MultiQC report is missing fastQC results on the dev branch

Description of the bug
When running the rnaseq pipeline using the dev branch, the fastQC results are no longer included in the MultiQC report, even though the fastqc zip files are available in the results.  This occurs regardless of whether trim_galor or fastp are used as the trimmer.
Command used and terminal output
nextflow run \
nf-core/rnaseq \
--input ${SAMPLES} \
--outdir ${OUTDIR} \
--save_merged_fastq \
--save_trimmed \
--trimmer fastp \
--remove_ribo_rna \
--fasta ${GENOME} \
--gtf ${GTF} \
--aligner star_salmon \
-r dev \
--save_reference \
-resume \
-c /gpfs/projects/GenomicsCore/nf-core/configs/conf/seawulf.config

Relevant files
seawulf_config.zip
nextflow.log.zip
multiqc_report.html.zip
System information
Nextflow version: 24.02.0-edge
Hardware: HPC
Executor: Slurm
Container: Singularity
OS: Rocky Linux 8.7
nf-core version: dev

Some more detail:  I compared the results from the dev branch with a previous successful run using the latest release version (different data sets).  The working directories are structured quite differently.
Release working directory:
.               .command.run    fastqc                        picard                     versions.yml
..              .command.sh     methods_description_mqc.yaml  samtools                   workflow_summary_mqc.yaml
.command.begin  .command.trace  multiqc_config.yml            software_versions_mqc.yml
.command.err    deseq2          multiqc_report_data           sortmerna
.command.log    dupradar        multiqc_report.html           star
.command.out    .exitcode       multiqc_report_plots          trim_log

Dev working directory:
.    117  137  157  177  197  216  236  256  276  296  315  335  355  375  395  414  434  454  474  494  513  533  57  77  97
..   118  138  158  178  198  217  237  257  277  297  316  336  356  376  396  415  435  455  475  495  514  534  58  78  98
1    119  139  159  179  199  218  238  258  278  298  317  337  357  377  397  416  436  456  476  496  515  535  59  79  99
10   12   14   16   18   2    219  239  259  279  299  318  338  358  378  398  417  437  457  477  497  516  536  6   8   .command.begin
100  120  140  160  180  20   22   24   26   28   3    319  339  359  379  399  418  438  458  478  498  517  537  60  80  .command.err
101  121  141  161  181  200  220  240  260  280  30   32   34   36   38   4    419  439  459  479  499  518  538  61  81  .command.log
102  122  142  162  182  201  221  241  261  281  300  320  340  360  380  40   42   44   46   48   5    519  539  62  82  .command.out
103  123  143  163  183  202  222  242  262  282  301  321  341  361  381  400  420  440  460  480  50   52   54   63  83  .command.run
104  124  144  164  184  203  223  243  263  283  302  322  342  362  382  401  421  441  461  481  500  520  540  64  84  .command.sh
105  125  145  165  185  204  224  244  264  284  303  323  343  363  383  402  422  442  462  482  501  521  541  65  85  .command.trace
106  126  146  166  186  205  225  245  265  285  304  324  344  364  384  403  423  443  463  483  502  522  542  66  86  .exitcode
107  127  147  167  187  206  226  246  266  286  305  325  345  365  385  404  424  444  464  484  503  523  543  67  87  multiqc_config.yml
108  128  148  168  188  207  227  247  267  287  306  326  346  366  386  405  425  445  465  485  504  524  544  68  88  multiqc_data
109  129  149  169  189  208  228  248  268  288  307  327  347  367  387  406  426  446  466  486  505  525  545  69  89  multiqc_plots
11   13   15   17   19   209  229  249  269  289  308  328  348  368  388  407  427  447  467  487  506  526  546  7   9   multiqc_report.html
110  130  150  170  190  21   23   25   27   29   309  329  349  369  389  408  428  448  468  488  507  527  547  70  90  versions.yml
111  131  151  171  191  210  230  250  270  290  31   33   35   37   39   409  429  449  469  489  508  528  548  71  91
112  132  152  172  192  211  231  251  271  291  310  330  350  370  390  41   43   45   47   49   509  529  549  72  92
113  133  153  173  193  212  232  252  272  292  311  331  351  371  391  410  430  450  470  490  51   53   55   73  93
114  134  154  174  194  213  233  253  273  293  312  332  352  372  392  411  431  451  471  491  510  530  550  74  94
115  135  155  175  195  214  234  254  274  294  313  333  353  373  393  412  432  452  472  492  511  531  551  75  95
116  136  156  176  196  215  235  255  275  295  314  334  354  374  394  413  433  453  473  493  512  532  56   76  96

Despite the fact that the fastqc zip files are present in the dev working directory:
find . -name "*.zip"
./69/SH52_1_fastqc.zip
./34/SH61_1_fastqc.zip
./37/SH59_2_fastqc.zip
./85/SH55_1_fastqc.zip
./80/SH46_2_fastqc.zip
./88/SH58_2_fastqc.zip
./83/SH45_1_fastqc.zip
./103/SH49_1_fastqc.zip
./7/SH56_2_fastqc.zip
./21/SH45_2_fastqc.zip
./24/SH58_1_fastqc.zip
./27/SH57_2_fastqc.zip
./75/SH51_1_fastqc.zip
./70/SH52_2_fastqc.zip
./78/SH47_2_fastqc.zip
./73/SH50_1_fastqc.zip
./43/SH44_2_fastqc.zip

The MultiQC log doesn't show that they were found:
 cat .command.log

  /// MultiQC 🔍 | v1.21

|           multiqc | MultiQC Version v1.22.1 now available!
|           multiqc | Only using modules: custom_content, fastqc, cutadapt, fastp, sortmerna, star, hisat2, rsem, salmon, kallisto, samtools, picard, preseq, rseqc, qualimap
|           multiqc | Search path : /gpfs/projects/GenomicsCore/nf-core/rnaseq/Futcher-05-24/work/c9/3c7c78f49d00d00096f2c0e664d85e
|            report | Skipping 17 file search patterns
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 1252/1252
|    custom_content | biotype_counts: Found 1 samples (bargraph)
|    custom_content | dupradar: Found 1 samples (linegraph)
|    custom_content | DupInt: Found 21 General Statistics columns
|    custom_content | star_salmon_deseq2_clustering: Found 21 samples (heatmap)
|    custom_content | biotype-gs: Found 21 General Statistics columns
|    custom_content | nf-core-rnaseq-summary: Found 1 sample (html)
|    custom_content | star_salmon_deseq2_pca: Found 1 samples (scatter)
|    custom_content | fail_strand_check: Found 1 samples (table)
|            picard | Found 21 MarkDuplicates reports
|          qualimap | Found 21 RNASeq reports
|             rseqc | Found 21 read_distribution reports
|             rseqc | Found 21 inner_distance reports
|             rseqc | Found 21 read_duplication reports
|             rseqc | Found 21 junction_annotation reports
|             rseqc | Found 21 junction_saturation reports
|             rseqc | Found 21 infer_experiment reports
|             rseqc | Found 21 bam_stat reports
|          samtools | Found 21 stats reports
|          samtools | Found 21 flagstat reports
|          samtools | Found 21 idxstats reports
|         sortmerna | Found 42 logs
|              star | Found 21 reports
|             fastp | Found 21 reports
|           multiqc | Report      : multiqc_report.html
|           multiqc | Data        : multiqc_data
|           multiqc | Plots       : multiqc_plots
|           multiqc | MultiQC complete

I also noticed that the multiQC version differs between the release (1.19) and dev (1.21) branch.  I ran multQC version 1.21 manually in the working directory, and encountered the same issue where the fastQC files were not located.
So, I'm not currently certain whether the issue is related to the updated MultiQC version or changes to how the working directory files are structured.
Let me know if you need any additional information!
Best,
Dave

Another update: I tried downgrading my local version of MultiQC to 1.19 (which is used in the release version of the pipeline, where it seems to be working fine) and ran it again on my working directory.  The issue persists - MultiQC did not locate the fastQC files and did not incorporate them into the report.

Thanks for reporting and the thorough investigation!  I could reproduce the issue and also figured out the reason for the failed inclusion.
MultiQC is run with the custom config file workflows/rnaseq/assets/multiqc/multiqc_config.yml that warrants that the FastQC reports are located in the raw and trim subdirectories of the fastqc folder:
module_order:
  - fastqc:
      name: "FastQC (raw)"
      info: "This section of the report shows FastQC results before adapter trimming."
      path_filters:
        - "./fastqc/raw/*.zip"
  - cutadapt
  - fastp
  - fastqc:
      name: "FastQC (trimmed)"
      info: "This section of the report shows FastQC results after adapter trimming."
      path_filters:
        - "./fastqc/trim/*.zip"

In reality, the publishDir directives will publish the raw reports in ${params.outdir}/fastqc and the trimmed reports in ${params.outdir}/${params.trimmer}/fastqc.  Hence, both are not included, if the custom MultiQC config is applied, but will be included otherwise, e.g. in a manual rerun after the pipeline has finished.
I will fix that later this week.

Thanks a lot, Matthias!

Just to keep you updated: I think, I fixed the bug in this branch, but the testing is somehow cursed at the moment. At first, I had issues with Nextflow not finding the images on our offline cluster and now the MultiQC reports won't load in my browser at all. (But also those from the regular pipeline).
Since it seems to work for you, you are welcome to test the version from my branch. Please include also umi_dedup_stats = true, because I think that botched MultiQC config was also behind another issue (#1277) that I had not really understood before.

Hi Matthias,
I cloned your fork, switched to the MultiQC_FastQC_bug branch and then ran the local version of the pipeline with the following command:
nextflow run \
./rnaseq \
--input ${SAMPLES} \
--outdir ${OUTDIR} \
--save_merged_fastq \
--save_trimmed \
--trimmer fastp \
--remove_ribo_rna \
--fasta ${GENOME} \
--gtf ${GTF} \
--umitools_dedup_stats true \
--aligner star_salmon \
--save_reference \
-c /gpfs/projects/GenomicsCore/nf-core/configs/conf/seawulf.config

Unfortunately, the fastQC results are still not present in the MultiQC report (see attached).
Did I run the test correctly?
Thanks!
Dave
multiqc_report.zip

Thanks for testing! No, you did not do anything wrong - I did not successfully fix it. The output publishing is not working as supposed clean and the custom config thus does not apply.
I am just working on it again, but I won't have much more time till next Wednesday for that.

Okay, thanks for the update!  Let me know if I can help with any additional testing.

I now opened a draft PR #1308 that currently doesn't fix anything because ... that escalated quickly.
There is at least one MultiQC bug (see also issue there), potentially even two, involved, and we also have additional issues with the pipeline. So unfortunately, instead of fixing one, I discovered it is a total of four issues.
I described them in detail in the draft PR, so if you feel like experimenting, please give any of it a go, since I won't have time for it until end of next week.

These bugs in MultiQC should be fixed now as of MultiQC v1.22.2 - hopefully the best solution here is to update the MultiQC nf-core module.

#1308 has just been merged to dev and will be released as part of rnaseq 3.15. I hope, this issue is solved by those changes. Hence, I am closing for now.


