jekyll-graph 0.0.2 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 670c6b66d66a56c3c63030637450336fa2d9e357b0499615d8799552b047329a
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+  data.tar.gz: fc17d253fed0a6bcb738d21ca2469c7025bdccd0abe476a223649ec0fb3c672a2417f38cbc4381ab92b60a6c69f2480f4daf73bad4c2536e9c8f477924ffec2a

data/CHANGELOG.md

@@ -1,3 +1,24 @@
+## [0.0.6] - 2022-01-24
+### Change
+- Move jekyll patch files to patch/ dir.
+- Bump jekyll-wikilinks version number (0.0.10).
+## [0.0.5] - 2021-11-23
+### Change
+- 'relatives' -> 'lineage' for tree nodes.
+
+## [0.0.4] - 2021-11-22
+### Fix
+- Custom path config related fix in scripts.
+
+## [0.0.3] - 2021-11-22
+### Change
+- Fix javascript inheritance.
+- Decrement missing node log messages from 'warn' to 'debug'.
+- Update license.
+### Fix
+- Display log messages related to dependencies (see [#2](https://github.com/manunamz/jekyll-graph/issues/2)).
+- Custom path configs.
+
 ## [0.0.2] - 2021-09-17
 ### Change
 - Liquid tag `force-graph` -> `jekyll_graph`.  

data/Gemfile

@@ -6,8 +6,8 @@ source "https://rubygems.org"
 gemspec
 
 gem "jekyll", "~> 4.2.0"
-gem "jekyll-namespaces", "~> 0.0.2"
-gem "jekyll-wikilinks", "~> 0.0.6"
+gem "jekyll-namespaces", "~> 0.0.3"
+gem "jekyll-wikilinks", "~> 0.0.10"
 
 gem "rake", "~> 13.0.3"
 gem "rspec", "~> 3.10"

data/README.md

@@ -6,7 +6,7 @@
 
 Jekyll-Graph generates data and renders a graph that allows visitors to navigate a jekyll site by clicking nodes in the graph. Nodes are generated from the site's markdown files. Links for the tree graph are generated from [`jekyll-namespaces`](https://github.com/manunamz/jekyll-namespaces) and links for the net-web graph from [`jekyll-wikilinks`](https://github.com/manunamz/jekyll-wikilinks).
 
-This gem is part of the [jekyll-bonsai](https://manunamz.github.io/jekyll-bonsai/) project. 🎋
+This gem is part of the [jekyll-bonsai](https://jekyll-bonsai.netlify.app/) project. 🎋
 
 ## Installation
 
@@ -37,41 +37,45 @@ Follow the instructions for installing a [jekyll plugin](https://jekyllrb.com/do
 ```javascript
 import JekyllGraph from './jekyll-graph.js';
 
-export default class JekyllGraphSubClass {
-  ...
-}
-
-// subclass
-// Hook up the instance properties
-Object.setPrototypeOf(JekyllGraphSubClass.prototype, JekyllGraph.prototype);
-
-// Hook up the static properties
-Object.setPrototypeOf(JekyllGraphSubClass, JekyllGraph);
+export default class JekyllGraphSubClass extends JekyllGraph {
 
+  constructor() {
+    super();
+    // access graph with 'this.graph'
+    // access graph div with 'this.graphDiv'
+  }
+  
+  // ...
+}
 ```
+
 Call `this.drawNetWeb()` and `this.drawTree()` to actually draw the graph. You could do this simply on initialization or on a button click, etc.
 
-Unless otherwise defined, the `jekyll-graph.js` file will be generated into `_site/assets/scripts/`.
+Unless otherwise configured (see `path` vars below), the `jekyll-graph.js` file will be generated into `_site/assets/js/`.
 
 ## Configuration
 
 Default configs look like this:
 
-```yml
+```yaml
 graph:
   enabled: true
   exclude: []
-  assets_path: "/assets"
-  scripts_path: "/assets/js"
-  tree:
+  path:
+    assets: "/assets"
+    scripts: "/assets/js"
+  net_web:
     enabled: true
+    exclude:
+      attrs: false
+      links: false
     force:
       charge:
       strength_x:
       x_val:
       strength_y:
       y_val:
-  net_web:
+  tree:
     enabled: true
     force:
       charge:
@@ -85,11 +89,13 @@ graph:
 
 `exclude`: Exclude specific jekyll document types (`posts`, `pages`, `collection_items`).
 
