Set NB wd as /home/notebooks/. Move data to wd. See details

- Added changelog for internal update notes
- Recent server updates change the default user working directory
- Set each notebook to move to /home/notebooks/ if not in a NB dir already
- Purged outputs from Interactive notebooks
- moved data to /notebooks/ for both modalities

Author: CBroz1

.gitignore

@@ -1,12 +1,14 @@
+# OSX and python intermediate files
 __pycache__/
 .DS_Store
 ~*
 *~
 *.pyc
 .ipynb_checkpoints/
-dj_local_conf.json
-
-.idea/
+debug.log
 
+# DataJoint and setup files
+dj_local_con*.json
 julia/setup.jl
-debug.log
+.idea/
+temp*

01-Calcium_Imaging/02-Imported Tables - Interactive.ipynb

@@ -67,8 +67,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sys\n",
-    "sys.path.append(\"..\")\n",
+    "import os\n",
+    "if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')\n",
     "from tutorial_pipeline.mouse_session import schema, Mouse, Session"
    ]
   },

01-Calcium_Imaging/03-Computed Table, Lookup Table, and Part Table - Interactive.ipynb

@@ -69,8 +69,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sys\n",
-    "sys.path.append(\"..\")\n",
+    "import os\n",
+    "if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')\n",
     "from tutorial_pipeline.imaging import schema, Mouse, Session, Scan, AverageFrame"
    ]
   },

02-Electrophysiology/02-Imported Tables - Interactive.ipynb

@@ -66,8 +66,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sys\n",
-    "sys.path.append(\"..\")\n",
+    "import os\n",
+    "if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')\n",
     "from tutorial_pipeline.mouse_session import schema, Mouse, Session"
    ]
   },
@@ -641,74 +641,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "image/svg+xml": [
-       "<svg height=\"185pt\" viewBox=\"0.00 0.00 75.50 185.00\" width=\"76pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
-       "<g class=\"graph\" id=\"graph0\" transform=\"scale(1 1) rotate(0) translate(4 181)\">\n",
-       "<title>%3</title>\n",
-       "<polygon fill=\"white\" points=\"-4,4 -4,-181 71.5,-181 71.5,4 -4,4\" stroke=\"none\"/>\n",
-       "<!-- Mouse -->\n",
-       "<g class=\"node\" id=\"node1\"><title>Mouse</title>\n",
-       "<g id=\"a_node1\"><a xlink:title=\"mouse_id             \r",
-       "------------------------------\r",
-       "dob=null             \r",
-       "sex=&quot;unknown&quot;        \r",
-       "\">\n",
-       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" points=\"59.75,-177 7.75,-177 7.75,-142 59.75,-142 59.75,-177\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\"/>\n",
-       "<text fill=\"darkgreen\" font-family=\"arial\" font-size=\"12.00\" text-anchor=\"start\" text-decoration=\"underline\" x=\"15.75\" y=\"-157.4\">Mouse</text>\n",
-       "</a>\n",
-       "</g>\n",
-       "</g>\n",
-       "<!-- Session -->\n",
-       "<g class=\"node\" id=\"node3\"><title>Session</title>\n",
-       "<g id=\"a_node3\"><a xlink:title=\"→ Mouse\r",
-       "session_date         \r",
-       "------------------------------\r",
-       "experiment_setup     \r",
-       "experimenter         \r",
-       "data_path=&quot;&quot;         \r",
-       "\">\n",
-       "<polygon fill=\"#00ff00\" fill-opacity=\"0.188235\" points=\"63.25,-106 4.25,-106 4.25,-71 63.25,-71 63.25,-106\" stroke=\"#00ff00\" stroke-opacity=\"0.188235\"/>\n",
-       "<text fill=\"darkgreen\" font-family=\"arial\" font-size=\"12.00\" text-anchor=\"start\" text-decoration=\"underline\" x=\"12.25\" y=\"-86.4\">Session</text>\n",
-       "</a>\n",
-       "</g>\n",
-       "</g>\n",
-       "<!-- Mouse&#45;&gt;Session -->\n",
-       "<g class=\"edge\" id=\"edge1\"><title>Mouse-&gt;Session</title>\n",
-       "<path d=\"M33.75,-141.797C33.75,-130.949 33.75,-116.867 33.75,-106.049\" fill=\"none\" stroke=\"#000000\" stroke-opacity=\"0.250980\" stroke-width=\"0.75\"/>\n",
-       "</g>\n",
-       "<!-- Neuron -->\n",
-       "<g class=\"node\" id=\"node2\"><title>Neuron</title>\n",
-       "<g id=\"a_node2\"><a xlink:title=\"→ Session\r",
-       "neuron_id            \r",
-       "------------------------------\r",
-       "activity             \r",
-       "\">\n",
-       "<ellipse cx=\"33.75\" cy=\"-17.5\" fill=\"#00007f\" fill-opacity=\"0.250980\" rx=\"33.5018\" ry=\"17.5\" stroke=\"#00007f\" stroke-opacity=\"0.250980\"/>\n",
-       "<text fill=\"#00007f\" font-family=\"arial\" font-size=\"12.00\" text-anchor=\"start\" text-decoration=\"underline\" x=\"14.75\" y=\"-15.4\">Neuron</text>\n",
-       "</a>\n",
-       "</g>\n",
-       "</g>\n",
-       "<!-- Session&#45;&gt;Neuron -->\n",
-       "<g class=\"edge\" id=\"edge2\"><title>Session-&gt;Neuron</title>\n",
-       "<path d=\"M33.75,-70.797C33.75,-59.9485 33.75,-45.8669 33.75,-35.0492\" fill=\"none\" stroke=\"#000000\" stroke-opacity=\"0.250980\" stroke-width=\"0.75\"/>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>"
-      ],
-      "text/plain": [
-       "<datajoint.diagram.Diagram at 0x21e2cbe7358>"
-      ]
-     },
-     "execution_count": 28,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "dj.Diagram(schema)"
    ]
@@ -728,7 +663,7 @@
    "formats": "ipynb,py:light"
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -742,9 +677,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.6"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

02-Electrophysiology/02-Imported Tables - Interactive.py

@@ -34,8 +34,8 @@
 
 # Now we would like to continue working with the tables we defined in the previous notebook. To do so, we would need the classes for each table: `Mouse` and `Session`. We can either redefine it here, but for your convenience, we have included the schema and table class definitions in a package called `tutorial_pipeline.mouse_session`, from which you can import the classes as well as the schema object. We will use the schema object again to define more tables.
 
-import sys
-sys.path.append("..")
+import os
+if os.path.basename(os.getcwd())!='notebooks': os.chdir('/home/notebooks')
 from tutorial_pipeline.mouse_session import schema, Mouse, Session
 
 Mouse()