Could not load genomicsdb native library

Hi,
Another issue for the RNA-seq variant calling regarding loading genomicsdb, logs are attached here:
logs.txt
Please let me know if you need more information.

Hi Komal,
Hm, I think the clue is here in the log:
Runtime.totalMemory()=460259328
Exception in thread "main" java.lang.ExceptionInInitializerError
        at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteOrCreateWorkspace(GenomicsDBImport.java:660)
        at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:461)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:982)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: com.intel.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library
        at com.intel.genomicsdb.importer.GenomicsDBImporter.<clinit>(GenomicsDBImporter.java:65)
        ... 9 more
Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1867)
        at java.lang.Runtime.loadLibrary0(Runtime.java:870)
        at java.lang.System.loadLibrary(System.java:1122)
        at com.intel.genomicsdb.GenomicsDBLibLoader.loadLibrary(GenomicsDBLibLoader.java:43)
        at com.intel.genomicsdb.importer.GenomicsDBImporter.<clinit>(GenomicsDBImporter.java:62)

Do you happen to have LD_LIBRARY_PATH set?

Yes.
[rathik@reslnrab01 ~]$ echo $LD_LIBRARY_PATH
:/cm/shared/apps/intel-tbb-oss/intel64/current/lib/gcc4.4:/usr/lib64:/cm/shared/apps/intel-tbb-oss/intel64/2017_20170807oss/lib/intel64/gcc4.4

Can you unset LD_LIBRARY_PATH before running? It looks like GATK is looking for a shared library and can't find it, sometimes having LD_LIBRARY_PATH set can cause these kinds of issues.

I tried this and it didn't work. I am clueless as to what is going on. If you aren't able to debug this then you can close it.

Hi Komal,
Guh, sorry for the problems. If you go into the work/log directory and do this:
grep GenomicsDB bcbio-nextgen-commands.log

it should show the failing command. For example on our tests:
unset JAVA_HOME && export PATH=/home/rdk4/local/share/bcbio/anaconda/bin:$PATH && gatk --java-options '-Xms454m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/n/app/bcbio/dev/rory-dev/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chrM/bcbiotx/tmp312_s1' GenomicsDBImport --reader-threads 1 --genomicsdb-workspace-path TestBatch1-chrM_0_16571_genomicsdb -L chrM:1-16571 --variant /n/app/bcbio/dev/rory-dev/bcbio-nextgen/tests/test_automated_output/variation/rnaseq/gatk-haplotype/Test1-gatk-haplotype.vcf.gz --variant /n/app/bcbio/dev/rory-dev/bcbio-nextgen/tests/test_automated_output/variation/rnaseq/gatk-haplotype/Test2-gatk-haplotype.vcf.gz

Could you post what that is for you? And if you run that command by itself, does it fail?

Here:
[2018-07-16T18:08Z] unset JAVA_HOME && export PATH=/mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/bin:$PATH && gatk --java-options '-Xms454m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/joint/gatk-haplotype-joint/CDL-634-13P/1/bcbiotx/tmp5vG0IL' GenomicsDBImport --reader-threads 1 --genomicsdb-workspace-path CDL-634-13P-1_0_249250621_genomicsdb -L 1:1-249250621 --variant /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/variation/rnaseq/gatk-haplotype/Sample_1__CDL-634-13P-gatk-haplotype-annotated-rnaedit-annotated-gemini.vcf.gz

Thanks! What happens if you run that command outside of bcbio?

It crashes with the same error:
[rathik@reslnrefo01 log]$ unset JAVA_HOME && export PATH=/mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/bin:$PATH && gatk --java-options '-Xms1g -Xmx99g -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/joint/gatk-haplotype-joint/CDL-634-13P/1/bcbiotx/tmpHA8ElG' GenomicsDBImport --reader-threads 1 --genomicsdb-workspace-path CDL-634-13P-1_0_249250621_genomicsdb -L 1:1-249250621 --variant /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/variation/rnaseq/gatk-haplotype/Sample_1__CDL-634-13P-gatk-haplotype-annotated-rnaedit-annotated-gemini.vcf.gz
Using GATK jar /mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/share/gatk4-<IP_ADDRESS>-0/gatk-package-<IP_ADDRESS>-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms1g -Xmx99g -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/joint/gatk-haplotype-joint/CDL-634-13P/1/bcbiotx/tmpHA8ElG -jar /mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/share/gatk4-<IP_ADDRESS>-0/gatk-package-<IP_ADDRESS>-local.jar GenomicsDBImport --reader-threads 1 --genomicsdb-workspace-path CDL-634-13P-1_0_249250621_genomicsdb -L 1:1-249250621 --variant /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/variation/rnaseq/gatk-haplotype/Sample_1__CDL-634-13P-gatk-haplotype-annotated-rnaedit-annotated-gemini.vcf.gz
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/mnt/isilon/cbmi/variome/tmp/rathik
15:00:09.002 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/share/gatk4-<IP_ADDRESS>-0/gatk-package-<IP_ADDRESS>-local.jar!/com/intel/gkl/native/libgkl_compression.so
15:00:09.373 INFO  GenomicsDBImport - ------------------------------------------------------------
15:00:09.373 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v<IP_ADDRESS>
15:00:09.373 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
15:00:09.374 INFO  GenomicsDBImport - Executing as<EMAIL_ADDRESS>on Linux v3.10.0-862.el7.x86_64 amd64
15:00:09.374 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_144-b01
15:00:09.375 INFO  GenomicsDBImport - Start Date/Time: July 17, 2018 3:00:08 PM EDT
15:00:09.375 INFO  GenomicsDBImport - ------------------------------------------------------------
15:00:09.375 INFO  GenomicsDBImport - ------------------------------------------------------------
15:00:09.375 INFO  GenomicsDBImport - HTSJDK Version: 2.16.0
15:00:09.375 INFO  GenomicsDBImport - Picard Version: 2.18.7
15:00:09.375 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:00:09.375 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:00:09.375 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:00:09.375 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:00:09.376 INFO  GenomicsDBImport - Deflater: IntelDeflater
15:00:09.376 INFO  GenomicsDBImport - Inflater: IntelInflater
15:00:09.376 INFO  GenomicsDBImport - GCS max retries/reopens: 20
15:00:09.376 INFO  GenomicsDBImport - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
15:00:09.376 INFO  GenomicsDBImport - Initializing engine
15:00:10.365 INFO  IntervalArgumentCollection - Processing 249250621 bp from intervals
15:00:10.370 INFO  GenomicsDBImport - Done initializing engine
Created workspace /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/log/CDL-634-13P-1_0_249250621_genomicsdb
15:00:11.673 INFO  GenomicsDBImport - Vid Map JSON file will be written to CDL-634-13P-1_0_249250621_genomicsdb/vidmap.json
15:00:11.674 INFO  GenomicsDBImport - Callset Map JSON file will be written to CDL-634-13P-1_0_249250621_genomicsdb/callset.json
15:00:11.674 INFO  GenomicsDBImport - Complete VCF Header will be written to CDL-634-13P-1_0_249250621_genomicsdb/vcfheader.vcf
15:00:11.674 INFO  GenomicsDBImport - Importing to array - CDL-634-13P-1_0_249250621_genomicsdb/genomicsdb_array
15:00:11.674 INFO  ProgressMeter - Starting traversal
15:00:11.675 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute
15:00:12.505 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
Buffer resized from 22684bytes to 32523
Buffer resized from 32523bytes to 32671
Buffer resized from 32671bytes to 32769
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fc5ff88d359, pid=30328, tid=0x00007fc5ff737700
#
# JRE version: OpenJDK Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01)
# Java VM: OpenJDK 64-Bit Server VM (25.144-b01 mixed mode linux-amd64 )
# Problematic frame:
# C  [libtiledbgenomicsdb7066406292930633618.so+0x155359]  BufferVariantCell::set_cell(void const*)+0x99
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/bcbio_out/log/hs_err_pid30328.log
#
# If you would like to submit a bug report, please visit:
#   http://www.azulsystems.com/support/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.

Hm, it looks like there have been some other issues in GenomicsDBImport:
https://github.com/broadinstitute/gatk/issues/4994

The error running it alone is different than the one when it is run inside of bcbio, though.

Komal;
Thanks for all these detailed reports and apologies about the issues with GenomicsDB. I'm not totally positive what is going on but for the two issues:

For the core dump that you're seeing in #2453 and above (BufferVariantCell::set_cell(void const*)+0x99) I wonder if this is an issue with using too much memory. How much available memory is on your compute machines? In the example above you're asking for 99Gb of memory and in #2453 it's 53Gb of memory. Is it possible that other processes are running on these machines or other things restrict memory?

For the no tiledbgenomicsdb in java.library.path it seems to be running into problems finding appropriate shared libraries that are meant to be bundled with the jar file. What type of machine are you running this on? If we can provide more system information I think the best approach would be to raise an issue in the gatk repository to see if they can help with tracking down what is happening.

Thanks again for the help debugging this.

