@figtreejs/core 0.0.1-alpha.1 → 0.0.1-beta.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@figtreejs/core",
-  "version": "0.0.1-alpha.1",
+  "version": "0.0.1-beta.0",
   "description": "A react component library for phylogenetic visualization and app building",
   "repository": {
     "type": "git",
@@ -19,6 +19,10 @@
   "main": "./dist/index.cjs",
   "module": "./dist/index.mjs",
   "types": "./dist/index.d.ts",
+  "files": [
+    "./dist/*",
+    "./src/*"
+  ],
   "scripts": {
     "build": "vite build",
     "check-types": "tsc --noEmit",
@@ -37,7 +41,6 @@
     ]
   },
   "dependencies": {
-    "@figtreejs/maybe": "0.0.1-alpha.1",
     "@react-spring/web": "^9.7.5",
     "abs-svg-path": "^0.1.1",
     "d3-array": "^3.2.4",
@@ -51,8 +54,8 @@
     "uuid": "^13.0.0"
   },
   "devDependencies": {
-    "@figtreejs/eslint-config": "0.0.1-alpha.0",
-    "@figtreejs/typescript-config": "0.0.1-alpha.0",
+    "@figtreejs/eslint-config": "*",
+    "@figtreejs/typescript-config": "*",
     "@microsoft/api-extractor": "^7.55.1",
     "@testing-library/react": "^16.3.0",
     "@types/abs-svg-path": "^0.1.3",

package/src/bauble-makers/set-up-baubles.ts

@@ -22,7 +22,7 @@ import type {
 } from "./makers";
 import { mapAttrsToProps, mapInteractionsToProps } from "./utils";
 import type { Clade } from "../components/hoc/with-clades";
-import { notNull } from "../utils";
+import { notNull } from "../utils/maybe";
 
 export type InternalBaubleOptions =
   | InternalNodeOptions

package/src/components/baubles/clades/highlight.tsx

@@ -5,7 +5,7 @@ import { withClades } from "../../hoc/with-clades";
 
 import { BasePath, BaseRectangle } from "../shapes";
 import type { PolarVertex, simplePolarVertex } from "../../../layouts/types";
-import { notNull } from "../../../utils";
+import { notNull } from "../../../utils/maybe";
 import { ScaleContext } from "../../../context/scale-context";
 import { layoutContext } from "../../../context/layout-context";
 import { animatedContext } from "../../../context/aminated-context";

package/src/components/decorations/axis/polar-axis.tsx

@@ -7,7 +7,7 @@ import { defaultAxisProps } from "./axis-types";
 
 import { normalizeAngle } from "../../../store/polar-scale";
 import type { dimensionType } from "../../figtree/figtree-types";
-import { unNullify } from "../../../utils";
+import { unNullify } from "../../../utils/maybe";
 import { DimensionContext } from "../../../context/dimension-context";
 import { ScaleContext } from "../../../context/scale-context";
 import PolarAxisBars from "./polar-axis-bars";

package/src/components/decorations/axis/rectangular-axis.tsx

@@ -9,7 +9,7 @@ import type {
 } from "./axis-types";
 import { defaultAxisProps } from "./axis-types";
 import { makeAxisScale } from "./polar-axis";
-import { unNullify } from "../../../utils";
+import { unNullify } from "../../../utils/maybe";
 import { DimensionContext } from "../../../context/dimension-context";
 import { ScaleContext } from "../../../context/scale-context";
 import RectangleAxisBars from "./rectangular-axis-bars";

package/src/components/figtree/figtree.tsx

@@ -4,7 +4,7 @@ import { defaultInternalLayoutOptions, rectangularLayout } from "../../layouts";
 import { ImmutableTree } from "../../evo/tree";
 import { getScale } from "../../store/store";
 import { extent } from "d3-array";
-import { unNullify } from "../../utils";
+import { unNullify } from "../../utils/maybe";
 import { Bauble } from "../baubles/bauble";
 
 import { ScaleContext } from "../../context/scale-context";

package/src/components/hoc/with-node.tsx

@@ -8,7 +8,7 @@ import { layoutClass } from "../../layouts";
 import { defaultNodeLabelData } from "../../store/store";
 import type { PolarVertex } from "../../layouts/types";
 import { textSafeDegrees } from "../../store/polar-scale";
-import { unNullify } from "../../utils";
+import { unNullify } from "../../utils/maybe";
 
