@haniffalab/cherita-react 1.4.1 → 1.4.2

package/dist/esm/utils/zarrData.js

@@ -1,10 +1,11 @@
-import { useMemo } from "react";
-import _ from "lodash";
-import { slice } from "zarr";
-import { OBS_TYPES } from "../constants/constants";
-import { useDataset } from "../context/DatasetContext";
-import { useSettings } from "../context/SettingsContext";
-import { GET_OPTIONS, useZarr, useMultipleZarr } from "../helpers/zarr-helper";
+import { useMemo } from 'react';
+import _ from 'lodash';
+import { slice } from 'zarr';
+import { useSelectedObs, useSelectedVar } from './Resolver';
+import { OBS_TYPES } from '../constants/constants';
+import { useDataset } from '../context/DatasetContext';
+import { useSettings } from '../context/SettingsContext';
+import { GET_OPTIONS, useZarr, useMultipleZarr } from '../helpers/zarr-helper';
 
 // @TODO: support specifying slice to load from context
 export const useObsmData = function () {
@@ -14,7 +15,7 @@ export const useObsmData = function () {
   obsm = obsm || settings.selectedObsm;
   const obsmParams = useMemo(() => ({
     url: dataset.url,
-    path: "obsm/" + obsm,
+    path: 'obsm/' + obsm,
     s: [null, slice(null, 2)] // load only [:, :2]
   }), [dataset.url, obsm]);
   return useZarr(obsmParams, GET_OPTIONS, {
@@ -32,21 +33,18 @@ const meanData = (_i, data) => {
 export const useXData = function () {
   let agg = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : meanData;
   const dataset = useDataset();
-  const settings = useSettings();
-  const xParams = useMemo(() => {
-    var _settings$selectedVar, _settings$selectedVar2, _settings$selectedVar3;
-    return !settings.selectedVar ? [] : !((_settings$selectedVar = settings.selectedVar) !== null && _settings$selectedVar !== void 0 && _settings$selectedVar.isSet) ? [{
+  const selectedVar = useSelectedVar();
+  const xParams = useMemo(() => !selectedVar ? [] : !(selectedVar !== null && selectedVar !== void 0 && selectedVar.isSet) ? [{
+    url: dataset.url,
+    path: 'X',
+    s: [null, selectedVar === null || selectedVar === void 0 ? void 0 : selectedVar.matrix_index]
+  }] : _.map(selectedVar === null || selectedVar === void 0 ? void 0 : selectedVar.vars, v => {
+    return {
       url: dataset.url,
-      path: "X",
-      s: [null, (_settings$selectedVar2 = settings.selectedVar) === null || _settings$selectedVar2 === void 0 ? void 0 : _settings$selectedVar2.matrix_index]
-    }] : _.map((_settings$selectedVar3 = settings.selectedVar) === null || _settings$selectedVar3 === void 0 ? void 0 : _settings$selectedVar3.vars, v => {
-      return {
-        url: dataset.url,
-        path: "X",
-        s: [null, v.matrix_index]
-      };
-    });
-  }, [dataset.url, settings.selectedVar]);
+      path: 'X',
+      s: [null, v.matrix_index]
+    };
+  }), [dataset.url, selectedVar]);
   return useMultipleZarr(xParams, GET_OPTIONS, {
     enabled: !!xParams.length
   }, agg);
@@ -55,13 +53,13 @@ export const useObsData = function () {
   var _obs3, _obs4;
   let obs = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
   const dataset = useDataset();
-  const settings = useSettings();
-  obs = obs || settings.selectedObs;
+  const selectedObs = useSelectedObs();
+  obs = obs || selectedObs;
   const obsParams = useMemo(() => {
     var _obs, _obs2;
     return {
       url: dataset.url,
-      path: "obs/" + ((_obs = obs) === null || _obs === void 0 ? void 0 : _obs.name) + (((_obs2 = obs) === null || _obs2 === void 0 ? void 0 : _obs2.type) === OBS_TYPES.CATEGORICAL ? "/codes" : "")
