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RinRuby is a Ruby library that integrates the R interpreter in Ruby, making R's statistical routines and graphics available within Ruby. The library consists of a single Ruby script that is simple to install and does not require any special compilation or installation of R. Since the library is 100% pure Ruby, it works on a variety of operating systems, Ruby implementations, and versions of R. RinRuby's methods are simple, making for readable code. The {website [rinruby.ddahl.org]}[http://rinruby.ddahl.org] describes RinRuby usage, provides comprehensive documentation, gives several examples, and discusses RinRuby's implementation.

Provides SMTP STARTTLS support for Ruby 1.8.6 (built-in for 1.8.7+). Simply require 'smtp_tls' and use the Net::SMTP#enable_starttls method to talk to servers that use STARTTLS. require 'net/smtp' begin require 'smtp_tls' rescue LoadError end smtp = Net::SMTP.new address, port smtp.enable_starttls smtp.start Socket.gethostname, user, password, authentication do |server| server.send_message message, from, to end You can also test your SMTP connection settings using mail_smtp_tls: $ date | ruby -Ilib bin/mail_smtp_tls smtp.example.com submission \ "your username" "your password" plain \ from@example.com to@example.com Using SMTP_TLS 1.0.3 -> "220 smtp.example.com ESMTP XXX\r\n" <- "EHLO you.example.com\r\n" -> "250-smtp.example.com at your service, [192.0.2.1]\r\n" -> "250-SIZE 35651584\r\n" -> "250-8BITMIME\r\n" -> "250-STARTTLS\r\n" -> "250-ENHANCEDSTATUSCODES\r\n" -> "250 PIPELINING\r\n" <- "STARTTLS\r\n" -> "220 2.0.0 Ready to start TLS\r\n" TLS connection started <- "EHLO you.example.com\r\n" -> "250-smtp.example.com at your service, [192.0.2.1]\r\n" -> "250-SIZE 35651584\r\n" -> "250-8BITMIME\r\n" -> "250-AUTH LOGIN PLAIN\r\n" -> "250-ENHANCEDSTATUSCODES\r\n" -> "250 PIPELINING\r\n" <- "AUTH PLAIN BASE64_STUFF_HERE\r\n" -> "235 2.7.0 Accepted\r\n" <- "MAIL FROM:<from@example.com>\r\n" -> "250 2.1.0 OK XXX\r\n" <- "RCPT TO:<to@example.com>\r\n" -> "250 2.1.5 OK XXX\r\n" <- "DATA\r\n" -> "354 Go ahead XXX\r\n" writing message from String wrote 91 bytes -> "250 2.0.0 OK 1247028988 XXX\r\n" <- "QUIT\r\n" -> "221 2.0.0 closing connection XXX\r\n" This will connect to smtp.example.com using the submission port (port 587) with a username and password of "your username" and "your password" and authenticate using plain-text auth (the submission port always uses SSL) then send the current date to to@example.com from from@example.com. Debug output from the connection will be printed on stderr.

RinRuby is a Ruby library that integrates the R interpreter in Ruby, making R's statistical routines and graphics available within Ruby. The library consists of a single Ruby script that is simple to install and does not require any special compilation or installation of R. Since the library is 100% pure Ruby, it works on a variety of operating systems, Ruby implementations, and versions of R. RinRuby's methods are simple, making for readable code. The {website [rinruby.ddahl.org]}[http://rinruby.ddahl.org] describes RinRuby usage, provides comprehensive documentation, gives several examples, and discusses RinRuby's implementation.

Galaaz brings the power of R to the Ruby community. Galaaz is based on TruffleRuby and FastR, GraalVM-based interpreters for Ruby and the R language for statistical computing respectively. Over the past two decades, the R language for statistical computing has emerged as the de facto standard for analysts, statisticians, and scientists. Today, a wide range of enterprises – from pharmaceuticals to insurance – depend on R for key business uses. FastR is a new implementation of the R language and environment for the Graal Virtual Machine. Galaaz tightly couples Ruby and R and allows the use of R inside a Ruby script. In a sense, Galaaz is similar to other solutions such as RinRuby, Rpy2, PipeR, and reticulate (https://blog.rstudio.com/2018/03/26/reticulate-r-interface-to-python/). However, since Galaaz couples TruffleRuby and FastR that both target the JVM there is no need to integrate both solutions and there is no need to send data between Ruby and R, as it all resides in the same VM. Further, installation of Galaaz does not require the installation of GNU R. When installing GraalVM, just install TruffleRuby and FastR.

A few graphic scripts can load below. No need "gruff". You can use "gnuplot","R",or some useful graphic aplications.) require "agri-controller/gruff"

Ruby script for data-mining biostars.org using web-crawling techniques as well as utilizing the Biostars RESTful API. Statistical analysis requires R (http://www.r-project.org).

Find the path for a given gem or require path for editing or greping. For examples, under [fish](http://fishshell.com/): cd (gem path gem-path) vim (gem path gem-path) grep require -R (gem path gem-path) Or checkout [gem-eit][], [gem-grep][] for shorthands. [gem-eit]: https://github.com/godfat/gem-eit [gem-grep]: https://github.com/godfat/gem-grep

RinRuby is a Ruby library that integrates the R interpreter in Ruby, making R's statistical routines and graphics available within Ruby. The library consists of a single Ruby script that is simple to install and does not require any special compilation or installation of R. Since the library is 100% pure Ruby, it works on a variety of operating systems, Ruby implementations, and versions of R. RinRuby's methods are simple, making for readable code. The {website [rinruby.ddahl.org]}[http://rinruby.ddahl.org] describes RinRuby usage, provides comprehensive documentation, gives several examples, and discusses RinRuby's implementation.

