agentopology 0.2.5 → 0.4.0

package/dist/visualizer/index.js

@@ -48,19 +48,11 @@ function loadDagreSrc() {
     throw new Error("Could not find dagre.min.js — run: npm install dagre@0.8.5");
 }
 const DAGRE_SRC = loadDagreSrc();
-// ---------------------------------------------------------------------------
-// Public API
-// ---------------------------------------------------------------------------
-/**
- * Generate a self-contained HTML string that visualizes the given topology.
- *
- * Save the returned string to a `.html` file and open it in any browser.
- */
-export function generateVisualization(ast) {
+export function generateVisualization(ast, opts = {}) {
     const dataJson = JSON.stringify(astToViewData(ast));
     const issues = validate(ast);
     const issuesJson = JSON.stringify(issues);
-    return buildHtml(dataJson, ast.topology.name, issuesJson);
+    return buildHtml(dataJson, ast.topology.name, issuesJson, opts.brains ?? []);
 }
 // ---------------------------------------------------------------------------
 // AST -> view data  (matches the DEFAULT_DATA shape in the advanced viewer)
@@ -218,7 +210,22 @@ function astToViewData(ast) {
 // ---------------------------------------------------------------------------
 // HTML builder
 // ---------------------------------------------------------------------------
-function buildHtml(dataJson, title, issuesJson) {
+function buildHtml(dataJson, title, issuesJson, brains = []) {
+    let brainLink = "";
+    if (brains.length === 1) {
+        brainLink = `<a class="header-btn brain-link" href="${escHtml(brains[0].href)}" title="Open the company brain graph">🧠 Open Brain →</a>`;
+    }
+    else if (brains.length > 1) {
+        // Several brains → a dropdown listing each by store id.
+        const items = brains
+            .map((b) => `<a href="${escHtml(b.href)}">🧠 ${escHtml(b.id)} →</a>`)
+            .join("");
+        brainLink =
+            `<div class="brain-menu">` +
+                `<button class="header-btn brain-link" onclick="this.parentNode.classList.toggle('open')">🧠 ${brains.length} Brains ▾</button>` +
+                `<div class="brain-menu-list">${items}</div>` +
+                `</div>`;
+    }
     return `<!DOCTYPE html>
 <html lang="en">
 <head>
@@ -257,6 +264,7 @@ ${CSS}
     <div id="header-actions">
       <div class="topo-desc" id="topo-desc"></div>
       <div class="pattern-badges" id="pattern-badges"></div>
+      ${brainLink}
       <input type="text" id="search-input" class="search-input" placeholder="Search nodes..." oninput="onSearchInput(this.value)" />
       <button class="header-btn" id="dataflow-btn" onclick="toggleDataFlow()">Data Flow</button>
       <button class="header-btn" id="orientation-btn" onclick="toggleOrientation()" title="Switch between vertical and horizontal layout">&#8596; Horizontal</button>
@@ -383,6 +391,13 @@ body{background:var(--bg);color:var(--t);font-family:var(--font-body);line-heigh
 .pattern-badge.fan-out{background:var(--orange-bg);color:var(--orange);border:1px solid var(--orange-br)}
 .pattern-badge.human-gate{background:var(--gold-bg);color:var(--gold);border:1px solid var(--gold-br)}
 .header-btn{background:var(--s2);border:1px solid var(--b);color:var(--t2);padding:5px 12px;border-radius:6px;font-size:11px;cursor:pointer;transition:all .15s;font-family:var(--font-mono);letter-spacing:.3px}
+.brain-link{text-decoration:none;color:var(--purple);border-color:var(--purple-br);background:var(--purple-bg)}
+.brain-link:hover{background:rgba(167,139,250,.18);border-color:var(--purple)}
+.brain-menu{position:relative;display:inline-block}
+.brain-menu-list{display:none;position:absolute;top:calc(100% + 4px);right:0;z-index:30;min-width:160px;background:var(--s);border:1px solid var(--b2);border-radius:8px;padding:4px;box-shadow:0 8px 24px rgba(0,0,0,.5)}
+.brain-menu.open .brain-menu-list{display:block}
+.brain-menu-list a{display:block;text-decoration:none;color:var(--purple);font-family:var(--font-mono);font-size:11px;padding:6px 10px;border-radius:5px}
+.brain-menu-list a:hover{background:var(--purple-bg)}
 .header-btn:hover{background:rgba(255,255,255,.06);color:var(--t);border-color:var(--b2)}
 .header-btn.active{background:var(--amber-bg);color:var(--amber);border-color:var(--amber-br)}
 

package/dist/visualizer/index.js.map

@@ -1 +1 @@
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package/examples/code-review.at

