Merge branch 'refs/heads/develop' into 464-design-updating

# Conflicts: # examples/notebooks/spm_electrode_design.ipynb
pybop-team · Sep 7, 2024 · 121187c · 121187c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## Features
 
+- [#411](https://github.com/pybop-team/PyBOP/pull/411) - Updates notebooks with README in `examples/` directory, removes kaleido dependency and moves to nbviewer rendering, displays notebook figures with `notebook_connected` plotly renderer
 - [#6](https://github.com/pybop-team/PyBOP/issues/6) - Adds Monte Carlo functionality, with methods based on Pints' algorithms. A base class is added `BaseSampler`, in addition to `PintsBaseSampler`.
 - [#353](https://github.com/pybop-team/PyBOP/issues/353) - Allow user-defined check_params functions to enforce nonlinear constraints, and enable SciPy constrained optimisation methods
 - [#222](https://github.com/pybop-team/PyBOP/issues/222) - Adds an example for performing and electrode balancing.

diff --git a/examples/README.md b/examples/README.md
@@ -0,0 +1,43 @@
+# Examples
+
+This directory contains example notebooks and scripts demonstrating how to use PyBOP.
+
+## Directory Structure
+
+- `notebooks/`: Jupyter notebooks of example functionality with explanations
+- `scripts/`: Python scripts for quick reference and command-line usage
+- `standalone/`: Example scripts for using standalone classes
+
+## Notebooks
+
+The `notebooks/` directory contains Jupyter notebooks that provide detailed, interactive examples of various features and use cases. These notebooks include explanations, code snippets, and visualisations.
+
+To view the notebooks with interactive figures without downloading the repository, please use nbviewer:
+
+<div align="center">
+
+[Notebooks on nbviewer](https://nbviewer.org/github/pybop-team/PyBOP/tree/develop/examples/notebooks/)
+
+</div>
+
+## Scripts
+
+The `scripts/` directory contains standalone Python scripts that demonstrate specific tasks or workflows. These scripts are designed for quick reference and can be run directly from the command line.
+
+## Getting Started
+
+1. Clone the repository: `git clone https://github.com/pybop-team/pybop.git`
+2. Navigate to the examples directory: `cd pybop/examples`
+3. Explore the notebooks and scripts in their respective directories.
+4. To run the Jupyter notebooks locally:
+   - Install Jupyter: `pip install jupyter`
+   - Start Jupyter Notebook: `jupyter notebook`
+   - Navigate to the `notebooks/` directory and open the desired notebook
+
+5. To run the Python scripts:
+   - Install PyBOP: `pip install pybop`
+   - Run a script using Python: `python scripts/script_name.py`
+
+## Contributing
+
+If you have additional examples or improvements to existing ones, please feel free to submit a pull request. We appreciate your contributions!
diff --git a/examples/notebooks/LG_M50_ECM/1-single-pulse-circuit-model.ipynb b/examples/notebooks/LG_M50_ECM/1-single-pulse-circuit-model.ipynb
diff --git a/examples/notebooks/comparing_cost_functions.ipynb b/examples/notebooks/comparing_cost_functions.ipynb
diff --git a/examples/notebooks/cost-compute-methods.ipynb b/examples/notebooks/cost-compute-methods.ipynb
@@ -23,7 +23,27 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Note: you may need to restart the kernel to use updated packages.\n",
+      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
     }
@@ -52,7 +72,9 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "import pybop"
+    "import pybop\n",
+    "\n",
+    "pybop.PlotlyManager().pio.renderers.default = \"notebook_connected\""
    ]
   },
   {
@@ -356,14 +378,14 @@
   "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": "2.7.6"
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/ecm_trust-constr.ipynb b/examples/notebooks/ecm_trust-constr.ipynb
diff --git a/examples/notebooks/electrode_balancing.ipynb b/examples/notebooks/electrode_balancing.ipynb
diff --git a/examples/notebooks/equivalent_circuit_identification.ipynb b/examples/notebooks/equivalent_circuit_identification.ipynb
diff --git a/examples/notebooks/multi_model_identification.ipynb b/examples/notebooks/multi_model_identification.ipynb
diff --git a/examples/notebooks/multi_optimiser_identification.ipynb b/examples/notebooks/multi_optimiser_identification.ipynb
diff --git a/examples/notebooks/optimiser_calibration.ipynb b/examples/notebooks/optimiser_calibration.ipynb
diff --git a/examples/notebooks/optimiser_interface.ipynb b/examples/notebooks/optimiser_interface.ipynb
@@ -17,15 +17,46 @@
    "execution_count": null,
    "id": "1",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
    "source": [
     "%pip install --upgrade pip ipywidgets -q\n",
     "%pip install pybop -q\n",
     "\n",
     "# Import the necessary libraries\n",
     "import numpy as np\n",
     "\n",
-    "import pybop"
+    "import pybop\n",
+    "\n",
+    "pybop.PlotlyManager().pio.renderers.default = \"notebook_connected\""
    ]
   },
   {
@@ -250,7 +281,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/pouch_cell_identification.ipynb b/examples/notebooks/pouch_cell_identification.ipynb
diff --git a/examples/notebooks/solver_selection.ipynb b/examples/notebooks/solver_selection.ipynb
@@ -28,11 +28,25 @@
     "outputId": "0d785b07-7cff-4aeb-e60a-4ff5a669afbf"
    },
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "Note: you may need to restart the kernel to use updated packages.\n",
+      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
     }
@@ -46,7 +60,9 @@
     "import numpy as np\n",
     "import pybamm\n",
     "\n",
-    "import pybop"
+    "import pybop\n",
+    "\n",
+    "pybop.PlotlyManager().pio.renderers.default = \"notebook_connected\""
    ]
   },
   {
@@ -172,10 +188,28 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Time Evaluate IDA KLU solver: 0.477\n",
-      "Time Evaluate CasADi solver with 'safe' mode: 0.464\n",
-      "Time Evaluate CasADi solver with 'fast' mode: 0.446\n",
-      "Time Evaluate CasADi solver with 'fast with events' mode: 0.443\n"
+      "Time Evaluate IDA KLU solver: 0.303\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Time Evaluate CasADi solver with 'safe' mode: 1.076\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Time Evaluate CasADi solver with 'fast' mode: 1.003\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Time Evaluate CasADi solver with 'fast with events' mode: 1.008\n"
      ]
     }
    ],
@@ -208,10 +242,28 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Time EvaluateS1 IDA KLU solver: 0.997\n",
-      "Time EvaluateS1 CasADi solver with 'safe' mode: 2.743\n",
-      "Time EvaluateS1 CasADi solver with 'fast' mode: 2.689\n",
-      "Time EvaluateS1 CasADi solver with 'fast with events' mode: 2.688\n"
+      "Time EvaluateS1 IDA KLU solver: 0.671\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Time EvaluateS1 CasADi solver with 'safe' mode: 4.479\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Time EvaluateS1 CasADi solver with 'fast' mode: 3.440\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Time EvaluateS1 CasADi solver with 'fast with events' mode: 3.287\n"
      ]
     }
    ],
@@ -253,7 +305,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/spm_AdamW.ipynb b/examples/notebooks/spm_AdamW.ipynb
diff --git a/examples/notebooks/spm_electrode_design.ipynb b/examples/notebooks/spm_electrode_design.ipynb
diff --git a/noxfile.py b/noxfile.py
@@ -83,6 +83,23 @@ def notebooks(session):
     )
 
