Memory error when doing evaluation

High Level Description
I encounter memory error when evaluating my trained agent from the second time onward due to memory error.
Desired SMARTS version
0.6.1
Operating System
Ubuntu 20.04.5 LTS
Problems
(smarts) zeyu@ZYNitro5:~/SMARTS/competition/track1/train$  python3.8 run.py --mode=evaluate --model="./logs/2022_10_05_01_33_42/checkpoint/PPO_1_100000_steps.zip"

Torch cuda is available:  True

Logdir: /home/zeyu/SMARTS/competition/track1/train/logs/2022_10_05_13_02_34

Model: ./logs/2022_10_05_01_33_42/checkpoint/PPO_1_100000_steps.zip

Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/intersection/1_to_2lane_left_turn_c/. ...
/home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/gym/logger.py:34: UserWarning: WARN: Box bound precision lowered by casting to float32
  warnings.warn(colorize("%s: %s" % ("WARN", msg % args), "yellow"))
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/intersection/1_to_2lane_left_turn_c/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/intersection/1_to_2lane_left_turn_t/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/intersection/1_to_2lane_left_turn_t/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/merge/3lane_single_agent/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/merge/3lane_single_agent/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/straight/3lane_cruise_single_agent/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/straight/3lane_cruise_single_agent/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/straight/3lane_overtake/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/straight/3lane_overtake/. ...

Evaluate policy.

== CURRENT SYSTEM INFO ==
OS: Linux-<IP_ADDRESS>-microsoft-standard-WSL2-x86_64-with-glibc2.17 #1 SMP Wed Mar 2 00:30:59 UTC 2022
Python: 3.8.13
Stable-Baselines3: 1.4.0
PyTorch: 1.12.1+cu113
GPU Enabled: True
Numpy: 1.21.5
Gym: 0.19.0

== SAVED MODEL SYSTEM INFO ==
OS: Linux-<IP_ADDRESS>-microsoft-standard-WSL2-x86_64-with-glibc2.17 #1 SMP Wed Mar 2 00:30:59 UTC 2022
Python: 3.8.13
Stable-Baselines3: 1.4.0
PyTorch: 1.12.1+cu113
GPU Enabled: True
Numpy: 1.21.5
Gym: 0.19.0

/home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/stable_baselines3/common/base_class.py:687: ResourceWarning: unclosed file <_io.BufferedReader name='logs/2022_10_05_01_33_42/checkpoint/PPO_1_100000_steps.zip'>
  data, params, pytorch_variables = load_from_zip_file(
ResourceWarning: Enable tracemalloc to get the object allocation traceback
Traceback (most recent call last):
  File "run.py", line 158, in <module>
    main(args)
  File "run.py", line 70, in main
    run(envs_train=envs_train, envs_eval=envs_eval, config=config)
  File "run.py", line 119, in run
    model = getattr(sb3lib, config["alg"]).load(
  File "/home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/stable_baselines3/common/base_class.py", line 730, in load
    model._setup_model()
  File "/home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/stable_baselines3/td3/td3.py", line 126, in _setup_model
    super(TD3, self)._setup_model()
  File "/home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/stable_baselines3/common/off_policy_algorithm.py", line 213, in _setup_model
    self.replay_buffer = self.replay_buffer_class(
  File "/home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/stable_baselines3/common/buffers.py", line 519, in __init__
    self.observations = {
  File "/home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/stable_baselines3/common/buffers.py", line 520, in <dictcomp>
    key: np.zeros((self.buffer_size, self.n_envs) + _obs_shape, dtype=observation_space[key].dtype)
numpy.core._exceptions.MemoryError: Unable to allocate 105. GiB for an array with shape (1000000, 1, 9, 112, 112) and data type uint8
sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='/home/zeyu/SMARTS/competition/track1/train/logs/2022_10_05_13_02_34/monitor.csv' mode='wt' encoding='UTF-8'>

I suspect the following process is not necessary from the second time onward when I do evaluation:
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/intersection/1_to_2lane_left_turn_c/. ...
/home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/gym/logger.py:34: UserWarning: WARN: Box bound precision lowered by casting to float32
  warnings.warn(colorize("%s: %s" % ("WARN", msg % args), "yellow"))
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/intersection/1_to_2lane_left_turn_c/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/intersection/1_to_2lane_left_turn_t/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/intersection/1_to_2lane_left_turn_t/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/merge/3lane_single_agent/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/merge/3lane_single_agent/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/straight/3lane_cruise_single_agent/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/straight/3lane_cruise_single_agent/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/straight/3lane_overtake/. ...
Waiting on /home/zeyu/anaconda3/envs/smarts/lib/python3.8/site-packages/smarts/scenarios/straight/3lane_overtake/. ...

From the looks of it it is trying to build the simulation env, which probably used up a lot of memory. I am not sure how to let it use the same env which was built during the first round of evaluation.
Edit: also I just realized 105. GiB  is abnornally large for my standard. Is that normal?

Hi @zyzhang1130,

The publicly available evaluation script at comp-1 : SMARTS/competition/evaluation/evaluate.py is the actual script used for scoring in Track1 and Track2. A separate environment is built for each scenario evaluated. Hence, kindly ensure your policy works with the evaluate script and also by submitting to the Validation Stage in Codalab.
It appears the available computer memory was exceeded while executing your policy.
This problem does not appear to be related to SMARTS.
Consider using a smaller buffer or array size in your policy.


Dedup almost identical methods into #create_compare_or_drift_report method

@dclarizio @h-kataria @martinpovolny Please review

@Fryguy renamed compare_or_drift to mode.


remove file path syntax for imports

Closes: #???
Description
Removes the file path imports since new versions of the flow cli don't need it. If we do this, you can use submodules to pull in standard repos so you don't have to copy other contracts anymore!

For contributor use:

[ ] Targeted PR against master branch
[ ] Linked to Github issue with discussion and accepted design OR link to spec that describes this work.
[ ] Code follows the standards mentioned here.
[ ] Updated relevant documentation
[ ] Re-reviewed Files changed in the Github PR explorer
[ ] Added appropriate labels

[ ] Update the version in package.json when there is a change in the smart contracts

shouldn't be something like: import "NonFungibleToken" instead of import NonFungibleToken from "NonFungibleToken"

shouldn't be something like: import "NonFungibleToken" instead of import NonFungibleToken from "NonFungibleToken"

You're right! Tried that just now and it works as well. I could have sworn when I tried it a week back, my imports didn't resolve. I will amend this to use:
import "MetadataViews"

instead of
import MetadataViews from "MetadataViews"

Looks like changing syntax made js tests break. Does flow-js-testing support that yet?

Yeah, we weren't ready to update to the new syntax because it wasn't compatible with our existing tests and repo organization yet, but this might work now. @sisyphusSmiling or @satyamakgec can you take a look at the js tests and see what might be going wrong?

Yeah, we weren't ready to update to the new syntax because it wasn't compatible with our existing tests and repo organization yet, but this might work now.

I can always revert the last commit of this PR and we can tackle the final bit of it once support is there, I'm not blocked on this so whatever folks on your end would rather


[help]How Do I Drag the Mouse?

I recently upgraded to version 0.11.17 of the tool and wanted to ask how to drag and drop the mouse.

Hi, this is a snipppet we use in out tests
fun dragAndDrop(startPoint: Point, endPoint: Point) = step("Drag and Drop from $startPoint to $endPoint") {
        remoteRobot.runJs(
            """
                    const pointStart = new Point(${startPoint.x}, ${startPoint.y})
                    const pointEnd = new Point(${endPoint.x}, ${endPoint.y})
                    try {
                        robot.moveMouse(pointStart)
                        Thread.sleep(300)
                        robot.pressMouse(MouseButton.LEFT_BUTTON)
                        Thread.sleep(500)
                        robot.moveMouse(pointEnd)
                    } finally {
                        Thread.sleep(500)
                        robot.releaseMouse(MouseButton.LEFT_BUTTON)
                    }
                """
        )
    }

thanks


SANDBOX_USER_ID,i use dockerdesktop on windows

version: '3.8'

services:
  opendevin:
    image: ghcr.io/opendevin/opendevin:0.5
    pull_policy: always
    container_name: opendevin_container
    environment:
    # can i get SANDBOX_USER_ID from?
      - SANDBOX_USER_ID=1000
      - LLM_API_KEY=ollama
      - LLM_MODEL="ollama/codellama:7b"
      - LLM_EMBEDDING_MODEL="local"
      - LLM_BASE_URL=http://host.docker.internal:11434
      - WORKSPACE_MOUNT_PATH=${WORKSPACE_BASE}
    volumes:
      - ${WORKSPACE_BASE}:/opt/workspace_base
      - /var/run/docker.sock:/var/run/docker.sock
    ports:
      - "3000:3000"
    extra_hosts:
      - "host.docker.internal:host-gateway"

all documentation I see says you will need to run it from within windows subsystem for linux, The issue is actually not SANDBOX_USER_ID but will likely be your docker.sock
volumes:
- ${WORKSPACE_BASE}:/opt/workspace_base
- /var/run/docker.sock:/var/run/docker.sock
Windows does not have /var/run/docker.sock so mapping a file /var/run/docker.sock as a volume will not work, and from my understanding without that, it will not be able to start the docker image that runs your sandbox
Take all my info with a grain of salt though, I am new to this project and I am making assumptions based on how I believe it is written, ( I know docker and linux very well, but I have only spent a few days playing with OpenDevin )

@ruanjianlun tholum is correct--you need to use WSL.
If that doesn't work, feel free to open a new issue with the template filled out (e.g. logs/errors you saw)


4.x: Add io.helidon.webclient.api.HttpClient#baseURI method

Environment Details

Helidon Version: 4
Helidon SE or Helidon MP: All
JDK version: 21
OS: Linux Mint

Problem Description
HttpClient needs to be instanced with a pre-configured base URI:
HttpClient<?> httpClient = Http1Client.builder().baseUri(uri).build();
This is different approach than jakarta.ws.rs.client.Client, where you are able to create the client without specifying the base URI:
Client client = ClientBuilder.newClient()
This forces you to create a new HttpClient for every different base URI, and this brings some usability issues. For example, imagine you have a class that makes HTTP requests to a bank URI. This class, lets say BankClient, knows the base URI of the bank. Problems:

If you want to pass an existing HttpClient in this class, you need to set the base URI in in advance (note the URI is known by BankClient and you are forcing the users of this class to know this URI).
Or in case you don't pass the existing HttpClient, and you let the BankClient to create it, there are other problems:

You cannot mock the client for testing
You cannot have multiple BankClient instances for the same HttpClient instance.
BankClient will need to care about closing the HttpClient.
BankClient will need to allow configuration of the HttpClient, like proxies, etc.

A solution could be that HttpClient is a wrapper of multiple HttpClient per URI.
I noticed this issue while I was working on https://github.com/helidon-io/helidon/issues/8909 . There, I have to create a class that speaks with OpenAI.
Steps to reproduce

Closing because you can specify the full URL in httpClient.post(uri.toString())


Waybar crashes on hyprland after boot

Details
When I start my hyprland session from gdm (hyprland starts waybar) I see waybar for a split second then it crashes with the following error log:
[2023-01-18 07:25:36.459] [info] Using configuration file /home/david/.config/waybar/config
[2023-01-18 07:25:36.460] [info] Using CSS file /home/david/.config/waybar/style.css
[2023-01-18 07:25:36.579] [warning] For a functional tray you must have libappindicator-* installed and export XDG_CURRENT_DESKTOP=Unity
[2023-01-18 07:25:36.579] [warning] As using a timezone, some format args may be missing as the date library haven't got a release since 2018.
[2023-01-18 07:25:36.612] [warning] Requested height: 20 is less than the minimum height: 34 required by the modules
[2023-01-18 07:25:36.612] [info] Bar configured (width: 1886, height: 34) for output: eDP-1
[2023-01-18 07:25:36.699] [error] '4294967295' is not a valid ID (returned by default-nodes-api)

What's really strange is that if I end the hyprland session with: loginctl kill-session self and start the hyprland session again, waybar does not crash. It only crashes after logging in the first time after boot.
Helpful info

waybar --version: Waybar v0.9.16
waybar was compiled with -Dexperimental=true
display manager: GDM
OS: NixOS, my config is here

I've gotten around this issue by enabling the home manager waybar systemd service, which just restarts waybar whenever it crashes. Not that great of a solution, but it is working for me for now.

I have the same issue on Arch, here's my output from waybar -l trace:
[2023-01-24 16:12:04.907] [debug] Try expanding: $XDG_CONFIG_HOME/waybar/config
[2023-01-24 16:12:04.907] [debug] Found config file: $XDG_CONFIG_HOME/waybar/config
[2023-01-24 16:12:04.907] [info] Using configuration file /home/nicky/.config/waybar/config
[2023-01-24 16:12:04.907] [debug] Try expanding: $XDG_CONFIG_HOME/waybar/style.css
[2023-01-24 16:12:04.907] [debug] Found config file: $XDG_CONFIG_HOME/waybar/style.css
[2023-01-24 16:12:04.907] [info] Using CSS file /home/nicky/.config/waybar/style.css
[2023-01-24 16:12:04.913] [debug] Output detection done: eDP-1 (AU Optronics 0xDE8E)
[2023-01-24 16:12:04.917] [debug] network: new default route via <IP_ADDRESS> on if3 metric 600
[2023-01-24 16:12:04.917] [debug] network: wlan0, new addr <IP_ADDRESS>/24
[2023-01-24 16:12:04.924] [debug] Cmd exited with code 0
[2023-01-24 16:12:04.924] [debug] Received SIGCHLD in signalThread
[2023-01-24 16:12:04.930] [debug] Cmd exited with code 0
[2023-01-24 16:12:04.930] [debug] Received SIGCHLD in signalThread
[2023-01-24 16:12:04.931] [warning] As using a timezone, some format args may be missing as the date library haven't got a release since 2018.
[2023-01-24 16:12:04.947] [debug] GTK widget tree:
window#waybar.background.eDP-1..mode-default:dir(ltr)
  decoration:dir(ltr)
  box.horizontal:dir(ltr)
    box.horizontal.modules-left:dir(ltr)
      widget:dir(ltr)
        label#custom-system76-power-graphics:dir(ltr)
      widget:dir(ltr)
        label#custom-system76-power-profile:dir(ltr)
      widget:dir(ltr)
        label#network:dir(ltr)
      widget:dir(ltr)
        label#wireplumber:dir(ltr)
      widget:dir(ltr)
        label#backlight:dir(ltr)
    box.horizontal.modules-center:dir(ltr)
      widget:dir(ltr)
        box#workspaces.horizontal:dir(ltr)
    box.horizontal.modules-right:dir(ltr)
      widget:dir(ltr)
        label#battery:dir(ltr)
      widget:dir(ltr)
        label#cpu:dir(ltr)
      widget:dir(ltr)
        label#memory:dir(ltr)
      widget:dir(ltr)
        label#custom-gpu:dir(ltr)
      widget:dir(ltr)
        label#clock:dir(ltr)

[2023-01-24 16:12:05.078] [info] Bar configured (width: 1920, height: 34) for output: eDP-1
[2023-01-24 16:12:05.095] [error] '4294967295' is not a valid ID (returned by default-nodes-api)

I'm using v0.9.17.

I fixed the issue by removing the wireplumber module from my config.

wireplumber seems to be the problem for me as well. Perhaps a duplicate of https://github.com/Alexays/Waybar/issues/1852.

I have the same issue on NixOS with sway. For anyone looking for a quick and dirty fix, replace wayland.windowManager.sway.config.bars.*.command with this:
{
  command = builtins.toString (pkgs.writeScript "start-waybar" ''
    #! ${pkgs.bash}/bin/bash
    while true;
      do ${config.programs.waybar.package}/bin/waybar $@; sleep 1;
    done
  '');
}

I can reproduce this same issue on sway.

@NiciTheNici is it the wireplumber module?

I get the same crash on first launch of waybar after boot. Like @ok-nick [error] '4294967295' on sway/arch

same error on arch, latest waybar-hyprland v0.9.17 from AUR and wireplumber enabled
[2023-04-12 18:51:11.485] [error] '4294967295' is not a valid ID (returned by default-nodes-api)

only when just booted

Think it has something to do with how the wireplumber module handles its response to wireplumber > socket pipewire.service activation. If I enable pipewire.service directly on boot, then it doesn't crash.

this issue has started happening after i updated my system

@IllustratedMan-code does it work for you? if so, please close the issue

I actually don't use the wireplumber module anymore, but it looks like #1852 is now closed. So I'll close this in favor of that issue. If anyone still has this issue, just ping me and I'll reopen.


Add RBS for enumerize gem

Add type definitions for enumerize gem.
The type definitions to be added are those generated by the rbs prototype rb command.
$ rbs prototype rb gems/enumerize/2.5/_src/lib/**/*.rb >> gems/enumerize/2.5/enumerize-generated.rbs

Sorry for the small amount of tests...
I can't find any cases where other methods are used for projects, and this is the only one.

I can't find any cases where other methods are used for projects, and this is the only one.

You can find examples from the README if you need them.
https://github.com/brainspec/enumerize
I guess the added example represents the main use case of this gem, so it is not necessary to add more test cases for the first step.


Fast fail when any exception occurs in the handler

@jponge ?

Do you have an example where the handler throws an exception?
In any case the exception will be handled and the test context will fail, but things like assertions must be wrapped using verify(() -> { ... }.

In the handler, there is not only assertion. Users may write any code here. And as a result, any exception may happen, not just assertion failures.

For example:
// `tc` is a `VertxTestContext`
tc. succeeding(it -> {
  // some other code <1>

  tc.verify(() -> {
    // assertions <2>
  });
});

When any exception occurs at <1>, it takes too long to get result.

You are right, but do you have any example of Vert.x-related code that throws an exception in <1>? Vert.x code typically forwards errors not as exceptions, but as asynchronous results with an exception.

Vert.x is fine. It's nothing about vertx, it's just about ergonomics.

This PR can be closed. The requested feature has been implemented in #81 that has been released in Vert.x 4.0.0.


Cached Uint32 memory remains uninitialized

Describe the Bug
The generated JS file creates helpers for cachedUint32Memory, but never initializes it.
See denoland/wasmbuild/issues/61
Steps to Reproduce

Run the generator, with a JS function that returns an array
Call that JS function from Rust

Repository showcasing
Expected Behavior
The function runs without throwing a TypeError
Actual Behavior
Throws Uncaught (in promise) TypeError: Cannot read properties of undefined (reading 'byteLength')

wasm-bindgen --target deno and wasm-bindgen --target web do initialize all memory views as needed. wasmbuild, however, appears to always only assign values to cachedInt32Memory0 and cachedUint8Memory0.

Wasmbuild is using the direct output afaik, though that was only from a quick skim of the code

Hm, it looks like the issue is fixed in the latest commits of denoland/wasmbuild, but they just haven't created a release yet

Wasmbuild is using the direct output afaik, though that was only from a quick skim of the code

Ah, you are right. The upgrade to wasm-bindgen in denoland/wasmbuild#52 made the code I was looking at redundant.


terragrunt output-module-groups fails if not run from a Terragrunt module

Describe the bug
The description of output-module-groups says:

This will recursively search the current working directory for any folders that contain Terragrunt modules and build the dependency graph based on dependency and dependencies blocks.

However, if I run terragrunt output-module-groups from the root of my repo, the command fails. I do not have a terragrunt.hcl at root, as all Terragrunt modules are organized within my repo. Here's an example of my layout:
- root
  - aws
    - aws.hcl (shared config for all AWS Terragrunt modules)
    - commercial
      - account1
        - terragrunt.hcl
        - test.tfvars
      - account2
        - terragrunt.hcl
        - test.tfvars
        - submodule
          - terragrunt.hcl
          - test.tfvars
  - azure
    - azure.hcl (shared config for all Azure Terragrunt modules)
    - ...

Here's the error I'm getting:
$ terragrunt output-module-groups
ERRO[0000] Error reading file at path /terragrunt_test/terragrunt.hcl: open /terragrunt_test/terragrunt.hcl: no such file or directory
ERRO[0000] Unable to determine underlying exit code, so Terragrunt will exit with error code 1

To Reproduce
Attempt to run terragrunt output-module-groups from a a directory that contains Terragrunt modules in subfolders, but is not a Terragrunt module itself.
Expected behavior
I would expect this command to recursively search the current directory for all Terragrunt modules and build the dependency graph, even if there is no terragrunt.hcl in the current dir.
Workaround
As a workaround, you can create an empty terragrunt.hcl in the root directory to get it to recursively search for all Terragrunt modules.
Versions

Terragrunt version: v0.50.6
Terraform version: v1.5.4
Environment details (Ubuntu 20.04, Windows 10, etc.): Rocky Linux 8

I'm also running into this bug (or misdocumentation?) with the latest terragrunt version (0.51.6)

Included in release: https://github.com/gruntwork-io/terragrunt/releases/tag/v0.52.6


Added PHPWomen to the list of organizations.

Added PHPWomen to the list of organizations so the PHP community is represented

@dreamingechoes fixed! thanks for catching the typo!

💖 😊


feat!: update some CLI arguments / env variables for consistency

Description

Rename --study_dir to --study-dir
Drop the S3 bucket gathering entirely, we can get it from workgroup
Rename CUMULUS_LIBRARY_SCHEMA to CUMULUS_LIBRARY_DATABASE
Mention CUMULUS_LIBRARY_WORKGROUP in the docs

I could add some safety fallbacks for old env names, if you like the renames, but feel they are too jarring / sudden.

Checklist

[x] Consider if documentation (like in docs/) needs to be updated
[x] Consider if tests should be added
[x] Run pylint if you're making changes beyond adding studies

on line 142 in study_parser.py, we should change the text in the error to refer to databases instead of schemas.

on line 142 in study_parser.py, we should change the text in the error to refer to databases instead of schemas.

Good catch! Fixed.


rafthttp: configurable stream reader retry timeout

Please consider this small improvement: rafthttp.streamReader dial timeout was hardcoded to 100ms which may be too frequent for some use-cases of rafthttp library. I would like to have this setting configurable.

Codecov Report

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  Hits              ?    19845
  Misses            ?     5224
  Partials          ?     1473

Impacted Files
Coverage Δ

rafthttp/transport.go
83.05% <ø> (ø)

rafthttp/stream.go
89.66% <100%> (ø)

rafthttp/peer.go
90.22% <100%> (ø)

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lgtm. defer @heyitsanthony

lgtm. Thanks!

@heyitsanthony my pleasure! Please notify me if I need to do any additional work to see this PR merged.


Output # of records not the same as input.

In order to help us troubleshoot issues with this project, you must provide the following details:

ElasticDump version
2.4.2
Elasticsearch version
2.3 on AWS
Full command you are having issue with (with inputs and outputs)
multielasticdump

If an index name in ElasticSearch begins with a "." the file is created as hidden in the output directory. Can that behavior be overriden?

I'm updating your title to reflect the content of your question

There are no defaults specific to elasticdump about the output file's name (or even if we output to a file), so I'll guess you are talking about multielasticdump, which does save out all indexes to disk.
The file being "hidden" is specific to your operating system, and then the setting you have enabled for your "finder" or "explorer".  Yes, on most "*nix" operating systems, the default would be to hide that file.
I personally don't think that modifying the default behavior of multielasticdump is a good idea in these circumstances.  The logs still say which files are created, and adding complexity to the tool in this way seems unnecessary.
That said, you can certainly submit a pull request on this topic and we can ask for feedback from others!

Sorry about the title, I was going to report something else but I decided to try multielasticdump first. I checked and the files are being hidden by the OS but they don't have an archive or hidden file attribute set. No big deal then.


chore(deps): upgrade dependencies

Upgrades project dependencies. See details in workflow run.

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

⚪ Backport skipped
The pull request was not backported as there were no branches to backport to. If this is a mistake, please apply the desired version labels or run the backport tool manually.
Manual backport
To create the backport manually run:
backport --pr 529

Questions ?
Please refer to the Backport tool documentation


Cannot copy color

Hello, I tested a bit your color picker and I find it awesome.
I just had one trouble, I get an error when I want to copy the color.

It's fixed now, thanks for the feedback


The most important operations runs in main thread.

I saw some lags in my app when i started to use Heneke. And i found this problem. Its happens because your fetchers perform their success blocks in main thread.
Image resize, loading image from disk works in main thread.
Some proves:

Having this issue as well.
Anyone tried wrapping any of those methods in a separate queue?

We have done a lot of work on the Foursquare fork to move everything off to other threads. Haven't had a chance to clean everything up and submit back to this repo yet though.
You could try using our version if you like, but no guarantees that things won't break or method names won't change.

Great!
I’ll check it out.
https://github.com/foursquare/Haneke https://github.com/foursquare/Haneke right?

On Apr 16, 2015, at 5:05 PM, Brian Dorfman<EMAIL_ADDRESS>wrote:
We have done a lot of work on the Foursquare fork to move everything off to other threads. Haven't had a chance to clean everything up and submit back to this repo yet though.
You could try using our version if you like, but no guarantees that things won't break or method names won't change.
—
Reply to this email directly or view it on GitHub https://github.com/Haneke/Haneke/issues/69#issuecomment-93865365.

Yep. We also have some other improvements, like the ability to load images synchronously when there is a cache hit, consolidating duplicate in-flight network requests, and the ability to set what network fetcher subclass is used in the built in UIKit category methods so you can provide a custom URLSession.

Awesome!
Giving it a try right now.

Would you consider making a cocoapod for your fork? There are some pretty nice changes in here.

I think the idea is to submit our changes back to the main repo once we have some free time to clean things up a bit. Hopefully in the next month or so. I'd much rather do that than start "officially" maintaining a separate fork.