 //The goal here is now to take a shape components that accepts Attrs: number | string , x/y
 // and return a component that takes a node / layout/ scale and attrs:number|string | function

package/src/evo/tree/normalized-tree/immutable-tree-helpers.ts

@@ -6,8 +6,8 @@
  * those can't be called by immer proxies.
  */
 
-import type { Maybe, Undefinable } from "@figtreejs/maybe/maybe";
-import { MaybeType, Nothing, Some } from "@figtreejs/maybe/maybe";
+import type { Maybe, Undefinable } from "../../../utils";
+import { Nothing, Some, MaybeType } from "../../../utils";
 import type { Annotation, NodeRef } from "../tree-types";
 import type { ImmutableTree, nodeIndex, Node } from "./immutable-tree";
 import type { Taxon } from "../taxa";

package/src/evo/tree/normalized-tree/immutable-tree.test.ts

@@ -1,6 +1,6 @@
 //TODO test immutable tree include tests that check nodes to roots update as well.
 
-import { notNull, u } from "../../../utils";
+import { notNull, u } from "../../../utils/maybe";
 import { ImmutableTree } from "./immutable-tree";
 import { describe, it, expect } from "vitest";
 

package/src/evo/tree/normalized-tree/immutable-tree.ts

@@ -28,7 +28,7 @@ import {
   type Undefinable,
   UnwrapErr,
   type Maybe,
-} from "@figtreejs/maybe/maybe";
+} from "../../../utils";
 import {
   maybeGetAnnotation,
   maybeGetNode,
@@ -37,7 +37,7 @@ import {
   maybeGetTaxon,
   maybeGetTaxonFromNode,
 } from "./immutable-tree-helpers";
-import { notNull, unNullify } from "../../../utils";
+import { notNull, unNullify } from "../../../utils/maybe";
 import { v4 as uuidv4 } from "uuid";
 
 export type nodeIndex = string | number | Taxon;

package/src/evo/tree/parsers/newick-character-parser.ts

@@ -3,7 +3,7 @@ import { TaxonSet } from "../taxa/taxon";
 import type { NodeRef } from "../tree-types";
 import { ImmutableTree } from "../normalized-tree/immutable-tree";
 import { parseAnnotation } from "./annotation-parser";
-import { notNull, unNullify } from "../../../utils";
+import { notNull, unNullify } from "../../../utils/maybe";
 
 export class NewickCharacterParser {
   done: boolean;

package/src/evo/tree/parsers/parsing.test.ts

@@ -1,4 +1,4 @@
-import { u } from "../../../utils";
+import { u } from "../../../utils/maybe";
 import { ImmutableTree } from "../normalized-tree/immutable-tree";
 import { processAnnotationValue } from "./annotation-parser";
 import { describe, it, expect } from "vitest";

package/src/evo/tree/parsers/stream-reader/nexus-importer.ts

@@ -1,4 +1,4 @@
-import { notNull } from "../../../../utils";
+import { notNull } from "../../../../utils/maybe";
 import type { ImmutableTree } from "../../normalized-tree";
 import { TaxonSet } from "../../taxa/taxon";
 

package/src/evo/tree/parsers/stream-reader/nexus-tokenizer.ts

@@ -1,4 +1,4 @@
-import { notNull } from "../../../../utils";
+import { notNull } from "../../../../utils/maybe";
 
 export enum STATUS {
   PARSING = "parsing",

package/src/evo/tree/taxa/helper-functions.ts

@@ -1,5 +1,5 @@
-import type { Maybe, Undefinable } from "@figtreejs/maybe/maybe";
-import { Nothing, Some, MaybeType } from "@figtreejs/maybe/maybe";
+import type { Maybe, Undefinable } from "../../../utils";
+import { Nothing, Some, MaybeType } from "../../../utils";
 import type { Taxon, TaxonSetData } from "./taxon";
 
 export function maybeGetNameFromIndex(

package/src/evo/tree/taxa/taxon.ts

@@ -1,4 +1,4 @@
-import { MaybeType } from "@figtreejs/maybe/maybe";
+import { MaybeType } from "../../../utils";
 import { maybeGetNameFromIndex, maybeGetTaxonByName } from "./helper-functions";
 
