labofsahil/github-event-dataset-2012 huggingface dataset:
Show Run As > JUnit Test when right clicking on a source that contains runnable
JUnit Test classes

If a source is closed (i.e., it hasn't been typechecked yet - this is
important!) and, through the package explorer, you right click and select Run
As, no "JUnit Test" option used to be shown.

The problem was that if the source is not opened (and typechecked), the
``@Test`` annotation can only be found in the AST, and not in the symbol. The
fix is to always initialize the member's symbol before looking if it declares
the ``@Test`` annotation.  By doing so, the ``@Test`` annotation is found also
for members inherited from a superclass or a trait!

In this commit I've also implemented the missing logic for considering the
JUnit4 ``@RunWith`` annotation. Basically, if a class or any of its inherited
types specify   the ``@RunWith`` annotation, then the class is a valid,
runnable, JUnit4 test class.

As part of this commit I've also made some improvements to the existing testing
class (formerly named ``LaunchableTesters``, now splitted into two distinct
classes: ``MainMethodFinderTest`` and ``RunAsTest``).

The work on these tickets (Re #1001379, Re #1001380) was somewhat motivated by
(or a consequence of) Re #1001304 and Re #1001275.

Finally, I'm quite convinced that the ``ScalaLaunchShortcut.getMainMethods``
could use some similar love, but this should be done in a separate PR(there is
already enough meat here).

Fix #1001234, Fix #1001379 and Fix #1001380
force commit message to be set for updates
prevented tests from failing due to missing property
!
reverted formatting changes
added mock identity prop to prevent NPE in some cases
guests are now accessible because host-only ips are assigned in the same network as the default vbox host-only network (vboxnet0)
Fix incorrect logo file name

Signed-off-by: Damien Regad <damien.regad@merckgroup.com>
Improve readability of CSS for sub-menus
Fix #15328: CSS for bracketed sub-menus

Make the bracketed sub-menus more similar to 1.2.x-style GUI by adding
padding between each line item and around current menu text.
Fix #15327: Removed unnecessary blank line above Account sub-menu
Fix #15329: use CSS to display admin page sub-menu
rename mapping file
some theme overhaul starters
better copy icon and other fallbacks
minor changes
stores 0.0.20 w/ customer control
Updated /create form for publication record searches
Support for search on record IDs
Create submodules. Create msysgit install. Update readme.
简单的社交关系映射
User Story U2

The user story U2 is implemented.
User story U3

The user story U3 is implemented.
[REFACTOR] Regex tightened

The regular expression are tightened to precisely match the entiry
line.
[REFACTOR] Uniformized the language

The language used in the scenario's is uniformized to allow code reuse.
User story U4

The user story u4 is implemented.
[FIX] Initially fail

The then clause should fail initially.
User story U5

The user story U5 is implemented.
Cucumber comment

The standard cucumber command is added to the method body to state
the intention.
[REFACTOR] Reorder code

The methods are grouped by given, when, then structure.
Fixed residual wall-hanging bug on corners of tiles.
Removed unused win margin constant.
Add bundler alias for installing to vendor. Add <Leader>l for :ls.
Move code around. Clear out old code.
rvenv support, including with pow.
Moom preferences - goes in ~/Library/Preferences
Merge branch 'rbenv'
A few git aliases and vim ignore tweaks.
Update demo deploy alias to push from current branch.
Add the osx file
Remove rvm.
Merge branch 'master' of github.com:dzello/dotfiles

Conflicts:
	gitignore
	zshrc
send x deletes to null register. gitignore only root tags file.
Merge branch 'master' into ubuntu

Conflicts:
	gitignore
ubuntu ami
added trackball config to xorg.conf
Add proxy-core-api to FraSCAti libraries
Refactoring start.js
Removed out-of-order retrieval of gene vector and version checking.
Se guardan las citas de las actuaciones nuevas
fixed low perfomance on big chunks writing
mofified .gitignore
removed hw2
should remove regression in add course, fix issue #51
search test should work better now
thread view refactoring, fix issue #43 #18
remove debug msg
fix logic problem in the state of processing document in course show
fix refresh error for processing document
implement overlay form in viewer document
revert to old css, margin-right/left to 30% is _fixed_, not variable...
deploy sortable on document viewer comments
inline with razor's style
Use packages properly.
Remove use for alloca.h
Add default arg for bookmark commands.
* helm.el (helm-execute-persistent-action): Fix persistent action is a lambda form.
sb-mainichi.el (shimbun-mainichi-get-headers, shimbun-mainichi-multi-next-url): Update regexps
sb-mainichi.el (shimbun-mainichi-ignored-subject): New variable
Removed hack that disabled role switching.
Merge remote-tracking branch 'nbites/master'
Merge pull request #288 from jzalinger/master

Role switching will work again.
Merge remote-tracking branch 'nbites/master'
Fix syntax error in config.rb
Don't show blank page in carousel - fixes #124
Fix list indent in docs
Update to 0.9.8
Fix debug message in bot.py (rate limit part)
ConversationManager, Preferences: Close tab button hiding, is now instantly applied
Make ordered lists ordered, at least...
Fix bug with application default setting
added onload callback for SpriteSheetUtils.extractFrame which is necessary when loading frames from larger spritesheets
reordered divs in float
changed edit link in description
Merge pull request #342 from enspiral/bug/member-request-fix-for-ie7