[FLINK-11241][table] - Enhance TableEnvironment to connect to a catalog via descriptor

What is the purpose of the change
Please see commits prefixed with FLINK-11241.
This PR builds on #7390 (catalog descriptor/factory), to provide a typed API on TableEnvironment for connecting to a catalog via descriptor.  You may see this API in action in the below snippet (from this example):
// register the taxi data tables under the "nyc" schema
tEnv.connect(new TaxiData()
        .ridesFile(ridesFile)
        .faresFile(faresFile)
        .maxEventDelaySecs(maxEventDelay)
        .servingSpeedFactor(servingSpeedFactor))
        .registerExternalCatalog("nyc");

// query across registered tables
tEnv.sqlQuery("SELECT f.rideId, f.driverId, f.totalFare FROM nyc.TaxiRides r INNER JOIN nyc.TaxiFares f ON r.rideId = f.rideId");

Brief change log

Added ConnectExternalCatalogDescriptor
Extended TableEnvironment with new connect method for catalogs

Verifying this change
This change added tests and can be verified as follows:

Added unit test ConnectExternalCatalogDescriptorTest for testing the new API

Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): no
The public API, i.e., is any changed class annotated with @Public(Evolving): yes
The serializers: no
The runtime per-record code paths (performance sensitive): no
Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Yarn/Mesos, ZooKeeper: no
The S3 file system connector: no

Documentation

Does this pull request introduce a new feature? yes
If yes, how is the feature documented? JavaDocs

AM closing since I think catalog subsystem is going in a different direction.


Badges in tabs for recipe contents

Include a badge in the tab label to indicate number of list items for
Dependencies and Selected Components.
Remove modified PF css since the Tabs component supports
defining class names.

Codecov Report

Merging #157 into master will increase coverage by 1.66%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #157      +/-   ##
==========================================
+ Coverage   37.66%   39.32%   +1.66%
==========================================
  Files          73       70       -3
  Lines        2257     2230      -27
  Branches      298      312      +14
==========================================
+ Hits          850      877      +27
+ Misses       1196     1134      -62
- Partials      211      219       +8

Impacted Files
Coverage Δ

components/ListView/ComponentDetailsView.js
1.21% <ø> (+0.01%)
:arrow_up:

components/ListView/RecipeContents.js
44.44% <100%> (+3.26%)
:arrow_up:

components/ListView/ComponentSummaryList.js
5.88% <0%> (-1.27%)
:arrow_down:

components/Modal/PendingChanges.js
6.66% <0%> (-1.03%)
:arrow_down:

core/reducers/modals.js
81.25% <0%> (ø)
:arrow_up:

pages/error/index.js
0% <0%> (ø)
:arrow_up:

core/reducers/inputs.js
66.66% <0%> (ø)
:arrow_up:

core/reducers/recipePage.js
50% <0%> (ø)
:arrow_up:

core/reducers/sort.js
30% <0%> (ø)
:arrow_up:

components/Layout/Layout.js
100% <0%> (ø)
:arrow_up:

... and 16 more

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Add setters for bound methods

Hello.
I want to use the @autobind decorator with this awesome React babel plugin by @gaearon
https://github.com/gaearon/react-transform-catch-errors
But when the page loads I get Cannot set property render of #<Component> which has only a getter error in the console.
The fix is to add a setter (see the code).

I would love this for testing!


Crash on macOS when importing textures with specific settings

Tested versions
4.3-rc1 (also happens in 4.3-beta3)
System information
macOS Sonoma (14.5) with Intel CPU - GPU: Radeon Pro Vega 20
Issue description
When opening the editor to import textures, the editor crashes with a segfault. I'm using the Compatibility renderer.

Stack trace
* thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT
  * frame #0: 0x00007ff810a4b14a libsystem_kernel.dylib`__pthread_kill + 10
    frame #1: 0x0000000107c57555 libsystem_pthread.dylib`pthread_kill + 262
    frame #2: 0x00007ff8109a9b19 libsystem_c.dylib`__abort + 145
    frame #3: 0x00007ff810997ab8 libsystem_c.dylib`__stack_chk_fail + 102
    frame #4: 0x00000001009d60d8 Godot`_compress_astc(Image*, Image::ASTCFormat) + 2168
    frame #5: 0x00000001046031c8 Godot`Image::compress_from_channels(Image::CompressMode, Image::UsedChannels, Image::ASTCFormat) + 200
    frame #6: 0x0000000102093ca5 Godot`ResourceImporterTexture::save_to_ctex_format(Ref<FileAccess>, Ref<Image> const&, ResourceImporterTexture::CompressMode, Image::UsedChannels, Image::CompressMode, float) + 837
    frame #7: 0x00000001020944b1 Godot`ResourceImporterTexture::_save_ctex(Ref<Image> const&, String const&, ResourceImporterTexture::CompressMode, float, Image::CompressMode, bool, bool, bool, bool, bool, bool, bool, bool, unsigned int, Ref<Image> const&, Image::RoughnessChannel) + 721
    frame #8: 0x00000001020960e1 Godot`ResourceImporterTexture::import(String const&, String const&, HashMap<StringName, Variant, HashMapHasherDefault, HashMapComparatorDefault<StringName>, DefaultTypedAllocator<HashMapElement<StringName, Variant>>> const&, List<String, DefaultAllocator>*, List<String, DefaultAllocator>*, Variant*) + 6257
    frame #9: 0x0000000101b78722 Godot`EditorFileSystem::_reimport_file(String const&, HashMap<StringName, Variant, HashMapHasherDefault, HashMapComparatorDefault<StringName>, DefaultTypedAllocator<HashMapElement<StringName, Variant>>> const&, String const&, Variant*) + 6178
    frame #10: 0x0000000101b6afe3 Godot`EditorFileSystem::reimport_files(Vector<String> const&) + 3091
    frame #11: 0x0000000101b68b8e Godot`EditorFileSystem::_update_scan_actions() + 5854
    frame #12: 0x0000000101b6f13d Godot`EditorFileSystem::_notification(int) + 621
    frame #13: 0x0000000104a469de Godot`Object::notification(int, bool) + 62
    frame #14: 0x0000000102898bb5 Godot`SceneTree::_process_group(SceneTree::ProcessGroup*, bool) + 405
    frame #15: 0x0000000102896ddf Godot`SceneTree::_process(bool) + 879
    frame #16: 0x000000010289748f Godot`SceneTree::process(double) + 223
    frame #17: 0x0000000100971f71 Godot`Main::iteration() + 1089
    frame #18: 0x000000010090314a Godot`OS_MacOS::run() + 154
    frame #19: 0x00000001009321f3 Godot`main + 387
    frame #20: 0x00007ff8106f8366 dyld`start + 1942

Only happens on macOS. On Linux and Windows it imports the texture just fine.
Disabling ETC2 ASTC makes it not crash but it does not import the texture correctly.
Steps to reproduce

Create a project.godot with these settings:

[importer_defaults]

texture={
"compress/channel_pack": 0,
"compress/hdr_compression": 1,
"compress/high_quality": true,
"compress/lossy_quality": 0.7,
"compress/mode": 2,
"compress/normal_map": 0,
"detect_3d/compress_to": 1,
"editor/convert_colors_with_editor_theme": false,
"editor/scale_with_editor_scale": false,
"mipmaps/generate": false,
"mipmaps/limit": -1,
"process/fix_alpha_border": true,
"process/hdr_as_srgb": false,
"process/hdr_clamp_exposure": false,
"process/normal_map_invert_y": false,
"process/premult_alpha": false,
"process/size_limit": 0,
"roughness/mode": 0,
"roughness/src_normal": "",
"svg/scale": 1.0
}

[rendering]

renderer/rendering_method="gl_compatibility"
renderer/rendering_method.mobile="gl_compatibility"
textures/vram_compression/import_etc2_astc=true

Include any texture in the project (can be the default icon.svg).
Open the editor to import the files.

Minimal reproduction project (MRP)
import-crash-macos.zip

Note: None of my custom builds cause the crash so I couldn't debug it properly. Even with ASAN enabled. Though none import the texture correctly.
Also, it gets to the message astcenc: Encoding took 558 ms. that happens at the end of the _compress_astc() function so the issue might be in some destructor that's causing the issue.

Do you reproduce the issue with 4.2.2 or earlier dev snapshots?

Note: None of my custom builds cause the crash so I couldn't debug it properly.

Can you reproduce the issue if you build with production=yes like official builds?

Even with ASAN enabled.

I can reproduce it with custom build without ASAN, but can't reproduce with ASAN (maybe since ASAN build increase stack size from 8 MB to 30, and trace indicate stack related issue).

Do you reproduce the issue with 4.2.2 or earlier dev snapshots?

I will try earlier snapshots. With 4.2.2 it does not crash, but it does not import the texture correctly, and it tries to reimport every time the window is focused (which takes a while in the actual project).

Checked the snapshots and 4.3-dev4 is the first that crashes. Still couldn't reproduce with my own builds even with production=yes.

It might some sort of conflict with ANGLE, which also include own copy of ASTC encoder (none of the symbols should be public), it's not crashing without ANGLE, but import is not working.

Edit: import is working, but MRP is set compatibility renderer, and ASTC is not supported by OpenGL on macOS.

Okay, this seems to be a different problem. When I disable "High Quality" in the import settings, it actually loads everything just fine, even if the ETC2 ASTC option is on.
Summary:

If "High Quality" import setting is OFF, everything works.
If "High Quality" import setting is ON, textures do not load, but it does not crash.
If "High Quality" import setting is ON and the ETC2 ASTC option is ON, the editor crashes.

It might some sort of conflict with ANGLE, which also include own copy of ASTC encoder (none of the symbols should be public), it's not crashing without ANGLE.

I got it working with enabled ANGLE (by keeping only Godot copy of ASTC encoder), will check if it's working on Windows (might need linking order adjusted for GCC builds), and open PR tomorrow.


PUPIL-478: Confirmic blocking the bottom nav in pupil lessons

Description
Music year: 1977
Moves the Confirmic widget above the footer nav in pupil lessons so that it no longer obscures and blocks interaction with the button beneath
How to test

Open an incognito browser window or clear your cookies + localStorage for thenational.academy
Go to https://deploy-preview-2311--oak-web-application.netlify.thenational.academy/pupils/lessons/prologue-grime-mix-ccuk0d
Observe the appearance of the Confirmic consent widget
You should be able to click on "Let's get ready"
The confirmic widget should work as before
The confirmic widget should not be affected in any other section of OWA

Screenshots
How it used to look (delete if n/a):
https://github.com/oaknational/Oak-Web-Application/assets/122096/1af63711-856c-4bca-8313-f4fe8f5898c2
How it should now look:

:tada: This PR is included in version 1.388.2 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


docs(readme): add package listing

See https://github.com/ipfs/js-ipfs/pull/385 for details

Usage should be above Packages. Not sure about Contribute vs Packages (I vote for Contribute first)

I vote for Contribute second, as you first have to use it and understand things before you contribute. Also this does not follow standard readme, so maybe we can get @RichardLitt to work his magic?

standard-readme 👼 :D

Will standardize this!


The docs/ directory should be a vaild Jekyll site for github pages

Currently, the release target in the Makefile outputs a bunch of markdown files, but doesn't take the logical next step(s) of turning them into a functional Github Pages website.  We should fix this so that users can easily browse the docs.

Fixed in https://github.com/Cray-HPE/cray-site-init/commit/ee0dec84e4af5d4772b1948242b29ee408b42744


perf: add ability to cache dataframe and series to session table

Thank you for opening a Pull Request! Before submitting your PR, there are a few things you can do to make sure it goes smoothly:

[ ] Make sure to open an issue as a bug/issue before writing your code!  That way we can discuss the change, evaluate designs, and agree on the general idea
[ ] Ensure the tests and linter pass
[ ] Code coverage does not decrease (if any source code was changed)
[ ] Appropriate docs were updated (if necessary)

Fixes #<issue_number_goes_here> 🦕

Very cool! I assume this is intended to be built on by other PRs?

For sure, right now you would have to manually invoke this functionality. We will want to soon apply this automatically in some circumstances.


cosmic-launcher: init at unstable-2023-11-08

Description of changes

Things done

Built on platform(s)

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

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] Tested, as applicable:

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

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

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

[x] Fits CONTRIBUTING.md.

* [ ]  Tested basic functionality of all binary files (usually in `./result/bin/`)

Have you tested that it works?  You should check the box if so!

