Trimming for polyA/T/C; improved runtimes for downstream alignment and variant calling

Shifu;
Congrats on the paper in bioRxiv and thanks for all the great work on fastp. We've been working on improving the runtimes for somatic variant calling workflows and exploring quality and polyX trimming. We did a test run with fastp and atropos and found that the major improvements in runtime were due to removal of polyX sequences at the 3' ends of reads:
https://github.com/bcbio/bcbio_validations/tree/master/somatic_trim
We'd used the new polyG trimming functionality (thank you), but a crude method of 3' polyA/T/C adapter removal, which appears to be less effective with fastp compared to atropos trimming. When additional polyX stretches get removed we get much better runtimes for alignment and variant calling.
I saw general polyX and low complexity trimming are on the roadmap for fastp and would like to express my support for this. We've been making great use of fastp for adapter conversion and would like to offer trimming as part of an effort to speed up alignment and variant calling both on NovaSeqs and more generally.
As a secondary help for integration, is streaming trimming a possibility for paired ends? To help improve preparation runtimes I'd been thinking of including trimming and streaming directly into bwa/minimap2 alignment, or being able to stream outputs into bgzip so we can index and parallelize variant calling.
Thanks again for all the work on fastp.

Thank you Brad!
Actually fastp only implemented polyG  trimming in 3' ends since I thought polyG is much more serious than poly A/T/C for NextSeq/NovaSeq. It's not difficult to support polyX trimming based on the polyG trimming implementation. And I will implement it, according to your good suggestion.
Since the paired-end processing will output two files, I cannot find a good solution to stream the output to aligners.
Thank you again for your support and good suggestions. I will continue to improve this tool.

Shifu,
thank you so much -- we are one of the NovaSeq sites that would positively benefit from a fast trimming implementation, particularly if it can handle polyX sequences. A +1 on the roadmap from us.

Hi Brad and Oliver,
I'd like to ask some questions about polyX trimming:

We know that polyG is caused by signal attenuation of SBS. When the signal is very weak, the base will be detected as G in a two-colour system like NovaSeq or NextSeq. But what causes poly A/T/C?
If polyX trimming is implemented, do we still need polyG trimming options?
Do you think polyX trimming should be enabled by default for preprocessing NovSeq / NextSeq data?

Thanks
Shifu

Shifu;
Thanks so much for considering this feature. In terms of motivation, I think the polyX trimming is separate from NovaSeq polyG trims. There isn't a NovaSeq mechanism contributing to polyA/T/C since this is also present in non-NovaSeq (HiSeq and friends) reads. Rather this is due to some kind of slippage issue or is sequencing real signal. But either way what happens with this during variant calling is that these reads pile up on A stretches of the genome, creating very deep pileups of noise which take a long time to variant call through especially when identifying low frequency somatic variants.
So, I'd suggest having these as separate options. Some users might want only polyG and to keep the other poly stretches. I think having both as optional flags is probably the best option for now until trimming these becomes more standard accepted practice.
Regarding streaming for paired end reads, there are a couple of use cases where we could take advantage of this;

Streaming interleaved reads directly into mappers like bwa and minimap2. So instead of -o and -O, stream both ends, interleaved, directly to standard out.
Streaming into bgzip preparation of reads, doing something like -o >(bgzip --threads 8 > out_R1.fq.gz) -O >(bgzip --threads 8 > out_R2.fq.gz). This would help us prepare bgzipped outputs which are indexable for looks like grabix (https://github.com/arq5x/grabix) so we could parallelize subsequent alignment over regions of the fastq file.

Thanks again for considering all these options and all the work on fastp.

Shifu,
I think both options are useful. polyG is a 2-color-chemistry specific problem and causes variant callers to fail depending on coverage depth (or at least stall for a long time). That in itself is valuable, but based on the preliminary results removing other polyX regions helps with both speed and precision, something I didn't anticipate.
For two color chemistry I'd suggest polyG as a default, with everything else up to the user.

Okay.
Another question: do you want to discard reads containing long polyX in the middle, I mean not in 3' or 5' ends.

Hi @chapmanb ,
Streaming both ends, interleaved, directly into STDOUT is a good suggestion. I have just confirmed that minimap2 also supports interleaved FASTQ, as well as bwa does.
I will add this feature to the roadmap.
Thanks
Shifu

@sfchen

But what causes poly A/T/C?

In RNA-seq one has polyA due to polyadenulation of mRNA, and therefore one would want to trim the polyA ends from the reads before aligning the reads. Some RNA-seq datasets, which come from non-stranded library preparation, will have the polyA showing up as polyT in the reads.

Hi all, I am just starting to implement 3' end polyX trimming.
Another important question:
1, in your opinion, how many continuously identical bases must be detected as a polyX? How about 10 bp?
2, to be error tolerant, how many mismatches are allowed? How about 1 mismatch per 10bp?
Although I will make these options configurable by command line, I still need these information to set the default configuration.
Thanks
Shifu

https://s3-ap-southeast-2.amazonaws.com/umccr/umccr/qc/polyg/ipmn2219-2_33_tumor_hotspot_fastqc.html#M9 is a FASTQC report including just one problematic region. I can only speak for poly-G tracks, but even removing just reads that consist of 50 consecutive Gs would allow most variant callers to finish the region in a reasonable amount of time; allowing one mismatch in 50 would get rid of all but the a small minority.
I think at least for the poly-G issue a conservative setting would work. Not sure what the Atropos defaults are though.

Currently in fastp's polyG implementation is a bit aggressive: 10 bp consecutive G will be categorised as polyG, with one mismatch allowed in per 8 bp.

Shifu;
The defaults you use for polyG -- 10 Gs with 1 mismatch per 8bp -- also seem reasonable to me for polyX. Having them consistent as defaults seems like a worthwhile strategy. Thanks again for working on this.

I just implemented this feature.
Please try to build fastp with latest code on master. Or download http://opengene.org/fastp/fastp to test.

Thanks so much for the quick work integrating this, we really appreciate it. I've re-run a test on the same dataset used above and this does provide some nice improvements in removing these stretches. In comparison to what we were seeing before, here are the top 3' ends for the first 10 million reads:
GTGTGTGTGT 1217
TGTGTGTGTG 1175
CACACACACA 1122
ACACACACAC 1089
TTTTTTTTTG 1083
TTTTTTTTTA 1009

The low complexity dinucleotide repeats are still expected with our current trimming, but the last two polyT with a different base end are ones I'd expect to remove. I dug into them and here are some example reads with these ends left after trimming:
AGGAATTCTGCAGCTTTTTCTTTTCTTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTGTTTTTTTTTAAGGAATTCTGCAGCTTTTTCTTTTCTTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTGTTTTTTTTTATTTTTTTGTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTGTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTA
CCCTTCTTTACGGTGAAGCTTATTCTGATTAAGCCTAGACTGTGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA
TGAAGGCCTGGGGATGGTGACTGAAGAAGGAACACGTAAGTAACTAATGAATGTGAAGGCCATTCTCTTCCTGATTAAAATCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
TGGGTGTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTG

Happy to provide more examples if it would help. Thanks again for the work on this.

@chapmanb how about trim the last base with -t 1 option? Are they from the 151st cycle?
Anyway, I can make a minor revision to trim polyX like TTTTTTTTTTTTTTTTTTTTTTTTA, but we should consider that whether it will cause over trimming. Should it impact MSI detection?

Shifu -- thanks for this. Generally I thought these should fall into the logic of being > poly_x_min_len (which I left at 10) and the logic of 1 allowed mismatch per 8bp with a maximum of 5 mismatches. Are you requiring that the polyX stretch initiate with the 3' most end and implicitly disallowing mismatches there?
MSIs should primarily by in more complex di-nucleotide+ repeats (like the first 4 examples in the remaining trim) and I agree the polyX shouldn't touch those to avoid messing with these. Exploring low complexity filters and the impact of this type of detection would be a useful secondary filter but something more long term. We're hoping to isolate the smaller set of trimming changes which help most with runtimes as a first pass, so clearing out the remaining noisy polyT and other reads would be helpful.
Thanks again for the discussion and help.

@chapmanb I just made an update to trim the polyX like TTTTTTTTTTTTTTTTTTTTTTTTA . Could you please try the latest build?

Shifu;
Thanks much for the fix and continuing to work on this. I've been testing this and comparing with atropos trimming and finding some reads where atropos trims and fastp does not. This is a list of ~1000 that atropos will trim after being fed the fastp trimmed outputs. I don't think atropos does the right thing in all of these cases but would especially like to remove a lot of these problematic reads that are almost all polyX. The file is two columns, with the first the remaining read and the second the part that gets trimmed, so adding those first two columns gives the original post-fastp read:
https://gist.github.com/chapmanb/a0f3ccb645079634dc1e733be29f3de5
I'm continuing to try to understand which reads specifically help with downstream speed improvements, and appreciate all the help trying to be able to be more aggressive in removing this polyX noise. Thanks again.

Thank you Brad, I will do a test with the file you provided.

Hi @chapmanb I cannot download the file you uploaded at https://gist.github.com/chapmanb/a0f3ccb645079634dc1e733be29f3de5
Would you please attach it in this issue? I think it's small enough to be attached here.
Thanks
Shifu

This direct link works, thanks.

Hi @chapmanb
With the latest build, I implemented low complexity filtering, which can filter out most of these reads. You can test it by specifying -y

Shifu;
Thanks so much for the implementation. I've been using this and working through different trimming comparisons with both fastp and atropos to try and find a good minimal combination of quality and polyX trimming that improves calling runtimes and helps with senstivity/specificity.
It looks in the end like the primary different is due to quality trimming differences, and polyX 3' ends up being a reflection of that:
https://github.com/bcbio/bcbio_validations/tree/master/somatic_trim
I'm trying to harmonize fastp and atropos trimming to better understand the differences but am having trouble replicating the runtime improvements we find with atropos trimming. For fastp I use:
--cut_by_quality3 --cut_mean_quality 5 --disable_quality_filtering

to get 3' only quality trimming and with atropos use:
--quality-cutoff 5

which I think should be roughly equivalent. I've tried increasing --cut_mean_quality without much change, so must be missing something.
I'll continue to dig but welcome any thoughts about how best to synchronize these, or if I'm missing anything obvious. Thank you again for all the help and happy to have two quality options to test with.

