matterviz 0.3.5 → 0.3.6

package/tests/extension.test.ts

@@ -0,0 +1,2041 @@
+import {
+  STRUCTURE_EXTENSIONS,
+  TRAJ_EXTENSIONS,
+  TRAJ_KEYWORDS,
+  VASP_VOLUMETRIC_REGEX,
+} from '$lib/constants'
+import type { ThemeName } from '$lib/theme/index'
+import { is_trajectory_file } from '$lib/trajectory/parse'
+import { Buffer } from 'node:buffer'
+import { beforeEach, describe, expect, test, vi } from 'vitest'
+import type { ExtensionContext, Tab, TextEditor, Uri } from 'vscode'
+import pkg_json from '../package.json' with { type: 'json' }
+import {
+  activate,
+  create_html,
+  get_defaults,
+  get_file,
+  get_theme,
+  handle_msg,
+  MessageData,
+  read_file,
+  render,
+  should_auto_render,
+} from '../src/extension'
+import { VOLUMETRIC_VASP_RE } from '../src/types'
+import type { FileData } from '../src/webview/main'
+
+// Mock modules
+const mock_fs = vi.hoisted(() => ({
+  readFileSync: vi.fn().mockReturnValue(`mock content`),
+  existsSync: vi.fn().mockReturnValue(true),
+  readdirSync: vi.fn().mockReturnValue([]),
+}))
+
+vi.mock(`node:fs`, () => mock_fs)
+vi.mock(`node:path`, async (importOriginal) => {
+  const actual = (await importOriginal()) as Record<string, unknown>
+  return {
+    ...actual,
+    basename: vi.fn((p: string) => p.split(`/`).pop() || ``),
+    dirname: vi.fn((p: string) => p.split(`/`).slice(0, -1).join(`/`) || `/`),
+    join: vi.fn((...paths: string[]) => paths.join(`/`)),
+    isAbsolute: vi.fn((p: string) => p.startsWith(`/`)),
+  }
+})
+
+const msg_args = {
+  // generic placeholder arguments for all messages
+  filename: `filename`,
+  request_id: `request_id`,
+  file_path: `file_path`,
+  frame_index: 0,
+} as const
+
+const mock_vscode = vi.hoisted(() => ({
+  window: {
+    showInformationMessage: vi.fn(),
+    showErrorMessage: vi.fn(),
+    showTextDocument: vi.fn(),
+    showSaveDialog: vi.fn(),
+    createWebviewPanel: vi.fn(),
+    activeTextEditor: null as TextEditor | null,
+    tabGroups: { activeTabGroup: { activeTab: null as Tab | null } },
+    registerCustomEditorProvider: vi.fn(),
+    activeColorTheme: { kind: 1 }, // Light theme by default
+    onDidChangeActiveColorTheme: vi.fn(() => ({ dispose: vi.fn() })),
+    onDidChangeActiveTextEditor: vi.fn(() => ({ dispose: vi.fn() })),
+  },
+  workspace: {
+    getConfiguration: vi.fn(() => ({
+      get: vi.fn((_key: string, default_val: string) => default_val),
+    })),
+    onDidChangeConfiguration: vi.fn(() => ({ dispose: vi.fn() })),
+    openTextDocument: vi.fn(),
+    onDidOpenTextDocument: vi.fn(() => ({ dispose: vi.fn() })),
+    onDidCreateFiles: vi.fn(() => ({ dispose: vi.fn() })),
+    onDidRenameFiles: vi.fn(() => ({ dispose: vi.fn() })),
+    createFileSystemWatcher: vi.fn(() => ({
+      onDidChange: vi.fn(),
+      onDidDelete: vi.fn(),
+      dispose: vi.fn(),
+    })),
+    fs: { stat: vi.fn(), readFile: vi.fn(), writeFile: vi.fn() },
+  },
+  commands: { registerCommand: vi.fn(), executeCommand: vi.fn() },
+  Uri: {
+    file: vi.fn((p: string) => ({ fsPath: p })),
+    joinPath: vi.fn((_base: unknown, ...paths: string[]) => ({
+      fsPath: paths.join(`/`),
+    })),
+    parse: vi.fn((url: string) => ({ toString: () => url })),
+  },
+  ViewColumn: { Active: 1, Beside: 2 },
+  ColorThemeKind: { Light: 1, Dark: 2, HighContrast: 3, HighContrastLight: 4 },
+  UIKind: { Desktop: 1, Web: 2 },
+  RelativePattern: class {
+    constructor(
+      public base: unknown,
+      public pattern: string,
+    ) {}
+  },
+  version: `1.99.0`,
+  env: {
+    appName: `VSCode`,
+    remoteName: undefined,
+    uiKind: 1, // Desktop
+    clipboard: {
+      writeText: vi.fn(() => Promise.resolve()),
+      readText: vi.fn(() => Promise.resolve(``)),
+    },
+    openExternal: vi.fn(() => Promise.resolve(true)),
+  },
+}))
+
+vi.mock(`vscode`, () => mock_vscode)
+
+describe(`MatterViz Extension`, () => {
+  let mock_file_system_watcher: {
+    onDidChange: ReturnType<typeof vi.fn>
+    onDidDelete: ReturnType<typeof vi.fn>
+    dispose: ReturnType<typeof vi.fn>
+  }
+  const supported_volumetric_filenames: [string, string][] = [
+    [`CHGCAR`, `VASP volumetric`],
+    [`AECCAR0`, `VASP volumetric`],
+    [`AECCAR1`, `VASP volumetric`],
+    [`AECCAR2`, `VASP volumetric`],
+    [`ELFCAR`, `VASP volumetric`],
+    [`LOCPOT`, `VASP volumetric`],
+    [`PARCHG`, `VASP volumetric`],
+    [`PARCHG.gz`, `VASP volumetric`],
+    [`PARCHG.BAND_1`, `VASP volumetric`],
+    [`run_PARCHG_001`, `VASP volumetric`],
+    [`density.cube`, `Gaussian cube`],
+    [`density.cube.gz`, `Gaussian cube`],
+  ]
+  const volumetric_auto_render_filenames: [string, boolean][] =
+    supported_volumetric_filenames.map(([filename]) => [filename, true] as [string, boolean])
+
+  test(`extensionKind should be configured as ["workspace"] to work locally and in remote SSH sessions`, () => {
+    // https://github.com/janosh/matterviz/issues/129#issuecomment-3193473225
+    expect(pkg_json.extensionKind).toEqual([`workspace`])
+  })
+
+  test(`extension volumetric regex stays in sync with app detection`, () => {
+    expect(VOLUMETRIC_VASP_RE.source).toBe(VASP_VOLUMETRIC_REGEX.source)
+    expect(VOLUMETRIC_VASP_RE.flags).toBe(VASP_VOLUMETRIC_REGEX.flags)
+  })
+
+  describe(`Custom Editor File Patterns`, () => {
+    const custom_editors = pkg_json.contributes.customEditors
+    const matterviz_editor = custom_editors.find(
+      (editor) => editor.viewType === `matterviz.viewer`,
+    )
+    const patterns = matterviz_editor?.selector.map((sel) => sel.filenamePattern) ?? []
+
+    // Tests if a filename matches any pattern (simplified glob matching).
+    const matches_any_pattern = (filename: string): boolean => {
+      for (const pattern of patterns) {
+        // Convert glob pattern to regex
+        const regex_str = pattern
+          .replace(/\./g, `\\.`) // escape dots
+          .replace(/\*/g, `.*`) // * → .*
+          .replace(/\{([^}]+)\}/g, (_, group) => `(${group.split(`,`).join(`|`)})`) // {a,b} → (a|b)
+        const regex = new RegExp(`^${regex_str}$`, `i`)
+        if (regex.test(filename)) return true
+      }
+      return false
+    }
+
+    test(`should have matterviz.viewer custom editor defined`, () => {
+      expect(matterviz_editor).toBeDefined()
+      expect(matterviz_editor?.displayName).toBe(`MatterViz Viewer`)
+    })
+
+    // Tests auto-synced with library constants to prevent regressions
+    test.each<[string, string]>([
+      // All trajectory extensions from library
+      ...TRAJ_EXTENSIONS.map(
+        (ext: string) => [`test${ext}`, `TRAJ_EXT ${ext}`] as [string, string],
+      ),
+      // All structure extensions from library (uncompressed, .gz, .bz2)
+      ...STRUCTURE_EXTENSIONS.flatMap(
+        (ext: string) =>
+          [
+            [`test${ext}`, `STRUCT_EXT ${ext}`],
+            [`test${ext}.gz`, `${ext}.gz`],
+          ] as [string, string][],
+      ),
+      // All trajectory keywords in filenames
+      ...TRAJ_KEYWORDS.map(
+        (kw: string) => [`${kw}_output.dat`, `TRAJ_KW ${kw}`] as [string, string],
+      ),
+      // VASP special filenames + additional VS Code-only formats
+      [`POSCAR`, `VASP`],
+      [`CONTCAR`, `VASP`],
+      [`XDATCAR`, `VASP`],
+      [`OUTCAR`, `VASP`],
+      [`simulation.h5`, `HDF5`],
+      [`data.hdf5`, `HDF5`],
+      [`dynamics.dcd`, `DCD`],
+      [`run.trr`, `TRR`],
+      [`molecule.xyz`, `XYZ`],
+      [`atoms.extxyz`, `extXYZ`],
+      ...supported_volumetric_filenames,
+    ])(`pattern matches "%s" (%s)`, (filename) => {
+      expect(matches_any_pattern(filename)).toBe(true)
+    })
+
+    test.each([
+      [`myCHGCARfile`],
+      [`prefixPARCHGsuffix`],
+      [`notes_ELFCARbackup`],
+      [`report-AECCARnotes`],
+      [`density.cube.bz2`],
+      [`structure.cif.bz2`],
+    ])(`pattern does not match unsupported near miss "%s"`, (filename) => {
+      expect(matches_any_pattern(filename)).toBe(false)
+    })
+  })
+
+  beforeEach(async () => {
+    vi.clearAllMocks()
+
+    // Import extension module and clear all watchers
+    const ext = await import(`../src/extension`)
+    ext.active_watchers.clear()
+    ext.active_frame_loaders.clear()
+    ext.auto_render_timers.clear()
+    ext.active_auto_render_panels.clear()
+
+    mock_fs.readFileSync.mockReturnValue(`mock content`)
+    mock_fs.existsSync.mockReturnValue(true)
+    mock_fs.readdirSync.mockReturnValue([])
+    mock_vscode.window.activeTextEditor = null
+
+    // Reset theme to default Light theme to avoid inter-test coupling
+    mock_vscode.window.activeColorTheme = { kind: 1 } // Light theme by default
+
+    // Set up file system watcher mock
+    mock_file_system_watcher = {
+      onDidChange: vi.fn(),
+      onDidDelete: vi.fn(),
+      dispose: vi.fn(),
+    }
+    mock_vscode.workspace.createFileSystemWatcher.mockReturnValue(mock_file_system_watcher)
+
+    // Set up default mock for vscode.workspace.fs.stat to return file stats
+    mock_vscode.workspace.fs.stat.mockResolvedValue({ size: 1000, type: 1 })
+    mock_vscode.workspace.fs.readFile.mockResolvedValue(
+      new Uint8Array(Buffer.from(`mock content`)),
+    )
+  })
+
+  // Test data consolidation
+  const mock_webview = {
+    cspSource: `vscode-webview:`,
+    asWebviewUri: vi.fn(
+      (uri: { fsPath: string }) =>
+        `vscode-webview://unit-test${encodeURIComponent(uri.fsPath)}`,
+    ),
+    onDidReceiveMessage: vi.fn(),
+    postMessage: vi.fn(),
+    html: ``,
+  }
+  const mock_context = {
+    extensionUri: { fsPath: `/test` },
+    subscriptions: [],
+  } as unknown as ExtensionContext
+
+  test.each([
+    [`test.gz`, true],
+    [`test.h5`, true],
+    [`test.traj`, true], // ASE binary files should be treated as compressed
+    [`test.hdf5`, true],
+    [`md_npt_300K.traj`, true], // Specific ASE ULM binary file
+    [`ase-LiMnO2-chgnet-relax.traj`, true], // Another ASE ULM binary file
+    [`test.cif`, false],
+    [`test.xyz`, false], // .xyz files are text format, not compressed binary
+    [`test.json`, false],
+    [``, false],
+  ])(`file reading: "%s" → compressed:%s`, async (filename, expected_compressed) => {
+    const result = await read_file(`/test/${filename}`)
+    expect(result.filename).toBe(filename)
+    expect(result.is_base64).toBe(expected_compressed)
+    // Assert payload differences instead of redundant API calls
+    if (expected_compressed) {
+      expect(result.content).toBe(Buffer.from(`mock content`).toString(`base64`))
+    } else {
+      expect(result.content).toBe(`mock content`)
+    }
+  })
+
+  test(`file reading: large file should return sentinel`, async () => {
+    const large_file_size = 2 * 1024 * 1024 * 1024 // 2GB, above MAX_VSCODE_FILE_SIZE (1GB)
+    const filename = `large-structure.cif`
+    const file_path = `/test/${filename}`
+
+    // Mock fs.stat to return a size above the threshold
+    mock_vscode.workspace.fs.stat.mockResolvedValue({
+      size: large_file_size,
+      type: 1,
+    })
+
+    const result = await read_file(file_path)
+
+    expect(result.filename).toBe(filename)
+    expect(result.content).toBe(`LARGE_FILE:${file_path}:${large_file_size}`)
+    expect(result.is_base64).toBe(false)
+    // readFile should not be called for large files
+    expect(mock_vscode.workspace.fs.readFile).not.toHaveBeenCalled()
+  })
+
+  test(`file reading: large binary file should return sentinel with base64 flag`, async () => {
+    const large_file_size = 2 * 1024 * 1024 * 1024 // 2GB, above MAX_VSCODE_FILE_SIZE (1GB)
+    const filename = `large-trajectory.traj`
+    const file_path = `/test/${filename}`
+
+    // Mock fs.stat to return a size above the threshold
+    mock_vscode.workspace.fs.stat.mockResolvedValue({
+      size: large_file_size,
+      type: 1,
+    })
+
+    const result = await read_file(file_path)
+
+    expect(result.filename).toBe(filename)
+    expect(result.content).toBe(`LARGE_FILE:${file_path}:${large_file_size}`)
+    expect(result.is_base64).toBe(true) // Binary files should have base64 flag
+    // readFile should not be called for large files
+    expect(mock_vscode.workspace.fs.readFile).not.toHaveBeenCalled()
+  })
+
+  test.each([
+    [`md_npt_300K.traj`, true, true], // ASE binary trajectory
+    [`ase-LiMnO2-chgnet-relax.traj`, true, true], // ASE binary trajectory
+    [`simulation_nvt_250K.traj`, true, true], // ASE binary trajectory
+    [`water_cluster_md.traj`, true, true], // ASE binary trajectory
+    [`optimization_relax.traj`, true, true], // ASE binary trajectory
+    [`regular_text.traj`, true, true], // .traj files are always binary
+    // filename-only based .xyz/.extxyz detection always assumes structure, requires file content to look for frames and recognize as trajectory
+    [`test.xyz`, false, false],
+    [`test.extxyz`, false, false],
+    [`test.cif`, false, false], // Not a trajectory file
+  ])(
+    `ASE trajectory file handling: "%s" → trajectory:%s, binary:%s`,
+    async (filename, is_trajectory, is_binary) => {
+      expect(is_trajectory_file(filename)).toBe(is_trajectory)
+      if (is_trajectory) {
+        const result = await read_file(`/test/${filename}`)
+        expect(result.is_base64).toBe(is_binary)
+      }
+    },
+  )
+
+  // Integration test for ASE trajectory file processing (simulates the exact failing scenario)
+  test(`ASE trajectory file end-to-end processing`, async () => {
+    const ase_filename = `ase-LiMnO2-chgnet-relax.traj`
+
+    // Step 1: Extension should detect this as a trajectory file
+    expect(is_trajectory_file(ase_filename)).toBe(true)
+
+    // Step 2: Extension should read this as binary (compressed)
+    const file_result = await read_file(`/test/${ase_filename}`)
+    expect(file_result.filename).toBe(ase_filename)
+    expect(file_result.is_base64).toBe(true)
+    expect(file_result.content).toBe(Buffer.from(`mock content`).toString(`base64`)) // base64 encoded binary data
+
+    // Step 3: Verify webview data structure matches expected format
+    const webview_data = {
+      type: `trajectory` as const,
+      data: file_result,
+    }
+
+    // Step 4: HTML generation should work with this data
+    const webview_data_with_theme = { ...webview_data, theme: `light` as const }
+    const html = create_html(mock_webview, mock_context, webview_data_with_theme)
+
+    expect(html).toContain(`<!DOCTYPE html>`)
+    expect(html).toContain(JSON.stringify(webview_data_with_theme))
+
+    // Step 5: Verify the exact data structure that would be sent to webview
+    const parsed_data = JSON.parse(/matterviz_data=(\{[\s\S]*?\});/.exec(html)?.[1] ?? `{}`)
+    expect(parsed_data.type).toBe(`trajectory`)
+    expect(parsed_data.data.filename).toBe(ase_filename)
+    expect(parsed_data.data.is_base64).toBe(true)
+    expect(parsed_data.data.content).toBe(Buffer.from(`mock content`).toString(`base64`))
+    expect(parsed_data.theme).toBe(`light`)
+  })
+
+  test.each([
+    [{ fsPath: `/test/file.cif` } as unknown as Uri, `file.cif`],
+    [{ fsPath: `/test/structure.xyz` } as unknown as Uri, `structure.xyz`],
+  ])(`get_file with URI`, async (uri, expected_filename) => {
+    const result = await get_file(uri)
