matterviz 0.3.5 → 0.3.7

package/dist/symmetry/index.js

@@ -23,6 +23,17 @@ export const default_sym_settings = {
 };
 let initialized = false;
 const OCCUPANCY_EPS = 1e-8;
+const to_unit = (value) => value - Math.floor(value);
+const near_zero = (value) => Math.min(value, 1 - value);
+const near_half = (value) => Math.abs(value - 0.5);
+const symmetry_position_key = (pos) => pos.map((coord) => to_unit(coord).toFixed(8)).join(`,`);
+const periodic_distance = (pos1, pos2) => Math.sqrt(pos1.reduce((sum, coord, idx) => {
+    // Wrap delta into [-0.5, 0.5) using safe modulo
+    const delta = coord - pos2[idx];
+    const wrapped = ((((delta + 0.5) % 1) + 1) % 1) - 0.5;
+    const distance = Math.abs(wrapped);
+    return sum + distance * distance;
+}, 0));
 export async function ensure_moyo_wasm_ready(wasm_url) {
     if (initialized)
         return;
@@ -117,9 +128,6 @@ export async function analyze_structure_symmetry(struct_or_mol, settings) {
 }
 // Helper function to score coordinate simplicity for Wyckoff table
 export function simplicity_score(vec) {
-    const to_unit = (v) => v - Math.floor(v);
-    const near_zero = (v) => Math.min(v, 1 - v);
-    const near_half = (v) => Math.abs(v - 0.5);
     const [ax, ay, az] = vec?.map(to_unit) ?? [];
     return (near_zero(ax) +
         near_zero(ay) +
@@ -180,8 +188,6 @@ export function wyckoff_positions_from_moyo(sym_data) {
 // Apply symmetry operations to find all equivalent positions for a given fractional coordinate
 export function apply_symmetry_operations(position, operations, _tolerance = 1e-6) {
     const seen = new Set();
-    const wrap = (coord) => coord - Math.floor(coord);
-    const key = (pos) => pos.map((coord) => wrap(coord).toFixed(8)).join(`,`);
     return operations
         .map(({ rotation, translation }) => {
         // Apply 3x3 rotation matrix and translation: new_pos = R * position + t
@@ -189,10 +195,10 @@ export function apply_symmetry_operations(position, operations, _tolerance = 1e-
             rotation[dim * 3 + 1] * position[1] +
             rotation[dim * 3 + 2] * position[2] +
             translation[dim]);
-        return new_pos.map(wrap);
+        return new_pos.map(to_unit);
     })
         .filter((pos) => {
-        const pos_key = key(pos);
+        const pos_key = symmetry_position_key(pos);
         if (seen.has(pos_key))
             return false;
         seen.add(pos_key);
@@ -204,13 +210,6 @@ export function map_wyckoff_to_all_atoms(wyckoff_positions, displayed_structure,
     if (!sym_data?.operations || !displayed_structure.sites || !orig_structure.sites) {
         return wyckoff_positions;
     }
-    const periodic_distance = (pos1, pos2) => Math.sqrt(pos1.reduce((sum, coord, idx) => {
-        // Wrap delta into [-0.5, 0.5) using safe modulo
-        const delta = coord - pos2[idx];
-        const wrapped = ((((delta + 0.5) % 1) + 1) % 1) - 0.5;
-        const d = Math.abs(wrapped);
-        return sum + d * d;
-    }, 0));
     return wyckoff_positions.map((wyckoff_pos) => {
         const indices = (wyckoff_pos.site_indices || [])
             .filter((idx) => idx < orig_structure.sites.length)

package/dist/table/HeatmapTable.svelte

@@ -28,6 +28,35 @@
   import type { HTMLAttributes } from 'svelte/elements'
   import { SvelteMap } from 'svelte/reactivity'
 