Bug/member request fix for ie7
standardize module naming
Update the order of item insertion in the menu.
Update docstring
Update the sample view
Added a timezone to the tests so they work with travis.
std.math.sqrt

daha temiz bir yol olduğu için bu hatayı Ali beyin gösterdiği şekilde
düzelttim
Correct error in problem 3
check bash minor version for shopt direxpand
Merge branch 'master' of http://github.com/ericvw/dotfiles
two line style prompt
Merge branch 'master' of http://github.com/ericvw/dotfiles
added control
Merge branch 'master' of https://github.com/ericz/touchbase
Made attitude_viz.py work on Mac OS X.
modified:   TODO
	modified:   bin/fakedns.rb
	modified:   doc/DNSQuery.html
	modified:   doc/FakeDNS.html
	modified:   doc/bin/fakedns_rb.html
	modified:   doc/created.rid
	modified:   doc/index.html
	modified:   doc/rdoc.css
	modified:   fakedns-1.0.gem
added clean exit on ctrl+c
bug 808943
 1. add phone lock state enabled/disabled under Phone Lock setting menu item
 2. update because of lazy-load patch of bug 806237
fadeIn + Slide text
Don't recorder Content-Length header

This header should be computed
Accept empty package
Change indicators default bounds
Adding dbus to launch session, for automounting of drives
Adds createTable method that backsoff and retries creating a dynamo table.
Cant actually get SQS to take posts, and something wack with really long URL's.  So, make MessageBatch.put just use individual saend message calls and lump them all together.
SWF-2162 : Add missing dep + reformat poms
PLF-3942 :[Top Navigation]Sanitization
PLF-3884 :[Top Navigation][Create Portlet] Implement PROFILE entry
Merge branch 'feature/navigation' of github.com:exodev/platform into feature/navigation
JCR-1867: PrimaryTypeNotFoundException when repairing data
JCR-1864: SessionDataManager.getLastOrderNumber returns incorrect value in some cases
testeando que pasa en tailf block
Defaulting to global is a stupid idea. Nevermind.
Fix for GCC compilation
Add more plug-ins
Ausblick - 162 Seiten
Changed the colors back to ea colors
sayfa 9
fixed setup.py and include test dependencies
logged_in var from simple and from class based view processed in main
template
Trim down code for item box tab hints a bit
Upgrade citeproc-js to version 1.0.394
jasmine's last changes
jasmine's most recent changeS
basic movement support via keyboard
- Code cleaning
- copyrights
go for the release
Update inline event handler map + dom member map
Fix test html/2183/issue2183.js correctly this time
Initial implementation of a simple Firebug server (so, we have something to connect to)
修正修改可疑物品信息，禁寄物品无法保存的问题
添加揽件信息插入验证信息
修改揽件导入，时间解析部分。
Merge branch 'master' of git@github.com:firefoxmmx2/jdy.git
重点人员预警处理
Merge branch 'master' of git@github.com:firefoxmmx2/jdy.git
添加预警参数的execute方法事务.
预警参数添加预警前处理和预警后处理
修改为个人身份查询和联系电话查询
better input checking
another big cleanup round
simple demo client for OAuth 2 authorization code profile
better handle http responses according to spec
prevent the authorize dialog from loading in an iframe
add some more software dependencies
implement CSRF protection by checking referrer
rename some exceptions to make more sense
fix coding mistake when resource owner does not approve request
refactor install scripts, update README file
support resource_owner_id hinting to preselect a resource_owner_id if the authentication backend supports it, this is a proprietary extension (get parameter user_address to the authorize endpoint)
merge with master
Add RULE, RULE DONE and SAVE ORIGINAL instructions.
Allow all subgoals to use SAVE ORIGINAL.
6/22/12
fixed lost use clause
fixed renaming ConsoleInitEvent in ConsoleEvent
fix tests for Console/Application
[doxygen] tell doxygen to ignore gcc extension __attribute__
Serial flashing for STM32
Makefile for submodule
[doxygen] change some TODO comments to doxygen @todo
so they show up in http://paparazzi.github.com/docs/latest/todo.html
[sw/ext] fix detection if submodules are already cloned
[sw/ext] update submodule with every make, init only if not already cloned
store luftboot version
[maps] extracting google maps version

It should not fail in case of lost connection or corrupted maps.xml file
Fix #187
[sw/ext] simplify updating of submodules in Makefile
worldwind fix for 32 bit, non-tested
fixes #106 - now loops with a 5 second wait between attempts to test the pagerduty connection, rather than raising (when we can't connect to pagerduty)
Join channels *after* VHOST/OPER. FFUU.
added a hacky fix to the jumping 'shift image up to new ribbon problem'...

Signed-off-by: Alex A. Naanou <alex.nanou@gmail.com>
add updates on berkshelf
changed graph switching to use links instead of event handlers. individual views can now be linked to and refresh works.
Item11879: adding rendering time for cached pages as well. sort of interesting numbers as well measuring foswiki performance ;)



git-svn-id: http://svn.foswiki.org/trunk@15666 0b4bb1d4-4e5a-0410-9cc4-b2b747904278
Item11992:

   * replaced all simplemodals with jquery-ui dialogs
   * added nullformat,nullheader,nullfooter to %ATTACHMENTS macro
   * removed dependency on !WebDAVLinkPlugin to render webdav-enabled urls 



git-svn-id: http://svn.foswiki.org/trunk@15127 0b4bb1d4-4e5a-0410-9cc4-b2b747904278
Item12237: Add ability to escape TML to NatEdit

git-svn-id: http://svn.foswiki.org/trunk@16003 0b4bb1d4-4e5a-0410-9cc4-b2b747904278
install: corrige inicializaçao da instalaçao para mssql.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
documents: referencia a coluna deve ser declarada em maiuscula.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
core: trata exceçao para inserçao de valor duplicado.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
core: suporte a execuçao de store procedures.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
core: permite que checked_select() trabalhe com inner join.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
shell: melhora performance para recuperar estilo da pagina.

seleciona estilo da pagina atraves de join.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
shell: implementaçao inicial de lista html.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
packagetool: reimplementaçao de indice dos itens do pacote.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
tasksel: desloca responsabilidade de instalaçao de tasksel para login.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
core: grava informaçoes restantes do usuario.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
usereditor: apresenta corretamente propriedades adicionais do usuario.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
core: create() deve gravar restante das informaçoes adicionais do usuario.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
core: trata MySQLNonTransientConnectionException em rollback().

