[Feature Request] Overlay font transparency to prevent OLED burn-in

Description of issue / Feature request
It would be nice to be able to set transparency for the overlay fonts to protect OLED displays from burn-in.

Great idea, I'll keep it in mind when I rework the overlay stuff which should be pretty soon.


enhancement - debug view of sphere / transparent live video view (optional)

Did you consider a kind of debug view to show spheres / perhaps with flexible radius?

http://paulbourke.net/dome/fish2/

I don't do the projections manually. They do happen automatically because of the arrangement of the 3D geometry and the camera in the scene. Therefore showing debug views such as those wouldn't be much useful. One could use special images to test the accuracy of the projections, but I don't think that it's something users really need. It'd be more like a gimmick at this point.

Thing is / I want to use/extend this library for augmented reality. Given its using SceneKit / did you know you can import 3D models out of the box? Also / consider that given this library is open source other developers may want to take this work on and chime in to help.(it's a pity all suggestions are bundled in as issues.) mapping the pixels to physical space would be critical for that kind of work to succeed (not a gimmick)

I'm aware that this was as suggestion and not an issue. I've started the project simply to display panoramic images and that's why haven't thought about its potential use cases in AR. Especially since it currently lacks features such as partial panorama support which are more relevant to its actual use cases I had in mind. Of course this doesn't mean that if someone does the work and sends a pull request, I'll ignore it :) It just isn't among my priorities right now.
Btw, SceneKit already has methods that project/unproject points that can be used to map the coordinates between the scene coordinates and pixel coordinates. So the mapping you're referring to should not be so hard to do even now, if that's what you're looking for.


Migrate pushrimkinetics to kineticstoolkit_instrumentedwheel extension

While pushrimkinetics is what started KTK, it's now too specific for my general vision of KTK. I started to create an extension system and pushrimkinetics should be an extension.

Related to #95

Done in kineticstoolkit_pushrimkinetics.


Cannot add using LuaRocks

This is the error:
mingw32-gcc -O2 -c -o src/luasocket.o -ID:\dev\deps\lua src/luasocket.c -DLUA_COMPAT_APIINTCASTS -DLUASOCKET_DEBUG -DLUASOCKET_INET_PTON -DWINVER=0x0501 -DLUASOCKET_API=__declspec(dllexport) -DMIME_API=__declspec(dllexport) -Ic:/mingw/include
In file included from src/socket.h:18,
                 from src/inet.h:18,
                 from src/luasocket.c:30:
src/wsocket.h:14:13: error: conflicting types for 'socklen_t'
   14 | typedef int socklen_t;
      |             ^~~~~~~~~
In file included from src/wsocket.h:12,
                 from src/socket.h:18,
                 from src/inet.h:18,
                 from src/luasocket.c:30:
c:\mingw\include\ws2tcpip.h:399:22: note: previous declaration of 'socklen_t' was here
  399 | typedef unsigned int socklen_t;
      |                      ^~~~~~~~~

Error: Failed installing dependency: https://luarocks.org/luasocket-3.0rc1-2.src.rock - Build error: Failed compiling object src/luasocket.o

me too. How to resolve this issue?

This is issue #302.

This is issue #302.


Evaluate performance on Scan->keyword->sink workflow

A basic workflow like Scan->keyword->sink was taking a lot of time (even going on till 20 min) while Source:Keyword-> Sink was very fast. So, we did experiment to test the root cause.

We took three data sizes - 10K, 50K and 100K and used YourKit profiler to note the time taken by scan and keyword operators. The graph below shows that as data size increases , the time taken by scan operator increases and is the main culprit for the long execution times.

Profiling setup
To profile the Scan->keyword->sink workflow, we need to use Yourkit as our tool. The procedure is as follow:

Change to the root of the texera maven folder:  cd texera/texera/
Run the build command for Texera: mvn clean install -DskipTests
Change to the texera-web module:  cd web/
Start the server with the command: java -jar ../web/target/web-0.1.0.jar server ../web/sample-config.yml
When the server is started, a process will appear in Yourkit main page. Connect to the process web-0.1.0 to profile our application.

If you have successfully attached to Texera application, you will see this page:

Open a new tab in the terminal, and navigate to gui folder.

Start the angular front end using the following command: npm start. Then the GUI will pop up from browser. (FYI: You need to install npm if you haven't done so. To install, use npm install)

Form the following diagram. Feel free to change tables/keywords/limits.

Don't run the application for now. We need to start CPU sampling first in the next step:
(CPU sampling is a statistical profiling method that shows you the functions that are doing most of the user mode work in the application)

Switch to Yourkit, and start CPU sampling by clicking the button in the red box:

After CPU sampling is started, switch back to Texera, and execute the application by clicking the "Run" button on the upper right corner.

When the execution is finished, you can examine your results in Yourkit in detail, to see the time consumption by each function.

Profiler validation
To make sure Yourkit profiles the application as expected, I implemented a small program to double check. In this program, b and c are two testers that sleep for a different amount of time, and are called and timed in the main program.

As shown, the time monitored by Yourkit has basically the same composition as compared with time shown in eclipse, so we can entrust Yourkit to profile our Scan->keyword->sink workflow .
Experiment Setup
In evaluating what took our Scan->keyword->sink workflow such a long time, I used a gibberish keyword to make sure that the selected table was entirely iterated through. Because the table doesn't contain gibberish keywords, inputting one will make sure Keyword Operator processes all the tuples. I did testing on table sizes of 10k, 50k, and 100k rows. Shown below is the call tree for 100k rows table. As you can see, the TupleSink.getNextTuple() function invokes ScanBasedSourceOperaor.getNextTuple() and KeywordMatcher.processOneInputTuple(Tuple) in the workflow:

After profiling with three tables, a graph that shows time consumption by Scan and Keyword operators can be generated:

In conclusion, the time taken by scan operator increases as the table size increases, and is the main culprit for the long execution time.


How exactly do errors work with this client? Can I catch the error somehow and figure out what the error is (without using typo-littered error messages)

The only error output provided by the API are the typo littered error messages. Whether you want to show them as-is to your users or want to built processing rules for them is up to you. A previous version of the client had some message matching, but even for InfinityFree the exact filtering got changed many times for my use case alone, so I gave up trying to come up with a system which works for everyone.

Do you have an example of what errors could look like?

For some inspiration, you could check the first version of this client: https://github.com/HansAdema/mofh-client/blob/0.1/src/Exception/Builder.php It has pattern matching and example messages.
But there is a reason I dropped this feature. Generic error handling didn't work out for me, and maintaining an exhaustive list of error patterns is impossible. Now I just make sure to validate data before sending it and match and handle error messages for the specific API functions.

Now I just make sure to validate data before sending it and match and handle error messages for the specific API functions.

Wouldn't you still have to keep a big list of all possible errors with that?

Wouldn't you still have to keep a big list of all possible errors with that?

No, not really. This is largely mitigated by having strong validation before sending it to the API. Sure, you could filter an error message saying .tk domains are not supported, but you can also check that the domain is not a .tk domain before sending it to the API.
The only error messages I filter are the ones which I cannot adequately check before sending the API call.
And unknown error messages are unknown and show a generic error message.

The first client version seems to just use strpos for finding errors. Seems like that would work.

Also regular expressions.

Hi, I had a question that is related to the replies.

The only error messages I filter are the ones which I cannot adequately check before sending the API call.
What information do you meant?

What information do you meant by this?

For example, you cannot host .tk domains. You could send the createacct request to the API and get the response that .tk domains are not allowed, or you can run your own validation rules on the domain and reject .tk domains before sending them to the API at all. That way, it doesn't make sense to setup filters for .tk domain errors, because your own validation makes sure that those error never occur.

@HansAdema, what I meant is: What information that you cannot adequately check before sending the API call?

I’m assuming by that he means errors like invalid IP address, a generic failure on MOFH’s end, or a domain being on another reseller.

@Dog2puppy I believe that the availability method can check if a domain is already hosted on MOFH or not, and Invalid IP Address and Generic Failures on MOFH's end is not information that we're about to send them. My question is about information that we cannot adequately check before sending.
Also if such errors occurred (Invalid IP Address, Generic Failure), do you think it's best to tell the user to try again later or our system will try again automatically?

For my client area I just return a 500 error for pretty much every error and say to try again. That’s mostly because I was too lazy to figure out how to do automatic retries though.

I second many of the things @Dog2puppy  said. I do have a generic "we were unable to create your account, try again later" error messages for those.
Retry mechanisms are an interesting suggestion. But some errors, like when a domain is not pointing to the nameservers yet, require user action to be completed properly, which is why I prefer to try the API call once synchronously, rather than multiple times asynchronously.
The availability call catches a lot of errors already, but it doesn't do nameserver checks and some reseller domain checks.


Code the course listing with a letter preceding it to use for user input's completed courses

Changed it to #13


Not working with wamp

Hi Sir,
I am using wampserver.
I am going to convert PDF to HTML. i am using your script but its not working.
My PHP version is 5.5.12
I am using following extensions for this.
extension=libfreetype-6.dll
extension=libgcc_s_sjlj-1.dll
extension=libjpeg-8.dll
extension=liblcms2-2.dll
extension=liblzma-5.dll
extension=libopenjpeg-1.dll
extension=libpng15-15.dll
extension=libpoppler-28.dll
extension=libpoppler-cpp-0.dll
extension=libstdc++-6.dll
extension=libtiff-5.dll
Please suggest how can i resolve it.
Thanks.

Unfortunately, this package is only available in *nix OS. I believe WAMP is in Windows, so sorry. Till right now, this package can fulfill what you need. I only test this package in Ubuntu.

Hi Sir,
Thanks, for your response.
I used Linux system and now its working fine.
I have got HTML code in the following format.
[bold tag]  Scott  [/close bold tag][break tag /]
[bold tag]  Scott & Borcher  [/close bold tag][break tag /]
[bold tag]  The Le Companies  [/close bold tag][break tag /]
[bold tag]  Pittsburg  [/close bold tag][break tag /]
I have a query here: Can i get "top" and "left" margin as well in the bold tag.
Because that would be more helpfull for me.
For eg:
[bold tag top="100" left="20"]  Scott  [/close bold tag][break tag /]
Thanks.

Hi Sir,
Please suggest me on the above issue. I can pay you for this.
Please reply me asap.
Thanks.

can you send me your pdf you are trying to convert to?
btw i didn't get it by what you mean : "Can i get "top" and "left" margin as well in the bold tag."
Mind to make it more clear?

Hi Sir,
Thanks for your response.
Please have a look following PDF file
http://1stbadges.com/pdfs/Badges995.pdf
I want to convert this PDF to HTML
Here you can see 3 rows(Louis, Louis Banda, PittsBurg) in the First page of the PDF.
and 4 rows(Harrison, Harrison Barnes, The Warriers, San Francisco) in the Second page of the PDF.
I want to know the top and left margin of all the 3 and 4 rows.
Please have a look, Is this possible for us to get margin properties..
Thanks.

@mgufrone do u plan to port this to windows? I urgently need a tool like this so in case u know any similar tool which may work for windows please tell me, it would be helpful. Thanks

@sunnypatial do u know any library or tool which converts PDF to HTML using php? Please share if u know. Thanks.

I'm still looking for poppler-utils for windows. If i can, i will make this package support on windows

Hai @zealfire, I've updated readme files for windows user like you. Please check it out at https://github.com/mgufrone/pdf-to-html. I've already test it in my local and it works like a charm


Migrated to portable simd

This PR replaces the packed_simd dependency by the nightly-available std::simd (aka portable simd).
 Given that it compiles, maybe just wait a bit and do a benchmark once in a while?

I agree that we should not merge with these numbers. I will reach the working group for feedback and advice.

Converted to draft to indicate that this is blocked by a perf. regression.

FYI, I also experimented with portable_simd today and created an llvm issue about a missing/incorrect optimization with from_bitmask on non-avx512 machines.

Wow, awesome finding and summary @jhorstmann  - thank you for reporting it over there 🙇

What do you think of keeping this one aside of current SIMD (until the performance is comparable)? Then there is already SIMD support for the stable compiler. And can people opt in to the nightly version for the maximal performance.

:) portable simd released the required APIs. I am re-benching this as of now to evaluate where we at wrt to performance. :)

🤞

There are still 2 regressions, so this continues blocked.
sum 2^20 f32            time:   [164.88 us 165.03 us 165.23 us]
                        change: [-1.3535% -0.2982% +0.8551%] (p = 0.62 > 0.05)
min 2^20 f32            time:   [211.05 us 212.38 us 214.02 us]
                        change: [-0.9052% +0.2757% +1.3189%] (p = 0.64 > 0.05)
sum 2^20 i32            time:   [167.82 us 168.38 us 169.12 us]
min 2^20 i32            time:   [165.78 us 166.48 us 167.59 us]
sum null 2^20 f32       time:   [858.64 us 860.01 us 861.73 us]
                        change: [+352.55% +356.83% +360.89%] (p = 0.00 < 0.05)
min null 2^20 f32       time:   [874.36 us 877.98 us 883.40 us]
                        change: [+128.24% +131.57% +136.81%] (p = 0.00 < 0.05)
f32 2^20                time:   [349.08 us 354.17 us 364.40 us]
                        change: [-3.7451% -2.3785% -0.2625%] (p = 0.00 < 0.05)
f32 scalar 2^20         time:   [201.41 us 202.66 us 204.41 us]
                        change: [-2.4794% -1.2193% -0.0931%] (p = 0.05 < 0.05)
bool 2^20               time:   [179.35 us 180.41 us 182.26 us]
                        change: [+4.1593% +5.9573% +8.4415%] (p = 0.00 < 0.05)
bool scalar 2^20        time:   [26.768 us 26.920 us 27.116 us]
                        change: [+0.2871% +1.5636% +2.6602%] (p = 0.00 < 0.05)
utf8 2^20               time:   [6.6215 ms 6.6433 ms 6.6747 ms]
                        change: [-3.8776% -3.2642% -2.6263%] (p = 0.00 < 0.05)

actually, the regression was only from the last commit, which tries to use the intrinsics for the from_bitmask. Without that, there is no regression. Just reverted that one and will post the updated benches.

There is some noise, but the overall is that we are now equal to packed simd:
sum 2^20 f32            time:   [166.41 us 167.83 us 169.74 us]
                        change: [-0.0800% +1.1867% +3.0513%] (p = 0.11 > 0.05)
min 2^20 f32            time:   [210.90 us 211.92 us 213.13 us]
                        change: [+0.2811% +1.5970% +2.8225%] (p = 0.02 < 0.05)
sum 2^20 i32            time:   [167.38 us 167.71 us 168.16 us]
                        change: [-6.1677% -4.9397% -3.5768%] (p = 0.00 < 0.05)
min 2^20 i32            time:   [198.58 us 199.09 us 199.78 us]
                        change: [+14.587% +16.306% +18.393%] (p = 0.00 < 0.05)
sum null 2^20 f32       time:   [186.71 us 188.37 us 190.54 us]
                        change: [-1.6255% +0.2482% +2.1276%] (p = 0.81 > 0.05)
min null 2^20 f32       time:   [368.12 us 370.28 us 373.81 us]
                        change: [-4.1516% -3.1519% -2.1852%] (p = 0.00 < 0.05)
f32 2^20                time:   [351.59 us 352.98 us 355.48 us]
                        change: [-0.8055% +0.4256% +1.7513%] (p = 0.52 > 0.05)
f32 scalar 2^20         time:   [235.50 us 237.09 us 239.49 us]
                        change: [-4.2012% -1.9893% -0.1382%] (p = 0.06 > 0.05)
bool 2^20               time:   [192.72 us 193.63 us 195.08 us]
                        change: [+14.066% +16.238% +19.238%] (p = 0.00 < 0.05
bool scalar 2^20        time:   [26.444 us 26.557 us 26.692 us]
                        change: [-2.1207% -0.6513% +0.5040%] (p = 0.36 > 0.05)
utf8 2^20               time:   [6.5841 ms 6.6033 ms 6.6358 ms]
                        change: [-0.3873% +0.1999% +0.8762%] (p = 0.57 > 0.05)

Awesome. Nice work!


TestAuthHelperTrait does too much magic

I think createTestingUser method does too much magic behind the scenes.
For example this line I don't think this is the best idea... Now in real tests you have to call $this->actingAs($user,'web') in order to "disable" the linked line.
I expect the method to "create user" not "create and authenticate it". Or just make it protected so users (developers) can override.

https://github.com/apiato/core/blob/master/Traits/TestsTraits/PhpUnit/TestsAuthHelperTrait.php#L113-L154
Now user of Apiato can not have its own table structure, what is my user does not have name? Its going to throw up.

Apiato ships with a pre-defined set of attributes for some models (e.g., the user model). The test cases reflect those attributes..
If you don't have a name, you can remove them (from the migration file and model) and adapt your tests..
However, I would recommend to still use the username and just "hide" it in respective Transformer in order to comply with the default version of Apiato..

No its not possible. TestsAuthHelperTrait is used in Core PHPUnit class which is later used in Abstract class (Ship). In private methods (see link above) attributes are hard-coded, User model factory is hardcoded as well.

hm, you're right.. however, this might be a bigger change?! not sure about it yet..
however, for now, i would suggest to keep "name" as an attribute for you ;9

What I did is the following:
function factoryCreateUser($userDetails = null)
{
    return is_null($userDetails) ? factory(User::class)->create() : factory(User::class)->create($userDetails);
}

As you can see I do not need shenanigans with preparing password & details, I trust myself that I will send only array -> thus factory will do its thing.
To be even more modular I would use not User::class at all but whatever class is stored in config file auth.php -> providers -> users -> model

Simplest solution is to change visibility of methods within the Trait to public so user can do whatever.

wouldn't setting the factoryCreateUser() method to protected solve your issue?


Sanitize all inputs, do not require residuals if errors are passed

Codecov Report

Merging #68 (37ccc5a) into master (069053e) will increase coverage by 0.14%.
The diff coverage is 91.89%.

@@            Coverage Diff             @@
##           master      #68      +/-   ##
==========================================
+ Coverage   84.29%   84.44%   +0.14%
==========================================
  Files          18       18
  Lines         866      887      +21
==========================================
+ Hits          730      749      +19
- Misses        136      138       +2

Impacted Files
Coverage Δ

hts/convenience.py
92.72% <91.89%> (-1.40%)
:arrow_down:

Continue to review full report at Codecov.

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[tests] delete test cases that became parsing error after<EMAIL_ADDRESS>

CI is failing after the release of<EMAIL_ADDRESS>4 days ago, which is a dependency of espree. https://github.com/acornjs/acorn-jsx/releases/tag/5.2.0. That release introduced a breaking change that forbids > and } in JSXText. Therefore codes like <p>></p> became a parsing error.
This PR removed test cases that became parsing error after<EMAIL_ADDRESS>An expensive alternative is to setup tests for both acorn-jsx < 5.2.0 and > 5.2.0. But that is expensive.

Has an issue been filed upstream for the breaking change in a minor release?

Looks like they unfortunately made an intentional breaking change in a minor version.

I've gone ahead and updated the tests so they're kept when acorn-jsx is < 5.2, and skipped when it's absent or when it's >= 5.2. That way they can still run on eslint 4, for example: https://travis-ci.org/yannickcr/eslint-plugin-react/builds/657558888


Support for Windows Server Nano

Maybe I'm missing something, but when I try to install this on Server Nano it says that the OS Type isn't supported.

The actual error is "The system cannot execute the specified program.".
Just for confirmation, the .msi pack isn't blocked or anything alike.

Nano Server does not include MSI as an installation technology due to dependencies and the open ended nature of MSI custom actions. See full blog here.
The only way I can suggest is you install the msi in a full window OS, back-up the C:\Program Files (x86)\Microsoft SDKs\Azure\CLI2 and you can then xcopy to any nano servers. Do remember to add C:\Program Files (x86)\Microsoft SDKs\Azure\CLI2\wbin (or others if the destination folder changes) to the PATH environment though.
I don't believe we will support WSA for nano in any near future. So i am closing this.

I completely understand that, but .msi certainly is not the only installation technology.
In my humble opinion, it is increasingly difficult to install Azure CLI in a Windows Container and the entire nature of a Nano Container becomes a no-go because of a limited range of installation options on Windows. Why is it that you have Bash installation scripts, yum, apt-get, pip options for Linux, but only an MSI installer package for Windows?
Certainly I didn't open this issue to learn that MSI is not supported on Windows Server Nano, but because I want Azure CLI on Windows Server Nano.
Would it be an idea to have an installer for Windows which copies to right files and adds the URI to the PATH environment variable instead of relying only on MSI packages?

You can also install the CLI directly with pip install azure-cli. It is highly recommended you do this inside a virtual environment.

@tjprescott, python installer for window is a .msi :)

This is about Windows Nano. Is pip available on Windows Nano?!
Get Outlook for iOShttps://aka.ms/o0ukef

From: Yugang Wang<EMAIL_ADDRESS>Sent: Wednesday, July 11, 2018 7:16 PM
To: Azure/azure-cli
Cc: Alex Mang; Author
Subject: Re: [Azure/azure-cli] Support for Windows Server Nano (#6723)
@tjprescotthttps://github.com/tjprescott, python installer for window is a .msi :)
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHubhttps://github.com/Azure/azure-cli/issues/6723#issuecomment-404227774, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFgX4XBBR8vwyIUCkklixY6Cf18qiqLdks5uFiTAgaJpZM4VDVwv.

Python has an embeddable zip that can be used on Windows without MSI.  You can also get the standalone get-pip.py installation script. If you run python get-pip.py, you should have pip on your machine, at which point you should be able to pip install azure-cli.

I ran into this today when trying to install Azure CLI on nanoserver.
It would be great if we could reconsider this.  It would allow us to get Azure CLI on nano without having to install python or pip as separate commands.
It doesn't look like too much work to create a WSA package.

Is this on the roadmap at all? We're going to be relying on Azure CLI for some scenarios to produce our Docker images from https://github.com/dotnet/dotnet-docker. Having it available from Nano Server would be very useful.

