labofsahil/github-event-dataset-2012 huggingface dataset:
yi12345s fixes
Add form add ad

This form allows to add ads.
Use Object#to_enum instead of Enumerator.new without a block

Fix warning
warning: Enumerator.new without a block is deprecated; use Object#to_enum
bar problem

aaa
added some more default paths for metasploit-autolaunch
Add a Thread.Sleep() during the busy loops calling DoEvents() while waiting for various things to complete.

At various points the code loops waiting for various things to complete (downloads, etc.) and this pushes the CPU 100%. Easy fix is to just a some sleeps. I'm not a .net guy (or even vb for that matter) so I didn't want to re-architect the code to eliminate them. From the little I've read, some of them might be better off with Thread.Join() instead.

Before, scraping would peg a couple cores at 100% and which would kick in the fans. Now barely registers while waiting for the network.

Doug
Pull request from John's master to my brach release 0.0.2

Pull request from John's master pcwerk/seck to cs454cpotts/seck release 0.0.2
Issue 1452 (Plugin cancel button doesn't work when using a PlaceholderField with a custom model)

The issue is fixed in placeholderadmin, but the 'cancel' button logic is duplicated with the one in pageadmin. However, the 'edit_plugin' (and other plugin handling methods) already has most of it's logic duplicated in the two modules. I could refactor the code and remove all duplication, but the changeset would be quite massive and would probably require some design decisions.

Besides the issue, also improved test coverage and fixed a couple of miss behaving tests.
From based on readable-stream

Again just an idea of how to implement it.
Fixes #4 - Remove ejs
Replace erroneous use of "throw" with "raise"

I also added a spec forn this case.
Fixed EZP-20158 Small typo in load DB Schema function of eZ Demo package

An easy one. :)
Add an arg "simple" to show explainations only

Sometime, especially when i am checking more than two words, the references and resources would disturb me and makes the interface a little more noisy.

By adding an argument "simple", program will show only explainations and it will be more effictive when check multiple words
renamed extension on another.file.here to another.php
AS7-4723 Clustering TS: add generation of the sync cache configs, make i...

...t default, don't wait on sync repl
WS authentication tests for EJB and POJO endpoints [JBQA-5249]
JBPAPP-9094 fix for branch 7.1

Throws deployment errors if library-directory value is not supported, and/or has modules as childs.
JBTM-1360 updated the path for orson in build-release-pkgs.xml (master)
IIS Web.config example

For thous of us who for some reason trying to run this on IIS added Web.config example to docs
Merge Ahausladen webdownload - download functionality

This is a pull request for the (not yet finished) ahausladen-webdownload branch. This branch is based on the work by @ahausladen at ashausladen/issrc. See 37c9728c6c4d6751ac51d9f587f95aaf50a884e1 and 71c32ede4d7de6732b9c28d24e3b60b4b11b807c for its documentation. Comments/ideas are welcome.

Did some cleanup work on it but got stalled:

-Tried called DownloadWebFile but its Cancel button didn't work very well and throws up VCL thread synchronization errors, at least under D2. I hate those. Also thinking calling this function from [Code] should be limited to from within PrepareToInstall events.

-The code is WinInet based, but WinInet doesn't work in services, so the download functionality doesn't work if Setup is called by a service. Not sure how much of a problem this is or isn't. Using WinHttp instead would work, but it has other limitations. See http://msdn.microsoft.com/en-us/library/windows/desktop/hh227297%28v=vs.85%29.aspx
added feature y
databaseupdate

No need to reinstall for this one.
Will auto apply.
LOG_AUTHPRIV and LOG_FTP may not be defined
Cascading selects

support for _one_ cascading select per worksheet... not sure what will happen if you try more.
Bug 800446 -  [email]'load more messages from server' box gets stuck und.er the toolbar

* Fix bug: https://bugzilla.mozilla.org/show_bug.cgi?id=800446
* "No message" text position will be affected in this fixing, but "No message" style will be replaced in this PR: https://github.com/mozilla-b2g/gaia/pull/5762
Helping this guy out :)

Test PR
Moving start screen inside main browser frame, closes #4641
Support loading app packages from multiple locations - install-gaia part

Gaia side of https://bugzilla.mozilla.org/show_bug.cgi?id=778079 - don't merge before this lands!
Merge with master - really
[SMS] Edit mode responsive to input selection

- When no threads/messages selected, button 'delete selected' is disabled
- When any thread/message is selected, button 'delete selected' is enabled and header shows the number of items selected
Bug 809039-reopened Updating images in contact list view after synchroni...

Some minor changes needed to enable it working in all cases
Treso

Ajout d'un module dans Scoobydoo permettant de voir le CA sur une période donnée.
Fix .organization_members. Implement media_types.

Fixes #158.

All requests will now be mashified. ~~This makes the use of the raw paramter
everywhere unnecessary since it is primarily used to get the status code of
the request instead of the response body. I will remove it later.~~ Edit: This 
actually won't be removed, I'm just tired and overlooked a small detail.

Mime types have started to begin due to a conflict with needing a request to
be "raw" to get the status code while also returning the mashified response
body and still working with the markdown results from the markdown api.
They are not fully implemented, just enough to keep the response.body
parser happy without breaking any code for the new changes.

This bunches a few things together that would usually be frowned upon
in a commit but I hope you will see it out.
Untitled

patched as supplied in bug http://www.pecl.php.net/bugs/bug.php?id=18658
Added "bypassCache" option to let the browser cache the images.

By default, image's URLs are prefixed with a timestamp which prevent
the browser from caching the image.

