galaaz 0.4.6 → 0.5.0

data/lib/gknit/knitr_engine.rb

@@ -572,8 +572,8 @@ class KnitrEngine
     plot = R.evaluate_plot_snapshot
 
     if (!(plot.is__null >> 0))
-      
       # create directory for the graphics files if does not already exists
+      # unless (R.dir__exists(@fig__path) >> 0)
       unless File.directory?(@fig__path)
         FileUtils.mkdir_p(@fig__path)
       end
@@ -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.
@@ -685,36 +687,3 @@ class KnitrEngine
   end
   
 end
-
-=begin
-module R
-
-  class Object
-
-    #--------------------------------------------------------------------------------------
-    # Redefine to_s in order to capture plots when in knitr
-    #--------------------------------------------------------------------------------------
-    
-    def to_s
-
-      STDERR.puts "+++++++++++++++++++++++++++"
-      STDERR.puts "in to_s"
-      STDERR.puts "+++++++++++++++++++++++++++"
-      
-      cap = nil
-      cap = R::Support.capture.call(r_interop)
-      str = String.new
-      (0...(cap.size - 1)).each do |i|
-        str << cap[i] << "\n"
-      end
-      str << cap[cap.size - 1] if cap.size >= 1
-      re = RubyEngine.instance
-      re.capture_plot
-      str
-    end
-
-  end
-  
-end
-
-=end

data/lib/util/exec_ruby.rb

@@ -24,72 +24,35 @@
 require 'stringio'
 
 #----------------------------------------------------------------------------------------
-# 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)
-
-    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
-
-    nil
-  end
-
-end
+class RC
 
+  attr_reader :out_list
 
-#----------------------------------------------------------------------------------------
-# 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 initialize
+    @out_list = R.list
+  end
 
-  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
+
 #----------------------------------------------------------------------------------------
 #
 #----------------------------------------------------------------------------------------
@@ -114,11 +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
@@ -135,7 +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)
+      # RChunk.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
@@ -173,30 +137,4 @@ module GalaazUtil
     
   end
   
-  #----------------------------------------------------------------------------------------
-  # Used by old gknit.  Will eventually be replaced by exe_ruby
-  #----------------------------------------------------------------------------------------
-
-  def self.exec_ruby_tor(code)
-
-    # the output should be a list with the proper structure to pass to
-    # function engine_output.
-    out_list = R.list(R.structure(R.list(src: code), class: 'source'))
-    
-    # Set up standard output as a StringIO object.
-    $stdout = StringIO.new
-    RubyChunk.instance_eval(code)
-
-    # this should have captured everything in the evaluation code
-    # it is not working since at least RC10.
-    out = $stdout.string
-
-    out_list = R.c(out_list, out)
-    
-    # return $stdout to standard output
-    $stdout = STDOUT
-    R::Support.parse_arg(out_list)
-
-  end
-  
 end

data/lib/util/inline_file.rb

@@ -49,12 +49,16 @@ module GalaazUtil
 
         if files != nil
           file = "#{path}/#{filename}"
-          break if File.exist?(file)
+          # break if File.exist?(file)
+          break if (R.file__exists(file) >> 0)
         end
       end
     end
-    
-    if File.exist?(file)
+
+    # There is a bug(?) in > RC15 that when the bellow command
+    # is called, there is a call to R Polyglot eval passing to_i 
+    # if File.exist?(file)
+    if (R.file__exists(file) >> 0)
       code = ""
       File.open(file, "r") do |fileObj|
         while (line = fileObj.gets)

data/specs/figures/bg.svg

@@ -3,7 +3,7 @@
 <svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' version='1.1' viewBox='0 0 506 506' style='fill:transparent'>
 <g style='stroke-width:1.4226377952755906;stroke-linejoin:round;stroke-linecap:round'>
 <rect x='0' y='0' width='506' height='506' style='stroke:#FFFFFF;fill:#FFFFFF'/>
-<rect x='31' y='6' width='469' height='473' style='stroke:rgb(0,0,0);stroke-opacity:0.000;fill:#EBEBEB'/>
+<rect x='31' y='6' width='469' height='473' style='stroke:rgb(0,0,0);stroke-opacity:0,000;fill:#EBEBEB'/>
 </g><g style='stroke-width:0.7113188976377953;stroke-linejoin:round;stroke-linecap:butt'>
 <polyline points='31,446 500,446' style='stroke:#FFFFFF'/>
 <polyline points='31,301 500,301' style='stroke:#FFFFFF'/>
@@ -54,4 +54,4 @@
 <text x='410' y='490' lengthAdjust='spacingAndGlyphs' textLength='5px' style='font-size:8.8px;fill:#4D4D4D'>2</text>
 <text x='253' y='500' lengthAdjust='spacingAndGlyphs' textLength='26px' style='font-size:11.0px;fill:#000000'>dose</text>
 <text x='13' y='252' lengthAdjust='spacingAndGlyphs' textLength='20px' style='font-size:11.0px;fill:#000000' transform='rotate(-90,13,252)'>len</text>
-</svg>
+</svg>

data/specs/figures/no_args.svg

@@ -3,7 +3,7 @@
 <svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' version='1.1' viewBox='0 0 506 506' style='fill:transparent'>
 <g style='stroke-width:1.4226377952755906;stroke-linejoin:round;stroke-linecap:round'>
 <rect x='0' y='0' width='506' height='506' style='stroke:#FFFFFF;fill:#FFFFFF'/>
-<rect x='31' y='6' width='469' height='473' style='stroke:rgb(0,0,0);stroke-opacity:0.000;fill:#EBEBEB'/>
+<rect x='31' y='6' width='469' height='473' style='stroke:rgb(0,0,0);stroke-opacity:0,000;fill:#EBEBEB'/>
 </g><g style='stroke-width:0.7113188976377953;stroke-linejoin:round;stroke-linecap:butt'>
 <polyline points='31,446 500,446' style='stroke:#FFFFFF'/>
 <polyline points='31,301 500,301' style='stroke:#FFFFFF'/>
@@ -54,4 +54,4 @@
 <text x='410' y='490' lengthAdjust='spacingAndGlyphs' textLength='5px' style='font-size:8.8px;fill:#4D4D4D'>2</text>
 <text x='253' y='500' lengthAdjust='spacingAndGlyphs' textLength='26px' style='font-size:11.0px;fill:#000000'>dose</text>
 <text x='13' y='252' lengthAdjust='spacingAndGlyphs' textLength='20px' style='font-size:11.0px;fill:#000000' transform='rotate(-90,13,252)'>len</text>
-</svg>
+</svg>

