v3.0.0-alpha.0 (#119)

* Convert pre-compiled model structures to `model` class * Rebuild code * Replace var with let * Add plotting with plotly for NodeJS (not for HTML) * Fix plotting with `com` module and rebuild code * Add plotting in the Web * Fix tests for plotly * [Deprecation] Deprecate `com` module (#118) * Rebuild code * Add documentation * Update documentation * Version Bump and Docs Rebuild * Apply suggestions from code review Co-authored-by: q9i <46249765+quantum9Innovation@users.noreply.github.com> * Remove unnecassary variable and rebuild code Co-authored-by: q9i <46249765+quantum9Innovation@users.noreply.github.com>
epispot · Jan 7, 2022 · 6117e2b · 6117e2b
1 parent 0a200ad
commit 6117e2b
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Showing 65 changed files with 906 additions and 1,774 deletions.
diff --git a/EpiJS/com.js b/EpiJS/com.js
diff --git a/EpiJS/comp.js b/EpiJS/comp.js
diff --git a/EpiJS/index.js b/EpiJS/index.js
@@ -1,5 +1,4 @@
 const pre = require('./pre')
-const com = require('./com')
 const comp = require('./comp')
 const model = require('./model')
 const package = require('../package.json');
@@ -13,7 +12,6 @@ let description = package.description;
 exports.pre = pre;
 exports.about = 'EpiJS \n'+description+'\n----------------------------------\n By @epispot \n GitHub - https://github.com/epispot/EpiJS \n Version - '+ version;
 exports.version = version;
-exports.com = com;
 exports.comp = comp;
 exports.model = model;
 exports.utils = utils;

diff --git a/EpiJS/model.js b/EpiJS/model.js
@@ -63,17 +63,17 @@ class Model {
 	 *model.get_data(100) // Get data for 100 days.
 	 */
 	get_data(time) { // skipcq: JS-0045
-		var key = {}
-		var newkey = {}
+		let key = {}
+		let newkey = {}
 
 		// For key in this.key, add it to newkey and key.
-		for (var key_key in this.key) {
+		for (let key_key in this.key) {
 			key[key_key] = this.key[key_key]
 			newkey[key_key] = this.key[key_key]
 		}
 
-		for (var x = 0; x < time; x++) {
-			var y; // skipcq: JS-0119
+		for (let x = 0; x < time; x++) {
+			let y; // skipcq: JS-0119
 			for (y in this.compartments) {
 				newkey[this.compartments[y][1]] = this.compartments[y][0].get_data(key)
 			}
@@ -88,7 +88,7 @@ class Model {
 							"population": key[this.compartments[y][1]],
 							"compartments": {}
 						}
-						for (var z in this.compartments[y][0].compartments) {
+						for (let z in this.compartments[y][0].compartments) {
 							return_val[this.compartments[y][1]].compartments[z] = this.compartments[y][0].getSubData(z, key)
 						}
 					}
@@ -121,7 +121,7 @@ class Model {
 	 * sirm.remove(recovered) // Removes the recovered compartment.
 	 */
 	remove(compartment) {
-		for (var x = 0; x < this.compartments.length; x++) {
+		for (let x = 0; x < this.compartments.length; x++) {
 			if (this.compartments[x][0] === compartment) {
 				this.compartments.splice(x, 1)
 			}
@@ -182,13 +182,13 @@ class Model {
  *mexport(sirm, "output.js", file_type=".js")
  */
 function mexport(model, output, file_type=".json") {
-	var jsonout = {
+	let jsonout = {
 		"compartments": {
 
 		},
 		"key": model.key
 	}
-	for (var x in model.compartments) {
+	for (let x in model.compartments) {
 		if (model.compartments[x][0].compartments === {}) {
 			delete model.compartments[x][0].compartments
 		}
@@ -213,14 +213,14 @@ function mexport(model, output, file_type=".json") {
  */
 function mimport(input, file_type=".json") {
 	if (file_type === ".json") {
-		var json = JSON.parse(fs.readFileSync(input))
+		let json = JSON.parse(fs.readFileSync(input))
 	} else if (file_type === ".js") {
-		var json = require(output)
+		let json = require(output)
 	}
 
-	var comp = []
+	let comp = []
 
-	for (var x in json.compartments) {
+	for (let x in json.compartments) {
 		// If compartments key does not exist in json.compartments[x], then add it
 		if (!Object.prototype.hasOwnProperty.call(json.compartments[x],"compartments")) {
 			json.compartments[x].compartments = {}

