Mutect2 error: java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN

Hello,
I'm running into an error with mutect2 (java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN) when using a pair of FASTQ files with yeast sequence reads. Other callers (vardict, freebayes, strelka2) seem to work fine with these files. Haplotypecaller also works fine in germline VC mode.
I have GATK <IP_ADDRESS>. I'm guessing these GATK issues is related: https://github.com/broadinstitute/gatk/issues/5821 and https://github.com/broadinstitute/gatk/issues/5880, but I'm not sure how I can get mutect2 to work with these files. Any idea what could be causing this?
Note: I'm using single-end reads (this came up in a separate issue: https://github.com/broadinstitute/gatk/issues/5553#issuecomment-485581531) and I've set up two batches, one treating a FASTQ file as normal and the other as tumor, and the second one with the samples reversed.
This is the stack trace:
21:53:45.495 INFO  FilterMutectCalls - Done initializing engine
21:53:45.887 INFO  ProgressMeter - Starting traversal
21:53:45.889 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
21:53:45.890 INFO  FilterMutectCalls - Starting pass 0 through the variants
21:53:46.089 INFO  FilterMutectCalls - Finished pass 0 through the variants
21:53:46.169 INFO  FilterMutectCalls - Shutting down engine
[May 20, 2019 9:53:46 PM EEST] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=922484736
java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN
	at org.broadinstitute.hellbender.utils.MathUtils.log10SumLog10(MathUtils.java:1023)
	at org.broadinstitute.hellbender.utils.MathUtils.log10SumLog10(MathUtils.java:995)
	at org.broadinstitute.hellbender.utils.MathUtils.log10SumLog10(MathUtils.java:999)
	at org.broadinstitute.hellbender.utils.MathUtils.normalizeLog10(MathUtils.java:1098)
	at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.clusterProbabilities(SomaticClusteringModel.java:201)
	at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.learnAndClearAccumulatedData(SomaticClusteringModel.java:120)
	at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.learnParameters(Mutect2FilteringEngine.java:152)
	at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.afterNthPass(FilterMutectCalls.java:151)
	at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:35)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:984)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
	at org.broadinstitute.hellbender.Main.main(Main.java:291)
Using GATK jar /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/share/gatk4-<IP_ADDRESS>-0/gatk-package-<IP_ADDRESS>-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms909m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/export/home/ncit/external/a.mizeranschi/yeast/CNV/BRF-BRS-somatic-CNV/work/bcbiotx/tmp50fhhyub -jar /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/share/gatk4-<IP_ADDRESS>-0/gatk-package-<IP_ADDRESS>-local.jar FilterMutectCalls --reference /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/genomes/Scerevisiae/sacCer3_BRF/seq/sacCer3_BRF.fa --variant /export/home/ncit/external/a.mizeranschi/yeast/CNV/BRF-BRS-somatic-CNV/work/bcbiotx/tmp50fhhyub/BRS-vs-BRF-som-NODE_1409_length_236_cov_0.961326_0_236-raw.vcf.gz --output /export/home/ncit/external/a.mizeranschi/yeast/CNV/BRF-BRS-somatic-CNV/work/bcbiotx/tmp50fhhyub/BRS-vs-BRF-som-NODE_1409_length_236_cov_0.961326_0_236-raw-filt.vcf.gz
' returned non-zero exit status 3.

And this is the YAML template that I use:
# Template for whole genome Illumina variant calling with GATK pipeline
---
details:
  - analysis: variant2
    genome_build: sacCer3_BRF
    resources:
      default:
        memory: 3G
        cores: 32
        jvm_opts: ["-Xms1000m", "-Xmx3500m"]
    algorithm:
      aligner: bwa
      effects: false
      mark_duplicates: true
      recalibrate: false
      realign: false
      variantcaller:
        somatic: mutect2
      ensemble:
        numpass: 2
      ploidy: 2
      tools_off: [gemini, contamination, peddy]
      tools_on: svplots
      min_allele_fraction: 1
      svcaller: [cnvkit, seq2c]
      variant_regions: /export/home/ncit/external/a.mizeranschi/yeast/GTF/variant_regions_BRF.bed
      sv_regions: /export/home/ncit/external/a.mizeranschi/yeast/GTF/sv_regions_genes_contigs_BRF.bed

Hello!
Sorry, maybe a little on the off-topic side, however, I'm curious:

Why are you using somatic calling on yeast? Isn't HC enough?
Is it diploid or haploid strain?
What is the estimate of the polymorphism level in the yeast population?

Sergey

Hi Sergey,
I'm not sure about the polymorphism level in the yeast population. The strain we're using is diploid and we found evidence for high allelism in the two samples that we're trying to analyze. I already ran HC on them and, in addition, I wanted to try out Mutect2 to see if there are any low-frequency variants present in one sample and not the other.
Alex

Hi Alex!
Thanks for reporting the issue and expanding the usage of bcbio into yeast genomics!
Unfortunately, it is not easy to debug such a unique case: single end reads on a custom yeast reference coupled with somatic(cancer) variant calling with mutect2. (Wow!)
The best advices I have are:

to use ensemble variant calling 1 of 3 or even 1 of 7 tools,
if you want to achieve really high sensitivity without opening the can of worms of somatic calling (use multiple callers: gatk, samtools, freebayes, up to 7 and set up the threshold to call a variant to 1).

Also, you may try to call variants in many samples together as a 'family'. There improved coverage and occurrence of variants in 2 samples may increase their chance to be picked up.

The third option is to consider relaxed filters in your vcf (expand your analysis beyond only PASS variants). The filters were tunned for human genome for the best sensitivity/specificity balance, and might not reflect the reality of variant calling it Yeast.

However, I hope you remember that gain in sensitivity does not come without loss in specificity (i.e. you will be getting more false positive trash calls).
Buy the way, have you done any measurements of variant calling precision and sensitivity in yeast with bcbio? (See the examples here, https://github.com/bcbio/bcbio_validations).
If you have done it, we might publish the results among the other validations, underlining this unique use case of bcbio.
Sergey

Thanks much for this report and apologies about the issue. This looks related to #2832 and we were able to reproduce when the MuTect2 associated .stats file has 0 callable reads. The latest development has a workaround which avoid this by flooring this stat at 1. It also leaves the intermediate files in the work directory (instead of transactional directory) to make it easier to debug if it still fails. If you still have issues after updating please share the input *.vcf.gz and *.vcf.gz.stats files to FilterMutectCalls and we can investigate more. Thanks again and hope this gets your analysis done.

Thanks a lot for the update. The MuTect2 issue went away after upgrading to the latest development version.

Hi Brad. I updated to the latest version of bcbio and am still getting this error. I am doing tumor only calling using mutect2. Version of bcbio is 1.1.6a and version of GATK is v<IP_ADDRESS> Here's the variants from the problematic vcf -
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  TUMOR_SAMPLE
13      19020627        .       A       G       .       .       DP=5;ECNT=1;FS=0.000;MBQ=0,31;MFRL=0,135;MMQ=60,58;MPOS=16;MQ=62.35;MQ0=0;POPAF=7.30;TLOD=14.62 GT:AD:AF:DP:F1R2:F2R1:SB        0/1:0,5:0.857:5:0,3:0,2:0,0,3,2
13      19020776        .       T       G       .       .       DP=3;ECNT=3;FS=0.000;MBQ=0,31;MFRL=0,230;MMQ=60,58;MPOS=8;MQ=58.56;MQ0=0;POPAF=7.30;TLOD=10.03  GT:AD:AF:DP:F1R2:F2R1:SB        0/1:0,3:0.800:3:0,1:0,2:0,0,2,1
13      19020857        .       G       A       .       .       ClippingRankSum=-0.431;DP=4;ECNT=3;FS=0.000;MBQ=31,30;MFRL=192,284;MMQ=58,64;MPOS=21;MQ=61.62;MQ0=0;MQRankSum=0.431;POPAF=7.30;ReadPosRankSum=-0.674;TLOD=5.48  GT:AD:AF:DP:F1R2:F2R1:SB
0/1:2,2:0.500:4:0,1:2,1:1,1,1,1
13      19020890        .       G       A       .       .       DP=1;ECNT=3;FS=0.000;MBQ=0,30;MFRL=0,154;MMQ=60,45;MPOS=15;MQ=45.00;MQ0=0;POPAF=7.30;TLOD=3.18  GT:AD:AF:DP:F1R2:F2R1:SB        0/1:0,1:0.667:1:0,0:0,1:0,0,0,1
13      19021019        .       AG      CA      .       .       DP=1;ECNT=1;FS=0.000;MBQ=0,31;MFRL=0,284;MMQ=60,70;MPOS=48;MQ=70.00;MQ0=0;POPAF=7.30;TLOD=4.20  GT:AD:AF:DP:F1R2:F2R1:SB        0/1:0,1:0.667:1:0,0:0,1:0,0,0,1
13      19021223        .       T       C       .       .       DP=1;ECNT=1;FS=0.000;MBQ=0,31;MFRL=0,171;MMQ=60,70;MPOS=32;MQ=70.00;MQ0=0;POPAF=7.30;TLOD=3.28  GT:AD:AF:DP:F1R2:F2R1:SB        0/1:0,1:0.667:1:0,1:0,0:0,0,1,0
13      19021651        .       A       G       .       .       DP=1;ECNT=1;FS=0.000;MBQ=0,31;MFRL=0,208;MMQ=60,59;MPOS=14;MQ=59.00;MQ0=0;POPAF=7.30;TLOD=3.28  GT:AD:AF:DP:F1R2:F2R1:SB        0/1:0,1:0.667:1:0,0:0,1:0,0,0,1
13      19022290        .       C       G       .       .       DP=5;ECNT=1;FS=0.000;MBQ=0,30;MFRL=0,152;MMQ=60,70;MPOS=21;MQ=66.93;MQ0=0;POPAF=7.30;TLOD=16.29 GT:AD:AF:DP:F1R2:F2R1:SB        0/1:0,5:0.857:5:0,3:0,2:0,0,5,0
Here's the output from the stats file for the same -
statistic       value
callable        1.0
Let me know if you need any further information to help debug this.
Thanks,
Moiz

Hi Moiz,
Could you post up the command that is failing along with the broken VCF file so we can have a mini test set while we try to fix this?

Hi Rory,
Here's the command that I see in the bcbio logs -
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm -jar bcbio_1.1.5/anaconda/share/gatk4-<IP_ADDRESS>-1/gatk-package-<IP_ADDRESS>-local.jar FilterMutectCalls --reference bcbio_1.1.5/genomes/Hsapiens/hs37d5/seq/hs37d5.fa --variant Tumor-raw.vcf.gz --output Tumor-raw-filt.vcf.gz
Let me know if you need anything else.
Thanks,
Moiz

Thanks, could you post up the VCF file that you sampled from above, but attach the actual gzipped file? That way we can use that to test against.

Hi Rory,
That's all the variants in the vcf. I can attach the actual vcf if you need it.

Yup! The actual VCF would be helpful, just so we'll have the header and it wil be formatted right and all of that.

