@rho-workspace/rho 0.5.4 → 0.5.6

package/protocol/operations/observation.snapshot.json

@@ -4776,6 +4776,35 @@
                   "type": "null"
                 }
               ]
+            },
+            "origin": {
+              "anyOf": [
+                {
+                  "type": "object",
+                  "properties": {
+                    "producer": {
+                      "type": "string",
+                      "minLength": 1
+                    },
+                    "where": {
+                      "type": "string",
+                      "minLength": 1
+                    },
+                    "copyOf": {
+                      "type": "string",
+                      "minLength": 1
+                    }
+                  },
+                  "required": [
+                    "producer",
+                    "where"
+                  ],
+                  "additionalProperties": true
+                },
+                {
+                  "type": "null"
+                }
+              ]
             }
           },
           "required": [

package/protocol/operations/project.work.read.json

@@ -68,7 +68,8 @@
                 "acp",
                 "claude-cli",
                 "native-transcript",
-                "external-acp"
+                "external-acp",
+                "external-session"
               ]
             },
             "sessionId": {
@@ -573,7 +574,7 @@
             "resourceRefs"
           ]
         },
-        "maxItems": 80
+        "maxItems": 88
       },
       "files": {
         "type": "array",

package/protocol/operations/session.grant.json

@@ -27,6 +27,8 @@
             "agent.activity.capture",
             "agent.activity.outputs",
             "agent.activity.read",
+            "agent.sessions.list",
+            "agent.sessions.read",
             "annotation.create",
             "annotation.decide",
             "annotation.list",
@@ -68,6 +70,13 @@
             "document.undoOwn",
             "evidence.export",
             "evidence.preview",
+            "extension.call",
+            "extension.content",
+            "extension.describe",
+            "extension.install",
+            "extension.list",
+            "extension.manage",
+            "extension.read",
             "feedback.read",
             "feedback.status",
             "feedback.submit",

package/protocol/operations/session.instructions.json

@@ -0,0 +1,43 @@
+{
+  "method": "session.instructions",
+  "inputSchema": {
+    "type": "object",
+    "additionalProperties": false,
+    "properties": {
+      "projectId": {
+        "type": "string",
+        "pattern": "^[A-Za-z0-9._:@-]{1,128}$"
+      }
+    },
+    "required": [
+      "projectId"
+    ]
+  },
+  "outputSchema": {
+    "type": "object",
+    "properties": {
+      "request": {
+        "type": "string",
+        "minLength": 1
+      },
+      "prompt": {
+        "type": "string",
+        "minLength": 1
+      },
+      "command": {
+        "type": "array",
+        "items": {
+          "type": "string",
+          "minLength": 1
+        }
+      }
+    },
+    "required": [
+      "request",
+      "prompt",
+      "command"
+    ],
+    "additionalProperties": true
+  },
+  "description": "Person at this machine or operator only: read a prompt for the person's own MCP client to connect itself to this existing project. Returns local launcher paths, never credential contents. Reading or copying grants no access, edits no client configuration and starts no runtime."
+}

