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

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@figtreejs/core",
-  "version": "0.0.1-alpha.1",
+  "version": "0.0.1-beta.1",
   "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;
@@ -143,9 +143,7 @@ export class ImmutableTree implements Tree, TaxonSetInterface {
     nexus: string,
     options?: newickParsingOptions,
   ): ImmutableTree {
-    const tree = new this();
-    return parseNexus(tree, nexus, options);
-    // throw new Error("Nexus parsing not implemented")
+    return parseNexus(nexus, options);
   }
   static fromString(
     string: string,

package/src/evo/tree/parsers/annotation-parser.ts

@@ -130,6 +130,12 @@ export function parseAnnotation(annotationString: string): ParsedAnnotationRaw {
   return annotations;
 }
 
+/**
+ * Process an annotation value and return the possibly transformed value and
+ * figtreejs annotation type
+ * @param values RawAnnotationValue
+ * @returns ClassifiedValue {type: BaseAnnotationType, value: ValueOf<BaseAnnotationType>};
+ */
 export function processAnnotationValue(
   values: RawAnnotationValue,
 ): ClassifiedValue {

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

@@ -3,7 +3,11 @@ 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";
+/**
+ * A class that contains the logic for parsing newick strings.
+ * It the tokens of the string should be split as in
+ *   /\s*('[^']+'|"[^"]+"|\[&[^[]+]|,|:|\)|\(|;)\s\*/
 
 export class NewickCharacterParser {
   done: boolean;
@@ -52,6 +56,10 @@ export class NewickCharacterParser {
     return this.tree;
   }
 
+  /**
+   * Parse the next token
+   * @param t token
+   */
   parseCharacter(t: string): void {
     if (this.done) {
       throw new Error("Parsing is done. We have seen a ';'");

package/src/evo/tree/parsers/newick-parsing.ts

@@ -2,6 +2,12 @@ import { NewickCharacterParser } from "./newick-character-parser";
 import type { ImmutableTree, newickParsingOptions } from "..";
 import { TaxonSet } from "..";
 
+/**
+ * An internal function to parse a newick string.
+ * @param newick
+ * @param options
+ * @returns
+ */
 export function parseNewick(
   newick: string,
   options: newickParsingOptions = {},

package/src/evo/tree/parsers/nexus-parsing.ts

@@ -1,12 +1,17 @@
 /* eslint-disable */
 import { ImmutableTree } from "../normalized-tree/immutable-tree";
+import { newickParsingOptions } from "../tree-types";
 import { parseNewick } from "./newick-parsing";
 
-//ONLY parses the first tree
+/**
+ * An internal helper function that parses the first tree in a nexus string
+ * @param nexus - The nexus string to be parsed.
+ * @param options - newickParsingOptions - parseAnnotations is set to true
+ * @returns
+ */
 export function parseNexus(
-  _tree: ImmutableTree,
   nexus: string,
-  options = {},
+  options: newickParsingOptions = {},
 ): ImmutableTree {
   // odd parts ensure we're not in a taxon label
   //TODO make this parsing more robust

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

@@ -1,10 +1,14 @@
-import { notNull } from "../../../../utils";
+import { notNull } from "../../../../utils/maybe";
 import type { ImmutableTree } from "../../normalized-tree";
 import { TaxonSet } from "../../taxa/taxon";
 
 import { NewickCharacterParser } from "../newick-character-parser";
 import { newickDeliminators, nexusTokenizer } from "./nexus-tokenizer";
 
+/**
+ * A nexus importing class that parses a stream and into an asynchronous
+ * iterator over trees.
+ */
 export class NexusImporter {
   reader: ReadableStreamDefaultReader<string>;
   taxonSet: TaxonSet;
@@ -27,7 +31,10 @@ export class NexusImporter {
     this.currentBlock = undefined;
     this.options = options;
   }
-
+  /**
+   * The main public api.
+   * an asynchronous iterator over the trees provided by the stream
+   */
   async *getTrees(): AsyncIterableIterator<ImmutableTree> {
     while (this.currentBlock !== "trees") {
       await this.parseNextBlock();

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",
@@ -7,6 +7,11 @@ export enum STATUS {
   IN_COMMENT = "in comment",
 }
 
