Error 500

Hello.
I install this module on my presta 1.7.3
I got php 7.1
I can't install from backoffice and load file from PC becouse is error.
But i send gamefications folder to the /modules and after check backoffice i got error 500.
When i ON debug mode it's error :
Compile Error: Gamifications::requireAutoloader(): Failed opening required '/var/www/prestashop/modules/gamifications/vendor/autoload.php' (include_path='/var/www/prestashop/vendor/pear/pear_exception:/var/www/prestashop/vendor/pear/console_getopt:/var/www/prestashop/vendor/pear/pear-core-minimal/src:/var/www/prestashop/vendor/pear/archive_tar:.:/usr/share/php')
500 Internal Server Error - FatalErrorException

Stack Trace
in modules/gamifications/gamifications.php at line 302   -
     */
    private function requireAutoloader()
    {
        require_once $this->getLocalPath().'vendor/autoload.php';
    }
}
Logs   -
1 error
INFO - The Sensio\Bundle\DistributionBundle\Controller\ConfiguratorController class extends Symfony\Component\DependencyInjection\ContainerAware that is deprecated since version 2.8, to be removed in 3.0. Use the ContainerAwareTrait instead.
INFO - Matched route "admin_module_manage".
DEBUG - Read existing security token from the session.
DEBUG - User was reloaded from a user provider.
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\DebugHandlersListener::configure".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\ProfilerListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\ValidateRequestListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Bundle\FrameworkBundle\EventListener\SessionListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\FragmentListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\RouterListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\LocaleListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "PrestaShopBundle\EventListener\UserLocaleListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\TranslatorListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\Security\Http\Firewall::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "PrestaShop\PrestaShop\Adapter\Security\Admin::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "PrestaShop\PrestaShop\Adapter\Security\SslMiddleware::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "PrestaShopBundle\EventListener\TokenizedUrlsListener::onKernelRequest".
DEBUG - Notified event "kernel.controller" to listener "PrestaShopBundle\EventListener\ActionDispatcherLegacyHooksSubscriber::callActionDispatcherBeforeHook".
DEBUG - Notified event "kernel.controller" to listener "Symfony\Bundle\FrameworkBundle\DataCollector\RouterDataCollector::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Symfony\Component\HttpKernel\DataCollector\RequestDataCollector::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\ControllerListener::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\ParamConverterListener::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\HttpCacheListener::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\SecurityListener::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\TemplateListener::onKernelController".
DEBUG - SELECT p0_.id AS id_0, p0_.id_employee AS id_employee_1, p0_.id_module AS id_module_2, p0_.date_add AS date_add_3, p0_.date_upd AS date_upd_4 FROM ps_module_history p0_ WHERE p0_.id_employee = ?
CRITICAL - Uncaught PHP Exception Symfony\Component\Debug\Exception\FatalErrorException: "Compile Error: Gamifications::requireAutoloader(): Failed opening required '/var/www/prestashop/modules/gamifications/vendor/autoload.php' (include_path='/var/www/prestashop/vendor/pear/pear_exception:/var/www/prestashop/vendor/pear/console_getopt:/var/www/prestashop/vendor/pear/pear-core-minimal/src:/var/www/prestashop/vendor/pear/archive_tar:.:/usr/share/php')" at /var/www/prestashop/modules/gamifications/gamifications.php line 302
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\DebugHandlersListener::configure".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\ProfilerListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\ValidateRequestListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Bundle\FrameworkBundle\EventListener\SessionListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\FragmentListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\RouterListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\LocaleListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "PrestaShopBundle\EventListener\UserLocaleListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\HttpKernel\EventListener\TranslatorListener::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "Symfony\Component\Security\Http\Firewall::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "PrestaShop\PrestaShop\Adapter\Security\Admin::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "PrestaShop\PrestaShop\Adapter\Security\SslMiddleware::onKernelRequest".
DEBUG - Notified event "kernel.request" to listener "PrestaShopBundle\EventListener\TokenizedUrlsListener::onKernelRequest".
DEBUG - SELECT name FROM ps_module WHERE active = 1
DEBUG - Notified event "kernel.controller" to listener "PrestaShopBundle\EventListener\ActionDispatcherLegacyHooksSubscriber::callActionDispatcherBeforeHook".
DEBUG - Notified event "kernel.controller" to listener "Symfony\Bundle\FrameworkBundle\DataCollector\RouterDataCollector::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Symfony\Component\HttpKernel\DataCollector\RequestDataCollector::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\ControllerListener::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\ParamConverterListener::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\HttpCacheListener::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\SecurityListener::onKernelController".
DEBUG - Notified event "kernel.controller" to listener "Sensio\Bundle\FrameworkExtraBundle\EventListener\TemplateListener::onKernelController".

Hi, you missed 2nd installation step. Before installing module, you should run composer install command. :)

Guys, do you know how to install this composer on debian 8, php 7.1  ?
Becouse i'm not perfect with this so i don't know how to use this composer install.

did you cd (change folder in ssh) to gamifications before launching the composer install?
i have shared hosting so everything is installed, sorry i cant help you any further

I have updated module with generated autoload files, there's no need to run composer install anymore.

Hey guys!
I tried to install the addons as registered in the ''readme''.
I got this answer when I typed ''composer install'':
Loading composer repositories with package information Updating dependencies (including require-dev) Nothing to install or update Generating autoload files
For your information, yes I did it in the right directory. Gamifications, there is another one without a ''s''.
I tried it wihout using the composer command and it doesn't appear in my addons list.
I also tried to zip it, both of them, the one with the composer install apllied and the other one without it.
I got: "500 Internal Server Error"
Help me please, I really want to use that addons. Thank you very much
I use:
Prestashop <IP_ADDRESS>
PHP 7.0.32
Ubuntu Server 16.04.1
Zend Engine v3.0.0,
Zend OPcache v7.0.32
Apache 2.4.35
Pagespeed <IP_ADDRESS>-stable

hi @xsteacy, this module was not tested on PS <IP_ADDRESS>. However, i cannot say why its not working, because error 500 Internal Server Error is too generic, you should enable debug mode on your shop and check for more accurate error. Let me know if you need more help. :)


Scalability issues: App shows excessive refreshes during use

@CTLocalGovTeam
We have received feedback indicating the 511 app does not scale.  Looking at Fiddler while using the app, we can see that there is a large number of refreshes when using the app.
To repro:

start fiddler
launch the 511 app and click okay to the splash screen
note that in Fiddler, you see a series of ~42 requests to the server for a single pan of the map.

Please look into this issue as soon as possible.  Do we need to change how the app fetches data?

This app has been replaced by the new Transportation 511.  No action required at this time.


Remove _symTransformer until official spec is worked out.

Prompted by cognitect-labs/transducers-js#20 from @tgriesser, removing
the internal transformer symbol until issues are worked out. This symbol
is currently only supported in jlongster/transducers.js and
interoperability is questionable as (Symbol('transformer') !==
Symbol('transformer')).
This feature was not documented, nor do the tests depend on it, and
only effects an undocumented feature of into. Better to remove it now
until details are worked out.  If an "official spec" is agreed upon,
I will open a new PR.

:cow2:

Removed parens in _isTransformer per @davidchambers

:deciduous_tree:


3299 allocation with codes

Context
Changes proposed in this pull request
Guidance to review
Checklist

[ ] Make sure all information from the Trello card is in here
[ ] Attach to Trello card
[ ] Rebased master
[ ] Cleaned commit history
[ ] Tested by running locally

 [M] Fix last years allocation on data


CTC ERROR WITH CUDA ILLEGAL MEMORY ACCESS ERROR

For bugs or installation issues, please provide the following information.
The more information you provide, the more likely people will be able to help you.
Environment info
Operating System: Ubuntu14.04
Compiler: install by pip
Package used (Python/R/Scala/Julia): python
MXNet version:0.11
Error Message:
Please paste the full error message, including stack trace.
  File "/usr/local/lib/python2.7/dist-packages/mxnet/module/module.py", line 680, in update_metric
[21:29:57] /home/travis/build/dmlc/mxnet-distro/mxnet-build/dmlc-core/include/dmlc/logging.h:304: [21:29:57] src/engine/./threaded_engine.h:329: [21:29:57] /home/travis/build/dmlc/mxnet-distro/mxnet-build/mshadow/mshadow/./stream_gpu-inl.h:55: Check failed: e == cudaSuccess CUDA: an illegal memory access was encountered

Stack trace returned 10 entries:
[bt] (0) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0x19fd3c) [0x7f6953c81d3c]
[bt] (1) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xcf7eb8) [0x7f69547d9eb8]
[bt] (2) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd4a300) [0x7f695482c300]
[bt] (3) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd32dfc) [0x7f6954814dfc]
[bt] (4) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd35a78) [0x7f6954817a78]
[bt] (5) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd35c75) [0x7f6954817c75]
[bt] (6) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd33b1b) [0x7f6954815b1b]
[bt] (7) /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb1a60) [0x7f69420bca60]
[bt] (8) /lib/x86_64-linux-gnu/libpthread.so.0(+0x8184) [0x7f6963d65184]
[bt] (9) /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7f6963a91ffd]

An fatal error occurred in asynchronous engine operation. If you do not know what caused this error, you can try set environment variable MXNET_ENGINE_TYPE to NaiveEngine and run with debugger (i.e. gdb). This will force all operations to be synchronous and backtrace will give you the series of calls that lead to this error. Remember to set MXNET_ENGINE_TYPE back to empty after debugging.

Stack trace returned 8 entries:
[bt] (0) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0x19fd3c) [0x7f6953c81d3c]
[bt] (1) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd33094) [0x7f6954815094]
[bt] (2) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd35a78) [0x7f6954817a78]
[bt] (3) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd35c75) [0x7f6954817c75]
[bt] (4) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd33b1b) [0x7f6954815b1b]
[bt] (5) /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb1a60) [0x7f69420bca60]
[bt] (6) /lib/x86_64-linux-gnu/libpthread.so.0(+0x8184) [0x7f6963d65184]
[bt] (7) /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7f6963a91ffd]

terminate called after throwing an instance of 'dmlc::Error'
  what():  [21:29:57] src/engine/./threaded_engine.h:329: [21:29:57] /home/travis/build/dmlc/mxnet-distro/mxnet-build/mshadow/mshadow/./stream_gpu-inl.h:55: Check failed: e == cudaSuccess CUDA: an illegal memory access was encountered

Stack trace returned 10 entries:
[bt] (0) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0x19fd3c) [0x7f6953c81d3c]
[bt] (1) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xcf7eb8) [0x7f69547d9eb8]
[bt] (2) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd4a300) [0x7f695482c300]
[bt] (3) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd32dfc) [0x7f6954814dfc]
[bt] (4) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd35a78) [0x7f6954817a78]
[bt] (5) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd35c75) [0x7f6954817c75]
[bt] (6) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd33b1b) [0x7f6954815b1b]
[bt] (7) /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb1a60) [0x7f69420bca60]
[bt] (8) /lib/x86_64-linux-gnu/libpthread.so.0(+0x8184) [0x7f6963d65184]
[bt] (9) /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7f6963a91ffd]

An fatal error occurred in asynchronous engine operation. If you do not know what caused this error, you can try set environment variable MXNET_ENGINE_TYPE to NaiveEngine and run with debugger (i.e. gdb). This will force all operations to be synchronous and backtrace will give you the series of calls that lead to this error. Remember to set MXNET_ENGINE_TYPE back to empty after debugging.

Stack trace returned 8 entries:
[bt] (0) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0x19fd3c) [0x7f6953c81d3c]
[bt] (1) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd33094) [0x7f6954815094]
[bt] (2) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd35a78) [0x7f6954817a78]
[bt] (3) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd35c75) [0x7f6954817c75]
[bt] (4) /usr/local/lib/python2.7/dist-packages/mxnet/libmxnet.so(+0xd33b1b) [0x7f6954815b1b]
[bt] (5) /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb1a60) [0x7f69420bca60]
[bt] (6) /lib/x86_64-linux-gnu/libpthread.so.0(+0x8184) [0x7f6963d65184]
[bt] (7) /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7f6963a91ffd]

Minimum reproducible example
if you are using your own code, please provide a short script that reproduces the error.
For mxHelper below, see https://github.com/jiarenyf/mxWrapper ...
# -*- coding: utf8 -*-

import os
os.environ['MXNET_CPU_WORKER_NTHREADS'] = '4'

import numpy as np
import mxnet as mx
import mxHelper as mh

class MyCTC(object):
    def __init__(self):
        self.model = './model'

        self.kind = 21
        self.labelLen = 8
        self.inputLen = 20
        self.batchSize = 100
        self.batchShape = (100, 3, 48, 160)

    def loadData(self):
        mean, std = np.array([128.0]), np.array([128.0])

        lines1 = open('./train_ctc.txt').readlines()
        for i, line in enumerate(lines1):
            path, labels = line.split()[:2]
            labels = map(lambda l: int(l)+1, labels.split(','))
            labels += [0]*(self.labelLen-len(labels))
            lines1[i] = [labels, path]

        self.trainI = mx.image.ImageIter(
            self.batchSize, self.batchShape[1:], self.labelLen,
            path_root='./', imglist=lines1, shuffle=True,
            data_name='datas', label_name='labels', mean=mean, std=std,
            brightness=0.5, contrast=0.5, saturation=0.5, pca_noise=0.5
        )

        lines2 = open('./test_ctc.txt').readlines()
        for i, line in enumerate(lines2):
            path, labels = line.split()[:2]
            labels = map(lambda l: int(l)+1, labels.split(','))
            labels += [0]*(self.labelLen-len(labels))
            lines2[i] = [labels, path]

        self.testI = mx.image.ImageIter(
            self.batchSize, self.batchShape[1:], self.labelLen,
            path_root='./', imglist=lines2, shuffle=False,
            data_name='datas', label_name='labels', mean=mean, std=std,
        )

    def initNet(self):
        self.x = mh.var('datas', self.batchShape)
        self.y = mh.var('labels', (self.batchSize, self.labelLen))

        layer = self.x

        layer = mh.convBnRelu(layer, 16, (3,3), (2,2), (1,1))

        layer = mh.ResBlocks(layer, 16, 3)
        layer = mh.ResBlock(layer, 16, 32)
        layer = mh.ResBlocks(layer, 32, 5)
        layer = mh.ResBlock(layer, 32, 64)
        layer = mh.ResBlocks(layer, 64, 10)

        layer = mh.convBnRelu(layer, self.kind, (6,1), (1,1))
        layer = mh.reshape(layer, (0, 0, -3))

        self.net = mh.ctcLoss(layer, self.y)

    def train(self):
        self.initNet()
        self.loadData()

        self.m = mh.MyModule(
            symbol=self.net, context=mx.gpu(),
            data_names=['datas'], label_names=['labels']
        )

        lr = mx.lr_scheduler.FactorScheduler(step=508*100, factor=0.1)
        self.m.fit(
            self.trainI, self.testI,
            model=self.model, numEpoch=1500,
            optimizer='sgd', optimizerParams={
                'learning_rate': 0.1, 'lr_scheduler': lr,
                'momentum': 0.9, 'wd': 0.0005,
            },
            metric=mh.ctcAccuracy(self.batchSize, self.inputLen, 100),
        )

if __name__ == '__main__':
    m = MyCTC()
    m.train()

###

Thank you very mush if any one can solve my problem ...

@szha

@jiarenyf Which version are you using? 0.11.0 or 0.11.1? What's the output of
python -c 'import os, mxnet; print open(os.path.join(os.path.dirname(mxnet.__file__), "COMMIT_HASH")).readline().strip()'

@szha
I install 2 versions of mxnet on different pc:
1, mxnet-cu80==0.10.0.post2 and "d220e192897da763ed8e8a6135f9e8b24cc1a2ce"
2, mxnet-cu80==0.11.0rc3 and "53274b4a2b0d73f3fbdb10cfb5f9ed0c8263fda7"
And both have the problem mention above ...

@szha
I install 2 versions of mxnet on different pc:
1, mxnet-cu80==0.10.0.post2 and "d220e192897da763ed8e8a6135f9e8b24cc1a2ce"
2, mxnet-cu80==0.11.0rc3 and "53274b4a2b0d73f3fbdb10cfb5f9ed0c8263fda7"
And both have the problem mention above ...

Do you mind sharing a small chunk of data so that I can run the program and debug?

@szha
Link：http://pan.baidu.com/s/1o7Zpc06
Password：plmp
Sometimes it could train for several epochs, but finally it always occurs the problem ...

@szha
Link：http://pan.baidu.com/s/1o7Zpc06
Password：plmp
Sometimes it could train for several epochs, but finally it always occurs the problem ...

@jiarenyf unfortunately I wasn't able to reproduce the problem. I'm using an EC2 p2 host which has K80 GPUs. I was able to run 70 epochs without problem. Also, I'm running from the current head of mxnet.
INFO:root:Epoch[100] Time cost=2.508 ...

Could it be hardware/driver issue?

@szha
I found that when adding forceResize in the imageIter-kwargs, the problem solved ...

Thanks. Good to know.

@szha
I found that the problem is not because of the data, but maybe because of the local variables in python functions that are collected by the gc, such that the cuda access illegal memory.
And I add "gc.disable()" at the beginning of each epoch, and then add "gc.enable()" at the end of each epoch, the problem never occurs at least for 5 days .
I think maybe this could help you to debug ...

@jiarenyf thanks. Does it still happen if you use the latest nightly build?

@szha
Yes. I have updated to the version 0.11.0 by "pip install mxnet-cu80==0.11.0".

@jiarenyf the nightly build is on 0.11.1. You can get it by using pip install -U --pre mxnet-cu80

@szha
I found another reason of that problem.
As in "https://github.com/jiarenyf/mxWrapper/blob/02fd9b0fcd37f7224648efad651a6f83a1f06d78/mxHelper/mxData.py#L158", the labels is initialize to empty, while in "https://github.com/jiarenyf/mxWrapper/blob/02fd9b0fcd37f7224648efad651a6f83a1f06d78/mxHelper/model/model.py#L98", it directly uses batch.label without considering the batch.pad.
So if not meets "data size % batch size ==0", the error occurs when accessing empty labels.
And the data set I offered you to debug has 800 images, and it meets: "800 % 100 == 0" (100 is batch size). So the problem never occurs on your workplace.
I found this problem because I happen to change the train set size to 111 and the test size to 33, where "111+33 % 100 != 0".
And after I add "https://github.com/jiarenyf/mxWrapper/blob/02fd9b0fcd37f7224648efad651a6f83a1f06d78/mxHelper/mxData.py#L169" (remove empty), and change "https://github.com/jiarenyf/mxWrapper/blob/02fd9b0fcd37f7224648efad651a6f83a1f06d78/mxHelper/mxData.py#L170" (set "pad" to 0), then the problem does not occur.
I wonder is there some error or bug in my implementation: "https://github.com/jiarenyf/mxWrapper/blob/master/mxHelper/model/model.py" ?


FancyZones not remembering window positions on second monitor.

Microsoft PowerToys version
0.67.0
Installation method
GitHub, PowerToys auto-update
Running as admin
Yes
Area(s) with issue?
FancyZones
Steps to reproduce
As of 0.66.0 windows that were placed on my second monitor no longer remember the zone they were in when closing and re-opening. When moving those windows to the primary monitor, they stick and open exactly where they were assigned. But when set to and closed on the secondary monitor, they'll open on the last zone they were set to on the primary monitor. The position data for secondary monitor apps doesn't appear to be getting saved properly.
Tried things such as refreshing the layout editor, restarting PT in and out of admin mode, and fully restarting..
W10H 22H2 (19045.2546)
WFEP 120.2212.4190.0
✔ Expected Behavior
Proper snapping to zones on secondary monitor.
❌ Actual Behavior
Snapping to previously known position on primary monitor.
Other Software
No response

Hi @BlackWyvern, can you please help me investigate the problem?
In case you have several locations saved for the app, first FancyZones will try to find a zone for the opened window on the active monitor. Does it work for you? To check, move your mouse to the secondary monitor and open the window.
If the window wasn't snapped on the active monitor, FancyZones will search for the location on the primary monitor and then on the others. So, it could help to unsnap the window from the primary monitor to always open the window in the zone on the secondary monitor.
Please let me know if it helps.

Yes, but also no. My main culprit is my explorer.exe window. I've managed to finally get it to close and re-open on the second monitor, but it will not snap to the zones it should be assigned to. but all my second-monitor programs exhibit this issue.
As for the troubleshooting, yes. If I make a new folder on the second monitor, and open it from there, it snaps in place properly. If I open explorer from my main monitor, or my start menu it opens at MS's last location; IE. not snapped into anything.
The same goes for my cmd, powershell, steam, discord, and firefox windows, as those all launch either on start, or exclusively from my main monitor start menu.
Looking at things a little closer though, you are absolutely right. I can see the behavior being tied to the cursor position as you say. But, that makes it a bit asinine.
The option is "Move newly created windows to their last known zone." Not "Move newly created windows to their last known zone (if you happen to have your mouse cursor on the monitor that they were last closed on.)"
Any way to disable that behavior? I'd like things to just stay where I stick em.

I guess you have also Move newly created windows to the current active monitor option enabled. Am I right?
It's a separate option that also affects what happens with the newly created window.

I do not have that option enabled. It does the exact opposite of what I want it to do, and the text is quite clear on that.
As I said, the windows are placed on the correct monitor, but will not snap into position unless I launch them directly from the second monitor.

Thank you for the clarification.

I have the same problem in the version  0.67.1

This was resolved with 0.68 build of PowerToys with PR #24290!


Move all classes used by blaze3d classes to com.mojang.blaze3d package

Some classes aren't really client-dedicated such as Snooper. Moreover, those used classes are more or less rendering libraries instead of classes that perform rendering logic.

Yes, based on the class name order, all classes between ctb and cut belong in blaze3d: https://gist.github.com/Runemoro/e8c45aabc8f7048d0414e42ea338d510
Snooper is probably misnamed. It has nothing to do with the snooper.

I think we should just wait for the full adaptation to your/jamierocks's notes and order-based information which I want to pull off on the 1.15 snapshot jump.

most mojang packaging is fine, though we maty revise some (like the package for text)

I want to close this one because this will cause some classes like SystemUtil be moved to b3d package (while it never belongs there)

SystemUtil isn't in the blaze3d package, it's in net.minecraft. See https://gist.github.com/Runemoro/e8c45aabc8f7048d0414e42ea338d510.

but it was used by b3d so according to my old logic it will go com mojamg, which is wrong

Still, I personally think the blaze3d classes should be separated from the rest. We don't have to use com.mojang.blaze3d (though I don't see why not), but putting everything in com.mojang.render doesn't make sense. It's clearly a separate, almost independent, library, and I'm guessing that they will eventually make it fully independent (are they still planning on open-sourcing it?)

I'd wait for mojang to cut it clean before we cut it clean


Migrate async to waitForAsync

async from @angular/core/testing is deprecated in Angular v12. Migrate to waitForAsync
See #410 for a wip example.

Hello, I would love to contribute!

Hi, I did a Pull request with the necessary change
see: #412

@manekinekko I think this one can be closed now that #412 has landed?


Mergify: configuration update

This change has been made by @thitch97 from https://mergify.io simulator.

Mergify commands and options

More conditions and actions can be found in the documentation.
You can also trigger Mergify actions by commenting on this pull request:

@Mergifyio refresh will re-evaluate the rules
@Mergifyio rebase will rebase this PR on its base branch
@Mergifyio update will merge the base branch into this PR
@Mergifyio backport <destination> will backport this PR on <destination> branch

Additionally, on Mergify dashboard you can:

look at your merge queues
generate the Mergify configuration with the simulator.

Finally, you can contact us on https://mergify.io/

Trying this out with the strict rebase option, it may cause issues when multiple PRs come in. If so, strict merge might be a suitable replacement.

I guess we can try and see how it works out


Convert examples to reusable controller agnostic apps

Add trait that implements necessary HCI features
Add example apps crate referenced by board crates

This approach deduplicates a lot of the example app logic to focus on BLE use cases, which can be reused for different boards. This ensures consistency and reduces maintenance.

/test


Uploading app to Teams issue

Hi Guys,
I have been in touch with Microsoft Support regarding this Icebreaker app. They have advised to reach out to the developers as there is an issue on both my end and their end when uploading. I have attached this error.
Could you advise the steps needed to be able to upload this app? Thanks

Hi @gavinbeere1 ,
Could you try validating the JSON with the 'App Studio' in Teams?
Follow these steps to add the App Studio to your Teams environment, then use the validator to check for manifest errors:
https://docs.microsoft.com/en-us/microsoftteams/platform/concepts/build-and-test/app-studio-overview

Hi @gavinbeere1 ,
Could you try validating the JSON with the 'App Studio' in Teams?
Follow these steps to add the App Studio to your Teams environment, then use the validator to check for manifest errors:
https://docs.microsoft.com/en-us/microsoftteams/platform/concepts/build-and-test/app-studio-overview

Hi @gavinbeere1  ,
Could you try validating the JSON with the 'App Studio' in Teams?
Follow these steps to add the App Studio to your Teams environment, then use the validator to check for manifest errors:
https://docs.microsoft.com/en-us/microsoftteams/platform/concepts/build-and-test/app-studio-overview

Hi @gavinbeere1  ,
Could you try validating the JSON with the 'App Studio' in Teams?
Follow these steps to add the App Studio to your Teams environment, then use the validator to check for manifest errors:
https://docs.microsoft.com/en-us/microsoftteams/platform/concepts/build-and-test/app-studio-overview

Hi Rutger,
So I ran the .zip package through the validator and it failed with the below error code:

I have also attached the .zip package too.
Icebreaker.zip
Let me know the next steps, thank you!

Hi Rutger,
So I ran the .zip package through the validator and it failed with the below error code:

I have also attached the .zip package too.
Icebreaker.zip
Let me know the next steps, thank you!

Hi @gavinbeere1 ,
Please update the manifest.json with the correct and valid privacyURL and termsofUseURL.
This should include 'https://' and shouldn't start with www.

Hi @gavinbeere1 ,
Please update the manifest.json with the correct and valid privacyURL and termsofUseURL.
This should include 'https://' and shouldn't start with www.

Hi there,
Thank you! That worked for me!
Kind regards,
On Tue, Jan 26, 2021 at 10:21 AM KnijnOps<EMAIL_ADDRESS>wrote:

Hi @gavinbeere1 https://github.com/gavinbeere1 ,
Please update the manifest.json with the correct and valid privacyURL and
termsofUseURL.
This should include 'https://' and shouldn't start with www.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/OfficeDev/microsoft-teams-apps-icebreaker/issues/122#issuecomment-767446761,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AIBBTOXVIFQWR5ZVZAR262LS32JSZANCNFSM4WOTYCGA
.

Hi there,
Thank you! That worked for me!
Kind regards,
On Tue, Jan 26, 2021 at 10:21 AM KnijnOps<EMAIL_ADDRESS>wrote:

Hi @gavinbeere1 https://github.com/gavinbeere1 ,
Please update the manifest.json with the correct and valid privacyURL and
termsofUseURL.
This should include 'https://' and shouldn't start with www.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/OfficeDev/microsoft-teams-apps-icebreaker/issues/122#issuecomment-767446761,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AIBBTOXVIFQWR5ZVZAR262LS32JSZANCNFSM4WOTYCGA
.

@gavinbeere1 Don't forget to close the report if it's still working :)


How to add a new version

I will try to compile the instructions for adding a new version to the build matrix, since cudatoolkit is only one part of the CUDA ecosystem on conda-forge and it's not trivial. We can extend this as needed and pin the issue, move to the documentation or whatever you prefer.

Add the cudatoolkit packages in this feedstock.
Submit the version migration to conda-forge-pinning-feedstock. This will stay open during the following steps.
For Linux, add the corresponding Docker images at docker-images. Copy the migration file manually to .ci_support/migrations. This copy should not specify a timestamp. Comment it out! Rerender.
For Windows, add the installer URLs and hashes in conda-forge-ci-setup. The manual migration must also be performed here. Rerender.
Create the new nvcc  packages for the new version. Again, manual migration must be added. Rerender.
After careful testing, consider merging the migration now so it can apply to all the downstream feedstocks.

Note: CUDA 11 and above might need manual edits to make sure the corresponding YML files under .ci_support specify cdt_name: cos7 and zipped_keys: - [docker_image, cuda_compiler_version, cdt_name].

Thanks for putting this together Jaime! 😄
Should we start moving this kind of information to the docs? 🙂

That'd work too! I'll add to my list for December :)

Added as part of https://github.com/conda-forge/conda-forge.github.io/pull/1226


BlockFetcher/BlockUploader: fix and add additional attributes

Close #3631

2024-10-23T08:34:53.2882722Z failed to load account: open wallet: open ./not-exist.json: no such file or directory
2024-10-23T08:34:53.2883695Z failed to decode container ID: invalid length 3
2024-10-23T08:34:53.2885040Z failed to create RPC client: failed to get network magic: Post "https://test": dial tcp: lookup test on <IP_ADDRESS>:53: server misbehaving
2024-10-23T08:34:53.2887105Z     logger.go:146: 2024-10-23T08:34:47.157Z	DEBUG	processing rpc request	{"method": "getversion", "params": "[]"}
2024-10-23T08:34:53.2889593Z     logger.go:146: 2024-10-23T08:34:47.157Z	DEBUG	processing rpc request	{"method": "getnativecontracts", "params": "[]"}
2024-10-23T08:34:53.2892126Z     logger.go:146: 2024-10-23T08:34:47.242Z	DEBUG	done processing headers	{"headerIndex": 2, "blockHeight": 1, "took": "167.934µs"}
2024-10-23T08:34:53.2894727Z     logger.go:146: 2024-10-23T08:34:47.343Z	DEBUG	done processing headers	{"headerIndex": 3, "blockHeight": 2, "took": "175.388µs"}
2024-10-23T08:34:53.2896538Z failed to dial NeoFS pool: at least one node must be healthy
2024-10-23T08:34:53.2897437Z     executor.go:239:
2024-10-23T08:34:53.2898879Z         	Error Trace:	/home/runner/work/neo-go/neo-go/internal/testcli/executor.go:239
2024-10-23T08:34:53.2901236Z         	            				/home/runner/work/neo-go/neo-go/internal/testcli/executor.go:244
2024-10-23T08:34:53.2903266Z         	            				/home/runner/work/neo-go/neo-go/cli/util/util_test.go:212
2024-10-23T08:34:53.2904473Z         	Error:      	Received unexpected error:
2024-10-23T08:34:53.2905309Z         	            	EOF
2024-10-23T08:34:53.2905991Z         	Test:       	TestUploadBin
2024-10-23T08:34:53.2907547Z     logger.go:146: 2024-10-23T08:34:47.380Z	INFO	shutting down RPC server	{"endpoint": "<IP_ADDRESS>:40959"}
2024-10-23T08:34:53.2910442Z     logger.go:146: 2024-10-23T08:34:47.380Z	INFO	persisted to disk	{"blocks": 3, "keys": 163, "headerHeight": 3, "blockHeight": 3, "took": "68.588µs"}
2024-10-23T08:34:53.2912386Z --- FAIL: TestUploadBin (0.24s)
2024-10-23T08:34:53.2912861Z FAIL


Demo not working

I've tried open the  demo to know the project, but the page don't load.

What exception do you have faced?

Aparently was an issue with my corporate proxy. Thank you.


Coverlet support SDK version 2.2.207

Description
Coverlet should be supported since SDK version 2.2.300 that was released in 2019-05-21.
After that a version 2.2.8 was released with SDK 2.2.207 in 2019-11-19 and in this version coverlet is no more supported and throws exception
Steps to reproduce
You can follow @PureKrome repro https://github.com/coverlet-coverage/coverlet/issues/1078#issue-798889883
Expected behavior
I think it should work because it was released after 2.2.300 version
Actual behavior
Throws exception
Starting test execution, please wait...
Data collector 'XPlat code coverage' message: [coverlet]System.MissingMethodException: Make sure to use .NET core SDK Version >= 2.2.300 ---> System.MissingMethodException: Method not found: '!!0 Microsoft.VisualStudio.TestPlatform.ObjectModel.DataCollection.SessionStartEventArgs.GetPropertyValue(System.String)'.
   at Coverlet.Collector.DataCollection.CoverletCoverageCollector.GetPropertyValueWrapper(SessionStartEventArgs sessionStartEventArgs)
   at Coverlet.Collector.DataCollection.CoverletCoverageCollector.GetTestModules(SessionStartEventArgs sessionStartEventArgs) in /_/src/coverlet.collector/DataCollection/CoverletCoverageCollector.cs:line 195
   --- End of inner exception stack trace ---
   at Coverlet.Collector.DataCollection.CoverletCoverageCollector.GetTestModules(SessionStartEventArgs sessionStartEventArgs) in /_/src/coverlet.collector/DataCollection/CoverletCoverageCollector.cs:line 206
   at Coverlet.Collector.DataCollection.CoverletCoverageCollector.OnSessionStart(Object sender, SessionStartEventArgs sessionStartEventArgs) in /_/src/coverlet.collector/DataCollection/CoverletCoverageCollector.cs:line 127.

