run package document msbuild

Author: xieguigang

man/.get_context.1

@@ -7,11 +7,12 @@
     <i>ssid</i> = <span style='color: blue !important;'>NULL</span>)\fR
 .SH OPTIONS
 .PP
-\fBssid\fB \fR\- NULL. 
+\fBssid\fB \fR\- NULL. the session id for multiple user environment, default NULL means global user environment
 .PP
 .SH VALUE
 .PP
-the context object which is generated via the ``init_context`` function.
+the context object which is generated via the
+``init_context`` function.
 .PP
 .SH FILES
 .PP

man/.internal_call.1

@@ -5,26 +5,59 @@
 \fI.internal_call(app, context)\fR
 .SH DESCRIPTION
 .PP
-This internal function executes an analysis application after validating its dependencies. It handles application execution, error reporting, and performance profiling.
+
+
+This internal function executes an analysis application after validating its dependencies.
+It handles application execution, error reporting, and performance profiling.
 .PP
 .SH OPTIONS
 .PP
-\fBapp\fB \fR\- . A list defining the analysis application. Must contain: - `name`: (character) Name of the application (for logging). - `call`: (function) The function to execute the application logic. - `profiler`: (list) Stores performance metrics (e.g., execution time).
+\fBapp\fB \fR\- . A list defining the analysis application. Must contain:
+- `name`: (character) Name of the application (for logging).
+- `call`: (function) The function to execute the application logic.
+- `profiler`: (list) Stores performance metrics (e.g., execution time).
 .PP
 .PP
-\fBcontext\fB \fR\- . A list or environment providing runtime context, such as input data paths, environment variables, or configuration settings required by the application.
+\fBcontext\fB \fR\- . A list or environment providing runtime context, such as input data paths,
+environment variables, or configuration settings required by the application.
 .PP
 .SH VALUE
 .PP
-Invisibly returns `NULL`. The function primarily updates `app$profiler` with execution time metrics and may modify the `context` during execution.
+Invisibly returns `NULL`. The function primarily updates `app$profiler` with execution
+time metrics and may modify the `context` during execution.
 .PP
 .SH DETAILS
 .PP
-### Key Steps: 1. ​**Dependency Check**: Validates if required context variables and files exist via `check_dependency(app, context)`. - If dependencies are met, proceeds to execute the application. - If dependencies are missing, throws an error with detailed missing resources. 2. ​**Execution**: - Logs start/end timestamps if `options(verbose = TRUE)`. - Executes `app$call` with arguments `app` and `context` using `do.call()`. 3. ​**Error Handling**: - Aggregates missing dependencies into readable error messages. - Calls `throw_err()` to terminate the workflow and report issues. 4. ​**Profiling**: Records total execution time in `app$profiler$time` using `time_span()` for human-readable formatting.
+### Key Steps:
+1. ​**Dependency Check**:
+Validates if required context variables and files exist via `check_dependency(app, context)`.
+- If dependencies are met, proceeds to execute the application.
+- If dependencies are missing, throws an error with detailed missing resources.
+2. ​**Execution**:
+- Logs start/end timestamps if `options(verbose = TRUE)`.
+- Executes `app$call` with arguments `app` and `context` using `do.call()`.
+3. ​**Error Handling**:
+- Aggregates missing dependencies into readable error messages.
+- Calls `throw_err()` to terminate the workflow and report issues.
+4. ​**Profiling**:
+Records total execution time in `app$profiler$time` using `time_span()` for human-readable formatting.
 .PP
 .SH EXAMPLES
 .PP
-\dontrun{ # Define a sample application app <- list( name = "demo_analysis", call = function(argv) { print(paste("Running:", argv$app$name)) }, profiler = list() ) # Execute with context .internal_call(app, context = list()) }
+#\dontrun{
+
+# Define a sample application
+app <- list(
+name = "demo_analysis",
+call = function(argv) {
+print(paste("Running:", argv$app$name))
+},
+profiler = list()
+)
+# Execute with context
+.internal_call(app, context = list())
+
+#}
 .PP
 .SH FILES
 .PP

man/__build_app.1

@@ -5,7 +5,13 @@ __build_app \- __build_app(f)
 \fI__build_app(f)\fR
 .SH OPTIONS
 .PP
-\fBf\fB \fR\- . the target function f which tagged the required attribute data inside: app, desc, context_env, workfiles
+\fBf\fB \fR\- . the target function f which tagged the required
+attribute data inside: app, desc, context_env, workfiles
+.PP
+.SH DETAILS
+.PP
+Build a new workflow app module object based on the
+custom attribute values that tagged on the target function
 .PP
 .SH FILES
 .PP

man/__runImpl.1

@@ -5,20 +5,45 @@ __runImpl \- __runImpl(context,
 .SH SYNOPSIS
 \fI__runImpl(context,
     <i>disables</i> = 'list'())\fR
+.SH DESCRIPTION
+.PP
+
+
+An internal function that drives the execution of a modular workflow.
+It sequentially processes analysis modules according to the pipeline
+configuration while respecting disablement rules.
+.PP
 .SH OPTIONS
 .PP
-\fBcontext\fB \fR\- . A workflow context object containing: \itemize{ \item{pipeline - character vector of module execution order} \item{workflow - list of module definitions} }
+\fBcontext\fB \fR\- . A workflow context object containing:
+\itemize{
+\item{pipeline - character vector of module execution order}
+\item{workflow - list of module definitions}
+}
 .PP
 .PP
-\fBdisables\fB \fR\- 'list'(). A named list specifying module disablement status. Format: `list(module_name = TRUE/FALSE)`. Modules with TRUE will be skipped.
+\fBdisables\fB \fR\- 'list'(). A named list specifying module disablement status.
+Format: `list(module_name = TRUE/FALSE)`. Modules with TRUE will be skipped.
 .PP
 .SH VALUE
 .PP
-Invisibly returns NULL. Modifies the workflow context object in-place through module executions.
+Invisibly returns NULL. Modifies the workflow context object in-place
+through module executions.
 .PP
 .SH DETAILS
 .PP
-This function: \enumerate{ \item Retrieves module execution order from `context$pipeline` \item Checks disablement status through two mechanisms: \itemize{ \item Explicit disablement via `disables` parameter \item Module's own `disable` property (set by upstream modules) } \item Executes non-disabled modules using `.internal_call()` \item Provides verbose logging when `options(verbose=TRUE)` } The workflow context is modified in-place by module execution.
+This function:
+\enumerate{
+\item Retrieves module execution order from `context$pipeline`
+\item Checks disablement status through two mechanisms:
+\itemize{
+\item Explicit disablement via `disables` parameter
+\item Module's own `disable` property (set by upstream modules)
+}
+\item Executes non-disabled modules using `.internal_call()`
+\item Provides verbose logging when `options(verbose=TRUE)`
+}
+The workflow context is modified in-place by module execution.
 .PP
 .SH SEE ALSO
 \code{\link{.internal_call}} for module execution logic

man/__workfile_uri_parser.1

@@ -5,11 +5,14 @@ __workfile_uri_parser \- __workfile_uri_parser(uri)
 \fI__workfile_uri_parser(uri)\fR
 .SH OPTIONS
 .PP
-\fBuri\fB \fR\- . 
+\fBuri\fB \fR\- . a character vector that contains the workfile
+reference expression.
 .PP
 .SH VALUE
 .PP
-a tuple list object that contains the necessary parameter value for call ``workfile`` function for gets the reference file path to the required data files.
+a tuple list object that contains the necessary
+parameter value for call ``workfile`` function for gets
+the reference file path to the required data files.
 .PP
 .SH FILES
 .PP

man/app.1

@@ -12,13 +12,17 @@ app \- app(name, analysis,
 \fBname\fB \fR\- . the analysis app name
 .PP
 .PP
-\fBanalysis\fB \fR\- . 
+\fBanalysis\fB \fR\- . a callable function for run the data analysis
+content. The function declare signature for this parameter
+value required of two parameter signature, see comment document
+of the ``app_check.delegate`` function.
 .PP
 .PP
 \fBdesc\fB \fR\- 'no description'. 
 .PP
 .PP
-\fBdependency\fB \fR\- NULL. usually be the environment context symbol dependency or the workspace file dependency
+\fBdependency\fB \fR\- NULL. usually be the environment context symbol
+dependency or the workspace file dependency
 .PP
 .SH FILES
 .PP

