scientify 2.1.0 → 3.1.0

package/dist/src/services/auto-updater.js

@@ -1,188 +0,0 @@
-import { exec } from "child_process";
-import { readFileSync, existsSync, lstatSync } from "fs";
-import { fileURLToPath } from "url";
-import { dirname, join } from "path";
-/**
- * Get the plugin root directory (where package.json lives).
- */
-function getPluginRoot() {
-    const __filename = fileURLToPath(import.meta.url);
-    const __dirname = dirname(__filename);
-    // From dist/src/services/ → go up 3 levels to plugin root
-    // Check for package.json at each level to find the correct root
-    let root = __dirname;
-    for (let i = 0; i < 5; i++) {
-        if (existsSync(join(root, "package.json"))) {
-            return root;
-        }
-        root = dirname(root);
-    }
-    // Fallback: assume dist/src/services structure
-    return join(__dirname, "../../..");
-}
-/**
- * Check if running in development mode.
- * Detection methods (no main package dependency):
- * 1. SCIENTIFY_DEV=1 environment variable
- * 2. tsconfig.json exists in plugin root (source checkout)
- * 3. Plugin directory is a symlink (npm link / pnpm link)
- * 4. Version contains "-dev" suffix
- * 5. NODE_ENV=development
- */
-function isDevMode() {
-    // 1. Explicit env var
-    const scientifyDev = process.env.SCIENTIFY_DEV;
-    if (scientifyDev === "1" || scientifyDev === "true") {
-        return true;
-    }
-    // 2. NODE_ENV
-    if (process.env.NODE_ENV === "development") {
-        return true;
-    }
-    const pluginRoot = getPluginRoot();
-    // 3. tsconfig.json exists (source checkout, not installed from npm)
-    if (existsSync(join(pluginRoot, "tsconfig.json"))) {
-        return true;
-    }
-    // 4. Plugin directory is a symlink (npm/pnpm link)
-    try {
-        if (lstatSync(pluginRoot).isSymbolicLink()) {
-            return true;
-        }
-    }
-    catch {
-        // ignore
-    }
-    // 5. Version contains "-dev"
-    try {
-        const pkg = JSON.parse(readFileSync(join(pluginRoot, "package.json"), "utf-8"));
-        if (pkg.version && pkg.version.includes("-dev")) {
-            return true;
-        }
-    }
-    catch {
-        // ignore
-    }
-    return false;
-}
-// Get current version from package.json
-function getCurrentVersion() {
-    try {
-        const packagePath = join(getPluginRoot(), "package.json");
-        const pkg = JSON.parse(readFileSync(packagePath, "utf-8"));
-        return pkg.version;
-    }
-    catch {
-        return "0.0.0";
-    }
-}
-// Check npm registry for latest version
-async function getLatestVersion(packageName) {
-    return new Promise((resolve) => {
-        exec(`npm view ${packageName} version`, { timeout: 10000 }, (error, stdout) => {
-            if (error) {
-                resolve(null);
-                return;
-            }
-            resolve(stdout.trim());
-        });
-    });
-}
-// Compare semver versions: returns true if latest > current
-function isNewerVersion(current, latest) {
-    const currentParts = current.split(".").map(Number);
-    const latestParts = latest.split(".").map(Number);
-    for (let i = 0; i < 3; i++) {
-        const c = currentParts[i] || 0;
-        const l = latestParts[i] || 0;
-        if (l > c)
-            return true;
-        if (l < c)
-            return false;
-    }
-    return false;
-}
-/**
- * Get the OpenClaw extensions directory.
- */
-function getExtensionsDir() {
-    const home = process.env.HOME || process.env.USERPROFILE || "";
-    return join(home, ".openclaw", "extensions");
-}
-/**
- * Run the update using npm pack + extract approach.
- * This avoids dependency on `openclaw` CLI being in PATH.
- */
-async function runUpdate(packageName, logger) {
-    const extensionsDir = getExtensionsDir();
-    const targetDir = join(extensionsDir, packageName);
-    return new Promise((resolve) => {
-        // Use npm pack to download the tarball, then extract
-        const cmd = `cd "${extensionsDir}" && npm pack ${packageName} --pack-destination . && tar -xzf ${packageName}-*.tgz && rm -rf "${targetDir}" && mv package "${targetDir}" && rm ${packageName}-*.tgz`;
-        exec(cmd, { timeout: 120000 }, (error, stdout, stderr) => {
-            if (error) {
-                logger.warn(`Scientify auto-update failed: ${stderr || error.message}`);
-                resolve(false);
-                return;
-            }
-            logger.info(`Scientify updated. Restart gateway to apply.`);
-            resolve(true);
-        });
-    });
-}
-export function createAutoUpdaterService(options) {
-    const { packageName, checkIntervalMs, logger } = options;
-    let intervalId = null;
-    let isChecking = false;
-    const checkAndUpdate = async () => {
-        if (isChecking)
-            return;
-        isChecking = true;
-        try {
-            const currentVersion = getCurrentVersion();
-            const latestVersion = await getLatestVersion(packageName);
-            if (!latestVersion) {
-                logger.debug?.(`Scientify update check: could not fetch latest version`);
-                return;
-            }
-            if (isNewerVersion(currentVersion, latestVersion)) {
-                logger.info(`Scientify update available: ${currentVersion} → ${latestVersion}`);
-                await runUpdate(packageName, logger);
-            }
-            else {
-                logger.debug?.(`Scientify is up to date (${currentVersion})`);
-            }
-        }
-        catch (err) {
-            logger.warn(`Scientify update check error: ${err}`);
-        }
-        finally {
-            isChecking = false;
-        }
-    };
-    return {
-        id: "scientify-auto-updater",
-        start: async () => {
-            // Skip auto-updates in development mode
-            if (isDevMode()) {
-                logger.debug?.("Scientify auto-updater skipped (dev mode)");
-                return;
-            }
-            logger.debug?.("Scientify auto-updater service started");
-            // Check once on startup (with a small delay to not block gateway start)
-            setTimeout(() => {
-                checkAndUpdate();
-            }, 5000);
-            // Then check periodically
-            intervalId = setInterval(checkAndUpdate, checkIntervalMs);
-        },
-        stop: () => {
-            if (intervalId) {
-                clearInterval(intervalId);
-                intervalId = null;
-            }
-            logger.debug?.("Scientify auto-updater service stopped");
-        },
-    };
-}
-//# sourceMappingURL=auto-updater.js.map

