genfrag 0.0.0.1
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- data/.bnsignore +16 -0
- data/History.txt +4 -0
- data/LICENSE.txt +58 -0
- data/README.rdoc +40 -0
- data/Rakefile +53 -0
- data/bin/genfrag +8 -0
- data/lib/genfrag.rb +129 -0
- data/lib/genfrag/app.rb +105 -0
- data/lib/genfrag/app/command.rb +145 -0
- data/lib/genfrag/app/index_command.rb +227 -0
- data/lib/genfrag/app/index_command/db.rb +105 -0
- data/lib/genfrag/app/search_command.rb +298 -0
- data/lib/genfrag/app/search_command/match.rb +165 -0
- data/lib/genfrag/app/search_command/process_file.rb +125 -0
- data/lib/genfrag/app/search_command/trim.rb +121 -0
- data/lib/genfrag/debug.rb +0 -0
- data/spec/data/index_command/in/a.fasta +109 -0
- data/spec/data/index_command/out/1-a_lookup.tdf +4 -0
- data/spec/data/index_command/out/2-a_lookup.db +0 -0
- data/spec/data/index_command/out/3-a_lookup.tdf +2 -0
- data/spec/data/index_command/out/4-a_lookup.db +0 -0
- data/spec/data/index_command/out/5-a_lookup.tdf +4 -0
- data/spec/data/index_command/out/6-a_lookup.db +0 -0
- data/spec/data/index_command/out/a.fasta.db +0 -0
- data/spec/data/index_command/out/a.fasta.tdf +6 -0
- data/spec/genfrag/app/command_spec.rb +55 -0
- data/spec/genfrag/app/index_command_spec.rb +258 -0
- data/spec/genfrag/app/search_command/match_spec.rb +77 -0
- data/spec/genfrag/app/search_command/process_file_spec.rb +185 -0
- data/spec/genfrag/app/search_command/trim_spec.rb +75 -0
- data/spec/genfrag/app/search_command_spec.rb +260 -0
- data/spec/genfrag/app_spec.rb +77 -0
- data/spec/genfrag_spec.rb +87 -0
- data/spec/spec_helper.rb +56 -0
- data/tasks/ann.rake +80 -0
- data/tasks/bones.rake +20 -0
- data/tasks/gem.rake +201 -0
- data/tasks/git.rake +40 -0
- data/tasks/notes.rake +27 -0
- data/tasks/post_load.rake +34 -0
- data/tasks/rdoc.rake +50 -0
- data/tasks/rubyforge.rake +55 -0
- data/tasks/setup.rb +300 -0
- data/tasks/spec.rake +54 -0
- data/tasks/svn.rake +47 -0
- data/tasks/test.rake +40 -0
- metadata +136 -0
data/spec/spec_helper.rb
ADDED
@@ -0,0 +1,56 @@
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# Equivalent to a header guard in C/C++
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# Used to prevent the spec helper from being loaded more than once
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unless defined? GENFRAG_SPEC_HELPER
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GENFRAG_SPEC_HELPER = true
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5
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6
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require 'stringio'
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7
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require 'tmpdir'
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8
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require File.expand_path(
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9
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File.join(File.dirname(__FILE__), %w[.. lib genfrag]))
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GENFRAG_SPEC_DATA_DIR = File.join(File.dirname(__FILE__), %w[data])
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12
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GENFRAG_SPEC_TMP_DIR = File.join(Dir.tmpdir, %w[genfrag])
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14
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puts "tmp dir is #{GENFRAG_SPEC_TMP_DIR}"
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15
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def compare(filename, ext)
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generated = File.join(@working_output_dir, filename + ext)
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frozen = File.join(@frozen_output_dir, filename + ext)
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FileUtils.compare_file(generated, frozen)
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20
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end
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21
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Spec::Runner.configure do |config|
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23
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# == Mock Framework
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24
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#
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25
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# RSpec uses it's own mocking framework by default. If you prefer to
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26
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# use mocha, flexmock or RR, uncomment the appropriate line:
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27
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#
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# config.mock_with :mocha
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29
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# config.mock_with :flexmock
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30
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# config.mock_with :rr
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31
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end
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33
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class StringIO
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34
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alias :_readline :readline
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35
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def readline
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36
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@_pos ||= 0
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seek @_pos
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38
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begin
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39
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_line = _readline
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40
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@_pos = tell
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_line.rstrip
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rescue EOFError
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nil
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end
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end
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46
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def clear
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48
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truncate 0
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seek 0
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@_pos = 0
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end
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end
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53
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+
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54
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end # unless defined?
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55
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56
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# EOF
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data/tasks/ann.rake
ADDED
@@ -0,0 +1,80 @@
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begin
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require 'bones/smtp_tls'
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rescue LoadError
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require 'net/smtp'
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6
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end
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7
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require 'time'
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8
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namespace :ann do
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# A prerequisites task that all other tasks depend upon
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task :prereqs
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file PROJ.ann.file do
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ann = PROJ.ann
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puts "Generating #{ann.file}"
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File.open(ann.file,'w') do |fd|
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fd.puts("#{PROJ.name} version #{PROJ.version}")
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fd.puts(" by #{Array(PROJ.authors).first}") if PROJ.authors
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20
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fd.puts(" #{PROJ.url}") if PROJ.url.valid?
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21
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fd.puts(" (the \"#{PROJ.release_name}\" release)") if PROJ.release_name
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22
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fd.puts
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23
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fd.puts("== DESCRIPTION")
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24
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fd.puts
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25
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fd.puts(PROJ.description)
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26
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fd.puts
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27
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fd.puts(PROJ.changes.sub(%r/^.*$/, '== CHANGES'))
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28
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fd.puts
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29
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ann.paragraphs.each do |p|
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30
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fd.puts "== #{p.upcase}"
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31
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fd.puts
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32
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fd.puts paragraphs_of(PROJ.readme_file, p).join("\n\n")
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33
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fd.puts
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34
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end
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35
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fd.puts ann.text if ann.text
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36
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end
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37
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end
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38
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39
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desc "Create an announcement file"
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40
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task :announcement => ['ann:prereqs', PROJ.ann.file]
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41
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42
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desc "Send an email announcement"
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43
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task :email => ['ann:prereqs', PROJ.ann.file] do
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44
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ann = PROJ.ann
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45
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from = ann.email[:from] || Array(PROJ.authors).first || PROJ.email
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46
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to = Array(ann.email[:to])
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47
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+
|
48
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### build a mail header for RFC 822
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49
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rfc822msg = "From: #{from}\n"
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50
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rfc822msg << "To: #{to.join(',')}\n"
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51
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rfc822msg << "Subject: [ANN] #{PROJ.name} #{PROJ.version}"
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52
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rfc822msg << " (#{PROJ.release_name})" if PROJ.release_name
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53
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rfc822msg << "\n"
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54
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rfc822msg << "Date: #{Time.new.rfc822}\n"
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rfc822msg << "Message-Id: "
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56
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rfc822msg << "<#{"%.8f" % Time.now.to_f}@#{ann.email[:domain]}>\n\n"
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57
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rfc822msg << File.read(ann.file)
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58
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+
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59
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params = [:server, :port, :domain, :acct, :passwd, :authtype].map do |key|
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60
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ann.email[key]
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61
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end
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62
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63
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params[3] = PROJ.email if params[3].nil?
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64
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65
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if params[4].nil?
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66
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STDOUT.write "Please enter your e-mail password (#{params[3]}): "
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67
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params[4] = STDIN.gets.chomp
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68
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end
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69
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### send email
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71
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Net::SMTP.start(*params) {|smtp| smtp.sendmail(rfc822msg, from, to)}
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72
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end
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73
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end # namespace :ann
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74
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75
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desc 'Alias to ann:announcement'
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76
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task :ann => 'ann:announcement'
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77
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CLOBBER << PROJ.ann.file
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79
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80
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# EOF
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data/tasks/bones.rake
ADDED
@@ -0,0 +1,20 @@
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if HAVE_BONES
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3
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namespace :bones do
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5
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desc 'Show the PROJ open struct'
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task :debug do |t|
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8
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atr = if t.application.top_level_tasks.length == 2
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9
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t.application.top_level_tasks.pop
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10
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end
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11
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12
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if atr then Bones::Debug.show_attr(PROJ, atr)
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else Bones::Debug.show PROJ end
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end
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end # namespace :bones
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end # HAVE_BONES
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20
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# EOF
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data/tasks/gem.rake
ADDED
@@ -0,0 +1,201 @@
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1
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2
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require 'find'
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3
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require 'rake/packagetask'
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4
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require 'rubygems/user_interaction'
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5
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require 'rubygems/builder'
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6
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7
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module Bones
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class GemPackageTask < Rake::PackageTask
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# Ruby GEM spec containing the metadata for this package. The
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# name, version and package_files are automatically determined
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# from the GEM spec and don't need to be explicitly provided.
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#
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attr_accessor :gem_spec
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# Tasks from the Bones gem directory
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attr_reader :bones_files
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# Create a GEM Package task library. Automatically define the gem
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# if a block is given. If no block is supplied, then +define+
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20
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# needs to be called to define the task.
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21
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#
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22
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def initialize(gem_spec)
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23
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init(gem_spec)
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24
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yield self if block_given?
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25
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define if block_given?
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26
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+
end
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27
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+
|
28
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# Initialization tasks without the "yield self" or define
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29
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# operations.
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30
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#
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31
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def init(gem)
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32
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super(gem.name, gem.version)
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@gem_spec = gem
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34
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@package_files += gem_spec.files if gem_spec.files
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@bones_files = []
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36
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37
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local_setup = File.join(Dir.pwd, %w[tasks setup.rb])
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38
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if !test(?e, local_setup)
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39
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Dir.glob(::Bones.path(%w[lib bones tasks *])).each {|fn| bones_files << fn}
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40
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end
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41
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end
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42
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+
|
43
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# Create the Rake tasks and actions specified by this
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44
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# GemPackageTask. (+define+ is automatically called if a block is
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45
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# given to +new+).
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46
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#
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47
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def define
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48
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super
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49
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task :prereqs
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50
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task :package => ['gem:prereqs', "#{package_dir_path}/#{gem_file}"]
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51
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file "#{package_dir_path}/#{gem_file}" => [package_dir_path] + package_files + bones_files do
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52
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when_writing("Creating GEM") {
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53
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chdir(package_dir_path) do
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54
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Gem::Builder.new(gem_spec).build
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55
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verbose(true) {
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56
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mv gem_file, "../#{gem_file}"
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57
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}
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58
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end
|
59
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}
|
60
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end
|
61
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+
|
62
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file package_dir_path => bones_files do
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63
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mkdir_p package_dir rescue nil
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64
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+
|
65
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gem_spec.files = (gem_spec.files +
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66
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bones_files.map {|fn| File.join('tasks', File.basename(fn))}).sort
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67
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+
|
68
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bones_files.each do |fn|
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69
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base_fn = File.join('tasks', File.basename(fn))
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70
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f = File.join(package_dir_path, base_fn)
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71
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fdir = File.dirname(f)
|
72
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mkdir_p(fdir) if !File.exist?(fdir)
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73
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+
if File.directory?(fn)
|
74
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mkdir_p(f)
|
75
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else
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76
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raise "file name conflict for '#{base_fn}' (conflicts with '#{fn}')" if test(?e, f)
|
77
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safe_ln(fn, f)
|
78
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+
end
|
79
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+
end
|
80
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+
end
|
81
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+
end
|
82
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+
|
83
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def gem_file
|
84
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if @gem_spec.platform == Gem::Platform::RUBY
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85
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"#{package_name}.gem"
|
86
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else
|
87
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"#{package_name}-#{@gem_spec.platform}.gem"
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88
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end
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89
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+
end
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90
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end # class GemPackageTask
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91
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end # module Bones
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92
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+
|
93
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namespace :gem do
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94
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+
|
95
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PROJ.gem._spec = Gem::Specification.new do |s|
|
96
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+
s.name = PROJ.name
|
97
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+
s.version = PROJ.version
|
98
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+
s.summary = PROJ.summary
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99
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+
s.authors = Array(PROJ.authors)
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100
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+
s.email = PROJ.email
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101
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s.homepage = Array(PROJ.url).first
|
102
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+
s.rubyforge_project = PROJ.rubyforge.name
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103
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+
|
104
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s.description = PROJ.description
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105
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+
|
106
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+
PROJ.gem.dependencies.each do |dep|
|
107
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s.add_dependency(*dep)
|
108
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+
end
|
109
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+
|
110
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+
PROJ.gem.development_dependencies.each do |dep|
|
111
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+
s.add_development_dependency(*dep)
|
112
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+
end
|
113
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+
|
114
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s.files = PROJ.gem.files
|
115
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+
s.executables = PROJ.gem.executables.map {|fn| File.basename(fn)}
|
116
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+
s.extensions = PROJ.gem.files.grep %r/extconf\.rb$/
|
117
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+
|
118
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+
s.bindir = 'bin'
|
119
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+
dirs = Dir["{#{PROJ.libs.join(',')}}"]
|
120
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+
s.require_paths = dirs unless dirs.empty?