Nano Server does not include MSI as an installation technology due to dependencies and the open ended nature of MSI custom actions. See full blog here.
The only way I can suggest is you install the msi in a full window OS, back-up the C:\Program Files (x86)\Microsoft SDKs\Azure\CLI2 and you can then xcopy to any nano servers. Do remember to add C:\Program Files (x86)\Microsoft SDKs\Azure\CLI2\wbin (or others if the destination folder changes) to the PATH environment variable though.
I don't believe we will support WSA for nano in any near future. So i am closing this.

I tested it in nanoserver, but it seems that it does not work, I can run az command, but I can't get any response.
I guess copy this folder is not enough... Do you have some other solutions?


Demo clarification

I am referring to the draggable demo here.
I don't really understand what's happening to the disObj or the objMoving in general.
is it cloned here objMoving = disObj; ?
why are you moving it here objMoving.elem.style.transform = "translate(" + (coords.x - mXo) + "px, " + (coords.y - mYo) + "px)";?
I would love to have you explain these questions as I am trying to achieve the same effect but for a scroll event instead of a drag. where basically I have a pinned element that get's in contact with another one when scrolling down and I want only the intersection part to disintegrate.
PS: I am disintegrating img tags and it's working fine with me (referring to this issue)

Hello. Glad to see someone using this :)
I just used objMoving to make it so that I didn't have to pass the variable into each listener manually. You could pass it into mouseDown, elMove, and mouseUp using bind if you'd like to instead. It points to the currently clicked on disObj.
As for your situation of disentegrating on scroll, you don't need the draggable functionality. I'd recommend using data-dis-type="contained" and telling what the container is. Then you can animate the element's movement outside of the container using whatever normal means that you move things on scroll.
I'm glad that img tags are working for you! If you get your project online and can link it (or a demo setup) I'd love to have you post in that issue.

Thank you for your fast reply!
I think I misunderstood how this library works, that's why I was confused with the code.
I thought that the effect of disintegration happening only at the border of the element was due to your snippet of code (and that's the effect I want to achieve ).
but the effect comes from the data-dis-type="contained" so now it all makes sense. I was also looking for where you were triggering the disintegration until your explanation just now.
Anyway, thank you very much for your help and have a good day.
PS: I will try to get the effect I want still work and if I do I will update this issue.


Eclipse plugin fails when I try to clean project.

This issue was originally filed by @giry

What steps will reproduce the problem?

In Eclipse: Project->clean

What is the expected output? What do you see instead?
Error log shows bunch of errors (attached below), things like: code completion, ctrl+click etc doesn't work.
What version of the product are you using?
Eclipse 4.4.1, dart plugin: 1.9.0.dev_09_01.
On what operating system?
Windows 8.1.
Please provide any additional information below.

Attachment:
eclipse.log (15.40 KB)

This issue has been moved to dart-lang/eclipse3#50.


<IP_ADDRESS>: Build failures on multiple systems

unix-compat-<IP_ADDRESS> fails to build on multiple Linux distributions.  The common factor appears to be old versions of glibc:

Debian 6 (i386 and x86_64), glibc 2.11.3
Fedora 19 (i386 and x86_64), glibc 2.17
Ubuntu 10.04 LTS (i386 and x86_64), glibc 2.11.1

The precise failure cause is unclear:
Failed to install unix-compat-<IP_ADDRESS>
Build log ( /app/sandbox/logs/unix-compat-<IP_ADDRESS>.log ):
Configuring unix-compat-<IP_ADDRESS>...
Building unix-compat-<IP_ADDRESS>...
Preprocessing library unix-compat-<IP_ADDRESS>...
[1 of 8] Compiling System.PosixCompat.User ( dist/dist-sandbox-a9165fb6/build/System/PosixCompat/User.hs, dist/dist-sandbox-a9165fb6/build/System/PosixCompat/User.o )
[2 of 8] Compiling System.PosixCompat.Unistd ( src/System/PosixCompat/Unistd.hs, dist/dist-sandbox-a9165fb6/build/System/PosixCompat/Unistd.o )
[3 of 8] Compiling System.PosixCompat.Types ( src/System/PosixCompat/Types.hs, dist/dist-sandbox-a9165fb6/build/System/PosixCompat/Types.o )
[4 of 8] Compiling System.PosixCompat.Extensions ( dist/dist-sandbox-a9165fb6/build/System/PosixCompat/Extensions.hs, dist/dist-sandbox-a9165fb6/build/System/PosixCompat/Extensions.o )
[5 of 8] Compiling System.PosixCompat.Time ( src/System/PosixCompat/Time.hs, dist/dist-sandbox-a9165fb6/build/System/PosixCompat/Time.o )
[6 of 8] Compiling System.PosixCompat.Temp ( src/System/PosixCompat/Temp.hs, dist/dist-sandbox-a9165fb6/build/System/PosixCompat/Temp.o )
[7 of 8] Compiling System.PosixCompat.Files ( dist/dist-sandbox-a9165fb6/build/System/PosixCompat/Files.hs, dist/dist-sandbox-a9165fb6/build/System/PosixCompat/Files.o )
[8 of 8] Compiling System.PosixCompat ( src/System/PosixCompat.hs, dist/dist-sandbox-a9165fb6/build/System/PosixCompat.o )
In-place registering unix-compat-<IP_ADDRESS>...
Creating package registration file: /tmp/pkgConf-unix-compat-0.4.117664.4

Actually, this failure doesn’t happen when installing manually in an ordinary ssh session.  I can only reproduce this in an installation process automated using Fabric.  The mind boggles!

I can now reproduce this failure over ssh — on Arch Linux only.

Do you get anything useful doing cabal build --verbose or cabal build --verbose=3?

For now, here’s the raw output:

Relevant part of cabal install --dependencies-only --verbose, 85 lines
Relevant part of cabal install --dependencies-only --verbose=3, 923 lines

Unfortunately, I don’t see any hints in it.

Hey just had a chance to look at this (I've been on holiday)
As you say, doesn't look like there's a whole lot of hints. I'm curious about why it fails over in some circumstances (Fabric) and not others (ssh) on the same setup.

I can reliably reproduce a build failure (maybe another one?) with a minimal Dockerfile:
#FROM          ubuntu:14.04.2
FROM          ubuntu:15.04

RUN          echo "Flush docker cache 1481"

RUN          DEBIAN_FRONTEND=noninteractive apt-get update && apt-get upgrade -y
RUN          DEBIAN_FRONTEND=noninteractive apt-get install -y cabal-install

#RUN          cabal update && cabal install unix-compat-<IP_ADDRESS>
RUN          cabal update && cabal install unix-compat-<IP_ADDRESS>

It can be executed with docker build -t foo ..
The relevant output is:
Downloading unix-compat-<IP_ADDRESS>...
Configuring unix-compat-<IP_ADDRESS>...
Building unix-compat-<IP_ADDRESS>...
Failed to install unix-compat-<IP_ADDRESS>
Build log ( /root/.cabal/logs/unix-compat-<IP_ADDRESS>.log ):
[1 of 1] Compiling Main             ( /tmp/unix-compat-<IP_ADDRESS>-8/unix-compat-<IP_ADDRESS>/dist/setup/setup.hs, /tmp/unix-compat-<IP_ADDRESS>-8/unix-compat-<IP_ADDRESS>/dist/setup/Main.o )
Linking /tmp/unix-compat-<IP_ADDRESS>-8/unix-compat-<IP_ADDRESS>/dist/setup/setup ...
Configuring unix-compat-<IP_ADDRESS>...
Building unix-compat-<IP_ADDRESS>...
Preprocessing library unix-compat-<IP_ADDRESS>...
[1 of 8] Compiling System.PosixCompat.User ( dist/build/System/PosixCompat/User.hs, dist/build/System/PosixCompat/User.o )
[2 of 8] Compiling System.PosixCompat.Unistd ( src/System/PosixCompat/Unistd.hs, dist/build/System/PosixCompat/Unistd.o )
[3 of 8] Compiling System.PosixCompat.Types ( src/System/PosixCompat/Types.hs, dist/build/System/PosixCompat/Types.o )
[4 of 8] Compiling System.PosixCompat.Extensions ( dist/build/System/PosixCompat/Extensions.hs, dist/build/System/PosixCompat/Extensions.o )
[5 of 8] Compiling System.PosixCompat.Time ( src/System/PosixCompat/Time.hs, dist/build/System/PosixCompat/Time.o )
[6 of 8] Compiling System.PosixCompat.Temp ( src/System/PosixCompat/Temp.hs, dist/build/System/PosixCompat/Temp.o )
[7 of 8] Compiling System.PosixCompat.Files ( dist/build/System/PosixCompat/Files.hs, dist/build/System/PosixCompat/Files.o )
[8 of 8] Compiling System.PosixCompat ( src/System/PosixCompat.hs, dist/build/System/PosixCompat.o )
In-place registering unix-compat-<IP_ADDRESS>...
Creating package registration file: /tmp/pkgConf-unix-compat-<IP_ADDRESS>
cabal: Error: some packages failed to install:
unix-compat-<IP_ADDRESS> failed during the final install step. The exception was:
/tmp/pkgConf-unix-compat-<IP_ADDRESS>: hGetContents: invalid argument (invalid
byte sequence)

The failure occurs for both <IP_ADDRESS> and <IP_ADDRESS>. The build succeeds when using ubuntu:14.0.2 as image base (just uncomment!).

@lpeterse awesome, thank you for this!

Too early to tell if it's a problem, but it certainly seems fishy that on Ubuntu 15 we end up with a relatively recent version of cabal-install but an ancient ghc, where as with Ubuntu 14 they are both from the same era:
Ubuntu 14.04.2:
$ cabal --version
cabal-install version <IP_ADDRESS>
using version 1.16.0 of the Cabal library
$ ghc --version
The Glorious Glasgow Haskell Compilation System, version 7.6.3
$ ghc-pkg list | grep Cabal
    Cabal-1.16.0

Ubuntu 15.04:
$ cabal --version
cabal-install version <IP_ADDRESS>
using version <IP_ADDRESS> of the Cabal library
$ ghc --version
The Glorious Glasgow Haskell Compilation System, version 7.6.3
$ ghc-pkg list | grep Cabal
    Cabal-1.16.0

@lpeterse your problem appears to be this issue: https://github.com/haskell/cabal/issues/1883
If you add ENV LANG "C.UTF-8" to your Dockerfile then it works on Ubuntu 15.

@jystic Thanks for pointing that out. I'm still a little puzzled of why just the unix-compat package broke, but this is/was definitely an cabal issue.


Some more terrain gen

Temperature is now used in worldgen. There are nine basic terrain types based on combinations of low/medium/high temperature and humidity, and a few extra ones based on the slopiness factor. Terrain varies from smooth to blocky, and the lerp, bilerp, and trilerp functions are replaced with serp, biserp, and triserp functions that produce a more S-shaped curve.
Fog is blue and less intense, and movement speed is faster.

Great stuff, thanks!


Access to devices

At this moment the devices at /dev don't allow to access to them by the users, being only accesible by root. There are several alternatives:

change their permissions to allow being read-write by everybody. This has some obvious security issues, and would require by the user to use the O_EXCL explicitly (and seems it would not work...).
craft an overlay filesystem (FUSE based?) on top of /dev that apply an O_EXCL open permission automatically so only can be accesed by the one that opened it until it's released. There could be some security issues on some of the devices (specially the memory ones), but the permissions could be restricted on them. Problem is that FUSE would slow the system...
left the permissions root only as they are now, and implement a "device manager" that would accept petitions for access to a device and return a file descriptor to it if nobody is using it. This is the most complex one, but also the most flexible, allowing to filter only the "secure" device (mouse, serial ports...) or also allow to fetch a component by type, and would also be extended to network ports. Depending of the implementation and system limitations it would allow access directly to the device using an open file descriptor (can be shared between unrelated process?) or using a pipe being the device manager as a proxy, problem is that it would be a somewhat complex component needing to run with root permissions that would depend the whole system, that it's not something I'm happy with... :-/

Thoughs? Opinions?

OMG, it's not only possible to share a file descriptor over a system socket but also there's a lot of documentation about it! :-D So, this way the Device Manager would open the device inode and share the file descriptor to the requester process so it can access to it directly, performance! :-D

After thinking on this, I think the best is in fact an overlay filesystem on top of /dev just for the shake of simplicity, since the usual is to simple use the device files. This overlay filesystem will run as root to have access to all the device files, and its behaviour should be

[ ] exclusive access to devices, only can be open once for write access (and maybe read access, too)
[ ] whitelist of safe devices, maybe also a blacklist
[ ] use sendmsg() to transfer the open file descriptors to the requester processes
[ ] don't list devices already being used by other processes/users

At this moment, seems the file descriptor can not be shared with FUSE, so although this got implemented I'll leave this issue open.

The device manager sounds like an excellent idea. How would we go about implementing it?

The device manager "as is" has been deprecated, but instead it has been implemented its functionality in a more generic way on ExclFS and it's currently integrated on NodeOS :-) This issue has been left open just waiting to know if the underlying filesystem file descriptor could be in the future being shared with FUSE to improve performance :-) Maybe should it be open in a new issue without a defined milestone and close this?


HAPI FHIR does not support stateless pagination

Describe the issue
FHIR pagination documentation states, that server may or may not use stateful pagination:

A server MAY add additional state tracking parameters to the links, as shown in the example above, though the server need not use a stateful paging method as shown in this example - it is at the discretion of the server how to best ensure that the continuation retains integrity in the context of ongoing changes to the resources

Currently HAPI FHIR forces to use stateful pagination and hides initial search parameters in next/prev links, so there is no way to get them except saving on the server side. That complicates implementation for most common cases, when each page request can be retrieved from the database with no need for full resultset cache or continuation control. To retrieve the search metadata by request id in multi-node environment, we need to introduce additional infrastructure (e.g. cache with TTL support) or use sticky sessions, while parameters can be available in the user request.
That is exactly why REST is intended to be stateless.
It would be very beneficial to have stateless pagination option, which won't remove initial search parameters from the next/prev links

I think the problem is more or less the whole search implementation. I've been working on some initial proof-of-concept of the stateless paging on the db level in !2059.


Avoid osbs.conf collision in import_image

Setting conf_file to None avoids the local file /etc/osbs.conf to be used if present.
This file can cause problems as it may have some uneeded configuration such as auth details.
This is the same approach taken by any other usage of Configuration object in this project: see koji_promote, store_metadata_in_osv3, check_and_set_rebuild.

Coverage remained the same at 88.284% when pulling a7681130e0fee0393cd980ce1314a30d875e2487 on chain-rebuild-fixes into 775a7012f5a656390a250f5ffc0c1644d6f0b55a on master.


[storage] Change generated code Uri.ToString to Uri.AbsoluteUri

Resolves #11368
Uri.ToString() unencodes the Uri before sending the request to storage. When using a source Uri that has non ascii characters, we will encode the Uri by putting it in the Uri object but unencode it when setting the header.
Switching to using Uri.AbsoluteUri fixes this problem. This fix applies to AppendBlobClient.AppendBlockFromUri. BlockBlobClient.StageBlockFromUri, PageBlobClient.UploadPagesFromUri, FileClient.StartCopy, FileClient.UploadRangeFromUri
This PR also has updates to DataLakeErrorDetails because of the regenerated code.

Updated generator to convert Uri.ToString to Uri.AbsoluteUri
Regenerated adding in Error to DataLakeErrorDetails
Added tests and recordings for non Ascii source blob/file names

Looks good.
Why did we make the Data Lake error change?

Hm. So I assumed someone from our team made the change to the storage swagger and we just haven't regenerated recently, but looks like the change was made by this PR
https://github.com/Azure/azure-rest-api-specs/pull/8739
Should I make a separate PR to make updates to the regenerated code?

Looks good.
Why did we make the Data Lake error change?

Hm. So I assumed someone from our team made the change to the storage swagger and we just haven't regenerated recently, but looks like the change was made by this PR
Azure/azure-rest-api-specs#8739
Should I make a separate PR to make updates to the regenerated code?

We shouldn't be touching generated code (otherwise process would become non-deterministic at some point). If we were to change this we'd edit readme with generator transforms. However, this is just internal type rename, so we're good.
On the side note. https://github.com/Azure/azure-rest-api-specs/pull/8739/files it seems that we don't have this in 2019-12-12 rest spec. Would be good to get it there as well.

Yes - we should make the same swagger change to 2019-12-12 as @kasobol-msft noted.  The new Track 2 generators being developed are a lot pickier about correct swagger syntax instead of silently swallowing issues.  It's a good thing overall, but will require small changes like this.


If the wizard is still open but the user clicks a lens or a recent activity link, we can close the wizard

duplicate
https://github.com/digma-ai/digma-intellij-plugin/issues/1175


Downgrade celery and kombu

More background can be found in https://github.com/celery/kombu/issues/870, Celery needs to be fixed at 4.1.0 until Kombu 4.2.2 arrives. Fixes #5221.

Codecov Report

Merging #5222 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #5222   +/-   ##
=======================================
  Coverage   63.45%   63.45%
=======================================
  Files         261      261
  Lines       19842    19842
  Branches     1998     1998
=======================================
  Hits        12591    12591
  Misses       7242     7242
  Partials        9        9

Continue to review full report at Codecov.

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@villebro so for iterating on the comment. When I tested this locally (to see if we still needed to pin kombu when using celery==4.1.0),
> pyenv version
2.7.13 (set by /Users/john_bodley/.pyenv/version)
> virtualenv env
> pip install celery==4.1.0
...
Collecting kombu<5.0,>=4.0.2 (from celery==4.1.0)
...
> pip freeze | grep kombu
kombu==4.2.1

It seems like the version of kombu might still be problematic given the range versioning defined from celery==4.1.0.

Oops, good call @john-bodley. I repinned Kombu at 4.1.0.

Actually @villebro they've recently released celery version 4.2.0 and I was wondering whether bumping the version higher would remedy the issue. If so we should pin celery==4.2.0 in requirements.txt and require celery>=4.2.0 in setup.py to ensure we bypass this issue.

Let's see what happens..

Looking at CI logs bumping to 4.2.0 seems to have resolved the issue!

Thanks @villebro.

For reference here’s the item in Celery 4.2.0 changelog which remedies the issue.


WASI threads support

I create this issue to track implementation of the WASI threads proposal, define technical approach and give opportunity for discussion.
High-level approach
The high-level approach for implementing WASI threads is to create a new module instance for every new thread and only share the memory between created instances.
API
As of today there's a single API that has to be added to the host:
int32_t thread_spawn(void * start_arg)

where start_arg is an opaque pointer and its value should not be inspected by the host environment; instead, it should be passed back to the WASM code. The function return unique non-negative thread identifier integer.
thread_spawn instantiates new thread, and must call the following exported function in a new thread once the thread is ready:
void wasi_thread_start(int thread_id, void *start_arg);

where the start_arg is exactly the same value as the one being passed to the thread_spawn, and thread_id is the same thread ID as the one returned from thread_spawn.
Project structure
We considered two approaches:

implement proposal in libc-wasi, given it is already part of wasi sdk
create a new library (in iwasm/core/libraries) that includes the implementation

The main benefit of the former approach is consistency with other APIs; however, we decided to go for the latter approach due to the following reasons:

WASI threads is still in progress and some of the concepts haven't been fully clarified yet; having it as a separate library help emphasizing the instability of the module to potential users
conditional compilation of the module won't require too many ifdef's here and there as the whole implementation will live in a separate place; that will enable us to have cleaner and more maintainable code

Compatibility
WAMR already allows for spawning new threads, either using pthread library or wasm_runtime_spawn_thread.
Our goal as part of wasi threads support is to provide a replacement for pthread library (through wasi-libc) therefore we won't guarantee compatibility with pthread library (i.e. both wasi threads and pthread library can not be used at the same time). If we see that using both implementations at the same time might actually be harmful, we might even restrict enabling both features at the same time at build time.
Users who are willing to use threads, should be instructed to use wasi-libc implementation on top of wasi threads in WAMR, so eventually pthread library can be deprecated and removed.
We see a value in keeping wasm_runtime_spawn_thread in parallel to wasi threads as this allows running concurrently multiple instances of a module from the native code (as opposed to spawning new threads from WASM code itself). wasi threads implementation should be able to work in parallel with wasm_runtime_spawn_thread functionality (with caveats, see sections below).
Thread instantiation & management
wasi threads implementation needs some sort of native thread management for multiple reasons, e.g.:

exception propagation - whenever the exception is being raised (e.g. out of bound memory access or division by zero), all the running threads should be notified and stopped
there's a discussion whether wasi_thread_exit-like API is needed in https://github.com/WebAssembly/wasi-threads/issues/7; if so, or if other syscalls are being added for threads (e.g. for setting thread priorities), thread manager must be able to locate the thread and interact with it accordingly.

WAMR already have a concept of WASM threads implemented using pthread library and thread management using thread manager. We'll use this thread manager for prototype as it gives us out of the box thread instantiation. However, because thread manager also enforces aux stack management, we'll have to refactor the module to allow pass aux stack control to the application.
Auxiliary stack management
Currently WAMR manages stack boundaries when threads are enabled:

Based on the maximum number of threads, WAMR segments aux stack so segments can be assigned to the thread code
When a new thread is created (here or here), one of the segments is being assigned to the thread using allocate_aux_stack method.
When thread finishes, stack segment has to be released using free_aux_stack so new threads can use the segment.

The approach is not ideal for a few reasons:

stack size, configured e.g. by -z stack-size=XXX is split across all the threads, therefore e.g. the main thread receives only a fraction of the stack size. This is inconsistent with LLD's -Wl,-stack_size, where the thread receives a full stack_size value.
WAMR's stack allocation might interfere with user space stack allocation; for example, wasi-libc's pthread_create (similarly to musl's pthread_create) allocates memory for the stack dynamically, so there's no need for the host to manage stack for multiple threads.

