chore(ci) build nightly releases from jenkins instead of travis-ci (#…

Moves the kong nightly builds off of travis-ci onto a internal private jenkins instance.
This has been running on a Kong fork for about a week successfully and jenkins is configured in such a way that it will not report failures back to github

@hutchic I split it into two commits

@hishamhm yeah it occurred to me that I squashed too far but the forgot to tease them apart thanks for that 👍


Add new web app - manual entry of GPS lat/long/time - to Safe Places suite

Add a 3rd web app to the Safe Places mix that allows a contact tracer to conduct a patient interview with no location history.
Allow GPS Long/Lat/Time to be entered manually using a Google Maps interface and then:
If (has_backend)
Publish via API spec to backend similar to the outcome of the Redaction tool
else
Publish to a json file similar to the outcome of the Redaction tool.
Slack interaction with Steve P on this to give context and some ideas of where to start:
Kyle Towle
Enable infected carriers to provide manually entered location data to a Health Authority (edited)
This one is big because it allows HAP's to start using the tool immediately, even before massive mobile app adoption
Steve Penrod  4 hours ago
I was picturing this as a an independent web app, the Builder.
Geocode a place/address, then get a start time and duration.  Drop 5 minute coordinates to match
Kyle Towle  3 hours ago
Yeah, I think you are correct. It would be a separate app, but in the same "SPL suite", right?
Kyle Towle  3 hours ago
I just think prior to massive adoption, this would be a good thing to get started with and several HA's have asked about it
Steve Penrod  3 hours ago
Yup!
I think it could be built in just a few hours, I bet.  Just use the Google geocoding API and hack up the reaction tool a little.  At least that's my Dr Hackenstein approach.

@kylemtowle @Utzel-Butzel
https://covidmaps.org/submit
Check out "Step 2. Manually enter Location History"
This component was written in React and could easily be brought into dev_react branch

Satoshi, I'm all for it!


Redesingning the contactUs form and map

Adding effects to buttons and input boxes of form

Aligning the map alongside the form for dense look

Are you working on this issue ?
Yes

May u please assign me this issue, I want to work on this part.

@smaranjitghose I want to work on this issue.

I would like to work on this issue if work hasn't completed yet

Hey, can I do it?

@smaranjitghose Can I work on this issue ?

@shreyakapoor08 Sure Give a PR, I will review it accordingly


Update depression compress

https://github.com/paradigmxyz/reth/pull/371#pullrequestreview-1212127516

PR is merged so closing the issue


chore(rockspec) use lua-resty-healthcheck 1.4.2

Approved. We're in the feature freeze now, I assume this update is needed for fixes, not features?


AnchorHandler and ProveCoGateway service

PR contains below:

AnchorHandler changes to support redeem and unstake.
ProveCoGateway service.

It should be merged after merge of PR #175
Fixes #154

working on the PR feedback 👨⚕

Available for review again 🚀


Browser: show aliases

from @szeke :
we should show aliases below the label, as in SQID

Aliases are now displayed in both the Ringgaard- and React-based KGTK browsers.  A finer degree of formatting may be implemented at a later time.


Introducing the OSCODE COPILOT: Your AI-Powered Voice and Text Assistant 🚀"

Closes
Closes #1328
Description
I'm thrilled to present my latest contribution to our community website - the OSCODE COPILOT, an innovative AI-powered voice and text assistant designed to enhance your browsing experience like never before!
Key Features

Seamless Voice Interaction: Say goodbye to conventional navigation! The OSCODE COPILOT allows you to interact with our website using natural language commands. Simply speak, and let the AI take care of the rest.

Smart Text Assistance: Have a question while browsing through code snippets? The OSCODE COPILOT is here to help! It can intelligently analyze your text queries and provide relevant suggestions and resources.

Personalized Recommendations: The AI assistant learns from your browsing patterns and offers personalized recommendations, making it easier for you to discover exciting projects and discussions.

Accessibility at its Core: Inclusivity matters. The OSCODE COPILOT is equipped with advanced accessibility features, ensuring everyone can navigate the website effortlessly.

How to Engage with OSCODE COPILOT

Look for the microphone icon in the website's header and click it to activate voice mode.

Alternatively, you can type your queries in the text input area to interact using text commands.

Experiment and explore! The more you use it, the better it gets at understanding your preferences.

Screenshots

Note to reviewers

Checklist:

[x] I have linked the PR to the correct issue.
[x] I have read the Contribution Guidelines
[x] I have built and tested the changes, and they do not break or show any errors.

@Vaishnavi-Patil2211 ,please review and merge my pull request ,I have added copilot bot with voice and text chat please consider my valuable contribution and assign me valauable contribution

@Vaishnavi-Patil2211 ,I have added valuable ai copilot  can you give me level3?


[5.8] Use application instead of container in console

https://github.com/laravel/framework/pull/25241
Inside \Illuminate\Console\Application class:

The $laravel property is commented as a Laravel application and we currently use more functions than just a container.
The getLaravel method is also commented \Illuminate\Contracts\Foundation\Application as the return type.
The \Illuminate\Tests\Console\ConsoleApplicationTest uses console mock by injecting a Laravel application instead of container instance.

So, I just change a bit at \Illuminate\Console\Application constructor by injecting application instead of container. It will be more clearly for someone who wants to extend this class. For example, building a package.

This limit the usage to just Laravel Framework, when you use console with Lumen or without a framework this would break. :-1:

@crynobone Because it is a breaking change, I send to the branch 5.8. This version is unreleased.

So explain to me again how do Lumen use Illuminate\Console\Application starting from 5.8?

5.8 is a major version. Such as all other breaking changes, a maintainer has to update his/her package.
If this is accepted and there is a conflict with Lumen, Taylor Otwell or other Laravel members will apply this to lumen and Lumen will be release v5.8 too.

Anyway, both in core frameowork or Lumen, the console application is also created by the same way.
// $this->app is \Illuminate\Contracts\Foundation\Application implementation.
if (is_null($this->artisan)) {
    return $this->artisan = (new Artisan($this->app, $this->app->make('events'), $this->app->version()))
                        ->resolveCommands($this->getCommands());
}

Sorry! I don't really understand your expectation.

@xuanquynh

// $this->app is \Illuminate\Contracts\Foundation\Application implementation.

This isn't true. In Lumen $this->app is an instance of Laravel\Lumen\Application which as you can see here doesn't (and shouldn't) implement Illuminate\Contracts\Foundation\Application.
Besides, the Illuminate\Contracts\Foundation\Application interface (and its implementation) is too specific for the Laravel framework so it should be separated into smaller interfaces as discussed in https://github.com/laravel/framework/pull/26477 and after some deprecation period be removed which means that all other services should rely only on the Container interface.

@crynobone @X-Coder264 Thanks for correcting me with the helpful information!


Use about info to determine which sections to archive

The groupinfo (captured by archive_about) tells us which sections we have access to. We should use this to prevent attempting to archive sections that we don't have permissions for.

Might also be able to use ygPerms for this.


Running cancer-syn3-chr6.yaml throws error

Hi,
I am new to this tool.
https://github.com/chapmanb/bcbio-nextgen/blob/master/config/teaching/cancer-syn3-chr6.yaml
The above mentioned pipeline (config/cancer-syn3-chr6.yaml)  gives me the following error.
I was under the impression that gatk is not required for this particular run.
May be I am wrong, any pointers?
Kind regards
[2017-01-04T15:42Z] GATK: VariantAnnotator
[2017-01-04T15:42Z] GATK jar file not found.  Have you run "gatk-register"?
' returned non-zero exit status 1
Traceback (most recent call last):
File "/home/LOCAL_NGS_TOOLS/tools/BCBIO-NEXTGEN/bin/bcbio_nextgen.py", line 234, in
main(**kwargs)
File "/home/LOCAL_NGS_TOOLS/tools/BCBIO-NEXTGEN/bin/bcbio_nextgen.py", line 43, in main
run_main(**kwargs)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 150, in variant2pipeline
samples = genotype.parallel_variantcall_region(samples, run_parallel)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py", line 181, in parallel_variantcall_region
"vrn_file", ["region", "sam_ref", "config"]))
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py", line 32, in grouped_parallel_split_combine
final_output = parallel_fn(parallel_name, split_args)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 758, in call
while self.dispatch_one_batch(iterator):
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 608, in dispatch_one_batch
self._dispatch(tasks)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 571, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 109, in apply_async
result = ImmediateResult(func)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 326, in init
self.results = batch()
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 131, in call
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, *args, **kwargs)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 216, in variantcall_sample
return genotype.variantcall_sample(*args)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py", line 316, in variantcall_sample
call_file = caller_fn(align_bams, items, sam_ref, assoc_files, region, call_file)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/variation/freebayes.py", line 95, in run_freebayes
assoc_files, region, out_file)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/variation/freebayes.py", line 203, in _run_freebayes_paired
config)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/variation/annotation.py", line 162, in annotate_nongatk_vcf
broad_runner.run_gatk(params)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/broad/init.py", line 311, in run_gatk
log_error=log_error)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; unset JAVA_HOME && export PATH=/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/bin:$PATH && /mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/bin/gatk -Xms454M -Xmx9G -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/bcbiotx/tmpmzSIBV -T VariantAnnotator -R /mnt/biousb2/BCBIO-NEXTGEN/share/genomes/Hsapiens/hg38/seq/hg38.fa --variant /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/freebayes/chr6/syn3-chr6_0_16129694.vcf.gz --out /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/bcbiotx/tmpy5Irea/syn3-chr6_0_16129694-gatkann.vcf.gz -L /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/freebayes/chr6/syn3-chr6_0_16129694.vcf.gz --dbsnp /mnt/biousb2/BCBIO-NEXTGEN/share/genomes/Hsapiens/hg38/variation/dbsnp-147.vcf.gz -I /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/align/syn3-normal/syn3-normal-sort.bam -I /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/align/syn3-tumor/syn3-tumor-sort.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
GATK jar file not found. Have you run "gatk-register"?
' returned non-zero exit status 1

Syed;
Thanks for the report and sorry about the issue. You're right that bcbio doesn't need GATK for this workflow and should be skipping this annotation step if not present. I've been trying to reproduce the issue using the latest development version without GATK installed but can not seem to do so.
Which version of bcbio are you running? If it's an older version I know we fixed some issues around this and you could try updating with:
bcbio_nextgen.py upgrade - u development

to see if that fixes the issue. If not, any information about how you installed bcbio would be helpful to trying to understand the source of the issue so we can fix. Thanks for the help debubbing.