|
121
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+
|
122
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+
incl = Regexp.new(PROJ.rdoc.include.join('|'))
|
123
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+
excl = PROJ.rdoc.exclude.dup.concat %w[\.rb$ ^(\.\/|\/)?ext]
|
124
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+
excl = Regexp.new(excl.join('|'))
|
125
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+
rdoc_files = PROJ.gem.files.find_all do |fn|
|
126
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+
case fn
|
127
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+
when excl; false
|
128
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+
when incl; true
|
129
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+
else false end
|
130
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+
end
|
131
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+
s.rdoc_options = PROJ.rdoc.opts + ['--main', PROJ.rdoc.main]
|
132
|
+
s.extra_rdoc_files = rdoc_files
|
133
|
+
s.has_rdoc = true
|
134
|
+
|
135
|
+
if test ?f, PROJ.test.file
|
136
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+
s.test_file = PROJ.test.file
|
137
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+
else
|
138
|
+
s.test_files = PROJ.test.files.to_a
|
139
|
+
end
|
140
|
+
|
141
|
+
# Do any extra stuff the user wants
|
142
|
+
PROJ.gem.extras.each do |msg, val|
|
143
|
+
case val
|
144
|
+
when Proc
|
145
|
+
val.call(s.send(msg))
|
146
|
+
else
|
147
|
+
s.send "#{msg}=", val
|
148
|
+
end
|
149
|
+
end
|
150
|
+
end # Gem::Specification.new
|
151
|
+
|
152
|
+
Bones::GemPackageTask.new(PROJ.gem._spec) do |pkg|
|
153
|
+
pkg.need_tar = PROJ.gem.need_tar
|
154
|
+
pkg.need_zip = PROJ.gem.need_zip
|
155
|
+
end
|
156
|
+
|
157
|
+
desc 'Show information about the gem'
|
158
|
+
task :debug => 'gem:prereqs' do
|
159
|
+
puts PROJ.gem._spec.to_ruby
|
160
|
+
end
|
161
|
+
|
162
|
+
desc 'Write the gemspec '
|
163
|
+
task :spec => 'gem:prereqs' do
|
164
|
+
File.open("#{PROJ.name}.gemspec", 'w') do |f|
|
165
|
+
f.write PROJ.gem._spec.to_ruby
|
166
|
+
end
|
167
|
+
end
|
168
|
+
|
169
|
+
desc 'Install the gem'
|
170
|
+
task :install => [:clobber, 'gem:package'] do
|
171
|
+
sh "#{SUDO} #{GEM} install --local pkg/#{PROJ.gem._spec.full_name}"
|
172
|
+
|
173
|
+
# use this version of the command for rubygems > 1.0.0
|
174
|
+
#sh "#{SUDO} #{GEM} install --no-update-sources pkg/#{PROJ.gem._spec.full_name}"
|
175
|
+
end
|
176
|
+
|
177
|
+
desc 'Uninstall the gem'
|
178
|
+
task :uninstall do
|
179
|
+
installed_list = Gem.source_index.find_name(PROJ.name)
|
180
|
+
if installed_list and installed_list.collect { |s| s.version.to_s}.include?(PROJ.version) then
|
181
|
+
sh "#{SUDO} #{GEM} uninstall --version '#{PROJ.version}' --ignore-dependencies --executables #{PROJ.name}"
|
182
|
+
end
|
183
|
+
end
|
184
|
+
|
185
|
+
desc 'Reinstall the gem'
|
186
|
+
task :reinstall => [:uninstall, :install]
|
187
|
+
|
188
|
+
desc 'Cleanup the gem'
|
189
|
+
task :cleanup do
|
190
|
+
sh "#{SUDO} #{GEM} cleanup #{PROJ.gem._spec.name}"
|
191
|
+
end
|
192
|
+
end # namespace :gem
|
193
|
+
|
194
|
+
|
195
|
+
desc 'Alias to gem:package'
|
196
|
+
task :gem => 'gem:package'
|
197
|
+
|
198
|
+
task :clobber => 'gem:clobber_package'
|
199
|
+
remove_desc_for_task 'gem:clobber_package'
|
200
|
+
|
