dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity (obsoletion query)

GO:0004584 - dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity
has the note
This term represents a deleted EC activity and is scheduled for obsoletion.
when will it go and does it have a replacement term?

Good question;

Hi @ValWood
So here is what ec said:
Four  EC numbers that have replaced EC <IP_ADDRESS>.
Now covered by
EC <IP_ADDRESS>8 (Dol-P-Man:Man5GlcNAc2-PP-Dol α-1,3-mannosyltransferase),
EC <IP_ADDRESS>9 (Dol-P-Man:Man6GlcNAc2-PP-Dol α-1,2-mannosyltransferase),
EC <IP_ADDRESS>0 (Dol-P-Man:Man7GlcNAc2-PP-Dol α-1,6-mannosyltransferase) and
EC <IP_ADDRESS>1 (Dol-P-Man:Man8GlcNAc2-PP-Dol α-1,2-mannosyltransferase).
EC <IP_ADDRESS> was too unspecific and covered several different enzymes with
non-overlapping catalytic activities.
So, I will

see if these ecs are in already
add any that aren't.
Then it's up to you to choose which one relevant for your use.

All 4 of these are in the GO already.
EC <IP_ADDRESS>8 is GO:0052925
EC <IP_ADDRESS>9 is GO:0052926
EC <IP_ADDRESS>60 is GO:0052917
EC <IP_ADDRESS>61 is GO:0052918
I will add this info to EC <IP_ADDRESS> and send out the obsoletion notice in a bit

Oh brilliant, I think that must be the 4 mannosyltransferases in
https://github.com/geneontology/go-ontology/issues/14204
That is what I was looking for yesterday.
Now, how do I know which one is which??????

Looks like you need to figure out the substrate

There are over 500 annotations using the term. wah

Hmm, I don't think it's these ones. These are (SGD) ALG2, ALG9, ALG12, ALG9
I was looking for
PIGX/PBN1
PIGM/GPI14
GPI18

Pombase has 3; not so much.
gip18, gip10, and alg3, via iso, and ic
You're lucky!

we have 28 mannosyltransferases, but I was trying to specify the activity for
glycosylphosphatidylinositol-mannosyltransferase I complex
and
glycosylphosphatidylinositol-mannosyltransferase II complex
It seemed that this might be it at first ....
(in GPI biosynthesis every eukaryote pretty much has the same 1:1  with a few extra for mammalian?)

Actually  the pathway is pretty much identical
GPI biosynthesis
mouse 31
human 32
pombe 31
cerevisae 30
Not "lucky" Harold, just "picky"


Cufflinks error

Dear
I'm was running the RNAseq DE pipeline on some samples. After aligning with tophat, the cufflinks command gave next error:
[2016-10-27T11:22Z] Assembling transcripts with Cufflinks using /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/align/CELL_R_DMSO/1_2016-10-11_CELL_SampleInfo-merged_tophat/CELL_R_DMSO.bam. [2016-10-27T11:22Z] Assembling transcripts with Cufflinks using /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/align/CELL_R_EVER/2_2016-10-11_CELL_SampleInfo-merged_tophat/CELL_R_EVER.bam. [2016-10-27T11:22Z] Assembling transcripts with Cufflinks using /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/align/CELL_S_DMSO/3_2016-10-11_CELL_SampleInfo-merged_tophat/CELL_S_DMSO.bam. [2016-10-27T11:22Z] You are using Cufflinks v2.2.1, which is the most recent release. [2016-10-27T11:22Z] You are using Cufflinks v2.2.1, which is the most recent release. [2016-10-27T11:22Z] You are using Cufflinks v2.2.1, which is the most recent release. [2016-10-27T11:22Z] Error: sort order of reads in BAMs must be the same [2016-10-27T11:22Z] Error: sort order of reads in BAMs must be the same [2016-10-27T11:22Z] Uncaught exception occurred Traceback (most recent call last):   File "/home/myNAME/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run     _do_run(cmd, checks, log_stdout)   File "/home/myNAME/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run     raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; cufflinks --output-dir /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/assembly/tx/tmpMu06ph/CELL_R_DMSO --num-threads 16 --frag-bias-correct /mnt/home_nfs3/myNAME/local/share/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --library-type fr-firststrand --multi-read-correct --upper-quartile-norm /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/align/CELL_R_DMSO/1_2016-10-11_CELL_SampleInfo-merged_tophat/CELL_R_DMSO.bam You are using Cufflinks v2.2.1, which is the most recent release. Error: sort order of reads in BAMs must be the same ' returned non-zero exit status 1 [2016-10-27T11:22Z] Uncaught exception occurred Traceback (most recent call last):   File "/home/myNAME/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run     _do_run(cmd, checks, log_stdout)   File "/home/myNAME/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run     raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; cufflinks --output-dir /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/assembly/tx/tmpj0FMtY/CELL_R_EVER --num-threads 16 --frag-bias-correct /mnt/home_nfs3/myNAME/local/share/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --library-type fr-firststrand --multi-read-correct --upper-quartile-norm /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/align/CELL_R_EVER/2_2016-10-11_CELL_SampleInfo-merged_tophat/CELL_R_EVER.bam You are using Cufflinks v2.2.1, which is the most recent release. Error: sort order of reads in BAMs must be the same ' returned non-zero exit status 1 [2016-10-27T11:22Z] Error: sort order of reads in BAMs must be the same [2016-10-27T11:22Z] Uncaught exception occurred Traceback (most recent call last):   File "/home/myNAME/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run     _do_run(cmd, checks, log_stdout)   File "/home/myNAME/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run     raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; cufflinks --output-dir /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/assembly/tx/tmpEWqxRC/CELL_S_DMSO --num-threads 16 --frag-bias-correct /mnt/home_nfs3/myNAME/local/share/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --library-type fr-firststrand --multi-read-correct --upper-quartile-norm /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/align/CELL_S_DMSO/3_2016-10-11_CELL_SampleInfo-merged_tophat/CELL_S_DMSO.bam You are using Cufflinks v2.2.1, which is the most recent release. Error: sort order of reads in BAMs must be the same ' returned non-zero exit status 1 [2016-10-27T11:22Z] Assembling transcripts with Cufflinks using /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/align/CELL_S_EVER/4_2016-10-11_CELL_SampleInfo-merged_tophat/CELL_S_EVER.bam. [2016-10-27T11:22Z] You are using Cufflinks v2.2.1, which is the most recent release. [2016-10-27T11:22Z] Error: sort order of reads in BAMs must be the same [2016-10-27T11:22Z] Uncaught exception occurred Traceback (most recent call last):   File "/home/myNAME/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run     _do_run(cmd, checks, log_stdout)   File "/home/myNAME/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run     raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; cufflinks --output-dir /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/assembly/tx/tmpoKZPpg/CELL_S_EVER --num-threads 16 --frag-bias-correct /mnt/home_nfs3/myNAME/local/share/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --library-type fr-firststrand --multi-read-correct --upper-quartile-norm /mnt/home_nfs3/myNAME/RNAseq/CELLdata/FastQs/CELL_SampleInfo-merged/config/align/CELL_S_EVER/4_2016-10-11_CELL_SampleInfo-merged_tophat/CELL_S_EVER.bam You are using Cufflinks v2.2.1, which is the most recent release. Error: sort order of reads in BAMs must be the same ' returned non-zero exit status 1
What's going wrong here?
Thank you in advance.

Hi MBeyens,
Thanks-- it looks like this is a problem with transcriptome assembly with Cufflinks. Do you need to do assembly for your DE project? If not you can turn that off and it should work fine. In the meantime I'll see if I can reproduce.
For doing DE calls with hg38 you'll want to use an aligner that is aware of the alt alleles, hisat2 should work great. I'd also recommend when you do the downstream analysis to not use the count tables and instead use the sailfish quantitated counts instead.

Hi
I am closing this because it seems an old issue. Come back if you find other issues  or want to continue with this one.
cheers


Added some Jest Tests for Customization Components

added dependency to react-test-renderer (used for jest snapshot testing)
added comments to IExtensionDetailProps
removed all uses of data-testid
modified ExtensionSupports to only create a Row if there is content
added 4 jest tests for customization components
adding jest snapshots for the 4 jest tests

@riccardo-forina I'm getting lots of the following when I run yarn test --watch:
   console.error ../../node_modules/react-dom/cjs/react-dom.development.js:506
      Warning: This synthetic event is reused for performance reasons. If you're seeing this, you're accessing the property `view` on a released/nullified synthetic event. This is set to null. If you must keep the original synthetic event around, use event.persist(). See https://fb.me/react-event-pooling for more information.

Was hoping you could take a look. Also:

I really thought the inline snapshots were really cluttering up the test file so I went with the generated snapshot file. Wdyt?
I wanted to test that the delete confirmation dialog was being displayed when I hit the delete button. The only way I could figure out how to do that was to do that in ExtensionDetail.spec.tsx was to do     expect(baseElement.classList).toContain('modal-open'); but doesn't feel like the right way to do it.

PR Storybook available here

PR Storybook available here

PR Storybook available here


Run shift commands one time

In time2backup.sh, move shift commands up to run once

Done in commit b2c1803f2c67d9f5510404a06a329844dd33058a


E2E Init.sh fails complaining about Git Repo branch

VM provisioning:

(base) ~/Documents/Code/Go/Nephio/test-infra$ gcloud compute instances create --machine-type e2-standard-8 --boot-disk-size 200GB --image-family=ubuntu-2004-lts --image-project=ubuntu-os-cloud --metadata=startup-script-url=https://raw.githubusercontent.com/nephio-project/test-infra/v1.0.0/e2e/provision/init.sh,nephio-test-infra-branch=v1.0.0 --zone=us-west1-a nephio-r1-e2e

Script logs:

(base) ~$ gcloud compute ssh ubuntu@nephio-r1-e2e -- sudo journalctl -u google-startup-scripts.service --follow
WARNING:  Python 3.5-3.7 will be deprecated on August 8th, 2023. Please use Python version 3.8 and up.

If you have a compatible Python interpreter installed, you can use it by setting
the CLOUDSDK_PYTHON environment variable to point to it.

