From 2ab5c8ea3324514d808185aecd74fb88de971849 Mon Sep 17 00:00:00 2001 From: Vivian Nguyen Date: Wed, 17 Apr 2024 12:05:41 -0500 Subject: [PATCH] Correct documentation --- libtiledbsoma/src/soma/soma_array.h | 7 +++---- libtiledbsoma/src/soma/soma_dataframe.h | 17 ++++++++++------- libtiledbsoma/src/soma/soma_dense_ndarray.h | 20 ++++++++++---------- libtiledbsoma/src/soma/soma_sparse_ndarray.h | 18 +++++++++--------- 4 files changed, 32 insertions(+), 30 deletions(-) diff --git a/libtiledbsoma/src/soma/soma_array.h b/libtiledbsoma/src/soma/soma_array.h index 7d0e379731..65049be95b 100644 --- a/libtiledbsoma/src/soma/soma_array.h +++ b/libtiledbsoma/src/soma/soma_array.h @@ -5,7 +5,7 @@ * * The MIT License * - * @copyright Copyright (c) 2022-2023 TileDB, Inc. + * @copyright Copyright (c) 2022-2024 TileDB, Inc. * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -102,8 +102,7 @@ class SOMAArray : public SOMAObject { * * @param mode read or write * @param uri URI of the array - * @param name Name of the array - * @param platform_config Config parameter dictionary + * @param ctx SOMAContext * @param column_names Columns to read * @param batch_size Read batch size * @param result_order Read result order: automatic (default), rowmajor, @@ -152,8 +151,8 @@ class SOMAArray : public SOMAObject { * * @param mode read or write * @param uri URI of the array + * @param ctx SOMAContext * @param name name of the array - * @param platform_config Config parameter dictionary * @param column_names Columns to read * @param batch_size Batch size * @param result_order Result order diff --git a/libtiledbsoma/src/soma/soma_dataframe.h b/libtiledbsoma/src/soma/soma_dataframe.h index f2e8a2aa63..fe95efdb66 100644 --- a/libtiledbsoma/src/soma/soma_dataframe.h +++ b/libtiledbsoma/src/soma/soma_dataframe.h @@ -5,7 +5,7 @@ * * The MIT License * - * @copyright Copyright (c) 2023 TileDB, Inc. + * @copyright Copyright (c) 2023-2024 TileDB, Inc. * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -53,8 +53,12 @@ class SOMADataFrame : public SOMAArray { * @brief Create a SOMADataFrame object at the given URI. * * @param uri URI to create the SOMADataFrame - * @param schema TileDB ArraySchema + * @param schema Arrow schema + * @param index_columns The index column names with associated domains + * and tile extents per dimension + * @param ctx SOMAContext * @param platform_config Optional config parameter dictionary + * @param timestamp Optional the timestamp range to write SOMA metadata info */ static void create( std::string_view uri, @@ -67,18 +71,17 @@ class SOMADataFrame : public SOMAArray { /** * @brief Open and return a SOMADataFrame object at the given URI. * - * @param mode read or write * @param uri URI to create the SOMADataFrame + * @param mode read or write + * @param ctx SOMAContext * @param column_names A list of column names to use as user-defined index * columns (e.g., ``['cell_type', 'tissue_type']``). All named columns must * exist in the schema, and at least one index column name is required. - * @param platform_config Platform-specific options used to create this - * DataFrame * @param result_order Read result order: automatic (default), rowmajor, or * colmajor * @param timestamp If specified, overrides the default timestamp used to * open this object. If unset, uses the timestamp provided by the context. - * @return std::shared_ptr SOMADataFrame + * @return std::unique_ptr SOMADataFrame */ static std::unique_ptr open( std::string_view uri, @@ -142,7 +145,7 @@ class SOMADataFrame : public SOMAArray { /** * Return the data schema, in the form of a ArrowSchema. * - * @return std::shared_ptr + * @return std::unique_ptr */ std::unique_ptr schema() const; diff --git a/libtiledbsoma/src/soma/soma_dense_ndarray.h b/libtiledbsoma/src/soma/soma_dense_ndarray.h index 18b8432cdd..a1997019a0 100644 --- a/libtiledbsoma/src/soma/soma_dense_ndarray.h +++ b/libtiledbsoma/src/soma/soma_dense_ndarray.h @@ -5,7 +5,7 @@ * * The MIT License * - * @copyright Copyright (c) 2023 TileDB, Inc. + * @copyright Copyright (c) 2023-2024 TileDB, Inc. * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -53,9 +53,9 @@ class SOMADenseNDArray : public SOMAArray { * @brief Create a SOMADenseNDArray object at the given