Ref issue https://github.com/coverlet-coverage/coverlet/issues/1078

A further note to the VSTest team: I understand that SDK 2.2.* is now classified as unsupported / EOF (and we should all be upgrading to 3.1.* or 5.*), but it feels like is an unfair regression which breaks compatability?

Based on talk with @MarcoRossignoli  closing this as won't fix.

Yep I think it's ok that SDK is also out of support.


Backport only if before Win32-<IP_ADDRESS>?

I understand that it was Win32-<IP_ADDRESS> that fixed the ntdll-related problem. Consequently, I wondered if the criteria for not backporting should be: # if MIN_VERSION_Win32(2,5,3) rather than the existing # if MIN_VERSION_Win32(2,5,0)?

None of Win32 versions 2.5.0 through 2.5.2 were ever bundled with GHC, so the chances of anyone building against them are quite slim. Still, I suppose it couldn't hurt to be safe here.

I've uploaded mintty-0.1.2 to Hackage with a fix.


Support for changing TextBlock text

 TextBlock Button_Text = Window.GetElementByName<TextBlock>("Button_Text");
Currently the above is not working as we cannot select the textblock in order to modify it's content.

Resolved, Should have selected the element as MGTextBlock


add unicode char literal

generic lexer
add support for unicode char literals
'\uxxx' and '\Uxxx'

version <IP_ADDRESS>


Negative affects of performance with execution by calling HostFunctions

Background
Hi cosmwasmers~ I got an issue regarding the execution performance.
We have migrated cosmwasm into OKTChain and OKBChain and now doing some requisite tests. while the pressure testing with contract interact, we found out that performance are limited by calling host-function.
this is a huge performance gap between WASM and EVM while calling host-function. here is the performance analysis
Phenomenon

The upper image shows that call db_read in wasm contract over 1m times and all time cost has been collected include do_db_read
The result indicated that over 75% time costs were used by cosmwasm dispatch code
I numbered those functions and calculate the time costs and separate it to the different functions
Read_region(388) + process_gas_info(423)+write_to_contract(2248) = 3059.  It means 62%(3059 / 4870) time costs were used by those functions
It should be optimized cause those codes are not requisite logical codes and I believe that codes can be optimized by someway. once the code has been optimized, there must have a considerable increases of performance for cosmwasm.

The issue purpose
We are highly requesting that your team members who could fix this issue asap as the performance is really important for the chains especially the WASM chain @ethanfrey  @webmaster128
Thank you very much and our team will keep touching on it ~
Sincerely Yours

Thank you for the detailed report. I have a few question before investigating further:

Which version of cosmwasm-vm or wasmvm do you use?
How large is the data you read in Store.get (both key and value)?
Why are those things so slow? I mean all values are incredibly huge. 4870ms round mean a 5 second execution time for the whole thing. Are you using a debug build?

@webmaster128 Hi, just want to know, is there any updates regard this issue?

That's interesting work here. It would be heavily breaking and hardly make it to main CosmWasm in the near future. But still worth exploring.
Some thoughts:

I still son't understand why the runtimes are so long. How many read operations do you test there in 1 benchmark?
I'd be surprised if the optimizations here matter much given the storage layer below is usually the bottleneck. Do you test this with a real IAVL storage from Cosmos SDK?
Can you reproduce it with the latest version of CosmWasm? 1.0.0 is quite old. Also with Wasmer 3 or 4 the situation can be better already from CosmWasm 1.3 on.
The short value optimization is interesting. However it adds some complexity. I wonder why host functions seem to be slow in the first place.
Since there is no concurrent access to ExternalStorage, you can move the vTemp there (and make it bigger?): e.g. vTemp: Box<[u8; 64]>

1000000 read operations in one benchmark test
when use the latest version of cosmwasm by using same computer, the performance was increased about 11% while calling function do_db_read
I am using profiler to trace the time cost of execution and it shows that over 40% time was cost by write_to_contract

After the optimization, the rate was decreased to 19%

In practice, we often see times between 40 microseconds to 100 microseconds when reading one value from the backing database.

1000000 read operations in one benchmark test

If your benchmark we run in a real blockchain, the IAVL overhead would likely be 40-100s.
This section you are looking to optimize takes around 2s.
My quick judgement is that it is not worth spending time optimizing this section until there is a 20-100x or more speedup in the data storage layer, and this section is a significant overhead for execution.
Furthermore, if a contract made 1 million read operations, it would likely use around 1-2 billion gas, which would never fit inside a blockchain transaction.
If that number were reduced to 100 or even 1000 read operations, then other fixed costs (like creating an Instance) would likely use a significantly more portion of the time. It is important to find the proper spots to optimize that will have impact in real world usecases.
While we could look into changes here, I think there are other areas that would be much more productive, like the IAVL tree in the SDK.

Glad to got your responds and let me share the key points for this optimization.
The influences of the changes are not only regarding the IO operations but also other calls of Host functions.
As I know, all of the host functions which were registered by cosmwasm are using the same way to passing the params and calculate gas such as write_to_contract, read_region, process_gas_info
Now we are focusing on optimizing those functions and got about 35% speedup of execution performance. I think it's worth to optimize.  and we are keep digging on that~


Including EVENT_PROP_TARGET in onLoad on Android

closed in favor of https://github.com/cuvent/react-native-fast-video/commit/6fc2472ba611ba7aa52c8a2d9b86490764f43536


Inverse of a matrix

Hello I am planning to use this library to create a multiple regression model. Is it possible to calculate the inverse of a matrix using the CKKS scheme?

Is the matrix guaranteed to be invertible?

Yes it is.

I actually don't know. No matter what matrix inversion method you choose, there is a division involved, either by the determinant or an element of the matrix. I suppose that you want to invert an encrypted matrix. This division by an encrypted value is not supported.

I see. Thank you for the information.

@prconcepcion BTW, this paper shows a method for matrix inversion with some limitations, maybe it can work in your scenario.


Monotonicity preserving C1 interpolation (continued)

Reported by beutlich on 2 Nov 2015 15:56 UTC
In #1717 I added the univariate Fritsch-Butland-spline interpolation to the MSL trunk.
Now I noticed that GSL 2.0 also added support for monotonicity preserving C1 interpolation based on "Steffen, M.; A Simple Method for Monotonic Interpolation in One Dimension; Astronomy and Astrophysics, Vol. 239, NO. NOV(II), P. 443, 1990".
What should be done for MSL 3.2.2?

Do nothing and keep Fritsch-Butland as it is now?
Replace Fritsch-Butland by Steffen.
Keep Fritsch-Butland and also add Steffen.

@haumer @otter Any feedback is appreciated.

Migrated-From: https://trac.modelica.org/Modelica/ticket/1814

Modified by beutlich on 2 Nov 2015 15:58 UTC

Comment by beutlich on 23 Nov 2015 21:27 UTC
I started a poll about the potential change alternatives to gain more feedback from the MSL shapers and users. Feel free to contribute (by the end of next week).
http://doodle.com/poll/txgxv2i58rs84hh8

Comment by hansolsson on 24 Nov 2015 16:15 UTC
I believe the most important question is to understand in what way the different schemes differ.
This is both necessary to make an informed decision in this poll and to present it in a reasonable way for the users.
Looking at http://adsabs.harvard.edu/full/1990A%26A...239..443S it seems that Steffens' variant looks better than Akima - while avoiding some problems with Fritsch-Butland (but I couldn't find any direct comparison between them). However, some of the issues seem related to derivatives at knot-points - which may be an advanced option that we do not use.
So, can anyone answer the following:
Is there a problem with Fritsch-Butland for this use-case?
If there is a problem with Fritsch-Butland, what is the reason for keeping it (if we only want to keep it for backward compatibility reasons we might use annotation choices to hide it).

Comment by hansolsson on 26 Nov 2015 11:32 UTC
Ok, I have now read the paper by Steffen in more detail. I still feel that it seems as if we hand over the decision to users since we haven't understood it ourselves.
Let's see if I understand it correctly - that in addition to Akima-interpolation the following interpolation alternatives exist:
1 Akima
2 Fritsch&Carlsson 1980
3 Fritsch&Butland 1984/Brodlie 1980
4 Steffen 1990
As I understand it 1 is already present, 2 is not considered.
The question is if we should add 3 and/or 4. Is that correct?
Akima can produce local extrema inside intervals.
Akima method is not always forward stable (i.e. infinitesimal changes in y-values can cause large changes in results)
However, Akima interpolation is already used and should thus be kept (even if problematic).
Fritsch&Carlsson potentially has the issues that it 2-pass, and non-local; thus we should not add it.
Fritsch&Butland does not match 2nd order polynomials
Akima completely matches 2nd order polynomials
Steffen completely matches 2nd order polynomials - if the extrema is on a knot-point
The difference between F&B and Steffen seems to be the difference between equation 30 and 11; and F&B seems more elegant.
But is it important to match 2nd order polynomials? If so is there any reason to assume that extrema are on knot-points?
Are there any other considerations that we need to consider?
E.g. are any of the interpolations linear (and is that important)? (I.e such that interpolation([x,y1+a*y2], t)=interpolation([x,y1],t)+a*interpolation([x,y2],t) ).

Comment by beutlich on 26 Nov 2015 11:53 UTC
Replying to [comment:4 hansolsson]:

The question is if we should add 3 and/or 4. Is that correct?

