Populate ASME Journal of Mechanical Design manuscript draft from repo context, with todonotes toggle, consolidated bibliography, Edison mock peer review, first-pass blocker fixes, cross-PR planned-methods refresh, a master synthesized bibliography, rea...#20
Populate ASME Journal of Mechanical Design manuscript draft from repo context, with todonotes toggle, consolidated bibliography, Edison mock peer review, first-pass blocker fixes, cross-PR planned-methods refresh, a master synthesized bibliography, rea...#20
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Agent-Logs-Url: https://github.com/vertical-cloud-lab/byu-mentored-research-tensegrity/sessions/a1b1a2fc-33ce-42f1-8240-a3b0ee027579 Co-authored-by: sgbaird <45469701+sgbaird@users.noreply.github.com>
Agent-Logs-Url: https://github.com/vertical-cloud-lab/byu-mentored-research-tensegrity/sessions/a1b1a2fc-33ce-42f1-8240-a3b0ee027579 Co-authored-by: sgbaird <45469701+sgbaird@users.noreply.github.com>
Agent-Logs-Url: https://github.com/vertical-cloud-lab/byu-mentored-research-tensegrity/sessions/a1b1a2fc-33ce-42f1-8240-a3b0ee027579 Co-authored-by: sgbaird <45469701+sgbaird@users.noreply.github.com>
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@copilot begin populating the draft based on all context in this repo. Leave placeholders for figures/tables and wherever else placeholders are needed. Use latex todonotes package (miktex will probably need to download) to make it easy to toggle on and off. Make sure to commit two versions: with todonotes enabled and regular (no todonotes enabled). Make sure to use a proper bib file, pullling in all existing edison queries across the repo (various PRs) to populate the bib file, even if not everything gets used right away. |
On it — populating the JMD draft from the proposal/repo context, switching the placeholder
Done in 9de8a4a (after groundwork in 9413a09). Manuscript draft populated from the proposal/repo context (IMRaD, Acknowledgment / Funding Data / Conflict of Interest, JMD-formatted abstract). Figures and tables are stubbed via
Built via
Side-by-side preview of page 1 (clean ↔ with todos):
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#18 crutch refs) Agent-Logs-Url: https://github.com/vertical-cloud-lab/tensegrity-optimization/sessions/03194806-e539-4fd3-b8d0-70f727e97b13 Co-authored-by: sgbaird-alt <71569943+sgbaird-alt@users.noreply.github.com>
…iKTeX Agent-Logs-Url: https://github.com/vertical-cloud-lab/tensegrity-optimization/sessions/03194806-e539-4fd3-b8d0-70f727e97b13 Co-authored-by: sgbaird-alt <71569943+sgbaird-alt@users.noreply.github.com>
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@copilot send to edison (analysis) for mock review for a characteristic mock set of likely reviewers and a mock editor. |
Submitted as Edison ANALYSIS task Attached: Prompt asks for four artifacts:
Plus a closing "Reviewers' bibliographic gaps" section flagging likely-missing references by topic. The prompt explicitly told the reviewers it is acceptable to call out the |
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@copilot fetch and analyze latest Edison results |
…lysis Agent-Logs-Url: https://github.com/vertical-cloud-lab/tensegrity-optimization/sessions/1ceeacbe-2d9f-4590-a507-53604d0429ed Co-authored-by: sgbaird-yolo <235173974+sgbaird-yolo@users.noreply.github.com>
Fetched in 639a15d. Trajectory (verbatim
Triaged analysis with priority ordering: Mock decision: Reject and Resubmit. All three reviewers (Design/Mech Eng, Biomechanics/Rehab, AM/Materials) returned Major Revision. Venue fit for ASME JMD is confirmed as a Research Paper; SMS and Additive Manufacturing are flagged as alternatives only if BO methodology is deprioritized. Blockers I verified against the source files:
