cant build with ubuntu 15.10

i tested it with following swift versions
a) => swift-DEVELOPMENT-SNAPSHOT-2016-04-12-a-ubuntu15.10
matt@matt-ubu:~/swifter$ which swift
/home/matt/swift-DEVELOPMENT-SNAPSHOT-2016-04-12-a-ubuntu15.10/usr/bin/swift
matt@matt-ubu:~/swifter$ swift build
error: MixedSources("/home/matt/swifter/Sources")
matt@matt-ubu:~/swifter$ cd Packages/
matt@matt-ubu:~/swifter/Packages$ cd NSLinux-1.1.0/
matt@matt-ubu:~/swifter/Packages/NSLinux-1.1.0$ swift build
Compiling Swift Module 'NSLinux' (2 sources) /home/matt/swifter/Packages/NSLinux-1.1.0/Sources/Dispatch.swift:47:57: error: 'COpaquePointer' has been renamed to 'OpaquePointer'     let unmanaged = Unmanaged<pthreadBlock>.fromOpaque( COpaquePointer( arg ) )                                                         ^~~~~~~~~~~~~~                                                         OpaquePointer /home/matt/swifter/Packages/NSLinux-1.1.0/Sources/Dispatch.swift:55:47: error: value of type 'Unmanaged<pthreadBlock>' has no member 'toOpaque'     let pointer = UnsafeMutablePointer<Void>( holder.toOpaque() )                                               ^~~~~~ ~~~~~~~~ /home/matt/swifter/Packages/NSLinux-1.1.0/Sources/Dispatch.swift:76:19: error: missing argument label 'queue:' in call     dispatch_async( queue, {                   ^                     queue:  /home/matt/swifter/Packages/NSLinux-1.1.0/Sources/NSString.swift:101:52: error: 'joinWithSeparator' has been renamed to 'joined'         return componentsSeparatedByString( str1 ).joinWithSeparator( str2 )                                                    ^~~~~~~~~~~~~~~~~                                                    joined Swift.Sequence:3:17: note: 'joinWithSeparator' has been explicitly marked unavailable here     public func joinWithSeparator(_ separator: String) -> String                 ^ /home/matt/swifter/Packages/NSLinux-1.1.0/Sources/NSString.swift:119:26: error: 'fromCString' is unavailable: Please use String.init?(validatingUTF8:) instead. Note that it no longer accepts NULL as a valid input. Also consider using String(cString:), that will attempt to repair ill-formed code units.             out = String.fromCString( bytes )!                          ^~~~~~~~~~~ Swift.String:4:24: note: 'fromCString' has been explicitly marked unavailable here     public static func fromCString(_ cs: UnsafePointer<CChar>) -> String?                        ^ /home/matt/swifter/Packages/NSLinux-1.1.0/Sources/NSString.swift:119:26: error: 'fromCString' is unavailable: Please use String.init?(validatingUTF8:) instead. Note that it no longer accepts NULL as a valid input. Also consider using String(cString:), that will attempt to repair ill-formed code units.             out = String.fromCString( bytes )!                          ^~~~~~~~~~~ Swift.String:4:24: note: 'fromCString' has been explicitly marked unavailable here     public static func fromCString(_ cs: UnsafePointer<CChar>) -> String?                        ^ /home/matt/swifter/Packages/NSLinux-1.1.0/Sources/NSString.swift:127:26: error: 'fromCString' is unavailable: Please use String.init?(validatingUTF8:) instead. Note that it no longer accepts NULL as a valid input. Also consider using String(cString:), that will attempt to repair ill-formed code units.             out = String.fromCString( bytes+index )!                          ^~~~~~~~~~~ Swift.String:4:24: note: 'fromCString' has been explicitly marked unavailable here     public static func fromCString(_ cs: UnsafePointer<CChar>) -> String?                        ^ <unknown>:0: error: build had 1 command failures error: exit(1): /home/matt/swift-DEVELOPMENT-SNAPSHOT-2016-04-12-a-ubuntu15.10/usr/bin/swift-build-tool -f /home/matt/swifter/Packages/NSLinux-1.1.0/.build/debug.yaml default
b)  => swift-DEVELOPMENT-SNAPSHOT-2016-02-08-a-ubuntu15.10
matt@matt-ubu:~/swifter$ which swift
/home/matt/swift-DEVELOPMENT-SNAPSHOT-2016-02-08-a-ubuntu15.10/usr/bin/swift
matt@matt-ubu:~/swifter$ swift build
Compiling Swift Module 'NSLinux' (2 sources)
Linking Library:  .build/debug/NSLinux.a
Compiling Swift Module 'Swifter' (19 sources)
/home/matt/swifter/Sources/HttpServerIO.swift:25:23: warning: extraneous '_' in parameter: 'listenPort' has no keyword argument name     public func start(_ listenPort: in_port_t = 8080) throws {                       ^~....error.txt
i find out in  my Test a) the NSLinux lib are not compatible !
in Test b) the dependent NSLinux lib runs fine.
Which swift version i need ?

hi @mtt2p
thank you for the report. I manage to solve all the problems for the latest toolchain (04-12-a) so please go for it :)
Linux
VirtualBox:~/Desktop$ export PATH=/home/swift-DEVELOPMENT-SNAPSHOT-2016-04-12-a-ubuntu15.10/usr/bin:"${PATH}"
VirtualBox:~/Desktop$ which swift
/home/swift-DEVELOPMENT-SNAPSHOT-2016-04-12-a-ubuntu15.10/usr/bin/swift
kolakowski@kolakowski-VirtualBox:~/Desktop$ git clone https://github.com/httpswift/swifter.git
Cloning into 'swifter'...
Checking connectivity... done.
VirtualBox:~/Desktop$ cd swifter/
VirtualBox:~/Desktop/swifter$ swift build
Compiling CSQLite sqlite.c
Linking CSQLite
Compiling Swift Module 'Swifter' (19 sources)
VirtualBox:~/Desktop/swifter$

Mac:
Damian:~ $ git clone https://github.com/httpswift/swifter.git
Cloning into 'swifter'...
Checking connectivity... done.
Damian:~ $ cd swifter/
Damian:swifter $ export SDKROOT=$(xcrun --show-sdk-path --sdk macosx)
Damian:swifter $ swift build
Compiling CSQLite sqlite.c
Linking CSQLite
Compiling Swift Module 'Swifter' (19 sources)
Damian:swifter $

thanks it works (swift-DEVELOPMENT-SNAPSHOT-2016-04-12-a-ubuntu15.10)
matt@matt-ubu:~/http$ ls -lsa
total 16
4 drwxrwxr-x  2 matt matt 4096 Apr 19 14:19 .
4 drwxr-xr-x 27 matt matt 4096 Apr 19 14:19 ..
4 -rw-rw-r--  1 matt matt  504 Apr 19 14:19 main.swift
4 -rw-rw-r--  1 matt matt  138 Apr 19 14:08 Package.swift

matt@matt-ubu:~/http$ cat main.swift
//
//  main.swift
//  SwifterSampleLinux
//  Copyright (c) 2015 Damian Kołakowski. All rights reserved.
//

import Foundation
import Swifter
import Glibc

let server = demoServer(NSBundle.mainBundle().resourcePath!)

do {
    server["/testAfterBaseRoute"] = { request in
        return .OK(.Html("ok !"))
    }
    try server.start(9080)
    print("Server has started ( port = 9080 ). Try to connect now...")

    while true {
      sleep(10)
    }
} catch {
    print("Server start error: \(error)")
}

matt@matt-ubu:~/http$ cat Package.swift
import PackageDescription

let package = Package(
  name:"matt",
  dependencies:[
    .Package(url:"../swifter", Version(2, 0, 0))
  ]
)

matt@matt-ubu:~/http$ swift build
Cloning /home/matt/swifter
Resolved version: 2.0.0
mkdir -p /home/matt/http/.build/debug/CSQLite.build
Compiling CSQLite sqlite.c
Linking CSQLite
Compiling Swift Module 'Swifter' (19 sources)
Compiling Swift Module 'matt' (1 sources)
Linking .build/debug/matt

matt@matt-ubu:~/http$ .build/debug/matt
/home/matt/http/.build/debug
Server has started ( port = 9080 ). Try to connect now...

please tag the swifter version new to deal with swift built , latest version is 1.1.3 or is it possible to build from the master  branche ?
great project


Why can't I install 0.4.7？

I ruled out the reasons for bad speed，and I also tried the network over the wall.

@flyBoyTLW did you get this resolved? If not, have you tried installing any other plugins?


Docs: Improve docs

Codecov Report
Base: 97.35% // Head: 97.35% // No change to project coverage :thumbsup:

Coverage data is based on head (05a0cf8) compared to base (2090fe8).
Patch has no changes to coverable lines.

Additional details and impacted files
@@           Coverage Diff           @@
##           master       #2   +/-   ##
=======================================
  Coverage   97.35%   97.35%
=======================================
  Files           4        4
  Lines         303      303
=======================================
  Hits          295      295
  Misses          8        8

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

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multible instances description not clear

I try to get the data of 3 inverters into venus-os.
First is working perfect. Now I'm not shure how the MQTT data has to look like. For my understanding there have to be differences to the first instance. I didn't try it now but can it be that the JSON structure has to start with "pv-2" for the second instance ?
Thank you very much for this implementation
Best regards

You just need a different topic for the second instance. The JSON structure is the same.

Thank you, that was it. I should have scoll down the config.ini , there is the topic for the instance I had missed.
I think it would be a improvement in the describtion to add at point 5 . Edit the topic for the new instance too.

Problem solved


How to implement object oriented programming using Matlab

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How to implement object oriented programming using Matlab
Introduction:
Object-oriented programming is a design approach that enables you to programmatically define structures called objects that combine data (properties) together with functions that operate on that data (methods). In Matlab, you can create objects that model the behavior of devices and systems in the real world. Those objects can then be used as building blocks in applications used to simulate and analyze complex systems.
Using object-oriented programming in Matlab, you can manage software complexity by organizing your code into logical components that are easier to maintain and extend. You can avoid code duplication by creating reusable objects with well-defined interfaces that hide the complexity of the underlying code. Furthermore, your objects can evolve and change over time without introducing incompatibilities in client code. In this tutorial, we will look at how to apply this in Matlab
Key takeaways:

understanding object oriented programming.
Importance of object oriented programming.
How to apply this skills in Matlab.

References:
Please list links to any published content/research that you intend to use to support/guide this article.
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Good afternoon and thank you for submitting your topic suggestion.
Your topic form has been entered into our queue and should be reviewed (for approval) as soon as a content moderator is finished reviewing the ones in the queue before it.  @collince777

@collince777
Sounds like a helpful topic - lets please be sure it add value beyond what is in the official docs and what is covered in other blog sites.
Please be sure to double check that it does not overlap with any existing EngEd articles or incoming topic suggestions (if you haven't already) to avoid any potential article closure, please reference any relevant EngEd articles in yours. - Approved
I know we have quite a few Mathlab artices in our EngEd library.