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
login: nao queremos que iocaste-login seja a aplicaçao inicial.

Signed-off-by: Francisco Prates <mad.kanie@gmail.com>
removed dependency on mongoid and moved to redis.
first functional 2D nurbs Surface interpolation
all phases of Nurbs 2D full multi-threaded
- point transformation, solver and batch interpolation are able to use 100% of the CPU for the  interpolation process
Adding Git note for current refs/heads/projects/calloutng
Adding Git note for current refs/heads/stable/9
Move the code around a bit to move two parts of code duplicated from
kern_close() close together.

Discussed with:	kib
Tested by:	pho
MFC after:	1 month
Merge two ifs into one to make the code almost identical to the code in
kern_close().

Discussed with:	kib
Tested by:	pho
MFC after:	1 month
Refine r237102 a bit:
- Anounce JTAG interfaces deliberately skipped.
- Bring back empty lines too eagerly removed.

MFC after:	3 days
Unbreak after r236658 by comparing the right things.
Always clear p_xthread if current thread no longer needs it, in theory, if
debugger exited without calling ptrace(PT_DETACH), there is a time window
that the p_xthread may be pointing to non-existing thread, in practical,
this is not a problem because child process soon will be killed by parent
process.
Don't print SCSI Queue Full and CAM_REQUEUE_REQ statuses as errors if they
were handled and retried. They are part of normal operation for SCSI TCQ.

MFC after:	3 days
Shuffle these initialisations to where they should be.
Attempt to make machine check handling a bit more robust:
- Don't malloc() new MCA records for machine checks logged due to a
  CMCI or MC# exception.  Instead, use a pre-allocated pool of records.
  When a CMCI or MC# exception fires, schedule a swi to refill the pool.
  The pool is sized to hold at least one record per available machine
  bank, and one record per CPU. This should handle the case of all CPUs
  triggering a single bank at once as well as the case a single CPU
  triggering all of its banks.  The periodic scans still use malloc()
  since they are run from a safe context.
- Since we have to create an swi to handle refills, make the periodic scan
  a second swi for the same thread instead of having a separate taskqueue
  thread for the scans.

Suggested by:	mdf (avoiding malloc())
MFC after:	2 weeks
Tweak the output to match FreeBSD's mtree when running on FreeBSD systems:
 - Emit ripemd160digest= keywords rather them rmd160=.
 - Output the size of all objects rather than just regular files.
 - Emit the trailing .. when leaving the root directory.
Correctly format the nanoseconds by padding out to 9 digits.
Document this with text from the FreeBSD manpage.

Without this change a file modified on the first nanosecond of a second
(N.000000001) would be reported to have been modified at precicely 100ms
into the second (N.100000000).
Save Button Working!
added a better MQ page
adding clean
removed useless engine stuff. cleaned Levels, removed get/set from grid, player spawning
fix: full test for rt runs does not have sound test
fix: removed extraneous lines
Merge pull request #23 from akeshavan/test_eq

fix: full test for rt runs does not have sound test
About tab - displays versions of DFU, HW, FPGA...
in bios.h was interesting bug - the function _Get was declared only with one argument, but the SYS module has implementation with two arguments :) I wonder why it didn't crash with such serious mistake.
use new method definition
[upstart] next attempt at a startup script
[upstart] Added .conf for roscore on startup
[upstart] Changed test .conf file
[upstart] Successfully got test program to start at boot
[upstart] Rename codename "Thanksgiving" program to Upstart
Translate link for user
add pager on tag views
Change show article
Fixed hard-coded offset on overview panel scroll into view.
modify sync.readme
finally, status display should now work
Merge pull request #484 from wkollernhm/master

finally, status display should now work
starting to implement batch retrieval
Table gotcha. Implemented uniprotxml2json for multiple entries retrieval. Next will be bring the json to ExtJs and display them at the table
uniprot2json ended but not working on client, some misyncronization
Multiple uniprot entries retrieval displayed by table
Set the foundation for panel creation through history events on viewport controller
Table working correctly for multiple targets
Merge branch 'panels-creation' into develop
EOD commit
Fixed multiple targets rendering
Added protein info panels based on conceptwiki calls and rendering. Added images directory and tdgui.css file for styles.
Merge branch 'multiple-targets-feat' into develop
Added PharmByTarget panel
Merge branch 'multiple-targets-feat' into develop
Uniprot XML parser done by using Nokogiri. Nokogiri gem was added. Uniprot protein info is not functional yet
Test for uniprot/coreAPI request (for proteinInfo at least) were developed. lib/coreapi_reponse_parser.rb modified and both coreApiCallsController and model. It still has to fit to ExtJs comps
Added functionality to make a request to string-db and convert the result to a valid json for JIT ForceDirected. In progress a component panel supporting the graph
Nothing remarkable
Merge branch 'target_info_uniprot' into develop
JIT ForceDirected already on the Interactions panel. Code not organized yet
ForceDirected integrated on panel. Lets set it up more convenient
upgraded api to svn trunk version, seems to work but needs testing
Updates to how cn-view in called in clin-seq main to accommodate updates to cn-view
Merge branch 'master' of ssh://git/srv/git/genome
Merge branch 'master' of ssh://git/srv/git/genome
remove test case for behavior that was removed
Cosmetic update to cn-view
Fix clin-seq update-analysis test and minor update to Main.pm
moved Uniprot to Entrez sub to Base.pm
added blacklist
Don't include inputs from the helper in type-specific parameters.

