Use a memtest.0 found on the Internet to optionally boot into a memtest instead of kickstart

This has been tested and it boots a Dell R640 and R740 BIOS (not UEFI) with an memtest86+ v5.01 from 2015.
Controlled by touching a file in memtest86/(mynodes short hostname). The file is removed before booting into memtest which autostarts. After memtest is done the server is waiting for a keystroke (escape) to quit and resume booting.
memtest86 has preference over reinstall (if both files exist the server runs a memtest86). On next boot it will reinstall.
Left some commits here to show off some earlier testing that I couldn't get working with 7.5 ISO or USB images.
https://www.memtest86.com/features.htm says one has to get the "site edition" of memtest86 for the network (PXE) boot feature.

Some background details about what we are booting (and what needs to be copied onto a web server which the nodes can reach via http within the iPXE script):
According to a forum post by an mcb30 Lead Developer of iPXE memtest.0 is:
" This is memtest in the form of a PXE NBP: it has the advantage that you can return to iPXE afterwards (and report the test result, and potentially capture a screenshot of the memtest output and send it to a reporting server via HTTP POST)."
I checked in version 7.5 of memtest86+ src.tgz from the ISO and it does
not contain "pxe" anywhere in the code. It is possible to make a
similar patch to 7.5's Makefile and add the pxe.S file to build a memtest.0 but with that build the server did not manage to boot into memtest. Maybe it would work if one took in more of the patches from https://git.ipxe.org/people/mcb30/memtest.git/shortlog/refs/heads/pxe501

waiting for travis.


borgbackup: 1.2.8 -> 1.4.0

Description of changes
Various fixes, new BORG_EXIT_CODES=modern and borg version, documentation improvements.
Changelog:
https://github.com/borgbackup/borg/blob/1.4.0/docs/changes.rst

If you currently use borg 1.2.5+: no upgrade steps needed
(if you already did them when upgrading to that version, otherwise see below).

Upgrade notes: https://github.com/borgbackup/borg/blob/1.4.0/docs/changes.rst#upgrade-notes
Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[x] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[x] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[x] Tested basic functionality of all binary files (usually in ./result/bin/)
24.11 Release Notes (or backporting 23.11 and 24.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

Result of nixpkgs-review pr 324323 run on x86_64-linux 1

13 packages built:

borgbackup
borgbackup.dist
borgbackup.doc
borgbackup.man
borgmatic
borgmatic.dist
emborg (python311Packages.emborg)
emborg.dist (python311Packages.emborg.dist)
pika-backup
python312Packages.emborg
python312Packages.emborg.dist
vorta
vorta.dist

Is BORG_EXIT_CODES=modern helpful for the NixOS module?

https://github.com/borgbackup/borg/blob/1.4.0/docs/internals/frontends.rst#message-ids
https://www.freedesktop.org/software/systemd/man/latest/systemd.service.html#SuccessExitStatus=
SuccessExitStatus=100 (FileChangedWarning)

Is BORG_EXIT_CODES=modern helpful for the NixOS module?

<EMAIL_ADDRESS>freedesktop.org/software/systemd/man/latest/systemd.service.html
SuccessExitStatus=100 (FileChangedWarning)

https://github.com/NixOS/nixpkgs/blob/9f4128e00b0ae8ec65918efeba59db998750ead6/nixos/modules/services/backup/borgbackup.nix#L36-L45
I'd rather use the 100 in borgWrapper and treat it as everything as expected (just like the rc 1 for generic warnings).

Since BORG_EXIT_CODES=modern is opt-in, I suggest we merge this PR and have a follow-up PR for the NixOS side of things.

borg 1.4.x is the current stable version (https://www.borgbackup.org/releases/); should we backport it to release-24.05, after a few weeks perhaps?


mixed_instances_policy for managed node groups

If I understand correctly, currently it is only possible to specify mixed_instances_policy for self-managed worker groups. For managed node groups, it is only possible to set all instances to either ON_DEMAND or SPOT. As mixed_instances_policy is an option for managed node groups in AWS, it would be a nice feature to add.

nope, AWS Node groups have own api which on backend is using a AWS autoscaling, but you cannot influence it.
Any changes directly to autoscaling is just a unsupported by AWS hack
There was some similar discussion under https://github.com/terraform-aws-modules/terraform-aws-eks/issues/1525

Ah, that's too bad. At this point, I don't want to switch to worker groups so I'll probably manually edit the ASG, I guess. Well, thanks a lot for clarifying it!


V2: Nervos Docs V2 Project

Context
It takes too many steps for 1st time devs to: test, build, and deploy DApps on CKB
Goals:
A first-time developer can quickly:

Test, build, and deploy DApps (and Contracts)
Find any information and help

Good Dev Experiences: https://stripe.com/docs
Phase 1: Issue Tracker
UI

[x] WireFrame: https://github.com/nervosnetwork/docs.nervos.org/issues/209 - (02/22 Thu)
[x] High Fidelity
[x] Implement UI on Docasarus

DApp Examples

[x] Create 4 tutorials to teach developers how to get started building DApps: https://github.com/nervosnetwork/docs.nervos.org/issues/211 -

Dev Tools

[x] Short introduction to DApp development tools + link to these applications: Lumos, Kuai? https://github.com/nervosnetwork/docs.nervos.org/pull/242
[x] RPC endpoints: list the RFC endpoints and status. https://github.com/nervosnetwork/docs.nervos.org/pull/244

Local Environment Setup

[x] Simplify Dev Env setup: https://github.com/nervosnetwork/docs.nervos.org/issues/210
[x] Supported environment: Docker, Mac, Linux, (Windows)
[x] Update Tutorial to configure local dev environment

Ecosystem

[x] Embedd Explorer, Faucet, Address Creator into documentation https://github.com/nervosnetwork/docs.nervos.org/pull/253

Support

[x] How to do this? Docasuarus, Chat, Discrod, Email?  https://github.com/nervosnetwork/docs.nervos.org/pull/242

Phase 2
Contracts Examples

Update content for contract deployment

Mining
Team: @RetricSu, @yfeng2824

Deployment checklist: https://github.com/nervosnetwork/docs.nervos.org/issues/268

Deployed: docs.nervos.org


[blog] Proposed blog post clarifying communication channels

I like this!
utACK (I'm not an english lector).

ACK

@btcdrak, does 14336b3e7c9d01833e782a9067a6d082f9faebc3 include all the recent updates?

@btcdrak, does 14336b3 include all the recent updates?

yes.

Very well-written!

ACK

ACK https://github.com/btcdrak/website/commit/0eb428a707d11b602ba509899508bd42d3df237d

ACK

ACK, needs the Twitter account linked to.

ACK

NACK
Good idea, but I think the tone is still wrong.
Recognizing that moderation is needed, but not recognizing that people feel that free discussion of ideas has been censored is erring on the wrong side.  Heavy handed moderation is a cop out.
If this document is meant to in part represent my views, I think it should explicitly state that we think discussion of rule changes to Bitcoin should be encouraged and happen freely in public forums.  That is not what has happened on /r/bitcoin.

@morcos "I think it should explicitly state that we think discussion of rule changes to Bitcoin should be encouraged and happen freely in public forums." Agree with this.

You should also note that the only communication the core devs care about is the one between Blockstream's bank account and their own pockets.

ACK as a first statement. Personally I dislike both moderation and censorship.  But it has to be conceded that no moderation does tend to have the side effect of a low signal to noise with all of the forums, with whichever moderators.

Comment:  thanks for all the work on this -- I think that the recent, increasing trend of referring to "core" and the "core team" could have some drawbacks.   Since this is an open source project it makes sense to be especially careful in speaking as if one monolithic entity is or speaks for "Core".
I'd recommend against using phrases like "core thinks X" or "core agrees that Y should occur" - ultimately these statements are written by individuals and are not unanimous -- saying that "core" says something gives more of an impression of consensus or weight than might be accurate, gives inordinate power to channel controllers and can stifle minority opinions (or potentially highlight them depending on who does the posting).
I'd suggest as an alternative to use phrases like "several members of the core development team" or "the undersigned developers" etc.

@BruceFenton Meh, there are many, many issues on which there is nearly universal support from all active Bitcoin Core contributors. No need to complicate things uneccessarily.

@BruceFenton I agree. In addition it enhances the perception of a perpetuated "us vs them" debate. "The Core team" as opposed to whom?

For the whole thread, this is worth a read regarding moderation. http://lesswrong.com/lw/c1/wellkept_gardens_die_by_pacifism/ It points out that on a practical level, online communities can be killed by spam and low-effort content.

Personally I dislike both moderation and censorship. But it has to be conceded that no moderation does tend to have the side effect of a low signal to noise with all of the forums, with whichever moderators.

In fact, it could be argued that a low SNR is itself a form of censorship.
Of course it depends on your interpretation of free speech and liberty. It's a deep political issue which I don't want to go into fully, except to say that it's not obvious that the greatest freedom comes from just leaving things alone.
There is also this article which shows that it is possible for large moneyed groups to 'hack free speech' so to say, by simply paying people to sit in offices and comment. Although I don't think this has happened in bitcoin today. http://consciouslifenews.com/paid-internet-shill-shadowy-groups-manipulate-internet-opinion-debate/1147073/

@BruceFenton Aree with @TheBlueMatt here, and if people what to know for sure, refer them back to these pull-reqs to see who ACKed what.
This isn't unlike the question "How do changes get approved to go into Bitcoin Core?"

For this topic, this is a relevant blog post. http://lesswrong.com/lw/c1/wellkept_gardens_die_by_pacifism/ It makes the point that forum can indeed die by not moderating themselves.

Personally I dislike both moderation and censorship. But it has to be conceded that no moderation does tend to have the side effect of a low signal to noise with all of the forums, with whichever moderators.

In fact it could be said that a low SNR is itself a form of censorship. If somebody's voice is not heard because of spam and mass downvoting, they are censored same way as if their post is simply deleted.
Of course it depends on your interpretation of free speech and liberty. It's a philosophical question which I don't want to go into except to point out that it's not at all obvious that the greatest freedom comes from just leaving things alone.
Something else to think about is this report: http://consciouslifenews.com/paid-internet-shill-shadowy-groups-manipulate-internet-opinion-debate/1147073/ Which writes about entities that do nothing but pay people to sit in offices and comment on internet forums. I don't think this has happened in the bitcoin space, but it's worth knowing that its certainly possible for powerful groups to 'hack free speech' so to speak.
It's unfortunate that so many people are angry at the r/bitcoin moderation/censorship. I wonder if there could be some kind of middle ground. For example, continuing the moderation policy but also linking to alternate places to discuss like r/btc.

