projects.yaml: RAL mirrors the laptop (development/, euclid→complete/); register retired storage trees

projects.yaml

@@ -90,7 +90,7 @@ subhalo:
 euclid:
   remote: none
   local_path: /mnt/c/Users/Jammy/Workspace/Science/complete/euclid
-  ral_root: /mnt/ral/jnightin/active/euclid
+  ral_root: /mnt/ral/jnightin/complete/euclid
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [push, pull, sync, status]
@@ -118,7 +118,7 @@ euclid_dr1_prelim:
 euclid_dr1:
   remote: none
   local_path: /mnt/c/Users/Jammy/Workspace/Science/active/euclid_dr1
-  ral_root: /mnt/ral/jnightin/euclid_dr1
+  ral_root: /mnt/ral/jnightin/active/euclid_dr1
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
@@ -132,10 +132,10 @@ euclid_dr1:
 analytic_gaussian:
   remote: none
   local_path: /mnt/c/Users/Jammy/Workspace/Science/development/analytic_gaussian
-  ral_root: /mnt/ral/jnightin/active/analytic_gaussian
+  ral_root: /mnt/ral/jnightin/development/analytic_gaussian
   mirror: none
   sync_cli: hpc/sync
-  sync_verbs: [push, pull, logs, sync, status, submit, push-submit, jobs, sacct, cancel, tail, du, check]
+  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
   ledger: wiki/project/state.md
   assistant: autofit_assistant
   witness_file: results/**/*.json
@@ -146,10 +146,10 @@ analytic_gaussian:
 ep_toy_gaussian:
   remote: PyAutoLabs/ep_toy_gaussian
   local_path: /mnt/c/Users/Jammy/Workspace/Science/development/ep_toy_gaussian
-  ral_root: /mnt/ral/jnightin/active/ep_toy_gaussian
+  ral_root: /mnt/ral/jnightin/development/ep_toy_gaussian
   mirror: none
   sync_cli: hpc/sync
-  sync_verbs: [push, pull, logs, sync, status, submit, push-submit, jobs, sacct, cancel, tail, du, check]
+  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
   ledger: wiki/project/state.md
   assistant: autofit_assistant
   witness_file: results/**/*.json
@@ -222,10 +222,10 @@ slope_hierarchy:
 slope_hierarchy_scale:
   remote: PyAutoLabs/slope_hierarchy_scale
   local_path: /mnt/c/Users/Jammy/Workspace/Science/development/slope_hierarchy_scale
-  ral_root: /mnt/ral/jnightin/active/slope_hierarchy_scale
+  ral_root: /mnt/ral/jnightin/development/slope_hierarchy_scale
   mirror: none
   sync_cli: hpc/sync
-  sync_verbs: [push, pull, sync, status, submit, push-submit, jobs, tail, check]
+  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
   ledger: wiki/project/state.md
   assistant: autolens_assistant
   witness_file: results/**/*.json
@@ -249,7 +249,7 @@ pj011646:
 
 concr:
   remote: Jammy2211/cosmology_and_cancer
-  local_path: /mnt/c/Users/Jammy/Science/archive/concr
+  local_path: /mnt/c/Users/Jammy/Workspace/Science/complete/concr_cosmology
   ral_root: /mnt/ral/jnightin/archive/concr
   mirror: none
   sync_cli: hpc/sync
@@ -259,12 +259,12 @@ concr:
   witness_file: results/**/*.json
   partition: both
   status: retired
-  note: "retired 2026-10-14: human moved the tree to z_vault 2026-10-14"
+  note: "retired 2026-10-14: human moved the tree to z_vault 2026-10-14; the tree is Science/complete/concr_cosmology (local_path repointed 2026-10-29)"
 