Can not install globally on debian 7 (1.6.3, 1.6.4)

Can not install by npm install -g strider (npm tries to install version 1.6.3). Can not install by git checkout v1.6.3 && npm install -g. Also can not install by git checkout v1.6.4 && npm install -g. npm install works fine on both v1.6.3 and v1.6.4 tags.
npm-debug.log from installation: https://gist.github.com/m00t/e66c9502b77884adb872
P.S.
Output from npm install -g: https://gist.github.com/m00t/28009a17abc03226fd73
P.P.S.
For those who will google this issue by error message:
System info:
Bower version: 1.3.12
Node version: 0.10.29
OS: Linux 3.2.0-4-amd64 x64
npm ERR! Linux 3.2.0-4-amd64
npm ERR! argv "node" "/usr/bin/npm" "install" "-g"
npm ERR! node v0.10.29
npm ERR! npm  v2.5.0
npm ERR! code ELIFECYCLE

npm ERR<EMAIL_ADDRESS>postinstall: `bower install --allow-root && npm run build`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the<EMAIL_ADDRESS>postinstall script 'bower install --allow-root && npm run build'.
npm ERR! This is most likely a problem with the strider package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     bower install --allow-root && npm run build
npm ERR! You can get their info via:
npm ERR!     npm owner ls strider
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR!     /root/strider/npm-debug.log

I think this has to do with the less dependency, since it doesn't install properly with the -g option when in dependencies.

How I can get output from bower install --allow-root && npm run build? Is there some sort of flags to keep node_modules/strider folder after npm install -g fail?

Things became even more strange after I run npm install -g less. Now npm install -g strider (or npm install -g within strider checkout directory) silently fails without any error and logs:
root@ci:/usr/lib# npm install -g strider
npm WARN deprecated<EMAIL_ADDRESS>v1.0.0 is a complete rewrite of Swig from the ground up. Previous versions are no longer supported
npm WARN engine<EMAIL_ADDRESS>wanted: {"node":">=0.6","npm":"1"} (current: {"node":"0.10.29","npm":"2.5.0"})
npm WARN optional dep failed, continuing<EMAIL_ADDRESS>
><EMAIL_ADDRESS>install /usr/lib/node_modules/strider/node_modules/bcrypt
> node-gyp rebuild

gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/.node-gyp/0.10.29"
gyp WARN EACCES attempting to reinstall using temporary dev dir "/usr/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
Killed
root@ci:/usr/lib# make: Entering directory `/usr/lib/node_modules/strider/node_modules/bcrypt/build'
  CXX(target) Release/obj.target/bcrypt_lib/src/blowfish.o
  CXX(target) Release/obj.target/bcrypt_lib/src/bcrypt.o
  CXX(target) Release/obj.target/bcrypt_lib/src/bcrypt_node.o
  SOLINK_MODULE(target) Release/obj.target/bcrypt_lib.node
  SOLINK_MODULE(target) Release/obj.target/bcrypt_lib.node: Finished
  COPY Release/bcrypt_lib.node
make: Leaving directory `/usr/lib/node_modules/strider/node_modules/bcrypt/build'

root@ci:/usr/lib#

@m00t did you see the note about global installs here?

@knownasilya nope, I used this manual: http://strider.readthedocs.org/en/latest/install.html
I will try it later, thanks.

@m00t were you successful?

@knownasilya Sorry, did not have time for testing yet.

Tried this. Got unlimited
gyp WARN EACCES attempting to reinstall using temporary dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp/0.10.29"
gyp WARN EACCES attempting to reinstall using temporary dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp/0.10.29"
gyp WARN EACCES attempting to reinstall using temporary dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp/0.10.29"
gyp WARN EACCES attempting to reinstall using temporary dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp/0.10.29"
gyp WARN EACCES attempting to reinstall using temporary dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp/0.10.29"
gyp WARN EACCES attempting to reinstall using temporary dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp/0.10.29"
gyp WARN EACCES attempting to reinstall using temporary dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp/0.10.29"
gyp WARN EACCES attempting to reinstall using temporary dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp"
gyp WARN EACCES user "root" does not have permission to access the dev dir "/root/npm/lib/node_modules/strider/node_modules/bcrypt/.node-gyp/0.10.29"

@m00t so if you follow that note about installing global modules, you shouldn't be using sudo.
If this isn't working, just clone the repo and do npm install inside.

@knownasilya what note should I follow to not using sudo? I use npm install -g strider without sudo, but other commands like npm config etc was ran with sudo because I forgot to remove sudo: yes from my ansible playbook. Can it be the case?
npm install inside repo works.

The one here under the npm install

@knownasilya This note says nothing about sudo. Also I followed it completely. Tried to install everything from scratch without sudo, no luck.

@knownasilya  Ow, I see. I should not install modules for root too?

You should never use sudo for npm modules global or local.

@knownasilya works fine when I do not try to install strider as root. I think this should be pointed clearly, because it is not obvious that ~ should not actually be /root

Also running into this problem. @knownasilya do you have any resources for not using sudo to install global modules? AFAIK this is common practice...

In fact, it looks like the official stance is that packages should work while being installed with sudo or else they are considered broken.

@chrisfosterelli run (as normal user) npm config set prefix ~/npm to set your global modules directory to '~/npm'. You will also have to add ~/npm/bin to your PATH environment variable. Also installing node with n or nvm is recommended, especially since ubuntu botches that install so often.
On the other end, node-gyp is a special case since it compiles the systems native c++ libraries to build certain modules, and if that doesn't work with sudo, it should be brought to their attention. I've not had any issues with it working with sudo, when I've tried.

@knownasilya I understand the process to reconfiguring that, I was wondering if you had any resources stating that you should not install modules globally when you said "You should never use sudo for npm modules global or local", which doesn't seem to be the official stance. I'd like to install my global modules globally, and I'm sure lots of other users would too.
At any rate, this is certainly a bug and saying "don't install Strider the standard, accepted way" isn't a fix.
It appears that npm scripts are ran as the user nobody, could it be that bower is trying to access the error directory (/home/cfoster/.cache/bower/registry/bower.herokuapp.com/lookup in my case) and the user nobody wouldn't have access?

The permission error appears to be what's happening, because if I add a whoami to the postinstall script then I get nobody as the result. As a temporary workaround, you can create a world-writeable directory that nobody can write to and use that as HOME.
mkdir /tmp/testhome ; chmod 777 /tmp/testhome ; HOME=/tmp/testhome sudo npm install -g strider ; rm -r /tmp/testhome

That works for me on Ubuntu with<EMAIL_ADDRESS>but isn't exactly a fix.
I guess this issue is that bower is trying to use the HOME variable to access it's cache, but the user nobody wouldn't have access to that directory. Strider could get around this by assigning HOME to a temporary dir as part of the postinstall script, but I've also created bower/bower#1715 to see what they think of building this into bower, since what node-gyp does if I understand right is create it's own temporary build directory if it can't access the one it needs to for whatever reason.
Also open to better suggestions :)

Yeah not sure, probably not using bower, or having a script for pulling out the used files from the dependencies and committing those.

If you're on ubuntu, you may have to install nodejs-legacy
Read more: http://stackoverflow.com/a/21171188
This was the solution for me.

If you're trying to install on an Ubuntu machine, you may have to install nodejs-legacy package.
Read more here: http://stackoverflow.com/a/21171188
This was the solution for me.

@ksgy thank you for the input!

@ksgy I think that may be a separate issue, I'm using the PPA which provides /usr/bin/node. If it's working to globally install Strider, that may because the debain package is a much older version of node that doesn't run scripts as nobody (just a guess, though). Can you clarify your node version?

@chrisfosterelli
My node version is: v0.10.25 on Ubuntu 14.04.2 LTS

like @ksgy im using nodejs-legacy v 0.10.25 on Ubuntu machine and have no problems installig globally

Closing this, since we no longer tell you to use -g to install strider. Feel free to continue discussion. If there are any other specific issues feel free to create a new issue.

Only worked after I installed strider like a node.js app without -g flag.


bluetooth: hci: enable BT_SPI from DT

Add dedicated Kconfig symbols for the two SPI backend variants. This
allows enabling the symbols by default from devicetree, and cleans up
the cmake logic.
The HCI_SPI symbol is now automatically selected from devicetree,
removing the need for board specific defaults.

Not sure if this is quite correct, due to this hackery in CMakeLists.txt (which I'd gladly get rid of, but it may require some refactoring somewhere):
https://github.com/zephyrproject-rtos/zephyr/blob/1aaea30adb62df1aff2ccb167966db443667d5f6/drivers/bluetooth/hci/CMakeLists.txt#L20-L26

Not sure if this is quite correct, due to this hackery in CMakeLists.txt (which I'd gladly get rid of, but it may require some refactoring somewhere):
https://github.com/zephyrproject-rtos/zephyr/blob/1aaea30adb62df1aff2ccb167966db443667d5f6/drivers/bluetooth/hci/CMakeLists.txt#L20-L26

Yea noticed this after pushing, working on it now

@HoZHel the changes in this PR are not modifying the form of any of the Kconfig text, just rearranging the symbols (And duplicating in the case of SPI_HCI_ZEPHYR).
I think substantive changes should be their own PR, so that all the symbols can be addressed at once/wording changes discussed independently.

@HoZHel the changes in this PR are not modifying the form of any of the Kconfig text, just rearranging the symbols (And duplicating in the case of SPI_HCI_ZEPHYR). I think substantive changes should be their own PR, so that all the symbols can be addressed at once/wording changes discussed independently.

Well, config BT_SPI_BLUENRG is not an rearrangement and it has a wrong definition.

Removed prompts from the new symbols as done in #77418

@JordanYates, recently PR #71352 added a new HCI board which possibly needs update before merging this PR.

@JordanYates, recently PR #71352 added a new HCI board which possibly needs update before merging this PR.

Done

@HoZHel the changes in this PR are not modifying the form of any of the Kconfig text, just rearranging the symbols (And duplicating in the case of SPI_HCI_ZEPHYR). I think substantive changes should be their own PR, so that all the symbols can be addressed at once/wording changes discussed independently.

Well, config BT_SPI_BLUENRG is not an rearrangement and it has a wrong definition.

I think this comment needs also to be addressed before merging this PR, since the information provided can be misleading.

The BT_SPI_BLUENRG symbol was updated mostly in line with the request
Ah, sorry I missed that.

Rebasing on main in the hope the unrelated CI failures are resolved

Rebase to resolve release notes conflict

@erwango any idea about the CI failures here? They don't seem to be related to this PR, rather something's off with mbedtls and wifi on ST platforms. Is that a know issue?

@erwango any idea about the CI failures here? They don't seem to be related to this PR, rather something's off with mbedtls and wifi on ST platforms. Is that a known issue?

