@saibolla/ada 0.1.2

package/LICENSE

@@ -0,0 +1,191 @@
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+   Copyright 2026 Sai Krishna Bolla
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+   limitations under the License.

package/README.md

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+# Ada
+
+The AI research agent for your terminal.
+
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue?style=flat-square)](LICENSE)
+[![Node](https://img.shields.io/badge/node-%3E%3D20.18.1-brightgreen?style=flat-square)](https://nodejs.org)
+[![Skills](https://img.shields.io/badge/skills-197-orange?style=flat-square)](#skills)
+[![Website](https://img.shields.io/badge/web-thinkwithada.com-0d9668?style=flat-square)](https://thinkwithada.com)
+
+Ada is an AI-powered research agent that runs in your terminal. Ask questions, search papers, run experiments, write drafts, and produce cited research artifacts. Built on [Pi](https://github.com/badlogic/pi-mono) with 197 scientific skills across 22 disciplines.
+
+---
+
+## Install
+
+```bash
+git clone https://github.com/saikrishnabolla/ada.git
+cd ada
+npm install
+npm run build
+npm run dev
+```
+
+On first launch, Ada will install packages and walk you through model setup.
+
+Requires Node.js 20.18.1 or newer.
+
+---
+
+## Usage
+
+Just ask anything:
+
+```
+$ ada "what do we know about scaling laws?"
+```
+
+Or use workflows for structured research:
+
+```
+$ ada deepresearch "mechanistic interpretability"
+$ ada litreview "mRNA vaccine efficacy"
+$ ada audit 2401.12345
+$ ada replicate "chain-of-thought improves math"
+```
+
+Inside the REPL, type naturally or use `/commands`:
+
+```
+/deepresearch <topic>     thorough multi-source investigation
+/litreview <topic>        literature review with citations
+/review <file>            simulated peer review
+/audit <paper>            verify paper claims against its codebase
+/replicate <paper>        replicate a paper's experiments
+/compare <topic>          compare sources on a topic
+/draft <topic>            write a paper-style draft
+/autoresearch <idea>      autonomous experiment loop
+/help                     all commands
+```
+
+---
+
+## What Ada can do
+
+**Research** -- Search papers via AlphaXiv and Semantic Scholar, traverse citation graphs, run literature reviews with verified citations, and produce source-grounded briefs.
+
+**Write** -- Generate LaTeX papers, conference posters, slide decks (PPTX), Word documents, and publication-quality figures. Every claim is backed by a source.
+
+**Experiment** -- Run code locally, in Docker containers, or on cloud GPUs (Modal, RunPod). Replicate paper results with isolated execution environments.
+
+**Analyze** -- 197 scientific skills covering genomics, proteomics, drug discovery, clinical research, chemistry, physics, ML, finance, geospatial, and more. 325 pre-built workflow procedures across 22 disciplines.
+
+---
+
+## Agents
+
+Four specialized subagents, dispatched automatically for complex tasks:
+
+| Agent | Role |
+|-------|------|
+| **Researcher** | Gather evidence across papers, web, repos, docs |
+| **Reviewer** | Simulated peer review with severity-graded feedback |
+| **Writer** | Structured drafts from research notes |
+| **Verifier** | Inline citations, source URL verification, dead link cleanup |
