New command: realpath

Resolves #93
Closes #92
Checklist

[x] I have made a change to this repository, be it functionality, testing, documentation, spelling, or grammar.
[x] I updated my branch with the master branch.
[x] I have added the necessary testing to prove my fix is effective/my feature works (or I did not modify functionality).
[x] I have added necessary documentation about the functionality in an appropriate .md file.
[x] I have appropriately commented any code I have modified

Short description of what this PR does:

A new command realpath is added to echo the path to the a note by the name provided.
If no note was provided, realpath would echo $NOTES_DIRECTORY.
If a note which does not exist was provided, realpath would echo the future path to that file.
As a consequence, A user can run cd "$(notes realpath)" to cd into $NOTES_DIRECTORY.

I have an issue by running a particular test case. If you have have a look at my test case here, it runs indefinitely. Funny enough, a Ctrl+C (SIGINT) does not stop the test case; force quitting the terminal is the only option. However, the other test cases work. Can someone please guide why this error occurs and how to fix it?

I have an issue by running a particular test case. If you have have a look at my test case here, it runs indefinitely.

You're not overriding EDITOR anywhere in the test case, so the notes new in that test is actually opening up your real editor somewhere, and blocking while until that exits.
You can use something like export EDITOR=touch to skip that, as in some of the other similar tests.
I think that's the only changed required here though, otherwise this all looks good to me! Very clean. If you patch that up and check it works, I'll merge this 👍

Thanks for your help. The test cases pass successfully now.

Perfect, thanks! :+1:


fix the generate_trie command parameter

The original file was changed into vocab.txt

Thanks a lot for the PR!
Can you please sign-off your commit (with git commit --amend -s for the existing commit)?

Thank you for fixing the issue!


Disable the Skia to Fuchsia Autoroller.

Currently, there are two auto-rollers that roll Skia in the Fuchsia and Flutter buildroots respectively. Consequently, the Flutter engine has to be compatible with two versions of Skia. Since this is not always possible, the version of Skia used by Fuchsia should be tied to the one referenced in DEPS file in the Flutter engine buildroot.
The side effect of this and the adherence to the "one version" dictum enforced in the Fuchsia buildroot is that existing targets in Fuchsia will be tied to the Skia version used by the Flutter. Such targets don't seem to be particularly common or complex but this may not be the case in the future.

Thanks, the link to the rollers in the wiki was old. Updated.

@rmistry: I think we are ready now. However, I am not able to disable the roller because of the following error "Failed to change the mode: [object Object]". Can you disable / help me troubleshoot the same please? Once the roller is disabled, I can reconcile the Skia version in Fuchsia with the one currently used by Flutter. Once that is settled, we can remove the roller completely.

Thanks to @rmistry for the troubleshooting. The roller has been disabled. Reconciling the changes in Fuchsia.

@chinmaygarde : Should I go ahead and delete the Skia->Fuchsia roller?

Can we wait till at least one roll has been completed into Fuchsia manually?

Sure, no rush. I am OOO tomorrow so will probably do it on Monday (once I get confirmation).

We are rolling manually into Fuchsia now and the latest roll has landed. Please delete the roller when able. Thanks.

Deleted the roller, Thanks.


Fixed the input and output utilities

After this PR, the input fields will work properly again and no errors will be swallowed.

Any reason why error() doesn't just output the message? Wrapping all occurrences of error() with console.error() isn't very DRY.

@Qix- @rauchg said it's very important that a function only does as less as possible (like composing a string) - he criticized that on Now Desktop as well, so I converted it into log statements that are logging a string that was composed by a function.
The statements you in the code here were written by him before, so I just extended that.

I just worry that someone is going to mistake error() for actually outputting an error message, thus running the risk of an error message silently being ignored.

@Qix- @leo we moved away from having output utilities to console.log because having side effects like that makes it very hard (if not impossible) to perform nested calls like this:
console.log(info(
  `AWS credentials found in ${param(AWS_CREDENTIALS_FILE_PATH)}.`,
  `  Would you like to use them?`
))

@matheuss but in that case, console.log wouldn't be necessary? I'm not following that specific logic.
I agree with the sentiment, but I don't necessarily like the non-DRY-ness of it all - especially since, as I mentioned before, it'd be easy for someone to forget a logging statement and accidentally hide an error message because they didn't know to output to the console.
We see this kind of problem frequently over at Chalk (where people don't realize they need to console.log() the result of chalk calls).


fix: openssl location on new installation

When running the build.sh script I noticed that, by default, brew doesn't install the openssl library on the OPENSSL_DIR default value and it was not working for me.
This PR changes the openssl configuration section of this script.
First, it looks up for an openssl installation and, if not found, tells the user to install it.
Second, it attempts to guess the openssl directory, in a certain order, using:

the current default value (to avoid breaking stuff that was working)
the directory where openssl now gets installed when using brew (fix for new people getting on-boarded)
the directory where openssl gets installed if the user used port instead

Also, changed which to command based on stackoverflow > How can I check if a program exists from a Bash script?.
Testing
I managed to used the build.sh script successfully on my M1 mac laptop with the changes I'm proposing.
$ grep OPENSSL_DIR 202206_*
202206_brew.log:OPENSSL_DIR=/opt/homebrew/opt/openssl@3
202206_macports.log:OPENSSL_DIR=/opt/local/libexec/openssl3

$ tail -n 1 202206_*
==> 202206_brew.log <==
Build completed successfully in 0:04:58

==> 202206_macports.log <==
Build completed successfully in 0:04:55

Complete builds logs:

202206_brew.log
202206_macports.log

disclaimer: I have no clue on the labels I should use or where. hopefully, this is useful but if it's not just let me know.

This is great, thanks! It wouldn't surprise me if this fixes #22.

if it doesn't, it could be the next roadblock. 😄


Importing geoviews breaks show_grid=True for matplotlib backend in holoviews

Importing geoviews breaks usage of show_grid=True for matplotlib backend in holoviews even when not using geoviews at all with the following error:
AttributeError: 'AxesSubplot' object has no attribute 'gridlines'

See minimal working example here for the full stacktrace: https://anaconda.org/zertrin/2019-04-03-holoview-reproduce-show_grid-bug/notebook?version=2<IP_ADDRESS>1
Commenting out import geoviews as gv restarting and re-running the notebook works. Thus it seems related to Geoviews and I post the issue here. If it is a Holoview bug, this issue can be moved over there instead.

It seems to only error with overlays; this works
(hv.Curve([0, 1, 2]) + hv.Curve([4, 5, 6])).opts('Curve', show_grid=True)

but not (hv.Curve([0, 1, 2]) * hv.Curve([4, 5, 6])).opts(show_grid=True)

I believe this was fixed in #308


Cannot make the SvelteKit default demo application to run on firebase: timeout when POSTing a new todo

Describe the bug
After creating a new SvelteKit project with the default demo app, intialized and firebase (firebase init) and installed the svelte-adapter-firebase, the ssrServer functions dies with a timeout error on the logs.
To Reproduce
Create a new SvelteKit Application,
npm init svelte@next adapter-error`
cd adapter-error
npm install

Choose SvelteKit demo app and leave all the other options by default
Go to firebase console and create a new project (https://console.firebase.google.com/), unselect google analytics
Add a web app adapter-error-app
Install firebase-tools
npm install -g<EMAIL_ADDRESS>

Got a nasty error using the lastest version<EMAIL_ADDRESS>
firebase init

choose functions and hosting
use an existing project, and choose the one you created before
accept all options by default

Note: check that the node version in function/package.json is 14

install the adapter:
npm install --save-dev svelte-adapter-firebase

update svelte.config.js
import firebase from "svelte-adapter-firebase";

/** @type {import('@sveltejs/kit').Config} */
export default {
  kit: {
    adapter: firebase(),
    target: "#svelte",
  },
};

update package.json
	"scripts": {
		"dev": "svelte-kit dev",
		"build": "npx rimraf myApp && svelte-kit build --verbose"
  }

update firebase.json
{
  "hosting": {
    "public": "myApp",
    "ignore": [
      "firebase.json",
      "**/.*",
      "**/node_modules/**"
    ],
    "rewrites": [
      {
        "source": "**",
        "function": "ssrServer"
      }
    ],
    "predeploy": ["npm run build"]
  },
  "functions": {
    "source": "functions"
  }
}

Deploy your app
firebase deploy

Follow the message on the terminal and add the following code to functions/index.js
  let ssrServerServer;
  exports.ssrServer = functions.https.onRequest(async (request, response) => {
        if (!ssrServerServer) {
                functions.logger.info("Initializing SvelteKit SSR Handler");
                ssrServerServer = require("./ssrServer/index").default;
                functions.logger.info("SvelteKit SSR Handler initialised!");
        }
        functions.logger.info("Requested resource: " + request.originalUrl);
        return ssrServerServer(request, response);
  });

Remember to change your plan to Blaze (pay-as-you-go)
Deploy your app
firebase deploy

I'll finish it later, sorry!

Expected behavior

Screenshots

Additional context

This is related to #87


Remove hover effect in checkboxes

When hovered, the checkboxes grow in size. They shouldn't. The scale of the element should remain the same. Only the color should change on hover.

Here is the current situation, which applies to all controls:
{
    // Expand hovered and active button frames:
    egui_style.visuals.widgets.hovered.expansion = 2.0;
    egui_style.visuals.widgets.active.expansion = 2.0;
    egui_style.visuals.widgets.open.expansion = 2.0;
}

Setting hovered.expansion to 0 removes the scaling on hover.
Questions:

Should the scaling be removed on click as well (active.expension = 0.0? I would say this is not necessary as there is already some click feedback with thickening of the white check mark.
How about open.expension? It refers buttons dropdown menu, see 2nd video.
Since this is a rather global setting, do we expect undesirable side-effects (e.g. other types of widgets would should scale on hover and/or activation)?

This is with both hovered and active set to 0.0:
https://github.com/rerun-io/rerun/assets/49431240/9ffef4a1-30c5-4801-a8e8-f2478e6e3ce9
Effect of open.expansion = 2.0 (current situation):
https://github.com/rerun-io/rerun/assets/49431240/9ae1b454-c5ff-4da0-8d3b-d3b030da779f

I think scaling is a disorienting pattern. I think we should remove it across the app. Colors + hover cursor should be enough to signify interactivity. So, I think we should remove scaling from any interactive elements for now.
If we remove it, we will spot where states are missing and then we can fix that upstream in the design system 🙂

#2796 reverted by #2824


sbcl: Increase default heap size to 3GB.

Things done

Built on platform(s)

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

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

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] Tested, as applicable:

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

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

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

[ ] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

After taking all views into account, I believe that the best move is to close the PR. Thanks.