Setting "bypassCache: false" disable this prefix, and allow the browser
to cache the images and do If-Modified-Since requests instead of
fetching the whole image.
Added support for setting NuGetCachePath environment variable to speed u...

...p nuget package install.
Fixes missing changes in #172

My IDE didn't push all changes for some reason in my commit.
This was includes missing changes for what would have been in pull request: #172
TK33612: Move deb creation from core/valve to installation.

TK33612: Move deb creation from core/valve to installation.
Allow populate method to set properties on children.

This code will allow users to set properties on child components using dot notation.  For example, a person component that has a child component of address a user could set properties on address by having a property in the request.context of address.line1.  

```cfm
<!-- to set child properties use dot notation -->
<input type="text" name="contact.address.line1">

<!-- this would call -->
getContact().getAddress().setLine1(value);
```

I've added a new parameter to the populate method called "deep", which by default is false so current functionality is not changed.  Only if trustkeys == true or deep == true child properties will be set.

I've also added some mxunit tests to confirm that the functionality is working, it assumes that mxunit is installed in a webroot becuase I didn't want to assume that you'd want that framework in this project.
Empty search expressions should return all objects, not none

When i create search using expressions array, i found that if the array is empty, the SQL generated will return no result:

```sql
SELECT DISTINCT (NSFKey),NSFPlist,NSFObjectClass FROM NSFKeys WHERE (NSFObjectClass = 'User') AND NSFKey IN ()
```

This pull request fix that and return all results with following SQL:

```sql
SQL: SELECT DISTINCT (NSFKey),NSFPlist,NSFObjectClass FROM NSFKeys WHERE (NSFObjectClass = 'User') AND NSFKey IN (SELECT NSFKEY FROM NSFValues)
```
fixed a bug where xml wouldn't pass Airbrake's validation

Problem was that <project-root> came after <environment-name> when, according to their xml schema, root should come first.
Amd wrapper cleanup

Just a few cleanups for the expectations of an AMD module. The commits are pretty obvious.
Adds trivial UnitGroup
Fix README link

Maybe you could also add link to github issues tracker to README

Best regards
Abstract away reporters for extensibility
Features/better configuration

The goal of this pull request is to move all the configuration into a kip.conf that can be overridden on a per user basis. 

The format supported format is : [ConfigParser](http://docs.python.org/library/configparser.html) 

I have also added some improvements to the `guess` method to ask the user to pick his choice among the list.

--yml
Added sBUS RSSI (Frame loss detection)

Not true RSSI but something to work with.
Also, smoothed out CameraTXControl to move servo slower.
Importing random in DevAppServer

The DevAppServer uses the random class to decide if it should randomly kill AppServers, but it wasn't importing it. Fixed this.
Fixed some minor es_ES translation typos
Load tableOrdering() function only when needed
Rudimentary unit test framework for the MobiPerf server.

At this point this only contains basic unit tests for the 'model.py'
module. It should be straightforward to add unit tests for other
modules by creating a corresponding <module>_test.py file and using a
similar structure to that in model_test.py.
Migration email

changes in migration
gz-10: Fixed an issue that prevented Zendesk tickets outside of the age limit from being filtered at some age limits

There was an issue that allowed Zendesk tickets with associated GitHub tickets that were outside of the age limit to escape from being filtered. Although this is a rare occurrence amongst Zendesk tickets, it can still be a problem at some age limits as these tickets will break the application when they pass through the main loop in the `build_enhancement_data` function.

In order to fix this, I rewrote the GitHub ticket filtering so that it removes any Zendesk tickets whose associated GitHub ticket can not be found in the list of GitHub tickets from the API calls.
Fixing success message alignment.
Fix for Issue #64

This is a fix for issue #64

In s3.createBucket if region is "us-east-1" send empty body.
Good part of French Translation

- Some files were saved using the UTF-8 encoding (can't work in ANSI)
- Should be good but the chars still need to be defined (the font). I believe Persalteas has started that.
pull request test

branch作ってpull requestしてみました。
Xml utils

This includes original patch I sent to ML, introducing TempXMLFile, XMLBackup, XMLBase.  In addition I found that in order to support proper and uniform XPath support, we need  to bundle another ElementTree sub-module: ElementPath.  This is key because it allows users to access elements structurally.  I've updated the unittests to make use of this but they also serve as a good example of how this can be used.  For example, assume you have an ElementTree containing the 'virsh capabilities' XML output and you want to change the architecture of a guest:

xml.find('guest/arch/wordsize').text = 32

Much easier than doing the same thing with minidom.
Added additional benchmarks for focal operations.

Added benchmarks comparing old-framework and new-framework focal operations, in preparation for optimization.

Removed some commented code in Build.scala.
モバイル用のbaseUrlが正常に取得されていなかったので修正

本家への反映をお願いします。
jquery-uiのカレンダーウィジェットの年月の背景色が見難いので変更。

本家にマージをお願いします。
quick fix for BUKKIT-1140

I encountered this bug when I first forked/cloned/mvn'd. Taking a run at contributing here, more to come I hope.
Ver 0.0.2 array support

I made some changes so this gem can support multiple return values for some arguments.
add setMute and isMuted function to SimpleAudioEngine. iOS & Mac is comp...

add setMute and isMuted function to SimpleAudioEngine. iOS & Mac is completed, other platform need to coding.
Do some changes before releasing
Change 'unless' to 'if' again because 'unless' is wrong here.