Thanks @chapmanb;
AFAIK - I have followed the following steps:

I have installed the tool using the following command
 wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py

bcbio_nextgen_install.py path/to/share --tooldir=path/to/tool/dir --genomes hg38 --distribution ubuntu

Configured the genomes and indexed it using the following command
 bin/bcbio_setup_genome.py -f /path/to/share/genomes/Hsapiens/hg38/seq/hg38.fa -n Hsapiens -b hg38 -i bowtie bowtie2 bwa novoalign rtg snap star ucsc seq --cores 8

Installed External Data
 bin/bcbio_nextgen.py upgrade -u skip --tooldir=path/to/tool/dir --genomes hg38 --data --datatarget vep --datatarget variation

Then upgraded it to the development version 1.0.1a0
bin/bcbio_nextgen.py upgrade -u development --tooldir=path/to/tool/dir

Preparing and Running
mkdir -p run
cd run
wget https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/teaching/cancer-syn3-chr6-prep.sh
bash cancer-syn3-chr6-prep.sh

Running test case
 cd cancer-syn3-chr6/work
 path/to/bin/bcbio_nextgen.py ../config/cancer-syn3-chr6.yaml -n 16

Thanks for all the details. This looks like the generally right procedure do I don't see any issues there. Apologies, I'm not sure why the check for gatk is indicating it is present and continuing, but I pushed a fix to attempt to resolve it. Could you try updating to the latest development:
bcbio_nextgen.py upgrade -u development

and re-running? Fingers crossed it will now do the right thing.
This isn't anything to do with your problem, but there is no need to do step 2 in your process as a separate step. bcbio_setup_genome.py is meant for other genomes bcbio doesn't support by default. You can install other indices for hg38 with the --aligners argument:
bcbion_nextgen.py upgrade --data --genomes hg38 --aligners bowtie --aligners bowtie2 --aligners bwa --aligners novoalign --aligners rtg --aligners snap --aligners star

Hope this helps.

Thank you for the patch and tips, much appreciated!
It ran but unfortunately it didn't finish the job.  It crashed with the following error in the end, any pointers please?
[2017-01-04T22:19Z] Prioritize: convert to tab delimited
[2017-01-04T22:19Z]
[2017-01-04T22:19Z] Uncaught exception occurred
Traceback (most recent call last):
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; zcat /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/structural/syn3-tumor/prioritize/syn3-tumor-lumpy-prioritize-wgts-prep-simple-prep.vcf.gz | vawk -v SNAME=syn3-tumor -v CALLER=lumpy '{if (($7 == "PASS" || $7 == ".") && (S$syn3-tumor$GT != "0/0")) print CALLER,SNAME,$1,$2,I$END,I$SVTYPE=="BND" ? I$SVTYPE":"$3":"I$MATEID : I$SVTYPE,I$LOF,I$SIMPLE_ANN,S$syn3-tumor$SR,S$syn3-tumor$PE,S$syn3-tumor$PR}' > /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/bcbiotx/tmpjbldwi/syn3-tumor-lumpy-prioritize.tsv
gzip: stdout: Broken pipe
' returned non-zero exit status 1
Traceback (most recent call last):
File "/home/arahman/LOCAL_NGS_TOOLS/tools/BCBIO-NEXTGEN/bin/bcbio_nextgen.py", line 234, in
main(**kwargs)
File "/home/arahman/LOCAL_NGS_TOOLS/tools/BCBIO-NEXTGEN/bin/bcbio_nextgen.py", line 43, in main
run_main(**kwargs)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 180, in variant2pipeline
samples = structural.run(samples, run_parallel, "ensemble")
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/structural/init.py", line 146, in run
for xs in to_process.values()))
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 758, in call
while self.dispatch_one_batch(iterator):
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 608, in dispatch_one_batch
self._dispatch(tasks)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 571, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 109, in apply_async
result = ImmediateResult(func)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 326, in init
self.results = batch()
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 131, in call
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, *args, **kwargs)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 244, in detect_sv
return structural.detect_sv(*args)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/structural/init.py", line 165, in detect_sv
for svdata in caller_fn(items):
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/structural/prioritize.py", line 38, in run
for vcaller, vfile, post_prior_fn in inputs]
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/structural/prioritize.py", line 122, in _prioritize_vcf
do.run(cmd.format(**locals()), "Prioritize: convert to tab delimited")
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; zcat /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/structural/syn3-tumor/prioritize/syn3-tumor-lumpy-prioritize-wgts-prep-simple-prep.vcf.gz | vawk -v SNAME=syn3-tumor -v CALLER=lumpy '{if (($7 == "PASS" || $7 == ".") && (S$syn3-tumor$GT != "0/0")) print CALLER,SNAME,$1,$2,I$END,I$SVTYPE=="BND" ? I$SVTYPE":"$3":"I$MATEID : I$SVTYPE,I$LOF,I$SIMPLE_ANN,S$syn3-tumor$SR,S$syn3-tumor$PE,S$syn3-tumor$PR}' > /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/bcbiotx/tmpjbldwi/syn3-tumor-lumpy-prioritize.tsv
gzip: stdout: Broken pipe
' returned non-zero exit status 1

Also, found an error in log file.
[2017-01-04T22:10Z] lumpyexpress : syn3-normal
[2017-01-04T22:10Z] Sourcing executables from /mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/bin/lumpyexpress.config ...
[2017-01-04T22:10Z]
[2017-01-04T22:10Z] Checking for required python modules (/mnt/biousb2/BCBIO-NEXTGEN/share/anaconda/bin/python)...
[2017-01-04T22:10Z]
[2017-01-04T22:10Z]     create temporary directory
[2017-01-04T22:10Z] Calculating insert distributions...
[2017-01-04T22:10Z] sambamba-view:  (Broken pipe)

Syed;
Glad that fixed the previous error. It looks like we're running into something new during structural variant prioritization. Could you try running the failing command outside of bcbio:
zcat /mnt/biousb2/NGS_DATA/cancer/cancer-syn3-chr6/work/structural/syn3-tumor/prioritize/syn3-tumor-lumpy-prioritize-wgts-prep-simple-prep.vcf.gz | vawk -v SNAME=syn3-tumor -v CALLER=lumpy '{if (($7 == "PASS" || $7 == ".") && (S$syn3-tumor$GT != "0/0")) print CALLER,SNAME,$1,$2,I$END,I$SVTYPE=="BND" ? I$SVTYPE":"$3":"I$MATEID : I$SVTYPE,I$LOF,I$SIMPLE_ANN,S$syn3-tumor$SR,S$syn3-tumor$PE,S$syn3-tumor$PR}' > syn3-tumor-lumpy-prioritize.tsv

Does it work, or fail consistently? Are there any useful error messages. It seems like something is slightly problematic with your setup but I'm not sure what. What type of system are you running this on and I'll see if I can reproduce.
The sambamba-view message you found is not a problem, that's an expected message. It reads the start of a BAM file, so the shell reports the pipe is broken when it doesn't read the full file.
Hope that helps.

Hi Brad;
Here is the output from the above mentioned command.
tail syn3-tumor-lumpy-prioritize.tsv
awk: line 1: illegal reference to array fmt
awk: line 1: illegal reference to array fmt
awk: line 1: illegal reference to array fmt
awk: line 1: illegal reference to array fmt
awk: line 1: illegal reference to array x

Thanks,

Syed;
Thanks for testing and for the file. This works cleanly on my system so from the error messages it looks like an incompatibility with the vawk command and your version of awk. What does:
awk --version

say? What type of system are you running bcbio on? I'll work on getting a fix in place for these, which will need an update of vawk to use an internally installed gawk (instead of your default system awk). I should have that settled early tomorrow and can report back here. In the short term you can disable prioritization by commenting out svprioritize: cancer/civic in your config. Hopefully this will help your test run get to completion. Thanks again for all the help debugging this.

@chapmanb 👍
I had to install gawk instead of vawk.
awk --version
GNU Awk 4.1.3, API: 1.1 (GNU MPFR 3.1.4, GNU MP 6.1.0)

Good news is that it works smoothy and yes creates far less noisy debugging logging info.
Thanks a lot for your help.
I am already liking the tool!

Syed;
Thanks for confirming that it was a gawk/awk issue and glad it now finishes correctly. I pushed a permanent fix so vawk will use an internally installed gawk and should no longer rely on the external installation. Hope things continue to run cleanly for you on real analyses.


chore(main): release 1.4.0

:robot: I have created a release beep boop
1.4.0 (2024-12-01)
Features

add action to test the build (#39) (82472f5)

This PR was generated with Release Please. See documentation.

:robot: Created releases:

v1.4.0
:sunflower:


JCenter and Maven Central serving two different artifacts for 4.1.1

Hi!
We have dependency verification enabled in our build and when updating to the latest version of Kotlin (1.5.20), we started seeing verification failures:
https://ge.gradle.org/s/dt6v732iuevd2
The Kotlin dependency is now bringing in a newer version of this plugin:
https://ge.gradle.org/s/dt6v732iuevd2/dependencies?dependencies=de.undercouch&expandAll&focusedDependency=Wzc4LDAsNzYzMSxbMTksMCxbMjNdXV0&focusedDependencyView=versions
The dependency verification report says that the signature doesn't match the jar file.
I took a look on Maven Central and downloaded the files from:
https://repo1.maven.org/maven2/de/undercouch/gradle-download-task/4.1.1/
gradle-download-task-4.1.1.jar -> 5da00a4a96829700216768887a8f3051 (MD5)
gradle-download-task-4.1.1.jar.asc -> 9889ae9893f6227893ee0828139c687a (MD5)
We have JCenter mirrored to our own repository, but JCenter is currently serving the same artifacts:
https://repo.gradle.org/artifactory/libs/de/undercouch/gradle-download-task/4.1.1/
gradle-download-task-4.1.1.jar -> 93578a8acb236688e2aebf33519b1dd2 (MD5)
gradle-download-task-4.1.1.jar.asc -> 9889ae9893f6227893ee0828139c687a (MD5)
This seems to be saying that the signature files are the same for both repositories, but the jar files are different somehow.
When I compared the jars, they seem to have identical contents, so I think the differences are not from something malicious. I'm not sure how JCenter and Maven Central wound up with two different jars, do you?
This is going to cause headaches/confusion whenever someone runs into this. I checked 4.0.4 and 4.1.0 and they looked identical.
I've attached the jars here as well (rename from .zip) in case one or the other repository changes behavior.
Could you contact JFrog and see if they can fix something on their side?
Or could you publish a 4.1.2?
Thanks!
From Maven Central
From JCenter

Thanks for bringing this up. Since JCenter is read-only now [1], I think the only possible solution is to publish a 4.1.2 to Maven only. I will try to do this within the next days.
[1] https://jfrog.com/blog/into-the-sunset-bintray-jcenter-gocenter-and-chartcenter/

gradle-download-task 4.1.2 has just been released to Maven Central and the Gradle plugin portal (alternative Maven URL: https://plugins.gradle.org/m2/).


