Ray engine implementation uses ray's private API

Currently, we use private ray's ._remote() function to override the remote function's parameters before its execution:
https://github.com/modin-project/modin/blob/51658b49b54ce89f1277f8b73bdef4cf909e53fd/modin/engines/ray/task_wrapper.py#L65
Ray provides public API to override function's parameters, the same behaviour could be achieved by combination of .options()  + .remote() methods.
@ray.remote
def foo(*args, **kwargs):
    return bar(args, kwargs)

# Previous approach:
id1, id2, id3 = foo._remote(args=args, kwargs=kwargs, num_returns=3)

# Proposal:
tuned_foo = foo.options(num_returns=3)
id1, id2, id3 = tuned_foo.remote(*args, **kwargs)

Files where ._remote is used:

modin/engines/ray/task_wrapper.py
modin/engines/ray/axis_partition.py
... maybe more?

@YarShev do you have more files/cases of using ray's private API on your mind?

@dchigarev , yes, I added some more files to the list at the top of this issue.


#4792 Downgrade Bitcoin Core reckless update to tested v27.1

addresses #4792

Merging for RaspiBlitz v1.11.3rc2


fix: Remove premature removal of finalizer from Default ArgoCD Instance

What type of PR is this?

Uncomment only one  /kind line, and delete the rest.
For example, > /kind bug would simply become: /kind bug

/kind bug

What does this PR do / why we need it:
Problem Description
When DISABLE_DEFAULT_ARGOCD_INSTANCE is changed from false to true. It is expected that all the associated RBAC resources too get cleaned up. But the clean up of RBAC resources does not remove the ClusterRoles and ClusterRoleBindings associated with the default ArgoCD instance. However, the ServiceAccount, Role and RoleBinding resources are cleaned up correctly.
Following ClusterRoles are not cleaned up
openshift-gitops-openshift-gitops-argocd-application-controller
openshift-gitops-openshift-gitops-argocd-server

Following ClusterRoleBindings are not cleaned up
openshift-gitops-openshift-gitops-argocd-application-controller             ClusterRole/openshift-gitops-openshift-gitops-argocd-application-controller
openshift-gitops-openshift-gitops-argocd-server                             ClusterRole/openshift-gitops-openshift-gitops-argocd-server

Solution
In gitopservice_controller.go, when DEFAULT_ARGOCD_INSTANCE is set to true it removes the finalizers, and then marks the ArgoCD CR for deletion. The ArgoCD controller, cleanup code depends on the finalizers to cleanup the RBAC resources.
Have you updated the necessary documentation?

[ ] Documentation update is required by this PR.
[ ] Documentation has been updated.

Which issue(s) this PR fixes:
Fixes GITOPS-2572
Test acceptance criteria:

[] Unit Test
[x] E2E Test

How to test changes / Special notes to the reviewer:
Related PR: https://github.com/redhat-developer/gitops-operator/pull/525

/retest-required

/test v4.13-kuttl-parallel
/test v4.14-kuttl-parallel

/retest-required

/lgtm
/approve


Python3 compatibility

It is good idea to start from something with least dependency.
I have tested at least I can edit the scene correctly using pytest.

I happened see Simon working on migrating to Py3 and I asked him about my work. And he commended changing the assignee to Ziyan.


BQ Table Schema - Maintaining Original Case of Spark DF Schema

Hi Sam,
Is it possible to retain the original case for the BQ Table schema generated?  Currently it makes all fields lowercase (customeraccountid) when the original is camel (customerAccountId) - this makes it quite hard for some of the business people to read.  Is this possible at all to retain the original case?
Cheers
K

Hey kurt
You can probably send a pr to the schema converter
It should be a small one and help you understand the code base
On Tue, 23 May 2017 at 11:52, kurtmaile<EMAIL_ADDRESS>wrote:

Hi Sam,
Is it possible to retain the original case for the BQ Table schema
generated? Currently it makes all fields lowercase (customeraccountid) when
the original is camel (customerAccountId) - this makes it quite hard for
some of the business people to read. Is this possible at all to retain the
original case?
Cheers
K
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
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.

cool will try - just looking at the code nothing jumps out as where this is explicitly happening - assume its implicitly (json4s library?) happening somewhere I cant see - a pointer?
fieldToJson - would appear the where this would happen?
Cheers

Hey Sam any hints as to why the schema casing is all lower case?  Nothing obvious jumps out, I may be missing the missing the obvous too :)

Hey @kurtmaile I believe its here https://github.com/samelamin/spark-bigquery/blob/master/src/main/scala/com/samelamin/spark/bigquery/converters/BigQueryAdapter.scala#L17
Give it a test locally after you do the pr to ensure it still saves to bq :)

Oh cool thanks - what is the reason you initially made this lower case though so that I dont break things?  Is there a BQ constraint to adhere to?  Thanks for the tip ;)

I think initially BQ didnt allow uppercase schemas but this has now been fixed, send a PR over when your free :)

This has now been released on v 0.1.7

Awesome thanks!
On Thu, 22 Jun 2017 at 22:52, Sam Elamin<EMAIL_ADDRESS>wrote:

This has now been released on v 0.1.7
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Stock Imagery

Change stock imagery on landing page

for now is just an image with the logos, we will wait for the production team


Pipeline fails when processing an image acquired in the visible spectrum

Pipeline fails when processing a image acquired in the visible spectrum
Context

Operating System: Windows
iris.version = 1.1.1

I'm using the IRIS pipeline to outline the pupil center and iris from images acquired with a "standard" camera (Canon EOS R).
I convert the RGB images to gray-scale using img_pixels = cv2.cvtColor(img_pixels, cv2.COLOR_RGB2GRAY), then run the pipeline as usual:
full_env = iris.Environment(
    pipeline_output_builder=build_simple_debugging_output,
    error_manager=store_error_manager,
    disabled_qa=[
        iris.nodes.validators.object_validators.Pupil2IrisPropertyValidator,
        iris.nodes.validators.object_validators.OffgazeValidator,
        iris.nodes.validators.object_validators.OcclusionValidator,
        iris.nodes.validators.object_validators.IsPupilInsideIrisValidator,
        iris.nodes.validators.object_validators.IsMaskTooSmallValidator,
        iris.nodes.validators.cross_object_validators.EyeCentersInsideImageValidator,
        iris.nodes.validators.cross_object_validators.ExtrapolatedPolygonsInsideImageValidator,
    ],
    call_trace_initialiser=iris.PipelineCallTraceStorage.initialise,
)

iris_pipeline = iris.IRISPipeline(env=full_env) # note using default env. here does not solve the problem
output = iris_pipeline(img_data=img_pixels, eye_side=eye_side)  # changing eye side does not solve the problem

This works very well in most cases but, in some of them (about 14%), it fails with the the following error message:
{'error_type': 'VectorizationError',
 'message': '_find_class_contours: Number of contours must be equal to 1.',
 'traceback': '  File "D:\\Sources\\IkomIris\\ImageProcessingAutomation\\dev\\env\\lib\\site-packages\\iris\\pipelines\\iris_pipeline.py", line 131, in run
    _ = self.nodes[node.name](**input_kwargs)
  File "D:\\Sources\\IkomIris\\ImageProcessingAutomation\\dev\\env\\lib\\site-packages\\iris\\io\\class_configs.py", line 67, in __call__
    return self.execute(*args, **kwargs)
  File "D:\\Sources\\IkomIris\\ImageProcessingAutomation\\dev\\env\\lib\\site-packages\\iris\\io\\class_configs.py", line 78, in execute
    result = self.run(*args, **kwargs)
  File "D:\\Sources\\IkomIris\\ImageProcessingAutomation\\dev\\env\\lib\\site-packages\\iris\nodes\\vectorization\\contouring.py", line 75, in run
    geometry_contours = self._find_contours(geometry_mask)
  File "D:\\Sources\\IkomIris\\ImageProcessingAutomation\\dev\\env\\lib\\site-packages\\iris\\nodes\\vectorization\\contouring.py", line 90, in _find_contours
    pupil_array = self._find_class_contours(mask.pupil_mask.astype(np.uint8))
  File "D:\\Sources\\IkomIris\\ImageProcessingAutomation\\dev\\env\\lib\\site-packages\\iris\\nodes\\vectorization\\contouring.py", line 117, in _find_class_contours
    raise VectorizationError("_find_class_contours: Number of contours must be equal to 1.")
'}

Unfortunately, I can't provide you with an image sample to respect subject anonymity. Looking at the call stack and source code, it seems to fail in the pupil detection.
I'm aware the pipeline is supposed to process IR images. Yet, are there some recommended pre-processing steps so I can sucessfully use the pipeline on visible images?
Thanks!

