galaaz 0.4.9 → 0.4.10

data/lib/R_interface/rvector.rb

@@ -115,18 +115,6 @@ module R
       puts "comparison called"
     end
 
-#=begin    
-    #--------------------------------------------------------------------------------------
-    # @TODO Need to understand why to_ary is being called here and what the effect is of
-    # returning the empty array.  For now, doing this returns better error messages in
-    # rspec
-    #--------------------------------------------------------------------------------------
-
-    def to_ary
-      []
-    end
-#=end
-    
   end
   
 end

data/lib/gknit/knitr_engine.rb

@@ -652,11 +652,13 @@ class KnitrEngine
         # function engine_output will format whatever is in out inside a white box
         out = R.engine_output(@options, out: res) if @echo
         
-        # ouputs the data in RubyChunk '@@outputs' variable. Everything that should
+        # ouputs the data in RubyChunk '@outputs' variable. Everything that should
         # be processed by 'pandoc' and not appear in the output block from
         # engine_output, should be outputed with the 'outputs' function and will be
-        # stored in the @@outputs variable
-        out = R.c(out, RubyChunk.get_outputs)
+        # stored in the @outputs variable
+        # out = R.c(out, RubyChunk.get_outputs)
+        out = R.c(out, RChunk.out_list)
+        RChunk.reset_outputs
         
         # @TODO: allow capturing many plots in the block.  For now, only the last
         # plot will be captured.  Not a very serious problem for now.

data/lib/util/exec_ruby.rb

@@ -22,77 +22,37 @@
 ##########################################################################################
 
 require 'stringio'
-=begin
+
 #----------------------------------------------------------------------------------------
-# Path StringIO puts... Already opened an issue in RC12
+# Class RC is used only as a context for all ruby chunks in the rmarkdown file.
+# This allows for chunks to access local variables defined in other chunks.
 #----------------------------------------------------------------------------------------
 
-class StringIO
-  
-  def puts(*args)
+class RC
 
-    print "========================\n"
-    print "Inside puts\n"
-    print "========================\n"
-    
-    if args.empty?
-      write(DEFAULT_RECORD_SEPARATOR)
-    else
-      args.each do |arg|
-
-        # method to_s is not being called when the output is diverted
-        # need to fix it
-        if (arg.is_a? R::Object)
-          arg = arg.to_s
-        end
-        
-        if arg.nil?
-          line = ''
-        elsif Thread.guarding? arg
-          line = '[...]'
-        else
-          begin
-            arg = Truffle::Type.coerce_to(arg, Array, :to_ary)
-            Thread.recursion_guard arg do
-              arg.each { |a| puts a }
-            end
-            next
-          rescue
-            line = arg.to_s
-          end
-        end
-
-        write(line)
-        write(DEFAULT_RECORD_SEPARATOR) # unless line[-1] == ?\n
-      end
-    end
+  attr_reader :out_list
 
-    nil
+  def initialize
+    @out_list = R.list
   end
 
-end
-=end
-#----------------------------------------------------------------------------------------
-# Class RubyChunk is used only as a context for all ruby chunks in the rmarkdown file.
-# This allows for chunks to access instance_variables (@)
-#----------------------------------------------------------------------------------------
-
-class RubyChunk
-
-  def self.init
-    @@outputs = R.list
+  def outputs(obj)
+    @out_list = R.c(@out_list, obj)
   end
-  
-  def self.get_outputs
-    @@outputs
+
+  def reset_outputs
+    @out_list = nil
   end
-  
-  def self.outputs(obj)
-    @@outputs = R.c(@@outputs, obj)
+
+  def get_binding
+    binding
   end
   
 end
 
+RChunk = RC.new
+RCbinding = RChunk.get_binding
+
 #----------------------------------------------------------------------------------------
 #
 #----------------------------------------------------------------------------------------
@@ -117,11 +77,11 @@ module GalaazUtil
 
   def self.exec_ruby(options)
 
-    RubyChunk.init
+    # RubyChunk.init
     
     # read the chunk code
     code = R.paste(options.code, collapse: "\n") >> 0
-
+    
     # the output should be a list with the proper structure to pass to
     # function engine_output.  We first add the souce code from the block to
     # the list
@@ -138,7 +98,8 @@ module GalaazUtil
       # Execute the Ruby code in the scope of class RubyChunk. This is done
       # so that instance variables created in one chunk can be used again on
       # another chunk
-      RubyChunk.instance_eval(code) if (options[["eval"]] >> 0)
+      # RubyChunk.instance_eval(code) if (options[["eval"]] >> 0)
+      eval(code, RCbinding, __FILE__, __LINE__ + 1) if (options[["eval"]] >> 0)
       
       # add the returned value to the list
       # this should have captured everything in the evaluation code

data/specs/tmp.rb

@@ -22,21 +22,35 @@
 ##########################################################################################
 
 require 'galaaz'
-# require 'ggplot'
 
-R.install_and_loads('nycflights13')
-R.library('dplyr')
+puts RChunk
+puts RCbinding
+
+eval("a = 10", RCbinding)
+eval("puts a", RCbinding)
+
+code = <<-EOC
+     def test
+       puts "hello from test"
+     end
+EOC
+
+eval(code, RCbinding)
+eval("test", RCbinding)
+
+
+
+=begin
+code6 = <<-EOC
+  test
+EOC
+
+puts code2
+
+eval(code2, RubyChunk.binding)
+=end
 
-@flights = ~:flights
-@flights = @flights.
-             mutate("Diff Chegada": :arr_time - :sched_arr_time,
-                    'Total Delay': :'Diff Chegada' *
-                                   E.if_else(((:arr_time - :sched_arr_time).eq 0), 1, 2),
-                    'Moeda.x': "R$",
-                    'Valor Nominal': :'Diff Chegada' *
-                                     E.if_else((:'Moeda.x'.eq "R$"), :'Total Delay', 100))
 
-puts @flights.head.as__data__frame
 
 ## Renaming columns
 

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "galaaz"
-$version="0.4.9"
+$version="0.4.10"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: galaaz
 version: !ruby/object:Gem::Version
-  version: 0.4.9
+  version: 0.4.10
 platform: ruby
 authors:
 - Rodrigo Botafogo
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-30 00:00:00.000000000 Z
+date: 2019-05-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
@@ -80,31 +80,21 @@ files:
 - Rakefile
 - bin/galaaz
 - bin/gknit
-- bin/gknit_old_r
 - bin/grun
 - bin/gstudio
 - bin/gstudio.rb
-- blogs/dev/dev.Rmd
-- blogs/dev/dev.md
-- blogs/dev/dev2.Rmd
-- blogs/dev/model.rb
-- blogs/dplyr/dplyr.Rmd
-- blogs/dplyr/dplyr.html
-- blogs/dplyr/dplyr.md
-- blogs/dplyr/dplyr.rb
 - blogs/galaaz_ggplot/galaaz_ggplot.Rmd
 - blogs/galaaz_ggplot/galaaz_ggplot.aux
 - blogs/galaaz_ggplot/galaaz_ggplot.html
-- blogs/galaaz_ggplot/galaaz_ggplot.log
-- blogs/galaaz_ggplot/galaaz_ggplot.md
 - blogs/galaaz_ggplot/galaaz_ggplot.out
 - blogs/galaaz_ggplot/galaaz_ggplot.pdf
-- blogs/galaaz_ggplot/galaaz_ggplot.tex
+- blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/midwest_rb.png
+- blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/scatter_plot_rb.png
+- blogs/galaaz_ggplot/galaaz_ggplot_files/figure-latex/midwest_rb.pdf
+- blogs/galaaz_ggplot/galaaz_ggplot_files/figure-latex/scatter_plot_rb.pdf
 - blogs/galaaz_ggplot/midwest.Rmd
 - blogs/galaaz_ggplot/midwest.html
-- blogs/galaaz_ggplot/midwest.png
 - blogs/galaaz_ggplot/midwest_external_png
-- blogs/galaaz_ggplot/scatter_plot.png
 - blogs/gknit/gknit.Rmd
 - blogs/gknit/gknit.html
 - blogs/gknit/gknit.md
@@ -118,10 +108,15 @@ files:
 - blogs/manual/manual.Rmd
 - blogs/manual/manual.html
 - blogs/manual/manual.md
+- blogs/manual/manual.pdf
+- blogs/manual/manual.tex
 - blogs/manual/manual_files/figure-html/diverging_bar.png
+- blogs/manual/manual_files/figure-latex/diverging_bar.pdf
 - blogs/nse_dplyr/nse_dplyr.Rmd
 - blogs/nse_dplyr/nse_dplyr.html
 - blogs/nse_dplyr/nse_dplyr.md
+- blogs/nse_dplyr/nse_dplyr.pdf
+- blogs/nse_dplyr/nse_dplyr.tex
 - blogs/oh_my/not_so.rb
 - blogs/oh_my/oh_my.Rmd
 - blogs/oh_my/oh_my.html
@@ -132,7 +127,6 @@ files:
 - blogs/ruby_plot/ruby_plot.html
 - blogs/ruby_plot/ruby_plot.md
 - blogs/ruby_plot/ruby_plot.pdf
-- blogs/ruby_plot/ruby_plot.tex
 - blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.png
 - blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.png
@@ -154,6 +148,17 @@ files:
 - blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.svg
 - blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.png
 - blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.svg
+- blogs/ruby_plot/ruby_plot_files/figure-latex/dose_len.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_delivery.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_dose.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color2.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_decorations.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_jitter.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_points.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/final_box_plot.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/final_violin_plot.png
+- blogs/ruby_plot/ruby_plot_files/figure-latex/violin_with_jitter.png
 - examples/50Plots_MasterList/Images/midwest-scatterplot.PNG
 - examples/50Plots_MasterList/ScatterPlot.rb
 - examples/50Plots_MasterList/scatter_plot.rb

