freebayes "Segmentation fault"

Dear Community,
I want to align some RAD data of a non-model organism to a genome of the same species.
For that I followed this tutorial so far: https://github.com/ekg/alignment-and-variant-calling-tutorial
When using freebayes I get the following error: "Segmentation fault" (nothing more except these two words, no number and no error code etc. )
I called freebayes as follows:
$ freebayes -f  genome.fasta fastQ-processradtags/Rad-seq.fq.raw.bam >output.vcf
I'm using it on a Debian Server:
Distributor ID: Debian
Description:    Debian GNU/Linux 9.3 (stretch)
Release:        9.3
Codename:       stretch
Do You have any Idea what I'm missing/ doing wrong here?
Thanks for your help, time and consideration
Lucy

That sounds like a compilation issue. Did you run into anything weird (error or failure messages) during installation (make then make install)?

I installed it locally on a server and only used following commands:
getting freebayes
git clone --recursive git://github.com/ekg/freebayes.git
go to folder
cd freebayes && make
Do you think I have to use the make install command (and therefore the Server Admin has to do this?)
Cheers and thanks for your fast feedback!

It should be enough to run make, make install just copies the content of bin/ to /usr/local/bin/.
What happens when you just run ./freebayes or ./bin/freebayes? You should see something like this:
$ ./freebayes
usage: ./freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]

Bayesian haplotype-based polymorphism discovery.

parameters:

   -h --help       For a complete description of options.

citation: Erik Garrison, Gabor Marth
          "Haplotype-based variant detection from short-read sequencing"
          arXiv:1207.3907 (http://arxiv.org/abs/1207.3907)

author:   Erik Garrison<EMAIL_ADDRESS>Marth Lab, Boston College, 2010-2014
version:  v1.1.0-56-ga180635

If the help menu doesn't show up, then there's an issue with compilation. I was also able to run a commmand like yours and a VCF file was being written.
I was going to say to try to run  make test from the freebayes directory but I'm noticing a couple of failed test on my end as well, even though freebayes appears to work, so I'm not sure how expected this is.
Maybe try to rebuild and see if it helps, and see if make ends with an error or anything suspicious:
make clean
make
Otherwise, can you paste the version of g++ and make?
$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-16) (GCC)

$ make -v
GNU Make 3.82
Built for x86_64-redhat-linux-gnu
Copyright (C) 2010  Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Do you have bin/freebayes at the end of compilation?
You don't have to make install. That target just copies freebayes and bamleftalign into /usr/local/bin/.  You can add freebayes/bin to you own $PATH, or copy it to a directory in your path that you have write access to. On multiuser systems I always add $HOME/bin and make that the first entry in my path.

I agree. Did you build this from scratch yourself?
On Thu, Feb 1, 2018, 18:30 Manuel Belmadani<EMAIL_ADDRESS>wrote:

That sounds like a compilation issue. Did you run into anything weird
(error or failure messages) during installation (make then make install)?
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What do you mean with "Did you build this from scratch yourself" ?
In regards to the compilation issue I posted the requested Calls and the outputs above.
As mentioned above I used the following commands to install the program
git clone --recursive git://github.com/ekg/freebayes.git
cd freebayes && make
afterwards I exported the PATH to the $PATH variable and was able to call it from every position.
When you agree that there is a compilation issue, what could I do differently during installation/compilation?

afterwards I exported the PATH to the $PATH variable and was able to call it from every position.

This makes it seem that there isn't an issue. I'm confused if you are still having a problem.

Could it be an issue with the input files?
Although I tried different data sets(input files)  I'm still open for any possible explanation?

What happens when you run "make test" in the freebayes directory?

when I call "make test" in the freebayes dirctorys it runs sucessfully through all test:
All tests successful.
Files=4, Tests=42, 26 wallclock secs ( 0.06 usr  0.01 sys + 23.39 cusr  0.63 csys = 24.09 CPU)
Result: PASS
make[1]: Leaving directory '/path/to/freebayes/test'

Good, this mean that the freebayes you built is working fine.
Con you verify that the data is correctly formatted by running another
variant caller or using samtools view on the BAM?
On Thu, Mar 1, 2018 at 12:23 PM LucysWorld<EMAIL_ADDRESS>wrote:

when I call "make test" in the freebayes dirctorys it runs sucessfully
through all test:
All tests successful.
Files=4, Tests=42, 26 wallclock secs ( 0.06 usr  0.01 sys + 23.39 cusr  0.63 csys = 24.09 CPU)
Result: PASS
make[1]: Leaving directory '/path/to/freebayes/test'
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I can use "samtools view" without problems on the bam file. But the file is 699Mb big. Could that be an issue?

The file size is not an issue. You can use any sized file as input to freebayes.
From your freebayes build directory, try running bin/freebayes -f ref.fa file.bam >out.vcf.

then the error still occurs
/programs/freebayes/bin$ ./freebayes -f ../../../genome.fasta ../../../bams/sample.fq.raw.bam >out.vcf
Segmentation fault

Is the input bam sorted? Add --debug and see where it stops.
On Thu, Mar 1, 2018, 14:08 LucysWorld<EMAIL_ADDRESS>wrote:

then the error still occurs
/programs/freebayes/bin$ ./freebayes -f ../../../genome.fasta
../../../bams/sample.fq.raw.bam >out.vcf
Segmentation fault
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here is the --debug output:
bin$ ./freebayes -f ../../../genome.fasta ../../../sample.fq.raw.bam --debug >out.vcf
loading fasta reference ../../../SNP-project/hirise-dovetail-original.fasta
Opening BAM format alignment input file: ../../../SNP-project/fastQ-processradtags/fastQ-proccessradtags-bams/P1-031.fq.raw.bam ...
done
Number of ref seqs: 2025248
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 1 samples in BAM file
Segmentation fault

Is the BAM file sorted? The fact it's called "raw" makes me wonder.

I've been running into an identical issue.
Freebayes appears to be compiled correctly (managed to complete the tutorial), yet every time I run one of my exon capture files I get
loading fasta reference Tg_ExoCap_orfs.fa Opening BAM format alignment input file: A01.clean.bam ...  done Number of ref seqs: 278057 Number of target regions: 0 no sample list file given, reading sample names from bam file found 1 samples in BAM file Segmentation fault: 11
This Segmentation fault error shows up both locally and when I attempt to run it on my institution's cluster.
The sequence files were trimmed using Trimmomatic, and mapped using bwa with only the trimmed pair files. I've tried adding tags with bamaddrg and then re-did the bwa mapping setting read group and sample id there. Files are sorted, indexed, and PCR duplicates are removed with samtools markdup.
I did try the make test command in the freebayes folder and got the following:
11 warnings and 1 error generated. make[2]: *** [src/cdflib.o] Error 1 make[1]: *** [../vcflib/bin/vcfuniq] Error 2 make: *** [test] Error 2
Would really appreciate any insight: if there's a compilation error I don't understand how was I able to run through the test data, or why the same segmentation fault come up on multiple platforms.

I have been working with dDocent for several datasets and have not had any issue with freebayes. On one of my more recent datasets though I keep getting this segmentation fault. I have tried freebayes v1.1.0-54-g49413aa and v1.2.0.
Originally when I used this dataset, I was using a genome assembly from masurka and everything was working well. I have some very long contigs (>1Mbp) though and it is likely that loci on opposite ends of this act differently. Scripting wise, I thought it would be easier to break the contigs in the reference rather than rename the contigs in the vcf file, so using bedtools I broke the contigs in my reference, and with bash I added a number to the end of the name of the contig to make them unique and then remapped my samples (with bwa via dDocent).
e.g.
Original contig: >jcf7180004243889_pilon
New contigs: >jcf7180004243889_pilon_1; >jcf7180004243889_pilon_2
of Original contigs = 154064
of New contigs = 508393
The mapping went fine. Visually I don't see an issue with the reference file, the bam file or the bed file. I can view the bam file with IGV on the reference file, but when I run freebayes I get a seg. fault.
Running the debug command suggested by @ekg results in:
$ ~/programs/freebayes/bin/freebayes --debug -f reference.fasta split.1.bam >out.vcf
loading fasta reference reference.fasta
Opening BAM format alignment input file: split.1.bam ...
 done
Number of ref seqs: 508393
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 32 samples in BAM file
Segmentation fault (core dumped)

file sizes:
172M split.1.bam
220M reference.fasta
0        out.vcf
I don't think this is an installation error or a sorting issue since I have run this dataset previously with dDocent and a different reference and it worked. The two things I see are:

the number of contigs is much higher, but I have other datasets that have a large number and freebayes doesn't have an issue
the naming of the contig is not quite conventional for me. Usually I only have 1 number in the name, but I have added a second number, but I didn't think this should matter.

I would appreciate any help with parsing this issue out. Thank.

I’d remove the second > from the reference header and additionally check
for any unmarked or hidden characters in the reference.
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Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881
Webpage: MarineEvoEco.com
Email:
<EMAIL_ADDRESS>Cell:<PHONE_NUMBER>
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"The most valuable of all talents is that of never using two words when one
will do.” -Thomas Jefferson
On June 13, 2018 at 10:46:56 AM, atfields<EMAIL_ADDRESS>wrote:
I have been working with dDocent for several datasets and have not had any
issue with freebayes. On one of my more recent datasets though I keep
getting this segmentation fault. I have tried freebayes v1.1.0-54-g49413aa
and v1.2.0.
Originally when I used this dataset, I was using a genome assembly from
masurka and everything was working well. I have some very long contigs
(>1Mbp) though and it is likely that loci on opposite ends of this act
differently. Scripting wise, I thought it would be easier to break the
contigs in the reference rather than rename the contigs in the vcf file, so
using bedtools I broke the contigs in my reference, and with bash I added a
number to the end of the name of the contig to make them unique and then
remapped my samples (with bwa via dDocent).
e.g.
Original contig: >jcf7180004243889_pilon
New contigs: >jcf7180004243889_pilon_1; >jcf7180004243889_pilon_2
of Original contigs = 154064 of New contigs = 508393
The mapping went fine. Visually I don't see an issue with the reference
file, the bam file or the bed file. I can view the bam file with IGV on the
reference file, but when I run freebayes I get a seg. fault.
Running the debug command suggested by @ekg https://github.com/ekg
results in:
$ ~/programs/freebayes/bin/freebayes --debug -f reference.fasta
split.1.bam >out.vcf
loading fasta reference reference.fasta
Opening BAM format alignment input file: split.1.bam ...
done
Number of ref seqs: 508393
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 32 samples in BAM file
Segmentation fault (core dumped)
file sizes:
172M split.1.bam
220M reference.fasta
0 out.vcf
I don't think this is an installation error or a sorting issue since I have
run this dataset previously with dDocent and a different reference and it
worked. The two things I see are:

the number of contigs is much higher, but I have other datasets that
have a large number and freebayes doesn't have an issue
the naming of the contig is not quite conventional for me. Usually I
only have 1 number in the name, but I have added a second number, but I
didn't think this should matter.