Hi Rory,
I have attached the bgzipped vcf file. Let me know if you need anything else.
Thanks,
Moiz
Tumor-raw.vcf.gz.gz

Sorry, could you post the error that you are seeing as well? The bcbio-nextgen-debug.log file would be helpful to look at.

Hi Rory,
The sample identifiers in the debug log file have PHI in them that I cannot share. It'll take me a lot of time to de-identify and validate it. I am attaching the stack trace from where the error occurred. Let me know if this is enough.
Traceback (most recent call last):
File "bcbio_nextgen/1.1.5/bin/bcbio_nextgen.py", line 238, in
main(**kwargs)
File "bcbio_nextgen/1.1.5/bin/bcbio_nextgen.py", line 46, in main
run_main(**kwargs)
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 53, in run_main
fc_dir, run_info_yaml)
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 89, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 152, in variant2pipeline
samples = genotype.parallel_variantcall_region(samples, run_parallel)
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 208, in parallel_variantcall_region
"vrn_file", ["region", "sam_ref", "config"]))
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/distributed/split.py", line 35, in grouped_parallel_split_combine
final_output = parallel_fn(parallel_name, split_args)
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/distributed/ipython.py", line 137, in run
for data in view.map_sync(fn, items, track=False):
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/view.py", line 344, in map_sync
return self.map(f,*sequences,**kwargs)
File "<bcbio_1.1.5/anaconda/lib/python3.6/site-packages/decorator.py:decorator-gen-140>", line 2, in map
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/view.py", line 52, in sync_results
ret = f(self, *args, **kwargs)
File "<bcbio_1.1.5/anaconda/lib/python3.6/site-packages/decorator.py:decorator-gen-139>", line 2, in map
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/view.py", line 37, in save_ids
ret = f(self, *args, **kwargs)
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/view.py", line 1114, in map
return pf.map(*sequences)
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/remotefunction.py", line 299, in map
return self(*sequences, __ipp_mapping=True)
File "<bcbio_1.1.5/anaconda/lib/python3.6/site-packages/decorator.py:decorator-gen-122>", line 2, in call
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/remotefunction.py", line 80, in sync_view_results
return f(self, *args, **kwargs)
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/remotefunction.py", line 285, in call
return r.get()
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/asyncresult.py", line 169, in get
raise self.exception()
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/asyncresult.py", line 228, in _resolve_result
results = error.collect_exceptions(results, self._fname)
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/error.py", line 233, in collect_exceptions
raise e
File "bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/error.py", line 231, in collect_exceptions
raise CompositeError(msg, elist)
ipyparallel.error.CompositeError: one or more exceptions from call to method: variantcall_sample
[20:apply]: CalledProcessError: Command 'set -o pipefail; unset JAVA_HOME && export PATH=bcbio_1.1.5/anaconda/bin:"$PATH" && gatk --java-options '-Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm' Mutect2 --annotation ClippingRankSumTest --annotation DepthPerSampleHC --reference bcbio_1.1.5/genomes/Hsapiens/hs37d5/seq/hs37d5.fa --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation FisherStrand --annotation MappingQuality --annotation DepthPerAlleleBySample --annotation Coverage --read-validation-stringency LENIENT -I bcbio_20180410/work_novoalign/align/Tumor_Sample/Tumor-sort.bam --tumor-sample TUMOR_SAMPLE -L bcbio_20180410/work_novoalign/mutect2/13/Tumor-regions.bed --interval-set-rule INTERSECTION -O bcbio_20180410/work_novoalign/mutect2/13/Tumor-raw.vcf.gz && sed -i 's/callable\t0.0/callable\t1.0/' bcbio_20180410/work_novoalign/mutect2/13/Tumor-raw.vcf.gz.
stats && unset JAVA_HOME && export PATH=bcbio_1.1.5/anaconda/bin:"$PATH" && gatk --java-options '-Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm' FilterMutectCalls --reference bcbio_1.1.5/genomes/Hsapiens/hs37d5/seq/hs37d5.fa --variant bcbio_20180410/work_novoalign/mutect2/13/Tumor-raw.vcf.gz --output bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm/Tumor-raw-filt.vcf.gz

Thanks, are there errors further up in the debug log? This is the generic
“this command failed” error, the root cause should be further up.
On Tue, Jun 11, 2019 at 5:15 PM Moiz Bootwalla<EMAIL_ADDRESS>wrote:

Hi Rory,
The sample identifiers in the debug log file have PHI in them that I
cannot share. It'll take me a lot of time to de-identify and validate it. I
am attaching the stack trace from where the error occurred. Let me know if
this is enough.
Traceback (most recent call last):
File "bcbio_nextgen/1.1.5/bin/bcbio_nextgen.py", line 238, in
main(**kwargs)
File "bcbio_nextgen/1.1.5/bin/bcbio_nextgen.py", line 46, in main
run_main(**kwargs)
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py",
line 53, in run_main
fc_dir, run_info_yaml)
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py",
line 89, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py",
line 152, in variant2pipeline
samples = genotype.parallel_variantcall_region(samples, run_parallel)
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py",
line 208, in parallel_variantcall_region
"vrn_file", ["region", "sam_ref", "config"]))
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/distributed/split.py",
line 35, in grouped_parallel_split_combine
final_output = parallel_fn(parallel_name, split_args)
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/bcbio/distributed/ipython.py",
line 137, in run
for data in view.map_sync(fn, items, track=False):
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/view.py",
line 344, in map_sync
return self.map(f,*sequences,**kwargs)
File
"<bcbio_1.1.5/anaconda/lib/python3.6/site-packages/decorator.py:decorator-gen-140>",
line 2, in map
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/view.py",
line 52, in sync_results
ret = f(self, *args, **kwargs)
File
"<bcbio_1.1.5/anaconda/lib/python3.6/site-packages/decorator.py:decorator-gen-139>",
line 2, in map
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/view.py",
line 37, in save_ids
ret = f(self, *args, **kwargs)
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/view.py",
line 1114, in map
return pf.map(*sequences)
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/remotefunction.py",
line 299, in map
return self(*sequences, __ipp_mapping=True)
File
"<bcbio_1.1.5/anaconda/lib/python3.6/site-packages/decorator.py:decorator-gen-122>",
line 2, in call
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/remotefunction.py",
line 80, in sync_view_results
return f(self, *args, **kwargs)
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/remotefunction.py",
line 285, in call
return r.get()
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/asyncresult.py",
line 169, in get
raise self.exception()
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/client/asyncresult.py",
line 228, in _resolve_result
results = error.collect_exceptions(results, self._fname)
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/error.py",
line 233, in collect_exceptions
raise e
File
"bcbio_1.1.5/anaconda/lib/python3.6/site-packages/ipyparallel/error.py",
line 231, in collect_exceptions
raise CompositeError(msg, elist)
ipyparallel.error.CompositeError: one or more exceptions from call to
method: variantcall_sample
[20:apply]: CalledProcessError: Command 'set -o pipefail; unset JAVA_HOME
&& export PATH=bcbio_1.1.5/anaconda/bin:"$PATH" && gatk --java-options
'-Xms681m -Xmx3181m -XX:+UseSerialGC
-Djava.io.tmpdir=bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm' Mutect2
--annotation ClippingRankSumTest --annotation DepthPerSampleHC --reference
bcbio_1.1.5/genomes/Hsapiens/hs37d5/seq/hs37d5.fa --annotation
MappingQualityRankSumTest --annotation MappingQualityZero --annotation
QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality
--annotation FisherStrand --annotation MappingQuality --annotation
DepthPerAlleleBySample --annotation Coverage --read-validation-stringency
LENIENT -I bcbio_20180410/work_novoalign/align/Tumor_Sample/Tumor-sort.bam
--tumor-sample TUMOR_SAMPLE -L
bcbio_20180410/work_novoalign/mutect2/13/Tumor-regions.bed
--interval-set-rule INTERSECTION -O
bcbio_20180410/work_novoalign/mutect2/13/Tumor-raw.vcf.gz && sed -i
's/callable\t0.0/callable\t1.0/'
bcbio_20180410/work_novoalign/mutect2/13/Tumor-raw.vcf.gz.
stats && unset JAVA_HOME && export PATH=bcbio_1.1.5/anaconda/bin:"$PATH"
&& gatk --java-options '-Xms681m -Xmx3181m -XX:+UseSerialGC
-Djava.io.tmpdir=bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm'
FilterMutectCalls --reference
bcbio_1.1.5/genomes/Hsapiens/hs37d5/seq/hs37d5.fa --variant
bcbio_20180410/work_novoalign/mutect2/13/Tumor-raw.vcf.gz --output
bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm/Tumor-raw-filt.vcf.gz
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub
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.

Hi Rory,
Is this what you were looking for -
[June 5, 2019 2:50:08 PM PDT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=691404800
java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN
at org.broadinstitute.hellbender.utils.NaturalLogUtils.logSumExp(NaturalLogUtils.java:84)
at org.broadinstitute.hellbender.utils.NaturalLogUtils.normalizeLog(NaturalLogUtils.java:51)
at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.clusterProbabilities(SomaticClusteringModel.java:203)
at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.learnAndClearAccumulatedData(SomaticClusteringModel.java:122)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.learnParameters(Mutect2FilteringEngine.java:156)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.afterNthPass(FilterMutectCalls.java:151)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Using GATK jar bcbio_1.1.5/anaconda/share/gatk4-<IP_ADDRESS>-1/gatk-package-<IP_ADDRESS>-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm -jar bcbio_1.1.5/anaconda/share/gatk4-<IP_ADDRESS>-1/gatk-package-<IP_ADDRESS>-local.jar FilterMutectCalls --reference bcbio_1.1.5/genomes/Hsapiens/hs37d5/seq/hs37d5.fa --variant bcbio_20180410/work_novoalign/mutect2/13/Tumor-raw.vcf.gz --output bcbio_20180410/work_novoalign/bcbiotx/tmp3gkzrbvm/Tumor-raw-filt.vcf.gz
' returned non-zero exit status 3.

@roryk any updates on this issue? Kindly let me know if you need any more details.

Moiz;
Thanks for following up on this. I was able to reproduce and it looks like the same error can happen in some cases with the callable reads in the stats file set at 1 (which was our workaround for 0 reads). Increasing to a bigger number seems to avoid it and the latest development now does this to try and work around the issue more generally. If you update to the latest development version of bcbio, remove the problematic Tumor-raw.vcf.gz (and .stats) files and re-run it should hopefully work cleanly now. Please let us know if you are still stuck. Thanks again for the help debugging.

Hi Brad,
I tested this and confirm that it works fine now. I will let you know if this issue crops up again.
Thank you so much for fixing this!

Thank you for following up Moiz!

Hello @chapmanb and @roryk . I have run into this issue again. I looked at the stats file for the variants where this is happening and the callable value is 4.0 which is what you had set it to in the previous fix for this problem. I don't know if continuing to set a higher value to avoid this error is the right approach to fixing this issue. There must be another approach to having a more permanent fix to this issue. Kindly let me know if you guys have any ideas or if you need files to test this out.
Thanks,
Moiz

Moiz;
Thanks for the report and apologies about the continued problems. I still have no clue about what causes the underlying issue and allows MuTect2 to make calls but report zero callable reads, but tried to keep going with the less than perfect solution we've been using and set it to a higher number. Hope this gets it working now and avoids the problem. Thanks again for your patience with this.


Show the last-updated time in the generated gh-pages docs?

I know we have the version history, but it'd be really cool if we could see the date that the docs were last updated. Any chance we can put that into the travis deployment build?

The site displays docs for the latest tagged version by default, so the last built date will always be the date of the latest version's release. We could use the GitHub api to get information that should work. For example, we can filter through https://api.github.com/repos/googlecloudplatform/gcloud-node/releases for the matching version and get the date.

Yeah GitHub API should work. Last update would not necessarily be the last release though, so we are better off using something like https://api.github.com/repos/GoogleCloudPlatform/gcloud-node/commits?sha=gh-pages&per_page=1

I think the most useful date to show on our docs is the one that matches when the version was released. Unless you meant we can fish through the commits to gh-pages to find some kind of indicator of a release's build?

Nope I meant the latest commit as per @jgeewax request for "date that the docs were last updated" which would coincide with the last push, regardless of release. If this is not what @jgeewax meant, then release date works for me.

OK so -- two scenarios I see:

I'm using version x.y -- I want to see the docs for x.y (and honestly, the date doesn't really matter... the version is the important piece).

I'm using master -- I want to see the docs for master (at which point, the date and/or last commit ID matter a bunch, the version not so much...)

For the first case, I think we're covered. This issue is to cover the second case. Can we make "master" also include a commit ID and date of the commit?

PR sent: #394


Do not ignore type parameters of receiver in method calls

For now I am special casing the treatment of method calls to fix #373. What I do not like about this solution:

previously there was no freshTypeVar in Typer--it all was encapsulated behind instantiate.
now the treatment of method and function calls is not entirely uniform and slightly differs.

To test this fix I added a few variations of #373. @dvdvgt could you double-check that this fix is working?

Looks good to me and also seems to reject the "crazy" examples. One note, though, you only tested this using handlers, however I think it would be more robust if we had at least one negative test for objects as well. While they should do the same, the implementation is different and we should also for this issue there. Besides, adding the more elaborate examples as negatives test too shouldn't hurt, right?

Yeah I thought about adding them as well, but then they are really only instances of the tests already there. Each test, at least, adds time to CI :) (which is an excuse for me not to add it)


Editor piece tree chunk management

I am playing around with reading and writing very large files (27 MB) when sandbox is enabled where the file service is implemented via remote IPC (same as when you are connected to a remote such as SSH).
For some unrelated reason, our call into IFileService.readFileStream ends up with a small chunk of 256kb and a large chunk of the rest instead of N chunks of 256kb each (which is what we end up getting when sandbox is not enabled). We end up passing this into the PieceTreeTextBufferBuilder#acceptChunk method.
Later, when I trigger save, we use the snapshot method to have a Readable we can iterate over to write to disk. I end up with the exact 2 chunks as before. So we end up with a small write and a very large write instead of smaller chunks.
Is this the intended behaviour or does the piece tree have some own logic for managing chunks?
Steps to reproduce:

produce a large text file with 1m lines
run with scripts/code.sh --__sandbox
open the file and have a breakpoint where we create the piece tree

Here is the file that I have used for reproduction:
Features.txt.zip


Fix for ts errors and other improves

This PR solve issues #13 #14

i think that this can be merged, if there are other issues i will fix them in a separate PR. Anyway i can not reproduce those errors again... i will make a last test to see if i can find any issue with this PR.


Option to lock aspect ratio of window to screen

Is your feature request related to a problem? Please describe.
I dont like it when there are extra black borders around the screen area and I think it would be nice to have a mode in which you can lock the aspect ratio of the screen to the phone screen being displayed.

I tried to force the other dimension on resize with SDL, but it didn't work as expected.
Note that you can remove the black bars afterwards either with Alt+w or by double-clicking inside the bars.
In theory, keeping the aspect ratio while resizing is possible (mpv supports it), but not via SDL.

@rp1231 https://github.com/Genymobile/scrcpy/issues/2317#issuecomment-841692150


Bugfix: Wrong ArtemisWebView height when the connection speed is slow

I've noticed that the webview can't set it's height property correctly when the loading takes too long (more than 2 seconds). This affects users having slow connection speeds.
What I did:

Added a timer that does the following:

Starts firing after the webView(..didFinish navigation: ) is called
Checks every 0.5 seconds for document.readyState to be set
If set, it starts sampling the document.body.scrollHeight value. The sampling occurs 5 times with an interval of 1 seconds.

This makes the webview start displaying content as it arrives, expanding its height

@sven0311  I noticed your latest commit also addresses this issue with clicks and preserved your implementation as well. With this PR both timer-based and click-based height adjustments should work fine. 🙂

I also found a retain cycle that prevented the Coordinator from being deallocated. 2c2dbe4 fixes that


feat: add react-dva-ts template

too many any and ts-nocheck🤔

Thanks for reminding, I am ready to resubmit


Can not swith to another app if the target app is not in the same window(MacBookAir M3 chip)

just as the title

needs to type the shortcut twice

I tested the latest beta version (15.0 Beta version (24A5327a)) and did not encounter the issue you mentioned. Could you please provide the version number of your macOS?


Trust: Missing settings link

Testing #122209
Follow the same steps as https://github.com/microsoft/vscode/issues/122541
🐛 There's no link to see which settings are affected by trust.

The link comes up if I untrust the workspace. 😕

duplicate https://github.com/microsoft/vscode/issues/122477


Auto complete custom element tags in TSX not working with hyphen in name

When using tsx to develop components for custom elements (web components), auto complete does not show element names that have a - in it's name.
I'm using https://stenciljs.com/ to create these components, and custom element names are added to an extended InstrinsicElements interface. Which looks like this:
interface StencilIntrinsicElements {
    'app-home': Components.AppHomeAttributes;
    'app-profile': Components.AppProfileAttributes;
    'app-root': Components.AppRootAttributes;
    'app-tester': Components.AppTesterAttributes;
    'tester2': Components.Tester2Attributes;
  }

VSCode Version:
Version: 1.29.1 (system setup)
Commit: bc24f98b5f70467bc689abf41cc5550ca637088e
Date: 2018-11-15T19:13:36.375Z
Electron: 2.0.12
Chrome: 61.0.3163.100
Node.js: 8.9.3
V8: 6.1.534.41
Architecture: x64

OS: Windows 10

Steps to Reproduce:
Repo here - https://github.com/Cammisuli/tsx-completion-bug
Preview of issue discussed:

Not working

Working

After either element is added, hovering over it shows the proper type of the element.

Does this issue occur when all extensions are disabled?: Yes

This is actually something I would like to see fix. If help is needed to get this going, I'm more than willing to try to create a PR; I would just need to get some direction on where to look/debug.
Thanks!

The Software Engineering Code of Ethics and Professional Practice

1.07. Consider issues of physical disabilities, allocation of resources, economic disadvantage and other factors that can diminish access to the benefits of software.

All React's Aria tags use hyphens. When people start typing aria for an attribute, they cannot discover it in VSCode because of this BUG! People are less likely to discover and pay attention to accessibility because of that.
STOP BREAKING SOFTWARE ENGINEERING CODE AND IMPLEMENT ESSENTIAL FUNCTIONALITY!!!

I think I can fix it. Let me have a try...
The reason of this bug is https://github.com/microsoft/TypeScript/blob/f9945f5acfe24664c446e990eeecc7c00f700c99/src/services/completions.ts#L2415 here filter out the hyphened name because TypeScript thinks it isn't a valid identifier name.

OK I get it

Another screenshot

This would be very helpful to fix, Jack-works!  Many thanks for your efforts.


[Login] Validation message is not consistant to required, when entering incorrect email address

Date Time
06-15-2021 10:35
Priority
Medium
Environment:
OS: Windows 10 x64 bit
Browser Chrome Version 91.0.4472.77
Reproducible always
Build found 20210614.3
Steps to Reproduce

Go to https://eventsexpress-test.azurewebsites.net/home/events
Click on 'Sign in/up' button in the left corner
Enter invalid email address into the 'Email Address' field
Enter password into the 'Password' field
Click on 'Sign in' button
Pay attention on the validation messages

Actual result
Validation message 'Incorrect email address' in red color appears under the 'Log in with facebook' and 'log in with google' buttons
Expected result
Validation message 'Incorrect login or password' in red color appears under the 'Log in with facebook' and 'log in with google' buttons
Screenshots
Actual result

Expected result

User story and test case links E.g.: "User story #181  Test case #662 "
Labels to be added "Bug", Priority Medium, Severity Minor, Type UI

Email validation is used for checking if email format is correct, therefore it cannot be used for whole login form


server/sandbox: fix add/release pod/ctr ids and names

Fix #127
@mrunalp @mikebrow PTAL
Signed-off-by: Antonio Murdaca<EMAIL_ADDRESS>

can't sign the CLA right now since I made the request with an old, wrong email address, I contacted the linux foundation, still waiting..

alright, fixed

alright, fixed

Looks good. I will test out locally and merge.

Looks better but after sudo ocic pod remove does not delete both containers from the /var/lib/ocid/containers directory. Thus trying to run my manual test twice results in a failure the second time around.

sudo ocic ctr list
ID: 6a487097ff18d03ac02e55d6ee73363288e1c92011ed02668fd93426dcf44165
Pod: 1035d00d5a2e8f2c37307eed1c493773f3704c1e40a3857d7e90d6a5c73edf67
Status: RUNNING
Created: 2016-10-13 11:28:36 -0500 CDT
ID: 617f2c3dd898356db711b980bf85567a9b718cb3378ab72eb64c8352c3dd5647
Pod: 1035d00d5a2e8f2c37307eed1c493773f3704c1e40a3857d7e90d6a5c73edf67
Status: RUNNING
Created: 2016-10-13 11:28:00 -0500 CDT
mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo ocic ctr status --id 6a487097ff18d03ac02e55d6ee73363288e1c92011ed02668fd93426dcf44165
ID: 6a487097ff18d03ac02e55d6ee73363288e1c92011ed02668fd93426dcf44165
Status: RUNNING
Created: 2016-10-13 11:28:36 -0500 CDT
Started: 2016-10-13 11:29:19 -0500 CDT
mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo ocic ctr status --id 617f2c3dd898356db711b980bf85567a9b718cb3378ab72eb64c8352c3dd5647
ID: 617f2c3dd898356db711b980bf85567a9b718cb3378ab72eb64c8352c3dd5647
Status: RUNNING
Created: 2016-10-13 11:28:00 -0500 CDT
Started: 2016-10-13 11:28:00 -0500 CDT
mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo ocic pod list
ID: 1035d00d5a2e8f2c37307eed1c493773f3704c1e40a3857d7e90d6a5c73edf67
Name: podsandbox1
Status: READY
Created: 2016-10-13 11:28:00 -0500 CDT
Labels:
	group -> test
Annotations:
	owner -> hmeng
mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo ocic pod remove --id 1035d00d5a2e8f2c37307eed1c493773f3704c1e40a3857d7e90d6a5c73edf67
1035d00d5a2e8f2c37307eed1c493773f3704c1e40a3857d7e90d6a5c73edf67
mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo runc list
ID          PID         STATUS      BUNDLE      CREATED

mike@mike-VirtualBox:/var/lib/ocid$ ls containers
6a487097ff18d03ac02e55d6ee73363288e1c92011ed02668fd93426dcf44165

Looks better but after sudo ocic pod remove does not delete both containers from the /var/lib/ocid/containers directory. Thus trying to run my manual test twice results in a failure the second time around.

I'll look into this as well...

seems that issue is wanted https://github.com/kubernetes-incubator/cri-o/blob/master/server/sandbox.go#L348 @mrunalp?

@runcom The pod infra container directory is removed after all the other containers in the pod have been removed. https://github.com/kubernetes-incubator/cri-o/blob/master/server/sandbox.go#L365. We can open and fix the issue @mikebrow reported separately.

Trying to keep the pause container alive?

@runcom The pod infra container directory is removed after all the other containers in the pod have been removed. https://github.com/kubernetes-incubator/cri-o/blob/master/server/sandbox.go#L365. We can open and fix the issue @mikebrow reported separately.

I have fixed it here, it was just Name vs ID, PTAL

@mikebrow please re-test

@runcom Nice! :)

mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo ocic pod create --config test/testdata/sandbox_config.jsonabadb43d94f84e389406ab50310b6053062976e61980566bc75301d2857da71e
mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo ocic ctr create --pod abadb43d94f84e389406ab50310b6053062976e61980566bc75301d2857da71e --config test/testdata/container_redis.json
FATA[0001] Creating container failed: rpc error: code = 2 desc = error getting container state for default-podsandbox1-0-podsandbox1-redis-0: wait: no child processes: [123 10 32 32 34 111 99 105 86 101 114 115 105 111 110 34 58 32 34 49 46 48 46 48 45 114 99 49 45 100 101 118 34 44 10 32 32 34 105 100 34 58 32 34 100 101 102 97 117 108 116 45 112 111 100 115 97 110 100 98 111 120 49 45 48 45 112 111 100 115 97 110 100 98 111 120 49 45 114 101 100 105 115 45 48 34 44 10 32 32 34 112 105 100 34 58 32 49 54 49 52 53 44 10 32 32 34 98 117 110 100 108 101 80 97 116 104 34 58 32 34 47 118 97 114 47 108 105 98 47 111 99 105 100 47 99 111 110 116 97 105 110 101 114 115 47 49 100 54 101 49 53 52 50 54 101 51 54 102 99 55 57 55 102 99 50 100 50 52 52 57 55 55 57 56 53 50 98 52 57 99 50 57 55 49 100 101 51 99 53 101 50 49 54 56 53 48 52 99 52 97 57 98 57 97 51 56 57 55 49 34 44 10 32 32 34 114 111 111 116 102 115 80 97 116 104 34 58 32 34 47 118 97 114 47 108 105 98 47 111 99 105 100 47 99 111 110 116 97 105 110 101 114 115 47 49 100 54 101 49 53 52 50 54 101 51 54 102 99 55 57 55 102 99 50 100 50 52 52 57 55 55 57 56 53 50 98 52 57 99 50 57 55 49 100 101 51 99 53 101 50 49 54 56 53 48 52 99 52 97 57 98 57 97 51 56 57 55 49 47 114 111 111 116 102 115 34 44 10 32 32 34 115 116 97 116 117 115 34 58 32 34 99 114 101 97 116 101 100 34 44 10 32 32 34 99 114 101 97 116 101 100 34 58 32 34 50 48 49 54 45 49 48 45 49 51 84 49 54 58 53 50 58 49 57 46 56 57 48 49 54 54 51 54 55 90 34 44 10 32 32 34 97 110 110 111 116 97 116 105 111 110 115 34 58 32 123 10 32 32 32 32 34 111 99 105 100 47 108 97 98 101 108 115 34 58 32 34 123 92 34 116 105 101 114 92 34 58 92 34 98 97 99 107 101 110 100 92 34 125 34 44 10 32 32 32 32 34 111 99 105 100 47 108 111 103 95 112 97 116 104 34 58 32 34 99 111 110 116 97 105 110 101 114 46 108 111 103 34 44 10 32 32 32 32 34 111 99 105 100 47 110 97 109 101 34 58 32 34 100 101 102 97 117 108 116 45 112 111 100 115 97 110 100 98 111 120 49 45 48 45 112 111 100 115 97 110 100 98 111 120 49 45 114 101 100 105 115 45 48 34 44 10 32 32 32 32 34 111 99 105 100 47 115 97 110 100 98 111 120 95 105 100 34 58 32 34 97 98 97 100 98 52 51 100 57 52 102 56 52 101 51 56 57 52 48 54 97 98 53 48 51 49 48 98 54 48 53 51 48 54 50 57 55 54 101 54 49 57 56 48 53 54 54 98 99 55 53 51 48 49 100 50 56 53 55 100 97 55 49 101 34 44 10 32 32 32 32 34 111 99 105 100 47 116 116 121 34 58 32 34 102 97 108 115 101 34 44 10 32 32 32 32 34 112 111 100 34 58 32 34 112 111 100 115 97 110 100 98 111 120 49 34 10 32 32 125 10 125]

not sure what's up rebooting..

@mikebrow Looks like another issue. Could you open one for it? (Thanks for testing and finding issues btw :) )

definitely not related? bad state of /var/lib/ocid/* or runc

LGTM

Not sure what's up but now I can't create a container.
mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo ocic pod create --config test/testdata/sandbox_config.json
[sudo] password for mike:
99fec541a30f381f55c51c8cf4a384294153321f808b8e1c61f1b4efe93f1916
mike@mike-VirtualBox:~/go/src/github.com/kubernetes-incubator/cri-o$ sudo ocic ctr create --pod 99fec541a30f381f55c51c8cf4a384294153321f808b8e1c61f1b4efe93f1916 --config test/testdata/container_redis.json
FATA[0008] Creating container failed: rpc error: code = 2 desc = `docker rm 080880564dae577b4518de756aa82742c59f7705032c186428b7fa692412180e` failed:  (wait: no child processes)

@mikebrow seems like you have a bad state between docker/runc/ocid. Can you purge everything and retry from scratch? (open an issue also)

@mrunalp would you merge this? :angel:

Sure what do I need to completely purge.. i deleted the stuff under /var/lib/ocid/containers/* and sandboxes/* and checked to make sure nothing was running via docker ps and runc...

Sure what do I need to completely purge.. i deleted the stuff under /var/lib/ocid/containers/* and sandboxes/* and checked to make sure nothing was running via docker ps and runc...

the failure you had seems related to docker itself, docker rm is failing I don't know why.. we hopefully get rid of docker soon also

Ok .. now it's working. So some sort of intermittent problems. The first one looked like processes were leaking so I ran out of pids.. The second one looks like some odd timing bug.
So for this one LGTM :-)


AsyncIterator API for Result consumption

The current driver implementation has only two options for record consumption, the default async/promise api and the reactive api.
In the async side, there is no simple way to interact over the results before consuming all the data stream and back-pressure the consumption. Meanwhile in the reactive, the back-pressure is implemented  but this api usage depends on the knowledge of reactive programming and RxJS.  Another issue with our current reactive implementation is not having the way to configure the back-pressure or pause the stream consumption.
The introduction of the Async Iterator is part of a group of improvements to make the driver more idiomatic and memory efficient.

Replace by https://github.com/neo4j/neo4j-javascript-driver/pull/831


Item editor - Attribute values do not support inf

use "1.79769313486232E+308d" in NBT Editor and it will become "Infinity"

I also just found out you can directly type "Infinity"


Kill Element.normal_name variable

See original issue on GitLab
In GitLab by [Gitlab user @tristanvb] on Mar 8, 2018, 11:33
This has been a constant source of confusion, even to me.

For BuildStream developers, it is needlessly confusing that there are effectively 2 names of an element
For users, there is no reason to give them inconsistent naming, just always give them the same name

The normal_name is currently used to construct artifact keys, and to create build directories.
It is also used to create log file names, these are also better off without the normal_name substitutions.
For this, it would be nice to replace the .bst with the .log extension here.

In GitLab by [Gitlab user @milloni] on Apr 1, 2018, 15:34
assigned to [Gitlab user @milloni]

In GitLab by [Gitlab user @milloni] on Apr 1, 2018, 15:34
unassigned [Gitlab user @milloni]

In GitLab by [Gitlab user @milloni] on Apr 1, 2018, 16:12
assigned to [Gitlab user @milloni]

In GitLab by [Gitlab user @milloni] on Apr 22, 2018, 20:10
unassigned [Gitlab user @milloni]

In GitLab by [Gitlab user @finnball] on May 11, 2018, 13:55
assigned to [Gitlab user @finnball]

In GitLab by [Gitlab user @finnball] on May 14, 2018, 14:12
mentioned in commit aa0964bc061388b6404bab40d1fbc84de5b010ec

In GitLab by [Gitlab user @finnball] on May 14, 2018, 14:19
mentioned in merge request !465

In GitLab by [Gitlab user @finnball] on May 14, 2018, 15:05
closed


Missing version.rc file for pyinstaller when using pyinstaller-versionfile

Hi
I'm using pyinstaller-versionfile in a prior to pyinstaller to generate the version.rc file. When the github action runs, the version.rc file is not present for pyinstaller.
What am I doing wrong?
Here is an example of my actions.yml file
name: CI

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

jobs:
  pyinstaller_build:
    runs-on: windows-latest
    outputs:
      version: ${{ steps.set_version.outputs.version }}
    steps:
      - name: Checkout code
        uses: actions/checkout@v2

      # Install dependencies
      - name: Setup Python
        uses: actions/setup-python@v2
        with:
          python-version: '3.11.7'
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install pyinstaller-versionfile

      # Add step to create version file before PyInstaller build
      - name: Create Version File
        run: create-version-file version_metadata.yml --outfile version.rc

      - name: LS version.rc (before pyinstaller)
        run: |
          ls ./
          mkdir test

      - name: Create Executable
        uses: sayyid5416/pyinstaller@v1
        with:
          python_ver: '3.11.7'
          pyinstaller_ver: '==6.3.0'
          spec: 'presenterfocus.py'
          requirements: 'requirements.txt'
          upload_exe_with_name: 'PresenterFocus'
          options: --onefile --windowed --icon "icon.png" --name "PresenterFocus"

      - name: LS version.rc (after pyinstaller)
        run: |
          ls ./
          # the version.rc and test dir are not present here

Use clean_checkout: false


Code extraction rewrite

RegExp based extraction was prone to a lot of errors and very hard to work with.
This version uses a (light) code parser and performs basic static analysis to extract data more accurately.
Extraction is done in a Worker, to let the main event loop breathing room, and let it give visual feedback to the user in the CLI.
The JavaScript code analyser and React extractor are tested

I added also Stepan as a reviewer since he is State Machines expert. 🤓

From code style perspective it's OK. Please consider tokenization or some more structured way of code parsing.

Superseded by #10


Now You can see three projects on Project Page.

It look like this:

This will fixed #281 .

Thank you very much for merging. 🔥

I believe we can improve the design even more. For example
Basically in terms of a technical portfolio, following should be there for the cards:

A gif or picture give a visual insight
Name of the project
Link to Code
Link to Deploy
Tags of technology
Description [ optional, nowadays we don't look for it much]

I believe we can improve the design even more. For example
Basically in terms of a technical portfolio, following should be there for the cards:

A gif or picture give a visual insight
Name of the project
Link to Code
Link to Deploy
Tags of technology
Description [ optional, nowadays we don't look for it much]

Additionally in the project page we could build a search option to look at a particular category of projects (with the help of the tags used for them]


homebridge-zp does NOT work with homebridge v0.4.39

homebridge v0.4.39 crashes when homebridge-zp is active, see https://github.com/nfarina/homebridge/issues/1841.

Fixed in homebridge v0.4.42.


Creating Average over two columns

I have a table that contains the following columns:
[Country, Department, Employee , Sales Target, Actual Sales]
I need to create a ratio to be the result of the sales target and the actual Sales either by aggregating the Country over department, Department over country or by employees over department and the result to be the ratio between the Sales and Actual.
The result could look something like this:
Country Target Actual Ratio
USA 100 150 150%
UK 80 70 87.5%
to be able to draw it and configure it as i want with different configurations
How can I implement this ??

You can generate this ratio using the "Sum over Sum" aggregator and passing in Actual and Target as the arguments, but you cannot create a table which simultaneously shows Target, Actual and Ratio, you can just show the Ratio.


How to Enabled CLEARTEXT communication?

Hi, i'm using this library to get some data from a rest service that has an HTTP base address  and i can't manage it to use HTTPS instead of HTTP. Every time i do a rest call, it's throw an exception:
System.Net.Http.HttpRequestException: CLEARTEXT communication not enabled for client
Now. i saw on internet that, for Android, I have to add a network configuration with CLEARTEXT enabled, and i did it, without any result. What should i do to enable CLEARTEXT communication?

Use TLSConfig.DangerousAllowInsecureHTTPLoads property.

In iOS you have to add this to the info.plist
<key>NSAppTransportSecurity</key>
<dict>
    <key>NSExceptionDomains</key>
    <dict>
        <key>gorest.co.in</key>
        <dict>
            <key>NSExceptionAllowsInsecureHTTPLoads</key>
            <true/>
        </dict>
    </dict>
</dict>


allow building for macCatalyst

This came up while using CocoaLumberjack as a framework dependency. Without SUPPORTS_MACCATALYST it didn't build for catalyst for me.
Adding this, allowed Xcode to use the targets as dependencies in a macCatalyst app.

@diederich Interesting... Have you tried archiving a macCatalyst app with this setting? In my (quick and dirty) experimentations with macCatalyst, I had to "disable" multi platform (iOS and macOS) support to get it running and only leave iOS enabled.

Oh - good call regarding archiving. I had not tried it, but just did and it seems to work just fine and the resulting archive looks good. Will do the notarising dance etc. later today and can report back if something else pops up.

@diederich Very interesting, thanks for trying. If that works, they've changed something recently. Last I tried was during the betas and there I still had problems.

Yeah, this looks fantastic. Archived, notarised, all works fine :-)

@diederich I'd sign off the changes as well, but Travis doesn't:
$ xcodebuild test -skip-testing:'iOS Tests/DDFileLoggerPerformanceTests' -project Tests/Tests.xcodeproj -scheme 'iOS Tests' -sdk iphonesimulator -destination 'platform=iOS Simulator,name=iPhone 7,OS=10.3.1' GCC_GENERATE_TEST_COVERAGE_FILES=YES | xcpretty -c
xcodebuild: error: Unable to find a destination matching the provided destination specifier:
		{ platform:iOS Simulator, OS:10.3.1, name:iPhone 7 }

	The requested device could not be found because no available devices matched the request.

	Available destinations for the "iOS Tests" scheme:
		{ platform:macOS, arch:x86_64, variant:Mac Catalyst, id:4221EC92-2283-E327-612C-E5D7AEA432B1 }
		{ platform:iOS Simulator, id:9F6D3D24-3BA6-46D3-86E9-901C33C51CB2, OS:13.0, name:iPad Air (3rd generation) }
		{ platform:iOS Simulator, id:44416935-7D92-4E30-8AFC-9E291C08BCF0, OS:13.0, name:iPad Pro (9.7-inch) }
		{ platform:iOS Simulator, id:B1461227-C5A0-40CD-B14B-CF68260EF531, OS:13.0, name:iPad Pro (11-inch) }
		{ platform:iOS Simulator, id:EF26324D-D481-4A8E-AEA8-E0A1185F2709, OS:13.0, name:iPad Pro (12.9-inch) (3rd generation) }
		{ platform:iOS Simulator, id:60CD9292-3EC7-4C1C-8166-E1C2F5A47F01, OS:13.0, name:iPhone 8 }
		{ platform:iOS Simulator, id:0836550B-8811-49DF-ADAE-E4A09C63B3B3, OS:13.0, name:iPhone 8 Plus }
		{ platform:iOS Simulator, id:426A786E-9F1E-4A72-BCE9-F0394A0574D0, OS:13.0, name:iPhone 11 }
		{ platform:iOS Simulator, id:40A536FE-B35B-4721-B390-6DF012892918, OS:13.0, name:iPhone 11 Pro }
		{ platform:iOS Simulator, id:F8BB5873-A04F-405F-908D-DB8AC9C942FA, OS:13.0, name:iPhone 11 Pro Max }

	Ineligible destinations for the "iOS Tests" scheme:
		{ platform:iOS, id:dvtdevice-DVTiPhonePlaceholder-iphoneos:placeholder, name:Generic iOS Device }
		{ platform:iOS Simulator, id:dvtdevice-DVTiOSDeviceSimulatorPlaceholder-iphonesimulator:placeholder, name:Generic iOS Simulator Device }
The command "xcodebuild test -skip-testing:'iOS Tests/DDFileLoggerPerformanceTests' -project Tests/Tests.xcodeproj -scheme 'iOS Tests' -sdk iphonesimulator -destination 'platform=iOS Simulator,name=iPhone 7,OS=10.3.1' GCC_GENERATE_TEST_COVERAGE_FILES=YES | xcpretty -c" exited with 70.

I changed the travis config when I enabled Xcode 11 support and it worked back then. I know that travis also updated their images (e.g. adding Xcode 11.1 and 11.2 support). I wonder if this breakage now results from the added catalyst support (as in Xcode no longer offers older targets because of this?) or are caused by the updated travis images... 🤔

It looks like it can't find the iPhone 7 for building anymore. Let me bump this to the 8 running iOS 13..

Codecov Report

Merging #1104 into master will increase coverage by 0.03%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #1104      +/-   ##
==========================================
+ Coverage   36.89%   36.92%   +0.03%
==========================================
  Files          23       23
  Lines        3754     3870     +116
==========================================
+ Hits         1385     1429      +44
- Misses       2369     2441      +72

Impacted Files
Coverage Δ

Sources/CocoaLumberjack/DDFileLogger.m
56.23% <0%> (-3.05%)
:arrow_down:

Sources/CocoaLumberjack/DDTTYLogger.m
0% <0%> (ø)
:arrow_up:

Sources/CocoaLumberjack/DDASLLogCapture.m
0% <0%> (ø)
:arrow_up:

Sources/CocoaLumberjack/DDLog.m
59.46% <0%> (+1.32%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update ded5f59...27b0276. Read the comment docs.

@diederich Yea, we had this to test the library against the "oldest possible" OS. But it seems like Xcode (and Travis) don't come with support for older OS by default anymore. So I think that's fine.


Research and install Prettier

Description
Research and install Prettier.io for better styling of code without having to discuss what style is better and saves a lot of time.
Create React App folks recommend using Prettier. Setting Up Your Editor
Initial install on a front-end
For initial install on a React front-end and to set up automatic code formatting execute the following. Skip this if someone else has set it up already.
Step 1
Add prettier to your project:
npm install prettier --save-dev --save-exact
Step 2
Verify by running against a file:
npx prettier --write src/index.js
Step 3
Run prettier when commiting files:
npm install pretty-quick husky --save-dev
Then add this config to package.json:
{ "husky": { "hooks": { "pre-commit": "pretty-quick --staged" } } }
Setting up Prettier on Sublime Text 3

Install package JSPrettier.

Setting up Prettier on VSCode
Not sure how to do this on VSCode but I would imagine it's quite simple. Here's a video tutorial I found for those using VSCode. VSCode ESLint, Prettier & Airbnb Style Guide Setup

Done


fix(applications/web): use a more specific field name for project updates content

Describe your changes
Use a more specific POST field name to allow a specific WAF exception
Issue ticket number and link
ASB-1692
Type of change 🧩

[x] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] Documentation update
[ ] Other (please explain in the description section above)

Checklist before requesting a review

[ ] I have performed a self-review of my own code
[ ] I have double checked this work does not include any hardcoded secrets or passwords
[ ] I have made corresponding changes to the documentation
[ ] I have provided details on how I have tested my code
[ ] I have referenced the ticket number above
[ ] I have provided a description of the ticket
[ ] I have included unit tests to cover any testable code changes

Forgot to update tests.


Enable test that failed with PSK

Revert the changes in this commit https://github.com/thaliproject/Thali_CordovaPlugin/pull/670/commits/7da7b77ceccd2bfed5e28265a79f806e7ae0591c and make the test work with PSK.

This test is now been enabled


Fuzzy sort / match when filtering

Provide fuzzy matching and sorting by default when using the filtering helpers. This will provide a better out of the box experience.

Implemented in 0.6.0


Delegate default region to aws sdk

Close https://github.com/apex/up/issues/250.
If regions is not present in up.json delegates default region to aws sdk. More info about how this process works can be found here and here. Also the added tests try to enumerate them all.

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

definitely want to get this in the next release, merging! Thanks again

actually I might leave it undocumented, for seasoned AWS people, but otherwise I think it's a little obscure, ideally up.json has the config.


Class name refactoring

Do you plan to namespace classes like Google_Service_Books along with PSR compatibility fixes in v3? Something like Google\Service\Books

In progress here: https://github.com/googleapis/google-api-php-client-services/pull/363
Will be available in the very near future!


Samples out of date

Hello,
I am trying to run some qiskit samples to test the JKU simulator, but I get errors. Could you please provide me with the latest versions of Qiskit these were tested and validated ? I would like to try this simulator (I understand that JKU is BDD-based?).
I currently cannot run the following sample (sample 1):
https://github.com/Qiskit/qiskit-jku-provider/blob/master/examples/jku_circuit.py
... or the main thing I want to run, sample 2, relying on qiskit_chemistry (eventually yields same error than sample 1 after a few fixes)
https://github.com/Qiskit/qiskit-chemistry/blob/master/qiskit_aqua_chemistry/drivers/pyscfd/README.md (with JKU as backend)
If you have a way for me to test / benchmark JKU that does not require the resolution of the errors described below, that would be useful on the very short-term (that being said I think it's very important that users are able to run your samples without troubles !)
========================================================
1 - Environment
Here is my current Qiskit environment, which I believe has the latest version of everything (pip freeze):
qiskit==0.7.2
qiskit-addon-jku==1.0.2
qiskit-aer==0.1.1
qiskit-aqua==0.4.1
qiskit-aqua-chemistry==0.4.0
qiskit-chemistry==0.4.2
qiskit-terra==0.7.0

2 - Error
For both samples, I eventually get a key error, raised in function compute_measurement_data: I have stopped investigating after reaching that point.
  File "/home/vsenicourt/Desktop/virtualenvs/simulators/lib/python3.6/site-packages/qiskit_addon_jku/qasm_simulator_jku.py", line 243, in compute_measurement_data
    measurement_data['mapping'][op['qubits'][0]] = op['clbits'][0]
KeyError: 'clbits'

Before reaching this error, a few straightforward ones appeared. For both these samples I'm running, a few namespaces have changed for the latest Qiskit:

In the "main" files, I need to import qiskit_addon_jku (and not qiskit_jku_provider)
qiskit.backends does not exist anymore. You have to go through qiskit.providers for various imports in qasm_simulator_JKU.py(a search in their Github for the classes you need to import solves it)

Several errors occurred in the main qiskit / qiskit_aqua modules in sample 2:
Qiskit accesses "configuration information" through a method that apparently returns an object and reads the fields, while the JKU package tries to access a dictionary whose name iOS preceded by "_". Example:
backend.configuration().simulator. # Latest Qiskit
backend._configuration['simulator'] # Latest JKU

After solving these kinds of error, I eventually reach the code section that returns the error I shared at the top of this post, the "key" error, for both samples. It would seem that the keys and values of the dictionaries used to created header and ops are not as expected: maybe you guys were relying on qiskit to build them and their implementation has changed since then. As a consequence, the  dictionary obj_circuit passed is not matching the fields the compute_measurement_data function is expecting.
Thanks for your efforts ! Again, If you guys were just able to point at the latest Qiskit environment (versions) your samples were tested and working, that would already allow me to try your simulator :)

Talking with @gadial seems this was fixed since, but Gadi will check again and comment

Thank you for your excellent feedback! We have just uploaded a new version of the JKU provider to PyPi and I hope all the problems you have raised were addressed. I explicitly verified that our samples work now with qiskit 0.7.2.
One thing I did not manage to check is working with Aqua; if you still encounter problems let us know.


maven: configure toolchains based on ASF infra jdk names

This adds toolchain configuration for CloudStack to use specific
toolchain for building per ASF infra's configured toolchain.
Reference: https://issues.apache.org/jira/browse/INFRA-19817
Signed-off-by: Rohit Yadav<EMAIL_ADDRESS>

not useful


Centos 7 systemd container on Fedora 31

Is this a BUG REPORT or FEATURE REQUEST? (leave only one on its own line)
/kind bug
Description
Running a centos 7 container with systemd fails to run on Fedora 31
Steps to reproduce the issue:

podman run -ti centos7-with-systemd /sbin/init

output shows the following:

Failed to mount cgroup at /sys/fs/cgroup/systemd: Operation not permitted
[!!!!!!] Failed to mount API filesystems, freezing.

This occurs when running as root and rootless

Describe the results you received:
Failed to mount cgroup at /sys/fs/cgroup/systemd: Operation not permitted
[!!!!!!] Failed to mount API filesystems, freezing.
Describe the results you expected:
Expect systemd to run
Additional information you deem important (e.g. issue happens only occasionally):
Output of podman version:
podman version
Version:            1.6.1
RemoteAPI Version:  1
Go Version:         go1.13
OS/Arch:            linux/amd64
Output of podman info --debug:
podman info --debug
debug:
compiler: gc
git commit: ""
go version: go1.13
podman version: 1.6.1
host:
BuildahVersion: 1.11.2
CgroupVersion: v2
Conmon:
package: conmon-2.0.1-1.fc31.x86_64
path: /usr/bin/conmon
version: 'conmon version 2.0.1, commit: 5e0eadedda9508810235ab878174dca1183f4013'
Distribution:
distribution: fedora
version: "31"
MemFree:<PHONE_NUMBER>4
MemTotal:<PHONE_NUMBER>4
OCIRuntime:
package: crun-0.10.1-1.fc31.x86_64
path: /usr/bin/crun
version: |-
crun version 0.10.1
spec: 1.0.0
+SYSTEMD +SELINUX +APPARMOR +CAP +SECCOMP +EBPF +YAJL
SwapFree: 0
SwapTotal: 0
arch: amd64
cpus: 16
eventlogger: journald
hostname: kubhost
kernel: 5.3.0-1.fc31.x86_64
os: linux
rootless: true
slirp4netns:
Executable: /usr/bin/slirp4netns
Package: slirp4netns-0.4.0-20.1.dev.gitbbd6f25.fc31.x86_64
Version: |-
slirp4netns version 0.4.0-beta.3+dev
commit: bbd6f25c70d5db2a1cd3bfb0416a8db99a75ed7e
uptime: 186h 43m 44.97s (Approximately 7.75 days)
registries:
blocked: null
insecure: null
search:

docker.io
registry.fedoraproject.org
quay.io
registry.access.redhat.com
registry.centos.org
store:
ConfigFile: /home/greg/.config/containers/storage.conf
ContainerStore:
number: 13
GraphDriverName: vfs
GraphOptions: {}
GraphRoot: /home/greg/.local/share/containers/storage
GraphStatus: {}
ImageStore:
number: 21
RunRoot: /run/user/1000
VolumePath: /home/greg/.local/share/containers/storage/volumes

Additional environment details (AWS, VirtualBox, physical, etc.):
running ZFS

My suspicion is that the systemd used in Cent 7 images is too early to support CGroups v2, as used in Fedora 31 by default

@mheon - agreed, will there be a work around or for users using Centos 7 systemd or should everything be rebuild with Centos 8

i dont think this is a podman problem?

@baude We should contact the systemd folks to be sure. If there's a trivial workaround on the Podman side it could be worthwhile

@greg-hydrogen could you open a bugzilla on this?  Open it on Podman and we will pull in the systemd team.

For reference: https://bugzilla.redhat.com/show_bug.cgi?id=1760645

@giuseppe  I am seeing the same problem with  a fedora:31 container (where presumable systemd is cgroup2 aware). Hangs at
INFO[0000] Running conmon under slice machine.slice and unitName
libpod-conmon-ddb15b914e83b432a44b9fa9726fb30d144e667f16b4c157d2c8aa54139ec61a.scope

@space88man that looks a different issue.
Could you please verify if the NOTIFY_SOCKET environment variable is defined in your session?

@giuseppe Fedora 31 terminal (as root and non-root) both do not have NOTIFY_SOCKET in the environment.

Sorry for the noise: my issue is was due to the existence of an upgraded package oci-systemd-hook from F30 to F31. This package prevents F31 podman from launching systemd based containers.
After removing it,  the cgroupv2-aware containers(F30,F31,CentOS 8) run and I get the same error as OP for older containers.

@lsm5 @rhatdan oci-systemd-hook is causing different issues on cgroups v2.  Should we change the  podman spec file to conflict with oci-systemd-hook?

We should obsolete it.  There are no users of oci-systemd-hook any longer.

@lsm5 @jnovy Could you guys obsolete oci-systemd-hook?

oci-systemd-hook no longer exists in Fedora 31/32

Added obsolet oci-systemd-hook


#60 names can include dashes or spaces

The variable names can now include dashes or spaces in the cheatsheets.

Hey @denisidoro, I am able to pass all test cases on my local system. please check once.

Are you on OSX? I believe your changes won't work with GNU utils

You can run your tests in a local container by running scripts/docker then /navi/test/run

No, I am not on OS X. I'll try running it in docker. Thanks. :)


Fix image/svg widget size allocation to use full_size, not raw_size

Previously only had an impact on the final size of dimensions set to Shrink. I'm guessing this was a mistake but anyway...
Before this change, setting Fill for height and width of an image, with ContentFit::Contain, caused it to take all available space in both dimensions. Where the ratio of the images differs from that of the space it has available, it preserves the ratio and centers along the dimension with extra space. I want to to allocate only the space it needs, without centering, and I don't see a way to do that currently.
The centering may be useful in some cases but should involve another property or widget.

Hm, looking at https://developer.mozilla.org/en-US/docs/Web/CSS/object-fit, I guess "letterboxing" is the behavior of contain there?
I haven't written much css there, I suppose I should see how what I'm trying to do would be done there...

Ah, I guess what I'd use in CSS is width: 100%; height: auto;. So I guess if it's trying to follow a CSS like model, we'd need a Length::Auto? Maybe not the way Iced wants to handle it though.

So I guess if it's trying to follow a CSS like model, we'd need a Length::Auto?

At least for this question with a fixed dimensiom image, Length::Shrink should do the same as your requested Length::auto
Length::Shrink meaning, as small as your smallest bound on this axis. Which is generally the same as what auto does in CSS

Which is generally the same as what auto does in CSS

This is not true when width and height are set differently, when scaling up, at least.
You can generate a 1x1 pixel image with convert -size 1x1 canvas:black 1x1.png. With this, <img style="width: 100%;" src="1x1.png"/> sets the width to fill the available space, and sets the height to the same to preserve aspect ratio (auto is the default behavior). In Iced, with Shrink, it doesn't allow a height greater than 1px here.
So CSS and GTK both have ways for the height allocated to depend on the width (and vice versa). Iced's image widget is supporting that only with Shrink.

It seems even width: 100%; height: min-content expands the height this way? I might expect min-content to be more link Shrink.
object-fit: contain; width: 100%; height: 100% does seem to match what Iced is doing with Fill and Contain though. (So this PR definitely isn't right if the behavior should match CSS, but the existing behavior isn't either.)

Since it's unclear what we actually want to do here, let's avoid breaking anything and have a proper discussion first about what the new behavior should be (RFC?).


Update sbt-scalafmt to 2.4.3

Superseded by https://github.com/sangria-graphql/sangria-ion/pull/95


Fixed typo in train api documentation

"It True" -> "If True". Fixed upstream as suggested by @drpngx.

Can one of the admins verify this patch?

Jenkins, test this please.