+  // Helper to check if value is invalid (null, undefined, NaN)
+  const is_invalid = (val: unknown) =>
+    val == null || (typeof val === `number` && Number.isNaN(val))
+
+  const NUMERIC_WITH_ERROR_RE =
+    /^([-+−]?(?:\d+\.?\d*|\d*\.\d+)(?:[eE][-+−]?\d+)?)\s*(?:±|\+[-−]|\()/
+
+  const parse_numeric_string = (val: string): number | null => {
+    const numeric_str = val.match(NUMERIC_WITH_ERROR_RE)?.[1] ?? val
+    if (numeric_str.trim() === ``) return null
+    const num = Number(normalize_unicode_minus(numeric_str))
+    return isNaN(num) ? null : num
+  }
+
+  // Get sort value from a cell (handles HTML data-sort-value and numbers with errors)
+  const get_sort_val = (val: CellVal): string | number => {
+    if (typeof val === `string`) {
+      // Check for HTML data-sort-value attribute first
+      const sort_attr_match = val.match(/data-sort-value="([^"]*)"/)
+      if (sort_attr_match) {
+        const num = Number(sort_attr_match[1])
+        return isNaN(num) ? sort_attr_match[1] : num
+      }
+      const num = parse_numeric_string(val)
+      if (num !== null) return num
+    }
+    return val as string | number
+  }
+
   let {
     data = $bindable([]),
     columns = [],
@@ -433,36 +462,6 @@
 
     if (!sort_state.column && multi_sort.length === 0) return filtered_data
 
-    // Helper to check if value is invalid (null, undefined, NaN)
-    const is_invalid = (val: unknown) =>
-      val == null || (typeof val === `number` && Number.isNaN(val))
-
-    // Get sort value from a cell (handles HTML data-sort-value and numbers with errors)
-    const get_sort_val = (val: CellVal): string | number => {
-      if (typeof val === `string`) {
-        // Check for HTML data-sort-value attribute first
-        const sort_attr_match = val.match(/data-sort-value="([^"]*)"/)
-        if (sort_attr_match) {
-          const num = Number(sort_attr_match[1])
-          return isNaN(num) ? sort_attr_match[1] : num
-        }
-        // Handle numbers with error notation: "1.23 ± 0.05" or "1.23 +- 0.05" or "1.23(5)"
-        // Extract the primary number before the ± or +- or (
-        // Supports: ± (U+00B1), ASCII +-, Unicode minus − (U+2212), with optional whitespace
-        const error_match = val.match(
-          /^([+-−]?\d+\.?\d*(?:[eE][+-−]?\d+)?)\s*(?:[±\u00B1]|[+][−-]|\()/,
-        )
-        if (error_match) {
-          const num = Number(error_match[1])
-          if (!isNaN(num)) return num
-        }
-        // Try parsing as a plain number (handles "1.23" strings)
-        const plain_num = Number(val)
-        if (!isNaN(plain_num) && val.trim() !== ``) return plain_num
-      }
-      return val as string | number
-    }
-
     // Build sort criteria: multi_sort takes precedence, fallback to single sort
     const sort_criteria = multi_sort.length > 0
       ? multi_sort
@@ -474,7 +473,7 @@
 
     return [...filtered_data].sort((row1, row2) => {
       for (const { column, ascending } of sort_criteria) {
-        const matched_col = ordered_columns.find((c) => get_col_id(c) === column)
+        const matched_col = ordered_columns.find((col) => get_col_id(col) === column)
         if (!matched_col) continue
 
         const col_id = get_col_id(matched_col)
@@ -548,7 +547,7 @@
   ) {
     // Find the column using both label and group if provided
     const col = ordered_columns.find(
-      (c) => c.label === column && c.group === group,
+      (candidate_col) => candidate_col.label === column && candidate_col.group === group,
     )
 
     if (!col) return // Skip if column not found
@@ -558,7 +557,7 @@
 
     // Shift+click for multi-column sort
     if (event.shiftKey) {
-      const existing_idx = multi_sort.findIndex((s) => s.column === col_id)
+      const existing_idx = multi_sort.findIndex((sort_entry) => sort_entry.column === col_id)
       if (existing_idx >= 0) {
         // Toggle direction or remove if clicked again
         const existing = multi_sort[existing_idx]
@@ -567,8 +566,8 @@
           multi_sort = multi_sort.filter((_, idx) => idx !== existing_idx)
         } else {
           // Toggle direction
-          multi_sort = multi_sort.map((s, idx) =>
-            idx === existing_idx ? { ...s, ascending: !s.ascending } : s
+          multi_sort = multi_sort.map((sort_entry, idx) =>
+            idx === existing_idx ? { ...sort_entry, ascending: !sort_entry.ascending } : sort_entry
           )
         }
       } else {
@@ -622,27 +621,7 @@
   // Extract numeric value from strings with uncertainty notation: "1.23 ± 0.05", "1.23 +- 0.05", "1.23(5)"
   function parse_numeric_val(val: CellVal): number | null {
     if (typeof val === `number`) return Number.isNaN(val) ? null : val
-    if (typeof val !== `string`) return null
-
-    // Handle numbers with error notation: "1.23 ± 0.05" or "1.23 +- 0.05" or "1.23(5)"
-    // Supports: ± (U+00B1), ASCII +-, Unicode minus − (U+2212), with optional whitespace
-    // Note: [-+−] has hyphen first to avoid regex range interpretation
-    // Pattern allows leading decimals like .5 or -.5 via (?:\d+\.?\d*|\d*\.\d+)
-    const error_match = val.match(
-      /^([-+−]?(?:\d+\.?\d*|\d*\.\d+)(?:[eE][-+−]?\d+)?)\s*(?:±|\+[-−]|\()/,
-    )
-    if (error_match) {
-      // Normalize unicode minus (U+2212) to ASCII hyphen for Number()
-      const normalized = normalize_unicode_minus(error_match[1])
-      const num = Number(normalized)
-      if (!isNaN(num)) return num
-    }
-    // Try parsing as a plain number (handles "1.23" strings)
-    // Also normalize unicode minus for plain numbers
-    const normalized_val = normalize_unicode_minus(val)
-    const plain_num = Number(normalized_val)
-    if (!isNaN(plain_num) && val.trim() !== ``) return plain_num
-    return null
+    return typeof val === `string` ? parse_numeric_string(val) : null
   }
 
   // Memoize parsed column values to avoid O(N²) re-parsing in calc_color
@@ -704,7 +683,7 @@
     const col_id = get_col_id(col)
 
     // Check multi-sort first
-    const multi_idx = multi_sort.findIndex((s) => s.column === col_id)
+    const multi_idx = multi_sort.findIndex((sort_entry) => sort_entry.column === col_id)
     if (multi_idx >= 0) {
       const arrow = multi_sort[multi_idx].ascending ? `↓` : `↑`
       const badge = multi_sort.length > 1 ? `<sup>${multi_idx + 1}</sup>` : ``
@@ -736,7 +715,7 @@
   // Row selection using WeakMap-based ID lookup instead of O(n) JSON.stringify comparison
   function toggle_row_select(row: RowData) {
     const row_id = get_row_id(row)
-    const idx = selected_rows.findIndex((r) => get_row_id(r) === row_id)
+    const idx = selected_rows.findIndex((selected_row) => get_row_id(selected_row) === row_id)
     if (idx >= 0) {
       selected_rows = selected_rows.filter((_, i) => i !== idx)
     } else {
@@ -746,7 +725,7 @@
 
   function is_row_selected(row: RowData): boolean {
     const row_id = get_row_id(row)
-    return selected_rows.some((r) => get_row_id(r) === row_id)
+    return selected_rows.some((selected_row) => get_row_id(selected_row) === row_id)
   }
 
