youplot 0.4.1 → 0.4.4

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@@ -1,7 +1,7 @@
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data/README.md

@@ -1,16 +1,16 @@
-<p align="center">
-  <img src="logo.svg" width="60%" height="60%" />
-</p>
-
-![Build Status](https://github.com/kojix2/youplot/workflows/test/badge.svg)
-[![Gem Version](https://badge.fury.io/rb/youplot.svg)](https://badge.fury.io/rb/youplot)
-[![Docs Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/youplot)
-[![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
-[![DOI](https://zenodo.org/badge/283230219.svg)](https://zenodo.org/badge/latestdoi/283230219)
-
-YouPlot is a command line tool for Unicode Plotting working with data from standard stream.
-
-:bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
+<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://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>
+  <a href="LICENSE.txt"><img alt="The MIT License" src="https://img.shields.io/badge/license-MIT-blue.svg"></a>
+  
+  YouPlot is a command line tool that draws plots on the terminal.
+
+  :bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
+</div>
 
 ## Installation
 
@@ -20,8 +20,9 @@ gem install youplot
 
 ## Quick Start
 
-* `cat data.tsv | uplot <command> [options]` or
-* `uplot <command> [options] <data.tsv>`
+<img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png" width=160> <img alt="histogram" src="https://user-images.githubusercontent.com/5798442/101999820-21cafc00-3d24-11eb-86db-e410d19b07df.png" width=160> <img alt="scatter" src="https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png" width=160> <img alt="density" src="https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png" width=160> <img alt="boxplot" src="https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png" width=160>
+
+`uplot <command> [options] <data.tsv>`
 
 ### barplot
 
@@ -33,7 +34,7 @@ curl -sL https://git.io/ISLANDScsv \
 ```
 
 <p align="center">
-<img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
+  <img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
 </p>
 
 ### histogram
@@ -100,10 +101,6 @@ curl -sL https://git.io/IRIStsv \
 
 ### count
 
-In this example, YouPlot counts the number of chromosomes where the gene is located from the human gene annotation file and it creates a bar chart. The human gene annotation file can be downloaded from the following website.
-
-* https://www.gencodegenes.org/human/
-
 ```sh
 cat gencode.v35.annotation.gff3 \
 | grep -v '#' | grep 'gene' | cut -f1 \
@@ -114,23 +111,21 @@ 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.
 This is fine in most cases, as long as the data size is small. If you want to visualize huge data, it is faster to use a combination of common Unix commands as shown below.
 
 ```sh
 cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
-| sort | uniq -c | sort -nrk2 | awk '{print $2,$1}' \
-| uplot bar -d ' ' -t "The number of human gene annotations per chromosome"  -c blue
+| sort | uniq -c | sort -nrk1 \
+| uplot bar --fmt yx -d ' ' -t "The number of human gene annotations per chromosome"  -c blue
 ```
 
 ## Usage
 
-### Why YouPlot?
-
-Wouldn't it be a pain to have to run R, Python, Julia, gnuplot or whatever REPL just to check your data?
-YouPlot is a command line tool for this purpose. With YouPlot, you can continue working without leaving your terminal and shell.
-
-### How to use YouPlot?
+### Commands
 
 `uplot` is the shortened form of `youplot`. You can use either.
 
@@ -140,18 +135,7 @@ YouPlot is a command line tool for this purpose. With YouPlot, you can continue
 | `uplot <command> [options] data.tsv ...`       | Take input from files             |
 | `pipeline1 \| uplot <command> -O \| pipeline2` | Outputs data from stdin to stdout |
 
-### Where to output the plot?
-
-By default, the plot is output to *standard error output*.
-The output file or stream for the plot can be specified with the `-o` option.
-
-### Where to output the input data?
-
-By default, the input data is not shown anywhere.
-The `-O` option, with no arguments, outputs the input data directly to the standard output. 
-This is useful when passing data to a subsequent pipeline.
-
-### What types of plots are available?
+### Subcommands
 
 The following sub-commands are available.
 
@@ -164,74 +148,83 @@ The following sub-commands are available.
 | scatter   | s     | draw a scatter plot                    |
 | density   | d     | draw a density plot                    |
 | boxplot   | box   | draw a horizontal boxplot              |
+|           |       |                                        |
+| count     | c     | draw a barplot based on the number of occurrences (slow) |
+|           |       |                                        |
+| colors    | color | show the list of available colors      |
 
-See Quick Start for `count`.
+### Output the plot
 
-| command   | short | how it works                                             |
-|-----------|-------|----------------------------------------------------------|
-| count     | c     |  draw a barplot based on the number of occurrences (slow) |
+* `-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 | `.
 
