galaaz 0.4.10 → 2.0.0

data/bin/gknit-draft

@@ -0,0 +1,105 @@
+#!/usr/bin/env ruby
+# 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 'optionparser'
+
+options = {}
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: gknit-draft [options] [path]"
+  opts.on("-f", "--filename FILE", "Directory and filename to create") do |opt|
+    options[:file] = opt
+  end
+  opts.on("-t", "--template TEMPLATE", "Latex template to use") do |opt|
+    options[:template] = opt
+  end
+  opts.on("-p", "--package PACKAGE", "R Package where the template is defined") do |opt|
+    options[:package] = opt
+  end
+  opts.on("-g", "--gem RubyGem", "Ruby Gem where the template is defined") do |opt|
+    options[:gem] = opt
+  end
+  opts.on("-n", "--no_dir", "If a new directory should not be created") do |opt|
+    options[:no_dir] = opt
+  end
+  opts.on("-e", "--edit EDITOR", "Editor to use to edit the file") do |opt|
+    options[:editor] = opt
+  end
+end.parse!
+
+#=========================================================================================
+# Only one of 'package' or 'gem' can be given
+#=========================================================================================
+
+raise "You should either specify an R package or Ruby Gem where the template is defined" if
+  !options[:package].nil? && !options[:gem].nil?
+
+#=========================================================================================
+# If gem given, then set it as the package name
+#=========================================================================================
+
+is_r_package = (options[:package].nil?)? false : true
+options[:package] =
+  (!options[:gem].nil?)? "%Q(#{options[:gem]})" : "%Q(#{options[:package]})"
+
+#=========================================================================================
+#
+#=========================================================================================
+
+options[:no_dir] = (options[:no_dir].nil?)? true : false
+
+#=========================================================================================
+#
+#=========================================================================================
+
+Dir.chdir(File.dirname(File.expand_path('.', __FILE__)))
+
+options[:file] = "%Q(#{options[:file]}-#{options[:template]})"
+
+code = <<-Ruby
+require 'gknit'
+R.install_and_loads 'xfun'
+
+GKnit.draft(file: #{options[:file]}, template: %Q(#{options[:template]}), 
+            package: #{options[:package]}, create_dir: #{options[:no_dir]}, 
+            is_package: #{is_r_package}, edit: true)
+Ruby
+
+libx = File.expand_path('../../lib', __FILE__)
+exec %Q(ruby --polyglot --jvm -I#{libx} -e "#{code}")
+
+# exec %Q(ruby --polyglot --jvm --experimental-options --single-threaded -I../lib -e "#{code}")
+
+=begin
+puts "=========="
+full_filename = Dir.glob("gknit-templates*", base: "#{Gem.default_dir}/gems")
+template_path = "#{Gem.default_dir}/gems/#{full_filename[0]/rmarkdown/templates/}"
+puts template_path
+puts "=========="
+=end
+
+#puts %Q(ruby --polyglot --jvm --experimental-options --single-threaded -I../lib -e "#{code}")
+
+#exec "ruby --polyglot --jvm --experimental-options --single-threaded \
+#-I../lib -S ./gknit-draft.rb #{options[:file]} #{options[:template]} #{options[:package]} #{options[:create_#dir]} #{is_r_package} #{options[:editor]}"

data/bin/gknit-draft.rb

@@ -0,0 +1,28 @@
+# 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 'gknit'
+
+R.install_and_loads 'xfun'
+
+GKnit.draft(file: ARGV[0], template: ARGV[1], package: ARGV[2],
+	    create_dir: ARGV[3], is_package: ARGV[4], edit: ARGV[5])

