matterviz 0.4.0 → 0.4.2

package/dist/xrd/parse.js

@@ -20,13 +20,24 @@ const parse_number_list = (text) => text
     .split(/\s+/)
     .map(parseFloat)
     .filter((val) => !isNaN(val));
+// Return the first parseable number from the text content of any of `tags`
+// (in order) that also passes the optional `ok` predicate. Null when none match.
+const query_first_number = (doc, tags, ok = () => true) => {
+    for (const tag of tags) {
+        const text = doc.querySelector(tag)?.textContent?.trim();
+        const val = text ? Number(text) : NaN;
+        if (!isNaN(val) && ok(val))
+            return val;
+    }
+    return null;
+};
 // Extract numeric value from header line matching "KEY=VALUE" or "KEY VALUE" pattern.
 // Returns null if not found or not a valid number.
 function extract_header_value(lines, key_pattern) {
     for (const line of lines) {
         const match = line.match(key_pattern);
         if (match?.[1]) {
-            const val = parseFloat(match[1]);
+            const val = Number(match[1]);
             if (!isNaN(val))
                 return val;
         }
@@ -53,17 +64,17 @@ function normalize_and_subsample(x_values, y_values) {
 }
 // Subsample data while preserving peaks (local maxima).
 // Uses a combination of uniform sampling and peak preservation.
-function subsample_preserve_peaks(x_values, y_values, target_points) {
-    const num_points = x_values.length;
+function subsample_preserve_peaks(x_vals, y_vals, target_points) {
+    const num_points = x_vals.length;
     if (num_points <= target_points)
-        return { x: x_values, y: y_values };
+        return { x: x_vals, y: y_vals };
     // Find peaks (local maxima with significant height)
     const peaks = [];
-    const threshold = Math.max(...y_values) * 0.05; // 5% of max as significance threshold
+    const threshold = Math.max(...y_vals) * 0.05; // 5% of max as significance threshold
     for (let idx = 1; idx < num_points - 1; idx++) {
-        if (y_values[idx] > y_values[idx - 1] &&
-            y_values[idx] > y_values[idx + 1] &&
-            y_values[idx] > threshold) {
+        if (y_vals[idx] > y_vals[idx - 1] &&
+            y_vals[idx] > y_vals[idx + 1] &&
+            y_vals[idx] > threshold) {
             peaks.push(idx);
         }
     }
@@ -72,7 +83,7 @@ function subsample_preserve_peaks(x_values, y_values, target_points) {
     const uniform_slots = target_points - peak_slots;
     // Select top peaks by height
     const top_peaks = peaks
-        .map((idx) => ({ idx, y: y_values[idx] }))
+        .map((idx) => ({ idx, y: y_vals[idx] }))
         .sort((a, b) => b.y - a.y)
         .slice(0, peak_slots)
         .map((peak) => peak.idx);
@@ -90,8 +101,8 @@ function subsample_preserve_peaks(x_values, y_values, target_points) {
     // Merge and sort all selected indices
     const selected = [...new Set([...uniform_indices, ...top_peaks])].sort((a, b) => a - b);
     return {
-        x: selected.map((idx) => x_values[idx]),
-        y: selected.map((idx) => y_values[idx]),
+        x: selected.map((idx) => x_vals[idx]),
+        y: selected.map((idx) => y_vals[idx]),
     };
 }
 // Parse a two-column ASCII file containing XRD data (2θ, intensity).
@@ -110,8 +121,8 @@ export function parse_xy_file(content) {
         const parts = trimmed.split(/[\s,]+/).filter(Boolean);
         if (parts.length < 2)
             continue;
-        const two_theta = parseFloat(parts[0]);
-        const intensity = parseFloat(parts[1]);
+        const two_theta = Number(parts[0]);
+        const intensity = Number(parts[1]);
         if (!isNaN(two_theta) && !isNaN(intensity)) {
             x_values.push(two_theta);
             y_values.push(intensity);
@@ -122,24 +133,17 @@ export function parse_xy_file(content) {
     const normalized = normalize_and_subsample(x_values, y_values);
     return { x: normalized.x, y: normalized.y };
 }
-// Parse a .xye file containing three-column XRD data (2θ, intensity, error).
-// Same as .xy but with an optional third column for uncertainties (ignored for plotting).
