Phase 4a: the nine core-loop ag_* skills

.claude/skills/ag_build_imaging_model.md

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+../../skills/ag_build_imaging_model.md

.claude/skills/ag_configure_search.md

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+../../skills/ag_configure_search.md

.claude/skills/ag_debug_fit_failure.md

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+../../skills/ag_debug_fit_failure.md

.claude/skills/ag_load_results.md

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+../../skills/ag_load_results.md

.claude/skills/ag_plot_fit.md

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+../../skills/ag_plot_fit.md

.claude/skills/ag_prepare_imaging_data.md

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+../../skills/ag_prepare_imaging_data.md

.claude/skills/ag_run_search.md

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+../../skills/ag_run_search.md

.claude/skills/ag_setup_environment.md

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+../../skills/ag_setup_environment.md

.claude/skills/ag_simulate_dataset.md

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+../../skills/ag_simulate_dataset.md

AGENTS.md

@@ -21,12 +21,11 @@ ask one focused question — never default to the longest possible explanation.
    ```
    Exit 0 = documented API matches the stack. Exit 1 = genuine drift: recommend the pinned
    version or an audit — [`skills/ag_audit_skill_apis.md`](./skills/ag_audit_skill_apis.md)
-   owns that procedure. Exit 2/3 = absent/broken stack: report the interpreter, then diagnose
-   and repair the environment directly
-   ([`wiki/core/operations/installation.md`](./wiki/core/operations/installation.md) for the
-   install routes, [`wiki/core/operations/sandbox.md`](./wiki/core/operations/sandbox.md) for
-   the cache env vars). The `ag_setup_environment` skill that will own the repair itself is not
-   written yet; `PENDING.md` tracks it. Skip this step by default in maintainer mode.
+   owns that procedure. Exit 2/3 = absent/broken stack: report the interpreter, then follow
+   [`skills/ag_setup_environment.md`](./skills/ag_setup_environment.md), which owns the repair
+   (`wiki/core/operations/installation.md` for the install routes and
+   `wiki/core/operations/sandbox.md` for the cache env vars are the pages it cites).
+   Skip this step by default in maintainer mode.
 