+      path: 'obs/' + ((_obs = obs) === null || _obs === void 0 ? void 0 : _obs.name) + (((_obs2 = obs) === null || _obs2 === void 0 ? void 0 : _obs2.type) === OBS_TYPES.CATEGORICAL ? '/codes' : '')
     };
   }, [dataset.url, (_obs3 = obs) === null || _obs3 === void 0 ? void 0 : _obs3.name, (_obs4 = obs) === null || _obs4 === void 0 ? void 0 : _obs4.type]);
   return useZarr(obsParams, GET_OPTIONS, {
@@ -71,13 +69,14 @@ export const useObsData = function () {
 export const useLabelObsData = () => {
   const dataset = useDataset();
   const settings = useSettings();
-  const labelObsParams = useMemo(() => _.map(settings.labelObs, obs => {
+  const labelObsParams = useMemo(() => _.map(settings.labelObs, obsName => {
+    const obs = settings.data.obs[obsName] || null;
     return {
       url: dataset.url,
-      path: "obs/" + obs.name + (obs.type === OBS_TYPES.CATEGORICAL ? "/codes" : ""),
+      path: 'obs/' + obs.name + (obs.type === OBS_TYPES.CATEGORICAL ? '/codes' : ''),
       key: obs.name
     };
-  }), [dataset.url, settings.labelObs]);
+  }), [dataset.url, settings.data.obs, settings.labelObs]);
   return useMultipleZarr(labelObsParams, GET_OPTIONS, {
     enabled: !!labelObsParams.length
   });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@haniffalab/cherita-react",
-  "version": "1.4.1",
+  "version": "1.4.2",
   "author": "Haniffa Lab",
   "license": "MIT",
   "keywords": [
@@ -64,6 +64,12 @@
     "@babel/plugin-proposal-private-property-in-object": "^7.21.11",
     "@babel/preset-env": "^7.22.5",
     "@babel/preset-react": "^7.22.5",
+    "@semantic-release/changelog": "^6.0.3",
+    "@semantic-release/commit-analyzer": "^13.0.1",
+    "@semantic-release/git": "^10.0.1",
+    "@semantic-release/github": "^11.0.6",
+    "@semantic-release/npm": "^12.0.2",
+    "@semantic-release/release-notes-generator": "^14.1.0",
     "@testing-library/dom": "^10.4.0",
     "@testing-library/jest-dom": "^6.6.3",
     "@testing-library/react": "^16.2.0",
@@ -71,19 +77,24 @@
     "babel-plugin-transform-define": "^2.1.4",
     "cpx": "^1.5.0",
     "eslint": "^8.57.1",
-    "eslint-config-prettier": "^8.10.0",
+    "eslint-config-prettier": "^8.10.2",
     "eslint-config-react-app": "^7.0.1",
-    "eslint-plugin-import": "^2.29.1",
-    "eslint-plugin-prettier": "^5.2.3",
+    "eslint-import-resolver-alias": "^1.1.2",
+    "eslint-plugin-import": "^2.32.0",
+    "eslint-plugin-prettier": "^5.5.4",
+    "eslint-plugin-react": "^7.37.5",
+    "eslint-plugin-unused-imports": "^4.3.0",
     "jest": "^29.7.0",
     "jest-environment-jsdom": "^29.7.0",
-    "prettier": "^3.5.3",
+    "prettier": "^3.6.2",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
     "sass": "1.77.6",
+    "semantic-release": "^24.2.9",
     "stylelint": "^16.10.0",
     "stylelint-config-prettier": "^9.0.5",
-    "stylelint-config-standard-scss": "^13.1.0"
+    "stylelint-config-standard-scss": "^13.1.0",
+    "stylelint-prettier": "^5.0.3"
   },
   "scripts": {
     "build:esm": "babel src/lib --out-dir dist/esm --copy-files --env-name esm",
@@ -93,7 +104,7 @@
     "copy:scss": "cpx 'src/scss/**/*' 'scss'",
     "copy:assets": "cpx 'src/assets/**/*' 'dist/assets'",
     "build": "npm run build:babel && npm run build:scss && npm run copy:scss && npm run copy:assets",
-    "test": "jest --watchAll",
+    "test": "jest",
     "test:ci": "jest --coverage --ci --no-watch",
     "lint:scss": "stylelint 'src/**/*.scss' --fix",
     "lint:js": "eslint 'src/**/*.js' --fix",