* [ ]  Tested basic functionality of all binary files (usually in `./result/bin/`)

Have you tested that it works? You should check the box if so!

Well it runs, so I guess that basic functionality

Since this package has some unusual stuff in it, like RUSTFLAGS, we should check it's using the right variables for cross-compilation:
@OfBorg test pkgsCross.riscv64.cosmic-launcher

Since this package has some unusual stuff in it, like RUSTFLAGS, we should check it's using the right variables for cross-compilation:
@ofborg test pkgsCross.riscv64.cosmic-launcher

Is this good to merge now?


Document Lane Splines Tool

add documentation for lane spline tool

where is the animated gif requested in https://github.com/monoDriveIO/documentation/pull/71#pullrequestreview-390850895


Allow reports to be analyzed even with incomplete data

This partially addresses #29 by allowing the report to be generated at all in the first place. Now only the parts of the bundle that failed to be analyzed don't contain sizes for Gzip or parsed parts, but will still render successfully.
I suspect this will also help in debugging the issue further a lot.

This solution allows the build to succeed in those cases when the modules couldn't be extracted correctly from the compiled bundles.
It might be useful to warn about this failure mode, though. The modules that don't have gzip nor parsed sizes are not sized appropriately in the treemap as they have nothing to compare against so every module takes the same space in all but "stat" based sorting.
#44 should fix the root cause properly. The webpack chunk module template doesn't seem to have any other new, unaddressed cases than what #44 adds support for:

https://github.com/webpack/webpack/blob/v1.14.0/lib/Template.js#L79
https://github.com/webpack/webpack/blob/v2.2.1/lib/Template.js#L94

I think #44 fixes the root of the issue so there is no need in this PR any more.


Added PostMaster website

*Fixed #1346

Description 📜
This website is used to create get and post request from a URL. We can add JSON request or set custom parameter. We get desired response after submitting. I have used html, css, javascript,  prism.js and prism.css to make this website.
Fixes #1346

Type of change 📝

[x] Add a new project

Domain of Contribution 📊

[x] Project using HTML, CSS & JS

Checklist ✅

[x] I have performed a self-review of my own code or work.
[x] I have commented on my code, particularly in hard-to-understand areas.
[x] My changes generate no new warnings.
[x] I'm GSSoC'22 contributor

Screenshots / Gif (Recommended) 📸

Creating GET request from URL

Creating POST request using JSON

Creating POST request using custom parameters

https://github.com/ravigithub19/postman-clone copied from here @Mrjoy832

@gurjeetsinghvirdee I have not copied their content. This pr is itself plagiarised from https://www.youtube.com/watch?v=g0gLojpleAg&list=PLu0W_9lII9ajyk081To1Cbt2eI5913SsL&index=63&t=4557s here. I have taken help fron online and tried to build it on my own

@gurjeetsinghvirdee I have not copied their content. This pr is itself plagiarised from https://www.youtube.com/watch?v=g0gLojpleAg&list=PLu0W_9lII9ajyk081To1Cbt2eI5913SsL&index=63&t=4557s here. I have taken help fron online and tried to build it on my own

Then mention you are taking refrence

Okay, I will do it surely next time. Thank you.


Integrate safe-npm/sockets

Recently, npm malware is incresing.

Security alert: social engineering campaign targets technology industry employees - The GitHub Blog
Social engineering campaign targeting tech employees spreading through npm malware - Socket

We want to integrate safe npm or something into ni.zsh
ni # check and install
ni add ... # check and install

Get issues by package
Issues - npm - Socket


chore(deps): upgrade dependencies

Upgrades project dependencies. See details in workflow run.

Automatically created by projen via the "upgrade-2.x" workflow

⚪ Backport skipped
The pull request was not backported as there were no branches to backport to. If this is a mistake, please apply the desired version labels or run the backport tool manually.
Manual backport
To create the backport manually run:
backport --pr 390

Questions ?
Please refer to the Backport tool documentation


Add NEWS file and update authors in README

@lchristm Once the conflicts are resolved, this can be merged imho


Bobbing causes weird shift in lighting

What you were trying to do
Test something unrelated. One would normally expect to be able to move around the world with consistent lighting/shadows
What actually happened
Only when walking with the "bobbing" gfx turned on: the lighting shifts subtly for each "bob" (every few steps). Doesn't happen if flying or if you turn off the effect.
How to reproduce

Run game normally and enter a world with "bobbing" enabled
Move forward, ideally with a hill or something in front of you
Observe subtle lighting shifts in tune with the head bobbing

Note:: It may be specific to time of day in-game - seemed to not happen in some cases but around World Time 0.5 it was strongly present.
It may relate to the recent JOML changes as I cannot replicate with the commit immediately preceding #3811 - but I haven't tested after that point commit-by-commit. @PS-Soundwave suspected as much, but upgrading to 1.9.23 from 1.9.19 didn't seem to have an effect.
Screenies
Easier to see the effect in-game, but it is there

I think #3885 resolves this.

Looks like! Thanks hunting it down :-)


MIVA Token on GnosisChain

为确保 Token Profile 的顺利通过，务必逐一确保以下检查项并补充项目资料：
.json 及 .png 文件检查项

[ ] logo 尺寸：120*120 px
[ ] logo 背景：透明
[ ] 代币有至少一笔成功的转账记录
[ ] 此项对于 ERC-20 项目方：合约地址有大小写（做 checksum）
[ ] .json 和 .png 文件名一致（包括大小写）

项目资料：
官方公告：
团队背景：
项目基本情况：
媒体报道：
收录的交易所：
转账所需 Gas Limit（对 ERC-20 项目方）：（默认为 60000）

Please check the following to ensure a successful verification of Token Profile
.json and .png document checklists

[x] logo dimensions: 120*120 px
[x] logo background: Transparent
[x] At least one transaction on the token contract
[x] For ERC-20 project teams: Upper and lower capitalized alphabets in token address (For checksum purposes)
[x] Same document name for both .json and .png (Including capitalization)

Project background:
Official announcement: https://mirror.xyz/minerva.eth/ZKt2VSGBTBdTj8jZ0gSX_XLA86NI0QfheiKafFkC9P0
Project team background: The Minerva Wallet gets developed by the lab10 collective, an austrian blockchain collective with +5 years of experience in the blockchain field.
Project basic information: The Minerva Wallet is a Android Wallet for EVM Chains. We support major EVM Networks, auto-detect Tokens&NFTs and can display active Superfluid Streams.
Media publications: https://mirror.xyz/minerva.eth/
Tradeable exchanges: Honeyswap, CowSwap, Balancer, Symmetric
Recommended Gas Limit (For ERC-20 project teams) for transaction: (Default is 60,000) 60,0000

Please provide at least one successful transfer record within the last 14 days. @seliqui

The Token is on GnosisChain, with a few hundred transfers in the last 14 days.
https://gnosisscan.io/token/0x63e62989d9eb2d37dfdb1f93a22f063635b07d51
Sorry for any confusion.

Or here's a direct tx of one transfer:
https://gnosisscan.io/tx/0x562625bf1563ea606fef4388179ff755dbfbe31774da6db6fe260d242e3ee785
Is that sufficient? Let me know if you need anything else :)

Sorry, token-profile can't support non-ERC20 or non-EOS20 tokens, we will add the MIVA token by other methods, Please wait a sec. @seliqui

Did you find another method to add MIVA? :)
Do you need any additional informations from us?


ENH: Fix vineyard compatibility issue

What do these changes do?
Fix vineyard compatibility issue. Note that there is a a workaround here: vineyard return a different class name (metadata), while the data values is correct.
Related issue number

Fixes #xxxx
Check code requirements

[x] tests added / passed (if needed)
[x] Ensure all linting tests pass

The vineyard CI error may be related to pandas 2.2.2.
See: https://github.com/v6d-io/v6d/issues/1930


Fixed #24728 -- Rename mime_type to content_type for syndication feeds

Renamed the mime_type properties of RssFeed and Atom1Feed to
content_type and start deprecation for the old names.

buildbot, test this please.

This wouldn't work if someone has subclassed the fields and set their own mime_type -- this doesn't seem like it would be common though, so maybe we can ignore that. We need to update the places that use the deprecated attribute, e.g. item['enclosure'].mime_type. Also a mention in docs/internals/ddeprecation.txt is missing.

No need for the "buildbot, test this please." comment -- builds will run automatically and that comment triggers extra builds.

Okay, I got that wrong about buildbot, thanks.
Concerning item['enclosure'].mime_type, I believe it is correct this way. The scope of the ticket was to remove the term "mime type" form everything related to HTTP (such as: the rendered feed), in order to match the terminology of the HTTP header Content-Type.
However, item['enclosure'].mime_type refers to the type of an Enclosure object. In this case, "mime type" is the commonly used term (see for example rssboard.org). Therefore, I did not deprecate this. (Although we could do, if we want, for consistency.)
Django itself never uses the mime_type attribute of Atom1Feed or RssFeed outside of tests, neither is it a documented attribute. Additionally, the attribute does not exist on the base SyndicationFeed class. Therefore, to my understanding it wasn't even a public API, so I think we can indeed ignore the subclassing issue.

Please ignore my last comment, I understood something wrong there. I will look into it.

I missed one usage when grepping. Fixed it now, complete test suite passes.
Also, I added it to the deprecation list. For enclosures, see my comment above. Thank you for the feedback! :)

This looks good to me, waiting to see if tests pass.

merged in 5c125f63f77e169a459c11bab0f639c83fabc6e2, thanks!


Update dartdoc to 0.28.1+2 and fix search text alignment

Fixes #22967.
Dartdoc release notes:  https://github.com/dart-lang/dartdoc/releases/tag/v0.28.1%2B2
Dartdoc's search box alignment has been off in both the mainline dartdoc for some browsers, and in Flutter for all browsers (#22967).  A combination of style tweaks in Dartdoc and Flutter's overrides fixes this for all platforms I have tested.
Screenshots (all on Mac unless specified):
Safari:

Firefox:

Chrome canary:

Chrome 72:

Chrome 72, Linux:


FIX: Move from pkg_resources to niworkflows.data.Loader

pkg_resources is deprecated as an API.

Ouch. Thanks
On Tue, Mar 19, 2024, 16:11 Chris Markiewicz @.***>
wrote:

@.**** commented on this pull request.
In mriqc/reports/individual.py
https://github.com/nipreps/mriqc/pull/1199#discussion_r1530585084:

from nireports.assembler.report import Report
+from niworkflows.data import Loader

+_load_data = Loader(package)
I don't think this is going to work quite how you want. I'm pretty sure
this will load relative to mriqc.reports.individual. I would suggest
instead having data/init.py define load_data and import from there.
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Support for Sentinel-1 Download

Is there planned support for downloading S1B data as SAFE files, eg. S1B_IW_GRDH_1SDV_20180911T054651_20180911T054716_012663_0175E1_E282?
Would this be alot of work? I'd be happy to contribute.

It was not on our high priority list for the moment. You are welcome to implement and do a PR/

I wouldn't mind looking at it. Do you have a broad idea of how it should be done? A couple of pointers would be appreciated. 💯


Allow disabling of CURLOPT_SSL_VERIFYHOST

Useful when the SSL cert has an invalid or non-resolvable hostname

@voodoodrul thanks for this! the tests are failing however, due to libcurl warning:
curl_setopt_array(): CURLOPT_SSL_VERIFYHOST with value 1 is deprecated and will be removed as of libcurl 7.28.1. It is recommended to use value 2 instead

please review the related docs of libcurl here: http://curl.haxx.se/libcurl/c/CURLOPT_SSL_VERIFYHOST.html
can you please make the appropriate changes so I can merge and release a new version?
thanks!

