Renamed example folder to examples (#83)

* fixes to present version of NYHeadModel code * renamed folder example > examples * prep examples for mybinder * prep for mybinder * add link button to mybinder
LFPy · Oct 12, 2020 · 1c5f706 · 1c5f706
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diff --git a/README.md b/README.md
@@ -60,6 +60,7 @@ Build Status
 ![Lintly flake8 checks](https://github.com/LFPy/lfpykit/workflows/Lintly%20flake8%20checks/badge.svg)
 ![Python application](https://github.com/LFPy/LFPykit/workflows/Python%20application/badge.svg)
 [![Upload Python Package](https://github.com/LFPy/LFPykit/workflows/Upload%20Python%20Package/badge.svg)](https://pypi.org/project/LFPykit)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LFPy/LFPykit.git/master)
 [![License](http://img.shields.io/:license-GPLv3+-green.svg)](http://www.gnu.org/licenses/gpl-3.0.html)
 
 Features

diff --git a/example/Example_EEG_NYHead.ipynb b/example/Example_EEG_NYHead.ipynb
diff --git a/example/LFPykit_demo.ipynb b/example/LFPykit_demo.ipynb
diff --git a/examples/Example_EEG_NYHead.ipynb b/examples/Example_EEG_NYHead.ipynb
diff --git a/example/Example_LFPy.ipynb → examples/Example_LFPy.ipynb b/example/Example_LFPy.ipynb → examples/Example_LFPy.ipynb
@@ -24,12 +24,24 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "## if running on mybinder or similar, uncomment and run the two following lines to install LFPy. \n",
+    "## Then restart the kernel.\n",
+    "#!conda install mpi4py -y\n",
+    "#!pip install -e git+https://github.com/LFPy/LFPy.git@2.2.dev0#egg=LFPy"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "/Users/ehagen/Repositories/LFPykit/example\n",
+      "/Users/ehagen/Repositories/LFPykit/examples\n",
       "sinsyn.mod\n",
       "sinsyn.mod\n",
       "\"/Users/ehagen/anaconda3/envs/lfpy/share/nrn/libtool\" --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H  -I. -I.. -I\"/Users/ehagen/anaconda3/envs/lfpy/include/nrn\" -I\"/Users/ehagen/anaconda3/envs/lfpy/lib\"    -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/ehagen/anaconda3/envs/lfpy/include  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/ehagen/anaconda3/envs/lfpy/include -fdebug-prefix-map=/usr/local/miniconda/conda-bld/neuron_1579771171236/work=/usr/local/src/conda/neuron-7.7.2 -fdebug-prefix-map=/Users/ehagen/anaconda3/envs/lfpy=/usr/local/src/conda-prefix -c -o mod_func.lo mod_func.c\n",
@@ -51,7 +63,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -66,7 +78,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -75,7 +87,7 @@
        "1.0"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -105,7 +117,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -129,7 +141,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,7 +154,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -164,7 +176,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -180,7 +192,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -210,7 +222,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -219,7 +231,7 @@
        "Text(0.5, 0, '$t$ (ms)')"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     },

diff --git a/example/Example_LFPy_MEG.ipynb → examples/Example_LFPy_MEG.ipynb b/example/Example_LFPy_MEG.ipynb → examples/Example_LFPy_MEG.ipynb
@@ -22,6 +22,18 @@
    "execution_count": 2,
    "metadata": {},
    "outputs": [],
+   "source": [
+    "## if running on mybinder or similar, uncomment and run the two following lines to install LFPy. \n",
+    "## Then restart the kernel.\n",
+    "#!conda install mpi4py -y\n",
+    "#!pip install -e git+https://github.com/LFPy/LFPy.git@2.2.dev0#egg=LFPy"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import LFPy, os, numpy as np, matplotlib.pyplot as plt\n",
     "from matplotlib.gridspec import GridSpec\n",
@@ -31,7 +43,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +67,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -77,16 +89,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x10e897610>"
+       "<matplotlib.legend.Legend at 0x13e61a6a0>"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     },

diff --git a/.../Example_LFPy_compare_forwardmodels.ipynb → .../Example_LFPy_compare_forwardmodels.ipynb b/.../Example_LFPy_compare_forwardmodels.ipynb → .../Example_LFPy_compare_forwardmodels.ipynb
@@ -29,12 +29,24 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "## if running on mybinder or similar, uncomment and run the two following lines to install LFPy. \n",
+    "## Then restart the kernel.\n",
+    "#!conda install mpi4py -y\n",
+    "#!pip install -e git+https://github.com/LFPy/LFPy.git@2.2.dev0#egg=LFPy"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "/Users/ehagen/Repositories/LFPykit/example\n",
+      "/Users/ehagen/Repositories/LFPykit/examples\n",
       "sinsyn.mod\n",
       "sinsyn.mod\n",
       "\"/Users/ehagen/anaconda3/envs/lfpy/share/nrn/libtool\" --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H  -I. -I.. -I\"/Users/ehagen/anaconda3/envs/lfpy/include/nrn\" -I\"/Users/ehagen/anaconda3/envs/lfpy/lib\"    -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/ehagen/anaconda3/envs/lfpy/include  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/ehagen/anaconda3/envs/lfpy/include -fdebug-prefix-map=/usr/local/miniconda/conda-bld/neuron_1579771171236/work=/usr/local/src/conda/neuron-7.7.2 -fdebug-prefix-map=/Users/ehagen/anaconda3/envs/lfpy=/usr/local/src/conda-prefix -c -o mod_func.lo mod_func.c\n",
@@ -56,7 +68,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -73,7 +85,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -122,7 +134,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -168,7 +180,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -254,7 +266,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -269,7 +281,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {

diff --git a/example/Example_LFPy_pt3d.ipynb → examples/Example_LFPy_pt3d.ipynb b/example/Example_LFPy_pt3d.ipynb → examples/Example_LFPy_pt3d.ipynb
@@ -30,6 +30,18 @@
    "execution_count": 2,
    "metadata": {},
    "outputs": [],
+   "source": [
+    "## if running on mybinder or similar, uncomment and run the two following lines to install LFPy. \n",
+    "## Then restart the kernel.\n",
+    "#!conda install mpi4py -y\n",
+    "#!pip install -e git+https://github.com/LFPy/LFPy.git@2.2.dev0#egg=LFPy"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import numpy as np\n",
     "import neuron\n",
@@ -41,7 +53,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +80,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -78,7 +90,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -87,7 +99,7 @@
        "1.0"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -129,7 +141,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -160,7 +172,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -180,7 +192,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -206,7 +218,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -242,7 +254,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {