferred)
Add round 2 engine review (12 items)
Engine review complete (10/12 done, 2 by-design)
Add round 2 inference CLI review (8 items, reformatted)
Inference review complete (6/8 done, 2 deferred)
Add Windows support proposal, replace 'special user' with 'Windows user'
Revise experiment spec → unified run spec (v0.4-draft)
(run-spec) Fix review items — ObsOutput enum, ConfigHasher, SBC, designs
Add run system review (25 items, 5 critical)
Mark run system review 23/25 complete, 2 deferred
Add compiler review (8 items, 1 critical — indexed observations)
Update compiler review — 4/8 fixed (#1/#2/#4/#6)
(spec) Mark coupling sugar §10 as not yet implemented (review #8)
(review) Mark compiler review as complete (8/8 items done)
Priors belong with parameter declarations, not in fit.toml
Docs + test(cas): run-spec §4.4/§4.5 + end-to-end integration tests
Docs + diagnostic: observation semantics for state-snapshot projections
(proposal) Mark Erlang implicit-sum as shipped in initial review
(proposal) Synthetic-data fits + fit-seed replicates
(proposal) Unify fit output shape under fit_/
(proposal) Add real/ subdirectory, analogous to synthetic/
(proposal) Incorporate downstream feedback + LOC comparison record
Docs + test: replicate fits section + end-to-end grid tests
Update for simulate batch rename + synthetic fit fields
Drop migration guidance; file future-model-overrides stub
(proposal) IC-free inference (conditioning on y_1)
(proposal) Gate refine on scout convergence
(proposal) Unify simulate and fit output trees
Update output-path references to unified tree
Cleanup.md — audit of unified-output-tree shipping
(fit/provenance) Clarify hash vocabulary boundaries
Update to content-hashed output tree (D1-D4)
(inference) Filtering-vs-smoothing section + 'the diagnostic plot' guide
Single-writer-per-fit-dir contract + mark hardening proposal implemented
(review) Clean up 2026-04-19 compiler review + add front matter
(ir-spec) Align wire format with emitter (M12, M13, m15)
(review) Mark 2026-04-19 compiler review mostly addressed
(review) Mark 2026-04-19 compiler review fully addressed
(review) Reformat 2026-04-19 engine review + front matter
(review) Mark 2026-04-19 engine review addressed
Align docs with current CLI + cleanups (RC2/M17/m24 followup)
(review) Reformat 2026-04-19 inference review + front matter
(inference) Cooling approximation, reset_flows invariant, likelihood corner tests (IM5/Im5/In4 + IC1 regression)
(review) Mark 2026-04-19 inference batch 1 addressed
(review) Append batch 2 (NUTS, pgas_grad, correlated_pf, PMMH)
(review) Batch 2 resolution status
(review) Append batch 3 inference review (diagnostics + CLI)
(review) Batch 3 resolution status
Pfilter single-stream note + Hinnant link (Im22, Im23)
(pgas) Clarify heated-rung re-warmup on resume (Im18)
(review) Follow-up pass resolution status (IM6, Im18, Im22, Im23, Im25, Im2)
(reviews) Add 2026-04-20 design review suite
(spec) Fix IR spec drift — Sd1-Sd14 (compartmental-ir-spec.md)
(proposal) REPL/inspector mode for IR exploration (proposed, deferred)
(book) Add cross-dimension features guide with seir_cross_dim example
(proposal) Prequential out-of-sample evaluation
(spec) Tag camdl fenced blocks + remove deferred data {} block
(spec) Fix tagging misses + projection indexing comment
(cli) Add Examples block to every subcommand's --help
(cli) Note camdlc delegation + real flag set in compile/check/inspect help
(review) Audit spec claims vs test coverage
Docs/dev/testing.md — test architecture + runbook
(dev) Rewrite observations-system.md to reflect shipped reality
(spec) Add §2.3 three-tier dimensional overview; flag GH #8 in §7
Incident report for iota TOML unit miscast (GH #11, #12)
Incident report for forcing rescale double-conversion (GH #11, #13)
(testing) Add L9 external validation layer
(testing) Book now external at ../camdl-book
(harness) Sabotage-procedure section in tests/external/README.md
Correct IF2 cooling semantics; create docs/methods/ + cooling.md
Stage cooling work + inflight proposal index
(dev) If2 unit a handoff note for session resume
Rhat → chain_agreement (Â) in MLE-pipeline spec; document clean-eval keys + compound gate (unit a step 9 follow-up)
(channel) Bring downstream up to date on Unit A + summary proposal; rename effective→resolved gate config
(channel) Summary command shipped — schema + migration notes for downstream
Fit-command audit + sharpen CLAUDE.md "delete dead code" policy
Workspace dead-code scan inventory (pre-cleanup)
(inference-spec) Delete _summary.json claims; per-stage JSON files no longer exist
(methods) Particle-methods.md — bootstrap PF, IF2, CSMC-AS, correlated PF
Fit experiment-management audit + proposal
Clean-eval strip rationale + audit trail
Post-strip sweep — audit table + particle-methods §7
(typed-cas) Check off camdl list profile surfacing in proposal
(types) Regenerate TYPES-REFERENCE.md for post-v1-cleanup state
(types) Mark four-PriorSpec smell resolved; delete CLEANUP note
(proposal) Prior types consolidation, 2026-04-30
(review) 2026-04-30 full-codebase correctness and design audit
(review) Mark M1-M5 resolved in 2026-04-30-design.md
(cli) Help-text quality sweep — umbrella examples, top-level workflows, fixed fit new bug
(language-spec) Surface consecutive(dim) as the aging-across-stratified-models primitive
Reply on typhoid-issues.md — three of four shipped, one was a docs gap
Per-chain init_method (gh#42)
Restore camdl survey proposal lost in PR #44 squash
ODE inference proposal — three phases (NLopt / MH / NUTS)
Refine ODE inference proposal — round 2 review feedback
ODE proposal — integrate survey rewiring into Phase 1
ODE proposal — clarify stage names are user-chosen
ODE proposal — fold in tuple schema, METHODS registry, nl-* renaming
CLAUDE.md — book handoff note for the fit.toml schema rename
(review) 2026-05-12 full-codebase audit (8C/14H/21M)
(handoff) Camdl-book agent briefing for audit remediation
AGENTS.md + README updates + EVSI proposal
(readme) Add Prerequisites + fix dune test-stanza ambiguity
(readme) IDM/Gates attribution; honest about ir/VERSION + schema.json
(readme) Fix quickstart so commands actually run from fresh clone (closes gh#61)

