[docs] Updated documentation for added validation functions

man/OGS6.Rd

@@ -13,8 +13,10 @@ Constructor for the OGS6 base class
 \item \href{#method-add_sim_output}{\code{OGS6$add_sim_output()}}
 \item \href{#method-add_mesh}{\code{OGS6$add_mesh()}}
 \item \href{#method-add_gml}{\code{OGS6$add_gml()}}
+\item \href{#method-add_python_script}{\code{OGS6$add_python_script()}}
 \item \href{#method-add_process}{\code{OGS6$add_process()}}
 \item \href{#method-add_time_loop}{\code{OGS6$add_time_loop()}}
+\item \href{#method-add_local_coordinate_system}{\code{OGS6$add_local_coordinate_system()}}
 \item \href{#method-add_medium}{\code{OGS6$add_medium()}}
 \item \href{#method-add_parameter}{\code{OGS6$add_parameter()}}
 \item \href{#method-add_curve}{\code{OGS6$add_curve()}}
@@ -22,6 +24,7 @@ Constructor for the OGS6 base class
 \item \href{#method-add_nonlinear_solver}{\code{OGS6$add_nonlinear_solver()}}
 \item \href{#method-add_linear_solver}{\code{OGS6$add_linear_solver()}}
 \item \href{#method-add_vtkdiff}{\code{OGS6$add_vtkdiff()}}
+\item \href{#method-add_insitu}{\code{OGS6$add_insitu()}}
 \item \href{#method-get_status}{\code{OGS6$get_status()}}
 \item \href{#method-clear}{\code{OGS6$clear()}}
 \item \href{#method-clone}{\code{OGS6$clone()}}
@@ -42,12 +45,13 @@ Constructor for the OGS6 base class
 
 \item{\code{sim_id}}{The ID of the simulation}
 
-\item{\code{sim_path}}{The path where all relevant files for the simulation will be saved}
+\item{\code{sim_path}}{The path where all relevant files for the simulation will be
+saved}
 
 \item{\code{ogs_bin_path}}{Path to OpenGeoSys6 /bin directory}
 
-\item{\code{test_mode}}{In test mode, sim_path and ogs_bin_path will not be validated. If you're not
-a developer, please leave this variable as it is :)}
+\item{\code{test_mode}}{In test mode, sim_path and ogs_bin_path will not be
+validated. If you're not a developer, please leave this variable as it is :)}
 }
 \if{html}{\out{</div>}}
 }
@@ -78,6 +82,15 @@ a developer, please leave this variable as it is :)}
 \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_gml(gml)}\if{html}{\out{</div>}}
 }
 
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_python_script"></a>}}
+\if{latex}{\out{\hypertarget{method-add_python_script}{}}}
+\subsection{Method \code{add_python_script()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_python_script(python_script)}\if{html}{\out{</div>}}
+}
+
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-add_process"></a>}}
@@ -96,6 +109,15 @@ a developer, please leave this variable as it is :)}
 \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_time_loop(time_loop)}\if{html}{\out{</div>}}
 }
 
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_local_coordinate_system"></a>}}
+\if{latex}{\out{\hypertarget{method-add_local_coordinate_system}{}}}
+\subsection{Method \code{add_local_coordinate_system()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_local_coordinate_system(local_coordinate_system)}\if{html}{\out{</div>}}
+}
+
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-add_medium"></a>}}
@@ -159,6 +181,15 @@ a developer, please leave this variable as it is :)}
 \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_vtkdiff(vtkdiff)}\if{html}{\out{</div>}}
 }
 
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_insitu"></a>}}
+\if{latex}{\out{\hypertarget{method-add_insitu}{}}}
+\subsection{Method \code{add_insitu()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_insitu(insitu)}\if{html}{\out{</div>}}
+}
+
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-get_status"></a>}}
@@ -174,11 +205,7 @@ a developer, please leave this variable as it is :)}
 \if{latex}{\out{\hypertarget{method-clear}{}}}
 \subsection{Method \code{clear()}}{
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$clear(
-  which = c("meshes", "geometry", "processes", "time_loop", "media", "parameters",
-    "curves", "process_variables", "nonlinear_solvers", "linear_solvers",
-    "test_definition")
-)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$clear(which = names(get_implemented_classes()))}\if{html}{\out{</div>}}
 }
 
 }

man/analyse_xml.Rd

@@ -4,18 +4,30 @@
 \alias{analyse_xml}
 \title{analyse_xml}
 \usage{
-analyse_xml(path, pattern, element_name)
+analyse_xml(
+  path,
+  pattern,
+  element_name,
+  xpath_prefix = "//",
+  print_findings = TRUE
+)
 }
 \arguments{
-\item{path}{A path}
+\item{path}{string: A path}
 
-\item{pattern}{A regex pattern}
+\item{pattern}{string: A regex pattern}
 
-\item{element_name}{The name of the XML element to look for}
+\item{element_name}{string: The name of the XML element to look for}
+
+\item{xpath_prefix}{string: Optional: The XPath prefix to use
+(defaults to "//")}
+
+\item{print_findings}{Optional: Should the results be printed to the console?}
 }
 \description{
-This is a helper function which can be used to combat missing documentation. It looks
- for files in a path which match the given pattern and then attempts to parse them as XML.
- For each occurence of the specified element, it documents its attributes and direct children and prints a little
- summary of its findings at the end.
+This is a helper function which can be used to combat missing
+documentation. It looks for files in a path which match the given pattern
+and then attempts to parse them as XML. For each occurence of the specified
+element, it documents its attributes and direct children and prints a little
+summary of its findings at the end.
 }

man/coerce_string_to_numeric.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{coerce_string_to_numeric}
+\alias{coerce_string_to_numeric}
+\title{coerce_string_to_numeric}
+\usage{
+coerce_string_to_numeric(obj, split = FALSE)
+}
+\arguments{
+\item{obj}{An object to check}
+
+\item{split}{flag: Should object be split at ' ' (whitespace) if it is a
+string?}
+}
+\value{
+The object as a numeric type (if 'obj' was a string, else the
+unchanged 'obj')
+}
+\description{
+If an object is of type string, coerces it to a numeric type:
+A double if 'split' is FALSE as per default, a numeric vector otherwise.
+If 'split' is set to true the string will be split at ' ' (whitespace)
+characters.
+}

man/download_benchmark.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/scrape_benchmarks.R
+\name{download_benchmark}
+\alias{download_benchmark}
+\title{download_benchmark}
+\usage{
+download_benchmark(prj_url, path)
+}
+\arguments{
+\item{prj_url}{The URL of a .prj file}
+
+\item{path}{The path the benchmark files should be saved to}
+}
+\description{
+Downloads a single benchmark (consisting of one .prj file and
+either one .gml and one .vtu file OR multiple .vtu files)
+}

man/find_read_in_func_call.Rd

@@ -10,8 +10,10 @@ find_read_in_func_call(node_name)
 \item{node_name}{The name of an XML node}
 }
 \value{
-A ready-to-call string if a corresponding function was found, an empty string otherwise
+A ready-to-call string if a corresponding function was found, an
+empty string otherwise
 }
 \description{
-Checks if a custom read_in function was defined for nodes with the given name
+Checks if a custom read_in function was defined for nodes
+with the given name
 }

man/flags_to_assign_str.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{flags_to_assign_str}
+\alias{flags_to_assign_str}
+\title{flags_to_assign_str}
+\usage{
+flags_to_assign_str(flags, print_result = FALSE)
+}
+\arguments{
+\item{flags}{vector: Flags}
+
+\item{print_result}{flag: Should the result be printed to the console?}
+}
+\description{
+Helper function to generate a string out of a flag vector
+}

man/flags_to_con_call_str.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{flags_to_con_call_str}
+\alias{flags_to_con_call_str}
+\title{flags_to_con_call_str}
+\usage{
+flags_to_con_call_str(flags, print_result = FALSE)
+}
+\arguments{
+\item{flags}{vector: Flags}
+
+\item{print_result}{flag: Should the result be printed to the console?}
+}
+\description{
+Helper function to generate a string out of a flag vector
+}

man/flags_to_con_str.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{flags_to_con_str}
+\alias{flags_to_con_str}
+\title{flags_to_con_str}
+\usage{
+flags_to_con_str(flags, print_result = FALSE)
+}
+\arguments{
+\item{flags}{vector: Flags}
+
+\item{print_result}{flag: Should the result be printed to the console?}
+}
+\description{
+Helper function to generate a string out of a flag vector
+}

man/flags_to_doc_str.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{flags_to_doc_str}
+\alias{flags_to_doc_str}
+\title{flags_to_doc_str}
+\usage{
+flags_to_doc_str(flags, print_result = FALSE)
+}
+\arguments{
+\item{flags}{vector: Flags}
+
+\item{print_result}{flag: Should the result be printed to the console?}
+}
+\description{
+Helper function to generate a string out of a flag vector
+}

man/flags_to_name_str.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{flags_to_name_str}
+\alias{flags_to_name_str}
+\title{flags_to_name_str}
+\usage{
+flags_to_name_str(flags, print_result = FALSE)
+}
+\arguments{
+\item{flags}{vector: Flags}
+
+\item{print_result}{flag: Should the result be printed to the console?}
+}
+\description{
+Helper function to generate a name string out of a flag vector
+}

man/generate_active_field.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{generate_active_field}
+\alias{generate_active_field}
+\title{generate_active_field}
+\usage{
+generate_active_field(parameter_name)
+}
+\arguments{
+\item{parameter_name}{The name of the OGS6 class parameter}
+}
+\description{
+Helper function to generate an R6 active field for a OGS6 class
+parameter
+}