== ABOUT A simple program and library to conjugate french verbs. Parses responses to requests to an online reference site. === Executable ConjugateFR comes with the executable binary +conjugatefr+. To view information about it's supported arguments, run conjugatefr --help === Custom Renderers To make a custom renderer, just type require conjugatefr/renderer and then make a class that extends +Renderer+. An example is as follows: require 'conjugatefr/renderer' class ExampleRenderer < Renderer def pre puts "This goes before the words." end def word (name, words) print "#{name}:" words.each do |word| print " #{word}" end end def post puts "This goes after the words." end def description; "Renders an example format."; end end # Add to the Renderers list (For CLI and other programs that use it.) $renderers["Example"] = ExampleRenderer.new To try this out, save it as +erend.rb+ and then run: conjugatefr -R ./erend.rb -r Example It will produce the output: This goes before the words. someword: someconjugation etc etc ... (more words will be here) This goes after the words. === The Library The library can be included with +require conjugatefr+. It includes the +ConjugateFR+ class.

The DevCreek gem enables programmers to collect and transmit metrics from their Ruby Test::Unit and RSpec test suites to a DevCreek server. Please visit the DevCreek site (http://devcreek.com/index.html) for more info. == FEATURES/PROBLEMS: Supported frameworks include Test::Unit and RSpec (> 1.10). == SYNOPSIS: The DevCreek Ruby Gem is library that, when loaded, will automatically listen to and collect metrics from your Test::Unit/RSpec unit tests. All you have to do is load the DevCreek library in your code and give it your DevCreek account info so that it can transmit the metrics to the server. Here is the simplest example of how to load DevCreek: -------- #Load the devcreek gem require 'rubygems' require 'devcreek' #set your account info DevCreek::Core.instance().load_from_yaml("#{ENV['HOME']}/.yoursettingsfile.devcreek.yml") -------- There are two ways to provide DevCreek with your account settings. The first (as shown above) is to point DevCreek to a settings file. The 'enabled' attribute tells devcreek whether or not it should actually transmit the metrics that it collects. The yaml file would like this: -------- user: your_devcreek_username password: your_devcreek_password project: your_devcreek_project enabled: true -------- The other way to provide DevCreek with your settings is via a hash. So, instead of loading a yaml file, you could do this: -------- #Load the devcreek gem require 'rubygems' require 'devcreek' #set your account info DevCreek::Core.instance().load( :user => 'your_devcreek_username', :password => 'your_devcreek_password', :project => 'your_devcreek_project', :enabled => true ) -------- The first method is preferrable because it allows you to keep your account settings outside of your project (and therefore your source control tool). If you only have 1 test file, you can place the code to load devcreek in the test file and your done. However, most projects will have many test files. In this case, you need to make sure that the Ruby interpreter loads devcreek before running the test classes. This can be done via the Ruby '-r' option. For example, assuming your code to load devcreek is in a file called foo.rb, you would run your tests from the command line like this: ruby -r foo.rb test/test_* If you run your tests from a Rakefile, then you need to tell rake to include the -r option when it runs the tests (rake runs it's tests in a separate Ruby process). You can do this pretty easily in your Rakefile, like so; -------- require 'rake/testtask' Rake::TestTask.new('all_tests') do |t| t.ruby_opts = ['-r foo.rb'] t.test_files = ['test/test_*.rb'] end --------

= Webservice Client Library for InterMine Data-Warehouses This library provides an interface to the InterMine webservices API. It makes construction and execution of queries more straightforward, safe and convenient, and allows for results to be used directly in Ruby code. As well as traditional row based access, the library provides an object-orientated record result format (similar to ActiveRecords), and allows for fast, memory efficient iteration of result sets. == Example Get all protein domains associated with a set of genes and print their names: require "intermine/service" Service.new("www.flymine.org/query"). new_query("Pathway") select(:name). where("genes.symbol" => ["zen", "hox", "h", "bib"]). each_row { |row| puts row[:name]} == Who is this for? InterMine data warehouses are typically constructed to hold Biological data, and as this library facilitates programmatic access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services may find it especially useful: * FlyMine (http://www.flymine.org/query) * YeastMine (http://yeastmine.yeastgenome.org/yeastmine) * RatMine (http://ratmine.mcw.edu/ratmine) * modMine (http://intermine.modencode.org/release-23) * metabolicMine (http://www.metabolicmine.org/beta) == How to use this library: We have tried to construct an interface to this library that does not require you to learn an entirely new set of concepts. As such, as well as the underlying methods that are common to all libraries, there is an additional set of aliases and sugar methods that emulate the DSL style of SQL: === SQL style service = Service.new("www.flymine.org/query") service.model. table("Gene"). select("*", "pathways.*"). where(:symbol => "zen"). order_by(:symbol). outerjoin(:pathways). each_row do |r| puts r end === Common InterMine interface service = Service.new("www.flymine.org/query") query = service.new_query("Gene") query.add_views("*", "pathways.*") query.add_constraint("symbol", "=", "zen") query.add_sort_order(:symbol) query.add_join(:pathways) query.each_row do |r| puts r end For more details, see the accompanying documentation and the unit tests for interface examples. Further documentation is available at www.intermine.org. == Support Support is available on our development mailing list: dev@intermine.org == License This code is Open Source under the LGPL. Source code for this gem can be checked out from https://github.com/intermine/intermine-ws-ruby

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