labofsahil/github-event-dataset-2012 huggingface dataset:
ClassLauncher: do not forget previous classpath additions

We want to re-use a ClassLoaderPlus if we created one previously,
not forget about it, when adding new elements to the class path.

The code used to work only because the default class loader is a
URLClassLoader and we play reflection games to access its addURL()
method.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'class-launcher'

Some change that was buried in the legacy mode work.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
CodeHacker: remove unused replaceMethod() method

For the legacy mode, we should avoid replacing methods in every case,
so we will not need this method anymore, ever.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
WIP: Introduce a legacy mode to the LegacyService

To fall back to original ImageJ1 (e.g. should some plugin or macro not
work in ImageJ2 as it did in ImageJ1), we'd like to be able to drive a
patched ImageJ1 in such a way that it behaves exactly like unpatched
ImageJ1 (except still synchronizing all the data with ImageJ2).

This change introduces a flag in the class LegacyService, and changes the
Javassist patches so that the legacy mode is heeded.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
WIP: Add Help>Legacy Mode

Since it is very hard (or might be impossible) to achieve full 100%
backwards-compatibility with ImageJ1, we want to have one last way out for
users whose plugin/macro might not work in ImageJ2, namely to show the old
ImageJ1 GUI and lose all the ImageJ2 goodness.

This is what Help>Legacy Mode does.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Make the ImageJ context known to scripts

Scripts can now access the current context via the local variable called
'imagej'.

Suggested by Lee Kamentsky.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add convenience method ImageJ#getService(String)

In some scripting language (Javascript, I am looking at you!), it is
pretty difficult to get at the java.lang.Class instance of a Java class
give its name. In such a case, the method added by this commit comes in
real handy. Now, we can call

	service = imagej.getService("imagej.display.DisplayService");

instead of the quite unwieldy

	loader = Thread.currentThread().getContextClassLoader();
	clazz = loader.loadClass("imagej.display.DisplayService");
	service = imagej.getService(clazz);

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
ScriptService: Test the Javascript backend

Javascript should be available in every Java 1.6 compliant system,
so let's just test the ScriptService using that backend.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add the top-level 'script' project with the 'script-beanshell' child

This commit may serve as example what it takes to add other Script
languages in the future.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add the Beanshell scripting adapter

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add tests for the Beanshell adapter

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'scripts'

This merges the enhanced scripting framework. We will add more languages
as we go, but the basic building blocks are now in place.

In particular, we have the current ImageJ context available to every
script under the name "IJ". This will become a delegator in the near
future, offering all the macro functions as non-static methods of a
Contextual as well as all the methods of the imagej.ImageJ class (which
are simply proxied through).

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Adaptive median func: improve algorithm readability
Fixed issue #264
remove test dir
initial commit
for appengine
[#41333699] Alert detail page with fake info
windows: small style fix in uv-win.h
windows: separate uv_tty_t read state from write state
windows: readable tty handles need access to console output

Readable tty handles need to be able to update the virtual window,
so if uv_tty_t is initialized with a console input fd, additionally
open the console output.
unix: move platform init out of loop.c

Move platform-specific initialization logic out of loop.c and into the
platform files (freebsd.c, sunos.c, etc).
unix: remove UV_REQ_BUFSML_SIZE
build: handle bad gcc -dumpversion output

`gcc -dumpversion` usually prints major.minor - but on sunos it prints
major.minor.patch.
unix: split up uv-unix.h
stream: use select for specific fds on osx

kqueue(2) on osx doesn't work (emits EINVAL error) with specific fds
(i.e. /dev/tty, /dev/null, etc). When given such descriptors - start
select(2) watcher thread that will emit io events.
fixes from jim
Remove powerline
Fixes PATH and set spell checker program
Use ⌘+arrows for moving through windows
I'm not using rvm anymore
Fix visual settings for when running in console mode
Initialize Emacs server if not running
Use Monaco 14pt as default font
Minibuffer settings
Add docs for m_spanningtree.
Manually merge changes by @neersighted.
Ready to work
Rename vars
WIP
Article Next / Prev correction : Simply gets the article.
Content Element rewrite.
Add ContentEditable plugin to Editor
Logging file handler is closed when the portlet is destroyed.
Correction of UrlFactory when setting an URL absolute.
Update to "minimal" version of #1689, without all the Lua changes, just
the buttons to enable the hungry autopilot.
Started min-max, working with example
Started epc7
building a path of the presentation steps
client and server support lower case characters in messages
working
set for turbo boosting
implemented affine turbo+
working
merged in affine_turbo+
Notations changes for location option
Missing a brace
Fix some bugs of new Schema object integration
Don't strip the U4/U6 port numbers if updated after login.
sat
A new layout
a new instance
justify some floder
modify the structure
good
change the structure of the director.
Add some navigation in.
New changelist2
Refactor parameter passing to IndexProvider. Added limit support and tests.
switch to bytebuffers for IO
pagos
Merge branch 'master' of https://github.com/jcordero/bind.git
presentation detalle de cheque
Tarjetas - BIND DMZ (Arreglos de filtros).
Merge branch 'master' of https://github.com/jcordero/bind.git
bug fixes
cache command and bug fixes
More README.md...
Bugfix in filemanager for:
TypeError: super(type, obj): obj must be an instance or subtype of type
DOC


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3920 42a5c34f-2066-0410-bec5-ba365beb4995
CHG: slight rewording


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3921 42a5c34f-2066-0410-bec5-ba365beb4995
OBS: "average_edt" tool obsoleted by "sba" and "sbai" tools.


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3922 42a5c34f-2066-0410-bec5-ba365beb4995
DOC


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3923 42a5c34f-2066-0410-bec5-ba365beb4995
FIX: MacPorts gcc configuration for packaging

git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3924 42a5c34f-2066-0410-bec5-ba365beb4995
CHG: rename system for separation from non=MacPorts builds


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3925 42a5c34f-2066-0410-bec5-ba365beb4995
TST: XML and man page baselines changed


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3926 42a5c34f-2066-0410-bec5-ba365beb4995
REF: moved SBA code into library class.


