From e44099c4dac75153708ee7af389c09165242d8f8 Mon Sep 17 00:00:00 2001 From: koji Date: Wed, 16 Sep 2026 03:36:46 -0400 Subject: [PATCH 1/5] update the website --- src/App.tsx | 2 + .../AiWorkflow/AiWorkflow.module.css | 74 ++++++++++++++++ src/components/AiWorkflow/AiWorkflow.test.tsx | 41 +++++++++ src/components/AiWorkflow/AiWorkflow.tsx | 84 +++++++++++++++++++ 4 files changed, 201 insertions(+) create mode 100644 src/components/AiWorkflow/AiWorkflow.module.css create mode 100644 src/components/AiWorkflow/AiWorkflow.test.tsx create mode 100644 src/components/AiWorkflow/AiWorkflow.tsx diff --git a/src/App.tsx b/src/App.tsx index aaff810..52ca598 100644 --- a/src/App.tsx +++ b/src/App.tsx @@ -3,6 +3,7 @@ import { useTheme } from './hooks/useTheme' import { Header } from './components/Header/Header' import { Hero } from './components/Hero/Hero' import { Features } from './components/Features/Features' +import { AiWorkflow } from './components/AiWorkflow/AiWorkflow' import { Screenshot } from './components/Screenshot/Screenshot' import { TryCta } from './components/TryCta/TryCta' import { Install } from './components/Install/Install' @@ -18,6 +19,7 @@ export default function App(): ReactNode {
+ diff --git a/src/components/AiWorkflow/AiWorkflow.module.css b/src/components/AiWorkflow/AiWorkflow.module.css new file mode 100644 index 0000000..9a96f1b --- /dev/null +++ b/src/components/AiWorkflow/AiWorkflow.module.css @@ -0,0 +1,74 @@ +.section { + padding-block: 32px 88px; +} + +.heading { + margin: 0 0 16px; + font-size: clamp(1.5rem, 3vw, 2rem); + letter-spacing: -0.01em; +} + +.lead { + max-width: 72ch; + margin: 0 0 32px; + color: var(--color-text-muted); + font-size: 1rem; + line-height: 1.6; +} + +.link { + color: var(--color-accent-strong); +} + +.figure { + margin: 0 0 32px; +} + +.video { + display: block; + width: 100%; + height: auto; + border: 1px solid var(--color-border); + border-radius: 16px; + background: var(--color-surface); +} + +.caption { + margin-top: 12px; + color: var(--color-text-muted); + font-size: 0.9rem; + text-align: center; +} + +.subHeading { + margin: 0 0 12px; + font-size: 1.05rem; +} + +.steps { + max-width: 72ch; + margin: 0; + padding: 24px 24px 24px 42px; + border: 1px solid var(--color-border); + border-radius: 14px; + background: var(--color-surface); + color: var(--color-text-muted); + font-size: 0.95rem; + line-height: 1.6; +} + +.steps li + li { + margin-top: 8px; +} + +.codeInline { + padding: 2px 6px; + border-radius: 6px; + background: color-mix(in srgb, var(--color-accent) 12%, transparent); + color: var(--color-accent-strong); + font-size: 0.85em; +} + +.muted { + font-size: 0.9em; +} diff --git a/src/components/AiWorkflow/AiWorkflow.test.tsx b/src/components/AiWorkflow/AiWorkflow.test.tsx new file mode 100644 index 0000000..ce2f0af --- /dev/null +++ b/src/components/AiWorkflow/AiWorkflow.test.tsx @@ -0,0 +1,41 @@ +import { render, screen } from '@testing-library/react' +import { describe, expect, it } from 'vitest' +import { AiWorkflow } from './AiWorkflow' + +describe('AiWorkflow', () => { + it('anchors at id=ai-workflow', () => { + render() + expect(screen.getByLabelText('Generate protocols with AI')).toHaveAttribute( + 'id', + 'ai-workflow', + ) + }) + + it('links to the protocol-fix-loop skill repo', () => { + render() + const links = screen.getAllByRole('link', { name: /protocol-fix-loop/i }) + expect(links.length).toBeGreaterThanOrEqual(1) + for (const link of links) { + expect(link).toHaveAttribute( + 'href', + 'https://github.com/koji/protocol-fix-loop', + ) + } + }) + + it('shows the demo video and usage steps', () => { + render() + const video = document.querySelector('video') + expect(video).not.toBeNull() + expect(video?.getAttribute('src')).toBe( + 'https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf', + ) + expect( + screen.getByText('npx skills add koji/protocol-fix-loop'), + ).toBeInTheDocument() + expect(screen.getByText('/protocol-fix-loop')).toBeInTheDocument() + expect( + screen.getByText(/Install VSCode or Cursor/i), + ).toBeInTheDocument() + }) +}) diff --git a/src/components/AiWorkflow/AiWorkflow.tsx b/src/components/AiWorkflow/AiWorkflow.tsx new file mode 100644 index 0000000..4a3ffca --- /dev/null +++ b/src/components/AiWorkflow/AiWorkflow.tsx @@ -0,0 +1,84 @@ +import type { ReactNode } from 'react' +import styles from './AiWorkflow.module.css' + +const DEMO_VIDEO = + 'https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf' +const SKILL_REPO = 'https://github.com/koji/protocol-fix-loop' +const SKILL_INSTALL_COMMAND = 'npx skills add koji/protocol-fix-loop' + +export function AiWorkflow(): ReactNode { + return ( +
+
+

+ Generate protocols with AI, verify with Protocol Visualizer +

+

+ Connect Protocol Visualizer to your LLM with{' '} + + protocol-fix-loop + + . Generate Opentrons protocols with GitHub Copilot or Cursor, then + simulate and fix them in a visual feedback loop. +

+ +
+ +
+ Generate a protocol from a prompt, then fix it while watching the + simulation +
+
+ +

How to use

+
    +
  1. Install VSCode or Cursor
  2. +
  3. + Install the skill:{' '} + {SKILL_INSTALL_COMMAND}{' '} + + (see{' '} + + koji/protocol-fix-loop + + ) + +
  4. +
  5. + Install the Protocol Visualizer extension (see{' '} + + Installation guide + + ) +
  6. +
  7. + Use /protocol-fix-loop{' '} + in chat and add your prompt to generate a protocol +
  8. +
+
+
+ ) +} From be8d956bebe4c0af1ce600129c9e73abb0906b9d Mon Sep 17 00:00:00 2001 From: koji Date: Wed, 16 Sep 2026 03:49:47 -0400 Subject: [PATCH 2/5] add verification skill --- .opencode/skills/verify-web/SKILL.md | 126 + .../ai-workflow/axtree.json | 12018 ++++++++++++++++ .../ai-workflow/dom.html | 616 + .../ai-workflow/result.json | 55 + .../ai-workflow/screenshot.png | Bin 0 -> 50645 bytes .../features-grid/axtree.json | 12018 ++++++++++++++++ .../features-grid/dom.html | 616 + .../features-grid/result.json | 35 + .../features-grid/screenshot.png | Bin 0 -> 51914 bytes .../2026-09-16T07-46-20-848Z/hero/axtree.json | 12018 ++++++++++++++++ .../2026-09-16T07-46-20-848Z/hero/dom.html | 616 + .../2026-09-16T07-46-20-848Z/hero/result.json | 45 + .../hero/screenshot.png | Bin 0 -> 185579 bytes .../install-guide/axtree.json | 12018 ++++++++++++++++ .../install-guide/dom.html | 616 + .../install-guide/result.json | 53 + .../install-guide/screenshot.png | Bin 0 -> 50301 bytes .../theme-toggle/axtree.json | 12018 ++++++++++++++++ .../theme-toggle/dom.html | 616 + .../theme-toggle/result.json | 37 + .../theme-toggle/screenshot.png | Bin 0 -> 185652 bytes .../2026-09-16T07-46-20-848Z/vite-server.log | 11 + .../skills/verify-web/features/README.md | 47 + .../skills/verify-web/features/ai-workflow.md | 36 + .../verify-web/features/features-grid.md | 31 + .opencode/skills/verify-web/features/hero.md | 35 + .../verify-web/features/install-guide.md | 36 + .../verify-web/features/theme-toggle.md | 32 + .../skills/verify-web/scripts/doctor.mjs | 50 + .opencode/skills/verify-web/scripts/drive.mjs | 486 + .../skills/verify-web/scripts/verify.mjs | 151 + docs/verification.md | 74 + 32 files changed, 64510 insertions(+) create mode 100644 .opencode/skills/verify-web/SKILL.md create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/dom.html create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/result.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/screenshot.png create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/axtree.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/dom.html create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/result.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/screenshot.png create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/axtree.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/dom.html create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/result.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/screenshot.png create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/axtree.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/result.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/screenshot.png create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/axtree.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/dom.html create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/result.json create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/screenshot.png create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/vite-server.log create mode 100644 .opencode/skills/verify-web/features/README.md create mode 100644 .opencode/skills/verify-web/features/ai-workflow.md create mode 100644 .opencode/skills/verify-web/features/features-grid.md create mode 100644 .opencode/skills/verify-web/features/hero.md create mode 100644 .opencode/skills/verify-web/features/install-guide.md create mode 100644 .opencode/skills/verify-web/features/theme-toggle.md create mode 100644 .opencode/skills/verify-web/scripts/doctor.mjs create mode 100644 .opencode/skills/verify-web/scripts/drive.mjs create mode 100644 .opencode/skills/verify-web/scripts/verify.mjs create mode 100644 docs/verification.md diff --git a/.opencode/skills/verify-web/SKILL.md b/.opencode/skills/verify-web/SKILL.md new file mode 100644 index 0000000..0da714f --- /dev/null +++ b/.opencode/skills/verify-web/SKILL.md @@ -0,0 +1,126 @@ +--- +name: verify-web +description: Drive and prove the protocol-visualizer-web landing page (Vite + React static marketing site) in real headless Chromium. Use when verifying any user-facing behavior of the site — hero, feature cards, AI workflow section, theme toggle, install guide — or after changing components under src/. +--- + +# Verify protocol-visualizer-web + +This skill drives the real landing page the way a user sees it: a local `vite` +dev server plus headless Chromium over CDP. No mocks, no test-only endpoints — +the page is rendered with JavaScript and asserted through DOM state, +accessibility tree, and screenshots. + +Facts established from the repo (do not re-derive unless the repo changed): + +- **Surface:** single static marketing page (`src/App.tsx` renders `Header`, + `Hero`, `Features`, `AiWorkflow`, `Screenshot`, `TryCta`, `Install`, + `Disclaimer`, `Footer`). No backend, no auth, no database, no router. +- **Run:** `bun x vite --host 127.0.0.1 --port --strictPort` from the repo + root. Ready means HTTP 200 plus `
` in the shell. + Default verify port is `5173` (`VERIFY_PORT` overrides). +- **Drive:** `scripts/drive.mjs` launches headless Chromium (Playwright-cached + build or system Chrome, resolved automatically) with a disposable profile, + navigates over CDP, evaluates DOM assertions, and captures evidence. + Zero npm dependencies — bun built-ins only. +- **Isolate:** stateless static page. Parallel runs isolate by app port + (`VERIFY_PORT`) and CDP port (`VERIFY_CDP_PORT`, default `19222`). + Each drive uses a fresh Chromium profile, so `localStorage` never leaks + between runs. Never drive a URL you did not start (e.g. someone's + `npm run dev`); refuse and start your own. +- **Shell lifetime:** background processes do not survive across separate tool + calls in this environment. Prefer the one-shot `verify.mjs` below, which + owns the server as its own child for the whole run. + +## Launch + +Recommended one-shot (launch + doctor + drive + cleanup in one command). +Run from the repo root: + +```powershell +bun .opencode/skills/verify-web/scripts/verify.mjs --feature --port 5173 +``` + +`` is one of `hero`, `features-grid`, `ai-workflow`, `theme-toggle`, +`install-guide` (see `features/`). The run directory is +`.opencode/skills/verify-web/artifacts//` (`VERIFY_RUN_ID` overrides). + +Manual launch (only for interactive debugging; must stay in the same shell +session for subsequent steps): + +```powershell +$p = Start-Process bun -ArgumentList @('x','vite','--host','127.0.0.1','--port','5173','--strictPort') -PassThru +# ... run doctor/drive against http://127.0.0.1:5173/ ... +Stop-Process -Id $p.Id -Force +``` + +Ready signal: `Vite ready` in the log AND `doctor.mjs` exit 0. + +## Doctor + +Read-only check. Run first whenever anything looks off: + +```powershell +bun .opencode/skills/verify-web/scripts/doctor.mjs --url http://127.0.0.1:5173/ +``` + +Exit 0 with `{"ok": true, ...}` means worth driving. It asserts HTTP 200, +`
`, and a dev (`/src/main.tsx`) or built (`/assets/`) client. +It never starts, stops, or mutates anything. + +## Drive + +```powershell +bun .opencode/skills/verify-web/scripts/drive.mjs --url http://127.0.0.1:5173/ --feature --out +``` + +Optional: `--chrome ` (or `CHROME_PATH` env) pins the browser binary; +`--cdp-port ` (or `VERIFY_CDP_PORT`) isolates parallel runs. + +Recipe per run: launch Chromium with a fresh profile → open CDP → +`Page.navigate` → wait for `#root h1` → evaluate the feature's checks from +`features/.md` → `Page.captureScreenshot` → dump `outerHTML` → +`Accessibility.getFullAXTree` → write `result.json` (exit 0 only if every +check passes). The theme-toggle recipe clicks twice so the page is left in +its original theme. + +Conventions: prefer the ARIA/semantic handles named in the feature files +(`aria-label`, roles, heading text) over CSS position. Treat every command +as literal. + +## Evidence + +Per feature, `//` (or `/` for a single feature) contains: + +- `screenshot.png` — rendered page (1280×900) with app identity visible +- `dom.html` — rendered DOM after React hydration (proves content, not shell) +- `axtree.json` — full accessibility tree (proves ARIA handles) +- `result.json` — each check id, pass/fail, observed value + +Proof standards: exercise the real user path (navigate, read, click — never +vitest/jsdom or internal setters); capture the action and the resulting state +(a green check alone is not proof — the screenshot and DOM must show the +state); verify side effects (theme-toggle asserts `documentElement` theme AND +`localStorage`); mocks nowhere — there is no network boundary in this app +other than the two external demo URLs, which are asserted as attributes, not +fetched. Report unreachable paths with the command and unmet precondition; +never report a skipped entry point as verified through another path. + +## Cleanup + +`verify.mjs` always kills the vite child it started and deletes the Chromium +profile, then confirms the artifacts still exist — a cleanup that eats the +proof fails the run. For manual launches: `Stop-Process` what you started +(PID, never by process name). Cleanup removes instances and scratch state +only; proof artifacts under +`.opencode/skills/verify-web/artifacts//` are retained. + +## Helpers + +All helpers are dependency-free `bun` scripts; invocations are shown above: + +- `scripts/verify.mjs` — full run: spawn server, doctor, drive, teardown. +- `scripts/doctor.mjs` — read-only health check of a running instance. +- `scripts/drive.mjs` — CDP drive + evidence capture for `--feature`. + +Feature recipes live in `features/`; read `features/README.md` first, then +the matching feature file, before driving. diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json new file mode 100644 index 0000000..64770ab --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json @@ -0,0 +1,12018 @@ +[ + { + "nodeId": "728", + "ignored": false, + "role": { + "type": "internalRole", + "value": "RootWebArea" + }, + "chromeRole": { + "type": "internalRole", + "value": 144 + }, + "name": { + "type": "computedString", + "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + }, + { + "type": "attribute", + "attribute": "aria-label", + "superseded": true + }, + { + "type": "relatedElement", + "value": { + "type": "computedString", + "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode" + }, + "nativeSource": "title" + } + ] + }, + "properties": [ + { + "name": "focusable", + "value": { + "type": "booleanOrUndefined", + "value": true + } + }, + { + "name": "url", + "value": { + "type": "string", + "value": "http://127.0.0.1:5180/" + } + } + ], + "childIds": [ + "835" + ], + "backendDOMNodeId": 728, + "frameId": "0F19F770020C1A63EA3E621076BF1C9D" + }, + { + "nodeId": "835", + "ignored": true, + "ignoredReasons": [ + { + "name": "uninteresting", + "value": { + "type": "boolean", + "value": true + } + } + ], + "role": { + "type": "role", + "value": "none" + }, + "chromeRole": { + "type": "internalRole", + "value": 0 + }, + "parentId": "728", + "childIds": [ + "860" + ], + "backendDOMNodeId": 835 + }, + { + "nodeId": "860", + "ignored": true, + "ignoredReasons": [ + { + "name": "uninteresting", + "value": { + "type": "boolean", + "value": true + } + } + ], + "role": { + "type": "role", + "value": "none" + }, + "chromeRole": { + "type": "internalRole", + "value": 0 + }, + "parentId": "835", + "childIds": [ + "861" + ], + "backendDOMNodeId": 860 + }, + { + "nodeId": "861", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "860", + "childIds": [ + "862" + ], + "backendDOMNodeId": 861 + }, + { + "nodeId": "862", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "861", + "childIds": [ + "863", + "880", + "1065", + "1071" + ], + "backendDOMNodeId": 862 + }, + { + "nodeId": "863", + "ignored": false, + "role": { + "type": "role", + "value": "banner" + }, + "chromeRole": { + "type": "internalRole", + "value": 94 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + }, + { + "type": "attribute", + "attribute": "title" + } + ] + }, + "properties": [], + "parentId": "862", + "childIds": [ + "864" + ], + "backendDOMNodeId": 863 + }, + { + "nodeId": "880", + "ignored": false, + "role": { + "type": "role", + "value": "main" + }, + "chromeRole": { + "type": "internalRole", + "value": 118 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + }, + { + "type": "attribute", + "attribute": "title" + } + ] + }, + "properties": [], + "parentId": "862", + "childIds": [ + "881", + "897", + "925", + "1023", + "1028", + "1033" + ], + "backendDOMNodeId": 880 + }, + { + "nodeId": "1065", + "ignored": false, + "role": { + "type": "role", + "value": "complementary" + }, + "chromeRole": { + "type": "internalRole", + "value": 22 + }, + "name": { + "type": "computedString", + "value": "Disclaimer", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "value": { + "type": "computedString", + "value": "Disclaimer" + }, + "attribute": "aria-label", + "attributeValue": { + "type": "string", + "value": "Disclaimer" + } + }, + { + "type": "attribute", + "attribute": "title", + "superseded": true + } + ] + }, + "properties": [], + "parentId": "862", + "childIds": [ + "1066" + ], + "backendDOMNodeId": 1065 + }, + { + "nodeId": "1071", + "ignored": false, + "role": { + "type": "role", + "value": "contentinfo" + }, + "chromeRole": { + "type": "internalRole", + "value": 85 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + }, + { + "type": "attribute", + "attribute": "title" + } + ] + }, + "properties": [], + "parentId": "862", + "childIds": [ + "1072" + ], + "backendDOMNodeId": 1071 + }, + { + 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"properties": [], + "parentId": "1084", + "childIds": [], + "backendDOMNodeId": 1085 + } +] \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/dom.html new file mode 100644 index 0000000..ed5bc63 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/dom.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + Protocol Visualizer — Simulate Opentrons protocols in VSCode + + + +

Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
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Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
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"backendDOMNodeId": 123 + } +] \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/dom.html new file mode 100644 index 0000000..ed5bc63 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/dom.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + Protocol Visualizer — Simulate Opentrons protocols in VSCode + + + +

Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
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"relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1945", + "childIds": [], + "backendDOMNodeId": 1946 + } +] \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html new file mode 100644 index 0000000..ed5bc63 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + Protocol Visualizer — Simulate Opentrons protocols in VSCode + + + +

Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
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Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
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z4sPQ&SkOGry=S(%jk=;ndc4*h=^Vbre_m=%#S8a+x{m3K97^Tl++uW)atqFh?99gO zsS>j9DZ77L+DX63aB|0oS^};5b~~lY%~NzRN~1rfVpU(oMMQbE0Q)2-<$Qtey=;bL zvOorp_|xc>=Tag4rVUo(wjyeKVkR|mC?l2Leq^{%Xe^b6n3#&eU_~7_gIS3i4mBIx z`D!~=rwIEcR9HsYApvkVbo{xpN{9SG9u3Ha_cnMzx4nIXit6mZA6x*=!BI|2UA_7H zNRkV}!W+x5xI%G$}sBD?~{8LH~~ zI%6Q@q7*|J$jsNR77bZ9)(O?^i~zxQFFVIJN>lGmYrWah|D3Wn^*IUy;!gu*f2pZx zx~Qa84|Pv?6zqk8%k#Lbvdup@UoGR~IdG<8D@@k@dU8eW%Vn(d_Zu!aRv$*|xfjEJ z;x|?`mB3#;11vhkJKk`H+bDjQh-G3;zGs&##+ki#6!pFuY=1-I4=d@nDoKe(p4_SWGo(HK!X{<2PVjx-h)y z4SJ%l5Pvg3$1C+xDFdq8-jLUXdUpM}l#uSU?Cwsxvz)QO3HqR8vHDWF(p+ul6tiGe z8j2Q#*0`cgYeCHCXnt%Z<@@YKXOX0bx` z_hq&&&nh13Hz()yl)hzHl0>c;MMmqC6g4uY_zcCn)>s!7F!Gn)y(e6)s#9l@?JVYP zF>`. +- The theme-toggle recipe restores the original theme. Do not remove proof artifacts during cleanup. + +## Proof and skip reporting + +- Capture the user action and the resulting state, not only the final screen. +- UI proof includes the rendered DOM, the accessibility tree, and a screenshot with the app identity visible. +- State-change proof (theme toggle) includes the before/after values plus the persisted value (`localStorage`). +- Mutation proof restores the prior state in-page (theme is clicked back). +- Record the feature ID and entry point used with every artifact. +- Report an unreachable path with the attempted command and the unmet precondition. +- Do not report a skipped entry point as verified through a different path. + +## Feature entry contract + +Each feature file starts with an H1 title and one paragraph describing the user-visible behavior. It then uses exactly four H2 sections in this order. + +1. `Sub-features` lists short IDs with one line for each behavior. +2. `How to get to it (user POV)` lists every user entry point. +3. `Driving it with drive.mjs` starts with `Preconditions:` and uses labeled bullets that pair each user action with an exact command and observable result. +4. `Gotchas` lists traps that can waste or invalidate a verification run. + +Keep implementation details out of the map. Name only user paths, stable handles, required state, commands, and observable proof. + +## Features + +- [Hero](./hero.md) covers headline, tagline, request-access CTAs, and the install-guide link. +- [Features grid](./features-grid.md) covers the six feature cards under "Everything you need to see your protocol run". +- [AI workflow](./ai-workflow.md) covers the protocol-fix-loop video, skill command, and repo links. +- [Theme toggle](./theme-toggle.md) covers dark/light switching and persistence. +- [Install guide](./install-guide.md) covers prerequisites, install methods, and header anchor navigation. diff --git a/.opencode/skills/verify-web/features/ai-workflow.md b/.opencode/skills/verify-web/features/ai-workflow.md new file mode 100644 index 0000000..1e3a2c8 --- /dev/null +++ b/.opencode/skills/verify-web/features/ai-workflow.md @@ -0,0 +1,36 @@ +# AI workflow + +AI workflow shows how `protocol-fix-loop` connects Protocol Visualizer to an LLM: an intro paragraph naming GitHub Copilot and Cursor, a demo video, and a four-step `How to use` list with the skill install command and the `/protocol-fix-loop` chat command. + +## Sub-features + +- `ai-intro` links `protocol-fix-loop` to the skill repo and names Copilot/Cursor. +- `ai-video` embeds the demo video with controls. +- `ai-howto` lists install-editor, install-skill, install-extension, run-command steps. +- `ai-links` cross-links the skill repo and the page's installation guide. + +## How to get to it (user POV) + +- Scroll to `Generate protocols with AI, verify with Protocol Visualizer` on `/` (between the features grid and the screenshot). +- Choose the `protocol-fix-loop` link to open `https://github.com/koji/protocol-fix-loop` in a new tab. +- Choose the `Installation guide` link in step 3 to jump to `#install`. + +## Driving it with drive.mjs + +Preconditions: + +- Doctor reports `"ok": true` at the run URL. +- Fresh page load; no prior interaction. + +- **Region.** Find the section. Run `bun .opencode/skills/verify-web/scripts/drive.mjs --url http://127.0.0.1:5173/ --feature ai-workflow --out

