matterviz 0.4.0 → 0.4.2

package/dist/composition/parse.d.ts

@@ -2,11 +2,10 @@ import type { ElementSymbol } from '../element';
 import type { CompositionType } from './';
 export declare const ATOMIC_NUMBER_TO_SYMBOL: Record<number, ElementSymbol>;
 export declare const SYMBOL_TO_ATOMIC_NUMBER: Partial<CompositionType>;
-export declare const ATOMIC_WEIGHTS: Map<"S" | "K" | "B" | "H" | "He" | "Li" | "Be" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "Cl" | "Ar" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og", number>;
-export declare const ELEMENT_ELECTRONEGATIVITY_MAP: Map<"S" | "K" | "B" | "H" | "He" | "Li" | "Be" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "Cl" | "Ar" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og", number>;
+export declare const ATOMIC_WEIGHTS: Map<"Ac" | "Ag" | "Al" | "Am" | "Ar" | "As" | "At" | "Au" | "B" | "Ba" | "Be" | "Bh" | "Bi" | "Bk" | "Br" | "C" | "Ca" | "Cd" | "Ce" | "Cf" | "Cl" | "Cm" | "Co" | "Cr" | "Cs" | "Cu" | "Db" | "Dy" | "Er" | "Es" | "Eu" | "F" | "Fe" | "Fm" | "Fr" | "Ga" | "Gd" | "Ge" | "H" | "He" | "Hf" | "Hg" | "Ho" | "Hs" | "I" | "In" | "Ir" | "K" | "Kr" | "La" | "Li" | "Lr" | "Lu" | "Md" | "Mg" | "Mn" | "Mo" | "Mt" | "N" | "Na" | "Nb" | "Nd" | "Ne" | "Ni" | "No" | "Np" | "O" | "Os" | "P" | "Pa" | "Pb" | "Pd" | "Pm" | "Po" | "Pr" | "Pt" | "Pu" | "Ra" | "Rb" | "Re" | "Rf" | "Rh" | "Rn" | "Ru" | "S" | "Sb" | "Sc" | "Se" | "Sg" | "Si" | "Sm" | "Sn" | "Sr" | "Ta" | "Tb" | "Tc" | "Te" | "Th" | "Ti" | "Tl" | "Tm" | "U" | "V" | "W" | "Xe" | "Y" | "Yb" | "Zn" | "Zr" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og", number>;
+export declare const ELEMENT_ELECTRONEGATIVITY_MAP: Map<"Ac" | "Ag" | "Al" | "Am" | "Ar" | "As" | "At" | "Au" | "B" | "Ba" | "Be" | "Bh" | "Bi" | "Bk" | "Br" | "C" | "Ca" | "Cd" | "Ce" | "Cf" | "Cl" | "Cm" | "Co" | "Cr" | "Cs" | "Cu" | "Db" | "Dy" | "Er" | "Es" | "Eu" | "F" | "Fe" | "Fm" | "Fr" | "Ga" | "Gd" | "Ge" | "H" | "He" | "Hf" | "Hg" | "Ho" | "Hs" | "I" | "In" | "Ir" | "K" | "Kr" | "La" | "Li" | "Lr" | "Lu" | "Md" | "Mg" | "Mn" | "Mo" | "Mt" | "N" | "Na" | "Nb" | "Nd" | "Ne" | "Ni" | "No" | "Np" | "O" | "Os" | "P" | "Pa" | "Pb" | "Pd" | "Pm" | "Po" | "Pr" | "Pt" | "Pu" | "Ra" | "Rb" | "Re" | "Rf" | "Rh" | "Rn" | "Ru" | "S" | "Sb" | "Sc" | "Se" | "Sg" | "Si" | "Sm" | "Sn" | "Sr" | "Ta" | "Tb" | "Tc" | "Te" | "Th" | "Ti" | "Tl" | "Tm" | "U" | "V" | "W" | "Xe" | "Y" | "Yb" | "Zn" | "Zr" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og", number>;
 export declare const ELEM_NAME_TO_SYMBOL: Record<string, ElementSymbol>;
 export declare const ELEM_SYMBOL_TO_NAME: Partial<Record<ElementSymbol, string>>;
-export declare const is_valid_element: (sym: string) => sym is ElementSymbol;
 export declare const atomic_num_to_symbols: (atomic_composition: Record<number, number>) => CompositionType;
 export declare const atomic_symbol_to_num: (symbol_composition: CompositionType) => Record<number, number>;
 export declare const parse_formula: (formula: string) => CompositionType;