This fixes model definitions broken by making processing profile an
input in 8fb1465afa56aafe2ab6a0baa8152dd4f3f51fd7.
fixed a bug so that RSID is matched to the right variant allele
move vcf_version into the get
invert conditional
improve debug message
ensure checks to common_name go through the default nomenclature ("WUGC" here")
fix typo

Change-Id: I5e4c644b5f05cc3bd8b74dc8e83e6b6b8fdf913c
improve reliability of the allocate with move test

Change-Id: I4f22ddbbd84d8c9973c6ef46783ac681a17469aa
refactor allocated_kb body into sub

Change-Id: I0c16bbcf5720a9b4f712b4f5e1a4f4892d89e3f3
add timer instrumentation

Change-Id: Id002688b67d5e6e5f84988bb6572b5babb6856d8
use UR::Object::Set's server-side aggregate logic

Change-Id: Ie0a9d9eb63b4508b443c7a405f2c4a462b159c1d
use set operation

This is still pretty hairy since we have to prevent UR from caching
aggregate value.

Change-Id: I4e776ad91612a34b379c168143d1765cf507eca5
Merge "fix typo"
Merge changes I4e776ad9,Ie0a9d9eb,Id002688b,I0c16bbcf,I4f22ddbb

* changes:
  use set operation
  use UR::Object::Set's server-side aggregate logic
  add timer instrumentation
  refactor allocated_kb body into sub
  improve reliability of the allocate with move test
Correct locking when software result has an object as input or param.

Previously the inputs and params were simply concatenated together; however
in the case of objects this would use their memory address, which is unsuitable
for a lock across processes.  The locks generated should be the same for
results without objects--only locks that currently don't work are changing!
Solexa: rm original fastqs after SX trimming
Update test with new expected outputs
Merge branch 'fix' into gb_master
Merge remote-tracking branch 'origin/master'
Ignore some files for build diffs in somatic variation.  This is necessary because of the strelka output files.  We also now grep out some lines from all .hq files such as fileDate,cmdline, and startTime
Merge branch 'fix' into gb_master
add optional --file-suffix option to gmt graph mutation-diagram
Test file, should have never put it in the publicly visible bin
gh-pages refactored to use the new conventions
Still needs testing before making it public
Readme updates, waiting for new deliver screenshots
Always try to use test instead of if [ ]
Because it's &&, false test will stop further execution
Without __exec, $SILENCE won't be DRY
This is only relevant for deliver devs, not for end-users
Ignore the gh-pages dir contents, not all gh-pages matches
man & README minor updates
deliver's default strategy is gh-pages
This check MUST remain in place
gh-pages strategy fully working
Merge pull request #22 from gerhard/gh-pages-strategy

github:pages strategy
Update notes for submitted changes

* Add pmtpa/eqiad Squid/Varnish servers as esams backends
Update notes for submitted changes

* Install cp3003 as Varnish upload
Merged with other code
Adding initial files.

Signed-off-by: Ben Corlett <bencorlett@me.com>
update to documentation files
add professor_all for auto complete
professor affiliation info update (with model relation)
remove useless devise views, devise auth config name to username
l10n: vi.po: update one message

* Translate message that updated from commit bb2ba06

Signed-off-by: Tran Ngoc Quan <vnwildman@gmail.com>
Add more Prolog samples

Closes #233
Removed unused file step
Renamed a step definition to better show its purpose
Changed around wording in feature description
Added the skeleton of a new feature "Help (--help)"
ahorcado con diseño
Deleted some files and changed port number.
use diff reputation for connection and ssl_connection
common task listener, error handling
Type should be 4 for the modules.
ver.1.1.5
added a global cache to allow methods to use the same caching-source
Initial qbs test
Complete jreen build with qbs
Some project refactoring
Successfuly built jreen with msvc compiler
Sync from qbs-labs
Framework probe
Refactoring
Use submodule for qbs files instead copy
Use symlink instead submodule.
Concat properties fix
Warning fixes
Merge pull request #13 from gorthauer/qbs

qbs build scripts
Update with upstream qbs
Messages draft
add range release finder
modification importante
Refactor away the Worker by combining it with the Minion. Refs PRGBPD-71
Continued refactor of Minion/Worker.  Seems to work now! Refs PRGBPD-71.
Continued swinging the refactoring hammer. Refs PRGBPD-71.
Finish the refactor of PerformanceEmitter. Refs PRGBPD-71.
Continue pinning down the refactor.  afaict everything works now.  Refs
PRGBPD-71.
Some doc fixes. Refs PRGBPD-71.
Continue cleaning up tests.
Still renaming things. Wahmp-Wahmp. Refs PRGBPD-71.
asdasd
Add more checks around sending messages so that it doesn't get caught
in an endless loop.
Remove catch that broke tests.
Merge branch 'master' into minion-refactor
Small refactors and some actual work on the table emptier minion.  Works
so far! Refs PRGBPD-71
Don't buffer responses from QueryRunner. Properly close various
resources as well. Refs PRGBPD-71.
Add bits to ResultSetWrapper to facilitate row deletion. Works! Refs
PRGBPD-71.
local json commit for tracking. Refs PRGBPD-71.
Turn off compression by setting the threshold stupid high. Refs
PRGWS-54.
Merge branch 'master' into minion-refactor
Actually merge in compression fix from PRGWS-54.
Remove some remnants of the emitter thread code that has been moved to a
minion. Refs PRGBPD-71.
better documentation for lsqfit
Components, Cody: improved localization of 'Identifier dictionary' dilaog and 'IDE Integration' settings tab; updated Russian translation. Inspired by barlone's patch, bug 21612.