 ## Safety invariants — default non-negotiable
 
@@ -44,10 +43,11 @@ deliberate refactor). Two are NEVER overridden: the real-data gate and never-rew
   real data. **If you can't plot it yourself — no code execution, e.g. a GitHub-connector chat
   — the gate is not waived: ask the user to plot and inspect the data, and to confirm both (a)
   contaminants and (b) the mask extent, before you compose the fit.** These are the questions
-  every real-data run must ask, on every harness. Ground the procedure in
+  every real-data run must ask, on every harness. The procedure itself is owned by
+  [`skills/ag_prepare_imaging_data.md`](./skills/ag_prepare_imaging_data.md) — read it before
+  the first real-data fit; it is grounded in
   `autogalaxy_workspace:scripts/imaging/data_preparation/start_here.py` and the
-  `imaging/start_here.py` masking section until the `ag_prepare_imaging_data` skill that will own
-  it is written (see `PENDING.md`). Simulated data is exempt.
+  `imaging/start_here.py` masking section. Simulated data is exempt.
 - **Code gate.** A PreToolUse hook validates PyAuto* symbols against the installed library
   and blocks ones written from memory. If blocked, don't guess — grep `skills/` or introspect
   `dir()`, then re-run. The hook fires only on harnesses with hook support (Claude Code);
@@ -81,10 +81,13 @@ Map every request onto one or more layers:
    task. Library-API skills are `ag_<task>.md` and produce/evolve a Python script;
    project-workflow skills (`start-new-project.md`, `contribute-upstream.md`) drive repo-level
    operations. Skills starting with `_` (`_style.md`, `_bootstrap_skill.md`) are meta-skills —
-   don't surface them when answering science questions. **No `ag_*` skill for doing galaxy
-   science is written yet**: the three that exist (`ag_audit_skill_apis`, `ag_update_wiki`,
-   `ag_refresh_api_docs`) are maintenance workflows for this repo's own content.
-   `skills/README.md` lists all seven live skills and catalogues the rest by phase with the
+   don't surface them when answering science questions. The **core modelling loop** is live —
+   `ag_setup_environment`, `ag_prepare_imaging_data`, `ag_simulate_dataset`,
+   `ag_build_imaging_model`, `ag_configure_search`, `ag_run_search`, `ag_plot_fit`,
+   `ag_load_results`, `ag_debug_fit_failure` — and is what a galaxy-science request routes to.
+   Three further `ag_*` skills (`ag_audit_skill_apis`, `ag_update_wiki`, `ag_refresh_api_docs`)
+   are maintenance workflows for this repo's own content, not science workflows.
+   `skills/README.md` lists all sixteen live skills and catalogues the rest by phase with the
    `autogalaxy_workspace` script that grounds each one. Never activate a skill name you
    have not confirmed is a file on disk.
 3. **Wiki** (`wiki/**/*.md`) — *content*: what a Sersic profile is, which searches exist,
@@ -226,16 +229,25 @@ When **not** in maintainer mode, commit at natural checkpoints (a script + its
 - **Working directories.** Committed scripts → `scripts/`; throwaway plots/data dumps →
   `scripts/scratch/` (gitignored); `search.fit(...)` output → `./output/`.
 - **Plot path announcement.** The plot API is **functional-only**: pass
-  `output_path="scripts/scratch/<context>/"`, `output_filename=...`, `output_format="png"`
-  straight to the `aplt.*` call (e.g. `aplt.subplot_imaging_dataset`, `aplt.subplot_fit_imaging`).
+  `output_path="scripts/scratch/<context>/"` and `output_format="png"` straight to the `aplt.*`
+  call (e.g. `aplt.subplot_imaging_dataset`, `aplt.subplot_fit_imaging`).
   **The object-oriented plotters (`aplt.FitImagingPlotter`, `ImagingPlotter`, `GalaxyPlotter`,
   `GalaxiesPlotter`, `InversionPlotter`, …) and the `aplt.MatPlot2D` / `aplt.Include2D` /
   `aplt.Output` objects have been removed — do not use them.
   They are the #1 stale-from-memory API error, especially on a harness with no code gate (a
   connector chat).** Wrong:
   `aplt.FitImagingPlotter(fit=fit, mat_plot_2d=aplt.MatPlot2D(...)).subplot_fit_imaging()`.
   Right:
-  `aplt.subplot_fit_imaging(fit=fit, output_path="scripts/scratch/ring/", output_filename="fit", output_format="png")`.
+  `aplt.subplot_fit_imaging(fit=fit, output_path="scripts/scratch/ngc1300/", output_format="png")`.
+  **`output_filename` is not universal** — passing it to a call that does not take it raises
+  `TypeError`. Only `plot_array`, `plot_grid`, `subplot_imaging_dataset`,
+  `subplot_imaging_dataset_list`, `subplot_interferometer_dataset` and
+  `subplot_interferometer_dirty_images` accept it;
+  `subplot_galaxies` names its file with `auto_filename`; and the remaining fit and galaxy
+  subplots write a **fixed stem** into `output_path` (`subplot_fit_imaging` → `fit.png`), so the
+  *directory* is what separates one context from another. Check the signature —
+  [`skills/ag_plot_fit.md`](./skills/ag_plot_fit.md) and
+  [`wiki/core/api/plotting.md`](./wiki/core/api/plotting.md) carry the full split.
   If unsure a PyAuto* symbol exists, ground it against `skills/` or `dir(aplt)` — never write it
   from memory. Then `print(...)` the absolute path, and after running **quote that absolute path**
   and offer to open it (platform opener: `open` on macOS, `xdg-open` on Linux,

PENDING.md

@@ -90,29 +90,14 @@ where it is acted on — the run-time and GPU sections of `concepts/non_linear_s
 