 export interface Taxon {

package/src/index.ts

@@ -3,4 +3,4 @@ export type { FigtreeProps } from "./components";
 export * from "./bauble-makers/makers";
 export * from "./evo";
 export * from "./layouts";
-export * from "./utils";
+export * from "./utils/dateUtils";

package/src/layouts/functional/radial-layout.ts

@@ -3,7 +3,7 @@
 import type { ImmutableTree, NodeRef } from "../../evo";
 import { preOrderIterator, tipIterator } from "../../evo";
 import type { NodeLabelType } from "../types";
-import { notNull } from "../../utils";
+import { notNull } from "../../utils/maybe";
 import type { FunctionalVertex } from "../types";
 import { layoutClass } from "../types";
 

package/src/layouts/functional/rectangular-layout.ts

@@ -3,7 +3,7 @@ import type { ImmutableTree, NodeRef } from "../../evo";
 import { postOrderIterator } from "../../evo";
 import type { NodeLabelType, FunctionalVertex } from "../types";
 import { layoutClass } from "../types";
-import { unNullify } from "../../utils";
+import { unNullify } from "../../utils/maybe";
 
 export function baseLayout(lc: layoutClass) {
   function layout(tree: ImmutableTree): (node: NodeRef) => FunctionalVertex {

package/src/path.helpers.ts

@@ -6,76 +6,93 @@
 
 // curve splitting by https://pomax.github.io/bezierinfo/#introduction
 
-import abs from 'abs-svg-path'
-import normalize from 'normalize-svg-path'
-import parse from 'parse-svg-path'
-import type { NormalizedCommand } from './@custom-types/svg-path-types';
-import { unNullify } from './utils';
+import abs from "abs-svg-path";
+import normalize from "normalize-svg-path";
+import parse from "parse-svg-path";
+import type { NormalizedCommand } from "./@custom-types/svg-path-types";
+import { unNullify } from "./utils/maybe";
 
-class point{
-    x:number;
-    y:number;
-    constructor(x:number,y:number){
-        this.x=x
-        this.y=y
-    }
+class point {
+  x: number;
+  y: number;
+  constructor(x: number, y: number) {
+    this.x = x;
+    this.y = y;
+  }
 }
 
-const NUMBER_OF_POINTS=6; // this should be more than needed by layouts 
+const NUMBER_OF_POINTS = 6; // this should be more than needed by layouts
 type curveArray = [string, number, number, number, number, number, number];
-export function normalizePath(path:string):string{ //TODO this might remove the fill on cartoons.
-    const parsedPath = parse(path) //as AnyCommand[]
-    const absPath = abs(parsedPath)
-    const normalizedPath = normalize(absPath) // normalized path is [M, x,y ] [C, x1,y1, x2,y2, x,y]....
+export function normalizePath(path: string): string {
+  //TODO this might remove the fill on cartoons.
+  const parsedPath = parse(path); //as AnyCommand[]
+  const absPath = abs(parsedPath);
+  const normalizedPath = normalize(absPath); // normalized path is [M, x,y ] [C, x1,y1, x2,y2, x,y]....
 
-    let newPath = `${normalizedPath[0][0]} ${normalizedPath[0][1]} ${normalizedPath[0][2]} `
-    const curves = normalizedPath.filter((d:NormalizedCommand)=>d[0]==="C").map((curve:curveArray)=>{return [new point(curve[1], curve[2]),new point(curve[3], curve[4]),new point(curve[5], curve[6])]})
+  let newPath = `${normalizedPath[0][0]} ${normalizedPath[0][1]} ${normalizedPath[0][2]} `;
+  const curves = normalizedPath
+    .filter((d: NormalizedCommand) => d[0] === "C")
+    .map((curve: curveArray) => {
+      return [
+        new point(curve[1], curve[2]),
+        new point(curve[3], curve[4]),
+        new point(curve[5], curve[6]),
+      ];
+    });
 