git-svn-id: http://svn.freepascal.org/svn/lazarus/trunk@36472 4005530d-fff6-0310-9dd1-cebe43e6787f
IDE: save state new project

git-svn-id: http://svn.freepascal.org/svn/lazarus/trunk@38756 4005530d-fff6-0310-9dd1-cebe43e6787f
codetools: skipped code is now converted to special comments

git-svn-id: http://svn.freepascal.org/svn/lazarus/trunk@38521 4005530d-fff6-0310-9dd1-cebe43e6787f
codetools: fixed reusing scanrange of implementation uses section

git-svn-id: http://svn.freepascal.org/svn/lazarus/trunk@38522 4005530d-fff6-0310-9dd1-cebe43e6787f
lcl: fixed function result

git-svn-id: http://svn.freepascal.org/svn/lazarus/trunk@36712 4005530d-fff6-0310-9dd1-cebe43e6787f
IDE: clean dir dlg: set default value, issue 22779

git-svn-id: http://svn.freepascal.org/svn/lazarus/trunk@38619 4005530d-fff6-0310-9dd1-cebe43e6787f
Reverts the help for OpenURL as per comments in bug 21659

git-svn-id: http://svn.freepascal.org/svn/lazarus/trunk@36934 4005530d-fff6-0310-9dd1-cebe43e6787f
updated var names, readme
use a template for nginx vhost config (to support UAT)
add --test option for trialling puppet config
bsd:  Another attempt at fixing the flex/yacc issues.

Guess I forgot to fully clean before declaring my previous
fix a fix.

Signed-off-by: Ben Greear <greearb@candelatech.com>
Update notes for submitted changes

* reduced the cost of the nbnxn OpenMP nb-force reduction
Fixes bug in g_hbond that makes it produce fatal error.

Rather than crashing with a range check error when there
are no hydrogen bonds the code now prints to stderr and
continues normally.

Change-Id: Idc9fddf8bfac9989bc1aa3a9c552b08580f99949
Merge "Fixes bug in g_hbond that makes it produce fatal error." into release-4-5-patches
Use stat for gmx_is_file. Fix get_libdir with symlinks.

In commit 4e057440520c1 I used lstat instead of stat confusing the
two. The commit tried to fix the misidentification of directories.
There is no need to distinquish between symlinks and files (and
thus break it if a binary is a symlink).

Change-Id: Ie964e826729a35f11516fb3d002ebc01cbb7a564
Fixes #1035 NaN in g_cluster output.

Now always initializes the masses of the atoms to prevent
division by zero downstream.

Change-Id: I1b38ccc7982d4340ed068535f7b7dd8e75e1a4c4
Merge "Use stat for gmx_is_file. Fix get_libdir with symlinks." into release-4-5-patches
Merge release-4-5-patches into release-4-6

Conflicts (both trivial):
	CMakeLists.txt
	src/config.h.cmakein

Change-Id: I363ce1c09c68c2be5aa926e893011d43c8ed3337
Merge "Merge release-4-5-patches into release-4-6" into release-4-6
Update notes for submitted changes

* Updates to CMake treatment of OpenMP
Report elapsed time
groonga-httpd: fix configure failure
doc: add missing row separators
Support for blast
document esearch in README
cleanup & test
CSS fixes

Removido arquivos não utilizados de css
Colocado o css minimalism dentro do conteúdo do editor de textos.
* Modification du listing des pages parentes

* Listing sous forme de tableaux (sortable)
* Ajout d'un sous menu pour gérer les "modules" (dropdown)
Make queueName configurable and other minor changes
fix some code and add tests
gem:168 github version one
gem:34 new file
gem:34 1
gem:34 2
gem:34 3
Fastplace check improved by @SuperSpyTX - Welcome to AntiCheat!
show_rd renders as if at build time
Improve release documentation
Path modification functions from Andrew Redd.
# 92
Use registry to find Rtools.
Contributed by Andrew Redd.  Fixes #92
Remove trailing whitespace
added support for OpenMP
Use tcc not gcc to compile osint.
Add declarations for dump_* locations in os.s. to be used to dumping registers to
assist in debuggin.
Update utility_sql/Orders.sql
Semi working rewrite
Cleaned up BuildCascade.m
Merge branch 'master' of github.com:haukuri/FaceLab
Rename read() methon in readFile()
added arrow to repo.
1. Added few more functionalities with jquery
2. Added the fb integration to be available inside the chat room
3. Restrucutred the code a little bit
===
To Do
1. Finalize the msg pull and friendlist
timeline - tonight.
Add/layout preface content.
カラースキームをGUI起動時にのみ読み込むように変更
Oh yeah, it supports files and resources.
Site updated at 2012-07-18 13:42:14 UTC
More for safely inherit/use multiple partial classes
重命名表名：DRIP_USER --> DRIP_USER_INFO
bug
minified
do not remove module from sys.modules
add download-baseline and restore-from-baseline
HORNETQ-1013 and JBPAPP-9737 - Paged Messages are overflowing the memory during a delete of core-queues (including JMS durable subscriptions)
getting rid of eclipse warning (since we use compilation level at 1.5 on
2.2)
Merge pull request #440 from clebertsuconic/Branch_2_2_AS7

HORNETQ-1013 and JBPAPP-9737 - Paged Messages are overflowing the memory
Need to track tables by tableid
Update to pybbm 0.11
add support for installing via composer http://getcomposer.org to create a symfony package
Fix headless binary path on Linux, add shebang and exec flag to test.py
removed the external reference to the jQuery library
Fixed form for Bank Accounts.
Use three states on StatusBarIndicator, active, inactive and invalid.

When the status is invalid no matter if the item is active or not, this
is used to show in the UI how many items he could have, so the non-used
slots are marked as invalid.

Reviewed-by: Rafael Brandão
PagedGrid should use a proper model.

Now we need a QAbstractItemModel to fill the PagedGrid so the previous
model in javascript needed to be implemented like the rest of our models.

Reviewed-by: Caio Oliveira
             Hugo Parente Lima
Implement a QAbstractItemModel for tabs.

This way we could use the same mechanism to display thumbs
for both favorites (aka topsites) and opened tabs.

Reviewed-by: Caio Oliveira
             Hugo Parente Lima
Blink the statusbar indicator when the load progress is 0%.