+    expect(result.filename).toBe(expected_filename)
+  })
+
+  test(`get_file with active editor`, async () => {
+    mock_vscode.window.activeTextEditor = {
+      document: { fileName: `/test/active.cif`, getText: () => `active content` },
+    } as TextEditor
+    const result = await get_file()
+    expect(result.filename).toBe(`active.cif`)
+    expect(result.content).toBe(`active content`)
+    expect(result.is_base64).toBe(false)
+  })
+
+  test(`get_file with active tab`, async () => {
+    mock_vscode.window.tabGroups.activeTabGroup.activeTab = {
+      input: { uri: { fsPath: `/test/tab.cif` } },
+    } as unknown as Tab
+    const result = await get_file()
+    expect(result.filename).toBe(`tab.cif`)
+  })
+
+  test(`get_file throws when no file found`, async () => {
+    mock_vscode.window.tabGroups.activeTabGroup.activeTab = null
+    await expect(get_file()).rejects.toThrow(
+      `No file selected. MatterViz needs an active editor to know what to render.`,
+    )
+  })
+
+  test.each([
+    [`structure`, { filename: `test.cif`, content: `content`, is_base64: false }],
+    [`trajectory`, { filename: `test.traj`, content: `YmluYXJ5`, is_base64: true }],
+    [
+      `structure`,
+      {
+        filename: `test"quotes.cif`,
+        content: `content`,
+        is_base64: false,
+      },
+    ],
+    [`structure`, { filename: `test.cif`, content: ``, is_base64: false }],
+    [
+      `structure`,
+      {
+        filename: `test.cif`,
+        content: `<script>alert("xss")</script>`,
+        is_base64: false,
+      },
+    ],
+    [
+      `structure`,
+      {
+        filename: `large.cif`,
+        content: `x`.repeat(100_000),
+        is_base64: false,
+      },
+    ],
+  ] as const)(`HTML generation: %s files`, (type, data) => {
+    const webview_data = { type, data, theme: `light` } as const
+    const html = create_html(mock_webview, mock_context, webview_data)
+    expect(html).toContain(`<!DOCTYPE html>`)
+    expect(html).toContain(`Content-Security-Policy`)
+    expect(html).toContain(`default-src 'none'`)
+    expect(html).toContain(`script-src 'nonce-`)
+    expect(html).toMatch(/nonce="[a-zA-Z0-9]{8,32}"/)
+    expect(html).toContain(JSON.stringify(webview_data).replace(/<\//g, `<\\/`))
+    expect(html).toContain(`matterviz-app`)
+  })
+
+  test.each([
+    [{ command: `info`, text: `Test message` }, `showInformationMessage`],
+    [{ command: `error`, text: `Error message` }, `showErrorMessage`],
+    [{ command: `info`, text: `"><script>alert(1)</script>` }, `showInformationMessage`],
+    [{ command: `error`, text: `javascript:alert(1)` }, `showErrorMessage`],
+  ] as const)(`message handling: %s`, async (message, expected_method) => {
+    await handle_msg(message)
+    expect(
+      mock_vscode.window[expected_method as keyof typeof mock_vscode.window],
+    ).toHaveBeenCalledWith(message.text)
+  })
+
+  test.each([
+    [{ command: `saveAs`, content: `content`, filename: `test.cif` }, true, `Saved: save.cif`],
+    [
+      {
+        command: `saveAs`,
+        content: `<script>alert("XSS")</script>`,
+        filename: `test.cif`,
+      },
+      true,
+      `Saved: save.cif`,
+    ],
+  ] as const)(`saveAs success: %s`, async (message, should_succeed, expected_info) => {
+    mock_vscode.window.showSaveDialog.mockResolvedValue({ fsPath: `/test/save.cif` })
+    await handle_msg(message)
+    if (should_succeed) {
+      const enc = new TextEncoder()
+      expect(mock_vscode.workspace.fs.writeFile).toHaveBeenCalledWith(
+        { fsPath: `/test/save.cif` },
+        enc.encode(message.content),
+      )
+      expect(mock_vscode.window.showInformationMessage).toHaveBeenCalledWith(expected_info)
+    }
+  })
+
+  test.each([
+    [
+      `PNG image`,
+      `data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAADUlEQVR42mNkYPhfDwAChwGA60e6kgAAAABJRU5ErkJggg==`,
+      `structure.png`,
+      true,
+    ],
+    [
+      `JPEG image`,
+      `data:image/jpeg;base64,/9j/4AAQSkZJRgABAQEASABIAAD/2wBDAAEBAQEBAQEBAQEBAQEBAQEBAQEBAQEBAQEBAQEBAQEB/8QAFBABAAAAAAAAAAAAAAAAAAAAAP/EABQRAQAAAAAAAAAAAAAAAAAAAAD/2gAMAwEAAhEDEQA/AP/Z`,
+      `plot.jpg`,
+      true,
+    ],
+    [
+      `PDF document`,
+      `data:application/pdf;base64,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`,
+      `report.pdf`,
+      true,
+    ],
+  ])(`saveAs binary data: %s`, async (_description, data_url, filename, is_binary) => {
+    mock_vscode.window.showSaveDialog.mockResolvedValue({ fsPath: `/test/${filename}` })
+    await handle_msg({
+      command: `saveAs`,
+      content: data_url,
+      ...msg_args,
+      filename,
+      is_binary,
+    })
+    const base64_data = data_url.replace(/^data:[^;]+;base64,/, ``)
+    const expected_buffer = Uint8Array.from(Buffer.from(base64_data, `base64`))
+    expect(mock_vscode.workspace.fs.writeFile).toHaveBeenCalledWith(
+      { fsPath: `/test/${filename}` },
+      expected_buffer,
+    )
+    expect(mock_vscode.window.showInformationMessage).toHaveBeenCalledWith(
+      `Saved: ${filename}`,
+    )
+  })
+
+  test(`saveAs error handling`, async () => {
+    mock_vscode.window.showSaveDialog.mockResolvedValue({
+      fsPath: `/test/save.cif`,
+    })
+    mock_vscode.workspace.fs.writeFile.mockRejectedValue(new Error(`Write failed`))
+
+    await handle_msg({
+      command: `saveAs`,
+      content: `content`,
+      ...msg_args,
+      filename: `test.cif`,
+    })
+    expect(mock_vscode.window.showErrorMessage).toHaveBeenCalledWith(
+      `Failed to save text file: Write failed`,
+    )
+  })
+
+  test(`saveAs user cancellation`, async () => {
+    mock_vscode.window.showSaveDialog.mockResolvedValue(undefined)
+
+    await handle_msg({
+      command: `saveAs`,
+      content: `content`,
+      ...msg_args,
+      filename: `test.cif`,
+    })
+    expect(mock_vscode.workspace.fs.writeFile).not.toHaveBeenCalled()
+  })
+
+  test(`saveAs binary data validation: empty base64 data`, async () => {
+    mock_vscode.window.showSaveDialog.mockResolvedValue({ fsPath: `/test/test.png` })
+
+    await handle_msg({
+      command: `saveAs`,
+      content: `data:image/png;base64,`,
+      ...msg_args,
+      filename: `test.png`,
+      is_binary: true,
+    })
+
+    expect(mock_vscode.window.showErrorMessage).toHaveBeenCalledWith(
+      `Failed to save binary data: Invalid data URL: missing base64 data`,
+    )
+    expect(mock_vscode.workspace.fs.writeFile).not.toHaveBeenCalled()
+  })
+
+  test.each([[{ command: `info` }], [{ command: `saveAs` }], [{ command: `unknown` }]])(
+    `malformed message handling: %s`,
+    async (msg) => {
+      await expect(
+        handle_msg({ ...msg, ...msg_args } as unknown as MessageData),
+      ).resolves.toBeUndefined()
+    },
+  )
+
+  test(`render creates webview panel`, async () => {
+    const mock_panel = {
+      webview: { ...mock_webview },
+      onDidDispose: vi.fn(),
+    }
+    mock_vscode.window.createWebviewPanel.mockReturnValue(mock_panel)
+    mock_vscode.window.activeTextEditor = {
+      document: { fileName: `/test/active.cif`, getText: () => `content` },
+    } as TextEditor
+
+    await render(mock_context)
+    expect(mock_vscode.window.createWebviewPanel).toHaveBeenCalledWith(
+      `matterviz`,
+      `MatterViz - active.cif`,
+      mock_vscode.ViewColumn.Active,
+      expect.any(Object),
+    )
+  })
+
+  test(`render handles errors`, async () => {
+    mock_vscode.window.activeTextEditor = null
+    mock_vscode.window.tabGroups.activeTabGroup.activeTab = null
+    await render(mock_context)
+    expect(mock_vscode.window.showErrorMessage).toHaveBeenCalledWith(
+      `Failed: No file selected. MatterViz needs an active editor to know what to render.`,
+    )
+  })
+
+  test(`extension activation`, () => {
+    activate(mock_context)
+    expect(mock_vscode.commands.registerCommand).toHaveBeenCalledWith(
+      `matterviz.open`,
+      expect.any(Function),
+    )
+    expect(mock_vscode.commands.registerCommand).toHaveBeenCalledWith(
+      `matterviz.report_bug`,
+      expect.any(Function),
+    )
+    expect(mock_vscode.window.registerCustomEditorProvider).toHaveBeenCalledWith(
+      `matterviz.viewer`,
+      expect.any(Object),
+      expect.any(Object),
+    )
+  })
+
+  describe(`Bug Reporting`, () => {
+    let mock_opened_document: { content: string; language: string } | null = null
+    let report_bug_command: (() => Promise<void>) | null = null
+    let mock_env: {
+      appName: string
+      remoteName: string | undefined
+      uiKind: number
+      clipboard: {
+        writeText: ReturnType<typeof vi.fn>
+        readText: ReturnType<typeof vi.fn>
+      }
+      openExternal: ReturnType<typeof vi.fn>
+    }
+
+    beforeEach(async () => {
+      // Reset state
+      mock_opened_document = null
+      report_bug_command = null
+
+      // Mock clipboard API (must be set up before activation)
+      mock_env = {
+        appName: `Cursor`,
+        remoteName: undefined,
+        uiKind: 1, // Desktop
+        clipboard: {
+          writeText: vi.fn(() => Promise.resolve()),
+          readText: vi.fn(() => Promise.resolve(``)),
+        },
+        openExternal: vi.fn(() => Promise.resolve(true)),
+      }
+      mock_vscode.env = mock_env as unknown as typeof mock_vscode.env
+
+      // Capture the report_bug command during activation
+      const command_registry = new Map<string, () => Promise<void>>()
+      mock_vscode.commands.registerCommand = vi.fn(
+        (command_name: string, callback: () => Promise<void>) => {