   // Select-all: checks if every row on the current page is selected
@@ -788,7 +767,7 @@
         return quote(strip_html(String(val)))
       })
     )
-    return [headers.join(delimiter), ...rows.map((r) => r.join(delimiter))].join(`\n`)
+    return [headers.join(delimiter), ...rows.map((row) => row.join(delimiter))].join(`\n`)
   }
 
   function export_csv(filename = `table-export`) {
@@ -890,7 +869,7 @@
 {/snippet}
 
 <div
-  {@attach tooltip()}
+  {@attach tooltip({ allow_html: true })}
   {...rest_props}
   bind:this={container_el}
   class="table-container {rest_props.class ?? ``}"
@@ -1155,13 +1134,13 @@
               {#if !col.group}
                 <th class:sticky-col={col.sticky}></th>
               {:else}
-                {@const group_cols = visible_columns.filter((c) =>
-              c.group === col.group
+                {@const group_cols = visible_columns.filter((column) =>
+              column.group === col.group
             )}
                 <!-- Only render the group header once for each group by checking if this is the first column of this group -->
-                {#if visible_columns.findIndex((c) => c.group === col.group) ===
-              visible_columns.findIndex((c) =>
-                c.group === col.group && c.label === col.label
+                {#if visible_columns.findIndex((column) => column.group === col.group) ===
+              visible_columns.findIndex((column) =>
+                column.group === col.group && column.label === col.label
               )}
                   <th title={col.description} colspan={group_cols.length}>
                     {@html sanitize_html(col.group)}

package/dist/table/HeatmapTable.svelte.d.ts

@@ -44,6 +44,6 @@ type $$ComponentProps = HTMLAttributes<HTMLDivElement> & {
     }]>;
     footer?: Snippet;
 };
-declare const HeatmapTable: import("svelte").Component<$$ComponentProps, {}, "sort" | "data" | "show_controls" | "controls_open" | "show_heatmap" | "column_order" | "selected_rows" | "hidden_columns" | "loading" | "heatmap_opacity">;
+declare const HeatmapTable: import("svelte").Component<$$ComponentProps, {}, "sort" | "data" | "show_controls" | "loading" | "controls_open" | "show_heatmap" | "column_order" | "selected_rows" | "hidden_columns" | "heatmap_opacity">;
 type HeatmapTable = ReturnType<typeof HeatmapTable>;
 export default HeatmapTable;

package/dist/table/ToggleMenu.svelte

@@ -24,24 +24,31 @@
   const col_id = (col: Label) => col.key ?? col.label
 
   // Snapshot default visibility when column set changes (new dataset).
-  // Compare by column keys to avoid re-snapshotting on internal columns = [...columns] reactivity.
-  // Intentionally non-reactive: mutated only inside snapshot_defaults() and compared manually.
-  let prev_col_keys = ``
-  let default_visibility: Record<string, boolean> = {}
+  // Compare by keys and visibility defaults. Internal updates opt out below.
+  // Signature state is non-reactive; default visibility is state so reset UI updates after snapshots.
+  let prev_default_signature = ``
+  let internal_default_signature: string | undefined
+  let default_visibility = $state<Record<string, boolean>>({})
+  const default_signature = () =>
+    columns.map((col) => `${col_id(col)}:${col.visible !== false}`).join(`\0`)
+
   function snapshot_defaults() {
     default_visibility = {}
     for (const col of columns) {
       default_visibility[col_id(col)] = col.visible !== false
     }
-    prev_col_keys = columns.map(col_id).join(`\0`)
+    prev_default_signature = default_signature()
   }
   snapshot_defaults()
 
   $effect(() => {
-    const current_keys = columns.map(col_id).join(`\0`)
-    if (current_keys !== prev_col_keys) {
-      snapshot_defaults()
+    const current_signature = default_signature()
+    if (current_signature === internal_default_signature) {
+      internal_default_signature = undefined
+      return
     }
+    if (current_signature === prev_default_signature) return
+    snapshot_defaults()
   })
 
   // Check if a column's visibility differs from its default
@@ -55,6 +62,7 @@
     for (const col of items) {
       col.visible = default_visibility[col_id(col)] ?? true
     }
+    internal_default_signature = default_signature()
     columns = [...columns]
   }
 
