Patch install instructions and notebook examples

docs/source/developer_guide/developer_installation.rst

@@ -41,23 +41,23 @@ The steps to install PyProBE wih developer settings are as follows:
             conda create -n pyprobe python=3.12
             conda activate pyprobe
 
-3. Install PyProBE as a package into your virtual environment:
+3. Install the developer dependencies:
 
    .. code-block:: bash
 
       cd /path/to/your/directory/PyProBE
+      pip install -r requirements-dev.txt
+
+4. Install PyProBE as a package into your virtual environment:
+
+   .. code-block:: bash
+
       pip install -e .
 
    The :code:`-e` flag installs in "editable" mode, which means changes that you 
    make to the code will be automatically reflected in the package inside your
    virtual environment.
 
-4. Install the developer dependencies:
-
-   .. code-block:: bash
-
-      pip install -r requirements-dev.txt
-
 5. Install the pre-commit hooks:
 
    .. code-block:: bash

docs/source/examples/LEAN-differentiation.ipynb

@@ -5,7 +5,8 @@
    "metadata": {},
    "source": [
     "# Differentiating with the LEAN algorithm\n",
-    "This example shows how to differentiate cycler data using the LEAN algorithm developed by "
+    "This example shows how to differentiate cycler data using the LEAN algorithm developed in: Feng X, Merla Y, Weng C, Ouyang M, He X, Liaw BY, et al. A reliable approach of differentiating discrete sampled-data for battery diagnosis. eTransportation. 2020;3: 100051. https://doi.org/10.1016/j.etran.2020.100051.\n",
+    " "
    ]
   },
   {
@@ -53,7 +54,8 @@
     "final_cycle= cell.procedure['Sample'].experiment('Break-in Cycles').cycle(-1)\n",
     "fig = pyprobe.Plot()\n",
     "fig.add_line(final_cycle, 'Time [hr]', 'Voltage [V]')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -86,7 +88,8 @@
     "fig = pyprobe.Plot()\n",
     "fig.add_line(discharge_dQdV, 'Capacity [Ah]', 'd(Capacity [Ah])/d(Voltage [V])', label='Discharge', color='blue')\n",
     "fig.add_line(charge_dQdV, 'Capacity [Ah]', 'd(Capacity [Ah])/d(Voltage [V])', label='Charge', color='red')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -107,7 +110,8 @@
     "fig = pyprobe.Plot()\n",
     "fig.add_line(discharge_dQdV, 'Capacity [mAh]', 'd(Capacity [mAh])/d(Voltage [V])', label='Discharge', color='blue')\n",
     "fig.add_line(charge_dQdV, 'Capacity [mAh]', 'd(Capacity [mAh])/d(Voltage [V])', label='Charge', color='red')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -128,7 +132,8 @@
     "fig = pyprobe.Plot()\n",
     "fig.add_line(discharge_dQdV, 'Cycle Capacity [Ah]', 'd(Cycle Capacity [Ah])/d(Voltage [V])', label='Discharge', color='blue')\n",
     "fig.add_line(charge_dQdV, 'Cycle Capacity [Ah]', 'd(Cycle Capacity [Ah])/d(Voltage [V])', label='Charge', color='red')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -151,7 +156,8 @@
     "\n",
     "fig = pyprobe.Plot()\n",
     "fig.add_line(pulse_rest, 'Time [s]', 'Voltage [V]')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   }
  ],
@@ -171,7 +177,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

docs/source/examples/filtering-data.ipynb

@@ -53,7 +53,8 @@
     "full_procedure = cell.procedure['Sample']\n",
     "fig = pyprobe.Plot()\n",
     "fig.add_line(full_procedure, 'Time [s]', 'Voltage [V]')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -95,7 +96,8 @@
     "fig.add_line(initial_charge, 'Procedure Time [s]', 'Voltage [V]', color = 'red', label='Initial Charge')\n",
     "fig.add_line(break_in, 'Procedure Time [s]', 'Voltage [V]', color = 'blue', label='Break-in Cycles')\n",
     "fig.add_line(pulses, 'Procedure Time [s]', 'Voltage [V]', color='purple', label='Discharge Pulses')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -116,7 +118,8 @@
     "fig = pyprobe.Plot()\n",
     "fig.add_line(break_in, 'Experiment Time [s]', 'Voltage [V]', color = 'blue', label='Break-in Cycles')\n",
     "fig.add_line(cycle_3, 'Experiment Time [s]', 'Voltage [V]', color='red', label='Cycle 3')\n",
-    "fig.show()\n"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -142,7 +145,8 @@
     "fig.add_line(rest_0, 'Experiment Time [s]', 'Voltage [V]', color='red', label='Rest 0')\n",
     "fig.add_line(charge, 'Experiment Time [s]', 'Voltage [V]', color='purple', label='Charge')\n",
     "fig.add_line(rest_1, 'Experiment Time [s]', 'Voltage [V]', color='green', label='Rest 1')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -167,7 +171,8 @@
     "fig.add_line(CC_discharge, 'Experiment Time [s]', 'Current [A]', color='green', label='CC Discharge')\n",
     "fig.add_line(CC_charge, 'Experiment Time [s]', 'Current [A]', color='red', label='CC Charge')\n",
     "fig.add_line(CV_hold, 'Experiment Time [s]', 'Current [A]', color='purple', label='CV Hold')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   }
  ],

