@genome-spy/core 0.19.0 → 0.21.0

package/dist/schema.json

@@ -478,6 +478,9 @@
         "baseUrl": {
           "type": "string"
         },
+        "columns": {
+          "type": "number"
+        },
         "concat": {
           "items": {
             "anyOf": [
@@ -575,7 +578,14 @@
           "type": "number"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -606,7 +616,8 @@
         }
       },
       "required": [
-        "concat"
+        "concat",
+        "columns"
       ],
       "type": "object"
     },
@@ -1335,7 +1346,14 @@
           "type": "number"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -1624,7 +1642,14 @@
           "type": "object"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -1633,7 +1658,7 @@
           "type": "array"
         },
         "view": {
-          "$ref": "#/definitions/ViewConfig"
+          "$ref": "#/definitions/ViewBackground"
         },
         "visible": {
           "description": "Visibility of the view. An invisible view is removed from the layout and not rendered.\n\n**Default:** `true`",
@@ -1791,9 +1816,6 @@
           "description": "The vertical offset between the text and its anchor point, in pixels. Applied after the rotation by `angle`.",
           "type": "number"
         },
-        "dynamicData": {
-          "type": "boolean"
-        },
         "fill": {
           "type": "string"
         },
@@ -2972,7 +2994,14 @@
               "type": "object"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -2981,7 +3010,7 @@
               "type": "array"
             },
             "view": {
-              "$ref": "#/definitions/ViewConfig"
+              "$ref": "#/definitions/ViewBackground"
             },
             "visible": {
               "description": "Visibility of the view. An invisible view is removed from the layout and not rendered.\n\n**Default:** `true`",
@@ -3137,7 +3166,14 @@
               "type": "object"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3146,7 +3182,7 @@
               "type": "array"
             },
             "view": {
-              "$ref": "#/definitions/ViewConfig"
+              "$ref": "#/definitions/ViewBackground"
             },
             "visible": {
               "description": "Visibility of the view. An invisible view is removed from the layout and not rendered.\n\n**Default:** `true`",
@@ -3292,7 +3328,14 @@
               "type": "boolean"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3432,7 +3475,14 @@
               "type": "number"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3597,7 +3647,14 @@
               "type": "number"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3641,6 +3698,9 @@
             "baseUrl": {
               "type": "string"
             },
+            "columns": {
+              "type": "number"
+            },
             "concat": {
               "items": {
                 "anyOf": [
@@ -3749,7 +3809,14 @@
               "type": "number"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3780,6 +3847,7 @@
             }
           },
           "required": [
+            "columns",
             "concat"
           ],
           "type": "object"
@@ -3947,7 +4015,14 @@
           "type": "boolean"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -4062,10 +4137,6 @@
           "description": "The exponent of the `pow` scale.",
           "type": "number"
         },
-        "fp64": {
-          "description": "Use emulated 64bit floating points on the GPU to increase precision.\n\nEmulation has a performance cost when compared to the native 32bit processing, but the effect is negligible in the most cases.\n\n__Default value:__ `true` for `\"locus\"` scale, `false` for others.",
-          "type": "boolean"
-        },
         "interpolate": {
           "anyOf": [
             {
@@ -4502,6 +4573,109 @@
         }
       ]
     },
+    "Title": {
+      "additionalProperties": false,
+      "properties": {
+        "align": {
+          "$ref": "#/definitions/Align",
+          "description": "Horizontal text alignment for title text. One of `\"left\"`, `\"center\"`, or `\"right\"`."
+        },
+        "anchor": {
+          "$ref": "#/definitions/TitleAnchor",
+          "description": "The anchor position for placing the title and subtitle text. One of `\"start\"`, `\"middle\"`, or `\"end\"`. For example, with an orientation of top these anchor positions map to a left-, center-, or right-aligned title."
+        },
+        "angle": {
+          "description": "Angle in degrees of title and subtitle text.",
+          "type": "number"
+        },
+        "baseline": {
+          "$ref": "#/definitions/Baseline",
+          "description": "Vertical text baseline for title and subtitle text. One of `\"alphabetic\"` (default), `\"top\"`, `\"middle\"`, or `\"bottom\"`."
+        },
+        "color": {
+          "description": "Text color for title text.",
+          "type": "string"
+        },
+        "dx": {
+          "description": "Delta offset for title and subtitle text x-coordinate.",
+          "type": "number"
+        },
+        "dy": {
+          "description": "Delta offset for title and subtitle text y-coordinate.",
+          "type": "number"
+        },
+        "font": {
+          "description": "Font name for title text.",
+          "type": "string"
+        },
+        "fontSize": {
+          "description": "Font size in pixels for title text.",
+          "minimum": 0,
+          "type": "number"
+        },
+        "fontStyle": {
+          "$ref": "#/definitions/FontStyle",
+          "description": "Font style for title text."
+        },
+        "fontWeight": {
+          "$ref": "#/definitions/FontWeight",
+          "description": "Font weight for title text. This can be either a string (e.g `\"bold\"`, `\"normal\"`) or a number (`100`, `200`, `300`, ..., `900` where `\"normal\"` = `400` and `\"bold\"` = `700`)."
+        },
+        "frame": {
+          "$ref": "#/definitions/TitleFrame",
+          "description": "The reference frame for the anchor position, one of `\"bounds\"` (to anchor relative to the full bounding box) or `\"group\"` (to anchor relative to the group width or height)."
+        },
+        "offset": {
+          "description": "The orthogonal offset in pixels by which to displace the title group from its position along the edge of the chart.",
+          "type": "number"
+        },
+        "orient": {
+          "$ref": "#/definitions/TitleOrient",
+          "description": "Default title orientation (`\"top\"`, `\"bottom\"`, `\"left\"`, or `\"right\"`)"
+        },
+        "style": {
+          "description": "A mark style property to apply to the title text mark. If not specified, a default style of `\"group-title\"` is applied.",
+          "type": "string"
+        },
+        "text": {
+          "description": "The title text.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "text"
+      ],
+      "type": "object"
+    },
+    "TitleAnchor": {
+      "enum": [
+        null,
+        "start",
+        "middle",
+        "end"
+      ],
+      "type": [
+        "null",
+        "string"
+      ]
+    },
+    "TitleFrame": {
+      "enum": [
+        "bounds",
+        "group"
+      ],
+      "type": "string"
+    },
+    "TitleOrient": {
+      "enum": [
+        "none",
+        "left",
+        "right",
+        "top",
+        "bottom"
+      ],
+      "type": "string"
+    },
     "Tooltip": {
       "anyOf": [
         {
@@ -4700,7 +4874,14 @@
           "type": "object"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -4709,7 +4890,7 @@
           "type": "array"
         },
         "view": {
-          "$ref": "#/definitions/ViewConfig"
+          "$ref": "#/definitions/ViewBackground"
         },
         "visible": {
           "description": "Visibility of the view. An invisible view is removed from the layout and not rendered.\n\n**Default:** `true`",
@@ -4859,7 +5040,14 @@
           "type": "number"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -4936,7 +5124,7 @@
       ],
       "type": "object"
     },
-    "ViewConfig": {
+    "ViewBackground": {
       "additionalProperties": false,
       "properties": {
         "cornerRadius": {