@@ -50,7 +50,14 @@ topology code-review : [pipeline, fan-out, human-gate] {
     role: analyzer
     model: sonnet
     permissions: supervised
-    prompt: "prompts/analyzer.md"
+    prompt {
+      Read the diff at workspace/pr-diff.md.
+
+      Report structural risk only — complexity, dependency changes, and blast
+      radius. Do not comment on security; a separate agent covers that.
+
+      Write your findings to workspace/analysis.md and set risk-level.
+    }
     phase: 1
     tools: [Read, Grep, Glob]
     reads: ["workspace/pr-diff.md"]
@@ -64,7 +71,14 @@ topology code-review : [pipeline, fan-out, human-gate] {
     role: security
     model: sonnet
     permissions: supervised
-    prompt: "prompts/security-scanner.md"
+    prompt {
+      Read the diff at workspace/pr-diff.md.
+
+      Look for injection, auth or authorization changes, secret handling, and
+      unsafe deserialization. Do not comment on style or complexity.
+
+      Write your findings to workspace/security.md and set has-vulnerabilities.
+    }
     phase: 1
     tools: [Read, Grep, Glob]
     reads: ["workspace/pr-diff.md"]
@@ -79,7 +93,14 @@ topology code-review : [pipeline, fan-out, human-gate] {
     role: reviewer
     model: opus
     permissions: supervised
-    prompt: "prompts/reviewer.md"
+    prompt {
+      Read the diff, workspace/analysis.md and workspace/security.md.
+
+      The two reports were produced independently. Where they disagree, say so
+      rather than silently picking one.
+
+      Write your review to workspace/review.md and set a verdict.
+    }
     phase: 2
     tools: [Read, Grep, Glob]
     reads: ["workspace/pr-diff.md", "workspace/analysis.md", "workspace/security.md"]
@@ -93,7 +114,14 @@ topology code-review : [pipeline, fan-out, human-gate] {
     role: reporter
     model: haiku
     permissions: autonomous
-    prompt: "prompts/reporter.md"
+    prompt {
+      Read workspace/analysis.md, workspace/security.md and workspace/review.md.
+
+      Produce one report a human can act on: the verdict, the reasons behind it,
+      and the specific changes required. No new analysis.
+
+      Write it to workspace/final-report.md.
+    }
     phase: 3
     tools: [Read, Write, Glob]
     reads: ["workspace/analysis.md", "workspace/security.md", "workspace/review.md"]