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3927 42a5c34f-2066-0410-bec5-ba365beb4995
DOC


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3928 42a5c34f-2066-0410-bec5-ba365beb4995
DOC


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3929 42a5c34f-2066-0410-bec5-ba365beb4995
REF: compute label flags when initializing SBA class


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3930 42a5c34f-2066-0410-bec5-ba365beb4995
REF: prepare for introduction of outlier detection code


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3931 42a5c34f-2066-0410-bec5-ba365beb4995
REF: identified more common code


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3932 42a5c34f-2066-0410-bec5-ba365beb4995
ADD: outlier detection in shape-based averaging


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3933 42a5c34f-2066-0410-bec5-ba365beb4995
TST: tests and baselines for SBA with outlier detection


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3934 42a5c34f-2066-0410-bec5-ba365beb4995
DOC


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3935 42a5c34f-2066-0410-bec5-ba365beb4995
REF: use std::vector instead of TypedArray


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3936 42a5c34f-2066-0410-bec5-ba365beb4995
REF: use generic type rather than "float"


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3937 42a5c34f-2066-0410-bec5-ba365beb4995
DOC: removed outdated \todo


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3938 42a5c34f-2066-0410-bec5-ba365beb4995
OBS: removed unused string.h include


git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@3939 42a5c34f-2066-0410-bec5-ba365beb4995
JERSEY-1291: fixed handling of generic types in proxy-client

Change-Id: I26344687fce0ca690dc90a7b0d6c7c59dfb06e35
Test Commit

Tidied up bootstrap-overrides.less. Linked to a number of less files, so development will be easier.

p.lead isn't showing in the correct font. Will see what's wrong.

Signed-off-by: Kenneth Lim <kenlimmj@gmail.com>
Tidied CSS

Cleaned up bootstrap_and_overrides.less - Removed all extraneous variables, and refactored excess code into font.less and ol.less. Font.less carries font loading information, and ol.less carries OL specific hacks for bootstrap.

Cleaned up the structure of the erbs in /pages.

Bug still exists where it is not possible to declare "is_user_signed_in" a second time on the same page without $end error popping.

Signed-off-by: Kenneth Lim <kenlimmj@gmail.com>
Fixed Pages Nav

Fixed the issue with the sign in blocks giving problems. Damn programming languages love to use "end" as a reserved name and not tell you that. Format is now

<%=render 'shared/start'%>
<%=render 'shared/about'%>
<%=render 'shared/last'%>

Start checks for sign in. If true, returns profile name and link. If false, returns login/register link. Links to toggle the next block will be added in due course

About is meant to be swappable. Provides context dependent links, e.g. "subjects" or "about us" related.

Last checks for sign in. If true, returns a log out link. If false, returns nothing.

Signed-off-by: Kenneth Lim <kenlimmj@gmail.com>
Fixed fonts
Don't run start-stop by default
integração com leitor digital
Install ruby.vim bundle as a submodule.
Install markdown.vim bundle as a submodule.
Install javascript.vim bundle as a submodule.
fix bug of focus urlbar with set homepage to 'about:blank'

Signed-off-by: jiaofeng <jiaofeng601@gmail.com>
Merge branch 'master' of github.com:jiaofeng/COBA
Update powerline plugin.
Update syntastic plugin.
Update tagbar plugin.
Update zencoding plugin.
Update fugitive plugin.
Update snipMate plugin.
Update tabular plugin.
Update zencoding plugin.
Update AsyncCommand plugin.
Update coffee-script plugin.
Update fugitive plugin.
Update lustyjuggler plugin.
Update ragtag plugin.
Update tlib plugin.
Update zencoding plugin.
[codegen] Fix bugs
Fix compiling error on some architecture after adding -Werror

Signed-off-by: Jiaju Zhang <jjzhang@suse.de>
Enable solarized
Removed old forgotten password function.
Trying to fix stuff
Fix try1
Edited instructions and added probability to axes.
hiscore toimimaan ja kysymään nimeä
drag and drop commence
daskldjhf
Add initial support for user interrupt.
Fix debugger connection not establishing.

Non-blocking socket listener function was not returning the socket and
address. Introduced this when I moved the listener into its own function
and didn't test my work :)
Document xdebug_break() behavior.

xdebug_break() is helpful when the debugger won't stop at a breakpoint.
The causes of this vary; for example some complex auto class loading may
be confusing xdebug. Using xdebug_break() is a last resort, but at least
it achieves the desired effect of breaking at a line of code when
nothing else works.
Merge pull request #7 from artnez/xdebug-hardcoded-break-docs

Added question about breakpoints to FAQ in help file: "Document xdebug_break() behavior."
Merge branch 'user-interrupt-support' of https://github.com/artnez/vdebug into user-interrupt
Some refactoring of artnez's connection interrupt code

Removed vim dependency from dbgp and created a new InputStream class
which is passed in to the Connection object. This is used to probe Vim's
input stream and check for keyboard interrupts.
Python omni completion is currently broken when Vdebug is installed.

Vdebug is currently overwriting the built in 'dir' function when adding
itself to the python path.  Changing the name of the temporary variable
fixes omni completion.
Merge pull request #8 from csomme/master

Vdebug is currently overwriting the built in 'dir' function when adding itself to the python path.  Changing the name of the temporary variable fixes omni completion.
Fixed bug with opening/closing tree nodes after eval
Merge branch 'master' into user-interrupt
Removed help tags from repo and added to gitignore, fixes #10
Deleted seperator line in WatchWindow.

