Non-ACGTN reference allele

Description of the bug
When running Tomte, it crashes for me at the SPLIT_MULTIALLELICS step due to non-regular base "B" being present.
It seems similar to the error found here: https://github.com/samtools/bcftools/issues/473 It seems to be due to mpileup sometimes generating the B base.
I further checked the reference genome and BAM file for this region. No non ACGTN letters were found there.
Here is the error:
ERROR ~ Error executing process > 'GENOMICMEDICINESWEDEN_TOMTE:TOMTE:CALL_VARIANTS:SPLIT_MULTIALLELICS (<ID>)'

Caused by:
  Process `GENOMICMEDICINESWEDEN_TOMTE:TOMTE:CALL_VARIANTS:SPLIT_MULTIALLELICS (<ID>)` terminated with an error exit status (255)

Command executed:

  bcftools norm \
      --fasta-ref GCA_000001405.15_GRCh38_no_alt_analysis_set_chr_masked.fna \
      --output <ID>_norm.vcf.gz\
      --output-type z --multiallelics -both \
      --threads 16 \
      <ID>.vcf.gz

  cat <<-END_VERSIONS > versions.yml
  "GENOMICMEDICINESWEDEN_TOMTE:TOMTE:CALL_VARIANTS:SPLIT_MULTIALLELICS":
      bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  Non-ACGTN reference allele at chr3:16902879 .. REF_SEQ:'TGTGNG' vs VCF:'TGTGBG'

Work dir:
  <workdir>/tomte/87/994c3113cd903794f7c9f5652d7379

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

Looking at that position in the input VCF, there is indeed a "B" present:
chr3    16902879        .       TGTGBG  TG      38.1334 .       INDEL;IDV=6;IMF=0.0521739;DP=7;VDB=0.400625;SGB=-0.590765;RPBZ=1.17689;MQBZ=0;MQSBZ=0;SCBZ=2.88819;MQ0F=0;AC=2;AN=2;DP4=1,0,2,3;MQ=20   GT:PL   1/1:65,9,0

I will continue investigating, starting with rerunning using the latest version of Tomte (I realized I ran using a version prior to the update of bcftools).
Command used and terminal output
No response
Relevant files
No response
System information
No response

Sorry, this comes originally from our reference. Closing!

Hello,
I have been experiencing a similar issue running the sarek v3.4.2 pipeline, where only some of the VCF ( 2 out of my 3 samples) generated by mpileup show ambiguous bases "R" in chromosome 7 (genome build GRCh38). I have seen this issue once more in a specific region of chromosome 3. I checked the igenomes reference from https://support.illumina.com/sequencing/sequencing_software/igenome.html, and found that the "R" bases are indeed coming from the reference itself. Does your pipeline uses the same reference from the s3 aws bucket (s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes/) ? could this be part of the same issue?
Thanks in advance!

Hello,
I have been experiencing a similar issue running the sarek v3.4.2 pipeline, where only some of the VCF ( 2 out of my 3 samples) generated by mpileup show ambiguous bases "R" in chromosome 7 (genome build GRCh38). I have seen this issue once more in a specific region of chromosome 3. I checked the igenomes reference from https://support.illumina.com/sequencing/sequencing_software/igenome.html, and found that the "R" bases are indeed coming from the reference itself. Does your pipeline uses the same reference from the s3 aws bucket (s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes/) ? could this be part of the same issue?
Thanks in advance!

It looks like it could be the same or a similar issue. I don't think we have downloaded our reference genome from that exact location, but it might very well be same / similar anyway.
I did a counting of all letters in our reference genome and found that there is a bunch of non ACGTNs:
defaultdict(<class 'int'>, {'N': 166087682, 'T': 868645206, 'A': 866149498, 'C': 598435124, 'G': 600604937, 'M': 8, 'R': 26, 'Y': 33, 'W': 13, 'K': 8, 'B': 2, 'S': 4})

Currently I am trying out an updated version where I have replaced non ACGTs with N:
sed '/^[^>]/ s/[^ACGTNacgtn]/N/g' orig.fna > updated_only_acgtn.fna

Thank you for your answer, this is very helpful!


Identify objects using custom id

Describe the bug
Identify objects using custom id like data-test-id
To Reproduce
We are able to identify objects in the following manner, using id, class and href
{class:"btn btn--big btn-primary continue-checkout mobile-hidden"}
{id:"form--checkout_signin_new_user--field--NEW_USER_EMAIL_ADDRESS"}
{href:"?edit_shipping_panel=1"}
We are not able to identify using custom id like data-test-id
{data-test-id:"cart_subtotal"}
For ease of automation this type of id is made available is most places in the application
We are not able to leverage that.
Is there any way to leverage id's like that

I am able to successfully locate an element with data attribute,

await goto("https://www.w3schools.com/tags/tryit.asp?filename=tryhtml5_global_data");
await highlight(listItem({"data-animal-type":"fish"}));

Can you please provide a sample where this doesn't work ?

Thanks for the clarification. I tried like the following,
await evaluate(link({"data-test-id":"cart_primarycheckout"}), ele => ele.click());
It is working.


Correct closing web socket connections in case of fatal server stopping

The current implementation doesn't send a correct close message to the client in case of abnormal server stopping.

@marci4 could you please take a look? Thanks.

@marci4  sorry I will reopen PR, looks like I've done incorrect merging thus commits from my last PR is added as well.


Rename depreciated strings

Resolve #117

Codecov Report

Merging #121 into master will not change coverage.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master     #121   +/-   ##
=========================================
  Coverage     55.77%   55.77%
  Complexity      376      376
=========================================
  Files            83       83
  Lines          1402     1402
  Branches        112      112
=========================================
  Hits            782      782
  Misses          584      584
  Partials         36       36

Impacted Files
Coverage Δ
Complexity Δ

...java/seedu/address/logic/commands/FindCommand.java
100.00% <ø> (ø)
6.00 <0.00> (ø)

src/main/java/seedu/address/model/Model.java
100.00% <ø> (ø)
1.00 <0.00> (ø)

...main/java/seedu/address/model/tag/FileAddress.java
70.00% <ø> (ø)
4.00 <0.00> (ø)

src/main/java/seedu/address/model/tag/Tag.java
79.16% <ø> (ø)
10.00 <0.00> (ø)

src/main/java/seedu/address/model/tag/TagName.java
80.00% <ø> (ø)
6.00 <0.00> (ø)

...in/java/seedu/address/model/tag/UniqueTagList.java
92.68% <ø> (ø)
20.00 <0.00> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update ffa1e08...76e1386. Read the comment docs.


Image upload in modal

Hi, i'm new in ruby ecosystem but i'll try to explain my problem, by the way, thank you for this gem :)
Im hurting to a wall, I'm trying to upload images through a one to many relationship and it dont works.
Nothing happen when i submit form and I have a console error :
Uncaught TypeError: $.rails.callFormSubmitBindings is not a function
I only see the parent entity change to 'Edit' view and datas are not persisted.
The line which is causing problem seems to be:
if (!$.support.submitBubbles && $().jquery < '1.7' && $.rails.callFormSubmitBindings(form) === false) return $.rails.stopEverything(e); in jquery.remotipart
If i dont put any images to my associated entity I have no problems so I tried with carrierwave and paperclip but the problem remains.
I hope you will be able to help me,
Cordially

I have exactly the same issue. Hope, somebody know, how to solve it.

Same for me when i use the modal upload to add a Rich media.

I have upgraded remotipart. Can you guys try again and reopen if it still shows up?

It's ok for me.
Thanks for your quick upgrade.

Still broken
Using rails_admin 0.8.1

Just had this problem too, I'm surprised there aren't more people commenting here. Thanks for your fix @bbenezech. For those flicking to the bottom of the issue to see the solution, just switch to the master branch and it will be fixed. (I have locked to the most recent commit, so it doesn't keep changing)
gem 'rails_admin', github: 'sferik/rails_admin', ref: '49aafbb'
I assume this issue will be fixed with the next release after 0.8.1. Thanks for the great gem guys!

I've just reproduced it on 0.8.1 as well:
TypeError: $.rails.callFormSubmitBindings is not a function. (In '$.rails.callFormSubmitBindings(form)', '$.rails.callFormSubmitBindings' is undefined)

Switching to 49aafbb resolved the problem.

The fix using the ref '49aafbb' makes another error pop in my app:
NoMethodError at /servicio/1/edit ================================= > undefined method to_sym' for nil:NilClass rails_admin_globalize_field (0.4.0) `

Hi
I am facing Same issue .
if (!$.support.submitBubbles && $().jquery < '1.7' && $.rails.callFormSubmitBindings(form) === false) return $.rails.stopEverything(e);
Can anybody have solution..?.
Thanks in advance.
Thanks
Shiva.A

if (!$.support.submitBubbles && $().jquery < '1.7' && $.rails.callFormSubmitBindings(form) === false) return $.rails.stopEverything(e);

This is because expression ('1.12.1' < '1.7') is a true ;)
Try to copy standard jquery.remotipart.js file from the last version of remotepart to the app/assets/javascripts/rails_admin/jquery.remotipart.fixed.js.

Novik, could you tell me how I can download your plugins for ruTorrent? Many thanks!

@ant919191 From the project's github repo of course.
And some correction to the above -

Try to copy standard jquery.remotipart.js file from the last version

This will not work, you need simply comment this line (if (!$.support.submitBubbles && $().jquery < '1.7'...) in the original jquery.remotipart.fixed.js
(Of course, this is correct only for case, when you use jQuery >= 1.7)


Bug:

What happened?
Tried to transcribe a file.
Steps to reproduce

step one...
step two...

What OS are you seeing the problem on?
Window
Relevant log output
options: {
  "path": "C:\\Users\\jmillet\\Documents\\2024-11-04 09-01-14.wav",
  "lang": "en",
  "verbose": false,
  "n_threads": 11,
  "init_prompt": "",
  "temperature": 0.6,
  "translate": null,
  "max_text_ctx": 3,
  "word_timestamps": false,
  "max_sentence_len": 1
}

Caused by:
    no segements found!

