pybamm-team#1330 add print_citations to notebooks

brosaplanella · Jan 24, 2021 · a17bac6 · a17bac6
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diff --git a/examples/notebooks/Creating Models/1-an-ode-model.ipynb b/examples/notebooks/Creating Models/1-an-ode-model.ipynb
diff --git a/examples/notebooks/Creating Models/2-a-pde-model.ipynb b/examples/notebooks/Creating Models/2-a-pde-model.ipynb
diff --git a/examples/notebooks/Creating Models/3-negative-particle-problem.ipynb b/examples/notebooks/Creating Models/3-negative-particle-problem.ipynb
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
@@ -47,7 +47,15 @@
    "cell_type": "code",
    "execution_count": 1,
    "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",
@@ -284,14 +292,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "2020-05-30 11:14:09,214 - [WARNING] processed_variable.get_spatial_scale(497): No scale set for spatial variable r_n. Using default of 1 [m].\n",
-      "2020-05-30 11:14:09,244 - [WARNING] processed_variable.get_spatial_scale(497): No scale set for spatial variable r_n. Using default of 1 [m].\n"
+      "2021-01-24 19:29:00,043 - [WARNING] processed_variable.get_spatial_scale(518): No length scale set for negative particle. Using default of 1 [m].\n",
+      "2021-01-24 19:29:00,105 - [WARNING] processed_variable.get_spatial_scale(518): No length scale set for negative particle. Using default of 1 [m].\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "c043c0f27ffc46f88fe69b0cbdf14d46",
+       "model_id": "143b65882ebc453292887b839483c1b2",
        "version_major": 2,
        "version_minor": 0
       },
@@ -367,12 +375,35 @@
     "In the [next notebook](./5-a-simple-SEI-model.ipynb) we consider a simple model for SEI growth, and show how to correctly pose the model in non-dimensional form and then create and solve it using pybamm."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## References\n",
+    "\n",
+    "The relevant papers for this notebook are:"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[1] Joel A. E. Andersson, Joris Gillis, Greg Horn, James B. Rawlings, and Moritz Diehl. CasADi – A software framework for nonlinear optimization and optimal control. Mathematical Programming Computation, 11(1):1–36, 2019. doi:10.1007/s12532-018-0139-4.\n",
+      "[2] Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, and others. Array programming with NumPy. Nature, 585(7825):357–362, 2020. doi:10.1038/s41586-020-2649-2.\n",
+      "[3] Valentin Sulzer, Scott G. Marquis, Robert Timms, Martin Robinson, and S. Jon Chapman. Python Battery Mathematical Modelling (PyBaMM). ECSarXiv. February, 2020. doi:10.1149/osf.io/67ckj.\n",
+      "[4] Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, and others. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods, 17(3):261–272, 2020. doi:10.1038/s41592-019-0686-2.\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "pybamm.print_citations()"
+   ]
   }
  ],
  "metadata": {
@@ -391,7 +422,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.7.4"
   }
  },
  "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
@@ -176,7 +176,15 @@
    "cell_type": "code",
    "execution_count": 1,
    "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",
@@ -538,7 +546,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "2020-05-30 11:30:30,931 - [WARNING] processed_variable.get_spatial_scale(497): No scale set for spatial variable x. Using default of 1 [m].\n"
+      "2021-01-24 19:29:11,759 - [WARNING] processed_variable.get_spatial_scale(518): No length scale set for SEI layer. Using default of 1 [m].\n"
      ]
     }
    ],
@@ -601,7 +609,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "03d0d8fd63324d16858941bfcbe513be",
+       "model_id": "d66f188c61a14a3682d48294f6e5d108",
        "version_major": 2,
        "version_minor": 0
       },
@@ -646,12 +654,35 @@
     "The purpose of this notebook has been to go through the steps involved in getting a simple model working within PyBaMM. However, if you plan on reusing your model and want greater flexibility then we recommend that you create a new class for your model. We have set out instructions on how to do this in the \"Adding a Model\" tutorial in the documentation. "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## References\n",
+    "\n",
+    "The relevant papers for this notebook are:"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 16,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[1] Joel A. E. Andersson, Joris Gillis, Greg Horn, James B. Rawlings, and Moritz Diehl. CasADi – A software framework for nonlinear optimization and optimal control. Mathematical Programming Computation, 11(1):1–36, 2019. doi:10.1007/s12532-018-0139-4.\n",
+      "[2] Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, and others. Array programming with NumPy. Nature, 585(7825):357–362, 2020. doi:10.1038/s41586-020-2649-2.\n",
+      "[3] Valentin Sulzer, Scott G. Marquis, Robert Timms, Martin Robinson, and S. Jon Chapman. Python Battery Mathematical Modelling (PyBaMM). ECSarXiv. February, 2020. doi:10.1149/osf.io/67ckj.\n",
+      "[4] Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, and others. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods, 17(3):261–272, 2020. doi:10.1038/s41592-019-0686-2.\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "pybamm.print_citations()"
+   ]
   }
  ],
  "metadata": {
@@ -670,7 +701,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.4"
   }
  },
  "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
@@ -83,7 +83,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.solvers.solution.Solution at 0x7f20b554f650>"
+       "<pybamm.solvers.solution.Solution at 0x7fc2b39da310>"
       ]
      },
      "execution_count": 4,
@@ -110,7 +110,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "2b323f5e668d4135834681aac97571ce",
+       "model_id": "0d24d4cdcfd1440aae72b0371ddcdec4",
        "version_major": 2,
        "version_minor": 0
       },
@@ -139,19 +139,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## References"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "We would be grateful if you could cite the papers relevant to your code. These will change depending on what models and solvers you use. To find out which papers you should cite, you can run:"
+    "## References\n",
+    "\n",
+    "If you write a paper that uses PyBaMM, we would be grateful if you could cite the papers relevant to your code. These will change depending on what models and solvers you use. To find out which papers you should cite, you can run:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -170,13 +165,6 @@
    "source": [
     "pybamm.print_citations()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/examples/notebooks/Getting Started/Tutorial 2 - Compare models.ipynb b/examples/notebooks/Getting Started/Tutorial 2 - Compare models.ipynb
@@ -89,7 +89,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b9ba084e8e6444c48e8ae6244b753040",
+       "model_id": "33d9970753e647a98da2824a1a72a6a9",
        "version_major": 2,
        "version_minor": 0
       },
@@ -103,7 +103,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x7f5d8b1e5a50>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x7fab1bee6490>"
       ]
      },
      "execution_count": 4,
@@ -126,20 +126,17 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## References"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "The relevant papers to this notebook are:"
+    "## References\n",
+    "\n",
+    "The relevant papers for this notebook are:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -157,13 +154,6 @@
    "source": [
     "pybamm.print_citations()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {