matterviz 0.3.7 → 0.4.1

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'
@@ -26,16 +27,17 @@
   import type { BroadeningParams } from './broadening'
   import { compute_broadened_pattern, DEFAULT_BROADENING } from './broadening'
   import type { Hkl, HklFormat, PatternEntry, XrdPattern } from './index'
+  import { to_error } from '../utils'
 
   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
     )
   }
 
@@ -137,7 +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
   })
@@ -158,7 +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[]>(() => {
@@ -167,7 +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))
@@ -279,7 +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
@@ -352,7 +354,7 @@
           }
         } catch (exc) {
           error_msg = `Failed to load file ${file.name}: ${
-            exc instanceof Error ? exc.message : String(exc)
+            to_error(exc).message
           }`
         }
       }
@@ -473,15 +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; ${rest.style ?? ``}`}
         {controls}
@@ -495,11 +489,11 @@
         {@const angle_text = `${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}
@@ -532,15 +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

@@ -5,6 +5,7 @@ import { is_crystal } from '../structure/validation';
 // Single source of truth for atomic scattering params
 import ATOMIC_SCATTERING_PARAMS from './atomic_scattering_params.json' with { type: 'json' };
 import { is_xrd_data_file, parse_xrd_file } from './parse';
+import { to_error } from '../utils';
 // XRD wavelengths in Angstrom (Å)
 export const WAVELENGTHS = {
     CuKa: 1.54184,
@@ -66,23 +67,13 @@ 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, max_radius, min_radius) {
+function enumerate_reciprocal_points(recip_rows, direct_rows, max_radius, min_radius) {
     const recip_b1 = recip_rows[0];
     const recip_b2 = recip_rows[1];
     const recip_b3 = recip_rows[2];
-    const n1 = Math.max(Math.hypot(...recip_b1), 1e-12);
-    const n2 = Math.max(Math.hypot(...recip_b2), 1e-12);
-    const n3 = Math.max(Math.hypot(...recip_b3), 1e-12);
-    const h_max = Math.ceil(max_radius / n1 + 2);
-    const k_max = Math.ceil(max_radius / n2 + 2);
-    const l_max = Math.ceil(max_radius / n3 + 2);
+    // Exact index bound: |h_i| = |g·a_i| ≤ R·|a_i| (since a_i·b_j = δ_ij). Bounds from
+    // reciprocal-row norms (R/|b_i| + 2) undercount for skewed cells, dropping reflections.
+    const [h_max, k_max, l_max] = direct_rows.map((row) => Math.ceil(max_radius * Math.hypot(...row)) + 1);
     // Safety cap to avoid pathological enumeration volume
     const CAP = 512;
     if (Math.max(h_max, k_max, l_max) > CAP) {
@@ -133,7 +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
@@ -143,7 +135,7 @@ export function compute_xrd_pattern(structure, options = {}) {
             const r_max = (2 * Math.sin((t_max / 2) * (Math.PI / 180))) / wavelength;
             return [r_min, r_max];
         })(two_theta_range);
-    const recip_points = enumerate_reciprocal_points(recip_rows, max_radius, min_radius);
+    const recip_points = enumerate_reciprocal_points(recip_rows, structure.lattice.matrix, max_radius, min_radius);
     const coeffs = [];
     const frac_coords = [];
     const occus = [];
@@ -163,7 +155,7 @@ export function compute_xrd_pattern(structure, options = {}) {
             if (Array.isArray(raw_coeff)) {
                 const a_arr = raw_coeff.map(([a]) => a);
                 const b_arr = raw_coeff.map(([_, b]) => b);
-                coeff_entry = { a: a_arr, b: b_arr };
+                coeff_entry = { a: a_arr, b: b_arr, z: ELEMENT_Z[element_symbol] };
             }
             else {
                 coeff_entry = { a: raw_coeff.a.slice(), b: raw_coeff.b.slice(), c: raw_coeff.c };
@@ -194,11 +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 } = 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 (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));
@@ -303,7 +299,9 @@ wavelength) {
             }
             // Get base extension (strip .gz if present) for error message
             const base_name = filename.toLowerCase().replace(/\.gz$/, ``);
-            const ext = base_name.split(`.`).pop()?.toUpperCase() || `XRD`;
+            // truthiness (not ??) so an empty extension (filename ending in `.`) falls back to XRD
+            const last_part = base_name.split(`.`).pop();
+            const ext = last_part ? last_part.toUpperCase() : `XRD`;
             const format_hints = {
                 XY: `Expected 2-column format: "2theta intensity" (space/tab/comma separated)`,
                 XYE: `Expected 3-column format: "2theta intensity error" (space/tab/comma separated)`,
@@ -329,7 +327,7 @@ wavelength) {
     }
     catch (exc) {
         return {
-            error: `Failed to compute XRD pattern: ${exc instanceof Error ? exc.message : String(exc)}`,
+            error: `Failed to compute XRD pattern: ${to_error(exc).message}`,
         };
     }
 }

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/dist/xrd/parse.js

@@ -343,7 +343,7 @@ function parse_bruker_raw_v1(view, bytes) {
         // Find where binary data starts (after header)
         let data_offset = 512;
         if (count_match) {
-            const expected_count = parseInt(count_match[1]);
+            const expected_count = parseInt(count_match[1], 10);
             // Binary data is typically 4 bytes per intensity (float32)
             data_offset = bytes.length - expected_count * 4;
         }
@@ -406,7 +406,7 @@ function parse_rigaku_raw_file(data) {
             return null; // Not a recognizable Rigaku format
         const start = start_match ? parseFloat(start_match[1]) : 0;
         const step = step_match ? parseFloat(step_match[1]) : DEFAULT_STEP_SIZE;
-        const expected_count = count_match ? parseInt(count_match[1]) : 0;
+        const expected_count = count_match ? parseInt(count_match[1], 10) : 0;
         // Find binary data section
         // Rigaku typically stores intensities as 32-bit floats or integers
         let data_offset = 0;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matterviz",
-  "version": "0.3.7",
+  "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": {
@@ -169,63 +178,69 @@
   "scripts": {
     "test": "vp test --run && playwright test",
     "knip": "knip --include dependencies,devDependencies",
-    "package-dist-assets": "NODE_OPTIONS=--experimental-strip-types node scripts/package-dist-assets.ts",
-    "package:dist": "svelte-package && npm run package-dist-assets",
-    "prepare": "NODE_OPTIONS=--experimental-strip-types svelte-kit sync && npm run package:dist",
-    "prepublishOnly": "npm run package:dist"
+    "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": "2.61.1",
+    "@spglib/moyo-wasm": "^0.12.0",
+    "@sveltejs/kit": "2.65.1",
     "@threlte/core": "^8.5.16",
-    "@threlte/extras": "^9.20.1",
+    "@threlte/extras": "^9.21.0",
     "d3-array": "^3.2.4",
     "d3-color": "^3.1.0",
     "d3-format": "^3.1.2",
     "d3-hierarchy": "^3.1.2",
     "d3-interpolate-path": "^2.3.0",
+    "d3-sankey": "^0.12.3",
     "d3-scale": "^4.0.2",
     "d3-scale-chromatic": "^3.1.0",
     "d3-shape": "^3.2.0",
     "d3-time-format": "^4.1.0",
-    "dompurify": "^3.4.7",
+    "dompurify": "3.4.7",
     "fflate": "^0.8.3",
-    "h5wasm": "^0.10.2",
-    "js-yaml": "^4.1.1",
-    "svelte-multiselect": "^11.7.1",
+    "h5wasm": "^0.10.3",
+    "js-yaml": "^4.2.0",
+    "svelte-multiselect": "^11.7.2",
     "three": "^0.184.0"
   },
   "devDependencies": {
+    "@janosh/vite-config": "github:janosh/dotfiles",
     "@playwright/test": "^1.60.0",
     "@sveltejs/adapter-static": "3.0.10",
-    "@sveltejs/package": "^2.5.7",
+    "@sveltejs/package": "^2.5.8",
     "@sveltejs/vite-plugin-svelte": "^7.1.2",
     "@types/d3-array": "^3.2.2",
     "@types/d3-color": "^3.1.3",
     "@types/d3-format": "^3.0.4",
     "@types/d3-hierarchy": "^3.1.7",
     "@types/d3-interpolate-path": "^2.0.3",
+    "@types/d3-sankey": "^0.12.5",
     "@types/d3-scale": "^4.0.9",
     "@types/d3-scale-chromatic": "^3.1.0",
     "@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.20260527.2",
-    "@vitest/coverage-v8": "4.1.7",
-    "@wooorm/starry-night": "^3.9.0",
-    "happy-dom": "^20.9.0",
-    "knip": "^6.14.2",
+    "@typescript/native-preview": "7.0.0-dev.20260614.1",
+    "@vitest/coverage-v8": "4.1.8",
+    "@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": "5.56.0",
-    "svelte-check-rs": "0.9.19",
+    "svelte": "^5.56.3",
+    "svelte-check-rs": "0.10.1",
     "typescript": "6.0.3",
-    "vite": "^8.0.14",
+    "vite": "^8.0.16",
     "vite-plus": "latest",
-    "vitest": "4.1.7"
+    "vitest": "4.1.8"
   },
   "peerDependencies": {
     "svelte": "^5.0.0"
@@ -233,9 +248,11 @@
   "engines": {
     "node": ">=24"
   },
+  "packageManager": "pnpm@11.5.0",
   "knip": {
     "entry": [
-      "svelte.config.ts"
+      "svelte.config.ts",
+      "src/site/**/*.{js,ts,svelte}"
     ],
     "ignore": [
       "extensions/**"