No zone specified. Using zone [us-west1-a] for instance: [nephio-r1-e2e].
Warning: Permanently added 'compute.7535939896876911728' (ECDSA) to the list of known hosts.
-- Logs begin at Fri 2023-07-07 02:04:30 UTC. --
Jul 07 02:04:54 nephio-r1-e2e google_metadata_script_runner[2763]: Found startup-script-url in metadata.
Jul 07 02:04:54 nephio-r1-e2e google_metadata_script_runner[2763]: startup-script-url: false, r1, false, https://github.com/nephio-project/test-infra.git, v1.0.0, ubuntu, /home/ubuntu, /home/ubuntu/test-infra
Jul 07 02:04:54 nephio-r1-e2e runuser[2799]: pam_unix(runuser:session): session opened for user ubuntu by (uid=0)
Jul 07 02:04:54 nephio-r1-e2e google_metadata_script_runner[2763]: startup-script-url: Cloning into '/home/ubuntu/test-infra'...
Jul 07 02:04:55 nephio-r1-e2e runuser[2799]: pam_unix(runuser:session): session closed for user ubuntu
Jul 07 02:04:55 nephio-r1-e2e runuser[2830]: pam_unix(runuser:session): session opened for user ubuntu by (uid=0)
Jul 07 02:04:55 nephio-r1-e2e google_metadata_script_runner[2763]: startup-script-url: fatal: 'origin/v1.0.0' is not a commit and a branch 'v1.0.0' cannot be created from it
Jul 07 02:04:55 nephio-r1-e2e runuser[2830]: pam_unix(runuser:session): session closed for user ubuntu
Jul 07 02:04:55 nephio-r1-e2e google_metadata_script_runner[2763]: startup-script-url: CPU usage: 12.5471 %
Jul 07 02:04:55 nephio-r1-e2e google_metadata_script_runner[2763]: startup-script-url: I/O Pressure Stall Information (PSI): 0.77
Jul 07 02:04:55 nephio-r1-e2e google_metadata_script_runner[2763]: startup-script-url: Memory free(Kb):32239040
Jul 07 02:04:55 nephio-r1-e2e google_metadata_script_runner[2763]: startup-script-url exit status 128
Jul 07 02:04:55 nephio-r1-e2e google_metadata_script_runner[2763]: Finished running startup scripts.
Jul 07 02:04:55 nephio-r1-e2e systemd[1]: google-startup-scripts.service: Succeeded.
Jul 07 02:04:55 nephio-r1-e2e systemd[1]: Finished Google Compute Engine Startup Scripts.

Ok, here is the issue with this. The init.sh expects a branch in nephio-test-infra-branch and fails with a tag. I am fixing this, but it is a code change and so would not go into effect until v1.0.1.
Therefore, I created a branch called branch-1.0.0 in the test-infra repo, and updated the docs in https://github.com/nephio-project/docs/pull/42
The branch-1.0.0 is locked and cannot be updated.
This is NOT the same branch we should use for 1.0.1, that would be something like "v1.0" or something.
/cc @s3wong @radoslawc @electrocucaracha


Problems with internal Exchange behind traefik - looking for tcp-timeout settings

Do you want to request a feature or report a bug?

Bug

What did you do?
We have an internal Exchange Server behind traefik.
We have lots of Errors in our traefik log.
reverse-proxy_1  | time="2021-06-04T12:57:43+02:00" level=error msg="Error during connection: read tcp <IP_ADDRESS>:56734->172.X.X.X:443: read: connection reset by peer"
reverse-proxy_1  | time="2021-06-04T12:57:43+02:00" level=error msg="Error during connection: read tcp <IP_ADDRESS>:56196->172.X.X.X:443: read: connection reset by peer"
reverse-proxy_1  | time="2021-06-04T12:57:43+02:00" level=debug msg="Error while terminating connection: close tcp <IP_ADDRESS>:56196->172.X.X.X:443: shutdown: transport endpoint is not connected"
reverse-proxy_1  | time="2021-06-04T12:57:43+02:00" level=debug msg="Error while terminating connection: close tcp <IP_ADDRESS>:56734->172.X.X.X:443: shutdown: transport endpoint is not connected"

We have many Users complaining about poor Outlook / Exchange Performance
While following this Guide (https://techcommunity.microsoft.com/t5/exchange-team-blog/checklist-for-troubleshooting-performance-related-issues-in/ba-p/604792) we stumbled across the Load Balance Section where they are talking about keep alives and TCP idle Timeouts.
Firewall time out = 40 minutes
LB TCP Idle time out = 35 minutes
Exchange Keep Alive = 30 minutes

Or even to a feature called "least connections".
I´ve googled a lot to come over to this settings in traefik but can´t find any.
Could you please help? Ist this a Bug or a Feature Request?
Its my first risen Issue so pls be kind.
I´ve also opened an entry in traefik-community: https://community.traefik.io/t/traefik-as-reverse-proxy-for-internal-exchange/10798
Output of traefik version: (What version of Traefik are you using?)

Feel free to request more if needed.
File-Provider
# tcp:
  routers:
    https.activesync.DOMAIN.de:
      rule: HostSNI(`activesync.DOMAIN.de`)
      entryPoints:
        - websecure
      service: activesync.DOMAIN.de
      tls:
       passthrough: true

  services:
    activesync.DOMAIN.de:
      loadBalancer:
        servers:
          - address: 172.X.X.X:443

If applicable, please paste the log output in DEBUG level (--log.level=DEBUG switch)
(paste your output here)

I answered on the community forum, therefore I close this issue as a question.


Publication title should be hyperlinked

Underline on mouseover (to make it more clear that it is a hyperlink):

Done and on production!


Helper to shutdown / stop /kill the relay server

I am trying to use GSN in a test environment with truffle + ganache, and gulp for running tests automatically (my guess is nodemon would also be affected). It seems like the relayer is reattaching to the parent node process when truffle finishes the test, so the relayer is kept alive after the test run ends, spamming messages and requiring to kill the gulp / nodemon process.

A straight forward way to avoid this would be to add an "after" hook in the test and calling a helper to shutdown the relayer server, but I have not seen this neither in the docs nor in the exported helpers for the package.
A workaround would be to keep ganache alive and instantiate the relayer "externally".
I will try to do it myself but don't count on it :joy:
EDIT. Oh well, diving into the source it seems like runRelayer actually returns the node subprocess. I will try to kill it and if sucessful, close the issue.
EDIT2. Done, I am leaving a code snippet
In a before hook:
relayHubProcess = await runRelayer({ web3, quiet: true, detach: true });

In the after hook:
after('kill relayhub', async () => {
    if (
      relayHubProcess &&
      !relayHubProcess.killed &&
      typeof relayHubProcess.kill === 'function'
    ) {
      await relayHubProcess.kill();
      if (!relayHubProcess.killed) {
        console.warn('Relayer was not killed');
      }
    }
  });

Closing the issue!

I'm glad to hear you got this sorted out @rrodriguezreche! For testing enviroments, you can also use the GSNDevProvider, which may simplify things further.


Adding PhysicalStorage into PhysicalChassis

This PR is able to:

Add the possibility of PhysicalStorage being inside a PhysicalChassis

@miq-bot assign @agrare

Sorry for the double review. Internet connection is making fun of me.

This looks fine to me but depends on https://github.com/ManageIQ/manageiq-schema/pull/224
@EsdrasVP please put any dependent PRs in the description, this would have failed if merged before the schema change.

@agrare : can you merge both?

@martinpovolny no we need @Fryguy to merge the schema one

This looks fine to me but depends on ManageIQ/manageiq-schema#224
@EsdrasVP please put any dependent PRs in the description, this would have failed if merged before the schema change.

@agrare Sorry for that, I fixed it now.

@agrare As the schema PR was merged, I think this one is ok too. Could you check it out?


Responsive/prettier statusbar

Make the status bar responsive (if possible, str.format() and str.rjust() doesn't apply)

fman.io will eventually implement independent status bars for each pane so this will solve the problem. Also did some text changes so it'll fit better no matter what the window size is.


SnackBar push FloatingActionButton upward

Hi!
Description:
When using the FloatingActionButton along with a SnackBar, I noticed that when the SnackBar is displayed, it pushes the FloatingActionButton upward, which can be visually disruptive. It would be helpful to have an option to prevent this behavior.
Proposed Solution:
I believe that setting the behavior of the SnackBar to floating could potentially resolve this issue. This way, the SnackBar would overlay on top of other UI elements without affecting their layout.
Video recording
https://github.com/GiYeongUM/flutter_icon_snackbar/assets/66636702/8773fdb2-30fe-4714-bbcf-d75b1fba354f

@MDeLuise Hi! I checked your issue content, I will revise and reflect it! BRB.

@MDeLuise I added the SnackBarBehavior option in version 1.1.7 The default value is fixed option, and I modified it to make floating available as well. Thank you so much for your comments.

Great, thanks so much!


juliaup

Project description
Juliaup is the new installer and version multiplexer for the Julia runtime. In a few weeks it is going to be the default installer for the Julia language, as just announced on the JuliaConference last week.
It would be great to have it available in nixpkgs.
Metadata

homepage URL: https://github.com/JuliaLang/juliaup
source URL: https://github.com/JuliaLang/juliaup
license: mit
platforms: unix, linux, darwin, ...

I just watched the Juliacon talk on this. It might be similar to the way rustup is packaged?

Ah this is interesting. I started working on a PR that uses BinaryBuilder (#211162) instead of system dependencies for packaging julia. I assume this means later versions don't use BinaryBuilder anymore?

BinaryBuilder is Julia's way to package non-julia dependencies in a architecture agnostic way.
juliaup is the main way to install julia nowadays. Hence this is unrelated to BinaryBuilder.

Indeed this is basically rustup but for Julia, it would be nice to have


An error occurred (AccessDenied) when calling the ListObjects operation: Access Denied

I am trying to sync two buckets, both of which I have access to:
# created destination bucket to store data
$ s3cmd ls s3://toil.20k
                       DIR   s3://toil.20k/gtex/
                       DIR   s3://toil.20k/pnoc/
                       DIR   s3://toil.20k/target/
                       DIR   s3://toil.20k/tcga/

# publicly accesible source bucket I am trying to get data from
# without --requester-pays I cannot even ls on this bucket
$ s3cmd --requester-pays ls s3://cgl-rnaseq-recompute-fixed/gtex
                       DIR   s3://cgl-rnaseq-recompute-fixed/gtex/
2016-06-03 17:02    435553   s3://cgl-rnaseq-recompute-fixed/gtex-manifest

I had two approaches:

Get-Put

# get from source bucket to an EBS volume
s3cmd get s3://cgl-rnaseq-recompute-fixed/gtex/$i ./
# put into destination bucket
s3cmd put ./$i s3://toil.20k/gtex/
# remove from EBS
rm ./$i

I have this working in the background but I wanted to test the second approach where you can just copy/sync between buckets without having to store them temporarily on an EBS volume.

Sync between buckets
I read that s4cmd is faster than s3cmd but when I use this:

$ s4cmd --dry-run sync s3://cgl-rnaseq-recompute-fixed/gtex s3://rnaseq.toil.20k/gtex

# I get the following error
[Exception] An error occurred (AccessDenied) when calling the ListObjects operation: Access Denied
[Thread Failure] An error occurred (AccessDenied) when calling the ListObjects operation: Access Denied

Like I said I cannot ls on the source bucket without --requester-pays. Would that be causing the error? I see there is no --requester-pays argument for s4cmd. How can I use s4cmd to sync two buckets?
Thanks!

I'm also getting this error.. and I swear it worked about a month ago when I was using it previously.
I'm also getting this error when trying to dsync:
[Exception] An error occurred (InvalidAccessKeyId) when calling the ListObjects operation: The AWS Access Key Id you provided does not exist in our records.
when an ls works fine:
$ s4cmd ls s3://cms-files/                     DIR s3://cms-files/uploads/ 2016-05-06 04:53  85351 s3://cms-files/01.pdf 2016-05-06 04:53 663665 s3://cms-files/06.pdf 2016-06-20 04:16 171308 s3://cms-files/17.pdf


Implement the insert “query”.