Also failing with nrf9160dk/nrf9160/ns, so I guess it's rather an issue with the test itself.

Also failing with nrf9160dk/nrf9160/ns, so I guess it's rather an issue with the test itself.

@erwango where do you see that? I only see stm32l562e_dk/stm32l562xx/ns failing in the CI logs.

Also failing with nrf9160dk/nrf9160/ns, so I guess it's rather an issue with the test itself.

@erwango where do you see that? I only see stm32l562e_dk/stm32l562xx/ns failing in the CI logs.

Reproduced locally. But I don't know why only stm32l562e_dk/stm32l562xx/ns is tested.

The CI failure should get fixed by #80381


spork -d fails

I am on rails 3.2.1 and spork 1.0.0.rc1
Since upgrade rails spork does not reload models, factories etc...
When I try to see what is cached via spork -d
I get this error
Using RSpec, Unknown
Loading Spork.prefork block...
wrong number of arguments (2 for 1) (ArgumentError)
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/spork-1.0.0rc1/lib/spork/diagnoser.rb:35:in `load'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/activesupport-3.2.1/lib/active_support/dependencies.rb:245:in `block in load'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/activesupport-3.2.1/lib/active_support/dependencies.rb:236:in `load_dependency'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/activesupport-3.2.1/lib/active_support/dependencies.rb:245:in `load'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/engine.rb:588:in `block (2 levels) in <class:Engine>'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/engine.rb:587:in `each'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/engine.rb:587:in `block in <class:Engine>'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/initializable.rb:30:in `instance_exec'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/initializable.rb:30:in `run'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/initializable.rb:55:in `block in run_initializers'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/initializable.rb:54:in `each'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/initializable.rb:54:in `run_initializers'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/application.rb:136:in `initialize!'
/Users/andrea/.rvm/gems/ruby-1.9.2-p180-patched/gems/railties-3.2.1/lib/rails/railtie/configurable.rb:30:in `method_missing'
/Users/andrea/dev/kemen/virgilio/config/environment.rb:8:in `<top (required)>'

are you sure it's related to fuubar?
Could you upload a simple app that reproduce this error? Thanks!

Fuubar is not the culprit.
Even removing it the issue perists.
Will try to reproduce in a test app

Hey Andrea,
Thanks for diving in. Could you start an issue in the Spork issue tracker for this? I'm sure they'll help you out. :)

sorry man .... posted int he wrong tracker !!!!!!!!!!!!!! I must be tired!!!


你好，mgan模块的 第32行  或者那个weight.appen(0)应该把0改成1 ？

因为mgan论文中，本意是要加大aspect词和靠近aspect的那些词的权重？

原文中提到

Specifically, we treat the weights of words within the aspect as 0 in order to focus on the context words in the sentence

所以应该没问题哈。


Prepare the MONDO outreach presentation materials

On 2023-09-22, we're giving a presentation at the Mondo Workshops / Outreach Call. The current title is "Classifying EFO/MONDO diseases as areas, roots, or subtypes". Daniel Korn from Every Cure will also present, so we should plan to not exceed 25 minutes.
We can use this issue to coordinate the slides and materials.

Some slides / topics for the presentation

Background on the task and desired classification levels https://github.com/related-sciences/nxontology-ml/issues/2
First application is EFO for OpenTargets integration, but can be easily adapted to MONDO
Subsets are helpful but not exhaustive https://github.com/related-sciences/nxontology-ml/issues/14
Features

ontology features
text-derived features: LLMs / embeddings
anything else

performance
data and repo availability
nxontology suite introduction

@yonromai it probably makes sense to tailor the next week of work to make sure we have a MVP dataset and analysis for the presentation.
I think the main things we're missing are:

https://github.com/related-sciences/nxontology-ml/issues/14
including gpt4 classifications as features in the model. Given that the cost is not so high, we can query all terms now, even if we think we're going to improve the prompts going forward and rerun everything.
store the classifications from the final model
with the final model, some analyses of feature importance, so we can give a general idea of which features matter most.

How does this sound? If it seems infeasible, we can restrict the scope of the MVP.

it's been bothering me that I have left all the data artifacts out so far

For this repo, we'll want to use a method where the data easily available to a public user, preferably integrated with the repo. I like Git LFS, but the GitHub billing for LFS can be excessive. The method we use for ensembl-genes and nxontolgoy-data is to commit the data directly to an output branch without LFS. Works if all datasets are < 100 MB, which I assume with be the case here. Kind of hacky but gets you version control, gratis storage, and good forkability and community accessibility.

Sure! In terms of feature importance, does something https://github.com/related-sciences/nxontology-ml/pull/7 work?

Yes that works, especially if those importance values can be aggregated, so we can show groupings of features.

Do you think you'd have some time tomorrow

Yes, let's find a time in slack.

For this repo, we'll want to use a method where the data easily available to a public user, preferably integrated with the repo. I like Git LFS, but the GitHub billing for LFS can be excessive. The method we use for ensembl-genes and nxontolgoy-data is to commit the data directly to an output branch without LFS. Works if all datasets are < 100 MB, which I assume with be the case here. Kind of hacky but gets you version control, gratis storage, and good forkability and community accessibility.

Right, usually I prefer to avoid putting large data files in git since (1) it makes git increasingly slow and (2) it becomes more likely to hit the 1GB GH size limit (unless erasing data file history). If the checked-in data is small and fairly static then none of these are an issue.
In the case of checking-in experiments, training set and output models (to increase reproducibility and preserve history) - it becomes more of a problem. Using a solution backed by something like S3 or GCS could work long term but is definitely too much work / out of scope for now. If history/reproducibility aren't super important, it's probably okay too keep being mindful about which dataset is persisted and only check-in essential datasets (like efo_otar_slim_v3.43.0_rs_classification.tsv).
=> I agree that checking the "final" model in git is the way to go forward at this point in time.

Yes that works, especially if those importance values can be aggregated, so we can show groupings of features.

Cool! Let's discuss all these points tomorrow

I put up a rough outline and template slide deck at https://slides.com/dhimmel/efo-disease-precision.

@dhimmel nice to prepare the seminar in the open. Just FYI, some people in Monarch have already asked that we look at some concrete examples of diseases where it is hard to classify them as grouping (area) or proper disease. Will you mention a few examples of clear-cut subtypes, groupings, and diseases, and a few questionable ones for debate?

Just a quick note here on the difficulties of establishing ground truth here, don't have time for a full summary here but see this as a quick literature proxy (usual caveats AI etc):
https://www.perplexity.ai/search/Is-Parkinson-disease-G_cC1TZOQ121Q2ZWmKjCZw?s=c

@dhimmel one of these might be worth including: https://github.com/related-sciences/nxontology-ml/issues/2#issuecomment-1728373390
I have no strong opinion one way or the other, but +1 to having a sampling of terms by precision label somewhere after https://github.com/related-sciences/nxontology-ml/issues/30.

@eric-czech the one area that I don't feel fully confident in presenting is how the initial RS labels that we use for training were calculated. Would you be able to jot down a few notes on that process here? I could then copy that to a slide and then you could present that slide.

a few notes on that process

Certainly.  The process went like this:

Start with an empty set of annotations, one for each EFO term and precision class (low, medium, high)
Repeat this loop:

Curate terms from these heuristic functions to bootstrap some positive / negative examples by class:

low: Has very low intrinsic IC
low: Has very high aggregate Open Targets evidence
¬low: Has clinical trials associated
medium: Has a lot of descendants with many of the same tokens in the label

e.g. familial hypertrophic cardiomyopathy -> hypertrophic cardiomyopathy {2,4,10,11,12,17,20,26}

medium: Has an OMIM PS xref and has descendants

Add the above to the set of annotations
Run these automatic labeling functions given the existing set of annotations

high: Is a terminal node descending from an OMIM PS term
high: Is a terminal node descending from an existing medium precision term
low: Ends with neoplasm and has cancer descendants
¬low: Has no descendants

Run separate binary ML light GBM models for each class and propose new terms for them
Manually review the top predictions for each class w/o a current label
Append new terms to the existing set of annotations

At any time, override existing annotations based on manual review

I went through this loop ~5 times and stopped once the top predictions for the low precision terms started to become more difficult to distinguish from medium precision terms.

Thanks @yonromai and @eric-czech for the help presenting. We can leave this issue up until the recording is online and we add a link to the recording/slides to the README.
Copying the zoom chat log here from today, since there are some good suggestions that we should follow up on.
11:58:38 From Sarah G. To Everyone:
	https://www.slido.com/
11:58:47 From Nicole Vasilevsky To Everyone:
	https://app.sli.do/event/4m6g4VAFFpHsAQTWwVAjve
12:13:41 From Chris Mungall To Everyone:
	We should talk about synergies with oaklib (but not on this call!)
12:14:01 From trish To Everyone:
	Reacted to "We should talk about..." with 👍
12:14:09 From Sarah G. To Everyone:
	Reacted to "We should talk about..." with 👍
12:23:51 From Chris Mungall To Everyone:
	Some of the text-based features could be replaced by axioms (e.g. “ends with neoplasm”) … this is awesome!
12:25:23 From Chris Mungall To Everyone:
	@Nicole I don’t know if we are ready to show our design patterns (or just the tags). The meta class is the most powerful feature I’d expect
12:26:42 From Nicole Vasilevsky To Everyone:
	Here are the design patterns: https://mondo.readthedocs.io/en/latest/editors-guide/patterns/
12:26:50 From Chris Mungall To Everyone:
	I would hope our prefixes are standardized!
12:29:02 From Joe Flack To Everyone:
	are the nxontology repos private?
12:29:14 From Eric Sid To Daniel Himmelstein(Direct Message):
	Hi Daniel, great talk so far - would you be able to share your slides afterwards?
12:32:58 From Sarah G. To Everyone:
	https://www.slido.com/
12:33:04 From Sarah G. To Everyone:
	Replying to "https://www.slido.co..."

	1342945
12:33:23 From trish To Everyone:
	Replying to "are the nxontology r..."

	Some repos are public https://github.com/related-sciences
12:34:25 From Chris Mungall To Everyone:
	My vote: Metaclass >> gut >> topology
12:34:38 From Chris Mungall To Everyone:
	Gpt not gut (feeling :-)
12:34:46 From Nico To Everyone:
	Reacted to "Gpt not gut (feeling…" with 😂
12:35:01 From Sarah G. To Everyone:
	Reacted to "Gpt not gut (feeling..." with 😂
12:35:18 From Sarah G. To Everyone:
	https://www.slido.com/     1342945
12:35:24 From Gioconda Alyea To Everyone:
	topology, description, cross reference
12:44:11 From Sarah G. To Everyone:
	https://github.com/related-sciences/nxontology
12:44:19 From Nico To Everyone:
	Super interesting guys, I have to run now, willl follow up
12:49:53 From Chris Mungall To Everyone:
	Yes! We have an evaluation happening if you want to join that
12:50:09 From Chris Mungall To Everyone:
	[for @Eric]
12:50:52 From Daniel Himmelstein To Eric Sid(Direct Message):
	Slides from our talk at https://slides.com/dhimmel/efo-disease-precision
12:51:14 From Eric Sid To Daniel Himmelstein(Direct Message):
	Replying to "Slides from our talk..."