package/scss/cherita-bootstrap.scss

@@ -1,2 +1,2 @@
-@use "bootstrap/scss/bootstrap";
-@import "cherita";
+@use 'bootstrap/scss/bootstrap';
+@import 'cherita';

package/scss/cherita.scss

@@ -1,12 +1,12 @@
 // Define $prefix only if it hasn't been set already
-$prefix: "bs-" !default;
+$prefix: 'bs-' !default;
 
-@import "components/accordions";
-@import "components/lists";
-@import "components/layouts";
-@import "components/plotly";
-@import "components/plots";
-@import "components/scrollbars";
+@import 'components/accordions';
+@import 'components/lists';
+@import 'components/layouts';
+@import 'components/plotly';
+@import 'components/plots';
+@import 'components/scrollbars';
 
 .loading-spinner {
   @extend .bg-light;
@@ -119,6 +119,7 @@ $prefix: "bs-" !default;
   white-space: nowrap;
   text-overflow: ellipsis;
   pointer-events: auto;
+
   .legend-text {
     overflow: hidden;
     text-overflow: ellipsis;
@@ -128,7 +129,7 @@ $prefix: "bs-" !default;
   }
 }
 
-@media (max-width: 600px) {
+@media (width <= 600px) {
   .cherita-spatial-footer {
     flex-direction: column;
     align-items: center;
@@ -232,13 +233,14 @@ $prefix: "bs-" !default;
 }
 
 .value-count-badge {
-  color: #000000 !important;
+  color: #000 !important;
   background-color: #dedede !important;
   font-weight: lighter;
 }
 
 .filtered-value-count-badge {
-  color: #ffffff !important;
+  color: #fff !important;
+
   // background-color: $alt-color !important;
   font-weight: normal;
 }
@@ -269,28 +271,32 @@ $gauge-padding: 0.15rem;
 
 .feature-histogram {
   @extend .feature-histogram-container;
-  border-radius: 5px;
 
+  border-radius: 5px;
   background-color: #dedede;
 }
 
+.feature-histogram-tooltip td > p {
+  font-size: 0.85rem !important;
+}
+
+/* stylelint-disable-next-line selector-class-pattern */
 .feature-histogram-tooltip .MuiChartsTooltip-markCell,
+/* stylelint-disable-next-line selector-class-pattern */
 .MuiChartsTooltip-labelCell {
   display: none;
 }
 
+/* stylelint-disable-next-line selector-class-pattern */
 .feature-histogram-tooltip .MuiChartsTooltip-valueCell {
   padding: 0.5rem !important;
 }
 
+/* stylelint-disable-next-line selector-class-pattern */
 .feature-histogram-tooltip .MuiChartsTooltip-valueCell > p {
   font-size: 0.85rem !important;
 }
 
-.feature-histogram-tooltip td > p {
-  font-size: 0.85rem !important;
-}
-
 .feature-disease-info-list {
   max-height: 300px;
   overflow-y: auto;
@@ -354,6 +360,7 @@ $gauge-padding: 0.15rem;
 
 .cherita-pseudospatial {
   width: 100%;
+  position: relative;
 }
 
 .cherita-pseudospatial-plot {
@@ -419,12 +426,31 @@ $gauge-padding: 0.15rem;
 
 .var-item-name {
   @extend .me-auto;
+
   padding-right: 0.5rem;
   white-space: nowrap;
   overflow: hidden;
   text-overflow: ellipsis;
 }
 
