Merge pull request #35 from stan-donarise/optimade-ns

Optimade namespace
tilde-lab · Jun 17, 2024 · 6274a7e · 6274a7e
2 parents 52fe447 + d91b84b
commit 6274a7e
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Showing 35 changed files with 124 additions and 120 deletions.
diff --git a/.github/workflows/deploy-to-gh-pages.yml b/.github/workflows/deploy-to-gh-pages.yml
@@ -14,10 +14,10 @@ jobs:
 
     - uses: hyoo-ru/mam_build@master2
       with:
-        package: mpds/cifplayer
+        package: optimade/cifplayer
         modules: app
 
     - uses: JamesIves/[email protected]
       with:
         branch: gh-pages
-        folder: mpds/cifplayer/app/-
+        folder: optimade/cifplayer/app/-
diff --git a/app/app.view.css.ts b/app/app.view.css.ts
@@ -1,6 +1,6 @@
 namespace $.$$ {
 
-	$mol_style_define( $mpds_cifplayer_app, {
+	$mol_style_define( $optimade_cifplayer_app, {
 
 		contain: 'none', // otherwise in fullscreen 'fixed' positions plot relative to parent is not in the viewport
 

diff --git a/app/app.view.tree b/app/app.view.tree
@@ -1,4 +1,4 @@
-$mpds_cifplayer_app $mol_drop
+$optimade_cifplayer_app $mol_drop
 	receive? <=> drop_file? null
 	Sub <= Book $mol_book2
 		plugins /
@@ -25,7 +25,7 @@ $mpds_cifplayer_app $mol_drop
 				<= Data_text $mol_textarea
 					value? <=> data_str?
 					hint \or paste here...
-		<= Player $mpds_cifplayer_player
+		<= Player $optimade_cifplayer_player
 			data <= data_str? \
 			vibrate? => vibrate?
 			unvibrate => unvibrate

diff --git a/app/app.view.web.ts b/app/app.view.web.ts
@@ -1,5 +1,5 @@
 namespace $.$$ {
-	export class $mpds_cifplayer_app extends $.$mpds_cifplayer_app {
+	export class $optimade_cifplayer_app extends $.$optimade_cifplayer_app {
 
 		@ $mol_mem
 		pages(): readonly any[] {

diff --git a/app/index.html b/app/index.html
@@ -7,7 +7,7 @@
 		<meta name="apple-mobile-web-app-capable" content="yes">
 	</head>
 	<body mol_view_root>
-		<div mol_view_root="$mpds_cifplayer_app"></div>
+		<div mol_view_root="$optimade_cifplayer_app"></div>
 		<script src="web.js" charset="utf-8"></script>
 	</body>
 </html>
diff --git a/demo/demo.view.tree b/demo/demo.view.tree
@@ -1,10 +1,10 @@
-$mpds_cifplayer_demo $mol_book2_catalog
+$optimade_cifplayer_demo $mol_book2_catalog
 	plugins /
 		<= Theme $mol_theme_auto
 	menu_title \Demo
 	Placeholder null
 	spreads *
-		app <= App $mpds_cifplayer_app
+		app <= App $optimade_cifplayer_app
 			title \App
-		phonons <= Phonons $mpds_cifplayer_phonons
+		phonons <= Phonons $optimade_cifplayer_phonons
 			title \Phonons example
diff --git a/demo/index.html b/demo/index.html
@@ -7,7 +7,7 @@
 		<meta name="apple-mobile-web-app-capable" content="yes">
 	</head>
 	<body mol_view_root>
-		<div mol_view_root="$mpds_cifplayer_demo"></div>
+		<div mol_view_root="$optimade_cifplayer_demo"></div>
 		<script src="web.js" charset="utf-8"></script>
 	</body>
 </html>
diff --git a/lib/cif/cif.meta.tree b/lib/cif/cif.meta.tree
@@ -1 +1 @@
-require \/mpds/cifplayer/lib/cif/_cif.js
+require \/optimade/cifplayer/lib/cif/_cif.js
diff --git a/lib/cif/cif.web.ts b/lib/cif/cif.web.ts
@@ -1,10 +1,10 @@
 namespace $ {
 
-	export class $mpds_cifplayer_lib_cif extends $mol_object2 {
+	export class $optimade_cifplayer_lib_cif extends $mol_object2 {
 
 		@ $mol_mem
 		static all() {
-			return require( '../mpds/cifplayer/lib/cif/_cif.js' ) as typeof import( './_cif' )
+			return require( '../optimade/cifplayer/lib/cif/_cif.js' ) as typeof import( './_cif' )
 		}
 
 		@ $mol_mem

diff --git a/lib/math/math.meta.tree b/lib/math/math.meta.tree
@@ -1 +1 @@
-require \/mpds/cifplayer/lib/math/_math.js
+require \/optimade/cifplayer/lib/math/_math.js
diff --git a/lib/math/math.web.ts b/lib/math/math.web.ts
@@ -1,5 +1,5 @@
 namespace $ {
 
-	export const $mpds_cifplayer_lib_math = require( '../mpds/cifplayer/lib/math/_math.js' ) //as typeof import( './build/_math' )
+	export const $optimade_cifplayer_lib_math = require( '../optimade/cifplayer/lib/math/_math.js' ) //as typeof import( './build/_math' )
 
 }
diff --git a/lib/spacegroups/spacegroups.meta.tree b/lib/spacegroups/spacegroups.meta.tree
@@ -1 +1 @@
-require \/mpds/cifplayer/lib/spacegroups/_spacegroups.js
+require \/optimade/cifplayer/lib/spacegroups/_spacegroups.js
diff --git a/lib/spacegroups/spacegroups.web.ts b/lib/spacegroups/spacegroups.web.ts
@@ -1,6 +1,6 @@
 namespace $ {
 
-	export const $mpds_cifplayer_lib_spacegroups = require( '../mpds/cifplayer/lib/spacegroups/_spacegroups.js' ) as typeof import( './_spacegroups' )
-	export type $mpds_cifplayer_lib_spacegroups_info = import( './_spacegroups' ).SpaceGroupInfo
+	export const $optimade_cifplayer_lib_spacegroups = require( '../optimade/cifplayer/lib/spacegroups/_spacegroups.js' ) as typeof import( './_spacegroups' )
+	export type $optimade_cifplayer_lib_spacegroups_info = import( './_spacegroups' ).SpaceGroupInfo
 
 }
diff --git a/lib/three/three.meta.tree b/lib/three/three.meta.tree
@@ -1 +1 @@
-require \/mpds/cifplayer/lib/three/_three.js
+require \/optimade/cifplayer/lib/three/_three.js
diff --git a/lib/three/three.web.ts b/lib/three/three.web.ts
@@ -1,5 +1,5 @@
 namespace $ {
 
-	export const $mpds_cifplayer_lib_three = require( '../mpds/cifplayer/lib/three/_three.js' ) as typeof import( './_three' )
+	export const $optimade_cifplayer_lib_three = require( '../optimade/cifplayer/lib/three/_three.js' ) as typeof import( './_three' )
 
 }
diff --git a/lib/three/view/view.view.css.ts b/lib/three/view/view.view.css.ts
@@ -1,6 +1,6 @@
 namespace $.$$ {
 
-	$mol_style_define( $mpds_cifplayer_lib_three_view, {
+	$mol_style_define( $optimade_cifplayer_lib_three_view, {
 
 		flex: {
 			grow: 1,

diff --git a/lib/three/view/view.view.tree b/lib/three/view/view.view.tree
@@ -1,4 +1,4 @@
-$mpds_cifplayer_lib_three_view $mol_view
+$optimade_cifplayer_lib_three_view $mol_view
 	sub /
 		<= canvas null
 	scene null

diff --git a/lib/three/view/view.view.web.ts b/lib/three/view/view.view.web.ts
@@ -1,9 +1,9 @@
 namespace $.$$ {
 
-	const THREE = $mpds_cifplayer_lib_three
+	const THREE = $optimade_cifplayer_lib_three
 	type THREE = typeof THREE
 
-	export class $mpds_cifplayer_lib_three_view extends $.$mpds_cifplayer_lib_three_view {
+	export class $optimade_cifplayer_lib_three_view extends $.$optimade_cifplayer_lib_three_view {
 
 		@ $mol_mem
 		start_render_loop() {
@@ -40,7 +40,7 @@ namespace $.$$ {
 		}
 
 		remove_object( obj: any ) {
-			$mpds_cifplayer_lib_three_view_dispose_deep( obj )
+			$optimade_cifplayer_lib_three_view_dispose_deep( obj )
 			this.scene()?.remove( obj )
 		}
 