Hey @cleosia,
Thank you for your interest in open-iris and raising that issue.
Regarding your issue, there is not much that I can recommend you here. The error that you are seeing is related to bad segmentation map being produced. Specifically, a semantic segmentation model produced a scattered segmentation map that contains more than 1 blobs for iris, pupil or eyeball class that are bigger than hardcoded in this function thresholds. For more context on that checkout ContouringAlgorithm.
Having said that there are two things you may try to improvement of overall working of open-iris for your data:

First thing you can test is modifying mentioned above threshold such that filtering blobs in contouring algorithm will lead to only one blob being considered for further processing.
Second idea you may try is to modify/improve input image such that it "reminds" more images that we used for training our semantic segmentation model. More details on that you can find in the SEMSEG_MODEL_CARD.md file. From our intuition, when we spend some time on analysing what our semantic segmentation model is guided by when doing inference, we find out that high frequencies (edges) are very frequently extracted as features for further semantic segmentation maps generation. Therefore, I can advise you to boost edges signal in your images. This may help to produce more consistent, not scattered, geometry segmentation maps and will remove the error you're encountering.

Hope that helps or at least gives you some intuition on what you may work on to improve your results!
Best regards,
Wiktor

Hey @cleosia,
Please, let me know if you manage to solve your problem, so we can close this issue, or you still would like some support from our side?
Best regards,
Wiktor

Hey Wiktor,
Thanks for your follow-up. I would have liked to give you a more complete feedback, but at least here is my current status on this:
Between my email and your answer, I basically tried several RGB to grayscale conversion methods, trying successively each channel of the RGB image, and this reduced the failure ratio to 4%.
The drawback of this improvement is that this issue fell down at the bottom of my "todo" stack, so that I couldn't try your improvement suggestions. Nor do I know when (and whether) it will become a priority again...
So I think the best is to close this issue for now. Thanks for your support on this!

Thank you for your feedback. I'm closing this issue for now. However, if at some point this becomes your priority again, please feel free to reach out to us. We can also hop on a call to discuss your issue and maybe give a better feedback.
Best regards,
Wiktor


Cors credentials headers is set even if cors isn't enabled at all.

During cool digging i noticed this issue, gonna work on fixing that. and focus on fixing the CORS issues on the project too.

This issue has been fixed at b535228 by including the CORs headers on the same if condition with the credentials.


make MAX_NUM_THREADS_PER_QUERY configurable

make MAX_NUM_THREADS_PER_QUERY configurable.
Currently it depends on Runtime.getRuntime().availableProcessors() , due to which user is forced request high number of CPU in k8 deployments
https://github.com/apache/incubator-pinot/blob/master/pinot-core/src/main/java/org/apache/pinot/core/operator/combine/CombineOperatorUtils.java#L38

created PR" https://github.com/apache/incubator-pinot/pull/6375

@samarth-gupta-traceable
is this still an issue? You have closed the related pull request
https://github.com/apache/pinot/pull/6375
If solved we d like to close this issue.

thank you!


[Bug Report] Poppover popper-options causes error

Element UI version
1.4.2
OS/Browsers version
OSX Chrome, OSX Safari
Vue version
2.4.2
Reproduction Link
https://jsfiddle.net/sammie/ondno3oe/
Steps to reproduce
Bind an object to popper-options declaring modifiers in the format specified by https://popper.js.org/popper-documentation.html#Popper.Defaults
What is Expected?
Popover appears with offset specified by popper-options
What is actually happening?
Popover appears at bottom: 0, left: 0.
[Vue warn]: Error in callback for watcher "showPopper": "TypeError: this._options.modifiers.map is not a function"
Javascript error: TypeError: this._options.modifiers.map is not a function

The solution was to refactor popper.js as a package dependency instead of relying on an internal, out-of-date popper.js file in src/utils. Then I had to refactor Vue-popper to reference vm.PopperJS.popper instead of vm.PopperJS._popper.
This required the popper.js to be imported as an es6 native module instead of a commonjs require() module, so its unclear how this might effect server-side rendering (not a feature I happen to care about).
My solution can be found in a fork here, with an example of popover's popper-options in updated documentation: https://github.com/sammieedwards/element

+1. I have the same issue. Refactoring dependency code isn't really an option for me.

Is there a fix for this issue?

这个问题有没有解决啊

Could this please be addressed? I can confirm the bug and the solution by @stablegeniusbestbrain works like a charm and looks clean, but obviously I don't want to edit files in my node_modules folder.

I have the same issue.How to fix it?


Fix for redundant calls to SQLNumResultCols and SQLRowCount

Coverage increased (+0.1%) to 73.329% when pulling cf03cbb6f7283be90f20ab609fba68ad97d27ce9 on david-puglielli:redundant-apis into 1e4f0147272af65589019ad290a52aa2010cb438 on Microsoft:dev.

Codecov Report

Merging #972 into dev will decrease coverage by 0.05%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev     #972      +/-   ##
==========================================
- Coverage   81.38%   81.32%   -0.06%
==========================================
  Files          25       25
  Lines        7758     7792      +34
==========================================
+ Hits         6314     6337      +23
- Misses       1444     1455      +11

Impacted Files
Coverage Δ

...c14/x86/php-7.1.28-src/ext/pdo_sqlsrv/pdo_stmt.cpp
84.19% <0%> (-0.92%)
:arrow_down:

...php-7.1.28-src/ext/pdo_sqlsrv/shared/core_stmt.cpp
78.78% <0%> (-0.4%)
:arrow_down:

...x86/php-7.1.28-src/ext/sqlsrv/shared/core_sqlsrv.h
86.49% <0%> (-0.37%)
:arrow_down:

...php-7.1.28-src/ext/pdo_sqlsrv/shared/core_sqlsrv.h
84.42% <0%> (ø)
:arrow_up:

...phpdev/vc14/x86/php-7.1.28-src/ext/sqlsrv/stmt.cpp
89.51% <0%> (+0.06%)
:arrow_up:

...x86/php-7.1.28-src/ext/sqlsrv/shared/core_stmt.cpp
86.64% <0%> (+0.3%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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Allow get() for large files

Also makes it slightly easier to browserify.
Increasing file limits on the other operations (add, update, remove) is next up, but a little more challenging.
@tmcw, mind taking a quick look?

:+1:


Run Saucelabs tests for internal PRs except if branch contains 'quick/'

Related to https://github.com/vaadin/vaadin-upload/pull/141
Run Saucelabs tests for:

internal PRs, except cases when branch contains 'quick/'
daily builds, triggered by cron

This change is

Reviewed 2 of 2 files at r1.
Review status: all files reviewed at latest revision, all discussions resolved.

Comments from Reviewable


Fix RUNNING information.

The information in https://github.com/agl/pond/blob/master/RUNNING is overly complicated and wrong at the moment. Go is not Python after all and you don't need a special environment to run Go programs.
All the Go libraries are statically linked an can safely be removed if you only want to run the client. (Just check ldd $GOPATH/bin/client)
For example after compiling Pond on Tails one could easily do
> cp $GOPATH/bin/client /home/amnesia/Persistent/pond
> unset GOPATH
> rm -rf $GOPATH
> /home/amnesia/Persistent/pond

and then forget about Go until one wants to update Pond. The C libraries are not statically linked, but they don't need $GOPATH either.
Would it be okay to remove RUNNING and mention this in doc/index.html instead?
Edit: Fix path in the last command.

+1 imho. I think there's a todo somewhere for better documenting the building of the non-gtk client as well, if you're in a tidying up mood...


[6.x] Resolve migration classes via the container

Resolve migration classes via the container to allow DI in migrations

Can you maybe explain more in detail why this is needed? Provide some use cases.

@driesvints
Personally, I'm not a big fan of using Facades, so in our apps we tend use DI everywhere to inject our classes, with the exception being our migrations. Aside from this, I'd say having the possibility to use DI here would never be a bad thing considering it's possible to use it virtually everywhere else as well.
As for the global helper, I forgot that illuminate/database is also a separate package. Seeing as this package is also depending on illuminate/container, I can change resolve($class) to Container::getInstance()->make($class) with a use Illuminate\Container\Container; statement at the top, to not break BC by changing the constructor.