Without that line, more variables are visible at once in the DebuggerWatch window. The hierarchy is still visible via the indentation.
Added some fixes for node debug support
Added HISTORY file for a changelog
Updated HISTORY with entire history so far
Merge branch 'master' of https://github.com/georgjaehnig/vdebug into watch-window-options
Added compact style option for watch window
Updated help file with new watch window style option
Added debug set up for NodeJS to the help file
scj: work around for scope sizing
tester

Signed-off-by: Joshua Michaels <joshuaiz@me.com>
Manually define LIBARCHSUFFIX PLIST entries.
Convert time/p5-Time-HiRes to multiarch.
Enable p5-* multiarch based on USE_LANGUAGES.

This will hopefully end up easier than maintaining USE_MULTIARCH entries
in lots of packages, and any packages which do not yet have
USE_LANGUAGES set correctly can be added and upstreamed to avoid extra
diffs.
initial esper based feed of LSD
get pylint.el from the offical pylint repo
* ADD:
 * FIX: compilation time
 * CHG: merge with main repo
 * CHG: creation of function to count characterd of fields in the table, and use this to create string for record
 * CHG: internal representation of Relation
 * CHG: internal representation of Relation
 * ADD: test scriptcompileBenchmarks_exampleND.py
 * DEL: NULL
 * ADD: String utilities class
Merge branch 'c++' of github.com:lalanne/goas into c++
 * CHG: name of test script
 * ADD: new design structure of the code, vector optimisations, polymorphism for Fields, reestructure of the print method
 * ADD: new design structure of the code, vector optimisations, polymorphism for Fields, reestructure of the print method
 * CHG: Record
 * CHG: hand made strlen-----> to------> strlen duh
 * DEL: includes
 * CHG: Records
 * CHG: Records
 * CHG: Records
 * CHG: Records
stripped version of mylbfgs - not running
Cleaned up the problem with Fzzz and The Fuzz
added sermon player and format to home page
Scrape *_pm.PL scripts in misc/perlcore.

Regenerates perlcore.mods-5.16.0 using the new script.
DynaLoader and some ext/ modules were missing.
Remove old unused tmp var from prepkg.
Better error handling in genpkg's dupver().
Just added the P2C site and testing 1st commit.

This is all graphics, .css, .php, .js, and fonts for the P2C site.
Added toString()

Signed-off-by: John Lawson <john@jwlawson.co.uk>
Added debug logging.

Signed-off-by: John Lawson <john@jwlawson.co.uk>
Sends som emock data to graphview.

Signed-off-by: John Lawson <john@jwlawson.co.uk>
Label class with text and position

Signed-off-by: John Lawson <john@jwlawson.co.uk>
Finally got it all working. 

Sets a size correctly, scales to fill size, displays graph nicely, can
have each edge padding adjusted.

Signed-off-by: John Lawson <john@jwlawson.co.uk>
Logging off

Signed-off-by: John Lawson <john@jwlawson.co.uk>
Scrollview with nested linearlayout added, so graphs can be added
programatically

Signed-off-by: John Lawson <john@jwlawson.co.uk>
Added a couple new graphs

Signed-off-by: John Lawson <john@jwlawson.co.uk>
add value types and error handling
miner.php by default don't display IP/Port numbers in error messages
set as version 2.7.5i
Very important!
Added persist method to staticactor so that they can be saved and loaded to from disk.
Added intellij settings.
Renamed intellij settings.
Added osx terminal settings.
Add ignore, cut, joinP combinators
Fixed #30
Fixed #31
faqs
pages
color, line width, eraser
Forward groups as well
Make sure IPs are only sent once when sending to ArrayPort on a subgraph
Make sending anything wait until downstream component is ready
Merge branch 'refs/heads/buffer_until_ready' into develop
Merge branch 'refs/heads/link_arrayport_on_subgraphs' into develop
Nomenclature
Merge branch 'refs/heads/buffer_until_ready' into develop
Buffer outgoing subgraph ports as well
Merge branch 'refs/heads/buffer_until_ready' into develop
aタグをhamlスタイルで書き換え
Purged no longer used translations.
Added username checking to DB and fixed async bugs with POST requests
Camera and config update
fixed alignments
Merge branch 'master' of https://github.com/kjlam/Ginwoo2
all edited
initial
Quick fix to possessive pronoun
Added theory of relations; modified stylsheet to use 1px instead of 1pt
Cleaned up relations page
devel version 0.400_1 based on iup-3.6 & co.
Fix pixel pattern calculating
Add a title helper
Add blueprint css
Merge branch master into bachelorproject.
dziwnie sie recty pierdola

caly czas probuje to do brze wyswietlic i nie wiem jakie wspolrzedne dac
oO
juz cos tam wykminilem ale jeszcze chwila zamin bedzie git
11:23

cale kupowanie juz smiga jaqk trzeba biore sie za sprzedarz
No 37 solved
No 39 solved but too slow...
make tests compatible with simpletest 1.1
update BDD tests, make compatible with behat 2.3.3

Also updated/removed tests to match Tonic's current feature-set.
Improved Examples
Implemented PathSmoothing, but not tested yet.
Compiles as C++, although still C-code
krfs: struct Tree_s is now a C++ class from the outside
Mostly ported from C to somewhat sane C++11.
globals variables
Bash completion script
Update @dayz/dayz_code/stringtable.xml
wrapping up. admin interface..
refine Makefil
parse node and output
Partially fixes #3. Will create new bug for remaining commands.
change file name to be compatible with cpp
去掉UserController
encode constants
fix another bitmask comparison
fix warnings, some sugested by http://www.jasoncavett.com/2012/05/better-aero-snap-with-openbox.html?showComment=1346609597742#c1018008963616724440
Started implementing some of the ll rep code. Created Ir to ll visitor converter class
return proof
fix bug in tools saving mutated command
fix waitresponse(1000) to waitresponse()
delete 's' word
Merge pull request #17 from huangnoah/fix-waitresponse