We'll disable stack allocation for new threads created with wasi_thread_spawn and instead, we off-load stack management to WASM application.
Similar approach can be used for wasm_runtime_spawn_thread; we'll use wasm_runtime_module_malloc/wasm_runtime_module_free to allocate aux stack either in libc heap (if malloc/free are exported) or app heap.
Stack overrun detection
At the moment WAMR has the information about stack boundaries so can detect aux stack overflow/underflow when it happens. This detection still will be possible for wasm_runtime_spawn_thread because the memory for those methods will be allocated in native code. However, WAMR won't have access to stack boundaries defined by wasi-libc's pthread implementation. This was already discussed in https://github.com/WebAssembly/wasi-threads/issues/12; one of the approach is to use binaryen's stack-check pass.
MVP Tasks

[X] Create a skeleton of the wasi threads library https://github.com/bytecodealliance/wasm-micro-runtime/pull/1783
[X] provide implementation for thread_spawn function https://github.com/bytecodealliance/wasm-micro-runtime/pull/1786
[X] refactor thread manager (and possibly interpreters) to enable aux stack management by the application https://github.com/bytecodealliance/wasm-micro-runtime/pull/1799
[x] improve thread ID allocation method to enable re-using unused thread ids and avoid integer overflow https://github.com/bytecodealliance/wasm-micro-runtime/pull/1809
[X] gracefully exit threads when the exception is thrown in one of the threads https://github.com/bytecodealliance/wasm-micro-runtime/pull/1812
[x] make sure proc_exit terminates all of the threads, and traps kill the process

[ ] https://github.com/bytecodealliance/wasm-micro-runtime/issues/1910
[x] https://github.com/bytecodealliance/wasm-micro-runtime/issues/1909

[x] build wasi-threads examples in the CI https://github.com/bytecodealliance/wasm-micro-runtime/pull/1819
[x] Fast JIT atomic operations implementation
[x] execute tests (update proposal repository with tests, use existing libc test suite etc)

[x] classic interpreter
[x] fast interpreter
[x] JIT
[x] AOT

[x] add examples

[X] add pure wasi examples https://github.com/bytecodealliance/wasm-micro-runtime/pull/1783
[x] add examples using pthread API and wasi-libc

[x] update documentation

Users who are willing to use threads, should be instructed to use wasi-libc implementation on top of wasi threads in WAMR, so eventually pthread library can be deprecated and removed.

Does it mean users have to write some glue code to satisfy wasi-threads requirements and can't keep their original version of code?

Users who are willing to use threads, should be instructed to use wasi-libc implementation on top of wasi threads in WAMR, so eventually pthread library can be deprecated and removed.

Does it mean users have to write some glue code to satisfy wasi-threads requirements and can't keep their original version of code?

embedder will need wasi initialization etc.
wasm apps will need a rebuild at least.
it might or might not need some code changes to accommodate for incompatibilities between pthread implementations.

Does it mean users have to write some glue code to satisfy wasi-threads requirements and can't keep their original version of code?

Glue code might or might not be needed depending on the features being used. At the moment wasi-libc does not implement all the pthread API (having said that, I don't think WAMR pthread implement it all either?) so there might be some limitations.
I'd suggest keeping pthread as an option for now and only if we achieve feature parity in wasi-libc (or we're close to that, and we're ok accepting potential gaps), we can drop pthread library.

I'm resolving the issue as the functionality has been already implemented and a lot of tests have been added. We'll continue testing and bugfixing the feature but any further problems will be tracked in separate github issue.


The 'eye' of the jan-glyph does not scale properly.

All eye-like features are svg filled circles, the current behavior is expected and for now, desired.


Small RNA report issue. (only see R codes, not generating full reports)

Hi @lpantano ,
I am using bcbio-nextgen small RNA pipeline to analyze miRNA sequencing data. The whole process executed correctly after upgrading to latest development version of bcbio-nextgen. There is a Rmarkdown file named srna_report.rmd in the final directory. Here is the full address to the rmarkdown file: /mnt/data/proj/guo/miRNA/brainTrauma/final/2019-01-25_brainTrauma/report. I tried to generate report by using the rmarkdown file but I did not get the full report. I can see some R codes, but no results.
Can you look into this please? Thank you in advance!
Best regards,
Jianxiang

Sorry for the late reply due to Chinese New Year vacation. Happy Chinese New Year!
I have the following folder in genome folder:
genomes/Hsapiens/GRCh37/srnaseq
And in genomes/Hsapiens/GRCh37/seq/GRCh37-resources.yaml:
srnaseq:
  srna_transcripts: ../srnaseq/srna-transcripts.gtf
  mirbase_hairpin: ../srnaseq/hairpin.fa
  mirbase_mature: ../srnaseq/mature.fa
  mirdeep2_fasta: ../srnaseq/Rfam_for_miRDeep.fa
  trna_fasta: ../srnaseq/trna_mature_pre.fa
  mint_lookup: ../srnaseq/LookupTable.tRFs.MINTmap_v1.txt
  mint_space: ../srnaseq/tRNAspace.Spliced.Sequences.MINTmap_v1.fa
  mint_other: ../srnaseq/OtherAnnotations.MINTmap_v1.txt

Thank you!
Jianxiang

No worries. I hope you got a nice holiday.
Can you show me the head of the ../srnaseq/srna-transcripts.gtf file?
Maybe there is chromosome mismatches and that is the reason for lack of
annotation.
As well, if you can find in the bcbio_nextgen_command.log file the
seqcluster cluster command and show me here, it would help.
Cheers
On Tue, Feb 12, 2019 at 8:22 AM jxshi<EMAIL_ADDRESS>wrote:

Sorry for the late reply due to Chinese New Year vacation. Happy Chinese
New Year!
I have the following folder in genome folder:
genomes/Hsapiens/GRCh37/srnaseq
And in genomes/Hsapiens/GRCh37/seq/GRCh37-resources.yaml:
srnaseq:
srna_transcripts: ../srnaseq/srna-transcripts.gtf
mirbase_hairpin: ../srnaseq/hairpin.fa
mirbase_mature: ../srnaseq/mature.fa
mirdeep2_fasta: ../srnaseq/Rfam_for_miRDeep.fa
trna_fasta: ../srnaseq/trna_mature_pre.fa
mint_lookup: ../srnaseq/LookupTable.tRFs.MINTmap_v1.txt
mint_space: ../srnaseq/tRNAspace.Spliced.Sequences.MINTmap_v1.fa
mint_other: ../srnaseq/OtherAnnotations.MINTmap_v1.txt
Thank you!
Jianxiang
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Here is the head of ../srnaseq/srna-transcripts.gtf file:
chr1    .       miRNA   17409   17431   .       -       .       ID MIMAT0027618;Alias MIMAT0027618;Name hsa-miR-6859-5p;Derives_from MI0022705
chr1    .       miRNA   17369   17391   .       -       .       ID MIMAT0027619;Alias MIMAT0027619;Name hsa-miR-6859-3p;Derives_from MI0022705
chr1    .       miRNA   30438   30458   .       +       .       ID MIMAT0005890;Alias MIMAT0005890;Name hsa-miR-1302;Derives_from MI0006363
chr1    .       miRNA   567762  567783  .       -       .       ID MIMAT0025855;Alias MIMAT0025855;Name hsa-miR-6723-5p;Derives_from MI0022558
chr1    .       miRNA   1102504 1102525 .       +       .       ID MIMAT0004571;Alias MIMAT0004571;Name hsa-miR-200b-5p;Derives_from MI0000342
chr1    .       miRNA   1102540 1102561 .       +       .       ID MIMAT0000318;Alias MIMAT0000318;Name hsa-miR-200b-3p;Derives_from MI0000342
chr1    .       miRNA   1103258 1103279 .       +       .       ID MIMAT0001620;Alias MIMAT0001620;Name hsa-miR-200a-5p;Derives_from MI0000737
chr1    .       miRNA   1103296 1103317 .       +       .       ID MIMAT0000682;Alias MIMAT0000682;Name hsa-miR-200a-3p;Derives_from MI0000737
chr1    .       miRNA   1104435 1104456 .       +       .       ID MIMAT0001536;Alias MIMAT0001536;Name hsa-miR-429;Derives_from MI0001641
chr1    .       miRNA   1231525 1231545 .       -       .       ID MIMAT0027353;Alias MIMAT0027353;Name hsa-miR-6726-5p;Derives_from MI0022571

Here is the seqcluster cluster command in the bcbio_nextgen_command.log:
[2019-01-24T07:00Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster collapse -o /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T1 -f /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T1/hanxiaoxiao.clean.fq.gz -m 1 --min_size 16
[2019-01-24T07:06Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster collapse -o /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/N1 -f /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/N1/haoyanlinzhengchangnaozuzhi.clean.fq.gz -m 1 --min_size 16
[2019-01-24T07:10Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster collapse -o /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T2 -f /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T2/houXLxuezhongzhouweinaozuzhi.clean.fq.gz -m 1 --min_size 16
[2019-01-24T07:15Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster collapse -o /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T3 -f /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T3/liguilanxuezhongzhouweinaozuzhi.clean.fq.gz -m 1 --min_size 16
[2019-01-24T07:20Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster collapse -o /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T4 -f /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T4/S3336205xuezhongzhouweinaozuzhi.clean.fq.gz -m 1 --min_size 16
[2019-01-24T07:25Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster collapse -o /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T5 -f /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/T5/tianguoyouxuezhongzhouweinaozuzhi.clean.fq.gz -m 1 --min_size 16
[2019-01-24T07:30Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster collapse -o /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/N2 -f /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/N2/tianguoyouzhengchangnaozuzhi.clean.fq.gz -m 1 --min_size 16
[2019-01-24T07:34Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster collapse -o /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/N3 -f /mnt/data/proj/guo/miRNA/brainTrauma/work/trimmed/N3/wangshunhua.clean.fq.gz -m 1 --min_size 16
[2019-01-24T07:40Z] /home/jshi/local/share/bcbio/galaxy/../anaconda/bin/STAR --genomeDir /home/jshi/local/share/bcbio/genomes/Hsapiens/GRCh37/star/ --readFilesIn /mnt/data/proj/guo/miRNA/brainTrauma/work/se cluster/prepare/seqs.fastq --runThreadN 12 --outFileNamePrefix /mnt/data/proj/guo/miRNA/brainTrauma/work/bcbiotx/tmplpvjc1/T1/T1 --outReadsUnmapped Fastx --outFilterMultimapNmax 1000 --outStd BAM_Unsorted --alignIntronMax 1 --limitOutSJcollapsed 2000000 --outSAMtype BAM Unsorted --outSAMmapqUnique 60 --outSAMunmapped Within --outSAMattributes NH HI NM MD AS  --outSAMattrRGline ID:T1 PL:illumina PU:T1 SM:T1  | /home/jshi/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 12 -m 2G  -T /mnt/data/proj/guo/miRNA/brainTrauma/work/bcbiotx/tmplpvjc1/T1/T1_star/T1-sorttmp -o /mnt/data/proj/guo/miRNA/brainTrauma/work/bcbiotx/tmplpvjc1/T1/T1_star/T1.bam /dev/stdin > /mnt/data/proj/guo/miRNA/brainTrauma/work/bcbiotx/tmplpvjc1/T1/T1_star/T1.bam
[2019-01-24T10:18Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster cluster -o /mnt/data/proj/guo/miRNA/brainTrauma/work/seqcluster/cluster -m /mnt/data/proj/guo/miRNA/brainTrauma/work/seqcluster/prepare/seqs.ma -a /mnt/data/proj/guo/miRNA/brainTrauma/work/align/seqs.bam -r /home/jshi/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -g /home/jshi/local/share/bcbio/genomes/Hsapiens/GRCh37/srnaseq/srna-transcripts.gtf
[2019-01-24T15:44Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster cluster -o /mnt/data/proj/guo/miRNA/brainTrauma/work/seqcluster/cluster -m /mnt/data/proj/guo/miRNA/brainTrauma/work/seqcluster/prepare/seqs.ma -a /mnt/data/proj/guo/miRNA/brainTrauma/work/align/seqs.bam -r /home/jshi/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -g /home/jshi/local/share/bcbio/genomes/Hsapiens/GRCh37/srnaseq/srna-transcripts.gtf
[2019-01-24T20:43Z] /home/jshi/local/share/bcbio/anaconda/bin/seqcluster report -o /mnt/data/proj/guo/miRNA/brainTrauma/work/seqcluster/report -r /home/jshi/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -j /mnt/data/proj/guo/miRNA/brainTrauma/work/seqcluster/cluster/seqcluster.json

Thank you for your help!