	Thanks Daniel. Great work, very interesting!
12:54:11 From Eric Czech To Everyone:
	Awesome, would love to take a look and/or get more involved
12:54:15 From Eric Czech To Everyone:
	How can we do that?
13:01:16 From Daniel Himmelstein To Everyone:
	Slides from our talk https://slides.com/dhimmel/efo-disease-precision
13:02:19 From Eric Sid To Everyone:
	Great talks!
13:02:32 From Gioconda Alyea To Everyone:
	Very interesting!  Great to know about all you do and will want to keep in contact
13:03:05 From Sarah G. To Everyone:
	I will leave you in the call to chat!
13:03:09 From Sarah G. To Everyone:
	Thank you!


 In practise, lots of apps report network unreachable. It is not matter of bandwidth (the connections do not do much). Switching DNS to useHostResolver: false did not help.
mstenber@lima-f34 ~>curl https://www.google.com -o ,x
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 15246    0 15246    0     0    737      0 --:--:--  0:00:20 --:--:--  3168

mstenber@lima-f34 ~>curl https://www.google.com -o ,x
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 15179    0 15179    0     0  26583      0 --:--:-- --:--:-- --:--:-- 26583
^ note ~instant fetch without connections going on

mstenber@lima-f34 ~>curl https://www.google.com -o ,x
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 15187    0 15187    0     0    955      0 --:--:--  0:00:15 --:--:--  3342

You can try if using VDE helps ?

#537

I had similar issues (but not quite) with podman machine too. I suppose it might be even qemu issue of some kind. I'll try the vmnet, it looked bit unnecessary (as all I need is really just container -> outer world connectivity) but if it works better..

Hmm, podman machine uses gvproxy

gvproxy seems to perform much worse in terms of speed (that's why I switched to lima to start with); the weird part is that it is most likely not (only) DNS, it seems that the result is 'network unreachable' from TCP connect().

Seems to work better with the vde.. initially it didn't though, as the slirp was preferred default route still:
mstenber@lima-f34 ~>ip route
default via <IP_ADDRESS> dev eth0 proto dhcp metric 100
default via <IP_ADDRESS> dev lima0 proto dhcp metric 101
<IP_ADDRESS>/24 dev eth0 proto kernel scope link src <IP_ADDRESS> metric 100
<IP_ADDRESS>/24 dev lima0 proto kernel scope link src <IP_ADDRESS> metric 101

Needed to run following:
mstenber@lima-f34 ~>sudo ip route delete default via <IP_ADDRESS>

The configuration I had was:
networks:
  - lima: shared

Maybe VDE should be packaged for Linux as well ? https://wiki.alienbase.nl/doku.php?id=slackware:vde

Maybe VDE should be packaged for Linux as well ?

No, because vde_vmnet doesn't work on Linux.
For Linux we should support TAP with qemu-ifup/qemu-ifdown.

I meant VDE (not vde_vmnet), but I think it's the same TUN/TAP.

Much to my surprise VDE is quite slow; in my testing it was 7 times slower than the slirp user mode networking in qemu. And that was after fixing a bug in the vde_bridge code; before it was almost 350 times slower. Timings in https://github.com/virtualsquare/vde-2/pull/35.
So it might be better to do TUN/TAP directly without going through VDE, but just a guess until we benchmark...

Trying to remember what libvirt uses, just know it gets two eth interfaces.
Which in turn is mostly legacy from the VirtualBox setup, NAT + Host-Only.

Very non-scientific benchmark but yeah, the VDE perf is pretty bad (most recent master built for the vde*):
slirp:
Fedora-Workstation-Live-aarch64-35-1.2.iso    100% 1831MB 343.3MB/s   00:05

vde:
Fedora-Workstation-Live-aarch64-35-1.2.iso    100% 1831MB  31.6MB/s   00:57

(Both of these are to the host machine, so no real network was harmed during the test)

I only get the desired behaviour on Lima with nerdctl running on user-level, even though the host has same behaviour.
Every other permutations of the following attempts has also reproduced the behaviour.

nerdctl at system level
docker
host-resolver on/off
Alpine and Ubuntu as distros
with/without vde_vmnet

I do notice the difference in nameserver in both user and system level nerdctl.
$ nerdctl run --rm -it alpine -- cat /etc/resolv.conf
nameserver <IP_ADDRESS>
nameserver <IP_ADDRESS>

# nerdctl run --rm -it alpine -- cat /etc/resolv.conf
nameserver <IP_ADDRESS>
nameserver <IP_ADDRESS>

I do notice the difference in nameservers on user and system level nerdctl.
$ nerdctl run --rm -it alpine -- cat /etc/resolv.conf
nameserver <IP_ADDRESS>
nameserver <IP_ADDRESS>

# nerdctl run --rm -it alpine -- cat /etc/resolv.conf
nameserver <IP_ADDRESS>
nameserver <IP_ADDRESS>

I don't actually know how containerd configures DNS (inside k3s it uses coredns; not sure how it works for user mode containerd).
The entries for system mode containerd look suspicious: <IP_ADDRESS> looks like a nameserver on the local network. How did that make it into the VM? Did you add it via dns in lima.yaml, or did you disable the host resolver?
<IP_ADDRESS> is either a qemu-forwarded nameserver from /etc/resolv.conf on the host, or the lima host resolver (we override the qemu one using iptables).
Either way, you (we) should not have both nameservers in there, as they are no equivalent. Multiple nameservers in /etc/resolv.conf are supported for high availability: if one server is unreachable, the resolver will try another one. But they are all supposed to be interchangable, all resolving all names the same way. There is no fallback from one nameserver to the other. If the first one responds with "domain not found", then that is the final answer.
FWIW, I only get the single expected nameserver when using system mode containerd:
jan@lima-default:~$ sudo nerdctl run --rm -it alpine -- cat /etc/resolv.conf
nameserver <IP_ADDRESS>

FWIW, I only get the single expected nameserver when using system mode containerd:
jan@lima-default:~$ sudo nerdctl run --rm -it alpine -- cat /etc/resolv.conf
nameserver <IP_ADDRESS>

Sorry for the confusion, that is with vmnet shared network enabled. Without that, it is same as yours.

I see, thanks! That will be a potential source of problems:
jan@lima-default:~$ sudo nerdctl run --rm -it alpine -- cat /etc/resolv.conf
search home
nameserver <IP_ADDRESS>
nameserver <IP_ADDRESS>
jan@lima-default:~$ resolvectl status
Global
       Protocols: -LLMNR -mDNS -DNSOverTLS DNSSEC=no/unsupported
resolv.conf mode: stub

Link 2 (eth0)
    Current Scopes: DNS
         Protocols: +DefaultRoute +LLMNR -mDNS -DNSOverTLS DNSSEC=no/unsupported
Current DNS Server: <IP_ADDRESS>
       DNS Servers: <IP_ADDRESS>

Link 3 (lima0)
    Current Scopes: DNS
         Protocols: +DefaultRoute +LLMNR -mDNS -DNSOverTLS DNSSEC=no/unsupported
Current DNS Server: <IP_ADDRESS>
       DNS Servers: <IP_ADDRESS>
        DNS Domain: home

Link 4 (nerdctl0)
Current Scopes: none
     Protocols: -DefaultRoute +LLMNR -mDNS -DNSOverTLS DNSSEC=no/unsupported

It does pick up a search domain from the host, but the simplistic /etc/resolv.conf mechanism doesn't support split-DNS, so all requests should really just go to <IP_ADDRESS> and the other nameserver should not be listed as a fallback.
The /etc/resolv/conf in the VM is correct though:
jan@lima-default:~$ cat /etc/resolv.conf
[...]
# This is a dynamic resolv.conf file for connecting local clients to the
# internal DNS stub resolver of systemd-resolved. This file lists all
# configured search domains.
[...]
nameserver <IP_ADDRESS>
options edns0 trust-ad
search home

Again, I don't know how nerdctl and/or containerd configure DNS, and why it picks up the incorrect second nameserver.
But you said you get the flaky networking even without the additional vde_vmnet network (and DNS), so it should be immaterial for this issue.

I do not know whether I should append in this issue , but in my case it do nothing with the DNS resolver , even with the pure IP:Port, the network issue seems existed .
In my case , I use lima nerdctl compose up to start 5 services at the same time , and this 5 services both depend on the outside register and discovery service (this is my outgoing traffic) to start . Things get weird that if we start 5 service at the same time , they can not start due to the disconnection or time-out with the outside register service but we reduce the service to 1 or 2 , it will start occasionally , after some times of retry , even the dig response with timeout .
After I  install the vde , things get better now.

I used raw qemu before and tested several options for networking. I found that vde is really slow compared to user-mode networking. I though we could attach two interfaces to vm: the user-mode device for out traffic and a vde for a connection between vms(if needed).

I used raw qemu before and tested several options for networking. I found that vde is really slow compared to user-mode networking. I though we could attach two interfaces to vm: the user-mode device for out traffic and a vde for a connection between vms(if needed).

I tried out PTP mode and it seems to be more stable for situations like https://github.com/lima-vm/lima/issues/561#issuecomment-1047132046. The download speed is okay and there is also a report of a better dns performance (when used for dns).
But there are still two main issues.

the upload speed is 90% slower.
it appears to be incompatible with vpn connections. There are multiple reports of unsuccessful outgoing requests when vpn connection is active.

It looks like the safest best is still your recommendation i.e. to limit vde to providing reachable address to the vm and retaining the user-mode for normal traffic.

Hi all - is this the root cause for the Slirp issues: https://gitlab.freedesktop.org/slirp/libslirp/-/issues/35 ?

Hi all - is this the root cause for the Slirp issues: https://gitlab.freedesktop.org/slirp/libslirp/-/issues/35 ?

that looks like it

Hi all - is this the root cause for the Slirp issues: https://gitlab.freedesktop.org/slirp/libslirp/-/issues/35 ?

Seems already fixed in libslirp v4.5.0 (18 May, 2021): https://gitlab.freedesktop.org/slirp/libslirp/-/merge_requests/73

Seems already fixed in libslirp v4.5.0 (18 May, 2021): https://gitlab.freedesktop.org/slirp/libslirp/-/merge_requests/73

I saw that, however the issue described is near identical to the current issue as well.

This particular one was fixed, but follow-up problem surfaced in 0.12 ( see https://github.com/lima-vm/lima/issues/1285 ). Closing this though.