Thanks for your PR though, and maybe it helps to know I constantly run into the 1GiB heap limit as well. Allowing for controlling the heap size through a setup hook has been on my todo list for ages so I completely empathize.
If you manage to convince upstream SBCL to change the default you have my +1.

For the record: SBCL from Nix can now have its memory controlled using an envvar:
$ sbcl --script <<<'(format T "~A~%" (sb-kernel::dynamic-space-size))'
1073741824
$ NIX_SBCL_DYNAMIC_SPACE_SIZE=3gb sbcl --script <<<'(format T "~A~%" (sb-kernel::dynamic-space-size))'
3221225472


Update balena.yml to new format

Change-type: patch
Signed-off-by: Chris Crocker-White<EMAIL_ADDRESS>

@balena-ci I self-certify!


Samples for GetOfferDetail get incorrect response

in https://github.com/PartnerCenterSamples/Partner-Center-Java-SDK/blob/master/Samples/src/main/java/com/microsoft/store/partnercenter/samples/offers/GetOfferDetails.java
line 44
Offer offer = partnerOperations.getOffers().byCountry( countryCode ).byId( "8AA7E78B-B265-4AC6-ADA0-14900A8A3F94" ).get();
a constant value 8AA7E78B-B265-4AC6-ADA0-14900A8A3F94 be used as a parameter for getOffers().byId(), need declare a private variables offerId get input as the parameter for getOffers().byId()
i write code as below,it's work well
String countryCode =
this.getContext().getConsoleHelper().readNonEmptyString( "Enter the 2 digit country code to get its supported offers",
"The country code can't be empty" );
String offerId =  	this.getContext().getConsoleHelper().readNonEmptyString("Enter offerId to get its supported offer detail",
"The offerId can't be empty" );
 this.getContext().getConsoleHelper().startProgress( MessageFormat.format( "Getting offers for {0}",
                                                                           countryCode ) );
 Offer offer = partnerOperations.getOffers().byCountry( countryCode ).byId(offerId).get();

pls help to fix it!

Hi @Ruodong, this issue has been resolved with the latest update. Please let us know if you have any other issues.


Shift Codebase to NextJS: Project Page

Work with the nextjs branch. Do not disturb the master branch please
Footer and Navbar should be called dynamically (for now don't do anything about it. It is a part of another issue)

I want to work on this


ValueError: The provided bam files don't have enough reads mapped to TE loci

Example pipeline and files to process 10X Visium data
The following is the processing of Visium_Souse-Olfactory_Sulb_possorted_genome_mam.bam data:

#Run get_cb.py to extract all cell barcodes from the bam file
#When it comes to your own data, you should change the directory of input bam file and output cell barcode file
!python get_cb.py

The barcodes obtained after using the above command are like the following:

CGATTTGTCATTAATG-1
GCAGCCTATATCACAT-1
TACACCGTCGTTAGTC-1
CTTAATCGACTTAGTA-1
...

Then I modified get_cb.py and got the barcodes again：

CGATTTGTCATTAATG
GCAGCCTATATCACAT
TACACCGTCGTTAGTC
CTTAATCGACTTAGTA
...

Afterwards, I ran the following code:

from MATES import bam_processor,data_processor,MATES_model,TE_quantifier
Step1: Generate coverage vector
bam_processor.split_count_10X_data('exclusive', '10X','sample_list.txt', 'path_to_bam.txt', 'path_to_cb.txt', bc_ind='CB', ref_path = 'TE_nooverlap.bed')

Step2: Generate the training and prediction sample
data_processor.calculate_UM_region('exclusive', '10X', 'sample_list.txt', bin_size=5, proportion=80, bc_path_file='path_to_cb.txt',cut_off=50)
data_processor.generate_training_sample('10X', 'sample_list.txt', bin_size=5, proportion=80,cut_off=50)
data_processor.generate_prediction_sample('exclusive','10X','sample_list.txt', bin_size=5, proportion=80, ref_path="TE_nooverlap.csv", bc_path_file='path_to_cb.txt',cut_off=50)
Step3:Training and prediction
MATES_model.train('10X', 'sample_list.txt', bin_size = 5, proportion = 80, BATCH_SIZE= 256,
AE_LR = 1e-4, MLP_LR = 1e-6, AE_EPOCHS = 2, MLP_EPOCHS = 2, DEVICE='cpu')
MATES_model.prediction('exclusive', '10X', 'sample_list.txt', bin_size = 5, proportion = 80,
AE_trained_epochs =2, MLP_trained_epochs=2,DEVICE='cpu')
##Step4: Quantify the TE
TE_quantifier.unique_TE_MTX('exclusive', '10X', 'sample_list.txt', 20, bc_path_file='path_to_cb.txt')
TE_quantifier.finalize_TE_MTX('10X', 'sample_list.txt')

Then the following result was obtained:

Unique matrix finished
uilding multi coverage vectors: 100%|██████████| 4992/4992 [00:00<00:00, 84351.43it/s]
Multi matrix finished
rocessing barcodes: 100%|██████████| 4992/4992 [00:00<00:00, 2063463.64it/s]
Directory MU_Stats created.
Start Calculating U/M region for cells in test_visium...
0%|          | 0/4992 [00:00<?, ?it/s]
Finish calculating U/M region for cells in test_visium, finalizing...
Finish finalizing U/M region information for test_visium.
enerating training samples: 100%|██████████| 1/1 [00:00<00:00, 20.31it/s]
Start generating training sample for unqiue read TE in test_visium...
Finish analyse generating sample for unqiue read TE in test_visium.
Start generating training sample for multi read TE in test_visium...
Finish analyse generating sample for multi read TE in test_visium.
Finish Sample test_visium
Directory MU_Stats created.
Generating prediction samples: 0it [00:00, ?it/s]
Start analyse full prediciton data of multi read...
100%|██████████| 4992/4992 [00:00<00:00, 95131.92it/s]
Generating prediction samples: 1it [00:02,  2.11s/it]
(0,)
(0,)
(2, 0)
(0,)
(3, 0)
(0,)
(4, 0)
(0,)
(5, 0)
(0,)
(6, 0)
(0,)
(7, 0)
(0,)
(8, 0)
(0,)
(9, 0)
Finish analyse full prediciton data of multi read.
Finish saving data for prediction.
Running on CPU.
Data Mode:  10X
AE Settings:  Epoch:      2, Learning Rate: 0.000100
MLP Settings: Epoch:      2, Learning Rate: 0.000001
Batch Size:    256
Searching Bin Size:      5
Dominate Proportion:     80
Loading training data for test_visium...

ValueError                                Traceback (most recent call last)
File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/MATES/scripts/train_model.py:384, in MATES_train(data_mode, file_name, bin_size, prop, BATCH_SIZE, AE_LR, MLP_LR, AE_EPOCHS, MLP_EPOCHS, DEVICE)
383 try:
--> 384     Batch_train = unique_TE_matrix.toarray().reshape(i,)
385 except:
ValueError: cannot reshape array of size 0 into shape (1,)
During handling of the above exception, another exception occurred:
ValueError                                Traceback (most recent call last)
Cell In[6], line 12
8 data_processor.generate_prediction_sample('exclusive','10X','sample_list.txt', bin_size=5, proportion=80, ref_path="TE_nooverlap.csv", bc_path_file='path_to_cb.txt',cut_off=50)
11 ## Step3:Training and prediction
---> 12 MATES_model.train('10X', 'sample_list.txt', bin_size = 5, proportion = 80, BATCH_SIZE= 256,
13                   AE_LR = 1e-4, MLP_LR = 1e-6, AE_EPOCHS = 2, MLP_EPOCHS = 2, DEVICE='cpu')
14 MATES_model.prediction('exclusive', '10X', 'sample_list.txt', bin_size = 5, proportion = 80,
15                        AE_trained_epochs =2, MLP_trained_epochs=2,DEVICE='cpu')
17 ##Step4: Quantify the TE
File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/MATES/MATES_model.py:16, in train(data_mode, sample_list_file, bin_size, proportion, BATCH_SIZE, AE_LR, MLP_LR, AE_EPOCHS, MLP_EPOCHS, DEVICE)
14         sample_name = [line.rstrip('\n') for line in sample_file]
15     for idx, sample in enumerate(sample_name):
---> 16         MATES_train(data_mode, sample, bin_size, proportion, BATCH_SIZE, AE_LR, MLP_LR,
17              AE_EPOCHS, MLP_EPOCHS, DEVICE)
19 elif data_mode == 'Smart_seq':
20     MATES_train(data_mode, sample_list_file, bin_size, proportion, BATCH_SIZE, AE_LR, MLP_LR,
21              AE_EPOCHS, MLP_EPOCHS, DEVICE)
File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/MATES/scripts/train_model.py:386, in MATES_train(data_mode, file_name, bin_size, prop, BATCH_SIZE, AE_LR, MLP_LR, AE_EPOCHS, MLP_EPOCHS, DEVICE)
384     Batch_train = unique_TE_matrix.toarray().reshape(i,)
385 except:
--> 386     raise ValueError("The provided bam files don't have enough reads mapped to TE loci.")
387 p3 = path + '/Multi_TE_train_'+BIN_SIZE + '' + PROP+'.npz'
388 p4 = path + '/Multi_Batch_train'+BIN_SIZE + '_' + PROP+'.npz'
ValueError: The provided bam files don't have enough reads mapped to TE loci.

May I ask if I should modify get_cb.py to obtain the barcode that appears to be correct?
If it should be modified, what is the reason for the above erroneous result?