package/scripts/third-party-acceptance.mjs

@@ -0,0 +1,77 @@
+#!/usr/bin/env node
+// An opt-in, real scientific episode. R packages must already be available;
+// this script never installs dependencies or touches an existing R session.
+import fs from 'node:fs/promises';
+import path from 'node:path';
+import os from 'node:os';
+import assert from 'node:assert/strict';
+import { fileURLToPath } from 'node:url';
+import { RhoService } from '../dist/server.js';
+import { RhoClient } from '../dist/client.js';
+
+const repo = fileURLToPath(new URL('../', import.meta.url));
+const source = process.env.RHO_SCLET_PLUGIN ?? path.resolve(repo, '../Rho-plugins/examples/sclet-plugin');
+const root = await fs.mkdtemp(path.join(os.tmpdir(), 'rho-third-party-'));
+await fs.mkdir(path.join(root, 'project'));
+const service = await new RhoService({ root, stateDir: path.join(root, 'state'), rscript: process.env.RHO_RSCRIPT ?? 'Rscript', example: false }).start();
+const client = new RhoClient({ url: service.url, token: service.adminToken });
+const project = await client.call('project.open', { path: 'project' });
+const notes = [];
+let sequence = 0;
+const text = cell => cell.outputs.map(output => output.text ?? '').join('\n') + (cell.error ? '\n' + JSON.stringify(cell.error) : '');
+const json = value => JSON.parse(value.slice(value.indexOf('{'), value.lastIndexOf('}') + 1));
+async function finished(cell) {
+  for (let i = 0; i < 600; i++) {
+    const current = (await client.call('kernel.read', { projectId: project.id, cellId: cell.cellId })).cells[0];
+    if (['done', 'error', 'unknown', 'interrupted'].includes(current.state)) return current;
+    await new Promise(resolve => setTimeout(resolve, 500));
+  }
+  throw new Error('Observation deadline reached; original cell: ' + cell.cellId);
+}
+try {
+  const plugin = await client.call('extension.install', { source });
+  const invoke = (operation, input = {}, changeId = 'acceptance-' + ++sequence) => client.call('extension.call', { projectId: project.id, pluginId: plugin.id, expectedDigest: plugin.digest, operation, input, changeId });
+  assert.deepEqual((await invoke('sessions')).value.sessions, []);
+  async function run(operation, input = {}) {
+    const receipt = await invoke(operation, input); assert.equal(receipt.state, 'completed', receipt.error);
+    const cell = await finished(receipt.value.cell); notes.push({ operation, cellId: cell.cellId, state: cell.state });
+    assert.equal(cell.state, 'done', text(cell)); return { receipt, cell, text: text(cell) };
+  }
+  const library = process.env.RHO_SCLET_LIBRARY;
+  const seedCode = `${library ? '.libPaths(c(' + JSON.stringify(library) + ', .libPaths()))\n' : ''}if (!requireNamespace("sclet", quietly=TRUE)) stop("Set RHO_SCLET_LIBRARY to an existing sclet library.")\nset.seed(19)\nsce <- scuttle::mockSCE(ncells=60, ngenes=200)`;
+  const seed = await client.call('kernel.run', { projectId: project.id, language: 'r', code: seedCode, purpose: 'Disposable third-party plugin trial', changeId: 'seed', waitMs: 0 });
+  const seeded = await finished(seed.cell); assert.equal(seeded.state, 'done', text(seeded));
+  const packages = await run('check');
+  const before = json((await run('ledger', { object: 'sce', includeArtifacts: true })).text);
+  await run('registry', { object: 'sce' }); await run('skill', { name: 'sclet-driver' });
+  const plan = { task: 'plugin-acceptance', context_fingerprint: before.fingerprint, actions: [
+    { id: 'normalize', action: 'normalize_data' },
+    { id: 'hvg', action: 'find_variable_features', params: { nfeatures: 50 }, depends_on: 'normalize' },
+    { id: 'scale', action: 'scale_data', depends_on: 'hvg' },
+    { id: 'pca', action: 'run_pca', params: { ncomponents: 5 }, depends_on: 'scale' },
+  ] };
+  const validated = json((await run('validate', { object: 'sce', plan })).text); assert.equal(validated.validation.valid, true);
+  const executeBody = { validationId: validated.validationId };
+  const execution = await invoke('execute', executeBody, 'execute-once'); assert.equal(execution.state, 'completed', execution.error);
+  const executed = await finished(execution.value.cell); assert.equal(executed.state, 'done', text(executed));
+  assert.equal(json(text(executed)).status, 'completed');
+  assert.equal((await invoke('execute', executeBody, 'execute-once')).value.cell.cellId, executed.cellId);
+  await run('record', { object: 'sce', recordId: 'smoke-report', result: {
+    task: 'plugin-acceptance', answer: 'A synthetic 200-gene, 60-cell input completed normalization, variable feature selection, scaling and PCA. This verifies software integration; no biological conclusion is claimed.',
+    findings: [], evidence: [], warnings: ['Synthetic input, not evidence for a biological hypothesis.'], recommendations: [], proposed_actions: [], success_criteria: [], stop_conditions: [], context: { fingerprint: json(text(executed)).fingerprint }, metadata: { provider: 'integration-test' },
+  } });
+  const report = await run('report', { object: 'sce', recordId: 'smoke-report' }); assert.match(report.text, /all checks passed/);
+  const after = json((await run('ledger', { object: 'sce', includeArtifacts: true })).text);
+  assert.equal(after.dataset.reductions, 'PCA'); assert.equal(after.features.hvg.n, 50);
+  assert.equal(json((await run('validate', { object: 'sce', plan })).text).validation.valid, false);
+  await client.call('extension.manage', { pluginId: plugin.id, expectedDigest: plugin.digest, action: 'disable' });
+  await assert.rejects(invoke('ledger', { object: 'sce' }), /disabled/);
+  await client.call('extension.manage', { pluginId: plugin.id, expectedDigest: plugin.digest, action: 'remove' });
+  assert.equal((await invoke('execute', executeBody, 'execute-once')).value.cell.cellId, executed.cellId);
+  const sessions = await client.call('kernel.read', { projectId: project.id, limit: 1 });
+  assert.ok(sessions.sessions.some(s => s.sessionId === seed.cell.sessionId && s.state !== 'ended'));
+  const output = path.resolve(process.env.RHO_THIRD_PARTY_OUTPUT ?? path.join(repo, 'output/third-party-plugins/acceptance.json'));
+  await fs.mkdir(path.dirname(output), { recursive: true });
+  await fs.writeFile(output, JSON.stringify({ at: new Date().toISOString(), node: process.version, platform: process.platform, source, digest: plugin.digest, packages: packages.text, notes, execution: json(text(executed)), report: report.text, lifecycle: 'disable/remove retained original cell and live R session', passed: true }, null, 2) + '\n');
+  console.log(JSON.stringify({ passed: true, output }));
+} finally { await service.close(); await fs.rm(root, { recursive: true, force: true }); }

package/vendor/composition.json

@@ -11,21 +11,21 @@
   "build": {
     "system": "github-actions",
     "workflow": "YuLab-SMU/Rho/.github/workflows/ci.yml@refs/heads/main",
-    "run": "https://github.com/YuLab-SMU/Rho/actions/runs/41975339969",
+    "run": "https://github.com/YuLab-SMU/Rho/actions/runs/42361803786",
     "attempt": 1
   },
   "application": {
     "repository": "https://github.com/YuLab-SMU/Rho",
-    "commit": "fd0f9de59a07f2208ea9a228430877b057f3cc18",
-    "tree": "4f81ab2396389fc66eb8557e3773cd7594bb1a24",
-    "buildInputsSha256": "9566fa300a68d068ff1b1010671e02ab995b09b3bd73b552562c21c857472258",
+    "commit": "cd559cc0f832cd4f68386caa351ddad942f41e21",
+    "tree": "f967ccbdda8e07be1bdad994db4d2340205b517b",
+    "buildInputsSha256": "e1a5c034aa93c580f6939643dd7d9681a736635092dd39067170aa2bb556259e",
     "localOverride": null
   },
   "plugins": {
     "repository": "https://github.com/YuLab-SMU/Rho-plugins",
-    "commit": "2e53dc2b0d7493ef074a49581a0908c6c1cb52cd",
-    "tree": "74f2c5dbecbdc0190080ef2dc0e4b7e173bccd92",
-    "buildInputsSha256": "1788587ff08ab4ef58308d99dcd8a03e4cf0b141d5b243852b7df6ca1a687dc1",
+    "commit": "434d9a33d82125e7b3f291fae83e7b33a0fc2a24",
+    "tree": "482c71685214c5437016592321221852c94b8327",
+    "buildInputsSha256": "8db139ca3c92937b265749637370ec2d79659d74e9e697e1d36867815838a31f",
     "localOverride": null,
     "selected": [
       "documents",
@@ -121,11 +121,11 @@
       {
         "id": "agent",
         "package": "@rho-workspace/plugin-agent",
-        "version": "0.4.28",
-        "filename": "rho-workspace-plugin-agent-0.4.28.tgz",
-        "bytes": 121829,
-        "sha256": "4ca47add5451d66c18538b1baf5d90639cc9ba5d643f0dc59dba7a0a1935dc47",
-        "integrity": "sha512-yaj11ytftsyEljSHJC5i2pplRLRb1ZIu1hg38/uJvSAVFoTYDZm5XZO6oxoavj4YuEYEuGVpV/mug1qrt7jOsQ=="
+        "version": "0.4.30",
+        "filename": "rho-workspace-plugin-agent-0.4.30.tgz",
+        "bytes": 140297,
+        "sha256": "eb3ece278bd163d727393e29126a52a686eee7e32f9d49e5bb88e195a5b2d9b7",
+        "integrity": "sha512-O6c276Js2JXwjPoUfPFBYFM2iXb6emIzyXoMd0qco0BCfDm9JE9kOq69JJFmf3m/TsY3U2RlgEl73xuP5z58XQ=="
       },
       {
         "id": "annotations",
@@ -167,12 +167,12 @@
   },
   "catalog": {
     "path": "dist/plugin-inventory.json",
-    "sha256": "35c66c5bdf7d5343ade0f267c37402b0c2c52c8a93fb82c2920bb1e0e9f1d16b",
-    "bytes": 39343,
+    "sha256": "c91b2283576672a2f4fb11fd9839e2b6f1adae47758434b560c06c071c5b0090",
+    "bytes": 40021,
     "source": {
-      "commit": "2e53dc2b0d7493ef074a49581a0908c6c1cb52cd",
-      "tree": "74f2c5dbecbdc0190080ef2dc0e4b7e173bccd92",
-      "buildInputsSha256": "1788587ff08ab4ef58308d99dcd8a03e4cf0b141d5b243852b7df6ca1a687dc1",
+      "commit": "434d9a33d82125e7b3f291fae83e7b33a0fc2a24",
+      "tree": "482c71685214c5437016592321221852c94b8327",
+      "buildInputsSha256": "8db139ca3c92937b265749637370ec2d79659d74e9e697e1d36867815838a31f",
       "localOverride": null
     },
     "scope": "Descriptive inventory of the reviewed owners; contributes no runtime entry or authority."
@@ -216,7 +216,7 @@
   "web": {
     "format": "rho.web-build/1",
     "uiProtocol": "0.1-draft",
-    "rendererBuild": "485f1b19e789f432be41a9566199b3dddf2ff479e48ab4e3c1cd4ea75fe16033",
+    "rendererBuild": "094bee327d7964c2c6ea9fe3db6d35899545d090074c964d0cdb056f556471f1",
     "ownerEntries": [
       {
         "plugin": "documents",
@@ -275,7 +275,7 @@
         "component": "rho.agent-note",
         "version": "0.2.0",
         "source": "web/entries/agent.tsx",
-        "packageVersion": "0.4.28",
+        "packageVersion": "0.4.30",
         "entrySha256": "0e18d175dfc25fd8e237ec0341422e0d1311d2d8882e487962e8c7c25794d69e"
       },
       {
@@ -470,7 +470,7 @@
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         "bytes": 23614,
-        "sha256": "3f5cd1589d4c851c00b0e6dedecf2df169dba3eae111302f38bdb6b7fed51460"
+        "sha256": "2dc60f63158b05c257607125515a2cdd1c31059f96cf596a31c88bb20dbf6576"
       },
       {
         "path": "assets/answer-board-CBkGbSLD.js",
@@ -478,59 +478,59 @@
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+        "path": "assets/console-Trqc0swD.js",
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@@ -548,9 +548,9 @@
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@@ -558,14 +558,14 @@
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@@ -878,14 +878,14 @@
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@@ -893,9 +893,9 @@
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package/web/theme.css

