Issue with multiple phenotype files

Hi there,
I am trying to use multiple phenotypes and have been getting the error 'NoneType' object is not subscriptable. I have used space and tab delimited files with and without column names without success.
I tried running:
import numpy as np
from fastlmm.association import single_snp
pheno_both =  "C:/Users/koapl/OneDrive/Desktop/data/double_pheno.txt"
bed_fn = "C:/Users/koapl/OneDrive/Desktop/data/leaf-files/Potri.001G385100.vcf.gz.bed"
results_df = single_snp(bed_fn, pheno_both, count_A1=False)

This is an example file:
double_pheno.txt
Do you know what is causing this error and how I can fix it? My single phenotype files have been running without issue.
Thanks in advance,
Koa

Koa,
Thanks for using FaST-LMM and thanks for including the sample pheno file!
Your sample pheno file works fine for me. So, let's try:
Specifying the files readers explicitly like this:
import numpy as np
from fastlmm.association import single_snp
from pysnptools.snpreader import Pheno, Bed
bed = Bed(r"C:/Users/koapl/OneDrive/Desktop/data/leaf-files/Potri.001G385100.vcf.gz.bed",count_A1=False)
print(bed.shape)
pheno = Pheno("C:/Users/koapl/OneDrive/Desktop/data/double_pheno.txt")
print(pheno.shape)
results_df = single_snp(bed, pheno, count_A1=False)
Also, please let me know what version of Python, fastlmm, pysnptools, and bed-reader you are using.
Yours,
Carl
Carl Kadie, Ph.D.
FaST-LMM & PySnpTools Teamhttps://fastlmm.github.io/
(Microsoft Research, retired)
https://www.linkedin.com/in/carlk/
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From: koa-planedin @.>
Sent: Monday, July 12, 2021 2:10 PM
To: fastlmm/FaST-LMM @.>
Cc: Subscribed @.***>
Subject: [fastlmm/FaST-LMM] Issue with multiple phenotype files (#20)
Importance: High
Hi there,
I am trying to use multiple phenotypes and have been getting the error 'NoneType' object is not subscriptable. I have used space and tab delimited files with and without column names without success.
I tried running:
import numpy as np
from fastlmm.association import single_snp
pheno_both =  "C:/Users/koapl/OneDrive/Desktop/data/double_pheno.txt"
bed_fn = "C:/Users/koapl/OneDrive/Desktop/data/leaf-files/Potri.001G385100.vcf.gz.bed"
results_df = single_snp(bed_fn, pheno_both, count_A1=False)
This is an example file:
double_pheno.txthttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffastlmm%2FFaST-LMM%2Ffiles%2F6804150%2Fdouble_pheno.txt&data=04|01||70cfb32f661c446eee9d08d945796906|84df9e7fe9f640afb435aaaaaaaaaaaa|1|0|637617210017927645|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|1000&sdata=PXrzk%2F%2FrGcCuL1PStjBFkrRj5MBTNxthh7tf85rNUcM%3D&reserved=0
Do you know what is causing this error and how I can fix it? My single phenotype files have been running without issue.
Thanks in advance,
Koa

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Hi Carl,
thank you for the quick reply!
I am using python 3.8.5, fastlmm 0.5.9, pysnptools 0.5.2, and bed-reader 0.2.5. Unfortunately, the suggested code is still giving me a 'NoneType' object is not subscriptable error.
Best,
Koa

Hi Carl,
Just wanted to follow up as I've been trying more solutions with no success. I have tried putting my own data into SnpData() the way it is shown in the example, but still get the same error on every multiple phenotype variation.
pheno_file_1 = "C:/Users/koapl/OneDrive/Desktop/data/leaf-files/pheno_Potri.001G385100.txt"
pheno_file_2 = "C:/Users/koapl/OneDrive/Desktop/data/leaf-files/pheno_Potri.001G395300.txt"
pheno1 = Pheno(pheno_file_1).read()
pheno2 = Pheno(pheno_file_2).read()
pheno3 = SnpData(iid=pheno1.iid,
                 sid=["Potri.001G385100","Potri.001G395300"],
                 val= np.c_[pheno1.val,pheno2.val]
)
pheno4 = SnpData(iid=pheno1.iid,
                sid=["original","sqrt","square"],
                 val= np.c_[pheno1.val,pheno1.val**2,pheno1.val**3]
                )

Could there be a problem with the bed file? The bed file works with my single phenotype files, but I'm not sure what else could be causing the issue. I would attach an example bed file I am working with, but they are not supported on this platform.
Thanks in advance,
Koa

Koa,
[If you want, you can email me directly at carlk [at]msn.com]
That looks pretty good.
What error messages are you getting?
Can you please print
pheno1.shape
pheno2.shape

Carl

From: koa-planedin @.>
Sent: Wednesday, July 21, 2021 4:39 PM
To: fastlmm/FaST-LMM @.>
Cc: Carl Kadie @.>; Comment @.>
Subject: Re: [fastlmm/FaST-LMM] Issue with multiple phenotype files (#20)
Importance: High
Hi Carl,
Just wanted to follow up as I've been trying more solutions with no success. I have tried putting my own data into SnpData() the way it is shown in the example, but still get the same error on every multiple phenotype variation.
pheno_file_1 = "C:/Users/koapl/OneDrive/Desktop/data/leaf-files/pheno_Potri.001G385100.txt"
pheno_file_2 = "C:/Users/koapl/OneDrive/Desktop/data/leaf-files/pheno_Potri.001G395300.txt"
pheno1 = Pheno(pheno_file_1).read()
pheno2 = Pheno(pheno_file_2).read()
pheno3 = SnpData(iid=pheno1.iid,
             sid=["Potri.001G385100","Potri.001G395300"],

             val= np.c_[pheno1.val,pheno2.val]

)
pheno4 = SnpData(iid=pheno1.iid,
            sid=["original","sqrt","square"],

             val= np.c_[pheno1.val,pheno1.val**2,pheno1.val**3]

            )

Could there be a problem with the bed file? The bed file works with my single phenotype files, but I'm not sure what else could be causing the issue. I would attach an example bed file I am working with, but they are not supported on this platform.
Thanks in advance,
Koa

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Hi Carl,
I sent you an email elaborating, please let me know if it didn't go through!
Best,
Koa

Koa,
I see it now. Thanks for the heads up. It should see future emails.

Carl

From: koa-planedin @.>
Sent: Friday, July 23, 2021 10:43 AM
To: fastlmm/FaST-LMM @.>
Cc: Carl Kadie @.>; Comment @.>
Subject: Re: [fastlmm/FaST-LMM] Issue with multiple phenotype files (#20)
Importance: High
Hi Carl,
I sent you an email elaborating, please let me know if it didn't go through!
Best,
Koa

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Feature/funding bugfix

Codecov Report

:exclamation: No coverage uploaded for pull request base (feature/funding@0d0e996). Click here to learn what that means.
The diff coverage is 100%.

@@                Coverage Diff                 @@
##             feature/funding       #9   +/-   ##
==================================================
  Coverage                   ?   99.67%
==================================================
  Files                      ?       26
  Lines                      ?      927
  Branches                   ?      117
==================================================
  Hits                       ?      924
  Misses                     ?        3
  Partials                   ?        0

Impacted Files
Coverage Δ

contracts/lib/Transfer.sol
100% <ø> (ø)

contracts/funding/BatchActions.sol
100% <100%> (ø)

contracts/exchange/Exchange.sol
100% <100%> (ø)

contracts/funding/LendingPool.sol
100% <100%> (ø)

contracts/lib/Events.sol
100% <100%> (ø)

contracts/lib/Requires.sol
100% <100%> (ø)

contracts/ExternalFunctions.sol
100% <100%> (ø)

contracts/funding/Auctions.sol
100% <100%> (ø)

contracts/lib/Consts.sol
100% <100%> (ø)

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Update typings to properly work for better-sqlite3

This was a mistake on my part initially, was partially resolved in #172 by @develogix however ended up still being broken once you actually wanted to import both better-sqlite3 (while having @types/better-sqlite3 from DefinitelyTyped) and Commando. This PR should truly fix the whole typing issue.
Previously this would not compile, despite it being correct syntax:
import * as Database from 'better-sqlite3';

const db = new Database(path.join(__dirname, 'data/databases/settings.sqlite3'));

as it gave the error:
Cannot use 'new' with an expression whose type lacks a call or construct signature.

For relatively obvious reasons as TypeScript was referencing the exported better-sqlite3 module from the Commando typings rather than the one from the @types/better-sqlite3 and in there the interface does indeed not have a construct signature.
Renaming the interface to SyncSqlite resolves this entirely.
While renaming I also changed the later variables from SQLite to Sqlite to be closed to their namings for the asynchronous sqlite3.
Furthermore I also updated the better-sqlite3 peer dependency as the author has told users to upgrade to v5.X and I added the @types/better-sqlite3 as peer dependency since the library won't work without that when using TypeScript.
One final note I should add that this is based on using TypeScript v3.1.6 which is latest stable at time of writing. For any testers I strongly recommend upgrading to that version prior to testing in order to get a clean test result.

No idea why this was closed .... I was just rebasing my fork. Regardless a new one covering it is upcoming anyway <_<

Yeah I was confused when it was closed as well, because the commit disappeared too.

There, the replacement commit is up. I think it was because I reset my master branch when I kinda borked that rebase I mentioned. Ohwell it's solved that's all that matters I guess.


Concurrent editing notifications are not cluster aware

I noticed we hadn't recorded this issue yet...
The current mechanism is a polling ajax call that returns a JSON representation of all the changes recorded on the current node by other users.  These concurrent notifications are stored in memory on the node where the changes were made, so a user accessing the gradebook from a different node will not receive these notifications.

This is stored in a cache via the MemoryService which can be setup as a distributed cache per installation. We'd probably have to either use a message queue or database if we wanted something different.

