ulla 0.9.3 → 0.9.4

data/.autotest

@@ -0,0 +1,5 @@
+#require 'autotest/screen'
+
+#Autotest::Screen.statusline = '%H %`%-w%{=b bw}%n %t%{-}%+w (your statusline)'
+#Autotest::Screen.statusline = '%{=b}%{G} Screen(s): %{b}%w %=%{kG}%C%A  %D, %M/%d/%Y (your statusline)'
+

data/History.txt

@@ -1,3 +1,7 @@
+== 0.9.4 18/03/2009
+
+* Fixed a bug for environment label and residue name when --cys 2 is set
+
 == 0.9.3 23/2/2009
 
 * Egor has been renamed to Ulla!

data/Manifest.txt

@@ -1,56 +1,4 @@
-.git/COMMIT_EDITMSG
-.git/HEAD
-.git/config
-.git/description
-.git/hooks/applypatch-msg.sample
-.git/hooks/commit-msg.sample
-.git/hooks/post-commit.sample
-.git/hooks/post-receive.sample
-.git/hooks/post-update.sample
-.git/hooks/pre-applypatch.sample
-.git/hooks/pre-commit.sample
-.git/hooks/pre-rebase.sample
-.git/hooks/prepare-commit-msg.sample
-.git/hooks/update.sample
-.git/index
-.git/info/exclude
-.git/logs/HEAD
-.git/logs/refs/heads/master
-.git/logs/refs/remotes/origin/HEAD
-.git/objects/06/9494e479f28b5751fb135b8e55e8fef3d3a02e
-.git/objects/22/0df784191ad94983ca1d943e49fe482c9d1069
-.git/objects/3b/b6f2b7f563175a13a0ccd723aab761552f448b
-.git/objects/41/f48aefb4d7a6a87eb423eaae77ae1e8a58dd6c
-.git/objects/44/d1f1782e3ea1d9fd2f9054784b53e8e810a8ca
-.git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace
-.git/objects/57/1326145a7a4b3e58f3d3008ba343135f213b05
-.git/objects/6c/4f0844f62b7345f0651b0fb2829a8f157469fb
-.git/objects/73/8dc79450de050f12d48a32602f2ddbe6807029
-.git/objects/7b/4acb3aee6616d80e295ee21fe8bb7ee93ebe96
-.git/objects/9e/0a9235b0d70a8029098070007fb414cb52504e
-.git/objects/9e/bfcad2906aac4a23a7c9689a47b76723f5d152
-.git/objects/a6/578c95f2f474303464b572e9dac716432472b2
-.git/objects/a8/65ef5700ff04601c6fc40fa5ede3cc25534723
-.git/objects/aa/285cb176668c5e49c54c6e1d3cc27bd47fd4f4
-.git/objects/b8/e3828a1082137c4aa4595386bdfb73e3c75b9d
-.git/objects/c2/fb6afc000952b56354fe195682645000d2aea2
-.git/objects/c4/a0553ca0e3c4628e688ecb5e3304a8a8ac0c28
-.git/objects/c8/d49f83c4a32cff2d87dd4aa5f83eb7aac3a753
-.git/objects/ca/c25e8049075ed4bff993705acb4750b2b62ba9
-.git/objects/d2/ff2e939339eb3fb776e064c258e71dfa1cf396
-.git/objects/d7/cedf9e2a8ff35b5d7dafdc0f20daed9c65ce44
-.git/objects/e2/e81af59e3a6c4aa8daac62add62860ae776ba4
-.git/objects/e5/7c47d183ce5dda1a944c7ee1c19c8a0c4bb278
-.git/objects/eb/f4a4e1e50bb30731597f776e56b0ccb0c9959f
-.git/objects/f6/39d6f6cf883fde4b9052012919c1df3288c7da
-.git/objects/f8/2346f308f49053df108b7c31ac3089e8b4b4ac
-.git/objects/fb/4b193bb1cbe9041d2f00176f6caa6acfb1fc12
-.git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.idx
-.git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.pack
-.git/packed-refs
-.git/refs/heads/master
-.git/refs/remotes/origin/HEAD
-.gitignore
+.autotest
 History.txt
 Manifest.txt
 PostInstall.txt
@@ -83,6 +31,7 @@ test/test_ulla.rb
 test/ulla/test_cli.rb
 test/ulla/test_environment_class_hash.rb
 test/ulla/test_environment_feature.rb
+ulla.gemspec
 website/index.html
 website/index.txt
 website/javascripts/rounded_corners_lite.inc.js