`. A `section#ai-workflow` with accessible name `Generate protocols with AI` exists. +- **Heading.** Read the section heading. The run asserts it contains `Generate protocols with AI`. +- **Video.** Inspect the player. The run asserts a `video` whose `src` is exactly `https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf` with `controls`. +- **Commands.** Read the steps. The run asserts the text contains `npx skills add koji/protocol-fix-loop` and `/protocol-fix-loop`. +- **Links.** Follow the references. The run asserts at least one link to `https://github.com/koji/protocol-fix-loop` and one link to `#install`. +- **Proof.** Inspect the artifacts. `/screenshot.png` shows the video and steps, `/dom.html` contains both commands, `/result.json` records all seven checks passing. + +## Gotchas + +- The video is remote media; the file asserts the `src` attribute and `controls`, it does not play the stream. A missing network still passes as long as the markup is correct. +- `/protocol-fix-loop` is a substring of the install command context too. The steps list must contain both the `npx skills add ...` line and the standalone chat command. +- External repo links open in a new tab (`target="_blank"`). The drive does not follow them; it asserts `href` values only. diff --git a/.opencode/skills/verify-web/features/features-grid.md b/.opencode/skills/verify-web/features/features-grid.md new file mode 100644 index 0000000..c786f18 --- /dev/null +++ b/.opencode/skills/verify-web/features/features-grid.md @@ -0,0 +1,31 @@ +# Features grid + +Features grid lists the six capability cards under the heading `Everything you need to see your protocol run`, each with a title and a one-paragraph description. + +## Sub-features + +- `features-heading` names the section's promise. +- `features-cards` renders all six cards with titles and descriptions. + +## How to get to it (user POV) + +- Scroll to `Everything you need to see your protocol run` on `/`. +- Choose `Features` in the header section navigation (jumps to `#features`). + +## Driving it with drive.mjs + +Preconditions: + +- Doctor reports `"ok": true` at the run URL. +- Fresh page load; no prior interaction. + +- **Region.** Find the section. Run `bun .opencode/skills/verify-web/scripts/drive.mjs --url http://127.0.0.1:5173/ --feature features-grid --out `. A `section#features` with accessible name `Features` exists. +- **Heading.** Read the section heading. The run asserts it equals `Everything you need to see your protocol run`. +- **Cards.** Count and name the cards. The run asserts exactly 6 `article` elements whose `h3` titles are `Real-time Deck Visualization`, `Auto-analysis on Save`, `Runtime Parameters UI`, `Custom Labware Support`, `Pop-out Window`, and `Step Jumper`. +- **Proof.** Inspect the artifacts. `/screenshot.png` shows the grid, `/axtree.json` exposes the six headings, `/result.json` records all three checks passing. + +## Gotchas + +- The grid collapses to 2 columns under 1024px and 1 column under 768px. Card count stays 6; assert count, not layout. +- Card hover lifts the card (`translateY`). Screenshots may differ on hover; capture without hovering. +- Titles are exact strings. `Runtime Parameters UI` and `Step Jumper` are easy to mistype — copy them verbatim. diff --git a/.opencode/skills/verify-web/features/hero.md b/.opencode/skills/verify-web/features/hero.md new file mode 100644 index 0000000..185b250 --- /dev/null +++ b/.opencode/skills/verify-web/features/hero.md @@ -0,0 +1,35 @@ +# Hero + +Hero is the first screen: the `Protocol Visualizer` headline with `Preview` badge, the Opentrons tagline, `Request access` buttons, and a link down to the installation guide. + +## Sub-features + +- `hero-headline` shows the product name and status badge. +- `hero-tagline` states the Opentrons simulation value proposition. +- `hero-request-access` offers the access form link in hero, header, and try-CTA band. +- `hero-install-link` jumps to the installation guide. + +## How to get to it (user POV) + +- Load `/` and look at the top of the page. +- Choose the `Request access` link in the hero copy, the header, or the `Want to try the extension?` band. +- Choose the `Installation guide ↓` link under the tagline. + +## Driving it with drive.mjs + +Preconditions: + +- Doctor reports `"ok": true` at the run URL. +- Fresh page load; no prior interaction. + +- **Headline.** Load the page. Run `bun .opencode/skills/verify-web/scripts/drive.mjs --url http://127.0.0.1:5173/ --feature hero --out `. The `h1` reads `Protocol Visualizer`. +- **Tagline.** Read the hero paragraph. The same run asserts it contains `Simulate your Opentrons`. +- **Request access.** Count the access links. The run asserts at least 3 links named `Request access` and every one targets `docs.google.com/forms`. +- **Install jump.** Follow `Installation guide ↓`. The run asserts one of the `#install` links (header nav also uses that href) reads `Installation guide`. +- **Proof.** Inspect the artifacts. `/screenshot.png` shows the headline and CTAs, `/dom.html` contains the tagline, `/result.json` records all four checks passing. + +## Gotchas + +- `Request access` appears 3+ times (header compact, hero, try-CTA). Asserting exactly one will fail; assert at least 3 with identical form hrefs. +- The install link text includes a `↓` arrow. Match by `href="#install"`, not exact text. +- The hero beaker visual is `aria-hidden`. Do not assert on it; it is decorative. diff --git a/.opencode/skills/verify-web/features/install-guide.md b/.opencode/skills/verify-web/features/install-guide.md new file mode 100644 index 0000000..7b540c0 --- /dev/null +++ b/.opencode/skills/verify-web/features/install-guide.md @@ -0,0 +1,36 @@ +# Install guide + +Install guide documents prerequisites (Python, `opentrons` package, OT-2 pin, interpreter selection) and the two extension install methods (Command Palette, `code --install-extension`). The header section navigation jumps to it and to the features grid. + +## Sub-features + +- `install-prereqs` lists the Python/opentrons prerequisites. +- `install-cli-method` shows the `code --install-extension` command. +- `header-nav` links `Features` and `Install` to their anchors. +- `anchor-navigation` scrolls to the install section on nav click. + +## How to get to it (user POV) + +- Scroll to `Installation` on `/`. +- Choose `Install` in the header section navigation (jumps to `#install`). +- Choose `Installation guide ↓` in the hero or `Installation guide` in the AI workflow steps. + +## Driving it with drive.mjs + +Preconditions: + +- Doctor reports `"ok": true` at the run URL. +- Fresh page load; no prior interaction. + +- **Region.** Find the section. Run `bun .opencode/skills/verify-web/scripts/drive.mjs --url http://127.0.0.1:5173/ --feature install-guide --out `. A `section#install` with accessible name `Installation guide` exists. +- **Prerequisites.** Read the block. The run asserts the text contains `Python 3.8 or later`, `pip install opentrons`, and `Python: Select Interpreter`. +- **CLI method.** Read the second method. The run asserts the text contains `code --install-extension protocol-visualizer.vsix`. +- **Nav links.** Inspect the header. The run asserts `Section navigation` contains `Features` → `#features` and `Install` → `#install`. +- **Anchor jump.** Choose `Install` in the header nav. The run clicks it and asserts `location.hash` becomes `#install` with the install section inside the viewport. +- **Proof.** Inspect the artifacts. `/screenshot.png` shows the page after the anchor jump, `/dom.html` contains the prerequisite texts, `/result.json` records all five checks passing. + +## Gotchas + +- Anchor navigation is the only in-page routing; there is no router and no other URL. Do not expect `/install` to exist. +- The OT-2 note pins `opentrons==9.0.0`. Asserting bare `pip install opentrons` as an exact string fails — the recipe asserts containment, not equality. +- The anchor click changes `location.hash` in the driven page only. Later recipes start from a fresh load, so no cleanup is needed. diff --git a/.opencode/skills/verify-web/features/theme-toggle.md b/.opencode/skills/verify-web/features/theme-toggle.md new file mode 100644 index 0000000..35f6218 --- /dev/null +++ b/.opencode/skills/verify-web/features/theme-toggle.md @@ -0,0 +1,32 @@ +# Theme toggle + +Theme toggle flips the site between dark and light themes from the header button and persists the choice in `localStorage`, so a reload keeps the selected theme. + +## Sub-features + +- `toggle-present` exposes a header button named `Switch to light theme` or `Switch to dark theme`. +- `toggle-flips-theme` changes `documentElement` theme and persists it. +- `toggle-restores` flips back, leaving the page as found. + +## How to get to it (user POV) + +- Choose the sun/moon button in the header (right side, next to `Request access`). + +## Driving it with drive.mjs + +Preconditions: + +- Doctor reports `"ok": true` at the run URL. +- Fresh Chromium profile, so `localStorage` starts empty. + +- **Presence.** Find the button. Run `bun .opencode/skills/verify-web/scripts/drive.mjs --url http://127.0.0.1:5173/ --feature theme-toggle --out `. A `button` whose accessible name starts with `Switch to` exists. +- **Flip.** Choose the toggle. The run clicks once, waits for React to flush the state update, and asserts `documentElement.dataset.theme` changed, is `dark` or `light`, and `localStorage.theme` equals the new value. +- **Restore.** Choose the toggle again. The run clicks a second time, waits, and asserts the theme flipped back (differs from the post-flip value), the persisted value matches, and the button label names the opposite theme — leaving the page as found. +- **Proof.** Inspect the artifacts. `/result.json` records the before/after/stored triple for the flip, `/screenshot.png` shows the restored page. + +## Gotchas + +- The toggle goes through React state, so the theme attribute updates asynchronously after the click. The drive waits ~400ms before reading; a synchronous read sees the stale theme and fails. +- The initial theme follows `prefers-color-scheme` (headless Chromium default), so never assert a specific starting theme — assert the flip and persistence instead. +- The button icon swaps (sun in dark mode, moon in light mode) but both are `aria-hidden` SVGs. Assert the button's accessible name, not the icon. +- `localStorage` persists per Chromium profile. Drives always use a fresh profile, so a stored value in `result.json` came from the clicks in that run. diff --git a/.opencode/skills/verify-web/scripts/doctor.mjs b/.opencode/skills/verify-web/scripts/doctor.mjs new file mode 100644 index 0000000..63eee01 --- /dev/null +++ b/.opencode/skills/verify-web/scripts/doctor.mjs @@ -0,0 +1,50 @@ +#!/usr/bin/env bun +// doctor.mjs — read-only health check for a running verification instance. +// Answers: "is this instance worth driving?" +// +// Usage: +// bun scripts/doctor.mjs --url http://127.0.0.1:5173 +// +// Exits 0 when healthy, 1 otherwise. Never starts, stops, or mutates anything. + +function parseArgs(argv) { + const out = {} + for (let i = 0; i < argv.length; i++) { + if (argv[i].startsWith('--')) { + const key = argv[i].slice(2) + const next = argv[i + 1] + out[key] = next && !next.startsWith('--') ? argv[++i] : 'true' + } + } + return out +} + +const args = parseArgs(process.argv.slice(2)) +const url = args.url ?? 'http://127.0.0.1:5173/' + +try { + const controller = new AbortController() + const timer = setTimeout(() => controller.abort(), 8000) + const res = await fetch(url, { signal: controller.signal }) + clearTimeout(timer) + const body = await res.text() + const hasRoot = body.includes('
') + const isDev = body.includes('/src/main.tsx') + const isBuild = body.includes('/assets/') + const report = { + ok: res.ok && hasRoot && (isDev || isBuild), + url, + status: res.status, + hasRoot, + mode: isDev ? 'dev' : isBuild ? 'preview/build' : 'unknown', + } + console.log(JSON.stringify(report, null, 1)) + if (!report.ok) { + console.error('doctor: instance is NOT worth driving (expected HTTP 200 +
+ vite client or built assets).') + process.exit(1) + } + console.log('doctor: instance is healthy.') +} catch (e) { + console.error(`doctor: unreachable at ${url} — ${e?.message ?? e}`) + process.exit(1) +} diff --git a/.opencode/skills/verify-web/scripts/drive.mjs b/.opencode/skills/verify-web/scripts/drive.mjs new file mode 100644 index 0000000..3361fac --- /dev/null +++ b/.opencode/skills/verify-web/scripts/drive.mjs @@ -0,0 +1,486 @@ +#!/usr/bin/env bun +// drive.mjs — drive the real protocol-visualizer-web landing page in headless +// Chromium over CDP (no npm dependencies; uses bun built-ins only). +// +// Usage: +// bun scripts/drive.mjs --url http://127.0.0.1:5173 --feature --out +// [--chrome ] [--cdp-port 19222] +// +// Exits 0 when every check passes, 1 otherwise. Always writes per-feature +// artifacts (screenshot.png, dom.html, axtree.json, result.json) into --out +// (or --out/ when --feature all). + +import fs from 'node:fs' +import os from 'node:os' +import path from 'node:path' + +const FEATURES = ['hero', 'features-grid', 'ai-workflow', 'theme-toggle', 'install-guide'] + +const EXPECTED_FEATURE_TITLES = [ + 'Real-time Deck Visualization', + 'Auto-analysis on Save', + 'Runtime Parameters UI', + 'Custom Labware Support', + 'Pop-out Window', + 'Step Jumper', +] + +const AI_VIDEO = + 'https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf' +const SKILL_REPO = 'https://github.com/koji/protocol-fix-loop' + +function parseArgs(argv) { + const out = {} + for (let i = 0; i < argv.length; i++) { + if (argv[i].startsWith('--')) { + const key = argv[i].slice(2) + const next = argv[i + 1] + out[key] = next && !next.startsWith('--') ? argv[++i] : 'true' + } + } + return out +} + +// Kill a spawned process AND its children. `bun x ` wraps the real +// server in a child process, so a bare kill() can orphan the listener. +function killTree(proc) { + try { + if (process.platform === 'win32') { + Bun.spawnSync(['taskkill', '/PID', String(proc.pid), '/T', '/F'], { + stdout: 'ignore', + stderr: 'ignore', + }) + } else { + proc.kill() + } + } catch {} +} + +function findChrome(explicit) { const candidates = [ + explicit, + process.env.CHROME_PATH, + `${process.env.LOCALAPPDATA}\\ms-playwright\\chromium-1208\\chrome-win64\\chrome.exe`, + 'C:\\Program Files\\Google\\Chrome\\Application\\chrome.exe', + 'C:\\Program Files (x86)\\Google\\Chrome\\Application\\chrome.exe', + 'C:\\Program Files\\Microsoft\\Edge\\Application\\msedge.exe', + ].filter(Boolean) + for (const c of candidates) { + try { + if (fs.existsSync(c)) return c + } catch {} + } + return null +} + +async function sleep(ms) { + return new Promise((r) => setTimeout(r, ms)) +} + +function createCdp(ws) { + let nextId = 1 + const pending = new Map() + const waiters = new Map() // method name -> [resolve] + ws.onmessage = (event) => { + let msg + try { + msg = JSON.parse(String(event.data)) + } catch { + return + } + if (msg.id !== undefined && pending.has(msg.id)) { + const { resolve, reject } = pending.get(msg.id) + pending.delete(msg.id) + if (msg.error) reject(new Error(`CDP error: ${JSON.stringify(msg.error)}`)) + else resolve(msg.result) + } else if (msg.method) { + const list = waiters.get(msg.method) + if (list) { + waiters.delete(msg.method) + for (const r of list) r(msg.params) + } + } + } + function send(method, params = {}, timeoutMs = 20000) { + const id = nextId++ + return new Promise((resolve, reject) => { + pending.set(id, { resolve, reject }) + ws.send(JSON.stringify({ id, method, params })) + setTimeout(() => { + if (pending.has(id)) { + pending.delete(id) + reject(new Error(`CDP timeout: ${method}`)) + } + }, timeoutMs) + }) + } + function waitForEvent(method, timeoutMs = 20000) { + return new Promise((resolve, reject) => { + if (!waiters.has(method)) waiters.set(method, []) + waiters.get(method).push(resolve) + setTimeout(() => { + const list = waiters.get(method) ?? [] + const idx = list.indexOf(resolve) + if (idx >= 0) { + list.splice(idx, 1) + reject(new Error(`CDP event timeout: ${method}`)) + } + }, timeoutMs) + }) + } + return { send, waitForEvent } +} + +async function evaluate(cdp, expression) { + const res = await cdp.send('Runtime.evaluate', { + expression, + returnByValue: true, + awaitPromise: true, + }) + if (res.exceptionDetails) { + throw new Error(`evaluate threw: ${JSON.stringify(res.exceptionDetails).slice(0, 500)}`) + } + return res.result?.value +} + +async function waitForReady(cdp, timeoutMs = 20000) { + const start = Date.now() + while (Date.now() - start < timeoutMs) { + const h1 = await evaluate(cdp, `document.querySelector('#root h1')?.textContent ?? null`) + if (h1) return h1 + await sleep(250) + } + throw new Error('timed out waiting for #root h1 to render') +} + +// Each check returns { id, pass, detail }. Expressions run in the page. +const CHECKS = { + hero: [ + { + id: 'hero-headline', + expr: `document.querySelector('#root h1')?.textContent ?? null`, + want: 'Protocol Visualizer', + }, + { + id: 'hero-tagline', + expr: `document.querySelector('#root section p')?.textContent ?? null`, + contains: 'Simulate your Opentrons', + }, + { + id: 'hero-request-access-links', + expr: `(() => { const a = [...document.querySelectorAll('#root a')].filter(e => e.textContent.trim() === 'Request access'); return { count: a.length, hrefs: a.map(e => e.href) }; })()`, + check: (v) => v.count >= 3 && v.hrefs.every((h) => h.includes('docs.google.com/forms')), + }, + { + id: 'hero-install-link', + expr: `[...document.querySelectorAll('#root a[href="#install"]')].map(a => a.textContent.trim())`, + check: (v) => Array.isArray(v) && v.some((t) => t.includes('Installation guide')), + }, + ], + 'features-grid': [ + { + id: 'features-region', + expr: `document.querySelector('section#features[aria-label="Features"]') !== null`, + want: true, + }, + { + id: 'features-heading', + expr: `document.querySelector('section#features h2')?.textContent ?? null`, + want: 'Everything you need to see your protocol run', + }, + { + id: 'features-cards', + expr: `[...document.querySelectorAll('section#features article')].map(a => a.querySelector('h3')?.textContent ?? '')`, + check: (v) => + Array.isArray(v) && + v.length === 6 && + EXPECTED_FEATURE_TITLES.every((t) => v.includes(t)), + }, + ], + 'ai-workflow': [ + { + id: 'ai-region', + expr: `document.querySelector('section#ai-workflow[aria-label="Generate protocols with AI"]') !== null`, + want: true, + }, + { + id: 'ai-heading', + expr: `document.querySelector('section#ai-workflow h2')?.textContent ?? null`, + contains: 'Generate protocols with AI', + }, + { + id: 'ai-video', + expr: `(() => { const v = document.querySelector('section#ai-workflow video'); return v ? { src: v.getAttribute('src'), controls: v.hasAttribute('controls') } : null; })()`, + check: (v) => v !== null && v.src === AI_VIDEO && v.controls === true, + }, + { + id: 'ai-skill-command', + expr: `document.querySelector('section#ai-workflow')?.textContent.includes('npx skills add koji/protocol-fix-loop') ?? false`, + want: true, + }, + { + id: 'ai-slash-command', + expr: `document.querySelector('section#ai-workflow')?.textContent.includes('/protocol-fix-loop') ?? false`, + want: true, + }, + { + id: 'ai-skill-links', + expr: `[...document.querySelectorAll('section#ai-workflow a[href="${SKILL_REPO}"]')].length`, + check: (v) => typeof v === 'number' && v >= 1, + }, + { + id: 'ai-install-link', + expr: `document.querySelector('section#ai-workflow a[href="#install"]') !== null`, + want: true, + }, + ], + 'theme-toggle': [ + { + id: 'toggle-present', + expr: `document.querySelector('button[aria-label^="Switch to"]')?.getAttribute('aria-label') ?? null`, + check: (v) => v === 'Switch to light theme' || v === 'Switch to dark theme', + }, + { + id: 'toggle-flips-theme', + expr: `(async () => { const b = document.querySelector('button[aria-label^="Switch to"]'); if (!b) return null; const before = document.documentElement.dataset.theme; b.click(); await new Promise(r => setTimeout(r, 400)); const after = document.documentElement.dataset.theme; const stored = localStorage.getItem('theme'); window.__verifyThemeFlipped = after; return { before, after, stored }; })()`, + check: (v) => + v !== null && v.before !== v.after && (v.after === 'dark' || v.after === 'light') && v.stored === v.after, + }, + { + id: 'toggle-restores', + expr: `(async () => { const b = document.querySelector('button[aria-label^="Switch to"]'); if (!b) return null; b.click(); await new Promise(r => setTimeout(r, 400)); return { theme: document.documentElement.dataset.theme, stored: localStorage.getItem('theme'), label: b.getAttribute('aria-label'), flipped: window.__verifyThemeFlipped ?? null }; })()`, + check: (v) => + v !== null && + (v.theme === 'dark' || v.theme === 'light') && + v.stored === v.theme && + v.theme !== v.flipped && + v.label === (v.theme === 'dark' ? 'Switch to light theme' : 'Switch to dark theme'), + }, + ], + 'install-guide': [ + { + id: 'install-region', + expr: `document.querySelector('section#install[aria-label="Installation guide"]') !== null`, + want: true, + }, + { + id: 'install-prereqs', + expr: `document.querySelector('section#install')?.textContent ?? ''`, + check: (v) => + typeof v === 'string' && + v.includes('Python 3.8 or later') && + v.includes('pip install opentrons') && + v.includes('Python: Select Interpreter'), + }, + { + id: 'install-cli-method', + expr: `document.querySelector('section#install')?.textContent.includes('code --install-extension protocol-visualizer.vsix') ?? false`, + want: true, + }, + { + id: 'header-nav', + expr: `[...document.querySelectorAll('header nav[aria-label="Section navigation"] a')].map(a => [a.textContent.trim(), a.getAttribute('href')])`, + check: (v) => + Array.isArray(v) && + v.some(([t, h]) => t === 'Features' && h === '#features') && + v.some(([t, h]) => t === 'Install' && h === '#install'), + }, + { + id: 'anchor-navigation', + expr: `(() => { const link = document.querySelector('header nav a[href="#install"]'); if (!link) return null; link.click(); const sec = document.querySelector('section#install'); const r = sec.getBoundingClientRect(); return { hash: location.hash, top: Math.round(r.top), vh: window.innerHeight }; })()`, + check: (v) => v !== null && v.hash === '#install' && v.top < v.vh, + }, + ], +} + +function judge(check, value) { + if (check.check) { + try { + return check.check(value) === true + } catch { + return false + } + } + if (check.want !== undefined) return JSON.stringify(value) === JSON.stringify(check.want) + if (check.contains !== undefined) return typeof value === 'string' && value.includes(check.contains) + return false +} + +async function driveFeature(cdp, pageUrl, feature, outDir) { + fs.mkdirSync(outDir, { recursive: true }) + + await cdp.send('Page.navigate', { url: pageUrl }) + await cdp.waitForEvent('Page.loadEventFired').catch(() => {}) + await waitForReady(cdp) + // Let entrance animations (e.g. hero 0.6s fade-in) finish so the + // screenshot shows the steady visual state. + await sleep(900) + + const results = [] + for (const check of CHECKS[feature]) { + let value = null + let pass = false + let error = null + try { + value = await evaluate(cdp, check.expr) + pass = judge(check, value) + } catch (e) { + error = String(e).slice(0, 300) + } + results.push({ id: check.id, pass, value, error }) + console.log(` [${pass ? 'PASS' : 'FAIL'}] ${check.id}${pass ? '' : ` — saw ${JSON.stringify(value)?.slice(0, 200)}${error ? ` (${error})` : ''}`}`) + } + + const shot = await (async () => { + // Show the driven feature in the screenshot, not just the page top. + const targets = { + hero: null, // top of page + 'features-grid': 'section#features', + 'ai-workflow': 'section#ai-workflow', + 'theme-toggle': null, // header, at top of page + 'install-guide': 'section#install', + } + const sel = targets[feature] + if (sel) { + await evaluate(cdp, `document.querySelector(${JSON.stringify(sel)})?.scrollIntoView({ block: 'start' }); window.scrollBy(0, -72)`) + } else { + await evaluate(cdp, `window.scrollTo(0, 0)`) + } + await sleep(500) + return cdp.send('Page.captureScreenshot', { format: 'png' }) + })() + fs.writeFileSync(path.join(outDir, 'screenshot.png'), Buffer.from(shot.data, 'base64')) + const dom = await evaluate(cdp, `document.documentElement.outerHTML`) + fs.writeFileSync(path.join(outDir, 'dom.html'), String(dom ?? '')) + let ax = null + try { + await cdp.send('Accessibility.enable', {}).catch(() => {}) + const tree = await cdp.send('Accessibility.getFullAXTree', {}) + ax = tree.nodes + fs.writeFileSync(path.join(outDir, 'axtree.json'), JSON.stringify(ax, null, 1)) + } catch (e) { + fs.writeFileSync(path.join(outDir, 'axtree.json'), JSON.stringify({ error: String(e).slice(0, 300) })) + } + const passed = results.filter((r) => r.pass).length + const result = { + feature, + url: pageUrl, + passed, + total: results.length, + ok: passed === results.length, + checks: results, + finishedAt: new Date().toISOString(), + } + fs.writeFileSync(path.join(outDir, 'result.json'), JSON.stringify(result, null, 1)) + return result +} + +async function main() { + const args = parseArgs(process.argv.slice(2)) + const pageUrl = args.url ?? 'http://127.0.0.1:5173/' + const featureArg = args.feature ?? 'all' + const outBase = args.out ?? 'artifacts' + const cdpPort = Number(args['cdp-port'] ?? process.env.VERIFY_CDP_PORT ?? 19222) + const features = featureArg === 'all' ? FEATURES : [featureArg] + for (const f of features) { + if (!CHECKS[f]) { + console.error(`unknown feature: ${f} (known: ${FEATURES.join(', ')})`) + process.exit(2) + } + } + + const chrome = findChrome(args.chrome) + if (!chrome) { + console.error('no Chromium/Chrome binary found. Set CHROME_PATH or install Chrome.') + process.exit(2) + } + console.log(`chrome: ${chrome}`) + + const profile = fs.mkdtempSync(path.join(os.tmpdir(), 'verify-web-profile-')) + const proc = Bun.spawn( + [ + chrome, + '--headless=new', + '--no-sandbox', + '--disable-gpu', + '--hide-scrollbars', + '--window-size=1280,900', + '--force-device-scale-factor=1', + '--no-first-run', + '--no-default-browser-check', + `--user-data-dir=${profile}`, + `--remote-debugging-port=${cdpPort}`, + 'about:blank', + ], + { stdout: 'ignore', stderr: 'ignore' }, + ) + + const cleanup = () => { + killTree(proc) + try { + fs.rmSync(profile, { recursive: true, force: true }) + } catch {} + } + process.on('SIGINT', () => { + cleanup() + process.exit(130) + }) + + try { + let targets = null + const start = Date.now() + while (Date.now() - start < 15000) { + try { + const res = await fetch(`http://127.0.0.1:${cdpPort}/json/list`) + const list = await res.json() + const page = list.find((t) => t.type === 'page' && t.webSocketDebuggerUrl) + if (page) { + targets = page + break + } + } catch {} + await sleep(250) + } + if (!targets) throw new Error('timed out waiting for Chrome remote debugging') + + const ws = new WebSocket(targets.webSocketDebuggerUrl) + await new Promise((resolve, reject) => { + const t = setTimeout(() => reject(new Error('websocket connect timeout')), 10000) + ws.onopen = () => { + clearTimeout(t) + resolve() + } + ws.onerror = (e) => { + clearTimeout(t) + reject(new Error(`websocket error: ${e?.message ?? 'unknown'}`)) + } + }) + const cdp = createCdp(ws) + await cdp.send('Page.enable', {}) + await cdp.send('Runtime.enable', {}) + + // Doctor-style precheck: the app must serve its shell before driving. + const probe = await fetch(pageUrl) + if (!probe.ok) throw new Error(`app probe failed: HTTP ${probe.status} at ${pageUrl}`) + + let allOk = true + for (const f of features) { + const outDir = featureArg === 'all' ? path.join(outBase, f) : outBase + console.log(`feature: ${f}`) + const result = await driveFeature(cdp, pageUrl, f, outDir) + console.log(` -> ${result.passed}/${result.total} passed — ${path.join(outDir, 'screenshot.png')}`) + if (!result.ok) allOk = false + } + ws.close() + try { + await cdp.send('Browser.close', {}).catch(() => {}) + } catch {} + cleanup() + process.exit(allOk ? 0 : 1) + } catch (e) { + console.error(`drive failed: ${e?.message ?? e}`) + cleanup() + process.exit(1) + } +} + +await main() diff --git a/.opencode/skills/verify-web/scripts/verify.mjs b/.opencode/skills/verify-web/scripts/verify.mjs new file mode 100644 index 0000000..f2f5833 --- /dev/null +++ b/.opencode/skills/verify-web/scripts/verify.mjs @@ -0,0 +1,151 @@ +#!/usr/bin/env bun +// verify.mjs — one-shot end-to-end verification for protocol-visualizer-web. +// Spawns its own `vite` server as a child process (same process tree, so no +// cross-shell lifetime issues), runs doctor, drives the requested features in +// real Chromium, then always tears the server down. Proof artifacts survive. +// +// Usage (run from the repo root): +// bun .opencode/skills/verify-web/scripts/verify.mjs --feature [--port 5173] [--run-id ] +// +// Env overrides: VERIFY_PORT, VERIFY_CDP_PORT, VERIFY_RUN_ID, CHROME_PATH. + +import fs from 'node:fs' +import path from 'node:path' +import { fileURLToPath } from 'node:url' + +const SKILL_DIR = path.dirname(path.dirname(fileURLToPath(import.meta.url))) +const ROOT = path.dirname(path.dirname(path.dirname(SKILL_DIR))) + +function parseArgs(argv) { + const out = {} + for (let i = 0; i < argv.length; i++) { + if (argv[i].startsWith('--')) { + const key = argv[i].slice(2) + const next = argv[i + 1] + out[key] = next && !next.startsWith('--') ? argv[++i] : 'true' + } + } + return out +} + +async function sleep(ms) { + return new Promise((r) => setTimeout(r, ms)) +} + +// Kill a spawned process AND its children. `bun x ` wraps the real +// server in a child process, so a bare kill() can orphan the listener. +function killTree(proc) { + try { + if (process.platform === 'win32') { + Bun.spawnSync(['taskkill', '/PID', String(proc.pid), '/T', '/F'], { + stdout: 'ignore', + stderr: 'ignore', + }) + } else { + proc.kill() + } + } catch {} +} + +const args = parseArgs(process.argv.slice(2)) +const feature = args.feature ?? 'all' +const port = Number(args.port ?? process.env.VERIFY_PORT ?? 5173) +const runId = + args['run-id'] ?? process.env.VERIFY_RUN_ID ?? new Date().toISOString().replace(/[:.]/g, '-') +const artifacts = path.join(SKILL_DIR, 'artifacts', runId) +const serverLog = path.join(artifacts, 'vite-server.log') + +fs.mkdirSync(artifacts, { recursive: true }) +const url = `http://127.0.0.1:${port}/` + +console.log(`launch: bun x vite --host 127.0.0.1 --port ${port} --strictPort`) +const server = Bun.spawn([process.execPath, 'x', 'vite', '--host', '127.0.0.1', '--port', String(port), '--strictPort'], { + cwd: ROOT, + stdout: 'pipe', + stderr: 'pipe', +}) +const logFile = fs.createWriteStream(serverLog) +server.stdout.pipeTo(new WritableStream({ write: (c) => logFile.write(c) })) +server.stderr.pipeTo(new WritableStream({ write: (c) => logFile.write(c) })) + +let exitCode = 1 +try { + // Wait for readiness: log line + HTTP 200. + let ready = false + const start = Date.now() + while (Date.now() - start < 30000) { + if (server.exitCode !== null && server.exitCode !== undefined) { + throw new Error(`vite exited early (code ${server.exitCode}); see ${serverLog}`) + } + try { + const res = await fetch(url) + if (res.ok) { + ready = true + break + } + } catch {} + await sleep(300) + } + if (!ready) throw new Error(`vite never became ready at ${url}; see ${serverLog}`) + console.log(`launch: ready at ${url}`) + + // Doctor (official read-only check, as a separate step). + console.log('doctor:') + const doctor = Bun.spawn(['bun', path.join(SKILL_DIR, 'scripts', 'doctor.mjs'), '--url', url], { + cwd: ROOT, + stdout: 'inherit', + stderr: 'inherit', + }) + const doctorCode = await doctor.exited + if (doctorCode !== 0) throw new Error('doctor reported the instance is not worth driving') + + // Drive. + console.log('drive:') + const drive = Bun.spawn( + ['bun', path.join(SKILL_DIR, 'scripts', 'drive.mjs'), '--url', url, '--feature', feature, '--out', artifacts], + { cwd: ROOT, stdout: 'inherit', stderr: 'inherit' }, + ) + const driveCode = await drive.exited + exitCode = driveCode + + // Cleanup never eats the proof: confirm artifacts still exist after teardown. + const walked = [] + const walk = (dir) => { + for (const e of fs.readdirSync(dir, { withFileTypes: true })) { + const p = path.join(dir, e.name) + if (e.isDirectory()) walk(p) + else walked.push(p) + } + } + walk(artifacts) + const hasShot = walked.some((p) => p.endsWith('screenshot.png')) + const hasResult = walked.some((p) => p.endsWith('result.json')) + console.log(`artifacts: ${artifacts} (${walked.length} files)`) + if (!hasShot || !hasResult) throw new Error('evidence missing after run (screenshot.png + result.json required)') +} catch (e) { + console.error(`verify failed: ${e?.message ?? e}`) + exitCode = 1 +} finally { + killTree(server) + await server.exited.catch(() => {}) + try { + logFile.end() + } catch {} + // Prove the teardown: the port must refuse connections afterwards. + let portFree = false + for (let i = 0; i < 20; i++) { + try { + await fetch(url) + await sleep(250) + } catch { + portFree = true + break + } + } + console.log(`cleanup: vite server stopped (port free: ${portFree}; artifacts retained).`) + if (!portFree) { + console.error(`cleanup: port ${port} is still owned after teardown`) + exitCode = 1 + } +} +process.exit(exitCode) diff --git a/docs/verification.md b/docs/verification.md new file mode 100644 index 0000000..2206433 --- /dev/null +++ b/docs/verification.md @@ -0,0 +1,74 @@ +# Verification + +This repo ships a scripted way to drive the real landing page and prove its behavior: the `verify-web` skill in `.opencode/skills/verify-web/`. It serves the site with `vite`, opens it in real headless Chromium over CDP, asserts DOM/accessibility state, and captures screenshots. No mocks, no test-only endpoints, no npm dependencies (bun built-ins only). + +## Prerequisites + +- `bun` on PATH. +- A Chromium/Chrome binary. Auto-detected in this order: `CHROME_PATH` env, Playwright-cached `chromium-1208`, system Chrome, Edge. Override with `CHROME_PATH` or `--chrome`. +- Ports free: app port (default `5173`) and CDP port (default `19222`). + +## Quick start + +Run from the repo root: + +```powershell +bun .opencode/skills/verify-web/scripts/verify.mjs --feature all +``` + +This spawns its own `vite` server, runs the doctor check, drives every mapped feature, tears the server down, and leaves proof under `.opencode/skills/verify-web/artifacts//`. Exit 0 only if every check passes. + +Verify a single feature: + +```powershell +bun .opencode/skills/verify-web/scripts/verify.mjs --feature ai-workflow --port 5173 +``` + +Feature IDs: `hero`, `features-grid`, `ai-workflow`, `theme-toggle`, `install-guide`. Recipes live in `.opencode/skills/verify-web/features/`. + +## Individual steps + +Health-check a running instance (read-only, never starts or stops anything): + +```powershell +bun .opencode/skills/verify-web/scripts/doctor.mjs --url http://127.0.0.1:5173/ +``` + +Drive an already-running instance and write evidence to ``: + +```powershell +bun .opencode/skills/verify-web/scripts/drive.mjs --url http://127.0.0.1:5173/ --feature --out +``` + +Manual server launch (only for interactive debugging — background processes do not survive across separate shell sessions, so prefer `verify.mjs`): + +```powershell +$p = Start-Process bun -ArgumentList @('x','vite','--host','127.0.0.1','--port','5173','--strictPort') -PassThru +bun .opencode/skills/verify-web/scripts/doctor.mjs --url http://127.0.0.1:5173/ +Stop-Process -Id $p.Id -Force +``` + +## Environment variables + +| Variable | Default | Purpose | +| --- | --- | --- | +| `VERIFY_PORT` | `5173` | App server port (also `--port`) | +| `VERIFY_CDP_PORT` | `19222` | Chrome remote-debugging port (also `--cdp-port`); change per parallel run | +| `VERIFY_RUN_ID` | timestamp | Artifact directory name (also `--run-id`) | +| `CHROME_PATH` | auto-detect | Browser binary (also `--chrome` for `drive.mjs`) | + +## Evidence + +Per feature, `///` contains `screenshot.png` (rendered page showing the feature), `dom.html` (post-hydration DOM), `axtree.json` (full accessibility tree), and `result.json` (per-check pass/fail with observed values). Plus `vite-server.log` at the run root. Cleanup never deletes evidence. + +## Gotchas + +- Never drive a URL you did not start. If the port is taken, pick another `--port` instead of reusing someone's dev server. +- Each drive uses a fresh Chromium profile, so `localStorage` starts empty and the theme starts from the browser default. Never assert a specific starting theme — assert the flip and persistence. +- The demo video is asserted by `src` attribute and `controls`, not by playing the remote stream. +- The hero fades in over 0.6s; the drive waits for the steady state before capturing. +- `result.json` with a failing check names the check id and the observed value — start there when a run goes red. + +## Maintenance + +The `features/` map is the maintained verification source. When the page changes, update the matching feature file first, then the checks in `scripts/drive.mjs`. See `/maintain-verification-skill` for the periodic audit loop. From 670b2c3e305c2e48b891d4fde12a1be8a07dc56a Mon Sep 17 00:00:00 2001 From: koji Date: Wed, 16 Sep 2026 03:52:56 -0400 Subject: [PATCH 3/5] fix format errors --- .../ai-workflow/axtree.json | 23158 ++++++++------- .../ai-workflow/dom.html | 1663 +- .../ai-workflow/result.json | 108 +- .../features-grid/axtree.json | 23148 ++++++++------- .../features-grid/dom.html | 1663 +- .../features-grid/result.json | 68 +- .../2026-09-16T07-46-20-848Z/hero/axtree.json | 23148 ++++++++------- .../2026-09-16T07-46-20-848Z/hero/dom.html | 1663 +- .../2026-09-16T07-46-20-848Z/hero/result.json | 84 +- .../install-guide/axtree.json | 23167 ++++++++-------- .../install-guide/dom.html | 1663 +- .../install-guide/result.json | 98 +- .../theme-toggle/axtree.json | 23167 ++++++++-------- .../theme-toggle/dom.html | 1663 +- .../theme-toggle/result.json | 72 +- .../skills/verify-web/scripts/doctor.mjs | 4 +- .opencode/skills/verify-web/scripts/drive.mjs | 105 +- .../skills/verify-web/scripts/verify.mjs | 69 +- docs/verification.md | 12 +- src/components/AiWorkflow/AiWorkflow.test.tsx | 4 +- src/components/AiWorkflow/AiWorkflow.tsx | 4 +- 21 files changed, 62087 insertions(+), 62644 deletions(-) diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json index 64770ab..53d7316 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json @@ -1,12018 +1,11418 @@ [ - { - "nodeId": "728", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { 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"childIds": [] - }, - { - "nodeId": "1083", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1082", - "childIds": [], - "backendDOMNodeId": 1083 - }, - { - "nodeId": "1085", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1084", - "childIds": [], - "backendDOMNodeId": 1085 - } -] \ No newline at end of file + }, + "properties": [], + "parentId": "827", + "childIds": [] + }, + { + "nodeId": "1083", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1082", + "childIds": [], + "backendDOMNodeId": 1083 + }, + { + "nodeId": "1085", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1084", + "childIds": [], + "backendDOMNodeId": 1085 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/dom.html index ed5bc63..41ef3bd 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
+
+
+
+ +
+
+
+
+
+
+

