youplot 0.4.4 → 0.4.6

checksums.yaml

@@ -1,7 +1,7 @@
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data/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>
@@ -14,10 +14,28 @@
 
 ## 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
+```
+
 ## Quick Start
 
 <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>
@@ -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)

data/lib/youplot/command.rb

@@ -40,24 +40,6 @@ 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
@@ -178,9 +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])

data/lib/youplot/parser.rb

@@ -29,53 +29,59 @@ module YouPlot
       )
 
       @params = Parameters.new
+    end
 
-      if @config_file = find_config_file
-        ENV['MYYOUPLOTRC'] = @config_file
-        @config = read_config_file(config_file)
-        configure(config)
-      end
+    def apply_config_file
+      return if !config_file && find_config_file.nil?
+
+      read_config_file
+      configure
     end
 
-    def candidate_paths
+    def config_file_candidate_paths
+      # keep the order of the 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']
+      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_path = nil
-      candidate_paths.each do |file|
+      config_file_candidate_paths.each do |file|
         path = File.expand_path(file)
-        if File.exist?(path)
-          config_file_path = path
-          break
-        end
+        next unless File.exist?(path)
+
+        @config_file = path
+        ENV['MYYOUPLOTRC'] = path
+        return @config_file
       end
-      config_file_path
+      nil
     end
 
-    def read_config_file(path)
+    def read_config_file
       require 'yaml'
-      YAML.load_file(path)
+      @config = YAML.load_file(config_file)
     end
 
-    def configure(config)
+    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
+          @options[k] ||= v
         elsif param_members.include?(k)
-          @params[k] = v
+          @params[k] ||= v
         else
-          raise Error, "Unknown option/param: #{k}"
+          raise Error, "Unknown option/param in config file: #{k}"
         end
       end
     end
@@ -154,6 +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
@@ -180,11 +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
@@ -192,10 +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
@@ -265,10 +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
@@ -291,14 +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
@@ -327,16 +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
 
@@ -344,7 +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
 
@@ -353,7 +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

data/lib/youplot/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module YouPlot
-  VERSION = '0.4.4'
+  VERSION = '0.4.6'
 end

metadata

@@ -1,15 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: youplot
 version: !ruby/object:Gem::Version
-  version: 0.4.4
+  version: 0.4.6
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2022-08-02 00:00:00.000000000 Z
+date: 2024-07-20 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: csv
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: unicode_plot
   requirement: !ruby/object:Gem::Requirement
@@ -50,7 +64,7 @@ homepage: https://github.com/red-data-tools/YouPlot
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -58,15 +72,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.4.0
+      version: 2.5.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.7
-signing_key: 
+rubygems_version: 3.5.11
+signing_key:
 specification_version: 4
 summary: A command line tool for Unicode Plotting
 test_files: []