@hongmaple0820/med-scale-research-os 0.43.0

package/dist/env/EnvironmentDoctor.js

@@ -0,0 +1,581 @@
+import { spawnSync } from 'node:child_process';
+import { existsSync } from 'node:fs';
+import { arch, platform, release } from 'node:os';
+import { delimiter, extname } from 'node:path';
+import { runGbrainCommandSync } from '../core/GbrainRuntime.js';
+import { resolveExternalCommandPath } from '../core/ExternalCommand.js';
+const CHECK_DEFINITIONS = [
+    {
+        id: 'git',
+        label: 'Git',
+        category: 'core',
+        required: true,
+        candidates: [{ command: 'git', args: ['--version'], display: 'git' }],
+        requiredFor: ['repository workflow', 'release verification'],
+        installHint: 'Install Git and re-open the shell so git is on PATH.',
+    },
+    {
+        id: 'npm',
+        label: 'npm',
+        category: 'core',
+        required: true,
+        candidates: [{ command: 'npm', args: ['--version'], display: 'npm' }],
+        requiredFor: ['scale install', 'codegraph install', 'node-library workflow'],
+        installHint: 'Install Node.js 20+; npm is bundled with Node.js.',
+    },
+    {
+        id: 'npx',
+        label: 'npx',
+        category: 'core',
+        required: true,
+        candidates: [{ command: 'npx', args: ['--version'], display: 'npx' }],
+        requiredFor: ['awesome-design-md', 'ui-ux-pro-max', 'frontend-design'],
+        installHint: 'Install Node.js 20+; npx is bundled with npm.',
+    },
+    {
+        id: 'powershell',
+        label: 'PowerShell',
+        category: 'shell',
+        required: false,
+        candidates: [
+            { command: 'pwsh', args: ['-NoProfile', '-Command', '$PSVersionTable.PSVersion.ToString()'], display: 'pwsh' },
+            { command: 'powershell', args: ['-NoProfile', '-Command', '$PSVersionTable.PSVersion.ToString()'], display: 'powershell' },
+        ],
+        requiredFor: ['Windows workflow wrappers', 'RTK Windows proxy'],
+        installHint: 'Install PowerShell 7+ or use Windows PowerShell where available.',
+    },
+    {
+        id: 'bash',
+        label: 'Bash',
+        category: 'shell',
+        required: false,
+        candidates: [{ command: 'bash', args: ['--version'], display: 'bash' }],
+        requiredFor: ['Unix workflow wrappers', 'make targets'],
+        installHint: 'Install Bash through Git for Windows, WSL, or the OS package manager.',
+    },
+    {
+        id: 'cargo',
+        label: 'Rust/Cargo',
+        category: 'runtime',
+        required: false,
+        candidates: [{ command: 'cargo', args: ['--version'], display: 'cargo' }],
+        requiredFor: ['rtk install'],
+        installHint: 'Install Rust with rustup, then re-open the shell so cargo is on PATH.',
+    },
+    {
+        id: 'bun',
+        label: 'Bun',
+        category: 'runtime',
+        required: false,
+        candidates: [{ command: 'bun', args: ['--version'], display: 'bun' }],
+        requiredFor: ['gbrain install'],
+        installHint: 'Install Bun from https://bun.sh and re-open the shell.',
+    },
+    {
+        id: 'python',
+        label: 'Python',
+        category: 'runtime',
+        required: false,
+        candidates: [
+            { command: 'python', args: ['--version'], display: 'python' },
+            { command: 'python3', args: ['--version'], display: 'python3' },
+            { command: 'py', args: ['--version'], display: 'py' },
+        ],
+        requiredFor: ['graphify install'],
+        installHint: 'Install Python 3.10+ and ensure it is on PATH.',
+    },
+    {
+        id: 'python-installer',
+        label: 'Python installer',
+        category: 'runtime',
+        required: false,
+        candidates: [
+            { command: 'uv', args: ['--version'], display: 'uv' },
+            { command: 'pipx', args: ['--version'], display: 'pipx' },
+            { command: 'pip', args: ['--version'], display: 'pip' },
+            { command: 'pip3', args: ['--version'], display: 'pip3' },
+            { command: 'python', args: ['-m', 'pip', '--version'], display: 'python -m pip' },
+            { command: 'python3', args: ['-m', 'pip', '--version'], display: 'python3 -m pip' },
+        ],
+        requiredFor: ['graphify install'],