@kyleblythe, we were seeing some lag in concurrent messages displaying while testing yesterday, so will investigate today before we close and forget this one ;)

Many of the classic Sakai tools use the SAKAI_LOCKS table to lock tables/rows across the cluster. There might be some other ways to do it, but I feel like in the past with Gradebook 1 there was no concurrent editing notification and the second grade would just overwrite the first grade in a cluster.
I don't think many places set up the memory cache right now as distributed because AFIAK you have to setup a secondary server like Terracotta since Hazelcast is not yet implemented (Maybe for Sakai 12 KNL-1272). That would be the best solution for a lot of tools though.

note: this can just be pasted in two different browsers

Confirmed using two browsers.


replace for-loop based initialization

replace structures like:
for i in 0..<len {
    buf.advanced(by: i).initialize(to: 0)
}

with:
buf.initialize(repeating: 0, count: len)

should bring small performance improvements

@swift-ci please test

@swift-ci please test and merge

It looks like this commit might have broken the Ubuntu 18.04 test runs: https://ci.swift.org/job/oss-swift-incremental-RA-linux-ubuntu-18_04/329/console

@rudkx It is not clear to me that it has — the log you linked now 404s, and while I see that the build is broken, it is broken in URLSession tests, not NSURL creation. What are you seeing?


[4.0] NPM update

To update the assets and create this branch, I've run:
cd vendor/backpack/crud
git checkout -b npm-update
npm install
npm update
npm audit fix
npm prod
git commit -am "updated css and js assets"
git push origin npm-update

Fixed in https://github.com/Laravel-Backpack/CRUD/pull/2424 which got merged


feat: add STARKNET_FEE_ESTIMATE_OVERRIDE env to hardcode fee

Summary
This PR adds VITE_FEE_ESTIMATE_OVERRIDE that can be used to override fees in starknet-tx and herodotus clients.
The fees are pretty high on Sepolia right now, over $4 to just propose on Sepolia. We could hardcode it to<PHONE_NUMBER>0000000 to be safe.
How to test

Uncomment mana filter from yarn dev script.
Run STARKNET_FEE_ESTIMATE_OVERRIDE=10000000000000000 VITE_MANA_URL=http://localhost:3001 yarn dev
You can propose/vote on Starknet spaces with EthSig/StarkSig.
Max fee is hardcoded in transaction.

I don't understand why it use a VITE_ config var, this is only for UI but the fee estimate happen on Mana, how would this work?

Good point, VITE_ doesn't matter for non-vite projects (so it still works on mana), but it doesn't have to be prefixed with VITE_ if we don't use it in UI.
The prefix ended up there because I was testing it on UI, removed it now.

Also does that config var apply for both SN sepolia and mainnet?

Also does that config var apply for both SN sepolia and mainnet?

It will and it might not be ideal (fees used shouldn't be affected as long as we have enough for max fee) - I can make it per-network though.

Per network would be nice


Mapper 256 419 and more

Hello, I have a question, will mappers 295 313 256 419 413 353 be added?

Probably next year.  I need to tidy up some things before I can add the
underlying features needed for any new mappers, especially if they rely on
interrupts.
On Fri, Oct 25, 2024 at 4:54 PM TheBoxGamePL @.***>
wrote:

Hello, I have a question, will mappers 295 313 256 419 413 be added?
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thanks


[tests-only][full-ci]Add api tests to assign role using graph api

Description
This scenario adds scenario assign a role to a user using the graph API and check if its correctly listed by the graph API and and by the settings API
Related Issue

https://github.com/owncloud/ocis/issues/5565#

Motivation and Context

How Has This Been Tested?

locally

Screenshots (if appropriate):
Types of changes

[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)
[ ] Technical debt
[x] Tests only (no source changes)

Checklist:

[ ] Code changes
[ ] Unit tests added
[x] Acceptance tests added
[ ] Documentation ticket raised:

blocked until this issue confirm as a bug from the developer side https://github.com/owncloud/ocis/issues/5583?


direct installation via pip

A useful top that you may add to the documentation:
You can directly clone the repo and install via pip in one step:
sudo -H pip3 install git+https://github.com/princeton-vl/lietorch.git

Thanks, didn't know pip could do that! Just added to documentation

Using sudo uses a different python than the one you might want to use. When I do it, I get ModuleNotFoundError: No module named 'torch', while I do have torch (python3 -c "import torch" succeeds)

tl;dr: If you installed torch without sudo, you also have to install lietorch without sudo.

Using sudo uses a different python than the one you might want to use.

Do you mean a different Python interpreter or a different environment? Where do you have torch installed?
The global system environment is different from the local user environment. If you install torch as local user (under ~/.local/lib/python3.10/site-packages/) and try to use it from a package installed system-wide (under /usr/local/lib/python3.10/dist-packages/) it will not be located. A locally installed package can use a system-wide installed package, but not the other way around.


Trigger: NoMorale Issues

So I have two encounters running in one quest. I set an event to trigger on NoMorale to end the first encounter (staying in the quest). Then it begins the next encounter. I set another event to trigger on NoMorale for the second encounter. However, it either doesn't work or freezes up on me. I tried Assigning  the &%morale back up but that isn't working either. How can I take that nomorale tag off mid quest so I can run it again? Is it possible? Is there a workaround? Thanks!
DeathOnTheWing.zip

I'm curious about "doesn't work or freezes up" what do you mean?  When Morale is reduced to less than 0 it is instead set to 0, and NoMorale is triggered.  This can happen any number of times.  If you provide a working example of the fault I can investigate.
That said, the best way to do encounters is as two different quests.  Set the second encounter to hidden and have the first encounter end by launching the second.  Use Campaign vars to transfer data between the two encounters.  This will also take care of resetting the board and round state.

Thanks!
I attached the quest in my original comment. After the first nomorale triggered and Encounter 2 started I reset morale but after the opening event series it looped back to that nomorale trigger even though I had reset morale. So it was in this loop that kept opening Encounter 2. I had to close the program to stop it.
I then used a variable and set the events that trigger nomorale to test for encounter1 & 2 before running. When the second encounter ends by morale dropping to less than 0, the event bugs out and you have to click the button numerous times to get past it and it won’t go to the next event.
Hope that’s clear. I’ll take your advice and work on separating the encounters though. What do I use to trigger the next quest though? Not sure how to do that.  Thanks again!

So I've looked through the pages and still can't find how to trigger a new quest from an active one.  Sorry for the constant questions.  Really enjoying the editor.

This is one of the few things that you can't do in the editor.  Here is what I recommend:
1 Copy your scenario in Valkyrie (off the main menu).
2 Set the copy to 'hidden' and name it as encounter 2
3 Locate the original and copy in %appdata%\Valkyrie\D2E\Editor
4 Move the copy INTO the the directory of the original ie:
%appdata%\Valkyrie\D2E\Editor\Original\quest.ini
%appdata%\Valkyrie\D2E\Editor\Original\Copy\quest.ini
But then rename Copy to be something like 'encounter2'
5: Add an event in the original which is something like 'EventNextEncounter', add a button and one next event (any)
6: Edit Original/events.ini and find EventNextEncounter and change the next event that was added above to 'encounter2/quest.ini' (or whereever you placed encounter 2).
Now anywhere you call EventNextEncounter from will start the next quest.
I will investigate the trigger issue.

Found the NoMorale bug, AdjustMorale function is assuming that the morale is reset to 0 when it goes negative, however this is only happening for the local variable, not the morale master.

It worked! Thank you so much! No "NoMorale" bug and it's so much cleaner to do it this way.  Just have to switch some things to a campaign variable and it should be complete!

From what I can read, a workaround is available.
I'm removing this from 2.1 scope.
@Maverick4jc, feel free to tell us if you think this issue should be fixed urgently.


feat: enhence rest api tools

Summary
This PR did some enhencement for app module(rest api).
Key Points

[ ] This is a breaking change
[x] New or existing documentation is updated

Description

[x] add global excepiton handler
[x] add logger example #192
[x] log exceptions
[x] add default value for request pagination parameter.

Does this close any open issues?
Current Behavior
New Behavior
Screenshots
Other Information

close due to language switch


Jupyter Notebook Don't save automatically even on autosave after delay enabled

Issue Type: Bug
Create a new jupyter notebook (using ctrl+shift+p and select create new jupyter notebook), startworking on it but new changes made on the notebook are not saved. Though I expect it to be saved. But If I close and reopen the notebook it works fine.
PS : I cannot be sure if its python extention issue of  Vscode.
Extension version: 2020.5.86806
VS Code version: Code 1.45.1 (5763d909d5f12fe19f215cbfdd29a91c0fa9208a, 2020-05-14T08:27:35.169Z)
OS version: Windows_NT x64 10.0.19041

System Info

Item
Value

CPUs
Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz (8 x 1800)

GPU Status
2d_canvas: enabledflash_3d: enabledflash_stage3d: enabledflash_stage3d_baseline: enabledgpu_compositing: enabledmultiple_raster_threads: enabled_onoop_rasterization: disabled_offprotected_video_decode: enabledrasterization: enabledskia_renderer: disabled_off_okvideo_decode: enabledviz_display_compositor: enabled_onviz_hit_test_surface_layer: disabled_off_okwebgl: enabledwebgl2: enabled

Load (avg)
undefined

Memory (System)
7.88GB (1.25GB free)

Process Argv

Screen Reader
no

VM
0%

@goyal-aman . Just to confirm (this is what I'm seeing when I try to repro this):

Turn autosave to "afterDelay"
Create a new blank notebook
Save the notebook
Type in the notebook some
At this point the file is not saved after typing and is still dirty
Close the file
Reopen the file
Type in the notebook some
At this point the file is saved after typing and is not dirty

Is that what you are seeing as well? Looks like after creating a new notebook that autosave doesn't work until the file is saved and reopened.

Exactly. Autosave after delay doesn't newly created blank notebook until closed and reopened.


status query is not working  as expected

Describe the bug
node shown as down while using status=up query
To Reproduce
Steps to reproduce the behavior:
check https://gridproxy.dev.grid.tf/nodes/18?status=up&size=1
Expected behavior
show list only up status node

as we discussed it is an invalid URL.
either filter the nodes endpoint /nodes?status=up&size=1 or call a single node /nodes/18


Laravel 5.3

Hi guys!
Can I use it with Laravel 5.3?

yaa i want to know that too

I've just tagged a new release, 2.2.0, which will work for Laravel 5.3

Great! Thanks!


Let's provide a link to roast for every documented feature!