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "BSD-2-Clause",
-  "version": "0.19.0",
+  "version": "0.21.0",
   "main": "dist/index.js",
   "module": "src/index.js",
   "exports": {
@@ -28,6 +28,7 @@
     "dev": "node dev-server.js",
     "build": "vite build && npm run build:schema",
     "prepublishOnly": "npm run build",
+    "test:vitest": "vitest run",
     "test:tsc": "tsc -p tsconfig.json",
     "checkSpec": "tsc --allowJs --checkJs --strict --noEmit --moduleResolution node --target es6 src/spec/root.d.ts",
     "build:schema": "mkdir -p dist && ts-json-schema-generator --path 'src/spec/*.ts' --type RootSpec > dist/schema.json"
@@ -43,7 +44,7 @@
     "d3-color": "^3.0.1",
     "d3-ease": "^3.0.1",
     "d3-format": "^3.0.1",
-    "flatqueue": "^1.2.1",
+    "flatqueue": "^2.0.3",
     "internmap": "^2.0.3",
     "lit-html": "^2.0.2",
     "twgl.js": "^4.19.1",
@@ -52,5 +53,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "282eb640bf4c29be3755ef5de3992b8d76ad5f4c"
+  "gitHead": "293e743d4b887427d8fadc49460a08a572eaff12"
 }

package/src/data/collector.test.js

@@ -1,3 +1,5 @@
+import { expect, test } from "vitest";
+
 import Collector from "./collector";
 
 const data = [1, 5, 2, 4, 3].map((x) => ({ x }));

package/src/data/dataFlow.test.js

@@ -1,3 +1,5 @@
+import { describe, test } from "vitest";
+
 describe("DataFlow", () => {
     test.todo("TODO");
 });

package/src/data/flow.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FilterTransform from "./transforms/filter";
 import FormulaTransform from "./transforms/formula";
 import Collector from "./collector";

package/src/data/flowNode.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FlowNode from "./flowNode";
 import { validateLinks } from "./flowOptimizer";
 

package/src/data/flowOptimizer.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FlowNode, { BEHAVIOR_CLONES } from "./flowNode";
 import { removeRedundantCloneTransforms, validateLinks } from "./flowOptimizer";
 import CloneTransform from "./transforms/clone";

package/src/data/formats/fasta.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import fasta from "./fasta";
 
 test("fasta", () => {

package/src/data/sources/inlineSource.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import Collector from "../collector";
 import InlineSource from "./inlineSource";
 

package/src/data/sources/sequenceSource.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import Collector from "../collector";
 import SequenceSource from "./sequenceSource";
 