@bdorfman It would be good to see these changes in main repo. Although it seems Haneke is no longer active.
Do you guys at foursquare/Haneke have a way to prefetch images in an array? Like SDWebImage does?
[[SDWebImagePrefetcher sharedImagePrefetcher] prefetchURLs:<NArray with image URLs>];

Then I would be using your fork right away.


create tofixed decimal feature in format number

The purpose of this PR is to add a toFixed option to the numberFormatter. Currently, there is not an easy way to display a fixed number of decimals, i.e. trailing zeros. This change allows users to toggle toFixed, using the number of decimals specified in the decimals option. Tests are written and passing for this feature.

clsoing because docs were rebuilt with forked repo instead of main


niri: 0.1.8 -> 0.1.9

tested on my own laptop

hiya. in general i'd like to fully implement all relevant settings before i feel comfortable updating the stable package - the idea is that if you use the stable package, the flake should "just work" for everything, whereas the unstable package may speed ahead of capability the flake provides. this includes, at least, the VRR on demand options, which i've already began to implement, but also some way to deal with /etc/niri/config.kdl which involves at least some sort of rework of how settings currently work (to allow this file to be generated by the nixos config)

makes sense, nyaa~ :3

but also some way to deal with /etc/niri/config.kdl which involves at least some sort of rework of how settings currently work (to allow this file to be generated by the nixos config)

yeah, can't be bothered to do that right now. i've removed teh relevant unstable option notes, and i'm going to merge this now.
i'm also very concerned about how to implement the config in a way that won't conflict with nixpkgs in the future, so i might hold off on that until i can upstream my NixOS module and it becomes clearer how to deal with it


Triangle CfA promo

Natalie - please add this to the marketing plan so we remember to do this in future years

Sent to meet-up group members on 9/6

@jhibbets Did you setup a meetup or send an e-mail to the mailing list?
Chris Mathews
On Wed, Sep 6, 2017 at 9:38 PM, Jason Hibbets<EMAIL_ADDRESS>wrote:

Closed #672 https://github.com/codeforraleigh/NCOpenPass/issues/672.
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Email to the mailing list. I can set-up an event meet-up too like we've
done in the past.
On Wed, Sep 6, 2017 at 9:52 PM, Chris Mathews<EMAIL_ADDRESS>wrote:

@jhibbets Did you setup a meetup or send an e-mail to the mailing list?
Chris Mathews
On Wed, Sep 6, 2017 at 9:38 PM, Jason Hibbets<EMAIL_ADDRESS>wrote:

Closed #672 https://github.com/codeforraleigh/NCOpenPass/issues/672.
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Remove C* 2.0 from build matrix

There seems to be an issue with the image used by Jenkins related to mono, but there isn't any mono installation on the image setup scripts (like apt install mono-devel) 🤔, should we add it?
Do you know how it used to work? (probably some base image?)

I am checking if that was missing on last image update, thanks for the heads up.

+1


Importing events to Aggregates

This PR implements importing events into aggregates.
Importing aggregates should have allowTrue flag set in @Apply annotations. Events to be imported are dispatched by ImportBus, which accepts registrations of AggregateRepositories.
By default, dispatching is based on producerId of Events to be imported, but can be easily changed to using first event message field.
Other notable changes:

UnicastBus was introduced as an abstract base for unicast dispatching.
Bus.AbstractBuilder was pushed to the top level and renamed to BusBuilder.
idAsString() was added to Entity to simplify diagnostic output.
Consolidated code in classes and interfaces responsible for event routing.
Introduced SystemRepository abstract base for system aggregate repository classes.
Removed Bounded infix in classes extending BoundedContext.
ImportEvent, CommandRounted types are removed.
added factory methods for creating TestEventFactory from BlackBoxBoundedContext.

@armiol, PTAL.


Implement shrink for Inlines and Blocks

Only caption is shrinked in tables for now.

It also makes sense to flatten the lists, e.g by removing emphasis or replacing lists that have one list item with the list item contents, but it is already good enough at this point.

Looks good. Does adding 'shrink' require a new lower bound for QuickCheck?

Does adding 'shrink' require a new lower bound for QuickCheck?

No, it was present since the beginning of QuickCheck 2: https://hackage.haskell.org/package/QuickCheck-<IP_ADDRESS>/docs/Test-QuickCheck-Arbitrary.html


[add][#1200] part support inside

Coverage increased (+0.001%) to 83.853% when pulling 61dac8e984416e904bf954c64b47eb136c4ca270 on sunny4381:features/ss-1200 into b884a588c8df9720a26ed4f4b3923c191092eaba on shirasagi:master.


using `vedo==2020.3.4 with dolfin inside Jupyter (docker container)

Hi Marco,
I was trying to use vedo.dolfin.plot to make 3D plots in Jupyter inside of a docker container. I have installed k3d using pip but I'm unable to render the plot. I am using an older version due to vtk version conflicts with dolfin 2019.2.0 ....
from dolfin import *
import numpy as np
from vedo.dolfin import plot as vplot, show as vShow, embedWindow
from vedo import settings
mesh  = UnitCubeMesh(5,5,5)
V = VectorFunctionSpace(mesh, "CG", 2)
u = Function(V)
u.vector()[:] = np.linspace(0,1,V.dim())
embedWindow("k3d")
vplot(u)
mesh = settings.plotter_instance.actors[0]
mesh.lw(0)
vShow(mesh, newPlotter=True, axes=1)

but this just gives
Plot(antialias=3, axes=['x', 'y', 'z'], axes_helper=1.0, background_color=16777215, camera=[0.0357292797817024…

Would you happen to know what could be going wrong?

