Correct documentation

single-cell-data · Apr 17, 2024 · 2ab5c8e · 2ab5c8e
1 parent 1e70f97
commit 2ab5c8e
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Showing 4 changed files with 32 additions and 30 deletions.
diff --git 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
@@ -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> SOMADataFrame
+     * @return std::unique_ptr<SOMADataFrame> SOMADataFrame
      */
     static std::unique_ptr<SOMADataFrame> 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<ArrowSchema>
+     * @return std::unique_ptr<ArrowSchema>
      */
     std::unique_ptr<ArrowSchema> schema() const;
 

diff --git 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<SOMADenseNDArray> 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> 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> SOMADenseNDArray
      */
     static std::unique_ptr<SOMADenseNDArray> 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
@@ -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<SOMASparseNDArray> 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> SOMASparseNDArray
+     * @return std::unique_ptr<SOMASparseNDArray> SOMASparseNDArray
      */
     static std::unique_ptr<SOMASparseNDArray> 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<ArrowSchema>
+     * @return std::unique_ptr<ArrowSchema>
      */
     std::unique_ptr<ArrowSchema> schema() const;
 };