-    if(curves.length>NUMBER_OF_POINTS){
-        throw new Error(`Path must have no more than ${NUMBER_OF_POINTS} nodes (excluding start point) detected ${curves.length} nodes update layout or path.helpers` )
-    }
-    if(curves.length==0){
-        throw new Error('Path must have at least 1 node (excluding start point) update layout or path.helpers' )
-    }
+  if (curves.length > NUMBER_OF_POINTS) {
+    throw new Error(
+      `Path must have no more than ${NUMBER_OF_POINTS} nodes (excluding start point) detected ${curves.length} nodes update layout or path.helpers`,
+    );
+  }
+  if (curves.length == 0) {
+    throw new Error(
+      "Path must have at least 1 node (excluding start point) update layout or path.helpers",
+    );
+  }
 
-    while(curves.length<NUMBER_OF_POINTS){
-        const toSplit = unNullify(curves.pop(),`Internal error in normalization`);
-        const {left,right} = splitCubicB(toSplit,0.5);
-        curves.push(left);
-        curves.push(right.reverse());
-    }
+  while (curves.length < NUMBER_OF_POINTS) {
+    const toSplit = unNullify(curves.pop(), `Internal error in normalization`);
+    const { left, right } = splitCubicB(toSplit, 0.5);
+    curves.push(left);
+    curves.push(right.reverse());
+  }
 
-    for(let i = 0; i<curves.length; i++){
-        const curve = curves[i];
-        newPath+=`C${curve[0].x},${curve[0].y} ${curve[1].x},${curve[1].y} ${curve[2].x},${curve[2].y} `
-    }
-    return newPath;
+  for (let i = 0; i < curves.length; i++) {
+    const curve = curves[i];
+    newPath += `C${curve[0].x},${curve[0].y} ${curve[1].x},${curve[1].y} ${curve[2].x},${curve[2].y} `;
+  }
+  return newPath;
 }
 
-function splitCubicB(curve:point[],t:number):{left:point[],right:point[]}{
-const left:point[]=[]
-const right:point[]=[]
+function splitCubicB(
+  curve: point[],
+  t: number,
+): { left: point[]; right: point[] } {
+  const left: point[] = [];
+  const right: point[] = [];
 
-function getCurve(points:point[],t:number){
-    if(points.length==1){
-        left.push(points[0])
-        right.push(points[0])
-    }else{
-        const newPoints:point[] = Array(points.length-1) as point[]
-        for(let i =0; i<newPoints.length; i++){
-            if(i==0){
-                left.push(points[0])
-            }
-            if(i==newPoints.length-1){
-                right.push(points[i+1])
-            }
-            newPoints[i]=new point((1-t)*points[i].x+t*points[i+1].x,(1-t)*points[i].y+t*points[i+1].y)
+  function getCurve(points: point[], t: number) {
+    if (points.length == 1) {
+      left.push(points[0]);
+      right.push(points[0]);
+    } else {
+      const newPoints: point[] = Array(points.length - 1) as point[];
+      for (let i = 0; i < newPoints.length; i++) {
+        if (i == 0) {
+          left.push(points[0]);
         }
-        getCurve(newPoints,t)
+        if (i == newPoints.length - 1) {
+          right.push(points[i + 1]);
+        }
+        newPoints[i] = new point(
+          (1 - t) * points[i].x + t * points[i + 1].x,
+          (1 - t) * points[i].y + t * points[i + 1].y,
+        );
+      }
+      getCurve(newPoints, t);
     }
+  }
+  getCurve(curve, t);
+  return { left, right };
 }
-    getCurve(curve,t);
-    return {left,right}
-}
-
-

package/src/tests/clades/cartoon.test.tsx

@@ -2,7 +2,7 @@ import { render } from "@testing-library/react";
 import { ImmutableTree } from "../../evo";
 import { FigTree } from "../../components";
 import { polarLayout, rectangularLayout } from "../../layouts";
-import { u } from "../../utils";
+import { u } from "../../utils/maybe";
 import { Branches, CartoonClades } from "../../bauble-makers/makers";
 
 const tree = ImmutableTree.fromNewick("((A:1,B:1):2,C:1);");

package/src/tests/clades/highlight.test.tsx

@@ -3,7 +3,7 @@ import { ImmutableTree } from "../../evo";
 import { FigTree } from "../../components";
 import { polarLayout, rectangularLayout } from "../../layouts";
 