Thanks.
For 1, I actually asked one of our systems engineer to help me debug it as well and he said the box I was running on has like 700GB of free memory. I did try to use -n 1 and jvm_opts: ["-Xms2g", "-Xmx4g"] so not sure how it could be a memory issue.
For 2, not sure if this helps:
[rathik@reslnrab01 ~]$ lscpu

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                96
On-line CPU(s) list:   0-95
Thread(s) per core:    2
Core(s) per socket:    12
Socket(s):             4
NUMA node(s):          4
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 85
Model name:            Intel(R) Xeon(R) Gold 5118 CPU @ 2.30GHz
Stepping:              4
CPU MHz:               2300.000
BogoMIPS:              4600.00
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              1024K
L3 cache:              16896K
NUMA node0 CPU(s):     0,4,8,12,16,20,24,28,32,36,40,44,48,52,56,60,64,68,72,76,80,84,88,92
NUMA node1 CPU(s):     1,5,9,13,17,21,25,29,33,37,41,45,49,53,57,61,65,69,73,77,81,85,89,93
NUMA node2 CPU(s):     2,6,10,14,18,22,26,30,34,38,42,46,50,54,58,62,66,70,74,78,82,86,90,94
NUMA node3 CPU(s):     3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63,67,71,75,79,83,87,91,95
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_ppin intel_pt mba tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local ibpb ibrs stibp dtherm ida arat pln pts pku ospke spec_ctrl intel_stibp

Also, how do I find tiledbgenomicsdb? I want to check where it is present on both the boxes so I can compare why is it missing.

Hi Rory,
I am closing this as I was able to circumvent this error by resetting my Java tmpdir. However, https://github.com/bcbio/bcbio-nextgen/issues/2453 still persists. But at least, now there is 1 less error to debug.
Thanks
Komal


web-encoding package causes problems with jest in env=node and env=jsdom

Describe the bug
When running the test in jest (with either env=jsdom or env=node setting) the TextDecoder or TextEncoder is not a constructor error makes it impossible to write unit tests using this module
To Reproduce
This simple test and code fails to run in jest
code:
https://github.com/Uniswap/uniswap-interface/blob/0aabf4856e6e90041caf4233db4b7defb01574a2/src/utils/contenthashToUri.ts
test:
https://github.com/Uniswap/uniswap-interface/blob/0aabf4856e6e90041caf4233db4b7defb01574a2/src/utils/contenthashToUri.test.skip.ts
error:
TypeError: TextDecoder is not a constructor

    TypeError: TextDecoder is not a constructor

    > 1 | import CID from 'cids'
        | ^
      2 | import { getCodec, rmPrefix } from 'multicodec'
      3 | import { decode, toB58String } from 'multihashes'
      4 |

      at Object.<anonymous> (node_modules/multibase/src/util.js:6:21)
      at Object.<anonymous> (node_modules/multibase/src/base.js:4:24)
      at Object.<anonymous> (node_modules/multibase/src/constants.js:5:14)
      at Object.<anonymous> (node_modules/multibase/src/index.js:9:19)
      at Object.<anonymous> (node_modules/multihashes/src/index.js:10:19)
      at Object.<anonymous> (node_modules/cids/src/index.js:3:12)
      at Object.<anonymous> (src/utils/contenthashToUri.ts:1:1)
      at Object.<anonymous> (src/utils/contenthashToUri.test.ts:1:1)

Expected behavior
TextDecoder from the environment (specifically, global for node and window for jsdom jest setting) is successfully loaded
Screenshots

Desktop (please complete the following information):

OS: MacOS

other issues:
https://github.com/discordjs/discord.js/issues/3971#issuecomment-602010271
potential solution for us https://stackoverflow.com/a/57713960

Going to suggest @Gozala is probably the one to take a look at this. If it's simple then it'd be great to fix. It seems that jsdom is just growing in use, not shrinking (which I wouldn't have expected!), so this might be fairly important.

@moodysalem I'm not yet sure what is going on there yet, and sadly I have no experience with jest which does no help either. I am however guessing that problem here is that build picks up a wrong module, more specifically there are bunch entry points provided by web-encodings:
https://github.com/Gozala/web-encoding/blob/default/package.json#L10-L19
And I'm guessing that one being pulled in is (which assumes modern node >= 11.0.0 with ESM and TextEncoder / TextDecoder globals:
https://github.com/Gozala/web-encoding/blob/default/src/lib.js
Instead of the common JS module targeted for non ESM, which does pretty much what linked stackoverflow solution describes:
https://github.com/Gozala/web-encoding/blob/default/src/lib.cjs
@moodysalem what's the version of the node you're testing on ?

And from stack trace it appears error is coming from https://github.com/multiformats/js-cid/blob/cbe44d41e19de9b5ae6de0607abf7027f84920af/src/index.js which no longer imports TextDecoder (directly).

@moodysalem what's the version of the node you're testing on ?

Node v12.18.3, and same with CI, which both have TextEncoder/TextDecoder in the global NS

And from stack trace it appears error is coming from https://github.com/multiformats/js-cid/blob/cbe44d41e19de9b5ae6de0607abf7027f84920af/src/index.js which no longer imports TextDecoder (directly).

The stack trace points at this line https://github.com/multiformats/js-multibase/blob/master/src/util.js#L6

The stack trace points at this line https://github.com/multiformats/js-multibase/blob/master/src/util.js#L6

Oh right stack trace point to that, but code snippet seems to point to something else 😳

Turns out problem is that react-scripts used by uniswap-interface uses old version of jest which does not recognize or support .cjs files. Unfortunately it does not appear to be a way to create a universal cjs / esm package without using .cjs files so we can't really work around this.
Good news is modern jest works without a problem and upcoming react-scripts also works (because it uses modern jest). With all that I think the best path forward would be to update to the upcoming react-scripts. If that is problematic, maybe work with react-scripts community to try an have minor release that just updates to new jest.

It is also might be worth looking into why lib.cjs is been pulled in, in first place. I'd expect lib.js (ESM one) to be used given that it's imported from ESM:
https://github.com/multiformats/js-multibase/blob/424709195b46ffb1d6f2f69a7707598ebe751e5e/src/util.js#L4-L6
I'm guessing that has something to do with jest implementing their own custom module loader that did not recognized export maps (modern jest might do that).

Thank you for the investigation, I tried updating just the jest package to ^26.0.0 and the test errored in the same way. However I didn't upgrade any other dependencies, so the jest config would be the same.

@moodysalem could you please try with new teact-scripts ? There could be more things going on there and would be good to confirm

with react-scripts 4.0.0-next.77 it fails with jsdom:
 FAIL  src/utils/contenthashToUri.test.ts
  ● Test suite failed to run

    ReferenceError: TextDecoder is not defined

      13 | }
      14 |
    > 15 | const UTF_8_DECODER = new TextDecoder()
         |                       ^
      16 |
      17 | /**
      18 |  * Returns the URI representation of the content hash for supported codecs

      at Object.<anonymous> (src/utils/contenthashToUri.ts:15:23)
      at Object.<anonymous> (src/utils/contenthashToUri.test.ts:1:1)

Test Suites: 1 failed, 1 total
Tests:       0 total
Snapshots:   0 total
Time:        0.711 s, estimated 1 s
Ran all test suites related to changed files.

and passes with env=node
 PASS  src/utils/contenthashToUri.test.ts
  #contenthashToUri
    ✓ 1inch.tokens.eth contenthash (3 ms)
    ✓ uniswap.eth contenthash
  #hexToUint8Array
    ✓ common case (1 ms)

Test Suites: 1 passed, 1 total
Tests:       3 passed, 3 total
Snapshots:   0 total
Time:        0.424 s
Ran all test suites related to changed files.

I'll look into this more. I'm suspecting that it may be loading lib.js in there instead of lib.cjs which just assumes TextDecoder global, which is not available because jest swaps node global for jsdom window which does not have TextEncoder / TextDecoder.

Relevant issue for JSDOM https://github.com/jsdom/jsdom/issues/2524

@moodysalem what branch of the uniswap-interface are those changes on ? I would like to try figure it out, but I can't seem to find linked files in the master

Never mind found it

Also created jest issue https://github.com/facebook/jest/issues/10431

@moodysalem as I started debugging I noticed that this time error is no longer coming from js-multibase or web-encoding packages it's coming from uniswap-interface itself:
https://github.com/Uniswap/uniswap-interface/blob/0aabf4856e6e90041caf4233db4b7defb01574a2/src/utils/contenthashToUri.ts#L15

@moodysalem I have created https://github.com/Uniswap/uniswap-interface/pull/1056 to illustarte the fix.
I'm closing this issue, because there is noting we can do other than encourage react-scripts adopt nodes ESM support sooner.

Thanks @Gozala !


Fix CI part2 test failures

@KevinRansom This is an attempt to fix the test failures in CI part2 by reinstating the xcopy to copy over missing dependencies
I think the problem is that FSharp.Core is not listed as a dependency and is not being copied over as part of the publish step.
The failure of the tests was previously being masked prior to #1729


profiling bazel compile time

Found bazel run takes about 9~10 minutes for every test run.
INFO: Elapsed time: 444.182s, Critical Path: 286.44s
...
INFO: Elapsed time: 126.192s, Critical Path: 102.18s
This is run.log before any vcs activity starts.
Please review bazel compile process to see if there is anything that can be improved this.

It is for @timothytrippel , I added others just for the reference.

hmmm that seems really long. When I run it locally or on the airgapped setups I don't recall it taking that long..
It could be that since i'm using the airgapped setup none of the dependencies need to be resolved

IIUC, @jdonjdon this only occured for you on the airgapped setup correct? and for more context, what do those above build times correspond to? I assume one is the test ROM? and the other is a chip-level test you were trying to build?

IIUC, @jdonjdon this only occured for you on the airgapped setup correct? and for more context, what do those above build times correspond to? I assume one is the test ROM? and the other is a chip-level test you were trying to build?

Let me put the log file here(#13929) you can grep 'Elapsed time' to get the same out and
the context where the output is created.

With the latest update, I don't see this issue anymore.
Close for now.