-export function parse_xye_file(content) {
-    // XYE is just XY with an extra error column - reuse parse_xy_file which already
-    // handles extra columns by only taking the first two
-    return parse_xy_file(content);
-}
 // Parse a Rigaku .ras file (ASCII format with structured header).
 // Format: *RAS_HEADER_START ... *RAS_HEADER_END followed by *RAS_INT_START ... *RAS_INT_END
 // Data can be single-column (intensity only) or multi-column (2-theta, intensity, [error])
 export function parse_ras_file(content) {
     const lines = content.split(/\r?\n/);
     // Extract header values (used as fallback for single-column data)
-    const header_start = extract_header_value(lines, /\*MEAS_SCAN_START\s*=\s*([\d.+-]+)/i) ??
-        extract_header_value(lines, /\*SCAN_START\s*=\s*([\d.+-]+)/i) ??
+    const header_start = extract_header_value(lines, /\*MEAS_SCAN_START\s*=\s*(?<value>[\d.+-]+)/i) ??
+        extract_header_value(lines, /\*SCAN_START\s*=\s*(?<value>[\d.+-]+)/i) ??
         0;
-    const header_step = extract_header_value(lines, /\*MEAS_SCAN_STEP\s*=\s*([\d.+-]+)/i) ??
-        extract_header_value(lines, /\*SCAN_STEP\s*=\s*([\d.+-]+)/i) ??
+    const header_step = extract_header_value(lines, /\*MEAS_SCAN_STEP\s*=\s*(?<value>[\d.+-]+)/i) ??
+        extract_header_value(lines, /\*SCAN_STEP\s*=\s*(?<value>[\d.+-]+)/i) ??
         DEFAULT_STEP_SIZE;
     // Find intensity data section between *RAS_INT_START and *RAS_INT_END
     // Also handle older format with *RAS_DATA_START
@@ -204,11 +208,11 @@ export function parse_ras_file(content) {
 export function parse_uxd_file(content) {
     const lines = content.split(/\r?\n/);
     // Extract header values (underscore-prefixed keys)
-    const start = extract_header_value(lines, /_2THETA_?START\s*=?\s*([\d.+-]+)/i) ??
-        extract_header_value(lines, /_START\s*=?\s*([\d.+-]+)/i) ??
+    const start = extract_header_value(lines, /_2THETA_?START\s*=?\s*(?<value>[\d.+-]+)/i) ??
+        extract_header_value(lines, /_START\s*=?\s*(?<value>[\d.+-]+)/i) ??
         0;
-    const step = extract_header_value(lines, /_STEP_?SIZE\s*=?\s*([\d.+-]+)/i) ??
-        extract_header_value(lines, /_STEPWIDTH\s*=?\s*([\d.+-]+)/i) ??
+    const step = extract_header_value(lines, /_STEP_?SIZE\s*=?\s*(?<value>[\d.+-]+)/i) ??
+        extract_header_value(lines, /_STEPWIDTH\s*=?\s*(?<value>[\d.+-]+)/i) ??
