Diagram survey Phase 1-2: 16 diagrams across Ch1-10, plus pre-PR hardening - #24
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…illustrate Z's addition to the spec, folded in as decision 7: the diagram sequence across the tutorial doubles as a visual-syntax curriculum, bridging diagram-first systems engineers and this tutorial's code-first approach. Simple structural diagrams establish the basic visual vocabulary before later chapters layer in notation that assumes it (structure -> interconnection -> action-flow -> state, the same order decision 2 already uses). Diagrams stay strictly derived views of the model (decision 1 unchanged); reviewing one is real work, the same construct-and-analyze loop the tutorial already teaches, exercised visually. Phase 1's method gains a concrete placement trigger from this: scan for cells with large, dense text/string output -- the exact signal Z named -- as the prime diagram-replacement candidates, not left to judgment alone. Phase 1's own output table gains a 'visual notation introduced' column (new vs. reused from an earlier chapter), and Verification gains a check that no chapter's proposed diagrams assume notation nothing earlier established.
…ssing) Decision 1 and Phase 0's Method discussed only 4 of the original trade study's 5 renderer paths -- DEMA SysML2Tools was never mentioned, adopted or rejected. Z confirmed (popup): rerun all 5 for Phase 0's real-fixture pass, matching decision 6's own stated rigor; OpenSysML's separate PlantUML render path stays out of scope since only its DOT/Graphviz path is actually in force (DL-001/DL-002).
… was just stale The model fix, the always-on guard (allocate-connector-end-accessibility, DEFERRED.md D-032), and four rounds of independent hardening (DL-059 and its three addenda) all landed 2026-09-29, the same day DL-058 ruled this gap -- this register entry's own 'Status: not yet drafted here' text was simply never updated afterward. No new work was needed; this corrects the record to point at D-032, the complete, current account, rather than restating or re-deriving a fix that already exists. Reconfirmed: uv run pytest tests/ -k allocat -- 37 passed.
…dd status banner All 4 tasks were already fully implemented and tested (containment_subgraph, model_to_dot's elements/layout params, build_interconnection_intent's depth param, decisions/diagram-tool-gaps.md seeded) but the plan's own checkboxes were never ticked when the work landed. Verified directly rather than assumed: all three test files pass (test_containment_subgraph.py, test_diagram_probe.py, test_interconnection.py), including two extra input-validation tests beyond what the plan originally specified. Also verified (no changes needed): DL-057's two action items -- the render_sysmld -> render_interconnection rename and the sysml-diagrams skill's renderer-choice table correction -- are both fully and correctly applied already.
…rvey.md) Ten read-only research agents, one per chapter, each given the fixed visual-syntax progression, Phase 0's capability matrix, and the already- built containment_subgraph()/model_to_dot()/render_interconnection() tooling. 16 diagram placements proposed across 9 of 10 chapters (Ch9 has a legitimate zero-candidate finding, not a gap). Progression ordering and tool choice both verified consistent against the fixed table and Phase 0's matrix; no chapter recommends the OMG pilot or SysMLD/sysml2d anywhere. Two things flagged for Z, not resolved here: Ch5's agent recommends upgrading the chapter's own existing, shipped interconnection figure from render_interconnection() to sysml-toolkit (real port boxes, not an edge label) since the chapter's whole point is a conjugated port; and a cross-chapter question on whether that upgrade should be a one-off or a standing rule, since Ch6 deliberately keeps the in-house renderer for its own allocation-edge diagrams. No implementation happens in this pass, per the spec's own Non-goals -- recommendations only.
…ix a second stale paper-trail gap (recipes.md) Z's decision (item 2 of the two open items from the diagram survey): make 'use sysml-toolkit when port identity itself is the pedagogical point, otherwise default to the in-house renderer' an explicit rule in the renderer-choice table, not an implicit per-chapter judgment call. While locating where to add it, found that references/recipes.md was never updated when DL-057 corrected SKILL.md's own table: it still told readers to use the OMG pilot for decomposition and state views, and SysMLD for interconnection -- all three confirmed to fail entirely on real content by Phase 0 (decisions/diagram-study-real-fixtures.md). Rewrote all three recipes to the current, confirmed-working pipelines (model_to_dot(), render_interconnection()/sysml-toolkit, OpenSysML CLI), added the explicit sysml-toolkit criterion with a worked command, and fixed the action-flow recipe's render form (plantuml -> dot, matching what's actually confirmed on real content). No PilotFigure.java/scripts/ dead references existed to clean up -- confirmed by search, not assumed.