data/bin/gknit_Rscript

@@ -0,0 +1,127 @@
+#!/usr/bin/env ruby
+# coding: utf-8
+
+require 'optionparser'
+
+options = {}
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: gknit [options]"
+  opts.on("-f", "--filename FILE", "The input file to be rendered.  This value can also be provided without the '-f' or '--filename' flag by just giving the name of the file as an input parameter.") do |opt|
+    options[:input_file] = opt
+  end
+  opts.on("--output_format OUT_FORMAT", "The R Markdown output format to convert to. The option 'all' will render all formats defined within the file. The option can be the name of a format (e.g. 'html_document') and that will render the document to that single format. One can also use a vector of format names to render to multiple formats. Alternatively, you can pass an output format object (e.g. html_document()). If using NULL then the output format is the first one defined in the YAML frontmatter in the input file (this defaults to HTML if no format is specified there).") do |opt|
+    options[:output_format] = opt
+  end
+  opts.on("-o", "--output_file OUT_FILE", "The name of the output file. If using nil then the output filename will be based on filename for the input file. If a filename is provided, a path to the output file can also be provided. Note that the output_dir option allows for specifying the output file path as well, however, if also specifying the path, the directory must exist.") do |opt|
+    options[:output_file] = opt
+  end
+  opts.on("-d", "--output_dir OUT_DIR", "The output directory for the rendered output_file. This allows for a choice of an alternate directory to which the output file should be written (the default output directory is that of the input file). If a path is provided with a filename in output_file the directory specified here will take precedence. Please note that any directory path provided will create any necessary directories if they do not exist.") do |opt|
+    options[:output_dir] = opt
+  end
+  opts.on("-a", "--output_options OUT_OPT", "List of output options that can override the options specified in metadata (e.g. could be used to force self_contained or mathjax = 'local'). Note that this is only valid when the output format is read from metadata (i.e. not a custom format object passed to output_format).") do |opt|
+    options[:output_options] = opt
+  end
+  opts.on("-i", "--intermediates_dir INTER_DIR", "FEATURE NOT YET IMPLEMENTED! Intermediate files directory. If a path is specified then intermediate files will be written to that path. If nil, intermediate files are written to the same directory as the input file.") do |opt|
+    options[:intermediates_dir] = opt
+  end
+  opts.on("-n", "--no_clean", "Will not clean intermediate files that are created during rendering.") do |opt|
+    options[:clean] = opt
+  end
+end.parse!
+
+# Sets the directory
+dir = Dir.pwd
+
+#=========================================================================================
+# Check if the name of the file to gKnit was given and that it exists. If not,
+# issue error.
+#=========================================================================================
+
+options[:input_file] = ARGV[0] if !ARGV[0].nil?
+raise "Input file name is required for gKnitting. Add -f FILE or --input_file FILE. For help, type gknit -h" if
+  options[:input_file].nil?
+options[:input_file] = "#{dir}/#{options[:input_file]}"
+raise "File #{options[:input_file]} does not exist!" if !File.exist?(options[:input_file])
+
+#=========================================================================================
+# Checks the output_format option. If none, pass NULL to the render function. Output
+# format needs to be quoted.
+#=========================================================================================
+
+options[:output_format] =
+  (options[:output_format].nil?)? "NULL" : "\"#{options[:output_format]}\""
+
+#=========================================================================================
+# Checks the output_file option. If none, pass NULL to the render function. Output
+# file name needs to be quoted.
+#=========================================================================================
+
+options[:output_file] =
+  (options[:output_file].nil?)? "NULL" : "\"#{options[:output_file]}\""
+
+#=========================================================================================
+# Checks if an output directory was given. If given and directory does not exist,
+# create the directory.  If no directory given, pass NULL to the render function.
+#=========================================================================================
+
+if (!options[:output_dir].nil?)
+  Dir.mkdir(options[:output_dir]) if !Dir.exist?(options[:output_dir])
+  options[:output_dir] = "\"#{options[:output_dir]}\""
+else
+  # If not, pass NULL to the render function
+  options[:output_dir] = "NULL"
+end
+
+#=========================================================================================
+# Checks if any intermediate directory given. If not, pass NULL to the render function
+# Calling render with options intermediates_dir is not working, requires further study
+#=========================================================================================
+
+if (!options[:intermediates_dir].nil?)
+  if !Dir.exist?(options[:intermediates_dir])
+    Dir.mkdir(options[:intermediates_dir])
+    options[:intermediates_dir] = "\"#{options[:intermediates_dir]}\""
+  else
+    options[:intermediates_dir] = "\"#{options[:intermediates_dir]}\""
+  end
+else
+  options[:intermediates_dir] = "NULL"
+end
+
+options[:clean] = (options[:clean].nil?)? "TRUE" : "FALSE" 
+
+#=========================================================================================
+# Sends message to user that the gKniting process has started
+#=========================================================================================
+puts "================================"
+puts "gKnitting #{options[:input_file]} with the following options:"
+puts "   * Output format: \t #{options[:output_format]}"
+puts "   * Output file: \t #{options[:output_file]}"
+puts "   * Output directory: \t #{options[:output_dir]}"
+puts "   * Clean: \t\t #{options[:clean]}"
+
+
+# Code to be evaluated by the R script
+code = <<EOF
+eval.polyglot("ruby", "$LOAD_PATH.unshift %q(/home/rbotafogo/desenv/galaaz/lib)")
+eval.polyglot("ruby", "require %q(gknit)")
+
+rmarkdown::render("#{options[:input_file]}", output_format = #{options[:output_format]}, 
+                  output_file = #{options[:output_file]}, 
+                  output_dir = #{options[:output_dir]}, 
+                  clean = #{options[:clean]})
+EOF
+
+
+exec "Rscript --jvm --polyglot -e '#{code}'"
+
+=begin
+# how to call rmarkdown::render with a parameter list
+# all params need to be defined in the YAML header
+rmarkdown::render("#{options[:input_file]}", output_format = #{options[:output_format]}, 
+                  output_file = #{options[:output_file]}, 
+                  output_dir = #{options[:output_dir]}, 
+                  clean = #{options[:clean]},
+                  params = list(rake_clean = TRUE))
+=end