Hello @DrmBee ,
Thank you for using MATES. If the barcode obtained by using get_cb.py is 'CGATTTGTCATTAATG-1', you should not change it to 'CGATTTGTCATTAATG'. Just use format like 'CGATTTGTCATTAATG-1' is correct.
Thanks,
Yumin

Hi! @Szym29 :
Thank you very much for your answer!
But if I continue to use the form 'CGATTTGTCATTAATG-1', it will report the following error:
[E::hts_open_format] Failed to open file "/home/jialu/ly/new/MATES/example/10X_visium_example/sub_bam_files/test_visium/multi/TAGCTCGCCTGATAAC-1.bam" : Too many open files

ummarizing reads statistics:   0%|          | 127902/45398537 [00:02<12:26, 60640.13it/s]
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
Cell In[10], line 3
      1 from MATES import bam_processor,data_processor,MATES_model,TE_quantifier
      2 ## Step1: Generate coverage vector
----> 3 bam_processor.split_count_10X_data('exclusive', '10X','sample_list.txt', 'path_to_bam.txt', 'path_to_cb.txt', bc_ind='CB', ref_path = 'TE_nooverlap.bed')
      5 ## Step2: Generate the training and prediction sample
      6 data_processor.calculate_UM_region('exclusive', '10X', 'sample_list.txt', bin_size=5, proportion=80, bc_path_file='path_to_cb.txt',cut_off=50)

File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/MATES/bam_processor.py:36, in split_count_10X_data(TE_mode, data_mode, sample_list_file, bam_path_file, bc_path_file, bc_ind, ref_path)

File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/MATES/scripts/split_count_10X.py:412, in start_split_count(barcode_field, path_to_bam, barcodes_file, sample, TE_mode, TE_ref_bed_path)

File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/MATES/scripts/split_count_10X.py:337, in generate_matrix(samp_bc, barcodes_file, path_to_bam, TE_ref_bed, coverage_stored_dir, tag_field)

File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/MATES/scripts/split_count_10X.py:31, in write_record_to_barcode(self, rec, barcode, option)

File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/MATES/scripts/split_count_10X.py:37, in _open_file_for_barcode(self, barcode, option)

File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/pysam/libcalignmentfile.pyx:751, in pysam.libcalignmentfile.AlignmentFile.__cinit__()

File ~/anaconda3/envs/mates_env/lib/python3.9/site-packages/pysam/libcalignmentfile.pyx:924, in pysam.libcalignmentfile.AlignmentFile._open()

OSError: [Errno 24] could not open alignment file `/home/jialu/ly/new/MATES/example/10X_visium_example/sub_bam_files/test_visium/multi/TAGCTCGCCTGATAAC-1.bam`: Too many open files

May I ask what error this is? Is it due to insufficient hardware performance?

Hi @DrmBee ,
This is an limit in the linux system. Ubuntu system has a default limit for the total number of files opening at the same time. If you are using ubuntu, check some solutions in stackoverflow.
In short, you can try ulimit -n 1000000 in the terminal before you run MATES. There are some other ways to permanently change this limit mentioned in the link.
Thanks,
Yumin

Hi! @Szym29 ：
Thank you very much for your friendly and accurate answer! I'm very sorry, I have another small question. In the example of Smart-seq2 Data, does the SRR3934350 output by the following command represent a cell data in human glioblastoma or a type of cell population data?
%%bash
echo -e 'sample_list_file:'
cat sample_list_subset.txt | head -n 5
echo -e '\n\nbam_path_file:'
cat bam_path_file_subset.txt | head -n 5

sample_list_file:
SRR3934350
SRR3934360
SRR3934371
SRR3934376
SRR3934387
bam_path_file:
../smart_seq/STAR_Solo_subset/SRR3934350/SRR3934350_Aligned.sortedByCoord.out.bam
../smart_seq/STAR_Solo_subset/SRR3934360/SRR3934360_Aligned.sortedByCoord.out.bam
../smart_seq/STAR_Solo_subset/SRR3934371/SRR3934371_Aligned.sortedByCoord.out.bam
../smart_seq/STAR_Solo_subset/SRR3934376/SRR3934376_Aligned.sortedByCoord.out.bam
../smart_seq/STAR_Solo_subset/SRR3934387/SRR3934387_Aligned.sortedByCoord.out.bam

Hi @DrmBee ,
One sample represent only one cell.
Thanks,
Yumin


Adding the ability to handle random IVs for security purposes

Opening a PR for initial review/feedback before submitting to the upstream

@joslynesser it's been a while, any thoughts of trying to get this submitted upstream?

@dangerp thanks for reminding me of this! I'll get this cleaned up, rebased, and get tests passing. :beer:


v2.0 roadmap

These changes will enhance the smart contract. Redeployment is required.
Increasing Smart contract functionality / Must haves

[ ] Initial seed list of categories enforced by the SC.
[ ] Ability to add categories (strict rules, only creators or public vote?)

Enchance / Should haves

[ ] None so far. We are open for suggestions

Experimental / Could haves

[ ] None so far. We are open for suggestions

NOTE this is not the final state of the v2.0 roadmap. Check back regularly to discover new features!
If there's a cool feature you'd like to see, do not hesitate to leave a comment 💯

State Management should go in #41 since it's intertwined with routing 😄


⚠ Bofrost.es has degraded performance

In c54b2f0, Bofrost.es (https://www.bofrost.es) experienced degraded performance:

HTTP code: 200
Response time: 1714 ms

Resolved: Bofrost.es performance has improved in 7b60a3a after 6 minutes.


Returning TypedResults.NotFound() actually returns no content and a 204

Code
internal class Test : EndpointWithoutRequest<NotFound>
{
    public override void Configure()
    {
        Get("/test");
    }

    public override async Task<NotFound> HandleAsync(CancellationToken ct)
    {
        await Task.CompletedTask;

        return TypedResults.NotFound();
    }
}

Expected result
A 404 response.
Actual result
204 No Content
< HTTP/1.1 204 No Content
< Date: Tue, 05 Sep 2023 04:09:23 GMT
< Server: Kestrel

you're overriding the wrong method. this is what it says in the docs:

setting the response DTO type of the endpoint's generic parameter to the desired union type and overriding the ExecuteAsync(...) handler method instead of the usual HandleAsync(...) method.

the following works as intended:
sealed class Test : EndpointWithoutRequest<NotFound>
{
    public override void Configure()
    {
        Get("/test");
        AllowAnonymous();
    }

    public override async Task<NotFound> ExecuteAsync(CancellationToken ct)
    {
        await Task.CompletedTask;
        return TypedResults.NotFound();
    }
}


API Client: Basic Auth credentials not properly encoded when password is empty

What happens?
When using the built-in API client with Basic Authentication and providing only a username with an empty password, an Authorization header is incorrectly generated.
The current behaviour produces a Bearer token instead of the expected Basic Auth format.
I am using package @scalar/hono-api-reference ^0.5.146
What did you expect to happen?
The API client's Authorization header should be prefixed with "Basic"
Credentials (username:password) should be Base64 encoded, even when the password is empty
OpenAPI Document
No response

True!

I can make PR for this 👀

This seems to be fixed already, but it’s not released yet.
Preview: https://client.scalar.com/

Almost there :)
Checked version 0.5.150 today. Authorization scheme is correct, but there's still an issue with the format of the credentials:
When a password isn't provided, the credentials divider : is missing.
So, the decoded credentials come out as just username instead of username:.


Graphical elements displaced, inspector claims they are in place

Graphical elements are displaced on screen after screenmanager changes screens. Inspector shows them in place. Tested with pygame & SDL2, happens in both.
When, for example Button, is clicked in place where it is supposed to be, its misplaced graphical element reacts where it is.
STR: Does not happen all the time, requires several launches to appear (sometimes 10+). No need to do anything in the app, it either loads next screen properly or not.
Source code

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The example is broken, make sure anyone can run it without bothering with dependencies and fixing things.

tested just before posting, but there (maybe) were some nonstandard imports, i removed it & reuploaded.

You're messing with graphics and widgets from a thread, which is not correct. If you can duplicate the problem without performing these actions from a thread, please reopen this or open another issue.
If you need to use a thread, you can use the @mainthread decorator on a function, and when called that function will execute in the main thread. You can also use Clock.schedule_once to call any function in the main thread (this is actually what @mainthread does).


responsive view, mobile: message actions menu overlays the message and can block interaction

Just noticed this on my phone (Pixel 3 XL, Chrome):

There's an open issue and pr for this.
-Tim Abbott (mobile)
On Thu, Feb 13, 2020, 08:21 Chris Heald<EMAIL_ADDRESS>wrote:

Just noticed this on my phone (Pixel 3 XL, Chrome):
[image: Screenshot_20200213-091834]
https://user-images.githubusercontent.com/9830/74455187-30196480-4e42-11ea-9cd6-bc469789948d.png
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You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
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i would like to work on this issue

Closing as a duplicate of https://github.com/zulip/zulip/issues/13642


Unable to configure

Trying to connect to my Thermia Atlas 12 via Modbus TCP.
Modbus TCP is enabled in my heatpump.
When I try to configure the integration I get the error message "User input malformed".

I do not know if it should be possible to connect to an Atlas 12 but it is running Genesis just like the inverter and mega heatpumps. I need help to point me in the right direction...
thanks,
Gustav

Hi!
I haven't touched this integration in quite some time, this was probably caused by some change in home assistant.
I have published a new version, 0.0.7, that should fix this!

Tackar för hjälpen.
Jag testar på nytt.
Mvh
Gustav
On Wed, Dec 8, 2021 at 1:00 AM Johan Isacsson @.***>
wrote:

Hi!
I haven't touched this integration in quite some time, this was probably
caused by some change in home assistant.
I have published a new version, 0.0.7, that should fix this!
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Still unable to configure. I updated to version 0.0.7 (via HACS) and the files are installed in the wrong directory.
To get the integration as an option I had to rename the directory under custom_components and make a symbolic link to  the .py-files.
/config/custom_components/thermiagenesis -> /config/custom_components/thermiagenesis_github/custom_components/thermiagenesis
The plugin is now shown in the integration but when I try to run it it just freezes. I cannot find any error messages in the home assistant logfiles.

I am running Home Assistant 2021.11.5 aarch64 on a Raspberrypi 4.
Please advice.
Thanks,
Gustav

It worked like a charm for me until the 0.0.7 update that stopped everthing. Backed down to 0.0.6 and it's back to working again.
It looks like 0.0.7 is moving the files to a catlog under the right one.

As a desperate move I rebooted the Pi and now everything started working.
I guess moving the files to the correct path and a reboot did the trick :-).

So to summarize. The problem is that the files are placed in the wrong path "/config/custom_components/thermiagenesis/custom_components/thermiagenesis"

My bad, i reorganized the directory structure, previously everything was located in the root directory of this repo and now it's in custom_components/thermiagenesis.
For new installations it works without any issues but when you update an existing install it seems to break.
So to get around this you can do this:

Remove the integration form home assistant integrations page
Uninstall the integration in HACS
Restart (don't skip this step otherwise it will install in the wrong dir)
Install the integratoin in HACS
Restart
Reload the browser window (might not be needed for you but i had to).
Add the integration on the integrations page.

Your entities should have the same id's so your history is preserved.
Nice to see that someone is using this, i'm going to add some features to it in the near future, like being able to write all values that are settable.

Jag har tom frågat tekniker på Thermia om de inte skulle släppa ett API (var tydligen inte aktuellt just nu) i vilket fall har jag en atlas 18 som fungerar fin fint. Å din plugin hjälper till att hålla lite koll och rita kurvor :-D

I will use it as well, if I can just figure out how to enable Modbus TCP on the Atlas 18 😅

I will use it as well, if I can just figure out how to enable Modbus TCP on the Atlas 18 😅

You can use the service code 607080 activate BMS in the display settings. There you can choose Modbus TCP or RTU.