Location:
    core\src\transcribe.rs:292:13
App Version: vibe 2.6.3
Commit Hash: d24ffccb0d05ea822ff1a3a6edb3b9871be9f368
Arch: x86_64
Platform: windows
Kernel Version: 10.0.19045
OS: windows
OS Version: 10.0.19045
Cuda Version: n/a
Models: ggml-distil-large-v3.bin, ggml-large-v3-turbo.bin, ggml-medium.bin
Default Model: "C:\\Users\\jmillet\\AppData\\Local\\github.com.thewh1teagle.vibe\\ggml-distil-large-v3.bin"
Cargo features: vulkan

{
    "avx": {
        "enabled": true,
        "support": true
    },
    "avx2": {
        "enabled": true,
        "support": true
    },
    "f16c": {
        "enabled": true,
        "support": true
    },
    "fma": {
        "enabled": true,
        "support": true
    }
}

Try with other file

Unfortunately I can't know from such error the cause. The only way we could know is running it from the terminal and see the error coming from whisper.cpp
taskkill /IM vibe.exe /F
set RUST_BACKTRACE=1
set RUST_LOG=vibe=debug,whisper_rs=debug
%localappdata%\vibe\vibe.exe

https://github.com/thewh1teagle/vibe/issues/370


Strong inaccuracy in calculation of atom positions from frames&torsion-angles

OpenFold/AF2 provide extensive and welll-documented code bases for working with protein structures, beyond structure prediction purposes. Thanks a lot for this work!
I wanted to make use of OpenFold's implementation for converting betwene atom positions and frames/torsion-angles. To test this, I wrote a little test script that

loads atom positions
calculates AA-based frames and torsion angles
calculates new atom positions from the frames and torsion angles
checks whether the two sets of atom positions are identical (as one would expect)

Although I would expect some numerical errors from angle-based positions calculations, the error is much larger than what seems  reasonable:

I commented and uploaded the script here along with the example protein (the script is on the bottom):
https://gist.github.com/moritzschaefer/2b2c97c266b93d0df2559ab1b9ef512f
I (unsuccesfully) checked multiple things to pinpount the error:

whether it might be a float-precision error (I set all tensors to float64)
whether alternative coordinates might be the issue (sometimes, a 180 degree turn results in the exact same conformation, where two C-atoms are swapped (such that it looks different for the model))
whether running on CPU or GPU makes a difference

Note: the atom error seems to increase with additional angles (e.g. Chi4-based atoms tend to be more off, as they depend on chi3, chi2 and chi1). The C-alpha atoms show no deviation (RMSD < 1e-8)
Is there something I missed?

Have you checked whether this also occurs w/ AF2 code?

As a next step, if gahdritz does not respond in the coming week, I should report to AF2 (and/or OpenFold)

I am not very familiar with AlphaFold/OpenFold implementation details, so I could be mistaken here, but I wonder if this issue results from the fact that the structure module uses idealized bond lengths and angles to construct sidechain atoms (see Section 1.8.4 AlphaFold Supplementary Material).
For instance, I see that you are using what seems to be the PDB file as downloaded from the RCSB website. This file likely does not have idealized bond lengths or angles. When converting to frames/angles and then back to coordinates, I am guessing that the new structure is different because it was rebuilt using the idealized angles.
If you repeat the process by taking your resultant structure (after rebuilding), converting it to angles, and converting back to structure, I hope that the final structure will be identical to the first rebuilt structure. I am not quite familiar with the code enough to test this myself.
Of course, perhaps you've already considered this! I am chiming in because I have encountered this in my own work - idealized bond lengths and angles can significantly impact reconstruction loss when using an angle-only representation of protein structure.

Hey @jonathanking, indeed I overlooked this. I'll check this and report back here. Thank you for the reply!

I'm glad that seemed to explain some of the discrepancies!
No, I don't know when or even if AlphaFold does any handling of idealized bond lengths or angles.
A quick search in their repo for "ideal/idealized" didn't turn up anything particularly telling either. It's my guess that they simply trained the model to predict the crystal structure/existing PDB files, without strictly accounting for the differences between the bond lengths/angles in the target structure and the angles/bonds in their prediction. In this manner, the model can certainly be trained but would have some limitations due to these differences. Perhaps they hoped relaxation would resolve the remaining differences.


[Auto-generated] Check & update dependencies (pyproject.toml)

Update dependencies (pyproject.toml)
Automatically created PR based on the 'CI - Check pyproject.toml dependencies' workflow in SINTEF/ci-cd.

Keep using the dev version of oteapi-core.


What settings do I change to make the inference_video.py more sensitive to shadows? (COM )

Or simply improve results overall. Mobilenet backbone and model seems to work best but Id still like to improve on it more.
Here is the background image:

A frame of the source video:

Frames of the result: There are  frames where the background is not completely replaced

python command:
python inference_video.py
--model-type mattingrefine
--model-backbone mobilenetv2
--model-backbone-scale 0.25
--model-refine-mode sampling
--model-refine-sample-pixels 80000
--model-checkpoint "path"
--video-src "xpath"
--video-bgr "ypath"
--video-resize 1920 1080
--output-dir "zpath"
--output-type com

I don't have any tricks that can help besides avoiding the shadow at its first place. Every method has its limitations. Shadow will cause problems even for green screen matting.

ok thank you very much!


Error: Could not find or load main class org.gradle.wrapper.GradleWrapperMain

React Native run-android build today and have issue , how can i solve it

Hey, thanks for reporting this issue!
It looks like your description is missing some necessary information, or the list of reproduction steps is not complete. Can you please add all the details specified in the template? This is necessary for people to be able to understand and reproduce the issue being reported.
I am going to close this, but feel free to open a new issue with the additional information provided. Thanks!


Checkout different frameworks for Website

Right now, there are three different frameworks I want to test for their suitability to make up the main website:
goHugo
Hugo is based around markdown files. They are flexible, can be read without the framework, and render nicely in github as well. Additionally, they can be directly included into streamlit if the content of the website should be loadable here as well.
The streamlit apps can be included via their own content page, which just hold a shortcode to a boarderless iframe linking the streamlit app.
sphinx
Sphinx is the de-facto documentation engine for python. It would be nice to have the introduction texts, streamlit apps, and code reference all in one place. Sphinx is built with restructured text, which is similar to markdown. I am as of now not 100% sure how to embed an iframe into a sphinx page.
A possible downside of sphinx is that most templates work with sidebar navigation, which we have to get rid of for the streamlit apps. The templates are built with jinja2 (I think), which is pretty straightforward and could enable us to build our own template.
react
Another option is to use react. We would go with material design here, which will be very familiar to most users, as most websites nowadays are built this way. The huge advantage is flexibility. I can build anything into the app. The downside is, that this will take time. As long as the website does not get too complicated, the effort to implement should be controllable.
@cojacoo any comment is welcome, otherwise, I will implement a minimal example for all three options and see how things are going:

[ ] minimal hugo example
[ ] minimal sphinx example
[ ] minimal react app

I like Hugo. I also like the option to work with markdownfiles for both, apps and websites. If I got you right, iframes would be mostly interactive content such as a streamlit app? A url-link would be ok too.

I guess we have a plan here, and made the decision in favor of an React app.


Add screen reader support for A11y

[x] each cell should have aria-label of sate with x,y position
[ ] top nav should have aria-label of game size & timer.

closing this as all are tracked in separate items


Posting discussion comments through osmcha gives error

I'm submitting a bug report
Brief Description

When I try add a discussion comment to a changeset using OSMCha, it gives error. "It was not possible to post your comment".  This error arose after the port of OSMCha on 13 Feb 2024
What is the motivation / use case for this feature?

What  is the current behaviour, (attach relevant screenshots) ?

Screenshot enclosed

What  is the expected behaviour ?

Discussion comment should be posted successfully
When does this occur ?

Everytime a comment posting is attempted
How do we replicate the issue ?

Take any changeset and try to post a comment.
The error shows

Please tell us about your environment:

Ubuntu 22.04, Firefox 123.0(64bit)
Other Information / context:

This error seems to be a result of the porting of Osmcha to new server on 13 Feb 2024

Are you still experiencing this issue? I could not reproduce it.

Yes, I tried with Chrome Version 121.0.6167.184 (Official Build) (64-bit) also and faced the same error

Looks like cookie issue. I logged out and then logged in. Now I am able to post comments.

@willemarcel I was having the same issue. Is there a way to invalidate cookies that belong to the old OAuth Process? Which I guess is the issue here…?


reportHTTP

A report that allows generic HTTP calls.
It can be used for integrating various messaging platforms (including #81).

missing documentation


Waypoint: Build Web Apps with Expressjs - Suggestion: Needs some context

Not a bug, just a suggestion:  I feel this waypoint would benefit from a brief introduction or a little context.  Perhaps adding an additional step to the waypoint that links to an article such as...
http://evanhahn.com/understanding-express/
...would be beneficial to other students?  That article gives a good, quick overview of Expressjs and, most importantly, directly connects it with the Node HTTP server material we just learned in the previous waypoints.  Without that connection, when I was going through the first few exercises, all I was thinking was:  What on earth is this?  Why am I doing this?  What's going on?

My experience was similar to Jeff's.

@FreeCodeCamp/issue-moderators I don't have Express.js experience to evaluate this sufficiently, but I'm all for giving context to lessons. Should we have this one check box before running the git clone command in the challenge? For quick access, here's a link to Waypoint: Build Web Apps with Expressjs.

[ ] ...
[ ] Read this article on Understanding Express.js (http://evanhahn.com/understanding-express/)
[ ] ...

How about :

[ ] Read this article on Understanding Express.js


transform does not respect value_offset in conversion

Describe the bug
I am converting a binary table to csv and a field in the table uses value_offset, however this offset is not applied to the values in the resulting output.
Expected behavior
Decoded values should be modified by value_offset - and also by scaling_factor if present (in my case it was not).
Desktop (please complete the following information):

OS: ubuntu 18.04
Version: transform 1.9 (cannot test on 1.10 due to #16)

Adding a sample file. Values in the raw data are: 0, 32768,<PHONE_NUMBER>,<PHONE_NUMBER>.
With <value_offset>1</value_offset> in the label the python viewer shows this correctly:
fits_test.zip

but the output of transform -a -f csv -t fits_test_k.xml gives:
0
32768
2147483648
4294967295

Ahhhh, I see - this is carried forward to the label of the CSV file - OK, my bad - feel free to close this ticket. I was expected the data to be transformed, and actually didn't care about the label in this case and had not looked at it. But understood now!


Add dir

if admin/admin.js is empty not commit instead use .gitkeep file

Add .gitkeep and alter validation

Nice! Thanks @FernandoCagale


Fix example for black background color in Objective 2

Please edit the description with 'Fixes #3870' on a separate line.
Thanks!

@XianPalin Thanks for catching and fixing this!


Styling

Try to use same bootstrap theme as the main NetworkCanvas site?

Could be tricky, but if you can get something rudimentary up, I will tweak it.
You mentioned this is react based. We actually have a UI component repo that is implementing some of our project style guide. Check out https://github.com/codaco/Network-Canvas-UI
If any of those components can be used again (perhaps only the utilities such as colors and typography), please go ahead.

Deployed a first pass styling with the Network Canvas font and color scheme. The existing styles are a bit of a hybrid bootstrap and custom CSS, I started moving toward more pure bootstrap. SASS source is here: https://github.com/codaco/feedback-site/tree/master/packages/networkcanvas-styles/lib/stylesheets


Move MOI, SCIP and HiGHS to extension folder

Get rid of the direct dependencies MathOptInterface, SCIP and HiGHS.
That includes the integer bounds. These can just be a dictionaries of Int and Float.

See https://pkgdocs.julialang.org/v1.9/creating-packages/#Conditional-loading-of-code-in-packages-(Extensions)

Related to #144

Update: We can move SCIP and HiGHS into the extensions but not MathOptInterface.
According to this discussion https://github.com/JuliaLang/Pkg.jl/issues/3499 one is not supposed to define new structs in an extension but only overwrite functions from the main package.
An alternative could be to create a BosciaExtras package. This would be a separate package that the user only has to load if they need it.

For now, let's watch the discussion and see how the extension feature is developing.
If, at one point, there is a nice way of defining structs in extension, we can do that. This shouldn't be a lot of work.
Else, if we have a lot of predefined BLMOs, maybe for graphs etc, we can always think about outsourcing those into an Extra package.


Some CI improvements

Add a config for catalog and database
Use more unique names for test tables

not sure what happened this PR got merged while we were discussing in the review comment section.
@kravets-levko could you please respond on this question:
https://github.com/databricks/databricks-sql-nodejs/pull/19#discussion_r911439511


/me endpoint

This PR implements #12599.

CR comments addressed, now waiting to CI to move this again to a new CR round.

@javitonino comment addressed, moving to Acceptance.

Merging, @matallo will tell us if it works. Endpoint is at /api/v3/me


Some extensions cannot be found

VSCode Version: 1.50.1
OS Version: 5.9.2-arch1-1

Steps to Reproduce:

Open VSCode
Search for extensions with explicit name like mshr-h.VerilogHDL
Or use command: ext install mshr-h.VerilogHDL
Says "No extensions found"

Does this issue occur when all extensions are disabled?: Yes
Other extensions such as ftsamoyed.theme-pink-cat-boo won't appear too, though can be downloaded from extension market online and installed via .vsix files. While some other extensions can still be found in search bar like dbaeumer.vscode-eslint.

This reoccured after reinstalling the system and vscode. I believe this to be due to some weird configurations or network errors instead of an internal bug, but reinstalling didn't work nor searching the Internet helped. No relavant Q&A was found in forums and thus I've to raise this issue. Any suggestion?

/duplicate
https://github.com/microsoft/vscode/issues/107034

Duplicate of https://github.com/microsoft/vscode/issues/107997#issuecomment-703245178

