@ivybiosciences/ivybloom-cli 0.8.20

package/README.md

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+# @ivybiosciences/ivybloom-cli
+
+CLI/TUI for computational biology and drug discovery on the .bloom* platform.
+
+## Installation
+
+```bash
+npm install -g @ivybiosciences/ivybloom-cli
+```
+
+Or with npx (no install):
+
+```bash
+npx @ivybiosciences/ivybloom-cli --help
+```
+
+## Quick Start
+
+```bash
+# Authenticate with .bloom* platform
+ivybloom auth login
+
+# Launch interactive TUI
+ivybloom tui
+
+# Run protein structure prediction
+ivybloom tools run esmfold --sequence "MKFLILLFN..."
+
+# List available tools
+ivybloom tools list
+```
+
+## Features
+
+- **Protein Structure Prediction** - ESMFold, AlphaFold integration
+- **Drug Molecule Generation** - REINVENT, molecular design
+- **Property Prediction** - ADMET, toxicity, solubility
+- **Molecular Docking** - Protein-ligand binding analysis
+- **Interactive TUI** - Full terminal interface with Charmbracelet
+
+## Platform Support
+
+| Platform | Architecture |
+|----------|--------------|
+| macOS    | x64, arm64   |
+| Linux    | x64, arm64   |
+| Windows  | x64          |
+
+## Environment Variables
+
+| Variable | Description |
+|----------|-------------|
+| `IVYBLOOM_API_KEY` | API key for authentication |
+| `IVYBLOOM_SKIP_INSTALL` | Set to `1` to skip binary download |
+
+## Alternative Installation
+
+### Go
+
+```bash
+go install github.com/ivybiosciences/ivybloom-cli/go@latest
+```
+
+### Direct Download
+
+Download binaries from [GitHub Releases](https://github.com/ivybiosciences/ivybloom-cli/releases).
+
+## Documentation
+
+- [Full Documentation](https://docs.ivybloom.com)
+- [API Reference](https://docs.ivybloom.com/api)
+- [GitHub Repository](https://github.com/ivybiosciences/ivybloom-cli)
+
+## License
+
+MIT - Ivy Biosciences

package/package.json

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+{
+  "name": "@ivybiosciences/ivybloom-cli",
+  "version": "0.8.20",
+  "description": "CLI/TUI for computational biology and drug discovery on the .bloom* platform",
+  "keywords": [
+    "cli",
+    "tui",
+    "biology",
+    "bioinformatics",
+    "drug-discovery",
+    "protein",
+    "science",
+    "ivybloom",
+    "computational-biology",
+    "esmfold",
+    "molecular-design"
+  ],
+  "homepage": "https://ivybloom.com",
+  "bugs": {
+    "url": "https://github.com/ivybiosciences/ivybloom-cli/issues"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/ivybiosciences/ivybloom-cli.git"
+  },
+  "license": "MIT",
+  "author": "Ivy Biosciences <admin@ivybiosciences.com>",
+  "bin": {
+    "ivybloom": "bin/ivybloom"
+  },
+  "files": [
+    "bin/",
+    "scripts/",
+    "README.md"
+  ],
+  "scripts": {
+    "postinstall": "node scripts/install.js",
+    "test": "node -e \"require('child_process').execSync('./bin/ivybloom --version', {stdio: 'inherit'})\""
+  },
+  "engines": {
+    "node": ">=16"
+  },
+  "os": [
+    "darwin",
+    "linux",
+    "win32"
+  ],
+  "cpu": [
+    "x64",
+    "arm64"
+  ]
+}

package/scripts/install.js

@@ -0,0 +1,334 @@
+#!/usr/bin/env node
+
+const { execSync, spawnSync } = require("child_process");
+const fs = require("fs");
+const https = require("https");
+const path = require("path");
+const { createWriteStream, chmodSync } = require("fs");
+
+const BIN_NAME = "ivybloom";
+const RELEASES_BASE_URL = "https://releases.ivybloom.com/releases";
+
+// ANSI color codes for terminal output
+const colors = {
+  reset: "\x1b[0m",
+  bright: "\x1b[1m",
+  dim: "\x1b[2m",
+  green: "\x1b[32m",
+  yellow: "\x1b[33m",
+  blue: "\x1b[34m",
+  magenta: "\x1b[35m",
+  cyan: "\x1b[36m",
+  red: "\x1b[31m",
+};
+
+// Brand colors (approximated for terminal)
+const brand = {
+  primary: colors.green,
+  accent: colors.cyan,
+  muted: colors.dim,
+};
+
+function log(message, color = colors.reset) {
+  console.log(`${color}${message}${colors.reset}`);
+}
+
+function logStep(step, message) {
+  console.log(`${brand.muted}[${step}]${colors.reset} ${message}`);
+}
+
+function logSuccess(message) {
+  console.log(`${colors.green}✓${colors.reset} ${message}`);
+}
+
+function logError(message) {
+  console.log(`${colors.red}✗${colors.reset} ${message}`);
+}
+
+// Map Node.js platform/arch to release asset names
+const PLATFORM_MAP = {
+  darwin: "darwin",
+  linux: "linux",
+  win32: "windows",
+};
+
+const ARCH_MAP = {
+  x64: "amd64",
+  arm64: "arm64",
+};
+
+const PLATFORM_DISPLAY = {
+  darwin: "macOS",
+  linux: "Linux",
+  win32: "Windows",
+};
+
+function getPlatformInfo() {
+  const platform = PLATFORM_MAP[process.platform];
+  const arch = ARCH_MAP[process.arch];
+
+  if (!platform || !arch) {
+    throw new Error(
+      `Unsupported platform: ${process.platform}-${process.arch}`
+    );
+  }
+
+  // Windows doesn't support arm64 in our builds
+  if (platform === "windows" && arch === "arm64") {
+    throw new Error("Windows ARM64 is not supported. Please use x64.");
+  }
+
+  return { platform, arch };
+}
+
+function getAssetName(version, platform, arch) {
+  const ext = platform === "windows" ? ".zip" : ".tar.gz";
+  return `ivybloom_${version}_${platform}_${arch}${ext}`;
+}
+
+async function getLatestVersion() {
+  return new Promise((resolve, reject) => {
+    // Fetch latest version from releases CDN
+    const url = `${RELEASES_BASE_URL}/latest.txt`;
+
+    https
+      .get(url, { headers: { "User-Agent": "ivybloom-npm-installer" } }, (res) => {
+        if (res.statusCode === 302 || res.statusCode === 301) {
+          // Follow redirect
+          https.get(res.headers.location, { headers: { "User-Agent": "ivybloom-npm-installer" } }, handleResponse);
+          return;
+        }
+        handleResponse(res);
+
+        function handleResponse(res) {
+          let data = "";
+          res.on("data", (chunk) => (data += chunk));
+          res.on("end", () => {
+            const version = data.trim().replace(/^v/, "");
+            if (version && /^\d+\.\d+\.\d+/.test(version)) {
+              resolve(version);
+            } else {
+              reject(new Error("No releases found"));
+            }
+          });
+        }
+      })
+      .on("error", reject);
+  });
+}
+
+async function downloadFile(url, dest, onProgress) {
+  return new Promise((resolve, reject) => {
+    const follow = (url) => {
+      https
+        .get(url, { headers: { "User-Agent": "ivybloom-npm-installer" } }, (res) => {
+          if (res.statusCode === 302 || res.statusCode === 301) {
+            follow(res.headers.location);
+            return;
+          }
+
+          if (res.statusCode !== 200) {
+            reject(new Error(`Download failed: HTTP ${res.statusCode}`));
+            return;
+          }
+
+          const totalSize = parseInt(res.headers["content-length"], 10);
+          let downloadedSize = 0;
+          const file = createWriteStream(dest);
+
+          res.on("data", (chunk) => {
+            downloadedSize += chunk.length;
+            if (onProgress && totalSize) {
+              onProgress(downloadedSize, totalSize);
+            }
+          });
+
+          res.pipe(file);
+          file.on("finish", () => {
+            file.close();
+            resolve();
+          });
+          file.on("error", (err) => {
+            fs.unlink(dest, () => {}); // Delete partial file
+            reject(err);
+          });
+        })
+        .on("error", reject);
+    };
+
+    follow(url);
+  });
+}
+
+function formatBytes(bytes) {
+  if (bytes < 1024) return bytes + " B";
+  if (bytes < 1024 * 1024) return (bytes / 1024).toFixed(1) + " KB";
+  return (bytes / (1024 * 1024)).toFixed(1) + " MB";
+}
+
+function renderProgressBar(current, total, width = 30) {
+  const percent = Math.round((current / total) * 100);
+  const filled = Math.round((current / total) * width);
+  const empty = width - filled;
+  const bar = "█".repeat(filled) + "░".repeat(empty);
+  const size = `${formatBytes(current)}/${formatBytes(total)}`;
+
+  process.stdout.write(`\r  ${brand.primary}${bar}${colors.reset} ${percent}% ${colors.dim}(${size})${colors.reset}`);
+}
+
+function extractArchive(archivePath, destDir, platform) {
+  if (platform === "windows") {
+    execSync(
+      `powershell -command "Expand-Archive -Path '${archivePath}' -DestinationPath '${destDir}' -Force"`,
+      { stdio: "pipe" }
+    );
+  } else {
+    execSync(`tar -xzf "${archivePath}" -C "${destDir}"`, { stdio: "pipe" });
+  }
+}
+
+function verifyInstallation(binPath) {
+  try {
+    const result = spawnSync(binPath, ["--version"], {
+      encoding: "utf8",
+      timeout: 5000,
+    });
+
+    if (result.status === 0) {
+      return result.stdout.trim() || result.stderr.trim();
+    }
+    return null;
+  } catch {
+    return null;
+  }
+}
+
+function printBanner() {
+  console.log();
+  console.log(`${brand.primary}${colors.bright}  ╭─────────────────────────────────────╮${colors.reset}`);
+  console.log(`${brand.primary}${colors.bright}  │${colors.reset}         ${brand.primary}IvyBloom CLI${colors.reset}               ${brand.primary}${colors.bright}│${colors.reset}`);
+  console.log(`${brand.primary}${colors.bright}  │${colors.reset}  ${colors.dim}Computational Biology Platform${colors.reset}     ${brand.primary}${colors.bright}│${colors.reset}`);
+  console.log(`${brand.primary}${colors.bright}  ╰─────────────────────────────────────╯${colors.reset}`);
+  console.log();
+}
+
+function printSuccessBanner(version, binPath) {
+  console.log();
+  console.log(`${brand.primary}${colors.bright}  ╭─────────────────────────────────────╮${colors.reset}`);
+  console.log(`${brand.primary}${colors.bright}  │${colors.reset}  ${colors.green}✓${colors.reset} Installation Complete            ${brand.primary}${colors.bright}│${colors.reset}`);
+  console.log(`${brand.primary}${colors.bright}  ╰─────────────────────────────────────╯${colors.reset}`);
+  console.log();
+  console.log(`  ${colors.dim}Version:${colors.reset}  ${version}`);
+  console.log(`  ${colors.dim}Binary:${colors.reset}   ${binPath}`);
+  console.log();
+  console.log(`  ${colors.dim}Get started:${colors.reset}`);
+  console.log(`    ${brand.accent}ivybloom --help${colors.reset}     Show available commands`);
+  console.log(`    ${brand.accent}ivybloom auth login${colors.reset} Authenticate with .bloom*`);
+  console.log(`    ${brand.accent}ivybloom tui${colors.reset}        Launch interactive interface`);
+  console.log();
+}
+
+async function main() {