docs/source/examples/getting-started.ipynb

@@ -174,7 +174,8 @@
    "source": [
     "figure = pyprobe.Plot()\n",
     "figure.add_line(cell.procedure['Sample'].experiment('Break-in Cycles'), 'Experiment Time [s]', 'Voltage [V]')\n",
-    "figure.show()"
+    "figure.show_image()\n",
+    "# figure.show() # This will show the plot interactively, it is commented out for the sake of the documentation\n"
    ]
   },
   {
@@ -230,7 +231,8 @@
     "figure.add_line(cycling.summary(), \n",
     "                x = 'Capacity Throughput [Ah]', \n",
     "                y = 'Discharge Capacity [Ah]')\n",
-    "figure.show()"
+    "figure.show_image()\n",
+    "# figure.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   }
  ],

docs/source/examples/ocv-fitting.ipynb

@@ -157,7 +157,8 @@
     "fig = pyprobe.Plot()\n",
     "fig.add_line(fitted_curve, x='SOC', y='Input Voltage [V]',label = \"Input\")\n",
     "fig.add_line(fitted_curve, x='SOC', y='Fitted Voltage [V]', color='red', label = 'Fit', dash='dash')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -183,7 +184,8 @@
     "fig = pyprobe.Plot()\n",
     "fig.add_line(fitted_curve, x='SOC', y='Input dSOCdV [1/V]',label = \"Input\")\n",
     "fig.add_line(fitted_curve, x='SOC', y='Fitted dSOCdV [1/V]', color='red', label = 'Fit', dash='dash')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   }
  ],

docs/source/examples/providing-valid-inputs.ipynb

@@ -238,7 +238,8 @@
     "fig = pyprobe.Plot()\n",
     "fig.add_line(pOCV_cycle.discharge(0).constant_current(0), x='SOC', y='Voltage [V]', label='Discharge', color='blue')\n",
     "fig.add_line(pOCV_cycle.charge(0).constant_current(0), x='SOC', y='Voltage [V]', label='Charge', color='purple')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   },
   {
@@ -257,7 +258,8 @@
     "averaged_ocv_dma = DMA.average_ocvs(input_data = pOCV_cycle, charge_filter=\"charge(0).constant_current(0)\", discharge_filter=\"discharge(0).constant_current(0)\")\n",
     "\n",
     "fig.add_line(averaged_ocv_dma.input_data, x='SOC', y='Voltage [V]', label='Average', color='red')\n",
-    "fig.show()"
+    "fig.show_image()\n",
+    "# fig.show() # This will show the plot interactively, it is commented out for the sake of the documentation"
    ]
   }
  ],

docs/source/user_guide/installation.rst

@@ -73,14 +73,20 @@ The steps to install PyProBE are as follows:
             conda create -n pyprobe python=3.12
             conda activate pyprobe
 
-3. Install PyProBE as a package into your virtual environment:
+3. Install PyProBE's dependencies:
 
-   .. code-block:: bash
+      .. code-block:: bash
 
       cd /path/to/your/directory/PyProBE
+      pip install -r requirements.txt
+
+4. Install PyProBE as a package into your virtual environment:
+
+   .. code-block:: bash
+
       pip install .
 
-4. In your working directory you can create a new python script or jupyter notebook to 
+5. In your working directory you can create a new python script or jupyter notebook to 
    process your data. You can import PyProBE into your script as follows:
 
    .. code-block:: python

pyprobe/plot.py

@@ -4,6 +4,7 @@
 import numpy as np
 import plotly.graph_objects as go
 import polars as pl
+from IPython.display import Image, display
 from numpy.typing import NDArray
 from plotly.express.colors import sample_colorscale
 from plotly.subplots import make_subplots
@@ -57,6 +58,11 @@ def show(self) -> None:
         """Show the plot."""
         self.fig.show()
 
+    def show_image(self) -> None:
+        """Show the plot as an image."""
+        img_bytes = self.fig.to_image(format="png")
+        display(Image(img_bytes))
+
     def add_line(
         self,
         result: "Result",

pyproject.toml

@@ -23,9 +23,10 @@ dependencies = [
     "distinctipy", 
     "streamlit", 
     "PyYAML", 
-    "nbformat", 
     "ordered-set",
     "pydantic",
+    "kaleido",
+    "IPython"
 ]
 
 [project.optional-dependencies]