Configurable product option redesign

Issue Reference
Configurable product option redesign

Checked the image related issue  in Arabic RTL view and also in English LTR view. Checked the admin and shop front, now the image issue has been fixed and working fine.  Please check the video for reference.
Video
https://github.com/bagisto/bagisto/assets/92721837/71abfee5-a964-4a33-8861-1b8272faecd8


HB-7035: Handle fullscreen ad memory leak

Fixes a memory leak for fullscreen ads.
Updated CHANGELOG, README, Adapter version to <IP_ADDRESS>.1

Yep, it's coming.  Thanks!


[PGAPI] Lab6 texture bug on non Windows systems

Bug Report
The issue is in m2::Lab6
When the archer texture is loaded, the parameters are not set correctly.
TextureManager::LoadTexture(PATH_JOIN(window->props.selfDir, RESOURCE_PATH::MODELS), "characters", "archer", "Akai_E_Espiritu.fbm", "akai_diffuse.png");

First, the path is not correct. PATH should contain everything up to the file name, but it is closed after the models folder.
The code works on Windows because when the texture is loaded, it is done like this:
glBindTexture(GL_TEXTURE_2D, TextureManager::GetTexture("Akai_E_Espiritu.fbm\\akai_diffuse.png")->GetTextureID());

The texture is there because it is loaded when the model is loaded. But in this manner, the path is not correct for non-Windows systems. PATH_JOIN should be used or the initial load should be corrected. I opted for the last one since it would be quite difficult for students to find out where is the texture loaded.

Hello, Mihnea!
Everything looks perfect. Thank you for your contribution!


InstallPlan/Update spam with multiple catalogsources containing different operator versions

Hi everybody,
using OKD 4.3 i've been running into a problem when installing Noobaa. First i could not find Noobaa in the standard catalogsource deployed in OKD 4.3 ( issue on OKD). I fixed this with installing the operatorhub.io catalogsource:
apiVersion: operators.coreos.com/v1alpha1
kind: CatalogSource
metadata:
  name: operatorhubio-catalog
spec:
  displayName: OperatorHub.io
  image: 'quay.io/operator-framework/upstream-community-operators:latest'
  publisher: OperatorHub.io
  sourceType: grpc

This works fine for installing Noobaa, but Noobaa also installs the AWS S3 Operator, which is available on both, the operatorhub.io catalogsource and the community-operator catalogsource from OKD, in different versions 1.0.0 and 1.0.1.
With having the installPlan for the AWS S3 operator set to automatic it gets stuck in an update loop going from version 1.0.0 to 1.0.1 to 1.0.0 ....... while always creating new serviceaccounts and rolebindings (about 2000 per night).
Setting the installPlan to manual it still continues to try to upgrade, but only creating installPlans (about 4000 per night). For example such an installPlan:
apiVersion: operators.coreos.com/v1alpha1
kind: InstallPlan
metadata:
  creationTimestamp: "2020-04-17T09:10:33Z"
  generateName: install-
  generation: 1
  name: install-9grr7
  namespace: noobaa
  ownerReferences:
  - apiVersion: operators.coreos.com/v1alpha1
    blockOwnerDeletion: false
    controller: false
    kind: Subscription
    name: noobaa
    uid: fa1e86ee-a111-4a26-a61e-f503b793da08
  resourceVersion: "2546748"
  selfLink: /apis/operators.coreos.com/v1alpha1/namespaces/noobaa/installplans/install-9grr7
  uid: c3d69d61-1171-49a1-9653-8e4cefc92b50
spec:
  approval: Manual
  approved: false
  clusterServiceVersionNames:
  - awss3operator.v1.0.1
  - awss3operator.v1.0.0
  generation: 4287

Is there something i'm missing or is this update loop/spam a bug? I think this also could happen with other operators if there is more than 1 version of a operator on 2 different catalogsources.
Greetings
Patrick

@lallinger-arbeit thanks for raising this. This looks like a bug indeed. Can you file it as an issue against OLM?
This repository only concerns itself with the community Operator content and using the operatorhub.io catalog is actually not supported on OpenShift. Though that's mainly because there are Operators in the OperatorHub.io catalog that will not work in OpenShift - it should not cause this behavior and OLM has special logic to resolve dependencies when there are multiple candidates from different catalogs.


Use PEP-621, replace setup.py and fix IDE error regarding the version file

Hi,
Minor nit-pick. When using an IDE like PyCharm, I get an error in setup.py due to the IDE not being smart enough to recognize that the version.py is being dynamically loaded.
With PEP-621, combining a pyproject.toml and setup.cfg, it is possible to get rid of setup.py without losing any functionality, simplifying the project metadata (you edit an cfg file, not a Python file).

Hi @kinow,
Yes I agree. We are working on a standard packaging for python repositories (we are using pyflow a bit as a guinea pig) and we'll probably use a setup.cfg instead.
Thanks!
Corentin

Hi @corentincarton ,
That's great! I have a branch with a work-in-progress. I will submit a draft in case there's anything useful there (but feel free to close that one whenever you want :+1: )
Thanks!
Bruno

Closing as #7 was merged :+1: (sorry, forgot to link the PR)


feat: check dataset and shapefile for compatibility

#23 requires a join between a user-specified dataset and a user-specified shapefile, using keys passed by the user. This feature will check that they are compatible:

dataset and shapefile have keys specified by user
keys are the same data type

Completing this as part of branch corresponding to #23


[RFE] Keep page number when back to resource list from detail page

Current situation

User go to page 5 and select one pod to check detail
User click back button, list will be page 1

Another way to keep context of list is


bug(apps/pano): Inconsistent Margins on Header Menu between https://pano-dev.fly.dev/ and https://pano-dev.fly.dev/login

Describe the bug
Description: There is an inconsistency with the margins on the header menu between the landing page (https://pano-dev.fly.dev/) and the login page (https://pano-dev.fly.dev/login). This can be observed when transitioning between the two pages.

Actual Result
The header menu has different margins on the landing page and login page
Possible Solution
Adjust the margins of the header menu to be consistent across both pages.
Steps to reproduce the behavior

Go to https://pano-dev.fly.dev/
Click on the "Log in" button on the top right corner
Observe the header menu during the transition between the two pages
Expected result: The header menu should have consistent margins on both pages

Expected behavior
The header menu should have consistent margins on both pages

When running the development branch locally, no issues appear. :smiley:

I didn't do a deep dive but what i have in my mind is; we have lots of posts in dev environment and this causes scrollbar to appear and makes screen move. This doesn't happen in local because we have a limited amount of posts.

I'm closing this since this isn't really a big much of problem for now. We'll consider opening a new one if this becomes unbearable.


Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1376055539,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONWHCXTFQSKBRLMAKF3WRRJDNANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

Yes, you can use the wildcard in the file names.

Hi Li,
Thank you. I have a question and thoughtmaybe you know about that. I am
going to run TRUST4 on a new set of fastq files, but it looks my fastq file
types are different from my previous files. Previously they were single
-end. But the new files I am not sure.
Both R1 and R2 are the same in terms of line length.
(I tried to run with my original run-trust4 command and got an error).
[image: image.png]
I put the contents of R1 and R2 here, in case the image is not clear
(length of lines in R1 and R2 are the same). :
for R1 it is:
@A00213:491:HNWYHDSX5:4:1101:2971:1000 1:N:0:TGTAGTCATT+TACGATCAAG
NCGCAACCACATTCGATCACTTACGATTTCTTATATGGGGGAGTGATGGCTGCCGGCGCTCTCTGCGTGGTTCTTCTTCTCGGCCGCTGAAACCCCCGCGG
+
#FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFF
@A00213:491:HNWYHDSX5:4:1101:5177:1000 1:N:0:TGTAGTCATT+TACGATCAAG
NACCACTGAGTACGTCCATCCAATCATGAACACTGTCCCAGCCTCCTTCACGTTCAAGGATATGACCCAACTGGACATTGTCTAAGTATTCCTTCAGTACT
+
for R2 it is:
@A00213:491:HNWYHDSX5:4:1101:2971:1000 2:N:0:TGTAGTCATT+TACGATCAAG
TATAAAATTAAATACTGTAAACTACGGCACAGAAACCGAGCTGGGGAGTTACTGCTATACGCTGCGTATGTGCATCTGTTGTCTGGGGTTTCTTTGGCTCA
+
F:FFFFFFFFFFFFFF::F:FFFFF::FFFFFFFFFFFFFFFFFFFFF::FFFFF:FFFFFFF::F:FFFFFFFFFFFFFF:FFFFFFFFF,FFFFFFFFF
@A00213:491:HNWYHDSX5:4:1101:5177:1000 2:N:0:TGTAGTCATT+TACGATCAAG
CGAGAAGATCAGAAAAGGAAGGGAATTTCTGACCTAGTACTGAAGGAATACTTAGACAATGTCCAGTTGGGTCATATCCTTGAACGTGAAGGAGGCTGGGA
+
Do you know what option in trust4 I should use for these group of fastq?
Are they pair-end? And in this case, how the run-trust4 command change:
run-trust4 -f hg38_bcrtcr.fa -t 8 --ref human_IMGT+C.fa -u R2.fastq.gz
--barcode R1.fastq.gz --barcodeRange 0 15 + --barcodeWhitelist
737K-august-2016_barcodes.txt --UMI R1.fastq.gz --umiRange 16 27 + -o
FR2 --od out --re
pseq
Thank you for your support!
Best,
Sara
On Tue, Jul 18, 2023 at 2:52 PM Li Song @.***> wrote:

Yes, you can use the wildcard in the file names.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1640777070,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONQ2JXZKRFYYOEPVPT3XQ3LN5ANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

The github could not show the image you attached in the email.
I think both ends contain meaningful genomic information, so you may need to use -1/-2 and configure the read1Range option to get that information. It depends on the kit, you may need to look into the manual/readme.

read1Range/barcodeRange/UMIRange specification is inherited from previous TRUST versions (<1.0.10). You can use --readFormat specification in newer versions, which has a much simpler syntax (I think).

thanks. Like this:
run-trust4 -t 8
-f /home/kkearns/hipc_trust4/hg38_bcrtcr.fa
--ref /home/kkearns/hipc_trust4/human_IMGT+C.fa
-1 /home/kkearns/hipc_trust4/tube5_fastq/R1.fastq.gz
-2 /home/kkearns/hipc_trust4/tube5_fastq/R2.fastq.gz
--barcode /home/kkearns/hipc_trust4/tube5_fastq/R1.fastq.gz
--barcodeRange 0 15 + --readFormat 16 -1
On Thu, Jul 20, 2023 at 1:55 PM Li Song @.***> wrote:

read1Range/barcodeRange/UMIRange specification is inherited from previous
TRUST versions (<1.0.10). You can use --readFormat specification in newer
versions, which has a much simpler syntax (I think).
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1644353399,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONWDEPMG4OP7RZYKXZ3XRFWJDANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

Li, would you please help me to fix my command for the pair-end fastq based
on new version?
Thanks!
On Thu, Jul 20, 2023 at 1:58 PM Sara Moien @.***> wrote:

thanks. Like this:
run-trust4 -t 8
-f /home/kkearns/hipc_trust4/hg38_bcrtcr.fa
--ref /home/kkearns/hipc_trust4/human_IMGT+C.fa
-1 /home/kkearns/hipc_trust4/tube5_fastq/R1.fastq.gz
-2 /home/kkearns/hipc_trust4/tube5_fastq/R2.fastq.gz
--barcode /home/kkearns/hipc_trust4/tube5_fastq/R1.fastq.gz
--barcodeRange 0 15 + --readFormat 16 -1
On Thu, Jul 20, 2023 at 1:55 PM Li Song @.***> wrote:

read1Range/barcodeRange/UMIRange specification is inherited from previous
TRUST versions (<1.0.10). You can use --readFormat specification in newer
versions, which has a much simpler syntax (I think).
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1644353399,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONWDEPMG4OP7RZYKXZ3XRFWJDANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

I guess it would be like this based on the command you sent:
run-trust4 -t 8
-f /home/kkearns/hipc_trust4/hg38_bcrtcr.fa
--ref /home/kkearns/hipc_trust4/human_IMGT+C.fa
-1 /home/kkearns/hipc_trust4/tube5_fastq/R1.fastq.gz
-2 /home/kkearns/hipc_trust4/tube5_fastq/R2.fastq.gz
--barcode /home/kkearns/hipc_trust4/tube5_fastq/R1.fastq.gz
--readFormat bc:0:15,r1:16:-1

Thank you so much, Li.
It worked.
I have a more general question: what are the main differences of trust4 vs
cellRanger. I just need that as an explanation in my paper.
Already have some justifications, but need to make sure I am giving the
best explanation.
Thanks,
Sara
On Thu, Jul 20, 2023 at 2:53 PM Li Song @.***> wrote:

I guess it would be like this based on the command you sent:
run-trust4 -t 8
-f /home/kkearns/hipc_trust4/hg38_bcrtcr.fa
--ref /home/kkearns/hipc_trust4/human_IMGT+C.fa
-1 /home/kkearns/hipc_trust4/tube5_fastq/R1.fastq.gz
-2 /home/kkearns/hipc_trust4/tube5_fastq/R2.fastq.gz
--barcode /home/kkearns/hipc_trust4/tube5_fastq/R1.fastq.gz
--readFormat bc:0:15,r1:16:-1
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1644432296,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONSWQ5HTB64OTRZKCSDXRF5C7ANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

The assembly algorithm is quite different. I think cellranger uses de bruijn graph to conduct the assembly, and TRUST4 is based on read overlaps found by read alignment. Theoretically, TRUST4 is more robust when the sequences are more divergent, either due to sequencing errors or somatic hypermutations. Furthermore, de bruijn graph usually expects higher read coverage to make sure the contiguous error-free k-mer's, the alignment approach allows certain mismatches in the overlap region. Therefore, TRUST4 might work better on low-coverage scenarios (data set without VDJ enrichment).
These are just part of theoretical differences. In practice, different heuristics, like the threshold for filtering, may play big roles too.