data/bin/gknit_old_r

@@ -1,236 +0,0 @@
-#!/usr/bin/env ruby
-# coding: utf-8
-
-dir = Dir.pwd
-puts "Knitting #{dir}/#{ARGV[0]}"
-
-code = <<EOF
-eval.polyglot("ruby", "$LOAD_PATH.unshift %q(/home/rbotafogo/desenv/galaaz/lib)")
-eval.polyglot("ruby", "require %q(galaaz)")
-eval.polyglot("ruby", "R.install_and_loads %q(knitr)")
-eval.polyglot("ruby", "R.install_and_loads %q(rmarkdown)")
-
-# graphics devices in base R, plus those in Cairo, cairoDevice, tikzDevice
-auto_exts = c(
-  bmp = "bmp", postscript = "eps", pdf = "pdf", png = "png", svg = "svg",
-  jpeg = "jpeg", pictex = "tex", tiff = "tiff", win.metafile = "wmf",
-  cairo_pdf = "pdf", cairo_ps = "eps",
-
-  quartz_pdf = "pdf", quartz_png = "png", quartz_jpeg = "jpeg",
-  quartz_tiff = "tiff", quartz_gif = "gif", quartz_psd = "psd",
-  quartz_bmp = "bmp",
-
-  CairoJPEG = "jpeg", CairoPNG = "png", CairoPS = "eps", CairoPDF = "pdf",
-  CairoSVG = "svg", CairoTIFF = "tiff",
-
-  Cairo_pdf = "pdf", Cairo_png = "png", Cairo_ps = "eps", Cairo_svg = "svg",
-
-  svglite = "svg",
-
-  tikz = "tex"
-)
-
-is_plot_output = function(x) {
-  evaluate::is.recordedplot(x) || inherits(x, "knit_image_paths")
-}
-
-# find recorded plots in the output of evaluate()
-find_recordedplot = function(x) {
-  vapply(x, is_plot_output, logical(1))
-}
-
-dev2ext = function(x) {
-  res = auto_exts[x]
-  if (any(idx <- is.na(res))) {
-    for (i in x[idx]) check_dev(i)
-    stop2(
-      "cannot find appropriate filename extensions for device ", x[idx], "; ",
-      "please use chunk option 'fig.ext' (https://yihui.name/knitr/options)"
-    )
-  }
-  unname(res)
-}
-
-# filter the dev.args option
-get_dargs = function(dargs, dev) {
-  if (length(dargs) == 0) return()
-  if (is.list(dargs) && all(sapply(dargs, is.list))) {
-    # dev.args is list(dev1 = list(arg1 = val1, ...), dev2 = list(arg2, ...))
-    dargs = dargs[[dev]]
-  }
-  dargs
-}
-
-# open a device for a chunk; depending on the option global.device, may or may
-# not need to close the device on exit
-chunk_device = function(
-  width, height, record = TRUE, dev, dev.args, dpi, options, tmp = tempfile()
-) {
-  dev_new = function() {
-    # actually I should adjust the recording device according to dev, but here I
-    # have only considered the png and tikz devices (because the measurement
-    # results can be very different especially with the latter, see #1066), and
-    # also the cairo_pdf device (#1235)
-    if (identical(dev, "png")) {
-      do.call(grDevices::png, c(list(
-        filename = tmp, width = width, height = height, units = "in", res = dpi
-      ), get_dargs(dev.args, "png")))
-    } else if (identical(dev, "tikz")) {
-      dargs = c(list(
-        file = tmp, width = width, height = height
-      ), get_dargs(dev.args, "tikz"))
-      dargs$sanitize = options$sanitize; dargs$standAlone = options$external
-      if (is.null(dargs$verbose)) dargs$verbose = FALSE
-      do.call(tikz_dev, dargs)
-    } else if (identical(dev, "cairo_pdf")) {
-      do.call(grDevices::cairo_pdf, c(list(
-        filename = tmp, width = width, height = height
-      ), get_dargs(dev.args, "cairo_pdf")))
-    } else if (identical(getOption("device"), "pdf_null")) {
-      if (!is.null(dev.args)) {
-        dev.args = get_dargs(dev.args, "pdf")
-        dev.args = dev.args[intersect(names(dev.args), c("pointsize", "bg"))]
-      }
-      do.call(pdf_null, c(list(width = width, height = height), dev.args))
-    } else dev.new(width = width, height = height)
-  }
-  if (!opts_knit$get("global.device")) {
-    dev_new()
-    dev.control(displaylist = if (record) "enable" else "inhibit")  # enable recording
-    # if returns TRUE, we need to close this device after code is evaluated
-    return(TRUE)
-  } else if (is.null(dev.list())) {
-    # want to use a global device but not open yet
-    dev_new()
-    dev.control("enable")
-  }
-  FALSE
-}
-