It's not needed. Use Facades. It seriously does not matter at all if you use facades in your migrations. It's good to just move past the superstition in this case.

I don't see why it's a problem to resolve the classes using the container, it doesn't remove any current features, it only adds new possibilities.
Besides that, the main reason I don't like Facades is because IDE's can't autocomplete their methods without a third party module, and I don't want to install or add unnecessary dependencies to my apps if I can help it. So honestly, I don't see the benefits of using Facades over DI.

@DuckThom I personally also don't use facades much myself but in this particularly use case I don't see how DI provides benefit here. The point of a migration is to change a DB structure which you generally want to test as an integration test with a real database. I don't think that DI provides any benefit here. If you need more logic inside your migration than the default structure changes it might be best to extract to a separate class and unit test that class.

@driesvints I agree that it doesn't provide a benefit to migrations but it also doesn't remove any existing functionality. It's more to be able to keep the code consistent with the rest of your codebase and to be able to use autocompletion in IDEs without adding extra dependencies in the app. This 2 line change just allows you to inject classes in the constructor of a migration in case it's needed.
I'll just keep my override then, just in case anyone else is looking for the same functionality, these are my changes:
In my service provider's register method I have:
$this->app->extend('migrator', function ($migrator, $app) {
    $repository = $app['migration.repository'];

    return new Database\Migrator($repository, $app['db'], $app['files'], $app['events']);
});

And the custom migrator class (removed some newlines to keep the codeblock shorter):
use Illuminate\Database\Migrations\Migrator as LaravelMigrator;

class Migrator extends LaravelMigrator {
    public function resolve($file) {
        $class = Str::studly(implode('_', array_slice(explode('_', $file), 4)));
        return Container::getInstance()->make($class);
    }
}

@DuckThom there's no need in adding code which won't be used.

@driesvints Well that's kind of my point for having to use the extra dependency for facade IDE autocompletion aswell :stuck_out_tongue:


IconTheme should also let you specify the size

...that way PaginatedDataTable could just set it to 24.0 and you wouldn't have to worry about it when specifying your IconButtons in the actions list.

I'm not really sure how I intended this to apply to PaginatedDataTable, so I may revisit this, but I have a size on IconTheme now at least.


White Smiling Face is undefined - bug

hi
i am using this great emojis, but there is 1 icon that is undefined :
☺ - this  is the native
and the emoticons: undefined

Sorry for the late response. I do not see the issue here though, the emoticons property is optional and not all the emojis have these.
This is a text representation of the emoji, such as =) for simile emoji.
In the emojis data library this is represented by texts and text properties, which are optional.
You can see these text representations in the emoji preview area at the bottom:

Here is another emoji, that doesn't have it:


[CARBONDATA-1914] [Dictionary Cache] Cache Access Rectification

Rectifying Cache Access. In order to mark Dictionary Caches are in-use, there is a Atomic access Count variable which is incremented and post  usage it is being decremented. In some of the places Cache access is not being cleared, therefore is was difficult to evict it from cache as AccessCount will be non zero.

[x] Any interfaces changed?
No

[x] Any backward compatibility impacted?
No

[x] Document update required?
No

[x] Testing done
Please provide details on
- Whether new unit test cases have been added or why no new tests are required?
- How it is tested? Please attach test report.
- Is it a performance related change? Please attach the performance test report.
- Any additional information to help reviewers in testing this change.
NA

[x] For large changes, please consider breaking it into sub-tasks under an umbrella JIRA.
NA

SDV Build Success , Please check CI http://<IP_ADDRESS>:8080/job/ApacheSDVTests/2442/

Retest this please.

Build Failed  with Spark 2.1.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder1/2221/

Build Success with Spark 2.2.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder/999/

Build Success with Spark 2.2.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder/1003/

Build Failed  with Spark 2.1.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder1/2226/

Build Failed  with Spark 2.1.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder1/2230/

SDV Build Fail , Please check CI http://<IP_ADDRESS>:8080/job/ApacheSDVTests/2485/

Retest this please

Build Success with Spark 2.1.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder1/2231/

LGTM

Build Success with Spark 2.2.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder/1007/

SDV Build Success , Please check CI http://<IP_ADDRESS>:8080/job/ApacheSDVTests/2490/


[Testing] Refactor locality integration tests

The goal here is to reduce the overall test time.

Run all tests with the same test suite (i.e. only deploy Istio once)

Run some tests in parallel. For some reason, running all tests in parallel doesn't work. I've added a TODO: to investigate.

[APPROVALNOTIFIER] This PR is APPROVED
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/lgtm
/approve

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prow/release-test.sh
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/lgtm
/approve
I'm on vacation until mid-May and then at KubeCon so probably won't get round to investigating for a while.

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/lgtm

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@geeknoid looks like prow/release-test is pretty broken ... can we make it non-required?

@nmittler I don't think the test is new, is it? Maybe it is a real, new failure - not sure though, the test-infra repo is not easy to navigate

/test release-test

@howardjohn not sure if it's new, but it's recently required and is problematic.

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/test istio_auth_sds_e2e

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New changes are detected. LGTM label has been removed.

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@ozevren PTAL ... I rebased to absorb your flaky label. I also changed the test to use Echo.

/lgtm

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/test istio-integ-k8s-tests

@ozevren could I get your LGTM again? Had to make the linter happy.

/test istio-pilot-e2e-envoyv2-v1alpha3

/lgtm

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GetData gives incorrect results

The Matrix.Transpose method seems to be broken for nonsquare arrays.
Example code to produce the error is shown below.  It seems that transpose assumes that the incoming matrix dimensions are switched perhaps.
Program.txt

change main to
    static void Main(string[] args)
    {
        ArrayFire.Array ArrayIn = Data.CreateArray(IndexMatrix(5, 7));

        Console.WriteLine("In:");
        Console.WriteLine(ArrayToString(Data.GetData2D<int>(ArrayIn)));

        Util.Print(ArrayIn);

        ArrayFire.Array ArrayOut = Matrix.Transpose(ArrayIn, false);

        Console.WriteLine("");
        Console.WriteLine("Out:");
        Console.WriteLine(ArrayToString(Data.GetData2D<int>(ArrayOut)));

        Util.Print(ArrayOut);

        Thread.Sleep(100000);
    }

and you see that GetData2D may be the issue

Command line output:
In:
0,1,2,3,4,5,6
7,8,9,10,11,12,13
14,15,16,17,18,19,20
21,22,23,24,25,26,27
28,29,30,31,32,33,34
No Name Array
[5 7 1 1]
0          5         10         15         20         25         30
1          6         11         16         21         26         31
2          7         12         17         22         27         32
3          8         13         18         23         28         33
4          9         14         19         24         29         34
Out:
0,5,10,15,20
25,30,1,6,11
16,21,26,31,2
7,12,17,22,27
32,3,8,13,18
23,28,33,4,9
14,19,24,29,34
No Name Array
[7 5 1 1]
0          1          2          3          4
5          6          7          8          9
10         11         12         13         14
15         16         17         18         19
20         21         22         23         24
25         26         27         28         29
30         31         32         33         34

ArrayFire is a column major library so consecutive values across the column are going to be represented as consecutive values in memory. The values returned by the array seems correct but the shape seems to be off. I think the IndexArray and ArrayToString need to be reworked to take this into account. If you look at the In array, the values already seem to be transposed.


docs: add GitHub Actions example for container image

As requested here: https://github.com/go-reform/reform/issues/299#issuecomment-945658555

Hi @AlekSi - let me know if this is on track or if there's anything else you'd like to see.

Looks great. Could you also add instructions for .tar.gz please? I use something like that:
      - name: Install Go
        run: |
          sudo rm -fr /opt/hostedtoolcache/go /usr/local/go /usr/bin/go /bin/go
          curl -o go.tar.gz -L \
            https://github.com/AlekSi/golang-tip/releases/download/tip/master.linux-amd64.tar.gz
          sudo tar -C /usr/local -xzf go.tar.gz
          sudo ln -s /usr/local/go/bin/* /usr/local/bin/
          go version
          rm go.tar.gz

But that probably could be simplified.

But that probably could be simplified.

TY for the example code. Doesn't get much simpler really! The .tar.gz example is much faster to run (48 seconds faster than container example) so I called that out also.


Exception when updating dynmap on first player join

Sometimes rebooting a server running both HuskTowns and Dynmap causes exceptions on first player join as seen below:
[22:06:09 INFO]: [HuskTowns] Loading claim data into cache...
[22:06:09 WARN]: [HuskTowns] An exception occurred updating the Dynmap:null
[22:06:09 WARN]: me.william278.husktowns.cache.Cache$CacheNotLoadedException: Exception attempting to access unloaded Player Data cache (current state: UPDATING)
[22:06:09 WARN]:        at HuskTowns-1.7.jar//me.william278.husktowns.cache.PlayerCache.getPlayerUsername(PlayerCache.java:127)
[22:06:09 WARN]:        at HuskTowns-1.7.jar//me.william278.husktowns.integrations.map.Map.getClaimInfoWindow(Map.java:50)
[22:06:09 WARN]:        at HuskTowns-1.7.jar//me.william278.husktowns.integrations.map.DynMap.addMarker(DynMap.java:101)
[22:06:09 WARN]:        at HuskTowns-1.7.jar//me.william278.husktowns.cache.ClaimCache.add(ClaimCache.java:96)
[22:06:09 WARN]:        at HuskTowns-1.7.jar//me.william278.husktowns.data.DataManager.lambda$updateClaimedChunkCache$49(DataManager.java:3047)
[22:06:09 WARN]:        at org.bukkit.craftbukkit.v1_18_R1.scheduler.CraftTask.run(CraftTask.java:101)
[22:06:09 WARN]:        at org.bukkit.craftbukkit.v1_18_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:57)
[22:06:09 WARN]:        at com.destroystokyo.paper.ServerSchedulerReportingWrapper.run(ServerSchedulerReportingWrapper.java:22)
[22:06:09 WARN]:        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
[22:06:09 WARN]:        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
[22:06:09 WARN]:        at java.base/java.lang.Thread.run(Thread.java:833)
[22:06:09 INFO]: [HuskTowns] Claim data caching complete (took 0 secs)

Possible steps to reproduce exception:

Restart server which has configured Dynmap
Join server as the first player to do so since restart
Observe console

Other notes:
Original user to report this had Dynmap saving map data to MySQL.  If this is a map cache issue, perhaps the SQL data and cache data are conflicting?

This should no longer be the case as 2.0 has a new Dynmap integration


strange result with mono_sc depth model

Hi, I got the normal result with the kitti_odom/stereo model, but when I did the evaluation with command
python run.py -c options/kitti/kitti_mono_sc_0.yml
Here's the result I got:
Evaluate result in result/mono_sc/0? [y/n]y
Sequence: 9
Translational error (%):<PHONE_NUMBER>392447
Rotational error (deg/100m):  0.31097519037206917
ATE (m):<PHONE_NUMBER>028094
RPE (m):  4.013671579698525
RPE (deg):  0.03655727300821237
Sequence: 10
Translational error (%):<PHONE_NUMBER>227918
Rotational error (deg/100m):  0.3488643421558913
ATE (m):<PHONE_NUMBER>38146
RPE (m):  2.9854127555332712
RPE (deg):  0.04222684748013362

The result is quite strange, do you know why?

Hi @Kewenjing1020 , since mono_sc depth model is not aligned with real-world scale. You have to use 7DoF alignment (to align the result to the real-world scale) in the evaluation.

Hi @Kewenjing1020 , since mono_sc depth model is not aligned with real-world scale. You have to use 7DoF alignment (to align the result to the real-world scale) in the evaluation.


Update documentation for FASTLINK

The documentation for FASTLINK had a few issues that this PR attempts to address:

The sentence about "executable is deployed on another computer" was confusing because deploying the executable isn't a problem if you are doing so to remote debug. The real problem is attempting to deploy the PDB.
The performance notes on FASTLINK were not correct for Visual Studio 2019 and later

CC @RussKeldorph

@corob-msft,
Can you review the proposed changes?
IMPORTANT: When the changes are ready for publication, add a #sign-off comment to signal that the PR is ready for the review team to merge.
#label:"aq-pr-triaged"
@MicrosoftDocs/public-repo-pr-review-team

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Thanks @gregg-miskelly and @corob-msft for taking care of this!


Additional Parameters for r.recognize_ibm()

IBM Watson's Speech to Text Service allows you to opt out of data collection when making requests. I do not want them to collect my data so I am trying to opt-out, which involves setting the parameter X-Watson-Learning-Opt-Out to True. See more details at: http://www.ibm.com/watson/developercloud/speech-to-text/api/v1/#authentication
When I use your  r.recognize_ibm() function, X-Watson_Learning-Opt-Out=True, is not valid. Is there a way for me to pass this argument in?
Thanks!

This will be a part of the next release (ref: ba8becc3f3ffea793eb0bf02d77acb06bbe5c173)

Fixed in 3.5.0!

Awesome, thanks!


updated versioning and release notes to fix innaccuracies

Bug 30063361: WebView2: Docs: Update versioning concept doc
Bug 30063385: WebView2: Docs: Update release notes with correct min runtime version

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@david-risney could you take another look when you get the chance?

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Acrolinx score: 92

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#sign-off offline and merged.


We can ad rating section in feedback form

Is your feature request related to a problem? Please describe.
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done by someone already


[ServiceBus] Abandon not needed if AutoComplete is false

Resolving issues Azure/azure-webjobs-sdk#2152 and Azure/azure-functions-servicebus-extension#142
If AutoComplete is false, then it should not attempt to abandon the message.
This change brings AbandonMessageIfNeededAsync in line with CompleteMessageIfNeededAsync.
I'm not sure if this counts as a breaking change. It's fixing an issue to bring it in line with the documentation, but that results in different behavior - throwing an exception will no longer cause the message to be abandoned if AutoComplete is false.
There were no existing unit tests for MessageReceivePump so I attempted to add some. Guidance welcome.
All SDK Contribution checklist:
This checklist is used to make sure that common guidelines for a pull request are followed.

[x] Please open PR in Draft mode if it is:

Work in progress or not intended to be merged.
Encountering multiple pipeline failures and working on fixes.

[n/a] If an SDK is being regenerated based on a new swagger spec, a link to the pull request containing these swagger spec changes has been included above.
[x] I have read the contribution guidelines.
[x] The pull request does not introduce breaking changes.

General Guidelines and Best Practices

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Testing Guidelines

[x] Pull request includes test coverage for the included changes.

SDK Generation Guidelines

[n/a] The generate.cmd file for the SDK has been updated with the version of AutoRest, as well as the commitid of your swagger spec or link to the swagger spec, used to generate the code. (Track 2 only)
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Note: Only applies to Microsoft.Azure.Management.[RP] or Azure.ResourceManager.[RP]

[n/a] Include updated management metadata.
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I'm not sure how I can "complete legal signoff" or get this code "fully code reviewed" as described in the Code Review Process

Hi @zamzowd.  Thank you for your contribution and for helping to improve the Azure SDK experience.  I've added some tags and routed to the team member best able to offer feedback.

Thanks for the assistance!
I noticed this morning that there's also SessionReceivePump and ReceiverManager that probably need to be updated in a similar manner.
Comparing the documentation, the wording for what AutoComplete does is different in Azure.Messaging.ServiceBus vs the Azure Functions Service Bus Trigger, even though their implementations are the same:

ServiceBusProcessor.AutoCompleteMessages
ServiceBusSessionProcessor.AutoCompleteMessages
Azure Functions ServiceBusTrigger

Ultimately, I'd like to be able to manually deadletter and then throw (for logging purposes). With AutoComplete off, I would expect what the ServiceBusTrigger documentation to describe: it also does not "AutoAbandon" when an exception is thrown.
Finally, and to reiterate, I'm not sure about my approach to unit testing this. I couldn't work out a way to unit test with any of the existing OnMessageQueueTests or uses of SenderReceiverClientTestBase.

@JoshLove-msft:   Would you be so kind as to offer your thoughts on the Azure.Messaging.ServiceBus observations?

I'd suggest splitting out the Microsoft.Azure.ServiceBus changes into a separate PR from the Azure.Messaging.ServiceBus changes. I'm ready to approve the changes for Azure.Messaging.ServiceBus, but the changes for Microsoft.Azure.ServiceBus would need to be reviewed by the other reviewers on this PR.

I rebased after the other PR was completed, as mentioned above. This PR no longer has anything in Azure.Messaging.ServiceBus, only in Microsoft.Azure.ServiceBus's MessageReceivePump and SessionReceivePump.

I'm not sure if there's anything further needed before exiting Draft on this PR, so I went ahead with Ready for Review.
As I understand it, primarily hoping for review from @DorothySun216 or @shankarsama as the code owners?


Moved startup settings to the preferences settings page

Validation
How did you test these changes?

[x] Built and ran the app
[x] Tested the changes for accessibility

Known issues
Startup settings combo box doesn't select the correct item when the app is opened

In my locale the combobox appears one row below:

In my locale the combobox appears one row below:

@gave92 I think there is an issue with the setting control template we're using, I'll work on a fix for this in a future PR.


Lastz error: terminated with an error exit status (1)

Hey I have beed tryin to run make_chains.py locally and keep getting shutdown by terminated with an error exit status (1).
(TOGA) hwaterma@cast-bio540ws02:~/Documents/MX_TOGA$ ../make_lastz_chains/make_chains.py MX DR MX_HiC_50chr_debris.fasta Danio.fa --pd test_out --chaining_memory 20 --executor local -f
Make Lastz Chains
Version 2.0.8
Commit: 88f4f390f032015816eef6bf69c574d683046fea
Branch: main

found run_lastz.py at /home/hwaterma/Documents/make_lastz_chains/standalone_scripts/run_lastz.py
found run_lastz_intermediate_layer.py at /home/hwaterma/Documents/make_lastz_chains/standalone_scripts/run_lastz_intermediate_layer.py
found chain_gap_filler.py at /home/hwaterma/Documents/make_lastz_chains/standalone_scripts/chain_gap_filler.py
found faToTwoBit at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/faToTwoBit
found twoBitToFa at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/twoBitToFa
found pslSortAcc at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/pslSortAcc
found axtChain at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/axtChain
found axtToPsl at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/axtToPsl
found chainAntiRepeat at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/chainAntiRepeat
found chainMergeSort at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/chainMergeSort
found chainCleaner at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/chainCleaner
found chainSort at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/chainSort
found chainScore at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/chainScore
found chainNet at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/chainNet
found chainFilter at /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/chainFilter
found lastz at /data/krablab/miniconda2/envs/TOGA/bin/lastz
found nextflow at /data/krablab/miniconda2/envs/TOGA/bin/nextflow
All necessary executables found.
Making chains for MX_HiC_50chr_debris.fasta and Danio.fa files, saving results to /home/hwaterma/Documents/MX_TOGA/test_out
Pipeline started at 2024-11-08 11:24:48.221388
Setting up genome sequences for target
genomeID: MX
input sequence file: MX_HiC_50chr_debris.fasta
is 2bit: False
planned genome dir location: /home/hwaterma/Documents/MX_TOGA/test_out/target.2bit
Initial fasta file MX_HiC_50chr_debris.fasta saved to /home/hwaterma/Documents/MX_TOGA/test_out/target.2bit
For MX (target) sequence file: /home/hwaterma/Documents/MX_TOGA/test_out/target.2bit; chrom sizes saved to: /home/hwaterma/Documents/MX_TOGA/test_out/target.chrom.sizes
Setting up genome sequences for query
genomeID: DR
input sequence file: Danio.fa
is 2bit: False
planned genome dir location: /home/hwaterma/Documents/MX_TOGA/test_out/query.2bit
Initial fasta file Danio.fa saved to /home/hwaterma/Documents/MX_TOGA/test_out/query.2bit
For DR (query) sequence file: /home/hwaterma/Documents/MX_TOGA/test_out/query.2bit; chrom sizes saved to: /home/hwaterma/Documents/MX_TOGA/test_out/query.chrom.sizes

Partition Step
Partitioning for target
Saving partitions and creating 26 buckets for lastz output
In particular, 0 partitions for bigger chromosomes
And 26 buckets for smaller scaffolds
Saving target partitions to: /home/hwaterma/Documents/MX_TOGA/test_out/target_partitions.txt
Partitioning for query
Saving partitions and creating 59 buckets for lastz output
In particular, 40 partitions for bigger chromosomes
And 19 buckets for smaller scaffolds
Saving query partitions to: /home/hwaterma/Documents/MX_TOGA/test_out/query_partitions.txt
Num. target partitions: 0
Num. query partitions: 40
Num. lastz jobs: 0
Lastz Alignment Step
LASTZ: making jobs
LASTZ: saved 1534 jobs to /home/hwaterma/Documents/MX_TOGA/test_out/temp_lastz_run/lastz_joblist.txt
Parallel manager: pushing job /data/krablab/miniconda2/envs/TOGA/bin/nextflow /home/hwaterma/Documents/make_lastz_chains/parallelization/execute_joblist.nf --joblist
/home/hwaterma/Documents/MX_TOGA/test_out/temp_lastz_run/lastz_joblist.txt -c /home/hwaterma/Documents/MX_TOGA/test_out/temp_lastz_run/lastz_config.nf
N E X T F L O W   ~  version 24.10.0
Launching /home/hwaterma/Documents/make_lastz_chains/parallelization/execute_joblist.nf [deadly_ekeblad] DSL2 - revision: 0432e25129
executor >  local (27)
[e2/21114c] execute_jobs (34) [  2%] 17 of 769, failed: 17, retries: 17
[80/3a5e0e] NOTE: Process execute_jobs (7) terminated with an error exit status (1) -- Execution is retried (1)
executor >  local (27)
[70/2f69ec] execute_jobs (12) [  2%] 18 of 824, failed: 18, retries: 18
[80/3a5e0e] NOTE: Process execute_jobs (7) terminated with an error exit status (1) -- Execution is retried (1)
[cb/61e398] NOTE: Process execute_jobs (26) terminated with an error exit status (1) -- Execution is retried (1)
[0f/1cc334] NOTE: Process execute_jobs (39) terminated with an error exit status (1) -- Execution is retried (1)
[7c/1aa0fe] NOTE: Process execute_jobs (16) terminated with an error exit status (1) -- Execution is retried (1)
[aa/6ec182] NOTE: Process execute_jobs (20) terminated with an error exit status (1) -- Execution is retried (1)
[b5/7cb776] NOTE: Process execute_jobs (21) terminated with an error exit status (1) -- Execution is retried (1)
[71/1845b5] NOTE: Process execute_jobs (27) terminated with an error exit status (1) -- Execution is retried (1)
[34/8005d1] NOTE: Process execute_jobs (25) terminated with an error exit status (1) -- Execution is retried (1)
[df/64091e] NOTE: Process execute_jobs (22) terminated with an error exit status (1) -- Execution is retried (1)
[f6/8f96ed] NOTE: Process execute_jobs (33) terminated with an error exit status (1) -- Execution is retried (1)
[04/06b5b4] NOTE: Process execute_jobs (10) terminated with an error exit status (1) -- Execution is retried (1)
[98/051c7e] NOTE: Process execute_jobs (5) terminated with an error exit status (1) -- Execution is retried (1)
[09/e4de98] NOTE: Process execute_jobs (3) terminated with an error exit status (1) -- Execution is retried (1)
[c2/153283] NOTE: Process execute_jobs (37) terminated with an error exit status (1) -- Execution is retried (1)
[36/f2dec6] NOTE: Process execute_jobs (29) terminated with an error exit status (1) -- Execution is retried (1)
[33/2420be] NOTE: Process execute_jobs (40) terminated with an error exit status (1) -- Execution is retried (1)
[e2/21114c] NOTE: Process execute_jobs (34) terminated with an error exit status (1) -- Execution is retried (1)
When I try to understand the error the run.log:
Lastz Alignment Step
LASTZ: making jobs
LASTZ: saved 1534 jobs to /home/hwaterma/Documents/MX_TOGA/test_out/temp_lastz_run/lastz_joblist.txt
Parallel manager: pushing job /data/krablab/miniconda2/envs/TOGA/bin/nextflow /home/hwaterma/Documents/make_lastz_chains/parallelization/execute_joblist.nf --joblist /home/hwaterma/Documents/MX_TOGA/test_out/temp_lastz_run/lastz_joblist.txt -c /home/hwaterma/Documents/MX_TOGA/test_out/temp_lastz_run/lastz_config.nf
and there is no .nextflow or .nextflow.log get crated.
I beed trying to trouble shoot on my own but just can;'t seem to understand what the code it getting stuck on.

Could you pls try to run a single lastz jobs on the command line? There is something systematically wrong. Likely some input files are not found or so.
@kirilenkobm Could you pls have a look? There must be log files that indicate why the lastz jobs die.

I ran one of the jobs from lastz_joblist.txt:
/home/hwaterma/Documents/make_lastz_chains/standalone_scripts/run_lastz_intermediate_layer.py BULK_1:/home/hwaterma/Documents/MX_TOGA/test_out/target.2bit:MYX_Chr1 /home/hwaterma/Documents/MX_TOGA/test_out/query.2bit:NC_007112_7:0-50000000 /home/hwaterma/Documents/MX_TOGA/test_out/pipeline_parameters.json /home/hwaterma/Documents/MX_TOGA/test_out/temp_lastz_psl_output/bucket_ref_bulk_1/BULK_1_NC_007112_7__1.psl /home/hwaterma/Documents/make_lastz_chains/standalone_scripts/run_lastz.py --output_format psl --axt_to_psl /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/axtToPsl
That has been running for a few hours now with no errors.

Well that is promising.
You align a whole chr1 (how large is that??) against a 50Mb chunk.
If you want to run the test faster, maybe align it to a 5 or 10 Mb chunk

Our first chromosome is 69,199,620 bp.
The command did run  to completion too.
I just do not understand why the larger script is not working.

I have no idea. Could you pls check how much memory the job required and how long it ran?

Maybe your jobs get killed by Slurm on the cluster because they don't get enough memory or runtime?
Did you test running lastz on the actual compute nodes that run the Slurm jobs? Maybe something is not correctly configured there.
Do the jobs die immediately or only after running for a few hours?
Also, maybe test splitting the genomes into much smaller chunks to see if these jobs succeed.

hwaterma@cast-bio540ws02:~/Documents/MX_TOGA$ /usr/bin/time -v lastz
You must specify a target file
lastz-- Local Alignment Search Tool, blastZ-like
(version 1.04.15 released 20210827)
usage: lastz target [query] [options]
(common options;  use --help for a more extensive list)
target, query          specifiers or files, containing sequences to align
(use --help=files for more details)
--seed=       set seed pattern (12of19, 14of22, or general pattern)
(default is<PHONE_NUMBER>010101111)
--[no]transition       allow (or don't) one transition in a seed hit
(by default a transition is allowed)
--[no]chain            perform chaining
(by default no chaining is performed)
--[no]gapped           perform gapped alignment (instead of gap-free)
(by default gapped alignment is performed)
--step=        set step length (default is 1)
--strand=both          search both strands
--strand=plus          search + strand only (matching strand of query spec)
(by default both strands are searched)
--scores=        read substitution and gap scores from a file
--xdrop=        set x-drop threshold (default is 10sub[A][A])
--ydrop=        set y-drop threshold (default is open+300extend)
--infer[=]    infer scores from the sequences, then use them
all inference options are read from the control file
--hspthresh=    set threshold for high scoring pairs (default is 3000)
ungapped extensions scoring lower are discarded
 can also be a percentage or base count
--gappedthresh= set threshold for gapped alignments
gapped extensions scoring lower are discarded
 can also be a percentage or base count
(default is to use same value as --hspthresh)
--include=       read command line arguments from a text file
--help                 list "all" options (but the online documentation is
more complete)
--help=files           list information about file specifiers
--help=shortcuts       list blastz-compatible shortcuts
--help=defaults        list scoring defaults for your current settings
--help=yasra           list yasra-specific shortcuts
See the online documentation at http://www.bx.psu.edu/~rsharris/lastz for
the most up-to-date information.
Command exited with non-zero status 1
Command being timed: "lastz"
User time (seconds): 0.00
System time (seconds): 0.00
Percent of CPU this job got: 33%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 2240
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 97
Voluntary context switches: 1
Involuntary context switches: 0
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 1
The job dies immediately on our local computer. This computer does not have a time window.
I have got it to run locally on our computer cluster but it does not run in the 3 day window we are allowed. It does not run on Slurm but, I am working with the computer cluster IT for that issue.

After /usr/bin/time -v
which is just the command to track time and mem consumption,
pls provide the full lastz command with all parameters

I don't think I am doing this right. I'm sorry for being a little slow to this computer coding but this is what I ran and got:
(TOGA) hwaterma@cast-bio540ws02:~/Documents/MX_TOGA$ /usr/bin/time -v lastz /home/hwaterma/Documents/MX_TOGA/test_out/target.2bit:MYX_Chr1 /home/hwaterma/Documents/MX_TOGA/test_out/query.2bit:NC_007112_7:0-50000000
FAILURE: fopen_or_die failed to open "/home/hwaterma/Documents/MX_TOGA/test_out/target.2bit:MYX_Chr1" for "rb"
Command exited with non-zero status 1
Command being timed: "lastz /home/hwaterma/Documents/MX_TOGA/test_out/target.2bit:MYX_Chr1 /home/hwaterma/Documents/MX_TOGA/test_out/query.2bit:NC_007112_7:0-50000000"
User time (seconds): 0.00
System time (seconds): 0.00
Percent of CPU this job got: 100%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 2880
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 227
Voluntary context switches: 1
Involuntary context switches: 0
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 1
It seems that it can not read the target file.

your command /usr/bin/time -v lastz etc is all correct, but it outputs an error
FAILURE: fopen_or_die failed to open "/home/hwaterma/Documents/MX_TOGA/test_out/target.2bit:MYX_Chr1" for "rb"
which means the lastz command without measuring time and mem consumption (via /usr/bin/time -v ) should also crash immediately.
Is the lastz command exactly the command that was running for a long time?
Maybe try this to see if your /usr/bin/time -v works.
/usr/bin/time -v find . | wc 	Command being timed: "find ." 	User time (seconds): 0.00 	System time (seconds): 0.00 	Percent of CPU this job got: 1% 	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.53 	Average shared text size (kbytes): 0 	Average unshared data size (kbytes): 0 	Average stack size (kbytes): 0 	Average total size (kbytes): 0 	Maximum resident set size (kbytes): 3032 	Average resident set size (kbytes): 0 	Major (requiring I/O) page faults: 0 	Minor (reclaiming a frame) page faults: 217 	Voluntary context switches: 66 	Involuntary context switches: 0 	Swaps: 0 	File system inputs: 0 	File system outputs: 0 	Socket messages sent: 0 	Socket messages received: 0 	Signals delivered: 0 	Page size (bytes): 4096 	Exit status: 0

when I run that I get:
/usr/bin/time -v find . | wc Command being timed: "find ." User time (seconds): 0.00 System time (seconds): 0.00 Percent of CPU this job got: 1% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.53 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 3032 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 217 Voluntary context switches: 66 Involuntary context switches: 0 Swaps: 0 File system inputs: 0 File system outputs: 0 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0
-bash: syntax error near unexpected token `('

Exit status: 0
means that this test works.
Where is this coming from?  -bash: syntax error near unexpected token `('

when I run /usr/bin/time -v find . | wc Command being timed: "find ." User time (seconds): 0.00 System time (seconds): 0.00 Percent of CPU this job got: 1% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.53 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 3032 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 217 Voluntary context switches: 66 Involuntary context switches: 0 Swaps: 0 File system inputs: 0 File system outputs: 0 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0
the output is:
-bash: syntax error near unexpected token `('

Really weird. Here is what I get.

You have a proper linux system?

no idea. Pls send me this folder gzipped for download somewhere and I'll run this lastz locally on my system.
Lets see if that works

I tar the files I am using. Could I get an email to send it to?
Thank you so much again for your time on this!

The 2bit files will be too large for email.
Pls also gzip it.
Then maybe put it on google drive for me to download.

I uploaded it to my google drive. Just need an email to share it with.

I downloaded the files, but I would need the exact command you are running.
The files are Danio and not target.2bit.
Also lastz takes parameters.