+        installHint: 'Install uv or pipx first; pip is supported only as a fallback.',
+    },
+    {
+        id: 'rtk',
+        label: 'RTK',
+        category: 'third-party',
+        required: false,
+        candidates: [{ command: 'rtk', args: ['--version'], display: 'rtk' }],
+        requiredFor: ['governed CLI proxy', 'token savings evidence'],
+        installHint: 'Install with cargo, then run `rtk init -g --codex` and `rtk gain`.',
+    },
+    {
+        id: 'gbrain',
+        label: 'GBrain',
+        category: 'third-party',
+        required: false,
+        candidates: [{ command: 'gbrain', args: ['doctor', '--json'], display: 'gbrain doctor --json' }],
+        requiredFor: ['memory provider routing', 'cross-session recall'],
+        installHint: 'Install with Bun and run `gbrain init --pglite` before autonomous recall.',
+    },
+    {
+        id: 'graphify',
+        label: 'Graphify',
+        category: 'third-party',
+        required: false,
+        candidates: [{ command: 'graphify', args: ['--version'], display: 'graphify' }],
+        requiredFor: ['knowledge graph provider'],
+        installHint: 'Install with `uv tool install graphify && graphify install --platform codex`.',
+    },
+    {
+        id: 'codegraph',
+        label: 'CodeGraph',
+        category: 'third-party',
+        required: false,
+        candidates: [{ command: 'codegraph', args: ['--version'], display: 'codegraph' }],
+        requiredFor: ['code intelligence provider'],
+        installHint: 'Install with `npm install -g @colbymchenry/codegraph` and run `codegraph init -i` per project.',
+    },
+];
+export function inspectEnvironment(options = {}) {
+    const env = options.env ?? process.env;
+    const currentPlatform = options.platform ?? platform();
+    const currentArch = options.arch ?? arch();
+    const currentRelease = options.release ?? release();
+    const currentNodeVersion = options.nodeVersion ?? process.version;
+    const currentExecPath = options.execPath ?? process.execPath;
+    const resolver = options.commandResolver ?? resolveExternalCommandPath;
+    const runner = options.commandRunner ?? runCommand;
+    const pathEntries = String(env.PATH ?? env.Path ?? '')
+        .split(currentPlatform === 'win32' ? ';' : delimiter)
+        .map(entry => entry.trim())
+        .filter(Boolean);
+    const checks = CHECK_DEFINITIONS.map(definition => inspectCommand(definition, resolver, runner, currentPlatform));
+    const nodeStatus = nodeVersionStatus(currentNodeVersion);
+    const warnings = buildWarnings(checks, nodeStatus);
+    const recommendations = buildRecommendations(checks, nodeStatus);
+    const requiredFailures = checks.filter(check => check.required && (check.status === 'missing' || check.status === 'fail')).length;
+    const warnCount = checks.filter(check => check.status === 'warn').length + (nodeStatus.status === 'warn' ? 1 : 0);
+    const status = nodeStatus.status === 'fail' || requiredFailures > 0
+        ? 'broken'
+        : warnCount > 0 ? 'degraded' : 'healthy';
+    return {
+        ok: status !== 'broken',
+        status,
+        generatedAt: new Date().toISOString(),
+        platform: currentPlatform,
+        arch: currentArch,
+        release: currentRelease,
+        node: {
+            version: currentNodeVersion,
+            execPath: currentExecPath,
+            status: nodeStatus.status,
+            reason: nodeStatus.reason,
+        },
+        shell: {
+            defaultShell: env.SHELL,
+            comspec: env.ComSpec,
+            detected: shellCandidates(currentPlatform).map(command => ({
+                id: command,
+                available: Boolean(resolver(command)),
+                path: resolver(command) ?? undefined,
+            })),
+        },
+        path: {
+            delimiter: currentPlatform === 'win32' ? ';' : delimiter,
+            entryCount: pathEntries.length,
+            entriesPreview: pathEntries.slice(0, 12),
+        },
+        checks,
+        warnings,
+        recommendations,
+    };
+}
+export function renderEnvironmentDoctor(report) {
+    const lines = [
+        '',
+        'SCALE Environment Doctor',
+        `  Status: ${report.status.toUpperCase()}`,