fix waitresponse(1000) to waitresponse()
update for form and print pdf for client
saldkfjaslkdjflksadjflk
Added .tmux.conf file.
Site updated at 2012-06-03 10:03:47 UTC
Octopress init
Site updated at 2012-10-06 05:46:53 UTC
TableLayout, fixed merging column defaults and cell defaults.
Merge remote-tracking branch 'origin/master'
NinePatch, added getTexture().
Added apache install, and moved git and misc services into own scripts
Added rvm as a submodule
change favorites model, add user_id + song_id cols, set up favorites controller
gemfile housekeeping
update mixtape index view, clean up mixtape show view
switch buy/own button colors shared song
add purchase date to purchase table + model
file cleanup
add ransack gem, add search and sort capabilities to song index -- revisit, associated fields are not working correctly
update search form fields
temporarily change fave logic to song.name -- revisit fave logic/naming
add search and sort to user song collection -- revisit sort for associated fields
clean up song index + user_table_head + remove search from song collection b/c returns results on song index page
create starter purchase form
Pleshds
se enter the commit message for your changes. Lines starting
Update zh/chp102-1.md
Update zh/chp101-4.md
Update Unit-1/Lesson-15.md
add va
Performance for ycbcr2rgb function
修复几个bug，增加日志
Merge branch 'master' of https://github.com/liuaifu/asio5
org.liveSense.service.captcha:
Parameter handling via PrameterProvider class.
clean up duplicate info in the readme
Skyrim ASPC (Acoustic Space) Record
Skyrim LVSP (leveled spell) Record
- Start Splitting game specific stuff in GenericChunks into
  separate source files/namespaces
Skyrim LVLN (Leveled Actor) Record
Fix warning (conversion to bool)
Macro for conditionally setting/clearing bit (slightly faster than branching method ( conditional ? do 1 : do 2)
- Skyrim ARTO (Art Object) Record
- Missing parsing code for new record types
started designing db
add autowire and property parse feature
Добавлено редактирование типа бумаги. Связь кол-ва нарушена. Баг!!!!
Добавлено работа с типом бумаги сохранение, востановление расчет цены. Нет передачи в корзину.
Added UIWebView
pending transactions
fixed javascripts in head
delete playlist functionality
list all playlists feature
RFCT Run hlint

Did not follow every suggestion, only where code was made simpler
RFCT Less code. Better docs
updated paths and references to whistle to kazoo
MIFOS-5649 changes in date validator
[equo] be more explicit when running with forced "--pretend" when not root

Fixes bug 2882
[dev-util/molecule] temp add, while waiting for Portage to propagate it
[www-misc/zoneminder] Version from dilfridge overlay
[www-misc/zoneminder] Fixed dependency on media-video/ffmpeg
[www-misc/zoneminder] Keyworded ebuild
[kde-misc/entropy-kioslaves] export CMAKE_REQUIRED=never as per Gentoo bug #409367
bugfix midi
Completely removed disabled opcodes (and one support function, MakeSameSize(), which was only used by the disabled opcodes). Fixes #1868.
added the missing welcome.tex
bar chart transition example
some starter code
added a basic grid functionarity
js para que se actualize el link del menu que se aprieta
Merge remote-tracking branch 'origin/master'
add:ga code
Fixed POMs so everything builds nicely from the root.
Signed CLA
Specify parent POMs
Specify issue management details in master POM
Updated scm url in POM
Remove inherited property from POMs
Updated module display names in POMs
Remove overly verbose comments and an outdated description from POM
Updated developer roles in POM
Specify url in master POM
Remove inherited and default properties from POMs
Merge branch 'maven' into master
Merge remote-tracking branch 'upstream/master' into fixes
Fix
Use *guard* as buffer name for guard
fix scroll spy.  it is so dumb.
DG MS; don't show the make button on the profile page
labels
don't load tests in browser
Add & export mapCollectionWithKey
Typoe fix, add test for mapCollection
Version bump (0.4.5.0)
Merge pull request #7 from jaspervdj/master

Add & export mapCollectionWithKey
Update mbutil/util.py

Fix fix tiles count error on compression
Merge pull request #36 from yellow-sky/master

Fix small bug on tiles compression
add more color to the visual test output
image_filter: extract apply_filter boilerplate, pass filter by reference
image_filter: make 'gray' and 'invert' filters honor alpha
Merge pull request #1541 from mapycz/compositing

Fix 'blur' and 'invert' image-filters to honor alpha
add mention of new 64 bit integer support for datasources and expressions
also clear out stale object files than scons my no longer know about
replace boost::trim with faster custom trim - closes #1633
Making our README even more fancy.
Margin for the right guy.
add right path to url
Corrected Added Starter Files
Fixing bug in unpaired mode, with --all-contigs and --single-best-mappings set, also added --min-mapq to mergesam and made mergesam report 0 MAPQ for MAPQ<4
Fixed a problem in the packaging script
update from SVN to GIT packaging, script was giving erro
Fixed default number of seeds in genome splitting scripts.
Fixed issue with --trim-illumina producing reads of length 0
Fixed writing of fasta/fastq when lines wrap around
Now original SHRiMP format outputs the posterior score instead of the raw SW score in colour space.
Updated version number
Fixed space issue in get_contigs.py in fasta names
replace linear contig search by binary search
Updated history with two brief notes
replaced binary search for contig starts by 17-way search, to fully utilize 64-byte cache lines (each node has 16 4-byte int keys)
use linear search for <100 contigs, use 17-way search after
changed search tree for contig offsets to uint32_t instead of int
hard-coded b=17 in search functions
Fixed a potential error when using mergesam with non-SHRiMP SAM files
While reading in from two input files, sometimes fasta2fastq would stop early because of differences in the bytes read from each file. This should now be fixed.
changed default window overlap from 20% to 90%
Some updates
do not drop clones when one read is smaller than any seed
included prettyprint editstring in sam extra flags
safer build: consider target dirty if depfile is missing
Merge pull request #407 from maximuska/proposed/dirty-on-missing-depfile

safer build: consider target dirty if depfile is missing
Use ruby methods to check class ancestors, instead of m_tbl directly
Merge pull request #24 from geoffyoungs/master

