galaaz 0.4.1 → 0.4.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 34f0d93c32e4c3f2deb6a15ff8d02ba684a28396
+  metadata.gz: 96f1e6bcd6650786b9e33356b100bec04177400c
+  data.tar.gz: e66eed26b93a6cb4eae16212027319a269af8ccb
 SHA512:
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+  metadata.gz: db82f43785fd763ff93d0f494d284536c3041fa0b68a69295192d3074b328fe6098b484e940d2c2de3a5eef2e63ef72b435b9442bf7685f527a565d0c1fcbe16
+  data.tar.gz: 63943f74c540a1dd96f48dbd874c20849f0a7fc92bb1f8eea643f8973c3920e19f061a11792f74c6054e8f3617ccb90409cbab6faf8a784f0ab9b4c49d6c4367

data/Rakefile

@@ -79,6 +79,7 @@ specs = FileList['specs/**/*.rb']
 master_list = FileList['examples/50Plots_MasterList/**/*.rb']
 islr = FileList['examples/islr/**/*.rb']
 misc = FileList['examples/misc/**/*.rb']
+blogs = Dir.entries("blogs")
 
 #===========================================================================================
 # Creates tasks for all specs.
@@ -147,6 +148,34 @@ end
 
 task :default => "sthda:all"
 
+#===========================================================================================
+# Creates task for running gknit
+#===========================================================================================
+
+blogs.each do |dir|
+  next if dir == '.' || dir == '..'
+  blog_rmd = "blogs/#{dir}/#{dir}.Rmd"
+  desc "run gknit to build #{dir} blog post"
+  task "blog:#{dir}" do
+    (sh %{ bin/gknit #{blog_rmd} })
+  end
+
+  desc "run gknit2 to build #{dir} blog post"
+  task "blog2:#{dir}" do
+    (sh %{ bin/gknit2 #{blog_rmd} })
+  end
+  
+end
+  
+#===========================================================================================
+# Loads R and require libraries to run Galaaz
+#===========================================================================================
+
+desc 'Prepare R for running'
+task :make_r do
+  (sh %{ gu install r })
+end
+
 
 =begin
 name = "#{$gem_name}-#{$version}.gem"

data/bin/gknit

@@ -1,26 +1,224 @@
 #!/usr/bin/env ruby
+# coding: utf-8
 
 dir = Dir.pwd
 puts "Knitting #{dir}/#{ARGV[0]}"
 
-req_gal = "require '../lib/galaaz'"
-
 code = <<EOF
-library('knitr');
-library('rmarkdown');
+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 galaaz engine for processing Ruby chunks in
+# define the ruby engine for processing Ruby chunks in
 # rmarkdown
-eng_galaaz = function(options) {
+eng_ruby = function(options) {
   block_code = paste(options$code, collapse = "\\n");
-  code = paste0("GalaazUtil.exec_ruby(", shQuote(block_code), ")");
+  code = paste0("GalaazUtil.exec_ruby(", 
+                   shQuote(block_code), 
+                  ")
+                ");
+
+  # png(paste0("gknit_files/figure-html/", options$label, ".png"));
+
+  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$dev)
+
+  # out = eval.polyglot("ruby", code);
+  res = eval.polyglot("ruby", code);
+
+# rearrange locations of figures
+#  figs = find_recordedplot(res)
+#  if (length(figs) && any(figs)) {
+#    if (keep == 'none') {
+#      res = res[!figs] # remove all
+#    } else {
+#      if (options$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, 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, block_code, out)
+  engine_output(options, include, out)
 }
 
-knit_engines$set(galaaz = eng_galaaz)
+knit_engines$set(include = eng_include)
 
