prompt: priors/messages census wrap-up — 09+11 shipped, 12+13 design deferred, census retired

draft/bug/priors/09_prior_property_tests.md → complete/2026/08/prior-property-tests.md

@@ -1,3 +1,53 @@
+Property-based correctness sweep over every concrete `Prior` subclass — census
+finding C3, the Phase 3 safety net of the priors/messages cleanup (hub
+PyAutoFit#1331). Issue PyAutoFit#1497; **PR PyAutoFit#1499, merged 2026-08-18
+as `21288bb` with all checks green** (unittest 3.12 + 3.13, docs). Closes the
+loop the census opened: the nine bug fixes shipped in July (#1345/#1348) are
+now locked as class-wide invariants, not just pointwise regressions.
+
+- New `test_autofit/mapper/prior/test_prior_properties.py` — 134 parametrised
+  tests, five properties over Uniform/LogUniform/Gaussian/LogGaussian/
+  TruncatedGaussian (two parameterisations each): P1 `cdf(value_for(u)) ≈ u`
+  (1e-6); P2 normalisation three ways — `exp(log_prior_from_value +
+  log_normalisation())` integrates to 1 (locks the #1331 Option A contract),
+  the message physical-density path integrates to 1, and the generic
+  exponential-family pdf integrates to 1 for direct messages **including
+  `TruncatedNormalMessage`** (the exclusion that let #1331-04 survive); P3
+  finite-difference gradient parity between `log_prior_from_value` and the
+  physical log density (the #1266 sign-convention canary); P4 `with_limits`
+  constructs for every family with documented semantics (hard-limit families
+  hit the limits exactly; Gaussian families centre between limits, and the
+  LogGaussian keeps positive support per the #1331-01 fix); P5
+  `from_mode(m, V)` reproduces mean and variance at V≠1 discriminating points
+  for Normal and Gamma (locks #1331-D3 — V=1 cannot discriminate the
+  historical inverted formula).
+- Also carried `bug/priors/11` §2 (see [[transformed-message-semantics-doc]]).
+- Every property was numerically validated against clean main before being
+  committed as an assertion; NumPy-only per the house rule (EP-level coverage
+  belongs to the EP framework review, [[ep-framework-review]]).
+
+**Key trap / new finding:** `TransformedMessage.logpdf`/`pdf` omit the
+transform Jacobian — the generic path returns the *base-space* density at
+physical coordinates (`UniformPrior(0,1).message.pdf` integrates to exactly
+1/(2√π) ≈ 0.282, not 1; LogUniform(0.01,100) to 15.83) while `factor()` is
+correct, and the #1334 module docstring claims the opposite. Same failure
+shape as #1331-04. Filed as **PyAutoFit#1498** + intaken as
+`draft/bug/priors/15_transformed_message_logpdf_jacobian.md`; the tests
+assert the physical density via `factor()` (`physical_log_density` helper)
+and cite #1498 at the site so they can be tightened once adjudicated.
+
+**API notes for future sweeps:** `with_limits` is an instance method on
+Uniform (abstract) but a classmethod on the Gaussian families;
+`GammaMessage.value_for` deliberately raises (no inverse CDF) so infinite
+supports are truncated at mean ± 40σ for integration; `prior.cdf` works on
+every family via the message and round-trips exactly.
+
+Sibling work filed the same day: the bundled 12+13 design issue
+PyAutoFit#1500 (single-source density + Prior/Message collapse), which the
+census retirement and this sweep were the groundwork for.
+
+## Original prompt
+
 # `@PyAutoFit` Add property-based correctness tests for every `Prior` subclass
 
 Type: bug

draft/bug/priors/11_transformed_message_semantics_doc.md → complete/2026/08/transformed-message-semantics-doc.md

@@ -1,11 +1,38 @@
+`TransformedMessage` semantics documentation — census finding C6,
+`bug/priors/11`. Shipped in two halves, both now on PyAutoFit main:
+
+- **§1 (asymmetric reversal convention)** — shipped 2026-07-10 via
+  PyAutoFit#1333 / PR#1334 as part of EP-review Phase 2: docstrings on
+  `_transform` / `_inverse_transform` in `messages/composed_transform.py`
+  plus the module docstring's worked `UniformPrior(0, 2).value_for(0.5)`
+  example and `autofit/graphical/README.md` §2 pointer.
+- **§2 (`LinearShiftTransform` stores the reciprocal of the intuitive
+  scale)** — shipped 2026-08-18 riding PR PyAutoFit#1499 (merged `21288bb`,
+  the [[prior-property-tests]] PR): class docstring stating that
+  `shift`/`scale` describe physical space, the stored parent Jacobian is
+  `DiagonalMatrix(1/scale)` because `transform()` runs physical → base, and
+  `log_det = -log(scale)` follows; cites #1266 as the historical cost of
+  getting the reciprocal backwards.
+
+The prompt's optional `physical_scale=` rename was **not** done — the audit's
+own leaning ("docs alone are fine if the bijector migration stays on the
+roadmap") applied, and the bijector question is now explicitly parked behind
+the PyAutoFit#1500 design decision.
+
+Note: the same PR's test work surfaced that `TransformedMessage.logpdf`
+contradicts the #1334 module docstring (Jacobian never accumulated) — that is
+PyAutoFit#1498 / `draft/bug/priors/15`, deliberately outside this doc task.
+
+## Original prompt
+
 # `@PyAutoFit` `TransformedMessage` reversal convention is undocumented foot-gun
 