package/examples/company-brain-team.at

@@ -0,0 +1,241 @@
+# company-brain-team.at — A team of agents that build & maintain a company brain
+#
+# The flagship "company brain" topology. A folder of Obsidian-format markdown,
+# fed and maintained by a TEAM — not one librarian:
+#
+#   📧 gmail-ingester    ─┐
+#   💬 slack-ingester    ─┼─► drop raw notes into brain/    ─► 👤 librarian wires them
+#   📅 calendar-ingester ─┘    (each owns ONE source)          (links, tags, hubs)
+#                                                              ─► 🔍 auditor heals the graph
+#
+# - Ingesters are scheduled — they pull from their source and write raw markdown.
+# - The librarian is custodian-of the brain: it wires dropped notes into the graph.
+# - The auditor is custodian-of the brain too: it heals broken links, surfaces
+#   ghost nodes, and flags duplicates.
+# - A researcher reads the brain to answer questions.
+#
+# This is the whitespace: declarative + multi-agent team + Obsidian-portable +
+# agents own memory layers. Demonstrates `brain` + `custodian-of` + ingestion.
+
+topology company-brain-team : [brain, event-driven, human-gate] {
+
+  meta {
+    version: "0.1.0"
+    description: "A team of agents that ingest, wire, and maintain a company brain"
+  }
+
+  # --- The brain: one Obsidian-format markdown vault, no database ---
+
+  memory {
+    store brain {
+      type: brain
+      description: "The company brain — fed by ingesters, wired by the librarian"
+      path: "brain/"
+      format: obsidian
+      scope: org
+
+      # Presentation only — colors/icons for the graph view, by provenance.
+      # A note's `source:` frontmatter (stamped by its ingester) maps to a look.
+      # Cosmetic: bindings ignore this; delete it and the brain works the same.
+      sources {
+        gmail {
+          color: "#EA4335"
+          icon: "./logos/gmail.svg"
+        }
+        slack {
+          color: "#4A154B"
+          icon: "./logos/slack.svg"
+        }
+        calendar {
+          color: "#4285F4"
+        }
+      }
+    }
+  }
+
+  # --- Ingesters: each owns ONE external source, writes raw notes ---
+
+  agent gmail-ingester {
+    model: sonnet
+    description: "Pulls notable emails and writes them as raw notes into the brain"
+    tools: [Read, Write, Grep, Glob]
+    mcp-servers: [gmail]
+    writes: ["brain/"]
+
+    prompt {
+        You ingest email into the brain. On each run:
+        - Pull recent notable threads (decisions, deals, intros, commitments).
+        - For each, write ONE raw markdown note into `brain/` with a clear title
+          and YAML frontmatter (date, source: gmail, participants).
+        - Do NOT wire links or tags — that is the librarian's job. Just capture
+          the content faithfully. Skip noise (newsletters, automated mail).
+    }
+  }
+
+  agent slack-ingester {
+    model: sonnet
+    description: "Captures key Slack decisions and threads as raw notes"
+    tools: [Read, Write, Grep, Glob]
+    mcp-servers: [slack]
+    writes: ["brain/"]
+
+    prompt {
+        You ingest Slack into the brain. On each run, capture threads where a
+        decision was made, a commitment given, or knowledge shared. Write each
+        as ONE raw markdown note in `brain/` with frontmatter (date, source:
+        slack, channel). Leave linking and tagging to the librarian.
+    }
+  }
+
+  agent calendar-ingester {
+    model: sonnet
+    description: "Turns meetings into raw notes (attendees, outcomes)"
+    tools: [Read, Write, Grep, Glob]
+    mcp-servers: [calendar]
+    writes: ["brain/"]
+
+    prompt {
+        You ingest calendar events into the brain. For meetings that mattered,
+        write ONE raw markdown note in `brain/` with frontmatter (date, source:
+        calendar, attendees) and any outcomes/notes you can infer. No linking —
+        that is the librarian's job.
+    }
+  }
+
+  # --- Librarian: custodian that WIRES dropped notes into the graph ---
+
+  agent librarian {
+    model: sonnet
+    description: "Wires raw notes into the brain graph — links, tags, hubs"
+    tools: [Read, Write, Edit, Grep, Glob]
+
+    custodian-of: [brain] {
+      does: [link, tag, index, dedupe]
+    }
+
+    prompt {
+        You are the brain's librarian. Raw notes arrive from the ingesters and
+        from humans. You never invent content — you wire what is dropped in.
+        Resolve mentions into [[wikilinks]], assign #nested/tags, keep the hub
+        notes current, and flag duplicates. Leave ghost links to mark gaps.
+    }
+  }
+
+  # --- Auditor: custodian that keeps the whole graph HEALTHY ---
+
+  agent auditor {
+    model: opus
+    description: "Heals the brain — broken links, ghost nodes, orphans, dupes"
+    tools: [Read, Edit, Grep, Glob]
+
+    custodian-of: [brain] {
+      does: [heal, dedupe, index]
+    }
+
+    prompt {
+        You audit the brain's health. Find and repair broken [[links]] after
+        renames, surface ghost nodes (links to notes that don't exist), flag
+        orphan notes (nothing links to them), and propose merges for duplicates.
+        Conservative: repair links and report issues — never delete a human's note.
+    }
+  }
+
+  # --- Researcher: READS the brain to answer questions ---
+
+  agent researcher {
+    model: sonnet
+    description: "Answers questions by traversing the brain"
+    tools: [Read, Grep, Glob]
+    memory: [brain]
+
+    prompt {
+        Answer questions using only the brain in `brain/`. Grep for relevant
+        notes, follow their [[wikilinks]] and #tags, and cite notes by filename.
+    }
+  }
+
+  # --- Actions (flow entry/exit points) ---
+
+  action wire-in {
+    kind: inline
+    description: "Fold a dropped or freshly-ingested note into the brain"
+  }
+
+  action audit {
+    kind: report
+    description: "Report the brain's health: ghosts, orphans, broken links, dupes"
+  }
+
+  action query {
+    kind: inline
+    description: "Ask the brain a question"
+  }
+
+  # --- Flow: ingesters feed the librarian; auditor runs after; researcher reads ---
+
+  flow {
+    gmail-ingester    -> wire-in
+    slack-ingester    -> wire-in
+    calendar-ingester -> wire-in
+    wire-in           -> librarian
+    librarian         -> auditor
+    auditor           -> audit
+    query             -> researcher
+  }
+
+  # --- Schedule: ingesters and the auditor run on their own cadence ---
+
+  schedule {
+    job pull-email {
+      cron: "0 */2 * * *"
+      agent: gmail-ingester
+    }
+    job pull-slack {
+      cron: "0 */2 * * *"
+      agent: slack-ingester
+    }
+    job pull-calendar {
+      cron: "0 8 * * *"
+      agent: calendar-ingester
+    }
+    job nightly-audit {
+      cron: "0 3 * * *"
+      agent: auditor
+    }
+  }
+
+  # --- Triggers: humans can wire a file or ask the brain anytime ---
+
+  triggers {
+    command wire-in {
+      pattern: "/wire-in <FILE>"
+      argument: FILE
+      description: "Fold a dropped markdown file into the brain"
+    }
+    command query {
+      pattern: "/ask <QUESTION>"
+      argument: QUESTION
+      description: "Ask the brain a question"
+    }
+  }
+
+  # --- External sources the ingesters connect to ---
+
+  mcp-servers {
+    gmail {
+      type: stdio
+      command: "npx"
+      args: ["-y", "gmail-mcp-server"]
+    }
+    slack {
+      type: stdio
+      command: "npx"
+      args: ["-y", "slack-mcp-server"]
+    }
+    calendar {
+      type: stdio
+      command: "npx"
+      args: ["-y", "calendar-mcp-server"]
+    }
+  }
+}