Great. Thanks.
On Wed, Jul 26, 2023 at 10:36 AM Li Song @.***> wrote:

The assembly algorithm is quite different. I think cellranger uses de
bruijn graph to conduct the assembly, and TRUST4 is based on read overlaps
found by read alignment. Theoretically, TRUST4 is more robust when the
sequences are more divergent, either due to sequencing errors or somatic
hypermutations. Furthermore, de bruijn graph usually expects higher read
coverage to make sure the contiguous error-free k-mer's, the alignment
approach allows certain mismatches in the overlap region. Therefore, TRUST4
might work better on low-coverage scenarios (data set without VDJ
enrichment).
These are just part of theoretical differences. In practice, different
heuristics, like the threshold for filtering, may play big roles too.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1651938279,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONSAWETMSBMVDYQ7VWTXSETNJANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

Dear Li,
One question I have:
Why the number of cells in file "out_airr.tsv" and "cluster_python.csv" are
different? cluster_python.csv is the output of python.cluster.py when
running on CDR3.out file.
Thanks,
Sara
On Wed, Jul 26, 2023 at 12:44 PM Sara Moien @.***> wrote:

Great. Thanks.
On Wed, Jul 26, 2023 at 10:36 AM Li Song @.***> wrote:

The assembly algorithm is quite different. I think cellranger uses de
bruijn graph to conduct the assembly, and TRUST4 is based on read overlaps
found by read alignment. Theoretically, TRUST4 is more robust when the
sequences are more divergent, either due to sequencing errors or somatic
hypermutations. Furthermore, de bruijn graph usually expects higher read
coverage to make sure the contiguous error-free k-mer's, the alignment
approach allows certain mismatches in the overlap region. Therefore, TRUST4
might work better on low-coverage scenarios (data set without VDJ
enrichment).
These are just part of theoretical differences. In practice, different
heuristics, like the threshold for filtering, may play big roles too.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1651938279,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONSAWETMSBMVDYQ7VWTXSETNJANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

airr doesn't do any filtering. cluster will only keep the contigs with both V,J gene identified, and some other filters.

Thank you so much for fast replying.
Therefore, do you recommend using the airr.tsv file for obtaining the
clones?
The problem we have here is that using the python_cluster.csv file we don't
see any clone on heavy chain, but we see clones on light chain.
So the question is why we don't see clone on heavy chain, but we see on
light chain.
With airr.tsv we are seeing some clonality on heavy chain as well.
Do you have any comments?
Thanks,
Sara
On Wed, Aug 30, 2023 at 10:40 AM Li Song @.***> wrote:

airr doesn't do any filtering. cluster will only keep the contigs with
both V,J gene identified, and some other filters.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1699314994,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONTKFD55LROCNYXYIJTXX5GFTANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

Hello Li,
I have a question: can I ask what is the strategy for identifying the
V-gene, J-gene, D-genes? Are you using igblast?
And is there any strategy for scoring to select which V/J/D genes you
select in final results?
Thanks,
Sara
On Wed, Aug 30, 2023 at 10:44 AM Sara Moien @.***> wrote:

Thank you so much for fast replying.
Therefore, do you recommend using the airr.tsv file for obtaining the
clones?
The problem we have here is that using the python_cluster.csv file we
don't see any clone on heavy chain, but we see clones on light chain.
So the question is why we don't see clone on heavy chain, but we see on
light chain.
With airr.tsv we are seeing some clonality on heavy chain as well.
Do you have any comments?
Thanks,
Sara
On Wed, Aug 30, 2023 at 10:40 AM Li Song @.***> wrote:

airr doesn't do any filtering. cluster will only keep the contigs with
both V,J gene identified, and some other filters.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1699314994,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONTKFD55LROCNYXYIJTXX5GFTANCNFSM6AAAAAASNQNL5E
.
You are receiving this because you authored the thread.Message ID:
@.***>

We implement our own alignment procedure. The score is based on the number of matched bases between the contig and the reference V,J,D genes.

Thanks Li.
I am running TRUST4 on my samples with the latest version. But in the final
results, some of the files are missing: such as the airr.tsv and few others.
This is what I have:
[image: Screen Shot 2023-12-28 at 9.54.21 AM.png]
What can be the possible reason?
Thanks!
On Fri, Dec 22, 2023 at 12:25 PM Li Song @.***> wrote:

We implement our own alignment procedure. The score is based on the number
of matched bases between the contig and the reference V,J,D genes.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1867919086,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONQEOCB5RMPNPWYNRE3YKW67NAVCNFSM6AAAAAASNQNL5GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRXHEYTSMBYGY
.
You are receiving this because you authored the thread.Message ID:
@.***>

I could not see the screenshot on github. Based on your description, I guess those are the samples without any VDJ readout, and TRUST4 exits in the middle of the program.

Thanks Li.
The error I am getting is this and I am not sure what can be the issue:
....
.....
......
[Fri Dec 29 11:43:28 2023] Processed 20700000 reads (20250666 are used for
assembly).
[Fri Dec 29 11:44:31 2023] Processed 20800000 reads (20338425 are used for
assembly).
[Fri Dec 29 11:45:01 2023] Assembled 20377447 reads.
[Fri Dec 29 11:45:01 2023] Try to rescue 5738 reads for assembly.
[Fri Dec 29 11:45:05 2023] Rescued 475 reads.
[Fri Dec 29 11:46:12 2023] SYSTEM CALL:
/athena/namlab/scratch/sam4032/trust/bin/annotator -f
/athena/namlab/scratch/sam4032/HL6/human_IMGT+C.fa -a
new_BCR_s1s2_dec2023/new_BCR_s1s2_dec2023_final.out -t 8 -o
new_BCR_s1s2_dec2023/new_
BCR_s1s2_dec2023 --barcode --UMI -r
new_BCR_s1s2_dec2023/new_BCR_s1s2_dec2023_assembled_reads.fa
--airrAlignment > new_BCR_s1s2_dec2023/new_BCR_s1s2_dec2023_annot.fa
[Fri Dec 29 11:46:13 2023] Start to annotate assemblies.
[Fri Dec 29 11:49:11 2023] Start to realign reads for CDR3 analysis.
[Fri Dec 29 11:54:42 2023] Compute CDR3 abundance.
*** Error in `/athena/namlab/scratch/sam4032/trust/bin/annotator': free():
invalid pointer: 0x000056052f58fbf0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7ff3027bf329]
/athena/namlab/scratch/sam4032/trust/bin/annotator(+0x7298)[0x5603ebe2c298]
/athena/namlab/scratch/sam4032/trust/bin/annotator(+0xce7a)[0x5603ebe31e7a]
/athena/namlab/scratch/sam4032/trust/bin/annotator(+0x502f)[0x5603ebe2a02f]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7ff302760555]
/athena/namlab/scratch/sam4032/trust/bin/annotator(+0x5da1)[0x5603ebe2ada1]
======= Memory map: ========
5603ebe25000-5603ebe27000 r--p 00000000 58b:914c8<PHONE_NUMBER>48986669
/athena/namlab/scratch/sam4032/trust/bin/annotator
5603ebe27000-5603ebe48000 r-xp 00002000 58b:914c8<PHONE_NUMBER>48986669
/athena/namlab/scratch/sam4032/trust/bin/annotator
5603ebe48000-5603ebe4b000 r--p 00023000 58b:914c8<PHONE_NUMBER>48986669
/athena/namlab/scratch/sam4032/trust/bin/annotator
5603ebe4b000-5603ebe4c000 r--p 00026000 58b:914c8<PHONE_NUMBER>48986669
/athena/namlab/scratch/sam4032/trust/bin/annotator
5603ebe4c000-5603ebe4d000 rw-p 00027000 58b:914c8<PHONE_NUMBER>48986669
/athena/namlab/scratch/sam4032/trust/bin/annotator
5603ebe4d000-5603ebe52000 rw-p 00000000 00:00 0
5603ec397000-560530018000 rw-p 00000000 00:00 0
[heap]
7ff14bffb000-7ff20bffc000 rw-p 00000000 00:00 0
7ff265ffc000-7ff295ffd000 rw-p 00000000 00:00 0
7ff2c0000000-7ff2c028a000 rw-p 00000000 00:00 0
7ff2c028a000-7ff2c4000000 ---p 00000000 00:00 0
7ff2c8000000-7ff2c84cc000 rw-p 00000000 00:00 0
7ff2c84cc000-7ff2cc000000 ---p 00000000 00:00 0
7ff2cc000000-7ff2cc2df000 rw-p 00000000 00:00 0
7ff2cc2df000-7ff2d0000000 ---p 00000000 00:00 0
7ff2d0000000-7ff2d038e000 rw-p 00000000 00:00 0
7ff2d038e000-7ff2d4000000 ---p 00000000 00:00 0
7ff2d8000000-7ff2d85da000 rw-p 00000000 00:00 0
7ff2d85da000-7ff2dc000000 ---p 00000000 00:00 0
7ff2e0000000-7ff2e05d5000 rw-p 00000000 00:00 0
7ff2e05d5000-7ff2e4000000 ---p 00000000 00:00 0
7ff2e8000000-7ff2e84aa000 rw-p 00000000 00:00 0
This is my command:
run-trust4 -f /athena/namlab/scratch/sam4032/HL6/hg38_bcrtcr.fa -t 8 --ref
/athena/namlab/scratch/sam4032/HL6/human_IMGT+C.fa -u
/athena/namlab/scratch/sam4032/HL2/all_BCR_R2.fastq.gz --barcode
/athena/namlab/scratch/sam4032/HL2/all_BCR_R1.fastq.gz --barcodeRange 0 15

--barcodeWhitelist
/athena/namlab/scratch/sam4032/HL1_GEX_BCR_TCR/737K-august-2016_barcodes.txt
--UMI /athena/namlab/scratch/sam4032/HL2/all_BCR_R1.fastq.gz  --umiRange 16
27 + -o new_BCR_s1s2_dec2023 --od new_BCR_s1s2_dec2023

On Thu, Dec 28, 2023 at 1:38 PM Li Song @.***> wrote:

I could not see the screenshot on github. Based on your description, I
guess those are the samples without any VDJ readout, and TRUST4 exits in
the middle of the program.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1871407527,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONSCRBT7FTC62SJZOIDYLW4DTAVCNFSM6AAAAAASNQNL5GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZRGQYDONJSG4
.
You are receiving this because you authored the thread.Message ID:
@.***>

There might be a bug in the annotator program. Which version of TRUST4 did you use? If it is the newest version, could you please share the _final.out file with me?
If it is not the newest version, you can download the new one, and rerun TRUST4 with an additional parameter "--stage 2" and see whether it still crashes.