This is an expression, and so returns a new set combining those of the
source set with the values provided.

Current coverage is 78.82%

Merging #1109 into master will increase coverage by +0.01% as of acbc946

@@            master   #1109   diff @@
======================================
  Files          171     171
  Stmts         9572    9580     +8
  Branches       316     316
  Methods          0       0
======================================
+ Hit           7544    7551     +7
  Partial          0       0
- Missed        2028    2029     +1

Review entire Coverage Diff as of acbc946

Powered by Codecov. Updated on successful CI builds.

👍🏼

This is merged. I think the lack of a merge commit in the way I did it failed to trigger the PR as merged.


ERR_CONNECTION_RESET on android emulator

Problem Description
Setting up mitmproxy on a default android-33 emulator always yields a connection reset error, regardless of HTTP or HTTPS.
Steps to reproduce the behavior:

Create emulator:
avdmanager create avd --name mitm --package 'system-images;android-33;default;arm64-v8a' -c 2048M -d pixel --force
Add CA certificate following instructions on Install System CA Certificate on Android Emulator
Start mitmproxy: mitmproxy
Configure android proxy
Visit any page (either http or https)

Expected behavior: traffic should flow through mitmproxy.
Actual behavior: ERR_CONNECTION_RESET.
Notes:

I can see the mitmproxy system CA certificate listed under Trusted credentials
http://mitm.it also yields the same ERR_CONNECTION_RESET error.
Quitting mitmproxy and trying to make requests again yields ERR_PROXY_CONNECTION_FAILED, which means the connection seems to be going through the proxy.
Turning off the proxy settings on the emulator makes pages load again (without flowing through mitmproxy, of course).

The event logs only show the client connecting/disconnecting:
Events
info: [10:54:07.496] HTTP(S) proxy listening at *:8080.
info: [10:54:33.817][<IP_ADDRESS>:60531] client connect
info: [10:54:33.829][<IP_ADDRESS>:60531] client disconnect

System Information
$ mitmproxy --version
Mitmproxy: 10.2.4 binary
Python:    3.12.2
OpenSSL:   OpenSSL 3.2.1 30 Jan 2024
Platform:  macOS-14.2.1-arm64-arm-64bit

What happens if you run with --set proxy_debug -vvv ?

Do you mean mitmproxy --set proxy_debug -vvv? If so, nothing really happened: I'm still not able to connect and I only see the exact same log entries:
info: [16:11:12.457] HTTP(S) proxy listening at *:8080.
info: [16:11:16.141][<IP_ADDRESS>:55893] client connect
info: [16:11:16.143][<IP_ADDRESS>:55893] client disconnect

For what it's worth, I just learned about android's <IP_ADDRESS> magic IP address, which does make the proxy work. Now I'm not sure if this problem is on the android side or mitmproxy. On one hand, the proxy works with the magic IP, but on the other hand, I can reach my local IP address from the emulator just the same (i.e. without any proxy settings, I can visit my local ip on a browser and make successful requests), so the network seems fine. 🤷

Closing as this very likely is an Android Emulator issue.


Initial implementation of tracing in the mixer with opentracing

Initial implementation of tracing in the mixer with opentracing. In opentracing a tracer starts spans, spans together form a trace. We generate a span which represents the entire stream of calls between a client and mixer, with a child span for each request served by the mixer. We also introduce a client interceptor which propagates the mixer's current span to the callee.
There's still a bit more to do to get opentracing into a better state, but I think this is a reasonable start.
Implementation notes:

I chose to handle the root span in the GRPCServer's streamLoop method rather than in gRPC's ServerStreamInterceptor (doesn't allow mutation of the context, so we can't propagate span metadata through the mixer) or its transport layer handler (allows mutating the context but
doesn't bookend the stream so we can't finish the root span) due to the shortcomes mentioned inline.
Quite a bit of this code should eventually migrate into github.com/grpc-ecosystem/grpc-opentracing.

This change is

Current coverage is 66.94% (diff: 60.00%)

Merging #158 into master will decrease coverage by 0.64%

@@             master       #158   diff @@
==========================================
  Files            28         30     +2
  Lines          1018       1086    +68
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
+ Hits            688        727    +39
- Misses          312        338    +26
- Partials         18         21     +3

Powered by Codecov. Last update 399a5f7...e836818

Here's mixs example spans for mixc making a check call to mixs:
2017-01-12 15:10:01.0511497 -0800 PST /istio.mixer.v1.Mixer/Check-1 101.428µs trace:<PHONE_NUMBER>738902926; span:<PHONE_NUMBER>754802239; parent:<PHONE_NUMBER>601980156; tags: map[]; logs: [{2017-01-12 15:10:01.051153826 -0800 PST [gRPC request:attribute_update:<dictionary:<key:0 value:"serviceName" > dictionary:<key:1 value:"peerId" > string_attributes:<key:0 value:"foo" > string_attributes:<key:1 value:"bar" > > ]} {2017-01-12 15:10:01.051249355 -0800 PST [gRPC response:result:<code:12 > ]}]
2017-01-12 15:10:01.050843885 -0800 PST /istio.mixer.v1.Mixer/Check 563.719µs trace:<PHONE_NUMBER>738902926; span:<PHONE_NUMBER>601980156; parent: 0; tags: map[span.kind:server component:gRPC]; logs: []

Where /istio.mixer.v1.Mixer/Check is the root span for the stream and /istio.mixer.v1.Mixer/Check-# are the children spans (with # incrementing with each message received).
mixc's single span for the same call is:
2017-01-12 15:10:01.049575332 -0800 PST /istio.mixer.v1.Mixer/Check 1.094139ms trace:<PHONE_NUMBER>585099018; span:<PHONE_NUMBER>75469219; parent: 0; tags: map[span.kind:client]; logs: []

I need to dig into why the parent wasn't propagated in the call, but that doesn't need to block the rest of the PR I think.

As far as WrappedServerStream is concerned, the only thing that would let us do is remove these two lines in streamLoop. I'm pro-using it if we need the mutable context elsewhere, otherwise I don't have a strong feeling either way.

Also updated how reporting is handled in mixs/mixc, PTAL.

Thanks for the example! That is a tremendous help.


Add interface to register callback when raft part elected

 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.liuyu seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.You have signed the CLA already but the status is still pending? Let us recheck it.

CLA issue, close this. open #546 instead


Travis CI failed for a fresh master fork

Hi, I test making a PR with only a comment line changed after forking from master branch and Travis failed while it's supposed to be passing . Maybe it's an issue on my part ?. Please have a look :) .
Related PR : (#866)
Output: (more details are in this Travis raw output log):
Tests run: 9, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 113.068 sec <<< FAILURE! - in fr.inria.spirals.repairnator.scanner.ProjectScannerTest
testGetBuildToBeInspectedWithPassingWithPreviousPassingFromPR(fr.inria.spirals.repairnator.scanner.ProjectScannerTest)  Time elapsed: 33.525 sec  <<< FAILURE!
java.lang.AssertionError: expected:<BuildToBeInspected{patchedBuild=Build{number='2774', state='PASSED', duration=445, eventType='PULL_REQUEST', previousState='PASSED', pullRequestTitle='review 2: Change local variable name refactoring', pullRequestNumber=1005, startedAt=Wed Mar 15 19:19:41 UTC 2017, finishedAt=Wed Mar 15 19:27:06 UTC 2017, repository=Repository{name='spoon', slug='INRIA/spoon', active=false, privateProperty=false, description='null', githubLanguage='null', starred=false, owner=null, defaultBranch=null}, branch=Branch{name='master', repository=null, defaultBranch=false, existsOnGithub=false, lastBuild=null}, commit=Commit{sha='74cc445c5cbd55cddb02164fa9ecee25c6f6d6d0', ref='refs/pull/1005/merge', message='feature: change LocalVariable name', compareUrl='https://github.com/INRIA/spoon/pull/1005', committedAt=Wed Mar 15 19:17:45 UTC 2017, committer=null, author=null}, jobs=Job{allowFailure=false, number='2774.1', state=PASSED, startedAt=Wed Mar 15 19:19:41 UTC 2017, finishedAt=Wed Mar 15 19:27:06 UTC 2017, build=Build{number='2774', state='PASSED', duration=445, eventType='PULL_REQUEST', previousState='PASSED', pullRequestTitle='review 2: Change local variable name refactoring', pullRequestNumber=1005, startedAt=Wed Mar 15 19:19:41 UTC 2017, finishedAt=Wed Mar 15 19:27:06 UTC 2017, repository=null, branch=null, commit=null, jobs=, updatedAt=null, tag='null', createdBy=null}, queue='builds.gce', repository=Repository{name='spoon', slug='INRIA/spoon', active=false, privateProperty=false, description='null', githubLanguage='null', starred=false, owner=null, defaultBranch=null}, commit=Commit{sha='74cc445c5cbd55cddb02164fa9ecee25c6f6d6d0', ref='refs/pull/1005/merge', message='feature: change LocalVariable name', compareUrl='https://github.com/INRIA/spoon/pull/1005', committedAt=Wed Mar 15 19:17:45 UTC 2017, committer=null, author=null}, owner=Owner{type=ORGANIZATION, login='INRIA', name='null', githubId=0, avatarUrl='null', isSyncing=false, syncedAt=null}, createdAt=Wed Mar 15 19:19:03 UTC 2017, updatedAt=Sat Jun 02 03:00:07 UTC 2018, log=fr.inria.jtravis.entities.Log@eddf281b, buildTool=null}, updatedAt=Thu Apr 11 10:57:12 UTC 2019, tag='null', createdBy=Owner{type=USER, login='pvojtechovsky', name='null', githubId=0, avatarUrl='null', isSyncing=false, syncedAt=null}}, buggyBuild=Build{number='2741', state='PASSED', duration=464, eventType='PULL_REQUEST', previousState='PASSED', pullRequestTitle='WiP: Change local variable name refactoring', pullRequestNumber=1005, startedAt=Sat Mar 11 17:53:01 UTC 2017, finishedAt=Sat Mar 11 18:00:45 UTC 2017, repository=Repository{name='spoon', slug='INRIA/spoon', active=false, privateProperty=false, description='null', githubLanguage='null', starred=false, owner=null, defaultBranch=null}, branch=Branch{name='master', repository=null, defaultBranch=false, existsOnGithub=false, lastBuild=null}, commit=Commit{sha='203c0973905fd932d763cd50049c1dadc73da4bc', ref='refs/pull/1005/merge', message='feature: change LocalVariable name', compareUrl='https://github.com/INRIA/spoon/pull/1005', committedAt=Sat Mar 11 17:50:36 UTC 2017, committer=null, author=null}, jobs=Job{allowFailure=false, number='null', state=null, startedAt=null, finishedAt=null, build=null, queue='null', repository=null, commit=null, owner=null, createdAt=null, updatedAt=null, log=null, buildTool=null}, updatedAt=Thu Apr 11 10:57:12 UTC 2019, tag='null', createdBy=Owner{type=USER, login='pvojtechovsky', name='null', githubId=0, avatarUrl='null', isSyncing=false, syncedAt=null}}, status=PASSING_AND_PASSING_WITH_TEST_CHANGES, runId='test'}> but was:<null>
	at fr.inria.spirals.repairnator.scanner.ProjectScannerTest.testGetBuildToBeInspectedWithPassingWithPreviousPassingFromPR(ProjectScannerTest.java:158)