+
+---
+
+## Skills
+
+Ada ships 197 skills organized into:
+
+- **Research tools** -- AlphaXiv paper search/Q&A, Semantic Scholar citation graphs, Crawl4AI web scraping, session search
+- **Scientific domains** -- Genomics (scanpy, biopython), drug discovery (rdkit, diffdock), clinical (clinvar, pubmed), proteomics, chemistry, physics, materials science, neuroscience, ecology, astronomy
+- **Databases** -- 250+ scientific databases including PubMed, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, OpenAlex, arXiv, KEGG, STRING, GnomAD
+- **Writing & visualization** -- LaTeX papers, posters, PPTX slides, DOCX, PDF manipulation, matplotlib, seaborn, plotly, Mermaid diagrams
+- **Compute** -- Docker sandbox, Modal (serverless GPU), RunPod (persistent GPU), Python REPL
+- **Workflow catalog** -- 325 pre-built procedures from data analysis to quantum circuit design
+
+---
+
+## Packages
+
+27 Pi packages provide tools, agents, and integrations:
+
+| Category | Packages |
+|----------|----------|
+| Research | AlphaXiv, arXiv, Tavily web search, session search |
+| Agents | Subagents, task tracking, ultrathink review loops |
+| Documents | Document parser, markdown preview, PowerPoint, Zotero |
+| Visualization | Charts, Mermaid diagrams, Excalidraw canvas |
+| Compute | Python REPL, sandbox, process management |
+| Infrastructure | MCP adapter, command palette, context management |
+
+---
+
+## Configuration
+
+On first launch, run `setup` inside Ada to configure services interactively. Or edit `~/.ada/.env` directly:
+
+```env
+# AI model (required -- at least one provider)
+ANTHROPIC_API_KEY=
+OPENAI_API_KEY=
+
+# Web search
+TAVILY_API_KEY=
+
+# Scientific databases (optional)
+S2_API_KEY=                    # Semantic Scholar
+OPENALEX_API_KEY=              # OpenAlex
+NCBI_API_KEY=                  # PubMed/NCBI
+
+# Citation management
+ZOTERO_API_KEY=
+ZOTERO_LIBRARY_ID=
+ZOTERO_LIBRARY_TYPE=user
+
+# Cloud compute (optional)
+MODAL_TOKEN_ID=
+MODAL_TOKEN_SECRET=
+RUNPOD_API_KEY=
+OPENROUTER_API_KEY=
+```
+
+Global config at `~/.ada/.env` works from any folder. Project-specific `.env` overrides per directory.
+
+---
+
+## Architecture
+
+```
+ada/
+├── packages/alpha-hub/     AlphaXiv CLI and library
+├── extensions/             Research tools (/help, /init, /outputs)
+├── prompts/                Workflow templates (11 orchestrated workflows)
+├── skills/                 197 scientific skills (SKILL.md files)
+├── .ada/
+│   ├── agents/             4 subagent prompts
+│   ├── themes/             Ada terminal theme
+│   ├── settings.json       Package configuration
+│   └── SYSTEM.md           Agent personality and rules
+├── src/                    TypeScript source
+└── bin/ada.js              CLI entry point
+```
+
+Built on the Pi agent runtime and Feynman by Companion AI. Scientific skills sourced from Claude Scientific Skills (MIT).
+
+---
+
+## Development
+
+```bash
+git clone https://github.com/saikrishnabolla/ada.git
+cd ada
+npm install
+npm run dev          # Run from source
+npm run build        # Compile TypeScript
+npm test             # Run tests (25 tests)
+npm run typecheck    # Type checking
+```
+
+---
+
+## License
+
+Apache 2.0 -- see [LICENSE](LICENSE).
+
+[thinkwithada.com](https://thinkwithada.com)