-`assets_path`: Custom graph file location from the root of the generated `_site/` directory.
+`path.assets`: An optional custom assets location for graph assets to generate into. Location is relative to the root of the generated `_site/` directory.
+
+`path.scripts`: An optional custom scripts location for the graph scripts to generate into. Location is relative to the assets location in the `_site/` directory (If `assets_path` is set, but `scripts_path` is not, the location will default to `_site/<assets_path>/js/`).
 
-`scripts_path`: Custom graph scripts location from the assets location of the generated `_site/` directory (If `assets_path` is set, but `scripts_path` is not, the location will default to `_site/<assets_path>/js/`).
+`net_web.exclude.attrs` and `net_web.exclude.links`: Determines whether wikilink attributes and/or links are added to the net-web graph from the link index.
 
-`tree.enabled` and `net_web.enabled`: Toggles on/off the `tree` and `net_web` graphs, respectively.
+`tree.enabled` and `net_web.enabled`: Toggles on/off the `tree` and `net_web` graphs, respectively. Be sure to disable graphs that are not in use.
 
 `tree.force` and `net_web.force`: These are force variables from d3's simulation forces. You can check out the [docs for details](https://github.com/d3/d3-force#simulation_force).
 
@@ -98,7 +104,6 @@ Force values will likely need to be played with depending on the div size and nu
 ```yaml
 graph:
   tree:
-    # enabled: true
     dag_lvl_dist: 100
     force:
       charge: -100
@@ -107,7 +112,6 @@ graph:
       strength_y: 0.1
       y_val: 0.9
   net_web:
-    # enabled: true
     force:
       charge: -300
       strength_x: 0.3
@@ -138,13 +142,13 @@ Graph colors are determined by css variables which may be defined like so -- any
   --graph-particles-color: grey;
   /* label text */
   --graph-text-color: black;
-  /*  */
 ```
 
 ## Data
 Graph data is generated in the following format:
 
 For the net-web graph, `graph-net-web.json`,`links` are built from `backlinks` and `attributed` metadata generated in `jekyll-wikilinks`:
+
 ```json
 // graph-net-web.json
 {
@@ -154,8 +158,8 @@ For the net-web graph, `graph-net-web.json`,`links` are built from `backlinks` a
       "url": "<relative-url>", // site.baseurl is handled for you here
       "label": "<note's-title>",
       "neighbors": {
-          "nodes": [<neighbor-node>, ...],
-          "links": [<neighbor-link>, ...],
+          "nodes": [<neighbor-node-id>, ...],
+          "links": [<neighbor-link-id>, ...],
       }
     },
     ...
@@ -169,18 +173,20 @@ For the net-web graph, `graph-net-web.json`,`links` are built from `backlinks` a
   ]
 }
 ```
+
 For the tree graph, `graph-tree.json`, `links` are built from a tree data structure constructed in `jekyll-namespaces`:
+
 ```json
 // graph-tree.json
 {
   "nodes": [
     {
       "id": "<some-id>",
-      "url": "<relative-url>", // site.baseurl wil be handled for you here
+      "url": "<lineage-url>", // site.baseurl wil be handled for you here
       "label": "<note's-title>",
-      "relatives": {
-          "nodes": [<relative-node>, ...],
-          "links": [<relative-link>, ...],
+      "lineage": {
+          "nodes": [<lineage-node-id>, ...],
+          "links": [<lineage-link-id>, ...],
       }
     },
     ...
@@ -194,4 +200,5 @@ For the tree graph, `graph-tree.json`, `links` are built from a tree data struct
   ]
 }
 ```
+
 Unless otherwise defined, both json files are generated into `_site/assets/`.

data/bin/console

@@ -2,7 +2,7 @@
 # frozen_string_literal: true
 
 require "bundler/setup"
-require "jekyll/graph"
+require "jekyll-graph"
 
 # You can add fixtures and/or initialization code here to make experimenting
 # with your gem easier. You can also use a different console, if you like.

