mind: CTI CI standardisation Phase 5 — two tasks shipped, one in flight

active.md

@@ -1,5 +1,25 @@
 # Active Tasks
 
+## phase5-smoke-ordered-trap-scripts
+- issue: https://github.com/PyAutoLabs/autocti_workspace/issues/27
+- issued: 2026-08-24
+- prompt: active/phase5_smoke_reenable_ordered_trap_scripts.md
+- status: workspace-dev
+- worktree: ~/Code/PyAutoLabs-wt/phase5-smoke-ordered-trap-scripts
+- repos:
+  - autocti_workspace: feature/phase5-smoke-ordered-trap-scripts
+- summary: |
+    CTI epic Phase 5. PR autocti_workspace#28 open, CI running. The prompt's
+    premise was wrong: autocti_workspace has no smoke_tests.txt and never had one
+    (no .github/, no config/build/, nothing deleted in history), so this creates
+    the repo's first CI rather than re-enabling anything — which also closes
+    pre-existing drift, since PyAutoHeart/config/repos.yaml already lists this
+    repo under `workspaces` with required checks "Smoke Tests" + "Navigator
+    Check". All nine modeling/start_here.py-class scripts verified running
+    bypassed against PyAutoFit 438f56fac; a curated three promoted (132s cold)
+    rather than all nine (~522s), per the repos' no-mass-promote convention.
+    Navigator Check deliberately left out of scope.
+
 ## transformed-message-factor-gradient-unpack
 - issue: https://github.com/PyAutoLabs/PyAutoFit/issues/1501 (issued 2026-08-19)
 - issued: 2026-08-19

draft/test/autocti/phase5_smoke_reenable_ordered_trap_scripts.md → active/phase5_smoke_reenable_ordered_trap_scripts.md

@@ -9,6 +9,7 @@ Autonomy: supervised
 Priority: normal
 Status: formalised
 Filed: 2026-08-24
+Issued: 2026-08-24
 Epic: CTI resurrection — Phase 5
 
