java.lang.NullPointerException: Cannot enter synchronized block because "this.logs" is null

Jenkins and plugins versions report

Environment

  Jenkins 2.479.1
  openjdk version "21.0.2" 2024-01-16 (build node)
  openjdk version "17.0.13" 2024-10-15 (controller node)
  Lockable Resources plugin Version 1327.ved786b_a_197e0

I would prefer not to make my whole environment public. Let me know if you need specific versions of specific other plugins.

What Operating System are you using (both controller, and any agents involved in the problem)?
controller: Ubuntu 20.04.6
build node: OpenBSD 7.5
Reproduction steps
Build two jobs that have the following in their Jenkinsfile:
pipeline {
    options {
        ....
        lock resource: 'foo'
    }

Expected Results
No stacktrace, successful build.
Actual Results
java.lang.NullPointerException: Cannot enter synchronized block because "this.logs" is null
	at PluginClassLoader for lockable-resources//org.jenkins.plugins.lockableresources.actions.LockedResourcesBuildAction.addLog(LockedResourcesBuildAction.java:97)
	at PluginClassLoader for lockable-resources//org.jenkins.plugins.lockableresources.actions.LockedResourcesBuildAction.addLog(LockedResourcesBuildAction.java:92)
	at PluginClassLoader for lockable-resources//org.jenkins.plugins.lockableresources.actions.LockedResourcesBuildAction.addLog(LockedResourcesBuildAction.java:84)
	at PluginClassLoader for lockable-resources//org.jenkins.plugins.lockableresources.LockStepExecution$Callback.finished(LockStepExecution.java:234)
	at PluginClassLoader for workflow-step-api//org.jenkinsci.plugins.workflow.steps.BodyExecutionCallback$TailCall.onSuccess(BodyExecutionCallback.java:119)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsBodyExecution$SuccessAdapter.receive(CpsBodyExecution.java:381)
	at PluginClassLoader for workflow-cps//com.cloudbees.groovy.cps.Block$Noop.eval(Block.java:30)
	at PluginClassLoader for workflow-cps//com.cloudbees.groovy.cps.Next.step(Next.java:83)
	at PluginClassLoader for workflow-cps//com.cloudbees.groovy.cps.Continuable.run0(Continuable.java:147)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.SandboxContinuable.access$001(SandboxContinuable.java:17)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.SandboxContinuable.run0(SandboxContinuable.java:49)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsThread.runNextChunk(CpsThread.java:180)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsThreadGroup.run(CpsThreadGroup.java:422)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsThreadGroup$2.call(CpsThreadGroup.java:330)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsThreadGroup$2.call(CpsThreadGroup.java:294)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsVmExecutorService.lambda$wrap$4(CpsVmExecutorService.java:140)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
	at hudson.remoting.SingleLaneExecutorService$1.run(SingleLaneExecutorService.java:139)
	at jenkins.util.ContextResettingExecutorService$1.run(ContextResettingExecutorService.java:28)
	at jenkins.security.ImpersonatingExecutorService$1.run(ImpersonatingExecutorService.java:68)
	at jenkins.util.ErrorLoggingExecutorService.lambda$wrap$0(ErrorLoggingExecutorService.java:51)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsVmExecutorService$1.call(CpsVmExecutorService.java:53)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsVmExecutorService$1.call(CpsVmExecutorService.java:50)
	at org.codehaus.groovy.runtime.GroovyCategorySupport$ThreadCategoryInfo.use(GroovyCategorySupport.java:136)
	at org.codehaus.groovy.runtime.GroovyCategorySupport.use(GroovyCategorySupport.java:275)
	at PluginClassLoader for workflow-cps//org.jenkinsci.plugins.workflow.cps.CpsVmExecutorService.lambda$categoryThreadFactory$0(CpsVmExecutorService.java:50)
	at java.base/java.lang.Thread.run(Thread.java:840)

What is even worse, the lock that is held by this build is not released, so no other can execute.
Anything else?
No response
Are you interested in contributing a fix?
I would like to, but it would probably take some time as I have no setup to develop / test Jenkins Plugins and have no idea how logs could be null here in the first place.

I just realized that this happened during the Jenkins Upgrade, not after.
So I guess this is not really an issue.


Add a S2I working sample

Is your feature request related to a problem? Please describe.
Add a S2I working sample
Describe the solution you'd like
Add a S2I working sample
Describe alternatives you've considered
Manually try.

@Akash-Nayak Can you please try converting the language platforms with s2i and check if we have any issues.

Yes Sure.

While running move2kube-demos git:(main) $ move2kube translate -s samples/language-platforms, in the first QA it asked me to select the services and there was one service named move2kube-demos.
? 1. Select all services that are needed:
Hints:
 [The services unselected here will be ignored.]
  [Use arrows to move, space to select, <right> to all, <left> to none, type to filter]
> [✓]  java-gradle
  [✓]  java-maven-war
  [✓]  python
  [✓]  move2kube-demos
  [✓]  golang
  [✓]  nodejs
  [✓]  php

golang, java-maven-war, nodejs, php, python, ruby, move2kube-demos, java-gradle-war, java-maven, java-gradle

java-maven and java-gradle-war which were not in the options also appeared in the selected services.
I got few warning messages after I selected S2I as the containerization technique.
? 2. Select all containerization modes that is of interest:
Hints:
 [The services which does not support any of the containerization technique you are interested will be ignored.]
 S2I
WARN[0039] Ignoring service java-gradle-war, since it does not support any selected containerization technique.
WARN[0039] Ignoring service java-gradle, since it does not support any selected containerization technique.
WARN[0039] Ignoring service java-maven-war, since it does not support any selected containerization technique.
WARN[0039] Ignoring service move2kube-demos, since it does not support any selected containerization technique.
? 3. Choose the artifact type:

After the translation was complete, I deployed the artifacts to the Kubernetes cluster and the below mentioned services are running successfully.
The services are accessible on the following paths:
golang : http://myproject.irlhc12-cf7808d3396a7c1915bd1818afbfb3c0-0000.us-south.containers.appdomain.cloud/golang
java-maven : http://myproject.irlhc12-cf7808d3396a7c1915bd1818afbfb3c0-0000.us-south.containers.appdomain.cloud/java-maven
nodejs : http://myproject.irlhc12-cf7808d3396a7c1915bd1818afbfb3c0-0000.us-south.containers.appdomain.cloud/nodejs
php : http://myproject.irlhc12-cf7808d3396a7c1915bd1818afbfb3c0-0000.us-south.containers.appdomain.cloud/php
python : http://myproject.irlhc12-cf7808d3396a7c1915bd1818afbfb3c0-0000.us-south.containers.appdomain.cloud/python
ruby : http://myproject.irlhc12-cf7808d3396a7c1915bd1818afbfb3c0-0000.us-south.containers.appdomain.cloud/ruby

Added S2I working example using the language-platforms sample usecase - https://github.com/konveyor/move2kube/pull/240


Research: Combined blast database.

Instead of using a bunch of separate database files per organism, what if we had 1 combined database and used the -taxids cli argument to filter the search to the correct organisms.
Testing on NCBI confirms that limiting the database to the selected tax-ids does impact the statistical significance of the result (as would running against a smaller database)
To accomplish this, MBlast would need to access the app database (which it may already be doing) to get the tax ids for the selected organism to build the CLI arg.

Things we are testing:

The creation of a combined database.
The performance of querying the combined database vs multiple files.


RefSeq GRCh38.p12 reference genome fails to build

I'm hitting some errors when attempting to index the current RefSeq Homo sapiens reference genome GCF_000001405.38_GRCh38.p12 using bcbio_setup_genome.py. Is RefSeq currently supported in bcbio?
Here's a link to the relevant files on the NCBI FTP server:
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.38_GRCh38.p12

GCF_000001405.38_GRCh38.p12_genomic.fna.gz
GCF_000001405.38_GRCh38.p12_genomic.gff.gz
GCF_000001405.38_GRCh38.p12_genomic.gtf.gz