package/dist/src/services/auto-updater.js.map

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package/dist/src/tools/arxiv-download.d.ts

@@ -1,24 +0,0 @@
-export declare const ArxivDownloadSchema: import("@sinclair/typebox").TObject<{
-    arxiv_ids: import("@sinclair/typebox").TArray<import("@sinclair/typebox").TString>;
-    output_dir: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-}>;
-/**
- * arxiv_download: Download papers by arxiv_id. Requires explicit output_dir.
- */
-export declare function createArxivDownloadTool(): {
-    label: string;
-    name: string;
-    description: string;
-    parameters: import("@sinclair/typebox").TObject<{
-        arxiv_ids: import("@sinclair/typebox").TArray<import("@sinclair/typebox").TString>;
-        output_dir: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-    }>;
-    execute: (_toolCallId: string, rawArgs: unknown) => Promise<{
-        content: {
-            type: "text";
-            text: string;
-        }[];
-        details: unknown;
-    }>;
-};
-//# sourceMappingURL=arxiv-download.d.ts.map

package/dist/src/tools/arxiv-download.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/tools/arxiv-download.js

@@ -1,177 +0,0 @@
-import { Type } from "@sinclair/typebox";
-import * as fs from "node:fs";
-import * as path from "node:path";
-import * as tar from "tar";
-import { Result } from "./result.js";
-// Rate limit: arXiv recommends ~3 seconds between requests
-const RATE_LIMIT_MS = 3000;
-/** Non-blocking delay that yields to event loop */
-const delay = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
-export const ArxivDownloadSchema = Type.Object({
-    arxiv_ids: Type.Array(Type.String(), {
-        description: "List of arXiv IDs to download (e.g. ['2401.12345', '2312.00001']).",
-    }),
-    output_dir: Type.Optional(Type.String({
-        description: "Directory to save files. Defaults to 'papers/' relative to cwd. Can be relative or absolute.",
-    })),
-});
-function readStringParam(params, key, opts) {
-    const value = params[key];
-    if (value === undefined || value === null) {
-        if (opts?.required) {
-            throw new Error(`Missing required parameter: ${key}`);
-        }
-        return undefined;
-    }
-    return String(value);
-}
-function readArrayParam(params, key) {
-    const value = params[key];
-    if (Array.isArray(value))
-        return value.map(String);
-    if (typeof value === "string") {
-        try {
-            const parsed = JSON.parse(value);
-            if (Array.isArray(parsed))
-                return parsed.map(String);
-        }
-        catch {
-            return [value];
-        }
-    }
-    return [];
-}
-async function downloadTexSource(arxivId, outputDir, logger) {
-    const log = (msg) => logger?.debug?.(`[arxiv:${arxivId}] ${msg}`);
-    const paperDir = path.join(outputDir, arxivId);
-    await fs.promises.mkdir(paperDir, { recursive: true });
-    const srcUrl = `https://arxiv.org/src/${arxivId}`;
-    const tarPath = path.join(paperDir, "source.tar.gz");
-    try {
-        log(`Fetching source from ${srcUrl}`);
-        const response = await fetch(srcUrl);
-        if (!response.ok) {
-            const reason = `Source download failed: HTTP ${response.status} ${response.statusText}`;
-            log(reason);
-            const result = await downloadPdf(arxivId, outputDir, logger);
-            return { ...result, fallbackReason: reason };
-        }
-        const buffer = Buffer.from(await response.arrayBuffer());
-        log(`Downloaded ${buffer.length} bytes`);
-        await fs.promises.writeFile(tarPath, buffer);
-        const isTarGz = buffer[0] === 0x1f && buffer[1] === 0x8b;
-        log(`Format check: ${isTarGz ? "tar.gz" : "single file"}`);
-        if (isTarGz) {
-            await tar.x({ file: tarPath, cwd: paperDir });
-            await fs.promises.unlink(tarPath);
-            const files = await findTexFiles(paperDir);
-            log(`Found ${files.length} .tex files: ${files.join(", ")}`);
-            if (files.length === 0) {
-                const reason = "No .tex files found in source archive";
-                log(reason);
-                const result = await downloadPdf(arxivId, outputDir, logger);
-                return { ...result, fallbackReason: reason };
-            }
-            return { success: true, format: "tex", path: paperDir, files };
-        }
-        else {