A handy wordaround is to manually edit /usr/share/code/products.config,
and change
"serviceUrl": "https://open-vsx.org/vscode/gallery",
"itemUrl": "https://open-vsx.org/vscode/item"
~~~~json
to

"serviceUrl": "https://marketplace.visualstudio.com/_apis/public/gallery",
"cacheUrl": "https://vscode.blob.core.windows.net/gallery/index",
"itemUrl": "https://marketplace.visualstudio.com/items"


Allow for validation of the entire collection

When creating, I have the need to validate the entire collection of items as a whole. For instance, there should be validation to ensure there are exactly three items present. At the moment, I do not see an easy way to accomplish this.

Not sure if it's still relevant for you @alex-netquity but here's how I handled the situation (admittedly not the most elegant fix).

Create a list validation method in the Serializer
Overwrite create() on the ModelViewSet so it's basically the same as inside BulkCreateModelMixin, with the exception of the added call to the list validation method:

def create(self, request, *args, **kwargs):
    self.serializer_class = CustomerBoxCreateSerializer

    # From here on copied from BulkCreateModelMixin in order to be able to call
    # the custom is_valid_across_list()
    bulk = isinstance(request.data, list)

    if not bulk:
        return super(BulkCreateModelMixin, self).create(request, *args, **kwargs)

    else:
        serializer = self.get_serializer(data=request.data, many=True)
        serializer.is_valid(raise_exception=True)

        # Call to custom list validation method
        self.serializer_class().is_valid_across_list(data=serializer.validated_data, raise_exception=True)

        self.perform_bulk_create(serializer)
        return Response(serializer.data, status=status.HTTP_201_CREATED)

Again, not the most elegant, but it works. I tried overwriting is_valid() directly on the serializer, but it never got executed since create() in BulkCreateModelMixin for some reason ends up calling the method on BaseSerializer.
Hope it helps! Let me know if you found a more elegant solution.


NaN or Inf found in input tensor

How are you @weixians ?
I have some issue about your code.
When i run run_dqn.py. there is a issue [NaN or Inf found in input tensor.]
Here is figure

Hello, have you resolved this issue? If it's resolved, I hope you can let me know. Thank you

How are you @XinLei-L.
I am so sorry... i am still in this issue.

I have trained on this project, and this situation has no impact on the training。

How are you @XinLei-L. I am so sorry... i am still in this issue.

@XinLei-L oh okay!
Thanks!


BUG: reciprocal GPU kernel for complex 1/1 division not found

System information

Have I written custom code (as opposed to using a stock example script provided in TensorFlow): yes
OS Platform and Distribution (e.g., Linux Ubuntu 16.04): Ubuntu 18.04
Mobile device (e.g. iPhone 8, Pixel 2, Samsung Galaxy) if the issue happens on mobile device:
TensorFlow installed from (source or binary): binary
TensorFlow version (use command below): 1.10.0
Python version: 3.6
Bazel version (if compiling from source):
GCC/Compiler version (if compiling from source):
CUDA/cuDNN version: 9.2/7.2.1
GPU model and memory: GeForce GTX 1050 mobile, 4096MiB
Exact command to reproduce:

import tensorflow as tf
import numpy as np

# create a lot of points
# CHANGE NUMBER BELOW (higher -> fails)
n_points = 670000  # fails around > 650'000 (e.g. 1'000'000) for np.linspace generation

# points creation
points = np.ones(n_points)
# alternate points creation
# low = 100.  # irrelevant, only > 0 -> no 0 (division)
# high = 200.  # irrelevant
# points = tf.random_uniform(shape=[n_points], minval=low, maxval=high)
# points = np.linspace(low, high, n_points)

with tf.Session() as sess:
    # just do complex division: 1.0+0j / points
    complex_1_0 = tf.cast(1., dtype=tf.complex128)
    denom = tf.cast(points, dtype=tf.complex128)
    division = complex_1_0 / denom
    result = sess.run(division)
    print(result)

Describe the problem
For a certain amount of points, the complex division kernel (or rather reciprocal kernel) "seems to not be available on the GPU".
It works for

a lower number of points
for floats
on CPU (tested with "tf.devices")

It seems to be independent of

the generation of the points (see commented lines for alternate creation)
GPU (also tested on Tesla K80) with lower TF/Cuda version

No idea where to start...
Source code / logs
relevant error:
NotFoundError (see above for traceback): No registered 'Reciprocal' OpKernel for GPU devices compatible with node truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"
(OpKernel was found, but attributes didn't match)
.  Registered:  device='GPU'; T in [DT_INT64]
device='GPU'; T in [DT_DOUBLE]
device='GPU'; T in [DT_HALF]
device='GPU'; T in [DT_FLOAT]
device='CPU'; T in [DT_COMPLEX128]
device='CPU'; T in [DT_COMPLEX64]
device='CPU'; T in [DT_DOUBLE]
device='CPU'; T in [DT_HALF]
device='CPU'; T in [DT_FLOAT]
[[Node: truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"]]
Full stacktrace of failure:
2018-09-19 17:18:40.965160: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 3010 MB memory) -> physical GPU (device: 0, name: GeForce GTX 1050, pci bus id: 0000:01:00.0, compute capability: 6.1)
2018-09-19 17:18:41.104747: E tensorflow/core/common_runtime/executor.cc:697] Executor failed to create kernel. Not found: No registered 'Reciprocal' OpKernel for GPU devices compatible with node truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"
(OpKernel was found, but attributes didn't match)
.  Registered:  device='GPU'; T in [DT_INT64]
device='GPU'; T in [DT_DOUBLE]
device='GPU'; T in [DT_HALF]
device='GPU'; T in [DT_FLOAT]
device='CPU'; T in [DT_COMPLEX128]
device='CPU'; T in [DT_COMPLEX64]
device='CPU'; T in [DT_DOUBLE]
device='CPU'; T in [DT_HALF]
device='CPU'; T in [DT_FLOAT]
[[Node: truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"]]
Traceback (most recent call last):
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1278, in _do_call
return fn(*args)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1263, in _run_fn
options, feed_dict, fetch_list, target_list, run_metadata)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1350, in _call_tf_sessionrun
run_metadata)
tensorflow.python.framework.errors_impl.NotFoundError: No registered 'Reciprocal' OpKernel for GPU devices compatible with node truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"
(OpKernel was found, but attributes didn't match)
.  Registered:  device='GPU'; T in [DT_INT64]
device='GPU'; T in [DT_DOUBLE]
device='GPU'; T in [DT_HALF]
device='GPU'; T in [DT_FLOAT]
device='CPU'; T in [DT_COMPLEX128]
device='CPU'; T in [DT_COMPLEX64]
device='CPU'; T in [DT_DOUBLE]
device='CPU'; T in [DT_HALF]
device='CPU'; T in [DT_FLOAT]
[[Node: truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"]]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2961, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
runfile('/home/jonas/Documents/uni/Master_thesis/code/test/tf_playground/test/gpu_div_bug.py', wdir='/home/jonas/Documents/uni/Master_thesis/code/test/tf_playground/test')
File "/usr/share/pycharm/helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile
pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
File "/usr/share/pycharm/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "/home/jonas/Documents/uni/Master_thesis/code/test/tf_playground/test/gpu_div_bug.py", line 20, in
result = sess.run(division)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 877, in run
run_metadata_ptr)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1100, in _run
feed_dict_tensor, options, run_metadata)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1272, in _do_run
run_metadata)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1291, in _do_call
raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.NotFoundError: No registered 'Reciprocal' OpKernel for GPU devices compatible with node truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"
(OpKernel was found, but attributes didn't match)
.  Registered:  device='GPU'; T in [DT_INT64]
device='GPU'; T in [DT_DOUBLE]
device='GPU'; T in [DT_HALF]
device='GPU'; T in [DT_FLOAT]
device='CPU'; T in [DT_COMPLEX128]
device='CPU'; T in [DT_COMPLEX64]
device='CPU'; T in [DT_DOUBLE]
device='CPU'; T in [DT_HALF]
device='CPU'; T in [DT_FLOAT]
[[Node: truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"]]
Caused by op 'truediv', defined at:
File "/usr/share/pycharm/helpers/pydev/pydevconsole.py", line 511, in
pydevconsole.start_server(host, int(port), int(client_port), client_host)
File "/usr/share/pycharm/helpers/pydev/pydevconsole.py", line 336, in start_server
process_exec_queue(interpreter)
File "/usr/share/pycharm/helpers/pydev/pydevconsole.py", line 192, in process_exec_queue
more = interpreter.add_exec(code_fragment)
File "/usr/share/pycharm/helpers/pydev/_pydev_bundle/pydev_console_utils.py", line 281, in add_exec
more = self.do_add_exec(code_fragment)
File "/usr/share/pycharm/helpers/pydev/_pydev_bundle/pydev_ipython_console.py", line 41, in do_add_exec
res = bool(self.interpreter.add_exec(code_fragment.text))
File "/usr/share/pycharm/helpers/pydev/_pydev_bundle/pydev_ipython_console_011.py", line 442, in add_exec
self.ipython.run_cell(line, store_history=True)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2907, in run_ast_nodes
if self.run_code(code, result):
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2961, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
runfile('/home/jonas/Documents/uni/Master_thesis/code/test/tf_playground/test/gpu_div_bug.py', wdir='/home/jonas/Documents/uni/Master_thesis/code/test/tf_playground/test')
File "/usr/share/pycharm/helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile
pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
File "/usr/share/pycharm/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "/home/jonas/Documents/uni/Master_thesis/code/test/tf_playground/test/gpu_div_bug.py", line 19, in
division = complex_1_0 / denom
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/ops/math_ops.py", line 850, in binary_op_wrapper
return func(x, y, name=name)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/ops/math_ops.py", line 958, in _truediv_python3
return gen_math_ops.real_div(x, y, name=name)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/ops/gen_math_ops.py", line 5881, in real_div
"RealDiv", x=x, y=y, name=name)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py", line 787, in _apply_op_helper
op_def=op_def)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/util/deprecation.py", line 454, in new_func
return func(*args, **kwargs)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/framework/ops.py", line 3155, in create_op
op_def=op_def)
File "/home/jonas/anaconda3/envs/zfit36/lib/python3.6/site-packages/tensorflow/python/framework/ops.py", line 1717, in init
self._traceback = tf_stack.extract_stack()
NotFoundError (see above for traceback): No registered 'Reciprocal' OpKernel for GPU devices compatible with node truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"
(OpKernel was found, but attributes didn't match)
.  Registered:  device='GPU'; T in [DT_INT64]
device='GPU'; T in [DT_DOUBLE]
device='GPU'; T in [DT_HALF]
device='GPU'; T in [DT_FLOAT]
device='CPU'; T in [DT_COMPLEX128]
device='CPU'; T in [DT_COMPLEX64]
device='CPU'; T in [DT_DOUBLE]
device='CPU'; T in [DT_HALF]
device='CPU'; T in [DT_FLOAT]
[[Node: truediv = ReciprocalT=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"]]

@mayou36 The fix has been pushed. #22420 Can you please confirm it?

Cool. Please post your findings once you have it.

I am also suffering from this bug. Since the pull request was not accepted, this issue is still active and should be reopened.

@azaks2 any updates here? I just stumbled in a completely different problem again on it (am I the only one doing complex divisions? :) )
For completeness the slighlty changed error message (from the example code above) which now incorporates the XLAs:
NotFoundError (see above for traceback): No registered 'Reciprocal' OpKernel for GPU devices compatible with node node truediv (defined at <ipython-input-2-fde784715ebe>:18)  = Reciprocal[T=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"](Cast_1)
	 (OpKernel was found, but attributes didn't match)
	.  Registered:  device='XLA_GPU'; T in [DT_FLOAT, DT_DOUBLE, DT_INT32, DT_COMPLEX64, DT_INT64, DT_BFLOAT16, DT_HALF]
  device='XLA_CPU'; T in [DT_FLOAT, DT_DOUBLE, DT_INT32, DT_COMPLEX64, DT_INT64, DT_HALF]
  device='XLA_CPU_JIT'; T in [DT_FLOAT, DT_DOUBLE, DT_INT32, DT_COMPLEX64, DT_INT64, DT_HALF]
  device='XLA_GPU_JIT'; T in [DT_FLOAT, DT_DOUBLE, DT_INT32, DT_COMPLEX64, DT_INT64, DT_BFLOAT16, DT_HALF]
  device='GPU'; T in [DT_INT64]
  device='GPU'; T in [DT_DOUBLE]
  device='GPU'; T in [DT_HALF]
  device='GPU'; T in [DT_FLOAT]
  device='CPU'; T in [DT_COMPLEX128]
  device='CPU'; T in [DT_COMPLEX64]
  device='CPU'; T in [DT_DOUBLE]
  device='CPU'; T in [DT_HALF]
  device='CPU'; T in [DT_FLOAT]

I encountered this bug on a much smaller scale -- trying to do division on a single complex number.
x = tf.random.uniform(shape=())  # change to tf.constant(1.0) and error disappears
cx_x = tf.cast(x, dtype=tf.complex128)

numerator = 1  # change to 1.1 (error disappears) or 1.0 (throws same error)

with tf.Session() as sess:
  sess.run(numerator/cx_x)

Here's the error message:

NotFoundError                             Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py in _do_call(self, fn, *args)
1333     try:
-> 1334       return fn(*args)
1335     except errors.OpError as e:
/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py in _run_fn(feed_dict, fetch_list, target_list, options, run_metadata)
1318       return self._call_tf_sessionrun(
-> 1319           options, feed_dict, fetch_list, target_list, run_metadata)
1320
/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py in _call_tf_sessionrun(self, options, feed_dict, fetch_list, target_list, run_metadata)
1406         self._session, options, feed_dict, fetch_list, target_list,
-> 1407         run_metadata)
1408
NotFoundError: No registered 'Reciprocal' OpKernel for GPU devices compatible with node {{node truediv_5}}
(OpKernel was found, but attributes didn't match) Requested Attributes: T=DT_COMPLEX128, _device="/job:localhost/replica:0/task:0/device:GPU:0"
.  Registered:  device='XLA_GPU'; T in [DT_FLOAT, DT_DOUBLE, DT_INT32, DT_COMPLEX64, DT_INT64, DT_BFLOAT16, DT_HALF]
device='XLA_CPU'; T in [DT_FLOAT, DT_DOUBLE, DT_INT32, DT_COMPLEX64, DT_INT64, DT_HALF]
device='XLA_CPU_JIT'; T in [DT_FLOAT, DT_DOUBLE, DT_INT32, DT_COMPLEX64, DT_INT64, DT_HALF]
device='XLA_GPU_JIT'; T in [DT_FLOAT, DT_DOUBLE, DT_INT32, DT_COMPLEX64, DT_INT64, DT_BFLOAT16, DT_HALF]
device='GPU'; T in [DT_INT64]
device='GPU'; T in [DT_DOUBLE]
device='GPU'; T in [DT_HALF]
device='GPU'; T in [DT_FLOAT]
device='CPU'; T in [DT_COMPLEX128]
device='CPU'; T in [DT_COMPLEX64]
device='CPU'; T in [DT_DOUBLE]
device='CPU'; T in [DT_HALF]
device='CPU'; T in [DT_FLOAT]
[[{{node truediv_5}}]]

@mayou36 , This issue has been fixed in the recent Tensorflow GPU version 2.4.1, please find the gist here.

Good to hear, many thanks for resolving this!


Add thread diagnostics

This change adds task diagnostics to the CBL thread manager.  On catastrophic failures, it will log useful information helpful for identifying the cause of the failure

A couple of notes:

While it is possible for SerialExecutor.execute to throw an RejectedExecutionException, it is pretty unlikely.  If it does happen, wrapping the exception doesn't seem to add any value.
In order to make it possible to dump the executor queue, I need a ThreadPoolExecutor.  Changed the Java Executor from a fixed pool to a TPE.  The parameters are approximately the same, but the threads can die back to only 2, after 30 seconds.


Fixed Quantity Button

Added a reusable component named QuantityButton.tsx under Cart component.

Fix the build Errors. @Disha-Hati


Remove incorrectly duplicated queries in SignOPT attack

Description
The current implementation of SignOPT sends duplicated queries when checking targeted/untargeted modes. This is because the model query happens before the mode checking. For example:
https://github.com/Trusted-AI/adversarial-robustness-toolbox/blob/22dbf830d0db590ce8cb85d600f8e63c2905d163/art/attacks/evasion/sign_opt.py#L309-L311
In untargeted mode, self.targeted = False would cost an unnecessary self._is_label call.
This PR moves the mode checks ahead of the self._is_label as a valid short-circuiting.
It is hard to determine the exact number of calls wasted due to this problem, but this PR should reduce half of the running time for this specific part.
Type of change
Please check all relevant options.

[ ] Improvement (non-breaking)
[x] Bug fix (non-breaking)
[ ] New feature (non-breaking)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update

Testing
Please describe the tests that you ran to verify your changes. Consider listing any relevant details of your test configuration.

[ ] Test A
[ ] Test B

Test Configuration:

OS
Python version
ART version or commit number
TensorFlow / Keras / PyTorch / MXNet version

Checklist

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[ ] I have commented my code
[ ] I have made corresponding changes to the documentation
[x] My changes generate no new warnings
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] New and existing unit tests pass locally with my changes

Codecov Report

Merging #2129 (4a9ef03) into dev_1.15.0 (b13f802) will decrease coverage by 59.37%.
The diff coverage is 0.00%.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more

@@               Coverage Diff               @@
##           dev_1.15.0    #2129       +/-   ##
===============================================
- Coverage       85.63%   26.26%   -59.37%
===============================================
  Files             297      297
  Lines           26521    26521
  Branches         4864     4864
===============================================
- Hits            22712     6967    -15745
- Misses           2571    19313    +16742
+ Partials         1238      241      -997

Impacted Files
Coverage Δ

art/attacks/evasion/sign_opt.py
9.15% <0.00%> (-77.66%)
:arrow_down:

... and 227 files with indirect coverage changes


fix: make sure devDependencies are marked as such

PR Checklist
Please check if your PR fulfills the following requirements:

[x] The commit message follows our guidelines: https://github.com/scullyio/scully/blob/master/CONTRIBUTING.md#commit
[ ] Tests for the changes have been added (for bug fixes / features)
[ ] Docs have been added / updated (for bug fixes / features)

PR Type
What kind of change does this PR introduce?

[ ] Bugfix
[ ] Feature
[ ] Code style update (formatting, local variables)
[x] Refactoring (no functional changes, no api changes)
[ ] Other... Please describe:

What is the current behavior?

This should be a start to tackle this issue:
Issue Number: #88
What is the new behavior?
Dependencies needed only during development are moved to the devDependencies object.
Does this PR introduce a breaking change?

[ ] Yes
[x] No

Other information
I checked these pages and found that almost none of the devDependencies are marked as such:
https://www.npmjs.com/package/@scullyio/scully?activeTab=dependencies
https://www.npmjs.com/package/@scullyio/init?activeTab=dependencies
There might be more deps that can be moved, but this should be a good start.

@beeman, we need to talk this one through. As Scully is a dev-time tool, arent all of them devDepedencies?
Also ,the top-level package.json is actually not being distributed to anywhere, but just four our own development mono-repo. That means that everything in there is a devDepdency right?

@SanderElias scully being a dev-time tool is not relevant here.
We should only list the dependencies that are needed in runtime in the dependencies object, the rest (what's needed to build scully itself) goes into devDependencies. This keeps the fotoprint small and prevents downloading and installing unneeded deps.
With regards to the top-level package, as it's not distributed it doesn't really matter but you are right, they could all be devDependencies.

This LGTM, but deferring to @SanderElias for approval.

We should only list the dependencies that are needed in runtime in the dependencies object, the rest (what's needed to build scully itself) goes into devDependencies. This keeps the fotoprint small and prevents downloading and installing unneeded deps.


environment variable ?

I use nxtend with Nx to generate a Ionic/Capacitor project but somehow i can't use .env environment variables. They're always undefined. I read that ionic uses Create React App under the hood, so it should work with REACT_APP_... variables. But i see no react-scripts dependency. How can i use environment variables with React?

This is supported by Nx directly. You should be able to add a variable in a .env file but it has to start with NX_* instead.
https://nx.dev/latest/react/guides/environment-variables#environment-variables


Deploying large contracts fails

When testing with ganache we use allowUnlimitedContractSize switch to allow contracts bigger than 234576 bytes to be deployed. However an out of gas error is thrown even though the contract was created, e.g:
Transaction: 0x702c95bfc4324122876c795d6175a62e1a8a75c04d37f3dc30c5a479dda54544
  Contract created: 0xe83ef66e898b65e1e202f3f554897943a0383f29
  Gas usage: 110000000
  Block Number: 430
  Block Time: Tue Apr 28 2020 16:44:45 GMT+0300 (Eastern European Summer Time)
  Runtime Error: out of gas

Your Environment

Version used: Ganache CLI v6.9.1 (ganache-core: 2.10.2)
Version of Truffle/Remix/Other tools used: etherlime
NodeJS Version: 10.12
Operating System and version (include distro if Linux): OSX
Link to your project or repro gist: https://github.com/argentlabs/argent-contracts

@elenadimitrova can you provide any steps to reproduce this?
We do test for this feature. However, our test case is extremely simple:
https://github.com/trufflesuite/ganache-core/blob/27d59d974664462d4152d9bb6ca213e1a6fc9b55/test/unlimitedContractSize.js#L46-L68
Using this contract:
https://github.com/trufflesuite/ganache-core/blob/27d59d974664462d4152d9bb6ca213e1a6fc9b55/test/contracts/customContracts/LargeContract.sol .

We're using the TestUpgradedMakerV2Manager here. And the contract  deployment that surfaced the issue is here

Example contract here with deployedBytecode size of 50908 nibbles or 50908/2 +1 = 25455 bytes just over the allowed 24576 bytes. Same contract when shrank below the limit is deployed successfully to ganache.


Making vector similarity functions pluggable

Description
There are two major reasons for adding a custom vector similarity function:

Adding new nuanced similarity functions (jaccard, hamming, etc.)
Have external support for unstable JVM APIs (Vector incubator)

I am not 100% sure Lucene itself should go through the work of consistently adding new similarity functions.
We should make these pluggable in such a way that developers using Lucene can provide specialized distance functions.
I think the main issue is that the Vector Similarity function is tied to the FieldType and currently that is not pluggable via any external configuration.
There are two ways I can think of for doing this:

The functions being provided in indexing and search configurations (not a fan of this option).
Using an SPI (seems like a more natural option).

Opening this issue for discussion.

What about doing this through vector formats: vector formats could take a similarity parameter, which would win over the one configured on the field type when set. The benefit is that it builds on the fact that vector formats are already pluggable, which makes things simpler in my view. The downside is that you can't plug in similarity functions independently from vectors formats.
This makes me wonder more generally if the similarity should have been an implementation detail of vector formats, like maxConn and beamWidth. Having it on the field type is a bit more user friendly if we think it's important for users to be able to choose between cosine, dot-product and euclidean, but a downside of this choice it that it requires any legal KNN vectors format to support all 3 similarity functions.

@msokolov what do you think about this?

It makes sense to me. I think we got where we are because initially all these things were field-level and then some of them got migrated to the format. Now we're in a middle place straddling two different APIs. Adrien's suggestion to override the field-level setting seems a bit odd from a user perspective though -- I guess a per-field vector format can choose to ignore the similarity function, but then it feels like we ought to avoid setting it in the first place. Maybe we could create a FieldType similarity function "DEFAULT" that is whatever default is provided by the format?

OK, I think this design would look like this:

When creating the format, a similarity function can be optionally provided

The vector similarity function will be a new java interface
We will default to the same default as the current vector similarity enumeration.

Add a new enum to the existing vector similarity enumeration indicating DEFAULT that indicates that the format similarity interface must be used. The implementation of this enum will throw UnsupportedOperationException for its similarity functions.
Add a vector similarity parameter for the vector reader & writer that the format will provide.

If we didn't do this, there would have to be some serialization support for storing custom vector similarity functions, this seems weird to me.

Sorry, I'm -1 to this. This is going with the approach that only those with the resources of amazon or elastic can have performance search. IMO it is OUR JOB AS A LIBRARY to implement these functions in a performant way, for everyone, not just those with the resources of big tech to plug in some custom shit because openjdk is a shitshow.
taking a stand.
I propose an alternative approach here: https://github.com/apache/lucene/issues/12302


Shadow veil changes todo

Make it use the vanish buff, that makes it so the unit can attack while invis?

make it target non-flying units


Use Hogan.js as default template engine

We recently incorporated consolidate.js into Connect so that the view engine is configurable. Now we want to replace the jade templating language with Hogan.js which has a syntax more friendly to non-Nodejs developers and performs substantially better as well.

Close #24.


B 20991 main - Add Counseling Office Column and Filtering to TIO Queue

Agility ticket
Summary
When a customer selects an origin duty location assigned to government counseling, then they will also be asked to select a counseling office within the same GBLOC. This field will be called "Counseling Office".
How to test

Login as a customer and create a 2 both with different counseling offices.
Login as a Services Counselor and submit the new move.
3 Login as TOO, approve both moves.
Crete multiple payment requests for each move
Login as TIO and filter the Counseling Office Task Order Queue for a move to verify filtering works.
Login as TIO and sort the Counseling Office Task Order Queue for a move to verify sort works.

Screenshots
B-20991-508Screenshots.pdf

Test coverage on server failed.
Last run: Wed 20 Nov 2024 12:33:12 AM UTC
Refer to this report to see coverage details for the server app.
Documentation for test coverage can be found at this link.


Add a function to get connection info in a structure format from data

Add a function to get connection info in a structure format from data so that it is easier for post processing.
Signed-off-by: Zang Li<EMAIL_ADDRESS>

test-me-please

Coverage increased (+0.06%) to 44.5% when pulling 09fd29afbb16887c1a5aaa6ab6d88804af40f885 on lzang:master into 864990a6017a7c00ae51953f2f6d72d9d000e6f4 on cilium:master.