Other genomes from Ensembl/GenBank and GENCODE (e.g. GRCh38 v29) install as expected on my virtual machine, so it appears that I'm running into some RefSeq-specific issues.
bowtie2, for example, errors out here, and I see this using either the GTF or GFF3 as input:
Total time for backward call to driver() for mirror index: 00:34:05
2019-04-05 16:14:23,509 - INFO - Committing changes: 3698000 features
2019-04-05 16:14:24,047 - INFO - Populating features table and first-order relations: 3698296 features
2019-04-05 16:14:24,047 - INFO - Creating relations(parent) index
2019-04-05 16:14:28,948 - INFO - Creating relations(child) index
2019-04-05 16:14:34,035 - INFO - Inferring transcript extents and writing to tempfile
2019-04-05 16:14:59,707 - INFO - Importing inferred features into db
2019-04-05 16:15:27,587 - INFO - Committing changes
2019-04-05 16:15:27,704 - INFO - Creating relations(parent) index
2019-04-05 16:15:32,459 - INFO - Creating relations(child) index
2019-04-05 16:15:37,302 - INFO - Creating features(featuretype) index
2019-04-05 16:15:40,852 - INFO - Creating features (seqid, start, end) index
2019-04-05 16:15:45,800 - INFO - Creating features (seqid, start, end, strand) index
2019-04-05 16:15:50,957 - INFO - Running ANALYSE features
invalid gffGroup detected on line: NC_000002.12 Curated Genomic stop_codon      88857361
        88857363        0.000000        -       0       gene_id "IGKC"; transcript_id "unknown_transcript_1";
GFF/GTF group unknown_transcript_1 on NC_000001.11-, this line is on NC_000002.12-, all group members must be on same seq and strand
1 errors
Creating gffutils database for /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.gtf.
'transcript' or 'gene' entries not found, so inferring their extent. This can be very slow.
Writing out merged GTF file to /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.gtf.
Traceback (most recent call last):
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 840, in <module>
    main(args.org_build, args.gtf, args.fasta, genome_dir, args.cores, args)
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 298, in main
    gtf_to_refflat(gtf_file)
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 439, in gtf_to_refflat
    genepred = gtf_to_genepred(gtf)
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 431, in gtf_to_genepred
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/data00/bcbio/stable/anaconda/lib/python2.7/subprocess.py", line 190, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'gtfToGenePred -allErrors -ignoreGroupsWithoutExons -genePredExt /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.gtf /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.genePred' returned non-zero exit status 255
Creating directories using /data00/bcbio/stable/genomes as the base.
Genomes will be installed into /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12.
Installed genome as /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/seq/GCF_000001405.38_GRCh38.p12.fa.
Installed GTF as /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/rnaseq/ref-transcripts.gtf.
Creating the seq index.
[localhost] local: samtools faidx GCF_000001405.38_GRCh38.p12.fa
[localhost] local: picard -Xms500m -Xmx3500m CreateSequenceDictionary REFERENCE=/data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/seq/GCF_000001405.38_GRCh38.p12.fa OUTPUT=/data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/seq/GCF_000001405.38_GRCh38.p12.dict
Creating the bowtie2 index.
[localhost] local: mkdir /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/seq/../bowtie2
[localhost] local: ln -sf ../seq/GCF_000001405.38_GRCh38.p12.fa /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/bowtie2/GCF_000001405.38_GRCh38.p12.fa
Traceback (most recent call last):
  File "/data00/bcbio/tools/bin/bcbio_setup_genome.py", line 312, in <module>
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/data00/bcbio/stable/anaconda/lib/python2.7/subprocess.py", line 190, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/data00/bcbio/stable/anaconda/bin/python /data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py --cores 28 --genome-dir /data00/bcbio/stable/genomes --gtf /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/rnaseq/ref-transcripts.gtf Hsapiens GCF_000001405.38_GRCh38.p12' returned non-zero exit status 1

Hi Mike,
It looks like it is throwing up on the stop_codon lines in the GTF file-- if you remove those and try to rerun, does it work? If so I can add stop_codon to the list of things we filter out from the GTF before going on with it.

Thanks, I'll try editing the GTF file to remove the stop_codons line and see if I can get it to index clean with bowtie2 directly first.

I think it is this that is failing: gtfToGenePred -allErrors -ignoreGroupsWithoutExons -genePredExt /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.gtf /data00/bcbio/stable/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.genePred -- hopefully a clean version of the GTF file will work.

I'm guessing the start_codon entries will have the same problem so you probably want to remove those too.

Thanks yeah I'll see if I can make a stripped down GTF file that works with gtfToGenePred.

Here's a minimal example that fixes gtfToGenePred on my end:
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.gtf.gz --output-document=ref-transcripts.gtf.gz
gunzip -c ref-transcripts.gtf.gz > ref-transcripts.gtf
grep -vwE "(start_codon|stop_codon|unknown_transcript_1)" ref-transcripts.gtf > ref-transcripts-sanitized.gtf
wc -l ref-transcripts*.gtf
# 3698302 ref-transcripts.gtf
# 3455709 ref-transcripts-sanitized.gtf
gtfToGenePred -allErrors -ignoreGroupsWithoutExons -genePredExt ref-transcripts-sanitized.gtf ref-transcripts.genePred
wc -l ref-transcripts.genePred
# 172088 ref-transcripts.genePred

Using the sanitized GTF that works directly with gtfToGenePred, now here's what I'm seeing with bcbio 1.1.4:
2019-04-08 15:15:48,162 - INFO - Running ANALYSE features
Unpaired type("")/val on end of gtf line 1 of /data00/bcbio/patched/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref$
transcripts.gtf
Creating gffutils database for /data00/bcbio/patched/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.gt$
.
'transcript' or 'gene' entries not found, so inferring their extent. This can be very slow.
Writing out merged GTF file to /data00/bcbio/patched/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.gt$
.
Traceback (most recent call last):
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 841, in <module>
    main(args.org_build, args.gtf, args.fasta, genome_dir, args.cores, args)
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 299, in main
    gtf_to_refflat(gtf_file)
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 440, in gtf_to_refflat
    genepred = gtf_to_genepred(gtf)
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 432, in gtf_to_genepred
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/data00/bcbio/patched/anaconda/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'gtfToGenePred -allErrors -ignoreGroupsWithoutExons -genePredExt /data00/bcbio/patch$
d/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/tmpcbl/ref-transcripts.gtf /data00/bcbio/patched/genomes/Hsapiens/GCF_0000014
05.38_GRCh38.p12/tmpcbl/ref-transcripts.genePred' returned non-zero exit status 255.
Creating directories using /data00/bcbio/patched/genomes as the base.
Genomes will be installed into /data00/bcbio/patched/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12.
Installed genome as /data00/bcbio/patched/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/seq/GCF_000001405.38_GRCh38.p12.fa.
Installed GTF as /data00/bcbio/patched/genomes/Hsapiens/GCF_000001405.38_GRCh38.p12/rnaseq/ref-transcripts.gtf.
Creating the seq index.
Creating the bowtie2 index.
Traceback (most recent call last):
  File "/data00/bcbio/tools-patched/bin/bcbio_setup_genome.py", line 308, in <module>
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/data00/bcbio/patched/anaconda/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/data00/bcbio/patched/anaconda/bin/python /data00/biodata/cloudbiolinux/utils/prepar
e_tx_gff.py --cores 28 --genome-dir /data00/bcbio/patched/genomes --gtf /data00/bcbio/patched/genomes/Hsapiens/GCF_000001405
.38_GRCh38.p12/rnaseq/ref-transcripts.gtf Hsapiens GCF_000001405.38_GRCh38.p12' returned non-zero exit status 1.

Can you send along the top of the ref-transcripts.gtf, the original gtf and the one that works from Ensembl? Like one gene from each. Like in files, not pasted in. I bet there is some trailing whitespace in the RefSeq GTF, but it would be good to test on something small.

That's totally it, the RefSeq GTF has trailing whitespace. If you trim that off during sanitizing it should fix that issue.
Is there a reason you're switching it up? There's a bunch of stuff in bcbio that is really useful that won't work with the RefSeq version of the genome.

Hi Rory,
I have no idea what is special about the RefSeq flavor of hg38. However, I was considering to try out the newest patchlevel of hg38. I noticed that bcbio is using a 1kG version of hg38 from 2016 without the patches released since then (if I read the provenance files correctly).
Do you have an idea if the patches provide any benefit in variant calling performance or any benefit at all?
TIA for your feedback.

@roryk Will do, I'll zip up these files and send you a link on O2. I need to use RefSeq for a multi-omics analysis using some proprietary aligned data that can't be reprocessed from the original FASTQs easily. Otherwise, I'm currently using the bcbio hg38 reference for my other projects.

@gabeng That's correct that bcbio hg38 is sourced from 1000 Genomes. Here's the recipe YAML from cloudbiolinux with more details: https://github.com/chapmanb/cloudbiolinux/blob/master/ggd-recipes/hg38/seq.yaml
Genome indices built from RefSeq (GCF_*) and GenBank (GCA_*; i.e. Ensembl, GENCODE) assemblies will have significant differences in the number of annotated genes and transcripts, so it's important to use a single reference genome per project.
The RefSeq FAQ has a nice explanation:

What is the difference between RefSeq and GenBank?
The GenBank archival sequence database includes publicly available DNA sequences submitted from individual laboratories and large-scale sequencing projects. GenBank is part of the International Nucleotide Sequence Database Collaboration (INSDC) along with the European Nucleotide Archive and the DNA Data Bank of Japan (DDBJ). Submitted sequence data is exchanged daily between the three collaborators to achieve comprehensive worldwide coverage. As an archival database, GenBank can be very redundant for some loci. GenBank sequence records are owned by the original submitter and cannot be altered by a third party.
RefSeq sequences are not part of the INSDC but are derived from INSDC sequences to provide non-redundant curated data representing our current knowledge of known genes. Some records include sequence information gathered from more than one INSDC record. Records may include sequence, descriptive information, publications, or feature annotation that is not available from any single INSDC record. RefSeq records are owned by NCBI and therefore can be updated as needed to maintain current annotation or to incorporate additional information. Also see the appendix provided in the NCBI Handbook, GenBank chapter.
Another distinction is that transcripts and proteins annotated on RefSeq genomic records are instantiated as separate records; in contrast, GenBank only instantiates the proteins annotated on genomic sequence records.

See also this post on Quora.

Okay, I can get bcbio to build bowtie2, minimap2, and STAR indices. However, I'm hitting an error with picard:
[localhost] local: picard -Xms500m -Xmx3500m CreateSequenceDictionary REFERENCE=/data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.fa OUTPUT=/data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.dict
Traceback (most recent call last):
  File "/data00/bcbio/tools/bin/bcbio_setup_genome.py", line 312, in <module>
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/data00/bcbio/stable/anaconda/lib/python2.7/subprocess.py", line 190, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/data00/bcbio/stable/anaconda/bin/python /data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py --cores 30 --genome-dir /data00/bcbio/stable/genomes --gtf /data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/rnaseq/ref-transcripts.gtf Hsapiens GRCh38_RefSeq_93' returned non-zero exit status 1

If you run picard -Xms500m -Xmx3500m CreateSequenceDictionary REFERENCE=/data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.fa OUTPUT=/data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.dict manually, does it give you more information about the error?

