fixed quickstart

docs/_templates/layout.html

@@ -0,0 +1,16 @@
+{% extends "!layout.html" %}
+
+{%- block footer %}
+<footer class="footer" style="border-top: 1px solid #ccc; padding-top: 10px">
+  <div class="container">
+    <div id="credits" style="width: 50%; float: left">
+      <p>
+      {% trans copyright=copyright|e %}&#169; Copyright {{ copyright }}, <a href="https://www.simonsfoundation.org/people/edoardo-balzani/">Edoardo Balzani</a>.{% endtrans %}<br/>
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> and the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/">PyData Theme</a>.<br/>
+      </p>
+    </div>
+    <div id="version" style="color: #999; float: right; margin: 15px">v{{ version }}</div>
+    </div>
+  </div>
+</footer>
+{%- endblock %}

docs/assets/stylesheets/custom.css

@@ -93,3 +93,45 @@ html[data-theme=light]{
 .toctree-l4 {
     font-weight: normal;
 }
+
+/* Add a line separator above the entire footnote list */
+aside.footnote-list {
+    border-top: 1px solid #ccc; /* Add a horizontal line */
+    margin-top: 2em; /* Space above the separator */
+    padding-top: 1em; /* Space below the separator */
+}
+
+/* Style each individual footnote */
+aside.footnote {
+    margin-bottom: 1em; /* Add space between footnotes */
+    font-size: 0.9em; /* Adjust font size */
+    color: #333; /* Text color */
+}
+
+/* Style the label (the bracketed number) */
+aside.footnote .label {
+    font-weight: bold; /* Make it stand out */
+    margin-right: 0.5em; /* Add space after the label */
+}
+
+/* Style the brackets */
+span.fn-bracket {
+    color: #666; /* Dim the brackets */
+}
+
+/* Style the links within the footnotes */
+aside.footnote a {
+    color: #007BFF; /* Blue link color */
+    text-decoration: none; /* Remove underline */
+}
+
+aside.footnote a:hover {
+    text-decoration: underline; /* Add underline on hover */
+}
+
+/* Adjust spacing for the paragraph inside the footnote */
+aside.footnote p {
+    margin: 0.5em 0;
+    line-height: 1.5; /* Improve readability */
+}
+

docs/conf.py

@@ -30,8 +30,8 @@
 
 
 project = 'nemos'
-copyright = '2024, SJ Venditto'
-author = 'SJ Venditto'
+copyright = '2024'
+author = 'E Balzani'
 version = release = nemos.__version__
 
 # -- General configuration ---------------------------------------------------

docs/quickstart.md

@@ -211,8 +211,11 @@ Once the basis is initialized, you can call `compute_features` on an input of sh
 `(n_samples, n_signals)` to perform the convolution. The output will be a 2-dimensional array of shape 
 `(n_samples, n_basis_funcs)` or `(n_samples, n_basis_funcs * n_signals)` respectively.
 
-!!! warning "Signal length and window size"
-    The `window_size` must be shorter than the number of samples in the signal(s) being convolved.
+:::{admonition} Signal length and window size
+:class: warning
+
+The `window_size` must be shorter than the number of samples in the signal(s) being convolved.
+:::
 
 ```python
 
@@ -279,11 +282,11 @@ You can specify the regularization scheme and its strength when initializing the
 ## **Pre-processing with `pynapple`**
 
 
-!!! warning
-
-    This section assumes some familiarity with the `pynapple` package for time series manipulation and data
-    exploration. If you'd like to learn more about it, take a look at the [`pynapple` documentation](https://pynapple-org.github.io/pynapple/).
+:::{info}
 
+This section assumes some familiarity with the `pynapple` package for time series manipulation and data
+exploration. If you'd like to learn more about it, take a look at the [`pynapple` documentation](https://pynapple-org.github.io/pynapple/).
+:::
 
 `pynapple` is an extremely helpful tool when working with time series data. You can easily perform operations such
 as restricting your time series to specific epochs (sleep/wake, context A vs. context B, etc.), as well as common
@@ -321,9 +324,10 @@ A canonical example of this behavior is the `predict` method of `GLM`.
 Let's see how you can greatly streamline your analysis pipeline by integrating `pynapple` and NeMoS.
 
 
-!!! note
-    You can download this dataset by clicking [here](https://www.dropbox.com/s/su4oaje57g3kit9/A2929-200711.zip?dl=1).
+:::{note}
 
+You can download this dataset by clicking [here](https://www.dropbox.com/s/su4oaje57g3kit9/A2929-200711.zip?dl=1).
+:::
 
 ```python
 
@@ -426,9 +430,11 @@ Fit a 5-fold cross-validation scheme for comparing two different regularizer str
 ```
 
 
-!!! info "Cross-Validation in NeMoS"
+:::{admonition} Cross-Validation in NeMoS
+:class: info
 
-    For more information and a practical example on how to construct a parameter grid and cross-validate hyperparameters across an entire pipeline, please refer to the [tutorial on pipelining and cross-validation](../generated/how_to_guide/plot_06_sklearn_pipeline_cv_demo).
+For more information and a practical example on how to construct a parameter grid and cross-validate hyperparameters across an entire pipeline, please refer to the [tutorial on pipelining and cross-validation](../generated/how_to_guide/plot_06_sklearn_pipeline_cv_demo).
+:::
 
 Finally, we can print the regularizer strength with the best cross-validated performance: