Enable workflow_dispatch for test

csv  is not part of the default gems since Ruby 3.4.0

.github/FUNDING.yml

@@ -1,2 +1 @@
-github: kojix2
 ko_fi: kojix2

.github/workflows/ci.yml

@@ -1,15 +1,15 @@
 name: test
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 jobs:
   build:
     name: ${{ matrix.os }} Ruby ${{ matrix.ruby }}
     runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
-        os:   ['ubuntu', 'macos']
-        ruby: [ '2.4', '2.5', '2.6', '2.7', '3.0' ]
+        os: ["ubuntu", "macos"]
+        ruby: ["2.6", "2.7", "3.0", "3.1", "3.2", "3.3", "3.4"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: ruby/setup-ruby@v1
         with:
           ruby-version: ${{ matrix.ruby }}

.github/workflows/doc.yml

@@ -0,0 +1,23 @@
+name: doc
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: ruby
+      - name: Generate document
+        run: gem install -N yard && yard doc
+      - name: Publish Documentation on GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc

README.md

@@ -1,7 +1,7 @@
 <div align="center">
   <img src="logo.svg">
   <hr>
-  <img alt="Build Status" src="https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg">
+  <a href="https://github.com/red-data-tools/YouPlot/actions/workflows/ci.yml"><img alt="Build Status" src="https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg"></a>
   <a href="https://rubygems.org/gems/youplot/"><img alt="Gem Version" src="https://badge.fury.io/rb/youplot.svg"></a>
   <a href="https://zenodo.org/badge/latestdoi/283230219"><img alt="DOI" src="https://zenodo.org/badge/283230219.svg"></a>
   <a href="https://rubydoc.info/gems/youplot/"><img alt="Docs Stable" src="https://img.shields.io/badge/docs-stable-blue.svg"></a>
@@ -15,6 +15,24 @@
 ## Installation
 
 ```
+brew install youplot
+```
+
+```
+gem install youplot
+```
+
+```
+nix shell nixpkgs#youplot
+```
+
+```
+guix install youplot
+```
+
+```
+conda install -c conda-forge ruby
+conda install -c conda-forge compilers
 gem install youplot
 ```
 
@@ -37,13 +55,20 @@ curl -sL https://git.io/ISLANDScsv \
   <img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
 </p>
 
+
+
+```sh
+# For offline user: Sorts files in a directory by size and shows a bar graph.
+ls -l | awk '{print $9, $5}' | sort -nk 2 | uplot bar -d ' '
+```
+
 ### histogram
 
 ```sh
 echo -e "from numpy import random;" \
         "n = random.randn(10000);"  \
         "print('\\\n'.join(str(i) for i in n))" \
-| python \
+| python3 \
 | uplot hist --nbins 20
 ```
 
@@ -63,6 +88,14 @@ curl -sL https://git.io/AirPassengers \
   <img alt="lineplot" src="https://user-images.githubusercontent.com/5798442/101999825-24c5ec80-3d24-11eb-99f4-c642e8d221bc.png">
 </p>
 
+```sh
+# For offline users: Calculates sin values (0-2*pi) and plots a sine wave.
+python3 -c '
+from math import sin, pi
+data = "\n".join(f"{i*pi/50}\t{sin(i*pi/50)}" for i in range(101))
+print(data)' | uplot line
+```
+
 ### scatter
 
 ```sh
@@ -75,6 +108,12 @@ curl -sL https://git.io/IRIStsv \
   <img alt="scatter" src="https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png">
 </p>
 
+
+```sh
+# For offline users
+cat test/fixtures/iris.csv | cut -f1-4 -d, | uplot scatter -H -d, -t IRIS
+```
+
 ### density
 
 ```sh
@@ -87,6 +126,11 @@ curl -sL https://git.io/IRIStsv \
   <img alt="density" src="https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png">
 </p>
 
