updating notebooks to newer updated dataset; changing wf.base_dir to /output (instead of /data/...); editing some markdown cells

Author: djarecka

notebooks/basic_function_nodes.ipynb

@@ -17,17 +17,14 @@
    "source": [
     "## Simple example\n",
     "\n",
-    "Let's consider the very simple example depicted at the top of this page (since `A` is not defined, the cell will crash if you try to run):"
+    "Let's consider the very simple example depicted at the top of this page:"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
+   "cell_type": "markdown",
+   "metadata": {},
    "source": [
+    "```python\n",
     "from nipype import Node, JoinNode, Workflow\n",
     "\n",
     "# Specify fake input node A\n",
@@ -51,7 +48,8 @@
     "workflow.connect([(a, b, [('subject', 'subject')]),\n",
     "                  (b, c, [('out_file', 'in_file')])\n",
     "                  (c, d, [('out_file', 'in_files')])\n",
-    "                  ])"
+    "                  ])\n",
+    "```"
    ]
   },
   {
@@ -72,7 +70,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {
     "collapsed": true
    },
@@ -84,7 +82,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {
     "collapsed": true
    },
@@ -99,7 +97,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {
     "collapsed": false
    },
@@ -120,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {
     "collapsed": false
    },
@@ -129,12 +127,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "170715-22:55:10,963 workflow INFO:\n",
+      "170727-22:26:31,403 workflow INFO:\n",
       "\t Workflow joinflow settings: ['check', 'execution', 'logging']\n",
-      "170715-22:55:10,997 workflow INFO:\n",
+      "170727-22:26:31,441 workflow INFO:\n",
       "\t Running serially.\n",
-      "170715-22:55:10,999 workflow INFO:\n",
-      "\t Executing node joinnode in dir: /tmp/tmp0mqxl90s/joinflow/joinnode\n"
+      "170727-22:26:31,444 workflow INFO:\n",
+      "\t Executing node joinnode in dir: /tmp/tmp4cldpdjt/joinflow/joinnode\n"
      ]
     }
    ],
@@ -154,7 +152,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {
     "collapsed": false
    },
@@ -166,7 +164,7 @@
        "sqrts = [1.0, 2.0, 3.0]"
       ]
      },
-     "execution_count": null,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -177,7 +175,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {
     "collapsed": false
    },
@@ -194,7 +192,7 @@
        "numbersJ3 = 9"
       ]
      },
-     "execution_count": null,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -221,9 +219,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 2
 }

notebooks/basic_import_workflows.ipynb

@@ -122,6 +122,19 @@
      "data": {
       "text/html": [
        "<div>\n",
+       "<style>\n",
+       "    .dataframe thead tr:only-child th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: left;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "</style>\n",
        "<table border=\"1\" class=\"dataframe\">\n",
        "  <thead>\n",
        "    <tr style=\"text-align: right;\">\n",
@@ -253,15 +266,15 @@
     {
      "data": {
       "text/plain": [
-       "[('onsets',\n",
+       "[('conditions', ['Finger', 'Foot', 'Lips']),\n",
+       " ('onsets',\n",
        "  [[10, 100, 190, 280, 370],\n",
        "   [40, 130, 220, 310, 400],\n",
        "   [70, 160, 250, 340, 430]]),\n",
        " ('durations',\n",
        "  [[15.0, 15.0, 15.0, 15.0, 15.0],\n",
        "   [15.0, 15.0, 15.0, 15.0, 15.0],\n",
-       "   [15.0, 15.0, 15.0, 15.0, 15.0]]),\n",
-       " ('conditions', ['Finger', 'Foot', 'Lips'])]"
+       "   [15.0, 15.0, 15.0, 15.0, 15.0]])]"
       ]
      },
      "execution_count": 5,
@@ -304,7 +317,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,

notebooks/basic_iteration.ipynb

@@ -3,7 +3,6 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true,
     "deletable": true,
     "editable": true
    },
@@ -79,23 +78,23 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.13"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 2
 }