Methodological gaps (next pass): BO rigor (kernel / categorical handling / constraints / batch size Bibliographic gaps the reviewers want added: ISO 11334-4 (walking-aid slip/friction); Caminero et al. 2019 (TPU/PETG FDM adhesion, not TPU/PLA); Garrido-Merchán & Hernández-Lobato 2020 + Ru et al. 2020/BOCS (categorical-variable BO); FFF resolution limits for elastomeric lattices. I've left the actual manuscript edits for a follow-up commit per your usual workflow — flag whether you want me to proceed with the blocker fixes (#1–#4) now, or hold for your read of the trajectory first. |
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@copilot address following #20 (comment) End with sending to Edison analysis and waiting to fetch and commit the artifacts, and report back the results |
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@copilot try again |
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We might need to create a new issue and pull request, pulling in all changes from this branch |
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@copilot try again |
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Stands up the journal-manuscript skeleton called for in the issue and populates it from existing repo context (proposal narrative, Edison literature trajectories across PR branches). Primary venue is ASME Journal of Mechanical Design (JMD); Smart Materials and Structures (SMS) is documented as a backup. Quantitative results remain
\todo{}placeholders pending experimental data.manuscript/(new)manuscript-body.tex— shared IMRaD body using theasmejourclass (CTAN; auto-installed by MiKTeX, not vendored). Uses the actual class macros (\JourName,\SetAuthorBlock{...\CorrespondingAuthor}{...},\title,\keywords,\maketitle),\DocumentMetadatafor PDF/A, JMD-formatted abstract, contributions list, three Background subsections (tensegrity, multi-material AM, BO), four Methods subsections (parameterization, fabrication, testing, BO loop), Results/Discussion stubs, Conclusions, and the JMD-required Acknowledgment (singular, per ASME) / Funding Data / Conflict of Interest blocks. Class options[lineno,singlecolumn,nocopyright,upint,varvw,hyphenate]give a single-column line-numbered draft; dropsinglecolumn/nocopyrightfor the two-column ASME final.manuscript.tex— thin wrapper that sets\def\TODOOPTS{disable}and\input{manuscript-body}→ clean reader-facing PDF (todonotes hidden).manuscript-todos.tex— thin wrapper that leaves\TODOOPTSempty → review PDF with margin annotations and\listoftodos.references.bib— consolidated working bibliography aggregating Edison-derived literature from across the repo's PR branches: proposal references, BO-algorithms PRECEDENT review (copilot/write-draft-abstract), NASA / aerospace literature (copilot/create-latex-template-proposal), tensegrity-impact extras (copilot/increase-experimentation-mentoring), and 27 new crutch-tip prior-art entries parsed from PR Explore tensegrity crutch-tip impact-absorber and industry partners via Edison literature queries #18'sedison-trajectories/01-...mdand02-...md(Segura 2007, Manocha 2021, Rasouli 2020, Brasil-Barros-da-Silva 2022, Dozono 2015, MacGillivray 2016, Zhang 2011, Mottaghi 2025, Stasiak-Cieślak 2025, Santos 2023, Yavas 2022, Arifvianto 2022, Ezeh 2018, Vanaei 2021, Ruwais 2025, plus footwear/insole lattice studies). Thepajunen2019overlap was deduped.