RandomSource update - Validated

Enables developers to supply their own custom RandomSource

Same four existing sources are still available
Updated RandomSource test to ensure test for randomness should always pass

PseudoDeviceAddress (PDA) now use SHA256 to cryptographically separate random address from random source

Existing non-blocking random source made it impractical to use observed addresses for tracking

Call time is inherently random due to real-world events as entropy source
Shared random seed source is inherently random as system initialisation time is unpredictable
Random values follow a uniform distribution, thus all values may be generated by all seeds
Random sequence follow a uniform distribution, thus knowledge of prior values offer minimal gain in reducing the total number of seeds that could have generated the consecutive addresses

Introduction of SHA256 hash and data trimming offer additional assurance that the random seed is cryptographically challenging to identify given observed addresses

Developers are free to adopt their own customer RandomSource that meets their specific requirements
Recommendation is to use the non-blocking random source in contact tracing applications as the impact of blocking, leading to non-detection of disease transmission, is far greater than the theoretical risk of tracking

Passes all unit tests

Signed-off-by: c19x<EMAIL_ADDRESS>closes #189

Would it be possible to add a higher level test for PseudoMacAddress that validated each byte value for the mac had an even distribution and was comparable in every byte position? (I.e. to ensure that the first byte being, say, 00 was just as likely as its other values, and that the frequency was comparable with bytes 2-6's frequency of 00 too).

Thanks for review.

Current tests have a high tolerance as they aim to test for obviously not random output (i.e. due to coding error), rather than confirm the output is random and uniformly distributed
Good idea to incorporate uniformity tests, considering incorporating existing standalone simulation code, but need to make it run within reasonable time
Also have an idea for non-blocking secure random, shall provide update, please hold PR

Added comment to clarify why the tolerance is so high for existing tests (to catch obviously not random output)
Added new uniformity tests with just 10% threshold for confirming if all values are equally likely in a sequence and as initial value given a seed

Uniformity test can run at lower threshold given more samples, current parameters have been set to ensure the automated tests should run quickly and passes almost all the time given uniformly distributed random sources

Introduced new Non-blocking CSPRNG based on the same concepts as SecureRandom except entropy is gathered from sources that won't exhaust in the target application environment. This is a simplified and quantified version of existing Non-blocking PRNG, enhanced with SHA256 for separating the observations (random values) generated by the one-time use PRNG from its seed that has been derived from a mixture of entropy sources, and also separating the seed source from the entropy source.

Passes all new unit tests
Delivers the best speed performance across all available random sources.
This is now the recommended default random source.
Validated on Pixel 3 and A20

Running overnight test to confirm new Non-Blocking CSPRNG really is non-blocking on idle devices

Code analysis has not identified any blocking calls in the new random source.
Planning to migrate uniformity test to server for statistical tests as separate standalone background task.

Conducted 18hr+ test on Pixel3 and A20 to confirm Non-Blocking CSPRNG is non-blocking

NonBlockingCSPRNG confirmed to be non-blocking after 44hr test on idle devices
Battery usage was 84% and 82% after 44 hours continuous use
Added new NonBlockingSecureRandom which is the recommended random source for the future as all reliance on LCG has been removed. The solution is based entirely on cryptographically secure functions only, yet remains non-blocking.
Conducting long running test to confirm NonBlockingSecureRandom now.

NonBlockingSecureRandom FAILED to perform continuously without any negative impact on wider systems

Test shows any call to SecureRandom is liable to exhaust system entropy which prevents BLE operation
Developing new algorithm to remove reliance on SecureRandom

New implementation of NonBlockingSecureRandom is guaranteed to be non-blocking

Eliminated reliance on SecureRandom for reseeding
Using a time-based truly unpredictable random source for reseeding

Solution is based on thread scheduling which is inherently unpredictable and determined by wider system events
Same concept as ThreadSeedGenerator that is used by Oracle and OpenJDK implementations of SecureRandom that acts as backup random source when /dev/random is exhausted

Running overnight test under stress testing condition to confirm solution is non-blocking

No logging to avoid generating storage events to minimise system entropy
Advert refreshes every 3 minutes to trigger generation of new pseudo device address
RandomSource gathering external entropy from just one target device (test conducted with 2 phones in a faraday bag)
NonBlockingSecureRandom set to reseed every minute

Tests have confirmed NonBlockingSecureRandom is non-blocking under continuous background use

Advert refresh set to once every 3 minutes to trigger unusually frequent use of random source
Reseed set to once every minute to trigger unusually frequent use of entropy source
Logging set to OFF to minimise system activities
Pixel3 and A20 placed in a single Faraday bag to eliminate external entropy
100% continuity in 5 hour test, shall continue testing for 24 hours

PR ready for merge as new solution is now validated and proven to be non-blocking

Design builds on accepted seed generation method in SecureRandom and addresses known vulnerabilities
2048 bit internal state, SHA256 based state updates, incorporates external truly random data when available

closes #189
closes #118
closes #110

Ready for merge

27hr test shows 100% continuity


Add ability for users to change custom file names

Use aliases for class config files instead of hardcoding file names. This way the user can choose their own file names instead of the now hardcoded 'class_c.cfg,' convention. For example this allows the user to avoid file clutter by putting class files in their own directory. As another example the files can be organised by class number instead of alphabetically by using file names like '1_scout.cfg.'

Thank you for your contribution to mastercomfig!


Update definition of  GO:0002144 - cytosolic tRNA wobble base thiouridylase complex

If you change the definition from "A complex of two proteins involved in the thiolation of U34 in glutamate, lysine, and glutamine tRNAs of eukaryotes."  to ""A complex of two proteins involved in the thiolation of uridine 34 (U34) of tRNAs decoding two-family box triplets." then it works for prokaryotes too, which is what I need it for. PMID: 17062623 if you want to check it out.

Done.


Missing EFFEXPTM keyword in headers

Hi @hover2pi!
Currently, awesimsoss simulations crash in the TSO3 outlier_detection step because the EFFEXPTM header keyword (effective exposure duration) is not populated (this defines the exposure time for the pipeline to read: https://github.com/spacetelescope/jwst/blob/04dad52af950a652becc79a6d8e3dcb44d255253/jwst/datamodels/schemas/core.schema.yaml#L793).  Currently, the similar DURATION keyword is included --- but from a quick read to the Keyword Dictionary (https://mast.stsci.edu/portal/Mashup/Clients/jwkeywords/index.html), it seems that one counts the entire real duration (including resets, dead time, etc.) --- whereas EFFEXPTM is just the photon-counting duration of the exposure.
N.

Thanks @nespinoza ! Fixed in #111 when I updated a bunch of TSO properties to reflect the datamode.xml PRD file.


set the supervisor strategy from the props

This seems to fix #289 . I couldn't see anywhere in the code where the supervisor is actually being set.

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.

Thank you very much for this PR.
But the issue should be fixed here:
https://github.com/AsynkronIT/protoactor-go/pull/291
So I'll close this PR for now!


Fixed-Function Media Engines in GPUs with HW Media Acceleration Features

Intel
Intel GPUs have fixed-function media engines for quite a while. The important parts to know about are:

VDBOX: Video Decoding
VEBOX: Video Enhancement
SFC: Scaling and format conversion
VDEnc: Video Encoding

SFC was introduced in Kaby Lake to achieve low-power video playback without using shaders for scaling via EUs (Execution Units). EUs are the primary workhorses which are used by games for 3D computations but also for desktop composition, overlay and scaling of gpu surfaces. This is also what accounts for "3D" usage percentage in task manager.
Some video processing features are provided as EU Kernels, some via VEBOX fixed function blocks, sometimes, both. It depends on the GPU generation. Scaling is done via SFC since Kaby Lake
References:

https://www.anandtech.com/show/9562/intels-skylake-gpu-analyzing-the-media-capabilities
https://www.x.org/docs/intel/LKF/intel-gfx-prm-osrc-lkf-vol11-mediaengines.pdf
https://www.x.org/docs/intel/KBL/intel-gfx-prm-osrc-kbl-vol15-sfc.pdf
https://github.com/intel/media-driver#components-and-features
https://github.com/intel/media-driver/blob/master/docs/media_features.md#supported-video-processing-feature-combination

SFC is not a generic and independent feature. It is part of the Media Engines and requires a media pipeline context  to be used. SFC cannot be used for generic scaling, such as is done for desktop composition. For desktop composition, scaling is done by EU kernels.
ffmpeg Implementation
The processing filter in ffmpeg as a scale_mode options which allows you to switch between shader-based (EU kernel) scaling and fixed-function block (SFC, also called 'low-power mode') scaling:
With EO Kernel Scaling
ffmpeg -hwaccel qsv -c:v h264_qsv -i video.mkv -vf "vpp_qsv=w=1920:h=1080:scale_mode=2" -f null -

ffmpeg speed=7.69x
CPU load: 25%

With Fixed-Function Scaling
ffmpeg -hwaccel qsv -c:v h264_qsv -i video.mkv -vf "vpp_qsv=w=1920:h=1080:scale_mode=1" -f null -

ffmpeg  speed=8.05x
CPU load: 25%

CPU Decoding and Scaling
ffmpeg -i  video.mkv -vf "scale=w=1920:h=1080" -f null -

speed=8.03x
CPU load: 100%
NOTE: The test file I used is "Samsung Dubai" which you can find on DemoLandia.net

DirectX VideoProcessor Scaling
Just few weeks ago I have added a new "Power Efficient" playback mode to our Windows app which is using mpv. MPV has its own presentation-side scaling implemented by custom shaders, which may provide good scaling quality but are also draining batteries quickly.
Our Win App with shader-based presentation scaling

Our Win App with D3D11 VideoProcessor Scaling
The presentation-layer scaling is disabled in this case

Windows Media Player
For comparison

Test file parameters:   Stream #0:0: Video: hevc (Main 10), yuv420p10le(tv, bt2020nc/bt2020/smpte2084), 3840x1600 [SAR 1:1 DAR 12:5], 24 fps, 24 tbr, 1k tbn (default)
Playback scenario: 4k TV with HDR enabled, but playing in a window of about half the size.

In that mpv based app, I also have an additional mode:

HW Prescaling means that D3D11 VideProcesor scaling is only applied when the video is significantly larger in resolution than the display on which the app window resides. Like 4k video on a laptop. These are often not capable to handle 4k frame downscaling via shaders (or at least pushes the GPUs 3D load very hard).
In that case it applies D3D11 VideoProcessor scaling but with a target size that is still somewhat larger than the window. This reduces the amount of data for the eventual scaling that is done for presentation via shaders (and also adapts to window resizing while the D3D11 VideoProcessor scale factor remains unchanged.