…eal viz CLI For when port identity itself is the pedagogical point (e.g. a conjugated port): sysml-toolkit draws real port names as their own boxes, where the in-house render_interconnection() only draws a single edge label. render_interconnection() stays the default everywhere else.
…fixture Exercises the real sysml-toolkit binary, sysml.library, PlantUML jar and java; skips with a clear reason if any of those four real paths is missing on the machine running it.
…t's viz CLI Cell 16 now calls render_toolkit_interconnection() instead of build_interconnection_intent()/render_interconnection(), per diagram-survey.md's Ch5 recommendation: this chapter's whole point is a conjugated port, and the new pipeline draws the real port names (durationIn, durationOut) as their own boxes instead of folding them into one edge label. Cells 17-18 now describe the real port names the figure shows, not only the interface-level connection. Regenerates the shipped figure and keeps its intermediate .puml alongside it for inspection, per the sysml-diagrams skill's convention for generated build products.
…tion Review found two real defects in render_toolkit_interconnection(): 1. The connector PlantUML draws by default between the two ports is a diagonal line that cuts straight through the nearer part's own <<part>> stereotype and title text (confirmed by rendering and rasterizing the real Ch5 output). skinparam linetype ortho routes it in axis-aligned segments along box edges instead, via a new _apply_interconnection_layout_fixes() post-processing step applied to the generated .puml before PlantUML renders it. 2. The same post-processing wraps each port's own auto-generated label at its ' : ' (e.g. durationIn / : ~DurationPort, same text, just line-broken) so it no longer overlaps the neighboring box's border -- also confirmed by rendering before and after. Both are presentation only: neither changes which elements or edges the .puml describes. Also tightens the lib/binary/plantuml_jar/java argument checks from a bare Path.exists() to what each path actually needs to be (a directory, an executable file, a file), so an empty string or a directory passed as binary now raises this function's own ToolkitRenderError instead of a raw PermissionError or NotADirectoryError surfacing from the subprocess call.
…ion fixes The old assertion 'durationIn' in puml is trivially true even when only the durationInterface edge label survives, since 'durationIn' is a literal substring of 'durationInterface' -- it could never actually detect losing the conjugated port, which is the one thing this upgrade exists to catch. Now asserts the full declaration text instead (with the layout fix's line-wrap undone first, so the check depends on what the label says, not how it is wrapped on screen). Verified against a copy of the real .puml with its port lines stripped: the old assertion passed on that regression, the new one correctly fails. Adds a test for the new ortho-routing skinparam, and a test that a directory passed as binary raises this module's own ToolkitRenderError rather than a raw PermissionError; updates the existing missing-binary test's match string for the new, more specific error wording.
Review found the comment cited 'the sysml-diagrams skill' by name -- an internal, builder-facing reference a learner has no context for (same class of violation AGENTS.md 1.10 already covers for Tall's three worlds). Reworded to state the actual reason in plain terms instead, without changing what the comment explains.
…ut fix Byproduct of render_toolkit_interconnection()'s layout fix: the shipped SVG and its intermediate .puml now reflect ortho connector routing and wrapped port labels, clear of both parts' own borders and title text.
… the new G-D003 layout residual
… pages
Every chapter's index.md and conclusion.md had an H1 identical (or near-
identical) to its myst.yml TOC group title ('Chapter N: ...'), so the
sidebar showed the bold group header immediately followed by a sub-item
repeating the same text. Each file now carries frontmatter title: Overview
or title: Conclusion, which becomes the page's own banner heading and
sidebar label; the body's own 'Chapter N: ...' heading is unchanged and
still renders as the page's first section, appearing correctly in the
in-page Contents outline.