Results :
Failed tests:
  ProjectScannerTest.testGetBuildToBeInspectedWithPassingWithPreviousPassingFromPR:158 expected:<BuildToBeInspected{patchedBuild=Build{number='2774', state='PASSED', duration=445, eventType='PULL_REQUEST', previousState='PASSED', pullRequestTitle='review 2: Change local variable name refactoring', pullRequestNumber=1005, startedAt=Wed Mar 15 19:19:41 UTC 2017, finishedAt=Wed Mar 15 19:27:06 UTC 2017, repository=Repository{name='spoon', slug='INRIA/spoon', active=false, privateProperty=false, description='null', githubLanguage='null', starred=false, owner=null, defaultBranch=null}, branch=Branch{name='master', repository=null, defaultBranch=false, existsOnGithub=false, lastBuild=null}, commit=Commit{sha='74cc445c5cbd55cddb02164fa9ecee25c6f6d6d0', ref='refs/pull/1005/merge', message='feature: change LocalVariable name', compareUrl='https://github.com/INRIA/spoon/pull/1005', committedAt=Wed Mar 15 19:17:45 UTC 2017, committer=null, author=null}, jobs=Job{allowFailure=false, number='2774.1', state=PASSED, startedAt=Wed Mar 15 19:19:41 UTC 2017, finishedAt=Wed Mar 15 19:27:06 UTC 2017, build=Build{number='2774', state='PASSED', duration=445, eventType='PULL_REQUEST', previousState='PASSED', pullRequestTitle='review 2: Change local variable name refactoring', pullRequestNumber=1005, startedAt=Wed Mar 15 19:19:41 UTC 2017, finishedAt=Wed Mar 15 19:27:06 UTC 2017, repository=null, branch=null, commit=null, jobs=, updatedAt=null, tag='null', createdBy=null}, queue='builds.gce', repository=Repository{name='spoon', slug='INRIA/spoon', active=false, privateProperty=false, description='null', githubLanguage='null', starred=false, owner=null, defaultBranch=null}, commit=Commit{sha='74cc445c5cbd55cddb02164fa9ecee25c6f6d6d0', ref='refs/pull/1005/merge', message='feature: change LocalVariable name', compareUrl='https://github.com/INRIA/spoon/pull/1005', committedAt=Wed Mar 15 19:17:45 UTC 2017, committer=null, author=null}, owner=Owner{type=ORGANIZATION, login='INRIA', name='null', githubId=0, avatarUrl='null', isSyncing=false, syncedAt=null}, createdAt=Wed Mar 15 19:19:03 UTC 2017, updatedAt=Sat Jun 02 03:00:07 UTC 2018, log=fr.inria.jtravis.entities.Log@eddf281b, buildTool=null}, updatedAt=Thu Apr 11 10:57:12 UTC 2019, tag='null', createdBy=Owner{type=USER, login='pvojtechovsky', name='null', githubId=0, avatarUrl='null', isSyncing=false, syncedAt=null}}, buggyBuild=Build{number='2741', state='PASSED', duration=464, eventType='PULL_REQUEST', previousState='PASSED', pullRequestTitle='WiP: Change local variable name refactoring', pullRequestNumber=1005, startedAt=Sat Mar 11 17:53:01 UTC 2017, finishedAt=Sat Mar 11 18:00:45 UTC 2017, repository=Repository{name='spoon', slug='INRIA/spoon', active=false, privateProperty=false, description='null', githubLanguage='null', starred=false, owner=null, defaultBranch=null}, branch=Branch{name='master', repository=null, defaultBranch=false, existsOnGithub=false, lastBuild=null}, commit=Commit{sha='203c0973905fd932d763cd50049c1dadc73da4bc', ref='refs/pull/1005/merge', message='feature: change LocalVariable name', compareUrl='https://github.com/INRIA/spoon/pull/1005', committedAt=Sat Mar 11 17:50:36 UTC 2017, committer=null, author=null}, jobs=Job{allowFailure=false, number='null', state=null, startedAt=null, finishedAt=null, build=null, queue='null', repository=null, commit=null, owner=null, createdAt=null, updatedAt=null, log=null, buildTool=null}, updatedAt=Thu Apr 11 10:57:12 UTC 2019, tag='null', createdBy=Owner{type=USER, login='pvojtechovsky', name='null', githubId=0, avatarUrl='null', isSyncing=false, syncedAt=null}}, status=PASSING_AND_PASSING_WITH_TEST_CHANGES, runId='test'}> but was:<null>

Tests run: 9, Failures: 1, Errors: 0, Skipped: 0

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] repairnator-root ................................... SUCCESS [ 10.641 s]
[INFO] repairnator-core ................................... SUCCESS [ 14.579 s]
[INFO] repairnator-pipeline ............................... SUCCESS [26:40 min]
[INFO] repairnator-scanner ................................ FAILURE [01:54 min]
[INFO] repairnator-dockerpool ............................. SKIPPED
[INFO] repairnator-checkbranches .......................... SKIPPED
[INFO] repairnator-realtime ............................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 29:06 min
[INFO] Finished at: 2019-07-15T16:39:55Z
[INFO] Final Memory: 184M/698M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.19.1:test (default-test) on project repairnator-scanner: There are test failures.
[ERROR]
[ERROR] Please refer to /home/travis/build/Spirals-Team/repairnator/repairnator/repairnator-scanner/target/surefire-reports for the individual test results.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :repairnator-scanner
travis_time:end:0b59b88f:start=1563207046635614720,finish=1563208795894318050,duration=1749258703330
The command "./.travis/travis-run.sh" exited with 1.

Done. Your build exited with 1.

Also related (travis build)[https://travis-ci.org/Spirals-Team/repairnator/jobs/559018886] where I just removed the comment right after the previous build.

Closed after discussion in #866

Duplicate of #744, which is becoming high priority


Always output the Out-of-sample start date even if its very short, or after the last backtest date

its useful info, if its available.  In screenshot, sounds like the out of sample date was less than 5 days from the end of the available backtest data from the test harness run, and thus an automatical 85%/15% split was used (which is totally fine, and a good default).  But if the out of sample date is available lets just show it

looks like this has been completed


Support .text as a text file extension in the Web UI

Change Description
Background
The lakeFS web UI supports .txt as a text file extension, but not .text. The latter is still a text file and used by, amongst other things, Apache Iceberg in its metadata.
This fix adds support for .text to the web UI.
New Feature
.text files are also supported for viewing and diff'ing.
Testing Details
Locally built and tested the change.
Object viewer

Diff

Breaking Change?
No

Added support for .yml files and dynamically rendered the list of supported file formats using Intl.ListFormat for the non-supported error message.


Alert color for modal primary button

Suggestion / feature request
We would like to use the modal for confirmation of delete on the UI. It would be nice to have an option to set the primary button color to red to emphasize the delete action.
Example:

Internal tracked [IX-364]

Closed by #1277


fix issues with stem3 for data-distribution

This PR fix issues and improves functionalities related to stem3 matlab function.
To see how works, it was tested for all examples in https://github.com/plotly/ssim_baselines/tree/main/matlab/code-examples/discrete-data-plots/stem3
As an example, a test code is shown bellow:
figure
X = linspace(-pi/2,pi/2,40);
Z = cos(X);
% Z = ones(size(Z));
stem3(Z);

f = fig2plotly(gcf, 'offline', 0);

Attach bellow results for all examples in  https://github.com/plotly/ssim_baselines/tree/main/matlab/code-examples/discrete-data-plots/stem3

Links to chart-studio
https://chart-studio.plotly.com/~galvisgilberto/4006/#/
https://chart-studio.plotly.com/~galvisgilberto/4008/#/
https://chart-studio.plotly.com/~galvisgilberto/4010/#/
https://chart-studio.plotly.com/~galvisgilberto/4012/#/
https://chart-studio.plotly.com/~galvisgilberto/4014/#/
https://chart-studio.plotly.com/~galvisgilberto/4016/#/
https://chart-studio.plotly.com/~galvisgilberto/4018/#/
https://chart-studio.plotly.com/~galvisgilberto/4020/#/
https://chart-studio.plotly.com/~galvisgilberto/4022/#/
https://chart-studio.plotly.com/~galvisgilberto/4024/#/
https://chart-studio.plotly.com/~galvisgilberto/4026/#/

This PR was updated with a new commit to work perfect with stem function too without any conflict with stem3.
This new commit was tested for all examples in https://github.com/plotly/ssim_baselines/tree/main/matlab/code-examples/discrete-data-plots/stem
Results bellow

Links to Chart-Studio:
https://chart-studio.plotly.com/~galvisgilberto/4030/#/
https://chart-studio.plotly.com/~galvisgilberto/4032/#/
https://chart-studio.plotly.com/~galvisgilberto/4034/#/
https://chart-studio.plotly.com/~galvisgilberto/4036/#/
https://chart-studio.plotly.com/~galvisgilberto/4038/#/
https://chart-studio.plotly.com/~galvisgilberto/4040/#/
https://chart-studio.plotly.com/~galvisgilberto/4042/#/
https://chart-studio.plotly.com/~galvisgilberto/4044/#/
https://chart-studio.plotly.com/~galvisgilberto/4046/#/
https://chart-studio.plotly.com/~galvisgilberto/4048/#/
https://chart-studio.plotly.com/~galvisgilberto/4052/#/
https://chart-studio.plotly.com/~galvisgilberto/4054/#/


Yandex Music not working

Hello.
C:\Users\RED\AppData\Roaming\AIMP\aimp_youtubedl>youtube-dl.exe https://music.yandex.ru/album/11817010/track/70116183 -v
[debug] System config: []
[debug] User config: []
[debug] Custom config: []
[debug] Command-line args: ['https://music.yandex.ru/album/11817010/track/70116183', '-v']
[debug] Encodings: locale cp1251, fs mbcs, out cp866, pref cp1251
[debug] youtube-dl version 2020.07.28
[debug] Python version 3.4.4 (CPython) - Windows-10-10.0.19041
[debug] exe versions: none
[debug] Proxy map: {}
[yandexmusic:track] 70116183: Downloading track JSON
[yandexmusic:track] 70116183: Downloading track location url JSON
[yandexmusic:track] 70116183: Downloading track location JSON
ERROR: An extractor error has occurred. (caused by KeyError('storageDir',)); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.
Traceback (most recent call last):
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpq2whuxta\build\youtube_dl\extractor\common.py", line 530, in extract
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpq2whuxta\build\youtube_dl\extractor\yandexmusic.py", line 112, in _real_extract
KeyError: 'storageDir'
Traceback (most recent call last):
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpq2whuxta\build\youtube_dl\extractor\common.py", line 530, in extract
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpq2whuxta\build\youtube_dl\extractor\yandexmusic.py", line 112, in _real_extract
KeyError: 'storageDir'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpq2whuxta\build\youtube_dl\YoutubeDL.py", line 797, in extract_info
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpq2whuxta\build\youtube_dl\extractor\common.py", line 543, in extract
youtube_dl.utils.ExtractorError: An extractor error has occurred. (caused by KeyError('storageDir',)); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.

