matterviz 0.3.6 → 0.4.0

package/dist/src/lib/constants.ts

@@ -1,134 +0,0 @@
-// Shared keyword constants for file type detection across the codebase
-
-// compression formats and their file extensions
-export const COMPRESSION_FORMATS = {
-  gzip: [`.gz`, `.gzip`] as const,
-  deflate: [`.deflate`] as const,
-  'deflate-raw': [`.z`] as const,
-  zip: [`.zip`] as const, // Browser DecompressionStream doesn't support ZIP
-  xz: [`.xz`] as const, // Browser DecompressionStream doesn't support XZ
-  bz2: [`.bz2`] as const, // Browser DecompressionStream doesn't support BZ2
-} as const satisfies Record<string, readonly string[]>
-
-// All detectable compression extensions
-export const COMPRESSION_EXTENSIONS = Object.freeze(
-  Object.values(COMPRESSION_FORMATS).flat(),
-) as readonly string[]
-
-// Keywords that indicate a file is likely a trajectory file
-export const TRAJ_KEYWORDS = Object.freeze([
-  `trajectory`,
-  `traj`,
-  `relax`,
-  `npt`,
-  `nvt`,
-  `nve`,
-  `qha`,
-  `md`,
-  `dynamics`,
-  `simulation`,
-])
-
-// Keywords that indicate a file is likely a structure file
-export const STRUCT_KEYWORDS = Object.freeze([
-  `structure`,
-  `phono`,
-  `vasp`,
-  `crystal`,
-  `material`,
-  `lattice`,
-  `geometry`,
-  `unit_cell`,
-  `unitcell`,
-  `atoms`,
-  `sites`,
-  `data`,
-  `phono3py`,
-  `phonopy`,
-])
-
-// More restrictive keywords for JSON/YAML files (excludes generic terms like "data")
-export const STRUCT_KEYWORDS_STRICT = Object.freeze([
-  `structure`,
-  `phono`,
-  `vasp`,
-  `crystal`,
-  `material`,
-  `lattice`,
-  `geometry`,
-  `unit_cell`,
-  `unitcell`,
-  `atoms`,
-  `sites`,
-  `phono3py`,
-  `phonopy`,
-])
-
-// Regex patterns for keyword matching
-export const TRAJ_KEYWORDS_REGEX = new RegExp(
-  `(^|[-_.])(${TRAJ_KEYWORDS.join(`|`)})([-_.]|$)`,
-  `i`,
-)
-
-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(`(${TRAJ_KEYWORDS.join(`|`)})`, `i`)
-
-// File extensions for different file types
-export const TRAJ_EXTENSIONS = Object.freeze([`.traj`, `.xtc`, `.lammpstrj`])
-export const TRAJ_EXTENSIONS_REGEX = new RegExp(
-  `\\.(${TRAJ_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`,
-  `i`,
-)
-export const STRUCTURE_EXTENSIONS = Object.freeze([
-  `.cif`,
-  `.mcif`,
-  `.poscar`,
-  `.vasp`,
-  `.cube`,
-  `.lmp`,
-  `.data`,
-  `.dump`,
-  `.pdb`,
-  `.mol`,
-  `.mol2`,
-  `.sdf`,
-  `.mmcif`,
-])
-export const STRUCTURE_EXTENSIONS_REGEX = new RegExp(
-  `\\.(${STRUCTURE_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`,
-  `i`,
-)
-export const TRAJ_FALLBACK_EXTENSIONS = Object.freeze([
-  `.dat`,
-  `.data`,
-  `.log`,
-  `.out`,
-  `.json`,
-])
-export const TRAJ_FALLBACK_EXTENSIONS_REGEX = new RegExp(
-  `\\.(${TRAJ_FALLBACK_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`,
-  `i`,
-)
-
-// Special regex patterns
-export const VASP_FILES_REGEX =
-  /(?:^|[\\/_.-])(poscar|contcar|potcar|incar|kpoints|outcar)(?:[\\/_.-]|$)/i
-export const VASP_VOLUMETRIC_REGEX =
-  /(?:^|[\\/_.-])(chgcar|aeccar[012]?|elfcar|locpot|parchg)(?:[\\/_.-]|$)/i
-export const XDATCAR_REGEX = /xdatcar/i
-export const CONFIG_DIRS_REGEX =
-  /(?:^|[\\/])(\.vscode|\.idea|\.nyc_output|\.cache|\.tmp|\.temp|node_modules|dist|build|coverage)(?:[\\/]|$)/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
-
-// Compression extensions regex (shared across files)
-export const COMPRESSION_EXTENSIONS_REGEX = new RegExp(
-  `\\.(${COMPRESSION_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`,
-  `i`,
-)

