Fixed nasty problem with z axis range set to null

lab-cosmo · Nov 6, 2024 · 21ddf7a · 21ddf7a
1 parent dcb7fd2
commit 21ddf7a
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Showing 5 changed files with 23 additions and 19 deletions.
diff --git a/python/chemiscope/jupyter.py b/python/chemiscope/jupyter.py
@@ -277,7 +277,6 @@ def show(
         # and error is only visible in the console
         if len(dict_input["properties"]) < 2:
             raise ValueError("Need at least two properties to visualize a map widget")
-
     return widget_class(dict_input, has_metadata=has_metadata)
 
 

diff --git a/python/jupyter/src/widget.ts b/python/jupyter/src/widget.ts
@@ -39,7 +39,7 @@ class ChemiscopeBaseView extends DOMWidgetView {
                 }
 
                 const settings = this.model.get('settings') as Partial<Settings>;
-
+                
                 // ignore pinned setting in jupyter, otherwise the pinned is changed
                 // by JS and then overwritten the first time by Python
                 delete settings.pinned;
@@ -51,7 +51,7 @@ class ChemiscopeBaseView extends DOMWidgetView {
     }
 
     protected _updatePythonSettings(): void {
-        if (this.visualizer !== undefined) {
+        if (this.visualizer !== undefined) {            
             const settings = this.visualizer.saveSettings();
             // ignore pinned setting in jupyter, otherwise the pinned is changed
             // by JS and then overwritten the first time by Python

diff --git a/src/map/options.ts b/src/map/options.ts
@@ -99,17 +99,17 @@ export class MapOptions extends OptionsGroup {
         super();
 
         // Setup axes
-        const propertiesName = Object.keys(properties);
-        if (propertiesName.length < 2) {
+        const propertiesNames = Object.keys(properties);
+        if (propertiesNames.length < 2) {
             throw new Error(
                 'Cannot show a map because the dataset contains fewer than two properties.'
             );
         }
-        this.x = new AxisOptions(propertiesName);
-        this.y = new AxisOptions(propertiesName);
+        this.x = new AxisOptions(propertiesNames);
+        this.y = new AxisOptions(propertiesNames);
         // For z and color '' is a valid value
-        this.z = new AxisOptions(propertiesName.concat(['']));
-
+        this.z = new AxisOptions(propertiesNames.concat(['']));
+        console.log('initialized z as', this.z);
         // Initialise symbol
         this.symbol = new HTMLOption('string', '');
         const validSymbols = [''];
@@ -131,7 +131,7 @@ export class MapOptions extends OptionsGroup {
             min: new HTMLOption('number', NaN),
             max: new HTMLOption('number', NaN),
         };
-        this.color.property.validate = optionValidator(propertiesName.concat(['']), 'color');
+        this.color.property.validate = optionValidator(propertiesNames.concat(['']), 'color');
         this.color.mode.validate = optionValidator(['linear', 'log', 'sqrt', 'inverse'], 'mode');
 
         // Initialise size
@@ -140,7 +140,7 @@ export class MapOptions extends OptionsGroup {
             mode: new HTMLOption('string', 'linear'),
             property: new HTMLOption('string', ''),
         };
-        this.size.property.validate = optionValidator(propertiesName.concat(['']), 'size');
+        this.size.property.validate = optionValidator(propertiesNames.concat(['']), 'size');
         this.size.factor.validate = (value) => {
             if (value < 1 || value > 100) {
                 throw Error(`size factor must be between 0 and 100, got ${value}`);
@@ -156,11 +156,11 @@ export class MapOptions extends OptionsGroup {
         this.joinPoints = new HTMLOption('boolean', false);
 
         // Setup default values
-        this.x.property.value = propertiesName[0];
-        this.y.property.value = propertiesName[1];
+        this.x.property.value = propertiesNames[0];
+        this.y.property.value = propertiesNames[1];
         this.z.property.value = '';
-        if (propertiesName.length > 2) {
-            this.color.property.value = propertiesName[2];
+        if (propertiesNames.length > 2) {
+            this.color.property.value = propertiesNames[2];
         } else {
             this.color.property.value = '';
         }

diff --git a/src/options.ts b/src/options.ts
@@ -357,7 +357,6 @@ export abstract class OptionsGroup {
     public applySettings(settings: Settings): void {
         // make a copy of the settings since we will be changing it below
         const copy = JSON.parse(JSON.stringify(settings)) as Settings;
-
         this.foreachOption((keys, option) => {
             /* eslint-disable */
             assert(keys.length >= 1);
@@ -374,10 +373,14 @@ export abstract class OptionsGroup {
             const lastKey = keys[keys.length - 1];
 
             if (lastKey in root) {
-                const value = root[lastKey];
+                var value = root[lastKey];
 
+                // convert null values for numeric options to NaN (useful for axis range)
+                if (typeof option.value === 'number' && value === null) {
+                    value = NaN;
+                }
                 // send warning if the value is invalid and omit applying it
-                if (value === undefined || value === null || Number.isNaN(value)) {
+                if (value === undefined || value === null) {
                     sendWarning(`ignored setting '${lastKey}' with invalid value '${value}'`);
                     return;
                 }

diff --git a/src/structure/viewer.ts b/src/structure/viewer.ts
@@ -587,7 +587,9 @@ export class MoleculeViewer {
             return;
         }
 
-        const active = this._environments.filter((e) => e !== undefined).map((e) => e.center);
+        const active = this._environments
+            .filter((e): e is Environment => e !== undefined)
+            .map((e) => e.center);
 
         // resets clickable and hoverable state interactions
         for (const atom of this._viewer.selectedAtoms({})) {