+          command_registry.set(command_name, callback)
+          return { dispose: vi.fn() }
+        },
+      )
+
+      // Mock workspace.openTextDocument to capture the document content (BEFORE activation)
+      mock_vscode.workspace.openTextDocument = vi.fn(
+        (options: { content: string; language: string }) => {
+          mock_opened_document = {
+            content: options.content,
+            language: options.language,
+          }
+          return Promise.resolve({
+            uri: { fsPath: `/tmp/bug-report.md` },
+            getText: () => options.content,
+          })
+        },
+      )
+
+      // Mock window.showTextDocument (BEFORE activation)
+      mock_vscode.window.showTextDocument = vi.fn(() => Promise.resolve())
+
+      // Mock showInformationMessage to return action choices (BEFORE activation)
+      mock_vscode.window.showInformationMessage = vi.fn(() => Promise.resolve(undefined))
+
+      // Activate extension to register commands
+      activate(mock_context)
+
+      // Get the report_bug command
+      report_bug_command = command_registry.get(`matterviz.report_bug`) ?? null
+    })
+
+    test(`should generate bug report with environment information`, async () => {
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      expect(mock_opened_document).not.toBeNull()
+      expect(mock_opened_document?.language).toBe(`markdown`)
+
+      const content = mock_opened_document?.content ?? ``
+
+      // Check for main sections
+      expect(content).toContain(`### Environment`)
+      expect(content).toContain(`### System Resources`)
+      expect(content).toContain(`### Active Files & Extension State`)
+      expect(content).toContain(`### Console Logs`)
+
+      // Check environment details
+      expect(content).toContain(`- **Editor**: Cursor`)
+      expect(content).toContain(`- **MatterViz Version**: ${pkg_json.version}`)
+      expect(content).toContain(`- **UI Kind**: Desktop`)
+      expect(content).toContain(`- **Remote Session**: No (Local)`)
+
+      // Check system resources
+      expect(content).toContain(`- **Total Memory**:`)
+      expect(content).toContain(`- **Free Memory**:`)
+      expect(content).toContain(`- **Process RSS**:`)
+      expect(content).toContain(`- **Process Heap Used**:`)
+      expect(content).toContain(`- **Process Heap Total**:`)
+
+      // Check console logs instructions
+      expect(content).toContain(`**Please check for console errors/warnings:**`)
+      expect(content).toContain(`Toggle Developer Tools`)
+
+      // Check GitHub link
+      expect(content).toContain(`https://github.com/janosh/matterviz/issues`)
+
+      // Check timestamp
+      expect(content).toMatch(/\*\*Generated\*\*: \d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}/)
+    })
+
+    test(`should detect remote session correctly`, async () => {
+      // Mock remote session
+      mock_env.remoteName = `ssh-remote`
+
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      const content = mock_opened_document?.content ?? ``
+      expect(content).toContain(`- **Remote Session**: Yes (ssh-remote)`)
+    })
+
+    test(`should include active files in report`, async () => {
+      // Start watching some files first
+      const file1_path = `/test/structure.cif`
+      const file2_path = `/test/trajectory.traj`
+
+      await handle_msg(
+        {
+          command: `startWatching`,
+          file_path: file1_path,
+          filename: `structure.cif`,
+          request_id: `req1`,
+          frame_index: 0,
+        } as MessageData,
+        mock_webview,
+      )
+
+      await handle_msg(
+        {
+          command: `startWatching`,
+          file_path: file2_path,
+          filename: `trajectory.traj`,
+          request_id: `req2`,
+          frame_index: 0,
+        } as MessageData,
+        mock_webview,
+      )
+
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      const content = mock_opened_document?.content ?? ``
+
+      // Should list both files with bold filenames (not headers)
+      expect(content).toContain(`**structure.cif**`)
+      expect(content).toContain(`**trajectory.traj**`)
+      expect(content).toContain(`- **Path**: \`${file1_path}\``)
+      expect(content).toContain(`- **Path**: \`${file2_path}\``)
+      expect(content).toContain(`- **Has Watcher**: true`)
+
+      // Check for combined section and extension state counters
+      expect(content).toContain(`### Active Files & Extension State`)
+      expect(content).toContain(`- **Active Watchers**: 2`)
+    })
+
+    test(`should handle files with no active watchers`, async () => {
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      const content = mock_opened_document?.content ?? ``
+      expect(content).toContain(`No files currently being watched/rendered.`)
+    })
+
+    test(`should copy to clipboard when user selects that option`, async () => {
+      mock_vscode.window.showInformationMessage = vi.fn(() =>
+        Promise.resolve(`Copy to Clipboard`),
+      )
+
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      const content = mock_opened_document?.content ?? ``
+
+      // Should have called clipboard.writeText with the content
+      expect(mock_env.clipboard.writeText).toHaveBeenCalledWith(content)
+
+      // Should show success message
+      expect(mock_vscode.window.showInformationMessage).toHaveBeenCalledWith(
+        `Debug information copied to clipboard!`,
+      )
+    })
+
+    test(`should open GitHub issues when user selects that option`, async () => {
+      mock_vscode.window.showInformationMessage = vi.fn(() =>
+        Promise.resolve(`Open GitHub Issues`),
+      )
+
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      // Should have opened GitHub issues URL
+      expect(mock_env.openExternal).toHaveBeenCalledWith(
+        expect.objectContaining({
+          toString: expect.any(Function),
+        }),
+      )
+
+      // Verify the URL contains the GitHub issues path
+      const call_args = mock_env.openExternal.mock.calls[0]
+      expect(call_args[0].toString()).toContain(
+        `https://github.com/janosh/matterviz/issues/new`,
+      )
+    })
+
+    test(`should format file sizes correctly`, async () => {
+      // Mock different file sizes
+      const test_cases = [
+        { size: 500, expected: `500 B` },
+        { size: 1024, expected: `1.00 KiB` },
+        { size: 1024 * 1024, expected: `1.00 MiB` },
+        { size: 1024 * 1024 * 1024, expected: `1.00 GiB` },
+      ]
+
+      // Create a map to track sizes for each file
+      const file_sizes = new Map<string, number>()
+
+      // Set up persistent mock that uses the file_sizes map
+      mock_vscode.workspace.fs.stat.mockImplementation((uri) => {
+        const size = file_sizes.get(uri.fsPath) ?? 1000
+        return Promise.resolve({ size, type: 1 })
+      })
+
+      // Add files to watchers with their sizes
+      const watcher_promises = test_cases.map((test_case) => {
+        const file_path = `/test/file_${test_case.size}.cif`
+        file_sizes.set(file_path, test_case.size)
+
+        return handle_msg(
+          {
+            command: `startWatching`,
+            file_path,
+            filename: `file_${test_case.size}.cif`,
+            request_id: `req_${test_case.size}`,
+            frame_index: 0,
+          } as MessageData,
+          mock_webview,
+        )
+      })
+
+      await Promise.all(watcher_promises)
+
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      const content = mock_opened_document?.content ?? ``
+
+      // Check that sizes are formatted correctly
+      for (const test_case of test_cases) {
+        if (test_case.size >= 1024) {
+          // Only check KB and above (bytes might be rounded)
+          expect(content).toContain(test_case.expected)
+        }
+      }
+    })
+
+    test(`should handle file stat errors gracefully`, async () => {
+      // Mock file that exists but throws error on stat
+      const file_path = `/test/error-file.cif`
+
+      await handle_msg(
+        {
+          command: `startWatching`,
+          file_path,
+          filename: `error-file.cif`,
+          request_id: `req_error`,
+          frame_index: 0,
+        } as MessageData,
+        mock_webview,
+      )
+
+      // Mock stat to throw error for this specific file
+      mock_vscode.workspace.fs.stat.mockRejectedValue(new Error(`File not found`))
+
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      const content = mock_opened_document?.content ?? ``
+
+      // Should still include the file but with "Unknown" size
+      expect(content).toContain(`**error-file.cif**`)
+      expect(content).toContain(`- **Size**: Unknown`)
+    })
+
+    test(`should include extension state counters`, async () => {
+      // Start watching multiple files
+      await handle_msg(
+        {
+          command: `startWatching`,
+          file_path: `/test/file1.cif`,
+          filename: `file1.cif`,
+          request_id: `req1`,
+          frame_index: 0,
+        } as MessageData,
+        mock_webview,
+      )
+
+      await handle_msg(
+        {
+          command: `startWatching`,
+          file_path: `/test/file2.cif`,
+          filename: `file2.cif`,
+          request_id: `req2`,
+          frame_index: 0,
+        } as MessageData,
+        mock_webview,
+      )
+
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      const content = mock_opened_document?.content ?? ``
+
+      // Check combined Active Files & Extension State section