+/**
+ * A helper function that converts an incoming stream into tokens in
+ * a nexus file.
+ * @returns A pipe string tokenizer for use in a transform stream.
+ */
 export function nexusTokenizer() {
   return {
     lastChunk: "",

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

@@ -1,7 +1,14 @@
-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";
 
+/**
+ * An internal maybe safe helper function for getting a taxon's name
+ * @param data - the underlying taxon set data.
+ * @param id
+ * @returns Maybe(name)
+ */
+
 export function maybeGetNameFromIndex(
   data: TaxonSetData,
   id: Maybe<number> | number,
@@ -23,6 +30,13 @@ export function maybeGetNameFromIndex(
   return Some(name);
 }
 
+/**
+ * An internal maybe safe helper function for getting a taxon by it's name
+ * @param data - the underlying taxon set data.
+ * @param id
+ * @returns Maybe(taxon)
+ */
+
 export function maybeGetTaxonByName(
   data: TaxonSetData,
   id: Maybe<string> | string,

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

@@ -1,12 +1,23 @@
-import { MaybeType } from "@figtreejs/maybe/maybe";
+import { MaybeType } from "../../../utils";
 import { maybeGetNameFromIndex, maybeGetTaxonByName } from "./helper-functions";
 
+/**
+ * A interface for taxon.
+ * There should only be one taxon per individual sampled.
+ * The taxon is meant to be synonymous with the individual and may be shared across multiple trees.
+ */
 export interface Taxon {
   name: string;
   number: number;
   annotations: { [annotation: string]: string | string[] | number | number[] };
 }
 
+/**
+ * An internal helper function for constructing a new taxon.
+ * @param name - taxon name
+ * @param number - taxon number
+ * @returns
+ */
 function newTaxon(name: string, number: number): Taxon {
   return {
     name,
@@ -15,19 +26,47 @@ function newTaxon(name: string, number: number): Taxon {
   };
 }
 
+/**
+ * An interface for a taxon set - a group of taxa in a tree.
+ */
 export interface TaxonSetInterface {
+  /**
+   * Add a taxon the the set
+   * @param name - Add a new taxon with this name
+   */
   addTaxon(name: string): TaxonSetInterface;
-  getTaxon(id: number): Taxon | undefined;
+  /**
+   * Get a taxon by it's number
+   * @param id -taxon number
+   */
+  getTaxon(id: number): Taxon | undefined; // remove this undefined?
+  /**
+   * Get a taxon object by it's name.
+   * @param name -the taxon name
+   */
   getTaxonByName(name: string): Taxon;
+  /**
+   * Return the number of taxa in the set.
+   */
   getTaxonCount(): number;
+  /**
+   * Lock the taxa set. No taxa can be added or removed at this point. The population is fixed.
+   */
   lockTaxa(): TaxonSetInterface;
 }
 
+/**
+ * The interface for a taxon set internal data structure.
+ */
 export interface TaxonSetData {
   allNames: string[];
   byName: { [taxon: string]: Taxon };
   finalized: boolean;
 }
+
+/**
+ * A concrete implementation of the taxonset interface
+ */
 export class TaxonSet implements TaxonSetInterface {
   _data: TaxonSetData;
   constructor(taxonSetData?: TaxonSetData) {

package/src/evo/tree/traversals/preorder-traversal.ts

@@ -1,5 +1,10 @@
 import type { Tree, NodeRef } from "../tree-types";
 import type { TreeTraversal } from "./traversal-types";
+
+/**
+ * A class for a cached pre-order traversal.
+ * This needs to be revisited before it can be used.
+ */
 export class PreOrderTraversalCache implements TreeTraversal {
   _forwardCache: Map<NodeRef, NodeRef>;
   _reverseCache: Map<NodeRef, NodeRef>;

package/src/evo/tree/traversals/traversal-types.ts

@@ -1,5 +1,8 @@
 import type { NodeRef, Tree } from "../tree-types";
 
+/**
+ * An interface for tree traversals
+ */
 export interface TreeTraversal {
   getNext(tree: Tree, node: NodeRef): NodeRef | undefined;
   getPrevious(tree: Tree, node: NodeRef): NodeRef | undefined;