\bibliographystyle{asmejour}(numeric).references-full.bib— master synthesized library (see "Master synthesized bibliography" below); the working superset pool, not wired into thepdflatexbuild.README.md— JMD limits (Research ≤9 000 words, Tech Brief ~4 000, Design Innovation ~7 000), 150–200-word Latin-only abstract rule, IMRaD requirement, ASME numeric refs, links to the submission portal/companion site/CTAN package; SMS aside (no hard word limit, 200–300-word abstract,iopart); description of the two-builds todonotes toggle; documentation ofreferences-full.biband its regeneration command.manuscript.pdf(clean, 9 pp),manuscript-todos.pdf(review with margin notes +\listoftodos, 10 pp), andmanuscript-diff.pdf(latexdiff, 9 pp) committed per repo convention.preview/manuscript-versions.png— side-by-side preview of page 1 (clean ↔ todos) for review;preview/manuscript-real-figures.png— preview of Fig 2 + Fig 3 with the harvested real photos.Placeholder system
todonotespackage wired through a single\TODOOPTSflag so both PDFs sharemanuscript-body.texand the same numbered structure.\figplaceholder{label}{caption}and\tabplaceholder{label}{caption}macros render visible placeholder boxes at every figure/table location, vanishing automatically when\TODOOPTS=disable. (The figure slots have since been populated — see "Real-image figure population" below; the remaining\tabplaceholderis the repeatability table, pending data.)\todo{...}so reviewers can audit them via\listoftodos.Build / repo plumbing
Makefile: newmanuscript(clean PDF),manuscript-todos(review PDF),manuscript-all(both), andclean-manuscript/distclean-manuscripttargets thatcd manuscript && pdflatex/bibtex/pdflatex/pdflatexagainst the appropriate wrapper. Existingproposalbuild is untouched.README.md: pointer to the new scaffold..gitignore: ignoremanuscript-orig.tex(latexdiff source artifact, matching the existingproposal-orig.texentry),manuscript/*.tdotodonotes build artefacts, Python bytecode (__pycache__/,*.pyc), and the Edison upload bundles/zips (edison-trajectories/review-followups/fabfig-bundle*,edison-trajectories/mechfig-feedback/bundle*,edison-trajectories/mock-jmd-review-2/*bundle*).Edison mock peer review (ANALYSIS task
6c140449-0426-490d-8fc2-67bcfdd0d1d9).texfiles,references.bib,manuscript/README.md) to Edison ANALYSIS with a prompt requesting three characteristic mock reviewers (Design / Mech Eng, Biomechanics / Rehab, AM / Materials) plus a mock JMD Associate Editor decision letter and a "bibliographic gaps" section.edison-trajectories/2026-05-09-mock-jmd-review-6c140449.md(formatted answer + query) and.json(full structuredtask.model_dump_json()for reproducibility), following the repo's Edison-trajectory convention.reviews/mock-jmd-review-analysis.mdmapping reviewer feedback to specific files/sections with a priority-ordered fix list. Mock decision: Reject and Resubmit; venue fit confirmed for ASME JMD as a Research Paper (alternatives flagged: SMS, Additive Manufacturing).First-pass blocker fixes (per PR comment)
(author?)bibtex artefacts fixed. Root cause was\citet{...}resolving against theasmejour.bstoutput, which emits raw author text without natbib's\bibinfo{author}annotation. All eight\citet{...}calls inmanuscript-body.texwere rewritten to inline-author form (e.g.Pajunen et~al.~\cite{...}). Two pre-existing unescaped&inreferences.bibjournalfields (requejo2005upperextremitykinetics,macgillivray2016theinfluenceof) were also fixed (& physics→\& physics). Verified viapdftotext manuscript.pdf | grep '(author?)'→ 0 hits.\todo{}\itemwith a substantive third contribution describing a planned two-fidelity escalation path (pretensioned tensegrity assemblies with true cables and measured pretension, per Sterling's "somewhat TBD" note); the surrogate / fusion-strategy choice (co-Kriging vs. nonlinear information-fusion priors) is left as an explicit\todo{}.iso11334-4, walking-aid test methods, Methods §3.3); Caminero et~al. 2019 (caminero2019printingparameters, FFF interface adhesion, Background §2.2); Garrido-Merchán & Hernández-Lobato 2020 (garridomerchan2020dealingwithcategorical) and Baptista & Poloczek 2018 BOCS (baptista2018bocs) for categorical-variable BO (Background §2.3 + Methods §3.4). The FFF resolution-limits reference was not added — left as a\todo{}placeholder pending a vetted citation, per Sterling's "don't guess" instruction.\todo{}placeholders per Sterling's "don't guess" instruction.Cross-PR planned-methods refresh (per PR comment)