Windows 64-bit wheel is missing for 0.3.3

System Info
Python 3.8, Windows 64-bit, Safetensors 0.3.3
Information

[ ] The official example scripts
[ ] My own modified scripts

Reproduction
Install safetensors using pip install safetensors in a new python environment, doing this you get this installation failure : error: can't find Rust compiler
Expected behavior
The rust compiler is either being handled automatically or not needed because of prebuilt wheels for this platform.

It's fixed. I messed up the windows 64 bit when rewriting the action.
Should be fixed now, can you confirm ?

Can confirm, I see the wheels on pypi and was able to install it on a machine that did not have rust installed.
I have resumed the rollout to the KoboldAI users, thanks!


Add a "just listen" option

If someone just wants to listen they shouldn't have to go through calibration

Or even give microphone permissions

Added to tutorial in https://github.com/gwillen/solstice-audio-test/pull/77
We should postpone asking for microphone permissions until they say they do want to participate


Functionality suggestion

Hi, I have a question, since Samira Soulfighter has her own damage font, which is really pretty, would you, if it's possible to implement it, add a toggle to make us able to activate that font not matter the champ or skin we are currently using? Thanks for the work.

What you ask will not happen because in april 2024 R3nzSkin will no longer work for all server because of Vanguard https://m.youtube.com/watch?v=t2niKNCmiUY&t=167s and on announcement it clearly said this R3nzSkin will no longer be supported by 2024 due to Riot Games implementing Valorant's Vanguard anti-cheat to League of Legends


Ipad does not work correctly

Describe the bug
A clear and concise description of what the bug is.
To Reproduce
https://ar-js-org.github.io/AR.js-Docs/#requirements
I used this sample, but it doesn't work.
The model appears to be successfully loaded, but there is no error log.
Smartphone (please complete the following information):

Device:Ipad(gen6)
OS: IOS13.5(IpadOS13)
Browser:safari

,@Teityan please close this and re-post the issue on the AR-js-org repository. Thank you. 🙂

Excuse me.
Thank you.


Update Electron to 17.4.3

Does this issue occur when all extensions are disabled?: Yes/No

VS Code Version: 1.67.1
OS Version: Win 7 x64

Steps to Reproduce:

Please update Electron to 17.4.3 https://github.com/electron/electron/releases/tag/v17.4.3

Does this fix the high CPU usage on OSX? (introduced in 1.67.0)

Does this fix the high CPU usage on OSX?

God I hope so. This editor is starting to turn into a real heater on my 2019 MBP. And all of a sudden after the April update I've got major performance issues and downgrading doesn't help. Ugh.


Support compression without export?

Hey!
Just found this plugin and really like it but I use zeplin and export directly to zeplin so the svg files end up as assets in the zeplin app.
Would it be possible to compress the svgs without the export so that they will be compressed in zeplin?

AFAIK, Zeplin does its own SVG compression: https://twitter.com/zeplin_io/status/837224316475441154 so I'm closing this issue : )


[kwokctl] support extension apiserver

What would you like to be added?
Add arguments "--requestheader-allowed-names", "--requestheader-group-headers", "--requestheader-username-headers", and "--requestheader-client-ca-file" when starting api server.
Why is this needed?
So that we can support extension apiserver as well as components profiling.

It looks like this will be a generic requirement, I plan to add a field in KwokctlConfiguration to configure it like this.
https://kwok.sigs.k8s.io/docs/user/configuration/
kind: KwokctlConfiguration
apiVersion: kwok.x-k8s.io/v1alpha1
componentsPatches:
  - name: <component-name>
    extraArgs:
      - key: <key>
      - value: <value>

/triage accepted

It looks like this will be a generic requirement, I plan to add a field in KwokctlConfiguration to configure it like this. WDYT?
https://kwok.sigs.k8s.io/docs/user/configuration/
kind: KwokctlConfiguration
apiVersion: kwok.x-k8s.io/v1alpha1
componentsPatches:
  - name: <component-name>
    extraArgs:
      - key: <key>
        value: <value>

I think it is great.

/good-first-issue

If there is no one working on this issue, maybe I can help

Thank you for your willingness to take on this work😄

/assign @KunWuLuan
/milestone v0.3
let's move it to milestone v0.3, and if you don't have time to continue this work you can reply /unassign 😄


Note around Animation Writer requirements

First of all, love this package!
I used this on an existing project, wish I had known about it before!
Run into a hurdle in that I didn't have any of the supported writers installed, so added note in the README for anyone else that runs into this.

Thank you for writing this. I've since made many changes, but will add an option for movie writers like you did.


TFLite Raspberry Pi object detection example code does not work with tensorflow.lite.python.interpreter, only works with tflite_runtime.interpreter

System information

Have I written custom code (as opposed to using a stock example script provided in TensorFlow): No
OS Platform and Distribution (e.g., Linux Ubuntu 16.04): Raspbian Buster
Mobile device (e.g. iPhone 8, Pixel 2, Samsung Galaxy) if the issue happens on mobile device: Raspberry Pi 4 4GB
TensorFlow installed from (source or binary): Binary (pip3 install tensorflow)
TensorFlow version (use command below): v1.12.1-3892-g127aae0 1.13.1
Python version: 3.7.3
Bazel version (if compiling from source): n/a
GCC/Compiler version (if compiling from source): n/a
CUDA/cuDNN version: n/a
GPU model and memory: n/a

Describe the behavior
I am following the TFLite object detection on Raspberry Pi guide (https://github.com/tensorflow/examples/tree/master/lite/examples/object_detection/raspberry_pi) using a Raspberry Pi 4 4GB model. The guide says to download and install the tflite_runtime from the Python quickstart page. However, I tried using it with my existing installation of TensorFlow since I already have it installed on my Pi 4, and the script exits with the error shown below.
It also doesn't work if I have regular TensorFlow and the tflite_runtime package installed at the same time. It does work if I uninstall TensorFlow using pip3 uninstall tensorflow and then install the tflite_runtime package.
Describe the expected behavior
It would be nice if the object detection example code worked without having to remove my existing TensorFlow install.
Code to reproduce the issue
I used the example code given here. When trying to use regular TensorFlow (rather than just the tflite_runtime package), I changed line 33 from from tflite_runtime.interpreter import Interpreter to from tensorflow.lite.python.interpreter import Interpreter.
I called the script using:
python3 detect_picamera.py \
  --model /tmp/detect.tflite \
  --labels /tmp/coco_labels.txt

Other info / logs
Traceback for the error I am getting:
Traceback (most recent call last):
File "TFLite_detection_picamera.py", line 113, in
interpreter = Interpreter(model_path=PATH_TO_CKPT)
File "/home/pi/.local/lib/python3.7/site-packages/tflite_runtime/interpreter.py", line 205, in init
_interpreter_wrapper.InterpreterWrapper_CreateWrapperCPPFromFile(
File "/home/pi/.local/lib/python3.7/site-packages/tensorflow_core/python/util/lazy_loader.py", line 62, in getattr
module = self._load()
File "/home/pi/.local/lib/python3.7/site-packages/tensorflow_core/python/util/lazy_loader.py", line 45, in _load
module = importlib.import_module(self.name)
File "/usr/lib/python3.7/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 677, in _load_unlocked
File "", line 728, in exec_module
File "", line 219, in _call_with_frames_removed
File "/home/pi/.local/lib/python3.7/site-packages/tensorflow_core/lite/python/interpreter_wrapper/tensorflow_wrap_interpreter_wrapper.py", line 28, in
_tensorflow_wrap_interpreter_wrapper = swig_import_helper()
File "/home/pi/.local/lib/python3.7/site-packages/tensorflow_core/lite/python/interpreter_wrapper/tensorflow_wrap_interpreter_wrapper.py", line 24, in swig_import_helper
_mod = imp.load_module('_tensorflow_wrap_interpreter_wrapper', fp, pathname, description)
File "/usr/lib/python3.7/imp.py", line 242, in load_module
return load_dynamic(name, filename, file)
File "/usr/lib/python3.7/imp.py", line 342, in load_dynamic
return _load(spec)
File "", line 696, in _load
File "", line 670, in _load_unlocked
File "", line 583, in module_from_spec
File "", line 1043, in create_module
File "", line 219, in _call_with_frames_removed
ImportError: /home/pi/.local/lib/python3.7/site-packages/tensorflow_core/lite/python/interpreter_wrapper/_tensorflow_wrap_interpreter_wrapper.so: undefined symbol: _ZN6tflite12tensor_utils24NeonVectorScalarMultiplyEPKaifPf

Update: I just tested this with TensorFlow v2.0 (downloaded and installed from https://github.com/lhelontra/tensorflow-on-arm/releases), and everything worked fine.

Thank you @EdjeElectronics, I had exactly the same issue and this solution also worked for me.

Update: I just tested this with TensorFlow v2.0 (downloaded and installed from https://github.com/lhelontra/tensorflow-on-arm/releases), and everything worked fine.

@petewarden will this get resolved any time soon? It looks like users are having this same error with TF v1.14, which is the latest version easily available for Raspbian Stretch (which uses Python 3.5 by default).
Seems there are two solutions:

Add wheel files for TF v2.0 on piwheels.org so users can easily install TF v2.0
Resolve the issue with TF v1.13 / TF v1.14.

A couple people following my guide for TF Lite on Raspberry Pi are encountering the same problem: https://github.com/EdjeElectronics/TensorFlow-Lite-Object-Detection-on-Android-and-Raspberry-Pi/issues/13

Hi There,
We are checking to see if you still need help on this, as you are using an older version of tensorflow which is officially considered end of life . We recommend that you upgrade to the latest 2.x version and let us know if the issue still persists in newer versions. Please open a new issue for any help you need against 2.x, and we will get you the right help.
This issue will be closed automatically 7 days from now. If you still need help with this issue, please provide us with more information.