+```sh
+# For offline users
+cat test/fixtures/iris.csv | cut -f1-4 -d, | uplot density -H -d, -t IRIS
+```
+
 ### boxplot
 
 ```sh
@@ -99,8 +143,21 @@ curl -sL https://git.io/IRIStsv \
   <img alt="boxplot" src="https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png">
 </p>
 
+```sh
+# For offline users
+cat test/fixtures/iris.csv | cut -f1-4 -d, | uplot boxplot -H -d, -t IRIS
+```
+
 ### count
 
+Count processes by user ID.
+
+```sh
+ps aux | awk '{print $1}' | uplot count
+```
+
+Count the number of chromosomes where genes are located. 
+
 ```sh
 cat gencode.v35.annotation.gff3 \
 | grep -v '#' | grep 'gene' | cut -f1 \
@@ -111,7 +168,6 @@ cat gencode.v35.annotation.gff3 \
   <img alt="count" src="https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png">
 </p>
 
-In this example, YouPlot counts the number of chromosomes where genes are located. 
 * [GENCODE - Human Release](https://www.gencodegenes.org/human/)
 
 Note: `count` is not very fast because it runs in a Ruby script.
@@ -157,7 +213,7 @@ The following sub-commands are available.
 
 * `-o`
   * By default, the plot is output to **standard error output**.
-  * If you want to output to standard input, Use hyphen ` -o -` or no argument `uplot s -o | `.
+  * If you want to output to standard output, Use hyphen ` -o -` or no argument `uplot s -o | `.
 
 ### Output the input data
 
@@ -211,6 +267,14 @@ The following sub-commands are available.
 
 * Not yet supported.
 
+### YouPlot Configuration (youplotrc)
+
+You can specify default options in a configuration file in YAML format. For more information, enter the following command.
+
+```
+uplot --config
+```
+
 ## Tools that are useful to use with YouPlot
 