@@ -125,7 +125,7 @@ namespace $.$$ {
 		}
 
 		destructor(): void {
-			$mpds_cifplayer_lib_three_view_dispose_deep( this.scene() )
+			$optimade_cifplayer_lib_three_view_dispose_deep( this.scene() )
 			this.renderer()?.dispose()
 		}
 
@@ -138,7 +138,7 @@ namespace $.$$ {
 	 * @param object  Object3D, BufferGeometry, Material or Texture
 	 * @param disposeMedia If set to true will dispose of the texture image or video element, default false
 	 */
-	export function $mpds_cifplayer_lib_three_view_dispose_deep(
+	export function $optimade_cifplayer_lib_three_view_dispose_deep(
 		object: InstanceType< THREE["Object3D"] > | InstanceType< THREE["BufferGeometry"] > | InstanceType< THREE["Material"] > | InstanceType< THREE["Texture"] >
 	) {
 		const dispose = ( object: InstanceType< THREE["BufferGeometry"] > | InstanceType< THREE["Material"] > | InstanceType< THREE["Texture"] > ) => {

diff --git a/lib/tween/tween.meta.tree b/lib/tween/tween.meta.tree
@@ -1 +1 @@
-require \/mpds/cifplayer/lib/tween/_tween.js
+require \/optimade/cifplayer/lib/tween/_tween.js
diff --git a/lib/tween/tween.web.ts b/lib/tween/tween.web.ts
@@ -1,5 +1,5 @@
 namespace $ {
 
-	export const $mpds_cifplayer_lib_tween = require( '../mpds/cifplayer/lib/tween/_tween.js' ) as typeof import( './_tween' )
+	export const $optimade_cifplayer_lib_tween = require( '../optimade/cifplayer/lib/tween/_tween.js' ) as typeof import( './_tween' )
 
 }
diff --git a/matinfio/cell/cell.ts b/matinfio/cell/cell.ts
@@ -1,12 +1,12 @@
 namespace $ {
 
-	const math = $mpds_cifplayer_lib_math
+	const math = $optimade_cifplayer_lib_math
 
 	function unit( vec: number[] ): number[] {
 		return math.divide( vec, math.norm( vec ) )
 	}
 
-	export type $mpds_cifplayer_matinfio_cell = {
+	export type $optimade_cifplayer_matinfio_cell = {
 		a: number,
 		b: number,
 		c: number,
@@ -16,7 +16,7 @@ namespace $ {
 	}
 
 	/** Crystalline cell parameters to 3x3 matrix */
-	export function $mpds_cifplayer_matinfio_cell_to_matrix( this : $, cell: $mpds_cifplayer_matinfio_cell ): number[][] {
+	export function $optimade_cifplayer_matinfio_cell_to_matrix( this : $, cell: $optimade_cifplayer_matinfio_cell ): number[][] {
 		const { a, b, c, alpha, beta, gamma } = cell
 		if( !a || !b || !c || !alpha || !beta || !gamma ) {
 			return this.$mol_fail( new $mol_data_error('Error: invalid cell definition') )
@@ -43,7 +43,7 @@ namespace $ {
 	}
 
 	/** 3x3 matrix to crystalline cell parameters */
-	export function $mpds_cifplayer_matinfio_cell_params_from_matrix( matrix: number[][] ) {
+	export function $optimade_cifplayer_matinfio_cell_params_from_matrix( matrix: number[][] ) {
 		const norms: number[] = matrix.map( vec => math.norm( vec ) )
 		const angles = []
 		let j = -1

diff --git a/matinfio/cif/cif.ts b/matinfio/cif/cif.ts
@@ -1,13 +1,13 @@
 namespace $ {
 
-	const math = $mpds_cifplayer_lib_math
+	const math = $optimade_cifplayer_lib_math
 