data/bin/grun

@@ -1,5 +1,31 @@
 #!/usr/bin/env ruby
+# 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.
+##########################################################################################
+
+
+libx = File.expand_path('../../lib', __FILE__)
+exec "ruby --polyglot --jvm -I#{libx} -S #{ARGV[0]}"
 
 # Dir.chdir(File.dirname(File.expand_path('.', __FILE__)))
+# exec "ruby --polyglot --jvm --experimental-options --single-threaded -I../lib -S #{ARGV[0]}"
 
-exec "ruby --polyglot --jvm --experimental-options --single-threaded -S #{ARGV[0]}"

data/bin/gstudio

@@ -1,8 +1,53 @@
 #!/usr/bin/env ruby
+# coding: utf-8
 
-Dir.chdir(File.dirname(File.expand_path('.', __FILE__)))
+##########################################################################################
+# @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.
+##########################################################################################
 
-puts "Loading IRB and Galaaz... Please wait!"
+require 'optionparser'
+require 'shellwords'
 
-# exec "ruby --polyglot --jvm -Xsingle_threaded -S pry -r ./gstudio.rb"
-exec "ruby --polyglot --jvm --experimental-options --single-threaded -S irb -r ./gstudio.rb"
+options = {}
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: gknit-draft [options] [path]"
+  opts.on("-i", "--irb", "Use IRB as shell") do |opt|
+    options[:irb] = opt
+  end
+  opts.on("-p", "--pry", "Use PRY as shell") do |opt|
+    options[:pry] = opt
+  end
+end.parse!
+
+# Dir.chdir(File.dirname(File.expand_path('.', __FILE__)))
+
+bin_dir = File.expand_path('..', __FILE__)
+libx = File.expand_path('../../lib', __FILE__)
+require File.join(libx, 'galaaz_jruby')
+jvm_args = GalaazJRuby.shell_j_arg_string
+
+if options[:pry]
+  puts "Loading PRY and Galaaz... Please wait!"
+  exec "jruby #{jvm_args} -I#{Shellwords.escape(libx)} -S pry -r #{Shellwords.escape(File.join(bin_dir, 'gstudio_pry.rb'))}"
+else
+  puts "Loading IRB and Galaaz... Please wait!"
+  exec "jruby #{jvm_args} -I#{Shellwords.escape(libx)} -S irb -r #{Shellwords.escape(File.join(bin_dir, 'gstudio_irb.rb'))}"
+end

data/bin/gstudio_pry.rb

@@ -0,0 +1,7 @@
+require 'galaaz'
+require 'ggplot'
+require 'pp'
+
+Pry.config.prompt = proc { |obj, nest_level, _| "galaaz:#{nest_level}> " }
+# Pry.config.history.file = '~/.galaaz.history'
+Pry.config.editor = "emacsclient"

data/bin/install-tinytex

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+# Install TinyTeX to ~/.TinyTeX with symlinks in ~/bin (no sudo).
+# Needed for rmarkdown pdf_document and specs/phase2_gknit_chunk_output_spec.rb.
+set -euo pipefail
+curl -fsSL https://raw.githubusercontent.com/rstudio/tinytex/master/tools/install-bin-unix.sh | sh
+echo "TinyTeX installed. Ensure ~/bin is on PATH for interactive shells, or rely on the Phase 2 spec prepending it for gknit."