package/bin/ada.js

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+#!/usr/bin/env node
+const MIN_NODE_VERSION = "20.18.1";
+
+function parseNodeVersion(version) {
+  const [major = "0", minor = "0", patch = "0"] = version.replace(/^v/, "").split(".");
+  return {
+    major: Number.parseInt(major, 10) || 0,
+    minor: Number.parseInt(minor, 10) || 0,
+    patch: Number.parseInt(patch, 10) || 0,
+  };
+}
+
+function compareNodeVersions(left, right) {
+  if (left.major !== right.major) return left.major - right.major;
+  if (left.minor !== right.minor) return left.minor - right.minor;
+  return left.patch - right.patch;
+}
+
+if (compareNodeVersions(parseNodeVersion(process.versions.node), parseNodeVersion(MIN_NODE_VERSION)) < 0) {
+  console.error(`ada requires Node.js ${MIN_NODE_VERSION} or later (detected ${process.versions.node}).`);
+  console.error("Switch to Node 20 with `nvm install 20 && nvm use 20`, or use the standalone installer:");
+  console.error("curl -fsSL https://ada.is/install | bash");
+  process.exit(1);
+}
+await import("../scripts/patch-embedded-pi.mjs");
+await import("../dist/index.js");

package/dist/bootstrap/sync.js

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+import { createHash } from "node:crypto";
+import { existsSync, mkdirSync, readdirSync, readFileSync, rmSync, writeFileSync } from "node:fs";
+import { dirname, relative, resolve } from "node:path";
+import { getBootstrapStatePath } from "../config/paths.js";
+function sha256(text) {
+    return createHash("sha256").update(text).digest("hex");
+}
+function readBootstrapState(path) {
+    if (!existsSync(path)) {
+        return { version: 1, files: {} };
+    }
+    try {
+        const parsed = JSON.parse(readFileSync(path, "utf8"));
+        return {
+            version: 1,
+            files: parsed.files && typeof parsed.files === "object" ? parsed.files : {},
+        };
+    }
+    catch {
+        return { version: 1, files: {} };
+    }
+}
+function writeBootstrapState(path, state) {
+    mkdirSync(dirname(path), { recursive: true });
+    writeFileSync(path, JSON.stringify(state, null, 2) + "\n", "utf8");
+}
+function listFiles(root) {
+    if (!existsSync(root)) {
+        return [];
+    }
+    const files = [];
+    for (const entry of readdirSync(root, { withFileTypes: true })) {
+        const path = resolve(root, entry.name);
+        if (entry.isDirectory()) {
+            files.push(...listFiles(path));
+            continue;
+        }
+        if (entry.isFile()) {
+            files.push(path);
+        }
+    }
+    return files.sort();
+}
+function removeEmptyParentDirectories(path, stopAt) {
+    let current = dirname(path);
+    while (current.startsWith(stopAt) && current !== stopAt) {
+        if (!existsSync(current)) {
+            current = dirname(current);
+            continue;
+        }
+        if (readdirSync(current).length > 0) {
+            return;
+        }
+        rmSync(current, { recursive: true, force: true });
+        current = dirname(current);
+    }
+}
+function syncManagedFiles(sourceRoot, targetRoot, scope, state, result) {
+    const sourcePaths = new Set(listFiles(sourceRoot).map((sourcePath) => relative(sourceRoot, sourcePath)));
+    for (const targetPath of listFiles(targetRoot)) {
+        const key = relative(targetRoot, targetPath);
+        if (sourcePaths.has(key))
+            continue;
+        const scopedKey = `${scope}:${key}`;
+        const previous = state.files[scopedKey] ?? state.files[key];
+        if (!previous) {
+            continue;
+        }
+        if (!existsSync(targetPath)) {
+            delete state.files[scopedKey];
+            delete state.files[key];
+            continue;
+        }
+        const currentTargetText = readFileSync(targetPath, "utf8");
+        const currentTargetHash = sha256(currentTargetText);
+        if (currentTargetHash !== previous.lastAppliedTargetHash) {
+            result.skipped.push(key);
+            continue;
+        }
+        rmSync(targetPath, { force: true });
+        removeEmptyParentDirectories(targetPath, targetRoot);
+        delete state.files[scopedKey];
+        delete state.files[key];
+    }
+    for (const sourcePath of listFiles(sourceRoot)) {
+        const key = relative(sourceRoot, sourcePath);
+        const targetPath = resolve(targetRoot, key);
+        const sourceText = readFileSync(sourcePath, "utf8");
+        const sourceHash = sha256(sourceText);
+        const scopedKey = `${scope}:${key}`;
+        const previous = state.files[scopedKey] ?? state.files[key];
+        mkdirSync(dirname(targetPath), { recursive: true });
+        if (!existsSync(targetPath)) {
+            writeFileSync(targetPath, sourceText, "utf8");
+            state.files[scopedKey] = {
+                lastAppliedSourceHash: sourceHash,
+                lastAppliedTargetHash: sourceHash,
+            };
+            delete state.files[key];
+            result.copied.push(key);
+            continue;
+        }
+        const currentTargetText = readFileSync(targetPath, "utf8");
+        const currentTargetHash = sha256(currentTargetText);
+        if (currentTargetHash === sourceHash) {
+            state.files[scopedKey] = {
+                lastAppliedSourceHash: sourceHash,
+                lastAppliedTargetHash: currentTargetHash,
+            };
+            delete state.files[key];
+            continue;
+        }
+        if (!previous) {
+            result.skipped.push(key);
+            continue;
+        }
+        if (currentTargetHash !== previous.lastAppliedTargetHash) {
+            result.skipped.push(key);
+            continue;
+        }
+        writeFileSync(targetPath, sourceText, "utf8");
+        state.files[scopedKey] = {
+            lastAppliedSourceHash: sourceHash,
+            lastAppliedTargetHash: sourceHash,
+        };
+        delete state.files[key];
+        result.updated.push(key);
+    }
+}
+export function syncBundledAssets(appRoot, agentDir) {
+    const statePath = getBootstrapStatePath();
+    const state = readBootstrapState(statePath);
+    const result = {
+        copied: [],
+        updated: [],
+        skipped: [],
+    };
+    syncManagedFiles(resolve(appRoot, ".ada", "themes"), resolve(agentDir, "themes"), "themes", state, result);
+    syncManagedFiles(resolve(appRoot, ".ada", "agents"), resolve(agentDir, "agents"), "agents", state, result);
+    syncManagedFiles(resolve(appRoot, "skills"), resolve(agentDir, "skills"), "skills", state, result);
+    writeBootstrapState(statePath, state);
+    return result;
+}