-import { u } from "../../utils";
+import { u } from "../../utils/maybe";
 import { Branches, HighlightClades } from "../../bauble-makers/makers";
 
 const tree = ImmutableTree.fromNewick("((A:1,B:1):2,C:1);");

package/src/tests/layouts/rectangularlayout.test.ts

@@ -1,7 +1,7 @@
 import { describe, it, expect } from "vitest";
 import { ImmutableTree } from "../../evo";
 import { rectangularLayout } from "../../layouts";
-import { u } from "../../utils";
+import { u } from "../../utils/maybe";
 
 describe("Test rectangular layout", () => {
   it("check x and y on root", function () {

package/src/tests/shapes/label.test.tsx

@@ -1,7 +1,7 @@
 import { describe, expect, test } from "vitest";
 import { render, screen } from "@testing-library/react";
 import { BaseLabel } from "../../components/baubles/shapes/label";
-import { unNullify } from "../../utils";
+import { unNullify } from "../../utils/maybe";
 
 describe("BaseLabel", () => {
   test("renders an SVG text element that uses transform to position", () => {

package/src/utils/dateUtils.ts

@@ -0,0 +1,41 @@
+import { timeParse, timeFormat } from "d3-time-format";
+import { unNullify } from "./maybe";
+
+//https://stackoverflow.com/questions/29400171/how-do-i-convert-a-decimal-year-value-into-a-date-in-javascript
+/**
+ * Helper function to determine if the provided year is a leap year
+ * @param year
+ * @return {boolean}
+ */
+export function leapYear(year: number): boolean {
+  return (year % 4 === 0 && year % 100 !== 0) || year % 400 === 0;
+}
+
+/**
+ * A function which converts a decimal float into a date object
+ * @param decimalDate
+ * @return {Date}
+ */
+export function decimalToDate(decimal: number): Date {
+  const year = Math.trunc(decimal);
+  const totalNumberOfDays = leapYear(year) ? 366 : 365;
+  const day = Math.round((decimal - year) * totalNumberOfDays);
+  const date = timeParse("%Y-%j")(`${year}-${day}`);
+  // notNull(date,`Could not convert ${decimal} to date tried (year:${year} - day: ${day})`)
+  return unNullify(
+    date,
+    `Could not convert ${decimal} to date tried (year:${year} - day: ${day})`,
+  );
+}
+
+/**
+ * A function that converts a date into a decimal.
+ * @param date
+ * @return {number}
+ */
+export function dateToDecimal(date: Date) {
+  const year = parseInt(timeFormat("%Y")(date));
+  const day = parseInt(timeFormat("%j")(date));
+  const totalNumberOfDays = leapYear(year) ? 366 : 365;
+  return year + day / totalNumberOfDays;
+}

package/src/utils/index.ts

@@ -0,0 +1,2 @@
+export * from "./maybe";
+export * from "./dateUtils";

package/src/utils/maybe.ts

@@ -0,0 +1,67 @@
+// types to avoid always checking for null values
+
+//https://engineering.dollarshaveclub.com/typescript-maybe-type-and-module-627506ecc5c8#950b
+export enum MaybeType {
+  Some = "some",
+  Nothing = "nothing",
+}
+
+export type Some<T> = {
+  type: typeof MaybeType.Some;
+  value: T;
+};
+
+export type Nothing = {
+  type: typeof MaybeType.Nothing;
+};
+
+export type Maybe<T> = Some<T> | Nothing;
+
+export const Nothing = (): Nothing => ({
+  type: MaybeType.Nothing,
+});
+
+export const Some = <T>(value: T): Some<T> => ({
+  type: MaybeType.Some,
+  value,
+});
+
+export const UnwrapErr = <T>(v: Maybe<T>, message: string): T => {
+  switch (v.type) {
+    case MaybeType.Some:
+      return v.value;
+    case MaybeType.Nothing:
+      throw new Error(message);
+  }
+};
+
+export const UnwrapOr = <T>(v: Maybe<T>, d: T): T => {
+  switch (v.type) {
+    case MaybeType.Some:
+      return v.value;
+    case MaybeType.Nothing:
+      return d;
+  }
+};
+// A helper type so we can appease the linters and check some accesses for undefined without having to check them all.
+export type Undefinable<T> = T | undefined;
+
+export function panic(message: string): never {
+  throw new Error(message);
+}
+
+export function u<T>(x: T | undefined): NonNullable<T> {
+  if (x === undefined) {
+    throw new Error("internal bug! unhandled undefined");
+  }
+  return x as NonNullable<T>;
+}
+
+export function notNull<T>(x: T, message: string): asserts x is NonNullable<T> {
+  if (x === undefined) throw new Error(message);
+}
+
+export function unNullify<T>(x: T, message: string): NonNullable<T> {
+  if (x === null) throw new Error(message);
+  return x as NonNullable<T>;
+}