Features

(ir) Implement IR layer — types, golden files, schema, tests
(rust) Implement sim runtime against real ir crate
(ocaml) Implement camdl DSL compiler + CLI; extend Rust CLI with simulate command
(ocaml) Implement inspect commands and accurate error diagnostics
Implement IR expression extensions and full compile-to-simulate pipeline
(compiler) Add indexed parameters (R0[patch] : positive = 2.5)
Strip param defaults from DSL; add layered --params TOML files
Add parameter bounds (in [lo, hi]) to DSL, IR, and spec
Browser-based visual editor (web app + WASM sim crate)
Add scenarios {} block and embed presets in IR
(web) Experiment redesign with multi-scenario ensemble visualization
(web) Three-column experiment layout, consistent ensemble modes
(ir) Add model_structure field for structural view building
(web) Base model canvas with swim lanes and birth/death stubs
(web) Add preset scenario menu to experiment sidebar
(web) Dark/light/auto theme, dynamic brush window, golden t_end updates
(web) Split pane, run all button, brush margin, Monaco keyboard fix
Scenario enable/disable, infectious_compartments fix, Layer 2 model
(ocaml/golden) Add Phase 1 model ladder — Layers 1, 3, 4
Rename IR field presets → scenarios, add new models to web
(cli) Add camdl experiment run/status with content-addressed output
(cli) Add camdl serve — static file server for experiment output
Remote experiment connect — load camdl serve results in web editor
(cli) Add camdl experiment summarize — per-seed scalar summaries
(web) Add MapPanel — choropleth for patch-stratified models
Add sir_patches_5 golden model + example for map panel demo
(cli) Geo pipeline for experiment serve; suppress flow cols by default
Indexed interventions, typed scenarios, family enable resolution
Add bernoulli likelihood, fix observations syntax, per-patch timing
(sim) Add ODE/RK4 backend; add intro.md and runtimes.md docs
(compiler) Fix time_unit normalization; add underscore literals + W100
(compiler) Replace read_csv/read_tsv with read_long + defines()
(compiler) Dimensions{} block, read(), origin/date(), indexed time functions
(experiment) Add sweep, design sampling, and analyze subcommand (v0.5)
Add camdl-analysis Python package and seir_age_sobol golden example
(voi) Add prior spec to design parameters; add VOI specification
(voi) Add camdl voi run command; add polio_es EVSI example
(sim) Add overdispersed() rate syntax and backend capabilities system
(dsl) Make t (simulation time) available in expressions
Wire math functions into expander; add cubic spline interpolation
(cli) Add camdl eval command for expression inspection
(cli) Add eval to unified camdl script; support .camdl input
(chain-binomial) Multinomial competing risks for shared source compartments
(inference) Stage 0-1 — module structure, obs loglik, resampling, PF
(inference) Stage 2 — step_one(), ChainBinomialProcess, camdl pfilter CLI
(inference) Stage 3 — IF2 (iterated filtering for MLE)
(inference) Discretized Normal observation model (He et al. 2010)
(dsl) Range-based periodic forcing (on = [7:100, 115:199, ...])
(pfilter) One-step-ahead prediction diagnostics in --trace output
(dsl) W301 warning for misaligned periodic range endpoints
(pfilter) Expose likelihood tolerance as --tol CLI flag
(inference) Camdl if2 CLI + fix iteration feedback loop
(inference) Camdl profile — parallel profile likelihoods with indicatif
(if2) Multi-chain with Rhat diagnostics and regime presets
(profile) 2D profile likelihood grids
(if2) IVP support + 3 integration tests
Camdl fit workflow, auto rw_sd, indicatif progress, --save-final-state
(golden) Add sir_spatial_sum — 4-patch spatial coupling via compile-time sum() expansion
(profile) Add --output/-o flag for file output
--output/-o on all data subcommands; clippy clean; CI
(if2) Variance ratio diagnostic (r_k) and --trace long-format output
Compile observation model from IR; remove --obs-model flag
(pfilter) Observation-space predictive quantiles via rmeasure
(fit) Per-stage configuration in fit.toml
Pfilter --replicates N; validate writes pfilter_trace.tsv
Provenance system — input_hash in fit_state, output manifest, experiment audit
Param_kind in IR; type-driven transforms replace bounds heuristic
Transform carries bounds; cooling_target = n_iterations; /20 log auto rw_sd
Boundary-hit diagnostic, preflight transform report, plan update
(profile) Add --fixed flag to exclude params from optimization
Deny_unknown_fields on fit.toml; Rhat basin-finding diagnostic
(scout) Seeded chains from start values + start_chains config
Out-of-sample validation via [holdout] in fit.toml + camdl data split
(data split) --fraction, --time-col, auto-detect time column
Warn when cooling exhausts before run ends
True (unperturbed) loglik evaluation in IF2 trace
Simplex (barycentric) parameter groups — softmax transform
Add balance compartment support (IR + runtime + OCaml)
(dsl) Add balance {} block parser
Add method = "constant" for piecewise-constant covariate interpolation
Add CAMDL_TRACE_STEPS=1 env var for per-substep diagnostics
Embed git hash + build date in all outputs, detect stale binaries
Add events {} block with add() action and at_day scheduling
Add PMMH posterior sampling (camdl fit pmmh)
Correlated pseudo-marginal MCMC (Deligiannidis et al. 2018)
(pmmh) Streaming traces + non-TTY progress