I'm running that right now actually

Weird, this works for me:
rm /data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.dict
picard -Xms500m -Xmx3500m CreateSequenceDictionary REFERENCE=/data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.fa OUTPUT=/data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.dict

Ah okay it's this step that's erroring out:
14:00:15.487 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data00/bcbio/stable/anaconda/share/picard-2.18.26-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Apr 09 14:00:15 EDT 2019] CreateSequenceDictionary OUTPUT=/data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.dict REFERENCE=/data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/seq/GRCh38_RefSeq_93.fa    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Apr 09 14:00:15 EDT 2019] Executing as mike@azlabapp35 on Linux 3.10.0-957.10.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_192-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.26-SNAPSHOT
[Tue Apr 09 14:00:32 EDT 2019] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=595591168
2019-04-09 14:13:25,968 - INFO - Committing changes: 3455000 features
2019-04-09 14:13:26,592 - INFO - Populating features table and first-order relations: 3455703 features
2019-04-09 14:13:26,593 - INFO - Creating relations(parent) index
2019-04-09 14:13:31,792 - INFO - Creating relations(child) index
2019-04-09 14:13:36,443 - INFO - Inferring transcript extents and writing to tempfile
2019-04-09 14:14:03,806 - INFO - Importing inferred features into db
2019-04-09 14:14:32,978 - INFO - Committing changes
2019-04-09 14:14:33,079 - INFO - Creating relations(parent) index
2019-04-09 14:14:38,089 - INFO - Creating relations(child) index
2019-04-09 14:14:42,692 - INFO - Creating features(featuretype) index
2019-04-09 14:14:46,100 - INFO - Creating features (seqid, start, end) index
2019-04-09 14:14:51,403 - INFO - Creating features (seqid, start, end, strand) index
2019-04-09 14:14:56,943 - INFO - Running ANALYSE features
Traceback (most recent call last):
  File "/data00/bcbio/stable/anaconda/lib/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py", line 51, in <module>
    for f in HTSeq.GFF_Reader( gtf_file ):
  File "/data00/bcbio/stable/anaconda/lib/python2.7/site-packages/HTSeq/__init__.py", line 208, in __iter__
    ( attr, name ) = parse_GFF_attribute_string( attributeStr, True )
  File "/data00/bcbio/stable/anaconda/lib/python2.7/site-packages/HTSeq/__init__.py", line 161, in parse_GFF_attribute_string
    raise ValueError, "The attribute string seems to contain mismatched quotes."
ValueError: The attribute string seems to contain mismatched quotes.
Creating gffutils database for /data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/tmpcbl/ref-transcripts.gtf.
'transcript' or 'gene' entries not found, so inferring their extent. This can be very slow.
Writing out merged GTF file to /data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/tmpcbl/ref-transcripts.gtf.
Traceback (most recent call last):
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 840, in <module>
    main(args.org_build, args.gtf, args.fasta, genome_dir, args.cores, args)
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 301, in main
    prepare_dexseq(gtf_file)
  File "/data00/biodata/cloudbiolinux/utils/prepare_tx_gff.py", line 811, in prepare_dexseq
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/data00/bcbio/stable/anaconda/lib/python2.7/subprocess.py", line 190, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/data00/bcbio/stable/anaconda/bin/python /data00/bcbio/stable/anaconda/lib/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py /data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/tmpcbl/ref-transcripts.gtf /data00/bcbio/stable/genomes/Hsapiens/GRCh38_RefSeq_93/tmpcbl/ref-transcripts.dexseq.gff3' returned non-zero exit status 1

It looks like the GTF file is malformed again, I bet if you look at it you'll see where the issue is.

Yeah the tmp file tmpcbl/ref-transcripts.gtf getting passed to dexseq_prepare_annotation.py is malformed. There's some step during the prepare_tx_gff.py call involving picard and gffutils that corrupts the original GTF input file.
Loading this up in R with rtracklayer confirms the embedded double-quote issue, although I'm not exactly sure where.
x <- rtracklayer::import("malformed.gtf")

Warning in readGFF(filepath, version = version, filter = filter) :
  the value part of some of the tag value pairs contains embedded double-quotes
Calls: <Anonymous> ... import -> import -> .local -> readGFFAsGRanges -> readGFF

Passing in the original GTF file in used in the bcbio_setup_genome.py call works though:
/data00/bcbio/stable/anaconda/bin/python /data00/bcbio/stable/anaconda/lib/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py /home/mike/refseq-trouble/GCF_000001405.38_GRCh38.p12_genomic-clean.gtf ref-transcripts.dexseq.gff3

I'd look at the malformed GTF and see if you can figure out where the issue is; it might be the original GTF file needs to get fixed some more.

Thanks, did you get this solved?

@roryk I punted on using RefSeq for this project and we've just been using Ensembl / GENCODE annotations here

Ok, thanks! Closing and we can re-visit if there is need for this particular build.

For the record, I've also been having trouble while running bcbio_setup_genome.py on a RefSeq GTF file. I'm guessing that the general RefSeq pipeline setup renders their GTF files unusable for bcbio by default, so I'm describing below what worked for me in case it helps anyone else.
I've also had to remove trailing spaces and any lines containing transcript_id "unknown_transcript_1", as described above. Then, in order to fix the error The attribute string seems to contain mismatched quotes (https://github.com/bcbio/bcbio-nextgen/issues/2760#issuecomment-481375203), I used the following perl command to replace any semicolons with & signs when enclosed within quotes inside the GTF annotations (as suggested here):
perl -e 'open(FILE, "original_file.gtf"); while(<FILE>){$_ =~ s/([^\"]);/\1\&/g; print $_;}' > edited_file.gtf

This got the GTF file usable with bcbio_setup_genome.py.

Thanks @amizeranschi, I'll try to circle back to this and see if it works on my end. bcbio currently uses gffutils internally to process GTF/GFF3 files. Maybe we can just add this step manually for RefSeq genome files prior to handing off to gffutils downstream in the genome build steps.

Good idea, it would be useful to have RefSeq GTF files automatically sanitized somehow.
Alternatively, this could be done directly from bcbio_setup_genome.py when the user mentions refseq in the --buildversion option, which was recently added (https://github.com/bcbio/bcbio-nextgen/commit/38badc09e1c0d2168c8b6105c21ff7726259ce91).

Thanks for the information, it is helpful to have-- unfortunately it's pretty tough to handle all GTF files since there is no actual specification for them, so I think it's best to just compile the workarounds necessary to get various ones to work, rather than implement fixes for all of the different types.


Inactive workspaces always showing in waybar

After #111 all the workspaces show in waybar using "hyprland/workspaces" module all the time.
That's pretty annoying because I can't tell anymore whether I have something in a workspace or if it's empty without navigating to it.
Is this an expected behavior?

Ah, we forgot to do this: https://github.com/Duckonaut/split-monitor-workspaces/pull/111#issuecomment-2266146252
@toamz I'll take care of it

That's pretty annoying because I can't tell anymore whether I have something in a workspace or if it's empty without navigating to it.

FYI: you can change css styles in waybar to make this clearer:

Active workspace has a light grey background with a white line, non-empty workspaces have a light grey background and empty workspaces have a dark grey background. You can see this in my waybar config: https://github.com/zjeffer/dotfiles/blob/main/.config/hypr/apps/waybar/style.css

Thank you for the advise.
I tried to target #workspaces button.empty and I can modify the background-color, however if I try to set a display: none; which is the behavior I'm trying to replicate, waybar just crashes.
It's been a while since I played with css properly, am I missing something?

Waybar does not implement full CSS. It is using GTK css subset and display is not one of the supported properties, as can be seen on https://docs.gtk.org/gtk3/css-properties.html, which is linked in waybar documentation.
The linked pull request should help you though.


Update Composer dependencies (2022-01-09-21-12)

Visual regression test passed!
View the visual regression test report


Read REMOTE_ADDR from server parameters

Currently server IP is reported in a User IP field because the library is checking for REMOTE_ADDR HTTP header.
REMOTE_ADDR is not an HTTP header, but rather a server variable.
This PR reads IP from the right place.

Good catch, thank you for your contribution!


Issue Notifier Discord Bot

Discord Bot to notify the DIscord Community about an open issue or a PR. Please explain how you did it and the resource you used or referred. And a brief guide on how to use it. Feel free to drop me a message if you need help :)

Hello! I've got a good knowlage in creating discord bots, but in JS (discord.js), but I can try writing one in python, is that good? Can I have this issue?

Yesh please go ahead and give it a try .Let me know If you need some help :) Have a great day

Hello, I've added solution files for this task. Let me know if I missing something!

Hello, I've added solution files for this task. Let me know if I missing something!