Thanks Li. This is the newest version of trust4.
v1.0.12-r465
Running it like this?
run-trust4 -f /athena/namlab/scratch/sam4032/HL6/hg38_bcrtcr.fa -t 8 --ref
/athena/namlab/scratch/sam4032/HL6/human_IMGT+C.fa -u
/athena/namlab/scratch/sam4032/HL2/all_BCR_R2.fastq.gz --barcode
/athena/namlab/scratch/sam4032/HL2/all_BCR_R1.fastq.gz --barcodeRange 0 15

--barcodeWhitelist
/athena/namlab/scratch/sam4032/HL1_GEX_BCR_TCR/737K-august-2016_barcodes.txt
--UMI /athena/namlab/scratch/sam4032/HL2/all_BCR_R1.fastq.gz  --umiRange 16
27 + -o new_BCR_s1s2_dec2023 --od new_BCR_s1s2_dec2023 --stage 2

On Fri, Dec 29, 2023 at 3:05 PM Li Song @.***> wrote:

There might be a bug in the annotator program. Which version of TRUST4 did
you use? If it is the newest version, could you please share the _final.out
file with me?
If it is not the newest version, you can download the new one, and rerun
TRUST4 with an additional parameter "--stage 2" and see whether it still
crashes.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1872312855,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONQ5HEQTXXBOMSYTU6TYL4PAFAVCNFSM6AAAAAASNQNL5GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZSGMYTEOBVGU
.
You are receiving this because you authored the thread.Message ID:
@.***>

Not sure how to share the final_out.
Some lines are:

CTGATAGGTCCTCTTG_0 IGKV3-11+IGKC

AGAGCCCTGGGGAGGAACTGCTCAGTTAGGACCCAGAGGGAACCATGGAAGCCCCAGCTCAGCTTCTCTTCCTCCTGCTACTCTGGCTCCCAGATACCACCGGAGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCT
CCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCCGGAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAACGAACTGTGGCTGCACCATCTGTCTTCATCTTCCC
GCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGC
5 0 5 0 0 0 0 0 0 0 0 0 74 0 0 80 80 0 0 0 0 0 0 92 0 0 0 97 0 0 99 0 0 0
104 0 107 0 0 0 114 116 1 0 122 0 0 0 123 126 0 0 0 0 0 130 0 0 0 0 126 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 161 0 0 0 0 0 0 0 0 0 1 0 196 0 196 0 194 1
1 195 0
0 0 0 193 0 196 195 201 0 0 0 0 0 0 0 0 200 0 204 0 205 0 0 1 1 0 0 209 0
0 1 209 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 233 0 0 0 0 225 225 228 0 223 0 0 0
210 0 0 0 0 0 0 0 0 0 0 0 214 0 0 0 2 0 207 0 0 0 204 0 207 0 0 0 0 0 210 0
0 209
0 0 0 213 0 0 0 215 0 1 0 0 0 0 0 214 0 0 211 214 0 214 0 216 212 216 0 0 0
0 0 0 0 216 0 1 0 0 0 0 0 220 0 0 0 0 0 0 0 1 229 0 0 0 234 0 0 235 0 0 0
222 1 1 0 214 213 0 221 0 0 0 0 1 221 0 0 0 0 0 226 0 0 0 0 223 0 0 0 219 0
0 1 0 0
221 0 0 0 0 0 219 0 0 0 0 0 0 0 0 0 0 0 220 0 215 0 210 1 0 0 0 201 0 0 0
0 0 199 0 0 189 0 0 182 0 0 175 0 0 0 0 165 0 163 0 0 0 0 0 159 161 1 139 0
0 0 0 0 0 137 0 0 0 0 135 0 0 139 0 0 0 0 0 128 0 0 129 0 0 0 0 124 0 0 118
119 0
0 0 0 0 0 0 0 0 0 0 103 0 0 99 0 97 0 0 0 0 0 0 0 0 0 89 0 0 0 0 83 0 0 82
83 0 0 0 0 0 85 1 84 1 0 78 78 79 0 0 77 78 0 0 0 0 0 0 0 0 0 0 84 1 1 83 0
0 0 0 0 1 0 0 0 75 0 0 0 0 0 0 0 0 0 0 72 0 0 0 0 80 0 0 104 0 1 622 0 0 0
0 617 6
11 613 1 1 0 0 0 613 612 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 595
595 0 592 587 2 0 0 0 0 580 0 1 1 0 573 0 574 0 575 0 0 0 2 574 573 569 0 0
570 0 570 0 0 0 0 569 566 0 0 0 0 1 562 0 555 548 0 0 0
0 0 0 0 5 6 6 0 0 0 0 0 0 0 0 0 0 81 0 0 84 0 87 0 0 0 0 0 0 0 0 99 99 103
0 0 0 0 0 0 0 0 115 118 0 0 0 0 0 0 0 128 127 130 131 0 0 129 0 124 0 0 135
0 0 138 0 143 0 0 157 162 0 159 166 0 0 165 0 0 170 0 176 0 0 0 184 0 191
195 196
0 0 0 0 0 192 193 0 197 196 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 201 0 205 0 0 0
208 0 207 211 0 0 215 208 0 212 217 214 0 0 0 224 0 0 0 0 0 227 0 231 233 1
0 0 0 0 0 0 0 0 0 0 222 213 1 212 214 210 0 221 0 222 222 0 0 214 0 0 0 0
208 210
1 0 0 204 0 0 0 0 0 0 0 0 0 0 215 0 0 208 0 0 214 0 0 0 0 218 217 2 0 0 0
0 212 213 0 0 213 0 0 0 0 1 215 217 0 0 0 216 217 0 0 0 218 0 214 215 215 1
0 0 224 0 223 224 0 228 2 0 236 0 0 1 0 0 0 0 226 0 0 221 223 1 1 218 0 0 0
0 228
222 0 221 0 0 0 222 0 1 225 223 221 0 0 217 215 0 0 0 0 0 220 0 0 0 0 0 218
0 0 0 0 0 0 0 231 0 0 0 0 0 221 0 0 0 211 0 0 202 0 203 0 198 0 195 0 197
197 0 0 186 0 0 177 0 0 171 168 0 0 0 0 0 159 161 0 0 0 0 0 0 0 0 0 0 0 145
0 0 0 0
0 0 0 0 0 139 0 0 0 128 0 0 130 0 0 125 0 0 0 0 116 0 0 120 0 0 0 120 113
0 109 109 0 0 0 0 0 0 100 0 97 0 0 0 0 0 0 92 92 0 0 0 0 0 0 83 82 0 0 0 83
0 0 0 0 0 0 0 80 1 1 0 81 0 0 0 81 0 0 0 0 0 84 0 0 84 0 82 82 0 0 80 0 0 0
73 0 0
75 0 0 74 0 0 71 72 73 0 72 72 0 0 70 0 0 0 0 0 0 0 619 0 1 0 0 0 0 2 4 0
616 0 0 0 0 1 613 0 0 608 609 1 606 0 0 0 0 0 0 0 0 0 599 599 0 0 595 0 0 0
0 0 0 1 589 0 0 587 1 3 0 582 576 576 1 1 0 0 1 0 0 576 572 0 0 3 1 0 0 571
0 0 0
0 0 0 0 0 0 0 0 0 0 1 0 0 550 0 519
0 5 0 5 0 0 0 0 40 59 68 74 0 75 75 0 0 0 0 84 0 0 0 0 94 0 0 0 98 98 0 0 0
0 0 106 0 110 109 111 0 0 0 0 0 0 126 126 0 0 127 0 0 0 0 0 130 0 0 0 0 133
0 0 0 0 0 0 1 0 0 0 0 0 0 0 167 0 0 0 0 0 0 0 181 184 0 0 0 0 0 0 196 0 0 0
0 0 0
0 0 192 193 0 201 0 3 0 0 0 200 0 198 0 0 199 0 0 0 0 0 207 0 0 0 0 0 0
213 0 0 0 0 0 0 3 219 0 0 0 1 0 232 0 0 1 0 0 0 235 236 231 230 2 1 0 229 0
225 0 0 0 0 0 0 1 0 1 0 0 0 217 0 0 210 210 211 0 0 0 208 0 0 0 208 0 209 0
210 0 0
0 215 0 0 211 0 0 0 0 0 2 0 218 0 0 0 212 211 0 0 0 0 0 0 0 0 216 0 0 0 0 0
0 214 212 0 0 0 220 216 0 0 0 0 0 0 218 221 0 0 0 0 0 0 0 0 0 0 0 1 235 0 0
231 0 0 0 1 0 0 0 0 0 228 230 229 1 0 0 0 0 224 225 0 0 0 0 0 0 0 223 0 0 0
219 2
19 0 0 0 0 222 0 219 216 0 0 228 0 230 223 227 0 0 0 231 226 222 0 0 1 216
0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 181 0 0 174 0 0 0 0 164 0 162 0 0 0 161
0 0 160 0 0 0 0 1 152 0 0 136 0 0 0 0 0 0 0 0 0 132 0 0 0 127 0 0 130 0 123
0 0 12
3 0 0 0 0 0 118 118 0 0 0 0 0 109 104 0 103 0 0 0 0 0 0 0 0 0 98 96 0 0 0
87 89 87 88 0 0 0 0 0 83 0 0 82 83 0 83 0 0 1 0 0 0 1 78 0 0 0 0 80 0 83 80
0 0 84 0 0 1 0 0 0 0 0 72 0 0 0 0 0 0 0 0 0 0 0 0 0 72 0 0 0 0 0 0 76 0 0
94 0 619
0 0 618 0 0 618 0 0 0 0 0 1 611 611 0 0 0 2 609 0 0 0 0 0 603 0 0 601 2 601
4 599 0 1 0 595 0 0 595 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 574 0 576 0 576 576
0 0 0 0 0 571 0 0 0 0 570 1 570 569 0 0 566 566 0 565 562 0 0 0 0 0 528 0
0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 0 0 0 84 0 0 87 0 0 0 94 97 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 0 126 0 0 0 0 0 0 0 0 0 0 0 0 124 0 0 0 0 140 138 0 138 0
141 147 0 0 159 0 0 167 0 0 164 0 0 174 0 178 0 0 0 185 0 0 0 0 1 0 195 0 0
0 0 0
0 1 0 1 0 0 0 0 199 200 0 198 0 197 197 0 0 0 0 0 0 0 209 0 207 0 0 0 0 0 0
0 0 0 0 215 0 222 0 223 226 228 0 228 0 228 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
0 0 1 216 0 219 0 0 220 0 0 0 0 0 0 0 0 0 0 207 1 1 0 0 0 210 0 211 210 0 1
0 0 0
2 211 0 0 214 211 0 0 0 0 211 0 1 211 0 0 0 0 0 0 0 1 0 0 0 0 0 209 0 1 0
0 0 2 0 0 215 0 0 0 0 1 0 0 221 0 0 225 0 0 234 0 236 0 232 0 0 235 0 0 0
220 0 0 1 1 0 0 0 1 0 0 0 0 0 221 0 0 0 1 224 0 0 0 0 0 0 0 0 0 0 214 213 0
0 0 220
0 0 0 0 0 227 0 3 1 228 0 228 1 0 0 0 0 0 0 0 0 207 202 0 1 0 197 0 196 0 1
0 0 0 189 0 0 0 0 0 0 0 0 166 0 0 0 0 0 0 160 0 0 0 0 18 157 159 161 158 0
0 0 0 135 135 136 1 139 143 0 0 133 1 129 0 0 0 0 1 0 0 0 123 0 0 0 1 0 0
118 1 0
0 0 110 0 0 0 1 0 0 100 1 0 1 0 100 101 101 99 0 0 0 0 0 1 0 0 1 0 0 0 0 0
0 0 83 1 0 0 0 0 81 0 0 0 0 0 0 0 0 0 79 1 83 0 0 0 84 0 0 0 0 0 0 81 0 79
0 72 0 74 74 0 0 75 0 71 71 0 0 0 1 0 0 0 70 0 73 0 0 79 0 0 4 2 0 1 620
618 0 0 4
0 616 0 613 2 2 0 0 0 611 0 0 0 605 0 604 1 604 602 0 599 0 597 1 0 0 596 1
1 594 0 0 0 595 0 4 0 590 587 0 584 0 582 0 0 0 2 1 2 0 0 0 0 0 0 0 1 0 0
572 1 0 0 0 569 0 1 0 2 1 0 566 0 0 0 557 0 2 0 4 1