Yard and custom “terminal type” show wrong icons

-create or edit new terminal
-select yard or custom.
Note the icon shown after selection and saving the artifact is wrong.
Yard shows a ship and custom shows a truck.

This would likely be addressed once @martareg gives us some guidance on overall ux.

This would likely be addressed once @martareg gives us some guidance on overall ux.


more thorough wire break test

It occurs to me that util.dbutils.db_to_df's filter_on_wire_break option seems to assume that CSIRO_wire_break test flags all levels that are affected by a wire break; I'm not sure that it does. Most profiles flagged by the wire break test look qualitatively like:

But the wire break reference and our qc test only check the very last level - meaning that the db util is only filtering out, at most, the last level of a profile. Is that really what we want, or do we want to filter out all the red points in the above figure? (the unlabeled color scale is originator qc code).
This PR tries to flag all such points at the end of a profile by flagging:

all the levels in a consecutive run from the end that fall outside of -2.8<t<36
all consecutive levels shallower than this run where the gradient from the next-shallower level is > 0.5 deg C / m in magnitude.

This is somewhat arbitrarily constructed - @s-good please let me know if I've misread something entirely, and also how we can make this a little more precise. Also before we merge, I'm going to run this over a few 10's of thousands of profiles just to check for edge cases.

Right! What do you think, @BecCowley? Is it fair to call all the red points above symptomatic of a wire break, or is that too heavy-handed? If these are all part of a wire break event, do you have a preferred algorithm that flags them all? I'd prefer to use something established if it exists, rather than the rough estimate I propose here.

@BillMills, all the red points are wire break points and should be flagged as bad. You will need some sort of gradient or difference test to get all the points. Then anything deeper than the point is bad.
Here is a link to our automatic wire break detection code used in our XBT QC gui (Mquest):
https://github.com/BecCowley/Mquest/blob/083b9a3dc7ec9076705aca0e90bcb500d241be03/GUI/detectwirebreak.m
You can see it has a range detection and a difference cutoff between points. This works really well in probably 90% of our high resolution data.

Sorry this took a while, I've been 100% focused on the track check for the past while. Anyway - this now reproduces Bec's suggestion linked above.


Move from Glide to Dep: dep ensure -add fails

Currently docs suggest the following method to import the SDK with dep however this fails with the latest version of dep
dep:
 version     : v0.4.1
 build date  : 2018-01-27
 git hash    : 37d9ea0
 go version  : go1.9.3
 go compiler : gc
 platform    : darwin/amd64

I created a new package with a main.go then ran dep init then tried to import the sdk:
~/ dep ensure -add<EMAIL_ADDRESS>Fetching sources...

Solving failure: No versions of github.com/Azure/azure-sdk-for-go met constraints:
   14.1.1: Could not introduce<EMAIL_ADDRESS>as its subpackage github.com/Azure/azure-sdk-for-go does not contain usable Go code (*build.NoGoError).. (Package is required by (root).)
   v14.1.1: Could not introduce<EMAIL_ADDRESS>as its subpackage github.com/Azure/azure-sdk-for-go does not contain usable Go code (*build.NoGoError).. (Package is required by (root).)
   v14.1.0: Could not introduce<EMAIL_ADDRESS>as it is not allowed by constraint ^14.1.1 from project github.com/lawrencegripper/azuresdkgotest.
   v14.0.2: Could not introduce<EMAIL_ADDRESS>as it is not allowed by constraint ^14.1.1 from project github.com/lawrencegripper/azuresdkgotest.
.....

It seems that adding a sub-directory succeeds.
✘ dep ensure -add<EMAIL_ADDRESS>Fetching sources...

"github.com/Azure/azure-sdk-for-go/services/batch/2017-09-01.6.0/batch" is not imported by your project, and has been temporarily added to Gopkg.lock and vendor/.
If you run "dep ensure" again before actually importing it, it will disappear from Gopkg.lock and vendor/.

This creates a gopkg.lock like so
[[projects]]
  name = "github.com/Azure/azure-sdk-for-go"
  packages = [
    "services/batch/2017-09-01.6.0/batch",
    "version"
  ]
  revision = "1e334c402ea1460704b0263e5d188f28ad946ce1"
  version = "14.1.1"

I can then go into my go code and start using it, at which point the warning isn't a problem any more.
It looks like this is being worked on by dep here and here
I'm relatively new to dep having spent some time getting my head around glide so this may simply be user error. If it's not then I think it would be good to update the docs to call this out.
Any help and pointers much appreciated!

Thanks for noting this @lawrencegripper. I think the solution may be to turn the root into a Go package by adding a doc.go file. Did so in #1310.

Awesome that sounds like it will do the trick - good call

Fixed by #1310


partial complement of the fs header

This PR try to complete header line content description and to clarify bit/area unknown for futher analyze.

Awesome!


Add .allSettled() method

Like https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Promise/allSettled

This one is a little more complicated but I think it should be possible. Precedent in p-all: https://github.com/sindresorhus/p-all/pull/9

Reworking those typings for Iterables like Sets might be a challenge because of how P in keyof Task may yield get, set, has, etc. instead of the indexes we want.


change-icon-for-page-previews

Have you read the Contributing Guidelines on issues?

[X] I have read the Contributing Guidelines on issues.

Description
I'd like to change the icon in the pink box in the screenshot attached, but I can't find guidance on how to do this in the docs. Is this possible?

Has this been requested on Canny?
No response
Motivation
Looking to add variation on pages with multiple link card previews.
API design
No response
Have you tried building it?
No response
Self-service

[x] I'd be willing to contribute this feature to Docusaurus myself.

We don't have an API for that apart using swizzle on the DocCard component.
It's unlikely we implement anything like this in the future because there are tons of way to provide an icon (React, emoji, font icon, SVG, SVGR...) and we wouldn't be able to find a good API that satisfies all usages. Swizzle remains the most flexible option for such use-cases.

thank you @slorber - can you point me to more information on the DocCard component?

thank you @slorber - can you point me to more information on the DocCard component?

I'm not sure what information you want exactly.
Have you read the doc and tried to swizzle? I won't write you a step by step tutorial so please read the doc and report what exactly is unclear. We'll improve the doc for all instead of helping a single user.


Use .class files instead of compiling the sources

The goal is to give certain project types, or their configurations, a chance to use existing .class files rather than compiling from .java. The primary motivation for this API is to support following usecase with mx based graal sources:
$ cd graal/truffle
$ mx build
$ netbeans --open .

The build command compiles everything and places the classes into bin directories. By using the API introduced in this pull request, the project can instruct the NetBeans Java support to copy those .class files and thus speed the initialization up.
The support shall be generally useful in all project types. Yet, it is up to individual projects to turn it on. There has been pushback against this copying approach in the past, so we definitely want opt-in behavior, the default should remain as it is.

Maybe it's good to mention that preferring class files to source files has some limitations.
The find usages (refactoring) will not work on source level annotations, static fields initialized by compilation time constant, etc.
I am not saying that's a big problem but should be known.

I am not sure how this will behave when the project is using annotation processors generating sources. Did you try that?
Thanks

Maybe it's good to mention that preferring class files to source files has some limitations.

Right. Another reason for the support to be opt-in only.

The find usages (refactoring) will not work on source level annotations, static fields initialized by compilation time constant, etc.

Right.

Another limitation comes from annotation processing. There will be no sources generated by AP only binaries.

In the mx based projects, I can put the src_gen folder on some classpath. E.g. the sources will be there, it is just a question whether IDE finds them... I will need to test this change on the real mx projects before merging it to make sure it really works.

Regarding APs, the tricky aspect might be when the APs need to read the sources from previous compilation iterations in incremental compilation. It may even be necessary to copy the sources as well.
I appreciate that the API was adjusted to a more common structure.
Overall, I don't have problem with this patch.

Here are the changes generated by ant -f ide/api.java.classpath check-sigtest -Dsigtest.check.type=strictcheck:
  [sigtest] Added Classes
  [sigtest] -------------
  [sigtest]
  [sigtest] org.netbeans.api.java.queries.BinaryForSourceQuery$Result2
  [sigtest] org.netbeans.spi.java.queries.BinaryForSourceQueryImplementation2
  [sigtest]
  [sigtest] Added Nested Classes
  [sigtest] --------------------
  [sigtest]
  [sigtest] org.netbeans.api.java.queries.BinaryForSourceQuery:         nested public abstract static org.netbeans.api.java.queries.BinaryForSourceQuery$Result2
  [sigtest]
  [sigtest] Added Methods
  [sigtest] -------------
  [sigtest]
  [sigtest] org.netbeans.api.java.queries.BinaryForSourceQuery:         method public final static org.netbeans.api.java.queries.BinaryForSourceQuery$Result2 org.netbeans.api.java.queries.BinaryForSourceQuery.findBinaryRoots2(java.net.URL)
  [sigtest]

I'd like to integrate the change into NetBeans 11. @lkishalmi, can you cherry pick it once it gets into master?

Seems OK to me.

I did testing on IGV and things seem to work relatively well. Let's integrated. @lkishalmi, please consider backporting this into release110 branch. That would make it easier for some future version of IGV to use the new API.


docs/peter.somogyvari/whitepaper

I made a pull-request
https://github.com/petermetz/blockchain-integration-framework/pull/1/


Convert all models to Typescript

Models have a central role in our code. They're used pretty much everywhere and are usually responsible for binding data inputs to the database. Having them converted to Typescript will therefore improve our coverage in many places, making the code safer.
Today, about half of our models are already using Typescript, and it's the default documented way to create new models. We want to convert the remaining ones.
For everyone willing to contribute to this: opening smaller pull requests with only one or a few converted models is very welcome and actually preferred to a giant one that would be more difficult to test & review!

[ ] server/models/Application.js => @rxbryan
[ ] server/models/Collective.js => Reserverd to the core team
[x] server/models/Comment.js => https://github.com/opencollective/opencollective-api/pull/8255
[x] server/models/ConnectedAccount.js => https://github.com/opencollective/opencollective-api/pull/8248
[x] server/models/Conversation.js => https://github.com/opencollective/opencollective-api/pull/8256
[ ] server/models/ConversationFollower.js
[x] server/models/DataTypes.js => https://github.com/opencollective/opencollective-api/pull/8250
[x] server/models/EmojiReaction.js => https://github.com/opencollective/opencollective-api/pull/8239
[x] server/models/Expense.js => https://github.com/opencollective/opencollective-api/pull/8340/files
[x] server/models/index.js => https://github.com/opencollective/opencollective-api/pull/8241
[ ] server/models/LegalDocument.js => @hjaintech
[ ] server/models/Member.js
[ ] server/models/MemberInvitation.js
[ ] server/models/Order.js => Reserverd to the core team
[ ] server/models/PaymentMethod.js
[x] server/models/RequiredLegalDocument.js => https://github.com/opencollective/opencollective-api/pull/8254
[ ] server/models/Subscription.js
[x] server/models/Tier.js => https://github.com/opencollective/opencollective-api/pull/8250
[ ] server/models/Transaction.js => Reserverd to the core team
[ ] server/models/Update.js
[x] server/models/User.js => https://github.com/opencollective/opencollective-api/pull/8245

I could work on this one if that's okey.

@jacoobanderson Sure! Feel free to open PRs linking to this issue, ideally small ones - one model per PR - to facilitate the review.

Hi, can I take up this issue if it's still available ? @Betree

Hi, can I take up this issue if it's still available ? @Betree

Sure! Contributions for this one are welcome, just don't do everything in one go; we recommend making one pull request per converted model to simplify the review & merge process.

@Betree Can I take up typescript migration for LegalDocument.js?

@hjaintech Be welcome! I've assigned it to you in the issue description.

Hi @Betree I can see that Application.js and collective.js has no been worked on.
Could you assign them to me? I would like to work on them.

Hi @rxbryan, we prefer to reserve the Collective model for the core team as it's a really large one used in many places.
Feel free to start working on Application, I've assigned it to you in the issue description.

@Betree take a look at the pr https://github.com/opencollective/opencollective-api/pull/8473

I would like to work on this issue

@ashutosh887 One at a time, please complete your already-assigned PRs and ask again once they're merged


only face detection but not recognition

Cant recognize but can only detect.

@nirjack  Do you solve this problem? I am trying to use face-api.js in RN but it seems not work


Timeline for releasing checkpoints/metrics

Hi Authors,
Thanks for this really cool work. May I kindly ask when the pre-trained checkpoints and code for evaluation (metrics) will be released?
Thanks,
Luke

Hi @DanielDauner
Will the route-extrapolation code also be released by then? Thank you!

@hamid54 Unlikely. The route-extrapolation will be part of a later release.

Hi @DanielDauner, I was wondering if you have any plans to release the checkpoints and metrics soon. It would be really helpful. Thanks in advance!


Add run_length encoding and decoding

This PR adds run_length.encode() and run_length.decode(), which compress and decompress iterables, respectively.
This python-ideas thread discusses such an addition, and we once discussed something related here.
There are a ton of (mostly homework?) questions about this on StackOverflow as well. I didn't see any that use the trick we use for ilen.

I'm used to the odd name "compression", which admittedly can be confused with data compression (zip, tar, etc.).  How did you come about the name run_length?

Wikipedia has a good overview of this topic. "Run length" is the standard name for this procedure. One presumes it comes from the output of the encoder - you get which element had a "run" of repeated elements, and the "length" of the repetition.
As you'll see in the Wikipedia article, run-length encoding is itself a basic form of data compression, and is a component of some modern compression methods in use today.

Any objections to this? I don't have a concrete idea of what's out of scope for this library, but this might be on the edge. I'm leaning toward yes because of all the questionable implementations on StackOverflow.
There's a clear use case for these functions, but they're both one-liners and apparently not that to come up with - this blog post had the same ideas for both encode and decode years ago.

OK, let's do this.


pytorch_pretrained_bert loading and path issues

Thanks a lot for the novel dataset and baselines!
The repository doesn't seem to be plug and play. The specialized bert model used here seems to not be loaded correctly by the run_webqa.py file.
Moving run_webqa.py one level up from the vlp/ folder seems to fix some but not all path issues. Most paths given in the file seem to be absolute paths and corresponding files and folders are missing from the repository

Thanks for asking! Please see our README for explanations of absolute path arguments. Let us know if there are still unclear arguments.
If you're having trouble import BERT model classes, please try sys.path.append("path to ./VLP")
Hope that helps!

Hi!
I just want to follow up to see if my previous answer addressed your problem. If yes, I will close the issue. Otherwise, I'm happy to address any follow-up questions!


Allow profiles to be window specific

Right now, when I open two different VSCode windows, if I switch to a profile in one window, it affects the other window and its profile changes as well. I would like to be able to have two different windows with different profiles. For example, I'd like to work on the same project but have one Python profile for the backend in one window and one Vue+TS profile in the other window, for the frontend.
I'm open to a solution with workspaces if it's an alternative but I don't really see it documented anywhere.
Current VSCode version:
1.90.1
611f9bfce64f25108829dd295f54a6894e87339d
arm64

Thanks

You can have two different profiles for two different windows and it should work. Can you please share a gif showing that it is not working for you?
Regarding opening same folder in multiple windows - we do not support this scenario.

Hi,
Yeah in the case of the monorepo I would've liked to be able to open the same project/folder in two different windows but with different profiles. Isn't there a workaround?

I would've liked to be able to open the same project/folder in two different windows

You can use multi folder workspace as an alternative

@sandy081
Any chance that setting up the profiles in multi-root workspaces would be possible like this?
{
	"folders": [
		{
			"name": "main",
			"path": "."
		},
		{
			"name": "backend",
			"path": "backend",
			"profile": "Python"
		},
		{
			"name": "frontend",
			"path": "frontend",
			"profile": "Vue"
		}
	],
	"settings": {}
}

Unfortunately not. You can have only one profile associated per workspace.

That's too bad, thx for the answers!


Update: KDE.Dolphin version 22.12.0 [FP-D]

Result: Installation Successful

Manifest
Add/Remove Programs

Name
Dolphin
Dolphin

Version
22.12.0
22.12.0

Publisher
KDE e.V.
KDE e.V.

ProductCode

Dolphin

Auto-updated by vedantmgoyal2009/winget-pkgs-automation in workflow run 4639

@msftbot reset feedback

Well I had guessed it wouldn't remove the Project-File label but was worth a try...😅

Close with reason: No changes in pull request;


Delivery charge not based on Delivery address

I noticed that the delivery charge is calulated on base of the address/postcode that a customer inputs when entering the site.
However, when you fill in an address/postcode (from a different area_id) as a delivery-address in the checkout-procedure, the delivery charges are not updated according to this new address/area.
Or am i doing something wrong?

Thanks for the very fast response!


Add ItemsView for Maui.Markup

This PR adds the ItemsView Extensions docs for CommunityToolkit.Maui.Markup

Microsoft authors of articles need to make updates through the private repository, so the updates can be staged and validated by current validation rules. After you review staging and fix all validation issues, you can add the sign-off comment to let the PR reviewers know the updates are ready to be merged.
It's easy to access the private repo version of your articles in GitHub. Just add -pr to the URL, as follows:
 Public repo URL: https://github.com/MicrosoftDocs/{docs-repo}
 Private repo URL: https://github.com/MicrosoftDocs/{docs-repo-pr}
We have closed this pull request. Please resubmit the updates through the private repo. For more information, see the contributor guide.

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Oh actually we should add this file also in to the markup.md table at the bottom.

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Oh actually we should add this file also in to the markup.md table at the bottom.

Done! ✅
I added in the other missing links to the table in markup.md too


Add an extended mode search example

Coverage remained the same at 30.064% when pulling ba0f42e3cbc6aac7a979c53cbc2d63ae9bd147e6 on joonro:patch-1 into 48412378b32b92ca6a0b80770f27158714008a9c on sixohsix:master.


[Sprint 42] XD-2672 Scala support for spark streaming module

Add ScalaProcessor trait that defines the process method

Handle the scala module that extends this trait

Update SparkStreamingPlugin and SparkStreamingDriverModule
to handle this appropriately

Add examples that extend this trait
Add tests

I've not gone into the details of this PR at all, but overall, seems like it's calling for the Strategy pattern, what do you think?

I agree with @ericbottard that the parameterized types for the Scala Processor would be clearer if I and O instead of A and B, respectively.

we need to add this to .gitignore (it appears after running a full 'clean build'):
spring-xd-spark-streaming/.cache

Queues created in Rabbit are not cleaned up properly, e.g.:
xdbus.SparkLogModuleTest958666173.0	0
xdbus.SparkProcessorModuleTest-1773612481.0	0
xdbus.SparkProcessorModuleTest-1773612481.1	0
xdbus.SparkScalaLogModuleTest-672629880.0	0
xdbus.SparkScalaProcessorModuleTest56289912.0	0
xdbus.SparkScalaProcessorModuleTest56289912.1	0

rebased, squashed and merged as https://github.com/spring-projects/spring-xd/commit/77bb4cb81b4ee6184696b8c68536e1a22759620c


Update Swift syntax for Xcode 8 Beta 6.

