diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2f588683..f1041109 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,4 +7,4 @@ repos: rev: v0.9.1 hooks: - id: snapper - files: ^2026-usrse/(stamped-abcd-poster-draft|orinoco-lite/README)\.md$ + files: ^2026-usrse/(stamped-abcd-poster-draft\.md|orinoco-lite/README\.md|stamped-ai-study/(?!logs/).*\.md)$ diff --git a/2026-usrse/README.md b/2026-usrse/README.md index d9afc27a..da228c85 100644 --- a/2026-usrse/README.md +++ b/2026-usrse/README.md @@ -3,6 +3,8 @@ This is folder to collect ideas/drafts for submissions for https://us-rse.org/us The Orinoco Lite poster is available as [editable poster](orinoco-lite_poster.html), with [editing, PDF export and release notes](orinoco-lite/README.md). Its [submitted abstract](orinoco-lite-poster-draft.md) remains alongside it. +The [STAMPED in Practice poster](stamped-ai-study/README.md) compares research-skill assistance across three rounds, with editable HTML, a verified PDF and links to the research evidence. + ### Meeting theme etc That meeting is about/for Software Research Engineers. And this particular meeting has following diff --git a/2026-usrse/stamped-ai-study/.gitattributes b/2026-usrse/stamped-ai-study/.gitattributes new file mode 100644 index 00000000..4a14175a --- /dev/null +++ b/2026-usrse/stamped-ai-study/.gitattributes @@ -0,0 +1,8 @@ +# Module-scoped equivalent for its binary types; works without MagicMime. +# Text sources remain in Git. Large SVGs retain the repository threshold. +* annex.largefiles=((include=*.png)or(include=*.pdf)or(include=*.jpg)or(include=*.jpeg)or(include=*.gif)or(include=*.webp)or(include=*.woff)or(include=*.woff2)or(include=*.ttf)or(include=*.otf)or(include=*.zip)or(include=*.gz)or(include=*.xz)or(include=*.zst)or(include=*.mp4)or(include=*.webm)or(include=*.bin)) +*.svg annex.largefiles=(largerthan=100K) + +# Poster-specific image assets are distributed through the annex remote. +assets/*.svg annex.largefiles=anything +*.npz annex.largefiles=anything diff --git a/2026-usrse/stamped-ai-study/.gitignore b/2026-usrse/stamped-ai-study/.gitignore new file mode 100644 index 00000000..0f00ac7c --- /dev/null +++ b/2026-usrse/stamped-ai-study/.gitignore @@ -0,0 +1,10 @@ +# Keep the exported poster in this module. +!exports/stamped-ai-poster.pdf +.pixi/ +pixi.lock +node_modules/ +exports/html-fullsize.png +exports/pdf-fullsize.png +exports/pdf-qr-*.png +exports/qr-source/*.png +exports/layout-review.png diff --git a/2026-usrse/stamped-ai-study/BUILDING.md b/2026-usrse/stamped-ai-study/BUILDING.md new file mode 100644 index 00000000..dd71c65e --- /dev/null +++ b/2026-usrse/stamped-ai-study/BUILDING.md @@ -0,0 +1,90 @@ +# Build and verify the poster + +Start with the [poster introduction](README.md) for downloads and interpretation. +This page covers editing, exact scientific sources, environment replay and verification. + +## Scientific sources and display copies + +The [benchmark figure workflow](https://github.com/leej3/stamped-in-practice/blob/codex/stamped-poster-analysis/scripts/POSTER-FIGURES.md) contains the scientific generators, frozen inputs, root Pixi environment, derived results and provenance. +This poster retains display copies and a [source binding](figures/benchmark-source.json), including the exact benchmark revision and SHA-256 values. +Overview links begin with guides on `main`; direct technical links open the named research branches. +The guides explain their role, while exact source revisions remain in the provenance. + +The group map shows formal round-two run 09: a one-sample group test on 54 participant maps, 9,999 sign-flip permutations and whole-brain FWE correction. +The spatial comparison uses all 48 analyses from rounds two and three, twelve per condition, on 168,285 shared tested voxels. +Every run retains its native corrected decisions and coverage; the source repository preserves masks, scientific code, reports and capture identities. + +The compact outcomes table pools the retained operational assessments from all three rounds: 72 original research runs, 70 primary scientific judgments and 68 valid primary checklists. +Native replay counts distinguish full selected-output matches from observed executions. +The [benchmark summary](https://github.com/leej3/stamped-in-practice/tree/codex/stamped-poster-analysis/experiments/retained-round-reporting/pooled) retains all grades, denominators, partial matches and separate round summaries. +The [outcomes](data/benchmark-outcomes.json), [checklist index](data/benchmark-checklists.json) and [source binding](data/benchmark-outcomes-source.json) identify the exact imported reports. +The table’s linked checklist scores average each valid primary response’s met-item count divided by all 31 checklist items, matching the app’s denominator. +Each condition mean links to its individual filled checklists, with exact original JSON responses alongside them. +The app rounds individual scores to integers; pooled means use the unrounded fractions and display one decimal. +Four unavailable checklists remain unscored; their retained responses are accessible with exclusion reasons. +The complete table includes 21 observed native reruns: 13 full selected-output matches, five partial matches and three nonzero exits. +Round-specific results and every original judgment remain retrievable. + +The progression chart shows each condition across the three rounds, with separate panels for scientific adequacy and mean evaluated checklist items met. +Each point summarizes designated primary judgments from six assigned fresh workers; science has 5–6 available judgments and the checklist has 4–6 per condition and round. +Scientific proportions have 95% Wilson intervals, conditional on independent runs with a common within-group probability. +The checklist panel shows each available run, connected means and ± one sample standard deviation, describing between-run spread rather than uncertainty in a mean. +Its denominator is evaluated items (met + partial + unmet), excluding unchecked and not-applicable items; this differs from the table’s all-31-item app measure. +The chart uses the same retained judgments as the table, with exact denominators in the linked round data. +Neither bar type accounts for missing judgments, assessor uncertainty, shared infrastructure or the adaptive protocol; these are descriptive comparisons, not causal effects. +Only the STAMPED condition receives the revised research-skill bundle; the other conditions retain their assigned instructions. +The baseline label is “No supplied research skills”: common task instructions, software resources and runtime system skills remain available to all conditions. + +The seven concise definitions follow the [STAMPED paper](https://github.com/stamped-principles/stamped-paper/blob/main/main.tex), including component and change provenance, versioned environment specifications, persistent retrieval and explicit licenses. +A spectrum note distinguishes incremental improvement from a single compliance threshold. + +The poster focuses on the scientific results and skill-development experiment. +Original reporting failures, additive extraction corrections and infrastructure diagnostics remain in the benchmark's linked reporting record. +Future directions draw on the [study lessons](https://github.com/leej3/stamped-in-practice/blob/main/LESSONS.md): stronger calibrated judges, clear completion rules, common tool guidance, measured coordinator effort, isolation, execution capture and new scientific tasks. + +## Retrieve and build + +Run from this directory: + +```sh +pixi install +pixi run datalad get ../orinoco-lite/assets/con-logo-outlined.svg \ + ../orinoco-lite/assets/con-ccn-dartmouth-letterhead.svg \ + ../orinoco-lite/assets/repronim_logo.svg \ + ../orinoco-lite/assets/orinoco-qr-con.svg assets figures exports +pixi run setup-browser +pixi run build +pixi run verify +pixi run links +``` + +`pixi run build` verifies the scientific display copies and outcome table against their bindings, then exports the local HTML/CSS poster. It does not regenerate scientific analyses or request live study data. Before replacing annexed exports, run `pixi run git annex unlock exports/stamped-ai-poster.pdf exports/pdf-preview.png`. The exact validated `pixi.lock` is preserved separately on [`codex/env-poster-ci-20261016`](https://github.com/con/talks/tree/codex/env-poster-ci-20261016). For an exact environment replay, retrieve its `2026-usrse/stamped-ai-study/pixi.lock` here before `pixi install --locked`. + +To import a new committed benchmark export: + +```sh +pixi run git annex unlock figures +pixi run python scripts/import-benchmark-figures.py --benchmark /path/to/stamped-in-practice +pixi run python scripts/import-benchmark-outcomes.py --benchmark /path/to/stamped-in-practice +pixi run build +``` + +The importer checks every source recorded in the benchmark export manifest and requires those files to match its committed revision. +Scientific regeneration and input refresh happen through the benchmark's documented root tasks. +The historical poster-side scientific pipeline remains in Git history; it is no longer a second source of truth. + +Institutional marks are reused from the ORINOCO Lite poster. +To change QR destinations, edit `make-logo-qrs.py` and run `pixi run python make-logo-qrs.py --check-dir exports/qr-source`. +QR regeneration additionally requires Inkscape and `rsvg-convert`; ordinary builds use the supplied QR assets. + +## Verification and provenance + +[HTML audit](exports/html-audit.json), [PDF audit](exports/pdf-audit.json), [link audit](exports/link-audit.json), [retrieval audit](exports/retrieval-audit.json) and [visual review](exports/agent-visual-review.json) describe the current export. +The retrieval audit records fresh full-payload checks for the current PDF, preview and changed figure assets, alongside earlier checks for unchanged assets. +Checks require one 44-inch square page, at least 24-point print text, no layout overflow, clickable PDF links, and four QR codes decoded from PDF pixels. +These are agent checks; author review remains part of poster preparation. + +Earlier designs remain in the [poster history](https://github.com/con/talks/commits/codex/stamped-example-poster/2026-usrse/stamped-ai-study). +[source-manifest.json](source-manifest.json) records the inherited layout and artwork. +Composition and prose are CC BY-SA 4.0; scripts are Apache-2.0. +Institutional marks and external scientific inputs retain their own rights, documented in [REUSE.toml](../../REUSE.toml) and the benchmark provenance. diff --git a/2026-usrse/stamped-ai-study/README.md b/2026-usrse/stamped-ai-study/README.md new file mode 100644 index 00000000..59cedea2 --- /dev/null +++ b/2026-usrse/stamped-ai-study/README.md @@ -0,0 +1,44 @@ +# STAMPED in Practice poster + +Can research guidance help AI agents do sound science and leave work others can inspect and reproduce? +This **44 × 44 inch** poster presents a comparison of four kinds of assistance across three rounds of a shared neuroscience task. +It shows both scientific results and how the research guidance was tested and revised. + +## Read the poster + +- [Download the current PDF](https://hub.centerforopenneuroscience.org/git-annex-p2phttp/git-annex/40d344f5-0628-494e-82e4-9fab0949ed12/key/MD5E-s908837--31099438fe11c5bd19df7b43513b8e42.pdf). +- [View the image preview](https://hub.centerforopenneuroscience.org/git-annex-p2phttp/git-annex/40d344f5-0628-494e-82e4-9fab0949ed12/key/MD5E-s1116391--0e3f41dd0df6a3610fb5b7634c75608e.png). +- [Read the poster and figure guide](https://github.com/leej3/stamped-in-practice/blob/main/docs/poster.md) for context before following individual research records. + +The PDF and preview are publicly downloadable; their contents have been checked against the reviewed local export. +GitHub