I have merged the PR


react-primitives Touchable doesn't work

First of all, thanks for this awesome project! I'm investigating how this could work at our company to get more client-facing component building in the design team realm and it seems really viable so far!
Now, I may be wrong about the expected behavior, but I thought that all of the react-primitives would work for react-sketchapp. I wouldn't expect Touchable to do anything in sketch, but I was hoping that it would transparently render so I could share components with interactions with the web and native.
When I attempt something like this:
import React from 'react';
import { Text, View, Touchable } from 'react-primitives';

const Button = (props) => (
    <Touchable onPress={() => console.log('hi')}>
        <View>
            <Text>{props.children}</Text>
        </View>
    </Touchable>
);

export default Button;

I am getting an error that says:
TypeError: this.touchableGetInitialState is not a function. See the screenshot below:

It works fine when I render it on the web, so it stands to reason this is not an issue with react-primitives. Let me know if I am expecting something that shouldn't work at all, but it seems logical to me that Touchable should at least render and not be interactive in Sketch.
I am using Sketch 43.2 and react-sketchapp 0.10.0

Thanks for reporting @tysoncadenhead - looks like we have a fix coming, bear with us 🙏

Should be fixed with<EMAIL_ADDRESS>

This is still happening for me in react-native (ios) with react-primitives 0.4.3

To confirm, it doesn't seem to be fixed in<EMAIL_ADDRESS>I'm using CRNA:
"dependencies": {     "expo": "^18.0.3",     "react": "16.0.0-alpha.12",     "react-native": "^0.45.1"   }
https://github.com/lelandrichardson/react-primitives/issues/71#issuecomment-312650514 states that "React 16" isn't compatible yet, but CRNA (and react-native init) only function correctly with React 16+
Any ideas on timings to resolve this?

cc @lelandrichardson

Yes. Still not working with 0.4.3. (using CRNA)
"react": "15.4.0",
"react-dom": "15.4.0",
"react-primitives": "^0.4.3",

Could you try with v0.4.4?
It's definitely defined here: https://github.com/lelandrichardson/react-primitives/blob/master/src/injection/react-sketchapp.js#L12-L24

just tried with v0.5 and it's working

Hi, is this working on react 16.3? I'm having this same issue using v0.5 and react 16.3


Writing on NdefFormatable does not work

Hello!
I am having issues with writing data on an NdefFormatable object which fails and invokes "fail to apply ndef tech" warning.
This issue is caused by line 1174 in android/src/main/java/community/revteltech/nfc/NfcManager.java:
try {
  Log.d(LOG_TAG, "ready to writeNdef");
  Ndef ndef = Ndef.get(tag);
  if (ndef == null) {
    callback.invoke("fail to apply ndef tech"); // line 1174
  } else if (!ndef.isWritable()) { ...

Instead of invoking error if ndef is null, I think we can follow Android developers documentation and use NdefFormatable.format to convert NdefFormatable to Ndef and then proceed to write on the NFC.
I am not too familiar with how to make changes to the repository and testing it so any help will be greatly appreciated :)
Thanks!
James

You find fix for this?

The way I remember solving this issue was by giving sufficient physical contact time (~3 seconds) between the NFC device and the tag for the data transmission to complete.
The error was invoked when the NFC device and the tag were in contact for too short.

It seems like they have updated the lib and it works well now on the version @3.13.0.


Ability to run via exe file (WinUI 3)

Give the ability to run applications through an exe file directly, and without certificates, in fact, like any classic WPF application, for example.
It is extremely unusual and inconvenient to do MSIX builds with certificates, I would like more freedom of action in this regard.

This is already possible and is called unpackaged distribution:
https://learn.microsoft.com/en-us/windows/apps/winui/winui3/create-your-first-winui3-app

Give unpackaged a try! Thanks


Support for Israel(Tel Aviv) Region "il-central-1"

The solution deployment is failing in Israel(Tel Aviv) Region "il-central-1"
Version: 2.1.3
Released: 12/2023
Additional context
S3 error: The unspecified location constraint is incompatible for the region specific endpoint this request was sent to. For more information check http://docs.aws.amazon.com/AmazonS3/latest/API/ErrorResponses.html

Israel is not a supported region. We have a full list of supported regions here: https://docs.aws.amazon.com/solutions/latest/workload-discovery-on-aws/supported-aws-regions.html.

Thanks, can this be added as enhancement in your roadmap?

Unfortunately, until this region has support for the AppSync service then it won't be possible to deploy the solution.


Screen for User Profile Setup

After registration, users will be directed to a profile page where they can fill in more details like medical history, current medications, allergies, etc.
Fields like blood type and whether they're willing to donate blood or organs will be collected.
Users can update their information at any time. Profile settings should include the ability to turn on/off notifications for donation-related events.

Hy, I would like to work on this issue , Can you please add Hactoberfest and gssoc tags.

hy, just noticed that there is no navigation happening when I press the registration button, Its missing
Navigator.push(
context, MaterialPageRoute(builder: (context) => const HomePage()));
Also , I think this is very inefficient to use , How about we use GoRouter package?
Can I open an issue for it?

Don't use GoRouter
as of now just work with MaterialPageRoute in future if it require then we will proced with it
as app don't much screen
Now just focus on Profile screen building

okay thanks, and what about navigation from registration page , should i add navigation on my own?
Also in profile page , for state management i was using Cubit, Is there any preference for other state management tools.
if yes, do tell.

Yes you can add your navigation but make sure it will properly works
You can use cubit and if it is required you can use shared-preference for caching

Okay Thanks

@may-tas are you comfotable with firebase, supabase or even nodejs and mongo??

If you encounter any new issue or problem raise new issue @may-tas
now i am closing this issue

Okay Got it.


Simplify nested reshapes

The find_reshaper is supposed to do this, but it doesnt work and there were no tests. So I updated for it to work and I added unit tests for it.

The find_reshaper is supposed to do this, but it doesnt work and there were no tests. So I updated for it to work and I added unit tests for it.

Does this mean we should remove the reshaper pass or is there some other function its providing we need to keep these seperate?

Does this mean we should remove the reshaper pass or is there some other function its providing we need to keep these seperate?

You mean the find_reshaper? I didnt remove it, I just changed it to work correctly.

Does this mean we should remove the reshaper pass or is there some other function its providing we need to keep these seperate?

You mean the find_reshaper? I didnt remove it, I just changed it to work correctly.

All good. Approved.


how to use this tool to break down a target compound?(Retrosynthesis)

I have some target compounds(SMILES), but I have no idea how to use your tool to break it down into some reactants.Any help would be appreciated.

If you simply want to predict potential reactants based on our method, you can refer to the "Environment Preparation" section in the readme document to set up the environment and download the pre-trained model for prediction.
We may develop a more user-friendly website in the future to provide reactant prediction services.

Since the questioner has not asked any further questions for a long time, I believe it is appropriate to close this issue.


Conflict with LapisReserve

The enchantment table cannot be opened with Lapis Reserve's presence:
[18:50:55] [Server thread/ERROR]: Failed to handle packet net.minecraft.class_2885@52bf6cc1, suppressing error
java.lang.NullPointerException: Cannot invoke "safro.apotheosis.util.FloatReferenceHolder.set(float)" because "this.eterna" is null
	at Not Enough Crashes deobfuscated stack trace.(1.18.2+build.3) ~[?:?]
	at safro.apotheosis.ench.table.ApothEnchantContainer.lambda$gatherStats$3(ApothEnchantContainer.java:251) ~[apotheosis-0.2.81.jar:?]
	at net.minecraft.class_3914$2.get(class_3914.java:22) ~[client-intermediary.jar:?]
	at safro.apotheosis.ench.table.ApothEnchantContainer.gatherStats(ApothEnchantContainer.java:228) ~[apotheosis-0.2.81.jar:?]
	at safro.apotheosis.ench.table.ApothEnchantContainer.lambda$slotsChanged$1(ApothEnchantContainer.java:163) ~[apotheosis-0.2.81.jar:?]
	at net.minecraft.class_3914$2.get(class_3914.java:22) ~[client-intermediary.jar:?]
	at safro.apotheosis.ench.table.ApothEnchantContainer.onContentChanged(ApothEnchantContainer.java:160) ~[apotheosis-0.2.81.jar:?]
	at net.minecraft.class_1718$1.markDirty(class_1718.java:32) ~[client-intermediary.jar:?]
	at net.minecraft.inventory.SimpleInventory.redirect$fha000$fabric_redirectMarkDirty(SimpleInventory:1043) ~[?:?]
	at net.minecraft.inventory.SimpleInventory.setStack(SimpleInventory:140) ~[?:?]
	at net.minecraft.screen.slot.Slot.setStack(Slot:61) ~[?:?]
	at net.minecraft.screen.EnchantmentScreenHandler.handler$hff000$open(EnchantmentScreenHandler:2530) ~[?:?]
	at net.minecraft.screen.EnchantmentScreenHandler.<init>(EnchantmentScreenHandler:92) ~[?:?]
	at safro.apotheosis.ench.table.ApothEnchantContainer.<init>(ApothEnchantContainer.java:62) ~[apotheosis-0.2.81.jar:?]
	at net.minecraft.block.EnchantingTableBlock.mdcc0c58$lambda$apothEnchMenu$0$0(EnchantingTableBlock:1039) ~[?:?]
	at net.minecraft.screen.SimpleNamedScreenHandlerFactory.createMenu(SimpleNamedScreenHandlerFactory:25) ~[?:?]
	at net.minecraft.server.network.ServerPlayerEntity.openHandledScreen(ServerPlayerEntity:1031) ~[?:?]
	at net.minecraft.block.EnchantingTableBlock.onUse(EnchantingTableBlock:87) ~[?:?]
	at net.minecraft.block.AbstractBlock$AbstractBlockState.onUse(AbstractBlock:939) ~[?:?]
	at net.minecraft.server.network.ServerPlayerInteractionManager.redirect$ckb000$activateWithOptionalCactus(ServerPlayerInteractionManager:4029) ~[?:?]
	at net.minecraft.server.network.ServerPlayerInteractionManager.interactBlock(ServerPlayerInteractionManager:336) ~[?:?]
	at net.minecraft.server.network.ServerPlayNetworkHandler.onPlayerInteractBlock(ServerPlayNetworkHandler:1081) ~[?:?]
	at net.minecraft.network.packet.c2s.play.PlayerInteractBlockC2SPacket.apply(PlayerInteractBlockC2SPacket:30) ~[?:?]
	at net.minecraft.network.packet.c2s.play.PlayerInteractBlockC2SPacket.apply(PlayerInteractBlockC2SPacket:8) ~[?:?]
	at net.minecraft.network.NetworkThreadUtils.method_11072(NetworkThreadUtils:22) ~[?:?]
	at net.minecraft.server.ServerTask.run(ServerTask:18) ~[?:?]
	at net.minecraft.util.thread.ThreadExecutor.redirect$cam000$redirectExecuteTask(ThreadExecutor:521) ~[?:?]
	at net.minecraft.util.thread.ThreadExecutor.runTask(ThreadExecutor:131) ~[?:?]
	at net.minecraft.server.MinecraftServer.runOneTask(MinecraftServer:17288) ~[client-intermediary.jar:?]
	at net.minecraft.server.MinecraftServer.runTask(MinecraftServer:784) ~[client-intermediary.jar:?]
	at net.minecraft.util.thread.ThreadExecutor.runTasks(ThreadExecutor:140) ~[?:?]
	at net.minecraft.server.MinecraftServer.runTasksTillTickEnd(MinecraftServer:769) ~[client-intermediary.jar:?]
	at net.minecraft.server.MinecraftServer.handler$chd000$modifiedRunLoop(MinecraftServer:5405) ~[client-intermediary.jar:?]
	at net.minecraft.server.MinecraftServer.runServer(MinecraftServer:676) ~[client-intermediary.jar:?]
	at net.minecraft.server.MinecraftServer.method_29739(MinecraftServer:273) ~[client-intermediary.jar:?]
	at java.lang.Thread.run(Thread.java:833) [?:?]

Mods that mixin to the Enchantment Table features won't work with Apotheosis unfortunately. There isn't much I can do so you will have to either uninstall Apotheosis or Lapis Reserve.

yeah but how about adding a feature of lapis reservoir within the table? or that's beyond scope due to upstream?


solved error with create_payment_gateway during install

@brosboss thanks for your contribution, the app has been improved, errors fixed, it is setup, testes and working fine for version-14. please install and test.


Update javaparser-symbol-solver-core to 3.25.2

About this PR
📦 Updates com.github.javaparser:javaparser-symbol-solver-core from 3.22.1 to 3.25.2
Usage
✅ Please merge!
I'll automatically update this PR to resolve conflicts as long as you don't change it yourself.
If you'd like to skip this version, you can just close this PR. If you have any feedback, just mention me in the comments below.
Configure Scala Steward for your repository with a .scala-steward.conf file.
Have a fantastic day writing Scala!

⚙ Adjust future updates
Add this to your .scala-steward.conf file to ignore future updates of this dependency:
updates.ignore = [ { groupId = "com.github.javaparser", artifactId = "javaparser-symbol-solver-core" } ]

Or, add this to slow down future updates of this dependency:
dependencyOverrides = [{
  pullRequests = { frequency = "30 days" },
  dependency = { groupId = "com.github.javaparser", artifactId = "javaparser-symbol-solver-core" }
}]

labels: library-update, early-semver-minor, semver-spec-minor, commit-count:1

Superseded by #1737.


Potentially confusing API next16 when operating on values with sizes < 2

I am implementing a custom error handling strategy for converting from UTF-16 to UTF-8. My raw bytes are held in a std::string.
I naively attempted to iterate this std::string by using next16. This fails since the iteration under next16 now iterates single bytes instead of pairs.
TEST(Foo, bar) {
  using namespace std::string_literals;
  std::string abc = "a\0b\0c\0"s;
  EXPECT_EQ(abc.size(), 6); // Precondition.

  auto &&x = abc;

  std::u16string abc16;
  const auto end = x.end();
  for (auto it = x.begin(); it < end;) {
    auto ch = utf8::next16(it, end);
    utf8::append16(ch, abc16);
  }

  EXPECT_TRUE(is_valid(abc16.begin(), abc16.end())); // Precondition.
  EXPECT_EQ(utf16to8(abc16), "abc"s); // FAIL.
}

With the right warnings enabled this raises a sign-conversion warning in the bowels of utfcpp. I however naively expected that next16 would already pick the right iteration strategy (it could in principle detect the sizes of the values behind the word_iterator passed to next16, but does not).
I get the correct behavior if I additionally wrap the string in a u16string_view which ensure the iterator advances like expected by next16.
auto x = std::u16string_view{reinterpret_cast<char16_t *>(abc.data()),
                             abc.size() / 2};

I think it would be great if utfcpp could either automatically pick the right iteration strategy based on the value type behind its iterators, or at least reject cases where an iterator over values of smaller size is passed than is expected.

I guess it would help to issue a compiler error if the value type is not the right size. I am not sure how I accomplish that, though. Any ideas?

What makes this slightly "ugly" is that next16's word_iterator is completely unconstrained, but I think we should be able to get the values it yields with a combination of declval and decltype, e.g., (slightly convoluted to also support C++11 where we cannot have the enable_if as a default template argument):
template<typename word_iterator>
typename std::enable_if<sizeof(decltype(*std::declval<word_iterator>())) == sizeof(char16_t), utfchar32_t>::type next16(
    word_iterator& it, word_iterator end) {
 ...

With this one can only invoke next16 with iterators which yield values of the same size as char16_t and my example would not compile anymore. Not sure whether it makes sense to allow iterators over bigger values.


[DevOps] automatic Workflow for container publish

This Repository needs an automatic Deploy job.
I started testing and found a way of doing this. The pipeline can be found in my fork of this (https://github.com/lightlike/docker-avorion)
The job currently only pushes to ghcr but that should be changable with some credentials.
There are still two points I need to discuss.
1. How should versioning work?
My pipeline is currently only setting the tag of the container statically (e.g. stable/beta)
It would be nice for compatibility to set the version for containers but this is only optional as this could bring instability.
This could be done using one of the following methods:

set version as manual parameter (only manual triggering) or via a push
get the version via https://api.steampowered.com/ISteamNews/GetNewsForApp/v2/?appid=445220&count=1&tags=patchnotes and grep

The second possibility is only as reliable as the posts from the dev team but would mean that the pipeline could run automatically.
2. Should this pipeline run automatically?
If the automatic versioning should be used. The build could run daily and the would be no maintanance except for errors.
This would not be a Problem when using the free plan as you get 2,000 min/month and the pipeline currently takes one minute.
This maybe could also be triggered using some e-mail hook or similar but that is not supported by github and one would need to run a third party tool for that.

I'd like to keep the full game version which I think rules out scraping patch notes. I currently get this from the server binary (AvorionServer --version). I'd also like the readme to be kept up to date automatically.
An automatic pipeline would be great though. Just a few ideas that could be worth looking into:

Does steam offer a way to download single binaries from a depot? If so, we could periodically download AvorionServer and run the job based off that.
Does steamdb offer an api (or some reliable way to know if a depot branch has been updated)?
Perhaps the devs would be open to providing a stable location for querying for the latest version of the game.

I have the version working by just Running a steamcmd container and installing Avorion there.
This will only get the current Version.
I have tried to find any way of getting the version otherwise or downloading a depot using the steam API but no luck.
The last thing missing is the checking if the build has to run. I would try to use Tags or (Pre-)Releases for that.
That would also allow to have the Readme static and let shields.io get the Version from the Releases.
After that the Builds could just run Daily and not publish if there are no changes.
The only Problem, that I could see with that is that the version for the beta tag show the stable number if there is a stable release later than the beta. I have no idea if or when this could come up but I'll try some stuff.

The Pipeline should be done.
The only changes needed are some small ones like the shields.io links, the trigger and the login to docker hub if you do not want to use ghcr.
I had to change the way latest works because I need a static way to set the tags. So that now constantly links to stable.
I already changed the Redme to reflect those changes.
Please look into my changes and tell me everything you might want changed.


is this designed to work in the saleshub app on a mobile device?

it appears to not work in the mobile apps.  is it designed to work there ?

Any progress or an answer on this?  I'm also hoping to use this functionality on the Mobile App.


CI: Re-enable integration tests and QC toolkit tests

Describe your changes

Storage access for these tests have been resolved. Azure ML tests are still blocked.
Fix lint issue due to new ruff release

Checklist before requesting a review

[ ] Add unit tests for this change.
[x] Make sure all tests can pass.
[ ] Update documents if necessary.
[x] Lint and apply fixes to your code by running lintrunner -a
[ ] Is this a user-facing change? If yes, give a description of this change to be included in the release notes.
[ ] Is this PR including examples changes? If yes, please remember to update example documentation in a follow-up PR.

(Optional) Issue link

/azp run


The functional test for changing title into the first script after  tag

Todo

[ ] Check the following case:

<head>
    <title>Test page title 1</title>
    <script>
        var log = [];

        log.push('head:after-first-title: ' + String(document.title));

Related to https://github.com/DevExpress/testcafe-hammerhead/issues/2374

We want to cover more test cases for document.title proxing.


2023-13-08: Tweets not embedding

Investigating this issue where Tweets are not embedding properly.
So far, I have found that Twitter is returning an empty response when I ask for info about a Tweet

A fix has been deployed, currently looking to see if this stabilizes things. It might take up to 30 minutes for Discord to update their cache

seems functional here

update : seems inconsistent. some links work fine but some dont

Made some other changes behind the scenes which should improve things, I hope

seems resolved but the tweet that was broken before seems broken still (maybe caching issue?)
problematic one : https://vxtwitter.com/eatery1234/status/1690615633757802496?s=20

Probably a caching issue. I reset the cache on my end of things so hopefully it all starts working again

yup seems resolved. was most likely expired cache 👍 thanks

Issue resolved I guess!

seems like the combined image tweets cant be maximized properly (4 images in 1 tweet for example)
the screenshot ive provided is what happens when i click on such embed image on android. could test on my iphone but i dont have access to it right now

This error usually happens if the tweet has been deleted

gotcha, ty👍


Stream load issue

I saw that streaming_load_max_mb is 10G. Can Stream load support 500GB data from mysql to doris。

Supported in theory, but not recommended, because stream load reads and processes data in a single thread


Still active

Is this project still active?