Oh, sorry about this. I think I forgot to correct the chromosome naming fo that genome. It should be without the chr word.
I normally use hg19, sorry about that. I will try to push a fix this week. Meanwhile, you can fix it your own removing that word from the file and changing the MT chromosome as well to the used by Ensembl.  You will need to repeat the analysis.
Cheers

Hi,
It finally worked. Thank you!
Cheers!


BUG:navbar in community chat page

Is there an existing issue for this?

[X] I have searched the existing issues

What happened?
Elements are getting outside of the navbar container and also it is not aligned correctly

Record

[X] I agree to follow this project's Code of Conduct
[X] I'm a GSSOC'24 contributor
[X] I want to work on this issue

Assigned!
Make sure to attach before & after screenshots in your PR and include the issue number.
Also, please star the repo before working on it.
i am the project mentor you can reach out to me for any help!
Happy open-source contributing! 🎉


Show ffmpeg progress

Is your feature request related to a problem? Please describe.
As av1 encoding on a cpu takes quite a long time, in my opinion, a progress indicator would be quite helpful.
Describe the solution you'd like
ffmpeg has an -stats output and -progress output  option. source
One of the solutions is to use ffprobe before ffmpeg, grab the frame counter from -progress output and calcutate the progress in percent. source.
There are also multiple wrappers available, most of them use js, python or php.
Bash implementation: https://github.com/zamanuhina/ffmpeg-progress

Added in v3.2.0


embedding old icons so we can upgrade to Daylight icons

Coverage remained the same at 88.235% when pulling c018ea490eb4a810448cfe96c55650435e8549fa on embed-icons into d69419b8504f43b191708d7a96910ab287ef195d on master.


Tapzone not working properly

Steps to reproduce
1.open any manga or manhwa
2.set reading mode to long strips
3tapzone for next won't work while tapzone for previous will be fine
Expected behavior
In long strips mode Next tap zone should work it should scroll the page it should work because it worked before recent updates and it works in latest version of tachiyomi
Actual behavior
In long strips mode Next tapzone doesn't work while previous one does
Crash logs
No response
Aniyomi version
<IP_ADDRESS>
Android version
Android 11
Device
OnePlus nord CE
Other details
No response
Acknowledgements

[X] I have searched the existing issues and this is a new ticket, NOT a duplicate or related to another open or closed issue.
[X] I have written a short but informative title.
[X] If this is an issue with an official extension, I should be opening an issue in the extensions repository.
[X] If this is an issue with an official manga extension and this issue can be replicated in the Tachiyomi app, that I should be opening an issue in Tachiyomi's extensions repository.
[X] I have gone through the FAQ and troubleshooting guide.
[X] I have updated the app to version <IP_ADDRESS>.
[X] I have updated all installed extensions.
[X] I will fill out all of the requested information in this form.

Duplicate of #1294


ignore the target directories in examples/*

This simply instructs git to ignore the target/ directories in the examples directory

@awoods, I'm not going to submit a jira ticket for this unless you feel it is necessary.


1.13.1

Hello there (:
I have a little question please, recently i updated my game in accident to 1.13.1
and i saw your mod not complitble with it, so i wanted to ask how can i downgrade the game
or ask when you gonna update it?
Thanks (:

You probably use ancient version of TrafficManager (v10.20).
Close game, unsubscribe it and subscribe to TM:PE v11 Stable or TMPE v11 Labs


Render a trailing newline on multipart close-delimiter

Adds a "\r\n" after the close-delimiter when encoding multipart bodies.  This is not required per specification, but is more robust with certain server implementations.

That's correct.  The epilogue is currently empty.  We don't provide a way to control it, because the recipient is supposed to ignore it.  This just helps it work with bad parsers in the wild.


Support for more equalizer filters

For the project I am working on we would like to EQ some sound effects. Rodio has a low pass filter (which is labelled as buggy in the docs but we haven't used it yet so I can't comment). A high pass filter, a band pass, and a band reject would be very useful.
Even if these never get implemented, thank you for working on Rodio, it is a great project and very helpful!

Slightly unrelated, but I noticed the low pass filter produces Infinity/NaN values if the frequency is set to (just below) half the sampling rate of the source, or higher. This causes the audio to cut out or to stutter.
You can see this for yourself if you play a 32 kHz audio file with source.low_pass(16_000) applied. I think this is because of Nyquist rate but I'm not sure.
If you want to detect this bug happening, you can force a panic:
if !result.is_finite() { panic!("{}", result); }


delete bitrise yml

this repo is using a remote config

Closing this as im learning there is some interplay here


Update gearley to cfg's latest version

There are a lot of changes to cfg crate, it's a good API now. This crate however, I could update it to latest version with some changes but the grammar.rs is very difficult to migrate
For example
fn populate_grammar_with_events_rhs(&mut self, grammar: &BinarizedGrammar) {
        self.events_rhs[1].extend(
            grammar.rules().map(|rule| rule.history().dot(1).event_without_tracing())

What's it's equivalent to the new cfg?

@trickster ,
I am migrating the API right now, while improving it too.

I am still working on making all tests pass for cfg after latest changes.


IntentDialog.onBegin( function (session, args, next)) Args is always undefined.

I am trying to capture the intent recognized on the onBegin handler. But I always see the args argument in the function called as undefined.
dH.onBegin = function (session,args,next){
if( args) {
// code here is not reached.
} else {
// this is always reached.
}
};
var dialog = new builder.IntentDialog({
recognizeMode : builder.RecognizeMode.onBegin,
recognizers : [recognizer]
});
dialog.onBegin(dH.onBegin);

IntentDialog.onBegin() is always called before the intent recognizers are run.  You'd need to use either matches() or onDefault() to receive the intents. Can I ask what you're trying to do? maybe I can make a suggestion.

I am trying to log to database all intents and entities chat users use. Uday
On Monday, 14 November 2016 4:24 AM, Steven Ickman<EMAIL_ADDRESS>wrote:

IntentDialog.onBegin() is always called before the intent recognizers are run. You'd need to use either matches() or onDefault() to receive the intents. Can I ask what you're trying to do? maybe I can make a suggestion.—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or mute the thread.

You could create a new custom recognizer that wraps the LuisRecognizer. This would let you log everything coming from LUIS.

Let us know if this does not work for you.

I am not getting dialog in args, I can get only entities in args.


Help with an advice - stuck in a browser window after pressing the button "Allow"

Hi, Yoshihiro. Thank you very much for the article on Medium!
May I ask you for some advice?
I've downloaded the example you provided (from GitHub) and tried to run it but when I try to authorise with my Google account I get stuck in a browser window on a page google.com after I press the button "Allow". It seems that the redirect doesn't work correctly or I did something wrong.
Thank you.
I added a credential in https://console.cloud.google.com/ for the OAuth Android app type.
In the project I put secret.txt file with ClientId

I guess there's a problem with your deep linking configuration if the app doesn't open after the approval process. I recommend checking the deep link documentation and OAuth client configuration for Google Cloud. Unfortunately, there is not much I can comment on.

Thanks for your response! will try to figure it out.


Configurable wait time for all agents

This will allow us to test how GEOPM overhead changes with sample rate.

Thanks for the suggestion from @sbtrasi

Consider making this a global GEOPM parameter available to all agents.

Superseeded by #1065.  There's more detail in that issue.


Add data on livestock and meat production

This is the start of an agriculture section. It adds data on meat and on livestock. This is to partially fulfill #214
This uses the meat data collected by @Bezzy1999 in #217
Screenshots
Nepal

Okhaldunga

@ravinepal
Would you have time to review this pull request and merge if it looks good?
Thanks.


Handle the situation where the recorded component type does not match the required type for the actual number of stored points

This situation arises when decoding certain malformed files, most notably it's seen in glb tiles from Google Earth's 3d tileset.
It's a port of the workaround used by Cesium native here:
https://github.com/CesiumGS/cesium-native/blob/d9172461e2d53f19d050ebc39f24a4f4ef5b9224/CesiumGltfReader/src/decodeDraco.cpp#L101

I think it'd be better to provide user callback functions for Draco decoding/encoding for flexibility, not implement workaround in the builtin Draco decoding function.
PR of callback functions for Draco decoding/encoding is much appreciated!

@syoyo would it be acceptable to you to follow the current approach but only use this logic when the permissive flag from https://github.com/syoyo/tinygltf/pull/445 is set?

@nyalldawson Yes, could you please modify this PR so that the situation is only considered when strictness flags is PERMISSIVE, like this?:
if (strictness == PERMISSIVE) {
  do PR 447
}

@syoyo ok, that's done. I've also made it add a warning string when the component type is upgraded when in permissive mode.

Awesome! Thanks! Merged!
TODO: This is still much appreciated 🥺 > PR of callback functions for Draco decoding/encoding is much appreciated!


Add Wasm assets for .NET 8

Depends on ericsink/cb#16
Resolves dotnet/efcore#29000

Acknowledging that I've seen this and will get it merged ASAP.


Feat: allow dynamic properties for PHP8.2

Add AllowDynamicProperties attribute to Entities.php for PHP8.2 compatibility. Not a permanent/final solution, but good enough to allow upgrades.
#1375

@TiiFuchs Happy to do this for now?

Yeah we had this coming. Need to add #[AllowDynamicProperties] for now...

(Those checks are not very useful at all at the moment 😞)

For the record I'l cross-reference this issue in which we discussed this topic before: https://github.com/php-telegram-bot/core/issues/1375


iOS Build Issue after Updating to Flutter 3.16.0

Is there an existing issue for this?