… I know it sounds scary, but wouldn't it be amazing?
Besides providing some extra examples and making stuff more clear in places where the documentation is not that great, it will also give us an easy way to find undertested features!
I think that it is a great idea, at least hypothetically. Now how do we implement this? Line numbers in roast are not permanent. Does it mean that we will have to put some kind of special markers in roast files?

Str::match (that is not documented, that's why I know) shows up in 12 different spec files. There are many such features. If you look for subscripts it's dozens of files.
The idea sounds appealing until you try to implement it. It's just way to much stuff to handle. If you want to find stuff in the spec you have to have good grep skills.

I think piggy backing off the existing markers is a good idea, and it's also a reasonable way to add new markers into roast.
I also think that if one doesn't try to be exhaustive about it -- i.e., accept that some documentation pages might not have all (or any) of the relevant references to roast -- it can still be very useful to have.  For example, with Str::match it might be okay to simply link to a few prominent instances of Str::match being used in roast, rather than try to find and link all of them.  If someone needs to know all of the occurrences, then do a grep.  :)
Pm

Should this be part of the documentation, or part of the site? Like, try and link every Type to a roast test file.

@JJ I think this can only be done section by section, so it'd need a lot of work and yes, it should be part of the documentation.

I wouldn't agree that the docs in this repo are intended for entry (level?) users. It's mostly reference type documentation which is generally read by more experienced users. Entry level users are probably better off reading tutorial type documentation (which is sadly lacking at the moment) as a primary resource and using reference documentation as a secondary resource (until they become more used to it).
I think the original idea of linking ref docs to roast tests is a excellent one and the original issue should be kept open.

Issues are better solved than kept open

Yes but closing a github issue does not solve the issue.

to a GitHub search query in the roast repo can be easily done

I don't think it'll give any meaningful (or usable) results.

Advanced users can probably figure out looking stuff up in roast without us taking them by the hand.

That's LTA.

Less Than Awesome.

if solving this issue involves reviewing every single doc page and adding something, as well as adding something else to the build system, I'd really rather not

Well… you don't have to do it…

So that's what you are looking for? Including some tag or metadata in every page indicating the corresponding roast test? Anything less than that would be LTA?

Also, we could try to figure out the link Class name → synopsis → roast line numbers that has been mentioned above. I don't know how hard it would be or how generalized are these markers. But hoping that they are good for every class here is a long shot.
I still think that in this case the best would be to arrive to a compromise option, like including that in the writing guide and make it more or less compulsory for every class file that is modified, maybe by including an author test.

I think we'd need to spend the time first in cleaning up roast so that it is clear what feature is being tested, at which point, we can use the information from tagging in roast to drive the documentation links. I don't think having this in raku/doc first makes sense. If someone is still exciting about this, please open a roast or problem-solving ticket to track this issue. Thanks.


intermittent crash in tests/portability/cmsis_rtos_v2 on qemu_x86

Describe the bug
starting test - test_mutex_lock_timeout
E: Page fault at address 0xe (error code 0x0)
E: Linear address not present in page tables
E:   PDE: 0x0000000000120827 Writable, User, Execute Enabled
E:   PTE: Non-present
E: EAX: 0xffffffff, EBX: 0x001579dc, ECX: 0x00000000, EDX: 0x00000000
E: ESI: 0x00000000, EDI: 0x00000286, EBP: 0x0012d194, ESP: 0x0012d188
E: EFLAGS: 0x00000046 CS: 0x0008 CR3: 0x00122000
E: call trace:
E: EIP: 0x00109424
E:      0x00107551 (0x1579dc)
E:      0x001017f8 (0x1579dc)
E:      0x001066d1 (0x1579dc)
E:      0x00104389 (0x1579dc)
E: >>> ZEPHYR FATAL ERROR 0: CPU exception on CPU 0
E: Current thread: 0x00122580 (Mutex_check)
E: Halting system

I checked the binary to get symbols for the reported call trace:
(gdb) x/fx 0x00109424
0x109424 <z_impl_k_mutex_lock+496>:	0x0e4abe0f
(gdb) x/fx 0x00107551
0x107551 <osMutexAcquire+89>:	0xf0f8835a
(gdb) x/fx 0x001017f8
0x1017f8 <tThread_entry_lock_timeout+66>:	0xfef8835e
(gdb) x/fx 0x001066d1
0x1066d1 <zephyr_thread_wrapper+13>:	0xe083c658
(gdb) x/fx 0x00104389
0x104389 <z_thread_entry+15>:	0xe80cc483

The fault seems to be here, where mutex->owner->base.prio is checked...maybe we have a race where mutex->owner is now NULL?
103	}
104
105	static bool adjust_owner_prio(struct k_mutex *mutex, s32_t new_prio)

106	{
107		if (mutex->owner->base.prio != new_prio) {
   0x00109424 <+496>:	movsbl 0xe(%edx),%ecx
   0x00109428 <+500>:	cmp    %ecx,%eax
   0x0010942a <+502>:	je     0x10944d <z_impl_k_mutex_lock+537>

108

To Reproduce
Seen in a sanitycheck run
ERROR   - qemu_x86                  tests/portability/cmsis_rtos_v2/portability.cmsis_rtos_v2 FAILED: Exited with 2
ERROR   - see: /dev/shm/sanity-out/qemu_x86/tests/portability/cmsis_rtos_v2/portability.cmsis_rtos_v2/handler.log

Expected behavior
The test should not crash like this.
I don't know whether this is some issue related to emulator timings, but at worst those issues should result in a failed assertion, and not a full-on page fault.
Hopefully this is a test case problem and not an issue with the CMSIS layer or the mutex code.
I don't know if this is limited to qemu_x86 or has been observed on other platforms.
Impact
Needs root-cause analysis to determine severity, currently only seen on a test case.

The locking looks right, all assignments to mutex->owner, as well as any entry to adjust_owner_prio() are held with the mutex code's spinlock. My suspicion is someone is calling k_mutex_init() on a mutex that is in use.

Investigating this bug but I'm having trouble reproducing it.

Still cannot reproduce. Closing for now.


Verify that IncludedConfigurations system property works

@drewtwitchell  based on your call with a customer asking to expand scopes, can you verify the following:
IncludedConfigurations can be set as system property.
They can then list the scopes they are interested in, comma separated.

@akamen I have just included you on an email with that company that asked about this. Please advise.

I have tested the IncludedConfigurations property.  Use a java -D option to set it on the command line.
In order to include the -D java option on the command line it looks like you need to use the gradle wrapper to execute the build.  Execute gradle wrapper to generate the gradle wrapper.  Then you can invoke the ./gradlew with the java property set.  An example is shown below.
example:  ./gradlew deployHubOutputAndCheckPolicies -DIncludedConfigurations="testCompile,runtime"

includedConfigurations will be a configurable property in the gradle tasks in the 3.2.0 version.  About to commit the changes to include it.


Get rid of execa

source: http://npm.broofa.com/?q=lint-unpushed

Wrote https://www.npmjs.com/package/@steelbrain/exec
Has zero dependencies and a decent API


Add Linux docker containers on Windows 2019 environment

Tool name
Linux docker containers
Tool license
?
Add or update?

[X] Add
[ ] Update

Desired version
latest
Approximate size
No response
Brief description of tool
At the moment it's not possible to use the Windows 2019 image within Azure DevOps Pipeline to build Linux based docker images. Now we need to use ubuntu-latest to get this working - but it would be nice that this is also available within the Windows 2019 image.
Problem is that the installation of Docker on Windows 2019 only supports platform 'windows' and not 'linux.
For this reason it's not possible to build image of: node or nginx which only supports linux containers.
URL for tool's homepage
https://docs.microsoft.com/en-us/virtualization/windowscontainers/deploy-containers/linux-containers
Provide a basic test case to validate the tool's functionality.
docker run --rm --platform linux alpine ls

Platforms where you need the tool

[X] Azure DevOps
[ ] GitHub Actions

Virtual environments where you need the tool

[ ] Ubuntu 18.04
[ ] Ubuntu 20.04
[ ] Ubuntu 22.04
[ ] macOS 10.15
[ ] macOS 11
[ ] macOS 12
[X] Windows Server 2019
[ ] Windows Server 2022

Can this tool be installed during the build?
Couldn't find a way to do this.

Tool installation time in runtime
No response
Are you willing to submit a PR?
Yes - if I've the solution

Hey @DanielOverdevest.
Unfortunately, we can't add linux container support due to Azure vm spec limitation we use, at that moment it is DSv2-series without supporting nested Hyper-V virtualization.

Thanks for swift response! I understand.


CI: Unable to ping endpoint with init policy. TTL exceeded

20:24:14     Cannot ping endpoint with init policy
20:24:14     Expected command: ping -W 2 -c 5 <IP_ADDRESS>
20:24:14     To succeed, but it failed:
20:24:14     Exitcode: 1
20:24:14     Stdout:
20:24:14      	 PING <IP_ADDRESS> (<IP_ADDRESS>) 56(84) bytes of data.
20:24:14     	 From <IP_ADDRESS> icmp_seq=1 Time to live exceeded
20:24:14     	 From <IP_ADDRESS>: icmp_seq=1 Redirect Host(New nexthop: <IP_ADDRESS>)
20:24:14     	 From <IP_ADDRESS> icmp_seq=2 Time to live exceeded
20:24:14     	 From <IP_ADDRESS>: icmp_seq=2 Redirect Host(New nexthop: <IP_ADDRESS>)
20:24:14     	 From <IP_ADDRESS>: icmp_seq=3 Redirect Host(New nexthop: <IP_ADDRESS>)
20:24:14     	 From <IP_ADDRESS> icmp_seq=3 Time to live exceeded
20:24:14     	 From <IP_ADDRESS>: icmp_seq=4 Redirect Host(New nexthop: <IP_ADDRESS>)
20:24:14     	 From <IP_ADDRESS> icmp_seq=4 Time to live exceeded
20:24:14     	 From <IP_ADDRESS> icmp_seq=5 Time to live exceeded
20:24:14
20:24:14     	 --- <IP_ADDRESS> ping statistics ---
20:24:14     	 5 packets transmitted, 0 received, +5 errors, 100% packet loss, time 4015ms
20:24:14
20:24:14
20:24:14     Stderr:

https://jenkins.cilium.io/job/cilium-ginkgo/job/cilium/job/master/1461/execution/node/96/log/?consoleFull
616c54a2_RuntimePolicies_Init_Policy_Test_Init_Ingress_Policy_Test.zip

Discussion with @joestringer we think it's because the endpoint's entry in the lxcmap is not written after the endpoint add API request is completed.