-            const texPath = path.join(paperDir, "main.tex");
-            await fs.promises.rename(tarPath, texPath);
-            log("Saved as single main.tex file");
-            return { success: true, format: "tex", path: paperDir, files: ["main.tex"] };
-        }
-    }
-    catch (error) {
-        const reason = `Source extraction error: ${error instanceof Error ? error.message : String(error)}`;
-        log(reason);
-        const result = await downloadPdf(arxivId, outputDir, logger);
-        return { ...result, fallbackReason: reason };
-    }
-}
-async function downloadPdf(arxivId, outputDir, logger) {
-    const log = (msg) => logger?.debug?.(`[arxiv:${arxivId}] ${msg}`);
-    try {
-        const pdfUrl = `https://arxiv.org/pdf/${arxivId}.pdf`;
-        log(`Downloading PDF: ${pdfUrl}`);
-        const response = await fetch(pdfUrl);
-        if (!response.ok) {
-            log(`PDF download failed: HTTP ${response.status}`);
-            return { success: false, format: "pdf", path: "", files: [], error: `PDF download failed: ${response.status}` };
-        }
-        const pdfPath = path.join(outputDir, `${arxivId}.pdf`);
-        const buffer = Buffer.from(await response.arrayBuffer());
-        await fs.promises.writeFile(pdfPath, buffer);
-        log(`PDF saved: ${pdfPath} (${buffer.length} bytes)`);
-        return { success: true, format: "pdf", path: pdfPath, files: [`${arxivId}.pdf`] };
-    }
-    catch (error) {
-        log(`PDF download error: ${error}`);
-        return { success: false, format: "pdf", path: "", files: [], error: String(error) };
-    }
-}
-async function findTexFiles(dir) {
-    const files = [];
-    const entries = await fs.promises.readdir(dir, { withFileTypes: true });
-    for (const entry of entries) {
-        const fullPath = path.join(dir, entry.name);
-        if (entry.isDirectory()) {
-            const subFiles = await findTexFiles(fullPath);
-            files.push(...subFiles.map((f) => path.join(entry.name, f)));
-        }
-        else if (entry.name.endsWith(".tex")) {
-            files.push(entry.name);
-        }
-    }
-    return files;
-}
-/**
- * arxiv_download: Download papers by arxiv_id. Requires explicit output_dir.
- */
-export function createArxivDownloadTool() {
-    return {
-        label: "ArXiv Download",
-        name: "arxiv_download",
-        description: "Download arXiv papers by ID. Downloads .tex source (with PDF fallback). output_dir defaults to 'papers/' if omitted.",
-        parameters: ArxivDownloadSchema,
-        execute: async (_toolCallId, rawArgs) => {
-            const params = rawArgs;
-            const arxivIds = readArrayParam(params, "arxiv_ids");
-            const outputDir = readStringParam(params, "output_dir") ?? "papers";
-            if (arxivIds.length === 0) {
-                return Result.err("invalid_params", "arxiv_ids must be a non-empty array");
-            }
-            const resolvedOutputDir = path.resolve(outputDir);
-            await fs.promises.mkdir(resolvedOutputDir, { recursive: true });
-            const logger = { debug: (msg) => console.log(`[arxiv-download] ${msg}`) };
-            const downloads = [];
-            for (let i = 0; i < arxivIds.length; i++) {
-                const arxivId = arxivIds[i];
-                // Rate limit: wait before each request (except first)
-                if (i > 0) {
-                    await delay(RATE_LIMIT_MS);
-                }
-                // Always try .tex first, fallback to PDF automatically
-                const result = await downloadTexSource(arxivId, resolvedOutputDir, logger);
-                downloads.push({
-                    arxiv_id: arxivId,
-                    success: result.success,
-                    format: result.format,
-                    path: result.path,
-                    files: result.files,
-                    error: result.error,
-                    fallback_reason: result.fallbackReason,
-                });
-            }
-            const successful = downloads.filter((d) => d.success).length;
-            const failed = downloads.filter((d) => !d.success).length;
-            return Result.ok({
-                output_dir: resolvedOutputDir,
-                total: arxivIds.length,
-                successful,
-                failed,
-                downloads,
-            });
-        },
-    };
-}
-//# sourceMappingURL=arxiv-download.js.map

package/dist/src/tools/arxiv-download.js.map

@@ -1 +0,0 @@
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package/dist/src/tools/github-search-tool.d.ts

@@ -1,25 +0,0 @@
-export declare const GithubSearchToolSchema: import("@sinclair/typebox").TObject<{
-    query: import("@sinclair/typebox").TString;
-    max_results: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-    language: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-    sort: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-}>;
-export declare function createGithubSearchTool(): {
-    label: string;
-    name: string;
-    description: string;
-    parameters: import("@sinclair/typebox").TObject<{
-        query: import("@sinclair/typebox").TString;
-        max_results: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-        language: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-        sort: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-    }>;
-    execute: (_toolCallId: string, rawArgs: unknown) => Promise<{
-        content: {
-            type: "text";
-            text: string;
-        }[];
-        details: unknown;
-    }>;
-};
-//# sourceMappingURL=github-search-tool.d.ts.map

package/dist/src/tools/github-search-tool.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"github-search-tool.d.ts","sourceRoot":"","sources":["../../../src/tools/github-search-tool.ts"],"names":[],"mappings":"AAOA,eAAO,MAAM,sBAAsB;;;;;EAqBjC,CAAC;AAyCH,wBAAgB,sBAAsB;;;;;;;;;;2BAOL,MAAM,WAAW,OAAO;;;;;;;EAsExD"}