data/jekyll-graph.gemspec

@@ -12,7 +12,8 @@ Gem::Specification.new do |spec|
   # spec.description   = "TODO: Write a longer description or delete this line."
   spec.homepage      = "https://github.com/manunamz/jekyll-graph"
   spec.required_ruby_version = Gem::Requirement.new(">= 2.4.0")
-
+  spec.licenses      = ["GPL3"]
+  
   # spec.metadata["allowed_push_host"] = "TODO: Set to 'http://mygemserver.com'"
 
   spec.metadata["homepage_uri"] = spec.homepage
@@ -29,11 +30,11 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   # Uncomment to register a new dependency of your gem
-  # spec.add_dependency "example-gem", "~> 1.0"
+  spec.add_dependency "jekyll", "~> 4.2.0"
 
   # For more information and examples about making a new gem, checkout our
   # guide at: https://bundler.io/guides/creating_gem.html
 
-  spec.add_runtime_dependency "jekyll-namespaces", "~> 0.0.2"
-  spec.add_runtime_dependency "jekyll-wikilinks", "~> 0.0.6"
+  spec.add_runtime_dependency "jekyll-namespaces", "~> 0.0.3"
+  spec.add_runtime_dependency "jekyll-wikilinks", "~> 0.0.10"
 end

data/lib/jekyll-graph/config.rb

@@ -5,12 +5,16 @@ module Jekyll
   module Graph
 
     class PluginConfig
+
+      ASSETS_KEY = "assets"
+      ATTRS_KEY = "attrs"
       CONFIG_KEY = "graph"
       ENABLED_KEY = "enabled"
       EXCLUDE_KEY = "exclude"
+      LINKS_KEY = "links"
       NET_WEB_KEY = "net_web"
-      PATH_ASSETS_KEY = "assets_path"
-      PATH_SCRIPTS_KEY = "scripts_path"
+      PATH_KEY = "path"
+      SCRIPTS_KEY = "scripts"
       TREE_KEY = "tree"
       TYPE_KEY = "type"
 
@@ -20,7 +24,7 @@ module Jekyll
         Jekyll.logger.debug("Excluded jekyll types in graph: ", option(EXCLUDE_KEY)) unless disabled?
       end
 
-      # options
+      # descriptors
 
       def disabled?
         return option(ENABLED_KEY) == false
@@ -39,22 +43,42 @@ module Jekyll
         return option(EXCLUDE_KEY).include?(type.to_s)
       end
 
-      def has_custom_write_path?
-        return !!option(PATH_ASSETS_KEY)
+      def has_custom_assets_path?
+        return option_path(ASSETS_KEY)
       end
 
       def has_custom_scripts_path?
-        return !!option(PATH_SCRIPTS_KEY)
+        return option_path(SCRIPTS_KEY)
+      end
+
+      def use_attrs?
+        return true if option_net_web_exclude(ATTRS_KEY).nil?
+        return !option_net_web_exclude(ATTRS_KEY)
+      end
+
+      def use_links?
+        return true if option_net_web_exclude(LINKS_KEY).nil?
+        return !option_net_web_exclude(LINKS_KEY)
       end
 
+      # options
+
       def option(key)
         @config[CONFIG_KEY] && @config[CONFIG_KEY][key]
       end
 
+      def option_path(key)
+        @config[CONFIG_KEY] && @config[CONFIG_KEY][PATH_KEY] && @config[CONFIG_KEY][PATH_KEY][key]
+      end
+
       def option_net_web(key)
         @config[CONFIG_KEY] && @config[CONFIG_KEY][NET_WEB_KEY] && @config[CONFIG_KEY][NET_WEB_KEY][key]
       end
 
+      def option_net_web_exclude(key)
+        @config[CONFIG_KEY] && @config[CONFIG_KEY][NET_WEB_KEY] && @config[CONFIG_KEY][NET_WEB_KEY][EXCLUDE_KEY] && @config[CONFIG_KEY][NET_WEB_KEY][EXCLUDE_KEY][key]
+      end
+
       def option_tree(key)
         @config[CONFIG_KEY] && @config[CONFIG_KEY][TREE_KEY] && @config[CONFIG_KEY][TREE_KEY][key]
       end
@@ -66,11 +90,11 @@ module Jekyll
       end
 
       def path_assets
-        return has_custom_write_path? ? option(PATH_ASSETS_KEY) : "/assets"
+        return has_custom_assets_path? ? option_path(ASSETS_KEY) : "/assets"
       end
 