(pmmh) --check-variance now includes CPM correlation diagnostic
(pgas) Implement Particle Gibbs with Ancestor Sampling
(pgas) Add Robbins-Monro adaptive proposal SD
(pgas) Parallelize chains via rayon
(pgas) Random starts for chains (overdispersed initialization)
(pgas) PF marginal likelihood for θ updates + trajectory renewal diagnostic
(pgas) Stochastic initial states for IVP posterior sampling
(autodiff) Symbolic differentiation pass + rate_grad in IR
(autodiff) Rust gradient evaluation + compiler wiring
(autodiff) NUTS sampler + PGAS integration
(pgas) Add --no-nuts flag for MH-within-Gibbs fallback
(autodiff) Close gradient gaps — gamma density, obs model, eval_expr_deriv
(nuts) Diagonal mass matrix adaptation from burn-in samples
(pgas) Posterior trajectory output
(nuts) Dense mass matrix for correlated posteriors
(fit) Prior specification in fit.toml [estimate] section
(fit) Add Beta prior support
(pgas) Chain resume infrastructure — serializable state + bincode
(pgas) --resume flag with config hash safety + bincode state
(fit) Multi-stream observation support
(cli) --verbosity flag for structured logging
TraceWriter + shared config hash, PGAS refactored
PMMH --resume + FitState loglik_type/acceptance_rate
(sim) Add ResolvedExpr — pre-resolved expression trees for hot-path eval
(sim) Add ResolvedModel to CompiledModel, resolve all Expr at construction
(pgas) Parallel tempering (replica exchange) for NUTS parameter updates
(pgas) Periodic swap rate logging during tempering
(pgas) Configurable max_treedepth for NUTS
(pgas) NUTS treedepth/divergence warnings + configurable max_treedepth
(pgas) LL decomposition in trace + trajectory warm-up
(pgas) Csmc_sweeps_per_nuts — multiple trajectory updates per param step
Review-zip.sh — targeted zips for external code review
(sim) Typed inference diagnostics — DiagnosticKind + DiagnosticCollector
(cli) Migrate inference diagnostics to typed DiagnosticCollector
(inference) Add ProcessModel, DensityProcess, ObservationModel traits
(compiler) Dimensional analysis checker
(dimcheck) Promote dimension errors to compilation errors
(dimcheck) Phase 2 — explicit [dim] annotations on parameters
(ir) Add param_dim field to Rust Parameter struct
(dsl) Support indexed syntax in scenario set/scale blocks
(compiler) Inspect --dims, W200 guard warning, seasonal docs
Windows support + single entry point (Phase 1+2)
Add pre-push hook for cargo check + dune build
Add clippy + OCaml tests to pre-push hook
(dsl) Typed let bindings for dimensional constants
(parser) Support (expr) 'unit syntax, error on ambiguous division
(cli) Synthetic observations for camdl simulate
(fit) New FitConfigV2 types + camdl fit run command
(fit) Provenance.json + config_hash staleness detection
(fit) Wire PGAS/PMMH dispatch through camdl fit run
(cli) --draws flag for posterior/prior predictive simulation
(fit) --sweep on camdl fit run for profile likelihood and grids
(fit) Camdl fit status for v2 configs and result directories
(cli) --batch flag on simulate, delegates to experiment runner
(fit) Write draws.tsv with complete parameter vectors (PGAS + PMMH)
(cli) --seeds and --scenario batch flags on simulate
(cli) --draws uniform for space-filling exploration
(fit) PFilter dispatch through camdl fit run
(fit) Camdl fit diff and camdl fit new utilities
(cli) Help system with examples and dim comments
(cli) --dry-run for simulate shows resolved parameters with provenance
(dsl) ~ prior syntax for parameter declarations
(prior) Wire IR priors through Rust runtime + simulate --draws prior
(dsl) Recurring intervention syntax — { every, from, until } block
(cas) New cas module — canonical CAS layout + meta types
(cas) --cas flag on camdl simulate — opt-in trajectory caching
(cas) Camdl list / show / cat — browse the content-addressable store
(wrapper) Route list/show/cat through camdl-sim + update --help
(dsl) extends for scenario inheritance (single-parent)
(cli) Simulate batch subcommand, retire --batch flag and experiment
(inference) State-snapshot projections in the particle filter
(fit) Add [synthetic] block + fit_seeds to FitConfigV2
(fit) Wrap all fit outputs under real/fit_/
(fit) Synthetic-data generator for [synthetic] fit configs
(fit) Replicate-grid dispatch for synthetic + fit_seeds
(fit) Summary.tsv + coverage.tsv for grid runs
(fit) Warn when priors are declared but no stage consumes them
(fit) Record pre-filter chain starts in chain_starts.tsv
(fit) IC-free inference via [fit] ic_free = true
(fit) Gate refine on scout convergence + loglik regression
(run_meta) Add unified Run/RunKind ADT types
(run_paths) Canonical output-path construction module
Unify output tree — output/sims/ and output/fits/
(cas) Human-readable dir names — -<hash[:8]> for fits and sims
(fit,list) Write Run::Fit at fit root + surface fits in camdl list
(list) --kind sim|fit|both filter (cleanup.md L2)
(fit,batch) V1 fit writes unified tree + manifest moves to sims/
(show,cat) Resolve fits by path or short-hash prefix
(sim/inference) Ancestor-trace primitive + opt-in recording in bootstrap PF
(cli/pfilter) --save-paths + --save-filtering flags
(fit) camdl fit where FIT.toml [--seed N]
(fit) --starts-from accepts short-hash prefix in addition to path
(simulate) Backend-provenance guardrail for --params from a fit MLE
(diagnostics) Add Info severity level (M5)