A toc-level title: override on the myst.yml entry itself does not affect
the rendered sidebar label in this mystmd version (v1.11.0) -- confirmed
by inspecting the built config.json before and after; frontmatter title:
on the file itself is what actually controls it.
…s the CLI-provisioning infrastructure they depend on
…w/render_state_flow
…g A)
The test corrupted only ("darwin", "arm64")'s own sha256 pin, so on any
other platform ensure_cli_binary() would look up and correctly verify
against its own real, uncorrupted hash -- silently not testing anything.
Now corrupts whichever pin opensysml.binary.detect_platform() (the same
lookup the real code performs) resolves to on the machine actually
running the test.
…composition+typing)
…o'd negative control)
PartUsage owned by a RequirementDefinition/RequirementUsage (a requirement's declared subject, e.g. TimelyToast's subject toaster : Toaster) is a reference binding, not real composition. model_to_dot() now resolves each PartUsage's owner @type via a once-per-call index and skips both the composition and typing edges when the owner is a requirement, leaving real part composition untouched.
…mily subject means the same reference-binding thing (not composition) on every kind that declares it, not just RequirementDefinition/RequirementUsage: ConcernDefinition/ConcernUsage, CaseDefinition/CaseUsage and its own specializations VerificationCaseDefinition/VerificationCaseUsage, UseCaseDefinition/UseCaseUsage, AnalysisCaseDefinition/AnalysisCaseUsage. Confirmed on the real Ch3 fixture: TimelyToastTest (a VerificationCaseDefinition) was still leaking its subject usage as false composition under the narrower skip-set. Also tighten the Ch2 test's vacuous 'Toaster' in dot substring check to the real node-declaration lines, and record the known narrow limitation (a subject usage's own further-nested parts are not suppressed) in the docstring.
…ocation An AllocationUsage is now only included in a diagram's allocs when its own owner is the diagram's fqn or something in the already-computed expanded containment set, resolved via to_api_json()'s own owner reference followed to that owner's record in the same payload (covers anonymous allocations too, which model.query() does not surface). Previously every AllocationUsage in the whole model was drawn regardless of which element it belonged to, so a HeatingAssembly-scoped diagram drew Toaster's own heatAllocation plus an orphan 'heating' box, just because one of its endpoints collided with a part name. flows extraction is untouched. Adds tests against the real Ch6/Ch5 fixtures proving the fix and that in-scope allocations are unaffected.
The second review (opus-5-5) confirmed REQUIREMENT_OWNER_TYPES's docstring claim of covering "the whole Requirement/Case family" is not spec-complete: two synthetic toolkit constructs it built (viewpoint def's own subject, satisfy requirement's own subject) still leak as false composition, and a third toolkit quirk (objective as a bare PartUsage) can't be caught by any type-list fix. None of these appear in any real fixture in this tutorial (ch01-ch10), where the only subject-bearing owner types actually observed are RequirementDefinition and VerificationCaseDefinition -- both already handled. Record the gap next to the existing nested-subject-parts note, same reasoning: tracked, not fixed. Also strengthens the Ch3 real-fixture test to assert "TimelyToast" (Ch2's requirement, carried into Ch3's cumulative fixture) is absent from the DOT output, not just "TimelyToastTest". No production behavior change: docstring text and one added test assertion.
Stops model_to_dot() from drawing a requirement's, concern's, or case's own subject reference as if it were real part composition. Confirmed systemic across Ch2, Ch3, Ch5, Ch8 and Ch10's diagrams; fixed at the shared rendering function rather than worked around per-chapter.
TimelyToast no longer leaks into the diagram as false composition.
Bridge or reorder each setup-cell-to-diagram-cell adjacency so no two code cells sit back to back without narration, per toaster-recipe's pacing rule.
…y fixes build_interconnection_intent() now scopes allocations to HeatingAssembly's own subtree, so the diagram shows exactly one allocation (heatGenAllocation), matching the narration. Rewrote the bridge and post-diagram cells, which previously described a removed print's output instead of the diagram's actual content; dropped a dead find_allocations() assignment.
cell-20 said heatGenAllocation and Chapter 5's heatAllocation are 'the same connection' -- they are different allocations with different ends; restored 'the same way... by query'. Also replaced two literal em-dash characters introduced by this task (nb03 cells 3 and 9) with a colon/comma per tutorial-style-guide's no-em-dash rule; the ASCII '--' used elsewhere in this diff is the established convention, not the banned character, and is left unchanged.