Protocol Visualizer

+ Preview +
+

+ Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

+ +
+ +
+
+
+
+

+ Everything you need to see your protocol run +

+
    +
  • +
    +

    + Real-time Deck Visualization +

    +

    + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

    +
    +
  • +
  • +
    +

    Auto-analysis on Save

    +

    + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

    +
    +
  • +
  • +
    +

    Runtime Parameters UI

    +

    + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

    +
    +
  • +
  • +
    +

    Custom Labware Support

    +

    + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

    +
    +
  • +
  • +
    +

    Pop-out Window

    +

    + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

    +
    +
  • +
  • +
    +

    Step Jumper

    +

    + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

    +
    +
  • +
+
+
+
+
+

+ Generate protocols with AI, verify with Protocol Visualizer +

+

+ Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

+
+ +
+ Generate a protocol from a prompt, then fix it while watching + the simulation +
+
+

How to use

+
    +
  1. Install VSCode or Cursor
  2. +
  3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
  4. +
  5. + Install the Protocol Visualizer extension (see + Installation guide) +
  6. +
  7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
  8. +
+
+
+
+
+
+ Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
+ Protocol Visualizer in action +
+
+
+
+
+
+

Want to try the extension?

+

+ Request access via our form — requests are handled individually. +

+ Request access +
+
+
+
+

Installation

+
+
+

Prerequisites

+
    +
  • + Python 3.8 or later, with + python3 available in PATH +
  • +
  • + The opentrons Python package: + pip install opentrons +
  • +
  • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
  • +
  • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
  • +
  • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
  • +
+
+
+

+ Method A: Command Palette +

+
    +
  1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
  2. +
  3. + Select Extensions: Install from VSIX... +
  4. +
  5. Choose the downloaded .vsix file
  6. +
+
+
+

Method B: Command line

+
code --install-extension protocol-visualizer.vsix
+
+
+
+
+
+ +
+
+ MIT License © 2026 Koji Kanao + +
+
+
+
- - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/result.json index f6766b0..738a632 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/result.json @@ -1,55 +1,55 @@ { - "feature": "ai-workflow", - "url": "http://127.0.0.1:5180/", - "passed": 7, - "total": 7, - "ok": true, - "checks": [ - { - "id": "ai-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "ai-heading", - "pass": true, - "value": "Generate protocols with AI, verify with Protocol Visualizer", - "error": null - }, - { - "id": "ai-video", - "pass": true, - "value": { - "src": "https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf", - "controls": true - }, - "error": null - }, - { - "id": "ai-skill-command", - "pass": true, - "value": true, - "error": null - }, - { - "id": "ai-slash-command", - "pass": true, - "value": true, - "error": null - }, - { - "id": "ai-skill-links", - "pass": true, - "value": 2, - "error": null - }, - { - "id": "ai-install-link", - "pass": true, - "value": true, - "error": null - } - ], - "finishedAt": "2026-09-16T07:46:30.548Z" -} \ No newline at end of file + "feature": "ai-workflow", + "url": "http://127.0.0.1:5180/", + "passed": 7, + "total": 7, + "ok": true, + "checks": [ + { + "id": "ai-region", + "pass": true, + "value": true, + "error": null + }, + { + "id": "ai-heading", + "pass": true, + "value": "Generate protocols with AI, verify with Protocol Visualizer", + "error": null + }, + { + "id": "ai-video", + "pass": true, + "value": { + "src": "https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf", + "controls": true + }, + "error": null + }, + { + "id": "ai-skill-command", + "pass": true, + "value": true, + "error": null + }, + { + "id": "ai-slash-command", + "pass": true, + "value": true, + "error": null + }, + { + "id": "ai-skill-links", + "pass": true, + "value": 2, + "error": null + }, + { + "id": "ai-install-link", + "pass": true, + "value": true, + "error": null + } + ], + "finishedAt": "2026-09-16T07:46:30.548Z" +} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/axtree.json index 6e67674..cbfd9e1 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/axtree.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/axtree.json @@ -1,12018 +1,11408 @@ [ - { - "nodeId": "367", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol 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"parentId": "720", - "childIds": [ - "724" - ], - "backendDOMNodeId": 723 - }, - { - "nodeId": "-1000000362", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Extensions: Install " - }, - "properties": [], - "parentId": "464", - "childIds": [] - }, - { - "nodeId": "-1000000363", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "from VSIX..." - }, - "properties": [], - "parentId": "464", - "childIds": [] - }, - { - "nodeId": "-1000000365", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": ".vsix" - }, - "properties": [], - "parentId": "466", - "childIds": [] - }, - { - "nodeId": "722", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "721", - "childIds": [], - "backendDOMNodeId": 722 - }, - { - "nodeId": "724", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "723", - "childIds": [], - "backendDOMNodeId": 724 - } -] \ No newline at end of file + }, + "properties": [], + "parentId": "466", + "childIds": [] + }, + { + "nodeId": "722", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "721", + "childIds": [], + "backendDOMNodeId": 722 + }, + { + "nodeId": "724", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "723", + "childIds": [], + "backendDOMNodeId": 724 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/dom.html index ed5bc63..41ef3bd 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
+
+
+
+ +
+
+
+
+
+
+

Protocol Visualizer

+ Preview +
+

+ Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

+ +
+ +
+
+
+
+

+ Everything you need to see your protocol run +

+
    +
  • +
    +

    + Real-time Deck Visualization +

    +

    + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

    +
    +
  • +
  • +
    +

    Auto-analysis on Save

    +

    + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

    +
    +
  • +
  • +
    +

    Runtime Parameters UI

    +

    + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

    +
    +
  • +
  • +
    +

    Custom Labware Support

    +

    + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

    +
    +
  • +
  • +
    +

    Pop-out Window

    +

    + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

    +
    +
  • +
  • +
    +

    Step Jumper

    +

    + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

    +
    +
  • +
+
+
+
+
+

+ Generate protocols with AI, verify with Protocol Visualizer +

+

+ Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

+
+ +
+ Generate a protocol from a prompt, then fix it while watching + the simulation +
+
+

How to use

+
    +
  1. Install VSCode or Cursor
  2. +
  3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
  4. +
  5. + Install the Protocol Visualizer extension (see + Installation guide) +
  6. +
  7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
  8. +
+
+
+
+
+
+ Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
+ Protocol Visualizer in action +
+
+
+
+
+
+

Want to try the extension?

+

+ Request access via our form — requests are handled individually. +

+ Request access +
+
+
+
+

Installation

+
+
+

Prerequisites

+
    +
  • + Python 3.8 or later, with + python3 available in PATH +
  • +
  • + The opentrons Python package: + pip install opentrons +
  • +
  • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
  • +
  • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
  • +
  • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
  • +
+
+
+

+ Method A: Command Palette +

+
    +
  1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
  2. +
  3. + Select Extensions: Install from VSIX... +
  4. +
  5. Choose the downloaded .vsix file
  6. +
+
+
+

Method B: Command line

+
code --install-extension protocol-visualizer.vsix
+
+
+
+
+
+ +
+
+ MIT License © 2026 Koji Kanao + +
+
+
+
- - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/result.json index 7230bc2..1b630c9 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/result.json @@ -1,35 +1,35 @@ { - "feature": "features-grid", - "url": "http://127.0.0.1:5180/", - "passed": 3, - "total": 3, - "ok": true, - "checks": [ - { - "id": "features-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "features-heading", - "pass": true, - "value": "Everything you need to see your protocol run", - "error": null - }, - { - "id": "features-cards", - "pass": true, - "value": [ - "Real-time Deck Visualization", - "Auto-analysis on Save", - "Runtime Parameters UI", - "Custom Labware Support", - "Pop-out Window", - "Step Jumper" - ], - "error": null - } - ], - "finishedAt": "2026-09-16T07:46:28.965Z" -} \ No newline at end of file + "feature": "features-grid", + "url": "http://127.0.0.1:5180/", + "passed": 3, + "total": 3, + "ok": true, + "checks": [ + { + "id": "features-region", + "pass": true, + "value": true, + "error": null + }, + { + "id": "features-heading", + "pass": true, + "value": "Everything you need to see your protocol run", + "error": null + }, + { + "id": "features-cards", + "pass": true, + "value": [ + "Real-time Deck Visualization", + "Auto-analysis on Save", + "Runtime Parameters UI", + "Custom Labware Support", + "Pop-out Window", + "Step Jumper" + ], + "error": null + } + ], + "finishedAt": "2026-09-16T07:46:28.965Z" +} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/axtree.json index 8cb9597..b609602 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/axtree.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/axtree.json @@ -1,12018 +1,11408 @@ [ - { - "nodeId": "2", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "aria-label", - "superseded": true - }, - { - "type": "relatedElement", - "value": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode" - }, - "nativeSource": "title" - } - ] - }, - "properties": [ - { - "name": "focusable", - "value": { - "type": "booleanOrUndefined", - "value": true - } - }, - { - "name": "url", - "value": { - "type": "string", - "value": "http://127.0.0.1:5180/" - } - } - ], - "childIds": [ - "19" - ], - "backendDOMNodeId": 2, - "frameId": "0F19F770020C1A63EA3E621076BF1C9D" - }, - { - "nodeId": "19", - "ignored": true, - "ignoredReasons": [ - { - "name": "uninteresting", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "2", - "childIds": [ - "44" - ], - "backendDOMNodeId": 19 - }, - { - "nodeId": "44", - "ignored": true, - "ignoredReasons": [ - { - "name": "uninteresting", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "19", - "childIds": [ - "45" - ], - "backendDOMNodeId": 44 - }, - { - "nodeId": "45", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "44", - "childIds": [ - "46" - ], - "backendDOMNodeId": 45 - }, - { - "nodeId": "46", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "45", - "childIds": [ - "47", - "65", - "255", - "261" - ], - "backendDOMNodeId": 46 - }, - { - "nodeId": "47", - "ignored": false, - "role": { - "type": "role", - "value": "banner" - }, - "chromeRole": { - "type": "internalRole", - "value": 94 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "title" - } - ] - }, - "properties": [], - "parentId": "46", - "childIds": [ - "48" - ], - "backendDOMNodeId": 47 - }, - { - "nodeId": "65", - "ignored": false, - "role": { - "type": "role", - "value": "main" - }, - "chromeRole": { - "type": "internalRole", - "value": 118 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "title" - } - ] - }, - "properties": [], - "parentId": "46", - "childIds": [ - "66", - "81", - "108", - "213", - "218", - "223" - ], - "backendDOMNodeId": 65 - }, - { - "nodeId": "255", - "ignored": false, - "role": { - "type": "role", - "value": "complementary" - }, - "chromeRole": { - "type": "internalRole", - "value": 22 - }, - "name": { - "type": "computedString", - "value": "Disclaimer", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "value": { - "type": "computedString", - "value": "Disclaimer" - }, - "attribute": "aria-label", - "attributeValue": { - "type": "string", - "value": "Disclaimer" - } - }, - { - "type": "attribute", - "attribute": "title", - "superseded": true - } - ] - }, - "properties": [], - "parentId": "46", - "childIds": [ - "256" - ], - "backendDOMNodeId": 255 - }, - { - "nodeId": "261", - "ignored": false, - "role": { - "type": "role", - "value": "contentinfo" - }, - "chromeRole": { - "type": "internalRole", - "value": 85 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": 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- + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
+
+
+
+ +
+
+
+
+
+
+

Protocol Visualizer

+ Preview +
+

+ Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

+ +
+ +
+
+
+
+

+ Everything you need to see your protocol run +

+
    +
  • +
    +

    + Real-time Deck Visualization +

    +

    + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

    +
    +
  • +
  • +
    +

    Auto-analysis on Save

    +

    + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

    +
    +
  • +
  • +
    +

    Runtime Parameters UI

    +

    + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

    +
    +
  • +
  • +
    +

    Custom Labware Support

    +

    + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

    +
    +
  • +
  • +
    +

    Pop-out Window

    +

    + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

    +
    +
  • +
  • +
    +

    Step Jumper

    +

    + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

    +
    +
  • +
+
+
+
+
+

+ Generate protocols with AI, verify with Protocol Visualizer +

+

+ Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

+
+ +
+ Generate a protocol from a prompt, then fix it while watching + the simulation +
+
+

How to use

+
    +
  1. Install VSCode or Cursor
  2. +
  3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
  4. +
  5. + Install the Protocol Visualizer extension (see + Installation guide) +
  6. +
  7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
  8. +
+
+
+
+
+
+ Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
+ Protocol Visualizer in action +
+
+
+
+
+
+

Want to try the extension?