-input[type="checkbox"] {
+input[type='checkbox'] {
   cursor: pointer;
-}
+}
+
+.ps-xs-1 {
+  padding-left: 0.15rem !important;
+}
+
+.resampled-tooltip-container {
+  position: absolute;
+  bottom: 16px;
+  right: 16px;
+  z-index: 10;
+  width: max-content;
+
+  @media (width >= 991px) {
+    top: 16px;
+    left: 16px;
+    bottom: auto;
+  }
+}

package/scss/components/accordions.scss

@@ -19,6 +19,7 @@
     height: 20px;
     margin-right: 10px;
   }
+
   .obs-accordion-header-span {
     font-size: 1rem;
     width: 100%;
@@ -36,6 +37,7 @@
       @extend .flex-nowrap;
     }
   }
+
   .active-icon {
     color: #0c63e4;
   }
@@ -43,5 +45,6 @@
 
 .obs-group-accordion-body {
   @extend .accordion-flush;
+
   padding: 0;
-}
+}

package/scss/components/layouts.scss

@@ -3,9 +3,7 @@
   display: flex;
   flex-direction: column;
   overflow: auto;
-}
 
-.cherita-app {
   .cherita-navbar {
     @extend .m-3;
     @extend .d-block;
@@ -17,16 +15,13 @@
     left: 0;
     right: 0;
     border-radius: 0.25rem;
-    @media (min-width: 992px) and (max-width: 1199px) {
-      margin-left: calc(33.33333333% + 1rem) !important;
+
+    @media (width >= 992px) and (width <= 1199px) {
+      margin-left: calc(33.3333% + 1rem) !important;
     }
   }
 }
 
-.cherita-app-canvas {
-  position: relative;
-}
-
 .cherita-app-obs {
   @extend .col;
   @extend .d-none;
@@ -73,8 +68,8 @@
     align-items: center;
     width: 100%;
 
-    &:after {
-      content: "";
+    &::after {
+      content: '';
       flex-shrink: 0;
       width: var(--geeks-accordion-btn-icon-width);
       height: var(--geeks-accordion-btn-icon-width);
@@ -90,28 +85,13 @@
     color: var(--geeks-accordion-active-color);
     background-color: var(--geeks-accordion-active-bg);
 
-    &:after {
+    &::after {
       background-image: var(--geeks-accordion-btn-active-icon);
       transform: var(--geeks-accordion-btn-icon-transform);
     }
   }
 }
 
-.sidebar-plotselector {
-  padding: 6px;
-  border-bottom: 1px solid #dee2e6;
-
-  .plotselector-icon {
-    padding-bottom: 2px;
-    cursor: pointer;
-
-    .active {
-      opacity: 1;
-      border-bottom: 2px solid #007bff;
-    }
-  }
-}
-
 .sidebar-pseudospatial {
   padding: 10px;
   border-bottom: 1px solid #dee2e6;
@@ -141,6 +121,7 @@
   .offcanvas-header {
     @extend .pb-0;
   }
+
   .offcanvas-body {
     @extend .pt-1;
 
@@ -160,6 +141,8 @@
 }
 
 .cherita-app-canvas {
+  position: relative;
+
   .cherita-plot {
     position: relative;
     height: 100%;
@@ -169,6 +152,7 @@
 
 .cherita-app-container {
   @extend .p-0;
+
   display: flex;
   flex-wrap: nowrap;
   width: 100%;
@@ -182,9 +166,10 @@
   }
 
   .cherita-app-canvas {
-    @extend .p-1;
+    @extend .p-0;
+
     flex: 1 1 auto;
-    min-width: 400px;
+    min-width: 375px;
     position: relative;
     max-height: 100%;
     display: flex;
@@ -193,6 +178,7 @@
     .cherita-navbar {
       @extend .m-0;
       @extend .d-block;
+
       position: relative;
     }
   }
@@ -204,14 +190,10 @@
     position: relative;
   }
 
