Summary and info Classes; Interface, navigation, bug fixes.

.readthedocs.yaml

@@ -10,6 +10,10 @@ build:
       - poetry config virtualenvs.create false
       - . "$READTHEDOCS_VIRTUALENV_PATH/bin/activate" && poetry install --with docs
       - pip freeze
+    post_install:
+      # RTD auto-upgrades sphinx (breaks myst-parser <9) and setuptools
+      # (82+ removes pkg_resources, breaking pybtex). Re-pin to safe versions.
+      - pip install "sphinx<9" "setuptools<82"
 
 sphinx:
   configuration: docs/conf.py

Makefile

@@ -15,6 +15,10 @@ clean.doc:
 	@$(RM) -rf docs/auto_examples/
 	@$(RM) -rf docs/sg_execution_times.rst
 
+.PHONY: doc-quick
+doc-quick: install.doc
+	@$(SPHINX) -b html docs/ docs/_build/html
+
 .PHONY: clean.py
 clean.py:
 	@find . -name __pycache__ -exec $(RM) -r {} +

README.md

@@ -85,6 +85,10 @@ pre-commit install
 ### Examples & Tutorials
 
 The `examples` folder contains a starting point if you want to launch your first scripts and notebook with the Leaspy package.
+<<<<<<< HEAD
+
+=======
+>>>>>>> upstream/v2.1
 
 ## Description
 Leaspy is a software package for the statistical analysis of **longitudinal data**, particularly **medical** data that comes in a form of **repeated observations** of patients at different time-points.

docs/_static/custom.css

@@ -1,6 +1,246 @@
-.wy-nav-content {
-    max-width: 96% !important;
+/* =============================================================================
+   Leaspy custom styles for PyData Sphinx Theme
+   CSS variables: https://pydata-sphinx-theme.readthedocs.io/en/stable/user_guide/styling.html
+   ============================================================================= */
+
+/* --- Viewcode: pastel blue highlights (hll lines + target blocks) --- */
+html[data-theme="light"] {
+    --pst-color-target: rgba(80, 150, 220, 0.18);
 }
+html[data-theme="dark"] {
+    --pst-color-target: rgba(80, 150, 220, 0.15);
+}
+html[data-theme="light"] .highlight .hll {
+    background-color: rgba(80, 150, 220, 0.18) !important;
+}
+html[data-theme="dark"] .highlight .hll {
+    background-color: rgba(80, 150, 220, 0.15) !important;
+}
+
+/* =============================================================================
+   Sphinx-Gallery
+   ============================================================================= */
+
+/* Hide download note, timing, and download footer */
+.sphx-glr-download-link-note,
+.sphx-glr-timing,
+.sphx-glr-footer {
+    display: none !important;
+}
+
+/* Gallery card thumbnails: text only, no images */
 .sphx-glr-thumbcontainer .xref.std.std-ref {
     display: none;
+}
+.sphx-glr-thumbcontainer img {
+    display: none !important;
+}
+.sphx-glr-thumbcontainer {
+    min-height: auto !important;
+    height: auto !important;
+}
+
+/* Input code blocks: green left border + grey/white outline */
+div.highlight-Python,
+div.highlight-python3,
+div.highlight-python {
+    border: 1px solid;
+    border-left: 4px solid var(--pst-color-success);
+    border-radius: 6px;
+    overflow: hidden;
+}
+html[data-theme="light"] div.highlight-Python,
+html[data-theme="light"] div.highlight-python3,
+html[data-theme="light"] div.highlight-python {
+    border-color: #c0c0c0;
+    border-left-color: var(--pst-color-success);
+}
+html[data-theme="dark"] div.highlight-Python,
+html[data-theme="dark"] div.highlight-python3,
+html[data-theme="dark"] div.highlight-python {
+    border-color: #555;
+    border-left-color: var(--pst-color-success);
+}
+
+/* Output blocks: grey/white outline, no green bar, tinted background */
+.sphx-glr-script-out div.highlight-none {
+    border: 1px solid;
+    border-radius: 6px;
+    overflow: hidden;
+}
+html[data-theme="light"] .sphx-glr-script-out div.highlight-none {
+    border-color: #989898;
+}
+html[data-theme="dark"] .sphx-glr-script-out div.highlight-none {
+    border-color: #555;
+}
+html[data-theme="light"] .sphx-glr-script-out .highlight,
+html[data-theme="light"] .sphx-glr-script-out pre {
+    background: #e1e1e1 !important;
+}
+html[data-theme="dark"] .sphx-glr-script-out .highlight,
+html[data-theme="dark"] .sphx-glr-script-out pre {
+    background: #272626 !important;
+}
+.sphx-glr-script-out pre {
+    color: var(--pst-color-text-base) !important;
+    font-size: 0.875em;
+    line-height: 1.5;
+}
+
+/* =============================================================================
+   Misc
+   ============================================================================= */
+
+/* Logo: white background patch for transparency on dark bg */
+img[src*="leaspy_logo.png"] {
+    background-color: white;
+    padding: 5px;
+    border-radius: 4px;
+}
+
+/* Pandas DataFrame styling */
+table.dataframe {
+    border: none !important;
+    border-collapse: collapse;
+    border-spacing: 0;
+    margin-bottom: 1em;
+    width: auto;
+    overflow-x: auto;
+    display: block;
+}
+table.dataframe thead {
+    border-bottom: 1px solid var(--pst-color-border);
+    vertical-align: bottom;
+}
+table.dataframe tr,
+table.dataframe th,
+table.dataframe td {
+    text-align: right;
+    vertical-align: middle;
+    padding: 0.5em;
+    line-height: normal;
+    white-space: normal;
+    max-width: none;
+    border: none;
+    color: var(--pst-color-text-base);
+}
+table.dataframe th {
+    font-weight: bold;
+    background: var(--pst-color-surface);
+}
+table.dataframe tbody tr:nth-child(odd) {
+    background: var(--pst-color-surface);
+}
+table.dataframe tbody tr:hover {
+    background: var(--pst-color-surface);
+    opacity: 0.85;
+}
+
+/* =============================================================================
+   API Reference Styling
+   ============================================================================= */
+
+/* 1. Class block separation */
+dl.py.class {
+    margin-bottom: 4rem !important;
+    padding-bottom: 2rem;
+    border-bottom: 2px solid var(--pst-color-border);
+}
+
+/* 2. Method / Function separation */
+dl.py.method,
+dl.py.function {
+    margin-bottom: 2rem !important;
+    padding-bottom: 1rem;
+    border-bottom: 1px solid var(--pst-color-border);
+}
+dl.py.class > dd > dl.py.method:last-child {
+    border-bottom: none;
+    margin-bottom: 0 !important;
+    padding-bottom: 0;
+}
+
+/* 3. Signature headers */
+dl.py.class > dt {
+    background-color: var(--pst-color-surface);
+    padding: 0.8rem;
+    border-radius: 4px;
+    margin-top: 1.5rem;
+    font-weight: bold;
+    border-left: 5px solid var(--pst-color-primary);
+    display: block;
+    text-indent: 0 !important;
+    margin-left: 0 !important;
+    width: 100%;
+    box-sizing: border-box;
+}
+dl.py.function > dt,
+dl.py.method > dt {
+    background-color: var(--pst-color-surface);
+    padding: 0.6rem;
+    border-radius: 4px;
+    margin-top: 1.0rem;
+    font-weight: bold;
+    border-left: 3px solid var(--pst-color-text-base);
+    display: block;
+    text-indent: 0 !important;
+    margin-left: 0 !important;
+    width: 100%;
+    box-sizing: border-box;
+}
+
+/* 4. Body indentation with vertical lines */
+dl.py.class > dd {
+    margin-left: 0 !important;
+    padding-left: 1.5rem;
+    border-left: 4px solid var(--pst-color-primary);
+}
+dl.py.method > dd,
+dl.py.function > dd {
+    margin-left: 0 !important;
+    padding-left: 1.5rem;
+    border-left: 2px solid var(--pst-color-text-base);
+}
+
+/* 5. Parameters / Returns / Attributes field lists */
+dl.field-list > dt {
+    font-weight: bold;
+    color: var(--pst-color-text-base);
+    margin-top: 1.0rem;
+    margin-bottom: 0.5rem;
+    padding: 0;
+    border: none;
+    background: none;
+}
+dl.field-list > dd {
+    margin-left: 0 !important;
+    padding-left: 1.0rem;
+}
+dl.field-list > dd > dl > dt {
+    background-color: transparent !important;
+    padding: 0 !important;
+    margin-top: 0 !important;
+    margin-bottom: 0 !important;
+    font-weight: bold;
+    border: none !important;
+    color: var(--pst-color-text-base);
+    font-family: var(--pst-font-family-monospace);
+    line-height: 1.2;
+}
+dl.field-list > dd > dl > dt::before {
+    content: "•";
+    color: var(--pst-color-text-muted);
+    margin-right: 0.5rem;
+    font-weight: normal;
+}
+dl.field-list > dd > dl > dd {
+    margin-top: 0 !important;
+    margin-bottom: 0.1rem !important;
+    margin-left: 1.0rem !important;
+}
+dl.field-list > dd > dl > dd > p {
+    margin-top: 0 !important;
+    margin-bottom: 0 !important;
+    line-height: 1.3;
 }