+        `  OS: ${report.platform} ${report.arch} ${report.release}`,
+        `  Node: ${report.node.version} (${report.node.status})`,
+        `  PATH entries: ${report.path.entryCount}`,
+    ];
+    for (const check of report.checks) {
+        lines.push(`  [${check.status.toUpperCase()}] ${check.id}: ${check.reason}`);
+        if (check.detectedCommand && check.version)
+            lines.push(`    detected: ${check.detectedCommand} (${check.version})`);
+        if ((check.status === 'missing' || check.status === 'fail' || check.status === 'warn') && check.installHint) {
+            lines.push(`    fix: ${check.installHint}`);
+        }
+    }
+    for (const warning of report.warnings)
+        lines.push(`  [WARN] ${warning}`);
+    for (const recommendation of report.recommendations)
+        lines.push(`  [NEXT] ${recommendation}`);
+    return lines.join('\n');
+}
+function inspectCommand(definition, resolver, runner, currentPlatform) {
+    let firstFailed;
+    for (const candidate of definition.candidates) {
+        const resolved = resolver(candidate.command);
+        if (!resolved)
+            continue;
+        const result = runner(candidate.command, candidate.args, resolved);
+        const output = `${result.stdout}\n${result.stderr}`.trim();
+        const interpreted = interpretSpecialCheckResult(definition.id, output, resolved, currentPlatform, result.exitCode);
+        const version = resolveSpecialVersion(definition.id, output, runner, resolved) ?? interpreted?.version ?? firstLine(output);
+        if (result.exitCode === 0) {
+            const status = interpreted ?? commandVersionStatus(definition.id, version);
+            return {
+                id: definition.id,
+                label: definition.label,
+                category: definition.category,
+                status: status.status,
+                required: definition.required,
+                candidates: definition.candidates.map(item => item.display),
+                detectedCommand: candidate.display,
+                resolvedPath: resolved,
+                version,
+                reason: status.reason ?? `${definition.label} is available via ${candidate.display}.`,
+                installHint: definition.installHint,
+                requiredFor: definition.requiredFor,
+            };
+        }
+        if (interpreted) {
+            return {
+                id: definition.id,
+                label: definition.label,
+                category: definition.category,
+                status: interpreted.status,
+                required: definition.required,
+                candidates: definition.candidates.map(item => item.display),
+                detectedCommand: candidate.display,
+                resolvedPath: resolved,
+                version,
+                reason: interpreted.reason,
+                installHint: definition.installHint,
+                requiredFor: definition.requiredFor,
+            };
+        }
+        firstFailed ??= {
+            id: definition.id,
+            label: definition.label,
+            category: definition.category,
+            status: 'warn',
+            required: definition.required,
+            candidates: definition.candidates.map(item => item.display),
+            detectedCommand: candidate.display,
+            resolvedPath: resolved,
+            reason: `${definition.label} was found but health/version command failed: ${summarizeFailureOutput(definition.id, output)}`,
+            installHint: definition.installHint,
+            requiredFor: definition.requiredFor,
+        };
+    }
+    if (firstFailed)
+        return firstFailed;
+    return {
+        id: definition.id,
+        label: definition.label,
+        category: definition.category,
+        status: definition.required ? 'fail' : 'missing',
+        required: definition.required,
+        candidates: definition.candidates.map(item => item.display),
+        reason: `${definition.label} was not detected on PATH.`,
+        installHint: definition.installHint,
+        requiredFor: definition.requiredFor,
+    };
+}
+function runCommand(command, args, resolvedPath) {
+    if (command === 'gbrain') {
+        const result = runGbrainCommandSync(args, {
