Results for style-r

Adapt between anstyle and roff

= 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

Parse and generate Portable Action Notation (PAN) strings for representing atomic actions in abstract strategy board games including chess, shogi, xiangqi, and others. PAN provides an intuitive operator-based syntax with six core operators: "-" (move to empty square), "+" (capture), "~" (special moves with side effects), "*" (drop to board), "." (drop with capture), and "=" (in-place transformation), plus "..." (pass turn). Supports coordinates via CELL specification and piece identifiers via EPIN specification. Handles transformations ("e7-e8=Q"), enhanced/diminished states ("+R", "-P"), and style derivation markers ("K'"). Provides comprehensive validation, immutable action objects, and functional API design. Examples: "e2-e4" (move), "d1+f3" (capture), "e1~g1" (castling), "P*e5" (drop), "e7-e8=Q" (promotion), "..." (pass), "+d4" (static capture), "e4=+P" (modify).

# Fancy Logger An easily customizable logger with style. ## Install ### Bundler: `gem 'fancy_logger'` ### RubyGems: `gem install fancy_logger` ## Usage Simply use as if you were using the normal Ruby `Logger` class: ```ruby require 'fancy_logger' logger = FancyLogger.new(STDOUT) logger.info "Hello" ``` ### Config The `config` instance method allows you to modify the configuration of the Logger within a DSL. Continuing with our last example: ```ruby logger.config do timestamp_format "%c" styles do info do foreground :yellow blink true end end end logger.debug 'Look here!' logger.info 'Doing things...' logger.warn 'Watch out!' logger.error 'Bad' logger.fatal 'VERY bad' logger.unknown 'Weird unknown stuff' ``` #### Output ![][output_example] ### Config ```ruby # The format of the timestamp in the log. Follows the strftime standards. timestamp_format "%F %r" # On the first logged message, FancyLogger will prepend a help message # containing a list of all the severities (debug, info, warn, etc) styled # according to your config as reference. # You can disable this by setting the below option to false. show_help_message true # Under styles, you have a configuration for each severity. # Each severity has a configuration with the following valid options: # Key: foreground # Value: # :default, :black, :red, :green, :yellow, :blue, :magenta, :cyan, :white # # Key: background # Value: # :default, :black, :red, :green, :yellow, :blue, :magenta, :cyan, :white # # Key: reset # Value: true or false # # Key: bright # Value: true or false # # Key: italic # Value: true or false # # Key: underline # Value: true or false # # Key: # blink # Value: true or false # # Key: inverse # Value: true or false # # Key: hide # Value: true or false styles do debug do foreground :black background :cyan end info do foreground :default background :default end warn do foreground :yellow background :default blink true end error do foreground :red background :default end fatal do foreground :black background :red bold true underline true end unknown do foreground :black background :white underline true end end ``` ## Contributing * Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet * Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it * Fork the project * Start or switch to a testing/unstable/feature/bugfix branch * Commit and push until you are happy with your contribution * Make sure to add tests for it. This is important so I don't break it in a future version unintentionally. * Please try not to mess with the Rakefile, VERSION or gemspec. ## Copyright Copyright © 2012 Ryan Scott Lewis <ryan@rynet.us>. The MIT License (MIT) - See LICENSE for further details. [output_example]: http://oi44.tinypic.com/sfwlkp.jpg

Ame Ame provides a simple command-line interface API for Ruby¹. It can be used to provide both simple interfaces like that of ‹rm›² and complex ones like that of ‹git›³. It uses Ruby’s own classes, methods, and argument lists to provide an interface that is both simple to use from the command-line side and from the Ruby side. The provided command-line interface is flexible and follows commond standards for command-line processing. ¹ See http://ruby-lang.org/ ² See http://pubs.opengroup.org/onlinepubs/9699919799/utilities/rm.html ³ See http://git-scm.com/docs/ § Usage Let’s begin by looking at two examples, one where we mimic the POSIX¹ command-line interface to the ‹rm› command. Looking at the entry² in the standard, ‹rm› takes the following options: = -f. = Do not prompt for confirmation. = -i. = Prompt for confirmation. = -R. = Remove file hierarchies. = -r. = Equivalent to /-r/. It also takes the following arguments: = FILE. = A pathname or directory entry to be removed. And actually allows one or more of these /FILE/ arguments to be given. We also note that the ‹rm› command is described as a command to “remove directory entries”. ¹ See http://pubs.opengroup.org/onlinepubs/9699919799/utilities/contents.html ² See http://pubs.opengroup.org/onlinepubs/9699919799/utilities/rm.html Let’s turn this specification into one using Ame’s API. We begin by adding a flag for each of the options listed above: class Rm &lt; Ame::Root flag 'f', '', false, 'Do not prompt for confirmation' flag 'i', '', nil, 'Prompt for confirmation' do |options| options['f'] = false end flag 'R', '', false, 'Remove file hierarchies' flag 'r', '', nil, 'Equivalent to -R' do |options| options['r'] = true end A flag¹ is a boolean option that doesn’t take an argument. Each flag gets a short and long name, where an empty name means that there’s no corresponding short or long name for the flag, a default value (true, false, or nil), and a description of what the flag does. Each flag can also optionally take a block that can do further processing. In this case we use this block to modify the Hash that maps option names to their values passed to the block to set other flags’ values than the ones that the block is associated with. As these flags (‘i’ and ‘r’) aren’t themselves of interest, their default values have been set to nil, which means that they won’t be included in the Hash that maps option names to their values when passed to the method. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#flag-class-method There are quite a few other kinds of options besides flags that can be defined using Ame, but flags are all that are required for this example. We’ll get to the other kinds in later examples. Next we add a “splus” argument. splus 'FILE', String, 'File to remove' A splus¹ argument is like a Ruby “splat”, that is, an Array argument at the end of the argument list to a method preceded by a star, except that a splus requires at least one argument. A splus argument gets a name for the argument (‹FILE›), the type of argument it represents (String), and a description. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#splus-class-method Then we add a description of the command (method) itself: description 'Remove directory entries' Descriptions¹ will be used in help output to assist the user in using the command. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#description-class-method Finally, we add the Ruby method that’ll implement the command (all preceding code included here for completeness): class Rm &lt; Ame::Root version '1.0.0' flag 'f', '', false, 'Do not prompt for confirmation' flag 'i', '', nil, 'Prompt for confirmation' do |options| options['f'] = false end flag 'R', '', false, 'Remove file hierarchies' flag 'r', '', nil, 'Equivalent to -R' do |options| options['r'] = true end splus 'FILE', String, 'File to remove' description 'Remove directory entries' def rm(files, options = {}) require 'fileutils' FileUtils.send options['R'] ? :rm_r : :rm, [first] + rest, :force =&gt; options['f'] end end Actually, another bit of code was also added, namely version '1.0.0' This sets the version¹ String of the command. This information is used when the command is invoked with the “‹--version›” flag. This flag is automatically added, so you don’t need to add it yourself. Another flag, “‹--help›”, is also added automatically. When given, this flag’ll make Ame output usage information of the command. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#version-class-method To actually run the command, all you need to do is invoke Rm.process This’ll invoke the command using the command-line arguments stored in ‹ARGV›, but you can also specify other ones if you want to: Rm.process 'rm', %w[-r /tmp/*] The first argument to #process¹ is the name of the method to invoke, which defaults to ‹File.basename($0)›, and the second argument is an Array of Strings that should be processed as command-line arguments passed to the command. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#process-class-method If you’d store the complete ‹Rm› class defined above in a file called ‹rm› and add ‹#! /usr/bin/ruby -w› at the beginning and ‹Rm.process› at the end, you’d have a fully functional ‹rm› command (after making it executable). Let’s see it in action: % rm --help Usage: rm [OPTIONS]... FILE... Remove directory entries Arguments: FILE... File to remove Options: -R Remove file hierarchies -f Do not prompt for confirmation --help Display help for this method -i Prompt for confirmation -r Equivalent to -R --version Display version information % rm --version rm 1.0.0 Some commands are more complex than ‹rm›. For example, ‹git›¹ has a rather complex command-line interface. We won’t mimic it all here, but let’s introduce the rest of the Ame API using a fake ‹git› clone as an example. ¹ See http://git-scm.com/docs/ ‹Git› uses sub-commands to achieve most things. Implementing sub-commands with Ame is done using a “dispatch”. We’ll discuss dispatches in more detail later, but suffice it to say that a dispatch delegates processing to a child class that’ll handle the sub-command in question. We begin by defining our main ‹git› command using a class called ‹Git› under the ‹Git::CLI› namespace: module Git end class Git::CLI &lt; Ame::Root version '1.0.0' class Git &lt; Ame::Class description 'The stupid content tracker' def initialize; end We’re setting things up to use the ‹Git› class as a dispatch in the ‹Git::CLI› class. The description on the ‹initialize› method will be used as a description of the ‹git› dispatch command itself. Next, let’s add the ‹format-patch›¹ sub-command: description 'Prepare patches for e-mail submission' flag ?n, 'numbered', false, 'Name output in [PATCH n/m] format' flag ?N, 'no-numbered', nil, 'Name output in [PATCH] format' do |options| options['numbered'] = false end toggle ?s, 'signoff', false, 'Add Signed-off-by: line to the commit message' switch '', 'thread', 'STYLE', nil, Ame::Types::Enumeration[:shallow, :deep], 'Controls addition of In-Reply-To and References headers' flag '', 'no-thread', nil, 'Disables addition of In-Reply-To and Reference headers' do |options, _| options.delete 'thread' end option '', 'start-number', 'N', 1, 'Start numbering the patches at N instead of 1' multioption '', 'to', 'ADDRESS', String, 'Add a To: header to the email headers' optional 'SINCE', 'N/A', 'Generate patches for commits after SINCE' def format_patch(since = '', options = {}) p since, options end ¹ See http://git-scm.com/docs/git-format-patch/ We’re using quite a few new Ame commands here. Let’s look at each in turn: toggle ?s, 'signoff', false, 'Add Signed-off-by: line to the commit message' A “toggle”¹ is a flag that also has an inverse. Beyond the flags ‘s’ and “signoff”, the toggle also defines “no-signoff”, which will set “signoff” to false. This is useful if you want to support configuration files that set “signoff”’s default to true, but still allow it to be overridden on the command line. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#toggle-class-method When using the short form of a toggle (and flag and switch), multiple ones may be juxtaposed after the initial one. For example, “‹-sn›” is equivalent to “‹-s -n›” to “git format-patch›”. switch '', 'thread', 'STYLE', nil, Ame::Types::Enumeration[:shallow, :deep], 'Controls addition of In-Reply-To and References headers' A “switch”¹ is an option that takes an optional argument. This allows you to have separate defaults for when the switch isn’t present on the command line and for when it’s given without an argument. The third argument to a switch is the name of the argument. We’re also introducing a new concept here in ‹Ame::Types::Enumeration›. An enumeration² allows you to limit the allowed input to a set of Symbols. An enumeration also has a default value in the first item to its constructor (which is aliased as ‹.[]›). In this case, the “thread” switch defaults to nil, but, when given, will default to ‹:shallow› if no argument is given. If an argument is given it must be either “shallow” or “deep”. A switch isn’t required to take an enumeration as its argument default and can take any kind of default value for its argument that Ame knows how to handle. We’ll look at this in more detail later, but know that the type of the default value will be used to inform Ame how to parse a command-line argument into a Ruby value. An argument to a switch must be given, in this case, as “‹--thread=deep›” on the command line. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#switch-class-method ² See http://disu.se/software/ame-1.0/api/user/Ame/Types/Enumeration/ option '', 'start-number', 'N', 1, 'Start numbering the patches at N instead of 1' An “option”¹ is an option that takes an argument. The argument must always be present and may be given, in this case, as “‹--start-number=2›” or “‹--start-number 2›” on the command line. For a short-form option, anything that follows the option is seen as an argument, so assuming that “start-number” also had a short name of ‘S’, “‹-S2›” would be equivalent to “‹-S 2›”, which would be equivalent to “‹--start-number 2›”. Note that “‹-snS2›” would still work as expected. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#option-class-method multioption '', 'to', 'ADDRESS', String, 'Add a To: header to the email headers' A “multioption”¹ is an option that takes an argument and may be repeated any number of times. Each argument will be added to an Array stored in the Hash that maps option names to their values. Instead of taking a default argument, it takes a type for the argument (String, in this case). Again, types are used to inform Ame how to parse command-line arguments into Ruby values. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#multioption-class-method optional 'SINCE', 'N/A', 'Generate patches for commits after SINCE' An “optional”¹ argument is an argument that isn’t required. If it’s not present on the command line it’ll get its default value (the String ‹'N/A'›, in this case). ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#optional-class-method We’ve now covered all kinds of options and one new kind of argument. There are three more types of argument (one that we’ve already seen and two new) that we’ll look into now: “argument”, “splat”, and “splus”. description 'Annotate file lines with commit information' argument 'FILE', String, 'File to annotate' def annotate(file) p file end An “argument”¹ is an argument that’s required. If it’s not present on the command line, an error will be raised (and by default reported to the terminal). As it’s required, it doesn’t take a default, but rather a type. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#argument-class-method description 'Add file contents to the index' splat 'PATHSPEC', String, 'Files to add content from' def add(paths) p paths end A “splat”¹ is an argument that’s not required, but may be given any number of times. The type of a splat is the type of one argument and the type of a splat as a whole is an Array of values of that type. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#splat-class-method description 'Display gitattributes information' splus 'PATHNAME', String, 'Files to list attributes of' def check_attr(paths) p paths end A “splus”¹ is an argument that’s required, but may also be given any number of times. The type of a splus is the type of one argument and the type of a splus as a whole is an Array of values of that type. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#splus-class-method Now that we’ve seen all kinds of options and arguments, let’s look on an additional tool at our disposal, the dispatch¹. class Remote &lt; Ame::Class description 'Manage set of remote repositories' def initialize; end description 'Shows a list of existing remotes' flag 'v', 'verbose', false, 'Show remote URL after name' def list(options = {}) p options end description 'Adds a remote named NAME for the repository at URL' argument 'name', String, 'Name of the remote to add' argument 'url', String, 'URL to the repository of the remote to add' def add(name, url) p name, url end end ¹ See http://disu.se/software/ame-1.0/api/user/Ame/Class#dispatch-class-method Here we’re defining a child class to Git::CLI::Git called “Remote” that doesn’t introduce anything new. Then we set up the dispatch: dispatch Remote, :default =&gt; 'list' This adds a method called “remote” to Git::CLI::Git that will dispatch processing of the command line to an instance of the Remote class when “‹git remote›” is seen on the command line. The “remote” method expects an argument that’ll be used to decide what sub-command to execute. Here we’ve specified that in the absence of such an argument, the “list” method should be invoked. We add the same kind of dispatch to Git under Git::CLI: dispatch Git and then we’re done. Here’s all the previous code in its entirety: module Git end class Git::CLI &lt; Ame::Root version '1.0.0' class Git &lt; Ame::Class description 'The stupid content tracker' def initialize; end description 'Prepare patches for e-mail submission' flag ?n, 'numbered', false, 'Name output in [PATCH n/m] format' flag ?N, 'no-numbered', nil, 'Name output in [PATCH] format' do |options| options['numbered'] = false end toggle ?s, 'signoff', false, 'Add Signed-off-by: line to the commit message' switch '', 'thread', 'STYLE', nil, Ame::Types::Enumeration[:shallow, :deep], 'Controls addition of In-Reply-To and References headers' flag '', 'no-thread', nil, 'Disables addition of In-Reply-To and Reference headers' do |options, _| options.delete 'thread' end option '', 'start-number', 'N', 1, 'Start numbering the patches at N