[IMPAC-670] Forecast transactions

UI improvements on Cash projection widget
Simulation mode replaced by add/remove forecast transactions capability

Dependencies

https://github.com/maestrano/impac/pull/521
https://github.com/maestrano/impac-finance-bolt/pull/72

@xaun can you please review?
I'm deploying it to https://mnoe-demo.maestrano.io for testing

@xaun thanks, that's a good point - will do


Add support for rocky linux and script cleanup

Additional changes related to 4.11 for new services
Tested on 4.8 and 4.11 with clean install and re-install for rocky/cent/aws/ubuntu

@jrich523 your installation script looks fine:

I also added a small commit for changing route to get files from e26c8e0

Making tests with this code deploying on ubuntu, Sidecar v4.12.2:

cc: @jrich523

Tests after commit 4e3f4d5
Running the script with export CYRAL_SIDECAR_VERSION="v4.12.2" I do see correct behavior:

Running it with export CYRAL_SIDECAR_VERSION="v4.6.0":

cc: @jrich523


Tests failing to run with BackendUnavailable since pip 19

It seems that since the release of pip 19, Setuptools' own tests fail to run thus:
setuptools fix_889_and_non-ascii_in_setup.cfg_take_2 $ tox -e py27
py27 create: /Users/jaraco/code/main/setuptools/.tox/py27
py27 installdeps: -rtests/requirements.txt
py27 develop-inst: /Users/jaraco/code/main/setuptools
ERROR: invocation failed (exit code 2), logfile: /Users/jaraco/code/main/setuptools/.tox/py27/log/py27-2.log
ERROR: actionid: py27
msg: developpkg
cmdargs: '/Users/jaraco/code/main/setuptools/.tox/py27/bin/pip install --exists-action w -e /Users/jaraco/code/main/setuptools'

DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///Users/jaraco/code/main/setuptools
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
Exception:
Traceback (most recent call last):
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_internal/cli/base_command.py", line 176, in main
    status = self.run(options, args)
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_internal/commands/install.py", line 315, in run
    resolver.resolve(requirement_set)
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_internal/resolve.py", line 131, in resolve
    self._resolve_one(requirement_set, req)
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_internal/resolve.py", line 294, in _resolve_one
    abstract_dist = self._get_abstract_dist_for(req_to_install)
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_internal/resolve.py", line 226, in _get_abstract_dist_for
    req, self.require_hashes, self.use_user_site, self.finder,
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_internal/operations/prepare.py", line 382, in prepare_editable_requirement
    abstract_dist.prep_for_dist(finder, self.build_isolation)
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_internal/operations/prepare.py", line 149, in prep_for_dist
    reqs = self.req.pep517_backend.get_requires_for_build_wheel()
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_vendor/pep517/wrappers.py", line 71, in get_requires_for_build_wheel
    'config_settings': config_settings
  File "/Users/jaraco/code/main/setuptools/.tox/py27/lib/python2.7/site-packages/pip/_vendor/pep517/wrappers.py", line 162, in _call_hook
    raise BackendUnavailable
BackendUnavailable

py27 installed: DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.,apipkg==1.5,atomicwrites==1.2.1,attrs==18.2.0,configparser==3.7.1,contextlib2==0.5.5,coverage==4.5.2,enum34==1.1.6,execnet==1.5.0,flake8==3.6.0,funcsigs==1.0.2,futures==3.2.0,importlib-metadata==0.8,mccabe==0.6.1,mock==2.0.0,more-itertools==5.0.0,path.py==11.5.0,pathlib2==2.3.3,pbr==5.1.1,pluggy==0.8.1,py==1.7.0,pycodestyle==2.4.0,pyflakes==2.0.0,pytest==3.10.1,pytest-cov==2.6.1,pytest-fixture-config==1.4.0,pytest-flake8==1.0.3,pytest-shutil==1.4.0,pytest-virtualenv==1.4.0,scandir==1.9.0,six==1.12.0,termcolor==1.1.0,virtualenv==16.3.0,zipp==0.3.3
________________________________________________________________________________________ summary ________________________________________________________________________________________
ERROR:   py27: InvocationError for command /Users/jaraco/code/main/setuptools/.tox/py27/bin/pip install --exists-action w -e /Users/jaraco/code/main/setuptools (see /Users/jaraco/code/main/setuptools/.tox/py27/log/py27-2.log) (exited with code 2)

I suspect this is related to #1642 if not just another manifestation of the same issue.

That's with the current pyproject.toml, no?

@benoit-pierre No, I added setuptools to the pyproject.toml. Without that, the install fails with or without --no-binary.

That's not how to show the issue:
> git diff
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
modified: pyproject.toml
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
@ pyproject.toml:2 @
[build-system]
requires = ["wheel"]
requires = ["wheel", "setuptools"]
build-backend = "setuptools.build_meta"

[tool.towncrier]
> python setup.py sdist
> pip download --no-binary :all: wheel -d dist
> pip install --no-binary :all: --no-index -f dist -t tmp -v setuptools

Trying to install from patched source with the index available will work because there's currently a setuptools sdist available on PyPI that itself does not depend on a version of (another version of) setuptools for building.

@benoit-pierre Ah, so as soon as we upload this version of setuptools it will start breaking. Good point.

Even if we discount the --no-binary :all: case, how would you start even build your first version of a PEP 517 backend? Do you need to have a separate code path to create the wheel?

Even if we discount the --no-binary :all: case, how would you build your first version of a PEP 517 backend? Do you need to have a separate code path to create the wheel?

That's the idea, yes. In practice what it means is that all PEP 517 backends will use a different, existing PEP 517 backend to bootstrap their first build. It's not terribly different from the situation with compilers, most compilers are built either by another compiler or by an older version of themselves (clang builds itself, for example), and they usually start out being built from other compilers.
It's possible for a project to bootstrap the process by manually creating a wheel, though I imagine no one would do that because wheels for setuptools and flit already exist.
Personally, I'm arguing in the discourse thread for adding a mechanism in PEP 517 to allow us to bootstrap ourselves, but if PEP 517 simply changes to mandate that front-ends must use wheels if available to satisfy the build requirements, that would neatly solve our problem.
Another possibility is that PEP 517 could change to mandate cycle detection and wheels would be required for the first package in a cycle. That seems much more complicated to implement than a bootstrapping mechanism, though.

At this point the discussion in Discourse does not seem to be going anywhere. I suggest we simply add setuptools to the build-system.requires. This will have the unfortunate side-effect of breaking --no-binary :all: for pretty much everyone using PEP 517 (and possibly everyone?), but I think pretty much everyone using PEP 517 will be broken anyway.
pip can decide whether or not to support --no-binary :all:. My understanding is that as PEP 517 stands right now, it's not intended to support bootstrapping, and I think that even if they revert the "pyproject.toml opts you in to PEP 517" change with pypa/pip#6229, we'll still be affected because we have a [build-system] in our pyproject.toml, so building from source will be broken anyway. Might as well just get into compliance with the spec and let pip decide what to do about --no-binary :all:.

I think the discussionin Discourse is still going somewhere, but the direction it's now going is the direction you describe here: projects that need bootstrapping should add themselves to their own build-system.requires, and then the onus is on frontends to detect that and halt the infinite regress.

Thinking about this, even if pip --no-binary :all: switches to resolving self-referential source distributions with wheels, if they don't handle long-range cycles, we're still going to break --no-binary :all: if we depend on wheel as part of the PEP 517 build.
That basically means that we cannot have any dependencies in build-system.requires, and we'll need to vendor wheel, so I think we have three options:

Specify 'setuptools' and 'wheel' in our build-system.requires and let pip fix --no-binary :all: or not, as desired.
Opt out of PEP 517 forever, meaning that we will never be installable by a PEP 517-only frontend except as a wheel.
Vendor wheel in our source tree and wait for PEP 517 to be extended to allow for self-bootstrapping builds.

I don't think number 3 is going to happen, so we're really choosing between options 1 and 2. I'm in favor of option 1, but we may want to give pip some fair warning that we'll be doing it, since it will likely cause at least some breakages.

Reading https://github.com/pypa/pip/issues/6222 (and based on the other threads), I think the pip folks already agree that the current interaction between --no-binary :all: and PEP 517 needs work, so Option 1 seems like a reasonable choice at the setuptools level to me.

So after the absurd amount of discussion on this, the final decision (around 9 months ago) was to modify PEP 517 to add backend-path for bootstrapping, but no front-ends are actually spec compliant as far as I can tell. pip doesn't seem to support it at all.
This makes it very difficult to install our own library from git. I suggest that we just go ahead with this configuration for now:
[build-system]
requires = ["wheel", "setuptools>=40.0"]
build-backend = "setuptools.build_meta"

We can continue to exclude pyproject.toml from the source distribution so that pip install setuptools --no-binary :all: will continue to work for now. Once pip implements this we can probably switch over to using backend-path.

So after the absurd amount of discussion on this, the final decision (around 9 months ago) was to modify PEP 517 to add backend-path for bootstrapping, but no front-ends are actually spec compliant as far as I can tell. pip doesn't seem to support it at all.

backend-path is now used on the main branch requiring pip >=20 or something like python-build.

I see two ways forward with this:
1. Fix this problem with `pip`, adjusting PEP 517 to allow this kind of situation if necessary.

2. Create a new "PEP 517 bootstrapper" backend, that simply delegates all backend tasks to a backend that exists in your local directory, then start using that.

After some consideration, I do think this project needs something like a bootstrapper backend, mainly to address the situation of a clean source checkout. In that situation, there is no metadata present. Setuptools currently works around that situation by requiring a separate copy of setuptools to build, which is okay, but also clumsy, because then when the sdist is built, it also declares a requirement on setuptools, even when it's not needed.

In the above referenced pull request, I figured out that Setuptools can supply its bootstrapping metadata in a separate metadata file. There's still no way to ever make Setuptools build properly on pip 19, so it will just have to break.


ci: adds codeql-analysis.yml for codeql execution

This enables codeql for this repo to meet the security and stability requirements of the octokit org.

@nickfloyd What do you think of adding all of these issues to our project so we can better track the work we've done?

@nickfloyd What do you think of adding all of these issues to our project so we can better track the work we've done?

I have them encapsulated in the existing issues (I didn't want to create 40+ issues) so I grouped them by JS SDK, tooling, plugins, and schemas/types


Riemann output

cc @allenj

@allenj I took your commit and added the godep dependencies as well as the docker container. You can see in the 3rd commit that I also removed some of the object reference/dereferencing by mostly storing and passing pointers, which should be more performant as well.
Let me know what you think, and if it looks good I'll merge it to master, thanks a bunch for your contribution!! a lot of people have been asking for this :+1:

Looks good. Thanks @sparrc . First thing I've written in golang so I'm glad you looked over and fixed those references/derefs.


Update main.py

Bhadve kahi aur jaake pr kar fir pr kiya toh teri gand mai danda daalunga

Bruh wtf ye repo public nhi hai ?
On Tue., 8 Feb. 2022, 12:30 pm The Guy, @.***> wrote:

Bhadve kahi aur jaake pr kar fir pr kiya toh teri gand mai danda daalunga
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Sorry
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Toh bhadve repo fork karke edit karna maa chudane original repo pe pr kar
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@grue47553 The heck


Adding set_paths to WasiNnCtx

This function will allow storage of the real paths
of the --mapdir values given to wasmtime. This is
needed because TensorFlow and possibly other
backends require a path to the model and other
files.