-### What if the header line is included?
+### Output the input data
 
-If your input data contains a header line, you need to specify the `-H` option.
+* `-O`
+  * By default, the input data is not shown anywhere.
+  * If you want to pass the input data directly to the standard output, Use hyphen `-O -` or no argument `uplot s -O |`.
+  * This is useful when passing data to a subsequent pipeline.
 
-### How to specify the delimiter?
+### Header
 
-Use the `-d` option. To specify a blank space, you can use `uplot bar -d ' ' data.txt`. 
-You do not need to use `-d` option for tab-delimited text since the default value is tab.
+* `-H`
+  * If input data contains a header line, you need to specify the `-H` option.
 
-### Is there a way to specify a column as the x-axis or y-axis?
+### Delimiter
 
-Not yet. 
-YouPlot treats the first column as the X axis and the second column as the Y axis. 
-When working with multiple series, the first column is the X axis, the second column is series Y1, the third column is series Y2, and so on. 
-If you pass only one column of data for `line` and `bar`, YouPlot will automatically use a sequential number starting from 1 as the X-axis. 
+* `-d`
+  * You do not need to use `-d` option for tab-delimited text since the default value is tab.
+  * To specify a blank space, you can use `uplot bar -d ' ' data.txt`. 
 
-* `--fmt xyy` `--fmt xyxy` `--fmt yx` options give you a few more choices. 
-See `youplot <command> --help` for more details. 
+### Real-time data
 
-* Use `awk '{print $2, $1}'` to swap lines.
-* Use `paste` to concatenate series.
+* `-p` `--progress`
+  * Experimental progressive mode is currently under development.
+  * `ruby -e 'loop{puts rand(100)}' | uplot line --progress`
 
-### How to plot real-time data?
+### Show detailed options for subcommands
 
-Experimental progressive mode is currently under development.
+* `--help`
+  * The `--help` option will show more detailed options for each subcommand.
+  * `uplot hist --help`
 
-```sh
-ruby -e 'loop{puts rand(100)}' | uplot line --progress
-```
+### Set columns as x-axis or y-axis
 
-### How to view detailed command line options?
+* YouPlot treats the first column as the X axis and the second column as the Y axis. When working with multiple series, the first column is the X axis, the second column is series Y1, the third column is series Y2, and so on. 
+* If you pass only one column of data for `line` and `bar`, YouPlot will automatically use a sequential number starting from 1 as the X-axis. 
 
-Use `--help` to print command-specific options.
+* `--fmt`
+  * `--fmt xyy` `--fmt xyxy` `--fmt yx` options give you a few more choices. See `youplot <command> --help` for more details. 
+  * The fmt option may be renamed in the future. 
+  * The `-x` and `-y` options might be used to specify columns in the future.
 
-`uplot hist --help`
+* Use `awk '{print $2, $1}'` to swap columns. Use `paste` to concatenate series.
 
-```
-Usage: uplot histogram [options] <in.tsv>
+### Categorical data
 
-Options for histogram:
-        --symbol VAL         character to be used to plot the bars
-        --closed VAL         side of the intervals to be closed [left]
-    -n, --nbins VAL          approximate number of bins
+* With GNU datamash, you can manage to handle categorized data. 
+  * `cat test/fixtures/iris.csv | sed '/^$/d' | datamash --header-in --output-delimiter=: -t, -g5 collapse 3,4 | cut -f2-3 -d: | sed 's/:/\n/g' | uplot s -d, -T --fmt xyxy`
+  * This is not so easy...
 
-Options:
-...
-```
+### Time series
 
-### How to view the list of available colors?
+* Not yet supported.
 
-```sh
-uplot colors
-```
+## Tools that are useful to use with YouPlot
+
+* [csvtk](https://github.com/shenwei356/csvtk)
+* [GNU datamash](https://www.gnu.org/software/datamash/)
+* [awk](https://www.gnu.org/software/gawk/)
+* [xsv](https://github.com/BurntSushi/xsv)
 
 ## Contributing
 
 YouPlot is a library under development, so even small improvements like typofix are welcome!
 Please feel free to send us your pull requests.
 
