pdidev · JAuriac · Jan 14, 2026 · Jan 14, 2026 · Jan 14, 2026 · Jan 14, 2026
@@ -1,4 +1,5 @@
-# %PDI examples {#PDI_example}
+\page PDI_example PDI example
+# %PDI examples
 
 The example is made of a single source file (one version in each supported
 programming language), this file loads its configuration and %PDI specification

@@ -121,7 +121,7 @@ LAYOUT_FILE            = ./_template/layout.xml
 CITE_BIB_FILES         = 
 QUIET                  = NO
 WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = YES
+WARN_IF_UNDOCUMENTED   = NO
 WARN_IF_DOC_ERROR      = YES
 WARN_IF_INCOMPLETE_DOC = YES
 WARN_NO_PARAMDOC       = YES
@@ -130,11 +130,13 @@ WARN_AS_ERROR          = NO
 WARN_FORMAT            = "$file:$line: $text"
 WARN_LINE_FORMAT       = at line $line of file $file
 WARN_LOGFILE           = 
-INPUT                  = @DOXYGEN_INPUT_SP@
+INPUT                  = @DOXYGEN_INPUT_SP@ \
+                         ../../plugins \
+						 ../../tutorial
 INPUT_ENCODING         = UTF-8
 INPUT_FILE_ENCODING    = 
 FILE_PATTERNS          = *.c *.cc *.cxx *.cxxm *.cpp *.cppm *.c++ *.c++m *.java *.ii *.ixx *.ipp *.i++ *.inl *.idl *.ddl *.odl *.h *.hh *.hxx *.hpp *.h++ *.ixx *.l *.cs *.d *.php *.php4 *.php5 *.phtml *.inc *.m *.markdown *.md *.mm *.dox *.py *.pyw *.f90 *.f95 *.f03 *.f08 *.f18 *.f *.for *.vhd *.vhdl *.ucf *.qsf *.ice
-RECURSIVE              = NO
+RECURSIVE              = YES
 EXCLUDE                = 
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = */.git/* */.svn/* */.hg/* */CMakeFiles/* */_CPack_Packages/* DartConfiguration.tcl CMakeLists.txt CMakeCache.txt

@@ -4,7 +4,7 @@
 |:----------------------------------------------------|:------------------------------------------------------------------|
 |\subpage Decl_HDF5_plugin "Decl'HDF5 plugin"         |Read and write data from HDF5 files in a declarative way.          |
 |\subpage Decl_NetCDF_plugin "Decl'NetCDF plugin"     |Read and write data from NetCDF files in a declarative way.        |
-|Deisa plugin                                         |Expose data to a Dask analysis script.                             |
+|\subpage deisa_plugin "Deisa plugin"                 |Expose data to a Dask analysis script.                             |
 |\subpage mpi_plugin "MPI plugin"                     |Enables MPI support in %PDI and plugins.                           |
 |\subpage pycall_plugin "Pycall plugin"               |Call python scripts from C application                             |
 |\subpage JSON_plugin "JSON plugin"                   |Export data in JSON format.                                        |

@@ -110,15 +110,15 @@ class PDI_EXPORT Datatype: public Datatype_template
 	 *
 	 * \param[in] to the pointer to the allocated memory to fill (dense data)
 	 * \param[in] from the pointer to the copied data (size of buffersize)
-	 * \return updated `to' pointer
+	 * \return updated 'to' pointer
 	 */
 	virtual void* data_to_dense_copy(void* to, const void* from) const = 0;
 
 	/** Creates a sparse deep copy of dense data
 	 *
 	 * \param[in] to the pointer to the allocated memory to fill (size of buffersize)
 	 * \param[in] from the pointer to the copied data (dense data)
-	 * \return updated `to' pointer
+	 * \return updated 'to' pointer
 	 */
 	virtual void* data_from_dense_copy(void* to, const void* from) const = 0;
 

@@ -114,7 +114,7 @@ class PDI_EXPORT Expression
 
 	/** Moves an expression
 	 *
-	 * \param[in] expr the expression to move`
+	 * \param[in] expr the expression to move
 	 * \return *this
 	 */
 	Expression& operator= (Expression&& expr);

@@ -1,4 +1,5 @@
-# The Decl'HDF5 plugin {#Decl_HDF5_plugin}
+\page Decl_HDF5_plugin Decl'HDF5 plugin
+# The Decl'HDF5 plugin
 