+            timeout: 20_000,
+            env: process.env,
+        });
+        return {
+            exitCode: result.exitCode,
+            stdout: result.stdout,
+            stderr: result.stderr,
+        };
+    }
+    const executable = resolveWindowsCommandShim(resolvedPath ?? command);
+    const wrapperArgs = isWindowsCommandWrapper(executable)
+        ? ['/d', '/c', 'call', executable, ...args]
+        : args;
+    const result = spawnSync(isWindowsCommandWrapper(executable) ? process.env.ComSpec ?? 'cmd.exe' : executable, wrapperArgs, {
+        encoding: 'utf8',
+        shell: false,
+        windowsHide: true,
+        timeout: 10_000,
+        maxBuffer: 1024 * 1024,
+    });
+    return {
+        exitCode: typeof result.status === 'number' ? result.status : 1,
+        stdout: String(result.stdout ?? ''),
+        stderr: String(result.stderr ?? result.error?.message ?? ''),
+    };
+}
+function resolveWindowsCommandShim(executable) {
+    if (process.platform !== 'win32')
+        return executable;
+    if (!/[\\/]/.test(executable) || extname(executable))
+        return executable;
+    for (const extension of ['.cmd', '.exe', '.bat', '.com']) {
+        const candidate = `${executable}${extension}`;
+        if (existsSync(candidate))
+            return candidate;
+    }
+    return executable;
+}
+function isWindowsCommandWrapper(executable) {
+    return process.platform === 'win32' && /\.(cmd|bat)$/i.test(executable);
+}
+function nodeVersionStatus(value) {
+    const version = parseSemver(value);
+    if (!version)
+        return { status: 'warn', reason: `Could not parse Node.js version: ${value}` };
+    if (version.major < 20)
+        return { status: 'fail', reason: `Node.js ${value} is below the required 20.x baseline.` };
+    return { status: 'ok', reason: `Node.js ${value} satisfies the 20+ baseline.` };
+}
+function commandVersionStatus(id, version) {
+    if (id === 'python') {
+        const parsed = parseSemver(version);
+        if (!parsed || parsed.major < 3 || (parsed.major === 3 && parsed.minor < 10)) {
+            return { status: 'warn', reason: `${version || 'Python'} is detected, but Graphify requires Python 3.10+.` };
+        }
+    }
+    if (id === 'python-installer' && version && !/^(uv|pipx)\b/i.test(version)) {
+        return { status: 'warn', reason: `${version} is available, but uv or pipx is preferred for isolated graphify installs.` };
+    }
+    return { status: 'ok' };
+}
+function buildWarnings(checks, nodeStatus) {
+    const warnings = [];
+    if (nodeStatus.status !== 'ok')
+        warnings.push(nodeStatus.reason);
+    for (const check of checks) {
+        if (check.required && (check.status === 'missing' || check.status === 'fail'))
+            warnings.push(`${check.id} is required: ${check.reason}`);
+        if (!check.required && check.status === 'warn')
+            warnings.push(`${check.id}: ${check.reason}`);
+    }
+    return warnings;
+}
+function buildRecommendations(checks, nodeStatus) {
+    const recommendations = new Set();
+    if (nodeStatus.status !== 'ok')
+        recommendations.add('Install Node.js 20+ before running SCALE workflow commands.');
+    for (const check of checks) {
+        if ((check.status === 'missing' || check.status === 'fail' || check.status === 'warn') && check.installHint) {
+            recommendations.add(check.installHint);
+        }
+    }
+    recommendations.add('Use `npm run smoke:setup` as the cross-platform setup smoke; use `make setup-smoke` only where make is installed.');
+    return [...recommendations];
+}
+function shellCandidates(currentPlatform) {
+    return currentPlatform === 'win32'
+        ? ['powershell', 'pwsh', 'cmd', 'bash']
+        : ['bash', 'sh', 'pwsh'];
+}
+function firstLine(value) {
+    return value.split(/\r?\n/).map(line => line.trim()).find(Boolean) ?? '';
+}
+function interpretSpecialCheckResult(id, output, resolvedPath, currentPlatform, exitCode) {
+    if (id === 'bash'
+        && currentPlatform === 'win32'
+        && isWindowsSystemBashLauncher(resolvedPath)
+        && typeof exitCode === 'number'
+        && exitCode !== 0) {
+        return {
+            status: 'missing',
+            reason: 'Windows bash launcher is present, but no usable Bash runtime is configured.',