-	export function $mpds_cifplayer_matinfio_cif_to_obj( this: $, str: string ): $mpds_cifplayer_matinfio_internal_obj {
+	export function $optimade_cifplayer_matinfio_cif_to_obj( this: $, str: string ): $optimade_cifplayer_matinfio_internal_obj {
 		const structures = []
 		let symops = []
 		let atprop_seq: any[] = []
 		let lines = str.toString().replace( /(\r\n|\r)/gm, "\n" ).split( "\n" )
-		let cur_structure: any | $mpds_cifplayer_matinfio_internal_obj = {
+		let cur_structure: any | $optimade_cifplayer_matinfio_internal_obj = {
 			cell: {},
 			atoms: [],
 			cartesian: false,
@@ -45,7 +45,7 @@ namespace $ {
 		const chem_element_idxs = [ 0, 1 ]
 		let overlayed_idxs = []
 
-		for( let oprop in $mpds_cifplayer_matinfio_custom_atom_loop_props ) {
+		for( let oprop in $optimade_cifplayer_matinfio_custom_atom_loop_props ) {
 			overlayed_idxs.push( loop_vals.length )
 			loop_vals.push( oprop )
 		}
@@ -127,7 +127,7 @@ namespace $ {
 					}
 					line_data = cur_line.replace( /\t/g, " " ).split( " " ).filter( function( o ) { return o ? true : false } )
 
-					const atom: any | $mpds_cifplayer_matinfio_internal_obj_atom = { overlays: {} }
+					const atom: any | $optimade_cifplayer_matinfio_internal_obj_atom = { overlays: {} }
 
 					for( let j = 0; j < atprop_seq.length; j++ ) { // TODO handle in-loop mismatch
 						const atom_index = loop_vals.indexOf( atprop_seq[ j ] )
@@ -148,7 +148,7 @@ namespace $ {
 							atom.overlays.label = atom.label
 							if( !atom.symbol ) atom.symbol = atom.label.replace( /[0-9]/g, '' )
 						}
-						if( !( $mpds_cifplayer_matinfio_chemical_elements.JmolColors as any )[ atom.symbol ]
+						if( !( $optimade_cifplayer_matinfio_chemical_elements.JmolColors as any )[ atom.symbol ]
 							&& atom.symbol
 							&& atom.symbol.length > 1
 						) {
@@ -187,18 +187,18 @@ namespace $ {
 
 
 	/** Convert internal repr into CIF */
-	export function $mpds_cifplayer_matinfio_cif_from_obj( this: $, crystal: any ) {
+	export function $optimade_cifplayer_matinfio_cif_from_obj( this: $, crystal: any ) {
 
 		let cif_str = "data_matinfio\n"
 		let cell_abc
 		let cell_mat
 
 		if( Object.keys( crystal.cell ).length == 6 ) {
 			cell_abc = crystal.cell
-			cell_mat = this.$mpds_cifplayer_matinfio_cell_to_matrix( crystal.cell )
+			cell_mat = this.$optimade_cifplayer_matinfio_cell_to_matrix( crystal.cell )
 			// cell_mat = this.cell2vec( ...( crystal.cell as [ number, number, number, number, number, number ] ) )
 		} else {
-			cell_abc = $mpds_cifplayer_matinfio_cell_params_from_matrix( crystal.cell )
+			cell_abc = $optimade_cifplayer_matinfio_cell_params_from_matrix( crystal.cell )
 			cell_mat = crystal.cell
 		}
 		cif_str += "_cell_length_a    " + cell_abc[ 0 ].toFixed( 6 ) + "\n"

diff --git a/matinfio/flatten/flatten.web.ts b/matinfio/flatten/flatten.web.ts
@@ -1,11 +1,11 @@
 namespace $ {
 
 	/** Convert internal repr into a flattened C-alike structure */
-	export function $mpds_cifplayer_matinfio_flatten_from_obj( this: $, crystal: any ) {
-		if( crystal.symops ) this.$mpds_cifplayer_matinfio_log.warning( "Reading of symmetry operations is not implemented, expect errors" )
+	export function $optimade_cifplayer_matinfio_flatten_from_obj( this: $, crystal: any ) {
+		if( crystal.symops ) this.$optimade_cifplayer_matinfio_log.warning( "Reading of symmetry operations is not implemented, expect errors" )
 
 		const cell = Object.keys( crystal.cell ).length == 6
-			? this.$mpds_cifplayer_matinfio_cell_to_matrix( crystal.cell ) // for CIF
+			? this.$optimade_cifplayer_matinfio_cell_to_matrix( crystal.cell ) // for CIF
 			: crystal.cell // for POSCAR
 
 		const xyzatoms = []