(expander) Warn when indexed obs has no data_stream (W203, m25)
(expander) E265 on intervention ASet to unknown compartment (m13)
(expander) E233 hints at mean/mu typo in priors (m19/C4/C10)
(compiler) Thread source locations into decl-level diagnostics (M9)
(cli) Run ir::validate on model load (RC1)
(inference) Implement BetaBinomial observation likelihood (IC1)
(correlated_pf) Preflight-reject multi-overdispersion CPM (IM8)
(fit) Prior × transform compatibility validator (IC4)
(compiler) Thread obs_decl.oloc + intervention_decl.ivloc into diagnostics (M9)
(compiler) Add init_entry.iloc field (M9 continuation)
(inspect) Add --tables flag to show loaded table values
(book+inspect) Add dimensions/data guide with working examples
(inference) Prequential trace + scoring kernels (Part I scaffolding)
(sim) SMCConfig.record_prequential flag
(sim) PF prequential sample recording + trace builder
(cli) Default backend is now chain_binomial
(pfilter) --save-prequential / --no-save-samples
(fit) Prequential trace for PFilter stage
(cli) Camdl compare — multi-model prequential table
(compare) E_T column + column-definition block in --help
(wave1/#1) Multi-source transitions — A + B --> C + D DSL syntax
(wave1/#4) Diagnostic_test likelihood sugar
(wave2/#2) Probabilistic branching X --> {A:p, B:1-p} @ r
(wave2/#3 gate 1) Hierarchical priors — parse + IR classification
(wave2/#3 gate 2) Hierarchical log-prior evaluator + scipy-oracle tests
(wave2/#3 gate 3a) Wire hierarchical priors into PMMH log-posterior
(obs) Multi-compartment prevalence() — GH #7 + proposal update
(inspect) Kind-grouped parameter summary + --parameters detail view
(forcing) Required tier-3 unit literal on every forcing declaration (GH #8)
(dim) Unchecked_dim per-expression dimensional escape
(cli) --progress {auto,pretty,plain,none} flag (GH #14)
(harness) External-validation harness v1 with sir_analytical case
(harness) He2010_forward case with R+pomp reference (regen path)
(harness) Boarding_school_sir case — pomp canonical SIR
(harness) Run-all mode + cargo test integration (L9 gate)
(harness) He2010_pfilter_loglik case + batch-replicated mode
(run_meta) Add RunKind::Profile + FitStage profile backrefs
(run_paths) Profile_run_dir / profile_point_dir / profile_point_start_dir
(profile) CAS integration for resume/mid-run-plotting (GH #15, v1)
(list) --parent HASH to enumerate a profile's grid-point runs
(compare) Evidence in decibans alongside nats (item 1 of 4)
(evidence) Add logmeanexp + sample_sd helpers for clean-eval PF replicates
(fit) Add CleanEvalConfig + GateConfig to IF2 stage (unit A step 3)
(fit) Plumb clean_eval / gate config through CLI + FitRunConfig (unit A step 4)
(fit) Clean_eval module — candidate construction + replicate scoring (unit A step 5)
(fit) Wire clean_eval into chain selection (unit A step 6)
(fit) Chain_evaluations.tsv + run-root final_params.toml (unit A step 7)
(fit) Compound scout-convergence gate (Â + decibans-spread, SE-aware floor) (unit A step 8)
(fit) Per-chain clean-eval keys in summary JSON + status decibans line (unit A step 9)
(fit) Persist resolved gate / clean-eval config in fit_state.toml (phase 3)
(fit) Camdl fit summary — single-fit interpretation surface (phase 1, closes #18)
(fit) Plumb ESS through clean-eval into chain_evaluations.tsv + summary JSON (phase 2)
(fit) Summary --format json|md|latex + --params-only (phases 4 + 5); spec docs
(fit) Foundation walker, MethodResult ADT, and v2 summary swap
(evidence) Add logmeanexp_with_se — delta-method SE on log scale
(fit) Cmd_fit_summary method-aware refactor + fit table + ConfigDiff + Deliverable C
(fit) Step 6 — archive fit.toml.original; fit table reads from archive
(fit) Step 8 — labels (--label, fit label, fit table/list integration)
(camdlc) -o / --output FILE writes IR JSON to file (closes #23)
(profile) --sweep accepts lin(min,max,n) and log10(min,max,n)
(cas) Typed CasInputs trait + ReplicateSet + profile migration with --seeds
(cas) Migrate simulate --cas to CasInputs
(cas) Migrate batch run to CasInputs; delete legacy run_hash
(cas) Migrate fit run to CasInputs (FitInputs + StageInputs)
(cas) Camdl show/cat handle RunKind::ReplicateSet umbrellas
(list) Surface profiles + replicate-set umbrellas in camdl list
(fit/config_v2) Add Gamma + Exponential to PriorSpec (parity with IR + sim)
(fit) --resume for PGAS / PMMH; identity vs. extension hash split
(fit) IF2 cooling_target_iters + simplex_groups (top-level)
(fit) Surface lost PGAS / PMMH / PFilter knobs in v2 schema + CLI
(fit) Default record_prequential = true for Stage::PFilter
(cli) Styled --help output (colorize after_help, clap structural styles, term-width cap)
(fit) [data] file = "..." shorthand for stratified models with one wide TSV
(fit) [estimate] start = defaults from bounds when omitted (gh#34)
(dsl) :rate (and other dim) cell-type annotations on tables (gh#32)
(fit) [fixed] from_scenario = "name" shorthand (gh#33)
(fit) Stream IF2 parameter_traces.tsv during run for tail -f diagnostics
(pfilter) Include observation projections in --save-paths output
Phase 1 ODE-inference — NLopt MLE + tuple-schema migration
(fit) Make [estimate.X].bounds optional, defaulting from model file
(fit) Default init_method = "lhs" across IF2 / PGAS / PMMH / NLopt
(fit) Transform-aware uniform start when [estimate] omits start