+

+ Request access via our form — requests are handled individually. +

+ Request access +
+
+
+
+

Installation

+
+
+

Prerequisites

+
    +
  • + Python 3.8 or later, with + python3 available in PATH +
  • +
  • + The opentrons Python package: + pip install opentrons +
  • +
  • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
  • +
  • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
  • +
  • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
  • +
+
+
+

+ Method A: Command Palette +

+
    +
  1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
  2. +
  3. + Select Extensions: Install from VSIX... +
  4. +
  5. Choose the downloaded .vsix file
  6. +
+
+
+

Method B: Command line

+
code --install-extension protocol-visualizer.vsix
+
+
+
+
+
+ +
+
+ MIT License © 2026 Koji Kanao + +
+
+
+
- - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/result.json index 5ab24c0..0fa0106 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/result.json @@ -1,45 +1,41 @@ { - "feature": "hero", - "url": "http://127.0.0.1:5180/", - "passed": 4, - "total": 4, - "ok": true, - "checks": [ - { - "id": "hero-headline", - "pass": true, - "value": "Protocol Visualizer", - "error": null - }, - { - "id": "hero-tagline", - "pass": true, - "value": "Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.", - "error": null - }, - { - "id": "hero-request-access-links", - "pass": true, - "value": { - "count": 3, - "hrefs": [ - 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without leaving VSCode.", + "error": null + }, + { + "id": "hero-request-access-links", + "pass": true, + "value": { + "count": 3, + "hrefs": [ + "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor", + "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor", + "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor" + ] + }, + "error": null + }, + { + "id": "hero-install-link", + "pass": true, + "value": ["Install", "Installation guide ↓", "Installation guide"], + "error": null + } + ], + "finishedAt": "2026-09-16T07:46:27.408Z" +} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/axtree.json index 675ab74..1ffffca 100644 --- 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"-1000001256" - ], - "backendDOMNodeId": 1686 - }, - { - "nodeId": "-1000001140", - "ignored": true, - "ignoredReasons": [ - { - "name": "presentationalRole", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "1658", - "childIds": [] - }, - { - "nodeId": "-1000001257", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Choose the downloaded " - }, - "properties": [], - "parentId": "1687", - "childIds": [] - }, - { - "nodeId": "1688", - "ignored": false, - "role": { - "type": "internalRole", - "value": "StaticText" - }, - "chromeRole": { - "type": "internalRole", - "value": 158 - }, - "name": { - "type": "computedString", - "value": ".vsix", - "sources": [ - { - "type": "contents", - "value": { + }, + "properties": [], + "parentId": "1616", + "childIds": [] + }, + { + "nodeId": "-1000001183", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "Enter any step number under Protocol Steps " + }, + "properties": [], + "parentId": "1617", + "childIds": [] + }, + { + "nodeId": "-1000001184", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "and hit Enter to jump the visualization state " + }, + "properties": [], + "parentId": "1617", + "childIds": [] + }, + { + "nodeId": "-1000001185", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "instantly." + }, + "properties": [], + "parentId": "1617", + "childIds": [] + }, + { + "nodeId": "1943", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1942", + "childIds": ["1944"], + "backendDOMNodeId": 1943 + }, + { + "nodeId": "1945", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1942", + "childIds": ["1946"], + "backendDOMNodeId": 1945 + }, + { + "nodeId": "-1000001255", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "Extensions: Install " + }, + "properties": [], + "parentId": "1686", + "childIds": [] + }, + { + "nodeId": "-1000001256", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "from VSIX..." + }, + "properties": [], + "parentId": "1686", + "childIds": [] + }, + { + "nodeId": "-1000001258", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { "type": "computedString", "value": ".vsix" - } - } - ] - }, - "properties": [], - "parentId": "1921", - "childIds": [ - "-1000001258" - ], - "backendDOMNodeId": 1688 - }, - { - "nodeId": "-1000001259", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "file" - }, - "properties": [], - "parentId": "1689", - "childIds": [] - }, - { - "nodeId": "-1000001261", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "code --install-extension protocol-visualizer.vsix" - }, - "properties": [], - "parentId": "1691", - "childIds": [] - }, - { - "nodeId": "-1000001161", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Real-time Deck Visualization" - }, - "properties": [], - "parentId": "1606", - "childIds": [] - }, - { - "nodeId": "-1000001162", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Deck state and liquid volume changes " - }, - "properties": [], - "parentId": "1607", - "childIds": [] - }, - { - "nodeId": "-1000001163", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "render in real time through an interactive " - }, - "properties": [], - "parentId": "1607", - "childIds": [] - }, - { - "nodeId": "-1000001164", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "panel while your protocol runs." - }, - "properties": [], - "parentId": "1607", - "childIds": [] - }, - { - "nodeId": "-1000001165", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Auto-analysis on Save" - }, - "properties": [], - "parentId": "1608", - "childIds": [] - }, - { - "nodeId": "-1000001166", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "The simulation automatically reruns " - }, - "properties": [], - "parentId": "1609", - "childIds": [] - }, - { - "nodeId": "-1000001167", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "whenever you save changes (Ctrl+S / " - }, - "properties": [], - "parentId": "1609", - "childIds": [] - }, - { - "nodeId": "-1000001168", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Cmd+S) to your protocol file." - }, - "properties": [], - "parentId": "1609", - "childIds": [] - }, - { - "nodeId": "-1000001169", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters UI" - }, - "properties": [], - "parentId": "1610", - "childIds": [] - }, - { - "nodeId": "-1000001170", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Input fields are generated for Opentrons " - }, - "properties": [], - "parentId": "1611", - "childIds": [] - }, - { - "nodeId": "-1000001171", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters; hit Analyze to apply " - }, - "properties": [], - "parentId": "1611", - "childIds": [] - }, - { - "nodeId": "-1000001172", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "them — your original code is never " - }, - "properties": [], - "parentId": "1611", - "childIds": [] - }, - { - "nodeId": "-1000001173", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "modified." - }, - "properties": [], - "parentId": "1611", - "childIds": [] - }, - { - "nodeId": "-1000001174", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Custom Labware Support" - }, - "properties": [], - "parentId": "1612", - "childIds": [] - }, - { - "nodeId": "-1000001175", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Place custom labware definition files (.json) " - }, - "properties": [], - "parentId": "1613", - "childIds": [] - }, - { - "nodeId": "-1000001176", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "in the same directory as your protocol file " - }, - "properties": [], - "parentId": "1613", - "childIds": [] - }, - { - "nodeId": "-1000001177", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and they just work." - }, - "properties": [], - "parentId": "1613", - "childIds": [] - }, - { - "nodeId": "-1000001178", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop-out Window" - }, - "properties": [], - "parentId": "1614", - "childIds": [] - }, - { - "nodeId": "-1000001179", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop the panel out to its own window or " - }, - "properties": [], - "parentId": "1615", - "childIds": [] - }, - { - "nodeId": "-1000001180", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "drag the tab to another monitor via " - }, - "properties": [], - "parentId": "1615", - "childIds": [] - }, - { - "nodeId": "-1000001181", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "VSCode's Auxiliary Window support." - }, - "properties": [], - "parentId": "1615", - "childIds": [] - }, - { - "nodeId": "-1000001182", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Step Jumper" - }, - "properties": [], - "parentId": "1616", - "childIds": [] - }, - { - "nodeId": "-1000001183", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Enter any step number under Protocol Steps " - }, - "properties": [], - "parentId": "1617", - "childIds": [] - }, - { - "nodeId": "-1000001184", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and hit Enter to jump the visualization state " - }, - "properties": [], - "parentId": "1617", - "childIds": [] - }, - { - "nodeId": "-1000001185", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "instantly." - }, - "properties": [], - "parentId": "1617", - "childIds": [] - }, - { - "nodeId": "1943", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1942", - "childIds": [ - "1944" - ], - "backendDOMNodeId": 1943 - }, - { - "nodeId": "1945", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1942", - "childIds": [ - "1946" - ], - "backendDOMNodeId": 1945 - }, - { - "nodeId": "-1000001255", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Extensions: Install " - }, - "properties": [], - "parentId": "1686", - "childIds": [] - }, - { - "nodeId": "-1000001256", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "from VSIX..." - }, - "properties": [], - "parentId": "1686", - "childIds": [] - }, - { - "nodeId": "-1000001258", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": ".vsix" - }, - "properties": [], - "parentId": "1688", - "childIds": [] - }, - { - "nodeId": "1944", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1943", - "childIds": [], - "backendDOMNodeId": 1944 - }, - { - "nodeId": "1946", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1945", - "childIds": [], - "backendDOMNodeId": 1946 - } -] \ No newline at end of file + }, + "properties": [], + "parentId": "1688", + "childIds": [] + }, + { + "nodeId": "1944", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1943", + "childIds": [], + "backendDOMNodeId": 1944 + }, + { + "nodeId": "1946", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1945", + "childIds": [], + "backendDOMNodeId": 1946 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html index ed5bc63..41ef3bd 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
+
+
+
+ +
+
+
+
+
+
+

Protocol Visualizer

+ Preview +
+

+ Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

+ +
+ +
+
+
+
+

+ Everything you need to see your protocol run +

+
    +
  • +
    +

    + Real-time Deck Visualization +

    +

    + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

    +
    +
  • +
  • +
    +

    Auto-analysis on Save

    +

    + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

    +
    +
  • +
  • +
    +

    Runtime Parameters UI

    +

    + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

    +
    +
  • +
  • +
    +

    Custom Labware Support

    +

    + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

    +
    +
  • +
  • +
    +

    Pop-out Window

    +

    + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

    +
    +
  • +
  • +
    +

    Step Jumper

    +

    + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

    +
    +
  • +
+
+
+
+
+

+ Generate protocols with AI, verify with Protocol Visualizer +

+

+ Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

+
+ +
+ Generate a protocol from a prompt, then fix it while watching + the simulation +
+
+

How to use

+
    +
  1. Install VSCode or Cursor
  2. +
  3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
  4. +
  5. + Install the Protocol Visualizer extension (see + Installation guide) +
  6. +
  7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
  8. +
+
+
+
+
+
+ Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
+ Protocol Visualizer in action +
+
+
+
+
+
+

Want to try the extension?

+

+ Request access via our form — requests are handled individually. +

+ Request access +
+
+
+
+

Installation

+
+
+

Prerequisites

+
    +
  • + Python 3.8 or later, with + python3 available in PATH +
  • +
  • + The opentrons Python package: + pip install opentrons +
  • +
  • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
  • +
  • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
  • +
  • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
  • +
+
+
+

+ Method A: Command Palette +

+
    +
  1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
  2. +
  3. + Select Extensions: Install from VSIX... +
  4. +
  5. Choose the downloaded .vsix file
  6. +
+
+
+

Method B: Command line

+
code --install-extension protocol-visualizer.vsix
+
+
+
+
+
+ +
+
+ MIT License © 2026 Koji Kanao + +
+
+
+
- - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/result.json index fd355d6..03db2a5 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/result.json @@ -1,53 +1,47 @@ { - "feature": "install-guide", - "url": "http://127.0.0.1:5180/", - "passed": 5, - "total": 5, - "ok": true, - "checks": [ - { - "id": "install-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "install-prereqs", - "pass": true, - "value": "InstallationPrerequisitesPython 3.8 or later, with python3 available in PATHThe opentrons Python package: pip install opentronsFor OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)Select the matching Python interpreter in VSCode via Python: Select InterpreterUsing both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.Method A: Command PaletteOpen the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)Select Extensions: Install from VSIX...Choose the downloaded .vsix fileMethod B: Command linecode --install-extension protocol-visualizer.vsix", - "error": null - }, - { - "id": "install-cli-method", - "pass": true, - "value": true, - "error": null - }, - { - "id": "header-nav", - "pass": true, - "value": [ - [ - "Features", - "#features" - ], - [ - "Install", - "#install" - ] - ], - "error": null - }, - { - "id": "anchor-navigation", - "pass": true, - "value": { - "hash": "#install", - "top": 0, - "vh": 749 - }, - "error": null - } - ], - "finishedAt": "2026-09-16T07:46:34.620Z" -} \ No newline at end of file + "feature": "install-guide", + "url": "http://127.0.0.1:5180/", + "passed": 5, + "total": 5, + "ok": true, + "checks": [ + { + "id": "install-region", + "pass": true, + "value": true, + "error": null + }, + { + "id": "install-prereqs", + "pass": true, + "value": "InstallationPrerequisitesPython 3.8 or later, with python3 available in PATHThe opentrons Python package: pip install opentronsFor OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)Select the matching Python interpreter in VSCode via Python: Select InterpreterUsing both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.Method A: Command PaletteOpen the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)Select Extensions: Install from VSIX...Choose the downloaded .vsix fileMethod B: Command linecode --install-extension protocol-visualizer.vsix", + "error": null + }, + { + "id": "install-cli-method", + "pass": true, + "value": true, + "error": null + }, + { + "id": "header-nav", + "pass": true, + "value": [ + ["Features", "#features"], + ["Install", "#install"] + ], + "error": null + }, + { + "id": "anchor-navigation", + "pass": true, + "value": { + "hash": "#install", + "top": 0, + "vh": 749 + }, + "error": null + } + ], + "finishedAt": "2026-09-16T07:46:34.620Z" +} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/axtree.json index 7211fc3..98c1e58 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/axtree.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/axtree.json @@ -1,12018 +1,11427 @@ [ - { - "nodeId": "1089", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "aria-label", - "superseded": true - }, - { - "type": "relatedElement", - "value": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode" - }, - "nativeSource": "title" - } - ] - }, - "properties": [ - { - "name": "focusable", - "value": { - "type": 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} -] \ No newline at end of file + }, + "properties": [], + "parentId": "1431", + "childIds": [] + }, + { + "nodeId": "1443", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1442", + "childIds": [], + "backendDOMNodeId": 1443 + }, + { + "nodeId": "1445", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1444", + "childIds": [], + "backendDOMNodeId": 1445 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/dom.html index ed5bc63..41ef3bd 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

Protocol Visualizer

Preview

Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

Everything you need to see your protocol run

  • Real-time Deck Visualization

    Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

  • Auto-analysis on Save

    The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

  • Runtime Parameters UI

    Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

  • Custom Labware Support

    Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

  • Pop-out Window

    Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

  • Step Jumper

    Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

Generate protocols with AI, verify with Protocol Visualizer

Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

Generate a protocol from a prompt, then fix it while watching the simulation

How to use

  1. Install VSCode or Cursor
  2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
  3. Install the Protocol Visualizer extension (see Installation guide)
  4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol
Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
Protocol Visualizer in action

Want to try the extension?

Request access via our form — requests are handled individually.

Request access

Installation

Prerequisites

  • Python 3.8 or later, with python3 available in PATH
  • The opentrons Python package: pip install opentrons
  • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
  • Select the matching Python interpreter in VSCode via Python: Select Interpreter
  • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

Method A: Command Palette

  1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Select Extensions: Install from VSIX...
  3. Choose the downloaded .vsix file

Method B: Command line

code --install-extension protocol-visualizer.vsix
+
+
+
+ +
+
+
+
+
+
+

Protocol Visualizer

+ Preview +
+

+ Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

+ +
+ +
+
+
+
+

+ Everything you need to see your protocol run +

+
    +
  • +
    +

    + Real-time Deck Visualization +

    +

    + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

    +
    +
  • +
  • +
    +

    Auto-analysis on Save

    +

    + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

    +
    +
  • +
  • +
    +

    Runtime Parameters UI

    +

    + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

    +
    +
  • +
  • +
    +

    Custom Labware Support

    +

    + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

    +
    +
  • +
  • +
    +

    Pop-out Window

    +

    + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

    +
    +
  • +
  • +
    +

    Step Jumper

    +

    + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

    +
    +
  • +
+
+
+
+
+

+ Generate protocols with AI, verify with Protocol Visualizer +

+

+ Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

+
+ +
+ Generate a protocol from a prompt, then fix it while watching + the simulation +
+
+

How to use

+
    +
  1. Install VSCode or Cursor
  2. +
  3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
  4. +
  5. + Install the Protocol Visualizer extension (see + Installation guide) +
  6. +
  7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
  8. +
+
+
+
+
+
+ Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
+ Protocol Visualizer in action +
+
+
+
+
+
+

Want to try the extension?

+

+ Request access via our form — requests are handled individually. +

+ Request access +
+
+
+
+

Installation

+
+
+

Prerequisites

+
    +
  • + Python 3.8 or later, with + python3 available in PATH +
  • +
  • + The opentrons Python package: + pip install opentrons +
  • +
  • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
  • +
  • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
  • +
  • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
  • +
+
+
+

+ Method A: Command Palette +

+
    +
  1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
  2. +
  3. + Select Extensions: Install from VSIX... +
  4. +
  5. Choose the downloaded .vsix file
  6. +
+
+
+