Walked every open PR and recent branch and folded the concrete planned-methods progress into
manuscript-body.tex. Results/Discussion remain\todo{}placeholders by design — the project is at the planned-methods phase. Citation slots for unreleased Edison briefs were left as\todo{}rather than guessing bib keys..gcode.3mfslice + re-importable project.3mf(H2D-only, supports enabled, scale 1.5× / cable_d 4.5 mm) + PLA-cables and PLA-struts/TPU-cables MM variants (with modeled-in PLA scaffo... #35 CAD).HierarchicalSearchSpacescaffolding (PR Scaffold Bayesian-optimization script with honegumi + customized tensegrity campaign #30);.gcode.3mfslice + re-importable project.3mf(H2D-only, supports enabled, scale 1.5× / cable_d 4.5 mm) + PLA-cables and PLA-struts/TPU-cables MM variants (with modeled-in PLA scaffo... #35); SAASBO + qNEHVI default acquisition pairing with TuRBO escalation only above $\sim$25 D (PR Explore TPU+PLA BO design variables and base structures (Edison literature result + PR #22 design-gaps synthesis, hierarchical search space) #24 follow-up).Master synthesized bibliography (per PR comment)
Synthesized a single master library from every branch and every Edison query in the repo into
manuscript/references-full.bib— 813 unique references (592 with DOIs, 213 with abstracts), drawn from 38 distinct Edison tasks plus the committed project bibs. This is a working superset pool and is intentionally not wired into thepdflatexbuild, which still cites the curatedmanuscript/references.bibto keep the printed bibliography focused.scripts/edison/build_master_bib.py(new) — reproducible extractor. Unshallows the clone and pulls all 34+ branches, content-deduplicates everyedison-trajectories/**/*.jsonand every committed project.bib(excluding thesterling-cv/personal-publication lists), and parses references from both representations the Edison jobs emit: rich inlineBibTex:blocks (author/title/journal/doi + a followingAbstract:block) and, as a fallback for tasks whose raw evidence blocks weren't retained, the numberedReferenceslist informatted_answerso no cited key is dropped. The citation key (<surname><year><titlewords>) is used to split author/title/venue robustly even for ALL-CAPS or non-Latin author names. Entries are deduplicated by key then DOI (richest record wins), with the union of source task IDs recorded in a leading% source:comment per entry for traceability; HTML entities are decoded and&is BibTeX-escaped to\&.*-SUBMITTED.jsonplaceholders were polled via the Edison API; most areANALYSISjobs with no bibliography, butPHASE4-context(f9804247…) was a completedLITERATURE_HIGHtask, so it was re-fetched (get_task(...).model_dump_json()) and folded in (+3 unique references). Separate-account tasks that the API can't return would need manual lookup; none were required to reach the current set.&/HTML entities are escaped.manuscript/README.mddocumentsreferences-full.bib, the% source:provenance scheme, and the regeneration command.One-by-one DOI verification / abstract enrichment (per PR comment)
Went through the master library DOI-by-DOI to confirm each DOI actually points at the cited paper, enrich abstracts, and find missing DOIs — driven by a reproducible tool that checks each DOI against its authoritative registered metadata rather than guessing.
