Improve citation information & app name (for now): EnrichmentMap:RNA-Seq

General information
Associated issues: #82
Checklist
Author:

[x] One or more reviewers have been assigned.
[x] N/A -- Automated tests have been included in this pull request, if possible, for the new feature(s) or bug fix.
[x] The associated GitHub issues are included (above).
[x] Notes have been included (below).

Reviewers:

[ ] All automated checks are passing (green check next to latest commit).
[ ] At least one reviewer has signed off on the pull request.  Reviewers have two business days to review the pull request, after which the author may merge in the pull request unilaterally.

Notes

Improves the citation information, as discussed.
Provisionally the shown app name to 'EnrichmenMap:RNA-Seq'.  This makes it clearer it's not exactly the same as EnrichmentMap:Cy3, and it's better for search.  We can change this later, but it's an improvement for now.

Just merging, as there's not much to this.  Basically text updates.


Indexer and scanner processes do not appear to be running on Windows

AppMaps are not indexed or scanned on Windows. None of the expected subprocesses are present in the task manager (assuming they're children of the IDE). No errors are reported.

It looks like the binaries are not downloaded. I'd expect binaries to exist in these subdirectories, but they're empty:
PS C:\Users\Dustin\AppData\Local\JetBrains\appland-plugin> Get-ChildItem -Recurse

    Directory: C:\Users\Dustin\AppData\Local\JetBrains\appland-plugin

Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
d-----          9/9/2022   2:10 PM                appmap
d-----          9/9/2022   2:12 PM                scanner

Thanks!
Fixed by https://github.com/applandinc/appmap-intellij-plugin/pull/81/commits/88382162181cf1d0e27bae79bd89a5381cf31aa3
This wasn't found by CI, because it was recently decided on Slack not to run the plugin tests on Windows CI

Fixed with 0.11.0-2, please reopen if it's still a bug on your machine.
https://github.com/applandinc/appmap-intellij-plugin/releases/tag/install-guide-preview


[backstage-plugin-jira] Hise issue filter by configuratin

Hello,
I installed the jira plugin to test it, and I met problem with the issue filter. The jira workflow configuration is very complicated and states on this filter are hard to apprehend. That's why I want to provide a patch hide this filter by configuration. Do you think this patch could be accepted and merged for the next release ?
Regards,
Stéphane Mori

Linked to pull request : https://github.com/RoadieHQ/roadie-backstage-plugins/pull/997

How can I link the pull request to this issue ? I can see "No branches or pull requests" in right menu.


chef-provisioning should not be a dependency

For some reason, chef-provisioning has been added to metadata.rb as a dependency.  While I understand chef-provisioning is used for testing this cookbook, I don't see the need for it to be in metadata.rb.  If anything, it should be in the Gemfile.  Please remove this dep.

Removed in this commit for 1.0.0.

Thanks


Vickel: Watch becky[\W_]*+shawver(?!.com(?<=beckyshawver.com))

Vickel requests the watch of the watch_keyword becky[\W_]*+shawver(?!\.com(?<=beckyshawver\.com)). See the MS search here and the Stack Exchange search in text, in URLs, and in code.

becky[\W_]*+shawver(?!\.com(?<=beckyshawver\.com)) has been seen in 1 true positive, 0 false positives, and 0 NAAs.

Approved by tripleee in Charcoal HQ


[Fix](full compaction) Full compaction should not do ordered data compaction

What problem does this PR solve?
Issue Number: close #xxx
Related PR: #xxx
Problem Summary:
Release note
None
Check List (For Author)

Test

[x] Regression test
[ ] Unit Test
[ ] Manual test (add detailed scripts or steps below)
[ ] No need to test or manual test. Explain why:

[ ] This is a refactor/code format and no logic has been changed.
[ ] Previous test can cover this change.
[ ] No code files have been changed.
[ ] Other reason

Behavior changed:

[x] No.
[ ] Yes.

Does this need documentation?

[x] No.
[ ] Yes.

Check List (For Reviewer who merge this PR)

[ ] Confirm the release note
[ ] Confirm test cases
[ ] Confirm document
[ ] Add branch pick label

run buildall

regression test will be added later.

please update "Problem Summary"

run buildall


Add configuration details to HTML report?

Is your feature request related to a problem? Please describe.
Yesterday evening I was able to produce a stryker report with an awesomly high score and it took close to an hour to run. I only remember that I used the command runner and that I had less test suites configured.
To improve performance I switched to jest and had many iterations until it worked, but only with a much lower resulting score (and many timeouts and runtime errors, but that's a topic for a different issue).
I still have that report open in a tab in my browser, but it's no longer on the disk.
So far I was not able to get back to my old configuration (I know, should have commited that, but I didn't...)
Describe the solution you'd like
If (at least) the configuration that was used (and ideally a list of the files that have been copied into the sandbox at that point in time) would be available from the HTML report, it would also be more easy to reproduce that report for others looking at it (or verify it was produced with what is in the repo, if needed).
There are many more ideas for information in the report:

OS and stryker/test runner versions
duration it took to generate the report
final result of test runner config (e.g. the resulting jest config that was actually applied after merging the many options)
But I think the config file/object would be the most valuable to be able to reproduce the report.

Describe alternatives you've considered
I will try to use the "Local history" feature of my IDE to recover the config, and for sure commit such beautiful setups into git in the future...
Additional context
Maybe this becomes less of an issue with the reduced amount of time it takes to produce a report soon, but it would still add transparency to a report, especially with the possible complexity of tools invoked.

It surprises me that there is no feedback on this feature request at all.
Is it more because you think that it's not worth investing time, or because you think it's hard to do?

Hi @karfau

Is it more because you think that it's not worth investing time, or because you think it's hard to do?

Neither. We are an open-source project and thus have limited time to invest in issues and features. Sometimes it happens that an issue is reported and goes unnoticed. That seems to have happened here, I'm sorry about that. We're not bad people, sorry.
On the bright side: I think we've already implemented this feature... sort of. StrykerJS will add your config to the mutation testing report, but it is currently not yet displayed in the HTML report.
StrykerJS uses the mutation-testing-elements, in which we recently added the ability to add configuration to the json report:
https://github.com/stryker-mutator/mutation-testing-elements/blob/e434aa9b1c56d90058396423a22bfe75300a8ab2/packages/report-schema/src/mutation-testing-report-schema.json#L9-L12
Since<EMAIL_ADDRESS>this "config" property is filled with the config object. The easiest way to see it is to use the "json" reporter, but you could also look in the source of the HTML reporter and search for "config".
We're planning to add it visually to the HTML report, if you have some ideas about that, please feel free to open an issue there.

Thanks for the update.
Although it doesn't solve the problem for the report that I used, since it was created by v4, I think anything relevant will happen in the new issue I created, so I'll close this one.


Etiquette note

Hello Cogstack (Amos right?). Just a quick etiquette poke - sorry! Provenance wise, it's bad form to start a new repo without acknowledging existing github projects. It's better to fork (e.g. here or here
:)

@RichJackson happy to acknowledge, we are tidying up KHPinformatics (and the original CogStack should have gone into this). Happy to cite work and papers however if you'd like.


yarn test:generators => attempt to override $UID readonly variable

When running $ yarn test:generators I get the following error : script/lib/docker: line 2: UID: readonly variable.
Indeed, script generators/root/templates/base/script/lib/docker attempts to set $UID global var, which is reserved by some shells.
Running environment :

Shell : zsh 5.8
OS : MacOS 12.0.1

That's strange, this script is only called by the scripts in the script directory that use a shebang of #!/bin/sh that doesn't have this special variable. Maybe MacOS implementation of sh doesn't work the same way.
Anyway we can easily rename this variable to fix this problem.

Apple ways 😅 :
$ which sh
/bin/sh

$ sh --version
GNU bash, version 3.2.57(1)-release (arm64-apple-darwin21)
Copyright (C) 2007 Free Software Foundation, Inc.


Enable checking against mypy with minimal set of fixes

4 significant checks are disabled:

strict_optional - check that an object might be None on access
warn_no_return - requiring a return
assignment - any assignment of a variable of a wrong type
var-annotated - a type annotation is missing

I'm sorry, this is is still way to much rewriting of code. I will not under any circumstances change the way I write code in a dynamically typed language to suite a type checker. The checker should only be verifying that existing annotations are correct.
The only edits which are acceptable are edits to the annotations. If you can't make that work, then mypy is not the right tool.

So, it seems that if you can configure mypy to not require any of the code changes included here, then it would be something we can use.
However, I will note that simply commenting lines of code may not be the best solution in some cases. For example. there is little difference in def __init__(self) -> None: and def __init__(self): # ignore. I would expect to be able to do def __init__(self):. And the same goes for every time we use Python's dynamic nature. There shouldn't need to be a comment on every such line. A global config option would be preferable. If mypy can't do that, then its not the right tool for the job.

Yes, it seems that the projects goals and this PR's goals are a bit at odds. It sounds like Python Markdown only cares about checking that types are defined, but type checking itself is not desired.
I will add one point though. There seems to be some disdain for explicitly defining a function has no return, but if that is disabled, it seems you have no actual way of checking if a return is required and missed? Maybe I'm wrong about this?

The only thing that should be checked is that existing annotations are correct.

In which way, just purely conceptually, do you think this is supposed to be accomplished? What is "correct" in isolation?
The only known way to do this is to check code that uses annotated members. If something doesn't match up then it shows an error, and you need to check if it's the code that is wrong or the annotation that is wrong.

I'm okay with that. The only thing that should be checked is that existing annotations are correct. Anything that is not annotated should be ignored. Seems like a simple concept. I don't understand why that is so hard... except that perhaps it is because the goal of the type checker is to enforce static typing, which is something I have repeatedly said I am not interested in.

That's fair, and it is possible I've misinterpreted some interaction. So yeah, I'm good with that.

The only known way to do this is to check code that uses annotated members. If something doesn't match up then it shows an error, and you need to check if it's the code that is wrong or the annotation that is wrong.

Yes, when its annotated that is reasonable. And when it is not annotated, it should be ignored.
In other words, suppose we have to functions, one of which is annotated and one which is not. The tool would see a line of code which calls the annotated function, It would see the annotation and confirm that the return value matches up. However, when it sees the unannotated function is would not confirm anything about the return value as there is nothing to confirm. That is what I expect to happen.
In the first case, the assumption would then be that perhaps the annotation is wrong. However, we could check for a potential bug in the code and fix that instead if need be. In the second case, we are alerted to nothing as it has been for many years.
And no, I don't want to have to add an ignore comment to every one of those lines. The tool should just ignore them either by default or via a global setting.

I think mypy in the current config matches what you describe - it validates only things that are annotated.
Which of the comment threads don't match this? There was an example where something clearly annotated as str | Element is being passed to something clearly annotated as str. How is that not a correct finding that either the annotation is wrong or the code can have a problem?
Although a big snag might be in the fact that the whole standard library is annotated, so usages (inside annotated functions) are checked against it as well.
And there was one consistently mentioned limitation of mypy - that it can't cope with reassigning a different-typed value to the same variable name, and it should be able to. I have replied with "limitation" to those threads. But it's a conceptually different problem. And if we do look at it separately, perhaps this pull request can be said to have only this as a blocker.

Which of the comment threads don't match this? There was an example where something clearly annotated as str | Element is being passed to something clearly annotated as str. How is that not a correct finding that either the annotation is wrong or the code can have a problem?

I've never suggested that that was the case. In fact, if the issue is that the annotation was wrong, I have made no objection. However, I have consistently stated that if the code is wrong, then each individual instance should be addressed as a separate bug, not included wholesale in this large PR. This PR (or one like it) should not be changing code. only annotations. And yet, you have repeatedly ignored that request.

And there was one consistently mentioned limitation of mypy - that it can't cope with reassigning a different-typed value to the same variable name, and it should be able to. I have replied with "limitation" to those threads. But it's a conceptually different problem. And if we do look at it separately, perhaps this pull request can be said to have only this as a blocker.

And a very big blocker is it, I have stated repeatedly that I will not change this lib to be statically typed, which mypy requires. In other words, I will not change the code to appease a tool which is designed to enforce something we are not enforcing. And it is unreasonable to expect us to ignore-comment every single dynamically typed object in our code line-by-line. If mypy had a global option to not enforce that, then it wouldn't be a tool which enforced static types. Therefore, it seems that if does not fit our needs.


ddev composer could have a config.yaml item to determine its expected composer.json location

Is your feature request related to a problem? Please describe.
I do not have the composer.json on the root level. I cannot use ddev composer then.
For convenience, I already have set the config.yaml setting working_dir= to the main web directory. I would expect that to influence composer's working directory as well.
$ ddev composer install

runs
Failed to run docker-compose [-f /home/jonas/www/ratbacher.de/.ddev/docker-compose.yaml -f /home/jonas/www/ratbacher.de/.ddev/docker-compose.env.yaml -f /home/jonas/www/ratbacher.de/.ddev/docker-compose.redis.yaml exec -w /var/www/html -T web bash -c composer install], err='exit status 1', stdout='', stderr='Composer could not find a composer.json file in /var/www/html

which ignores the working_dir= - setting but instead uses explicitly exec -w /var/www/html
Describe the solution you'd like
ddev composer should either have the possibility to use a composer_root_dir= setting or just use the already existing working_dir=. Both would make sense to me. The 1st implementation would not be breaking, though.
Describe alternatives you've considered
ddev composer --working-dir=/var/www/html/webroot ... works, but is tedious.
ddev ssh, then composer works also, but defeats the purpose of a ddev composer command and the according *-composer hooks.
Thank you for considering!

I'm sure you already know that you can ddev ssh and composer install -d .... On macOS and Linux this is completely equivalent, and it might be on Windows with NFS. However, ddev composer... on regular Windows is hugely better because of its handling of symlinks in the container.

That's why it would be great when teams could use ddev composer... even when composer.json is not on the root dir.

It looks like it is here https://github.com/drud/ddev/blob/6ba9fd61c8f1984b165e928523de282b6e412fcf/pkg/ddevapp/composer.go#L20 where the fixed dir is given. Sorry, I am a Go noob.
Could we get the configured working_dir (or a new option composer_root_dir) there?

In v1.11, ddev composer install -d <somedir> works fine. I'm going to close this assuming that works for you @jonaseberledmind
ddev composer install -d junk1 will install into /var/www/html/junk1 (assuming a composer.json there)
ddev composer install -d /var/www/html/junk1 does the same.

Maybe we could revisit this topic @rfay?
I think ddev exec composer (which respects the working_dir) should be the same as ddev composer.

ddev exec composer works fine for non-Windows OS. And it should also work with -d. I'm not sure the question you're asking @jonaseberle - The reason ddev composer exists really is for Windows, where symlinks have to be cleaned up.

I am not taking this. We are a mixed team and ddev composer is  way easier to remember for all. ddev exec... is for the specialists.
Please let ddev composer use the working directory specified in config.yaml.

Sorry, I didn't understand most anything you were saying. Ever. For most people, defaulting to working dir for would break all composer builds. For example, with Drupal the composer.json is in root, and working dir is web.
Reopening this, but please propose a robust solution that might work for most people.  The vast majority of composer builds for anything I'm familiar with put composer.json in repo root .
I suspect you need a new config element, not working dir?

A configuration option in the yml file to change the working dir would be great!
I dont want to add a directive -d /var/www/html/Source on each execution.

That's a really good workaround. And it goes ahead and provides the extra fixup that ddev does on Windows because it still uses ddev composer

It's worth noting that you can place that in .ddev/commands/web/composer, which means it'll replace the standard ddev composer command, which is a bit easier cognitively and means there's no real benefit to a config property for it.
Although it's worth noting that you'll probably want to also add something like PATH=$PATH:/var/www/html/SUBPATH/vendor/bin to .ddev/homeadditions/.bash_aliases so it picks up the compose bin path!

@andrewbelcher No, it is not possible to replace the default command.

Apologies, you are completely right! Perhaps allowing that would be worth considering.

ddev composer is mostly a wrapper on composer, but it has the subcommand ddev composer create, which is a wrapper on composer create-project, which is a different animal. Maybe we'll figure out how to do that differently some day.

Maybe there is an argument for allowing the composer dir to be configurable then. Would resolve the bin path issue too. Though it's such an edge case it's probably better to just discourage that set up and leave a bit of pain for those that plough on or inherit something like that!

I definitely think there's some improvement for ddev composer down the pike.
See also

https://github.com/drud/ddev/issues/2680
https://github.com/drud/ddev/issues/2547
and especially https://github.com/drud/ddev/issues/2422


Training ended with code 139 at 185215 step

Hi @kan-bayashi ,
I am trying  ParallelWaveGAN trainng for test dataset, which generated Tacotron2 model in espnet TTS.
The training stopped with error code 139 in the middle of processing.
The voice generation with checkpoint-185000steps.pkl (and elder) is poor. Some words are skipped.
How may I investigate this case and fix it?

Thank you in advance

I am trying ParallelWaveGAN trainng for test dataset, which generated Tacotron2 model in espnet TTS.

This means that you try to train the PWG with mel-spectrogram generated by Tacotron 2 using teacher forcing?

The training stopped with error code 139 in the middle of processing.

Please attach the train.log.

This means that you try to train the PWG with mel-spectrogram generated by Tacotron 2 using teacher forcing?

I used "How to make the recipe for your own dateset" from https://github.com/kan-bayashi/ParallelWaveGAN/blob/master/egs/README.md
train.log:
train.log.zip

Sorry, I misunderstood your post.
You made the recipe using your dataset, which is also used for the training of Tacotron 2, right?
I've never met this error code and no information in the log.
Actually, I have no idea.
Why don't you resume the training from the checkpoint?

The voice generation with checkpoint-185000steps.pkl (and elder) is poor. Some words are skipped.

You decode with the tacotron2 generated features, did not perform analysis-synthesis, right? If so, it is better to separate the problem.
Basically, the word skipping does not happen in the vocoder.
That is a problem of the text2mel model.

One of the possible reason is the mismatch of cuda version.
What is the your cuda version and pytorch version?
And how did you install pytorch?

Let me to reboot and repeat training.

OK. If you find the reproducible procedure, please re-open.

Yes it was a hardware issue. After reboot It resumes to train normal way from the last checkpoint.
Sorry for bothering
The machine is a new. I did not meet any hardware trouble before it.


First version direct link

At the moment the first tag doesn't have any href (CHANGELOG.md)
v0.0.1

31 December 2015

It would be nice to have a direct link to the first tag
v0.0.1

31 December 2015

All other tags are a comparison link to see commits since the previous version. It feels like it would be inconsistent and potentially confusing to link the first release to something else.
If there was a link to show commits from the start of time up to a certain tag, that would be ideal, but last time I checked I couldn't find a way to do this (on GitHub, let alone other platforms).

You could compare from the initial commit to the tag, no?

I think that makes sense. The only weird thing is that it excludes the initial commit from the comparison, but maybe that's ok.

Unfortunately there is no clean way to achieve this. Namely because we need to support multiple platforms, some of which explicitly use versions in their comparison URLs (like visualstudio or dev.azure repos). Without some heavy refactoring, I'm inclined to leave this as a wontfix until it possibly becomes easier in the future. Apologies!

Keep a Changelog seems to suggest just linking to the tag directly;

The lack of link on the first release breaks our initial builds that use this changelog reader: https://github.com/mindsers/changelog-reader-action/blob/master/src/get-entries.js#L5
I'm not really sure which repository to file this issue against, because I don't think either side is really doing anything "wrong" here - keep a changelog doesn't really have a hard spec, so it's hard to call this a "spec violation". Any thoughts on whether this is easily fixable now?


grafana dashboard

Do you have a nice grafana dashboard for this to share?

Found your libsonets now! :)


Confusion about the filling rule.

The documentation for NVG claims that "NanoVG uses even-odd filling rule and by default the paths are wound in counter clockwise order." It then goes on to describe how shapes should be wound CCW and holes CW. I am doing a little bit of research on how to render SVG images using NVG and all documentation I have found on the subject suggests that the Even-Odd filling rule does not care about the winding, while the Non-Zero rule does. Eg:
https://developer.mozilla.org/en-US/docs/Web/SVG/Attribute/fill-rule
https://www.w3.org/TR/SVG2/painting.html#WindingRule
https://en.wikipedia.org/wiki/Even–odd_rule
Also I am a bit confused what it means that "NanoVG uses even-odd filling rule" in the first place. It would seem to me that whether or not a shape is filled is determined by (and only by) the winding order of the shape points. Am I right, or does the NVG library actually perform any filling rule tests at runtime? (Ie. fire a ray in any direction and counting intersections etc.)

Actually, it seems I misunderstood the NVG docs a little. In nvg__flattenPaths() there is a piece of code labeled "Enforce winding" which makes sure the winding is what the path->winding variable specifies. Because of this it seems like the winding for shapes fed into NVG doesn't really matter, only the winding set with nvgPathWinding().
The docs make it seem like you can create holes by feeding shapes with CW winding into NVG: "In order to wind one of the predefined shapes as a hole, you should call nvgPathWinding(vg, NVG_HOLE)". (Emphasis on predefined by me).
Anyway, my original question remains. Does NVG perform any kind of even-odd filling rule logic, or is the solidness of a shape determined by the winding only?

Hey, I've also stumbled across this today.
From my testing, it seems that nanovg actually uses the non-zero fill rule:

(The documentation for nvgArc is wrong too: It does not start a new path. You have to nvgMoveTo manually.)

Oh, by the way: NVG_SOLID == NVG_CCW and NVG_HOLE == NVG_CW.


Support optional components or targeted components

As a: someone that uses Fabrikate.
I want: To optionally use some components when using generate.
So that: the tool is more flexible.
Describe the solution you'd like: support component top level field that is an array of tags (e.g: environments) that when those tags are used in generate, components eligible for creation need to have those tags present in the array.
Describe alternatives you've considered: None.
Additional context: Maybe issue #73 was meant for this ... #18 would most likely address this feature and more but might more complex to implement.

Duplicate of #277


Update --update-parallelism docs

Update documentation to account for the changes in #24952.
docs/swarm/swarm-tutorial/rolling-update.md doesn't need any changes,
but the CLI reference pages should show the current help text.
drain-node.md no longer needs to specify --update-parallelism 1 in its
example.
ping @stevvooe @sfsmithcha

LGTM
(we may want to look for a shorter flag description to make the output fit in smaller terminals)


Allow setting the default language

The default language can be set in the dashboard by an admin but the front-end is not respecting that setting.

@micahwalter this should be working now. It will use the default language. But if user switches languages, it will store a cookie and that will become the default language from that point on.


TypeError when using auto-shap on Naive Bayes models or SVC models

Hi,
I enjoy auto-shap for it simplied my workflow a lot. thank you for the great work!
Recectly I was playing with Naive Bayes models (e.g. sklearn.naive_bayesBernoulliNB ) and SVC models (sklearn.svm.SVC), the auto-shap failed on me by giving the following TypeError. :

TypeError                                 Traceback (most recent call last)
/var/folders/ns/fwk51rq51_92t1bw24g3136cq5vk8m/T/ipykernel_40545/67005119.py in
2 shap_dir = inputdir + 'shap_output/'
3 save_path = shap_dir + tag
----> 4 produce_shap_values_and_summary_plots(model=model, x_df=shap_df_train, save_path=save_path,n_jobs=10)
~/opt/miniconda3/envs/brain_ai/lib/python3.9/site-packages/auto_shap/auto_shap.py in produce_shap_values_and_summary_plots(model, x_df, save_path, linear_model, tree_model, boosting_model, calibrated_model, regression_model, voting_or_stacking_model, use_kernel, file_prefix, n_jobs)
338         ]
339     )
--> 340     shap_values_df, shap_expected_value, global_shap_df = generate_shap_values(
341         model, x_df, linear_model, tree_model, boosting_model, calibrated_model, regression_model,
342         voting_or_stacking_model, use_kernel, n_jobs
~/opt/miniconda3/envs/brain_ai/lib/python3.9/site-packages/auto_shap/auto_shap.py in generate_shap_values(model, x_df, linear_model, tree_model, boosting_model, calibrated_model, regression_model, voting_or_stacking_model, use_kernel, n_jobs)
287             voting_or_stacking_model
288         )
--> 289     shap_values_df, shap_expected_value, global_shap_df = produce_raw_shap_values(
290         model, x_df, use_kernel, linear_model, tree_model, calibrated_model, boosting_model, regression_model,
291         voting_or_stacking_model, n_jobs
TypeError: cannot unpack non-iterable NoneType object

Could you please take look at this?
Thanks,
Yang

Sorry for the issue! An interim solution would be to turn on the Kernel Explainer, which is model agnostic.
produce_shap_values_and_summary_plots(model=model, x_df=shap_df_train, save_path=save_path, use_kernel=True)
However, the Kernel Explainer can be slow, so you might want to subset the x_df.
Here's what I'll do in an upcoming release. First, I want to replace the Kernel Explainer with a faster model-agnostic alternative (probably the Partition Explainer). Second, I should have auto-shap fallback on the model-agnostic explainer for any type of model it doesn't "know" (such as the two you mentioned).

@conge, I have released auto-shap 0.2.1 to address this issue. Any time we cannot use a specialized explainer, like the tree explainer, we will fallback to the kernel explainer.
https://pypi.org/project/auto-shap/

Sorry for the issue! An interim solution would be to turn on the Kernel Explainer, which is model agnostic.
produce_shap_values_and_summary_plots(model=model, x_df=shap_df_train, save_path=save_path, use_kernel=True)
However, the Kernel Explainer can be slow, so you might want to subset the x_df.
Here's what I'll do in an upcoming release. First, I want to replace the Kernel Explainer with a faster model-agnostic alternative (probably the Partition Explainer). Second, I should have auto-shap fallback on the model-agnostic explainer for any type of model it doesn't "know" (such as the two you mentioned).

I want to propose a possible solution to the "the Kernel Explainer can be slow" problem. It look something like this:
def produce_shap_output_with_agnostic_explainer(model: callable, x_df: pd.DataFrame, boosting_model: bool,
                                                regression_model: bool, linear_model: bool,
                                                return_df: bool = True, n_jobs: int = None,
                                                sample_size: int = None, k: int = None) -> tuple:

    # Initialize background samples for the SHAP explainer. Data will be subsampled if  sample_size or k is provided.
    if sample_size:
        background_samples = shap.sample(x_df, sample_size)  # Use randomly sampled background samples
    elif k:
        # Initialize the SHAP explainer with reduced background samples
        background_samples = shap.kmeans(x_df, k)  # Use k-means summarized background samples
    else:
         background_samples = x_df

if regression_model:
        explainer = shap.KernelExplainer(model.predict, background_samples)
else:
        explainer = shap.KernelExplainer(model.predict_proba, background_samples)

# Calculate SHAP values for all samples

What do you think?

I like this idea a lot. I will work to get this functionality in the next release. Thank you!

I have made an update in version 0.3.0 to reflect this suggestion! (Slight modifications). Thank you so much for the help on this.


Feature/map search

Overview
This pr adds new design update for the search panel.

there are a few style changes for previous content, but basically kept the colors the same as defined colors where not in our config.
Modified styles to make sure only search results are overflowed, otherwise the entire menu will move when results overflow the container
As previous statement, i decided to make sure the search box is always visible on desktop when scrolling, so you dont loose context of what you searched for.
Mobile layout is handled mostly by flex logic, as we will only show eather menu/result container and let flex grow deal with the layout. For this change the logic became a bit more complex in the search component; so did some splitting of logic there to make it easier to work with in the future.
Created a vertical-menu component that we can re-use when we need it, as of now its quite simple and we can extend if we need more logic there.

Demo

Notes
We still use "one" component for datasets/locations, as the behaviour is still similar. and when switching between the location/dataset menu it behaves like a "filter" and you dont loose the previous context.
...
Testing

Make sure search works as it was before, as nothing should have been changed there, but all old logic should still work.
Make sure navigation works as expected.
Make sure styles are correct (as i didnt use the colors in (invision).
Tested in webkit,ff edge not sure if we need to check ie 11 ?
Make sure mobile/desktop layouts behave as expected both in reload/resize browser window.

There is a whole other issue of how to access this menu on mobile but we can address that is another PR.

fixes amended ! @edbrett

added an issue to notion related to search on mobile: here

This is looking great! Im not going to merge yet as we are missing the results from geocoding service which we are still waiting for confirmation on. I will tag as on hold or similar.


Repackaging-ZoomReports

Required items, please complete
Change(s):

See guidance below

Reason for Change(s):

Adding new workbook into solution.

Version Updated:

Required only for Detections/Analytic Rule templates
See guidance below

Testing Completed:

Checked that the validations are passing and have addressed any issues that are present:

See guidance below

we have close this PR because description display issue in content hub will reopen this pr once fix that issue.


UI for Market Makers/Liquidity Providers

This may just be a matter of making the Liquidity interface of the Create Market form available outside of the create market form.
Or, maybe the main order form should be changed so that multiple orders can be added at once.
Talk to Alex, Jack, Chwy, and do some research on standard interfaces for this.
...
@achapman Just FYI, I've added this ticket to track the need. I'm not sure how highly prioritized it should be compared to all of our other priorities. We'll discuss.
-sharkcrayon
...
This may just be a matter of making the Liquidity interface of the Create Market form available outside of the create market form.
-joeykrug
...
That’s what I’d do ^
-joeykrug

Do you imagine this is a feature only available to a market maker, on a market they have already created? @joeykrug

No it should be available to all users

for people who want to add a lot of orders

So this is something that would be triggered from the new trading page, will keep this in mind as we look at the liquidity step for market creation. cc: @Chwy5 @matt-bullock

yeah

@joeykrug @Chwy5 -- Does this still sit as a priority in the current flow of things?
If so I'll add this to the Liquidity Dev epic to make sure it can be accessed stand-alone on a market, but that may require some design.

dont think it matters, no other trading UI has this

I dont believe it is a big priority. Most users will input through the order ticket and imo anyone wanting to add multiple orders at once will do it through bot trading.
Can either close and reconsider later or just punt until later


imagePullSecrets v/s secrets

Hello,
I have a question,
why has Chains been designed to read credentials from the service account's imagePullSecrets instead of secrets - given that we are really pushing ( and not pulling ) to the registry.
kubectl patch serviceaccount $SERVICE_ACCOUNT_NAME \
  -p "{\"imagePullSecrets\": [{\"name\": \"registry-credentials\"}]}" -n $NAMESPACE

.. though I'm aware that imagePullSecrets is a reserved API for specifying 'how to authenticate with a registry'.


Fix scope of allowedToProxy flag

Merged https://github.com/Jasig/cas/pull/933 into master/4.1 to address #904

+1


Update cleanup in STLPriorityQueue

https://github.com/AbePralle/Rogue/blob/develop/Source/Libraries/CPP/STLPriorityQueue.rogue#L23
Should be on_cleanup now, yes?

Quite right - fixed in develop.


Applying changes to a template doesn't work

PDNS: 4.1.3
Powerdns Admin: Latest pull from git (01.08.18)
When changing a template it can't be saved, applying does not not work:
Oops! You're lost The page you requested could not be found. You may return to the dashboard
It appears when "/template/templatename/apply" is posted.
The error page that pops up is also damaged - the full html code of the error page is visibible (<!DOCTYPE html> <html> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title>DNS Control Panel - 404 Error</title> and so on) not the formatted error page.
Maybe 2 or 3 weeks ago edit and saving a template works on my installation

Hmm, we don't have any changes on domain template recently. I cannot reproduce the issue. Can you give more information on how did you setup the PowerDNS-Admin, Web browsers, template/domain name used, etc.?

Found that on Firefox debugger console:
Fehler beim Laden der folgenden Adresse: Could not load the source for blob:http://pdns.mydomain.tld/f5e245c9-c425-f54d-a876-ed5d8034039a.
Error: Failed to fetch blob:http://pdns.mydomain.tld/f5e245c9-c425-f54d-a876-ed5d8034039a. Code<PHONE_NUMBER>.
Stack: onResponse@resource://devtools/shared/base-loader.js -> resource://devtools/shared/DevToolsUtils.js:558:23
onStopRequest@resource://gre/modules/NetUtil.jsm:126:17
Line: 558, column: 23

Template works till ~2-3 weeks ago, I've made an powerdns-admin update via git pull since then. Also some python source may be updated
Browser: Firefox and Safari
PowerDNS-Admin Installation on FreeBSD 11.2,
Webserver: Lighttpd with uwsgi,
Database: PostgreSQL 10

Hmm, it looks like we have more issue with PostgreSQL...I will need to test with the same PostgreSQL 10 to verify this case.

I'm using pgsql 10.4. -  A data record in the table "domain_template" is createt.  I've testing in debugging modus, logging all statements and it seems that no input  is arriving in pgsql for the table "domain_template_record" so no inserts are made.

I've made more test. This is shown on Firefox Browser Console as the error message in
error/static/generated/main.js?d56aea7b
on "5130:71"
if(refreshPage){location.reload(true);}},error:function(jqXHR,status){console.log(jqXHR);var modal=$("#modal_error");modal.find('.modal-body p').text(jqXHR["responseText"]);modal.modal('show');}});}

Behavior changed with newest version 9a4eebf  - No Error message is shown, but the green validation window doesn't appear and the template record isn't saved

Just my feedback,
are you sure its javascript? because for me (mysql (MariaDB 10.3)) its working perfect....
Cheers :-)

No - I'm not sure about anything. But I don't know how to debug it. Any ideas are wellcome.

debug mode in firefox and you can activate debugging in config.py...
but you are uing totally different setup... which python version do you are on?

Python 3.6.
I've debuged the postgresql communication. There is no insert at this time I fired a domain template change
Maybe there's something wrong with the generated main.js - Firefox sees a fault at line 5130
At line 5130 there is a function to change the domain table but not the domain_template or domain_template_record table
Error at Firefox
prototype: {…}
constructor: function state()
<prototype>: Object { … }
<prototype>: function ()
status: 404
statusCode: statusCode()
length: 1
name: "statusCode"
prototype: Object { … }
<prototype>: function ()
statusText: "Not Found"
then: function then()
<prototype>: Object { … }
main.js:5130:71
SyntaxError: JSON.parse: unexpected character at line 1 column 1 of the JSON data[Weitere Informationen] main.js:5130:135
error
http://pdns.domain.tld/error/static/generated/main.js:5130:135
fire
http://pdns.domain.tld/error/static/generated/main.js:239:213
fireWith
http://pdns.domain.tld/error/static/generated/main.js:245:181
done
http://pdns.domain.tld/error/static/generated/main.js:659:157
callback/<
http://pdns.domain.tld/error/static/generated/main.js:672:314

./app/static/generated/main.js, line 5128-5132:
function applyChanges(data,url,showResult,refreshPage){$.ajax({type:"POST",url:url,data:JSON.stringify(data),contentType:"application/json; charset=utf-8",crossDomain:true,dataType:"json",success:function(data,status,jqXHR){console.log("Applied changes successfully.")
if(showResult){var modal=$("#modal_success");modal.find('.modal-body p').text("Applied changes successfully");modal.modal('show');}
if(refreshPage){location.reload(true);}},error:function(jqXHR,status){console.log(jqXHR);var modal=$("#modal_error");var responseJson=jQuery.parseJSON(jqXHR.responseText);modal.find('.modal-body p').text(responseJson['msg']);modal.modal('show');}});}
function applyRecordChanges(data,domain){$.ajax({type:"POST",url:$SCRIPT_ROOT+'/domain/'+domain+'/apply',data:JSON.stringify(data),contentType:"application/json; charset=utf-8",crossDomain:true,dataType:"json",success:function(data,status,jqXHR){$.getJSON($SCRIPT_ROOT+'/domain/'+domain+'/info',function(data){$(".button_apply_changes").val(data['serial']);});console.log("Applied changes successfully.")


Delete stale Firestore instances after FIRApp is deleted.

This fixes #683.

Why is delete special for Firestore?   Wouldn't other components want the same thing and there be a FIRApp implementation?

@paulb777 right now FIRApp just fires a notification for other SDKs to handle - Database and Auth do similar things as well.
Once Core takes over the management of instances, this code should be able to go away.


_MultiThreadedRendezvous error

Description of the bug:
when i am trying to ask a question to the model by adding the image ,sometimes i am getting below error
grpc._channel._MultiThreadedRendezvous: <_MultiThreadedRendezvous of RPC that terminated with:
status = StatusCode.INTERNAL
details = "An internal error has occurred. Please retry or report in https://developers.generativeai.google/guide/troubleshooting"
debug_error_string = "UNKNOWN:Error received from peer ipv4:<IP_ADDRESS>:443 {created_time:"2024-01-24T11:30:58.841912+00:00", grpc_status:13, grpc_message:"An internal error
has occurred. Please retry or report in https://developers.generativeai.google/guide/troubleshooting"}"
the code i am using is below
genai.configure(api_key=GOOGLE_API_KEY)
model = genai.GenerativeModel("gemini-pro-vision")
img = PIL.Image.open(f"output_images_and_tables/{value}.png")
response = model.generate_content([item[1], img], stream=True)
Actual vs expected behavior:
No response
Any other information you'd like to share?
No response

Same here! Did you figure it out?

We are having trouble reproducing this one - if you have any more info on how to repro the issue, it would help. Any environmental information too - e.g. was this colab, are you using a proxy, what OS, etc.


[bug] Environment variables from entrypoint.sh ain't exported

Environment variables from ./compose/django/entrypoint.sh ain't exported.
To reproduce, run
docker-compose -f dev.yml build
docker-compose -f dev.yml up -d
docker-compose -f dev.yml exec django env

The last command's output contains no REDIS_URL, DATABASE_URL, or CELERY_BROKER_URL variables declared in the entrypoint.

It's weird, but now I've noticed they are indeed being exported... Have no idea what it was all about, but I guess the issue can be closed.

I'm not seeing this behavior, I pinged you on another thread but I see different behavior when using docker-compose -f local.yml run vs docker-compose -f local.yml exec


EES-4591 Logger returns if it is running in debug mode

Logger is aware if debug mode is enabled, so it returns corresponding flag, so that other parts can enable some debug features based on this flag.
Not used right now, but going to be used in upcoming PRs.

+1


Compare to requires 2 clicks

Steps to reproduce:
Have multiple builds.

Click "Compare" checkbox
Click the dropdown(up?) and select a build to compare against
Click the dropdown to select another build: dropdown does not open
Click the dropdown a 2nd time: it will now open

No longer reproduceable after some code refactoring from https://github.com/frzyc/genshin-optimizer/pull/1724.


Update L01 Intro.ipynb

Added "use school email for zybooks account" under zyboks

Awesome, merging.


[Chart] Add support for deploying Notary

Assuming Harbor FQDN is specified as harbor.my.domain by the user,
the Notary server FQDN will be set to notary-harbor.my.domain.
So the user must point both Harbor FQDN and Notary FQDN to the K8s
ingress controller IP in the DNS server.
Fix issue https://github.com/vmware/harbor/issues/4394

Coverage increased (+0.08%) to 64.485% when pulling 78c1be1ae4dc40400b220608dcd49a75f4a3d86e on jessehu:notary-in-chart into 9d13842a294932cf55b5951086cc1e99c830e373 on vmware:master.


Added network cache

Added a network & unit cache to be able to connect to the unit without having to contact the Casambi servers.
You need to connect once to get the necessary info.
Then you can call the connect method without password.
In the client-code I had to replace
get_device(self.address) by BleakScanner.find_device_by_address(self.address, timeout=10.0)
because the get_device code doesn't work on Windows. The BleakScanner-code works on windows. Didn't test on Linux.
Also corrected some minor spelling mistakes.

This isn't quite what I had in mind but I think we had different goals when thinking about this feature. I wanted the library to keep working even if there is no internet access. If I understand it correctly your goal is to avoid contacting the casambi servers unless it is absolutely necessary.
The problem is that your current implementation is somewhat incompatible with my goal. But now that I've refactored caching the solution I was thinking of shouldn't be that much more work. I think I can get it done next week and also add a flag to disable communication with the api even if there is internet access. Sadly this means that I can't merge this PR but thanks for your effort nevertheless.

Hi,
ok sorry to hear that.
My goal was to have one "bootstrap" where all the necessary info was loaded from the network and that not needing the network anymore. I don't see it to be incompatible to what you do and is an additional feature that people might want.


nested expressions

including weighted objectives and combinations of +/- operators.
Ongoing work in 'ortools_flatten' branch

implemented with pull request #24


How do you update table data?

I see you can specify initialData but when the data changes how would you update it in a DataTable component?

I just pushed a change to fix this in v1.0.2, if you update the component with the new data it will refresh now.

Nice, thanks!


chore: update rust dependencies

Changes

Updated rust dependencies

/kind enhancement

Fixes #1111

Release Note

Docs

@vyasgun this requires also update of the zz_* file.

@vyasgun looks good, but you should exclude the generated docs, I'll update it in separate PR.

@matejvasek Thanks for the review. I updated the PR accordingly.

/approve

/lgmt
/hold for tests

@vyasgun thanks for your contribution.

/lgtm

/unhold


Basic statistical tests to compare two datasets

This is useful to built more generic comparison tests in examples. Please suggest other names for the function if the proposed one doesn't make sense.

Current coverage is 100.00%

Merging #220 into master will not affect coverage as of cd9cd39

@@            master    #220   diff @@
======================================
  Files           38      38
  Stmts         1486    1491     +5
  Branches         0       0
  Methods
======================================
+ Hit           1486    1491     +5
  Partial          0       0
  Missed           0       0

Review entire Coverage Diff as of cd9cd39

Powered by Codecov. Updated on successful CI builds.

Ok, I added ks-test because all the other tests in scipy are either buggy or not working properly. I can remove that, but then the user will probably get wrong results if he uses a buggy module.

That is fine. If there really is a bug in scipy we can add a warning. But do you have three lines of code that can reproduce the scipy bug(s)?

Ok, I removed the default and updated the test accordingly.
Example of problematic test:
data = np.array([1., 1., 2., 2.])
data_same = np.array([1.0, 1.0, 2.0, 2.0])
stats.compare_two(data, data_same, test='ks_2samp')
Stats(dist=0.0, pvalue=1.0) # ok

stats.compare_two(data, data_same, test='mannwhitneyu')
Stats(dist=8.0, pvalue=0.43433053149553336) # wrong

I mean code that unambiguously shows a bug in scipy, not our own code.

Updated example of problematic test:
from scipy import stats
data = np.array([1., 1., 2., 2.])
data_same = np.array([1.0, 1.0, 2.0, 2.0])

stats.mannwhitneyu(data, data_same)
(8.0, 0.43433053149553336) #wrong, same as before

Maybe it would make sense to be explicit about the one method we do support:
stats.compare_ks(data, data_same) # two is implicit from the number of parameters

We could also have a stats.compare_two(a, b, str) where we restrict the values of the strings.

But we want to support any type of test in principle. Compare two is not a good name, but compare_ks is too restricted and I would like to avoid assumptions unless we only allow ks-tests to be applied.
What do you mean restrict the string values? Could I generate a list of accepted distributions and check if the string is in the list? Otherwise I would raise an error. Does that make sense?

If only KS works at the moment, then we should only support that. There is no ambiguity because the name expresses the intent clearly. So which tests "work" besides Ks?
About the string, yes, that makes sense. We could also use an enum I guess.

I would prefer the second option (enum will do) in order to avoid rewriting the same function if new tests are needed. If scipy has bugs-errors we cannot usually predict this (only if we try the tests one by one :P).
We can start simple: [ks_2samp, wilcoxon] and build from this set of tests adding anything that will make sense and is available in scipy.

That sounds good. If you want to see an example of Enum use, see neurom/core/types.py.


[python3] Python3 needs Pyhon3 to build Python3

Till four days ago, it was possible to install Python3 in vcpkg without having Python3 system-wide installed. Since 4 days ago (and specifically, this commit and line: https://github.com/microsoft/vcpkg/commit/c6928dfb9eb7f333f988d2ce70d1e771b7606849#diff-f682e6e46ef0d0dae2ceba81d191975da58a84cbdab4811a0e84683442265461R245 ) that is no longer the case.
We use vcpkg to build a linux-generic binary with a very old libc so as many people as possible can run it on their system. Basically, it based on quay.io/pypa/manylinux2014_x86_64. Sadly, having a system-wide Python3 on that is very challenging, one that vcpkg was resolving for us. But .. no longer :(
Would be really appreciated if Python3 can be build again without needing Python3 to start with! Tnx :)
Package: python3:x64-linux -> 3.11.4#1
Host Environment

Host: x64-linux
Compiler: GNU 10.2.1
vcpkg-tool version: 2023-08-09-9990a4c9026811a312cb2af78bf77f3d9d288416
vcpkg-scripts version: 0fa8459 2023-08-11 (34 hours ago)

To Reproduce
vcpkg install python3
Failure logs
-- Downloading https://github.com/python/cpython/archive/v3.11.4.tar.gz -> python-cpython-v3.11.4.tar.gz...
-- Extracting source /vcpkg/downloads/python-cpython-v3.11.4.tar.gz
-- Applying patch 0001-only-build-required-projects.patch
-- Applying patch 0003-use-vcpkg-zlib.patch
-- Applying patch 0004-devendor-external-dependencies.patch
-- Applying patch 0005-dont-copy-vcruntime.patch
-- Applying patch 0008-python.pc.patch
-- Applying patch 0010-dont-skip-rpath.patch
-- Applying patch 0012-force-disable-curses.patch
-- Applying patch 0014-fix-get-python-inc-output.patch
-- Applying patch 0015-dont-use-WINDOWS-def.patch
-- Applying patch 0002-static-library.patch
-- Applying patch 0011-gcc-ldflags-fix.patch
-- Using source at /vcpkg/buildtrees/python3/src/v3.11.4-101b2af427.clean
CMake Error at scripts/cmake/vcpkg_find_acquire_program.cmake:163 (message):
  Could not find python3.  Please install it via your package manager:

      sudo apt-get install python3
Call Stack (most recent call first):
  ports/python3/portfile.cmake:254 (vcpkg_find_acquire_program)
  scripts/ports.cmake:147 (include)

Disabling the following lines fixes my issue:
https://github.com/microsoft/vcpkg/blob/c6928dfb9eb7f333f988d2ce70d1e771b7606849/ports/python3/portfile.cmake#L245-L246
After which Python builds and functions as expected.

Since we don't touch stuff that needs regeneration, we don't need to set PYTHON_FOR_REGEN. Please test #33132

As that is exactly the patch I am currently applying to my builds, can confirm, fixes the issue :)


Windows CI currently failing; wants chocolatey credentials ?

Currently, the CI on Windows is broken:
https://github.com/chipsalliance/verible/actions/runs/8218621248/job/22479126298#step:5:17
Looks like the package manager used there is needing some sort of credentials. Why would credentials be needed to download from the package manager ? Maybe the URL changed ?

I have no idea how things work on Windows, paging @corco for expertise.

Hold on, maybe it fixed itself ...

The info I found seems to point to a server issue with Chocolatey (or Cloudflare) or an environment issue. I did a PR to update Windows runner to 2022 (from 2019).
Otherwise I would give it a day or two and hope it solves itself.


Cannot find symbol error for java.io.File.toPath

I am getting this error.
fileName.java:154 error: cannot find symbol Files.delete(file.toPath());
symbol:   method toPath()
location: variable file of type java.io.File
I am using java 8 and the method is there since 1.7.

Thanks a lot ☺


[5.8]Let release method has return value

The releaseLock function is used in release function.  ReleaseLock function has return value 0 or 1, but release function doesn't has return value.
I think sometimes we may use return value determine the lock succeed or fail to be release. Then we may do something according the successful or fail status.
Below is source code of the releaseLock:
<?php
namespace Illuminate\Cache;
class LuaScripts
{
    /**
     * Get the Lua script to atomically release a lock.
     *
     * KEYS[1] - The name of the lock
     * ARGV[1] - The owner key of the lock instance trying to release it
     *
     * @return string
     */
    public static function releaseLock()
    {
        return <<<'LUA'
if redis.call("get",KEYS[1]) == ARGV[1] then
    return redis.call("del",KEYS[1])
else
    return 0
end
LUA;
    }
}

Unfortunately this breaks the contract of the Lock interface and other drivers aren't updated. Seeing that the DynamoDB driver and the Memcached driver can return booleans, maybe it's an idea to also return a boolean in the Redis implementation, update the Lock interface and also update the other drivers?


Clarify menvcfg.SSE is 0 then henvcfg.SSE/senvcfg.SSE are read-only zero

I think there is a typo in your change will are

@kacouane thanks. Fixed.


Make subgraph deployments persistent across restarts

For this, nodes that we deploy for hackathons need to have a persistent Postgres database and persistent IPFS node. Any subgraph that is deployed over the JSON-RPC admin API should be resumed after restarting a node.
So basically: Need a persistent IPFS node. Need to remember subgraphs that are registered in Postgres.

I've deployed a persistent IPFS node on our infra. Now it's just the Postgres side and re-loading previously registered subgraphs at startup.

stealing this

Major work on this has been done on the tim/persistent-subgraphs branch (and is in ethsf). There's still a bit more work to do before merging it to master, but it's working well enough for this weekend.


LineRenderer shown in wrong position during first frame of controller activation

Overview
Pulling the trigger of the motion controller makes the beam appear infront of it. It kinda snaps into position, because during the first frame of visibility, its in a wrong position
Expected Behavior
Line just appears in front of the motion controller
Actual Behavior
First frame is wrong
Steps to reproduce
put on MR HMD and pull the trigger on the motion controller
Unity Editor Version
2018.3.8f1
Mixed Reality Toolkit Release Version
mrtk_development

@StephenHodgson this is also caused by the wrong order of execution:

LinePointer PreRaycast: the current position is read and BaseMixedRealityLineDataProvider's First and LastPosition get set.
LinePointer PostRaycast: the BaseMixedRealityLineDataProvider gets Enabled and gets its matrix saved for the first time

It's the second time the matrix is old the moment it's needed.
Nonetheless, the MixedRealityToolkit seems to have a problem with execution orders. I'm going to do a diagram for who needs what and when it will get it.

@Alexees,
We very much appreciate all of the investigation you have been putting into your issue reports. It helps immensely!

@davidkline-ms,
thanks for the appreciation. im actually ging to work full time in the kit at least until the end of the month. we will be replacing a pretty crippled version of a year old HTK and I want to make sure the conversion goes as smooth as possible

Tagging with Input, but specifically this is pointers within Input

@Alexees , this seems to have been fixed via PR #3626. Can you confirm and close the issue if appropriate?

this issue is pretty old, but at that time some errors I found got doubled in issues I've written and from the sounds of these two, these are two of those.
I'm pretty sure this is fixed.

@luis-valverde-ms my assumption is wrong, it's not fixed

Thanks @Alexees . With the repro in that one it should be relatively straightforward to get to the bottom of it.


Advanced Queries for the command line utility

The utility script meticulous also offers some advanced database operations that allow you to extract precisely the experiments of interest as well as some interesting aggregates.
The operations supported are filtering, grouping, sorting and selecting columns, and they are applied in exactly this order.
Note this convention on the column names: All arguments of the experiment are prefixed with args_ whereas all results in the summary dictionary are prefixed with summary_.
Filtering allows you to specify a pandas query <https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.query.html>_ for experiments using the --filter argument.
We groups experiments based on a given comma-separated list of columns using the --groupby argument. The remaining columns are aggregated: For real-valued columns, a mean and standard deviation are reported, which is particularly helpful for machine learning metrics like accuracy or loss. All other columns are aggregated by count.
To sort the results, we can specify a comma-separated list of columns to sort by using --sort argument. To reverse the order, specify the --sort_reverse flag.
If we're only interested in a subset of all columns, we can specify a comma-separated list of column-names using the --columns argument. Note that the --groupby option changes the names of aggregated attributes.
We can also limit the output to only the last k columns with th e --tails k argument.

This is amazing!
I don't have any tests for the meticulous script, so I'm just going to accept it for now. If any breakages happen, I'll open issues or fix them myself.


Add ORPO within README.md files

Description
This PR adds the ORPO fine-tuning technique among the existing README.md files where the available techniques are mentioned, as well as adding https://huggingface.co/HuggingFaceH4/zephyr-orpo-141b-A35b-v0.1 within the "News" section.
Additionally, this PR also fixes a small typo in the ModelArguments from adatpers to adapters.
Thanks @nisten for realising that the docs were missing https://github.com/huggingface/alignment-handbook/pull/143#issuecomment-2051497473

The docs for this PR live here. All of your documentation changes will be reflected on that endpoint. The docs are available until 30 days after the last update.


chore(master): release 1.1.177

:robot: I have created a release beep boop
1.1.177 (2023-09-04)
Miscellaneous

deps: update dependency archiver to v6.0.1 (944ad38)

This PR was generated with Release Please. See documentation.

:robot: Release is at https://github.com/wayofdev/keywind/releases/tag/v1.1.177 :sunflower:


Error: Running stisla installing generator

Stack

Ruby 2.5.3p105 (2018-10-18 revision 65156) [x86_64-linux]
Rails 5.2.2
Bundler version 2.0.1

Flow

Add stisla-rails in Gemfile

gem 'stisla-rails'

Running bundle command.

$> bundle

Use aplication.scss instead application.css

$> mv app/assets/stylesheets/application.css app/assets/stylesheets/application.scss

Remove all *= require_self or *= require_tree
Running install stisla

$> rails g stisla_rails:install

Expected
All dependencies in stisla will installed and will sync with package.json file.
Actual
The command, not available.
Running via Spring preloader in process 31838
Could not find generator 'stisla_rails:install'. Maybe you meant 'test_unit:system', 'test_unit:model' or 'integration_test'
Run `rails generate --help` for more options.

This is the issue or I'm missing something?
Thank you

what is the output of this command
rails g -h

My output for that command.
$> rails g -h
Running via Spring preloader in process 4111
Usage: rails generate GENERATOR [args] [options]

General options:
  -h, [--help]     # Print generator's options and usage
  -p, [--pretend]  # Run but do not make any changes
  -f, [--force]    # Overwrite files that already exist
  -s, [--skip]     # Skip files that already exist
  -q, [--quiet]    # Suppress status output

Please choose a generator below.

Rails:
  application_record
  assets
  channel
  controller
  generator
  helper
  integration_test
  jbuilder
  job
  mailer
  migration
  model
  resource
  scaffold
  scaffold_controller
  system_test
  task

ActiveRecord:
  active_record:application_record

Coffee:
  coffee:assets

Js:
  js:assets

TestUnit:
  test_unit:generator
  test_unit:plugin

please update your stisla-rails
gem update stisla-rails

That still not appears.
$> gem update stisla-rails
Updating installed gems
Nothing to update

$> rails g -h | grep stisla_rails
Running via Spring preloader in process 843

try this
gem list stisla-rails

$ gem list stisla-rails
*** LOCAL GEMS ***

stisla-rails (0.1.5, 0.0.2)


chore(deps): rm unused arb feature

this doesn't change lockfile so this must get pulled in from somewhere else as well, checking next


RAW / DNG File type support

RAW pictures don't seem to load correctly on AVES.
Adobe Lightroom (Mobile) supports RAW pictures. Could something be implemented to support RAW pictures
For further discussion I am willing to provide a comparison screenshot of a RAW image on AVES and Lightroom.

For image support, the app relies on the codecs on the device (except for Tiff and SVG), and I don't intend to ship with extra codecs.


⚠ T:Riza Docs has degraded performance

In 5607253, T:Riza Docs (https://docs.triza.dev) experienced degraded performance:

HTTP code: 200
Response time: 5679 ms

Resolved: T:Riza Docs performance has improved in ff7ac4b.


iOS 8.1: Focus on input (filled with text) pushes cursor out of bounds

Can use http://ftlabs.github.io/fastclick/examples/input.html or http://ftlabs.github.io/fastclick/examples/focus.html to test.
Seems to only show up on iOS 8 Safari. When an input element is filled with text, and then refocused, cursor moves to the end of the text, but incorrectly places the cursor outside of the input's bounds.
This can lead to user confusion, especially when the text string is long enough to push the cursor off-screen.

I'm having the same problem with an input field, on iOS 8, did you managed somehow to not show the caret out of the input field.
Any help would be appreciated.
Thanks.

This it what I did for textarea. See the comments.
FastClick.prototype.needsClick = function(target) {
	case 'textarea':
		if (target.disabled || target.value.length) {
    	// Request click when textarea has content.
			return true;
		}

		break;
};

FastClick.prototype.needsFocus = function(target) {
	case 'textarea':
		return !target.value.length;    // Request focus when textarea has no content.
};

What it does is firing a fast click (focus) when textarea is empty and a regular click when there is content.
This way the caret will appear into correct position, which is more important for us than fast click. I did not manage to get the best of both words, meaning fast click and correct caret position but something like this could work for input fields as well

I had the same issue those days but only on IOS 8.1, so maybe my solution will help somebody. The issue came from a div tag which had set a transform CSS property. I solve the problem with the following code:
#your-parent-div {
    -webkit-transform: none;
    -moz-transform: none;
    -o-transform: none;
}


Bump docker/docker to silence vuln scanner warnings for CVE-2024-41110

We don't actually embed any of the Docker runtime stuff, nor do we interact in any way with docker authz plugins, but scanners are still flagging our use of a version of docker/docker affected by CVE-2024-41110 in go.mod.
We should bump this, just to get the scanners to stop flagging it.

https://github.com/k3s-io/k3s/security/dependabot/77

Verified via go.mod https://github.com/k3s-io/k3s/blob/0ee714d62b257c90f2f6ace9caa2fb0e78b06e96/go.mod#L12


wiremock: 3.3.1 -> 3.4.0

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.
meta.description for wiremock is: A flexible tool for building mock APIs
meta.homepage for wiremock is: https://wiremock.org/
meta.changelog for wiremock is: https://github.com/wiremock/wiremock/releases/tag/3.4.0
Updates performed

Ran passthru.UpdateScript

To inspect upstream changes
Impact
Checks done

built on NixOS
The tests defined in passthru.tests, if any, passed
found 3.4.0 in filename of file in /nix/store/362mfw5kv2la9fq79hym7gq3krxj503x-wiremock-3.4.0

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

1 total rebuild path(s)

1 package rebuild(s)

First fifty rebuilds by attrpath
wiremock

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/362mfw5kv2la9fq79hym7gq3krxj503x-wiremock-3.4.0 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A wiremock https://github.com/r-ryantm/nixpkgs/archive/95ce2ea4cff2d69e8eea990eec8168ac3b7f83dd.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/95ce2ea4cff2d69e8eea990eec8168ac3b7f83dd#wiremock

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/362mfw5kv2la9fq79hym7gq3krxj503x-wiremock-3.4.0
ls -la /nix/store/362mfw5kv2la9fq79hym7gq3krxj503x-wiremock-3.4.0/bin

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

1 package built:

wiremock

Maintainer pings
cc @bobvanderlinden @anthonyroussel for testing.

@NixOS/nixpkgs-merge-bot merge


[NEW] Starred messages

Your Rocket.Chat.Android version:
2.0.1
Rocket version 0.63.1 - Docker install
Phone:
Samsung S6 - Android 7.0
With the new app I can see Pinned messages, but Starred messages are not available?

Changed to a feature, it's not a bug. 👍

LOL.....
Starred messages appear in the desktop app and browser. They are used.
They DID appear in the old app.
So the functionality has been lost, removed, or broken (especially as the update was effectively forced)
That's a bug not a feature. I digress.

@reetp I think what @rafaelks meant is that this feature not appearing on 2.0.0 onwards is something new to the redesign so in order for us to best organize our tasks it fits better as a new feature to the redesigned app.
Moreover, starring messages is still up to debate if we should include or deprecate it.

We also have pin message functionality. You can pin your messages.

@reetp In order to fully support star/unstar messages, we need some changes in our APIs and improve the way it is handled, because today is a mess. That's why we didn't implement it yet. I'll let this issue opened for now and we'll discuss what do to about it. Thank you!

I get all the comments.
Just frustrating that having had the use of starred messages, and messages being starred, it is not possible to see them now.
So we have the option if going through them and converting to pinned, or not being able to see them on mobile.
I'll keep watch for developments :-)

Closing this due to duplicate of https://github.com/RocketChat/Rocket.Chat.Android/issues/1009.

This not a dupe of #1009 which refers to starring Rooms
This references starred Messages in rooms.
Please reopen.

Yeah, you're right. There are about three different issues relating to favoriting things, I think I got dizzy.

LOL - know that feeling ;-)
Thanks


Add a community part to the README

[ ] BearStudio's YouTube videos that are about 🚀 Start UI
[ ] BearStudio's Twitch channel that streams a lot of 🚀 Start UI content
[ ] Any other content on the web about 🚀 Start UI

Hey @yoannfleurydev ! I would like to work on this issue if its alright

Hi sure, feel free to list contents here before submitting a Pull Request.


how to process backend on multi-gpus?

how to process backend on multi-gpus?

can the frontend and backend be processed  respectively in two GPUS？

I process the froentend in 5 GPUs ，and report errors：
ii, jj = torch.as_tensor(es, device=self.device).unbind(dim=-1)
ValueError: not enough values to unpack (expected 2, got 0)
how to process the backend in multi GPUS ？

Hi, I also encountered this problem, did you solve it?

no😅😅
---Original---
From: @.>
Date: Wed, Apr 27, 2022 12:48 PM
To: @.>;
Cc<EMAIL_ADDRESS>Subject: Re: [princeton-vl/DROID-SLAM] how to process backend on multi-gpus?(Issue #42)
Hi, I also encountered this problem, did you solve it?
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.Message ID: @.***>

Having same issue, anyone can help?

这是来自QQ邮箱的假期自动回复邮件。

您好，已经收到您的邮件，无法亲自回复，还请见谅。


[Quest/Malawi Core] Show expanding list of patient's guardians on patient profile

THIS IS A DRAFT
Is your feature request related to a problem? Please describe.
There is no place to view guardians who have been registered.
Describe the solution you'd like
In the patient's profile, there needs to be a expandable list of the patient's guardians. This is applicable for all patient categories.
Describe alternatives you've considered
N/A
Additional context
The guardians will be mapped to the RelatedPerson resource.

Replaced with this issue


Battlefield Rich Presence is not using the latest version of GameDataReader

Last week, I opened a pull request so that Battlefield Rich Presence would use the latest version of GameDataReader (0.0.4).  However today, I noticed that the 1.4.7 Release build of Battlefield Rich Presence was not working correctly with Discord.  The 1.4.7 build of Battlefield Rich Presence exhibits the same behavior as the previous versions.  I looked at the install directory for Battlefield Rich Presence and it appears that it is using version 0.0.2 of GameDataReader based on the timestamp of the DLL file and the release date of GameDataReader 0.0.2.
I was able to fix the issue by building the Battlefield Rich Presence solution locally and then installing the 1.4.7 Debug build of Battlefield Rich Presence.  I have attached screenshots showing the timestamp of the GameDataReader DLL when the Debug and Release versions are installed.  It appears that the Battlefield rich presence.csproj project file is setup to use the correct version of GameDataReader, so I am not sure where the issue lies.
1.4.7 Debug Build:

1.4.7 Release Build:

rebuilding 1.4.7 as 1.4.8, apparently I forgot to pull before making release... https://github.com/community-network/Battlefield-rich-presence/actions/runs/4466116786/jobs/7843899822

@zefanjajobse Thank you for creating a new release build.  I installed 1.4.8 and it appears that Battlefield Rich Presence is now using the 0.0.4 version of GameDataReader.  I tested the new build with BF1942 and my game information showed up in Discord correctly.  I would say that this issue can be closed.


Wrong .cpp filename in the code snippet

Type of issue
Code doesn't work
Description
No.3 of step 3 - Set up the project files, in the line:
add_executable(HelloWorld main.cpp)
"main.cpp" is used even though the source file is named "helloworld.cpp"
This causes the code execution to fail
Page URL
https://learn.microsoft.com/en-gb/vcpkg/get_started/get-started-vs
Content source URL
https://github.com/Microsoft/vcpkg-docs/blob/main/vcpkg/get_started/get-started-vs.md
Document Version Independent Id
94e7a328-84e7-33e6-9e9f-9bb95cbd99cb
Article author
@JavierMatosD
Metadata

ID: 94e7a328-84e7-33e6-9e9f-9bb95cbd99cb
Service: vcpkg

Fixed in #404


shown.bs.dropdown Related target

Hi there!
Im using Bootstrap v3.3.5 and I'm having some troubles using the dropdown menu and accessing to the dropdown events. According to documentation (http://getbootstrap.com/javascript/#dropdowns-events) all dropdown events (show, shown, hide and hidden) has a relatedTarget property to access the anchor that fired the event. It works perfect in show and hide events, but shows undefined in shown and hidden events.
Is there an error in the documentation or did you miss to put that property when the event was built?
Here is an example of my code:
$('.dropup').on('show.bs.dropdown', function(e){
	console.log(e.relatedTarget);
});

$('.dropup').on('shown.bs.dropdown', function(e){
	console.log(e.relatedTarget);
});

$('.dropup').on('hide.bs.dropdown', function(e){
	console.log(e.relatedTarget);
});

$('.dropup').on('hidden.bs.dropdown', function(e){
	console.log(e.relatedTarget);
});

And their results:

Thanks in advance.
Regards,
Diego.
PS: I'm using Windows 7 with Chrome 43.0.2357.132 m
EDIT: I've been checking all events objects through console.log(e) and they all have the same properties with exactly same values, only "timestamp" property is the one that is not the same in all event objects, and I found that hidden and shown events has not defined the relatedTarget property, but in the bootstrap.js file there is this piece code:
$parent.trigger(e = $.Event('hide.bs.dropdown', relatedTarget))
if (e.isDefaultPrevented()) return
$this.attr('aria-expanded', 'false')
$parent.removeClass('open').trigger('hidden.bs.dropdown', relatedTarget)

relatedTarget is theorically sent, correct me if I'm wrong, in both hide events and the same where show events are thrown.

Solved You call the hide and show events like this:
$parent.trigger(e = $.Event('hide.bs.dropdown', relatedTarget))
$parent.trigger(e = $.Event('show.bs.dropdown', relatedTarget))

But for some reason you call hidden and shown events like this:
$parent.removeClass('open').trigger('hidden.bs.dropdown', relatedTarget)
$parent.removeClass('open').trigger('shown.bs.dropdown', relatedTarget)

Why would you do that? This solved my problem and probably you have to add it into new Bootstrap versions:
$parent.removeClass('open').trigger(e = $.Event('hidden.bs.dropdown', relatedTarget))
$parent.removeClass('open').trigger(e = $.Event('shown.bs.dropdown', relatedTarget))

According to jQuery Event, the event never gets the relatedTarget parameter doing it like you did it. You need to call the jQuery Event to send the extra parameter.


Bigger picture & wider sidebar?!

Hi Stuart and other friendly people that might be able to help me out here,
I've been trying to adjust the size of the picture for a whlie now, and while I have found some hints in the issues, I haven't been able to succeed. I am imagining putting a significantly larger picture (square) in the sidebar. I have been playing around with the _sidebar.scss file a bunch, but somehow neither succeeded in getting the picture to be a square, nor for it to get larger.
Now, when uploading a very skinn, vertically long picture I have been managing to get it to be quite large -- so I presume the issue with width is related to the size of the sidebar. Does that sound right? And if so, how do I make the sidebar wider?
Second, how do I get the picture to be square and without the border? I tried copying out the border-radious line that somebody suggested on here but that didn't change anything.
Any help would obviously be highly appreciated and loving the template :)

I have the same question. Any help will be greatly appreciated!

Hi, you can change the sidebar width here, when specified in each screen size (x-large, large, etc.) https://github.com/academicpages/academicpages.github.io/blob/25c30de2b4ce3e3f23559384699bb4b9865d6473/_sass/_sidebar.scss#L28
Just add a width property and it would work.

Any examples of this?

I'm don't know how to change the side bar size, but I was able to change the shape of the photo by editing border-radius.  In my case, I did border-radius: 10% , which gives a square with rounded edges.

Information for adjusting the sidebar can be found in the wiki.


Allow PredicatePermissions to return a PermissionResult

A few things:

Will add a better PR description tomorrow, probably
Will javadoc and fix checkstyle issues tomorrow, probably
It seems like AndPermission and OrPermission had loose definitions of what to do when empty. OrPermission already resulted in false, but I added a check for AndPermission so that it now also results in false. I was thinking of requiring a non-empty Set in their constructors, and also moving the iteration to the respective classes. Can't move much more up without introducing a generic to CommandPermission, which seems yucky.
I was originally going to make PermissionLevelResult with a private constructor and a static factory method. But then I figured that it wouldn't hurt to allow the class to be extended. So then I was looking at a protected constructor and a static factory method, and I figured to just have a public constructor. It feels like I'm getting bureaucratic. Maybe a middle ground?

as mentioned on discord, the result for an empty and permission shouldn't be changed. but requiring a non empty set also sounds reasonable.

thank you - got busy the last couple days. I'll be able to finish this today or tomorrow

thank you - got busy the last couple days. I'll be able to finish this today or tomorrow

absolutely no rush, I just figured I'd help keep it up to date with 2.0.0-dev as it's still moving quite fast :sweat_smile:

@jpenilla can i get some guidance/clarification on the direction i should take with AndPermission/OrPermission :)

I merged in the changes from #578, hopefully I didn't butcher it too badly.

thank you... a bit taken by life right now 😆


Update nGraph PythonAPI - P1 ops

Inthis PR following ops were updated or added to Python API:

Broadcast,
Clamp,
Concat,
LRN,
NonMaxSuppression,
NonZero,
RELU,
ROIAlign,
ShapeOf
TopK

TESTNOW_DLDT_E2E

This PR was merged to the PR https://github.com/NervanaSystems/ngraph/pull/2553


Wrong Season/Grass

I finally got around to hacking my acnl game, but when I put in my garden.dat file, it only gave me options for winter grass. (It's summer!) I think it might have something to do with the fact that as I was installing the Checkpoint app on my 3ds, it somehow reset the date to 2/2/2001. I changed the date back to present day, and saved my down to the SD card again, but it still only gives me winter grass options. Any fixes? I really want to be able to hack my game.

The winter bit is just the second part.
So for the first option it's triangle in summer, but square in winter.