Miscellaneous

Gitignore output/ and diagnostics.tsv artifacts
Docs refresh, golden file cleanup, web formatter pass
Move proposals to docs/dev/proposals/
Move dev-blog to docs/dev/blog/
Tidy pass — trace OnceLock, remove stale dead_code, wire PMMH status
(pmmh) Add experimental warning for long time series
Clean up root — 65 .md files → 3
Add zip-for-review-with-docs.sh for comprehensive review packages
Add Apache 2.0 license + NOTICE
Remove dead compile_joint_obs_loglik + dead_code suppression
Move web/ to web-archive branch — not a priority, eats context
Update golden files for autodiff simplifier fixpoint
(fit) Drop the 3-line iter-0 preamble from parameter_traces.tsv
(compiler) Delete dead Source_cache.load (m6)
(parser) Delete empty tag_opt from inline transition (m14)
(inference) Batch 2 minor cleanups (Im14, Im15, Im17)
Delete observe/ crate (stub, never built out)
(gitignore) Fix .claire/ → .claude/ typo; untrack settings.local.json
(harness) Re-bootstrap pfilter_loglik MANIFEST after .gitignore edit
(ci) Untrack stray .claude/worktrees/* gitlinks
(fit) Delete v1 FitToml schema; v2 is the only fit-config path
(fit) Silence too_many_arguments on run_stage entry points
Remove camdl-wasm crate + web-editor Makefile targets
(cli) Clean up stale doc-string references after RunStatus + run_meta migrations
Remove dead camdl-analysis / VOI / sensitivity-experiment subgraph

