ulla 0.9.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (91) hide show
  1. data/.git/COMMIT_EDITMSG +13 -0
  2. data/.git/HEAD +1 -0
  3. data/.git/config +11 -0
  4. data/.git/description +1 -0
  5. data/.git/hooks/applypatch-msg.sample +15 -0
  6. data/.git/hooks/commit-msg.sample +24 -0
  7. data/.git/hooks/post-commit.sample +8 -0
  8. data/.git/hooks/post-receive.sample +15 -0
  9. data/.git/hooks/post-update.sample +8 -0
  10. data/.git/hooks/pre-applypatch.sample +14 -0
  11. data/.git/hooks/pre-commit.sample +18 -0
  12. data/.git/hooks/pre-rebase.sample +169 -0
  13. data/.git/hooks/prepare-commit-msg.sample +36 -0
  14. data/.git/hooks/update.sample +107 -0
  15. data/.git/index +0 -0
  16. data/.git/info/exclude +6 -0
  17. data/.git/logs/HEAD +3 -0
  18. data/.git/logs/refs/heads/master +3 -0
  19. data/.git/logs/refs/remotes/origin/HEAD +1 -0
  20. data/.git/objects/06/9494e479f28b5751fb135b8e55e8fef3d3a02e +0 -0
  21. data/.git/objects/22/0df784191ad94983ca1d943e49fe482c9d1069 +0 -0
  22. data/.git/objects/3b/b6f2b7f563175a13a0ccd723aab761552f448b +0 -0
  23. data/.git/objects/41/f48aefb4d7a6a87eb423eaae77ae1e8a58dd6c +0 -0
  24. data/.git/objects/44/d1f1782e3ea1d9fd2f9054784b53e8e810a8ca +0 -0
  25. data/.git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace +2 -0
  26. data/.git/objects/57/1326145a7a4b3e58f3d3008ba343135f213b05 +4 -0
  27. data/.git/objects/6c/4f0844f62b7345f0651b0fb2829a8f157469fb +3 -0
  28. data/.git/objects/73/8dc79450de050f12d48a32602f2ddbe6807029 +0 -0
  29. data/.git/objects/7b/4acb3aee6616d80e295ee21fe8bb7ee93ebe96 +2 -0
  30. data/.git/objects/9e/0a9235b0d70a8029098070007fb414cb52504e +2 -0
  31. data/.git/objects/9e/bfcad2906aac4a23a7c9689a47b76723f5d152 +0 -0
  32. data/.git/objects/a6/578c95f2f474303464b572e9dac716432472b2 +0 -0
  33. data/.git/objects/a8/65ef5700ff04601c6fc40fa5ede3cc25534723 +0 -0
  34. data/.git/objects/aa/285cb176668c5e49c54c6e1d3cc27bd47fd4f4 +0 -0
  35. data/.git/objects/b8/e3828a1082137c4aa4595386bdfb73e3c75b9d +0 -0
  36. data/.git/objects/c2/fb6afc000952b56354fe195682645000d2aea2 +0 -0
  37. data/.git/objects/c4/a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 +2 -0
  38. data/.git/objects/c8/d49f83c4a32cff2d87dd4aa5f83eb7aac3a753 +5 -0
  39. data/.git/objects/ca/c25e8049075ed4bff993705acb4750b2b62ba9 +0 -0
  40. data/.git/objects/d2/ff2e939339eb3fb776e064c258e71dfa1cf396 +0 -0
  41. data/.git/objects/d7/cedf9e2a8ff35b5d7dafdc0f20daed9c65ce44 +0 -0
  42. data/.git/objects/e2/e81af59e3a6c4aa8daac62add62860ae776ba4 +0 -0
  43. data/.git/objects/e5/7c47d183ce5dda1a944c7ee1c19c8a0c4bb278 +0 -0
  44. data/.git/objects/eb/f4a4e1e50bb30731597f776e56b0ccb0c9959f +0 -0
  45. data/.git/objects/f6/39d6f6cf883fde4b9052012919c1df3288c7da +0 -0
  46. data/.git/objects/f8/2346f308f49053df108b7c31ac3089e8b4b4ac +0 -0
  47. data/.git/objects/fb/4b193bb1cbe9041d2f00176f6caa6acfb1fc12 +0 -0
  48. data/.git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.idx +0 -0
  49. data/.git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.pack +0 -0
  50. data/.git/packed-refs +8 -0
  51. data/.git/refs/heads/master +1 -0
  52. data/.git/refs/remotes/origin/HEAD +1 -0
  53. data/.gitignore +8 -0
  54. data/History.txt +42 -0
  55. data/Manifest.txt +90 -0
  56. data/PostInstall.txt +5 -0
  57. data/README.rdoc +259 -0
  58. data/Rakefile +32 -0
  59. data/bin/ulla +10 -0
  60. data/config/website.yml +2 -0
  61. data/config/website.yml.sample +2 -0
  62. data/lib/math_extensions.rb +7 -0
  63. data/lib/narray_extensions.rb +22 -0
  64. data/lib/nmatrix_extensions.rb +245 -0
  65. data/lib/string_extensions.rb +17 -0
  66. data/lib/ulla/cli.rb +1742 -0
  67. data/lib/ulla/environment.rb +34 -0
  68. data/lib/ulla/environment_class_hash.rb +20 -0
  69. data/lib/ulla/environment_feature.rb +26 -0
  70. data/lib/ulla/environment_feature_array.rb +12 -0
  71. data/lib/ulla/heatmap_array.rb +111 -0
  72. data/lib/ulla.rb +6 -0
  73. data/script/console +10 -0
  74. data/script/destroy +14 -0
  75. data/script/generate +14 -0
  76. data/script/txt2html +71 -0
  77. data/test/test_helper.rb +2 -0
  78. data/test/test_math_extensions.rb +11 -0
  79. data/test/test_narray_extensions.rb +14 -0
  80. data/test/test_nmatrix_extensions.rb +16 -0
  81. data/test/test_string_extensions.rb +11 -0
  82. data/test/test_ulla.rb +11 -0
  83. data/test/ulla/test_cli.rb +9 -0
  84. data/test/ulla/test_environment_class_hash.rb +25 -0
  85. data/test/ulla/test_environment_feature.rb +29 -0
  86. data/website/index.html +16 -0
  87. data/website/index.txt +217 -0
  88. data/website/javascripts/rounded_corners_lite.inc.js +285 -0
  89. data/website/stylesheets/screen.css +158 -0
  90. data/website/template.html.erb +57 -0
  91. metadata +215 -0
@@ -0,0 +1,13 @@
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+ ulla.gemspec generated
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+ # Please enter the commit message for your changes. Lines starting
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+ # with '#' will be ignored, and an empty message aborts the commit.
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+ # On branch master
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+ # Your branch is ahead of 'origin/master' by 1 commit.
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+ #
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+ # Changes to be committed:
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+ # (use "git reset HEAD <file>..." to unstage)
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+ #
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+ # modified: Manifest.txt
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+ # modified: Rakefile
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+ # new file: ulla.gemspec
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+ #
data/.git/HEAD ADDED
@@ -0,0 +1 @@
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+ ref: refs/heads/master
data/.git/config ADDED
@@ -0,0 +1,11 @@
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+ [core]
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+ repositoryformatversion = 0
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+ filemode = true
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+ bare = false
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+ logallrefupdates = true
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+ [remote "origin"]
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+ url = git@github.com:semin/ulla.git
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+ fetch = +refs/heads/*:refs/remotes/origin/*
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+ [branch "master"]
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+ remote = origin
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+ merge = refs/heads/master
data/.git/description ADDED
@@ -0,0 +1 @@
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+ Unnamed repository; edit this file to name it for gitweb.
@@ -0,0 +1,15 @@
1
+ #!/bin/sh
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+ #
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+ # An example hook script to check the commit log message taken by
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+ # applypatch from an e-mail message.
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+ #
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+ # The hook should exit with non-zero status after issuing an
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+ # appropriate message if it wants to stop the commit. The hook is
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+ # allowed to edit the commit message file.
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+ #
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+ # To enable this hook, rename this file to "applypatch-msg".
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+
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+ . git-sh-setup
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+ test -x "$GIT_DIR/hooks/commit-msg" &&
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+ exec "$GIT_DIR/hooks/commit-msg" ${1+"$@"}
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+ :
@@ -0,0 +1,24 @@
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+ #!/bin/sh
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+ #
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+ # An example hook script to check the commit log message.
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+ # Called by git-commit with one argument, the name of the file
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+ # that has the commit message. The hook should exit with non-zero
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+ # status after issuing an appropriate message if it wants to stop the
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+ # commit. The hook is allowed to edit the commit message file.
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+ #
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+ # To enable this hook, rename this file to "commit-msg".
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+
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+ # Uncomment the below to add a Signed-off-by line to the message.
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+ # Doing this in a hook is a bad idea in general, but the prepare-commit-msg
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+ # hook is more suited to it.
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+ #
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+ # SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
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+ # grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
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+
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+ # This example catches duplicate Signed-off-by lines.
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+
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+ test "" = "$(grep '^Signed-off-by: ' "$1" |
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+ sort | uniq -c | sed -e '/^[ ]*1[ ]/d')" || {
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+ echo >&2 Duplicate Signed-off-by lines.
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+ exit 1
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+ }
@@ -0,0 +1,8 @@
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+ #!/bin/sh
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+ #
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+ # An example hook script that is called after a successful
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+ # commit is made.
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+ #
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+ # To enable this hook, rename this file to "post-commit".
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+
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+ : Nothing
@@ -0,0 +1,15 @@
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+ #!/bin/sh
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+ #
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+ # An example hook script for the "post-receive" event.
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+ #
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+ # The "post-receive" script is run after receive-pack has accepted a pack
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+ # and the repository has been updated. It is passed arguments in through
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+ # stdin in the form
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+ # <oldrev> <newrev> <refname>
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+ # For example:
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+ # aa453216d1b3e49e7f6f98441fa56946ddcd6a20 68f7abf4e6f922807889f52bc043ecd31b79f814 refs/heads/master
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+ #
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+ # see contrib/hooks/ for an sample, or uncomment the next line and
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+ # rename the file to "post-receive".
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+
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+ #. /usr/share/doc/git-core/contrib/hooks/post-receive-email
@@ -0,0 +1,8 @@
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+ #!/bin/sh
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+ #
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+ # An example hook script to prepare a packed repository for use over
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+ # dumb transports.
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+ #
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+ # To enable this hook, rename this file to "post-update".
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+
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+ exec git-update-server-info
@@ -0,0 +1,14 @@
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+ #!/bin/sh
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+ #
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+ # An example hook script to verify what is about to be committed
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+ # by applypatch from an e-mail message.
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+ #
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+ # The hook should exit with non-zero status after issuing an
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+ # appropriate message if it wants to stop the commit.
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+ #
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+ # To enable this hook, rename this file to "pre-applypatch".
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+
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+ . git-sh-setup
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+ test -x "$GIT_DIR/hooks/pre-commit" &&
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+ exec "$GIT_DIR/hooks/pre-commit" ${1+"$@"}
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+ :
@@ -0,0 +1,18 @@
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+ #!/bin/sh
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+ #
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+ # An example hook script to verify what is about to be committed.
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+ # Called by git-commit with no arguments. The hook should
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+ # exit with non-zero status after issuing an appropriate message if
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+ # it wants to stop the commit.
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+ #
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+ # To enable this hook, rename this file to "pre-commit".
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+
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+ if git-rev-parse --verify HEAD 2>/dev/null
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+ then
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+ against=HEAD
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+ else
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+ # Initial commit: diff against an empty tree object
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+ against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
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+ fi
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+
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+ exec git diff-index --check --cached $against --
@@ -0,0 +1,169 @@
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+ #!/bin/sh
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+ #
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+ # Copyright (c) 2006, 2008 Junio C Hamano
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+ #
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+ # The "pre-rebase" hook is run just before "git-rebase" starts doing
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+ # its job, and can prevent the command from running by exiting with
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+ # non-zero status.
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+ #
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+ # The hook is called with the following parameters:
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+ #
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+ # $1 -- the upstream the series was forked from.
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+ # $2 -- the branch being rebased (or empty when rebasing the current branch).
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+ #
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+ # This sample shows how to prevent topic branches that are already
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+ # merged to 'next' branch from getting rebased, because allowing it
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+ # would result in rebasing already published history.
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+
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+ publish=next
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+ basebranch="$1"
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+ if test "$#" = 2
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+ then
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+ topic="refs/heads/$2"
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+ else
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+ topic=`git symbolic-ref HEAD` ||
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+ exit 0 ;# we do not interrupt rebasing detached HEAD
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+ fi
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+
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+ case "$topic" in
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+ refs/heads/??/*)
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+ ;;
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+ *)
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+ exit 0 ;# we do not interrupt others.
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+ ;;
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+ esac
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+
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+ # Now we are dealing with a topic branch being rebased
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+ # on top of master. Is it OK to rebase it?
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+
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+ # Does the topic really exist?
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+ git show-ref -q "$topic" || {
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+ echo >&2 "No such branch $topic"
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+ exit 1
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+ }
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+
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+ # Is topic fully merged to master?
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+ not_in_master=`git-rev-list --pretty=oneline ^master "$topic"`
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+ if test -z "$not_in_master"
48
+ then
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+ echo >&2 "$topic is fully merged to master; better remove it."
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+ exit 1 ;# we could allow it, but there is no point.
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+ fi
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+
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+ # Is topic ever merged to next? If so you should not be rebasing it.
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+ only_next_1=`git-rev-list ^master "^$topic" ${publish} | sort`
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+ only_next_2=`git-rev-list ^master ${publish} | sort`
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+ if test "$only_next_1" = "$only_next_2"
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+ then
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+ not_in_topic=`git-rev-list "^$topic" master`
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+ if test -z "$not_in_topic"
60
+ then
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+ echo >&2 "$topic is already up-to-date with master"
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+ exit 1 ;# we could allow it, but there is no point.
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+ else
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+ exit 0
65
+ fi
66
+ else
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+ not_in_next=`git-rev-list --pretty=oneline ^${publish} "$topic"`
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+ perl -e '
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+ my $topic = $ARGV[0];
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+ my $msg = "* $topic has commits already merged to public branch:\n";
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+ my (%not_in_next) = map {
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+ /^([0-9a-f]+) /;
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+ ($1 => 1);
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+ } split(/\n/, $ARGV[1]);
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+ for my $elem (map {
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+ /^([0-9a-f]+) (.*)$/;
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+ [$1 => $2];
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+ } split(/\n/, $ARGV[2])) {
79
+ if (!exists $not_in_next{$elem->[0]}) {
80
+ if ($msg) {
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+ print STDERR $msg;
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+ undef $msg;
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+ }
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+ print STDERR " $elem->[1]\n";
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+ }
86
+ }
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+ ' "$topic" "$not_in_next" "$not_in_master"
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+ exit 1
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+ fi
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+
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+ exit 0
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+
93
+ ################################################################
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+
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+ This sample hook safeguards topic branches that have been
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+ published from being rewound.
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+
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+ The workflow assumed here is:
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+
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+ * Once a topic branch forks from "master", "master" is never
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+ merged into it again (either directly or indirectly).