may show annexed files as pointers, so use the download links above rather than expecting those pointers to display the poster. + +## Follow the story + +The left column introduces STAMPED and the experiment. +The centre shows one agent's brain analysis and where repeated analyses agree. +The right compares scientific adequacy and research practices, including their progression across rounds. +The scientific and checklist measures describe different outcomes; an improvement in one does not establish an improvement in the other. +The plot shows 95% Wilson intervals for scientific adequacy and individual checklist scores with means ± one standard deviation. +Each linked table score opens the condition’s individual filled checklists and original responses. +The table uses mean app scores out of all 31 items; the plot uses the fraction of evaluated items met, a separate measure. + +Choose a starting point for the part you want to explore: + +- [Results and interpretation](https://github.com/leej3/stamped-in-practice/blob/main/docs/results.md) explains the measures, missing assessments and limits of the comparison, then leads to the underlying tables. +- [Scientific figures](https://github.com/leej3/stamped-in-practice/blob/main/docs/poster.md#interpret-the-scientific-figures) explains what each image represents and where its inputs and plotting code live. +- [Research skills and assessment](https://github.com/leej3/stamped-in-practice/blob/main/docs/skills.md) introduces the workflows, the independent assessor and the revisions tested in each round. +- [Repository map](https://github.com/leej3/stamped-in-practice/blob/main/docs/repository-map.md) explains why evidence links open different branches and how to read an individual research delivery. + +The poster's general links and QR codes lead to these introductions. +Links labelled **Analysis code**, **Numerical results**, **Figure code**, **Map inputs** or **Round data + denominators** open the named material directly. + +## Edit or reproduce the poster + +This directory is in the presentation repository, `con/talks`, on the `codex/stamped-example-poster` branch. +The scientific records and figure-generation workflow belong to `leej3/stamped-in-practice`; this directory holds display copies, their source bindings and the editable [HTML](index.html) and [CSS](poster.css). +The [build guide](BUILDING.md) covers retrieval, source imports, the exact environment and export checks. + +The exported poster passes checks for its page size, minimum 24-point text, links, QR codes and public downloads, plus a visual review. +These agent checks support author review. +The [build guide's verification records](BUILDING.md#verification-and-provenance) contain the details; the [completion record](completion-plan.md) and [poster history](https://github.com/con/talks/commits/codex/stamped-example-poster/2026-usrse/stamped-ai-study) preserve how the poster developed. diff --git a/2026-usrse/stamped-ai-study/assets/stamped-qr-poster.svg b/2026-usrse/stamped-ai-study/assets/stamped-qr-poster.svg new file mode 120000 index 00000000..202bed22 --- /dev/null +++ b/2026-usrse/stamped-ai-study/assets/stamped-qr-poster.svg @@ -0,0 +1 @@ +../../../.git/annex/objects/7P/pg/MD5E-s71326--5efd8ccdbf4534a4377167b6e72e77a8.svg/MD5E-s71326--5efd8ccdbf4534a4377167b6e72e77a8.svg \ No newline at end of file diff --git a/2026-usrse/stamped-ai-study/assets/stamped-qr-skills.svg b/2026-usrse/stamped-ai-study/assets/stamped-qr-skills.svg new file mode 120000 index 00000000..3b4bf9e6 --- /dev/null +++ b/2026-usrse/stamped-ai-study/assets/stamped-qr-skills.svg @@ -0,0 +1 @@ +../../../.git/annex/objects/x2/Fp/MD5E-s71260--1996f2b5c3ec7072029d9ccb4c6291a5.svg/MD5E-s71260--1996f2b5c3ec7072029d9ccb4c6291a5.svg \ No newline at end of file diff --git a/2026-usrse/stamped-ai-study/assets/stamped-qr-study.svg b/2026-usrse/stamped-ai-study/assets/stamped-qr-study.svg new file mode 120000 index 00000000..9d208ddb --- /dev/null +++ b/2026-usrse/stamped-ai-study/assets/stamped-qr-study.svg @@ -0,0 +1 @@ +../../../.git/annex/objects/jp/qZ/MD5E-s67623--fad8037a2c4eac1c81b0f96a75bb69e2.svg/MD5E-s67623--fad8037a2c4eac1c81b0f96a75bb69e2.svg \ No newline at end of file diff --git a/2026-usrse/stamped-ai-study/build-poster.cjs b/2026-usrse/stamped-ai-study/build-poster.cjs new file mode 100644 index 00000000..0aebe808 --- /dev/null +++ b/2026-usrse/stamped-ai-study/build-poster.cjs @@ -0,0 +1,112 @@ +#!/usr/bin/env node +// SPDX-FileCopyrightText: 2026 Center for Open Neuroscience +// SPDX-License-Identifier: Apache-2.0 +// Build one editable HTML poster with a strict 32 CSS px print-text floor. +const fs = require('node:fs'); +const path = require('node:path'); +const os = require('node:os'); +const crypto = require('node:crypto'); +const { pathToFileURL } = require('node:url'); +let playwright; +try { playwright = require('playwright'); } +catch { + const moduleRoot = process.env.CODEX_NODE_MODULES || path.join(os.homedir(), + '.cache/codex-runtimes/codex-primary-runtime/dependencies/node/node_modules'); + playwright = require(path.join(moduleRoot, 'playwright')); +} +const root = __dirname; +const outArg = process.argv.indexOf('--out-dir'); +if (outArg < 0 || !process.argv[outArg + 1]) { + throw new Error('Usage: node build-poster.cjs --out-dir /absolute/review-directory [--check-only]'); +} +const output = path.resolve(process.argv[outArg + 1]); +const checkOnly = process.argv.includes('--check-only'); +fs.mkdirSync(output, { recursive: true }); +const sha = file => crypto.createHash('sha256').update(fs.readFileSync(file)).digest('hex'); + +(async () => { + const browser = await playwright.chromium.launch({ headless: true }); + try { + const page = await browser.newPage({ viewport: { width: 4224, height: 4224 }, deviceScaleFactor: 1 }); + const errors = []; + page.on('pageerror', e => errors.push(String(e))); + // Every asset is local; building never needs website content. + await page.route(/^https?:/, route => route.abort()); + await page.goto(pathToFileURL(path.join(root, 'index.html')).href, { waitUntil: 'load' }); + await page.emulateMedia({ media: 'print' }); + await page.evaluate(async () => { await document.fonts.ready; await Promise.all([...document.images].map(i => i.decode())); }); + const audit = await page.evaluate(() => { + const poster = document.querySelector('.poster'); + const bounds = poster.getBoundingClientRect(); + const rect = r => ({ x: r.x - bounds.x, y: r.y - bounds.y, width: r.width, height: r.height }); + const text = [], small = [], outside = [], regionOverflow = [], internalOverflow = [], unlinkedImages = [], sectionOverlap = []; + const walker = document.createTreeWalker(poster, NodeFilter.SHOW_TEXT); + while (walker.nextNode()) { + const node = walker.currentNode; + if (!node.textContent.trim()) continue; + const el = node.parentElement; + const style = getComputedStyle(el); + if (style.display === 'none' || style.visibility === 'hidden') continue; + const range = document.createRange(); range.selectNodeContents(node); + if (!range.getClientRects().length) continue; + const row = { text: node.textContent.trim(), px: parseFloat(style.fontSize), element: el.tagName }; + text.push(row); + if (row.px < 32) small.push(row); + } + for (const el of poster.querySelectorAll('*')) { + const r = el.getBoundingClientRect(); + if (!r.width || !r.height) continue; + if (r.left < bounds.left - 1 || r.top < bounds.top - 1 || r.right > bounds.right + 1 || r.bottom > bounds.bottom + 1) { + outside.push({ element: el.tagName, class: el.className, rect: rect(r) }); + } + const s = getComputedStyle(el); + if (s.display !== 'inline' && el.clientWidth && el.scrollWidth > el.clientWidth + 2) { + internalOverflow.push({ element: el.tagName, class: el.className, width: el.clientWidth, scroll: el.scrollWidth }); + } + } + // The page can contain an overlapping footer even if every element fits + // its outer canvas. Check the four original template regions separately. + for (const region of poster.children) { + const area = region.getBoundingClientRect(); + for (const el of region.querySelectorAll('*')) { + const r = el.getBoundingClientRect(); + if (r.width && r.height && (r.top < area.top - 1 || r.bottom > area.bottom + 1)) { + regionOverflow.push({ region: region.className, element: el.tagName, class: el.className, rect: rect(r) }); + } + } + } + for (const parent of poster.querySelectorAll('.method-column, .science-column, .outcomes')) { + const sections = [...parent.children]; + for (let i = 1; i < sections.length; i++) { + const previous = sections[i - 1].getBoundingClientRect(); + const next = sections[i].getBoundingClientRect(); + if (next.top < previous.bottom - 1) sectionOverlap.push({ parent: parent.className, previous: sections[i - 1].className, next: sections[i].className }); + } + } + const images = [...poster.querySelectorAll('img')].map(img => { + const link = img.closest('a'); + if (!link || !link.href.startsWith('https://')) unlinkedImages.push(img.src); + return { src: img.getAttribute('src'), loaded: img.complete && img.naturalWidth > 0, href: link?.href, rect: rect(img.getBoundingClientRect()) }; + }); + const qrs = [...poster.querySelectorAll('[data-qr]')].map(a => ({ name: a.dataset.qr, url: a.href, rect: rect(a.querySelector('img').getBoundingClientRect()) })); + const links = [...new Set([...poster.querySelectorAll('a')].map(a => a.href))]; + const commitNavigationLinks = links.filter(url => /\/(tree|blob)\/[0-9a-f]{40}(\/|$)/.test(url)); + const blocks = [...poster.querySelectorAll('.property-section, .property-table, .property-table tbody tr, .stages-section, .section-heading, .stage-cards, .stages-figure, .scientific-results, .scope-note, .outcomes > section')].map(el => ({ element: el.tagName, class: el.className, rect: rect(el.getBoundingClientRect()) })); + return { size_css_px: { width: bounds.width, height: bounds.height }, minimum_text_px: Math.min(...text.map(t => t.px)), text_node_count: text.length, small, outside, regionOverflow, internalOverflow, sectionOverlap, unlinkedImages, commitNavigationLinks, images, qrs, links, blocks }; + }); + audit.browser = browser.version(); + audit.created_utc = new Date().toISOString(); + audit.source_sha256 = Object.fromEntries(['index.html', 'template.css', 'poster.css', 'build-poster.cjs', 'verify-pdf.py', 'verify-links.py', 'make-logo-qrs.py', 'source-manifest.json', 'figures/benchmark-source.json', 'scripts/import-benchmark-figures.py', 'scripts/import-benchmark-outcomes.py', 'data/benchmark-outcomes.json', 'data/benchmark-checklists.json', 'data/benchmark-outcomes-source.json', 'pixi.toml', 'package-lock.json'].map(n => [n, sha(path.join(root, n))])); + audit.errors = errors; + fs.writeFileSync(path.join(output, 'html-audit.json'), JSON.stringify(audit, null, 2) + '\n'); + await page.screenshot({ path: path.join(output, 'layout-review.png'), fullPage: true }); + if (errors.length || audit.small.length || audit.outside.length || audit.regionOverflow.length || audit.internalOverflow.length || audit.sectionOverlap.length || audit.unlinkedImages.length || audit.commitNavigationLinks.length || audit.images.some(i => !i.loaded)) { + throw new Error('HTML layout or asset audit failed; inspect html-audit.json.'); + } + if (!checkOnly) { + await page.pdf({ path: path.join(output, 'stamped-ai-poster.pdf'), preferCSSPageSize: true, printBackground: true, tagged: true }); + await page.screenshot({ path: path.join(output, 'html-fullsize.png'), fullPage: true }); + } + console.log(JSON.stringify({ output, check_only: checkOnly, minimum_text_px: audit.minimum_text_px, qrs: audit.qrs.length, links: audit.links.length })); + } finally { await browser.close(); } +})().catch(e => { console.error(e.stack); process.exitCode = 1; }); diff --git a/2026-usrse/stamped-ai-study/completion-plan.md b/2026-usrse/stamped-ai-study/completion-plan.md