-* [Report bugs](https://github.com/kojix2/youplot/issues)
-* Fix bugs and [submit pull requests](https://github.com/kojix2/youplot/pulls)
+* [Report bugs](https://github.com/red-data-tools/YouPlot/issues)
+* Fix bugs and [submit pull requests](https://github.com/red-data-tools/YouPlot/pulls)
 * Write, clarify, or fix documentation
   * English corrections by native speakers are welcome.
 * Suggest or add new features
@@ -245,11 +238,15 @@ git clone https://github.com/your_name/YouPlot
 bundle install             # Install the gem dependencies
 bundle exec rake test      # Run the test
 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
 
-* [Red Data Tools](https://github.com/red-data-tools) - Technical support
 * [sampo grafiikka](https://jypg.net/sampo_grafiikka) - Project logo creation
 * [yutaas](https://github.com/yutaas) - English proofreading
 

data/lib/youplot/backends/unicode_plot.rb

@@ -6,6 +6,27 @@
 require_relative 'processing'
 require 'unicode_plot'
 
+# If the line color is specified as a number, the program will display an error
+# message to the user and exit. Remove this patch when UnicodePlot is improved.
+
+module UnicodePlot
+  class << self
+    alias lineplot_original lineplot
+    def lineplot(*args, **kw)
+      if kw[:color].is_a? Numeric
+        warn <<~EOS
+          YouPlot: Line colors cannot be specified by numerical values.
+
+          For more information, please see the following issue.
+          https://github.com/red-data-tools/unicode_plot.rb/issues/34
+        EOS
+        YouPlot.run_as_executable ? exit(1) : raise(Error)
+      end
+      lineplot_original(*args, **kw)
+    end
+  end
+end
+
 module YouPlot
   # plotting functions.
   module Backends
@@ -106,11 +127,10 @@ module YouPlot
 
       def plot_xyxy(data, method1, params)
         headers = data.headers
-        series = data.series
+        series2 = data.series
+                      .map { |s| s.map(&:to_f) }
+                      .each_slice(2).to_a
         method2 = get_method2(method1)
-        series.map! { |s| s.map(&:to_f) }
-        series2 = series.each_slice(2).to_a
-        series = nil
         params.name ||= headers[0] if headers
         params.xlim ||= series2.map(&:first).flatten.minmax # why need?
         params.ylim ||= series2.map(&:last).flatten.minmax # why need?
@@ -182,7 +202,7 @@ module YouPlot
         series = data.series
         if series.size == 1
           warn <<~EOS
-            youplot: There is only one series of input data. Please check the delimiter.
+            YouPlot: There is only one series of input data. Please check the delimiter.
 
             Headers: \e[35m#{data.headers.inspect}\e[0m
             The first item is: \e[35m\"#{series[0][0]}\"\e[0m

data/lib/youplot/command.rb

@@ -40,6 +40,24 @@ module YouPlot
         return
       end
 
+      # config command
+      if @command == :config
+        if ENV['MYYOUPLOTRC']
+          puts "config file : #{ENV['MYYOUPLOTRC']}"
+          puts parser.config.inspect
+        else
+          puts <<~EOS
+            You don't have a config file. The default config file paths are:
+            ./.youplot.yml, ./.youplotrc, ~/.youplot.yml, ~/.youplotrc
+            You can specify a config file with the environment variable MYYOUPLOTRC.
+            File format is YAML. For example:
+            width : 40
+            height : 20
+          EOS
+        end
+        return
+      end
+
       # progressive mode
       if options[:progressive]
         stop = false
@@ -63,9 +81,15 @@ 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 +159,12 @@ 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
@@ -169,7 +198,7 @@ module YouPlot
     def output_data(input)
       # Pass the input to subsequent pipelines
       case options[:pass]
-      when IO
+      when IO, StringIO
         options[:pass].print(input)
       else
         if options[:pass]

data/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
@@ -28,6 +29,55 @@ module YouPlot
       )
 
       @params = Parameters.new
+
+      if @config_file = find_config_file
+        ENV['MYYOUPLOTRC'] = @config_file
+        @config = read_config_file(config_file)
+        configure(config)
+      end
+    end
+
+    def candidate_paths
+      paths = []
+      paths << ENV['MYYOUPLOTRC'] if ENV['MYYOUPLOTRC']
+      paths << '.youplot.yml'
+      paths << '.youplotrc'
+      paths << File.join(ENV['HOME'], '.youplotrc') if ENV['HOME']
+      paths << File.join(ENV['HOME'], '.youplot.yml') if ENV['HOME']
+      paths
+    end
+
+    def find_config_file
+      config_file_path = nil
+      candidate_paths.each do |file|
+        path = File.expand_path(file)
+        if File.exist?(path)
+          config_file_path = path
+          break
+        end
+      end
+      config_file_path
+    end
+
+    def read_config_file(path)
+      require 'yaml'
+      YAML.load_file(path)
+    end
+
+    def configure(config)
+      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: #{k}"
+        end
+      end
     end
 