Exactly.
I studied why the GSL implemented Steffen and not F&B. They discussed it: https://www.sourceware.org/ml/gsl-discuss/2014-q1/msg00036.html It looks like GSL preferred Steffen over F&B due to the three reasons Steffen stated in his paper.
I have the patch for Steffen interpolation ready. The differences (both in sense of source and the resulting interpolant) are marginal only. And for that reason I cannot see why Steffen claims his three aspects.
So the difference in slope approximation simply is:
--- fb.c	Do Nov 26 12:51:08 2015
+++ s.c	Do Nov 26 13:03:38 2015
@@ -1,13 +1,12 @@
-static CubicHermite1D* fritschButlandSpline1DInit(const double* table,
-                                                  size_t nRow, size_t nCol,
-                                                  const int* cols,
-                                                  size_t nCols) {
+static CubicHermite1D* steffenSpline1DInit(const double* table,
+                                           size_t nRow, size_t nCol,
+                                           const int* cols,
+                                           size_t nCols) {
   /* Reference:

-     Frederick N. Fritsch and Judy Butland. A method for constructing local
-     monotone piecewise cubic interpolants. SIAM Journal on Scientific and
-     Statistical Computing, 5(2), 300-304, June 1984.
-     (http://dx.doi.org/10.1137/0905021)
+     Matthias Steffen. A simple method for monotonic interpolation in one
+     dimension. Astronomy and Astrophysic, 239, 443-450, August 1990.
+     (https://trac.modelica.org/Modelica/attachment/ticket/1814/1990A%2BA___239__443S.pdf)
   */

     CubicHermite1D* spline = NULL;
@@ -55,7 +54,15 @@
             }
             else {
                 const double dx_ = TABLE_COL0(i + 2) - TABLE_COL0(i + 1);
-                c2 = 3*(dx + dx_)/((dx + 2*dx_)/d[i] + (dx_ + 2*dx)/d[i + 1]);
+                double abs_c2_d2, abs_di, abs_di1;
+                c2 = (d[i]*dx_ + d[i + 1]*dx)/(dx + dx_);
+                abs_c2_d2 = 0.5*fabs(c2);
+                abs_di = fabs(d[i]);
+                abs_di1 = fabs(d[i + 1]);
+                if (abs_c2_d2 > abs_di || abs_c2_d2 > abs_di1) {
+                    const double two_a = d[i] > 0 ? 2 : -2;
+                    c2 = two_a*(abs_di < abs_di1 ? abs_di : abs_di1);
+                }
             }
             c[1] = (3*d[i] - 2*c[2] - c2)/dx;
             c[0] = (c[2] + c2 - 2*d[i])/(dx*dx);

Comment by hansolsson on 26 Nov 2015 14:41 UTC
Replying to [comment:5 beutlich]:

Replying to [comment:4 hansolsson]:

The question is if we should add 3 and/or 4. Is that correct?
Exactly.

I studied why the GSL implemented Steffen and not F&B. They discussed it: https://www.sourceware.org/ml/gsl-discuss/2014-q1/msg00036.html It looks like GSL preferred Steffen over F&B due to the three reasons Steffen stated in his paper.

Now I am getting confused again:
I thought the three reasons was why Steffen is preferred over F&C, but compared to F&B there is only the "doesn't match 2nd order polynomial where extrema is at knotpoint" argument.

Comment by beutlich on 26 Nov 2015 15:08 UTC
OK, I always thought that F&C (1980) gives the idea, but lacks a real implementation, which than was added by F&B (1984).

Comment by hansolsson on 26 Nov 2015 15:42 UTC
Replying to [comment:7 beutlich]:

OK, I always thought that F&C (1980) gives the idea, but lacks a real implementation, which than was added by F&B (1984).

And I think that F&C (1980) had one idea, which was found wanting and a better solution proposed in F&B (1984).
Steffen (1990) independently found another solution without knowing about these; the reviewers found them for him - and he added references, but in such a way that it could be mis-interpreted as above.  (I might be too jaded.)
Obviously this needs to be resolved.

Comment by beutlich on 26 Nov 2015 15:57 UTC
I doubt that we'll find a resolution. I also tried to reproduce Steffen's Akima figures with his datasets (reconstructed from the figures) but failed. I neither observed the numerical instabilities nor the oscillations he mentioned.
I also doubt that we'll see some other user's input since most simply do not care in such a detail. See #1153 for an example.
For me there is no major difference between F&B and Steffen and I also cannot judge if one is superior than the other. You said that F&B does not match 2nd order polynomials whereas Steffen does. This might be the only reason to go for one, the other or even both. I mean I can simply add both and let the user have the choice (that we cannot or do not want to take).

Comment by hansolsson on 26 Nov 2015 16:14 UTC
Replying to [comment:9 beutlich]:

I doubt that we'll find a resolution. I also tried to reproduce Steffen's Akima figures with his datasets (reconstructed from the figures) but failed. I neither observed the numerical instabilities nor the oscillations he mentioned.

Even more confusing.

I also doubt that we'll see some other user's input since most simply do not care in such a detail. See #1153 for an example.

Well, there are two kinds of user input:

I prefer x over y due to z.
This is too complicated, can you give me a simpler variant?

We get less of the 2nd kind, but I still see some.

For me there is no major difference between F&B and Steffen and I also cannot judge if one is superior than the other. You said that F&B does not match 2nd order polynomials whereas Steffen does. This might be the only reason to go for one, the other or even both. I mean I can simply add both and let the user have the choice (that we cannot or do not want to take).

Well, even that claim is less complete: Steffen claims his method matches 2nd order polynomials IF the extrema is at a knot-point; otherwise not.
Letting users choose between two different interpolation formulas where we don't know the real difference and we doubt that users care is not good library design to me.

Comment by beutlich on 26 Nov 2015 20:03 UTC
Replying to [comment:10 hansolsson]:

Even more confusing.

Steffen mentions Akima (1970) that also is used as reference for the MSL tables (in function akimaSpline1DInit). Somewhere I read that there is an improved Akima variant. That might be one reason.
For sake of completeness, this is the (reconstructed) data set of figure 3: [0,8.5;1,8;2,7.5;3,7;4,6.5;4.25,3.25;4.5,0.5;7,0.5;8,0.5;9,0.5;10,0.5]

Letting users choose between two different interpolation formulas where we don't know the real difference and we doubt that users care is not good library design to me.

You are right, to be honest.
I read Steffen's conclusion again. The paragraph after formula (30) shows the differences he observed with respect to F&B (1984). He states that the approximated slopes of F&B are always lower in comparison to his algorithm. And the difference can be up to 25%.
And on page 2 Steffen states the his algorithm gives exact results if the data points are derived from a 2nd order polynomial (which is not true for F&B/Brodlie).
Thus, if we won't let the user decide between F&B or Steffen we could reason that we chose Steffen over F&B for exactly this point.

Comment by beutlich on 30 Nov 2015 12:37 UTC
In http://doodle.com/poll/txgxv2i58rs84hh8 there are now three votes to have both F&B and Steffen. Hans, would you agree on replacing F&B by Steffen?

Comment by otter on 10 Dec 2015 10:54 UTC
Interpolation has always the difficulty that it is not possible to know which is suitable/best for the problem at hand. The only way is to concretly try it out with the concrete task and then compare what looks best for this problem at hand.
Therefore, if there are already two implementations, I would include them both in MSL.

Modified by beutlich on 10 Dec 2015 11:12 UTC

Comment by beutlich on 16 Dec 2015 13:07 UTC
Option 3. resolved by 7631ba7a0c5dab286bb065d198bd36fd5bfb1274.
CombiTable2D gives a not-implemented error for smoothness=MonotoneContinuousDerivative1 or smoothness=MonotoneContinuousDerivative2.

Changelog modified by beutlich on 16 Dec 2015 13:07 UTC
Added univariate Steffen-spline interpolation (for CombiTimeTable, CombiTable1D and CombiTable1Ds)


Packit rebase command

As a follow-up of https://github.com/packit/packit/issues/1724 expose a new packit command
/packit rebase
for both pull-from-upstream and propose-downstream jobs,
for updating Packit's pull requests that are supposed to be fast-forwarded by Pagure but are now out-of-sync.
The comment command has to be written in the Pagure PR the user wants to updated.
The original request is here

I've just tried the rebase option in Pagure (it shows as an option under the Merge button when it's yellow) in this PR and it worked like a charm (the PR was rebased, the Merge button turned green and CI is running). So I'm not sure if this is really needed.


Fixed Bug in pythogorean calculator

Related Issuse

Info about Issue or bug

fix #2133
Describe the changes you've made
A clear and concise description of what you have done to successfully close your assigned issue. Any new files? or anything you feel to let us know!
Checklist:

[x] My code follows the style guidelines of this project.
[x] I have performed a self-review of my own code.
[x] I have commented my code, particularly in hard-to-understand areas.
[x] I have made corresponding changes to the documentation.
[x] My changes generate no new warnings.

Screenshots

@sairish2001 resolved conflicts :)


do not adjust location being passed to the managed side

// cc: @mhegazy

👍

Does this fix the "Exception in loose file typing if / else block" bug?


Readme: clarify plans for plugin implementations

Current coverage is 74.23% (diff: 100%)

Merging #225 into master will not change coverage

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==========================================
  Files            16         16
  Lines          1110       1110
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Prepare quill 2.x for use in replace frontend

Copied types into repo because typescript cannot understand that @engoo/quill should use @types/quill types
Fixed formatting errors
Disabled unused modules because Quill does not take options into account for some reason. Probably this is one of the “develop” branch woes
Replaced npm usage with yarn
Enabled minification in production build
Made both production and develop build generate quill.js instead of .min and no-suffix version
Added a filtering function to the clipboard matchers to take care of GDocs issue

As discussed on a call, upstreaming the changes is very likely impossible due to overall lethargic state of maintenance.
I removed webpack build step from package distribution and pointed the main entry to the raw quill.js file, letting our own build pipeline to take care of minification and bundling.
I also went back and restored original package-lock.json, then converted it to yarn.lock properly. ESLint issues did not go away so the fixes stay.
Agree that specific module configuration could be done client-side instead of being hard pinned in the library, but that will be a follow up: https://github.com/iknow/issues/issues/2973


Design: Text to align with coded Text

The coded Heading has margin-top and margin-bottom values which the Figma component does not have. Add spacing to Figma Headings to mimic margins so they appear consistent with coded outputs.
Acceptance criteria

[x] All variants should have margin-bottom: 400
[x] Text component must have boolean property: Vertical margins?
[x] Poster to recommend space component for margin values outside of the default
[ ] Work done in EN and in FR

Done when

[x] Reviewed by designers
[x] Reviewed by developers
[x] EN component is merged and published
[x] FR component is merged and published
[ ] Poster content design review
[ ] Poster translations
[ ] EN poster merged and published
[ ] FR poster merged and published

Deliverables

[x] EN component in Figma
[x] FR component in Figma
[x] EN poster in Figma
[ ] FR postert in Figma

Dev impact
None

EN updates in branch for review:
https://www.figma.com/design/mh2maMG2NBtk41k1O1UGHV/branch/omJPAgCAbhtOrk6hVH3zi1/GC-Design-System?node-id=10053-348&node-type=CANVAS&t=yCdsQLXrViMXPwAG-0

FR updates in branch for review:
https://www.figma.com/design/o4SguSZdar2CCFzSkWNrmB/branch/qPi2DnQiMXDTY955DnMqz3/Système-de-design-GC?node-id=114-3353&node-type=CANVAS&t=ImVDu8s57JyJSIwK-0

Figma updates done, poster work in EN done and awaiting review, translation to be started.


[incubator/gitea] Initial commit of chart.

/ok-to-test

Marking this a stale. Please update within one week.

Closing as stale.


Review remain pull request

The remaining PR reviews are not being reviewed for a long time. Please give us your opinion on what to do from now on.

Sorry for the late response. 😢 I think my personal work will be done at the end of September. I will be able to participate actively in October.

As personal schedule is over, I can participate more actively from this month.

@taehwanno @gnujoow
The Pull Request is currently being left unattended. Maintainers are too busy to manage. Why don't you lower the limit with an approve?

@hg-pyun yes :cry: I agree.

@reactjs/reactjs-org-korean-translation When I looked at https://github.com/reactjs/reactjs.org/issues/3308, the React docs will be likely to change to hooks-first in 2021 early. Although the scope of the change is uncertain, it seems good that the PRs submitted so far are quickly merged. I wonder if you can help :)

Every pull request was closed. So I will close this :)


.tex Latex support

Is it possible to get support for .tex Latex files?

@impredicative What do you specifically have in mind with .tex support? In general, parsing .tex files and removing all LaTeX code is a non trivial task. There are tools such as DeTex and pandoc that allow converting .tex to .txt files which can be parsed with textract.
If this is sufficient, I encourage you to open a PR that adds support for either of these tools. If you have anything else in mind, please elaborate.

Support for .tex files will be added in the upcoming version with pandoc and opendetex as parsers.


WIP: event cleanup (golden files)

Golden files for: https://github.com/fabric8-services/fabric8-wit/pull/2212

Ike Plugins (test-keeper)
Thank you @kwk for this contribution!

It appears that no tests have been added or updated in this PR.
Automated tests give us confidence in shipping reliable software. Please add some as part of this change.
If you are an admin or the reviewer of this PR and you are sure that no test is needed then you can use the command /ok-without-tests as a comment to make the status green.
For more information please head over to official documentation. You can find there how to configure the plugin.

Codecov Report

:exclamation: No coverage uploaded for pull request base (kwk_event_cleanup_code@78e21fd). Click here to learn what that means.
The diff coverage is n/a.

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=========================================================
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[test]

/ok-without-test


Feature/aanderaa app configs

This PR includes:

:bug: the rtc value from the on-board aggregation is basically always 0, because the system starts the aggregation before the UTC fix from Spotter comes in. -> use rtc_end
replace the hardcoded CURRENT_SAMPLE_PERIOD_MS with a config named "CURRENT_READING_INTERVAL_MS. Currently this is hard-coded to 2s, but we actually set them up for 1s...
implement a baud rate configuration
configify nSkipReadings
configify readingIntervalMs
configify payloadWdToS

sc-194765

sc-194765

SC-194765

https://app.shortcut.com/sofar/story/194765/implement-bristlemouth-current-meter-module-firmware


Issue involving lime.ndll

After an failed to attempt to compile on Windows, this just now happens
I'm on the latest git lime, and haxe 4.3.3
Called from ? line 1
Called from CommandLineTools.hx line 1903
Called from CommandLineTools.hx line 22
Called from a C function
Called from CommandLineTools.hx line 125
Called from CommandLineTools.hx line 640
Called from lime/tools/PlatformTarget.hx line 107
Called from WindowsPlatform.hx line 305
Called from a C function
Called from lime/tools/ProjectHelper.hx line 57
Called from hxp/Log.hx line 50
Called from hxp/Log.hx line 152
Called from a C function
Called from C:\HaxeToolkit\haxe\std/neko/Lib.hx line 43
Uncaught exception - load.c(237) : Failed to load library : D:\HaxeToolkit\haxe\lib\lime\git//ndll/Windows/lime.ndll

EDIT: tried to delete it, now this happens
Called from ? line 1
Called from CommandLineTools.hx line 1903
Called from CommandLineTools.hx line 22
Called from a C function
Called from CommandLineTools.hx line 125
Called from CommandLineTools.hx line 640
Called from lime/tools/PlatformTarget.hx line 107
Called from WindowsPlatform.hx line 305
Called from a C function
Called from lime/tools/ProjectHelper.hx line 57
Called from hxp/Log.hx line 50
Called from hxp/Log.hx line 152
Called from a C function
Called from C:\HaxeToolkit\haxe\std/neko/Lib.hx line 43
Uncaught exception - load.c(237) : Failed to load library : lime.ndll

great
great

You can copy lime.ndll from the latest Haxelib release of Lime.

You can copy lime.ndll from the latest Haxelib release of Lime.
If this happened because you switched to 8.2.0-Dev, you'll need to get it from an actions run, or go through the trouble of rebuilding it yourself.

I'm using develop, and I can't find it in actions

okay well
@player-03 same issue
Called from ? line 1
Called from CommandLineTools.hx line 1903
Called from CommandLineTools.hx line 22
Called from a C function
Called from CommandLineTools.hx line 125
Called from CommandLineTools.hx line 640
Called from lime/tools/PlatformTarget.hx line 107
Called from WindowsPlatform.hx line 305
Called from a C function
Called from lime/tools/ProjectHelper.hx line 57
Called from hxp/Log.hx line 50
Called from hxp/Log.hx line 152
Called from a C function
Called from C:\HaxeToolkit\haxe\std/neko/Lib.hx line 43
Uncaught exception - load.c(237) : Failed to load library : D:\HaxeToolkit\haxe\lib\lime\git//ndll/Windows/lime.ndll

Make sure you copied both Windows/lime.ndll and Windows64/lime.ndll into their respective folders, just in case it's telling you the wrong one.
Try reinstalling hxp.
Run lime rebuild tools, even though this isn't the usual error for that.
Delete lime.ndll from Export/windows/bin and try again.
Try building with -eval (e.g., lime test windows -eval).

It's crashing while trying to print a "source path does not exist" error message, so if you start seeing that message instead, you'll know it's fixed.

okay, so, seems like that fixed it, but an issue unrelated to lime came back, so I'mma close this


Engine: add field to Command model to link analysis commands to run commands

Overview
TBD

Duplicate of #8986, which is more fleshed out


Reorganise item groups

Add item subgroup for SpaceX components

Put on SCT tab, if enabled. Else intermediates tab

Remove override of Centrifuge subgroup & order
Stop nilling item groups bob-gems and bob-fluid-products
Instead, move anything in bob-resource-products or bob-fluid-products to Intermediate Products
Move Battery and Iron gear wheel to bob intermediates
Move Rocket part to SCT
Move Blasting Charges to Angel's Petrochem
Move Solid Fuel from Hydrogen to Angel's Petrochem

Circuits moved in Circuit Processing https://github.com/KiwiHawk/CircuitProcessing/issues/19


Icon request: Bitcoin.de

URL for the brand / site / app
https://www.bitcoin.de/
Logo resources for the icon
https://www.bitcoin.de/build/images/svg/bc_logo.svg
Anything else?
I can only find a .svg with the logo and the text "bitcoin.de", so it would need to be modified.
There's a press kit, but it seems unavailable at the moment: https://www.bitcoin.de/en/presse
Confirmation

[X] I have read and followed the issue guidelines.

Here you go!
https://github.com/aegis-icons/aegis-icons/blob/master/SVG/Bitcoin.de.svg

:question: How to add icon(s) to Aegis?
:star: Support this project by giving a star! Just adding like to this comment is also appreciated.


Reseller.php unable to load base classes.

Reseller API's file Reseller.php located at (src/Google/Service/Reseller.php) is unable to load all the base classes. Have to manually insert autoload file of the API.

This is expected behavior. You need to include autoload.php.


ci: skip no-unexpected-packet-drops for cilium dualstack e2e

Reason for Change:
Skip no-unexpected-packet-drops test cases for ACN PR cilium dualstack e2e -- case is passing in other cilium dualstack scenarios for release pipeline + locally. There are some known issues upstream with this connectivity test case failing.
Issue Fixed:

Requirements:

[ ] uses conventional commit messages

[ ] includes documentation
[ ] adds unit tests
[ ] relevant PR labels added

Notes:

/azp run Azure Container Networking PR


i can not find a properties file, the name is src/resources/samoa-storm-cluster.properties,help me please.

this file locates in samoa-storm,i find something where i can not understand,here is the code in  /src/com/yahoo/labs/samoa/topology/impl/StormSamoaUtils.java.
File f = new File("src/resources/samoa-storm-cluster.properties"); // FIXME it does not exist anymore
should i just remove  codes like this?

Ported to SAMOA-30.


Modals and Global Modal Controller

Features:

Global Modal Context added for all application to use more easy modals.
Types of modals were created.
Client service was implemented.

well, it's fine I think


The signal on one end of pseudochromosomes is missing

Dear developers,
Thanks for your great software!
I am working on assembling a putative hexaploid or octoploid plant genome with a genome size of ~1.45 Gb by flow cytometry. In addition, the only one published closely related species has 2n=2X=28 karyotype, 400 Mb haploid genome size, and the CCDB shows the chromosome base number of this genus may be 9 or 14.
I obtained 54 pseudochromosomes by scaffolding the primary assembly generated by hifiasm with ~41x hifi reads and ~140x Hi-C reads. The colinear plot between this genome and the relative species indicated it may have undergone chromosome fusion events.  I have several questions doing scaffolding.
(1) Can I determine how many the chromosome sets are by Hi-C analysis of haphic?
(2) Is there any possibility of a complex chromosome number variations occurring? like ((14 x 2) - 1 ) x 2
(3) The signal on one end of a considerable number of pseudochromosomes is missing, should I break the contigs and move this regions to debris?

(4) Some pseudochromosomes centromeric regions or ends are just consist of debris which have nearly no signal, should I remove them?

According to the interaction signal among pseudochromosomes, I think it should be an octoploid. Typically, a pseudochromosome has one strongly and two weakly interacting pseudochromosomes.

(1) Can I determine how many the chromosome sets are by Hi-C analysis of haphic?

This information can be inferred from 1) self-alignment, 2) alignment to other species, and (3) diagonally distributed Hi-C signals on contact maps.

(2) Is there any possibility of a complex chromosome number variations occurring? like ((14 x 2) - 1 ) x 2

For bioinformatics analysis, drawing such a conclusion requires more information and experience. For example: a full version of contact map without clustering errors, the locations of telomeres and centromeres on each chromosome, alignments to closely related species using dot plots, read depth distribution across each chromosome, etc.

(3) The signal on one end of a considerable number of pseudochromosomes is missing, should I break the contigs and move this regions to debris?
(4) Some pseudochromosomes centromeric regions or ends are just consist of debris which have nearly no signal, should I remove them?

Regions lacking Hi-C signals are typically either repetitive sequences or regions that are extremely similar among different haplotypes. During BAM filtering, these signals are filtered out by the MAPQ ≥ 1 criterion due to multiple alignments. The handling of these sequences should be considered case by case. If assemblers join these regions with signal-rich regions into the same contig, I generally regard the results as reliable, as the assemblers use additional information from overlapping HiFi reads. Conversely, the placements of independently existing signal-lacking contigs are considered unreliable if their placements rely solely on weak Hi-C signals. The placements of these sequences can be manually determined based on the GFA files generated by assemblers. If their placements remain uncertain, they can be moved to debris.

According to the interaction signal among pseudochromosomes, I think it should be an octoploid. Typically, a pseudochromosome has one strongly and two weakly interacting pseudochromosomes.

Before providing further comments, I need to know how this genome was assembled, including the version of the assembly used (p_ctg, p_utg, hap*.p_ctg).