I would appreciate any help with parsing this issue out. Thank.
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"I’d remove the second > from the reference header and additionally check
for any unmarked or hidden characters in the reference." -jpuritz

There isn't actually two > in the reference header. That was just an example of how the reference contig name was split. I have not found any hidden characters.
reference file output:
>jcf7180004243889_pilon_1
AATTTGTTTACTCGGGTTAGCTCGAATGCTAGCTTTGACAGTTAGCCTTCAGTGTTGCTTTGCTAACGGCCTTCCACCCGGTCGGAACGTACAAATATCTATAACTGCACAGTCATTCCTTGACATACCTTTTTATGATAAGCTTTCTTTGGCGCTCCAGTCCGATAGATTCCTTCATTTTGTCCATAATTAGCTGTTTTAACAAGTTTAAGGGGCTATTGTTTCTCGAAAACACAGACGATATCGTCTGAGCACACCGGAGAGGGCCTCCAAAATGTCTCTCTGGTTTGTAAGGAGCTCGGTGATTGGTCCGTTTCAGAAAACCAGGGGGCTCGATTCATTTAAGGGCGTTGCCTGGCAACACTACTGATAGAAGCTCCAGTCTGTAGAACCACAGCATAGCTGATTACGTAATATGTTTACCAAGATGTTGTTCCATGTTTACCCTGCAATCACTCAAAAAGGCGAGGCTACAACAATATGGTATCATCATATAATTTCTCACAACAATATTTATTTTAAGTAATAACATCATAACAACATAACATAACATATAATATT
>jcf7180004243889_pilon_2
CGGTGAAAGCGGGTCTCCTCAGCAGAGAGCCCCTTGTGAGGAGAATACCCAGCGTCTGTCAGGCCTGCCTGGTGCTCAAACTTCTGTAGATTCTCATGTGTCTGCTCTAAGTGAAGATGGAGATACAGTTGACAGTGGATATAAAATTAGTTAATGTTTTAATATGCTGCCCTATATTGTTGCTCGCTGATACTCTGCACTGAATACTGTTCATCCATATTTGGAAATCAAGGCAGCAGCTATTTAGACAATCAGCGATAACGCTTGCACAATTCTGTCACATGTGGCCTTGTGAAGGAATT

Hannes,
The message you posted indicates that there were no samples found in the BAM file. Is this right? Could that be a source of your error? I don't know if that should cause a seg fault.

Hannes,
The message you posted indicates that there were no samples found in the BAM file. Is this right? Could that be a source of your error? I don't know if that should cause a seg fault.

It is true, when mapping I did not assign read groups and so freebayes does not find "samples". But this did not stop freebayes from readily processing a similar file (albeit with fewer contigs).
bash-4.2$ ~/git_repos/freebayes/bin/freebayes --debug -f ~/assemblies/Tetraploid/EuphrasiaNBER_Pacbio_Canu.unitigs.fasta /media/Euphrasia_backup/ArcCanuMappings/ArcIll_sorted_dedupped.bam | head
loading fasta reference /localdisk/home/hbecher/assemblies/Tetraploid/EuphrasiaNBER_Pacbio_Canu.unitigs.fasta
Opening BAM format alignment input file: /media/Euphrasia_backup/ArcCanuMappings/ArcIll_sorted_dedupped.bam ...
 done
Number of ref seqs: 28582
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 0 samples in BAM file
##fileformat=VCFv4.2
##fileDate=20181028
##source=freeBayes v1.2.0-2-g29c4002
##reference=/localdisk/home/hbecher/assemblies/Tetraploid/EuphrasiaNBER_Pacbio_Canu.unitigs.fasta
##contig=<ID=tig00000001,length=26900>
##contig=<ID=tig00000002,length=33549>
##contig=<ID=tig00000003,length=39058>
##contig=<ID=tig00000004,length=27392>
##contig=<ID=tig00000005,length=107765>
##contig=<ID=tig00000006,length=341136>

Would one of you please provide a minimal test case which reproduces the
segfault?
On Sun, Oct 28, 2018, 19:37 Hannes Becher<EMAIL_ADDRESS>wrote:

Hannes,
The message you posted indicates that there were no samples found in the
BAM file. Is this right? Could that be a source of your error? I don't know
if that should cause a seg fault.
It is true, when mapping I did not assign read groups and so freebayes
does not find "samples". But this did not stop freebayes from readily
processing a similar file (albeit with fewer contigs).
bash-4.2$ ~/git_repos/freebayes/bin/freebayes --debug -f ~/assemblies/Tetraploid/EuphrasiaNBER_Pacbio_Canu.unitigs.fasta /media/Euphrasia_backup/ArcCanuMappings/ArcIll_sorted_dedupped.bam | head
loading fasta reference /localdisk/home/hbecher/assemblies/Tetraploid/EuphrasiaNBER_Pacbio_Canu.unitigs.fasta
Opening BAM format alignment input file: /media/Euphrasia_backup/ArcCanuMappings/ArcIll_sorted_dedupped.bam ...
done
Number of ref seqs: 28582
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 0 samples in BAM file
##fileformat=VCFv4.2
##fileDate=20181028
##source=freeBayes v1.2.0-2-g29c4002
##reference=/localdisk/home/hbecher/assemblies/Tetraploid/EuphrasiaNBER_Pacbio_Canu.unitigs.fasta
##contig=<ID=tig00000001,length=26900>
##contig=<ID=tig00000002,length=33549>
##contig=<ID=tig00000003,length=39058>
##contig=<ID=tig00000004,length=27392>
##contig=<ID=tig00000005,length=107765>
##contig=<ID=tig00000006,length=341136>
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Dear Erik
Found the same issue. A segmentation fault occurring when calling SNPs against a transcriptome (no genome available). Read groups are present, bam files have been sorted and duplicates marked.
Specifying a few or a single contig as a region didn't help.
Our same installation of freebayes has been working through 315 bams and a genomic reference without complaint.
The command:
$ freebayes -r contig0_c1550_g31432_i1:0-4545 -f /path/to/hedin_transcriptome_v2.fasta -L /path/to/faba_bams.txt --debug --vcf /path/to/all_faba_SNPs1.vcf
yields:
"
Opening output file: /path/to/all_faba_SNPs1.vcf ...
loading fasta reference /path/to/hedin_transcriptome_v2.fasta
Opening 13 BAM format alignment input files
done
Number of ref seqs: 200293
will process reference sequence contig0_c1550_g31432_i1:0..4545
Number of target regions: 1
no sample list file given, reading sample names from bam file
found 13 samples in BAM file
Segmentation fault
"
and an empty output file.
Test case:
I replicated the issue with the same ref but my two smallest of bam files, is there a way of transferring ~ 7Gb of files to you in private so you look at it?
Regards,
A. Webb

That'd be good!

An update on this. Getting the same issue on version v1.2.0-4-gd15209e. Happy to provide a small reproducible case if needed.
loading fasta reference CassavaPangenomev0.1.fa
Opening BAM format alignment input file: sorted_bam_test ...
done
Number of ref seqs: 231785
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 25 samples in BAM file
Segmentation fault

Yes, I definitely need an example that reproduces this.
On Thu, Apr 11, 2019, 16:48 bacms2<EMAIL_ADDRESS>wrote:

An update on this. Getting the same issue on version v1.2.0-4-gd15209e.
Happy to provide a small reproducible case if needed.
loading fasta reference CassavaPangenomev0.1.fa
Opening BAM format alignment input file: sorted_bam_test ...
done
Number of ref seqs: 231785
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 25 samples in BAM file
Segmentation fault
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First,  I also encountered this issue when I execute
freebayes -f ref.fa aln.bam >var.vcf
It shows "Segmentation fault",and I find lots of solutions posted were about "install freebayes", so I choose to use a docker to avoid "install issue".
Second, In the docker ,I also get "Segmentation fault",when I get into docker's bash and execute
**ulimit -s 81920** to Expand stack space ten times,then  execute freebayes -f ref.fa aln.bam >var.vcf Successfully.
This means stack limit is the key to solve the "Segmentation fault". I recommend anyone who encounter this problem should try ulimit -s though you don't use docker.
At last , via docker I execute
docker run -ti --ulimit stack=8277716992:8277716992 -v /media:/media ctomlins/freebayes_polish freebayes -f /media/test.fa /media/test.bam >/media/test.bam.vcf
successfully run freebayes.
If this can help anyone ,it's my pleasure.

That's interesting. Segfaults can be caused by several things. This does
suggest that there may be a problem with recursion running out of control,
and I can investigate possible causes.
On Wed, Jun 19, 2019, 16:05 TiMaCi<EMAIL_ADDRESS>wrote:

First, I also encountered this issue when I execute
freebayes -f ref.fa aln.bam >var.vcf
It shows "Segmentation fault",and I find lots of solutions posted were
about "install freebayes", so I choose to use a docker
https://hub.docker.com/r/ctomlins/freebayes_polish to avoid "install
issue".
Second, In the docker ,I also get "Segmentation fault",when I get into
docker's bash and execute
ulimit -s 81920 to Expand stack space ten times,then execute freebayes
-f ref.fa aln.bam >var.vcf Successfully.
This means stack limit is the key to solve the "Segmentation fault". I
recommend anyone who encounter this problem should try ulimit -s though
you don't use docker.
At last , via docker I execute
docker run -ti --ulimit stack=8277716992:8277716992 -v /media:/media
ctomlins/freebayes_polish freebayes -f /media/test.fa /media/test.bam

/media/test.bam.vcf
successfully run freebayes.

If this can help anyone ,it's my pleasure.
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I actually managed to sort the problem. There is a limit on the number of reference sequences you can have on your bam file. I am assuming this is probably related to the BAM library using a variable that is too small to store this number but not followed through into it to confirm. But splitting the bam files and the headers manually by chromosome solved the problem

What's the limit? Perhaps the problem is that the header is stored on the
stack, and not that the number in the library is small. I'd be surprised if
it were less than 32 bits, which is an awful lot of reference sequences.
On Wed, Jun 19, 2019 at 7:00 PM bacms2<EMAIL_ADDRESS>wrote:

I actually managed to sort the problem. There is a limit on the number of
reference sequences you can have on your bam file. I am assuming this is
probably related to the BAM library using a variable that is too small to
store this number but not followed through into it to confirm. But
splitting the bam files and the headers manually by chromosome solved the
problem
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I got the same issue of segmentation fault with freebayes version 1.3.1-17-gaa2ace8.
I used freebayes 2 years ago with dDocent and it worked fine on the same data.
I installed my freebayes into a container : https://singularity-hub.org/collections/3319
 git clone --recursive https://github.com/ekg/freebayes.git
    cd freebayes
    make
    cd bin
    chmod +x *
    cp -f * /usr/local/bin
    cd ..
    cd ./vcflib/
    make
    chmod +x ./bin/*
    cp -f ./bin/* /usr/local/bin
    cd ../..

a command to test
singularity exec seaconnect.simg freebayes --debug -f 04-ddocent/mullus/reference.fasta 04-ddocent/mullus/C100_M100i10E2-RG.bam > ou.vcf

and the results : (same for all my others .bam files)
loading fasta reference 04-ddocent/mullus/reference.fasta
Opening BAM format alignment input file: 04-ddocent/mullus/C100_M100i10E2-RG.bam ...
 done
Number of ref seqs: 361602
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 1 samples in BAM file
Erreur de segmentation

reducing the number of scaffolds (ref seqs) solved the problem.

Hello all,
After using FB for a while without any problems, but recently I am having the same problem described here:
loading fasta reference 3_Tms_b3v08.fasta
Opening 46 BAM format alignment input files
 done
Number of ref seqs: 189023
Number of target regions: 0
no sample list file given, reading sample names from bam file
found 46 samples in BAM file
Segmentation fault

And the command line:
 freebayes -f 3_Tms_b3v08.fasta --bam-list trim3bam --min-mapping-quality 30 --min-coverage 5 --debug > Tms.trim3.fb.vcf
I re-sorted the bam files, re-indexed the fasta, increased memory, and tried calling SNPs with only 2 of the bams and still get the same "Segmentation fault"
I ran FB on another dataset (with a different reference genome) and it ran without problems.
Did any of you find a solution (apart from reducing the number of scaffolds in the ref genome)?
Many thanks!!

I forgot to mention that I am using version 1.2.0 (installed as a model in my server), but I also get the same error if I use the most recent FB version.
It would be great if anyone had some suggestion or could help...
Thanks!

Hi SusanaFreitas,
If you are running on linux, have you tried gagayuan's suggestion of changing the ulimit (ulimit -s 81920)? I found that if I have a very large number of contigs in my reference fasta file, then increasing this limit would allow me to run freebayes.
Good luck!

yey, it works!
Sorry for not having tried it before, I wasnt sure how to add that option to my sbatch script. I tried it with srun and I didnt get the segfault (and my output started pilling up SNP calls).
I am still waiting to see if when I add the option on my sbatch script it works, but I cant see why it wouldnt...
Thanks again!!
#SBATCH options(...)

srun -p normal -t 2:00:00 --cpus-per-task=4 --mem=10GB --pty bash
ulimit -s 81920
freebayes -f 3_Tms_b3v08.fasta --bam-list trim3bam --min-mapping-quality 30 --min-coverage 5 --debug > Tms.trim3.fb.vcf
FB v1.3.1-19-g54bf409


Camera only north option is available

Please check if your issue is not a duplicate by searching existing issues
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:

Go to '...'
Click on '....'
Scroll down to '....'
See error

Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
Environment (please complete the following information):

OS: [e.g. Windows, Ubuntu, macOS]
RuneLite version: [e.g 1.4.6]
Launcher version: [e.g 1.5.2]

Additional context
Add any other context about the problem here, e.g. logs. Your client logs can usually be found in
C:\Users\<your_user_name>\.runelite\logs on Windows and ~/.runelite/logs on Linux and macOS.

 Is it by chance possible to make it possible to
change angles with a simple click? This would be great if you want to play
on windows touchscreen devices
Op wo 5 feb. 2020 om 05:06 schreef ThePharros<EMAIL_ADDRESS>
it should work if you right click on the compass
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What if the Camera plugin was extended so clicking the compass quickly in succession (within a configurable reset time) would cycle between N S E and W, so players could double tap compass to look south, and after timeout tapping compass would again return to north?
I have this partially implemented. Could also do a simple config option dropdown for default compass direction, but I find the multiple tapping would be more useful. Touch players could make the timeout as long as they need.


Search and sharing options

What feature or improvement do you think would benefit Files?

There is no information about the file search status in the program. Immediately after starting the search for files, the word "search results" appears in the directory path bar. It is not known whether the search is over or whether it is still necessary to wait for the next results.
Besides, I don't know if in the search results window it is possible to add a column where the file / folder is located. This is useful when you want to browse the list and find out where the files / folders are, and especially when you can sort the list by location on the disk or disks.
I also didn't find advanced / extended search, so I can't search for files within their size or date range.
There is no sharing option in folder / drive properties.
After clicking on the left bar icon it is not possible to display all disks or all library folders but you have to decide (drop-down menu) on one disk or folder. This makes it impossible, for example, to check a free space on all disks. You have to use the "home" icon, which is not intuitive for me.

Requirements

Add search progress information
Add more columns like path (in search results), movie length, resolution of image files, bitrate of music files
Add extended search options
Add sharing options
Add view of all libraries, disks (with information about their size and free space) just like on the main page.

Files Version
Wersja: <IP_ADDRESS>
Windows Version
Windows 10 Pro 22H2 19045.2130
Comments
Without these functions, I am often forced to use the default windows application or Total Commander, and I hope that your great idea for the appearance, arrangement of elements, customization options and of course tabs will allow me to use only your program.
BTW this is the first time i'm using github to ask for extra features. I would like to thank you for a great job on this project and wish you perseverance and creativity in the future.

Thanks for the feedback, please make them separate issue in future.

There is a loading indicator in the tab and performance improvements to it are being tracked here #6825 when complete search would hopefully be quick or instant.
 If it not what you mean please say.
The home button has a drive widget showing all drives and free/total space

Great! I'm not familiar with GitHub. I will wait for update.    Pozdrawiam  Rafał Kotarba
    Dnia 8 listopada 2022 07:03 Josh-65<EMAIL_ADDRESS>napisał(a):

Thanks for the feedback, please make them separate issue in future.
There is a loading indicator in the tab and performance improvements to it are being tracked here  github.com #6825  when complete search would hopefully be quick or instant.
 If it not what you mean please say.
The home button has a drive widget showing all drives and free/total space
—  Reply to this email directly,  github.com view it on GitHub , or  github.com unsubscribe .  You are receiving this because you authored the thread. Message ID:  <files-community/Files/issues/10431/1306678573 @ github . com>


A working setup of Javalin 3.11.2 with Pac4J 4.0.3 breaks once Pac4J is upgraded to 4.1.0

When I upgrade the Pac4J to version 4.1.0 the ctx.body() and ctx.formParamMap() become empty (form submit body is not received by the handler although I see the form data in the chrome console in the body section).
The security is working fine, the path parameters are correct, the handler of the endpoint is called, its just the ctx.body() is empty.
I have made a compare between de dependencies of Pac4J version 4.0.3 and 4.1.0 and downgraded them in the pom to the versions used in 4.0.3 or upgraded them to the latest versions but that did not help.
List of dependencies I modified in the pom:
        <dependency>
            <groupId>org.pac4j</groupId>
            <artifactId>pac4j-core</artifactId>
            <version>4.1.0</version>
        </dependency>
        <dependency>
            <groupId>org.pac4j</groupId>
            <artifactId>pac4j-oidc</artifactId>
            <version>4.1.0</version>
        </dependency>
        <!-- Force downgrade the jackson from 2.11.2 to 2.11.0 and the nimbusds did not help, upgrading to the latest version did not help too -->
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-core</artifactId>
            <version>2.11.3</version><!{1}** 4.0.3: 2.11.0, 4.1.0: 2.11.2 **{1}>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-annotations</artifactId>
            <version>2.11.3</version><!{1}** 4.0.3: 2.11.0, 4.1.0: 2.11.2 **{1}>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-databind</artifactId>
            <version>2.11.3</version><!{1}** 4.0.3: 2.11.0, 4.1.0: 2.11.2 **{1}>
        </dependency>
        <dependency>
            <groupId>com.nimbusds</groupId>
            <artifactId>oauth2-oidc-sdk</artifactId>
            <version>8.23.1</version><!{1}** 4.0.3: 8.9, 4.1.0: 8.22 **{1}>
            <scope>runtime</scope>
        </dependency>
        <dependency>
            <groupId>com.nimbusds</groupId>
            <artifactId>content-type</artifactId>
            <version>2.1</version><!{1}** 4.0.3: 2.0, 4.1.0: 2.1 **{1}>
        </dependency>
        <dependency>
            <groupId>com.nimbusds</groupId>
            <artifactId>nimbus-jose-jwt</artifactId>
            <version>8.20.1</version><!{1}** 4.0.3: 8.19, 4.1.0: 8.20.1 **{1}>
        </dependency>

I made a code compare between Pac4J versions 4.0.3 and 4.1.0 but I did not find something that might cause a problem.
I wonder if any of you has experienced such an issue or has a pointer to what might be the cause and of course how to fix it.

The Pac4J version 4.2.0 has been released couple of days ago and it resolves the above issue.


Assertion `args[1]->IsString()' failed error while trying to rebuild the "react-content-query-webpart"

Use the following form to submit an issue only if it's related to samples in this repo. If you have an issue related to the SharePoint Framework or its documentation, please submit the issue at https://github.com/SharePoint/sp-dev-docs/issues/new. This will help us respond to your issue faster.

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Category

[ ] Question
[x ] Bug
[] Enhancement

Hi,
I am trying to rebuild the webpart here "https://github.com/SharePoint/sp-dev-fx-webparts/tree/master/samples/react-content-query-webpart" but getting the error (Please see the attachment).
I tried to run "npm install --unsafe-perm=true" but it start the gulp --clean but getting lot of errors,
Could you please suggest how to build this webpart. Thanks for the help.
-Devendra

Quick update: When I tried from another machine its started working..

I am having the same issue. Any updates on this?

I experience same issue when try to run "gulp serve" for react-file-upload.
sigh... I am getting various kind of error try to setup each samples. I think entire sample library is out-dated.


Create Matrix-Merlin

Description:
Describe your changes.
Related issue:
Add link to the related issue.
Check list:

[ ] Mark if documentation changes are required.
[ ] Mark if tests were added or updated to cover the changes.

Closing this PR as it seems like spam


Add support for using the gRPC-JSON transcoder in envoy

Envoy supports mapping gRPC services to RESTful ones (https://www.envoyproxy.io/docs/envoy/latest/configuration/http_filters/grpc_json_transcoder_filter). Please add support to pass the additional configuration options from ambassador to envoy.
The minimal required options are proto_descriptor_bin and services

In envoy 1.6.x there will be support for inline protobuf descriptors in configuration files (proto_descriptor_bin)
https://www.envoyproxy.io/docs/envoy/latest/api-v2/config/filter/http/transcoder/v2/transcoder.proto.html#envoy-api-msg-config-filter-http-transcoder-v2-grpcjsontranscoder

See also #456.

+1

I'm closing this in favor of #456

So this means grpc streaming is also supported. What is the roadmap for grpc support?

@richarddli this issue should be re-opened as #456 added support for gRPC HTTP/1.1 bridge and gRPC-Web but not for gRPC-JSON transcoder which is distinct and requested in this issue and not in any others I can find. The reason I'm here is we now have also have a need for this.

@ctoomey thanks! I'll reopen -- we'd welcome a PR for this!

is there any update?

@npuichigo I don't about an update here. But what I will say is that you might prefer using the envoy http2bridge. Thats what lift uses internally and it works fine. the http2bridge is a simple and robust solution that actually works. If you need details on suing it let me know.

Can it be used to transcode a streaming grpc response to a chunked http response?

I see its marked stale but the milestone is set to future cycle. Is team really looking forward to enable/support this?


DateTimePicker defaults to current minutes and seconds rather than 00

Duplicates

[X] I have searched the existing issues

Latest version

[X] I have tested the latest version

Current behavior 😯
If you go to https://mui.com/components/date-time-picker/#api and try selecting a day on the "Clear Initial State" input you will notice that the minutes are initially set to the minutes of the current hour. The seconds of the Date value will also be set to the current seconds of the minute (althought that is not visible unless you inspect the value object).
This is almost never desired and breaks naive integrations with libraries such as React Final Form or React Hook Form.
Also, if you have set minutesStep={5} it will not be respected.
A similar issue has already been addressed on the TimePicker in #24887 but was not fixed for DateTimePicker (and maybe even DatePicker and DateRangePicker?).

This is also present within DatePicker, minutes and seconds are being set instead of 00


eip712_encode_hash encode string bytes and string uint256

Closes #424

Add test for string uint
Add test for string bytes

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
3 unchanged lines in 1 file lost coverage.
Overall coverage decreased (-0.08%) to 90.233%

Files with Coverage Reduction
New Missed Lines
%

gnosis/util/util.py
3
66.67%

Totals

Change from base Build<PHONE_NUMBER>:
-0.08%

Covered Lines:
3520

Relevant Lines:
3901

💛  - Coveralls


tried to pip install mujoco-mjx on MacBook , I got the error:

tried to pip install mujoco-mjx on MacBook , I got the error:
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for mujoco
Failed to build mujoco
ERROR: Could not build wheels for mujoco, which is required to install pyproject.toml-based projects
Any suggestions ? appreciate it
Originally posted by @Alpslee in https://github.com/google-deepmind/mujoco/discussions/1101#discussioncomment-7317317

Is this an M1 mac or x86? We test on both.
Can you try it in a clean venv?
python3 -m venv /tmp/mujoco
. /tmp/mujoco/bin/activate
pip install mujoco-mjx


undefined method `analytics'

Hello Guys,
I installed the gems
gem 'chartkick'
gem 'chartable'

in my Gemfile and bundle install & also bundle update
And in my controller  I added this code
@users =User.analytics(:daily)
In my local laptop every thing going well, But when I deployed it to the server I found its giving me the below issue.
NoMethodError (undefined method analytics for #<User::ActiveRecord_Relation:0x000000070f3708>):
BTW, I checked the gems in my Gemfile and find them installed on the server.
How I can fix it?!

@AstmDesign Hello, can you post the code that is causing this error? You posted the case with the User model but you have an error for Content

Hi @rubyhero,
I copied the error from another page, I edited the post.

@AstmDesign Thank you. What Ruby and Rails version do you use?

@rubyhero :
This is my server ruby version:  ruby 2.2.1p85 (2015-02-26 revision 49769) [x86_64-linux]

@AstmDesign can you add also your Rails version? It will help me to debug the issue

@rubyhero , it's the  Rails <IP_ADDRESS>, I found It the same version on my local laptop also.
Maybe this is not the issue because the Gem working well with me locally

@rubyhero, This is all the versions on server
$gem -v
2.6.14
$bundle -v
Bundler version 1.16.3
$ruby -v
ruby 2.2.1p85 (2015-02-26 revision 49769) [x86_64-linux]
$rails -v
Rails <IP_ADDRESS>

@AstmDesign thank you, I will take a look at it during this weekend

@AstmDesign I tried to reproduce this issue with the same setup as you have but the only way to reproduce this on the development is to wrap the gem definition into production group in the Gemfile:
group :production do
  gem 'chartable'
end

are you sure you didn't do the same but in the development group that's why it doesn't work in the production environment?

HI @rubyhero,
This issue makes me crazy and decided to discover why the server doing something like that?!
so checked the server today & upgraded the ruby version and the gems and the bundle and unicorn, notes that the unicorn still using the old ruby version so restarted it again and deployed new version then found it working well.
Many thanks for you @rubyhero, Now I'm finally enjoying myself by using your amazing Gem.
Regards


Make sortText on completions be enum-typed

We've had a couple issues in the past where the value of a member of the SortText enum has changed when adding a new member. This has caused bugs in editors that use TSServer.
Here, we ensure that the sortText property of completion entries is specifically typed with the SortText enum, so that it's properly represented in the protocol.

So if VS relies on specific string-numbers for the sort text, does that mean that VS/vscode couldn't handle LS plugins that provide arbitrary alphanumeric content for the sortText? I always assumed the content was an arbitrary relative "string to sort by".

For reference: The angular language service plugin definitely passes full on arbitrary strings. The sort they map into sortText is the full alphanumeric name of a thing.

@weswigham VS code uses string sorting logic: https://github.com/microsoft/vscode/blob/9f474febfee5330f7a9a7456862ef73d0b6f0bf5/src/vs/editor/contrib/suggest/suggest.ts#L229
So you could use 'a', 'b', 'c', ... instead of '0', 1, ...

Right - all that matters is that whoever is sending the sortText is internally consistent in that case. @uniqueiniquity how is it used elsewhere? And why is it not used as an opaque string in those cases? As I've pointed out - the angular LS plugin does make use of it as not-internal-numbering-scheme, so this'd definitely break it.

agree with @weswigham here.. this needs to be string so that any string value can be passed in.. Its enum in services layer internally so that it can easily be labeled instead of making them "1" or "2"

@weswigham @sheetalkamat we don't generally care about the text - we specifically care about the JavaScriptIdentifiers entries, as since they're basically guesses, we want to handle those a little differently than the others. In all other cases, interpreting it as "a string to sort by" is fine.
My goal here is to either prevent these values from being changed or, if that's not feasible, to at least have a way to get notified when they get changed. I'd also be open to an additional property saying "this entry is a js-only guess" if that's preferred.

I think making a property for js-only guess is better than having enum for the sorting text

Superseded by #36063.


Fast way switch picks

Contributing guidelines

[X] I have read CONTRIBUTING.md
[X] I have read CODE_OF_CONDUCT.md

Module(s)
mini.pick
Description
Open buffers pick and input fuzzy text, but not found my want result.
I need exit buffers pick and open files pick, and re input fuzzy text.
Any way shortcut or actions for switch between picks?

That's a very nice suggestion! Thank you!
I don't think having this built-in is undoubtedly a good thing (built-in mappings is already quite crowded). But it can be implemented via custom action. For example, something like this:
local switch_picker = function()
  local ok, picker_name = pcall(vim.fn.input, 'Picker name: ')
  if not ok or MiniPick.registry[picker_name] == nil then return end

  local query = MiniPick.get_picker_query()
  MiniPick.stop()

  vim.cmd('Pick ' .. picker_name)
  local transfer_query = function() MiniPick.set_picker_query(query) end
  vim.api.nvim_create_autocmd('User', { pattern = 'MiniPickStart', once = true, callback = transfer_query })
end

require('mini.pick').setup({
  mappings = {
    switch = { char = '<C-z>', func = switch_picker },
  },
})

With this you can press <C-z>, type a picker name you want to switch to (should be present in registry, i.e. executable via :Pick command), press <CR>, and it should switch picker while transferring the current query.

Closing as "doable but seems to be too much to be built-in". Although it is a very good candidate for a possible future wiki entry.

Input picker name is slow. It would be better to open a picker for selecting from registry and retain the previous query.

Input picker name is slow. It would be better to open a picker for selecting from registry and retain the previous query.

This can also be achieved because registry is available to the user. I'd suggest either using MiniPick.ui_select() to get the registry entry name or supply completion to  vim.fn.input().

Input picker name is slow. It would be better to open a picker for selecting from registry and retain the previous query.

This can also be achieved because registry is available to the user. I'd suggest either using MiniPick.ui_select() to get the registry entry name or supply completion to  vim.fn.input().

Thanks for the suggestion.
  local switch_picker = function()
    local query = MiniPick.get_picker_query() or {}
    MiniPick.stop()
    MiniPick.ui_select(vim.tbl_keys(MiniPick.registry), {
      prompt = 'Switch picker with query: ' .. table.concat(query, ''),
    }, function(picker)
      vim.cmd('Pick ' .. picker)
      local transfer_query = function() MiniPick.set_picker_query(query) end
      vim.api.nvim_create_autocmd('User', { pattern = 'MiniPickStart', once = true, callback = transfer_query })
    end)
  end
  require('mini.pick').setup({
    mappings = {
      switch = { char = '<C-k>', func = switch_picker },
    },
  })


Add Autobalancing

Drive backward at full speed until the gyro detects the robot is on the charge station (the robot is no longer level)
Backup slowly until the gyro becomes level again (engage brake mode)

code exists, never worked in reality. The slower part didn't activate at the end


Lorem ipsum detector

Crawler or other.. why not have a heuristic to fail when "lorem ipsum" on page?

What would be the use case?

The use case would be to check site for accidentally leaving lorem ipsums on some place.

I agree that it is good check, but is that something which belongs to core library or would it better live as extension?

There are several heuristical (or”common” pattern based) tests to make. Maybe templating might be better place for this


Remove absurdity

Are you sure we'll never inherit from it? Why not just remove throw()?

If we don't need dynamic polymorphism right now, I don't see a reason not to remove it. This is in details so backward-compatibility is not required.

Are you sure we'll never inherit from it? Why not just remove throw()?

std::exception <- std::logic_error <- ArborX::SearchException
std::exception has virtual constructor


[MenuItem] Remove fixed height

[x] I have followed (at least) the PR section of the contributing guide.

Closes #6216
Breaking change
Remove the fixed height of the menu Item. The padding and line-height are used by the browser to compute the height.

@KyruCabading It's a great first pull request on Material-UI 👌🏻. Thank you for working on it!

Thank you @oliviertassinari! Hope to be able to contribute more in the future. Thank you to you and the mui-org team for creating material-ui!

We would love that 🙏


bind_zones_play' is undefined

I have insert file group_vars/dns-server/bind with zone and file group_vars/dns-server/dnssec with keys
TASK [bind : create zone folder] ******************************************************************************************
task path: /GIT/nnxx-bind-server/roles/bind/tasks/zones.yml:6
fatal: [dns.nnxx.ninux.org]: FAILED! => {"msg": "'bind_zones_play' is undefined"}

What could be the problem?

I add file in group_vars with name different from bind .... merge only file bind and dnssec


Add process_model as a submodule

Re-add the process_model code as a submodule to this repo.  This should include the necessary tests that take an example model, run process_model on it, and then compile the resulting output, linking it against this library.

Looking to review, but I can only see the adding of process_model as a git submodule?
Are there more commits to come, or did you want review on the code in the submodule?

More commits to come.


Inner Classes fail to properly encode

I have a class Foo with an inner class (within Foo) named Bar, within module 'm'. When encoding the object, this is what would show up:
{"py/object": "m.Bar" ...
This causes decoding to fail, as a dictionary will be created instead of the object.
Perhaps this is what should appear in the json?
{"py/object": "m.Foo.Bar" ...

This is already supported, but unfortunately it only works under python3, where we have a __qualname__ identifier provided by the language.
Without that, it's not really possible to implement support for these classes.  You can workaround it by making the class available at module scope, through an alias:
class Foo(object):
    class Bar(object):
        ...

Bar = Foo.Bar

The Bar = Foo.Bar workaround makes it work on python2, and is not needed on python3.

I just realized we have a really simple workaround, better than exposing a new global symbol (which might clash with existing symbols at module scope).
Instead of doing that, provide the __qualname__ yourself for python2, and jsonpickle will pick that up.
class Foo(object):
    class Bar(object):
        __qualname__ = 'Foo.Bar'

Please try that out.  The only downside is that you might want to remove that line in the future if things ever move over to python3 fully.
jsonpickle itself will remain 2+3 compatible for the foreseeable future.

Thanks davvid! Your reply pointed me in the right direction to solve my own issue.
This method turns out to be a good workaround if you move the location of your classes but still want to decode old files for backwards compatibility.
class LocalClass:
    ... #implementation

class _LocalClass(LocalClass):
    __module__ = "old.location.of"
    __qualname__ = "LocalClass"

data = jsonpickle.decode(json_data, classes=[_LocalClass])


Te Adapters floods the DB with new states with no reason

Describe the bug
The Adapter creates Thousands of states in the DB with absolut rubbish.
To Reproduce
I just configured the Adapter to watch my two Pi-Holes. Everything works fine until my iobroker admin-Interface starts suddenly to become slower and slower
Screenshots & Logfiles
host.ioBroker Counted 2 instances of pi-hole
host.ioBroker Counted 1 meta of pi-hole
host.ioBroker Counted 1 adapter for pi-hole
host.ioBroker Counted 44 channels of pi-hole
host.ioBroker Counted 80417 states of pi-hole
host.ioBroker Counted 29 states of system.adapter.pi-hole
host.ioBroker Counted 80413 states (io.pi-hole.*) from states
host.ioBroker Counted 24 states (system.adapter.pi-hole.*) from states

Versions:

Adapter version: Latest
JS-Controller version: 3.1.6
Node version: 12.18.3
Operating system: Raspbian GNU/Linux 10 (buster)

Hello Keno,
I can not confirm this issue in my installation. How many seconds did you enter in the admin interface of the adapter to pull new values?
Where did get the logs from? In my installation a lot of adapters are spamming the events log, too. This log provides each change of states and objects. So every 60 seconds (standard settings) for every state of the pi-hole adapter.

This was the deinstallation Log. The Maul deinstallation would take round about 12 Hours so I decided to copy the objects and states.json to my Mac and edit them manually to remove those entries. After that the DB was "only" 4MB left in size compared to 30MB. After the manual removing I could relogin to the admin-Adapter very quick and deinstalled the Adapter within the Admin interface to remove some left entries in the DB.
The waiting time to enter the admin Interface was near infinite. I left the tab open for round about 15 Minutes without any result. Only saw the loading bar.
I will read out my backup and send some entries out of the states/objects.json in a few minutes

Here are some states created by the pihole adapter. Those were created round about 80000 times in one file
{"val":"�","ack":true,"ts":1599955452725,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287265},"pi-hole.0.version.928":{"val":"$","ack":true,"ts":1599955452726,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287266},"pi-hole.0.version.929":{"val":"Q","ack":true,"ts":1599955452726,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287266},"pi-hole.0.version.930":{"val":"\u0018","ack":true,"ts":1599955452726,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287266},"pi-hole.0.version.931":{"val":"�","ack":true,"ts":1599955452726,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287267},"pi-hole.0.version.932":{"val":"\u0015","ack":true,"ts":1599955452726,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287267},"pi-hole.0.version.933":{"val":"�","ack":true,"ts":1599955452727,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287267},"pi-hole.0.version.934":{"val":"�","ack":true,"ts":1599955452727,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287267},"pi-hole.0.version.935":{"val":"!","ack":true,"ts":1599955452727,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287268},"pi-hole.0.version.936":{"val":"�","ack":true,"ts":1599955452727,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287268},"pi-hole.0.version.937":{"val":"g","ack":true,"ts":1599955452728,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287268},"pi-hole.0.version.938":{"val":"q","ack":true,"ts":1599955452728,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287268},"pi-hole.0.version.939":{"val":"�","ack":true,"ts":1599955452728,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287269},"pi-hole.0.version.940":{"val":"_","ack":true,"ts":1599955452728,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287269},"pi-hole.0.version.941":{"val":"�","ack":true,"ts":1599955452728,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287270},"pi-hole.0.version.942":{"val":"w","ack":true,"ts":1599955452729,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287270},"pi-hole.0.version.943":{"val":"�","ack":true,"ts":1599955452729,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287270},"pi-hole.0.version.944":{"val":"`","ack":true,"ts":1599955452729,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287270},"pi-hole.0.version.945":{"val":"�","ack":true,"ts":1599955452729,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287271},"pi-hole.0.version.946":{"val":"l","ack":true,"ts":1599955452729,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287271},"pi-hole.0.version.947":{"val":"�","ack":true,"ts":1599955452730,"q":0,"from":"system.adapter.pi-hole.0","user":"system.user.admin","lc":1588418287271},"pi-hole.0.version.948":{"val":"\u0001","ack":true,"ts":1599955452730,"q":0,"from":"system.adapter.pi-

Did I get you right? These logs are coming from a database adapter?


Add public method for getting back all permission status

Or requesting specific statuses.
Also, a Parse extension to plop these all into a permission class unique by user id + installation id

all permission status
configuredPermissions ?

Also, a Parse extension to plop these all into a permission class unique by user id + installation id
Can be done with reduce

Did this in 13710e8
As for the Parse stuff... it probably just belongs in my main project for now.


Non ascii characters in trigger name

Hi, great library, thank you for sharing it with the rest of the world!
Its not a big issue but I'm wondering if it is possible to use . , ( - % symbols as triggers. If so how?
The reason I need this is that I'm using FSM for static code analysis, for example code below allows SQL injection:
session.execute('select * from users where user.id = %s' % request.args['id'])

And it would be nice to trigger state transition using exact symbol without needing to translate it into symbol name, f.e:
code_stmt.trigger('%')

Not sure I understand the example... why would this present a problem from an injection standpoint? You can always sanitize the params in the request if you need to, no?
More generally, the issue I see here is that triggers need to be valid Python method names, since they get bound to the model. So I'm not sure how we could add special characters, since something like model.%my_trigger() isn't valid Python. (In theory we could add a Machine flag to prevent dynamic method binding, and then you could call the trigger directly, but that seems like an edge case, so I incline to not support it unless there's more demand.)

Yes your right, it is possible to sanitize arguments before interpolating those into string. But sometimes developer (including me) forget to do that. And I want to have static code analysis to detect that during automate testing stage.