How to fire event when click the old selected option

Hi - Is it possible to fire select event when click a option, even it's a old selected option?

This appears to be more of a usage question than a bug report or common feature request.  As we continue to keep the Select2 issue tracker geared towards these two areas, bug reports and common feature requests, we are redirecting usage questions to other communities such as the mailing list, IRC, or Stack Overflow.


Updates to AWS ECS deploy guide

Why:

Following the steps in the guide, errors will occur running the workflow due to these syntax problems.

Example failed run with the guide syntax for environment variables before these changes: https://github.com/cal-itp/docker-django-aws-test/actions/runs/494684748

Example successful run with the updated environment variable syntax reflected in this PR: https://github.com/cal-itp/docker-django-aws-test/actions/runs/494699023

Example failed run with the output redirect to $GITHUB_ENV before these changes: https://github.com/cal-itp/docker-django-aws-test/runs/1724635263

Example successful (step) with the updated ::set-ouput syntax reflected in this PR: https://github.com/cal-itp/docker-django-aws-test/runs/1724692920

What's being changed:

Syntax of environment variables used in jobs.<job_id>.steps[*].with, from $ENV_VAR to ${{ env.ENV_VAR }}
Fix to output command, from redirecting to $GITHUB_ENV to using ::set-output name=variable::

Check off the following:

[x] I have reviewed my changes in staging. (look for the deploy-to-heroku link in your pull request, then click View deployment)
[x] For content changes, I have reviewed the localization checklist
[x] For content changes, I have reviewed the Content style guide for GitHub Docs.

Direct link to staging deploy: https://docs-3002--aws-ecs-updates.herokuapp.com/en/actions/guides/deploying-to-amazon-elastic-container-service

@thekaveman Thanks so much for opening a PR! I'll get this triaged for review ✨

@thekaveman Thanks so much for opening a PR! I'll get this triaged for review ✨

Please don't close!

Please don't close!


"Feleacu", "Casele Micești", "Gheorghieni", "Sărădiș", "Vâlcele" are listed in the drop-down

Description:
When user writes "Feleacu", "Casele Micești", "Gheorghieni", "Sărădiș" and "Vâlcele" the locations appear in the drop-down menu next to the comune and the county which is a part according to the law
Precondition:
The website is up an running.

Step 1
Write in the search bar "Feleacu"
Expected results
The location appears in the drop-down menu as "Sat Feleacu, CLUJ (Feleacu)"

Step 3
Write in the search bar "Casele Micești"
Expected results
The location appears in the drop-down menu as "Sat Casele Micești, CLUJ (Feleacu)"

Step 8
Press "x" button.
Expected results
The location was deleted from the search bar.

Step 9
Write in the search bar "Vâlcele"
Expected results
The location appears in the drop-down menu as "Sat Vâlcele, CLUJ (Feleacu)"


Questions about the competing method in Figure 5 (c)

Hello,
Thank you for the fantastic work. May I ask a question about Figure 5 (c)? I notice the Core-set is listed as a competing method on COCO, which is an important result, and I believe this is the first paper that presents it.
In fact, I am trying to realize the same result on COCO. However, I find that to get the result I need to infer the model on the whole COCO training set (~ 118k images) and compute the distance for every pair of images, which is memory and time consuming: the distance matrix size is nearly 40GB. Moreover, running mixed integer programming (MIP) is even more expensive.
Therefore, may I ask how did you work this out? Did you run the full Core-set algorithm that contains the MIP? Or only the Greedy K-Centroid was used?
Additionally, could you please provide the initial COCO training set (the 2% one)? As active learning is prone to variation in initialization. Starting from the same initialization can make sure the following works to have a fair comparison with yours.
Looking forward to your answer :-)

Hello,
Thanks for your attention to our work.
For Core-set, we use the function in this repository for implementation. So we only use the Greedy K-Centroid method.
For COCO training set, we set the random seed here before initialization. You may use the same random seed 666.
Hope this answer would be useful to you :-)

Cool!. Thank you for the quick reply. It's very helpful. :-)

Hi. Sorry for bothering again. May I ask how many epochs did you train for the competing methods that did not require adversarial training? Is it still 26 epochs?

Yes.

Hi. But I found that a simple ResNet50 RetinaNet model with 26 epoch training can achieve ~14 AP using your initial set (2% images), which is far better than the numbers reported in the paper. Is there anything wrong?

Oh sorry, just found a bug in my code.... My bad :-(


os.sched_getaffinity error

while running molbart.predict in macos I got the error i received the error AttributeError: module 'os' has no attribute 'sched_getaffinity' in molbart/modules/data/base.py. Similary I received error `AttributeError: module 'os' has no attribute 'sched_getaffinity'  in molbart/models/chemformer.py. Currently I handled the issue with
try:
           self._num_workers = len(os.sched_getaffinity(0))
except AttributeError:
           self._num_workers = os.cpu_count() or 1

try:
           n_cpus = len(os.sched_getaffinity(0))
except AttributeError:
           n_cpus = os.cpu_count() or 1  # Default to 1 if cpu_count() is None

I am wondering if this serves the original purpose of sched_getaffinity(0) and is there a better way to handle it in mac ?

Looks like it could be a Mac-specific issue. The main idea behind using sched_getaffinity() is to get the correct number of CPUs that the user has access to (cpu_count() will not always give the correct number when running the code on a server).
For efficient training/inference it's important to make sure the dataloaders use multiple workers so that the data processing and loading is not the bottleneck. If you're not running on a server cpu_count() should give you the correct answer, otherwise you can always just set num_workers to a small number (I think 4 should be sufficient).

Thank you very much for the clarification.


Add CL_FORK env to create genesis at arbitrary forks (phase0, altair, merge)

Pull protolambda/eth2-testnet-genesis instead of skylenet/eth2-testnet-genesis as the changes were merged from the latter to the former.
Added CL_FORK environment variable to pass to eth2-testnet-genesis for genesis at forks other than phase0
Workaround for a bug where sed -i fails for Docker on Mac with VirtioFS enabled (see https://github.com/docker/for-mac/issues/6277)
I know that's not necessary, but it alleviates some pain for Mac peoples without hurting others, so why not? :-)
Updated README.md

For the record, I only tested Altair genesis so far, and it works just fine :)


YUNIKORN-462: Streamline core to shim update on allocation change

What is this PR for?
SI changes to remove ReSyncSchedulerCache plugin and added new fields in AllocationRelease message
What type of PR is it?

[ ] - Improvement

Todos

[ ] - Task

What is the Jira issue?
https://issues.apache.org/jira/browse/YUNIKORN-462
How should this be tested?
Screenshots (if appropriate)
Questions:

[ ] - The licenses files need update.
[ ] - There is breaking changes for older versions.
[ ] - It needs documentation.

Sorry that it has taken so long to get back to you :-(
Way to long an update but it sets the direction for the other two repos involved
We have one change in mind remove the ReSyncSchedulerCache call. The call is made twice from the core to the shim:

for new allocations
for removed allocations

First new allocations: the message we send is a RMNewAllocationsEvent with all allocations that are new. That event is currently async. That is why we first we call a sync cache update with partial info. The change is that the event will become a sync call. We have enough information in the current Allocations array. This is part of the event we send and we can also call the assume of the pod inside the cache on the shim side by pulling that key from the allocation. We always call assume pod for every new allocation.
Simple change on the SI side: we can remove the AssumedAllocation message. Leverage existing information for the AllocationKey
On the remove side we have 4 locations where we send a RMReleaseAllocationEvent. Only in one location, as you pointed out, we also call the sync of the cache. The sync of the cache triggers the forget of an assumed pod. Only looking at the path that sends events back. The cache sync is part of one of these calls.

handleRMUpdateApplicationEvent handles removal of an application. Does not call the cache sync.
updateNode handles the node removal. Does not call the cache sync.
schedule triggers the release of a placeholder. Does not call the cache sync.
processAllocationReleases is processing release requests send by the shim. This calls the cache sync.
The termination type for call 1,2 and 4 is STOPPED_BY_RM. For call 2 it is PLACEHOLDER_REPLACED.
Every single allocation is assumed as per above description. So we should also forget a pod, remove it, from the assumed pod list when we remove the pod without exception. If we do not we could leak the entry in the assumed pod cache structure. There should be no difference in the communication for any of these cases between core and shim.

Simple change on the SI side: we can remove the ForgotAllocation message. Add the allocationKey to the AllocationRelease message (check case for the new field!)
The core sends the events synchronously. The shim collapses the assume call into the event processing for new allocations, returns as soon as possible forking of the long running tasks. The shim collapses the forget call into the event processing for the remove. If there is any special cases to not forget the assumption of a removed pod then the shim must implement it. The core should not be the one that decides this.
After this we also need to completely remove the ReSyncSchedulerCacheArgs and the ReSyncSchedulerCache call from the interface.

Thanks for your detailed explanation and giving me a clear picture.
Have taken care of SI and Core accordingly. As discussed, once YUNIKORN-876 goes in, we can work on the shim. Summary is, We should call clear the cache on shim side for all these 4 calls. Since we need to clear cache in all 4 calls, then probably we should make all these calls sync?


Available communication methods

I would like to make language server for Pascal but I'm not sure which methods LSP uses for communication with the server. I think the options are named pipes and sockets, is that correct? If sockets are used is there a default port to listen on and if named pipes a specific name to be used?
I looked over the spec at https://microsoft.github.io/language-server-protocol/ but they just say the data format is JSON-RPC but nothing as to how the tools communicate (I guess that application specific details).

Named pipes (stdout and stderr) are the most common.
Some servers (also) support TCP, this package currently only allows users to hardcode the port as an argument to the server (there is no default)
In the future this package will select the port automatically and pass it to the server as an argument - this is what the LSP spec suggests

Thanks, I see in the preference there is a "tcp_port" setting.  If I use sockets can I run the server from the terminal so I debug input from LSP? I think LSP is meant to spawn the process itself but using sockets means this isn't strictly necessary.
I've never used named pipes before but I think you mean that if I simply write to stdout then LSP will parse the output? That sounds easiest for sure.