package/dist/composition/parse.js

@@ -1,4 +1,5 @@
-import { element_data } from '../element';
+import { default as element_data } from '../element/data';
+import { is_elem_symbol } from '../element/helpers';
 import { ELEM_SYMBOLS } from '../labels';
 // Create symbol/number/mass/electronegativity lookup maps for O(1) access
 export const ATOMIC_NUMBER_TO_SYMBOL = {};
@@ -16,8 +17,6 @@ for (const element of element_data) {
     ELEM_NAME_TO_SYMBOL[element.name] = element.symbol;
     ELEM_SYMBOL_TO_NAME[element.symbol] = element.name;
 }
-// Type guard: check if a string is a valid element symbol
-export const is_valid_element = (sym) => ELEM_SYMBOLS.includes(sym);
 // Check if object has atomic numbers as keys (1-118)
 const is_atomic_number_composition = (obj) => {
     const keys = Object.keys(obj);
@@ -26,7 +25,7 @@ const is_atomic_number_composition = (obj) => {
         atomic_nums.every((atomic_num) => Number.isInteger(atomic_num) && Object.hasOwn(ATOMIC_NUMBER_TO_SYMBOL, atomic_num)));
 };
 const format_state = (state) => (state > 0 ? `+` : ``) + state;
-const parse_count = (count) => (count ? parseFloat(count) : 1);
+const parse_count = (count) => (count ? Number(count) : 1);
 const format_count = (count) => {
     if (!Number.isFinite(count))
         return `${count}`;
@@ -51,7 +50,7 @@ export const atomic_num_to_symbols = (atomic_composition) => {
 export const atomic_symbol_to_num = (symbol_composition) => {
     const atomic_composition = {};
     for (const [symbol, amount] of Object.entries(symbol_composition)) {
-        if (!is_valid_element(symbol))
+        if (!is_elem_symbol(symbol))
             throw new Error(`Invalid element symbol: ${symbol}`);
         const atomic_num = SYMBOL_TO_ATOMIC_NUMBER[symbol];
         if (!atomic_num)
@@ -65,9 +64,9 @@ export const atomic_symbol_to_num = (symbol_composition) => {
 // Expand parentheses in chemical formulas
 const expand_parentheses = (formula) => {
     while (formula.includes(`(`)) {
-        const expanded = formula.replaceAll(/\(([^()]+)\)(\d+(?:\.\d+)?|\.\d+)?/g, (_match, group, multiplier) => {
+        const expanded = formula.replaceAll(/\((?<group>[^()]+)\)(?<multiplier>\d+(?:\.\d+)?|\.\d+)?/g, (_match, group, multiplier) => {
             const mult = parse_count(multiplier);
-            return group.replaceAll(/([A-Z][a-z]?)(\d+(?:\.\d+)?|\.\d+)?/g, (_m, element, count) => {
+            return group.replaceAll(/(?<element>[A-Z][a-z]?)(?<count>\d+(?:\.\d+)?|\.\d+)?/g, (_m, element, count) => {
                 const count_str = format_count(parse_count(count) * mult);
                 return element + (count_str === `1` ? `` : count_str);
             });
@@ -89,11 +88,11 @@ export const parse_formula = (formula) => {
     for (const [seg_idx, segment] of segments.entries()) {
         // only hydrate segments (after a separator) carry a leading multiplier
         const coeff = seg_idx > 0 ? /^(?:\d+(?:\.\d+)?|\.\d+)/.exec(segment)?.[0] : undefined;
-        const multiplier = coeff ? parseFloat(coeff) : 1;
+        const multiplier = coeff ? Number(coeff) : 1;
         const expanded = expand_parentheses(segment.slice(coeff?.length ?? 0));
-        for (const match of expanded.matchAll(/([A-Z][a-z]?)(\d+(?:\.\d+)?|\.\d+)?/g)) {
+        for (const match of expanded.matchAll(/(?<element>[A-Z][a-z]?)(?<count>\d+(?:\.\d+)?|\.\d+)?/g)) {
             const [, element, count] = match;
-            if (!is_valid_element(element))
+            if (!is_elem_symbol(element))
                 throw new Error(`Invalid element symbol: ${element}`);
             composition[element] = (composition[element] ?? 0) + parse_count(count) * multiplier;
         }
@@ -107,7 +106,7 @@ export const normalize_composition = (composition) => {
     }
     const normalized = {};
     for (const [element, amount] of Object.entries(composition)) {
-        if (typeof amount === `number` && amount > 0 && is_valid_element(element)) {
+        if (typeof amount === `number` && amount > 0 && is_elem_symbol(element)) {