+      expect(content).toContain(`### Active Files & Extension State`)
+      expect(content).toContain(`- **Active Watchers**: 2`)
+      expect(content).toMatch(/- \*\*Active Frame Loaders\*\*: \d+/)
+      expect(content).toMatch(/- \*\*Auto-Render Timers\*\*: \d+/)
+      expect(content).toMatch(/- \*\*Active Auto-Render Panels\*\*: \d+/)
+    })
+
+    test(`should handle errors during report generation`, async () => {
+      // Mock openTextDocument to throw an error
+      mock_vscode.workspace.openTextDocument = vi.fn(() =>
+        Promise.reject(new Error(`Failed to create document`)),
+      )
+
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      // Should show error message
+      expect(mock_vscode.window.showErrorMessage).toHaveBeenCalledWith(
+        expect.stringContaining(`Failed to collect debug information`),
+      )
+    })
+
+    test(`should include console logs instructions in bug report`, async () => {
+      expect(report_bug_command).not.toBeNull()
+      if (!report_bug_command) return
+
+      await report_bug_command()
+
+      const content = mock_opened_document?.content ?? ``
+
+      // Check for console logs section with instructions
+      expect(content).toContain(`### Console Logs`)
+      expect(content).toContain(`**Please check for console errors/warnings:**`)
+      expect(content).toContain(`Toggle Developer Tools`)
+      expect(content).toContain(`Tip: You can filter console messages`)
+    })
+  })
+
+  test(`performance benchmarks`, () => {
+    // Trajectory detection performance
+    const filenames = Array.from({ length: 10000 }, (_, idx) => `test_${idx}.xyz`)
+    const start = performance.now()
+    filenames.forEach((name) => is_trajectory_file(name))
+    expect(performance.now() - start).toBeLessThan(100)
+
+    // HTML generation performance
+    const large_data = {
+      type: `structure`,
+      data: { filename: `large.cif`, content: `x`.repeat(100_000), is_base64: false },
+      theme: `light`,
+    } as const
+    const html_start = performance.now()
+    create_html(mock_webview, mock_context, large_data)
+    expect(performance.now() - html_start).toBeLessThan(50)
+  })
+
+  test(`nonce uniqueness`, () => {
+    const data = {
+      type: `structure`,
+      data: { filename: `test.cif`, content: `content`, is_base64: false },
+      theme: `light`,
+    } as const
+    const nonces = new Set<string>()
+
+    for (let idx = 0; idx < 1000; idx++) {
+      const html = create_html(mock_webview, mock_context, data)
+      const nonce_match = /nonce="([a-zA-Z0-9]+)"/.exec(html)
+      if (nonce_match) nonces.add(nonce_match[1])
+    }
+
+    expect(nonces.size).toBe(1000)
+  })
+
+  test(`XSS prevention`, () => {
+    const dangerous_payloads = [
+      `<script>alert("XSS")</script>`,
+      `<img src="x" onerror="alert(1)">`,
+      `javascript:alert(1)`,
+      `"><script>alert(1)</script>`,
+      `';alert(1);//`,
+      `</script><script>alert(document.cookie)</script>`,
+    ]
+
+    dangerous_payloads.forEach((payload) => {
+      const data = {
+        type: `structure`,
+        data: { filename: `test.cif`, content: payload, is_base64: false },
+        theme: `light`,
+      } as const
+      const html = create_html(mock_webview, mock_context, data)
+      const escaped_json = JSON.stringify(data).replace(/<\//g, `<\\/`)
+
+      expect(html).toContain(escaped_json)
+      // Ensure no raw </script> inside the JSON data breaks out of the script tag
+      const data_script = /window\.matterviz_data=(.*?);/s.exec(html)
+      if (data_script) {
+        expect(data_script[1]).not.toContain(`</script>`)
+      }
+    })
+  })
+
+  test(`concurrent operations`, async () => {
+    const promises = Array.from({ length: 50 }, (_, idx) =>
+      handle_msg({ command: `info`, text: `Message ${idx}`, ...msg_args }),
+    )
+    await Promise.all(promises)
+    expect(mock_vscode.window.showInformationMessage).toHaveBeenCalledTimes(50)
+  })
+
+  describe(`Theme functionality`, () => {
+    test.each([
+      [mock_vscode.ColorThemeKind.Light, `auto`, `light`], // Light VSCode theme, auto setting → light
+      [mock_vscode.ColorThemeKind.Dark, `auto`, `dark`], // Dark VSCode theme, auto setting → dark
+      [mock_vscode.ColorThemeKind.HighContrast, `auto`, `black`], // High contrast VSCode theme, auto setting → black
+      [mock_vscode.ColorThemeKind.HighContrastLight, `auto`, `white`], // High contrast light VSCode theme, auto setting → white
+      [mock_vscode.ColorThemeKind.Light, `light`, `light`], // Light VSCode theme, light setting → light
+      [mock_vscode.ColorThemeKind.Light, `dark`, `dark`], // Light VSCode theme, dark setting → dark
+      [mock_vscode.ColorThemeKind.Light, `white`, `white`], // Light VSCode theme, white setting → white
+      [mock_vscode.ColorThemeKind.Light, `black`, `black`], // Light VSCode theme, black setting → black
+      [mock_vscode.ColorThemeKind.Dark, `light`, `light`], // Dark VSCode theme, light setting → light
+      [mock_vscode.ColorThemeKind.Dark, `dark`, `dark`], // Dark VSCode theme, dark setting → dark
+      [mock_vscode.ColorThemeKind.Dark, `white`, `white`], // Dark VSCode theme, white setting → white
+      [mock_vscode.ColorThemeKind.Dark, `black`, `black`], // Dark VSCode theme, black setting → black
+    ] as const)(
+      `theme detection: VSCode theme %i, setting '%s' → '%s'`,
+      (vscode_theme_kind: number, setting: string, expected: ThemeName) => {
+        const mock_config = {
+          get: vi.fn((key: string, default_value?: string) =>
+            key === `theme` ? setting : default_value,
+          ),
+        }
+        mock_vscode.workspace.getConfiguration = vi.fn(() => mock_config) as ReturnType<
+          typeof vi.fn
+        >
+        mock_vscode.window.activeColorTheme = { kind: vscode_theme_kind }
+
+        const result = get_theme()
+        expect(result).toBe(expected)
+      },
+    )
+
+    test(`webview data includes theme`, () => {
+      const mock_config = {
+        get: vi.fn((key: string, default_value?: string) =>
+          key === `theme` ? `dark` : default_value,
+        ),
+      }
+      mock_vscode.workspace.getConfiguration = vi.fn(() => mock_config) as ReturnType<
+        typeof vi.fn
+      >
+
+      const data = {
+        type: `structure` as const,
+        data: { filename: `test.cif`, content: `content`, is_base64: false },
+        theme: get_theme(),
+      }
+
+      const html = create_html(mock_webview, mock_context, data)
+
+      const parsed_data = JSON.parse(/matterviz_data=(\{[\s\S]*?\});/.exec(html)?.[1] || `{}`)
+      expect(parsed_data.theme).toBe(`dark`)
+    })
+
+    test(`invalid theme setting falls back to auto`, () => {
+      const mock_config = {
+        get: vi.fn((key: string, default_value?: string) =>
+          key === `theme` ? `invalid-theme` : default_value,
+        ),
+      }
+      mock_vscode.workspace.getConfiguration = vi.fn(() => mock_config) as ReturnType<
+        typeof vi.fn
+      >
+      mock_vscode.window.activeColorTheme = {
+        kind: mock_vscode.ColorThemeKind.Light,
+      }
+
+      const result = get_theme()
+      expect(result).toBe(`light`) // Should fall back to system theme
+    })
+
+    test(`high contrast themes are mapped correctly`, () => {
+      const mock_config = {
+        get: vi.fn((key: string, default_value?: string) =>
+          key === `theme` ? `auto` : default_value,
+        ),
+      }
+      mock_vscode.workspace.getConfiguration = vi.fn(() => mock_config) as ReturnType<
+        typeof vi.fn
+      >
+
+      // Test high contrast dark → black
+      mock_vscode.window.activeColorTheme = {
+        kind: mock_vscode.ColorThemeKind.HighContrast,
+      }
+      expect(get_theme()).toBe(`black`)
+
+      // Test high contrast light → white
+      mock_vscode.window.activeColorTheme = {
+        kind: mock_vscode.ColorThemeKind.HighContrastLight,
+      }
+      expect(get_theme()).toBe(`white`)
+    })
+  })
+
+  describe(`Theme listener cleanup`, () => {
+    const setup_panel = (options = {}) => {
+      const mock_dispose = vi.fn()
+      const mock_panel = {
+        webview: { ...mock_webview },
+        onDidDispose: vi.fn(),
+        visible: true,
+        ...options,
+      }
+
+      mock_vscode.window.createWebviewPanel.mockReturnValue(mock_panel)
+      mock_vscode.window.onDidChangeActiveColorTheme.mockReturnValue({
+        dispose: mock_dispose,
+      })
+      mock_vscode.workspace.onDidChangeConfiguration.mockReturnValue({
+        dispose: mock_dispose,
+      })
+      mock_vscode.window.activeTextEditor = {
+        document: { fileName: `/test/active.cif`, getText: () => `content` },
+      } as TextEditor
+
+      return { mock_dispose, mock_panel }
+    }
+
+    test(`sets up and cleans up theme listeners`, async () => {
+      const { mock_dispose, mock_panel } = setup_panel()
+
+      await render(mock_context)
+
+      expect(mock_vscode.window.onDidChangeActiveColorTheme).toHaveBeenCalled()
+      expect(mock_panel.onDidDispose).toHaveBeenCalled()
+
+      // Test cleanup
+      mock_panel.onDidDispose.mock.calls[0][0]()
+      expect(mock_dispose).toHaveBeenCalledTimes(2)
+    })
+
+    test(`respects panel visibility for theme updates`, async () => {
+      const mock_panel = {
+        webview: { ...mock_webview },
+        onDidDispose: vi.fn(),
+        visible: false,
+      }
+
+      mock_vscode.window.createWebviewPanel.mockReturnValue(mock_panel)
+      mock_vscode.window.onDidChangeActiveColorTheme.mockReturnValue({
