update docs to include github auth feature (#75)

* update docs to include github auth feature

* pr feedback for more verbose context

* move github auth instructions to pacakge management document

* remove github specific link from readme

README.md

@@ -170,7 +170,8 @@ Use your pool configuration JSON file to define your pool in Azure.
   },
   "rPackages": {
     "cran": ["some_cran_package", "some_other_cran_package"],
-    "github": ["username/some_github_package", "another_username/some_other_github_package"]
+    "github": ["username/some_github_package", "another_username/some_other_github_package"],
+    "githubAuthenticationToken": {}
   },
   "commandLine": []
 }

docs/20-package-management.md

@@ -18,6 +18,41 @@ You can install packages by specifying the package(s) in your JSON pool configur
 }
 ```
 
+## Installing packages from a private GitHub repository
+
+Clusters can be configured to install packages from a private GitHub repository by setting the __githubAuthenticationToken__ property. If this property is blank only public repositories can be used. If a token is added then public and the private github repo can be used together.
+
+When the cluster is created the token is passed in as an environment variable called GITHUB\_PAT on start-up which lasts the life of the cluster and is looked up whenever devtools::install_github is called.
+
+```json
+{
+    {
+    "name": <your pool name>,
+    "vmSize": <your pool VM size name>,
+    "maxTasksPerNode": <num tasks to allocate to each node>,
+    "poolSize": {
+        "dedicatedNodes": {
+            "min": 2,
+            "max": 2
+        },
+        "lowPriorityNodes": {
+            "min": 1,
+            "max": 10
+        },
+        "autoscaleFormula": "QUEUE"
+    },
+    "rPackages": {
+        "cran": [],
+        "github": ["<project/some_private_repository>"],
+        "githubAuthenticationToken": "<github_authentication_token>"
+    },
+    "commandLine": []
+    }
+}
+```
+
+_More information regarding github authentication tokens can be found [here](https://help.github.com/articles/creating-a-personal-access-token-for-the-command-line/)_
+
 ## Installing Packages per-*foreach* Loop
 You can also install packages by using the **.packages** option in the *foreach* loop. Instead of installing packages during pool creation, packages (and it's dependencies) can be installed before each iteration in the loop is run on your Azure cluster.
 
@@ -35,5 +70,6 @@ results <- foreach(i = 1:number_of_iterations, .packages=c('package_1', 'package
 
 Installing packages from github using this method is not yet supported.
 
+
 ## Uninstalling packages
 Uninstalling packages from your pool is not supported. However, you may consider rebuilding your pool.

docs/README.md

@@ -19,7 +19,7 @@ This section will provide information about how Azure works, how best to take ad
    
 4. **Package Management** [(link)](./20-package-management.md)
 
-   Best practices for managing your R packages across your Azure pool 
+   Best practices for managing your R packages in code. This includes installation at the cluster or job level as well as how to use different package providers.
    
 5. **Distributing your Data** [(link)](./21-distributing-data.md)
 
@@ -36,3 +36,4 @@ This section will provide information about how Azure works, how best to take ad
 8. **Customize Cluster** [(link)](./30-customize-cluster.md)
 
    Setting up your cluster to user's specific needs
+