[X] I have searched the existing issues
[X] I have read the guide to filing a bug

Steps to reproduce
Updated Flutter to 3.16.0
VS Code -> Start Debugging (by selecting iOS Simulator)
Using XCode Version 14.1 (14B47b)
Expected results
Myself resolved all issues from Android part, but couldn't resolve issues raised from iOS (as I am not that having that much deeper knowledge in Swift development)
iOS App was running fine before updating to 3.16.0...
Actual results

Whenever I try to debug with iOS, I get this error... Tried all methods from StackOverflow and GitHub, even deleted my ios folder and recreated it using flutter create . . any idea how to solve this??
Code sample
Podfile
# Uncomment the next line to define a global platform for your project
platform :ios, '11.0'

# CocoaPods analytics sends network stats synchronously affecting flutter build latency.
ENV['COCOAPODS_DISABLE_STATS'] = 'true'

project 'Runner', {
  'Debug' => :debug,
  'Profile' => :release,
  'Release' => :release,
}

def flutter_root
  generated_xcode_build_settings_path = File.expand_path(File.join('..', 'Flutter', 'Generated.xcconfig'), __FILE__)
  unless File.exist?(generated_xcode_build_settings_path)
    raise "#{generated_xcode_build_settings_path} must exist. If you're running pod install manually, make sure flutter pub get is executed first"
  end

  File.foreach(generated_xcode_build_settings_path) do |line|
    matches = line.match(/FLUTTER_ROOT\=(.*)/)
    return matches[1].strip if matches
  end
  raise "FLUTTER_ROOT not found in #{generated_xcode_build_settings_path}. Try deleting Generated.xcconfig, then run flutter pub get"
end

require File.expand_path(File.join('packages', 'flutter_tools', 'bin', 'podhelper'), flutter_root)

flutter_ios_podfile_setup

target 'Runner' do
  use_frameworks!
  use_modular_headers!
  pod 'GoogleUtilities'
  flutter_install_all_ios_pods File.dirname(File.realpath(__FILE__))
end

target 'ImageNotification' do
  use_frameworks!
  pod 'GoogleUtilities'
  pod 'Firebase/Auth'
  pod 'Firebase/Messaging'
end

post_install do |installer|
  installer.pods_project.targets.each do |target|
    flutter_additional_ios_build_settings(target)
    target.build_configurations.each do |config|
      config.build_settings['ENABLE_BITCODE'] = 'YES'
      config.build_settings['GCC_PREPROCESSOR_DEFINITIONS'] ||= [
        '$(inherited)',
        'PERMISSION_MICROPHONE=1',
        'PERMISSION_LOCATION=1',
        'PERMISSION_NOTIFICATIONS=1',
      ]
    end
  end
end

Screenshots or Video

Screenshots / Video demonstration
[Upload media here]

Logs
Logs
[Paste your logs here]

Flutter Doctor output
Doctor output
[✓] Flutter (Channel stable, 3.16.0, on macOS 12.7.1 21G920 darwin-x64, locale en-IN)
    • Flutter version 3.16.0 on channel stable at /usr/local/Caskroom/flutter/3.3.8/flutter
    • Upstream repository https://github.com/flutter/flutter.git
    • Framework revision db7ef5bf9f (3 weeks ago), 2023-11-15 11:25:44 -0800
    • Engine revision 74d16627b9
    • Dart version 3.2.0
    • DevTools version 2.28.2

[✓] Android toolchain - develop for Android devices (Android SDK version 33.0.0)
    • Android SDK at /Users/rishigesan/Library/Android/sdk
    • Platform android-34, build-tools 33.0.0
    • Java binary at: /Applications/Android Studio.app/Contents/jbr/Contents/Home/bin/java
    • Java version OpenJDK Runtime Environment (build 11.0.15+0-b2043.56-8887301)
    • All Android licenses accepted.

[✓] Xcode - develop for iOS and macOS (Xcode 14.1)
    • Xcode at /Applications/Xcode.app/Contents/Developer
    • Build 14B47b
    • CocoaPods version 1.14.3

[✓] Chrome - develop for the web
    • Chrome at /Applications/Google Chrome.app/Contents/MacOS/Google Chrome

[✓] Android Studio (version 2022.1)
    • Android Studio at /Applications/Android Studio.app/Contents
    • Flutter plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build 11.0.15+0-b2043.56-8887301)

[✓] VS Code (version 1.84.2)
    • VS Code at /Applications/Visual Studio Code.app/Contents
    • Flutter extension version 3.78.0

[✓] Connected device (4 available)
    • RMX3491 (mobile)       • 5aa5238f                             • android-arm64  • Android 13 (API 33)
    • iPhone 8 Plus (mobile) • 230EC1C9-7D46-46E3-A22A-753F2315A852 • ios            • com.apple.CoreSimulator.SimRuntime.iOS-16-1
      (simulator)
    • macOS (desktop)        • macos                                • darwin-x64     • macOS 12.7.1 21G920 darwin-x64
    • Chrome (web)           • chrome                               • web-javascript • Google Chrome 120.0.6099.62

[✓] Network resources
    • All expected network resources are available.

• No issues found!

Have you tried with newer iOS simulators like iPhone 14 / 15?

Have you tried with newer iOS simulators like iPhone 14 / 15?

no... i'll try it now

Have you tried with newer iOS simulators like iPhone 14 / 15?

still the same issue

Hi @NOTtheKRish
Please provide the error log in text format instead of a screenshot for better readability and investigation. And it would be more helpful if you can provide the entire output of flutter run -v. If the log is too long, please save it into a file and attach it here or you can use 3rd tool like pastebin.com.
Please also check this and the underlying comments to see if it works.

Hi @NOTtheKRish Please provide the error log in text format instead of a screenshot for better readability and investigation. And it would be more helpful if you can provide the entire output of flutter run -v. If the log is too long, please save it into a file and attach it here or you can use 3rd tool like pastebin.com.
Please also check this and the underlying comments to see if it works.

ok... will check it and will provide you the output of flutter run -v soon...

@huycozy I've tried the one in StackOverflow and 2 of the issues got solved... Just getting 1 error... also, this is my output for flutter run -v
run-log.txt

[   +3 ms] Error (Xcode): Undefined symbol: _swift_FORCE_LOAD$_swiftCompatibility56

This seems to be an issue because the library was built with an incompatible Swift version compared to Xcode's. I see you are using Xcode 14.1, you may try upgrading to XCode 14.3, please check this https://github.com/CocoaPods/CocoaPods/issues/11960#issuecomment-1612161476.

@huycozy Alright buddy... Thanks!

Closing as this doesn't seem to be a Flutter issue. If you disagree, please write in the comments and I will reopen it. Thanks!


require("fennel") from .lua file breaks provide_require_fennel on a macro file

I finally got to reproduce the bug we were talking about: https://github.com/rktjmp/hotpot.nvim/issues/38#issuecomment-927229883.
It seems that requiring Fennel from the init.lua file breaks the provide_require_fennel configuration option for the macro files.
How to reproduce
I created this repository to reproduce the issue using Docker: datwaft/hotpot-issue_39.

Btw, executing the following snippet using :Fnl also reproduces the issue:
(macro test []
  (local {: view} (require :fennel))
  (print view))
(test)

If you change macro to fn it's no longer reproduced.

Seems fixed...


Remove Styled Components

This project looks great but I won't want to add styled-components as a dependency to my application. Is there any future in which that is no longer a dependency?

Sorry, this library is heavily based on the concepts of styled-components. I am planning to add the ability to swap out styled-components for something like emotion, but I don't plan to move to vanilla react.


Update baseConfig.md

I noticed some of the documentation for base options are out-of-date. I diffed with the source and updated the documentation.

Thanks :)


let's encrypt cron jobs get overwritten on each successive pass.

Notice this while using this playbook to create multiple sites that after completion there was only one cron job in the crontab for the root.  Right now each successive letsencrypt cert creation is overwriting the previous renewal job.

Switching to use certbot instead for letsencrypt cert setup might work better.


Add predictive gene scores as Decipher does

Is your feature request related to a problem? Please describe.
Decipher has a number of useful predictive scores. We don't.
Describe the solution you'd like
Add the predictive scores just like Decipher has.
Describe alternatives you've considered
N/A
Additional context

Skipping sHet for now.


As a Pod Provider Operator, I'd like to run different components on different hosts to have a simple division of labor

add to readme

Opening this as part of moving all user stories into issues again.


Fixes bug in watchman.js that constructs invalid queries

Summary
This addresses the watchman issue shown here:

This happens when dirExpr isn't a valid query and it causes watchman to crash
Test plan

npm run build && npm run test

Current coverage is 87.42% (diff: 100%)

Merging #1807 into master will increase coverage by 0.02%

@@             master      #1807   diff @@
==========================================
  Files            38         38
  Lines          1215       1217     +2
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
+ Hits           1062       1064     +2
  Misses          153        153
  Partials          0          0

Powered by Codecov. Last update 63ac0fd...5f4181c

thank you!


MySQL Bug? - [Server Crash]

Hello!
I posted in the SAMP forum the following bug: http://forum.sa-mp.com/showthread.php?t=633682
Any help to solve this?
Thanks!

This doesn't look like a MySQL plugin issue, as the crash happens somewhere in the SA-MP server itself.


None of the methods to stop autoplay works

.slick('slickPause'), .slick('slickSetOption', 'autoplay', false); don't seem to have any effect on the slick object. Can someone verify this?

$('.autoplay').slick('slickPause')

The above works on the live demo

Hey Ken! I found the issue. I was trying to pause indefinitely until a video in the carousel finishes playing. The thing with pausing is that as soon as you mouseout, there's a trigger that sets paused = false.
The fix was to set autoplay to false using setOption. However on line 369 in the autoPlay method, it doesn't check the _options.autoplay before setting the interval:
if (_.slideCount > _.options.slidesToShow && _.paused !== true) {
    _.autoPlayTimer = setInterval(_.autoPlayIterator,
    _.options.autoplaySpeed);
}

Changing the if-block to the following fixed my issue:
if (_.options.autoplay === true && _.slideCount > _.options.slidesToShow && _.paused !== true) {
    _.autoPlayTimer = setInterval(_.autoPlayIterator,
    _.options.autoplaySpeed);
}


Enable track-2 SDK automation for all the SDKs in azure-rest-api-specs repo

Enable track-2 sdk automation for all the services in the specs repo. If the service is new or the sdk doesn't exists in azure-sdk-for-net repo, it won't affect anything. It will only generate code for existing swagger updates.
For more details: https://github.com/Azure/azure-sdk-for-net/issues/15585

CC: @weshaggard @PhoenixHe-msft

CC: @weshaggard @PhoenixHe-msft

@ShivangiReja do you know what the current status of this work is? Have we configured any of the track 2 sdk's to use this automation?


Scaling Exact Multi-Objective Combinatorial Optimization by Parallelization

paper link: http://dl.acm.org/citation.cfm?id=2642971&CFID=609852226&CFTOKEN=49731104
data link: http://www.splot-research.org/

heading

dot1
dot2

asda italic asdas

Context Notes
Download Models From
http://www.splot-research.org/

Summary

Needs new context notes. See this example or this example as a reference.
Context notes are directly inserted into the actual repository (like this), so good context notes are necessary for putting the datasets into the repo in a timely fashion.

