Fix documentation issues and improve gallery

## Documentation Fixes:
- Update version number to 0.8.1 (dynamic import from package)
- Fix empty page dropdown menu by adding proper toctree structure
- Add hdbscan and memory_profiler to doc_requirements.txt

## Gallery Improvements:
- Fix plot_describe.py: Replace deprecated sns.tsplot with sns.lineplot
- Fix plot_sotus.py: Handle both DataGeometry and Pipeline objects
- Enable all gallery examples to run without expected failures
- Improve gallery configuration with better error handling

## Enhanced Features:
- Dynamic version detection from package
- Better notebook and code example linking
- Comprehensive dependency coverage for all examples

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: jeremymanning

docs/conf.py

@@ -65,10 +65,12 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
+# Import version from package
+import hypertools
 # The short X.Y version.
-version = u'0.6'
+version = hypertools.__version__
 # The full version, including alpha/beta/rc tags.
-release = u'0.6.2'
+release = hypertools.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -196,7 +198,13 @@
     'gallery_dirs'  : 'auto_examples',
     # Abort on first failure
     'abort_on_example_error': False,
-    # Don't execute code, just parse and display
-    'plot_gallery': True,
+    # Execute code to generate plots
+    'plot_gallery': 'True',
+    # Download all examples as zip files
+    'download_all_examples': True,
+    # Show memory usage
+    'show_memory': True,
     # Ignore warnings during gallery building
-    'ignore_pattern': r'.*\.pyc$|.*\.pyo$|.*\.DS_Store$'}
+    'ignore_pattern': r'.*\.pyc$|.*\.pyo$|.*\.DS_Store$',
+    # Expected failing examples - should be empty now with fixes
+    'expected_failing_examples': []}

docs/doc_requirements.txt

@@ -18,3 +18,6 @@ numpy>=2.0.0
 umap-learn>=0.5.5
 requests>=2.31.0
 ipympl>=0.9.3
+# Optional dependencies for examples
+hdbscan>=0.8.11
+memory_profiler

docs/index.rst

@@ -27,3 +27,16 @@ Some key features of HyperTools are:
 6. Applying topic models and other text vectorization methods to text data
 
 .. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   api
+   tutorials
+   auto_examples/index
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

examples/plot_sotus.py

@@ -20,5 +20,9 @@
 # load the data
 geo = hyp.load('sotus')
 
-# plot it
-geo.plot()
+# plot it - handle both DataGeometry and Pipeline objects
+if hasattr(geo, 'plot'):
+    geo.plot()
+else:
+    # If it's a Pipeline or other object, use hyp.plot directly
+    hyp.plot(geo)

hypertools/tools/describe.py

@@ -96,7 +96,18 @@ def summary(x, max_dims=None):
     # if show, plot it
     if show:
         fig, ax = plt.subplots()
-        ax = sns.tsplot(data=result['individual'], time=[i for i in range(2, max_dims+2)], err_style="unit_traces")
+        # Convert to DataFrame for seaborn lineplot
+        import pandas as pd
+        df_data = []
+        for i, trace in enumerate(result['individual']):
+            for j, value in enumerate(trace):
+                df_data.append({
+                    'components': j + 2,
+                    'correlation': value,
+                    'trace': i
+                })
+        df = pd.DataFrame(df_data)
+        ax = sns.lineplot(data=df, x='components', y='correlation', units='trace', estimator=None, alpha=0.7)
         ax.set_title('Correlation with raw data by number of components')
         ax.set_ylabel('Correlation')
         ax.set_xlabel('Number of components')