 
+@nox.session(name="notebooks-overwrite")
+def notebooks_overwrite(session):
+    """Run the Jupyter notebooks."""
+    session.install("setuptools", "wheel")
+    session.install("-e", ".[all,dev]", silent=False)
+    if PYBOP_SCHEDULED:
+        session.run("pip", "install", f"pybamm=={PYBAMM_VERSION}", silent=False)
+    session.run(
+        "pytest",
+        "--notebooks",
+        "--nbmake",
+        "--overwrite",
+        "--nbmake-timeout=1000",
+        "examples/",
+    )
+
+
 @nox.session(name="tests")
 def run_tests(session):
     """Run all the tests."""

diff --git a/pybop/plotting/nyquist.py b/pybop/plotting/nyquist.py
@@ -1,5 +1,3 @@
-import sys
-
 from pybop import StandardPlot
 from pybop.parameters.parameter import Inputs
 
@@ -17,8 +15,7 @@ def nyquist(problem, problem_inputs: Inputs = None, show=True, **layout_kwargs):
         Input parameters for the problem. If not provided, the default parameters from the problem
         instance will be used. These parameters are verified before use (default is None).
     show : bool, optional
-        If True, the plots will be displayed. If running in an IPython kernel (e.g., Jupyter Notebook),
-        the plots will be shown using SVG format for better quality (default is True).
+        If True, the plots will be displayed.
     **layout_kwargs : dict, optional
         Additional keyword arguments for customising the plot layout. These arguments are passed to
         `fig.update_layout()`.
@@ -134,10 +131,7 @@ def nyquist(problem, problem_inputs: Inputs = None, show=True, **layout_kwargs):
 
         # Overwrite with user-kwargs
         fig.update_layout(**layout_kwargs)
-
-        if "ipykernel" in sys.modules and show:
-            fig.show("svg")
-        elif show:
+        if show:
             fig.show()
 
         figure_list.append(fig)

diff --git a/pybop/plotting/plot2d.py b/pybop/plotting/plot2d.py
@@ -1,4 +1,3 @@
-import sys
 import warnings
 from typing import Union
 
@@ -149,8 +148,8 @@ def plot2d(
         title_y=0.9,
         width=600,
         height=600,
-        xaxis=dict(range=bounds[0]),
-        yaxis=dict(range=bounds[1]),
+        xaxis=dict(range=bounds[0], showexponent="last", exponentformat="e"),
+        yaxis=dict(range=bounds[1], showexponent="last", exponentformat="e"),
     )
     if hasattr(cost, "parameters"):
         name = cost.parameters.keys()
@@ -204,9 +203,7 @@ def plot2d(
 
     # Update the layout and display the figure
     fig.update_layout(**layout_kwargs)
-    if "ipykernel" in sys.modules and show:
-        fig.show("svg")
-    elif show:
+    if show:
         fig.show()
 
     if gradient:
@@ -225,9 +222,7 @@ def plot2d(
             )
             grad_fig.update_layout(**layout_kwargs)
 
-            if "ipykernel" in sys.modules and show:
-                grad_fig.show("svg")
-            elif show:
+            if show:
                 grad_fig.show()
 
             # append grad_fig to list

diff --git a/pybop/plotting/plot_convergence.py b/pybop/plotting/plot_convergence.py
@@ -1,5 +1,3 @@
-import sys
-
 from pybop import StandardPlot
 
 
@@ -35,17 +33,17 @@ def plot_convergence(optim, show=True, **layout_kwargs):
         x=iteration_numbers,
         y=cost_log,
         layout_options=dict(
-            xaxis_title="Iteration", yaxis_title="Cost", title="Convergence"
+            xaxis_title="Iteration",
+            yaxis_title="Cost",
+            title="Convergence",
         ),
         trace_names=optim.name(),
     )
 
     # Generate and display the figure
     fig = plot_dict(show=False)
     fig.update_layout(**layout_kwargs)
-    if "ipykernel" in sys.modules and show:
-        fig.show("svg")
-    elif show:
+    if show:
         fig.show()
 
     return fig