labgate 0.5.40 → 0.5.43

package/dist/lib/display-mcp.js

@@ -3,8 +3,8 @@
  * LabGate Display MCP Server
  *
  * A Model Context Protocol server that allows Claude to render rich
- * interactive content (markdown, tables, plots, molecular structures,
- * DNA/protein sequences) directly in the LabGate web UI.
+ * lightweight rich content (markdown, tables, images, PDFs, and file previews)
+ * directly in the LabGate web UI.
  *
  * Usage: node dist/lib/display-mcp.js [--db /path/to/display.json]
  */
@@ -49,18 +49,9 @@ function parseDbPathFromArgs(args) {
 const WIDGET_TYPES = [
     'markdown',
     'table',
-    'plot',
     'image',
     'pdf',
-    'molecule',
-    'sequence',
-    'alignment',
     'file_preview',
-    'tree',
-    'heatmap',
-    'tracks',
-    'domains',
-    'network',
 ];
 async function main(args = process.argv.slice(2)) {
     const dbPath = parseDbPathFromArgs(args);
@@ -75,11 +66,8 @@ async function main(args = process.argv.slice(2)) {
             tools: {},
         },
         instructions: 'LabGate display widgets. Use display_widget to render rich interactive content ' +
-            'directly in the LabGate web UI — markdown with formatting, data tables, Plotly charts, ' +
-            '3D molecular structures (PDB), PDF documents, DNA/RNA/protein sequences with coloring, ' +
-            'multiple sequence alignments, phylogenetic trees, clustered heatmaps, ' +
-            'genome feature tracks, protein domain architectures, network graphs, ' +
-            'images, and file previews. ' +
+            'directly in the LabGate web UI — markdown with formatting, data tables, ' +
+            'images, PDF documents, and file previews. ' +
             'The widget appears inline in the chat transcript for the researcher to interact with.',
     });
     // ── Tool: display_widget ──────────────────────────────
@@ -89,39 +77,26 @@ async function main(args = process.argv.slice(2)) {
             'Supported widget types:\n' +
             '- markdown: Formatted text with headings, code blocks, tables, math\n' +
             '- table: Structured data table with sortable columns\n' +
-            '- plot: Interactive chart (Plotly.js specification)\n' +
             '- image: Display an image from the container filesystem\n' +
             '- pdf: PDF document viewer with page navigation\n' +
-            '- molecule: 3D molecular structure viewer (PDB ID, inline data, or file)\n' +
-            '- sequence: Colored DNA/RNA/protein sequence display\n' +
-            '- alignment: Multiple sequence alignment with conservation highlighting\n' +
-            '- file_preview: Preview of CSV, TSV, FASTA, or other data files\n' +
-            '- tree: Phylogenetic tree from Newick format string\n' +
-            '- heatmap: Clustered heatmap with optional dendrograms\n' +
-            '- tracks: Genome feature track viewer (GFF3, BED, VCF via igv.js)\n' +
-            '- domains: Protein domain/feature architecture diagram\n' +
-            '- network: Interactive network/graph visualization\n\n' +
+            '- file_preview: Preview of CSV, TSV, text, or other data files\n' +
+            '\n' +
             'Data shapes per widget type:\n' +
             '  markdown: { content: string }\n' +
             '  table: { columns: string[], rows: (string|number)[][], caption?: string }\n' +
-            '  plot: { plotly: { data: PlotlyTrace[], layout?: PlotlyLayout } }\n' +