data/specs/r_dataframe.spec.rb

@@ -72,6 +72,179 @@ describe R::DataFrame do
     end
 
   end
+
+  #----------------------------------------------------------------------------------------
+  context "Subsetting with '['" do
+
+    before(:each) do
+      @mtcars = ~:mtcars
+    end
+
+    it "should subset with [ with only the column index" do
+      slice = @mtcars[1]
+      expect(slice.typeof).to eq "list"
+      expect(slice.rclass).to eq "data.frame"
+      expect(slice.length).to eq 1
+      expect(slice[[1]][1]).to eq 21.0
+      expect(slice[[1, 1]]).to eq 21.0
+      # undefined columns selected (RError)
+      expect { slice['Mazda RX4'] }.to raise_error(RuntimeError)
+      expect(slice[['Mazda RX4']]).to eq nil
+    end
+    
+    it "should subset with [ with a column range" do
+      slice = @mtcars[(1..3)]
+      expect(slice.typeof).to eq "list"
+      expect(slice.rclass).to eq "data.frame"
+      expect(slice.length).to eq 3
+      expect(slice[[2]][10]).to eq 6.0
+      expect(slice[10, 2]).to eq 6.0
+    end
+
+    it "should subset with [ by row and column indices" do
+      expect(@mtcars[1, 1]).to eq 21.0
+      expect(@mtcars[6, 5]).to eq 2.76
+    end
+
+    it "do not use R style missing value idexing with [" do
+      # This array bellow is equivalent to [6]. This can bring some surprises for
+      # R people that are used to this indexing notation, as in this case the ','
+      # is ignored
+      arr = [6, ]
+      expect(arr).to eq [6]
+      
+      # This will output the sixth column of the mtcars dataframe
+      slice = @mtcars[6, ]
+      expect(slice.typeof).to eq "list"
+      expect(slice.rclass).to eq "data.frame"
+      expect(slice.length).to eq 1
+      expect(slice[[1]][1]).to eq 2.62
+    end
+
+    it "should subset with [ by row index and :all" do
+      # Hornet Sportabout 18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2      
+      slice = @mtcars[5, :all]
+      expect(slice.rclass).to eq "data.frame"
+      expect(slice[1, 1]).to eq 18.7
+      expect(slice[1, 1]).not_to eq 360.0
+      expect(slice.names).to eq R.c("mpg", "cyl", "disp", "hp", "drat",
+                                    "wt", "qsec", "vs", "am", "gear", "carb")
+    end
+
+    it "should subset with [ by row index, :all and allowing for drop parameter" do
+      # will transform the data into a list
+      lst = @mtcars[1, :all, drop: true]
+      expect(lst.typeof).to eq "list"
+      expect(lst[[1]]).to eq 21.0
+      expect(lst[1]).to eq R.list(mpg: 21.0)
+    end
+
+    it "should subset with [ by :all and column index" do
+      # [1] 110 110  93 110 175 105 245  62  95 123 123 180 180 180 205 215 230  66  52
+      # [20]  65  97 150 150 245 175  66  91 113 264 175 335 109
+      slice = @mtcars[:all, 4]
+      expect(slice.rclass).to eq "numeric"
+      expect(slice.typeof).to eq "double"
+      expect(slice[10]).to eq 123.0
+    end
+
+    it "should subset with [ by :all, column index and allowing for 'drop' parameter" do
+      expect(@mtcars[:all, 1]).to eq @mtcars[:all, 1, drop: true]
+    end
+
+    it "should subset with [ and column name" do
+      slice = @mtcars['drat']
+      expect(slice.typeof).to eq "list"
+      expect(slice.rclass).to eq "data.frame"
+      expect(slice.length).to eq 1
+      expect(slice[[1]][1]).to eq 3.90
+      expect(slice[[1, 1]]).to eq 3.90
+      # undefined columns selected (RError)
+      expect { slice['Mazda RX4'] }.to raise_error(RuntimeError)
+      expect(slice[['Mazda RX4']]).to eq nil
+    end
+
+    it "should subset with [ and row name" do
+      slice = @mtcars['Merc 450SE', :all]
+      expect(slice[[1]]).to eq 16.4
+      expect(slice[['hp']]).to eq 180.0
+    end
+
+    it "should subset with [ and row and column name" do
+      slice = @mtcars['Merc 450SL', 'drat']
+      expect(slice).to eq 3.07
+    end
+    
+  end
+  
+  #----------------------------------------------------------------------------------------
+  context "Subsetting with '[['" do
+
+    before(:each) do
+      @mtcars = ~:mtcars
+    end
+
+    it "should subset with [[ and a column index" do
+      slice = @mtcars[[1]]
+      expect(slice.typeof).to eq "double"
+      expect(slice.rclass).to eq "numeric"
+      expect(slice[1]).to eq 21.0
+      expect(slice[16]).to eq 10.4
+    end
+
+    it "should subset with [[ and a row index" do
+      slice = @mtcars
+    end
+
+    it "should subset with [[ and row and column indices" do
+      expect(@mtcars[[6, 1]]).to eq 18.1
+      expect(@mtcars[[6, 5]]).to eq 2.76
+      expect(@mtcars[[15, 1]]).to eq 10.4
+      expect(@mtcars[[15, 7]]).to eq 17.98
+    end
+
+    it "should subset with [[ and row and column names" do
+      expect(@mtcars[['Valiant', 'mpg']]).to eq 18.1
+      expect(@mtcars[['Valiant', 'drat']]).to eq 2.76
+      expect(@mtcars[['Cadillac Fleetwood', 'mpg']]).to eq 10.4
+      expect(@mtcars[['Cadillac Fleetwood', 'qsec']]).to eq 17.98
+    end
+
+  end
+  
+  #----------------------------------------------------------------------------------------
+  context "Assigning with '[<-'" do
+
+    before(:each) do
+      @mtcars = ~:mtcars
+    end
+
+    it "should add a column to a dataframe indexing by column" do
+      @mtcars["New Column"] = R.c((1..32))
+      expect(@mtcars[[1, 12]]).to eq 1
+      expect(@mtcars[['Mazda RX4', 'New Column']]).to eq 1
+    end
+
+    it "should add a column to a dataframe indexing with :all in the row" do
+      @mtcars[:all, 'New Column'] = R.c((1..32))
+      expect(@mtcars[[1, 12]]).to eq 1
+      expect(@mtcars[['Mazda RX4', 'New Column']]).to eq 1
+    end
+    
+    it "should assign to an element of a dataframe indexing with row and column by number" do
+      @mtcars[17, 6] = 1000
+      expect(@mtcars[[17, 6]]).to eq 1000.0
+      expect(@mtcars[['Chrysler Imperial', 'wt']]).to eq 1000.0
+    end
+
+    it "should assign to a range" do
+      @mtcars[(10..12)] = R.list((1..32), nil, "New Col": R.c(32..1))
+      expect(@mtcars[['Fiat 128', 'gear']]).to eq 18
+      expect(@mtcars[['Chrysler Imperial', 'New Col']]).to eq 16
+    end
+
+  end
+  
   #----------------------------------------------------------------------------------------
   context "Ruby 'each'" do
     