URI. * * @param uri URI to create the SOMADenseNDArray - * @param schema TileDB ArraySchema - * @param platform_config Optional config parameter dictionary - * @return std::shared_ptr opened in read mode + * @param schema Arrow schema + * @param ctx SOMAContext + * @param timestamp Optional the timestamp range to write SOMA metadata info */ static void create( std::string_view uri, @@ -66,18 +66,17 @@ class SOMADenseNDArray : public SOMAArray { /** * @brief Open and return a SOMADenseNDArray object at the given URI. * - * @param mode read or write * @param uri URI to create the SOMADenseNDArray + * @param mode read or write + * @param ctx SOMAContext * @param column_names A list of column names to use as user-defined index * columns (e.g., ``['cell_type', 'tissue_type']``). All named columns must * exist in the schema, and at least one index column name is required. - * @param platform_config Platform-specific options used to create this - * SOMADenseNDArray - * @param timestamp If specified, overrides the default timestamp used to - * open this object. If unset, uses the timestamp provided by the context. * @param result_order Read result order: automatic (default), rowmajor, or * colmajor - * @return std::shared_ptr SOMADenseNDArray + * @param timestamp If specified, overrides the default timestamp used to + * open this object. If unset, uses the timestamp provided by the context. + * @return std::unique_ptr SOMADenseNDArray */ static std::unique_ptr open( std::string_view uri, @@ -104,6 +103,7 @@ class SOMADenseNDArray : public SOMAArray { * @param mode read or write * @param uri URI of the array * @param ctx TileDB context + * @param column_names Columns to read * @param result_order Read result order: automatic (default), rowmajor, or * colmajor * @param timestamp Timestamp diff --git a/libtiledbsoma/src/soma/soma_sparse_ndarray.h b/libtiledbsoma/src/soma/soma_sparse_ndarray.h index e212dee78b..db3b251a53 100644 --- a/libtiledbsoma/src/soma/soma_sparse_ndarray.h +++ b/libtiledbsoma/src/soma/soma_sparse_ndarray.h @@ -53,9 +53,9 @@ class SOMASparseNDArray : public SOMAArray { * @brief Create a SOMASparseNDArray object at the given URI. * * @param uri URI to create the SOMASparseNDArray - * @param schema TileDB ArraySchema - * @param platform_config Optional config parameter dictionary - * @return std::shared_ptr opened in read mode + * @param schema Arrow schema + * @param ctx SOMAContext + * @param timestamp Optional the timestamp range to write SOMA metadata info */ static void create( std::string_view uri, @@ -66,18 +66,17 @@ class SOMASparseNDArray : public SOMAArray { /** * @brief Open and return a SOMASparseNDArray object at the given URI. * - * @param mode read or write * @param uri URI to create the SOMASparseNDArray + * @param mode read or write + * @param ctx SOMAContext * @param column_names A list of column names to use as user-defined index * columns (e.g., ``['cell_type', 'tissue_type']``). All named columns must * exist in the schema, and at least one index column name is required. - * @param platform_config Platform-specific options used to create this - * SOMASparseNDArray * @param result_order Read result order: automatic (default), rowmajor, or * colmajor * @param timestamp If specified, overrides the default timestamp used to * open this object. If unset, uses the timestamp provided by the context. - * @return std::shared_ptr SOMASparseNDArray + * @return std::unique_ptr SOMASparseNDArray */ static std::unique_ptr open( std::string_view uri, @@ -104,6 +103,7 @@ class SOMASparseNDArray : public SOMAArray { * @param mode read or write * @param uri URI of the array * @param ctx TileDB context + * @param column_names Columns to read * @param result_order Read result order: automatic (default), rowmajor, or * colmajor * @param timestamp Timestamp @@ -138,7 +138,7 @@ class SOMASparseNDArray : public SOMAArray { using SOMAArray::open; /** - * Return whether the NDArray is sparse. + * Return whether the SOMASparseNDArray is sparse. * * @return true */ @@ -149,7 +149,7 @@ class SOMASparseNDArray : public SOMAArray { /** * Return the data schema, in the form of an ArrowSchema. * - * @return std::shared_ptr + * @return std::unique_ptr */ std::unique_ptr schema() const; };