GGGCATCCATTATCTC_1 IGKV3-20+IGKC

GAAGAGCTGCTCAGTTAGGACCCAGAGGGAACCATGGAAACCCCAGCGCAGTTTCTCTTCCTCCTGCTACTCTGGCTCCCAGATACCACCGGAGAAATTGTGTTGACGCAGTCTCCAGACACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGACACTTAGCACCTACTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAAACT
CCTCATCTATCGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTGAGAACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAGACGAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATG
AGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGC
0 19 19 0 19 0 0 0 0 0 0 0 21 0 0 0 21 0 0 21 0 0 0 22 0 22 0 0 0 24 26 0 0
26 0 1 0 24 23 23 0 0 0 0 23 0 0 0 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
26 0 0 0 0 0 0 0 0 0 0 0 24 0 24 0 23 0 0 24 0 0 0 0 21 0 22 22 23 0 0 0 0
0 0 0
0 23 0 0 0 24 0 0 0 0 0 0 29 0 28 0 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0
0 0 0 23 23 23 0 25 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 24 0 0 0 0 0 24 0 0 0 27
0 28 0 27 0 0 0 28 0 0 27 0 0 0 27 0 0 27 0 0 0 26 0 0 0 0 0 0 0 21 0 0 21
0 0 20
0 22 24 25 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 27 27 27 0 0 0 0 0 0 28 0 0 0 27
0 0 0 0 0 0 27 0 0 0 27 0 0 27 0 0 0 0 0 25 0 0 0 0 0 27 0 0 0 0 26 0 28 0
28 0 0 0 0 0 30 0 0 0 0 0 28 0 0 0 0 0 0 0 0 0 0 0 30 0 27 0 26 0 0 0 0 25
0 0 0 0
0 24 0 0 24 0 0 22 0 0 21 0 19 0 0 0 0 24 0 0 0 0 0 22 21 0 21 0 0 0 0 0 0
20 0 0 0 0 20 0 0 18 0 0 0 0 0 18 0 1 17 0 0 17 0 0 0 0 17 0 0 0 0 17 0 1 0
0 18 0 14 15 0 15 0 0 0 0 0 0 0 0 0 15 0 0 0 0 13 0 0 12 12 0 0 0 0 0 14 0
14 0 0
14 0 13 0 0 11 12 0 0 0 0 0 0 0 0 0 0 12 0 0 11 0 0 0 0 0 0 0 0 0 10 0 0 0
0 0 0 0 0 0 0 9 0 0 0 0 8 0 0 13 0 0 69 0 0 0 0 68 68 67 0 0 0 0 0 67 67 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 64 65 0 64 63 0 0 0 0 0 64 0 1
0 0 64
0 62 0 63 0 0 0 1 62 62 62 0 0 63 0 63 0 0 0 0 61 61 0 0 0 0 0 60 0 61 61 0
0 0
0 0 0 0 0 0 19 0 0 20 0 21 0 0 0 0 0 0 0 0 21 21 21 0 0 0 0 0 0 0 0 26 26 0
0 0 0 0 0 0 23 23 23 23 0 0 22 0 22 0 0 0 0 0 25 0 25 0 0 25 24 0 25 26 0 0
26 0 0 28 0 28 0 0 0 27 0 24 24 24 0 0 0 0 0 23 24 0 24 24 0 0 0 0 0 0 0 0
0 0 0
0 0 0 0 0 23 0 24 0 0 0 30 0 29 29 0 0 0 28 0 26 26 25 0 0 0 25 0 0 0 0 0
27 0 25 26 0 0 0 0 0 0 0 0 0 0 0 25 25 0 25 24 23 0 22 1 25 25 0 0 24 0 0 0
0 24 24 0 0 0 28 0 0 0 28 0 28 0 0 0 0 29 0 28 28 0 0 27 0 0 27 0 0 0 0 26
26 0 0 0
0 0 21 21 0 0 20 0 0 0 0 0 25 26 0 0 0 27 26 0 0 0 28 0 28 27 26 0 0 0 29
0 30 30 0 28 0 0 27 0 0 0 28 0 0 0 26 0 0 28 27 0 0 27 0 0 0 0 27 25 0 23 0
0 0 27 0 0 26 26 26 0 0 0 28 0 0 0 0 0 30 0 0 0 0 0 30 0 0 0 0 0 0 0 30 0 0
0 0 0
28 0 0 0 26 0 0 25 0 23 0 24 0 24 0 24 24 0 0 24 0 0 21 0 0 2 21 0 0 0 0 0
23 23 0 0 0 0 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 0 0 18 0 0 0 18 0 0 17 0 0 0 0
0 0 0 0 0 0 17 0 17 0 17 16 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 15 15 0 0 0 0 0
0 13 12
0 0 0 12 0 0 0 0 0 0 0 14 0 0 0 13 0 0 0 12 0 0 0 0 0 11 0 0 11 0 12 11 0
0 11 0 0 0 11 0 0 11 0 0 11 0 0 11 10 10 0 10 10 0 0 8 0 0 0 0 0 0 0 69 0 0
0 0 0 0 0 1 0 68 0 0 0 0 0 67 0 0 67 67 0 67 0 0 0 0 0 0 0 0 0 66 65 0 0 65
0 0 0
0 0 0 0 64 0 0 64 0 0 0 63 64 64 0 0 0 0 0 0 0 63 62 0 0 0 0 0 0 63 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 61 0 56
16 0 0 19 0 19 0 0 20 0 0 0 0 21 0 0 0 21 21 0 0 0 0 0 22 0 22 24 24 0 0 0
0 0 0 25 25 0 0 0 0 0 0 0 0 23 0 22 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 0
0 0 0 0 0 0 28 28 0 0 0 0 0 0 24 0 0 0 0 0 0 0 0 24 21 0 22 0 0 0 0 0 22 0
22 0 0
23 0 0 23 0 0 25 0 0 0 0 0 0 28 0 0 0 0 0 0 0 25 0 0 0 0 0 27 0 0 0 0 0 0
25 25 25 25 0 0 0 24 0 25 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 24 24 24 0 0 0 26
0 0 1 28 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 26 0 0 0 27 26 0 0 0 0
0 21 0 0
20 0 0 0 0 0 0 26 26 0 0 0 28 27 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
28 0 29 0 0 0 0 0 0 27 0 0 27 29 29 0 0 0 0 0 26 27 0 0 0 0 0 0 0 26 0 0 0
28 28 0 0 0 0 30 0 30 30 0 0 28 0 28 28 28 0 0 0 31 31 31 0 0 0 27 0 0 0 0
0 0 0 0
0 0 0 0 0 0 0 0 0 0 22 0 0 20 0 0 0 22 23 0 24 0 0 0 22 0 0 21 0 0 0 0 0 21
0 0 20 0 20 0 0 0 0 0 0 0 18 0 0 0 18 0 0 17 0 0 0 14 17 0 0 17 0 0 0 0 0 0
0 17 0 18 0 0 0 0 15 0 0 0 0 15 15 0 0 0 15 15 15 13 0 0 0 0 0 12 0 0 12 14
0 14
0 0 0 0 13 0 0 12 0 0 0 0 12 0 12 12 0 0 11 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0
0 0 0 0 0 1 0 10 0 0 0 0 0 0 8 0 0 9 0 69 0 0 69 0 0 67 0 0 0 0 0 0 67 68 0
0 0 0 67 0 0 0 0 0 67 0 0 66 0 67 0 67 0 0 0 64 0 0 64 1 0 0 0 0 0 0 0 0 0
0 1 0 0
0 0 64 0 62 0 63 62 0 0 0 0 0 63 0 0 0 0 62 0 62 62 0 0 62 62 0 62 62 0 0
0 0 0 59 0
0 0 0 0 0 0 0 19 0 0 20 0 0 0 21 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26
0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 20 25 25 0 25 0 25 24 0 0 24 0 0 27 0 0 26
0 0 28 0 28 0 0 0 25 0 0 0 0 0 0 24 0 0 0 0 0 0 0 0 0 0 0 0 0 23 22 0 23 0
23 23 0
0 0 0 0 0 0 27 0 29 0 0 0 0 0 0 0 0 0 0 25 0 25 0 25 26 26 0 27 0 25 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 0 21 0 0 23 0 0 0 0 0 0 0 0 0 0 28 0 0 0
0 0 0 0 28 29 1 0 0 1 0 0 27 0 0 28 0 0 26 26 0 0 0 0 27 0 0 24 0 0 0 0 0 0
0 0 0
0 0 0 0 26 0 0 0 0 0 0 0 0 28 0 0 0 0 0 0 0 29 0 0 29 0 0 28 0 27 0 27 0 0
28 0 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 2 26 0 0 0 0 27 0 0 0 0 0 0 0 0 0 0 30
30 0 0 0 30 0 0 0 0 0 28 0 0 0 31 1 31 0 0 0 0 0 0 0 0 0 26 26 0 0 0 24 0
23 0 0 0
0 0 24 0 0 0 0 0 1 0 0 22 0 0 0 0 0 0 23 0 0 0 0 0 21 21 21 21 0 0 0 0 20 0
20 0 19 19 0 0 18 0 18 0 0 0 0 0 0 17 0 17 0 0 17 0 0 0 17 0 0 0 0 17 0 0 0
1 0 0 0 0 15 14 14 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 14 0 0 0
0 0 0
1 0 0 12 0 12 0 0 0 11 0 0 0 0 0 0 11 0 11 0 11 0 11 11 0 0 10 0 11 11 0 0
0 0 0 0 1 10 0 8 0 0 8 0 0 0 0 0 0 69 68 1 0 0 0 68 0 68 1 0 0 0 0 67 0 0 0
67 0 67 0 67 67 1 67 0 67 0 0 0 65 1 0 65 1 0 0 65 0 1 0 64 64 0 64 0 63 0
0 0 0
0 1 1 0 0 1 0 0 1 1 1 0 63 0 0 0 0 62 0 0 1 1 0 0 62 0 0 1 61 0 0 0 1 0
On Fri, Dec 29, 2023 at 3:24 PM Sara Moien @.***> wrote:

Thanks Li. This is the newest version of trust4.
v1.0.12-r465
Running it like this?
run-trust4 -f /athena/namlab/scratch/sam4032/HL6/hg38_bcrtcr.fa -t 8 --ref
/athena/namlab/scratch/sam4032/HL6/human_IMGT+C.fa -u
/athena/namlab/scratch/sam4032/HL2/all_BCR_R2.fastq.gz --barcode
/athena/namlab/scratch/sam4032/HL2/all_BCR_R1.fastq.gz --barcodeRange 0
15 + --barcodeWhitelist
/athena/namlab/scratch/sam4032/HL1_GEX_BCR_TCR/737K-august-2016_barcodes.txt
--UMI /athena/namlab/scratch/sam4032/HL2/all_BCR_R1.fastq.gz  --umiRange
16 27 + -o new_BCR_s1s2_dec2023 --od new_BCR_s1s2_dec2023 --stage 2
On Fri, Dec 29, 2023 at 3:05 PM Li Song @.***> wrote:

There might be a bug in the annotator program. Which version of TRUST4
did you use? If it is the newest version, could you please share the
_final.out file with me?
If it is not the newest version, you can download the new one, and rerun
TRUST4 with an additional parameter "--stage 2" and see whether it still
crashes.
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1872312855,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONQ5HEQTXXBOMSYTU6TYL4PAFAVCNFSM6AAAAAASNQNL5GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZSGMYTEOBVGU
.
You are receiving this because you authored the thread.Message ID:
@.***>

Can you send them through a dropbox, or email attachment if it is small? My email is<EMAIL_ADDRESS>.

I emailed to @.***
On Fri, Dec 29, 2023 at 4:01 PM Li Song @.***> wrote:

Can you send them through a dropbox, or email attachment if it is small?
My email is @.*** .
—
Reply to this email directly, view it on GitHub
https://github.com/liulab-dfci/TRUST4/issues/169#issuecomment-1872335843,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVVJONRAKUAGQDIJ5LC5KBTYL4VUPAVCNFSM6AAAAAASNQNL5GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZSGMZTKOBUGM
.
You are receiving this because you authored the thread.Message ID:
@.***>


clientconfig: Deprioritize Environment Variables

Currently, environment variables will override any authentication setting that was explicitly defined in the AuthInfo struct.
The behaviour should really be the opposite: only use an environment variable if the auth setting is currently empty.

Fixed in #70


Link functionalities

Related Issue

Issue No. #307

Changes you made :

Wrote code to open the links in a new tab
corrected links and the respective names given on pages
created input field for mail to sign-in for newsletter
created a proper feedback to be given to user once their mail-id is submitted for newsletter

Describe the changes :

Check list :

[x] I have followed code style of this project.
[x] I have read the CONTRIBUTING document.
[x] All the aspects mentioned in the issue are covered.
[x] The website is properly working after my changes.
[x] 🌟 ed the repo

Type of change :

[x] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)

Output Screenshots :

@Srish-ty Again there have been some branch conflicts
Plz resolve for merging

Can you try merging now please

Can you please try merging now

@Srish-ty Good to go
LGTM 🌟


Rewrite HudRender.class to support conditional rendering, and add order field.

This PR changes two things.

The ability to swap out hud renders on the same power by putting the hud render into an array.
An order field supported in the base directory of the hud render. Requires a separate hud_render (supports a hud render object or an array) field for the "inner" hud render itself.

