R7.3

Hi Jared (and colleagues),
I have recently put a genome together and want to see if there is evidence for methylation. A previous paper reported some evidence using an antibody on polytene chromosomes. So I am excited by the possibility that it can be detected at the sequence level with nanopore data.
Can the methylation detection for nanopolish still work with R7.3 data? That is all I have for this organism. Well I have the following:
SQK-MAP002, r7.3 (5mer)
SQK-MAP004, r7.3 (5mer)
SQK-MAP005, r7.3 (5mer)
SQK-MAP006, r7.3_e6_70bps_6mer, MkI
If the newest code doesn't support it, is there a way to access an older version that does?
Many thanks,
John

The current version (github master) branch still supports R7.3 data but only from the MAP005/MAP006 kits. I suggest only using the MAP006 data if possible, as the older sets tend to be lower quality.
Do you know the candidate methylation motif or do you hope to discover it?

Excellent question. I know nothing about it yet. There is some evidence that methyl-C exists. This would be exploratory and entirely new territory for us.

So to answer your question directly: I hope to discover a motif if one exists. I would even be happy to use this to build more evidence that methylation exists in this organism and evidence to approximately what regions of the genome. A motif would be icing on the cake.

The MAP006 data makes up ~67% of the data anyway -- so I will stick to that as per your recommendation.

Ok - my suggestion is to use the methyltrain machinery to learn a new set of k-mer parameters and see if the trained parameters deviate from what you expect. See supp table 1/2 in our methylation preprint. When we trained on enzymatically methylated DNA (supp table 2) we saw many k-mers whose mean changed and almost all of them contained a CG dinucleotide.

Also, was your assembly polished with nanopolish or Illumina reads? If the former this will get a bit circular as any methylation motifs would probably be miscalled.

Actually it was polished with Quiver/PacBio followed by Pilon/Illumina. I reasoned that I do not really have enough nanopore data for polishing -- maybe 6-7X considering all reads, less for 2D only but likely >= 2-3x.

Thanks for your advice -- I will try to get to this in the coming week or 2 and let you know how it went. If I don't get to it in that time-frame, then we are looking at January or February due to other constraints.

Sure, let me know if you need more help.

Alright I see that the usage is:
nanopolish methyltrain [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa

Presumably aligning with bwa mem -x ont2d is fine...(?)
I see there are plenty of options:
  -v, --verbose                        display verbose output
      --version                        display version
      --help                           display this help and exit
  -m, --models-fofn=FILE               read the models to be trained from the FOFN
      --train-kmers=STR                train methylated, unmethylated or all kmers
  -c  --calibrate                      recalibrate aligned reads to model before training
      --no-update-models               do not write out trained models
      --output-scores                  optionally output read scores during training
  -r, --reads=FILE                     the 2D ONT reads are in fasta FILE
  -b, --bam=FILE                       the reads aligned to the genome assembly are in bam FILE
  -g, --genome=FILE                    the reference genome is in FILE
  -t, --threads=NUM                    use NUM threads (default: 1)
      --filter-policy=STR              filter reads for [R7] or [R9] project
  -s, --out-suffix=STR                 name output files like <strand>.out_suffix
      --out-fofn=FILE                  write the names of the output models into FILE
      --rounds=NUM                     number of training rounds to perform
      --progress                       print out a progress message
      --stdv                           enable stdv modelling

...and I was wondering about your recommendations/thoughts on:

--train-kmers  -- should specify 'methylated' or 'all'?
should I specify --calibrate ?
What information might the read scores give me for --output-scores?
How many rounds? What is the default?
Do you recommend --stdv?
I'm guessing there is a manual somewhere that explains all this. Feel free to tell me to RTFM if so. I will search for it after I post this. :)

I am getting it going with Loman data found here:
wget ftp://ftp.era.ebi.ac.uk/vol1/ERA540/ERA540530/oxfordnanopore_native/MAP006-1.tar

When I do:
nanopolish methyltrain --reads pass.nanopolish.fa --bam pass.nanopolish.bam --genome ecoli_k12_mg1655_NC_000913.3.fasta

I get the error:
methyltrain: a --models file must be provided

I only found R9 model info that came with the download here:
./nanopolish/etc/r9-models/

...which contains:
nanopolish_models.fofn
template_median68pA.5mers.model
template_median68pA.model

I tried it anyway by copy pasting those files into the working dir and doing:
nanopolish methyltrain --reads pass.nanopolish.fa --bam pass.nanopolish.bam --genome ecoli_k12_mg1655_NC_000913.3.fasta --models-fofn=nanopolish_models.fofn

...and received this message:
registering model t.007-base
registering model t.007-ONT
Starting round 0
Error: cannot find model t.006 for type reftrained

Any ideas on how to proceed?
Thanks.

Hi John,

--train-kmers -- should specify 'methylated' or 'all'?

you should use "all", which is the default (so you don't need to pass this parameter)

should I specify --calibrate ?

no

What information might the read scores give me for --output-scores?

this is for debugging, you don't need to use this option

How many rounds? What is the default?

the default is 5, which I recommend

Do you recommend --stdv?

no
I'll send you the R7.3 input models (R9 works by default)

Thanks for the clear directions. I look forward to trying the R7.3 models.

It looks like we have lift off!
registering model t.006-ONT
registering model c.p1.006-ONT
registering model c.p2.006-ONT
Starting round 0

Thanks for the R7.3 models.
After running methyltrain and getting tables like the supp tables 1/2 in your preprint, assuming we see a difference. What is the next step?
Do I just run methyltest?
It does not appear at first glance that methyltest depends on any output from methyl train - is that correct? I'm guessing it runs methyltrain for itself...(?)
As a final question (can't thank you enough if you've made it this far), does it just find CG dinucleotides in the given genome sequence and test them or is it looking for other possible methylation sites as well?
Thanks again.

After running methyltrain and getting tables like the supp tables 1/2 in your preprint, assuming we see a difference. What is the next step?

You're doing something a little different than what we did in our paper - we knew the motif, you are trying to discover it (if there is one). I suggest making a table of differences between the ONT-provided mean and the trained mean for each k-mer and seeing if a consistent motif pops out. I can help with this if you provide the table (or the trained model files).

Do I just run methyltest?

You won't be able to run methyltest since you don't know the motif

It does not appear at first glance that methyltest depends on any output from methyl train - is that correct? I'm guessing it runs methyltrain for itself...(?)

methyltest takes in new model files, which you have to provide from the output of methyltrain

As a final question (can't thank you enough if you've made it this far), does it just find CG dinucleotides in the given genome sequence and test them or is it looking for other possible methylation sites as well?

Right now you are just fitting new Gaussian distributions to each k-mer. Methyltrain doesn't assume anything about motifs or which bases might be methylated, it simple aligns events to k-mers (like eventalign) then fits a new Gaussian to every k-mer that it sees. You'll have to build your own method to interpret the trained parameters (I suggested one way above)

Thanks. Do you recommend using only pass reads, or would it be okay to use all fast5s with 2D reads? or would it be ok to use all pass/ fail/ files that contain 2d or templates that align?
I am guessing there is a balance between read coverage and read quality. Below are coverage values from read lengths for subsets of decreasing quality reads. The coverage values are from summing the read lengths before aligning -- so they are the max possible.
For 2D pass, I have 1.8x coverage.
For all 2D, I have 4.7x coverage.
For all 2D and template, I have 6.9x coverage (only ~5.47x when only counting templates with mean qualities > 4).
This is from my MAP006 data.

Alright - rereading your preprint I see you used 2D from pass and fail given that reads with base-modifications likely have lower mean quality scores and get sent to the fail bin. I will assume that is still your thinking. If your thinking has changed on that let me know (e.g. if you think I should also include the templates for reads in the fail bin that do not have a 2D).

Yes, I still suggest using both pass and fail.

Hi Jared,
Do you know how to get past this error:
registering model t.006-ONT
registering model c.p1.006-ONT
registering model c.p2.006-ONT
Starting round 0
nanopolish: ./src/common/nanopolish_alphabet.h:173: virtual std::__cxx11::string Alphabet::disambiguate(const string&) const: Assertion `IUPAC::isValid(out[i])' failed.

Aborted (core dumped)

It is being thrown immediately. I saw IUPAC and searched my sequence for some non-ACGT letters, but didn't find any. Is it possible that it is throwing the error on lower-case letters?

Yeah, lower-case bases are the problem

Thanks for the quick reply. Yeah these lowercase bases are from Quiver output -- typically at the ends of contigs. I will make everything uppercase.

I tried re-running several times before contacting you again, but I keep getting the same error regardless of the amount of memory I throw at it.
Starting round 0
/var/spool/slurmd/job14011507/slurm_script: line 35: 44012 Segmentation fault      nanopolish methyltrain --reads $R --bam $B --genome $G -t $T --models-fofn=ont.alphabet_nucleotide.R7.fofn --train-kmers all --rounds=5 --progress

It made it to realigning ~17,000 reads (last message before error was ^MRealigned 17280 reads in 0.0s)
SLURM says the max amount of memory used was only around 26GB. Since it has 150GB available to it, I am guessing that is not the problem.

In my experience this is always caused by running out of memory but it looks like you have that covered. Could you capture the segfault in gdb and provide a stack trace?

Ok - this was my first experience using gdb, so I will tell you how I did it to make sure it was the right way.
I requested 32 threads and 150GB RAM for an interactive SLURM session.
T=32
R=map006.fa
B=map006.bam
G=1.canu.corcov500minrl500.aspb-e02.pball.ont2d.quiverfinal1.pilon2x.UPPERCASE.fasta

gdb --args nanopolish methyltrain --reads $R --bam $B --genome $G -t $T --models-fofn=ont.alphabet_nucleotide.R7.fofn --train-kmers all --rounds=5 --progress

(gdb) run

The messages after that are:
Starting program: /gpfs/data/sgerbi/jurban/software/nanopolish/nanopolish/nanopolish methyltrain --reads map006.fa --bam map006.bam --genome 1.canu.corcov500minrl500.aspb-e02.pball.ont2d.quiverfinal1.pilon2x.UPPERCASE.fasta -t 32 --models-fofn=ont.alphabet_nucleotide.R7.fofn --train-kmers all --rounds=5 --progress
warning: File "/gpfs/runtime/opt/gcc/5.2.0/lib64/libstdc++.so.6.0.21-gdb.py" auto-loading has been declined by your `auto-load safe-path' set to "$debugdir:$datadir/auto-load".
To enable execution of this file add
	add-auto-load-safe-path /gpfs/runtime/opt/gcc/5.2.0/lib64/libstdc++.so.6.0.21-gdb.py
line to your configuration file "/users/jurban/.gdbinit".
To completely disable this security protection add
	set auto-load safe-path /
line to your configuration file "/users/jurban/.gdbinit".
For more information about this security protection see the
"Auto-loading safe path" section in the GDB manual.  E.g., run from the shell:
	info "(gdb)Auto-loading safe path"
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
registering model t.006-ONT
registering model c.p1.006-ONT
registering model c.p2.006-ONT
Starting round 0
[New Thread 0x7fffdfdda700 (LWP 64563)]
[New Thread 0x7fffc1592700 (LWP 64564)]
[New Thread 0x7fffa2d4a700 (LWP 64565)]
[New Thread 0x7fff84502700 (LWP 64566)]
[New Thread 0x7fff65cba700 (LWP 64567)]
[New Thread 0x7fff47472700 (LWP 64568)]
[New Thread 0x7fff28c2a700 (LWP 64569)]
[New Thread 0x7fff0a3e2700 (LWP 64570)]
[New Thread 0x7ffeebb9a700 (LWP 64571)]
[New Thread 0x7ffecd352700 (LWP 64572)]
[New Thread 0x7ffeaeb0a700 (LWP 64573)]
[New Thread 0x7ffe902c2700 (LWP 64574)]
[New Thread 0x7ffe71a7a700 (LWP 64575)]
[New Thread 0x7ffe53232700 (LWP 64576)]
[New Thread 0x7ffe349ea700 (LWP 64577)]
[New Thread 0x7ffe161a2700 (LWP 64578)]
[New Thread 0x7ffdf795a700 (LWP 64579)]
[New Thread 0x7ffdd9112700 (LWP 64580)]
[New Thread 0x7ffdba8ca700 (LWP 64581)]
[New Thread 0x7ffd9c082700 (LWP 64582)]
[New Thread 0x7ffd7d83a700 (LWP 64583)]
[New Thread 0x7ffd5eff2700 (LWP 64584)]
[New Thread 0x7ffd407aa700 (LWP 64585)]
[New Thread 0x7ffd21f62700 (LWP 64586)]
[New Thread 0x7ffd0371a700 (LWP 64587)]
[New Thread 0x7ffce4ed2700 (LWP 64588)]
[New Thread 0x7ffcc668a700 (LWP 64589)]
[New Thread 0x7ffca7e42700 (LWP 64590)]
[New Thread 0x7ffc895fa700 (LWP 64591)]
[New Thread 0x7ffc6adb2700 (LWP 64592)]
[New Thread 0x7ffc4c56a700 (LWP 64593)]
Realigned 24704 reads in 0.0s
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7ffe902c2700 (LWP 64574)]
0x00000000005518c8 in H5F_addr_decode ()

I then did:
(gdb) backtrace

And the message was:
#0  0x00000000005518c8 in H5F_addr_decode ()
#1  0x00000000006824d7 in H5T_vlen_disk_isnull ()
#2  0x000000000061a342 in H5T__conv_vlen ()
#3  0x000000000060f4b9 in H5T_convert ()
#4  0x0000000000516dd8 in H5A_read ()
#5  0x0000000000511b7b in H5Aread ()
#6  0x00000000004411e9 in wrap<int (&)(int, int, void*), int&, int&, void*&> (f=<optimized out>) at ./fast5/src/hdf5_tools.hpp:472
#7  operator() (dest=<optimized out>, mem_dtype_id=<optimized out>, __closure=<optimized out>) at ./fast5/src/hdf5_tools.hpp:804
#8  _ZNSt17_Function_handlerIFviPvEZN10hdf5_tools6detail11Reader_BaseC4EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEUliS0_E0_E9_M_invokeERKSt9_Any_dataOiOS0_ (__functor=..., __args#0=<optimized out>, __args#1=<optimized out>) at /gpfs/runtime/opt/gcc/5.2.0/include/c++/5.2.0/functional:1871
#9  0x0000000000446194 in operator() (__args#1=0x7ffb3a716050, __args#0=50331759, this=0x7ffe902c0e98)
    at /gpfs/runtime/opt/gcc/5.2.0/include/c++/5.2.0/functional:2271
#10 _ZNK10hdf5_tools6detail13String_readerclB5cxx11ERNS0_11Reader_BaseEPKSt5dequeIPKNS0_27Compound_Member_DescriptionESaIS7_EE (
    this=this@entry=0x7ffe902c0cd2, reader_base=..., mptr_l_ptr=mptr_l_ptr@entry=0x0) at ./fast5/src/hdf5_tools.hpp:887
#11 0x0000000000447217 in operator() (this=<optimized out>, out=0x7ffe902c0fe0, reader_base=...) at ./fast5/src/hdf5_tools.hpp:1022
#12 operator()<> (out=..., name=..., grp_id=<optimized out>, this=<optimized out>) at ./fast5/src/hdf5_tools.hpp:1103
#13 hdf5_tools::File::read<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >>(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const (this=<optimized out>,
    loc_full_name=..., out=...) at ./fast5/src/hdf5_tools.hpp:1529
#14 0x0000000000463ec8 in get_basecall_model_file (_bc_gr=..., st=0, this=0x7ffb381e5ac0) at ./fast5/src/fast5.hpp:612
#15 PoreModel::PoreModel (this=0x7ffe902c1220, f_p=0x7ffb381e5ac0, strand=0, bc_gr=..., alphabet=<optimized out>) at src/nanopolish_poremodel.cpp:239
#16 0x00000000004705c5 in SquiggleRead::_load_R7 (this=0x7ffe902c1910, si=0) at src/nanopolish_squiggle_read.cpp:183
#17 0x0000000000476bcb in SquiggleRead::load_from_fast5 (this=this@entry=0x7ffe902c1910, flags=flags@entry=0) at src/nanopolish_squiggle_read.cpp:136
#18 0x0000000000477883 in SquiggleRead::SquiggleRead (this=0x7ffe902c1910, name=..., path=..., flags=0) at src/nanopolish_squiggle_read.cpp:25
#19 0x000000000045aca6 in add_aligned_events (name_map=..., fai=0x7789c80, hdr=0x9b8580, record=0x779fbb0, read_idx=24754, region_start=-1, region_end=-1,
    round=0, training=...) at src/nanopolish_methyltrain.cpp:317
#20 0x000000000045bbb6 in train_one_round () at src/nanopolish_methyltrain.cpp:623
#21 0x00007fffe05b113e in gomp_thread_start (xdata=<optimized out>) at ../../../libgomp/team.c:118
#22 0x00007fffe0176aa1 in start_thread () from /lib64/libpthread.so.0
#23 0x00007fffdfec393d in clone () from /lib64/libc.so.6

Thanks, the backtrace looks right.
It got further this time (~24,000 reads instead of ~17,000) and the function that segfaulted is in libhdf5, not nanopolish, so I'm not sure what the problem is yet. Could you try running with fewer threads (maybe 8)?

Update.
Nanopolish seems to be working well(ish) when specifying 4 threads.
Command used:
nanopolish methyltrain --reads map006.fa --bam map006.bam --genome 1.canu.corcov500minrl500.aspb-e02.pball.ont2d.quiverfinal1.pilon2x.UPPERCASE.fasta -t 4 --models-fofn=ont.alphabet_nucleotide.R7.fofn --train-kmers all --rounds=5 --progress
The good news is that it made it up to Round3 (i.e. the 4th round). The bad news is that it crashed during Round3 with this error:
registering model t.006-ONT
registering model c.p1.006-ONT
registering model c.p2.006-ONT
Starting round 0
[methyltrain]                            [==================================================] 100% in 0s
Starting round 1
[methyltrain]                            [==================================================] 100% in 0s
Starting round 2
[methyltrain]                            [==================================================] 100% in 0s
Starting round 3
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread<PHONE_NUMBER>45152:
  #000: H5F.c line 604 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: H5Fint.c line 990 in H5F_open(): unable to open file: time = Sun Nov 20 23:09:50 2016
, name = 'lib14/pass/newt_sciara_coprophila_library_014_restart_maleEmbryo_48hr_Mk1_map006_ontprotocol_FAA70180_5246_1_ch258_file150_strand.fast5', tent_flags = 0
    major: File accessibilty
    minor: Unable to open file
  #002: H5FD.c line 992 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #003: H5FDsec2.c line 343 in H5FD_sec2_open(): unable to open file: name = 'lib14/pass/newt_sciara_coprophila_library_014_restart_maleEmbryo_48hr_Mk1_map006_ontprotocol_FAA70180_5246_1_ch258_file150_strand.fast5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
    major: File accessibilty
    minor: Unable to open file
terminate called after throwing an instance of 'hdf5_tools::Exception'
  what():  /Analyses/Basecall_2D_000/BaseCalled_2D/Alignment: lib14/pass/newt_sciara_coprophila_library_014_restart_maleEmbryo_48hr_Mk1_map006_ontprotocol_FAA70180_5246_1_ch258_file150_strand.fast5: error in H5Fopen
/var/spool/slurmd/job14038462/slurm_script: line 39: 14393 Aborted                 nanopolish methyltrain --reads $R --bam $B --genome $G -t $T --models-fofn=ont.alphabet_nucleotide.R7.fofn --train-kmers all --rounds=5 --progress

It is odd that a file that must have been fine during previous rounds caused this error in a later round. Do you think this file became corrupt at some point (not necessarily due to nanopolish but in the same time frame)?
Also, the trained models up to this point seem to be suspicious. For example if I do:
paste <( tail -n +6 t.006.ont.alphabet_nucleotide.model ) <( tail -n +7 t.006.trained ) | awk '{print $1,$2,$8,$2-$8}' | awk '$4<=-1 || $4>=1'

There are 1318 6mers that differ by at least 1 pA.

Does this look abnormal to you? Perhaps it is because I used 2d-or-template for all pass/ and fail/ reads for nanopolish extract?
This was my pipeline:
T=4
R=map006.fa
B=map006.bam
G=1.canu.corcov500minrl500.aspb-e02.pball.ont2d.quiverfinal1.pilon2x.UPPERCASE.fasta

if [ ! -f ${G}.fai ]; then samtools faidx $G; fi
bwa index $G

nanopolish extract ${lib}/pass/ -o pass.fa -t 2d
nanopolish extract ${lib}/fail/ -o fail.fa -t 2d-or-template

cat pass.fa fail.fa > ${R}
bwa mem -M -x ont2d $G $R -t $T | samtools sort -T ${lib}.pass --threads $T | samtools view -F 4 -q 1 -bSh - > $B
samtools index $B

nanopolish methyltrain --reads $R --bam $B --genome $G -t $T --models-fofn=ont.alphabet_nucleotide.R7.fofn --train-kmers all --rounds=5 --progress

Perhaps next I should just do 2D......
As a final thought, is there a way to resume the training from where I left off?
Thanks for any of your thoughts.
best,
John


Added dummy client data

Added dummy client data.

Figure: Dummy client card response from the SophieBot.

Codecov Report

Merging #486 (368c59c) into main (a830a58) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #486   +/-   ##
=======================================
  Coverage   32.84%   32.84%
=======================================
  Files          76       76
  Lines        2128     2128
=======================================
  Hits          699      699
  Misses       1429     1429

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update a830a58...368c59c. Read the comment docs.


How to upload multiple file in MatBlazor File Upload component . This feature is missing.please can you add these feature

Closing this as an duplicate of #435


Additional enum changes per commit comment on https://github.com/IBM-…

There was a comment on my last PR that the enums will need to be compliant with the spec here: https://github.com/apple/swift-evolution/blob/master/proposals/0036-enum-dot.md
Description
Changed several enums and constants to be camelCase.
Motivation and Context

How Has This Been Tested?
Tests passed.
Checklist:

[ ] I have submitted a CLA form
[ ] If applicable, I have updated the documentation accordingly.
[ ] If applicable, I have added tests to cover my changes.

Reviewed. Looks good. Merging


[FEAT]

Would be cool to have more testnets to test this with. The idea is incredible. I get it.

Which testnets would you like to see?


Add bower.json + grunt

Hi, it would be nice if a bower.json was defined in order to get the dependencies (they are as submodules), and also a Grunfile.js definition, in order to generate the build using grunt as an alternative to make.
Thanks!

Hi there,
This project is no longer being maintained so this issue is being closed. Thank you for using r2d3 and taking the time to report this issue.


change all commands use org/env flags

environment cmd uses org/env flags for environment name
deployment cmd uses org/env flags for environment name
disable API proxy bundle creation cmd until its new use is determined
update verbose printing to only print used variables
update README to reflect changes

way out of date and not very necessary right now


[Marker.io] (mobile)(suggestion) user should be able to view different images by sliding on screen

Steps to reproduce:

go to any project details page
scroll down to images section (with navigation arrows)
try to slide on screen to view diffrent image

Actual result: it is not changing
Expected result: we can ignore this if we are ok with current behaviour .else we can fix this

Reported by: vinod<EMAIL_ADDRESS>- Contact via Marker.io
Source URL: https://kensway.webflow.io/projects/wellington-city-mission---whakamaru-6
Issue details: Open in Marker.io
Device typemobileBrowserChrome Mobile <IP_ADDRESS>Screen Size412 x 892OSAndroid 11.0.0Viewport Size412 x 812Pixel<EMAIL_ADDRESS>
🤖 Marker.io bot - 💬 Vinod commented:

working now

Reply here

🤖 Marker.io bot - This issue was marked as ✅ Resolved in Marker.io


using llavar

maybe a dumb question,
I tried LlaVa and it did not succeed in processing text, so I found this LlaVar model. Which might be exactly what im looking for.
just wondering how I should run it.
do you load it up with Gradio ? or ?
could you provide some insights into using the llavar model.

We provide the snapshot of the LLaVA codebase we used in this repo (the llava folder, is kind of outdated now). You can host it via Gradio following the instructions.

Hi Steven,
Thank you for your answer :-)
not sure if you read it right, but I mentioned LLaVar,,,, ((notice the "r" at the end).
did your answer take that into account ?
if so , then I will take a look at this better.
Im only asking because the llava model had some difficulty understanding numbers on an Icelandic Invoice.... But it did alright with numbers on an english invoice.
So, its my understanding that LLaVar (with an rrrr :-) is a model that is better with text and numbers.
trying to figure out where and how I can try out that LLaVar.

Hi, thanks for the follow-up.
The current release of LLaVAR uses the same architecture as LLaVA. So, hosting LLaVAR should be similar to hosting LLaVA. All you need is to change the model checkpoint you used. You can find more details in the README and other issues.


range with more then 1 parameter causes flicker and app crash on Android

Godot version:
v3.2.2
OS/device including version:
Multiple Android devices, both actual hardware and emulator
Issue description:
Using range with more then 1 parameter causes app to crash / screen flicker on Android.
The only useful bit from Logcat is the following:
**SCRIPT ERROR**: Parse Error: Too many arguments for 'hash()' call. Expected at most 1.
At: res://hello_world.gdc:7:GDScript::load_byte_code() - Parse Error: Too many arguments for 'hash()' call. Expected at most 1.

Steps to reproduce:
for i in range(0, 25, 1)

Can you provide a reproduction project?
I tried and I can't reproduce it. No problem with this script:
extends Label

func _ready():
	for i in range(0, 25, 1):
		text += " " + str(i)

The Label properly lists all numbers from 0 to 24.

Are you maybe using export templates which do not match your Godot version? That's the usual suspect when getting bytecode errors, as the bytecode of different Godot versions is not compatible.

I'll check export templates
I Just added a Node and then a script with the following:
func _ready(): 	for i in range(0, 25, 1): 		print_debug(i)

Right.  Had forgotten to point my Path to Godot I was using. Many apologies. Will keep the export template bytecode error in mind in the futre!

Great, closing then.


Bug: an extra space is inserted after the return statement if the function returns void

Bug: an extra space is inserted after the return statement inserted by code completion if the function explicitly returns void:
function foo(): Void
{
  return ;
}

Expected result:
function foo(): Void
{
  return;
}

FD version: https://github.com/fdorg/flashdevelop/commit/c4264e9f73

duplicate #3229


Supporting fix for #949

supporting for fix #949

After setting IdentityModelEventSource.ShowPII = true;, I also tried to force a resolution to the StringFormatter class.  Now, I'm getting this:
https://imgur.com/a/8x9Okp9

It would appear that whatever process attempts to instantiate System.FormattableString, that process will blow up Azure,  In the case of the Microsoft.IdentityLibrary, we have the issue in:
The type initializer for 'Microsoft.IdentityModel.Protocols.HttpDocumentRetriever' threw an exception.
with an innner exception of:
Could not load type 'System.FormattableString' from assembly 'mscorlib, Version=<IP_ADDRESS>, Culture=neutral, PublicKeyToken=b77a5c561934e089'.
When I tried to instantiate a System.FormattableString in the method that called configManager.GetConfigurationAsync(), I took the exception in that method instead of the Microsoft.Identity library.


Disallow non-empty timezone for CSV reader (#3841)

Which issue does this PR close?

Closes #3841
Rationale for this change

This is a temporary "fix" for #3841 pending a more holisitic rework of the parser interface to properly support timezones #1936
Rather than silently being broken for timezones, this change makes it fail loud
What changes are included in this PR?

Are there any user-facing changes?

The only thing I think this PR needs is a test -- otherwise 👍

Is this PR superceded by  https://github.com/apache/arrow-rs/pull/3908 ?

Is this PR superceded by https://github.com/apache/arrow-rs/pull/3908 ?

Yes, sorry, meant to close


DMF_VirtualHidKeyboard

This example module is missing?

I believe they replaced it with https://github.com/Microsoft/DMF/blob/master/Dmf/Modules.Library/Dmf_HidPortableDeviceButtons.txt

DMF_HidPortableDeviceButtons is an example of how to make a Virtual HID device. But, it does not replace the DMF_VirtualHidKeyboard. I will investigate this and update here.

I have just submitted a fix for this.


SFTP - Authentication via RSA token

Hi,
I am using RSA token authentication for my servers, How can I connect using SFTP plugin with asking password every time instead of configuring directly in config.
Regards,
Santhoshkumar Murugesan.

Config Like the one below.
{
  host: 'host',
  port: 22,
  username: 'username',
  password: null,
  protocol: 'sftp',
  interactiveAuth: true,
  ...
}

And Make sure to set this in /etc/ssh/sshd_config on your server:
ChallengeResponseAuthentication yes

Thanks mate.. It's working...!!!!!


Enable CI for dubbo-ops

We should enable CI (e.g. travis ci) for dubbo-ops, and each pull request should pass CI check before getting merged.

close via https://github.com/apache/incubator-dubbo-ops/pull/40


Updates for spec split & pending 1.0-beta

Related Issue(s): #
Proposed Changes:

Updated stac api to not link internally, but mentioned it and linked to the new repo.
Updated warning to reflect that we aren't super early any more
Some updates to static vs dynamic catalogs, as that hadn't been revisited in awhile (there may be a better place to talk about this than the readme, maybe just in best practices)

PR Checklist:

[x] This PR has no breaking changes.
[ ] I have added my changes to the CHANGELOG or a CHANGELOG entry is not required.
[ ] API only: I have run npm run generate-all to update the generated OpenAPI files.

I may continue to add more edits on this PR, but it's also ok to merge at most any point.

Merging this state as it enables/fixes the CI.


"contextmenu"

Describe the bug
When you right-click on a node, the system context menu opens correctly; when you click outside to discard the context menu and move the mouse, the mouse starts dragging around the node on which you initially opened the context menu.
Your Example Website or App
https://antv-g6.gitee.io/en/examples/net/radialLayout#interactRadial
Steps to Reproduce the Bug or Issue

Open official G6 examples;
Go to "Interactively Expand a Node" example; in this sample, you can select nodes with a click and drag them keeping the left button down and moving the mouse;
Right click on a node and watch the browser context menu open;
Click somewhere else on the graph and watch the browser context menu close;
Now mouse interaction with the graph is corrupted: moving the mouse causes the node to be dragged around even if no mouse button is pressed; if you single click another node, you don't select it but instead you start dragging it even if no mouse button is pressed; If you double click the graph, the mouse behavior sometimes appears to reset and graph starts behaving like in bullet 2, but things may start to behave weirdly (e.g. more than one node can have the selected status, a thing that doesn't happen in the initial condition of bullet 2).

Expected behavior
As a user, I expected that opening the context menu doesn't corrupt mouse interaction with the graph (i.e. that you can continue to select nodes with a click and drag them keeping the left button down and moving the mouse).
Screenshots or Videos
https://user-images.githubusercontent.com/10465876/214839219-cb14a612-8788-456f-b2de-a17e013d4a02.mov
Platform

OS: macOS Ventura 13.1 (22C65)
Browser: Chrome Version 108.0.5359.124 (Official build) (arm64)
Version: 4.3.2

Additional context
No response

Demos and docs on the domain https://antv-g6.gitee.io is outdated, and we are not able to update it currently. See the demo on https://g6.antv.antgroup.com/en/examples/net/radialLayout#interactRadial
And it is correct as expected

Thanks for the reply. You are correct, the demo at your link works correctly so the issue can be closed.
Do you have any hint on what can cause that problem?

Thanks for the reply. You are correct, the demo at your link works correctly so the issue can be closed. Anyway I still have the same issue in an application I am writing, even using 4.8.5, so I suspect it's something else than G6; in case you have any hint on what can cause the problem on the https://antv-g6.gitee.io/ sample, please reply. Thanks anyway!

Sorry, I rushed the test in reply to your post didn't realise that I was using Firefox; both https://antv-g6.gitee.io/en/examples/net/radialLayout#interactRadial and https://g6.antv.antgroup.com/en/examples/net/radialLayout#interactRadial using Chrome Version 109.0.5414.119 (Official build) (arm64) do fail in the same way as the video. So they do in Safari Version 16.2 (186<IP_ADDRESS>.5). Firefox 108.0.2 (64 bit) instead works.

The problem is already solved by 4.8.x. You could see the demo here https://codesandbox.io/s/epic-wescoff-t41ve9
(codesandbox has the latest dependencies by default)
G6's website depends on<EMAIL_ADDRESS>now, I will upgrade the it ASAP. You could upgrade @antv/g6 in your project to see whether the problem still exist.

Upgrade g6 to v4.8.7 in your project and try again pls.
P.S. the g6 website's dependency is not updated yet, so you might not get the latest result on the website currently. I will update it ASAP

I am sticking to 4.8.1 as when I install 4.8.7 in an Angular app I get the following error on ng serve (using typescript 4.8.2), so I thought typings were broken in latest releases:
Error: node_modules/@antv/g6-pc/lib/graph/tree-graph.d.ts:124:5 - error TS2416: Property 'data' in type 'TreeGraph' is not assignable to the same property in base type 'ITreeGraph'.
  Type '(data?: TreeGraphData | undefined) => void' is not assignable to type '(data?: TreeGraphData | GraphData | undefined) => void'.
    Types of parameters 'data' and 'data' are incompatible.
      Type 'TreeGraphData | GraphData | undefined' is not assignable to type 'TreeGraphData | undefined'.
        Property 'id' is missing in type 'GraphData' but required in type 'TreeGraphData'.

124     data(data?: TreeGraphData): void;
        ~~~~

  node_modules/@antv/g6-core/lib/types/index.d.ts:386:5
    386     id: string;
            ~~
    'id' is declared here.

I manually applied the Typescript definition fixes of PR https://github.com/antvis/G6/pull/4312 to test 4.8.7, and still context menu doesn't work properly.
Even in the official example https://g6.antv.antgroup.com/en/examples/net/radialLayout#interactRadial in Chrome 109.0.5414.119 (Official build) (arm64), if one opens the context menu then mouse clicks begin to behave strangely (nodes can't be dragged, or you can select multiple nodes, and so on). 4.8.7 seems to fix only the fact that after closing the context menu the right-clicked node is not dragged on mousemove.


Adding API messages

@blueorangutan package

@rhtyd a Jenkins job has been kicked to build primate packages. I'll keep you posted as I make progress.

Packaging result: :heavy_check_mark:centos :heavy_check_mark:debian :heavy_check_mark:archive.
QA: http://primate-qa.cloudstack.cloud:8080/client/pr/407 (JID-1996)


Could not activate remote peer 'org.projectatomic.rpmostree1' & ConditionPathExists=/ostree was not met

After Kinoite Aurora upgraded to 40, all rpm-ostree commands fail with an error -
 rpm-ostree update
error: Loading sysroot: Failed to invoke RegisterClient: GDBus.Error:org.freedesktop.DBus.Error.NameHasNoOwner: Could not activate remote peer 'org.projectatomic.rpmostree1': unit failed

 systemctl status rpm-ostreed
○ rpm-ostreed.service - rpm-ostree System Management Daemon
     Loaded: loaded (/usr/lib/systemd/system/rpm-ostreed.service; static)
    Drop-In: /usr/lib/systemd/system/service.d
             └─10-timeout-abort.conf
     Active: inactive (dead) since Wed 2024-04-24 02:42:41 PDT; 18h ago
   Duration: 1min 41.713s
  Condition: start condition unmet at Wed 2024-04-24 20:54:38 PDT; 1min 6s ago
             └─ ConditionPathExists=/ostree was not met
       Docs: man:rpm-ostree(1)
   Main PID: 10611 (code=exited, status=0/SUCCESS)
     Status: "Exiting due to idle"
        CPU: 17.211s

systemctl start rpm-ostreed has no effect.
Related: https://github.com/ublue-os/main/issues/170

Update: seems working fine now


Tests

Let's add missed tests.

@rultor hello

@rultor hello

@vssekorin Hi there! I understand a few simple commands: "merge", "deploy", etc. This page explains them briefly. Any questions or bug reports are welcome. Have fun :)


Session affinity scenario is broken in the sample app

Session affinity doesn't work in ReverseProxy.Config.Sample. It might have got broken when transformation pieces were added.

How does it fail?

Clearing the milestone so this shows up in triage.

Triage: Create PR to fix it and we can review what is left / removed.


[Notifications] Bot does not send a message if a notification is a substring of another existing notification

Steps to reproduce:

Add 3 notifications where the next notification is a substring of the previous one.

-notification add mmmtest
-notification add mmmt
-notification add mmm

Use a different user and type in mmmt

Expected Behavior:
sushii-bot notifies the user that someone mentioned the keyword mmmt.
Observed Behavior:
sushii-bot does not notify the user.

Tested on the lucky sushii server

Thanks, the fix should be in place now.


payload should have id field

Below is the source code:
await this.oa.payloadStore.setContactPayload(this.id, { } as any)

It save empty object as ContactPayload, which will cause id not found error.

id is the required field for payload

Thanks for fixing this!
Please feel free to merge this PR by yourself, cheers!


Blade Extends Layouts.app not minify

layouts.app not minify but blade extends from layouts.app is minify
im sorry for my bad english

thanks

Probably clear your compiled view cache. If not, then it's not being minified because it's not safe to do so. You could force it by enabling the force option.
Alternatively, for best results (smallest output, not fastest execution time), use the minification http middleware. TBH, in most applications, minification is not needed, because the amount it time it takes to minify is larger than the time it takes to transfer those extra bytes across the network.


s2i: use fix-permssions script from s2i core image

Replace the various chmod and chgrp commands with a script from
Red Hat Software Collections that does all of this for us.
See: https://github.com/bucharest-gold/centos7-s2i-nodejs/issues/122
This fixes one part of the issue referenced above.

@helio-frota agree that we are making these changes much earlier in the process. I did this due to the fact that the NPM cache causes permission problems if this step is not taken very early - e.g. when the the image is being created.

@lance Our example is working with that new assemble, so "looks good to me".

The fix-permissions must also be run at the end of the assemble script on whatever directory hierarchy you installed stuff into. If you don't, an application when run, as different user ID, will not be able to do an npm install. So is needed so that everything is writable via group in running container.

Should make clear that the issue with not running fix-permissions will arise in normal use case for the image, not when doing special magic with odo where mounting persistent volume on /opt/app-root.

@GrahamDumpleton so this is confusing to me. Instead of putting fix-permissions in install_node.sh if I run it during the assemble script, npm install fails.
npm ERR! path /opt/app-root/src/.npm/_cacache/tmp/git-clone-0b3f3c89
npm ERR! code EACCES
npm ERR! errno -13
npm ERR! syscall mkdir
npm ERR! Error: EACCES: permission denied, mkdir '/opt/app-root/src/.npm/_cacache/tmp/git-clone-0b3f3c89'
npm ERR!  { [Error: EACCES: permission denied, mkdir '/opt/app-root/src/.npm/_cacache/tmp/git-clone-0b3f3c89']

And I don't understand the benefit of running it twice - once in install_node.sh and once in assemble. We already test post-assemble directory permissions here. Is there something not correct with this test? As far as I can tell, we are doing this correctly - but maybe I am missing something.

@GrahamDumpleton could you provide me with a test scenario that illustrates what you are describing here?

I didn't say to remove it from install_node.sh. My comment about not running it earlier, was in reference to running it earlier in the assemble script. Originally you had some chmod commands near the start of assemble which as far as I could tell would serve no purpose.
There are two places you need to run fix-permissions.
You should run it at the end of any RUN step done from the Dockerfile to fix up permissions on any directories updated which user at runtime needs to write to. This is during the build phase of the base image itself.
It should then also be run at the end of the assemble script during the S2I build phase.
A key thing fix-permissions does is grant write access to group for directories. If this is not done and a action run creates a directory, if something later on at runtime for the container attempts to write to that same directory, it will fail due to lacking write access to the directory. This is because at runtime it runs as random uid and relies on having group write access. Group write access works because permissions on the directory will have directory group being root, which is what the random user at runtime also runs as.
As a test, you want to be seeing if at runtime you can write to a directory which was only created during the assemble and which didn't exist before then.

@GrahamDumpleton this fix should resolve that issue https://github.com/bucharest-gold/centos7-s2i-nodejs/commit/12aa3a2fb594e880c1f4e86cb74a6757b980e5d8


REPL tab completion does not work through webrepl_client.py

/webrepl_client.py tab completion is not working:
Instead of the REPL printing completed variable and module names, the REPL prints six spaces, like a tab. The lack of tab completion substantially slows interactive work.

I agree, but have no access to my ESPs for the next 3 weeks.
Needs new case handling before inp is send to websocket.
PR welcome.

I would submit a pull request myself if I knew enough about this. As it is, it would require quite a lot of digging on my part to come up to speed and implement this, and consequently it would probably not be the elegant solution you would come up with. I hope you have time to do this. I'll remind you in couple of  weeks if I don't see anything, and I'm happy to beta test it on my ESPs.


[Analysis] State-owned enterprises and censorship

Motivating questions: Are SOE-related cases more likely to get censored?

Summary statistics for firm state-ownership:
We observe 1,230,849 firms in total, among which:

78.78% are State-owned enterprises,

0.008% are central SOE,

21.20% are SOE-connected firms,

1.56% are central-SOE-connected firms


ADD: 增加wxml压缩插件

基于html-minifier实现的用于压缩小程序wxml文件的插件
https://www.npmjs.com/package/html-minifier

Codecov Report

Merging #17 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #17   +/-   ##
=======================================
  Coverage   95.26%   95.26%
=======================================
  Files          62       62
  Lines         971      971
  Branches      259      259
=======================================
  Hits          925      925
  Misses         40       40
  Partials        6        6

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5f591ed...6f1f048. Read the comment docs.


Problem with resolving alias...

Hi guys...
Currently I've a problem with creating an alias. When I try to create some alias in webpack.config.js (resolve.alias.someAlias) then webpack throw error:
ERROR in ./src/main.js Module not found: Error: Cannot resolve 'file' or 'directory' ./config/project.config in /home/***/***/project/src  @ ./src/main.js 23:15-48
My configuration in webpack.config.js is:
  resolve : {     root  : project.paths.client(),     alias: {       '~config': './home/path/to/config/dir'     },     extensions : ['', '.js', '.jsx', '.json']   },
and I try to refer project.config.js from /src/main.js
import $config from '~config/project.config'
So, my question is what is wrong?

I tried with relative path and absolute path, but the result is same.

One problem with this is that you can't import any modules that rely on Node bindings (e.g. fs) into webpack, because they won't be running on the same platform in the browser.
If you were to create a config that webpack could package, and you wanted to import that across your project, it would look like this:
// ./src/app.config.js
export default {
  foo: 'bar'
}

// ./build/webpack.config.
alias: {
  // points to `./src/app.config.js`
  config: inProject(project.srcDir, 'app.config'),
}

// src/path/to/some/nested/file.js
import $config from 'config'

$config.foo // => 'bar'

Hope that helps.


SQL failed because table is not created.

Bug Report
Please answer these questions before submitting your issue. Thanks!
1. Minimal reproduce step (Required)

add a failpoint in InterpreterCreateQuery::createTable before res->startup();
start a cluster and make the failpoint enabled.
drop table if exists test.t;create table test.t(a int);alter table test.t set tiflash replica 1;set session tidb_isolation_read_engines='tiflash'; select * from test.t;
and run the sql set session tidb_isolation_read_engines='tiflash'; select * from test.t; in another seesion

2. What did you expect to see? (Required)
ERROR 1105 (HY000): other error for mpp stream: Code: 0, e.displayText() = DB::TiFlashException: Table 111 doesn't exist., e.what() = DB::TiFlashException,
3. What did you see instead (Required)
sql not return when failpoint enabled.
4. What is your TiFlash version? (Required)
master

change the severity from critical to major as the error will automatically disappear if user retry the query


added example: changefeed sync with redux app state boilerplate

[x] I have read and agreed to the RethinkDB Contributor License Agreement http://rethinkdb.com/community/cla/

Description
I've pieced together a working boilerplate for changefeed interaction demonstration with a Redux store.
boilerplate documentation will be included over time - however, it's fairly simple to follow how Redux is alternatively triggered by RethinkDB changefeeds as opposed to immediately triggering redux action creators. User actions in this case trigger a RethinkDB query which in-turn send changefeeds to trigger redux action creators.

Thank you.  I've merged this to master.  It might take some time to get on the website.

you're the man, sam


RSComposite>>#adjustToChildren is wrong

from issue https://github.com/ObjectProfile/Roassal3/issues/452

Moved to Roassal3


SPIKE Enable query logging for the DNS(BIND) server.

Context:
This ticket has been spun off from ticket 182 where we encountered DNS errors.
We need to look into enabling query logging for the DNS(BIND) server for improved monitoring. This could be an off the shelf solution or in house. We need to review the work and tools required to do this.

More of a strategic ticket than something that impacts the infrastructure

Message from Shreya about potential off the shelf options.  'Off the shelf is ok - I just need to know roughly, what's the problem statement e.g. we're seeing spikes in traffic and the impact could be x. We need logging to be able to investigate. If we implemented this ourselves it would take x amount of time, and x offers an off the shelf package that costs x and provides x.'


Error: unable to resolve actions/conda-skeleton-publish@v1

I am trying to use this action but I get Error: Unable to resolve actionactions/conda-skeleton-publish@v1, repository not found
Any hints on how to fix it?

Hi @ubaldot, you will need to specify the user/org in the YAML uses key for your workflow definition:
uses: silvxlabs/conda-skeleton-publish@v2

The example in the README only works for local tests. I'm closing this issue; feel free to reopen it if you continue to experience issues.

Ah ok! Now it works! It is a bit confusing that sometimes you just use actions some other times user (not a critique on your tool which looks great!).
But now I have another issue though:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpqbeqwoasconda_skeleton_dymoval-0.5.2.tar.gz/dymoval-0.5.2/setup.py'
My project does not have any setup.py as it uses the new pyproject.toml file.
Shall I open a dedicated issue (even if that seems more a conda related problem. It seems they haven't updated their build system for projects that only have pyproject.toml files)?
Also, I have
with:
    pypi_package: dymoval
    python_version: [3](https://github.com/VolvoGroup/dymoval/actions/runs/3421083499/jobs/5696740008#step:3:3).10
    upload_channel: conda-forge
    access_token: ***
    stable: true
    package_version: latest
    build_channels: conda-forge
    platforms: win-6[4](https://github.com/VolvoGroup/dymoval/actions/runs/3421083499/jobs/5696740008#step:3:4) osx-[6](https://github.com/VolvoGroup/dymoval/actions/runs/3421083499/jobs/5696740008#step:3:6)4 osx-arm64 linux-64 linux-aarch64
    wait: false

but I got
=======================================
Creating build recipe from PyPI package
=======================================
/opt/conda/lib/python3.9/site-packages/requests/__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.8) or chardet (5.0.0)/charset_normalizer (2.0.4) doesn't match a supported version!

i.e. I asked for Python 3.10 but it seems it is using Python 3.9

I have not tried this action with a .toml file, so I'm not sure if that's the issue. If you find a solution feel free to submit a PR, and we'll incorporate the fix in the next release.


Feedback: demo issues

First of all, slick library and good work.  Thanks.
However, the demo that you have at http://react-redux-grid.herokuapp.com does not show the vast capabilities of this component:

Dragging Column Orderring (does not refresh).
Sortable Columns (clicked but nothing happen).
Delete of rows (clicked but nothing happen, not sure if this is intended).

Tested using chrome (50.0.2661.102) and firefox (47.0.1).

Agreed, I've been meaning to update the demo page to include the newest feature set. I will spend some time this weekend updating the demo page, to get it current with the newest version. I'll let you know when the changes have been made.
Thanks!

I've updated the demo site to include the newest version of the grid (which fixes the bugs you mentioned). Thanks for the feedback!

Thanks @bencripps, may i know which demo show the sorting capabilities.

@kayazinc the complex demo now has sorting enabled.

Closing this issue for now -- if you have other issues/requests, please let me know.

@bencripps, thanks for the quick response, its a beauty!


Prevent loading overly long samples

The Tracker has a limit on sample length, avoid loading samples that go over this limit. (TODO: figure out this limit).
There should be a notification to the user when this happens.

The longest recorded audio file can be 30 seconds long max.

https://polyend.com/manuals/tracker/#the-sampler


scan stuck after finished running tests

New Issue Checklist

[ ] Updated fastlane to the latest version
[ ] I have read the Contribution Guidelines

Issue Description
I have installed the latest version of scan, but not fastlane.
It's awesome and works well in my server mac pro if directly open the server mac pro command line and enter
 scan --workspace myApp.xcworkspace --scheme myApp --device 'iPhone 6' clean
However, if I put this command in the Jenkins job, it's always loading after finished running the tests. I try to use another mac to access the server mac pro through ssh, the same problem happens even I use the same command line.
Complete output when running fastlane, including the stack trace and command used
15:38:52: ▸ ValidatorTest
15:38:52: ▸ ✓ Password (0.007 seconds)
15:38:52: ▸ ✓ Number (0.005 seconds)
15:38:52: ▸ ✓ NewLine (0.005 seconds)
15:38:52: ▸ ✓ Hash (0.006 seconds)
15:38:52: ▸ ✓ At (0.005 seconds)
15:38:52: ▸ ✓ Mail (0.008 seconds)
15:38:52: ▸ ✓ Phone (0.252 seconds)
15:38:52: ▸ ✓ URL (0.039 seconds)
15:38:52: ▸ Executed 38 tests, with 0 failures (0 unexpected) in 16.332 (17.564) seconds

^C^C
Cancelled... use --verbose to show the stack trace
XXXXs-Mac-Pro:XXX xxx$ scan --verbose
INFO [2016-09-26 16:10:50.04]: $ xcodebuild -list -workspace ./XXX.xcworkspace
Select Scheme:
1. XXX
2. XXXCore
3. socketio
4. Analytics
5. DTCoreText
6. DTFoundation
7. IDMPhotoBrowser
8. JTCalendar
9. MGSwipeTableCell
10. Pods
11. SDWebImage
12. SnapKit
13. TTTAttributedLabel
14. YYText
?

========
If I run the command line directly in the mac server, here is the success output
[15:08:50]: ▸ ValidatorTest
[15:08:50]: ▸ ✓ Password (0.001 seconds)
[15:08:50]: ▸ ✓ Number (0.001 seconds)
[15:08:50]: ▸ ✓ NewLine (0.001 seconds)
[15:08:50]: ▸ ✓ Hash (0.001 seconds)
[15:08:50]: ▸ ✓ At (0.001 seconds)
[15:08:50]: ▸ ✓ Mail (0.001 seconds)
[15:08:50]: ▸ ✓ Phone (0.003 seconds)
[15:08:50]: ▸ ✓ URL (0.010 seconds)
[15:08:50]: ▸ 	 Executed 38 tests, with 0 failures (0 unexpected) in 0.240 (0.302) seconds
[15:08:50]: ▸
[15:08:50]: ▸ Test Succeeded
+--------------------+-------+
|        Test Results        |
+--------------------+-------+
| Number of tests    | 38    |
| Number of failures | 0     |
+--------------------+-------+

Configuration Files
Please copy the complete content of your Fastfile and any other configuration files you use below:
Fastfile:
Environment
fastlane version (run fastlane -v):
Xcode 7.3.1,  OS X 10.11.6
Do you use bundler to execute fastlane (i.e. bundle exec fastlane)?
Do you use a Ruby environment manager (e.g. chruby, rbenv, rvm)?

?  ^C/Library/Ruby/Gems/2.0.0/gems/highline-1.7.8/lib/highline.rb:870:in `gets': Interrupt
	from /Library/Ruby/Gems/2.0.0/gems/highline-1.7.8/lib/highline.rb:870:in `get_line'
	from /Library/Ruby/Gems/2.0.0/gems/highline-1.7.8/lib/highline.rb:891:in `get_response'
	from /Library/Ruby/Gems/2.0.0/gems/highline-1.7.8/lib/highline.rb:264:in `ask'
	from /Library/Ruby/Gems/2.0.0/gems/highline-1.7.8/lib/highline.rb:365:in `choose'
	from /Library/Ruby/Gems/2.0.0/gems/fastlane_core-0.52.0/lib/fastlane_core/project.rb:137:in `select_scheme'
	from /Library/Ruby/Gems/2.0.0/gems/scan-0.13.0/lib/scan/detect_values.rb:21:in `set_additional_default_values'
	from /Library/Ruby/Gems/2.0.0/gems/scan-0.13.0/lib/scan.rb:27:in `config='
	from /Library/Ruby/Gems/2.0.0/gems/scan-0.13.0/lib/scan/manager.rb:4:in `work'
	from /Library/Ruby/Gems/2.0.0/gems/scan-0.13.0/lib/scan/commands_generator.rb:41:in `block (2 levels) in run'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.4.0/lib/commander/command.rb:178:in `call'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.4.0/lib/commander/command.rb:178:in `call'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.4.0/lib/commander/command.rb:153:in `run'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.4.0/lib/commander/runner.rb:444:in `run_active_command'
	from /Library/Ruby/Gems/2.0.0/gems/fastlane_core-0.52.0/lib/fastlane_core/ui/fastlane_runner.rb:36:in `run!'
	from /Library/Ruby/Gems/2.0.0/gems/commander-4.4.0/lib/commander/delegates.rb:15:in `run!'
	from /Library/Ruby/Gems/2.0.0/gems/scan-0.13.0/lib/scan/commands_generator.rb:60:in `run'
	from /Library/Ruby/Gems/2.0.0/gems/scan-0.13.0/lib/scan/commands_generator.rb:14:in `start'
	from /Library/Ruby/Gems/2.0.0/gems/scan-0.13.0/bin/scan:6:in `<top (required)>'
	from /usr/local/bin/scan:23:in `load'
	from /usr/local/bin/scan:23:in `<main>'

@yeyimilk Thanks for reaching out. Can you try setting the --scheme parameter of scan?


Removed Alpha Bots

Removed Alpha Bots
The API endpoint for the alphabots(which is https://hoaxbot3000.herokuapp.com/), is no longer working and it's bringing back 404s. For the time being, I am removing them from being called.

This PR looks good!


[REQUEST] push to all remote repositories

I would really like another option in the git push menu - a * or "all" to designate push to all of the remote repositories. I often work on two remotes and it would be great to be able to push to all of them in a single command (I recall TextMate has this option).

I'm trying not to add particular features that are less commonly used across all git users.
This seems like a great candidate for a custom command though. You can read about custom commands here and try it out.


Adds hyperterm-duotone-darkspace theme

Checklist:

[ x] The title for my package or theme uses its npm title (hyperterm-plugin-example)

[ x] The link for my package or theme uses the npmjs.com link (https://npmjs.com/package/hyperterm-plugin-example)

[ x] There is a visual representation of what my plugin does in the repo. (Plugin: screenshot or gif || Theme: screenshot of the colors within HyperTerm)

[x ] VERY IMPORTANT: I've written a short (one sentence) description for my package or theme of why it's awesome and deserves to be on the list.

hyperterm-duotone-darkspace

Do we really want to add all six of them? Why not link to the main one and write in the description that the others exist?

Sure, works for me.
On Sat, Jul 23, 2016, 5:37 AM Max Stoiber<EMAIL_ADDRESS>wrote:

Do we really want to add all six of them? Why not link to the main one and
write in the description that the others exist?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/bnb/awesome-hyperterm/pull/55#issuecomment-234709477,
or mute the thread
https://github.com/notifications/unsubscribe-auth/ADdjNNWNIDbzpQxdZjHoHIb-D4rBHYlDks5qYeDsgaJpZM4JTIt4
.

@kkemple Pointing to the main one would be ideal! If you could push that, I'd merge!

@bnb made the requested updates, let me know if i need to do anything else!

Merged! Thanks!


