investigate delivering annotations as contours instead of rendered images

Deliver annotations as contours (represented using JSON) instead of rendered images.
Allows for more user interactivity in ndviz. Also cleanly separates annotation channels from image channels (removes blending, etc from the equation). It is also preferable to paint for some neuroscientists.
@randalburns @jovo thoughts? Let's pretend time is not a factor and just discuss the scientific merits.

totally open to it.
that is how jeremy does it for his codeneuro data.
i don't understand the pro's and con's sufficiently yes,
but if there were a table listing them, i'd be interested in discussing....
On Fri, Jul 29, 2016 at 3:30 PM, Alex Baden<EMAIL_ADDRESS>wrote:

Deliver annotations as contours (represented using JSON) instead of
rendered images.
Allows for more user interactivity in ndviz. Also cleanly separates
annotation channels from image channels (removes blending, etc from the
equation). It is also preferable to paint for some neuroscientists.
@randalburns https://github.com/randalburns @jovo
https://github.com/jovo thoughts? Let's pretend time is not a factor
and just discuss the scientific merits.
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neurodata.io, jovo calendar
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The key idea is delivering contours instead of rendered images allows the
client to identify a given annotation without contacting the server. Mouse
over color changes and metadata would then be possible. The downside is the
client has to do the rendering, but my theory is the performance hit is
minimal.
On Fri, Jul 29, 2016 at 17:12 joshua vogelstein<EMAIL_ADDRESS>wrote:

totally open to it.
that is how jeremy does it for his codeneuro data.
i don't understand the pro's and con's sufficiently yes,
but if there were a table listing them, i'd be interested in discussing....
On Fri, Jul 29, 2016 at 3:30 PM, Alex Baden<EMAIL_ADDRESS>wrote:

Deliver annotations as contours (represented using JSON) instead of
rendered images.
Allows for more user interactivity in ndviz. Also cleanly separates
annotation channels from image channels (removes blending, etc from the
equation). It is also preferable to paint for some neuroscientists.
@randalburns https://github.com/randalburns @jovo
https://github.com/jovo thoughts? Let's pretend time is not a factor
and just discuss the scientific merits.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/neurodata/ndviz/issues/132, or mute the thread
<
https://github.com/notifications/unsubscribe-auth/AACjcteGqpUyN9m7PC3hmxOBtNzijRL0ks5qalTsgaJpZM4JYgGx
.

--
the glass is all full: half water, half air.
neurodata.io, jovo calendar
<
https://calendar.google.com/calendar/embed?src=joshuav%40gmail.com&ctz=America/New_York

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You are receiving this because you were assigned.
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.

We can identify annotations and render as closed (colored) contours in v2. Seems like the best of both worlds.


CSP MCQ practice corrections/reflection

What you learned from quiz?
I learned from this quiz that I still have a lot to learn, but also that the quiz not only contains questions about coding, but also descriptions of things like IPs, reading graphs and tables, how to prevent things like copyright strikes, binary sequences, and things that include some cybersecurity knowledge.
What type of questions do you feel you are weak on?
I was weak on questions that had multiple right answers, as with other questions I could use the process of elimination to identify questions that make the most sense, but with multiple choice the questions were more vague.
Corrections on anything you got wrong.

Q1.
Which of the following best describes one of the benefits of using an iterative and incremental process of program development?
My answer: A, It allows programmers to implement algorithmic solutions to otherwise unsolvable problems.
Correction: D, It helps programmers identify errors as components are added to a working program.
D is the correct answer because adding small segments at a time to code allows programmers to identify errors in the newer components so that they can focus on those new components.

Q3.
Which of the following best compares the values displayed by programs A and B?
My answer: B, Program A and program B display the same values in different orders.
Correction: C, Program A and program B display the same number of values, but the values differ.
C is correct, as program A lists 1-10 while program B lists 2-11.

Q5.
A user reads reviews of a popular artist’s new album and then downloads the album from the Web site of a licensed online music seller. Which of the following is LEAST likely to be a consequence of this action?
My answer: B, Album reviews from other people who live nearby will be displayed to the user.
Correction: D, The user will be in violation of the Digital Millennium Copyright Act (DMCA).
The user downloads the music from a licensed online music seller's website, so it is unlikely that they would face a violation of the DMCA.

Q9.
For which of the following strings is it NOT possible to use byte pair encoding to shorten the string’s length?
My answer: C, "MEET_ME_LATER"
Correction: B, "LEVEL_UP"
Byte pair encoding cannot shorten this string because it lacks repeating character pairs.

Q12.
The following grid shows a robot in a square grid. Which of the following replacements for missing code can be used to move the robot to the gray square?
My answer: B
Correction: A
The robot cannot rotate right at the beginning, so it will move forward regardless of the if statement.

Q18.
A video-streaming service uses a procedure that takes approximately 1 hour to return results for each genre. What is the total execution time of the program?
My answer: A, 1 hour
Correction: D, 5 hours
It takes 1 hour for each of the 5 genres, resulting in 5 hours total.

Q29.
For which of the following input values will the circuit have an output of false?
My answer: D
Correction: A
A is correct because the AND gate will output false, and the OR gates will not convert it to true.

Q64.
Which of the following statements describe how cloud computing has affected Internet communication?
My answer: A, B
Correction: B, C
C is correct because cloud computing has introduced new data security concerns.

Q65.
A program is created to perform arithmetic operations on positive and negative integers. Under which conditions will the procedure NOT return the correct product?
My answer: B, C
Correction: B, D
D is correct because if y is negative, then count = y will never be met.

Q66.
For which of the following values of theList will Smallest(theList) NOT return the intended value?
My answer: B, C
Correction: C, D
B is incorrect because 10 is the first value smaller than the first number, so it will return 10.
D is correct because the procedure will incorrectly return 30.

Good job, with some more studying you will be able to get close to all of them correct


Breakout Response creation into separate method

As a workaround to folks who would like the headers from a requests.Response but also the nice, neat tweepy.Response data type? I think #1984 and #1989 might be related?

I did no testing of this code because I don't know how. I'm new to Python.


Improve redirection in resend account confirmation scenario

Describe the issue:

It was observed that the Resend Account Confirmation email link in WSO2 redirects to the My Account application. The scenario that is being tested is as follows:

A user self-registers through an application registered in WSO2 IS v7.0.0 (not the My Account application).
After the confirmation email is sent, attempt to log in using the created username and password. A warning appears indicating the account is not verified, along with a Resend Code link.
Then click the Resend Code link to initiate the email.
Upon receiving the email and accessing the confirmation URL, you will be redirected to the My Account application.

The ability to redirect users to the application where the self-registration originated, rather than the My Account application should be available out-of-the-box in WSO2 Identity Server v7.0.0.

Optional Fields
Related issues:

Suggested labels:

This fix is not needed for IS 7 and Master, as this is the self-registration complete page.

Here the user will redirected by the Application Access URL if it's set in the profile.


Implement BGP groups

Fixes:

Closes #110.
This feature will help grouping BGP sessions that are not part of Internet Exchanges. This will be a requirement to be able to deploy configuration of these BGP sessions on routers.
Also it's a good opportunity to have an abstract model of a BGP group that could be use for both standard groups and Internet Exchanges.

Coverage remained the same at ?% when pulling 7ec3847d8cef565766f5d66c652ce5fde3b5cdf6 on bgp-groups into f2080026b7e28582b3054504b7d2c6b92d4f4a29 on master.


Segmentation Code

hello,
I am a student studying knowledge distillation in semantic segmentation.
I want to study your method with implementation detail.
Is it possible to upload your segmentation task code?

Hi @seok-hwa ,
Thanks for your attention on our work.
You can download our code on segmentation via the following link:
https://drive.google.com/file/d/1S8ZE_sMb3xlkA8kiqc-f71-bjkjNzB3A/view?usp=sharing
For implementation instructions, see the README.md included in the archive. I also include the training log and checkpoint of dv3-r101_dv3-r18 setting for your reference. I will upload a more official code of segmentation to this repo once I have time to refactor it.
If you have any questions, please feel free to ask me.
Thanks,
Tao

Thank you very much for your work. Could you provide the code for object detection?

Thank you very much for your work. Could you provide the code for object detection?

Sorry for the late reply. Please allow us some time to prepare the detection code cause currently we are busy in other projects :)

DiffKD for object detection is cool! Could you provide the code for object detection?
Thank you very much for your work.


Add client side for QR code generator

Is your feature request related to a problem? Please describe.
The QR code generator project has only the backend side, not any interface.
Describe the solution you'd like
I want to make an interface where the user can write the URL see the generated QR code and save it in local storage.

please assign this issue under hectoberfest


python311Packages.gradio-pdf: 0.0.7 -> 0.0.9

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.
meta.description for python311Packages.gradio-pdf is: Python library for easily interacting with trained machine learning models
meta.homepage for python311Packages.gradio-pdf is: https://pypi.org/project/gradio-pdf/
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 0.0.9 with grep in /nix/store/wpr810q96fmdgxwgp08kw5zhpc4liyx5-python3.11-gradio-pdf-0.0.9
found 0.0.9 in filename of file in /nix/store/wpr810q96fmdgxwgp08kw5zhpc4liyx5-python3.11-gradio-pdf-0.0.9

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

7 total rebuild path(s)

7 package rebuild(s)

First fifty rebuilds by attrpath

private-gpt
python311Packages.gradio
python311Packages.gradio-pdf
python311Packages.private-gpt
python312Packages.gradio
python312Packages.gradio-pdf

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/wpr810q96fmdgxwgp08kw5zhpc4liyx5-python3.11-gradio-pdf-0.0.9 \
  --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 python311Packages.gradio-pdf https://github.com/r-ryantm/nixpkgs/archive/8f6fbde6a0a2e34d3cb38be1f157fa8700057ac4.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/8f6fbde6a0a2e34d3cb38be1f157fa8700057ac4#python311Packages.gradio-pdf

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/wpr810q96fmdgxwgp08kw5zhpc4liyx5-python3.11-gradio-pdf-0.0.9
ls -la /nix/store/wpr810q96fmdgxwgp08kw5zhpc4liyx5-python3.11-gradio-pdf-0.0.9/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.
nixpkgs-review took longer than 120m and timed out

Maintainer pings
cc @pbsds for testing.

superseeded by https://github.com/NixOS/nixpkgs/pull/316222


Chaise config not copied for Travis tests

Chaise config is copied properly per test when you run the tests locally against the dev.isrd server.
When you run the tests in travis the chaise config isn't copied per test. I noticed it was only using the sample chaise config.

This was failing because the chaise-config was getting copied to some other place.
cp /home/travis/build/informatics-isi-edu/chaise/test/e2e/specs/navbar/data-dependent/chaise-config.js /home/travis/build/informatics-isi-edu/chaise/chaise-config.js

The path should have been
cp /var/www/html/chaise/test/e2e/specs/navbar/data-dependent/chaise-config.js /var/www/html/informatics-isi-edu/chaise/chaise-config.js


Ukrainian supported?

Are there any plans to support Ukrainian and Russian languages? great product would like to try it

Please see demo_part2.ipynb for support

@majestica I'm totally voting for Ukrainian. But russian?
But unfortunately it is not.
 But unfortunately it is not. Very sad.

Slava Ukraini

@ke1ne
SLAVA ROSSII!
Glory to Russia, glory to heroes who won the World War II, defeated nazism and will defeat it again, proving the name of the biggest, the most powerfull and simply the best country in the world.
Sorry, but "country 404" has no chance against mighty Russia in this war.
Слава России! за победу!

Somebody call the doctor

All languages are beautiful, but not all people are. Liberate people from idiocy.

@jarcoder Thank you for understanding this obvious fact, really. I am Russian and I have many Ukrainian friends; we have good time playing games and chatting together and nobody thinks about politics, this military conflict. We don't blame each other because some of us were born in a specific country. We share our problems, they tell me stories about how they suffer and I tell what problems we also have in Russia because of this situations (believe, we have). But we are adequate people and we don't do such things like this @ke1ne does.


Remaking of Sign Up and  Sign In page and validations

Feature request:
The sign up and sign in page should be more graceful and must have validations.
I want to work on this issue under GSSoC'21 participant can i ?

@kumarishalini6 Can you please show a glimpse of the change you wanna make?

The pages are too short in full screen i want to make it perfect according to screen and want to add some images like:-

I'll send you the final image  after working on it

now can i work on it?

@kumarishalini6 Looks good. But you've already been assigned an issue, so you'll have to first finish that one and then you can start with this one.

I have fixes#217 now assign me

I have fixes#217 now assign me

I have requested a few changes, once that PR gets merged, this issue will be assigned to you.

Ok

Can I work over this issue as a GSSOC'21 participant?

i have send PR please review it.

Please review my PR


Direct Download to Ceph Primary storage fails

ISSUE TYPE

Bug Report

COMPONENT NAME
KVM
Direct Download

CLOUDSTACK VERSION
master / 4.12

CONFIGURATION
Trying to deploy a direct download template on Ceph / RBD.
OS / ENVIRONMENT

Ubuntu 18.04
Ceph Luminous 12.2.8

SUMMARY
Deployment of the template fails on RBD.
STEPS TO REPRODUCE
Try to deploy a Direct Download template on RBD shared storage and you will see it fails.
EXPECTED RESULTS
deployment should work

The direct download feature needs to be supported for ceph cc @nvazquez

@wido @rhtyd currently NFS is supported, needs to be extended for Ceph

Moved to the next major milestone

Do we have some work in progress around improving direct downloads @nvazquez - I recall we discussed this at some point for various storage types (Ceph and SolidFire included)?

Yes @andrijapanicsb but the improvement will not include managed storage atm. This will need to be moved to the next release/milestone

I think we added support for direct download agnostic of storage cc @nvazquez @shwstppr ? Is this still an issue then?

We don't support Ceph atm, the framework is storage-agnostics, but the implementation for Ceph/SolidFire is not done.

I've renamed the title and added this to the GSOC 2023 ideas list


plotly installation

Add a note to the trainer.fit method documentation which tells the user to install plotly if they wish to plot the latent space during training.

Print warning if the plotly html import line fails. Then skip plotting.


Fix lines kubernetes-cluster-architecture.svg

Little bit fixed lines in kubernetes-cluster-architecture.svg

Preview of updated related page: https://deploy-preview-45066--kubernetes-io-main-staging.netlify.app/docs/concepts/architecture/
/approve


Install python mysql module dependencies whenever necessary.

The MySQL python module requires either MySQLdb or PyMySQL so the cookbook must ensure they are installed.
My concern here is that by default all modules are enabled but remain silent unless they are able to monitor something.
To avoid having to install unnecessary dependencies a chef attribute was created:

['netdata']['plugins']['python']['mysql']['enabled']

...which is set to false by default. On nodes that have MySQL installed users will need to set this to true which kinda makes sense because chances are they will also need to update the mysql.conf file as well.

+1


Muyang/test helm

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.3 out of 4 committers have signed the CLA.:white_check_mark: pierrelamarche:white_check_mark: FahadBSyed:white_check_mark: acohen4:x: MuyangZangHPEYou have signed the CLA already but the status is still pending? Let us recheck it.


⚠ Bofrost.nl has degraded performance

In 85219a0, Bofrost.nl (https://www.bofrost.nl) experienced degraded performance:

HTTP code: 200
Response time: 1300 ms

Resolved: Bofrost.nl performance has improved in e1749ae.


Allow scrape basic_auth password as a bcryp hash like in the web.yml

Proposal
It seems like basic_auth.password in the prometheus.yml accepts only passwords in clear.
Could it be possible to allow a bcrypt hash like in the web.yml?
web.yml:
basic_auth_users:
  admin: $2y$12$c5H2g88o6KjelhUxOPFJ8eaF5L26XZOKM619XaK5c/SZEuWB0SE42

prometheus.yml:
global:
  scrape_interval: 15s
  evaluation_interval: 15s

scrape_configs:
  - job_name: prometheus
    scrape_interval: 10s
    static_configs:
      - targets: ["prometheus:9090"]
    basic_auth:
      username: admin
      password: $2y$12$c5H2g88o6KjelhUxOPFJ8eaF5L26XZOKM619XaK5c/SZEuWB0SE42

Hello,
Thanks for taking the time to open this request. Unfortunately, this is technically not possible.
A hash can be used to verify a password, it can not be used to use it or decrypt it.
Therefore it can be used to verify that a given password matches, but not to provide a password.
Hashing is a one-way operation.

Note: If for some reason you do not want the password in your prometheus.yml, you can write it in its own file and use password_file. But it would still be cleartext.


Add new company: [company name]

Company Name?
Mentor Graphics
What's the company main business today?
Electronic design automation and CAD Software
What did the company do in the early days?
Sold turn-key CAD workstations (i.e. pre-installed EDA and CAD software, pre-configured network, on Apollo (Unix-like) workstations.
What caused the company to pivot?
Selling workstations with pre-installed software made sense in the 1980s because often the customers had no other computers (except for finance's mainframe) and certainly no LAN.  New competitors sold just software and thus had lower overhead and thus a business model that was more friendly to Wall St. analysts. At the same time customers got more sophisticated they didn't need the white-glove, managed, workstations.
Source?
https://en.m.wikipedia.org/wiki/Mentor_Graphics

Oh wow! This is my first time hearing Mentor Graphics and electronic design automation. That field is almost entirely new to me. I had to summarize the paragraph a bit, hopefully I still got the main idea correct. Let me know if I miss something.
Thanks for the contribution!

Glad to submit. At the time everyone pointed at another company's recent failure to make the same pivot and claimed MG could do no better.  They had some tough years but succeeded.  (Though, one can question if that success was real or not because years later they got bought out by Siemens.)


pandoc breaking change

pandoc realeased a breaking change in 2017: Rename --latex-engine to --pdf-engine, and --latex-engine-opt to --pdf-engine-opt.
I managed to fix the error I was getting about this breaking change, altering mk2pdf-plugin's renderer.py
def write_pdf(self,  mk_filename: str, pdf_filename: str):
        if os.path.isfile(self.template) and os.path.exists(self.template):
            os.system('pandoc --pdf-engine=xelatex --template=%s  %s -o %s'%(self.template,mk_filename,pdf_filename))
        else:
            os.system('pandoc --pdf-engine=xelatex %s -o %s'%(mk_filename,pdf_filename))

maybe you can propose a merge request

Sure, thank you!


Bugfix: adds extension to register SQL TPS

What this PR changes/adds
Adds the previously forgotten service extension to register the SQL TPS.
Why it does that
It wasn't there before.
Further notes
n/a
Linked Issue(s)
Closes #1027
Checklist

[x] added appropriate tests?
[x] performed checkstyle check locally?
[x] added/updated copyright headers?
[x] documented public classes/methods?
[x] added/updated relevant documentation?
[x] added relevant details to the changelog? (skip with label no-changelog)
[x] formatted title correctly? (take a look at the CONTRIBUTING and styleguide for details)

Codecov Report

Merging #1030 (b25a0aa) into main (949451a) will increase coverage by 0.04%.
The diff coverage is 33.33%.

@@             Coverage Diff              @@
##               main    #1030      +/-   ##
============================================
+ Coverage     63.12%   63.16%   +0.04%
- Complexity     2624     2643      +19
============================================
  Files           640      645       +5
  Lines         13964    14048      +84
  Branches        982      987       +5
============================================
+ Hits           8815     8874      +59
- Misses         4698     4722      +24
- Partials        451      452       +1

Impacted Files
Coverage Δ

...nsferprocess/SqlTransferProcessStoreExtension.java
0.00% <0.00%> (ø)

.../sql/transferprocess/store/PostgresStatements.java
100.00% <100.00%> (ø)

...onnector/dataplane/selector/DataPlaneSelector.java
0.00% <0.00%> (ø)

...api/controller/ContainerRequestContextApiImpl.java
83.87% <0.00%> (ø)

...dataplane/sync/DataPlaneTransferSyncExtension.java
0.00% <0.00%> (ø)

...controller/DataPlaneTransferSyncApiController.java
100.00% <0.00%> (ø)

...ne/api/controller/DataPlaneTransferController.java

...plane/sync/DataPlaneTransferSyncConfiguration.java

...ataplane/flow/DataPlaneTransferFlowController.java
91.30% <0.00%> (ø)

...aplane/client/EmbeddedDataPlaneTransferClient.java
100.00% <0.00%> (ø)

... and 5 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 949451a...b25a0aa. Read the comment docs.

@MoritzKeppler Would you like to hit the merge-button?


Update IAM service definitions

This is an auto-generated PR with IAM service updates.

:tada: This PR is included in version 1.1.38 :tada:
The release is available on:

Visual Studio Marketplace
GitHub release

Your semantic-release bot :package::rocket:


Backend Selection for IJulia Notebooks

For plots with a large number of elements (e.g. scatterplots with a bunch of points) the resulting SVG can gum up the browser, which isn't unexpected.
It would be nice to be able to select a backend or something (i.e. render the image as a PNG and show it) that wouldn't have the browser doing so much work for those types of plots.
At the moment, my workaround for plots like this is to use Winston, but it would be nice to be able to use Gadfly all the way through an analysis, even when the dataset has a lot of points.

@timothyrenner Did you end up finding a way to set PNG as the default for all plots in IJulia?

I didn't, I just use the draw(PNG(...), p) trick.


[Feature Request] Horror Game Recommendations

It's that spooky time of the year, and there's no better time to turn off the lights and cower in fear in front of a screen! To also keep up with the gaming spirit, what game should you play? Ask Spookybot!
Implementation details

[ ] Return an embed containing information on a random popular horror game

Information in the embed

Summary of the game
Developer of the game
Publisher of the game
Rating
Release Date
IGN score

@kosayoda I would like to work on it.

@HeroicHitesh You can go for it!


Need for documentation : Style.block wrt. Dimensions & Overflow

In the current state of athlete, one should call

Style.block [ Display.dimensions [...]]

and

Style.blockProperties [ Display.overflow [...]]

It appears as a naming inconsistency that is pretty much

impossible to guess since it does not seem to follow CSS logic (no blockProperty property)
really hard to resolve in the absence of usage documentation.

I had to analyze a dozen type signatures in the source code of athlete to find the blockProperty function.
This is not what you want when using a library.

Hello,
You are right. We'll do it when we can. If you want, you can write the doc as a base and we'll merge it.

I would gladly write a doc if I had the knowledge.

why blockProperties in addition to block in the first place ?
how to use block and blockProperties calls on the same node ?

It appears that
B.div [ Attr.style [ Style.block [ Display.overflow [...]]
but that
B.node [ Attr.style [ Style.block [ Display.overflow [...]]
is ok.
It has to do with the first argument of div being a Modifiers BlockAttributes and that of node being a Modifiers NodeAttributes, which in turn point to a difference of type in the block field.
Overflow being obviously a block attribute, I think something the current behaviour is incorrect. I lack the athlete knowledge to precise how it should work with node, however I am pretty sure it should be ok with div.

did you try
    div [ style [ Style.blockProperties [ Display.overflow [...]] ]

?

Yes It tried and it works - it is actually the point reported initially in this issue.
The actual problem then (outside the lack of documentatio)  is in the use of other block properties such as Display.dimensions, which are valid arguments for Style.block but not for Style.blockProperties.
I feel there is a rationale for all this - and probably a right way to organize the code -  but I can't get my head around how it is supposed to work.

can you mention something that doesn't compile and should ?
Thank you again for your dedication :)


Bezier fixes 2

I'll be testing this tonight.

Please rebase the branch over to material_overlay (current dev branch).


How to use cache in github action when using dip

Reference

https://evilmartians.com/chronicles/journey-from-circleci-to-github-actions
https://evilmartians.com/chronicles/ruby-on-whales-docker-for-ruby-rails-development

When using dip.yml it is convenient to use it in github actions as well. Example from a repo of mine
    - name: Build Images
        run: dip build
        shell: bash

      - name: Pull Images
        run: dip compose pull redis minio caddy
        shell: bash

      - name: Provision
        run: touch .dockerdev/.bashrc && dip provision
        shell: bash

      - name: Integration Tests
        run: dip test system
        shell: bash

By default this doesn't cache the images created in dip build step. How can we do that?

Hey!
Pushed an example GitHub Action which I use in one of the apps: https://github.com/evilmartians/ruby-on-whales/blob/main/example/.github/workflows/test.yml
The key is to use buildx (which supports GitHub Actions cache out-of-the-box).
Note that since we store bundled gems in a volume, it's not cached. That could be fixed by using different volume drivers, though I haven't tried this approach yet.

Thanks you!
So the build args and tags have to be kept in sync between github actions and compose file.


Update README.MD for prototype version 7 documentation

PR Checklist

[ ] If you are proposing a new decision record document, used the right template for that
- (ADR, decision-record, engagement, research)
[ ] Set yourself as the Assignee
[ ] Tag anyone you would like to review, or @forms-design or @forms-devs
[ ] Fill in the template below

What
Describe what you have changed and why.
How to review
Describe the steps required to test the changes.
For example:

Semantic: Do you agree with the changes?
Syntactic: Spelling, grammar, etc.

Who can review
Describe who can review the changes. Or more importantly, list the people
that can't review, because they worked on it.

I have documented the pages for the forms admin and preview forms runner for the prototype version 7.
At first it appeared as if this version was what was tested in sprint 9, but I think this version was not tested. What was tested in sprint 9 has some slight variations on some pages. I am still looking at the murals and other documentation to ascertain and then I will update on this version.

Sorry, accidentally closed this.
Thanks for doing this Betty. I think the screenshots could do with more detail about what is on the screens as well as some of the details of what was changed based on the change logs.
I think you are right this wasn’t tested. It was the content and changes based on Sprint 9 (prototype version 6) which still needs written up properly.

I think the screenshots could do with more detail about what is on the screens as well as some of the details of what was changed based on the change logs.

You mean like mention what was changed according to the change logs, per screen in comparison to the previous version 6? Or elaborate the changes in a separate section?

Yeah pretty much just that.
One way I did this previously was to write up a quick comparison of the screens like https://github.com/alphagov/forms/tree/main/design/prototype-version-4#what-we-changed-from-the-previous-version and a quick summary of those things that changed https://github.com/alphagov/forms/tree/main/design/prototype-version-4#some-things-we-changed-since-last-time
It might also be worth noting to exclude email addresses and names from the write up. So anywhere my email pops up for instance you could just replace it with<EMAIL_ADDRESS>or something similar if that’s ok :)

@bettymw @christophercameron-ixd Hello this has been open for a while can it be progressed any further?

@chao-xian will be progressing this documentation this week

Hi @christophercameron-ixd pls have a review of the updates I have made:

have added more explanations of the changes on the narration below the screenshots for different pages.
Added a new section for new journeys we introduced
created a file to show the changes on the task list page and linked to the main version 7 file
updated the context section
fixed typos and grammatical errors


mTLS needs client secret for requests

We tested this with ADP using omniauth_openid_connect.  Without the client secret for mTLS requests, we received "invalid_client".

Not seeing that as a requirement in the OAuth mTLS draft https://tools.ietf.org/html/draft-ietf-oauth-mtls-15#section-2
Is ADP falling back to reading the parameters being posted in the request body as outlined here? https://tools.ietf.org/html/rfc6749#section-2.3.1

This was a while ago, but I'm almost certain this was not a fallback.  I think they were doing both.

I am reviewing this with jgoerz.  We are still maintaining a patch to support the PR above.  I think ADP may be using the client secret to pass the DN.  We have to go back and research this as time allows.  We do still have an interest in this.  We also understand that it needs to follow the outlined protocols of Openid to be included in a standard implementation.

Sorry for my late response.
Since RFC 6749 prohibits Client to use multiple authentication methods in one request, I'm not going to merge this change.

I am ok with closing this for now.  I think the standard that we are looking at is RFC8705, which extends RFC6749.  I think what we have is an early adopter of a standard that only recently was finalized.  We will review what this client is doing and make sure it fits in the extension.  We may come back later with a new request.  Once we have evaluated what is being done.  Thank you for considering the change.


update Master with first running version of Snow17 BMI development

Complete first version of snow17 with BMI driver. Rewrite and restructure of original NCAR version archived at: https://github.com/NCAR/NWS_hydro_models
Includes a test case with two snowbands for the SF Flathead R / Hungry Horse Reservoir inflows, with restart capabilities. The rewrite converted to using BMI functions to drive the model and consolidated datatype classes.
It was tested against the original version on NCAR Cheyenne with the gfortran compiler, and found to a very close but not perfect match to output from a prior run. This is likely due to converting many datatypes to single precision from double precision and omitting the use of nrtype specifications.

@Keith and Naoki, perhaps take a quick look.  I'm not sure this is reviewable since the version in master before was incomplete.  Let me know if you have any comments or want to test it yourself, otherwise I will go ahead and merge it.


Add Operating System property to KissMetrics events (UPLOAD-766)

Addresses UPLOAD-766.

@krystophv I changed from suing ua-parser to using the UA Client Hints API instead.

@krystophv Some minor changes since your last review. Mind having a quick look?


FAIL  test/example_api.test.js on master

Hello guys,
The test/example_api.test.js is currently broken on master. Stack (npm run test):
`● Link parameters as constants and variables with request payload
expect(received).toEqual(expected)

Difference:

- Expected
+ Received

  Object {
-   "data": Object {
-     "postScanner": Object {
-       "body": "req.body: body, req.query.query: query, req.path.path: path",
-       "everythingLink2": Object {
-         "body": "http://localhost:3002/api/scanner/path_post_200_body_query_path_application/json_req.body: body, req.query.query: query, req.path.path: path_query_path_close",
-       },
-     },
-   },
+   "errors": Array [
+     [GraphQLError: Cannot query field "everythingLink2" on type "Scanner". Did you mean "everythingLink"?],
+   ],
  }

  286 |   }`
  287 |   return graphql(createdSchema, query).then(result => {
> 288 |     expect(result).toEqual({
      |                    ^
  289 |       data: {
  290 |         "postScanner": {
  291 |           "body": "req.body: body, req.query.query: query, req.path.path: path",

  at toEqual (test/example_api.test.js:288:20)

`

Hmmm... this is very strange. I just ran the test and I didn't get any errors. Travis should also report errors like these before a pull request. I will reclone the repository and reinstall the node modules and see if the error still appears. In the mean time, can you make sure you are on the right branch (git remote -v) and commit (git log)?

I just recloned the repository and I didn't experience any problems. Tell me if you have any ideas.
I tried:
git clone https://github.com/strongloop/oasgraph.git
cd oasgraph
lerna bootstrap
npm test

and
git clone https://github.com/strongloop/oasgraph.git
cd oasgraph/packages/oasgraph
npm i
npm test

Maybe it comes from my setup... I will re-check now from fresh clone !

Hum same error from a fresh clone, I use "graphql": "^14.1.1"
Steps were:
cd /tmp
git clone https://github.com/strongloop/oasgraph.git
cd oasgraph/packages/oasgraph
npm i
npm install graphql
npm test

Basicaly, I just added the dependency to graphql. Maybe it has to do with it ???

Very strange... I tried your build process along with a number of other things and I could not replicate this error. I also verified that I am using<EMAIL_ADDRESS>I'm not too sure how to resolve this to be honest...

@ErikWittern Maybe you can help us out with this issue as well 😅

Maybe the node version ? I use :
node -v                                           v11.10.0

@thejibz I was also not able to recreate your issue. I followed your steps (that you listed one hour ago) exactly. My node version is v10.9.0.

@thejibz I think the problem is "exposed by" the node version. I updated my node from v10.14.2 to v11.10.1 and I was able to replicate this error.
However, I believe the core problem is quite involved. I will try my best to try to explain what is going on.

The first thing to I want to explain is why the test failed in v11 and not v10, and that is because the GraphQL interface can change depending on the order in which operations are processed and this order is influenced by a number of factors including the node implementation.
This is a separate issue and we should look into trying to make the behavior more consistent. However, I am not sure how much we can do as even making innocuous changes to the OAS, for example adding a completely unrelated operation, can drastically change the order.

The following is just speculation as I haven't had time to a deep dive but I think it's plausible.
Regarding the core problem, OASGraph tries to reuse object types. It determines if an object type can be reused if 1) the preferredName is the same and 2) the schema matches.
There are two operations in the Example API that have the same preferredName and the same schema, and they are GET /scanner and POST /scanner/{path}. Their preferredName is Scanner and their schema, aka response body, is just a string.
I believe that in v10 both operations get an object type that was produced by POST /scanner/{path} but in v11 both get an object type produced by GET /scanner.
You may think that this shouldn't be a problem -- after all, reusing object types is a critical part to OASGraph -- but it is!
The problem is that OASGraph supplements schemas with link definitions and these links are not considered when an object type is reused.
We only found this problem now because the links in GET /scanner is a subset of POST /scanner/{path}. The aftermath is that in v10, you could query for more than what is stated in the OAS (and we simply didn't know) but in v11, you can only query for less, which broke the test.

Hopefully resolving the issue is only a matter of changing the line here to consider links as well...

Whoa, you did some deep investigation ! Hum don't know what to say ^^ Kudo :)

@thejibz No need to say anything! These notes are mostly for me 😄 But they're also there for anyone who needs them in the future. I think it's a good habit to go in-depth, kind of like providing a distributed form of documentation. Anyway, thanks for filling this issue! Will look into fixing it in the next few days!

Fixed in #133 by collapsing links. An unintended consequence of previous versions is that only links from a single operation would be processed. We will now try to collapse the links, i.e. determine the superset of links for a particular return type, before trying to create objects.

Fixed in #138


Force HTTPS-only on domain

Would love a feature (perhaps I'm missing something) for a domain to only be accessible via HTTPS. Ideally, HTTP requests would be redirected to HTTPS as well for such a domain.

Or maybe even deactivate port 80 for a route?

@philiplb Do you mean return an error instead of a redirect when served over HTTP? What is the use case for that?

With the Amazon ELB, I can just not open port 80, no response there. Use case here: We want to open HTTP APIs only via HTTPs. The app developers would get an error if they even try to use unencrypted requests on port 80.

Ah, I see, so Flynn would not listen on port 80 at all? That makes sense. Please file a separate issue.

Exact, will do. :)

This is a duplicate of #2310.


Editor: Popup showing function arguments only displayed for 3 seconds

Description
In the editor, when I type the name of a function and a left parenthesis, Spyder displays a helpful popup showing the function's arguments.  Unfortunately, this is only displayed for 3 seconds, and then disappears.  It would be helpful if this popup stayed visible for longer, possibly until I type the closing parenthesis or move the text cursor off of the line.
What steps will reproduce the problem?

Type the name of a function, followed by the left parenthesis
The helpful popup appears
Wait 3 seconds
The helpful popup disappears, and I am sad

Version and main components

Spyder Version: 3.0.0b1 (happens in 2.3.x as well)
Python Version: 2.7.10
Qt Versions: 4.8.6, PyQt4 (API v2) 4.10.4 on Windows

Optional dependencies
pyflakes >=0.5.0:  0.9.2 (OK)
pep8 >=0.6      :  1.6.2 (OK)
pygments >=1.6  :  2.0.2 (OK)
IPython >=3.0   :  3.2.0 (OK)
zmq >=13.0.0    :  14.7.0 (OK)
pandas >=0.13.1 :  0.16.2 (OK)
sphinx >=0.6.6  :  1.3.1 (OK)
rope >=0.9.4    :  0.9.4 (OK)
jedi >=0.8.1    :  0.8.1 (OK)
matplotlib >=1.0:  1.4.3 (OK)
sympy >=0.7.3   :  0.7.6 (OK)
pylint >=0.25   :  None (NOK)

If you put the mouse over the popup before it disappears, it will remain visible until you do a right-click over the popup or move the mouse somewhere else.

So the user is happily typing away, and has to move their hands to the mouse and put it over the popup in the next three seconds, or the helpful info goes away?  That seems less than ideal.
I would argue that it should be treated the same as the code completion popup, which gets left in place indefinitely, unless the user dismisses it by hitting ESC.
Finally, if the info is not going to be left there indefinitely, it should at least be for longer than three seconds.  Three seconds isn't generally enough time for me to even read the function definition, let along process it and make use of the information.

Same problem I am facing..

I mean, having the tooltip visible seems to me very distracting. But we could add an option for users who prefer that.
@joshburnett, @akhouribhanu, what do you think?

@ccordoba12 : Definitely, there should be an option to customise. As you wrote earlier, as long as you keep your mouse over menu, it will be visible. But, as soon as you start typing code, It will be gone. As you know, there are many parameters/arguments available with a function, and one cannot memorise it all after looking it once. When you are in middle of writing a function, and you are stuck as you forget the parameter/arguments you are suppose to use.

@akhouribhanu, ok, I understand the use case better now. Then perhaps it'd be better to add a close button to the tooltip.
@goanpeca, @jitseniesen, what do you think about this one?

Actually @ccordoba12 I do agree with the user suggestion,  I have find myself deleting the ( and retyping it to get the info.

@goanpeca wrote down exactly what I thought: leave the tooltip until the corresponding closing parenthesis is typed (or the user moves the cursor past the automatically inserted closing parenthesis), or the cursor is moved to another line, or the user presses Esc, or another tooltip is displayed.
Not sure what to do if the argument list spans more than one line; does the tooltip move down or is it closed?
PS: Visual Studio displays the argument that you are currently at in bold in the tooltip, which I think is pretty neat.

These are all very good suggestions. I'll create a PR to test how this works :-)
@Nodd, I think this would require some changes in your spyder_vim plugin because if a tooltip is visible, users will need to press Esc twice now: one time to hide the tooltip and another one to enter command mode.

Visual Studio displays the argument that you are currently at in bold in the tooltip

Interesting idea, but for another PR ;-)

@ccordoba12 If the problem is just pressing Esc I think it's fine. But I'm afraid that it could be more problematic because the same shortcut would be used for 2 different things in the same context (the editor). And using something else than Esc for vim is not realistic either. Maybe it will depend on how the tooltip thing will be implemented.

So I tried VS Code, which maintains the tooltip open until the user decides to close it (by typing Up or Down arrows), and it works quite nicely!!
So now I fully agree with you guys, and you can expect a PR at the end of this weekend ;-)


BottomBar not visible properly

Here is the screenshot of my activity, am not able to figure out what is wrong. Plz Help

Seems those icons are way too big. Are they 24 dp?

Yep, @jd-alexander is right.
See here how to create the icons properly.


Install script didnt compile .exe

During compile I have this error
SetOutPath: "$INSTDIR"
File: "..\Frog3.exe" -> no files found.
Usage: File [/nonfatal] [/a]([/r] [/x filespec [...]] filespec [...] |
/oname=outfile one_file_only)
Error in script "C:\Users\VS\Downloads\frog-master\frog-master\FROG\installer\Installer.nsi" on line 107 -- aborting creation process

See the link in the ReadMe file


Fixing marketplace

This PR fixes the collect_marketplace method.
It collects 2 tokens, and passes a parameter sorting[date]=desc to the request

got fixed with
https://github.com/alaingilbert/pyogame/commit/3fa35a9d09bff8b1653057707f582efab962957c


The "File Transformation Task" needs to be renamed to include "And Pipeline Variable Substitution"

I just spent several hours of time trying to figure out how the resulting deployed web.config file for an application is getting a value for a connection string that is not specified in the web.config, the web..config, or any other file in the project.
It was only after copying the build definition json to a text editor and searching did I find that there was a pipeline variable that was the potential source, but it took a while longer (more reading) to realize that while the "File Transformation Task" does perform that intended service, it does something else - replaces content in those files with pipeline variables.

The naming for the task is misleading in one of the worst ways - an unrelated or nonsense name that does not describe the functionality of the task would be a safer choice than the one it has now that very specifically describes only half of the total functionality (and you cant even opt out of the unsaid half)
The documentation is slightly misleading as it does not mention that the variables its discussing are pipeline variables until a teeny little blue "Note" after the examples.
The log messages that are emitted reinforce that like its name implies, this task is yet another XDT task. It doesnt state what variables its using or what values, or that its even using pipeline variables and not environment or other variables.

@StingyJack  Most of the points you've highlighted are mentioned in the doc here: https://docs.microsoft.com/en-us/azure/devops/pipelines/tasks/transforms-variable-substitution?view=azure-devops&tabs=Classic
However, we will keep your suggestion in mind. Thankyou for your contribution.

@github-actions - please have your configurer use a stale age that is longer than the time it takes to add new features from customer requests. AFAIK that takes years

naming things like this properly is not hard

necrobump


Support uint32 sampling in random.RandomState.interval

In this PR, random.RandomState.interval supports sampling up to 0xffffffff.
It returns numpy.int32 array if mx <= 0x7fffffff for backward compatibility.
Otherwise it returns numpy.uint32.

LGTM!


Why is the property of OrderViewModel.cs lowercase

@SrushtiPasari94  can you PR this

Raised PR https://github.com/dotnet/eShop/pull/350


Pump up third party

Denpends on vesoft-inc/nebula-common#466

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

@bright-starry-sky @critical27 Please take a look at this PR.

Compile failure, dependent library version problem?
`terminate called after throwing an instance of 'terminate called after throwing an instance of 'terminate called after throwing an instance of 'terminate called after throwing an instance of 'terminate called after throwing an instance of 'boost::filesystem::filesystem_errorboost::filesystem::filesystem_errorboost::filesystem::filesystem_errorboost::filesystem::filesystem_error'
'
boost::filesystem::filesystem_error'
'
'
what():    what():  boost::filesystem::status: Function not implemented: "."boost::filesystem::status: Function not implemented: "."  what():    what():  boost::filesystem::status: Function not implemented: "."
boost::filesystem::status: Function not implemented: "."  what():
boost::filesystem::status: Function not implemented: "."`

Compile failure, dependent library version problem?
`terminate called after throwing an instance of 'terminate called after throwing an instance of 'terminate called after throwing an instance of 'terminate called after throwing an instance of 'terminate called after throwing an instance of 'boost::filesystem::filesystem_errorboost::filesystem::filesystem_errorboost::filesystem::filesystem_errorboost::filesystem::filesystem_error'
'
boost::filesystem::filesystem_error'
'
'
what(): what(): boost::filesystem::status: Function not implemented: "."boost::filesystem::status: Function not implemented: "." what(): what(): boost::filesystem::status: Function not implemented: "."
boost::filesystem::status: Function not implemented: "." what():
boost::filesystem::status: Function not implemented: "."`

working on these weirdos...


Added redirect client

In the Client.ts i had to add a check to se if we have embedded items when we have pagination properties, since the new endpoint is paginated but we dont have embedded data.

For the RedirectClient I would assume we need to override this standard api version header, so we send api-version: 2.3 for the redirect requests.
Ref.: https://github.com/umbraco/Umbraco.Headless.Client.NodeJs/blob/master/src/ApiRequest.ts#L19

Do you think it's enough to just bump it to 2.3 ? I mean if this version works with the apis which are defined in version 2.0 it should be enough right?
It's funny, because i did test the code without noticing this header, and it worked fine so i'm a bit confused

The way I understand it from the discussion on Slack - if we send 2.3 as the default header, then the CMS instance will reject the request, because it only supports up until 2.2.
If we keep the api-version as is in this library I would expect the CDP to not serve the Redirects API as its api-version is 2.3. But what did you test it against? The Redirects API has been deployed to both DEV and PROD now, so maybe do a test against PROD with a project that has the latest bundle?

The cms doesn't know about version 2.3, so that is as expected. I just wasn't sure if the Redirects api would respond if the api-version sent was 2.2 (which is lower than what this api is released under).


[Feature Request] Sega sound at launch

Hello emoose,
We have in the sound folder, a typical Sega sound : sega441.ogg.
Surprisingly, I have never heard it in games, I would like to know if it is possible to add an option to make it work when launching the game at the same time as the presented by Sega screen appears.
Thank you.

+1 for this, I heard it when experimenting with the new SwitcherShuffleTracks setting.

There are at least 3 unused audio files including that: https://github.com/emoose/OutRun2006Tweaks/issues/9#issuecomment-2184261474

Does OR2 share engines with any other AM2 game ?
Left over asset that Sumo didn't delete, maybe.

I remember in an interview one of the devs said that they really wanted to have a button combo to play the classic sega sound on startup, but it was implemented too late and caused issues so the sound is in the files but unused.

Yeah, you "Cheat Activated" when successfully inputting a code on Xbox OR2.

So... is this considered "closed" because whoever opened the issue ragequit GitHub or there's really nothing that could be done? (will someone here ever read this message, anyway?)

The opening video is a bk file, you could just edit the SFX in I think. I believe Howard (FXT) released some hacking tools.

Build at https://github.com/emoose/OutRun2006Tweaks/issues/39#issuecomment-2221028992 includes something for this, but sound has some popping/crackling at the start for me, I guess the sound code hasn't fully initialized yet or something by that time, could be why they didn't add it too :/

It also crackles for me. Bummer!

Just replace the Sega441.ogg file with this one and it works perfectly.
sega441.zip

Just replace the Sega441.ogg file with this one and it works perfectly.
sega441.zip

Where did you get it?

Just replace the Sega441.ogg file with this one and it works perfectly.
sega441.zip

Where did you get it?

I made it myself.

Huh, I wonder why it works, because the original ogg file sounds fine when played by itself. Sometimes the solution is just that obvious lol.

Build at #39 (comment) includes something for this, but sound has some popping/crackling at the start for me, maybe the sound code hasn't fully initialized yet or something by that time, could be why they didn't add it too :/

Is this included in the action build you linked (https://github.com/emoose/OutRun2006Tweaks/actions/runs/9921117465)? It doesn't play sega441.flac like it did with your other DLL, which is the fix mentioned above.

Whatever part of the shadow fix DLL that played the SEGA boot sound doesn't seem to be included in the newer DLLs, it'd be cool to see it restored.

Are you telling me this is not yet on any stable release?

Whatever part of the shadow fix DLL that played the SEGA boot sound doesn't seem to be included in the newer DLLs, it'd be cool to see it restored.

Is it still MIA as of today? @emoose

This is in Tweaks now, all is well.


Add {7SNT}: {SavnSent}

[ Y ] I understand that token listing is not required to use the Polygon Wallet with a token.

Please provide the following information for your token.
Token Name: SavnSent
Token Symbol: 7SNT
Decimals: 14
Polygon Address:0xe74657b0b89ad676F7B2953A8ca393b4A43FeBd5
Ethereum Address:
Logo URI (svg):
Project Name: SavnSent
Project Summary: SavnSent is a deflationary virtual currency created as a store of value. It features built-in parameters to encourage holding, discourage day trading and provide p2p transactions for .07%.
Project Contact<EMAIL_ADDRESS>Project Website: https://www.savnsent.com/
Mainnet/Testnet: Mainnet
Additonal Notes: Please add logo

@mayanks1211 let me know if you need anything on my end. Thanks


[ML]: Resolve the cross references for MLClient, Resource and OnlineDeployment

Resolve the cross references for MLClient, Resource and Online Deployment and Endpoint.
Add description for project, modules and classes.
Description
Please add an informative description that covers that changes made by the pull request and link all relevant issues.
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.
All SDK Contribution checklist:

[x] The pull request does not introduce [breaking changes]
[x] CHANGELOG is updated for new features, bug fixes or other significant changes.
[ ] I have read the contribution guidelines.

General Guidelines and Best Practices

[x] Title of the pull request is clear and informative.
[ ] There are a small number of commits, each of which have an informative message. This means that previously merged commits do not appear in the history of the PR. For more information on cleaning up the commits in your PR, see this page.

Testing Guidelines

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

Existing documentation for the packages (Empty table):

Updated the documentation for the packages:

Broken reference links for Online Deployment:

Resolved reference links for Online Deployment:


Fixed UI Changes

Issue #103 📐

I KeshavAneja have worked for #103

Guidelines 🔐
I accept the fact that I have followed the guidelines and have not copied the codes from around the internet

[x] Contribution Guidelines
[x] Code of Conduct

Issue to be closed 🛅

My pull request closes #103

Provide screenshots also in this PR

Rename PR title to Issue name as previous PR's

Here are the screenshots of the Changes Made:

recording-2023-10-04-19-19-55.webm

Rename PR title to Issue name as previous PR's

Done Sir


Infinite Loop error after upgrading to Yii 2.0.50

After upgrading to Yii 2.0.50, while trying to display a gridview using yii2-elasticsearch, an infinite loop is reported by XDebug.
What steps will reproduce the problem?
Using the yii2-elasticsearch ActiveDataProvider class to display paginated listing is causing this infinite loop error
What's expected?
Display the listing normally which works on reverting the package updates (list of packages updated given below)
What do you get instead?

Packages that got updated on running composer update:
  - Removing symfony/process (v7.0.7)
- Upgrading aws/aws-sdk-php (3.308.4 => 3.313.0)
- Upgrading bower-asset/inputmask (3.3.11 => 5.0.9)
- Upgrading bower-asset/punycode (v1.3.2 => v2.3.1)
- Upgrading components/flag-icon-css (v7.2.2 => v7.2.3)
- Upgrading phpstan/phpstan (1.11.2 => 1.11.4)
- Upgrading psy/psysh (v0.12.3 => v0.12.4)
- Upgrading roave/security-advisories (dev-latest 37f84fe => dev-latest cac81dc)
- Upgrading symfony/browser-kit (v6.4.7 => v6.4.8)
- Upgrading symfony/config (v7.0.7 => v7.1.1)
- Upgrading symfony/console (v7.0.7 => v7.1.1)
- Upgrading symfony/css-selector (v7.0.7 => v7.1.1)
- Upgrading symfony/dependency-injection (v7.0.7 => v7.1.1)
- Upgrading symfony/dom-crawler (v6.4.7 => v6.4.8)
- Upgrading symfony/event-dispatcher (v7.0.7 => v7.1.1)
- Upgrading symfony/filesystem (v7.0.7 => v7.1.1)
- Upgrading symfony/finder (v7.0.7 => v7.1.1)
- Upgrading symfony/string (v7.0.7 => v7.1.1)
- Upgrading symfony/var-dumper (v7.0.7 => v7.1.1)
- Upgrading symfony/var-exporter (v7.0.7 => v7.1.1)
- Upgrading symfony/yaml (v7.0.7 => v7.1.1)
- Upgrading yiisoft/yii2 (<IP_ADDRESS> => 2.0.50)
Writing lock file
Installing dependencies from lock file (including require-dev)
Package operations: 0 installs, 5 updates, 0 removals
- Downloading bower-asset/jquery (3.7.1)
- Downloading aws/aws-sdk-php (3.313.0)
- Downloading psy/psysh (v0.12.4)
- Downloading components/flag-icon-css (v7.2.3)
- Upgrading bower-asset/jquery (3.6.4 => 3.7.1): Extracting archive
- Upgrading aws/aws-sdk-php (3.311.1 => 3.313.0): Extracting archive
- Upgrading psy/psysh (v0.12.3 => v0.12.4): Extracting archive
- Upgrading components/flag-icon-css (v7.2.2 => v7.2.3): Extracting archive
- Upgrading roave/security-advisories (dev-latest eaf1054 => dev-latest cac81dc)

I'm guessing there has been some change in either Yii2 or one of the symfony packages that is causing this but I haven't been able to figure out what it is...

Q
A

Yii version
2.0.50

PHP version
8.2

Operating system
Linux

@lav45 seems to be connected with pagination fix.

I can confirm same issue. Quick fix was to replace BaseDataProvider.php from <IP_ADDRESS>

Q
A

Yii version
2.0.50

PHP version
7.4

Operating system
Linux

Hosted
Docker


Run lintreview through modernize

Relates to https://github.com/markstory/lint-review/pull/149
I'm going to send individual PRs for each part of that PR.

Codecov Report

Merging #150 into master will increase coverage by 0.27%.
The diff coverage is 92.59%.

@@            Coverage Diff             @@
##           master     #150      +/-   ##
==========================================
+ Coverage   83.16%   83.43%   +0.27%
==========================================
  Files          35       35
  Lines        1681     1721      +40
==========================================
+ Hits         1398     1436      +38
- Misses        283      285       +2

Impacted Files
Coverage Δ

lintreview/tools/gpg.py
0% <0%> (ø)
:arrow_up:

lintreview/cli.py
0% <0%> (ø)
:arrow_up:

lintreview/repo.py
95.45% <100%> (+0.06%)
:arrow_up:

lintreview/tools/csslint.py
100% <100%> (ø)
:arrow_up:

lintreview/tools/rubocop.py
97.22% <100%> (+0.07%)
:arrow_up:

lintreview/diff.py
93.4% <100%> (+0.07%)
:arrow_up:

lintreview/tools/jsonlint.py
90.32% <100%> (+0.32%)
:arrow_up:

lintreview/tools/foodcritic.py
40.62% <100%> (+1.91%)
:arrow_up:

lintreview/tools/eslint.py
100% <100%> (ø)
:arrow_up:

lintreview/tools/swiftlint.py
60% <100%> (+1.66%)
:arrow_up:

... and 25 more

Continue to review full report at Codecov.

Legend - Click here to learn more
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I think it would also be wise to add py3 builds to travis. Without those it will be very easy to break py3 support and not know.

How do we handle currently failing tests?

The Py3 builds can be marked as allow failure until they are passing as a whole.

Hi @markstory any progress on this?

@adrianmoisey I've not had the time to dedicate to this. I'm hoping to get to it next week.


Support for WSL2?

Hi,
When I install this repo on WSL 2, the system error ImageMagick. Before I installed sudo apt-get install imagemagick  on Ubuntu WSL2, ImageMagick still not working.

I found setup https://cn.linux-console.net/?p=16978
It work!


document is not defined

Hi,
iam trying to use Photon, but after I wrote this line(const Photon = require("electron-photon");) in my script I get this error.

i also installed the package via npm

Oh man I found the issue... you can close this


GPS Action Remote ?

store.insta360.com
Reddit "Insta360 X3 app recording with GPS location attached to the video file"

Mapillary forum


Generated Filling recipes cannot be removed

I'm using Minecraft 1.16.5, Forge 36.1.4, CraftTweaker 1.16.5-<IP_ADDRESS>, Create 1.16.4+ 0.3.1c, and CreateTweaker <IP_ADDRESS> (and some others like JEI, but nothing that should affect this).
Short version: read the title.
Long version: It seems that Create generates recipes such as filling bottles with potion and buckets with fluid, alongside some recipes added via datapacks. These manually added recipes (such as create:filling/blaze_cake) can be removed with the IRecipeManager functions. However, generated recipes (such as create:fill_minecraft_bucket_with_create_honey) cannot. If I try to add <recipetype:create:filling>.removeByName("create:fill_minecraft_bucket_with_create_honey"); to a script, CrafttTweaker complains it cannot find any recipe with such a name, even though JEI shows it exists and it can be crafted.

I am having a similar issue on 1.18.2. However, it seems to be spread across multiple different crafting managers, including the crushing wheels.

There is nothing that can be done about this.
The recipes you are seeing in JEI are fake recipes, they don't actually exist, Create is just creating recipes for all generic fluid containers (bucket for example) to be filled with all the different types of fluids.
The actual interaction of filling the containers isn't a recipe that can be removed and is hard coded in Create itself.


Fix Bandwidth Reduction envvar table formatting

Fix markdown table typo

Connects to #1076 ?

@lurch Ah, yes. Didn't realize there was an issue filed. Thanks!

Closing for #1083


Non steering comittee members should not have right to close issues

Especially without reasons as for #6871

This has nothing to do about steering comittee @CSurieux. If you have a problem with me then it is a different problem. And I'm not the only one closing your issues because they lack respect of people in here. And don't expect me to not be arrogant if you are. Thanks.
I will leave this one open.

I have no problem with you.
You are a problem for Orchard.
There is no continuing to discuss with you.
I will stop reporting errors because this project is going out of control.

Please file complaints against me here.

@CSurieux yes please do us all a favor and stop participating in this project.

You are the instigator of all this.
I leave.

De : Daniel<EMAIL_ADDRESS>Envoyé : 07/05/2016 19:12
À<EMAIL_ADDRESS>Cc<EMAIL_ADDRESS><EMAIL_ADDRESS>Objet : Re: [OrchardCMS/Orchard] Non steering comittee members should not have right to close issues (#6874)
@CSurieux yes please do us all a favor and stop participating in this project.

You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:
https://github.com/OrchardCMS/Orchard/issues/6874#issuecomment-217652698

To be clear, the steering committee has no particular bug-closing privileges. It's just there to decide the general direction of the project, to take care of mostly administrative tasks related to the project, and to approve new committers, who are then trusted to close bugs, integrate PRs, etc.
See http://orchardproject.net/governance for more details on roles in Orchard.

I want to add that I, as everyone else, can be wrong sometimes. And I do appreciate people that can tell me when I'm wrong. I don't hold the absolute thruth and I believe no one does. This is why, I think that respecting each others is the most important thing if we want to achieve better things. We don't have all the same experience with Orchard. We all learn new things about it every day.
I deliberately closed my eyes on the lack of respect that happened here to make sure this was not aimed to only one person. I tried to be polite and answered even passed those "insults". The reasons are that beyond his arrogance @CSurieux has contributed on some issues and had good points on some. Also at some point I thought that we would come to reason with him over time. We don't want to question his integrity ; but we think that he reached point of no return where anything that we would write to him would never be enough.
I don't mind arguing with someone as long as it stays positive for the project.
Thanks


Disabling/Enabling extension that requires reload does not full sync automatically

Testing #103613

enable settings sync (including extension sync)
enable/disable an extension that requires a reload
reload
go to other VS Code instance and force settings sync manually

Observe:
extension is not yet in the same state as on the first VS Code instance because a reload is required.
It would be be nice if a notification would pop up in this case.

@weinand Not sure about the notification you mean. When you go to second machine/instance sync gets kicked off and extension gets disabled (for eg.,). Since it happens behind the scenes are you suggesting to show a notification that inform user that some extensions are disabled by sync and needs reload for the change to have affect?

@sandy081 yes, exactly what you explain.
Users probably expect that settings sync takes care of everything and assume that an enabled or disabled extension will be enabled or disabled in the other VS Code instance automatically. But this is not the case.

/duplicate
https://github.com/microsoft/vscode/issues/69620 - This is also similar - how to notify user about background updates to an extension.


[TASK][EASY] JDBC Engine supports ClickHouse

Code of Conduct

[X] I agree to follow this project's Code of Conduct

Search before creating

[X] I have searched in the task list and found no similar tasks.

Mentor

[ ] I have sufficient knowledge and experience of this task, and I volunteer to be the mentor of this task to guide contributors to complete the task.

Skill requirements

Basic knowledge of Scala programming language
Basic knowledge of JDBC concepts
Basic knowledge of Docker and Testcontianers

Background and Goals
Currently, Kyuubi supports JDBC engines with limited dialects, e.g. Doris, Phoenix, we can easily extend the dialects to support more databases.
Reference https://www.bilibili.com/video/BV1UT411m7LR
Implementation steps

Implement a ClickHouse dialect in the JDBC engine
Leverage the Testcontainers to add integration tests
Update document correspondingly

Additional context
No response

Sure, could please

... leave a comment with a reasonable estimated deadline

Support other popular DB is fine too, feel free to make PRs, all your contribution will be counted :)

hey guys, any progress on this ?

@cekicbaris there is a draft PR https://github.com/apache/kyuubi/pull/5644, as the original author has no response, you can take over it if you like


Reduce memory footprint of thumbnails

We have discussed on IRC that it might be helpful to package rendered thumbnails as PNG to reduce their memory consumption. This should be done when the viewer is idle, i.e., not when the user is scrolling.

I want to work for it. Can you tell me what exactly needs to be done?

Probably all code you need is in https://github.com/mozilla/pdf.js/blob/master/web/pdf_thumbnail_view.js. At https://github.com/mozilla/pdf.js/blob/master/web/pdf_thumbnail_view.js#L242-L261 we render the page onto a thumbnail canvas.
The idea is that when thumbnails are created, they are drawn on a separate canvas. We have to keep these canvases in memory such that the thumbnail viewer can be used at all times. The goal of this issue is to package the rendered thumbnails as PNG instead of keeping them as canvases in order to reduce the memory we need for them (canvas is essentially a plain pixel map and PNG is more compressed). Maybe we can just use canvas.toDataURL("image/png");, otherwise we have a "convert image data to PNG" function at https://github.com/mozilla/pdf.js/blob/d10573468634e5b1f431821ec2f8cf80d5a64ef6/src/display/svg.js#L29-L219. If we must use that here, we should extract it into a separate component and apply that to the thumbnails.
For more details I hereby ping @yurydelendik, but he is currently on vacation, so it might take some time before he responds here.
For starters it would be nice to have a benchmark of how much memory the thumbnails use in the current implementation. Take the PDF reference for example with 1310 pages: https://www.adobe.com/content/dam/Adobe/en/devnet/acrobat/pdfs/pdf_reference_1-7.pdf. Theoretically, here (http://logs.glob.uno/?c=mozilla%23pdfjs&s=19+May+2015&e=19+May+2015&h=package#c34123) is the size of one thumbnail, so multiplying that by 1310 should give an upper bound for the memory usage of the thumbnails, but we do not know if that theoretical bound is also true in practice. Once we have an idea of the current memory usage, you can create this PNG patch and see if it indeed helps to reduce memory usage.

as for the benchmarks of how memory have been saved, is there any similar test in the existing pdf.js tests?

@zinking No, that should be done manually by measuring memory consumption of the process.


Can not add an assignment within an existing assignment

I'm getting an error message when trying to create an assignment within an existing assignment.
$ nipap address list test
Searching for prefixes in any VRF...
VRF            Prefix                             #  Node                Order          Customer       Description
==================================================================================================================
-              <IP_ADDRESS>/8                       R -  None                None           None           test
-                <IP_ADDRESS>/24                   A -  None                None           None           test /24
-                  <IP_ADDRESS>/24                H -  None                None           None           test host
$ nipap address add prefix <IP_ADDRESS>/29 type assignment description "test smaller subnet"
Could not add prefix to NIPAP: Parent prefix (<IP_ADDRESS>/24) is of type assignment but must be of type 'reservation'

This is per design. An "assignment" is supposed to map up with the prefixes you have configured in your network (that you see in your routing table). You wouldn't configured <IP_ADDRESS>/24 on one interface and then try to configure <IP_ADDRESS>/28 on another interface, right!?
So the larger prefixes need to be "reservation" (those can be infinitely nested) and then there's just one assignment and hosts in that assignment.

ok, but you could have <IP_ADDRESS>/28 point to a next hop in that same subnet, say <IP_ADDRESS>. In that case there are hosts and assignments within the larger assignment.

It's typically a broken configuration right? Hosts in <IP_ADDRESS>/24 probably just have two entries in their routing table - the locally connected <IP_ADDRESS>/24 and a default route. They will ARP for things in <IP_ADDRESS>/28 but as they are nor directly connected this won't work properly. So while it is possible to build in real life it is not possible to cleanly document it in NIPAP. NIPAP does try to give some "guidance" in the sense that it won't allow "senseless" subnetting. I believe it is a good thing to provide such guidance rather than providing maximum freedom to users. Most time it will save people from doing the wrong thing.
If you really want to document it you'll have to use a reservation for <IP_ADDRESS>/24, the <IP_ADDRESS>/28 can be an assignment if you want. The "hosts" in <IP_ADDRESS>/24 can't be "hosts" in NIPAP but will have to be saved as "assignments" or so.
What does your routing actually look like?

In our specific case we have the .1 out of the /24 assigned to a SVI/IRB interface. Other machines on the same broadcast domain are numbered out of that same /24 prefix. Some of those devices announce smaller subnets from the /24 prefix.
We're now using reservations for everything, including the end-hosts. So far that works fine.
Another scenario that comes to mind is 'delegating' a smaller subnet to another department/team. To document that you should be able to add assignments within assignments.

Ok, so you are doing funny subnetting then ;)
Sorry to say but NIPAP was not built for that so you have to do what you are currently doing, i.e. use type "reservation" for all of it.
As for the last use case - no, I don't think that's true. It's a rather common misconception, largely based on the naming of the types in NIPAP, but a NIPAP assignment is not the same thing as a RIPE assignment, so there is nothing that prevents you from "delegating" (whatever that means in this context). You can "delegate" a prefix with type "reservation" too.

Sure, fair enough.
As for the 'delegation' scenario. It's still not possible if you already have end-hosts assigned in the assignment prefix and you decided that you want to 'delegate' a part of the subnet to another team.
But, I get that this is by design.


Update setup-rethinkdb.md

Change the wording From:
If you wish to use Redis as an actor store, append the following to the yaml.
To:
If you wish to use RethinkDB as an actor store, append the following to the yaml.
Thank you for helping make the Dapr documentation better!
Please follow this checklist before submitting:

[ ] Commits are signed with Developer Certificate of Origin (DCO - learn more)
[ ] Read the contribution guide
[ ] Commands include options for Linux, MacOS, and Windows within codetabs
[ ] New file and folder names are globally unique
[ ] Page references use shortcodes instead of markdown or URL links
[ ] Images use HTML style and have alternative text
[ ] Places where multiple code/command options are given have codetabs

In addition, please fill out the following to help reviewers understand this pull request:
Description

Issue reference

close this PR


Build fails due to warnings C4267: '=': conversion from 'size_t' to 'uInt', possible loss of data

Describe the bug
strm.avail_in aws-sdk-cpp/src/aws-cpp-sdk-core/source/client/RequestCompression.cpp
has improper conversions at 2 locations:
Line 159:
strm.avail_in = (flush == Z_FINISH)?toRead-1:toRead; //skip EOF if included
and Line 280:
strm.avail_in = toRead;
Found when building custom client.
Worked around with adding #pragma warning(suppress: 4267) on the source.
Expected Behavior
Build should not fail
Current Behavior
Build fails when building custom clients with warning treated as error:
C4267: '=': conversion from 'size_t' to 'uInt', possible loss of data
Reproduction Steps
Build custom client with cmake ( flag -DLEGACY_BUILD=ON and -DADD_CUSTOM_CLIENTS=<your_service_name>)
Possible Solution
Fix the conversion issue
Additional Information/Context
No response
AWS CPP SDK version used
1.11.169
Compiler and Version used
Visual Studio 2022
Operating System and version
Windows 10

Can you try turning off warning as errors? You can do this with this cmake flag:
-DAWS_SDK_WARNINGS_ARE_ERRORS=OFF

Yes, turning off warning as errors works, but ideally one shouldn't.

Should be fixed with the above PR. closing issue


runtime error from clap

I get a runtime error from clap:
 cargo run --locked --bin freenet

Command freenet: Argument names must be unique, but 'address' is in use by more than one argument or group
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

I fixed the problem, but the code is like that since a very long time. So I assume it is working for everybody else, that is why I did not create a pull-request.
diff --git a/crates/core/src/config.rs b/crates/core/src/config.rs
index 7f90315e..d1cac401 100644
--- a/crates/core/src/config.rs
+++ b/crates/core/src/config.rs
@@ -377,7 +377,7 @@ impl Config {
 #[derive(clap::Parser, Debug, Default, Copy, Clone, Serialize, Deserialize)]
 pub struct NetworkArgs {
     /// Address to bind to for the network event listener, default is <IP_ADDRESS>
-    #[arg(long = "network-address", env = "NETWORK_ADDRESS")]
+    #[arg(name = "network_address", long = "network-address", env = "NETWORK_ADDRESS")]
     #[serde(rename = "network-address", skip_serializing_if = "Option::is_none")]
     pub address: Option<IpAddr>,

@@ -436,7 +436,7 @@ const fn default_network_port() -> u16 {
 #[derive(clap::Parser, Debug, Default, Copy, Clone, Serialize, Deserialize)]
 pub struct WebsocketApiArgs {
     /// Address to bind to for the websocket API, default is <IP_ADDRESS>
-    #[arg(long = "ws-api-address", env = "WS_API_ADDRESS")]
+    #[arg(name = "ws_api_address", long = "ws-api-address", env = "WS_API_ADDRESS")]
     #[serde(rename = "ws-api-address", skip_serializing_if = "Option::is_none")]
     pub address: Option<IpAddr>,

cc: @iduartgomez


Do not display document type for Topical Events

In a previous commit, the conditional for Topical Events was removed. This previously had the effect of not displaying the document type for Topical Events. As there is no published edition for these document types, the display_type_key method fails due to a undefined method 'published_edition' for nil:NilClass and a 500 error is returned.
Therefore adding the conditional back in so we don't attempt to show a document type for Topical Events.
This resolves https://sentry.io/organizations/govuk/issues/2328381368/.
Trello card: https://trello.com/c/GL03zuU5

Sentry issue: APP-WHITEHALL-7XH


Ivf c example

Add examples of ivf-flat and ivf-pq in C language

/ok to test

/ok to test

/ok to test


version 8.7 of highlight.js

Addresses the first part of https://github.com/elm-lang/elm-lang.org/issues/342, but not yet the actual replacing of haskell tags by elm tags throughout the site.
The languages included are: "elm", "javascript", "haskell", "bash". (Previously it was the same without "elm".)

Awesome, thanks again!

Want to do a find-and-replace on ```haskell? I'm happy to do it, so if you are on the fence say no :)

Yes, I can do that.


WorldEdit Compatiability

Having WorldEdit and this mod running at the same time causes Worldedit commands to not autofill.
To replicate: install both mods and type "//replace whi"
Expected behavior "//replace white_concrete" Bold characters should be suggested for autofill

I couldn't reproduce this in singleplayer and multiplayer on 1.18.2 with WE 7.2.10 and Suggestion Tweaker 1.2.0. If you still have this issue I'd recommend specifying the environment in greater detail.

I have this same problem. Here are the mods I have installed: https://github.com/ChristopherHaws/mc-craftersmc-modpack/tree/41dbffc63638b5df151b84fc70227152126a3274/mods
If I get a chance I will see if I can break it down into a minimum list of mods to repro.


Added sequence spawner to fix #133

Usage in development console:
app.addFile(new File([app.unparseFASTA(app.generateSeqs("gen-", 50, 20))], "generated.fasta"))
#133

This is SO COOL! Thanks for tackling this project! One tiny modification requested: that seed string is already available in app.dataSkeleton().reference. Moreover, it makes sense to me to simply default to the session reference string (session.data.reference), instead of hard-coding one in like this.

@AABoyles, I implemented your requested change.
After reading your response on https://github.com/CDCgov/SeqSpawnR/issues/1, I also tried to tweak the algorithm so as to always do codon replacement, but because this seems likely to me to change statistical properties a little, this change is on a separate branch at
https://github.com/gmkarl/MicrobeTrace/compare/seqgen...gmkarl:seqgen-tweak.  The untweaked algorithm looks to me like it will skip codon replacement increasingly as it works with increasingly mutated seeds.
I'm not sure how to actually measure the statistical properties of genetic sequences, or I would have only presented the right solution =)

Thanks @gmkarl! Sorry, I should've been a little more explicit than just saying "statistical properties." The only thing I really care about is that the pairwise genetic distances across the entire matrix are normally distributed. You can confirm this by loading up your random sequences in MicrobeTrace, launching the network, and then clicking settings. The settings modal has a small black histogram in it. If that histogram shows a normal curve, we're good. I'll test it right now.

...And it looks great! Thanks again, @gmkarl!


Refactor based on flutter_lints

Hi amazing developer,
This pull request is related to https://github.com/Jamalianpour/easy_sidemenu/pull/8
I have made the following fixes.

Added flutter_lints to pubspec.yaml
Added analysis_options.yaml
Fixed some lines based on flutter_lints suggestions (Not destructive)
Renamed files based on flutter_lints suggestions (Not destructive)
Fixed typo

Please merge it if it's okay :)
Thank you.

Hello @myConsciousness, and thank you very much.


qemu-networking: consider changing virtio backend default

The default backend for QEMU virtio-net is vhost-net.  This is efficient for performance, but a concern from security perspective.
I recommend for 1.10 that we change the default to disable vhost net. I expect this may result in lowered performance and/or I/O efficiency. This is configurable already in the toml, and users can opt-in to vhost-net still.
Note, on Firecracker and when enabling Cloud Hypervisor, vhost-net is not used.
Feedback?
@sameo @gnawux @amshinde @mcastelino

The performance drop could be less than marginal, so this should be a big fat warning in our release notes. Otherwise I'm all for it.

@gnawux do you have input here?


Attempt SemVer action again

Codecov Report

Merging #15 (d8af77d) into main (af301aa) will not change coverage.
The diff coverage is n/a.

@@          Coverage Diff          @@
##            main     #15   +/-   ##
=====================================
  Coverage   0.00%   0.00%
=====================================
  Files          5       5
  Lines        248     248
=====================================
  Misses       248     248

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Completion toolbar not accessible

Testing #172029
Ctrl+k, Ctrl+I should move focus into the completion toolbar. Or there should be some command that does this.
Then the usual toolbar navigation should work (left/right arrow, space to trigger action).

When the toolbar always shows, there is currently no way to focus it without using the mouse (but this is also not the default).
When it only shows in the hover, Ctrl+K, Ctrl+I should work (if it doesn't work that's a bug of the hover).


Datamap this.data.get(key) should return undefined

Datamap's this.data.get(key) method returns null for data attributes that are not defined. I use TypeScript and find myself doing a lot of checks/casting when comparing something against values returned from that method. Javascript Element.dataset getter methods return undefined, and it feels more correct that an undefined data attribute's value is undefined since, well, it's undefined.

On second thought, null seems to be the more correct return value.

To follow up, DataMap#get(key) returns string | null because that's the return type of Element#getAttribute(name). I agree that string | undefined would be the appropriate type if the Data Map API exposed getter properties instead of a get(key) method.
The proposed Values API avoids this problem entirely: when their underlying attributes are missing, value properties return their type's default value.


Reduced memory usage with a pre-generated index

Here’s a draft proposal for reducing memory requirements.
As discussed in #173, each entry in the index hash table (mers_index) maps a randstrobe to an (offset, count) pair that point to a slice of the flat vector, where the actual information about the randstrobe is stored. For CHM13, ~500 million unique randstrobes are generated, so the hash table has 500 million entries. However, 97.4% of the randstrobes occur only once, so to store one of those, we need an (offset, count) pair (8 bytes) and the ReferenceMer entry in the flat vector itself (another 8 bytes). The idea implemented here is to store those randstrobes directly in the hash table:

The most significant bit of the "count" value is used as a marker
If it is set, the (offset, count) pair is re-interpreted as a ReferenceMer, where offset is interpreted as position and count is interpreted as the "packed" reference index and strobemer offset.
If the bit is not set, (offset, count) are interpreted as before.

On constructing the index, we only add randstrobes with count greater than one to the flat vector, which gives us the memory savings.
The reason why I’ve marked this as "draft" is that peak memory on index construction is a bit larger because I had to undo the optimization of throwing away the hash values and filling the mers_index afterwards because I now need both to be available. One option would be to fall back to the previous way of doing things if --use-index is not provided.
I also have been working on a way to reduce the memory usage even during index creation time, but that is in a different branch
Here are some numbers on CHM13 using the 10 M 200 bp paired-end reads from your evaluation dataset.

main
this branch

Size of .sti file
11.7 GiB
8.2 GiB

Peak mem when creating index
28.6 GiB
29.6 GiB

Time to create index
~5:00
~5:00

Peak mem with -t 8 --use-index
24.4 GiB
20.7 GiB

(User) runtime mapping 10 M paired-end reads
~2500s
~2500s

I think there is something fishy going on with the huge peak memory usage while mapping reads. I only discovered this just now when I wanted to see whether runtime changes when mapping a large number of reads. That is a separate issue however. Fixed by #181. (Edit: Changed table above to no longer show peak memory for mapping 10 million reads. It’s the same as when mapping any number of reads. main includes the fix in #181.)
Note also how the index itself only contains 8.2 GiB of data. When it’s loaded, that becomes 17 GiB because of the maximum load factor of the hashtable and because its size can only be a power of two. If we could reduce this to the absolute minimum somehow, strobealign would only need ~12 GiB of RAM (3.2 GiB for the reference plus 8.2 GiB for the index plus a little extra).

Also, FWIW, ~12 GiB looks suspiciously close to minimap2's peak memory usage. Perhaps Heng has though exactly about this in his hash table implementation.

1. Wouldn't this also give us a tad speedup if reads mostly have unique seeds? (since we do not have to access the flat_vector as much?

If there is a speedup, it’s not much. The runtime was a bit lower (maybe 1-2%), but I didn’t run it often enough so that I could say anything with statistical certainty.

2. Wouldn't the following reduce peak memory during indexing?
   A. construct and sort `flat_vector`
   B. save `flat_vector` to disk
   C. Read `flat_vector`as a stream and construct the hash table (using your new approach of storing randstorbes directly in hash table). Keeping offset incrementing only for non-unique entries. (here things over hard cutoff of 1000 can also be ignored)
   D. Read in the `flat_vector` again (only randstrobes occurring more than once).

It would only increase indexing runtime slightly I think. While keeping peak memory as low as for alignment.

That’s a good suggestion!
Maybe I should mention the other thing I have actually already implemented (in branch index). It doesn’t quite work (yet) as I want it, but I want to mention the idea: The reason the flat vector is created in full in memory at all is that this is needed for sorting it. But we no longer need the hashes with count==1 to be sorted. (And technically, we don’t even need the hashes with count > 1 to be sorted, the ones with the same hash value just need to be adjacent to each other so that they can be looked up together.)
So we can just iterate over all randstrobes and directly insert them into the hash table and the flat vector. More precisely:

Check if the randstrobe is already in the table. If not, add it as a "direct" entry.
If it is, convert the entry to an "indirect" one if count=1 (extract the existing entry, add it to the flat vector), then add the new randstrobe.
At the end, sort the flat vector, and go over its entries to fix up the "offset" fields in the hash table.
(This requires that the flat vector still contains the hashes.)
The issue I have at the moment is that I need to iterate over the all randstrobes once in the beginning to count the unique hashes so that I can reserve the correct size. If I don’t do that, the hash table gets resized when adding entries, which blows up memory usage and runtime.

3. I am also interested in what you wrote about the hash table. Potentially a big gain to be made! Did you try if the other implementation in robin_hood is better? It should be more memory sparse, but not near the minimum I predict.

I tried it just now. Peak memory usage with unordered_node_map is 24 GB.

That’s a good suggestion! Maybe I should mention the other thing I have actually already implemented (in branch index).

When I suggest something, you typically have something better going on ^^. Do you have any estimate on how much the peak memory for this approach would be? Would be great have a peak memory that is not much more than during alignment. Maybe wishful thinking.
Also, to challenge your approach with 'extreme scenarios', the approach would not have as much gain over our previous approach for very repetitive genomes withour many unique seeds. However, CHM13 is a good standard. Just pointing it out for extreme cases such as repetitive plant genomes. Good that we have those datasets to benchmark on.

The issue I have at the moment is that I need to iterate over the all randstrobes once in the beginning to count the unique hashes so that I can reserve the correct size. If I don’t do that, the hash table gets resized when adding entries, which blows up memory usage and runtime.

Indexing time is not crucial imo. Better to have a stable peak memory. Also, since hash table look ups are not a major part of the runtime, maybe it is worth looking at other header-only memory sparse implementations, for example sparsepp, or find any other alternative from this benchmark? This seems to be minimap2's hash table implementation. Something about quadratic probing. Haven't looked up what it means yet.
Another direction is to use 32bit hashes that I played around with a bit before and suggested in https://github.com/ksahlin/strobealign/issues/27. My main concern with the 32bit int hash table are collisions for very large genomes as we are capped by 4.2billion entries.
Just brainstorming a bit. Of course, the trade-off with how much slower it gets should IMO always be consulted.

I tried it just now. Peak memory usage with unordered_node_map is 24 GB.

Okay, that wasn't a viable direction.

I was curious so I checked the results for rye (7.3G) and maize (2.4G) genomes with seeds from 2*150nt reads.
For rye, 83% of the seeds occur once out of 668M total distinct hash values. Maize has about 86% of the seeds occurring only once from a total of 208M distinct hash values. So still big gain to be made with your approach.

Nice results for rye and maize!

Do you have any estimate on how much the peak memory for this approach would be? Would be great have a peak memory that is not much more than during alignment. Maybe wishful thinking.

It would indeed be nearly the same as during alignment. I suggest that I open a separate PR for this. I think it is still valuable to first get this PR to a stage where it can be merged because that other method is a bit slower, so maybe it’s worth to have both and then be able to switch between them (high memory/fast vs low memory/slow).

Indexing time is not crucial imo. Better to have a stable peak memory. Also, since hash table look ups are not a major part of the runtime, maybe it is worth looking at other header-only memory sparse implementations, for example sparsepp, or find any other alternative from this benchmark?

I tested gtl::flat_hash_map a couple of days ago. It used more memory and was a lot slower when creating the index. I’ll need to test sparsepp, but it claims to also have one byte overhead per entry, so this would be the same as what we have now. I haven’t systematically tried the other hash table implementations.

This seems to be minimap2's hash table implementation. Something about quadratic probing. Haven't looked up what it means yet.

To try this, I think we would need to find a C++ wrapper for it (haven’t searched, this probably exists somewhere).

Another direction is to use 32bit hashes that I played around with a bit before and suggested in #27. My main concern with the 32bit int hash table are collisions for very large genomes as we are capped by 4.2billion entries.

I’ll comment over at #27.

... and this can be closed because it has been superseded by #191.


Add helper descriptions on new repo page

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signature trust model

Signed-off-by: Bagas Sanjaya<EMAIL_ADDRESS>

@bagasme would you please add some screenshot on pull description. Thanks.

review ping

Codecov Report

Merging #14591 (e71f482) into master (487f2ee) will decrease coverage by 0.00%.
The diff coverage is 42.15%.

@@            Coverage Diff             @@
##           master   #14591      +/-   ##
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- Coverage   42.21%   42.21%   -0.01%
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  Lines       81624    82078     +454
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+ Hits        34458    34647     +189
- Misses      41531    41783     +252
- Partials     5635     5648      +13

Impacted Files
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models/action.go
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models/migrations/migrations.go
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models/migrations/v166.go
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models/migrations/v172.go
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models/migrations/v173.go
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models/session.go
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models/user.go
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modules/context/context.go
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modules/indexer/code/elastic_search.go
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Code cleanup after GSoC 2023

I need to clean up things. Some things I'm considering:

Adding more comments documenting things, as well as additions to tutorial READMEs
Replace struct name to name_t to make code a bit more compact.
Variable declaration/initialization at the start of scopes. So far, some times I've created variables as and when needed. I will move them to the start to follow the styles of the rest of the code.

Also fixed a small bug here, where the default version in a YAML file needed to be defined at the start of a file (before queries).
Fixed it to follow YAML rules, ie. the order should not be important.


Allow action to force push

@njooma I think you may want to update rdk/app to mention that we are now pinned to API versions and must explicitly ask for them (particularly for web assets)


Tn update

Description
Updated TN profile for the new checks/profile organization.

Hi @felipesanches, I finished reviewing the checks :)

Great, thanks!
I'm starting to review the PR now.

Work on reviewing this PR continues at #4879