 ## Phase 4a — the core modelling loop (9 skills)
 
-- [ ] `skills/ag_setup_environment.md` — grounding: `guides/modeling/bug_fix.py`, plus
-      `wiki/core/operations/installation.md` and `wiki/core/operations/sandbox.md` (both live
-      since Phase 3) and the RTD installation pages they were written from. `AGENTS.md`'s
-      session-start step and `skills/ag_audit_skill_apis.md` route environment failures here;
-      until it exists they route to `--check-install` and those two pages.
-- [ ] `skills/ag_prepare_imaging_data.md` — grounding:
-      `imaging/data_preparation/start_here.py`, `imaging/data_preparation/examples/`,
-      `imaging/data_preparation/gui/`. **This skill owns the real-data inspection gate's
-      procedure**, which `AGENTS.md` currently points at the workspace scripts for.
-- [ ] `skills/ag_simulate_dataset.md` — grounding: `imaging/simulator.py`,
-      `imaging/simulator_sersic.py`, `imaging/simulator_sample.py`.
-- [ ] `skills/ag_build_imaging_model.md` — grounding: `imaging/start_here.py`,
-      `imaging/modeling.py`, `guides/modeling/cookbook.py`.
-- [ ] `skills/ag_configure_search.md` — grounding: `guides/modeling/searches.py`,
-      `guides/modeling/customize.py`.
-- [ ] `skills/ag_run_search.md` — grounding: `imaging/modeling.py`,
-      `guides/modeling/bug_fix.py`.
-- [ ] `skills/ag_plot_fit.md` — grounding: `imaging/plot.py`, `guides/plot/start_here.py`,
-      `guides/plot/plotters.py`.
-- [ ] `skills/ag_load_results.md` — grounding: `guides/results/start_here.py`,
-      `guides/results/aggregator/`, `guides/results/latent_variables.py`.
-- [ ] `skills/ag_debug_fit_failure.md` — grounding: `guides/modeling/bug_fix.py`,
-      HowToGalaxy `chapter_2_modeling/tutorial_4_dealing_with_failure`.
+**Delivered.** All nine core-loop skills are on disk with `.claude/skills/` symlinks, rows in
+`wiki/core/external/skill_citation_map.md` and entries in the `skills/README.md` Index:
+`ag_setup_environment`, `ag_prepare_imaging_data`, `ag_simulate_dataset`,
+`ag_build_imaging_model`, `ag_configure_search`, `ag_run_search`, `ag_plot_fit`,
+`ag_load_results`, `ag_debug_fit_failure`. Two `AGENTS.md` hand-offs closed with them: the
+session-start environment repair now routes to `ag_setup_environment`, and the real-data
+inspection gate's procedure is owned by `ag_prepare_imaging_data` rather than pointing at the
+workspace scripts directly.
 
 ## Phase 4b — features beyond a single smooth profile (8 skills)
 

llms.txt

@@ -18,9 +18,9 @@ from memory.
 
 Read order: [AGENTS.md](./AGENTS.md) → [skills/README.md](./skills/README.md) → the relevant skill → [wiki/](./wiki). **In chat, lead by engaging.** Ask what the user is trying to do, ask them to describe or plot their data (you can't inspect files on their machine), plan the model, and draft the scripts — do this *first*, and never open a reply with what you can't do. The assistant can also route to examples, explain galaxy morphology and surface-brightness fitting, and review pasted scripts / errors / figures. It cannot run code or guarantee drafts against the installed PyAutoGalaxy version, so switching to a local coding agent (Claude Code, Codex, or Codex web with the repo connected) is the step for **actually running the fit or iterating live** — raise that handoff when execution becomes the blocker, not as an opening disclaimer.
 