 Type: bug
 Target: priors
-Difficulty: large
+Difficulty: small
 Autonomy: supervised
 Priority: normal
-Status: HALF SHIPPED — edge 1 is documented, edge 2 is not (2026-08-09)
+Status: HALF SHIPPED — edge 1 is documented, edge 2 is not (2026-08-09; Difficulty dropped large → small per the note below, 2026-08-18)
 
 ## 2026-08-09 — the reversal-convention half landed; the reciprocal half did not
 

complete/index.md

@@ -6,7 +6,7 @@ Token-light navigation over the finished-work records (schema:
 only then grep a dated bucket. Curators: edit the band between the CURATED
 markers; everything below GENERATED is rebuilt.
 
-1023 records across 7 buckets.
+1025 records across 7 buckets.
 
 <!-- CURATED:START -->
 ## Highlights
@@ -111,6 +111,7 @@ _(curate hard-won records here — survives regeneration.)_
 - [power-law-omega-convergence](2026/08/power-law-omega-convergence.md) — Bounded the fixed 20-term JAX PowerLaw omega recurrence across the packaged slope and ellipticity priors, meas…
 - [pr-ci-for-own-test-suite](2026/08/pr-ci-for-own-test-suite.md)
 - [pre-build-stages-untracked-wip](2026/08/pre-build-stages-untracked-wip.md) — CLOSED completed
+- [prior-property-tests](2026/08/prior-property-tests.md)
 - [prior-support-clipper](2026/08/prior-support-clipper.md) — Shipped `AbstractClipper` / `ClipperNone` / `ClipperPriorBox` in
 - [profile-validation-resample-recovery](2026/08/profile-validation-resample-recovery.md) — Shipped the approved narrow compatibility fix: invalid profile construction is now both a direct `ValueError` …
 - [purge-autocti-dataset-1d-overview](2026/08/purge-autocti-dataset-1d-overview.md) — no GitHub issue — the leftover from `autocti-util-dataset-export`, executed on direct human instruction "do th…
@@ -144,6 +145,7 @@ _(curate hard-won records here — survives regeneration.)_
 - [tenant-firewall-hygiene-extras](2026/08/tenant-firewall-hygiene-extras.md) — auto-closed by the merge
 - [test-mode-fit-exception-finalization](2026/08/test-mode-fit-exception-finalization.md) — `PYAUTO_TEST_MODE=1` no longer finalizes a model point whose reconstruction raises `FitException`; it substitu…
 - [test-mode-samples-info-hook-contract](2026/08/test-mode-samples-info-hook-contract.md) — `NonLinearSearch._test_mode_samples_info()`'s docstring told subclasses
+- [transformed-message-semantics-doc](2026/08/transformed-message-semantics-doc.md)
 - [uniform-prior-bounds-numpy-path](2026/08/uniform-prior-bounds-numpy-path.md) — auto-closed by the merge's `Closes` line
 - [version-skew-yank-awareness](2026/08/version-skew-yank-awareness.md)
 - [wiki-provenance-restamp](2026/08/wiki-provenance-restamp.md)

dashboard.md

@@ -8,10 +8,10 @@ Tasks only — the organism's health lives with the Heart (`/health`), not here.
 
 | Where | Count |
 |-------|------:|
-| [In flight](#in-flight) (`active/`) | 3 |
-| [Parked](#parked) (`parked.md`) | 1 |
+| [In flight](#in-flight) (`active/`) | 5 |
+| [Parked](#parked) (`parked.md`) | 3 |
 | [Planned](#planned) (`planned.md`) | 7 |
-| [Backlog](#backlog) (`draft/`) | 127 |
+| [Backlog](#backlog) (`draft/`) | 124 |
 
 Live on GitHub: [open issues](https://github.com/search?q=org%3APyAutoLabs+is%3Aissue+is%3Aopen&type=issues) · [open pull requests](https://github.com/search?q=org%3APyAutoLabs+is%3Apr+is%3Aopen&type=prs)
 
@@ -45,6 +45,8 @@ Live on GitHub: [open issues](https://github.com/search?q=org%3APyAutoLabs+is%3A
 
 Issued — each has an open GitHub issue and usually a branch. The full record for each is in [`active.md`](active.md).
 