 Re-homed from `draft/test/autofit/` by the filing session. Intake set

complete/2026/08/arcticpy-install-standardisation.md

@@ -0,0 +1,256 @@
+- completed: 2026-08-24
+- issue: https://github.com/PyAutoLabs/PyAutoHeart/issues/170
+- prs:
+  - https://github.com/PyAutoLabs/PyAutoHeart/pull/171 (merged) — the canonical action
+  - https://github.com/PyAutoLabs/autocti_workspace_test/pull/18 (merged)
+  - https://github.com/PyAutoLabs/autocti_assistant/pull/22 (merged)
+  - https://github.com/PyAutoLabs/PyAutoCTI/pull/109 (merged)
+  - https://github.com/PyAutoLabs/autocti_workspace/pull/26 (merged)
+- summary: |
+    One canonical Heart-owned arcticpy install — a composite action at
+    `PyAutoHeart/.github/actions/install-arcticpy`, holding the single
+    `arcticpy==2.6` pin — consumed by every CTI repo, replacing four divergent
+    shell copies. Four documented recipes fixed to match. Verified end-to-end:
+    the action builds and clocks charge through arctic on Python 3.12 and 3.13
+    in CI, PyAutoCTI's lib-tests are green through it, and autocti_workspace_test
+    smoke is green through it.
+
+## Audit correction — the site list in the prompt was wrong
+
+The prompt flagged PyAutoCTI's own lib-tests CI as UNREAD and counted two copies.
+Audited: `PyAutoCTI/.github/workflows/main.yml` is a *thin caller* of
+`PyAutoHeart/.github/workflows/lib-tests.yml@main` and carries no recipe of its
+own — but that reusable workflow carries **two** copies, one per job (`unittest`,
+`unittest-nojax`). So there were **four** shell copies, not two:
+
+| # | site | had `setuptools wheel`? |
+|---|------|---|
+| 1 | `PyAutoHeart/.github/workflows/lib-tests.yml` job `unittest` | yes |
+| 2 | `PyAutoHeart/.github/workflows/lib-tests.yml` job `unittest-nojax` | yes |
+| 3 | `autocti_workspace_test/.github/scripts/smoke_install.sh` | no |
+| 4 | `autocti_assistant/.github/workflows/wiki-currency.yml` | yes |
+
+`autocti_workspace` has no `.github/` at all — docs-only consumer.
+
+## Correction — smoke_install.sh was NOT one runner-image change from breaking
+
+The prompt described it as relying on the runner image's ambient `setuptools`.
+It was not: Heart's `smoke-tests.yml` runs `pip install --upgrade pip setuptools
+wheel` immediately before invoking the epilogue. The real defect was weaker but
+still worth removing — the epilogue's correctness depended implicitly on a step
+in a *different repository's* workflow, with nothing on either side stating it.
+The canonical step is self-contained, so the coupling is gone rather than
+merely documented.
+
+## Two things the specified recipe got wrong (found by building it, not reading it)
+
+1. **`--no-deps` suppresses arcticpy's RUNTIME dependencies too.**
+   `arcticpy/read_noise.py` does `from scipy.optimize import curve_fit` and
+   `import matplotlib as mpl`, and `__init__.py` imports `read_noise`. Installing
+   only the build deps leaves `import arcticpy` raising `ModuleNotFoundError:
+   No module named 'scipy'`. The prompt's prose called out matplotlib only.
+2. **arcticpy exposes NO `__version__` attribute.** The assertion the prompt
+   specified — `import arcticpy; print(arcticpy.__version__)` — raises
+   `AttributeError` on a perfectly good install. The same broken command was
+   already documented in `autocti_assistant/skills/ac_setup_environment.md`,
+   i.e. the assistant would have told a user their healthy arcticpy was broken.
+   Use `importlib.metadata.version("arcticpy")`.
+
+Both were caught because the self-test was written and run, not assumed. Two
+further API mistakes surfaced the same way: `add_cti` needs an `ac.CCD`, not an
+`ac.CCDPhase` (else `AttributeError: fraction_of_traps_per_phase`), and
+`parallel_roe` is not optional in practice (else `AttributeError: dwell_times`).
+
+## Verified
+
+- **Negative case reproduced**: with setuptools uninstalled the build dies at
+  `BackendUnavailable: Cannot import 'setuptools.build_meta'`. And a fresh
+  **Python 3.12 venv ships no setuptools at all** — checked directly — so the
+  omission was a real hazard, not a style nit.
+- **Canonical recipe builds** on 3.11 and 3.12 locally, 3.12 and 3.13 in CI.
+- **arctic actually clocks**: bright pixel 1000.0 -> 997.2389438265325, trail
+  [1.18249389, 0.77773508, 0.50869121, 0.33114622, 0.21469258] (decaying),
+  charge conserved to 5.8e-4. Byte-identical numbers locally and in CI.
+- PyAutoCTI `unittest` (3.12, 3.13) and `unittest-nojax` green through the action.