It is currently inactive due to a lack of time and need on my end. That said, if there is interest and I have the ability to do so, I'd love to see this get off the ground. I haven't kept up with changes to openmct in the past year or so, nor to new ros packages, so I don't know f this would still fill the need it was intended to two years ago.

@DWatkins I would like to help get this project going again, are you open to contributions? Also, any chance you could write a wiki article with some installation steps? To get going, I'd like to be able to see a plot of the linear and angular velocity of my robot from the odometry messages, I also have battery voltage information and such.

Let me look through the current state of open mct and see how compatible things are, and then I will get back to you on this.

Also interested

I am going to need something like this for my current project, and am happy to contribute my time to getting this off the ground and working again.

FWIW, inspired by this project we've got a plugin for the current version of Open MCT that's working with ROS2:
https://github.com/traclabs/openmct-ros
I haven't tested extensively, but I think it also works with ROS 1.


Playbook fails when Vault is not initialized.

This issue is similar to #83 Vault API reachable? - fails. To use this role in a larger playbook, where auto-init and auto-unseal are implemented, it would help if the health_check at the end simply reports the status. Now it seems stuck in the loop when the status is just how this role delivers Vault: not initialized.
TASK [ansible-hashicorp-vault : Vault API reachable?] **************************
FAILED - RETRYING: Vault API reachable? (30 retries left).
FAILED - RETRYING: Vault API reachable? (29 retries left).
FAILED - RETRYING: Vault API reachable? (28 retries left).
FAILED - RETRYING: Vault API reachable? (27 retries left).
FAILED - RETRYING: Vault API reachable? (26 retries left).
FAILED - RETRYING: Vault API reachable? (25 retries left).
FAILED - RETRYING: Vault API reachable? (24 retries left).
FAILED - RETRYING: Vault API reachable? (23 retries left).
FAILED - RETRYING: Vault API reachable? (22 retries left).
FAILED - RETRYING: Vault API reachable? (21 retries left).
FAILED - RETRYING: Vault API reachable? (20 retries left).
FAILED - RETRYING: Vault API reachable? (19 retries left).
FAILED - RETRYING: Vault API reachable? (18 retries left).
FAILED - RETRYING: Vault API reachable? (17 retries left).
FAILED - RETRYING: Vault API reachable? (16 retries left).
FAILED - RETRYING: Vault API reachable? (15 retries left).
FAILED - RETRYING: Vault API reachable? (14 retries left).
FAILED - RETRYING: Vault API reachable? (13 retries left).
FAILED - RETRYING: Vault API reachable? (12 retries left).
FAILED - RETRYING: Vault API reachable? (11 retries left).
FAILED - RETRYING: Vault API reachable? (10 retries left).
FAILED - RETRYING: Vault API reachable? (9 retries left).
FAILED - RETRYING: Vault API reachable? (8 retries left).
FAILED - RETRYING: Vault API reachable? (7 retries left).
FAILED - RETRYING: Vault API reachable? (6 retries left).
FAILED - RETRYING: Vault API reachable? (5 retries left).
FAILED - RETRYING: Vault API reachable? (4 retries left).
FAILED - RETRYING: Vault API reachable? (3 retries left).
FAILED - RETRYING: Vault API reachable? (2 retries left).
FAILED - RETRYING: Vault API reachable? (1 retries left).
fatal: [myhost]: FAILED! => {"attempts": 30, "cache_control": "no-store", "changed": false, "connection": "close", "content": "{\"initialized\":false,\"sealed\":true,\"standby\":true,\"performance_standby\":false,\"replication_performance_mode\":\"unknown\",\"replication_dr_mode\":\"unknown\",\"server_time_utc\":1570612414,\"version\":\"1.2.2\"}\n", "content_length": "199", "content_type": "application/json", "date": "Wed, 09 Oct 2019 09:13:34 GMT", "elapsed": 0, "json": {"initialized": false, "performance_standby": false, "replication_dr_mode": "unknown", "replication_performance_mode": "unknown", "sealed": true, "server_time_utc":<PHONE_NUMBER>, "standby": true, "version": "1.2.2"}, "msg": "Status code was 501 and not [200, 503]: HTTP Error 501: Not Implemented", "redirected": false, "status": 501, "url": "https://<IP_ADDRESS>:8200/v1/sys/health"}

Fixed by https://github.com/brianshumate/ansible-vault/pull/120


Termius crash on launch.

After jailbreaking with Dopamine 1.0.4 the "Termius" app from AppStore crashes on launch.
Any solutions?
App url:
https://apps.apple.com/gr/app/termius-terminal-ssh-client/id549039908

Duplicate of #139

Install the Choicy Tweak  from "opa334's Repo" and disable tweak injection into the "Termius" app


When exported label map is added to 3D ROI Manager, overlapping areas are counted as new labels

Hi,
Firstly, thank you for this resource, it is working really well for me. I am using it to generate ground-truth images for use with the StarDist Segmentation, and it is easy to use and has great functionality. I have come across a problem however, but I'm not sure if it is because I am doing something wrong.
I colour each nucleus in an image with a separate label, and some of my labels overlap in lab kit. In lab kit this is fine, the overlapping area belongs to both labels as it should. However when I export the label map into imageJ and add the image to the 3D Roi Manager, these overlapping areas are counted as new labels, which is not ideal. From 200 labels on lab kit, I have 258 in the Roi Manager. I'm worried that, as well as skewing the 3D Measure values, this may also be leading to errors in the training of my segmentation model with StarDist, if it too is erroneously attributing nuclear identity to these overlapping areas.
I was wondering how I could prevent this.
Thanks again, and look forward to hearing from you,
Michael Schwimmer

Apologies, I just noticed a solution from another user!

Hi,
I noticed a solution from another user @maweigert (#31), involving the override checkbox. This seems to not make a difference if it was not checked during label drawing. Is there a way to achieve the same result after all the labels have been drawn, I would really like to not have to redraw a lot of labels!
Thankyou very much,
Michael

Hi @michaelschwimmer
Indeed, checking override is very important for generating stardist training  data.

Is there a way to achieve the same result after all the labels have been drawn, I would really like to not have to redraw a lot of labels!

This is going to be hard in general. If the overlap only affects small regions of the annotations, you could try to filter the overlap regions and set them to one of the two adjacent regions.
This can be done in python like so:
from skimage import measure, segmentation

def fix_labels(lbl):
    y = np.zeros_like(lbl)
    for r in measure.regionprops(lbl):
        outer = list(x[segmentation.find_boundaries(lbl==r.label, mode=  "outer")])
        outer_label = max(outer,key=outer.count)
        y[lbl==r.label] = r.label if outer_label==0 else outer_label
    return y

img = ... # load the 2D label image

img_fixed = fix_labels(img)

Which results in something like this:

Maybe this helps...
Martin

Hi @maweigert ,
Will this work for 3D images? Just noticing the img = # load the 2D label image.
Thank you very much!
Michael Schwimmer

Will this work for 3D images?

Yes


Make twister dig deeper in directory structure to find additional .yaml files

Is your enhancement proposal related to a problem? Please describe.
We want to add application/sample specific tests in projects. When adding a my_sample /tests/ folder side by side with the my_sample/src/ folder of a project we experience that twister cannot find the our testcase.yaml files inside the /tests/ folder as it stops searching further down the folder structure when it finds a .yaml file. In this case /my_sample/sample.yaml
The reason for having the application specific tests together with the application and not together with the other tests is that we want to be able to make out of tree copies of the application where the user can update the tests together with changes they make in the application.
Describe the solution you'd like
I would like twister to be modified somehow to dig deeper to find my testcase.yaml
I would like to keep directory structure as proposed.
Describe alternatives you've considered
Either dig into all folders, or possibly make a hint in the  my_sample/sample.yaml that it should look for more files.
It should be scalable in such a way that you do not have to change any central configuration to make twister find the test file such as e.g  add -T samples/my_sample/tests to the twister call
Additional context

@PerMac @nashif @carlescufi

I am not clear exactly what the ask is and why is this useful.

The ask is to make it possible for twister to find .yaml files in subfolders in a samples. The use case is to have sample specific tests in a subfolder within a sample. We want CI to find these tests automatically with twister. In its current form twister will stop searching at the root level of the sample when it finds the sample.yml
The reason for having tests bundled with the sample in the sample folder is that we want customers to take the entire folder out of tree and customize both the sample and the tests for their own needs.  Here is an example where we add tests: https://github.com/nrfconnect/sdk-nrf/pull/4173
We want our CI to pick up these tests without specifying the exact path. That will get ugly when we add more samples and applications with their own tests.
Here we have an out of tree setup of the asset tracker v2 application: https://github.com/NordicSemiconductor/asset-tracker-cloud-firmware

@nashif did I manage to explain it?