package/src/data/transforms/clone.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import CloneTransform from "./clone";
 

package/src/data/transforms/coverage.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import CoverageTransform from "./coverage";
 import { processData } from "../flowTestUtils";
 

package/src/data/transforms/filter.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FilterTransform from "./filter";
 

package/src/data/transforms/flattenDelimited.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FlattenDelimitedTransform from "./flattenDelimited";
 

package/src/data/transforms/flattenSequence.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FlattenSequenceTransform from "./flattenSequence";
 

package/src/data/transforms/formula.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FormulaTransform from "./formula";
 

package/src/data/transforms/identifier.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { range } from "d3-array";
 import { processData } from "../flowTestUtils";
 import IdentifierTransform, { BLOCK_SIZE, DEFAULT_AS } from "./identifier";

package/src/data/transforms/pileup.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import PileupTransform from "./pileup";
 import { processData } from "../flowTestUtils";
 

package/src/data/transforms/project.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import ProjectTransform from "./project";
 

package/src/data/transforms/regexExtract.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 
 import RegexExtractTransform from "./regexExtract";

package/src/data/transforms/regexFold.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import RegexFoldTransform from "./regexFold";
 

package/src/data/transforms/sample.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import SampleTransform from "./sample";
 import { extent } from "d3-array";
 import { createChain } from "../../view/flowBuilder";

package/src/data/transforms/stack.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import StackTransform from "./stack";
 

package/src/encoder/accessor.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import AccessorFactory from "./accessor";
 
 const af = new AccessorFactory();

package/src/encoder/encoder.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import AccessorFactory from "./accessor";
 import { scale as vegaScale } from "vega-scale";
 

package/src/genome/genome.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import Genome from "./genome";
 
 describe("Human genome, chromosome names prefixed with 'chr'", () => {

package/src/genome/scaleIndex.js

@@ -24,7 +24,7 @@ export default function scaleIndex() {
     let numberingOffset = 0;
 
     const scaleFunction = (/** @type {number} */ x) =>
-        ((x - domain[0]) / domainSpan) * rangeSpan + range[0];
+        ((x + align - domain[0]) / domainSpan) * rangeSpan + range[0];
 
     /**
      * In principle, the domain consists of integer indices. However,
@@ -34,7 +34,8 @@ export default function scaleIndex() {
      */
     const scale = /** @type {any} */ (scaleFunction);
 
-    scale.invert = (y) => ((y - range[0]) / rangeSpan) * domainSpan + domain[0];
+    scale.invert = (y) =>
+        ((y - range[0]) / rangeSpan) * domainSpan + domain[0] - align;
 
     // @ts-expect-error
     scale.domain = function (_) {

package/src/genome/scaleIndex.test.js

@@ -1,23 +1,40 @@
+import { expect, test } from "vitest";
 import scaleIndex from "./scaleIndex";
 
 test("Scale with defaults works as expected", () => {
     const scale = scaleIndex();
 
-    expect(scale(-1)).toEqual(-1);
-    expect(scale(0)).toEqual(0);
-    expect(scale(1)).toEqual(1);
-    expect(scale(2)).toEqual(2);
+    // Align is 0.5 by default
+    expect(scale(-1)).toEqual(-0.5);
+    expect(scale(0)).toEqual(0.5);
+    expect(scale(1)).toEqual(1.5);
+    expect(scale(2)).toEqual(2.5);
 });
 
 test("Scale scales correctly with custom domain and range", () => {
-    const scale = scaleIndex().domain([0, 10]).range([100, 200]);
+    const scale = scaleIndex().domain([0, 10]).range([100, 200]).align(0.0);
 
     expect(scale(0)).toEqual(100);
     expect(scale(10)).toEqual(200);
 });
 
 test("Invert works as expected", () => {
-    const scale = scaleIndex().domain([0, 10]).range([100, 200]);
+    const scale = scaleIndex().domain([0, 10]).range([100, 200]).align(0.0);
+
+    expect(scale.invert(scale(0))).toEqual(0);
+    expect(scale.invert(scale(5))).toEqual(5);
+    expect(scale.invert(scale(10))).toEqual(10);
+});
+
+test("Scale scales correctly with custom domain, range, and align", () => {
+    const scale = scaleIndex().domain([0, 10]).range([100, 200]).align(0.5);
+
+    expect(scale(0)).toEqual(105);
+    expect(scale(10)).toEqual(205);
+});
+
+test("Invert works as expected with align", () => {
+    const scale = scaleIndex().domain([0, 10]).range([100, 200]).align(0.5);
 
     expect(scale.invert(scale(0))).toEqual(0);
     expect(scale.invert(scale(5))).toEqual(5);

package/src/genome/scaleLocus.test.js

@@ -1,3 +1,4 @@
+import { test } from "vitest";
 import scaleLocus from "./scaleLocus";
 
 test.todo("Write some tests!");