diff --git a/example/README.md b/example/README.md index 3b5752e3c..817ff1541 100644 --- a/example/README.md +++ b/example/README.md @@ -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 diff --git a/pdi/docs/Doxyfile b/pdi/docs/Doxyfile index 5e2307d4f..9b56f9e86 100644 --- a/pdi/docs/Doxyfile +++ b/pdi/docs/Doxyfile @@ -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 diff --git a/pdi/docs/Plugins.md b/pdi/docs/Plugins.md index 65b349830..970ac0fca 100644 --- a/pdi/docs/Plugins.md +++ b/pdi/docs/Plugins.md @@ -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. | diff --git a/pdi/include/pdi/datatype.h b/pdi/include/pdi/datatype.h index 09a28d202..6d1ef35d4 100644 --- a/pdi/include/pdi/datatype.h +++ b/pdi/include/pdi/datatype.h @@ -110,7 +110,7 @@ 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; @@ -118,7 +118,7 @@ class PDI_EXPORT Datatype: public Datatype_template * * \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; diff --git a/pdi/include/pdi/expression.h b/pdi/include/pdi/expression.h index 1aa8f3c75..8bf43c47b 100644 --- a/pdi/include/pdi/expression.h +++ b/pdi/include/pdi/expression.h @@ -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); diff --git a/plugins/decl_hdf5/README.md b/plugins/decl_hdf5/README.md index e39821594..3a693ce19 100644 --- a/plugins/decl_hdf5/README.md +++ b/plugins/decl_hdf5/README.md @@ -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. diff --git a/plugins/decl_hdf5/dataset_op.h b/plugins/decl_hdf5/dataset_op.h index 8d58df0da..d1c0ec722 100644 --- a/plugins/decl_hdf5/dataset_op.h +++ b/plugins/decl_hdf5/dataset_op.h @@ -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, diff --git a/plugins/decl_hdf5/hdf5_wrapper.h b/plugins/decl_hdf5/hdf5_wrapper.h index 5c9e77225..56fa7fde9 100644 --- a/plugins/decl_hdf5/hdf5_wrapper.h +++ b/plugins/decl_hdf5/hdf5_wrapper.h @@ -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 space(PDI::Datatype_sptr type, bool dense = false); diff --git a/plugins/decl_netcdf/README.md b/plugins/decl_netcdf/README.md index 5d8f2b732..12ae12da7 100644 --- a/plugins/decl_netcdf/README.md +++ b/plugins/decl_netcdf/README.md @@ -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. diff --git a/plugins/decl_netcdf/dnc_group.h b/plugins/decl_netcdf/dnc_group.h index 0645be8c1..ca5a58f92 100644 --- a/plugins/decl_netcdf/dnc_group.h +++ b/plugins/decl_netcdf/dnc_group.h @@ -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 = {}); diff --git a/plugins/decl_netcdf/dnc_io.h b/plugins/decl_netcdf/dnc_io.h index 9c578adef..7d21fd493 100644 --- a/plugins/decl_netcdf/dnc_io.h +++ b/plugins/decl_netcdf/dnc_io.h @@ -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); diff --git a/plugins/decl_netcdf/dnc_netcdf_file.h b/plugins/decl_netcdf/dnc_netcdf_file.h index 203d25d15..b390f58cd 100644 --- a/plugins/decl_netcdf/dnc_netcdf_file.h +++ b/plugins/decl_netcdf/dnc_netcdf_file.h @@ -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(); diff --git a/plugins/decl_netcdf/dnc_variable.h b/plugins/decl_netcdf/dnc_variable.h index 18307d277..f0a1df92d 100644 --- a/plugins/decl_netcdf/dnc_variable.h +++ b/plugins/decl_netcdf/dnc_variable.h @@ -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); diff --git a/plugins/deisa/README.md b/plugins/deisa/README.md index 74d0b64c3..b58d21452 100644 --- a/plugins/deisa/README.md +++ b/plugins/deisa/README.md @@ -1,4 +1,5 @@ -# 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. @@ -6,17 +7,17 @@ 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. --- @@ -24,7 +25,7 @@ The DEISA plugin uses the following configuration: # 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 diff --git a/plugins/json/README.md b/plugins/json/README.md index 1d95039d0..a60e4b988 100644 --- a/plugins/json/README.md +++ b/plugins/json/README.md @@ -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. diff --git a/plugins/mpi/README.md b/plugins/mpi/README.md index 2ca50611e..dbdea9c87 100644 --- a/plugins/mpi/README.md +++ b/plugins/mpi/README.md @@ -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. diff --git a/plugins/pycall/README.md b/plugins/pycall/README.md index b85f6680f..5e222c71e 100644 --- a/plugins/pycall/README.md +++ b/plugins/pycall/README.md @@ -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. diff --git a/plugins/serialize/README.md b/plugins/serialize/README.md index c4641955c..14932581a 100644 --- a/plugins/serialize/README.md +++ b/plugins/serialize/README.md @@ -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. diff --git a/plugins/set_value/README.md b/plugins/set_value/README.md index d5293598a..abcb5f97c 100644 --- a/plugins/set_value/README.md +++ b/plugins/set_value/README.md @@ -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. diff --git a/plugins/set_value/operation.h b/plugins/set_value/operation.h index 172416f49..ebae8c7d6 100644 --- a/plugins/set_value/operation.h +++ b/plugins/set_value/operation.h @@ -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); diff --git a/plugins/trace/README.md b/plugins/trace/README.md index 88186c9e9..2e61d0286 100644 --- a/plugins/trace/README.md +++ b/plugins/trace/README.md @@ -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". diff --git a/plugins/user_code/README.md b/plugins/user_code/README.md index 1a7d0a48c..5e5d03eb8 100644 --- a/plugins/user_code/README.md +++ b/plugins/user_code/README.md @@ -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.