Other

Initial import
Normalize formatting across IR schema, spec, golden files, and Cargo configs
Merge inference-v0: particle filter, IF2, profiles, DSL improvements
Merge worktree-profile: 3-4x inference speedup via scratch buffers + rayon particles
Remove EkRng dead code + ahash dependency
Add CAMDL_TRACE_STEPS logging to event Add actions
Revert "fix(cpm): track particle identity through resampling for z-value sync"
(pgas) Sanity check LL immediately after simulate_reference
(pgas) Enhanced spatial -inf diagnostics + targeted step_one test
(pgas) Definitive diagnostics for spatial -inf
(pgas) Add consistency assertions for counts_before/flows pairing
(pgas) Observation density is the -inf source, not transitions
IF2Param → EstimatedParam throughout
Remove ObsStreamSpec and joint_obs_weight
(pgas) Pre-allocate ancestor weights, swap gamma buffers
Remove resolved issue file, gitignore parser artifacts
Camdl experiment and camdl profile with migration notes
Remove camdl experiment analyze, deprecation notes
Remove deprecated CLI commands, tidy dispatch
(ir) Remove dead error variants WrongIndexCount and UnknownCompartmentInInitialConditions (review #5)
(prior) Self-review of prior-syntax PR with bugs + test gaps
Spec wording + PIndexed catch-all is an internal invariant
(list) Switch to borderless layout for readability at scale
(browse,fit) Drop dead shim, mark incomplete stages explicitly
Tick L5 (book fit paths migrated to stem-glob helpers)
Three-stage review zip bundlers for external code-review agent
Drop diff-scoped review zips in favor of canonical scripts/review-zip.sh
Canonical review-zip.sh + scripts/README.md
Review-request.md — paste-ready reviewer prompt + staging order
Expose PF latent trajectories + the (1-vs-2) diagnostic
(pf) Reframe --save-filtering as PF-diagnostic tool, not 'less-useful alternative'
(pf-traj) Mark implemented + record shipping commits
Output-tree hardening (addresses post-ship review findings)
Default output root back to 'results/' (post-ship review)
Proposal + incident: backend-provenance guardrail for simulate --params
(backend-provenance) Mark implemented, record shipping commit
(sim) Minor review cleanups (RM10, Rm4, Rm5, Rm8, Rn2)
Permissive mode inside observation likelihoods (gh #4)
Scrub remaining experiment / --batch references (gh #2)
Scrub stale CLI refs for alpha (sweep)
DSL features for first-class malaria modelling
(malaria) Add verified pre-proposal fixture + show inspect output
(demography) Split vital dynamics into separate proposal
(malaria) Document already-shipped features; add #5b state-read
(malaria) Waves + checkboxes; #3 stays in parameters{}
(wave1/#1) Design note + failing TDD tests for multi-source
(wave1) Check off #1 multi-source — landed d88eb7f
(wave1) Check off #4 diagnostic_test — landed 674c451
Request Ross-Macdonald fit vignette (Wave 1 demo)
(wave2) Check off #2 branching — landed 9c6530a
(wave2/#3 gate 2) Hierarchical log-prior evaluation — risk catalog + test battery
Check off Wave 2 #3 Gates 1+2+3a; notify book agent
Obs sampler evaluated likelihood args against zero scratch (GH #5, #6)
Update with meta-incident (first fix missed the actual path)
Update with third strike + audit-technique lesson
Verify perf intact after helper deletion
(note) Defer --no-dim-check hardening (require reason + loud warn)
(note) Defer unchecked_dim per-expression dimensional escape
External validation harness (post-GH #11 lessons)
Revise external-validation harness after design review
Nightly external-validation regen CI (deferred)
Evidence in decibans for model-comparison output
Camdl profile CAS integration (supersedes GH #15 approach)
IF2 scout findings + remediation (silent-wrong-answer class)
Camdl fit summary — single-fit interpretation surface
Clean_eval → loglik_eval (file, types, fields, CLI flags, TOML key)
Typed CAS runs, replicate sets, profile-as-stage (2026-04-28)
(typed-cas) Scope to single push; drop migration tool; Phase 2 → future work
(typed-cas) Mark Implemented; check off implementation checklist
Init_method = single | uniform | lhs for IF2 chain starts
Extend init_method to PGAS and PMMH
Per-start init draws in camdl profile
Gh42 follow-up: honour fit.toml [estimate].bounds in IF2/LHS/transform
Camdl survey — likelihood-landscape diagnostic (#44)
Gh43 follow-up: --eval auto picks pfilter/simulate from model capabilities
Gh43 follow-up: bound-clustering + start-rank silent-miss diagnostics
Gh43 follow-up: auto-scale --n-points and bump --eval-replicates 3 → 5
Gh43 fix: pairplot subplot axis assignment off-by-one
Gh43 fix: pair-plot diagonal histograms — overlay subsets, not partitions
Gh43 fix: pair-plot 1:1 aspect ratio
Gh43 fix: color-coord normalisation uses displayed top-K, not all rows
Merge Phase 1 ODE-inference into main
Add InitMethod::SurveyTopK variant + proposal
Stage config fields survey_path + survey_top_k_n
SurveyTopK reader + IF2 dispatch wiring
CLI overrides --survey-path and --survey-top-k
Chain_init_source provenance + chain_starts.tsv sidecar
Cross_check + end-to-end survey-top-k unit tests
Richardson dt-convergence check at θ̂ + IF2 wiring
CLI overrides --no-dt-check / --dt-check-strict / --dt-check-halvings
Render dt-check verdict in camdl fit summary
Proposal — record v1 ship status + deferred work
Gh#53: dt-check verdict text — flag high-magnitude failures (≥100·τ) as
Gh#53 fix: store dt-invariant fire_times on CompiledModel; resolve
Gh#53 incident report — cohort fire-step dt misalignment
Gh#53 audit: consolidate the 5 remaining inline time-to-step
Gh#53 incident report — seed-resampling test results + audit findings
Gh#53 audit: 2 new ladder-dimension regression tests
Proposal for dt primitive + L401 lint + warning catalog
OCaml side — Ir.Dt variant + reserved name + dim/expander wiring
Rust side — Expr::Dt + EvalCtx threading
L401 lint — Euler-correction with fixed time literal
Round-trip + runtime tests for dt primitive
Mark proposal v1 complete + cross-repo hand-off
Proposal — trig primitives (sin/cos/tanh + pi/e)
Add Sin / Cos / Tanh + pi / e (trig primitives)
Tests + end-to-end smoke for trig primitives
Proposal + forcing-kinds taxonomy doc
Add Fourier + PeriodicSpline forcings
Tests + DSL smoke for Fourier + PeriodicSpline forcings
Gh#59 follow-up: proposal — proper periodic B-spline algorithm
Gh#59 v2: proper periodic B-spline algorithm (de Boor)
Gh#59 v2: cross-validate periodic B-spline + Fourier against external oracles
Bump to 0.4 with envelope + version handshake (audit C8)