Correct, tcp mode makes it easy to run from a debugger.
Some challenge with named pipes exists - for example in PHP on Windows stdio communication blocks the process/threads - only TCP mode works there. But most other languages have no such issues.

Then do we even need the "command" setting? I'm trying my first tests by running the server on <IP_ADDRESS> and listening on port 6050 but I don't get any data back from LSP when I enable it in the project.
Does that setting look correct? I'm thinking I can omit "command" because the server is already running and so LSP shouldn't need to spawn the process itself. Looking at the ST console I don't get any feedback either (I was expected LSP errors to appear at least)
"clients": {
"fpc-language-server":
{
"command": ["/Users/ryanjoseph/Desktop/symbols/fpcls"],
"scopes": ["source.pascal"],
"syntaxes": ["Packages/FPC/FPC.sublime-syntax"],
"languageId": "pascal",
"tcp_port": 6050,
}
},

Correct, command can be omitted in this  case (did you try it?)
I'd like to invite you to the gitter chat (gitter.im/SublimeLSP/Lobby) as this is turning more into a support discussion.

I asked my question again on gitter. Thanks.


Address bonsai self-destruct stale code present

PR description
During an initial worldstate sync, a self-destruct that occurs between the initial pivot block and final heal pivot block will leave stale code in bonsai code storage.  If subsequently the code is redeployed via create2 to the same contract address, the bonsai db will fail to roll code changes to the block where the redeployment occurs.  This presents in a handful of ways such as 'worldstate not present' or 'unable to copy layered worldstate'.
Discussing with @matkt, since the repivot and heal process does not presently have an opportunity to 'heal' the code storage, and we should be able to trust the trielogs, this PR changes the rollCodeForward behavior to overwrite stale code if/when it is found.  This should resolve #4784 and give the besu team an opportunity to revisit this in flat database heal work that is ongoing.
Fixed Issue(s)

addresses #4784
Documentation

[ ] I thought about documentation and added the doc-change-required label to this PR if
updates are required.

Changelog

[ ] I thought about the changelog and included a changelog update if required.

Testing with a database that exhibited this error on block 16369752.  A self-destruct for contract this occurred during the initial sync/heal phase of besu, and was subsequently recreated on the problem block which exhibited the "unable to copy layered worldstate" error:  https://etherscan.io/address/0x0000000000a1c1accd070e0003838859fe4f7046#internaltx
testing with main yields the error state with this database (empty optional returned for the worldstate)
testing with this PR yields no error and this log output:
2023-01-12 11:08:01.756-08:00 | vert.x-worker-thread-6 | WARN  | BonsaiWorldStateUpdater | At Address=0x0000000000a1c1accd070e0003838859fe4f7046, expected to create code, but code exists. Overwriting.


The section vsphere cpi in Rancher is not visible when creating a custom RKE2 cluster selecting v1.23.14 or 1.24.8

Internal reference: SURE-5747
Reported in 2.6.8
The section vsphere cpi in Rancher is not visible when creating a custom RKE2 cluster selecting v1.23.14 or 1.24.8.
Troubleshooting steps:
The user is running Rancher 2.6.8 in RKE2 cluster, but Support could reproduce the issue deploying Rancher in RKE1.
Repro steps:

Fresh installation: Rancher 2.6.8
From Cluster Management ==> Create ==> Toggle switch to RKE2/K3s ==> Custom
In Cluster Configuration ==> Basics ==> Kubernetes Version: 1.24.8+rke2r1 and Cloud Provider set to vSphere.  Note that a new message appears: "Important: Configure the vSphere Cloud Provider and Storage Provider options in the Add-On Config tab."
Click on the Add-On Config
The "vSphere CPI Configuration" is missing:

If version 1.22.14 is selected, the CPI Configuration is showed (CF image cluster122yaml)

When v1.22.16+rke2r1 is selected, using Chrome dev tools, the redirect goes to:

rancher-rke2-charts?link=info&chartName=rancher-vsphere-csi&version=2.5.1-rancher101
rancher-rke2-charts?link=info&chartName=rancher-vsphere-cpi&version=1.2.201

When v1.24.8 is selected,  using Chrome dev tools, the redirect goes to

rancher-rke2-charts?link=info&chartName=rancher-vsphere-csi&version=2.6.2-rancher100

Workaround: none
Actual behavior:
The CPI configuration is missing for Kubernetes version 1.23.14 and 1.24.8
Expected behavior:
The CPI Configuration should be visible for the 3 versions of Kubernetes
Additional notes:
According to https://github.com/rancher/rancher/issues/36987, the vSphere CPI and CSI should be visible for 1.122 and 1.23, but in the UI, it is only visible for 1.22.

Possibly caused by https://github.com/rancher/rancher/issues/39462#issuecomment-1306433102. @jiaqiluo , could you please look into it?

The bug is reproduced on rancher v2.7.5 when the local cluster version is k3s v1.26.4+k3s1;
the bug is NOT reproduced when the local cluster version is k3s v1.25.5+k3s1.
When reproduced, there are no sections for vSphere-CSI or vSphere-CPI under the "Add-on Config" in Rnacher UI when creating a custom RKE2 1.23.17+rke2r1 cluster with the cloud provider being vSphere.
The things that make the RKE2 1.23.17 different from other versions are the following annotations  on its associated  rancher-vsphere-csi (2.6.1-rancher101) and rancher-vsphere-cpi (1.4.101) charts:
catalog.cattle.io/kube-version: '>= 1.20.0-0 < 1.26.0-0'
catalog.cattle.io/rancher-version: '>= 2.6.0-0'

As a result, when Rancher v2.7.5 is installed on a k3s 1.26.4 cluster, those two charts are hidden from the index returned from the following endpoint
/v1/catalog.cattle.io.clusterrepos/rancher-rke2-charts?link=index

However, it is important to know that those two specific versions of the charts are still accessible via the following endpoint:
v1/catalog.cattle.io.clusterrepos/rancher-rke2-charts?link=info&chartName=<chart-came>&version=<version>

Ideally, when the cluster k8s version is changed on the cluster creation page, UI should retrieve the chart info for the associated versions via the above endpoint (if the chart info is not already in the local cache). However, it looks like UI does the retrieval only if the version exists in the chart index file. (This is proven by monitoring the network activities when changing the versions).
With that being said, we would like the UI team to confirm whether the above behavior is true. And if it is true, we can fix the bug in the UI: drop the check for the existence of the chart version before retrieving the chart info in this scenario.
ping the UI team - @gaktive @codyrancher
cc @snasovich

As per https://github.com/rancher/dashboard/issues/9520#issuecomment-1702869821, moving this back to rancher/dashboard


feature: Metadata query endpoint

Note to self: Fix that flaky queue test

Note to self: Fix that flaky queue test


Change how --config flag is working

Currently you can use --config flag to set the config file path. But there is no option to change the place where completed uploads database is storing the upload files or where secrets backend is keeping the credentials.
If you use --config /home/user/my_config/config.hjson:
/home/user/my_config
|-- config.hjson (file)
|
.config/gphotos-uploader-cli
|-- uploads.db (folder)
|-- secrets (folder)

This makes --config flag useless for:

Mounting all configuration files inside a mounted volume in a docker.
Using completed uploads database for different accounts. Currently the database is the same for all the accounts, and it would be interesting to maintain different one per account.
Havng configuration files per environment. Let's imagine you want to have different PRE/PRO env.

Describe the solution you'd like
I would like to change --config to set the folder where all these configuration is kept.
If you use --config /home/user/my_config:
/home/user/my_config
|-- config.hjson (file)
|-- uploads.db (folder)
|-- secrets (folder)

and by default (if you don't set any config file ~/.config/gphotos-uploader-cli will be used:
.config/gphotos-uploader-cli
|-- config.hjson (file)
|-- uploads.db (folder)
|-- secrets (folder)

You will be able to use --config or GPHOTOS_UPLOADER_CONFIG_DIR environment variable to set configuration folder. --config will override environment variable. WDYT?
Thanks @rfgamaral for raising it up

Looks good to me 🙂


First pass implementation of chords

The most important part of this is that it gets the structure of the control flow right for doing chords.
The Entity -> Set DateTime lookup function is really stupid/slow but this can be improved in a later PR.

the C looks fine :+1:

:+1:


The 500th closed issue!

@AlexHGaming Please do not make any more pointless issues, its the reason why we even have 500 issues in the first place.

@Megabyte918 oh ok, sorry lol


Volume.delete method

Wanted this for an integration test thing. Also we had no tests for VolumeDelete so I added that

@prbot approve


Can we raise a more informative error when papermill is not installed?

Context
When papermill is not in environment the job fails without any sensible description. There are some ideas to solve it with LBYL (https://github.com/nebari-dev/nebari/issues/1838):
https://github.com/nebari-dev/argo-jupyter-scheduler/blob/1d9f1d175dd40a2dfc25497f215f60e4fec24e56/argo_jupyter_scheduler/utils.py#L135-L137
but I think what would be neat is if we could return an informative error from the container itself:
currently it just shows "Workflow failed"

Maybe it is as simple as adjusting these lines:
https://github.com/nebari-dev/argo-jupyter-scheduler/blob/1d9f1d175dd40a2dfc25497f215f60e4fec24e56/argo_jupyter_scheduler/utils.py#L207-L210
?
Value and/or benefit
Less user confusion. Users using the scheduler function rather than giving up after first attempt because it is not working.
Anything else?
No response

Definitely agree with this :+1:

I've implemented this in #10.


Update pthreads.php

Updated stubs

Hello. Please, sync your fork and create PR without conflicts.

It might be better to take the version of bakedpotat0.

See issue WI-44013


Modelling of organizations

Discussed during the 16 April meeting.
The initial proposal has three distinct subclasses of StatisticalOrganization: NationalStatisticalInstitute, OtherNationalAuthority and InternationalAgency.
Luca makes the following observations:

In the context of the ESS, « Other National Authority » has a very precise signification and its reuse in the context of COOS could bring confusion since non-European organization could use it in a different way.

So there are two solutions:

Find a new name to replace the term currently proposed.
Only define two classes of « Statistical Organisation »: « International Agency »  et « National Statistical Institute ». The ONAs would the simply be direct instances of « Statistical Organisation ».

Agreed on 2 July meeting: just drop the ONA.


problem in 3D recon on ETH. Points shifted from reference images

Hi ! Thank you for the great work and sharing! ASLfeat is a very competitive method and is currently one of the best in MMA.
So, I have been interested in the ASLfeat's performance on 3D reconstruction as it seems that ASLfeat is doing very well in providing high registered images and sparse points.
So, I run a small test using the output from your package and integrate it into ETH Benchmark evaluation on Herzjesu.