已收到您发送的邮件！

Thank you very much for your suggestion! I also think keeping the original assembling results should be more reliable instead of breaking up contigs. And for the Hi-C link near-absent small contigs, I will check their read mapping depth.
We vastly underestimated the size of this genome before sequencing. I think the sequencing depth (~43x) was not enough for accurately separate haplotypes, let alone it may be a autopolyploid, even if we have enough Hi-C reads. So I chose the p_ctg as input for scaffolding a haplotype collapsed genome. Do you think haplotyping is better?
As for this plot, I noticed haphic uses MAPQ ≥ 1 as the default filtering settings. I am not sure this may erase the inter-pseudochromosomes contact signals or not, so I kept the reads whose MAPQ = 0 to draw this plot for a test.

According to the interaction signal among pseudochromosomes, I think it should be an octoploid. Typically, a pseudochromosome has one strongly and two weakly interacting pseudochromosomes.

So I chose the p_ctg as input for scaffolding a haplotype collapsed genome.

The p_ctg version is not correctly phased. The contigs in it may contain randomly joined long phased blocks. We typically use hap*.p_ctg for diploids and p_utg for autotetraploids. For more information, please refer to https://lh3.github.io/2021/04/17/concepts-in-phased-assemblies and https://hifiasm.readthedocs.io/en/latest/interpreting-output.html#interpreting-output.

As for this plot, I noticed haphic uses MAPQ ≥ 1 as the default filtering settings. I am not sure this may erase the inter-pseudochromosomes contact signals or not, so I kept the reads whose MAPQ = 0 to draw this plot for a test.

The MAPQ ≥ 1 criterion does not specifically filter out inter-chromosome Hi-C signals. Instead, it mainly removes multiple alignments. The diagonally distributed Hi-C links between homologous chromosomes stem from mapping errors and assembly errors.

Thank you for you advice!
I have tried unitigs for scaffolding, but the utg N50 (1.2Mb) is much smaller than ctg N50 (21Mb), resulting much more fragmented pseudochromosomes and making it more complicated to scaffold. Besides, the final size of pseudochromosomes is only a few Mb larger than ctg version. So we decide using ctg for scaffolding.
As for Hi-C signal filtering, I am curious about that if the sequences of two or multiple chromosomal regions are near the same, will this MAPQ ≥ 1 filtering criterion cause all the signals in these regions to disappear?

I have tried unitigs for scaffolding, but the utg N50 (1.2Mb) is much smaller than ctg N50 (21Mb), resulting much more fragmented pseudochromosomes and making it more complicated to scaffold. Besides, the final size of pseudochromosomes is only a few Mb larger than ctg version. So we decide using ctg for scaffolding.

You are free to persist in how you conduct your research and take responsibility for it, and the heatmaps you provided do not appear to have obvious anomalies, however, considering that GitHub Issues are also visible to other users, as the author of HapHiC and the maintainer of this GitHub repository, I still need to express my personal opinion and stance: I think these reasons are not sufficient to convince me to choose a conceptually incorrect assembly version. A lower contiguity is preferable to being incorrect.

As for Hi-C signal filtering, I am curious about that if the sequences of two or multiple chromosomal regions are near the same, will this MAPQ ≥ 1 filtering criterion cause all the signals in these regions to disappear?

Although MAPQ is defined as −10 log10 Pr{mapping position is wrong} in the Sequence Alignment/Map Format Specification, the calculation of MAPQ varies among different read mappers. I can only say that the MAPQ  ≥ 1 criterion is the minimum requirement to prevent multiple mappings. This threshold is also used by several Hi-C-related software tools, including 3D-DNA and chromap.
Here is a comparison of various MAPQ cutoffs in the genome assembly of the autotetraploid potato C88:

A lower contiguity is preferable to being incorrect.

I think this statement makes sense, however, there are about 2500 unitigs which have been assigned to pseudochromosomes by haphic. The complexity of scaffolding these thousands of unitigs by only Hi-C evidence raises the concern that I can not determine whether unitig scaffolding is more correct than the potential chimeric contigs generated by assembler or not. Do you have any suggestions?
In addition, the Hi-C signals among contigs generally looks good, like the heatmaps I posted. The author of hifiasm suggested usually >=13x HiFi reads per haplotype are desired. Higher coverage might be able to improve the contiguity of assembly. We may not phase eight sets of haplotypes by only ~43x reads, so the haplotype-collapsed genome is acceptable. Maybe I should ask my boss for more sequencing depth and other scaffolding evidences ~
By the way, I am confused about the "primary assembly" described here (Are polyploid genomes supported), whether it is p_ctg or p_utg? I used --n-hap 8 in running hifiasm.

Here is a comparison of various MAPQ cutoffs in the genome assembly of the autotetraploid potato C88:

Thanks for your example, it seems more obvious than my case. In my opinion, we should make use of the multiple mapping reads instead of filtering them along with the low mapping quality reads, I am not sure it is correct or not, do you think multiple mapping reads should be treated as the same as low mapping quality reads?

Thanks to your suggestion, I found some assembly error in contigs by checking the hifi reads mapping depth on the pseudochromosomes where the depth changes suddenly and Hi-C signals are absent. There may be more such errors hiding in the contigs. And I face the issue how to find out them and how to revise them. Do you think it makes sense using contigs to assist scaffolding those unitigs or using corresponding unitigs to replace those flawed contigs?
Hope these ignorant questions won't take up too much of your time, thank you very much！

I think this statement makes sense, however, there are about 2500 unitigs which have been assigned to pseudochromosomes by haphic. The complexity of scaffolding these thousands of unitigs by only Hi-C evidence raises the concern that I can not determine whether unitig scaffolding is more correct than the potential chimeric contigs generated by assembler or not. Do you have any suggestions?

They are different types of errors. Short contigs (often < 100 kb) do have a higher potential to be erroneously ordered and oriented. These kinds of errors can be alleviated by using the assembly graph output by the assemblers. However, the primary assembly (p_ctg) can introduce phasing errors (see the top right panel in the figure below).

We may not accurately phase eight sets of haplotypes by ~40x reads, a haplotype-collapsed genome is acceptable.

First, the concepts of the primary assembly and the haplotype-collapsed assembly are different. Furthermore, in your case, the primary assembly contains four times the haploid genome size due to high heterozygosity.

By the way, I am confused about the "primary assembly" described here (Are polyploid genomes supported), whether it is p_ctg or p_utg?

The "primary assembly" is p_ctg, while the sequences in p_utg are unitigs. p_ctg may not be correctly phased. For diploids, when you have provided trio data or Hi-C data, the generated hap*.p_ctg files are often correctly phased. If you did not provide trio data or Hi-C data, adding the --n-hap parameter puts hifiasm in "dual" mode, and the generated hap*.p_ctg files are not correctly phased (see the top middle panel in the figure above). However, for autopolyploids, hifiasm may generate imbalanced haplotypes (hap*.p_ctg). Therefore, researchers often choose unitigs (p_utg) for scaffolding, which are typically correctly phased but not assigned to haplotypes. This is why the authors of hifiasm drew the conclusion in their [documentation].(https://hifiasm.readthedocs.io/en/latest/faq.html#are-polyploid-genomes-supported):

The *r_utg.gfa and *p_utg.gfa are lossless so that they also work for polyploid genomes.

I used --n-hap 8 in running hifiasm.

In your case, as the species may be an allotetraploid, I recommend reassembling the genome as a diploid by using Hi-C data and the --n-hap 2 parameter. I hope this can solve all the other problems you are facing.

Close this issue as there has been no response for two weeks.

Sorry for the late reply, I went on a meeting trip recently. Thank you very much for your patient answers, they are very helpful for me!


Model without Tangent and Normal is Black

Why does the model became almost black and you can't see the texture if you don't export the tangent and normal?
Looking at the same GLTF file with an online preview won't cause this issue.

And seen online it's perfect: https://gltf-viewer.donmccurdy.com/
Here the GLTF model file as txt, rename it to .gltf to make it work:
noNormalorTangent.txt

Sounds like normals are not being calculated.  Per glTF spec:

Implementation note: When normals are not specified, client implementations should calculate flat normals.

@emackey this should be fixable in the plugin side right?  Which file/class should calcolate them?

Sorry, I'm not a Unity expert.  Maybe one of the maintainers here can chime in.

I just checked this on the latest and it renders correctly now.


Add information in Readme.md + change the file name Readme.md to Surr…

…ogate Modeling Toolbox.md

:white_check_mark: Build SMT 0.1.344 completed (commit https://github.com/SMTorg/SMT/commit/e0c7f719af by @bouhlelma)

Why renaming? A side-effect is that the landing page of the github repo does not display any information anymore, so I would suggest to keep README.md.

I agree!

:white_check_mark: Build SMT 0.1.345 completed (commit https://github.com/SMTorg/SMT/commit/eb445316a3 by @bouhlelma)

:white_check_mark: Build SMT 0.1.346 completed (commit https://github.com/SMTorg/SMT/commit/d2ab86b7bd by @bouhlelma)


Add openapi tags to Instance,Binding types

This patch would allow this PR to work: https://github.com/kubernetes/kubernetes/pull/41354
Explanation
By tagging api types with +k8s:openapi-gen=x-kubernetes-display-all:true, we would be able to use the kubectl discovery client to identify the resources that should be printed as part of the "all" alias in kubectl get all.
Why
Right now, kubectl get all fails with the error the server doesn't have a resource type "pods" every time, due to k8s.io/kubernetes/pkg/kubectl/cmd/util/shortcut_restmapper.go defaulting to a hardcoded list of resources any time it attempts to lookup a resource alias (which happens any time a resource is retrieved using kubectl get...).
Why not just make shortcut_restmapper.go use the list of discovered resources from the server every time, instead of defaulting to using the hard-coded list in kubectl?
Right now that is what the linked PR does, however defaulting to a list of resources returned by the discovery client would involve filtering such list in order to conform to the definition of "all". That is not possible to do with the default information returned by the openapi spec. Hence why using this PR to add tags to all of resources we intend to return as part of kubectl get all is the proposed way to move forward. This would allow us to lookup these tags with kubectl and use those resouces, or keep current behavior of defaulting to the hardcoded list of resources in shortcut_restmapper.go for backwards compatibility.
cc @pwittrock @pmorie @fabianofranz

Why am I including a copy of openapi-gen in this repo, rather than updating the version of k8s.io/kubernetes that we are vendoring, to support tagging?
I tried, turns out this would break a few packages due to apimachinery no longer being under k8s.io/kubernetes/pkg/apimachinery, but under k8s.io/kubernetes/staging/src/apimachinery. If you have a painless / simple way of making this work, I would be more than happy to update this PR to do that instead :)

Is there a change made to openapi-gen for our repo and purpose, or is this strictly an upstream copy?
If it is more than a copy, I would like that change split out as a separate commit as well.
I accept the explanation for needing a copy.
Pending that and a working build, it's lgtm. I will re-review as necessary.