Reviewed-by: Rafael Brandão
Use the correct asset for page slots in StatusBarIndicator.

Reviewed-by: Marcelo Lira
Add small side shadows to all screens.

Reviewed-by: Marcelo Lira
Swiping the tab indicator bar to left and right moves through tabs.

Reviewed-by: Hugo Parente Lima
The WebView overlay is just a swipe area now.

Swipe left and right to move through open tabs, click in the
SwipeArea to go back to fullscreen view.

The SwipeArea is in fact transparent, so the user will be under
the impression of interacting with the WebView.

Reviewed-by: Hugo Parente Lima
Fix build caused by commit c855af4fc467c5d1a759724e584432e8f6cef466

Reviewed-by: Trust me
Make PagedGrid support empty slot delegate

Put a page with empty slots behind the last page with actual items
and also display a new one (also filled with empty slots) to the right
of the last page when we didn't reach the limit of pages yet.

Reviewed-by: Hugo Parente Lima
Implement the toolbar relayout.

The new toolbar goes below navigation bar.
Buttons added: "Share" and "Settings"
Buttons modified: "Favorite" becomes "Pin"

Reviewed by: Rafael Brandao
Fix a warning on TopSitesPanel.qml file.

It was complaining about a "Binding loop detected for property "visible""
on line 66. Now we use a property to link both components.

Reviewed by: Hugo Parente
Use new assets on PanelToggle bar and simplify a bit their logic.

Reviewed-by: Rafael Brandão
Removed the toolbar that shows tab indicators and url only.

Previously there was three states for the navigation toolbar in the
bottom of the screen:

1. Only the tab indicators (the little circles).
2. The tab indicators and the url entry.
3. The tab indicators, the url entry and option buttons.

The state #2 was removed for the sake of simplicity.

Reviewed-by: Luciano Wolf
Modify grid's item overlay image

Now using a smaller overlay since we don't have pin buttons
any more on "Tabs" screen, just on "My Sites".

Reviewed by: Marcelo Lira
item_row weights
set number according to taps
Merge pull request #76 from hweng/heroku

calendar controller rspec tests for admin_index and index
closes #68, closes #76, closes #53
Merge pull request #77 from sheelc/cuke_fix

Cuke fix
Use tomorrow-night-bright-theme : https://github.com/chriskempson/tomorrow-theme/tree/master/GNU%20Emacs
charges proof of concept working
damn pyc files
add tweet button to unlocked clan page
Merge branch 'feature-clans' of github.com:iRail/Ghendetta into feature-clans
add :active states
added multiplier to selected list checkins
fixed codes multiple lines
Changed the interface to Poracle. It's now a static method, since it turns out that there's no need to maintain state across multiple calls
Fixed code style in node.js examples for chapter 1
Revert "apply ideeli patches (revert to 3.0.2)"

This reverts commit 26b7a54855f9a6881101866797ef98b25c6f44c3.
[udev rules] Add local rules for radeon and hdd power management

and at the same time, remove these from the rc.local file.
[xbindkeys] add config file
refresh
Merge branch 'master' of github.com:ijse/formHelper
Build into a directory with the proper structure
Shop metro design.
Add pdf of lab exam... thanks to @haider92
fix a bug with prettify reduction calling undoAdd() in the wrong place, and another where under certain circumstances extra nodes would be created over the top of others
Rework events for initial touch support.

Provides a better abstraction layer for the events, and make both touch
and mouse events correspond to that API.

This doesn't yet support multitouch, and trying to use multitouch will
result in some pretty hilarious effects, like resistors changing start
nodes, or things flying all over the screen.

Progress on #24
Support for multitouch move tool.

Progress on #24
Working multitouch for wires and resistors.

Except it kind of sucks, because its really hard to get them to actually
hittest the nodes.

Progress on #24
тестирование подсветки синтаксиса в документации
new functioanality

added Linear Algebra and Matrix math modules
added new Feature detectors
improved matrix_t initiation with custom data
Fix safe_branches
Merge branch 'hotfix/0.9.43'
Fixed a bug in 1.8.7 and added a test case.
Preserve unavailable_pythons list for post_pr_test script.
Make print syntax in GUI integration examples Python 3 compatible.
Update print syntax in parallel examples.
Use print_function in example-embed
Tidy up references to ipclusterz in parallel examples.
Merge pull request #1595 from takluyver/examples-syntax

Update examples syntax to be Python3 compliant (this avoids errors when installing on Python 3, since examples don't get modified by 2to3 at installation time).
clean up of typos and awkward wording
clean build dir in test_pr
separate pull from commit in test_pr
time test run
Merge pull request #1714 from minrk/testpr

minor adjustments to test_pr
edited link in registration process
Updating C++ unit testing to match conventions used for C code base.
Adding parameter unescaping for operators.
core_operators, lua: Remove trailing whitespace.
config.h, util.h, engine.hpp: Fix doxygen issue.
IronBee++/Tests: Fix to work again after recent breaking change.
field: Change all creation routines to take nlen argument and remove _ex.   Update all uses.
field: API doc update.
Field (and everything else): Field overhaul.  See below.