#3655 was merged by accident but tests for `seed_aspects` ~~are~~were missing. ~~Tests will follow, please **do not merge** until the tests are here...~~
Default style fix and add recurse=true to layer.delete

Two small fixes mostly related to Geonode.

An aborted data upload in Geonode will leave a resource but no default style, so when cascading_delete is run if errors when it tries to find the default style to delete. The first fix allows the default style to be None.

The second fixes adds the "recurse=true" option when deleting layers. This will delete both the layer and any associated resources.
Acertando bug de excluir modelo

Acertando bug de excluir modelo
Python fixes

Fixed python forking -- children processes now die off when a paren gets killed.

Tweaked logging and a backlog parameter of the python servers.
lib/flatiron.js: Replace deprecated __defineGetter/__defineSetter__

@coderarity and I weren't sure how to document this, and not sure if the set change will be welcomed.

The only difference between the original set/get is that the new set also allows options to be passed, instead of an instance of `flatiron.App`. You can still use an instance of `flatiron.App` for backwards capability, so no major API change was implemented.

Feedback welcome, especially on the documentation.
flow_matches

This is in reference to conformance test-cases section --6 flow-matches"

1. All tests are passing with reference and some physical switches , except for VlanPCP . 
it seems like switch is not letting me insert a flow entry matching on vlan_priority

2. Two test-cases are missing "match on ip src and ip destination ". Will add them soon .
make escapeMarkup optional

This is my pull request on refactoring the place where the `escapeMarkup` lives and making it optional with an `doEscapeMarkup` parameter. 

## Disclaimer

I'm no JS developer and I hope those changes makes sense.

## Reasoning

I'm using select2 with Django by supplying an `ajax` object and I'm generating the rich format of a selection items on server side (i.e. values from db wrapped by some nice tables and images). I want to display those items "as is" and I'm escaping all the user inputed data on server side (in json). So my json looks something like this:

    {

    "id": "2",
    "value": "Pear",
    "label": "\n <table class=\"selectable_table\">\n <tr>\n <td rowspan=\"2\" class=\"image\">\n <img src=\"/media/fruitimages/pear.jpg\" alt=\"\" width=\"50px\" height=\"50px\">\n </td>\n <td>Pear</td>\n </tr>\n <tr>\n <td class=\"small\">this is a pear! and it is  &lt;script&gt;alert(&#39;hacked&#39;);&lt;/script&gt;</td>\n </tr>\n </table>"

     },

and format funcs look like this:

            formatResult     :  function (state) {
              return state.label;
            },
            formatSelection  :  function (state) {
              return state.value;
            },

because i want to display:

    this is a pear! and it is  <script>alert('hacked');</script>

In current implementation of select2 it seems that i can't do that because theres is no option to ignore the client side escaping.
Modified the regular expression in language debugger to include dot sign as a valid KEY character

More info: http://code.joomla.org/gf/project/joomla/tracker/?action=TrackerItemEdit&tracker_item_id=28908
Keycuts

This branch adds basic keyboard shortcut support for Fulcrum.

Implemented shortcuts:
Help -> ?
New story -> a
Save currently edited story -> <Ctrl> + s
Toggle backlog <Shift> + b
Toggle don <Shift> + d
Toggle chilly bin -> <Shift> + i
Toggle In progress <Shift> + p
Dev/genomecomparison

- Updated Styling on buttons (test)
- Genome name editing via genome table now working
- Tooltips for RGB colour values
- Manual comparison now set to compare the newer genome with older genome (same as Auto Compare in main genome window)
- Signal blocking of tables on row insert. Stopping 70+ signals being sent every insert.
Kudos

* Slightly modified kudos css
+ Added small basic animation of kudos
Refactoring of C# GUI components.
CADMIUM-77: Added logic to force the ".war" extension on the cadmium

init-war cli command.
code optimizations & gitignore
Clarifying placeholder text in login form. Field is called username but ...

...form accepts e-mails, not IRC usernames.

jjw
Fix: port of the PR #319 from Propel

See https://github.com/propelorm/Propel/pull/319
add ability for script to work even when the GPG file is read-only

I want to encourage users on my system to use 'viencrypt'.  While it's certainly not too difficult
to have them use GPG by itself to look at read-only files, not all of my users are
super sophisticated, so I want viencrypt to *just work*.

Also included in this pull request are: 2) an additional error-check in case the GPG file is `chmod -r`, 3) two documentation-only changes
2.1 Compatibility

Made the module 2.1 compatible
adding RSpec for test
Constant stubbing

This is the implementation of constant stubbing for #144.

I want to do the work in rspec-fire to ensure that it works with this before merging it in, but it's done as far as I know for now, so I figured I'd submit the pull request to get implementation feedback.
Support for %j and %C

%j: The day of the year as a decimal number (range 001 to 366).
%C: The century number (year/100) as a 2-digit integer.
strftime() offers AM/PM and am/pm
The json when you delete an index contains acknowledged

The method isOperationSucceed search for "found:true" to determine if the operation succeed in case of a DELETE method.
However for a DELETEINDEX operation, the json is {ok:true, acknowledged : true}
Code clean up

Don't use strlen()
Fix type delemeter->delimiter
Remove useless method
Patch for issue #119

Just realized it was very straight forward to get the desired behavior.
Only clean-up left. :)

Added support for bundling and minifying (introduces dependency on yui compressor).
Moved HtmlHelper to seperate project.
Generate ruby thrift client  for cassandra 1.1.2 using thrift 0.8.0

Please merge this change so that we can continue working on the changes for the latest version of cassandra (1.1.2)
Fixed URL to use corsproxy :-)
Macでビルドするためのfix

