matterviz 0.4.0 → 0.4.1

package/dist/trajectory/plotting.js

@@ -32,18 +32,9 @@ function extract_property_statistics(trajectory, data_extractor) {
             if (typeof value !== `number` || key === `Step` || key.startsWith(`constant_`)) {
                 return;
             }
-            if (!property_stats.has(key)) {
-                const stats = { values: [], sum: 0, sum_squares: 0, min: value, max: value };
-                property_stats.set(key, stats);
-            }
-            const stat = property_stats.get(key);
-            if (stat) {
-                stat.values.push(value);
-                stat.sum += value;
-                stat.sum_squares += value * value;
-                stat.min = Math.min(stat.min, value);
-                stat.max = Math.max(stat.max, value);
-            }
+            const stat = property_stats.get(key) ?? { values: [] };
+            property_stats.set(key, stat);
+            stat.values.push(value);
         });
     });
     // Convert to final format with variation detection
@@ -201,94 +192,6 @@ const is_default_visible = (property_key, default_properties) => {
     }
     return false;
 };
-// Optimized series visibility toggling
-export function toggle_series_visibility(series, target_series_idx) {
-    if (target_series_idx < 0 || target_series_idx >= series.length)
-        return series;
-    const target_series = series[target_series_idx];
-    const new_visibility = !target_series.visible;
-    // Create unit groups from current state
-    const unit_groups = create_unit_groups_from_series(series);
-    const target_group = unit_groups.find((group) => group.series.includes(target_series));
-    if (!target_group)
-        return series;
-    // Start with updating the target series visibility
-    const updated_series = series.map((srs) => srs === target_series ? { ...srs, visible: new_visibility } : { ...srs });
-    // Handle smart group replacement for new groups
-    if (new_visibility && !target_group.is_visible) {
-        const visible_groups = unit_groups.filter((group) => group.is_visible);
-        if (visible_groups.length >= 2) {
-            // Hide lowest priority group (highest priority number)
-            const lowest_priority_group = visible_groups
-                .sort((g1, g2) => g1.priority - g2.priority)
-                .pop(); // Get the last (lowest priority) group
-            if (lowest_priority_group) {
-                lowest_priority_group.is_visible = false;
-                // Also hide the actual series in this group
-                lowest_priority_group.series.forEach((srs1) => {
-                    const series_idx = updated_series.findIndex((srs2) => srs2.label === srs1.label && srs2.unit === srs1.unit);
-                    if (series_idx !== -1) {
-                        updated_series[series_idx] = { ...updated_series[series_idx], visible: false };
-                    }
-                });
-            }
-        }
-        target_group.is_visible = true;
-    }
-    // Recalculate group visibility and reassign axes
-    update_group_visibility_and_axes(updated_series, unit_groups);
-    return updated_series;
-}
-function create_unit_groups_from_series(series) {
-    const unit_map = new Map();
-    for (const srs of series) {
-        const unit = srs.unit ?? `dimensionless`;
-        const group = unit_map.get(unit) ?? [];
-        group.push(srs);
-        unit_map.set(unit, group);
-    }
-    return Array.from(unit_map.entries())
-        .map(([unit, group_series]) => ({
-        unit,
-        series: group_series,
-        priority: calculate_priority(unit, group_series),
-        is_visible: group_series.some((srs) => srs.visible),
-    }))
-        .sort((a, b) => a.priority - b.priority);
-}
-function update_group_visibility_and_axes(series, unit_groups) {
-    // Update group visibility based on series
-    for (const group of unit_groups) {
-        group.is_visible = group.series.some((srs1) => series.find((srs2) => srs2.label === srs1.label && srs2.unit === srs1.unit)?.visible);
-    }
-    // Apply 2-group limit
-    if (unit_groups.filter((unit_group) => unit_group.is_visible).length > 2) {
-        for (const group of unit_groups.filter((unit_group) => unit_group.is_visible).slice(2)) {
-            group.is_visible = false;
-            for (const srs1 of group.series) {
-                const idx = series.findIndex((srs2) => srs2.label === srs1.label && srs2.unit === srs1.unit);
-                if (idx !== -1)
-                    series[idx] = { ...series[idx], visible: false };
-            }
-        }
-    }
-    // Assign axes
-    const final_visible = unit_groups
-        .filter((group) => group.is_visible)
-        .sort((g1, g2) => g1.priority - g2.priority);
-    const axis_map = new Map();
-    if (final_visible.length > 0)
-        axis_map.set(final_visible[0], `y1`);
-    if (final_visible.length === 2)
-        axis_map.set(final_visible[1], `y2`);
-    // Apply to series
-    for (const [idx, srs] of series.entries()) {
-        const group = unit_groups.find((unit_group) => unit_group.series.some((member) => member.label === srs.label && member.unit === srs.unit));
-        if (group && axis_map.has(group)) {
-            series[idx] = { ...srs, y_axis: axis_map.get(group) };
-        }
-    }
-}
 // Utility functions
 export function should_hide_plot(trajectory, plot_series, tolerance = 1e-10) {
     if (!trajectory || trajectory.frames.length <= 1 || plot_series.length === 0) {

package/dist/utils.d.ts

@@ -1,3 +1,4 @@
+export declare const is_plain_object: (val: unknown) => val is Record<string, unknown>;
 export declare function merge_nested<T extends Record<string, unknown>>(obj1: T, obj2?: Partial<T>): T;
 export declare const escape_html: (unsafe_string: string) => string;
 export declare const normalize_unicode_minus: (value: string) => string;

package/dist/utils.js

@@ -1,5 +1,5 @@
 // Check if value is a plain object (not array, null, or other types)
-const is_plain_object = (val) => typeof val === `object` && val !== null && !Array.isArray(val);
+export const is_plain_object = (val) => typeof val === `object` && val !== null && !Array.isArray(val);
 // Merge nested objects (1 level deep).
 export function merge_nested(obj1, obj2) {
     const result = { ...obj1, ...obj2 };

package/dist/xrd/XrdPlot.svelte

@@ -6,6 +6,7 @@
     decompress_data_binary,
     decompress_file,
     detect_compression_format,
+    drag_over_handlers,
     handle_url_drop,
   } from '../io'
   import { format_value } from '../labels'
@@ -31,12 +32,12 @@
   function is_xrd_pattern(obj: unknown): obj is XrdPattern {
     if (!obj || typeof obj !== `object`) return false
     const pattern_obj = obj as { x?: unknown; y?: unknown }
-    const x = pattern_obj.x
-    const y = pattern_obj.y
+    const x_vals = pattern_obj.x
+    const y_vals = pattern_obj.y
     return (
-      Array.isArray(x) &&
-      Array.isArray(y) &&
-      x.length === y.length
+      Array.isArray(x_vals) &&
+      Array.isArray(y_vals) &&
+      x_vals.length === y_vals.length
     )
   }
 
@@ -138,7 +139,7 @@
   const global_max_intensity = $derived.by(() => {
     let max_val = 0
     for (const entry of pattern_entries) {
-      for (const y of entry.pattern.y) if (y > max_val) max_val = y
+      for (const intensity of entry.pattern.y) if (intensity > max_val) max_val = intensity
     }
     return max_val || 1
   })
@@ -159,7 +160,7 @@
   })
 
   // Scaled intensities are normalized to 0..100, add 10% top padding for peak labels
-  const intensity_range: [number, number] = [0, 110]
+  const intensity_range: Vec2 = [0, 110]
 
   // Build BarPlot series from entries (for Discrete/Stick view)
   const bar_series = $derived.by<BarSeries[]>(() => {
@@ -168,7 +169,7 @@
     const include_name = pattern_entries.length > 1
     // Add transparency when multiple series overlap
     const alpha = pattern_entries.length > 1 ? 0.6 : 1
-    const scale = (y: number) => (y / global_max_intensity) * 100
+    const scale = (y_val: number) => (y_val / global_max_intensity) * 100
     return pattern_entries.map((entry, entry_idx) => {
       const xs = entry.pattern.x
       const ys = entry.pattern.y.map((val) => scale(val || 0))
@@ -280,7 +281,7 @@
         const all_ys = all_processed.flatMap((processed) => processed.broadened.y)
         const max_y = Math.max(...all_ys, 1) // Avoid div by zero
 
-        const scale = (y: number) => (y / max_y) * 100
+        const scale = (y_val: number) => (y_val / max_y) * 100
         const base_color = entry.color ?? PLOT_COLORS[entry_idx % PLOT_COLORS.length]
         // Add transparency when multiple series overlap
         const alpha = all_processed.length > 1 ? 0.6 : 1
@@ -474,15 +475,7 @@
         }}
         {tooltip}
         ondrop={handle_file_drop}
-        ondragover={(event) => {
-          event.preventDefault()
-          if (!allow_file_drop) return
-          dragover = true
-        }}
-        ondragleave={(event) => {
-          event.preventDefault()
-          dragover = false
-        }}
+        {...drag_over_handlers({ allow: () => allow_file_drop, set_dragover: (over) => dragover = over })}
         class={(rest.class ?? ``) + (dragover ? ` dragover` : ``)}
         style={`overflow: visible; ${rest.style ?? ``}`}
         {controls}
@@ -496,11 +489,11 @@
         {@const angle_text = `${format_value(info.x, `.2f`)}°`}
         {@const intensity_text = `${format_value(info.y, `.1f`)}`}
         {@const hkls = info.metadata?.hkls}
-        {@const d = info.metadata?.d}
+        {@const d_spacing = info.metadata?.d}
         {@const hkl_text = hkls && hkl_format
       ? hkls.map((hkl: Hkl) => format_hkl(hkl, hkl_format)).join(`, `)
       : ``}
-        {@const d_text = d != null ? `${format_value(d, `.3f`)} Å` : ``}
+        {@const d_text = d_spacing != null ? `${format_value(d_spacing, `.3f`)} Å` : ``}
         {@html sanitize_html(info.metadata?.label ?? ``)}<br />
         2θ: {angle_text}<br />
         Intensity: {intensity_text}
@@ -533,15 +526,7 @@
         }}
         {tooltip}
         ondrop={handle_file_drop}
-        ondragover={(event) => {
-          event.preventDefault()
-          if (!allow_file_drop) return
-          dragover = true
-        }}
-        ondragleave={(event) => {
-          event.preventDefault()
-          dragover = false
-        }}
+        {...drag_over_handlers({ allow: () => allow_file_drop, set_dragover: (over) => dragover = over })}
         class={(rest.class ?? ``) + (dragover ? ` dragover` : ``)}
         style={`overflow: visible; ${rest.style ?? ``}`}
         show_controls={controls.show}

package/dist/xrd/broadening.d.ts

@@ -1,3 +1,4 @@
+import type { Vec2 } from '../math';
 import type { XrdPattern } from './index';
 export type BroadeningParams = {
     U: number;
@@ -16,5 +17,5 @@ fwhm: number, // Full Width at Half Maximum
 eta: number): number;
 export declare function compute_broadened_pattern(pattern: XrdPattern, // Discrete XRD pattern (peaks)
 params: BroadeningParams, // Broadening parameters (U, V, W, shape_factor)
-range: [number, number], // Angular range [min, max] in degrees
+range: Vec2, // Angular range [min, max] in degrees
 step_size?: number): XrdPattern;