Is the endpoint add API request always synchronous? I think this was changed for the CNI plugin some time ago, I wonder if this was changed in the core API code or if there is some difference in the client request which needs to also occur from the docker plugin.

@aanm how frequently do we hit this?

@joestringer so far only one time.

I believe that in this scenario, we don't know how to deliver to the destination because the endpoint no longer exists on the local node. Even if we handled this more gracefully, I think it would involve explicitly checking this condition and dropping the packet rather than forwarding on to another device which loops the packet back and ends up dropping the packet by looping and dropping TTL until the packet expires.

This was fixed by #5663


Typo fixes

Fixes some typos in german translation

@AlkoholLiga Thanks for the fixes but translation work is done on Transifex platform and then po files are pulled back to this repository. So any fixes to translations should be done there, otherwise they will likely be overwritten at the next pull. Please join the german team.


[Status] SE-0136 is accepted and implemented

Closing due to merge conflict; will re-open and ping someone for merging.


Add debugging code for ETH not getting updated when creating market

CH-issue

Coverage increased (+0.01%) to 63.817% when pulling 0405e00016f1ed12f346c17bc89ab804e1cddc1e on adrake/ch16152/add-debugging-code-for-eth-not-getting-updated into 120e6dceb2836cc5fdc5d0c0648889f765663ea5 on master.


fix: Detect title of commits with both line ending

GitHub's Dependabot has commits that contain both CR/LF and LF, the previous logic did not always split the commit message correctly
Fixes: #1042
Context

Checklist

[x] Review Contribution Guidelines.
[x] Make sure all contributed code can be distributed under the terms of the
Apache License 2.0, e.g. the code was written by
you or the original code is licensed under a license compatible to Apache License 2.0.
[ ] Update documentation when applicable.

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

I'm not sure the test added fits the conventions used here, feel free to suggest an alternative approach 😄

Thank you! 😄


Cache not working

 PROC_SHOPIFY_CACHE = 12 * 60 * 60 async def proc_shopify(order_no):     url = f"https://alfuuktopkh.myshopify.com/admin/api/2023-07/orders.json?name={order_no}&status=any"     headers = {         'Content-Type': 'application/json',         'X-Shopify-Access-Token': ADMIN_token,         "cache-control": f"max-age={PROC_SHOPIFY_CACHE}"     }     async with httpx_cache.AsyncClient() as client:         response = await client.get(url, headers=headers)
I don't think caching is working on the request, as the response is similar in multiple runs.

I don't think caching is working on the request, as the response is similar in multiple runs.

Can you give more details about the issue ?
If my understanding is correct, you mean multiple runs of your app/script, and not multiple runs of the request in the same program. I see you are using the default memory cache in your httpx_cache.AsyncClient, so maybe just switching that to a FileCache or a RedisCache wuld solve your issue.
More in cache type and how to use them: https://obendidi.github.io/httpx-cache/guide/#cache-types
The (default) in-memory dict cache is cleared at the end of your script (it's a simple python dict), so you can't reuse cache across multiple runs of your script.
The file/redis cache are more consistent.

I'm using fastapi and Uvicorn, so the the request is basically to our other servers, so it's not a complete re-run, i'll still consider running redis or something though

Does httpx_cache support caching of POST requests as well, or do we have to use custom transport

I'm using fastapi and Uvicorn, so the the request is basically to our other servers, so it's not a complete re-run, i'll still consider running redis or something though

If you are using httpx_cache in fastapi endpoints, you can keep a single cache lient in the app state so that it shared by all endpoints and request instances, creating a different httpx_cache.Client for each request, will discard the cache at the end of that request, example:
from fastapi import FastAPI, Depends, Request
import httpx_cache

async def lifespan(app: FastAPI):
    print("startup ...")
    httpx_client = httpx_cache.AsyncClient()
    app.state.client = httpx_client
    yield
    print("shutdown ...")
    await httpx_client.aclose()

app = FastAPI(lifespan=lifespan)

async def get_httpx_client(request: Request) -> httpx_cache.AsyncClient:
    return request.app.state.httpx_client

@app.get("/")
async def get_httpbin(
    httpx_client: httpx_cache.AsyncClient = Depends(get_httpx_client),
):
    response = await httpx_client.get("https://httpbin.org/get")
    response.raise_for_status()
    return response.json()

Does httpx_cache support caching of POST requests as well, or do we have to use custom transport
Not by default, but you can easily add it if you want, links in the docs:

https://obendidi.github.io/httpx-cache/cache_control/
https://obendidi.github.io/httpx-cache/api/#client

httpx_cache.Client(cacheable_methods=["GET", "POST"])

You should keep in mind that you probably don't want to cache POST request, because they are requests that make changes in the requested server, so it doesn't make sens to cache them (it might be different for your use case, so you know better :) )

So yeah, i was having some issues with the remote redis-server hosted by redis, so i move to file cache, which is working great..
Actually i'm trying to cache the response of the POST, as it's for checking the status of an order, and post value has a 2step key in the body.
But i'm thinking of a different approach now, i'll instead host that particular script seprately, and have a get request to get data from that script, that way, i have more control over caching.

Closing as the issue is no longer related to httpx-cache


First coordinate skipped when populating alignment arrays

Hi Jon,
I'm not sure if I've followed your code exactly right, but in the align_tracks() routine while loop, you maintain i > 0 || j > 0.
The children if statements then decide which alignment sequence to apply the coordinate to.
If I'm right, this means the final coordinate track1[0] and track2[0] NEVER get prepended onto a1 and a2
My testing seems to support this, but I have rewritten a lot of this in PHP so it may be a flaw on my part, but logically I see the same issue with the python code.
Your images on your blog seem to support this as well with the initial coordinate not being blue.
I'm trying to figure this out on my end, unfortunately, I'm not extremely familiar with these matrixes, and obviously if i == 0, i-1 is an undefined index which would break these if statements.
Any insight?

Oh, and I should have prefaced this by saying, thank you for sharing your code. It has been interesting to tinker with it and consider this algorithm for comparing GPS tracks.


Add fastlane

needed for #17
see: https://gitlab.com/fdroid/rfp/-/issues/1456#note_401907057
when creating a release a changelog txt should be added to fastlane/metadata/android/en-US/changelogs/ !

@vikulin thanks - and wow this was fast!!!


Lack of documents for deployment

I want to deploy a tf-operator on my cluster, but I can't find documents about it.
does anybody have tutorials about it?

@hykych Thanks for the issue. We do not have a separate doc to deploy tf-operator. Maybe you could refer to doc https://www.kubeflow.org/docs/started/getting-started/#installing-kubeflow to setup kubeflow.


Persistent 419 error

Hi,
My Success Story is repeatedly showing an authentication error (see image below). I have tried re-authenticating as well as re-installing the extension. New achievements are not being tracked and the extension seems overall unresponsive. I've also attached a log package in case that is of use, but any help or guidance would be appreciated, thanks!
SuccessStory_2024-02-29.zip

Well, I also had this problem and I swear I tried to find a solution everywhere, and apparently some people say that the Plugin works for them, not all of them say it works but for example, in my case, it doesn't work either.
And I didn't see anyone talking about a solution or anything like that, nothing at all. But the fact that I heard people saying that the plugin works and I did everything they said and the official guide sites said to do and still got this error, made me think that maybe the new version (3.1.7) was everything was bugged, and I got it right.
If you install version (3.1.5) of SuccesStory, it works minimally better. So for now I recommend you and everyone who has this problem to install this version (3.1.5), version (3.1.6) also has some bugs. For me it worked better (3.1.5) and I literally spent a whole day figuring it out and so far it's working well, the only thing that doesn't work well is the update but at least it shows the achievements and manually you can edit it.
Now we have to wait until the version (3.1.8) comes out.
Link - https://github.com/Lacro59/playnite-successstory-plugin/releases/tag/v3.1.5

Can you try this?
https://github.com/Lacro59/playnite-successstory-plugin/issues/479#issuecomment-2191342743


Feature/user defined functions

Codecov Report

Merging #29 (a22d75c) into master (499a1d8) will increase coverage by 3.74%.
The diff coverage is 58.69%.

@@             Coverage Diff              @@
##             master      #29      +/-   ##
============================================
+ Coverage     43.81%   47.56%   +3.74%
- Complexity      188      243      +55
============================================
  Files            54       63       +9
  Lines           986     1169     +183
  Branches        109      123      +14
============================================
+ Hits            432      556     +124
- Misses          510      564      +54
- Partials         44       49       +5

Impacted Files
Coverage Δ

...tlin/org/actorlang/ast/printer/AstPrettyPrinter.kt
0.00% <0.00%> (ø)

...rg/actorlang/interpreter/eval/BehaviorEvaluator.kt
59.25% <0.00%> (-7.41%)
:arrow_down:

...interpreter/exceptions/UnknownFunctionException.kt
0.00% <0.00%> (ø)

...kotlin/org/actorlang/ast/visitor/BaseAstVisitor.kt
24.00% <17.64%> (-1.43%)
:arrow_down:

...in/org/actorlang/interpreter/eval/RootEvaluator.kt
39.28% <50.00%> (+4.28%)
:arrow_up:

...rg/actorlang/interpreter/eval/AbstractEvaluator.kt
36.00% <70.00%> (+6.90%)
:arrow_up:

...rg/actorlang/interpreter/eval/FunctionEvaluator.kt
72.97% <72.97%> (ø)

src/main/kotlin/org/actorlang/ast/CallNode.kt
100.00% <100.00%> (ø)

.../main/kotlin/org/actorlang/ast/FunctionCallNode.kt
100.00% <100.00%> (ø)

...c/main/kotlin/org/actorlang/ast/FunctionDefNode.kt
100.00% <100.00%> (ø)

... and 9 more

:mega: Codecov can now indicate which changes are the most critical in Pull Requests. Learn more


Top Upcoming anime list not being retrieved

Is there an existing issue for this?