LICENSEとlicense/が大文字小文字でコンフリクトしたので
LICENSE -> LICENSE.txtとしました。

そのほか、OSX10.7環境でビルドするためのFixをしました。

なお、MacのXで動作させるためにはconf.hを

diff --git a/conf.h b/conf.h
index b26f080..a6d6f0d 100644
--- a/conf.h
+++ b/conf.h
@@ -34,8 +34,8 @@ enum {
 	WALLPAPER = false,
 	OFFSET_X = 32,
 	OFFSET_Y = 32,
-	TERM_WIDTH = 0,
-	TERM_HEIGHT = 0,
+	TERM_WIDTH = 600,
+	TERM_HEIGHT = 380,
 	TABSTOP = 8,
-	SELECT_TIMEOUT = 1000000, /* usec */
+	SELECT_TIMEOUT = 20000, /* usec */
 };

とする必要がありました。
Ryu gre tunnel oct 11 2012

Stop DevStack install. -> Delete '#'. -> Install DevStack.
removed anchor after redirect for validate host

for when a url is redirected to another where there is anchor
Hotfix random integer generator rand() in Zend\Math\Math

Fixed the integer random generator. The previous implementation didn't provide a uniform distribution (because the usage of %). See: http://www.php.net/manual/en/function.openssl-random-pseudo-bytes.php#104322
I also added a new test case for the randomness using an idea present in the PHP-CryptLib project.
I added a note in the Zend\Crypt documentation for thanks the PHP-CryptLib project.
Improved integer random generator rand() in Zend\Math\Math

Improved version of the integer random generator. The previous implementation didn't provide a uniform distribution (because the usage of %). See: http://www.php.net/manual/en/function.openssl-random-pseudo-bytes.php#104322
I also added a new test case for the randomness using an idea present in the PHP-CryptLib project.
Class construct to allow the min and max year to be specified

Class construct to allow the min and max year to be specified
Just need code review.

issue A24Group/Triage#661
changed update and delete methods

/cc @nbryan  @daveknapik 
STAGING-SITE : 
STORY: 28113981
Notifications : 
Notification Message :
  
Test Cases :
 see https://github.com/Adaptly/adaptly_pi/pull/3/files#diff-5

Has Migration : No
Notes :
Importing jon's code
Frontend merge back to master
Fix xKI insanity

In external builds, the python pak thinks xKI.py == xKI. This is understanable--having two modules with the same name is naughty.
Speedup for debugging: don't create std::string on every call to glCheckError

Hi,

I was getting ~10 FPS when debugging in VS2012, and doing a performance analysis seems to indicate a lot of the time spent is simply creating std::strings on each call to ```sf::priv::glCheckError(__FILE__, __LINE__);```.

This seems really unnecessary as the string is only needed once something actually goes wrong, so I changed it accordingly.

With the patch I get ~100 instead of ~10 FPS when debugging.

Cheers,
\-\-
Christian
[Fixes bug #1079680] Cleared selection polygons before creating new selection
atulizacao final das ultimas alteracoes
Published Categories

Adds an adapters object that is passed through from a category to a card instance. It also only loads categories into a cache if they have a published : true flag.
New behavior for `tests\mocks\core\MockCallable`

Example of use case:

```php
<?php
$callable = new MockCallable();
Adaptable::config(array(
	'test_config' => array(
		'object' => $callable
	)
));
Adaptable::method(array(...));
var_dump($callable->call);
//or
var_dump($callable::staticCall);
```
Updated interface names for ZF2 master
Fix for FormButton API change

This should remove the current errors on the Login and Register pages.
Add the option to whitelist ip's. 

Added the full description into the readme.

I added tests and they work, but they are a little clunky. I'm not incredibly familiar with shoulda.
X教授初步框架重新发布

删了node_modules文件夹下的文件，并加了.gitignore文件来忽略这个文件下的内容更新，这个文件下的内容改由npm来手动安装
Remove exiting_a_business BusinessStage.

This shouldn't have been there. It came across with the data from the BusinessLink tool.
Removed an accidental debug line that was causing issues with our use case

Hey, just so you know we're using your library!

My colleagues and I are writing a new testing framework for lua (with all the same features as rspec, mocha or jasmine). In fact, we're about to release it. It should be on luarocks in a few days. We use cliargs for everything command line.

Expect more pull requests from us in the future =) Thanks for your great work!

http://olivinelabs.com
Add /delete to protected routes
Move/trash an array of paths

See issue #16 for reference and inspiration.
I did lots of stufz
Fixed link to menu.
Issue #205

Также исправил, чтобы при экспорте не было выделенных элементов
Tilauksen mitätöintiin tuki valmistusriveille joilla var P.

Jatkossa tyhjennetään var P ja mitätöidään ne tyyppi D:ksi, jotta ei jää varaamaan myytävissä määrää.
Laskun viivakoodin korjaus.

Käytetään laskurow summaa viivakoodissa.
Added help on couch-lucene/ celeryd settings
Bug #1514 - Rewrite S2PropGroup.pm to use pure CSS positioning instead o...

http://bugs.dwscoalition.org/show_bug.cgi?id=1514
Patch for NavStripChooser.pm to use CSS positioning (does not change custom color-picker table)
Fix/1.2.x/soc 2609

Fix wrong default focus on My connections page.
Allow disabling notifications

#709
Added bzr support

I've implemented bzr support and I've added the groovy-mode pkg that uses it.
fix critical issue with utf-8 urls - infinity 301 redirects

 string  $identifier containing symbols newer be compare with  urldecoded string $requestUri
Bug 740302 404 on login

Add URL to the error email
Adding tests for products page

Products page tests
Clean up nav bar and uplevel Edit Profile button. bug 743709
Added constants + various

Hi,

* Added costants for almost every "magical"/hardcoded value
* Reduced the lines of code of several functions
* Switched a few if/else branches around, hoping to hit the more common cases more often
* Added memoization of len(values) several places

All tests pass.