man/app_check.delegate.1

@@ -5,11 +5,20 @@ app_check.delegate \- app_check.delegate(analysis)
 \fIapp_check.delegate(analysis)\fR
 .SH OPTIONS
 .PP
-\fBanalysis\fB \fR\- . 
+\fBanalysis\fB \fR\- . a callable function to check, just check of the required
+parameters is exists in the definition or not.
 .PP
 .SH DETAILS
 .PP
-the analysis function should contains only two required parameters with specific name defined: 1. app: a list object that defines the app object itself 2. context: a list object that accept the workflow environment context due to the reason of analysis app function is called via the ``do.call`` function from the RENV base environment, so that the parameter value is aligned with the invoke function target strictly, so you can not change the parameter name or the parameter will not be aligned properly when call this analysis app function.
+the analysis function should contains only two
+required parameters with specific name defined:
+1. app: a list object that defines the app object itself
+2. context: a list object that accept the workflow environment context
+due to the reason of analysis app function is called via the ``do.call``
+function from the RENV base environment, so that the parameter value is
+aligned with the invoke function target strictly, so you can not change
+the parameter name or the parameter will not be aligned properly when
+call this analysis app function.
 .PP
 .SH FILES
 .PP

man/check_dependency.1

@@ -7,14 +7,22 @@ check_dependency \- check_dependency(app,
     <i>context</i> = '.get_context'())\fR
 .SH OPTIONS
 .PP
-\fBapp\fB \fR\- . 
+\fBapp\fB \fR\- . the analysis app object list which is construct
+via the ``app`` function.
 .PP
 .PP
 \fBcontext\fB \fR\- '.get_context'(). 
 .PP
 .SH VALUE
 .PP
-this function returns a data list that contains the dependency check result. there are some data symbol inside this result object list: 1. check: logical, for indicate the dependency check success or not; 2. context: a tuple list object that contains of context symbol names which are not check success, and the reason of failure; 3. file: character vector of dependency of local workspace file check not success
+this function returns a data list that contains the
+dependency check result. there are some data symbol inside
+this result object list:
+1. check: logical, for indicate the dependency check success or not;
+2. context: a tuple list object that contains of context symbol names
+which are not check success, and the reason of failure;
+3. file: character vector of dependency of local workspace file
+check not success
 .PP
 .SH FILES
 .PP

man/check_dependency.context_env.1

@@ -10,6 +10,11 @@ check_dependency.context_env \- check_dependency.context_env(requires, context)
 .PP
 \fBcontext\fB \fR\- . 
 .PP
+.SH DETAILS
+.PP
+the environment symbols from the analysis context should be
+set via the ``set_config`` function.
+.PP
 .SH FILES
 .PP
 SMRUCC/R#.declare_function.check_dependency.context_env at context_env.R:line 6

man/check_dependency.localfiles.1

@@ -5,14 +5,18 @@ check_dependency.localfiles \- check_dependency.localfiles(requires, context)
 \fIcheck_dependency.localfiles(requires, context)\fR
 .SH OPTIONS
 .PP
-\fBrequires\fB \fR\- . 
+\fBrequires\fB \fR\- . the required temp work files, should be a tuple list
+object that contains the app reference and the related temp workfile,
+example data format of this tuple list would be:
+list(app1 = [file1, file2, ...], app2 = file3, ...)
 .PP
 .PP
 \fBcontext\fB \fR\- . 
 .PP
 .SH DETAILS
 .PP
-the workfile path in the ``requires`` tuple file list should be a relative file path which is relative to the app workdir
+the workfile path in the ``requires`` tuple file list should be
+a relative file path which is relative to the app workdir
 .PP
 .SH FILES
 .PP