data/README.rdoc

@@ -94,7 +94,7 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
 
 == Usage
 
-1. Prepare an environmental class definition file. For more details, please check this notes (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES).
+1. Prepare an environmental class definition file. For more details, please check this notes (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES). You can download a sample environmental class definition file from http://www-cryst.bioc.cam.ac.uk/~kenji/subst/classdef.dat 
 
         ~user $ cat classdef.dat
         #
@@ -104,7 +104,7 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
         secondary structure and phi angle;HEPC;HEPC;T;F
         solvent accessibility;TF;Aa;F;F
 
-2. Prepare structural alignments and their annotations of above environmental classes in PIR format.
+2. Prepare structural alignments and their annotations of above environmental classes in PIR format. You can download sample alignments from http://www-cryst.bioc.cam.ac.uk/~kenji/subst/alltem-allmask.tar.gz
 
         ~user $ cat sample1.tem
         >P1;1mnma
@@ -153,13 +153,13 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
 
         ~user $ ulla -l TEMLIST --output 2 -o substlogo.mat
 
-7. To produce substitution data only from the sequence pairs within a given PID range, type (if you don't provide any name for output, 'allmat.dat' will be used.)
+7. To produce substitution probability matrices only from the sequence pairs within a certain PID range, type (if you don't provide any name for output, 'allmat.dat' will be used.)
 
         ~user $ ulla -l TEMLIST --pidmin 60 --pidmax 80 --output 1
 
-8. To change the clustering level (default 60), type
+8. To change the clustering level (default 60) to PID 80, type
 
-        ~user $ ulla -l TEMLIST --weight 80 --output 2
+        ~user $ ulla -l TEMLIST --weight 80 --output 1
 
 9. In case positions are masked with the character 'X' in any environmental features, all mutations from/to the position will be excluded from the calculation of substitution counts.
 
@@ -235,7 +235,6 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
 == TODO
 
 * Substitution table generation considering both the source and the target environmental classes
-* Remove dependency on NMatrix package
 
 == Repository
 

data/lib/ulla/cli.rb

@@ -502,9 +502,7 @@ Options:
                       'X'
                     else
                       if ei == 0 # Amino Acid Environment Feature
-                        (disulphide.has_key?(key) &&
-                         (disulphide[key][pos] == 'F') &&
-                         (sym == 'C')) ? 'J' : sym
+                        (disulphide.has_key?(key) && (disulphide[key][pos] == 'F') && (sym == 'C') && ($cys != 2)) ? 'J' : sym
                       else
                         ec.labels[ec.symbols.index(sym)]
                       end
@@ -569,8 +567,8 @@ Options:
                       next
                     end
 
-                    aa1 = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C')) ? 'J' : aa1
-                    aa2 = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C')) ? 'J' : aa2
+                    aa1 = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C') && ($cys != 2)) ? 'J' : aa1
+                    aa2 = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C') && ($cys != 2)) ? 'J' : aa2
 
                     if $cst_features.empty?
                       $env_classes[env_labels[id1][pos]].increase_residue_count(aa2)
@@ -684,8 +682,8 @@ Options:
                       next
                     end
 
-                    aa1   = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C')) ? 'J' : aa1
-                    aa2   = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C')) ? 'J' : aa2
+                    aa1   = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C') && ($cys != 2)) ? 'J' : aa1
+                    aa2   = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C') && ($cys != 2)) ? 'J' : aa2
                     cnt1  = 1.0 / cluster1.size
                     cnt2  = 1.0 / cluster2.size
                     jnt_cnt = cnt1 * cnt2

data/lib/ulla.rb

@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
 module Ulla
-  VERSION = '0.9.3'
+  VERSION = '0.9.4'
 end

data/ulla.gemspec

@@ -0,0 +1,53 @@
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{ulla}
+  s.version = "0.9.4"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Semin Lee"]
+  s.date = %q{2009-03-18}
+  s.default_executable = %q{ulla}
+  s.description = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
+  s.email = ["seminlee@gmail.com"]
+  s.executables = ["ulla"]
+  s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
+  s.files = [".autotest", "History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
+  s.has_rdoc = true
+  s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
+  s.post_install_message = %q{PostInstall.txt}
+  s.rdoc_options = ["--main", "README.rdoc"]
+  s.require_paths = ["lib"]
+  s.rubyforge_project = %q{ulla}
+  s.rubygems_version = %q{1.3.1}
+  s.summary = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
+  s.test_files = ["test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "test/test_helper.rb", "test/test_ulla.rb"]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 2
+
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
+      s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
+      s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
+      s.add_development_dependency(%q<newgem>, [">= 1.3.0"])
+      s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
+    else
+      s.add_dependency(%q<narray>, [">= 0.5.9.5"])
+      s.add_dependency(%q<bio>, [">= 1.2.1"])
+      s.add_dependency(%q<facets>, [">= 2.4.5"])
+      s.add_dependency(%q<rmagick>, [">= 2.9.1"])
+      s.add_dependency(%q<newgem>, [">= 1.3.0"])
+      s.add_dependency(%q<hoe>, [">= 1.8.0"])
+    end
+  else
+    s.add_dependency(%q<narray>, [">= 0.5.9.5"])
+    s.add_dependency(%q<bio>, [">= 1.2.1"])
+    s.add_dependency(%q<facets>, [">= 2.4.5"])
+    s.add_dependency(%q<rmagick>, [">= 2.9.1"])
+    s.add_dependency(%q<newgem>, [">= 1.3.0"])
+    s.add_dependency(%q<hoe>, [">= 1.8.0"])
+  end
+end

data/website/index.html

@@ -9,8 +9,18 @@
 </head>
 <body>
     <p>
-    Egor has been renamed to Ulla, and an official web site for Ulla will be available when our new web contents management system is ready. Until then, this page will be redirected to its Git repository, <a href="http://http://github.com/semin/ulla/">http://github.com/semin/ulla</a> in 5 seconds.
+    Egor has been renamed to Ulla, and an official web site for Ulla will be available when our new web contents management system is ready. Until then, this page will be redirected to its Git repository, <a href="http://github.com/semin/ulla/">http://github.com/semin/ulla</a> in 5 seconds.
     </p>
     - Semin
+    <script type="text/javascript">
+        var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+        document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+    </script>
+    <script type="text/javascript">
+        try {
+            var pageTracker = _gat._getTracker("UA-7633498-1");
+            pageTracker._trackPageview();
+        } catch(err) {}
+    </script>
 </body>
 </html>

data/website/index.txt

@@ -30,7 +30,6 @@ Following RubyGems will be automatically installed if you have rubygems installe
 * narray (http://narray.rubyforge.org/)
 * facets (http://facets.rubyforge.org/)
 * bio (http://bioruby.open-bio.org/)
-* simple_memoize (http://github.com/JackDanger/simple_memoize/tree/master)
 
 
 h2. Basic Usage

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ulla
 version: !ruby/object:Gem::Version 
-  version: 0.9.3
+  version: 0.9.4
 platform: ruby
 authors: 
 - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-02-23 00:00:00 +00:00
+date: 2009-03-18 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -60,7 +60,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.2.3
+        version: 1.3.0
     version: 
 - !ruby/object:Gem::Dependency 
   name: hoe
@@ -86,59 +86,7 @@ extra_rdoc_files:
 - README.rdoc
 - website/index.txt
 files: 
-- .git/COMMIT_EDITMSG
-- .git/HEAD
-- .git/config
-- .git/description
-- .git/hooks/applypatch-msg.sample
-- .git/hooks/commit-msg.sample
-- .git/hooks/post-commit.sample
-- .git/hooks/post-receive.sample
-- .git/hooks/post-update.sample
-- .git/hooks/pre-applypatch.sample
-- .git/hooks/pre-commit.sample
-- .git/hooks/pre-rebase.sample
-- .git/hooks/prepare-commit-msg.sample
-- .git/hooks/update.sample
-- .git/index
-- .git/info/exclude
-- .git/logs/HEAD
-- .git/logs/refs/heads/master
-- .git/logs/refs/remotes/origin/HEAD
-- .git/objects/06/9494e479f28b5751fb135b8e55e8fef3d3a02e
-- .git/objects/22/0df784191ad94983ca1d943e49fe482c9d1069
-- .git/objects/3b/b6f2b7f563175a13a0ccd723aab761552f448b
-- .git/objects/41/f48aefb4d7a6a87eb423eaae77ae1e8a58dd6c
-- .git/objects/44/d1f1782e3ea1d9fd2f9054784b53e8e810a8ca
-- .git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace
-- .git/objects/57/1326145a7a4b3e58f3d3008ba343135f213b05
-- .git/objects/6c/4f0844f62b7345f0651b0fb2829a8f157469fb
-- .git/objects/73/8dc79450de050f12d48a32602f2ddbe6807029
-- .git/objects/7b/4acb3aee6616d80e295ee21fe8bb7ee93ebe96
-- .git/objects/9e/0a9235b0d70a8029098070007fb414cb52504e
-- .git/objects/9e/bfcad2906aac4a23a7c9689a47b76723f5d152
-- .git/objects/a6/578c95f2f474303464b572e9dac716432472b2
-- .git/objects/a8/65ef5700ff04601c6fc40fa5ede3cc25534723
-- .git/objects/aa/285cb176668c5e49c54c6e1d3cc27bd47fd4f4
-- .git/objects/b8/e3828a1082137c4aa4595386bdfb73e3c75b9d
-- .git/objects/c2/fb6afc000952b56354fe195682645000d2aea2
-- .git/objects/c4/a0553ca0e3c4628e688ecb5e3304a8a8ac0c28
-- .git/objects/c8/d49f83c4a32cff2d87dd4aa5f83eb7aac3a753
-- .git/objects/ca/c25e8049075ed4bff993705acb4750b2b62ba9
-- .git/objects/d2/ff2e939339eb3fb776e064c258e71dfa1cf396
-- .git/objects/d7/cedf9e2a8ff35b5d7dafdc0f20daed9c65ce44
-- .git/objects/e2/e81af59e3a6c4aa8daac62add62860ae776ba4
-- .git/objects/e5/7c47d183ce5dda1a944c7ee1c19c8a0c4bb278
-- .git/objects/eb/f4a4e1e50bb30731597f776e56b0ccb0c9959f
-- .git/objects/f6/39d6f6cf883fde4b9052012919c1df3288c7da
-- .git/objects/f8/2346f308f49053df108b7c31ac3089e8b4b4ac
-- .git/objects/fb/4b193bb1cbe9041d2f00176f6caa6acfb1fc12
-- .git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.idx
-- .git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.pack
-- .git/packed-refs
-- .git/refs/heads/master
-- .git/refs/remotes/origin/HEAD
-- .gitignore
+- .autotest
 - History.txt
 - Manifest.txt
 - PostInstall.txt
@@ -171,6 +119,7 @@ files:
 - test/ulla/test_cli.rb
 - test/ulla/test_environment_class_hash.rb
 - test/ulla/test_environment_feature.rb
+- ulla.gemspec
 - website/index.html
 - website/index.txt
 - website/javascripts/rounded_corners_lite.inc.js

data/.git/COMMIT_EDITMSG

@@ -1,13 +0,0 @@
-ulla.gemspec generated
-# Please enter the commit message for your changes. Lines starting
-# with '#' will be ignored, and an empty message aborts the commit.
-# On branch master
-# Your branch is ahead of 'origin/master' by 1 commit.
-#
-# Changes to be committed:
-#   (use "git reset HEAD <file>..." to unstage)
-#
-#	modified:   Manifest.txt
-#	modified:   Rakefile
-#	new file:   ulla.gemspec
-#

data/.git/HEAD

@@ -1 +0,0 @@
-ref: refs/heads/master

data/.git/config

@@ -1,11 +0,0 @@
-[core]
-	repositoryformatversion = 0
-	filemode = true
-	bare = false
-	logallrefupdates = true
-[remote "origin"]
-	url = git@github.com:semin/ulla.git
-	fetch = +refs/heads/*:refs/remotes/origin/*
-[branch "master"]
-	remote = origin
-	merge = refs/heads/master

data/.git/description

@@ -1 +0,0 @@
-Unnamed repository; edit this file to name it for gitweb.