ACK 920704bae0d1928101aac204f83d8aa29ea779f2

ACK

ACK 920704bae0d1928101aac204f83d8aa29ea779f2

ACK https://github.com/btcdrak/website/commit/920704bae0d1928101aac204f83d8aa29ea779f2

ACK 920704b

ACK 920704b

ACK 920704b

ACK 920704b

Thanks for everyone's hard work on this. This will be posted live shortly.


Automatic private key renewal on decryption error

Current behavior:
If the private key cannot be decrypted or if it doesn't match the public key, then the private/public key pair is re-generated resulting in a new system ID and another entry in the public directory (reg2 system). The administrator doesn't notice it unless they require the system ID or look in their log files. This is dangerous.
It is easy to trigger a decryption error if you create a tenant using the same database connection, but one has the privkey_secret.inc.php and one does not (or have a different one). Or if you switch the database connection in the baseconfig and forget to change the privkey_secret.inc.php
I suggest the following change:
(1) Instead of re-generating a new system ID on the silent, the system should stop and warn the user that the private key file is missing, doesn't match the database or is corrupted. This way, the administrator notices the problem and can fix the privkey_secret file.
(2) It is complex to keep track of the contents of privkey_secret.inc.php . So I guesst that each system ID gets their own privkey_secret.inc.php by including the system Id into that filename. For example, the file could be named privkey_secret1234567.inc.php if 1234567 is the system ID. This way, the system can tell the administrator "hey, I am missing the file privkey_secret1234567.inc.php!"
(3) In case the system owner actually lost the privkey_secret file, they must remove the config entry from the database, e.g. using phpMyAdmin. The error message should tell what to do.
(4) I was wondering if the reg2 system should auto-unregister a previously assigned system ID in case another system registeres with the same URL and the ViaThinkSoft server can verify the URL (this is VERY important, otherwise you could force-delete foreign systems!!!)

System "X" with URL "A" registers to reg2
System ID gets regenerated because the administrator deleted the config database entry after loosing the secret PHP file. New system ID is "Y"
System "Y" with URL "A" registers to reg2
reg2 sees hat URL "A" belongs to system ID "X".
It will auto-unregister system ID "X"  if  (AND ONLY IF)  it can verify that URL "A" replies to the challenge for private/public key "Y"

Issue 4 fixed.
# --- If the same URL has another system ID, and we can verify this URL with this key, then auto-unregister the previous system
$systemid = $payload['system_id'];
$sysurl = $payload['system_url'];
$verified_sysurl = oidplus_verify_system_url($sysurl, $public_key);
if ($verified_sysurl) {
        $res = mysql_query("select systemid from directory ".
                           "where url = '".mysql_real_escape_string($sysurl)."' ".
                           "and   systemid <> '".mysql_real_escape_string($systemid)."';");
        while ($row = mysql_fetch_array($res)) {
                reg2_unregister($row['systemid']);
        }
}

Fixed issues 1, 2 and 3!
Release:
        {
                "version": "<IP_ADDRESS>",
                "date": "2024-07-19 13:00:00 +0200",
                "author": "Daniel Marschall (ViaThinkSoft)",
                "changes": [
                        "In case the private/public key pair is broken or cannot be decrypted, it will not be regenerated automatically.",
                        "The privkey secret file filename now contains the system ID, so it is easier to recognize"
                ]
        },


'Test it on a minimal dataset by running' does not work

Hi again.
Today, I installed metaGT on our machine using git clone.
After installing it, I tried to test the minimal dataset described in README - 'Quick Start' - 4, but it did not work.
(metaGT) pclee@bio507-3:/analysis/users/wycho/Project/metaGT$ nextflow run metaGT -profile test,conda
N E X T F L O W  ~  version 22.10.6
Launching `metaGT/main.nf` [distraught_bardeen] DSL2 - revision: 53a1fce0fe

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  metaGT v1.0dev
------------------------------------------------------

WARN: Found unexpected parameters:
* --single_end: false
- Ignore this warning: params.schema_ignore_params = "single_end"

Core Nextflow options
  runName                   : distraught_bardeen
  container                 : metaGT:dev
  launchDir                 : /analysis/users/wycho/Project/metaGT
  workDir                   : /analysis/users/wycho/Project/metaGT/work
  projectDir                : /analysis/users/wycho/Project/metaGT/metaGT
  userName                  : pclee
  profile                   : test,conda
  configFiles               : /analysis/users/wycho/Project/metaGT/metaGT/nextflow.config

Input/output options
  dna_reads                 : null
  rna_reads                 : null

Pipeline options
  transcriptome             : /analysis/users/wycho/Project/metaGT/metaGT/data/transcriptome.fasta
  genome                    : /analysis/users/wycho/Project/metaGT/metaGT/data/genome.fasta

Generic options
  enable_conda              : true

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 2d

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

------------------------------------------------------
 Only displaying parameters that differ from defaults.
------------------------------------------------------
executor >  local (2)
[e0/189a38] process > MINIMAP2 (genome) [  0%] 0 of 1
executor >  local (2)
[e0/189a38] process > MINIMAP2 (genome) [100%] 1 of 1, failed: 1 ✘
[93/35c80a] process > PROKKA (genome)   [100%] 1 of 1, failed: 1 ✘
executor >  local (2)
[e0/189a38] process > MINIMAP2 (genome) [100%] 1 of 1, failed: 1 ✘
[93/35c80a] process > PROKKA (genome)   [100%] 1 of 1, failed: 1 ✘
[-        ] process > COVERED_CDS       -
[-        ] process > TRANSDECODER      -
[-        ] process > MMSEQS_CLUSTER    -
Execution cancelled -- Finishing pending tasks before exit
- Ignore this warning: params.schema_ignore_params = "single_end"
WARN: Found unexpected parameters:
* --single_end: false
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.
Error executing process > 'MINIMAP2 (genome)'

Caused by:
  Process `MINIMAP2 (genome)` terminated with an error exit status (127)

Command executed:

  minimap2 -t 2 -aY --MD genome.fasta transcriptome.fasta > genome.align.sam

  samtools sort genome.align.sam -o genome.align.sorted.bam

  change_name.py  transcriptome.fasta transcriptome.all_transcripts.fasta

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: minimap2: command not found

Work dir:
  /analysis/users/wycho/Project/metaGT/work/e0/189a3802f3a24a22cbc95071249249

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Unknown method invocation `checkHostname`

 -- Check script 'metaGT/main.nf' at line: 270 or see '.nextflow.log' file for more details

Is this caused by my incorrect command? Then, how can I solve it?
Best,
Lafmas

Hi again
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.
Error executing process > 'MINIMAP2 (genome)'

this issue was solved when I installed graphviz using conda install -c bioconda perl-graphviz
but
`WARN: Found unexpected parameters:

--single_end: false`

this is issue still remain

Dear @Lafmas
I haven't seen the graphvis warning before. The one about single-end can be ignored, it should not affect the run.
Conda is installed, correct?
Best
Andrey

Dear @andrewprzh
Thank you for your reply.
Warning for graphviz already solved.
How can I ignore the warning about single-end? Insert nextflow run metaGT -profile test --params.schema_ignore_params = "single_end" command only displayed Unexpected error [StackOverflowError].
I installed nextflow and metaGT using conda environment.
Best,
Lafmas

Dear @Lafmas
As far as I understand this warning does not affect the run, right? It sill completes despite the warning?
Best
Andrey

I update the code, the warning should not appear anymore.
Best
Andrey

Dear @andrewprzh
Unfortunately, the error we previously discussed unfortunately still exists.
I have attached a screenshot of my terminal to give you a clearer picture. It seems minimap2 and prokka still do not working properly.
Thank you for your consistent help and support.
Best,
Lafmas
(metaGT) pclee@bio507-3:/analysis/users/wycho/Project$ nextflow run metaGT -profile test,conda N E X T F L O W  ~  version 22.10.6 Launching metaGT/main.nf [festering_curran] DSL2 - revision: 53a1fce0fe

Dear @andrewprzh
Sure. I will try it.
As soon as the results are confirmed, I will share them here
Best
Lafmas

I deleted the existing conda environment and installed Nextflow & metaGT newly again.
Afterward, I am running the test file and this time the process appears to be working well!
The analysis is currently underway and I will share the results here once it's complete.
Best
Lafmas

Dear @andrewprzh
Unfortunately, the process was stopped.
I have attached screenshot of the error. And I'll see if there are any problems with my conda environment.
Best
Lafmas

Dear @Lafmas
Looks like a conda problem - the environment was not created and it does not even tell what the error is.
Could you try running the same command manually:
conda create -n metagt --file metaGT/environment.yml
?
Best
Andrey

Dear @andrewprzh
I write because I have the same problem, it has not been possible to create the environment, it generates the same error seen in the thread, it seems that conda is able to install minimap2. Even trying to create the environment directly with the conda command, it never finishes creating. What I find strange is that with the command "conda install -c bioconda minimap2" it is able to install minimap2.

here is a part of the problem shown in the nextflow.log file
"Aug-14 00:37:39.031 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
[process] MINIMAP2
status=ACTIVE
port 0: (queue) closed; channel: -
port 1: (queue) OPEN  ; channel: -
port 2: (cntrl) -     ; channel: $
[process] COVERED_CDS
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (queue) OPEN  ; channel: -
port 2: (queue) OPEN  ; channel: -
port 3: (queue) OPEN  ; channel: -
port 4: (cntrl) -     ; channel: $
[process] TRANSDECODER
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (cntrl) -     ; channel: $
[process] MMSEQS_CLUSTER
status=ACTIVE
port 0: (queue) OPEN  ; channel: -
port 1: (queue) OPEN  ; channel: -
port 2: (cntrl) -     ; channel: $
Aug-14 00:37:39.272 [Actor Thread 9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=MINIMAP2 (1); work-dir=null
error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to create Conda environment
command: conda env create --prefix /home/call/MetaGT/work/conda/metaGT-1.0-f7c8dc3121d55495d60aeb53bd2259e3 --file /home/call/MetaGT/metaGT/environment.yml
status : 143
message:
Aug-14 00:37:39.282 [Actor Thread 9] ERROR nextflow.processor.TaskProcessor - Error executing process > 'MINIMAP2 (1)'
Caused by:
Failed to create Conda environment
command: conda env create --prefix /home/call/MetaGT/work/conda/metaGT-1.0-f7c8dc3121d55495d60aeb53bd2259e3 --file /home/call/MetaGT/metaGT/environment.yml
status : 143
message:
java.lang.IllegalStateException: java.lang.IllegalStateException: Failed to create Conda environment
command: conda env create --prefix /home/call/MetaGT/work/conda/metaGT-1.0-f7c8dc3121d55495d60aeb53bd2259e3 --file /home/call/MetaGT/metaGT/environment.yml
status : 143
message:
"
I hope there is a solution to this problem
Best,
Cesar

conda create -n metagt --file metaGT/environment.yml

I am having the same minimap2 issue as mentioned in this thread. This quoted command returns:
CondaValueError: could not parse 'name: metaGT-1.0' in: metaGT/environment.yml
which I think is a typo from not using conda env ? Because when I instead run:
conda env create -n metagt --file metaGT/environment.yml
It seems to complete without errors.
However, running the test still doesn't work, with the same error read out as shown in @cesar2598 's most recent post.