The problem is that I have got the following results. The sparse points projected on images are shifted from where it supposed to be (as shown in the image number 8 on the right).

Could you advice if I should set anything in addition ?
Here is the results of ASLfeat.

Also, just to give a reference. Here is the results of SIFT. The other methods seem to do ok too.

Also, I attached my setting in the config here.
If it happened that I did not set something right, please let me know:.
data_name: 'eth'
data_split: ['Herzjesu', 'Fountain', 'South-Building']  #['Gendarmenmarkt', 'Madrid_Metropolis', 'Tower_of_London']
data_root: '/mnt/HDD4TB1/local-feature-evaluation/datasets'
dump_root:
truncate: [0, null]
model_path: 'pretrained/aslfeat/model.ckpt-380000' # 'pretrained/aslfeat/model.ckpt-60000'  #
overwrite: true
net:
  max_dim: 2048 #1600 #
  config:
    kpt_n: 20000 # 20000
    kpt_refinement: true
    deform_desc: 1
    score_thld: 0.5
    edge_thld: 10
    multi_scale: true
    multi_level: true
    nms_size: 3
    eof_mask: 5
    need_norm: true
    use_peakiness: true
post_format:
  suffix: '_aslfeat20K2048_380'

Just to update. I think I found a big bug in your code...
In L 59, feat_model, you have made an extract scaling which leads to the wrong scaling....
So, the scalling   np.array([W / data_size[1], H / data_size[0]], dtype=np.float32)    should be removed.
So, instead of this .....
kpts = kpts[idxs] *** np.array([W / data_size[1], H / data_size[0]], dtype=np.float32)**
It should be this ....
kpts = kpts[idxs]

Hi,
Thank you very much for this observation! We checked the code and find this is indeed a scaling bug.  We have fixed it in the latest commit. This bug causes issues when input size exceeds config['max_dim'], which is set as 2048 by default. We will investigate the bug's influence on our previous results.
The shifting issue in your case mighted be caused by this scaling bug. Could you please try our latest code and tell us if the probelm is solved?

Thanks for letting me know. I have seen the commit id 4ca6cf4.... You have removed that line and that fixed the issue on 3D recon. ....But that is as far as I know.

@GabbySuwichaya Hi, When you do 3D reconstruction, what kind of matching method did you using on ASLfeat?

@DHNicoles  I used the NN Matching, just like those in https://github.com/ahojnnes/local-feature-evaluation.

Thanks! I have used SuperPoint+SuperGlue for 3D reconstruction, and visualized with colmap, it works well.
So I'm a little interested in the result of ASLFeat+SuperGlue, but no relevant discussion was found.

@DHNicoles I am not sure about the size of ASLFeat's descriptor... So far what I know is that SuperGlue was trained with SuperPoints, and the pre-trained model is based on the descriptor size of 256.
Moreover, if you read SuperGlue's paper carefully, you'll find that the SuperGlue has been tested with SuperPoint as well as SIFT. In some way, you may need to train SuperGlue + ASLFeat features.....by yourself..... as far as I can remember. The author of SuperGlue does not release the training script. [But if you find one, I would appreciate if you can share the code.]
However, I think the match of SuperGlue + ASLFeat should work well, because ASLFeat has very high repeatability, just like SuperPoint [This is an underlying condition of SuperGlue].

Hi ! Thank you for the great work and sharing! ASLfeat is a very competitive method and is currently one of the best in MMA.
So, I have been interested in the ASLfeat's performance on 3D reconstruction as it seems that ASLfeat is doing very well in providing high registered images and sparse points.
So, I run a small test using the output from your package and integrate it into ETH Benchmark evaluation on Herzjesu.

The problem is that I have got the following results. The sparse points projected on images are shifted from where it supposed to be (as shown in the image number 8 on the right).

Could you advice if I should set anything in addition ?
Here is the results of ASLfeat.

Also, just to give a reference. Here is the results of SIFT. The other methods seem to do ok too.

Also, I attached my setting in the config here.
If it happened that I did not set something right, please let me know:.
data_name: 'eth'
data_split: ['Herzjesu', 'Fountain', 'South-Building']  #['Gendarmenmarkt', 'Madrid_Metropolis', 'Tower_of_London']
data_root: '/mnt/HDD4TB1/local-feature-evaluation/datasets'
dump_root:
truncate: [0, null]
model_path: 'pretrained/aslfeat/model.ckpt-380000' # 'pretrained/aslfeat/model.ckpt-60000'  #
overwrite: true
net:
  max_dim: 2048 #1600 #
  config:
    kpt_n: 20000 # 20000
    kpt_refinement: true
    deform_desc: 1
    score_thld: 0.5
    edge_thld: 10
    multi_scale: true
    multi_level: true
    nms_size: 3
    eof_mask: 5
    need_norm: true
    use_peakiness: true
post_format:
  suffix: '_aslfeat20K2048_380'

hello,I'm a beginner ,can you tell me how to use the aslfeat in colmap ? I can use colmap but don't konw how to use aslfeat in colmap together.

Hi, I follow the standard way ....https://github.com/ahojnnes/local-feature-evaluation.
So, please check https://github.com/ahojnnes/local-feature-evaluation/blob/master/INSTRUCTIONS.md

Hi, I follow the standard way ....https://github.com/ahojnnes/local-feature-evaluation.
So, please check https://github.com/ahojnnes/local-feature-evaluation/blob/master/INSTRUCTIONS.md

than you very much!

Hi, I follow the standard way ....https://github.com/ahojnnes/local-feature-evaluation.
So, please check https://github.com/ahojnnes/local-feature-evaluation/blob/master/INSTRUCTIONS.md

Hi bother you again,I follow the instructions to build the colmap successful,and I use aslfeat compute the keypoints and descriptor like this:

but when I run the vocab_tree_builder_float,it reports this:

I debug the code found that when the code read database to get the images,there are no images in the database.db,can you tell me what you did when run the 'vocab_tree_builder_float'?

Hi! I am not quite sure about this ....
I think it is best to post this question to the original repo:  https://github.com/ahojnnes/local-feature-evaluation ... It is more related to how to set up and build COLMAP ( I guess) ....
Also, maybe you should check this one as well. I also use the following repo for using COLMAP with Custom Features:
https://github.com/tsattler/visuallocalizationbenchmark/tree/master/local_feature_evaluation#using-colmap-with-custom-features
https://github.com/tsattler/visuallocalizationbenchmark/tree/master/local_feature_evaluation
So, maybe you should tag the author of the ASLFeat repo. I am not a contributor; I am just a loyal fan .... just like you  :)   .

Hi! I am not quite sure about this ....
I think it is best to post this question to the original repo: https://github.com/ahojnnes/local-feature-evaluation ... It is more related to how to set up descriptor size and build COLMAP ( I guess) ....
Also, maybe you should check this one as well. I also use the following repo for using COLMAP with Custom Features:
https://github.com/tsattler/visuallocalizationbenchmark/tree/master/local_feature_evaluation#using-colmap-with-custom-features
https://github.com/tsattler/visuallocalizationbenchmark/tree/master/local_feature_evaluation
Or, maybe you should tag the author of the ASLFeat repo, as well. I am not a contributor; I am just a loyal fan .... just like you :) .

OK，I'll try,thank you!


Alpha

Codecov Report

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 Consider uploading reports for the commit 65d971f to get more accurate results

Additional details and impacted files
@@           Coverage Diff           @@
##             main      #31   +/-   ##
=======================================
  Coverage        ?   88.32%
=======================================
  Files           ?      313
  Lines           ?    19293
  Branches        ?      939
=======================================
  Hits            ?    17041
  Misses          ?     2252
  Partials        ?        0

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ros_reader: fix error converting camera distortion

intrinsics.model was missing in create_video_stream_profile and ci.D is a vector of double instead of float in my setup.

I prefer not to add from_string APIs to librealsense, since given how enums are constructed you can always implement it by iterating over all enum values until _COUNT and calling to_string for each.
Otherwise, we will be adding a lot of new APIs

@dorodnic I cleaned this up.


Support abbreviated image name when using Sealer Image offline

Issue Description
Type: feature request
Describe what feature you want
When create the build content, the address of the image to be cached needs to be filled in completely, image address such as nginx:latest are not supported now. We need to be able to support it.
Additional context
Add any other context or screenshots about the feature request here.

/assign

@YTGhost , do you mean that sealer could download container image address looks like : nginx:latest ? set default address domain and repository  docker.io/library ?


mgmt, local generation for Compute 2023-10-02

relate to issue#4850
Description
Fixed PlatformImageNotFound exception for test case VirtualMachinePopularImageTests#canCreateAllPopularImageVM.
Please add an informative description that covers that changes made by the pull request and link all relevant issues.
If an SDK is being regenerated based on a new swagger spec, a link to the pull request containing these swagger spec changes has been included above.
All SDK Contribution checklist:

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

General Guidelines and Best Practices

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

Testing Guidelines

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

API change check
API changes are not detected in this pull request.

Added <revapi.skip>true</revapi.skip> in pom.xml for fix ci analyze exception.
The detail infomation following as:
https://dev.azure.com/azure-sdk/public/_build/results?buildId=3390320&view=results

Yes, the handwritten code change is only on the 2 Known###VirtualMachineImage.


New version: Tauri.create-tauri-app version 4.5.4

Created by 🥟 Dumplings in workflow run #9116.

Log
Updated: 4.5.3 → 4.5.4
Submitting WinGet manifests
Creating manifests
Uploading manifests and making commits
Creating a pull request

Microsoft Reviewers: Open in CodeFlow

/azp run


Can't login using a cookie

Prerequisites

[x] Did you read FAQ section?
[x] Did you test with the latest releases or commit ?

Description
Getting the following error while trying to login with a cookie:
Trying to log in with saved cookie
Error at doLogin(): (<class 'mechanize._response.get_seek_wrapper_class.<locals>.httperror_seek_wrapper'>, <ht
tperror_seek_wrapper (urllib.error.HTTPError instance) at 0x3250418 whose wrapped object = <HTTPError 403: 'Fo
rbidden'>>, <traceback object at 0x03256248>)
Cannot Login!

version tested: 20201025, however it was the same on previous versions
PHPSESSID was copied right after logging to the website through browser, and pasted into the config file.
Also tested the password - can't login with it either, getting the captcha error.
Can login on the website itself just fine.