test-me-please

test-me-please

test-me-please

restart-ginkgo

restart-ginkgo

@pchaigno, thanks for the tip!  How to restart the Ginkgo-GKE test,  test-gke?

@lzang Yep, test-gke exactly. The GKE pipeline isn't required to merge at the moment though. So I wouldn't bother re-running if you've already checked that the failing tests are not the same between two runs (i.e., they are flakes).


Zooming in manim

I've been trying to figure out how to zoom in on a specific point in manim on my own without success. How do I make some kind of zoom animation? It's about settheory and I want to zoom in on one of the more centered points in the set in the picture below and then zoom out to continue in the same scene. How can I make that happen? :-)

Check this and this.

But I keep on getting this attribute error:
self.camera_frame.save_state()
AttributeError: 'introset' object has no attribute 'camera_frame'
How do I fix that?

Check this and this.

These examples were deprecated

what about 3D animation?


fix: test without fetch dept

:tada: This PR is included in version 8.9.0 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


feat(website): automatically publish latest blog posts to website

#12277

In darkmode the author name should be pink.
I don't think the authors dictionary is such a good idea..

@Jaapiehetaapie thank you for working on this. Could you please resolve the conflits?

The author name should be pink.
I don't think the authors dictionary is such a good idea..

Lets remove the author's name and avatar.

The other dependicies are needed for my code. Is their a way to resolve these confilcts?

Sorry for the mess. I'm not sure how to resolve the conflicts.

The deployed preview doesn't show blogs fetched successfully! @Jaapiehetaapie

Thank you for resolving the conflicts, @Jaapiehetaapie. I wonder if you can also display the blog entries as placeholders while the content is being fetched. Otherwise, during the loading period, that section looks wierd.
See https://jamesinkala.com/blog/make-animated-content-placeholders-with-html-and-css/

I added the loading animation. The only problem there is right now is that i am using https://proxy.cors.sh/ to fetch the mirror site for the images. I'm am doing this to avoid CORS errors. I was wondering i someone knows a more robust fix for this?

I added the loading animation. The only problem there is right now is that i am using https://proxy.cors.sh/ to fetch the mirror site for the images. I'm am doing this to avoid CORS errors. I was wondering i someone knows a more robust fix for this? When fetching the post data from the arweave API i get an imgURI aswell, but i dont know where this points to, maybe that can help.

Does this article help?
https://dev.mirror.xyz/GjssNdA6XK7VYynkvwDem3KYwPACSU9nDWpR5rei3hw

I added the loading animation. The only problem there is right now is that i am using https://proxy.cors.sh/ to fetch the mirror site for the images. I'm am doing this to avoid CORS errors. I was wondering i someone knows a more robust fix for this? When fetching the post data from the arweave API i get an imgURI aswell, but i dont know where this points to, maybe that can help.

Does this article help?
https://dev.mirror.xyz/GjssNdA6XK7VYynkvwDem3KYwPACSU9nDWpR5rei3hw

Yeah, I used this to get most of the post data. This data also includes a ImgURI but I don't know where that points to, or how to convert that imgURI to an url.

Maybe the people that's place the post know where the imgURI points to.

What's the URI look like?
The images on mirror.xyz are hosted at https://mirror-media.imgix.net, one example is:
https://mirror-media.imgix.net/publication-images/5Ed-TXJIB3LTC2HJdPuEN.png?height=512&width=1024&h=512&w=1024&auto=compress

This is an example of the imgURI : QmeN9jeFWF4TnH6L9xCHPmvkodbWc83ex2yxvHzpvsfSmT

one idea i'm thinking which could be simpler is like this (not sure if the arweave graphql API exposes this)

query for all of the posts made by the taiko labs mirror account on ARWeave (fetch), and get the content ID
for each of these, take the 3 most recent, then we can use the open graph metadata to render the image title and short description.

if this is simpler, i think we should do this instead and we can drop the reading time, author, etc. and the additional dependencies. whatever is exposed by the open graph metadata (like if you just share a mirror link), i think should be sufficient for this preview.
let me know if you need any help on it, or what you think of this idea.

I see that you managed to get the images now, well done! Also nice getReadingTime solution

looks good, thanks @Jaapiehetaapie ! however I am not able to see the images on the preview deploy: https://website-k6ktlpx1o-taikoxyz.vercel.app/

do you know why?

Weird. It's working for me, can you maybe check the logs to see if there are any erros when fetching from ipfs.

Weird. It's working for me, can you maybe check the logs to see if there are any erros when fetching from ipfs.

here is the error. it won't resolve in my browser either, if i just navigate to it in a separate tab. is there another indexer we can use? does https://ipfs.io/ipfs/QmeN9jeFWF4TnH6L9xCHPmvkodbWc83ex2yxvHzpvsfSmT resolve for you? if i open it up in IPFS itself yes I can see it, just can't retrieve it from here.

Website  and ipfs are working for me

@Jaapiehetaapie there are some merge conflicts with package.json and pnpm-lock.yaml, i think because i updated the packages on main branch. could you please resolve them? if you need any help let me know. once again thank you so much for your effort!

I don't know how to resolve the last conflict, because arweave is needed for the scripts to work

I'm having problems resolving the conflict, does anyone know how to do this?

@dantaik i think you are queued to review this, this PR is quite old now.


SentencePiece Models for Chinese Models Missing?

It seems that the SPM model files are missing from the tar files for Chinese models.

For Chinese models, we use word piece model provided by Jacob as sentence piece get worse performance on reading comprehension tasks for Chinese.

For Chinese models, we use word piece model provided by Jacob as sentence piece get worse performance on reading comprehension tasks for Chinese.

hi, may you share the word piece model used in albert Chinese model? Thanks!

The vocab file is in the same folder with the model. For word piece, you only need the vocab file, not the model. You can skip the model part for the input.

@beamind I think it's mean that you have to use --vocab_file instead of --spm_model_file.
But @Danny-Google I encouter a problem when I do this change in run_squad_v1.py, when it goes to squad_utils.convert_examples_to_features, spm model must be used in tokenization.encode_pieces.
I'm not familiar with spm so i have no idea how to modify it currently.

@Danny-Google @beamind @penut85420 @0x0539
Are you able to solve it. I want to use albert chinese and I am using huggingface pipeline for sequence classification which gives error as spiece.model is missing?
We assumed '/home/transformers/albert_base_zh/' was a path or url to a directory containing vocabulary files named ['spiece.model'] but couldn't find such vocabulary files at this path or url.

@beamind Currently, Squad_utils is meant to be used only for squad dataset. If you use Chinese models, you may want to take a look at the clue code (https://github.com/CLUEbenchmark/CLUE/tree/master/baselines/models/albert).
@008karan The Chinese model use wordpiece and you want to disable the sentence piece part of the code.

@Danny-Google thanks! i will keep on researching.


cmd/compile: -m flag unexpectedly affects compilation output

I am currently working on some changes to the inliner for #15561, the current state of my work is https://go-review.googlesource.com/c/go/+/72490
While testing my changes, I noticed a very odd behavior, namely that code miscompiled when my inliner changes where triggered, was compiled correctly when passing the -m flag.
The following code is reduced reproducer from a failure observed in generateTrace from cmd/trace/trace.go

import (
	"fmt"
)

type elem struct {
	f uint64
}

func f() int {
	m := make(map[uint64]*elem)
	getOrCreate := func(g uint64) *elem {
		info, ok := m[g]
		if !ok {
			info = &elem{}
			m[g] = info
		}
		return info
	}
	getOrCreate(42)
	return len(m)
}

func main() {
	fmt.Println(f())
}

Diffing a disassembly of this program, compiled with - l -l and -l -l -m respectively, gives the following:
16c16
<   0x1091a6e<PHONE_NUMBER>		MOVQ AX, 0x20(SP)
---
>   0x1091a6e<PHONE_NUMBER>		MOVQ AX, 0x30(SP)
27c27
<   0x1091a9a		488b442420		MOVQ 0x20(SP), AX
---
>   0x1091a9a		488b442430		MOVQ 0x30(SP), AX
47c47
<   0x1091adf		488b4c2420		MOVQ 0x20(SP), CX
---
>   0x1091adf		488b4c2430		MOVQ 0x30(SP), CX

The only other reference to the 0x20(SP) slot is, in both cases, the return value of the mapaccess call inside the inlined closure body :
0x1091a8c             e86f7ff7ff              CALL runtime.mapaccess2_fast64(SB)
0x1091a91             0fb6442420              MOVZX 0x20(SP), AX

I realize that there is probably something wrong with my inliner changes. However, I'm submitting this bug nonetheless because I find it very surprising that the -m flag somehow fixes this issue, even though it should only affect compiler logs and not the resulting binary. This seems like it might be a latent issue in the compiler that would be worth fixing.
I have manually audited all locations that read Debug['m'] inside the compiler and didn't notice anything suspicious/side-effecty so I'm pretty stumped at this point and could use another pair of eyes.

\cc @randall77 @cherrymui

I cannot reproduce it, with both Go 1.9 and tip (006bc57095),  at least on darwin/amd64.
$ go1.9 build -gcflags="-l -l" -o x1 x.go
cherryyz-macbookair:tmp cherryyz$ go1.9 build -gcflags="-l -l -m" -o x2 x.go
# command-line-arguments
./x.go:13:17: can inline f.func1
./x.go:16:17: &elem literal escapes to heap
./x.go:12:11: f make(map[uint64]*elem) does not escape
./x.go:13:17: f func literal does not escape
./x.go:26:15: f() escapes to heap
./x.go:26:13: main ... argument does not escape
$ diff x1 x2
$ go-tip build -gcflags="-l -l" -o x1 x.go
$ go-tip build -gcflags="-l -l -m" -o x2 x.go
# command-line-arguments
./x.go:13:17: can inline f.func1
./x.go:16:17: &elem literal escapes to heap
./x.go:12:11: f make(map[uint64]*elem) does not escape
./x.go:13:17: f func literal does not escape
./x.go:26:15: f() escapes to heap
./x.go:26:13: main ... argument does not escape
$ diff x1 x2
$ go-tip version
go version devel +006bc57095 Sun Oct 22 15:50:50 2017 +0000 darwin/amd64

@huguesb, which version of Go, and what GOARCH/GOOS are you using?

@cherrymui  I'm on darwin/amd64. This issue is reliably reproducible with CL72490 applied on top of tip (006bc57095):
$ git fetch https://go.googlesource.com/go refs/changes/90/72490/2 && git cherry-pick FETCH_HEAD
$ ./make.bash
$ PATH=~/go/bin go run -gcflags='-l -l -m' closure.go
# command-line-arguments
./closure.go:14:17: can inline f.func1
./closure.go:23:13: inlining call to f.func1
./closure.go:12:11: make(map[uint64]*elem) escapes to heap
./closure.go:23:13: &elem literal escapes to heap
./closure.go:17:17: &elem literal escapes to heap
./closure.go:14:17: f func literal does not escape
./closure.go:29:15: f() escapes to heap
./closure.go:29:13: main ... argument does not escape
1
$ PATH=~/go/bin go run -gcflags='-l -l' closure.go
unexpected fault address 0xb01dfacedebac1e
fatal error: fault
[signal SIGSEGV: segmentation violation code=0x1 addr=0xb01dfacedebac1e pc=0x100898e]

goroutine 1 [running]:
runtime.throw(0x10c2c0c, 0x5)
	/Users/hugues/go/src/runtime/panic.go:616 +0x81 fp=0xc420045de8 sp=0xc420045dc8 pc=0x1026bc1
runtime.sigpanic()
	/Users/hugues/go/src/runtime/signal_unix.go:383 +0x200 fp=0xc420045e38 sp=0xc420045de8 pc=0x1039bd0
runtime.hashGrow(0x10a9480, 0xc420076100)
	/Users/hugues/go/src/runtime/hashmap.go:910 +0xfe fp=0xc420045e98 sp=0xc420045e38 pc=0x100898e
runtime.mapassign_fast64(0x10a9480, 0xc420076100, 0x2a, 0x1159c00)
	/Users/hugues/go/src/runtime/hashmap_fast.go:498 +0x181 fp=0xc420045ef0 sp=0xc420045e98 pc=0x100a4f1
main.f.func1(...)
	/Users/hugues/go/src/closure.go:18
main.f(0x10a1e00)
	/Users/hugues/go/src/closure.go:23 +0xc7 fp=0xc420045f30 sp=0xc420045ef0 pc=0x1091b07
main.main()
	/Users/hugues/go/src/closure.go:29 +0x22 fp=0xc420045f88 sp=0xc420045f30 pc=0x1091b72
runtime.main()
	/Users/hugues/go/src/runtime/proc.go:195 +0x200 fp=0xc420045fe0 sp=0xc420045f88 pc=0x1028200
runtime.goexit()
	/Users/hugues/go/src/runtime/asm_amd64.s:2374 +0x1 fp=0xc420045fe8 sp=0xc420045fe0 pc=0x104f291
exit status 2

Ok, it seems there is something racy here, which may or may not be related to your CL.
With your CL applied, I run go build -gcflags='-l -l' x.go in a loop, and see sporadic crashes of the compiler. Since Go 1.9 the compiler, if invoked by cmd/go, by default runs concurrently. But cmd/go disables concurrent compilation if -m is specified, so the race does not happen there.
Without concurrent compilation, it still generates identical binaries:
$ go tool compile -l -l -o x1.o x.go
$ go tool compile -l -l -m -o x2.o x.go
x.go:13:17: can inline f.func1
x.go:21:13: inlining call to f.func1
x.go:12:11: make(map[uint64]*elem) escapes to heap
x.go:21:13: &elem literal escapes to heap
x.go:16:17: &elem literal escapes to heap
x.go:13:17: f func literal does not escape
x.go:26:15: f() escapes to heap
x.go:26:13: main ... argument does not escape
$ diff x1.o x2.o

@josharian

@cherrymui thanks for taking a look, I did not think of concurrent compilation. Is there an easy way of building the compiler with the race detector enabled? The naive GO_GCFLAGS=-race ./make.bash doesn't seem to work

I'm actually not sure. I guess go install -race cmd/compile will build a  compiler with race detector enabled, and then you can test it by using it to build other programs.