package/dist/src/tools/github-search-tool.js

@@ -1,114 +0,0 @@
-import { Type } from "@sinclair/typebox";
-import { Result } from "./result.js";
-const GITHUB_SEARCH_API = "https://api.github.com/search/repositories";
-const DEFAULT_MAX_RESULTS = 10;
-const MAX_RESULTS_LIMIT = 30;
-export const GithubSearchToolSchema = Type.Object({
-    query: Type.String({
-        description: "Search query for GitHub repositories (e.g. 'graph neural network recommendation').",
-    }),
-    max_results: Type.Optional(Type.Number({
-        description: "Maximum number of results (1-30). Default: 10.",
-        minimum: 1,
-        maximum: MAX_RESULTS_LIMIT,
-    })),
-    language: Type.Optional(Type.String({
-        description: "Filter by programming language (e.g. 'python', 'typescript').",
-    })),
-    sort: Type.Optional(Type.String({
-        description: 'Sort by: "stars" (default), "updated", or "best-match".',
-    })),
-});
-function readStringParam(params, key, opts) {
-    const value = params[key];
-    if (value === undefined || value === null) {
-        if (opts?.required) {
-            throw new Error(`Missing required parameter: ${key}`);
-        }
-        return undefined;
-    }
-    return String(value);
-}
-function readNumberParam(params, key, opts) {
-    const value = params[key];
-    if (value === undefined || value === null)
-        return undefined;
-    const num = Number(value);
-    if (isNaN(num))
-        return undefined;
-    return opts?.integer ? Math.floor(num) : num;
-}
-function resolveGithubToken() {
-    return ((process.env.GITHUB_TOKEN ?? "").trim() ||
-        (process.env.GH_TOKEN ?? "").trim() ||
-        (process.env.GITHUB_AI_TOKEN ?? "").trim() ||
-        undefined);
-}
-export function createGithubSearchTool() {
-    return {
-        label: "GitHub Search",
-        name: "github_search",
-        description: "Search GitHub repositories by keyword. Returns repo names, descriptions, star counts, and URLs. Reads GITHUB_TOKEN from environment for authentication.",
-        parameters: GithubSearchToolSchema,
-        execute: async (_toolCallId, rawArgs) => {
-            const params = rawArgs;
-            const query = readStringParam(params, "query", { required: true });
-            const maxResults = Math.min(readNumberParam(params, "max_results", { integer: true }) ?? DEFAULT_MAX_RESULTS, MAX_RESULTS_LIMIT);
-            const language = readStringParam(params, "language");
-            const rawSort = readStringParam(params, "sort") ?? "stars";
-            // Build GitHub search query
-            let searchQuery = query;
-            if (language) {
-                searchQuery += ` language:${language}`;
-            }
-            const sort = rawSort === "best-match" ? undefined : rawSort;
-            const urlParams = new URLSearchParams({
-                q: searchQuery,
-                per_page: String(maxResults),
-                order: "desc",
-            });
-            if (sort) {
-                urlParams.set("sort", sort);
-            }
-            const url = `${GITHUB_SEARCH_API}?${urlParams.toString()}`;
-            const token = resolveGithubToken();
-            const headers = {
-                Accept: "application/vnd.github+json",
-                "User-Agent": "scientify-agent",
-            };
-            if (token) {
-                headers.Authorization = `Bearer ${token}`;
-            }
-            let response;
-            try {
-                response = await fetch(url, { headers });
-            }
-            catch (error) {
-                return Result.err("network_error", `Failed to reach GitHub API: ${error instanceof Error ? error.message : String(error)}`);
-            }
-            if (response.status === 403) {
-                return Result.err("rate_limited", "GitHub API rate limit exceeded. Set GITHUB_TOKEN environment variable for higher limits.");
-            }
-            if (!response.ok) {
-                return Result.err("api_error", `GitHub API returned ${response.status}: ${response.statusText}`);
-            }
-            const data = (await response.json());
-            const repos = (data.items ?? []).map((repo) => ({
-                name: repo.full_name,
-                url: repo.html_url,
-                description: repo.description ?? "",
-                stars: repo.stargazers_count,
-                language: repo.language ?? "unknown",
-                updated: repo.updated_at,
-                topics: repo.topics ?? [],
-            }));
-            return Result.ok({
-                query,
-                total_count: data.total_count ?? 0,
-                returned: repos.length,
-                repos,
-            });
-        },
-    };
-}
-//# sourceMappingURL=github-search-tool.js.map

package/dist/src/tools/github-search-tool.js.map

@@ -1 +0,0 @@
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package/dist/src/tools/openreview-lookup.d.ts

@@ -1,31 +0,0 @@
-export declare const OpenReviewLookupSchema: import("@sinclair/typebox").TObject<{
-    query: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-    paper_id: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-    forum_id: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-    external_id: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-    max_results: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-    include_reviews: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
-    review_limit: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-}>;
-export declare function createOpenReviewLookupTool(): {
-    label: string;
-    name: string;
-    description: string;
-    parameters: import("@sinclair/typebox").TObject<{
-        query: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-        paper_id: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-        forum_id: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-        external_id: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
-        max_results: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-        include_reviews: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
-        review_limit: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
-    }>;
-    execute: (_toolCallId: string, rawArgs: unknown) => Promise<{
-        content: {
-            type: "text";
-            text: string;
-        }[];
-        details: unknown;
-    }>;
-};
-//# sourceMappingURL=openreview-lookup.d.ts.map

package/dist/src/tools/openreview-lookup.d.ts.map

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