+- [`@PyAutoFit` Refactor: each density should live in one place, not](active/12_single_source_density_refactor.md) — [issue #1500](https://github.com/PyAutoLabs/PyAutoFit/issues/1500)
+- [`@PyAutoFit` Refactor: collapse the `Prior` / `Message` two-layer hierarchy](active/13_collapse_prior_and_message.md) — [issue #1500](https://github.com/PyAutoLabs/PyAutoFit/issues/1500)
 - [PyAutoReduce validation: slacs1430+4105 ACS reduction vs trusted legacy dataset](active/pyautoreduce_slacs1430_acs_comparison.md)
 - [Reconstructing a stored sample raises through `ignore_assertions=True`](active/to_instance_guard_gap.md) — [issue #1486](https://github.com/PyAutoLabs/PyAutoFit/issues/1486) — library-dev — WORKSPACE HALF SHIPPED; the PyAutoFit hardening (#1486) is what remains
 - [Version-stamp sync to 2026.8.17.1 + release-sed guards](active/version_stamp_sync_and_release_sed_guards.md) — [issue #235](https://github.com/PyAutoLabs/PyAutoHands/issues/235) — pr-open (https://github.com/PyAutoLabs/PyAutoLens/pull/700)
@@ -54,8 +56,10 @@ Issued — each has an open GitHub issue and usually a branch. The full record f
 Started or scoped, not currently in flight — resume by moving the row back to `active.md`. Full detail in [`parked.md`](parked.md).
 
 <details>
-<summary><b>1</b> task(s)</summary>
+<summary><b>3</b> task(s)</summary>
 
+- **single-source-density-design** — [issue #1500](https://github.com/PyAutoLabs/PyAutoFit/issues/1500)
+- **prior-message-collapse-design** — [issue #1500](https://github.com/PyAutoLabs/PyAutoFit/issues/1500)
 - **pyautoreduce-slacs1430-acs-comparison**
 
 </details>
@@ -79,10 +83,10 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 
 ## Backlog
 
-**127** filed prompts, not started. Each section is sorted most-pickable first (priority, then size).
+**124** filed prompts, not started. Each section is sorted most-pickable first (priority, then size).
 
 <details>
-<summary><b>bug</b> — 35</summary>
+<summary><b>bug</b> — 32</summary>
 
 - [EP hierarchical parent-scale collapse: cure the basin, or document the](draft/bug/autofit/ep_scale_collapse_basin_cure_or_caveat.md) — autofit · too-large · human-required · high
 - [`NFWTruncatedSph.potential_2d_from`: MGE potential fails `grad(psi)=alpha` self-consistency](draft/bug/autogalaxy/nfw_truncated_potential_accuracy.md) — autogalaxy · too-large · supervised · high
@@ -110,11 +114,8 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 - [interferometer Delaunay pixelization — non-PD FitException in test-mode bypass](draft/bug/autolens/interferometer_delaunay_nonpd_fitexception.md) — autolens · medium · supervised · normal
 - [JAX point-source smoke sentinel: point.py returns -1e99 instead of -83.38](draft/bug/autolens/jax_point_source_point_smoke_sentinel.md) — autolens · medium · supervised · normal
 - [JIT cache not hit in modeling_visualization delaunay/rectangular scripts](draft/bug/autolens/jit_cache_not_hit_modeling_visualization.md) — autolens · medium · supervised · normal
-- [`@PyAutoFit` Add property-based correctness tests for every `Prior` subclass](draft/bug/priors/09_prior_property_tests.md) — priors · large · supervised · normal
-- [`@PyAutoFit` `TransformedMessage` reversal convention is undocumented foot-gun](draft/bug/priors/11_transformed_message_semantics_doc.md) — priors · large · supervised · normal
+- [`@PyAutoFit` `TransformedMessage.logpdf`/`pdf` omit the transform Jacobian](draft/bug/priors/15_transformed_message_logpdf_jacobian.md) — priors · medium · supervised · normal
 - [Resolve release-profile timeout scripts deliberately](draft/bug/health_fixes/release_timeout_policy.md) — health_fixes · too-large · supervised · normal
-- [`@PyAutoFit` Refactor: each density should live in one place, not](draft/bug/priors/12_single_source_density_refactor.md) — priors · too-large · supervised · normal
-- [`@PyAutoFit` Refactor: collapse the `Prior` / `Message` two-layer hierarchy](draft/bug/priors/13_collapse_prior_and_message.md) — priors · too-large · supervised · normal
 - [`@PyAutoFit` Refactor: replace hand-rolled `AbstractDensityTransform` with `tfp.bijectors` / `numpyro.distributions.transforms`](draft/bug/priors/14_replace_transform_stack_with_bijectors.md) — priors · too-large · supervised · normal
 - [Priors & Messages cleanup — tracker](draft/bug/priors/z_features.md) — priors · too-large · supervised · normal
 - [`add_notebook_quotes` mistakes a code string literal's closing delimiter for a](draft/bug/hands/notebook_quotes_string_literal_closing_delimiter.md) — hands · small · safe · low