         DEFAULT_STEP_SIZE;
     // Find intensity data after _COUNTS marker
     let in_data_section = false;
@@ -247,13 +251,13 @@ export function parse_gsas_file(content) {
     let bin_type = `CONST`; // CONST, RALF, or others
     let found_bank = false;
     for (const line of lines) {
-        const bank_match = /BANK\s+\d+\s+(\d+)\s+\d+\s+(\w+)\s+([\d.+-]+)\s+([\d.+-]+)/i.exec(line);
+        const bank_match = /BANK\s+\d+\s+(?<npts>\d+)\s+\d+\s+(?<bin_type>\w+)\s+(?<bcoef1>[\d.+-]+)\s+(?<bcoef2>[\d.+-]+)/i.exec(line);
         if (bank_match) {
             bin_type = bank_match[2].toUpperCase();
             // For CONST type: BCOEF1 is start*100 (centidegrees), BCOEF2 is step*100
             if (bin_type === `CONST`) {
-                start = parseFloat(bank_match[3]) / 100; // Convert centidegrees to degrees
-                step = parseFloat(bank_match[4]) / 100;
+                start = Number(bank_match[3]) / 100; // Convert centidegrees to degrees
+                step = Number(bank_match[4]) / 100;
             }
             else if (bin_type !== `FXYE`) {
                 // Other bin types like RALF (time-of-flight) are not fully supported
@@ -335,15 +339,15 @@ function parse_bruker_raw_v1(view, bytes) {
         // V1 has ASCII header with scan parameters followed by binary data
         const header_text = String.fromCharCode(...bytes.slice(0, 512));
         // Try to find scan parameters in ASCII header
-        const start_match = /START\s*=\s*([\d.+-]+)/i.exec(header_text);
-        const step_match = /STEP\s*=\s*([\d.+-]+)/i.exec(header_text);
-        const count_match = /(?:COUNT|POINTS|NPTS)\s*=\s*(\d+)/i.exec(header_text);
-        const start = start_match ? parseFloat(start_match[1]) : 0;
-        const step = step_match ? parseFloat(step_match[1]) : DEFAULT_STEP_SIZE;
+        const start_match = /START\s*=\s*(?<value>[\d.+-]+)/i.exec(header_text);
+        const step_match = /STEP\s*=\s*(?<value>[\d.+-]+)/i.exec(header_text);
+        const count_match = /(?:COUNT|POINTS|NPTS)\s*=\s*(?<value>\d+)/i.exec(header_text);
+        const start = start_match ? Number(start_match[1]) : 0;
+        const step = step_match ? Number(step_match[1]) : DEFAULT_STEP_SIZE;
         // Find where binary data starts (after header)
         let data_offset = 512;
         if (count_match) {
-            const expected_count = parseInt(count_match[1], 10);
+            const expected_count = Math.trunc(Number(count_match[1]));
             // Binary data is typically 4 bytes per intensity (float32)
             data_offset = bytes.length - expected_count * 4;
         }
@@ -399,14 +403,14 @@ function parse_rigaku_raw_file(data) {
         const bytes = new Uint8Array(data);
         // Try to find ASCII header section with scan parameters
         const header_text = String.fromCharCode(...bytes.slice(0, Math.min(2048, bytes.length)));
-        const start_match = /(?:START|2THETA_START|SCAN_START)\s*[:=]?\s*([\d.+-]+)/i.exec(header_text);
-        const step_match = /(?:STEP|STEP_SIZE|SCAN_STEP)\s*[:=]?\s*([\d.+-]+)/i.exec(header_text);
-        const count_match = /(?:COUNT|POINTS|NPTS|STEPS)\s*[:=]?\s*(\d+)/i.exec(header_text);
+        const start_match = /(?:START|2THETA_START|SCAN_START)\s*[:=]?\s*(?<value>[\d.+-]+)/i.exec(header_text);
+        const step_match = /(?:STEP|STEP_SIZE|SCAN_STEP)\s*[:=]?\s*(?<value>[\d.+-]+)/i.exec(header_text);
+        const count_match = /(?:COUNT|POINTS|NPTS|STEPS)\s*[:=]?\s*(?<value>\d+)/i.exec(header_text);
         if (!start_match && !step_match && !count_match)
             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], 10) : 0;
+        const start = start_match ? Number(start_match[1]) : 0;
+        const step = step_match ? Number(step_match[1]) : DEFAULT_STEP_SIZE;
+        const expected_count = count_match ? Math.trunc(Number(count_match[1])) : 0;
         // Find binary data section
         // Rigaku typically stores intensities as 32-bit floats or integers
         let data_offset = 0;
@@ -538,7 +542,7 @@ function extract_scan_parameters_xml(doc) {
         const intensity_elements = doc.querySelectorAll(`I, Count`);
         if (intensity_elements.length > 0) {
             intensities = Array.from(intensity_elements)