In PC Chromium browsers, Accessory buttons only work if I click them a bunch of times quickly

Describe The Bug:

Up until now, the web UI has functioned flawlessly. However after an unknown change (homebridge upgrade? homebridge-ui-x upgrade?) the accessory buttons register a click (they "grow" on a click) but do not change the accessory state or toggle appearance in PC Chrome and Edge (Chromium). However, if I click them a bunch of times, like 5 or so, very fast, they work. They work normally in PC Firefox, Mac Chrome, Safari Mac, Firefox Mac, Safari iOS, and Chrome iOS. Interestingly, the button "grow on click" feature doesn't appear to be implemented in any of the browsers that actually work? Is this a new feature? Is it possibly broken somehow?
To Reproduce:

Use PC Chrome or Edge Chromium
Expected behavior:

I expected the accessories to change state.
Logs:

Show the Homebridge / Homebridge Config UI X logs here.

[1/2/2021, 1:12:14 PM] [Homebridge UI] Restarting the docker container, make sure you have --restart=always turned on or the container will not come back online
Thank you for using the oznu/homebridge docker image!

 Syncing with Govee...
 Setup complete. Don't forget to ? this plugin on GitHub if you're finding it useful!
HAP Warning: Characteristic E863F126-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10C-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F110-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10A-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10D-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F126-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10C-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F110-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10A-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10D-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F126-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10C-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F110-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10A-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10D-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F126-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10C-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F110-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10A-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10D-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F126-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10C-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F110-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10A-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
HAP Warning: Characteristic E863F10D-079E-48FF-8F27-9C2605A29F52 not in required or optional characteristics for service 00000047-0000-1000-8000-0026BB765291. Adding anyway.
[1/2/2021, 1:12:30 PM] [Govee] Brightness issues? Please create an issue on GitHub with your model number!
[1/2/2021, 1:12:32 PM] [Homebridge UI] Homebridge Config UI X v4.36.0 is listening on :: port 58004
[1/2/2021, 1:12:31 PM] [LgThinqAirConditioner] Discover found 1 total devices
[1/2/2021, 1:12:31 PM] [LgThinqAirConditioner] Existing accessory: Bedroom AC
Homebridge Config:
Show your homebridge config.json here

{
"bridge": {
"name": "Homebridge Oznu",
"username": "0E:2E:FE:B4:1D:CE",
"port": 53055,
"pin": "031-45-154"
},
"accessories": [],
"platforms": [
{
"name": "Config",
"port": 58004,
"auth": "form",
"theme": "dark-mode",
"tempUnits": "f",
"lang": "auto",
"sessionTimeout": 604800,
"proxyHost": "synology.gcc.bitboy.com:58004",
"platform": "config"
},
{
"name": "TplinkSmarthome",
"addCustomCharacteristics": true,
"deviceTypes": [
"plug",
"bulb"
],
"platform": "TplinkSmarthome"
},
{
"name": "Govee",
"apiKey": "6a6517c6-37b3-454c-8246-91cc3552e4dd",
"debug": false,
"debugReqRes": false,
"disablePlugin": false,
"refreshTime": 10,
"platform": "Govee"
},
{
"country_code": "US",
"language_code": "en-US",
"auth_login_url": "XXX",
"auth_redirected_url": "XXX",
"auth_login_state": "XXX",
"refresh_interval": 1,
"platform": "LgThinqAirConditioner",
"auth_access_token": "XXX",
"auth_refresh_token": "XXX",
"auth_user_number": "XXX"
}
]
}
Screenshots:

Environment:

Node.js Version:  14.15.3
NPM Version:  6.14.9
Homebridge Version:  1.2.5
Homebridge Config UI X Version: 4.36.0
Operating System: Docker
Process Supervisor: Docker

This behavior is no longer repeatable, so I am closing the issue.

This behavior is no longer repeatable, so I am closing the issue.


Check kernel testing on stable branches

ginkgo not testing net-next. There are a lot of tests that only run when the kernel == "net-next". By switching to a "stable" kernel we are effectively removing that coverage. We need to address this for 1.15 as well.
I recognize this is making the CI results more stable, but it also gets me wondering what if a newer kernel breaks an older release, do we have any early warning system for that? Or we just rely on the kernel breaking the main branch and then figure out whether we need to apply mitigations back to older releases?
One more minor interesting note here - 6.6 is the current LTS, but bpf-next is closer to 6.10. This is subtly changing the target tests. Though that said, over the lifetime of maintaining v1.16 it makes sense to test 6.6 (EOL ETA end of 2026)

Fixed by https://github.com/cilium/cilium/pull/33733


Add onSeek support for Youtube player

Hello.
Im making a "watch together" app and the "onSeek" event for youtube is not working.
I found this tutorial on google: https://simplernerd.com/js-youtube-seek/
i thought it would help other developer if they are using the player.
I just added a little code to the tutorial to detect seek when the player is paused.
else if (data === PAUSED) {
    const seekTimer = setInterval(() => {
        if (
          this.prevTime !== this.getCurrentTime() &&   // Paused seek
          isSubArrayEnd(this._sequence, [PAUSED])
        ) {
          onSeek(this.getCurrentTime())
          // this._sequence = []
          this.prevTime = this.getCurrentTime()
        }
     }, 750)
}

Implements the onSeek event for YouTube. Fixes https://github.com/cookpete/react-player/issues/1243

Hi, I got same issue.
Vimeo works, but Youtube is not.

I cannot calculate elapsed time unless I trigger my seek bar, it does not work until then. So it doesn't work when the video plays unless I use my seek bar.
Is this because this function doesn't work? I'm a little confused because it works in the demo.

I cannot calculate elapsed time unless I trigger my seek bar, it does not work until then. So it doesn't work when the video plays unless I use my seek bar.
Is this because this onSeek function doesn't work? I'm a little confused because it works in the demo.

This behavior is not the same when it is deployed. I guess its a cross origin thing? I thought it was related to this function, but I guess not

Any updates on this?

@cookpete We're still facing the issue is there any updates?

I cannot calculate elapsed time unless I trigger my seek bar, it does not work until then. So it doesn't work when the video plays unless I use my seek bar.
Is this because this onSeek function doesn't work? I'm a little confused because it works in the demo.

onSeek will only be triggered when you seek on the bar, if you want to get the elapsed time every second you can have a setInteval function that will trigger every second to calculate the elapsed time based on the currentTime on the player

thanks for the contribution, closing due to out of date.


EmitterConfigV3 (particle-emitter v5) output?

It looks like the JSON files created by the editor don't work with the newest version of @pixi/particle-emitter, at least by default. Is there an option to pick a different type of config to export? Or do people just manually convert the JSON format? Thanks for any help!

Nevermind, just found upgradeConfig (https://pixijs.io/particle-emitter/docs/modules.html#upgradeConfig). Thank you!


Custom Materials with Atomic Counter

What problem does this solve or what need does it fill?
After #6988 I've questioned myself if it would be also possible to make custom materials use atomic counter for their AsBindGroup, instead of TypeUUID.
What solution would you like?
Make the AsBindGroup derive also increasing the atomic counter, so that lines like https://github.com/bevyengine/bevy/blob/b6066c30b6cfa7bffa598d45706dbe6e46ad24fc/examples/shader/shader_material.rs#L57 don't need to exist anymore.

That line is for the TypeUuid derive. It's required to support using it as an asset. The use case is entirely different and definitely needs a stable independent unique ID that is the same across compilations and executions of the same binary.

Oh I See.. should this be closed?


Update rdflib to v7.0.0 and Python >= 3.8.1

Increasing the Python base version is required for rdflib 7, though Python 3.8 is already no longer receiving security updates.

Thank you.


[Discussion] Are you still using norbert library?

In the paper it says that spleeter uses multi-channel Wiener filtering with the Norbert library, but I couldn't find the library anywhere in the code. Also spleeter seems to be running fine without norbert installed. Did you remove it?
I was wondering about the effect of multi-channel Wiener filtering on the results and would like to have some audio examples for comparison.

Hi @ManuelFritsche
Yes we still use norbert for instance here.  If you want to try the effect of Wiener Filtering, you need to add the --mwf option to your command (see more details on the options in the wiki
Best


Include VSS 3.0 and use it as default

Signed-off-by: Erik Jaegervall<EMAIL_ADDRESS>

Draft for discussion/test

Replaced by https://github.com/eclipse/kuksa.val/pull/331


How to apply a "what-if" parameter in the advanced query editor for a query copied in from kusto?

So I added a what-if parameter("Last N Days") from the ribbon and it gave me a slider that I can happily drag between 1 and 30 (for number of days ago to use in the query). Problem is - I don't know how to connect the user-supplied value from this slider into the Kusto query I am using for a funnel chart on the side. Using  this in the query - & #"Last N Days" & - doesn't work because the advanced query editor doesn't recognize the what-if parameter as it would a vanilla parameter

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 3ec5fb9d-8962-7e64-2768-b04b498f2db4
Version Independent ID: f82bc4a7-476c-20e6-71cb-5406a3577a74
Content: Best practices for using Power BI to query and visualize Azure Data Explorer data
Content Source: data-explorer/power-bi-best-practices.md
Service: data-explorer
GitHub Login: @orspod
Microsoft Alias: orspodek

@hasridha  Thanks for the question! We are investigating and will update you shortly.

@Gabilehner can you assist with this question?

@Gabilehner can you assist with this question?

You currently can't use WhatIf parameters in the Power Query Editor, as you've found out.
We are working on improving these kind of scenarios with the PBI team, but don't have anything to share yet.
Depending on what you are trying to do, you might be able to just use a filter on a column of your dataset.

@saguiitay - thanks for the answer
@hasridha hope this answered your question. Please let us know if you have additional questions

@hasridha I am closing this issue. If you have additional questions feel free to comment.


Link libc++ statically on Linux

Locally, I get this output:

I believe libunwind and libc++abi are only needed through libc++ and included in static libc++, so linking them statically is not needed.

Out of curiosity, how much bigger are our linux binaries after this change? (I'd probably eat any size, but worth bringing up.)

Out of curiosity, how much bigger are our linux binaries after this change? (I'd probably eat any size, but worth bringing up.)

Good question! Locally I'm seeing < 1MB size increase for debug binaries, not sure how that translates to release binaries but it feels reasonable.


A general error occurred.

No need to use template just a question. Is there a maintenance on going now with Firebase Remote Config we can no longer update value on any Firebase Account?

@ArcherEmiya05 looks like you're having an issue in production with the Firebase console. This repo is just for the android quickstart sample apps (hence the tempalte).  Please file an issue with Firebase support who can help you get the console working again:


MIC-389 send events from listeners rather than function on csip record

Codecov Report
Attention: Patch coverage is 88.93805% with 25 lines in your changes missing coverage. Please review.

Project coverage is 87.34%. Comparing base (e7c97c8) to head (83a805c).

Files
Patch %
Lines

...challengesupportinterventionplanapi/entity/Plan.kt
69.23%
1 Missing and 3 partials :warning:

...rtinterventionplanapi/entity/event/EventFactory.kt
78.94%
2 Missing and 2 partials :warning:

...esupportinterventionplanapi/DeleteEventListener.kt
85.71%
0 Missing and 3 partials :warning:

...lengesupportinterventionplanapi/entity/Referral.kt
66.66%
1 Missing and 2 partials :warning:

...supportinterventionplanapi/entity/Investigation.kt
71.42%
1 Missing and 1 partial :warning:

...ionplanapi/entity/audit/CsipEventEntityListener.kt
95.23%
0 Missing and 2 partials :warning:

...ngesupportinterventionplanapi/entity/CsipRecord.kt
87.50%
0 Missing and 1 partial :warning:

...rtinterventionplanapi/entity/DecisionAndActions.kt
50.00%
1 Missing :warning:

...tionplanapi/entity/SaferCustodyScreeningOutcome.kt
50.00%
1 Missing :warning:

...tinterventionplanapi/entity/audit/AuditRevision.kt
92.30%
0 Missing and 1 partial :warning:

... and 3 more

Additional details and impacted files
@@             Coverage Diff              @@
##               main     #106      +/-   ##
============================================
- Coverage     89.70%   87.34%   -2.36%
+ Complexity      661      582      -79
============================================
  Files           117      117
  Lines          2039     1762     -277
  Branches        112      100      -12
============================================
- Hits           1829     1539     -290
- Misses          170      178       +8
- Partials         40       45       +5

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:loudspeaker: Have feedback on the report? Share it here.


[Feature Request] Be able to adds scrap items in the list of Remnants

Would let us be able to add any items as remnants,
The point would be for mods that adds usefull scrap like Abandoned Company Assets (adds store items with malfunctions like abandonned flashlight, abandonned walkie-talkie), to add them to the list of remnants so they can spawn next to bodies.
The way this could work could be by entering the scrap name in a text field in the config.
Since I play with 100% chance for body to spawn next to a remnant, that would be usefull and more immersive.

Normally, the Remnants mod is compatible with other mods having store items and registering them as remnant items.
But the way I understand, it does not work with Abandoned Company Assets mod?
If that is the case, I will take a look at this issue and see If I can find a possible fix for it.
Thank you for reporting the issue.

This seems because the items are already scrap and the Remnant items do not register scrap.
So like you suggested, I could add a config feature where you can add the item name for it, to force add it to the remnants list.
If it works you will see then the item then in the config section called Remnants.
Do take in mind that you would need to type in the name perfectly, otherwise it would not work.
This feature will be added probably on the next update.


No caching for ADD instruction via HTTP

Description
I've searched issues for "cache add http" but didn't find anything relevant. This may be a dupe.
Instructions like the following don't appear to be cached, but RUN instructions invoking curl do get cached.
Step 4 : ADD https://storage.googleapis.com/golang/go1.7.4.linux-armv6l.tar.gz ./
The net effect is that this very useful way of downloading for a container becomes slow / repetitive / wasteful.

Steps to reproduce the issue:

Use ADD http(s):// ./ in a Dockerfile

Describe the results you received:
No caching of instruction
Describe the results you expected:
Caching on subsequent runs similar to the use of curl
Additional information you deem important (e.g. issue happens only occasionally):
Output of docker version:
Client:
 Version:      1.12.3
 API version:  1.24
 Go version:   go1.6.3
 Git commit:   6b644ec
 Built:        Wed Oct 26 19:06:36 2016
 OS/Arch:      linux/arm

Server:
 Version:      1.12.3
 API version:  1.24
 Go version:   go1.6.3
 Git commit:   6b644ec
 Built:        Wed Oct 26 19:06:36 2016
 OS/Arch:      linux/arm

Same behaviour on other Docker engine/CLI versions.

Looks like this is a duplicate of https://github.com/docker/docker/issues/15717; also see the issues linked from that issue (which contain some prior discussion)
I'll close this one 👍


Add access log filter based on response time

Do you want to request a feature or report a bug?
Feature
What did you expect to see?
It would be useful to have a filter to log requests that took longer than a defined threshold. The response times of a request ca be used in for example SLOs to define whether a request was successful or not. Currently, Traefik only supports this kind of filter on status code level.

I can take this :)


The system shuts down right after the start

I am using Docker (Version <IP_ADDRESS>-win81 (29211)) on Windows 10. Following exactly your example "Getting started" provided in README.md, I got the following log, mentioning "s6-applyuidgid: fatal: unable to exec /startapp.sh: No such file or directory":
C:\Users\Sofke\Desktop\dockerGui>docker build -t docker-xterm .
Sending build context to Docker daemon   5.12kB
Step 1/4 : FROM jlesage/baseimage-gui:alpine-3.6
---> 03c81ba1677f
Step 2/4 : RUN add-pkg xterm
---> Using cache
---> b8433a4f4a96
Step 3/4 : COPY startapp.sh /startapp.sh
---> 3ba17dfd408f
Step 4/4 : ENV APP_NAME="Xterm"
---> Running in c3d4798cc140
Removing intermediate container c3d4798cc140
---> 37268c153245
Successfully built 37268c153245
Successfully tagged docker-xterm:latest
SECURITY WARNING: You are building a Docker image from Windows against a non-Windows Docker host. All files and directories added to build context will have '-rwxr-xr-x' permissions. It is recommended to double check and reset permissions for sensitive files and directories.
C:\Users\Sofke\Desktop\dockerGui>docker run --rm -p 5800:5800 -p 5900:5900 docker-xterm
[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] 00-app-niceness.sh: executing...
[cont-init.d] 00-app-niceness.sh: exited 0.
[cont-init.d] 00-app-script.sh: executing...
[cont-init.d] 00-app-script.sh: exited 0.
[cont-init.d] 00-app-user-map.sh: executing...
[cont-init.d] 00-app-user-map.sh: exited 0.
[cont-init.d] 00-clean-logmonitor-states.sh: executing...
[cont-init.d] 00-clean-logmonitor-states.sh: exited 0.
[cont-init.d] 00-clean-tmp-dir.sh: executing...
[cont-init.d] 00-clean-tmp-dir.sh: exited 0.
[cont-init.d] 00-set-app-deps.sh: executing...
[cont-init.d] 00-set-app-deps.sh: exited 0.
[cont-init.d] 00-set-home.sh: executing...
[cont-init.d] 00-set-home.sh: exited 0.
[cont-init.d] 00-take-config-ownership.sh: executing...
[cont-init.d] 00-take-config-ownership.sh: exited 0.
[cont-init.d] 00-xdg-runtime-dir.sh: executing...
[cont-init.d] 00-xdg-runtime-dir.sh: exited 0.
[cont-init.d] 10-certs.sh: executing...
[cont-init.d] 10-certs.sh: exited 0.
[cont-init.d] 10-cjk-font.sh: executing...
[cont-init.d] 10-cjk-font.sh: exited 0.
[cont-init.d] 10-nginx.sh: executing...
[cont-init.d] 10-nginx.sh: exited 0.
[cont-init.d] 10-vnc-password.sh: executing...
[cont-init.d] 10-vnc-password.sh: exited 0.
[cont-init.d] 10-web-index.sh: executing...
[cont-init.d] 10-web-index.sh: exited 0.
[cont-init.d] done.
[services.d] starting services
[services.d] starting s6-fdholderd...
[services.d] starting xvfb...
[xvfb] starting...
[services.d] starting openbox...
[openbox] starting...
Openbox-Message: Openbox was compiled without image loading support. Icons in menus will not be loaded.
[services.d] starting certsmonitor...
[services.d] starting logmonitor...
[services.d] starting nginx...
[logmonitor] no file to monitor: disabling service...
[certsmonitor] disabling service: secure connection not enabled.
[services.d] starting statusmonitor...
[nginx] starting...
[services.d] starting x11vnc...
[statusmonitor] no file to monitor: disabling service...
[x11vnc] starting...
[services.d] starting app...
14/12/2018 20:36:41 passing arg to libvncserver: -rfbport
14/12/2018 20:36:41 passing arg to libvncserver: 5900
14/12/2018 20:36:41 passing arg to libvncserver: -rfbportv6
14/12/2018 20:36:41 passing arg to libvncserver: -1
14/12/2018 20:36:41 passing arg to libvncserver: -httpportv6
14/12/2018 20:36:41 passing arg to libvncserver: -1
14/12/2018 20:36:41 passing arg to libvncserver: -desktop
14/12/2018 20:36:41 passing arg to libvncserver: Xterm
[app] starting Xterm...
14/12/2018 20:36:41 x11vnc version: 0.9.14 lastmod: 2015-11-14  pid: 749
s6-applyuidgid: fatal: unable to exec /startapp.sh: No such file or directory
14/12/2018 20:36:41 Using X display :0
14/12/2018 20:36:41 rootwin: 0x43 reswin: 0x400001 dpy: 0x35eea00
14/12/2018 20:36:41
14/12/2018 20:36:41 ------------------ USEFUL INFORMATION ------------------
[services.d] done.
14/12/2018 20:36:41 X DAMAGE available on display, using it for polling hints.
14/12/2018 20:36:41   To disable this behavior use: '-noxdamage'
14/12/2018 20:36:41
14/12/2018 20:36:41   Most compositing window managers like 'compiz' or 'beryl'
14/12/2018 20:36:41   cause X DAMAGE to fail, and so you may not see any screen
14/12/2018 20:36:41   updates via VNC.  Either disable 'compiz' (recommended) or
14/12/2018 20:36:41   supply the x11vnc '-noxdamage' command line option.
14/12/2018 20:36:41 X COMPOSITE available on display, using it for window polling.
14/12/2018 20:36:41   To disable this behavior use: '-noxcomposite'
14/12/2018 20:36:41
14/12/2018 20:36:41 Wireframing: -wireframe mode is in effect for window moves.
14/12/2018 20:36:41   If this yields undesired behavior (poor response, painting
14/12/2018 20:36:41   errors, etc) it may be disabled:
14/12/2018 20:36:41    - use '-nowf' to disable wireframing completely.
14/12/2018 20:36:41    - use '-nowcr' to disable the Copy Rectangle after the
14/12/2018 20:36:41      moved window is released in the new position.
14/12/2018 20:36:41   Also see the -help entry for tuning parameters.
14/12/2018 20:36:41   You can press 3 Alt_L's (Left "Alt" key) in a row to
14/12/2018 20:36:41   repaint the screen, also see the -fixscreen option for
14/12/2018 20:36:41   periodic repaints.
14/12/2018 20:36:41 GrabServer control via XTEST.
14/12/2018 20:36:41
14/12/2018 20:36:41 Scroll Detection: -scrollcopyrect mode is in effect to
14/12/2018 20:36:41   use RECORD extension to try to detect scrolling windows
14/12/2018 20:36:41   (induced by either user keystroke or mouse input).
14/12/2018 20:36:41   If this yields undesired behavior (poor response, painting
14/12/2018 20:36:41   errors, etc) it may be disabled via: '-noscr'
14/12/2018 20:36:41   Also see the -help entry for tuning parameters.
14/12/2018 20:36:41   You can press 3 Alt_L's (Left "Alt" key) in a row to
14/12/2018 20:36:41   repaint the screen, also see the -fixscreen option for
14/12/2018 20:36:41   periodic repaints.
14/12/2018 20:36:41
14/12/2018 20:36:41 XKEYBOARD: number of keysyms per keycode 7 is greater
14/12/2018 20:36:41   than 4 and 51 keysyms are mapped above 4.
14/12/2018 20:36:41   Automatically switching to -xkb mode.
14/12/2018 20:36:41   If this makes the key mapping worse you can
14/12/2018 20:36:41   disable it with the "-noxkb" option.
14/12/2018 20:36:41   Also, remember "-remap DEAD" for accenting characters.
14/12/2018 20:36:41
14/12/2018 20:36:41 X FBPM extension not supported.
14/12/2018 20:36:41 X display is not capable of DPMS.
14/12/2018 20:36:41 --------------------------------------------------------
14/12/2018 20:36:41
14/12/2018 20:36:41 Default visual ID: 0x21
[services.d] stopping services
14/12/2018 20:36:41 Read initial data from X display into framebuffer.
14/12/2018 20:36:41 initialize_screen: fb_depth/fb_bpp/fb_Bpl 24/32/5120
14/12/2018 20:36:41
14/12/2018 20:36:41 X display :0 is 32bpp depth=24 true color
14/12/2018 20:36:41
14/12/2018 20:36:41 Listening for VNC connections on TCP port 5900
14/12/2018 20:36:41
14/12/2018 20:36:41 Xinerama is present and active (e.g. multi-head).
14/12/2018 20:36:41 Xinerama: number of sub-screens: 1
14/12/2018 20:36:41 Xinerama: no blackouts needed (only one sub-screen)
14/12/2018 20:36:41
14/12/2018 20:36:41 fb read rate: 1851 MB/sec
14/12/2018 20:36:41 fast read: reset -wait  ms to: 10
14/12/2018 20:36:41 fast read: reset -defer ms to: 10
14/12/2018 20:36:41 The X server says there are 10 mouse buttons.
14/12/2018 20:36:41 screen setup finished.
14/12/2018 20:36:41
The VNC desktop is:      94c38ecbd105:0
PORT=5900