+        dispose: vi.fn(),
+      })
+      mock_vscode.workspace.onDidChangeConfiguration.mockReturnValue({
+        dispose: vi.fn(),
+      })
+      mock_vscode.window.activeTextEditor = {
+        document: { fileName: `/test/active.cif`, getText: () => `content` },
+      } as TextEditor
+
+      await render(mock_context)
+
+      // Store initial HTML after render (render always sets HTML initially)
+      const initial_html = mock_panel.webview.html
+
+      const theme_calls = mock_vscode.window.onDidChangeActiveColorTheme.mock
+        .calls as unknown as unknown[][]
+      const theme_callback = theme_calls[0]?.[0] as (() => Promise<void>) | undefined
+      expect(theme_callback).toBeDefined()
+
+      // Should not update when invisible
+      await theme_callback?.()
+      expect(mock_panel.webview.html).toBe(initial_html)
+
+      // Should update when visible
+      mock_panel.visible = true
+      await theme_callback?.()
+      expect(mock_panel.webview.html).not.toBe(initial_html)
+    })
+
+    test(`multiple panels dispose independently`, async () => {
+      const dispose1 = vi.fn()
+      const dispose2 = vi.fn()
+      const panel1 = { webview: { ...mock_webview }, onDidDispose: vi.fn() }
+      const panel2 = { webview: { ...mock_webview }, onDidDispose: vi.fn() }
+
+      mock_vscode.window.createWebviewPanel
+        .mockReturnValueOnce(panel1)
+        .mockReturnValueOnce(panel2)
+      mock_vscode.window.onDidChangeActiveColorTheme
+        .mockReturnValueOnce({ dispose: dispose1 })
+        .mockReturnValueOnce({
+          dispose: dispose2,
+        })
+      mock_vscode.workspace.onDidChangeConfiguration
+        .mockReturnValueOnce({ dispose: dispose1 })
+        .mockReturnValueOnce({
+          dispose: dispose2,
+        })
+
+      mock_vscode.window.activeTextEditor = {
+        document: { fileName: `/test/active.cif`, getText: () => `content` },
+      } as TextEditor
+
+      await render(mock_context)
+      await render(mock_context)
+
+      panel1.onDidDispose.mock.calls[0][0]()
+      expect(dispose1).toHaveBeenCalledTimes(2)
+      expect(dispose2).not.toHaveBeenCalled()
+    })
+  })
+
+  describe(`File Watching`, () => {
+    describe(`message handling`, () => {
+      test(`should handle startWatching message`, async () => {
+        const message = {
+          command: `startWatching` as const,
+          ...msg_args,
+          file_path: `/test/file.cif`,
+        }
+        await handle_msg(message, mock_webview)
+
+        expect(mock_vscode.workspace.createFileSystemWatcher).toHaveBeenCalledWith(
+          expect.objectContaining({
+            base: expect.anything(),
+            pattern: `file.cif`,
+          }),
+        )
+        expect(mock_file_system_watcher.onDidChange).toHaveBeenCalledWith(expect.any(Function))
+        expect(mock_file_system_watcher.onDidDelete).toHaveBeenCalledWith(expect.any(Function))
+      })
+
+      test(`should handle stopWatching message`, async () => {
+        // First start watching
+        const start_message = {
+          command: `startWatching` as const,
+          ...msg_args,
+          file_path: `/test/file.cif`,
+        }
+        await handle_msg(start_message, mock_webview)
+
+        // Then test stopping
+        const stop_message = {
+          command: `stopWatching` as const,
+          ...msg_args,
+          file_path: `/test/file.cif`,
+        }
+        await handle_msg(stop_message, mock_webview)
+
+        expect(mock_file_system_watcher.dispose).toHaveBeenCalled()
+      })
+
+      test(`should handle startWatching without webview gracefully`, async () => {
+        const message = {
+          command: `startWatching` as const,
+          ...msg_args,
+          file_path: `/test/file.cif`,
+        }
+
+        await expect(handle_msg(message)).resolves.not.toThrow()
+        expect(mock_vscode.workspace.createFileSystemWatcher).not.toHaveBeenCalled()
+      })
+
+      test(`should handle startWatching without file_path gracefully`, async () => {
+        const message = {
+          command: `startWatching` as const,
+          ...msg_args,
+        }
+
+        await expect(handle_msg(message, mock_webview)).resolves.not.toThrow()
+        expect(mock_vscode.workspace.createFileSystemWatcher).not.toHaveBeenCalled()
+      })
+
+      test(`should send error message when file watching fails`, async () => {
+        mock_vscode.workspace.createFileSystemWatcher.mockImplementation(() => {
+          throw new Error(`File system watcher creation failed`)
+        })
+
+        const message = {
+          command: `startWatching` as const,
+          ...msg_args,
+          file_path: `/test/large-file.cif`,
+        }
+
+        await handle_msg(message, mock_webview)
+
+        expect(mock_webview.postMessage).toHaveBeenCalledWith({
+          command: `error`,
+          text: expect.stringContaining(`Failed to start watching file`),
+        })
+      })
+    })
+
+    describe(`file change notifications`, () => {
+      test(`should send file change notification to webview`, async () => {
+        const message = {
+          command: `startWatching` as const,
+          ...msg_args,
+          file_path: `/test/file.cif`,
+        }
+
+        await handle_msg(message, mock_webview)
+
+        // Get the change handler
+        const change_handler = mock_file_system_watcher.onDidChange.mock.calls[0][0]
+
+        // Trigger file change
+        await change_handler()
+
+        // Wait for postMessage to be called (it's async)
+        await vi.waitFor(() => {
+          expect(mock_webview.postMessage).toHaveBeenCalledWith({
+            command: `fileUpdated`,
+            data: expect.objectContaining({
+              filename: `file.cif`,
+              content: `mock content`,
+              is_base64: false,
+            }),
+            type: `structure`,
+            ...msg_args,
+            file_path: `/test/file.cif`,
+            theme: `light`,
+          })
+        })
+      })
+
+      test(`should handle file deletion notifications`, async () => {
+        const message = {
+          command: `startWatching` as const,
+          ...msg_args,
+          file_path: `/test/file.cif`,
+        }
+
+        await handle_msg(message, mock_webview)
+
+        // Get the delete handler
+        const delete_handler = mock_file_system_watcher.onDidDelete.mock.calls[0][0]
+
+        // Trigger file deletion
+        delete_handler()
+
+        expect(mock_webview.postMessage).toHaveBeenCalledWith(
+          expect.objectContaining({
+            command: `fileDeleted`,
+            file_path: `/test/file.cif`,
+          }),
+        )
+      })
+    })
+
+    describe(`lifecycle management`, () => {
+      test(`should handle activation gracefully`, () => {
+        const mock_context = {
+          extensionUri: { fsPath: `/test/extension` },
+          subscriptions: [],
+        } as unknown as ExtensionContext
+
+        expect(() => activate(mock_context)).not.toThrow()
+
+        expect(mock_vscode.commands.registerCommand).toHaveBeenCalledWith(
+          `matterviz.open`,
+          expect.any(Function),
+        )
+      })
+    })
+  })
+
+  describe(`Auto-Render Functionality`, () => {
+    test.each([
+      // Supported structure files
+      [`structure.cif`, true],
+      [`molecule.xyz`, true],
+      [`crystal.poscar`, true],
+      [`data.json`, false], // "data" is too broad, will not auto-render without structure-specific keywords in filename
+      [`structure.xml`, true],
+      [`molecule.pdb`, true],
+      [`compound.mol`, true],
+      [`structure.mol2`, true],
+      [`data.sdf`, true],
+      [`crystal.mmcif`, true],
+      // Supported trajectory files
+      [`trajectory.traj`, true],
+      [`simulation.h5`, true],
+      [`data.hdf5`, false],
+      [`traj.xtc`, true],
+      // Compressed supported files
+      [`trajectory.xyz.gz`, true],
+      [`data.json.gz`, false], // "data" is too broad, will not auto-render without structure-specific keywords in filename
+      [`structure.cif.gz`, true],
+      // Special filenames
+      [`POSCAR`, true],
+      [`CONTCAR`, true],
+      [`XDATCAR`, true],
+      [`trajectory.dat`, true],
+      [`md.xyz`, true],
+      [`relax.out`, true],
+      [`npt.log`, true],
+      [`nvt.data`, true],
+      [`nve.traj`, true],
+      // Files with special characters
+      [`structure (1).cif`, true],
+      [`trajectory[test].xyz.gz`, true],
+      [`crystal@test.poscar`, true],
+      [`molecule#test.xyz`, true],
+      [`structure$test.json`, true],
+      [`trajectory%test.h5`, true],
+      [`crystal^test.traj`, true],
+      [`molecule&test.extxyz`, true],
+      [`structure*test.xml`, true],
+      [`trajectory+test.pdb`, true],
+      [`crystal=test.mol`, true],
+      [`molecule|test.mol2`, true],
+      [`structure\`test.sdf`, true],
+      [`trajectory~test.mmcif`, true],
+      // Case sensitivity tests
+      [`STRUCTURE.CIF`, true],
+      [`structure.CIF`, true],
+      [`Structure.cif`, true],
+      [`TRAJECTORY.XYZ`, true],
+      [`trajectory.XYZ`, true],
+      [`Trajectory.xyz`, true],
+      [`POSCAR`, true],
+      [`poscar`, true],
+      [`Poscar`, true],
+      [`CONTCAR`, true],
+      [`contcar`, true],
+      [`Contcar`, true],
+      [`XDATCAR`, true],
+      [`xdatcar`, true],
+      [`Xdatcar`, true],
+      // Fermi surface files
+      [`band.bxsf`, true],
+      [`fermi.frmsf`, true],
+      [`BAND.BXSF`, true],
+      [`fermi.FRMSF`, true],