new file mode 100644 index 00000000..f565402a --- /dev/null +++ b/2026-usrse/stamped-ai-study/completion-plan.md @@ -0,0 +1,34 @@ +# Completing the STAMPED in Practice poster + +The poster now contains measured outcomes from the retained operational assessments of all three rounds, plus scientific spatial results from all 48 round-two and round-three analyses. +The original development comparison is not included in these summaries. +The invitation remains to use STAMPED, try the skills and contribute example studies. + +## Completed + +- Corrected reporting recognizes the authorized research and skill revisions while preserving original reports, raw judgments and every individual admission failure. +- The condition table gives each original research run equal weight, uses its designated primary judge and retains separate round summaries. +- Science, checklist and native replay observations have explicit denominators; missing measurements and partial output matches remain distinct. +- Scientific figure code, native maps, coverage, source records and provenance live in the benchmark. +The poster imports verified display copies. +- The formal example is round-two run09. +The variability figure includes twelve analyses per condition from rounds two and three, on 168,285 shared tested voxels. +- The revised PDF is inspected and checked for layout, legible text, links and QR destinations. + +## Final integration + +All 96 assigned operational judgments are closed. +The benchmark reporting layer recognizes the authorized source revisions, recovers exact retained links and preserves every original judgment, rejection report and individual admission failure. +The table pools 72 original runs with 70 primary scientific judgments and 68 valid primary checklists. +Duplicate judges remain separate. + +The final pool includes 21 native rerun executions: 13 full selected-output matches, five partial matches and three nonzero exits. +Unobserved or unavailable execution remains distinct. +The published benchmark retains separate round summaries and the source revisions behind the pool. + +The poster imports that committed summary, and its PDF is rebuilt, inspected and verified. +No research, replay or judging was repeated. +The original coordinator checkout and frozen judging runtime remain unchanged by this reporting work. + +The infrastructure history and detailed exclusions belong in the linked research object. +They are not additional poster panels. diff --git a/2026-usrse/stamped-ai-study/data/benchmark-checklists.json b/2026-usrse/stamped-ai-study/data/benchmark-checklists.json new file mode 100644 index 00000000..62cbfa58 --- /dev/null +++ b/2026-usrse/stamped-ai-study/data/benchmark-checklists.json @@ -0,0 +1,3360 @@ +{ + "branch": "codex/stamped-poster-analysis", + "conditions": [ + { + "app_all_items_mean_met_percent": 19.758064516129032, + "checklist_list_url": "https://github.com/leej3/stamped-in-practice/tree/codex/stamped-poster-analysis/experiments/narps-poster/checklists#no-supplied-research-skills", + "checklist_n": 16, + "condition": "baseline", + "label": "No supplied research skills" + }, + { + "app_all_items_mean_met_percent": 19.53405017921147, + "checklist_list_url": "https://github.com/leej3/stamped-in-practice/tree/codex/stamped-poster-analysis/experiments/narps-poster/checklists#find-useful-skills", + "checklist_n": 18, + "condition": "discover-general", + "label": "Find useful skills" + }, + { + "app_all_items_mean_met_percent": 18.975332068311197, + "checklist_list_url": "https://github.com/leej3/stamped-in-practice/tree/codex/stamped-poster-analysis/experiments/narps-poster/checklists#find-research-skills", + "checklist_n": 17, + "condition": "discover-science", + "label": "Find research skills" + }, + { + "app_all_items_mean_met_percent": 27.703984819734345, + "checklist_list_url": "https://github.com/leej3/stamped-in-practice/tree/codex/stamped-poster-analysis/experiments/narps-poster/checklists#use-stamped-skills", + "checklist_n": 17, + "condition": "stamped-explicit", + "label": "Use STAMPED skills" + } + ], + "definitions": { + "app_all_items_mean_met_percent": "Equal-run mean of the unrounded all-item percentages among admitted primary responses in a condition; this is separate from the plot's evaluated-item mean.", + "app_all_items_met_percent": "100 * met / all 31 checklist items; the checklist app rounds this to a whole percentage.", + "app_projection": "The frozen encoder maps met to yes, partial/unmet to no, and not-checked/not-applicable to blank. The web form omits evidence, source and assessor metadata; it truncates reasons to 250 characters and shows reasons only for no. The raw JSON is the authoritative complete response.", + "app_transport": "URLs must fit within 8,000 bytes. Only when necessary, undisplayed reasons for yes/blank answers are omitted before invoking the frozen encoder; every answer state and visible no reason is preserved. Per-run app_projection records this display-only loss. Exact original reasons remain in the raw response JSON.", + "evaluated_met_percent": "100 * met / (met + partial + unmet), exactly the per-run fraction used in the progression plot.", + "source": "Every response is copied byte-for-byte from the member selected by its retained primary judgment, after archive and response hash verification. App URLs are generated from these canonical responses, not reused from potentially stale retained URL files. No responses are regraded or repaired.", + "unavailable": "Invalid or unadmitted primary responses have null scores and app links. Their unchanged raw responses and counts are retained for inspection, never included in means." + }, + "encoder": { + "commit": "9852d8360f9519d21d11099b45f5deb8ba80cb28", + "files": [ + { + "bytes": 20858, + "path": "skills/stamped-conventions/scripts/encode_response.py", + "sha256": "5ce518f59c6a5a2ac0121b1105a675ca29ddfb1fd7eab9fcb784f645789f8969" + }, + { + "bytes": 781, + "path": "skills/stamped-conventions/checklist/lock.json", + "sha256": "4c353484adcb2210b8041f21366c7de04c4eaace7f8f52e7a30f6a279110a2ad" + }, + { + "bytes": 10709, + "path": "skills/stamped-conventions/checklist/stamped-checklist-0.3.1.json", + "sha256": "da2eb88ed49dff64f098ad92200dec81c1b4404cc2d3ba1e1e1404d0e10e7bba" + }, + { + "bytes": 3433, + "path": "skills/stamped-conventions/references/response-schema.json", + "sha256": "56a5339cac45d4a142eccf81f5b902cf2f3c4d85ddff3af949598bb7a9e8f0a4" + } + ], + "operation": "encode canonical answers for display; no assessment", + "repository": "https://github.com/con/skills" + }, + "repository": "https://github.com/leej3/stamped-in-practice", + "runs": [ + { + "admission": "eligible", + "all_item_count": 31, + "app_all_items_met_percent": 16.129032258064516, + "app_projection": { + "maximum_url_bytes": 8000, + "reason_character_limit": 250, + "undisplayed_reasons_omitted": false, + "url_bytes": 6052 + }, + "app_url": 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"82d480f105a75d2cf765cbabc189c90a96e5ecf64ffa754de455ad57669c7175", + "bytes": 146614, + "source_path": "experiments/narps-poster/figures/narps-spatial-agreement.svg" + }, + { + "path": "figures/narps-spatial-agreement.png", + "sha256": "4439f80e4fd4fffaf6093db4994f6ca89f041035703d9229913aab20b41c7d54", + "bytes": 219089, + "source_path": "experiments/narps-poster/figures/narps-spatial-agreement.png" + }, + { + "path": "figures/round-progression.svg", + "sha256": "59e5cb8a3995f4594d15bc757a2054c1d647d35119f5ace42eb07fbb298020b3", + "bytes": 44560, + "source_path": "experiments/narps-poster/figures/round-progression.svg" + }, + { + "path": "figures/round-progression.png", + "sha256": "6ff7af81684f6b9287519d9afbf364440077c394ef0f710ee9e3eaceb0c42038", + "bytes": 146510, + "source_path": "experiments/narps-poster/figures/round-progression.png" + } + ], + "scope": "Verified display copies. Scientific code, inputs, environment and provenance are retained in the benchmark repository." +} diff --git a/2026-usrse/stamped-ai-study/figures/narps-group-map.png b/2026-usrse/stamped-ai-study/figures/narps-group-map.png new file mode 120000 index 00000000..fd8b651e --- /dev/null +++ b/2026-usrse/stamped-ai-study/figures/narps-group-map.png @@ -0,0 +1 @@ +../../../.git/annex/objects/PP/q2/MD5E-s147376--edb524418ea5236eed62734e960ce400.png/MD5E-s147376--edb524418ea5236eed62734e960ce400.png \ No newline at end of file diff --git a/2026-usrse/stamped-ai-study/figures/narps-group-map.svg b/2026-usrse/stamped-ai-study/figures/narps-group-map.svg new file mode 100644 index 00000000..08a7383b --- /dev/null +++ b/2026-usrse/stamped-ai-study/figures/narps-group-map.svg @@ -0,0 +1,393 @@ + + + + + + + + image/svg+xml + + + Matplotlib v3.11.2, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + P + + + A + + + Sagittal + x = 0 mm + + + + + + + + + + + + + + + + L + + + R + + + Coronal + y = 40 mm + + + + + + + + + + + + + + + + + + + L + + + R + + + Axial + z = -3.6 mm + + + + + + + + + + + + ≤−6 + + + + + + 0 + + + + + + ≥6 + + + + + + + + + + Unthresholded group t + + + + Gray anatomy: outside common coverage + + + + + + + vmPFC region + + + + + + Positive FWE p ≤ .05 + + + + + + + + + + + + + + + diff --git a/2026-usrse/stamped-ai-study/figures/narps-spatial-agreement.png b/2026-usrse/stamped-ai-study/figures/narps-spatial-agreement.png new file mode 120000 index 00000000..fc8776e8 --- /dev/null +++ b/2026-usrse/stamped-ai-study/figures/narps-spatial-agreement.png @@ -0,0 +1 @@ +../../../.git/annex/objects/z8/1Z/MD5E-s219089--f17ba04b417e7010dbc86e431f4124bd.png/MD5E-s219089--f17ba04b417e7010dbc86e431f4124bd.png \ No newline at end of file diff --git a/2026-usrse/stamped-ai-study/figures/narps-spatial-agreement.svg b/2026-usrse/stamped-ai-study/figures/narps-spatial-agreement.svg new file mode 120000 index 00000000..b0940c91 --- /dev/null +++ b/2026-usrse/stamped-ai-study/figures/narps-spatial-agreement.svg @@ -0,0 +1 @@ +../../../.git/annex/objects/Mq/4G/MD5E-s146614--470b74b11f39bfdcbb48dbf7ca61d7e5.svg/MD5E-s146614--470b74b11f39bfdcbb48dbf7ca61d7e5.svg \ No newline at end of file diff --git a/2026-usrse/stamped-ai-study/figures/round-progression.png b/2026-usrse/stamped-ai-study/figures/round-progression.png new file mode 120000 index 00000000..8c0b9e48 --- /dev/null +++ b/2026-usrse/stamped-ai-study/figures/round-progression.png @@ -0,0 +1 @@ +../../../.git/annex/objects/7q/Jf/MD5E-s146510--1797d5bf189d882ca0150f07f3de2455.png/MD5E-s146510--1797d5bf189d882ca0150f07f3de2455.png \ No newline at end of file diff --git a/2026-usrse/stamped-ai-study/figures/round-progression.svg b/2026-usrse/stamped-ai-study/figures/round-progression.svg new file mode 100644 index 00000000..cbbaeab2 --- /dev/null +++ b/2026-usrse/stamped-ai-study/figures/round-progression.svg @@ -0,0 +1,741 @@ + + + + + + + + image/svg+xml + + + Matplotlib v3.11.2, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + 2 + + + + + + 3 + + + + Round + + + + + + + + + + 0 + + + + + + + + + 50 + + + + + + + + + 100 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Analyses supported (%) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + 2 + + + + + + 3 + + + + Round + + + + + + + + + + 0 + + + + + + + + + 50 + + + + + + + + + 100 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Evaluated items met (%) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + No supplied research skills + + + + + + + + + + + + Find research skills + + + + + + + + + + + + Find useful skills + + + + + + + + + + + + Use STAMPED skills + + + + + + + + + + + + diff --git a/2026-usrse/stamped-ai-study/index.html b/2026-usrse/stamped-ai-study/index.html new file mode 100644 index 00000000..88892069 --- /dev/null +++ b/2026-usrse/stamped-ai-study/index.html @@ -0,0 +1,154 @@ + + + + + + + + STAMPED in Practice: Improving research skills through reproducible experiments + + + + + + + +
+
+
+

