Pre-JOSS code review: correctness, robustness, and test fixes

.gitignore

@@ -14,4 +14,20 @@ LocalPreferences.toml
 _*
 tutorials/build
 .env
-.ipynb_checkpoints
+.ipynb_checkpoints
+
+# Local workspace and tooling artifacts (do not commit)
+.claude-plugin/
+.craft-agent/
+.agents/
+.pi-agent/
+.pi-sessions/
+/config.json
+/events.jsonl
+/views.json
+/theme.json
+/labels/
+/statuses/
+/sessions/
+/skills/
+/sources/

CHANGELOG.md

@@ -0,0 +1,99 @@
+# Changelog
+
+All notable changes to CEEDesigns.jl are documented in this file.
+
+## [Unreleased]
+
+This update resolves a set of correctness, reproducibility, and API/usability
+issues identified during a pre-JOSS code review. Each item lists the previous
+behavior and the change. Issue tags (S#, C#, M#, N#, D#, P#) are internal
+review references.
+
+### Fixed — correctness & crashes
+
+- **Categorical distance direction (S1).** `DiscreteDistance` returned `λ` for a
+  *match* and `0` for a *mismatch* — the opposite of a distance. After collation
+  through the `Exponential` similarity, historical rows that *matched* the
+  evidence received the *lowest* weight. It now returns `0` on a match and `λ` on
+  a mismatch, consistent with `QuadraticDistance`, so matching rows receive the
+  highest similarity weight.
+  *Note:* this changes the numerical output of any model that uses categorical
+  features.
+
+- **Symbol-keyed constraints crashed at run time (C1).**
+  `ConditionalUncertaintyReductionMDP` validated `target_condition` keys by
+  stringifying them but stored the original keys, so a `Dict(:Col => …)`
+  constructed successfully and then threw "Column … not found" during
+  `isterminal`. Keys are now normalized to `String` (and ranges validated) at
+  construction, and `conditional_likelihood` accepts both `String` and `Symbol`
+  keys.
+
+- **Columns with missing values were rejected (C2).** The numeric check
+  `eltype(col) <: Real` excluded `Union{Missing, Float64}` columns. It now uses
+  `nonmissingtype(...) <: Real`, and the membership mask uses
+  `coalesce(…, false)` so rows with `missing` in a constraint column are excluded
+  rather than erroring.
+
+- **`max_experiments` counted evidence entries (M1).** The budget check counted
+  evidence dictionary entries (including prior evidence and each feature of a
+  multi-feature experiment) instead of completed experiments. It now counts
+  experiments whose features are all present.
+
+- **Constant feature column produced an opaque error (M4).** A zero-variance
+  column made `QuadraticDistance` divide by zero, surfacing as the unrelated
+  "weights cannot contain Inf or NaN values". It now raises a clear
+  `ArgumentError`, and `σ` is recomputed per call (removing a latent
+  cross-column memoization bug).
+
+- **`importance_weights` length was unchecked (N3).** A wrong-length vector failed
+  later with an opaque broadcasting error. The length is now validated against
+  `nrow(data)` with a clear `ArgumentError`.
+
+### Fixed — reproducibility & concurrency
+
+- **Shared RNG across parallel simulations (S2).** All `Sim` runoffs shared a
+  single RNG object (a data race under `run_parallel`), and one solver instance
+  was reused across thresholds and ensemble runs. Each `Sim` now gets an
+  independent RNG derived from the caller's RNG; `default_solver(rng)` is
+  seedable; `efficient_designs` / `conditional_efficient_designs` use a fresh
+  solver and RNG per threshold; and `perform_ensemble_designs` uses an
+  independent RNG per ensemble run. Results are reproducible from a single seed.
+
+- **Static arrangement search used the global RNG (S3).** `optimal_arrangement`
+  built its `DPWSolver` with the implicit `Random.GLOBAL_RNG`, which the threaded
+  `StaticDesigns.efficient_designs` accessed concurrently. `optimal_arrangement`
+  now takes an `rng`, and the threaded driver pre-seeds one independent RNG per
+  task.
+
+### Changed — API, documentation, robustness
+
+- **Input validation uses `ArgumentError` (C3).** User-facing `@assert`s in the
+  MDP constructors, `conditional_likelihood`, and `Entropy` now throw
+  `ArgumentError` with stable messages.
+- **`EfficientValueMDP` value signature (D1).** Docstring corrected from
+  `value(evidence)` to `value(evidence, costs)`.
+- **Documentation / defaults / naming (D2).** `Exponential` docstring corrected to
+  `λ = 1/2` and `exp(-λ x)`; fixed typos; unified the `terminal_condition`
+  default; added `tau_set` as the keyword for `perform_ensemble_designs` (the
+  previous `thred_set` is still accepted).
+- **Static designs & plotting (D3).** Experiment feature lists are normalized to
+  `String` so `Symbol` features work; `plot_front` guards against empty input; a
+  docstring referenced a nonexistent `get_labels` (now `make_labels`); and the
+  ensemble output column `Average_Utility` was renamed to `Average_Cost` to
+  reflect that it holds cost.
+- **Ensemble frequency counting (M2).** `ensemble_to_dataframe` now de-duplicates
+  identical points within a single run, so collapsed points (under
+  `realized_uncertainty = true`) no longer inflate frequencies / MLASP votes.
+- **Documentation note (P1/P2).** Documented that the uncertainty measure is
+  normalized (thresholds on `[0, 1]`) and that the terminal information term is
+  realized as a hard terminal condition rather than an additive penalty.
+
+### Added
+
+- Regression tests covering the above: `test/GenerativeDesigns/test_review_fixes.jl`
+  (S1/C1/C2/M1/M4/N3), ensemble within-run de-duplication, and static arrangement
+  reproducibility.
+
+### Testing
+
+- Full test suite passes with `JULIA_NUM_THREADS=4`.

Project.toml

@@ -13,8 +13,6 @@ POMDPTools = "7588e00f-9cae-40de-98dc-e0c70c48cdd7"
 POMDPs = "a93abf59-7444-517b-a68a-c42f96afdd7d"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
@@ -30,8 +28,6 @@ POMDPTools = "0.1"
 POMDPs = "0.9"
 Plots = "1.39"
 Random = "1.9"
-Reexport = "1.2"
-Requires = "1.3"
 ScientificTypes = "3.0"
 Statistics = "1.9"
 StatsBase = "0.34"

docs/src/api.md

@@ -25,6 +25,7 @@ CEEDesigns.GenerativeDesigns.Entropy
 CEEDesigns.GenerativeDesigns.efficient_design
 CEEDesigns.GenerativeDesigns.efficient_designs
 CEEDesigns.GenerativeDesigns.efficient_value
+CEEDesigns.GenerativeDesigns.default_solver
 ```
 
 ### Distance-Based Sampling