but 0.1.2 → 0.1.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 853bfa5259d6c243f2728c71d7dd1575914cb38a29c1b40dcf39b78833fd670f
-  data.tar.gz: b4d65cf498abbc277d1ec5280d6de2542a48810ac20f58f36c449dbf3410f493
+  metadata.gz: abd129d50d267af66d41279fbb6ae787a66110f1ad1f16953a1bead04b377bc9
+  data.tar.gz: 23264ed3f2984516b6dee0e4580cb7310ab6776935d0499bf85153b35ba38f61
 SHA512:
-  metadata.gz: b90007c89eaa18486ebae63374caa47c3b32526fc58ac90b48542e0aa0cb67253caaf2336d56331218f84a7e319a023738718c1dc16a61c85ddef6937f93e68b
-  data.tar.gz: 74ea9639c7aaaaf9bf06db499e3031d97b3e48ccf332d9aa699ea18e93b7ad257a5065bf451018dce7672a02e045e75e5d50c488e776ff87b3fe73456e7536ca
+  metadata.gz: 17d68c15cdb023b8551ce7dce30a512662db12292eabfb8d8d7a91512b5e325739916dc9f495e43002c391599f872f8d77e94bcdbc1c9ea45906c1881f2da495
+  data.tar.gz: dfe73f4d8d3bda17e89b24f84b24e6039db08137e432eccc9d3bc1bdf8beca2dfce84961c2d9742630b77a88abc48b36f8cba85c3fafd774131175967a1caf2a

data/Gemfile.lock

@@ -1,8 +1,10 @@
 PATH
   remote: .
   specs:
-    but (0.1.2)
+    but (0.1.7)
       colorize
+      ruby-prof
+      ruby-progressbar
       thor
 
 GEM
@@ -129,6 +131,7 @@ GEM
       unicode-display_width (>= 1.4.0, < 2.0)
     rubocop-ast (0.0.3)
       parser (>= 2.7.0.1)
+    ruby-prof (1.4.1)
     ruby-progressbar (1.10.1)
     shellany (0.0.1)
     sys-uname (1.2.1)

data/README.md

@@ -95,9 +95,42 @@ After checking out the repo, run `bin/setup` to install dependencies. Then, run
 
 To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
 
+### Benchmarking and Profiling
+
+#### Benchmarking
+
+Each subcommand can be benchmarked by
+
+```
+### Garbage collector enabled
+but command subcommand --measure --gc
+
+#or
+
+### Garbage collector disabled
+but command subcommand --measure --nogc
+```
+
+#### Profiling
+
+Each subcommand can be profiled using ruby prof
+
+```
+but command --profile <MEASURING METHOD>
+```
+
+where possible options are
+
+```
+but command --profile WALL_TIME
+but command --profile PROCESS_TIME
+but command --profile ALLOCATIONS
+but command --profile MEMORY
+```
+
 ### Contributing
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/but. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+Bug reports and pull requests are welcome on GitLab at https://git.computational.bio.uni-giessen.de/rmueller/bcf_user_tools. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
 
 ### License
 
@@ -105,5 +138,5 @@ The gem is available as open source under the terms of the [MIT License](https:/
 
 ### Code of Conduct
 
-Everyone interacting in the But project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/but/blob/master/CODE_OF_CONDUCT.md).
+Everyone interacting in the But project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://git.computational.bio.uni-giessen.de/rmueller/bcf_user_tools/-/blob/master/CODE_OF_CONDUCT.md).
 

data/but.gemspec

@@ -9,6 +9,7 @@ Gem::Specification.new do |spec|
   spec.email         = ["raphael.mueller@computational.bio.uni-giessen.de"]
   spec.homepage    = 'https://git.computational.bio.uni-giessen.de/rmueller/bcf_user_tools'
   spec.license       = "MIT"
+  spec.required_ruby_version = '>=2.6.0'
   spec.summary     = "Tools, to help users to improve their experience with the BCF infrastructure."
   spec.description = "BCF admins have a hard live. Their user's don't keep their $HOMES and other working places clean. It appears that some users don't know that they use too much space in their home or don't clean used directories on cluster (or other) machines. This tools helps users find unused and unwanted directories, which could make BCF admins happier."
 
@@ -48,6 +49,8 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency 'thor'
   spec.add_dependency 'colorize'
+  spec.add_dependency 'ruby-prof'
+  spec.add_dependency 'ruby-progressbar'
 
 
   spec.metadata    = { "source_code_uri" => "https://git.computational.bio.uni-giessen.de/rmueller/bcf_user_tools" }

data/lib/but/cli.rb

@@ -17,6 +17,7 @@ module But
   class How < Thor
     class_option :measure, :type => :boolean, :default => false
     class_option :gc, :type => :boolean, :default => true
+    class_option :profile, :aliases => '-p', required: false, desc: 'create a ruby prof profile; Possible values: MEMORY, ALLOCATIONS, WALL_TIME, PROCESS_TIME'
 
     desc "messy am I?", "How messed up is your home?"
     def messy(*words)
@@ -24,6 +25,10 @@ module But
         measure(options) do
           say But::HomeKeeper.judge
         end
+      elsif options[:profile]
+        profile(options) do
+          say But::HomeKeeper.judge
+        end
       else
         say But::HomeKeeper.judge
       end

data/lib/but/dev_wrapper.rb

@@ -1,5 +1,7 @@
 require "json"
 require "benchmark"
+require "rubygems"
+require "ruby-prof"
 
 #inspired by Ruby Performance Optimization: Alexander Dymo
 def measure(options={}, &block)
@@ -31,3 +33,36 @@ def measure(options={}, &block)
     }
   }.to_json)
 end
+
+
+def profile(options={}, &block)
+  measure_mode = options[:profile].upcase
+  RubyProf.measure_mode = RubyProf.const_get(measure_mode)
+
+  case measure_mode
+  when "WALL_TIME" 
+    GC.disable
+  when "PROCESS_TIME" 
+    GC.disable
+  when "ALLOCATIONS" 
+    #GC.enable_stats
+  when "MEMORY" 
+    #GC.enable_stats
+  else
+  end
+
+  result = RubyProf.profile do
+    yield
+  end
+
+  printer_g = RubyProf::GraphHtmlPrinter.new(result)
+  printer_f = RubyProf::FlatPrinter.new(result)
+  printer_c = RubyProf::CallTreePrinter.new(result)
+  unless measure_mode == "MEMORY"
+    printer_g.print(File.open(measure_mode + "_graph.html","w"))
+    printer_f.print(File.open(measure_mode + "_flat.txt","w"))
+  end
+  printer_c.print(options)
+
+  puts "Profiles written for #{measure_mode}"
+end

data/lib/but/home_keeper.rb

@@ -1,9 +1,11 @@
 require 'open3'
 require 'tempfile'
 require 'colorize'
+require 'ruby-progressbar'
 
 module But
   module HomeKeeper
+    BLOCK_SIZE = 1024
 
     def self.info(options = {})
       file = ENV['BUTHOMEKEEPER'] || create_disk_usage_file(options)
@@ -21,22 +23,68 @@ module But
       end
     end
 
+    def self.all_eof(files)
+      files.find { |f| !f.eof }.nil?
+    end
 
     # Q: is $HOME always set?
     def self.create_disk_usage_file(options = {})
       tmpfile = ::Tempfile.new("diskusage")
       dir = options[:dir] || ENV['HOME']
-      ::Open3.popen3("du","-d 0", dir) do |stdin, stdout, stderr, wait_thr|
 
-        if wait_thr.value != 0
-          STDERR.write "Exitcode: #{wait_thr.value}\n".light_black
-          STDERR.write stderr.gets(nil).light_black
+      total_lines = `ls -d ~/.*/ ~/*/ | wc -l`.to_i
+      #puts total_lines
+      progressbar = ProgressBar.create(title: "inspecting #{dir}", total: total_lines , 
+                                       :format         => "%a %c/%C %b\u{15E7}%i %p%% %t",
+                                       :progress_mark  => ' ',
+                                       :remainder_mark => "\u{FF65}",
+                                      )
+
+      ::Open3.popen3("du","-d 1", dir) do |stdin, stdout, stderr, wait_thr|
+        # inspired by from https://gist.github.com/chrisn/7450808
+
+        stdin.close_write
+        begin
+          files = [stdout, stderr]
+          until all_eof(files) do
+            ready = IO.select(files)
+            progressbar.refresh
+
+            if ready
+              readable = ready[0]
+              readable.each do |f|
+                fileno = f.fileno
+
+                begin
+                  data = f.read_nonblock(BLOCK_SIZE)
+
+                  #puts "fileno: #{fileno}, data: #{data.inspect}"
+                  progressbar.progress += data.lines.count
+                  progressbar.title = "just completed: %s" % data.split(/\s+/).last
+                  tmpfile.write(data)
+                rescue EOFError => e
+                  #puts "fileno: #{fileno} EOF"
+                  files.delete f
+                end
+              end
+            end
+          end
+        rescue IOError => e
+          puts "IOError: #{e}"
         end
 
-        tmpfile.write(stdout.gets(nil))
+
+        #if wait_thr.value != 0
+        #  STDERR.write "Exitcode: #{wait_thr.value}\n".light_black
+        #  STDERR.write stderr.gets(nil).light_black
+        #end
+
+        #tmpfile.write(stdout.gets(nil))
       end
+      progressbar.finish
       tmpfile.rewind
       return tmpfile.path
     end
+
   end
 end

data/lib/but/version.rb

@@ -1,3 +1,3 @@
 module But
-  VERSION = "0.1.2"
+  VERSION = "0.1.7"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: but
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.7
 platform: ruby
 authors:
 - Raphael Müller
@@ -178,6 +178,34 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: ruby-prof
+  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: ruby-progressbar
+  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'
 description: BCF admins have a hard live. Their user's don't keep their $HOMES and
   other working places clean. It appears that some users don't know that they use
   too much space in their home or don't clean used directories on cluster (or other)
@@ -229,7 +257,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 2.6.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="