This is also made in a way where datapacks and addons (if they're just referencing the data type) shouldn't break.
Example JSONs:
{
  "hud_render": [
    {
      "sprite_location": "apoli:colored_bar.png",
      "bar_index": 0,
      "condition": {
        "type": "apoli:resource",
        "resource": "*:*",
        "comparison": "==",
        "compare_to": 1
      }
    },
    {
      "sprite_location": "apoli:colored_bar.png",
      "bar_index": 1,
      "condition": {
        "type": "apoli:resource",
        "resource": "*:*",
        "comparison": "==",
        "compare_to": 2
      }
    }
  ]
}

{
  "hud_render": {
    "order": 1,
    "hud_render": [
        {
          "sprite_location": "apoli:colored_bar.png",
          "bar_index": 0,
          "condition": {
            "type": "apoli:resource",
            "resource": "*:*",
            "comparison": "==",
            "compare_to": 1
          }
        },
        {
          "sprite_location": "apoli:colored_bar.png",
          "bar_index": 1,
          "condition": {
            "type": "apoli:resource",
            "resource": "*:*",
            "comparison": "==",
            "compare_to": 2
          }
        }
    ]
  }
}

The error message has the wrong field name. I'll get to fixing it when I can.

Fixed.

Sharing eggo's word on this PR here.


Update logic for handling externally set values

Fix a bug causing debounced value updates to get cancelled erroneously

 Failing E2E tests after bumping up Codemirror version


Added ability to translate strings

Adds string translations.
You can add custom strings by setting the strings property on the config object.
Depending on the application, you could also override or update the insightStrings service.

Thanks @jpmitche11. What caused you to change your mind on forking the partials to do translations?
Also, if you haven't seen it here's a good article on how i18n will eventually work in Angular: http://blog.thoughtram.io/angular/2015/03/21/angular-and-i18n-the-new-world.html

I'd like to integrate Rev with angular-gettext after our current release. One of the benefits is that we'd use the templates as is, without the need for magic values or anything. In that case, forking the insight partials makes more sense than merging this, unfortunately.

I chose to include translations here so we didn't have to maintain a forked template. This shouldnt interfere with gettext, since the translations still live in our partial, not in insight.


Add functionality for Postgres Listen and Notify

Postgres offers a pub / sub listen and notify, it would be amazing if Vapor 3 could implement this. Perfect for realtime updates.

I can dig in on this. assuming just like redis then we should be able to mimick command names in appliance
Subscribe
Info (https://www.postgresql.org/docs/10/static/sql-listen.html)
conn.listen(_  channel: String,   @escaping (PostgreSQLData) -> Void) -> Futue<Conn>

Publish
Info (https://www.postgresql.org/docs/10/static/sql-notify.html)
conn.notify(_ channel: String, payload: PostgrSQLData) -> Futue<Void>

In Progress no one complained so I am implementing

Publicized in #72:
let conn = try PostgreSQLConnection.makeTest(transport: .cleartext)
let done = conn.listen("foo") { message in
    XCTAssertEqual(message, "hi")
    return true
}
do {
    let conn = try PostgreSQLConnection.makeTest(transport: .cleartext)
    _ = try conn.notify("foo", message: "hi").wait()
}
try done.wait()


Unban request

Hi there,
I tried to join for the first time tonight and was kicked then kb'd immediately.  I'm guessing it has something to do with your current spam issues and me joining at a really bad time.   This is the message I see when I try to connect:
devbot: You are banned. If you feel this was a mistake, please reach out at github.com/quackduck/devzat/issues or email
<EMAIL_ADDRESS>Please include the following information: [ID
        42ae49dc6cdbb80b81ba2144385996e1b10cbb33896a062efbb68f9fe6cb1578]

Thanks for taking a look!

You should be good now!

 If you feel this was a mistake, please reach out at github.com/quackduck/devzat/issues or email
<EMAIL_ADDRESS>Please include the following information: [ID
        42ae49dc6cdbb80b81ba2144385996e1b10cbb33896a062efbb68f9fe6cb1578]

I wonder if it might be my IP? I could also regen my ssh-key if that would help.

That is super weird. Are you joining the same way you were before? If you're okay with sending me your public IP, you can email me with it (that would definitely get you unbanned)

Ok will do

Fixed 👍

Woo thanks! Successfully connected 😁

Great!


storage: One more persist error code path discovered

@brian-brazil Found one more code path that creates a persistErr, but was still returning false in writeMemorySeries.
The weird thing is: This codepath should never really happen, only upon obscure data corruption. I'll let this fix run on my high-load test server again. The (only) one server where I could observe #2409 so far.

:+1:

I also adjusted the chunkDescOffset for the series to be quarantined now because the special meaning of -1 was throwing other things off before the quarantine is completed.

And of course, this has to go to release-1.5


Look into issue automation with a PR

Figure out how to properly link a PR to an issue so issue automation applies when the PR is merged.

What I found when I looked into this is that pushing to a non-default branch would not close the github issue when the pull request is merged. So, I would suggest changing the default branch from master to develop and try that out!
To close an issue when a pull request is merged, these keywords can be used: close, closes, closed, fix, fixes, fixed, resolve, resolves, resolved
For more info: https://docs.github.com/en/free-pro-team@latest/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue#closing-an-issue-in-the-same-repository!


amplifyPush --simple fails when removing graphql API model

Before opening, please confirm:

[X] I have checked to see if my question is addressed in the FAQ.
[X] I have searched for duplicate or closed issues.
[X] I have read the guide for submitting bug reports.
[X] I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.

App Id
d1he6253vtkqx8
Region
us-east-2
Amplify Console feature
Backend builds
Describe the bug
We removed an api graphql model and we are unable to deploy using the amplify CI/CD due to the following error:
2022-01-31T03:25:00.558Z [INFO]: DestructiveMigrationError: Removing a model from the GraphQL schema will also remove the underlying DynamoDB table.
                                 This update will remove table(s) [XXXXXXXX]
                                 ALL EXISTING DATA IN THESE TABLES WILL BE LOST!
                                 If this is intended, rerun the command with '--allow-destructive-graphql-schema-updates'.
                                     at cantRemoveTableAfterCreation (/root/.nvm/versions/node/v14.18.1/lib/node_modules/@aws-amplify/cli/node_modules/graphql-transformer-core/src/util/sanity-check.ts:422:11)
                                     at sanityCheckDiffs (/root/.nvm/versions/node/v14.18.1/lib/node_modules/@aws-amplify/cli/node_modules/graphql-transformer-core/src/util/sanity-check.ts:59:9)
                                     at sanityCheckProject (/root/.nvm/versions/node/v14.18.1/lib/node_modules/@aws-amplify/cli/node_modules/graphql-transformer-core/src/util/sanity-check.ts:41:21)
                                     at buildProject (/root/.nvm/versions/node/v14.18.1/lib/node_modules/@aws-amplify/cli/node_modules/graphql-transformer-core/src/util/amplifyUtils.ts:68:5)
                                     at transformGraphQLSchema (/root/.nvm/versions/node/v14.18.1/lib/node_modules/@aws-amplify/cli/node_modules/amplify-provider-awscloudformation/src/transform-graphql-schema.ts:534:29)
                                     at Object.run (/root/.nvm/versions/node/v14.18.1/lib/node_modules/@aws-amplify/cli/node_modules/amplify-provider-awscloudformation/src/push-resources.ts:166:5) {
                                   removedModels: [ 'XXXXXXXXX' ],
                                   replacedModels: [],
                                   toString: [Function (anonymous)]
                                 }

I tried adding a parameter to the amplifyPush command in the build.yml file, but still no luck.
I understand why the protection is there, but we would like to move forward with the change.
Expected behavior
Ability to use the Amplify CI/CD web ui console to deploy a change that involves removing an api graphql model
Reproduction steps

Remove a graphql schema type that is annotated with @model
Start deploy process

Build Settings
No response
Additional information
No response

In my case what I have done is to come to my branch (the intended one to be deployed) and deploy from my local machine using the flag --allow-destructive-graphql-schema-updates in the end amplifyPush suppose to be a script to deploy detecting the right env to deploy but if we manually deploy from local we know what and where to deploy. In my case:

git checkout develop
git pull
amplify env checkout staging
amplify push --allow-destructive-graphql-schema-updates
Then I re-run the failed build (to make sure the deploy to the custom url take place)

🎉
Nonetheless, I am agree we need to have a solution to make sure the CI does this and avoid developers to manually have to update the infrastructure before being able to deploy.

Hi @gakinson thank you for raising this issue. Can you please try @duranmla's suggestion so you can move forward with this change? We will further investigate this behavior on our end.

Hello,
I was able to do this for our beta environment, but for some reason, when I did another deploy after using the CI/CD, it was still failing saying it was destructive. Not sure if there was some sort of amplicy cli issues with the staged/tiered deploy.
In the end we were able to overcome this by changing our deploy pattern, but we are still unable to delete the tables. This is something we will be doing in the future and would like to do it through the CI/CD, but if it comes to it, we can deploy from our local.
It would be great to get this feature though on the CI/CD deployment process. Even if it was an ENV variable or something.
Thank you,
Geoffrey Kinson

+1.
This issue appears to prevent anyone from removing graphql models while using the Amplify CI/CD pipeline.
@gakinson, how did you modify your deploy pattern to get your subsequent CI/CD builds to work?

@myartsev Instead of deleting the resource, I just ended up leaving it existing until the amplify team can resolve this issue. But if we wanted to, we could pull the environment locally and push the change, but we are refraining from that for now since it is okay that the resource sits there unused until this is addressed.

@myartsev Sorry, I didn't really answer your question. I should have mentioned that my initial goal was to delete and rename a model with different indexes. We ended up keeping the same model name, but deployed each key change. I should have clarified this on my earlier comment as it was kind of irrelevant to the main issue.

@hloriana I was wondering if there was any progress/update on this issue?

Hi all 👋 Thanks for your patience. We have released support for these type of operations via CI/CD as well. To be able to use Amplify CI/CD for changes which requires replacement of the underlying DynamoDB table, including removing a graphql model, please add an environment variable AMPLIFY_DESTRUCTIVE_UPDATES and set it to true.
Please feel free to re-open this issue if you encounter any problems

@shubhamsharma04 thank you! does this require an update to the CLI (which version?) or is it purely a backend fixed that's already been deployed on your side?

@myartsev Of course! This does not require an update to CLI. It is purely a backend fix


Error: Cannot generate signature for type - aztec_macros/src/utils/hir_utils.rs:103 when compiling counter contract

Description:
While following the Counter Contract tutorial (https://docs.aztec.network/tutorials/contract_tutorials/counter_contract) from the Aztec documentation, I encountered an error during the compilation step using aztec-nargo. The error indicates that the compiler cannot generate a signature for a specific type, pointing to aztec_macros/src/utils/hir_utils.rs:103.
Error Message:

Steps to Reproduce:

Follow the steps in the Counter Contract tutorial.
Set up the project environment as described in the tutorial.
Run the command to compile the contract: aztec-nargo compile

Observe the error message in the terminal.
Expected Behavior:
The contract should compile without any errors.
Actual Behavior:
Compilation fails with the above error message.
Environment:
Operating System: Ubuntu 24.04 LTS
Compiler version : >=0.30.0
Aztec Packages version : v0.47.1

Closing this as it should be resolved with newer versions. Please lmk if this is not the case.


[Doc]: update user guide: "finetune.md, inference.md"

Thanks for your contribution and we appreciate it a lot. The following instructions would make your pull request more healthy and more easily get feedback. If you do not understand some items, don't worry, just make the pull request and seek help from maintainers.
Motivation
Update user guide based on English version.
Modification
Update
Two user guides were updated based on English version

docs/zh_cn/user_guides/finetune.md
docs/zh_cn/user_guides/inference.md
Fixed
Fixed a misspelling in inference.md
docs/en/user_guides/finetune.md

BC-breaking (Optional)
Does the modification introduce changes that break the backward-compatibility of the downstream repos?
If so, please describe how it breaks the compatibility and how the downstream projects should modify their code to keep compatibility with this PR.
Use cases (Optional)
If this PR introduces a new feature, it is better to list some use cases here, and update the documentation.
Checklist

Pre-commit or other linting tools are used to fix the potential lint issues.
The modification is covered by complete unit tests. If not, please add more unit test to ensure the correctness.
If the modification has potential influence on downstream projects, this PR should be tested with downstream projects, like MMDet or MMCls.
The documentation has been modified accordingly, like docstring or example tutorials.