     def create_base_parser
@@ -58,13 +108,13 @@ module YouPlot
         parser.on('-t', '--title STR', String, 'print string on the top of plot') do |v|
           params.title = v
         end
-        parser.on('-x', '--xlabel STR', String, 'print string on the bottom of the plot') do |v|
+        parser.on('--xlabel STR', String, 'print string on the bottom of the plot') do |v|
           params.xlabel = v
         end
-        parser.on('-y', '--ylabel STR', String, 'print string on the far left of the plot') do |v|
+        parser.on('--ylabel STR', String, 'print string on the far left of the plot') do |v|
           params.ylabel = v
         end
-        parser.on('-w', '--width INT', Integer, 'number of characters per row') do |v|
+        parser.on('-w', '--width INT', Numeric, 'number of characters per row') do |v|
           params.width = v
         end
         parser.on('-h', '--height INT', Numeric, 'number of rows') do |v|
@@ -95,7 +145,7 @@ module YouPlot
         parser.on('-M', '--monochrome', TrueClass, 'no colouring even if writing to a tty') do |_v|
           UnicodePlot::IOContext.define_method(:color?) { false } # FIXME
         end
-        parser.on('--encoding STR', String, 'Specify the input encoding') do |v|
+        parser.on('--encoding STR', String, 'specify the input encoding') do |v|
           options[:encoding] = v
         end
         # Optparse adds the help option, but it doesn't show up in usage.
@@ -118,7 +168,7 @@ module YouPlot
 
           Program: YouPlot (Tools for plotting on the terminal)
           Version: #{YouPlot::VERSION} (using UnicodePlot #{UnicodePlot::VERSION})
-          Source:  https://github.com/kojix2/youplot
+          Source:  https://github.com/red-data-tools/YouPlot
 
           Usage:   uplot <command> [options] <in.tsv>
 
@@ -130,10 +180,9 @@ module YouPlot
               scatter    s             draw a scatter plot
               density    d             draw a density plot
               boxplot    box           draw a horizontal boxplot
-              colors     color         show the list of available colors
-
               count      c             draw a baplot based on the number of
                                        occurrences (slow)
+              colors     color         show the list of available colors
 
           General options:
               --help                   print command specific help menu
@@ -171,13 +220,13 @@ module YouPlot
 
     def sub_parser_add_xlim
       sub_parser.on_head('--xlim FLOAT,FLOAT', Array, 'plotting range for the x coordinate') do |v|
-        params.xlim = v
+        params.xlim = v.map(&:to_f)
       end
     end
 
     def sub_parser_add_ylim
       sub_parser.on_head('--ylim FLOAT,FLOAT', Array, 'plotting range for the y coordinate') do |v|
-        params.ylim = v
+        params.ylim = v.map(&:to_f)
       end
     end
 
@@ -278,6 +327,8 @@ module YouPlot
           options[:color_names] = v
         end
 
+      when :config
+
       else
         error_message = "uplot: unrecognized command '#{command}'"
         if YouPlot.run_as_executable?

data/lib/youplot/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module YouPlot
-  VERSION = '0.4.1'
+  VERSION = '0.4.4'
 end

data/lib/youplot.rb

@@ -6,6 +6,12 @@ require_relative 'youplot/parameters'
 require_relative 'youplot/command'
 
 module YouPlot
+  # @run_as_executable = true / false
+  # YouPlot behaves slightly differently when run as a command line tool
+  # and when run as a script (e.g. for testing). In the event of an error,
+  # when run as a command line tool, YouPlot will display a short error message
+  # and exit abnormally. When run as a script, it will just raise an error.
+  @run_as_executable = false
   class << self
     attr_accessor :run_as_executable
 
@@ -13,5 +19,4 @@ module YouPlot
       @run_as_executable
     end
   end
-  @run_as_executable = false
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: youplot
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.4.4
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2021-06-03 00:00:00.000000000 Z
+date: 2022-08-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: unicode_plot
@@ -16,84 +16,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.0.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rubocop
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: simplecov
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: test-unit
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.0.5
 description: A command line tool for Unicode Plotting
 email:
 - 2xijok@gmail.com
@@ -116,7 +46,7 @@ files:
 - lib/youplot/parameters.rb
 - lib/youplot/parser.rb
 - lib/youplot/version.rb
-homepage: https://github.com/kojix2/youplot
+homepage: https://github.com/red-data-tools/YouPlot
 licenses:
 - MIT
 metadata: {}
@@ -135,7 +65,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.15
+rubygems_version: 3.3.7
 signing_key: 
 specification_version: 4
 summary: A command line tool for Unicode Plotting