Merge branch 'main' into MMathisLab-setup

Author: MMathisLab

.github/workflows/docs.yml

@@ -9,6 +9,12 @@ on:
       - main
       - public
       - dev
+    paths:
+      - '**.py'
+      - '**.ipynb'
+      - '**.js'
+      - '**.rst'
+      - '**.md'
 
 jobs:
   build:
@@ -69,6 +75,7 @@ jobs:
           pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
           pip install '.[docs]'
 
+
       - name: Build docs
         run: |
           ls docs/source/cebra-figures

cebra/integrations/plotly.py

@@ -28,6 +28,7 @@
 import numpy.typing as npt
 import plotly.graph_objects
 import torch
+import plotly.graph_objects as go
 
 from cebra.integrations.matplotlib import _EmbeddingPlot
 
@@ -154,7 +155,7 @@ def _plot_3d(self, **kwargs) -> plotly.graph_objects.Figure:
 def plot_embedding_interactive(
     embedding: Union[npt.NDArray, torch.Tensor],
     embedding_labels: Optional[Union[npt.NDArray, torch.Tensor, str]] = "grey",
-    axis: Optional[plotly.graph_objects.Figure] = None,
+    axis: Optional["go.Figure"] = None,
     markersize: float = 1,
     idx_order: Optional[Tuple[int]] = None,
     alpha: float = 0.4,
@@ -163,7 +164,7 @@ def plot_embedding_interactive(
     figsize: Tuple[int] = (5, 5),
     dpi: int = 100,
     **kwargs,
-) -> plotly.graph_objects.Figure:
+) -> "go.Figure":
     """Plot embedding in a 3D dimensional space.
 
     This is supposing that the dimensions provided to ``idx_order`` are in the range of the number of

docs/Makefile

@@ -18,6 +18,11 @@ help:
 html:
 	PYTHONPATH=.. $(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
+# Build multiple versions
+html_versions:
+	for v in latest v0.2.0 v0.3.0 v0.4.0; do \
+		PYTHONPATH=.. $(SPHINXBUILD) -b html "$(SOURCEDIR)" "$(BUILDDIR)/$$v"; \
+	done
 # Remove the current temp folder and page build
 clean:
 	rm -rf build

docs/source/_static/css/custom.js

@@ -0,0 +1,6 @@
+requirejs.config({
+    paths: {
+        base: '/static/base',
+        plotly: 'https://cdn.plot.ly/plotly-2.12.1.min.js?noext',
+    },
+});

docs/source/_templates/layout.html

@@ -1,11 +1,15 @@
 {% extends "pydata_sphinx_theme/layout.html" %}
 
-{% block fonts %}
+{% block extrahead %}
+    <!-- Load require.js locally from _static -->
+    <script src="{{ pathto('_static/css/custom.js', 1) }}"></script>
+
+{% endblock %}
 
+{% block fonts %}
 <link rel="preconnect" href="https://fonts.googleapis.com">
 <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
 <link href="https://fonts.googleapis.com/css2?family=IBM+Plex+Mono:wght@300&display=swap" rel="stylesheet">
-
 {% endblock %}
 
 {% block docs_sidebar %}

docs/source/conf.py

@@ -47,8 +47,8 @@ def get_years(start_year=2021):
 
 # -- Project information -----------------------------------------------------
 project = "cebra"
-copyright = f"""{get_years(2021)}, Steffen Schneider, Jin H Lee, Mackenzie Mathis"""
-author = "Steffen Schneider, Jin H Lee, Mackenzie Mathis"
+copyright = f"""{get_years(2021)}"""
+author = "See AUTHORS.md"
 # The full version, including alpha/beta/rc tags
 release = cebra.__version__
 
@@ -57,6 +57,13 @@ def get_years(start_year=2021):
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
+
+#https://github.com/spatialaudio/nbsphinx/issues/128#issuecomment-1158712159
+html_js_files = [
+    "require.min.js",  # Add to your _static
+    "custom.js",
+]
+
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.napoleon",
@@ -68,13 +75,13 @@ def get_years(start_year=2021):
     "sphinx_tabs.tabs",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
-    # "sphinx_panels", # Note: package to avoid: no longer maintained.
     "sphinx_design",
     "sphinx_togglebutton",
     "sphinx.ext.doctest",
     "sphinx_gallery.load_style",
 ]
 
+
 coverage_show_missing_items = True
 panels_add_bootstrap_css = False
 
@@ -137,6 +144,21 @@ def get_years(start_year=2021):
 # a list of builtin themes.
 html_theme = "pydata_sphinx_theme"
 
+html_context = {
+    "default_mode": "light",
+    "switcher": {
+        "version_match": "latest",  # Adjust this dynamically per version
+        "versions": [
+            ("latest", "/latest/"),
+            ("v0.2.0", "/v0.2.0/"),
+            ("v0.3.0", "/v0.3.0/"),
+            ("v0.4.0", "/v0.4.0/"),
+            ("v0.5.0rc1", "/v0.5.0rc1/"),
+        ],
+    },
+    "navbar_start": ["version-switcher", "navbar-logo"],  # Place the dropdown above the logo
+}
+
 # More info on theme options:
 # https://pydata-sphinx-theme.readthedocs.io/en/latest/user_guide/configuring.html
 html_theme_options = {
@@ -197,6 +219,8 @@ def get_years(start_year=2021):
 ]
 
 nbsphinx_thumbnails = {
+    "demo_notebooks/CEBRA_best_practices":
+    "_static/thumbnails/cebra-best.png",
     "demo_notebooks/Demo_primate_reaching":
         "_static/thumbnails/ForelimbS1.png",
     "demo_notebooks/Demo_hippocampus":