Simplify docs a bit and remove other modules

README.md

@@ -69,32 +69,18 @@ $ cbioportal-api-client getProfileData -s gbm_tcga_cnaseq -p gbm_tcga_mutations
 
 ## API Reference
 
-## Modules
-
-<dl>
-<dt><a href="#module_cbioportal-api-client">cbioportal-api-client</a> ⇒ <code>cbioPortal</code></dt>
-<dd><p>Creates a new cBio Portal API client</p>
-</dd>
-<dt><a href="#module_cbioportal-api-client/utils/convertResponse">cbioportal-api-client/utils/convertResponse</a> ⇒ <code>Promise</code></dt>
-<dd><p>Converts tab delimited responses to JSON format</p>
-</dd>
-<dt><a href="#module_cbioportal-api-client/utils/summarizeAlterations">cbioportal-api-client/utils/summarizeAlterations</a></dt>
-<dd><p>Exports utility functions for summarizing gene alterations</p>
-</dd>
-</dl>
-
 <a name="module_cbioportal-api-client"></a>
 ## cbioportal-api-client ⇒ <code>cbioPortal</code>
 Creates a new cBio Portal API client
 
-**See**: [cbioPortal](#module_cbioportal-api-client..cbioPortal)  
+**See**: [cbioPortal](#module_cbioportal-api-client..cbioPortal)
 
 | Param | Type | Description |
 | --- | --- | --- |
 | config | <code>Object</code> | Configuration options object. |
 | config.includeRaw | <code>Boolean</code> | Include the raw TSV response |
 
