single-cell-data · johnkerl · Nov 5, 2024 · Nov 2, 2024 · Nov 2, 2024 · Nov 2, 2024
diff --git a/doc/source/python-tiledbsoma-axis.rst b/doc/source/python-tiledbsoma-axis.rst
@@ -0,0 +1,24 @@
+tiledbsoma.Axis
+===============
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: Axis
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~Axis.__init__
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~Axis.name
+      ~Axis.unit
+
diff --git a/doc/source/python-tiledbsoma-axiscolumnnames.rst b/doc/source/python-tiledbsoma-axiscolumnnames.rst
@@ -0,0 +1,35 @@
+tiledbsoma.AxisColumnNames
+==========================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: AxisColumnNames
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~AxisColumnNames.__init__
+      ~AxisColumnNames.clear
+      ~AxisColumnNames.copy
+      ~AxisColumnNames.fromkeys
+      ~AxisColumnNames.get
+      ~AxisColumnNames.items
+      ~AxisColumnNames.keys
+      ~AxisColumnNames.pop
+      ~AxisColumnNames.popitem
+      ~AxisColumnNames.setdefault
+      ~AxisColumnNames.update
+      ~AxisColumnNames.values
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~AxisColumnNames.obs
+      ~AxisColumnNames.var
+
diff --git a/doc/source/python-tiledbsoma-axisquery.rst b/doc/source/python-tiledbsoma-axisquery.rst
@@ -0,0 +1,24 @@
+tiledbsoma.AxisQuery
+====================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: AxisQuery
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~AxisQuery.__init__
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~AxisQuery.value_filter
+      ~AxisQuery.coords
+
diff --git a/doc/source/python-tiledbsoma-collection.rst b/doc/source/python-tiledbsoma-collection.rst
@@ -0,0 +1,54 @@
+tiledbsoma.Collection
+=====================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: Collection
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~Collection.__init__
+      ~Collection.exists
+      ~Collection.create
+      ~Collection.open
+      ~Collection.reopen
+      ~Collection.close
+      ~Collection.verify_open_for_writing
+
+      ~Collection.items
+      ~Collection.keys
+      ~Collection.values
+      ~Collection.members
+      ~Collection.get
+      ~Collection.set
+      ~Collection.setdefault
+      ~Collection.update
+      ~Collection.clear
+      ~Collection.pop
+      ~Collection.popitem
+
+      ~Collection.add_new_collection
+      ~Collection.add_new_dataframe
+      ~Collection.add_new_dense_ndarray
+      ~Collection.add_new_sparse_ndarray
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~Collection.uri
+      ~Collection.closed
+      ~Collection.context
+      ~Collection.metadata
+
+      ~Collection.mode
+      ~Collection.soma_type
+      ~Collection.tiledb_timestamp
+      ~Collection.tiledb_timestamp_ms
+
diff --git a/doc/source/python-tiledbsoma-coordinatespace.rst b/doc/source/python-tiledbsoma-coordinatespace.rst
@@ -0,0 +1,27 @@
+tiledbsoma.CoordinateSpace
+==========================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: CoordinateSpace
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~CoordinateSpace.__init__
+      ~CoordinateSpace.count
+      ~CoordinateSpace.from_axis_names
+      ~CoordinateSpace.index
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~CoordinateSpace.axes
+      ~CoordinateSpace.axis_names
+
diff --git a/doc/source/python-tiledbsoma-dataframe.rst b/doc/source/python-tiledbsoma-dataframe.rst
@@ -0,0 +1,58 @@
+tiledbsoma.DataFrame
+====================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: DataFrame
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~DataFrame.__init__
+      ~DataFrame.exists
+      ~DataFrame.create
+      ~DataFrame.open
+      ~DataFrame.reopen
+      ~DataFrame.close
+      ~DataFrame.read
+      ~DataFrame.write
+      ~DataFrame.verify_open_for_writing
+
+      ~DataFrame.keys
+
+      ~DataFrame.tiledbsoma_upgrade_domain
+      ~DataFrame.change_domain
+      ~DataFrame.tiledbsoma_resize_soma_joinid_shape
+      ~DataFrame.tiledbsoma_upgrade_soma_joinid_shape
+      ~DataFrame.non_empty_domain
+
+      ~DataFrame.config_options_from_schema
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~DataFrame.uri
+      ~DataFrame.soma_type