             normalized[element] = amount;
         }
     }
@@ -125,7 +124,7 @@ export const sanitize_composition_keys = (composition) => {
         if (typeof amount !== `number` || amount <= 0)
             continue;
         // Extract first valid element symbol from key (e.g. "B0." -> "B", "Fe2+" -> "Fe")
-        const elem = (key.match(/[A-Z][a-z]?/g) ?? []).find(is_valid_element);
+        const elem = (key.match(/[A-Z][a-z]?/g) ?? []).find(is_elem_symbol);
         if (elem)
             sanitized[elem] = (sanitized[elem] || 0) + amount;
     }
@@ -139,7 +138,7 @@ export const fractional_composition = (composition, by_weight = false) => {
     const filtered = Object.fromEntries(Object.entries(composition).filter(([, amount]) => amount > 0));
     if (by_weight) {
         const element_weights = Object.fromEntries(Object.entries(filtered).map(([element, amount]) => {
-            if (!is_valid_element(element))
+            if (!is_elem_symbol(element))
                 throw new Error(`Unknown element: ${element}`);
             const atomic_mass = ATOMIC_WEIGHTS.get(element);
             if (!atomic_mass)
@@ -191,14 +190,14 @@ export const get_reduced_formula = (composition) => {
         return composition;
     const reduced = {};
     for (const [elem, amt] of Object.entries(composition)) {
-        if (is_valid_element(elem))
+        if (is_elem_symbol(elem))
             reduced[elem] = amt / divisor;
     }
     return reduced;
 };
 // Calculate molecular weight (sum of atomic masses * amounts)
 export const get_molecular_weight = (composition) => Object.entries(composition).reduce((total, [elem, amount]) => {
-    const mass = is_valid_element(elem) ? (ATOMIC_WEIGHTS.get(elem) ?? 0) : 0;
+    const mass = is_elem_symbol(elem) ? (ATOMIC_WEIGHTS.get(elem) ?? 0) : 0;
     return total + mass * amount;
 }, 0);
 // Parse oxidation state string (e.g. "+2", "2+", "-", "[2-]") to number
@@ -208,12 +207,12 @@ const parse_oxidation_state = (oxidation_str) => {
         return oxidation_str === `+` ? 1 : -1;
     }
     // Handle formats like "2+", "+2", "2-", "-2"
-    const ox_match = /([+-]?)(\d+)([+-]?)/.exec(oxidation_str);
+    const ox_match = /(?<sign_before>[+-]?)(?<number>\d+)(?<sign_after>[+-]?)/.exec(oxidation_str);
     if (!ox_match)
         return 0;
     const [, sign_before, number, sign_after] = ox_match;
     const sign = sign_before || sign_after || `+`;
-    return sign === `-` ? -parseInt(number, 10) : parseInt(number, 10);
+    return sign === `-` ? -Number(number) : Number(number);
 };
 // Parse chemical formula string with oxidation states into structured data.
 // Supports both ^2+ and [2+] syntax for oxidation states.
@@ -231,7 +230,7 @@ export const parse_formula_with_oxidation = (formula, strict = false) => {
     //          - just oxidation: (?:\^([+-]?\d+[+-]?|[+-])|\[([+-]?\d+[+-]?|[+-])\])
     //          - just count: count
     //          - neither
-    const regex = /([A-Z][a-z]?)(?:(?:\^([+-]?\d+[+-]?|[+-])|\[([+-]?\d+[+-]?|[+-])\])((?:\d+(?:\.\d+)?|\.\d+)?)|((?:\d+(?:\.\d+)?|\.\d+))(?:\^([+-]?\d+[+-]?|[+-])|\[([+-]?\d+[+-]?|[+-])\])?)?/g;
+    const regex = /(?<element>[A-Z][a-z]?)(?:(?:\^(?<oxi_caret>[+-]?\d+[+-]?|[+-])|\[(?<oxi_bracket>[+-]?\d+[+-]?|[+-])\])(?<count_after>(?:\d+(?:\.\d+)?|\.\d+)?)|(?<count_before>(?:\d+(?:\.\d+)?|\.\d+))(?:\^(?<oxi_caret_2>[+-]?\d+[+-]?|[+-])|\[(?<oxi_bracket_2>[+-]?\d+[+-]?|[+-])\])?)?/g;
     let match;
     let orig_idx = 0;
     while ((match = regex.exec(cleaned_formula)) !== null) {
@@ -241,7 +240,7 @@ export const parse_formula_with_oxidation = (formula, strict = false) => {
         const oxidation_str = match[2] || match[3] || match[6] || match[7];
         const count_str = match[4] || match[5];
         const count = parse_count(count_str);
-        if (!is_valid_element(element))
+        if (!is_elem_symbol(element))
             throw new Error(`Invalid element symbol: ${element}`);
         const oxidation_state = oxidation_str ? parse_oxidation_state(oxidation_str) : undefined;
         // Find or add element entry