package/examples/company-brain.at

@@ -0,0 +1,104 @@
+# company-brain.at — A plug-and-play company brain
+#
+# A folder of Obsidian-format markdown, maintained by agents, not by hand.
+# - Humans drop a new note and run /wire-in. The librarian links & tags it.
+# - The researcher traverses the [[link]] graph (with grep) to answer questions.
+# - No vector DB, no MCP server. The brain is a folder you can git clone and
+#   open in Obsidian for the graph view.
+#
+# Demonstrates the `brain` PATTERN + the `custodian-of` PRIMITIVE.
+
+topology company-brain : [brain, human-gate] {
+
+  meta {
+    version: "0.1.0"
+    description: "An agent-maintained, Obsidian-portable company brain"
+  }
+
+  # --- The brain itself: one markdown store, no backend ---
+
+  memory {
+    store brain {
+      type: brain                 # NEW store type — no DB, just files
+      description: "The company brain — a folder of linked markdown"
+      path: "brain/"              # this folder IS a valid Obsidian vault
+      format: obsidian            # [[wikilinks]], #nested/tags, YAML frontmatter
+      scope: org
+    }
+  }
+
+  # --- The librarian: KEEPER of the brain (the new primitive) ---
+
+  agent librarian {
+    model: sonnet
+    description: "Maintains the brain — wires new notes into the graph"
+    tools: [Read, Write, Edit, Grep, Glob]
+
+    custodian-of: [brain] {       # owns upkeep, not just read access
+      does: [link, tag, index, dedupe]   # OPTIONAL verbs — visible strategy
+    }
+
+    prompt {
+        You are the brain's librarian. The brain lives in `brain/` as Obsidian
+        markdown. You never invent content — you wire what's dropped in.
+
+        When a note is added or changed:
+        - link:   find mentions of existing notes and turn them into [[wikilinks]]
+        - tag:    add #nested/tags consistent with the existing tag hierarchy
+        - index:  update the relevant hub note (a Map-of-Content that [[links]]
+                  the cluster) so the new note is reachable
+        - dedupe: flag near-duplicate notes for human review; never auto-delete
+
+        Backlinks are computed from the [[links]] you write — never author them
+        by hand. If a note links to something that doesn't exist yet, leave the
+        ghost link; it marks a gap to fill later.
+    }
+  }
+
+  # --- The researcher: READS the brain to answer questions ---
+
+  agent researcher {
+    model: sonnet
+    description: "Answers questions by traversing the brain"
+    tools: [Read, Grep, Glob]
+    memory: [brain]               # read access — the ordinary wiring
+
+    prompt {
+        Answer questions using only the brain in `brain/`. Start by grepping for
+        relevant notes, then follow their [[wikilinks]] and #tags to gather the
+        full picture. Cite the notes you used by filename.
+    }
+  }
+
+  # --- What the human can do (actions are the flow entry points) ---
+
+  action wire-in {
+    kind: inline
+    description: "Fold a dropped markdown file into the brain"
+  }
+
+  action query {
+    kind: inline
+    description: "Ask the brain a question"
+  }
+
+  triggers {
+    command wire-in {
+      pattern: "/wire-in <FILE>"
+      argument: FILE
+      description: "Fold a dropped markdown file into the brain"
+    }
+    command query {
+      pattern: "/ask <QUESTION>"
+      argument: QUESTION
+      description: "Ask the brain a question"
+    }
+  }
+
+  # --- Flow ---
+
+  flow {
+    wire-in -> librarian          # human drops a file → librarian wires it
+    query   -> researcher         # human asks → researcher traverses & answers
+  }
+}