I confirm. I have this problem too. OS Archlinux.
youtube-dl --verbose https://music.yandex.ru/album/11522234/track/69096002

[debug] System config: []
[debug] User config: []
[debug] Custom config: []
[debug] Command-line args: ['--verbose', 'https://music.yandex.ru/album/11522234/track/69096002']
[debug] Encodings: locale UTF-8, fs utf-8, out utf-8, pref UTF-8
[debug] youtube-dl version 2020.09.06
[debug] Python version 3.8.5 (CPython) - Linux-5.4.63-1-lts-x86_64-with-glibc2.2.5
[debug] exe versions: ffmpeg 4.3.1, ffprobe 4.3.1, rtmpdump 2.4
[debug] Proxy map: {}
[yandexmusic:track] 69096002: Downloading track JSON
[yandexmusic:track] 69096002: Downloading track location url JSON
[yandexmusic:track] 69096002: Downloading track location JSON
ERROR: An extractor error has occurred. (caused by KeyError('storageDir')); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; see  https://yt-dl.org/update  on how to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.
Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/youtube_dl/extractor/common.py", line 530, in extract
    ie_result = self._real_extract(url)
  File "/usr/lib/python3.8/site-packages/youtube_dl/extractor/yandexmusic.py", line 112, in _real_extract
    storage = track['storageDir'].split('.')
KeyError: 'storageDir'
Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/youtube_dl/extractor/common.py", line 530, in extract
    ie_result = self._real_extract(url)
  File "/usr/lib/python3.8/site-packages/youtube_dl/extractor/yandexmusic.py", line 112, in _real_extract
    storage = track['storageDir'].split('.')
KeyError: 'storageDir'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/youtube_dl/YoutubeDL.py", line 797, in extract_info
    ie_result = ie.extract(url)
  File "/usr/lib/python3.8/site-packages/youtube_dl/extractor/common.py", line 543, in extract
    raise ExtractorError('An extractor error has occurred.', cause=e)
youtube_dl.utils.ExtractorError: An extractor error has occurred. (caused by KeyError('storageDir')); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; see  https://yt-dl.org/update  on how to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.

I confirm. I have this problem too.
youtube-dl --verbose https://music.yandex.ru/album/540508/track/4878838
[debug] System config: []
[debug] User config: []
[debug] Custom config: []
[debug] Command-line args: ['--verbose', 'https://music.yandex.ru/album/540508/track/4878838']
[debug] Encodings: locale cp1251, fs mbcs, out cp866, pref cp1251
[debug] youtube-dl version 2020.09.06
[debug] Python version 3.4.4 (CPython) - Windows-10-10.0.19041
[debug] exe versions: none
[debug] Proxy map: {}
[yandexmusic:track] 4878838: Downloading track JSON
[yandexmusic:track] 4878838: Downloading track location url JSON
[yandexmusic:track] 4878838: Downloading track location JSON
ERROR: An extractor error has occurred. (caused by KeyError('storageDir',)); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.
Traceback (most recent call last):
  File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\common.py", line 530, in extract
  File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\yandexmusic.py", line 112, in _real_extract
KeyError: 'storageDir'
Traceback (most recent call last):
  File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\common.py", line 530, in extract
  File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\yandexmusic.py", line 112, in _real_extract
KeyError: 'storageDir'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\YoutubeDL.py", line 797, in extract_info
  File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\common.py", line 543, in extract
youtube_dl.utils.ExtractorError: An extractor error has occurred. (caused by KeyError('storageDir',)); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.

also with cookies.txt
youtube-dl https://music.yandex.ru/album/540508/track/4878838 --cookies cookies.txt
[yandexmusic:track] 4878838: Downloading track JSON
[yandexmusic:track] 4878838: Downloading track location url JSON
[yandexmusic:track] 4878838: Downloading track location JSON
ERROR: An extractor error has occurred. (caused by KeyError('storageDir',)); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.

the same here
[debug] System config: []
[debug] User config: []
[debug] Custom config: []
[debug] Command-line args: ['--verbose', '--username', 'PRIVATE', '--password', 'PRIVATE', 'https://music.yandex.ru/album/4923330']
[debug] Encodings: locale cp1252, fs mbcs, out cp437, pref cp1252
[debug] youtube-dl version 2020.09.06
[debug] Python version 3.4.4 (CPython) - Windows-10-10.0.17763
[debug] exe versions: none
[debug] Proxy map: {}
[yandexmusic:album] 4923330: Downloading album JSON
[download] Downloading playlist: Billie Eilish - dont smile at me (2017)
[yandexmusic:album] playlist Billie Eilish - dont smile at me (2017): Collected 9 video ids (downloading 9 of them)
[download] Downloading video 1 of 9
[yandexmusic:track] 36083710: Downloading track JSON
[yandexmusic:track] 36083710: Downloading track location url JSON
[yandexmusic:track] 36083710: Downloading track location JSON
ERROR: An extractor error has occurred. (caused by KeyError('storageDir',)); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.
Traceback (most recent call last):
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\common.py", line 530, in extract
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\yandexmusic.py", line 112, in _real_extract
KeyError: 'storageDir'
Traceback (most recent call last):
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\common.py", line 530, in extract
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\yandexmusic.py", line 112, in _real_extract
KeyError: 'storageDir'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\YoutubeDL.py", line 797, in extract_info
File "C:\Users\dst\AppData\Roaming\Build archive\youtube-dl\ytdl-org\tmpquf06fea\build\youtube_dl\extractor\common.py", line 543, in extract
youtube_dl.utils.ExtractorError: An extractor error has occurred. (caused by KeyError('storageDir',)); please report this issue on https://yt-dl.org/bug . Make sure you are using the latest version; type  youtube-dl -U  to update. Be sure to call youtube-dl with the --verbose flag and include its complete output.

same on Linux

I confirm. I have this problem too. Win 10

Fix.
File ./youtube-dl/extractor/yandexmusic.py  Line: 112-113
Find:
storage = track['storageDir'].split('.')
f_url = 'http://%s/get-mp3/%s/%s?track-id=%s ' % (fd_data['host'], key, fd_data['ts'] + fd_data['path'], storage[1])

Replace to:
storage = track['realId']
f_url = 'http://%s/get-mp3/%s/%s?track-id=%s ' % (fd_data['host'], key, fd_data['ts'] + fd_data['path'], storage)

repack youtube-dl binary with new yandexmusic.py


Adds minimum requirements

Which issue(s) this PR addresses:

Closes #243

/approve
/ok-to-test

/lgtm

/lgtm


Restrict scope of intial release shadow JCL scope

Earlier, we were attempting to contain the entire scope of any classes we wanted to support in the shadow JCL.  Some omissions were required, earlier on, due to:  references to classes not supported (ie Stream) or functionality which was incompatible with the blockchain (ie Math.random()).
This still leaves a very large surface area which must be tested and secured, despite probably not being relevant to the blockchain contracts (consider all that Character can do regarding specialized unicode parsing, for instance).
Instead, this item will track any discussion around changing our philosophy to assume exclusion from the AVM shadow JCL, unless a case can be made for why a given method should be included.
It is a safer position to start with a restricted library and only open that up in future hard-forks instead of risk inconsistencies or errors due to exposing a large class library which couldn't be as exhaustively tested.

Note that we should also do a basic audit of whether we correctly map/handle all the exceptions thrown from the underlying JDK calls while verifying what is left in scope.

During the review, usage of internal methods in final classes should be evaluated.


UX issues

Add Room button doesnt look like Add, looks like groups or contact button
()you could just put a simple + sign next to titles of Groups and Contacts)

Once I hit info button, info displays on a row that is hidden under row name

its not obvious which chatroom i am in

avatars as Initials capitals letters: are blurry + could have random colours assigned insteas of grey

when you click on Close group, the arrow also should be clikable

its not clear how to filter the contacts... maybe put 2 dropdown side by side? Its confusing having icons to the right that change something to their left...

Add Room button doesnt look like Add
Fixed in converse 4.0.1

Once I hit info button, info displays on a row that is hidden under row name
Fixed in converse 4.0.1

Maybe add a bgcolor on the row to the left
Fixed in converse 4.0.1

avatars as Initials capitals letters: are blurry + could have random colours assigned insteas of grey
Fixed in Pade version 0.5.2

having the trash icon next to the contact.. isnt it too much? I would put it in the profile of the person..
Fixed in converse 4.0.1


[JOSS Review] Comments on Modular structure and Optimized Version

https://github.com/openjournals/joss-reviews/issues/5160#issuecomment-1453048277

This issue shall resolve the following comments from https://github.com/openjournals/joss-reviews/issues/5160#issuecomment-1453048277:

Modular structure

[ ]   Since most scientific software is modular, I would request the author to elaborate more on the modularity of QuaCa and discuss any intentional choices made from a software design perspective to make the package extensible. This was briefly mentioned in lines 67-73, but a more clear justification would be helpful.

Optimized version

[ ] Though the authors have cited MEEP, I would like the authors to clearly describe the current state of other open-source packages and the exact gap that QuaCa is trying to address.

[ ] Specifically, they have mentioned that QuaCa uses a numerically optimized version of $F_{\mathrm fric}$. I would request the authors briefly describe the approach that is unique to QuaCa when compared with other FDTD packages that offer subroutines to calculate the Casimir force.

[ ] Additionally, I would request the authors to comment on the applicability of the implemented optimizations and limitations of the same, if any.

Concerning point 1.
We replaced the sentence in line 67
"On the other hand (ii), we have chosen an implementation strategy where any of the physical quantities, such as the permittivity, the polarizability, the Green tensor or the power spectrum, are assigned to individual objects in the package. These can be tested, replaced, computed or used independently. By virtue of this modular structure, the QuaCa package can be easily adapted to different geometries and materials, parts of the code can be used as a library performing a subroutine in a larger project, or it can even be extended to compute other observables of fluctuation-induced light-matter interactions."

with
"On the other hand (ii), we have chosen a modular implementation strategy guided by physical principles. We assigned each meaningful physical observable in the setup to individual objects in the package which can be tested, replaced, computed or used independently. Irrespective of the particular intricacies that come with the calculation of quantum friction (i), the code structure reflects the individual building blocks of the physical setup, i.e. the atom (polarizability), the electromagnetic vacuum field in the presence of the given geometry (Green tensor) as well as the respective material properties (permittivity). By virtue of this modular structure, the QuaCa package can be easily adapted to different geometries and materials in the calculation of quantum friction, (physically relevant) objects of the code can be used as a library performing a subroutine in a larger project, or they can be used to compute other observables of fluctuation-induced light-matter interactions."