Fix ancestor checking
Changed XML routing system

More flexible with the power of xpath
Added tests emphasizing current behavior of gcd()
Fixed patch readme
Restored _getCookieName function
Merge branch 'dev' into gh-pages
Added creation of inner SceneModels for the GUI
Added documentation
Added tests for kata-002 from Bruno's branch
aggiunto test-004
inserito test
corretto test
comments in english :)
Merge remote-tracking branch 'swat/master'
Cosmetics
Merge remote-tracking branch 'swat/master'
Fix mayen plugins versions after 2.1 rollback

Signed-off-by: Alin Dreghiciu <adreghiciu@gmail.com>
NXCM-4516: Walker fix

When Walker invoked with starting path that was not pointing to
collection, it simply returned doing nothing. Otherwise, it would
recursively "dive" in.

This simply fix contains a small refactoring, pulling out
the "walkItem" part, and in main entry point, if the starting
item is not a collection, then direct call to this method is made.

UT added covering this case, that asserts that walk does happen
to the 1 targeted file item.
Merge pull request #490 from sonatype/nxcm-4516-walker-not-walking

NXCM-4516: Walker fix
Added a soname to the Ruby cqpid extension build.
Bumped the Ruby release version to 0.16.
Created a build environment for non-blocking I/O modules.

This module is for use by language bindings and is not a part of the
public APIs.
The non-blocking I/O commands for language bindings.

The commands are based on the TrackerAdaptor and TrackerEventHandler
classes, which enable the commands to run in a separate thread. This
allows languages that have a global interpreter to not be blocked when a
blocking I/O command is executed.

The commands are:

 * Receiver.fetch
 * Receiver.get
 * Sender.send
 * Session.acknowledge
 * Session.next_receiver
 * Session.sync
Automake environment for the nonblocking I/O library.
Ruby extensions to use the non-blocking I/O commands.

Provides Ruby native extensions that take advantage of the non-blocking
I/O commands provided in the non-public APIs.

The following APIs are provided:

 * Qpid::Messaging::Receiver.get
 * Qpid::Messaging::Receiver.fetch
 * Qpid::Messaging::Sender.send
 * Qpid::Messaging::Session.acknowledge
 * Qpid::Messaging::Session.next_receiver
 * Qpid::Messaging::Session.sync

Removed the previous implementation of each method since they are no
longer used.
Updated the Rakefile to build the nonblockio code.
Modified the Qpid Ruby code to load the non-blocking I/O bits.

If the non-blocking code is present, then this change attempts to load
it to replace the standard blocking I/O code seamlessly.
Modified the testing environment to accomodate non-blocking I/O.

Modified the Rspec tests to check for the existence of non-blocking I/O
code. It doesn't change the actual tests but instead provides a few
expectation checks.
Updated the spout and drain ruby examples.
Cleaned up the Ruby bindings documentation.
More cleanups on the Ruby documentation.
Added a compile-time macro for the Ruby version for native extensions.

This version allows for Ruby 1.8 and 1.9 development in the same
codebase. So we can support both development streams in one codebase.
Updated the Rakefile to work under both Ruby 1.8 and 1.9.

It determines at startup which Ruby is in use and then adjusts the
requires and RSpec setup accordingly.
Modified the Ruby native extensions for Ruby 1.9.

Moved the Ruby 1.8 code into conditional areas that will only compile
when Ruby 1.8 is the target. When Ruby 1.9 is the target then the
updated threading model is used.
Created a build environment for non-blocking I/O modules.

This module is for use by language bindings and is not a part of the
public APIs.
The non-blocking I/O commands for language bindings.

The commands are based on the TrackerAdaptor and TrackerEventHandler
classes, which enable the commands to run in a separate thread. This
allows languages that have a global interpreter to not be blocked when a
blocking I/O command is executed.

The commands are:

 * Receiver.fetch
 * Receiver.get
 * Sender.send
 * Session.acknowledge
 * Session.next_receiver
 * Session.sync
Automake environment for the nonblocking I/O library.
Ruby extensions to use the non-blocking I/O commands.

Provides Ruby native extensions that take advantage of the non-blocking
I/O commands provided in the non-public APIs.

The following APIs are provided:

 * Qpid::Messaging::Receiver.get
 * Qpid::Messaging::Receiver.fetch
 * Qpid::Messaging::Sender.send
 * Qpid::Messaging::Session.acknowledge
 * Qpid::Messaging::Session.next_receiver
 * Qpid::Messaging::Session.sync

Removed the previous implementation of each method since they are no
longer used.
Updated the Rakefile to build the nonblockio code.
Modified the Qpid Ruby code to load the non-blocking I/O bits.

If the non-blocking code is present, then this change attempts to load
it to replace the standard blocking I/O code seamlessly.
Modified the testing environment to accomodate non-blocking I/O.

Modified the Rspec tests to check for the existence of non-blocking I/O
code. It doesn't change the actual tests but instead provides a few
expectation checks.
Updated the spout and drain ruby examples.
Cleaned up the Ruby bindings documentation.
More cleanups on the Ruby documentation.
Added a compile-time macro for the Ruby version for native extensions.

This version allows for Ruby 1.8 and 1.9 development in the same
codebase. So we can support both development streams in one codebase.
Updated the Rakefile to work under both Ruby 1.8 and 1.9.

It determines at startup which Ruby is in use and then adjusts the
requires and RSpec setup accordingly.
Updated the Ruby extensions to selectively check for dependencies.

For either Ruby 1.8 or 1.9 it looks for the standard header files
provided by the QPID development package.