Hi @chapmanb
A quick update, fastp 0.16.0 supports streaming to STDOUT, and also supports interleaved input. Please see the update on README: https://github.com/OpenGene/fastp#input-and-output
output to STDOUT
fastp supports streaming the passing-filter reads to STDOUT, so that it can be passed to other compressors like bzip2, or be passed to aligners like bwa and bowtie2.

specify --stdout to enable this mode to stream output to STDOUT
for PE data, the output will be interleaved FASTQ, which means the files will contain records like record1-R1 -> record1-R2 --> record2-R1 -> record2-R2 --> record3-R1 -> record1-R3 ...

I hope you will like this new feature.
BTW, I think it's you that maintain fastp on BioConda, am I right? If yes, can you please add me as one collaborator so that I can update it after new version released?

Shifu;
Thanks so much for these improvements, that is really helpful. I'll look at incorporating this into bcbio's use of fastp.
For the bioconda package, you don't need to be a collaborator or anything special. If you update the recipe, send a PR and cc me I'd be happy to merge:
https://bioconda.github.io/contributing.html
or you can also ask to become a contributor to the project to merge them yourself:
https://bioconda.github.io/contrib-setup.html#request-to-be-added-to-the-bioconda-team-optional
It's pretty lightweight meant to enable as many contributors as we can. Note that right nowe we're in the middle of a huge transition to a new compiler system and rebuild so things are bogged down on new recipes. Hopefully that backlog will get cleared soon. Thanks again.

Hi @chapmanb
I sent u an email yesterday. Just wondering that whether you have received it?
Thanks
Shifu

Shifu;
Sorry, I don't think I got this. I'm not sure what happened, but could you resend or we can discuss here? My e-mail is in my GitHub profile. Thanks again.

I sent the email to your Harvard mailbox, and probably it was filtered to the junk box. So I just resent it to your fastmail.com mailbox :)


Introduction to the VMware Tanzu Portfolio Link Fail

I was able to add Introduction to the VMware Tanzu Portfolio to my page (https://modernappsninjas.github.io/bburnz1985/), but the link fails to load (404 error).

This is not supposed to be an answer key submission. This is an issue from the ModernAppsNinja Course enrollment.


Support for Playwright

Playwright Supports Reporters: https://playwright.dev/docs/test-reporters#custom-reporters
It would be nice to have test-analytics around those.

FYI: this is a duplicate of https://github.com/buildkite/test-collector-javascript/issues/41


Add the ability to Stop Search API

If I'm not actively using Ava, it would be nice to be able to stop the search API so that it is not running all the time in the background. Especially since it generates a ton of notifications. But also because I assume it is updating the embeddings constantly, which has a cost.
Of course, it's possible to simply disable Ava, but that is more time consuming than a simple command to disable the search API.

We'll be shipping a major iteration soonish (tomorrow or the day after)

Search API is in the cloud now !


#2014 Use React Testing Library for common-properties tests - pt1 Actions

Fixes #2014
Developer's Certificate of Origin 1.1
   By making a contribution to this project, I certify that:

   (a) The contribution was created in whole or in part by me and I
       have the right to submit it under the Apache License 2.0; or

   (b) The contribution is based upon previous work that, to the best
       of my knowledge, is covered under an appropriate open source
       license and I have the right under that license to submit that
       work with modifications, whether created in whole or in part
       by me, under the same open source license (unless I am
       permitted to submit under a different license), as indicated
       in the file; or

   (c) The contribution was provided directly to me by some other
       person who certified (a), (b) or (c) and I have not modified
       it.

   (d) I understand and agree that this project and the contribution
       are public and that a record of the contribution (including all
       personal information I submit with it, including my sign-off) is
       maintained indefinitely and may be redistributed consistent with
       this project or the open source license(s) involved.

Hi @mikieyx there seems to be some build issue could you please fix it ?

@srikant-ch5 can you approve if this PR is complete?

Hi @JesusGuerrero PR looks good to me.
Just wanted to check regarding my comments above.

Rest looks fine.

Hi @mikieyx Is there any alternative to below ?

@JesusGuerrero If there is no alternative for above in RTL, you can approve this PR as the coverage and other things looks good.

I agree that there should be a better way of validating this then getting the parent x times.  That seems very easy to break in the future.

Hi @mikieyx Is there any alternative to below ?
@JesusGuerrero If there is no alternative for above in RTL, you can approve this PR as the coverage and other things looks good.

Hi @JesusGuerrero PR looks good to me. Just wanted to check regarding my comments above.  It looks good.

Also I was able to use querySelector to check for the button using data-id.

Why can't you use the wrapper to get find the className instead of getting the img and search up the chain?

Why can't you use the wrapper to get find the className instead of getting the img and search up the chain?

I ended up rewriting to avoid going up the chain.


"yarn start" error

Describe the bug
A clear and concise description of what the bug is.
I got the error after I executed the following command as below document says.
https://hawkins.gitbook.io/consoleme/quick-start/local-development
Can I ignore the below error? I am wondering if there is any solution.
cd home/service/consoleme/ui
yarn start
...
WARNING in<EMAIL_ADDRESS>Module Warning (from ./node_modules/source-map-loader/dist/cjs.js):
Failed to parse source map from<EMAIL_ADDRESS>file: Error: ENOENT: no such file or directory, open<EMAIL_ADDRESS>@ ./node_modules/react-semantic-ui-datepickers/dist/react-semantic-ui-datepickers.esm.js 5:0-67 108:41-54
@ ./src/components/selfservice/SelfServiceStep1.js 10:0-63 309:49-67
@ ./src/components/selfservice/SelfService.js 9:0-50 262:47-63
@ ./src/App.js 12:0-72 40:19-39
@ ./src/index.js 8:0-24 11:38-41
....
To Reproduce
Steps to reproduce the behavior:

Go to '...'
Click on '....'
Scroll down to '....'
See error

Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

OS: [e.g. iOS] : Ubuntu 20.04 LTS
Browser [e.g. chrome, safari]
Version [e.g. 22]

Smartphone (please complete the following information):

Device: [e.g. iPhone6]
OS: [e.g. iOS8.1]
Browser [e.g. stock browser, safari]
Version [e.g. 22]

Additional context
Add any other context about the problem here.

Hi @adenkang , what version of yarn and node are you using? Can you try upgrading to the latest LTS releases? Here are the versions I have. After upgrading, remove your node_modules directory and try running yarn again to install frontend packages.
✗ yarn --version
1.22.19
✗ node --version
v15.14.0
✗ node --version
v15.14.0
✗ yarn
yarn install v1.22.19
[1/4] 🔍  Resolving packages...
[2/4] 🚚  Fetching packages...
.......

@castrapel
I get the same error
re install nodejs & yarn install

node version 16.x
yarn 1.22.19

: Error: ENOENT: no such file or directory, open<EMAIL_ADDRESS>


Design language: logo and favicons

Get rid of current silhouette and create a logo that draws emphasis on flash. Generate new favicons based on this logo.

Done in 845320238d33f30c2926dd1b9c558c247c2b3921


VSCode freezes up using more than 6% CPU when pasting text from the clipboard in Linux

Does this issue occur when all extensions are disabled?: Yes, without any user plugins or settings.

VS Code Version: 1.79.2 (695af097c7bd098fbf017ce3ac85e09bbc5dda06) x64
OS Version: Arch Linux  / 6.4.1-arch1-1 (64-bit)
KDE Plasma Version: 5.27.6
KDE Frameworks Version: 5.107.0
Qt Version: 5.15.10
Kernel Version: 6.4.1-arch1-1 (64-bit)
Graphics Platform: X11

Steps to Reproduce:

Create New Window (Ctrl+Shift+N)
Try to save a file (Ctrl+Shift+S)
Once the OS File manager window appears then just copy the name of the file without saving it and close that window (as shown in the video below)
Now, in your file's VSCode tab just paste what you copied into the editor
Congrats! Your editor is frozen now.

For more details see the video that reproduces the bug.
https://github.com/microsoft/vscode/assets/1700322/20d299a1-dafb-4399-b76b-7e240af8bf64

Same issue, VSCode freeze when I switch to vscode ui from other apps, and mouse pointer is always in "text mode".
Platform: VSCode 1.80 on Windows 11
By the way, Microsoft Edge Broswer also has this problem. So I think it caused by Chromium upstream.
Temp workaround: switch between ENG ime and other ime, for example, press Win+Space twice, Chinese->ENG->Chinese.

Can you check if the issue repros with latest stable 1.84 ?

@deepak1556 in 1.84.2 the issue still happens.

Hey @deepak1556, this issue might need further attention.
@joseluisq, you can help us out by closing this issue if the problem no longer exists, or adding more information.

@joseluisq, you can help us out by closing this issue if the problem no longer exists, or adding more information.

Sure, let me try to check it again and I will report here.

@VSCodeTriageBot I can confirm that the problem unfortunately still exists in 1.86.2.

Hey @deepak1556, this issue might need further attention.
@joseluisq, you can help us out by closing this issue if the problem no longer exists, or adding more information.

@deepak1556 @VSCodeTriageBot this issue is still not fixed. For example, in VSCode 1.89.1 is still happening.
What is strange is when I paste from the clipboard then a loader spinner shows up in the editor.

Operating System: Debian GNU/Linux 12
KDE Plasma Version: 5.27.5
KDE Frameworks Version: 5.103.0
Qt Version: 5.15.8
Kernel Version: 6.1.0-17-amd64 (64-bit)
Graphics Platform: X11

@deepak1556 I couldn't reproduce the issue on 1.92.0. It works as expected when using the latest KDE 6.1 and Wayland.
Operating System: Arch Linux
KDE Plasma Version: 6.1.3
KDE Frameworks Version: 6.4.0
Qt Version: 6.7.2
Kernel Version: 6.10.3-arch1-1 (64-bit)
Graphics Platform: Wayland
VSCode: 1.92.0 - b1c0a14de1414fcdaa400695b4db1c0799bc3124

I will try reproducing it again using KDE 5 and X11 in the next few hours.

@deepak1556 I tested VSCode 1.91.1 on Debian 12 x86_64 and works as expected with KDE 5 and X11. It does not hang anymore and the clipboard text gets pasted into the editor correctly.
Operating System: Debian GNU/Linux 12
KDE Plasma Version: 5.27.5
KDE Frameworks Version: 5.103.0
Qt Version: 5.15.8
Kernel Version: 6.1.0-23-amd64 (64-bit)
Graphics Platform: X11
VSCode: 1.91.1 - f1e16e1e6214d7c44d078b1f0607b2388f29d729


Add storage-secret-store, resizer image, and node label image

This pulls in the latest changes from https://github.com/IBM/ibm-vpc-block-csi-driver-operator master that are needed for the driver and operator to ship in 4.10. In particular, these two changes are essential:
https://github.com/IBM/ibm-vpc-block-csi-driver-operator/pull/8
https://github.com/IBM/ibm-vpc-block-csi-driver-operator/pull/10
Additionally, this PR includes:

bumping .ci-operator.yaml to golang-1.17
go mod tidy && go mod vendor
make update-gofmt

/cc @openshift/storage

/hold
to sort out licensing issue that Fabio pointed out above.

/unhold

/retest


Feat add pytest to ci

Solves #128
Todos:

[ ] Add separate cleanup script, needed since container are not delete in case of a timeout or canceled pipeline
[ ] Add test execution for exporter tests (local and git)
[ ] Check for which other images the tests need to be run in the pipeline
[ ] Write documentation for the changes/new gitlab ci template

@Wuestengecko mentioned that Gitlab offers a feature called "service containers". These are managed by Gitlab and are also killed automatically (this should solve the "Cancelled" case). More information here: https://docs.gitlab.com/ee/ci/yaml/#services
However, it will be a major restructuring (as our pytests currently depend on managing the container startup and shutdown themselves).
Communication seems to be difficult in the default setup, but it should work with FF_NETWORK_PER_BUILD enabled (it creates a Docker network for each build). https://gitlab.com/gitlab-org/gitlab-selenium-server/-/issues/1


[SPARK-13165][STREAMING] Replace deprecated synchronizedBuffer in streaming

Building with Scala 2.11 results in the warning trait SynchronizedBuffer in package mutable is deprecated: Synchronization via traits is deprecated as it is inherently unreliable. Consider java.util.concurrent.ConcurrentLinkedQueue as an alternative - we already use ConcurrentLinkedQueue elsewhere so lets replace it.
Some notes about how behaviour is different for reviewers:
The Seq from a SynchronizedBuffer that was implicitly converted would continue to receive updates - however when we do the same conversion explicitly on the ConcurrentLinkedQueue this isn't the case. Hence changing some of the (internal & test) APIs to pass an Iterable. toSeq is safe to use if there are no more updates.

Test build #50706 has started for PR 11067 at commit 9dfb313.

Test build #50706 has finished for PR 11067 at commit 9dfb313.

This patch fails Scala style tests.
This patch merges cleanly.
This patch adds no public classes.

Merged build finished. Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/50706/
Test FAILed.

jenkins, retest this please

Test build #50707 has started for PR 11067 at commit 716e4b3.

Test build #50708 has started for PR 11067 at commit 716e4b3.

Test build #50708 has finished for PR 11067 at commit 716e4b3.

This patch fails Spark unit tests.
This patch merges cleanly.
This patch adds no public classes.

Merged build finished. Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/50708/
Test FAILed.

Test build #50707 has finished for PR 11067 at commit 716e4b3.

This patch passes all tests.
This patch merges cleanly.
This patch adds no public classes.

Merged build finished. Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/50707/
Test PASSed.

cc @srowen

also @zsxwing

Minor questions; seems fine. It's actually the same simple changes in many files and mostly touches tests

@srowen simplified those two places in the test code :)

Test build #50836 has started for PR 11067 at commit 605bb84.

Test build #50836 has finished for PR 11067 at commit 605bb84.

This patch passes all tests.
This patch merges cleanly.
This patch adds no public classes.

Merged build finished. Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/50836/
Test PASSed.

@tdas  want to take a look or since its mostly tests is that not needed?

@tedyu I've cherry-picked in your DirectKafkaStreamSuite changes let me know if that looks ok to you.

Test build #50905 has started for PR 11067 at commit 2567ef0.

It's nice of you to put related changes under one PR.

Test build #50905 has finished for PR 11067 at commit 2567ef0.

This patch passes all tests.
This patch merges cleanly.
This patch adds no public classes.

Merged build finished. Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/50905/
Test PASSed.

Seems OK to me. This is all of the occurrences then? so we could add a scalastyle rule banning SynchronizedBuffer after this?

Yah @tedyu has a follow up PR that adds the scalastyle rule ready to rebase once this gets merged in.

merged to master


[Feature Request] Make scopes project-specific rather than sharing across all projects

This makes much more sense.
You can store configuration in .vscode/settings.json or other project local files.

You can set scopes per project in .vscode/settings.json already. But we could certainly have those be editable via the GUI (which will always edit user settings right now).


Missing control-plane workloads

Type of change

[ ] Refactor
[x] New feature
[ ] Bug fix
[ ] Optimization
[ ] Documentation Update

Description
Missing

crd-scale
node-density

Related Tickets & Documents

Related Issue #
Closes #

Checklist before requesting a review

[ ] I have performed a self-review of my code.
[ ] If it is a core feature, I have added thorough tests.

Testing

Please describe the System Under Test.
Please provide detailed steps to perform tests related to this code change.
How were the fix/results from this change verified? Please provide relevant screenshots or results.

Thanks for the adding more tests.. /lgtm


fs functions: remove_file, move_file, move_dir

https://github.com/foundpatterns/torchbear/issues/1


aws-google-auth: use python36 (#52445)

Motivation for this change
Fix #52445.
Things done

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)

[x] NixOS
[ ] macOS
[ ] other Linux distributions

[x] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[ ] Assured whether relevant documentation is up to date
[ ] Fits CONTRIBUTING.md.

What's happening here is that keyring wants secretstorage 2.x.x when python is older than 3.5.
https://github.com/jaraco/keyring/blob/1b8ab570b2b392f253d004bf325c7e6013d40f95/setup.cfg#L38
python 3.5 is a requirement for  secretstorage 3.x.x.
Since we can't mix another version of secretstorage into nixpkgs, this is the appropriate fix :+1:

Merged in d268e3b2c07b9e99ab02c6d3f3241d5182675a21
@memberbetty Thanks :sparkles:


Revive the Persons who got Killed by a Cheater

Revive Players that got Killed with spoofed bullets damage multi and more

nice idea, we will implement this.


index.html could be configurable

Currently there is no options to use diffrent index.html file to ex. production and development. It' ll be nice if this could be configurable.

You can handle it with your server using url rewriting in ASPNET Core for example or reverse proxy in your web server. Or even with conditions on your csproj file.

As part of our work on Razor Components we'll have a project template that uses server-side rendering for the initial HTML.


add According to to market cards

if market has a resolution source add it to the market card's market title.
if the resolution source is www.espn.com then the market title for the market card should say
Will NY Giants win Superbowl XXIV According to www.espn.com

removed resolution source in V2. this can be closed


Unsupported (17C5046a) iPhone 11 Pro Max

Getting the unsupported message.

@khojames You're supposed to be on iOS 13.0 - 13.3. Not beta versions are are supported. Please close the ticket.

And never will support beta firmwares


Track_infos keyerror

Running anything gives:
Traceback (most recent call last):
  File "/home/me/beatstar-tools/get_rewards.py", line 42, in <module>
    config = GameConfig(session)
  File "/home/me/beatstar-tools/gameconfig.py", line 21, in __init__
    self.tracks = {track['id']: track for track in self.config["track_infos"]}
KeyError: 'track_infos'

No clues how to solve this issue.

Looks like they've changed how they store the game data. You can work around this for now by just commenting out everything that's broken.

FYI: I've commented everything and obviously nothing is working. I'd suggest to put a disclaimer in the README remarking that you'll no longer work on this.
It's a pity, I used to love this small tool! :(

I don't do python but the point is they've removed the song info from the GameConfig and have instead put it into a SongConfig with the following proto
songconfig_proto = {
	1: ("version", String()),
	3: ("GameSKUs", Packed({
		1: ("id", Varint()),
		2: ("idLabel", String())
	})),
	4: ("Beatmaps", {
		1: ("id", Varint()),
		5: ("availability", Varint()),
		21: ("Song_id", Varint()),
		37: ("idLabel", String()),
		46: ("BeatmapVariantReference_id", Varint()),
	}),
	5: ("BeatmapVariants", {
		1: ("id", Varint()),
		2: ("idLabel", String()),
		3: ("Song_id", Varint()),
		4: ("MaxNumLanes", Varint()),
		5: ("MaxScore", Varint()),
		6: ("Difficulty_id", Varint()),
		9: ("IsComplete", Varint()),
		10: ("InteractionsReference_id", Varint()),
		12: ("NumStars", Varint()),
		13: ("InteractionsAsset_id", String()),
		15: ("Description", String()),
	}),
	7: ("SongDifficulties", Packed({
		1: ("id", Varint()),
		3: ("difficulty", Varint()),
		15: ("idLabel", String())
	})),
	8: ("SongTags", Packed({
		1: ("id", Varint()),
		14: ("idLabel", String()),
		21: ("sku_id", Varint())
	})),
	10: ("SongWeightingTags", Packed({
		1: ("id", Varint()),
		2: ("idLabel", String())
	})),
	11: ("BanGroups", Packed({
		1: ("id", String()),
		4: ("blankedBanned", Varint())
	})),
	12: ("SongGroups", Packed({
		1: ("id", Varint()),
		2: ("idLabel", String())
	})),
	13: ("SongMetas", Packed({
		1: ("id", Varint()),
		2: ("idLabel", String())
	}))
}

login.py has a list of CMS files you can request: https://github.com/DavidBuchanan314/beatstar-tools/blob/main/login.py#L121
Add a SongConfig to that to grab that once it's run.
In the case of list_all_songs
https://github.com/DavidBuchanan314/beatstar-tools/blob/main/login.py#L121
You no longer want GameConfig you'd want SongConfig which you'd have to make and parse with the new proto like with gameconfig.py: https://github.com/DavidBuchanan314/beatstar-tools/blob/main/login.py#L121
You'd then have to modify the data relationships using the SongConfig instead.


check-block sometimes Segmentation fault: 11

$ ./target/debug/substrate check-block --dev 2 --pruning=archive
2020-02-13 22:59:06 Importing 1 blocks
2020-02-13 22:59:08 Imported 1 blocks. Best: #6
Completed in 1256 ms.
Segmentation fault: 11

But seems working regardless. I guess some exit handler not configured correctly?
Also saw a few instance where it didn't seg fault, so some timing / ordering issue.
And it will complain pruning mode is not achieve if I didn't specify --pruning=archive, which seems redundant.

