galaaz 2.0.0 → 2.1.0

data/blogs/test/test.md

@@ -0,0 +1,10 @@
+Minimal gknit callback test
+================
+
+``` ruby
+# Minimal ruby chunk: triggers process_options and options['fig.ext'].unboxed_get(0).
+# Same R code path as oh_my.Rmd first ruby chunk (sends .GlobalEnv$g2_vN <- g2_vM[[1]] for fig.ext).
+puts "ok"
+```
+
+    ## ok

data/examples/50Plots_MasterList/ScatterPlot.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 module CorpTheme
@@ -156,4 +157,4 @@ sp.add_smoothing_line(method: "glm")
 sp.plot
 
 
-a = gets.chomp
+a = gets.chomp if $stdin.tty?

data/examples/50Plots_MasterList/scatter_plot.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 # load package and data

data/examples/bioconductor_deseq2_airway/bench_galaaz_three_same_process.rb

@@ -9,6 +9,7 @@
 
 require 'galaaz'
 
+using Galaaz::SymbolDSL
 root = File.expand_path('../..', __dir__)
 Dir.chdir(root)
 

data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz.rb

@@ -1,5 +1,6 @@
 require 'galaaz'
 
+using Galaaz::SymbolDSL
 R.library('DESeq2')
 R.library('airway')
 R.data('airway')

data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz_optimized.rb

@@ -1,5 +1,6 @@
 require 'galaaz'
 
+using Galaaz::SymbolDSL
 R.library('DESeq2')
 R.library('airway')
 R.data('airway')

data/examples/islr/all.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 # load ISLR and MASS Libraries

data/examples/islr/ch2.spec.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 context "ISLR" do

data/examples/islr/ch3.spec.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 context "ISLR" do

data/examples/islr/ch3_boston.rb

@@ -21,6 +21,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.install_and_loads('ISLR', 'MASS')

data/examples/islr/ch3_multiple_regression.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.install_and_loads('ISLR', 'MASS')

data/examples/islr/ch6.spec.rb

@@ -23,6 +23,7 @@
 
 require 'galaaz'
 
+using Galaaz::SymbolDSL
 R.install_and_loads('ISLR', 'MASS')
 
 context "ISLR" do

data/examples/misc/ggplot.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 module LightBlueTheme
@@ -154,7 +155,7 @@ R.grid__newpage
  R.geom_point('')).print
 =end
 
-a = gets.chomp
+a = gets.chomp if $stdin.tty?
 
 
 =begin

data/examples/misc/moneyball.rb

@@ -2,6 +2,7 @@
 
 require 'galaaz'
 
+using Galaaz::SymbolDSL
 local_dir = File.expand_path File.dirname(__FILE__)
 
 # This dataset comes from Baseball-Reference.com.

data/examples/misc/subsetting.rb

@@ -2,6 +2,7 @@
 
 require 'galaaz'
 
+using Galaaz::SymbolDSL
 # This examples were extracted from "Advanced R", by Hadley Wickham, available on the
 # web at: http://adv-r.had.co.nz/Subsetting.html#applications
 

data/examples/multithread_shards_to_r/shards_to_r.rb

@@ -16,6 +16,7 @@
 
 require 'galaaz'
 
+using Galaaz::SymbolDSL
 SHARD_COUNT = 3
 ROWS_PER_SHARD = 200
 

data/examples/sthda_ggplot/all.rb

@@ -21,6 +21,7 @@
 
 require 'galaaz'
 