Max Transaction Size

Problem
Currently, the CLI Collate process does not check that the final transaction size is below the max transaction size of 6,144 bytes. This can result in an invalid transaction being submitted to the network and failing.
Solution
Once the CLI collate process has been completed and confirmed all required signers have signed the transactions, it should then check that the resulting transaction that includes signatures is below the max transaction size of 6,144 bytes. If the file size exceeds the max transaction size the collate process should fail and return an error indicating the specific transaction that exceeds the file size.
Alternatives
No response

In that case, the collator should include only the minimum number of
signatures needed. To minimize the size. (Yes finding the true minimum is
NP-complete, but it could use a greedy algorithm).
On Wed, Oct 19, 2022 at 9:22 AM Mark Williamson @.***>
wrote:

Problem
Currently, the CLI Collate process does not check that the final
transaction size is below the max transaction size of 6,144 bytes. This can
result in an invalid transaction being submitted to the network and failing.
Solution
Once the CLI collate process has been completed and confirmed all required
signers have signed the transactions, it should then check that the
resulting transaction that includes signatures is below the max transaction
size of 6,144 bytes. If the file size exceeds the max transaction size the
collate process should fail and return an error indicating the specific
transaction that exceeds the file size.
Alternatives
No response
—
Reply to this email directly, view it on GitHub
https://github.com/hashgraph/hedera-transaction-tool-demo/issues/426,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/ABDBYW7PBYC4KIGDUMAX5P3WD772FANCNFSM6AAAAAARJFXIOE
.
You are receiving this because you are subscribed to this thread.Message
ID: @.***>

This issue still exists in v0.13.0 release


Added 4 unit tests

Added 4 unit tests. Added missing "=". Removed extra whitespace from GCD and LCM

@D-T-666 Hey, your tests disappeared during the rebase.


Fire base caching for publish cloudrun

https://gist.github.com/steren/03d3e58c58c9a53fd49bb78f58541872 has a recipe for this, via https://twitter.com/steren/status/1477038411114446848
Could this enable easier vanity URLs of the format https://$project_id.web.app/? How about CDN caching?

API tutorial: https://firebase.google.com/docs/hosting/api-deploy

API tutorial: https://firebase.google.com/docs/hosting/api-deploy


Update Japanese toc.yaml

Updated ./translations/ja/toc.yaml based on the resent translation.

thank you!


Fix username typo while setting up an user for the service

Thanks for the patch. I will merge it around the next weend, when I get around fixing some other issues.

Thanks for the patch! ^^

Finally, after 5 years!
Thank you, @q3k. 😄


controls don't autohide from mouse input if device also has touch input

control bar autohide only triggers when mouse is out of the video area. but in fullscreen it can never be moved out since video covers the screen. so control bar never autohides in fullscreen

@anonghuser can you please provide some extra information? Can you send a video of the issue so that I can create a better internal ticket?
Thank you!

just play the sample videos on the fluidplayer homepage and see how the control bar at the bottom never disappears if you are in fullscreen...

@ZentoDH can you please confirm if this is a bug or a new feature? Thank you!

Hi there, just checked a couple of sites where this is used and it was working as expected.
Note that the auto hide behaviour is set to false by default. If you do want an auto hide in your app, you can check here in the control bar documentation where to flip that flag. As for the fluid player website, it's configured for that video have autohide set to false, so we would expect it not to hide. Now I did notice that it hides it when you leave it with your mouse, as you pointed out. So I'll raise an internal ticket so we can discuss this. Thanks for bringing this to our attention!

Hello,
I'm not actually using fluid-player myself, I'm just visiting many other sites that use it and see the control bar gets in the way. But I guess despite that I should've made a test page earlier to investigate/demonstrate the issue earlier.
Here is an example that sets it to true. The code for it was copied from the docs. It still doesn't hide in fullscreen, and additionally stops autohiding it in normal mode now.

Ah yes I see. On my side, if you go full screen using the shortcutF, it stays on the screen unless you move the mouse and wait for a couple of seconds. The other way to replicate it is on clicking full screen, then you can see it starting to fade away but quickly going back to full opacity. Then you have to move you mouse again to trigger the autohide so it fades away 3 seconds later.
That's how it is for you right?

On my side the control bar never ever disappears in fullscreen. Not when i use F, not when i use the mouse, not with autohide: true, not with autohide: false.
In addition, in non-fullscreen it only disappears when autohide: false and I move the mouse outside of the video. I.e. it never disappears from the mouse being idle, only from the mouse being outside it.

Your claim that it mostly works fine for you after moving the mouse (some edge cases about the very first time you go fullscreen aside) made me wonder what else could be different in my setup.
Not even sure how one could detect it from javascript, but my laptop also has a touch screen. I didn't use it in the tests as I very rarely use it in my normal browsing as well, but maybe that causes the difference?
Now I tried to use the touch screen to press the fullscreen button, and the control bar disappeared 3 seconds later, along with my mouse cursor. Then even moving the mouse didn't bring them back.

@ZentoDH Can you please provide extra feedback here? Thank you!

@sergiomcsousa No feedback extra feedback I can give yet. I want to get my hands on a 2in1 so I can see if it has something to do with touchscreens on laptops

    Object.defineProperty(navigator, 'maxTouchPoints', {value:0})

This is what I use right now in a tampermonkey script to work-around the issue and trick fluid-player to not treat my device as touch-capable. I guess you could do the opposite, and run this with value:1 before loading fluid player while you don't have a suitable device to test. It won't let you test actual touch inputs of course, but it will at least show you how mouse inputs get affected.

Nice one, that's really helpful thanks! It probably has something to do with how we detect if it's a mobile device and not taking into account that computers can have touch screens too. We'll look into it.

I just remembered that chrome dev tools also has "device emulation" mode (icon right next to the inspect element icon in to top left) which sets maxTouchPoints to 1 and emulates touch events from clicks when enabled, maybe that can help with your testing as well.


Fix 'Can't find variable: React'

Border example throws "Can't find variable: React" error.
This simply includes React (using old 'require' syntax to keep syntax consistent)

Thanks! Tested out locally, all good.
@facebook-github-bot shipit

PS. @mkonicek @satya164 there seem to be quite a few other issues re: that, e.g. BoxShadow example does not work as well.
@nicholaspsmith would you mind checking all pages when you have time and submitting relevant PR with fixes once again? :)

No problem.


Lettuce cluster topology refresh querying known failed nodes

Bug Report
Two of the nodes in our cluster were marked as failed on several of the nodes and handshake on the others. These nodes had been replaced with new nodes, so they were gone and never coming back, but not yet forgotten.
I expected that Lettuce would filter out known failed nodes (or suspicious) from the information it gets from the cluster.
Current Behavior
Currently Lettuce appears to attempt to query known failed nodes when refreshing the cluster topology:

Stack trace
io.lettuce.core.cluster.topology.ClusterTopologyRefresh - Unable to connect to <IP_ADDRESS>:6379
 java.util.concurrent.CompletionException: io.netty.channel.AbstractChannel$AnnotatedConnectException: finishConnect(..) failed: No route to host: /<IP_ADDRESS>:6379
 	at java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:292)
 	at java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:308)
 	at java.util.concurrent.CompletableFuture.uniApply(CompletableFuture.java:593)
 	at java.util.concurrent.CompletableFuture$UniApply.tryFire(CompletableFuture.java:577)
 	at java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:474)
 	at java.util.concurrent.CompletableFuture.completeExceptionally(CompletableFuture.java:1977)
 	at io.lettuce.core.AbstractRedisClient.lambda$initializeChannelAsync0$4(AbstractRedisClient.java:329)
 	at io.netty.util.concurrent.DefaultPromise.notifyListener0(DefaultPromise.java:577)
 	at io.netty.util.concurrent.DefaultPromise.notifyListeners0(DefaultPromise.java:570)
 	at io.netty.util.concurrent.DefaultPromise.notifyListenersNow(DefaultPromise.java:549)
 	at io.netty.util.concurrent.DefaultPromise.notifyListeners(DefaultPromise.java:490)
 	at io.netty.util.concurrent.DefaultPromise.setValue0(DefaultPromise.java:615)
 	at io.netty.util.concurrent.DefaultPromise.setFailure0(DefaultPromise.java:608)
 	at io.netty.util.concurrent.DefaultPromise.tryFailure(DefaultPromise.java:117)
 	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.fulfillConnectPromise(AbstractEpollChannel.java:629)
 	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.finishConnect(AbstractEpollChannel.java:648)
 	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.epollOutReady(AbstractEpollChannel.java:522)
 	at io.netty.channel.epoll.EpollEventLoop.processReady(EpollEventLoop.java:407)
 	at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:317)
 	at io.netty.util.concurrent.SingleThreadEventExecutor$6.run(SingleThreadEventExecutor.java:1044)
 	at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
 	at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
 	at java.lang.Thread.run(Thread.java:748)
 Caused by: io.netty.channel.AbstractChannel$AnnotatedConnectException: finishConnect(..) failed: No route to host: /<IP_ADDRESS>:6379
 Caused by: java.net.ConnectException: finishConnect(..) failed: No route to host
 	at io.netty.channel.unix.Errors.throwConnectException(Errors.java:112)
 	at io.netty.channel.unix.Socket.finishConnect(Socket.java:269)
 	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.doFinishConnect(AbstractEpollChannel.java:665)
 	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.finishConnect(AbstractEpollChannel.java:642)
 	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.epollOutReady(AbstractEpollChannel.java:522)
 	at io.netty.channel.epoll.EpollEventLoop.processReady(EpollEventLoop.java:407)
 	at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:317)
 	at io.netty.util.concurrent.SingleThreadEventExecutor$6.run(SingleThreadEventExecutor.java:1044)
 	at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
 	at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
 	at java.lang.Thread.run(Thread.java:748)

Input Code

Input Code
ClusterTopologyRefreshOptions topologyRefreshOptions = ClusterTopologyRefreshOptions.builder()
        .enablePeriodicRefresh(Duration.of(60, ChronoUnit.SECONDS))
        .enableAllAdaptiveRefreshTriggers()
        .build();
client.setOptions(ClusterClientOptions.builder()
		.autoReconnect(true)
		.pingBeforeActivateConnection(true)
		.topologyRefreshOptions(topologyRefreshOptions)
		.build());

Expected behavior/code
I expected Lettuce would exclude the nodes that are known to be failed, or not yet known to be good (handshaking) from its probes.
I have my Redis cluster running in Docker Swarm and nodes may fail and be replaced automatically, but remain in the CLUSTER NODES list until I get around to forgetting them.
Environment

Lettuce version(s): 5.1.4, 5.2.0
Redis version: 5.0.5

Possible Solution
Perhaps add a check for RedisClusterNode.NodeFlag.FAIL and RedisClusterNode.NodeFlag.HANDSHAKE to ClusterTopologyRefresh.validNode?
Note that after I CLUSTER FORGET <node> each of the failed nodes lettuce recovered by itself and stopped looking for those bad nodes and the stack traces went away.

The current behavior is a matter of perspective. One node's view on another one is very likely to be different from the view from the application perspective. Nodes can e.g. be distributed across data networks and one server might not be able to connect to another one while your application is able to connect to both nodes.

@mp911de thanks for your quick response. Yes, I agree about the perspective. In this case no node saw the failed nodes as good—could that not be a signal that it's rogue?
I'm not sure that this actually caused a disturbance in our app, apart from the stack traces, although we observed some odd but not reproduced behaviour.
Would it be bad for Lettuce to talk to a Redis node that was denied by the bulk of the cluster?

Lettuce tries to do its best without applying filters.
Let's dig a bit into detail.
If we consider how we learn that a node is probably failed then what needs to happen first is fetching the topology first, including attempting to query the failed node. Once the topology refresh has finished, we have the indication that nodes have seen the failed node and likely that we weren't able to connect to that node.
On the next attempt, that happens after the previous one (that can be seconds, minutes or hours) in terms of time-dependency, we know that a particular node was considered a failed node back then. We don't know whether that assumption is still valid. What do we want to do now?

Do we reach out to that node?
Do we exclude it?
What if that node is down?
What if it is back up in the meantime?

There are plenty of approaches. One could be of interest which is dynamicRefreshSources. That is, Lettuce discovers the topology from the initial seed nodes and tries to reach out to the discovered nodes. If you have a known set of nodes, that remains intact, then you could disable dynamicRefreshSources and topology refresh uses only the seed nodes to discover the topology.
Another option, which is already in place, is overriding RedisClusterClient.determinePartitions so you clean up Partitions yourself to avoid reaching out to a particular node. determinePartitions receives the old Partition and Map<RedisURI, Partitions> as input parameters so you could hook into filtering yourself.
I could also think of an approach using filtering by applying a Predicate so you can hand in a filter to prevent nodes from being contacted. Such a feature isn't available (yet).

Related to this; we've found that when we start our application, if there are failed redis nodes, our application spends a lot of time trying to contact them and timing out, which impacts all of our queries. We are using ANY for the cluster node to connect to. Applications that were running at the time of the Redis node failure still log the topology error (as above) but their general usage of Redis is unaffected. We are doing more investigation of this...

There's no good pattern to approach this pattern than reducing dynamicRefreshSources and if you have topological information available, then you might want to override RedisClusterClient.getTopologyRefreshSource() for increased control.
Closing this ticket without a change. We can revisit this ticket once we have found an approach that works.


[catalogs] use secrets

Hello,
Once catalogs have username/password, instead of configmap use a secret
Note: I'm also using this secrets approach to configure authentication with password file + ldap, in order to create the property files (I've seen this approach for ldap, but I would rather avoid to use env vars with passwords)

This is a good improvement!
Worth noting in changelog as breaking tho

@luismacosta can you rebase and address comments?

This looks abandoned.


[BUG] handle case where there is an existing catalog that doesn't conform to new catalog format

Describe the bug
Of course I realized something just after the PR #243 was merged... (following on from #191)
The catalog builder is going to have issues the first time we run it, because there is an existing catalog in the live directory, but it doesn't match the new catalog.yaml structure. Specifically, there isn't a min or max version in the old catalog, so cli::build will throw a KeyError when it tries to read them.
To Reproduce
Will only occur if a live build process is triggered (not recommended right now).
Additional context
We could, of course, solve this outside code by simply deleting the existing catalog.yaml before we do our first new catalog build. However, this would leave users inexplicably unable to access intake.cat.access_nri for a few hours while that happens.
My solution will be to effectively treat this situation as if there is no existing catalog.yaml, but without having to cripple the system while the new catalog builds.

The complication is we want to keep the storage flags from the old catalog. I'm re-jigging the catalog overwrite/move logic to accommodate this.


chore(delete-user-data): added prepare script

Checklist

[x] Added prepare script
[x] Removed cleanup script from build script
[x] Updated external TSConfig to the extensions root
[x] Add .gitignore
[x] Updated typescript and moved from developer dependencies

Testing
Updated engine

Successful Installation and configuration

User data

Successfully ran function console

@googlebot I consent.

@googlebot I consent.

Codecov Report

Merging #800 (920a511) into next (641092c) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             next     #800   +/-   ##
=======================================
  Coverage   50.19%   50.19%
=======================================
  Files          30       30
  Lines        1329     1329
  Branches      192      192
=======================================
  Hits          667      667
  Misses        661      661
  Partials        1        1


mix.sourceMaps() does not work

Laravel Mix Version: 2.1.14
Node Version (node -v): 10.12.0
NPM Version (npm -v): 6.4.1
OS: macOS

Description:
Following the documentation here: https://laravel.com/docs/5.7/mix#css-source-maps
mix.sourceMaps() doesn't work. It's not adding source maps.
Steps To Reproduce:
Add mix.sourceMaps() to your webpack.mix.js file and then npm run dev.
Here is my webpack.mix.js file:
const mix = require('laravel-mix');

/*
 |--------------------------------------------------------------------------
 | Mix Asset Management
 |--------------------------------------------------------------------------
 |
 | Mix provides a clean, fluent API for defining some Webpack build steps
 | for your Laravel application. By default, we are compiling the Sass
 | file for the application as well as bundling up all the JS files.
 |
 */

mix.js('resources/js/app.js', 'public/js')
   .sass('resources/sass/app.scss', 'public/css');

I ran into a similar problem earlier. #879 fix worked for me when I added the following to my options:
mix.options({
    processCssUrls: false,
})
   .sourceMaps()
   .js(...)
   .sass(...);

For me there was an upstream issue with the resolve-url-loader dependency, but it recently got a re-write to postCSS and should resolve the issue. I don't have the time right now to work on a PR for this right now, however.
https://github.com/bholloway/resolve-url-loader/releases/tag/v3.0.0

Thanks, this workaround worked for me:
if ( ! mix.inProduction()) {
    mix.webpackConfig({
        devtool: 'inline-source-map'
    })
}

I'm going to leave this issue open though as I believe the original option isn't working.

Another workaround: .sourceMaps(true, 'source-map'). That first parameter is a boolean value for if you would source maps when ran as production as well.
The interesting thing is that if you use the default value of eval-source-map everything seems to work fine. I'm not sure why it would work fine when you pass it in but not when you let it default to the value.
https://github.com/JeffreyWay/laravel-mix/blob/52582c120f2eaef0146d63a43c41235f40e3f030/src/Api.js#L12

Well, I got the sass sourcemap to generate, the problem is now that the references point to the wrong files when viewed in the browser inspector.

Omg, has this seriously been open since 18th of October? Isn't this kinda like an official package with laravel?

@SimonEast's fix doesn't work for me. I cannot get any CSS sourcemaps to be generated, either inline or separate, either in development or production.

@75th Have you tried putting both?
mix.webpackConfig({
        devtool: 'inline-source-map'
    })

AND mix.sourceMaps()
I used to only have the webpackConfig() method and it was working fine. I haven't been debugging in Chrome lately (2+ weeks) but when I did today, I noticed that source maps weren't working anymore. Adding in mix.sourceMaps() worked.
It's a quick, and dirty fix but I just needed to get the source maps up and running.

I, too, have them both (on Mix 2.1.14) and it's working well:
...
.sourceMaps()
.webpackConfig({devtool: 'source-map'})
...

The sourcemaps might generate, but they point to totally wrong files.
For example:
I have a main style.sass file that imports a partial _base.sass.

@import 'base'

In _base.sass I have a simple sass rule:
body
   background: green

When I open the inspector in ChromeDevTools the rule is attributed to style.sass instead of _base.sass.

This is a fundamental thing that works flawlessly in gulp.

Another workaround: .sourceMaps(true, 'source-map'). That first parameter is a boolean value for if you would source maps when ran as production as well.
The second parameter is the type of of source map. The interesting thing is that if you use the default value of eval-source-map everything seems to work fine. I'm not sure why it would work fine when you pass it in but not when you let it default to the value.
https://github.com/JeffreyWay/laravel-mix/blob/52582c120f2eaef0146d63a43c41235f40e3f030/src/Api.js#L12

I found that .sourceMaps(false, 'source-map') forced source maps in development mode.

I was experiencing same with mix 4.0. I rearranged my webpack.mix.js so that mix.sourceMaps() is called  before anything else. Problem resolved; no workarounds needed.

Can confirm here.
mix version: 4.0.15
Node Version (node -v): 10.13.0
NPM Version (npm -v): 6.4.1
OS: Windows
With default webpack.mix.js file just added mix.sourceMaps(); and no CSS maps is created

I have also a lot of problems with sourceMaps, but by doing this:
mix.webpackConfig({     devtool: 'source-map' })
It seems to be working now.
Thanks to the information here:
https://stackoverflow.com/a/37653167
https://webpack.js.org/configuration/devtool/

I was experiencing same with mix 4.0. I rearranged my webpack.mix.js so that mix.sourceMaps() is called before anything else. Problem resolved; no workarounds needed.

This worked for me, but only when combined with...

I have also a lot of problems with sourceMaps, but by doing this:
mix.webpackConfig({ devtool: 'source-map' })
It seems to be working now.

Thank you @arxeiss and @filipve1994 .
I'm on node v8.11.2, npm 6.1.0, Laravel Mix 4.1.2, using outside of Laravel by way of the instructions in the docs, and using mix.less().

I am facing the same problem as @bonovski, the source map is generated, but it's pointing to the wrong file or line.

I had to use a combination of things here and other threads, this might help some people;
My file, with production stuff removed (note that this is from Laravue and running npm run hot not dev;
mix
	.options({
		processCssUrls: false,
	})
	.sourceMaps()
  .js('resources/js/app.js', 'public/js')
  .extract([
    'vue',
    'axios',
    'vuex',
    'vue-router',
    'vue-i18n',
    'element-ui',
    'echarts',
  ])
  .options({
    processCssUrls: false,
  }).sass('resources/js/styles/index.scss', 'public/css/app.css', {
    implementation: require('node-sass'),
    outputStyle: 'compressed',
    sourceMap: true,
	}).eslint()
	.sourceMaps()
	.webpackConfig({
    devtool: 'inline-source-map',
  });

@bonovski did you find a solution to your issue? I'm having the same problem myself and have tried all the solutions suggested here.

tried all workarounds posted here, the only thing that worked is to inline the map, if not, the map will generate but won't work, all the rules point to style.css as @bonovski mentioned above.
here's my webpack.mix.js
mix
.sourceMaps()
.options({
	processCssUrls: false
})
.webpackConfig({devtool: 'inline-source-map'})
.sass('./style.scss', './assets/styles/style.min.css', {implementation: require('node-sass')})
.tailwind('./tailwind.config.js')

Any solutions to @bonovski 's sass source map problem yet?

Pull request #2282 resolves the prod source map issue for sass files.
Details:
Sass sourcemaps fail to generate in production builds due to cssnano combined with OptimizeCSSAssetsPlugin. Moving cssnano into postcss-loader resolves issue. More detail https://www.webfoobar.com/node/109
Note eval-source-maps still will not work at all for CSS, so implementers must use Mix.sourceMaps(true, 'source-map') to allow development builds to successfully generate sourcemaps.

I can't get any sourcemap files to be generated at all.
My webpack.mix.js file:
mix.webpackConfig({ devtool: 'inline-source-map' })
.sourceMaps( true, 'source-map' )
.js( 'resources/js/app.js', 'public/js' )
.sass( 'resources/sass/app.scss', 'public/css' );

<EMAIL_ADDRESS>

@bentaber Thank you! I was wrestling with this problem for hours, and after manually patching Mix with the code from your PR, it's working perfectly. Let's hope it's merged in soon.

Anyone got any of the eval* sourcemap options working?

I, too, have them both (on Mix 2.1.14) and it's working well:
...
.sourceMaps()
.webpackConfig({devtool: 'source-map'})
...

It Worked for me aswell! tnks!

