galaaz 0.4.6 → 0.5.0

data/Rakefile

@@ -33,7 +33,10 @@ require_relative 'version'
 class MakeTask < Rake::TaskLib
 
   # Create class variables for the polyglot options and libs
-  @@polyglot_options = "--polyglot --jvm -Xsingle_threaded"
+  # not yet possible to run native with R it seems...
+  # @@polyglot_options = "--polyglot --experimental-options --single_threaded"
+  # @@polyglot_options = "--polyglot --jvm --experimental-options --single-threaded"
+  @@polyglot_options = "--polyglot --jvm"
   @@libs = "-Ilib/" # -Ir_requires/"
 
   #----------------------------------------------------------------------------------------
@@ -74,12 +77,16 @@ class MakeTask < Rake::TaskLib
   
 end
 
+
+task :default => "sthda:all"
+
 geoms = FileList['examples/sthda_ggplot/**/*.rb']
 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")
+bugs = FileList['bugs/**/*.rb']
 
 #===========================================================================================
 # Creates tasks for all specs.
@@ -146,7 +153,17 @@ misc.each do |f|
   Desc
 end
 
-task :default => "sthda:all"
+#===========================================================================================
+# Creates tasks for bug examples
+#===========================================================================================
+
+bugs.each do |f|
+  task_name = File.basename(f, ".rb")
+  dir_name = File.dirname(f)
+  MakeTask.new("bugs", dir_name, task_name, false, <<-Desc)
+    Executes misc #{task_name}
+  Desc
+end
 
 #===========================================================================================
 # Creates task for running gknit
@@ -157,11 +174,11 @@ blogs.each do |dir|
   blog_rmd = "blogs/#{dir}/#{dir}.Rmd"
   desc "run gknit to build #{dir} blog post"
   task "blog:#{dir}" do
-    (sh %{ bin/gknit #{blog_rmd} })
+    (sh %{ bin/gknit #{blog_rmd} } )
   end
 
 end
-  
+
 #===========================================================================================
 # Loads R and require libraries to run Galaaz
 #===========================================================================================

data/bin/gknit

@@ -1,15 +1,161 @@
 #!/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
-puts "Knitting #{dir}/#{ARGV[0]}"
 
+#=========================================================================================
+# 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?)? "nil" : "\"#{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?)? "nil" : "\"#{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] = "nil"
+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] = "nil"
+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 polyglot Ruby script
 code = <<EOF
-eval.polyglot("ruby", "$LOAD_PATH.unshift %q(/home/rbotafogo/desenv/galaaz/lib)")
-eval.polyglot("ruby", "require %q(gknit)")
+require %q(galaaz)
+require %q(gknit)
 
-gknit_file = "#{dir}/#{ARGV[0]}"
-rmarkdown::render("#{dir}/#{ARGV[0]}")
+R::Rmarkdown.render(
+     %q(#{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}'"
+libx = File.expand_path('../../lib', __FILE__)
+exec "ruby --polyglot --jvm --experimental-options --single-threaded -I#{libx} -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/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