Created a PR for this issue: #34041

PR merged, closing issue.


could I select the db ?

hi,dear
as I see the db in redis
help(redis.StrictRedis)
__init__(self, host='localhost', port=6379, db=0, password=None, socket_timeout=None, socket_connect_timeout=None, socket_keepalive=None, socket_keepalive_options=None, connection_pool=None, unix_socket_path=None, encoding='utf-8', encoding_errors='strict', charset=None, errors=None, decode_responses=False, retry_on_timeout=False, ssl=False, ssl_keyfile=None, ssl_certfile=None, ssl_cert_reqs='required', ssl_ca_certs=None, ssl_check_hostname=False, max_connections=None, single_connection_client=False, health_check_interval=0, client_name=None, username=None)

but in rediscluster can't find the parameter?
help(rediscluster.RedisCluster)
__init__(self, host=None, port=None, startup_nodes=None, max_connections=None, max_connections_per_node=False,
init_slot_cache=True, readonly_mode=False, reinitialize_steps=None, skip_full_coverage_check=False, nodemanager_fol
low_cluster=False, connection_class=None, read_from_replicas=False, cluster_down_retry_attempts=3, host_port_remap=
None, **kwargs)

So could I set the parameter ??
thx

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.5/dist-packages/rediscluster/client.py", line 336, in __init__
    raise RedisClusterException("Argument 'db' is not possible to use in cluster mode")
rediscluster.exceptions.RedisClusterException: Argument 'db' is not possible to use in cluster mode

@ucasiggcas The error message is very descriptive enough to say what is happening. I would recommend you to read up on the basics of redis cluster before you continue to know all of these more basic questions. You can find the docs and tutorial here https://redis.io/topics/cluster-tutorial and https://redis.io/topics/cluster-spec
In short, the concept of databases and selecting different ones in a cluster mode do not exists any longer. The concept of segmenting the data into smaller logic databases is not possible in a clustered environment.
In general what you do is to build a good key space pattern and then data can live along side each other w/o problem in a single database.

thanks a lot


[#1 Attention Performance] raise non-block pointer to block pointer

in the test python/tutorial/06-fused-attention.py, we have non block pointer operation
    m_ptrs = M + off_hz * N_CTX + offs_m
    tl.store(m_ptrs, m_i)

however, we can raise it to block pointer for this simple pattern.
M_block_ptr = tl.make_block_ptr(
    base=M + qvk_offset,
    shape=(N_CTX),
    strides=(1),
    offsets=(start_m * BLOCK_M),
    block_shape=(BLOCK_M),
    order=(0),
 )
tl.store(M_block_ptr, m_i)

an analysis and rewriter pass is needed to do this.

This can be changed in the tutorial as a workaround to unblock the process.

the store is for backward, now we can workaround it


feat: add support for byte range requests

fixes https://github.com/supabase/storage-api/issues/20
Video and Audio files should play better now

Sweeeeet

Will be deployed to prod next week :)

Does Supabase broadcast when production gets deployed?

Hey @quicksnap, not at the moment. Usually happens in a week or two after new storage, realtime, gotrue versions are released.


CAMEL-14886: Add camel-component-maven-plugin

This is to separate GenerateComponentMojo into separate maven plugin for 3rd party developers.
Tested on @oscerd Cassandra component.
Next on my list is to add it to the maven archetype and add documentation about its usage, for example the required annotations to be used in order to generate the metadata

No problems @oscerd . You can give it a test, you just need to add all the annotations, e.g: Component, UriEndpoint .. etc and it should generate all the metadata/java files. To run it:
mvn org.apache.camel:camel-component-maven-plugin:3.4.0-SNAPSHOT:generate

Added the plugin to the archetypes


Internal Server Error when trying to create a recipe

How to reproduce:

/mineflow
Click recipe
Type anything
Internal Server Error

Thank you for the report.
I tried it, but I couldn't reproduce. So, could you show me the details of the error statement?

Yes sorry for the long time for reply. Here you go:

thread/CRITICAL ErrorException: "file_put_contents(/plugin_data/Mineflow/recipes/hello.json): failed to open stream: Permission denied" (EXCEPTION) in "plugins/Mineflow_dev-31.phar/src/aieuo/mineflow/recipe/Recipe" at line 307
Not sure if it is my internet but the error doesn’t show in the blocks above so I reposted without it just incase

Thank you. Fixed.
Please delete the plugin_data/Mineflow/recipes folder, update the plugin and restart it.

Thanks so much!


material-select retain "selected" state on second opening only

Using material-select dropdown directive, the selected option will show only if you select one option, then select the same one again in the dropdown.
Steps to reproduce

Open the select options.
No selected item is shown even if one is selected by default.
Select an option (or the default selected one)
Click to open again and Select the same option again (if you have selected the default selected one it will show as selected...)
Finally your new choice is visible as selected in the dropdown.

What exactly is supposed to happen
The selected option should happens on first click or with the default value
What exactly does happens
The selected option only shows on second click (or first for the default selected one)

        store
        <select id="job" name="job" ng-model="usrEdit.user_edit.user.job" ng-options="job.name as job.label for job in usrEdit.user_edit.jobs" material-select>
        </select>
    Rôle

I tried the watch property but it changes nothing.
I could give you access to the related site but I can't post access code here. So either contact me in private or ask me what you need.
Thanks.
EDIT: NEW FOUND EVIDENCES
I were able to reprodcue this exact behavior from the Angularjs directives for Materialize official doc on selects !
Just here : https://goo.gl/SYvt5L

Can confirm

To be clear, the bug is that there isn't a grey background behind the selected item, when you open the select.

Yes, this is exactly what I mean.
It happens to me on the own documentation of this very plug-in... https://goo.gl/SYvt5L
You have to click two time on an option to get it with a greyed background, or just one if this is the "default" selected one.
I looked into this but can't find the faulty code there.

I suspect it has something to do with the select re-initializing all the time, every time something change, the initSelect method is invoked. And i think that resets the grey background.
It is however not invoked the second time one selects the same option, since nothing changes, and thereby the grey background is not reset.
I might have time to look further into it later today.

If I find a way to solve it, I'll just post a commit here. Not sure I get the time either today but will do what I can. !

I feels cheated as I almost spent all the day trying to solve this and didn't find the way to do it. Hope you'll have better ideas than mine.

Seeing that you failed, I gave it a go. I had a pretty good idea going in though.
It should be fixed now, and you should be able to see that in the documentation (might need to clear your cache).

Thanks for this.
That's true it's fixed on the demo website... But not for me... It's not fixed at all... It's even worse, now the dropdown is getting truncated by the lower part of my form container... Really curious, isn't it?
I'll have to find where this come from...
Thanks anyway.

If you think the issue is caused by angular-materialize, feel free to raise a new issue.


Windows support

[ ] add windows target to release builds
[ ] fix span bugs? is this related to unicode? document.offsetAt seems character based and not byte-based

Consolidated into #33.


fails to build when added as a stack dependency

upon building my project:
• Couldn't match kind ‘*’
                         with ‘(ghc-prim-<IP_ADDRESS>:GHC.Types.Symbol, *)’
          When matching the kind of ‘ZipTypes b_names b_rs’
          Expected type: b Identity
                         -> Frames.Rec.Record (ZipTypes b_names b_rs)
            Actual type: b Identity
                         -> Data.Vinyl.Core.Rec
                              Data.Vinyl.Functor.Identity (ZipTypes b_names b_rs)
        • In the first argument of ‘map’, namely ‘createRecId’
          In the expression: map createRecId bQRes
          In an equation for ‘bRecs’: bRecs = map createRecId bQRes
        • Relevant bindings include
            bRecs :: [Frames.Rec.Record (ZipTypes b_names b_rs)]
              (bound at src/Frames/SQL/Beam/Postgres/Query.hs:66:5)
            join2 :: JoinQueryResults a b
                     -> FrameRec (ZipTypes a_names a_rs ++ ZipTypes b_names b_rs)
              (bound at src/Frames/SQL/Beam/Postgres/Query.hs:61:1)

using this stack.yaml
resolver: lts-11.7
packages:
- .
extra-deps:
- Frames-0.5.0
- beam-core-<IP_ADDRESS>
- beam-migrate-<IP_ADDRESS>
- beam-postgres-<IP_ADDRESS>
- vinyl-0.10.0
- Frames-beam-<IP_ADDRESS>

Looks like this is an issue with vinyl-0.10.0; vinyl-<IP_ADDRESS> compiles.

The source of this appears to be the fact the dependency on Frames-0.5.0, which in turn depends on vinyl >= 0.10.0.
More specifically, in Frames-0.4.0:
type Record = Rec Identity

But in Frames-0.5.0:
type Record = FieldRec
-- and
type FieldRec = Rec ElField

I think, for now, putting an upper bound on Frames and vinyl should fix this. Let me push an update. Thanks for raising this.

Frames-beam-<IP_ADDRESS> is on Hackage now. Can I close this ?

I'm not familiar with the reasons behind the change in Frames-0.5.0, but I'd suggest to instead modify Frames-beam to use the new Frames representation, rather than being locked to an obsolete version.

It is likely that it has to do with the new Categorical representation in Frames. This allows many useful things, like the use of discrimination for joins. I would think supporting 5.0 would be preferable.
Sent from my iPhone

On Sep 1, 2018, at 4:11 PM, Marco Zocca<EMAIL_ADDRESS>wrote:
I'm not familiar with the reasons behind the change in Frames-0.5.0, but I'd suggest to instead modify Frames-beam to use the new Frames representation, rather than being locked to an obsolete version.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or mute the thread.

@o1lo01ol1o New version with support for Frames-0.5.0 and vinyl-0.10.0 is on Hackage now. Do give it another try and let me know how it goes.


How can i update server code without restart server

Hi,
Thanks for your work.
I have a question.
How can i update server code without restart node server?

Hi @trananhmanh89 :wave:
If you'd like to not have to manually restart node server every time you change code, you can use nodemon package, so that every time you make a code change, it will automatically restart your server. If what you want is to have some kind of hot replacement of server-side code without restarting the node process then unfortunately I won't be able to help you.