The biggest change was the JSON type changing from [String: AnyObject] to [String: Any].
I believe that is the best approach for the change on the way id gets imported from Objective-C.
I also had to rewrite KeyPathTests.testNestedKeyPathToJSON.

I updated the commit, I'm not sure if Github sends you a notification about that.

thanks! it does not


add .json extension for webpack targeting node

Superagent cannot be webpacked targeting node due to the missing .json extension.
ERROR in ./~/mime/index.js
Module not found: Error: Can't resolve './types/standard' in '/Users/user/project/node_modules/mime'
 @ ./~/mime/index.js 4:26-53
 @ ./~/superagent/lib/node/index.js
 @ ./src/lib/api.ts
 @ ./src/index.ts
 @ multi ./src/index.ts

ERROR in ./~/mime/index.js
Module not found: Error: Can't resolve './types/other' in '/Users/user/project/node_modules/mime'
 @ ./~/mime/index.js 4:55-79
 @ ./~/superagent/lib/node/index.js
 @ ./src/lib/api.ts
 @ ./src/index.ts
 @ multi ./src/index.ts

Adding .json, and using a json loader in webpack:
    {
      test: /\.json$/,
      loader: 'json-loader'
    }

resolves this issue.
Superagent needs to be webpacked with target: node outside of web environments.
https://github.com/visionmedia/superagent/wiki/Superagent-for-Webpack
Its possible there is a better way to resolve this in webpack.

'Just discussed this in issue #172
Note the bit at the bottom about the CommonJS spec explicitly saying module names should not include extensions.
'Curious to hear your thoughts once you've read through that.

@broofa thanks for the reply.
If this is meant to be a CommonJS module it does not make sense to include the extension.
However, if there is no harm in adding it, I don't think CommonJS module system makes any sense.
Being more explicit should be the default.
I've encountered a similar issue with bundling Scrypt which uses such an import, and there is no way to distinguish between the .json, .js and .node files in that package other than the extension.
I agree with what you are saying, and for a module like this that is used by so many projects, its extra important not to break it to resolve a problem with bundlers which can be resolved by the consumer normally.
I've actually repro'd this with both webpack and rollup, here is a relevant ticket for rollup for posterity: https://github.com/rollup/rollup/issues/480
Just another day as a JS dev :)


preventDefault on enter keydown

Hi
We need to call e.preventDefault() there to avoid the form submission.

Forgot to dist, made another pull request: https://github.com/hakib/MassAutocomplete/pull/23


Import ExchangeIssuance audit fixes and test updates from public repo

LGTM!
One thing to note is that there is a slightly improved version of this contract here:
https://github.com/SetProtocol/index-coop-smart-contracts/blob/ncitron/reduce-dust-II/contracts/exchangeIssuance/ExchangeIssuance.sol
It has a different interface for two of the functions though so it would require changes to the frontend. Its probably fine with we don't use it (it just reduces dust for the issueExactInput functions)

@ncitron Yes, that work is also open here at #35.
(For the moment we just need a quick deploy to patch Polygon. Will definitely revisit - alex has ideas for additional work on  ExchangeIssuance)


WIP: Add resource requests / limits information

Playing with how to best represent this information.

[ ] Tests
[ ] Documentation
[ ] Release note

None required

Deploy preview for calico ready!
Built with commit 5adfb91b8aecabb334d0212d059efc1a950d5252
https://deploy-preview-2439--calico.netlify.com


ES6 import with brackets makes first variable not documented

Input code

import {b} from 'b'

/** x */
const x = 0

/** y */
const y = 0

JSDoc debug output

DEBUG: JSDoc 3.6.3 (Sun, 14 Jul 2019 17:01:26 GMT)
DEBUG: Environment info: {"env":{"conf":{"plugins":[],"recurseDepth":10,"source":{"includePattern":".+\\.js(doc|x)?$","excludePattern":"(^|\\/|\\\\)_"},"sourceType":"module","tags":{"allowUnknownTags":true,"dictionaries":["jsdoc","closure"]},"templates":{"monospaceLinks":false,"cleverLinks":false,"default":{"outputSourceFiles":true}}},"opts":{"_":["."],"debug":true,"destination":"./out/","encoding":"utf8"}}}
DEBUG: Parsing source files: ["%PROJECT_DIRECTORY%\\a.js","%PROJECT_DIRECTORY%\\b.js"]
Parsing %PROJECT_DIRECTORY%\a.js ...
Parsing %PROJECT_DIRECTORY%\b.js ...
DEBUG: Finished parsing source files.
DEBUG: Adding inherited symbols, mixins, and interface implementations...
DEBUG: Adding borrowed doclets...
DEBUG: Post-processing complete.
Generating output files...
Finished running in 0.60 seconds.

Expected behavior
Both x and y should be documented.
Current behavior
x is not documented. Only the first declaration (variables, functions) in file is not documented.
This doesn't happen when I write import b from 'b'. Bracket seems to break something, I suppose?
Or am I doing something wrong?
Your environment

Software
Version

JSDoc
3.6.3

Node.js
8.10.0

npm
5.10.0

Operating system
Windows 10

Same issue here!
My workaround is to add an ugly constant after all the imports
/**
 * JSDoc Hack for import {}
 * @see https://github.com/jsdoc/jsdoc/issues/1718
 */
const jsdocHack = '' // eslint-disable-line

Software
Version

JSDoc
3.6.3

Node.js
10.17.0

npm
6.11.3

Operating system
MacOs 10.14.5

Seems related to #1706. Same result.

The workaround that worked for me is to add a semicolon at the end of brackets import.


Decrease max number of fragments?

It's happening that the fragmenter do not get broadcasted a trnasaction with a tx-size error
INFO[1384] sending transactions...
[tdex] sendrawtransaction RPC error: {"code":-26,"message":"tx-size (code 64)"}

To debug this issue, we should

add a flag --debug that prints the raw hex transaction in the terminal
add a flag --max_fragments  to decrese the number of outputs created


Improve with providing Nuclear Norm Constraint

Hello!
I have updated the conditional_gradient optimizer with providing the option of nuclear norm constraint option, as described in issue #1105,
with using following formula:
variable -= (1-learning_rate) * (variable
    + lambda_ * top_singular_vector(gradient))

Thank you!

Hello @facaiy @WindQAQ @Squadrick!
Can you provide some feedback for the update of CG optimizer?
Thank you!

@googlebot I consent

I've merged master into your branch to update it and fixed any formatting/conflicts it might have. If you need to do some more modifications, please do git pull beforehand.

@gabrieldemarmiesse Got it! Thank you a lot!

@Squadrick when you have the time, could you look into this pull request? Thank you.

@pkan2 There's a merge conflict, can you fix that? Once it's done, this should get merged.

Hello @Squadrick.Thank you for your feedback! I have fixed the merging conflict.
Thank you!

I'll merge this as it was approved by @Squadrick


⚠ ClamAV has degraded performance

In d7a2003, ClamAV (https://spamassassin.apache.org/) experienced degraded performance:

HTTP code: 200
Response time: 594 ms

Resolved: ClamAV performance has improved in e0ae726.


Regression: alertmanager.url flag ignores basic auth

What did you do?

Upgraded Prometheus from 1.1.3 to 1.4.1

What did you expect to see?
I expect that Prometheus will still parse the flag in the same way it used to do in 1.1.3. Especially when docs discourages using alertmanager_config and recommends the "stable" alternative, which is just alertmanager.url flag.
Our -alertmanager.url flag is set to https://<login>:<password>@<static_url>. With this flag our Prometheus instances were able to reach alertmanager with basic auth encoded.
What did you see instead? Under which circumstances?
time="2017-01-16T12:47:40Z" level=error msg="Error sending alerts: bad response status 401 Unauthorized" alertmanager="https://<static_url>:443/api/v1/alerts" count=1 source="notifier.go:335"
Clearly no basic auth is provided.
I can see that here  https://github.com/prometheus/prometheus/blob/master/cmd/prometheus/main.go#L271 u.User data is just ignored (where the basic auth is). Previously whole  -alertmanager.url url was just used.
Mitigation
Changing from flag to alertmanager_config with filled basic_auth options and removing flag obviously helped alert are propagating.
Second issue is that when both flag and alertmanager_config was specified, Prometheus was not able to reach alertmanager entirely as well.
Environment

System information:

uname -srm
Linux 4.7.3-coreos-r3 x86_64

Prometheus version:

./prometheus --version
prometheus, version 1.4.1 (branch: master, revision: 2a89e8733f240d3cd57a6520b52c36ac4744ce12)
  build user:       root@e685d23d8809
  build date:       20161128-09:59:22
  go version:       go1.7.3

Alertmanager version:
Not relevant, but:

/bin/alertmanager --version
alertmanager, version 0.5.1 (branch: master, revision: fddd88400b7264a6873d886fb9bf9321c631f53a)
  build user:       nev@pc-nev
  build date:       20170110-18:40:49
  go version:       go1.7.3

