add documentation.yaml and update readme links to work in github/locally/docs

Author: omargfh

README.md

@@ -1,4 +1,3 @@
-
 # NetLogo View2.5D Extension
 
 The `view2.5d` extension allows you to visualize 2d models on a 3d surface, using height to represent agent properties.
@@ -44,40 +43,38 @@ Send comments, bugs, or other feedback to [CCL Feedback](mailto:ccl-feedback@ccl
 
 ## Primitives
 
-[`view2.5d:patch-view`](#view2.5dpatch-view)
-[`view2.5d:decorate-patch-view`](#view2.5ddecorate-patch-view)
-[`view2.5d:undecorate-patch-view`](#view2.5dundecorate-patch-view)
-[`view2.5d:turtle-view`](#view2.5dturtle-view)
-[`view2.5d:update-all-patch-views`](#view2.5dupdate-all-patch-views)
-[`view2.5d:update-patch-view`](#view2.5dupdate-patch-view)
-[`view2.5d:update-turtle-view`](#view2.5dupdate-turtle-view)
-[`view2.5d:get-z-scale`](#view2.5dget-z-scale)
-[`view2.5d:set-z-scale`](#view2.5dset-z-scale)
-[`view2.5d:set-turtle-stem-thickness`](#view2.5dset-turtle-stem-thickness)
-[`view2.5d:set-turtle-stem-color`](#view2.5dset-turtle-stem-color)
-[`view2.5d:show-links-xy-plane`](#view2.5dshow-links-xy-plane)
-[`view2.5d:show-links-xyz`](#view2.5dshow-links-xyz)
-[`view2.5d:get-observer-angles`](#view2.5dget-observer-angles)
-[`view2.5d:set-observer-angles`](#view2.5dset-observer-angles)
-[`view2.5d:get-observer-xy-focus`](#view2.5dget-observer-xy-focus)
-[`view2.5d:set-observer-xy-focus`](#view2.5dset-observer-xy-focus)
-[`view2.5d:get-observer-distance`](#view2.5dget-observer-distance)
-[`view2.5d:set-observer-distance`](#view2.5dset-observer-distance)
-[`view2.5d:remove-patch-view`](#view2.5dremove-patch-view)
-[`view2.5d:remove-turtle-view`](#view2.5dremove-turtle-view)
-[`view2.5d:remove-all-patch-views`](#view2.5dremove-all-patch-views)
-[`view2.5d:remove-all-turtle-views`](#view2.5dremove-all-turtle-views)
-[`view2.5d:count-windows`](#view2.5dcount-windows)
-
+[`view2.5d:patch-view`](https://docs.netlogo.org/view2.5d#patch-view)
+[`view2.5d:decorate-patch-view`](https://docs.netlogo.org/view2.5d#decorate-patch-view)
+[`view2.5d:undecorate-patch-view`](https://docs.netlogo.org/view2.5d#undecorate-patch-view)
+[`view2.5d:turtle-view`](https://docs.netlogo.org/view2.5d#turtle-view)
+[`view2.5d:update-all-patch-views`](https://docs.netlogo.org/view2.5d#update-all-patch-views)
+[`view2.5d:update-patch-view`](https://docs.netlogo.org/view2.5d#update-patch-view)
+[`view2.5d:update-turtle-view`](https://docs.netlogo.org/view2.5d#update-turtle-view)
+[`view2.5d:get-z-scale`](https://docs.netlogo.org/view2.5d#get-z-scale)
+[`view2.5d:set-z-scale`](https://docs.netlogo.org/view2.5d#set-z-scale)
+[`view2.5d:set-turtle-stem-thickness`](https://docs.netlogo.org/view2.5d#set-turtle-stem-thickness)
+[`view2.5d:set-turtle-stem-color`](https://docs.netlogo.org/view2.5d#set-turtle-stem-color)
+[`view2.5d:show-links-xy-plane`](https://docs.netlogo.org/view2.5d#show-links-xy-plane)
+[`view2.5d:show-links-xyz`](https://docs.netlogo.org/view2.5d#show-links-xyz)
+[`view2.5d:get-observer-angles`](https://docs.netlogo.org/view2.5d#get-observer-angles)
+[`view2.5d:set-observer-angles`](https://docs.netlogo.org/view2.5d#set-observer-angles)
+[`view2.5d:get-observer-xy-focus`](https://docs.netlogo.org/view2.5d#get-observer-xy-focus)
+[`view2.5d:set-observer-xy-focus`](https://docs.netlogo.org/view2.5d#set-observer-xy-focus)
+[`view2.5d:get-observer-distance`](https://docs.netlogo.org/view2.5d#get-observer-distance)
+[`view2.5d:set-observer-distance`](https://docs.netlogo.org/view2.5d#set-observer-distance)
+[`view2.5d:remove-patch-view`](https://docs.netlogo.org/view2.5d#remove-patch-view)
+[`view2.5d:remove-turtle-view`](https://docs.netlogo.org/view2.5d#remove-turtle-view)
+[`view2.5d:remove-all-patch-views`](https://docs.netlogo.org/view2.5d#remove-all-patch-views)
+[`view2.5d:remove-all-turtle-views`](https://docs.netlogo.org/view2.5d#remove-all-turtle-views)
+[`view2.5d:count-windows`](https://docs.netlogo.org/view2.5d#count-windows)
 