 * [csvtk](https://github.com/shenwei356/csvtk)
@@ -241,6 +305,10 @@ bundle exec rake install   # Installation from source code
 bundle exec exe/uplot      # Run youplot (Try out the edited code)
 ```
 
+    Do you need commit rights to my repository?
+    Do you want to get admin rights and take over the project?
+    If so, please feel free to contact us.
+
 ### Acknowledgements
 
 * [sampo grafiikka](https://jypg.net/sampo_grafiikka) - Project logo creation

lib/youplot/command.rb

@@ -63,9 +63,15 @@ module YouPlot
       # normal mode
       else
         # Sometimes the input file does not end with a newline code.
-        while (input = Kernel.gets(nil))
+        begin
+          begin
+            input = Kernel.gets(nil)
+          rescue Errno::ENOENT => e
+            warn e.message
+            next
+          end
           main(input)
-        end
+        end until input
       end
     end
 
@@ -135,7 +141,12 @@ module YouPlot
       rescue CSV::MalformedCSVError => e
         warn 'Failed to parse the text. '
         warn 'Please try to set the correct character encoding with --encoding option.'
-        raise e
+        warn e.backtrace.grep(/youplot/).first
+        exit 1
+      rescue ArgumentError => e
+        warn 'Failed to parse the text. '
+        warn e.backtrace.grep(/youplot/).first
+        exit 1
       end
 
       data
@@ -149,9 +160,9 @@ module YouPlot
         @backend.barplot(data, params, count: true, reverse: options[:reverse])
       when :hist, :histogram
         @backend.histogram(data, params)
-      when :line, :lineplot
+      when :line, :lineplot, :l
         @backend.line(data, params, options[:fmt])
-      when :lines, :lineplots
+      when :lines, :lineplots, :ls
         @backend.lines(data, params, options[:fmt])
       when :scatter, :s
         @backend.scatter(data, params, options[:fmt])

lib/youplot/parser.rb

@@ -9,7 +9,8 @@ module YouPlot
     class Error < StandardError; end
 
     attr_reader :command, :options, :params,
-                :main_parser, :sub_parser
+                :main_parser, :sub_parser,
+                :config_file, :config
 
     def initialize
       @command = nil
@@ -30,6 +31,61 @@ module YouPlot
       @params = Parameters.new
     end
 
+    def apply_config_file
+      return if !config_file && find_config_file.nil?
+
+      read_config_file
+      configure
+    end
+
+    def config_file_candidate_paths
+      # keep the order of the paths
+      paths = []
+      paths << ENV['MYYOUPLOTRC'] if ENV['MYYOUPLOTRC']
+      paths << '.youplot.yml'
+      paths << '.youplotrc'
+      if ENV['HOME']
+        paths << File.join(ENV['HOME'], '.youplotrc')
+        paths << File.join(ENV['HOME'], '.youplot.yml')
+        paths << File.join(ENV['HOME'], '.config', 'youplot', 'youplotrc')
+        paths << File.join(ENV['HOME'], '.config', 'youplot', 'youplot.yml')
+      end
+      paths
+    end
+
+    def find_config_file
+      config_file_candidate_paths.each do |file|
+        path = File.expand_path(file)
+        next unless File.exist?(path)
+
+        @config_file = path
+        ENV['MYYOUPLOTRC'] = path
+        return @config_file
+      end
+      nil
+    end
+
+    def read_config_file
+      require 'yaml'
+      @config = YAML.load_file(config_file)
+    end
+
+    def configure
+      option_members = @options.members
+      param_members = @params.members
+      # It would be more useful to be able to configure by plot type
+      config.each do |k, v|
+        k = k.to_sym
+        if option_members.include?(k)
+          @options[k] ||= v
+        elsif param_members.include?(k)
+          @params[k] ||= v
+        else
+          raise Error, "Unknown option/param in config file: #{k}"
+        end
+      end
+    end
+
     def create_base_parser
       OptionParser.new do |parser|
         parser.program_name  = 'YouPlot'
@@ -104,6 +160,9 @@ module YouPlot
           puts parser.help
           exit if YouPlot.run_as_executable?
         end
+        parser.on('--config FILE', 'specify a config file') do |v|
+          @config_file = v
+        end
         parser.on('--debug', TrueClass, 'print preprocessed data') do |v|
           options[:debug] = v
         end
@@ -130,11 +189,12 @@ module YouPlot
               scatter    s             draw a scatter plot
               density    d             draw a density plot
               boxplot    box           draw a horizontal boxplot
-              count      c             draw a baplot based on the number of
+              count      c             draw a barplot based on the number of
                                        occurrences (slow)
               colors     color         show the list of available colors
 
           General options:
+              --config                 print config file info
               --help                   print command specific help menu
               --version                print the version of YouPlot
         MSG
@@ -142,10 +202,36 @@ module YouPlot
       # Help for the main parser is simple.
       # Simply show the banner above.
       main_parser.on('--help', 'print sub-command help menu') do
-        puts main_parser.banner