+- autocti_workspace_test `smoke` (3.12, 3.13) green through the action.
+
+## Caching decided with a measurement, not an assumption
+
+The prompt asked for before/after timings rather than an assumed win. GitHub's
+per-step timings from the self-test run (32769526194, job `build (3.12)`):
+
+```
+Install GSL headers (apt-get)            15.9 s
+Build deps (setuptools/wheel/numpy/cython) 9.0 s
+Runtime deps (scipy/matplotlib)            9.9 s
+Build and install arcticpy 2.6            16.8 s   <- compile is ~14 s of this
+Verify import                              0.8 s
+                                   total  ~52 s
+```
+
+**Recommendation: do not cache the wheel.** It would eliminate ~14 s, against
+which `actions/cache` restore+save costs several seconds, and a stale key costs
+more than no cache. The larger costs are `apt-get` (15.9 s) and the pip
+downloads (18.9 s), neither addressed by caching the wheel. The premise that
+"arcticpy compiles on every CI run" is true, but the compile turns out to be
+cheap — arctic is a small C++ extension. If revisited, target `apt-get`.
+
+## Design note — why a composite action, and how consumers reference it
+
+PyAutoHeart had no `.github/actions/` before this. It is the right shape because
+PyAutoHeart is **public**, so `uses: PyAutoLabs/PyAutoHeart/.github/actions/
+install-arcticpy@main` resolves from any consumer with no checkout of Heart —
+the same reach and reference style the reusable workflows already have. A shell
+script in Heart would have needed each consumer to fetch it first.
+
+`smoke_install.sh` is bash and cannot `uses:` an action, so the arcticpy install
+moved OUT of the workspace epilogue into Heart's `smoke-tests.yml` behind a new
+`arcticpy: true` input (default false, so every non-CTI caller is byte-identical).
+That matches the precedent already in `lib-tests.yml`, which gates its arcticpy
+step on `inputs.package == 'autocti'`.
+
+## The self-test, and why it exists
+
+`PyAutoHeart/.github/workflows/arcticpy-action.yml` +
+`.github/scripts/arcticpy_smoke.py`. Because consumers reference the action at
+`@main`, a recipe change would otherwise reach four repos with nothing having
+exercised it. The self-test references the action by **local** path so it builds
+the branch's version, and asserts a real CTI trail rather than "pip exited 0".
+It is what caught both recipe bugs above.
+
+## Docs fixed
+
+`PyAutoCTI/AGENTS.md` §arcticpy (the note the other repos cite as canonical, and
+the least complete — it omitted Cython *and* setuptools *and* the runtime deps),
+`autocti_workspace/AGENTS.md`, `autocti_workspace_test/AGENTS.md`, and
+`autocti_assistant/skills/ac_setup_environment.md` (whose broken
+`arcticpy.__version__` verification is also fixed). All four now point at the
+action as the recipe's single owner and the home of the pin.
+
+Note: the assistant's `.claude/skills/*.md` are symlinks into `skills/` (git
+mode 120000) — confirmed on the branch; one edit covers both surfaces.
+
+## Original prompt
+
+# Standardise the arcticpy CI install across every CTI repo
+
+Type: maintenance
+Target: pyautoheart
+Repos:
+- @PyAutoHeart
+- @autocti_workspace_test
+- @autocti_assistant
+- @PyAutoCTI
+- @autocti_workspace
+Difficulty: medium
+Autonomy: supervised
+Priority: normal
+Status: formalised
+Filed: 2026-08-24
+Issued: 2026-08-24
+
+`import autocti` hard-requires **arcticpy**, which is not a pip dependency: its
+sdist is source-only (needs `libgsl-dev` + a C++ toolchain + Cython) and its own
+requirements downgrade numpy below 2.0. Every CTI repo that runs CI therefore
+carries its own copy of the install recipe. There is no single owner, the copies
+have already **diverged in a way that matters**, and the recipe as documented is
+incomplete for a clean environment.
+
+Make one canonical arcticpy install step, owned by the organ that owns the
+reusable CI workflows, and have every CTI repo consume it.
+
+## The duplication today (verified by reading the files)
+
+- `autocti_workspace_test/.github/scripts/smoke_install.sh` — the install
+  epilogue for PyAutoHeart's reusable Smoke Tests workflow.
+- `autocti_assistant/.github/workflows/wiki-currency.yml`, step "Install the
+  stack (source @ main, or a pinned release)" (~L120-138). Its own comment says
+  *"Recipe mirrors autocti_workspace_test/.github/scripts/smoke_install.sh"* —
+  copy-paste, acknowledged in a comment rather than factored out.
+- `autocti_workspace/AGENTS.md` §arcticpy and
+  `autocti_assistant/skills/ac_setup_environment.md` document the same recipe
