Fix broken API docs search and expose Metadata (#2153)

* Fix the broken search functionality in docs.
* Resolve multiple minor errors and warnings encountered during the docs build process.
* Expose the Metadata class as tiledb.Metadata.

Author: kounelisagis

doc/source/conf.py

@@ -23,7 +23,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "TileDB-Py"
-copyright = "2024, TileDB, Inc."
+copyright = "2025, TileDB, Inc."
 author = "TileDB, Inc."
 
 # The full version, including alpha/beta/rc tags
@@ -41,7 +41,17 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ["sphinx.ext.autodoc", "sphinx.ext.doctest", "sphinx.ext.intersphinx"]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "nbsphinx",
+    "sphinxcontrib.jquery",
+]
+
+autosummary_generate = True
 
 # Mapping for linking between RTD subprojects.
 if readthedocs:
@@ -55,9 +65,14 @@
             % rtd_version,
             None,
         ),
-        "python": ("https://docs.python.org/", None),
+        "python": (
+            "https://docs.python.org/3",
+            None,
+        ),
     }
 
+napoleon_custom_sections = ["Lifecycle"]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 

doc/source/gensidebar.py

@@ -6,15 +6,13 @@
 # https://github.com/robotpy/robotpy-docs, licensed under Apache v2.
 #
 
-import os
-
 
 def write_if_changed(fname, contents):
 
     try:
         with open(fname, "r") as fp:
             old_contents = fp.read()
-    except:
+    except Exception:
         old_contents = ""
 
     if old_contents != contents:

doc/source/python-api.rst

@@ -15,6 +15,7 @@ There is also a submodule ``libtiledb`` which contains the necessary bindings to
 .. code-block:: python
 
    import tiledb
+   tiledb.version()  # TileDB-Py package version number
    tiledb.libtiledb.version()  # Native TileDB library version number
 
 Getting Started
@@ -176,17 +177,14 @@ Group
    .. automethod:: __contains__(member)
    .. automethod:: __len__
 
-.. autoclass:: tiledb.Group.GroupMetadata
+.. autoclass:: tiledb.Metadata
    :members:
 
    .. automethod:: __setitem__(key, value)
    .. automethod:: __getitem__(key)
    .. automethod:: __delitem__(key)
    .. automethod:: __contains__(key)
    .. automethod:: __len__
-   .. automethod:: __keys__
-   .. automethod:: __values__
-   .. automethod:: __items__
 
 Object
 ------
@@ -246,11 +244,6 @@ Filestore
 
    .. automethod:: __len__
 
-Version
--------
-
-.. autofunction:: tiledb.libtiledb.version
-
 Statistics
 ----------
 

pyproject.toml

@@ -44,9 +44,10 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 doc = [
-    "jinja2==3.0.0",
-    "sphinx-rtd-theme==2.0.0",
-    "Sphinx",
+    "jinja2==3.1.5",
+    "sphinx-rtd-theme==3.0.2",
+    "Sphinx==8.1.3",
+    "nbsphinx==0.9.6",
     "breathe",
 ]
 test = [

tiledb/__init__.py

@@ -88,6 +88,7 @@
     walk,
 )
 from .libtiledb import TileDBError
+from .metadata import Metadata
 from .multirange_indexing import EmptyRange
 from .object import Object
 from .parquet_ import from_parquet

tiledb/dense_array.py

@@ -138,7 +138,7 @@ def query(
             Consuming this iterable returns a result set for each TileDB incomplete query.
             See usage example in 'examples/incomplete_iteration.py'.
             To retrieve the estimated result sizes for the query ranges, use:
-                `A.query(..., return_incomplete=True)[...].est_result_size()`
+            `A.query(..., return_incomplete=True)[...].est_result_size()`
             If False (default False), queries will be internally run to completion by resizing buffers and
             resubmitting until query is complete.
         :return: A proxy Query object that can be used for indexing into the DenseArray
@@ -164,6 +164,7 @@ def query(
         ...                {"a1": np.zeros(5)})
 
         """
+
         if not self.isopen:
             raise tiledb.TileDBError("Array is not opened")
 

tiledb/filter.py

@@ -265,10 +265,8 @@ class DeltaFilter(CompressionFilter):
     Filter that compresses using run-length encoding (RLE).
 
     :param level: -1 (default) sets the compressor level to the default level as specified in TileDB core. Otherwise, sets the compressor level to the given value.
-    :type level: int
-    :param reinterp_dtype: (optional) sets the compressor to compress the data treating
-    as the new datatype.
-    :type reinterp_dtype: numpy, lt.DataType
+    :param reinterp_dtype: (optional) sets the compressor to compress the data treating as the new datatype.
+
     **Example:**
 
     >>> import tiledb, numpy as np, tempfile