-                .map((el) => parseFloat(el.textContent || ``))
+                .map((el) => Number(el.textContent?.trim() || NaN))
                 .filter((val) => !isNaN(val));
         }
     }
@@ -559,9 +563,9 @@ function extract_scan_parameters_xml(doc) {
                 const parts = text.split(`,`);
                 // Need at least 5 columns: time, flag, 2Theta, Theta/Omega, Intensity
                 if (parts.length >= 5) {
-                    const two_theta = parseFloat(parts[2]);
+                    const two_theta = Number(parts[2]);
                     // Intensity is always the last column
-                    const intensity = parseFloat(parts[parts.length - 1]);
+                    const intensity = Number(parts[parts.length - 1]);
                     if (!isNaN(two_theta) && !isNaN(intensity)) {
                         two_theta_values.push(two_theta);
                         intensities.push(intensity);
@@ -582,9 +586,7 @@ function extract_scan_parameters_xml(doc) {
     if (!intensities?.length)
         return null;
     // Extract scan range parameters
-    let start_angle = 0;
-    let step_size = DEFAULT_STEP_SIZE;
-    // Try to find start angle - multiple possible locations
+    // Try multiple possible tag names, returning the first that parses (and passes `ok`)
     const start_candidates = [
         `Start`,
         `TwoThetaStart`,
@@ -593,17 +595,6 @@ function extract_scan_parameters_xml(doc) {
         `ScanAxisBeginPosition`,
         `Begin`,
     ];
-    for (const tag of start_candidates) {
-        const el = doc.querySelector(tag);
-        if (el?.textContent) {
-            const val = parseFloat(el.textContent);
-            if (!isNaN(val)) {
-                start_angle = val;
-                break;
-            }
-        }
-    }
-    // Try to find step size - multiple possible locations
     const step_candidates = [
         `Step`,
         `StepSize`,
@@ -612,23 +603,15 @@ function extract_scan_parameters_xml(doc) {
         `ScanAxisIncrement`,
         `StepWidth`,
     ];
-    for (const tag of step_candidates) {
-        const el = doc.querySelector(tag);
-        if (el?.textContent) {
-            const val = parseFloat(el.textContent);
-            if (!isNaN(val) && val > 0) {
-                step_size = val;
-                break;
-            }
-        }
-    }
+    const start_angle = query_first_number(doc, start_candidates) ?? 0;
+    let step_size = query_first_number(doc, step_candidates, (val) => val > 0) ?? DEFAULT_STEP_SIZE;
     // Alternative: calculate step from start/end and count
     if (step_size === DEFAULT_STEP_SIZE) {
         const end_candidates = [`Stop`, `TwoThetaEnd`, `EndPosition`, `2ThetaEnd`, `End`];
         for (const tag of end_candidates) {
             const el = doc.querySelector(tag);
             if (el?.textContent) {
-                const end_val = parseFloat(el.textContent);
+                const end_val = Number(el.textContent);
                 if (!isNaN(end_val) && end_val > start_angle && intensities.length > 1) {
                     step_size = (end_val - start_angle) / (intensities.length - 1);
                     break;
@@ -660,8 +643,8 @@ export function parse_xrdml_file(content) {
         const end_el = two_theta_positions.querySelector(`endPosition`);
         if (!start_el?.textContent || !end_el?.textContent)
             return null;
-        const start_angle = parseFloat(start_el.textContent);
-        const end_angle = parseFloat(end_el.textContent);
+        const start_angle = Number(start_el.textContent);
+        const end_angle = Number(end_el.textContent);
         if (isNaN(start_angle) || isNaN(end_angle))
             return null;
         // Extract intensities

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matterviz",
-  "version": "0.4.0",
+  "version": "0.4.2",
   "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": {
@@ -168,15 +177,16 @@
   },
   "scripts": {
     "test": "vp test --run && playwright test",
-    "knip": "knip --include dependencies,devDependencies",
+    "knip": "knip --include dependencies,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": "^0.14.0",
+    "@sveltejs/kit": "2.69.2",