Best regards,
Alexander Rødseth
Add cocoapods.org in black list.
Add idp metadata

This patch adds IdP metadata to make the settings configuration easier.  No messing around with fingerprints and target URLs.  Additionally, it's more secure since many IdP's (Shibboleth especially) require the SP to have metadata when configuring permissions.

I also:
* Added response X.509 cert comparison with IdP metadata
* Supports IdP HTTP-Redirect and HTTP-POST SSO bindings
* Added option to skip signature validations
* Added some extra settings
* Created tests
* Updated the README with some extra fun.

This is probably the last feature that I needed from ruby-saml, but I might work on a nice rails3 example application to submit.
Fixes #67 & #69 (IE8 perfomance issues).
No more tenses
1.4.0 dev

- workaround for window problem in issue #37 (if you have better idea how to solve this issue please do :)
- functionality to use standard init to load plugin (by supplying usePlugin in options with plugin name)
Nebraska and Columbus assets
make suggestion output on failed comparison more descriptive for arrays ...

...of things

I ran in to an issue when comparing two arrays of objects. The output message told me to check the Array#== method, even though the comparison was being done on each element of the array and I needed to redefine an Object#== for the objects in the array. I thought this was a bit confusing and wanted to make it more specific. I added support for this in the patch.
support  for go

as title 
ah, and I change the README into README.md too
Branch1

Save new changes
Testing pull request

just to see what happens.
Supports numbers configured that are bigger then Long limits

Will create a BigInteger if the number parsed from the config goes outside the limits of the long type.   I'm catching the NumberFormatException, ideally a regex check would probably be more performant but I'm not sure the exact regex Java would be using parsing the int to throw the exception.  By using the NumberFormatException I'm guaranteeing I'm conforming to java's spec of what is a long.

Also, I might be missing a few test cases, I added what I could see needed checking.
tertertet
Added iPad 3 data caching

My fork caches validation data from iPad 3's. Unfortunately, however, the data from an iPad 3 is only good for dictation and not Siri.
A myriad of filter improvements and a new pixel filter

- Updated Swirl and Bulge and Pinch filters to be correct for aspect ratio
- Vignette filter has center and color parameters
- Added new filter PixellatePosition for blotting out logos or faces
- Added synchronous version of processImage in case you want to immediately generate a full image right after (i.e. changing the force output param to full size, calling processImage and then saving the image)
Fixed javadoc errors that occurred when moving from Eclipse Helios to Eclipse Indigo.

Also fixed a pom error that occurred when upgrading Eclipse.
Tweaks to the OCLA description

As suggested by @dustinsenos. Thanks, Dustin!

R=ds
I started writing ls

#LS
motherfuckers
#3 Create function return limit.

Create function limit of returns.
Oops, wrong file. Missing import
Gallery3d

Gallery3d gingerbread update works much faster than before
Extension system, independent wrappers. Init change.

Beginnings of an extension system, already tested with a clientside HUD, works fine. More changes to come in regards to read-only, and extension registry.
adding gnome to the 'know terminals' list

solves #30
SeqUtils.ProtParam: Add AA monoisotopic weights

Support for calculating the monoisotopic weights of proteins to simplify calculation for mass spec data.

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
Bug Fixes + New modules

- Bug fixes (see Google Docs)
- New module XYZoomNavigator (for loading plot)
- Loading plot can now send its center position, viewport and zoom (0-1)
- Loading plot can now be in a "navigator" mode, without zoom or drag, but with a red rectangle describing the viewport of another loading plot.
- Remove tools in header, but implement them on right click
- etc...
BUG 10037 Error in ws_sendMessage & ws_sendEmailMessage in wsClient.php SOLVED

- Incorrect parameters sent in the functions ws_sendEmailMessage and ws_sendMessage
- Now we use and send the correct parameters
Mime helper capitalized file extension fix

Added strtolower to passed extension in mimeFromExtension to handle capitalized file extensions.
Diferent changes in GUI and Data Model
pull pablo's changes as on 7/15/2012
Fix #93 Anti Sleep while playing
Release/releases 1.2.1
1 of 7 update to utype.c

Big update, but these smaller 'chunks' should help make it easier to accept small blocks at a time.
Just a small fix.
fixes in diabook-derivates

move the "common tabs" to right_aside on seetings-page in diabook-derivates
SUP!

Just changed it to say sup..
Another test

PR description
38
Added proxy implementation

Change-Id: Id96b3e29c812c96a04866c7c8f2045fe49254ab3
Test pull request from a branch

I created this branch at the end of the day, checked in a change, merged it, and pushed the branch to the origin (i.e, my fork). Now github will let me specify it as a place to pull from. 

I'm curious to see if it shows up as a branch when you pull, or if it just lands on your master. I presume the latter since that's what I've specified. After you've pulled, I presume that I'll be able to delete this branch from my origin, and treat it simply as my local daily branch in the future.
Fix creating a button with a type under IE7

A `<button>`'s type cannot be changed with `setAttribute` under IE7:

```javascript
var button = document.createElement("button");
button.setAttribute("type", "submit");

console.log(button.getAttribute("type")); // "submit" (even in IE7)
console.log(button.type);                 // "button" in IE7
```

The button continues to act like `<button type="button">`, and it cannot be used to submit a form in IE7 without adding a click event handler.