Step 1. go to pixiv website.
Step 2. change password or type current password in all 3 fields, press change password
step 3. on the new page with the text "your password has been changed", press F12 in browser and go to "application tab" (chrome) or "storage tab" (Firefox) and search for your new phpsessid -> should be in the new format.
step 4. paste the new format cookie in config.ini
hope this will help u...
//Onii

I'm experiencing the same issue, I tried Onii's method to no avail, I'm also on 20201025.

try the latest version, if still not working then better post on #814


Fix the notification get request

Summary of the Pull Request
Read the notification request  parmeters from the body of the request instead of the uri
related to #2589

Codecov Report

Merging #2591 (94adcd9) into main (33e2d5c) will decrease coverage by 5.09%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##             main    #2591      +/-   ##
==========================================
- Coverage   29.89%   24.80%   -5.10%
==========================================
  Files         289      120     -169
  Lines       35764    12483   -23281
==========================================
- Hits        10692     3096    -7596
+ Misses      25072     9387   -15685

Impacted Files
Coverage Δ

...c/ApiService/ApiService/Functions/Notifications.cs
0.00% <0.00%> (ø)

src/agent/coverage/src/pdb.rs

...c/agent/onefuzz-task/src/tasks/analysis/generic.rs

...nt/onefuzz-task/src/tasks/report/dotnet/generic.rs

src/agent/debugger/src/breakpoint.rs

src/agent/onefuzz-agent/src/work/double.rs

src/agent/debugger/src/module.rs

src/agent/onefuzz-agent/src/reboot/double.rs

src/agent/dynamic-library/src/lib.rs

src/agent/coverage/src/sancov.rs

... and 160 more

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Prompt Template for few-shot sentence-level translation.

I'm a bit confused about the Prompt Template for the few-shot sentence-level translation. Could you please give an example of the prompt template for the few-shot sentence-level translation? Thanks.

Addressed in commit 89b2ffb.


auth: Make getSession synchronous

Actually fixes: https://github.com/microsoft/vscode-azurefunctions/issues/3878
This PR broke everything. 😡
Apparently AzureAuthentication doesn't like getSession being async. So we need to be able to get the session and pass that along before we create the authentication object.
The async call must have somehow caused some parts of the zipfile not to get deployed since the stream was constantly making requests. Not sure why it only reproduces on Windows either. I'm assuming the auth provider was fast enough on a Mac to never actually be an issue.
Anyway, I'm making scopes an optional parameter on createSubscriptionClient. I think that should resolve the problem of not being able to pass scopes.
Also could someone double check to make sure that I reverted everything? I think that this is all, but my sanity bar is nearly depleted atm.

Can confirm (after multiple tries) this does in fact fix.

Also could someone double check to make sure that I reverted everything? I think that this is all, but my sanity bar is nearly depleted atm.

Don't Starve intensifies


[#FLAT-639] Fix collecting domain parent categories

https://sourceclear.atlassian.net/browse/FLAT-639

:+1:


Support for vlines and hlines from Matplotlib

Support for axes lines like these should be added to deepforge figure plots.
Example:
>>> from matplotlib import pyplot as plt
>>> plt.vlines(50, 1, 100, 'r')
<matplotlib.collections.LineCollection object at 0x7fd15d2ea890>
>>> plt.hlines(50, 1, 100, 'g')
<matplotlib.collections.LineCollection object at 0x7fd16577c4d0>
>>> plt.show()

These lines are rendered in matplotlib as lineCollections (axes.collections). And contain multiple Path Objects.


Apply patch from ilinsky/xmlhttprequest

Apply patch: https://github.com/ilinsky/xmlhttprequest/commit/9f1d0fd49b0583073c1ca19e220dc13fe0f509b4

I was expecting more changes. This is the only diff between the version in OL and the master?

See http://trac.osgeo.org/openlayers/ticket/3519

Hi,
I applied only the changes of the two lines, I thought we would expect a release of Sergey.
I am studying the actual code is a little bit cleaner than before ;-)
I do not know if Sergey plans to continue publishing versions.
Do you see interesting that I prepare an application current code of https://github.com/ilinsky/xmlhttprequest?

It should also close the ticket http://trac.osgeo.org/openlayers/ticket/3593 ?

I don't know if Sergey makes actual releases of his xmlhttprequest code.
Anyway, yes, it would be interesting to study how his code has evolved and if OpenLayers should be updated.

Ok, see the changes https://github.com/jorix/openlayers/commit/fd6a23e5ccac6be0ebd2a27b58c85bafaf3a9032


Implement JohnBakery's login fixes

This addresses the login failure glitch by implementing JohnBakery's fix from: https://github.com/ArthurG/Kijiji-Repost-Headless/issues/198
SSID needs to be manually pasted into an empty text file during setup. Instructions added to readme.

I think there may be a bug with option repost. You deleted the category_id for delete_ad_using_title however the call in __main__.py still references it.

What's the reason for taking out category_id?

I get the following, when I try to use your new ssid method.
Traceback (most recent call last):
  File "/usr/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/zeus/kijiji/kijiji_repost_headless/__main__.py", line 209, in <module>
    main()
  File "/home/zeus/kijiji/kijiji_repost_headless/__main__.py", line 51, in main
    args.function(args)
  File "/home/zeus/kijiji/kijiji_repost_headless/__main__.py", line 152, in repost_ad
    delete_ad(args, api)
  File "/home/zeus/kijiji/kijiji_repost_headless/__main__.py", line 130, in delete_ad
    api.login(args.username, args.password)
  File "/home/zeus/kijiji/kijiji_repost_headless/kijiji_api.py", line 125, in login
    if not self.is_logged_in():
  File "/home/zeus/kijiji/kijiji_repost_headless/kijiji_api.py", line 132, in is_logged_in
    resp = self.session.get('https://www.kijiji.ca/my/ads.json', headers=request_headers)
  File "/home/zeus/.local/lib/python3.7/site-packages/requests/sessions.py", line 543, in get
    return self.request('GET', url, **kwargs)
  File "/home/zeus/.local/lib/python3.7/site-packages/requests/sessions.py", line 530, in request
    resp = self.send(prep, **send_kwargs)
  File "/home/zeus/.local/lib/python3.7/site-packages/requests/sessions.py", line 643, in send
    r = adapter.send(request, **kwargs)
  File "/home/zeus/.local/lib/python3.7/site-packages/requests/adapters.py", line 449, in send
    timeout=timeout
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 600, in urlopen
    chunked=chunked)
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 354, in _make_request
    conn.request(method, url, **httplib_request_kw)
  File "/usr/lib/python3.7/http/client.py", line 1244, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/lib/python3.7/http/client.py", line 1285, in _send_request
    self.putheader(hdr, value)
  File "/usr/lib/python3.7/http/client.py", line 1222, in putheader
    raise ValueError('Invalid header value %r' % (values[i],))
ValueError: Invalid header value b'ssid=

I get the following, when I try to use your new ssid method.
Traceback (most recent call last):
  File "/usr/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/zeus/kijiji/kijiji_repost_headless/__main__.py", line 209, in <module>
    main()
  File "/home/zeus/kijiji/kijiji_repost_headless/__main__.py", line 51, in main
    args.function(args)
  File "/home/zeus/kijiji/kijiji_repost_headless/__main__.py", line 152, in repost_ad
    delete_ad(args, api)
  File "/home/zeus/kijiji/kijiji_repost_headless/__main__.py", line 130, in delete_ad
    api.login(args.username, args.password)
  File "/home/zeus/kijiji/kijiji_repost_headless/kijiji_api.py", line 125, in login
    if not self.is_logged_in():
  File "/home/zeus/kijiji/kijiji_repost_headless/kijiji_api.py", line 132, in is_logged_in
    resp = self.session.get('https://www.kijiji.ca/my/ads.json', headers=request_headers)
  File "/home/zeus/.local/lib/python3.7/site-packages/requests/sessions.py", line 543, in get
    return self.request('GET', url, **kwargs)
  File "/home/zeus/.local/lib/python3.7/site-packages/requests/sessions.py", line 530, in request
    resp = self.send(prep, **send_kwargs)
  File "/home/zeus/.local/lib/python3.7/site-packages/requests/sessions.py", line 643, in send
    r = adapter.send(request, **kwargs)
  File "/home/zeus/.local/lib/python3.7/site-packages/requests/adapters.py", line 449, in send
    timeout=timeout
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 600, in urlopen
    chunked=chunked)
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 354, in _make_request
    conn.request(method, url, **httplib_request_kw)
  File "/usr/lib/python3.7/http/client.py", line 1244, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/lib/python3.7/http/client.py", line 1285, in _send_request
    self.putheader(hdr, value)
  File "/usr/lib/python3.7/http/client.py", line 1222, in putheader
    raise ValueError('Invalid header value %r' % (values[i],))
ValueError: Invalid header value b'ssid=

I think you might have an extra line break somewhere in your SSID file. Make sure there's only one line containing the SSID itself.


Symmetric improvements

This implments the GCM mode of operation for several ciphers. It also has support for AESNOMAC (which users should steer clear of). It will require a change to trousseu for the function calls.

@oleiade - I changed this to use GCM as the default but left the ability to use the old AES in there as discussed in trousseau/#157. This requires more changes to trousseau, mainly editing the command line so that you can choose the algo - i will work on them as well.
Please let me know what you think of the API changes. The other route is to make a separate encrypter for each algo - but went this way instead.

Hi @jd1123
Thanks a lot for the hardwork on this. Even though I think it goes in the right direction, I think the changes it implies are a bit too brutal :-)
The main idea and goal with the Encrypter and Decrypter interfaces was to provide an as minimalist and simplistic API as possible. I made them with the idea of passing them around to functions agnostically of their type, algorithm, mode and so on.
I do believe that a SymmetricEncrypter and AsymmetricEncrypter have their reasons to be, but as interfaces, definetly not as implementations, and not without each other. With this goes my intuition that it is necessary to keep the subpackages model -> interfaces.go + aes package + openpgp package + salsa20 package etc...
Plus, I can't think of a generic model enough for AsymmetricEncrypter, and unfortunately that is because of the Go language design itself: recipients of asymmetric encryption can be of very mixed types, and it would be a hell to make them fit inside a single interface type.
However I think you work on AES mode is to be kept, but integrated as part of the AES256Encrypter, using a cipher attribute or something that would define with a switch statement which aes cipher to use.
Plus, I ignored twofish and blowfish algorithms on purpose because I've read here and there that were kind of considered as deprecated and unsafe by the community when used by themselves. I was considering to add a salsa20 package instead: https://github.com/oleiade/serrure/issues/3
Let me know what you think :-)

@oleiade -
Noted and done - I will change this PR to reflect this (push the commit later tonight or tomorrow).
I will hold off on twofish and blowfish if you'd like (blowfish does not work with GCM as its blocksize is incompatible) - but frankly I use twofish myself locally with trousseau.
For Salsa20 - I will have to look into this more deeply as it it not a block cipher and doesn't fit the mold of AES or Twofish so easily. After some research I will consider doing another PR with its implementation.
After I finish this PR, I'll change the trousseau PR as well.

closing this PR


Feature: ArtifactCard component

Adds a new ArtifactCard component used for both lists and summary displays on artifact (results) pages

I might stack these dates on the condensed view so that things line up a little better.


Pawn vaildate

check if square chossen is 1 ahead or behind unless on rank 2 or 7 then let it be up to 2 ahead or behind
check pawn colour if black let it only advance down and vis-a-versa
run check for enPassent https://en.wikipedia.org/wiki/En_passant
add promation promt if required and implment in main

Some Issues will cont to look into


Question :: Support to image borders

Hi there,
First of all, congrats on the project. It seems really promising.
I am currently trying to add borders to the image, however, it seems that the project does not support it right now.
Is there any plan on including it? or do you know what is the best way to achieve it?
I tried a couple of possibilities to achieve it with a single URL such as

using padding and applying  "round corner"
applying filters multiple times
/filters:round_corner(310,310,ff0000)/filters:round_corner(305:305)
/filters:round_corner(310,310,ff0000):round_corner(305:305)

For some reason, the padding does not seem to work fully with the crop/round corner.

What about
docker run -p 8000:8000 shumc/imagor:0.9.7 -imagor-unsafe

http://localhost:8000/unsafe/0x0/10x10/filters:background_color(white):fill(green)/raw.githubusercontent.com/cshum/imagor/master/testdata/gopher-front.png

Or with added round corner
http://localhost:8000/unsafe/0x0/10x10/filters:background_color(white):round_corner(20):fill(green)/raw.githubusercontent.com/cshum/imagor/master/testdata/gopher-front.png

Hey @cshum
Thanks very much.
That worked perfectly with:
/unsafe/413x111:723x421/3x3:3x3/smart/filters:grayscale():format(png):round_corner(310):fill(green):round_corner(310,310,transparent)/image/image.jpg

I missed the fill() in between round_corner filters. Without it, the padding area wasn't been fulfilled.
Without fill:

With fill:


Kinesis firehose instructions incomplete

File: themes/default/content/docs/reference/pkg/aws/kinesis/firehosedeliverystream.md
The instructions for setting up kinesis firehose with an S3 destinations are incomplete. The kinesis firehose role needs permissions to write to the S3 bucket as documented here https://docs.aws.amazon.com/firehose/latest/dev/controlling-access.html#using-iam-s3
The s3 destination also appears to be deprecated with extendedS3 being the recommended replacement.

This is the destination to where the data is delivered. The only options are s3 (Deprecated, use extendedS3 instead), extendedS3, redshift, elasticsearch, splunk, and httpEndpoint.

Hi, thanks for the issue!
Our examples and documentation are autogenerated from the upstream provider, so this isn't something that we control. And we do link to the firehose documentation for more in-depth guidance on using firehose.
We also do have an example for the extendedS3 destination


Cassandra Datacenter deletion hangs on finalizer

When helm delete command is executed to delete helm deployment containing cassandra datacenter (and operator), cassandra data center resource is not deleted. Doing kubectl delete cassdc $name_of_cassdc_object doesn't do any good either - the command hangs indefinitely and object is not removed. Using grace-period=0 and force flags also doesn't help - command terminates immediately but the object is still there.
Workaround is to do kubectl edit cassdc $name_of_cassdc_object and delete lines presented at screenshot. After that action object disappears.

We're using latest version of CRD and Cassandra operator (1.5.0) on kubernetes 1.19.4

@jsanda is this related to how K8ssandra installs things with helm? The cassdc needs to be explicitly deleted, and then the operator can reconcile that change and do some cleanup on other resources (namely PVCs) and then it removes the finalizer.
The deletion procedure is outlined in the README.
https://github.com/datastax/cass-operator#uninstall

@jsanda is this related to how K8ssandra installs things with helm? The cassdc needs to be explicitly deleted, and then the operator can reconcile that change and do some cleanup on other resources (namely PVCs) and then it removes the finalizer.
The deletion procedure is outlined in the README.
https://github.com/datastax/cass-operator#uninstall

@mgorsk1 did you hit this with k8ssandra? If so, what version of the charts?
The problem is that there are no ordering guarantees when you delete with Helm. The cass-operator deployment can get deleted before the CassandraDatacenter, and then you end up in this situation.
In k8ssandra we implemented a pre-delete hook that will make sure any CassandraDatacenters created via the k8ssandra chart get deleted before the cass-operator deployment. This functionality was introduced in version 0.24.0 of the k8ssandra chart.

@mgorsk1 did you hit this with k8ssandra? If so, what version of the charts?
The problem is that there are no ordering guarantees when you delete with Helm. The cass-operator deployment can get deleted before the CassandraDatacenter, and then you end up in this situation.
In k8ssandra we implemented a pre-delete hook that will make sure any CassandraDatacenters created via the k8ssandra chart get deleted before the cass-operator deployment. This functionality was introduced in version 0.24.0 of the k8ssandra chart.

Thanks for replies ! We are using our own chart, installing operator and cassandra datacenter. Something much simpler than k8ssandra. We'll try adding the pre-delete job similar to the cleaner one, thanks for the tip !

Thanks for replies ! We are using our own chart, installing operator and cassandra datacenter. Something much simpler than k8ssandra. We'll try adding the pre-delete job similar to the cleaner one, thanks for the tip !

Just to update - added a pre-delete job and worked like a charm, thanks for the help !

Just to update - added a pre-delete job and worked like a charm, thanks for the help !


Add import of operation types from weboob.

First PR for https://github.com/bnjbvr/kresus/issues/40

Thanks for the PR, it looks really nice! I think you'll need to rebase your code (please use git rebase :)).
Also, thinking about it, it seems that the OperationType only has one useful field (the name), which is finally stored in the Operation itself. It could show useful to save the OperationType in database, if we

either plan to add some attributes to the OperationType
or plan to use OperationType on the server

As of today, I can't see any good reason to do either 1. or 2. Moreover, storing only the operation type as of today and storing the OperationType instances seems overkill, so I'd rather link the OperationType id to the Operation, for better use in the future, but that will take strictly more storage space than just having the OperationType itself! (which sounds like an argument to just get rid of the OperationType structure entirely).
What do you think? Do you have any ideas in mind? Otherwise, I'd suggest just removing entirely the OperationType, and using only the map to retrieve the operation type, when storing it.

OK, I'll start over, and propose a fresh new PR.
The idea to have OperationType inside the DB was to be able to add an operation type filter in the research (why? it could be useful to retrieve an operation).
For that, it seems necessary to have a stble list of operation types (with stable values of labels, which is not the case right now, I know :-), as the value of operationtype is not updated inside the OperationType structure (nor in the operations).
Maybe linking operations  with operationTypeID would be better, instead of label.
But by using this solution, I fear the operation types are messed up in all operations if the value for operationstypes changes in weboob (thats why I finally harcoded them)


Compiler details - Copy to clipboard [object Object]

Found this on the compile tab, clicking on details to see the abi and bytecode.
Every section has a 'copy value to clipboard' button, which works fine for metadata, abi, webdeploy, etc.
However  FUNCTIONHASHES and GASESTIMATES  return '[object Object]' to my clipboard.
Shouldn't this be the raw version like it is displayed? (JSON.stringify)

fixed by https://github.com/ethereum/browser-solidity/pull/886


Typical cost for ghost blog on azure?

Can anyone speak on the typical monthly cost involved with a ghost blog azure at various traffic levels?
Thanks

sure, although that doesn't pertain to this particular project.
I ran ghost on 1 basic webapp service which costs around 30USD...that being said I bet it would probably work fine on the shared app pool which is only 7USD, but that is an untested assumption.

I'm running it on Shared. It works fine, although does go down briefly from time to time (Shared is still in Preview I believe).

Thx! Nice info about shared pool. I'm going that way. Thx for lib.

to stop the site going down on Azure...on the azure portal (old version) on the config tab
set:
Always On – ON
Web Sockets – ON
Platform – 64BIT
Managed Pipeline mode – INTEGRATED
PHP – 5.6
Otherwise the site goes to sleep and you need to restart it and wait 2 min for everything to kick in

The Always On setting is sufficient. These are the settings I use in the Application settings on the new portal (https://portal.azure.com/):

My settings are the same as yours @blustemy. I never use 64-bit unless I have to as it wastes memory - as pointed out by Scott Hanselman: https://www.hanselman.com/blog/PennyPinchingInTheCloudYourWebAppDoesntNeed64bit.aspx

Is there still the problem that the site goes down in shared app pool? I ask this because it is not possible to set AlwaysOn parameter for shared apps.

you could try using a free ping service like uptime robot to keep your site alive.


add module exception

With this PR, I hope to make it easier to catch errors while using bayesian-optimization.

Added reference/exception.rst.


Beta

Doneness:

[X] Build is okay - I made sure that this change is building successfully.
[X] No Bugs - I made sure that this change is working properly as expected. It doesn't have any bugs that you are aware of.
[X] Branching - If this is not a hotfix, I am making this request against develop branch

:x: Build Titanium-Web-Proxy 3.0.107 failed (commit https://github.com/justcoding121/Titanium-Web-Proxy/commit/edc78cc068 by @justcoding121)


Add option to configure nodePort

I'm deploying wg-access-server by helm chart to my self hosted k8s. I would like to use service type nodePort and point dnat firrewall rule on it.
Because of this I need to configure static nodePort. This is currently not possible as I looked into service template.

https://github.com/freifunkMUC/wg-access-server/pull/125 adds the ability to configure port and targetPort, but that's probably not enough for you, right? You also need the ability to configure the nodePort option?

yes, nodePort is additional setting

Now, when #125 is merged I can make PR for this enhancement. It will be pretty simple.
@DasSkelett are you interested in this contribution?

Yes, please go ahead! We are very thankful for contributions, especially regarding Helm.

@DasSkelett PR ready, can you approve it for tests?