This is an overhaul of the field API.  The most important change is that the expected types for pval parameters are made explicit and helper functions (ib_ftype_*) are provided to assert those types at compile time.  E.g.,

  rc = ib_field_value(field, ib_ftype_num_out(&n));

Other changes include:

- ib_field_value now returns an ib_status_t and uses out variables.  This also simplifies getters.
- API to extract mutable values from non-dynamic fields.
- ib_field_create_dynamic instead of the register dynamic functions.
- API documentation improvement.
- Change setv_static to make_static.
- Add no-copy setv's.
- Add ib_field_util_log_debug.
Fixed a couple build problems
field.h: API doc fix.
field.c: Fix bug with ib_field_setv_ex() with IB_FTYPE_LIST and IB_FTYPE_SBUFFER.
field.h: Spell check.
field.h: API doc fixes.  static functions now documented to allow for static inline's.
Removed '\n' from several debug log messages
Various: Minor API doc improvements.
core_tfns.c: Fix minor bug found by static analyzer.
Fixed build problems caused by field API changes
Fixing 32-bit architecture pointer/integer errors.
GCC/G++ 4.1.2 requires a virtual destructor for test class.
Using PRIu64 and PRId64 for printing ibnum_t fields.
customer tab

Signed-off-by: irwan subaya <subayairwan@yahoo.com>
perseus smith updates as noted by B. Almas
Merge branch 'master' into gh-pages
allow an empty environment
Made the gui a little more compact.
Now completly static
Remove uesless comments from Ticket
added ido support for choosing paths for the new-term function
Added fixture data for the layer application. We need to re visit how we are handling fixtures.
Missed a geonode GeoNodeException import.
Update the layer tests to work with the new app layout.
Switched the owslib version we are using to trunk. This is a tmp fix.
had fun with pointers and smart pointers yesterday.
wrote Commons as a readers-writer lock
Make all the headers public
Bug fix for MemcachedCache.delete()
Utility for generating sample user data for demonstration purposes.
Tweaks to teacher panel display to deal with username overflow.
Merge branch 'develop' of github.com:jamalex/ka-lite into develop
Added nested if statement to save button to give user control over already saved file names.
Added a 'material.' prefix to material strings in localStorage. Making way for recipe files in storage.
Fix: addSorted was adding first word twice
AS7-5361 Fix race condition
AS7-5134 Unable to not set key-alias for ssl - with new xsd + fallback for 1.1 schema
AS7-5369 Allow direct text value in parameter element.
AS7-5363 NPE on tab completion
JBQA-6037 added a property for IPv4 and IPv6 interoperability testing in LDAP login modules
AS7-4685 module schemas are missing from documentation

The schemas for the jboss module system are missing from the
docs/schemas
folder. I just copied them over from the jboss-modules project.
Make ds.xml, ra.xml, and ironjacamar.xml follow the property substitution settings
Switch the default for jboss descriptor property replacement to true
AS7-4700 refactor connector subsystems to make easier to browse for us and GSS
re-dding org.jboss.connetor.ConnectorServies class and depracate it
Resolve merge issues
AS7-4702 mod_cluster takes up to 10 seconds to register with load balancer
Use named thread pool for AsynchronousService
AS7-4614 Allow expressions in JSSE keystore and truststore configuration attributes.
AS7-4614 Convert strings coming in via mgmt ops; add parsing/marshalling test
AS7-4310 Upgrade to 1.0.9.Final of jboss-ejb-client library
Use the release version (just a tag for the java part).
Added translations properties files.
Web 7.0.16
AS7-4458 Include subsystem version info in ExtensionAdd response; use it on DC to update TransformationTarget
AS7-4687 Use InheriableThreadLocal for application client
Fix the exception returned for non existent view on EJB
Ignore properties that are not present on the data source class
Remove unused messages and move exception message out of the logging class
removed LaTeX compilation files
Cache Ticker Integration

+major changes to 0mq and rx implementations
march 25 5:55
files to dir
form-4.0_p20120529
Cambio Miercoles Noche
Add authentication support via Google OpenID

Can be enabled via command line options --authgmaillist and
--cookiesecret. "authgmaillist" is comma separated gmail IDs that will
be allowed to access the http interface.
cleanup
Fix the realtime vs. onetime switching logic

We do querying only via websockets now. One time queries are fulfilled
instantly. Tailing queries are fulfilled via a background thread.
StopTailing terminates the thread used for tailing.
Use wp_enqueue_scripts() to add styles instead of wp_print_styles(). See http://wpdevel.wordpress.com/2011/12/12/use-wp_enqueue_scripts-not-wp_print_styles-to-enqueue-scripts-and-styles-for-the-frontend/
including the example app I'm using for testing right now..a simply Todos. Doesn't actually let you add any yet.
[#32] Fix Reset PW flow through app.

* Add domain_helper for future domain 
  related helpers
* Add default_domain option to devise mailer views
* Clean up views a little bit.
* Remove default url_for host config in dev so as 
  to allow for accurate smoke tests.
[#61] Style private topics

* Both in topics and posts index actions
* slight cleanup
Merge pull request #62 from jayroh/61-private-topics-styling

[#61] Style private topics
Updated the specs
Merge pull request #14 from jaytaph/spec-update2

Updated the specs
Removed obsolete code
Merge branch 'master' of github.com:saffire/saffire into syntaxcheck
Small fixes. Made examples work
inching back to the prior level of performance
updates
a couple changes
Added MKVToolnix download support on OS X
lease client compiling
changeColors
changeColors
Merge branch 'master' of https://github.com/jceipek/pyShiva
Merge branch 'master' of github.com:jceipek/pyShiva
Added groups. Don't work yet because they segfault when drawn.
Added groups to Cython; fixed the drawing of groups.
Merge branch 'master' into resize-rect
Made resize_rect work, added demo file. -Chaz
papier.sprites: fix tests by adding combinators to using.
Merge pull request #1 from mrjbq7/patch-1

papier.sprites: fix tests by adding combinators to using.
Added BaseComputeServiceLiveTest.testConcurrentUseOfComputeServiceToCreateNodes
Merge pull request #639 from aledsage/AddedTest-ConcurrentUseOfComputeService

Added BaseComputeServiceLiveTest.testConcurrentUseOfComputeServiceToCreateNodes
added statement to rebase dist packages
Replaced the deprecated BlobStoreContextFactory with the new-style BlobStoreContextBuilder for runatcloud-tweetstore
Issue #830 vcloud-director: QueryClient live tests and fixes
Merge pull request #463 from aledsage/issue-830-query