@@ -269,7 +268,7 @@ export const parse_formula_with_oxidation = (formula, strict = false) => {
 };
 // Convert OxiComposition to ElementWithOxidation array
 // Does not preserve original order since objects don't have a defined order
-export const oxi_composition_to_elements = (composition) => Object.entries(composition).flatMap(([element, { amount, oxidation_state }], idx) => is_valid_element(element) ? [{ element, amount, oxidation_state, orig_idx: idx }] : []);
+export const oxi_composition_to_elements = (composition) => Object.entries(composition).flatMap(([element, { amount, oxidation_state }], idx) => is_elem_symbol(element) ? [{ element, amount, oxidation_state, orig_idx: idx }] : []);
 // Extract element symbols from a chemical formula.
 // Default (unique=true, sorted=true): "NbZr2Nb" -> ["Nb", "Zr"]
 // unique=false: Fast token extraction preserving order without parentheses expansion
@@ -283,12 +282,12 @@ export function extract_formula_elements(formula, { unique = true, sorted = true
         const matches = formula.match(/[A-Z][a-z]?/g) ?? [];
         const elements = [];
         for (const match of matches) {
-            if (is_valid_element(match))
+            if (is_elem_symbol(match))
                 elements.push(match);
         }
         return elements;
     }
-    const symbols = Object.keys(parse_formula(formula)).filter(is_valid_element);
+    const symbols = Object.keys(parse_formula(formula)).filter(is_elem_symbol);
     return sorted ? symbols.sort() : symbols;
 }
 // Generate all non-empty subsets of a chemical system as hyphenated strings.
@@ -302,7 +301,7 @@ export function generate_chem_sys_subspaces(input) {
     else if (Array.isArray(input)) {
         const uniq = [...new Set(input)];
         for (const elem of uniq) {
-            if (!is_valid_element(elem))
+            if (!is_elem_symbol(elem))
                 throw new Error(`Invalid element symbol: ${elem}`);
         }
         elements = uniq;
@@ -310,7 +309,7 @@ export function generate_chem_sys_subspaces(input) {
     else {
         elements = [];
         for (const elem of Object.keys(input)) {
-            if (!is_valid_element(elem))
+            if (!is_elem_symbol(elem))
                 throw new Error(`Invalid element symbol: ${elem}`);
             elements.push(elem);
         }
@@ -354,7 +353,7 @@ export function parse_chemsys_with_wildcards(input) {
         if (token === `*`) {
             wildcard_count++;
         }
-        else if (is_valid_element(token)) {
+        else if (is_elem_symbol(token)) {
             elements.push(token);
         }
         else {
@@ -389,7 +388,7 @@ export function parse_formula_with_wildcards(formula) {
     // Regex to match either:
     // 1. Standard element symbol with optional decimal count
     // 2. Wildcard with optional decimal count
-    const regex = /([A-Z][a-z]?)((?:\d+(?:\.\d+)?|\.\d+)?)|(\*)((?:\d+(?:\.\d+)?|\.\d+)?)/g;
+    const regex = /(?<element>[A-Z][a-z]?)(?<count>(?:\d+(?:\.\d+)?|\.\d+)?)|(?<wildcard>\*)(?<wildcard_count>(?:\d+(?:\.\d+)?|\.\d+)?)/g;
     let match;
     while ((match = regex.exec(cleaned)) !== null) {
         if (match[3] === `*`) {
@@ -401,7 +400,7 @@ export function parse_formula_with_wildcards(formula) {
             // Element symbol match
             const element = match[1];
             const count = parse_count(match[2]);
-            if (!is_valid_element(element)) {
+            if (!is_elem_symbol(element)) {
                 throw new Error(`Invalid element symbol: ${element}`);
             }
             tokens.push({ element, count });
@@ -422,7 +421,7 @@ export function matches_chemsys_wildcard(formula, explicit_elements, wildcard_co
         // Must contain all explicit elements
         const formula_set = new Set(formula_elements);
         for (const elem of explicit_elements) {
-            if (!is_valid_element(elem) || !formula_set.has(elem))
+            if (!is_elem_symbol(elem) || !formula_set.has(elem))
                 return false;
         }
         return true;