Fixed by #129


New option for global limit

Hey guys
First, thank you to allow this plugin to continue to live.
I reported an issue here about global limit ("default" limit in limitsv2.yml) https://github.com/megoesrawr/Modern-LWC/issues/97, but it wasn't a bug.
So I think it could be interesting to add an option to choose behaviour of global limit

current way: global limit is used only if any other limit is mentionned
new behaviour: global limit is a maximum number of protections allowed per player

default_limit_behaviour: if_nothing_else
default_limit_behaviour: max_limit

I think it could be an interesting behaviour to add a maximum number of protections per player/group, but still allow them to choose the type of protections they want to use
Cheers

I'm not sure I understand your issue. I believe you can simply change "unlimited" to whatever number you want in limitsv2.yml to achieve this effect. There is also a groups, and players section where you can set limits per group or per player.

So to translate this to logic
doorProtectionsOfPlayer <= globalDoorProtections
chestProtectionsOfPlayer <= globalChestProtections
globalChestProtections + globalDoorProtections <= globalProtectionLimit

Yeah I think it is a good translation

I think the current behaviour is understandable but weird, because it takes into account per block protections limits for display it, but it is binding only if there is not any defined per block limit

@JohOply Would you mind sharing your configuration files (core and limitsv2)? Also, assuming you start with a fresh database, what would be the steps to reproduce this issue? If you could detail in words, or leave a video, explaining the exact steps to take to break the limits, it would help a lot. I have never needed to change LWC's limits in the 5+ years I've used it, so I do need a little hand holding here as I don't quite have experience with it.
PS: Sorry for mistakenly closing your issue on this in the other repository. We were trying to clean up fixed issues so that we can focus on ones that still need attention. It seems like this may in fact be a bug in LWC and not "working as intended" as implied by megoesrawr.

This should be fixed in the latest development build. The limits module seems to now correctly block every case where the player exceeds either the default limit, or some individual block limit.
Screenshots:
https://imgur.com/a/D3zr8BK

Sorry I did not available last days
Thank you for fixing, on your screens it seems work!


⚠ Bofrost.com has degraded performance

In 5f213b2, Bofrost.com (https://www.bofrost.com) experienced degraded performance:

HTTP code: 200
Response time: 605 ms

Resolved: Bofrost.com performance has improved in 3336040 after 6 minutes.


Fix max transfer amount

Description
Add regex to validate transfer amount
Related Issues

https://github.com/threefoldtech/tfgrid-sdk-ts/issues/1670

Checklist

[ ] Tests included
[ ] Build pass
[ ] Documentation
[ ] Code format and docstrings
[ ] Screenshots/Video attached (needed for UI changes)

I have question, the fee excluded from the transfer amount or from my balance ?

@AlaaElattar I think the transaction (extrinsic) fee is deducted from the user who did it,


Infer# integration

Dear Infer team,
To contribute to Infer community, I would like to integrate infer#'s language agnostic layer into Infer.
Please help to review, discuss and consider to merge this feature.
Thanks,
Xiaoyu

I was able to figure out ocamlformat installation issue and ran make fmt successfully. It turns out that ocamlformat needs to be reinstalled first and then install nebuchadnezzar version.
Now all comments are resolved and this PR is ready for a second round of review.

I was able to figure out ocamlformat installation issue and ran make fmt successfully. It turns out that ocamlformat needs to be reinstalled first and then install nebuchadnezzar version.
Now all comments are resolved and this PR is ready for a second round of review.

Hi~
I saw there might be some tests failed in Facebook Internal Builds & Tests. I can't see what exactly caused the failure, but if it is about infersharp unit tests, I can either check in compressed json files (they are ready and good to go) or remove all of them from DIRECT_TESTS in make file.
Let me know what is the best option for you.
Thanks!

Hi~
I saw there might be some tests failed in Facebook Internal Builds & Tests. I can't see what exactly caused the failure, but if it is about infersharp unit tests, I can either check in compressed json files (they are ready and good to go) or remove all of them from DIRECT_TESTS in make file.
Let me know what is the best option for you.
Thanks!

The compilation failures are due to a small amount of extra code we have in the internal repo that needs to be updated by us. I'll do that.

The compilation failures are due to a small amount of extra code we have in the internal repo that needs to be updated by us. I'll do that.

The compilation failures are due to a small amount of extra code we have in the internal repo that needs to be updated by us. I'll do that.

I see. Thanks!
Now all compressed jsons are in. Feel free to give it a run simply with make direct_tests.

The compilation failures are due to a small amount of extra code we have in the internal repo that needs to be updated by us. I'll do that.

I see. Thanks!
Now all compressed jsons are in. Feel free to give it a run simply with make direct_tests.


Error loading dxf 2018

When I load dxf 2018, dxf::Drawing::load_ File() will give an error, such as: err: an unexpected code '90' was encountered at line/offset 11
Here is a dxf 2018 file for testing
test2018.zip

When I load dxf 2018, dxf::Drawing::load_ File() will give an error, such as: err: an unexpected code '90' was encountered at line/offset 11 Here is a dxf 2018 file for testing test2018.zip

try using git
dxf = { git = "https://github.com/ixmilia/dxf-rs.git" }


Support allowLinkng and cache setting on tomcat 8+

Is your feature request related to a problem? Please describe.

Describe the solution you'd like
tomcatdir/conf/Catalina/localhost/appname.xml is configurable to fix this as a best practice,See https://stackoverflow.com/a/43673455/4037224
But SmartTomcat now create appname.xml without this.
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<Context docBase="mydocpath">
  <Resources>
 </Resources >
</Context>

What expected is
<Context docBase="mydocpath">
  <Resources allowLinking="true" cacheMaxSize="100000" cachingAllowed="true">
 </Resources >
</Context>

Go through the source ,I found a solution
Change com.poratu.idea.plugins.tomcat.conf.TomcatCommandLineState.java createResourcesElementIfNecessary() mthod should add this
private Element createResourcesElementIfNecessary(Document doc, Element contextRoot) {
    Element resources = (Element) contextRoot.getElementsByTagName("Resources").item(0);
    if (resources == null) {
        resources = doc.createElement("Resources");
        // fix cache and linking
        resources.setAttribute("allowLinking", "true");
        resources.setAttribute("cachingAllowed", "true");
        resources.setAttribute("cacheMaxSize", "100000");
        contextRoot.appendChild(resources);
    }
    return resources;
}

Describe alternatives you've considered
The above options can be configuable.This is just a example to show how to suit this suitation.

Thanks for the report and look into this.
According to the documentation (https://tomcat.apache.org/tomcat-9.0-doc/config/resources.html
), cachingAllowed is true by default. And the default value for cacheMaxSize is 10240 (10 M). Is the default configuration good for you?
allowLinking is false by default, but it's not commonly used, for your case, I'm going to add a registry so that you can enable it on your needs.
Any questions?

Thanks , my company project is so large, in mycase, 10240 is not enough, so also add a registry for cacheMaxSize  will be better.

I tried thhe latest updated version4.3.8. it works great！
Thanks very much!

How to configure cacheMaxSize and allowLinking for SmartTomcat?
Search the Registry action then:


Babel plugin doesn't run with dev-server.

I can't get the babel plugin to run with the dev-server. It seems to load fine, but the code is never transpiled. I'm assuming it's a config error? I've tried looking through the source code but I don't quite understand where the plugins are supposed to be applied.
My config is here: https://github.com/eldh/jour/blob/master/dev-server.js. And I guess cloning that repo and doing npm i && npm start would reproduce the issue.

Investigating

Fixed in<EMAIL_ADDRESS>and<EMAIL_ADDRESS>

On a side note you might want to execute loadPlugins and activate in a series like
server.pundle.loadPlugins([
  [require.resolve('babel-pundle'), babelConfig],
]).catch((e) => console.log('Plugin load error', e)).then(function() {
  server.activate().catch((e) => console.log('activation failed', e))
})

Awesome, thanks a lot! Great work on Pundle!


Reenable e2e xla ctests

Will disable failing tests after running the CI once. My local system might behave different.


[Doc] Updated documentation

Description
This PR fixes #9
Notes for Reviewers
If desired, this PR can be kept as draft/wip for a little while (it is labelled). Please feel free to add and modify documentation.
Signed commits

[x] Yes, I signed my commits.

@leecalcote could you please clarify which changes in the documentation you request? I can't seem to find that, sorry.
Otherwise, we could just merge this PR. Documentation should not be a separate activity anyway, this was intended as kick-start - because I didn't add any initially, of course.


Test the network blocking

We may want to try writing a test Django app that tries to do something malicious to make sure that we don't have problems when we go live.

Fixed


Add ability to find and automatically tag images given a user supplied tag

Use the functionality similar to search for finding and applying tags.

Or possibly use a model like Florence for adding captions: https://huggingface.co/microsoft/Florence-2-large


NgIf structural directive with angular-cesium

Dear all,
I have problem using NgIf structural directive.This issue may effect  another angular important features (like ngSwitch Routing etc.).
Intended outcome:
*NgIf structural directive should respond as expected.
related links:
https://angular.io/guide/template-syntax#ngIf
https://angular.io/api/common/NgIf
https://angular.io/guide/structural-directives
Actual outcome: / How to reproduce the issue:
*ngIf=true/false (hard coded value expression) seem to work as expected.
*ngIf=isMap (variable expression) crash
Version
"angular-cesium": "0.0.49"
thank you for your great work and technical support :)

Hi there, Thanks for submitting an issue!
From my understanding ngIf doesnt work on ac-map (wasnt implemented) and ac-layer(maybe a bug).
Hopefully we will make it work soon

Should be resolved when #245 PR is merged


Enhancement suggestion:  On the product drive page, the filter by name box, when it has the drop down, can that be in alpha order?

Summary
Make the filter by name drop down on the product drive page come up in alpha order
Why
User convenience
Details
Recreation:  Product Drives | All Product Drives  -- click in Filter by name box.  This is currently in ... probably order that the product drives were created?   It should be in alpha order.
This obviously matters more for banks that have a lot of product drives.
Criteria for completion
[] The list of product drives in the filter by name drop down on the product drive page comes up in alphabetical order
[] Tests to demonstrate
Additional notes (origin of request)
Suggested by Judi Meighan on 2023-08-14: On the product drive page, the filter by name box, when it has the drop down, can that be in alpha order?

I can take this.

We can sort, but currently it is ordered based on the start date in descending order, if we want to change the filter to be in alphabetical order, then the list would change, is that fine? Or do we want only the names in the filter to be in alphabetical order, but leave the actual list as such.
Current:

After the change:

The actual list should stay in the current, reverse chronological by start date order so that, in general, active drives will end up at the top of the list.
The filter allows for finding specific drives by name, so it makes sense for that to be in the easiest order for finding a name, which is alpha.

This should be good for review now.