Merge pull request #49 from sinhaharsh/master

adding required packages to ease notebook usage
raamana · Oct 11, 2022 · b559eba · b559eba
2 parents 7c40b22 + b5857db
commit b559eba
Showing 1 changed file with 35 additions and 21 deletions.
diff --git a/docs/usage.ipynb b/docs/usage.ipynb
@@ -32,6 +32,17 @@
     "<a id='motivation'></a>"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "!pip install matplotlib"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -434,7 +445,7 @@
    "source": [
     "The dataset can be populated by adding all subjects belonging to a one class (referred to by `cls_id` here), done by adding one samplet at a time, using the `.add_samplet()` method. Let's go ahead and add some samplets based on id lists we just created.\n",
     "\n",
-    "*Note*: `samplet` here refers to a single in the sample feature matrix X. This new term `samplet` is defined to distinguish individual row elements of X from X itself and minimized confusion."
+    "*Note*: `samplet` here refers to a single row in the sample feature matrix X. This new term `samplet` is defined to distinguish individual row elements of X from X itself and minimized confusion."
    ]
   },
   {
@@ -817,11 +828,11 @@
      "evalue": "'dlfjdjf not found in dataset.'",
      "output_type": "error",
      "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-22-4b19d52bac71>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mdataset\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'dlfjdjf'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
-      "\u001b[0;32m~/dev/pyradigm/pyradigm/base.py\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, item)\u001b[0m\n\u001b[1;32m   1020\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_data\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mitem\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1021\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1022\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'{} not found in dataset.'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mitem\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1023\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1024\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mKeyError\u001b[0m: 'dlfjdjf not found in dataset.'"
+      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[0;31mKeyError\u001B[0m                                  Traceback (most recent call last)",
+      "\u001B[0;32m<ipython-input-22-4b19d52bac71>\u001B[0m in \u001B[0;36m<module>\u001B[0;34m\u001B[0m\n\u001B[0;32m----> 1\u001B[0;31m \u001B[0mdataset\u001B[0m\u001B[0;34m[\u001B[0m\u001B[0;34m'dlfjdjf'\u001B[0m\u001B[0;34m]\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m",
+      "\u001B[0;32m~/dev/pyradigm/pyradigm/base.py\u001B[0m in \u001B[0;36m__getitem__\u001B[0;34m(self, item)\u001B[0m\n\u001B[1;32m   1020\u001B[0m             \u001B[0;32mreturn\u001B[0m \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m_data\u001B[0m\u001B[0;34m[\u001B[0m\u001B[0mitem\u001B[0m\u001B[0;34m]\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m   1021\u001B[0m         \u001B[0;32melse\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m-> 1022\u001B[0;31m             \u001B[0;32mraise\u001B[0m \u001B[0mKeyError\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m'{} not found in dataset.'\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mformat\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mitem\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m   1023\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m   1024\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;31mKeyError\u001B[0m: 'dlfjdjf not found in dataset.'"
      ]
     }
    ],
@@ -879,24 +890,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
-   "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'sample' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-24-3c3646e8c9b1>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0msamplet\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfeatures\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdataset\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"{} : {:>10} : {}\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msample\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdataset\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtargets\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msamplet\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfeatures\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m: name 'sample' is not defined"
-     ]
+   "execution_count": null,
+   "metadata": {
+    "pycharm": {
+     "is_executing": true
     }
-   ],
+   },
+   "outputs": [],
    "source": [
     "for samplet, features in dataset:\n",
-    "    print(\"{} : {:>10} : {}\".format(sample, dataset.targets[samplet], features))"
+    "    print(\"{} : {:>10} : {}\".format(samplet, dataset.targets[samplet], features))"
    ]
   },
   {
@@ -1846,6 +1849,17 @@
     "This is all well and good. How does it interact with other packages out there, you might ask? It is as simple as you can imagine:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "!pip install scikit-learn"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
   {
    "cell_type": "code",
    "execution_count": 51,