package/dist/constants.js

@@ -61,9 +61,11 @@ export const TRAJ_KEYWORDS_REGEX = new RegExp(`(^|[-_.])(${TRAJ_KEYWORDS.join(`|
 export const STRUCT_KEYWORDS_REGEX = new RegExp(`(${STRUCT_KEYWORDS.join(`|`)})`, `i`);
 export const STRUCT_KEYWORDS_STRICT_REGEX = new RegExp(`(${STRUCT_KEYWORDS_STRICT.join(`|`)})`, `i`);
 export const TRAJ_KEYWORDS_SIMPLE_REGEX = new RegExp(`(${TRAJ_KEYWORDS.join(`|`)})`, `i`);
+// Build a case-insensitive `\.(ext1|ext2|...)$` regex from extensions (leading dots stripped)
+const ext_regex = (exts) => new RegExp(`\\.(${exts.map((ext) => ext.slice(1)).join(`|`)})$`, `i`);
 // File extensions for different file types
 export const TRAJ_EXTENSIONS = Object.freeze([`.traj`, `.xtc`, `.lammpstrj`]);
-export const TRAJ_EXTENSIONS_REGEX = new RegExp(`\\.(${TRAJ_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`, `i`);
+export const TRAJ_EXTENSIONS_REGEX = ext_regex(TRAJ_EXTENSIONS);
 export const STRUCTURE_EXTENSIONS = Object.freeze([
     `.cif`,
     `.mcif`,
@@ -79,7 +81,7 @@ export const STRUCTURE_EXTENSIONS = Object.freeze([
     `.sdf`,
     `.mmcif`,
 ]);
-export const STRUCTURE_EXTENSIONS_REGEX = new RegExp(`\\.(${STRUCTURE_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`, `i`);
+export const STRUCTURE_EXTENSIONS_REGEX = ext_regex(STRUCTURE_EXTENSIONS);
 export const TRAJ_FALLBACK_EXTENSIONS = Object.freeze([
     `.dat`,
     `.data`,
@@ -87,13 +89,13 @@ export const TRAJ_FALLBACK_EXTENSIONS = Object.freeze([
     `.out`,
     `.json`,
 ]);
-export const TRAJ_FALLBACK_EXTENSIONS_REGEX = new RegExp(`\\.(${TRAJ_FALLBACK_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`, `i`);
+export const TRAJ_FALLBACK_EXTENSIONS_REGEX = ext_regex(TRAJ_FALLBACK_EXTENSIONS);
 // Special regex patterns
-export const VASP_FILES_REGEX = /(?:^|[\\/_.-])(poscar|contcar|potcar|incar|kpoints|outcar)(?:[\\/_.-]|$)/i;
-export const VASP_VOLUMETRIC_REGEX = /(?:^|[\\/_.-])(chgcar|aeccar[012]?|elfcar|locpot|parchg)(?:[\\/_.-]|$)/i;
+export const VASP_FILES_REGEX = /(?:^|[\\/_.-])(?:poscar|contcar|potcar|incar|kpoints|outcar)(?:[\\/_.-]|$)/i;
+export const VASP_VOLUMETRIC_REGEX = /(?:^|[\\/_.-])(?:chgcar|aeccar[012]?|elfcar|locpot|parchg)(?:[\\/_.-]|$)/i;
 export const XDATCAR_REGEX = /xdatcar/i;
-export const CONFIG_DIRS_REGEX = /(?:^|[\\/])(\.vscode|\.idea|\.nyc_output|\.cache|\.tmp|\.temp|node_modules|dist|build|coverage)(?:[\\/]|$)/i;
-export const MD_SIM_EXCLUDE_REGEX = /md_simulation\.(out|txt|yml|py|csv|html|css|md|js|ts)$/i;
-export const XYZ_EXTXYZ_REGEX = /\.(xyz|extxyz)$/i;
+export const CONFIG_DIRS_REGEX = /(?:^|[\\/])(?:\.vscode|\.idea|\.nyc_output|\.cache|\.tmp|\.temp|node_modules|dist|build|coverage)(?:[\\/]|$)/i;
+export const MD_SIM_EXCLUDE_REGEX = /md_simulation\.(?:out|txt|yml|py|csv|html|css|md|js|ts)$/i;
+export const XYZ_EXTXYZ_REGEX = /\.(?:xyz|extxyz)$/i;
 // Compression extensions regex (shared across files)
-export const COMPRESSION_EXTENSIONS_REGEX = new RegExp(`\\.(${COMPRESSION_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`, `i`);
+export const COMPRESSION_EXTENSIONS_REGEX = ext_regex(COMPRESSION_EXTENSIONS);

