Update example for converting DLC project to benchmark (v2)

docs/source/api_index.rst

@@ -2,7 +2,7 @@ API
 ===
 
 io
-----
+--
 
 .. currentmodule:: poseinterface.io
 
@@ -11,15 +11,30 @@ io
     :template: function.rst
 
     annotations_to_poseinterface
-    video_to_poseinterface
+    frames_to_poseinterface
     predictions_to_poseinterface
+    video_to_poseinterface
+
 
 clips
 -----
+
 .. currentmodule:: poseinterface.clips
 
 .. autosummary::
     :toctree: api_generated
     :template: function.rst
 
     extract_clip
+
+
+utils
+-----
+
+.. currentmodule:: poseinterface.utils
+
+.. autosummary::
+    :toctree: api_generated
+    :template: function.rst
+
+    tree

docs/source/benchmark-dataset.md

@@ -17,6 +17,7 @@ We mark requirements with italicised *keywords* that should be interpreted as de
 
 The current scope is limited to **single-animal pose estimation** from a **single camera view**. Support for multi-camera setups is planned for a future version.
 
+(target-dataset-folder-structure)=
 ## Folder structure
 
 :::{note}

docs/source/conf.py

@@ -76,6 +76,9 @@
 autosummary_generate = True
 autodoc_default_flags = ["members", "inherited-members"]
 
+# sphinx-autodoc-typehints configuration
+always_use_bars_union = True
+
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
@@ -86,6 +89,12 @@
     "**/includes/**",
     # Auto-generated by sphinx-gallery; contains dangling refs to ignored examples
     "sg_execution_times.rst",
+    # exclude .py and .ipynb files in examples generated by sphinx-gallery
+    # this is to prevent sphinx from complaining about duplicate source files
+    "auto_examples/*.ipynb",
+    "auto_examples/*.py",
+    "auto_examples/**/*.ipynb",
+    "auto_examples/**/*.py",
 ]
 
 # -- Options for HTML output -------------------------------------------------
@@ -138,14 +147,12 @@
 }
 
 # -- Sphinx-Gallery configuration -------------------------------------------
+
 sphinx_gallery_conf = {
     "examples_dirs": ["../../examples"],
     "gallery_dirs": ["auto_examples"],
-    # Patterns of example filenames to ignore (not built or shown in gallery).
-    # Use this for scripts that depend on data/resources not available in CI
-    # or on the developer's machine (e.g. files on a specific mount point).
-    # To re-enable an example, remove its pattern from this list.
-    "ignore_pattern": r"SWC-plusmaze_to_benchmark",
+    "reference_url": {"poseinterface": None},
+    "filename_pattern": "/*.py",  # which files to execute before inclusion
 }
 
 # -- linkcheck configuration -------------------------------------------------