+        };
+    }
+    if (id === 'gbrain')
+        return interpretGbrainDoctorOutput(output);
+    return null;
+}
+function summarizeFailureOutput(id, output) {
+    const line = firstLine(output);
+    if (id === 'gbrain') {
+        const interpreted = interpretGbrainDoctorOutput(output);
+        if (interpreted)
+            return interpreted.reason;
+    }
+    if (!line)
+        return 'no output';
+    if (id === 'gbrain') {
+        const parsed = parseGbrainDoctorReport(output);
+        if (parsed) {
+            const failingChecks = gbrainDoctorChecks(parsed)
+                .filter(check => check.status && check.status !== 'ok')
+                .map(check => check.name)
+                .filter(Boolean);
+            if (failingChecks.length > 0) {
+                return `gbrain doctor reported ${failingChecks.length} non-ok check(s): ${failingChecks.slice(0, 4).join(', ')}`;
+            }
+            if (typeof parsed.status === 'string')
+                return `gbrain doctor status=${parsed.status}`;
+        }
+    }
+    return compactText(line);
+}
+function interpretGbrainDoctorOutput(output) {
+    const parsed = parseGbrainDoctorReport(output);
+    if (!parsed)
+        return null;
+    if (gbrainCoreRecallReady(parsed)) {
+        const optionalIssues = gbrainDoctorChecks(parsed)
+            .filter(check => check.status !== 'ok' && !GBRAIN_CORE_RECALL_CHECKS.has(check.name))
+            .map(check => check.name)
+            .filter(Boolean);
+        return {
+            status: 'ok',
+            reason: optionalIssues.length > 0
+                ? `GBrain core recall is available; optional doctor warnings: ${optionalIssues.slice(0, 4).join(', ')}`
+                : 'GBrain core recall is available.',
+        };
+    }
+    const coreIssues = gbrainDoctorChecks(parsed)
+        .filter(check => check.status !== 'ok' && GBRAIN_CORE_RECALL_CHECKS.has(check.name))
+        .map(check => check.name)
+        .filter(Boolean);
+    if (coreIssues.length > 0) {
+        return {
+            status: 'warn',
+            reason: `gbrain doctor reported core recall issue(s): ${coreIssues.join(', ')}`,
+        };
+    }
+    const nonOkChecks = gbrainDoctorChecks(parsed)
+        .filter(check => check.status !== 'ok')
+        .map(check => check.name)
+        .filter(Boolean);
+    if (nonOkChecks.length > 0) {
+        return {
+            status: 'warn',
+            reason: `gbrain doctor reported ${nonOkChecks.length} non-ok check(s): ${nonOkChecks.slice(0, 4).join(', ')}`,
+        };
+    }
+    if (typeof parsed.status === 'string') {
+        return {
+            status: 'ok',
+            reason: `gbrain doctor status=${parsed.status}`,
+        };
+    }
+    return null;
+}
+function compactText(value, maxLength = 200) {
+    const normalized = value.replace(/\s+/g, ' ').trim();
+    if (normalized.length <= maxLength)
+        return normalized;
+    return `${normalized.slice(0, maxLength - 1)}…`;
+}
+function resolveSpecialVersion(id, output, runner, resolvedPath) {
+    if (id !== 'gbrain')
+        return undefined;
+    return resolveGbrainVersion(output, runner, resolvedPath);
+}
+function parseSemver(value) {
+    const match = value.match(/(\d+)\.(\d+)(?:\.(\d+))?/);
+    if (!match)
+        return null;
+    return {
+        major: Number.parseInt(match[1], 10),
+        minor: Number.parseInt(match[2], 10),
+        patch: Number.parseInt(match[3] ?? '0', 10),
+    };
+}
+function isWindowsSystemBashLauncher(resolvedPath) {
+    if (!resolvedPath)
+        return false;
+    return /[\\/]windows[\\/]system32[\\/]bash\.exe$/i.test(resolvedPath);
+}
+const GBRAIN_CORE_RECALL_CHECKS = new Set(['connection', 'schema_version', 'brain_score']);
+function resolveGbrainVersion(output, runner, resolvedPath) {
+    const versionProbe = runner('gbrain', ['--version'], resolvedPath);
+    const versionLine = firstLine(`${versionProbe.stdout}\n${versionProbe.stderr}`);
+    if (versionProbe.exitCode === 0 && versionLine && !looksLikeJson(versionLine)) {
+        return compactText(versionLine, 80);
+    }
+    const parsed = parseGbrainDoctorReport(output);
+    if (typeof parsed?.status === 'string') {