instead of 1' multioption '', 'to', 'ADDRESS', String, 'Add a To: header to the email headers' optional 'SINCE', 'N/A', 'Generate patches for commits after SINCE' def format_patch(since = '', options = {}) p since, options end description 'Annotate file lines with commit information' argument 'FILE', String, 'File to annotate' def annotate(file) p file end description 'Add file contents to the index' splat 'PATHSPEC', String, 'Files to add content from' def add(paths) p paths end description 'Display gitattributes information' splus 'PATHNAME', String, 'Files to list attributes of' def check_attr(paths) p paths end class Remote &lt; Ame::Class description 'Manage set of remote repositories' def initialize; end description 'Shows a list of existing remotes' flag 'v', 'verbose', false, 'Show remote URL after name' def list(options = {}) p options end description 'Adds a remote named NAME for the repository at URL' argument 'name', String, 'Name of the remote to add' argument 'url', String, 'URL to the repository of the remote to add' def add(name, url) p name, url end end dispatch Remote, :default =&gt; 'list' end dispatch Git end If we put this code in a file called “git” and add ‹#! /usr/bin/ruby -w› at the beginning and ‹Git::CLI.process› at the end, you’ll have a very incomplete git command-line interface on your hands. Let’s look at what some of its ‹--help› output looks like: % git --help Usage: git [OPTIONS]... METHOD [ARGUMENTS]... The stupid content tracker Arguments: METHOD Method to run [ARGUMENTS]... Arguments to pass to METHOD Options: --help Display help for this method --version Display version information Methods: add Add file contents to the index annotate Annotate file lines with commit information check-attr Display gitattributes information format-patch Prepare patches for e-mail submission remote Manage set of remote repositories % git format-patch --help Usage: git format-patch [OPTIONS]... [SINCE] Prepare patches for e-mail submission Arguments: [SINCE=N/A] Generate patches for commits after SINCE Options: -N, --no-numbered Name output in [PATCH] format --help Display help for this method -n, --numbered Name output in [PATCH n/m] format --no-thread Disables addition of In-Reply-To and Reference headers -s, --signoff Add Signed-off-by: line to the commit message --start-number=N Start numbering the patches at N instead of 1 --thread[=STYLE] Controls addition of In-Reply-To and References headers --to=ADDRESS* Add a To: header to the email headers % git remote --help Usage: git remote [OPTIONS]... [METHOD] [ARGUMENTS]... Manage set of remote repositories Arguments: [METHOD=list] Method to run [ARGUMENTS]... Arguments to pass to METHOD Options: --help Display help for this method Methods: add Adds a remote named NAME for the repository at URL list Shows a list of existing remotes § API The previous section gave an introduction to the whole user API in an informal and introductory way. For an indepth reference to the user API, see the {user API documentation}¹. ¹ See http://disu.se/software/ame-1.0/api/user/Ame/ If you want to extend the API or use it in some way other than as a command-line-interface writer, see the {developer API documentation}¹. ¹ See http://disu.se/software/ame-1.0/api/developer/Ame/ § Financing Currently, most of my time is spent at my day job and in my rather busy private life. Please motivate me to spend time on this piece of software by donating some of your money to this project. Yeah, I realize that requesting money to develop software is a bit, well, capitalistic of me. But please realize that I live in a capitalistic society and I need money to have other people give me the things that I need to continue living under the rules of said society. So, if you feel that this piece of software has helped you out enough to warrant a reward, please PayPal a donation to now@disu.se¹. Thanks! Your support won’t go unnoticed! ¹ Send a donation: https://www.paypal.com/cgi-bin/webscr?cmd=_donations&amp;business=now@disu.se&amp;item_name=Ame § Reporting Bugs Please report any bugs that you encounter to the {issue tracker}¹. ¹ See https://github.com/now/ame/issues § Authors Nikolai Weibull wrote the code, the tests, the documentation, and this README. § Licensing Ame is free software: you may redistribute it and/or modify it under the terms of the {GNU Lesser General Public License, version 3}¹ or later², as published by the {Free Software Foundation}³. ¹ See http://disu.se/licenses/lgpl-3.0/ ² See http://gnu.org/licenses/ ³ See http://fsf.org/

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