+      [`band.bxsf.gz`, true],
+      [`fermi.frmsf.gz`, true],
+      // Volumetric data files
+      ...volumetric_auto_render_filenames,
+      [`DENSITY.CUBE`, true],
+      [`CHGCAR.lobster`, true],
+      // Files that look like structure files but are supported
+      [`structure_copy.cif`, true],
+      [`trajectory_backup.xyz`, true],
+      [`trajectory.log`, true], // Contains "trajectory" keyword
+      // Very long filenames
+      [`structure`.repeat(100) + `.cif`, true],
+      // Unsupported files
+      [`config.yaml`, false],
+      [`simulation.trr`, false], // .trr files not supported
+      [`md.dcd`, false], // .dcd files not supported
+      [`document.txt`, false],
+      [`script.py`, false],
+      [`data.csv`, false],
+      [`image.png`, false],
+      [`archive.zip`, false],
+      [`fake.gz`, false],
+      [`config.ini`, false],
+      [`log.txt`, false],
+      [`README.md`, false],
+      [`readme.md`, false],
+      [`ReadMe.Md`, false],
+      [`vite.config.ts`, false],
+      [`test.spec.ts`, false],
+      [`index.html`, false],
+      [`style.css`, false],
+      [`app.js`, false],
+      [`data.sql`, false],
+      [`backup.tar`, false],
+      [`compressed.7z`, false],
+      [`binary.bin`, false],
+      [`.pre-commit-config.yaml`, false],
+      [`changelog.md`, false],
+      [`.prettierrc`, false],
+      [`.gitignore`, false],
+      [`dockerfile`, false],
+      [`makefile`, false],
+      [`.env`, false],
+      [`.env.local`, false],
+      [`.env.production`, false],
+      [`.github/workflows/ci.yml`, false],
+      [`dist/bundle.js`, false],
+      [`build/index.html`, false],
+      [`coverage/lcov.info`, false],
+      [`.cache/build.js`, false],
+      [`structure.json.bak`, false],
+      [`crystal.poscar.lock`, true],
+      [`simulation.log`, true],
+      [`backup.old`, false],
+      [`original.orig`, false],
+      [`patch.diff`, false],
+      [`structure.txt`, false],
+      [`crystal.md`, false],
+      [`molecule.doc`, false],
+      [`poscar.bak`, true],
+      [`contcar.old`, true],
+      [`document.txt.gz`, false],
+      [`script.py.gz`, false],
+      [`data.csv.gz`, false],
+      [`image.png.gz`, false],
+      [`archive.zip.gz`, false],
+      [`structure.cif.bz2`, false],
+      [`density.cube.bz2`, false],
+      [`PARCHG.bz2`, false],
+      [`myCHGCARfile`, false],
+      [`prefixPARCHGsuffix`, false],
+      [`structure.cif.bak`, false],
+      [`crystal.poscar.old`, true],
+      [`molecule.xyz~`, false],
+      [`structure.cif.swp`, false],
+      [`DOCUMENT.TXT`, false],
+      [`document.TXT`, false],
+      [`Document.txt`, false],
+      [`SCRIPT.PY`, false],
+      [`script.PY`, false],
+      [`Script.py`, false],
+      [`DATA.CSV`, false],
+      [`data.CSV`, false],
+      [`Data.csv`, false],
+      // Configuration files that should never auto-render
+      [`package.json`, false],
+      [`tsconfig.json`, false],
+      [`vite.config.ts`, false],
+      [`webpack.config.js`, false],
+      [`rollup.config.js`, false],
+      [`eslint.config.js`, false],
+      [`prettier.config.js`, false],
+      [`babel.config.js`, false],
+      [`jest.config.js`, false],
+      [`karma.conf.js`, false],
+      [`cypress.json`, false],
+      [`playwright.config.ts`, false],
+      [`.eslintrc.json`, false],
+      [`.prettierrc`, false],
+      [`.babelrc`, false],
+      [`.jest.config.js`, false],
+      [`.karma.conf.js`, false],
+      [`.cypress.json`, false],
+      [`.playwright.config.ts`, false],
+      [`.npmrc`, false],
+      [`.yarnrc`, false],
+      [`.vscode/settings.json`, false],
+      [`.idea/workspace.xml`, false],
+      [`.nyc_output/coverage.json`, false],
+      [`.tmp/temp.json`, false],
+      [`.temp/structure.json`, false],
+      [`node_modules/package.json`, false],
+      // Edge cases
+      [``, false],
+      [`   `, false],
+      [`.`, false],
+      [`..`, false],
+      [`/`, false],
+      [`\\`, false],
+      [`a`.repeat(1000) + `.txt`, false],
+      // Null/undefined inputs
+      [null as unknown as string, false],
+      [undefined as unknown as string, false],
+    ])(`should detect auto-render for "%s" as %s`, (filename, expected) => {
+      expect(should_auto_render(filename)).toBe(expected)
+    })
+
+    test(`should register auto-render functionality`, () => {
+      const mock_context = {
+        subscriptions: { push: vi.fn() },
+      } as unknown as ExtensionContext
+      activate(mock_context)
+      expect(mock_vscode.workspace.onDidOpenTextDocument).toHaveBeenCalledWith(
+        expect.any(Function),
+      )
+    })
+
+    test(`should handle rapid file detection efficiently`, () => {
+      const filenames = Array.from({ length: 100 }, (_, idx) => `test_${idx}.cif`)
+      const start = performance.now()
+      filenames.forEach(should_auto_render)
+      expect(performance.now() - start).toBeLessThan(10)
+    })
+
+    test(`should not trigger on non-file URIs`, () => {
+      const mock_context = {
+        subscriptions: { push: vi.fn() },
+      } as unknown as ExtensionContext
+
+      activate(mock_context)
+
+      // Get the registered callback
+      const open_doc_calls = mock_vscode.workspace.onDidOpenTextDocument.mock
+        .calls as unknown as unknown[][]
+      const on_did_open_text_document_callback = open_doc_calls[0]?.[0] as
+        | ((doc: unknown) => void)
+        | undefined
+      expect(on_did_open_text_document_callback).toBeDefined()
+
+      // Mock document with non-file URI
+      const mock_document = {
+        uri: { scheme: `untitled` },
+      }
+
+      expect(() => on_did_open_text_document_callback?.(mock_document)).not.toThrow()
+    })
+
+    test(`should respect auto_render configuration setting`, () => {
+      const mock_context = {
+        subscriptions: { push: vi.fn() },
+      } as unknown as ExtensionContext
+
+      // Mock configuration to disable auto_render
+      mock_vscode.workspace.getConfiguration.mockReturnValue({
+        get: vi.fn((key: string, default_val: string) => {
+          if (key === `auto_render`) return false
+          return default_val
+        }),
+      })
+
+      activate(mock_context)
+
+      const open_doc_calls = mock_vscode.workspace.onDidOpenTextDocument.mock
+        .calls as unknown as unknown[][]
+      const on_did_open_text_document_callback = open_doc_calls[0]?.[0] as
+        | ((doc: unknown) => void)
+        | undefined
+      expect(on_did_open_text_document_callback).toBeDefined()
+
+      // Mock document with supported file
+      const mock_document = {
+        uri: { scheme: `file`, fsPath: `/test/structure.cif` },
+      }
+
+      expect(() => on_did_open_text_document_callback?.(mock_document)).not.toThrow()
+    })
+
+    test(`should handle file reading errors gracefully during auto-render`, async () => {
+      const mock_context = {
+        subscriptions: { push: vi.fn() },
+      } as unknown as ExtensionContext
+
+      // Mock vscode.workspace.fs.stat to throw an error
+      mock_vscode.workspace.fs.stat.mockRejectedValue(new Error(`File not found`))
+
+      // Enable auto_render in config
+      mock_vscode.workspace.getConfiguration.mockReturnValue({
+        get: vi.fn((_key: string, default_val: string) =>
+          _key === `auto_render` ? `true` : default_val,
+        ),
+      })
+
+      activate(mock_context)
+
+      const open_doc_calls = mock_vscode.workspace.onDidOpenTextDocument.mock
+        .calls as unknown as unknown[][]
+      const on_did_open_text_document_callback = open_doc_calls[0]?.[0] as
+        | ((doc: unknown) => void)
+        | undefined
+      expect(on_did_open_text_document_callback).toBeDefined()
+
+      // Mock document with supported file
+      const mock_document = {
+        uri: { scheme: `file`, fsPath: `/test/structure.cif` },
+      }
+
+      // Should show error message when file reading fails
+      expect(() => on_did_open_text_document_callback?.(mock_document)).not.toThrow()
+
+      await vi.waitFor(() => {
+        expect(mock_vscode.window.showErrorMessage).toHaveBeenCalledWith(
+          expect.stringContaining(`MatterViz auto-render failed:`),
+        )
+      })
+    })
+  })
+
+  describe(`Multi-frame xyz/extxyz handling`, () => {
+    test(`should correctly identify multi-frame XYZ as trajectory using content`, () => {
+      // Multi-frame XYZ content (2 frames)
+      const multi_frame_xyz_content = `3
+frame 1
+H 0.0 0.0 0.0
+O 0.0 0.0 1.0
+H 0.0 1.0 0.0
+3
+frame 2
+H 0.1 0.0 0.0
+O 0.0 0.1 1.0
+H 0.0 1.0 0.1`
+
+      // Single-frame XYZ content
+      const single_frame_xyz_content = `3
+water molecule
+H 0.0 0.0 0.0
+O 0.0 0.0 1.0
+H 0.0 1.0 0.0`
+
+      // Test 1: Verify is_trajectory_file directly detects multi-frame content
+      expect(is_trajectory_file(`multi-frame.xyz`, multi_frame_xyz_content)).toBe(true)
+      expect(is_trajectory_file(`single-frame.xyz`, single_frame_xyz_content)).toBe(false)
+
+      // Test 2: Verify filename-only detection doesn't identify .xyz as trajectory
+      expect(is_trajectory_file(`multi-frame.xyz`)).toBe(false) // filename-only should be false
+      expect(is_trajectory_file(`single-frame.xyz`)).toBe(false) // filename-only should be false
+
+      // Test 3: Test with FileData objects (simulating what infer_view_type receives)
+      const multi_frame_file: FileData = {
+        filename: `multi-frame.xyz`,
+        content: multi_frame_xyz_content,
+        is_base64: false,
+      }
+
+      const single_frame_file: FileData = {
