Fix or doc warnings due to previous snippets refactoring

Author: jctophefabre

doc/contents/dev_createsim.md

@@ -53,14 +53,14 @@ including source code and build configuration using the OpenFLUID CMake module.
 
 ### File ExampleSimulator.cpp containing the simulator source code {#dev_createsim_exmpl_cpp}
 
-@snippet help.snippets.example/ExampleSimulator.cpp example_full
+@snippet wares/ExampleSimulator.cpp example_full
 
 
 ### File CMake.in.config containing the build configuration {#dev_createsim_exmpl_config}
 
-@include help.snippets.example/CMake.in.cmake.snippet
+@include wares/CMake.in.cmake.snippet
 
 
 ### File CMakeLists.txt defining the build process {#dev_createsim_exmpl_cmakelists}
 
-@include help.snippets.example/CMakeLists.txt.snippet
+@include wares/CMakeLists.txt.snippet

doc/contents/dev_signature.md

@@ -2,8 +2,8 @@
 
 [TOC]
 
-The signature has to be defined between the @if DocIsLaTeX **BEGIN_SIMULATOR_SIGNATURE** @else #BEGIN_SIMULATOR_SIGNATURE @endif
- and the @if DocIsLaTeX **END_SIMULATOR_SIGNATURE** @else #END_SIMULATOR_SIGNATURE @endif 
+The signature has to be defined between the @if DocIsLaTeX **BEGIN_SIMULATOR_SIGNATURE** @else BEGIN_SIMULATOR_SIGNATURE @endif
+ and the @if DocIsLaTeX **END_SIMULATOR_SIGNATURE** @else END_SIMULATOR_SIGNATURE @endif 
  instructions.  
 The signature is usually placed in the upper part of the simulator main source file, before the C++ class of the simulator.
 
@@ -12,23 +12,23 @@ The signature is usually placed in the upper part of the simulator main source f
 
 The identification part of the signature must contain at least the ID of the simulator. 
 This ID will be used by the framework to load simulators. It is declared in 
-the signature as an argument of the @if DocIsLaTeX **BEGIN_SIMULATOR_SIGNATURE** @else #BEGIN_SIMULATOR_SIGNATURE @endif
+the signature as an argument of the @if DocIsLaTeX **BEGIN_SIMULATOR_SIGNATURE** @else BEGIN_SIMULATOR_SIGNATURE @endif
  instruction.   
 Other optional informations can be included for better description of the simulator:
 
-* the simulator name, declared through the @if DocIsLaTeX **DECLARE_NAME** @else #DECLARE_NAME @endif
+* the simulator name, declared through the @if DocIsLaTeX **DECLARE_NAME** @else DECLARE_NAME @endif
  instruction,
 allowing to assign a long name to the simulator
-* the simulator description, declared through the @if DocIsLaTeX **DECLARE_DESCRIPTION** @else #DECLARE_DESCRIPTION @endif
+* the simulator description, declared through the @if DocIsLaTeX **DECLARE_DESCRIPTION** @else DECLARE_DESCRIPTION @endif
  instruction,
 allowing to provide a detailed description of what the simulator actually does 
-* the name(s) of the author(s) and corresponding email address(es), declared through the @if DocIsLaTeX **DECLARE_AUTHOR** @else #DECLARE_AUTHOR @endif
+* the name(s) of the author(s) and corresponding email address(es), declared through the @if DocIsLaTeX **DECLARE_AUTHOR** @else DECLARE_AUTHOR @endif
  instruction.
-There may be multiple @if DocIsLaTeX **DECLARE_AUTHOR** @else #DECLARE_AUTHOR @endif
+There may be multiple @if DocIsLaTeX **DECLARE_AUTHOR** @else DECLARE_AUTHOR @endif
  instructions in the signature in case of multiple authors
-* the software version of the simulator, declared through the @if DocIsLaTeX **DECLARE_VERSION** @else #DECLARE_VERSION @endif
+* the software version of the simulator, declared through the @if DocIsLaTeX **DECLARE_VERSION** @else DECLARE_VERSION @endif
  instruction
-* the software status of the simulator, declared through the @if DocIsLaTeX **DECLARE_STATUS** @else #DECLARE_STATUS @endif
+* the software status of the simulator, declared through the @if DocIsLaTeX **DECLARE_STATUS** @else DECLARE_STATUS @endif
  instruction. The value can be
 _openfluid::ware::EXPERIMENTAL_, _openfluid::ware::BETA_ or _openfluid::ware::STABLE_
 
@@ -42,11 +42,11 @@ The informations about scientific applications are only indicative.
 It has no effects on simulator consistency or computational code.
 These informations can be :
 
-* the domain in which the simulator can be applied, declared through the @if DocIsLaTeX **DECLARE_DOMAIN** @else #DECLARE_DOMAIN @endif
+* the domain in which the simulator can be applied, declared through the @if DocIsLaTeX **DECLARE_DOMAIN** @else DECLARE_DOMAIN @endif
  instruction
-* the processes simulated by the simulator, declared through the @if DocIsLaTeX **DECLARE_PROCESS** @else #DECLARE_PROCESS @endif
+* the processes simulated by the simulator, declared through the @if DocIsLaTeX **DECLARE_PROCESS** @else DECLARE_PROCESS @endif
  instruction
-* the numerical methods used by the simulator, declared through the @if DocIsLaTeX **DECLARE_METHOD** @else #DECLARE_METHOD @endif
+* the numerical methods used by the simulator, declared through the @if DocIsLaTeX **DECLARE_METHOD** @else DECLARE_METHOD @endif
  instruction
 
 
@@ -77,7 +77,7 @@ The declarations of spatial data access include constraint levels:
 
 Simulator parameters are values provided to each simulator, 
 and are declared using the @if DocIsLaTeX **DECLARE_REQUIRED_PARAMETER** or **DECLARE_USED_PARAMETER**
-@else #DECLARE_REQUIRED_PARAMETER or #DECLARE_USED_PARAMETER @endif
+@else DECLARE_REQUIRED_PARAMETER or DECLARE_USED_PARAMETER @endif
  instructions.
 These instructions takes 3 arguments
 
@@ -87,15 +87,15 @@ These instructions takes 3 arguments
 
 
 _Example of a declaration of a required simulator parameter:_
-@snippet help.snippets.signature-parts/SignaturePartsSim.cpp signature_params
+**TOIMPL**
 
 
 ### Spatial attributes {#dev_signature_data_attrs}
 
 Spatial attributes are constant properties attached to each spatial units, 
 and are declared using @if DocIsLaTeX **DECLARE_REQUIRED_ATTRIBUTE**, **DECLARE_USED_ATTRIBUTE** 
 or **DECLARE_PRODUCED_ATTRIBUTE**
-@else #DECLARE_REQUIRED_ATTRIBUTE, #DECLARE_USED_ATTRIBUTE or #DECLARE_PRODUCED_ATTRIBUTE @endif
+@else DECLARE_REQUIRED_ATTRIBUTE, DECLARE_USED_ATTRIBUTE or DECLARE_PRODUCED_ATTRIBUTE @endif
  instructions
 
 These instructions take 4 arguments:
@@ -106,22 +106,18 @@ These instructions take 4 arguments:
 * the SI unit of the attribute (may be empty)
 
 
-_Example of attributes declaration:_
-@snippet help.snippets.signature-parts/SignaturePartsSim.cpp signature_attributes
-
-
 ### Simulation variables {#dev_signature_data_vars}
 
 Simulation variables are attached to spatial units. They are produced, accessed and modified
 by simulators during simulations.  
 Accessed variables are declared using @if DocIsLaTeX **DECLARE_REQUIRED_VARIABLE** or **DECLARE_USED_VARIABLE**
-@else #DECLARE_REQUIRED_VARIABLE or #DECLARE_USED_VARIABLE @endif
+@else DECLARE_REQUIRED_VARIABLE or DECLARE_USED_VARIABLE @endif
  instructions,
 produced variables are declared using @if DocIsLaTeX **DECLARE_PRODUCED_VARIABLE**
-@else #DECLARE_PRODUCED_VARIABLE @endif
+@else DECLARE_PRODUCED_VARIABLE @endif
  instruction, 
 updated variables are declared using @if DocIsLaTeX **DECLARE_UPDATED_VARIABLE**
-@else #DECLARE_UPDATED_VARIABLE @endif
+@else DECLARE_UPDATED_VARIABLE @endif
  instruction.
 
 These instructions take 4 arguments:
@@ -170,36 +166,36 @@ simulator B requires/uses/updates a _typed_ variable _var1_ of type `matrix`
 
 
 _Example of variable declarations:_
-@snippet help.snippets.signature-parts/SignaturePartsSim.cpp signature_variables
+**TOIMPL**
 
 
 ### Discrete events {#dev_signature_data_events}
 
 Discrete events are attached to spatial units, They are accessed or appended by simulators during simulations,
 and are declared using the @if DocIsLaTeX **DECLARE_USED_EVENTS**
-@else #DECLARE_USED_EVENTS @endif
+@else DECLARE_USED_EVENTS @endif
  instruction.  
 
 The declaration instruction takes 1 argument: the units class.
 
 _Example of events declaration:_
-@snippet help.snippets.signature-parts/SignaturePartsSim.cpp signature_events
+**TOIMPL**
 
 
 ### Extra files {#dev_signature_data_extrafiles}
 
 Simulators can declare files that they load and manage. This helps users to provide the needed files, and also  
 notifies the OpenFLUID framework to check the presence of the file if it is required.   
 These files are declared using the @if DocIsLaTeX **DECLARE_USED_EXTRAFILE**
-@else #DECLARE_USED_EXTRAFILE @endif
+@else DECLARE_USED_EXTRAFILE @endif
  or @if DocIsLaTeX **DECLARE_REQUIRED_EXTRAFILE**
-@else #DECLARE_REQUIRED_EXTRAFILE @endif
+@else DECLARE_REQUIRED_EXTRAFILE @endif
  instructions. 
 
 The declaration instruction takes 1 argument: the file name with relative path to the dataset path.
 
 _Example of extra file declarations:_
-@snippet help.snippets.signature-parts/SignaturePartsSim.cpp signature_extrafiles
+**TOIMPL**
 
 
 ### Spatial units graph {#dev_signature_data_spatial}
@@ -208,7 +204,7 @@ The spatial units graph representing the landscape can be modified by simulators
 These modifications are declared in the signature function using two instructions.  
 
 The @if DocIsLaTeX **DECLARE_UPDATED_UNITSGRAPH**
-@else #DECLARE_UPDATED_UNITSGRAPH @endif
+@else DECLARE_UPDATED_UNITSGRAPH @endif
  instruction is used for declaration of the global units graph modification
 that will occur during simulation. 
 It is for information purpose only, and takes a description as a single argument.  
@@ -223,11 +219,11 @@ It takes two arguments:
 
 
 _Example of declarations for spatial units graph:_
-@snippet help.snippets.signature-parts/SignaturePartsSim.cpp signature_spatial
+**TOIMPL**
 
 
 ## Complete signature example {#dev_signature_exmpl}
 
 The signature code below shows an example of a possible signature for a simulator.  
 
-@snippet help.snippets.signature/SignatureSim.cpp signature_full
+**TOIMPL**

doc/contents/dev_sim2doc.md

@@ -28,7 +28,7 @@ LaTeX
 
 
 _Example of a part of source code including sim2doc informations:_
-@snippet help.snippets.sim2doc/Sim2DocSim.cpp sim2doc
+**TOIMPL**
 
 
 <br/>

doc/contents/dev_srccode.md

@@ -48,10 +48,10 @@ to never be executed again
 
 
 _Example for a fixed time step simulator, with a time step equal to the default DeltaT value given in the input dataset:_
-@snippet help.snippets.sched-fixed/SchedFixedSim.cpp scheduling_fixed
+@snippet wares/SchedFixedSim.cpp scheduling_fixed
 