Infrastructure task plus all 9 chapter tasks merged. Records the two cross-cutting render.py bugs found and fixed at the root mid-batch (model_to_dot's requirement/case-subject leak, build_interconnection_intent's allocation scoping) and the known gaps carried forward.
… renderer Both still described build_interconnection_intent()/render_interconnection() (notebook 03 has used render_toolkit_interconnection() since the sysml-toolkit upgrade). Found independently by the Novice and SE Practitioner personas and the longitudinal Returning Learner run during the pre-PR user-testing pass.
- Ch3 nb02: join exercise-pointer cell's two sentences into one (semicolon, matching this tutorial's own established convention). - Ch4 index.md: name both new diagrams in the Ingredients table. - Ch5: rename 01-concept-selection.ipynb to 01-model-navigation.ipynb -- its content teaches model.find()/model.get() navigation, not selection among alternatives; already flagged in decisions/pass4-backlog.md and decisions/audits/ch05-layer-audit.md but never actioned. Updated myst.yml's toc and index.md's link accordingly.
…h1-7's plain style
Two issues found while reviewing the local build:
1. Every chapter notebook (all 32, including Ch1) rendered its own first
heading twice -- once as the implicit page banner/sidebar label (MyST's
fallback when no frontmatter title is set), once again as the first
in-body heading. Fixed by adding a short YAML frontmatter title
(ChN-NN) to each notebook's first cell, the same mechanism already used
for index.md/conclusion.md. Sidebar entries are now uniformly terse
(Ch1-01, Ch1-02, ...) across all ten chapters, matching what Ch8-10
already showed before this fix.
2. Starting at Chapter 8, every notebook's own heading drifted from Ch1-7's
plain, construct-named style ("abstract part def", "requirement def",
"level-2 function and logical carrier") into a "ChN-NN -- <essay-style
clause>" format ("A hand-restated lemma of the same shape", "Proof,
point evaluation, a genuine violation, and a genuine 'not sure'").
Rewrote all 9 Ch8-10 notebook headings to match the established plain
style; the ChN-NN prefix moved into the new frontmatter title instead
of living in the heading text.
…tUsage, draw specialization edges Defect 1: a PartUsage owned directly by a Package (e.g. nominal, slow) is not real part composition, so the composition diamond is no longer drawn for that owner kind; the usage's own typing edge is unaffected. Defect 2: model_to_dot() never drew specialization (:>) edges at all. Adds one edge per direct specializes target (resolved from the raw API-JSON payload's own specializes reference field, handling both single-dict and list shapes), styled as a solid line with an open/hollow arrowhead to stay visually distinct from both composition (filled diamond) and typing (dashed, open arrow). When elements is a scoped subset, an edge is only drawn when both ends are in that scope, the same discipline already applied to flows and allocs elsewhere in this file.
…dge fixes test_model_to_dot_draws_specialization_edge_on_real_ch08_fixture: proves Defect 2's fix against the real Ch8 fixture (ResistanceCoil :> HeatGenerator), asserting the literal DOT line and that it differs from the typing edges also present in the same output. test_model_to_dot_excludes_package_composition_on_real_ch02_fixture: proves Defect 1's fix against the real Ch2 fixture (nominal/slow owned directly by the ToasterDemo package), asserting the false composition line is absent while the usages' own typing edges and the fixture's real composition elsewhere are still present. test_model_to_dot_real_composition_is_unaffected (existing, unmodified) already covers the negative-control case for Defect 1 (a PartUsage owned by a real PartDefinition) since its own fixture's owner is a PartDefinition, not a Package -- no new test needed for that case.