If the code is compiled under Ruby 1.8 then it checks for the
qpidnonblockio shared library and the related header files.

Merge with the Rakefile changes
Updated the Rspec tests to accomodate both Ruby 1.8 and Ruby 1.9.

There are conditionals on the expectations that let the simpler Ruby 1.9
tests run while the 1.8 tests remain unchanged.
Modified the Ruby native extensions for Ruby 1.9.

Moved the Ruby 1.8 code into conditional areas that will only compile
when Ruby 1.8 is the target. When Ruby 1.9 is the target then the
updated threading model is used.
Created the new CommandRunner type for the dynamic language bindings.

CommandRunner executes in a separate thread and processes instances of
SynchioCommand. Refactored all existing synchio commands to extend this
new SynchioCommand type and eliminated their running a thread per
object.
Added "ruby_gemfile" as a build target.

This generates the file "qpid_messaging-${VER}.gem" in the build output
directory.
Remove install instructions for now
added height and is balance to BST, also shouldn't have taken the return out of the recursive call
sort: added some commetns
String Functions Complete.
11 functions complete. Stuck on the last array function.
Modified sortArray function to have a second argument...

User can now literally pass the key through this second argument.
Modified completion date in HTML...

Refactored some of the functions to make for cleaner code.

Added Flowchart
Reverted sortArrayByKey() function...

reverted due to issues w/Firefox although it works in Safari correctly.

Added Flowchart links to JS and HTML
pykeg: added STATIC_URL as per documentation

added STATIC_URL as per documentation and updated MEDIA_ROOT path to match STATIC_ROOT path. When i first set this up i thought i needed full URL but i have gone back and tested that it does not require this.
new format for sending
new format for sending
шаблон работает, походу заскоки самого гема
remove unneeded operations from Makefile
deref latest and next symbolic names
minor enhancements.

* SIGHUP to reload caches.
* Use argparse for arguments.
* Optionally use setproctitle to set process name
Remove obsolete scripts and dirs
Added form states usage example
IE7 throws an error if you use unquoted false or true as a key in object literals.

Quoting it works (and x[false] and x[true] work).
Basic email support
new accounts-ui spinner, has height of line
Emails, emails and more emails...
#1 Add targets and influencers. Add chosen.js
Add seec::cm::ProcessState, the start of the SeeC-Clang-mapped interface to recreated process states.
more experimenting with recall/identify
added unit test for application status, implemented application status request
Add filters
Add ColorMatrix copyright
InteractiveShell.restore_sys_module_state actually restores main

previously restored it only as a string, rather than the module itself.
test re-entrant embed_kernel
undo initial clobbering done by init_sys_modules in embed_kernel

revealed by test added in previous commit.
Added tags to the post lits
Dokumentacja gestów
New formula: `bup`
readded soft links
Merge branch 'pollvaultrv2' of github.com:mlutsky/PVdev into pollvaultrv2
async flag for threaded create_source in api
Added bindings to copy and paste from/to system clipboard
set noesckeys to make esc quit insert mode faster
Add help game state (F1 to enter)
Fixed pad not centering on input position
Merge branch 'userInput' of https://github.com/mogge/BluPong into userInput
Support logging out of a database in AuthorizationManager SERVER-7572
SERVER-7572 Introduce PrincipalName type, instead of using a pair of strings everywhere.
+ npm packake.
Tests for cron job
Merge remote branch 'origin/expectations' into expectations
Non-4x4 matrices now set correctly as shader constants
3x4, 4x3 and 3x3 matrices are not set correctly in EffectParameter.
The number of vectors used by an EffectParameter is now used to advance the offset.
Matrix transpose is now done in the assignment of the unrolled loop.
Save a bucketload of runtime memory allocations
Setting a Vector2, Vector3, Vector4 or an array of them on an EffectParameter would allocate new float arrays for each vector.  It now re-uses the float array that was already there for that parameter.
Merge pull request #1088 from slygamer/constant-buffer-transpose

Non-4x4 matrices now set correctly as shader constants
Fix cut-n-paste wording error
states work
Adding S3 storage
More LinkedList documentation.
Fix image width setter to use actual argument. Fix hasInstance checks to reflect the Handle changes in the JSAPI.
more scraper doc modifications
Bug 728433 - Get rid of ts_cold and head and tail scripts;r=jmaher
follow up to https://bugzilla.mozilla.org/show_bug.cgi?id=728433; remove file
Add "我要索取 DVD 光碟" & "我也想辦放映會" two sections in sdf2012 event page
Merge pull request #8 from RJking/master

Add "我要索取 DVD 光碟" & "我也想辦放映會" two sections in sdf2012 event page
partially revert r4448

git-svn-id: https://mpc-hc.svn.sourceforge.net/svnroot/mpc-hc/trunk@4450 10f7b99b-c216-0410-bff0-8a66a9350fd8
use a fixed value (10000) for MAXPACKETS_AVI and MAXPACKETS_RV

git-svn-id: https://mpc-hc.svn.sourceforge.net/svnroot/mpc-hc/trunk@5223 10f7b99b-c216-0410-bff0-8a66a9350fd8
File associations improvements (part 3): improve const-correctness.

git-svn-id: https://mpc-hc.svn.sourceforge.net/svnroot/mpc-hc/trunk@5224 10f7b99b-c216-0410-bff0-8a66a9350fd8
Updated Catalan translation by Xiulet.
This commit fixes ticket #2408.

git-svn-id: https://mpc-hc.svn.sourceforge.net/svnroot/mpc-hc/trunk@5225 10f7b99b-c216-0410-bff0-8a66a9350fd8
Interpolation of player movement.
Fleshing out component renderer extension method
see: more information on built-in classes.
Add a script for checking algorithmics AE1.
update index.html
adding video
adding video
MY EYES
Merge pull request #24 from kfc35/master

server client stuff connected
fix crash in tail text handling utility functions

--HG--
extra : transplant_source : %B9%B6%DEM%CA%1A%D7%24%09Qw%B7%C4%5E%82%5E%1B%E2%29K
docstring fixes in QName class