 **WARNING** This documentation is a work in progress and does not reflect the
 full Decl'HDF5 potential.

@@ -119,6 +119,7 @@ class Dataset_op
 	 * \param dir the operation direction
 	 * \param name the value name
 	 * \param default_when the default "when" clause as read from the file level (optional)
+	 * \param file_collision_policy the collision policy string
 	 */
 	Dataset_op(Direction dir, std::string name, PDI::Expression default_when, Collision_policy file_collision_policy = Collision_policy::WRITE_INTO);
 	/** Builds a Dataset_op from its yaml config
@@ -127,6 +128,7 @@ class Dataset_op
 	 * \param name the value name
 	 * \param default_when the default "when" clause as read from the file level (optional)
 	 * \param tree the configuration tree
+	 * \param collision_policy the collision policy string
 	 */
 	Dataset_op(
 		Direction dir,

@@ -148,7 +148,7 @@ Raii_hid make_raii_hid(hid_t value, Destroyer&& dst, const char* message = NULL)
 /** builds a HDF5 dataspace that represents a PDI Datatype
  *
  * \param type the datatype to represent in HDF5
- * \param select whether to create a dense type instead of a type with a selection
+ * \param dense whether to create a dense type instead of a type with a selection
  * \return a tuple containing the Raii_hid for (dataspace, datatype)
  */
 std::tuple<Raii_hid, Raii_hid> space(PDI::Datatype_sptr type, bool dense = false);

@@ -1,4 +1,5 @@
-# The Decl'NetCDF plugin {#Decl_NetCDF_plugin}
+\page Decl_NetCDF_plugin Decl'NetCDF plugin
+# The Decl'NetCDF plugin
 
 The Decl'NetCDF plugin was created to read from and write to NetCDF files in a declarative way.
 

@@ -50,6 +50,7 @@ class Dnc_group
 	/** Creates a NetCDF group information from yaml
 	 *
 	 * \param ctx Context of this group
+	 * \param path File name of the netCDF dataset
 	 * \param config (optional) config with group attributes
 	 */
 	Dnc_group(PDI::Context& ctx, const std::string& path, PC_tree_t config = {});

@@ -55,7 +55,6 @@ class Dnc_io
 	/** Creates I/O operation (read or write) on NetCDF file
 	 *
 	 * \param ctx Context of this I/O
-	 * \param file File associated with this I/O operation
 	 * \param config Configuration node of this I/O
 	 */
 	Dnc_io(PDI::Context& ctx, PC_tree_t config);

@@ -94,7 +94,7 @@ class Dnc_netcdf_file
 	 * \param right_flag right flag which be used to open file
 	 * \param mpi_comm_expr if not empty, opens NetCDF file in parallel using this MPI_Comm
 	 */
-	Dnc_netcdf_file(PDI::Context& ctx, const std::string& filename, int rights_flag, PDI::Expression mpi_comm_expr);
+	Dnc_netcdf_file(PDI::Context& ctx, const std::string& filename, int right_flag, PDI::Expression mpi_comm_expr);
 
 	/// Deleted copy constructor
 	Dnc_netcdf_file(const Dnc_netcdf_file& other) = delete;
@@ -140,7 +140,7 @@ class Dnc_netcdf_file
 	/** Gets variable from the file
 	 *
 	 * \param variable variable to get
-	 * \param write Dnc_io that deteremines the read operation
+	 * \param read Dnc_io that deteremines the read operation
 	 * \param ref_w reference where the data will be written
 	 */
 	void get_variable(const Dnc_variable& variable, const Dnc_io& read, PDI::Ref_w ref_w);
@@ -151,7 +151,7 @@ class Dnc_netcdf_file
 	 * \param sizeof_variable variable to read its size
 	 * \param ref reference where the data will be written
 	 */
-	void get_sizeof_variable(const std::string& variable, const std::string& sizeof_var, PDI::Ref ref);
+	void get_sizeof_variable(const std::string& variable, const std::string& sizeof_variable, PDI::Ref ref);
 
 	/// Destructor
 	~Dnc_netcdf_file();

@@ -60,6 +60,7 @@ class Dnc_variable
 	/** Creates NetCDF variable information from yaml
 	 *
 	 * \param ctx Context of this variable
+	 * \param path File name of the netCDF dataset
 	 * \param config Configuration node of this variable
 	 */
 	Dnc_variable(PDI::Context& ctx, const std::string& path, PC_tree_t config);

@@ -1,30 +1,31 @@
-# The DEISA plugin {#deisa_plugin}
+\page deisa_plugin Deisa plugin
+# The DEISA plugin
 
 **WARNING** This documentation is a work in progress and does not reflect the full DEISA plugin potential.
 
 The DEISA plugin is used to expose data to [Dask](https://www.dask.org/).
 This mechanism decouples analytics code from simulation code by providing an asynchronous pipeline for analytics.
 