Escape strings when interpolating into Markdown

At present, Markdown comments can result in unexpected formatting if the user or path includes Markdown formatting directives. (For example, __snapshots__.) We should handle this more gracefully by escaping those directives as needed.
For now, this pulls in a library to handle the escaping, although we might just want to vendor it in instead, given the transitive dependencies this adds to go.mod. Thoughts?

The dependency does seem to be a bit heavyweight. Famous last words, but it seems like writing a function to escape the 13 special characters in markdown would be easy to inline instead of adding a dependency: https://www.markdownguide.org/basic-syntax/#characters-you-can-escape
Another alternative would neither require a dependency nor extra extra escaping would be to wrap filenames in backtics. Kind of ugly though:

Notifying subscribers in CODENOTIFY files for diff 12da28213a6dafe0037d691c4e10a6236401014e...9afbed62fb9edb505e92fcdc9aa54ef81a61d2b2.

Notify
File(s)

@foo
internal/workerutil/dbworker/store/store.gointernal/workerutil/__dbworker__/store/store_test.go

What do you think?

Can you figure out why this build is red? Here is what I tried: https://sourcegraph.slack.com/archives/CMBA8F926/p1606932873200700


chore: remove scripts/fix-by-linebreaks.sh

This script is currently unused; it was created during and for the port, and its functionality is incorporated into lint-style.py.

Helps with #14539.

Thanks!
bors r+


Versions of spack-stack and modules need to be updated

The current versions of the spack-stack and module files are out of dated.

The Jedi run (analysis or run_ana task)  fails on the Rocky8 of Hera:
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 2140722 RUNNING AT h5c53
=   KILLED BY SIGNAL: 9 (Killed)
===================================================================================


Cleaned up the app with styling and consistency, and fixed pin bug

Addressed Issue #42

LOOKS GREAT!


Cannot Use Latest Chat and Calling SDK in same application (iOS)

Describe the bug
I have tried to add the following pod to our project but getting an error resolving dependencies.
podfile:
pod 'AzureCommunicationCalling', '~> 1.0.1'
pod 'AzureCommunicationChat', '~> 1.0.0-beta.11'

errors:
[!] CocoaPods could not find compatible versions for pod "AzureCore":
  In Podfile:
    AzureCommunicationCalling (~> 1.0.1) was resolved to 1.0.1, which depends on
      AzureCommunicationCommon (= 1.0.0) was resolved to 1.0.0, which depends on
        AzureCore (= 1.0.0-beta.12)

    AzureCommunicationChat (~> 1.0.0-beta.11) was resolved to 1.0.0-beta.11, which depends on
      AzureCore (= 1.0.0-beta.11)

To Reproduce
Steps to reproduce the behavior:

Add:

pod 'AzureCommunicationCalling', '~> 1.0.1'
pod 'AzureCommunicationChat', '~> 1.0.0-beta.11'

Run pod install --project-directory=ios --repo-update
See error

Expected behavior
A clear and concise description of what you expected to happen.
Desktop (please complete the following information):

OS: macOS Big Sur 11.3.1
XCode: 12.4

Logs
pod install --project-directory=ios --repo-update
/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/universal-darwin20/rbconfig.rb:229: warning: Insecure world writable dir /Users/rashid/Projects/Likewise/code/radiant in PATH, mode 040777
Auto-linking React Native modules for target `Likewise`: BVLinearGradient, CodePush, RNAppleAuthentication, RNCAsyncStorage, RNCPicker, RNCPushNotificationIOS, RNDateTimePicker, RNDefaultPreference, RNDeviceInfo, RNFS, RNFastImage, RNGestureHandler, RNGoogleSignin, RNImageCropPicker, RNLocalize, RNRate, RNReactNativeHapticFeedback, RNReanimated, RNScreens, RNShare, RNSharedElement, RNVectorIcons, ReactNativePermissions, lottie-ios, lottie-react-native, react-native-appsflyer, react-native-blur, react-native-color-thief, react-native-config, react-native-contacts, react-native-fbsdk-next, react-native-geolocation, react-native-google-analytics-bridge, react-native-image-sequence, react-native-mixpanel, react-native-netinfo, react-native-shake, react-native-share-extension, react-native-shared-group-preferences, react-native-splash-screen, react-native-switch-audio-output, react-native-tcp-socket, react-native-tracking-transparency, react-native-udp, react-native-video, react-native-viewpager, react-native-webview, react-native-zeroconf, and rn-fetch-blob
Auto-linking React Native modules for target `Kismet`: BVLinearGradient, CodePush, RNAppleAuthentication, RNCAsyncStorage, RNCPicker, RNCPushNotificationIOS, RNDateTimePicker, RNDefaultPreference, RNDeviceInfo, RNFS, RNFastImage, RNGestureHandler, RNGoogleSignin, RNImageCropPicker, RNLocalize, RNRate, RNReactNativeHapticFeedback, RNReanimated, RNScreens, RNShare, RNSharedElement, RNVectorIcons, ReactNativePermissions, lottie-ios, lottie-react-native, react-native-appsflyer, react-native-blur, react-native-color-thief, react-native-config, react-native-contacts, react-native-fbsdk-next, react-native-geolocation, react-native-google-analytics-bridge, react-native-image-sequence, react-native-mixpanel, react-native-netinfo, react-native-shake, react-native-share-extension, react-native-shared-group-preferences, react-native-splash-screen, react-native-switch-audio-output, react-native-tcp-socket, react-native-tracking-transparency, react-native-udp, react-native-video, react-native-viewpager, react-native-webview, react-native-zeroconf, and rn-fetch-blob
Updating local specs repositories
Analyzing dependencies
[!] CocoaPods could not find compatible versions for pod "AzureCore":
  In Podfile:
    AzureCommunicationCalling (~> 1.0.1) was resolved to 1.0.1, which depends on
      AzureCommunicationCommon (= 1.0.0) was resolved to 1.0.0, which depends on
        AzureCore (= 1.0.0-beta.12)

    AzureCommunicationChat (~> 1.0.0-beta.11) was resolved to 1.0.0-beta.11, which depends on
      AzureCore (= 1.0.0-beta.11)

The latest version of Chat (beta 12) resolves this conflict.


Update to Angular 8 - web-animations-js

🐞 Bug report
After updating our projects form Angular 7 to Angular 8, our Jenkins was not able run npm install due to this line in the package.json file
"web-animations-js": "angular/web-animations-js#release_pr208"
The thing is that our Jenkins is behind a corporate proxy that does not allow calls to github.com
Command (mark with an x)

- [ ] new
- [ ] build
- [ ] serve
- [ ] test
- [ ] e2e
- [ ] generate
- [ ] add
- [x] update
- [ ] lint
- [ ] xi18n
- [ ] run
- [ ] config
- [ ] help
- [ ] version
- [ ] doc

Is this a regression?

Yes, this did not happen with previous versions of Angular
Description
When running npm ci, our Jenkins is not able to get the web-animation-js dependency on the angular github for of the original project.
🔬 Minimal Reproduction

Create a project using @angular/cli 7
Install web-animation-js package
Add the dependency in the polyfill.ts file
Update to Angular 8 using ng update @ancular/cli @angular/core

I don't understand why the Angular team did not uploaded this dependency under @angular/web-animation-js or something instead of just pointing to a PR of a for of the original project.
I realise this is not really a bug since it is a feature of NPM to be able to fetch dependencies directly on github, but it is the first time since I'm using Angular that this happens.

@yodi-n the dependency uri is incorrect it should be github:angular/web-animations-js#release_pr208 and not angular/web-animations-js#release_pr208
The main reason why it's not an NPM package is that this is a temporary solution which wouldn't ideally be published as a separate NPM package, and also @angular doesn't own web-animations-js package and it won't be correct to publish the web-animations-js under the angular namespace.
That being said we are still waiting on the web-animations-js team to cut an official release containing the fix.
Some worksarounds would be;

Allow the corporate proxy to access github.com
Fork the above mentioned PR and host it locally

Lets continue tracking this in: https://github.com/angular/angular-cli/issues/14518

Also of note, is that the project may not actually need the polyfill anymore.  It is only needed by Angular if the project is using the AnimationBuilder class.  Declarative animations do not require the polyfill.


Unhandled exceptions in Light mode

What is wrong?
This appeared when running Trinity with --light
 WARNING  06-06 12:07:02  lightchain  LESAnnouncementProcessingError('Too many timeouts when fetching headers from LESPeer <Node(0x374a@<IP_ADDRESS>)>',)
   ERROR  06-06 12:07:02  base_events  Task exception was never retrieved
future: <Task finished coro=<LightPeerChain._process_announcements() done, defined at /home/cburgdorf/Documents/hacking/ef/py-evm/p2p/lightchain.py:141> exception=RuntimeError('Cannot cancel a service that has not been started',)>
Traceback (most recent call last):
  File "/home/cburgdorf/Documents/hacking/ef/py-evm/p2p/lightchain.py", line 217, in process_announcement
    batch = await self.fetch_headers(start_block, peer)
  File "/home/cburgdorf/Documents/hacking/ef/py-evm/p2p/lightchain.py", line 172, in fetch_headers
    raise TooManyTimeouts()
p2p.exceptions.TooManyTimeouts

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/cburgdorf/Documents/hacking/ef/py-evm/p2p/lightchain.py", line 150, in _process_announcements
    await self.process_announcement(peer, head_info)
  File "/home/cburgdorf/Documents/hacking/ef/py-evm/p2p/lightchain.py", line 220, in process_announcement
    "Too many timeouts when fetching headers from {}".format(peer))
p2p.exceptions.LESAnnouncementProcessingError: Too many timeouts when fetching headers from LESPeer <Node(0x374a@<IP_ADDRESS>)>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/cburgdorf/Documents/hacking/ef/py-evm/p2p/lightchain.py", line 157, in _process_announcements
    await self.drop_peer(peer)
  File "/home/cburgdorf/Documents/hacking/ef/py-evm/p2p/lightchain.py", line 82, in drop_peer
    await peer.cancel()
  File "/home/cburgdorf/Documents/hacking/ef/py-evm/p2p/service.py", line 93, in cancel
    raise RuntimeError("Cannot cancel a service that has not been started")
RuntimeError: Cannot cancel a service that has not been started
    INFO  06-06 12:07:22        peer  Connected peers: 0 inbound, 0 outbound

How can it be fixed
:hear_no_evil:

This might get fixed by the bonus change in #905

That code has been removed as we're now using BaseHeaderChainSyncer for light syncing, so this should no longer happen


Fix scripts to work with frzr-tweaks

Scripts fixed to work with frzr-tweaks

Need to make changes to prevent breakage with frzr-tweaks when chroot


[avocado-122] Tested and reintegrated EM algorithm.