package/CHANGELOG.md

@@ -1,17 +0,0 @@
-# @figtreejs/core
-
-## 0.0.1-alpha.1
-
-### Patch Changes
-
-- includes dist files for publication
-- Updated dependencies
-  - @figtreejs/maybe@0.0.1-alpha.1
-
-## 0.0.1-alpha.0
-
-### Patch Changes
-
-- This version marks the initial version of several packages, and the start of a new developement system
-- Updated dependencies
-  - @figtreejs/maybe@0.0.1-alpha.0

package/eslint.config.js

@@ -1,9 +0,0 @@
-import { defineConfig } from "eslint/config";
-import defaultConfig  from "@figtreejs/eslint-config";
-
-export default defineConfig({
-  "extends": [defaultConfig],
-  "rules":{
-   "@typescript-eslint/restrict-template-expressions": ["error", { allowNumber: true }]
-  }
-})

package/src/utils.ts

@@ -1,57 +0,0 @@
-import {timeParse, timeFormat} from "d3-time-format";
-
-//https://stackoverflow.com/questions/29400171/how-do-i-convert-a-decimal-year-value-into-a-date-in-javascript
-/**
- * Helper function to determine if the provided year is a leap year
- * @param year
- * @return {boolean}
- */
-export function leapYear(year:number):boolean {
-    return ((year % 4 === 0) && (year % 100 !== 0)) || (year % 400 === 0);
-}
-
-/**
- * A function which converts a decimal float into a date object
- * @param decimalDate
- * @return {Date}
- */
-export function decimalToDate(decimal:number):Date{
-    const year = Math.trunc(decimal);
-    const totalNumberOfDays = leapYear(year)? 366:365;
-    const day = Math.round(((decimal-year)*totalNumberOfDays));
-    const date = timeParse("%Y-%j")(`${year}-${day}`)
-    // notNull(date,`Could not convert ${decimal} to date tried (year:${year} - day: ${day})`)
-    return unNullify(date,`Could not convert ${decimal} to date tried (year:${year} - day: ${day})`);
-}
-
-/**
- * A function that converts a date into a decimal.
- * @param date
- * @return {number}
- */
-export function dateToDecimal(date:Date){
-    const year = parseInt(timeFormat("%Y")(date));
-    const day = parseInt(timeFormat("%j")(date));
-    const totalNumberOfDays = leapYear(year)? 366:365;
-    return year+day/totalNumberOfDays
-}
-export function panic(message: string): never { throw new Error(message); }
-
-
-export function u<T>(x: T | undefined): NonNullable<T> {
-  if (x === undefined) {
-    throw new Error('internal bug! unhandled undefined');
-  }
-  return x as NonNullable<T>;
-}
-
-
-export function notNull<T>(x: T,message:string): asserts x is NonNullable<T> {
-  if (x === undefined) throw new Error(message);
-}
-
-export function unNullify<T>(x: T,message:string):  NonNullable<T> {
-  if (x === null) throw new Error(message);
-  return x as NonNullable<T>
-}
-

package/tsconfig.json

@@ -1,12 +0,0 @@
-{
-  "extends": "@figtreejs/typescript-config/vite.json",
-  "compilerOptions": {
-    "allowSyntheticDefaultImports": true,
-    "noEmit": true,
-    "noUncheckedIndexedAccess": false,
-    "jsx": "react-jsx",
-    "types": ["vitest/globals"], // gives types for describe/test/expect
-    "lib": ["ES2020", "DOM", "DOM.Iterable"] // DOM types for `document`
-  },
-  "include": ["src/**/*.ts", "src/**/*.tsx", "*.js", "*.ts"] // /src files and config files
-}