@tensorflow-jenkins test this please


Fix mango json index selection

Overview
JSON index selection in Mango previously deemed an index to be usable if a range scan on the first component of its compound key could be generated from the query selector.
For instance, if I had an index:
[A, B]
is_usable would return true for the selector:
{"A": "foo"}
This is incorrect because JSON indexes only index documents that contain all the fields in the index; null values are ok, but the field must be present. That means that for the above selector, the index would implicitly include only documents where B exists, missing documents where {"A":5} matched but field B was not present.
This commit changes is_usable so that it only returns true if all the keys in the index are required to exist by the selector. This means that in the worst case e.g. none of the predicates can be used to generate a range query, we should end up performing a full index scan, but this is still more efficient
than a full database scan.
We leave the generation of the optimal range for a given index as a separate exercise - currently this happens after index selection.
Potentially we'd want to score indexes during index selection based on their ability to restrict the result set, etc.
Testing recommendations
Run the mango test suite. Manually run some mango queries with/without JSON indexes and check that the results are as expected.
Checklist

[ ] Code is written and works correctly;
[ ] Changes are covered by tests;
[ ] Documentation reflects the changes;

@davisp thanks for the review! I'll have a think about the naming and overloaded function issues.
To your last point, my thought there is that all predicates except, by definition, "$exists":false, "operate" on the index because selection of the index restricts the result set to documents where the indexed fields exist.

@davisp I went with your second suggestion and implemented a has_required_fields function


improve enable move memtable in routine load

Proposed changes
Issue Number: close #xxx

Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run buildall

run buildall

run buildall


feat: add awscrt 1.2.2 release

update awscrt with release 1.2.2

:tada: This PR is included in version 1.163.0 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Amazon Sync Error

Hi,
I am running the S3 Sync step, but I'm getting an error but i can't actually see the error, see the log below:
+------------------------------------------------------------------------------+
| (2<EMAIL_ADDRESS>                                                 |
+------------------------------------------------------------------------------+
| id: amazon-s3-upload                                                         |
| version: 3.1.2                                                               |
| collection: https://github.com/bitrise-io/bitrise-steplib.git                |
| time: 2016-06-23T07:45:58-07:00                                              |
+------------------------------------------------------------------------------+
|                                                                              |
INFO[07:46:01] (awscli) isn't installed, installing...
INFO[07:46:11]  * [OK] awscli installed
INFO[07:46:11]  * [OK] Step dependency (awscli) installed, available.
Configs:

access_key_id: ***
secret_access_key: ***
upload_bucket: nm-mobile-resources
upload_local_path: IPA/
acl_control: private
set_acl_only_on_changed_objets: true
aws_region:

/var/folders/lb/8n5bn9k975qgw662jpqdy7mm0000gn/T/bitrise419836257/step_src/step.sh: line 123: print_failed_message: command not found
|                                                                              |
+----+--------------------------------------------------------------+----------+
| 🚫  |<EMAIL_ADDRESS>(exit code: 127)                      | 15 sec   |
+----+--------------------------------------------------------------+----------+
| Issue tracker: https://github.com/bitrise-io/steps-amazon-s3-upload/issues   |
| Source: https://github.com/bitrise-io/steps-amazon-s3-upload                 |
+----+--------------------------------------------------------------+----------+

Thanks for reporting! We'll look into it ASAP!

Hi @Reedyuk ,
we fixed the issue, new release will be available in steplib soon.
Thanks for reporting!


Hot fixes for dbscan

Changes proposed in this pull request:

Fixed behavior for very small datasets (nRows < 64)
Optimized copyCoreObservations for current oneapi state

/intelci ru

/intelci run

/intelci run


Cyclops No Armour versions etc. not in new character list

add this into generation

put a creature default version in.


Make a comment field as an optional

According to aries rfcs
https://github.com/hyperledger/aries-rfcs/tree/master/features/0036-issue-credential
https://github.com/hyperledger/aries-rfcs/tree/master/features/0453-issue-credential-v2
the comment field is an optional field.
However, libvcx expects this as a mandatary, so if  the comment is empty it causes Json parsing error
Caused by: Cannot deserialize A2A message: missing field 'comment'

This PR fixes this issue.

FYI: I made PR in indy-sdk as well, and Daniel Hardman reviewed it already.
https://github.com/hyperledger/indy-sdk/pull/2220


Test script read username and password from GITHUB Secret dynamically while running test

List of changes:

Test script read username and password from GITHUB Secret dynamically while running test

Precondition :
Create Username and Password and update below repository secret (Refer Screenshot)

ORTELIUS_APP_USERNAME
ORTELIUS_APP_PASSWORD

Username and Password removed from serenity.properteis file for security purpose
Updated feature file name based on functionality
Added Thread count 3 in POM.xml file

I don't have write access to update conflicts changes.   Please provide write access

I have fixed merge conflict.  Please merge it and create a username and password in Repository SECRECT
List of changes:
Test script read username and password from GITHUB Secret dynamically while running test
Precondition :
Create Username and Password and update below repository secret (Refer Screenshot)
ORTELIUS_APP_USERNAME
ORTELIUS_APP_PASSWORD


update vtkvolume model to works with new bokeh build

fix : https://github.com/pyviz/panel/issues/728

Looks good. I must have overlooked this recent addition when rebasing PR #626. It would be good to test if this and all other models are importable in notebooks and under other embedding methods, especially in light of issue #727. Though I wouldn't block merging this PR on that.


nil as an arg for single arity + is valid

I just noticed (+ nil) => nil is apparently totally valid. I cannot fathom why, and interestingly (- nil) returns error. Other arities of + with nil as an argument produce an expected NullPointerException.
Interesting, looking at the source:
(defn +
  "Returns the sum of nums. (+) returns 0. Does not auto-promote
  longs, will throw on overflow. See also: +'"
  {:inline (nary-inline 'add 'unchecked_add)
   :inline-arities >1?
   :added "1.2"}
  ([] 0)
  ([x] (cast Number x))
  ([x y] (. clojure.lang.Numbers (add x y)))
  ([x y & more]
     (reduce1 + (+ x y) more)))

So (cast Number x), apparently thinks nil is a valid Number.
Digging some more because this smells like a bug, I finally found this:
https://stackoverflow.com/questions/35626096/clojure-behaviour-with-nil-values
I agree with the answer that this is indeed a bug.

Would you like to send it to Alex Miller? Or would like me to do it? I agree that it's a bug.

Oh, I would love to. How do I do that?

I sent you Alex's email.

This now corresponds to https://github.com/Clojure-Intro-Course/babel/issues/44 in the migration repository.


Ionic 2 Build Errors

Hi i got this Build Errors at my Ionic 2 Application
[04:21:57]  build prod failed: Template parse errors: Can't bind to 'inputText' since it isn't a known property of
            'tag-input-form'. 1. If 'tag-input-form' is an Angular component and it has 'inputText' input, then verify
            that it is part of this module. 2. If 'tag-input-form' is a Web Component then add "CUSTOM_ELEMENTS_SCHEMA"
            to the<EMAIL_ADDRESS>of this component to suppress this message. (" (onKeyup)="fireEvents('keyup',
            $event)" [ERROR ->][(inputText)]="inputText" [validators]="validators" "): TagInputComponent@38:12
[04:21:57]  ionic-app-script task: "build"
[04:21:57]  Error: Template parse errors: Can't bind to 'inputText' since it isn't a known property of 'tag-input-form'.
            1. If 'tag-input-form' is an Angular component and it has 'inputText' input, then verify that it is part of
            this module. 2. If 'tag-input-form' is a Web Component then add "CUSTOM_ELEMENTS_SCHEMA" to the
<EMAIL_ADDRESS>of this component to suppress this message. (" (onKeyup)="fireEvents('keyup', $event)"
            [ERROR ->][(inputText)]="inputText" [validators]="validators" "): TagInputComponent@38:12
Error: Template parse errors:
Can't bind to 'inputText' since it isn't a known property of 'tag-input-form'.
1. If 'tag-input-form' is an Angular component and it has 'inputText' input, then verify that it is part of this module.
2. If 'tag-input-form' is a Web Component then add "CUSTOM_ELEMENTS_SCHEMA" to the<EMAIL_ADDRESS>of this component to suppress this message.
 ("
            (onKeyup)="fireEvents('keyup', $event)"

            [ERROR ->][(inputText)]="inputText"

            [validators]="validators"
"): TagInputComponent@38:12
    at SyntaxError.BaseError [as constructor] (/Users/danielehrhardt/projekte/netz-app/node_modules/@angular/compiler/bundles/compiler.umd.js:1597:31)
    at new SyntaxError (/Users/danielehrhardt/projekte/netz-app/node_modules/@angular/compiler/bundles/compiler.umd.js:1795:20)
    at TemplateParser.parse (/Users/danielehrhardt/projekte/netz-app/node_modules/@angular/compiler/bundles/compiler.umd.js:11444:23)
    at AotCompiler._compileComponent (/Users/danielehrhardt/projekte/netz-app/node_modules/@angular/compiler/bundles/compiler.umd.js:24815:72)
    at /Users/danielehrhardt/projekte/netz-app/node_modules/@angular/compiler/bundles/compiler.umd.js:24717:117
    at Array.forEach (native)
    at AotCompiler._compileSrcFile (/Users/danielehrhardt/projekte/netz-app/node_modules/@angular/compiler/bundles/compiler.umd.js:24701:24)
    at /Users/danielehrhardt/projekte/netz-app/node_modules/@angular/compiler/bundles/compiler.umd.js:24676:95
    at Array.map (native)
    at /Users/danielehrhardt/projekte/netz-app/node_modules/@angular/compiler/bundles/compiler.umd.js:24676:60

very odd, @Input() inputText is there.

You can reproduce if you you create a new ionic app
Ionic 2
and add this package
Thank you for your fast reply

Yeah can reproduce it, when building prod. Still, very odd :|

Hi @danielehrhardt,
can you try with the new version? seems to build fine for me

I have the same problem on ionic2

@dkd051 can you create a new issue and fill out the template? to get a better understanding of your issue :)


sets

How about having sets, which is really just arrays that can have predefined values at most one time?
Proposed syntax:
+ privileges (set[string], required)
    + network
    + mailman
    + procmod
    + procview
    + lpadmin
    + lpoperator

+ privileges (array[string], fixed)
    + network
    + mailman
    + procmod
    + procview
    + lpadmin
    + lpoperator

Is what you looking at. Do not forget that the required there makes privileges key mandatory in its parent object.

fixed is essentially saying the instance of this type should appear exactly as defined below.

oh wait, you want just one value to be there?

or any number of those values? but only the values from the set?

Either way I think it might have a solution with combination of array enum and maybe fixed

I want the following objects to be considered valid:
{ "privileges": [] }
{ "privileges": [ "procmod" ] }
{ "privileges": [ "procmod", "lpoperator", "network" ] }

And the following to be considered invalid:
{}
{ "privileges": [ "somethingelse" ] }
{ "privileges": [ "procmod", "procmod", "network" ] }

I personally understand "set" as something like array, but with unique
members and unsorted.
The uniqueness could be theoretically achieved by a validation rule. The
fact it's unsorted... not sure how much that's important in web API
contracts.
On 17 Mar 2016 10:14 p.m., "Linus Unnebäck"<EMAIL_ADDRESS>wrote:

I want the following objects to be considered valid:
{ "privileges": [] }
{ "privileges": [ "procmod" ] }
{ "privileges": [ "procmod", "lpoperator", "network" ] }
And the following to be considered invalid:
{}
{ "privileges": [ "somethingelse" ] }
{ "privileges": [ "procmod", "procmod", "network" ] }
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly or view it on GitHub
https://github.com/apiaryio/mson/issues/55#issuecomment-198085019

@zdne Does "s1: awaiting input" mean that you are waiting on more information from me? I'm happy to help or provide more info 👍

@LinusU I think we are waiting for more feedback from other users here.
I also wonder how JSON Schema handles this.