 _Example for a variable time step simulator, based on the internal computation of the simulator:_
-@snippet help.snippets.sched-variable/SchedVariableSim.cpp scheduling_variable
+@snippet wares/SchedVariableSim.cpp scheduling_variable
 
 
 
@@ -146,7 +146,7 @@ The source code below shows examples of spatial graph parsing.
 The first part of the source code shows how to browse all units of the SU units class, 
 and how to browse the "From" units for each SU unit.
 The second part of the source code shows how to browse all units of the spatial domain. 
-@snippet help.snippets.spatial-parsing-seq/SpatialParsingSeqSim.cpp spatial_parsing_seq
+@snippet wares/SpatialParsingSeqSim.cpp spatial_parsing_seq
 
 
 #### Parallel processing using multithreading {#dev_srccode_space_parse_par}
@@ -167,10 +167,10 @@ a pointer to an @if DocIsLaTeX **openfluid::core::SpatialUnit** @endif
 <br/>
 In order to enable the parallel processing in the spatial graph, 
 the following inclusion must be added at the top of the simulator source code:
-@snippet help.snippets.spatial-parsing-parallel/SpatialParsingParallelSim.cpp spatial_parsing_parallel_include
+@snippet wares/SpatialParsingParallelSim.cpp spatial_parsing_parallel_include
 
 The code below shows how to apply a method in parallel over the spatial graph:
-@snippet help.snippets.spatial-parsing-parallel/SpatialParsingParallelSim.cpp spatial_parsing_parallel
+@snippet wares/SpatialParsingParallelSim.cpp spatial_parsing_parallel
 
 
 @note 
@@ -267,7 +267,7 @@ In order to add and remove connections, you can use the following methods, whene
 
 
 _Example:_
-@snippet help.snippets.spatial-connect/SpatialConnectSim.cpp spatial_connect
+@snippet wares/SpatialConnectSim.cpp spatial_connect
 
 
 #### Generating spatial domain graphs automatically {#dev_srccode_space_mod_gen}
@@ -340,7 +340,7 @@ and is available from the runStep() and finalizeRun() methods of the simulator
 
 
 _Example of code:_
-@snippet help.snippets.params-env-time/ParamsEnvTimeSim.cpp time
+@snippet wares/ParamsEnvTimeSim.cpp time
 
 
 ## Simulator parameters {#dev_srccode_simparams}
@@ -364,7 +364,7 @@ and used in the model.fluidx file (see @ref user_fluidx_sections_model of the si
 <br/>
 
 _Example of initParams method:_
-@snippet help.snippets.params-env-time/ParamsEnvTimeSim.cpp params
+@snippet wares/ParamsEnvTimeSim.cpp params
 
 
 To be used in other part of the simulator, 
@@ -406,7 +406,7 @@ The names of the attributes must match the names in the input dataset (see @ref
 or the name of an attribute created by a simulator.
 
 _Example of use:_
-@snippet help.snippets.attributes/AttributesSim.cpp attributes
+@snippet wares/AttributesSim.cpp attributes
 
 
 ## Simulation variables {#dev_srccode_vars}
@@ -466,7 +466,7 @@ and finalizeRun() parts of the simulator.
 
 
 _Example:_
-@snippet help.snippets.variables/VariablesSim.cpp variables
+@snippet wares/VariablesSim.cpp variables
 
 
 ## Events {#dev_srccode_events}
@@ -508,7 +508,7 @@ An event can be added on a specific spatial unit at a given date using:
 <br/>
 
 _Example of process of events occurring on the current time step:_
-@snippet help.snippets.events/EventsSim.cpp events
+@snippet wares/EventsSim.cpp events
 
 
 
@@ -569,11 +569,11 @@ openfluid::core::IDSerieOfDoubleValuePtrMap
 
 
 _Example of declaration of ID-map structures in private members of the simulator class:_
-@snippet help.snippets.internal-state/InternalStateSim.cpp internal_state_decl
+@snippet wares/InternalStateSim.cpp internal_state_decl
 