data/bin/run_all_rspec

@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+# Run default galaaz specs (specs/) and NewBridge gatekeeper specs (new_bridge_specs/)
+# in a single RSpec process so SimpleCov produces one merged report under coverage/.
+#
+# Compiles ext/new_bridge (incremental make) first — required for integration specs.
+#
+# Usage:
+#   bin/run_all_rspec
+#   bin/run_all_rspec --format documentation
+#   bin/run_all_rspec new_bridge_specs/phase0_protocol_spec.rb
+#
+# If the first argument is an option (starts with -), default dirs are prepended
+# so `bin/run_all_rspec --format doc` still runs specs/ + new_bridge_specs/.
+#
+# For specs/ only (faster day-to-day): bin/run_rspec
+set -e
+ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+# shellcheck source=galaaz_jruby_env.inc.sh
+source "$ROOT/bin/galaaz_jruby_env.inc.sh"
+
+echo "[run_all_rspec] compiling gatekeeper: ext/new_bridge"
+make -C "$ROOT/ext/new_bridge" -s all
+
+# Same top-level file set as bin/run_rspec (maxdepth 1), plus whole new_bridge_specs/ tree.
+DEFAULT_SPECS=()
+while IFS= read -r f; do
+  DEFAULT_SPECS+=("$f")
+done < <(find "$ROOT/specs" -maxdepth 1 -type f \( -name '*_spec.rb' -o -name '*.spec.rb' \) | sort)
+DEFAULT_SPECS+=( "$ROOT/new_bridge_specs" )
+
+# With no args, run those paths. If args are only RSpec options (e.g. --format progress),
+# prepend defaults so flags alone do not mean "run zero files".
+if [ $# -eq 0 ]; then
+  set -- "${DEFAULT_SPECS[@]}"
+elif [[ "${1:-}" == -* ]]; then
+  set -- "${DEFAULT_SPECS[@]}" "$@"
+fi
+exec jruby -I "$ROOT/lib" \
+  $GALAAZ_REQUIRED_JRUBY_J_ARGS \
+  ${GALAAZ_JRUBY_OPTS:-} \
+  -S bundle exec rspec \
+  -r "$ROOT/specs/spec_helper.rb" \
+  "$@"

data/bin/run_example

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+# Run a Galaaz example with required JRuby JVM flags (lib/galaaz_jruby.rb).
+# Optional: GALAAZ_JRUBY_OPTS.
+#
+# Usage: bin/run_example examples/sthda_ggplot/all.rb
+#        bin/run_example examples/sthda_ggplot/one_variable_continuous/geom_density.rb
+set -e
+ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+# shellcheck source=galaaz_jruby_env.inc.sh
+source "$ROOT/bin/galaaz_jruby_env.inc.sh"
+exec jruby -I "$ROOT/lib" \
+  $GALAAZ_REQUIRED_JRUBY_J_ARGS \
+  ${GALAAZ_JRUBY_OPTS:-} \
+  "$@"

data/bin/run_old_rspec

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+# Run legacy specs moved to old_specs/.
+# Usage:
+#   bin/run_old_rspec
+#   bin/run_old_rspec old_specs/r_environment.spec.rb
+set -e
+ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+# shellcheck source=galaaz_jruby_env.inc.sh
+source "$ROOT/bin/galaaz_jruby_env.inc.sh"
+if [ $# -eq 0 ]; then
+  shopt -s nullglob
+  SPECS=( "$ROOT"/old_specs/*.spec.rb "$ROOT"/old_specs/*_spec.rb )
+  IFS=$'\n' SPECS=( $(printf '%s\n' "${SPECS[@]}" | sort) )
+  set -- "${SPECS[@]}"
+fi
+exec jruby -I "$ROOT/lib" \
+  $GALAAZ_REQUIRED_JRUBY_J_ARGS \
+  ${GALAAZ_JRUBY_OPTS:-} \
+  -S bundle exec rspec "$@"