scripts/edison/verify_bib_dois.py(new) — fetches each DOI's CSL JSON via doi.org content negotiation + Crossref, compares the registered title to the cited title (jaccard /SequenceMatchersimilarity plus containment coverage), and conservatively applies only hand-verified edits. LaTeX-escaped DOIs (\_,\&, etc.) are unescaped before querying so they don't spuriously 404. The Crossref polite-pool contact is configurable via theCROSSREF_MAILTOenv var. Contains hand-verified decision tables (DOI_FIX,NODOX_FIX,CONFIRM_ABSTRACT,SUSPECT).manuscript/references-full.bib: all 592 DOIs checked against their registered titles; +179 abstracts added from each entry's own DOI record (JATS/HTML stripped,&escaped) → 213 → 393 abstracts; 1 wrong DOI fixed (zhang2015tensegrity, which pointed at an unrelated squash-mode-vibration paper, corrected to10.1063/1.5040850— the real Tensegrity cell mechanical metamaterial, APL 2018 — with abstract + year); +12 missing DOIs found via Crossref and confirmed by author+title → 592 → 604 DOIs. bibtexparser confirmed the edit was lossless (no original fields dropped/changed beyond the intended ones).fraternali2015tensegrity→ ceramics,witze2023osirisrex→ rural health,wang2022bayesian→ polyelectrolyte gel,lee2023bayesian404,grosu2025methodsforassessing404,wang2024simbencharulebasedtitle mismatch).edison-trajectories/bib-doi-verification/needs-list.mdand submitted as EdisonLITERATURE_HIGHtaskdbd490f6-edbc-4b8e-8778-b41e166b42ca(viascripts/edison/submit_bib_doi_verification.py) asking for correct DOIs and link verification. The task is async; its results are to be fetched in a future session and folded back into the bib. The submission and its provenance are recorded inedison-trajectories/bib-doi-verification/(README.md,needs-list.md,bib-doi-verification-SUBMITTED.json).manuscript/README.mddocuments this verification/enrichment pass.Reviewer-feedback corrections (per @me-madsen review)
Folded @me-madsen's inline review of
manuscript-body.texinto the draft and rebuilt all three PDFs:\todo{}now flags that the analogy must be verified (against PR Explore and validate joint design for PETG/PLA + TPU prints (5 candidate joints + OpenSCAD CAD + anchor-upset shape variants + Design F captive-core + Edison Phase-1/2/3/5 + Phase-4 submitted + lander-context reco + TPU-inside vs TPU-outside comparison... #39 / PR Add T3-prism (3-strut tensegrity) parametric CAD with Bambu PETG.gcode.3mfslice + re-importable project.3mf(H2D-only, supports enabled, scale 1.5× / cable_d 4.5 mm) + PLA-cables and PLA-struts/TPU-cables MM variants (with modeled-in PLA scaffo... #35) before it is claimed.\todo{}.Mechanism-oriented data figure example (side-task, per PR comment 4664748222)
Per @sgbaird's request, a standalone example of a mechanism-oriented data figure — processed drop-test deceleration curves with callouts to the specific structural features being tested. At the time it was a self-contained mock-up; it has since been wired into the manuscript as the §3.3
fig:dropcurveillustrative example (see "Real-image figure population" below).scripts/figures/mechanistic_data_figure_example.py(new) — matplotlib generator producing synthetic (clearly watermarked) but physically plausible curves anchored to the documented issue-Get a video and record data for a first crush/drop test #36 drop-test behaviour (125 kHz TP4/PicoScope-class capture, SAE J211 CFC-180 filtering, impact ≈4.2 ms, control CFC-180 peak ≈1792 G, tensegrity ≈370–463 G ⇒ ~74–79 % reduction). No experimental file is read; the script is meant to have real processed channels + camera frames swapped in later.figures/examples/mechanistic-data-figure-example.{png,pdf}— rendered example, embedded in the PR reply.figures/examples/README.md— documents the figure as an illustrative mock-up (synthetic data) with the regeneration command.Edison feedback on the mechanistic data figure (side-task, per PR comment 4664873230)
Per @sgbaird's follow-up ("send this to edison analysis for feedback"), the mechanistic data-figure example was submitted to Edison ANALYSIS and the result folded back in. The example figure and the manuscript were left unchanged in this round — feedback only.