package/dist/src/lib/controls.ts

@@ -1,42 +0,0 @@
-// Controls visibility configuration for visualization components
-// Manages visibility of control buttons in Structure, Trajectory, BrillouinZone
-
-export type ControlsVisibility = `always` | `hover` | `never`
-
-export type ShowControlsConfig = {
-  mode?: ControlsVisibility
-  hidden?: string[]
-  style?: string
-}
-
-// Prop type: boolean shorthand, mode string, or full config
-export type ShowControlsProp = ControlsVisibility | ShowControlsConfig | boolean
-
-// Normalize show_controls prop into consistent config with helper methods
-export function normalize_show_controls(prop: ShowControlsProp | undefined) {
-  // Extract mode, hidden, style from various prop forms
-  let mode: ControlsVisibility = `hover`
-  let hidden_arr: string[] | undefined
-  let style: string | undefined
-
-  if (typeof prop === `boolean`) {
-    mode = prop ? `always` : `never`
-  } else if (typeof prop === `string`) {
-    mode = prop
-  } else if (prop) {
-    mode = prop.mode ?? `hover`
-    hidden_arr = prop.hidden
-    style = prop.style
-  }
-
-  const hidden = new Set(hidden_arr)
-  return {
-    mode,
-    hidden,
-    style,
-    // Helper: check if a control should be visible
-    visible: (name: string) => !hidden.has(name),
-    // CSS class for visibility mode
-    class: mode === `never` ? `` : `${mode}-visible`,
-  }
-}

package/dist/src/lib/convex-hull/ConvexHull.svelte

@@ -1,157 +0,0 @@
-<script lang="ts">
-  import { extract_formula_elements } from '$lib/composition/parse'
-  import type { AxisConfig } from '$lib/plot'
-  import { DEFAULTS } from '$lib/settings'
-  import type { Component } from 'svelte'
-  import { SvelteSet } from 'svelte/reactivity'
-  import ConvexHull2D from './ConvexHull2D.svelte'
-  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>>
-  }
-
-  let {
-    entries = [],
-    // bindable props not part of rest because Svelte 5 doesn't support spreading bindable props.
-    fullscreen = $bindable(false),
-    wrapper = $bindable(),
-    show_stable = $bindable(true),
-    show_unstable = $bindable(true),
-    show_hull_faces = $bindable(true),
-    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),
-    max_hull_dist_show_phases = $bindable(0.1),
-    max_hull_dist_show_labels = $bindable(0.1),
-    show_stable_labels = $bindable(true),
-    show_unstable_labels = $bindable(false),
-    energy_source_mode = $bindable(`precomputed`),
-    phase_stats = $bindable(null),
-    display = $bindable({ x_grid: false, y_grid: false }),
-    stable_entries = $bindable([]),
-    unstable_entries = $bindable([]),
-    highlighted_entries = $bindable([]),
-    selected_entry = $bindable(null),
-    temperature = $bindable(),
-    gas_pressures = $bindable({}),
-    ...rest
-  }: ConvexHullProps = $props()
-
-  // Lightweight element extraction - count unique elements, stripping oxidation states
-  // (e.g. "V4+" -> "V") to avoid counting the same element multiple times
-  function extract_unique_elements(
-    hull_entries: { composition: Record<string, number> }[],
-  ): string[] {
-    const elements = new SvelteSet<string>()
-    for (const entry of hull_entries) {
-      for (const key of Object.keys(entry.composition)) {
-        // Extract valid element symbols, stripping oxidation states
-        for (const elem of extract_formula_elements(key, { unique: false })) {
-          elements.add(elem)
-        }
-      }
-    }
-    return Array.from(elements).toSorted()
-  }
-
-  // Detect dimensionality by counting unique elements (lightweight operation)
-  const elements = $derived(extract_unique_elements(entries))
-  const element_count = $derived(elements.length)
-
-  // Resolve hull face opacity: use caller's value if provided,
-  // otherwise pick the right default for the dimensionality (ternary=30%, quaternary=3%).
-  // Use writable derived so child bind updates can sync back to parent.
-  const default_opacity = $derived(
-    element_count === 4
-      ? DEFAULTS.convex_hull.quaternary.hull_face_opacity
-      : DEFAULTS.convex_hull.ternary.hull_face_opacity,
-  )
-  let hull_face_opacity = $derived(hull_face_opacity_prop ?? default_opacity)
-  $effect(() => {
-    if (hull_face_opacity_prop === hull_face_opacity) return
-    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)
-  const ConvexHullComponent = $derived(
-    { 2: ConvexHull2D, 3: ConvexHull3D, 4: ConvexHull4D }[element_count] ??
-      null,
-  ) as Component<ConvexHullProps> | null
-</script>
-
-{#if ConvexHullComponent}
-  <ConvexHullComponent
-    {entries}
-    {...rest}
-    bind:fullscreen
-    bind:wrapper
-    bind:show_stable
-    bind:show_unstable
-    bind:show_hull_faces
-    bind:hull_face_opacity
-    bind:color_mode
-    bind:color_scale
-    bind:info_pane_open
-    bind:legend_pane_open
-    bind:max_hull_dist_show_phases
-    bind:max_hull_dist_show_labels
-    bind:show_stable_labels
-    bind:show_unstable_labels
-    bind:energy_source_mode
-    bind:phase_stats
-    bind:display
-    bind:stable_entries
-    bind:unstable_entries
-    bind:highlighted_entries
-    bind:selected_entry
-    bind:temperature
-    bind:gas_pressures
-  />
-{: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)"
-    >
-      <h3 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`
-        }:
-      </p>
-      <p style="margin: 0.5em 0 0 0; font-weight: bold">
-        {elements.join(`, `)}
-      </p>
-    </div>
-  </div>
-{/if}
-
-<style>
-  .convex-hull-error {
-    display: flex;
-    align-items: center;
-    justify-content: center;
-    box-sizing: border-box;
-    height: var(--convex-hull-height, 500px);
-    border: 1px solid var(--convex-hull-border-color, #ccc);
-    border-radius: var(--border-radius, 3pt);
-    background: var(--convex-hull-bg, transparent);
-  }
-</style>