I tried building a race-enabled compiler with go install -a -race cmd/compile (and same for cmd/go) but it did not make any observable difference. The issue is still reproducible and I'm not seeing any logs from the race detector when I use the newly built compiler to build other programs

I finally figured out the problem: there was a subtle bug in my change which resulted in references to captured variables inside the inlined body using the same node as inside the regular closure body, instead of being substituted with local temporaries in every inlined location. I'm guessing the SSA phase either modifies the AST in-place or uses AST nodes as map keys, which leads to the observed issue when the regular closure body and a function with the inlined closure are compiled concurrently. Is this documented somewhere?

I'm guessing the SSA phase either modifies the AST in-place

Yes, order and walk mutate the function's AST.

Is this documented somewhere?

Not sure. The general rule is the goroutine that's compiling a function has exclusive ownership over that function during concurrent compilation.
Some stuff is safe to inspect externally. For example, the ONAME Nodes representing the function name and parameters are safe for basic use, but these basically become read-only once the early analysis phases are done.

Yes, order and walk mutate the function's AST.

That's not the issue here though. Order and walk are not executed concurrently at this point, only the SSA phase is.

uses AST nodes as map keys

Yes, there are a few in cmd/compile/internal/gc/ssa.go.


addresses https://github.com/Openscapes/series/issues/16

@jules32 does this do "everything" you wanted it to do?
 I was expecting a GH Action for rendering but .gitignore did not set ignore json etc.
Also, thanks for reminding me of this issue I had opened 😆

Thanks @stefaniebutland , the content looks great - I will look into the GA and .gitignore because all those files shouldn't be there. I'll work on it locally and push when I figure it out.

deleting and pushing then rebuilding seems to have solved it; .quarto/ files were already in .gitignore


ollama tries to contact registry even when adding a local model

What is the issue?
I have a Modelfile which has a full path to the model I wish to load, however I get an error when running ollama create regarding an invalid certificate from registry.ollama.ai (see #3336)
For stability and privacy reasons, it would be best if ollama does not try to connect to external resources when creating models from the local filesystem.
What did you expect to see?
ollama create succeeds
Steps to reproduce
No response
Are there any recent changes that introduced the issue?
No response
OS
No response
Architecture
No response
Platform
No response
Ollama version
0.1.29
GPU
No response
GPU info
No response
CPU
No response
Other software
No response

This was pilot error, it seems


Getting Blank Map

Thank you so much for this plugin.  I have been using the js api for years, but have decided to make the switch to this plugin to support offline maps using downloaded local tiles.
I was hoping you could tell me what I am doing wrong.  I am running the master of the plugin.  Xcode 8.0, iOS 10.0.2, and cordova 6.3.1.
I have the background color option set to blue and I am getting a blue div.  Running map.showDialog() in the javascript console does produce the map with proper zoom and center.
Below is my initialization code...
var options = plugin.google.maps.Map.getMap({
          'backgroundColor': 'blue',
          'mapType': plugin.google.maps.MapTypeId.HYBRID,
          'controls': {
            'compass': true,
            'myLocationButton': false,
            'indoorPicker': true,
            'zoom': true
          },
          'gestures': {
            'scroll': true,
            'tilt': true,
            'rotate': true,
            'zoom': true
          },
          'camera': {
            'latLng': new plugin.google.maps.LatLng(params.googleLat, params.googleLon),
            'tilt': 30,
            'zoom': parseInt(params.googleZoom),
            'bearing': 50
          }
        });
        googleMap = plugin.google.maps.Map.getMap(document.getElementById("map_canvas"), options);
        googleMap.on(plugin.google.maps.event.MAP_READY, refreshGoogleMap);

When I run that code these are my Xcode logs:
2016-10-04 09:45:23.931861 AssessDamage[560:560920] FUNCTION = login()
2016-10-04 09:45:52.108033 AssessDamage[560:560920] $(window)  =====   0: 768X1024
2016-10-04 09:45:52.108257 AssessDamage[560:560920] avail  ======= 0: 768X1024
2016-10-04 09:45:52.108382 AssessDamage[560:560920] creating google map with zoom:8

When I run googleMap.showDialog()  after that this is my log:
2016-10-04 09:47:18.968298 AssessDamage[560:560920] THREAD WARNING: ['GoogleMaps'] took '30.750000' ms. Plugin should use a background thread.

Let me know if there is anything else you need.

First of all, you need to use the master branch version for iOS10.
$> cordova plugin add https://github.com/mapsplugin/cordova-plugin-googlemaps --variable ...

The backgroundColor property is for specifying the background color when you want to use the embed map mode.
The backgroundColor option does not work for map.showDialog()
And if you can see the Google Logo but no map, double check your API key.
https://github.com/mapsplugin/cordova-plugin-googlemaps/wiki/TroubleShooting:-Blank-Map

Thank you for the quick response...
-I think I am using the master branch..
cordova-plugin-googlemaps 1.3.9 "phonegap-googlemaps-plugin"
-showDialog() is working no blue background the map is correct.
-getMap with backgroundColor:blue shows a blue div no Google logo, no zoom controls, just all blue.

Did you install from npm or github branch?

github I believe..
cordova plugin add https://github.com/mapsplugin/cordova-plugin-googlemaps

I see. In that case, please check the background color of your HTML elements (, ,
 and the parent elements of the map div) are transparent using the chrome dev tool or safari dev tool.

Debugging iOS PhoneGap Apps with Safari's Web Inspector
http://phonegap-tips.com/articles/debugging-ios-phonegap-apps-with-safaris-web-inspector.html
Remote Debugging Android Devices
https://developers.google.com/web/tools/chrome-devtools/remote-debugging/?utm_source=dcc&utm_medium=redirect&utm_campaign=2016q3

Body, map_page div, map_content div, and map_canvas div all show the grey checker board and rgba (0, 0, 0, 0)

Thank you for inspecting.
Um, I see... Please try the below code in the MAP_READY callback.
document.body.style.backgroundColor = "rgba(0,0,0,0)";
document.body.style.display='none';
document.body.offsetHeight;
document.body.style.display='';

As far as I tested on iOS10, the UIWebKit does not redraw the background sometimes.
The plugin does that automatically, but if it does not work, you need to redraw the background mandatory.
http://stackoverflow.com/a/21947628/697856

I added the code to the MAP_READY callback function.  The map div is blank no google logo.  Let me know if there is anything else I can provide you.

I see. Could you try with very simple code?
Create a new project, then install the plugin from github.
Then write the below code into the index.html.
<!DOCTYPE html>

    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1">

PhoneGap-GoogleMaps-Plugin

    <button id="button">Full Screen</button>

Will do.  In the meantime I put breakpoints in GoogleMaps.m  One the first line of each function pageDidLoad, getMap, setDiv, and resizeMap.  The only breakpoint it stopped at was the pageDidLoad function.  Not sure if that helps.

I see. In that case, please confirm JS errors using safari debugger.
Open safari debug tool, then inspect the simulator/your device, then reload the HTML file using the debugger.

Simple project works.  Looking for js errors in existing project.

There was a js error I just had introduced trying to simple my project down so I could better test.  I fixed the js error.  Now the getMap function gets called twice.  The second time shouldLoad = NO after running through this.
BOOL shouldLoad = YES;
if ([_delegate respondsToSelector:@selector(webView:shouldStartLoadWithRequest:navigationType:)]) {
    shouldLoad = [_delegate webView:webView shouldStartLoadWithRequest:request navigationType:navigationType];
}

Do I have to have the WKWebView plugin installed for the master branch of this plugin to work?

no

The plugin js code does not call getMap() twice internally. Please double check your js code.

ok will do. Thanks

I copy and pasted the following into the safari javascript console.  And getMap breakpoint was still hit twice...
var options = plugin.google.maps.Map.getMap({
//'backgroundColor': 'blue',
'mapType': plugin.google.maps.MapTypeId.HYBRID,
'controls': {
'compass': true,
'myLocationButton': false,
'indoorPicker': true,
'zoom': true
},
'gestures': {
'scroll': true,
'tilt': true,
'rotate': true,
'zoom': true
},
'camera': {
'latLng': new plugin.google.maps.LatLng(params.googleLat, params.googleLon),
'tilt': 30,
'zoom': parseInt(params.googleZoom),
'bearing': 50
}
});
googleMap = plugin.google.maps.Map.getMap(document.getElementById("map_canvas"), options);
googleMap.on(plugin.google.maps.event.MAP_READY, refreshGoogleMap);

The first time it hits the if (self.mapCtrl) and goes into that if and hits the return.
The second time it goes into the else of that if (self.mapCtrl) .

Ok we are good.  Can't believe I didn't see that!  Thanks for your help and your patience.

in ionic 2:
ionViewDidEnter(){
this.map = new GoogleMap('map', options);
}

and after initializing the map, it should be removed click-block-enabled
const elem = document.getElementsByClassName('click-block-enabled')[0];
                    elem.parentNode.removeChild(elem);


Stack-overflow link

I want to add my stack overflow link  in [params.social] .
Does it support ?

It does now... https://github.com/shenoybr/hugo-goa/commit/3bab75b6da63a30076a2cb2f4ccd017de9b0d0bb


Percentage displayed as Infinity in Slow Endpoint insight

Note: Infinity literal appears due to JS limitations to work with large numbers (greater than Number.MAX_VALUE = 1.7976931348623157e+308)

Closed by https://github.com/digma-ai/digma-collector-backend/issues/1517


Upgrade poison version

Update an example Phoenix app
Upgrade Poison library to the v2.1.0 in order to use with some app that required Poison > 2.0.0

:tada: :tada: :tada:


feat: add RFC about external data

Description of how we could potentially handle external data sources in Renku.

This RFC contains many details about implementation, but I still am finding it difficult to imagine how it would be used in practice.
As someone who uses AWS S3, it would be really great to have something like:
renku dataset add --name [name of the dataset] --external s3://[bucket]/[path]

What I would expect this to do is to:

create a dataset
if the path is to a file, the dataset contains just the file; if the path ends in a /, the dataset contains, recursively, everything below and including the path
If I have the aws cli set up, the command should do an aws s3 cp [--recursive] [s3-url] to get the contents into my project

A nice extension would be the following:
renku dataset add --name [name of the dataset] --external s3://[bucket]/[path] --local-path [some location where the contents should be stored]

When I work with s3, the contents there are often very large, and I do not want my local file system. In those cases, I would put them on an external disk or NAS, or, I guess, FUSE-mount the contents as a new volume. But, I would like to have all of those options and as a user be able to decide if I want the S3 content brought in to: a folder of the project, an external volume, or FUSE-mounted volume

Thanks @ciyer - yes, this last one was exactly what I had in mind as the default. But maybe there are use-cases where copying data into the project and using git-LFS from there (as is done now for e.g. grabbing data from zenodo) would still be desired?
imo the --external flag is not needed because we can guess that from the URL.

One more clarification - the reason I thought we might need a new command such as stage is because the local path to that fuse-mounted S3 bucket might be different from system to system. I can imagine we'll need a way to manage/query that, which requires new functionality and interface.

When I use s3, I do it in one of two ways:
Amount of data is small

write a script to fetch the data and store it in a subfolder of the project
add the script to git
add the subfolder to gitignore

This way, if I clone the project to a new computer, I can easily retrieve the data again. I do not add the files to LFS (or, in my annex) because I can always retrieve them again if necessary, and I trust them to be available from S3 at a future data.
Amount of data is large

write a script to fetch the data and store it on an external drive
add the script to git
write scripts that reference the external drive and reduce the data to a manageable size
add those scripts to git
if the reduced data is very small, I will add it to git as well, if it is too large, I will put it in a gitignored subfolder

In this case, if I clone the project to a new computer, I either have the reduced data that I need for day-to-day work available, or, I plug in the external drive and re-run the scripts to re-compute the reduced data.

@ciyer so I think what I proposed would basically replace the need to write one-off scripts for managing the data in S3, in the way that you have described.

One more thing I wanted to add is that using the cli in a csi driver written specifically for Renku would allow us to use the same code for mounting stuff locally and in k8s. The go code from the csi driver would call the renku cli to mount stuff.
I have been trying to write a simple csi driver for mounting s3 buckets with s3 fuse (mostly on the side) I just have not had time to finish this.