@ahmadnassri I committed a fix for this. As a side note, this functionality can also be accomplished in the existing codebase - without Request::verifyHost() - using:
Unirest\Request::curlOpt(CURLOPT_SSL_VERIFYHOST, false);

@voodoodrul yep, curlOpt is there precisely for that reason, though having helper methods is also good (and free!)


fix(docs): docs api property example open change status error

question:

When docs api property example opened, i change to other components,this api property example open status is not change.

method:

I watch the route change,when route changed,i get all toggleBtn and nextCode,if it has open status class ,remove them.

why this pr has three commits ,i change the branch not last pr branch


feat: New info about HGVS_OFFSET behavior (e109)

Description
Alteration to inform HGVS_OFFSET value behavior.
Test
Just check new text information.
http://wp-np2-11.ebi.ac.uk:7080/info/docs/tools/vep/vep_formats.html#vcfout
http://wp-np2-11.ebi.ac.uk:7080/info/docs/tools/vep/script/vep_options.html

Prefer text in vep_formats.html to be: "Value must be greater than 0."
Otherwise looks good.


Algo for assigning proctor and candidates to room

Problem Statement
Write workflow for assigning the candidates and proctors to the room.

Candidate and proctor must be join to same room if somehow he left the room.
More than configurable no of candidates should not be visible to particular proctor.
If there are more than one proctor in room, candidate must be assigned to proctor in the first come first served basis.
If Proctor left the room somehow. He must joined the same room .

Impact Analysis:
Algorithm for assigning the candidates and proctors:

How will candidates or proctors join?

As soon as the candidate page loads in the browser.
Candidates or proctors need to join the 100ms room.
For Joining the 100ms room required attributes:

userName
authToken

After joining the room, the candidate will be connected to a room.

How to generate authentication tokens?

A request will be sent from the browser to the application server for the authentication token.
Authentication token is a jwt token
To Create authentication token following attributes are required:

app_access_key -> will be fetched from the application credentials.
app_secret -> will be fetched from the application credentials.
user_id -> will be passed on the api request.
role -> will be passed on the api  request
room_id -> will re-use some old room_id or create new one.

How to generate a room_id for auth token?

For creating new room, we need to make api request to the 100ms server with attributes:
Management Token -> Is a jwt token created by the application.

Template Id -> For now from application credentials or can be created using the api request to 100ms.
S3 bucket -> from application credentials
Bucket location -> from application credentials
Folder prefix -> can be same as event_id
Credentials s3 -> from application credentials

How will management token be generated?

Management token is a jwt token.
Management token attributes:

app_access_key
app_secret

When do we need to generate an authentication token?

First time Page Load -> First time when the candidate or proctor loads the browser then the authentication token will be fetched from server.
Page Reload -> If candidate reload the page then
Authentication token will be fetched from the local storage on the basis of event id.
If the fetched authentication token is expired then the authentication token will be again fetched from the server.

Algorithm for creating the room?

When this algorithm will be triggered: Whenever the user request a authentication token.

Creating Room depends on -> the no of candidates, no of proctors

Room creation algorithm:

#44 closes this one


Drastically Improve Performance

Use multiple threads to process faster.

Do you have any benchmarks to actually show the performance of this versus the single-threaded version?

The .ToList() calls were actually so the library wouldn't try to enumerate multiple times when it isn't a simple collection.  Like for example, if this was an IQueryable that was being passed in from a database query.  The suggestion was made from ReSharper and I thought it was a good one.
I can add some performance benchmarks to show the differences with the multi-threaded changes.

Yeah, I'd be interested to see how much of a boost it gets with a big data set. Would be cool to see if it's a big improvement! :smile:

Some benchmarks using code from https://gist.github.com/issafram/b4bc98de575235456786
With the current processing logic in production (<IP_ADDRESS>), we see results like these:
Time for 1000 rows on execution 1: 00:00:00.1144958
Time for 1000 rows on execution 2: 00:00:00.0402236
Time for 1000 rows on execution 3: 00:00:00.0342082
Time for 1000 rows on execution 4: 00:00:00.0391841
Time for 1000 rows on execution 5: 00:00:00.0421885
Average time for 1000 rows with 5 executions: 00:00:00.0540600
Time for 10000 rows on execution 1: 00:00:00.6753164
Time for 10000 rows on execution 2: 00:00:00.6652991
Time for 10000 rows on execution 3: 00:00:00.6625778
Time for 10000 rows on execution 4: 00:00:00.6550143
Time for 10000 rows on execution 5: 00:00:00.6464313
Average time for 10000 rows with 5 executions: 00:00:00.6609278
Time for 100000 rows on execution 1: 00:00:32.8842859
Time for 100000 rows on execution 2: 00:00:32.5784661
Time for 100000 rows on execution 3: 00:00:32.5285126
Time for 100000 rows on execution 4: 00:00:32.5694837
Time for 100000 rows on execution 5: 00:00:32.4996665
Average time for 100000 rows with 5 executions: 00:00:32.6120830
With the new processing logic contained in this PR, we see results like the following:
Time for 1000 rows on execution 1: 00:00:00.0905472
Time for 1000 rows on execution 2: 00:00:00.0237432
Time for 1000 rows on execution 3: 00:00:00.0170057
Time for 1000 rows on execution 4: 00:00:00.0219092
Time for 1000 rows on execution 5: 00:00:00.0220426
Average time for 1000 rows with 5 executions: 00:00:00.0350496
Time for 10000 rows on execution 1: 00:00:00.2325847
Time for 10000 rows on execution 2: 00:00:00.2193486
Time for 10000 rows on execution 3: 00:00:00.2311276
Time for 10000 rows on execution 4: 00:00:00.2297525
Time for 10000 rows on execution 5: 00:00:00.2263789
Average time for 10000 rows with 5 executions: 00:00:00.2278385
Time for 100000 rows on execution 1: 00:00:02.2678210
Time for 100000 rows on execution 2: 00:00:02.3526032
Time for 100000 rows on execution 3: 00:00:02.2568745
Time for 100000 rows on execution 4: 00:00:02.2974694
Time for 100000 rows on execution 5: 00:00:02.2818754
Average time for 100000 rows with 5 executions: 00:00:02.2913287
Time for 500000 rows on execution 1: 00:00:11.6423330
Time for 500000 rows on execution 2: 00:00:11.6322395
Time for 500000 rows on execution 3: 00:00:11.7896660
Time for 500000 rows on execution 4: 00:00:12.7939964
Time for 500000 rows on execution 5: 00:00:12.2637361
Average time for 500000 rows with 5 executions: 00:00:12.0243942
Time for 1000000 rows on execution 1: 00:00:25.1888954
Time for 1000000 rows on execution 2: 00:00:25.7263118
Time for 1000000 rows on execution 3: 00:00:25.7460554
Time for 1000000 rows on execution 4: 00:00:27.1094301
Time for 1000000 rows on execution 5: 00:00:25.3239448
Average time for 1000000 rows with 5 executions: 00:00:25.8189275
So basically,  this change can process 1 million rows faster than the current logic can process even one hundred thousand rows.


Introduce non-generic type descriptor method descriptor.Type(System.Type).

#1058
For dynamic schema creating it would be useful to have a new Type description method that can be used to dynamically set types.
We need to write some validation logic that ensures the type context is always correct (input vs output).
Places where we have a type context:

Object Fields
Object Field Arguments
Interface Fields
Interface Field Arguments
Input Fields
Directive Arguments

@michaelstaib I've created a PR for this enhancement. Is it ok like this?

I will have a look at it later or in the morning.

@michaelstaib did you already manage to have a look? :)

https://github.com/ChilliCream/hotchocolate/releases/tag/10.2.0-preview.4


feat: everything looks green color + noremove

Do what we do for the other "Everything Looks" effects but for Green.

The design goals that were articulated by Hola (and some others) decades ago have lost relevance so I am also fine with waiting for complaints but figured it was worth noting.


Update MeleeCombatFeats.cs

Check the battle variable to make sure the ref exists; handles a bug where using a weapon outside of combat causes a null deref.
I don't just early return because this will allow blademaster rogues to apply the feat on a back stab; the validator should still pass and battle is only used in the early exit for the special case -- I'm not familiar enough with the codebase to understand precisely what that case is handling.

correct. thanks for the fix.


cgltf_free uses file release callback for base64 buffers

cgltf_load_buffers loads base64-encoded buffers with the memory.alloc callback, but cgltf_free frees all buffers with file.release. This is incorrect for cases where memory.free actually frees memory but file.read doesn't (e.g. using static embedded files), leading to a memory leak.

I've added a change in PR #160 that allows the library to track where the buffer data comes from. Does that help in your case?

Yep, that fixes it. Appreciate the timely fix!


Stereoscopic side-by-side plots?

Again, awesome project!! Any plans to add (or call for) stereoscopic side-by-side plots?

Thanks, try clicking the eye icon in the toolbar, Google cardboard
recommended :)
(from mobile phone)
On 15 Feb 2018 18:21, "deeplook"<EMAIL_ADDRESS>wrote:

Again, awesome project!! Any plans to add (or call for) stereoscopic
side-by-side plots?
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Hell, yeah, it works! Even without a cardboard! I'm intrigued! 🤓

👍

Have played a bit more with it, and wonder if the spacing between the left and right sides (and any horizontal centering) can be controlled? I see quite a small distance between left/right image resulting in a significant overlap when trying to zoom and find the sweet spot for the effect to occur.

yes, see https://github.com/maartenbreddels/ipyvolume/issues/24


jQuery does not work at all

i have this code
// Main javascript entry point
// Should handle bootstrapping/starting application
'use strict';
import $ from 'jquery';
$(() => {
let licenses = $('.license-item');
licenses.click(() => {
$(this).hide();
});
});
I have tried with many other functions such as .css and .animate, they do not work either.

Hey @MaximilianLloyd,
I can't seem to replicate the issue you are having, can you post the contents of your .yo-rc.json file (it's a hidden file found in the root folder of your project). This will help me diagnose the issue quicker.
In the meantime, sometimes deleting the node_modules folder and then re-running npm install in the root folder of your project can fix some issues. Feel free to try that out.

I am having the same issue, except with ES5.
I don't appear to be able to get Jquery to work at all, I am deleting the node_modules and reinstalling them as I am writing this, but if I can shed some light on this issue I will do my best to help with error logs etc.

{
"generator-yeogurt": {
"config": {
"projectName": "GSK",
"htmlOption": "nunjucks",
"jsPreprocessor": "none",
"cssOption": "sass",
"sassSyntax": "scss",
"testFramework": "none"
},
"version": "1.5.3"
}
}
This is the contents of my yo-rc file.


Disable automatic http to https transformation

Chrome 130 automatically converts http to https even if the target URL is http. We disable this behavior because some target sites simply don't have https.

Relevant: https://github.com/puppeteer/puppeteer/issues/10791


SQLite alternative?

SQLite is frequently used instead of MySQL for unit testing.
But some functions differ.
Would you be interested by Pull Requests for SQLite alternatives?
This is a quite easy implement, for example with YEAR:
public function getSql(SqlWalker $sqlWalker)
{
    if ($sqlWalker->getConnection()->getDriver() instanceof AbstractSQLiteDriver) {
        return "DATE('%Y', {$this->dateExpression->dispatch($sqlWalker)})";
    }

    return 'YEAR('.$this->dateExpression->dispatch($sqlWalker).')';
}

What do you think?

Yes!!!! If the result of the different function are equal, it's OK for me

@luxifer I think the tests should be rethink in this case, to test the result of a query on real databases, right?

I don't think it's useful to test that as it will introduce a lot of overhead in the test suite. As long as the MySQL and SQlite doc specify the same value for the return, it's OK for me


feat: add batch remove optimization script (optional)

Now that there is a feature for additional scripts, here is a script I have been using for a long time.
Problem: When batch removing many rows via Editor, and the rows contain large amounts of data, the remove requests become slow and sometimes even fail due to server limits.
That's because Datatables adds all the column data to the remove request, which is unnecessary in most of the cases. This script modifies the data before it's sent to the server and removes all data from it except the DT_RowId, which is enough for the removal. This results in a more stable and efficient batch removal.
Usage:
/**
 * Optional method if you want to use the html builder.
 */
public function html(): HtmlBuilder
{
	return $this->builder()
		[...]
		->addScript('datatables::functions.batch_remove');
}

Great idea, love it!
Had the same struggle and I think what I did was to use something like "submit only changed" option but the request is still big, especially for very large rows.

Released on v10.11.0 🚀 Thanks!
Feel free to submit a PR if you can for docs 🍻 :)


Wait container stuck in a loop while main container finished successfully

Summary
Wait container is occasionally stuck, workflow keeps running until it times out, while the main pod has finished successfully.
wait container log:
time="2021-06-09T18:01:47.217Z" level=info msg="docker ps --all --no-trunc --format={{.Status}}|{{.Label \"io.kubernetes.container.name\"}}|{{.ID}}|{{.CreatedAt}} --filter=label=io.kubernetes.pod.namespace=workflows --filter=label=io.kubernetes.pod.name=workflow-analytics-pipeline-cron-1623258000-2189159064"
time="2021-06-09T18:01:47.256Z" level=info msg="ignoring container \"main\" created at 2021-06-09 17:00:04 +0000 UTC, too long before process started"
time="2021-06-09T18:01:47.257Z" level=info msg="ignoring container \"wait\" created at 2021-06-09 17:00:03 +0000 UTC, too long before process started"
time="2021-06-09T18:01:48.257Z" level=info msg="docker ps --all --no-trunc --format={{.Status}}|{{.Label \"io.kubernetes.container.name\"}}|{{.ID}}|{{.CreatedAt}} --filter=label=io.kubernetes.pod.namespace=workflows --filter=label=io.kubernetes.pod.name=workflow-analytics-pipeline-cron-1623258000-2189159064"
time="2021-06-09T18:01:48.307Z" level=info msg="ignoring container \"main\" created at 2021-06-09 17:00:04 +0000 UTC, too long before process started"
time="2021-06-09T18:01:48.307Z" level=info msg="ignoring container \"wait\" created at 2021-06-09 17:00:03 +0000 UTC, too long before process started"

pod is in Completed status, main container is in terminated - Completed (exit code: 0) status, wait container is in running, ready status. And the workflow (it's a multi-step DAG workflow) hangs on running (eventually terminating after exceeding active deadline).
The main container is a very simple bash step of recording timestamp (sh -c 'date +%s > /tmp/timestamp.txt) that takes perhaps seconds to complete.
Diagnostics
Running self-managed Kubernetes on AWS.
Argo version 3.1.0-rc12
Docker executer
We've had this issue from time to time, we can't pinpoint the version in which we started seeing it.
Examining controller logs with the wf name in them:
time="2021-06-09T17:00:00.066Z" level=info msg="Processing workflow" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:00.105Z" level=info msg="Updated phase -> Running" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:00.108Z" level=info msg="Retry nodeworkflow-analytics-pipeline-cron-1623258000 initialized Running" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:00.109Z" level=info msg="All of nodeworkflow-analytics-pipeline-cron-1623258000(0).generate-timestamp dependencies [] completed" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:00.109Z" level=info msg="DAG node workflow-analytics-pipeline-cron-1623258000-1105574991 initialized Running" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:00.110Z" level=info msg="Pod node workflow-analytics-pipeline-cron-1623258000-2189159064 initialized Pending" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:00.110Z" level=info msg="Retry node workflow-analytics-pipeline-cron-1623258000-2617208257 initialized Running" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:00.134Z" level=info msg="Created pod: workflow-analytics-pipeline-cron-1623258000(0).generate-timestamp(0) (workflow-analytics-pipeline-cron-1623258000-2189159064)" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:00.157Z" level=info msg="Workflow update successful" namespace=workflows phase=Running resourceVersion=165964949 workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:10.068Z" level=info msg="Updating node workflow-analytics-pipeline-cron-1623258000-2189159064 message: ContainerCreating" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:10.084Z" level=info msg="Workflow update successful" namespace=workflows phase=Running resourceVersion=165965126 workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:20.086Z" level=info msg="Processing workflow" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:32.164Z" level=info msg="Processing workflow" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:32.169Z" level=info msg="Updating node workflow-analytics-pipeline-cron-1623258000-2189159064 status Pending -> Running" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:32.416Z" level=info msg="Workflow update successful" namespace=workflows phase=Running resourceVersion=165965421 workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:00:42.418Z" level=info msg="Processing workflow" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:20:42.420Z" level=info msg="Processing workflow" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T17:40:42.421Z" level=info msg="Processing workflow" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T18:00:00.027Z" level=info msg="stopping 'workflow-analytics-pipeline-cron-1623258000'" namespace=workflows workflow=workflow-analytics-pipeline-cron
time="2021-06-09T18:00:10.049Z" level=info msg="Processing workflow" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000
time="2021-06-09T18:00:10.055Z" level=info msg="Applying shutdown deadline for pod workflow-analytics-pipeline-cron-1623258000-2189159064" namespace=workflows workflow=workflow-analytics-pipeline-cron-1623258000

Message from the maintainers:
Impacted by this bug? Give it a 👍. We prioritise the issues with the most 👍.

Excellent. Thank you. Can I please ask you to test the argoexec:dev-docker image? I think this should fix your issue.

what do you suggest I test for? We weren't able to reproduce this every time, it just happens sporadically.

can you soak it and see?

This issue is still happening in v3.1.0-rc14
Main container status is terminated - Completed (exit code: 0), Wait container is still in running, ready Pod status is Completed, but workflow still running.
wait pod stuck in loop:
time="2021-06-15T08:08:21.528Z" level=info msg="docker ps --all --no-trunc --format={{.Status}}|{{.Label \"io.kubernetes.container.name\"}}|{{.ID}}|{{.CreatedAt}} --filter=label=io.kubernetes.pod.namespace=workflows --filter=label=io.kubernetes.pod.name=workflow-analytics-pipeline-cron-1623740400-3832141026"
time="2021-06-15T08:08:21.570Z" level=info msg="ignoring container \"main\" created at 2021-06-15 07:00:08 +0000 UTC, too long before process started"
time="2021-06-15T08:08:21.570Z" level=info msg="ignoring container \"wait\" created at 2021-06-15 07:00:04 +0000 UTC, too long before process started"

Running the following command manually inside the pod:
docker ps --all --no-trunc --format='{{.Status}}|{{.Label "io.kubernetes.container.name"}}|{{.ID}}|{{.CreatedAt}}' --filter=label=io.kubernetes.pod.namespace=workflows --filter=label=io.kubernetes.pod.name=workflow-analytics-pipeline-cron-1623740400-3832141026

Exited (0) About an hour ago|main|fd3f4355ca5538e0dbfa449c5f1c6a2d4b9dc913eb76527bdefc25cf7e0cafc2|2021-06-15 07:00:08 +0000 UTC
Up About an hour|wait|e7adf5bf1b185788a8d1418d76a05f841bc720a5ba0ffdd2a4001c743941e15a|2021-06-15 07:00:04 +0000 UTC
Up About an hour|POD|d64fc515554fa0cbbc10e31a015f18c6d5983506052366c930f56783cae300c7|2021-06-15 07:00:00 +0000 UTC

This was not fixed.

@avifried1 can you please attach the full logs? I don't have quite enough logs to diagnose.

Status:       Running
IP:           <IP_ADDRESS>
IPs:
IP:           <IP_ADDRESS>
Controlled By:  Workflow/hello-world-xr5lw
Containers:
wait:
Container ID:  containerd://707783fb47ba124b65e408a9e263c727f9518ed6d90cf9863ad31ae943d166c8
Image:         argoproj/argoexec:v3.0.3
Image ID:      docker.io/argoproj/argoexec@sha256:cf79ea62b8c9bf23bc5f5fd4dd1027d89c69353a83f62dd9d72d3e06f2e4c7a8
Port:
Host Port:
Command:
argoexec
wait
--loglevel
info
State:          Running
Started:      Sat, 03 Jul 2021 09:14:10 +0800
Ready:          True
Restart Count:  0
Environment:
ARGO_POD_NAME:        hello-world-xr5lw (v1:metadata.name)
GODEBUG:              x509ignoreCN=0
ARGO_CONTAINER_NAME:  wait
Mounts:
/argo/podmetadata from podmetadata (rw)
/argo/secret/my-minio-cred from my-minio-cred (ro)
/var/run/docker.sock from docker-sock (ro)
/var/run/secrets/kubernetes.io/serviceaccount from kube-api-access-jfqfk (ro)
main:
Container ID:  containerd://73d5862ea4fb2e605798c2d1cde2ec4af74876b720bfd09cc16744bfafc8ac99
Image:         docker/whalesay:latest
Image ID:      sha256:c717279bbba020bf95ac72cf47b2c8abb3a383ad4b6996c1a7a9f2a7aaa480ad
Port:
Host Port:
Command:
cowsay
Args:
hello world
State:          Terminated
Reason:       Completed
Exit Code:    0
Started:      Sat, 03 Jul 2021 09:14:15 +0800
Finished:     Sat, 03 Jul 2021 09:14:15 +0800
Ready:          False
Restart Count:  0
Environment:
ARGO_CONTAINER_NAME:  main
Mounts:
/var/run/secrets/kubernetes.io/serviceaccount from kube-api-access-jfqfk (ro)
Conditions:
Type              Status
Initialized       True
Ready             False
ContainersReady   False
PodScheduled      True
Volumes:
podmetadata:
Type:  DownwardAPI (a volume populated by information about the pod)
Items:
metadata.annotations -> annotations
docker-sock:
Type:          HostPath (bare host directory volume)
Path:          /var/run/docker.sock
HostPathType:  Socket
my-minio-cred:
Type:        Secret (a volume populated by a Secret)
SecretName:  my-minio-cred
Optional:    false
kube-api-access-jfqfk:
Type:                    Projected (a volume that contains injected data from multiple sources)
TokenExpirationSeconds:  3607
ConfigMapName:           kube-root-ca.crt
ConfigMapOptional:
DownwardAPI:             true
QoS Class:                   BestEffort
Node-Selectors:
Tolerations:                 node.kubernetes.io/not-ready:NoExecute op=Exists for 300s
node.kubernetes.io/unreachable:NoExecute op=Exists for 300s
Events:
Type    Reason     Age   From               Message

Normal  Scheduled  14m   default-scheduler  Successfully assigned argo/hello-world-xr5lw to <IP_ADDRESS>
Normal  Pulled     14m   kubelet            Container image "argoproj/argoexec:v3.0.3" already present on machine
Normal  Created    14m   kubelet            Created container wait
Normal  Started    14m   kubelet            Started container wait
Normal  Pulling    14m   kubelet            Pulling image "docker/whalesay:latest"
Normal  Pulled     14m   kubelet            Successfully pulled image "docker/whalesay:latest" in 5.1757762s
Normal  Created    14m   kubelet            Created container main
Normal  Started    14m   kubelet            Started container main

wait container logs are basically an endless loop of:
time="2021-07-01T23:00:04.335Z" level=info msg="docker ps --all --no-trunc --format={{.Status}}|{{.Label \"io.kubernetes.container.name\"}}|{{.ID}}|{{.CreatedAt}} --filter=label=io.kubernetes.pod.namespace=workflows --filter=label=io.kubernetes.pod.name=workflow-analytics-pipeline-cron-1625173200-1458802104"
time="2021-07-01T23:00:04.379Z" level=info msg="ignoring container \"main\" created at 2021-07-01 21:01:02 +0000 UTC, too long before process started"
time="2021-07-01T23:00:04.379Z" level=info msg="ignoring container \"wait\" created at 2021-07-01 21:00:56 +0000 UTC, too long before process started"
time="2021-07-01T23:00:04.379Z" level=info msg="ignoring container \"init\" created at 2021-07-01 21:00:37 +0000 UTC, too long before process started"

Had the same issue as others. main container finishes successfully. wait container keeps looping with docker ps...
Did not see this issue on local minikube cluster, but ran into it on digitalocean cluster.
For now, I've switched the executor to k8sapi and I'm not seeing any issues.

@raviatmaryh thank you ,the issue has been solve.

not sure why this was closed, the issue hasn't been solved - it has been circumvented by using k8sapin executor. Using the default Docker executor still has this issue.

The Docker executor is being sunset. You should switch to using either PNS or Emissary:
https://blog.argoproj.io/sunsetting-docker-executor-support-in-argo-workflows-77d352d601c?source=collection_home---------3-------------------------------

I think this has been fixed.


ci: Update action to 'released' type

https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#release

Seems the released type is what we want --
Note: The prereleased type will not trigger for pre-releases published from draft releases, but the published type will trigger. If you want a workflow to run when stable and pre-releases publish, subscribe to published instead of released and prereleased.


Chart.js doesn't work with the latest version

Versions
dependencies :
"@nuxt/http": "0.6.4",
"chart.js": "3.7.1",
"nuxt": "2.15.8",
"reqlim": "^0.0.0",
"vue-chartjs": "3.5.1"
Reproduction
Just try to render a chart with chart.js : the following error appears :
TypeError: chart_js__WEBPACK_IMPORTED_MODULE_0__.default is not a constructor
./node_modules/vue-chartjs/es/BaseCharts.js 62:32-37 "export 'default' (imported as 'Chart') was not found in 'chart.js'
Here is a sandbox to demonstrate the issue :
not working codesandbox
It's working with the chart.js version 2.9.4, you can change it in codesandbox to see the expected result
working codesandbox
What is Expected?
The chart should appear
What is actually happening?
The chart doesn't appear
Thank you,
Florent

This doesn't seem like a Nuxt issue.


DATABASE won't load

anytime I go to select a database it just sits there and I'm unable to select the database for my lab.
Version: 1.94.0
Commit: d78a74bcdfad14d5d3b1b782f87255d802b57511
User Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/<IP_ADDRESS> Safari/537.36 Edg/<IP_ADDRESS>
Embedder: codespaces

/question please use your course support channel.


Create Arrow schemas for each mmsdm struct/table

this is now done in https://github.com/eigenmo-de/mmsdm-rs/tree/sql-fixes for python and rust


[6.0] [PackageCMO] Override flags that prevent inlining with diagnostics.

Explanation: Override flags that prevent inlining with diagnostics.
Scope: Affected only if -experimental-allow-non-resilient-access is passed.
Original PR: https://github.com/apple/swift/pull/73717
Risk: Low. Changes are behind a flag and only affects builds that use the flag.
Testing: Added new cases to tests.
Issue: rdar://128413200&128647016
Reviewer: @tshortli

@swift-ci test

Included in https://github.com/apple/swift/pull/73993


Official Docker image for production needed

Describe the feature you'd like
Please provide official Docker image for production use. thanks.

Hi @krswin,
Can you describe why this is needed?
Is there something lacking in the linuxserver.io bookstack container?

using the linuxserver.io image in production for around 100 users, everything runs fine.
You can always modify the docker-compose.yaml for specific configurations.

Hi @krswin,
Can you describe why this is needed?
Is there something lacking in the linuxserver.io bookstack container?

Yes in linuxserver.io External MySql server with port other then 3306(default mysql port) not working. DB_PORT is not mapping to the app.

using the linuxserver.io image in production for around 100 users, everything runs fine.
You can always modify the docker-compose.yaml for specific configurations.

@Dayflare
Thanks for reply. Can you please also mention how do you connect to MySql server? Is it running on some IP address with random port(other then 3306)?
Actually problem is this that port other then 3306 with linuxserver.io image not working I was checking for a long time.
If you have some solution please share. thanks

using the linuxserver.io image in production for around 100 users, everything runs fine.
You can always modify the docker-compose.yaml for specific configurations.

@Dayflare
Thanks for reply. Can you please also mention how do you connect to MySql server? Is it running on some IP address with random port(other then 3306)?
Actually problem is this that port other then 3306 with linuxserver.io image not working I was checking for a long time.
If you have some solution please share. thanks

i'm using a mariadb container with default 3306 port as database.
Both containers need to be in the same docker network to find each other.

I'll now close this off, since the linuxserver.io team have responded to the main cause for this request, and since propose reasoning does not justify the effort in maintaining an official docker image.


Use all url templates provided by terrain config file

Ready to review.

Thanks for the contribution, @oterral.
I don't believe we have a Contributor's License Agreement (CLA) for you or your organization.  Can you send one in?  See https://github.com/AnalyticalGraphicsInc/cesium/blob/master/CONTRIBUTING.md
Also, check out the pull request guidelines in that doc.  For example, I imagine we will want to include a unit test and update to CHANGES.md for this change.

Yep I can try.

Great, thanks @oterral.  If there's any questions about the CLA, feel free to contact me directly.

We have a CLA now.
@kring can you review this?

And a test :)

Thanks @oterral.
@kring this looks good to me.  Can you confirm and merge?

@kring  I've fixed the test.

Thanks @oterral!

Thx for the review!!!


Feature/allow to group projects dirs issue #89

Include config directories support
mentioned in the issue https://github.com/ivaaaan/smug/issues/89

Thanks for your contribution!

Thanks for your contribution!

Thanks, would it be possible to create a new tag for a release ?


Ignore vim swap files

As the title says.
Submitted with employer's permission.

…and thanks again! Keep up the good work.


Elaborate on background around group signatures

Because the concept of a "group signature" is a lesser known term in the wider community that uses digital signature technology it would provide a good opportunity for education around some of the novel features of these types of cryptographic schemes provide if the spec included some of this background

@mikelodder7

There is now sufficient elaboration around the schemes unique properties in the introduction therefore closing this issue.


Disable PQDM in earthaccess.open

Please add an optional argument to earthaccess.open to disable PQDM progress bars. The progress bars clog up my Jupyter notebook output very badly.

@simonhatcher I agree it's a good idea to provide this control.
For now, since pqdm wraps tqdm, I believe you can set this environment variable to disable the progress bars. You can do this in a shell beforehand:
export TQDM_DISABLE=1

Or in Python ahead of any TQDM imports:
import os

os.environ["TQDM_DISABLE"] = "1"

The environment variable requires tqdm v4.66.0+, but you can also hack it for older versions ahead of any TQDM imports like:
from tqdm import tqdm
from functools import partialmethod

tqdm.__init__ = partialmethod(tqdm.__init__, disable=True)

@jhkennedy Thank you! That does work, but the one challenge is that I'm using TQDM elsewhere and I don't want to globally disable it in the long run.

That does work, but the one challenge is that I'm using TQDM elsewhere and I don't want to globally disable it in the long run.

yes, definitely exactly why we should provide a way to disable it for Earthaccess.
:thinking: I think you could write a context manager that would disable it temporarily... but that's getting to be a lot. Something like (I'm sure there are much cleaner ways to do this):
from tqdm import tqdm
from functools import partialmethod

class DisableTqdm(object):
    def __init__(self):
        self._tqdm_init = tqdm.__init__

    def __enter__(self):
        tqdm.__init__ = partialmethod(tqdm.__init__, disable=True)

    def __exit__(self, type, value, traceback):
        tqdm.__init__ = self._tqdm_init

with DisableTqdm():
    # Do stuff
    ...


Add CatólicaSC (Brasil)

Website URL:
https://www.catolicasc.org.br/
Software engineering course (4 years)
https://www.catolicasc.org.br/cursos/graduacao/engenharia-de-software/?unidade=joinville
Student page with the domain
https://prnt.sc/17icred

[
file.zip
](url)

ssts.txt
https://www.sst.edu.sg/

ssts.txt
https://www.sst.edu.sg/

pls add this

Waiting for this domain....

The thing is that I don't know how to add

@VitorPetri I am sorry, I cannot add this domain. The reasons are:

You seem to graduate from the university already. If you did not, please apply with official document at https://www.jetbrains.com/shop/eform/students (OFFICIAL DOCUMENT tab).
The official university website does not mention this domain at all.
I am not sure if the university withdraw the access to the email domain when the students graduate. If it does not, we'd refrain from adding the domain to this repository.

Thank you for your understanding!

@Asmaagamall @DakshRocks21 @Douglas-Strey Please send an email to<EMAIL_ADDRESS>about the domain that you wish to add. You can also familiarize with this repository rules located at the bottom of this page and submit a new separate request with correct information. Thank you for the understanding!


[backport] Dynamically import matplotlib.pyplot in PlotReport

Backport of #2740

Jensen, test this please

LGTM


Remove use of always_comb that Icarus does not support

Attempt to close #2253. Still a WiP.

@rachitnigam, I just tried this change on the unsigned-dot-product example in interp/, and It seems to have simulated fine?

Was it previously erroring out?

I just checked on my checkout of main (which is on commit f4e80ec0). It looks like Icarus executes correctly and produces a waveform. So no, it looks like Icarus was not erroring out. I'm just worried about the warning message Icarus prints.
$ ./target/debug/fud2 ./interp/tests/complex/unsigned-dot-product.futil --from calyx -o test.vcd --through icarus -s sim.data=./interp/tests/complex/unsigned-dot-product.futil.data
[WARN  calyx_frontend::attribute] The attribute @static is deprecated and will be ignored by the compiler.
[WARN  calyx_frontend::attribute] The attribute @static is deprecated and will be ignored by the compiler.
[WARN  calyx_frontend::attribute] The attribute @static is deprecated and will be ignored by the compiler.
[WARN  calyx_frontend::attribute] The attribute @static is deprecated and will be ignored by the compiler.
verilog-noverify.sv:149: sorry: constant selects in always_* processes are not currently supported (all bits will be included).

[nix-shell:~/Repos/calyx] 09:57:03 $ ll test.vcd
-rw-r--r-- 1 karljoad users 46415 Sep 30 09:57 test.vcd

Okay, then let's trigger the remaining tests and see if there are any failures. You need to mark the PR ready for review when you're ready.

@ekiwi wanted another pair of eyes on this in case you think there could be any problems changing the always_comb to always @*. I'm going to fix the failing tests and get this merge ready. If you think it's good, let's merge.

Closing in favor of https://github.com/calyxir/calyx/pull/2330.


new sponsors - please push asap

please push asap

Conflict with branch. Moved new sponsors over manually in separate commit


SorbetExtensionConfig uses only workspace configurations

Motivation

Test plan

See included automated tests.

This fix is more correct but requires too much work at the time.