US-RSE 2026 · Research in the open

STAMPED in PracticeImproving research skills through
reproducible experiments

+ +
+

John A. LeeAustin MacdonaldCody C. BakerYaroslav O. Halchenko

Center for Open Neuroscience
Dartmouth College

+ QR code for the poster guide, download and evidencePoster guide +
+
+
+

Our experiment: iteratively improve STAMPED research skills by validating the scientific results and research objects they produce.

+

Make the improvement process inspectable.Link the skills, data, runs, assessments and revisions, so others can evaluate both the science and how the guidance evolved.

+
+
+
+
+

01 · STAMPED

The seven principles

+
+
Self-contained
Reach all essential components from one project root.
+
Tracked
Identify every component and record changes and computational provenance.
+
Actionable
Provide executable procedures and reproduction instructions.
+
Modular
Separate components for reuse and recombination.
+
Portable
Version environment specifications and avoid undocumented host dependencies.
+
Ephemeral
Run in fresh, disposable environments built from recorded specifications.
+
Distributable
Make components persistently retrievable in their recorded state, with explicit licenses.
+
+

Each principle is a spectrum, supporting incremental improvement. STAMPED paper.

+
+
+

The experiment

Test the skills
through the work

+ +

Do successive revisions improve scientific adequacy, reproducibility and consistency?

+
    +
  1. RunFresh agents address the same scientific question.
    2. +
  2. AssessIndependent judges inspect the research object and attempt replay.
    3. +
  3. ReviseUse recurring findings to improve and compress the skills.
    4. +
  4. RepeatTest the next pinned revision with fresh agents.
    5. +
+

Three iterations of testing and revision. In the final iteration, evaluate without further tuning.

+
+
+

The study is itself a research object

Follow the evidence

+
+ Scientific task + inputs↓ + Guidance + tested revisions↓ + Reports + code + results↓ + Assessments + lessons +
+

Inspect both the scientific result and the decisions that shaped the experiment through the repository map. Apply the STAMPED checklist to your own research object.

+
+
+
+
+

02 · Scientific results

Replicating a gain-response analysis

+

Tom et al. asked how the brain represents potential gains and losses during risky choices.

+

Our replication: does potential gain increase ventromedial prefrontal cortex (vmPFC) activity? Agents test NARPS H1 using the same 54 equal-indifference AO86 participant maps.

+

NARPS paper · OpenNeuro data · AO86 maps · Scientific task

+
+
+

Group-level gain response

+
+ Orthogonal views of the NARPS group gain-effect t map, vmPFC region, and corrected positive signal +
Round 2, run 09. One-sample test, 9,999 sign flips, whole-brain family-wise error (FWE) correction at 0.05. Analysis code · Numerical results
+
+
No corrected positive vmPFC signal

24 posterior voxels survived correction; none overlapped the analysis’s Harvard–Oxford vmPFC proxy.

+
+
+

Where do repeated analyses agree?

+
+ Spatial agreement of corrected positive findings across twelve runs in each assistance condition, from rounds two and three +
Corrected findings vary across repeated analyses. Colour shows the fraction of 12 runs per condition reporting a positive FWE-corrected result in rounds 2 and 3. Each run retains its chosen method; 168,285 voxels share tested coverage. Figure code · Map inputs
+
+ +
+
+ +
+
+

Use STAMPED. Try the skills. Bring us a study.

Share a hypothesis, accessible data and a reference result. Help us test the skills on your science—and discuss what better guidance should do.