-        puts
-        exit if YouPlot.run_as_executable?
+        show_main_help
       end
+
+      main_parser.on('--config', 'show config file info') do
+        show_config_info
+      end
+    end
+
+    def show_main_help(out = $stdout)
+      out.puts main_parser.banner
+      out.puts
+      exit if YouPlot.run_as_executable?
+    end
+
+    def show_config_info
+      if ENV['MYYOUPLOTRC']
+        puts "config file : #{ENV['MYYOUPLOTRC']}"
+        puts config.inspect
+      else
+        puts <<~EOS
+          Configuration file not found.
+          It should be a YAML file, like this example:
+            width : 40
+            height : 20
+          By default, YouPlot will look for the configuration file in these locations:
+          #{config_file_candidate_paths.map { |s| '  ' + s }.join("\n")}
+          If you have the file elsewhere, you can specify its location with the `MYYOUPLOTRC` environment variable.
+        EOS
+      end
+      exit if YouPlot.run_as_executable?
     end
 
     def sub_parser_add_symbol
@@ -215,10 +301,13 @@ module YouPlot
       case command
 
       # If you type only `uplot` in the terminal.
+      # Output help to standard error output.
       when nil
-        warn main_parser.banner
-        warn "\n"
-        exit 1 if YouPlot.run_as_executable?
+        show_main_help($stderr)
+
+      # Output help to standard output.
+      when :help
+        show_main_help
 
       when :barplot, :bar
         sub_parser_add_symbol
@@ -241,14 +330,14 @@ module YouPlot
           params.nbins = v
         end
 
-      when :lineplot, :line
+      when :lineplot, :line, :l
         sub_parser_add_canvas
         sub_parser_add_grid
         sub_parser_add_fmt_yx
         sub_parser_add_ylim
         sub_parser_add_xlim
 
-      when :lineplots, :lines
+      when :lineplots, :lines, :ls
         sub_parser_add_canvas
         sub_parser_add_grid
         sub_parser_add_fmt_xyxy
@@ -277,14 +366,19 @@ module YouPlot
           options[:color_names] = v
         end
 
+      # Currently it simply displays the configuration file,
+      # but in the future this may be changed to open a text editor like Vim
+      # to edit the configuration file.
+      when :config
+        show_config_info
+
       else
-        error_message = "uplot: unrecognized command '#{command}'"
-        if YouPlot.run_as_executable?
-          warn error_message
-          exit 1
-        else
-          raise Error, error_message
-        end
+        error_message = "YouPlot: unrecognized command '#{command}'"
+        raise Error, error_message unless YouPlot.run_as_executable?
+
+        warn error_message
+        exit 1
+
       end
     end
 
@@ -292,7 +386,7 @@ module YouPlot
       begin
         create_main_parser.order!(argv)
       rescue OptionParser::ParseError => e
-        warn "uplot: #{e.message}"
+        warn "YouPlot: #{e.message}"
         exit 1 if YouPlot.run_as_executable?
       end
 
@@ -301,7 +395,14 @@ module YouPlot
       begin
         create_sub_parser&.parse!(argv)
       rescue OptionParser::ParseError => e
-        warn "uplot: #{e.message}"
+        warn "YouPlot: #{e.message}"
+        exit 1 if YouPlot.run_as_executable?
+      end
+
+      begin
+        apply_config_file
+      rescue StandardError => e
+        warn "YouPlot: #{e.message}"
         exit 1 if YouPlot.run_as_executable?
       end
     end

lib/youplot/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module YouPlot
-  VERSION = '0.4.3'
+  VERSION = '0.4.6'
 end

test/youplot/iris_test.rb

@@ -69,6 +69,12 @@ class YouPlotIRISTest < Test::Unit::TestCase
     assert_equal fixture('iris-lineplot.txt'), @stderr_file.read
   end
 
+  # l is an undocumented alias of lineplot.
+  test :l do
+    YouPlot::Command.new(['l', '-H', '-d,', '-t', 'IRIS-LINEPLOT']).run
+    assert_equal fixture('iris-lineplot.txt'), @stderr_file.read
+  end
+
   test :lineplots do
     YouPlot::Command.new(['lineplots', '-H', '-d,', '-t', 'IRIS-LINEPLOTS']).run
     assert_equal fixture('iris-lineplots.txt'), @stderr_file.read
@@ -79,6 +85,12 @@ class YouPlotIRISTest < Test::Unit::TestCase
     assert_equal fixture('iris-lineplots.txt'), @stderr_file.read
   end
 
+  # ls is an undocumented alias of lineplots.
+  test :ls do
+    YouPlot::Command.new(['lines', '-H', '-d,', '-t', 'IRIS-LINEPLOTS']).run
+    assert_equal fixture('iris-lineplots.txt'), @stderr_file.read
+  end
+
   test :scatter do
     YouPlot::Command.new(['scatter', '-H', '-d,', '-t', 'IRIS-SCATTER']).run
     assert_equal fixture('iris-scatter.txt'), @stderr_file.read

youplot.gemspec

@@ -12,12 +12,13 @@ Gem::Specification.new do |spec|
   spec.description   = 'A command line tool for Unicode Plotting'
   spec.homepage      = 'https://github.com/red-data-tools/YouPlot'
   spec.license       = 'MIT'
-  spec.required_ruby_version = Gem::Requirement.new('>= 2.4.0')
+  spec.required_ruby_version = Gem::Requirement.new('>= 2.5.0')
 
   spec.files         = Dir['*.{md,txt}', '{lib,exe}/**/*']
   spec.bindir        = 'exe'
   spec.executables   = %w[uplot youplot]
   spec.require_paths = ['lib']
 
+  spec.add_dependency 'csv'
   spec.add_dependency 'unicode_plot', '>= 0.0.5'
 end