 ic50_workspace:
   remote: Jammy2211/ic50_workspace
   local_path: /mnt/c/Users/Jammy/Workspace/Science/development/ic50_workspace
-  ral_root: /mnt/ral/jnightin/active/ic50_workspace
+  ral_root: /mnt/ral/jnightin/development/ic50_workspace
   mirror: none
   sync_cli: hpc/sync
   sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
@@ -372,3 +372,45 @@ cowls_ansofi:
   partition: ral
   status: retired
   note: "retired 2026-10-29: defunct; local tree deleted by the human 2026-10-29"
+
+euclid_group:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Workspace/Science/complete/euclid_group
+  ral_root: /mnt/ral/jnightin/complete/euclid_group
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: README.md
+  assistant: none
+  witness_file: results/**/*.json
+  partition: both
+  status: retired
+  note: "registered retired 2026-10-29 by human decision: storage tree, non-git; no RAL tree verified"
+
+cti:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Workspace/Science/archive/cti
+  ral_root: /mnt/ral/jnightin/archive/cti
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: notes
+  assistant: none
+  witness_file: results/**/*.json
+  partition: both
+  status: retired
+  note: "registered retired 2026-10-29 by human decision: archived CTI storage tree (COSMA era), non-git; no RAL tree verified"
+
+vignette:
+  remote: none
+  local_path: /mnt/c/Users/Jammy/Workspace/Science/archive/vignette
+  ral_root: /mnt/ral/jnightin/archive/vignette
+  mirror: none
+  sync_cli: hpc/sync
+  sync_verbs: [pull]
+  ledger: text.md
+  assistant: none
+  witness_file: results/**/*.json
+  partition: both
+  status: retired
+  note: "registered retired 2026-10-29 by human decision: archived vignette figures and DR1 material, non-git; no RAL tree"

projects/analytic_gaussian.md

@@ -11,6 +11,7 @@ Wave 1 (342413, 200 seeds at N=5) is accepted as the baseline: autofit EP is exa
 
 ## Log
 
+- 2026-10-29 — note — moved to the development/ category on the laptop and on RAL (ral_root in its row) on the human's decision (2026-10-29); hpc/sync.conf HPC_BASE updated, hpc/sync check passes
 - 2026-10-23 — note — second wave-1 finding closed (PyAutoFit#1713, PR #1714 merged, autofit_workspace_test#116): the `invalid value encountered in add` warnings on seeds 25 and 172 are a readout-only defect — under the mode projection an accepted truncated-normal scatter message sits ~19 sigma into its tail, its log_partition underflows to −inf (true log Z ≈ −187.9), the sigma evidence goes +inf and the EP log_evidence NaN from sweep 4; posteriors bit-identical to the ens_n5 sidecars. The library now names the term once per fit and returns an explicit NaN. The cure (tail-stable log_partition via log_ndtr) is message maths, filed in the Mind as draft/bug/autofit/truncated_normal_log_partition_tail_underflow.md for the human.
 - 2026-10-23 — note — criterion 6 amended (PyAutoFit#1711, PR #1712): the 19/400 zero-SUCCESS seed-legs of wave 1 split into 13 NO_CHANGE-only prior factors (zero-iteration Laplace convergence at the start point, projection accepted, closed-form match a 5e-5 / b 2e-5 on seed 140 leg A — a converged update, not stale; library reporting aligned, no EP maths changed) and 6 BAD_PROJECTION-only hierarchical factors (the #1405 scatter state, cured by projection="moments" #1656; seeds 29 and 71 re-run under moments give HierarchicalFactor SUCCESS 28 and 23). Criterion 6 now counts SUCCESS or NO_CHANGE as a completed update; the matching ensemble_seed.py any_factor_never_succeeded change is the human's to apply in the science checkout. Side finding: seed 29 leg B under moments still misses the sigma cell (a 0.225 / b 0.416) while sigma stays inside [q05, q95].
 - 2026-10-14 — note — PyAutoFit#1656 (merged 2026-09-30, released 2026.10.7.1) ports the minimal-EP referee's moment matching as LaplaceOptimiser(projection="moments"); on analytic_gaussian.py leg B autofit EP sigma 6.3401 ± 2.4609 vs closed form 6.5667 ± 2.8832 (mode path 9.3722, BAD_PROJECTION=19). A wave-2 ensemble on the moments path needs a private PyAutoFit checkout on RAL: the shared mirror is 404b3e5f7 and lacks it. The criterion-2 mu-threshold diagnostic is still unrun.