@@ -733,6 +733,18 @@ ol.md-list { list-style-type: decimal; }
 /* The message box: one rounded surface holding what is written, the model and the send action. */
 .conversation-composer { position: sticky; bottom: 0; z-index: 2; display: flex; flex-direction: column; gap: 6px; margin-top: auto; padding: 6px 14px 10px; background: var(--color-surface); }
 .conversation-composer [role="alert"] { display: flex; flex-wrap: wrap; align-items: center; gap: 8px; padding: 0 4px; color: var(--color-failed); font-size: 12px; }
+/* A session opened from another window: where it started, whether it is open there now, and the
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+.session-notice { display: flex; flex-wrap: wrap; align-items: baseline; gap: 2px 10px; padding: 0 4px; color: var(--color-muted); font-size: 12px; line-height: 1.5; }
+.session-notice p { flex: 1 1 260px; margin: 0; }
+.session-notice strong { color: var(--color-amber-text); font-weight: 600; }
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+.session-command { display: inline-flex; align-items: center; gap: 5px; color: var(--color-muted); }
+.turn-where { color: var(--color-meta); }
+.outside-results { display: flex; flex-direction: column; gap: 4px; margin: 6px 0; padding: 0; list-style: none; font-size: 12.5px; }
+.outside-results li { display: flex; flex-wrap: wrap; align-items: baseline; gap: 6px; min-width: 0; overflow-wrap: anywhere; }
+.outside-results small { color: var(--color-meta); }
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package/dist/web/assets/choices-DU9kHlyQ.js

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Redo what depends on it and update the notes.`),[l,u]=(0,g.useState)(!1),[d,f]=(0,g.useState)(``),p=(0,g.useRef)(null);async function m(){if(s.trim()&&!l){p.current?.text!==s&&(p.current={text:s,changeId:`choice-`+crypto.randomUUID()}),u(!0),f(``);try{await t.call(`conversation.send`,{projectId:n,conversationId:e,changeId:p.current.changeId,text:s}),p.current=null,o(e)}catch(e){f(e instanceof Error?e.message:`The message could not be sent.`)}finally{u(!1)}}}return(0,C.jsxs)(`form`,{className:`choice-send`,onSubmit:e=>{e.preventDefault(),m()},onKeyDown:e=>{e.key===`Escape`&&a()},children:[(0,C.jsx)(`textarea`,{rows:3,value:s,"aria-label":`Message to the Agent`,onChange:e=>c(e.target.value),autoFocus:!0}),d&&(0,C.jsx)(`p`,{className:`inline-error`,role:`alert`,children:d}),(0,C.jsxs)(`div`,{className:`choice-send-actions`,children:[(0,C.jsx)(`button`,{type:`button`,onClick:a,children:`Cancel`}),(0,C.jsx)(`button`,{type:`submit`,className:`primary`,disabled:l||!s.trim(),children:l?`Sending…`:`Send to the Agent`})]})]})}export{S as n,y as r,w as t};