docs/_static/custom.js

@@ -19,5 +19,8 @@ document.addEventListener("DOMContentLoaded", function() {
             // Change cursor to pointer
             el.style.cursor = 'pointer';
         }
+
+        // Remove the tooltip attribute to prevent the description from popping up
+        el.removeAttribute('tooltip');
     });
 });

docs/_templates/navbar-nav.html

@@ -0,0 +1,22 @@
+{# Navbar navigation links.
+   On toctree-rooted pages, generate_header_nav_html produces the links.
+   On orphan pages (e.g. viewcode _modules/), it returns empty — fall back to
+   a hardcoded list so navigation is always visible.
+#}
+<nav>
+  <ul class="bd-navbar-elements navbar-nav">
+    {% set nav_html = generate_header_nav_html(
+        n_links_before_dropdown=theme_header_links_before_dropdown,
+        dropdown_text=theme_header_dropdown_text
+    ) %}
+    {{ nav_html }}
+    {% if not nav_html.strip() %}
+    <li class="nav-item"><a class="nav-link nav-internal" href="{{ pathto('install') }}">Installation</a></li>
+    <li class="nav-item"><a class="nav-link nav-internal" href="{{ pathto('auto_examples/index') }}">Examples gallery</a></li>
+    <li class="nav-item"><a class="nav-link nav-internal" href="{{ pathto('user_guide') }}">User guide</a></li>
+    <li class="nav-item"><a class="nav-link nav-internal" href="{{ pathto('references') }}">References</a></li>
+    <li class="nav-item"><a class="nav-link nav-internal" href="{{ pathto('changelog') }}">Changelog</a></li>
+    <li class="nav-item"><a class="nav-link nav-internal" href="{{ pathto('reference/api/index') }}">API Reference</a></li>
+    {% endif %}
+  </ul>
+</nav>