This is caused by https://github.com/rust-lang/futures-rs/issues/1470  (duplicate of https://github.com/rust-lang/futures-rs/issues/1349)
The fact that ThreadPool leaves threads running after being dropped is totally unexpected. Main thread terminates while the thread pool tasks are still being cleaned up.
I'll see if a workaround is possible.

oh yes this is the same bug! On my machine it displays like this:
[134] [17:04:39] ~/r/substrate cecton-cli-service-configurations > ./target/debug/substrate check-block --dev 2 --pruning=archive
2020-02-13 18:04:42 Importing 1 blocks
2020-02-13 18:04:44 Imported 1 blocks. Best: #3
Completed in 1213 ms.
pure virtual method called
terminate called without an active exception
fish: “./target/debug/substrate check-…” terminated by signal SIGABRT (Abort)

Related issue: https://github.com/paritytech/parity-ethereum/pull/7695


feat: regen to consume state cache reload api

Motivation

for block processing (getPreState api), we want to reload state if needed
regen state does not work because we don't even need it in goerli/holesky/mainnet since our state cache is so big, but we used to see regen error in Sepolia https://discord.com/channels/593655374469660673/605818244036821012/1201646674628583515

Jan-29 19:30:06.015[rest]            error: Req req-7ml getStateV2 error - REGEN_ERROR_NO_SEED_STATE
Error: REGEN_ERROR_NO_SEED_STATE:
    at StateRegenerator.getState (file:///usr/app/packages/beacon-node/src/chain/regen/regen.ts:162:13)
    at StateRegenerator.getBlockSlotState (file:///usr/app/packages/beacon-node/src/chain/regen/regen.ts:122:38)
    at JobItemQueue.QueuedStateRegenerator.jobQueueProcessor [as itemProcessor] (file:///usr/app/packages/beacon-node/src/chain/regen/queued.ts:239:35)

Description

consume reload apis of checkpoint state cache
fix regen code. Since the regen logics relate to different modules, it's worth to only have e2e test for it which will come in the next PR
handle INVALID_STATE_ROOT error during regen and add logs
add metric to tell where epoch transition comes from

this is cherry-picked from #6359, it does not affect production code because we haven't configured new state caches yet, getOrReload* is just the same to get*
part of https://github.com/ChainSafe/lodestar/issues/5968

:tada: This PR is included in v1.17.0 :tada:


workflow: add workaround for failing tmt tests

Looks like tmt is fixed :tada: so I think we may not need this one


Improve QueryResultDynamicReturnTypeExtension

Same as https://github.com/phpstan/phpstan-doctrine/pull/453#issue-1695849185
With the commit https://github.com/phpstan/phpstan-doctrine/commit/1b0a1b09da00f3acabc3873460d34b514461d7ab
I changed the strategy to be easily accepted and then easier to merge:

If I can precisely infer the type, I return the type
If not, I rely on the default return type rather than returning an half-precise type like array<mixed> => This way we have the same behavior than before and people doesn't get error moving from level 9 to 7-8.

From https://github.com/phpstan/phpstan-doctrine/pull/453#issuecomment-1895364180

Real world project number 2: 21 new errors, some queries use getScalarResult and getResult(AbstractQuery::HYDRATE_SCALAR). In these cases the inferred type is mixed which should be improved. Example query (anonymized):
 $qb = $this->createQueryBuilder('a');
 $result = $qb
            ->select('a.one, a.two, a.three')
            ->andWhere($qb->expr()->in('a.four', $four))
            ->orderBy('a.date', 'ASC')
            ->getQuery()
            ->getResult(AbstractQuery::HYDRATE_SCALAR);

This is fixed by the commit https://github.com/phpstan/phpstan-doctrine/commit/1b0a1b09da00f3acabc3873460d34b514461d7ab

Real world project number 1: 48 new errors, most are "Casting to int something that's already int.". A few real bugs found. But the PR is not currently usable because COUNT(pr.id) AS count as inferred as int<0, max>|numeric-string which will be solved by #506.

I'm curious about this "bug" because COUNT(pr.id) AS count is supposed to be inferred as __benevolent(int<0, max>|numeric-string) in this PR. It's tested here:
https://github.com/phpstan/phpstan-doctrine/pull/520/files#diff-28394df5dba3e85fe86f9c8d9b05d6087fe897d0efa1d0c0ad3533a1f0252b99R381-R413
Did you kept any example of query with your issue @ondrejmirtes ?

I'm sorry, I want to wait for https://github.com/phpstan/phpstan-doctrine/pull/506 to be finished before trying #520 again.

Please fix the conflicts.

Hey, I just merged the most important part of this PR: https://github.com/phpstan/phpstan-doctrine/commit/5745ea60dc5b68ff13fd1295091b6663e3e6de61
Please let me know if I missed anything and open a new PR, thanks.

One note here: are we sure TypedExpressions are not wrongly deduced with this? Because getSingleScalarResult is NOT using result set mapping and thus it never gets casted by the type.

If more hydratation modes are now supported, I believe all those getXxxResult calls should be added to platform test and verified that it matches.

One note here: are we sure TypedExpressions are not wrongly deduced with this? Because getSingleScalarResult is NOT using result set mapping and thus it never gets casted by the type. Maybe it even affects more than just TypedExpressions

I dunno bout TypedExpressions but I just found a special case, and a pretty simple one. BigInt field on Dbal 3.

HYDRATE_OBJECT and HYDRATE_ARRAY is returning a numeric-string value
HYDRATE_SCALAR, HYDRATE_SINGLE_SCALAR and HYDRATE_SCALAR_COLUMN are returning an int value.

But since the query is already considered as a Query<null, array{id: numeric-string}> I'm not sure it will be easy to get back the int value for such hydration mode.
Should revert most of the PR (HYDRATE_SCALAR / HYDRATE_SINGLE_SCALAR / HYDRATE_SCALAR_COLUMN) to only keep the HYDRATE_ARRAY inference (cc @ondrejmirtes) or do you see a way to improve the dbal inference @janedbal ?

I'd need to dig deeper into it, but basically, for those hydratation modes you need to use getDatabaseInternalTypeForDriver and not getWritableToPropertyType in the walker. So if we know the mode beforehand, it should be easy. If not, hard.

I'd need to dig deeper into it, but basically, for those hydratation modes you need to use getDatabaseInternalTypeForDriver and not getWritableToPropertyType in the walker. So if we know the mode beforehand, it should be easy. If not, hard.

I don't think we know the mode before because the order things are done for $qb->getQuery()->getResult($hydrationMode) is

On the getQuery call, compute the Query type in QueryResultTypeWalker to hydrate the templates of the stub

/**
 * @template-covariant TKey The type of column used in indexBy
 * @template-covariant TResult The type of results returned by this query in HYDRATE_OBJECT mode
 */
abstract class AbstractQuery

Then, on the getResult compute the result with the hydration mode and the Query<TKey, TResult> type already computed.

That's why it may require to have something like
/**
 * @template-covariant TKey The type of column used in indexBy
 * @template-covariant TResult The type of results returned by this query in HYDRATE_OBJECT mode
 * @template-covariant TResult2 The type of results returned by this query in HYDRATE_SCALAR mode
 */
abstract class AbstractQuery

which is not really satisfying

Yeah, that is not very nice.
Btw, we are using only analysable methods since the query type inference was added and you actually dont need all the other methods. Everything can be replaced by the supported ones. We have this backed up by a rule. Thereotically, such rule can be even in phpstan-doctrine under some flag.

Should revert most of the PR

So I'd say yes.

Btw, we are using only analysable methods since the query type inference was added and you actually dont need all the other methods. Everything can be replaced by the supported ones. We have this backed up by a rule. Thereotically, such rule can be even in phpstan-doctrine under some flag.

I don't understand

Should revert most of the PR

So I'd say yes.

Done https://github.com/phpstan/phpstan-doctrine/pull/588

I'm just saying that codebase can still have 100% type coverage in terms of DQLs even when some of the methods are not supported:

getScalarResult or getArrayResult

replace by getResult

getSingleScalarResult

replace by getSingleResult(Query::HYDRATE_OBJECT)['column']

getSingleColumnResult

replace by getResult() + array_column

and pass Query::HYDRATE_OBJECT to getOneOrNullResult, getSingleResult, toIterable and you are safe.

The main method i use was getSingleColumnResult, I find silly to always have to add an extra array_column.
But yeah this can be avoided...

Silly, but type-safe :)

I have trouble to understand why we have a such different behavior with hydration mode. I created https://github.com/doctrine/orm/issues/11527 to know more about it if you're interested.
But I feel like you may already know the answer, or at least know way more things than me about this subject.

If you look at AbstractHydrator descendants, you will se that some (e.g. SingleScalarHydrator) is not using parent's ResultSetMapping. And that is the reason why result types are different.


change(ci): Run Zcash parameter downloads with trace logging

Motivation
We don't know why Zcash parameter downloads are failing, so we need to log more diagnostic info.
Diagnostics for #5091.
Solution

Run GitHub Runner Zcash parameter downloads with trace logging
Run Docker Zcash parameter downloads with trace logging

We might need to use --no-default-features or run cargo run --example download-params to make this work

Review
This is important but not critical.
Before Approving the PR
Does trace logging actually work in GitHub Runners and Docker?
Reviewer Checklist

[ ] Will the PR name make sense to users?

[ ] Does it need extra CHANGELOG info? (new features, breaking changes, large changes)

[ ] Are the PR labels correct?
[ ] Does the code do what the ticket and PR says?
[ ] How do you know it works? Does it have tests?

Follow Up Work
Look at the diagnostics to help fix the bug.

The OS workflow didn't give us any more logs, so I'm trying the Docker workflow here:
https://github.com/ZcashFoundation/zebra/actions/runs/3125512247/jobs/5069952746

This didn't work, we also need to compile Zebra without the compile-time debug/trace logging removal feature, and revert the switch to Rust 1.63.

I handed this ticket over to Marek, I'm happy to help out once I've finished the lightwalletd tests.

Marek diagnosed the issue as a performance regression, so we don't need this PR.


Provide design for generating simple "Hello World" models from Cadl description

Provide design for https://github.com/Azure/autorest.csharp/issues/2396

Duplicate of https://github.com/Azure/autorest.csharp/issues/2372


Dev: Web - EXpensify signup text appears on epub and mp4 uploads

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Action Performed:

Go to any chat
Upload attachments
Select any epub files or mp4 records and send
Notice that after the attachment is uploaded, extra text about expensify is displayed.
P.S doesn't happen with pdfs and jpgs.

Expected Result:
Extra text about expensify should not be  displayed.
Actual Result:
Extra text about expensify should is displayed after attachments
Workaround:
Unknown
Platforms:

Which of our officially supported platforms is this issue occurring on?