draft/bug/priors/15_transformed_message_logpdf_jacobian.md

@@ -0,0 +1,69 @@
+# `@PyAutoFit` `TransformedMessage.logpdf`/`pdf` omit the transform Jacobian
+
+Type: bug
+Target: priors
+Difficulty: medium
+Autonomy: supervised
+Priority: normal
+Status: formalised — issue filed (PyAutoFit#1498), awaiting adjudication
+
+Found 2026-08-18 while implementing the #1497 property sweep (prompt
+`bug/priors/09`). Same failure *shape* as census finding A4 (#1331-04): a
+generic-interface density path is silently wrong while the direct paths are
+right.
+
+## The finding
+
+`TransformedMessage` inherits `MessageInterface.logpdf` (the natural-parameter
+path). Its overrides forward `natural_parameters`, `calc_log_base_measure` and
+`to_canonical_form` to the base message — `to_canonical_form` is
+`@transform`-decorated, so the physical input is mapped to base coordinates —
+but **no `log_det` change-of-variables term is ever added**. `logpdf(x)` at a
+physical `x` therefore returns the *base-space* density at the mapped point,
+not the physical density. `TransformedMessage.factor(x)` does it correctly
+(`base.logpdf(transform(x)) + log_det`).
+
+Reproduction on `main` @ `7d4d931` (exact numbers):
+
+- `af.UniformPrior(0,1).message.logpdf(0.7)` = −1.05644 (physical density is
+  1.0 → expect 0.0); `factor(0.7)` = 0.0 ✓
+- `∫ exp(logpdf)` over [0,1] = **0.282095 = 1/(2√π)**, not 1.0;
+  `∫ exp(factor)` = 1.000000 ✓
+- `LogUniformPrior(0.01, 100)`: generic-path pdf integrates to **15.83**.
+
+Every `TransformedMessage`-wrapped prior (Uniform, LogUniform, LogGaussian) is
+affected. `NormalMessage` / `TruncatedNormalMessage` priors are not.
+`value_for`, `cdf`, `log_prior_from_value` and `factor` are all verified
+correct — sampling and MCMC/MLE log-priors are unaffected; the exposure is
+anything treating `transformed_message.pdf()` as a physical density.
+
+## Doc contradiction
+
+The `composed_transform.py` module docstring (added by #1334) claims `logpdf`
+accumulates the log-Jacobian. The code does not. Either the docstring states
+the intended contract (then `logpdf` needs the `log_det` term) or `logpdf` is
+deliberately base-space for EP message arithmetic (then the docstring and
+`pdf()` are misleading and should say so).
+
+## What adjudication needs
+
+1. Inventory callers of `TransformedMessage.logpdf`/`pdf` vs `factor` —
+   especially whether any EP projection / `log_norm` path evaluates `logpdf`
+   on transformed messages at physical coordinates.
+2. `logpdf_gradient` returns the base `log_likelihood` with a
+   Jacobian-corrected *gradient* (value base-space, gradient physical) — a
+   third convention to settle in the same pass.
+3. Decide: add `log_det` to the generic path, or document base-space `logpdf`
+   as the contract and fix the module docstring + `pdf()`.
+
+The #1497 property tests assert the physical density via `factor` and cite
+#1498 at the site (`physical_log_density` helper in
+`test_autofit/mapper/prior/test_prior_properties.py`); tighten them to
+`logpdf` once resolved.
+
+## Sequencing
+
+Adjudicate alongside the parked single-source-density design (census C1/C4,
+prompts `bug/priors/12`+`13`) — this is a fourth density-convention divergence
+of exactly the kind that design exists to eliminate. The 12+13 design issue
+should cite PyAutoFit#1498 as fresh evidence.