Concerning point 2.
We are not aware of any open-source software that is designed to compute the steady-state atom-surface quantum friction, other than brute force implementations of the coupled integrals occurring in $F_{\mathrm{fric}}$. As explained in lines 60-66, previous code projects that focus on other fluctuation-induced effects are, to the best of our knowledge, not directly applicable to the situation.

Concerning point 3.
As in point 2., other open-source software can not, we think, be directly applied to the situation of steady-stae atom-surface quantum friction. The term "optimized" in the draft refers to a particular analytical form of $F_{\mathrm{fric}}$, "where some nested integrals decouple" (line 64), which allows for an optimized performance with respect to a brute-force implementation. We acknowledge that this can lead to a misunderstanding. To make it more clear, we have modified the sentence in line 64 which now reads:
"Here, QuaCa uses an analytically equivalent version of $F_{\mathrm{ fric}}$, which is particularly suited for numerical computations. We decouple nested integrals and take explicit care of the occurring poles. This allows for an efficient and reliable computation of the force. For details of the procedure, we refer to Ref<EMAIL_ADDRESS>

Concerning point 4.
The in point 3 (and the paper) described "optimizations" have made a numerical calculation of $F_{\mathrm{fric}}$, in the situation described in the paper, possible in the first place. By implication, the QuaCa package is somewhat limited to an efficient calculation of steady-state quantum friction. Due to the modular structure driven by physical arguments, we may regain some flexibility, since many other fluctuation-induced forces can be computed from the same building blocks. We try to demonstrate this flexibility by additionally providing an executable for computing atomic decays rates. However, we have no intention to be in competition with other open-source software here. The strength of the package is the computation of (nonequilibrium) steady-state atom-surface quantum friction.

looks good to me :)

Received positive feedback from the review.


[Aio] Disable testing AsyncIO for versions that it doesn't exist yet

The CI build prod:grpc/core/master/linux/grpc_interop_matrix is failing due to the matrix trying to test pythonasyncio in all previous versions. By explicitly specify the runtime, we might be able to stop the failure.

prod:grpc/core/experimental/linux/grpc_interop_matrix_adhoc


add balancing for uncertain matrices

Codecov Report

Merging #85 (35166b7) into master (2db5d79) will increase coverage by 0.05%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #85      +/-   ##
==========================================
+ Coverage   90.04%   90.09%   +0.05%
==========================================
  Files          18       18
  Lines        2601     2605       +4
==========================================
+ Hits         2342     2347       +5
+ Misses        259      258       -1

Impacted Files
Coverage Δ

src/uncertainty_interface.jl
84.17% <100.00%> (+0.21%)
:arrow_up:

... and 1 file with indirect coverage changes
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.


FabricProxyLite support

As discussed on discord, here's a funky fix for #56  - thanks for all the helpful input, especially Tim203, Camotoy, and Konica!
I'm implementing this workaround to make sure Velocity servers with modern player info forwarding, send-floodgate-data & global linking set to true can properly send players & forward data to Fabric server backends with FabricProxyLite and Floodgate-fabric installed.
To fix the issue of too long handshake packets, a mixin extends the limit of 255 to the Short.MAX_VALUE when the mod fabricproxylite is present, as this fix isn't needed otherwise.
I've tested this with a Velocity proxy + Fabric 1.19.3 server - worked fine with a linked bedrock player. I haven't tested java players & unlinked bedrock players yet; but since those worked without this fix i couldn't imagine this messing with it; will test it later today though.

here's a .zip with the built floodgate-fabric.jar if anyone wants to test it -
floodgate-fabric.zip

Tested with unlinked bedrock account, and unlinked java account, and linked java account, and linked bedrock account - this thingy works!
as suggested by Camotoy; there's now a mixinconfigplugin to only load the hacky new mixin when the mod FabricProxyLite is present.
Finally, i think i was able to make the mixin less of a wildcard now; as it still works, i think i got it down? not 100% sure on if that's the best it can be though.
Also changed the name of the function in the mixin to properly reflect on what it is doing.

new floodgate-fabric jar incase you want to further test this:
floodgate-fabric (2).zip

new floodgate-fabric jar incase you want to further test this: floodgate-fabric (2).zip

sadly linked bedrock players, still not able to connect on my server :(
com.velocitypowered.proxy.util.except.QuietRuntimeException: The connection to the remote server was unexpectedly closed.
will this build only work for a specific version ??
as it works ok with plain bedrock users, just not users that are linked...
(also, probably not related to this/floodgate ?? but oddly, others can see the selected skin ok, but doing a "selfie" i have the default alex/steve skin)

Do you have FabricProxyLite installed & configured with Modern forwarding?
If not, what's your setup?

As for the skin issue, that's just https://github.com/GeyserMC/Geyser/issues/3540, and that's thanks to 1.19.60

Do you have FabricProxyLite installed & configured with Modern forwarding from Velocity? If not, what's your setup?
yes velocity, (velocity-proxy-3.1.2-SNAPSHOT with modern forwarding) with FabricProxy-Lite-2.3.0.jar on the fabric servers
Additionally, I've only tested this on 1.19.3 fabric; although 1.19.2 might work
yeah maybe its that ? ...

Just checked, it won't work on 1.19.2. I could make it work, but it would require adding another mixin for that version.. I'm not sure if it's even possible to add multiple mixins that target different versions in one .jar
Tbh, I might just end up making a 1.19.1/2 standalone mod with just that fix, as I could use it for my servers. However, that brings up the bigger issue that floodgate-fabric only supports the latest version and has no releases for older versions

Just checked, it won't work on 1.19.2. I could make it work, but it would require adding another mixin for that version.. I'm not sure if it's even possible to add multiple mixins that target different versions in one .jar
Tbh, I might just end up making a 1.19.1/2 standalone mod with just that fix, as I could use it for my servers. However, that brings up the bigger issue that floodgate-fabric only supports the latest version and has no releases for older versions

arrr ok, thankyou for checking ! ..
sasly theres still a few mods im waiting for updates on to upgrade to 1.19.3
(i may wait it out untill i upgrade, as i have viaversion on proxy. so 1.19.3 clients can connect atm)

handshakelengthadjust-1.0.0.zip
@gadget78 try adding this (keep the normal version of floodgate-fabric). It's a lil mod i quickly threw together with this mixin, but for 1.19.1/1.19.2 - it's a pain to upgrade fabric servers xD
if this doesn't work either, feel free to contact me on discord (onebeastchris#7281)

also, how were you able to test the build that i uploaded here? that whole floodgate-fabric build is 1.19.3 only
if this doesn't work either, feel free to contact me on discord (onebeastchris#7281)

odd that it didnt complain, you would think it would,
so, just checked the logs, and couldnt find anyrefferances to it,
so checked the files where there etc, where i realized the  files are all .zip, DOH ...
so that would be why it didnt work, or have have any referances lol...

handshakelengthadjust-1.0.0.zip @gadget78 try adding this (keep the normal version of floodgate-fabric). It's a lil mod i quickly threw together with this mixin, but for 1.19.1/1.19.2 - it's a pain to upgrade fabric servers xD

Thankyou for this, just gave this a whirl !
i have confirmed that this IS running.. lol
[main/INFO]: FabricProxy-Lite is present, we will mixin into the handshake length!
but bedrock/floodgate uses cannot still connect ...
(well in logs they connect then get disconnect, with a error on the player screen of forwarding issues...


unknown type and function name errors while building examples

I'm assuming this is some sort of a version mismatch
Steps

make minimal

  MKDIR    .output
  MKDIR    .output/libbpf
  LIB      libbpf.a
  MKDIR    /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/bpf.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/btf.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/libbpf.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/libbpf_errno.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/netlink.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/nlattr.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/str_error.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/libbpf_probes.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/bpf_prog_linfo.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/btf_dump.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/hashmap.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/ringbuf.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/strset.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/linker.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/gen_loader.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/relo_core.o
  CC       /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/usdt.o
usdt.c:566:56: error: unknown type name 'GElf_Nhdr'; did you mean 'GElf_Shdr'?
  566 | static int parse_usdt_note(Elf *elf, const char *path, GElf_Nhdr *nhdr,
      |                                                        ^~~~~~~~~
      |                                                        GElf_Shdr
usdt.c: In function 'collect_usdt_targets':
usdt.c:583:9: error: unknown type name 'GElf_Nhdr'; did you mean 'GElf_Shdr'?
  583 |         GElf_Nhdr nhdr;
      |         ^~~~~~~~~
      |         GElf_Shdr
usdt.c:615:23: error: implicit declaration of function 'gelf_getnote'; did you mean 'gelf_getsym'? [-Werror=implicit-function-declaration]
  615 |         while ((off = gelf_getnote(data, off, &nhdr, &name_off, &desc_off)) > 0) {
      |                       ^~~~~~~~~~~~
      |                       gelf_getsym
usdt.c:621:23: error: implicit declaration of function 'parse_usdt_note'; did you mean 'parse_usdt_spec'? [-Werror=implicit-function-declaration]
  621 |                 err = parse_usdt_note(elf, path, &nhdr, data->d_buf, name_off, desc_off, &note);
      |                       ^~~~~~~~~~~~~~~
      |                       parse_usdt_spec
usdt.c: At top level:
usdt.c:1089:56: error: unknown type name 'GElf_Nhdr'; did you mean 'GElf_Shdr'?
 1089 | static int parse_usdt_note(Elf *elf, const char *path, GElf_Nhdr *nhdr,
      |                                                        ^~~~~~~~~
      |                                                        GElf_Shdr
cc1: all warnings being treated as errors
make[1]: *** [Makefile:131: /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output//libbpf/staticobjs/usdt.o] Error 1
make: *** [Makefile:86: /home/akshat/wrkspc/libbpf-bootstrap/examples/c/.output/libbpf.a] Error 2

Other Details

pkg-config libelf --cflags

-I/nix/store/aa36qd0ahm65pjpx1xcp645rcqafwarr-libelf-0.8.13/include/libelf -I/nix/store/aa36qd0ahm65pjpx1xcp645rcqafwarr-libelf-0.8.13/include

pkg-config zlib --cflags

-I/nix/store/w99lhkib7z3hx9lcmlz17apzcm1qpsr7-zlib-1.2.13-dev/include

uname -a

Linux xps 6.3.8-200.fc38.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jun 15 02:15:40 UTC 2023 x86_64 GNU/Linux

Closing this issue. I was using the libelf package to build this but should have used elfutils package.