package/examples/data-processing.at

@@ -103,7 +103,15 @@ topology data-processing : [pipeline, fan-out] {
     role: extractor
     model: sonnet
     permissions: autonomous
-    prompt: "prompts/extractor.md"
+    prompt {
+      Read source documents from workspace/raw/.
+
+      Extract their text and structure using the extract-pdf and extract-doc
+      tools. Preserve tables and headings — downstream classification depends
+      on them.
+
+      Write one extracted file per source into workspace/extracted/.
+    }
     phase: 1
     tools: [Read, Write, extract-pdf, extract-doc]
     skills: [extraction]
@@ -123,7 +131,14 @@ topology data-processing : [pipeline, fan-out] {
     role: classifier
     model: haiku
     permissions: autonomous
-    prompt: "prompts/classifier.md"
+    prompt {
+      Read extracted documents from workspace/extracted/.
+
+      Assign each one a category and confidence. Run validate-output on your
+      result before writing it.
+
+      Write classified records into workspace/classified/.
+    }
     phase: 2
     tools: [Read, Write, validate-output]
     skills: [classification]
@@ -143,7 +158,14 @@ topology data-processing : [pipeline, fan-out] {
     role: synthesizer
     model: opus
     permissions: autonomous
-    prompt: "prompts/synthesizer.md"
+    prompt {
+      Read all classified records from workspace/classified/.
+
+      Merge them with merge-results into a single structured view. Where records
+      conflict, keep both and mark the conflict rather than choosing.
+
+      Write the result to workspace/synthesis.json.
+    }
     phase: 3
     tools: [Read, Write, merge-results]
     reads: ["workspace/classified/"]
@@ -154,7 +176,14 @@ topology data-processing : [pipeline, fan-out] {
     role: reporter
     model: sonnet
     permissions: autonomous
-    prompt: "prompts/reporter.md"
+    prompt {
+      Read workspace/synthesis.json.
+
+      Produce a report for a human reader: what was processed, what was found,
+      and what remains unresolved. No new analysis.
+
+      Write workspace/report.md and workspace/report.pdf, then set quality.
+    }
     phase: 4
     tools: [Read, Write]
     reads: ["workspace/synthesis.json"]

package/examples/logos/gmail.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 48 48" width="48" height="48"><path fill="#fff" d="M6 12h36v26H6z"/><path fill="#EA4335" d="M6 14v3l18 12L42 17v-3l-18 12z"/><path fill="#FBBC04" d="M6 14v22h6V18l12 8 12-8v18h6V14l-18 12z" opacity=".9"/><path fill="#34A853" d="M6 36h6V18l-6-4z"/><path fill="#4285F4" d="M42 36h-6V18l6-4z"/><path fill="#C5221F" d="M6 14l18 12L42 14v-2H6z"/></svg>

package/examples/logos/slack.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 48 48" width="48" height="48"><path fill="#36C5F0" d="M18 6a4 4 0 100 8h4V10a4 4 0 00-4-4z"/><path fill="#2EB67D" d="M42 18a4 4 0 10-8 0v4h4a4 4 0 004-4z"/><path fill="#ECB22E" d="M30 42a4 4 0 100-8h-4v4a4 4 0 004 4z"/><path fill="#E01E5A" d="M6 30a4 4 0 108 0v-4h-4a4 4 0 00-4 4z"/><path fill="#36C5F0" d="M18 18h8v8h-8z" opacity=".7"/></svg>

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agentopology",
-  "version": "0.2.5",
+  "version": "0.4.0",
   "description": "The declarative language for multi-agent systems. Write once, scaffold for any platform.",
   "author": "Nadav Naveh",
   "license": "Apache-2.0",