+      ~DataFrame.schema
+      ~DataFrame.index_column_names
+
+      ~DataFrame.count
+      ~DataFrame.domain
+      ~DataFrame.maxdomain
+      ~DataFrame.tiledbsoma_has_upgraded_domain
+
+      ~DataFrame.mode
+      ~DataFrame.closed
+
+      ~DataFrame.context
+      ~DataFrame.tiledb_timestamp
+      ~DataFrame.tiledb_timestamp_ms
+
+      ~DataFrame.metadata
+
diff --git a/doc/source/python-tiledbsoma-densendarray.rst b/doc/source/python-tiledbsoma-densendarray.rst
@@ -0,0 +1,53 @@
+tiledbsoma.DenseNDArray
+=======================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: DenseNDArray
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~DenseNDArray.__init__
+      ~DenseNDArray.exists
+      ~DenseNDArray.create
+      ~DenseNDArray.open
+      ~DenseNDArray.reopen
+      ~DenseNDArray.close
+      ~DenseNDArray.read
+      ~DenseNDArray.write
+      ~DenseNDArray.verify_open_for_writing
+
+      ~DenseNDArray.non_empty_domain
+      ~DenseNDArray.resize
+
+      ~DenseNDArray.config_options_from_schema
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~DenseNDArray.uri
+      ~DenseNDArray.soma_type
+      ~DenseNDArray.schema
+      ~DenseNDArray.is_sparse
+
+      ~DenseNDArray.ndim
+      ~DenseNDArray.nnz
+      ~DenseNDArray.shape
+      ~DenseNDArray.maxshape
+      ~DenseNDArray.tiledbsoma_has_upgraded_shape
+
+      ~DenseNDArray.mode
+      ~DenseNDArray.closed
+
+      ~DenseNDArray.context
+      ~DenseNDArray.tiledb_timestamp
+      ~DenseNDArray.tiledb_timestamp_ms
+
+      ~DenseNDArray.metadata
diff --git a/doc/source/python-tiledbsoma-experiment.rst b/doc/source/python-tiledbsoma-experiment.rst
@@ -0,0 +1,59 @@
+tiledbsoma.Experiment
+=====================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: Experiment
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~Experiment.__init__
+      ~Experiment.exists
+      ~Experiment.create
+      ~Experiment.open
+      ~Experiment.reopen
+      ~Experiment.close
+      ~Experiment.verify_open_for_writing
+
+      ~Experiment.items
+      ~Experiment.keys
+      ~Experiment.values
+      ~Experiment.members
+      ~Experiment.get
+      ~Experiment.set
+      ~Experiment.update
+      ~Experiment.clear
+      ~Experiment.pop
+      ~Experiment.popitem
+      ~Experiment.setdefault
+
+      ~Experiment.add_new_collection
+      ~Experiment.add_new_dataframe
+      ~Experiment.add_new_dense_ndarray
+      ~Experiment.add_new_sparse_ndarray
+
+      ~Experiment.axis_query
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~Experiment.closed
+      ~Experiment.context
+      ~Experiment.metadata
+      ~Experiment.mode
+      ~Experiment.ms
+      ~Experiment.obs
+      ~Experiment.obs_spatial_presence
+      ~Experiment.soma_type
+      ~Experiment.spatial
+      ~Experiment.tiledb_timestamp
+      ~Experiment.tiledb_timestamp_ms
+      ~Experiment.uri
+
diff --git a/doc/source/python-tiledbsoma-experimentaxisquery.rst b/doc/source/python-tiledbsoma-experimentaxisquery.rst
@@ -0,0 +1,38 @@
+tiledbsoma.ExperimentAxisQuery
+==============================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: ExperimentAxisQuery
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~ExperimentAxisQuery.X
+      ~ExperimentAxisQuery.__init__
+      ~ExperimentAxisQuery.close
+      ~ExperimentAxisQuery.obs
+      ~ExperimentAxisQuery.obs_joinids
+      ~ExperimentAxisQuery.obs_scene_ids
+      ~ExperimentAxisQuery.obsm
+      ~ExperimentAxisQuery.obsp
+      ~ExperimentAxisQuery.to_anndata
+      ~ExperimentAxisQuery.var
+      ~ExperimentAxisQuery.var_joinids
+      ~ExperimentAxisQuery.var_scene_ids
+      ~ExperimentAxisQuery.varm
+      ~ExperimentAxisQuery.varp
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~ExperimentAxisQuery.indexer
+      ~ExperimentAxisQuery.n_obs
+      ~ExperimentAxisQuery.n_vars
+
diff --git a/doc/source/python-tiledbsoma-intindexer.rst b/doc/source/python-tiledbsoma-intindexer.rst
@@ -0,0 +1,17 @@
+tiledbsoma.IntIndexer
+=====================
+
+.. currentmodule:: tiledbsoma
+
+.. autoclass:: IntIndexer
+
+   .. automethod:: __init__
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: _generated
+
+      ~IntIndexer.__init__
+      ~IntIndexer.get_indexer
+