galaaz 0.4.1 → 0.4.2

data/lib/{R/rclosure.rb → R_interface/rdevices.rb~}

@@ -21,14 +21,7 @@
 # OR MODIFICATIONS.
 ##########################################################################################
 
-module R
+dir = File.dirname(File.expand_path('.', __FILE__))
+src = "#{dir}/capture_plot.R"
 
-  class Closure < Object
-
-    def call(*args)
-      R::Support.exec_function(@r_interop, *args)
-    end
-    
-  end
-
-end
+R.source(src)

data/lib/{R → R_interface}/robject.rb

@@ -283,7 +283,12 @@ module R
     #--------------------------------------------------------------------------------------
 
     def to_s
+
+      cap = nil
+      # dev = R::Device.new('png', width: 5, height: 7, dpi: 300, record: true) {
       cap = R::Support.capture.call(r_interop)
+      # cap = R::Support.capture_output.call(r_interop)
+      # }
       str = String.new
       (0...(cap.size - 1)).each do |i|
         str << cap[i] << "\n"

data/lib/{R → R_interface}/rsupport.rb

@@ -57,11 +57,14 @@ module R
 
   module Support
 
+    @@exec_counter = 0
+    
     # Using this method gives us more control over what happens when calling do.call
     # and allows for debugging.  Use it in exec_function when debugging is needed.
     @@exec_from_ruby = Polyglot.eval("R", <<-R)
       function(build_method, ...) {
         # print(build_method);
+        # print("exec_from_ruby")
         # args = list(...);
         # print(args);
         res = do.call(...);
@@ -102,6 +105,7 @@ module R
       when Truffle::Interop
         arg
       when R::Object
+        # return (Truffle::Interop.null?(arg.r_interop)) ? nil : arg.r_interop
         arg.r_interop
       when NegRange
         final_value = (arg.exclude_end?)? (arg.last - 1) : arg.last
@@ -127,14 +131,14 @@ module R
     #----------------------------------------------------------------------------------------
     
     def self.parse2list(*args)
-      
+
       params = Polyglot.eval("R", "list()")
       
       args.each_with_index do |arg, i|
         if (arg.is_a? Hash)
           arg.each_pair do |key, value|
             k = key.to_s.gsub(/__/,".")
-            # HAS CHANGED IN RC6... FIX THIS TO THE NEW API
+            # HAS CHANGED IN RC6... FIXME: THIS TO THE NEW API
             # When evaluating to NA, Interop treats it as FALSE.  This breaks
             # all expectations about NA.  We need to protect NA from Interop
             # unboxing.  Class NotAvailable
@@ -157,7 +161,10 @@ module R
         end
       end
 
-      params
+      # if the parameter is an empty list, then add the element NULL to the list
+      (Polyglot.eval("R", "length").call(params) == 0) ?
+        Polyglot.eval("R", "list").call(nil) : params
+      # params
       
     end
     
@@ -194,25 +201,54 @@ module R
     #----------------------------------------------------------------------------------------
     
     def self.exec_function(function, *args)
+
+      # If the execution counter is 0, function was not recursively called
+      # Starts capturing output
+      if (@@exec_counter == 0)
+        R::Support.eval("unlockBinding('r_capture', globalenv())")
+        @@con = R::Support.start_capture.call("r_capture")
+      end
+
+      @@exec_counter = @@exec_counter + 1
+      
       # function has no arguments, call it directly
       if (args.length == 0)
-        return R::Object.build(function.call) # if args.length == 0
+        res = R::Object.build(function.call)
+      else
+        pl = R::Support.parse2list(*args)
+        res = @@exec_from_ruby.call(R::Object.method(:build), function, pl)
+        # R::Object.build(R::Support.eval("do.call").call(function, pl))
       end
 
-      pl = R::Support.parse2list(*args)
-      @@exec_from_ruby.call(R::Object.method(:build), function, pl)
-      # R::Object.build(R::Support.eval("do.call").call(function, pl))
+      @@exec_counter = @@exec_counter - 1
+
+      # When execution counter back to 0, print the captured output if the lenght
+      # of the output is greater than 0
+      if (@@exec_counter == 0)
+        R::Support.stop_capture.call(@@con)
+        
+        if (R::Support.eval("length(r_capture) > 0")[0])
+          cap = R::Object.build(R::Support.eval("r_capture"))
+          # puts ~:r_capture if (R::Support.eval("length(r_capture) > 0")[0])
+          (0...cap.size).each do |i|
+            puts cap << i
+          end
+        end
+        
+      end
+
+      res
     end
     
     #----------------------------------------------------------------------------------------
     # @param function_name [String] Name of the R function to execute
-    # @param internal [Boolean] true if returning to an internal object, i.e., does not
-    # wrap the return object in a Ruby object
     # @args [Array] Array of arguments for the function
     #----------------------------------------------------------------------------------------
     
     def self.exec_function_name(function_name, *args)
-      R::Support.exec_function(R::Support.eval(function_name), *args)
+      # TODO: should check the function name before calling eval
+      f = R::Support.eval(function_name)
+      R::Support.exec_function(f, *args)
     end
 
     #----------------------------------------------------------------------------------------
@@ -253,10 +289,10 @@ module R
       name = R::Support.convert_symbol2r(symbol)
       
       case name
-      # missing method has an '=' sign in it...
+      # when missing method has an '=' sign in it...
       when ->(x) { x =~ /(.*)=$/ }
         R::Support.set_symbol($1, *args)
-      # missing method is 'eval'... needs special treatment
+      # when missing method is 'eval'... needs special treatment
       when "eval"
         R::Support.r_evaluate(*args)
       else
@@ -264,7 +300,7 @@ module R
         internal ? R::Support.exec_function_i(function, *args) :
           R::Support.exec_function(function, *args)
       end
-      
+
     end
     
     #----------------------------------------------------------------------------------------

data/lib/{R → R_interface}/rsymbol.rb

@@ -36,6 +36,7 @@ module R
     #--------------------------------------------------------------------------------------
     
     def =~(other_object)
+      # puts "doing #{self} =~ #{other_object}"
       exec_oper("`~`", other_object, true)
     end
 

data/lib/{R → R_interface}/ruby_extensions.rb

@@ -60,7 +60,8 @@ class Symbol
   #--------------------------------------------------------------------------------------
 
   def +@
-    R::Object.build(R::Support.eval("as.name").call(to_s))
+    var = (self == :all)? '.' : to_s
+    R::Object.build(R::Support.eval("as.name").call(var))
   end
 
   #--------------------------------------------------------------------------------------

data/lib/galaaz.rb

@@ -21,8 +21,10 @@
 # OR MODIFICATIONS.
 ##########################################################################################
 
-require_relative 'R/r'
-require_relative 'util/exec_ruby'
+require 'pry'
 
 $LOAD_PATH << File.dirname(File.expand_path('..', __FILE__)) + "/r_requires"
 
+require_relative 'R_interface/r'
+require_relative 'util/exec_ruby'
+require_relative 'util/inline_file'

data/lib/gknit.rb

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+
+require_relative 'gknit/knitr_engine'
+require_relative 'gknit/ruby_engine'

data/lib/gknit.rb~

@@ -0,0 +1,26 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+
+puts "gknit loaded"