@@ -94,13 +102,14 @@
 
   function toggle_section(name: string) {
     collapsed_sections = collapsed_sections.includes(name)
-      ? collapsed_sections.filter((s) => s !== name)
+      ? collapsed_sections.filter((section) => section !== name)
       : [...collapsed_sections, name]
   }
 
   function toggle_column_visibility(col: Label, event: Event) {
     if (!(event.target instanceof HTMLInputElement)) return
     col.visible = event.target.checked
+    internal_default_signature = default_signature()
     columns = [...columns] // trigger reactivity on parent binding
   }
 
@@ -140,7 +149,7 @@
   <label
     class="toggle-label"
     class:disabled={col.disabled}
-    {@attach tooltip({ content: col.description })}
+    {@attach tooltip({ allow_html: true, content: sanitize_html(col.description ?? ``) })}
   >
     <input
       type="checkbox"

package/dist/theme/themes.mjs

@@ -148,6 +148,18 @@ const themes = {
 
   // Tooltips
   'tooltip-bg': tooltip_bg(`243, 244, 246`, `0, 40, 60`),
+  'canvas-tooltip-bg': {
+    light: `rgba(226, 232, 240, 0.96)`,
+    dark: `rgba(15, 23, 42, 0.96)`,
+    white: `rgba(241, 245, 249, 0.98)`,
+    black: `rgba(20, 20, 20, 0.98)`,
+  },
+  'canvas-tooltip-text-color': {
+    light: `#0f172a`,
+    dark: `#f8fafc`,
+    white: `#0f172a`,
+    black: `#f8fafc`,
+  },
   'tooltip-border': {
     light: `1px solid rgba(0, 0, 0, 0.15)`,
     dark: `1px solid rgba(255, 255, 255, 0.15)`,

package/dist/tooltip/index.d.ts

@@ -1,2 +1,2 @@
 export { default as TooltipContent } from './TooltipContent.svelte';
-export * from './types';
+export type * from './types';

package/dist/tooltip/index.js

@@ -1,2 +1 @@
 export { default as TooltipContent } from './TooltipContent.svelte';
-export * from './types';

package/dist/trajectory/Trajectory.svelte

@@ -10,6 +10,7 @@
   import { sanitize_html } from '../sanitize'
   import { toggle_fullscreen } from '../layout'
   import type { ControlsConfig, DataSeries, Orientation, Point } from '../plot'
+  import type { ScatterHandlerProps } from '../plot/types'
   import { Histogram, ScatterPlot } from '../plot'
   import { toggle_series_visibility } from '../plot/utils/series-visibility'
   import { DEFAULTS } from '../settings'
@@ -229,6 +230,7 @@
 
   // Current frame - load on demand for indexed trajectories
   let current_frame = $state<TrajectoryFrame | null>(null)
+  let frame_load_request_id = 0
 
   // Auto-play when trajectory changes (handles both props and file loading)
   $effect(() => {
@@ -254,15 +256,25 @@
 
   // Load frame on demand - works for both indexed files and external streaming
   async function load_frame_on_demand(frame_idx: number) {
-    if (!trajectory?.frame_loader) return
+    const load_trajectory = trajectory
+    const frame_loader = load_trajectory?.frame_loader
+    if (!load_trajectory || !frame_loader) return
+
+    const request_id = ++frame_load_request_id
+    const request_is_current = () =>
+      request_id === frame_load_request_id &&
+      trajectory === load_trajectory &&
+      current_step_idx === frame_idx
 
     try {
-      const frame = await trajectory.frame_loader.load_frame(
+      const frame = await frame_loader.load_frame(
         orig_data || ``, // Use original_data for indexed files, empty string for external streaming
         frame_idx,
       )
+      if (!request_is_current()) return
       current_frame = frame
     } catch (error) {
+      if (!request_is_current()) return
       console.error(`Failed to load frame ${frame_idx}:`, error)
       current_frame = null
       on_error?.({
@@ -292,8 +304,10 @@
       if (step_labels > 0) {
         return scaleLinear().domain([0, total_frames - 1]).nice()
           .ticks(Math.min(step_labels, total_frames))
-          .map((t) => Math.round(t))
-          .filter((t, i, arr) => t >= 0 && t < total_frames && arr.indexOf(t) === i)
+          .map((tick) => Math.round(tick))
+          .filter((tick, idx, ticks) =>
+            tick >= 0 && tick < total_frames && ticks.indexOf(tick) === idx
+          )
       }
       if (step_labels < 0) {
         const spacing = Math.abs(step_labels)
@@ -760,7 +774,8 @@
 