diff --git a/EpiJS/plots.js b/EpiJS/plots.js
@@ -7,102 +7,119 @@
  * ```
  */
 
-
- const chart = require('chart.js') // skipcq: JS-0502
+const http = require('http')
+const Plotly = require('plotly.js-dist-min')
 
 /**
- * Plots a output of a model from the pre module.
- * @param {Array} model - The output from the pre module function.
- * @param {HTMLCanvasElement} canvas - The canvas to show the output.
- * @param {Number} days - The amount of days to plot
- * @param {Array} colors - Custom colors for the graph, in the same order the compartments are.
- * @param {Object} options - Optional. Custom configuration to pass into the options parameter for chart.js, defaults to:
- * 
- * ```JSON
- * {
- *  title: {
- *      display: true,
- *      text: "Total Cases"
- *  },
- *  scales: {
- *      yAxes: [{
- *          ticks: {
- *              beginAtZero: true
- *          }
- *      }]
- *  }
- * }
- * ```
- * 
- * @returns Returns the chart.js chart, if needed for modification.
- * 
+ * Plots models from pre or model modules. If in Node, this will generate a localhost, otherwise it will plot it in the HTML div element provided.
+ * @param {Object} model A model class from the pre or model modules.
+ * @param {Number} time The number of days to plot.
+ * @param {String} name The ID of the plot. If this is in HTML, it will be the ID of the div element for the graph.
+ * @param {String} title The title of the graph.
  * @example
  * 
- * let sirout1 = sir(4, 9999, 1000, 100, 1/21, 10999, true)
+ * let susceptible = new Idiom("S-(B*S*I/p)");
+ * let infected = new Idiom("I+(B*S*I/p)-(u*I)");
+ * let recovered = new Idiom("R+(u*I)");
+ * 
+ * let key = {
+ *     "S": 10000,
+ *     "B": 0.3,
+ *     "I": 100,
+ *     "R": 0,
+ *     "p": 10100,
+ *     "u": 0.2
+ * };
  *
- * plot(sirout1, "canvas-pre1", 100) // Plots data for 100 days onto the canvas-pre1 chart, with the data from the SIR model.
+ * let sirm = new Model([[susceptible2, "S"], [infected2, "I"], [recovered2, "R"]], key)
+ * 
+ * plot(sirout1, 100, "SIR", "SIR Model (Population vs. Time)")
  */
-function plot(model, canvas, days, colors=null, options={title: {display: true, text: 'Total Cases'}, scales: {yAxes: [{ticks: {beginAtZero: true}}]}}) {
-    let data = {// skipcq: JS-0502
-        labels: [],
-        datasets: []
-    }
-    for (let i = 0; i < days; i++) {// skipcq: JS-0502
-        data.labels.push('Day '+i)
-    }
-    if (colors !== null) {
-        for (let i = 0; i < model.length; i++) {// skipcq: JS-0502
-            data.datasets.push({
-                label: model[i].name,
-                data: model[i].data,
-                borderColor: colors[i]
-            })
-        } 
+function plot(model, time, name, title='Cases vs. Time') {
+    // Get model data for every day up to and including `time`
+    let data = {
+        xvals: [],
+        yvals: {}
     }
-    else {
-        for (let i = 0; i < model.length; i++) {// skipcq: JS-0502
-            data.datasets.push({
-                label: model[i].label,
-                data: model[i].data,
-                borderColor: '#'+Math.floor(Math.random()*16777215).toString(16)
-            })
-        } 
+
+    for (let x in model.compartments) {
+        data.yvals[model.compartments[x][1]] = []
     }
 
-    let sirChart = new Chart(canvas, {// skipcq: JS-0502
-        type: 'line',
-        data: data,
-        options: options 
-    });
-    return sirChart;
-}
+    // For every day until `time`, get the data
+    for (let x = 0; x < time; x++) {
+        let current = model.get_data(x+1)
 
-/**
- * Manipulate the chart.js graph
- * 
- * @param id The chart.js graph
- * @param {String} mvalue The value to manipulate in `chart.data.datasets[x]`. This can be any valid chart.js parameter. See https://www.chartjs.org/docs/latest/charts/line.html#line-styling
- * @param value The value to insert into the graph
- * @returns The chart.js graph
- * 
- * @example
- * 
- * let sirout1 = sir(4, 9999, 1000, 100, 1/21, 10999, true)
- *
- * let sirplot = plot(sirout1, "canvas-pre1", 100)
- * 
- * sirplot.manipulate(sirplot, "fill", true) // Set fill to true
- */
-function manipulate(id, mvalue, value) {
-    var manip = Chart.getChart(id)// skipcq: JS-0502
+        // For every compartment, get the data
+        for (let y in model.compartments) {
+            // If the compartment data is an object, get .population
+            if (typeof current[model.compartments[y][1]] === 'object') {
+                data.yvals[model.compartments[y][1]].push(current[model.compartments[y][1]].population)
+            } else {
+                data.yvals[model.compartments[y][1]].push(current[model.compartments[y][1]])
+            }
+        }
+        data.xvals.push(x+1)
+    }
 
-    for (var x in manip.data.datasets) {
-        manip.data.datasets[x][mvalue] = value
+    // Create the plot
+    let plotlyData = []
+    for (let x in data.yvals) {
+        plotlyData.push({
+            x: data.xvals,
+            y: data.yvals[x],
+            name: x,
+            mode: 'lines'
+        })
     }
 
-    manip.update()
-    return manip
+    if (typeof process === 'object' && String(process) === '[object process]') { // Is running in NodeJS
+        // Create http server
+        let server = http.createServer((req, res) => {
+            // Send the plot as HTML
+            res.writeHead(200, {'Content-Type': 'text/html'})
+            res.write(`<!DOCTYPE html>
+            <html>
+            <head>
+            <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
+            </head>
+            <body>
+            <div id="plot"></div>
+            <script>
+            let data = ${JSON.stringify(plotlyData)}
+            let layout = {
+                title: '${title}',
+                xaxis: {
+                    title: 'Days'
+                },
+                yaxis: {
+                    title: 'Cases'
+                }
+            }
+            Plotly.newPlot('plot', data, layout)
+            </script>
+            </body>
+            </html>`)
+            res.end()
+        })
+
+        // Start the server
+        server.listen(8080)
+        console.log('[@epispot/epijs] Plotly server running on http://localhost:8080')
+    }
+    else { // Is running in the browser
+        // Create the plot
+        let layout = {
+            title: title,
+            xaxis: {
+                title: 'Days'
+            },
+            yaxis: {
+                title: 'Cases'
+            }
+        }
+        Plotly.newPlot(name, plotlyData, layout)
+    }
 }
 
-exports.plot = plot;
-exports.manipulate = manipulate;
+exports.plot = plot