--HG--
extra : transplant_source : %86%8E%1E%ED%3D%B0%97_%B4k%7D/%EA%C5KaU%0B%B33
Fix documentation link to etreepublic.pxd

The file has moved to src/lxml/include in
6d33615e46e4a2316331c1bfe8051875abf59ed3

--HG--
extra : transplant_source : %EC%DC%26%BC%E7%21%15%82FE%14%CALcTRM%D6o%9D
added .hgignore file

--HG--
extra : transplant_source : 9%E1%CF%C9%DA%D0P%91%7B%AF%94%20%ACG%F3m%40%8Bb%98
generate less aggressive cleanup code: lxml.etree types imported by lxml.objectify may still be required after cleanup

--HG--
extra : transplant_source : n%99%C8%E8Y.%B7%F5p%7B%2A2%D3%8D%04%F1%18E%CC%1C
Add .gitignore
Add tox.ini for tox (http://tox.testrun.org/)
Make selftest.py and selftest2.py exit with a non-zero exit code when
one or more tests fail.
Add .travis.yml for Travis CI (http://travis-ci.org/)
code format
quick fix for compilation in old libxml2 versions - to be revisited
added .hgignore file
added build option to enable cygdb debugging
Fix documentation link to etreepublic.pxd

The file has moved to src/lxml/include in
6d33615e46e4a2316331c1bfe8051875abf59ed3
Merge pull request #56 from SimonSapin/patch-1

Fix documentation link to etreepublic.pxd
code cleanup

--HG--
extra : rebase_source : 7575b17725fbcc3eb46d656ba12159df8902962f
code simplification

--HG--
extra : rebase_source : 3f0b3ba324cb309c8ca56ffdd2e38855066c499a
docstring fixes in QName class
moved EXSLT tests into their own test class
use a more straight forward (and more low-level) way to store XSLT parameters and avoid storing parameter values in the global thread dict
Added tags
Implemented the tagging feature.

The tagging feature implements the relationship between posts and tags.
A tag can index multiple posts, and posts may have multiple tags.
Fixed deprecation warning on the Guardfile
Polishing
Added more tests for the tagging feature
weapons have damage points. view displays relevent/correct info. weapons equip on pickup, and weight added is permanent.
Removing stuff moved to separate repositories.
scct repo now only has the core scct component.
- Fixed a bunch of tests
 - Add an explicit dependency on nokogiri 1.4.1, which still works, later versions break prism
 - Changed the way datetime.rb interprets some dates. Certain date-like strings (phone numbers)
	could be interpreted as dates, which is not something we want.
Fixed issue 5 (can't convert String into Integer (TypeError)).
See https://github.com/mwunsch/prism/issues/5
Merge pull request #6 from Nimlhug/master

Fix for issue 5: can't convert String into Integer (TypeError)
lua: revert to 5.1.4

Closes #14974.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
lua: use sha1, remove skip_clean :all

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
clojure: Add --devel build

Closes #14294.

Signed-off-by: Charlie Sharpsteen <source@sharpsteen.net>
superenv: Add brewed-python bin to PATH

A required special case since formula that use python can optionally use system python or Homebrew python. We'll probably need more of this sort of thing.
pil: fix crash in 64-bit mode

Closes #15563.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
z 1.2

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Detect http://svn... as svn
Remove redundant :using => :svn
Adding python class which can read dcdfl's files
Using python's date&time -types for time handling
[bug 791067] Fix favicon.
Casper.resourceExists() now checks for non 404 HTTP status
added Tester.assertTitleMatch() method
Default scheme program set to chicken scheme
Updated parser to produce POINTER return types (NOTE:!! ctypes does not like
restype speced as c_void_p -- it will use c_int instead and is not good on 64 bit
systems.  Improved enough to autogen JS stuff too.
remove browserify cache file from source control
general awesomefaction
add humblebundle ebook wget thingy
some error handling
migrate zenburn for awesome 3.5
migrate rc.lua to awesome 3.5
add vim key bindings for copying/pasting
add virtualenvwrapper
* added log record cursor for ascending/descending iteration
 * replaced query result file format (file buffer list to logstorage
file)
 * renamed sort2/stats2/timechart2 to sort/stats/timechart
 * refactored logstorage file package
 * logstorage file now support non-compressed format for performance
 * offset and limit type is changed to 'long' type
Merge branch 'master' of https://github.com/nchovy/kraken
- Created MiMBuilder object
MDL-32479 - RTL Theme fixes for Moodle 2 (theme/base)

Support for blocks columns switch when in rtl mode:
theme/base/layout/frontpage.php
theme/base/layout/general.php

Right align course completion checkbox to the right side of the activities and resources, when in RTL mode
theme/base/style/course.css

Right align DOCK bar, when in RTL mode
theme/base/style/dock.css

First-name and Last-name Initials (filter) bar (on every users list) letters spacing (usability issue, NOT RTL issue)
theme/base/style/core.css

Conflicts:

	theme/base/style/core.css
	theme/base/style/course.css
MDL-32479 - RTL Theme fixes for Moodle 2 (theme/base)
Right align content (when viewing a Lesson activity in RTL mode)
MDL-32479 - RTL Theme fixes for Moodle 2 (theme/base)
Right align item's content (when viewing a Glossary activity in RTL mode)

Conflicts:

	mod/glossary/styles.css
MDL-32479 - RTL Theme fixes for Moodle 2 (theme/base)
Right align Fields in forms (when in RTL mode)