Review findings on the package-composition/specialization fix: the docstring's own Nodes/Edges summary didn't mention either new behavior, and two real-but-unexercised edge cases (untyped package-owned usages now disappear entirely; a non-PartDefinition specialization target gets an unstyled node) were undocumented. Recorded both, not fixed, matching this function's own established gap-tracking pattern. Also fixed: source is now iterated twice (once for scoped_qnames, once in the main loop), so a one-shot iterable passed as elements would silently exhaust after the first pass. Materialized to a list once; no behavior change for any real caller, all of which already pass a list.
…zation edges A package is not a part and does not compose anything, but model_to_dot() drew every package-owned PartUsage (nominal, slow, rated, weak, heatGenCheck) with a false composition diamond from the package. Fixed by skipping that edge when the owner's @type is Package. Also adds specialization (:>) edges, previously never drawn at all -- Ch8's own caption had to carry the entire 'typed by' vs 'specializes' distinction in prose with no visual reinforcement.
…o_dot notation fix Package-owned usages (nominal, slow, rated, weak, heatGenCheck) no longer show a false composition diamond; specialization edges (Toaster's own :> ToastingSystem, and in Ch8/Ch10 also HeatingAssembly :> HeatingSystem, ResistanceCoil :> HeatGenerator) now appear as their own solid, hollow-triangle edges, distinct from composition and typing. Caption fixes: Ch8's own caption previously said the ResistanceCoil :> HeatGenerator link 'is not drawn' -- now false, since the diagram draws it directly; rewrote to describe what's actually shown. Ch2 and Ch5's 'containment skeleton' captions didn't account for the new specialization edge appearing alongside composition; added one clause naming it. Ch3's caption makes no composition-only claim and needed no change; Ch10's rooting/reachability claim is unaffected by either change.
…er edge Review finding: 'drawn as a package sibling of rated and weak' still implied a shared owner edge, which the package-composition fix just removed entirely. All three are now free-standing nodes with no owner edge at all.
…activity action names Formalizes the two render_action_flow()/render_state_flow() gaps found during Phase 2 and the pre-PR user-testing pass (decisions/log.md DL-087 known gap (b), DL-088 finding 5a). Z's decision: track only for now.
…cts found by direct local-build review
MyST's YAML frontmatter block in cell 0 fixed MyST's own double-heading display, but plain CommonMark (jupyter nbconvert, JupyterLab, GitHub notebook preview) misparses the --- delimiters as a horizontal rule plus a setext heading literally reading title: "ChN-NN", visible to the primary learner workflow (docs/setup.md line 29). Investigated and empirically tested on a correctly-scoped local MyST dev server (myst 1.11.0, reading /opt/homebrew/lib/node_modules/mystmd/dist/myst.cjs): - notebook metadata.title (top-level .ipynb metadata key): confirmed to have zero effect on the rendered banner/tab title. getPageFrontmatter() auto-fills frontmatter.title from the body's first heading before the notebook-level metadata (nbFrontmatter) is ever consulted, so the filled value always wins over metadata.title. - notebook metadata.short_title: confirmed this DOES change the sidebar/ TOC label (fileInfo3.short_title read at the TOC-render call site), but it does not touch the banner/tab title or the in-body heading, so it only satisfies half of the constraint. - a raw cell containing YAML frontmatter: confirmed no effect, matching the prior investigation; raw cells never reach the markdown-only frontmatter parser (processNotebookFull only calls parseMyst, which does the frontmatter detection, on cell_type markdown). - the literal YAML block in cell 0: the only mechanism that sets a page title distinct from the body heading, and it is exactly what breaks plain CommonMark rendering. No mechanism found inside the 32 notebooks themselves satisfies both constraints at once. Per the contract's own fallback instruction, reverting restores the known, already-tracked MyST double-heading regression rather than compounding it with the worse plain-CommonMark regression.
The notebook declares assert constraint deliveredEnergyBoundedBySupply (models/ch08-cumulative.sysml line 263); 'invariant' never appears anywhere else in the notebook's own prose. Matches Ch1-7's own name-the-actual-construct heading style (## action def, ## requirement def). Already flagged once in decisions/audits/ch08-layer-audit.md line 140.
The 9 table entries still quoted the old essay-style headings. Updated each to match its notebook's own current heading text exactly (post-F3 for Ch8-01).