Hi Bhavesh,
the message seems to say that the graphical canvas is returned but it is not rendered as such.
does it work outside jupyter? (e.g.setting embedWindow(False)). Unfortunately I have no experience with docker.. at some point I had this magic recipe:
sudo apt install libgl1-mesa-dev xvfb

export DISPLAY=:99.0
which Xvfb
Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
sleep 3
exec "$@"

but i'm not sure if it applies in this case.
ps: dolfin.plot() has many keywords, one is lw so this should also work
vplot(u, lw=0, axes=1)
also, vplot already returns the Plotter object.

at some point I had this magic recipe:

I can give this a try. Thanks!

does it work outside jupyter?

It has worked outside Jupyter without any problems in the past (though not Docker but Singularity).
This is a slightly esoteric way I am trying primarily to cater to windows users for a demo (who can pull the image, run fenics on jupyter (inside Docker), and vedo can render the embedded plots).


Require cycle: value.js -> object.js -> value.js

Hey! I'm getting the same require cycle again as mentioned in #97, I believe a change has overridden those fixes.
 WARN  Require cycle: node_modules/d3-interpolate/src/value.js -> node_modules/d3-interpolate/src/object.js -> node_modules/d3-interpolate/src/value.js

Require cycles are allowed, but can result in uninitialized values. Consider refactoring to remove the need for a cycle.

Causes issues when using react-native. Breaks end-to-end tests and strict environments.


V2 now without import errors - Opus and Dawiki downloader classes added to datasets.

Opus corpuses and danish wikipedia is available for download via their respective classes. The data is in raw text suitable for language modeling or training of word embeddings.
Corpuses has very little preprocessing and may require so dependant on the application. Could be a future feature.
Note that wikipedia data is download via a shell script.

Merges via download_frontend.


Synchronize with MailDir

See #212 for the reason of this enhancement
basic functionality of disc access is implemented
File names are incorrect so far

filenames are now consistent


Remove Rosetta as requirement for Docker Desktop on Apple Silicon

It's been some time now since the first release of Docker Desktop supporting Apple Silicon, but it stills holds Rosetta as a requirement.
Apple has always said that Rosetta is a temporary translation layer allowing software developers to have enough time to deliver specific ARM versions, and they will shut it off after some months.
Meanwhile I've been using remote development with Visual Studio Code against a remote machine running Linux x64, but this is not an ideal situation. Docker has become a central piece on any kind of software development, and Mac is one of the preferred ecosystems used by developers. I think that fully native M1 support should be put as top priority in the roadmap.
Thanks!!

Thank you for your comments, @jfernandezr. This has already been done in Docker Desktop 4.3. https://docs.docker.com/desktop/mac/release-notes/#docker-desktop-430

No worries, it's new, we only just released it last week!


blasting then voicemail doesn't work if there is an invalid or disconnected number among the volunteers

Describe the bug (or maybe it's an enhancement??)
If one of the volunteers has a disconnected number, blasting then voicemail never goes to voicemail -- it just keeps ringing.
What version are you running?
4.3.1-beta1
Did this happen on prior versions to the one you are running?
Yes, something like this happened also with 4.2.11.
To Reproduce
Steps to reproduce the behavior:

Set up yap for blasting then voicemail.
Add a disconnected or otherwise bad number to the volunteers list.  (To reproduce, I used a recently released Twilio number.)
Call the helpline and ask to talk with a volunteer.

Expected behavior
If one of the numbers is bad, I would expect yap in blast mode to still go to voicemail after the timeout.  Ideally there would be a report also regarding the bad number.
Additional context
The Twilio log for the test helpline number says that the released number was busy; there wasn't an error otherwise. I encountered something similar when trying to bring a new area on to yap.  It turns out the helpline coordinator just copied over the numbers from their old installation but didn't test them.  One of those numbers was bad -- not sure how since I didn't try to debug carefully at the time -- but that one gave an error on the Twilio log (which is how we discovered the problem). Same thing happened -- calls just kept ringing and never went to voicemail.

I was able to reproduce this.  This is an old bug and it deserves to be fixed!

The same issue occurs for any call strategy and anytime you use a number that doesn't exist.

fix coming in 4.3.4

I tried the fix in 4.3.4-beta1, and alas it's still hanging and not sending the call to voicemail when there is a bad number -- at least of a particular kind -- in the volunteer list.  (The number that causes this problem  is a Twilio number that we returned to the pool.)  I'll send you a screenshot similar to the one above, and the laravel log, as a DM.  (It's got my own number in it as well so I won't put it here.)
Then I tried it with the bad number in the screenshot above<PHONE_NUMBER>) and it did send the call to voicemail.

Ok I’ll test this other use case.
Get Outlook for iOShttps://aka.ms/o0ukef

From: Alan B @.>
Sent: Saturday, May 4, 2024 7:40:31 PM
To: bmlt-enabled/yap @.>
Cc: Danny Gershman @.>; Assign @.>
Subject: Re: [bmlt-enabled/yap] blasting then voicemail doesn't work if there is an invalid or disconnected number among the volunteers (Issue #971)
I tried the fix in 4.3.4-beta1, and alas it's still hanging and not sending the call to voicemail when there is a bad number -- at least of a particular kind -- in the volunteer list. (The number that causes this problem is a Twilio number that we returned to the pool.) I'll send you a screenshot similar to the one above, and the laravel log, as a DM. (It's got my own number in it as well so I won't put it here.)
Then I tried it with the bad number in the screenshot above<PHONE_NUMBER>) and it did send the call to voicemail.
—
Reply to this email directly, view it on GitHubhttps://github.com/bmlt-enabled/yap/issues/971#issuecomment-2094502534, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAOD3O22EKNFL52A3C7KZ5TZAVWW7AVCNFSM6AAAAABE4OF3O6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJUGUYDENJTGQ.
You are receiving this because you were assigned.Message ID: @.***>

figured out what the difference is.  these released numbers return a busy signal, not a failure.

working on a fix now.