With a csi driver we get a storage class (for example renku-storage) and then we can create a PVC (that uses said storage class) that will result in a s3 bucket, database or whatever the cli supports being mounted in a session. So if we write our own csi driver we would not have to use a privileged sidecar to run the renku cli and mount stuff in a session in k8s.

One more thing I wanted to add is that using the cli in a csi driver written specifically for Renku would allow us to use the same code for mounting stuff locally and in k8s. The go code from the csi driver would call the renku cli to mount stuff.

I wanted to ask you about this! I imagined it could work the way that you describe but I wasn't sure. The potential benefit of a sidecar is that we could (I think) make it mount volumes dynamically... whereas with the PVC we would always need to recreate the pod.

The potential benefit of a sidecar is that we could (I think) make it mount volumes dynamically

That is true. It is worth asking then the BIT how much of a problem such a feature will be. They want to limit the number of stuff that runs as root. And I think that this would require root / elevated permissions.
I can send them a message just to get a sense.

Root is not necessary, but the container will need to be run with elevated privileges afaik.

I had some manifests to test mounting stuff from a container sidecar. I can dig them up and confirm exactly what security context is needed to run this. It would be good to know and have this yaml snippet.

Does this RFC intend to support reading and writing to external data systems, or only reading?

So far it was talking about sources specifically. Not sure if we should include writing as well...

So far it was talking about sources specifically. Not sure if we should include writing as well...

I added a third user story for a researcher project use case, which motivates the need to write to the data system as well. I think the use cases that only need read-access are fairly limited.

I think the use cases that only need read-access are fairly limited.

That probably depends on the domain. There are plenty of cases where large raw data needs to be made accessible but downstream data products will be stored separately and be much smaller in size.

use data from remote storage as-is by remote-mounting it and remembering the source in renku metadata. This should support reading and writing.
use external storage as a source/sink but make local copies to speed up access for iterative calculations. In principle, this should also support reading and writing.

I think this would work. 👍 Having local copies (2) is necessary to support use outside renkulab, though I think that just reading in that case is an acceptable limitation.

Why do you say it's necessary to make local copies to use it outside of renkulab? We should be able to do mounts also on at least macos and linux systems.

@rokroskar I think clarifying the 2 use cases is helpful, thank you! To summarize Use Case 1:

User can read and write to a mounted external file source (with expected network performance penalties)
User will be able to view metadata for data that came from an external file source: url, perhaps s3 bucket name...
User will be able to run renku run/update/rerun as with local data sources, where the data in the external file source is pulled/checked for updates, likely with network performance penalties (is this right?)

And I second your question to @ciyer about why (2) is necessary for outside renkulab/renku session?

Good point -- if you make the assumption that FUSE is available on the user's machine, then you could enable access to S3 with just use-case 1, but that would not cover my use case detailed above.
I need to be certain that I can access the data even if I am not connected to the internet or if the bucket owner fails to pay their AWS bill, rendering the S3 bucket inaccessible ;) . I have not looked into the the details of how the FUSE/S3 file system is implemented, but I suspect that the data would not be accessible in those cases, and in any case, I like the security of knowing that I have a straightforward local copy of the data.

@ciyer yes, I think what you describe is covered by my use-case 2

@rokroskar Is this an accurate description of the different modes of data access we have to consider, and the current suggestions/contenders?

I have ... via a ...
small data
big data

renkulab session
mount (FUSE)
mount (FUSE)

local session
copy OR install FUSE
access remote programmatically OR install FUSE

Apologies @lokijuhy @ciyer @Panaetius and @olevski but I reworked significant sections of this based on feedback and discussions we had over the past few days. Most importantly, it seems to me that copy as default makes the most sense and will lead to least friction. otoh we might also want to support some way of simple designating some external data as being used but never actually copying or mounting it (this is what "Mode 3: reference" refers to). Thanks for all the comments and feedback so far, I think it's slowly becoming clearer.

@lokijuhy @ciyer @Panaetius @mohammad-sdsc @olevski I believe I've addressed all the comments and concerns that have come up during the various discussions. It would be great if we can finalize this (for now) and start to think about next steps.


Restic hang in check

Output of restic version
debug enabled
restic 0.9.2 (v0.9.2-110-g6bc99ce4) compiled with go1.10.3 on linux/amd64

How did you run restic exactly?
RESTIC_PASSWORD_FILE=/etc/restic/restic_pwd.txt
RESTIC_REPOSITORY=sftp:backup:/ovh-backup/vanaheim/restic/myhost
# ./restic check --cleanup-cache

What backend/server/service did you use to store the repository?
SFTP
Expected behavior
Ending of check command without error :-)
Actual behavior
debug enabled
using temporary cache in /tmp/restic-check-cache-631445418
repository 802cfbf3 opened successfully, password is correct
created new cache in /tmp/restic-check-cache-631445418
create exclusive lock for repository
load indexes
check all packs
check snapshots, trees and blobs
Processus arrêté

Steps to reproduce the behavior
GSOC=10 ./restic check --cleanup-cache
Do you have any idea what may have caused this?
I have been using Restic Backup for a few months on several machines and everything is working fine except for one, or the 'check' operation will fail. I suspected a moment memory pb because its use increases with the progress of the 'check'. So I added the intruction 'GSOC = 10' before the execution of the command but that did not solve the pb, and the reading of the logs does not look in this direction.
The only difference with other machines is the contents of the backup, which is not indicated by the '--files-from' parameter but by '--one-file-system'.
I generated the log file with the command:
GSOC=10 DEBUG_FILES = * ./restic check --cleanup-cache 2> ../debug_check.log
but the file is very big, i put a link : https://mon-partage.fr/f/9uNTqvHO/
Do you have an idea how to solve the issue?
No
Did restic help you or made you happy in any way?
Normaly yes :-)

Hi,
So I do not really know what happened, but a re-creation of the repository solved the question. I closed the issue.
Regards

Hm, interesting. What is GSOC=10? Do you maybe mean GOGC=10 to make the garbage collector more aggressive so that restic uses less memory?
I think restic was still at work, this step in the check process unfortunately has no progress output (yet). Did you see any network traffic?

Hm, interesting. What is GSOC=10? Do you maybe mean GOGC=10 to make the garbage collector more aggressive so that restic uses less memory?

yes, a mispelling

I think restic was still at work, this step in the check process unfortunately has no progress output (yet). Did you see any network traffic?

I did not check if there was network traffic, but it seems to me that the process is stopped.
Today the 'crash' is reproduced (with 8 snapshots in the repo), so I'll be able to check that (tomorrow)

I'm not sure what happens here, but I just had another look at the log file:
sftp/sftp.go:77 sftp.startClient.func2  13  ssh command exited, err signal: killed

This is odd.
In addition, I don't know what the last line in your output means, I've never seen this error before:
Processus arrêté

I can translate that (with the remains of the bit of French I learned in school) as "Process stopped", that seems to be a message from your shell. It's surely not something restic prints...
You mentioned a 'crash', what you do mean by that? A stack trace?

Hm, interesting.

Ok, still no idea. The "err signal: killed" means the OS (Linux) has killed the SSH process, which is different from when a timeout or network interruption occurs. Usually, there's an entry in the kernel log about it...
I'll close this for now, please let us know when it occurs again, and please feel free to add further comments. Thanks!

Hi
I know a little more now, and my initial idea was the good one. It is a memory consumption pb, Restic is executed in a container and the hypervisor kills it because it consumes too much memory.
My question then becomes, how to limit memory usage when Restic run a check?

You can't. I haven't found the cause yet, but it feels to me restic uses too much memory in some circumstances. You can try making the Go runtime garbage collector a lot more aggressive by setting GOGC=20 (or even 10), but that's about it for now. Did you try with the corrected environment variable yet?


What is the format for 'parameters'

Im trying this but dont show like the example.
In the controller
  $searchParams= ["value", "id"];

In my view
<nit-advanced-searchbox
    ng-model="searchModel"
    parameters="searchParams"
    placeholder="Search...">
</nit-advanced-searchbox>

I got this

availableSearchParams: [
{ key: "MMM", name: "ZZZ", placeholder: "VVV... "},
{ key: "MMM1", name: "ZZZ1", placeholder: "VVV1... "},
]

@hendrix85 is right, please take a look at the demo page:
Parameter declaration in controller:
https://github.com/dnauck/angular-advanced-searchbox/blob/gh-pages/index.html#L33
Directive declaration:
https://github.com/dnauck/angular-advanced-searchbox/blob/gh-pages/index.html#L80

Thanks!


Add heats-of-reaction directory that contains the jupyter notebook & supporting files

Add heats-of-reaction directory that contains the jupyter notebook used to calculate heats of reaction and required input files, heats-25C.csv which is produced by running the jupyter notebook, and nasa-polynomial-doc.pdf which details calculations using nasa polynomial coefficients.

Looks like you included the checkpoints file which typically isn't put into version control. Please remove it from the pull request.

Also, make sure you have a .gitignore file on your computer. You can set it up globally on your computer so it works with all your repositories. See here for more info about the ignore file. And this site is handy for creating such files.

Thanks Gavin! That site is great, I will be using that for my future projects now. I added the .gitignore and removed the .ipynb_checkpoints file. Let me know if there's anything else you'd like me to fix!

@megcrow I merged everything into the master branch. Notice that I moved the gitignore file into the root directory so it will apply to the whole repository. I also added some items to the ignore file. You can pull down the latest changes to your master branch and you'll be good to go. Thank you for the contribution. 👍


Feature: destroyDOM callback

It'll be great to have a controllable callback for destroying DOM that's been generated by the node. It'd be useful for removing event listeners and removing the DOM nodes from some kind of maps and caches. I'm working on some tooltip that should be shown when a DOM node is hovered and for now don't have an idea how to unsubscribe an event handler correctly.

Can you use a mutation listener for this?
https://lexical.dev/docs/concepts/listeners#registermutationlistener
const removeMutationListener = editor.registerMutationListener(
  MyCustomNode,
  (mutatedNodes) => {
    // mutatedNodes is a Map where each key is the NodeKey, and the value is the state of mutation.
    for (let [nodeKey, mutation] of mutatedNodes) {
      if (mutation === "destroyed") {
        const dom = editor.getElementByKey(nodeKey);
        // do whatever
      }
    }
  },
);

Yeah, I've already used this way as a workaround, but I had to implement and maintain the plugin instead of just using the node. Moreover, mutation listeners aren't executed during the editor unmounting, so I had to collect all DOM elements in some special array, that is used for removing listeners to avoid memory leaks. I have to keep the array relevant throughout the entire life cycle of the editor. And how knows, maybe I missed some more pitfalls

Yeah, I've already used this way as a workaround, but I had to implement and maintain the plugin instead of just using the node. Moreover, mutation listeners aren't executed during the editor unmounting, so I had to collect all DOM elements in some special array, that is used for removing listeners to avoid memory leaks. I have to keep the array relevant throughout the entire life cycle of the editor. And how knows, maybe I missed some more pitfalls

I don't think you need to worry about explicitly cleaning up those listeners. The runtime GC should get those for your once the underlying DOM Nodes are dereferenced.

As @acywatson already explained, the reason Lexical doesn't need this method is because cleanup is handled for you in almost all cases by the GC working as expected with unreferenced DOM nodes. Closing as I don't see the need for more code in core around this, but feel free to re-open if you feel this discussion needs more nuance.


Enclosures does not contain all media content

I have been using MWFeedParser for quite some time and at this point, it does not parse all media content associated with the feed. In my case, if there is media attached, it only parses the first item. Any reason for this or quick fix?

Any news on this issue?

No, none yet.

how to parse image in this framework ?