scripts/edison/submit_mechfig_feedback.py(new) — bundles the figure (png/pdf), its generator, and README into a single zipped collection (required for ANALYSIS uploads) and submits ANALYSIS taske0c4e062-15c7-4a62-b931-1746211fe8b1asking for prioritized, actionable critique (mechanism storytelling, highest-value additional panels, camera-frame registration, synthetic-vs-real honesty / uncertainty reporting, layout/color/accessibility, and physics red flags).scripts/edison/fetch_mechfig_feedback.py(new) — polls the task to terminal state and writes the verbatim trajectory.edison-trajectories/mechfig-feedback/(new) —README.md, the*-SUBMITTED.jsonplaceholder, and the fetchedmechfig-feedback-e0c4e062….{md,json}trajectory; the upload bundle/zip are gitignored per the existing fabfig precedent.Mechanistic data figure — Edison feedback implemented (side-task, per PR comment 4673512526)
Per @sgbaird's request to implement the Edison ANALYSIS changes (PR comment 4664958219), the recorded feedback above was folded into
scripts/figures/mechanistic_data_figure_example.pyand thefigures/examples/mechanistic-data-figure-example.{png,pdf}were regenerated.figures/examples/README.mdwas updated to describe the revised panels and the impulse-conservation framing.Ax-generated example fills for the empty figure slots (side-task, per PR comment 4673509625)
Per @sgbaird's request ("create actual placeholder figures for any of the figures that are actually just empty slots, e.g. an example of LOO-CV plots obtained from Ax using dummy data"), produced drop-in example fills for the four data-figure slots in
manuscript-body.tex(fig:loocv,fig:sensitivity,fig:convergence,fig:pareto). These are self-contained, watermarked illustrative examples and have since been wired into the manuscript (see "Real-image figure population" below).scripts/figures/ax_placeholder_figures_example.py(new) — runs a real Ax Bayesian-optimization loop (ax.api.Client: Sobol initialization + BoTorch model-based trials — the SAASBO/qNEHVI machinery the manuscript describes) over a tensegrity-flavoured search space (strut diameter, twist, pretension, categorical cable diameterevaluate()), so the diagnostics are genuine Ax/BoTorch output; the access to the fitted adapter (client._generation_strategy.adapter, no public accessor in Ax 1.3.1) is centralized in one documented helper.figures/examples/, each.png+.pdf) —ax-loocv-example(leave-one-out cross-validation of the GP surrogate viaax.adapter.cross_validation.cross_validate, predicted vs. observed SEA & peak force with model error bars andax-sensitivity-example(parameter-sensitivity ranking from model length-scale importances per objective);ax-convergence-example(best-so-far SEA vs. number of experiments, BO vs. an independent uniform random-search baseline, shadedax-pareto-example(Pareto front in (peak transmitted force, SEA) space with all evaluated designs).ax-placeholder-figures-contact-sheet.pngis a 2×2 preview embedded in the PR reply.figures/examples/README.md— documents the four fills, their slot mapping, the synthetic-objectives caveat, and the regeneration command (requiresax-platform, which pulls inbotorch/torch).Real-image figure population (per PR comment 4677526117)
Per @sgbaird's request to wire the Ax (comment 4673681822) and mechanistic (comment 4673786958) example figures into the manuscript and to fill Fig 2 / Fig 3 with real images extracted from the repo's issue & PR comment history (using the GitHub API on the full comment JSON):
manuscript-body.tex. The mechanistic drop-test figure is now §3.3fig:dropcurve(Fig 4); the four Ax diagnostics fill the formerly-empty\figplaceholderslotsfig:loocv/fig:sensitivity/fig:convergence/fig:pareto(Figs 5–8). All five are honestly captioned "Illustrative example (synthetic data)" and keep their watermarks, with in-text references added for each. The redundant BO-loop schematic was replaced by the surrogate diagnostics.fig:printed-prototypes) populated with a parametric CAD render (a) beside a real as-printed T3-prism photo (b) carrying TikZ callouts for the strut diameterasmejourgotcha in the process: itssubfigureenvironment auto-emits the(a)/(b)sublabels and forbids an inner\caption— using one spawns phantom figures and corrupts the main figure numbering; rewrote the block to use the class's nativesubfigurecorrectly.fig:fab-workflow) populated — the fabrication/characterization workflow TikZ nodes now