Hi @trananhmanh89 👋 If you'd like to not have to manually restart node server every time, you can use nodemon package, so that every time you make a code change, it will automatically restart your server. If what you want is to have some kind of hot replacement of server-side code without restarting the node process then unfortunately I won't be able to help you.

I tried with node --watch and it creates an infinite loop.
I'm pretty sure this is because when the frontend code is run, some file gets modified or created, and  causes the server code to restart.

@angelhdzmultimedia I found - it every time generates vite.config.ts.timestamp-1721912890454-4d4be18b59d59.mjs file in root folder
So you should ignore it:
# tsx watch example
tsx watch --ignore "vite.config.*" server/index.js


cool paper. Uncertainty Calibration in Bayesian Neural Networks via Distance-Aware Priors

https://arxiv.org/pdf/2207.08200
this paper provides a different way to optimize the priors using distance aware priors.
Maybe i can try to implement it.

Great idea!


feat(Config): not init on import of module

What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)

Changing the default behaviour of the Config module
Allowing the hostname for the class to be changed on the init method (vs modifying the environment variables)

What is the current behavior? (You can also link to an open issue here)

Current behaviour has the module class setup on import - this lends itself to some undesirable code (by moving the import into further down, conditionally doing imports as it cannot be modified after import)

Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)

In [1]: from staxapp.config import Config
   ...: from staxapp.openapi import StaxClient

In [2]: Config.secret_key = "xxx"

In [3]: Config.access_key = "yyy"

In [4]: stax_workloads = StaxClient("workloads", Config=Config)

In [5]: len(stax_workloads.ReadWorkloads(filter='ACTIVE')["Workloads"])
Out[5]: 742

Or

In [4]: stax_workloads = StaxClient("workloads")

In [5]: len(stax_workloads.ReadWorkloads(filter='ACTIVE')["Workloads"])
Out[5]: 742

This has been completed by the following pull request
https://github.com/stax-labs/lib-stax-python-sdk/pull/86

This has been completed by the following pull request
https://github.com/stax-labs/lib-stax-python-sdk/pull/86


build: fix build warn on cygwin.

Signed-off-by: MaYuming<EMAIL_ADDRESS>

Could you help me start a CI test for this patch.  I have no permission.

We have no cygwin CI, but here is a run nonetheless: https://ci.nodejs.org/view/libuv/job/libuv-test-commit/1586/

@saghul It seems that the fails didn’t caused by this PR.

What should I do to merge it？

Sorry for the delay! Landed in 0ff717e3, thanks!


[BUG] Seek Player Function

Describe the bug
The seek function always makes the bot stop playback, but only when auto completion is active (I think).

I use node v20.12.1.

Screenshots

Log File
There is no error logs.

Thanks for the report! I'll take a look at this and see if I can find a fix. Does it happen with all songs or just long ones? (Over 10 minutes)

Thanks for the report! I'll take a look at this and see if I can find a fix. Does it happen with all songs or just long ones? (Over 10 minutes)

All songs, but only when there is no next song in the queue.


HTML5Setup.sh problems

/c/UEHTML5/UnrealEngine/Engine/Platforms/HTML5
Cloning into 'emsdk-3.1.4'...
remote: Enumerating objects: 3580, done.
remote: Counting objects: 100% (11/11), done.
remote: Compressing objects: 100% (8/8), done.
remote: Total 3580 (delta 3), reused 5 (delta 3), pack-reused 3569
Receiving objects: 100% (3580/3580), 2.11 MiB | 2.55 MiB/s, done.
Resolving deltas: 100% (2356/2356), done.
Python
I think problem is here: "Python"
GenerateProjectFiles.bat also have errors
$ cmake --version
cmake version 3.26.0-rc3
CMake suite maintained and supported by Kitware (kitware.com/cmake).
$ python3 --version
Python
$ python --version
Python 3.7.9
$ ./GenerateProjectFiles.bat
Setting up Unreal Engine 4 project files...
ERROR: EMSCRIPTEN NOT FOUND: C:\UEHTML5\UnrealEngine\Engine\Platforms\HTML5\Build\emsdk\emsdk-3.1.4\upstream\emscripten
*** EMSCRIPTEN_ROOT directory NOT FOUND: error_emscripten_not_found
ERROR: NODEJS NOT FOUND: C:\UEHTML5\UnrealEngine\Engine\Platforms\HTML5\Build\emsdk\emsdk-3.1.4\node\14.18.2_64bit\bin\node.exe
*** NODE_JS NOT FOUND: error_nodejs_not_found
ERROR: LLVM NOT FOUND: C:\UEHTML5\UnrealEngine\Engine\Platforms\HTML5\Build\emsdk\emsdk-3.1.4\upstream\bin
*** LLVMROOT directory NOT FOUND: error_llvm_not_found
*** PYTHON NOT FOUND: C:\UEHTML5\UnrealEngine\Engine\Platforms\HTML5\Build\emsdk\emsdk-3.1.4\python\3.9.2_64bit\python.exe
*** EMSCRIPTEN_ROOT directory NOT FOUND: error_emscripten_not_found
*** NODE_JS NOT FOUND: error_nodejs_not_found
*** LLVMROOT directory NOT FOUND: error_llvm_not_found
*** PYTHON NOT FOUND: C:\UEHTML5\UnrealEngine\Engine\Platforms\HTML5\Build\emsdk\emsdk-3.1.4\python\3.9.2_64bit\python.exe
Binding IntelliSense data... 100%
Writing project files... 100%

Currently this plugin is very outdated with internal dev branch, I recommend to use https://github.com/SpeculativeCoder/UnrealEngine-HTML5-ES3


Redirection depend on roles of user

Closes

https://github.com/Real-Dev-Squad/website-my/issues/426

This issue depend on pr:

https://github.com/Real-Dev-Squad/website-my/pull/435

What is the change?

If user choose role developer on new-signup form then user will redirect to www.realdevsquad.com/join
If user choose any of these role i.e. designer, mavens, developers on new-signup then user will redirect to www.realdevsquad.com

After video
https://github.com/Real-Dev-Squad/website-www/assets/107163260/c30864f3-a572-4ab3-899f-ec3dac7add63

use the strict equality comparator wherever you are comparing values
@shubhamsigdar1
I still see == instead of === at 4 places. Please update.

@shubhamsigdar1 can we have the tests for the changed line updated as well. Also 1 of the workflow seems to be failing.

Hi @heyrandhir, website-www testing is not setup and this pr is pending from long. The feature is behind feature flag
Please approve now from next time I will account this thing in my deadline.


Corrects example usages for HDNode.Mnemonic.toSeed method

Hey @christroutner !  The docs shown at https://bchjs.fullstack.cash/#api-HDNode-fromSeed are incorrect for most of the examples using HDNode.Mnemonic.toSeed .  I've fixed it in this PR :)

Thank you, @uncletammy! This is a great PR. Much appriciated.

Thank you, @uncletammy! This is a great PR. Much appriciated.

:tada: This PR is included in version 4.8.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:

:tada: This PR is included in version 4.8.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Project Maintainers, Where Art Thou?

Who are the project maintainers for this project? It seems like the past maintainer(s) aren't interested in maintaining the project. That's fine, however, there are a couple of critical issues with this particular version of gelf-rb that are pretty wide scope and it would be great if we could get some eyes on it or at least the new features and fixes merged?
https://github.com/graylog-labs/gelf-rb/pull/78
https://github.com/graylog-labs/gelf-rb/issues/88

@edmundoa @jalogisch Any input / plans forward for this gem? We may begin using it soon, in which case I'd be interested in helping out. Though I'll only know by the end of April.

I think its time for someone else to maintain this project.

Looks like no one wants to fork it and takeover.

This project using by many companies so the project should updated. If you're okay, I can stay update the project until when you're find a new maintainer.
Also, In my opinion, you can open this project for Hacktoberfest. The Hacktoberfest new rules is here. You may find a new maintainer on this way.

Hi @tessie @joaocv3 @milgner @Stexxen @jsmucr @andreycizov could one of you please respond to this thread or point us in the direction of who could assist? I think its important to the community.

@chriscz Actually I thought this project was maintained by the Graylog devs. My only two cents here were the #70 PR.

My apologies @jsmucr I ran through the last few contributors in the hope that one of them might know more. Thanks for responding!

I have gone ahead and made a post in the community forum: https://community.graylog.org/t/gelf-ruby-library-maintainers-not-responsive/17832

Hi everyone, I've received a response from Aaron Sachs. This gem is considered experimental and the Graylog team believes it's best if the project is forked.

That is... unfortunate.

Even if it has been about two years since the last message in this issue: We created a new project to keep up the development of gelf-rb. It's pretty sad that all maintainers of this gem went silent because I think there are still a lot of people out there using this gem. We mirrored the existing codebase and started from there with some old pull requests that were already open here (and have never been merged) and we added support for logging over http(s) - So feel free to try it out: https://github.com/manet-marketing/gelf_redux


Feat: allow editable comments for model year report - ZEVA 168

Please re-target this pr to release-1.42.0


Flutter uniFFI

This is a PR to allow Flutter and Kotlin/Swift to share the binary with flutter_rust_bridge and uniFFI interfaces

Closed in favor of #510


cowsay: add COWPATH wrapper

Description of changes

Cowsay currently cannot find its pre-installed cowfiles when installed into the user or system profile, failing with:
cowsay: Could not find cowfile for 'default.cow'!

This patch adds a wrapper that explicitly sets the COWPATH environment variable to fix this.
Things done

Built on platform(s)

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

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

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

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[x] Tested basic functionality of all binary files (usually in ./result/bin/)
23.05 Release Notes (or backporting 22.11 Release notes)

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

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 223054 run on x86_64-linux 1

3 packages built:

cowsay
cowsay.man
pokemonsay