Issue #830 vcloud-director: QueryClient live tests and fixes
cloudservers and aws-ec2 work with tags now
prevent credentialstore from leaking across tests
Allow operable_on_all on ActiveRecord
Bump version for release
fix a cache warning

you can now call vips_cache_set_max() and friends just after
vips_init() ... previously you had to wait for the cache to be built
Added additional reversal on appended polygon point
implement get-board in terms of authorized-api-result
added some new convenient stuff to the end
update
configure Mono.Addins add-in cache to be located in user-specific directory
skip input lines whose first non-ws character is the comment character '#'
allow 0 as a value for the HA property, since the GNU regression test scripts use it, but log it as a parse warning message
relocate layer loading to GtpParameters and call the new method in DoFixedHandicap to avoid NPE when boardsize command not yet issued
add GTP debug commands plugin
fix regression introduced in last change to BoardCollector, revealed by strategy1.sgf, and add unit-test for same
ensure that the proper layer is loaded each time loadsgf is executed, and fix silly array element indexing bug
ensure that loadsgf sets the komi from the input game record in the resulting game object
ensure that the quit command replies to the controller, as required by the GTP 2 spec
support reverse komi (negative komi)
log warnings instead of throwing parse exceptions for bad values found for decimal or integer properties
be even more lenient about properties that have no values - log them instead of throwing ParseException
allow parsers to include input file path in any parse exceptions thrown, update SGFReader to do so
avoid NPE due to board arrays (neighbors, diagonals, translation) not having been initialized
fix SGF parsing bugs revealed by parsing GNU regression test SGF files, primarily SGFReader.ReadRawListValue was not properly handling left/right parens and EOL tokens
remove board size hack in TestFile_wing_yuhiko_gnugo
assign non-standard properties to GameInfo until SGFReader encounters a sub-branch of the main branch
license and description
release 0.1.0
changed title from 'groups' to 'user groups'
add create/access time to virtual membership object
highlight instances in main menu if instance overview is shown
better description what user groups are
change column type from string to unicode
Changed directories where to put releases and nightlies build
bugfix after name change

Signed-off-by: Jens Moser <jenmo917@student.liu.se>
Add missing type conversions.
Adding Your Own Bookmarks and Bookmarklets to the iOS Simulator's Mobile Safari
Make streaming kind of working.
got sliding dft to work
Strength/Match Indicator Bug Fixes
Added Config option to application.php for local email debug
Write files to log path
Moved test scaffolding into common class Test_InstrumentLogic and fixed compile errors.
Moved constructor testing code to testConstructor().
Deleted methods and arguments.
Updated documentation.
Updated documentation in GameEvent.
Fixed compile errors.
Deleted unnecessary file testHangman.
Deleted methods necessary for multiplayer.
Project chart.
Updated documentation.
Updated test coverage.
Added a makefile.
fix a bug in tmp attribute handling
Added a three tests for the GReQL function "theElement".
Added a test for the GReQL function "entrySet".
Modified test for function "keySet".
Added a test for the GReQL function "values".
Added three tests for the GReQL function "faltten".
Documentation has changed, because the documented exception was incorrect.
Swapped some variables for expectedValue und actualValue of an assertion function.
Merge with 330374052e75c47715bb70162028d53a082b2e4b
Minimal changes.
extracted random graph creator from "TryAStar"
created first version of "GraphDbPerformance"
Added some additional tests for the functions "contains" and "containsKey".
Added some additional tests for the function "containsValue".
Added some additional tests for the function "count".
Added some additional tests for the functions "contains" and "difference".
Moved testElements() before testEntrySet().
Modified test for function "elements".
Modified tests for function "get".
Added a class to test for the record access.
Modified tests for functions "intersection" and "isEmpty".
Modified tests for functions "isSubSet" and "isSuperSet".
Changing font size.
Better padding on main.
Add auth_type to object constructors

- Remove comment about not supporting OAuth in this version
- Fix incomplete object initialization in FriendFeed_OAuth

Future:
- Use auth_type to move logic outside of fetch.
Fix trace swallowing task name arguments.
Merge branch 'master' into next-major-release

* master:
  Fix trace swallowing task name arguments.
Fix trace/backtrace swallowing task name arguments.
Merge branch 'master' into next-major-release

* master:
  Fix trace/backtrace swallowing task name arguments.
Version handling => ignored version.properties + creating version.properties from scratch if needed
RM3764 fix (move before_destroy callbacks)

This fixes RM3764 but also other shortcomings that didn't get caught by
specs previously.

The problem is that when before_destroy callbacks are put *below*
association definitions, they are executed *after* `destroy` is called
on associated objects that are `:dependent => :destroy`. This is
currently an open issue in Rails [1]. It causes problems with our
`destroyable?` callbacks, as their whole purpose is to prevent `destroy`
from happening if needed. They should prevent destroy from happening at
the very beginning, not halfway through.

When `destroy` only manipulates data in relational DB, the issue is not
critical, because the transaction gets rolled back. However, the objects
in memory stay in `destroyed?` state, which is what caused RM3764 spec
to fail. The objects get into correct state again when `reload` is
called on them.

The situation is more problematic when `destroy` is not fully
transactional. This is the case of Instance and InstanceKey. When
attempting to destroy undestroyable instance previously, the
`destroy_instance_key` filter on InstanceKey, which deletes an instance
key via Deltacloud API, would get called before `destroyable?` filter on
Instance. The `destroyable?` filter would roll back the transaction in
Conductor's DB, but wouldn't revert the operation with Deltacloud. This
is now fixed, as `destroyable?` gets called first.

[1] https://github.com/rails/rails/issues/3458
First cut of new SOAP parser
Adding missing dnsmasq config file.
Add the 'fork' command to cabal-install.

This command reads the source-repositories from a package's description,
determines which VCS to use, and then creates a local repository or branch
of the package's repository.
Initial work on Java env var wrapper script.