Method B: Command line

+
code --install-extension protocol-visualizer.vsix
+
+
+
+
+
+ +
+
+ MIT License © 2026 Koji Kanao + +
+
+
+
- - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/result.json index 803c67f..1283dc5 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/result.json @@ -1,37 +1,37 @@ { - "feature": "theme-toggle", - "url": "http://127.0.0.1:5180/", - "passed": 3, - "total": 3, - "ok": true, - "checks": [ - { - "id": "toggle-present", - "pass": true, - "value": "Switch to light theme", - "error": null - }, - { - "id": "toggle-flips-theme", - "pass": true, - "value": { - "before": "dark", - "after": "light", - "stored": "light" - }, - "error": null - }, - { - "id": "toggle-restores", - "pass": true, - "value": { - "theme": "dark", - "stored": "dark", - "label": "Switch to light theme", - "flipped": "light" - }, - "error": null - } - ], - "finishedAt": "2026-09-16T07:46:33.030Z" -} \ No newline at end of file + "feature": "theme-toggle", + "url": "http://127.0.0.1:5180/", + "passed": 3, + "total": 3, + "ok": true, + "checks": [ + { + "id": "toggle-present", + "pass": true, + "value": "Switch to light theme", + "error": null + }, + { + "id": "toggle-flips-theme", + "pass": true, + "value": { + "before": "dark", + "after": "light", + "stored": "light" + }, + "error": null + }, + { + "id": "toggle-restores", + "pass": true, + "value": { + "theme": "dark", + "stored": "dark", + "label": "Switch to light theme", + "flipped": "light" + }, + "error": null + } + ], + "finishedAt": "2026-09-16T07:46:33.030Z" +} diff --git a/.opencode/skills/verify-web/scripts/doctor.mjs b/.opencode/skills/verify-web/scripts/doctor.mjs index 63eee01..01d0cd8 100644 --- a/.opencode/skills/verify-web/scripts/doctor.mjs +++ b/.opencode/skills/verify-web/scripts/doctor.mjs @@ -40,7 +40,9 @@ try { } console.log(JSON.stringify(report, null, 1)) if (!report.ok) { - console.error('doctor: instance is NOT worth driving (expected HTTP 200 +
+ vite client or built assets).') + console.error( + 'doctor: instance is NOT worth driving (expected HTTP 200 +
+ vite client or built assets).', + ) process.exit(1) } console.log('doctor: instance is healthy.') diff --git a/.opencode/skills/verify-web/scripts/drive.mjs b/.opencode/skills/verify-web/scripts/drive.mjs index 3361fac..25d3c8a 100644 --- a/.opencode/skills/verify-web/scripts/drive.mjs +++ b/.opencode/skills/verify-web/scripts/drive.mjs @@ -14,7 +14,13 @@ import fs from 'node:fs' import os from 'node:os' import path from 'node:path' -const FEATURES = ['hero', 'features-grid', 'ai-workflow', 'theme-toggle', 'install-guide'] +const FEATURES = [ + 'hero', + 'features-grid', + 'ai-workflow', + 'theme-toggle', + 'install-guide', +] const EXPECTED_FEATURE_TITLES = [ 'Real-time Deck Visualization', @@ -56,7 +62,8 @@ function killTree(proc) { } catch {} } -function findChrome(explicit) { const candidates = [ +function findChrome(explicit) { + const candidates = [ explicit, process.env.CHROME_PATH, `${process.env.LOCALAPPDATA}\\ms-playwright\\chromium-1208\\chrome-win64\\chrome.exe`, @@ -90,7 +97,8 @@ function createCdp(ws) { if (msg.id !== undefined && pending.has(msg.id)) { const { resolve, reject } = pending.get(msg.id) pending.delete(msg.id) - if (msg.error) reject(new Error(`CDP error: ${JSON.stringify(msg.error)}`)) + if (msg.error) + reject(new Error(`CDP error: ${JSON.stringify(msg.error)}`)) else resolve(msg.result) } else if (msg.method) { const list = waiters.get(msg.method) @@ -137,7 +145,9 @@ async function evaluate(cdp, expression) { awaitPromise: true, }) if (res.exceptionDetails) { - throw new Error(`evaluate threw: ${JSON.stringify(res.exceptionDetails).slice(0, 500)}`) + throw new Error( + `evaluate threw: ${JSON.stringify(res.exceptionDetails).slice(0, 500)}`, + ) } return res.result?.value } @@ -145,7 +155,10 @@ async function evaluate(cdp, expression) { async function waitForReady(cdp, timeoutMs = 20000) { const start = Date.now() while (Date.now() - start < timeoutMs) { - const h1 = await evaluate(cdp, `document.querySelector('#root h1')?.textContent ?? null`) + const h1 = await evaluate( + cdp, + `document.querySelector('#root h1')?.textContent ?? null`, + ) if (h1) return h1 await sleep(250) } @@ -168,12 +181,15 @@ const CHECKS = { { id: 'hero-request-access-links', expr: `(() => { const a = [...document.querySelectorAll('#root a')].filter(e => e.textContent.trim() === 'Request access'); return { count: a.length, hrefs: a.map(e => e.href) }; })()`, - check: (v) => v.count >= 3 && v.hrefs.every((h) => h.includes('docs.google.com/forms')), + check: (v) => + v.count >= 3 && + v.hrefs.every((h) => h.includes('docs.google.com/forms')), }, { id: 'hero-install-link', expr: `[...document.querySelectorAll('#root a[href="#install"]')].map(a => a.textContent.trim())`, - check: (v) => Array.isArray(v) && v.some((t) => t.includes('Installation guide')), + check: (v) => + Array.isArray(v) && v.some((t) => t.includes('Installation guide')), }, ], 'features-grid': [ @@ -237,13 +253,17 @@ const CHECKS = { { id: 'toggle-present', expr: `document.querySelector('button[aria-label^="Switch to"]')?.getAttribute('aria-label') ?? null`, - check: (v) => v === 'Switch to light theme' || v === 'Switch to dark theme', + check: (v) => + v === 'Switch to light theme' || v === 'Switch to dark theme', }, { id: 'toggle-flips-theme', expr: `(async () => { const b = document.querySelector('button[aria-label^="Switch to"]'); if (!b) return null; const before = document.documentElement.dataset.theme; b.click(); await new Promise(r => setTimeout(r, 400)); const after = document.documentElement.dataset.theme; const stored = localStorage.getItem('theme'); window.__verifyThemeFlipped = after; return { before, after, stored }; })()`, check: (v) => - v !== null && v.before !== v.after && (v.after === 'dark' || v.after === 'light') && v.stored === v.after, + v !== null && + v.before !== v.after && + (v.after === 'dark' || v.after === 'light') && + v.stored === v.after, }, { id: 'toggle-restores', @@ -253,7 +273,10 @@ const CHECKS = { (v.theme === 'dark' || v.theme === 'light') && v.stored === v.theme && v.theme !== v.flipped && - v.label === (v.theme === 'dark' ? 'Switch to light theme' : 'Switch to dark theme'), + v.label === + (v.theme === 'dark' + ? 'Switch to light theme' + : 'Switch to dark theme'), }, ], 'install-guide': [ @@ -300,8 +323,10 @@ function judge(check, value) { return false } } - if (check.want !== undefined) return JSON.stringify(value) === JSON.stringify(check.want) - if (check.contains !== undefined) return typeof value === 'string' && value.includes(check.contains) + if (check.want !== undefined) + return JSON.stringify(value) === JSON.stringify(check.want) + if (check.contains !== undefined) + return typeof value === 'string' && value.includes(check.contains) return false } @@ -327,7 +352,9 @@ async function driveFeature(cdp, pageUrl, feature, outDir) { error = String(e).slice(0, 300) } results.push({ id: check.id, pass, value, error }) - console.log(` [${pass ? 'PASS' : 'FAIL'}] ${check.id}${pass ? '' : ` — saw ${JSON.stringify(value)?.slice(0, 200)}${error ? ` (${error})` : ''}`}`) + console.log( + ` [${pass ? 'PASS' : 'FAIL'}] ${check.id}${pass ? '' : ` — saw ${JSON.stringify(value)?.slice(0, 200)}${error ? ` (${error})` : ''}`}`, + ) } const shot = await (async () => { @@ -341,14 +368,20 @@ async function driveFeature(cdp, pageUrl, feature, outDir) { } const sel = targets[feature] if (sel) { - await evaluate(cdp, `document.querySelector(${JSON.stringify(sel)})?.scrollIntoView({ block: 'start' }); window.scrollBy(0, -72)`) + await evaluate( + cdp, + `document.querySelector(${JSON.stringify(sel)})?.scrollIntoView({ block: 'start' }); window.scrollBy(0, -72)`, + ) } else { await evaluate(cdp, `window.scrollTo(0, 0)`) } await sleep(500) return cdp.send('Page.captureScreenshot', { format: 'png' }) })() - fs.writeFileSync(path.join(outDir, 'screenshot.png'), Buffer.from(shot.data, 'base64')) + fs.writeFileSync( + path.join(outDir, 'screenshot.png'), + Buffer.from(shot.data, 'base64'), + ) const dom = await evaluate(cdp, `document.documentElement.outerHTML`) fs.writeFileSync(path.join(outDir, 'dom.html'), String(dom ?? '')) let ax = null @@ -356,9 +389,15 @@ async function driveFeature(cdp, pageUrl, feature, outDir) { await cdp.send('Accessibility.enable', {}).catch(() => {}) const tree = await cdp.send('Accessibility.getFullAXTree', {}) ax = tree.nodes - fs.writeFileSync(path.join(outDir, 'axtree.json'), JSON.stringify(ax, null, 1)) + fs.writeFileSync( + path.join(outDir, 'axtree.json'), + JSON.stringify(ax, null, 1), + ) } catch (e) { - fs.writeFileSync(path.join(outDir, 'axtree.json'), JSON.stringify({ error: String(e).slice(0, 300) })) + fs.writeFileSync( + path.join(outDir, 'axtree.json'), + JSON.stringify({ error: String(e).slice(0, 300) }), + ) } const passed = results.filter((r) => r.pass).length const result = { @@ -370,7 +409,10 @@ async function driveFeature(cdp, pageUrl, feature, outDir) { checks: results, finishedAt: new Date().toISOString(), } - fs.writeFileSync(path.join(outDir, 'result.json'), JSON.stringify(result, null, 1)) + fs.writeFileSync( + path.join(outDir, 'result.json'), + JSON.stringify(result, null, 1), + ) return result } @@ -379,7 +421,9 @@ async function main() { const pageUrl = args.url ?? 'http://127.0.0.1:5173/' const featureArg = args.feature ?? 'all' const outBase = args.out ?? 'artifacts' - const cdpPort = Number(args['cdp-port'] ?? process.env.VERIFY_CDP_PORT ?? 19222) + const cdpPort = Number( + args['cdp-port'] ?? process.env.VERIFY_CDP_PORT ?? 19222, + ) const features = featureArg === 'all' ? FEATURES : [featureArg] for (const f of features) { if (!CHECKS[f]) { @@ -390,7 +434,9 @@ async function main() { const chrome = findChrome(args.chrome) if (!chrome) { - console.error('no Chromium/Chrome binary found. Set CHROME_PATH or install Chrome.') + console.error( + 'no Chromium/Chrome binary found. Set CHROME_PATH or install Chrome.', + ) process.exit(2) } console.log(`chrome: ${chrome}`) @@ -432,7 +478,9 @@ async function main() { try { const res = await fetch(`http://127.0.0.1:${cdpPort}/json/list`) const list = await res.json() - const page = list.find((t) => t.type === 'page' && t.webSocketDebuggerUrl) + const page = list.find( + (t) => t.type === 'page' && t.webSocketDebuggerUrl, + ) if (page) { targets = page break @@ -440,11 +488,15 @@ async function main() { } catch {} await sleep(250) } - if (!targets) throw new Error('timed out waiting for Chrome remote debugging') + if (!targets) + throw new Error('timed out waiting for Chrome remote debugging') const ws = new WebSocket(targets.webSocketDebuggerUrl) await new Promise((resolve, reject) => { - const t = setTimeout(() => reject(new Error('websocket connect timeout')), 10000) + const t = setTimeout( + () => reject(new Error('websocket connect timeout')), + 10000, + ) ws.onopen = () => { clearTimeout(t) resolve() @@ -460,14 +512,17 @@ async function main() { // Doctor-style precheck: the app must serve its shell before driving. const probe = await fetch(pageUrl) - if (!probe.ok) throw new Error(`app probe failed: HTTP ${probe.status} at ${pageUrl}`) + if (!probe.ok) + throw new Error(`app probe failed: HTTP ${probe.status} at ${pageUrl}`) let allOk = true for (const f of features) { const outDir = featureArg === 'all' ? path.join(outBase, f) : outBase console.log(`feature: ${f}`) const result = await driveFeature(cdp, pageUrl, f, outDir) - console.log(` -> ${result.passed}/${result.total} passed — ${path.join(outDir, 'screenshot.png')}`) + console.log( + ` -> ${result.passed}/${result.total} passed — ${path.join(outDir, 'screenshot.png')}`, + ) if (!result.ok) allOk = false } ws.close() diff --git a/.opencode/skills/verify-web/scripts/verify.mjs b/.opencode/skills/verify-web/scripts/verify.mjs index f2f5833..f264f64 100644 --- a/.opencode/skills/verify-web/scripts/verify.mjs +++ b/.opencode/skills/verify-web/scripts/verify.mjs @@ -51,7 +51,9 @@ const args = parseArgs(process.argv.slice(2)) const feature = args.feature ?? 'all' const port = Number(args.port ?? process.env.VERIFY_PORT ?? 5173) const runId = - args['run-id'] ?? process.env.VERIFY_RUN_ID ?? new Date().toISOString().replace(/[:.]/g, '-') + args['run-id'] ?? + process.env.VERIFY_RUN_ID ?? + new Date().toISOString().replace(/[:.]/g, '-') const artifacts = path.join(SKILL_DIR, 'artifacts', runId) const serverLog = path.join(artifacts, 'vite-server.log') @@ -59,11 +61,23 @@ fs.mkdirSync(artifacts, { recursive: true }) const url = `http://127.0.0.1:${port}/` console.log(`launch: bun x vite --host 127.0.0.1 --port ${port} --strictPort`) -const server = Bun.spawn([process.execPath, 'x', 'vite', '--host', '127.0.0.1', '--port', String(port), '--strictPort'], { - cwd: ROOT, - stdout: 'pipe', - stderr: 'pipe', -}) +const server = Bun.spawn( + [ + process.execPath, + 'x', + 'vite', + '--host', + '127.0.0.1', + '--port', + String(port), + '--strictPort', + ], + { + cwd: ROOT, + stdout: 'pipe', + stderr: 'pipe', + }, +) const logFile = fs.createWriteStream(serverLog) server.stdout.pipeTo(new WritableStream({ write: (c) => logFile.write(c) })) server.stderr.pipeTo(new WritableStream({ write: (c) => logFile.write(c) })) @@ -75,7 +89,9 @@ try { const start = Date.now() while (Date.now() - start < 30000) { if (server.exitCode !== null && server.exitCode !== undefined) { - throw new Error(`vite exited early (code ${server.exitCode}); see ${serverLog}`) + throw new Error( + `vite exited early (code ${server.exitCode}); see ${serverLog}`, + ) } try { const res = await fetch(url) @@ -86,23 +102,37 @@ try { } catch {} await sleep(300) } - if (!ready) throw new Error(`vite never became ready at ${url}; see ${serverLog}`) + if (!ready) + throw new Error(`vite never became ready at ${url}; see ${serverLog}`) console.log(`launch: ready at ${url}`) // Doctor (official read-only check, as a separate step). console.log('doctor:') - const doctor = Bun.spawn(['bun', path.join(SKILL_DIR, 'scripts', 'doctor.mjs'), '--url', url], { - cwd: ROOT, - stdout: 'inherit', - stderr: 'inherit', - }) + const doctor = Bun.spawn( + ['bun', path.join(SKILL_DIR, 'scripts', 'doctor.mjs'), '--url', url], + { + cwd: ROOT, + stdout: 'inherit', + stderr: 'inherit', + }, + ) const doctorCode = await doctor.exited - if (doctorCode !== 0) throw new Error('doctor reported the instance is not worth driving') + if (doctorCode !== 0) + throw new Error('doctor reported the instance is not worth driving') // Drive. console.log('drive:') const drive = Bun.spawn( - ['bun', path.join(SKILL_DIR, 'scripts', 'drive.mjs'), '--url', url, '--feature', feature, '--out', artifacts], + [ + 'bun', + path.join(SKILL_DIR, 'scripts', 'drive.mjs'), + '--url', + url, + '--feature', + feature, + '--out', + artifacts, + ], { cwd: ROOT, stdout: 'inherit', stderr: 'inherit' }, ) const driveCode = await drive.exited @@ -121,7 +151,10 @@ try { const hasShot = walked.some((p) => p.endsWith('screenshot.png')) const hasResult = walked.some((p) => p.endsWith('result.json')) console.log(`artifacts: ${artifacts} (${walked.length} files)`) - if (!hasShot || !hasResult) throw new Error('evidence missing after run (screenshot.png + result.json required)') + if (!hasShot || !hasResult) + throw new Error( + 'evidence missing after run (screenshot.png + result.json required)', + ) } catch (e) { console.error(`verify failed: ${e?.message ?? e}`) exitCode = 1 @@ -142,7 +175,9 @@ try { break } } - console.log(`cleanup: vite server stopped (port free: ${portFree}; artifacts retained).`) + console.log( + `cleanup: vite server stopped (port free: ${portFree}; artifacts retained).`, + ) if (!portFree) { console.error(`cleanup: port ${port} is still owned after teardown`) exitCode = 1 diff --git a/docs/verification.md b/docs/verification.md index 2206433..0b8e195 100644 --- a/docs/verification.md +++ b/docs/verification.md @@ -50,12 +50,12 @@ Stop-Process -Id $p.Id -Force ## Environment variables -| Variable | Default | Purpose | -| --- | --- | --- | -| `VERIFY_PORT` | `5173` | App server port (also `--port`) | -| `VERIFY_CDP_PORT` | `19222` | Chrome remote-debugging port (also `--cdp-port`); change per parallel run | -| `VERIFY_RUN_ID` | timestamp | Artifact directory name (also `--run-id`) | -| `CHROME_PATH` | auto-detect | Browser binary (also `--chrome` for `drive.mjs`) | +| Variable | Default | Purpose | +| ----------------- | ----------- | ------------------------------------------------------------------------- | +| `VERIFY_PORT` | `5173` | App server port (also `--port`) | +| `VERIFY_CDP_PORT` | `19222` | Chrome remote-debugging port (also `--cdp-port`); change per parallel run | +| `VERIFY_RUN_ID` | timestamp | Artifact directory name (also `--run-id`) | +| `CHROME_PATH` | auto-detect | Browser binary (also `--chrome` for `drive.mjs`) | ## Evidence diff --git a/src/components/AiWorkflow/AiWorkflow.test.tsx b/src/components/AiWorkflow/AiWorkflow.test.tsx index ce2f0af..9594d44 100644 --- a/src/components/AiWorkflow/AiWorkflow.test.tsx +++ b/src/components/AiWorkflow/AiWorkflow.test.tsx @@ -34,8 +34,6 @@ describe('AiWorkflow', () => { screen.getByText('npx skills add koji/protocol-fix-loop'), ).toBeInTheDocument() expect(screen.getByText('/protocol-fix-loop')).toBeInTheDocument() - expect( - screen.getByText(/Install VSCode or Cursor/i), - ).toBeInTheDocument() + expect(screen.getByText(/Install VSCode or Cursor/i)).toBeInTheDocument() }) }) diff --git a/src/components/AiWorkflow/AiWorkflow.tsx b/src/components/AiWorkflow/AiWorkflow.tsx index 4a3ffca..98779aa 100644 --- a/src/components/AiWorkflow/AiWorkflow.tsx +++ b/src/components/AiWorkflow/AiWorkflow.tsx @@ -74,8 +74,8 @@ export function AiWorkflow(): ReactNode { )
  • - Use /protocol-fix-loop{' '} - in chat and add your prompt to generate a protocol + Use /protocol-fix-loop in + chat and add your prompt to generate a protocol
  • From 4725df5721a87191eb4c20c824f5bbd46b0cd41c Mon Sep 17 00:00:00 2001 From: koji Date: Wed, 16 Sep 2026 03:57:07 -0400 Subject: [PATCH 4/5] modify the contents order --- .../ai-workflow/axtree.json | 11418 --------------- .../ai-workflow/dom.html | 1089 -- .../ai-workflow/result.json | 55 - .../ai-workflow/screenshot.png | Bin 50645 -> 0 bytes .../features-grid/axtree.json | 11408 --------------- .../features-grid/dom.html | 1089 -- .../features-grid/result.json | 35 - .../2026-09-16T07-46-20-848Z/hero/axtree.json | 11408 --------------- .../2026-09-16T07-46-20-848Z/hero/dom.html | 1089 -- .../2026-09-16T07-46-20-848Z/hero/result.json | 41 - .../install-guide/axtree.json | 11427 --------------- .../install-guide/dom.html | 1089 -- .../install-guide/result.json | 47 - .../theme-toggle/axtree.json | 11427 --------------- .../theme-toggle/dom.html | 1089 -- .../theme-toggle/result.json | 37 - .../2026-09-16T07-46-20-848Z/vite-server.log | 11 - .../ai-workflow/axtree.json | 11967 ++++++++++++++++ .../ai-workflow/dom.html | 616 + .../ai-workflow/result.json | 55 + .../ai-workflow/screenshot.png | Bin 0 -> 50696 bytes .../features-grid/axtree.json | 11967 ++++++++++++++++ .../features-grid/dom.html | 616 + .../features-grid/result.json | 35 + .../features-grid/screenshot.png | Bin 51914 -> 51556 bytes .../2026-09-16T07-56-03-875Z/hero/axtree.json | 11967 ++++++++++++++++ .../2026-09-16T07-56-03-875Z/hero/dom.html | 616 + .../2026-09-16T07-56-03-875Z/hero/result.json | 45 + .../hero/screenshot.png | Bin .../install-guide/axtree.json | 11967 ++++++++++++++++ .../install-guide/dom.html | 616 + .../install-guide/result.json | 53 + .../install-guide/screenshot.png | Bin .../theme-toggle/axtree.json | 11967 ++++++++++++++++ .../theme-toggle/dom.html | 616 + .../theme-toggle/result.json | 37 + .../theme-toggle/screenshot.png | Bin .../2026-09-16T07-56-03-875Z/vite-server.log | 13 + src/App.tsx | 2 +- 39 files changed, 63154 insertions(+), 62760 deletions(-) delete mode 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.opencode/skills/verify-web/artifacts/{2026-09-16T07-46-20-848Z => 2026-09-16T07-56-03-875Z}/theme-toggle/screenshot.png (100%) create mode 100644 .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/vite-server.log diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json deleted file mode 100644 index 53d7316..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/axtree.json +++ /dev/null @@ -1,11418 +0,0 @@ -[ - { - "nodeId": "728", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "aria-label", - "superseded": true - }, - { - "type": "relatedElement", - "value": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode" - }, - "nativeSource": "title" - } - ] - }, - "properties": [ - { - "name": "focusable", - "value": { - "type": "booleanOrUndefined", - "value": true - } - }, - { - "name": "url", - "value": { - "type": "string", - "value": "http://127.0.0.1:5180/" - } - } - ], - "childIds": ["835"], - "backendDOMNodeId": 728, - "frameId": "0F19F770020C1A63EA3E621076BF1C9D" - }, - { - "nodeId": "835", - "ignored": true, - "ignoredReasons": [ - { - "name": "uninteresting", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "728", - "childIds": ["860"], - "backendDOMNodeId": 835 - }, - { - "nodeId": "860", - "ignored": true, - "ignoredReasons": [ - { - "name": "uninteresting", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "835", - "childIds": ["861"], - "backendDOMNodeId": 860 - }, - { - "nodeId": "861", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "860", - "childIds": ["862"], - "backendDOMNodeId": 861 - }, - { - "nodeId": "862", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "861", - "childIds": ["863", "880", "1065", "1071"], - "backendDOMNodeId": 862 - }, - { - "nodeId": "863", - "ignored": false, - "role": { - "type": "role", - "value": "banner" - }, - "chromeRole": { - "type": "internalRole", - "value": 94 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "title" - } - ] - }, - "properties": [], - "parentId": "862", - "childIds": ["864"], - "backendDOMNodeId": 863 - }, - { - "nodeId": "880", - "ignored": false, - "role": { - "type": "role", - "value": "main" - }, - "chromeRole": { - "type": "internalRole", - "value": 118 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "title" - } - ] - }, - "properties": [], - "parentId": "862", - "childIds": ["881", "897", "925", "1023", "1028", "1033"], - "backendDOMNodeId": 880 - }, - { - "nodeId": "1065", - "ignored": false, - "role": { - "type": "role", - "value": "complementary" - }, - "chromeRole": { - "type": "internalRole", - "value": 22 - }, - "name": { - "type": "computedString", - "value": "Disclaimer", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "value": { - "type": "computedString", - "value": "Disclaimer" - }, - "attribute": "aria-label", - "attributeValue": { - "type": "string", - "value": "Disclaimer" - } - }, - { - "type": "attribute", - "attribute": "title", - "superseded": true - } - ] - }, - "properties": [], - "parentId": "862", - "childIds": ["1066"], - "backendDOMNodeId": 1065 - }, - { - "nodeId": "1071", - "ignored": false, - "role": { - "type": "role", - "value": "contentinfo" - }, - "chromeRole": { - "type": "internalRole", - "value": 85 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "title" - } - ] - }, - "properties": [], - "parentId": "862", - "childIds": ["1072"], - "backendDOMNodeId": 1071 - }, - { - "nodeId": "864", - "ignored": true, - "ignoredReasons": [ - { - "name": "uninteresting", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "863", - "childIds": ["865", "872", "874"], - "backendDOMNodeId": 864 - }, - { - "nodeId": "865", - "ignored": false, - "role": { 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    Protocol Visualizer

    - Preview -
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    - Simulate your Opentrons Python protocols and inspect deck - layout and liquid volumes in real time — without leaving - VSCode. -

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    - Everything you need to see your protocol run -

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      - Real-time Deck Visualization -

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      - Deck state and liquid volume changes render in real time - through an interactive panel while your protocol runs. -

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      Auto-analysis on Save

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      - The simulation automatically reruns whenever you save - changes (Ctrl+S / Cmd+S) to your protocol file. -

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      Runtime Parameters UI

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      - Input fields are generated for Opentrons Runtime - Parameters; hit Analyze to apply them — your original code - is never modified. -

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      Custom Labware Support

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      - Place custom labware definition files (.json) in the same - directory as your protocol file and they just work. -

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      Pop-out Window

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      - Pop the panel out to its own window or drag the tab to - another monitor via VSCode's Auxiliary Window support. -

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      Step Jumper

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      - Enter any step number under Protocol Steps and hit Enter - to jump the visualization state instantly. -

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    - Generate protocols with AI, verify with Protocol Visualizer -

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    - Connect Protocol Visualizer to your LLM with - protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, - then simulate and fix them in a visual feedback loop. -

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    - Generate a protocol from a prompt, then fix it while watching - the simulation -
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    How to use

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    1. Install VSCode or Cursor
    2. -
    3. - Install the skill: - npx skills add koji/protocol-fix-loop - (see - koji/protocol-fix-loop) -
    4. -
    5. - Install the Protocol Visualizer extension (see - Installation guide) -
    6. -
    7. - Use - /protocol-fix-loop - in chat and add your prompt to generate a protocol -
    8. -
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    - Protocol Visualizer visualizing an Opentrons protocol on a simulated deck -
    - Protocol Visualizer in action -
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    Want to try the extension?

    -

    - Request access via our form — requests are handled individually. -

    - Request access -
    -
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    Installation

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    Prerequisites

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    • - Python 3.8 or later, with - python3 available in PATH -
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    • - The opentrons Python package: - pip install opentrons -
    • -
    • - For OT-2 use - pip install opentrons==9.0.0 - (opentrons 9.1.0+ dropped OT-2 support) -
    • -
    • - Select the matching Python interpreter in VSCode via - Python: Select Interpreter -
    • -
    • - Using both Flex and OT-2? Keep them in a separate virtual - environment each and switch per protocol. -
    • -
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    - Method A: Command Palette -

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    1. - Open the Command Palette (Cmd+Shift+P / - Ctrl+Shift+P) -
    2. -
    3. - Select Extensions: Install from VSIX... -
    4. -
    5. Choose the downloaded .vsix file
    6. -
    -
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    Method B: Command line

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    code --install-extension protocol-visualizer.vsix
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    - MIT License © 2026 Koji Kanao - -
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    - - - diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/result.json deleted file mode 100644 index 738a632..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/ai-workflow/result.json +++ /dev/null @@ -1,55 +0,0 @@ -{ - "feature": "ai-workflow", - "url": "http://127.0.0.1:5180/", - "passed": 7, - "total": 7, - "ok": true, - "checks": [ - { - "id": "ai-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "ai-heading", - "pass": true, - "value": "Generate protocols with AI, verify with Protocol Visualizer", - "error": null - }, - { - "id": "ai-video", - "pass": true, - "value": { - "src": "https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf", - "controls": true - }, - "error": null - }, - { - "id": "ai-skill-command", - "pass": true, - "value": true, - "error": null - }, - { - "id": 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    Protocol Visualizer

    - Preview -
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    - Simulate your Opentrons Python protocols and inspect deck - layout and liquid volumes in real time — without leaving - VSCode. -

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    - Everything you need to see your protocol run -

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      - Real-time Deck Visualization -

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      - Deck state and liquid volume changes render in real time - through an interactive panel while your protocol runs. -

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      Auto-analysis on Save

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      - The simulation automatically reruns whenever you save - changes (Ctrl+S / Cmd+S) to your protocol file. -

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      Runtime Parameters UI

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      - Input fields are generated for Opentrons Runtime - Parameters; hit Analyze to apply them — your original code - is never modified. -

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      Custom Labware Support

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      - Place custom labware definition files (.json) in the same - directory as your protocol file and they just work. -

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      Pop-out Window

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      - Pop the panel out to its own window or drag the tab to - another monitor via VSCode's Auxiliary Window support. -

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      Step Jumper

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      - Enter any step number under Protocol Steps and hit Enter - to jump the visualization state instantly. -

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    - Generate protocols with AI, verify with Protocol Visualizer -

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    - Connect Protocol Visualizer to your LLM with - protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, - then simulate and fix them in a visual feedback loop. -

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    - Generate a protocol from a prompt, then fix it while watching - the simulation -
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    How to use

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    1. Install VSCode or Cursor
    2. -
    3. - Install the skill: - npx skills add koji/protocol-fix-loop - (see - koji/protocol-fix-loop) -
    4. -
    5. - Install the Protocol Visualizer extension (see - Installation guide) -
    6. -
    7. - Use - /protocol-fix-loop - in chat and add your prompt to generate a protocol -
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    - Protocol Visualizer visualizing an Opentrons protocol on a simulated deck -
    - Protocol Visualizer in action -
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    Want to try the extension?