Swift build error: Duplicate interface definition for class GRXWriteable

Error: Duplicate interface definition for class GRXWriteable
Warning: Duplicate protocol definition for GRXWriteable is ignored
Podspec
Pod::Spec.new do |s|
  s.name     = 'octopus'
  s.version  = '0.0.1'
  s.license  = 'New BSD'
  s.authors = { "programmers" => "Manana LLC" }
  s.homepage = "https://github.com/jorgeolivero/manana"
  s.summary = "gRPC Generated Code to Communicate with Octopus Server"
  s.source = { :git => "https://github.com/jorgeolivero/manana.git" }

  s.ios.deployment_target = '7.1'
  s.osx.deployment_target = '10.9'

  # Base directory where the .proto files are
  src = "../../octopus/proto"

  # We'll use protoc with the gRPC plugin
  s.dependency '!ProtoCompiler-gRPCPlugin', '~> 0.14'

  # Pods directory corresponding to this app's Podfile, relative to the location of this podspec
  pods_root = './Pods'

  # Path where Cocoapods downloads protoc and the gRPC plugin
  protoc_dir = "#{pods_root}/!ProtoCompiler"
  protoc = "#{protoc_dir}/protoc"
  plugin = "#{pods_root}/!ProtoCompiler-gRPCPlugin/grpc_objective_c_plugin"

  # Directory where you want the generated files to be placed
  dir = "Pods/" + s.name

  # Run protoc with the Objective-C and gRPC plugins to generate protocol messages and gRPC clients
  s.prepare_command = <<-CMD
    mkdir -p #{dir}
    #{protoc} \
        --plugin=protoc-gen-grpc=#{plugin} \
        --objc_out=#{dir} \
        --grpc_out=#{dir} \
        -I #{src} \
        -I #{protoc_dir} \
        #{src}/*.proto
  CMD

  # The --objc_out plugin generates a pair of .pbobjc.h/.pbobjc.m files for each .proto file.
  s.subspec "Messages" do |ms|
    ms.source_files = "#{dir}*.pbobjc.{h,m}", "#{dir}/**/*.pbobjc.{h,m}"
    ms.header_mappings_dir = dir
    ms.requires_arc = false
    ms.dependency "Protobuf", "~> 3.0.0-beta-2"
  end

  # The --objc_out plugin generates a pair of .pbobjc.h/.pbobjc.m files for each .proto file.
  # The --objc_out plugin generates a pair of .pbobjc.h/.pbobjc.m files for each .proto file.
  s.subspec 'Messages' do |ms|
    ms.source_files = "#{dir}/*.pbobjc.{h,m}"
    ms.header_mappings_dir = dir
    ms.requires_arc = false
    # The generated files depend on the protobuf runtime.
    ms.dependency 'Protobuf'
    # This is needed by all pods that depend on Protobuf:
    ms.pod_target_xcconfig = {
      'GCC_PREPROCESSOR_DEFINITIONS' => '$(inherited) GPB_USE_PROTOBUF_FRAMEWORK_IMPORTS=1',
    }
  end

  s.subspec 'Services' do |ss|
    ss.source_files = "#{dir}/*.pbrpc.{h,m}"
    ss.header_mappings_dir = dir
    ss.requires_arc = true
    # The generated files depend on the gRPC runtime, and on the files generated by `--objc_out`.
    ss.dependency 'gRPC-ProtoRPC'
    ss.dependency "#{s.name}/Messages"
  end

end

Podfile
source 'https://github.com/CocoaPods/Specs.git'
platform :ios, '8.0'

install! 'cocoapods', :deterministic_uuids => false

target 'manana' do
  pod 'BoringSSL', :podspec => "https://raw.githubusercontent.com/grpc/grpc/release-0_14/src/objective-c/BoringSSL.podspec"
  pod 'octopus', :path => '.'
end

Bridging Header File:
//
//  octopus-Bridging-Header.h
//  manana
//
//  Created by Jorge Olivero on 4/17/16.
//  Copyright © 2016 JOS. All rights reserved.
//

#ifndef octopus_Bridging_Header_h
#define octopus_Bridging_Header_h

#import <gRPC/GRPCCall.h>
#import <gRPC-ProtoRPC/ProtoMethod.h>
#import <gRPC-RxLibrary/GRXWriteable.h>

#import <octopus/Octopus.pbobjc.h>
#import <octopus/Octopus.pbrpc.h>

#endif

Image of Build Failure:

Image of Pods Directory:

I've grep-ed the entire project for:
@interface GRXWriteable
@protocol GRXWriteable
and only found the single definition in Pods/gRPC-RxLibrary/GRXWriteable.h - is there somewhere else where a duplicate definition could be lurking?
I've also tried cleaning the build folder with CMD + SHIFT + K and clearing out the folders in $HOME/Library/Developer/Xcode/DerivedData without any luck.
Doesn't seem that others are having this problem, but I've followed the README and the example code for generating the iOS swift client closely. How can I further debug this?
Appreciate the help!

Hi @jorgeolivero .. I'm also getting the same issue in my app ... Have you found any solution or do u get your app working after this issue. Please suggest if found any solution over this issue.
Thanks.


If no eventId given for testing pick up the latest problem via the Zabbix API

Currently for troubleshooting the eventId must be entered in order to allow a new mailGraph cycle to complete.
Code enhancement to pickup a random latest problem via the Zabbix API if eventId is set to zero.

Factored into v2.11


Replacing deprecated React.PropTypes with standalone dependency 'prop-types'

In the next release of React, it's export 'PropTypes' will be deprecated.
PropTypes now has it's own package on npm, called 'prop-types'.

Looks great! @Redmega can you make releases yet?

Don't have a lot of time to devote to this so if you want to take over maintaining this more directly that'd be great! Lemme know if that'd be alright and if you're missing any admin privileges here or on NPM!

Thanks @KyleAMathews
@jeldriks Tomorrow I'll get the chance to work on merging this in and stuff.

Sorry this got lost in the wind, was busy with work. I'll merge this later today!


Pickup Manager doesn't start properly

Description:
Followed the guide [1] and installed the pickup manager successfully. Started the PickupManager application and it shows following page.

Note: I have entered all the information requested in the setup, inluding the Callback URL, but this UI again requested me to enter Callback URL although other entered values were populated properly.
I entered only the Callback URL (running the application as Administrator) and tried to proceed. It showed the same UI, with Callback URL filled.
Only after updating UserInfo, Logout, Callback, PostLogout in above UI, I was directed to below UI.

When clicking the 'LOGIN' in above UI, application was closed after not responding for a while.
When
[1] https://github.com/wso2-extensions/identity-samples-dotnet/releases/tag/v0.9.0
Suggested Labels:
Type/Bug, Severity/Blocker
Affected Product Version:
v0.9.0
OS, DB, other environment details and versions:
OS: Windows 10 Enterprise

I also experienced the same behaviour. When I clicked the Login button the app closed.

(As per the fix: https://github.com/wso2-extensions/identity-sdks-dotnet/pull/2)
Configuring Callback URL as http://localhost:8080/ worked with v0.9.0 release.
Note the trailing backslash.

Updated the release note to,

Enter all fields during the setup
Have trailing backslash for the Callback URLs


Use an interface library to configure common compile options

Currently when we want to set an option across all targets we have to manually call target_compile_options() on each one.  I recently learned a nice technique to make this cleaner.  You define an interface library with the options:
add_library(bigtable_common_options INTERFACE)

such libraries do not create an actual file, but you can add compile options to them, and to anything that links them, e.g.,
target_compile_options(bigtable_common_options PUBLIC -Wall -Werror)

add_executable(foo)
target_link_libraries(foo PRIVATE bigtable_common_options)

Fixed in #283.


push_transaction with type "bytes" fails unless action.data is hex

action.data as object
api error => { message: 'Failed to deserialize data for eosio:buyrambytes',
  file: 'abi_serializer.hpp',
  line_number: 417,
  method: 'extract' } http://<IP_ADDRESS>:8888/v1/chain/push_transaction {"compression":"none","transaction":{"expiration":"2018-06-12T15:43:49","ref_block_num":623,"ref_block_prefix":4050859248,"net_usage_words":0,"max_cpu_usage_ms":0,"delay_sec":0,"context_free_actions":[],"actions":[{"account":"eosio","name":"newaccount","authorization":[{"actor":"eosio","permission":"active"}],"data":{"creator":"eosio","name":"myaccount","owner":{"threshold":1,"keys":[{"key":"EOS6MRyAjQq8ud7hVNYcfnVPJqcVpscN5So8BhtHuGYqET5GDW5CV","weight":1}],"accounts":[],"waits":[]},"active":{"threshold":1,"keys":[{"key":"EOS6MRyAjQq8ud7hVNYcfnVPJqcVpscN5So8BhtHuGYqET5GDW5CV","weight":1}],"accounts":[],"waits":[]}}},{"account":"eosio","name":"buyrambytes","authorization":[{"actor":"eosio","permission":"active"}],"data":{"payer":"eosio","receiver":"myaccount","bytes":8192}},{"account":"eosio","name":"delegatebw","authorization":[{"actor":"eosio","permission":"active"}],"data":{"from":"eosio","receiver":"myaccount","stake_net_quantity":"10.0000 SYS","stake_cpu_quantity":"10.0000 SYS","transfer":0}}],"transaction_extensions":[]},"signatures":["SIG_K1_Jy2oHSmkKyn7bXWzgGVjBJhSfYh8uJ1yvsfWj8muXLiWUup2C1dYUs3pzDvcESmicyetsDVaFNC64B9kyUFgm2R917kXgh"]}

action.data as hex
api > http://<IP_ADDRESS>:8888/v1/chain/push_transaction {"compression":"none","transaction":{"expiration":"2018-06-12T15:47:16","ref_block_num":25,"ref_block_prefix":1888660601,"net_usage_words":0,"max_cpu_usage_ms":0,"delay_sec":0,"context_free_actions":[],"actions":[{"account":"eosio","name":"newaccount","authorization":[{"actor":"eosio","permission":"active"}],"data":"0000000000ea30550000c85353848c9701000000010002c0ded2bc1f1305fb0faac5e6c03ee3a1924234985427b6167ca569d13df435cf0100000001000000010002c0ded2bc1f1305fb0faac5e6c03ee3a1924234985427b6167ca569d13df435cf01000000"},{"account":"eosio","name":"buyrambytes","authorization":[{"actor":"eosio","permission":"active"}],"data":"0000000000ea30550000c85353848c9700200000"},{"account":"eosio","name":"delegatebw","authorization":[{"actor":"eosio","permission":"active"}],"data":"0000000000ea30550000c85353848c97a0860100000000000453595300000000a086010000000000045359530000000000"}],"transaction_extensions":[]},"signatures":["SIG_K1_KVKNDaxxu23CRGsLYCoj4humPrvJMRpN8FdqpMcH9FpoMAoozy7pPynKGD4rjc8nwSKysNNUvQgweP882tMwd9GXouoFyo"]}
api < { transaction_id: '588ac8e814f64ef886d2fe6418c4b4c4a6bbbe7dbc43f0edaa8378a1536d2c25',
  processed:
   { id: '588ac8e814f64ef886d2fe6418c4b4c4a6bbbe7dbc43f0edaa8378a1536d2c25',
     receipt: { status: 'executed', cpu_usage_us: 293, net_usage_words: 42 },
     elapsed: 293,
     net_usage: 336,
     scheduled: false,
     action_traces: [ [Object], [Object], [Object] ],
     except: null } }

@jcalfee Please tell me how you make object to hex?

I just realized something.. I was testing this with eosio.bios deployed (not eosio.system) so this test must be invalid.  The buyrambytes does not exist until the system contract is deployed.  I think I need to add some RAM bits to the market to test this properly .. This is not your bug.
Although it would be better to report something along these lines:
Action eosio:buyrambytes does not exist

Back to your question.  The hex in action.data it is the serialized bytes just like what is stored on the blockchain..  Mostly you can use either JSON or HEX there and the back-end code will convert either to the same binary.  HEX is binary as-is and JSON must have all known FC_REFLECT types.
This is one way to create those bytes:
> require('eosjs)().fc.toBuffer('buyrambytes', {payer: 'eosio',receiver: 'myaccount',bytes: 8192}).toString('hex')
'0000000000ea30550000c85353848c9700200000'

It looks like you can use abi_json_to_bin to do this too.  Here is the API call docs:
"abi_json_to_bin": {
    "brief": "Manually serialize json into binary hex.  The binayargs is usually stored in Action.data.",
    "params": {
      "code": "name",
      "action": "name",
      "args": "bytes"
    },
    "results": {
      "binargs": "bytes"
    }
  }

> Buffer.from('{"payer":"eosio","receiver":"myaccount","bytes":8192}').toString('hex')
'7b227061796572223a22656f73696f222c227265636569766572223a226d796163636f756e74222c226279746573223a383139327d'

$ curl -X POST -d '{"code":"eosio","action":"buyrambytes","args":"7b227061796572223a22656f73696f222c227265636569766572223a226d796163636f756e74222c226279746573223a383139327d"}' http://localhost:8888/v1/chain/abi_json_to_bin
{"binargs":""}

This looks like a cool way to create the HEX data: https://github.com/EOSIO/abieos
I wonder if this will compile to wasm..