   // Handle click outside to close dropdowns
   function handle_click_outside(event: MouseEvent) {
-    const target = event.target as Element
+    const target = event.target
+    if (!(target instanceof Element)) return
     if (view_mode_dropdown_open) {
       const dropdown_wrapper = target.closest(`.view-mode-dropdown-wrapper`)
       // Don't close if clicking on dropdown wrapper (contains both button and menu)
@@ -773,10 +788,10 @@
     if (!trajectory) return
 
     // Don't handle shortcuts if user is typing in an input field (but allow if it's our step input and not focused)
-    const target = event.target as HTMLElement
-    const is_step_input = target.classList.contains(`step-input`)
-    const is_input_focused = target.tagName === `INPUT` ||
-      target.tagName === `TEXTAREA`
+    const target = event.target instanceof HTMLElement ? event.target : null
+    const is_step_input = target?.classList.contains(`step-input`) ?? false
+    const is_input_focused =
+      target?.tagName === `INPUT` || target?.tagName === `TEXTAREA`
 
     // Skip if typing in an input that's not our step input
     if (is_input_focused && !is_step_input) return
@@ -784,7 +799,7 @@
     // If typing in step input, only handle certain navigation keys
     if (is_step_input && is_input_focused) {
       // Allow normal typing, but handle special navigation keys
-      if ([`Escape`, `Enter`].includes(event.key)) target.blur() // Remove focus from input
+      if ([`Escape`, `Enter`].includes(event.key)) target?.blur() // Remove focus from input
       return
     }
 
@@ -905,7 +920,7 @@
             <button
               class="filename"
               title="Click to copy filename <code>{current_filename}</code>"
-              {@attach tooltip()}
+              {@attach tooltip({ allow_html: true })}
               onclick={() => {
                 if (current_filename) {
                   navigator.clipboard.writeText(current_filename)
@@ -1170,14 +1185,19 @@
             {...scatter_props}
             legend={{
               ...scatter_props.legend ?? {},
-              on_toggle: (series_idx) => {
+              on_toggle: (series_idx: number) => {
                 handle_legend_toggle(series_idx)
                 scatter_props.legend?.on_toggle?.(series_idx)
               },
             }}
             class="plot {scatter_props.class ?? ``}"
           >
-            {#snippet tooltip({ x, y, metadata, label })}
+            {#snippet tooltip({
+              x,
+              y,
+              metadata,
+              label,
+            }: ScatterHandlerProps)}
               {@const formatted_y = typeof y === `number` ? format_num(y) : y}
               Step: {Math.round(x)}<br />
               {@html sanitize_html(metadata?.series_label || label || `Value`)}: {formatted_y}
@@ -1195,7 +1215,7 @@
             mode={histogram_props.mode ?? `overlay`}
             show_legend={histogram_props.show_legend ?? plot_series.length > 1}
             legend={histogram_props.legend}
-            on_series_toggle={(series_idx) => {
+            on_series_toggle={(series_idx: number) => {
               handle_legend_toggle(series_idx)
               histogram_props.on_series_toggle?.(series_idx)
             }}
@@ -1203,7 +1223,15 @@
             class="plot {histogram_props.class ?? ``}"
             --ctrl-btn-top="6ex"
           >
-            {#snippet tooltip({ value, count, property })}
+            {#snippet tooltip({
+              value,
+              count,
+              property,
+            }: {
+              value: number
+              count: number
+              property?: string
+            })}
               {#if property}<div><strong>{property}</strong></div>{/if}
               <div>Value: {format_num(value)}</div>
               <div>Count: {count}</div>