+ QR code for the STAMPED in Practice research objectStudy + data + QR code for the guide to STAMPED research skillsUse the skills +
+ +
+
+ + + diff --git a/2026-usrse/stamped-ai-study/make-logo-qrs.py b/2026-usrse/stamped-ai-study/make-logo-qrs.py new file mode 100644 index 00000000..0ffa3714 --- /dev/null +++ b/2026-usrse/stamped-ai-study/make-logo-qrs.py @@ -0,0 +1,239 @@ +# SPDX-FileCopyrightText: 2026 Center for Open Neuroscience +# SPDX-License-Identifier: Apache-2.0 +# /// script +# requires-python = ">=3.11" +# dependencies = ["qrcode==8.2", "Pillow==11.3.0", "zxing-cpp==2.3.0"] +# /// +"""Generate three poster QR codes, reuse the repository CON QR, and verify all four destinations. + +Run with `uv run make-logo-qrs.py --check-dir /tmp/con-qr-checks`. +Requires Inkscape (only to measure the already outlined logo) and rsvg-convert +(for independent rasterization). New SVG assets are written to assets/; shared artwork is read only. Check images and +the JSON report stay in --check-dir, outside the repository by default. +""" + +import argparse +import copy +import json +from pathlib import Path +import shutil +import subprocess +import tempfile +import xml.etree.ElementTree as ET + +from PIL import Image, ImageDraw, ImageFilter +import qrcode +import zxingcpp + + +ROOT = Path(__file__).resolve().parent +SVG = "http://www.w3.org/2000/svg" +INK = "#193c4d" +BORDER = 4 # Four completely clear modules on every side. +LOGO_WIDTH_FRACTION = 0.42 +DESTINATIONS = { + "poster": "https://github.com/leej3/stamped-in-practice/blob/main/docs/poster.md", + "study": "https://github.com/leej3/stamped-in-practice", + "skills": "https://github.com/leej3/stamped-in-practice/blob/main/docs/skills.md", + "con": "https://dev.centerforopenneuroscience.org/", +} + +ET.register_namespace("", SVG) + + +def element(tag, attrs=None, text=None): + node = ET.Element(f"{{{SVG}}}{tag}", attrs or {}) + node.text = text + return node + + +def load_logo(inkscape): + """Reuse the corrected paths and original blue; never regenerate its type.""" + source = ROOT.parent / "orinoco-lite/assets/con-logo-outlined.svg" + original = ET.parse(source).getroot() + # The source retains hidden alternate artwork and wide canvas margins. + # Query the visible blue layer, then convert page-pixel bounds to its + # original SVG coordinates. Only our embedding viewport is cropped. + measured = subprocess.run( + [inkscape, str(source), "--query-id=layer1", "--query-x", "--query-y", + "--query-width", "--query-height"], + check=True, text=True, capture_output=True, + ) + x, y, width, height = map(float, measured.stdout.split()) + vx, vy, vw, vh = map(float, original.get("viewBox").split()) + scale_x = vw / float(original.get("width")) + scale_y = vh / float(original.get("height")) + # A tiny margin absorbs rounding in Inkscape's reported bounds. + margin = 0.05 + logo = element("svg", {"viewBox": ( + f"{vx+x*scale_x-margin:.6f} {vy+y*scale_y-margin:.6f} " + f"{width*scale_x+2*margin:.6f} {height*scale_y+2*margin:.6f}" + )}) + + def visible_copy(node): + if not node.tag.startswith(f"{{{SVG}}}"): + return None + if node.tag in {f"{{{SVG}}}{tag}" for tag in ("metadata", "title", "desc")}: + return None + if "display:none" in node.get("style", "").replace(" ", ""): + return None + result = ET.Element(node.tag, { + key: value for key, value in node.attrib.items() + if not key.startswith("{") # Drop editor-only namespaced metadata. + }) + for child in node: + copied = visible_copy(child) + if copied is not None: + result.append(copied) + return result + + for child in original: + copied = visible_copy(child) + if copied is not None: + logo.append(copied) + assert not logo.findall(f".//{{{SVG}}}text"), "Visible logo must be outlined" + assert not logo.findall(f".//{{{SVG}}}image"), "Logo must remain native vector" + return logo + + +def write_qr(name, url, logo): + qr = qrcode.QRCode(error_correction=qrcode.constants.ERROR_CORRECT_H, + border=BORDER, box_size=1) + qr.add_data(url) + qr.make(fit=True) + modules = qr.get_matrix() + size = len(modules) + body_size = size - 2 * BORDER + assert all(not any(row) for row in modules[:BORDER] + modules[-BORDER:]) + assert all(not any(row[:BORDER] + row[-BORDER:]) for row in modules) + root = element("svg", { + "version": "1.1", "width": "45mm", "height": "45mm", + "viewBox": f"0 0 {size} {size}", "role": "img", + "aria-labelledby": "qr-title qr-description", + }) + root.append(element("title", {"id": "qr-title"}, f"CON QR code: {name}")) + root.append(element("desc", {"id": "qr-description"}, + f"{url}; high error correction; four-module quiet zone.")) + root.append(element("rect", {"width": str(size), "height": str(size), + "fill": "#ffffff"})) + # Combine consecutive dark cells into horizontal runs, retaining square + # module geometry and avoiding hairline seams between adjacent cells. + runs = [] + for y, row in enumerate(modules): + x = 0 + while x < size: + if not row[x]: + x += 1 + continue + start = x + while x < size and row[x]: + x += 1 + runs.append(f"M{start},{y}h{x-start}v1h-{x-start}z") + root.append(element("path", {"d": "".join(runs), "fill": INK})) + + _, _, logo_vw, logo_vh = map(float, logo.get("viewBox").split()) + logo_width = body_size * LOGO_WIDTH_FRACTION + logo_height = logo_width * logo_vh / logo_vw + padding = 1.0 + pad_width, pad_height = logo_width + 2 * padding, logo_height + 2 * padding + root.append(element("rect", { + "x": f"{(size-pad_width)/2:.6f}", "y": f"{(size-pad_height)/2:.6f}", + "width": f"{pad_width:.6f}", "height": f"{pad_height:.6f}", + "rx": "0.55", "fill": "#ffffff", + })) + logo_box = element("svg", { + "x": f"{(size-logo_width)/2:.6f}", "y": f"{(size-logo_height)/2:.6f}", + "width": f"{logo_width:.6f}", "height": f"{logo_height:.6f}", + "viewBox": logo.get("viewBox"), "preserveAspectRatio": "xMidYMid meet", + }) + for child in logo: + # Inkscape export may retain metadata/hidden layers; only SVG drawing + # content belongs in the embedded mark. + if not child.tag.startswith(f"{{{SVG}}}"): + continue + if child.tag in {f"{{{SVG}}}metadata", f"{{{SVG}}}title", f"{{{SVG}}}desc"}: + continue + if "display:none" in child.get("style", "").replace(" ", ""): + continue + logo_box.append(copy.deepcopy(child)) + root.append(logo_box) + assert not root.findall(f".//{{{SVG}}}text") + assert not root.findall(f".//{{{SVG}}}image"), "Logo must remain native vector" + if name == "con": + destination = ROOT.parent / "orinoco-lite/assets/orinoco-qr-con.svg" + generated = ET.tostring(root, encoding="utf-8", xml_declaration=True) + assert destination.read_bytes() == generated, "Shared CON QR differs from the expected composition" + else: + destination = ROOT / f"assets/stamped-qr-{name}.svg" + if destination.is_symlink(): + raise SystemExit(f"Unlock the annexed output before rebuilding: {destination}") + ET.ElementTree(root).write(destination, encoding="utf-8", xml_declaration=True) + assert destination.stat().st_size < 100_000, "QR should remain a small SVG" + return { + "name": name, "url": url, "file": str(destination), + "qr_version": qr.version, "error_correction": "H", + "modules_including_border": size, "quiet_border_modules": BORDER, + "logo_source": "../orinoco-lite/assets/con-logo-outlined.svg", + "logo_width_fraction_of_body": LOGO_WIDTH_FRACTION, + "file_bytes": destination.stat().st_size, + "logo_pad_percent_of_body_area": round(100*pad_width*pad_height/body_size**2, 2), + } + + +def check_code(row, check_dir): + checks = [] + # 200–220 px cover the planned poster CSS sizes; 144/180 retain earlier + # screen-size checks. These are raster checks, not physical-camera scans. + # 177/266 px approximate 30/45 mm at + # 150 dpi; 354/531 px approximate 30/45 mm at 300 dpi. + for pixels in (144, 177, 180, 200, 210, 220, 240, 266, 354, 531, 720): + raster = check_dir / f"qr-{row['name']}-{pixels}px.png" + subprocess.run(["rsvg-convert", "-w", str(pixels), "-h", str(pixels), + "-o", str(raster), row["file"]], check=True) + image = Image.open(raster).convert("RGB") + variants = {"original": image, "rotated-90": image.transpose(Image.Transpose.ROTATE_90)} + if pixels >= 177: + variants["grayscale-softened"] = image.convert("L").filter(ImageFilter.GaussianBlur(0.35)) + variants["rotated-13"] = image.rotate( + 13, resample=Image.Resampling.BICUBIC, expand=True, fillcolor="white" + ) + for variant, candidate in variants.items(): + decoded = zxingcpp.read_barcodes(candidate) + ok = len(decoded) == 1 and decoded[0].text == row["url"] + checks.append({"pixels": pixels, "variant": variant, "passed": ok, + "decoded": [code.text for code in decoded]}) + row["checks"] = checks + return all(check["passed"] for check in checks) + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--check-dir", type=Path, + default=Path(tempfile.gettempdir()) / "con-qr-checks") + parser.add_argument("--inkscape", default=shutil.which("inkscape") or + "/Applications/Inkscape.app/Contents/MacOS/inkscape") + args = parser.parse_args() + args.check_dir.mkdir(parents=True, exist_ok=True) + logo = load_logo(args.inkscape) + report = [write_qr(name, url, logo) for name, url in DESTINATIONS.items()] + success = True + for row in report: + passed = check_code(row, args.check_dir) + success = passed and success + print(f"{row['name']}: version {row['qr_version']} / H; " + f"{sum(check['passed'] for check in row['checks'])}/" + f"{len(row['checks'])} decoding checks passed") + (args.check_dir / "decode-report.json").write_text(json.dumps(report, indent=2)+"\n") + overview = Image.new("RGB", (len(report)*360, 400), "white") + draw = ImageDraw.Draw(overview) + for i, row in enumerate(report): + image = Image.open(args.check_dir / f"qr-{row['name']}-354px.png") + overview.paste(image, (360*i+3, 5)) + draw.text((360*i+20, 370), row["name"], fill=INK) + overview.save(args.check_dir / "qr-overview.png") + if not success: + raise SystemExit("QR verification failed; inspect decode-report.json") + + +if __name__ == "__main__": + main() diff --git a/2026-usrse/stamped-ai-study/package-lock.json b/2026-usrse/stamped-ai-study/package-lock.json new file mode 100644 index 00000000..9bbc0d39 --- /dev/null +++ b/2026-usrse/stamped-ai-study/package-lock.json @@ -0,0 +1,58 @@ +{ + "name": "stamped-in-practice-poster", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "stamped-in-practice-poster", + "license": "Apache-2.0", + "dependencies": { + "playwright": "1.62.1" + } + }, + "node_modules/fsevents": { + "version": "2.3.2", + "resolved": "https://registry.npmjs.org/fsevents/-/fsevents-2.3.2.tgz", + "integrity": "sha512-xiqMQR4xAeHTuB9uWm+fFRcIOgKBMiOBP+eXiyT7jsgVCq1bkVygt00oASowB7EdtpOHaaPgKt812P9ab+DDKA==", + "hasInstallScript": true, + "license": "MIT", + "optional": true, + "os": [ + "darwin" + ], + "engines": { + "node": "^8.16.0 || ^10.6.0 || >=11.0.0" + } + }, + "node_modules/playwright": { + "version": "1.62.1", + "resolved": "https://registry.npmjs.org/playwright/-/playwright-1.62.1.tgz", + "integrity": "sha512-0M+L3LAD8/nm554LOla9Ayx0j0tmFZ0FBcoQ7F1VuVHpM/XpiC8RcDzBQB8W5+hA8L22THxELzeF+2WcUzvcLg==", + "license": "Apache-2.0", + "dependencies": { + "playwright-core": "1.62.1" + }, + "bin": { + "playwright": "cli.js" + }, + "engines": { + "node": ">=20" + }, + "optionalDependencies": { + "fsevents": "2.3.2" + } + }, + "node_modules/playwright-core": { + "version": "1.62.1", + "resolved": "https://registry.npmjs.org/playwright-core/-/playwright-core-1.62.1.tgz", + "integrity": "sha512-wPYSwEBJY9GHraISXqyqtx0na0LpO3XEX7jNDhntbex7tzUS7kLnZsOlFruFJB4Hi/rhDMjXGqHewDZ68nYZVw==", + "license": "Apache-2.0", + "bin": { + "playwright-core": "cli.js" + }, + "engines": { + "node": ">=20" + } + } + } +} diff --git a/2026-usrse/stamped-ai-study/package.json b/2026-usrse/stamped-ai-study/package.json new file mode 100644 index 00000000..c7d56c49 --- /dev/null +++ b/2026-usrse/stamped-ai-study/package.json @@ -0,0 +1,6 @@ +{ + "name": "stamped-in-practice-poster", + "private": true, + "license": "Apache-2.0", + "dependencies": { "playwright": "1.62.1" } +} diff --git a/2026-usrse/stamped-ai-study/pixi.toml b/2026-usrse/stamped-ai-study/pixi.toml new file mode 100644 index 00000000..7047a7ec --- /dev/null +++ b/2026-usrse/stamped-ai-study/pixi.toml @@ -0,0 +1,28 @@ +# SPDX-License-Identifier: Apache-2.0 +[workspace] +name = "stamped-in-practice-poster" +channels = ["conda-forge"] +platforms = [{ platform = "osx-arm64", macos = "14.0" }, "linux-64"] + +[dependencies] +python = ">=3.12,<3.14" +pillow = ">=11,<13" +pypdf = ">=6,<7" +qrcode = ">=8,<9" +poppler = "*" +nodejs = ">=22,<23" +pre-commit = "*" +git = "*" + +[pypi-dependencies] +zxing-cpp = "==2.3.0" +datalad = "*" +git-annex = "*" + +[tasks] +setup-browser = "npm ci && npx playwright install chromium" +figures = "python scripts/import-benchmark-figures.py" +outcomes = "python scripts/import-benchmark-outcomes.py" +build = { cmd = "node build-poster.cjs --out-dir exports", depends-on = ["figures", "outcomes"] } +verify = "python verify-pdf.py --review-dir exports" +links = "python verify-links.py --review-dir exports" diff --git a/2026-usrse/stamped-ai-study/poster.css b/2026-usrse/stamped-ai-study/poster.css new file mode 100644 index 00000000..f885a484 --- /dev/null +++ b/2026-usrse/stamped-ai-study/poster.css @@ -0,0 +1,75 @@ +/* SPDX-License-Identifier: CC-BY-SA-4.0 */ +.poster { grid-template-rows: 324px 240px 