+        filename: `single-frame.xyz`,
+        content: single_frame_xyz_content,
+        is_base64: false,
+      }
+
+      const compressed_file: FileData = {
+        filename: `trajectory.xyz.gz`,
+        content: `base64encodedcontent`,
+        is_base64: true,
+      }
+
+      // Test what infer_view_type logic would do:
+      // For non-compressed files, pass content
+      expect(is_trajectory_file(multi_frame_file.filename, multi_frame_file.content)).toBe(
+        true,
+      )
+      expect(is_trajectory_file(single_frame_file.filename, single_frame_file.content)).toBe(
+        false,
+      )
+
+      // For compressed files, don't pass content (falls back to filename-only)
+      expect(is_trajectory_file(compressed_file.filename)).toBe(true) // .xyz.gz with trajectory keyword is detected as trajectory by filename
+
+      // Test 4: Test webview creation scenario directly with content-based detection
+      const multi_frame_html = create_html(mock_webview, mock_context, {
+        type: is_trajectory_file(multi_frame_file.filename, multi_frame_file.content)
+          ? `trajectory`
+          : `structure`,
+        data: multi_frame_file,
+        theme: `light`,
+      })
+
+      const multi_frame_parsed_data = JSON.parse(
+        /matterviz_data=(\{[\s\S]*?\});/.exec(multi_frame_html)?.[1] ?? `{}`,
+      )
+
+      expect(multi_frame_parsed_data.type).toBe(`trajectory`)
+      expect(multi_frame_parsed_data.data.filename).toBe(`multi-frame.xyz`)
+      expect(multi_frame_parsed_data.data.content).toBe(multi_frame_xyz_content)
+
+      // Test 5: Test single-frame for comparison
+      const single_frame_html = create_html(mock_webview, mock_context, {
+        type: is_trajectory_file(single_frame_file.filename, single_frame_file.content)
+          ? `trajectory`
+          : `structure`,
+        data: single_frame_file,
+        theme: `light`,
+      })
+
+      const single_frame_parsed_data = JSON.parse(
+        /matterviz_data=(\{[\s\S]*?\});/.exec(single_frame_html)?.[1] ?? `{}`,
+      )
+
+      expect(single_frame_parsed_data.type).toBe(`structure`)
+
+      // Test 6: Test compressed file falls back correctly
+      const compressed_html = create_html(mock_webview, mock_context, {
+        type: is_trajectory_file(compressed_file.filename) ? `trajectory` : `structure`,
+        data: compressed_file,
+        theme: `light`,
+      })
+
+      const compressed_parsed_data = JSON.parse(
+        /matterviz_data=(\{[\s\S]*?\});/.exec(compressed_html)?.[1] ?? `{}`,
+      )
+
+      expect(compressed_parsed_data.type).toBe(`trajectory`) // Should be trajectory since filename contains trajectory keyword
+    })
+
+    test(`should handle compressed XYZ files by falling back to filename-only detection`, () => {
+      // Test compressed file (should fall back to filename-only detection)
+      const compressed_file = {
+        filename: `trajectory.xyz.gz`,
+        content: `base64encodedcontent`, // This is binary/compressed
+        is_base64: true,
+      }
+
+      // For compressed files, infer_view_type should fall back to filename-only detection
+      // Since .xyz.gz with trajectory keyword is detected as trajectory by filename, it should be 'trajectory'
+      expect(is_trajectory_file(compressed_file.filename)).toBe(true) // filename-only detection
+
+      // Test the HTML generation scenario
+      const html = create_html(mock_webview, mock_context, {
+        type: is_trajectory_file(compressed_file.filename) ? `trajectory` : `structure`,
+        data: compressed_file,
+        theme: `light`,
+      })
+
+      const parsed_data = JSON.parse(/matterviz_data=(\{[\s\S]*?\});/.exec(html)?.[1] ?? `{}`)
+
+      // Should be 'trajectory' since filename contains trajectory keyword
+      expect(parsed_data.type).toBe(`trajectory`)
+    })
+  })
+
+  describe(`Default Settings`, () => {
+    // Helper to create mock config and test setting
+    const test_setting = (
+      result_path: string,
+      expected_value: unknown,
+      config_key: string,
+    ) => {
+      const parts = config_key.split(`.`)
+
+      const mock_config = {
+        get: vi.fn((key: string, default_val?: unknown): unknown => {
+          if (parts.length === 2 && key === parts[0]) {
+            return { [parts[1]]: expected_value }
+          } else if (parts.length === 1 && key === parts[0]) return expected_value
+          return default_val
+        }),
+      }
+      // @ts-expect-error: Mock type override needed for testing
+      mock_vscode.workspace.getConfiguration.mockReturnValue(mock_config)
+
+      const result = get_defaults()
+      const value = result_path
+        .split(`.`)
+        .reduce(
+          (obj: Record<string, unknown>, key: string) => obj?.[key] as Record<string, unknown>,
+          result,
+        )
+
+      return Array.isArray(expected_value)
+        ? expect(value).toEqual(expected_value)
+        : expect(value).toBe(expected_value)
+    }
+
+    test(`should merge user settings with defaults`, () => {
+      const user_config = {
+        structure: { atom_radius: 1.5, show_bonds: `always`, bond_color: `#ff0000` },
+        trajectory: { auto_play: true },
+      }
+      const mock_config = {
+        get: vi.fn((key: string, default_val?: unknown) => {
+          if (key === `structure`) return user_config.structure
+          if (key === `trajectory`) return user_config.trajectory
+          return default_val
+        }),
+      }
+      // @ts-expect-error: Mock type override needed for testing
+      mock_vscode.workspace.getConfiguration.mockReturnValue(mock_config)
+
+      const result = get_defaults()
+
+      expect(result.structure.atom_radius).toBe(1.5)
+      expect(result.structure.show_bonds).toBe(`always`)
+      expect(result.structure.bond_color).toBe(`#ff0000`)
+      expect(result.trajectory.auto_play).toBe(true)
+      expect(result.structure.same_size_atoms).toBe(false) // Falls back to default
+    })
+
+    test.each([
+      // Numbers
+      [`structure.atom_radius`, 1.5],
+      [`structure.sphere_segments`, 24],
+      [`structure.bond_thickness`, 0.2],
+      [`structure.rotation_damping`, 0.2],
+      [`structure.zoom_speed`, 1.0],
+      [`structure.pan_speed`, 1.0],
+      [`structure.auto_rotate`, 2.0],
+      [`structure.site_label_size`, 14],
+      [`structure.site_label_padding`, 4],
+      [`structure.ambient_light`, 0.6],
+      [`structure.directional_light`, 0.8],
+      [`structure.vector_scale`, 2.0],
+      [`structure.vector_origin_gap`, 0.25],
+      [`structure.cell_edge_opacity`, 0.5],
+      [`structure.cell_surface_opacity`, 0.2],
+      [`background_opacity`, 0.8],
+      [`trajectory.fps`, 10],
+      [`trajectory.step_labels`, 10],
+
+      // Booleans
+      [`structure.same_size_atoms`, true],
+      [`structure.show_atoms`, false],
+      [`structure.show_bonds`, `always`],
+      [`structure.show_site_labels`, true],
+      [`structure.show_cell`, true],
+      [`structure.show_cell_vectors`, true],
+      [`structure.show_image_atoms`, true],
+      [`structure.show_gizmo`, false],
+      [`trajectory.auto_play`, true],
+      [`trajectory.show_controls`, false],
+
+      // Colors (strings)
+      [`structure.bond_color`, `#ff0000`],
+      [`structure.site_label_color`, `#00ff00`],
+      [`structure.site_label_bg_color`, `#333333`],
+      [`structure.cell_edge_color`, `#aaaaaa`],
+      [`structure.cell_surface_color`, `#bbbbbb`],
+      [`structure.vector_color`, `#ffff00`],
+      [`background_color`, `#111111`],
+
+      // String enums
+      [`structure.bonding_strategy`, `solid_angle`],
+      [`structure.camera_projection`, `orthographic`],
+      [`color_scheme`, `Jmol`],
+      [`composition.color_scheme`, `Alloy`],
+      [`trajectory.display_mode`, `scatter`],
+      [`trajectory.layout`, `vertical`],
+      [`composition.display_mode`, `bar`],
+
+      // Arrays
+      [`structure.camera_position`, [1, 2, 3]],
+      [`structure.site_label_offset`, [0.5, 1.0, 0]],
+      [`trajectory.fps_range`, [0.5, 60]],
+    ])(`should handle setting: %s = %s`, (result_path, expected_value) => {
+      test_setting(result_path, expected_value, result_path)
+    })
+
+    test.each([
+      [{ get: vi.fn(() => undefined) }, `missing config`],
+      [
+        {
+          get: vi.fn((key: string, default_val?: unknown) =>
+            key === `defaults`
+              ? {
+                  structure: {
+                    atom_radius: `invalid`,
+                    show_bonds: `invalid-value`,
+                    bond_color: 123,
+                  },
+                }
+              : default_val,
+          ),
+        },
+        `invalid values`,
+      ],
+    ])(`should handle %s gracefully`, (mock_config, _description) => {
+      // @ts-expect-error: Mock type override needed for testing
+      mock_vscode.workspace.getConfiguration.mockReturnValue(mock_config)
+
+      expect(() => get_defaults()).not.toThrow()
+      const result = get_defaults()
+
+      expect(result).toEqual(
+        expect.objectContaining({
+          structure: expect.any(Object),
+          trajectory: expect.any(Object),
+          composition: expect.any(Object),
+        }),
+      )
+    })
+
+    test(`should handle workspace config errors`, () => {
+      mock_vscode.workspace.getConfiguration.mockImplementation(() => {
+        throw new Error(`Config access failed`)
+      })
+
+      expect(() => get_defaults()).not.toThrow()
+    })
+  })
+})