data/.git/hooks/applypatch-msg.sample

@@ -1,15 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to check the commit log message taken by
-# applypatch from an e-mail message.
-#
-# The hook should exit with non-zero status after issuing an
-# appropriate message if it wants to stop the commit.  The hook is
-# allowed to edit the commit message file.
-#
-# To enable this hook, rename this file to "applypatch-msg".
-
-. git-sh-setup
-test -x "$GIT_DIR/hooks/commit-msg" &&
-	exec "$GIT_DIR/hooks/commit-msg" ${1+"$@"}
-:

data/.git/hooks/commit-msg.sample

@@ -1,24 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to check the commit log message.
-# Called by git-commit with one argument, the name of the file
-# that has the commit message.  The hook should exit with non-zero
-# status after issuing an appropriate message if it wants to stop the
-# commit.  The hook is allowed to edit the commit message file.
-#
-# To enable this hook, rename this file to "commit-msg".
-
-# Uncomment the below to add a Signed-off-by line to the message.
-# Doing this in a hook is a bad idea in general, but the prepare-commit-msg
-# hook is more suited to it.
-#
-# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
-# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
-
-# This example catches duplicate Signed-off-by lines.
-
-test "" = "$(grep '^Signed-off-by: ' "$1" |
-	 sort | uniq -c | sed -e '/^[ 	]*1[ 	]/d')" || {
-	echo >&2 Duplicate Signed-off-by lines.
-	exit 1
-}

data/.git/hooks/post-commit.sample

@@ -1,8 +0,0 @@
-#!/bin/sh
-#
-# An example hook script that is called after a successful
-# commit is made.
-#
-# To enable this hook, rename this file to "post-commit".
-
-: Nothing

data/.git/hooks/post-receive.sample

@@ -1,15 +0,0 @@
-#!/bin/sh
-#
-# An example hook script for the "post-receive" event.
-#
-# The "post-receive" script is run after receive-pack has accepted a pack
-# and the repository has been updated.  It is passed arguments in through
-# stdin in the form
-#  <oldrev> <newrev> <refname>
-# For example:
-#  aa453216d1b3e49e7f6f98441fa56946ddcd6a20 68f7abf4e6f922807889f52bc043ecd31b79f814 refs/heads/master
-#
-# see contrib/hooks/ for an sample, or uncomment the next line and
-# rename the file to "post-receive".
-
-#. /usr/share/doc/git-core/contrib/hooks/post-receive-email

data/.git/hooks/post-update.sample

@@ -1,8 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to prepare a packed repository for use over
-# dumb transports.
-#
-# To enable this hook, rename this file to "post-update".
-
-exec git-update-server-info

data/.git/hooks/pre-applypatch.sample

@@ -1,14 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to verify what is about to be committed
-# by applypatch from an e-mail message.
-#
-# The hook should exit with non-zero status after issuing an
-# appropriate message if it wants to stop the commit.
-#
-# To enable this hook, rename this file to "pre-applypatch".
-
-. git-sh-setup
-test -x "$GIT_DIR/hooks/pre-commit" &&
-	exec "$GIT_DIR/hooks/pre-commit" ${1+"$@"}
-:

data/.git/hooks/pre-commit.sample

@@ -1,18 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to verify what is about to be committed.
-# Called by git-commit with no arguments.  The hook should
-# exit with non-zero status after issuing an appropriate message if
-# it wants to stop the commit.
-#
-# To enable this hook, rename this file to "pre-commit".
-
-if git-rev-parse --verify HEAD 2>/dev/null
-then
-	against=HEAD
-else
-	# Initial commit: diff against an empty tree object
-	against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
-fi
-
-exec git diff-index --check --cached $against --

data/.git/hooks/pre-rebase.sample

@@ -1,169 +0,0 @@
-#!/bin/sh
-#
-# Copyright (c) 2006, 2008 Junio C Hamano
-#
-# The "pre-rebase" hook is run just before "git-rebase" starts doing
-# its job, and can prevent the command from running by exiting with
-# non-zero status.
-#
-# The hook is called with the following parameters:
-#
-# $1 -- the upstream the series was forked from.
-# $2 -- the branch being rebased (or empty when rebasing the current branch).
-#
-# This sample shows how to prevent topic branches that are already
-# merged to 'next' branch from getting rebased, because allowing it
-# would result in rebasing already published history.
-
-publish=next
-basebranch="$1"
-if test "$#" = 2
-then
-	topic="refs/heads/$2"
-else
-	topic=`git symbolic-ref HEAD` ||
-	exit 0 ;# we do not interrupt rebasing detached HEAD
-fi
-
-case "$topic" in
-refs/heads/??/*)
-	;;
-*)
-	exit 0 ;# we do not interrupt others.
-	;;
-esac
-
-# Now we are dealing with a topic branch being rebased
-# on top of master.  Is it OK to rebase it?
-
-# Does the topic really exist?
-git show-ref -q "$topic" || {
-	echo >&2 "No such branch $topic"
-	exit 1
-}
-
-# Is topic fully merged to master?
-not_in_master=`git-rev-list --pretty=oneline ^master "$topic"`
-if test -z "$not_in_master"
-then
-	echo >&2 "$topic is fully merged to master; better remove it."
-	exit 1 ;# we could allow it, but there is no point.
-fi
-
-# Is topic ever merged to next?  If so you should not be rebasing it.
-only_next_1=`git-rev-list ^master "^$topic" ${publish} | sort`
-only_next_2=`git-rev-list ^master           ${publish} | sort`
-if test "$only_next_1" = "$only_next_2"
-then
-	not_in_topic=`git-rev-list "^$topic" master`
-	if test -z "$not_in_topic"
-	then
-		echo >&2 "$topic is already up-to-date with master"
-		exit 1 ;# we could allow it, but there is no point.
-	else
-		exit 0
-	fi
-else
-	not_in_next=`git-rev-list --pretty=oneline ^${publish} "$topic"`
-	perl -e '
-		my $topic = $ARGV[0];
-		my $msg = "* $topic has commits already merged to public branch:\n";
-		my (%not_in_next) = map {
-			/^([0-9a-f]+) /;
-			($1 => 1);
-		} split(/\n/, $ARGV[1]);
-		for my $elem (map {
-				/^([0-9a-f]+) (.*)$/;
-				[$1 => $2];
-			} split(/\n/, $ARGV[2])) {
-			if (!exists $not_in_next{$elem->[0]}) {
-				if ($msg) {
-					print STDERR $msg;
-					undef $msg;
-				}
-				print STDERR " $elem->[1]\n";
-			}
-		}
-	' "$topic" "$not_in_next" "$not_in_master"
-	exit 1
-fi
-
-exit 0
-
-################################################################
-
-This sample hook safeguards topic branches that have been
-published from being rewound.
-
-The workflow assumed here is:
-
- * Once a topic branch forks from "master", "master" is never
-   merged into it again (either directly or indirectly).
-
- * Once a topic branch is fully cooked and merged into "master",
-   it is deleted.  If you need to build on top of it to correct
-   earlier mistakes, a new topic branch is created by forking at
-   the tip of the "master".  This is not strictly necessary, but
-   it makes it easier to keep your history simple.
-
- * Whenever you need to test or publish your changes to topic
-   branches, merge them into "next" branch.
-
-The script, being an example, hardcodes the publish branch name
-to be "next", but it is trivial to make it configurable via
-$GIT_DIR/config mechanism.
-
-With this workflow, you would want to know:
-
-(1) ... if a topic branch has ever been merged to "next".  Young
-    topic branches can have stupid mistakes you would rather
-    clean up before publishing, and things that have not been
-    merged into other branches can be easily rebased without
-    affecting other people.  But once it is published, you would
-    not want to rewind it.
-
-(2) ... if a topic branch has been fully merged to "master".
-    Then you can delete it.  More importantly, you should not
-    build on top of it -- other people may already want to
-    change things related to the topic as patches against your
-    "master", so if you need further changes, it is better to
-    fork the topic (perhaps with the same name) afresh from the
-    tip of "master".
-
-Let's look at this example:
-
-		   o---o---o---o---o---o---o---o---o---o "next"
-		  /       /           /           /
-		 /   a---a---b A     /           /
-		/   /               /           /
-	       /   /   c---c---c---c B         /
-	      /   /   /             \         /
-	     /   /   /   b---b C     \       /
-	    /   /   /   /             \     /
-    ---o---o---o---o---o---o---o---o---o---o---o "master"
-
-
-A, B and C are topic branches.
-
- * A has one fix since it was merged up to "next".
-
- * B has finished.  It has been fully merged up to "master" and "next",
-   and is ready to be deleted.
-
- * C has not merged to "next" at all.
-
-We would want to allow C to be rebased, refuse A, and encourage
-B to be deleted.
-
-To compute (1):
-
-	git-rev-list ^master ^topic next
-	git-rev-list ^master        next
-
-	if these match, topic has not merged in next at all.
-
-To compute (2):
-
-	git-rev-list master..topic
-
-	if this is empty, it is fully merged to "master".

data/.git/hooks/prepare-commit-msg.sample

@@ -1,36 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to prepare the commit log message.
-# Called by git-commit with the name of the file that has the
-# commit message, followed by the description of the commit
-# message's source.  The hook's purpose is to edit the commit
-# message file.  If the hook fails with a non-zero status,
-# the commit is aborted.
-#
-# To enable this hook, rename this file to "prepare-commit-msg".
-
-# This hook includes three examples.  The first comments out the
-# "Conflicts:" part of a merge commit.
-#
-# The second includes the output of "git diff --name-status -r"
-# into the message, just before the "git status" output.  It is
-# commented because it doesn't cope with --amend or with squashed
-# commits.
-#
-# The third example adds a Signed-off-by line to the message, that can
-# still be edited.  This is rarely a good idea.
-
-case "$2,$3" in
-  merge,)
-    perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;;
-
-# ,|template,)
-#   perl -i.bak -pe '
-#      print "\n" . `git diff --cached --name-status -r`
-#	 if /^#/ && $first++ == 0' "$1" ;;
-
-  *) ;;
-esac
-
-# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
-# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"

data/.git/hooks/update.sample

@@ -1,107 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to blocks unannotated tags from entering.
-# Called by git-receive-pack with arguments: refname sha1-old sha1-new
-#
-# To enable this hook, rename this file to "update".
-#
-# Config
-# ------
-# hooks.allowunannotated
-#   This boolean sets whether unannotated tags will be allowed into the
-#   repository.  By default they won't be.
-# hooks.allowdeletetag
-#   This boolean sets whether deleting tags will be allowed in the
-#   repository.  By default they won't be.
-# hooks.allowdeletebranch
-#   This boolean sets whether deleting branches will be allowed in the
-#   repository.  By default they won't be.
-#
-
-# --- Command line
-refname="$1"
-oldrev="$2"
-newrev="$3"
-
-# --- Safety check
-if [ -z "$GIT_DIR" ]; then
-	echo "Don't run this script from the command line." >&2
-	echo " (if you want, you could supply GIT_DIR then run" >&2
-	echo "  $0 <ref> <oldrev> <newrev>)" >&2
-	exit 1
-fi
-
-if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
-	echo "Usage: $0 <ref> <oldrev> <newrev>" >&2
-	exit 1
-fi
-
-# --- Config
-allowunannotated=$(git config --bool hooks.allowunannotated)
-allowdeletebranch=$(git config --bool hooks.allowdeletebranch)
-allowdeletetag=$(git config --bool hooks.allowdeletetag)
-
-# check for no description
-projectdesc=$(sed -e '1q' "$GIT_DIR/description")
-if [ -z "$projectdesc" -o "$projectdesc" = "Unnamed repository; edit this file to name it for gitweb." ]; then
-	echo "*** Project description file hasn't been set" >&2
-	exit 1
-fi
-
-# --- Check types
-# if $newrev is 0000...0000, it's a commit to delete a ref.
-if [ "$newrev" = "0000000000000000000000000000000000000000" ]; then
-	newrev_type=delete
-else
-	newrev_type=$(git-cat-file -t $newrev)
-fi
-
-case "$refname","$newrev_type" in
-	refs/tags/*,commit)
-		# un-annotated tag
-		short_refname=${refname##refs/tags/}
-		if [ "$allowunannotated" != "true" ]; then
-			echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
-			echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
-			exit 1
-		fi
-		;;
-	refs/tags/*,delete)
-		# delete tag
-		if [ "$allowdeletetag" != "true" ]; then
-			echo "*** Deleting a tag is not allowed in this repository" >&2
-			exit 1
-		fi
-		;;
-	refs/tags/*,tag)
-		# annotated tag
-		;;
-	refs/heads/*,commit)
-		# branch
-		;;
-	refs/heads/*,delete)
-		# delete branch
-		if [ "$allowdeletebranch" != "true" ]; then
-			echo "*** Deleting a branch is not allowed in this repository" >&2
-			exit 1
-		fi
-		;;
-	refs/remotes/*,commit)
-		# tracking branch
-		;;
-	refs/remotes/*,delete)
-		# delete tracking branch
-		if [ "$allowdeletebranch" != "true" ]; then
-			echo "*** Deleting a tracking branch is not allowed in this repository" >&2
-			exit 1
-		fi
-		;;
-	*)
-		# Anything else (is there anything else?)
-		echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
-		exit 1
-		;;
-esac
-
-# --- Finished
-exit 0