[ ] Android / native
[ ] Android / Chrome
[ ] iOS / native
[ ] iOS / Safari
[x] MacOS / Chrome / Safari
[ ] MacOS / Desktop

Version Number: Dev <IP_ADDRESS>
Reproducible in staging?: no
Reproducible in production?: no
If this was caught during regression testing, add the test name, ID and link from TestRail:
Email or phone of affected tester (no customers):
Logs: https://stackoverflow.com/c/expensify/questions/4856
Notes/Photos/Videos: Any additional supporting documentation
https://github.com/Expensify/App/assets/93399543/489d39fc-3f4a-4058-86b0-eb7659f22364
Expensify/Expensify Issue URL:
Issue reported by: @ashimsharma10
Slack conversation: https://expensify.slack.com/archives/C049HHMV9SM/p1693306268579329
View all open jobs on GitHub

Apologies. Accidentally I tested this on the really old dev version. Could not reproduce on latest v1.3.58-1 dev.

Apologies. Accidentally I tested this on the really old dev version. Could not reproduce on latest v1.3.58-1 dev.

All good! closing


[mac OS] Set flags for curl invocations

Description
Set -fsS flags for curl to catch errors early. Also add -L flag to handle redirects and improve build stability.
Related issue: -
Check list

[ ] Related issue / work item is attached
[ ] Tests are written (if applicable)
[ ] Documentation is updated (if applicable)
[ ] Changes are tested and related VM images are successfully generated

/azp run macos11, macos12


alt animation

What is your question?
how do i add alt animation to spritesheet

Draw it

What is your question?
how do i add alt animation to spritesheet

then use https://github.com/UncertainProd/FnF-Spritesheet-and-XML-Maker/releases/tag/v4.2.5

where on the sheet do you draw it

This isn't psych engine related


Migration Fails - System.TypeLoadException: Could not load type 'Microsoft.WebTools.Shared.FeatureDetection.FeatureContext' from assembly 'Microsoft.WebTools.Shared

Hey guys,
The migration seems to be failing via the extension.
System.TypeLoadException: Could not load type 'Microsoft.WebTools.Shared.FeatureDetection.FeatureContext' from assembly 'Microsoft.WebTools.Shared, Version=<IP_ADDRESS>, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a'.

Also wanted to say, I am very happy you guys are working on this.
We've been looking at the migration for a long time, even though we have a very modern WebForms app, we've wanted a pathway to .NET 6+.
So thanks for doing this.

Just installed the extension, and having the same issue.

Thanks for the feedback. An update will be pushed out soon that should fix this

Working now! Thanks!


https://developer.mozilla.org/en-US/docs/Mozilla/Testing/ASan_Nightly_Project

Request type

[ ] Please close this issue, I accidentally submitted it without adding any details
[ ] New documentation
[x] Correction or update

Details

Download links on https://developer.mozilla.org/en-US/docs/Mozilla/Testing/ASan_Nightly_Project#Requirements are broken.
You likely just need to replace the v57 with v68. (and possibly keep it up-to-date, or use a symbolic link/redirection or so, so it does not break again.)

@choller, the docs under /Mozilla are no longer maintained by the MDN team, but since I saw you've updated this page recently, I thought you might want to be aware of this bug report.

Thanks for pinging me on this. It looks like Kwan already changed the page to directly link to TC, so this should be fixed.


force REQUESTS_CA_BUNDLE=/etc/pki/tls/cert.pem

we install jenkins-jobs via pip, which pulls in certifi, which contains
the old DST X3 root cert, which makes OpenSSL 1.0.x on EL7 freak out and
fail to verify the perfectly valid certs of ci.theforeman.org and
ci.centos.org

The commit message might could use a change from foce to force as well. More typing @evgeni !


How to simulate a battery with given macroscopic 3d geometry

Is there a way to simulate a lithium-ion battery with a given arbitrary 3d macroscopic geometry (e.g. cylindrical, rectangular-shaped) and dimensions? I found a few sources that suggest it is possible with the current PyBaMM functionalities:
https://pybamm.readthedocs.io/en/latest/source/spatial_methods/finite_volume.html
https://github.com/pybamm-team/PyBaMM/blob/269629fc83774dbdea2288f466195b8805e72df2/pybamm/geometry/battery_geometry.py#L7
https://github.com/pybamm-team/PyBaMM/blob/269629fc83774dbdea2288f466195b8805e72df2/pybamm/meshes/scikit_fem_submeshes.py#L11
I was also able to use the "arbitrary" geometry of the "lumped" thermal submodel with the DFN model and calculate area and volume according to my geometry, but I was not able to find any usage example on how to adapt the rest of the model to an arbitrary macroscopic 3d geometry.
Could you give me a hint how to approach this problem?

At the moment you can only do single layer pouch cells in 3D by doing e.g.
dfn = pybamm.lithium_ion.DFN(
    {"current collector": "potential pair", "dimensionality": 2, "thermal": "x-lumped"},
)

this will solve a "2+1D" model where the temperature doesn't vary across the thickness of the pouch but does vary in the other two dimensions. See this paper for details.
The arbitrary option in the lumped thermal model uses an electrochemical model coupled to a lumped thermal model which has a cooling term that has a factor area/volume in it. The point of this option is to let the user specify the surface area available for cooling and volume for their cell, rather than letting the code calculate it from the other dimensions assuming a pouch cell.

Thank you for the quick reply. For my use case, I need to simulate macroscopic 3d lithium ion cells of cylindrical and rectangular-shaped geometry using the DFN model with the thermal, SEI, lithium plating and swelling + cracking submodels. What modifications will I have to make to PyBaMM to add support for my geometries?

You would need to add a new geometry for the cylindrical cell and update the spatial methods to work in cylindrical coordinates. I have an issue open #1311 to add some homogenised cylindrical models, which I'm hoping to work on soon, but it has been open for a year haha... other things have gotten in the way.
Do you actually need spatially resolved simulations? I.e. do you care about, say, how SEI thickness varies with macroscale r and theta? Or do you just want a 1D model that represents a cylindrical cell and tells you how quantities vary across the thickness of the electrode/separator/electrode sandwich? If it is the latter, the Chen2020 set is for a cylindrical cell, so would be a good starting point to see how to add your parameters.

Yes, I need spatially resolved simulations, ideally I should be able to create them for an arbitrary geometry. I would not expect the SEI thickness to vary with theta, but with r, eventually. And also the temperature will be dependent on r. I need to write a submodel that produces T(r, theta, z), or T(x, y, z), also with external cooling options, and swelling / SEI / lithium plating variables in a similar way.
I will have a look at the Chen2020 set, thanks.

A good starting point might be to just get the cylindrical geometry and spatial methods set up to solve something easy like the heat equation with a prescribed source term. Then once that is all set up you can figure out how to couple the electrical and thermal problem at the cell scale to the local electrochemistry. Solving something like a DFN at each point in space in the jelly roll might be computationally expensive, and you might find the homogenised models described in #1311 are enough.
We also did some work coupling pybamm with openpnm to solve jelly roll problems, see here and here.

But the rectangular model should work already for a single-layer pouch. There are ways you can make the single-layer model behave like it represents a multi-layer pouch, e.g. by scaling the parameters as in this paper, or by doing homogenisation (hoping to add this in the future, will open an issue now so you can track progress).

Thanks, I will take some time to have a look through all of this information.

Can we close this now we have #1777?

Ok I close this now... I will reopen in case it is necessary.


unable to run - gf180mcu_fd_io__bi_t.cdl file on ngspice

Expected Behavior
when the gf180mcu_fd_io__bi_t.cdl is run on ngspice by making the necessary connections of the pins to configure it to IE mode and drive a PULSE signal on PAD and plot output on Y port - the digital signals driven on PAD must show up on 'Y'
Actual Behavior
certain devices are not found in ngspice libs - and their symbols (example pfet_06v0_dss,nfet_06v0_dss) are not available in ngspice

Steps to Reproduce the Problem
take gf180mcu_fd_io__bi_t.cdl file in this repo and run on ngspice. Ngspice sims should run and you should be able to run digital signals on the PAD and plot the same on Y, A outputs (depending on digital pad configuration) as per -

Specifications

Platform: proppy/conda

@proppy

ngspice test bench attached
pads-tb.zip

The same issue persists when I extract the same pad via magic and run the extracted .spice file in the same test bench.

/cc @atorkmabrains

Looking at https://github.com/google/globalfoundries-pdk-libs-gf180mcu_fd_pr/blob/main/models/ngspice/sm141064.ngspice it seems that devices should be named:
pmos_06v0_dss nmos_06v0_dss

@mithro do you have a link to the naming convention for standard cells and primitive devices so that we can track the inconsistencies?

@FaragElsayed2 Could you please check?

@atorkmabrains No, we don't.
https://github.com/google/globalfoundries-pdk-libs-gf180mcu_fd_io/tree/main/cells/bi_t

@spnadig CDL is mainly used for LVS not for simulation. As @FaragElsayed2 mentioned, we don't have spice netlist for simulation unfortunately. You could rewrite the CDL to make it ng-spice compatible.

But the issue remains even after I extract the ngspice netlist via magic extraction- the screenshot is in the description

@spnadig Could you share the netlist?
\cc @RTimothyEdwards

To be more precise - I was able to get the netlist via magic extraction for analog and power pads. However, when I run extraction on digital pads (from PDK) I get segmentation fault.  Attached is the extraction script and the corresponding GDS file
digital_pads_extraction.zip
Error:

The digital pads are flattened prior to extraction

@spnadig :  Segfaults in magic should be reported to the https://github.com/RTimothyEdwards/magic issue tracker.  But since you have posted the netlist here, I'll take care of this one from here.
FYI, I can duplicate the crash condition here with the files you posted.

Sure @RTimothyEdwards will do

@spnadig :  The crash condition is now fixed in magic version 8.3.396.  Thanks for the detailed bug report and the files to reproduce the error.
Please note that I am aware of some issue with gf180mcu when running "extresist"---the routine will get confused over the device types.  I am not sure if that has any actual impact on the output or if it just causes "extresist" to dump a bunch of error messages, but I do need to fix it.


Do not close popup action in case withdraw on IOS

Describe the bug
Do not close the popup action in case withdraw on IOS
To reproduce the bug
Steps:
1. Go to the staking detail then open the action stake
2. Select withdraw action and observe the displayed screen
Actual: Do not close the popup action
https://github.com/Koniverse/SubWallet-Mobile/assets/117999489/14194fd2-0d3e-4088-b597-dbf2c5b7e82f
Expect: Close popup action and open withdraw screen.

Version test: v1.0.2(154)
Devices test: IP 11
Validation passed.