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

Hi @DanShouzhu ,
Thanks for your kind contribution. Would you like to fix the lint issue so that we could merge this PR?
The details can be found by clicking the item of lint check as shown below

@zytx121
Thanks for your review and suggestions, all changes have been accepted.
However, it still did not pass the tests, would you mind taking a look again?

Hi @DanShouzhu , Thanks for your kind contribution. Would you like to fix the lint issue so that we could merge this PR? The details can be found by clicking the item of lint check as shown below

Sure, I have already applied the suggested code changes given by @zytx121.
But, it still did not pass the test system, we will continue to deal with it.

seems the lint has failed, please fix the lint

you can follow https://github.com/open-mmlab/mmcv/blob/master/CONTRIBUTING.md

All checks have passed after using pre-commit!
Thank you so much!

Hi @DanShouzhu ,
Is there any progress in this PR?

Hi @DanShouzhu , Is there any progress in this PR?

Hello Wayne,
I made some updates.
Could you do a code review?
Best Regards,
Cecil Dan

Hi @DanShouzhu ,
The overall PR LGTM now and can be merged after fixing these small issues

Hi @DanShouzhu
please also add Objects365 in English documents. Thx!

This PR can be merged after fixing these small issues

Hi @DanShouzhu please also add Objects365 in English documents. Thx!

Thanks for your reminder, Objects365 has been added.

Hi @DanShouzhu ！First of all, we want to express our gratitude for your significant PR in the MMDet project. Your contribution is highly appreciated, and we are grateful for your efforts in helping improve this open-source project during your personal time. We believe that many developers will benefit from your PR.
We would also like to invite you to join our Special Interest Group (SIG) private channel on Discord, where you can share your experiences, ideas, and build connections with like-minded peers. To join the SIG channel, simply message moderator— OpenMMLab on Discord or briefly share your open-source contributions in the #introductions channel and we will assist you. Look forward to seeing you there! Join us ：https://discord.gg/UjgXkPWNqA
If you have WeChat account，welcome to join our community on WeChat. You can add our assistant ：openmmlabwx. Please add "mmsig + Github ID" as a remark when adding friends：）
Thank you again for your contribution！❤


go.mod is set to v2 sdk instead of v3

Hello!

Vote on this issue by adding a 👍 reaction
To contribute a fix for this issue, leave a comment (and link to your pull request, if you've opened one already)

Issue details
go.mod needs to be updated for v3 sdk.

Steps to reproduce

1.go get github.com/pulumi/pulumi-mongodbatlas/sdk/v3
Expected: Updated to latest version
Actual:
go: downloading github.com/pulumi/pulumi-mongodbatlas v1.7.0
go: downloading github.com/pulumi/pulumi-mongodbatlas/sdk v1.7.0
go: downloading github.com/pulumi/pulumi-mongodbatlas v3.1.0+incompatible
go get: module github.com/pulumi/pulumi-mongodbatlas/sdk@upgrade found (v1.7.0), but does not contain package github.com/pulumi/pulumi-mongodbatlas/sdk/v3

Hi @jacobfoard
I am so sorry about this - I have opened a PR to fix and will release it within the next hour - it will be v3.1.1 as it's a patch to the current version
Paul


JSON Audit Log (v3/master)

Hi,
This is not a real issue... but maybe can be useful. I'm reading the JSON audit log, i think that the "request method" is in the wrong parameter key on the JSON object:
{
    "transaction": {
        "client_ip": "<IP_ADDRESS>",
        "time_stamp": "Tue Feb 21 08:52:17 2017",
        "server_id": "21f343330a49bdd82b0ed58322ecf1bf7d72013b",
        "client_port": 58005,
        "host_ip": "<IP_ADDRESS>",
        "host_port": 80,
        "id": "14876671370.793770",
        "request": {
            **"protocol": "GET",**
            "http_version": 1.1,
            "uri": "/?asd=asd",
...
}

Don't you think that using "protocol" for describe the request method can lead to misinterpretations? Isn't "method" a better description for it?
Thank you,
Best Regards.
-theMiddle

Hi @theMiddleBlue,
You are absolutely right! Maybe it was a copy&paste error. I dunno. It is fixed already. Changes are available here: https://github.com/SpiderLabs/ModSecurity/tree/v3/dev/parser
Thank you!


Take out  in readme

helps it look nicer especially on the website

Codecov Report
Patch and project coverage have no change.

Comparison is base (188bd5c) 99.60% compared to head (6a71da7) 99.60%.

:exclamation: Current head 6a71da7 differs from pull request most recent head 50393cd. Consider uploading reports for the commit 50393cd to get more accurate results

:exclamation: Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more.
Additional details and impacted files
@@           Coverage Diff           @@
##           master     #261   +/-   ##
=======================================
  Coverage   99.60%   99.60%
=======================================
  Files         226      226
  Lines        3323     3323
=======================================
  Hits         3310     3310
  Misses         13       13

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.


Enhancing zUnitConfig processing

These two contributions cover following updates:
Externalising the BZUPLAY Options , see #162

Options for the zUnit Runner are now externalised as build properties and can be also overridden as file properties. For a full list of options, please see the zUnit/VTP documentation

Externalising the DT Test Runtime Options

Options for the IBM Debug Tool Test Options for the zUnitConfig.groovy are externalised; so users can select their test runtimes according to their needs. IBM Debug Tool Test Runtime Options

Extended behaviour in userBuild scenarios with debug flag when executing bzucfg files , see #163
The behaviour when leveraging the cli option --debug and --ccczUnit (see Build Cmdline Opts)  when processing a --userBuild was enhanced:

--userBuild , --debug and --ccczUnit configures the //CEEOPTS DD * to direct the code coverage session to the logged on user.
--debugzUnitTestcase introduced a new CLI option to tell zAppBuild, if the user would like to init a DT session of the application under test. So,  --userBuild  and --debugzUnitTestcase configure the //CEEOPTS DD * in the zUnit JCL to direct the debug session to the logged on user.

Thank you for the review @jbyibm


HDDS-3000. Update guava version to 28.2-jre.

What changes were proposed in this pull request?
Update Ozone's guava dependency to the latest.
(Please fill in changes proposed in this fix)
What is the link to the Apache JIRA
https://issues.apache.org/jira/browse/HDDS-3000
How was this patch tested?
(Please explain how this patch was tested. Ex: unit tests, manual tests)
(If this patch involves UI changes, please attach a screen-shot; otherwise, remove this)

Looks like the newer Guava versions updated the annotation for the API
void onSuccess(@Nullable V result);
(it didn't have the @Nullable annotation in Gauva 11.) Updated the PR to add the nullity check.
See also: https://github.com/spotbugs/spotbugs/issues/633


fix chocolatey provider correctly handle no newline

seems like chocolatey now outputting newlines when listing --exact

@patriksvensson 👈 Would be nice to get this in 😊

Sorry! 😄

@patriksvensson Sorry I poked, I thought it might be prudent as I know how easy it is to get lost with notification without direct mentions 😄

No worries.


Using a reserved name

list is a reserved keyword and should not be used for a method name.
Maybe use to_list? or items?
The affected methods are:

Collection#list
Inputs#list
Jobs#list

Where is it noted that it is a reserved keyword? All the Python docs I can find don't have it (they have others).

Pydev warns saying it is an assignment built-in symbol: list
Maybe it's just wrong and think you're overwriting the list() function?

Yeah, I'm unconvinced. It may very well change as we change our object model to something more descriptive, but I won't guarantee it.

I am reluctant to make a breaking change for this one. We chose "list" because it is the term used by the REST API for the functionality. In retrospect we might have chosen a different term, but I don't think its worth a breaking change at this point.
This doesn't appear to do any actual harm other than confusing pylint and incorrectly color coding the method as a keyword in vi.
(leaving the issue open for now pending additional feedback).


Fixed options

Fixes gcc build error

Appveyor pulled the commit from the wrong pull request. There should be no reason for it not to work on Windows using Visual Studio.


What archive module should be used?

https://github.com/camptocamp/puppet-archive/blob/master/manifests/init.pp seems incorrect as it does not contain the source attribute. The puppet run fails when https://github.com/camptocamp/puppet-archive/blob/master/manifests/init.pp is called.

https://github.com/jenkinsci/puppet-jenkins/blob/master/metadata.json#L26
We recently migrated because there were several complaints of module name conflicts.


HTTP 103 - Early Hints

Describe the feature you'd like to add to nginx
Support for the 103 Early Hints HTTP status code in Nginx. Early Hints allows sending preliminary HTTP headers to the browser before the final response is fully generated, enabling browsers to start loading critical resources earlier. This feature would significantly improve the performance of websites by allowing the browser to initiate requests for CSS, JavaScript, and other assets before the entire HTML document is delivered.
Describe the problem this feature solves
This feature solves the problem of delayed loading of critical resources on the web. Currently, browsers wait for the full HTML response before they can request resources like CSS or JavaScript files. Early Hints allows the server to "hint" to the browser which assets it should start fetching before the full response is ready. This can reduce Total Page Load Time and enhance perceived performance for users by optimizing resource delivery.
Additional context
Cloudflare has documented their experience with Early Hints and its performance benefits in production use. According to Cloudflare's blog, Early Hints can reduce load times by allowing resources to be fetched and processed sooner, thus speeding up rendering and improving user experience. By adding Early Hints support to Nginx, this widely-used server would gain a feature that is becoming essential for web performance optimizations in modern web development.
There is an experimental module, but it is 8 years old and not adapted to current versions of nginx: https://github.com/nginx-modules/ngx_http_early_hints

This should be a high priority addition. The benefits of this are pretty big.

https://github.com/freenginx/nginx/issues/3

Will be very useful. Make it high prio

May I Pick this up?

I believe 103 support was removed in favour of http/2 push, but in cases where the main response is not immediately ready, early hints will speed up FCP / LCP times greatly. Should be very high priority imo.

@chrisai-dev http/2 has been deprecated by Google, in favour of 103: https://developer.chrome.com/blog/removing-push
I understand the NGINX team don’t want to move too quickly with adding new features but Google made that announcement in 2022.
It feels like NGINX is being left behind by newer webservers like Caddy, who have has 103 support for some time.
Early hints have a very significant impact on page load times for complex pages.


/proxy/ doesn't map to designated url

I was testing the proxy functionality according to part 3 of the generator guide and it doesn't seem to map to the provided url.
The gulp command I'm passing is:
gulp watch --proxyPath=/proxy --proxyMapTo=http://localhost:55173
The proxy configuration generated is :
[proxy] Proxy Configuration:      Path: C:/Program Files/Git/proxy    Map to: http://localhost:55173
(I'm not sure why it's setting the Path on Git like that)
And when I make a call to
$http('/proxy/api/getData')
I get the response:
Cannot POST /proxy/api/getData↵
(Arrow symbol as returned in console.)
Is the issue that I'm issuing a call from localhost to localhost or is there some other configuration step I'm missing? It doesn't seem like it's actually parsing the proxy flag.

Hi @nonsenseless, I'm not sure whats going wrong. If you provide a sample repository I can clone with a description on how to reproduce the error, I might be able to help you.

closing due to inactivity. Please comment if you have updates.


stack build fails due to relative paths outside of repo in stack.yaml

stack build fails with the following error:
/home/tripped/src/odin/../gelatin/gelatin-core: canonicalizePath: does not exist (No such file or directory)

It looks like this was introduced in commit cd59ca10, when the stack.yaml dependencies were replaced with relative paths outside of the repo. I was going to try fixing the dependencies myself and submitting a PR along with this issue, but as the change appears deliberate I'm not sure if there was a specific way you were planning to get the dependencies in a working order.

Ah, yes - the dependencies are in flux but will be cleaned up shortly. You might want to try the part-one release https://github.com/schell/odin/releases/tag/part-one. I'll have master up and running soon enough, hopefully tonight.

Ah, cool; didn't see the tag. Thanks for the update.

This appears have regressed again on master: [https://github.com/schell/odin/blob/e8f1bad7949a2adce204e1a4d3e65061ea0b334b/stack.yaml#L4]

Yes, I keep doing this 👎. I'll get a patch in tomorrow and do my experimental work in a branch from now on.

@bwbaugh please let me know if that last patch does it for you. Thanks :)


pkg/trace/{agent,writer}: simplify channels

This change ensures that incoming client buckets get the same treatment as concentrator generated buckets. Additionally, it simplifies channel use.
Follows from #6870

Went for this change, so closing...


Cannot read property 'getAll' of undefined

Hi,
I am faced with the same issue as this: https://github.com/facebook/react-native/issues/1274
This is roughly my code:
var CookieManager = require('react-native-cookies');
CookieManager.getAll((err, res) => {
console.log('cookies!');
console.log(err);
console.log(res);
});
The cookie manager is defined, and so is the getAll method.
Someone suggested that maybe the files where not properly added to the xcode project. Do I need to "add files to.." the most top level name of the app (the one that states the sdk under it) or to the folder which has the same app name?
Thanks!