The only workaround I know of is IE's proprietary `createElement` syntax where you can specify attributes inline, and this pull request implements that workaround.
List snapshots separately from volumes+filesystems

Listing snapshots with full properties takes a significant amount of
time, increasing the time for a 'vmadm list' from less than a second to
almost a minute on some systems. Since we're really only interested in
the snapshot names, issue a separate 'zfs list' for just that and merge
the data afterwards.

You might hate declaring a named function in the middle/end of another function. I did it that way to minimize the amount of changes and make the diff easier to review. If you want this refactored differently I'd be happy to do so.

The patched VM.js Works For Me(tm), but I'm not entirely sure where the snapshot data is used. I'm currently building and installing a system to run the test suite on, if that fails I'll retract the push request or fix it.
Line 47 Corrected for Bananas

Returns nickname correctly now.
Add Makefile for building PDF

I added this so I can build the PDF from Vim easily.

If you are not interested, I can also add it to `.gitignore`. Probably needs some tweaking to work on both Mac OS X and whatever Linux distro you run anyway.
Apple pancakes!
Hide the cursor when printing

When keyboard shortcuts are used to print (e.g. `Ctrl` + `P`), focus is not removed from the editor (at least in Firefox 14-), and if the cursor is visible at that precise moment, it is also printed, which can be misleading (could be the cursor or `|`?). This simple fix makes sure it's always hidden when printing.

Note: I wasn't sure where you wanted to place the media query, but I figured throwing it at the end would be the safest, especially if more print-specific styles are added later.
Add semicolons and remove trailing space

Hi,

Apologies, my previous patch committed the twin sins of missing semicolons and containing trailing space :-). Fixed.

Cheers,
Lorenzo
Move warnings from fatalErrors array to warningErrors

I'm not sure if there is a justification i'm missing here, but a PHP warning was being classed as a fatal error and throwing an exception, rather than just logging the warning. This changes that behaviour so warnings are treated as warnings.

Either way, this was throwing an exception which was breaking our code.
Update of readme and new image file

I've added example image file and added some characters to readme
BZ 848639: The force kill was leaving SystemV IPC entities around
Changed .button to .uni-button and fixed IE opacity

The class .button is widely used by many other libraries on the web. The jquery.uniform CSS conflicts with those libraries, and so should be namespaced. I have changed all instances of the 'button' class to 'uni-button'. I have also namespaced the other classes with "uni-", e.g. .uni-selector, etc.

Also, the IE filter's for opacity were incorrectly written. http://www.quirksmode.org/css/opacity.html
They were: filter: alpha(opacity:50);
They are now: filter: alpha(opacity=50);
Add quoting to the values of the data-id attributes used to identify elements.

Ran into a problem where we had some complex data-ids(UUIDs), that contain punctuation like '-'. This broke quicksand, because the element lookup filters didnt have quoting, and the expression would look like:
[data-id=435ce-3242e]
which would break jquery.

So, here's a really small pull request to add in quoting for data-id values :)  Makes it look like:
[data-id="435ce-3242e"]
Filter package version properly, retry and mark changelog sync as down
Update formula generation scripts to use stack.xml, not stack.yaml

The existing formula generation scripts do not reflect recent changes to catkin. This patch updates them to reflect these changes.
html.htmlfrom
Devguide - Add Message Bus Section to APIs chapter

Reviewed https://github.com/markhealy/liferay-docs/pull/6 and ready to merge into master. Thanks.
TskAuto Warning Cleanup

Moved definitions of trivial virtual functions in TskAuto to cpp to keep 'unused variable' warnings out of user code.

I updated the Doxygen to reflect the default return values. Really kind of a silly change, but tsk_auto.h otherwise generates warnings when used in other code (at least with -Wall), which is annoying. Let me know if you have other ideas... the other way to do it is to remove the function parameter names in the header file, but I don't know doxygen well enough to know whether this would make it unhappy. Also, it's kind of nice to have the parameter names in the declarations for the sake of being explicit.
Spanish translation for widget settings (ignore the previous one)

I made a little but important change in one of the strings.
Please, ignore my previous commit, and do this one instead of it.
Sorry.
Gremlin Base Functionality

<i>[Edited by @aseemk: see previous discussion at issue #44.]</i>

Hey guys,

So I believe I finished a basic, working support of the Gremlin plugin for this module. I did not update the documentation, README, or module version as I know there are other features in the works that pertain to all of those.

Included some starter tests that seem to indicate it is working, I'm sure further testing and usage will prove otherwise but I'll keep working on it. My next steps are to see if transactional & multi-line gremlin work as intended with it as well.

Let me know if you need anything else on this though!

Usage: db.execute(script, optional: params, callback)
Test: npm run gremlin
grid fixes & example
I complete one further on branch b3

line 1
line 2
and line 3
Bug fix in `fromJSON`

Great little plugin!!  Coming in very handy on a project I am working on.  Thanks for the good work.

The bug is that `el` was being set to the `id` rather than the element, the fix was just to move the expression to it's own line.
Just to let you know I changed a bit the way backups are organized

I merged your master branch before doing this, so you'll see only the real changes in this request.