Ch4 (01-action-def-ffbd.ipynb) renders ToastBread, not ApplyHeat as the bullet claimed; only Ch6 (01-subsystem-requirements.ipynb) renders ApplyHeat. Confirmed against grep of both evidence SVGs' <text> elements: neither figures/ch04-toastbread-flow.svg (ToastBread's own flows and its applyHeat:ApplyHeat sub-action's flows) nor figures/ch06-applyheat-flow.svg (ApplyHeat's own flows and its generateHeat:GenerateHeat sub-action's flows) draws any flow-pin text at all.
Ch2-03 cell 3 and Ch5-01 cell 3 were each one semicolon-joined sentence (31 and 32 words); split each into two sentences (16/15 and 18/15 words) stating what the figure shows and what conclusion it supports, re-verified against the single existing Toaster->ToastingSystem specialization edge in figures/ch02-structure.svg and figures/ch05-structure.svg. Ch8-01 cell 4 had two sentences, both over the ceiling (33 and 26 words); split into five short sentences (13/15/7/12/16 words), also dropping a stray double-hyphen em-dash, re-verified against figures/ch08-structure.svg's own heatGenCheck/rated/weak/ResistanceCoil edges for the sibling/no-owner-edge distinction.
Traced mystmd v1.11.0's own getFrontmatter() (node_modules/mystmd, not the stale homebrew v1.9.1 install): when a markdown cell's first block is a level-1 heading, mystmd auto-derives frontmatter.title from it and deletes the heading from the body -- this only fires for H1 (depth 1), never H2, which is exactly why the prior "## heading" text rendered twice no matter what frontmatter was added around it. Changed all 32 chapter notebooks' cell 0 first line from "## heading" to "# heading" (same text, H1 instead of H2) and added notebook.metadata. short_title = "ChN-NN" (confirmed via fillProjectFrontmatter/ manifestPagesFromProject in myst.cjs to drive the sidebar/TOC label through a separate code path from the page's own banner/tab title, which now shows the real heading text, promoted by the H1 lift). Verified empirically: `jupyter nbconvert --to html` on 3 notebooks across 3 chapters shows zero <hr>, zero stray frontmatter text, exactly one heading matching the real text. A MyST dev server confirmed scoped to this worktree (lsof -a -p <pid> -d cwd) shows the sidebar as "ChN-NN", the page banner/tab title as the full heading text, and exactly one heading rendered on the page.
Ch2-03 and Ch5-01 cell 3's trim from the prior pass opened with "This
figure shows...", the only self-referential caption phrasing in the
32 notebooks, banned by tutorial-style-guide's no-metanarration rule
(a caption states the fact directly, it does not point at itself).
Restored the original direct phrasing ("The containment skeleton this
model carries so far...") as sentence one, kept sentence two unchanged;
both sentences stay under the 20-word ceiling, re-verified against the
single Toaster->ToastingSystem specialization edge in figures/
ch02-structure.svg and figures/ch05-structure.svg.
Ch8-01 cell 4's trim from the prior pass crammed five sentences into the
word ceiling, violating the style guide's exactly-two-sentences caption
rule, and lost the causal link between "no owner edge" and "declared at
package scope." Split the content instead, matching Chapter 6's own
bridge-then-caption pattern: cell 4 (before the diagram) is now a short
bridge narrating the typed-directly/specializes distinction and the
package-scope reasoning across four sentences, each under the ceiling;
a new cell after the diagram is the terse, exactly-two-sentence caption
(13 and 15 words). Re-verified against figures/ch08-structure.svg's own
edge styles: ResistanceCoil->HeatGenerator is solid with a hollow
(unfilled) triangle, the three others are dashed with filled triangles.
…n edges Ch8-01's caption (cell-03d) and bridge (cell-03a) claimed the ResistanceCoil-to-HeatGenerator edge was the only solid, hollow-triangle specialization edge in ch08-structure.svg. Third-pass review found and I confirmed directly against the SVG that three such edges exist (Toaster->ToastingSystem, HeatingAssembly->HeatingSystem, ResistanceCoil->HeatGenerator), because Ch8's diagram is unscoped unlike Ch2/Ch5's genuinely single-edge figures. Reworded both sentences to describe that edge's own styling without claiming uniqueness.