-**Example**  
+**Example**
 Basic usage:
 
 ```javascript
@@ -124,8 +110,8 @@ cbioPortal.getCancerStudies()
 cbioPortal API Object Prototype. Used as the object prototype
 when creating an API client object via the module factory method.
 
-**Kind**: inner constant of <code>[cbioportal-api-client](#module_cbioportal-api-client)</code>  
-**See**: Use [CbioPortal()](#module_cbioportal-api-client) for object creation.  
+**Kind**: inner constant of <code>[cbioportal-api-client](#module_cbioportal-api-client)</code>
+**See**: Use [CbioPortal()](#module_cbioportal-api-client) for object creation.
 
 * [~cbioPortal](#module_cbioportal-api-client..cbioPortal) : <code>Object</code>
     * [.getTypesOfCancer()](#module_cbioportal-api-client..cbioPortal+getTypesOfCancer) ⇒ <code>Promise</code>
@@ -141,19 +127,19 @@ when creating an API client object via the module factory method.
 #### cbioPortal.getTypesOfCancer() ⇒ <code>Promise</code>
 Retrieves a list of all the clinical types of cancer stored on the server.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
-**Returns**: <code>Promise</code> - See fullfills/rejects  
-**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
+**Returns**: <code>Promise</code> - See fullfills/rejects
+**Fulfills**: <code>Array</code> response data converted from TSV to JSON
 
 -----
 
 <a name="module_cbioportal-api-client..cbioPortal+getCancerStudies"></a>
 #### cbioPortal.getCancerStudies() ⇒ <code>Promise</code>
 Retrieves meta-data regarding cancer studies stored on the server.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
-**Returns**: <code>Promise</code> - See fullfills/rejects  
-**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
+**Returns**: <code>Promise</code> - See fullfills/rejects
+**Fulfills**: <code>Array</code> response data converted from TSV to JSON
 
 -----
 
@@ -162,9 +148,9 @@ Retrieves meta-data regarding cancer studies stored on the server.
 Retrieves meta-data regarding all genetic profiles, e.g.
 mutation or copy number profiles, stored about a specific cancer study.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
-**Returns**: <code>Promise</code> - See fullfills/rejects  
-**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
+**Returns**: <code>Promise</code> - See fullfills/rejects
+**Fulfills**: <code>Array</code> response data converted from TSV to JSON
 
 | Param | Type | Description |
 | --- | --- | --- |
@@ -182,8 +168,8 @@ For example, a within a particular study, only some cases may have sequence data
 
 Multiple case lists may be associated with each cancer study, and this method enables you to retrieve meta-data regarding all of these case lists.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
-**Fulfill**: JSON formatted response  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
+**Fulfill**: JSON formatted response
 
 | Param | Type | Description |
 | --- | --- | --- |
@@ -197,8 +183,8 @@ Multiple case lists may be associated with each cancer study, and this method en
 #### cbioPortal.getProfileData(query) ⇒ <code>Promise</code>
 Retrieves genomic profile data for one or more genes.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
-**Fulfill**: JSON formatted response  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
+**Fulfill**: JSON formatted response
 
 | Param | Type | Description |
 | --- | --- | --- |
@@ -210,71 +196,3 @@ Retrieves genomic profile data for one or more genes.
 
 -----
 
-<a name="module_cbioportal-api-client/utils/convertResponse"></a>
-## cbioportal-api-client/utils/convertResponse ⇒ <code>Promise</code>
-Converts tab delimited responses to JSON format
-
-**Returns**: <code>Promise</code> - Resolves with the response JSON  
-
-| Param | Type | Description |
-| --- | --- | --- |
-| response | <code>string</code> | TSV string |
-
-
------
-
-<a name="module_cbioportal-api-client/utils/summarizeAlterations"></a>
-## cbioportal-api-client/utils/summarizeAlterations
-Exports utility functions for summarizing gene alterations
-
-
-* [cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)
-    * [.summarizeMutations(mutations)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeMutations) ⇒ <code>Array</code>
-    * [.summarizeCopyNumberAlterations(copyNumberAlterations)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations) ⇒ <code>Array</code>
-    * [.summarizeAlterations(response)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations) ⇒ <code>Promise</code>
-
-
------
-
-<a name="module_cbioportal-api-client/utils/summarizeAlterations.summarizeMutations"></a>
-### cbioportal-api-client/utils/summarizeAlterations.summarizeMutations(mutations) ⇒ <code>Array</code>
-Summarize mutations
-
-**Kind**: static method of <code>[cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)</code>  
-**Returns**: <code>Array</code> - Array of summaries  
-
-| Param | Type | Description |
-| --- | --- | --- |
-| mutations | <code>Array</code> | Array of mutation rows as parsed by this library |
-
-
------
-
-<a name="module_cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations"></a>
-### cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations(copyNumberAlterations) ⇒ <code>Array</code>
-Summarize copy number alterations
-
-**Kind**: static method of <code>[cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)</code>  
-**Returns**: <code>Array</code> - Array of summaries  
-
-| Param | Type | Description |
-| --- | --- | --- |
-| copyNumberAlterations | <code>Array</code> | Array of copy number alteration rows as parsed by this library |
-
-
------
-
-<a name="module_cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations"></a>
-### cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations(response) ⇒ <code>Promise</code>
-Converts tab delimited responses to JSON format
-
-**Kind**: static method of <code>[cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)</code>  
-**Returns**: <code>Promise</code> - Resolves with the response JSON  
-
-| Param | Type | Description |
-| --- | --- | --- |
-| response | <code>string</code> | TSV string |
-
-
------
-

lib/utils/index.js

@@ -1,4 +1,4 @@
-import SummarizeAlterations from './summarizeAlterations';
+import * as SummarizeAlterations from './summarizeAlterations';
 import ConvertResponse from './convertResponse';
 
 export const summarizeAlterations = SummarizeAlterations;

lib/utils/summarizeAlterations.js

@@ -11,7 +11,14 @@ import _merge from 'lodash/merge';
 /**
  * Exports utility functions for summarizing gene alterations
  *
- * @exports summarizeAlterations
+ * @example
+ * ```javascript
+ * import {
+ *   summarizeMutations,
+ *   summarize
+ * } from 'cbioportal-api-client/dist/utils/summarizeAlterations';
+ * ```
+ *
  * @module cbioportal-api-client/utils/summarizeAlterations
  */
 

package.json

@@ -15,7 +15,7 @@
     "coverage": "npm run clean:coverage && babel-node node_modules/.bin/isparta cover --report lcov --report text --report html test/index.js",
     "coveralls": "cat ./coverage/lcov.info | coveralls",
     "dev": "nodemon -w lib -w test --exec \"npm run -s lint && npm run -s test:dev\"",
-    "docs": "jsdoc2md --src \"lib/**/*.js\" -t docs/README.md.hbs -d 2 --partial \"./docs/partials/**/*.hbs\" --separators  -l JavaScript > README.md",
+    "docs": "jsdoc2md --src \"lib/index.js\" -t docs/README.md.hbs -d 2 --partial \"./docs/partials/**/*.hbs\" --separators  -l JavaScript > README.md",
     "lint": "eslint lib",
     "precommit": "npm run docs",
     "prepublish": "in-publish && npm run build || not-in-publish",