#### Backups are organized differently in folders
Instead of putting zip files in separate folders:

    backups/world/2012-07-01-00-00-00.zip
    backups/world_nether/2012-07-01-00-00-00.zip
    backups/world_the_end/2012-07-01-00-00-00.zip

a single zip is created that contains all worlds:

    backups/2012-07-01-00-00-00.zip

Same thing if zipping is disabled, instead of this:

    backups/world/2012-07-01-00-00-00
    backups/world_nether/2012-07-01-00-00-00
    backups/world_the_end/2012-07-01-00-00-00

we do this:

    backups/2012-07-01-00-00-00/world
    backups/2012-07-01-00-00-00/world_nether
    backups/2012-07-01-00-00-00/world_the_endm

This way it is easier to manage the backups in explorer for example if you need to move old archives to another media. It also makes restoring easier, because you can restore all worlds at once, instead of one by one. And if the user needs to restore a single world only, it is still easy, this change does not make it harder.

#### The delete functionality now works with copied backups as well (when zipping is disabled)
Unfortunately, I had to do a lot of refactoring to allow the delete algorithm to work with both kinds of backups. You'll see that it uses IBackupFileManager to list available backups and to request deletions. The IBackupFileManager can be either ZipBackup or CopyBackup which knows how to list and how to delete each type of archive. 

I mostly did these changes, because it is more convenient for me that way - the machine that runs my server crashes a lot and restoring worlds one by one was really cumbersome. If you like the changes you can incorporate them in the plugin.

Best,
mantun
fix

revive limit
AntiCheat Support

Please note that this should only affect you if you wished to use the AntiCheat plugin.
Also, please note that this is an untested fix. However, due to the way it is implemented, it DOES NOT affect the operation of Vampire for non-AntiCheat users.

P.S.
The weird part about this is that it acts like I deleted and then re-wrote the entire plugin.yml, when in actuality the only change was in line 5.
Non-tracked manifest files

I'm now generating manifests on the fly in the bash scripts. "__" prefix means generated.
TRUNK-3501

Pull request for TRUNK-3501 - Show helpful message when purging in-use Field Types
Add bBBrainz
Fixes

Fix handling the preference for automatically checking a new update, and fix some visual glitches.
Support conditional paper trail on destroy

Howdy!

Background: We have a paper-trailed `Contact` model which `has_many :email_addresses`. The `EmailAddress` model also has a paper trail. We have a custom way of undo-ing deletes of parents, and all their children.

Problem: If someone blanks out an email in the web UI, then we destroy that email row. But, we don't want a `EmailAddress` version to be created in that case.

Other problem: However, we _do_ want to save a version of both the `EmailAddress` and the `Contact`, when a contact is deleted.

Solution: Pass along the `:if` conditional to the destroy code. We have a conditional expression that knows the difference between the parent `Contact` delete, versus the one-off deletion of an `EmailAddress` due to blanking it out in the UI.

Thanks!
Saving 2D coordinates of skeleton as well. (#35)
Disallowing decimal and negative quantities

Fixes andrrr/shopping_cart#8
Changed `pre code` block's highlighting color scheme to Zenburn

It is a nice scheme.

If any elements that should be highlighted are not, we can customize it.
Add an example config to run cleanbot on cloud foundry instead of heroku

After today, I figured I'd try running cleanbot on cloudfoundry instead of heroku.

Here's what I had to do:

First, I set the API endoint for `vmc`:

    vmc target api.cloudfoundry.com

Then I set the login credentials

    vmc login

After this, because cloudfoundry doesn't seem to let you set vars using `export` in bash scripts, you need to set them explicitly, like so:

    vmc env cleanishbot
    vmc env-add cleanishbot HUBOT_IRC_SERVER="irc.freenode.net"
    vmc env-add cleanishbot HUBOT_IRC_ROOMS="##cleanweb"

Once you have this, you can then try pushing it

    vmc push

The output should look a bit like this. the `Y` or `N` commands are my responses to the prompts when running the deploy for the first time.

    Would you like to deploy from the current directory? [Yn]: Y
    Application Name: cleanishbot
    Detected a Standalone Application, is this correct? [Yn]: y
    1: java
    2: java7
    3: node
    4: node06
    5: node08
    6: ruby18
    7: ruby19
    Select Runtime: 5
    Selected node08
    Start Command: bin/hubot -a irc -n cleanishbot
    Application Deployed URL [None]: 
    Memory reservation (128M, 256M, 512M, 1G, 2G) [64M]: 128
    How many instances? [1]: 1
    Create services to bind to 'cleanishbot'? [yN]: n
    Would you like to save this configuration? [yN]: y
    Manifest written to manifest.yml.
    Creating Application: OK
    Uploading Application:
      Checking for available resources: OK
      Packing application: OK
      Uploading (10K): OK   
    Push Status: OK
    Staging Application 'cleanishbot': OK                                           
    Starting Application 'cleanishbot': OK

And that seems to be it! It's up!
Build system fixes and UFEM enhancements
Created and Updated dates in entity constructor and fixed action
Improvements to TEB and TLV access that lead to performance improvements with C-R-T


As it stands, this will work on clang 3.2+ and gcc.

clang 3.1 should ignore it.
DOC-2239 Escape { in the wiki file to make sure the content display is c...
Add support for sFlow Nvidia GPU metrics from hsflowd,  and apache workers metrics from mod-sflow

hsflowd now supports sending Nvidia GPU metrics according to this spec: http://sflow.org/sflow_nvml.txt,  so this commit adds support for that sFlow structure to gmond.   This commit also adds support for the receipt of Apache worker-thread information,  because mod-sflow for apache now sends that along with the other sFlow-HTTP counters (see the "Application Workers" structure here: http://sflow.org/sflow_application.txt).
Support for managing scalarium apps and couds

It's very basic yet, but works as expected and is very hepful to deploy an app from chat
Support for Cassandras DoubleType and FloatType

As discussed on the user group [1], I have added support for Cassandras DoubleType and FloatType. It's just a few lines of code and I tested it with my application, storing and retrieving double and float values. Code review would be very much appreciated, though.