@eyaleizenberg the folder which has the same app name. Ensure Copy items if needed and Create groups are checked.

@joeferraro Cool that worked. You should really update the read me for this.
Thanks! :smile:

:+1:


Fasten lane_manager No live threads left Deadlock?

Hei I get stage error above. This is after updating to fastlane 0.12.5. I updated all the gems but not sure what the problem is.
/Library/Ruby/Gems/2.0.0/gems/fastlane-0.12.5/lib/fastlane/lane_manager.rb:57:in `join': No live threads left. Deadlock? (fatal)
	from /Library/Ruby/Gems/2.0.0/gems/fastlane-0.12.5/lib/fastlane/lane_manager.rb:57:in `finish_fastlane'
	from /Library/Ruby/Gems/2.0.0/gems/fastlane-0.12.5/lib/fastlane/lane_manager.rb:43:in `cruise_lane'
	from /Library/Ruby/Gems/2.0.0/gems/fastlane-0.12.5/bin/fastlane:39:in `block (2 levels) in run'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.3.3/lib/commander/command.rb:178:in `call'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.3.3/lib/commander/command.rb:178:in `call'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.3.3/lib/commander/command.rb:153:in `run'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.3.3/lib/commander/runner.rb:428:in `run_active_command'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.3.3/lib/commander/runner.rb:68:in `run!'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.3.3/lib/commander/delegates.rb:15:in `run!'
	from /Library/Ruby/Gems/2.0.0/gems/fastlane-0.12.5/bin/fastlane:118:in `run'
	from /Library/Ruby/Gems/2.0.0/gems/fastlane-0.12.5/bin/fastlane:124:in `<top (required)>'
	from /usr/bin/fastlane:23:in `load'
	from /usr/bin/fastlane:23:in `<main>'

Fixed with the next version, thanks for reporting :+1:

Thanks man will try Tomorrow.

Fix was not working for us. I created a pull request with a new fix.
https://travis-ci.org/KrauseFx/fastlane/builds/61267159

Thank you @bkockx :+1:


nvim needs multicursor support

Currently <C-v>  enters visual mode but can't enter insert mode from there to perform edit over multiple lines.
Need a plugin support for this

<C-v> to enter visual mode
j or k to highlight
I to enter insert mode
Exit to apply changes to highlighted lines


feat: count lgtm only for review approval

close #561
close #555

drop suppurt for /lgtm & /lgtm cancel everywhere
drop redundant review_acts_as_lgtm config
update document

cc: @Mini256  PTAL~  Thanks!
This is a breaking changes:

/lgtm [cancel] is no longer supported
Authors cannot apply for re-review

The documentation for the PR workflow also needs to be adjusted.

We need a Q&A to explain why /lgtm support was removed?

Other than this issue, rest LGTM.
/lgtm

I think this PR will also close https://github.com/ti-community-infra/tichi/issues/555. I will update it into desc.

/assign @Mini256

/test all

/test pull-tichi-unit-test

/test pull-tichi-unit-test

/test pull-tichi-unit-test

It looks like two seconds is basically stable enough to pass the test.

/test pull-tichi-unit-test

We need a Q&A to explain why /lgtm support was removed?

I would like to have a Q&A, with a detailed explanation of why.
This way we can simply reply in the autoresponder to use the approve feature and link to that Q&A.

We need a Q&A to explain why /lgtm support was removed?

I would like to have a Q&A, with a detailed explanation of why.
This way we can simply reply in the autoresponder to use the approve feature and link to that Q&A.

Make sense. Let me write one.

Could you mind update the description in the common plugin list? rest LGTM.

what should be updated there?

Remove the "Add command to" term?

Could you mind update the description in the common plugin list? rest LGTM.

db866f9737942977600b8c695170e3d32cd6fead

what should be updated there?

We can modify it to 'add or delete the status/lgt* label by submitting approve or request changes review' because it is no longer command driven.

Remove the "Add command to" term?

I think it’s a legacy typo.

what should be updated there?

We can modify it to 'add or delete the status/lgt* label by submitting approve or request changes review' because it is no longer command driven.

updated.

/megre
@tisonkun Thank you for your excellent contribution, we will bump a beta version image for testing the new feature later.

/merge


[WFLY-8475]: JBoss-Product-Release-Name has changed in eap manifest, breaking tools expectations.

Verifying the servlet and full distributions :

bin/product.conf exists
bin/product.conf has slot correctly set
jboss-modules.jar must exist
standalone/configuration/standalone.xml must exist
modules/system/layers/base/org/jboss/as/product/wildfly-full/dir/META-INF/MANIFEST.MF exists
JBoss-Product-Release-Name key in manifest.mf above has correct value
JBoss-Product-Release-Version key in manifest.mf has correct value

Jira: https://issues.jboss.org/browse/WFLY-8475
JBEAP: https://issues.jboss.org/browse/JBEAP-3664

This patch seems solid ;) +1


upgrade zig build api to 0.12.0-dev.891+2254882eb

addCSourceFiles now needs a Options struct, and build.zig.zon needs a paths key.
this fixes the build, but i haven't figured out why the "facil.io" artifact is not found on the zap side

I have pinned zap to zig 0.11 release as I didn't see a point for playing catch-up constantly since 0.11 was released. Please put your changes into a separate 0.12 branch so we can point to that or use it once 0.12 gets released


Is there a plan to support the new Activity Stream payloads?

https://dev.twitter.com/overview/api/upcoming-changes-to-tweets

Hi, we will eventually  add the new entities to the model, but I didn't see any comunity pull-request. No ETA for now.

Version 2.0.0 has the support.


How to keep previously rendered shapes?

Thank you for the library! Is there an easy way to simply draw shapes in main without using the update and render functions. I am trying to draw a large number of shapes, one on top of the other, but they keep erasing when update is called. Any help is much appreciated.

Hi @josiah-brown. Sorry, nothing like that is built in. Behind the scenes, the graphics engine clears the back buffer, draws the contents in your render() function, then swaps the back buffer to the front buffer, or what is visible in the window. I'm sure it's possible to retain the contents drawn, but would have to figure out how to do that in a dual-buffered system, something like this. Alternatively, you might be interested in something like Cairo instead.


ci(workflow): apply latest turbopack when build next-swc

Description

closes WEB-763.

This PR expands current daily integration setup to apply local patch to the turbopack when build next-swc. This'll allow to run integartion against latest TOT where possible.
Since we expect there are breaking changes makes incompatible build with next-* codes in next.js to the turbopack, workflow falls back to building normal next-swc with latest published turbopack if build fails for any reason. We do not have fine grained way to determine if build fails due to incompatiblity or other reason - simply falls back as soon as build fails.

This job is an example for failing build of next-swc falls back
https://github.com/vercel/turbo/actions/runs/4580249232/jobs/8088807766


Music will not play, then all sound will cut out

System:
Arch Linux, using java-10-openjdk
AMD RX 480
RuneLite 1.4.24
Oldschool revision: Rev 176
Launcher: 1.6.1
I have the following audio setup:
1 pair of headphones that plug into the stereo jack (this is the default device)
1 pair of speakers that plug in to a simple usb to audio jack device
While using the headphones, the client will fail to play music at all, and will only play game sounds, such as casting sounds or attacking sounds. It may randomly cut out after a few minutes.
If I attempt to switch my audio device to my usb speakers, the game sounds will cut out after a few seconds, making the game totally silent.
Application.log: http://ix.io/1qXA
Launcher log: http://ix.io/1qXB
Edit: Low Detail mode is not on either. temporarily moving the .runelite directory and letting it re-build did not affect the bug's behavior.
Edit2: It's possible this is a oldschool client issue, as OSBuddy exhibited having no sound.

Duplicate of #4891


fix(frontend): Fix common OIDC issues

Summary
This PR addresses 2 common OIDC issues we've seen, which both cause the "red screen of death" experience for users

Issue 1: Caused by: javax.crypto.AEADBadTagException: Tag mismatch!
This issue occurs because each time you deploy datahub-frontend, a new encryption key is being used to store browser-side state for our OIDC session (by Pac4j). The implications are that logging out / in with OIDC enabled, after a new deployment of datahub can give the red screen. Previously, clearing browser state addressed this. This PR fixes this by enabling a stable encryption key across deployments.
Issue 2:  Caused by: org.pac4j.core.exception.HttpAction: Performing a 401 HTTP action
This issue occurs when a user who previously did not have access to DataHub over OIDC (because they were not configured as users in Okta, for example) have tried to login, failed, but then are subsequently granted access. Previously a cached version of the previous login attempt was saved and replayed in such cases, meaning that the user would continually be denied until they cleared browser state. This PR addresses is by clearing the cached "previous attempt" prior to trying to authenticate again.
Status
Ready. Reproduced each issue and verified the solve locally with Okta.
Checklist

[ ] The PR conforms to DataHub's Contributing Guideline (particularly Commit Message Format)
[ ] Links to related issues (if applicable)
[ ] Tests for the changes have been added/updated (if applicable)
[ ] Docs related to the changes have been added/updated (if applicable)

@jjoyce0510 What would someone who was facing this issue do now? Will this be auto-resolved or someone needs to do some cleanup for existing deployments?


CMake: Build Type Release is not honored through ccmake.

Description:
When changing Build Type property through ccmake from Debug to Release, the resulting build remains in Debug mode.

Fixed by PR #1139


Adding dep version to fix logging_external_types

Fixes the failure seen in this artman build:
https://circleci.com/gh/googleapis/artman/6524?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link
cc @alexander-fenster

Codecov Report

Merging #2104 into master will not change coverage.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master    #2104   +/-   ##
=========================================
  Coverage     86.77%   86.77%
  Complexity     5000     5000
=========================================
  Files           450      450
  Lines         19829    19829
  Branches       2095     2095
=========================================
  Hits          17206    17206
  Misses         1904     1904
  Partials        719      719

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update b732351...cdb337d. Read the comment docs.


Some time functions derived from SDK

I discovered these functions in sntp.h and found a way to use them.
The time is synced after one hour, which can be observed by Serial.setDebugOutput(true).
To start the service call configTime() when WiFi is turned on.
You need $(SDK_BASE) to compile
Just a few suggestions...

Thanks, I have merged this into esp8266/Arduino, might be useful not only for TLS.


Why I can not drag out the tabitem?

I want to use this package. But I can not drag the tabitem.  When I try to drag out . It will get an error.Can you help me to solve it? Thanks.
Test.zip

Please post the stack trace and error message.

When I drag out the tabitem .  It will like this.


Errors about --port

Dud, I can host it from localhost:8080 but cannot set the special port.

Thank you for the detailed report @scillidan, sorry for the trouble! I forgot the Websocket port was hard-coded in the UI, this is fixed now.


A useful suggestion

Add the ability to track the miner via iplogger (the startup log, the installation log and the log that it started working), because I have not understood for 2 days whether I am doing something wrong or it is just not working

I'm not planning on adding any external services but you can use an IPLogger redirect for the 'Remote Configuration' to get logs.

I don't understand how to do this

Let's say you use something like https://iplogger.org/ then you can enter the 'Remote Configuration' URL there and enter the redirect URL you get into the builder. Then when it tries to get the 'Remote Configuration' it will first call the IPLogger which will log everything and then it be redirected to the 'Remote Configuration'.

I didn't understand anything(
I have an xmr miner in which this is quite conveniently implemented and I can see when a person started\installed\ and when the miner started working

Well I won't implement any external services that I have not made myself since they are all unsafe to use so I don't want to encourage the usage of them. But as I said you can just use an IPLogger URL (either redirect or normal) as the 'Remote Configuration' URL and it will contact the IPLogger when it gets the 'Remote Configuration' https://github.com/UnamSanctam/SilentETHMiner/wiki#remote-configuration.

I upload a file via DCRAT and nothing works, what is the problem?

Which file? The miner?


Refactoring

The 'modules' section was reworked. A new 'repositories' section was
added (which replaced the top level 'dependencies') and another
'install' was added to be able to list all modules that need to be
"installed/processed" to generate the image.
Renamed 'file' to 'path' references in resources (artifacts, modules).
Specifying cache_url in configuration file was moved from artifact
to common section.
For resources, if you specify only path to resource and at the same time
the cache_url will be set in configuration file - Concreate will still
try to fetch it from cacher, even if it was defined as 'local' path.
Dropped using 'dependencies' word across the code in favor of 'module repositories'.
Resource classes were moved to resource.py. Same happened to unit tests
for these classes.
Cleaned up logging across the tool.
The prepare_external_repositories method code from tools.py
was moved to generator.py and combined with prepare_repositories.
Handling of additional repository files is now done via resources too.
Fixes #40 #29

Documentation still needs to be updated (I'll do it after actual code review), but I would get feedback on it ASAP so we can finally release Concreate 1.0.