package/dist/xrd/calc-xrd.js

@@ -67,13 +67,6 @@ function get_unique_families(hkls) {
     }
     return family_map;
 }
-function compute_reciprocal_lattice_rows(structure) {
-    // For row-wise lattice matrix A (rows are a, b, c), reciprocal rows are inv(A)^T
-    const direct = structure.lattice.matrix;
-    const inv = math.matrix_inverse_3x3(direct);
-    const recip = math.transpose_3x3_matrix(inv);
-    return recip;
-}
 function enumerate_reciprocal_points(recip_rows, direct_rows, max_radius, min_radius) {
     const recip_b1 = recip_rows[0];
     const recip_b2 = recip_rows[1];
@@ -131,7 +124,8 @@ export function compute_xrd_pattern(structure, options = {}) {
     // Symmetry refinement (symprec > 0) is not implemented in TS version.
     // Option retained for API parity.
     // const symprec = options.symprec ?? 0
-    const recip_rows = compute_reciprocal_lattice_rows(structure);
+    // For row-wise lattice matrix A (rows are a, b, c), reciprocal rows are inv(A)^T
+    const recip_rows = math.transpose_3x3_matrix(math.matrix_inverse_3x3(structure.lattice.matrix));
     // Bragg condition bounds: reciprocal vector length r = 2 sin(theta) / lambda
     const two_theta_range = options.two_theta_range === null ? null : (options.two_theta_range ?? [0, 180]);
     const [min_radius, max_radius] = two_theta_range === null
@@ -192,14 +186,15 @@ export function compute_xrd_pattern(structure, options = {}) {
         const g_dot_r_all = frac_coords.map((frac_coord) => math.dot(frac_coord, hkl));
         // Atomic scattering factors (vectorized style)
         const f_scattering = coeffs.map((coeff_entry) => {
-            const { a: a_arr, b: b_arr, z } = coeff_entry;
+            const { a: a_arr, b: b_arr, z: atomic_number } = coeff_entry;
             const num_terms = Math.min(a_arr.length, b_arr.length);
             const sum_terms = a_arr
                 .slice(0, num_terms)
                 .reduce((sum, a_i, term_idx) => sum + a_i * Math.exp(-b_arr[term_idx] * sin_theta_over_lambda_sq), 0);
             // pymatgen-style fitted params: f = Z − 41.78214·s²·Σ aᵢ·exp(−bᵢ·s²)
-            if (z !== undefined)
-                return z - 41.78214 * sin_theta_over_lambda_sq * sum_terms;
+            if (atomic_number !== undefined) {
+                return atomic_number - 41.78214 * sin_theta_over_lambda_sq * sum_terms;
+            }
             return sum_terms + (coeff_entry.c ?? 0);
         });
         const dw_corr = dw_factors.map((dw_b) => Math.exp(-dw_b * sin_theta_over_lambda_sq));