[1] https://groups.google.com/forum/?fromgroups=#!topic/hector-users/pG3FMdpMaFo
Provide :setDefaults() for overriding defaults

Because we re-use the same instance of UniReader object (i.e. PDFReader, DJVUReader, CREReader and PICViewer) we have to re-initialize the defaults on closing the document. The clean way to do this which allows to keep the default values in a single place is in a :setDefaults() method which this commit provides, together with the example of usage in DJVUReader and PICViewer.
Fix french issue (related to bug 10784) 

This set of modifications fix french issue (using charset Windows-1252).
The plugin can parse ChangeSet from the french version of tf.exe.
Merge blocking-insertion into master, solving timing issues

I think that all the timing problems that happened while using avr-alarm in conjunction with avr-tone are now **gone**!! \o/

So, I propose to merge the fix into master. What I did was basically:

1. To avoid **buffer underflow** (the queue getting empty while *insert* calls are still trying to finish):  I greatly reduced the amount of time spent in relative_queue_insert. Now, to append elements to the queue takes **O(1)** time, and since appends are the MOST COMMON case, a great speedup results...

2. To avoid **buffer overflow** (too many insertions causing the queue to get too big and corrupt memory):  In alarm.h there is a macro that defines a reasonable value for a maximum queue size. In alarm.c, in alarm_insert, there's a **busy-wait**, so that insertion is only performed when the queue is smaller than the maximum value.

Let's merge this?  I'll test everything in actual hardware (my arduino), and if it goes well, I'll merge tomorrow :)
Opening popup from within a listview does not restore button state

When I open a popup from within a listview, the button is always marked as active.
The code to restore this does not check if the button is inside a listview.
Abstract LibGit2Sharp away in testing context

This pull request is related to #138, and is a follow-up of #182.

Changes:
- An ``IRepository`` interface has been introduced.
- The most commonly used classes have been made mockable.
- I also added a ``MockedRepositoryFixture``, which shows how to abstract LibGit2sharp in a testing context. If you have a better name for this fixture, please tell!

@Haacked @nulltoken Would you please be so kind as to review this PR?
Implement time formatting, sorting, ranking, layout fixes

Needs further testing, but I think it will work.
Support for Selenium tests

please merge
Added a README.md to the generated site, redirecting pull requests to the mongoid-site repo

I didn't notice the "DO NOT EDIT DIRECTLY" text in the repo description for [mongoid/mongoid.github.com](https://github.com/mongoid/mongoid.github.com), but probably would have noticed it if a README file was present.

There are a few other pull requests on [mongoid/mongoid.github.com](https://github.com/mongoid/mongoid.github.com) that confirm that a README might be helpful.
V2.1.1a - 8 commits

see log
CHEF-3674 Adding PATH to the postgresql users .profile
换了下收藏页的背景。
make gorun pip installable

This is to fix issue #1.

What changed:

- new requirements.txt file to list pyinotify
- "translated" README.md to README.rst (compatible with long_description)
- modified "installation" in the README.rst (to use pip)
- improved and complete setup.py (use requirements.txt and README.rst)
- MANIFEST.in to add README.rst and requirements.txt to the package
- new LICENSE file

Please note that I've used the BSD license, as it's the one I'm used too, but obviously, feel free to change it by:

- changing the content of the LICENSE file
- changing the "license" parameter in the setup.py
Update lib/devise/rails/routes.rb comments
Add an isTablet property
Update .gitmodules - fix url of socket.io

Socket.IO repository has been moved to new path
31204583 add context links to the right hand side information box
Branch a

綴り修正
Fix for latest version of leiningen 2, which privatizes leiningen.core.project/merge-profile

...core.project/merge-profiles to accommodate recent privatization of former
fixbug for heartbeat context, add on('close') event to deal close socket
Add propel chapter on Symfony2 doc
fix indent of "Customizing Form Output..." => css bug
Fixing minor rst errors

Should fix warning about Inline literal start-string without end-string by moving the space from just before the closing string to afterwards but should not make any difference to how it displays.
Add bootstrap 2.0.3

This includes separate definition calls for each plugin ('bootstrap/...')
and adds and 'bootstrap' definition which depends on all plugins.
BCrypt

Fixes issue #140.

* Makes BCrypt the default strategy
* Provides a strategy to migrate from SHA1 to BCrypt
* Changes the strategy API.
Automatic building on ci.onarandombox.com

If you pull this PR, add this web-hook url in the administration->service hooks tab of this git repo
http://ci.onarandombox.com/github-webhook/ and builds will automatically occur @ http://ci.onarandombox.com/view/Other%20Great%20Plugins/job/Votifier/ when changes are pushed to github.
Rrdd-related changes to xen-api-libs.
Adding new test: equalsreplace
refactor AR::AttributesMethods and fix time zone dirty issue

Initially was to fix issue #3965 but found some inconsistent code.
Empty hash assignments no longer make the mutation fail

For #5

This allows mutations to be checked to ensure that they can actually be mutated. If they can't, they are rejected from the mutation list.

So far, this only applies to hashes, but can easily be applied to other classes by overriding changes_on_swap? for that class.