Hi @aisbaa,
what you describe is expected behaviour. Transitions binds events to model attributes with setattr. Since all object attribute and method names are more or less keys in the object's __dict__ dictionary, every string which is a valid dictionary key should work with getattr. But as @tyarkoni mentions, you cannot call these functions directly because even though they are bound to the object they do not follow the python function naming scheme.
If you do not mind the -- a bit indirect -- getattr approach, it should work just fine for your field of application.  A second approach would be to call the event trigger directly (for instance machine.events['event_%'].trigger()) as Tal suggests. This might be a bit more comprehensible.
You could extend your model like this to get your desired behaviour.
class TestModel(object):
    def trigger(self, key):
        self.machine.events[key].trigger()

If using special characters cause problems elsewhere in transitions. Let us know.


Update Manifests to Swift 4.2

This updates SPM support to Swift 4.2. The version matching rules described here state that:

In particular, packages should not adopt this syntax for tagging versions supporting the latest GM Swift version.

In the spirit of this assertion, I renamed the existing root manifest to<EMAIL_ADDRESS>and copied the existing<EMAIL_ADDRESS>to<EMAIL_ADDRESS>and<EMAIL_ADDRESS>to ensure that pre-4.2 Swift versions are appropriately supported. The root manifest, Package.swift, uses the latest SPM version and has no version tag.
(This is the same strategy used in the Kitura repo, for example.)

 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.


Task3

Issue: #4
Commands Used:
sudo su
chmod +x

Hey @AdityaKishore29
Thanks for opening this PR 🚀. Mentor will review your pull request soon and till then, keep contributing and stay calm.
Thanks for contributing in OpenCode'24 ✨✨!

Hey @AdityaKishore29
Your PR has been merged 🥳🥳 and you have earned 10 points.
Thanks for contributing in OpenCode'24 ✨✨


test(connector-fabric-socketio): add functional test, bug fix

Added functional jest test fabric-socketio-connector.test that can be run during CI process. It checks evaluate/sending transactions and monitoring for new events. Connector had to be refactored to be testable, tests also discovered some bugs that had to be fixed in order to pass.
SocketIOApiClient refactors:

Added option for supplying validatorKeyValue instead of validatorKeyPath.
JWT validation function works with key value now (instead of reading the key).
Validator can now return messages that are not encrypted (it throwed error previously).
Adjusted unit tests.

connector-fabric-socketio refactors:

Connector can be run both as a standalone app and loaded as a module www.js. Caller can use exported startFabricSocketIOConnector function to run the connector. Configuration must be supplied in file or in env variable like it's done in functional test.
All cryptographic data (keys, certificates, etc…) can now be supplied as a value (previously it supported only path to a file).
sendSignedTransaction can now be called synchronously (it had wrong response format before).
Fixed a bug introduced during my last changes in this component, which caused fabric-client session to be disconnected but still reused by follow-up requests. I didn't know that gateway disconnects client it operates on.
Increased JWT expiration to 15 minutes to prevent constant JWT expiration error (I'm pretty sure 15 minutes is still secure period).
Minor improvements (logging, formatting, etc…)

fabric-test-ledger-v1 changes:

Added adminCredentials() to have programatic access to admin credentials on currently used ledger
(unlikely, but can change in the future).

Depends on: https://github.com/hyperledger/cactus/pull/1975
Closes: https://github.com/hyperledger/cactus/issues/1976
Signed-off-by: Michal Bajer<EMAIL_ADDRESS>

@petermetz @izuru0 Please review


Switch to Typescript

My Anycubic Photon had a hard time with the generated .pws file, so I wanted to add support for .photon. I had a hard time understanding the code and thought some types would greatly help.
I also dropped the checked in libraries and switched to npm packages.
Oh, and I also changed the anti-alias count from 0 to 1. UVTools had a division by zero before...
What do you think?

Oh wow, thanks for the contribution. This is a lot of work. It may take me a bit to review this but I'm absolutely open to making the switch to TS

Great, nice to hear. Looking forward to your feedback.

Mostly looks good! We still have some .js files I see, is that going to cause a problem? (I've never worked in a hybrid environment)

No, it should not cause any issues. But you don't have typing for the .js files...

Apologies. I caught COVID. I will try to take a look this weekend
On Mon, Aug 14, 2023, 12:12 Ruedi Steinmann @.***>
wrote:

Any news on this? Waiting for me?
—
Reply to this email directly, view it on GitHub
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AWs Instance Profile Support

What kind of request is this (question/bug/enhancement/feature request):
Feature Enhancement
Description:
It would be great if Rancher supported Instance profiles for AWS. Right now to use S3 etcd backups or to make an EC2 or EKS cluster you must provide Rancher with a set of AWS API Keys. We have setup our environment to prevent long lived AWS keys through the use of AWS Instance Profiles. We even use them for Kubernetes pods through the use of KIAM. We are hesitant to make an exception on our security policy for Rancher with regards to keys, as instance profile support is pretty standard across most products and sdks now.
Environment information
Rancher 2.2.2
gz#7072

BUMP, can we get an update to this?
Close the "issue" with a "won't fix" or something.

In a multi-account environment, the ability to provide an IAM role per-cluster to assume would allow the Rancher to assume IAM roles in other accounts.
https://docs.aws.amazon.com/IAM/latest/UserGuide/id_roles_use_switch-role-ec2.html#Allowing-an-instance-profile-role-to-switch-to-a-role-in-another-account


Preserve order in collections.

This MR tries to solve https://github.com/spdx/Spdx-Java-Library/issues/146
It replaces the use of HashMap with LinkedHashMap, which preserves the performance improvement done in https://github.com/spdx/Spdx-Java-Library/pull/144 but keeps the insertion order in collections.
Because LinkedHashMap is not synchronized, it has been wrapped using Collections.synchronizedMap method.

@goneall any ETA for a new release in June? This is a great improvement, thanks.

@beltran-rubo - would you want a complete release of all the java tools or just this library?  I could spin the library version pretty quickly if it helps.  Otherwise, it will probably be towards the end of June for a release of the complete set of Java tools as I'm working on a release of the online tools over the next week or two.

We are using the Java library itself, it would be great to get it sooner than later including this improvement. Thanks!

We are using the Java library itself, it would be great to get it sooner than later including this improvement. Thanks!

In that case I'll plan on producing a release of this library over the next couple of days.

Thanks! Still a bit early to move to version 3 on our side but we can help with the revision and testing.


MSID: 97612 Version: 1 DOI: 10.1101/2<IP_ADDRESS>2617

MSID: 97612
Version: 1
Preprint DOI: https://doi.org/10.1101/2<IP_ADDRESS>2617
Step 1. Awaiting reviews
Editorial to post reviews via hypothesis
Useful links:

DocMap: https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v2/by-publisher/elife/get-by-manuscript-id?manuscript_id=97612
New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
Reviews on sciety: https://sciety.org/articles/activity/10.1101/2<IP_ADDRESS>2617

For trouble shooting (e.g. no Docmaps available):

DocMap issue addressing: https://miro.com/app/board/uXjVNCwK6EI=/
Explore DataHub DocMaps API: https://lookerstudio.google.com/reporting/4c2f0368-babb-4beb-b5b3-497e7e7b0f08/page/ejphD
Unmatched submissions and preprints: https://lookerstudio.google.com/u/0/reporting/9f86204f-3bf7-477c-9b18-5c5ef141bf69/page/p_gxi57ha93c
Unmatched manuscripts spreadsheet: https://docs.google.com/spreadsheets/d/15QcK8w-ssB7109RQEDtFpJPZ0J5HTGxoHa_2TtpMBbg/edit#gid=1336081641

Step 2. Preview reviewed preprint
Production QC content ahead of publication
Instructions:

QC preview: https://prod--epp.elifesciences.org/previews/97612v1
Update ticket with any problems (add blocked label)
When QC OK, add QC OK label to ticket and add publication date and time to https://docs.google.com/spreadsheets/d/1amAlKvdLcaDp5W8Z8g77NmkwbMF5n_u89ArSqPMO8jg
Move card to next column
(At end of the day post link in #enhanced-preprint and ask for PDF to be generated)

Useful links:

Preprint DOI :  https://doi.org/10.1101/2<IP_ADDRESS>2617
Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/97612/v1/reviews
To update the MECA path in the docmap: https://docs.google.com/spreadsheets/d/1mctCQuNFBjSn97Lihy7_vBO6z7-N-oqyLv4clyi6zHg

Step 3: Awaiting search reindex
This step adds the reviewed preprint to the homepage: https://elifesciences.org
The search reindex is triggered once an hour. We need the reviewed preprint to be indexed as the search application serves the journal homepage.
Useful links:

Jenkins pipeline to reindex search can be triggered sooner or monitored here: https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/

Step 4: Published! PDF requested
Waiting for PDF to be generated
Useful links:

PDF tracking: https://docs.google.com/spreadsheets/d/106_XeDjmuBae7gexOTNzg60lapeqjl2aRn9DzupGyS8/

Step 5: Introduce PDF to data folder and git repo
Upload PDF to relevent folder in git repo https://github.com/elifesciences/enhanced-preprints-data/
Step 6: Done!

[ ] Kettle is on!

Hi @fred-atherden, multiple equations have been captured as figures, please can this be fixed?

@rkcook312, will merge the above when the tests pass. Then it'll take a few hours for the change to be deployed before the package can be reimported via temporal to fix the issue (might be one for tomorrow).
I also notice that bioRxiv did a poor job of capturing the authors code:

But unfortunately EPP will not be able to handle this being captured properly either. So I'll make a change to the package to use images for these instead.


Coloring labels by a continuous variable appears to be broken (labels associated with wrong colors)

My testing code:
import spatialdata as sd
import spatialdata_plot
import matplotlib.pyplot as plt
import numpy as np

sdata = sd.datasets.blobs()
sdata.pl.render_labels("blobs_labels", color="channel_0_sum").pl.show()

Previously (here I used commit c6575e2f5e49b495f97b6c7fc08fe9c16e0684d7) this would look something like this:

However, since e97a7fcb86762f66713c4cf0047d8353fc61984c, this looks like this:

Just to make sure that the first plot is correct, I extracted the labels where channel_0_sum is high, which shows that the two labels shown in yellow and green in the first plot are indeed the ones with the highest values:
highid = sdata.table.obs[sdata.table[:,'channel_0_sum'].X.toarray() > 1000].instance_id
plt.imshow(np.isin(sdata['blobs_labels'], highid))

Thank you for the issue @clwgg, will fix now


Update to node20

Getting the following warning:
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20<EMAIL_ADDRESS>For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

v2.1.2


Review the Contact component for Visual Stories

We currently have a Contact component.
We'd like to use it for Visual Stories (as seen in mockups), but it would need to allow icons before the information, and kind of refactor how it's displayed.
We've discussed allowing this using a checkbox (current layout vs new layout), but also just using the new layouts across the site. I need to confirm this as part of this ticket.

@DominiqueMarshall can I confirm with you the last paragraph?

In the future yes, but I wouldn't want to use the new layout across the site just yet. I need to spend some time looking at where the current component is used to see if the new layout would work well elsewhere before we consider completely switching over

Looks good! Thanks @rcantin-w  😊


Send Event to Dynatrace

This enhancement would see the jira-service sending a notification back to Dynatrace whenever a JIRA ticket is created (or a creation attempt is made).
This feature should have a corresponding enable / disable flag.
Thoughts

Is this the best place for this logic? Should it not live elsewhere?
Can this notification be made more generic for any tool (not just Dynatrace)?

@christian-kreuzberger-dtx interested on your thoughts. A generic "here's a payload, send an event" type facility would be great - perhaps this logic lives in the dynatrace-service or an extension of the notification-service?

That's definately something for dynatrace-service. Feel free to post a Feature Request for this service.


Change ScrollView to NestedScrollView for RepCallActivity to fix issu…

…e #117
Outcome buttons aren't always all displaying. Seems to be related to using a RecyclerView in a ScrollView. Changing to a NestedScrollView changes the problem.
I also have a few questions about the status of the 5calls Android app in general and how volunteers can contribute to the codebase.

This is great @chadschultz! Definitely something we've dealt with in the past too like #102. I will review this on my test android device this weekend.

I was able to reproduce and then see the fix, thanks @chadschultz!


Error parsing device info data.

PowerToys version: 0.20.1
PowerToy Utility: FancyZones
Running PowerToys as Admin: Yes
Windows build number: [run "winver"]

📝 Provide detailed reproduction steps (if any)

… I get this error on my work laptop but not on my personal laptop
… I have uninstalled and reinstalled it including .Net
…

✔ Expected result
Fancy Zones to work/Open
❌ Actual result
Exception handler
📷 Screenshots
Are there any useful screenshots? WinKey+Shift+S and then just paste them directly into the form

Hi @Lotzof
let's move the discussion to https://github.com/microsoft/PowerToys/issues/4873


Scoreboard is showing every 2 secs

I have a problem with the scoreboard and its like realoading every 2-3 seconds hides and shows up again

I have a problem with the scoreboard and its like realoading every 2-3 seconds hides and shows up again

Hi, what version are you having this issue with? Are there any errors in the console? I'll try and reproduce this, but I need to know the version.

Unable to replicate this.. Will reopen if further information is added to the issue.


trace panic in external lg mode

Just install this nice tool and played around for awhile and noticed that I got a panic when trying to do trace on external looking glass mode. It works correct in local mode.
local> lg
lg> trace www.google.com
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x48 pc=0x404a82]

goroutine 1 [running]:
panic(0x8fd8e0, 0xc42000c180)
	/usr/local/go/src/runtime/panic.go:500 +0x1a1
main.trace()
	/home/vagrant/golang/src/github.com/mehrdadrad/mylg/mylg.go:312 +0xb2
main.main()
	/home/vagrant/golang/src/github.com/mehrdadrad/mylg/mylg.go:157 +0x1e6

Thank you for reporting this bug. once the lg selected user needs to connect to a provider like telia then a node (like Los Angeles). I'll commit a code to set  a default to cover this issue.


M3-4128 Refactor User details, NodeBalancer details, and Profile tabs

Description
Switching over to the Reach pattern for the above sections + cleanup.
Type of Change

Non breaking change ('update')

Note to Reviewers
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration.

@WilkinsKa1 I looked a bit more into the issue I mentioned above. I think we could solve this with a custom TabPanel component:
// Only renders its children when the tab is selected.
const _TabPanel: React.FC<{ index: number } & TabPanelProps> = props => {
  const { index, ...tabPanelProps } = props;

  const { selectedIndex } = useTabsContext();
  const isSelected = selectedIndex === index

  return (
    <TabPanel {...tabPanelProps}>
      {isSelected ? props.children : null}
    </TabPanel>
  );
};

Then, in the <TabPanels/> sequence:
<TabPanels>
  <_TabPanel index={0}>
    <DisplaySettings />
  </_TabPanel>
  <_TabPanel index={1}>
    <AuthenticationSettings />
  </_TabPanel>
  {/* ...etc */}
</TabPanels>

It's not as fast moving between tabs of course, but it makes initial load quicker and doesn't request a ton of data we might not need,

@johnwcallahan I like that idea alot! I can work on that- would we apply this new component anywhere we're not using the TabbedPanel component, I'm thinking?

I apologize for the scope change in this PR- I wanted to see if the TabPanel abstraction would fix the Longview issue mentioned in the PR referenced above, looks like it does! I did have to do some strange checking for conditional tabPanels (LV apps) but there is likely a much better way to handle this.

would we apply this new component anywhere we're not using the TabbedPanel component, I'm thinking?

I think anywhere we are requesting data when a component mounts. If it's a simple component that is purely presentation, we could get by with the regular TabPanel and there'd be a slight performance benefit in doing so.


mypy 1.10.0 fails with matplotlib wrappers

What is your issue?
Pyright is a full-featured, standards-based static type checker for Python, recently I tried it with xarray and get an error.
And mypy generates the same error.
So I wonder if we can fix this error, although  this error won't have any impacts except for static type checker errors.

I have been using xarray for several years and recently began using Pyright. However, I encountered the following error: Argument missing for parameter 'self' Although my code still executes normally, I am curious about the cause of this error. Is this behavior expected?
import xarray as xr
import matplotlib.pyplot as plt
data = xr.DataArray([1, 2, 3], dims=['x'])
fig, ax= plt.subplots(ncols=1, nrows=1)
data.plot(ax=ax)

It seems to related to the codes here:
    plot = utils.UncachedAccessor(DataArrayPlotAccessor)

class UncachedAccessor(Generic[_Accessor]):
    """Acts like a property, but on both classes and class instances

    This class is necessary because some tools (e.g. pydoc and sphinx)
    inspect classes for which property returns itself and not the
    accessor.
    """

    def __init__(self, accessor: type[_Accessor]) -> None:
        self._accessor = accessor

    @overload
    def __get__(self, obj: None, cls) -> type[_Accessor]: ...

    @overload
    def __get__(self, obj: object, cls) -> _Accessor: ...

    def __get__(self, obj: None | object, cls) -> type[_Accessor] | _Accessor:
        if obj is None:
            return self._accessor

        return self._accessor(obj)  # type: ignore  # assume it is a valid accessor!

Here is my xarray version:
xarray                    2023.2.0           pyhd8ed1ab_0    conda-forge

Originally posted by @singledoggy in https://github.com/pydata/xarray/discussions/9150

Pyright is behaving correctly here. Not surprisingly, mypy generates the same error.
The problem appears to be in the xarray library here:
class DataArrayPlotAccessor:
    ...
    @functools.wraps(dataarray_plot.plot, assigned=("__doc__", "__annotations__"))
    def __call__(self, **kwargs) -> Any:
        return dataarray_plot.plot(self._da, **kwargs)

Originally posted by @erictraut in https://github.com/microsoft/pyright/discussions/8203#discussioncomment-9846958

Is the error still present on a recent version of xarray?

Before, I only read through the latest code and didn't find any relevant changes. I just had time to test the latest version, but the issue still persists.

OK. Mypy does pass — so if you find a mypy error in the current version then that's news, we'd like to understand that.
We do have a pyright job in CI, but it doesn't pass. We're definitely open to contributions that improve it, and probably we'd be happy to turn on the check if we could get everything to pass.
Though it's not feasible to have an open issue for every pyright error so we can close this unless there's more info; hope that's reasonable.

mypy also get this error
As  @erictraut points out here, mypy wil generate the same error.
I also tested it with command: mypy test.py with the latest version (v2024.06.0) by myself.
It's reasonable if you choose to close this issue.
import xarray as xr
import matplotlib.pyplot as plt

data = xr.DataArray([1, 2, 3], dims=["x"])
fig, ax = plt.subplots(ncols=1, nrows=1)
data.plot(ax=ax)

test.py:6: error: Missing positional argument "self" in call to "__call__" of "_Wrapped"  [call-arg]
Found 1 error in 1 file (checked 1 source file)

Version information
INSTALLED VERSIONS
------------------
commit: None
python: 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:39:40) [Clang 15.0.7 ]
python-bits: 64
OS: Darwin
OS-release: 22.3.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.9.1

xarray: 2024.6.0
pandas: 2.2.2
numpy: 1.25.2
scipy: 1.11.2
netCDF4: 1.6.3
pydap: None
h5netcdf: None
h5py: None
zarr: None
cftime: 1.6.2
nc_time_axis: None
iris: None
bottleneck: None
dask: 2023.8.1
distributed: 2023.8.1
matplotlib: 3.8.4
cartopy: 0.23.0
seaborn: 0.13.2
numbagg: None
fsspec: 2023.6.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 68.1.2
pip: 23.2.1
conda: None
pytest: None
mypy: 1.10.0
IPython: 8.14.0

Thanks for the example and mypy output.
I see now — it's that our mypy version in CI is a bit out of date, and it does indeed raise an error with the newer mypy 1.10.0. Thanks for helping debug it.
I'll adjust the title of the issue if that's OK

I immediately see what's going on, so I'll have to leave it for the moment. (If anyone wants to dive in, that would be great).
Thanks for finding it @singledoggy

Just ran into the same problem. Also when running mypy on xarray codebase (-> 70 errors)

Looks like https://github.com/python/mypy/issues/17166

I think this is mostly covered now — we have ignores, we can wait for the mypy upstream issue before removing.


