Merge pull request pybamm-team#1061 from ferranbrosa/issue-1044-googl…

…e-colab Issue 1044 google colab
brosaplanella · Jun 21, 2020 · 17460e8 · 17460e8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## Features
 
+-   Adapted examples to be run in Google Colab ([#1061](https://github.com/pybamm-team/PyBaMM/pull/1061))
 -   Added `length_scales` attribute to models ([#1058](https://github.com/pybamm-team/PyBaMM/pull/1058))
 -   Added averaging in secondary dimensions ([#1057](https://github.com/pybamm-team/PyBaMM/pull/1057))
 

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![Build](https://github.com/pybamm-team/PyBaMM/workflows/PyBaMM/badge.svg)](https://github.com/pybamm-team/PyBaMM/actions?query=workflow%3APyBaMM+branch%3Adevelop)
 [![readthedocs](https://readthedocs.org/projects/pybamm/badge/?version=latest)](https://pybamm.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/pybamm-team/PyBaMM/branch/master/graph/badge.svg)](https://codecov.io/gh/pybamm-team/PyBaMM)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pybamm-team/PyBaMM/master?filepath=examples%2Fnotebooks)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/master/)
 [![black_code_style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
 PyBaMM (Python Battery Mathematical Modelling) solves physics-based electrochemical DAE models by using state-of-the-art automatic differentiation and numerical solvers. The Doyle-Fuller-Newman model can be solved in under 0.1 seconds, while the reduced-order Single Particle Model and Single Particle Model with electrolyte can be solved in just a few milliseconds. Additional physics can easily be included such as thermal effects, fast particle diffusion, 3D effects, and more. All models are implemented in a flexible manner, and a wide range of models and parameter sets (NCA, NMC, LiCoO2, ...) are available. There is also functionality to simulate any set of experimental instructions, such as CCCV or GITT, or specify drive cycles.

diff --git a/examples/notebooks/Creating Models/1-an-ode-model.ipynb b/examples/notebooks/Creating Models/1-an-ode-model.ipynb
@@ -29,6 +29,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt"
@@ -278,7 +279,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Creating Models/2-a-pde-model.ipynb b/examples/notebooks/Creating Models/2-a-pde-model.ipynb
@@ -31,6 +31,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt"
@@ -308,7 +309,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Creating Models/3-negative-particle-problem.ipynb b/examples/notebooks/Creating Models/3-negative-particle-problem.ipynb
@@ -54,6 +54,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
@@ -330,7 +331,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb b/examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb
@@ -49,6 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
@@ -390,7 +391,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Creating Models/5-a-simple-SEI-model.ipynb b/examples/notebooks/Creating Models/5-a-simple-SEI-model.ipynb
@@ -178,6 +178,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",
@@ -669,7 +670,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Getting Started/Tutorial 1 - How to run a model.ipynb b/examples/notebooks/Getting Started/Tutorial 1 - How to run a model.ipynb
@@ -24,6 +24,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },
@@ -139,7 +140,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Getting Started/Tutorial 2 - Setting Parameter Values.ipynb b/examples/notebooks/Getting Started/Tutorial 2 - Setting Parameter Values.ipynb
@@ -20,6 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },
@@ -431,7 +432,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Getting Started/Tutorial 3 - Basic Plotting.ipynb b/examples/notebooks/Getting Started/Tutorial 3 - Basic Plotting.ipynb
@@ -31,6 +31,7 @@
     }
    ],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "model = pybamm.lithium_ion.SPMe()\n",
     "sim = pybamm.Simulation(model)\n",
@@ -851,7 +852,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Getting Started/Tutorial 4 - Model Options.ipynb b/examples/notebooks/Getting Started/Tutorial 4 - Model Options.ipynb
@@ -20,6 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm"
    ]
   },
@@ -136,7 +137,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/README.md b/examples/notebooks/README.md
@@ -4,7 +4,7 @@ For new users we recommend the [Getting Started](./Getting%20Started/) notebooks
 
 # Examples
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pybamm-team/PyBaMM/master)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/master/)
 
 This page contains a number of examples showing how to use PyBaMM.
 

diff --git a/examples/notebooks/change-input-current.ipynb b/examples/notebooks/change-input-current.ipynb
@@ -27,10 +27,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",
@@ -329,7 +338,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/change-settings.ipynb b/examples/notebooks/change-settings.ipynb
@@ -30,6 +30,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",
@@ -518,7 +519,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/compare-comsol-discharge-curve.ipynb b/examples/notebooks/compare-comsol-discharge-curve.ipynb
@@ -27,6 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",
@@ -207,7 +208,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/compare-ecker-data.ipynb b/examples/notebooks/compare-ecker-data.ipynb
@@ -22,6 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import os\n",
     "import pandas as pd\n",
@@ -237,7 +238,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/expression_tree/broadcasts.ipynb b/examples/notebooks/expression_tree/broadcasts.ipynb
@@ -16,6 +16,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np"
    ]
@@ -260,7 +261,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/expression_tree/expression-tree.ipynb b/examples/notebooks/expression_tree/expression-tree.ipynb
@@ -22,6 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "\n",
@@ -220,7 +221,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/models/DFN.ipynb b/examples/notebooks/models/DFN.ipynb
@@ -108,6 +108,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",
@@ -278,7 +279,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/models/SPM.ipynb b/examples/notebooks/models/SPM.ipynb
@@ -59,6 +59,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",
@@ -1092,7 +1093,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/models/SPMe.ipynb b/examples/notebooks/models/SPMe.ipynb
@@ -108,6 +108,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",
@@ -269,7 +270,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/models/compare-lithium-ion.ipynb b/examples/notebooks/models/compare-lithium-ion.ipynb
@@ -38,6 +38,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import os\n",
     "os.chdir(pybamm.__path__[0]+'/..')\n",
@@ -442,7 +443,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/models/lead-acid.ipynb b/examples/notebooks/models/lead-acid.ipynb
@@ -22,6 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import numpy as np\n",
     "import os\n",
@@ -424,7 +425,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/models/pouch-cell-model.ipynb b/examples/notebooks/models/pouch-cell-model.ipynb
@@ -53,6 +53,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "import pybamm\n",
     "import sys\n",
     "import pickle\n",
@@ -808,7 +809,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,