       def path_scripts
-        return has_custom_scripts_path? ? option(PATH_SCRIPTS_KEY) : File.join(path_assets, "js")
+        return has_custom_scripts_path? ? File.join(path_assets, option_path(SCRIPTS_KEY)) : File.join(path_assets, "js")
       end
 
       def testing

data/lib/jekyll-graph/jekyll-graph.js

@@ -1,4 +1,5 @@
 // don't need frontmatter because liquid is handled internally...somehow...
+
 export default class JekyllGraph {
 
   constructor() {
@@ -7,7 +8,7 @@ export default class JekyllGraph {
 
   // d3
   drawNetWeb () {
-    let assetsPath = '{{ site.graph.assets_path }}' !== '' ? '{{ site.graph.assets_path }}' : '/assets';
+    let assetsPath = '{{ site.graph.path.assets }}' !== '' ? '{{ site.graph.path.assets }}' : '/assets';
     fetch(`{{ site.baseurl }}${assetsPath}/graph-net-web.json`).then(res => res.json()).then(data => {
 
       // neighbors: replace ids with full object
@@ -29,9 +30,11 @@ export default class JekyllGraph {
       let hoverNode = null;
       let hoverLink = null;
 
-      const Graph = ForceGraph()
+      if (this.graph) {
+        this.graph._destructor();
+      }
 
-      (this.graphDiv)
+      const Graph = ForceGraph()(this.graphDiv)
         // container
         .height(this.graphDiv.parentElement.clientHeight)
         .width(this.graphDiv.parentElement.clientWidth)
@@ -101,35 +104,47 @@ export default class JekyllGraph {
             Graph.height(el.offsetHeight);
           }
         );
+
+        this.graph = Graph;
       });
   }
 
   drawTree () {
-    let assetsPath = '{{ site.graph.assets_path }}' !== '' ? '{{ site.graph.assets_path }}' : '/assets';
+    let assetsPath = '{{ site.graph.path.assets }}' !== '' ? '{{ site.graph.path.assets }}' : '/assets';
     fetch(`{{ site.baseurl }}${assetsPath}/graph-tree.json`).then(res => res.json()).then(data => {
+      
+      if (this.graph) {
+        this.graph._destructor();
+      }
 
-      // relatives: replace ids with full object
-      data.nodes.forEach(node => {
-        let relativeNodes = [];
-        node.relatives.nodes.forEach(nNodeId => {
-          relativeNodes.push(data.nodes.find(node => node.id === nNodeId));
-        });
-        let relativeLinks = [];
-        node.relatives.links.forEach(nLink => {
-          relativeLinks.push(data.links.find(link => link.source === nLink.source && link.target === nLink.target));
-        });
-        node.relatives.nodes = relativeNodes;
-        node.relatives.links = relativeLinks;
-      });
+      // node height vars
+      this.shifted = [];
+      this.numSiblingsLeft = [];
 
+      // hover vars
       const highlightNodes = new Set();
       const highlightLinks = new Set();
       let hoverNode = null;
       let hoverLink = null;
 
-      const Graph = ForceGraph()
+      // lineage: replace ids with full objects
+      data.nodes.forEach(node => {
+        // lineage
+        let lineageNodes = [];
+        node.lineage.nodes.forEach(nNodeId => {
+          lineageNodes.push(data.nodes.find(node => node.id === nNodeId));
+        });
+        let relativeLinks = [];
+        node.lineage.links.forEach(nLink => {
+          relativeLinks.push(data.links.find(link => link.source === nLink.source && link.target === nLink.target));
+        });
+        node.lineage.nodes = lineageNodes;
+        node.lineage.links = relativeLinks;
+        // siblings
+        this.numSiblingsLeft[node.parent] = node.siblings.length;
+      });
 
-      (this.graphDiv)
+      const Graph = ForceGraph()(this.graphDiv)
         // dag-mode (tree)
         .dagMode('td')
         .dagLevelDistance(Number('{{ site.graph.tree.dag_lvl_dist }}'))
@@ -141,6 +156,8 @@ export default class JekyllGraph {
         // .nodePointerAreaPaint((node, color, ctx, scale) => nodePaint(node, nodeTypeInNetWeb(node), ctx))
         .nodeId('id')
         .nodeLabel('label')
+        // todo-shift: this shiftNodeHeight() always renders, but animatation is choppy
+        // .nodeVal(node => this.shiftNodeHeight(node))
         .onNodeClick((node, event) => this.goToPage(node, event))
         // link
         .linkSource('source')
@@ -171,8 +188,8 @@ export default class JekyllGraph {
           highlightLinks.clear();
           if (node) {
             highlightNodes.add(node);
-            node.relatives.nodes.forEach(node => highlightNodes.add(node));
-            node.relatives.links.forEach(link => highlightLinks.add(link));
+            node.lineage.nodes.forEach(node => highlightNodes.add(node));
+            node.lineage.links.forEach(link => highlightLinks.add(link));
           }
           hoverNode = node || null;
         })
@@ -202,12 +219,29 @@ export default class JekyllGraph {
             Graph.height(el.offsetHeight);
           }
         );
+
+        this.graph = Graph;
       });
   }
 
   // draw helpers
 
+  shiftNodeHeight(node) {
+    if (node.namespace !== 'root' && !this.shifted.includes(node)) {
+      const padding = 5;
+      let areSiblingsLeftEven = (this.numSiblingsLeft[node.parent] % 2) === 1;
+      let altrntr = areSiblingsLeftEven ? 1 : -1;
+      node.fy = node.fy + (altrntr * (this.numSiblingsLeft[node.parent] * padding));
+      this.numSiblingsLeft[node.parent] -= 1;
+      this.shifted.push(node);
+    }
+  }
+
   nodePaint(node, ctx, hoverNode, hoverLink, gType) {
+    // todo-shift: this shiftNodeHeight() animates more smoothly, but suffers from a race condition
+    // if (gType === "tree") {
+    //   this.shiftNodeHeight(node);
+    // }
     let fillText = true;
     let radius = 6;
     //
@@ -216,7 +250,7 @@ export default class JekyllGraph {
     if (this.isVisitedPage(node)) {
       ctx.fillStyle = getComputedStyle(document.documentElement).getPropertyValue('--graph-node-visited-color');
     } else if (this.isMissingPage(node)) {
-      ctx.fillStyle = getComputedStyle(document.documentElement).getPropertyValue('--graph-node-missing-color')
+      ctx.fillStyle = getComputedStyle(document.documentElement).getPropertyValue('--graph-node-missing-color');
     } else if (!this.isVisitedPage(node) && !this.isMissingPage(node)) {
       ctx.fillStyle = getComputedStyle(document.documentElement).getPropertyValue('--graph-node-unvisited-color');
     } else {
@@ -235,9 +269,9 @@ export default class JekyllGraph {
     } else if (hoverNode !== null && gType === "net-web" && !hoverNode.neighbors.nodes.includes(node)) {
       // non-neighbor to hoverNode
       fillText = false;
-    } else if (hoverNode !== null && gType === "tree" && hoverNode.relatives.nodes.includes(node)) {
+    } else if (hoverNode !== null && gType === "tree" && hoverNode.lineage.nodes.includes(node)) {
       // neighbor to hoverNode
-    } else if (hoverNode !== null && gType === "tree" && !hoverNode.relatives.nodes.includes(node)) {
+    } else if (hoverNode !== null && gType === "tree" && !hoverNode.lineage.nodes.includes(node)) {
       // non-neighbor to hoverNode
       fillText = false;
     } else if ((hoverNode === null && hoverLink !== null) && (hoverLink.source === node || hoverLink.target === node)) {
@@ -255,11 +289,11 @@ export default class JekyllGraph {
     //
     if (this.isCurrentPage(node)) {
       // turn glow on
-      ctx.shadowBlur = 30;
+      ctx.shadowBlur = 40;
       ctx.shadowColor = getComputedStyle(document.documentElement).getPropertyValue('--graph-node-current-glow');
     } else if (this.isTag(node)) {
       // turn glow on
-      ctx.shadowBlur = 30;
+      ctx.shadowBlur = 40;
       ctx.shadowColor = getComputedStyle(document.documentElement).getPropertyValue('--graph-node-tagged-glow');
     } else if (this.isVisitedPage(node)) {
       // turn glow on

data/lib/jekyll-graph/version.rb

@@ -3,7 +3,7 @@
 module Jekyll
   module Graph
 
-    VERSION = "0.0.2"
+    VERSION = "0.0.6"
 
   end
 end

data/lib/jekyll-graph.rb

@@ -1,8 +1,8 @@
 # frozen_string_literal: true
 require "jekyll"
 
-require_relative "jekyll-graph/context"
-require_relative "jekyll-graph/page"
+require_relative "jekyll-graph/patch/context"
+require_relative "jekyll-graph/patch/page"
 require_relative "jekyll-graph/version"
 
 # setup config
@@ -30,13 +30,14 @@ module Jekyll
       CONVERTER_CLASS = Jekyll::Converters::Markdown
 
       def generate(site)
+        # check what's enabled
         return if $graph_conf.disabled?
-        if !$graph_conf.disabled_net_web? && site.link_index.nil?
-          Jekyll.logger.error("To generate the net-web graph, please add and enable the 'jekyll-wikilinks' plugin")
+        if !$graph_conf.disabled_net_web? && !site.respond_to?(:link_index)
+          Jekyll.logger.error("Jekyll-Graph: To generate the net-web graph, please either add and enable the 'jekyll-wikilinks' plugin or disable the net-web in the jekyll-graph config")
           return
         end
-        if !$graph_conf.disabled_tree? && site.tree.nil?
-          Jekyll.logger.error("To generate the tree graph, please add and enable the 'jekyll-namespaces' plugin")
+        if !$graph_conf.disabled_tree? && !site.respond_to?(:tree)
+          Jekyll.logger.error("Jekyll-Graph: To generate the tree graph, please either add and enable the 'jekyll-namespaces' plugin  or disable the tree in the jekyll-graph config")
           return
         end
 
@@ -50,7 +51,7 @@ module Jekyll
         docs += @site.docs_to_write.filter { |d| !$graph_conf.excluded?(d.type) }
         @md_docs = docs.filter { |doc| markdown_extension?(doc.extname) }
         if @md_docs.empty?
-          Jekyll.logger.debug("No documents to process.")
+          Jekyll.logger.warn("Jekyll-Graph: No documents to process.")
         end
 
         # write graph
@@ -64,25 +65,23 @@ module Jekyll
           )
           # create json file
           json_net_web_graph_file = self.new_page($graph_conf.path_assets, "graph-net-web.json", net_web_graph_content)
-          self.register_static_file(json_net_web_graph_file)
         end
         if !$graph_conf.disabled_tree?
           # generate json data
           json_tree_nodes, json_tree_links = self.generate_json_tree(@site.tree.root)
-          self.set_relatives(json_tree_nodes, json_tree_links)
+          self.set_lineage(json_tree_nodes, json_tree_links)
           tree_graph_content = JSON.dump(
             nodes: json_tree_nodes,
             links: json_tree_links,
           )
           # create json file
           json_tree_graph_file = self.new_page($graph_conf.path_assets, "graph-tree.json", tree_graph_content)
-          self.register_static_file(json_tree_graph_file)
         end
         # add graph drawing scripts
         script_filename = "jekyll-graph.js"
         graph_script_content = File.read(source_path(script_filename))
+        # create js file
         static_file = self.new_page($graph_conf.path_scripts, script_filename, graph_script_content)
-        self.register_static_file(static_file)
       end
 
       # helpers
@@ -116,13 +115,12 @@ module Jekyll
         return new_file
       end
 
-      def register_static_file(static_file)
-        # tests fail without manually adding the static file, but actual site builds seem to do ok
-        # ...although there does seem to be a race condition which causes a rebuild to be necessary in order to detect the graph data file
-        if $graph_conf.testing
-          @site.static_files << static_file if !@site.static_files.include?(static_file)
-        end
-      end
+      # keeping this around in case it's needed again
+      # # tests fail without manually adding the static file, but actual site builds seem to do ok
+      # # ...although there does seem to be a race condition which causes a rebuild to be necessary in order to detect the graph data file
+      # def register_static_file(static_file)
+      #   @site.static_files << static_file if !@site.static_files.include?(static_file)
+      # end
 
       # json population helpers
       #  set ids here, full javascript objects are populated in client-side javascript.
@@ -140,18 +138,24 @@ module Jekyll
         end
       end
 
-      def set_relatives(json_nodes, json_links)
+      def set_lineage(json_nodes, json_links)
         # TODO: json nodes have relative_url, but node.id's/urls are doc urls.
         json_nodes.each do |json_node|
-          ancestor_node_ids, descendent_node_ids = @site.tree.get_all_relative_ids(json_node[:id])
-          relative_node_ids = ancestor_node_ids.concat(descendent_node_ids)
-          json_node[:relatives][:nodes] = relative_node_ids if !relative_node_ids.nil?
+          # set lineage
+
+          ancestor_node_ids, descendent_node_ids = @site.tree.get_all_lineage_ids(json_node[:id])
+          lineage_node_ids = ancestor_node_ids.concat(descendent_node_ids)
+          json_node[:lineage][:nodes] = lineage_node_ids if !lineage_node_ids.nil?
 
           # include current node when filtering for links along entire relative lineage
-          lineage_ids = relative_node_ids.concat([json_node[:id]])
+          lineage_ids = lineage_node_ids.concat([json_node[:id]])
+
+          json_lineage_links = json_links.select { |l| lineage_ids.include?(l[:source]) && lineage_ids.include?(l[:target]) }
+          json_node[:lineage][:links] = json_lineage_links if !json_lineage_links.nil?
+
+          # set siblings
 
-          json_relative_links = json_links.select { |l| lineage_ids.include?(l[:source]) && lineage_ids.include?(l[:target]) }
-          json_node[:relatives][:links] = json_relative_links if !json_relative_links.nil?
+          json_node[:siblings] = @site.tree.get_sibling_ids(json_node[:id])
         end
       end
 
@@ -163,14 +167,13 @@ module Jekyll
         @md_docs.each do |doc|
           if !$graph_conf.excluded?(doc.type)
 
-            Jekyll.logger.debug "Processing graph nodes for doc: ", doc.data['title']
+            Jekyll.logger.debug("Jekyll-Graph: Processing graph nodes for doc: ", doc.data['title'])
             #
             # missing nodes
             #
             @site.link_index.index[doc.url].missing.each do |missing_link_name|
               if net_web_nodes.none? { |node| node[:id] == missing_link_name }
-                Jekyll.logger.warn "Net-Web node missing: ", missing_link_name
-                Jekyll.logger.warn " in: ", doc.data['title']
+                Jekyll.logger.warn("Jekyll-Graph: Net-Web node missing: #{missing_link_name}, in: #{doc.data['title']}")
                 net_web_nodes << {
                   id: missing_link_name, # an id is necessary for link targets
                   url: '',
@@ -200,10 +203,27 @@ module Jekyll
               },
             }
             # TODO: this link calculation ends up with duplicates -- re-visit this later.
-            @site.link_index.index[doc.url].attributes.each do |link| # link = { 'type' => str, 'urls' => [str, str, ...] }
-              # TODO: Header + Block-level wikilinks
-              link['urls'].each do |lu|
-                link_no_anchor = lu.match(/([^#]+)/i)[0]
+            if $graph_conf.use_attrs?
+              @site.link_index.index[doc.url].attributes.each do |link| # link = { 'type' => str, 'urls' => [str, str, ...] }
+                # TODO: Header + Block-level wikilinks
+                link['urls'].each do |lu|
+                  link_no_anchor = lu.match(/([^#]+)/i)[0]
+                  link_no_baseurl = @site.baseurl.nil? ? link_no_anchor : link_no_anchor.gsub(@site.baseurl, "")
+                  linked_doc = @md_docs.select{ |d| d.url == link_no_baseurl }
+                  if !linked_doc.nil? && linked_doc.size == 1 && !$graph_conf.excluded?(linked_doc.first.type)
+                    # TODO: add link['type'] to d3 graph
+                    net_web_links << {
+                      source: doc.url,
+                      target: linked_doc.first.url,
+                    }
+                  end
+                end
+              end
+            end
+            if $graph_conf.use_links?
+              @site.link_index.index[doc.url].forelinks.each do |link| # link = { 'type' => str, 'url' => str }
+                # TODO: Header + Block-level wikilinks
+                link_no_anchor = link['url'].match(/([^#]+)/i)[0]
                 link_no_baseurl = @site.baseurl.nil? ? link_no_anchor : link_no_anchor.gsub(@site.baseurl, "")
                 linked_doc = @md_docs.select{ |d| d.url == link_no_baseurl }
                 if !linked_doc.nil? && linked_doc.size == 1 && !$graph_conf.excluded?(linked_doc.first.type)
@@ -215,19 +235,6 @@ module Jekyll
                 end
               end
             end
-            @site.link_index.index[doc.url].forelinks.each do |link| # link = { 'type' => str, 'url' => str }
-              # TODO: Header + Block-level wikilinks
-              link_no_anchor = link['url'].match(/([^#]+)/i)[0]
-              link_no_baseurl = @site.baseurl.nil? ? link_no_anchor : link_no_anchor.gsub(@site.baseurl, "")
-              linked_doc = @md_docs.select{ |d| d.url == link_no_baseurl }
-              if !linked_doc.nil? && linked_doc.size == 1 && !$graph_conf.excluded?(linked_doc.first.type)
-                # TODO: add link['type'] to d3 graph
-                net_web_links << {
-                  source: doc.url,
-                  target: linked_doc.first.url,
-                }
-              end
-            end
 