I've actually added initial documentation already.


popovers: Fix incorrect "Manage this user" link for deactivated users.

If a user is deactivated Reactivate this user will be
shown as one of the links in user profile popover, in
place of Manage this user.
show_manage_user_option rename to can_manage_user
because now it will also be used as a condition for
reactivating user.
code for reactivating user follows the almost same procedure
as deactivate a user from manage this user, including
confirmation modal's code.

[x] Remove the "Manage this user" link for deactivated users. Just this change would be a fine, mergeable, quick fix.
[x] Instead show a "Reactivate user" link for users who have permission to do so. Clicking the link should pop up a confirmation modal.
[x] While we're here, we should also change "(This user has been deactivated)" -> "This user has been deactivated." for consistency with other parts of the app.

Fixes: #21428
CZO discussion
GIFs or screenshots:

Reactivate user

Thanks for working on this, posted one comment, looks fine otherwise.
Also are you working on the Reactivate user part mentioned in the issue or should I take it?

Yes, I am working on Reactivate user.

Looks good to me. Also, we should take care when we fix this popover for bots because for bots, their owners and (even if they are not realm owner or realm admin) also have permission to reactivate them. And we also check for organization setting for bots creation.

I don't think it's a problem for the API to use the same endpoint for reactivation; probably in an ideal world we'd do the same for deactivation too but I haven't investigated how those endpoints differ. Could be a good #api design conversation.

I think for the reactivation confirmation, the text can just say something like:
<user name> will have the same role, stream subscriptions, and other settings and permissions as they did prior to deactivation.
Other details can just be documented on the help page, and we don't need to explicitly pose the confirmation question, as it should be clear from context.

Visually, I think it would be good to have a bit more space to the left of the question mark link.

Merged, with the following changes:

Integrated that revised string in the modal.
Fixed the missing period at the end of "This user has been deactivated.".
Cleaned up the commit messages to motivate the changes.

Thanks @yogesh-sirsat!
In terms of follow-ups, I'd really like to see the following happen in the next week so we can have a consistent story in 5.0:

We should make the "reactivate user" option in "Deactivated users" settings use this same modal.  @yogesh-sirsat can you work on this?
@alya and @laurynmm should collaborate to fix the "deactivate/reactivate a user" help center page to include these additional details on what deactivating a user actually does.

Additionally:

We should improve the design for help center links in these modals in general. @ganpa3 FYI but @yogesh-sirsat you should feel free to attempt this.

I will happy to work on follow-ups.


Bridged Basic Info attribute storage broken (CON-1212)

When these attributes are reported, the buffer size is not set correctly.  Bridged Basic Info is a derived from Basic Info, so these attributes should match characteristics.  Attribute 1, name, String32.  Attribute E, Product Label, String 64. Attribute F, Serial Number, String 32. etc....  See page 659 in the Core Spec.
I am trying to get the Manufacturer, Model, Serial Number fields to display for a bridged device in Apple Home.  So far I haven't figured out how to do that.
I (16172) esp_matter_attribute: ********** R : Endpoint 0x000D's Cluster 0x00000039's Attribute 0x00000011 is 1 **********
I (16173) esp_matter_attribute: ********** R : Endpoint 0x000D's Cluster 0x00000039's Attribute 0x00000001 is Lowpan **********
E (16174) esp_matter_attribute: Insufficient space for reading Endpoint 0x000D's Cluster 0x00000039's Attribute 0x00000001: required: 7, max: 1
I (16175) esp_matter_attribute: ********** R : Endpoint 0x000D's Cluster 0x00000039's Attribute 0x00000002 is 65523 **********
I (16176) esp_matter_attribute: ********** R : Endpoint 0x000D's Cluster 0x00000039's Attribute 0x00000005 is init_bridged **********
I (16178) esp_matter_attribute: ********** R : Endpoint 0x000D's Cluster 0x00000039's Attribute 0x0000000E is Thermostat **********
E (16179) esp_matter_attribute: Insufficient space for reading Endpoint 0x000D's Cluster 0x00000039's Attribute 0x0000000E: required: 11, max: 1
I (16180) esp_matter_attribute: ********** R : Endpoint 0x000D's Cluster 0x00000039's Attribute 0x0000000F is 12345ABCDEF **********
E (16181) esp_matter_attribute: Insufficient space for reading Endpoint 0x000D's Cluster 0x00000039's Attribute 0x0000000F: required: 12, max: 1

Hi @jonsmirl we've identified and fix will be out soon


Error loading 'livecell_coco_train.json' using pycocotools

Hello.
I am trying to write a data generator to use LiveCell data to train a Keras model. While trying to read the annotation file 'livecell_coco_train.json' using pycocotools with the following code:
from pycocotools.coco import COCO
coco = COCO(annFile)
The following error is raised:

loading annotations into memory...
Done (t=28.31s)
creating index...

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/tmp/ipykernel_57/539935055.py in <module>
     12     json.dump(dataset, f)
     13
---> 14 check_ANNT = COCO(ANNT_TRAIN_COPY)

/opt/conda/lib/python3.7/site-packages/pycocotools/coco.py in __init__(self, annotation_file)
     87             print('Done (t={:0.2f}s)'.format(time.time()- tic))
     88             self.dataset = dataset
---> 89             self.createIndex()
     90
     91     def createIndex(self):

/opt/conda/lib/python3.7/site-packages/pycocotools/coco.py in createIndex(self)
     96         if 'annotations' in self.dataset:
     97             for ann in self.dataset['annotations']:
---> 98                 imgToAnns[ann['image_id']].append(ann)
     99                 anns[ann['id']] = ann
    100

TypeError: string indices must be integers

I am not sure how to correct this error or if this is the wrong approach  to read the annotation file.

This seems to be a duplicate of #4, please check if that is helpful.

Thanks. I will try that solution.


Composing keys are also being output

I just installed the extension through chrome-store, logged out and in again.
Now when I key in "alt-gr + ' + a", I get the sequence " 'áa ", that is single-quote + composed character + "a".
Any ideas what could be wrong ?
thanks!!

Same issue.
Platform: 10895.10.0 (Official Build) dev-channel setzer
Firmware: Google_Setzer.7287.381.0


menu key applied to the wrong item in explorer

Issue Type: Bug

ctrl-shift-e to switch input focus to the explorer panel
select a file
press menu key
another item's context menu is shown

VS Code version: Code 1.46.0 (a5d1cc28bb5da32ec67e86cc50f84c67cc690321, 2020-06-10T09:03:20.462Z)
OS version: Windows_NT x64 10.0.18363

System Info

Item
Value

CPUs
Intel(R) Core(TM) i3-6100 CPU @ 3.70GHz (4 x 3696)

GPU Status
2d_canvas: enabledflash_3d: enabledflash_stage3d: enabledflash_stage3d_baseline: enabledgpu_compositing: enabledmultiple_raster_threads: enabled_onoop_rasterization: disabled_offprotected_video_decode: unavailable_offrasterization: enabledskia_renderer: disabled_off_okvideo_decode: enabledviz_display_compositor: enabled_onviz_hit_test_surface_layer: disabled_off_okwebgl: enabledwebgl2: enabled

Load (avg)
undefined

Memory (System)
31.90GB (17.61GB free)

Process Argv

Screen Reader
no

VM
0%

Extensions (29)

Extension
Author (truncated)
Version

theme-verdandi
be5
2.0.1

vscode-custom-css
be5
3.0.9

markdown-mermaid
bie
1.5.1

better-toml
bun
0.3.2

thief-book
C-T
0.0.9

vscode-autohotkey-plus
cwe
2.4.1

autoit
Dam
1.0.5

vscode-eslint
dba
2.1.5

githistory
don
0.6.5

xml
Dot
2.5.0

EditorConfig
Edi
0.15.1

prettier-vscode
esb
5.0.0

shell-format
fox
7.0.1

toml-formatter
ice
0.0.3

sublime-babel-vscode
jos
0.2.10

vscode-language-pack-zh-hans
MS-
1.46.3

node-debug2
ms-
1.42.4

snippet-creator
nik
0.0.5

java
red
0.62.0

rust
rus
0.7.8

trailing-spaces
sha
0.3.1

language-stylus
sys
1.11.0

stylus-supremacy
thi
2.14.5

html-preview-vscode
tht
0.2.5

ghosttext
tok
1.1.0

vim
vsc
1.14.5

markdown-auto-toc
wib
0.3.0

markdown-pdf
yza
1.4.4

markdown-all-in-one
yzh
3.0.0

(1 theme extensions excluded)

Thanks for filling this issue. This works fine fine for me.
Can you reproduce using Visual Studio Code Insiders https://code.visualstudio.com/insiders/

@isidorn just tried the insiders (freshly downloaded one) and the same happened :-(

@glacjay can you please post a picture, or a short gif? What is the menu key?

This is the menu key, and it's usually being used to call out the context menu, just like the right mouse button, but without a mouse.

Thanks for providing more details. However this works just fine for me on Mac and Win.
However I do not have the menu key so I triggered the context menu via Ctrl+Shift+F10.
For know let's keep this issue opened and we see if more people hit it.

shift-f10 works fine for me, so I think I must use this instead for now.
Thank you anyway. Waiting for your good news.

/confirm
Screen recording from stable after reloading with all extensions disabled and enabling screencast mode:

Compare the first menu that appears (right-click on filename) with the second one (after pressing ContextMenu key).
Version: 1.46.0 (user setup)
Commit: a5d1cc28bb5da32ec67e86cc50f84c67cc690321
Date: 2020-06-10T09:03:20.462Z
Electron: 7.3.1
Chrome: 78.0.3904.130
Node.js: 12.8.1
V8: 7.8.279.23-electron.0
OS: Windows_NT x64 10.0.18363

@gjsjohnmurray thanks for confirming.
@joaomoreno why would the tree handle the context menu differently based on the trigger key? I once case trigger is shift + F10, in another trigger is the menu key.

It really shouldn't since both come from: https://github.com/microsoft/vscode/blob/86e6f8121ffec29243881374cc71352042c39231/src/vs/base/browser/ui/list/listWidget.ts#L1131-L1131
You can start debugging there.

I'm having the same issue and it was driving me crazy (I'm a VIM user and this completely breaking my work flow - since I could not create a simple folder any longer without needing the mouse). Thanks for shift+F10 suggestion, it really saved me (I've managed to map "ctrl+contextmenu" to "editor.action.showContextMenu" as a workaround).
I've noticed two interesting things with this, though:

Trying to bind to "contextmenu" is pointless - it continues having the same behaviour. Mapping to "ctrl+contextmenu" worked as intended, though. So I believe there is something on the "contextmenu" by itself that is overriding any custom mapping.

The "contextmenu" key seems to get fixed on the last selected item (the one that was selected when you hit "ctrl+shift+e" or the last you clicked). It's like when you move with the arrow keys the selected item is not updated correctly.

So, my wild guess is: the arrow keys are not updating the selected items properly, and hitting the "contextmenu" key does not use the "editor.action.showContextMenu" but another similar function that considers only the "properly selected" item.

I had to change my keybindings.json and add this shortcut to use contextmenu with ctrl
{
    "key": "ctrl + contextmenu",
    "command": "editor.action.showContextMenu",
    "when": "textInputFocus"
 }

@isidorn this is not vscode's problem?

This is happening for me as well in:
VS Code 1.50.1
Windows 10.0.18363
Shift + F10 works fine.

Adding verified since I just verified a potential duplicate https://github.com/microsoft/vscode/issues/116083
Users please let me know if you still see this.

/verified


Provide mixin steps to mixin during build

When a mixin is run, we provide the step mixin to it knows what to do. But when we ask the mixin to provide the lines for the Dockerfile, we don't give it any context from the steps it will be asked to run.
Depending on the mixin, it would really help it to know what it's going to need to do at runtime. So we should pass in a list of all the steps associated with it on STDIN and let the mixin use that information to maybe do extra work during build.
Here is an example of what the data will look like that is passed to the mixin on STDIN:
install:
- helm:
    description: install mysql
    chart: stable/mysql
    ...
- helm:
    description: install wordpress
    ...
uninstall:
- helm:
    description: uninstall wordpress
    ...

Examples of what the other mixins will do with this information:

azure mixin can install extensions
terraform mixin can initialize providers