Conflicts:

	theme/base/style/course.css
MDL - RTL Theme fixes for Moodle 2 (theme/canvas)
Right align Forms in Report pages (when in RTL mode)
Automatically generated installer lang files
Automatically generated installer lang files
MDL-33583 really keep all automated backup files when told to do so
Merge branch 'install_20_STABLE' of git://github.com/amosbot/moodle into MOODLE_20_STABLE
weekly release 2.0.9+
java interface snippet
Nabla keybinding
Snippets: org-mode as latex-mode child
Added examples to ensure extraction works regardless of the subject nested.
Removed redundant example.
Remove redundant code.
Throw Sourcify::NoMatchingProcError when no matching proc is found.
Added examples for proc & attache not on same line.
Ignore rvmrc configuration file
Issue #49: fix libv8 problem when bundle install/update on OS X 10.2.8
Merge pull request #51 from nightire/hotfix/libv8-issue

Issue #49: Hotfix/libv8 issue
ad auto close brousers
Fixes

include in controller was clashing with default scope (clusters)
modified default scope to remove join
FIX: save_montage with non black background issue #18
Language system rewritten.
Rename nodes directory to routes.
Update views to use t() instead of L() for translations.
Tweaks and fixes to language system.
Use .sass style for CSS isntead of .scss
Fixed link to the K8055 page
wtf
Merge branch 'gh-pages' of https://github.com/nklsrh/bbgame into gh-pages
improved data attr
Merge branch 'master' of github.com:nlintz/pyBros
wrote an example
implement repetition for numbers up to 10.
--remove INode--
--add hp view--
Taking care of other ! vs undefined. Removed doubled _masquerade method
more missed headers for 304 reply
Update mocha ver
default push to upstream
add alias for stash, pull, stash pop
Successfully consuming a bottle.  No flash.  No confirm.
A consumed bottle is now asking for confirmation.  No flash.  No after_find.
Sriram:Adding tap gesture for quadrants
Sriram:Binding swipe for radar to dashboard
Merge branch 'master' of github.com:nsriram/Gumba
SchemaCache and Join bug fix

Signed-off-by: Thomas Pasch <thomas.pasch@gmx.de>

(cherry picked from commit 86ba3bebca72e3d789e2a114e1f5b01302521778)

Conflicts:
	nuclos-server/src/main/java/org/nuclos/server/report/SchemaCache.java

git-svn-id: https://svn.novabit.de/nov_nucleus/branches/prod/3.7@9465 33553225-e83a-40c5-8946-3093c540bf14
Fix pivot column sorting

Signed-off-by: Thomas Pasch <thomas.pasch@gmx.de>

(cherry picked from commit 9528e1b18e57aed15508fd1b038028fc027bca61)

Conflicts:
	nuclos-client/src/main/java/org/nuclos/client/ui/collect/model/SortableCollectableTableModelImpl.java

git-svn-id: https://svn.novabit.de/nov_nucleus/branches/prod/3.7@9466 33553225-e83a-40c5-8946-3093c540bf14
Add convenience method to access the full path.

The "full path" is terminology for the request's path plus the query
string.

The term is borrowed from Django, which implements the get_full_path()
method on requests.
[#263, #314] Undo revert of "Ensure that $terminfo values are valid"

This reverts commit ed4e9af9c41d08876a76a54a3dece174b92c066d.
[Fix #263, Fix #314] Ensure application mode is valid before use
Fallback to standard cabal location on OS X

If ~/Library/Haskell does not exist, fall back to ~/.cabal/bin.

Ideally, we'd parse ~/.cabal/config here, but cabal does not provide an
interface to get configuration settings.
Merge remote-tracking branch 'upstream/master'
can add text and upload pics
manage, display added
src/utils_rrdcreate.c: Handle "last update" in a saner way.
src/utils_db_query.[ch]: Remove duplicate "const" modifier.
network.c: workaround for broken OSX compilers issuing false warnings

Signed-off-by: Florian Forster <octo@collectd.org>
disk plugin: Multiply the average read/write latency with the interval.

The counter/derive will later be divided by the interval, resulting in too
small rates (for interval > 1.0).

Should fix issue #150. Thanks to Manuel Sanmartin for identifying this problem!
Merge branch 'collectd-4.10' into collectd-5.0

Conflicts:
	src/utils_db_query.c
	src/utils_db_query.h
Render 404 when resource not found in Rails controller template.
Update rvm, cucumber, coffee modes.
も少し編集。
change the name for tag-branch script
Added logic for entering flying state.
using require instead of require_once
- added function umountSystemFileSystems() which is used
  to umount system filesystems like proc within the given
  root tree. This is called after a custom script call to
  cleanup the environment
- v4.85.45 released
updated geoserver-exts submodule
Second draft of Creating a WPS process (#SUITE-392)
More tweaks to extended tests
Add logic to handle when permissions are changed and when token is already present

Added logic that checks to see if the user has changed the level of
access the application should have to their account. If it has changed,
it requests a new token. I also added logic that checks to see if a
token is already present. If it is present, it simply logs the user in
instead of requesting a new token.
added sms website code
don't allow empty cms_id
remove erroneous key from templates array
automatically scan template (and parents) for additional styles to include
disallow duplicate stylesheet entries
Zurb Foundation

v2.2.1
save->close
Merge pull request #12 from ospalh/profiles-mod

Changes to the profile selection dialog
catch platform io error
Merge branch 'master' of github.com:dae/ankiqt
add option to paste as pngs; compress pngs
flag anki text on cut, too
add roland to about
change current deck if user specified different one when adding
copy/paste updates

- unify handling of shortcut key and context menu cut/copy/paste
- don't adjust selection on window/popup focus, so context works on win32 now
- remove undocumented shift to keep behaviour
make sure to start the timebox from a click too
fix refresh timer firing during sync
reverse order of history
always write js errors to stdout, as users pull in bad js when pasting
Merge branch 'master' of github.com:dae/ankiqt
Gallery: More cleanup