…irect edits
Four rounds of independent review. F1: the notebook title-duplication fix
previously broke plain Jupyter/nbconvert/GitHub rendering (a stray
'title: "ChN-NN"' heading); replaced with mystmd's own H1-heading
title-lifting plus a short_title metadata field, which fixes MyST's
sidebar/banner duplication with zero visible artifacts in any other
renderer. F2: synced Ch8-10's index.md tables to corrected headings.
F3: Ch8-01's heading named a construct ('invariant') the notebook
doesn't use; corrected to 'assert constraint'. F4: DEFERRED.md D-037
cited the wrong action-flow call site; corrected. F5: trimmed captions
to the style guide's own word-count ceiling without introducing
self-reference, breaking the two-sentence caption rule, or losing the
causal content the originals carried.
…audit, and the fix
…convention Per skill-editor's own protocol (DL-091): DL-090 found and fixed a real duplicate-heading bug whose actual mechanism -- cell 0 must use a level-1 heading, and the notebook's metadata must carry short_title -- was never written down anywhere a future builder or reviewer would see it. Added one paragraph to the skeleton template and one clause to the A6 checklist.
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Summary
Implements the diagram-survey mission's Phase 1 (per-chapter survey) and Phase 2 (implementation): 16 new diagrams across Chapters 1, 2, 3, 4, 5, 6, 7, 8, and 10 (Chapter 9 has no diagram candidates by design — it adds no new model element). Diagrams are generated from the model via
model_to_dot()/containment_subgraph(), OpenSysML's own-renderCLI (action-flow, state), and sysml-toolkit'svizCLI (port-level interconnection, where port identity is the pedagogical point).decisions/diagram-survey.md): 10 parallel per-chapter survey agents inventoried every notebook against Phase 0's own real-fixture capability matrix (merged separately as Phase 0: re-run the diagram trade study against real chapter fixtures #22), producing a concrete, reviewed table of where a diagram should be added.What's in this PR beyond the diagram implementation
Two things surfaced after Phase 2 landed and are included here, since they were found reviewing this same branch before opening the PR:
A pre-PR user-testing pass (29 reports: 2-3 personas × 9 chapters, plus 3 new longitudinal Ch1→Ch10 runs) — zero blocking issues. Found and fixed one real cross-chapter inconsistency (stale prose in Ch5 naming a superseded renderer).
Two real, cross-cutting bugs in
model_to_dot(), found mid-implementation by independent review and fixed at the root rather than worked around per chapter:subjectreference was drawn as false part composition.:>) edges were never drawn at all.Both required re-rendering and re-reviewing the five already-built chapters they affected.
A harness-discipline incident and its remediation. Partway through the pre-PR pass, a stretch of edits were made directly instead of through this repo's own builder/reviewer contracts — a real process violation, confirmed by an independent audit to have produced four real regressions (the worst: a notebook-title fix that broke plain Jupyter rendering for all 32 chapter notebooks). All four were fixed and independently re-verified across four review rounds before merging; the real fix mechanism is now documented in
toaster-recipe/SKILL.mdso it isn't lost. Recorded in full indecisions/log.mdDL-090/DL-091, for the record.Known, tracked gaps (not fixed here, by design)
Recorded in
DEFERRED.mdanddecisions/log.md's own "not determined" sections — all confirmed to affect no real fixture in this tutorial today:model_to_dot():PartUsagelabels show qualified names, not short names; the composition diamond is drawn at the opposite end from UML/SysML convention.render_action_flow()/render_state_flow(): OpenSysML's own-renderCLI drops typed flow pins and a state's own performed-action name (DEFERRED.mdD-037).build_interconnection_intent(): three narrow allocation-scoping edge cases (package-root allocations, inherited allocations, non-part-owned allocations).Test plan
uv run pytest tests/ glossary/tests/ -q— 444 passed, 7 deselecteduv run python scripts/check_construction.py --check— clean, all 10 chapters consistentuv run python -m glossary lint(chapters/) — 16 pre-existing hits, zero newdecisions/log.mdDL-086 through DL-091)