 ### `view2.5d:patch-view`
 
 ```NetLogo
 view2.5d:patch-view Title Reporter
 ```
 
-
-This command must be called from the Observer context.  (Attempting to call from another context causes an error)
+This command must be called from the Observer context. (Attempting to call from another context causes an error)
 The Title is a string, which will be used to label the new Window and to call for subsequent updates and modifications.
 Specification of the Reporter uses the NetLogo anonymous procedure syntax, from the Observer perspective.
 
@@ -87,17 +84,15 @@ Example:
 view2.5d:patch-view "Test"  [ [the-patch] -> [pxcor] of the-patch ]
 ```
 
-
 ### `view2.5d:decorate-patch-view`
 
 ```NetLogo
 view2.5d:decorate-patch-view Title
 ```
 
-
-This command must be called from the Observer context.  (Attempting to call from another context causes an error)
+This command must be called from the Observer context. (Attempting to call from another context causes an error)
 The Title is a string, the label of an existing Patch View Window.
-Effect:  draws the turtles of the model at their current location, on top of the Patch view display
+Effect: draws the turtles of the model at their current location, on top of the Patch view display
 
 > NOTE: only has an effect in the "structures" patch view (in the others, the patch value is inclined based on neighbors & gradient)
 
@@ -109,34 +104,30 @@ Example:
 view2.5d:decorate-patch-view "Test"
 ```
 
-
 ### `view2.5d:undecorate-patch-view`
 
 ```NetLogo
 view2.5d:undecorate-patch-view Title
 ```
 
-
-This command must be called from the Observer context.  (Attempting to call from another context causes an error)
+This command must be called from the Observer context. (Attempting to call from another context causes an error)
 
 The Title is a string, the label of an existing Patch View Window.
-Effect:  STOPS drawing the turtles of the model at their current location, on top of the Patch view display
+Effect: STOPS drawing the turtles of the model at their current location, on top of the Patch view display
 
 Example:
 
 ```NetLogo
 view2.5d:undecorate-patch-view "Test"
 ```
 
-
 ### `view2.5d:turtle-view`
 
 ```NetLogo
 view2.5d:turtle-view Title Agents Reporter
 ```
 
-
-This command must be called from the Observer context.  (Attempting to call from another context causes an error)
+This command must be called from the Observer context. (Attempting to call from another context causes an error)
 The Title is a string, which will be used to label the new Window and to call for subsequent updates.
 The turtle-set is any selector for turtles.
 Reporter is an anonymous reporter that should take a turtle as input, and report some number from it.
@@ -148,83 +139,69 @@ view2.5d:turtle-view "Test" turtles with [color = red] [ the-turtle -> [energy]
 ; This would create a new 2.5d window, plotting the ENERGY value of all turtles that are red.
 ```
 
-
 ### `view2.5d:update-all-patch-views`
 
 ```NetLogo
 view2.5d:update-all-patch-views
 ```
 
-
 This command must be called from the Observer context.
 Updates all existing patch-view windows according to the latest values.
 
-
 ### `view2.5d:update-patch-view`
 
 ```NetLogo
 view2.5d:update-patch-view Title
 ```
 
-
 This command must be called from the Observer context.
 Updates only the patch-view window with the specified title (if any).
 
-
 ### `view2.5d:update-turtle-view`
 
 ```NetLogo
 view2.5d:update-turtle-view Title Agents
 ```
 
-
 This command must be called from the Observer context.
 Updates only the turtle-view window with the specified title (if any).
 The turtle-set selector must be supplied to refresh the set of turtles.
 
-
 ### `view2.5d:get-z-scale`
 
 ```NetLogo
 view2.5d:get-z-scale title
 ```
 
-
 This reporter must be called from the Observer context.
 Returns the current z-scale of the turtle-view or patch-view window with the specified title (if any).
 
-
 ### `view2.5d:set-z-scale`
 
 ```NetLogo
 view2.5d:set-z-scale Title new-z-scale
 ```
 
-
 This command must be called from the Observer context.
 Updates only the turtle-view or patch-view window with the specified title (if any).
 The view is now displayed with the new z-scale.
 
-
 ### `view2.5d:set-turtle-stem-thickness`
 
 ```NetLogo
 view2.5d:set-turtle-stem-thickness Title thickness
 ```
 
-
 This command must be called from the Observer context.
 Updates only the turtle-view window with the specified title (if any).
 Turtles are now drawn with "pins" or "stems" that have the specified thickness (instead of the hairline default).
 
-
 ### `view2.5d:set-turtle-stem-color`
 