I see, thx

this is transaction
transaction =     {         actions =         (                         {                 account = eosio;                 authorization =                 (                                         {                         actor = eosio;                         permission = active;                     }                 );                 data =<PHONE_NUMBER>00263d0000000000a0929b010000000100039c5cfda31d5d4cf4f04225ac7cffccce19216a80dd0d39cf52361a0cc957086a0100000001000000010003f3d3de7d6210d3ae204a276bb9ff9c5154968b3b2073906a7597307419cb5bfb01000000;                 name = newaccount;             }         );         "context_free_actions" =         (         );         "context_free_data" =         (         );         "delay_sec" = 0;         expiration = "2018-06-29T11:26:28";         "max_kcpu_usage" = 0;         "max_net_usage_words" = 0;         "ref_block_num" = 54223;         "ref_block_prefix" =<PHONE_NUMBER>;         signatures =         (         );     };
and this is action.data
 {     action = newaccount;     args =     {         active =         {             accounts =             (             );             keys =             (                                 {                     key = EOS8gcn9TJv8daUqCurjP5QfprFwUoxbL3LoXVLBMJtF2VibaygEY;                     weight = 1;                 }             );             threshold = 1;             waits =             (             );         };         creator = eosio;         name = nide;         owner =         {             accounts =             (             );             keys =             (                                 {                     key = EOS826csYH9LxEt6FwmjaJL71jSioX4zEo5ktbXkXq5wbmqbossxc;                     weight = 1;                 }             );             threshold = 1;             waits =             (             );         };     };     code = eosio; }

probably unrelated

We haven't received any update for this. I think the behaviour described in this ticket is by designed. If you still have the problem and wish to discuss further, please post it in https://eosio.stackexchange.com.


Adding the choice of Pygments style

Hi,
If you're using Terminal256Formatter() instead of TerminalFormatter() in this line with the parameter style instead of bg, and set 'default' as default value in this line and this line we could change the Pygments style with CHEAT_COLORSCHEME.
You can see the different styles here.
It could be useful for everyone if we can adapt the syntax color with our terminal.

Hi, @chietsuki
I just released cheat v3, which re-implements this project from scratch in Go. The feature you requested is now available there, thanks to the wonderful Chroma library. Please upgrade and give it a try. Thanks.


feat: Dynamic target latency

This adds a new feature for adjusting the target latency closer to the live edge when playback is stable and back off away from the live edge when playback rebuffers. It is off by default and will only run a default of 5 times before it will stop trying to adjust the target latency.
Closes https://github.com/shaka-project/shaka-player/issues/6131.

This PR supercedes https://github.com/shaka-project/shaka-player/pull/6193. I marked it as a draft because while the functionality is there and the build passes locally, I hadn't yet gotten a chance to confirm that it's working as intended. It's possible there may be tweaks necessary. I'll get back to it on Thursday.

I'll take a look. At first glance they seemed unrelated, but who knows.

I don't have time to review this before I go on leave.  I trust @avelad, @theodab, and @gkatsev to review and figure out when it's ready.


Soundflower installs in Mojave but then can't find app

HI,
I successfully installed Soundflower on Mojave but then I can't find the application anywhere! I have done a "search this Mac" and all that comes up is the install disk image.

I experienced the same. After running the pkg file, granting the necessary security exceptions, and selecting the default destination directory, the installer reports success. However Soundflower does  not appear in the Applications folder, and not all files were installed.
According to the uninstall script, running the pkg file should have installed the following:
/System/Library/Extensions/Soundflower.kext
/Library/Extensions/Soundflower.kext
/Library/Receipts/Soundflower*
/var/db/receipts/com.cycling74.soundflower.*
/Applications/Soundflower
However after running the pkg file all items marked bold, above, are missing; only the following files were installed:
/Library/Extensions/Soundflower.kext
/var/db/receipts/com.cycling74.soundflower.bom
/var/db/receipts/com.cycling74.soundflower.plist
Thanks.

same problem for me
any solution?

hi, probably it is perfectly normal
https://github.com/mattingalls/Soundflower/releases/tag/2.0b2
can someone confirm that? 2.0b2 ver work without app interface, but only as kernel extension?


Adding basic description to README.md

Adding basic description to README.md
As Lettuce.IO is cool, we wanted to contribute some basic description to it so other users could enjoy this tool!

@oriagranat9 @atlasyonatan

@zigelboim-misha thanks 😎


[FLINK-28574] Bump the JOSDK version to 3.2.1

What is the purpose of the change
Java Operator SDK has released 3.2.1 version. Bump the JOSDK version to 3.2.1.
Brief change log

Bump the Java Operator SDK to 3.2.1

Verifying this change

(Please pick either of the following options)
This change is a trivial rework / code cleanup without any test coverage.
(or)
This change is already covered by existing tests, such as (please describe tests).
(or)
This change added tests and can be verified as follows:
(example:)

Added integration tests for end-to-end deployment with large payloads (100MB)
Extended integration test for recovery after master (JobManager) failure
Manually verified the change by running a 4 node cluster with 2 JobManagers and 4 TaskManagers, a stateful streaming program, and killing one JobManager and two TaskManagers during the execution, verifying that recovery happens correctly.

Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): (yes / no)
The public API, i.e., is any changes to the CustomResourceDescriptors: (yes / no)
Core observer or reconciler logic that is regularly executed: (yes / no)

Documentation

Does this pull request introduce a new feature? (yes / no)
If yes, how is the feature documented? (not applicable / docs / JavaDocs / not documented)

Thanks @SteNicholas, it seems that bumping the fabric8 client has further implications - please double check the test failures:
[INFO] Running org.apache.flink.kubernetes.operator.kubeclient.factory.StandaloneKubernetesJobManagerFactoryTest
Error:  Tests run: 7, Failures: 0, Errors: 7, Skipped: 0, Time elapsed: 0.182 s <<< FAILURE! - in org.apache.flink.kubernetes.operator.kubeclient.factory.StandaloneKubernetesJobManagerFactoryTest
Error:  org.apache.flink.kubernetes.operator.kubeclient.factory.StandaloneKubernetesJobManagerFactoryTest.testDeploymentMetadata  Time elapsed: 0.101 s  <<< ERROR!
java.lang.NoSuchMethodError: 'io.fabric8.kubernetes.api.model.ServicePortFluent io.fabric8.kubernetes.api.model.ServiceSpecFluent$PortsNested.withNewTargetPort(java.lang.Integer)'
	at org.apache.flink.kubernetes.operator.kubeclient.factory.StandaloneKubernetesJobManagerFactoryTest.setup(StandaloneKubernetesJobManagerFactoryTest.java:75)

Error:  org.apache.flink.kubernetes.operator.kubeclient.factory.StandaloneKubernetesJobManagerFactoryTest.testTemplateMetadata  Time elapsed: 0.015 s  <<< ERROR!
java.lang.NoSuchMethodError: 'io.fabric8.kubernetes.api.model.ServicePortFluent io.fabric8.kubernetes.api.model.ServiceSpecFluent$PortsNested.withNewTargetPort(java.lang.Integer)'
	at org.apache.flink.kubernetes.operator.kubeclient.factory.StandaloneKubernetesJobManagerFactoryTest.setup(StandaloneKubernetesJobManagerFactoryTest.java:75)

Error:  org.apache.flink.kubernetes.operator.kubeclient.factory.StandaloneKubernetesJobManagerFactoryTest.testFlinkConfConfigMap  Time elapsed: 0.003 s  <<< ERROR!
java.lang.NoSuchMethodError: 'io.fabric8.kubernetes.api.model.ServicePortFluent io.fabric8.kubernetes.api.model.ServiceSpecFluent$PortsNested.withNewTargetPort(java.lang.Integer)'
	at org.apache.flink.kubernetes.operator.kubeclient.factory.StandaloneKubernetesJobManagerFactoryTest.setup(StandaloneKubernetesJobManagerFactoryTest.java:75)

Thanks @SteNicholas for the contrib! Few thoughts on this change:

Why do we need to bump the fabric8 client? I guess nor Flink neither JOSDK itself has made this step yet.
All .0 upgrades on JOSDK have brought some unexpected surprises so far :/ So, if there's no specific feature we are after from JOSDK I'd put this PR on hold at least till we release 1.2 from the Operator.

@morhidi

Why do we need to bump the fabric8 client? I guess nor Flink neither JOSDK itself has made this step yet.
I follow the bump step of JOSDK and bump the fabric8 client to 6.1.1.

All .0 upgrades on JOSDK have brought some unexpected surprises so far :/ So, if there's no specific feature we are after from JOSDK I'd put this PR on hold at least till we release 1.2 from the Operator.
Holding this PR at least till we release 1.2 makes sense to me.

Hi @SteNicholas
It'd be great if you could try to fix the CI errors, i.e. NoSuchMethod. There is also the KubernetesClientMetrics class which introduces an interceptor to be able to measure the Kubernetes API Server access that might break due to the version bump.
Thanks,
Matyas

@morhidi, I will update this pull request to fix the CI errors today.

@morhidi, @mbalassi, the java-operator-sdk released the 3.2.1 version which reverts the upgrade made in 3.2.0 to Fabric8 Client 6.1. I will bump the version of the  java-operator-sdk to 3.2.1 later. WDYT?

@morhidi, @mbalassi, the java-operator-sdk released the 3.2.1 version which reverts the upgrade made in 3.2.0 to Fabric8 Client 6.1. Hence the version of the Fabric8 Client in v3.2.1 is 5.12.3. I will bump the version of the java-operator-sdk to 3.2.1 later. WDYT?

Somewhat expected :) Makes sense.

@morhidi, the Java Operator SDK releases the 3.2.1 and 4.0.0 version, in which the Fabric Client version is 5.12.3 in v3.2.1 and the version is 6.1.1 in v4.0.0. IMO, Fabric8 Kubernetes Client 6.1.1 is most likely a breaking change, hence we could bump the version to 4.0.0 in Flink K8S operator 1.3 version. WDYT?

@morhidi, the Java Operator SDK releases the 3.2.1 and 4.0.0 version, in which the Fabric Client version is 5.12.3 in v3.2.1 and the version is 6.1.1 in v4.0.0. I have bumped the version of Java Operator SDK to v3.2.1. PTAL.
BTW, Fabric8 Kubernetes Client 6.1.1 is most likely a breaking change, hence we could bump the version to 4.0.0 in Flink K8S operator 1.3 version. WDYT?

Hi @SteNicholas, if we stick with the current fabric8 version I don't see any problems merging this PR with the upcoming FOv1.2 release.


[PLAT-1187] Remove dead v1 code registration.

Purpose
For partial registrations we moved all the functionality of registering a draft to v2, abandoning a lot of v1 tests and views. Also with the removal of the Prereg Challenge options we can remove a lot of dead code.
Changes

removes v1 register route
removes old register with/without review buttons and waffling
removes old v1 tests for that view.

QA Notes
should be no noticeable changes.
Documentation
tech task, no docs.
Side Effects
None that I know of.
Ticket
https://openscience.atlassian.net/browse/PLAT-1187

Merging into feature branch feature/raticate for testing on staging3