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+
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+ * Once a topic branch is fully cooked and merged into "master",
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+ it is deleted. If you need to build on top of it to correct
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+ earlier mistakes, a new topic branch is created by forking at
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+ the tip of the "master". This is not strictly necessary, but
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+ it makes it easier to keep your history simple.
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+
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+ * Whenever you need to test or publish your changes to topic
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+ branches, merge them into "next" branch.
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+
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+ The script, being an example, hardcodes the publish branch name
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+ to be "next", but it is trivial to make it configurable via
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+ $GIT_DIR/config mechanism.
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+
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+ With this workflow, you would want to know:
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+
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+ (1) ... if a topic branch has ever been merged to "next". Young
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+ topic branches can have stupid mistakes you would rather
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+ clean up before publishing, and things that have not been
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+ merged into other branches can be easily rebased without
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+ affecting other people. But once it is published, you would
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+ not want to rewind it.
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+
125
+ (2) ... if a topic branch has been fully merged to "master".
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+ Then you can delete it. More importantly, you should not
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+ build on top of it -- other people may already want to
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+ change things related to the topic as patches against your
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+ "master", so if you need further changes, it is better to
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+ fork the topic (perhaps with the same name) afresh from the
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+ tip of "master".
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+
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+ Let's look at this example:
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+
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+ o---o---o---o---o---o---o---o---o---o "next"
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+ / / / /
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+ / a---a---b A / /
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+ / / / /
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+ / / c---c---c---c B /
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+ / / / \ /
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+ / / / b---b C \ /
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+ / / / / \ /
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+ ---o---o---o---o---o---o---o---o---o---o---o "master"
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+
145
+
146
+ A, B and C are topic branches.
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+
148
+ * A has one fix since it was merged up to "next".
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+
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+ * B has finished. It has been fully merged up to "master" and "next",
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+ and is ready to be deleted.
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+
153
+ * C has not merged to "next" at all.
154
+
155
+ We would want to allow C to be rebased, refuse A, and encourage
156
+ B to be deleted.
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+
158
+ To compute (1):
159
+
160
+ git-rev-list ^master ^topic next
161
+ git-rev-list ^master next
162
+
163
+ if these match, topic has not merged in next at all.
164
+
165
+ To compute (2):
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+
167
+ git-rev-list master..topic
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+
169
+ if this is empty, it is fully merged to "master".
@@ -0,0 +1,36 @@
1
+ #!/bin/sh
2
+ #
3
+ # An example hook script to prepare the commit log message.
4
+ # Called by git-commit with the name of the file that has the
5
+ # commit message, followed by the description of the commit
6
+ # message's source. The hook's purpose is to edit the commit
7
+ # message file. If the hook fails with a non-zero status,
8
+ # the commit is aborted.
9
+ #
10
+ # To enable this hook, rename this file to "prepare-commit-msg".
11
+
12
+ # This hook includes three examples. The first comments out the
13
+ # "Conflicts:" part of a merge commit.
14
+ #
15
+ # The second includes the output of "git diff --name-status -r"
16
+ # into the message, just before the "git status" output. It is
17
+ # commented because it doesn't cope with --amend or with squashed
18
+ # commits.
19
+ #
20
+ # The third example adds a Signed-off-by line to the message, that can
21
+ # still be edited. This is rarely a good idea.
22
+
23
+ case "$2,$3" in
24
+ merge,)
25
+ perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;;
26
+
27
+ # ,|template,)
28
+ # perl -i.bak -pe '
29
+ # print "\n" . `git diff --cached --name-status -r`
30
+ # if /^#/ && $first++ == 0' "$1" ;;
31
+
32
+ *) ;;
33
+ esac
34
+
35
+ # SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
36
+ # grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
@@ -0,0 +1,107 @@
1
+ #!/bin/sh
2
+ #
3
+ # An example hook script to blocks unannotated tags from entering.
4
+ # Called by git-receive-pack with arguments: refname sha1-old sha1-new
5
+ #
6
+ # To enable this hook, rename this file to "update".
7
+ #
8
+ # Config
9
+ # ------
10
+ # hooks.allowunannotated
11
+ # This boolean sets whether unannotated tags will be allowed into the
12
+ # repository. By default they won't be.
13
+ # hooks.allowdeletetag
14
+ # This boolean sets whether deleting tags will be allowed in the
15
+ # repository. By default they won't be.
16
+ # hooks.allowdeletebranch
17
+ # This boolean sets whether deleting branches will be allowed in the
18
+ # repository. By default they won't be.
19
+ #
20
+
21
+ # --- Command line
22
+ refname="$1"
23
+ oldrev="$2"
24
+ newrev="$3"
25
+
26
+ # --- Safety check
27
+ if [ -z "$GIT_DIR" ]; then
28
+ echo "Don't run this script from the command line." >&2
29
+ echo " (if you want, you could supply GIT_DIR then run" >&2
30
+ echo " $0 <ref> <oldrev> <newrev>)" >&2
31
+ exit 1
32
+ fi
33
+
34
+ if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
35
+ echo "Usage: $0 <ref> <oldrev> <newrev>" >&2
36
+ exit 1
37
+ fi
38
+
39
+ # --- Config
40
+ allowunannotated=$(git config --bool hooks.allowunannotated)
41
+ allowdeletebranch=$(git config --bool hooks.allowdeletebranch)
42
+ allowdeletetag=$(git config --bool hooks.allowdeletetag)
43
+
44
+ # check for no description
45
+ projectdesc=$(sed -e '1q' "$GIT_DIR/description")
46
+ if [ -z "$projectdesc" -o "$projectdesc" = "Unnamed repository; edit this file to name it for gitweb." ]; then
47
+ echo "*** Project description file hasn't been set" >&2
48
+ exit 1
49
+ fi
50
+
51
+ # --- Check types
52
+ # if $newrev is 0000...0000, it's a commit to delete a ref.
53
+ if [ "$newrev" = "0000000000000000000000000000000000000000" ]; then
54
+ newrev_type=delete
55
+ else
56
+ newrev_type=$(git-cat-file -t $newrev)
57
+ fi
58
+
59
+ case "$refname","$newrev_type" in
60
+ refs/tags/*,commit)
61
+ # un-annotated tag
62
+ short_refname=${refname##refs/tags/}
63
+ if [ "$allowunannotated" != "true" ]; then
64
+ echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
65
+ echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
66
+ exit 1
67
+ fi
68
+ ;;
69
+ refs/tags/*,delete)
70
+ # delete tag
71
+ if [ "$allowdeletetag" != "true" ]; then
72
+ echo "*** Deleting a tag is not allowed in this repository" >&2
73
+ exit 1
74
+ fi
75
+ ;;
76
+ refs/tags/*,tag)
77
+ # annotated tag
78
+ ;;
79
+ refs/heads/*,commit)
80
+ # branch
81
+ ;;
82
+ refs/heads/*,delete)
83
+ # delete branch
84
+ if [ "$allowdeletebranch" != "true" ]; then
85
+ echo "*** Deleting a branch is not allowed in this repository" >&2
86
+ exit 1
87
+ fi
88
+ ;;
89
+ refs/remotes/*,commit)
90
+ # tracking branch
91
+ ;;
92
+ refs/remotes/*,delete)
93
+ # delete tracking branch
94
+ if [ "$allowdeletebranch" != "true" ]; then
95
+ echo "*** Deleting a tracking branch is not allowed in this repository" >&2
96
+ exit 1
97
+ fi
98
+ ;;
99
+ *)
100
+ # Anything else (is there anything else?)
101
+ echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
102
+ exit 1
103
+ ;;
104
+ esac
105
+
106
+ # --- Finished
107
+ exit 0
data/.git/index ADDED
Binary file
data/.git/info/exclude ADDED
@@ -0,0 +1,6 @@
1
+ # git-ls-files --others --exclude-from=.git/info/exclude
2
+ # Lines that start with '#' are comments.
3
+ # For a project mostly in C, the following would be a good set of
4
+ # exclude patterns (uncomment them if you want to use them):
5
+ # *.[oa]
6
+ # *~
data/.git/logs/HEAD ADDED
@@ -0,0 +1,3 @@
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+ 0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000 clone: from git@github.com:semin/ulla.git
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+ c87d9b5b7bf5161f25e71698f85f8fac2602ed5d c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 Semin Lee <seminlee@gmail.com> 1235419011 +0000 commit: egor has been renamed to ulla
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+ c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 956112dd5ba2da60f043f4152a846c6922474bd4 Semin Lee <seminlee@gmail.com> 1235419394 +0000 commit: ulla.gemspec generated
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+ 0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000 clone: from git@github.com:semin/ulla.git
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+ c87d9b5b7bf5161f25e71698f85f8fac2602ed5d c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 Semin Lee <seminlee@gmail.com> 1235419011 +0000 commit: egor has been renamed to ulla
3
+ c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 956112dd5ba2da60f043f4152a846c6922474bd4 Semin Lee <seminlee@gmail.com> 1235419394 +0000 commit: ulla.gemspec generated
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+ 0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000 clone: from git@github.com:semin/ulla.git
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1
+ x�NMK1��_1!� �Ӣ ���<d�i7�Nj&Q�כ�h/��e�7��G���:;La��6��2/�s7o�'�{�W�OK���1�w?6PB��W*�k�@g�|Y�g}���yO�q�NV&�� �J�Gʢ1*n��0���04��
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+ )�y�#X���mA(�C��k`
@@ -0,0 +1,4 @@
1
+ x}��j�0�{�S̡�������[)�z2F�պ�%��?��k�I
2
+ %�A,�hf��Pa{��h����l2��������>
3
+ y�T5�ּ9�,��gK-���NXZT
4
+ o�t�T�z
@@ -0,0 +1,3 @@
1
+ xE��
2
+ �0F���vi�MD��$���b1���ط�fq�8��h�jX-֓|*bOB[/п��X�r��
3
+ h���o��/��
@@ -0,0 +1,2 @@
1
+ x�SkK�0��~ť��,�o��o�o����H���N���M߭
2
+ j��{s�9���z�{�3��<�)�;JQ��HJ�W"8 1S�@J �>�� ��0�c�~v0dq�aQ�y�V�T� �ޫT$��%E�L��P2�\�����)FA�|`�І\��h�`|xt|rv~1������x<5lQ��^ϲ���u���q�d%.���ׁ<YB�NZM�%KDmIs`��&���]��R'l”��̖zb ����r��ԩ�k�ܿ�� ���ͥf�E���d_`$�+�$A�]�������5ᶽU��v��ea~3�G�f��a�I�3�Zb�~\�U�]��0,;D�� �:f����}���.I�]�Ā�V�bh����W��ےl��GI����,}?�g
@@ -0,0 +1,2 @@
1
+ x5��
2
+ �0D=�{�"T������=�Ď4c�l��$�iv�Ό�oK�a�0>�1ht��8��Z���E���;��~�l��i��71�=?&�
@@ -0,0 +1,2 @@
1
+ x��M
2
+ �0�]��$��t"��'��L[hZi���G�ߗ�Z��ҩ�� ކ��g!�R���vF� 2��(%�w�ym�i(!�4$q�Q��} !'$1�
@@ -0,0 +1,5 @@
1
+ xmTmO�0��J����-k����*ul0�L�����M.��cg�S�(�}��EU%��9?w��͕�������3[�W�����/N
2
+
3
+ ���1-�+*��S�t��;�z����'}��ŷ�� o.R��Co�ϯ���LoBO�M�;�u�V�H�o�r|I�4a�ݸ�LNÓ�)R3IAc�`=���͘�_$�I�kY�&W��w[5�J��kX�7u�v��|���j����!n��/�6��n���L����f�!��y���0���`W�^<flD� �N�֭t�[� �H,!�2TH�E�Дi���hxQ���'��+"n&7HR�A{�7y�~o_�kn�T��ʞ��_�(VI��F��
4
+ M�N���G�]��������|�h,h�iM�M�D��I'��W�M\��&9
5
+ _[tԯA[�(
data/.git/packed-refs ADDED
@@ -0,0 +1,8 @@
1
+ # pack-refs with: peeled
2
+ dfa502c200e3bedb9574f484264a898c2aed09cb refs/tags/REL-0.9.3
3
+ dfa502c200e3bedb9574f484264a898c2aed09cb refs/tags/REL-0.9.0
4
+ b20ce7072cbf7801ab72bd464bb77a0154aafbdf refs/tags/REL-0.0.5
5
+ 31ee2a6788abc7036e30175fc8c96ae808725feb refs/tags/REL-0.0.4
6
+ f617333d5f3bda259d927074fe5ff4332db99412 refs/tags/REL-0.0.3
7
+ 18609e3b5637c7b102c0d7bdec44a1dcedc4c2e3 refs/tags/REL-0.0.2
8
+ c87d9b5b7bf5161f25e71698f85f8fac2602ed5d refs/remotes/origin/master
@@ -0,0 +1 @@
1
+ 956112dd5ba2da60f043f4152a846c6922474bd4
@@ -0,0 +1 @@
1
+ ref: refs/remotes/origin/master
data/.gitignore ADDED
@@ -0,0 +1,8 @@
1
+ pkg
2
+ doc
3
+ .DS_Store
4
+ tmp
5
+ data
6
+ *.log
7
+ *.swp
8
+ *~
data/History.txt ADDED
@@ -0,0 +1,42 @@
1
+ == 0.9.3 23/2/2009
2
+
3
+ * Egor has been renamed to Ulla!
4
+
5
+ == 0.9.0 13/2/2009
6
+
7
+ * Added --heatmap option for heat map generation from substitution tables
8
+ * Added --heatmap-format option for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
9
+ * Added --heatmap-stem option to set a file name of total heat maps figure when --heatmap 1 or 2 is set
10
+ * Added --heatmap-columns option to set the number of tables in a row when --heatmap 1 or 2 is set
11
+ * Added --heatmap-values option to print values in the cells of heat maps
12
+ * Renamed --noround option to --noroundoff
13
+ * 'simple_memoize' RubyGem package is no longer required
14
+
15
+ == 0.0.5 23/1/2009
16
+
17
+ * Warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
18
+ * Added --augosigma option to avoid excessive influence of background frequencies
19
+ * Added --noround option was added to get original log odds ratios
20
+ * Added --p1smooth option was added to enable p1 probability smoothing when partial smoothing
21
+ * Fixed a bug in p2 probability calculation of the partial smoothing procedure
22
+ * Fixed a bug in total probability/log odds ratio calculation
23
+ * Changed default verbosity from ERROR to WARN
24
+ * Refactored codes to be more human readable and DRY
25
+
26
+ == 0.0.4 15/12/2008
27
+
28
+ * Fixed a bug to generated log-odds ratio matrices with --nosmooth option
29
+ * Copes with no observations or mutations
30
+
31
+ == 0.0.3 09/12/2008
32
+
33
+ * Added --cys (-j) 2 not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
34
+ * Fixed a bug to make masking works for target amino acid, too
35
+
36
+ == 0.0.2 13/11/2008
37
+
38
+ * Supports user provided constrained environment features are properly handled
39
+
40
+ == 0.0.1 07/11/2008
41
+
42
+ * Initial release