Manage access permission test

Until refactored access dialog is released, this test needs to run as org admin and requires a secondary user to test if the permission was really applied and works as expected.
The prerequisite for this is this PR to mas-ci: https://gitlab.cee.redhat.com/mk-ci-cd/mas-ci/-/merge_requests/677

Will add some condition to skip steps that need a second user if credentials are not supplied tomorrow.

Forgot to wait for the instance to be ready 🤦♂. Next build should pass 😀


how to modify traceId

Please answer these questions before submitting your issue.

Why do you submit this issue?
[*] Question or discussion
[ ] Bug
[ ] Requirement
[ ] Feature or performance improvement

Question

What do you want to know?

how can i trace my project myself

the client is just
<dependency>
  <groupId>org.apache.skywalking</groupId>
  <artifactId>apm-toolkit-trace</artifactId>
  <version>${skywalking.version}</version>
  <scope>provided</scope>
</dependency>

or more

can i modify traceId, so it can associate another

Bug

Which version of SkyWalking, OS and JRE?

Which company or project?

What happened?
If possible, provide a way to reproduce the error. e.g. demo application, component version.

Requirement or improvement

Please describe your requirements or improvement suggestions.

You cannot do that via the toolkit. We don't support that now. If the trace breaks, you should find out why, simply modifying the trace id may make things worse.

As for how to trace by yourself, please read the doc, it's clearly documented.

As i publish a topic to redis, when i subscribe it, the traceId lose
I wanna add the traceId to data, and modify subscribe traceId, so the to trace linked

As i publish a topic to redis, when i subscribe it, the traceId lose
I wanna add the traceId to data, and modify subscribe traceId, so the to trace linked

I personally don't suggest to do that (and the toolkit doesn't have such APIs, as I said above), in my opinion, you should consider enhancing the Redis plugin(or create one) to propagate the tracing context in the PubSub mode, maybe the Redis plugin currently doesn't support that mode


Ability to crop profile picture before setting

Many social apps offer the ability to crop your profile picture from an image before setting it. Without this ability, users have to do so from a third-party app and it is a major introductory hassle when one is first making an account.
Having this ability in-app would thus be very useful.

Even better if it had a circle crop so you can see what it will actually look like.

Yes, good point.
On September 20, 2018 2:18:35 PM UTC, Coffee<EMAIL_ADDRESS>wrote:

Even better if it had a circle crop so you can see what it will
actually look like.
--
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub:
https://github.com/vector-im/riot-android/issues/2598#issuecomment-423200620

Hello I'm interested to add this functionality. May I try to implement it.

Thanks, I'm on it.

Cool, thanks!

How's your progress on this issue @Martinc4321?

I've committed some changes.

I am not sure ,but what review proces u have. Do I i need to push it to branch ? Then to which one.

Hello @Martinc4321,
You have forked the repository and commited changes on your version of the code. Once you have pushed your change to Github, you can then open a pull request to vector-im/riot-android and we will review what you have done.
Benoît

@bmarty I created PR. I hope it will work. I didn't work with GIT through PR yet. If there will be any problems (probably there will be) please wrote them down I definitely try to fix them.


Weird term "framework-dependent"

The page describes term "framework-dependent". But the definition says that in such case an app depends on "runtime". Why it is not called "runtime-dependent" then? Is there another term "runtime-dependent" which means something different than "framework-dependent"?
Personally I find the term "framework" pretty confusing nowadays. If I'm not mistaking it was used to describe something which is called "SDK" today. But here it was used as a synonym to "runtime". And I also assume that the vast majority of devs today clearly understand the difference between "SDK" and "runtime". Maybe "framework" is a good word for marketing or whatever. I am not good at that. But I find it not quite correct for technical documentation.

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 85eba478-0374-bb9b-8fa7-d5cf7d520603
Version Independent ID: 89967250-8c3b-1999-078f-94ad7518ed49
Content: Application publishing - .NET
Content Source: docs/core/deploying/index.md
Product: dotnet-fundamentals
GitHub Login: @adegeo
Microsoft Alias: adegeo

Hi 👋 @victor-yarema
Thank you so much for posting this issue. We really appreciate it.
In all honesty, I agree with you. The term is confusing and runtime-dependent makes more sense. I can only assume it was originally derived from the notion of .NET Framework. I labeled this issue as both product feedback and question. I'll tag a few folks here who might have a bit more insight.
@bartonjs @terrajobst and @davidfowl - do any of you have any idea where the term "framework-dependent" came from, see the ask above.

I thought along the same lines about a year ago and actually edited this and maybe another doc to replace framework with runtime. However, this caused even more confusion because the term "framework-dependent" is used in other tools and programs such as Visual Studio. We had to revert those changes almost a year ago in #20165
From a product standpoint this is the name of the feature. It needs to be changed there and in Visual Studio before we can change it in the docs.
Your best bet is to search/discuss it over at https://github.com/dotnet/sdk or https://github.com/dotnet/runtime
😦


Punt pause task to the end of the queue

Fixes #8294, probably.
It's unclear to me exactly what the original implementation did, though it's likely it slept the thread instead of allowing other closures to execute first.

Restarted CI that failed because of the GoogleUtilities 7.4.2 to 7.4.3 transition

Thanks for addressing Morgan.
Please investigate the integration test failure - https://github.com/firebase/firebase-ios-sdk/pull/8296/checks?check_run_id=2900576792

I think the fix doesn't work because it's unable to invoke dispatch_group_wait as the original method does here, which is causing the callbacks to not be executed.


Using Trezor with MultiBit HD requires zapping existing wallet stored in the Trezor

I have a Trezor that I have been using with MyTrezor and Electrum 2.0.  Both programs work with the same wallet with its private keys held by the Trezor.  Both programs found the contents of the wallet after initial installation by automatically querying the Trezor.  I can access the bitcoins in this Trezor on multiple computers, running MyTrezor or  Electrum 2.0.  I expected similar behavior from Multibit HD 0.0.7beta.  However, after connecting the Trezor to my computer and starting Multibit HD, the only Trezor option that I was offered involved zapping the wallet already in the Trezor and creating a new wallet.
Is there some way to use Multibit HD to access an existing Trezor hardware wallet?  If so, then I suggest the startup dialog be revised to make it clear how to do this.  If not, then this capability needs to be added.
( I downloaded the following installer: multibit-hd-windows-x64-0.0.7beta.exe)

Thanks for your feedback.
For a Trezor wallet WITHOUT a password the usage is starightforward:

Start up MultiBit HD and plug in your Trezor.
You get an alert saying 'Trezor "your trezor label' attached. Do you want to use it ?". Click 'Yes'.
You then get a PIN challenge from your Trezor where you type in our PIN in MBHD.
You then get a screen asking you to 'Press Next to unlock your Trezor (this generates a password used to decrypt your local wallet)
MBHD then syncs the wallet (take about 10 minutes first time) and then you are ready to go.

If your Trezor has a password protected wallet then we are not supporting that type of wallet in MBHD. We found with MultiBit Classic that a small proportion of people forget their password (it is about once incident in 30,000 user-months). These cause a lot of angst and ultimately loss of bitcoins. For this reason we have added into MBHD password recovery for the regular (non-Trezor) wallets worked out from the user's wallet words (aka seed phrase). We cannot offer this facility with the Trezor password so are not supporting this type of wallet..

I got it to work, by plugging in the Trezor before starting Multibit.  I also got it to work by starting Multibit first and then connecting Trezor.  However, the reaction of Multibit was a bit unexpected, which is why I probably got confused initially.  I did not expect the Enter Wallet Password dialog box to be blown away as soon as I connected the Trezor USB connector and replaced by the Trezor unlock dialog box.
The user interface for wallet selection between software wallets and hardware wallets might warrant additional thought.  I prefer the way Electrum 2.0 works, where the wallet type is set when the wallet is created or restored and where the normal program startup uses a default wallet.

We did consider having a default "Trezor type" wallet that prompted for a Trezor to be plugged in if it was absent, but user feedback indicated that the act of plugging in the Trezor should automatically detect the appropriate wallet (or create it if it is the first time it has been presented).
On balance we felt this was more intuitive for people with several Trezors and several "soft" wallets.
The reasoning behind the the "blowing away" of the password screen is that the credentials and wallet selection are now being provided entirely by the Trezor device. Consequently there is no need for a password or wallet selector or unlock button. Thus the screen adapts to reflect this simplification.

In my case, I am just using a single Trezor.  However, if later you want to implement a Trezor based "watch only" capability then I believe some wallet selection dialog will be needed. (I find it convenient to keep my Trezor locked away and have access to my wallet addresses and balance on my office computer. When testing Multibit HD, I found it inconvenient to have to unlock the storage, fetch the Trezor, connect it to my computer and then enter the PIN before I could check my balances.)

Adding a "watch only" wallet is not on our roadmap at the moment. There are two principle reasons behind this decision:

the wallet is encrypted using entropy that is only available from the Trezor device so the device must be physically present to unlock it - this greatly improves security (including an attacker gaining knowledge of a balance)
user feedback indicated that the idea of a wallet without send capability was quite confusing to the less technically capable and they were unlikely to use it

One workaround would be to use the Trezor to unlock the wallet at the start of the session and then detach it and place it in the secure box. So long as you don't attempt an operation involving the Trezor like a spend then you should be operating in a pseudo-watching mode.

I have two Trezors, one as yet unused in a sealed box.  I bought them so that I would not have to worry about my bitcoins being stolen if malware ended up on my computers.  Previously, I had been using off-line wallets, but this was a complex and tiresome procedure. I see the hardware wallet as an "ease of use" component as a security enhancement.  Others may have different feelings.  I would be much more likely to use Multibit HD if you were to implement a "watch only" capability. But this is a question of "features" not "bugs".
I don't worry about my bitcoin balance becoming public as a result of my computers/ being compromised. If my computers are compromised, I will have worse problems. I also don't view any of the Multibit files stored on disk as having any real value, since they can easily be recreated from the block chain and my Trezor (or my Trezor seed file that is locked up in a vault). (It takes about 10 minutes.)

Fair enough. One point to note about the MultiBit files stored on disk is that they contain more information than what is present on the block chain: exchange rates; contacts; private notes and so on. While the wallet words protect your bitcoins, you need your encrypted backups to protect that information.

Closing due to inacitvity.