data/bin/run_rspec

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+# Run rspec with JVM options required for Apache Arrow (see lib/galaaz_jruby.rb).
+# Optional JVM/jruby extras: GALAAZ_JRUBY_OPTS (space-separated).
+#
+# Usage:
+#   bin/run_rspec              # run fast specs in specs/ only
+#   bin/run_all_rspec          # top-level specs/ + new_bridge_specs/ + gatekeeper compile (see docs/testing.md)
+#   bin/run_slow_rspec         # run slow specs in slow-specs/
+#   bin/run_rspec specs/protocol_result_spec.rb
+#   GALAAZ_DEBUG=1 bin/run_rspec specs/r_vector_subsetting.spec.rb:61 ...
+set -e
+ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+# shellcheck source=galaaz_jruby_env.inc.sh
+source "$ROOT/bin/galaaz_jruby_env.inc.sh"
+if [ $# -eq 0 ]; then
+  set -- $(find "$ROOT/specs" -maxdepth 1 -type f \( -name '*_spec.rb' -o -name '*.spec.rb' \) | sort)
+fi
+exec jruby -I "$ROOT/lib" \
+  $GALAAZ_REQUIRED_JRUBY_J_ARGS \
+  ${GALAAZ_JRUBY_OPTS:-} \
+  -S bundle exec rspec \
+  -r "$ROOT/specs/spec_helper.rb" \
+  "$@"

data/bin/run_rspec_subset

@@ -0,0 +1,38 @@
+#!/usr/bin/env bash
+# Run a small subset of specs (see Documentation/Spec_Subsets.md).
+# Usage: bin/run_rspec_subset <number>
+# Example: bin/run_rspec_subset 1
+
+set -e
+ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+cd "$ROOT"
+
+SUBNUM="${1:?Usage: bin/run_rspec_subset <number> [rspec-args...]}"
+[ "$#" -ge 1 ] && shift
+
+case "$SUBNUM" in
+  1)  SPECS="specs/protocol_result_spec.rb" ;;
+  2)  SPECS="specs/r_vector_creation.spec.rb" ;;
+  3)  SPECS="specs/r_eval.spec.rb" ;;
+  4)  SPECS="specs/r_vector_subsetting.spec.rb" ;;
+  5)  SPECS="specs/r_list.spec.rb" ;;
+  6)  SPECS="specs/r_vector_operators.spec.rb" ;;
+  7)  SPECS="specs/r_dataframe.spec.rb" ;;
+  8)  SPECS="specs/r_matrix.spec.rb" ;;
+  9)  SPECS="specs/r_vector_object.spec.rb" ;;
+  10) SPECS="specs/r_vector_functions.spec.rb" ;;
+  11) SPECS="specs/r_language.spec.rb" ;;
+  12) SPECS="specs/r_formula.spec.rb" ;;
+  13) SPECS="specs/r_function.spec.rb" ;;
+  14) SPECS="specs/r_list_apply.spec.rb" ;;
+  15) SPECS="specs/r_nse.spec.rb" ;;
+  16) SPECS="specs/ruby_expression.spec.rb" ;;
+  17) SPECS="specs/r_environment.spec.rb" ;;
+  18) SPECS="specs/r_devices.spec.rb specs/r_plots.spec.rb" ;;
+  *)
+    echo "Unknown subset: $SUBNUM (use 1–18). See Documentation/Spec_Subsets.md"
+    exit 1
+    ;;
+esac
+
+exec "$ROOT/bin/run_rspec" $SPECS "$@"

data/bin/run_slow_rspec

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+# Run slower rspec suites from slow-specs/.
+# Usage:
+#   bin/run_slow_rspec
+#   bin/run_slow_rspec slow-specs/phase2_gknit_chunk_output_spec.rb
+set -e
+ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+# shellcheck source=galaaz_jruby_env.inc.sh
+source "$ROOT/bin/galaaz_jruby_env.inc.sh"
+if [ $# -eq 0 ]; then
+  shopt -s nullglob globstar
+  SPECS=( "$ROOT"/slow-specs/**/*_spec.rb "$ROOT"/slow-specs/**/*.spec.rb )
+  IFS=$'\n' SPECS=( $(printf '%s\n' "${SPECS[@]}" | sort) )
+  set -- "${SPECS[@]}"
+fi
+exec jruby -I "$ROOT/lib" \
+  $GALAAZ_REQUIRED_JRUBY_J_ARGS \
+  ${GALAAZ_JRUBY_OPTS:-} \
+  -S bundle exec rspec "$@"