Prometheus configuration file:
Not relevant, no <alertmanager_config> is configured.
Alertmanager configuration file:
Not relevant.
Logs:

time="2017-01-16T12:47:40Z" level=error msg="Error sending alerts: bad response status 401 Unauthorized" alertmanager="https://<static_url>:443/api/v1/alerts" count=1 source="notifier.go:335"
```

Created proposition for the fix ^
https://github.com/prometheus/prometheus/pull/2345

Fix merged.


Use Result conjunction operator in launchTask()

This restores the structure replaced with flatMapping in c852a5c without use of zipWith().
See also antitypical/Result#47 and Carthage/Carthage#547.

Carthage/Carthage#547 was merged.

Thanks! :sparkles:

You, too! :sparkling_heart:


Chore: External table test flake with flight sql

Description
02:06:01.333 ERROR testing::slt::cli: Error while running test `sqllogictests/external_table` error=test fail: query result mismatch:
[SQL] select count(*) from glare_catalog.tables where builtin = false;
[Diff] (-expected|+actual)
-   1
+   4
at /home/runner/work/glaredb/glaredb/testdata/sqllogictests/external_table.slt:30

@scsmithr I just tried to reproduce this on commit 66c2f6bc (main) and was not able to reproduce this
> just slt 'sqllogictests/external_table' --protocol=flightsql

cargo build --bin glaredb
    Finished dev [unoptimized + debuginfo] target(s) in 0.70s
just slt-bin sqllogictests/external_table --protocol=flightsql
./target/debug/glaredb sql-logic-tests sqllogictests/external_table --protocol=flightsql
15:13:05.648  INFO metastore::local: starting local metastore path="/var/folders/tt/gj5kpg1d6q76s1m4k1s3xjlw0000gn/T/.tmpjQiogY"
15:13:05.650  INFO metastore::srv: Creating new Metastore service process_id=9b85211b-d974-406a-badb-77598449e950
15:13:05.656  INFO glaredb::server: Starting GlareDB 0.8.0
Connect via RPC: grpc://<IP_ADDRESS>:49660

15:13:05.656  INFO glaredb::server: enabling flight sql service
15:13:05.657  INFO glaredb::args::slt: Running test: `sqllogictests/external_table`
Tests took 145.758375ms to run

was this only observed in CI?

I think we should:

run this 1000 times and see if we can provoke a failure. Locally or in CI (if we can just run a tight loop around this)
do a bit a poking around the glaredb catalog -> flightsql code path. I think the interesting thing here is that in sean's initial copy of the test failure, the catalog has more tables than it should, which makes me think that there's just some stale data that's hanging around.

Potential theories, lacking any other evidence:

there's something stateful in the test harness: a previous test created some external tables that aren't being cleaned up, or that expire when run against other harnesses.
the glare catalogue could be cached in the flightsql service or session, so we have a stale view.
for completeness: "something about the query just executes incorrectly on flightsql," and that seems much less likely, but if we're doing any kind of special handling or parsing of queries in this code path then maybe that would be a reasonable explanation.

I think if we can't get it to reproduce in 1000 runs, and a couple of us read through the code for the above three options, then it's probably worth closing this and calling it good for now. It could resurface, but I'm less worried because the failure is "there are more things in the catalog than we expect" and not fewer things that we expect. both are potentially bad, but the former might not represent data loss, where the later definitely is. Particularly because most of the explanations that I can come up with are basically "there's a problem with the test" rather than "there's a problem with the implementation" (or at least 2/3rds are) and it's extremely rare... that's something at least.

A separate flake: https://github.com/GlareDB/glaredb/actions/runs/7672628076/job/20913590679?pr=2498
These failures lead me to believe there's something in the flightsql code path that's intermingling databases when they shouldn't be.

https://github.com/glaredb/glaredb/blob/main/crates/rpcsrv/src/flight/handler.rs#L156 <- this is the obvious suspicious line. I've read through basically all of the flight code that I could find, and nothing else jumped out even a little.

https://github.com/glaredb/glaredb/blob/main/crates/rpcsrv/src/flight/handler.rs#L156 <- this is the obvious suspicious line. I've read through basically all of the flight code that I could find, and nothing else jumped out even a little.
the proxy bits seem like they would error if a db_name wasn't present, but if you connect directly (as I suspect these tests do), seems possible to trip this.

Yup! This is something I was trying to find during my initial investigation. Will look more into it. There's a good chance this is it.


Joy-Con motion detection

I haven't done much on GitHub before so I hope I'm not accidentally misusing this feature, but here's my situation:
-My knowledge of how JS works is minimal, but I'm interested in adding a way to use controller motion detection in my game
-I'm aware that there are already ways to connect a Joy-Con to TurboWarp, but they don't seem to support the accelerometer or gyroscope
Can anyone confirm or deny if making Joy-Con motion detection work in a TurboWarp extension is possible? Ideally allowing multiple controllers, with numerical reporters for the current sensor values
(might also be worth mentioning that there's a Joy-Con driver for the WebHID API, which Chrome supports, though I'm not sure if that's relevant here or not)

sensing + can sense gyroscopes? check if it can detect the joycons one

I haven't done much on GitHub before so I hope I'm not accidentally misusing this feature, but here's my situation:
-My knowledge of how JS works is minimal, but I'm interested in adding a way to use controller motion detection in my game
-I'm aware that there are already ways to connect a Joy-Con to TurboWarp, but they don't seem to support the accelerometer or gyroscope
Can anyone confirm or deny if making Joy-Con motion detection work in a TurboWarp extension is possible? Ideally allowing multiple controllers, with numerical reporters for the current sensor values
(might also be worth mentioning that there's a Joy-Con driver for the WebHID API, which Chrome supports, though I'm not sure if that's relevant here or not)

I'm on it!


Filter does not match exact case

If you search for a test using the exact case instead of lower case, the filter doesn't match.

This seem to have been fixed in 1.18.0. Sorry. Closing issue.


Create README

Is your feature request related to a problem? Please describe.
Some readme data is needed for the landing page, guiding users.
Describe the solution you'd like
Have directing data on landing page.
Describe alternatives you've considered
I don't think there are any.
Additional context
None

This is done with #4


[Bug] exercise "en/python/variables/4.md" has an issue

When i wrong an a exercise and I’ll rewrite the right answer, i press again on the retry’s button but it gives me the possibility to go to the next page.

Hello, I found a bug on the app.
I'm releasing the version 2.0.16 that fixes this issue.
Thank you for your report.
@all-contributors please add @lolrida for bug

Please update the app to the latest version, you should see the issue resolved.
If you encounter any other bug, please consider opening a new issue.


Running app for development on Windows is painful

Running Scout from source on windows is pretty painful. You cannot run it directly from the rake tasks unless you manually install several components like jruby, bundler, and then comment out other rake tasks when trying to run "rake" itself.

Adobe Air, Java, and Ruby are all no longer required for Scout-App.
Scout-App 2 was developed primarily on Windows 7. It runs smoothly and happily. The pain is gone, and I do believe this is the last issue I have to clean up.
Closed.


fix: DX around duplicate links

Feature or Problem

This PR:

Introduces some changes to wasmcloud-test-util to enable easier testing
Updates the HTTP server provider to have consistent behavior when overlapping links are used

Now, the HTTP server provider can deal with multiple link names that are essentially overlapping, in FIFO order, popping as links are deleted.

Adds a regression test for the behavior

While this doesn't fundamentally solve the different-link-name-same-interface issue, it should resolve https://github.com/wasmCloud/wasmCloud/issues/2806 as far as the HTTP server goes, at least fixing the accessibility after delete.
Related Issues

Release Information

Consumer Impact

Testing

Unit Test(s)

Acceptance or Integration

Manual Verification

Hey @brooksmtownsend could I get a review here -- I think this PR is the most important one!


preprocess was killed due to large dataset.

I was trying to binarize a huge dataset ~200G. but my server CPU size is 16v with 128G. I tried multiple times with different number of workers. seems that each worker works fine but when the entire process tried to merge, the process was auto-killed. regardless to the number of workers when the bin size reach about 120G, the process was killed without generating idx file.
my previous question was closed.
https://github.com/pytorch/fairseq/issues/2588
so I opened a new one here.

You can try splitting your input file into k chunks, and then call fairseq-preprocess k times.  You can then specify all data paths separated by colons.  See the data argument for more details.

@lematt1991 thanks! I will try and get back to you if it works. before that, let us keep this issue open.

tried multiple ways. split is the only way works.  Thanks

I am facing with same issue however I need to create dict.txt in this step with the fairseq-preprocess. I split my dataset into ~40 chunks but it seems in this way we will create 40 different dict.txt. Do you think it is a problem? What is the recommended data size to create proper dict.txt? Maybe I can first create dict.txt then preprocess data? Any idea?
Thanks

@lematt1991 @akalieren

You can try splitting your input file into k chunks, and then call fairseq-preprocess k times. You can then specify all data paths separated by colons. See the data argument for more details.

Hi, just like @akalieren said, the preprocess step will create multiple dict files, what is your suggestion to this problem?


Cancel in progress builds

A small GitHub Actions change, as specified here: https://docs.github.com/en/actions/learn-github-actions/workflow-syntax-for-github-actions#concurrency
This is primarily useful to automatically cancel jobs while updating PRs repeatedly in short succession, especially since macOS and Windows builds take quite a bit of time (and the number of parallel jobs is limited).
One note: this could cancel a main job if two PRs were merged right after each other, but that's fine: the checks with the final merge would eventually get run.