I think I found the problem. While 48.4% of the danio assembly is lower case = softmasked, you don't have any masking for the query.
twoBitToFa MX.2bit stdout | faSize stdin<PHONE_NUMBER> bases (65000 N's<PHONE_NUMBER> real<PHONE_NUMBER> upper 0 lower) in 384 sequences in 1 files
Pls run RepeatModeler2 on it, and use the resulting lib for repeatMasking.
Then the lastz pipe will likely work.
Not (properly) masking is the #1 issue that people have when the pipe is not running smoothly :-)

I masked my genome and it still not running. I have reached out to our school tech support. Hoping to get this figured out and will let you know if we ever get to the bottom of this.

Pls send me the masked genome files such that we test the same thing.
Pls let me know if any of your lastz jobs finish or run at all (if not, that is most likely a technical problem).
And pls send me the exact lastz command that you are running

Great!, thank you, Michael.
I just sent you the Google Drive link. So far, none of my commands work and I do not have any .nextflow.log file to check.
This is the current command that I'm running:
./make_chains.py dog ferret run_01/c_familiaris.2bit run_01/m_putorius_furo.2bit --pd run-01_out -f --chaining_memory 16 --seq1_limit 175 --seq2_limit 50 --cluster_executor slurm --cluster_queue togaslurm*

When you mention the lastz command, I checked the first the run.log:
LASTZ: making jobs
LASTZ: saved 3996 jobs to /localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/run-01_out/temp_lastz_run/lastz_joblist.txt
Parallel manager: pushing job /home/mmora30/.local/bin/nextflow /localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/parallelization/execute_joblist.nf --joblist /localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/run-01_out/temp_lastz_run/lastz_joblist.txt -c /localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/run-01_out/temp_lastz_run/lastz_config.nf

then the individual command:
/localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/standalone_scripts/run_lastz_intermediate_layer.py BULK_20:/localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/run-01_out/target.2bit:JAAUVH010000216:JAAUVH010000171:JAAUVH010000025:JAAUVH010000271:JAAUVH010000217:JAAUVH010000165:JAAUVH010000019:JAAUVH010000275:JAAUVH010000230:JAAUVH010000016:JAAUVH010000078:JAAUVH010000221:JAAUVH010000282:JAAUVH010000014:JAAUVH010000013:JAAUVH010000326:JAAUVH010000117:JAAUVH010000101:JAAUVH010000128:JAAUVH010000325:JAAUVH010000018:JAAUVH010000072:JAAUVH010000021:JAAUVH010000181:JAAUVH010000094:JAAUVH010000135:JAAUVH010000126:JAAUVH010000169:JAAUVH010000273:JAAUVH010000077:JAAUVH010000350:JAAUVH010000254:JAAUVH010000152:JAAUVH010000227:JAAUVH010000263:JAAUVH010000341:JAAUVH010000145:JAAUVH010000112:JAAUVH010000001:JAAUVH010000156 BULK_134:/localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/run-01_out/query.2bit:AEYP01117455:AEYP01117479:AEYP01117478:AEYP01117477:AEYP01117476:AEYP01117475:AEYP01117474:AEYP01117473:AEYP01117472:AEYP01117471:AEYP01117470:AEYP01117469 /localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/run-01_out/pipeline_parameters.json /localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/run-01_out/temp_lastz_psl_output/bucket_ref_bulk_20/BULK_20_BULK_134__3996.psl /localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/standalone_scripts/run_lastz.py --output_format psl --axt_to_psl /localData/workspace_mm/temporal_tasks/lastz-chains/make_lastz_chains/HL_kent_binaries/axtToPsl

Any comments?

Actually, it could be easier if you tell me the NCBI accession of the dog and the ferret genome.
I'll try to run the alignments on our system. and if it works, I can send you the chains

Seems like your ferret is a very old assembly. I would recommend GCF_011764305.1.
For dog, I would recommend GCA_011100685.1 = canFam4, which is better than the more recent assemblies.
I have both assemblies ready and repeat-masked.
Let me know if that would help you

Sounds great!
Actually, I'm using Ensembl genomes, and I tried to use the latest version available for three options:
Human-ferret, Mouse-ferret and Dog-ferret. I know that there are results available for the first two, however, those are from 2020-21. So I pretend to run it again with the release 113 from Ensembl.
Here is the ID accession:
ferret
https://ftp.ensembl.org/pub/release-113/fasta/mustela_putorius_furo/dnaMustela_putorius_furo.MusPutFur1.0.dna_rm.toplevel.fa.gz
dog
https://ftp.ensembl.org/pub/release-113/fasta/canis_lupus_familiaris/dna/Canis_lupus_familiaris.ROS_Cfam_1.0.dna_rm.toplevel.fa.gz
mice
https://ftp.ensembl.org/pub/release-113/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna_rm.toplevel.fa.gz
human
https://ftp.ensembl.org/pub/release-113/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_rm.toplevel.fa.gz

Please, let me know if I can help in something with the pairwise alignments to obtain the chains!
Thank you for your help!

@MichaelHiller Please let me know if I can help with something, I will be attentive to any comment! Thank you again

Dog to ferret chains are done. I'll send you everything via a download link

Sounds great, I answered you by mail!
Thank you again for the help!

I can try. Which is the reference? danRer11?

Yes please :)

Is running now. Pls send me a quick email and I'll share the chains once they are done.

Pls find the chains and nets on https://genome.senckenberg.de/download/forHannahFish/
and send me a ping when you downloaded it.


Marvell DPU Needed

Hi Dhruv!

Waiting on HW with onboard BMC.

Putting in PO but the BMC onboard isn't ready


RFC: Phase 3

Once the IPFS devgrant, and the Substrate grant is complete, we will have the following done:

HTTP API Scaffolding

/pubsub/{ publish, subscribe, unsubscribe, peers, ls }
/swarm/{connect, peers, addrs, localAddrs, disconnect }
/id
/version
/shutdown
/block/{ get, add, rm, stat }
/dag/{ put, resolve }
/refs and /refs/local
/bitswap/{ stat, wantlist }
/cat
/get
/add

client or server DHT + swarming support
UnixFS support

We would love your input for what direction to move toward next. There are some things we're thinking about:

pinning and different gc strategies
keygen
pubsub fixes

There are also some acute items from @stebalien already that we haven't forgotten about... but what else? Some time has passed so it bears repeating the question. Also, no guarantees but we'll do our best :crossed_fingers:

@aphelionz @vmx I don't monitor this repo too closely: hit me up<EMAIL_ADDRESS>when you are ready to do the add portion of the work: there's a lot of stuff "ready to translate 1:1", but still a bit in flux.

Thanks @ribasushi . Tagging @koivunej here as well.

Thanks everybody! We'll be revisiting this discussion in a future issue.


Batch insert is slow either using query or execute

Is your feature request related to a problem? Please describe.
We are trying to use either query or execute methods to do a batch insert and it's working. However, the insert is very slow, and we tried several ways to speed up it a little, like:

Creating the indexes just after the insert
Changing the Pragma Mode to MEMORY and turning off the synchronization
Create a batch insert instead of individual inserts
Have focused ways per OS. It seems that Query works better for iOS and Execute works better for Android.

None of them solved the problem, but they made the app slightly faster. It's not sufficient to solve our problems, tough.
Describe the solution you'd like
Do you have any suggestions on how to handle it?
Is there a specific method for batch inserts?
Describe alternatives you've considered
Additional context

@fbalbinoribeiro Well query method is not made to make insert but only select. Can you give more info on your batch and how large is it. looking at your execute method i do not thing it is a good idea to saveToStore after each execute command as this is time consuming but this apply only for Web. The best is to share a small repro of your app so i can look at it with more detail.

@fbalbinoribeiro Any news can you share your code and your batch insert commands so i can have a look

@jepiqueau sorry for the delay. I'll send some piece of codes for you.
A little more context:

We tried to use just execute method for everything, but the iOS froze when doing massive sequential insert operations.
Before we were wrongly using the query method for everything, and it made memory leaks on Android. Then, when we changed to always use the execute method, we started seeing iOS frozen. That's why we are splitting it up.
Our code is a little tricky because we use NgRX and the logic is within it. I will try to show some piece of code that does the calls.

1 - This is called sequentially and a huge amount of times on the loading functionality:
  saveTheDownloaded$ = createEffect(() =>
    this.actions$.pipe(
      ofType(Actions.newDownloaded),
      concatMap(({ info }) => from(this.databaseService.upsertByQuery(info))),
      map(() => Actions.saved()),
    )
  );

It has a big size of information (like some MB's).
2 - Then, we are using that wrapper that I've created:
 async upsertByQuery(query: string): Promise<boolean> {
      if (this.infoService.isIos()) {
        await this.query(query);
      } else {
        await this.execute(query);
      }

      return true;
  }

All these codes that I show you run several times. In the end, about 1GB of information could be inserted.
That combination was the best insert result that we had found specifically.
3 - These are the pragma journal codes:
  async setPragmaJournalModeToWal() {
    await this.query('PRAGMA journal_mode = MEMORY; PRAGMA synchronous = OFF');
  }

  async setPragmaJournalModeToDelete() {
    await this.query('PRAGMA journal_mode = DELETE; PRAGMA synchronous = ON');
  }

We set the pragma to memory at the very beginning of the loading operation and set it back only when everything is inserted.
4 - To try to speed up a little more, I'm only creating the indexes after all the inserts have been made.
Thanks a lot for your help.
Any further questions that you want for me, feel free to ask me.

@fbalbinoribeiro Can you give the database schema and some  insert command that you do with some data  example so i can trye recreating the issue. I never used NgRx and neither modifies the pragma journal_mode and synchronous like you did. May be the issue is due to the cache_size so you may play with this

@fbalbinoribeiro as i do not get feedback i close the issue


Take care of the reported Security issues reported by github

https://github.com/srcfl/srcful-gateway/security

Updated the offending modules and the issues were automatically closed.


Fix the conflict of the same identifier during encoding.

Description

Related Issues

Checklist

[ ] Is this code covered by new or existing unit tests or integration tests?
[ ] Did you run make unit_testing and make integration-testing successfully?
[ ] Do new classes, functions, methods and parameters all have docstrings?
[ ] Were existing docstrings updated, if necessary?
[ ] Was external documentation updated, if necessary?

Additional Notes or Comments

I approved, but we can add a test!

Sure, done


Weight Update with Padding for NHWC_Custom and NHWC_RSCK

I have added support in Weight Update kernel for NHWC_custom and NHWC_RSCK format. Currently it is giving correct result for convolutions with padding and without padding.

Can you please fix the CI issues, then we can merge

This is about C89 conformance or mixed declaration and code: https://travis-ci.org/hfp/libxsmm/jobs/200193853#L3393 (and following lines).
Moving variable declarations into the leading block is the typical solution, but if it's destroying locality of the code one can also introduce an additional scope {} (curly braces), and start (additional) variable declarations inside).

can you please remove src/generator_convolution_weight_update_avx512.c.backup  from the changeset?


[Bug] Changing status when editing seedlot on review page

Describe the Bug
The seedlot status is changing whenever the admin makes a change and save it.
Expected Behaviour
Status should stay the same after editing it.
Actual Behaviour
Status always going back to pending.
Steps To Reproduce
Steps to reproduce the behaviour:

Go to an Approved or Complete seedlot
Click the button to edit it
Change a field
Click the save butotn
Notice the status is back to Submitted

@mgaseta I registered a seedlot and got it into Approved status. When I updated a comment on the form in APP status, it stayed that way after saving so it looks like this is good. We will need to get this into test/production to see if it works on COM status seedlots too


e2e: Add test to pd that disk contents are preserved

Issue #11012 reported that disk contents may be lost (sometimes).
We should have an e2e test to verify this is not happening.
(If it is happening, we should then fix it!)

Doing a WIP PR to get results from GCE while I concurrently test with AWS

thanks!  Much needed

Tweaked to change the image to busybox so we get /bin/sh, and I think this will pass on AWS now.  (Worked when I ran the test directly using hack/e2e.go, and now trying a full-run).   However, because GCE e2e passed before, I don't think GCE e2e is actually running this test, perhaps the Github runner doesn't but the full test suite does though (?)
I'm going to try running directly on GCE.
The good news (I guess) is that this didn't immediately show a problem, so hopefully #11012 is caused by something else.

@k8s-bot test this please
(seemingly unrelated failure in should serve a basic endpoint from pods)

No longer WIP;  passes for me on AWS & GCE (when run directly for GCE).  I'm not sure why this test is skipped on GCE (if it indeed is); it seems fairly important that this work reliably!  Maybe whatever flake it is that causes us to skip it on GCE is in fact the scenario which causes data loss in #11012 (I've asked for clarification there in the hope of getting a clue as to what could be going wrong).
In terms of merging: Low risk, because only e2e tests, and I think it is important to test this, but given that it hasn't (yet) shown a problem I don't think there's any urgency in merging this pre v1.  I'm going to keep it on my integration branch anyway for AWS.

Saad, do you have time for this one?  Not critical for 1.0 (test only)

Yep, I'll take a look.

LGTM Thanks @justinsb!


Running the script on different platforms

Would Running the script on different platforms generate different binaries from the same source files and same options? (seems like it's the case on windows vs osx)
Any way around it? (it's  git related issue.. Too many modified files at every commit)

I'm not sure, but I imagine running e.g. optipng on two different systems could result in different images, yes. Might differ if it's version mismatches too.
I wouldn't really keep generated files under version control though.

Me neither but unfortunately it wasn't my decision, some folks still live in the era of "build and copy over the server" instead of deployment scripts. Thank you!


JVM Crash: Fullscreen doesnt work

Issue details
If i try to toggle fullscreen mode while playing, i get an JVM crash.
Reproduction steps/code
Graphics.DisplayMode primaryMode = Gdx.graphics.getDisplayMode();
Gdx.graphics.setFullscreenMode(primaryMode);

Full Code:
//toggle fullscreen mode
if ((Gdx.input.isKeyPressed(Input.Keys.CONTROL_LEFT) || Gdx.input.isKeyPressed(Input.Keys.CONTROL_RIGHT)) && Gdx.input.isKeyJustPressed(Input.Keys.F)) {
    //toggle fullscreen mode
    if (Gdx.graphics.isFullscreen()) {
        Gdx.graphics.setWindowedMode(this.lastWidth, this.lastHeight);
    } else {
        Graphics.DisplayMode primaryMode = Gdx.graphics.getDisplayMode();
        Gdx.graphics.setFullscreenMode(primaryMode);
    }
}

Version of LibGDX and/or relevant dependencies
Please provide the version(s) affected.
Stacktrace
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x00007ffcbadcaceb, pid=10456, tid=1724
#
# JRE version: Java(TM) SE Runtime Environment (8.0_91-b15) (build 1.8.0_91-b15)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.91-b15 mixed mode windows-amd64 compressed oops)
# Problematic frame:
# C  [glfw.dll+0xaceb]
#
# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
#
# An error report file with more information is saved as:
# D:\Users\Justin\IdeaProjects\island-exploration-rts\hs_err_pid10456.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
AL lib: (EE) alc_cleanup: 1 device not closed

hs_err_pid10456.log
Please select the affected platforms

[ ] Android
[ ] iOS (robovm)
[ ] iOS (MOE)
[ ] HTML/GWT
[x] Windows
[ ] Linux
[ ] MacOS

I have already found the solution:
Gdx.input.isKeyJustPressed(Input.Keys.F) fixed this issue.

Maybe the render call is trying to avoid/reduce misshapen rendering when the window is resized?

During normal window resizing, which happens through call to GLFW.glfwPollEvents(), normal rendering loop seems to stop, as it is blocked by GLFW.glfwPollEvents() for the duration of window resize dragging (at least on Mac). I don't know if this blocking is a bug or intended, but resizing the window triggers the resize callback, and the window never shows garbage (LWJGL2 did, IIRC), so it works well.
However, setFullscreen/WindowedMode triggers the resize callback immediately, which, as it is usually called inside render(), causes nested render() invocation. This is likely not desired behavior.
Two ways to fix this come to mind:

Disable the resize callback when setFullscreen/WindowedMode is called
Postpone the real window mode change so that it happens at the beginning of next frame.

Option 1. feels more intuitive, but could still lead to bugs, as application may not expect screen resolution to change mid-frame. The frame may then still show incorrectly resized frame, as it is rendering for the original screen size. 2. therefore is probably more correct. Without any modifications to resize callback, render() would still get called twice per frame. I don't know if GLFW expects glfwSwapBuffers to be called inside the callback, but if not, it may be worthwhile to disable the render() call from the resize callback when it happens during window mode change, so that it doesn't delay the whole operation.

Noncontinuous rendering could be a problem if the frame is drawn with the wrong size. #2 sounds good to me.