Merge pull request #44 from clockor2/relative-imports

Relative imports

.eslintignore

@@ -1,3 +1,4 @@
 src/types/global.d.ts
 webpack.config.js
-docs
+docs
+test

src/io/readers/neXML.ts

@@ -1,5 +1,5 @@
-import { Tree, Node } from '@phylojs';
-import { SkipTreeException } from '@phylojs/utils/error';
+import { Tree, Node } from '../../';
+import { SkipTreeException } from '../../utils/error';
 
 const neXMLNS = 'http://www.nexml.org/2009';
 

src/io/readers/newick.ts

@@ -1,6 +1,5 @@
-import { Tree, Node } from '@phylojs';
-import { SkipTreeException, ParseException } from '@phylojs/utils/error';
-
+import { Tree, Node } from '../../';
+import { SkipTreeException, ParseException } from '../../utils/error';
 
 /**
  * Reads .newick string and returns a tree.

src/io/readers/nexus.ts

@@ -1,5 +1,5 @@
-import { Tree } from '@phylojs';
-import { SkipTreeException } from '@phylojs/utils/error';
+import { Tree } from '../../';
+import { SkipTreeException } from '../../utils/error';
 import { readNewick } from './newick';
 
 // Function to extract the translate mapping

src/io/readers/phyloXML.ts

@@ -1,5 +1,5 @@
-import { Tree, Node } from '@phylojs';
-import { SkipTreeException } from '@phylojs/utils/error';
+import { Tree, Node } from '../../';
+import { SkipTreeException } from '../../utils/error';
 
 function parse(phyloxml: string): HTMLCollectionOf<Element> {
   const parser = new DOMParser();
@@ -8,7 +8,7 @@ function parse(phyloxml: string): HTMLCollectionOf<Element> {
 }
 
 /**
- * Read a tree from phyloXML format. If a list of trees is 
+ * Read a tree from phyloXML format. If a list of trees is
  * @param {string} phyloxml
  * @returns {Tree}
  */

src/io/readers/tree.ts

@@ -4,7 +4,7 @@ import {
   readTreesFromNeXML,
   readTreesFromPhyloXML,
   readTreesFromNexus,
-} from '@phylojs';
+} from '../../';
 
 type Schema = 'newick' | 'nexus' | 'phyloxml' | 'nexml';
 

src/io/writers/newick.ts

@@ -1,4 +1,4 @@
-import { Node, Tree } from '@phylojs';
+import { Node, Tree } from '../../';
 
 /**
  * Writes tree in .newick format. Undefined branch lengths set to 0.

src/io/writers/nexus.ts

@@ -1,4 +1,4 @@
-import { Tree } from '@phylojs';
+import { Tree } from '../../';
 import { newickRecurse } from './newick';
 
 /** Writes tree in .nexus format. Undefined branch lengths set to 0.

test/io/readers.spec.ts

@@ -1,5 +1,5 @@
-import { writeNewick } from '@phylojs';
 import {
+  writeNewick,
   readNewick,
   readNexus,
   readPhyloXML,
@@ -8,7 +8,7 @@ import {
   readTreesFromNexus,
   readTreesFromPhyloXML,
   readTreesFromNeXML,
-} from '@phylojs';
+} from '../../src';
 
 describe('Newick', () => {
   test('read', () => {

test/io/writers.spec.ts

@@ -1,5 +1,5 @@
 // phyloWriter.test.ts
-import { Node, Tree, writeNewick, writeNexus } from '@phylojs';
+import { Node, Tree, writeNewick, writeNexus } from '../../src';
 
 describe('PhyloWriter', () => {
   const rootNode = new Node(0);

test/tree/node.spec.ts

@@ -1,4 +1,4 @@
-import { Node } from '@phylojs';
+import { Node } from '../../src';
 
 describe('Node', () => {
   test('create node and check basic properties', () => {

test/tree/tree.spec.ts

@@ -1,7 +1,7 @@
-import { readNewick } from '@phylojs';
-import { Node } from '@phylojs/tree/node';
-import { Tree } from '@phylojs/tree';
-import { writeNewick } from '@phylojs';
+import { readNewick } from '../../src';
+import { Node } from '../../src/tree/node';
+import { Tree } from '../../src/tree';
+import { writeNewick } from '../../src';
 import { readFileSync } from 'fs';
 
 describe('Tree', () => {
@@ -27,20 +27,14 @@ describe('Tree', () => {
 
   test('reroot', () => {
     expect(
-      tree
-        .nodeList
-        .map(n => n.label)
-        .filter(n => n !== undefined)
+      tree.nodeList.map(n => n.label).filter(n => n !== undefined)
     ).toStrictEqual(['A', 'B', 'C']);
     tree.reroot(childNode4);
     const newick = writeNewick(tree);
     expect(newick).toBe('("C":0.5,("B":1,"A":2):0.5):0.0;');
     expect(tree.root.children.length).toBe(2);
     expect(
-      tree
-        .nodeList
-        .map(n => n.label)
-        .filter(n => n !== undefined)
+      tree.nodeList.map(n => n.label).filter(n => n !== undefined)
     ).toStrictEqual(['C', 'B', 'A']);
   });
 });

tsconfig.json

@@ -45,10 +45,10 @@
     /* Module Resolution Options */
     "moduleResolution": "node",                  /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */
     "baseUrl": "./",                             /* Base directory to resolve non-absolute module names. */
-    "paths": {
-      "@phylojs": ["src"],
-      "@phylojs/*": ["src/*"],
-    },                                 /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */
+    // "paths": {
+    //   "@phylojs": ["src"],
+    //   "@phylojs/*": ["src/*"],
+    // },                                 /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */
     // "rootDirs": [],                              /* List of root folders whose combined content represents the structure of the project at runtime. */
     // "typeRoots": [],                             /* List of folders to include type definitions from. */
     // "types": [],                                 /* Type declaration files to be included in compilation. */
@@ -71,5 +71,5 @@
     "skipLibCheck": true,                           /* Skip type checking of declaration files. */
     "forceConsistentCasingInFileNames": true        /* Disallow inconsistently-cased references to the same file. */
   },
-  "include": ["src/**/*.ts"]
+  "include": ["src/**/*.ts"],
 }