-**⚠️ API currency — read before writing any PyAutoGalaxy code.** Older PyAutoGalaxy releases are heavily represented in model training data and their API is **out of date**. Do **not** write PyAutoGalaxy from memory. The single most common stale error: **plotting is functional now.** Use `aplt.subplot_fit_imaging(fit=fit, output_path=..., output_filename=..., output_format="png")` and `aplt.subplot_imaging_dataset(dataset=..., ...)`. The old object-oriented plotters — `aplt.FitImagingPlotter`, `aplt.ImagingPlotter`, `aplt.GalaxyPlotter`, `aplt.GalaxiesPlotter`, `aplt.InversionPlotter` — and the `aplt.MatPlot2D` / `aplt.Include2D` / `aplt.Output` configuration objects have all been **removed**; never emit them. The whole plotting surface is module-level functions, and `dir(autogalaxy.plot)` is the authoritative list. If you can't point at a live example or a `dir()` listing for a call, say it's unverified rather than guessing.
+**⚠️ API currency — read before writing any PyAutoGalaxy code.** Older PyAutoGalaxy releases are heavily represented in model training data and their API is **out of date**. Do **not** write PyAutoGalaxy from memory. The single most common stale error: **plotting is functional now.** Use `aplt.subplot_fit_imaging(fit=fit, output_path=..., output_format="png")` and `aplt.subplot_imaging_dataset(dataset=..., output_path=..., output_filename=..., output_format="png")` — note that `output_filename` is accepted by the dataset subplots, `plot_array` and `plot_grid`, but **not** by `subplot_fit_imaging`, which writes a fixed `fit.png` into `output_path` (passing it raises `TypeError`). The old object-oriented plotters — `aplt.FitImagingPlotter`, `aplt.ImagingPlotter`, `aplt.GalaxyPlotter`, `aplt.GalaxiesPlotter`, `aplt.InversionPlotter` — and the `aplt.MatPlot2D` / `aplt.Include2D` / `aplt.Output` configuration objects have all been **removed**; never emit them. The whole plotting surface is module-level functions, and `dir(autogalaxy.plot)` is the authoritative list. If you can't point at a live example or a `dir()` listing for a call, say it's unverified rather than guessing.
 
-**⚠️ This assistant is young.** Four skills exist (two meta, two project-workflow); the `ag_*` task skills and most of `wiki/core/` are still being written, phase by phase. [`skills/README.md`](./skills/README.md) and [`PENDING.md`](./PENDING.md) say exactly what is present and what is planned, and every planned item names the `autogalaxy_workspace` script that grounds it. **Answer from those grounding scripts and say that you did** — never describe a pending skill or wiki page as though you had read it.
+**⚠️ This assistant is young.** Sixteen skills exist: the nine-skill core modelling loop (environment, data preparation, simulation, model building, search configuration, running the fit, plotting, results, debugging), two meta, two project-workflow and three maintenance. The Phase-4b **feature** skills (bases and MGE, pixelisations, ellipse fitting, multi-dataset, interferometry, multi-galaxy, search chaining), the literature wiki and the benchmark suite are still being written, phase by phase. [`skills/README.md`](./skills/README.md) and [`PENDING.md`](./PENDING.md) say exactly what is present and what is planned, and every planned item names the `autogalaxy_workspace` script that grounds it. **Answer from those grounding scripts and say that you did** — never describe a pending skill or wiki page as though you had read it.
 
 ## Agent instructions (canonical)
 
@@ -32,7 +32,7 @@ Read order: [AGENTS.md](./AGENTS.md) → [skills/README.md](./skills/README.md)
 
 ## Reference
 
-- [wiki/core/index.md](./wiki/core/index.md): curated PyAuto\* reference. The `stack/` pages (one per library) are live; concepts, API catalogues, operations and external routing arrive in a later phase, and the index itself marks the gap.
+- [wiki/core/index.md](./wiki/core/index.md): curated PyAuto\* reference. The `stack/`, `api/`, `concepts/`, `operations/` and `external/` sections are live; the index itself names the pages still missing (dataset layout, HPC).
 - [PENDING.md](./PENDING.md): the authoritative ledger of every unwritten skill and wiki page, with its grounding script and target phase.
 
 ## Runnable examples & tutorials (elsewhere)