Resolves #122. Reintegrated EM algorithm for estimating frequency of reference allele, which is used as a prior when genotyping.

Test PASSed.
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Test PASSed.

This now depends on #129.

Test PASSed.
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Test PASSed.

@fnothaft Can you rebase this?

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https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/43/Build result: FAILUREGitHub pull request #128 of commit f6da7583fcda511d09b5e4c9f56aa64e512729fa automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/128/merge^{commit} # timeout=10Checking out Revision 63afcbaa68e41526be701283991ec3e4e864c43a (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 63afcbaa68e41526be701283991ec3e4e864c43a > git rev-list 343b70dcf07f0ee0ae1f8489fffc541aafd47b71 # timeout=10Triggering avocado-prb ? 2.3.0,centosTriggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.2.0,centosavocado-prb ? 2.3.0,centos completed with result SUCCESSavocado-prb ? 1.0.4,centos completed with result FAILUREavocado-prb ? 2.2.0,centos completed with result FAILURE
Test FAILed.

Jenkins, retest this please.

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Test PASSed.

With the switch to log probabilities in #134 to fix #133, I just rewrote this to use all log probabilities in the EM loop as well. So, this now depends on #134, which depends in turn on #130.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/51/Build result: FAILUREGitHub pull request #128 of commit 956a1854b15a44d554f36456efed3d45c86faf78 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/128/merge^{commit} # timeout=10Checking out Revision a56fba5c0c9c5496681d9823d46b6dafed40785b (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f a56fba5c0c9c5496681d9823d46b6dafed40785b > git rev-list 63afcbaa68e41526be701283991ec3e4e864c43a # timeout=10Triggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.2.0,centosTriggering avocado-prb ? 2.3.0,centosavocado-prb ? 1.0.4,centos completed with result FAILUREavocado-prb ? 2.2.0,centos completed with result SUCCESSavocado-prb ? 2.3.0,centos completed with result SUCCESS
Test FAILed.

Jenkins, retest this please.

Test PASSed.
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Test PASSed.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/54/Build result: FAILUREGitHub pull request #128 of commit e823d7fdecb39c784db0da719d955c6db7362dd2 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/128/merge^{commit} # timeout=10Checking out Revision 390983fcf77ac5ff77b6bad08b975b1126e1c4fb (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 390983fcf77ac5ff77b6bad08b975b1126e1c4fb > git rev-list a56fba5c0c9c5496681d9823d46b6dafed40785b # timeout=10Triggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.2.0,centosTriggering avocado-prb ? 2.3.0,centosavocado-prb ? 1.0.4,centos completed with result FAILUREavocado-prb ? 2.2.0,centos completed with result SUCCESSavocado-prb ? 2.3.0,centos completed with result FAILURE
Test FAILed.

Jenkins, retest this please.

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Test PASSed.

Is this rebased, @fnothaft ?

@fnothaft I'm going to be offline for about 2 hours, will merge this (LGTM!) when I come back if you've rebased.

@tdanford rebased!

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https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/59/Build result: FAILUREGitHub pull request #128 of commit 4e1b3dce0d0dfa4d79df85d5a575950efed6ad75 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/128/merge^{commit} # timeout=10Checking out Revision 4bf5d887ad74675797cd00f22afd952fb1bb7e01 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 4bf5d887ad74675797cd00f22afd952fb1bb7e01 > git rev-list 390983fcf77ac5ff77b6bad08b975b1126e1c4fb # timeout=10Triggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.2.0,centosTriggering avocado-prb ? 2.3.0,centosavocado-prb ? 1.0.4,centos completed with result SUCCESSavocado-prb ? 2.2.0,centos completed with result SUCCESSavocado-prb ? 2.3.0,centos completed with result FAILURE
Test FAILed.

Test FAILed.
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Test FAILed.

Jenkins, retest this please.

Jenkins, retest this please.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/62/Build result: ABORTEDGitHub pull request #128 of commit 866c0768d18c70098076a16cf4518e19e8ba9b58 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/128/merge^{commit} # timeout=10Checking out Revision 077f0cde55fbb2bb52ffb5c2750b0a5c268b6fe3 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 077f0cde55fbb2bb52ffb5c2750b0a5c268b6fe3 > git rev-list 077f0cde55fbb2bb52ffb5c2750b0a5c268b6fe3 # timeout=10Triggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.2.0,centosTriggering avocado-prb ? 2.3.0,centosavocado-prb ? 1.0.4,centos completed with result SUCCESSAbortedAborted by fnothaftInterrupting #62
Test FAILed.

Jenkins, retest this please.

Jenkins, retest this please.

Jenkins, retest this please.

Jenkins, retest this please.

Jenkins, test this please.

Test PASSed.
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Test PASSed.

@fnothaft ... thanks!


Plugin: Network state

Is there a way to check and monitor network connectivity in flutter? I'd love to show a warning message if we can reliably identify the user has no connectivity.

"no connectivity" is very hard to define. If I'm on a subway and have a 10 Mbits connection every 5 minutes for 30 seconds, is that "no connectivity"? What about if I'm connected to a wifi network with DNS, but most packets are blocked silently? What about if I'm on a network with 90% packet loss?
I think https://github.com/flutter/flutter/issues/1051 presents a more effective long-term solution, but it's not on our near-term roadmap.

However, couldn't the developer ask "do I have a link light?". I should be able to tell if I definitely have no network access if I have zero "up" network interfaces.
Agreed that if I have at least one link light, that I can't assume that it means I have connectivity.
But, the absence of link lights should tell me "there's no way I have connectivity".

Android:
https://developer.android.com/reference/android/net/ConnectivityManager.html
and iOS:
https://developer.apple.com/library/tvos/documentation/SystemConfiguration/Reference/SCNetworkReachabilityRef/index.html#//apple_ref/doc/uid/TP40007260
It seems reasonable to ask for a x-platform wrapper around these two.  We don't have one currently.

We should probably switch customer: fast over to FlutterView so that they can integrate with whatever platform services they like without needing us to turn a crank for them.

@sethladd My point is that having the app work differently when there's no network (briefly) is suboptimal UI. Better to just buffer up sends, provide what cached data we have, and show an indicator that we want more data but are having trouble getting it. It's fine for apps to talk straight to the OS to find this information, but flutter's API IMHO shouldn't support that model natively, we can do better.

React Native API: https://facebook.github.io/react-native/docs/netinfo.html
A plugin for Xamarin: https://github.com/jamesmontemagno/Xamarin.Plugins/tree/master/Connectivity
(There is no out-of-the-box Xamarin API for x-plat network connectivity. There is an Android API and an iOS API.)

We have this already: https://pub.dartlang.org/packages/connectivity I will tentatively close this.

thanks!


Entitas Chat Poll

Hi,
it has been requested to consider other chat solutions other than gitter.
Since I'm revamping the repo and working on Entitas 2.0 it would also be a good time to ask you which platform you want to use to communicate moving forward.
Let's do a simple poll so I can get an overview what the community thinks and prefers

Gitter: 👀
Discord: 🚀
Slack: 🎉

Click the react button to vote. Comment, if you know great reasons why to pick a certain platform
Thanks!

I have preemptively created this Discord server.  Note that is is entirely unofficial unless @sschmid gives it his blessing.  All moderators of the existing Gitter chat room who join the Discord server will be granted equivalent privileges.  And if @sschmid joins and endorses the Discord, I will transfer ownership to him.

Thank god for a discord server

Discord
Sent with GitHawk

discord

I think I can already see a clear trend ;)

@sschmid Join the Discord I linked and post your Discord in this thread.  When you do, I will transfer ownership to you.

joined :D

For future readers: I have granted @sschmid total ownership of the linked Discord server. It is now official.


Add block to page (inline)

User Story
As a CMS user, I want to be able to add new content blocks within a page level between current content blocks, so that I can do this quickly and in context with the other page blocks.
Acceptance Criteria

[x] Hover-over between current page blocks presents styling as per wireframe: https://projects.invisionapp.com/share/ZRL4T2HQAGB#/screens/301918525
[x] Clicking a “+” button in between blocks presents a pop-up with all blocks available in a format that’s easy to view
[x] Clicking a new block type adds the block to the present gap between blocks. Styling animation pushes current page blocks below new block as per wireframe: https://projects.invisionapp.com/share/ZRL4T2HQAGB#/screens/301918523
[x] As per designs, when hovering between blocks there is a indicator that a block can be added between/above/below existing blocks (delayed interaction so the line isn’t triggered as you move the cursor across the screen).  https://invis.io/BYMQXG07QZH#/307488192_Adding_Blocks-_In-Page

Notes

Pop-up work is also covered in: https://github.com/dnadesign/silverstripe-elemental/issues/293

Done https://github.com/dnadesign/silverstripe-elemental/pull/443
in tandem with #340


Initial analysis

This shows the entire workflow mostly in Jupyter notebooks.

The wrongly imputed genotypes using tskit.lshmm are far too high to make sense. In contrast, the imputed genotypes from BEAGLE almost perfectly agree with truth. I suspect that the step adding new sample edges to the reference tree seqsuence is not done correctly. So, next thing is to investigate that step.


Revert "refactoring of jp.co.yahoo.yosegi.message.objects"

Reverts yahoojapan/yosegi#18
remove refactoring

LGTM


python3Packages.adafruit-platformdetect: 3.15.1 -> 3.15.3

Motivation for this change
Update to latest upstream release 3.15.3
Change log: https://github.com/adafruit/Adafruit_Python_PlatformDetect/releases/tag/3.15.3
Things done

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

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

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
21.11 Release Notes (or backporting 21.05 Relase notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 130433 run on x86_64-linux 1

2 packages built:

python38Packages.adafruit-platformdetect
python39Packages.adafruit-platformdetect

Result of nixpkgs-review pr 130433 at e528c779 run on aarch64-linux 1

2 packages built successfully:

python38Packages.adafruit-platformdetect
python39Packages.adafruit-platformdetect


Maintenance banner: Add endpoint to activate/deactivate status banner

Description
See #2315 for detailed explanation
Proposed solution
Add an endpoint to activate or deactivate the status banner. This endpoint should only be accessible by superadmins.
If activating, the endpoint will need to take in the severity level and user-facing message for the outage.
If deactivating, the endpoint will mark the banner as disabled/deactivated.

taking a new direction on the banner, so closing this issue


fix(hybrid) broadcast CRUD changes to DPs cluster

This change fixes a bug which manifested itself when Kong:

It is working on hybrid mode.
The CP role is being executed by several Kong nodes in a
cluster.
A change (any successful CRUD operation) happens in one of these
nodes.