+using Galaaz::SymbolDSL
 # Package Hmisc does not yet install on graalvm because of
 # problems with package data.table
 # install.packages('Hmisc')

data/examples/sthda_ggplot/one_variable_continuous/density_gg.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/one_variable_continuous/geom_area.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/one_variable_continuous/geom_density.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/one_variable_continuous/geom_dotplot.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/one_variable_continuous/geom_freqpoly.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/one_variable_continuous/geom_histogram.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/one_variable_continuous/histogram_density.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/one_variable_continuous/stat.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/one_variable_discrete/bar.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 # puts ~:mpg

data/examples/sthda_ggplot/qplots/box_violin_dot.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.set__seed(1234)

data/examples/sthda_ggplot/qplots/scatter_plots.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 # Load the data

data/examples/sthda_ggplot/scatter_gg.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.awt

data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_bin2d.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 diamonds = ~:diamonds

data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_density2d.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 faithful = ~:faithful

data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_hex.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.install_and_loads('hexbin')

data/examples/sthda_ggplot/two_variables_cont_cont/geom_point.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 mtcars = ~:mtcars

data/examples/sthda_ggplot/two_variables_cont_cont/geom_smooth.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 mtcars = ~:mtcars

data/examples/sthda_ggplot/two_variables_cont_cont/misc.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.install_and_loads('quantreg')

data/examples/sthda_ggplot/two_variables_cont_function/geom_area.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 economics = ~:economics

data/examples/sthda_ggplot/two_variables_disc_cont/geom_bar.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 df = R.data__frame(dose: R.c("D0.5", "D1", "D2"),

data/examples/sthda_ggplot/two_variables_disc_cont/geom_boxplot.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 tooth_growth = ~:ToothGrowth

data/examples/sthda_ggplot/two_variables_disc_cont/geom_dotplot.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.install_and_loads('Hmisc')

data/examples/sthda_ggplot/two_variables_disc_cont/geom_jitter.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 R.install_and_loads('Hmisc')
 

data/examples/sthda_ggplot/two_variables_disc_cont/geom_line.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 df = R.data__frame(supp: R.rep(R.c("VC", "OJ"), each: 3),

data/examples/sthda_ggplot/two_variables_disc_cont/geom_violin.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 R.install_and_loads('Hmisc')
 

data/examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 diamonds = ~:diamonds

data/examples/sthda_ggplot/two_variables_error/geom_crossbar.rb

@@ -22,6 +22,7 @@
 ##########################################################################################
 
 require 'galaaz'
+using Galaaz::SymbolDSL
 require 'ggplot'
 
 R.install_and_loads('Hmisc')

data/lib/R_interface/rvector.rb

@@ -177,6 +177,21 @@ module R
       end
     end
 
+    # CRuby Enumerable#sum probes begin/end (range fast-path). R::Object#respond_to?
+    # always returns true, so that probe would hit method_missing and call R's begin.
+    # Implement sum in Ruby so MRI matches JRuby Enumerable behavior for blocks;
+    # without a block, forward to R's sum via method_missing.
+    def sum(*args, &block)
+      if block
+        ::Kernel.raise(::ArgumentError, "wrong number of arguments (given #{args.size}, expected 0..1)") if args.size > 1
+        acc = args.empty? ? 0 : args[0]
+        each { |el| acc = acc + block.call(el) }
+        acc
+      else
+        method_missing(:sum, *args)
+      end
+    end
+
     #--------------------------------------------------------------------------------------
     # Need to override each_with_index, as R indexing starts at 1
     #--------------------------------------------------------------------------------------

data/lib/galaaz_ruby.rb

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+require 'shellwords'
+
+# Interpreter selection for Ruby launchers (bin/gknit, bin/gbookdown, bin/gstudio, Rake).
+# Default is `ruby` on PATH (JRuby or CRuby). Override with GALAAZ_RUBY=jruby / ruby / path.
+# JVM flags are applied only when the selected interpreter is JRuby (see galaaz_jruby.rb).
+module GalaazRuby
+  def self.interpreter
+    bin = ENV['GALAAZ_RUBY'].to_s.strip
+    bin.empty? ? 'ruby' : bin
+  end
+
+  def self.jruby?(bin = interpreter)
+    base = File.basename(bin.to_s)
+    return true if base == 'jruby' || base.start_with?('jruby.')
+
+    engine = `#{Shellwords.escape(bin)} -e 'print RUBY_ENGINE' 2>/dev/null`.to_s.strip
+    engine == 'jruby'
+  rescue StandardError
+    false
+  end
+
+  # Shell prefix: "<bin> [jvm-args] -I<lib_path>"
+  def self.shell_invocation(lib_path)
+    bin = interpreter
+    if jruby?(bin)
+      require_relative 'galaaz_jruby'
+      "#{bin} #{GalaazJRuby.shell_j_arg_string} -I#{lib_path}"
+    else
+      "#{bin} -I#{lib_path}"
+    end
+  end
+end