[X] I have searched the existing issues

Current Behavior
Request I tried:
https://api.jikan.moe/v4/top/anime?filter=upcoming&limit=5
returns:
{"pagination":{"last_visible_page":1,"has_next_page":false,"current_page":1,"items":{"count":0,"total":0,"per_page":5}},"data":[]}
Expected Behavior
Expected return:
a list of top upcoming anime
Steps To Reproduce
No response
Environment
Browser: Microsoft Edge Version 109.0.1518.100

Anything else?
No response

duplicate of #388
fixed in: #408  -> not yet deployed

Resolved


Channel Updates : Database and Server Code Updates PART 2

9eb9ca4 : This issue Contains insertion of DB when user is added by other group


[BUGFIX] Fix workspace of BoxNMS

Description
This commit fixes 2 problems:

previously in the calculation of the workspace size of NMS operator the space for the buffer was not included, resulting in potentially too small allocation
because the type requested for uint8_t, the maximum workspace size without setting large tensor support was 2GB, which was too small for some cases, without any error reporting (going over that limit would make the index_t in Shape1 overflow, resulting in negative value, which would later be cast to size_t in the allocator and MXNet would try to allocate a huge amount of memory, resulting in OoM). This PR changes the type of the allocation to double so that the size limit for workspace rises to 16 GB when large tensor support is not enabled.

Checklist
Essentials

[x] PR's title starts with a category (e.g. [BUGFIX], [MODEL], [TUTORIAL], [FEATURE], [DOC], etc)
[x] Changes are complete (i.e.


STYLE: Remove private ImageScanlineConstIterator member Increment()

ImageScanlineConstIterator::Increment() was only called once, by
ImageScanlineConstIterator::NextLine().

@dzenanz Thanks for your approval! I'm sorry I forgot how to rerun a specific machine. ITK.macOS.Python, in this case. Something like /AZP run...?

/azp run ITK.macOS.Python


Fixed spacing and removed Sean from Contributors since he's in the maintainers list

Merging my own pull request again, mostly to fix the spacing issue introduced in the last commit.


feat: handle org config dump if not present

Resolves #9

Create a Dockerfile for custom peribolos binary that solves this issue. This binary is then used in the updated dump-config task.
Add an CustomResourceApiCall to create a taksrun for the dump-config task

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Skipping CI for Draft Pull Request.
If you want CI signal for your change, please convert it to an actual PR.
You can still manually trigger a test run with /test all

/hold
Need to update app-id in the GIT_EMAIL parameter.

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66dd39479312d21ebaa8b826cda6de29d24f16da
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/unhold

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PR updated, thanks for the suggestions!

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Add azure-sdk-for-js to compute/resource-manager/readme.md

This checklist is used to make sure that common issues in a pull request are addressed. This will expedite the process of getting your pull request merged and avoid extra work on your part to fix issues discovered during the review process.
PR information

[ ] The title of the PR is clear and informative.
[ ] There are a small number of commits, each of which have an informative message. This means that previously merged commits do not appear in the history of the PR. For information on cleaning up the commits in your pull request, see this page.
[ ] Except for special cases involving multiple contributors, the PR is started from a fork of the main repository, not a branch.
[ ] If applicable, the PR references the bug/issue that it fixes.
[ ] Swagger files are correctly named (e.g. the api-version in the path should match the api-version in the spec).

Quality of Swagger

[ ] I have read the contribution guidelines.
[ ] My spec meets the review criteria:

[ ] The spec conforms to the Swagger 2.0 specification.
[ ] The spec follows the guidelines described in the Swagger checklist document.
[ ] Validation tools were run on swagger spec(s) and have all been fixed in this PR.

Automation for azure-sdk-for-ruby

Automation for azure-sdk-for-java

Automation for azure-sdk-for-go

Can one of the admins verify this patch?

Blocked by https://github.com/Azure/azure-rest-api-specs/pull/3939.

Automation for azure-sdk-for-js


Rust Medium - Temperature Converter

I'm not sure about the last two tests

I'm not sure about the last two tests

This code and tests are really well done, props for that! I think the last two tests should also work just fine and they are good for simulating how real user would behave.

Merged

This is an automated message from Fork, Commit, Merge [BOT].

Thank you for your contribution! Your pull request has been merged. The files have been reset for the next contributor.
What's next?
If you're looking for more ways to contribute, I invite you to check out my other projects. Just click here to find more. These projects contain real issues that you can help resolve.
Also please leave a star to this project if you feel it helped you, i would really appreciate it.
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The response object no work properly

This pull request reference the issue #3

We integrated the changes upstream.


nixpkgs.config and nixpkgs.overlays do not seem to work

Setting the nixpkgs.config and nixpkgs.overlays options in my home-manager configuration does not seem to do anything. This can probably most easily be replicated by setting:
nixpkgs.config = { allowUnfree = true; }
and trying to install a nonfree package via nix-env.
I am using the NixOS module to set my configuration.

That's intended behaviour, these setting only apply to the pkgs set in the module evaluation. This is the same behaviour for nixos' nixpkgs.* options.
I guess this could be made clearer in the options description.

Yeah, this is by design. In my configuration I have
nixpkgs.config = import dotfiles/nixpkgs-config.nix;
xdg.configFile."nixpkgs/config.nix".source = dotfiles/nixpkgs-config.nix;

to have the same configuration in both places.

I'll close this issue now but I opened #230 to improve the option descriptions a bit. Please have a look and comment on the phrasing (which I didn't spend much time on).

How does one allow nonfree packages in the scope of their home.nx?

@taohansen Sorry for the delay. It should be possible with something like nixpkgs.config.allowUnfree = true; in your home.nix.

@taohansen Sorry for the delay. It should be possible with something like nixpkgs.config.allowUnfree = true; in your home.nix.

I just tried replacing the file in ~/.config/nixpkgs/config.nix with the above in home.nix, but when switching HM complained about a non-free package - so it seems this is not working.


Intellij project error

when ever I start an express project in intellij it gives me this error.
Error creating Node.js Express App. Failed command:
/usr/bin/node /usr/bin/npm install<EMAIL_ADDRESS>Exit code: 1
Standard error:
npm WARN locking Error: EACCES, open '/home/taylor/.npm/_locks/express-generator-e52dc05ea52f878b.lock'
npm WARN locking  /home/taylor/.npm/_locks/express-generator-e52dc05ea52f878b.lock failed { [Error: EACCES, open '/home/taylor/.npm/_locks/express-generator-e52dc05ea52f878b.lock']
npm WARN locking   errno: 3,
npm WARN locking   code: 'EACCES',
npm WARN locking   path: '/home/taylor/.npm/_locks/express-generator-e52dc05ea52f878b.lock' }
npm ERR! Linux 3.13.0-55-generic
npm ERR! argv "/usr/bin/node" "/usr/bin/npm" "install"<EMAIL_ADDRESS>npm ERR! node v0.10.25
npm ERR! npm  v2.11.3

npm ERR! Attempt to unlock /tmp/intellij-express-generator3.tmp/node_modules/express-generator, which hasn't been locked
npm ERR!
npm ERR! If you need help, you may report this error at:
npm ERR!     <https://github.com/npm/npm/issues>

npm ERR! Please include the following file with any support request:
npm ERR!     /tmp/intellij-express-generator3.tmp/node_modules/npm-debug.log

Unfortunately that is an error with permissions on your machine. You can always try to ack for help on npm at https://github.com/npm/npm/ or try to run sudo rm -rf /home/taylor/.npm/ and see if that helps.


Bump alpine to 3.19.1

How to categorize this PR?

/area compliance
/kind enhancement
What this PR does / why we need it:
Bump alpine to 3.19.1 to address https://github.tools.sap/kubernetes/compliance-reporting/issues/6533
Which issue(s) this PR fixes:
Fixes #
Special notes for your reviewer:
Release note:

Bump alpine to 3.19.1

/cherry-pick release-v1.90

/cherry-pick release-v1.89

/cherry-pick release-v1.88


Testing: Platform/integration test for manual approval use case

Platform and integration tests for the manual approval use case need to be implemented.
Supported combinations of the property approval_strategy:

evaluation result: pass
evaluation result: warning
expected behavior

combi 1:
pass:automatic
warning:automatic
configuration-change for next stage is sent out

combi 2:
pass:automatic
warning:manual
if the evaluation result is a warning, an approval.triggered event is sent out

combi 3:
pass:manual
warning:automatic
if the evaluation result is a pass, an approval.triggered event is sent out

combi 4:
pass:manual
warning:manual
regardless of the evaluation result, an approval.triggered event is sent out

Test scenario:

Create a project based on the following shipyard file:

stages:
  - name: "dev"
    deployment_strategy: "direct"
    test_strategy: "functional"
  - name: "combi1"
    approval_strategy:     # approve based on evaluation result from dev
      pass: "automatic"
      warning: "automatic"
    deployment_strategy: "blue_green_service"
    test_strategy: "performance"
  - name: "combi2"
    approval_strategy:     # approve based on evaluation result from combi1
      pass: "manual"
      warning: "automatic"
    deployment_strategy: "blue_green_service"
    test_strategy: "performance"
  - name: "combi3"
    approval_strategy:     # approve based on evaluation result from combi2
      pass: "automatic"
      warning: "manual"
    deployment_strategy: "blue_green_service"
    test_strategy: "performance"
  - name: "combi4"
    approval_strategy:     # approve based on evaluation result from combi3
      pass: "manual"
      warning: "manual"
    deployment_strategy: "blue_green_service"
    test_strategy: "performance"
  - name: "production"
    deployment_strategy: "blue_green_service"
    remediation_strategy: "automated"

Send 3 evaluation-done events (result: pass, warning, failed) for each stage (dev, combi1, combi2, combi3) using the CLI.

Retrieve the open approvals using the CLI and verify the number of open approvals as shown below:
keptn get event approval.triggered --project=PROJECTNAME --stage=[combi1, combi2, combi3, combi4]

Expected number of open approvals:

Stage
No. of open approvals

combi 1:
0 open approvals

combi 2:
1 open approvals

combi 3:
1 open approvals

combi 4:
2 open approvals

For stage combi1, send an approval.finished event to Keptn specified by keptncontext:
keptn send event approval-finished --project=PROJECTNAME --stage=combi1 --id=1234.5432
--> verify CLI output

For stage combi2, send an approval.finished event to Keptn that has a different image/tag compared to the approval.triggered:
keptn send event approval-finished --project=PROJECTNAME --stage=combi2 --id=1234.5432
--> verify CLI output

For stage combi4, send a valid approval.finished event to Keptn.
keptn send event approval-finished --project=PROJECTNAME --stage=combi4 --id=1234.5432
--> verify the number of open approvals for this stage (using the command keptn get events approval.triggered)

Definition of Done:

[ ] Travis-CI is extended by the test script test_manual_approval.sh covering the above test scenarios of this use case
[ ] Test script is executed as part of a Keptn test on GKE: https://github.com/keptn/keptn/blob/master/.travis.yml#L111

I moved this back into the backlog in favor of #1896


Type safe fetched results controller

Added a type safe Fetched Results Controller thanks to @jgallagher and @zwaldowski
Updated the sample project with an example
Wrote unit test cases around the FRC
Updated the docs with better Markdown sugar

I believe I've addressed everything if someone else wants to give a quick run through.

@zwaldowski gotcha. Updated

:+1: We're well on our way to a great next release!


Add more resiliency features

Need to think about some additional resiliency features. Some loose ideas:

When not all messages in a batch are produced, keep retrying the remainder, instead of breaking off the production loop

This is particularly important if using pure push approaches, like PostgreSQL with WAL, where we can't mark things partially completed
Not relevant for polling providers

When there are issues with message production, have some backoff to avoid retying too much in a short amount of time
Retry acknowledging produced messages
Include some sort of "health check" abstraction, that the user can implement and OutboxKit checks, in order to pause trying to produce when either the database or the messaging infrastructure is having problems
Handle poison messages?

Not a fan of this, given it might mess up ordering guarantees, but may be worth having the option

Detect when the database is in readonly mode (e.g. during a blue/green deployment) and stop trying to produce, as it won't be able to mark messages as completed

You probably already have good solutions for these features in mind, but here are my 2 cents:

Retry acknowledging produced messages

Consumers need to be idempotent. I think this problem is inherent to the pattern itself, it’s a known problem, but to try to mitigate it may make sense the implementation.
So, thinking in a scenario in which it is not possible to mark the record in the outbox table as processed or delete it, an already produced message will return in the next loop. There may be some in-memory state mechanism of the latest successfully produced messages, so if you can't mark it in the database, you could mark it in memory and avoid processing it in the next loop. At some point, this state in memory may be released, or persisted in bulk when the database is operational again. (probably this is a bad solution, there must be another better way to avoid this problem, but I’m not reaching at the moment).

Include some sort of "health check" abstraction, that the user can implement and OutboxKit checks, to pause trying to produce when either the database or the messaging infrastructure is having problems

With the result of the "health check", you could have something like a "Circuit Breaker" when your infrastructure (database, broker) has N failures in X time, so you can pause the processing. I think this should not be left to the user to implement, but it could be a core feature of the OutboxKit, or the user could have the option to enable/disable this feature.

Handle poison messages?

Maybe it makes sense to have a "retry_count" and "failure_reason" in the outbox table. Imagine that you are trying to publish a certain message, and it always fails for some reason, mark that tried X times, until a limit in which it does not try this message, and then raises an alert. With the option to enable/disable in the OutboxKit configuration.

You probably already have good solutions for these features in mind, but here are my 2 cents:

I have some ideas, not sure if "good solutions" 😅

Retry acknowledging produced messages

This can go from simple(ish) to very complex, depending on how much one wants to invest in this. Personally, I'm tilting towards simple(ish). Not sure how yet, but my idea is indeed to keep the messages pending ack in memory, then keep retrying to ack them on an interval, not producing any additional messages in the meantime (to ensure order).

Include some sort of "health check" abstraction...

I think this should not be left to the user to implement

It has to be left to the user to implement. OutboxKit may include some database specific features to aid, but having an extensibility point for unaccounted for possibilities might be useful. Additionally, OutboxKit will not include broker specific code, so if we want to pause trying to produce in the face of broker issues, we'll need to rely on the users to do it.

Handle poison messages?

Yeah, that's probably the way to go, have something opt-in, for scenarios where order isn't relevant and we don't want all the messages to get blocked due to a problematic one.


Added fuzzer with oss-fuzz build script

This PR adds a fuzzer for decodeRequest along with the build script in case there is interest in setting up continuous fuzzing for Sarama by way of oss-fuzz.
I have the build files available for the oss-fuzz side and I will be happy to integrate Sarama.

Does anyone have a solution for the failed CI tests? It sure looks like an issue with the tests and not with the files in the commit

@AdamKorcz I re-based your branch on master (as the test flakiness has been much improved recently. Looks like just one failure on 1.15x + 2.6.1 for the new test you added --- FAIL: TestFuncConsumerGroupFuzzy (52.18s)
Please could you take a look?

Thank you for the rebase. The last failing test also looks unrelated to the code committed in this PR.
As a sidenote: The code in this PR should not affect any code in Sarama since the fuzzer is not called by Sarama itself, and a build comment has been added as well.

This is a flaky test on CI I'm afraid, I've re-run actions and it failed on another version/step.

👋🏼 Is this still something we want? /cc @dnwe @d1egoaz @vvuibert

@bai I think fuzzing in general would be a useful addition. However, if we want to look at doing some fuzzing in Sarama then I think that as the official fuzzing proposal has been accepted (since this PR was originally proposed) we would ideally look at adding an additional build in the GitHub actions to use tip and checkout the dev.fuzz branch (as per https://go.dev/blog/fuzz-beta) and use testing.F and the // +build gofuzzbeta build flags.
@AdamKorcz is that something you'd like to explore under this PR, or would you prefer we write that up as a separate backlog issue?

Looks like the dev.fuzz branch just merged to main and should be available in regular Golang tip now

Ref: https://twitter.com/katie_hockman/status/1440082486692773897?s=21

I'd wait for that then.


Fix usePrometheus bug that sends unnecessary requests

Description
Changes proposed in this pull request:

Fix bug that caused unnecessary prometheus request
Remove needless useeffect
Add function that gives list of timespans based on the given metric

Related issue(s)
Resolves #1141

/retest


KAFKA-8944: Fixed KTable compiler warning.

https://issues.apache.org/jira/browse/KAFKA-8944
More detailed description of your change,
if necessary. The PR title and PR message become
the squashed commit message, so use a separate
comment to ping reviewers.
Summary of testing strategy (including rationale)
for the feature or bug fix. Unit and/or integration
tests are expected for any behaviour change and
system tests should be considered for larger changes.
Committer Checklist (excluded from commit message)

[ ] Verify design and implementation
[ ] Verify test coverage and CI build status
[ ] Verify documentation (including upgrade notes)

Call for review @bbejeck @vvcephei @abbccdda

retest this please.

Java 11/2.12 build timed out
Java 11/2.13 failed with ERROR: Error cloning remote repo 'origin'
Java 8/2.11 failed with
# There is insufficient memory for the Java Runtime Environment to continue.
# Cannot create GC thread. Out of system resources.

retest this please

@huxihx Can you rebase this PR to resolve the merge conflicts?

@mjsax Please review again. Thanks

Merged 7393 into trunk.


[BUG] markmap.min.js

想在网页中集成Markmap而不使用服务器环境，该怎么办呢？有没有纯js版本的markmap.
I want to integrate Markmap into a webpage without relying on a server environment. Is there a pure JavaScript version of Markmap available?

To use the libraries:
https://markmap.js.org/docs/packages--markmap-lib
https://markmap.js.org/docs/packages--markmap-view
To render automatically:
https://github.com/markmap/markmap/tree/master/packages/markmap-autoloader


version 1.12.0 remove Sortable.js file

version 1.12.0

version 1.10.2

why？
There is a problem with the project，now
Module not found: Error: Cannot resolve module 'sortablejs/Sortable'

hey!
just updated some modules and stumbled about this too.
I fixed it by adding the import as a module relative to your path:
  <script type="module">
    import Sortable from "/node_modules/sortablejs/modular/sortable.core.esm.js";

    window.Sortable = Sortable;
  </script>

Then you can use Sortable.create(whatever.... again.
Hope this helps!

The change was intended.
@HopeMa Are you importing sortablejs/Sortable? Import sortablejs instead.
@yougene did import Sortable from 'sortablejs'not work for you?

@waynevanson presumably dist/sortable.umd.js is the same as Sortable.min.js in 1.10.2?
What's the reason for not including an unminified file like before?

The change was intended.
@HopeMa Are you importing sortablejs/Sortable? Import sortablejs instead.
@yougene did import Sortable from 'sortablejs'not work for you?

I tried that, but e.g. Firefox gives me:
Uncaught SyntaxError: import declarations may only appear at top level of a module
I'm currtently just doing some flat layouting with Bulma, so this was a quick workaround.

Stumbled over this, too.
Using the node module only to get "sortable.js" into my ASP.NET Core project.

The change was intended.

Can you please tell me, @waynevanson, what the intention was?
Not being a Nodejs developer, I still love to use npm to pull dependencies into my C# ASP.NET Core project. Your intended change makes life more difficult now.

@bytestream theres no real reason. Do you have a reason for needing it? Files are minified for production, so I don't think it makes much of a difference leaving it out.
The reasoning behind some of these accidental changes are that were trying to get typescript compiling with tools that we can manage in the future. Before we had no typescript in the code base.
@UweKeim i didn't realise users would be importing it from sortablejs/Sortable.
I'll try add it back.

I was using in gulpjs to concatenate and minify multiple library files.

Hi @waynevanson ! I'm in the same boat! I use yarn for dependencies management but I'm not using a module bundler to pack my javascript, just Rails with the good old asset pipeline. So for all of us working on "legacy" projects, having a precompiled version of sortable.js is really useful. Would be great if you could add it back or else I'll just stick with version 1.10.2.

So for all of us working on "legacy" projects, having a precompiled version of sortable.js

Which file are you after? The non minified version that is sortablejs/Sortable.js?

So for all of us working on "legacy" projects, having a precompiled version of sortable.js

@pomartel Which file are you after? The non minified version that is sortablejs/Sortable.js?