The desired behaviour is that when this happens, all the CPs in the cluster
would trigger a DP refresh. The bug consists in that only the workers in the
same Kong node as the one which received the CRUD operation do such
refresh.
Example setup: Two Kong nodes in CP role. Node A has workers A1 and A2, and Node
B has workers B1 and B2. The admins use A1's admin API to create a new Service.
Before this fix, A1 would trigger the CP reload, then A2 would "see" the change
(via a worker event) and refresh its DPs. But B1 and B2 would not perform such
refresh.
This fix makes A1 trigger a cluster event in addition of the previous
worker-level event. It also makes all workers look for this new cluster event,
and do a DP refresh.
Note that the test accompanying this fix does not exactly replicate the above
setup. There is a concern that the amount of memory this would need (at least 3
kong nodes, with several workers each) would trigger a CI shutdown. Instead, we
reduced the example to the minimum (only A1 and B1 are created) and we check
B1's logs for the reception of the change. The fact that B1 reliably
communicates refreshes its DPs when it receives this notification is assumed,
since the function triggered by the event is the same one used in worker-level
updates, which are already tested.

Update: after discussing with @bungle , it seems that the invalidations event is always triggered at least for all of the core entities and all the bundled plugin entries. If this became an issue, then we will fire our own cluster events from dao:crud instead. But this PR should make the situation better regardless, so it is decided to merge it first.


Support for Pioneer quadcopter

Plugins for editing Pioneer quadcopter programs and generating them to Lua, also installer script.

Merged rebased version (https://github.com/qreal/qreal/pull/1813) instead


FROM kubernetes:v1.19.8
COPY helm ./charts
COPY linux-amd64/helm ./bin
CMD helm install open-local ./charts/helm


Time profiling for PCA, LDA, and ICA

As each algorithm becomes functionally correct in the C code, we should do some profiling so that we can analyze the code for bottlenecks and eventually have a way to measure performance.
For now we can do this by measuring the time before and after the code in question and print the difference:
clock_t start, end;

start = clock();
// ...
end = clock();

printf("time to do [task]: %g s\n", 1000.0 * (end - start) / CLOCKS_PER_SEC);

The timing code should be controlled by a command line argument, something like --timing.
Later on we might be able to find better ways to manage the timing code. For example, I would like to store all timing information in a structure so that all of it can be printed at the end instead of throughout the code.

A timing library will soon be added in the lda-timing branch, which can be pulled into master. The problem with g++ linking was solved by continuing to use gcc as the c compiler, with g++ used for *.cpp files, and the addition of -lstdc++ to the LFLAGS variable, which includes the library definitions for c++ types.

lda-timing has been merged into master


feat(keepInView): add keepInView prop

Closes #14

Coverage increased (+1.5%) to 99.057% when pulling 2719bec3fcc91c215ad31b1a44dc2b173d61312e on feature/14-remain-in-screen into faeb98c577ad267905808fd086112ea7fcd4bc0b on master.

@hotpxl check out the preview and let me know if this is what you are wanting.
https://deploy-preview-15--react-block-ui.netlify.com/components/blockui/

Thanks. That's exactly what I want.
Although to make it a little better, I would want a little padding at the bottom and top so it will not be cut by the parent box when you scroll too further down. But anyways this is already good enough for what I want. Thanks again.

Coverage increased (+1.5%) to 99.074% when pulling 089c84fa7c7adb3d581461cf20e72314fb275a9c on feature/14-remain-in-screen into faeb98c577ad267905808fd086112ea7fcd4bc0b on master.

Ok, I made it so that it will take into account the height of the loader/message container when calculating. It makes sure that the loader/message will not get cut off even when using custom loaders and/or long messages (or have custom styles to make them bigger or smaller). Padding itself can be added via CSS to the .block-ui-message (or .block-ui-message-container) if you want additional padding around the loader/message, but I will leave that in user-land since it is custom styles.
In total, this entire feature didn't add that much code to the min (~1.18 kB). Though, because the package is so small, that technically is ~28% increase in size (4.17 kB -> 5.35 kB). I am fine with that, but my fear is this feature is missing some use-cases which would increase the code size a lot more.
Use-cases such as resize (I am not watching for window resizing or element resizing (from things such as child content changing or other external factors)), scrolling within another element (I only attach to the window's scroll event), horizontal scrolling.
If any of those use-cases become an issue, I will look at tackling them at that time. If the effort or code becomes too large when resolving those issues, I may move the entire feature to a custom loader or something at that point.


Update README.md

fixing pet peeve - SQLite
Description
[Describe what this change achieves]
Issues Resolved
[List any issues this PR will resolve]
Check List

[ ] Commits are signed per the DCO using --signoff

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.
For more information on following Developer Certificate of Origin and signing off your commits, please check here.

Few other typo's I'll want to fix as well. Can re-open later.


CollectD example config using SNMP plugin to send performance data to Azure Log Anayltics

Hello,
Please update docs page - https://docs.microsoft.com/en-us/azure/azure-monitor/agents/data-sources-collectd
and provide CollectD working configuration example with CollectD SNMP Plugin
https://collectd.org/wiki/index.php/Plugin:SNMP
That collects SNMP poll data and sends performance data to Azure Log Analytics.
usable for monitoring network equipment (switches, routers) or any other SNMP information using SNMP poll or trap.
Thank you,
Kind regards
Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: f36baa52-ce5b-95a3-522f-abc8600024f7
Version Independent ID: f30640f0-7cd0-c7ba-b6e0-093a0a94e8c8
Content: Collect data from CollectD in Azure Monitor - Azure Monitor
Content Source: articles/azure-monitor/agents/data-sources-collectd.md
Service: azure-monitor
Sub-service: agents
GitHub Login: @bwren
Microsoft Alias: bwren

@hkusulja Thanks for your comment! We will review and provide an update as appropriate.

We appreciate the request. I'll go ahead and create a work item to add this, but I'm not sure what priority we're going to be able to give it since we're focusing our efforts on the Azure Monitor agent  which is in the process of replacing the Log Analytics agent.
#please-close


Color contrast is not optimal

Run lighthouse test or similar on https://dom99.now.sh/
The text contrast between foreground and background should be WAI AAA

i'd like to try to take this on

just sent #33 tell me if these changes work for you!


[PLUGIN-1293] Gcs plugin Bug for buckets having delete multi part upload policy.

Bug:
Pipeline fails with warning and error for the GCS buckets with delete multi part upload policy.
Bugfix:
Plugin should support the buckets with this policy enabled in it. Bumped up the library version to fix this.
https://cdap.atlassian.net/browse/PLUGIN-1293

https://github.com/data-integrations/google-cloud/pull/1307 raised the new PR for this bug.


Horizontal Scroller Width Fix

The width of the horizontal scroller needs to be matched with the vertical scroller.

Resolved


5214.bugfix - Fixed the aria-label and button accessibility

Fixed the aria-label for close/clear search button and added circled border to it.
Issue reference #5214

@aadarsh-nagrath Look at this PR, please. Something was done here to improve accessibility using the mouse; now, we need to find a way to make it work with the keyboard as well


Documentation📄: Remove IBM Cloud Pak references from OH

What is the current documentation state?
There are a variety of Open Horizon documentation files which reference cloudctl and, by extension, IBM Cloud Pak common services.  This doesn't seem to make sense in the OH documentation.
A deep review of the following files is required:
docs/cli/index.md
docs/cli/cloudctl_oc_cli.md
docs/developing/container_registry.md
docs/user_management/rbac.md
docs/user_management/gdpr.md
docs/installing/preparing_edge_cluster.md
docs/admin/backup_recovery.md
docs/SUMMARY.md
docs/hub/gather_files.md
docs/hub/prepare_for_edge_nodes.md

Where is this stated?
No response
Why do you want to improve the statement?
No response
Proposed Statement
No response
Additional context.
No response

@johnwalicki A while back, @Abhijay007 mentioned this issue to me...I am not sure if he was planning to work on it, or if we need some in-depth Dev analysis before removing/replacing these references. And these files are probably also in the IEAM repo, so we will need to discuss how to handle that too.
Thanks!!

The IEAM documentation is correct to include these pages.  IEAM, by design, works within OpenShift.
I think we need to decide if Open Horizon (the open source project) also supports installation into OpenShift Container Platform.  It most certainly works.   I would think Yes.  It should be a supported target (on any cloud platform - IBM Cloud, AWS, Azure)
Then, separate from supporting OCP, we need to understand how the IBM Cloud Pak common services fits into the Open Horizon open source project.  That's a harder discussion (for which I do not know all the nuances)

This issue is still valid


Deprecation notice using HMSET with object

Version: node v4.4.5, node_redis v2.5.3.
Platform: Docker container based on Alpine linux
Description:

Calling HMSET with an object as an argument, I get the following

node_redis: Deprecated: The HMSET command contains a argument of type Object.
This is converted to "[object Object]" by using .toString() now and will return an error from v.3.0 on.
Please handle this in your code to make sure everything works as you intended it to.

Is this accurate?

@jbergknoff hmset still accepts an object as second argument like in: client.hmset('key', {field: 'value'}[, callback]). If you have a nested object, this was always converted to [object Object] but without any notice. So the only thing that changed is the added warning.

Thanks, I see what you mean now.


Rename rbenv repo url.

start rbenv organization. https://github.com/rbenv
(see http://www.hsbt.org/diary/20151126.html#p01)

@riywo Can you merge this? :octocat:

Thanks!

:star:


feat(runtime-vapor): add beforeUpdate hook for custom directive

close #65
By the way, I adjusted the trigger timing of the updated hook to after the effect in the render function.

Because it is implemented in #65, close this PR.


Understanding kata-fc

Explanation for kata-fc how that's associated with overhead.

Deployment preview : https://deploy-preview-45454--kubernetes-io-main-staging.netlify.app/docs/concepts/scheduling-eviction/pod-overhead/#understanding-kata-fc

This PR fixes : #45452

@tallclair changes made as suggested PTAL!

Can anyone PTAL! at this PR.

@sftim Thanks for the suggestion
PTAL!


51 reduce memory burden of pipeline

https://github.com/flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1/issues/51
I incorporated a test validating the numerical identity of the output, so I am confident there are no errors on that side.
Before there was batch normalization and masking for all the gt maps. Since only one map is loaded in at a time, this is done on-the-fly inside the local distance computation.

The metrics should not care if the input is low memory or not, they should only care about volumes1, volumes2, and some arguments if necessary. The whole low memory stuff should come at the pipeline level. Here is what I would do

Implement functions that normalize volumes the way you want it, they should take a stack of volumes or a single volumes. Don't do this things inside an if-statement.