@humancalico  I'm also facing the same issue while I try to build another repo.
I invoke build by using make.
It throws
pegasus@pegasus:~/Documents/eBPF/xdp-tutorial$ make -B
clang: 19.0.0git (https://github.com/llvm/llvm-project.git 815644b4dd882ade2e5649d4f97c3dd6f7aea200)
libbpf support: submodule
ELF support: yes
zlib support: yes
libxdp support: submodule
Configuring libxdp to use our libbpf submodule
Found clang binary 'clang' with version 19 (from 'clang version 19.0.0git (https://github.com/llvm/llvm-project.git 815644b4dd882ade2e5649d4f97c3dd6f7aea200)')
not using emacs:
using bpftool v7.3.0
libbpf support: custom v1.2.0
  perf_buffer__consume support: yes
  btf__load_from_kernel_by_id support: yes
  btf__type_cnt support: yes
  bpf_object__next_map support: yes
  bpf_object__next_program support: yes
  bpf_program__insn_cnt support: yes
  bpf_program__type support: yes
  bpf_program__flags support: yes
  bpf_program__expected_attach_type support: yes
  bpf_map_create support: yes
  perf_buffer__new_raw support: yes
  bpf_xdp_attach support: yes
  bpf_map__set_autocreate support: yes
  bpf_prog_test_run_opts support: yes
  bpf_xdp_query support: yes
zlib support: yes
ELF support: yes
pcap support: yes
secure_getenv support: yes

lib

  libbpf
    CC       install/lib/libbpf.a
usdt.c:566:56: error: unknown type name ‘GElf_Nhdr’; did you mean ‘GElf_Shdr’?
  566 | static int parse_usdt_note(Elf *elf, const char *path, GElf_Nhdr *nhdr,
      |                                                        ^~~~~~~~~
      |                                                        GElf_Shdr
usdt.c: In function ‘collect_usdt_targets’:
usdt.c:583:9: error: unknown type name ‘GElf_Nhdr’; did you mean ‘GElf_Shdr’?
  583 |         GElf_Nhdr nhdr;
      |         ^~~~~~~~~
      |         GElf_Shdr
usdt.c:615:23: error: implicit declaration of function ‘gelf_getnote’; did you mean ‘gelf_getsym’? [-Werror=implicit-function-declaration]
  615 |         while ((off = gelf_getnote(data, off, &nhdr, &name_off, &desc_off)) > 0) {
      |                       ^~~~~~~~~~~~
      |                       gelf_getsym
usdt.c:621:23: error: implicit declaration of function ‘parse_usdt_note’; did you mean ‘parse_usdt_spec’? [-Werror=implicit-function-declaration]
  621 |                 err = parse_usdt_note(elf, path, &nhdr, data->d_buf, name_off, desc_off, &note);
      |                       ^~~~~~~~~~~~~~~
      |                       parse_usdt_spec
usdt.c: At top level:
usdt.c:1089:56: error: unknown type name ‘GElf_Nhdr’; did you mean ‘GElf_Shdr’?
 1089 | static int parse_usdt_note(Elf *elf, const char *path, GElf_Nhdr *nhdr,
      |                                                        ^~~~~~~~~
      |                                                        GElf_Shdr
cc1: all warnings being treated as errors
make[2]: *** [Makefile:131: staticobjs/usdt.o] Error 1
make[1]: *** [Makefile:42: install/lib/libbpf.a] Error 2
make: *** [Makefile:27: lib] Error 2

Can you guide me how to fix it?

It looks like you don't have recent enough libelf, but seems like you are working with libxdp project, so I suggest asking question there as well, maybe others ran into this and solved it already.

@anakryiko
The issue is mainly with libbpf. I've asked there too.

I solved the issue. It was an issue with libelf. I downloaded a latest libelf version. Then Configured and installed it. libelf also had some dependency missing like specific versions of sqlite, libcurl, libarchive


[GLUTEN-8043] Use spark.shuffle.spill.diskWriteBufferSize if shuffle compression is disabled

Does hash shuffle writer or rss writer need to respect this config?

@jinchengchenghh The implementation detail of hash shuffle writer is quite different from Vanilla spark's, and we do not have an entry to support this config.
RSS writer doesn't spill to disks. It sends data to remote service when spill happens.


Separate merge buttons

In my team we mainly use squashing, but once in a while we have to do a merge commit or rebase. This sometimes causes accidents because when a team member switches their merge setting to do a merge commit, the next time they want to merge a PR by squashing, that setting is remembered and they accidentally merge all their commits to the branch. This could easily be avoided by laying out all buttons next to each other.
I took a quick shot at it and got the layout right, however the behaviour needs more work. When selecting from the dropdown, various things are changed in the DOM. I'm not sure how that would work when moving from a 2 step process to just 1 step.

This would be useful 👍

Our team also regularly experiences the issue described 👍

Our team needs this. I actually implemented this extension  in effort to fix this problem in that we always "squash" unless someone adds a label "DontSquash".
This forces squashing unless the label exists. Unfortunately github had a code change and the extension was brittle and doesnt work properly anymore. I'd love it if I can just suggest everyone switch to refined-github


[Feature] Add FMV to purchases index

Summary
Add FMV (fair market value) to Purchase index page
Why
It's useful info for at least one bank (lincoln)
Details

add a FMV column to the purchases index, after the amount spent  This will contain the total FMV for each purchase.

Criteria for completion
-[ ] purchases index has FMV column containing the total FMV for each purchase.
-[ ] tests that demonstrate that this feature works.

@cielf I'd be happy to take this one

Go for it!


crash when synchronizing with AFL

Hi
I'm trying to run in parallel angora and afl, since there's an option in the source code. But angora crashes.
Steps to reproduce:
wget http://xmlsoft.org/sources/libxml2-2.9.8.tar.gz
sudo apt-get install python-dev
sudo apt-get install libtool
cd libxml2-2.9.8
autoreconf --install
autoconf
CC=/path/to/afl-clang-fast ./configure --without-zlib --disable-shared
[...] compile for afl
reproduce the above but compile for angora.
then run:
timeout 24h /path/to/afl-fuzz -i in/ -o with_afl -S afl1 ./xmllint.afl @@
timeout 24h /path/to/angora/bin/fuzzer --input ./in/ --sync_afl --output with_afl/ -t ./xmllint.track -- ./xmllint.fast @@
2
ERROR angora::executor::executor > Crash or hang while tracking! -- Crash,  id: 0
Note: I don't think this has anything to do with libxml... it's just the first one I tried :)

seems the problem was because of the stack limit (ulimit -s) being set to unlimited on my machine. Setting it to 8092 fixed the problem. Not sure why...


CSS Caching

Hi there, so with installed bulma, bulma-heleprs and icons, after visiting page where I am using your library to display PDF, styling in entire application is messed up, so is there a way to prevent that by either not using that at all and providing my own style to PDFViewer component or some other solution you are suggesting?

you can remove bulma and provide your own css classes. You can check this example code & css classes


Move git refresh status task to long running task (Bug #9544)

Description of the Change
This PR addresses #9544. The issue here is that upon gaining focus, Atom spins off a new task to update the repository status. Profiling Atom during this time shows that there is a lengthy (~ 2 seconds on my machine, longer on others') delay on the rendering thread due to the child_process.fork(). This PR changes it so that each repository has its own there is a single long running task that receives a message upon needing to update repo status. This moves the overhead of the child_process.fork() into a single hit per repo (I am experiencing zero noticeable delay upon focus now).
Alternate Designs
An alternate design would be to have a single task that handled messages for all repositories. I didn't go this route as I didn't want to change the method signatures in the areas I touched. If we did it at the workspace level, we would need to allow for passing in a reference to the task. And potentially add a few .destroy() methods to the layer that housed the task. I figure that it would be rare to have a number of repositories open at any given time that would cause negative effects due to the number of helper tasks alive.
I managed to implement the alternate design without making a change to the API
Why Should This Be In Core?
This fixes an issue within core itself.
Benefits
Usability of Atom is increased as you spend less time per day waiting on a blocked rendering thread.
Possible Drawbacks
If you have a high number of repos open on Atom, you will have a high number of child processes.
n/a
Applicable Issues
n/a

Awesome!  Looks like there's quite a few lint and test failures though - could you please address those?

Yeah sorry about that. Forgot to run the lint script. Fixing now =]

Finally fixed the tests =]. Seems that window.requestIdleCallback() was causing the tests to fail. Not sure why though. The experience was useful as I found a few areas where tests weren't cleaning themselves up correctly, fixed that too. All tests are passing locally and in the CIs, with the exception of AppVeyor which seems to be having issues right now (same apm issue on other people's builds too)

@50Wliu, what is the usual turnaround time in a PR for Atom?

It depends.  There's a lot of changes happening right now, so I can't give you an estimate.  It is in the todo list however. (I know that's not the answer you were looking for, but it's the best I can give.)

Thanks for the PR, and thanks for being patient as we worked through it!
There are a few concerns I have regarding this change as it stands. Items 1 and 2 are addressable, but 3 and 4 I'm not sure about for the short term. Definitely open to feedback especially from @smashwilson and @kuychaco.

It doesn't look like we do any handling of the status handler instance if it crashes unexpectedly — we'd want to detect this and clear the appropriate state in the helper so the next call to refreshStatus properly restarts it.
It also doesn't look like we do any handling in the task itself of any errors. I know this was all just copy/pasted from the old code, but I think wrapping at least the call to repo.release() in a try/finally would be a good idea.
This creates a new long-running sidecar process for every Atom window. Probably not the biggest deal, but the GitHub package already does this for its own Git handling; a proper solution to the problem being addressed here (and, in general, for providing Git information to other parts of Atom) is to expose a service from the GitHub package that core and other packages can consume. Unfortunately this isn't trivial and probably not a viable short-term solution.
The Task API uses ChildProcess#send for communication, which (as we discovered while working on the GitHub package) has a bug that causes a quadratic growth in time as the size of the input grows. Eventually the version of Node contained in Electron will provide a fix for this, but in the meantime we were still seeing a lot of UI jank and freezing during large repositories simply due to the size of the output when calling status. @kuychaco fixed this by using a sidecar Electron process/IPC instead of native Node IPC — again, exposing a service from the GitHub package, which already has this feature, makes the most sense to address this.

Thanks for the review! I have updated with changes addressing items 1 and 2. I'm unsure of how to move forward with items 3 and 4 however.

Anything else I can add to the PR? I'm eager to work on this to address any concerns. It seems like the bug im addressing is getting a lot of attention from people this PR could help.

What's the holdup on merging this?

I'm still concerned about the remaining issues I commented on above. Pinging @atom/core for additional 💭 s around this feature.

No worries, if it gets merged, I want it to be the right code for the job =]

My opinion, based on 3 and 4 in @BinaryMuse's comment, is that we should hold off merging this until the GitHub package exposes a service it can call. We've begun thinking about the right way to implement that.

Abandoning until #1089 is resolved. The new PR at that time will likely share little code with this.

Alright, after considerable discussion with the rest of the team, I'm opting to reopen this PR, get it up to date with the new changes in https://github.com/atom/atom/pull/15415, and get it merged in. Apologies for the back and forth as we've explored the various ways to fix the underlying issue, and thanks again @Xapphire13 for the PR.


Update apigee-x-core to allow consumer_accept_list as a param

Quality of life change in case others use seperate projects for their Loadbalancers to route to apigee in apigee-x-core  tf module
What's changed, or what was fixed?

add consumer_accept_list to apigee-x-core module

update docs to reflect new field

[x] I have run all the tests locally and they all pass.

[x] I have followed the relevant style guide for my changes.

Thanks @g-greatdevaks, I dont have the power to merge, would you be able to do it?