package/dist/controls.d.ts

@@ -5,6 +5,7 @@ export type ShowControlsConfig = {
     style?: string;
 };
 export type ShowControlsProp = ControlsVisibility | ShowControlsConfig | boolean;
+export type ShowControlsState = ReturnType<typeof normalize_show_controls>;
 export declare function normalize_show_controls(prop: ShowControlsProp | undefined): {
     mode: ControlsVisibility;
     hidden: Set<string>;

package/dist/controls.js

@@ -1,6 +1,5 @@
 // Controls visibility configuration for visualization components
 // Manages visibility of control buttons in Structure, Trajectory, BrillouinZone
-// Normalize show_controls prop into consistent config with helper methods
 export function normalize_show_controls(prop) {
     // Extract mode, hidden, style from various prop forms
     let mode = `hover`;

package/dist/convex-hull/ConvexHull.svelte

@@ -8,18 +8,15 @@
   import ConvexHull3D from './ConvexHull3D.svelte'
   import ConvexHull4D from './ConvexHull4D.svelte'
   import type { BaseConvexHullProps, Hull3DProps } from './index'
-  import type { GasSpecies, GasThermodynamicsConfig } from './types'
 
   // Union type combining all possible props from 2D, 3D, and 4D components
   // each specific component will only use its relevant props from this super set
-  type ConvexHullProps = BaseConvexHullProps & Hull3DProps & {
-    x_axis?: AxisConfig
-    y_axis?: AxisConfig
-    // Gas thermodynamics config - enables atmosphere-controlled phase diagrams
-    gas_config?: GasThermodynamicsConfig
-    // Gas pressure binding - enables two-way binding for atmosphere control
-    gas_pressures?: Partial<Record<GasSpecies, number>>
-  }
+  // (gas_config/gas_pressures already come from BaseConvexHullProps)
+  type ConvexHullProps = BaseConvexHullProps &
+    Hull3DProps & {
+      x_axis?: AxisConfig
+      y_axis?: AxisConfig
+    }
 
   let {
     entries = [],
@@ -28,14 +25,13 @@
     wrapper = $bindable(),
     show_stable = $bindable(true),
     show_unstable = $bindable(true),
+    hidden_categories = $bindable([]),
     show_hull_faces = $bindable(true),
-    hull_face_opacity: hull_face_opacity_prop = $bindable(
-      undefined as number | undefined,
-    ),
+    hull_face_opacity: hull_face_opacity_prop = $bindable(undefined as number | undefined),
     color_mode = $bindable(`energy`),
     color_scale = $bindable(`interpolateViridis`),
     info_pane_open = $bindable(false),
-    legend_pane_open = $bindable(false),
+    controls_open = $bindable(false),
     max_hull_dist_show_phases = $bindable(0.1),
     max_hull_dist_show_labels = $bindable(0.1),
     show_stable_labels = $bindable(true),
@@ -87,12 +83,11 @@
     hull_face_opacity_prop = hull_face_opacity
   })
 