Load a chunk of the gt volumes, run all the preprocessing you need, and then get that submatrix of the full distance matrix. This should use the distance matrices you already have implemented. Populate that distance matrix on-the-fly. This way you can do a vmap to compute a submatrix, and then a simple stack operation to get the full matrix.

I would also create a low_memory_pipeline and a regular memory pipeline. All those if statements make the code very messy, and I think it'd be easy to miss something being wrong.

Yes, good point! I forgot that the getitem takes care of indexing into sub-batches
I did the masking and normalization in the subbatch. This prevents a duplication of reading it  into memory (once for normalization / masking, another right before doing the m2m distance call)
There is still some if low memory mode control flow. To reduce code duplication.

Also, now the gt maps should be a .npy file, not a .pt file.
I hope that torch.from_numpy(np.load(fname.npy)) is not a lot slower than torch.load(fname.pt) for the big 160 GB file.


Services table should drop "Format" column

Feature Request
Since the format of a service is always "SERVICE", AFAIK, it serves no purpose and takes up extra space. Suggest that column be removed.
Goto https://staging.dockstore.org/services

┆Issue is synchronized with this Jira Story
┆Issue Type: Story
┆Issue Number: DOCK-984

In the future, this would probably be mapped to subclass for services


Issue rendering component in Demo

When trying to render the demo below, docfy cannot find the component to render resulting in an error:
Module not found: Error: Can't resolve '#embroider_compat/components/hkds-button'
// src/components/button/button-demo/appearance.md
<div class="flex justify-center">
  <HkdsButton @appearance="default">Default</HkdsButton>
  <HkdsButton @appearance="outline">Outline</HkdsButton>
  <HkdsButton @appearance="minimal">Minimal</HkdsButton>
</div>

The markdown renders Ok; just with no demos.
This isn't working when the component is in the components folder or in the button folder. Where should this be located?

This was an issue with my addon. I moved to default-style colocated template naming (src/components/hkds-button.gts) which fixed it.


blackscreen after startup

Hyprland Version
0.27.2
Bug or Regression?
Bug
Description
black screen after startup
Thinkpad T60,T5500 ATI GPU,3+120
How to reproduce
try use hyprland on some old thing
Crash reports, logs, images, videos
hyprlandCrashReport357.txt
https://1drv.ms/v/s!AvKideWdko8ngbVCuzK4_zu6hW9FLA

you sure you have all graphics drivers installed? i don't know if the linux kernel bundles ATI drivers with it.

I use archinstall to install the system and choose the "ATI/AMD" choice, and KDE plasm wayland run well on my computer

after swich to hyprland-legacyrender, the problem fixed!

Humm it is running but with some render problem

iirc there might be some rendering issues when using legacy render (https://wiki.hyprland.org/Getting-Started/Installation/#custom-installation-legacy-renderer-etc)

It is something like, when I am in a clean workspace, everything work well,all animations(WiFi and mako) work on full frame, but if I open any window(kate,Vivaldi,konsole,dolphin,etc), the global fps suddenly drop to about ten, even just moving mouse is very stuck, and when I switch to another clean workspace, everything work well again,also there are some black square flashing on some app like thunar and konsole.

T5500,ATI x1300,3gb ddr2, 120g hdd,no vram
when using Hyprland with a konsole open
but no command running, cpu 5%, ram 30% HDD 1%, unable to see gpu usage but I promise it is not run in full speed, and the fps is low

Full fps when the same scene happened in plasm

https://www.techpowerup.com/gpu-specs/radeon-x1300.c947 256MB of vram
use nvtop for gpu usage
get a newer version of hyprland for better performance
maybe turn blur off or the number of passes down if the gpu is struggling

Sorry I miss understand what vram is, I thought that was swap
nvtop:No GPU to monitor
version is newest
blur was already off

0.28.0 is newest arch repo hasn't been updated for some reason

nvtop:No GPU to monitor

this probably means gpu isn't working properly
like I said above it's likely you need to use mesa-amber instead of mesa due to the gpu's age

If I switch to mesa-amber, hyprland will just stop working

I will try build the version 28

m_sWLRRenserer wall null

send output of sudo lspci -v

00:00.0 Host bridge: Intel Corporation Mobile 945GM/PM/GMS, 943/940GML and 945GT Express Memory Controller Hub (rev 03)
Subsystem: Lenovo ThinkPad T60
Flags: bus master, fast devsel, latency 0
Capabilities: [e0] Vendor Specific Information: Len=09 <?>
Kernel modules: intel_agp
00:01.0 PCI bridge: Intel Corporation Mobile 945GM/PM/GMS, 943/940GML and 945GT Express PCI Express Root Port (rev 03) (prog-if 00 [Normal decode])
Subsystem: Lenovo Mobile 945GM/PM/GMS, 943/940GML and 945GT Express PCI Express Root Port
Flags: bus master, fast devsel, latency 0, IRQ 24
Bus: primary=00, secondary=01, subordinate=01, sec-latency=0
I/O behind bridge: 2000-2fff [size=4K] [16-bit]
Memory behind bridge: ee100000-ee1fffff [size=1M] [32-bit]
Prefetchable memory behind bridge: d8000000-dfffffff [size=128M] [32-bit]
Capabilities: [88] Subsystem: Lenovo Mobile 945GM/PM/GMS, 943/940GML and 945GT Express PCI Express Root Port
Capabilities: [80] Power Management version 2
Capabilities: [90] MSI: Enable+ Count=1/1 Maskable- 64bit-
Capabilities: [a0] Express Root Port (Slot+), MSI 00
Capabilities: [100] Virtual Channel
Capabilities: [140] Root Complex Link
Kernel driver in use: pcieport
00:1b.0 Audio device: Intel Corporation NM10/ICH7 Family High Definition Audio Controller (rev 02)
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, fast devsel, latency 0, IRQ 31
Memory at ee400000 (64-bit, non-prefetchable) [size=16K]
Capabilities: [50] Power Management version 2
Capabilities: [60] MSI: Enable+ Count=1/1 Maskable- 64bit+
Capabilities: [70] Express Root Complex Integrated Endpoint, MSI 00
Capabilities: [100] Virtual Channel
Capabilities: [130] Root Complex Link
Kernel driver in use: snd_hda_intel
Kernel modules: snd_hda_intel
00:1c.0 PCI bridge: Intel Corporation NM10/ICH7 Family PCI Express Port 1 (rev 02) (prog-if 00 [Normal decode])
Subsystem: Lenovo ThinkPad R60e
Flags: bus master, fast devsel, latency 0, IRQ 25
Bus: primary=00, secondary=02, subordinate=02, sec-latency=0
I/O behind bridge: 3000-3fff [size=4K] [16-bit]
Memory behind bridge: ee000000-ee0fffff [size=1M] [32-bit]
Prefetchable memory behind bridge: c0000000-c01fffff [size=2M] [32-bit]
Capabilities: [40] Express Root Port (Slot+), MSI 00
Capabilities: [80] MSI: Enable+ Count=1/1 Maskable- 64bit-
Capabilities: [90] Subsystem: Lenovo ThinkPad R60e
Capabilities: [a0] Power Management version 2
Capabilities: [100] Virtual Channel
Capabilities: [180] Root Complex Link
Kernel driver in use: pcieport
00:1c.1 PCI bridge: Intel Corporation NM10/ICH7 Family PCI Express Port 2 (rev 02) (prog-if 00 [Normal decode])
Subsystem: Lenovo ThinkPad R60e
Flags: bus master, fast devsel, latency 0, IRQ 26
Bus: primary=00, secondary=03, subordinate=03, sec-latency=0
I/O behind bridge: 4000-5fff [size=8K] [16-bit]
Memory behind bridge: ec000000-edffffff [size=32M] [32-bit]
Prefetchable memory behind bridge: e4000000-e40fffff [size=1M] [32-bit]
Capabilities: [40] Express Root Port (Slot+), MSI 00
Capabilities: [80] MSI: Enable+ Count=1/1 Maskable- 64bit-
Capabilities: [90] Subsystem: Lenovo ThinkPad R60e
Capabilities: [a0] Power Management version 2
Capabilities: [100] Virtual Channel
Capabilities: [180] Root Complex Link
Kernel driver in use: pcieport
00:1c.2 PCI bridge: Intel Corporation NM10/ICH7 Family PCI Express Port 3 (rev 02) (prog-if 00 [Normal decode])
Subsystem: Lenovo ThinkPad R60e
Flags: bus master, fast devsel, latency 0, IRQ 27
Bus: primary=00, secondary=04, subordinate=0b, sec-latency=0
I/O behind bridge: 6000-7fff [size=8K] [16-bit]
Memory behind bridge: e8000000-e9ffffff [size=32M] [32-bit]
Prefetchable memory behind bridge: e4100000-e41fffff [size=1M] [32-bit]
Capabilities: [40] Express Root Port (Slot+), MSI 00
Capabilities: [80] MSI: Enable+ Count=1/1 Maskable- 64bit-
Capabilities: [90] Subsystem: Lenovo ThinkPad R60e
Capabilities: [a0] Power Management version 2
Capabilities: [100] Virtual Channel
Capabilities: [180] Root Complex Link
Kernel driver in use: pcieport
00:1c.3 PCI bridge: Intel Corporation NM10/ICH7 Family PCI Express Port 4 (rev 02) (prog-if 00 [Normal decode])
Subsystem: Lenovo ThinkPad R60e
Flags: bus master, fast devsel, latency 0, IRQ 28
Bus: primary=00, secondary=0c, subordinate=13, sec-latency=0
I/O behind bridge: 8000-9fff [size=8K] [16-bit]
Memory behind bridge: ea000000-ebffffff [size=32M] [32-bit]
Prefetchable memory behind bridge: e4200000-e42fffff [size=1M] [32-bit]
Capabilities: [40] Express Root Port (Slot+), MSI 00
Capabilities: [80] MSI: Enable+ Count=1/1 Maskable- 64bit-
Capabilities: [90] Subsystem: Lenovo ThinkPad R60e
Capabilities: [a0] Power Management version 2
Capabilities: [100] Virtual Channel
Capabilities: [180] Root Complex Link
Kernel driver in use: pcieport
00:1d.0 USB controller: Intel Corporation NM10/ICH7 Family USB UHCI Controller #1 (rev 02) (prog-if 00 [UHCI])
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, medium devsel, latency 0, IRQ 16
I/O ports at 1800 [size=32]
Kernel driver in use: uhci_hcd
00:1d.1 USB controller: Intel Corporation NM10/ICH7 Family USB UHCI Controller #2 (rev 02) (prog-if 00 [UHCI])
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, medium devsel, latency 0, IRQ 17
I/O ports at 1820 [size=32]
Kernel driver in use: uhci_hcd
00:1d.2 USB controller: Intel Corporation NM10/ICH7 Family USB UHCI Controller #3 (rev 02) (prog-if 00 [UHCI])
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, medium devsel, latency 0, IRQ 18
I/O ports at 1840 [size=32]
Kernel driver in use: uhci_hcd
00:1d.3 USB controller: Intel Corporation NM10/ICH7 Family USB UHCI Controller #4 (rev 02) (prog-if 00 [UHCI])
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, medium devsel, latency 0, IRQ 19
I/O ports at 1860 [size=32]
Kernel driver in use: uhci_hcd
00:1d.7 USB controller: Intel Corporation NM10/ICH7 Family USB2 EHCI Controller (rev 02) (prog-if 20 [EHCI])
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, medium devsel, latency 0, IRQ 19
Memory at ee404000 (32-bit, non-prefetchable) [size=1K]
Capabilities: [50] Power Management version 2
Capabilities: [58] Debug port: BAR=1 offset=00a0
Kernel driver in use: ehci-pci
00:1e.0 PCI bridge: Intel Corporation 82801 Mobile PCI Bridge (rev e2) (prog-if 01 [Subtractive decode])
Subsystem: Lenovo ThinkPad R60e
Flags: bus master, fast devsel, latency 0
Bus: primary=00, secondary=15, subordinate=18, sec-latency=32
I/O behind bridge: a000-dfff [size=16K] [16-bit]
Memory behind bridge: e4300000-e7ffffff [size=61M] [32-bit]
Prefetchable memory behind bridge: e0000000-e3ffffff [size=64M] [32-bit]
Capabilities: [50] Subsystem: Lenovo ThinkPad R60e
00:1f.0 ISA bridge: Intel Corporation 82801GBM (ICH7-M) LPC Interface Bridge (rev 02)
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, medium devsel, latency 0
Capabilities: [e0] Vendor Specific Information: Len=0c <?>
Kernel driver in use: lpc_ich
Kernel modules: intel_rng, lpc_ich, leds_ss4200
00:1f.1 IDE interface: Intel Corporation 82801G (ICH7 Family) IDE Controller (rev 02) (prog-if 8a [ISA Compatibility mode controller, supports both channels switched to PCI native mode, supports bus mastering])
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, medium devsel, latency 0, IRQ 16
I/O ports at 01f0 [size=8]
I/O ports at 03f4
I/O ports at 0170 [size=8]
I/O ports at 0374
I/O ports at 1880 [size=16]
Kernel driver in use: ata_piix
Kernel modules: ata_piix, pata_acpi, ata_generic
00:1f.2 SATA controller: Intel Corporation 82801GBM/GHM (ICH7-M Family) SATA Controller [AHCI mode] (rev 02) (prog-if 01 [AHCI 1.0])
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: bus master, 66MHz, medium devsel, latency 0, IRQ 29
I/O ports at 18c8 [size=8]
I/O ports at 18ac [size=4]
I/O ports at 18c0 [size=8]
I/O ports at 18a8 [size=4]
I/O ports at 18b0 [size=16]
Memory at ee404400 (32-bit, non-prefetchable) [size=1K]
Capabilities: [80] MSI: Enable+ Count=1/1 Maskable- 64bit-
Capabilities: [70] Power Management version 2
Kernel driver in use: ahci
00:1f.3 SMBus: Intel Corporation NM10/ICH7 Family SMBus Controller (rev 02)
Subsystem: Lenovo ThinkPad R60/T60/X60 series
Flags: medium devsel, IRQ 23
I/O ports at 18e0 [size=32]
Kernel driver in use: i801_smbus
Kernel modules: i2c_i801
01:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] RV515/M52 [Mobility Radeon X1300] (prog-if 00 [VGA controller])
Subsystem: Lenovo RV515/M52 [Mobility Radeon X1300]
Flags: bus master, fast devsel, latency 0, IRQ 16
Memory at d8000000 (32-bit, prefetchable) [size=128M]
I/O ports at 2000 [size=256]
Memory at ee100000 (32-bit, non-prefetchable) [size=64K]
Expansion ROM at 000c0000 [virtual] [disabled] [size=128K]
Capabilities: [50] Power Management version 2
Capabilities: [58] Express Legacy Endpoint, MSI 00
Capabilities: [80] MSI: Enable- Count=1/1 Maskable- 64bit+
Kernel driver in use: radeon
Kernel modules: radeon, amdgpu
02:00.0 Ethernet controller: Intel Corporation 82573L Gigabit Ethernet Controller
Subsystem: Lenovo ThinkPad T60
Physical Slot: 2
Flags: bus master, fast devsel, latency 0, IRQ 30
Memory at ee000000 (32-bit, non-prefetchable) [size=128K]
I/O ports at 3000 [size=32]
Capabilities: [c8] Power Management version 2
Capabilities: [d0] MSI: Enable+ Count=1/1 Maskable- 64bit+
Capabilities: [e0] Express Endpoint, MSI 00
Capabilities: [100] Advanced Error Reporting
Capabilities: [140] Device Serial Number 00-15-58-ff-ff-2d-20-43
Kernel driver in use: e1000e
Kernel modules: e1000e
03:00.0 Network controller: Intel Corporation PRO/Wireless 3945ABG [Golan] Network Connection (rev 02)
Subsystem: Intel Corporation ThinkPad R60e
Physical Slot: 3
Flags: bus master, fast devsel, latency 0, IRQ 32
Memory at edf00000 (32-bit, non-prefetchable) [size=4K]
Capabilities: [c8] Power Management version 2
Capabilities: [d0] MSI: Enable+ Count=1/1 Maskable- 64bit+
Capabilities: [e0] Express Legacy Endpoint, MSI 00
Capabilities: [100] Advanced Error Reporting
Capabilities: [140] Device Serial Number 00-19-d2-ff-ff-07-1a-cf
Kernel driver in use: iwl3945
Kernel modules: iwl3945
15:00.0 CardBus bridge: Texas Instruments PCI1510 PC card Cardbus Controller
Subsystem: Lenovo ThinkPad T60/R60 series
Physical Slot: 1
Flags: bus master, medium devsel, latency 168, IRQ 16
Memory at e4300000 (32-bit, non-prefetchable) [size=4K]
Bus: primary=15, secondary=16, subordinate=17, sec-latency=176
Memory window 0: e0000000-e3ffffff (prefetchable)
Memory window 1: c4000000-c7ffffff
I/O window 0: 0000a000-0000a0ff
I/O window 1: 0000a400-0000a4ff
16-bit legacy interface ports at 0001
Capabilities: [a0] Power Management version 2
Kernel driver in use: yenta_cardbus
Kernel modules: yenta_socket