Is there a change made to openapi-gen for our repo and purpose, or is this strictly an upstream copy?
If it is more than a copy, I would like that change split out as a separate commit as well.

it's strictly an updated upstream copy

What do you mean by 'updated'?
Can we get the kubernetes/kubernetes sha-ish that was used as the base?

What do you mean by 'updated'?

The copy in this PR, uses the openapi-gen changes introduced in 317376de307407b377753c4539be607400f43115 which allows for tagging. The copy found in our vendored version of kube, is from commit 6b9a9442855d16e0ff0c02ab0c82b1c1665cccaf

Yup, looks good.
There are some strange whitespace changes. But it is otherwise an exact copy.

The EDIT is what is clear to me. Thank you.

How important is it to be discoverable before we have a working product? I'd argue not very.
Shortly after we have this actually working, I'd anticipate that we rebase against stable upstream k8s. (@pmorie correct me if that's wrong.) When we do so, won't we get this for free?
Seems better to wait and get this for free in a few weeks than do apply this stop-gap now, have it not actually buy us anything since this project doesn't work yet, and then have to remember to remove that band-aid later.

@krancour As i understand this, it is less discoverability and more having kubectl work in a pleasing fashion.

@juanvallejo is working on other stuff now, so I will reopen this once our PR backlog is down.

@pmorie should we close this for now?

Yeah - I'm going to rebase and resubmit this PR today.


Add grouping to Python sklearn interface

Adds support to pass through groups & group_sizes to XGBoost's sklearn interface.
This is more of a proof of concept, I want to rework the interface so that groups is used the way the sklearn does things.  With sklearn groups should be a group identifier, while for xgboost it expects the data to be sorted by group, and then given group sizes.  I was thinking about making a group_sizes parameter, and then having a groups parameter that works the sklearn way.  Let me know if that sounds good!
This adds ability to build ranking models through the sklearn API, by setting .fit(X, y, groups=groups), which will now:

resort the data so groups are next to each other (based on groups)
on the created dmatrix, it will call DMatrix.set_group(...) with the calculated group sizes
goes through existing Booster.predict(...) code path
resorts the results back to what they original were
returns back to what called the sklearn API

I also passed through group_sizes if the programmer would rather use the XGBoost style of handing grouping, instead of how sklearn handles it (which is to assign a group number for every row).
#815 seems related, but it looks like they just jumped down to using DMatrix & train directly... but I have a bunch of parameter tuning setup so I don't want to rework that code. 😄

Closing as inactive for more than six months


Mobile nav layout issues.

Need to remove button icons on mobile view.

Adjusted mobile nav: 1b41b9c483a09bf8b4ed624019689ac3161be5fc


cloud: failure in deployment can lead to invalid/missing entries

E0417 20:26:58.263683       1 provisioner.go:288] Provider machine dad64412-0a1d-4523-9c5d-74782657af11 has no corresponding machine in BMDB.
E0417 20:26:58.263756       1 provisioner.go:296] Provider device ID b7e8894f-687b-4465-94cb-871d269d83e3 referred to in BMDB (from TODO) but missing in provider.
E0417 20:26:58.263766       1 provisioner.go:296] Provider device ID 5ade97e3-fe2e-471b-a712-e52418744396 referred to in BMDB (from TODO) but missing in provider.
E0417 20:26:58.263809       1 provisioner.go:296] Provider device ID 7361d3ab-67b7-453f-a3c2-bd98aa3af0c9 referred to in BMDB (from TODO) but missing in provider.
E0417 20:26:58.263821       1 provisioner.go:296] Provider device ID 2cd72fd6-c5c4-406d-b610-c0725c27c3ab referred to in BMDB (from TODO) but missing in provider.
E0417 20:26:58.263832       1 provisioner.go:303] Something's very wrong. Bailing early and refusing to do any work.
E0417 20:26:58.263841       1 provisioner.go:130] Processing failed: reconciliation failed: fatal discrepency between BMDB and provider

And we smh made it lockup the /root/agent file:
I0417 20:48:40.822884       1 sessions.go:354] Adding backoff for "ShepherdAccess" on machine "077a9aa4-736c-450b-9663-23bce09fcb79" (60 seconds)
W0417 20:48:41.032716       1 initializer.go:342] Agent stderr: "bash: /root/agent: Text file busy"
E0417 20:48:41.032788       1 initializer.go:283] Failed to initialize: while starting the agent: while starting the agent executable: Process exited with status 126

The list of machines that are missing always changes. Maybe we hit some kind of pagination:
I0417 20:54:21.474131       1 provisioner.go:181] Got 1049 machines managed in provider.
I0417 20:54:21.474148       1 provisioner.go:256] Reconciling...
E0417 20:54:21.474608       1 provisioner.go:288] Provider machine dad64412-0a1d-4523-9c5d-74782657af11 has no corresponding machine in BMDB.
E0417 20:54:21.474711       1 provisioner.go:296] Provider device ID 1378b8ec-6eeb-40e4-84ae-1ad6d96ac20b referred to in BMDB (from TODO) but missing in provider.
E0417 20:54:21.474724       1 provisioner.go:296] Provider device ID 1c05ff8e-50c8-4ee6-979c-447f241b0548 referred to in BMDB (from TODO) but missing in provider.
E0417 20:54:21.474736       1 provisioner.go:296] Provider device ID 5d82498a-9dfe-47e3-88b6-1d89ca4d99a8 referred to in BMDB (from TODO) but missing in provider.
E0417 20:54:21.474747       1 provisioner.go:303] Something's very wrong. Bailing early and refusing to do any work.
E0417 20:54:21.474754       1 provisioner.go:130] Processing failed: reconciliation failed: fatal discrepency between BMDB and provider

Found the culprit. I dont know yet why, but the loop https://github.com/monogon-dev/monogon/blob/main/cloud/shepherd/equinix/manager/shared_config.go#L250 overrides hosts. Apparently equinix returns wrong ids?

I0418 00:14:58.476655       1 provisioner.go:257] Reconciling...
E0418 00:14:58.477038       1 provisioner.go:289] Provider machine 220f6a62-7a1d-4f4b-b329-4a778aaa0573 has no corresponding machine in BMDB.
E0418 00:14:58.477191       1 provisioner.go:297] Provider device ID a3ccb7de-3d5e-4116-8132-88328372b9ee referred to in BMDB (from TODO) but missing in provider.
E0418 00:14:58.477223       1 provisioner.go:304] Something's very wrong. Bailing early and refusing to do any work.
E0418 00:14:58.477231       1 provisioner.go:130] Processing failed: reconciliation failed: fatal discrepency between BMDB and provider

https://review.monogon.dev/c/monogon/+/1555


Feature / Yarn 3 Upgrade

Provides Yarn upgrade to version 3.x, package dependencies cleanup on all 3 plugins and on general project.

@ionSurf the pipeline has failed, are you plaining to revisit it ?


Multisite about page (stub)

The default about page checked into the project should be a stub suitable for multisite installs.
The www.spee.ch about page should be a local page the same way it is for other installs.
Internal Use
Acceptance Criteria

Definition of Done

[ ]  Tested against acceptance criteria
[ ] Tested against the assumptions of the user story
[ ] The project builds without errors
[ ] Unit tests are written and passing
[ ] Tests on devices/browsers listed in the issue have passed
[ ] QA performed & issues resolved
[ ] Refactoring completed
[ ] Any configuration or build changes documented
[ ] Documentation updated
[ ] Peer Code Review performed

related to #637


Sequence to Sequence Problem Type

Closes https://github.com/h2oai/h2o-llmstudio/issues/100
Adds a new problem Type Sequence to Sequence Modeling. For now tested for different T5 models.
We can probably go step by step adding more functionality if this will be frequently used.
I tried to reuse as much as possible to not have much duplicate code.
@maxjeblick please take an initial look, it might need 1-2 iterations
Todo:

[ ] README
[x] Rework dataset?
[x] Check padding
[x] Check merging / pipeline
[x] Default settings for dtype etc?
[x] Model card

Thx for the comments @maxjeblick - tried to address them.

The PR is probably good to merge after hf has been added to the config.

Yes, I just noticed that I also need to adjust the summary model card now. On it.


[Feature Request] Add suport for AWS Athena

Is your feature request related to a problem? Please describe.
I need to run tests on tables using AWS Athena as backend. This would enable us to test a great amount of data on a data lake using dbt features.
Describe the solution you'd like
Enable the expectations to be run against an AWS Athena connection.
Describe alternatives you've considered
I tried to use athena_utils with compatibility "shims" but it does not work with all expectations. And it seems that its not possible to make all expectations compatible in this way because some of then does not use a adapter.dispatch . This turns harder to overwrite some of the dbt package tests code.
Additional context
Some expectations that does not work with athena_utils "shims" package:
-expect_column_to_exist
-expect_row_values_to_have_recent_data

Hi @joaopedro02, we currently have no way to test against AWS Athena during our CI process, so we can't support this platform at this time.

Hi @clausherther, now that dbt-athena is trusted adapter, please could this be reopened and explored? 😄 thanks!


Pairs in c++

Description 📜
Pairs in C++ standard template library #2257
There is basic introduction to pair.

Type of change 📝

[ ] Au#dio (Should be in mp3 format Includes speech clarity, Concise ,Low distortion)
[ ] Vi#deo (Animations, screen-recordings, presentations and regular explanatory films are all possibilties etc)
[x] Documentation (Content Creation in the form of codes or tutorials)
[ ] Other (If you choose other, Please mention changes below)

Domain of Contribution 📊

[ ] Android Dev #(Flutter)
[ ] Android Dev #(Java)
[ ] Android Dev #(Kotlin)
[ ] Backend Dev #(Java)
[ ] Backend Dev #(.NET)
[ ] Backend Dev #(PHP)
[ ] Backend Dev #(Python)
[x] C/CPP
[ ] Competitive #Programming
[ ] Cyber #Security
[ ] DS#A
[ ] Data#base
[ ] Datascience with #Python
[ ] Datascience with #R
[ ] Frontend Dev #HTML/CSS/JS
[ ] Frontend Dev #React/Angular/Vue
[ ] Go#lang
[ ] Interview #Prep
[ ] Java_#Domain
[ ] Java#Script
[ ] ME#RN
[ ] Machine #Learning
[ ] Open #Source
[ ] Python_#Domain
[ ] Ru#st
[ ] Statis#tics
[ ] UI/#UX

Checklist ✅

[x] I follow Contributing Guidelines & Code of conduct of this project.
[x] I have performed a self-review of my own code or work.
[x] I have commented my code, particularly in hard-to-understand areas.
[x] My changes generates no new warnings.
[x] I'm GWOC'21 contributor

Screenshots / Gif (Optional) 📸

ok i will do that

Note : You can only put your content in C/CPP's Subdirectories.

Is it ok now

Also, add a link of your code in Standard Template Library/readme.md.

add this line in Standard Template Library/readme.md
- [Pair](./pair.md)

Done with the changes ,please check it now.

@vasu-1  Excellent reviewing ❤
@geetika005  Perfect & neat explanation... Would love if it was atleast a 2 minute read
Try adding make_pair & tie() etc...

Made the changes sir.