Usually both: using the non-minified in debug builds and the minified in release builds.

@waynevanson The Rails asset pipeline has its own minifier so for my use case the non-minified sortablejs/Sortable.js would be enough. But it could be either one, as long as it doesn't require a module bundler such as Webpack to be usable.


Feature/redmo

Codecov Report

Merging #44 (a1e8add) into main (f3213eb) will increase coverage by 0.03%.
The diff coverage is 91.66%.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
@@            Coverage Diff             @@
##             main      #44      +/-   ##
==========================================
+ Coverage   92.86%   92.90%   +0.03%
==========================================
  Files          43       43
  Lines        2368     2381      +13
==========================================
+ Hits         2199     2212      +13
  Misses        127      127
  Partials       42       42

Impacted Files
Coverage Δ

mizugos/redmos/major.go
100.00% <ø> (ø)

mizugos/redmos/mxget.go
70.96% <75.00%> (+1.47%)
:arrow_up:

mizugos/redmos/mxindex.go
86.36% <75.00%> (+2.15%)
:arrow_up:

mizugos/redmos/minor.go
100.00% <100.00%> (+13.04%)
:arrow_up:

mizugos/redmos/mixed.go
100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes
:mega: We’re building smart automated test selection to slash your CI/CD build times. Learn more


Last Seen time should be much lower for Dev

Incorporate env specific time for last seen
dev should be 15 min and 45 min
staging and live should be 15 days and 45 days

Tested on Dev app version 1.3.1(164)


🛠 Refactor DGD Fusion Standardization

Description
A recent change in DGD output formatting has necessitated a change in the formatting script. I also updated the docker pull references. I will note that, unless a final standard is achieved, it's likely that every data release will require code tweaks.
Fixes # https://github.com/d3b-center/bixu-tracker/issues/2212
Type of change
Please delete options that are not relevant.

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

How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

[ ] Implemented and tested here: https://cavatica.sbgenomics.com/u/d3b-bixu/d3b-dgd-collab-dev/tasks/ec87f434-52ea-4926-872c-e963a97c7bdd/
[ ] Test B

Test Configuration:

Environment:
Test files:

Checklist:

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have made corresponding changes to the documentation
[x] My changes generate no new warnings
[x] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes
[x] Any dependent changes have been merged and published in downstream modules
[x] I have checked my code and corrected any misspellings
[x] I have committed any related changes to the PR

Thanks, @migbro - I'll take a look when I can. The fusion table format should not change in the future. I may make some suggestions here to do an auto pull of the fusion table from the warehouse (same one I gave you) so that this can just be run as we add more fusions without worrying about the input file being manually added - I have some R code for that in another repo. That'll make this more seemless. Thoughts?


[Fix] #1678 "view file" tooltip text positioning switch to mouse position

Purpose
This PR initially set out to resolve issue #1678 . Tooltips automatic placement was causing problems for long files in any case  so a solution was to show the tooltip where the mouse hovered over the item name which would eliminate the problem with the long file tooltips not being visible.
Changes

Separated function to reapplyTooltips which assigns tooltips and takes care of placement
Added this function to Fangorn.Utils for use by others
Additionally found out that Dataverse file names did not have tooltips so added them as well.

Side Effects

None, placement is working everytime provided there is a hover which is the same as previous tooltip requirement.
Tested in Chrome, Safari, Firefox, IE 9, 10, 11: All work as expected, tooltip shows where the mouse is.
One caveat is that sometimes (not always and not as often) there will be a minor difference between mosue position and tooltip but it is often because tooltip appears where mouse first entered and if the mouse position is slid a little bit they will be slightly off (a couple of pixels); I think this isn't an issue and does not harm the feature.

@caneruguz Can you please resend this as a feature branch?

So branch this into a branch called feature/....
Do I change anything in the commits?

@caneruguz You should just be able to send a new PR based off of develop

@Steve are you waiting for me to resend this? Was this not the one you were going to add in?


        ,     0.        , ...,
            0.        ,     0.        ,     0.        ],
...
       [    0.        ,     0.        ,     0.        , ...,
            0.        ,     0.        , 11987.55364268]])
full_matrices = False, compute_uv = True, hermitian = False

    @array_function_dispatch(_svd_dispatcher)
    def svd(a, full_matrices=True, compute_uv=True, hermitian=False):
        """…"""
        import numpy as _nx
        a, wrap = _makearray(a)

        if hermitian:
            […]

        _assert_stacked_2d(a)
        t, result_t = _commonType(a)

        extobj = get_linalg_error_extobj(_raise_linalgerror_svd_nonconvergence)

        m, n = a.shape[-2:]
        if compute_uv:
            if full_matrices:
                if m < n:
                    gufunc = _umath_linalg.svd_m_f
                else:
                    gufunc = _umath_linalg.svd_n_f
            else:
                if m < n:
                    gufunc = _umath_linalg.svd_m_s
                else:
                    gufunc = _umath_linalg.svd_n_s

            signature = 'D->DdD' if isComplexType(t) else 'd->ddd'
>           u, s, vh = gufunc(a, signature=signature, extobj=extobj)
E           ValueError: On entry to DGESDD parameter number 10 had an illegal value

/usr/lib/python3/dist-packages/numpy/linalg/linalg.py:1660: ValueError
----------------------------- Captured stderr call -----------------------------
init_dgesdd failed init

The same failure happens on TestFitting.test_mcmclc_arg_mutation, TestFitting.test_fit_lc, and TestFitting.test_flatten_result.
Full build/test log here.
On all other platforms, these tests pass.
Versions:

Python 3.10.6
sncosmo 2.8.0
astropy 5.1
numpy 1.21.5

Googling, this seems to be an SVD issue in scipy, likely associated with inverting a matrix. I think it might be because these tests use noise free simulations. That is my first theory at least.

OK, thanks. Since Riscv64 is not an official Debian architecture yet, I would just do nothing here; so, there is no Riscv64 package of sncosmo in the moment, and once scipy fixes this, I'd retrigger the build.
Scipy version used in the build was 1.8.1.
Just for reference: do you have the corresponding Scipy issues?


[SCHEMA] Reorganize schema code into a package

This stems from https://github.com/bids-standard/bids-specification/pull/885#issuecomment-934535138. The idea is to make the schema code operate as a proper Python package, so we can also start writing tests for it.
We still may want to move schema-related code into a different repository at some point (e.g., bids-schema, pybids), but for now I'd just like to have the code organized nicely within this repo.
Changes proposed:

Reorganize schemacode into a Python package, so that it can be installed and tests can be written for it.

This involves symlinking the schema files in src/schema to tools/schemacode/schemacode/data/schema. Thanks to @effigies for that.

Write a few initial tests for schemacode. These can be improved in future PRs.
Add a GitHub Action to run continuous integration for the new package and upload a coverage report to CodeCov.
Add new schema-related folders to the CODEOWNERS file with myself listed.

@tsalo Made several updates. RTD is fixed. The PDF build looks like it needs updating to new modules. I assume you'll be able to figure that out faster than me, but let me know if you want me to tackle it.

Thanks @effigies! How does it work? It looks like the schema files are duplicated in tools/schemacode/schemacode/data/schema/. Are those files updated automatically when the files in src/schema/ are updated?

It's just a symlink, so they will be copied into the package. If you're going to develop, it probably makes sense to pip install -e so you don't freeze them into a package and keep using the symlink. But from a CI build perspective, it's all based on the current commit, so fine to freeze.

Awesome! I fixed the module paths, so I think everything is good to go.

I'd like to have a CI job that runs the package's tests (at least with Python 3.7, if not other supported versions). Is there any preference for CircleCI vs. GitHub Action?

GHA.

Okay, I think it's looking good. I've added a few tests and a GitHub Action to run said tests. The tests are passing and the coverage report is uploading to CodeCov.
In a perfect world, I think we'd only run the tests when files in src/schema/ or tools/schemacode/ have been edited, but I don't want to hold this up on that basis. We could always try it in a future PR.

the linkchecker issue seems to have to do with the glossary PR we recently merged. Is that an easy one to fix here as well @tsalo? Or separate PR?

@sappelhoff I think it's just because there's a "canonical" link on all pages that goes to the stable version based on the MkDocs config file (which says that the site_url is the stable version). Until we have a new release with the glossary page included, I think that linkchecker is going to fail.

@sappelhoff I think it's just because there's a "canonical" link on all pages that goes to the stable version based on the MkDocs config file (which says that the site_url is the stable version). Until we have a new release with the glossary page included, I think that linkchecker is going to fail.

Mh, perhaps this could be solved by changing the site_url value as part of the release protocol. During release (and the version bumps) we change site_url to stable ... then after release (when changing the version to the dev version), we change it to "dev"
would that work?
https://github.com/bids-standard/bids-specification/blob/89115cd9ef0d4676ae78cfa1e9e78fa1048869a2/mkdocs.yml#L2

I think so, but I don't know if it's worth the effort. I don't think the links are a real problem outside of linkchecker. When you click links to other pages in the specification, they go to the same version you started from, rather than defaulting to stable. I believe that the messed up links only appear in HTML comments in the built site.

@bendhouseart sorry for not requesting your review earlier. I know you wanted to take a look, though we didn't end up trying out poetry.

I believe that the messed up links only appear in HTML comments in the built site.

I see :| but it's still annoying to have linkchecker now fail until we release ...

We could add a small Python script that checks whether the current commit is tagged (=stable), or not (=dev), and then in CI before building with mkdocs, that Python scripts changes stable to latest in the following line:
https://github.com/bids-standard/bids-specification/blob/98ca3fa8795a2ad29910cc54327c3cedb8f84906/mkdocs.yml#L2
:thinking: or would we screw up search engine results with that? I am not very familiar with "canonical URL" metadata in HTML headers.

We could add a small Python script that checks whether the current commit is tagged (=stable), or not (=dev), and then in CI before building with mkdocs, that Python scripts changes stable to latest

I have no clue if that's possible, but having the ability to update content files with Python scripts within CI would be really useful for adding tooltips (#954). The problem I have been bumping into for that is that the macros-generated content is not available for the auto-linked tooltips to grab onto. Generating the glossary within CI would circumvent that issue, I believe.
That said, I don't even know where to start to do it.

CircleCI disagrees, but eh.