embed real photos (OpenSCAD render, Bambu Studio dual-nozzle slice, H2D mid-print, post-processed specimen, drop-tower fixture) instead of text-only boxes; removed the "populate nodes"\todo.figures/photos/(new) — six harvested, cropped, and EXIF-orientation-corrected photographs plus aREADME.mdprovenance table mapping each to its source comment and manuscript usage.scripts/figures/fetch_repo_photos.py(new) — reproducible extractor that re-downloads the exact source attachments (handlinguser-attachmentsS3 redirects viacurland rewritinggithub.com/.../blob/...?raw=truelinks toraw.githubusercontent.com) and re-applies the recorded crops; 5/6 photos reproduce byte-identically, the sixth visually identically.figures/examples/README.mdupdated (no longer "not wired in"); rebuilt all three PDFs —manuscript.pdf(9 pp),manuscript-todos.pdf(10 pp), andmanuscript-diff.pdf(9 pp). Addedpreview/manuscript-real-figures.png. The only remaining figure-area placeholder is the\tabplaceholder{repeatability}table, pending data.Pretensioning correction (per @sgbaird-alt review)
Per @sgbaird-alt's note that there should be no pretensioning in Figure 2 (the only pretensioning belongs in the scale-up validation of the final Pareto front), removed the "and pre-tension geometry imposed during printing" phrase from the TPU tension-elements design-variable description in Methods §3.1. The current BO-loop specimens and the Fig 2 prototype are now described as unpretensioned; pretensioning remains only in Contributions item 3 as a future high-fidelity validation step on the Pareto-optimal designs. Rebuilt
manuscript.pdf(7 pp, two-column layout),manuscript-todos.pdf(10 pp), andmanuscript-diff.pdf(9 pp, showing the deletion markup) from source so the committed PDFs reflect the fix.Second-round Edison mock peer review (per PR comment 4686431615)
Per @sgbaird's request ("send to Edison analysis for another round of mock reviewer feedback and report back the results … Commit all Edison artifacts"), the revised draft was submitted to Edison ANALYSIS for a second pass of the same three-reviewer + Associate-Editor panel.
scripts/edison/submit_mock_jmd_review2.py(new) — bundles the rebuilt PDFs + all three.texwrappers +manuscript-body.tex+references.bib+manuscript/README.mdinto a single zipped collection (required for ANALYSIS uploads) and submits ANALYSIS task3fde560e-1bb9-4c6b-8fcc-eaeef4570bf4, with a prompt summarizing what changed since round 1 so the panel focuses on the current state. Writes a*-SUBMITTED.jsonplaceholder (including the verbatim query) for a later fetch.scripts/edison/fetch_mock_jmd_review2.py(new) — polls the task to terminal state and writes the verbatim trajectory (.mdanswer + query,.jsonfullmodel_dump_json).edison-trajectories/mock-jmd-review-2/(new) —README.md, the*-SUBMITTED.jsonplaceholder, and the fetchedmock-jmd-review-2-3fde560e….{md,json}trajectory; the upload bundle/zip are gitignored per the existing precedent.Notes for review
\documentclass[12pt]{iopart}and the bibstyle toiopart-num;manuscript/README.mdflags this.asmejour-specific gotchas were uncovered while populating: the class redefinesenumerate/itemizeand rejectsenumitem-style options (no[leftmargin=*]), and theasmejour.bstbibstyle requires BibTeX-canonical" and "author separators (Edison-trajectory comma-separated lists were converted automatically).asmejour.bstdoes not wrap author fields in natbib's\bibinfo{author}{...}macro, so\citet{...}always renders as(author?) [n]. Use\cite{...}with an inline author surname instead.references.bibjournalfields containing&must be escaped as\&.asmejour's built-insubfigureenvironment auto-generates the(a)/(b)sublabels and forbids an inner\caption/\subcaption; an inner\captionincrements the main figure counter and creates phantom figures, so subpanels must use\begin{subfigure}[b]{width} ... \label{} \end{subfigure}with all descriptive text in the single outer\caption.pdfmanagementandxkeyvalpre-installed beforepdflatex --enable-installer -interaction=nonstopmodewill succeed end-to-end. On a TeXLive sandbox theasmejourclass title additionally needs the TeX Gyre Heros Condensed fonts (tex-gyre) installed and registered viaupdmap, or the build fails withec-qhvcr not loadable. Theasmejourclass/bst itself is fetched from CTAN (macros/latex/contrib/asmejour.zip) and the.bstinstalled into thebibtex/bst/texmf tree;latexdiff(TeX Livetexlive-extra-utils) is needed for the diff PDF.