data/lib/gknit/knitr_engine.rb

@@ -0,0 +1,120 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+R.install_and_loads('knitr', 'rmarkdown')
+
+# dir = File.dirname(File.expand_path('.', __FILE__))
+# src = "#{dir}/R/eng_ruby.R"
+
+class KnitrEngine
+
+  attr_reader :options
+  attr_reader :keep
+
+  #--------------------------------------------------------------------------------------
+  # opens a device for plot recording.  Method chunk_device in knitr is not exported,
+  # so it cannot yet be accessed by Galaaz.  Need to develop a local function that calls
+  # the non-exported function.
+  #--------------------------------------------------------------------------------------
+
+  R::Support.eval(<<-R)
+    _ck_dv = function(width, height, record = TRUE, dev, dev.args, dpi, options, 
+                      tmp = tempfile()) {
+        knitr:::chunk_device(width, height, record, dev, dev.args, dpi, options, tmp)
+      }
+    R
+
+  #--------------------------------------------------------------------------------------
+  # The showtext package, is able to support more font formats and more graphics
+  # devices, and avoids using external software such as Ghostscript. showtext makes it
+  # even easier to use various types of fonts (TrueType, OpenType, Type 1, web fonts,
+  # etc.) in R graphs.
+  #--------------------------------------------------------------------------------------
+
+  R::Support.eval(<<-R)
+    showtext = function() {
+      showtext::showtext_begin()
+    }
+  R
+    
+  #--------------------------------------------------------------------------------------
+  # Process the fig.keep chunk option
+  # @param keep [String/Numeric] a string or a number.  If it is a string then it should
+  #   be one of the following: 
+  #   * high: only keep high-level plots (merge low-level changes into high-level plots);
+  #   * none: discard all plots;
+  #   *  all: keep all plots (low-level plot changes may produce new plots)
+  #   * first: only keep the first plot
+  #   * last: only keep the last plot
+  #   if set to a numeric vector: interpret value as index of (low-level) plots to keep
+  #   In this case, set variable @keep to "index" and variable @keep_ind as the numeric
+  #   index.
+  #--------------------------------------------------------------------------------------
+
+  def self.fig_keep
+    @keep = @options.fig__keep
+    @keep_idx = nil
+
+    if (@keep.is__numeric << 0)
+      @keep_idx = @keep
+      @keep = "index"
+    end
+
+  end
+
+  #--------------------------------------------------------------------------------------
+  # 
+  #--------------------------------------------------------------------------------------
+
+  def self.file_ext
+    # guess plot file type if it is NULL
+    if (@keep != 'none' && @options.fig__ext.is__null)
+      @options.fig__ext = R.dev2ext(@options.dev)
+    end
+  end
+    
+  #--------------------------------------------------------------------------------------
+  # Process the chunk options
+  #--------------------------------------------------------------------------------------
+  
+  def self.process_options(options)
+    @options = options
+    
+    # verifies if figures should be kept
+    fig_keep
+    
+    # if figures are to be kept, take or guess the file extension
+    # file_ext
+  end
+
+  #--------------------------------------------------------------------------------------
+  # Adds the new knitr engine to the list of engines
+  # @param spec [Hash] hash with only one pair containing the machine key and the engine
+  #    function
+  #--------------------------------------------------------------------------------------
+  
+  def add(spec)
+    (~:knit_engines).set.call(spec)
+  end
+  
+end

data/lib/gknit/knitr_engine.rb~

@@ -0,0 +1,102 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+R.install_and_loads('knitr', 'rmarkdown')
+
+# dir = File.dirname(File.expand_path('.', __FILE__))
+# src = "#{dir}/R/eng_ruby.R"
+
+class KnitrEngine
+
+  attr_reader :keep
+
+  #--------------------------------------------------------------------------------------
+  # opens a device for plot recording.  Method chunk_device in knitr is not exported,
+  # so it cannot yet be accessed by Galaaz.  Need to develop a local function that calls
+  # the non-exported function.
+  #--------------------------------------------------------------------------------------
+
+  R::Support.eval(<<-R)
+    _ck_dv = function(width, height, record = TRUE, dev, dev.args, dpi, options, 
+                      tmp = tempfile()) {
+        knitr:::chunk_device(width, height, record, dev, dev.args, dpi, options, tmp)
+      }
+    R
+
+  #--------------------------------------------------------------------------------------
+  # The showtext package, is able to support more font formats and more graphics
+  # devices, and avoids using external software such as Ghostscript. showtext makes it
+  # even easier to use various types of fonts (TrueType, OpenType, Type 1, web fonts,
+  # etc.) in R graphs.
+  #--------------------------------------------------------------------------------------
+
+  R::Support.eval(<<-R)
+    showtext = function() {
+      print("showtext beginning")
+      showtext::showtext_begin()
+    }
+  R
+    
+  #--------------------------------------------------------------------------------------
+  # Process the fig.keep chunk option
+  # @bug this does not what it should
+  #--------------------------------------------------------------------------------------
+
+  def self.fig_keep(keep)
+    puts "checking fig_keep options"
+    
+    @keep = keep
+    puts @keep
+    
+    @keep.idx = nil
+    
+    if (@keep.is__numeric << 0)
+      puts "keep is numeric"
+      
+      @keep.idx = keep
+      @keep = "index"
+    end
+
+    puts @keep
+    
+  end
+
+  #--------------------------------------------------------------------------------------
+  # Process the chunk options
+  #--------------------------------------------------------------------------------------
+  
+  def self.process_options(options)
+    fig_keep(options.fig__keep)
+  end
+
+  #--------------------------------------------------------------------------------------
+  # Adds the new knitr engine to the list of engines
+  # @param spec [Hash] hash with only one pair containing the machine key and the engine
+  #    function
+  #--------------------------------------------------------------------------------------
+  
+  def add(spec)
+    (~:knit_engines).set.call(spec)
+  end
+  
+end