Kernel driver in use: radeon

you're using a driver that's provided by mesa amber https://wiki.archlinux.org/title/OpenGL

thanks let me check

I have checked, that is just a tag but not what you are exactly using, even you are using a modern and gpu it may also shown as readon

The gpu driver is installed by arch install and it work well in KDE plasma so I don’t think it is the problem of driver

what happens when you use mesa-amber and run nvtop in the tty, does the gpu appear?

I think I found the problem, after I shut down swww, everything goes smoothly

nvtop is not just for nvidia, not sure if radeontop will work on older gpu's

I think I found the real problem, I need to shut down all the “shadow” things

Also the border rander cause some performance problem

I would like to know how could I disable the color change gradually of the active window border and the inactive border

Ok I found it

why is this open?


Connecting via TS gateway not working anymore

**Useful description of the bug
I have succefully been using FreeRDP to connect to a computer at work via a TS Gateway. What i understand from out IT guys, nothing on the server side has changed. Normal updates to my debian system has been performed. Could it be a change to any of those packages that have made the problem occur? I did not do any updates to the freerdp prior to the problem occured.
No failed connections are shown in the server log. I can still connect via Windows and Android RDP clients. These connections are shown as NTLM authentication in the server log.
Tried using different sec-parameters and other parameters.
deleted .config/freerdp directory
Tried with and without /gu /gd and /gp
Is there any way i can debug this issue further
**command line you have used
xfreerdp /f /v:computername /cert-ignore /log-level:TRACE /d:DOMAIN /u:USERNAME /p:PASSWORD /g:IP_TO_GATEWAY
**to what system did you connect to? (win8, 2008, ..)
Windows SBS 2011
**what actually happened?
[05:25:44:264] [25133:25134] [DEBUG][com.freerdp.client.x11] - Searching for XInput pointer device
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.client.x11] - Pointer device: 8
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.core.nego] - Enabling security layer negotiation: TRUE
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.core.nego] - Enabling restricted admin mode: FALSE
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.core.nego] - Enabling RDP security: TRUE
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.core.nego] - Enabling TLS security: TRUE
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.core.nego] - Enabling NLA security: TRUE
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.core.nego] - Enabling NLA extended security: FALSE
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.core.nego] - state: NEGO_STATE_NLA
[05:25:44:265] [25133:25134] [DEBUG][com.freerdp.core.nego] - Attempting NLA security
[05:25:44:353] [25133:25134] [DEBUG][com.freerdp.core.gateway.rpc] - VIRTUAL_CONNECTION_STATE_INITIAL
[05:25:44:444] [25133:25134] [ERROR][com.freerdp.core] - freerdp_set_last_error ERRCONNECT_TLS_CONNECT_FAILED [0x00020008]
[05:25:44:444] [25133:25134] [ERROR][com.freerdp.core.gateway.tsg] - rpc_connect error!
[05:25:44:444] [25133:25134] [ERROR][com.freerdp.core.nego] - Protocol Security Negotiation Failure
[05:25:44:444] [25133:25134] [ERROR][com.freerdp.core.connection] - Error: protocol security negotiation or connection failure
[05:25:44:444] [25133:25134] [ERROR][com.freerdp.client.x11] - Freerdp connect error exit status 1

**freerdp version (e.g. xfreerdp --version) or package version or git commit
$ xfreerdp --version
This is FreeRDP version 2.0.0-dev (git 3b8352690)

also tried freerdp-nightly without success.
**operating System, architecture, distribution e.g. linux, amd64, debian
$uname -s -r -v -m -o
Linux 4.3.0-1-amd64 #1 SMP Debian 4.3.5-1 (2016-02-06) x86_64 GNU/Linux

**if you built it yourself add some notes which branch you have used, also your cmake parameters can help
Build using instructions in wiki. Master branch
Nightlys installed via apt

is it possible that the certificate on the SBS server has expired (as nothing changed except that some time has passed) ?

I have checked the certificate on the server and it is still valid for 6 months.
Is there any way to get more debug information from FreeRDP than using loglevel:TRACE?

@jcfolke might not be related but did you try with differen /gateway-usage-method settings?

Maybe this is a duplicate of  #3602 - does it work with /gt:rpc ?