JSON Schema:
{
  "type": "array",
  "uniqueItems": true,
  "items": {
    "enum": [ "network", "mailman", "procmod", "procview", "lpadmin", "lpoperator" ]
  }
}

@LinusU

I want the following objects to be considered valid
{ "privileges": [] }
{ "privileges": [ "procmod" ] }
{ "privileges": [ "procmod", "lpoperator", "network" ] }

@LinusU in that case, this should be the solution:
# Permitted Values (enum[string))
- procmod
- lpoperator
- network

# My Object
- set (array[Permitted Values])

Does it work?

@zdne That would work for the happy case, but then this array would also be considered valid:
[ "procmod", "procmod" ]

@LinusU fair point. I think we have a case for set or a new type modifier (unique)?


App crashed when i clicked on idol

Descriptions
When I launched the app and clicked on idol, the app crashed. This happens while data connection was off. However, it keeps loading anytime I'm connected and click on it.
Steps to reproduce
Launch the app without data connection

click on idol
note the crash.

You can also switch data on and click on it again. It will keep loading without any display.

Reproducing the bug

Device used
Tekno spark k7
Android 7.0
App version

Thank for your report. I had seen some bug reports and wondered what happened. It don't have check data connection function, so app crashes. I will add this. About idols tab, I don't know. I will check later.

https://github.com/MagiCircles/SchoolIdolAPI/issues/339

Released new version. It fixed the bugs.


opt speed up deepEquals of TreeNode

Proposed changes
Issue Number: close #xxx

Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run buildall

(From new machine)TeamCity pipeline, clickbench performance test result:
the sum of best hot time: 49.91 seconds
stream load tsv:          535 seconds loaded<PHONE_NUMBER>9 Bytes, about 133 MB/s
stream load json:         20 seconds loaded<PHONE_NUMBER> Bytes, about 112 MB/s
stream load orc:          64 seconds loaded<PHONE_NUMBER> Bytes, about 16 MB/s
stream load parquet:          32 seconds loaded 861443392 Bytes, about 25 MB/s
insert into select:          29.0 seconds inserted 10000000 Rows, about 344K ops/s
storage size:<PHONE_NUMBER>0 Bytes


Convert-WindowsImage

The readme here says this code is going to be moved to its own repo. The link to the new repo doesn't work and I'm not getting any response from the email address listed. Is this going to be moved? I'd like to be able to put in a pull request but wasn't sure what the plan is for this code.

@mebersol -- Do you know who might be able to get this link fixed up?

HELLLLLLLLLLLLLLLLLLLLOOOOOOOOOOOOOOOOOOOOO  this has been broke for a few months now.  Anyone have any idea when this is going to be fixed?  is this project just abandoned?

Checking on this.
From: Thomas Malkewitz<EMAIL_ADDRESS>Sent: Tuesday, February 14, 2017 7:38 AM
To: Microsoft/Virtualization-Documentation<EMAIL_ADDRESS>Cc: Kallie Bracken<EMAIL_ADDRESS>Comment<EMAIL_ADDRESS>Subject: Re: [Microsoft/Virtualization-Documentation] Convert-WindowsImage (#483)
HELLLLLLLLLLLLLLLLLLLLOOOOOOOOOOOOOOOOOOOOO this has been broke for a few months now. Anyone have any idea when this is going to be fixed? is this project just abandoned?
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHubhttps://github.com/Microsoft/Virtualization-Documentation/issues/483#issuecomment-279742024, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVdoi1Ip_KwIzUMZEETObd89wvL3r-dAks5rccp1gaJpZM4KzHCI.

The development effort on this private repo has stalled - I haven't heard from the developer in weeks.  @mud5150 - feel free to submit your PR to this repo for now, Artem can mirror the change when he gets back to the separate repo.

@mebersol Thanks for letting me know.

FYI: There is a project https://github.com/docker/communitytools-image2docker-win


RNTester - Unable to resolve module 'TouchHistoryMath'

 I have reviewed the documentation
 I have searched existing issues
 I am using the latest React Native version

After cloning the React-Native repository, and running the RNTester.xcodeproj, I received an error message stating: Unable to resolve module 'TouchHistoryMath', from ../react-native/Libraries/Interaction/PanResponder.js
Environment
Environment:
OS: macOS High Sierra 10.13.4
Node: 9.10.1
Yarn: 1.5.1
npm: 5.8.0
Watchman: 4.9.0
Xcode: Xcode 9.3 Build version 9E145
Android Studio: 3.1 AI-173.4670197
Packages: (wanted => installed)
react: ^16.3.0-alpha.1 => 16.3.0
react-native: 0.54.4 => 0.54.4
Steps to Reproduce

Clone React-Native repository, open the RNTester project in Xcode, and run.
I also followed the guidelines in the warning, and the error is still present.
Expected Behavior

For the app to load up and work, showing examples etc.
Actual Behavior

I fixed the problem by prepending the file directory locator ("./") to the 'TouchHistoryMath' module call in PanResponder.js


[elasticsearch][logstash] Add support to PodDisruptionBudget policy/v1

This PR adds support to PodDisruptionBudget policy/v1 & backward compatibility with policy/v1beta1, it will fix the deprecated message you might be getting during charts installation:
helm install es ../elasticsearch/ -f ../elasticsearch/values.yaml
W1015 15:55:59.468680   45578 warnings.go:67] policy/v1beta1 PodDisruptionBudget is deprecated in v1.21+, unavailable in v1.25+; use policy/v1 PodDisruptionBudget
W1015 15:56:01.261764   45578 warnings.go:67] policy/v1beta1 PodDisruptionBudget is deprecated in v1.21+, unavailable in v1.25+; use policy/v1 PodDisruptionBudget
NAME: es
LAST DEPLOYED: Fri Oct 15 15:55:59 2021
NAMESPACE: default
STATUS: deployed

Fix #1454
Fix #1568
Replace #1453, #1526 and #1564

Hey 👋
What about this PR? Are we going to merge these changes?

Any plans to merge to the 6.8 branch?  We are stuck on 6.8 for a while as it's a big refactor job to update to the newer client libraries.


SSE2 implementation of i_to_float32(const float64x4& a) is broken

the operation
    r2 = move4_l<2>(r2);
shifts the wrong way and leaves r2 full of zeros. The upper 2 lanes of the result wind up being filled with zeros.
Furthermore, it looks like merging the two intermediate vectors with _mm_movelh_ps() might be more efficient than shifting and oring. Compiler optimization might produce that anyway, but _mm_movelh_ps() seems more straightforward.

the incorrect shift appears to have been fixed in a7f191d5, however use of _mm_movelh_ps() might still make for more efficient code.

Thanks, this improvement has been applied in 227cc0a8e79ceab4eda89126ca1e98b3ddc82c85.


[ENH] Implementing predict_interval in ColumnEnsembleForecaster

Implementing predict_interval for the multivariate case in ColumnEnsembleForecaster

Reference Issues/PRs

What does this implement/fix? Explain your changes.

FYI, I tried this here https://github.com/alan-turing-institute/sktime/pull/2356 since I needed it for sth else (testing multivariate proba predictions).
It turns out that there were a few bugs in the sktime framework that would have prevented this from going smoothly (see the PR and the bugfixes it depends on)

Should I close this issue?

I'd say, let's keep it open until #2356 is reviewed and potentially merged.
(your approach is different as far as I can tell)

#2356 is merged and seems to work fine, so closing this. Thanks for your work, @kejsitake, and sorry for the bugs that were overlaying this.


bcm43xxx: fixed issues with unaligned buffers for DMA transfers.

Summary
bcm43xxx: fixed issues with unaligned buffers for DMA transfers.
This fixes the following errors:

"stm32_dmacapable: stm32_dmacapable: burst crosses 1KiB
up_assert: Assertion failed at file:chip/stm32_sdio.c line: 2890 task: init"

"stm32_dmacapable: stm32_dmacapable: burst crosses 1KiB
up_assert: Assertion failed at file:chip/stm32_sdio.c line: 2808 task: bcmf"

Impact
bcm43xxx driver
Photon board
EMW3162 board

Hi Xiang,
Alternatively, I've added CONFIG_IEEE80211_BROADCOM_SDIO_DMA_BUF_ALIGNMENT parameter in menuconfig for bcm43xxx driver.

@xiaoxiang781216, possibly you know, for some reason CI tests on github sometimes fail despite the code is good and normally is built locally. Sometimes, I just sent the new commit (by adding a space character to the commit memo) just to restart CI tests on github (I do not know how else I can restart them). Usually just the restarting this way helped. However, now it always fails on arm-09 step. Possibly some build cache should be cleared? I do not know how I can do this, I do not have access.

The fail due to CI check defconfig in the normalized form, please try this command to say the difference:
./tools/refresh.sh --silent photon/wlan

The fail due to CI check defconfig in the normalized form, please try this command to see the difference:
./tools/refresh.sh --silent photon/wlan

Thank you very much! This helped.


Indexers

ref:

https://github.com/scientist-softserv/hykuup_knapsack/issues/85

Closing per Kirk's PR
Indexers were examined and no changes were needed


Demo app with toolbar, filter, and sort components

Added toolbar, filter, filter-field, filter-results, and Dana's sort component from Angular Patternfly. These separate components were built together in order to be consumed by the toolbar. This Angular2 conversion includes all existing Patternfly unit tests as well as examples.
I also created a demo app, built using webpack, to showcase new components. To view the demo, run "npm run start" and point your browser to http://localhost:3001.
Note that the styles are a little off for the toolbar view icons. The build also occasionally generates a "stack level too deep" error with sass-loader -- a rebuild often clears that up. Will need to evaluate how the CSS is built with Patternfly.
There is more work to be done here, but this is a good stopping point as the number of changes are getting large.
Toolbar Example:

Filter Example:

Sort Example:

FYI @dgutride

Added exports to index.ts and modified package versions per code review comments.

@dlabrecq there are failing tests.

@dlabrecq when I ran the demo with "npm start" I got the following error.
ERROR in ./~/css-loader!./~/sass-loader!./src/app/filters/filter.component.scss
Module build failed:
@include navbar-vertical-align($line-height-computed);
^
Stack level too deep
in /home/josh/git/fabric8-ui/ngx-widgets/src/assets/vendor/patternfly/stylesheets/bootstrap/_navbar.scss (line 360, column 12)
@ ./src/app/filters/filter.component.scss 4:13-138
@ ./src/app/filters/filter.component.ts
@ ./src/app/filters/filters.module.ts
@ ./src/app/filters/examples/filter-example.module.ts
@ ./src/app/app.module.ts
@ ./src/main.ts
@ multi (webpack)-dev-server/client?http://<IP_ADDRESS>:3001 ./src/main.ts