man/generate_add_method.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{generate_add_method}
+\alias{generate_add_method}
+\title{generate_add_method}
+\usage{
+generate_add_method(tag_name, parent_tag_name)
+}
+\arguments{
+\item{tag_name}{The tag name of the XML element represented by the class
+object}
+
+\item{parent_tag_name}{The tag name of the parent of the XML element
+represented by the class object}
+}
+\description{
+Helper function to generate an R6 add_* method for a
+r2ogs6 class object
+}

man/generate_all_benchmarks.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_benchmark_script.R
+\name{generate_all_benchmarks}
+\alias{generate_all_benchmarks}
+\title{generate_all_benchmarks}
+\usage{
+generate_all_benchmarks(
+  path = "extdata/benchmarks/",
+  dest_dir = "extdata/benchmark_scripts/"
+)
+}
+\arguments{
+\item{path}{Optional: A path to a benchmark directory to generate scripts from
+(defaults to 'extdata/benchmarks' package folder)}
+
+\item{dest_dir}{Optional: The directory to write the scripts to
+(defaults to 'extdata/benchmark_scripts' package folder)}
+}
+\description{
+Collector function to generate benchmarks from all .prj files in a directory
+}

man/generate_benchmark_script.Rd

@@ -4,7 +4,7 @@
 \alias{generate_benchmark_script}
 \title{generate_benchmark_script}
 \usage{
-generate_benchmark_script(prj_path, dest_dir = "")
+generate_benchmark_script(prj_path, dest_dir = "extdata/benchmark_scripts/")
 }
 \arguments{
 \item{prj_path}{The path to the project file the script will be based on}

man/generate_constructor.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{generate_constructor}
+\alias{generate_constructor}
+\title{generate_constructor}
+\usage{
+generate_constructor(tag_name, param_flags, prefix = "", print_result = FALSE)
+}
+\arguments{
+\item{tag_name}{The name of the XML element the class will be based on}
+
+\item{param_flags}{The parameters for the class and if they are required or
+not (i.e. 'c(a = TRUE, b = FALSE)')}
+
+\item{prefix}{Optional: For subclasses whose represented elements have
+the same tag name as an element for which a class was already specified,
+a prefix must be appended to the class name}
+
+\item{print_result}{flag: Should the result be printed to the console?}
+}
+\description{
+Helper function to generate a constructor out of a tag name
+and a flag vector
+}

man/generate_helper.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_class.R
+\name{generate_helper}
+\alias{generate_helper}
+\title{generate_helper}
+\usage{
+generate_helper(tag_name, param_flags, prefix = "", print_result = FALSE)
+}
+\arguments{
+\item{tag_name}{The name of the XML element the helper will be based on}
+
+\item{param_flags}{The parameters for the class and if they are required or
+not (i.e. 'c(a = TRUE, b = FALSE)')}
+
+\item{prefix}{Optional: For subclasses whose represented elements have
+the same tag name as an element for which a class was already specified,
+a prefix must be appended to the class name}
+
+\item{print_result}{flag: Should the result be printed to the console?}
+}
+\description{
+Helper function to generate a helper out of a tag name
+and a flag vector
+}

man/get_class_tag_name.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{get_class_tag_name}
+\alias{get_class_tag_name}
+\title{get_class_tag_name}
+\usage{
+get_class_tag_name(class_name)
+}
+\arguments{
+\item{class_name}{string: The name of a r2ogs6 class}
+}
+\value{
+string: The tag name corresponding to class_name
+}
+\description{
+Utility function, returns the tag name of a r2ogs6 class
+}

man/get_grandchild_length_vector.Rd

@@ -10,9 +10,10 @@ get_grandchild_length_vector(xml_node)
 \item{xml_node}{An XML node}
 }
 \value{
-A numeric vector containing the number of children of each child of xml_node
+A numeric vector containing the number of children of each child of
+xml_node
 }
 \description{
-Helper function to check the number of children of children of an XML node
-(i.e. grandchildren)
+Helper function to check the number of children of children of
+an XML node (i.e. grandchildren)
 }

man/get_implemented_classes.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{get_implemented_classes}
+\alias{get_implemented_classes}
+\title{get_implemented_classes}
+\usage{
+get_implemented_classes()
+}
+\description{
+Utility function, returns the names of all classes implemented
+so far. Change this if you implement new classes or delete old ones!
+If you implement a new class, you add the following to the character vector:
+<name_of_corresponding_OGS6_parameter> = <name_of_your_class>
+}

man/get_list_status.Rd

@@ -13,8 +13,9 @@ get_list_status(flag, obj_list, element_type = "list element", is_opt = FALSE)
 
 \item{element_type}{Optional: What kind of elements are in the list?}
 
-\item{is_opt}{Does the list need at least one element?}
+\item{is_opt}{flag: Does the list need at least one element?}
 }
 \description{
-Helper function for get_status() to check if a list has at least one element.
+Helper function for get_status() to check if a list has at least
+one element.
 }