Categorization (effort, requirements, model, defect, etc.)
If it doesn't fit nicely into one of these categories, put "other" and propose a category name
Pick from the categories in the navbar on the OpenScience website.
Author list for the paper (including emails)
General overview of the data
Note that this is not the abstract of the paper. If you can find an overview of the dataset in the author's own words, just copy those words. If not, make your own overview. Paragraph long (if you are making it yourself)
Link to the paper associated with the dataset
This should be either a link to the ACM digital library (e.g. http://dl.acm.org/citation.cfm?id=2635868.2635905), IEEE digital library (e.g. http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6982619), or some other standard library
Paper abstract
BibTeX reference for the paper
Link to the datasets
If multiple files come with it, include links to all files, not just the parent file
Red flags should go up if, after downloading all the data, it is larger than 100 MB (compressed)
Is this dataset part of a larger series or collection?
If so, link to the master index of the series or collection (if possible)

Added as splot.
http://openscience.us/repo/model/splot.html


Adding custom --help content sections

In a CLI am developing using Click I would like to have an Examples: section to complement the Usage: section. Sample output would look something like:
Usage: my-tool my-command [OPTIONS]

    Does something.

    Some explanation of more complicated use-cases.

Examples:
    Do something simple
    $ my-tool my-command --default

    Do something complicated
    $ my-tool my-command --some --other --set --of --options

Options:
    --default  doc
    --some     doc
    --other    doc
    --set      doc
    --of       doc
    --options  doc

Is this possible? What is the suggested way to do this?

Adding my Examples: section into my docstring does not result in the correct level of indentation:
@click.command()
def my-command()
    '''
    Does something.

    Some explanation of more complicated use-cases.

\b
Examples:
    Do something simple
    $ my-tool my-command --default

    Do something complicated
    $ my-tool my-command --some --other --set --of --options
    '''

Results in:
$ my-tool my-command --help
Usage: my-tool my-command [OPTIONS]
    Does something.

    Some explanation of more complicated use-cases.

  Examples:
    Do something simple
    $ my-tool my-command --default

    Do something complicated
    $ my-tool my-command --some --other --set --of --options

This is currently not possible. We might want to add this with a custom decorator instead of relying on more special characters.

@untitaker thanks for the quick reply!
A custom field created with a decorator would be great, but I think that perhaps the Examples field should be available as a first-class citizen, as in my opinion a CLI without example usage is more difficult to use. Often users starting out simply want to know "how do I do THIS" and only delve into the available options, etc. later.

If an Examples field were a first-class member, it would be nice if proper practice were to never use a string literal as the command name in the examples, but evaluate it at run-time and therefore allow "copy-paste-able" examples that would take their command from the name used to invoke it. This would also allow for refactoring command structures to be less labor-intensive.

If we're going this far, this might be a candidate for https://github.com/click-contrib

Very interested in this feature as well. I think it is a common and useful pattern to include examples in the help.


minor changes in grammar prevent highlighting

It appears that the treesitter julia grammar has recently changed in (at least) the following ways which break this package:

global_declaration and local_declaration are now global_statement and local_statement
in a type_clause, "<:" is now parsed as "operator" instead of the literal string

The changes to font-lock settings are easy, but I have no idea how to enforce consistency with versions of the grammar.

RalphAS : thank you for posting. Yesterday I installed emacs 29.0.92, tree-sitter, and julia-ts-mode and found that syntax highlighting was not working for me (ubuntu 22.04). Perhaps it is the same issue? Here is the error message:
Error during redisplay: (jit-lock-function 1) signaled (treesit-query-error "Node type error at" 350 "(assignment (identifier) @font-lock-variable-name-face (_)) (assignment (field_expression (identifier) \".\" (identifier) @font-lock-variable-name-face) (operator)) (assignment (bare_tuple (identifier) @font-lock-variable-name-face)) (assignment (bare_tuple (field_expression (identifier) \".\" (identifier) @font-lock-variable-name-face)) (operator)) (local_declaration (identifier) @font-lock-variable-name-face) (let_binding (identifier) @font-lock-variable-name-face) (global_declaration (identifier) @font-lock-variable-name-face)" "Debug the query with `treesit-query-validate'") [2 times]

Yes, that is is the critical symptom. You can try the changes in PR #11 on your system.

changes in PR #11 work for me to have syntax highlighting with treesit-font-lock-level 1, 2, or 3.  Thanks so much RalphAS.  Also thanks to ronisbr and team for putting this together.
Note, treesit-font-lock-level 4 gives an error
Query pattern is malformed: "Node type error at", 371, "(adjoint_expression \"'\" @font-lock-type-face) (let_binding \"=\" @font-lock-type-face) (for_binding [\"=\" \"∈\"] @font-lock-type-face) (function_expression \"->\" @font-lock-type-face) (operator) @font-lock-type-face (slurp_parameter \"...\" @font-lock-type-face) (splat_expression \"...\" @font-lock-type-face) (ternary_expression [\"?\" \":\"] @font-lock-type-face) (type_clause [\"<:\" \">:\"] @font-lock-type-face) ([\".\" \"::\"] @font-lock-type-face)", "Debug the query with `treesit-query-validate'"

Hi @ggebbie !
Can you please provide a MWE with the code that gives the error?
@RalphAS thank you very much for fixing the issue!

Never mind, the type_clause also changed. I fixed this error but I found a bug in the grammar reported here:
https://github.com/tree-sitter/tree-sitter-julia/issues/108

thanks @ronisbr  -- you beat me to it. nice work!


:bug: ALL_BROKERS_DOWN doesn't really mean anything to librdkafka

Summary
ref to https://github.com/confluentinc/confluent-kafka-dotnet/issues/957 https://github.com/confluentinc/librdkafka/issues/1072

Also, ALL_BROKERS_DOWN doesn't really mean anything to librdkafka, it is just a friendly indication to the application that currently there are no brokers to communicate with. But librdkafka will continue to try to reconnect indefinately, and it will attempt to re-send messages until message.timeout.ms or message.max.retries are exceeded.

It throws error in our case so that the sourceclient or agentclient will be restarted. that is not our desired behaviour.
Related issue(s)
Fixes #
E0515 11:14:48.057462    6304 baseclient.go:92] the cloudevents client is disconnected, client error 2/2 brokers are down
I0515 11:14:48.058680    6304 baseclient.go:199] stop the cloudevents receiver
{"level":"info","ts":1715742888.094746,"logger":"fallback","caller":"v2/protocol.go:186","msg":"Closing consumer [^sourceevents.*.local-cluster ^sourcebroadcast.*]"}
E0515 11:14:48.546987    6304 baseclient.go:172] failed to receive cloudevents, error while opening the inbound connection: context canceled
I0515 11:14:55.622359    6304 baseclient.go:60] reconnecting the cloudevents client

I0515 11:14:55.636559    6304 baseclient.go:74] the cloudevents client is reconnected
I0515 11:14:55.636726    6304 baseclient.go:190] restart the cloudevents receiver
E0515 11:14:55.637462    6304 clientbuilder.go:191] failed to send resync request, the cloudevents client is not ready

LGTM


Table Information no vertical scroll bar

Fix https://github.com/sosedoff/pgweb/issues/140

Thanks. Next time please make sure to run make assets before submitting pr so that update bindata.go is included.


[WIP] Improve Vagrant Remote Docker Host Support

Continuation of the earlier work in #100 and #110
TODO:

[x] detection of remote docker host via DOCKER_HOST env var
[ ] config option to disable remote docker host detection (=> fallback to host_vm approach)
[ ] ...

this is partially superseded by #130 now...


Did you guys remove the ability to drive trains?

One of my favorite features of locomotion was the ability to press insert, type "DRIVER," then release it to be able to drive the trains. However, in openloco, when I press insert, NOTHING HAPPENS! Did you guys remove it? And if you did, can you like, not?

Not intentionally.

Any chance you guys can fix it? I loved the driver feature.

It's a bug. It will get fixed eventually. We will likely break quite a few things along the way. We can't test everything.


SignUp link is not shown while loading

Issue: #231
Now the signup link is conditionally rendered. Hence the issue can be resolved.
Screenshot: While loading, the signup is not shown.
Note: Else it is shown.

@sanjay270899 review the request
I am done with my review


Fix panic when passing empty status field

When DeepCopy is called on objects that have gone through this conversion, they may panic as DeepCopy doesn't handle non-pointers, and the conversion logic has Status as a non-pointer.
This PR does two things:

Make Status a pointer, which I think it should be since we are expected to always have pointers for protos. golang/protobuf makes this requirement more explicit which we will likely move to soon anyways
Makes DeepCopy robust to non-pointer types and adds a bunch of tets.

@howardjohn: The following test failed, say /retest to rerun all failed tests or /retest-required to rerun all mandatory failed tests:

Test name
Commit
Details
Required
Rerun command

lint_istio
10f842a2fc288ffb9e5b72ae65af63c88feab272
link
true
/test lint_istio

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.


Extend functionality openapi type converter

Description
This PR:

Extend OpenAPI type converter with features required by lsm extension.
Bugfix: Ensure OpenAPI enum values always have the type field set.
Bugfix: Ensure that the OpenAPI type reference resolver populates the allOf and oneOf properties of the OpenAPI schema.
Bugfix: Ensure that the OpenApiTypeConverter.get_openapi_type_of_parameter() method populates the default value of a parameter.

Part of inmanta/inmanta-lsm#1169
Self Check:

[x] Attached issue to pull request
[x] Changelog entry
[x] Type annotations are present
[x] Code is clear and sufficiently documented
[x] No (preventable) type errors (check using make mypy or make mypy-diff)
[x] Sufficient test cases (reproduces the bug/tests the requested feature)
[x] Correct, in line with design
[x] End user documentation is included or an issue is created for end-user documentation (add ref to issue here: )
[ ] If this PR fixes a race condition in the test suite, also push the fix to the relevant stable branche(s) (see test-fixes for more info)

Processing this pull request

Merged into branches master, iso6 in 6902b49996bd3b094a5bb2cea3c5b0321c616c46


[#4000] improvement(client-python): Support simple auth for PyGVFS

What changes were proposed in this pull request?
Support simple auth for gravitino client in PyGVFS. The integration test depends on this PR: #3876 #3931 . When #3876 #3931 is merged, I will add integration tests and docs for this PR.
Why are the changes needed?
Fix: #4000
How was this patch tested?
Add UTs and ITs.

Unrelated to the PR here, I'm curious how do you support Kerberos HDFS for python gvfs, have you tried it?

Unrelated to the PR here, I'm curious how do you support Kerberos HDFS for python gvfs, have you tried it?

When I tested pygvfs locally, I directly connected to the online HDFS cluster which enabled Kerberos authentication. There are two ways I know:

Add some configurations in the core-site.xml of the Hadoop environment:

<property>
<name>hadoop.security.authentication</name>
<value>kerberos</value>
</property>
<property>
<name>hadoop.client.kerberos.principal</name>
<EMAIL_ADDRESS></property>

<property>
<name>hadoop.client.keytab.file</name>
<value>/tmp/xxx.keytab</value>
</property>

Execute kinit in the test local and log in to Kerberos

@jerryshao This PR is ready, please take a look, thanks.