@abrown Here is the proposed change needed to provide the mapdir location so the Tensorflow backend can work.


Fix small typo in README file

Changing from "In can be useful" to "It can be useful". No big deal :-)

Coverage remained the same at 99.52% when pulling 43fe3b8ea91e0a60e418f1da1dc084077ac0bf97 on igormoreno:patch-1 into 55664f7d73252f5127b9b654cfd35f3c66f50c9f on watsonbox:master.

Coverage remained the same at 99.52% when pulling 43fe3b8ea91e0a60e418f1da1dc084077ac0bf97 on igormoreno:patch-1 into 55664f7d73252f5127b9b654cfd35f3c66f50c9f on watsonbox:master.

Coverage remained the same at 99.52% when pulling 43fe3b8ea91e0a60e418f1da1dc084077ac0bf97 on igormoreno:patch-1 into 55664f7d73252f5127b9b654cfd35f3c66f50c9f on watsonbox:master.


Could you make an english bot too?

Heres the full dictionary of bombparty https://pastebin.com/raw/K54aJ5ez

There are already some forks that have been updated with an English dictionary:

imthe666st/sparklin-exploder
Beatbox309/sparklin-exploder

You could do so yourself:

Fork the repo, so that you will be able to edit any file you want
Create a new dictionary.js with the following content

var words = ["aa","aah","aahed", ... ,"zzzs"]

Update the dictionary.js on your repository, and your own version will be automatically aviable at  http://fyzick5.github.io/sparklin-exploder/exploder.js !

Of course there is too many words to do it manually, but here is the challenge 😉
You can do it with a little Python script, or even with Notepad++ macros
Have fun !

Ok, thank you!


[c#] Syntax highlighting problem with SQL text strings

From @mikestre on January 26, 2017 23:0

VSCode Version: Code 1.8.1 (ee428b0eead68bf0fb99ab5fdc4439be227b6281, 2016-12-19T14:41:20.664Z)
OS Version: Linux x64 3.10.0-514.6.1.el7.x86_64
Extensions:

Extension
Author
Version

vscode-docker
PeterJausovec
0.0.11

csharp
ms-vscode
1.6.2

mono-debug
ms-vscode
0.12.0

Steps to Reproduce:
1.Reading  the .NET Core in Action eBook and entered the following code:

CodeSample.txt
2.Syntax highlighting is incorrect for the SQL syntax strings.
Code sample provided as a text file.
Copied from original issue: Microsoft/vscode#19464

Thanks for the report! This is already fixed for the next release:


Invalid TypeScript declaration files in 4.13.0 release

Starting with 4.13.0 release dist contains only bundled index.js and index.d.ts instead of whole directory tree from previous versions.
This generated index.d.ts isn't valid (with typescript 4.7.3 and 4.9.3).
node_modules/starknet/dist/index.d.ts:1124:41 - error TS2708: Cannot use namespace 'Sequencer' as a value.

1124 declare const index$1_Sequencer: typeof Sequencer;
                                             ~~~~~~~~~

node_modules/starknet/dist/index.d.ts:1125:35 - error TS2708: Cannot use namespace 'RPC' as a value.

1125 declare const index$1_RPC: typeof RPC;
                                       ~~~

To reproduce, try building TS project that uses<EMAIL_ADDRESS>for example this.
This change in .d.ts file fixes it, but I'm not sure why broken file was produced:
1124,1125d1123
< declare const index$1_Sequencer: typeof Sequencer;
< declare const index$1_RPC: typeof RPC;
1137,1138c1135,1136
<     index$1_Sequencer as Sequencer,
<     index$1_RPC as RPC,
---
>     Sequencer,
>     RPC,

Thanks! cc: @penovicp

Looks like it's down to how rollup-plugin-dts does the bundling for nested namespaces. I'll see if it can be avoided and if not add a script to adjust the .d.ts with the changes that @Sekhmet identified.

@Sekhmet please check with the new release https://github.com/0xs34n/starknet.js/releases/tag/v4.13.1

@ivpavici it works with 4.13.1, thanks!


Updated ruamel.yaml import to avoid setup.py develop wheels issue

Hi @usmanazFIU, thanks for this fix and going through the tutorials. This fix looks safe to me, but let's also double check which ruamel.yaml version was installed in your venv to be sure, could please do these following things:

run pip freeze | grep yaml:

❯ pip freeze | grep yaml
ruamel.yaml==0.17.19
ruamel.yaml.clib==0.2.6

Could you also try to install this NApp again, without this PR, but instead of running python3 setup.py develop you run pip install -e .? For me it worked without this change here (although we should merge since the instructions/tutorials still use python3 setup.py develop, let's take this opportunity to confirm this on your end too.

Make sure to also update the CHANGELOG.RST file accordingly mentioning what this change is doing, you can insert a line under the UNRELEASED Fixed section.

pip freeze | grep yaml gave me same output. how ever pip install -e did not work out for me.  also I have changed CHANGELOG.RST and pushed the work again

pip freeze | grep yaml gave me same output. how ever pip install -e did not work out for me.  also I have changed CHANGELOG.RST and pushed the work again

@usmanazFIU, thanks for pushing this commit.
1 - Did you try to reinstall in the same venv?  It's worth removing it entirely.
2 - Could you these commands below? Let's see if would work on your end too:
cd /tmp/
git clone https://github.com/kytos-ng/kytos-utils
cd kytos-utils
virtualenv -p python39 venv
source ./venv/bin/activate
pip install -e .
kytos napps list

3 - Let me know also which operating system you're using.

kytos napps list

I have tried a new virtual env and the command now works and it installed successfully. should i now replace python3 setup.py develop with pip install -e.

2 - Could you these commands below? Let's see if would work on your end too:
Yes it worked on my end with new virtual environment

@usmanazFIU, great. The commans will be replaced in a next opportunity on issue #28


AMP Web UI Whitelist page: hit Enter key after entering a user name in text kicks UI back to Status page

Repro steps:

go to the Whitelist screen
click the Add User button
select the text box, enter a name
if you just hit enter while the cursor is still in the text box, the UI goes back to the log in page or the Status page

Expected behavior: hit enter should be the same as clicking the "Whitelist" button

I can reproduce this issue, it's due to a form being incorrectly submitted.

Whitelist UI was removed pending a rewrite.


Added int i and j declarations

Fixed issue with C99 declarations of i,j counters in for loop.

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.


Updating nlohman_json to 3.11 to match MRC

Description
This PR update nlohmann_json to 3.11 to match MRC.
By Submitting this PR I confirm:

I am familiar with the Contributing Guidelines.
When the PR is ready for review, new or existing tests cover these changes.
When the PR is ready for review, the documentation is up to date with these changes.

/merge

/merge


Async Interface IAfterInteract()

I re-wrote the interface and implementations of void IAfterInteract to make it a async Task, rather then a void, so it could be compatible with more functions such as DoAfter().
Please refuse the changes to the yml file and the removal of "IAfterInteract" in the components list of the mop, I tried removing those myself and making a separate commit but git doesn't read it as "changed", so the only way is to be cancelled by maintainers, thanks for your attention,

lmao im retarded revert that latest review

You didn't modify the code in InteractionSystem so the tasks are not consumed correctly there.

Fixed, please review if results are properly coded

Did you forget to push? You didn't make any changes to InteractionSystem.

Yes, something went wrong with the push. Changes are now commited.

Does this build locally? github is saying it dun build

You should honestly go take a crash course on git or get a decent git gui, you've made a couple PRs here now that are completely borked due to you committing seemingly random stuff...

You should honestly go take a crash course on git or get a decent git gui, you've made a couple PRs here now that are completely borked due to you committing seemingly random stuff...

Reasonable, some of the things which get into my commits I myself wonder how did they work out in such a way, but for right now I'd like to first finish this piece of work so I can go work on something simpler, which in turn relies on this being implemented.
Is there anything else need fixing at the moment?

Are there any parts which need alteration or is something so deeply wrong it is better to just close the pull request?

Are there any parts which need alteration or is something so deeply wrong it is better to just close the pull request?

It still doesn't build so you'll need to fix that before it can be reviewed https://github.com/space-wizards/space-station-14/pull/2735/checks?check_run_id=1539144916

Understood. Will be working on it during this week.

Checks run good. Merge?

All done.

All done.
EDIT: You were wrong, the Injector has to be a public function, it causes errors otherwise.

I can make mistakes but in this case I'm right.
Source: Half of these are still explicit implementations.

The function does not compile if not stated as a public async and causes a build error.

You seem to be confused because I'm talking about the ones you changed from explicit interface implementations to just being public methods like the one I commented on.

Are there more explicit implementations or other then the injector everything else seems in order?


Updated the Prime Minister list & Added Tamil Language of Prime Minister Name.

Hi @amir1611 ,
Accepted your pull request.
Thanks for contributing to this repo =)


Dmd uploader is not reseting when the reset button is clicked

During a single file upload the queue is not getting rest

See my response to issue 54. https://github.com/danielm/uploader/issues/54


collections: portalbox text overflow

Hi guys,
I installed the demo site and in home page, in right bar, the text doesn't respect the width of the box.
This css seems to fix the issue:
.panel-body {
word-wrap: break-word;
}

Before

After

From: https://github.com/inveniosoftware/invenio-demosite/issues/38

+1, tested working and browser support seems to be there: http://caniuse.com/#feat=wordwrap

Can you make a PR?


summary error when nn.LSTM(batch_first=True)

File "C:\Users\simon\Desktop\DeepRL.old\deep_rl\agent\PPO_agent.py", line 25, in init
torchsummary.summary(self.network,(100, 2, 11))
......
File "C:\Users\simon\Desktop\DeepRL.old\deep_rl\network\network_bodies.py", line 149, in forward
y, (h_n,c_n) = self.lstm1(x)
File "C:\Anaconda\lib\site-packages\torch\nn\modules\module.py", line 491, in call
hook_result = hook(self, input, result)
File "C:\Anaconda\lib\site-packages\torchsummary\torchsummary.py", line 23, in hook
[-1] + list(o.size())[1:] for o in output
File "C:\Anaconda\lib\site-packages\torchsummary\torchsummary.py", line 23, in
[-1] + list(o.size())[1:] for o in output
AttributeError: 'tuple' object has no attribute 'size'
where:
self.lstm1 = nn_init(nn.LSTM(input_size=self.trace_length, hidden_size=self.n_lstm_units,batch_first=True))

wow,the same question.

Hi,I solve this question#11,have a try!