Frontmatter Keywords Convention

I'm getting the following error in dev-environment
Mdx.frontmatter.keywords:
 - type: array
   value: [ ..., 'collators', ... ]
 - type: string
   value: 'client, wasm, rpc, node'

This is mainly the result of different files using different types.
Currently we don't do much with Keywords, other than just pass the info to LunrIndex for scoring.  But this will become a bigger problem as we move forward.  We should decide if this is going to be an array or string and then just stick with it.  I personally prefer an array of strings, as it'll be a bit easier to work with when it comes to filtering, search, etc.
Currently some documents have this, while the others don't.
null
null
null
null
template, contribute, style guide
contribute, style guide, bounties
contribute, style guide
contribute, style guide
node, client, tooling
runtime, tooling
[
  'collators',
  'parachains',
  'upgrade',
  'cumulus',
  'storage',
  'migration'
]
storage migration, testing, runtime, tooling
[
  'collator',
  'parachain',
  'cumulus',
  'design',
  'selection',
  'economic',
  'game theory'
]

Think we should surface this and perhaps have a pass to update it across all docs.

Sorry - I didn't report this injected it :sweat_smile:
+1 array of strings. ie:
keywords: [
"cumulus", "relay chain", "parachain",
]

also words with small phrases like "relay chain" / "chain spec" if we deem appropriate

ah I see that YAML is the frontmatter setion by convention, so then yes idiomatically it should by as you say
https://github.com/exquo/github-docs/blob/main/content/README.md#frontmatter
https://jekyllrb.com/docs/front-matter/
https://yaml.org/
keywords:
  - things
  - stuff
  - more things


pac solution Import fails with error but does not stop script

When running the pac solution import command in a PowerShell script, errors do not fail the script. When using pac solution pack errors do fail the script.

Hi @craig-lund,
Can you try to use the $? automatic variable available in PowerShell to detect if there is an error?
You can find an example of implementation I have done here.

Note: In my case I run again the command to get the error it returns because I am catching it in a variable in the first execution.

I hope this idea will help you.


update promlog to latest version

Revendor prometheus/common for the latest promlog version, in order to support changes from prometheus/common#136 (and prometheus/common#156); this resolves #3219 (i.e. adding JSON support for log output format).
Note: when revendoring (via go mod) promlog, this ended up retrieving the latest version of the entire prometheus/common repo; is there a good way of having a more granular update? I'm unsure what effects there are for updating the other parts of the prometheus/common repo (running tests locally with make test didn't seem to cause any errors).

when revendoring (via go mod) promlog, this ended up retrieving the latest version of the entire prometheus/common repo;

This is working as intended regarding Go modules. I would say that in general, the old way of mixing different revisions for packages from the same repository (module) was more prone to errors.

Updated again so we only need to initialize the config; also modified remote_storage_adapter/main.go to use kingpin, since promlog's AddFlags method requires a kingpin application.

That looks good bar Simon's comments.

Cleaned up the imports as per Simon's CR.

LGTM


Do not force disconnect for stalled nodes on sync

Looks like this was not such a good idea. They might be simply busy serving us another data (i.e. headers are in the tail of that queue).

ACK, tested locally with Dynamic codebase (https://github.com/duality-solutions/dynamic)

utACK


"Input file contains unsupported image format" running in Docker container

At first glance, I thought this might be related to #2003, but the circumstances are different enough to warrant a separate look. I have a project that implements one simple pipeline:

Fetch a TIFF from an Amazon S3 bucket to a temp file.
Load that file into sharp, convert it to a 15k-max-per-dimension, JPEG compressed, tiled pyramid TIFF, output to a buffer.
Send that buffer back to a different S3 bucket.

It runs inside a Docker container on Amazon Elastic Container Service, because it needs too much temporary disk space to run in a Lambda. The Docker container was, for a long time, based on the node:11-alpine base image (NodeJS 11.x running on Alpine Linux), but in the process of trying to fix this issue, I've changed it to node:13-buster (NodeJS 13.8.0 running on Debian Buster).
The processor has been chugging along nicely for some time, but yesterday, I noticed that there were 16 images that it failed to convert. The error it was throwing was Input file contains unsupported image format.
Here comes the weird part. When I run the node application on my Mac, it processes the outlier TIFFs just fine. When I run the Docker container on my Mac, it throws the error. Both are running the same version of NodeJS with the same version of sharp and the prebuilt VIPS installed by sharp's installer. Obviously, one of them is compiled for Darwin and the other for Linux x86_64.
In an effort to narrow down the issue, I decided to see if Alpine was the problem, so I rebuilt the container on Debian Buster. This time, the containerized version was able to read 13 of the 16 outliers, but 3 still failed with Input file contains unsupported image format. 1 of those 3 works under Docker on my Mac using the Buster-based container; the other two don't.
I'll try to attach one of the failing test images later, but I have to get my employer to give the OK to share it. In the meantime, I'm not sure what I should be looking at next. Could this be a resource issue of some kind? RAM? CPU? ulimits?

Please can you provide a sample image and complete, standalone code to trigger this error.

Welp, this one is on me. In whittling down my app to create a test case, I discovered that in some very narrow circumstances based on the size of the file and the chunk size of the download, the function responsible for downloading the source image was resolving its promise before the file was completely written to temp storage and closed. In this case, sharp would end up trying to read an incomplete file and report an error. I'm leaving this open so you can read this resolution, but feel free to close it as there's nothing to fix.


feat: Adds InformationIcon and LeftIcon

Summary of Changes
Adds LeftIcon
Adds Information Icon and uses it within the InfoButton
Tests
Updated tests
Documentation
Added stories
CheckList
Make sure you have checked all steps below to ensure a timely review.

[ ] PR title addresses the issue accurately and concisely. Example: "Updates the version of Flask to v1.0.2"

In case you are adding a dependency, check if the license complies with the ASF 3rd Party License Policy.

[ ] PR includes a summary of changes, including screenshots of any UI changes.
[ ] PR adds unit tests, updates existing unit tests, OR documents why no test additions or modifications are needed.
[ ] In case of new functionality, my PR adds documentation that describes how to use it.

All the public python functions and the classes in the PR contain docstrings that explain what it does

[ ] PR passes all tests documented in the developer guide

Closing in favor of https://github.com/amundsen-io/amundsenfrontendlibrary/pull/715


fix: Make default templates refer to GUI pages (DSP-763)

This PR changes the default URL templates so they refer to DSP-UI routes instead of to Knora API routes. This should help with DSP-763.

@subotic I can't merge this because Travis is waiting for something, but I don't understand what it's waiting for.

@benjamingeer should work now. although travis is not used anymore, it was still configured as required. I've changed the repo config.

@subotic  OK thanks!


Query only uses the default AF Server and AF Database

Hello,
I updated to version 2.0.0 and I encountered an issue with the query editor. When you have a default AF Server and AF Database set in the DataSource settings than you can't choose a different AF Server or AF Database when you want to create a new query.
The query only allows the selection of the defined AF Database and AF Server from DataSource settings.
If you don't set default AF Server and AF Database you can freely query for any AF Server or Database.
The problem here is, that if you want to use Annotations you need to set a default AF Server in order to use them. The best approach here would be to allow the selection of AF Server in the annotation query control.
Kind regards
Michael

@clackner-gpa @ritchiecarroll can you help what is the best option here? Thank you.

@Coding-Mike  I'm not quite sure I fully understand the issue. If you need annotations from a second PI instance you should be able to add a second datasource. There is no restriction on how many datasources of the same type can exists. I would caution against not setting a default server and database in the first place.

@clackner-gpa On our side we have the situation, that we have many different PI server and AF server.
This would lead to many data sources that makes it difficult to find the right settings.
Also the amount of AF databases is high. Many users also need the usage of different PI server, AF server and AF databases to query their data.
It would be easier if you can create one datasource for PI and the users can choose their PI server, AF server and AF database for all query types.
With this approach you can have one datasource for each kind of data - one for PI, one for postgres ...
I hope this helps to understand the issue.
Kind regards
Michael

@Coding-Mike I think you can set the PI server and AF server and leave the AF database empty. This would be a similar situation as a MySQL database that the user can select the tables. Different database means different datasource entry.
I will check if I can add AF database selection to annotation.

@Coding-Mike can you check v3.0.0. If all is ok, I will close this issue

This has been fixed. Version 4.0.0 will also fix annotations.


adding boxplot to pyplot

@ssunkara1 is this good to merge?

yep!!  this is all set.

Looks good to me, merging


Conditionally append port to endpoint

Fixes a bug where generated configs have an extra port added in some cases.

Pull Request Test Coverage Report for Build 3329a03aca0a61016d8f4f99038e15a55874ff3d-PR-1247

5 of 6 (83.33%)  changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.02%) to 66.168%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

apps/fz_http/lib/fz_http/devices.ex
5
6
83.33%

Totals

Change from base Build 427edb9d5f7822aad69215b336fe6d08235c37fc:
0.02%

Covered Lines:
1195

Relevant Lines:
1806

💛  - Coveralls


Paddy fix vendor tests

The tests were written to run as InApp, but InApp excludes everything
that has "vendor" in its import path. This only becomes a problem when
raven-go is vendored, and you run go test ./... for the package. On
the one hand, the package can be tested separately. On the other, it's
nice to know that all your dependencies pass their tests, and it's
pretty trivial to support making this pass when vendored.
Basically, we just need to update the test to detect when it's running
in a situation that's not considered "InApp", and then make sure that
the Stacktrace reports that correctly. Fortunately, we know how to
decide if something is InApp: does it have "vendor" in its path?
So we just check if the current file (retrieved using runtime.Caller)
has "vendor" in its path, and use that to decide whether the test passes
or fails, instead of the hardcoded true.

Seems reasonable to me. :) Thanks!

Late on this, but thanks @paddyforan!


samples: Bluetooth: direction_finging_connectionless_rx: Update config. to allow build for nRF5340 APP core

Move BLE controller configuration to board specific *.conf overlay.
That is required to make possible to build sample code for nRF5340,
where BLE controller is part of separate image aimed for network
core.
The PR may be merged when this PR: #36047 is merged into main.

Removed files that didn't belong to the PR.

@jhedberg @joerchan could you take a look on the PR?

Can we avoid turning on CONFIG_BT_CTLR_ADV_EXT=y, as this is still experimental (until we complete conformance tests) ?

Can we avoid turning on CONFIG_BT_CTLR_ADV_EXT=y, as this is still experimental (until we complete conformance tests) ?

@cvinayak without advertising extensions the features is not working. Maybe it would be better to put an information about use of experimental features?

Can we avoid turning on CONFIG_BT_CTLR_ADV_EXT=y, as this is still experimental (until we complete conformance tests) ?

@cvinayak without advertising extensions the features is not working. Maybe it would be better to put an information about use of experimental features?

Ok, I will send a PR adding CMake warning message when advertising extensions in Controller is enabled.

Ok, I will send a PR adding CMake warning message when advertising extensions in Controller is enabled.