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    - Request access via our form — requests are handled individually. -

    - Request access -
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    Installation

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    Prerequisites

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    • - Python 3.8 or later, with - python3 available in PATH -
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    • - The opentrons Python package: - pip install opentrons -
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    • - For OT-2 use - pip install opentrons==9.0.0 - (opentrons 9.1.0+ dropped OT-2 support) -
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    • - Select the matching Python interpreter in VSCode via - Python: Select Interpreter -
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    • - Using both Flex and OT-2? Keep them in a separate virtual - environment each and switch per protocol. -
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    - Method A: Command Palette -

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    1. - Open the Command Palette (Cmd+Shift+P / - Ctrl+Shift+P) -
    2. -
    3. - Select Extensions: Install from VSIX... -
    4. -
    5. Choose the downloaded .vsix file
    6. -
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    Method B: Command line

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    code --install-extension protocol-visualizer.vsix
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    - MIT License © 2026 Koji Kanao - -
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    - - - diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/result.json deleted file mode 100644 index 1b630c9..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/features-grid/result.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "feature": "features-grid", - "url": "http://127.0.0.1:5180/", - "passed": 3, - "total": 3, - "ok": true, - "checks": [ - { - "id": "features-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "features-heading", - "pass": true, - "value": "Everything you need to see your protocol run", - "error": null - }, - { - "id": "features-cards", - "pass": true, - "value": [ - "Real-time Deck Visualization", - "Auto-analysis on Save", - "Runtime Parameters UI", - "Custom Labware Support", - "Pop-out Window", - "Step Jumper" - ], - "error": null - } - ], - "finishedAt": "2026-09-16T07:46:28.965Z" -} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/axtree.json deleted file mode 100644 index b609602..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/axtree.json +++ /dev/null @@ -1,11408 +0,0 @@ -[ - 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    -
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    Protocol Visualizer

    - Preview -
    -

    - Simulate your Opentrons Python protocols and inspect deck - layout and liquid volumes in real time — without leaving - VSCode. -

    - -
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    - Everything you need to see your protocol run -

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      - Real-time Deck Visualization -

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      - Deck state and liquid volume changes render in real time - through an interactive panel while your protocol runs. -

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      Auto-analysis on Save

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      - The simulation automatically reruns whenever you save - changes (Ctrl+S / Cmd+S) to your protocol file. -

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      Runtime Parameters UI

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      - Input fields are generated for Opentrons Runtime - Parameters; hit Analyze to apply them — your original code - is never modified. -

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      Custom Labware Support

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      - Place custom labware definition files (.json) in the same - directory as your protocol file and they just work. -

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      Pop-out Window

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      - Pop the panel out to its own window or drag the tab to - another monitor via VSCode's Auxiliary Window support. -

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      Step Jumper

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      - Enter any step number under Protocol Steps and hit Enter - to jump the visualization state instantly. -

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    - Generate protocols with AI, verify with Protocol Visualizer -

    -

    - Connect Protocol Visualizer to your LLM with - protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, - then simulate and fix them in a visual feedback loop. -

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    - Generate a protocol from a prompt, then fix it while watching - the simulation -
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    How to use

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    1. Install VSCode or Cursor
    2. -
    3. - Install the skill: - npx skills add koji/protocol-fix-loop - (see - koji/protocol-fix-loop) -
    4. -
    5. - Install the Protocol Visualizer extension (see - Installation guide) -
    6. -
    7. - Use - /protocol-fix-loop - in chat and add your prompt to generate a protocol -
    8. -
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    - Protocol Visualizer visualizing an Opentrons protocol on a simulated deck -
    - Protocol Visualizer in action -
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    Want to try the extension?

    -

    - Request access via our form — requests are handled individually. -

    - Request access -
    -
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    Installation

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    Prerequisites

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    • - Python 3.8 or later, with - python3 available in PATH -
    • -
    • - The opentrons Python package: - pip install opentrons -
    • -
    • - For OT-2 use - pip install opentrons==9.0.0 - (opentrons 9.1.0+ dropped OT-2 support) -
    • -
    • - Select the matching Python interpreter in VSCode via - Python: Select Interpreter -
    • -
    • - Using both Flex and OT-2? Keep them in a separate virtual - environment each and switch per protocol. -
    • -
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    - Method A: Command Palette -

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    1. - Open the Command Palette (Cmd+Shift+P / - Ctrl+Shift+P) -
    2. -
    3. - Select Extensions: Install from VSIX... -
    4. -
    5. Choose the downloaded .vsix file
    6. -
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    Method B: Command line

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    code --install-extension protocol-visualizer.vsix
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    - MIT License © 2026 Koji Kanao - -
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    - - - diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/result.json deleted file mode 100644 index 0fa0106..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/hero/result.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "feature": "hero", - "url": "http://127.0.0.1:5180/", - "passed": 4, - "total": 4, - "ok": true, - "checks": [ - { - "id": "hero-headline", - "pass": true, - "value": "Protocol Visualizer", - "error": null - }, - { - "id": "hero-tagline", - "pass": true, - "value": "Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.", - "error": null - }, - { - "id": "hero-request-access-links", - "pass": true, - "value": { - "count": 3, - "hrefs": [ - "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor", - "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor", - 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"childIds": [] - }, - { - "nodeId": "-1000001261", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "code --install-extension protocol-visualizer.vsix" - }, - "properties": [], - "parentId": "1691", - "childIds": [] - }, - { - "nodeId": "-1000001161", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Real-time Deck Visualization" - }, - "properties": [], - "parentId": "1606", - "childIds": [] - }, - { - "nodeId": "-1000001162", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Deck state and liquid volume changes " - }, - "properties": [], - 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}, - "properties": [], - "parentId": "1611", - "childIds": [] - }, - { - "nodeId": "-1000001172", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "them — your original code is never " - }, - "properties": [], - "parentId": "1611", - "childIds": [] - }, - { - "nodeId": "-1000001173", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "modified." - }, - "properties": [], - "parentId": "1611", - "childIds": [] - }, - { - "nodeId": "-1000001174", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Custom Labware Support" - }, - "properties": [], - "parentId": "1612", - "childIds": [] - }, - { - "nodeId": "-1000001175", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Place custom labware definition files (.json) " - }, - "properties": [], - "parentId": "1613", - "childIds": [] - }, - { - "nodeId": "-1000001176", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "in the same directory as your protocol file " - }, - "properties": [], - "parentId": "1613", - "childIds": [] - }, - { - "nodeId": "-1000001177", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and they just work." - 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"properties": [], - "parentId": "1943", - "childIds": [], - "backendDOMNodeId": 1944 - }, - { - "nodeId": "1946", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1945", - "childIds": [], - "backendDOMNodeId": 1946 - } -] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html deleted file mode 100644 index 41ef3bd..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/dom.html +++ /dev/null @@ -1,1089 +0,0 @@ - - - - - - - - - - - - - - - Protocol Visualizer — Simulate Opentrons protocols in VSCode - 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    Protocol Visualizer

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    - Simulate your Opentrons Python protocols and inspect deck - layout and liquid volumes in real time — without leaving - VSCode. -

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    - Everything you need to see your protocol run -

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      - Real-time Deck Visualization -

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      - Deck state and liquid volume changes render in real time - through an interactive panel while your protocol runs. -

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      Auto-analysis on Save

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      - The simulation automatically reruns whenever you save - changes (Ctrl+S / Cmd+S) to your protocol file. -

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      Runtime Parameters UI

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      - Input fields are generated for Opentrons Runtime - Parameters; hit Analyze to apply them — your original code - is never modified. -

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      Custom Labware Support

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      - Place custom labware definition files (.json) in the same - directory as your protocol file and they just work. -

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      Pop-out Window

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      - Pop the panel out to its own window or drag the tab to - another monitor via VSCode's Auxiliary Window support. -

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      Step Jumper

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      - Enter any step number under Protocol Steps and hit Enter - to jump the visualization state instantly. -

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    - Generate protocols with AI, verify with Protocol Visualizer -

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    - Connect Protocol Visualizer to your LLM with - protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, - then simulate and fix them in a visual feedback loop. -

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    - Generate a protocol from a prompt, then fix it while watching - the simulation -
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    How to use

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    1. Install VSCode or Cursor
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    3. - Install the skill: - npx skills add koji/protocol-fix-loop - (see - koji/protocol-fix-loop) -
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    5. - Install the Protocol Visualizer extension (see - Installation guide) -
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    7. - Use - /protocol-fix-loop - in chat and add your prompt to generate a protocol -
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    - Protocol Visualizer visualizing an Opentrons protocol on a simulated deck -
    - Protocol Visualizer in action -
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    Want to try the extension?

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    - Request access via our form — requests are handled individually. -

    - Request access -
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    Installation

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    Prerequisites

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    • - Python 3.8 or later, with - python3 available in PATH -
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    • - The opentrons Python package: - pip install opentrons -
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    • - For OT-2 use - pip install opentrons==9.0.0 - (opentrons 9.1.0+ dropped OT-2 support) -
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    • - Select the matching Python interpreter in VSCode via - Python: Select Interpreter -
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    • - Using both Flex and OT-2? Keep them in a separate virtual - environment each and switch per protocol. -
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    - Method A: Command Palette -

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    1. - Open the Command Palette (Cmd+Shift+P / - Ctrl+Shift+P) -
    2. -
    3. - Select Extensions: Install from VSIX... -
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    5. Choose the downloaded .vsix file
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    Method B: Command line

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    code --install-extension protocol-visualizer.vsix
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    - MIT License © 2026 Koji Kanao - -
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    -
    -
    - - - diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/result.json deleted file mode 100644 index 03db2a5..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/install-guide/result.json +++ /dev/null @@ -1,47 +0,0 @@ -{ - "feature": "install-guide", - "url": "http://127.0.0.1:5180/", - "passed": 5, - "total": 5, - "ok": true, - "checks": [ - { - "id": "install-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "install-prereqs", - "pass": true, - "value": "InstallationPrerequisitesPython 3.8 or later, with python3 available in PATHThe opentrons Python package: pip install opentronsFor OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)Select the matching Python interpreter in VSCode via Python: Select InterpreterUsing both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.Method A: Command PaletteOpen the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)Select Extensions: Install from VSIX...Choose the downloaded .vsix fileMethod B: Command linecode --install-extension protocol-visualizer.vsix", - "error": null - }, - { - "id": "install-cli-method", - "pass": true, - "value": true, - "error": null - }, - { - "id": "header-nav", - "pass": true, - "value": [ - ["Features", "#features"], - ["Install", "#install"] - ], - "error": null - }, - { - "id": "anchor-navigation", - "pass": true, - "value": { - "hash": "#install", - "top": 0, - "vh": 749 - }, - "error": null - } - ], - "finishedAt": "2026-09-16T07:46:34.620Z" -} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/axtree.json deleted file mode 100644 index 98c1e58..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/axtree.json +++ /dev/null @@ -1,11427 +0,0 @@ -[ - 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    Protocol Visualizer

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    - Simulate your Opentrons Python protocols and inspect deck - layout and liquid volumes in real time — without leaving - VSCode. -

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    - Everything you need to see your protocol run -

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      - Real-time Deck Visualization -

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      - Deck state and liquid volume changes render in real time - through an interactive panel while your protocol runs. -

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      Auto-analysis on Save

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      - The simulation automatically reruns whenever you save - changes (Ctrl+S / Cmd+S) to your protocol file. -

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      Runtime Parameters UI

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      - Input fields are generated for Opentrons Runtime - Parameters; hit Analyze to apply them — your original code - is never modified. -

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      Custom Labware Support

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      - Place custom labware definition files (.json) in the same - directory as your protocol file and they just work. -

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      Pop-out Window

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      - Pop the panel out to its own window or drag the tab to - another monitor via VSCode's Auxiliary Window support. -

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      Step Jumper

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      - Enter any step number under Protocol Steps and hit Enter - to jump the visualization state instantly. -

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    - Generate protocols with AI, verify with Protocol Visualizer -

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    - Connect Protocol Visualizer to your LLM with - protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, - then simulate and fix them in a visual feedback loop. -

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    - Generate a protocol from a prompt, then fix it while watching - the simulation -
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    How to use

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    1. Install VSCode or Cursor
    2. -
    3. - Install the skill: - npx skills add koji/protocol-fix-loop - (see - koji/protocol-fix-loop) -
    4. -
    5. - Install the Protocol Visualizer extension (see - Installation guide) -
    6. -
    7. - Use - /protocol-fix-loop - in chat and add your prompt to generate a protocol -
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    - Protocol Visualizer visualizing an Opentrons protocol on a simulated deck -
    - Protocol Visualizer in action -
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    Want to try the extension?

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    - Request access via our form — requests are handled individually. -

    - Request access -
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    Installation

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    Prerequisites

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    • - Python 3.8 or later, with - python3 available in PATH -
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    • - The opentrons Python package: - pip install opentrons -
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    • - For OT-2 use - pip install opentrons==9.0.0 - (opentrons 9.1.0+ dropped OT-2 support) -
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    • - Select the matching Python interpreter in VSCode via - Python: Select Interpreter -
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    • - Using both Flex and OT-2? Keep them in a separate virtual - environment each and switch per protocol. -
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    - Method A: Command Palette -

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    1. - Open the Command Palette (Cmd+Shift+P / - Ctrl+Shift+P) -
    2. -
    3. - Select Extensions: Install from VSIX... -
    4. -
    5. Choose the downloaded .vsix file
    6. -
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    Method B: Command line

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    code --install-extension protocol-visualizer.vsix
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    - MIT License © 2026 Koji Kanao - -
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    - - - diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/result.json deleted file mode 100644 index 1283dc5..0000000 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/result.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "feature": "theme-toggle", - "url": "http://127.0.0.1:5180/", - "passed": 3, - "total": 3, - "ok": true, - "checks": [ - { - "id": "toggle-present", - "pass": true, - "value": "Switch to light theme", - "error": null - }, - { - "id": "toggle-flips-theme", - "pass": true, - "value": { - "before": "dark", - "after": "light", - "stored": "light" - }, - "error": null - }, - { - "id": "toggle-restores", - "pass": true, - "value": { - "theme": "dark", - "stored": "dark", - "label": "Switch to light theme", - "flipped": "light" - }, - "error": null - } - ], - "finishedAt": "2026-09-16T07:46:33.030Z" -} diff --git 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"properties": [], + "parentId": "1081", + "childIds": [], + "backendDOMNodeId": 1082 + } +] \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html new file mode 100644 index 0000000..d99e238 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + Protocol Visualizer — Simulate Opentrons protocols in VSCode + + + +

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
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"properties": [], + "parentId": "721", + "childIds": [], + "backendDOMNodeId": 722 + } +] \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html new file mode 100644 index 0000000..d99e238 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + Protocol Visualizer — Simulate Opentrons protocols in VSCode + + + +

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
    + + + + \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/result.json new file mode 100644 index 0000000..24d195c --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/result.json @@ -0,0 +1,35 @@ +{ + "feature": "features-grid", + "url": "http://127.0.0.1:5181/", + "passed": 3, + "total": 3, + "ok": true, + "checks": [ + { + "id": "features-region", + "pass": true, + "value": true, + "error": null + }, + { + "id": "features-heading", + "pass": true, + "value": "Everything you need to see your protocol run", + "error": null + }, + { + "id": "features-cards", + "pass": true, + "value": [ + "Real-time Deck Visualization", + "Auto-analysis on Save", + "Runtime Parameters UI", + "Custom Labware Support", + "Pop-out Window", + "Step Jumper" + ], + "error": null + } + ], + "finishedAt": 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"backendDOMNodeId": 128 + } +] \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html new file mode 100644 index 0000000..d99e238 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + Protocol Visualizer — Simulate Opentrons protocols in VSCode + + + +

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
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"relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1932", + "childIds": [], + "backendDOMNodeId": 1933 + } +] \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html new file mode 100644 index 0000000..d99e238 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + Protocol Visualizer — Simulate Opentrons protocols in VSCode + + + +

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
    + + + + \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/result.json new file mode 100644 index 0000000..4b083f1 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/result.json @@ -0,0 +1,53 @@ +{ + "feature": "install-guide", + "url": "http://127.0.0.1:5181/", + "passed": 5, + "total": 5, + "ok": true, + "checks": [ + { + "id": "install-region", + "pass": true, + "value": true, + "error": null + }, + { + "id": "install-prereqs", + "pass": true, + "value": "InstallationPrerequisitesPython 3.8 or later, with python3 available in PATHThe opentrons Python package: pip install opentronsFor OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)Select the matching Python interpreter in VSCode via Python: Select InterpreterUsing both Flex and OT-2? 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"relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1303", + "childIds": [], + "backendDOMNodeId": 1304 + } +] \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/dom.html new file mode 100644 index 0000000..d99e238 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/dom.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + Protocol Visualizer — Simulate Opentrons protocols in VSCode + + + +

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
    + + + + \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/result.json new file mode 100644 index 0000000..36b65d3 --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/result.json @@ -0,0 +1,37 @@ +{ + "feature": "theme-toggle", + "url": "http://127.0.0.1:5181/", + "passed": 3, + "total": 3, + "ok": true, + "checks": [ + { + "id": "toggle-present", + "pass": true, + "value": "Switch to light theme", + "error": null + }, + { + "id": "toggle-flips-theme", + "pass": true, + "value": { + "before": "dark", + "after": "light", + "stored": "light" + }, + "error": null + }, + { + "id": "toggle-restores", + "pass": true, + "value": { + "theme": "dark", + "stored": "dark", + "label": "Switch to light theme", + "flipped": "light" + }, + "error": null + } + ], + "finishedAt": "2026-09-16T07:56:16.174Z" +} \ No newline at end of file diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/screenshot.png b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/screenshot.png similarity index 100% rename from .opencode/skills/verify-web/artifacts/2026-09-16T07-46-20-848Z/theme-toggle/screenshot.png rename to .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/screenshot.png diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/vite-server.log b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/vite-server.log new file mode 100644 index 0000000..c7dbace --- /dev/null +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/vite-server.log @@ -0,0 +1,13 @@ + + VITE v8.2.2 ready in 192 ms + + ➜ Local: http://127.0.0.1:5181/ +3:56:10 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html +3:56:10 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html +3:56:12 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html +3:56:12 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html +3:56:13 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html +3:56:13 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html +3:56:16 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/dom.html +3:56:17 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html +3:56:17 AM [vite] (client) page reload .opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html diff --git a/src/App.tsx b/src/App.tsx index 52ca598..36b001a 100644 --- a/src/App.tsx +++ b/src/App.tsx @@ -19,8 +19,8 @@ export default function App(): ReactNode {
    - +
    From 669955dc129ed170c535bfff2b21e3edee392913 Mon Sep 17 00:00:00 2001 From: koji Date: Wed, 16 Sep 2026 03:59:34 -0400 Subject: [PATCH 5/5] fix format errors --- .../ai-workflow/axtree.json | 23059 ++++++++------- .../ai-workflow/dom.html | 1663 +- .../ai-workflow/result.json | 108 +- .../features-grid/axtree.json | 23049 ++++++++------- .../features-grid/dom.html | 1663 +- .../features-grid/result.json | 68 +- .../2026-09-16T07-56-03-875Z/hero/axtree.json | 23049 ++++++++------- .../2026-09-16T07-56-03-875Z/hero/dom.html | 1663 +- .../2026-09-16T07-56-03-875Z/hero/result.json | 84 +- .../install-guide/axtree.json | 23068 ++++++++-------- .../install-guide/dom.html | 1663 +- .../install-guide/result.json | 98 +- .../theme-toggle/axtree.json | 23068 ++++++++-------- .../theme-toggle/dom.html | 1663 +- .../theme-toggle/result.json | 72 +- 15 files changed, 61703 insertions(+), 62335 deletions(-) diff --git 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"ignoredReasons": [ - { - "name": "presentationalRole", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "794", - "childIds": [] - }, - { - "nodeId": "-1000000602", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Choose the downloaded " - }, - "properties": [], - "parentId": "823", - "childIds": [] - }, - { - "nodeId": "824", - "ignored": false, - "role": { - "type": "internalRole", - "value": "StaticText" - }, - "chromeRole": { - "type": "internalRole", - "value": 158 - }, - "name": { - "type": "computedString", - "value": ".vsix", - "sources": [ - { - "type": "contents", - "value": { + }, + "properties": [], + "parentId": "753", + "childIds": [] + }, + { + "nodeId": "-1000000529", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "Enter any step number under Protocol Steps " + }, + "properties": [], + "parentId": "754", + "childIds": [] + }, + { + "nodeId": "-1000000530", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "and hit Enter to jump the visualization state " + }, + "properties": [], + "parentId": "754", + "childIds": [] + }, + { + "nodeId": "-1000000531", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "instantly." + }, + "properties": [], + "parentId": "754", + "childIds": [] + }, + { + "nodeId": "1079", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1078", + "childIds": ["1080"], + "backendDOMNodeId": 1079 + }, + { + "nodeId": "1081", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1078", + "childIds": ["1082"], + "backendDOMNodeId": 1081 + }, + { + "nodeId": "-1000000600", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "Extensions: Install " + }, + "properties": [], + "parentId": "822", + "childIds": [] + }, + { + "nodeId": "-1000000601", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "from VSIX..." + }, + "properties": [], + "parentId": "822", + "childIds": [] + }, + { + "nodeId": "-1000000603", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { "type": "computedString", "value": ".vsix" - } - } - ] - }, - "properties": [], - "parentId": "1057", - "childIds": [ - "-1000000603" - ], - "backendDOMNodeId": 824 - }, - { - "nodeId": "-1000000604", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "file" - }, - "properties": [], - "parentId": "825", - "childIds": [] - }, - { - "nodeId": "-1000000606", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "code --install-extension protocol-visualizer.vsix" - }, - "properties": [], - "parentId": "827", - "childIds": [] - }, - { - "nodeId": "-1000000507", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Real-time Deck Visualization" - }, - "properties": [], - "parentId": "743", - "childIds": [] - }, - { - "nodeId": "-1000000508", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Deck state and liquid volume changes " - }, - "properties": [], - "parentId": "744", - "childIds": [] - }, - { - "nodeId": "-1000000509", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "render in real time through an interactive " - }, - "properties": [], - "parentId": "744", - "childIds": [] - }, - { - "nodeId": "-1000000510", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "panel while your protocol runs." - }, - "properties": [], - "parentId": "744", - "childIds": [] - }, - { - "nodeId": "-1000000511", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Auto-analysis on Save" - }, - "properties": [], - "parentId": "745", - "childIds": [] - }, - { - "nodeId": "-1000000512", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "The simulation automatically reruns " - }, - "properties": [], - "parentId": "746", - "childIds": [] - }, - { - "nodeId": "-1000000513", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "whenever you save changes (Ctrl+S / " - }, - "properties": [], - "parentId": "746", - "childIds": [] - }, - { - "nodeId": "-1000000514", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Cmd+S) to your protocol file." - }, - "properties": [], - "parentId": "746", - "childIds": [] - }, - { - "nodeId": "-1000000515", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters UI" - }, - "properties": [], - "parentId": "747", - "childIds": [] - }, - { - "nodeId": "-1000000516", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Input fields are generated for Opentrons " - }, - "properties": [], - "parentId": "748", - "childIds": [] - }, - { - "nodeId": "-1000000517", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters; hit Analyze to apply " - }, - "properties": [], - "parentId": "748", - "childIds": [] - }, - { - "nodeId": "-1000000518", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "them — your original code is never " - }, - "properties": [], - "parentId": "748", - "childIds": [] - }, - { - "nodeId": "-1000000519", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "modified." - }, - "properties": [], - "parentId": "748", - "childIds": [] - }, - { - "nodeId": "-1000000520", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Custom Labware Support" - }, - "properties": [], - "parentId": "749", - "childIds": [] - }, - { - "nodeId": "-1000000521", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Place custom labware definition files (.json) " - }, - "properties": [], - "parentId": "750", - "childIds": [] - }, - { - "nodeId": "-1000000522", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "in the same directory as your protocol file " - }, - "properties": [], - "parentId": "750", - "childIds": [] - }, - { - "nodeId": "-1000000523", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and they just work." - }, - "properties": [], - "parentId": "750", - "childIds": [] - }, - { - "nodeId": "-1000000524", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop-out Window" - }, - "properties": [], - "parentId": "751", - "childIds": [] - }, - { - "nodeId": "-1000000525", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop the panel out to its own window or " - }, - "properties": [], - "parentId": "752", - "childIds": [] - }, - { - "nodeId": "-1000000526", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "drag the tab to another monitor via " - }, - "properties": [], - "parentId": "752", - "childIds": [] - }, - { - "nodeId": "-1000000527", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "VSCode's Auxiliary Window support." - }, - "properties": [], - "parentId": "752", - "childIds": [] - }, - { - "nodeId": "-1000000528", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Step Jumper" - }, - "properties": [], - "parentId": "753", - "childIds": [] - }, - { - "nodeId": "-1000000529", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Enter any step number under Protocol Steps " - }, - "properties": [], - "parentId": "754", - "childIds": [] - }, - { - "nodeId": "-1000000530", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and hit Enter to jump the visualization state " - }, - "properties": [], - "parentId": "754", - "childIds": [] - }, - { - "nodeId": "-1000000531", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "instantly." - }, - "properties": [], - "parentId": "754", - "childIds": [] - }, - { - "nodeId": "1079", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1078", - "childIds": [ - "1080" - ], - "backendDOMNodeId": 1079 - }, - { - "nodeId": "1081", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1078", - "childIds": [ - "1082" - ], - "backendDOMNodeId": 1081 - }, - { - "nodeId": "-1000000600", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Extensions: Install " - }, - "properties": [], - "parentId": "822", - "childIds": [] - }, - { - "nodeId": "-1000000601", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "from VSIX..." - }, - "properties": [], - "parentId": "822", - "childIds": [] - }, - { - "nodeId": "-1000000603", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": ".vsix" - }, - "properties": [], - "parentId": "824", - "childIds": [] - }, - { - "nodeId": "1080", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1079", - "childIds": [], - "backendDOMNodeId": 1080 - }, - { - "nodeId": "1082", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1081", - "childIds": [], - "backendDOMNodeId": 1082 - } -] \ No newline at end of file + }, + "properties": [], + "parentId": "824", + "childIds": [] + }, + { + "nodeId": "1080", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1079", + "childIds": [], + "backendDOMNodeId": 1080 + }, + { + "nodeId": "1082", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1081", + "childIds": [], + "backendDOMNodeId": 1082 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html index d99e238..ad39db5 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    +