Performance

(sim) Add sparse incremental propensity updates to Gillespie
(web) Fix Connect hang + Map tab crash for slug-based patch models
Add criterion benchmark suite for simulation and inference
Pre-allocate scratch buffers in step_one, eliminating 4.2M allocs/run
Rayon parallel particle propagation in bootstrap_filter and IF2
Cache check, double-buffer resampling, initial_loglik pfilter
(cpm) Parallelize correlated PF + seed RNG from gamma noise
(sim) Migrate eval_propensities to pre-resolved expressions
(sim) Migrate chain_binomial overdispersion to pre-resolved expressions
(sim) Migrate gillespie, tau-leap, ODE backends to pre-resolved expressions
(sim) Migrate all inference code to pre-resolved expressions
(expander) Fix O(n^2) list append in collect_declarations
(expander) Add Hashtbl lookups in resolve_expr for O(1) name resolution
(expander) Incremental scenario bindings fold, O(N) not O(N²) (m23)
(obs) Thread-local scratch IntState eliminates hot-loop alloc (IM2)

Refactor

Restructure defaults/ presets and update experiment spec
(web) Auto-discover golden examples via import.meta.glob
(cli) Extract resolve_ir_path; add enable/disable to experiments
(experiment) Hierarchical run dirs + correct cache invalidation
(sim) Introduce EvalCtx; replace 6-arg eval_expr signature
(dsl) Rename functions {} to forcing {}
(ir) Replace overdispersion field with DrawMethod enum; add deterministic() and mod()
Unify threading — one rayon pool for all parallelism
(if2) Replace r_k with weighted-variance ratio + q_ratio diagnostics
(pfilter) Predictions are Option; state quantiles on obs scale
ParamSpec + build_if2_params_from_specs (Phase 0-1)
If2 + profile use compiled dmeasure from IR (Phase 5)
Reuse compute_rhat (Phase 6); scout_best_params.toml (Phase 7)
Unify model loading + flow resolution + error handling (Phase 3-4, 8)
Remove MAD auto-calibration; loud auto rw_sd with source tracking
Rename dmeasure → obs_loglik, rmeasure → obs_sample
(obs) ObsStreamSpec + joint_obs_weight — one function for all pipelines
(pgas) Centralize RATE_EPSILON, clean up debug diagnostics
Shared mcmc_diagnostics + rename if2_params → estimated_params
Run_chain_binomial calls step_one instead of inline copy
(pgas) Extract patch_population helper
(inference) Extract restore_z_values helper
(pgas) Extract sample_categorical_log helper
(inference) Consolidate transform_deriv into EstimatedParam
(pgas) Delegate prior density to Prior::log_density
(pgas) Precompute obs_at_substep mapping
(pgas) Extract RungState struct for parallel tempering
(inspect) Remove dead code — pp_one and unused neq binding
(expander) Deduplicate strides computation in load_table_data
(inspect) Extract read_file helper, eliminating duplicate file reads
(expander) Extract read_csv_rows helper for CSV/TSV file loading
(ir) Merge serialize.ml + deserialize.ml into serde.ml
(expander) Make expanded_comp_cache non-optional
(inference) Extract shared cholesky_lower to linalg.rs, add log::warn
(obs_model) Use binom_logpmf for Binomial observation likelihood
(runner) Extract median/MAD utility functions
(inference) Rewrite PF + IF2 to use trait-based API
(pgas) Replace ObsStreamSpec with MultiStreamObsModel
(cli) Build helpers, collector non-optional, auto_rw_sd dedup
Trait-ify correlated PF, finish PMMH migration, delete compat fields
(sim) Extract Prior to shared inference/prior.rs
(list) Use comfy-table + strip model path to basename
(hashing) Consolidate hash helpers into crate::hashing
(cas) Simulate writes Run/RunKind::Simulate, drop cas::RunMeta
(fit) Stage writes Run::FitStage, drop StageProvenance
(cas) Wire run_paths helpers into production, drop duplicated path code
(run_meta,browse) Collapse duplicated loader + drop redundant stage_hash
Delete dead data_contract field (m20)
Delete dead simplex parameter_groups plumbing (M17/m24)
Scrub stale EKRNG design references (RC2)
(inference) Propagate resolve_likelihood errors (IM3) + reject mismatched obs_times (Im3)
(cli) Delete dead legacy fit entry points (cmd_fit_scout/refine/validate/pmmh/pgas)
(ocaml) Design quality fixes from 2026-04-20 review
(cli) Migrate to clap 4 derive API and consolidate inference types
Cargo clippy --fix sweep across sim + cli
(cli) Util helpers for chain-seed derive, dir-create, die
(obs) Revert prevalence(x,y) sugar; support DerivedExpr emission (GH #7)
(progress) Extract DEFAULT_THROTTLE constant + Throttle::default
(fit) Rename rhat → chain_agreement (Â) in MLE pipeline only
(cli) Collapse duplicate args::Cli/Command/FitCommand into main.rs's tree
(fit) Delete v1 stage entry points + helpers (~2,000 lines)
(fit) Delete fit/status.rs — dead v1 status printer (~360 lines)
(fit) Rename fit/summary.rs → fit/grid_summary.rs
(fit) Remove all #[allow(dead_code)] in fit/; delete fields and methods that aren't read
Workspace-wide dead-code cleanup (~1,400 lines + 0 #[allow(dead_code)])
(fit) Strip clean-eval to FinalIter + clean re-evaluation
(fit) Typed-prior helpers; resolve_prior takes v2 estimate map
(fit) FitRunConfig::build + build_if2_params take v2 types
(fit) Pgas/pmmh as v2-native run_stage; drop to_legacy_toml + compute_config_hash
(run) Lift label from FitMeta to Run; add --label to simulate/profile
(cli) Rename camdl fit label → camdl label; add HASH column
(profile) Collapse single-seed Profile into ReplicateSet-of-1
(browse) Collapse Resolved enum; cover all kinds in show
(types) Swap stringly-typed backend / method for typed enums
(run) Replace wall_time_seconds==0.0 sentinel with RunStatus
(cli) Replace v2 PriorSpec enum with re-export of ir::PriorDist
(cli) Delete prior_spec_to_prior; resolve_prior calls Prior::from_ir directly
(cli) Replace sampling::PriorSpec with ir::PriorDist
(ir) Replace stringly-typed HierarchicalPrior.kind with enum (M1)
(fit) Rename internal format-dispatch helpers cmd_* → format_*
(run-meta) Drop legacy empty-string stage_hash deserialize shim