+        return `gbrain doctor status=${parsed.status}`;
+    }
+    return 'gbrain doctor --json';
+}
+function parseGbrainDoctorReport(output) {
+    const json = extractFirstJsonObject(output);
+    if (!json)
+        return null;
+    try {
+        const parsed = JSON.parse(json);
+        return isRecord(parsed) ? parsed : null;
+    }
+    catch {
+        return null;
+    }
+}
+function extractFirstJsonObject(output) {
+    const start = output.indexOf('{');
+    if (start === -1)
+        return null;
+    let depth = 0;
+    let inString = false;
+    let escaped = false;
+    for (let index = start; index < output.length; index += 1) {
+        const char = output[index];
+        if (inString) {
+            if (escaped) {
+                escaped = false;
+            }
+            else if (char === '\\') {
+                escaped = true;
+            }
+            else if (char === '"') {
+                inString = false;
+            }
+            continue;
+        }
+        if (char === '"') {
+            inString = true;
+            continue;
+        }
+        if (char === '{')
+            depth += 1;
+        if (char === '}') {
+            depth -= 1;
+            if (depth === 0)
+                return output.slice(start, index + 1);
+        }
+    }
+    return null;
+}
+function looksLikeJson(value) {
+    const trimmed = value.trim();
+    return trimmed.startsWith('{') || trimmed.startsWith('[');
+}
+function gbrainCoreRecallReady(report) {
+    const connection = gbrainDoctorCheckStatus(report, 'connection');
+    const schema = gbrainDoctorCheckStatus(report, 'schema_version');
+    const brainScore = gbrainDoctorCheckStatus(report, 'brain_score');
+    return connection === 'ok' && (schema === 'ok' || brainScore === 'ok');
+}
+function gbrainDoctorCheckStatus(report, name) {
+    return gbrainDoctorChecks(report).find(check => check.name === name)?.status;
+}
+function gbrainDoctorChecks(report) {
+    if (!Array.isArray(report.checks))
+        return [];
+    return report.checks
+        .filter(isRecord)
+        .map(check => ({
+        name: String(check.name ?? ''),
+        status: String(check.status ?? ''),
+    }))
+        .filter(check => check.name);
+}
+function isRecord(value) {
+    return Boolean(value) && typeof value === 'object' && !Array.isArray(value);
+}
+//# sourceMappingURL=EnvironmentDoctor.js.map

package/dist/env/EnvironmentDoctor.js.map

@@ -0,0 +1 @@
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package/dist/eval/BenchmarkPublisher.d.ts

@@ -0,0 +1,25 @@
+export interface BenchmarkData {
+    timestamp: string;
+    version: string;
+    summary: {
+        passAt1: number;
+        passAt3: number;
+        totalCases: number;
+        avgDurationMs: number;
+        avgTokens: number;
+        avgCostUsd: number;
+    };
+    byCategory: Record<string, {
+        total: number;
+        passed: number;
+        avgDurationMs: number;
+        avgTokens: number;
+    }>;
+    trends: Array<{
+        date: string;
+        passAt1: number;
+        totalCases: number;
+    }>;
+}
+export declare function publishBenchmark(data: BenchmarkData, outputDir?: string): string;
+export declare function createBenchmarkSummary(version: string): BenchmarkData;

package/dist/eval/BenchmarkPublisher.js

@@ -0,0 +1,27 @@
+import { writeFileSync, mkdirSync, existsSync } from 'node:fs';
+import { join } from 'node:path';
+export function publishBenchmark(data, outputDir = '.scale/benchmarks') {
+    if (!existsSync(outputDir))
+        mkdirSync(outputDir, { recursive: true });
+    const filename = `benchmark-${data.version}-${data.timestamp.replace(/[:.]/g, '-')}.json`;
+    const path = join(outputDir, filename);
+    writeFileSync(path, JSON.stringify(data, null, 2));
+    return path;
+}
+export function createBenchmarkSummary(version) {
+    return {
+        timestamp: new Date().toISOString(),
+        version,
+        summary: {
+            passAt1: 0,
+            passAt3: 0,
+            totalCases: 0,
+            avgDurationMs: 0,
+            avgTokens: 0,
+            avgCostUsd: 0,
+        },
+        byCategory: {},
+        trends: [],
+    };
+}
+//# sourceMappingURL=BenchmarkPublisher.js.map