-  @media (max-width: 1400px) {
+  @media (width <= 1400px) {
     .cherita-app-obs,
     .cherita-app-sidebar {
       max-width: 25%;
     }
   }
 }
-
-.ps-xs-1 {
-  padding-left: 0.15rem !important;
-}

package/scss/components/lists.scss

@@ -1,11 +1,13 @@
 .list-group.cherita-list {
   .virtualized-list-wrapper {
-    padding: 0 0.25rem 0.25rem 0.25rem;
+    padding: 0 0.25rem 0.25rem;
   }
+
   .list-group-item.unstyled {
     background-color: transparent;
     padding-left: 1rem;
   }
+
   .list-group-item {
     border: 0;
     padding: 0.375rem 0.75rem;
@@ -14,13 +16,15 @@
     background-color: var(--#{$prefix}tertiary-bg);
     border-radius: var(--#{$prefix}border-radius);
   }
+
   .list-group-item.active {
     background-color: var(--#{$prefix}secondary-bg);
   }
 }
+
 .obs-statistics {
   border: 0;
-  margin: 0 0.25rem 0.25rem 0.25rem;
+  margin: 0 0.25rem 0.25rem;
   padding: 0.375rem 0.75rem;
   line-height: 1.5;
   color: var(--#{$prefix}body-color);
@@ -29,7 +33,7 @@
 }
 
 .cherita-list.var-set-list > .list-group-item {
-  filter: brightness(0.95); // darken background
+  filter: brightness(0.95);
   padding-right: 0;
   padding-left: 0.35rem;
 }
@@ -40,4 +44,4 @@
       cursor: pointer;
     }
   }
-}
+}

package/scss/components/plotly.scss

@@ -1,35 +1,47 @@
-.js-plotly-plot .plotly .modebar {
+// Plotly modebar customisation
+.js-plotly-plot {
+  .plotly {
+    .modebar {
+      top: 16px;
+      right: 0;
 
-  .modebar-group {
-    @extend .bg-primary;
-    @extend .mx-1;
-    border-radius: 5px;
-    padding: 4px !important;
+      // Each button group in the modebar
+      .modebar-group {
+        @extend .bg-primary;
+        @extend .mx-1;
 
-    .modebar-btn {
-      display: inline-flex;
-      justify-content: center;
-      position: relative;
-      font-size: 1.25rem;
-      padding: 0.25rem;
-      height: auto;
-      cursor: pointer;
-      line-height: normal;
+        border-radius: 5px;
+        padding: 4px !important;
 
-      svg {
-        position: relative;
-        top: 1px;
+        // Individual buttons
+        .modebar-btn {
+          display: inline-flex;
+          justify-content: center;
+          align-items: center;
+          position: relative;
+          font-size: 1.25rem;
+          padding: 0.25rem;
+          height: auto;
+          cursor: pointer;
+          line-height: normal;
 
-        path {
-          fill: white !important;
-          color: white !important;
+          svg {
+            position: relative;
+            top: 1px;
+
+            path {
+              fill: white !important;
+              color: white !important;
+            }
+          }
         }
       }
+
+      // Hover effect for modebar buttons except watermark
+      &--hover > :not(.watermark) {
+        opacity: 1;
+        transition: opacity 0.3s;
+      }
     }
   }
 }
-
-.js-plotly-plot .plotly .modebar--hover > :not(.watermark) {
-  opacity: 0.5;
-  transition: opacity 0.3s;
-}

package/scss/components/plots.scss

@@ -1,11 +1,24 @@
 .cherita-spatial-controls {
   position: absolute;
-  z-index: 10;
   top: 1rem;
   left: 1rem;
+  z-index: 10;
   width: 3rem;
+
+  // Target buttons inside the controls
   .btn {
     padding-left: 0;
     padding-right: 0;
   }
 }
+
+.plotselector {
+  padding: 0 10px;
+  border-bottom: 1px solid #dee2e6;
+
+  // Individual plot selector icons
+  .plotselector-icon {
+    padding: 6px;
+    cursor: pointer;
+  }
+}