    Protocol Visualizer

    + Preview +
    +

    + Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

    + +
    + +
    +
    +
    +
    +

    + Everything you need to see your protocol run +

    +
      +
    • +
      +

      + Real-time Deck Visualization +

      +

      + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

      +
      +
    • +
    • +
      +

      Auto-analysis on Save

      +

      + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

      +
      +
    • +
    • +
      +

      Runtime Parameters UI

      +

      + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

      +
      +
    • +
    • +
      +

      Custom Labware Support

      +

      + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

      +
      +
    • +
    • +
      +

      Pop-out Window

      +

      + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

      +
      +
    • +
    • +
      +

      Step Jumper

      +

      + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

      +
      +
    • +
    +
    +
    +
    +
    +
    + Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
    + Protocol Visualizer in action +
    +
    +
    +
    +
    +
    +

    + Generate protocols with AI, verify with Protocol Visualizer +

    +

    + Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

    +
    + +
    + Generate a protocol from a prompt, then fix it while watching + the simulation +
    +
    +

    How to use

    +
      +
    1. Install VSCode or Cursor
    2. +
    3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
    4. +
    5. + Install the Protocol Visualizer extension (see + Installation guide) +
    6. +
    7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
    8. +
    +
    +
    +
    +
    +

    Want to try the extension?

    +

    + Request access via our form — requests are handled individually. +

    + Request access +
    +
    +
    +
    +

    Installation

    +
    +
    +

    Prerequisites

    +
      +
    • + Python 3.8 or later, with + python3 available in PATH +
    • +
    • + The opentrons Python package: + pip install opentrons +
    • +
    • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
    • +
    • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
    • +
    • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
    • +
    +
    +
    +

    + Method A: Command Palette +

    +
      +
    1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
    2. +
    3. + Select Extensions: Install from VSIX... +
    4. +
    5. Choose the downloaded .vsix file
    6. +
    +
    +
    +

    Method B: Command line

    +
    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    +
    +
    + +
    +
    + MIT License © 2026 Koji Kanao + +
    +
    +
    +
    - - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/result.json index 0fd499c..5eb66ca 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/ai-workflow/result.json @@ -1,55 +1,55 @@ { - "feature": "ai-workflow", - "url": "http://127.0.0.1:5181/", - "passed": 7, - "total": 7, - "ok": true, - "checks": [ - { - "id": "ai-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "ai-heading", - "pass": true, - "value": "Generate protocols with AI, verify with Protocol Visualizer", - "error": null - }, - { - "id": "ai-video", - "pass": true, - "value": { - "src": "https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf", - "controls": true - }, - "error": null - }, - { - "id": "ai-skill-command", - "pass": true, - "value": true, - "error": null - }, - { - "id": "ai-slash-command", - "pass": true, - "value": true, - "error": null - }, - { - "id": "ai-skill-links", - "pass": true, - "value": 2, - "error": null - }, - { - "id": "ai-install-link", - "pass": true, - "value": true, - "error": null - } - ], - "finishedAt": "2026-09-16T07:56:13.724Z" -} \ No newline at end of file + "feature": "ai-workflow", + "url": "http://127.0.0.1:5181/", + "passed": 7, + "total": 7, + "ok": true, + "checks": [ + { + "id": "ai-region", + "pass": true, + "value": true, + "error": null + }, + { + "id": "ai-heading", + "pass": true, + "value": "Generate protocols with AI, verify with Protocol Visualizer", + "error": null + }, + { + "id": "ai-video", + "pass": true, + "value": { + "src": "https://github.com/user-attachments/assets/812fbcdf-a84a-49fd-b631-ae925b64dddf", + "controls": true + }, + "error": null + }, + { + "id": "ai-skill-command", + "pass": true, + "value": true, + "error": null + }, + { + "id": "ai-slash-command", + "pass": true, + "value": true, + "error": null + }, + { + "id": "ai-skill-links", + "pass": true, + "value": 2, + "error": null + }, + { + "id": "ai-install-link", + "pass": true, + "value": true, + "error": null + } + ], + "finishedAt": "2026-09-16T07:56:13.724Z" +} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/axtree.json index 0b9c977..e5a1905 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/axtree.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/axtree.json @@ -1,11967 +1,11360 @@ [ - { - "nodeId": "366", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol 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} - } - ] - }, - "properties": [], - "parentId": "697", - "childIds": [ - "-1000000362" - ], - "backendDOMNodeId": 464 - }, - { - "nodeId": "-1000000363", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "file" - }, - "properties": [], - "parentId": "465", - "childIds": [] - }, - { - "nodeId": "-1000000365", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "code --install-extension protocol-visualizer.vsix" - }, - "properties": [], - "parentId": "467", - "childIds": [] - }, - { - "nodeId": "-1000000266", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Real-time Deck Visualization" - }, - "properties": [], - "parentId": "383", - "childIds": [] - }, - { - "nodeId": "-1000000267", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Deck state and liquid volume changes " - }, - "properties": [], - "parentId": "384", - "childIds": [] - }, - { - "nodeId": "-1000000268", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "render in real time through an interactive " - }, - "properties": [], - "parentId": "384", - "childIds": [] - }, - { - "nodeId": "-1000000269", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "panel while your protocol runs." - }, - "properties": [], - "parentId": "384", - "childIds": [] - }, - { - "nodeId": "-1000000270", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Auto-analysis on Save" - }, - "properties": [], - "parentId": "385", - "childIds": [] - }, - { - "nodeId": "-1000000271", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "The simulation automatically reruns " - }, - "properties": [], - "parentId": "386", - "childIds": [] - }, - { - "nodeId": "-1000000272", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - 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"value": 101 - }, - "name": { - "type": "computedString", - "value": "Step Jumper" - }, - "properties": [], - "parentId": "393", - "childIds": [] - }, - { - "nodeId": "-1000000288", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Enter any step number under Protocol Steps " - }, - "properties": [], - "parentId": "394", - "childIds": [] - }, - { - "nodeId": "-1000000289", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and hit Enter to jump the visualization state " - }, - "properties": [], - "parentId": "394", - "childIds": [] - }, - { - "nodeId": "-1000000290", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - 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"parentId": "718", - "childIds": [ - "722" - ], - "backendDOMNodeId": 721 - }, - { - "nodeId": "-1000000359", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Extensions: Install " - }, - "properties": [], - "parentId": "462", - "childIds": [] - }, - { - "nodeId": "-1000000360", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "from VSIX..." - }, - "properties": [], - "parentId": "462", - "childIds": [] - }, - { - "nodeId": "-1000000362", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": ".vsix" - }, - "properties": [], - "parentId": "464", - "childIds": [] - }, - { - "nodeId": "720", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "719", - "childIds": [], - "backendDOMNodeId": 720 - }, - { - "nodeId": "722", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "721", - "childIds": [], - "backendDOMNodeId": 722 - } -] \ No newline at end of file + }, + "properties": [], + "parentId": "464", + "childIds": [] + }, + { + "nodeId": "720", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "719", + "childIds": [], + "backendDOMNodeId": 720 + }, + { + "nodeId": "722", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "721", + "childIds": [], + "backendDOMNodeId": 722 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html index d99e238..ad39db5 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    +

    Protocol Visualizer

    + Preview +
    +

    + Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

    + +
    + +
    +
    +
    +
    +

    + Everything you need to see your protocol run +

    +
      +
    • +
      +

      + Real-time Deck Visualization +

      +

      + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

      +
      +
    • +
    • +
      +

      Auto-analysis on Save

      +

      + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

      +
      +
    • +
    • +
      +

      Runtime Parameters UI

      +

      + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

      +
      +
    • +
    • +
      +

      Custom Labware Support

      +

      + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

      +
      +
    • +
    • +
      +

      Pop-out Window

      +

      + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

      +
      +
    • +
    • +
      +

      Step Jumper

      +

      + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

      +
      +
    • +
    +
    +
    +
    +
    +
    + Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
    + Protocol Visualizer in action +
    +
    +
    +
    +
    +
    +

    + Generate protocols with AI, verify with Protocol Visualizer +

    +

    + Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

    +
    + +
    + Generate a protocol from a prompt, then fix it while watching + the simulation +
    +
    +

    How to use

    +
      +
    1. Install VSCode or Cursor
    2. +
    3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
    4. +
    5. + Install the Protocol Visualizer extension (see + Installation guide) +
    6. +
    7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
    8. +
    +
    +
    +
    +
    +

    Want to try the extension?

    +

    + Request access via our form — requests are handled individually. +

    + Request access +
    +
    +
    +
    +

    Installation

    +
    +
    +

    Prerequisites

    +
      +
    • + Python 3.8 or later, with + python3 available in PATH +
    • +
    • + The opentrons Python package: + pip install opentrons +
    • +
    • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
    • +
    • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
    • +
    • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
    • +
    +
    +
    +

    + Method A: Command Palette +

    +
      +
    1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
    2. +
    3. + Select Extensions: Install from VSIX... +
    4. +
    5. Choose the downloaded .vsix file
    6. +
    +
    +
    +

    Method B: Command line

    +
    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    +
    +
    + +
    +
    + MIT License © 2026 Koji Kanao + +
    +
    +
    +
    - - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/result.json index 24d195c..cb9001d 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/features-grid/result.json @@ -1,35 +1,35 @@ { - "feature": "features-grid", - "url": "http://127.0.0.1:5181/", - "passed": 3, - "total": 3, - "ok": true, - "checks": [ - { - "id": "features-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "features-heading", - "pass": true, - "value": "Everything you need to see your protocol run", - "error": null - }, - { - "id": "features-cards", - "pass": true, - "value": [ - "Real-time Deck Visualization", - "Auto-analysis on Save", - "Runtime Parameters UI", - "Custom Labware Support", - "Pop-out Window", - "Step Jumper" - ], - "error": null - } - ], - "finishedAt": "2026-09-16T07:56:12.143Z" -} \ No newline at end of file + "feature": "features-grid", + "url": "http://127.0.0.1:5181/", + "passed": 3, + "total": 3, + "ok": true, + "checks": [ + { + "id": "features-region", + "pass": true, + "value": true, + "error": null + }, + { + "id": "features-heading", + "pass": true, + "value": "Everything you need to see your protocol run", + "error": null + }, + { + "id": "features-cards", + "pass": true, + "value": [ + "Real-time Deck Visualization", + "Auto-analysis on Save", + "Runtime Parameters UI", + "Custom Labware Support", + "Pop-out Window", + "Step Jumper" + ], + "error": null + } + ], + "finishedAt": "2026-09-16T07:56:12.143Z" +} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/axtree.json index 5ea9d87..6ce5d9f 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/axtree.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/axtree.json @@ -1,11967 +1,11360 @@ [ - { - "nodeId": "2", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "aria-label", - "superseded": true - }, - { - "type": "relatedElement", - "value": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode" - }, - "nativeSource": "title" - } - ] - }, - "properties": [ - { - "name": "focusable", - "value": { - "type": "booleanOrUndefined", - "value": 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} - } - ] - }, - "properties": [], - "parentId": "250", - "childIds": [ - "-1000000121" - ], - "backendDOMNodeId": 359 - }, - { - "nodeId": "-1000000122", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "file" - }, - "properties": [], - "parentId": "360", - "childIds": [] - }, - { - "nodeId": "-1000000124", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "code --install-extension protocol-visualizer.vsix" - }, - "properties": [], - "parentId": "362", - "childIds": [] - }, - { - "nodeId": "-1000000013", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Real-time Deck Visualization" - }, - "properties": [], - "parentId": "277", - "childIds": [] - }, - { - "nodeId": "-1000000014", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Deck state and liquid volume changes " - }, - "properties": [], - "parentId": "278", - "childIds": [] - }, - { - "nodeId": "-1000000015", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "render in real time through an interactive " - }, - "properties": [], - "parentId": "278", - "childIds": [] - }, - { - "nodeId": "-1000000016", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "panel while your protocol runs." - }, - "properties": [], - "parentId": "278", - "childIds": [] - }, - { - "nodeId": "-1000000017", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Auto-analysis on Save" - }, - "properties": [], - "parentId": "279", - "childIds": [] - }, - { - "nodeId": "-1000000018", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "The simulation automatically reruns " - }, - "properties": [], - "parentId": "280", - "childIds": [] - }, - { - "nodeId": "-1000000019", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "whenever you save changes (Ctrl+S / " - }, - "properties": [], - "parentId": "280", - "childIds": [] - }, - { - "nodeId": "-1000000020", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Cmd+S) to your protocol file." - }, - "properties": [], - "parentId": "280", - "childIds": [] - }, - { - "nodeId": "-1000000021", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters UI" - }, - "properties": [], - "parentId": "281", - "childIds": [] - }, - { - "nodeId": "-1000000022", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - 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}, - "name": { - "type": "computedString", - "value": "in the same directory as your protocol file " - }, - "properties": [], - "parentId": "284", - "childIds": [] - }, - { - "nodeId": "-1000000029", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and they just work." - }, - "properties": [], - "parentId": "284", - "childIds": [] - }, - { - "nodeId": "-1000000030", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop-out Window" - }, - "properties": [], - "parentId": "285", - "childIds": [] - }, - { - "nodeId": "-1000000031", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - 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"value": 101 - }, - "name": { - "type": "computedString", - "value": "Step Jumper" - }, - "properties": [], - "parentId": "287", - "childIds": [] - }, - { - "nodeId": "-1000000035", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Enter any step number under Protocol Steps " - }, - "properties": [], - "parentId": "288", - "childIds": [] - }, - { - "nodeId": "-1000000036", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and hit Enter to jump the visualization state " - }, - "properties": [], - "parentId": "288", - "childIds": [] - }, - { - "nodeId": "-1000000037", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "instantly." - }, - "properties": [], - "parentId": "288", - "childIds": [] - }, - { - "nodeId": "125", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "124", - "childIds": [ - "126" - ], - "backendDOMNodeId": 125 - }, - { - "nodeId": "127", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - 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"childIds": [] - }, - { - "nodeId": "126", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "125", - "childIds": [], - "backendDOMNodeId": 126 - }, - { - "nodeId": "128", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "127", - "childIds": [], - "backendDOMNodeId": 128 - } -] \ No newline at end of file + }, + "properties": [], + "parentId": "359", + "childIds": [] + }, + { + "nodeId": "126", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "125", + "childIds": [], + "backendDOMNodeId": 126 + }, + { + "nodeId": "128", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "127", + "childIds": [], + "backendDOMNodeId": 128 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html index d99e238..ad39db5 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    +

    Protocol Visualizer

    + Preview +
    +

    + Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

    + +
    + +
    +
    +
    +
    +

    + Everything you need to see your protocol run +

    +
      +
    • +
      +

      + Real-time Deck Visualization +

      +

      + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

      +
      +
    • +
    • +
      +

      Auto-analysis on Save

      +

      + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

      +
      +
    • +
    • +
      +

      Runtime Parameters UI

      +

      + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

      +
      +
    • +
    • +
      +

      Custom Labware Support

      +

      + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

      +
      +
    • +
    • +
      +

      Pop-out Window

      +

      + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

      +
      +
    • +
    • +
      +

      Step Jumper

      +

      + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

      +
      +
    • +
    +
    +
    +
    +
    +
    + Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
    + Protocol Visualizer in action +
    +
    +
    +
    +
    +
    +

    + Generate protocols with AI, verify with Protocol Visualizer +

    +

    + Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

    +
    + +
    + Generate a protocol from a prompt, then fix it while watching + the simulation +
    +
    +

    How to use

    +
      +
    1. Install VSCode or Cursor
    2. +
    3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
    4. +
    5. + Install the Protocol Visualizer extension (see + Installation guide) +
    6. +
    7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
    8. +
    +
    +
    +
    +
    +

    Want to try the extension?

    +

    + Request access via our form — requests are handled individually. +

    + Request access +
    +
    +
    +
    +

    Installation

    +
    +
    +

    Prerequisites

    +
      +
    • + Python 3.8 or later, with + python3 available in PATH +
    • +
    • + The opentrons Python package: + pip install opentrons +
    • +
    • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
    • +
    • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
    • +
    • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
    • +
    +
    +
    +

    + Method A: Command Palette +

    +
      +
    1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
    2. +
    3. + Select Extensions: Install from VSIX... +
    4. +
    5. Choose the downloaded .vsix file
    6. +
    +
    +
    +

    Method B: Command line

    +
    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    +
    +
    + +
    +
    + MIT License © 2026 Koji Kanao + +
    +
    +
    +
    - - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/result.json index dab9497..2c7f913 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/hero/result.json @@ -1,45 +1,41 @@ { - "feature": "hero", - "url": "http://127.0.0.1:5181/", - "passed": 4, - "total": 4, - "ok": true, - "checks": [ - { - "id": "hero-headline", - "pass": true, - "value": "Protocol Visualizer", - "error": null - }, - { - "id": "hero-tagline", - "pass": true, - "value": "Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.", - "error": null - }, - { - "id": "hero-request-access-links", - "pass": true, - "value": { - "count": 3, - "hrefs": [ - "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor", - "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor", - "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor" - ] - }, - "error": null - }, - { - "id": "hero-install-link", - "pass": true, - "value": [ - "Install", - "Installation guide ↓", - "Installation guide" - ], - "error": null - } - ], - "finishedAt": "2026-09-16T07:56:10.567Z" -} \ No newline at end of file + "feature": "hero", + "url": "http://127.0.0.1:5181/", + "passed": 4, + "total": 4, + "ok": true, + "checks": [ + { + "id": "hero-headline", + "pass": true, + "value": "Protocol Visualizer", + "error": null + }, + { + "id": "hero-tagline", + "pass": true, + "value": "Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.", + "error": null + }, + { + "id": "hero-request-access-links", + "pass": true, + "value": { + "count": 3, + "hrefs": [ + "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor", + "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor", + "https://docs.google.com/forms/d/e/1FAIpQLSee8RapmgEfDE2QQtonDNmai44tuyidFQx5A4CiPfXO7_lFgQ/viewform?usp=publish-editor" + ] + }, + "error": null + }, + { + "id": "hero-install-link", + "pass": true, + "value": ["Install", "Installation guide ↓", "Installation guide"], + "error": null + } + ], + "finishedAt": "2026-09-16T07:56:10.567Z" +} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/axtree.json index 8d6d23a..35a4497 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/axtree.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/axtree.json @@ -1,11967 +1,11379 @@ [ - { - "nodeId": "1577", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "aria-label", - "superseded": true - }, - { - "type": "relatedElement", - "value": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode" - }, - "nativeSource": "title" - } - ] - }, - "properties": [ - { - "name": "focusable", - "value": { - "type": 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"-1000001245" - ], - "backendDOMNodeId": 1673 - }, - { - "nodeId": "-1000001130", - "ignored": true, - "ignoredReasons": [ - { - "name": "presentationalRole", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "1645", - "childIds": [] - }, - { - "nodeId": "-1000001246", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Choose the downloaded " - }, - "properties": [], - "parentId": "1674", - "childIds": [] - }, - { - "nodeId": "1675", - "ignored": false, - "role": { - "type": "internalRole", - "value": "StaticText" - }, - "chromeRole": { - "type": "internalRole", - "value": 158 - }, - "name": { - "type": "computedString", - "value": ".vsix", - "sources": [ - { - "type": "contents", - "value": { + }, + "properties": [], + "parentId": "1604", + "childIds": [] + }, + { + "nodeId": "-1000001173", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "Enter any step number under Protocol Steps " + }, + "properties": [], + "parentId": "1605", + "childIds": [] + }, + { + "nodeId": "-1000001174", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "and hit Enter to jump the visualization state " + }, + "properties": [], + "parentId": "1605", + "childIds": [] + }, + { + "nodeId": "-1000001175", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "instantly." + }, + "properties": [], + "parentId": "1605", + "childIds": [] + }, + { + "nodeId": "1930", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1929", + "childIds": ["1931"], + "backendDOMNodeId": 1930 + }, + { + "nodeId": "1932", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1929", + "childIds": ["1933"], + "backendDOMNodeId": 1932 + }, + { + "nodeId": "-1000001244", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "Extensions: Install " + }, + "properties": [], + "parentId": "1673", + "childIds": [] + }, + { + "nodeId": "-1000001245", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "from VSIX..." + }, + "properties": [], + "parentId": "1673", + "childIds": [] + }, + { + "nodeId": "-1000001247", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { "type": "computedString", "value": ".vsix" - } - } - ] - }, - "properties": [], - "parentId": "1908", - "childIds": [ - "-1000001247" - ], - "backendDOMNodeId": 1675 - }, - { - "nodeId": "-1000001248", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "file" - }, - "properties": [], - "parentId": "1676", - "childIds": [] - }, - { - "nodeId": "-1000001250", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "code --install-extension protocol-visualizer.vsix" - }, - "properties": [], - "parentId": "1678", - "childIds": [] - }, - { - "nodeId": "-1000001151", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Real-time Deck Visualization" - }, - "properties": [], - "parentId": "1594", - "childIds": [] - }, - { - "nodeId": "-1000001152", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Deck state and liquid volume changes " - }, - "properties": [], - "parentId": "1595", - "childIds": [] - }, - { - "nodeId": "-1000001153", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "render in real time through an interactive " - }, - "properties": [], - "parentId": "1595", - "childIds": [] - }, - { - "nodeId": "-1000001154", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "panel while your protocol runs." - }, - "properties": [], - "parentId": "1595", - "childIds": [] - }, - { - "nodeId": "-1000001155", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Auto-analysis on Save" - }, - "properties": [], - "parentId": "1596", - "childIds": [] - }, - { - "nodeId": "-1000001156", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "The simulation automatically reruns " - }, - "properties": [], - "parentId": "1597", - "childIds": [] - }, - { - "nodeId": "-1000001157", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "whenever you save changes (Ctrl+S / " - }, - "properties": [], - "parentId": "1597", - "childIds": [] - }, - { - "nodeId": "-1000001158", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Cmd+S) to your protocol file." - }, - "properties": [], - "parentId": "1597", - "childIds": [] - }, - { - "nodeId": "-1000001159", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters UI" - }, - "properties": [], - "parentId": "1598", - "childIds": [] - }, - { - "nodeId": "-1000001160", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Input fields are generated for Opentrons " - }, - "properties": [], - "parentId": "1599", - "childIds": [] - }, - { - "nodeId": "-1000001161", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters; hit Analyze to apply " - }, - "properties": [], - "parentId": "1599", - "childIds": [] - }, - { - "nodeId": "-1000001162", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "them — your original code is never " - }, - "properties": [], - "parentId": "1599", - "childIds": [] - }, - { - "nodeId": "-1000001163", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "modified." - }, - "properties": [], - "parentId": "1599", - "childIds": [] - }, - { - "nodeId": "-1000001164", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Custom Labware Support" - }, - "properties": [], - "parentId": "1600", - "childIds": [] - }, - { - "nodeId": "-1000001165", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Place custom labware definition files (.json) " - }, - "properties": [], - "parentId": "1601", - "childIds": [] - }, - { - "nodeId": "-1000001166", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "in the same directory as your protocol file " - }, - "properties": [], - "parentId": "1601", - "childIds": [] - }, - { - "nodeId": "-1000001167", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and they just work." - }, - "properties": [], - "parentId": "1601", - "childIds": [] - }, - { - "nodeId": "-1000001168", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop-out Window" - }, - "properties": [], - "parentId": "1602", - "childIds": [] - }, - { - "nodeId": "-1000001169", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop the panel out to its own window or " - }, - "properties": [], - "parentId": "1603", - "childIds": [] - }, - { - "nodeId": "-1000001170", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "drag the tab to another monitor via " - }, - "properties": [], - "parentId": "1603", - "childIds": [] - }, - { - "nodeId": "-1000001171", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "VSCode's Auxiliary Window support." - }, - "properties": [], - "parentId": "1603", - "childIds": [] - }, - { - "nodeId": "-1000001172", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Step Jumper" - }, - "properties": [], - "parentId": "1604", - "childIds": [] - }, - { - "nodeId": "-1000001173", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Enter any step number under Protocol Steps " - }, - "properties": [], - "parentId": "1605", - "childIds": [] - }, - { - "nodeId": "-1000001174", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and hit Enter to jump the visualization state " - }, - "properties": [], - "parentId": "1605", - "childIds": [] - }, - { - "nodeId": "-1000001175", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "instantly." - }, - "properties": [], - "parentId": "1605", - "childIds": [] - }, - { - "nodeId": "1930", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1929", - "childIds": [ - "1931" - ], - "backendDOMNodeId": 1930 - }, - { - "nodeId": "1932", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1929", - "childIds": [ - "1933" - ], - "backendDOMNodeId": 1932 - }, - { - "nodeId": "-1000001244", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Extensions: Install " - }, - "properties": [], - "parentId": "1673", - "childIds": [] - }, - { - "nodeId": "-1000001245", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "from VSIX..." - }, - "properties": [], - "parentId": "1673", - "childIds": [] - }, - { - "nodeId": "-1000001247", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": ".vsix" - }, - "properties": [], - "parentId": "1675", - "childIds": [] - }, - { - "nodeId": "1931", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1930", - "childIds": [], - "backendDOMNodeId": 1931 - }, - { - "nodeId": "1933", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1932", - "childIds": [], - "backendDOMNodeId": 1933 - } -] \ No newline at end of file + }, + "properties": [], + "parentId": "1675", + "childIds": [] + }, + { + "nodeId": "1931", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1930", + "childIds": [], + "backendDOMNodeId": 1931 + }, + { + "nodeId": "1933", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1932", + "childIds": [], + "backendDOMNodeId": 1933 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html index d99e238..ad39db5 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    +