-eval.polyglot("ruby", "require %q(galaaz)")
 
 rmarkdown::render("#{dir}/#{ARGV[0]}")
 EOF

data/bin/gknit2

@@ -0,0 +1,14 @@
+#!/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(gknit)")
+
+rmarkdown::render("#{dir}/#{ARGV[0]}")
+EOF
+
+exec "Rscript --jvm --polyglot -e '#{code}'"

data/bin/gknit2~

@@ -0,0 +1,6 @@
+#!/usr/bin/env ruby
+# coding: utf-8
+
+dir = Dir.pwd
+puts "Knitting #{dir}/#{ARGV[0]}"
+

data/bin/prepareR.rb

@@ -0,0 +1,3 @@
+# gu install r
+# configure r
+R.install_and_loads('knitr')

data/bin/prepareR.rb~

@@ -0,0 +1 @@
+R.install_and_loads('knitr')

data/bin/tmp.py

@@ -0,0 +1,51 @@
+  eval.polyglot("python", code);
+  code = paste0("out = sys.stdout.getvalue()",
+                "sys.stdout.close()",
+                "sys.stdout = backup",
+                "out"
+               )
+
+
+
+
+
+
+import sys
+from cStringIO import StringIO
+
+# setup the environment
+backup = sys.stdout
+
+# ####
+sys.stdout = StringIO()     # capture output
+write()
+out = sys.stdout.getvalue() # release output
+# ####
+
+sys.stdout.close()  # close the stream 
+sys.stdout = backup # restore original stdout
+
+print out.upper()   # post processing
+
+
+
+
+
+
+
+code = paste0("from contextlib import contextmanager",
+                "@contextmanager",
+                "def stdout_redirector(stream):",
+                "    old_stdout = sys.stdout",
+                "    sys.stdout = stream",
+                "    try:",
+                "       yield",
+                "    finally:",
+                "       sys.stdout = old_stdout",
+                "f = io.StringIO()",
+                "with stdout_redirector(f):",
+                "     exec(",
+                        shQuote(block_code), 
+                        ")",
+                "f.getvalue()"
+                ");

data/blogs/dev/dev.Rmd

@@ -0,0 +1,70 @@
+---
+title: "gKnit - Ruby and R Knitting with Galaaz in GraalVM"
+author: "Rodrigo Botafogo"
+tags: [Galaaz, Ruby, R, TruffleRuby, FastR, GraalVM, knitr]
+date: "19 October 2018"
+output:
+  html_document:
+    self_contained: true
+    keep_md: true
+  pdf_document:
+    includes:
+      in_header: ["../../sty/galaaz.sty"]
+    number_sections: yes
+---
+
+```{r setup, echo=FALSE}
+
+```
+
+# Introduction
+
+
+```{r bubble}
+# load package and data
+library(ggplot2)
+data(mpg, package="ggplot2")
+# mpg <- read.csv("http://goo.gl/uEeRGu")
+
+mpg_select <- mpg[mpg$manufacturer %in% c("audi", "ford", "honda", "hyundai"), ]
+
+# Scatterplot
+theme_set(theme_bw())  # pre-set the bw theme.
+g <- ggplot(mpg_select, aes(displ, cty)) + 
+  labs(subtitle="mpg: Displacement vs City Mileage",
+       title="Bubble chart")
+
+g + geom_jitter(aes(col=manufacturer, size=hwy)) + 
+  geom_smooth(aes(col=manufacturer), method="lm", se=F)
+```
+
+### Plotting
+
+```{ruby diverging_bar}
+require 'ggplot'
+
+R.theme_set R.theme_bw
+
+# Data Prep
+mtcars = ~:mtcars
+mtcars.car_name = R.rownames(:mtcars)
+# compute normalized mpg 
+mtcars.mpg_z = ((mtcars.mpg - mtcars.mpg.mean)/mtcars.mpg.sd).round 2
+mtcars.mpg_type = mtcars.mpg_z < 0 ? "below" : "above"
+mtcars = mtcars[mtcars.mpg_z.order, :all]
+# convert to factor to retain sorted order in plot
+mtcars.car_name = mtcars.car_name.factor levels: mtcars.car_name
+
+# Diverging Barcharts
+gg = mtcars.ggplot(E.aes(x: :car_name, y: :mpg_z, label: :mpg_z)) + 
+     R.geom_bar(E.aes(fill: :mpg_type), stat: 'identity',  width: 0.5) +
+     R.scale_fill_manual(name: "Mileage", 
+                         labels: R.c("Above Average", "Below Average"), 
+                         values: R.c("above": "#00ba38", "below": "#f8766d")) + 
+     R.labs(subtitle: "Normalised mileage from 'mtcars'", 
+            title: "Diverging Bars") + 
+     R.coord_flip()
+
+print gg
+```
+