1fr 286px 220px; gap: 32px; } +.masthead { grid-template-columns: 1.2fr 690px 1fr; gap: 60px; } +.con-logo { width: 690px; } +h1 { font-size: 92px; } +h1 span { font-size: 48px; } +.authors { font-size: 38px; } +.authors .affiliation { font-size: 32px; } +.author-panel { gap: 38px; } +.lead p { font-size:42px; } +.lead .pitch strong { font-size:44px; } +.lead .pitch span { font-size:36px; } +.principles-grid { display:grid; gap:10px; margin:0; } +.principles-grid > div { display:grid; grid-template-columns:300px 1fr; gap:24px; padding:10px 0; border-bottom:2px solid var(--rule); } +.principles-section > p:last-child { margin:14px 0 0; } +.principles-grid dt { font-size:36px; font-weight:700; color:var(--green); } +.principles-grid dd { font-size:32px; line-height:1.3; margin:0; } +.columns { grid-template-columns: 0.95fr 1.2fr 1.3fr; gap: 48px; } +.columns > * { min-width: 0; } +.columns p { font-size: 36px; line-height: 1.35; margin: 0 0 24px; } +.columns h2 { font-size: 61px; margin-bottom: 28px; } +.columns h3 { font-size: 44px; margin-bottom: 24px; } +.columns .section-label { font-size: 32px; margin-bottom: 18px; } +.columns .small, .columns .source-links { font-size: 32px; line-height: 1.35; } +.method-column, .science-column { display:flex; flex-direction:column; gap: 40px; } +.science-column { border-left:2px solid var(--rule); padding-left:44px; gap:24px; } +.ruled { border-top: 3px solid var(--rule); padding-top: 30px; } +.loop { list-style: none; padding:0; margin:34px 0; display:grid; gap:18px; counter-reset: step; } +.loop li { display:grid; grid-template-columns: 160px 1fr; gap:22px; padding:24px; background:var(--tint); font-size:36px; line-height:1.25; border-left:7px solid var(--green); } +.loop b { color:var(--green); font-size:38px; } +.evidence-chain { background:var(--tint); padding:28px; margin-bottom:28px; display:grid; text-align:center; gap:12px; font-size:34px; line-height:1.25; } +.evidence-chain span { color:var(--green); font-size:34px; } +.source-links { color:var(--green); } +.science-result { border-top:7px solid var(--green); padding-top:24px; } +.brain-figure { width:100%; display:block; } +figcaption { font-size:32px; line-height:1.32; margin:18px 0 0; } +.finding { margin-top:28px; background:var(--tint); padding:28px 32px; border-left:7px solid var(--green); } +.finding b { font-size:41px; display:block; margin-bottom:18px; } +.finding p { margin:0; } +.variability-figure { width:100%; display:block; } +.result-slot { border:3px dashed #8da49c; padding:24px 28px; margin-top:28px !important; color:var(--muted); } +.result-slot strong { display:block; color:var(--ink); } +.outcomes { padding-left:42px; } +.outcomes > section + section { margin-top:26px; } +.outcomes .revision-section p { margin-bottom:0; } +.outcomes .results-matrix { margin-top:10px; } +.outcome-table { width:100%; border-collapse:collapse; table-layout:fixed; font-size:32px; line-height:1.25; } +.outcome-table th, .outcome-table td { padding:24px 12px; text-align:left; border-bottom:2px solid var(--rule); vertical-align:middle; } +.outcome-table thead th { background:var(--green); color:white; font-size:32px; padding:22px 12px; } +.outcome-table col:first-child { width:34%; } +.outcome-table col:nth-child(2) { width:10%; } +.outcome-table col:nth-child(3) { width:17%; } +.outcome-table col:nth-child(4) { width:16%; } +.outcome-table col:nth-child(5) { width:23%; } +.columns .summary-key { margin-top:24px; } +.progression-figure { width:100%; display:block; } +.method-column .evidence-chain { gap:8px; padding:22px; margin-bottom:22px; } +.progression-section { padding-top:24px; } +.lessons-section > p:last-child { margin-bottom:0; } +.revision { border-left:6px solid var(--con-blue); padding:18px 26px; margin-bottom:20px; } +.revision b { font-size:37px; } +.revision p { font-size:34px; margin:12px 0 0; } +.skills-use p { line-height:1.65; margin-bottom:0; } +.invitation { background:var(--green); color:white; margin:0 -88px; padding:30px 88px; display:grid; grid-template-columns:1fr 240px 240px; gap:48px; align-items:center; } +.invitation h2 { font-size:61px; margin:0 0 20px; } +.invitation p { font-size:40px; line-height:1.3; margin:0; max-width:2900px; } +.invitation .qr-badge { color:white; font-size:32px; } +.invitation .qr-badge img { width:180px; height:180px; } +.footer { grid-template-columns:1.1fr 1fr; padding-top:16px; border:0; } +.footer p, .footer .thanks { font-size:32px; } +.partners .qr-badge img { max-height:none; height:155px; width:155px; } +.qr-badge { font-size:32px; } +.repronim-support { display:flex; align-items:center; gap:22px; font-size:32px; text-decoration:none; } + +.variability-section { padding-top:24px; } diff --git a/2026-usrse/stamped-ai-study/scripts/import-benchmark-figures.py b/2026-usrse/stamped-ai-study/scripts/import-benchmark-figures.py new file mode 100644 index 00000000..cffc119d --- /dev/null +++ b/2026-usrse/stamped-ai-study/scripts/import-benchmark-figures.py @@ -0,0 +1,77 @@ +#!/usr/bin/env python3 +# SPDX-FileCopyrightText: 2026 Center for Open Neuroscience +# SPDX-License-Identifier: Apache-2.0 +"""Import or verify display copies; scientific generation belongs to the benchmark.""" +from __future__ import annotations +import argparse +import hashlib +import json +from pathlib import Path +import shutil +import subprocess + +ROOT = Path(__file__).resolve().parents[1] +MANIFEST = Path('experiments/narps-poster/figures/poster-figure-manifest.json') +BINDING = ROOT / 'figures/benchmark-source.json' +EXPECTED = {f'{name}.{ext}' for name in ('narps-group-map', 'narps-spatial-agreement', 'round-progression') for ext in ('svg', 'png')} + + +def digest(path): + return hashlib.sha256(path.read_bytes()).hexdigest() + + +def checked_path(root, relative): + path = Path(relative) + if path.is_absolute() or '..' in path.parts: + raise ValueError(f'Expected repository-relative path: {relative}') + return root / path + + +def verify(root, entries): + for entry in entries: + path = checked_path(root, entry['path']) + if digest(path) != entry['sha256'] or path.stat().st_size != entry['bytes']: + raise ValueError(f'Figure source or display copy changed: {path}') + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument('--benchmark', type=Path, help='Import from a committed benchmark checkout; omit to verify existing display copies') + args = parser.parse_args() + if args.benchmark: + benchmark = args.benchmark.resolve() + raw = (benchmark / MANIFEST).read_bytes() + source = json.loads(raw) + if {Path(row['path']).name for row in source['figures']} != EXPECTED: + raise ValueError('Benchmark must export the expected three SVG and three PNG figures') + entries = source['figures'] + source['sources'] + verify(benchmark, entries) + paths = [MANIFEST.as_posix(), *[row['path'] for row in entries]] + subprocess.run(['git', '-C', str(benchmark), 'ls-files', '--error-unmatch', '--', *paths], check=True, stdout=subprocess.DEVNULL) + subprocess.run(['git', '-C', str(benchmark), 'diff', '--quiet', 'HEAD', '--', *paths], check=True) + revision = subprocess.check_output(['git', '-C', str(benchmark), 'rev-parse', 'HEAD'], text=True).strip() + rows = [] + for row in source['figures']: + destination = ROOT / 'figures' / Path(row['path']).name + destination.parent.mkdir(parents=True, exist_ok=True) + # Preserve existing annex symlinks when the exported bytes are unchanged. + if not destination.exists() or digest(destination) != row['sha256']: + if destination.is_symlink(): + raise ValueError(f'Unlock annexed display copy before replacing it: {destination}') + shutil.copyfile(benchmark / row['path'], destination) + rows.append({**row, 'source_path': row['path'], 'path': destination.relative_to(ROOT).as_posix()}) + binding = { + 'schema_version': 1, 'repository': source['repository'], + 'branch': source['branch'], 'revision': revision, + 'source_manifest': {'path': MANIFEST.as_posix(), 'sha256': hashlib.sha256(raw).hexdigest()}, + 'source_manifest_content': source, 'figures': rows, + 'scope': 'Verified display copies. Scientific code, inputs, environment and provenance are retained in the benchmark repository.' + } + BINDING.write_text(json.dumps(binding, indent=2) + '\n') + binding = json.loads(BINDING.read_text()) + verify(ROOT, binding['figures']) + print(json.dumps({'verified_display_copies': len(binding['figures']), 'benchmark_revision': binding['revision']})) + + +if __name__ == '__main__': + main() diff --git a/2026-usrse/stamped-ai-study/scripts/import-benchmark-outcomes.py b/2026-usrse/stamped-ai-study/scripts/import-benchmark-outcomes.py new file mode 100644 index 00000000..bdbd5c67 --- /dev/null +++ b/2026-usrse/stamped-ai-study/scripts/import-benchmark-outcomes.py @@ -0,0 +1,143 @@ +#!/usr/bin/env python3 +# SPDX-License-Identifier: Apache-2.0 +"""Import committed summaries and render linked primary checklist scores.""" +from __future__ import annotations + +import argparse +import hashlib +from html import escape +import json +from pathlib import Path +import re +import subprocess +from urllib.parse import urlsplit + +ROOT = Path(__file__).resolve().parents[1] +SOURCE = Path("experiments/retained-round-reporting/pooled/poster-outcomes.json") +CONFIG = SOURCE.parent.parent / "poster-pool.json" +COPY = ROOT / "data/benchmark-outcomes.json" +BINDING = ROOT / "data/benchmark-outcomes-source.json" +CHECKLIST_SOURCE = Path("experiments/narps-poster/checklists/index.json") +CHECKLIST_COPY = ROOT / "data/benchmark-checklists.json" +FIGURE_MANIFEST = Path("experiments/narps-poster/figures/poster-figure-manifest.json") +START = "" +END = "" + + +def digest(path): + return hashlib.sha256(path.read_bytes()).hexdigest() + + +def table_rows(summary, checklists): + rows = [] + runs = checklists["runs"] + if len(runs) != 72 or len({run["run_id"] for run in runs}) != 72: + raise ValueError("Expected one checklist slot for each of 72 research runs") + for row in summary["conditions"]: + group = [run for run in runs if run["condition"] == row["condition"]] + if any(sum(run["round"] == number for run in group) != 6 for number in summary["retained_rounds"]): + raise ValueError("Expected six assigned runs per condition and round") + valid = [] + for run in group: + score = run["evaluated_met_percent"] + if score is None: + if run["checklist_valid"] or run["app_url"] is not None or run["app_all_items_met_percent"] is not None: + raise ValueError("Unavailable checklist must not carry a score link") + continue + url = urlsplit(run["app_url"]) + if not run["checklist_valid"] or url.scheme != "https" or url.netloc != "checklist.stamped-principles.org": + raise ValueError("Expected a valid primary checklist app URL") + if not run["evaluated_count"] or abs(score - 100 * run["met_count"] / run["evaluated_count"]) > 1e-9: + raise ValueError("Evaluated-item score and counts disagree") + if run["all_item_count"] != 31 or abs(run["app_all_items_met_percent"] - 100 * run["met_count"] / 31) > 1e-9: + raise ValueError("App score and all-item counts disagree") + valid.append(run) + if len(valid) != row["checklist_n"] or abs(sum(run["evaluated_met_percent"] for run in valid) / len(valid) - row["checklist_mean_met_percent"]) > 1e-9: + raise ValueError("Individual scores do not reproduce the original condition summary") + aggregate, = [item for item in checklists["conditions"] if item["condition"] == row["condition"]] + mean = aggregate["app_all_items_mean_met_percent"] + if aggregate["checklist_n"] != len(valid) or abs(mean - sum(run["app_all_items_met_percent"] for run in valid) / len(valid)) > 1e-9: + raise ValueError("App-score mean differs from the exported individual scores") + url = urlsplit(aggregate["checklist_list_url"]) + if (url.scheme != "https" or url.netloc != "github.com" or not url.fragment + or url.path != "/leej3/stamped-in-practice/tree/codex/stamped-poster-analysis/experiments/narps-poster/checklists"): + raise ValueError("Expected a condition checklist list in the benchmark") + science = f'{row["science"]["supported"]}/{row["scientific_n"]}' if row["scientific_n"] else "—" + replay = f'{row["replay_matched_n"]}/{row["replay_executed_n"]}' if row["replay_executed_n"] else "—" + label = escape(f'{row["label"]}: mean app score {mean:.1f}% across {len(valid)} primary checklists; open the checklist list', quote=True) + score = f'{mean:.1f}%
n={len(valid)}' + rows.append(f'{escape(row["label"])}{row["assigned_runs"]}{science}{replay}{score}') + if len(rows) != 4: + raise ValueError("Expected four assistance conditions") + return "\n".join(" " + row for row in rows) + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--benchmark", type=Path) + args = parser.parse_args() + if args.benchmark: + benchmark = args.benchmark.resolve() + source = benchmark / SOURCE + summary = json.loads(source.read_text()) + paths = [SOURCE, CONFIG, Path("scripts/summarize_poster_outcomes.py")] + for row in summary["sources"]: + relative = Path(row["path"]) + if relative.is_absolute() or ".." in relative.parts: + raise ValueError("Summary source escapes its experiment directory") + path = CONFIG.parent / relative + if digest(benchmark / path) != row["sha256"]: + raise ValueError("Summary input changed: " + str(path)) + paths.append(path) + if digest(benchmark / CONFIG) != summary["config_sha256"]: + raise ValueError("Summary configuration changed") + if digest(benchmark / "scripts/summarize_poster_outcomes.py") != summary["generator_sha256"]: + raise ValueError("Summary generator changed") + subprocess.run(["git", "-C", str(benchmark), "ls-files", "--error-unmatch", "--", *map(str, paths)], check=True, stdout=subprocess.DEVNULL) + subprocess.run(["git", "-C", str(benchmark), "diff", "--quiet", "HEAD", "--", *map(str, paths)], check=True) + revision = subprocess.check_output(["git", "-C", str(benchmark), "rev-parse", "HEAD"], text=True).strip() + figure_manifest = json.loads((benchmark / FIGURE_MANIFEST).read_text()) + checklist_entry, = [row for row in figure_manifest["sources"] if row["path"] == CHECKLIST_SOURCE.as_posix()] + if digest(benchmark / CHECKLIST_SOURCE) != checklist_entry["sha256"]: + raise ValueError("Checklist export differs from the benchmark figure manifest") + subprocess.run(["git", "-C", str(benchmark), "ls-files", "--error-unmatch", "--", str(CHECKLIST_SOURCE), str(FIGURE_MANIFEST)], check=True, stdout=subprocess.DEVNULL) + subprocess.run(["git", "-C", str(benchmark), "diff", "--quiet", "HEAD", "--", str(CHECKLIST_SOURCE), str(FIGURE_MANIFEST)], check=True) + COPY.parent.mkdir(parents=True, exist_ok=True) + COPY.write_bytes(source.read_bytes()) + CHECKLIST_COPY.write_bytes((benchmark / CHECKLIST_SOURCE).read_bytes()) + BINDING.write_text(json.dumps({ + "schema_version": 2, + "repository": "https://github.com/leej3/stamped-in-practice", + "branch": "codex/stamped-poster-analysis", "revision": revision, + "source": SOURCE.as_posix(), "sha256": digest(COPY), + "checklists": {"source": CHECKLIST_SOURCE.as_posix(), "sha256": digest(CHECKLIST_COPY), + "manifest": FIGURE_MANIFEST.as_posix(), "manifest_sha256": digest(benchmark / FIGURE_MANIFEST)}, + "scope": "Display copy; aggregation and run-level evidence remain in the benchmark.", + }, indent=2) + "\n") + binding = json.loads(BINDING.read_text()) + if digest(COPY) != binding["sha256"]: + raise ValueError("Poster outcome display copy changed") + if digest(CHECKLIST_COPY) != binding["checklists"]["sha256"]: + raise ValueError("Poster checklist display copy changed") + summary = json.loads(COPY.read_text()) + rows = table_rows(summary, json.loads(CHECKLIST_COPY.read_text())) + rounds = summary["retained_rounds"] + description = "Rounds " + ", ".join(map(str, rounds)) + f'; {sum(row["assigned_runs"] for row in summary["conditions"])} research runs.' + html_path = ROOT / "index.html" + html = html_path.read_text() + block = START + "\n" + rows + "\n " + END + rendered, count = re.subn(re.escape(START) + ".*?" + re.escape(END), lambda _: block, html, flags=re.S) + if count != 1: + raise ValueError("Expected one benchmark outcome table") + rendered, count = re.subn(r'().*?()', lambda m: m[1] + description + m[2], rendered) + if count != 1: + raise ValueError("Expected one retained-round description") + if args.benchmark: + html_path.write_text(rendered) + elif rendered != html: + raise ValueError("Poster table differs from its benchmark summary; reimport it") + print(json.dumps({"verified_condition_rows": 4, "retained_rounds": rounds, "benchmark_revision": binding["revision"]})) + + +if __name__ == "__main__": + main() diff --git a/2026-usrse/stamped-ai-study/source-manifest.json b/2026-usrse/stamped-ai-study/source-manifest.json new file mode 100644 index 00000000..cf5b0b1a --- /dev/null +++ b/2026-usrse/stamped-ai-study/source-manifest.json @@ -0,0 +1,49 @@ +{ + "reference": { + "repository": "https://github.com/con/talks", + "pull_request": 20, + "commit": "8a15964ed5cbcd07b04d1f325e848c788e672b05", + "html": "2026-usrse/orinoco-lite_poster.html" + }, + "submitted_title": "STAMPED in Practice: Reproducing a Scientific Result Using ABCD Neuroimaging Data", + "current_scope": "NARPS group gain-effect reproduction and STAMPED skill development, with retained results from three rounds and guides to interpreting the evidence.", + "authors": [ + "John A. Lee", + "Austin Macdonald", + "Cody C. Baker", + "Yaroslav O. Halchenko" + ], + "assets": { + "con-logo-outlined.svg": { + "bytes": 125811, + "md5": "5429db5139ba49cc5a94dceb1532abe0", + "sha256": "076adc1bf4e2d9dba5983e22f753f562a7408c8a3393adea281c5478f64f7ee1", + "source": "2026-usrse/orinoco-lite/assets/con-logo-outlined.svg", + "local_path": "../orinoco-lite/assets/con-logo-outlined.svg", + "reused_from_repository": true + }, + "con-ccn-dartmouth-letterhead.svg": { + "bytes": 379034, + "md5": "be7ae71a14ff2301bb0cf1cde08457e9", + "sha256": "69dfcc6cd70367b7a03b19982589ac7d2180fdf6723bbb17ae2361c6c356d625", + "source": "2026-usrse/orinoco-lite/assets/con-ccn-dartmouth-letterhead.svg", + "local_path": "../orinoco-lite/assets/con-ccn-dartmouth-letterhead.svg", + "reused_from_repository": true + }, + "repronim_logo.svg": { + "bytes": 33939, + "md5": "cfe9b83acfb1f1292027c0a214c4b0f9", + "sha256": "0e1101fa2dca811587d0ad4caa040961da5156e11b9b23f64f29ca3463d84870", + "source": "2026-usrse/orinoco-lite/assets/repronim_logo.svg", + "local_path": "../orinoco-lite/assets/repronim_logo.svg", + "reused_from_repository": true + }, + "orinoco-qr-con.svg": { + "bytes": 67605, + "sha256": "9f5725bea98bf4b3b4b4a9479bdc734529b19db205089b291ee86e43320b1d49", + "source": "2026-usrse/orinoco-lite/assets/orinoco-qr-con.svg", + "local_path": "../orinoco-lite/assets/orinoco-qr-con.svg", + "reused_from_repository": true + } + } +} diff --git a/2026-usrse/stamped-ai-study/template.css b/2026-usrse/stamped-ai-study/template.css new file mode 100644 index 00000000..32100f02 --- /dev/null +++ b/2026-usrse/stamped-ai-study/template.css @@ -0,0 +1,128 @@ +/* SPDX-License-Identifier: CC-BY-SA-4.0 + * Adapted from con/talks PR 20, 8a15964ed5cbcd07b04d1f325e848c788e672b05. + * All poster text has a minimum 32 CSS px (24 pt) at full size. */ + + /* Editable 44 × 44 inch poster. Screen and print share the same canvas. */ + :root { + --paper: #f6f2e9; --ink: #193c4d; --green: #286857; + --muted: #526c76; --rule: #cbd6ce; --tint: #e6eee5; + --body-text: 36px; --con-blue: #87aade; + --warm: #b55c28; --canvas-width: 4224px; --canvas-height: 4224px; + } + * { box-sizing: border-box; } + body { margin: 0; background: #d8ddd9; color: var(--ink); font-family: Arial, Helvetica, sans-serif; } + a { color: inherit; text-decoration-thickness: 2px; text-underline-offset: 5px; } + a:focus-visible { outline: 6px solid var(--warm); outline-offset: 6px; } + .screen-tools { display: flex; gap: 18px; align-items: center; padding: 14px 24px; font-size: 32px; } + .screen-tools button { padding: 7px 14px; border: 1px solid #94a49a; border-radius: 5px; color: var(--ink); background: white; cursor: pointer; } + .screen-tools a { margin-left: auto; } + #viewport { position: relative; margin: 0 auto 24px; } + .poster { width: var(--canvas-width); height: var(--canvas-height); transform-origin: top left; + background: var(--paper); border-top: 24px solid var(--green); padding: 60px 88px 58px; + display: grid; grid-template-rows: 350px 286px 1fr 280px; gap: 36px; } + .masthead { display: grid; grid-template-columns: 1.15fr 840px 1fr; gap: 78px; align-items: center; } + .eyebrow { color: var(--green); font-size: 32px; font-weight: 700; text-transform: uppercase; letter-spacing: 2px; margin: 0 0 22px; } + h1 { margin: 0; font-size: 91px; line-height: 1.03; letter-spacing: -2px; } + h1 span { display: block; margin-top: 22px; font-size: 48px; font-weight: 400; letter-spacing: 0; line-height: 1.17; } + .con-logo { display: block; width: 840px; } + .author-panel { display: flex; align-items: center; gap: 52px; justify-self: end; } + .authors { font-size: 43px; line-height: 1.25; } + .authors p { margin: 0; } + .authors .name { display: block; } + .authors .affiliation { font-size: 32px; margin-top: 22px; color: var(--muted); line-height: 1.3; } + .lead { background: var(--ink); color: white; margin: 0 -88px; padding: 34px 88px; + display: grid; grid-template-columns: 1fr 1fr; gap: 76px; align-items: center; } + .lead p { margin: 0; font-size: 39px; line-height: 1.33; } + .lead .pitch { border-left: 3px solid #647d86; padding-left: 64px; } + .pitch strong { display: block; font-size: 45px; line-height: 1.2; margin-bottom: 18px; } + .pitch span { font-size: 35px; } + .columns { display: grid; grid-template-columns: 2fr 1fr; gap: 44px; min-height: 0; } + .comparison { display: grid; grid-template-columns: 1fr 1fr; grid-template-rows: auto 1fr; gap: 36px 42px; min-height: 0; } + .deployment { min-width: 0; } + .deployment + .deployment { border-left: 2px solid var(--rule); padding-left: 40px; } + .outcomes { border-left: 2px solid var(--rule); padding-left: 40px; display: flex; flex-direction: column; min-height: 0; } + .outcomes > * { flex-shrink: 0; } + .section-label { margin: 0 0 14px; color: var(--green); font-size: 32px; letter-spacing: 1.7px; text-transform: uppercase; font-weight: 700; } + h2 { margin: 0 0 22px; font-size: 63px; line-height: 1.08; } + h3 { margin: 0 0 24px; font-size: 46px; line-height: 1.15; } + .intro { font-size: 37px; line-height: 1.34; margin: 0; } + .column-head { height: 350px; position: relative; } + .with-video h2, .with-video .intro { margin-right: 242px; } + .with-video .video-qr { position: absolute; top: 45px; right: 0; } + figure { margin: 0; } + .image-link { display: block; } + .component-art { height: 550px; } + .component-art img { width: 100%; height: 100%; object-fit: contain; display: block; } + .diagram-note { min-height: 238px; display: grid; grid-template-columns: 1fr 214px; gap: 32px; align-items: center; } + .component-figure { margin-bottom: 18px; } + figcaption { font-size: 32px; line-height: 1.35; color: var(--muted); } + figcaption strong { color: var(--ink); } + .art-credit { display: block; font-size: 32px; margin-top: 12px; } + .qr-badge { display: flex; flex-direction: column; align-items: center; gap: 8px; width: 214px; color: var(--ink); text-decoration: none; text-align: center; font-size: 32px; line-height: 1.15; font-weight: 700; } + .qr-badge img { width: 204px; height: 204px; display: block; background: white; border-radius: 7px; } + .site-pair { display: grid; grid-template-columns: 1fr 1fr; gap: 20px; } + .figure { background: white; border: 2px solid var(--rule); border-radius: 12px; overflow: hidden; } + .figure img { display: block; width: 100%; height: 100%; object-fit: contain; } + .webshot { height: 740px; } + .webshot img { object-fit: contain; object-position: top center; } + .site-pair figcaption { font-size: 32px; margin-top: 12px; } + .site-caption { display: grid; grid-template-columns: 1fr 214px; gap: 30px; align-items: center; min-height: 242px; } + .site-caption h3 { font-size: 39px; margin: 0 0 13px; } + .site-caption p { font-size: 32px; line-height: 1.35; margin: 0; color: var(--muted); } + .shared-editor { grid-column: 1 / -1; border-top: 6px solid var(--green); padding-top: 32px; display: grid; grid-template-columns: 1.6fr 1fr; gap: 46px; align-items: center; min-height: 0; } + .editor { height: 730px; } + .editor img { object-fit: contain; object-position: center; } + .shared-editor figcaption { margin-top: 14px; } + .editor-copy h2 { font-size: 61px; margin: 0 0 30px; } + .editor-copy p { font-size: 40px; line-height: 1.4; margin: 0 0 27px; } + .editor-copy .editor-caption { color: var(--muted); font-size: 32px; } + .workflow-example { display: grid; grid-template-columns: 1fr 214px; gap: 28px; align-items: center; border-top: 2px solid var(--rule); padding-top: 22px; } + .editor-copy .workflow-example p { font-size: 32px; line-height: 1.35; margin: 0; } + .value-section { margin-top: 28px; } + .value-section p { margin: 0 0 28px; font-size: var(--body-text); line-height: 1.4; } + .local-value { display: grid; grid-template-columns: .75fr 1.25fr; gap: 30px; align-items: center; } + .local-value .graph-description { margin: 0; } + .graph-copy .qr-badge { margin-top: 30px; } + .graph { height: 890px; background: transparent; border: 0; } + .graph img { object-fit: contain; } + .local-value figcaption { font-size: 32px; margin-top: 12px; } + .meaning { margin-top: 52px; border-top: 3px solid var(--rule); padding-top: 32px; } + .meaning h3 { font-size: 50px; } + .meaning p { font-size: 36px; } + .linked-records { margin: 18px 0 28px; } + .linked-records svg { display: block; width: 100%; height: auto; } + .linked-records .source { fill: var(--ink); font-size: 32px; font-weight: 700; } + .linked-records .node { fill: var(--tint); stroke: var(--rule); stroke-width: 2px; } + .linked-records .name { fill: var(--ink); font-size: 32px; font-weight: 700; } + .linked-records .match { fill: var(--green); font-size: 32px; font-weight: 700; } + .linked-records .relation { fill: var(--ink); font-size: 32px; } + .linked-records .vocabulary { fill: var(--muted); font-size: 32px; } + .ai-copy { border-top: 3px solid var(--rule); padding-top: 32px; } + .report-example { font-size: 34px; line-height: 1.4; padding: 28px; background: var(--tint); margin-top: 32px; } + .report-example strong { display: block; font-size: 38px; margin-bottom: 15px; } + .callout { margin-top: auto; border-top: 7px solid var(--warm); background: #f0e4d5; padding: 32px; font-size: 37px; line-height: 1.4; } + .callout h3 { font-size: 42px; margin-bottom: 20px; } + .callout p { margin: 0; } + .callout p + p { margin-top: 18px; } + .footer { border-top: 3px solid var(--rule); padding-top: 28px; display: grid; grid-template-columns: 1.1fr 1fr; gap: 70px; align-items: center; } + .footer p { margin: 0 0 14px; font-size: 32px; line-height: 1.3; } + .footer .thanks { color: var(--muted); font-size: 32px; } + .snapshot strong { color: var(--green); } + .snapshot a { white-space: nowrap; } + .partners { display: flex; align-items: center; justify-content: space-between; gap: 35px; } + .partners img { max-height: 140px; max-width: 440px; object-fit: contain; } + .partners .repronim { width: 146px; height: 146px; } + .partners .dartmouth { width: 126px; height: 136px; object-fit: fill; } + .partner-affiliation { display: flex; gap: 22px; align-items: center; font-size: 32px; line-height: 1.3; color: #00693e; } + .partner-affiliation strong { display: block; font-size: 33px; } + .partner-affiliation a { text-decoration: none; } + .partners .psychoinformatics { display: flex; align-items: center; gap: 20px; font-size: 32px; color: var(--ink); text-decoration: none; } + .partners .psychoinformatics img { width: 108px; height: 140px; } + @page { size: 44in 44in; margin: 0; } + @media print { + html, body { width: 44in; height: 44in; background: white; print-color-adjust: exact; -webkit-print-color-adjust: exact; } + .screen-tools { display: none; } + #viewport { width: 44in !important; height: 44in !important; margin: 0; } + .poster { transform: none !important; break-inside: avoid; } + } + diff --git a/2026-usrse/stamped-ai-study/verify-links.py b/2026-usrse/stamped-ai-study/verify-links.py new file mode 100644 index 00000000..596a6de1 --- /dev/null +++ b/2026-usrse/stamped-ai-study/verify-links.py @@ -0,0 +1,72 @@ +#!