Yeah, the problem is that the "eval-source-map" (or any other eval* option for that matter) doesn't work and since it's set as default for sourceMaps() in production, it seems like sourceMaps() doesn't work.
More elegant solution is for example
.sourceMaps(true, 'inline-source-map')
The third parameter defaults to source-map anyway (for production), so we can leave it empty.

source map created
.sourceMaps()
.webpackConfig({devtool: 'source-map'})

How can remove the "webpack:///" prefix  in styles ?
This solution output error
 mix .webpackConfig({
output: {
    devtoolModuleFilenameTemplate: '[resource-path]'
  }
})

source map created
.sourceMaps()
.webpackConfig({devtool: 'source-map'})

How can remove the "webpack:///" prefix for files.less path in Styles ?
This solution output error
 mix.webpackConfig({
output: {
    devtoolModuleFilenameTemplate: '[resource-path]'
  }
})

sadly not working for me :(
my setup:
{   "private": true,   "scripts": {     "dev": "npm run development",     "development": "cross-env NODE_ENV=development node_modules/webpack/bin/webpack.js --progress --hide-modules --config=node_modules/laravel-mix/setup/webpack.config.js",     "watch": "cross-env NODE_ENV=development node_modules/webpack/bin/webpack.js --watch --progress --hide-modules --config=node_modules/laravel-mix/setup/webpack.config.js",     "watch-poll": "npm run watch -- --watch-poll",     "hot": "cross-env NODE_ENV=development node_modules/webpack-dev-server/bin/webpack-dev-server.js --inline --hot --config=node_modules/laravel-mix/setup/webpack.config.js",     "prod": "npm run production",     "build": "cross-env NODE_ENV=production node_modules/webpack/bin/webpack.js --progress --hide-modules --config=node_modules/laravel-mix/setup/webpack.config.js",     "production": "cross-env NODE_ENV=production node_modules/webpack/bin/webpack.js --progress --hide-modules --config=node_modules/laravel-mix/setup/webpack.config.js && grunt update-theme && grunt git-push",     "test": "grunt dusk-test"   },   "dependencies": {     "bootstrap": "^4.5.0",     "compress": "^0.99.0",     "cross-env": "^5.2.1",     "current-device": "^0.8.2",     "dev-ip": "^1.0.1",     "dotenv": "^6.2.0",     "dotenv-expand": "^5.0.0",     "ekko-lightbox": "^5.3.0",     "flatpickr": "^4.6.3",     "isotope": "^1.0.0-alpha.3",     "isotope-layout": "^3.0.6",     "jquery": "^3.5.1",     "laravel-mix": "^5.0.4",     "mobile-detect": "^1.4.4",     "npm": "^6.14.6",     "popper.js": "^1.16.1",     "sass-loader": "^7.3.1",     "slick-carousel": "^1.8.1",     "vue-typer": "^1.2.0"   },   "browserslist": [     ">0.25%",     "not ie 11",     "not op_mini all"   ],   "devDependencies": {     "animate.css": "^3.7.2",     "archiver": "^3.1.1",     "browser-sync": "^2.26.7",     "browser-sync-webpack-plugin": "^2.2.2",     "ekko-lightbox": "^5.3.0",     "fs": "0.0.1-security",     "fs-finder": "^1.8.1",     "grunt": "^1.2.1",     "grunt-contrib-clean": "^2.0.0",     "grunt-contrib-compress": "^1.6.0",     "grunt-ftp-push": "^1.2.1",     "grunt-git": "^1.0.14",     "grunt-json-generator": "^0.1.0",     "grunt-phpunit": "^0.3.6",     "grunt-string-replace": "^1.3.1",     "load-grunt-config": "^1.0.2",     "load-grunt-tasks": "^4.0.0",     "read-file": "^0.2.0",     "resolve-url-loader": "^2.3.2",     "sass": "^1.26.10",     "vue-template-compiler": "^2.6.11",     "webpack-cli": "^3.3.12"   } }
webpack.mix.js:
`const mix = require("laravel-mix");
var myEnv = require("dotenv").config();
var dotenvExpand = require("dotenv-expand");
dotenvExpand(myEnv);
/*
|--------------------------------------------------------------------------

Mix Asset Management

Mix provides a clean, fluent API for defining some Webpack build steps

for your Laravel application. By default, we are compiling the Sass

file for your application, as well as bundling up your JS files.

*/

const theme = process.env.WP_THEME;
mix.setResourceRoot("../");
mix.setPublicPath(public/themes/${theme}/assets);
mix.sourceMaps()
mix.webpackConfig({devtool: 'source-map'})
mix.webpackConfig({
output: {
devtoolModuleFilenameTemplate: '[resource-path]'
}
})
mix.js("resources/assets/scripts/app.js", "scripts");
mix.sass("resources/assets/styles/app.sass", "styles");
mix.js('resources/assets/backend/scripts/admin.js', 'backend/scripts');
mix.sass('resources/assets/backend/styles/admin.sass', 'backend/styles');
mix.options({
module: {
loaders: [
{
test: /.(woff|woff2|eot|ttf|otf)$/,
use: ["file-loader"],
},
],
},
});
if (mix.inProduction()) {
mix.options({
terser: {
terserOptions: {
compress: {
drop_console: true,
},
},
},
});
}
else{
mix.browserSync({
proxy: process.env.WP_HOME
});
}`

correct code:
 mix   .webpackConfig({      output: {       devtoolModuleFilenameTemplate: '[resource-path]'      },   })   .sourceMaps(false, 'inline-source-map');
but i don't change path, for example
devtoolModuleFilenameTemplate: 'file:///D:/[namespace]'
output: webpack:///./resources/less/style.less?13c8


Users need to understand what "As soon as possible" means

I believe this should be resolved by #313

Assigning this to @Lizzie to advice on how we could improve the content of this page
This is still an issue, as evidenced by Cambridgeshire's UR:

Re: "as soon as possible" how many users found this unclear? (And why?)
"Immediately" and "Straightaway" are alternative wording but are technically incorrect, especially for any councils that don't wish to offer temporary permits. If it's only 1 or 2 users who've found "as soon as possible" unclear I suggest we close this issue.
Re: different start dates for different vehicles, the prototype has been updated since this UR was carried out. Please see screenshot below.
Re: buying a permit for someone who doesn't live there, this links to the V5C discussion #264 #292

Content solution linked to #598 - preparing user expectations of permit start date in advance of permit summary page
Verify route

Non-Verify route / councils that don't issue temporary permits

@sanjaypoyzer might be a bug but the "different dates for different vehicles" radio button isn't showing when you chose more than one permit... the code for it is on the page:

@lizziebruce Can you create a different issue for that bug please as it doesn't relate to the user need on this card


PDK_ROOT environment variable path not found

I got warning: PDK_ROOT environment variable is set but path not found
Help me to solve  this

PDK_ROOT points to a place on the system where the PDK is installed.
On my system PDK_ROOT=/home/schippes/share/pdk, and this directory contains the process data:
ls /home/schippes/share/pdk
gf180mcuA  gf180mcuB  gf180mcuC  gf180mcuD  scripts  sky130A  sky130B

The error message you get is telling you you have set a path on PDK_ROOT but the path does not exist on the system. This means the PDK is not installed or is installed in a different place.
Set a correct path for PDK_ROOT:
export PDK_ROOT=/correct/path/to/pdk/data

I set the PDK_ROOT=/correct/path/to/pdk/data in  bashrc but I got again error
May i change the edit xschemrc file
I still not install open_pdk this may cause warning

I request you to suggest on this error

It looks linke the open_pdks installation was broken due to connection errors. Delete the git workspace and do the open_pdks install again.
remember that /correct/path/to/pdk/data is not an actual path. You must provide the location of the pdk (on some systems it is /usr/local/share/pdk, but it depends on your system installation).

I try to find but can't see any were is I need to to download only pdk file or other any way to find the pdk


xcversion install reinstalls installed versions

I installed Xcode with xcversion install 10
if i check the installed versions with xcversion installed Xcode 10 is listed as installed but if I enter xcversion install 10 he is redownloading Xcode every time on our runner.
Version: xcode-install 2.4.4

Found the issue: its installed as 10.0
if I install it with xcversion install 10 it is stored as 10.0

Just ran into this bug.

Apple lists the version as "10".
It is installed to /Applications/Xcode-10.app
xcversion list shows "10".

So, where is "10.0" coming from?
If xcversion is internally representing the value as "10.0", that is unfortunately inconsistent with the standard representation of the version and leads to problems.


Documentation does not build

Missing ALL in target?
CMake 3.9.0, CentOS 7.2
This fixes it.
--- a/documents/CMakeLists.txt
+++ b/documents/CMakeLists.txt
@@ -9,12 +9,12 @@ find_package(Doxygen)

 if(DOXYGEN_FOUND)
     configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
-    add_custom_target(MaterialXDocs ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+    add_custom_target(MaterialXDocs ALL ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile

That seems like a very reasonable improvement, and we'll test it on our local machines when we return from Siggraph.  At Lucasfilm we most commonly build the MaterialX documentation in Visual Studio, issuing a manual build request for the MaterialXDocs project, but it seems logical that documentation should be part of the "default" build target as well.

Alas, this proposed change would run into a known limitation of CMake, which is that a custom target has no output file, and thus is always considered "out of date":
https://cmake.org/cmake/help/v3.2/command/add_custom_target.html
Given this limitation, if we were to make MaterialXDocs part of the default build target (i.e. by adding the ALL keyword), it would be rebuilt every single time, rather than only building when one of its inputs has been modified.
To my mind, it may be better to leave this pattern as it stands, where the MaterialXDocs project is not part of the default build target, and documentation builds must be specifically requested by the developer.
Any thoughts on alternative approaches?

Now I understand your motivation. Thank you for clearing this up.
Let me make a point for making the documentation part of the ALL build target anyway.
I was just a bit confused as with other packages I am used to generate the documentation when an option to generate documentation is given and set.
Usually I do not build any specific targets as I have no knowledge about them as a "client" user.
I can imagine that a lot of people might find the same to be true if it is only their job to build dependencies.
The reason why I stumbled upon this is because here our build process is handled by rez. With an external/automated build process having to specify explicit targets might be at least a bit inconvenient.
For the use case you mention (developers who do frequent builds) I would expect them to simply leave MATERIALX_GENERATE_DOCS to OFF. I believe this option would satisfy their needs, until the point where they build for deployment with the documentation.
This is just how I see it but it certainly is not a big issue at all as is. Since their is no real standard for build scripts I feel both standpoints are valid. Usually I am used to the described behavior. At least I did not encounter any package yet where I would need to specify a target (for deployment) if there is an option for it. Maybe this is different with visual studio where you are used to opening the solution and picking targets. Still I could argue that "ALL" semantically implies all (valid) targets.
Anyhow thanks for the attention. Let's not waste more time over this. You provide good online documentation anyway, so feel free to do as you feel right.
All the best.

You bring up some very good points here, but for now I think it's best to maintain a separate build step for documentation (e.g. by calling make MaterialXDocs or cmake --build . --target MaterialXDocs).  On the Lucasfilm side, we're often developing code and documentation at once, and it would be awkward to have a build step that never "completes".
If anyone has a suggestion for a robust solution that generates the full set of dependencies (i.e. between the ALL project, MaterialXDocs, and the generated output), feel free to create a pull request and we're happy to check it out.

One more note:  I've updated the instructions for building API documentation in the Developer Guide (https://github.com/materialx/MaterialX/blob/master/documents/DeveloperGuide/MainPage.md), since our original instructions implied that you could just build the "ALL" target and get documentation as well.


can't be found on npm

This is a great idea very pleased I found it. Currenty I am unable to find it  the npm to install.
Could this be added?

This is just a demo for Cropper.js. You can install the Cropper.js directly:
npm i cropperjs


Hide tooltips behind panels

Before

After

Fixes https://github.com/AtomLinter/linter-ui-default/issues/51
Related https://github.com/atom/one-dark-ui/pull/127
Related https://github.com/atom/one-light-ui/pull/54
Related https://github.com/atom/atom-light-ui/pull/27

See https://github.com/atom/one-dark-ui/pull/127#issuecomment-198509440.

Closed in favor of https://github.com/atom/atom/issues/11249