data/blogs/dev/dev.Rmd~

@@ -0,0 +1,104 @@
+---
+title: "gKnit - Ruby and R Knitting with Galaaz in GraalVM"
+author: "Rodrigo Botafogo"
+tags: [Galaaz, Ruby, R, TruffleRuby, FastR, GraalVM, knitr]
+date: "19 October 2018"
+output:
+  html_document:
+    self_contained: true
+    keep_md: true
+  pdf_document:
+    includes:
+      in_header: ["../../sty/galaaz.sty"]
+    number_sections: yes
+---
+
+```{r setup, echo=FALSE}
+
+```
+
+# Introduction
+
+
+```{r bubble}
+# load package and data
+library(ggplot2)
+data(mpg, package="ggplot2")
+# mpg <- read.csv("http://goo.gl/uEeRGu")
+
+mpg_select <- mpg[mpg$manufacturer %in% c("audi", "ford", "honda", "hyundai"), ]
+
+# Scatterplot
+theme_set(theme_bw())  # pre-set the bw theme.
+g <- ggplot(mpg_select, aes(displ, cty)) + 
+  labs(subtitle="mpg: Displacement vs City Mileage",
+       title="Bubble chart")
+
+g + geom_jitter(aes(col=manufacturer, size=hwy)) + 
+  geom_smooth(aes(col=manufacturer), method="lm", se=F)
+```
+
+### Plotting
+
+```{ruby diverging_bar}
+require 'ggplot'
+
+R.theme_set R.theme_bw
+
+# Data Prep
+mtcars = ~:mtcars
+mtcars.car_name = R.rownames(:mtcars)
+# compute normalized mpg 
+mtcars.mpg_z = ((mtcars.mpg - mtcars.mpg.mean)/mtcars.mpg.sd).round 2
+mtcars.mpg_type = mtcars.mpg_z < 0 ? "below" : "above"
+mtcars = mtcars[mtcars.mpg_z.order, :all]
+# convert to factor to retain sorted order in plot
+mtcars.car_name = mtcars.car_name.factor levels: mtcars.car_name
+
+# Diverging Barcharts
+gg = mtcars.ggplot(E.aes(x: :car_name, y: :mpg_z, label: :mpg_z)) + 
+     R.geom_bar(E.aes(fill: :mpg_type), stat: 'identity',  width: 0.5) +
+     R.scale_fill_manual(name: "Mileage", 
+                         labels: R.c("Above Average", "Below Average"), 
+                         values: R.c("above": "#00ba38", "below": "#f8766d")) + 
+     R.labs(subtitle: "Normalised mileage from 'mtcars'", 
+            title: "Diverging Bars") + 
+     R.coord_flip()
+
+print gg
+```
+
+### Plotting with keep value
+
+```{ruby diverging_bar2, fig.keep = 1, fig.showtext = TRUE}
+require 'ggplot'
+
+R.theme_set R.theme_bw
+
+# Data Prep
+mtcars = ~:mtcars
+mtcars.car_name = R.rownames(:mtcars)
+# compute normalized mpg 
+mtcars.mpg_z = ((mtcars.mpg - mtcars.mpg.mean)/mtcars.mpg.sd).round 2
+mtcars.mpg_type = mtcars.mpg_z < 0 ? "below" : "above"
+mtcars = mtcars[mtcars.mpg_z.order, :all]
+# convert to factor to retain sorted order in plot
+mtcars.car_name = mtcars.car_name.factor levels: mtcars.car_name
+
+# Diverging Barcharts
+# R.png
+gg = mtcars.ggplot(E.aes(x: :car_name, y: :mpg_z, label: :mpg_z)) + 
+     R.geom_bar(E.aes(fill: :mpg_type), stat: 'identity',  width: 0.5) +
+     R.scale_fill_manual(name: "Mileage", 
+                         labels: R.c("Above Average", "Below Average"), 
+                         values: R.c("above": "#00ba38", "below": "#f8766d")) + 
+     R.labs(subtitle: "Normalised mileage from 'mtcars'", 
+            title: "Diverging Bars") + 
+     R.coord_flip()
+
+# print gg
+
+
+# R.dev__off
+# R.include_graphics("Rplot001.png")
+```