             '  image: { path: string, alt?: string, caption?: string }\n' +
             '  pdf: { path: string, page?: number }\n' +
-            '  molecule: { pdb_id?: string, pdb_data?: string, path?: string, style?: "cartoon"|"ball-and-stick"|"surface" }\n' +
-            '  sequence: { sequence: string, type: "dna"|"rna"|"protein", label?: string }\n' +
-            '  alignment: { sequences: { id: string, seq: string }[], format?: "clustal"|"fasta" }\n' +
-            '  file_preview: { path: string, format?: string, head_lines?: number }\n' +
-            '  tree: { newick: string, layout?: "rectangular"|"radial" }\n' +
-            '  heatmap: { matrix: number[][], row_labels?: string[], col_labels?: string[], colorscale?: "viridis"|"inferno"|"plasma"|"blues"|"reds", cluster_rows?: boolean, cluster_cols?: boolean }\n' +
-            '  tracks: { genome?: string, locus?: string, tracks: { name: string, path?: string, url?: string, format: string }[] }\n' +
-            '  domains: { length: number, label?: string, features: { type: string, name: string, start: number, end: number, color?: string }[] }\n' +
-            '  network: { nodes: { id: string, label?: string, color?: string }[], edges: { source: string, target: string, label?: string, weight?: number }[], layout?: "cose"|"circle"|"grid"|"concentric"|"breadthfirst", directed?: boolean }',
+            '  file_preview: { path: string, format?: string, head_lines?: number }\n\n' +
+            'IMPORTANT: Always provide a "description" parameter with a manuscript-quality figure/table legend. ' +
+            'Write it as you would for a publication — describe what the widget shows, key observations, and relevant context. ' +
+            'Example: "Summary table of benchmark runs showing runtime, exit status, and output artifact paths for each configuration."',
         inputSchema: {
             widget: zod_1.z.enum(WIDGET_TYPES).describe('Widget type to render'),
             title: zod_1.z.string().optional().describe('Optional title displayed above the widget'),
+            description: zod_1.z.string().optional().describe('Manuscript-style figure/table description displayed below the widget (e.g. "Superposition of wild-type and mutant active sites showing key residue shifts")'),
             data: zod_1.z.record(zod_1.z.string(), zod_1.z.unknown()).describe('Widget-specific data payload (see tool description for shapes per widget type)'),
         },
-    }, async ({ widget, title, data }) => {
+    }, async ({ widget, title, description, data }) => {
         try {
             // Validate payload size — reject oversized inline data
             const payloadSize = JSON.stringify(data).length;
@@ -129,10 +104,14 @@ async function main(args = process.argv.slice(2)) {
                 return asError(`Widget data too large (${Math.round(payloadSize / 1024)}KB). ` +
                     'For large files, use a path reference instead of inline data.');
             }
+            // Merge description into data payload so UI can render it below the widget
+            const mergedData = { ...data };
+            if (description)
+                mergedData.description = description;
             const event = store.appendEvent({
                 widget,
                 title: title || null,
-                data: data,
+                data: mergedData,
                 session_id: null,
             });
             const label = title ? `"${title}"` : widget;

package/dist/lib/display-mcp.js.map

@@ -1 +1 @@
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package/dist/lib/doctor.js

@@ -324,6 +324,14 @@ function runDoctor() {
         detail: sandboxHomeCheck.detail,
         hint: sandboxHomeCheck.hint,
     });
+    const imagesDirCheck = checkDirectoryWriteability((0, config_js_1.getImagesDir)());
+    findings.push({
+        id: 'sif_cache_dir',
+        status: imagesDirCheck.status,
+        summary: `SIF cache dir: ${imagesDirCheck.summary}`,
+        detail: imagesDirCheck.detail,
+        hint: imagesDirCheck.hint,
+    });
     findings.push(checkDatasets(config.datasets || [], configPath));
     const counts = countStatuses(findings);
     return {

package/dist/lib/doctor.js.map

@@ -1 +1 @@
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package/dist/lib/explorer-claude.js

@@ -197,6 +197,38 @@ function ensureDisplayDbFile() {
         mode: config_js_1.PRIVATE_FILE_MODE,
     });
 }
+function buildClaudeHeadlessAddDirArgs(config) {
+    const dirs = new Set();
+    let hasExtraMounts = false;
+    let hasDatasets = false;
+    for (const mount of config.filesystem.extra_paths || []) {
+        if (!mount || typeof mount.path !== 'string')
+            continue;
+        const resolved = mount.path.replace(/^~/, (0, os_1.homedir)());
+        const target = `/mnt/${(0, path_1.basename)(resolved)}`;
+        hasExtraMounts = true;
+        dirs.add(target);
+    }
+    for (const ds of config.datasets || []) {
+        if (!ds || typeof ds.name !== 'string')
+            continue;
+        const name = ds.name.trim();
+        if (!name)
+            continue;
+        hasDatasets = true;
+        dirs.add(`/datasets/${name}`);
+    }
+    if (hasExtraMounts)
+        dirs.add('/mnt');
+    if (hasDatasets)
+        dirs.add('/datasets');
+    return Array.from(dirs).flatMap((dir) => ['--add-dir', dir]);
+}
+function buildClaudeHeadlessAllowedToolsArgs() {
+    // Keep approvals enabled globally, but pre-allow the tools needed for
+    // headless discovery + web lookups in mounted workspaces.
+    return ['--allowed-tools', 'Glob,Read,Grep,WebFetch'];
+}
 function buildContainerPrefixArgs(config, worktreePath, sifPath) {
     const sandboxHome = (0, config_js_1.getSandboxHome)();
     const args = [
@@ -292,7 +324,8 @@ function normalizeTimeout(raw) {
     return Math.max(30, Math.min(4 * 60 * 60, Math.floor(parsed)));
 }
 function runClaudeHeadlessInWorktree(input) {
-    const worktreePath = (0, path_1.resolve)(String(input.worktree_path || '').trim());
+    const worktreePathRaw = String(input.worktree_path || '').trim();
+    const worktreePath = worktreePathRaw ? (0, path_1.resolve)(worktreePathRaw) : '';
     const prompt = String(input.prompt || '').trim();
     const resumeSessionId = String(input.resume_session_id || '').trim();
     const timeoutSec = normalizeTimeout(input.timeout_sec);
@@ -324,6 +357,8 @@ function runClaudeHeadlessInWorktree(input) {
         '--output-format',
         'stream-json',
         '--include-partial-messages',
+        ...buildClaudeHeadlessAddDirArgs(config),
+        ...buildClaudeHeadlessAllowedToolsArgs(),
         ...((0, config_js_1.shouldClaudeHeadlessRunWithAllowedPermissions)(config) ? ['--dangerously-skip-permissions'] : []),
         ...(resumeSessionId ? ['--resume', resumeSessionId] : []),
         prompt,

package/dist/lib/explorer-claude.js.map

@@ -1 +1 @@
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package/dist/lib/explorer-eval.js

@@ -17,13 +17,14 @@ function shellForCurrentPlatform() {
     if (process.platform === 'win32') {
         return process.env.COMSPEC || 'cmd.exe';
     }
-    return process.env.SHELL || '/bin/sh';
+    // Keep evaluation runs isolated from interactive shell startup files.
+    return '/bin/sh';
 }
 function shellArgsForCommand(command) {
     if (process.platform === 'win32') {
         return ['/d', '/s', '/c', command];
     }
-    return ['-lc', command];
+    return ['-c', command];
 }
 function runEvaluation(opts) {
     const worktreePath = (0, path_1.resolve)(opts.worktree_path);

package/dist/lib/explorer-eval.js.map

@@ -1 +1 @@
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package/dist/lib/init.js

@@ -93,6 +93,11 @@ const CONFIG_WITH_COMMENTS = `{
   // Container image used for sandboxes
   "image": "${config_js_1.DEFAULT_CONFIG.image}",
 
+  // Optional persistent shared SIF cache path (for multi-user HPC).
+  // Leave empty to use the default under ~/.labgate/images.
+  // Env var LABGATE_IMAGES_DIR overrides this when set.
+  "images_dir": "${config_js_1.DEFAULT_CONFIG.images_dir || ''}",
+
   // Max session duration (hours). Container is killed after this.
   "session_timeout_hours": ${config_js_1.DEFAULT_CONFIG.session_timeout_hours},
 
@@ -114,7 +119,10 @@ const CONFIG_WITH_COMMENTS = `{
 
   "commands": {
     // Commands that cannot be executed inside the sandbox.
-    "blacklist": ${JSON.stringify(config_js_1.DEFAULT_CONFIG.commands.blacklist, null, 6).replace(/\n/g, '\n    ')}
+    "blacklist": ${JSON.stringify(config_js_1.DEFAULT_CONFIG.commands.blacklist, null, 6).replace(/\n/g, '\n    ')},
+    // Commands to ensure inside Claude containers before startup.
+    // If a command is missing, LabGate tries a best-effort install (root only).
+    "ensure_commands": ${JSON.stringify(config_js_1.DEFAULT_CONFIG.commands.ensure_commands ?? [], null, 6).replace(/\n/g, '\n    ')}
   },
 