-  // Map element count to corresponding component
-  // Note: Type assertion needed because TypeScript can't infer that all components
-  // accept a compatible superset of props (BaseConvexHullProps + dimension-specific)
+  // Map element count to component. Deliberate cast: the wrapper passes the prop superset
+  // while each component declares only its dimension's props (2D lacks Hull3DProps, 3D/4D
+  // lack x/y_axis), so a constructor union wouldn't compile. Svelte ignores extra props.
   const ConvexHullComponent = $derived(
-    { 2: ConvexHull2D, 3: ConvexHull3D, 4: ConvexHull4D }[element_count] ??
-      null,
+    { 2: ConvexHull2D, 3: ConvexHull3D, 4: ConvexHull4D }[element_count] ?? null,
   ) as Component<ConvexHullProps> | null
 </script>
 
@@ -104,12 +99,13 @@
     bind:wrapper
     bind:show_stable
     bind:show_unstable
+    bind:hidden_categories
     bind:show_hull_faces
     bind:hull_face_opacity
     bind:color_mode
     bind:color_scale
     bind:info_pane_open
-    bind:legend_pane_open
+    bind:controls_open
     bind:max_hull_dist_show_phases
     bind:max_hull_dist_show_labels
     bind:show_stable_labels
@@ -127,14 +123,13 @@
 {:else}
   <!-- Error state for unsupported dimensionalities -->
   <div class="convex-hull-error">
-    <div
-      style="text-align: center; padding: 2em; color: var(--convex-hull-text-color, #666)"
-    >
+    <div style="text-align: center; padding: 2em; color: var(--convex-hull-text-color, #666)">
       <h3 id="unsupported-chemical-system" style="margin: 0 0 1em 0">Unsupported Chemical System</h3>
       <p style="margin: 0">
-        Convex hulls require 2, 3, or 4 elements. Found {element_count} element{
-          element_count === 1 ? `` : `s`
-        }:
+        Convex hulls require 2, 3, or 4 elements. Found {element_count} element{element_count ===
+        1
+          ? ``
+          : `s`}:
       </p>
       <p style="margin: 0.5em 0 0 0; font-weight: bold">
         {elements.join(`, `)}

package/dist/convex-hull/ConvexHull.svelte.d.ts

@@ -1,13 +1,10 @@
 import type { AxisConfig } from '../plot';
 import type { Component } from 'svelte';
 import type { BaseConvexHullProps, Hull3DProps } from './index';
-import type { GasSpecies, GasThermodynamicsConfig } from './types';
 type ConvexHullProps = BaseConvexHullProps & Hull3DProps & {
     x_axis?: AxisConfig;
     y_axis?: AxisConfig;
-    gas_config?: GasThermodynamicsConfig;
-    gas_pressures?: Partial<Record<GasSpecies, number>>;
 };
-declare const ConvexHull: Component<ConvexHullProps, {}, "temperature" | "display" | "fullscreen" | "show_hull_faces" | "hull_face_opacity" | "color_mode" | "color_scale" | "show_stable" | "show_unstable" | "show_stable_labels" | "show_unstable_labels" | "max_hull_dist_show_phases" | "max_hull_dist_show_labels" | "info_pane_open" | "legend_pane_open" | "wrapper" | "energy_source_mode" | "stable_entries" | "unstable_entries" | "phase_stats" | "highlighted_entries" | "selected_entry" | "gas_pressures">;
+declare const ConvexHull: Component<ConvexHullProps, {}, "display" | "fullscreen" | "wrapper" | "controls_open" | "color_scale" | "info_pane_open" | "temperature" | "show_hull_faces" | "hull_face_opacity" | "color_mode" | "show_stable" | "show_unstable" | "show_stable_labels" | "show_unstable_labels" | "max_hull_dist_show_phases" | "max_hull_dist_show_labels" | "hidden_categories" | "energy_source_mode" | "stable_entries" | "unstable_entries" | "phase_stats" | "highlighted_entries" | "selected_entry" | "gas_pressures">;
 type ConvexHull = ReturnType<typeof ConvexHull>;
 export default ConvexHull;