Please, add english translation

这个新特性和一个问题相关吗？简单描述下，比如我什么场景下，需要解决什么问题，发现表格不支持这个功能 Is your feature request related to a problem? Please describe.
描述下，你希望得到的什么解决方案 Describe the solution you'd like
是否有不错的替代方案 Describe alternatives you've considered

Due to too much translation content, it may be processed later


[explorer] Make binary event log optional

Since we are now dumping the replay files directly for all best
candidates found, the binary event log is only needed for performance
analysis (of the search algorithm, or of Telamon more generally).
This patch hence allows not generating it at all, and makes this the
default configuration.  Users that do want the event log should
explicitely set it in the configuration.

Since we are now dumping the replay files directly for all best
candidates found, the binary event log is only needed for performance
analysis (of the search algorithm, or of Telamon more generally).
This patch hence allows not generating it at all, and makes this the
default configuration. Users that do want the event log should
explicitely set it in the configuration.

explicitly


Support for IPython %magics, like %timeit

Hi, thanks for pdbr!
Since IPython is already baked into RichPdb (if available), it itched me to unlock some IPython features, so I started with %magic commands.
This is something that I've wanted to do for some time now; pdbr stands for a lot of things I enjoy: terminal debuggers, IPython and rich library.
I've added 2 functions in _pdbr.py, wrote a test in test_pdbr.py, and added a description of the feature in the README.md.
I had trouble testing the actual magic functionality, because when trying to init a rich_pdb_klass(IPython.terminal.debugger.TerminalPdb) inside a test, it raises an exception, complaining about stdout not being a terminal. I couldn't get past that.
Additionally, some magics don't work out of the box, for example %lsmagic. This can be fixed by overriding onecmd(), but I wanted to know if you're at all interested in this PR's idea before adding more changes. Let me know if you want this fixed as well :)
Thanks,
Gilad

@giladbarnea When i run a command and run magic secondly, i always see the last result with magic result. Can you have a look at it as well?

@cansarigol thanks for the quick reply :)
It looks like we're dealing with more than 1 issue, what do you think about writing tests for individual magics? I'd be happy to do it. There are a few dozen, I guess we'll find out we're not interested in some, or that others are working weirdly and require a more comprehensive fix.
About that bug with the repeating output, maybe it has to do with self.cmdqueue in pdb.Pdb.precmd(), or cmd.Cmd.emptyline(). I'll have to check that.
By the way, maybe it's worth sharing, I've made a pseudocode gist of the main loop. It helps me sort out the inheritance / method overload mess (cmd.Cmd > pdb.Pdb > IPython.core.debugger.Pdb > IPython.terminal.debugger.TerminalPdb > RichPdb):

Are there any magics that you don't want altogether?

@giladbarnea  writing tests for individual magics and making out TerminalPdb class and overriding its cmdloop are great ideas, please go ahead. My only objection would be for the %pdb but I don't have too much experience with magics.

Hi @giladbarnea your PR looks great 👍.  If you don't have time to put inherited TerminalPdb class, let's merge it as is and you can pursue with a new PR. Thanks for your effort btw

Hi @giladbarnea your PR looks great +1. If you don't have time to put inherited TerminalPdb class, let's merge it as is and you can pursue with a new PR. Thanks for your effort btw

Hi, you're right, I couldn't find the time (had my first kid a week ago :))
Let me see what quick wins I can get us within the next 45 minutes, I'll prepare a good-enough commit and hopefully it'll be ok.

@giladbarnea tests fail for me. Are they same for you as well?

@giladbarnea tests fail for me. Are they same for you as well?

@cansarigol Yes, I think at the very least the session.install() statement in noxfile.test() should include a . to install pdbr itself, and session.run() should include a "--capture=no" arg.
This fixes some tests but others are still failing, I'll update when it's fixed

@cansarigol That's it, f13020f succeeded through the CI pipeline.

@giladbarnea Great, thanks for your effort again. I am looking forward to using it myself first :smiley_cat:
we can fix windows test errors later.


Add the ability to add multiple sliders

It would be great if we could have multiple sliders and not just one. Would also be pretty cool if we could restrict clients from adding and deleting sliders using permissions.

I made a branch with that functionality.
https://github.com/mamarmite/PyroCMS-Slider-Module/tree/Multi-Sliders
I'm open to all point of view for the better implementation.

I made multiple changes to the module. I add the user's permissions to the multiples sliders parts.
https://github.com/mamarmite/PyroCMS-Slider-Module/tree/Multi-Sliders
Would you like a pull request? It may have a lot of merge conflitcs.

Hey,
Many thanks for your message.
Looks like you've done a pretty good job of extending this module.
I am no longer developing this module. So I'm happy to transfer this repository to you if you would like to maintain it?

Hi, Chris, I will be please to maintain it.
What are the steps to do that though?

Hi @mamarmite,
I'll transfer this repository to you now. The only think I ask is that you mention that I was the original author in the license file and it has the MIT license.
Cheers,
Chris

I'll add the license file now.
I tried transferring this repository to you, but it failed because you already have a repository named "PyroCMS-Slider-Module". If you could rename or delete this repository and let me know, then I'll transfer this one to you.

Ok, I deleted my fork of the project.
Thanks!

Brilliant! I have started the transfer process.

All done! Looking forward to see what you do with this plugin.
I'm really glad you're able to maintain it.


ci: use github actions

Before submitting the PR, please make sure you do the following

[x] Read the Contributing Guidelines.
[x] Read the Pull Request Guidelines and follow the Commit Convention.
[x] Check that there isn't already a PR that solves the problem the same way to avoid creating a duplicate.
[x] Provide a description in this PR that addresses what the PR is solving, or reference the issue that it solves (e.g. fixes #123).
[ ] Ideally, include relevant tests that fail without this PR but pass with it.

What is the purpose of this pull request?

[ ] Bug fix
[ ] New Feature
[ ] Documentation update
[x] Other

Description
#2604
This adds a CI script to the repo so GitHub Actions are used
This will provide warnings from eslint inside reviews in the GUI of GitHub
Also it may replace CircleCI in the long run
Additional context
I have added also some outcommented steps that are arguable if we should use them
In my smaller repos these are quite okay, but for such a big sized repo as Vite it's really questionable

:eyes: The tests on windows seems to fail successfully hihi 🤭
So I think I discovered a real issue

I think this is a good idea, but I have not enough experience with GitHub actions to review this one. Let's wait for @antfu and @underfin's input

You should also probably remove CircleCI and Appveyor to stop them from testing something that is already being tested by GitHub Actions. This prevents wasting energy that is consumed for running those extra virtual machines.
CircleCI has a "stop building" button in its settings, and Appveyor can be turned off from the repository settings.
If you don't have access to these, you can do some tricks. For Appveyor for example:
# empty appveyor
build: off

branches:
  only:
  - non-existing

The errors in the failing tests on Windows are irrelevant to these changes and should probably be fixed in a separate PR.

=> https://github.com/vitejs/vite/pull/2631

WHAT :eyes:
https://github.com/vitejs/vite/pull/2622/checks?check_run_id=2298098539#step:8:31
FATAL ERROR: Ineffective mark-compacts near heap limit Allocation failed - JavaScript heap out of memory
 1: 019FE94A v8::internal::Heap::PageFlagsAreConsistent+3050
 2: 019F50B0 v8::internal::Heap::CollectGarbage+1200
error Command failed with exit code 134.

The error message now look different :thinking:
https://github.com/vitejs/vite/pull/2622/checks?check_run_id=2298256877#step:8:31
<--- Last few GCs --->

[5388:039FC9C8]    66391 ms: Mark-sweep (reduce) 1021.0 (1027.0) -> 1019.6 (1028.0) MB, 1545.6 / 0.0 ms  (average mu = 0.099, current mu = 0.022) allocation failure scavenge might not succeed
[5388:039FC9C8]    67785 ms: Mark-sweep (reduce) 1022.1 (1030.0) -> 1019.4 (1029.0) MB, 1388.3 / 0.0 ms  (average mu = 0.053, current mu = 0.004) allocation failure scavenge might not succeed

<--- JS stacktrace --->

FATAL ERROR: Ineffective mark-compacts near heap limit Allocation failed - JavaScript heap out of memory
 1: 0086E5C9 v8::internal::Heap::PageFlagsAreConsistent+2169
 2: 00864651 v8::internal::Heap::CollectGarbage+1985
 3: 00862D03 v8::internal::Heap::AllocateExternalBackingStore+1155

Sorry @aminya but we had some GH Action issues with windows-2016_x86 due to out of memory while testing
Therefore we decided to just kick it :shrug:
We want to have a bit more simple CI

I think the scope of the issue is largen than this pull request, but it seems like a genuine issue in the native code. Doesn't Esbuild support Windows x86?


More Composability

Added environment variable to make fallback fetching of missing artifact dependencies from remote repos optional
Moved most composable values to Dockerfile as environment variables
Made expected names of all artifacts fully composable

@DieterReuter Re-thinking about this pull request, I'm not 100% happy with it.
I think the change in the nature of the environment variables is good as it allows more composition in the artifact names (for example, in the project as it currently stands, a debian arm 64 bits root fs is assumed, but with my modification, you can override that to any root fs which makes sense).
For having environment variables in a config file vs having them in the Dockerfile, it depends on your view of the project I think (either as the master orchestration of the HypriotOS build in which case a config file makes sense or simply as the final step in the HypriotOS build in which case variables in the Dockerfile make more sense).
With my current modifications, however, it's 75% in the Dockerfile and 25% in the config file which suits my needs (all the environment variables I need are in the Dockerfile), but for maintainers, it just puts the config in two places. I could move the remaining variables from the config file to the Dockerfile, but it might be unsatisfying for those who view this project as a top-level orchestrator.
Instead, what I could do as a compromise is put the defaults back in the config file, but only set each environment variable in the config file ONLY if they aren't already defined in the running container (that way you can still pass select environment variable overrides to the build container at runtime).
Let me know what you think.

I would prefer to have all the variable at a single place. For example, when I want to upgrade the os-rootfs, I have to change the version number in Dockerfile and the file checksum in version.config.
Right now there are only 4-5 settings left in version.config, I think it's best to move them over to the Dockerfile. Then we'll have everything together and it's simple to change/update and makes maintaining way easier.

Sounds good, I'll make the adjustment when I get back home.

Thanks, this LGTM now!