@cvinayak We don't do that for any of the other experimental features, so I don't think we should add it now.
I think having it enabled in this sample is fine.


Add pdb to helm chart

1. Issue, if available:
2. Description of changes:
Adds a pod disruption budget to the helm chart.
It's not exposed as a variable/value. Should it be?
3. How was this change tested?
Googling and copy pasting
4. Does this change impact docs?

[ ] Yes, PR includes docs updates
[ ] Yes, issue opened: link to issue
[x] No

No, unless we want to add a variable to disable it or change the value. I'm not sure that's a good idea.
By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

min-available should probably be in values.yaml IMO


Add hashtag capabilities to activities

It would be nice to be able to do something like this:
friends add activity "Went for a run. #exercise"
and then later filter activities like:
friends list activities --tagged exercise
or
friends list activities --with James --tagged restaurants
For now this would only support one tag to be passed to the --tagged argument (see #88 for more details on lifting that limitation).

I'd like to be able to tag friends as well, so I can search for people that I worked with, or people I know from school.

Ah interesting, so you're saying there might be friends under the #work tag as well as activities under the #work tag. That makes sense to me. I just created #90 for this; let me know if that looks like what you were thinking.


Building Julia dependencies

We also need to support dependencies for Julia. Discuss implementations etc here!

I'm gonna close this in favor of the repo2docker issue: https://github.com/jupyter/repo2docker/issues/23


[k8s>=1.30] switch off NodeSwap feature gate for AL2 based images

As of https://github.com/kubernetes/kubernetes/pull/122745, NodeSwap has been switched to true by default. Since we know that NodeSwap works only with cgroupv2 and AL2 defaults to cgroupv1, can we switch off the feature gate?
See https://github.com/kubernetes/test-infra/pull/32876 for context where we had to do this to ensure CI jobs are stabilized with AL2.
cc @cartermckinnon @njtran

We'd need to add some logic for older (and future) k8s versions where the feature flag doesn't exist, and since using swap requires you to also disable failOnSwap and configure the swap volumes, I'm not sure it makes sense to have this additional guardrail/callout. @ndbaker1 what do you think here?

add some logic for older (and future) k8s versions where the feature flag doesn't exist

we don't need to do anything for older version right?
If we already had logic in place to enforce NodeSwap=false it would make a lot of sense, but it sounds like the default makes sense from the PR since it won't be configures as NoSwap
I'm also not eager to track more featureGates besides the ones we currently set (which are all related to credentials afaict)

we don't need to do anything for older version right?

the feature gate was added in 1.22, so we can't specify it for 1.21 or kubelet will complain. When the feature gate is removed in the future, we'll have to come back and add a check for that boundary as well

If we already had logic in place to enforce NodeSwap=false it would make sense, but sounds like the default from the PR is NoSwap which works as expected?

yeah that's my thinking, the feature gate default changing was a no-op anyway, since you have to opt-in with several other config options

I think we'll leave things as-is for now


Added streamAst utility function

Added an option to TreeStreamImpl to include the root node
Added streamAst function as alternative to streamAllContents to include the root node
Use the new function where it makes sense
Changed streamCst to include the root node to be consistent with the new function (the name is almost the same)

Right, but I think in that case it actually makes sense to handle the root node separately. The comparedRange check is not necessary for the root node.


add a link to Spotify's homebrew tap

In case anyone gets confused looking for helios in the default homebrew formulas.

:+1:


release again

@rultor release, tag is 0.1.1

@rultor release, tag is 0.1.1

@yegor256 OK, I will release it now. Please check the progress here

@rultor release, tag is 0.1.1

@yegor256 Done! FYI, the full log is here (took me 1min)

@rultor release, tag is 0.1.2

@yegor256 OK, I will release it now. Please check the progress here

@rultor release, tag is 0.1.2

@yegor256 Oops, I failed. You can see the full log here (spent 1min)
Preparing to unpack .../python3-pygments_2.3.1+dfsg-1ubuntu2.2_all.deb ...
Unpacking python3-pygments (2.3.1+dfsg-1ubuntu2.2) ...
Setting up python3-pygments (2.3.1+dfsg-1ubuntu2.2) ...
+ sudo -i pip3 install pygments
Requirement already satisfied: pygments in /usr/lib/python3/dist-packages (2.3.1)
\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager.  Done

Building dependency tree... 0%

Building dependency tree... 0%

Building dependency tree... 50%

Building dependency tree... 50%

Building dependency tree

Reading state information... 0%

Reading state information... 0%

Reading state information... Done

aspell is already the newest version (0.60.8-1ubuntu0.1).
aspell set to manually installed.
0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+ sudo -i tlmgr --verify-repo=none update --self
tlmgr: package repository https://ftp.mpi-inf.mpg.de/pub/tex/mirror/ftp.dante.de/pub/tex/systems/texlive/tlnet (not verified: gpg unavailable)
tlmgr: saving backups to /usr/local/texlive/2022/tlpkg/backups
tlmgr: no self-updates for tlmgr available
+ sudo -i tlmgr --verify-repo=none install l3build
tlmgr: package repository https://ftp.rrze.uni-erlangen.de/ctan/systems/texlive/tlnet (not verified: gpg unavailable)
tlmgr install: package already present: l3build
+ make VERSION=0.1.2 set-version
date=$(date +%Y/%m/%d)
sed -i "s|00\.00\.0000|${date}|" ppt-slides.sty
sed -i "s/0\.0\.0/0.1.2/g" ppt-slides.sty
sed -i "s|00\.00\.0000|${date}|" ppt-slides.tex
sed -i "s/0\.0\.0/0.1.2/g" ppt-slides.tex
sed -i "s/0\.0\.0/0.1.2/g" build.lua
/bin/sh: 0: Illegal option -o pipefail
make: *** [Makefile:40: set-version] Error 2
container 1f64d2c8950aa26b75e8602495a57bd9dc8d92a190667e39cfca07d81a4aa278 is dead
Mon 12 Sep 2022 09:10:26 PM CEST

@rultor release, tag is 0.1.2

@rultor release, tag is 0.1.2

@yegor256 OK, I will release it now. Please check the progress here

@rultor release, tag is 0.1.2

@yegor256 Done! FYI, the full log is here (took me 1min)


Roadmap: x-ref to applications

Example query to fetch relationships between apps and roadmap/scenarios:
select distinct r.name, r.id, s.name, s.id
from roadmap r
inner join scenario s on s.roadmap_id = r.id
inner join scenario_rating_item si on si.scenario_id = s.id
where si.domain_item_kind = 'APPLICATION' and si.domain_item_id = 405
and s.lifecycle_status = 'ACTIVE'


Upgrade lodash to 4.0.0

lodash 4.0.0 contains many break changes: https://github.com/lodash/lodash/wiki/Changelog#v400

Close this pr in favour of #245.


Recompute deltas

r_0 = 0
e = 0.01
r_k = ((new-old)/new) + e*r_{k-1}

Maybe do an automatic computation and allow the user to set e?


Azure AD Registered Devices

Does this work with Azure AD Registered Devices or only Azure AD Join/Hybrid Joined devices?

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 0d912434-0693-e158-f371-51b010f8a533
Version Independent ID: 51892e2c-8bd5-df84-28a1-548bbf0d8d96
Content: How SSO to on-premises resources works on Azure AD joined devices
Content Source: articles/active-directory/devices/azuread-join-sso.md
Service: active-directory
Sub-service: devices
GitHub Login: @MicrosoftGuyJFlo
Microsoft Alias: joflore

@ElanShudnow
Thanks for your Question! We are currently investigating and will get back on this.

From my understanding, it should only work with joined devices and registered devices will work for cloud SSO.

Registered Devices

Key capabilities
SSO to cloud resources

Conditional Access when enrolled into Intune

Conditional Access via App protection policy

Enables Phone sign in with Microsoft Authenticator app

https://docs.microsoft.com/en-us/azure/active-directory/devices/concept-azure-ad-register
Hope this helps! CCing @MicrosoftGuyJFlo for additional comments.


Why was Alphapose chosen?

Why was Alphapose chosen? What about Mediapipe holistic or OpenPose?

Alphapose was chosen as it allowed us to use the Halpe dataset format, which we found useful for sign language representation, and also for performance reasons as it can run on 8GB of RAM.
Probably Mediapipe and Openpose could work as well, but we didn't find any particular advantage.

What is the particular special advantage of Halpe dataset format for sign language representation if you could answer? Would you be able to show an example of sign language representation?

Halpe dataset format, which we found useful for sign language representation

Err.. it has more finger keypoints than other formats/models. Also
Alphapose was (is?) significantly easier to work with since it is based on
pytorch.
Can I ask why the interest in such a specific detail? Also, you can always
run openpose on the videos...
El jue, 23 feb. 2023 23:11, Alexey Prikhodko @.***>
escribió:

What is the particular special advantage of Halpe dataset format for sign
language representation if you could answer? Would you be able to show an
example of sign language representation?
Halpe dataset format, which we found useful for sign language
representation
—
Reply to this email directly, view it on GitHub
https://github.com/midusi/LSA-T/issues/7#issuecomment-1442697185, or
unsubscribe
https://github.com/notifications/unsubscribe-auth/AAMA6B6JZCU6TZEFQZ5OPBLWZAKDNANCNFSM6AAAAAAVCU5SL4
.
You are receiving this because you are subscribed to this thread.Message
ID: @.***>

Yes, you can. The main problem with tracked skeletal fingers for sign language recognition task is that I'm interested in a specific detail. I tried OpenPose before, but there is a devops problem with python. Now I use Mediapipe Hands and Pose, Holistic, it's easier to do something there and it's convenient to analyze the finger skeletal model, see my video example.
I know more about Mediapipe than Alphapose. Alphapose and Mediapipe hands are the same number - 21 finger key points. I'm asking you, do you use a 2D or 3D finger skeletal model from Alphapose? Any other specific detail?:)

Err.. it has more finger keypoints than other formats/models. Also Alphapose was (is?) significantly easier to work with since it is based on pytorch. Can I ask why the interest in such a specific detail? Also, you can always run openpose on the videos... El jue, 23 feb. 2023 23:11, Alexey Prikhodko @.> escribió:
…
What is the particular special advantage of Halpe dataset format for sign language representation if you could answer? Would you be able to show an example of sign language representation? Halpe dataset format, which we found useful for sign language representation — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAMA6B6JZCU6TZEFQZ5OPBLWZAKDNANCNFSM6AAAAAAVCU5SL4 . You are receiving this because you are subscribed to this thread.Message ID: @.>