projects/cti.md

@@ -0,0 +1,14 @@
+# cti — Charge transfer inefficiency modelling, archived COSMA-era storage
+
+Project: cti
+Issue: none
+
+## Now
+
+Archived; registered retired so drift tracks the folder.
+
+## Runs
+
+## Log
+
+- 2026-10-29 — note — ledger opened

projects/ep_toy_gaussian.md

@@ -12,6 +12,7 @@ Wave 1 (n50_seed42: 342639 + 342640_[0-2]) failed on infrastructure — EP x3 on
 
 ## Log
 
+- 2026-10-29 — note — moved to the development/ category on the laptop and on RAL (ral_root in its row) on the human's decision (2026-10-29); hpc/sync.conf HPC_BASE updated, hpc/sync check passes
 - 2026-10-14 — note — Wave 2 still unsubmitted. RAL shared mirror 404b3e5f7 already carries the EMFILE fixes (#1632/#1634) wave 2 needs; it lacks #1655 (ProjectionException recovery), so a private PyAutoFit checkout is optional here but advisable.
 - 2026-10-14 — note — output/ vaulted to z_vault/ on laptop and RAL (mv, nothing deleted), anticipating reruns; output/ left empty, results/ untouched; z_vault/ gitignored locally
 - 2026-09-30 — note — RAL mirror PyAutoFit now 404b3e5f7 (2026-09-27), contains #1632 (b82fb3f69) and #1634 (fa2d540ac); 5 commits behind origin/main, none in blackjax/graphical/dynesty; deps at floor except anesthetic 2.8.14 < 2.9.0 (plots only). Sample n50_seed42_w2 is free locally and on RAL but must be added to toy.SAMPLES (scripts/toy.py) before submission, and SAMPLE must be exported to the job (hpc/sync submit does not forward laptop env)

projects/euclid.md

@@ -11,6 +11,7 @@ Dormant: superseded by euclid_dr1 (euclid_dr1_prelim is defunct). The tree is ke
 
 ## Log
 
+- 2026-10-29 — note — RAL tree moved to the complete/ category to mirror the laptop, on the human's decision (2026-10-29); hpc/sync.conf HPC_BASE updated
 - 2026-10-15 — note — superseded by euclid_dr1 (euclid_dr1_prelim defunct) per the human; stays dormant; folder under Science/active and RAL active/; ral_root repointed to the category layout (PyAutoCortex#67)
 - 2026-08-28 — note — question: Do we recover Sersic indices or is prior pile-up artefact — planned, never run [archive/tasks/euclid/sersic_index_recovery.md]
 - 2026-08-28 — note — question: Can a fitted Euclid lens be resimulated and recovered — planned, never run [archive/tasks/euclid/resimulate_fitted_lens_simulator.md]

projects/euclid_group.md

@@ -0,0 +1,14 @@
+# euclid_group — Euclid group-scale lens modelling, complete; kept for reference
+
+Project: euclid_group
+Issue: none
+
+## Now
+
+Complete; registered retired so drift tracks the folder.
+
+## Runs
+
+## Log
+
+- 2026-10-29 — note — ledger opened

projects/ic50_workspace.md

@@ -12,6 +12,7 @@ The scale ladder is in. EP passes N=5/10/25 with coef_mean within 3σ and cost g
 
 ## Log
 
+- 2026-10-29 — note — moved to the development/ category on the laptop and on RAL (ral_root in its row) on the human's decision (2026-10-29); hpc/sync.conf HPC_BASE updated, hpc/sync check passes
 - 2026-10-14 — note — output/ vaulted to z_vault/ on laptop and RAL (mv, nothing deleted), anticipating reruns; output/ left empty, results/ untouched; z_vault/ gitignored locally
 - 2026-09-30 — note — Ladder read: EP s/sweep 26/50/140/~300 s at N=5/10/25/50 vs graphical wall 21/42/119/281 s. EP hill_coef widths flat at ~0.8 because util.py reports factor-message (likelihood) widths and the global factor freezes hill_coef; graphical widths shrink but fall to 56/75 and 65/150 within 3 sigma at N=25/50 (overconfident). coef_mean passes 3 sigma for both methods on every completed rung.
 - 2026-09-30 — note — 342411 N=50 failure diagnosed: AssertionError at autofit/messages/abstract.py:316 while projecting the global factor after EP sweep 4 (mirror 66f9f8d5d); the 4th global search had max logL -337 (vs -69 at sweep 3) and logz +/- nan. Library defect: project asserts on non-finite suff_stats and factor_step (optimiser.py:150) does not catch AssertionError, so one bad projection kills the run; no later commit touches the path. A local rerun at 66f9f8d5d converged in sweep 3 without failing (unseeded Dynesty, non-deterministic). Mind bug prompt draft/bug/autofit/ep_project_nonfinite_suff_stats_ic50_n50.md

projects/slope_hierarchy_scale.md

@@ -12,6 +12,7 @@ The N=25 graphical baselines are in: per-lens fits (342348) give a naive parent
 
 ## Log
 
+- 2026-10-29 — note — moved to the development/ category on the laptop and on RAL (ral_root in its row) on the human's decision (2026-10-29); hpc/sync.conf HPC_BASE updated, hpc/sync check passes
 - 2026-10-14 — note — output/ vaulted to z_vault/ on laptop and RAL (mv, nothing deleted), anticipating reruns; output/ left empty, results/ untouched; z_vault/ gitignored locally
 - 2026-09-30 — note — graphical baselines recorded late at the 2026-09-30 check-in. 342348_[0-24] per-lens (one_by_one Nautilus, A100, 25/25, 6.9-8.8 min/task, 0 float32 truncations): naive parent mean 1.9992 +/- 0.0178 (SEM), std of medians 0.0889, deconvolved scatter 0.0852 (rms 1-sigma half-width 0.0255); truth inside the 1-sigma interval for 17/25 lenses; per-lens JSONs on RAL at results/one_by_one_sample_n25_seed42/dataset_*.json (not pulled; aggregate never written by the array). 342350_0 joint hierarchical NUTS: science completed despite the post-processing OOM — 500 warm-up (8h08m) + 1000 samples (7h17m), 1 chain, 0 divergences, acceptance 0.84, rhat_max 1.012, ess_min 133/302 params; parent mean 1.9936 [1.9761, 2.0136] 68%, sigma 0.0871 [0.0744, 0.1041] 68% (95% [0.0636, 0.1190]) vs truth 2.0/0.1 and realised draws 1.9917/0.0864 — the N=5 high-scatter bias (0.143) is gone at N=25. Computed from RAL samples.csv (graphical_nuts/f16c32e17f570603a1dc061f95792798/files); results/graphical_nuts_sample_n25_seed42.json never written (killed at 64 GB in latent/arviz post-processing) — pull samples.csv and write the summary offline
 - 2026-09-30 — run — 342351_0 failed — wall 27:41: n25_scale_up: EP arm on the CPU partition, hpc/batch_cpu/submit_ep, max_steps 12; RAL PyAutoFit mirror 68ff9bd57 predates PyAutoFit#1580, so this arm runs without the stale-mask fixed-point fix — CANCELLED 2026-09-09 20:56:19 BST (sacct 1-03:41:06): log stops at the first Nautilus status line 2026-09-08 17:15:36, no factor finished; superseded by 342410 then 343299, output parked as ep_dead_342351; recorded late at the 2026-09-30 check-in

projects/vignette.md

@@ -0,0 +1,14 @@
+# vignette — Strong-lens vignette figures and mosaic, archived
+
+Project: vignette
+Issue: none
+
+## Now
+
+Archived; registered retired so drift tracks the folder.
+
+## Runs
+
+## Log
+
+- 2026-10-29 — note — ledger opened

state.json

@@ -4,7 +4,7 @@
   "repo": "PyAutoCortex",
   "status": "yellow",
   "headline": "YELLOW \u2014 9 active \u00b7 16 running",
-  "updated": "2026-10-29T12:49:17Z",
+  "updated": "2026-10-29T13:59:06Z",
   "pages_url": "https://pyautolabs.github.io/PyAutoCortex/",
   "items": [
     {