+  for humans/agents. `PyAutoCTI/AGENTS.md` is cited by both as holding the
+  canonical note plus a no-root header workaround — **not verified, PyAutoCTI
+  was not checked out for this prompt.**
+- **To audit:** PyAutoCTI's own lib-tests CI must install arcticpy somehow too;
+  that site is unread here. Any other repo whose CI imports `autocti` counts.
+
+## The divergence that matters
+
+`wiki-currency.yml` runs `python -m pip install --upgrade pip setuptools wheel`
+*before* the arcticpy build. `smoke_install.sh` does **not** — it installs only
+`numpy cython` and relies on the runner image's ambient `setuptools`.
+
+`--no-build-isolation` means every build dependency must already be present, and
+arcticpy does not declare them. So `smoke_install.sh` is one runner-image change
+away from breaking, and Python 3.12+ venvs no longer ship setuptools by default.
+This is a latent failure, not a style nit.
+
+## Verified build requirements (measured 2026-08-24, clean Ubuntu container)
+
+Built arcticpy 2.6 successfully from a bare Python 3.12 venv. Each missing build
+dep failed the build with an error naming the next one:
+
+1. `setuptools` missing → build fails (`ModuleNotFoundError: setuptools`)
+2. `Cython` missing → build fails (`ModuleNotFoundError: No module named 'Cython'`)
+3. with both present → **builds and works**
+
+Working recipe:
+
+```bash
+apt-get install -y libgsl-dev          # g++/gcc/make already present on the image
+pip install numpy scipy setuptools wheel Cython matplotlib
+pip install arcticpy==2.6 --no-build-isolation --no-deps
+```
+
+`matplotlib` is a *runtime* import (`arcticpy/read_noise.py`), needed only
+because `--no-deps` suppresses it; the CTI stack installs it anyway, so it is
+not a build dep. Verified working end-to-end: `add_cti` on a single bright pixel
+produced a correct exponential CTI trail with charge conserved.
+
+**Consequence for the docs:** the recipe in `autocti_workspace/AGENTS.md` and
+`ac_setup_environment.md` says "after numpy+cython" and omits `setuptools`. That
+is incomplete for a clean venv on modern Python — a first-time user following it
+verbatim hits the same `ModuleNotFoundError: setuptools` I did. Fix the prose in
+the same task.
+
+## Work
+
+1. **Put the canonical step in PyAutoHeart**, alongside the reusable workflows
+   the CTI repos already call (`smoke-tests.yml`, `lib-tests.yml`,
+   `docs-build.yml`). A composite action (`.github/actions/install-arcticpy/`)
+   is the natural shape — callable from a plain step, version-pinned in one
+   place. **Check PyAutoHeart's actual layout and conventions before choosing
+   the shape**; do not assume a composite action is how that repo does things.
+2. **Add the missing `setuptools wheel`** to the canonical step, so the
+   `smoke_install.sh` latent failure cannot recur anywhere.
+3. **Assert the install worked** — end the step with
+   `python -c "import arcticpy; print(arcticpy.__version__)"`. Today a broken
+   arcticpy surfaces much later as a confusing `import autocti` failure in an
+   unrelated job.
+4. **Repoint every consumer** at the canonical step and delete the local copies.
+5. **Fix the documented recipe** in `autocti_workspace/AGENTS.md`,
+   `autocti_assistant/skills/ac_setup_environment.md` and (if it carries the
+   same omission) `PyAutoCTI/AGENTS.md`, so human/agent instructions match CI.
+6. **Single pin.** `arcticpy==2.6` is currently written out in every copy;
+   after this, bumping it should be a one-line change.
+
+## Optional, decide deliberately
+
+arcticpy compiles from source on **every** CI run in every CTI repo. Caching the
+built wheel (`actions/cache` keyed on arcticpy version + Python version + runner
+image) would cut that repeatedly. Not required for correctness — raise it as a
+measured proposal with before/after timings rather than assuming it is worth the
+cache-invalidation complexity.
+
+## Why now
+
+Filed after `test-mode-bypass-assertion-ties` and `testmode-assertion-note-removal`
+(both shipped 2026-08-24). Two tasks in that sequence were deferred on the
+belief that arcticpy could not be built outside a prepared machine — a belief
+that turned out to be false, and cost real work. A canonical, documented,
+CI-owned install is what stops that assumption forming again.
+
+Unblocks: `draft/test/autocti/phase5_smoke_reenable_ordered_trap_scripts.md`
+(CTI epic Phase 5) and helps `draft/bug/autocti/wiki_currency_baseline_drift.md`,
+whose baseline regeneration needs the same stack.