@@ -148,7 +321,7 @@ describe R::DataFrame do
   end
 
   #----------------------------------------------------------------------------------------
-  context "Boostraping" do
+  context "Bootsraping" do
     
     before(:each) do
       @df = R.data__frame(x: R.rep((1..3), each: 2), y: (6..1), z: (~:letters)[(1..6)])
@@ -158,8 +331,8 @@ describe R::DataFrame do
     it "should do reordering with integer subsetting" do
       
       table = @df[R.sample(@df.nrow), :all]
-      expect(table.x[3]).to eq 3
-      expect(table.y[2]).to eq 5
+      expect(table.x[3]).to eq 1
+      expect(table.y[2]).to eq 6
       expect(table.z.levels[6]).to eq "f"
       
     end
@@ -167,17 +340,17 @@ describe R::DataFrame do
     it "should select random rows with integer subsetting" do
       table = @df[R.sample(@df.nrow, 3), :all]
       
-      expect(table.x[3]).to eq 3
-      expect(table.y[1]).to eq 3
-      expect(table.z.levels[table.z[2]]).to eq "b"
+      expect(table.x[3]).to eq 1
+      expect(table.y[1]).to eq 4
+      expect(table.z.levels[table.z[2]]).to eq "a"
     end
     
     it "should randomly reorder a dataframe" do
       df2 = @df[R.sample(@df.nrow), (3..1)]
       
-      expect(df2.z.levels[df2.z[4]]).to eq "c"
-      expect(df2.y[2]).to eq 5
-      expect(df2.x[5]).to eq 1
+      expect(df2.z.levels[df2.z[4]]).to eq "f"
+      expect(df2.y[2]).to eq 6
+      expect(df2.x[5]).to eq 2
     end
     
     it "should reorder by a given variable" do
@@ -185,8 +358,8 @@ describe R::DataFrame do
       df2 = df2[df2.x.order, :all]
       
       expect(df2.x[1]).to eq 1
-      expect(df2.y[1]).to eq 5
-      expect(df2.z.levels[df2.z[1]]).to eq "b"
+      expect(df2.y[1]).to eq 6
+      expect(df2.z.levels[df2.z[1]]).to eq "a"
     end
     
     it "should reorder variables" do