Mkdocs conversion

.github/workflows/documentation-build.yml

@@ -35,15 +35,9 @@ jobs:
 
     - name: Build documentation
       run: pixi run --environment dev docs-build
-
-    # - name: Build and Commit
-    #   uses: sphinx-notes/pages@master
-    #   with:
-    #     install_requirements: true
-    #     documentation_path: docs/src
 
     - name: Deploy to GitHub Pages
       uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./docs/_build/html
+        publish_dir: ./site

Examples/base/README.md

@@ -0,0 +1,3 @@
+# Subclassing Examples
+
+This section gathers examples which correspond to subclassing the `easyscience.base_classes.ObjBase` class.

Examples/base/plot_baseclass1.py

@@ -1,14 +1,14 @@
 """
-Subclassing ObjBase - Simple Pendulum
-=====================================
-This  example shows how to subclass :class:`easyscience.base_classes.ObjBase` with parameters from
-:class:`EasyScience.variable.Parameter`. For this example a simple pendulum will be modeled.
+# Subclassing ObjBase - Simple Pendulum
 
-.. math::
+This  example shows how to subclass `easyscience.base_classes.ObjBase` with parameters from
+`EasyScience.variable.Parameter`. For this example a simple pendulum will be modeled.
+
+$$
     y = A \sin (2 \pi f t + \phi )
+$$
 
-Imports
-*******
+## Imports
 
 Firstly the necessary imports. Notice that we import numpy from easyscience. This is not done for any reason other than
 saving time from multiple imports.
@@ -21,8 +21,8 @@
 from easyscience.variable import Parameter
 
 # %%
-# Subclassing
-# ***********
+# ## Subclassing
+#
 # To include embedded rST, use a line of >= 20 ``#``'s or ``#%%`` between your
 # rST and your code. This separates your example
 # into distinct text and code blocks. You can continue writing code below the
@@ -53,8 +53,8 @@ def plot(self, time, axis=None, **kwargs):
 
 
 # %%
-# Single Example
-# **************
+# ## Single Example
+#
 # To include embedded rST, use a line of >= 20 ``#``'s or ``#%%`` between your
 # rST and your code. This separates your example
 # into distinct text and code blocks. You can continue writing code below the
@@ -82,8 +82,8 @@ def plot(self, time, axis=None, **kwargs):
 fig.show()
 
 # %%
-# Multiple Examples
-# *****************
+# ## Multiple Examples
+#
 # To include embedded rST, use a line of >= 20 ``#``'s or ``#%%`` between your
 # rST and your code. This separates your example
 # into distinct text and code blocks. You can continue writing code below the

Examples/fitting/README.rst → Examples/fitting/README.md

@@ -1,6 +1,3 @@
-.. _fitting_examples:
-
-Fitting Examples
-----------------
+# Fitting Examples
 
 This section gathers examples which demonstrate fitting functionality using EasyScience's fitting capabilities.

Examples/fitting/plot_fitting1.py

@@ -0,0 +1,80 @@
+"""
+# Simple Fitting Example
+
+This example demonstrates a simple fitting procedure using `easyscience.fitting.Fitter`.
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+from easyscience.fitting import Fitter
+from easyscience.base_classes import ObjBase
+from easyscience.variable import Parameter
+
+# %%
+# ## Define the Model
+#
+# We define a simple linear model with parameters `m` (slope) and `c` (intercept).
+
+
+class Line(ObjBase):
+    def __init__(self, m: Parameter, c: Parameter):
+        super().__init__('line', m=m, c=c)
+
+    def __call__(self, x):
+        return self.c.value + self.m.value * x
+
+
+# Initialize parameters
+m = Parameter('m', 1)
+c = Parameter('c', 1)
+b = Line(m, c)
+
+# %%
+# ## Define the Fitting Function
+#
+# The fitting function takes the independent variable `x` and returns the model prediction.
+
+
+def fit_fun(x):
+    return b(x)
+
+
+# %%
+# ## Setup the Fitter
+#
+# Initialize the Fitter with the model object and the fitting function.
+
+f = Fitter(b, fit_fun)
+
+# %%
+# ## Generate Data
+#
+# Create some synthetic data to fit.
+
+x = np.array([1, 2, 3])
+y = np.array([2, 4, 6]) - 1
+# x=1, y=1. x=2, y=3. x=3, y=5.
+# Expected result: m=2, c=-1.
+
+# %%
+# ## Perform Fit
+#
+# Run the fit.
+
+# We need to provide weights for the fit. Since we don't have experimental errors, we use equal weights.
+weights = np.ones_like(x)
+f_res = f.fit(x, y, weights=weights)
+
+print(f'Goodness of fit (chi2): {f_res.chi2}')
+print(f'Reduced chi2: {f_res.reduced_chi}')
+print(f'Fitted m: {b.m.value}')
+print(f'Fitted c: {b.c.value}')
+
+# %%
+# ## Plot Results
+
+plt.scatter(x, y, label='Data')
+plt.plot(x, fit_fun(x), label='Fit', color='red')
+plt.legend()
+plt.show()

docs/base_examples/index.md

@@ -0,0 +1,33 @@
+# Subclassing Examples
+
+This section gathers examples which correspond to subclassing the `easyscience.base_classes.ObjBase` class.
+
+
+
+<div class="mkd-glr-thumbcontainer" tooltip="This  example shows how to subclass easyscience.base_classes.ObjBase with parameters from EasyS...">
+    <!--div class="figure align-default" id="id1"-->
+        <img alt="Subclassing ObjBase - Simple Pendulum" src="images\thumb\mkd_glr_plot_baseclass1_thumb.png" />
+        <p class="caption">
+            <span class="caption-text">
+                <a class="reference internal" href="plot_baseclass1">
+                    <span class="std std-ref">Subclassing ObjBase - Simple Pendulum</span>
+                </a>
+            </span>
+            <!--a class="headerlink" href="#id1" title="Permalink to this image"></a-->
+        </p>
+    <!--/div-->
+</div>
+
+<div class="mkd-glr-clear"></div>
+
+<!-- docs_base_examples -->
+
+
+<div id="download_links"></div>
+
+[:fontawesome-solid-download: Download all examples in Python source code: base_examples_python.zip](./base_examples_python.zip){ .md-button .center}
+
+[:fontawesome-solid-download: Download all examples in Jupyter notebooks: base_examples_jupyter.zip](./base_examples_jupyter.zip){ .md-button .center}
+
+
+[Gallery generated by mkdocs-gallery](https://smarie.github.io/mkdocs-gallery){: .mkd-glr-signature }