    Protocol Visualizer

    + Preview +
    +

    + Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

    + +
    + +
    +
    +
    +
    +

    + Everything you need to see your protocol run +

    +
      +
    • +
      +

      + Real-time Deck Visualization +

      +

      + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

      +
      +
    • +
    • +
      +

      Auto-analysis on Save

      +

      + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

      +
      +
    • +
    • +
      +

      Runtime Parameters UI

      +

      + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

      +
      +
    • +
    • +
      +

      Custom Labware Support

      +

      + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

      +
      +
    • +
    • +
      +

      Pop-out Window

      +

      + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

      +
      +
    • +
    • +
      +

      Step Jumper

      +

      + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

      +
      +
    • +
    +
    +
    +
    +
    +
    + Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
    + Protocol Visualizer in action +
    +
    +
    +
    +
    +
    +

    + Generate protocols with AI, verify with Protocol Visualizer +

    +

    + Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

    +
    + +
    + Generate a protocol from a prompt, then fix it while watching + the simulation +
    +
    +

    How to use

    +
      +
    1. Install VSCode or Cursor
    2. +
    3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
    4. +
    5. + Install the Protocol Visualizer extension (see + Installation guide) +
    6. +
    7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
    8. +
    +
    +
    +
    +
    +

    Want to try the extension?

    +

    + Request access via our form — requests are handled individually. +

    + Request access +
    +
    +
    +
    +

    Installation

    +
    +
    +

    Prerequisites

    +
      +
    • + Python 3.8 or later, with + python3 available in PATH +
    • +
    • + The opentrons Python package: + pip install opentrons +
    • +
    • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
    • +
    • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
    • +
    • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
    • +
    +
    +
    +

    + Method A: Command Palette +

    +
      +
    1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
    2. +
    3. + Select Extensions: Install from VSIX... +
    4. +
    5. Choose the downloaded .vsix file
    6. +
    +
    +
    +

    Method B: Command line

    +
    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    +
    +
    + +
    +
    + MIT License © 2026 Koji Kanao + +
    +
    +
    +
    - - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/result.json index 4b083f1..773f3b3 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/install-guide/result.json @@ -1,53 +1,47 @@ { - "feature": "install-guide", - "url": "http://127.0.0.1:5181/", - "passed": 5, - "total": 5, - "ok": true, - "checks": [ - { - "id": "install-region", - "pass": true, - "value": true, - "error": null - }, - { - "id": "install-prereqs", - "pass": true, - "value": "InstallationPrerequisitesPython 3.8 or later, with python3 available in PATHThe opentrons Python package: pip install opentronsFor OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)Select the matching Python interpreter in VSCode via Python: Select InterpreterUsing both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.Method A: Command PaletteOpen the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)Select Extensions: Install from VSIX...Choose the downloaded .vsix fileMethod B: Command linecode --install-extension protocol-visualizer.vsix", - "error": null - }, - { - "id": "install-cli-method", - "pass": true, - "value": true, - "error": null - }, - { - "id": "header-nav", - "pass": true, - "value": [ - [ - "Features", - "#features" - ], - [ - "Install", - "#install" - ] - ], - "error": null - }, - { - "id": "anchor-navigation", - "pass": true, - "value": { - "hash": "#install", - "top": 0, - "vh": 749 - }, - "error": null - } - ], - "finishedAt": "2026-09-16T07:56:17.778Z" -} \ No newline at end of file + "feature": "install-guide", + "url": "http://127.0.0.1:5181/", + "passed": 5, + "total": 5, + "ok": true, + "checks": [ + { + "id": "install-region", + "pass": true, + "value": true, + "error": null + }, + { + "id": "install-prereqs", + "pass": true, + "value": "InstallationPrerequisitesPython 3.8 or later, with python3 available in PATHThe opentrons Python package: pip install opentronsFor OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)Select the matching Python interpreter in VSCode via Python: Select InterpreterUsing both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.Method A: Command PaletteOpen the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)Select Extensions: Install from VSIX...Choose the downloaded .vsix fileMethod B: Command linecode --install-extension protocol-visualizer.vsix", + "error": null + }, + { + "id": "install-cli-method", + "pass": true, + "value": true, + "error": null + }, + { + "id": "header-nav", + "pass": true, + "value": [ + ["Features", "#features"], + ["Install", "#install"] + ], + "error": null + }, + { + "id": "anchor-navigation", + "pass": true, + "value": { + "hash": "#install", + "top": 0, + "vh": 749 + }, + "error": null + } + ], + "finishedAt": "2026-09-16T07:56:17.778Z" +} diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/axtree.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/axtree.json index c814280..3990a35 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/axtree.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/axtree.json @@ -1,11967 +1,11379 @@ [ - { - "nodeId": "1086", - "ignored": false, - "role": { - "type": "internalRole", - "value": "RootWebArea" - }, - "chromeRole": { - "type": "internalRole", - "value": 144 - }, - "name": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - }, - { - "type": "attribute", - "attribute": "aria-label", - "superseded": true - }, - { - "type": "relatedElement", - "value": { - "type": "computedString", - "value": "Protocol Visualizer — Simulate Opentrons protocols in VSCode" - }, - "nativeSource": "title" - } - ] - }, - "properties": [ - { - "name": "focusable", - "value": { - "type": 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"-1000001006" - ], - "backendDOMNodeId": 1182 - }, - { - "nodeId": "-1000001012", - "ignored": true, - "ignoredReasons": [ - { - "name": "presentationalRole", - "value": { - "type": "boolean", - "value": true - } - } - ], - "role": { - "type": "role", - "value": "none" - }, - "chromeRole": { - "type": "internalRole", - "value": 0 - }, - "parentId": "1154", - "childIds": [] - }, - { - "nodeId": "-1000001009", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Choose the downloaded " - }, - "properties": [], - "parentId": "1183", - "childIds": [] - }, - { - "nodeId": "1184", - "ignored": false, - "role": { - "type": "internalRole", - "value": "StaticText" - }, - "chromeRole": { - "type": "internalRole", - "value": 158 - }, - "name": { - "type": "computedString", - "value": ".vsix", - "sources": [ - { - "type": "contents", - "value": { + }, + "properties": [], + "parentId": "1113", + "childIds": [] + }, + { + "nodeId": "-1000000770", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "Enter any step number under Protocol Steps " + }, + "properties": [], + "parentId": "1114", + "childIds": [] + }, + { + "nodeId": "-1000000771", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "and hit Enter to jump the visualization state " + }, + "properties": [], + "parentId": "1114", + "childIds": [] + }, + { + "nodeId": "-1000000772", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "instantly." + }, + "properties": [], + "parentId": "1114", + "childIds": [] + }, + { + "nodeId": "1301", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1300", + "childIds": ["1302"], + "backendDOMNodeId": 1301 + }, + { + "nodeId": "1303", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1300", + "childIds": ["1304"], + "backendDOMNodeId": 1303 + }, + { + "nodeId": "-1000001005", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "Extensions: Install " + }, + "properties": [], + "parentId": "1182", + "childIds": [] + }, + { + "nodeId": "-1000001006", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { + "type": "computedString", + "value": "from VSIX..." + }, + "properties": [], + "parentId": "1182", + "childIds": [] + }, + { + "nodeId": "-1000001010", + "ignored": false, + "role": { + "type": "internalRole", + "value": "InlineTextBox" + }, + "chromeRole": { + "type": "internalRole", + "value": 101 + }, + "name": { "type": "computedString", "value": ".vsix" - } - } - ] - }, - "properties": [], - "parentId": "1426", - "childIds": [ - "-1000001010" - ], - "backendDOMNodeId": 1184 - }, - { - "nodeId": "-1000001011", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "file" - }, - "properties": [], - "parentId": "1185", - "childIds": [] - }, - { - "nodeId": "-1000000847", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "code --install-extension protocol-visualizer.vsix" - }, - "properties": [], - "parentId": "1187", - "childIds": [] - }, - { - "nodeId": "-1000000748", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Real-time Deck Visualization" - }, - "properties": [], - "parentId": "1103", - "childIds": [] - }, - { - "nodeId": "-1000000749", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Deck state and liquid volume changes " - }, - "properties": [], - "parentId": "1104", - "childIds": [] - }, - { - "nodeId": "-1000000750", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "render in real time through an interactive " - }, - "properties": [], - "parentId": "1104", - "childIds": [] - }, - { - "nodeId": "-1000000751", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "panel while your protocol runs." - }, - "properties": [], - "parentId": "1104", - "childIds": [] - }, - { - "nodeId": "-1000000752", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Auto-analysis on Save" - }, - "properties": [], - "parentId": "1105", - "childIds": [] - }, - { - "nodeId": "-1000000753", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "The simulation automatically reruns " - }, - "properties": [], - "parentId": "1106", - "childIds": [] - }, - { - "nodeId": "-1000000754", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "whenever you save changes (Ctrl+S / " - }, - "properties": [], - "parentId": "1106", - "childIds": [] - }, - { - "nodeId": "-1000000755", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Cmd+S) to your protocol file." - }, - "properties": [], - "parentId": "1106", - "childIds": [] - }, - { - "nodeId": "-1000000756", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters UI" - }, - "properties": [], - "parentId": "1107", - "childIds": [] - }, - { - "nodeId": "-1000000757", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Input fields are generated for Opentrons " - }, - "properties": [], - "parentId": "1108", - "childIds": [] - }, - { - "nodeId": "-1000000758", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Runtime Parameters; hit Analyze to apply " - }, - "properties": [], - "parentId": "1108", - "childIds": [] - }, - { - "nodeId": "-1000000759", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "them — your original code is never " - }, - "properties": [], - "parentId": "1108", - "childIds": [] - }, - { - "nodeId": "-1000000760", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "modified." - }, - "properties": [], - "parentId": "1108", - "childIds": [] - }, - { - "nodeId": "-1000000761", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Custom Labware Support" - }, - "properties": [], - "parentId": "1109", - "childIds": [] - }, - { - "nodeId": "-1000000762", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Place custom labware definition files (.json) " - }, - "properties": [], - "parentId": "1110", - "childIds": [] - }, - { - "nodeId": "-1000000763", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "in the same directory as your protocol file " - }, - "properties": [], - "parentId": "1110", - "childIds": [] - }, - { - "nodeId": "-1000000764", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and they just work." - }, - "properties": [], - "parentId": "1110", - "childIds": [] - }, - { - "nodeId": "-1000000765", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop-out Window" - }, - "properties": [], - "parentId": "1111", - "childIds": [] - }, - { - "nodeId": "-1000000766", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Pop the panel out to its own window or " - }, - "properties": [], - "parentId": "1112", - "childIds": [] - }, - { - "nodeId": "-1000000767", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "drag the tab to another monitor via " - }, - "properties": [], - "parentId": "1112", - "childIds": [] - }, - { - "nodeId": "-1000000768", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "VSCode's Auxiliary Window support." - }, - "properties": [], - "parentId": "1112", - "childIds": [] - }, - { - "nodeId": "-1000000769", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Step Jumper" - }, - "properties": [], - "parentId": "1113", - "childIds": [] - }, - { - "nodeId": "-1000000770", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Enter any step number under Protocol Steps " - }, - "properties": [], - "parentId": "1114", - "childIds": [] - }, - { - "nodeId": "-1000000771", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "and hit Enter to jump the visualization state " - }, - "properties": [], - "parentId": "1114", - "childIds": [] - }, - { - "nodeId": "-1000000772", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "instantly." - }, - "properties": [], - "parentId": "1114", - "childIds": [] - }, - { - "nodeId": "1301", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1300", - "childIds": [ - "1302" - ], - "backendDOMNodeId": 1301 - }, - { - "nodeId": "1303", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1300", - "childIds": [ - "1304" - ], - "backendDOMNodeId": 1303 - }, - { - "nodeId": "-1000001005", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "Extensions: Install " - }, - "properties": [], - "parentId": "1182", - "childIds": [] - }, - { - "nodeId": "-1000001006", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": "from VSIX..." - }, - "properties": [], - "parentId": "1182", - "childIds": [] - }, - { - "nodeId": "-1000001010", - "ignored": false, - "role": { - "type": "internalRole", - "value": "InlineTextBox" - }, - "chromeRole": { - "type": "internalRole", - "value": 101 - }, - "name": { - "type": "computedString", - "value": ".vsix" - }, - "properties": [], - "parentId": "1184", - "childIds": [] - }, - { - "nodeId": "1302", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1301", - "childIds": [], - "backendDOMNodeId": 1302 - }, - { - "nodeId": "1304", - "ignored": false, - "role": { - "type": "role", - "value": "generic" - }, - "chromeRole": { - "type": "internalRole", - "value": 88 - }, - "name": { - "type": "computedString", - "value": "", - "sources": [ - { - "type": "relatedElement", - "attribute": "aria-labelledby" - }, - { - "type": "attribute", - "attribute": "aria-label" - } - ] - }, - "properties": [], - "parentId": "1303", - "childIds": [], - "backendDOMNodeId": 1304 - } -] \ No newline at end of file + }, + "properties": [], + "parentId": "1184", + "childIds": [] + }, + { + "nodeId": "1302", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1301", + "childIds": [], + "backendDOMNodeId": 1302 + }, + { + "nodeId": "1304", + "ignored": false, + "role": { + "type": "role", + "value": "generic" + }, + "chromeRole": { + "type": "internalRole", + "value": 88 + }, + "name": { + "type": "computedString", + "value": "", + "sources": [ + { + "type": "relatedElement", + "attribute": "aria-labelledby" + }, + { + "type": "attribute", + "attribute": "aria-label" + } + ] + }, + "properties": [], + "parentId": "1303", + "childIds": [], + "backendDOMNodeId": 1304 + } +] diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/dom.html b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/dom.html index d99e238..ad39db5 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/dom.html +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/dom.html @@ -1,19 +1,31 @@ - - + + + - - - - - - + + + + + + - + Protocol Visualizer — Simulate Opentrons protocols in VSCode - + + + + + + + + + + + + + -

    Protocol Visualizer

    Preview

    Simulate your Opentrons Python protocols and inspect deck layout and liquid volumes in real time — without leaving VSCode.

    Everything you need to see your protocol run

    • Real-time Deck Visualization

      Deck state and liquid volume changes render in real time through an interactive panel while your protocol runs.

    • Auto-analysis on Save

      The simulation automatically reruns whenever you save changes (Ctrl+S / Cmd+S) to your protocol file.

    • Runtime Parameters UI

      Input fields are generated for Opentrons Runtime Parameters; hit Analyze to apply them — your original code is never modified.

    • Custom Labware Support

      Place custom labware definition files (.json) in the same directory as your protocol file and they just work.

    • Pop-out Window

      Pop the panel out to its own window or drag the tab to another monitor via VSCode's Auxiliary Window support.

    • Step Jumper

      Enter any step number under Protocol Steps and hit Enter to jump the visualization state instantly.

    Protocol Visualizer visualizing an Opentrons protocol on a simulated deck
    Protocol Visualizer in action

    Generate protocols with AI, verify with Protocol Visualizer

    Connect Protocol Visualizer to your LLM with protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, then simulate and fix them in a visual feedback loop.

    Generate a protocol from a prompt, then fix it while watching the simulation

    How to use

    1. Install VSCode or Cursor
    2. Install the skill: npx skills add koji/protocol-fix-loop (see koji/protocol-fix-loop)
    3. Install the Protocol Visualizer extension (see Installation guide)
    4. Use /protocol-fix-loop in chat and add your prompt to generate a protocol

    Want to try the extension?

    Request access via our form — requests are handled individually.

    Request access

    Installation

    Prerequisites

    • Python 3.8 or later, with python3 available in PATH
    • The opentrons Python package: pip install opentrons
    • For OT-2 use pip install opentrons==9.0.0 (opentrons 9.1.0+ dropped OT-2 support)
    • Select the matching Python interpreter in VSCode via Python: Select Interpreter
    • Using both Flex and OT-2? Keep them in a separate virtual environment each and switch per protocol.

    Method A: Command Palette

    1. Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
    2. Select Extensions: Install from VSIX...
    3. Choose the downloaded .vsix file

    Method B: Command line

    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    +

    Protocol Visualizer

    + Preview +
    +

    + Simulate your Opentrons Python protocols and inspect deck + layout and liquid volumes in real time — without leaving + VSCode. +

    + +
    + +
    +
    +
    +
    +

    + Everything you need to see your protocol run +

    +
      +
    • +
      +

      + Real-time Deck Visualization +

      +

      + Deck state and liquid volume changes render in real time + through an interactive panel while your protocol runs. +

      +
      +
    • +
    • +
      +

      Auto-analysis on Save

      +

      + The simulation automatically reruns whenever you save + changes (Ctrl+S / Cmd+S) to your protocol file. +

      +
      +
    • +
    • +
      +

      Runtime Parameters UI

      +

      + Input fields are generated for Opentrons Runtime + Parameters; hit Analyze to apply them — your original code + is never modified. +

      +
      +
    • +
    • +
      +

      Custom Labware Support

      +

      + Place custom labware definition files (.json) in the same + directory as your protocol file and they just work. +

      +
      +
    • +
    • +
      +

      Pop-out Window

      +

      + Pop the panel out to its own window or drag the tab to + another monitor via VSCode's Auxiliary Window support. +

      +
      +
    • +
    • +
      +

      Step Jumper

      +

      + Enter any step number under Protocol Steps and hit Enter + to jump the visualization state instantly. +

      +
      +
    • +
    +
    +
    +
    +
    +
    + Protocol Visualizer visualizing an Opentrons protocol on a simulated deck +
    + Protocol Visualizer in action +
    +
    +
    +
    +
    +
    +

    + Generate protocols with AI, verify with Protocol Visualizer +

    +

    + Connect Protocol Visualizer to your LLM with + protocol-fix-loop. Generate Opentrons protocols with GitHub Copilot or Cursor, + then simulate and fix them in a visual feedback loop. +

    +
    + +
    + Generate a protocol from a prompt, then fix it while watching + the simulation +
    +
    +

    How to use

    +
      +
    1. Install VSCode or Cursor
    2. +
    3. + Install the skill: + npx skills add koji/protocol-fix-loop + (see + koji/protocol-fix-loop) +
    4. +
    5. + Install the Protocol Visualizer extension (see + Installation guide) +
    6. +
    7. + Use + /protocol-fix-loop + in chat and add your prompt to generate a protocol +
    8. +
    +
    +
    +
    +
    +

    Want to try the extension?

    +

    + Request access via our form — requests are handled individually. +

    + Request access +
    +
    +
    +
    +

    Installation

    +
    +
    +

    Prerequisites

    +
      +
    • + Python 3.8 or later, with + python3 available in PATH +
    • +
    • + The opentrons Python package: + pip install opentrons +
    • +
    • + For OT-2 use + pip install opentrons==9.0.0 + (opentrons 9.1.0+ dropped OT-2 support) +
    • +
    • + Select the matching Python interpreter in VSCode via + Python: Select Interpreter +
    • +
    • + Using both Flex and OT-2? Keep them in a separate virtual + environment each and switch per protocol. +
    • +
    +
    +
    +

    + Method A: Command Palette +

    +
      +
    1. + Open the Command Palette (Cmd+Shift+P / + Ctrl+Shift+P) +
    2. +
    3. + Select Extensions: Install from VSIX... +
    4. +
    5. Choose the downloaded .vsix file
    6. +
    +
    +
    +

    Method B: Command line

    +
    code --install-extension protocol-visualizer.vsix
    +
    +
    +
    +
    +
    + +
    +
    + MIT License © 2026 Koji Kanao + +
    +
    +
    +
    - - - \ No newline at end of file + + diff --git a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/result.json b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/result.json index 36b65d3..ab1f1c5 100644 --- a/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/result.json +++ b/.opencode/skills/verify-web/artifacts/2026-09-16T07-56-03-875Z/theme-toggle/result.json @@ -1,37 +1,37 @@ { - "feature": "theme-toggle", - "url": "http://127.0.0.1:5181/", - "passed": 3, - "total": 3, - "ok": true, - "checks": [ - { - "id": "toggle-present", - "pass": true, - "value": "Switch to light theme", - "error": null - }, - { - "id": "toggle-flips-theme", - "pass": true, - "value": { - "before": "dark", - "after": "light", - "stored": "light" - }, - "error": null - }, - { - "id": "toggle-restores", - "pass": true, - "value": { - "theme": "dark", - "stored": "dark", - "label": "Switch to light theme", - "flipped": "light" - }, - "error": null - } - ], - "finishedAt": "2026-09-16T07:56:16.174Z" -} \ No newline at end of file + "feature": "theme-toggle", + "url": "http://127.0.0.1:5181/", + "passed": 3, + "total": 3, + "ok": true, + "checks": [ + { + "id": "toggle-present", + "pass": true, + "value": "Switch to light theme", + "error": null + }, + { + "id": "toggle-flips-theme", + "pass": true, + "value": { + "before": "dark", + "after": "light", + "stored": "light" + }, + "error": null + }, + { + "id": "toggle-restores", + "pass": true, + "value": { + "theme": "dark", + "stored": "dark", + "label": "Switch to light theme", + "flipped": "light" + }, + "error": null + } + ], + "finishedAt": "2026-09-16T07:56:16.174Z" +}