 ```NetLogo
 view2.5d:set-turtle-stem-color Title colorReporter
 ```
 
-
 This command must be called from the Observer context.
 Updates only the turtle-view window with the specified title (if any).
 colorReporter is an anonymous reporter that should take a turtle as input, and report some number representing a color from it.
@@ -251,152 +228,125 @@ view2.5d:set-turtle-stem-color "Test" [ the-turtle -> [ color ] of the-turtle ]
 view2.5d:set-turtle-stem-color "Test" [ orange ]
 ```
 
-
 ### `view2.5d:show-links-xy-plane`
 
 ```NetLogo
 view2.5d:show-links-xy-plane Title
 ```
 
-
-  This command must be called from the Observer context.
-  Updates only the turtle-view  or patch-view window with the specified title (if any).
-  Links are drawn in the xy-plane (instead of the turtle to turtle default).
-  This option can be selected using the Link Options xy-plane radio Button in the 3D view.
-
+This command must be called from the Observer context.
+Updates only the turtle-view or patch-view window with the specified title (if any).
+Links are drawn in the xy-plane (instead of the turtle to turtle default).
+This option can be selected using the Link Options xy-plane radio Button in the 3D view.
 
 ### `view2.5d:show-links-xyz`
 
 ```NetLogo
 view2.5d:show-links-xyz Title
 ```
 
-
-  This command must be called from the Observer context.
-  Updates only the turtle-view  or patch-view window with the specified title (if any).
-  Links are drawn from turtle to turtle (this is the default way links are displayed).
-  This option can be selected using the Link Options xyz radio Button in the 3D view.
-
+This command must be called from the Observer context.
+Updates only the turtle-view or patch-view window with the specified title (if any).
+Links are drawn from turtle to turtle (this is the default way links are displayed).
+This option can be selected using the Link Options xyz radio Button in the 3D view.
 
 ### `view2.5d:get-observer-angles`
 
 ```NetLogo
 view2.5d:get-observer-angles Title
 ```
 
-
 This reporter must be called from the Observer context.
 Returns a list reflecting the observer's angular perspective { heading pitch } (the place on an imaginary sphere at the zoom distance is updated to obey heading & pitch given)
 
-
 ### `view2.5d:set-observer-angles`
 
 ```NetLogo
 view2.5d:set-observer-angles Title heading pitch
 ```
 
-
 This command must be called from the Observer context.
 Updates only the turtle-view window with the specified title (if any).
 Sets the observer's angular perspective (the place on an imaginary sphere at the zoom distance is updated to obey heading & pitch given)
 
-
 ### `view2.5d:get-observer-xy-focus`
 
 ```NetLogo
 view2.5d:get-observer-xy-focus Title
 ```
 
-
 This reporter must be called from the Observer context.
 Returns a list reflecting the x and y coordinates the observer is "looking at" in the patch plane.
 
-
 ### `view2.5d:set-observer-xy-focus`
 
 ```NetLogo
 view2.5d:set-observer-xy-focus Title number ycor
 ```
 
-
 This command must be called from the Observer context.
 Updates only the turtle-view window with the specified title (if any).
 Sets the x and y coordinates the observer that is "looking at" in the patch plane.
 
-
 ### `view2.5d:get-observer-distance`
 
 ```NetLogo
 view2.5d:get-observer-distance Title
 ```
 
-
 This reporter must be called from the Observer context.
 Returns the observer's distance from its "focus point"
 
-
 ### `view2.5d:set-observer-distance`
 
 ```NetLogo
 view2.5d:set-observer-distance Title new-distance
 ```
 
-
 This command must be called from the Observer context.
 Updates only the turtle-view window with the specified title (if any).
 Sets the observer's distance from its "focus point"
 
-
 ### `view2.5d:remove-patch-view`
 
 ```NetLogo
 view2.5d:remove-patch-view Title
 ```
 
-
 This command closes and removes the specified patch view programmatically (equivalent to closing the window manually).
 
-
 ### `view2.5d:remove-turtle-view`
 
 ```NetLogo
 view2.5d:remove-turtle-view Title
 ```
 
-
 This command closes and removes the specified turtle view programmatically (equivalent to closing the window manually).
 
-
 ### `view2.5d:remove-all-patch-views`
 
 ```NetLogo
 view2.5d:remove-all-patch-views
 ```
 
-
 This command closes and removes all patch views programmatically (equivalent to closing the windows manually).
 
-
 ### `view2.5d:remove-all-turtle-views`
 
 ```NetLogo
 view2.5d:remove-all-turtle-views
 ```
 
-
 This command closes and removes all turtle views programmatically (equivalent to closing the windows manually).
 
-
 ### `view2.5d:count-windows`
 
 ```NetLogo
 view2.5d:count-windows
 ```
 
-
 This reporter returns the number of turtle and patch views that are currently active.
 
-
 ## Acknowledgement
 
 For development of the View 2.5D NetLogo Extension, we acknowledge financial support from Joshua M. Epstein's NIH Director's Pioneer Award (DP1).