Tried
/gateway-usage-method:detect
/gateway-usage-method:direct
/gt:rpc
No sucess, still same problem.
I am trying to get a better understanding about the protocols etc and will do some more trials. Hopefully i will find something out.
//Johan

I removed the git master, removed some old FreeRDP-packages and dependencies in the package manager.
After that i got the FreeRDP-nightly (20171104)installed by the package manager to work.


feat: replace async-std dependency with futures

The async-std runtime shares traits with the futures crate, and async-native-tls doesn't really use anything else besides those traits. Therefore, we can just switch the async-std dependency with futures.
This PR inherits #14.
Closes #10.

I wonder if we should just call it futures runtime instead

Maybe, but "futures" is not really a runtime...

Maybe, but "futures" is not really a runtime...

fair enough


No reduction in model size

I use this command to quantize llama2-7b-chat model, but the model size dosen't change.
CUDA_VISIBLE_DEVICES=0 python3 main.py
--model /mnt/home/model/llama2-7b-chat-hf
--epochs 20 --output_dir ./log/llama2-7b-w2a8
--eval_ppl --wbits 2 --abits 8 --lwc --let
--tasks piqa,arc_easy,arc_challenge,boolq,hellaswag,winogrande
--real_quant
--save_dir /mnt/home/model/abq-llm/llama2-7b-w2a8

Hello, the weights obtained through this way are the calibrated fake quantization weights. To achieve actual weight compression, a packing operation is required to store the weights. For example, using INT2 quantization, the pack operation will use an INT32 to store 16 INT2 element values.

We are developing a complete link from pseudo-quantized models to real packing weights and directly executing WxAy quantized inference in Torch, which is expected to be released within a week after the National Day. We did not release this link before because the engine inside ByteDance is a pure C++ solution.

We are developing a complete link from pseudo-quantized models to real packing weights and directly executing WxAy quantized inference in Torch, which is expected to be released within a week after the National Day. We did not release this link before because the engine inside ByteDance is a pure C++ solution.

Thank you for your work. May I ask when you guys are planning to release the code related to real packing weight and Torch inference

It is expected that this quarter
From: @.>
Date: Tue, Oct 15, 2024, 18:58
Subject: [External] Re: [bytedance/ABQ-LLM] No reduction in model size
(Issue #15)
To: @.>
Cc: @.>, "Comment"<
@.>
We are developing a complete link from pseudo-quantized models to real
packing weights and directly executing WxAy quantized inference in Torch,
which is expected to be released within a week after the National Day. We
did not release this link before because the engine inside ByteDance is a
pure C++ solution.
Thank you for your work. May I ask when you guys are planning to release
the code related to real packing weight and Torch inference
—
Reply to this email directly, view it on GitHub
https://github.com/bytedance/ABQ-LLM/issues/15#issuecomment-2413564994,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AL4LCKNANSLUL2V2UTNCHHTZ3TYMDAVCNFSM6AAAAABPETUI6SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJTGU3DIOJZGQ
.
You are receiving this because you commented.Message ID:
@.***>

@lswzjuer
Did you release the code?
I quantized the model,and the model size of save_dir is still the same as before.


Potential Incompatibility with Act

Hi, I was very excited to see this, and wanted to look into using it. I have never used GitHub Actions before, and decided to use the amazing act tool. When I use act within an NUR repo and the demo action used, I get the following error:
| Warning: the flag --darwin-use-unencrypted-nix-store-volume
|          is no longer needed and will be removed in the future.
|
| warning: installing Nix as root is not supported by this script!
| performing a single-user installation of Nix...
| directory /nix does not exist; creating it by running 'mkdir -m 0755 /nix && chown root /nix' using sudo
| copying Nix to /nix/store...........................................
| installing 'nix-2.5.1'
| error: cannot set host name: Operation not permitted
| (use '--show-trace' to show detailed location information)
| /tmp/nix-binary-tarball-unpack.Vqotj11fBM/unpack/nix-2.5.1-x86_64-linux/install: unable to install Nix into your default profile
| node:child_process:899
|     throw err;
|     ^
|
| Error: Command failed<EMAIL_ADDRESS>|     at checkExecSyncError (node:child_process:861:11)
|     at Object.execFileSync (node:child_process:896:15)
|     at Object.<anonymous> (/run/act/actions/cachix-install-nix-action@v17/lib/main.js:4:17)
|     at Module._compile (node:internal/modules/cjs/loader:1196:14)
|     at Object.Module._extensions..js (node:internal/modules/cjs/loader:1250:10)
|     at Module.load (node:internal/modules/cjs/loader:1074:32)
|     at Function.Module._load (node:internal/modules/cjs/loader:909:12)
|     at Function.executeUserEntryPoint [as runMain] (node:internal/modules/run_main:81:12)
|     at node:internal/main/run_main_module:22:47 {
|   status: 1,
|   signal: null,
|   output: [ null, null, null ],
|   pid: 11,
|   stdout: null,
|   stderr: null
| }
[Build and populate cache/tests-2]   ❌  Failure - Main Install nix
[Build and populate cache/tests-2] exitcode '1': failure
[Build and populate cache/tests-2] 🏁  Job failed
Error: Job 'tests' failed

I am unsure if this is a bug, or user error, but any help would be greatly appreciated. Thanks!

That's an issue with https://github.com/cachix/install-nix-action and a newer version might help. Alternatively, you can use the DetSys Nix Installer like the README:
      - uses: DeterminateSystems/nix-installer-action@main
      - uses: DeterminateSystems/magic-nix-cache-action@main

If I remember correctly this can also be solved by running the container with container-option privileged

Ah, now I may be seeing the issue: I am using Podman with the socket symbolically linked to /var/run/docker.sock, which does work, but may be causing that incompatibility....

That's an issue with https://github.com/cachix/install-nix-action and a newer version might help. Alternatively, you can use the DetSys Nix Installer like the README:
      - uses: DeterminateSystems/nix-installer-action@main
      - uses: DeterminateSystems/magic-nix-cache-action@main

I am using the README example.

But then the error comes from the Cachix Nix Installer, which you may want to remove:

<EMAIL_ADDRESS>

With podman I have the following in my .actrc:
--platform ubuntu-latest=catthehacker/ubuntu:act-latest
--container-daemon-socket /run/user/1000/podman/podman.sock
--container-options --privileged

Looks like you missed the dashes. Also I had to set the container daemon socket to get it to work with podman.

Ah, now I am understanding the issue, I had leftover github actions that I forgot to delete. The actrc helped a lot as well, thanks! Unfortunately I still have an error I am unsure how to fix:
[CI/check]   🐳  docker exec cmd=[bash --noprofile --norc -e -o pipefail /var/run/act/workflow/1-composite-0.sh] user= workdir=
| Set NIX_INSTALLER_EXTRA_CONF=trusted-users = root root
| Set NIX_INSTALLER_URL=https://install.determinate.systems/nix?ci=github
| Set NIX_INSTALLER_DIAGNOSTIC_ENDPOINT=https://install.determinate.systems/nix/diagnostic
| Set NIX_INSTALLER_NO_CONFIRM=true
|   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
|                                  Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 16008  100 16008    0     0  18201      0 --:--:-- --:--:-- --:--:-- 41687
| info: downloading installer https://install.determinate.systems/nix/tag/v0.10.0/nix-installer-x86_64-linux
| Error:
|    0: Planner error
|    1: Error executing action
|    2: Action `configure_init_service` errored
|    3: Could not detect systemd; you may be able to get up and running without systemd with `nix-installer install linux --init none`.
|       See https://github.com/DeterminateSystems/nix-installer#without-systemd-linux-only for documentation on usage and drawbacks.
|
| Location:
|    src/cli/subcommand/install.rs:193
|
| Backtrace omitted. Run with RUST_BACKTRACE=1 environment variable to display it.
| Run with RUST_BACKTRACE=full to include source snippets.
|

Huzzah! I have fixed the last issue by setting the versions of installer and cache to v4 and v1 respectively. Thank you all for the help!


Change the name of core-docs to docs

The name core-docs made sense when this repo would be dedicated to the documentation for .NET Core. Its scope has grown, so its name should change.
When we change the repo name on GitHub, GitHub will issue 301 redirects for almost everything referenced with the existing name.  See here for details. Remotes will automatically redirect, as will forks.
Community members with active forks can continue using them. However, when the reach a point where they don't have open work in progress, recreating the fork using the new repo name is advised.
Community members that have cloned the repo (not through a fork) can follow these instructions to update the remote URL.

Rename is done and URLs on our content have been updated. External links will be redirected to the new repo name appropriately.


Reorganizing so the pull request stuff is collapseable!

This came from a great idea from @kweav and @avahoffman ! Some people know how to do pull requests already so this makes it so people can skip that section if they know.
Also rearranged and re-ordered some of the titles and sections! Shrunk some of the images that were a little too obnoxiously big.

Sorry, accidentally pushed docs/ folder

This PR also inspired https://github.com/jhudsl/OTTR_Template_Website/pulls Because the collapseable menus aren't displayed by htmlpreview so I realized we needed a back up way to still allow people to see a comprehensive preview more easily.


C_CPP : Valid Brackets using Stack in C++

Description 📜
I've completed my issue work , I raised an issue on the Valid Brackets using Stack in C++.
This documentation will explain Valid Brackets using Stack with the help of a problem in C++ :

It is a beginner friendly documentation of Valid Brackets using Stack includes a problem and its solution in C++ code with proper comments ahead.
Explained functions involved in the C++ code.

Fixes #5426

Type of change 📝

[x] Documentation (Content Creation in the form of codes or tutorials)

Domain of Contribution 📊

[x] C/CPP

Checklist ✅

[x] I follow Contributing Guidelines & Code of conduct of this project.
[x] I have performed a self-review of my own code or work.
[x] I have commented my code, particularly in hard-to-understand areas.
[x] My changes generates no new warnings.
[x] I'm GWOC'21 contributor

/unassign

First, implement code, then add input and output blocks.

@kashishahuja2002
It's just an example of the algorithm I explained, you can see down there after implementing the code I've shown the output properly.


send in-Game chat

ttestbetterthanftest on NexusMods:

do you think it would be possible to report on discord the conversation of the inGame chat?

I feel convinced that say and whisper leave one client and go to other clients in range when they are sent. These never seem to be visible to a dedicated server, and when running on the client-hosted server, I can only see the say and whisper messages from the host.


Notes on Tasks (Typos)

Hello @BrooklinJazz ,
Typos

Instead, we should instead rely on the Task module.

A computer with a multi-core processor can perform these cpmcirremt computations in parallel,

Alernatively, you can use the convenient Taskl.await_many/1 function instead.

Hope it helps!

These typos have already been taken cared of right? Taking a look at the files/prs, seems to have been corrected via

#599

Yup!