   "network": {
@@ -146,9 +154,9 @@ const CONFIG_WITH_COMMENTS = `{
   },
 
   "headless": {
-    // Claude headless mode cannot handle interactive tool permission prompts.
-    // When enabled, headless runs pass --dangerously-skip-permissions.
-    "claude_run_with_allowed_permissions": ${config_js_1.DEFAULT_CONFIG.headless?.claude_run_with_allowed_permissions ?? true},
+    // Deprecated safety flag (kept for backward compatibility).
+    // Runtime ignores this and keeps per-tool approvals enabled.
+    "claude_run_with_allowed_permissions": ${config_js_1.DEFAULT_CONFIG.headless?.claude_run_with_allowed_permissions ?? false},
     // Show "Continue in terminal via labgate continue ..." in the terminal footer.
     "continuation_in_other_terminals": ${config_js_1.DEFAULT_CONFIG.headless?.continuation_in_other_terminals ?? true},
     // Enable Git UI integration (Git DAG sidebar + footer branch switcher).
@@ -174,12 +182,6 @@ function ensureBundledIrisDatasetFiles(opts = {}) {
         });
     }
 }
-function stripJsonComments(text) {
-    return text
-        .split('\n')
-        .filter((line) => !line.trimStart().startsWith('//'))
-        .join('\n');
-}
 function bundledIrisDatasetEntry() {
     return {
         path: IRIS_SAMPLE_DATASET_DIR,
@@ -193,9 +195,7 @@ function ensureBundledIrisDatasetRegistration() {
     if (!(0, fs_1.existsSync)(configPath))
         return;
     try {
-        const raw = (0, fs_1.readFileSync)(configPath, 'utf-8');
-        const stripped = stripJsonComments(raw).trim();
-        const obj = (stripped ? JSON.parse(stripped) : {});
+        const obj = (0, config_js_1.readRawConfigFile)(configPath);
         const datasets = Array.isArray(obj.datasets)
             ? obj.datasets
             : [];
@@ -214,11 +214,7 @@ function ensureBundledIrisDatasetRegistration() {
             return;
         datasets.push(bundledIrisDatasetEntry());
         obj.datasets = datasets;
-        (0, fs_1.writeFileSync)(configPath, JSON.stringify(obj, null, 2) + '\n', {
-            encoding: 'utf-8',
-            mode: config_js_1.PRIVATE_FILE_MODE,
-        });
-        (0, config_js_1.ensurePrivateFile)(configPath);
+        (0, config_js_1.writeRawConfigFile)(obj, configPath);
     }
     catch (err) {
         log.warn(`Could not ensure bundled Iris dataset registration: ${err?.message ?? String(err)}`);

package/dist/lib/init.js.map

@@ -1 +1 @@
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package/dist/lib/slurm-cli-passthrough.d.ts

@@ -16,9 +16,17 @@ export interface StageSlurmCliOptions {
      * When set, generated wrappers will prefer proxy execution via this socket.
      */
     hostProxySocketInContainer?: string | null;
+    /**
+     * Prefer host proxy execution over full binary/plugin staging when a proxy
+     * socket is configured and host SLURM commands are available.
+     */
+    preferHostProxy?: boolean;
 }
 export interface StageSlurmCliResult {
     ok: boolean;
+    mode: 'staged' | 'proxy-only';
+    reused: boolean;
+    hostCommands: string[];
     staged: string[];
     skipped: string[];
     errors: string[];
@@ -30,7 +38,9 @@ export interface StageSlurmCliResult {
  * in $HOME/.labgate-bin so they are available inside the container even when the image
  * does not ship with SLURM.
  *
- * This is intentionally simple: copy binaries + ldd libraries + slurm.conf (if found).
- * The host-side session launcher is responsible for bind-mounting /run/munge when present.
+ * When host proxy mode is preferred, this writes proxy-only wrappers without paying the
+ * binary/plugin copy cost on every startup. Otherwise it stages binaries + ldd libraries
+ * + slurm.conf (if found). The host-side session launcher is responsible for bind-mounting
+ * /run/munge when present.
  */
 export declare function stageSlurmCliPassthrough(options: StageSlurmCliOptions): StageSlurmCliResult;