package/dist/xrd/index.d.ts

@@ -1,5 +1,5 @@
 import type { CompositionType } from '../composition';
-import type { Vec3 } from '../math';
+import type { Vec2, Vec3 } from '../math';
 import type { RadiationKey } from './calc-xrd';
 export * from './broadening';
 export * from './calc-xrd';
@@ -26,7 +26,7 @@ export type XrdOptions = {
     symprec?: number;
     debye_waller_factors?: CompositionType;
     scaled?: boolean;
-    two_theta_range?: [number, number] | null;
+    two_theta_range?: Vec2 | null;
     peak_merge_tol?: number;
     scaled_intensity_tol?: number;
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matterviz",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "description": "Interactive visualizations for materials science: periodic tables, 3D structures, MD trajectories, heatmaps, scatter plots.",
   "keywords": [
     "chemistry",
@@ -19,6 +19,9 @@
     "dist"
   ],
   "type": "module",
+  "sideEffects": [
+    "**/*.css"
+  ],
   "exports": {
     ".": {
       "types": "./dist/index.d.ts",
@@ -30,7 +33,6 @@
       "default": "./dist/element/data.js"
     },
     "./app.css": {
-      "types": "./dist/app.css.d.ts",
       "default": "./dist/app.css"
     },
     "./brillouin": {
@@ -109,10 +111,18 @@
       "types": "./dist/plot/index.d.ts",
       "default": "./dist/plot/index.js"
     },
+    "./plot/*": {
+      "types": "./dist/plot/*/index.d.ts",
+      "default": "./dist/plot/*/index.js"
+    },
     "./rdf": {
       "types": "./dist/rdf/index.d.ts",
       "default": "./dist/rdf/index.js"
     },
+    "./scene": {
+      "types": "./dist/scene/index.d.ts",
+      "default": "./dist/scene/index.js"
+    },
     "./spectral": {
       "types": "./dist/spectral/index.d.ts",
       "default": "./dist/spectral/index.js"
@@ -138,7 +148,6 @@
       "default": "./dist/theme/index.js"
     },
     "./theme/themes": {
-      "types": "./dist/theme/themes.d.ts",
       "default": "./dist/theme/themes.mjs"
     },
     "./tooltip": {
@@ -169,14 +178,16 @@
   "scripts": {
     "test": "vp test --run && playwright test",
     "knip": "knip --include dependencies,devDependencies",
+    "knip:exports": "knip --include exports,types,nsExports",
+    "publint": "publint",
     "package-dist-assets": "node scripts/package-dist-assets.ts",
     "package:dist": "svelte-package && pnpm run package-dist-assets",
     "prepare": "svelte-kit sync && pnpm run package:dist",
     "prepublishOnly": "pnpm run package:dist"
   },
   "dependencies": {
-    "@spglib/moyo-wasm": "^0.10.0",
-    "@sveltejs/kit": "2.63.0",
+    "@spglib/moyo-wasm": "^0.12.0",
+    "@sveltejs/kit": "2.65.1",
     "@threlte/core": "^8.5.16",
     "@threlte/extras": "^9.21.0",
     "d3-array": "^3.2.4",
@@ -189,11 +200,11 @@
     "d3-scale-chromatic": "^3.1.0",
     "d3-shape": "^3.2.0",
     "d3-time-format": "^4.1.0",
-    "dompurify": "3.4.8",
+    "dompurify": "3.4.7",
     "fflate": "^0.8.3",
-    "h5wasm": "^0.10.2",
+    "h5wasm": "^0.10.3",
     "js-yaml": "^4.2.0",
-    "svelte-multiselect": "^11.7.1",
+    "svelte-multiselect": "^11.7.2",
     "three": "^0.184.0"
   },
   "devDependencies": {
@@ -213,18 +224,19 @@
     "@types/d3-shape": "^3.1.8",
     "@types/d3-time-format": "^4.0.3",
     "@types/js-yaml": "^4.0.9",
-    "@types/node": "^25.9.1",
+    "@types/node": "^25.9.3",
     "@types/three": "^0.184.1",
-    "@typescript/native-preview": "7.0.0-dev.20260605.1",
+    "@typescript/native-preview": "7.0.0-dev.20260614.1",
     "@vitest/coverage-v8": "4.1.8",
-    "@wooorm/starry-night": "^3.9.0",
-    "happy-dom": "^20.10.1",
-    "knip": "^6.16.0",
+    "@wooorm/starry-night": "^3.10.0",
+    "happy-dom": "^20.10.3",
+    "knip": "^6.16.1",
     "mdsvex": "^0.12.7",
+    "publint": "^0.3.21",
     "rehype-katex": "^7.0.1",
     "remark-math": "3.0.1",
-    "svelte": "^5.56.2",
-    "svelte-check-rs": "0.9.20",
+    "svelte": "^5.56.3",
+    "svelte-check-rs": "0.10.1",
     "typescript": "6.0.3",
     "vite": "^8.0.16",
     "vite-plus": "latest",
@@ -239,7 +251,8 @@
   "packageManager": "pnpm@11.5.0",
   "knip": {
     "entry": [
-      "svelte.config.ts"
+      "svelte.config.ts",
+      "src/site/**/*.{js,ts,svelte}"
     ],
     "ignore": [
       "extensions/**"