Merge pull request #87 from UBC-MDS/85-notebook-cleanup

85 notebook cleanup

README.md

@@ -12,7 +12,7 @@ We utilized a subset of a dataset originally compiled from 680,333 participants,
 ## Report
 
 The final report can be found
-[here](notebooks/english_language_learning_ability_prediction_analysis.pdf).
+[here](https://github.com/UBC-MDS/522-workflows-group-18/docs/english_language_learning_ability_prediction_analysis.html)
 
 ---
 
@@ -84,6 +84,43 @@ jupyter notebook English Language Learning Ability Prediction.ipynb
 
 2. Navigate through the notebook to view our data analysis process, model training, and predictions.
 
+3. To run the analysis,
+enter the following commands in the terminal in the project root:
+
+```
+# Get train/test data:
+python src/scripts/english_score_get_data.py\
+   --url="https://osf.io/download/g72pq/" \
+   --output_folder_path="./data/raw"
+
+# Perform EDA: 
+python src/scripts/english_score_eda.py -v \
+   --training-data="data/raw/train_data.csv" \
+   --plot-to="results/figures/" \
+   --pickle-to="results/models/preprocessor/" \
+   --tables-to="results/tables/"
+
+# Tune Models:
+python src/scripts/english_score_tuning.py -v \
+    --train="data/raw/train_data.csv" \
+    --test="data/raw/test_data.csv" \
+    --output_dir="results/" \
+    --preprocessor_path="results/models/preprocessor/preprocessor.pkl"
+
+# Get Optimal Model Results:
+python src/scripts/english_score_results.py -v \
+    --train="data/raw/train_data.csv" \
+    --test="data/raw/test_data.csv" \
+    --plot-to="results/figures/" \
+    --tables-to="results/tables/" \
+    --preprocessor_path="results/models/preprocessor/preprocessor.pkl"
+    --best_model_path="results/models/ridge_best_model.pkl"
+
+# Build HTML report and copy build to docs folder
+jupyter-book build notebooks
+cp -r notebooks/_build/html/ docs
+```
+
 ---
 
 ## 🔍 Methodology

docs/_sphinx_design_static/design-tabs.js

@@ -0,0 +1,27 @@
+var sd_labels_by_text = {};
+
+function ready() {
+  const li = document.getElementsByClassName("sd-tab-label");
+  for (const label of li) {
+    syncId = label.getAttribute("data-sync-id");
+    if (syncId) {
+      label.onclick = onLabelClick;
+      if (!sd_labels_by_text[syncId]) {
+        sd_labels_by_text[syncId] = [];
+      }
+      sd_labels_by_text[syncId].push(label);
+    }
+  }
+}
+
+function onLabelClick() {
+  // Activate other inputs with the same sync id.
+  syncId = this.getAttribute("data-sync-id");
+  for (label of sd_labels_by_text[syncId]) {
+    if (label === this) continue;
+    label.previousElementSibling.checked = true;
+  }
+  window.localStorage.setItem("sphinx-design-last-tab", syncId);
+}
+
+document.addEventListener("DOMContentLoaded", ready, false);

docs/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,134 @@
+/*
+ * _sphinx_javascript_frameworks_compat.js
+ * ~~~~~~~~~~
+ *
+ * Compatability shim for jQuery and underscores.js.
+ *
+ * WILL BE REMOVED IN Sphinx 6.0
+ * xref RemovedInSphinx60Warning
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}