data/.git/info/exclude

@@ -1,6 +0,0 @@
-# git-ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
-# exclude patterns (uncomment them if you want to use them):
-# *.[oa]
-# *~

data/.git/logs/HEAD

@@ -1,3 +0,0 @@
-0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000	clone: from git@github.com:semin/ulla.git
-c87d9b5b7bf5161f25e71698f85f8fac2602ed5d c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 Semin Lee <seminlee@gmail.com> 1235419011 +0000	commit: egor has been renamed to ulla
-c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 956112dd5ba2da60f043f4152a846c6922474bd4 Semin Lee <seminlee@gmail.com> 1235419394 +0000	commit: ulla.gemspec generated

data/.git/logs/refs/heads/master

@@ -1,3 +0,0 @@
-0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000	clone: from git@github.com:semin/ulla.git
-c87d9b5b7bf5161f25e71698f85f8fac2602ed5d c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 Semin Lee <seminlee@gmail.com> 1235419011 +0000	commit: egor has been renamed to ulla
-c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 956112dd5ba2da60f043f4152a846c6922474bd4 Semin Lee <seminlee@gmail.com> 1235419394 +0000	commit: ulla.gemspec generated

data/.git/logs/refs/remotes/origin/HEAD

@@ -1 +0,0 @@
-0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000	clone: from git@github.com:semin/ulla.git

data/.git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace

@@ -1,2 +0,0 @@
-x
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-x
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data/.git/packed-refs

@@ -1,8 +0,0 @@
-# pack-refs with: peeled 
-dfa502c200e3bedb9574f484264a898c2aed09cb refs/tags/REL-0.9.3
-dfa502c200e3bedb9574f484264a898c2aed09cb refs/tags/REL-0.9.0
-b20ce7072cbf7801ab72bd464bb77a0154aafbdf refs/tags/REL-0.0.5
-31ee2a6788abc7036e30175fc8c96ae808725feb refs/tags/REL-0.0.4
-f617333d5f3bda259d927074fe5ff4332db99412 refs/tags/REL-0.0.3
-18609e3b5637c7b102c0d7bdec44a1dcedc4c2e3 refs/tags/REL-0.0.2
-c87d9b5b7bf5161f25e71698f85f8fac2602ed5d refs/remotes/origin/master

data/.git/refs/heads/master

@@ -1 +0,0 @@
-956112dd5ba2da60f043f4152a846c6922474bd4

data/.git/refs/remotes/origin/HEAD

@@ -1 +0,0 @@
-ref: refs/remotes/origin/master

data/.gitignore

@@ -1,8 +0,0 @@
-pkg
-doc
-.DS_Store
-tmp
-data
-*.log
-*.swp
-*~