201
|
+
# EOF
|
data/tasks/git.rake
ADDED
@@ -0,0 +1,40 @@
|
|
1
|
+
|
2
|
+
if HAVE_GIT
|
3
|
+
|
4
|
+
namespace :git do
|
5
|
+
|
6
|
+
# A prerequisites task that all other tasks depend upon
|
7
|
+
task :prereqs
|
8
|
+
|
9
|
+
desc 'Show tags from the Git repository'
|
10
|
+
task :show_tags => 'git:prereqs' do |t|
|
11
|
+
puts %x/git tag/
|
12
|
+
end
|
13
|
+
|
14
|
+
desc 'Create a new tag in the Git repository'
|
15
|
+
task :create_tag => 'git:prereqs' do |t|
|
16
|
+
v = ENV['VERSION'] or abort 'Must supply VERSION=x.y.z'
|
17
|
+
abort "Versions don't match #{v} vs #{PROJ.version}" if v != PROJ.version
|
18
|
+
|
19
|
+
tag = "%s-%s" % [PROJ.name, PROJ.version]
|
20
|
+
msg = "Creating tag for #{PROJ.name} version #{PROJ.version}"
|
21
|
+
|
22
|
+
puts "Creating Git tag '#{tag}'"
|
23
|
+
unless system "git tag -a -m '#{msg}' #{tag}"
|
24
|
+
abort "Tag creation failed"
|
25
|
+
end
|
26
|
+
|
27
|
+
if %x/git remote/ =~ %r/^origin\s*$/
|
28
|
+
unless system "git push origin #{tag}"
|
29
|
+
abort "Could not push tag to remote Git repository"
|
30
|
+
end
|
31
|
+
end
|
32
|
+
end
|
33
|
+
|
34
|
+
end # namespace :git
|
35
|
+
|
36
|
+
task 'gem:release' => 'git:create_tag'
|
37
|
+
|
38
|
+
end # if HAVE_GIT
|
39
|
+
|
40
|
+
# EOF
|
data/tasks/notes.rake
ADDED
@@ -0,0 +1,27 @@
|
|
1
|
+
|
2
|
+
if HAVE_BONES
|
3
|
+
|
4
|
+
desc "Enumerate all annotations"
|
5
|
+
task :notes do |t|
|
6
|
+
id = if t.application.top_level_tasks.length > 1
|
7
|
+
t.application.top_level_tasks.slice!(1..-1).join(' ')
|
8
|
+
end
|
9
|
+
Bones::AnnotationExtractor.enumerate(
|
10
|
+
PROJ, PROJ.notes.tags.join('|'), id, :tag => true)
|
11
|
+
end
|
12
|
+
|
13
|
+
namespace :notes do
|
14
|
+
PROJ.notes.tags.each do |tag|
|
15
|
+
desc "Enumerate all #{tag} annotations"
|
16
|
+
task tag.downcase.to_sym do |t|
|
17
|
+
id = if t.application.top_level_tasks.length > 1
|
18
|
+
t.application.top_level_tasks.slice!(1..-1).join(' ')
|
19
|
+
end
|
20
|
+
Bones::AnnotationExtractor.enumerate(PROJ, tag, id)
|
21
|
+
end
|
22
|
+
end
|
23
|
+
end
|
24
|
+
|
25
|
+
end # if HAVE_BONES
|
26
|
+
|
27
|
+
# EOF
|
@@ -0,0 +1,34 @@
|
|
1
|
+
|
2
|
+
# This file does not define any rake tasks. It is used to load some project
|
3
|
+
# settings if they are not defined by the user.
|
4
|
+
|
5
|
+
PROJ.exclude << ["^#{Regexp.escape(PROJ.ann.file)}$",
|
6
|
+
"^#{Regexp.escape(PROJ.ignore_file)}$",
|
7
|
+
"^#{Regexp.escape(PROJ.rdoc.dir)}/",
|
8
|
+
"^#{Regexp.escape(PROJ.rcov.dir)}/"]
|
9
|
+
|
10
|
+
flatten_arrays = lambda do |this,os|
|
11
|
+
os.instance_variable_get(:@table).each do |key,val|
|
12
|
+
next if key == :dependencies \
|
13
|
+
or key == :development_dependencies
|
14
|
+
case val
|
15
|
+
when Array; val.flatten!
|
16
|
+
when OpenStruct; this.call(this,val)
|
17
|
+
end
|
18
|
+
end
|
19
|
+
end
|
20
|
+
flatten_arrays.call(flatten_arrays,PROJ)
|
21
|
+
|
22
|
+
PROJ.changes ||= paragraphs_of(PROJ.history_file, 0..1).join("\n\n")
|
23
|
+
|
24
|
+
PROJ.description ||= paragraphs_of(PROJ.readme_file, 'description').join("\n\n")
|
25
|
+
|
26
|
+
PROJ.summary ||= PROJ.description.split('.').first
|
27
|
+
|
28
|
+
PROJ.gem.files ||= manifest
|
29
|
+
|
30
|
+
PROJ.gem.executables ||= PROJ.gem.files.find_all {|fn| fn =~ %r/^bin/}
|
31
|
+
|
32
|
+
PROJ.rdoc.main ||= PROJ.readme_file
|
33
|
+
|
34
|
+
# EOF
|