The built site looks good to me, as does the PDF. Now that we have two approvals, is this alright to merge or do we want to wait 5 days?

The 5 days is more for semantic changes than infrastructure.


Adds hint, some linting and a release drafter

Codecov Report

Merging #449 into master will decrease coverage by 0.16%.
The diff coverage is 72.22%.

@@            Coverage Diff             @@
##           master     #449      +/-   ##
==========================================
- Coverage   90.76%   90.60%   -0.17%
==========================================
  Files          44       44
  Lines        2933     2883      -50
==========================================
- Hits         2662     2612      -50
  Misses        271      271

Impacted Files
Coverage Δ

django_q/brokers/aws_sqs.py
0.00% <0.00%> (ø)

django_q/brokers/ironmq.py
0.00% <0.00%> (ø)

django_q/conf.py
74.75% <ø> (ø)

django_q/core_signing.py
84.61% <75.00%> (ø)

django_q/brokers/__init__.py
94.25% <100.00%> (ø)

django_q/brokers/disque.py
98.03% <100.00%> (+0.03%)
:arrow_up:

django_q/brokers/mongo.py
100.00% <100.00%> (ø)

django_q/brokers/orm.py
97.95% <100.00%> (ø)

django_q/brokers/redis_broker.py
96.00% <100.00%> (+0.08%)
:arrow_up:

django_q/cluster.py
91.97% <100.00%> (ø)

... and 16 more

Continue to review full report at Codecov.

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tar.gz module has been deprecated warning

Description
Getting warnings on create-react-native-app AwesomeProject command. This one tar.gz module has been deprecated and your application is vulnerable is especially concerning
Observed Behavior
Here is command output
yarn add v0.27.5
info No lockfile found.
[1/4] Resolving packages...
warning react-native-scripts > xdl ><EMAIL_ADDRESS>⚠  WARNING ⚠ tar.gz module has been deprecated and your application is vulnerable. Please use tar module instead: https://npmjs.com/tar
warning react-native-scripts > xdl > auth0-js > xtend ><EMAIL_ADDRESS>[2/4] Fetching packages...
[3/4] Linking dependencies...
warning<EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>|| ^15.0.0-0 || ^16.0.0-0".
[4/4] Building fresh packages...

Environment
Please run these commands in the project folder and fill in their results:

npm ls react-native-scripts<EMAIL_ADDRESS>npm ls react-native<EMAIL_ADDRESS>npm ls expo<EMAIL_ADDRESS>node -v: v7.10.1
npm -v: 4.2.0
yarn --version: 0.27.5

Also specify:

Operating system: macOs Sierra 10.12.6

Update your node version!
Cleared up the issue for me right away :)

fix coming in next release


Questions on Tests

Thanks so much for this project. I am working on getting a new yet-to-be formally published mutable state library tested in concurrent mode.  Adding it to this project produced failures on test 4 and 6 which is not surprising.  I do want to make sure I truly understand, the tests themselves and want to make sure these assumptions are correct:

Test 2 is just making sure that after a transition when rendering sub-components that get shared state and are slow rendering that the screen will never show a mix of the old and new values for these components as does  Dan's subscription example in the reactwg/react-18
Test 4 goes further and ensures that while the transition is pending that the original results stay on the screen.
Test 6 try's to demonstrate tearing due to changes in state that come in from user events during a series of related renders.

I also curious as to why the redux example with useMutableSource fails on test 4 & 6.  Is this because the one that is being used (unstable_useMutableSource) is not final?

You get Test 2 right.
Test 5 and 6 (corresponding to Test 1 and 2 respectively) are a trial to distinguish userland solution like useSubscription and native solution like unstable_useMutableSource. It used to work better in some experimental versions of React, but now it behaves weirdly and can't explain well. At least the pure useState passes those two tests.
Test 4 is for "branching". If branching works like useState, the update during pending is queued with priority, and flushed in that order. It shows "6" before "10".
Redux has a store externally, and branching doesn't work at the moment.

I had planned to use useMutableSource to manage a state version number and then branch accordingly within my proxy.  After reading your response on useMutableSource not yet being ready I have been experimenting with the alternative of just keeping the state version number in useState and using that to drive the internal branching which shows promise. I do think that proper support of branching (showing the previous state) is important in state libraries and maybe even more so in transitions that involve long delays like fetching data (e.g the Beatles examples in the WG). Thanks again for your insight and especially for the set of tests in this project.

Please note that uMS will be replaced with uSES. https://github.com/reactwg/react-18/discussions/86

(showing the previous state)

What Test 4 does is more than this. It's more or less nitpicking at this point.

Things are changing quickly on the R18 front indeed.  I am making good progress on using useState in a context just to track a transition version number and then delivering the corresponding snapshot from within my proxy.  All 6 tests are passing with my local version so there is hope that a mutable state manager could pass all tests without using uSES.  Hope to have the full proof published soon.
On the subject of uSES, When Andrew says "Updates triggered by a store change will always be synchronous, even when wrapped in startTransition" I assume that means that when an external state manager, using uSES, triggers an expensive render, the app would not be responsive to events until the entire synchronous render was complete.
So I am wondering if test 3 would start failing on state managers that use uSES.

I am throwing in the towel on making test 4 & 6 working.  Too much overhead and complexity to commit it.  Will wait to see uSES.
You are right that test 4 is somewhat nitpicking but it does represent a difference that useState/useContext based mechanisms offer.  Mutable state managers tend not to defer updates but rather offer snapshots for the un-transitioned state.  I assume that is what Valtio is doing with useSnapshot and that is what I am doing as well by taking snapshots during transitions.  So to offer an un-transitioned state to an event (doubleIncrement) which is how it would get from 3 to 6 seemed a bridge too far in the end.
However one other branching related issue that the tests do not currently address is ensuring what is rendered while isPending is true is the original and not the transitioned state.  This is not as much of a nit as long transitions that depend on suspense to complete may be displaying the old state for a visible amount of time.
To that end I propose that test 2 should ensure that the count obtained from useCount remains unchanged. You can see that change here in a branch of my fork of your project.  It does make a couple libraries fail test 2.  It just seems to me that a test described as "updated properly with transition" should include the period of the transition as well.  Alternatively another test could be added.
Also I have to say this project really helped me to give Proxily a shakeout with React 18 (at least in its current form).  I contributed an update script to run the tests and automatically update  the README.md
Let me know if you want me to file PRs for any of this.

the tests do not currently address is ensuring what is rendered while isPending is true is the original and not the transitioned state.

Great catch. It's a nice idea to add this. Isn't it test 1 instead of test 2? Feel free to file a PR and we discuss there.

an update script to run the tests and automatically update the README.md

Can you do it for this project? A PR would be nice. ref: https://github.com/dai-shi/will-this-react-global-state-work-in-concurrent-rendering/issues/44#issuecomment-870352907

Yes sorry it is test 1 that I modified to add this.  I should mention that there are also some minor changes to common to default-parameterize items for proxy-based state management libraries like mobx, Proxily, react-easy-state which use a wrapper other than React.memo.    Will file separate PRs for each topic so discussion can be tracked for each.

Will file separate PRs for each topic so discussion can be tracked for each.

That sounds great.

Improved with #56, closing for now. Feel free to continue working on them.


Update random_sampler.py

Temporary fix for torch.randperm, from: https://github.com/open-mmlab/mmdetection/pull/5014

Thanks for your contribution!


[gui] Incorrect handling of expanding/collapsing tree nodes when a node is selected

When there is a selection in the tree, expanding or collapsing any tree node causes the effect(s) of left click on selected node.
Steps to reproduce

Click on any class node in the tree (for the node to become selected and editor tab to be opened).
Close opened editor tab.
Expand or collapse any node in the tree .

Expected behavior

Tree node gets expanded/collapsed, state of the editor doesn't get changed.

Observed behavior

Tree node gets expanded/collapsed, new editor tab for class that is selected in the tree gets opened.

The issue seems to be caused by the change to implementation of getJNodeUnderMouse method in 82712776cc5097fe004f12ec5f70526df697c3c2 (or the fact that here it is called with trySelection parameter being true).

@CmP-lt I commit a fix for this issue, please check :smiley:

@skylot in latest nightly build expanding/collapsing tree nodes works as expected, thank you.

@skylot in latest nightly build expanding/collapsing tree nodes works as expected, thank you.


Custom URL patterns

Should custom patterns extend default ones that are defined in connectors.js?
In current implementation default patterns aren't used if at least one custom pattern is defined by user. I suppose it's made intentionally (and code comment proves that).
I don't use this feature but I was confusing when I tried to use it at first time. I mean if user wants to add a custom pattern to Bandcamp, for example, they should to define default Bandcamp URL patterns too; otherwise the extension won't scrobble tracks from bandcamp.com. That's not obvious behaviour and should be changed/documented/whatever.
I suggest two options:

Append custom patterns to default ones.
Leave all of it as is, but add default patterns to the configuration popup automatically.

I prefer the first one as the simplest way. The second option requires more changes.

IMHO they should extend the default options. Go with the first approach :+1:


web_cam camera not working when camera is uplugged

Describe the bug
when i use web_cam the video will disconnect when the camera is unplugged
To reproduce
i added a bat_init() to try and see if that would allow the video to play when the camera is unplugged but it disconnects after 30 seconds
Expected behavior
i expect the camera to rely on its battery and keep streaming
Screenshots
No response
Environment

OS:
IDE &IDE Version:
Repository Version:

Additional context
No response
Issue checklist

[X] I searched for previous reports in the issue tracker
[X] My report contains all necessary details

So why is it so strange? This example originally displays the contents of the camera on the web page. The camera has been unplugged, indicating that a fault has occurred. Shouldn't the device stop running?


No matching distribution found for torchvision==0.3.0 / torchvision==0.4.0 & other versions

From yesterday I can't download most versions of torchvision package.
I'm getting this exception:
ERROR: Could not find a version that satisfies the requirement torchvision==0.4.0
ERROR: No matching distribution found for torchvision==0.4.0

same for version 0.4.1 / 0.4.2 / 0.5.0 etc.

Hi, this issue tracker is for issues with the codebase behind https://pypi.org itself, not the projects hosted on PyPI.
You should report this issue to the tracker for the project in question instead.