+  // Skip if IVYBLOOM_SKIP_INSTALL is set (for CI or manual installs)
+  if (process.env.IVYBLOOM_SKIP_INSTALL === "1") {
+    console.log("Skipping binary download (IVYBLOOM_SKIP_INSTALL=1)");
+    return;
+  }
+
+  try {
+    printBanner();
+
+    const { platform, arch } = getPlatformInfo();
+    const platformDisplay = PLATFORM_DISPLAY[process.platform] || process.platform;
+
+    logStep("1/4", `Detected ${colors.cyan}${platformDisplay}${colors.reset} (${arch})`);
+
+    // Get version from package.json or fetch latest
+    const pkg = require("../package.json");
+    let version = pkg.version;
+
+    if (version === "0.0.0") {
+      logStep("2/4", "Fetching latest release...");
+      version = await getLatestVersion();
+    } else {
+      logStep("2/4", `Using version ${colors.cyan}v${version}${colors.reset}`);
+    }
+
+    const assetName = getAssetName(version, platform, arch);
+    const downloadUrl = `${RELEASES_BASE_URL}/${version}/${assetName}`;
+
+    const binDir = path.join(__dirname, "..", "bin");
+    const tmpDir = path.join(__dirname, "..", ".tmp");
+    const archivePath = path.join(tmpDir, assetName);
+
+    // Create directories
+    fs.mkdirSync(binDir, { recursive: true });
+    fs.mkdirSync(tmpDir, { recursive: true });
+
+    logStep("3/4", `Downloading ${colors.dim}${assetName}${colors.reset}`);
+
+    await downloadFile(downloadUrl, archivePath, (current, total) => {
+      renderProgressBar(current, total);
+    });
+    console.log(); // New line after progress bar
+
+    logStep("4/4", "Extracting and installing...");
+    extractArchive(archivePath, tmpDir, platform);
+
+    // Move binary to bin directory
+    const binName = platform === "windows" ? `${BIN_NAME}.exe` : BIN_NAME;
+    const srcBin = path.join(tmpDir, binName);
+    const destBin = path.join(binDir, binName);
+
+    // Check if extracted binary exists
+    if (!fs.existsSync(srcBin)) {
+      // Sometimes the binary is in a subdirectory
+      const extracted = fs.readdirSync(tmpDir);
+      for (const item of extracted) {
+        const itemPath = path.join(tmpDir, item);
+        if (fs.statSync(itemPath).isDirectory()) {
+          const nestedBin = path.join(itemPath, binName);
+          if (fs.existsSync(nestedBin)) {
+            fs.copyFileSync(nestedBin, destBin);
+            break;
+          }
+        }
+      }
+    } else {
+      fs.copyFileSync(srcBin, destBin);
+    }
+
+    if (!fs.existsSync(destBin)) {
+      throw new Error("Binary not found in archive");
+    }
+
+    if (platform !== "windows") {
+      chmodSync(destBin, 0o755);
+    }
+
+    // Cleanup temp directory
+    fs.rmSync(tmpDir, { recursive: true, force: true });
+
+    // Verify installation
+    const versionOutput = verifyInstallation(destBin);
+    if (versionOutput) {
+      logSuccess(`Binary verified: ${colors.dim}${versionOutput}${colors.reset}`);
+    }
+
+    printSuccessBanner(version, destBin);
+
+  } catch (error) {
+    console.log();
+    logError(`Installation failed: ${error.message}`);
+    console.log();
+    console.log(`  ${colors.dim}Manual installation:${colors.reset}`);
+    console.log(`    ${brand.accent}https://ivybloom.com/downloads${colors.reset}`);
+    console.log();
+    console.log(`  ${colors.dim}Or install via curl:${colors.reset}`);
+    console.log(`    ${brand.accent}curl -fsSL https://ivybloom.com/install.sh | bash${colors.reset}`);
+    console.log();
+    process.exit(1);
+  }
+}
+
+main();