Tests

Add experiment pipeline integration tests + fixture TOMLs
(cli) Extract plan_runs ADT + cache invalidation tests
(sim) Add unit tests for all UnOp variants (neg, log, sqrt, abs, floor, ceil)
(chain-binomial) Add invariant tests (conservation, non-negativity, large-N regression)
(sim) Validate CubicSpline against scipy.interpolate.CubicSpline
(sim) Add external validation tests
(inference) Particle filter validation tests
(if2) Tighten convergence test with loglik stability check
(autodiff) Gradient check — analytical vs finite differences
Resume hash + multi-stream observation tests
Joint_obs_weight tests with actual ObsStreamSpec
Spatial density reproduction tests — all pass
Downstream SEIR spatial model round-trip — PASSES with realistic params
Multi-seed spatial density — 0/100 seeds produce -inf
Golden spatial SEIR model for inference density round-trip
(sim) Add resolved_expr unit tests — 13 tests covering all variants
Diagnostic collector severity + JSON round-trip
Update all sim tests for trait-based inference API
Add obs-level parameter tests
(dimcheck) 56 tests + 6 negative golden files
(dimcheck) Add QCheck property-based tests
Add 25 tests for run system (65 → 90 total)
14 parameter precedence tests (90 → 104 total)
(compiler) 7 prior-syntax tests + sir_priors golden fixture
(cli) Prior-draws integration + resolve_prior precedence chain
(compiler) E230–E235 prior validation error codes
(compiler) Uniform/normal/exponential parse + const arithmetic in prior args
(cli) Prior draws bounds/scenarios/seeds + parse_prior coverage
(cli) Moment-matching sanity check for sample_from_prior_raw
(cli) End-to-end prior round-trip through golden IR
(inference) Regression tests for state-snapshot projections
Close gaps around prevalence-on-stratified-compartment fix
Regression guards for unified output tree + show-for-fits
(pfilter) Integration tests for --save-paths and --save-filtering
(backend_provenance) Behavior tests that read run.json, not just stderr
(compiler) Register 12 unlisted golden fixtures (C8)
Assert W310 actually fires in extends-dedup test (T4)
(golden) Regenerate IR golden files after OcM3 zero-grad filter
(compiler) P1.5 + P3.1 / P3.2 / P3.5 spec-claim regression tests
(compiler) P3.4 consecutive(k) → k-1 adjacent pairs
(sim) Numpy/scipy-reference tests for linear + constant interp
(sim) P1.3 Erlang-k statistical test + runtime-test design doc
(wave1/#1) Close multi-source coverage gaps
(fit) Spec sweep + Deliverables A & B for the v2 layout bug
(fit) Empirical anchor for clean-eval's bias-reduction claim
Add 11 missing tests + fix 3 bugs surfaced by them
(fit) Unit tests for nlopt_stage convergence gate + config extraction
Fix make test post-audit (envelope + degenerate-rates fallout)

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Changelog

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Performance

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[0.1.0-alpha] - 2026-05-15

Bug Fixes

Build

CI

Documentation

Features

Miscellaneous

Other

Performance

Refactor

Tests