 The DEISA plugin uses the following configuration:
-- `scheduler_info`: File name defined by the dask scheduler. This file contains information on how to connect to the dask cluster.
-- `init_on`: Name of the PDI event called after sharing all metadata.
-- `time_step`: Timestep variable.
-- `deisa_arrays`: List of Deisa virtual arrays.
-  - `type`: Type of the Deisa array. Usually: `array`.
-  - `subtype`: Type stored in the `Deisa array.
-  - `size`: Size of the Deisa array.
-  - `subsize`: How the Deisa array is chunked. In other words, the size of each chunk.
-  - `start`: How to find the start of each chunk.
-  - `+timedim`: Define where the time dimension is. Currently, only dimension 0 is supported.
-- `map_in`: Define how a local data is mapped to a Deisa array.
+- 'scheduler_info': File name defined by the dask scheduler. This file contains information on how to connect to the dask cluster.
+- 'init_on': Name of the PDI event called after sharing all metadata.
+- 'time_step': Timestep variable.
+- 'deisa_arrays': List of Deisa virtual arrays.
+  - 'type': Type of the Deisa array. Usually: 'array'.
+  - 'subtype': Type stored in the 'Deisa array.
+  - 'size': Size of the Deisa array.
+  - 'subsize': How the Deisa array is chunked. In other words, the size of each chunk.
+  - 'start': How to find the start of each chunk.
+  - '+timedim': Define where the time dimension is. Currently, only dimension 0 is supported.
+- 'map_in': Define how a local data is mapped to a Deisa array.
 
 
 ---
 
 
 # Example: A 2D MPI space with ghost cells.
 
-```yaml
+@code{.yaml}
 metadata:
   nx: int               # Domain size per proc
   ny: int               # Domain size per proc
@@ -51,5 +52,5 @@ plugins:
         start: [$nstep, '$mpi_coords_x*($nx+2)', '$mpi_coords_y*($ny+2)']
         +timedim: 0
     map_in: 
-      main_field: global_t            # `main_field` is mapped to `global_t`
-```
+      main_field: global_t            # 'main_field' is mapped to 'global_t'
+@endcode
@@ -1,4 +1,5 @@
-# JSON plugin {#JSON_plugin}
+\page JSON_plugin JSON plugin
+# JSON plugin
 
 **WARNING** This documentation is a work in progress and does not 
 reflect the full potential of the JSON plugin.

@@ -1,4 +1,5 @@
-# The MPI plugin {#mpi_plugin}
+\page mpi_plugin MPI plugin
+# The MPI plugin
 
 **WARNING** This documentation is a work in progress and does not reflect the
 full MPI plugin potential.

@@ -1,4 +1,5 @@
-# Pycall plugin {#pycall_plugin}
+\page pycall_plugin Pycall plugin
+# Pycall plugin
 
 The Pycall plugin allows calling python scripts from yaml file, that can work either if wanted data was shared or program calls specific event.
 

@@ -1,4 +1,5 @@
-# Serialize plugin {#serialize_plugin}
+\page serialize_plugin Serialize plugin
+# Serialize plugin
 
 Serialize plugin allows to serialize shared data. The plugin will convert all
 arrays from sparse to dense and dereference all pointers.

@@ -1,4 +1,5 @@
-# Set_value plugin {#set_value_plugin}
+\page set_value_plugin Set Value plugin
+# Set_value plugin
 
 The Set_value plugin allows setting values to data and metadata descriptors from
 the yaml file.

@@ -43,7 +43,6 @@ class Operation
 public:
 	/** Creates operation
      * \param[in] ctx context of the operation
-     * \param[in] release_value_node yaml config tree of operation
      */
 	Operation(PDI::Context& ctx);
 

@@ -1,4 +1,5 @@
-# Trace plugin {#trace_plugin}
+\page trace_plugin Trace plugin
+# Trace plugin
 
 The trace plugin is intended to generate a trace of what happens in 
 \ref Data_store "PDI data store".

@@ -1,4 +1,5 @@
-# The user-code plugin {#user_code_plugin}
+\page user_code_plugin user-code plugin
+# The user-code plugin
 
 The `user-code` plugin enables one to call a user-defined function 
 when a specified event occur or certain data becomes available.