Have you tried the x11vnc '-ncache' VNC client-side pixel caching feature yet?
The scheme stores pixel data offscreen on the VNC viewer side for faster
retrieval.  It should work with any VNC viewer.  Try it by running:
x11vnc -ncache 10 ...

One can also add -ncache_cr for smooth 'copyrect' window motion.

Issue solved:
line ending set to UNIX-format (LF) instead of Windows (CR LF)
Great Docker image!

Using dos2unix in Windows 10 - Ubuntu works well


evaluate polynomials with degree < 255

I've removed an outdated comment for the exposed Commit method. Could we use that one instead of commit for the get_tree_key? Then we would not need to change commit


Improve the visibility of contributor cards

The cards can use some shadows and hover effects. It will provide better visibility that way, also a fixed size would look better since some cards have really long texts on them.

Can I work on this issue?

sure, i'll assign it to you now


[FR] Be able to run more than one jax process concurrently

GPU/TPU cannot be found after jax process is imported in another open session
Please:

[x] Check for duplicate issues.

This looks different - running 1 piece of code on multiple devices
Concerned here, unsure if "we haven't published an API for multi-host GPU" is relevant here.

jax version 0.2.17
jaxlib version 0.1.67
Steps to replicate:
On a system with multiple devices (in my case, google cloud v2-8 TPU VM).
Open a terminal.
>>> import jax
>>> jax.devices()
[TpuDevice(id=0, process_index=0, coords=(0,0,0), core_on_chip=0), TpuDevice(id=1, process_index=0, coords=(0,0,0), core_on_chip=1), TpuDevice(id=2, process_index=0, coords=(1,0,0), core_on_chip=0), TpuDevice(id=3, process_index=0, coords=(1,0,0), core_on_chip=1), TpuDevice(id=4, process_index=0, coords=(0,1,0), core_on_chip=0), TpuDevice(id=5, process_index=0, coords=(0,1,0), core_on_chip=1), TpuDevice(id=6, process_index=0, coords=(1,1,0), core_on_chip=0), TpuDevice(id=7, process_index=0, coords=(1,1,0), core_on_chip=1)]

With that python session still open, open another terminal/tmux session in my case.
export TF_CPP_MIN_LOG_LEVEL=0:
>>> import jax
>>> jax.devices()
2021-12-03 14:10:23.408083: I external/org_tensorflow/tensorflow/compiler/xla/service/service.cc:171] XLA service 0x2d12d00 initialized for platform Interpreter (this does not guarantee that XLA will be used). Devices:
2021-12-03 14:10:23.408126: I external/org_tensorflow/tensorflow/compiler/xla/service/service.cc:179]   StreamExecutor device (0): Interpreter, <undefined>
2021-12-03 14:10:23.419007: I external/org_tensorflow/tensorflow/compiler/xla/service/service.cc:171] XLA service 0x2cd8ea0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2021-12-03 14:10:23.419039: I external/org_tensorflow/tensorflow/compiler/xla/service/service.cc:179]   StreamExecutor device (0): Host, Default Version
2021-12-03 14:10:23.475845: I external/org_tensorflow/tensorflow/compiler/xla/pjrt/tpu_client.cc:222] TPU platform initialization failed: Invalid argument: Invalid fd: -1; Couldn't open device: /dev/accel0 (Operation not permitted); Unable to create Node RegisterInterface for node 0, config: device_path: "/dev/accel0" mode: KERNEL debug_data_directory: "" dump_anomalies_only: true crash_in_debug_dump: false allow_core_dump: true; could not create driver instance
WARNING:absl:No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
[CpuDevice(id=0)]

I expected it to still find all the TPUs, and want to run a script on one TPU at a time.
In a more recent version of jax: jax-0.2.25 and jaxlib-0.1.73, the error is more descriptive (which made me realise this is known, possibly not a bug per-se):
>>> import jax
WARNING: Logging before InitGoogle() is written to STDERR
I1203 14:15:18.362570  117716 tpu_initializer_helper.cc:94] libtpu.so already in use by another process. Not attempting to load libtpu.so in this process.
>>> jax.devices()
WARNING:absl:No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
[<jaxlib.xla_extension.Device object at 0x7f042db18570>]

It seems libtpu.so cannot be used in two separate python processes importing jax, and it would be helpful if this were possible?

want to run a script on one TPU at a time

We have some "secret menu items" for running multiple processes on subsets of the available TPU chips. Each TpuDevice corresponds to a TPU core, and there are 2 cores per chip (see https://cloud.google.com/tpu/docs/system-architecture-tpu-vm), so you can run up to 4 Python processes, each with 1 chip / 2 TpuDevices. See https://gist.github.com/skye/f82ba45d2445bb19d53545538754f9a3 for how to do this. Let me know if you need help with any of this.
Do you mind sharing what your use case is? We're trying to decide if and how to officially support these kinds of setups, so it's useful to understand what you're trying to do (there might be better APIs than setting a bunch of mysterious environment variables...).

I will have a look at this suggestion and get back to you, thanks!
The use case is I am trying to run RL experiments. The data space is not large enough such that there's any benefit mapping calculations across N TPUs, but I would like to run N experiments in parallel using 1 TPU each. I guess this is the same for other types of experiments too, e.g. searching hyperparameter space for image classification you'd want to run many in parallel?

This seems to have worked perfectly - I'm up and running. Thanks for your help, skye!
I'll defer to you on whether to close the request. Perhaps this is a workaround and the request still stands to make this 'just work', but it's as you wish.
Jamie

(Sorry for the delay) Glad to hear this worked for you! And thanks for sharing your use case, that makes sense and is useful feedback. I'll go ahead and close this issue.


[Skeleton] Wave animation is light in dark mode

[x] The issue is present in the latest release.
[x] I have searched the issues of this repository and believe that this is not a duplicate.

Current Behavior 😯

A bright wave
Expected Behavior 🤔
A dark wave

Steps to Reproduce 🕹
https://material-ui.com/components/skeleton/
Steps:

Dark mode
Observe the wave animation

Context 🔦
N/A
Your Environment 🌎

Tech
Version

Material-UI
v4.9.0

@mbrookes I believe the issue was addressed in the latest version, could you confirm?
It behaves similarly to Facebook than further distinguishes the wave color from the overall background color. (in a light background -> darker, in a dark background -> lighter).

Yep, LGTM.


swagger-core does work with Jackson 2.7.0

The current master for swagger-jaxrs does not work with Jackson 2.7.0 (latest stable version) because such version removes com.fasterxml.jackson.databind.type.TypeFactory.constructType(Type, Class<?>) which is used by Reader.
Please note that, while being built against Jackson 2.4.5, everything works fine up to Jackson 2.6.4, e.g. the former stable version.

It's tricky to keep up with the Jacksons, many implementations don't move as fast.
What is the new syntax in 2.7.x?  Is it back compatible?

It seems that 2.7.0 accidentally removed the method, which is now back and will be available again in 2.7.1, even though deprecated.
By looking at current implementation, though, it seems that the Class<?> argument is ignored, so one could replace the current class in Swagger's Reader from
final Type type = TypeFactory.defaultInstance().constructType(genericParameterTypes[i], cls);

to
final Type type = TypeFactory.defaultInstance().constructType(genericParameterTypes[i]);

and have this call working with all Jackson variants (once 2.7.1 will be out, naturally).

Thank you for investigating.  Let's hold on 2.7.1 then, and I believe it should work as-is?

If you want to keep using the deprecated method, yes, we can leave as-is: I was suggesting the change above for relying on a non-deprecated method which is also available in older releases.

Got it, if the method is available in the 2.4.x libraries, we should change it.  Do you mind sending a PR?

Not at all, tomorrow morning I'll send it.

It seems I was wrong: the change proposed above makes at least 1 unit test to fail:
scanModelWithGenericType(io.swagger.GenericsTest)  Time elapsed: 0.017 sec  <<< FAILURE!
java.lang.AssertionError: expected object to not be null
        at io.swagger.GenericsTest.scanModelWithGenericType(GenericsTest.java:225

so it seems that in 2.7 the change should be invariant (not considering deprecation, though) while in 2.4.6 there is a difference.
I'd leave things as they currently are, then.