 
 _Example of usage of the ID-map structures:_
-@snippet help.snippets.internal-state/InternalStateSim.cpp internal_state_impl
+@snippet wares/InternalStateSim.cpp internal_state_impl
 
 
 ## Runtime environment {#dev_srccode_runenv}
@@ -591,7 +591,7 @@ They are accessible from simulators using:
 
 
 _Example:_
-@snippet help.snippets.params-env-time/ParamsEnvTimeSim.cpp env
+@snippet wares/ParamsEnvTimeSim.cpp env
 
 
 The keys for requesting runtime environment information are:
@@ -656,7 +656,7 @@ Using these methods is the recommended way to log and display messages. Please a
 or similar C++ facilities in production or released simulators.
 
 _Example:_
-@snippet help.snippets.infos-debug/InfosDebugSim.cpp infowarning
+@snippet wares/InfosDebugSim.cpp infowarning
 
 The messages logged to file are put in the `openfluid-messages.log` file
 placed in the simulation output directory. 
@@ -676,7 +676,7 @@ Errors can be raised using
 @endif
 
 _Example:_
-@snippet help.snippets.infos-debug/InfosDebugSim.cpp error 
+@snippet wares/InfosDebugSim.cpp error 
 
 
 ## Debugging {#dev_srccode_debug}
@@ -721,7 +721,7 @@ to log and display debug messages simultaneously
 
 
 _Example:_
-@snippet help.snippets.infos-debug/InfosDebugSim.cpp debug
+@snippet wares/InfosDebugSim.cpp debug
 
 
 Additional instructions are available for debugging, see file debug.hpp:
@@ -742,21 +742,21 @@ You are invited to read the FortranCPP.hpp file to get more information about th
 
 
 In order to enable the call of Fortran code, the following inclusion must be added at the top of the simulator source code: 
-@snippet help.snippets.fortran/FortranSim.cpp fortran_include
+@snippet wares/FortranSim.cpp fortran_include
 
 
 
 _Example of Fortran source code (e.g. FortranSubr.f90):_
-@include help.snippets.fortran/FortranSubr.f90
+@include wares/FortranSubr.f90
 
 
 _Example of declaration block int the .cpp file (e.g. FortranSim.cpp):_
-@snippet help.snippets.fortran/FortranSim.cpp fortran_decl
+@snippet wares/FortranSim.cpp fortran_decl
 
 
 
 _Example of call of the fortran subroutine from the initializeRun method (e.g. FortranSim.cpp):_
-@snippet help.snippets.fortran/FortranSim.cpp fortran_use
+@snippet wares/FortranSim.cpp fortran_use
 
 
 
@@ -776,14 +776,14 @@ It also relies on the [Rcpp package](http://dirk.eddelbuettel.com/code/rcpp.html
 for handling data from and to the [R environment](https://www.r-project.org/).
 
 In order to embed R code using RInside, the following inclusion must be added at the top of the simulator source code:
-@snippet help.snippets.R/RSim.cpp R_include
+@snippet wares/RSim.cpp R_include
 
 A unique RInside variable is used to run R code, it should be declared as a member of the simulator class (named `m_R` in this example).
-@snippet help.snippets.R/RSim.cpp R_decl
+@snippet wares/RSim.cpp R_decl
 
 The R environment can be acessed through the RInside variable
 and R commands can be run using its `parseEvalQ()` method.
-@snippet help.snippets.R/RSim.cpp R_use
+@snippet wares/RSim.cpp R_use
 
 In this short example, simple variables and commands are used. 
 It is possible to perform complex operations involving external R packages, 
@@ -794,7 +794,7 @@ See the [RInside package](http://dirk.eddelbuettel.com/code/rinside.html) docume
 To help configuring the simulator which is using the RInside package, a CMake module is provided with OpenFLUID 
 to setup the configuration variables when building the simulator.
 It should be used in the `CMake.in.cmake` file of the simulator.
-@include help.snippets.R/CMake.in.cmake
+@include wares/CMake.in.cmake.snippet
 
 An adjustment of the CMake module path prefix may be required to find the provided R module for CMake
 ```