     "@threlte/core": "^8.5.16",
     "@threlte/extras": "^9.21.0",
     "d3-array": "^3.2.4",
@@ -189,19 +199,19 @@
     "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",
-    "js-yaml": "^4.2.0",
-    "svelte-multiselect": "^11.7.1",
-    "three": "^0.184.0"
+    "h5wasm": "^0.10.3",
+    "js-yaml": "^5.2.1",
+    "svelte-multiselect": "^11.8.0",
+    "three": "^0.185.1"
   },
   "devDependencies": {
     "@janosh/vite-config": "github:janosh/dotfiles",
-    "@playwright/test": "^1.60.0",
+    "@playwright/test": "^1.61.1",
     "@sveltejs/adapter-static": "3.0.10",
     "@sveltejs/package": "^2.5.8",
-    "@sveltejs/vite-plugin-svelte": "^7.1.2",
+    "@sveltejs/vite-plugin-svelte": "^7.2.0",
     "@types/d3-array": "^3.2.2",
     "@types/d3-color": "^3.1.3",
     "@types/d3-format": "^3.0.4",
@@ -212,23 +222,21 @@
     "@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/three": "^0.184.1",
-    "@typescript/native-preview": "7.0.0-dev.20260605.1",
-    "@vitest/coverage-v8": "4.1.8",
-    "@wooorm/starry-night": "^3.9.0",
-    "happy-dom": "^20.10.1",
-    "knip": "^6.16.0",
+    "@types/three": "^0.185.1",
+    "@vitest/coverage-v8": "4.1.10",
+    "@wooorm/starry-night": "^3.10.0",
+    "happy-dom": "^20.10.6",
+    "knip": "^6.25.0",
     "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",
-    "typescript": "6.0.3",
-    "vite": "^8.0.16",
-    "vite-plus": "latest",
-    "vitest": "4.1.8"
+    "svelte": "^5.56.4",
+    "svelte-check": "^4.7.2",
+    "typescript": "^6.0.3",
+    "vite": "^8.1.4",
+    "vite-plus": "^0.2.4",
+    "vitest": "4.1.10"
   },
   "peerDependencies": {
     "svelte": "^5.0.0"
@@ -238,15 +246,48 @@
   },
   "packageManager": "pnpm@11.5.0",
   "knip": {
-    "entry": [
-      "svelte.config.ts"
-    ],
-    "ignore": [
-      "extensions/**"
-    ],
     "ignoreDependencies": [
-      "@typescript/native-preview",
-      "svelte-check-rs"
-    ]
+      "svelte-check"
+    ],
+    "workspaces": {
+      ".": {
+        "entry": [
+          "svelte.config.ts",
+          "src/site/**/*.{js,ts,svelte}"
+        ],
+        "paths": {
+          "$lib": [
+            "./src/lib"
+          ],
+          "$lib/*": [
+            "./src/lib/*"
+          ],
+          "$site": [
+            "./src/site"
+          ],
+          "$site/*": [
+            "./src/site/*"
+          ]
+        },
+        "ignore": [
+          "extensions/anywidget/**",
+          "extensions/dash/**"
+        ]
+      },
+      "extensions/vscode": {
+        "entry": [
+          "src/extension.ts",
+          "src/webview/main.ts"
+        ],
+        "paths": {
+          "$lib": [
+            "../../src/lib"
+          ],
+          "$lib/*": [
+            "../../src/lib/*"
+          ]
+        }
+      }
+    }
   }
 }

package/dist/api/mp.d.ts

@@ -1,6 +0,0 @@
-export declare const mp_bucket = "https://materialsproject-build.s3.amazonaws.com/collections/2022-10-28";
-export declare function fetch_material_data<T extends Record<string, unknown>>(material_id: string, bucket?: string): Promise<{
-    summary: T | null;
-    similarity: T | null;
-    robocrys: T | null;
-}>;

package/dist/api/mp.js

@@ -1,22 +0,0 @@
-import { fetch_zipped } from '../io/fetch';
-// Materials Project S3 bucket for pre-computed data (may be outdated)
-export const mp_bucket = `https://materialsproject-build.s3.amazonaws.com/collections/2022-10-28`;
-// Fetch all material data in parallel
-export async function fetch_material_data(material_id, bucket = mp_bucket) {
-    try {
-        const results = await Promise.allSettled([
-            fetch_zipped(`${bucket}/summary/${material_id}.json.gz`),
-            fetch_zipped(`${bucket}/similarity/${material_id}.json.gz`),
-            fetch_zipped(`${bucket}/robocrys/${material_id}.json.gz`),
-        ]);
-        return {
-            summary: results[0].status === `fulfilled` ? results[0].value : null,
-            similarity: results[1].status === `fulfilled` ? results[1].value : null,
-            robocrys: results[2].status === `fulfilled` ? results[2].value : null,
-        };
-    }
-    catch (err) {
-        console.error(`Failed to fetch material data:`, err);
-        return { summary: null, similarity: null, robocrys: null };
-    }
-}