data/lib/new_bridge/envelope.rb

@@ -22,7 +22,7 @@ module NewBridge
       raise InvalidEnvelope, "unknown keys: #{extra.join(', ')}" unless extra.empty?
 
       MessagePack.pack(h)
-    rescue MessagePack::MalformedFormatError, MessagePack::UnpackError => e
+    rescue MessagePack::MalformedFormatError, MessagePack::UnpackError, EOFError => e
       raise Error, "MsgPack pack failed: #{e.message}"
     end
 
@@ -39,7 +39,7 @@ module NewBridge
       raise InvalidEnvelope, "missing keys: #{missing.join(', ')}" unless missing.empty?
 
       h
-    rescue MessagePack::MalformedFormatError, MessagePack::UnpackError => e
+    rescue MessagePack::MalformedFormatError, MessagePack::UnpackError, EOFError => e
       raise Error, "invalid MsgPack envelope: #{e.message}"
     end
 

data/specs/gknit_include_engine_spec.rb

@@ -13,10 +13,10 @@ describe 'gknit include engine' do
     ].select { |dir| File.directory?(dir) }
     path = ENV.fetch('PATH', '')
     path = ([*extra, path].join(File::PATH_SEPARATOR)) unless extra.empty?
-    {
+    ENV.to_h.merge(
       'JAVA_OPTS' => '--add-opens=java.base/java.nio=ALL-UNNAMED',
       'PATH' => path
-    }
+    )
   end
 
   it 'loads include file code so constants are available in following ruby chunks' do

data/specs/gknit_install_timeout_report_spec.rb

@@ -13,10 +13,10 @@ describe 'gknit install timeout reporting' do
     ].select { |dir| File.directory?(dir) }
     path = ENV.fetch('PATH', '')
     path = ([*extra, path].join(File::PATH_SEPARATOR)) unless extra.empty?
-    {
+    ENV.to_h.merge(
       'JAVA_OPTS' => '--add-opens=java.base/java.nio=ALL-UNNAMED',
       'PATH' => path
-    }
+    )
   end
 
   it 'continues processing and prints timeout in final report' do

data/specs/gknit_internal_error_report_spec.rb

@@ -13,10 +13,10 @@ describe 'gknit internal error report' do
     ].select { |dir| File.directory?(dir) }
     path = ENV.fetch('PATH', '')
     path = ([*extra, path].join(File::PATH_SEPARATOR)) unless extra.empty?
-    {
+    ENV.to_h.merge(
       'JAVA_OPTS' => '--add-opens=java.base/java.nio=ALL-UNNAMED',
       'PATH' => path
-    }
+    )
   end
 
   it 'prints chunk-scoped report only when internal errors are detected' do

data/specs/gknit_vector_map_output_spec.rb

@@ -13,10 +13,10 @@ describe 'gknit vector map output' do
     ].select { |dir| File.directory?(dir) }
     path = ENV.fetch('PATH', '')
     path = ([*extra, path].join(File::PATH_SEPARATOR)) unless extra.empty?
-    {
+    ENV.to_h.merge(
       'JAVA_OPTS' => '--add-opens=java.base/java.nio=ALL-UNNAMED',
       'PATH' => path
-    }
+    )
   end
 
   it 'renders vec.map in ruby chunks without missing bridge methods' do

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "galaaz"
-$version="2.0.0"
+$version="2.1.0"