@mohaldu - Please use Release v0.17.0 for the latest changes.


Rename 'master' branch to 'main'

Is your feature request related to a problem? Please describe.
Using the name 'master' for the main branch of the repository has become insulting and offensive to some. The industry as a whole is shifting to using 'main' as the name of the main branch in GitHub repositories, and GitHub has even made it the new default name when you create a new repository.
Describe the solution you'd like
I'm suggesting that the Azure Bicep project shift to using 'main' as the name of the primary branch within the repository.

Is this assigned?

If not, can I take?

I'm fine with anyone picking it up, and it would be great to get this changed. I want @anthony-c-martin / @majastrz to take a look first as I'm guessing our build systems might be depending on this being called master so we should inventory what the change requires.

@olsenme Unfortunately this is going to require administrator rights on this repo to make the change. I'm going to get this done shortly. If there are any other open issues you'd like to help out with, please let us know!

I've made this change now. Thank you @crpietschmann for pointing this out!
For anyone who has the repo checked out locally still referencing the 'master' branch, you will need to run the following to use 'main' instead:
# rename your local 'master' branch to 'main'
git branch -m master main
# configure the local 'main' branch to track the remote 'main' branch
git branch main --set-upstream-to origin/main


Autohide Menu for cleaner fullscreen closes #437

Resolving issues #437. Autohiding the electron menu makes fullscreen clean on windows. Menu can be accessed at anytime by pressing the 'Alt' key

Thanks for the contribution. Lets get this merged


pysal.cg.sphere.fast_knn bug

Hello, I wanted to use this function, but I read the source code and I believe I found a bug:
pts = numpy.array(pts)
kd = scipy.spatial.KDTree(pts)
d, w = kd.query(pts, k + 1)

I can't understand how this is supposed to work while scipy.spatial.KDTree supports cartesian coordinates and NOT circular. Mapping from a sphere to a plane can make two close points very distant leading to wrong answer.
Moreover calculating distance directly from (lon, lat) coordinates using euclidean metric can lead to wrong results (it can mess the order of closest points.

Yes, that is true. To do the knn search using arc distances in PySAL see Arc_KDTree.


Fix setting the emails subject a second time with an undefined variable

In the \Concrete\Core\Mail\Service::load() method, the emails subject is set again, with for the most cases, a not defined variable.
If the subject of a mail was set like the example below, the load() method will override the value of the subject again. The $subject may or may not be set with the extract function  shown here.
If the Mail\Service class has a proper setter for the Subject, which it does, it should be the only way in setting the emails subject.
$mailHelper = $app->make('helper/mail')
$mailHelper->to('some@person.io);
// Set Subject
$mailHelper->setSubject('Some Title');
// Subject would be overridden under certain circumstances
$mailHelper->load('my_mail_template');

This would break existing code that sets the subject in the templates.
What about using this code?
if (isset($subject)) {
    $this->subject = $subject;
}

the Mail\Service class has a proper setter for the Subject, which it does, it should be the only way in setting the emails subject.

This would also be true for the body, isn't it?

What about using this code?
if (isset($subject)) {
    $this->subject = $subject;
}

@mlocati Jepp, you're right. (I hate brocken code. )😄 I'll the pull request with your solution.

This would also be true for the body, isn't it?

It depends on how you see it. I always saw the email template just being responsible only for the email body. But giving it a second thought, the $subject in the load() method has its justification.


[PowerToys Run] Which folders does it search? I'd like to customize them!

Summary of the new feature/enhancement
I'd like to know how to control the folders that Run searches for matches. Currently even used it to launch scripts (despite that folder being contained in %PATH%). It would be nice to have more control over the list of folders that it scans...

@mbaas2 Run is leveraging indexer to populate results. You can customize them in "Indexing Options" from Control Panel.

Thanks!


Register address top bit

In RV32E mode the RTL clears the top bit of all register addresses for all purposes. The Sail does not do this, creating the following issues:

Attempts to read or write from a register >= 16 is an internal error in the Sail.
handle_cheri_reg_exception(..., cs1) will put cs1 into MTVAL with its top bit potentially set, unlike in the RTL. This happens in

LoadCapImm/StoreCapImm
ext_data_get_addr as auth_idx
CJALR

CSpecialRW checks if cs1 = zeros(). This should presumably also fail if cs1 = 16.

I am of the opinion that this is a specification bug, so I would have the Sail force the top bit of the register indices to zero as well.

@rmn30 let me know what you think..

Yes, the Sail is lax about the unused register indexes. I guess it should raise Reserved Instruction exception if bit 4 is set in register operand?

If it would be useful I would be happy to prove the line numbers of everywhere in the Sail where I clear the top bit of a register index.
The decision is of course yours, but depending on how the exceptions are raised in the Sail there is the possibility for this to be a much harder to prove correctness of than the version with truncation as is already seen in the RTL.
If you do choose to raise an exception, ideally this would be done during decoding, or during some stage between decode and execute.

From an implementation point of view, it's much easier and performant to ignore the top register index bit rather than throwing an exception.

Yeah implementation-wise ignoring bit 4 is easier (that's why I did it ;) I think the verbal version of risc-v spec didn't really say what's supposed to happen in this case (running RV32I code on RV32E hardware). @rmn30, is there a sail model for RV32E or it's just us?

Yes, the Sail is lax about the unused register indexes. I guess it should raise Reserved Instruction exception if bit 4 is set in register operand?

Is that not what https://github.com/microsoft/cheriot-sail/commit/4185ba2e89087d4062dd0f5a7efa5ecd814b88de does?

I have checked in RTL changes in the decoder design (9a23c81) to generate illegal instruction exceptions when rd/rs1/rs2 address >=16.
@mndstrmr, this is a relatively involved change so if you could prioritize verifying this I'd really appreciate it.

Hi Kunjan,
I'm using the Cheri Ibex as part of the Sonata System. I ran into a problem  when register x26 was accessed and came across this Issue. I see (9a23c81) now will cause an error when this happens.
I was wondering if there is a reason for not replacing CheriLimit16Regs with the RV32E parameter? My understanding is that now the encoding of the opcode auicgp has been changed there is no longer a 16 register limit when Cheri is enabled, so tying CheriLimit16Regs to CHERIoTEn is maybe no longer appropriate?
Cheers

Hi Colin,
32-register is not an allowed configuration for CHERIoT (CHERIoTEn == 1 && cheri_pmode_i == 1), which is why in that mode the core always faults if it seems an attempt to access the upper 16 registers. It has to do with the arch and rtos design (e.g., spilling/scrubbing extra registers actually hurts performance and security). When pmode_i = 0 (RV32 mode) we do support both 16 and 32 registers (controlled by the RV32E parameter).
BTW I was running some verification in the background and it turns the earlier checkin didn't quite do what it supposed (still not generating exception when the upper registers are referred). The latest check in (5e4798f should fix it.
Thx

Hi Kunyan,
Thanks for the quick reply on this. Unfortunately, I'm on holiday at the moment, so can't enter into a proper discussion on this. I'm back on the 15/16-Jul. So will come back to you then. For now, thanks for the heads up about the 5e4798fhttps://github.com/microsoft/cheriot-ibex/commit/5e4798f67417bcf87c831c56b8980af0e5d3966c change.
Cheers,
Colin

From: Kunyan Liu @.>
Sent: 04 July 2024 01:38
To: microsoft/cheriot-ibex @.>
Cc: Colin Bates @.>; Comment @.>
Subject: Re: [microsoft/cheriot-ibex] Register address top bit (Issue #30)
Hi Colin,
32-register is not an allowed configuration for CHERIoT (CHERIoTEn == 1 && cheri_pmode_i == 1), which is why in that mode the core always faults if it seems an attempt to access the upper 16 registers. It has to do with the arch and rtos design (e.g., spilling/scrubbing extra registers actually hurts performance and security). When pmode_i = 0 (RV32 mode) we do support both 16 and 32 registers (controlled by the RV32E parameter).
BTW I was running some verification in the background and it turns the earlier checkin didn't quite do what it supposed (still not generating exception when the upper registers are referred). The latest check in (5e4798fhttps://github.com/microsoft/cheriot-ibex/commit/5e4798f67417bcf87c831c56b8980af0e5d3966c should fix it.
Thx
—
Reply to this email directly, view it on GitHubhttps://github.com/microsoft/cheriot-ibex/issues/30#issuecomment-2207677953, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BGFCAZ2G4ZEQDMGDMHDHXNLZKSKOTAVCNFSM6AAAAABF7G4HRSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBXGY3TOOJVGM.
You are receiving this because you commented.

I have checked in RTL changes in the decoder design (9a23c81) to generate illegal instruction exceptions when rd/rs1/rs2 address >=16.
@mndstrmr, this is a relatively involved change so if you could prioritize verifying this I'd really appreciate it.

Seems to be proving, thanks for the work. I do have local spec changes to help this, specifically I fail to decode instead of throwing Sail exceptions, which I am not convinced about: A store instruction would complete the store then throw an illegal instruction exception in Sail, but not in the RTL.

A CSR would mutate the CSR then throw an illegal instruction exception in Sail, but not in the RTL.

That is indeed be very strange and look like a bug in the current Sail specification. Failing to decode is preferable but we took the exception route to avoid having to make extensive changes to the upstream sail-riscv spec. I wonder if there are other instructions that are broken in this way? This would apply to  any instruction that has side-effects prior to writing the destination register for example jump and link, or store-conditional.


test_besttrack_ensemble test failing

The files in the output directory did not match those in the reference one.

If the reference files have not been updated since recent commits, then need to check make sure there is no mistake for the recent commits, assuming it was correct in the old implementation.

@zacharyburnettNOAA

the newest code seems to fix this problem by updating the dataframe setter and reference files


Rust Spanish Resources

What does this PR do?
Add resource(s)
For resources
Description
Basic learning resources for Rust programming language in Spanish.
The book Spanish translation, and a Microsoft basic course
Why is this valuable (or not)?
Many people are eager to learn Rust
How do we know it's really free?
The book is translated for the community. And Microsoft is offering this course for free.
For book lists, is it a book? For course lists, is it a course? etc.
Book.
Course
Checklist:

[x] Read our contributing guidelines.
[x] Search for duplicates.
[x] Include author(s) and platform where appropriate.
[x] Put lists in alphabetical order, correct spacing.
[x] Add needed indications (PDF, access notes, under construction).
[x] Used an informative name for this pull request.

Follow-up

Check the status of GitHub Actions and resolve any reported warnings!

please see CONTRIBUTING for info on how to list translators.

@eshellman Do you mean to include the translator name?

https://github.com/EbookFoundation/free-programming-books/blob/main/docs/CONTRIBUTING.md#creators

Thanks, and welcome to free-programming-books!


Add soft error stream for minidump-writer #31

This is a pretty simple change to allow Minidump-Writer to have the new soft error stream.
See: https://github.com/rust-minidump/minidump-writer/issues/31

Obviously the new stream needs to be actually integrated into the reader, but since the minidump reader will ignore streams it doesn't recognize, I consider that it can be done later once the minidump-writer code is done.