Documentation and more CI configuration changes

Author: peekxc

.circleci/config.yml

@@ -3,6 +3,8 @@
 language: R
 sudo: false
 cache: packages
+warnings_are_errors: false 
+r_check_args: #--as-cran
 
 # Run on both linux and OS X
 os:

.travis.yml

@@ -1,24 +1,26 @@
 Package: Mapper
 Type: Package
-Title: Open source implementation of the Mapper algorithm often used in Topological Data Analysis 
+Title: Open source implementation of the Mapper algorithm often used in Topological Data Analysis
 Version: 0.1.0
-Authors@R: c(person("Matt", "Piekenbrock", email = "[email protected]", role = c("aut", "ctb", "cph")), 
+Authors@R: c(person("Matt", "Piekenbrock", email = "[email protected]", role = c("aut", "cre", "cph")), 
              person("Daniel", "Muellner", role = c("ctb","cph")), 
              person("Gurjeet","Singh", role = c("ctb","cph")))
 Author: Matt Piekenbrock [aut, cre, ctb],
         Daniel Muellner [ctb, cph],
         Gurjeet Singh [ctb, cph]
 Maintainer: Matt Piekenbrock <[email protected]>
-Description: Open source implementation of the Mapper algorithm often used in Topological Data Analysis 
+Description: This package interfaces an open source implementation of the Mapper algorithm often used in Topological Data Analysis. 
 Imports: Rcpp, DT, htmlwidgets, methods, parallelDist, shiny
 LinkingTo: Rcpp
-License: GPL-3
-Suggests: network,
+License: file LICENSE
+BugReports: https://github.com/peekxc/mapper
+Suggests: 
+    network,
     testthat,
     igraph,
     knitr
-Copyright: The Mapper construction was originally developed by Gurjeet Singh, Facundo Memoli, and Gunnar Carlsson. 
-    Some of the code was inspired from direct translation from the Python Mapper library, copyright by Daniel Muellner and Aravindakshan Babu.  
+Copyright: The Mapper construction was originally developed by Gurjeet Singh, Facundo Mémoli, and Gunnar Carlsson. 
+    Some of the code was inspired by source scripts in the Python Mapper library, copyright by Daniel Müellner and Aravindakshan Babu.  
     All other code is copyright by Matt Piekenbrock.
 Encoding: UTF-8
 LazyData: true

DESCRIPTION

@@ -5,7 +5,6 @@ export()
 export(cutoff_first_bin)
 export(dashboard)
 export(mapper)
-export(multiscale)
 exportClasses(FixedRectangularCover)
 exportClasses(MapperRef)
 exportClasses(RestrainedRectangularCover)

NAMESPACE

@@ -19,33 +19,33 @@ dashboard <- function(mapper_obj, X = mapper_obj$X, node_color_f = "default"){
 
   ## Make sure shorthand 'M' is defined
   if (!"MapperRef" %in% class(mapper_obj)){ stop("'dashboard' must take as input a mapper reference object.") }
-  M <- mapper_obj
-  G <- Mapper::grapher(M)
-  if (is(X, "dist")){ X <- data.frame(index=1:attr(M$X, "Size")) }
-  else { X <- as.data.frame(X) }
-
-  ## Get the UI components
-  ui_file <- system.file(file.path("dashboard", "ui.R"), package = "Mapper")
-  source(file = ui_file, local = TRUE)
-
-  ## Node color functions
-  if (missing(node_color_f) || node_color_f == "default"){
-    if (is(X, "dist")){ stop("Default color functions cannot be applied when 'X' is given as a dist object.") }
-    if (is.null(colnames(X))) { colnames(X) <- paste0("dim", 1:dim(X)[2]) }
-    color_funcs <- new.env(parent = .BaseNamespaceEnv)
-    color_file <- system.file(file.path("dashboard", "components", "default_color_functions.R"), package = "Mapper")
-    source(color_file, local = color_funcs)
-    sapply(colnames(X), function(dim_name){ color_funcs[[dim_name]] <- make_Dim_f(dim_name) })
-  } else {
-    color_funcs <- node_color_f
-  }
-
-  ## Get the server components
-  server_file <- system.file(file.path("dashboard", "server.R"), package = "Mapper")
-  source(file = server_file, local = TRUE)
-
-  ## Return the shiny app
-  shiny::shinyApp(ui = ui, server = server)
+  # M <- mapper_obj
+  # G <- Mapper::grapher(M)
+  # if (is(X, "dist")){ X <- data.frame(index=1:attr(M$X, "Size")) }
+  # else { X <- as.data.frame(X) }
+  # 
+  # ## Get the UI components
+  # ui_file <- system.file(file.path("dashboard", "ui.R"), package = "Mapper")
+  # source(file = ui_file, local = TRUE)
+  # 
+  # ## Node color functions
+  # if (missing(node_color_f) || node_color_f == "default"){
+  #   if (is(X, "dist")){ stop("Default color functions cannot be applied when 'X' is given as a dist object.") }
+  #   if (is.null(colnames(X))) { colnames(X) <- paste0("dim", 1:dim(X)[2]) }
+  #   color_funcs <- new.env(parent = .BaseNamespaceEnv)
+  #   color_file <- system.file(file.path("dashboard", "components", "default_color_functions.R"), package = "Mapper")
+  #   source(color_file, local = color_funcs)
+  #   sapply(colnames(X), function(dim_name){ color_funcs[[dim_name]] <- make_Dim_f(dim_name) })
+  # } else {
+  #   color_funcs <- node_color_f
+  # }
+  # 
+  # ## Get the server components
+  # server_file <- system.file(file.path("dashboard", "server.R"), package = "Mapper")
+  # source(file = server_file, local = TRUE)
+  # 
+  # ## Return the shiny app
+  # shiny::shinyApp(ui = ui, server = server)
 }
 
 ## Auxillary function to make a closure for each dimension of X

R/dashboard.R

@@ -113,8 +113,10 @@ mapper <- function(X, filter_values, cover_type = "fixed rectangular", return_re
 }
 
 #' S3 method for default printing
+#' @param x Mapper object.
+#' @param ... unused. 
 #' @export
-print.Mapper <- function(x){
+print.Mapper <- function(x, ...){
   writeLines(attr(x, ".summary"))
 }