Please see https://github.com/FasterXML/jackson-databind/blob/master/src/main/java/com/fasterxml/jackson/databind/type/TypeFactory.java

https://github.com/FasterXML/jackson-databind/issues/1087 addresses the re-introduction of constructType

FYI with Jackson 2.7.1 (fresh release) everything works fine.

Since it was a Jackson issue in the first place, I wonder if we should upgrade now or hold off on it.

But good to know that 2.7.1 is fine with swagger-core.

Unfortunately 2.7.1 and swagger 1.5.6 now work correctly, but 1.5.7 is quite broken. Roughly 1/3 of all values in swagger.json end up as nulls. I also pulled the Jackson 2.7.2 snapshot build with one more fix for the constructType issue, but that does not make a difference

Todd, please check the release notes for 1.5.7 to see if the issue is the '@Provider' change we made.

ah - that is it - definitely not an obvious failure mode as many fields still have expected values. I also had to remove the code that was setting SNAKE_CASE on the io.swagger.util.Json.mapper()
    @Provider
    @Produces({MediaType.APPLICATION_JSON})
    private static class JacksonJsonProvider extends JacksonJaxbJsonProvider {
        JacksonJsonProvider(final ObjectMapper mapper) {
            super.setMapper(mapper);
        }
    }

        register(new JacksonJsonProvider(new ObjectMapper()));

Actually - this doesn't work with a shaded jar or maybe because that causes a different load order. I don't see how a provider can be set based on looking at the code. io.swagger.util.json does not provide a way to set the ObjectMapper because io.swagger.util. ObjectMapperFactory.CreateJson() has no public way to pass in the ObjectMapper - it always forces null which ends up using the Jackson default ObjectMapper()
I also need the default Jackson provider to work in SNAKE_CASE form to translate between java and json keyname conventions. However, Swagger must work in normal mode or else things like basePath get translated incorrectly

Played around for another couple of hours w/o luck. When running under Eclipse from it's build, I don't need the extra @Provider - swagger.json has all expected elements. However, I cannot get a shaded jar to work under any circumstance with any combination of provider code
I did notice one significant difference running the 2 Swagger releases. Shaded jar w/ 1.5.6 shows an info log for Reflections but 1.5.7 does not. Is there something that is supposed to initiate this that just happened to work automagically before?

Reflections Reflections took 1691 ms to scan 1 urls, producing 21317 keys and 38210 values

Hi @todd-richmond can you provide a simple sample project?

that will take quite some effort - let me see if it is possible after I ship a release this week

Will this issue be resolved with jackson being upgraded to 2.7.2?
I also noticed that the joda packages are old. I updated these to
        <joda-version>1.8.1</joda-version>
        <joda-time-version>2.9.2</joda-time-version>

as well in my environment.

Note that the current version of Jackson is 2.7.2.

I spent some time today attempting to see if 1.5.8 solved my problem (it didn't), but went through the integration docs again and decided to move my Swagger() object creation to my ResourceConfig based constructor as well as register(ApiListingResource.class) and SwaggerSerializers directly. Everything now works as expected for my embedded jetty app even when shaded.
Jackson 2.7.2 is out so I think this bug can be closed

Master is upgraded to 2.8.4.

This seems to be broken again with Jackson 2.9.0.
Unhandled exception: java.lang.NoSuchMethodError: com.fasterxml.jackson.databind.introspect.AnnotatedMember.annotations()Ljava/lang/Iterable;
at io.swagger.jackson.ModelResolver.resolve(ModelResolver.java:379)
at io.swagger.jackson.ModelResolver.resolve(ModelResolver.java:185)
at io.swagger.converter.ModelConverterContextImpl.resolve(ModelConverterContextImpl.java:100)
at io.swagger.jackson.ModelResolver.resolve(ModelResolver.java:236)
at io.swagger.jackson.ModelResolver.resolve(ModelResolver.java:185)
at io.swagger.converter.ModelConverterContextImpl.resolve(ModelConverterContextImpl.java:100)
at io.swagger.jackson.ModelResolver.resolveProperty(ModelResolver.java:161)
at io.swagger.jackson.ModelResolver.resolveProperty(ModelResolver.java:112)
at io.swagger.converter.ModelConverterContextImpl.resolveProperty(ModelConverterContextImpl.java:80)
at io.swagger.converter.ModelConverters.readAsProperty(ModelConverters.java:58)
at io.swagger.jaxrs.DefaultParameterExtension.createProperty(DefaultParameterExtension.java:204)
at io.swagger.jaxrs.DefaultParameterExtension.extractParameters(DefaultParameterExtension.java:75)
at io.swagger.jaxrs.ext.AbstractSwaggerExtension.extractParameters(AbstractSwaggerExtension.java:33)
at io.swagger.jersey.SwaggerJersey2Jaxrs.extractParameters(SwaggerJersey2Jaxrs.java:63)
at io.swagger.jaxrs.Reader.getParameters(Reader.java:1036)
at io.swagger.jaxrs.Reader.parseMethod(Reader.java:975)
at io.swagger.jaxrs.Reader.read(Reader.java:322)
at io.swagger.jaxrs.Reader.read(Reader.java:172)
at io.swagger.jaxrs.listing.BaseApiListingResource.scan(BaseApiListingResource.java:65)
at io.swagger.jaxrs.listing.BaseApiListingResource.process(BaseApiListingResource.java:122)
at io.swagger.jaxrs.listing.BaseApiListingResource.getListingJsonResponse(BaseApiListingResource.java:167)
at io.swagger.jaxrs.listing.ApiListingResource.getListing(ApiListingResource.java:33)
Jackson 2.8.9 works fine

@eduramiba got the same

https://github.com/FasterXML/jackson-core/issues/395
This is likely the cause of the problem in 2.9.0. I'm having it too - can we get swagger updated to use the new 2.9.0 api?

Works fine again with jackson 2.9.1

Well, then I guess we'll have to stick with 2.8.9 until 2.9.1 is published (it's not found on maven central).


run lightning run app app.py --cloud from lightning notebook

🚀 Feature
run lightning run app app.py --cloud from a lightning notebook
Motivation
need to access bigger CPU and GPU instances when developing a lightning app.
the local laptop environment does not provide sufficient resources when developing a complex app.   more info at https://pytorch-lightning.slack.com/archives/CRBLFHY79/p1658770802365889
Pitch
Use Lightning Notebook app as my laptop in the cloud.
running lightning run app app.py --cloud --name quick-start-workshop  results in the following:

waits on this message
Your Lightning App is starting. This won't take long.

ctl-c and received this message
AttributeError: Authentication Failed, no authentication header available.

tried lightning login

lightning login
INFO: login started for lightning.ai, opening https://lightning.ai/sign-in?redirectTo=http%3A%2F%2Flocalhost%3A56207%2Flogin-complete

tried copying tried copying .lightning/crednential.json file from my laptop and putting in /home/zeus and resulted in the above issues

Alternatives
Additional context
If you enjoy Lightning, check out our other projects! ⚡

@robert-s-lee Thanks for the ticket. The login mechanism currently requires us to have UI opened  which isn’t great. As a workaround, you can either copy the credential file from your local machine to /home/zeus/.lightning/ inside your notebook machine or set the credentials using the env variables LIGHTNING_USER_ID  and LIGHTNING_API_KEY.
We should ideally fix the login flow but about your current bug reported, I wasn’t able to reproduce. Could you verify if your credential file is exactly as same as what you have in local and and the location is right
$ pwd
/home/zeus/.lightning
$ ls
cache  credentials.json
$

ran
lightning run app app.py --cloud --open-ui false

received the following
  File "/content/venv/lib/python3.8/site-packages/lightning_app/utilities/packaging/lightning_utils.py", line 107, in _prepare_lightning_wheels_and_requirements
    tar_name = _copy_tar(_PROJECT_ROOT, root)
  File "/content/venv/lib/python3.8/site-packages/lightning_app/utilities/packaging/lightning_utils.py", line 73, in _copy_tar
    tar_files = os.listdir(dist_dir)
FileNotFoundError: [Errno 2] No such file or directory: '/content/venv/lib/python3.8/dist'

that’s odd and looks like a regression on the packaging function (could you create another issue please?). As a work around, can you set the env variable PACKAGE_LIGHTNING to 0 and try?

@hhsecond I got the a success run from the cloud.  the issue was https://github.com/Lightning-AI/lightning/issues/13942.  The steps to make this work:
cd
mkdir ~/.lightning
cat  ~/.lightning/credentials.json <<EOF
copy credentials from laptop
EOF

the output here.
zeus@lightningwork-01g9an3ze5h1z2x4ksrwyfgj7v:~/test$ lightning run app app.py --cloud --open-ui false
Your Lightning App is starting. This won't take long.
The name of the app is: singing-tesla-4089
upload ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0%
Application is ready in the cloud


[No QA] Cross-check the files touched by a PR in typecheck

Details
This PR shows an example of this JS-ban typecheck thing giving a false negative. This PR fixes that.
Fixed Issues
$ https://github.com/Expensify/App/issues/31598
Tests
You can run this locally using whatever PR you want:
gh pr checkout 31494
comm -1 -2 <(git diff --name-only --diff-filter=A origin/main HEAD -- 'src/libs/*.js' 'src/hooks/*.js' 'src/styles/*.js' 'src/languages/*.js') <(gh pr view 31494 --json files | jq -r '.files | map(.path) | .[]')

[x] Verify that no errors appear in the JS console

Offline tests
None.
QA Steps
None.

[x] Verify that no errors appear in the JS console

PR Author Checklist

[x] I linked the correct issue in the ### Fixed Issues section above
[x] I wrote clear testing steps that cover the changes made in this PR

[x] I added steps for local testing in the Tests section
[x] I added steps for the expected offline behavior in the Offline steps section
[x] I added steps for Staging and/or Production testing in the QA steps section
[x] I added steps to cover failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[x] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)
[x] I tested this PR with a High Traffic account against the staging or production API to ensure there are no regressions (e.g. long loading states that impact usability).