           end
         end
@@ -235,12 +242,12 @@ module Jekyll
         return net_web_nodes, net_web_links
       end
 
-      def generate_json_tree(node, json_parent="", tree_nodes=[], tree_links=[])
+      def generate_json_tree(node, json_parent="", tree_nodes=[], tree_links=[], level=0)
         #
         # missing nodes
         #
         if node.missing
-          Jekyll.logger.warn("Document for tree node missing: ", node.namespace)
+          Jekyll.logger.warn("Jekyll-Graph: Document for tree node missing: ", node.namespace)
 
           leaf = node.namespace.split('.').pop()
           missing_node = {
@@ -248,18 +255,22 @@ module Jekyll
             label: leaf.gsub('-', ' '),
             namespace: node.namespace,
             url: "",
-            relatives: {
+            level: level,
+            lineage: {
               nodes: [],
               links: [],
             },
+            siblings: [],
           }
-          tree_nodes << missing_node
+          # non-root handling
           if !json_parent.empty?
+            missing_node[:parent] = json_parent[:id]
             tree_links << {
               source: json_parent[:id],
               target: node.namespace,
             }
           end
+          tree_nodes << missing_node
           json_parent = missing_node
         #
         # existing nodes
@@ -270,22 +281,26 @@ module Jekyll
             label: node.title,
             namespace: node.namespace,
             url: relative_url(node.url),
-            relatives: {
+            level: level,
+            lineage: {
               nodes: [],
               links: [],
             },
+            siblings: [],
           }
-          tree_nodes << existing_node
+          # non-root handling
           if !json_parent.empty?
+            existing_node[:parent] = json_parent[:id]
             tree_links << {
               source: json_parent[:id],
               target: node.url,
             }
           end
+          tree_nodes << existing_node
           json_parent = existing_node
         end
         node.children.each do |child|
-          self.generate_json_tree(child, json_parent, tree_nodes, tree_links)
+          self.generate_json_tree(child, json_parent, tree_nodes, tree_links, (level + 1))
         end
         return tree_nodes, tree_links
       end

metadata

@@ -1,43 +1,57 @@
 --- !ruby/object:Gem::Specification
 name: jekyll-graph
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.6
 platform: ruby
 authors:
 - manunamz
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2021-09-17 00:00:00.000000000 Z
+date: 2022-01-24 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: jekyll
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.2.0
 - !ruby/object:Gem::Dependency
   name: jekyll-namespaces
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.0.2
+        version: 0.0.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.0.2
+        version: 0.0.3
 - !ruby/object:Gem::Dependency
   name: jekyll-wikilinks
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.0.6
+        version: 0.0.10
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.0.6
+        version: 0.0.10
 description:
 email:
 - manunamz@pm.me
@@ -59,13 +73,14 @@ files:
 - jekyll-graph.gemspec
 - lib/jekyll-graph.rb
 - lib/jekyll-graph/config.rb
-- lib/jekyll-graph/context.rb
 - lib/jekyll-graph/jekyll-graph.js
-- lib/jekyll-graph/page.rb
+- lib/jekyll-graph/patch/context.rb
+- lib/jekyll-graph/patch/page.rb
 - lib/jekyll-graph/tags.rb
 - lib/jekyll-graph/version.rb
 homepage: https://github.com/manunamz/jekyll-graph
-licenses: []
+licenses:
+- GPL3
 metadata:
   homepage_uri: https://github.com/manunamz/jekyll-graph
   source_code_uri: https://github.com/manunamz/jekyll-graph
@@ -85,7 +100,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.17
+rubygems_version: 3.2.27
 signing_key:
 specification_version: 4
 summary: Add d3 graph generation to jekyll.