Hi Puyu,
Thank you. But nn.LSTM(batch_first=True) still returns a tuple.
File "C:\Users\simon\Desktop\DeepRL.old\deep_rl\agent\PPO_agent.py", line 25, in init
torchsummary.summary(self.network,(100, 2, 11))
File "C:\Anaconda\lib\site-packages\torchsummary\torchsummary.py", line 89, in summary
model(*x)
File "C:\Anaconda\lib\site-packages\torch\nn\modules\module.py", line 489, in call
result = self.forward(*input, **kwargs)
File "C:\Users\simon\Desktop\DeepRL.old\deep_rl\network\network_heads.py", line 173, in forward
phi = self.network.phi_body(obs)
File "C:\Anaconda\lib\site-packages\torch\nn\modules\module.py", line 489, in call
result = self.forward(*input, **kwargs)
File "C:\Users\simon\Desktop\DeepRL.old\deep_rl\network\network_bodies.py", line 149, in forward
y, (h_n,c_n) = self.lstm1(x)#(torch.Size([22, 8]), torch.Size([22, 8])), (torch.Size([1, 2, 8]), torch.Size([1, 2, 8]))
File "C:\Anaconda\lib\site-packages\torch\nn\modules\module.py", line 491, in call
hook_result = hook(self, input, result)
File "C:\Anaconda\lib\site-packages\torchsummary\torchsummary.py", line 37, in hook
[-1] + list(o.size())[1:] for o in output
File "C:\Anaconda\lib\site-packages\torchsummary\torchsummary.py", line 37, in
[-1] + list(o.size())[1:] for o in output
AttributeError: 'tuple' object has no attribute 'size'

Hi,
I think that  you don't replace this version of pytorch-summary to Bond-SYSU/pytorch-summary successfully.When I do this,this error doesn't appear.Have a try!

Hi, I actually have the exact same error with lstm and torchsummary and replacing the version didn't help. any ideas on how to solve this?

I couldn't pass multiple inputs to Bond-SYSU version.

Using SummaryX solved my probelm

Using SummaryX solved my probelm

Can you please share the link? Because I either get the error mentioned above or "input must have 3 dimensions, got 4".

Using SummaryX solved my probelm

Can you please share the link? Because I either get the error mentioned above or "input must have 3 dimensions, got 4".

Using SummaryX solved my probelm

Very helpful answer! It works nicely now!
https://github.com/nmhkahn/torchsummaryX

Thank you very much~~

Using SummaryX solved my probelm

Thank you very much!!!


kubevpn: 2.0.1 -> 2.1.0

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://github.com/KubeNetworks/kubevpn/releases.
meta.description for kubevpn is: Create a VPN and connect to Kubernetes cluster network, access resources, and more
meta.homepage for kubevpn is: https://github.com/KubeNetworks/kubevpn
meta.changelog for kubevpn is: https://github.com/KubeNetworks/kubevpn/releases/tag/v2.1.0
Updates performed

Golang update

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
found 2.1.0 with grep in /nix/store/j3bwc996zfk2ha2hik3a7zk56w9dnmlw-kubevpn-2.1.0
found 2.1.0 in filename of file in /nix/store/j3bwc996zfk2ha2hik3a7zk56w9dnmlw-kubevpn-2.1.0

Rebuild report (if merged into master) (click to expand)

1 total rebuild path(s)

1 package rebuild(s)

First fifty rebuilds by attrpath
kubevpn

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/j3bwc996zfk2ha2hik3a7zk56w9dnmlw-kubevpn-2.1.0 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A kubevpn https://github.com/r-ryantm/nixpkgs/archive/e722cec9f858c133f9ecb64733ef64e0bd0e76e7.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/e722cec9f858c133f9ecb64733ef64e0bd0e76e7#kubevpn

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/j3bwc996zfk2ha2hik3a7zk56w9dnmlw-kubevpn-2.1.0
ls -la /nix/store/j3bwc996zfk2ha2hik3a7zk56w9dnmlw-kubevpn-2.1.0/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

1 package built:

kubevpn

Maintainer pings
cc @mig4ng for testing.

2.1.2 is out, please open a new PR.


Adapt checks to fit repo's merge strategy

GitHub PR can be merged in three ways. Let's call them merge, squash, and rebase.

This bot should check the repo's merge button configuration and change its behavior accordingly:

If merge or rebase, then a semantic PR title is not adequate, as it won't become a commit message. In this case, at least one semantic commit is required in the PR.
If squash, then a semantic PR title is required, as any semantic commits in the PR will be squashed.

Further info:
https://developer.github.com/v3/pulls/#merge-a-pull-request-merge-button API can be used to explicitly set the merge_method to squash. This would work if the bot was merging the PRs.
Humans could summon the bot to merge by either adding a label (e.g. merge) or with a comment (e.g. /merge). Note that in the case of using a comment, the bot would have to check that the commenter actually has permission to merge the PR.
Also, an edge case for squash commits (via @francisfuzz):

I was reminded of something I learned about how we treat squash merges recently and would like to share it here in the case it hasn’t been considered by the Electron team.
Squashing a pull request with one commit would use that commit’s message, but squashing a pull request with more than one commit will use the pull request’s title for the commit message.
We have a help-docs issue for it here: https://github.com/github/help-docs/issues/7621

This issue was mostly resolved by #19; the unresolved part is now #17


Trying to reify (M4?.reflect x)) gives error: Bound term variable not found

M4 is a layered effect and I try to write something like: reify (M4?.reflect x) == x. I am not sure if this is the correct way to do it, but it gives me the error F* may be in an inconsistent state. Please file a bug report,.
Code:
module Bug2135

open FStar.Exn

type maybe (a:Type) = either a exn

let m4_post a = maybe a -> Type0
let m4_wpty a = m4_post a -> Type0

unfold
let m4_return_wp (a:Type) (x:a) : m4_wpty a = fun p -> p (Inl x)

unfold
let compute_post (a b:Type) (kw : a -> m4_wpty b) (p:m4_post b)
  : m4_post a =
      (fun result ->
        match result with
        | Inl v -> kw v (fun r' -> p r')
        | Inr err -> p (Inr err))

unfold
let m4_bind_wp (a b:Type) (w : m4_wpty a) (kw : a -> m4_wpty b) : m4_wpty b =
  fun p -> w (compute_post a b kw p)

type io (a:Type) =
| Return : a -> io a

let m4_interpretation #a (m : io a) (p : m4_post a) : Type0 = True

let io_return (a:Type) (x: a) : io a = Return x

// REFINED COMPUTATION MONAD (repr)
let irepr (a:Type) (wp:m4_wpty a) =
  post:m4_post a ->
    Pure (io a)
      (requires (wp post))
      (ensures (fun (t:io a) -> m4_interpretation t post))

let ireturn (a : Type) (x : a) : irepr a (m4_return_wp a x) =
  fun _ -> io_return a x

let w = m4_wpty

unfold
val w_ord (#a : Type) : w a -> w a -> Type0
let w_ord wp1 wp2 = forall p. wp1 p ==> wp2 p

let io_bind (a:Type) (b:Type) (l:io a) (k:a -> io b) : io b =
  match l with
  | Return x -> k x

let ibind (a b : Type) (wp_v : w a) (wp_f: a -> w b) (v : irepr a wp_v)
  (f : (x:a -> irepr b (wp_f x))) : irepr b (m4_bind_wp _ _ wp_v wp_f) =
  fun p ->
    let t = (io_bind a b
        (v (compute_post a b wp_f p))
        (fun x ->
          assume (wp_f x p);
           f x p)) in
    assume (m4_interpretation t p);
    t

unfold
let isubcomp (a:Type) (wp1 wp2: w a) (f : irepr a wp1) :
  Pure (irepr a wp2) (requires w_ord wp2 wp1) (ensures fun _ -> True) = f

unfold
let wp_if_then_else (#a:Type) (wp1 wp2:w a) (b:bool) : w a =
  fun p -> (b ==> wp1 p) /\ ((~b) ==> wp2 p)

unfold
let i_if_then_else (a : Type) (wp1 wp2 : w a) (f : irepr a wp1) (g : irepr a wp2) (b : bool) : Type =
  irepr a (wp_if_then_else wp1 wp2 b)

total
reifiable
reflectable
layered_effect {
  M4wp : a:Type -> wp : m4_wpty a -> Effect
  with
       repr       = irepr
     ; return     = ireturn
     ; bind       = ibind

     ; subcomp      = isubcomp
     ; if_then_else = i_if_then_else
}

let elim_pure #a #wp ($f : unit -> PURE a wp) p
 : Pure a (requires (wp p)) (ensures (fun r -> p r))
 //: PURE a (fun p' -> wp p /\ (forall r. p r ==> p' r))
 // ^ basically this, requires monotonicity
 = FStar.Monotonic.Pure.wp_monotonic_pure ();
   f ()

let lift_pure_m4wp (a:Type) (wp:pure_wp a) (f:(eqtype_as_type unit -> PURE a wp)) :
  Pure (irepr a (fun p -> wp (fun r -> p (Inl r)))) (requires True)
                    (ensures (fun _ -> True))
  = fun p -> let r = elim_pure f (fun r -> p (Inl r)) in io_return _ r

sub_effect PURE ~> M4wp = lift_pure_m4wp

let interstinglemma () : Lemma (
  forall a (x:io a). (
    reify (M4wp?.reflect (fun _ -> x) <: M4wp a (fun p -> forall res. p res)) (fun _ -> True) == x)
) = ()

Error:
(Error) ASSERTION FAILURE: Bound term variable not found  a#21453 in environment: ...,Return, x#22036, x#22032, uu___#22034, uu___#22029, uu___#22028, p#22035, a#22031
F* may be in an inconsistent state.
Please file a bug report, ideally with a minimized version of the program that triggered the error.

Saving here a quick fix given by Guido:
let ref #a (x : io a) : irepr a (fun p -> forall res. p res) = (fun _ -> x)

let interstinglemma () : Lemma (
  forall a (x:io a). (
    reify (M4wp?.reflect (ref x) <: M4wp a (fun p -> forall res. p res)) (fun _ -> True) == x)
) = ()


Question: Can I mount volumes to Cloud Run?

Some of my applications need to store configuration files on volumes inside the cluster (the Grafana container, for example) and I sometimes use volumes to store service accounts (Pub/Sub publisher and reader, storage owned and so on). I do that by configuring my volumeMounts and volumes on my deployment.yaml.

Today, the answer depends on whether you’re using Cloud Run –OR– Cloud Run on GKE.
Which one are you using?

Hi ahmetb, thanks for answering.
Currently we are trying with Cloud Run on GKE.
Our plan is to use Cloud Run to autoscale some of our APIs that have high usage during the day and 0 at night.

The answer would be yes on GKE. It appears like this is not documented very well, so I'm raising a ticket to Knative documentation (https://github.com/knative/docs/issues/1413) and we'll be looking at documenting this on Cloud Run website as well.
If you’re writing YAML manifests as you said, take a look at Knative Secrets sample which uses volumes & volumeMounts fields, just like in Kubernetes. Any valid Kubernetes volume spec that works in your cluster should be also working on your Knative Service spec.