-showtext = function(show) if (isTRUE(show)) showtext::showtext_begin()
-
-#########################################################################################
-
-# define the ruby engine for processing Ruby chunks in
-# rmarkdown
-eng_ruby = function(options) {
-  block_code = paste(options$code, collapse = "\\n");
-  code = paste0("GalaazUtil.exec_ruby_tor(", 
-                   shQuote(block_code),
-                  ")
-                ");
-
-  keep = options$fig.keep
-  keep.idx = NULL
-  if (is.numeric(keep)) {
-    keep.idx = keep
-    keep = "index"
-  }
-
-  tmp.fig = tempfile(); on.exit(unlink(tmp.fig), add = TRUE)
-
-  # open a device to record plots
-  if (chunk_device(options$fig.width[1L], options$fig.height[1L], keep != "none",
-                   options$dev, options$dev.args, options$dpi, options, tmp.fig)) {
-    # preserve par() settings from the last code chunk
-    if (keep.pars <- opts_knit$get("global.par"))
-      par2(opts_knit$get("global.pars"))
-    showtext(options$fig.showtext)  # showtext support
-    dv = dev.cur()
-    on.exit({
-      if (keep.pars) opts_knit$set(global.pars = par(no.readonly = TRUE))
-      dev.off(dv)
-    }, add = TRUE)
-   }
-
-  # guess plot file type if it is NULL
-  # if (keep != "none" && is.null(options$fig.ext))
-  #   options$fig.ext = dev2ext(options$dev)
-
-  res = eval.polyglot("ruby", code);
-
-# rearrange locations of figures
-#  figs = find_recordedplot(res)
-#  if (length(figs) && any(figs)) {
-#    if (keep == 'none') {
-#      res = res[!figs] # remove all
-#    } else {
-#      if (options$fig.show == 'hold') res = c(res[!figs], res[figs]) # move to the end
-#      figs = find_recordedplot(res)
-#      if (length(figs) && sum(figs) > 1) {
-#        if (keep %in% c('first', 'last')) {
-#          res = res[-(if (keep == 'last') head else tail)(which(figs), -1L)]
-#        } else {
-#          # keep only selected
-#          if (keep == 'index') res = res[which(figs)[keep.idx]]
-#          # merge low-level plotting changes
-#          if (keep == 'high') res = merge_low_plot(res, figs)
-#        }
-#      }
-#    }
-#}
-
-  engine_output(options, out = res)
-
-#  out_list = list(source = block_code, text = res, message = "message from Galaaz",
-#                  warning = "Warning from Galaaz", error = "Error from Galaaz",
-#                  value = "Value from Galaaz")
-#  engine_output(options, out = out_list)
-   # engine_output(options, block_code, res)
-}
-
-knit_engines$set(ruby = eng_ruby)
-
-#########################################################################################
-
-# define the rb engine for inline Ruby code
-eng_rb = function(options) {
-  code = paste0("GalaazUtil.exec_ruby(", 
-                   shQuote(options$label), 
-                  ")
-                ");
-  out = eval.polyglot("ruby", code)
-  return(out)
-}
-
-knit_engines$set(rb = eng_rb)
-
-#########################################################################################
-
-# define the include engine for including Ruby files
-# in place
-
-eng_include = function(options) {
-  if (is.null(options$relative) | isTRUE(options$relative)) {
-    req = "require_relative "
-  } else {
-    req = "require "
-  }
-
-  # read the file and store it to output in the code block
-  code = paste0("GalaazUtil.inline_file(", 
-                   shQuote(options$label),
-                   ", ",
-                   shQuote(req),
-                  ")
-                ");
-  include = eval.polyglot("ruby", code);
-
-  # require the file
-  require = paste0(req, shQuote(options$label));
-  code = paste0("GalaazUtil.exec_ruby(", 
-                   shQuote(require), 
-                  ")
-                ");
-
-  out = eval.polyglot("ruby", code);
-  engine_output(options, include, out)
-}
-
-knit_engines$set(include = eng_include)
-
-
-rmarkdown::render("#{dir}/#{ARGV[0]}")
-EOF
-
-exec "Rscript --jvm --polyglot -e '#{code}'"