Thanks @weisers !


Collusion analysis on the arbitrum governance forum

Objective: The main aim is to gain a deeper understanding of the key group of individuals who are actively involved in submitting proposals to the governance forum.
Hypothesis: It is believed that there might be a certain group of individuals with shared interests who consistently support each other's proposals on the governance forum. This could lead to a bias in decision-making, potentially causing a centralization of power.
The Issue is Structured as Follows:
Data Extraction Algorithm Development:
Develop an open-source algorithm to extract data from the governance forum.
Ensure the algorithm is reusable and formats the data for subsequent analysis.
Data Analysis:
Develop a strategy to analyze the data and identify patterns in proposal support.
Consider analyzing who supports or comments on proposals, including sentiment analysis to determine if the responses are favorable or against the proposals.
Relationship Analysis:
Investigate if the most frequent proposal submitters are also acting as delegators.
Examine how these delegators support each other.
Cluster Analysis:
Determine if there are any obvious clusters of individuals who support each other.
Investigate if these clusters are also influencing proposal votes.
Voting Influence Assessment:
Analyze the extent of influence these clusters have in terms of voting power.
Reporting:
Compile a report detailing the methodology and findings.
Additional Notes:
This is a comprehensive project that might require breaking down into smaller, manageable tasks. Any feedback or suggestions to refine this project are welcome.

Hey @poupou-web3 building off of your insights re structuring the issues - would you want to split this into TWO issues, one building a pipeline looking at governance forums etc. and the second doing the analysis?

I believe that that most of the delegates do not leave data on arbitrum governance forum to enable a comprehensive analysis.

https://forum.arbitrum.foundation/t/self-voting-policy-discussion-arbitrumdao-constitution/20886/8?u=pfedprog
With Incentive Program Delegate this should be possible in the near future

Superseding this one with 16


Auto format on file save doesn't work

When I save the file in my editor (Vim & VS Code) prettier doesn't auto-format .prisma files. It does auto-format .js and .json files though.
When I run npx prettier --write ./ manually - it formats .prisma files correctly.
Can prettier-plugin-prisma auto-format on save?
$ node --version
v16.13.2

$ npx os-name-cli
macOS Big Sur

$ npx npm-why prettier

  Who required prettier:

  serverless-functions > eslint-plugin-prettier ><EMAIL_ADDRESS>  serverless-functions ><EMAIL_ADDRESS>  serverless-functions > prettier-plugin-prisma ><EMAIL_ADDRESS>
$ npx npm-why prettier-plugin-prisma

  Who required prettier-plugin-prisma:

  serverless-functions ><EMAIL_ADDRESS>

@umidbekk Thanks for the prompt answer man. That worked out in VS Code, and for Vim I did it the "hacky" way, by adding this line to ~/.vimrc:
" prettier-prisma
autocmd BufWritePre *.prisma Prettier

(This triggers vim-prettier on .prisma buffer write events)


Improvement to Swedish translation of "confirm"

Use the word "bekräfta" instead of "konfirmera". Both are technically correct, but "bekräfta" is more commonly used (e.g. according to frequency of use in Google Translate).

thank you

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 97.573%

Totals

Change from base Build<PHONE_NUMBER>:
0.0%

Covered Lines:
2573

Relevant Lines:
2637

💛  - Coveralls


Cull x axis ticks via css for more flexibility

With this pull request and by adding your own css, you can go from the current enforced choice:

to something as random as this:

[Current coverage][cc-pull] is 64.04%

Merging [#1724][cc-pull] into [master][cc-base-branch] will not change coverage

@@             master      #1724   diff @@
==========================================
  Files             1          1
  Lines          4400       4400
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
  Hits           2818       2818
  Misses         1582       1582
  Partials          0          0

Powered by Codecov. Last updated by [223404a...9f2309f][cc-compare]
[cc-base-branch]: https://codecov.io/gh/c3js/c3/branch/master?src=pr
[cc-compare]: https://codecov.io/gh/c3js/c3/compare/223404a79246c61d150d8a209dbdc81f6955083b...9f2309f6aa86dee9389cb4050f4ec0e042c5e322
[cc-pull]: https://codecov.io/gh/c3js/c3/pull/1724?src=pr


Add syscalls to operator seccomp profile

What type of PR is this?
/kind bug
What this PR does / why we need it:
Looks like we have to add the following syscalls to the default operator profile:
11     munmap
201    time
273    set_robust_list
97     getrlimit

Beside that, I now ensured that the list of syscalls is sorted alphabetically.
Which issue(s) this PR fixes:

Fixes #1404
Does this PR have test?

None
Special notes for your reviewer:
None
Does this PR introduce a user-facing change?

Modified default operator seccomp profile for Amazon Linux 2 (5.4.226-129.415.amzn2.x86_64)

/lgtm


GO:0070985 transcription factor TFIIK complex/GO:0019907 cyclin-dependent protein kinase activating kinase holoenzyme complex same?

From @pgarmiri
https://github.com/geneontology/go-annotation/issues/2941
GO:0070985
transcription factor TFIIK complex
Cellular Component
Definition (GO:0070985 GONUTS page)
A transcription factor complex that forms part of the holo TFIIH complex. In Saccharomyces/human, TFIIK contains Ccl1p/Cyclin H, Tfb3p/MAT1 and Kin28p/CDK7. PMID:19818408 PMID:22572993
GO:0019907
cyclin-dependent protein kinase activating kinase holoenzyme complex
Cellular Component
Definition (GO:0019907 GONUTS page)
A cyclin-dependent kinase activating kinase complex capable of activating cyclin-dependent kinases by threonine phosphorylation, thus regulating cell cycle progression. consists of a kinase, cyclin and optional assembly factors, in human CDK7, CCNH and MNAT1. CAK activity is itself regulated throughout the cell cycle by T-loop phosphorylation of its kinase component (CDK7 in human). Phosphorylation of serine residues during mitosis inactivates the enzyme. Also capable of CAK phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II and other transcription activating proteins, as part of the general transcription factor TFIIH. PMID:8752210
Synonyms
Synonym Type
CAK complex exact
CDK-activating kinase complex exact
seem as though they are describing the same process

@bmeldal Should we merge those 2 ?

I actually think that
GO:0070985 is a type of GO:0019907
GO:0019907 is  a broader term, BUT it is defined as GO:0070985  (or maybe the def is saying that  GO:0070985 is one type of GO:0019907
(there is more than one GO:0019907)

I actually think that
GO:0070985 is a type of GO:0019907

if this is the case, maybe a relation could be added to show that.


[ENHANCEMENT] Lexer improvements + bugfix

fixed line and column counting to start from zero, '\n' now checked before whitespace
simplified lexer errors
return value of lex function changed to include the position of tokens to be used for error handling

Looks pretty good. But please use one of the templates (https://github.com/I-Language-Development/I-language-rust/issues/new/choose) next time.


Output model to a pandas DataFrame

Added trees_to_dataframe method to Booster class in python API. Based on issue #2578.

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.:x: pford221 sign nowYou have signed the CLA already but the status is still pending? Let us recheck it.

This is embarrassing. I left a python debugger set_trace() call in the unit test. Would you like me to resubmit the PR with it removed?

You can simply add new commits in the df_trees branch and they will appear here.
And it seems that your new unit test fails itself. Please fix it along with PEP8 errors (you can find them here https://travis-ci.org/microsoft/LightGBM/jobs/616989890#L502). Thanks!

Hi,
I have formatted according to pep8 standard and the unit test I added is working.

Tests fail due to bad indents in the file. One more reminder: you are NOT restricted to 80 chars line length. I guess it was the reason you decided to change indents.
https://github.com/microsoft/LightGBM/tree/master/python-package#development-guide

Hi. I appreciate your patience! I'm not too familiar with PEP 8 so I relied on the PEP 8 auto formatting python library and maybe it doesn't exactly conform to LightGBM's standards or maybe something happened in the copy and paste from the PEP 8 formatted .py file to basic.py.
I went through all the travis-ci logs and corrected the formatting issues that I found. I then committed and squashed all the commits into one for easier review.
Thanks!

No problem! Thank you very much for this PR! I'll review it shortly.

Thank you for the thorough review, Striker. I will make these edits in the next day or two!

Hello. I can't debug why the Travis CI build failed. It appears to be related to Too Many Requests network error. Please let me know if it's something in this PR that's causing the issue.
Thanks!

Thank you for your updates! I'll review them soon.
Speaking about Travis, I'm sorry for making you confused with failed test. That test checks all URLs in our docs and is quite unstable due to obvious reasons. I've simply re-run it and now everything seems to be OK.

For auto-closing mechanism: fixed #2578. Also I think it can be treated as a fix for #2320, because with this PR it would be possible to obtain actual values as following: actual_min_gain_to_split = model.trees_to_dataframe()['split_gain'].min()

@jameslamb Were your comments fully addressed?

@jameslamb Were your comments fully addressed?

ah, totally missed the followup comment and commit in my GitHub emails!  Yes they were, thank you for the fix @pford221


login via twitter and github not needed

Login to nmrXiv.org provides three options: 1) login with nmrXiv login, 2) login with Twitter and 3) login with GitHub.

This enhancement request would point on the question: What do researchers need to log in?
Researchers would probably need to create a login which could be the nmrXiv login. Handiest would be DFN-AAI as with RADAR, which is, to my knowledge, work in process.
I could understand the possibility of login via GitHub, if there would be no nmrXiv login but only DFN-AAI (as with RADAR), as some (external) developers might not log in via DFN-AAI. However, the nmrXiv login is present, hence, login via GitHub could be omitted. Same applies to "login via Twitter".

Closing in favor of #157


BrainFuck FizzBuzz with no loops

A hardcoded version of FizzBuzz written in brainfuck with no loops, one with comments and then one one-liner with 2222 chars

awesome! thank you :D