[x] I included screenshots or videos for tests on all platforms
[x] I ran the tests on all platforms & verified they passed on:

[x] Android: Native
[x] Android: mWeb Chrome
[x] iOS: Native
[x] iOS: mWeb Safari
[x] MacOS: Chrome / Safari
[x] MacOS: Desktop

[x] I verified there are no console errors (if there's a console error not related to the PR, report it or open an issue for it to be fixed)
[x] I followed proper code patterns (see Reviewing the code)

[x] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick)
[x] I verified that the left part of a conditional rendering a React component is a boolean and NOT a string, e.g. myBool && <MyComponent />.
[x] I verified that comments were added to code that is not self explanatory
[x] I verified that any new or modified comments were clear, correct English, and explained "why" the code was doing something instead of only explaining "what" the code was doing.
[x] I verified any copy / text shown in the product is localized by adding it to src/languages/* files and using the translation method

[x] If any non-english text was added/modified, I verified the translation was requested/reviewed in #expensify-open-source and it was approved by an internal Expensify engineer. Link to Slack message:

[x] I verified all numbers, amounts, dates and phone numbers shown in the product are using the localization methods
[x] I verified any copy / text that was added to the app is grammatically correct in English. It adheres to proper capitalization guidelines (note: only the first word of header/labels should be capitalized), and is approved by marketing by adding the Waiting for Copy label for a copy review on the original GH to get the correct copy.
[x] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named "index.js". All platform-specific files are named for the platform the code supports as outlined in the README.
[x] I verified the JSDocs style guidelines (in STYLE.md) were followed

[x] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[x] I followed the guidelines as stated in the Review Guidelines
[x] I tested other components that can be impacted by my changes (i.e. if the PR modifies a shared library or component like Avatar, I verified the components using Avatar are working as expected)
[x] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[x] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[x] I verified that if a function's arguments changed that all usages have also been updated correctly
[x] If any new file was added I verified that:

[x] The file has a description of what it does and/or why is needed at the top of the file if the code is not self explanatory

[x] If a new CSS style is added I verified that:

[x] A similar style doesn't already exist
[x] The style can't be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(themeColors.componentBG))

[x] If the PR modifies code that runs when editing or sending messages, I tested and verified there is no unexpected behavior for all supported markdown - URLs, single line code, code blocks, quotes, headings, bold, strikethrough, and italic.
[x] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[x] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.
[x] If the PR modifies a component or page that can be accessed by a direct deeplink, I verified that the code functions as expected when the deeplink is used - from a logged in and logged out account.
[x] If a new page is added, I verified it's using the ScrollView component to make it scrollable when more elements are added to the page.
[x] If the main branch was merged into this PR after a review, I tested again and verified the outcome was still expected according to the Test steps.

Screenshots/Videos

Android: Native

Android: mWeb Chrome

iOS: Native

iOS: mWeb Safari

MacOS: Chrome / Safari

MacOS: Desktop

No C+ review needed here

Nope, the GITHUB_TOKEN is just needed in the env anywhere we use the gh cli. The command is the main thing that changed

thanks for the approval @hayata-suenaga, and your understanding is correct, so I think this should be ready for checklist + merge

Reviewer Checklist

[ ] I have verified the author checklist is complete (all boxes are checked off).
[ ] I verified the correct issue is linked in the ### Fixed Issues section above
[ ] I verified testing steps are clear and they cover the changes made in this PR

[ ] I verified the steps for local testing are in the Tests section
[ ] I verified the steps for Staging and/or Production testing are in the QA steps section
[ ] I verified the steps cover any possible failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[ ] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)

[ ] I checked that screenshots or videos are included for tests on all platforms
[ ] I included screenshots or videos for tests on all platforms
[ ] I verified tests pass on all platforms & I tested again on:

[ ] Android: Native
[ ] Android: mWeb Chrome
[ ] iOS: Native
[ ] iOS: mWeb Safari
[ ] MacOS: Chrome / Safari
[ ] MacOS: Desktop

[ ] If there are any errors in the console that are unrelated to this PR, I either fixed them (preferred) or linked to where I reported them in Slack
[ ] I verified proper code patterns were followed (see Reviewing the code)

[ ] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick).
[ ] I verified that the left part of a conditional rendering a React component is a boolean and NOT a string, e.g. myBool && <MyComponent />.
[ ] I verified that comments were added to code that is not self explanatory
[ ] I verified that any new or modified comments were clear, correct English, and explained "why" the code was doing something instead of only explaining "what" the code was doing.
[ ] I verified any copy / text shown in the product is localized by adding it to src/languages/* files and using the translation method
[ ] I verified all numbers, amounts, dates and phone numbers shown in the product are using the localization methods
[ ] I verified any copy / text that was added to the app is grammatically correct in English. It adheres to proper capitalization guidelines (note: only the first word of header/labels should be capitalized), and is approved by marketing by adding the Waiting for Copy label for a copy review on the original GH to get the correct copy.
[ ] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named "index.js". All platform-specific files are named for the platform the code supports as outlined in the README.
[ ] I verified the JSDocs style guidelines (in STYLE.md) were followed

[ ] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[ ] I verified that this PR follows the guidelines as stated in the Review Guidelines
[ ] I verified other components that can be impacted by these changes have been tested, and I retested again (i.e. if the PR modifies a shared library or component like Avatar, I verified the components using Avatar have been tested & I retested again)
[ ] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[ ] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[ ] If a new component is created I verified that:

[ ] A similar component doesn't exist in the codebase
[ ] All props are defined accurately and each prop has a /** comment above it */
[ ] The file is named correctly
[ ] The component has a clear name that is non-ambiguous and the purpose of the component can be inferred from the name alone
[ ] The only data being stored in the state is data necessary for rendering and nothing else
[ ] For Class Components, any internal methods passed to components event handlers are bound to this properly so there are no scoping issues (i.e. for onClick={this.submit} the method this.submit should be bound to this in the constructor)
[ ] Any internal methods bound to this are necessary to be bound (i.e. avoid this.submit = this.submit.bind(this); if this.submit is never passed to a component event handler like onClick)
[ ] All JSX used for rendering exists in the render method
[ ] The component has the minimum amount of code necessary for its purpose, and it is broken down into smaller components in order to separate concerns and functions

[ ] If any new file was added I verified that:

[ ] The file has a description of what it does and/or why is needed at the top of the file if the code is not self explanatory

[ ] If a new CSS style is added I verified that:

[ ] A similar style doesn't already exist
[ ] The style can't be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(themeColors.componentBG)

[ ] If the PR modifies code that runs when editing or sending messages, I tested and verified there is no unexpected behavior for all supported markdown - URLs, single line code, code blocks, quotes, headings, bold, strikethrough, and italic.
[ ] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[ ] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.
[ ] If the PR modifies a component or page that can be accessed by a direct deeplink, I verified that the code functions as expected when the deeplink is used - from a logged in and logged out account.
[ ] If a new page is added, I verified it's using the ScrollView component to make it scrollable when more elements are added to the page.
[ ] If the main branch was merged into this PR after a review, I tested again and verified the outcome was still expected according to the Test steps.
[ ] I have checked off every checkbox in the PR reviewer checklist, including those that don't apply to this PR.

Screenshots/Videos

Android: Native

Android: mWeb Chrome

iOS: Native

iOS: mWeb Safari

MacOS: Chrome / Safari

MacOS: Desktop

Oh, interesting. You should both install jq on your laptops with brew install jq, because it's great! However, not to worry – the GitHub-hosted runners ship with jq pre-installed:

https://github.com/actions/runner-images/blob/main/images/ubuntu/Ubuntu2204-Readme.md
https://github.com/actions/runner-images/blob/main/images/macos/macos-13-Readme.md

:hand: This PR was not deployed to staging yet because QA is ongoing. It will be automatically deployed to staging after the next production release.

🚀 Deployed to staging by https://github.com/neil-marcellini in version: 1.4.3-0 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
cancelled 🔪

🕸 web 🕸
success ✅

🚀 Deployed to staging by https://github.com/neil-marcellini in version: 1.4.3-0 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
success ✅

🕸 web 🕸
success ✅

🚀 Deployed to production by https://github.com/AndrewGable in version: 1.4.3-11 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
success ✅

🕸 web 🕸
success ✅


fix: removes layout shift caused due to ads

The ads don't have proper height and width so it causes the content to shift from left to right and top to bottom in different pages. So we give explicit height for the ad banners to avoid those shifts
https://user-images.githubusercontent.com/32865581/169266152-65e498bb-6287-4161-aca7-f6f8708a8bb9.mov
https://user-images.githubusercontent.com/32865581/169265443-3f28d8f7-a73f-4ddf-ba2f-5bf055a9903f.mov
https://user-images.githubusercontent.com/32865581/169265457-0fb12361-c2c8-43e2-8c97-937168fe4220.mov

Thanks. Just FYI that this site will be retired in about a month.


Setup fixes

Fixes for issues found during project setup, following standalone instructions in INSTALL.md
Additions

add command for running setup.sh - it was unclear from the written instructions that you need to run this as step 1 of the install in both vagrant + standalone scenarios. I found this out for standalone, because the MySQL script fails until you run setup.sh first.

Removals

duplicate browser-sync dependency. During setup.sh got this warning message:
npm WARN package.json Dependency 'browser-sync' exists in both dependencies and devDependencies, using<EMAIL_ADDRESS>from dependencies`

- setup.sh step in front end section is redundant since i added it in step 1. I kept the note about re-installing, though.

## Changes

- change 'frontend' references in `backend.sh` script to say 'backend'

## Testing

-

## Review

- @user

## Screenshots

## Notes

-

## Todos

-

## Checklist

* [ ] Changes are limited to a single goal (no scope creep)
* [ ] Code can be automatically merged (no conflicts)
* [ ] Code follows the standards laid out in the [front end playbook](https://github.com/cfpb/front-end)
* [ ] Passes all existing automated tests
* [ ] New functions include new tests
* [ ] New functions are documented (with a description, list of inputs, and expected output)
* [ ] Placeholder code is flagged
* [ ] Visually tested in supported browsers and devices
* [ ] Project documentation has been updated (including the "Unreleased" section of the CHANGELOG)

There's one semi-significant issue with this PR: You can't run (well, you can't successfully complete) setup.sh if you don't have your system-level dependencies installed.

There's one semi-significant issue with this PR: You can't run (well, you can't successfully complete) setup.sh if you don't have your system-level dependencies installed.

Is that an issue with this PR or an existing issue? We should keep the scope small and document outside issues.

It's an issue with the PR, because her updated doc instructs people to run setup.sh before installing those dependencies.

That explanation is helpful. So it's an issue with the documentation.

But I updated the documentation because you need to run setup.sh because the MySQL script fails until you run the script first. In the current order, the MySQL step comes first.

@cfarm If one hasn't done the stuff in "Front end setup", the first run of setup.sh (where you added it at the very start of the Standalone section) will fail.

I think it will also fail because the virtualenv hasn't been created when the bit at the end of .env tries to activate it. Well, it won't fail, but the pip dependencies will be installed globally, which is no bueno.

Closing in favor of #2217. Please open a new PR to reorganize devDependencies, if someone want to do that work.