package/dist/trajectory/TrajectoryInfoPane.svelte

@@ -5,7 +5,7 @@
   import DraggablePane from '../overlays/DraggablePane.svelte'
   import { get_electro_neg_formula } from '../composition'
   import { SETTINGS_CONFIG } from '../settings'
-  import { type AnyStructure } from '../structure'
+  import type { AnyStructure } from '../structure'
   import type { ComponentProps } from 'svelte'
   import type { TrajectoryType } from './index'
 
@@ -260,7 +260,7 @@
           { structure },
         ) => (`lattice` in structure && structure.lattice?.volume))
           .filter(is_valid_number)
-          .filter((v) => v > 0)
+          .filter((volume) => volume > 0)
 
         if (volumes.length > 1) {
           const vol_change = (Math.max(...volumes) - Math.min(...volumes)) /

package/dist/trajectory/extract.js

@@ -1,5 +1,5 @@
 // Data extraction functions for trajectory analysis and plotting
-import { get_density } from '../structure';
+import { get_density } from '../structure/index';
 // Common data extractor that extracts energy and structural properties
 export const energy_data_extractor = (frame) => {
     const data = {

package/dist/trajectory/frame-reader.js

@@ -104,7 +104,7 @@ export class TrajFrameReader {
         return this.load_ase_frame(data, frame_number);
     }
     async extract_plot_metadata(data, options, on_progress) {
-        const { sample_rate = 1, properties } = options || {};
+        const { sample_rate = 1, properties } = options ?? {};
         const metadata_list = [];
         const total_frames = await this.get_total_frames(data);
         if (this.format === `xyz`) {
@@ -240,11 +240,11 @@ export class TrajFrameReader {
             const frame_offset = Number(view.getBigInt64(offsets_pos + frame_number * 8, true));
             const json_length = Number(view.getBigInt64(frame_offset, true));
             const frame_data = JSON.parse(new TextDecoder().decode(new Uint8Array(data, frame_offset + 8, json_length)));
-            const positions_ref = frame_data[`positions.`] || frame_data.positions;
+            const positions_ref = frame_data[`positions.`] ?? frame_data.positions;
             const positions = positions_ref?.ndarray
                 ? read_ndarray_from_view(view, positions_ref)
                 : positions_ref;
-            const numbers_ref = frame_data[`numbers.`] || frame_data.numbers || this.global_numbers;
+            const numbers_ref = frame_data[`numbers.`] ?? frame_data.numbers ?? this.global_numbers;
             const numbers = numbers_ref?.ndarray
                 ? read_ndarray_from_view(view, numbers_ref).flat()
                 : numbers_ref;
@@ -266,7 +266,7 @@ export class TrajFrameReader {
                     console.warn(`Failed to calculate volume for frame ${frame_number}:`, error);
                 }
             }
-            return create_trajectory_frame(positions, convert_atomic_numbers(numbers), cell, frame_data.pbc || [true, true, true], frame_number, metadata);
+            return create_trajectory_frame(positions, convert_atomic_numbers(numbers), cell, frame_data.pbc ?? [true, true, true], frame_number, metadata);
         }
         catch (error) {
             console.warn(`Failed to load ASE frame ${frame_number}:`, error);

package/dist/trajectory/helpers.d.ts

@@ -1,9 +1,10 @@
-import type { ElementSymbol } from '../element';
+import type { ElementSymbol } from '../element/types';
 import * as math from '../math';
-import type { AnyStructure, Pbc } from '../structure';
+import type { AnyStructure } from '../structure/index';
+import type { Pbc } from '../structure/pbc';
 import type { TrajectoryFrame } from './index';
-export declare function is_valid_element_symbol(symbol: string): symbol is ElementSymbol;
-export declare function coerce_element_symbol(symbol: string): ElementSymbol | undefined;
+export declare const is_valid_element_symbol: (symbol: string) => symbol is ElementSymbol;
+export declare const coerce_element_symbol: (symbol: string) => ElementSymbol | undefined;
 export declare function validate_3x3_matrix(data: unknown): math.Matrix3x3;
 export declare const convert_atomic_numbers: (numbers: number[]) => ElementSymbol[];
 export declare const create_structure: (positions: number[][], elements: ElementSymbol[], lattice_matrix?: math.Matrix3x3, pbc?: Pbc, force_data?: number[][]) => AnyStructure;

package/dist/trajectory/helpers.js

@@ -3,25 +3,20 @@ import { ATOMIC_NUMBER_TO_SYMBOL } from '../composition/parse';
 import { ELEM_SYMBOLS } from '../labels';
 import * as math from '../math';
 const element_symbol_set = new Set(ELEM_SYMBOLS);
-export function is_valid_element_symbol(symbol) {
-    return element_symbol_set.has(symbol);
-}
-export function coerce_element_symbol(symbol) {
-    return is_valid_element_symbol(symbol) ? symbol : undefined;
-}
+const is_valid_row = (row) => {
+    if (!(Array.isArray(row) || (ArrayBuffer.isView(row) && `length` in row)))
+        return false;
+    return math.is_finite_vec3_like(row);
+};
+const is_valid_vec3 = (coords) => Array.isArray(coords) && math.is_finite_vec3_like(coords);
+export const is_valid_element_symbol = (symbol) => element_symbol_set.has(symbol);
+export const coerce_element_symbol = (symbol) => is_valid_element_symbol(symbol) ? symbol : undefined;
 // Validate that data is a proper 3x3 matrix
 // Accepts both regular arrays and typed arrays (Float32Array, Float64Array, etc.)
 export function validate_3x3_matrix(data) {
     if (!Array.isArray(data) || data.length !== 3) {
         throw new Error(`Expected 3x3 matrix, got array of length ${Array.isArray(data) ? data.length : `non-array`}`);
     }
-    const is_valid_row = (row) => {
-        if (Array.isArray(row))
-            return row.length === 3;
-        if (!ArrayBuffer.isView(row))
-            return false;
-        return `length` in row && typeof row.length === `number` && row.length === 3;
-    };
     if (!data.every(is_valid_row)) {
         throw new Error(`Invalid 3x3 matrix structure`);
     }
@@ -39,9 +34,6 @@ export const create_structure = (positions, elements, lattice_matrix, pbc, force
         throw new Error(`create_structure requires matching positions and elements lengths, got positions=${positions.length}, elements=${elements.length}`);
     }
     const cart_to_frac = lattice_matrix ? math.create_cart_to_frac(lattice_matrix) : null;
-    const is_valid_vec3 = (coords) => Array.isArray(coords) &&
-        coords.length === 3 &&
-        coords.every((value) => typeof value === `number` && Number.isFinite(value));
     const sites = positions.map((pos, idx) => {
         if (!is_valid_vec3(pos)) {
             throw new Error(`Invalid position at index ${idx}: expected 3 finite coordinates`);
@@ -64,7 +56,7 @@ export const create_structure = (positions, elements, lattice_matrix, pbc, force
             lattice: {
                 matrix: lattice_matrix,
                 ...math.calc_lattice_params(lattice_matrix),
-                pbc: pbc || [true, true, true],
+                pbc: pbc ?? [true, true, true],
             },
         }
         : { sites };

package/dist/trajectory/index.d.ts

@@ -1,6 +1,6 @@
-import type { AnyStructure } from '../structure';
-import type Trajectory from './Trajectory.svelte';
 import type { ComponentProps } from 'svelte';
+import type { AnyStructure } from '../structure/index';
+import type Trajectory from './Trajectory.svelte';
 export { default as Trajectory } from './Trajectory.svelte';
 export { default as TrajectoryError } from './TrajectoryError.svelte';
 export { default as TrajectoryExportPane } from './TrajectoryExportPane.svelte';