/usr/bin/env python3 +# SPDX-FileCopyrightText: 2026 Center for Open Neuroscience +# SPDX-License-Identifier: Apache-2.0 +"""Check published destinations from a current poster layout audit. + +This read-only network check records endpoint availability, not scientific +validity or the retrievability of every asset linked from those pages. +""" +import argparse +from concurrent.futures import ThreadPoolExecutor +from datetime import datetime, timezone +import hashlib +import json +from pathlib import Path +import urllib.error +import urllib.parse +import urllib.request + + +def inspect(url): + parsed = urllib.parse.urlsplit(url) + if parsed.scheme != 'https' or parsed.username or parsed.password: + return {'url': url, 'passed': False, 'error': 'Expected public HTTPS URL'} + row = {'url': url, 'checked_at': datetime.now(timezone.utc).isoformat()} + for method in ('HEAD', 'GET'): + try: + request = urllib.request.Request(url, method=method, + headers={'User-Agent': 'STAMPED-poster-link-check/1.0'}) + with urllib.request.urlopen(request, timeout=30) as response: + row.update(method=method, http_status=response.status, + final_url=response.url, passed=200 <= response.status < 300) + if method == 'GET': + row['body_read_limit'] = 65536 + row['prefix_sha256'] = hashlib.sha256(response.read(65536)).hexdigest() + return row + except urllib.error.HTTPError as error: + if method == 'HEAD' and error.code in (403, 405): + continue + row.update(method=method, http_status=error.code, passed=False) + return row + except (urllib.error.URLError, TimeoutError) as error: + row.update(method=method, passed=False, error=str(error)) + return row + return row + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument('--review-dir', required=True, type=Path) + args = parser.parse_args() + root = args.review_dir.resolve(strict=True) + audit_path = root / 'html-audit.json' + raw = audit_path.read_bytes() + audit = json.loads(raw) + links = sorted(set(audit['links'])) + if not links: + raise SystemExit('No poster links in the layout audit') + with ThreadPoolExecutor(max_workers=4) as pool: + results = list(pool.map(inspect, links)) + report = {'html_audit_sha256': hashlib.sha256(raw).hexdigest(), + 'checked_at': datetime.now(timezone.utc).isoformat(), + 'authentication': 'none', 'results': results, + 'all_passed': all(row['passed'] for row in results), + 'scope': 'Public destination HTTP availability; annex content integrity is checked separately.'} + (root / 'link-audit.json').write_text(json.dumps(report, indent=2) + '\n') + print(json.dumps({'links': len(links), 'passed': sum(r['passed'] for r in results), + 'report': str(root / 'link-audit.json')})) + raise SystemExit(0 if report['all_passed'] else 1) + + +if __name__ == '__main__': + main() diff --git a/2026-usrse/stamped-ai-study/verify-pdf.py b/2026-usrse/stamped-ai-study/verify-pdf.py new file mode 100644 index 00000000..52473352 --- /dev/null +++ b/2026-usrse/stamped-ai-study/verify-pdf.py @@ -0,0 +1,99 @@ +# SPDX-FileCopyrightText: 2026 Center for Open Neuroscience +# SPDX-License-Identifier: Apache-2.0 +# /// script +# requires-python = ">=3.11" +# dependencies = ["pypdf==6.0.0", "Pillow==11.3.0", "zxing-cpp==2.3.0"] +# /// +"""Verify the exported page, PDF links, and every QR from the actual PDF raster. + +uv run verify-pdf.py --review-dir /absolute/review-directory +Requires pdftoppm. The report does not replace human visual review. +""" +import argparse +import hashlib +import json +from math import hypot +from pathlib import Path +import subprocess + +from PIL import Image +from pypdf import PdfReader +import zxingcpp + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--review-dir", required=True, type=Path) + args = parser.parse_args() + root = args.review_dir.resolve() + pdf = root / "stamped-ai-poster.pdf" + audit = json.loads((root / "html-audit.json").read_text()) + reader = PdfReader(pdf) + assert len(reader.pages) == 1, f"Expected one page, got {len(reader.pages)}" + page = reader.pages[0] + width, height = float(page.mediabox.width), float(page.mediabox.height) + assert abs(width - 3168) < 0.1 and abs(height - 3168) < 0.1, (width, height) + uris = [] + for ref in page.get("/Annots", []): + ann = ref.get_object() + action = ann.get("/A", {}) + if action.get("/S") == "/URI": + uris.append(str(action.get("/URI"))) + missing = sorted(set(audit["links"]) - set(uris)) + assert not missing, f"Missing clickable PDF links: {missing}" + assert audit["minimum_text_px"] >= 32 + font_sizes = [] + + def inspect_text(text, current_matrix, text_matrix, font, font_size): + if not text.strip(): + return + # Transform the text-space vertical unit vector into page points. + # Chromium records CSS font sizes with a 0.75 page scale. Include both + # matrices so a transformed text node cannot evade the 24-point floor. + cm, tm = current_matrix, text_matrix + scale = hypot(tm[2] * cm[0] + tm[3] * cm[2], + tm[2] * cm[1] + tm[3] * cm[3]) + font_sizes.append({"text": text.strip()[:100], "points": font_size * scale}) + + page.extract_text(visitor_text=inspect_text) + assert font_sizes, "No inspectable PDF text; cannot establish font sizes" + small_pdf_text = [row for row in font_sizes if row["points"] < 24 - 0.001] + assert not small_pdf_text, f"PDF text smaller than 24 pt: {small_pdf_text}" + # The full page is also the visual-review image. Actual PDF pixels are the + # source for QR checks, not the original SVG or a browser screenshot. + dpi = 150 + subprocess.run(["pdftoppm", "-f", "1", "-singlefile", "-r", str(dpi), + "-png", str(pdf), str(root / "pdf-fullsize")], check=True) + Image.MAX_IMAGE_PIXELS = 100_000_000 + raster = Image.open(root / "pdf-fullsize.png").convert("RGB") + sx, sy = raster.width / 4224, raster.height / 4224 + qrs = [] + for qr in audit["qrs"]: + r = qr["rect"] + # White quiet zone is already in the SVG; add only a two-pixel margin. + crop = raster.crop((int(r["x"] * sx) - 2, int(r["y"] * sy) - 2, + round((r["x"] + r["width"]) * sx) + 2, + round((r["y"] + r["height"]) * sy) + 2)) + crop.save(root / f"pdf-qr-{qr['name']}.png") + decoded = [b.text for b in zxingcpp.read_barcodes(crop)] + rotated = [b.text for b in zxingcpp.read_barcodes(crop.transpose(Image.Transpose.ROTATE_90))] + qrs.append({"name": qr["name"], "expected": qr["url"], "decoded": decoded, + "decoded_rotated": rotated, "passed": decoded == [qr["url"]] and rotated == [qr["url"]]}) + preview = raster.copy() + preview.thumbnail((1600, 1600)) + preview.save(root / "pdf-preview.png") + report = {"pdf_sha256": hashlib.sha256(pdf.read_bytes()).hexdigest(), + "page_count": len(reader.pages), "page_points": [width, height], + "minimum_html_text_px": audit["minimum_text_px"], "minimum_html_text_pt": audit["minimum_text_px"] * 72 / 96, + "minimum_pdf_text_pt": round(min(row["points"] for row in font_sizes), 4), + "inspected_pdf_text_runs": len(font_sizes), + "link_annotation_count": len(uris), "unique_expected_links": len(audit["links"]), + "missing_links": missing, "raster_dpi": dpi, "qr_results": qrs, + "visual_review": "Required separately; not established by this script."} + (root / "pdf-audit.json").write_text(json.dumps(report, indent=2) + "\n") + assert qrs and all(q["passed"] for q in qrs), "A PDF QR failed; inspect pdf-audit.json" + print(json.dumps({"page_inches": [width / 72, height / 72], "qrs_passed": len(qrs), "links_present": len(set(uris)), "report": str(root / "pdf-audit.json")})) + + +if __name__ == "__main__": + main() diff --git a/INDEX.md b/INDEX.md index e07f1110..9734539c 100644 --- a/INDEX.md +++ b/INDEX.md @@ -532,6 +532,12 @@ Cross-references in the per-topic lookup point at the shelved path ## Posters +### `2026-usrse/stamped-ai-study/index.html` — *STAMPED in Practice* + +- US-RSE 2026 poster comparing research-skill assistance across three rounds. +- [Editable poster, verified PDF and research evidence](2026-usrse/stamped-ai-study/README.md). + + Posters are not reveal.js decks and have no slide IDs. HTML posters live in their venue directory; `tools/create_index.sh` lists them (with a *poster* tag) on `index.html` from its hand-maintained `LISTED` array — diff --git a/REUSE.toml b/REUSE.toml index 32896a00..804a679e 100644 --- a/REUSE.toml +++ b/REUSE.toml @@ -499,3 +499,80 @@ path = "2026-usrse/orinoco-lite/assets/repronim_logo.svg" precedence = "aggregate" SPDX-FileCopyrightText = "NOASSERTION" SPDX-License-Identifier = "LicenseRef-ThirdPartyLogo" + +# STAMPED example poster source and verification reports. +# Institutional artwork retains its separate attribution below. +[[annotations]] +path = [ + "2026-usrse/stamped-ai-study/index.html", + "2026-usrse/stamped-ai-study/*.css", + "2026-usrse/stamped-ai-study/*.md", + "2026-usrse/stamped-ai-study/*.json", + "2026-usrse/stamped-ai-study/.gitattributes", + "2026-usrse/stamped-ai-study/.gitignore", + "2026-usrse/stamped-ai-study/exports/*.json", + "2026-usrse/stamped-ai-study/exports/qr-source/decode-report.json", + "2026-usrse/stamped-ai-study/assets/stamped-qr-*.svg", + "2026-usrse/stamped-ai-study/exports/pdf-qr-*.png", + "2026-usrse/stamped-ai-study/exports/qr-source/*.png", +] +precedence = "closest" +SPDX-FileCopyrightText = "2026 Center for Open Neuroscience" +SPDX-License-Identifier = "CC-BY-SA-4.0" + +# Reference layout from con/talks PR 20, pinned in source-manifest.json. +[[annotations]] +path = "2026-usrse/stamped-ai-study/template.css" +precedence = "aggregate" +SPDX-FileCopyrightText = ["2026 John Lee", "2026 Isaac To", "2026 Yaroslav O. Halchenko", "2026 Center for Open Neuroscience"] +SPDX-License-Identifier = "CC-BY-SA-4.0" + +[[annotations]] +path = [ + "2026-usrse/stamped-ai-study/build-poster.cjs", + "2026-usrse/stamped-ai-study/make-logo-qrs.py", + "2026-usrse/stamped-ai-study/verify-links.py", + "2026-usrse/stamped-ai-study/verify-pdf.py", +] +precedence = "closest" +SPDX-FileCopyrightText = "2026 Center for Open Neuroscience" +SPDX-License-Identifier = "Apache-2.0" + +# Shared institutional artwork and CON QR retain the existing PR 20 annotations. + +# CC-BY-SA covers the poster composition, not its embedded institutional marks. +[[annotations]] +path = [ + "2026-usrse/stamped-ai-study/exports/stamped-ai-poster.pdf", + "2026-usrse/stamped-ai-study/exports/html-fullsize.png", + "2026-usrse/stamped-ai-study/exports/pdf-fullsize.png", + "2026-usrse/stamped-ai-study/exports/pdf-preview.png", +] +precedence = "aggregate" +SPDX-FileCopyrightText = ["2026 Center for Open Neuroscience (composition)", "Dartmouth College (institutional artwork)", "NOASSERTION"] +SPDX-License-Identifier = "CC-BY-SA-4.0 AND LicenseRef-ThirdPartyLogo" + +# Reproducible NARPS poster code and generated evidence. +[[annotations]] +path = ["2026-usrse/stamped-ai-study/scripts/*.py", "2026-usrse/stamped-ai-study/pixi.toml", "2026-usrse/stamped-ai-study/package*.json"] +precedence = "closest" +SPDX-FileCopyrightText = "2026 Center for Open Neuroscience" +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "2026-usrse/stamped-ai-study/figures/*.json" +precedence = "closest" +SPDX-FileCopyrightText = "2026 Center for Open Neuroscience" +SPDX-License-Identifier = "CC-BY-SA-4.0" + +[[annotations]] +path = ["2026-usrse/stamped-ai-study/figures/narps-group-map.*", "2026-usrse/stamped-ai-study/figures/narps-spatial-agreement.*"] +precedence = "override" +SPDX-FileCopyrightText = ["2026 Center for Open Neuroscience (composition)", "NOASSERTION"] +SPDX-License-Identifier = "CC-BY-SA-4.0 AND LicenseRef-ThirdPartyMixed" + +[[annotations]] +path = "2026-usrse/stamped-ai-study/figures/round-progression.*" +precedence = "override" +SPDX-FileCopyrightText = "2026 Center for Open Neuroscience" +SPDX-License-Identifier = "CC-BY-SA-4.0"