Try with 4.3.4-beta2

Working for both numbers now (the one that fails and the one that gives a busy signal).  One thing I did not test is having a volunteer who never answers and who does not have voicemail -- I don't have a number handy with that behavior.  Is that already known to work?

If they don't press 1 after answering it will result in a timeout.

What happens if they never answer?

It times out after whatever the setting is.
Get Outlook for iOShttps://aka.ms/o0ukef

From: Alan B @.>
Sent: Saturday, May 4, 2024 11:11:45 PM
To: bmlt-enabled/yap @.>
Cc: Danny Gershman @.>; Assign @.>
Subject: Re: [bmlt-enabled/yap] blasting then voicemail doesn't work if there is an invalid or disconnected number among the volunteers (Issue #971)
What happens if they never answer?
—
Reply to this email directly, view it on GitHubhttps://github.com/bmlt-enabled/yap/issues/971#issuecomment-2094564530, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAOD3O6ZO62EWZY5YKB6ZTLZAWPPDAVCNFSM6AAAAABE4OF3O6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJUGU3DINJTGA.
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chore: move logout functionality into auth crate

Closes TURBO-2405

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#7407
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Add DecimalMoneyFormatter

This formatter outputs a simple decimal string which is always in a consistent format independent of locale.
Related: #78
The workaround in https://github.com/moneyphp/money/issues/78#issuecomment-202262198 is inadequate now that we have subunits.
@sagikazarmark I hope this is not just "convenience stuff"?

There's duplicated code, because it's just IntlMoneyFormatter without for the last step.

I have nothing to add here. The PR looks good. Maybe the name of class. I think we could drop String from the name. That results in DecimalMoneyFormatter which I think covers the purpose of the class.

Alrighty, up to @frederikbosch then

@teohhanhui There is nothing wrong with that code duplication. There is no need for abstraction.

Oh, I did agree with @sagikazarmark comment though. Amount is already string. So please change that. I only wanted to say that I have no more comments on the PR than that.

Will merge after Travis is happy.

@teohhanhui Great PR, thanks for your help!

before this was merged, i solved it like this:
        $numberFormatter = new \NumberFormatter('en_US', \NumberFormatter::PATTERN_DECIMAL, '0.00');
        $decimalFormatter = new IntlMoneyFormatter($numberFormatter, $currencies);

Not a bad solution either.

yeah, the duplicated code (not a bad thing i know), could probably be removed and the DecimalMoneyFormatter could be composed with the IntlMoneyFormatter

DecimalMoneyFormatter has no dependency on the intl component. Can't say the same about IntlMoneyFormatter...

good point


Automatic hide on selection

Hi,
How can I hide the datepicker as soon as a date has been selected?
Thanks,

The picker should close automatically if using a format that does not include time.
format: "MM/DD/YYYY" or format: "L" amongst others
http://momentjs.com/docs/#/displaying/format/

listen for the change event dp.change then call the hide() function


Include monomorphic sites in VCF

Hi!
I miss an option to report all sites in VCF outupt, even the ones without genomic variants.
That would allow me to flag potentially non-informative sites, e.g. with low read depth. Applications in the comparison of multiple bacterial isolates, phylogeny, etc.
P.S. MapCaller is rocking on my 6-core i7-9750H 2.60GHz CPU. ~ 2 min for 2x5GB fastq. Congratulations for your work!

Hi, what do you mean by "all sites without genomic variants". Could you please explain with more detail? Thank you.

Perhaps best explained in GATK documentation

The key difference between a regular VCF and a GVCF is that the GVCF has records for all sites, whether there is a variant call there or not. The goal is to have every site represented in the file in order to do joint analysis of a cohort in subsequent steps. The records in a GVCF include an accurate estimation of how confident we are in the determination that the sites are homozygous-reference or not.

Thank you for the explanation. I'll study the details of GVCF and try to add this feature.

Hi,  I've added basic support for gVCF (v0.9.9.b). To output gVCF, Run MapCaller with "-gvcf". I read the format specification and follow Freebayes's tags to output gVCF file. Let me know if you find any problems with gVCF output. Thank you!

Hi! Thanks for the update!
I did some tests and noticed the tool is just reporting the genomic position immediately after a called variant.
-gvcf output:

MTB_anc 4394210 .       C       G       30      PASS    DP=90;AD=90;AF=1.000;GT=1|1;TYPE=SUBSTITUTE
MTB_anc 4394211 .       A       <*>     0       .       END=4395386;DP=90;MIN_DP=73

However, I needed a VCF file reporting from position 1 to the last genomic coordinate of the reference genome.
To clarify, here follows the corresponding FreeBayes option:

--report-monomorphic
Report even loci which appear to be monomorphic, and report all
considered alleles, even those which are not in called genotypes.
Loci which do not have any potential alternates have '.' for ALT.

I've updated a new version (0.9.9.c) to report all loci which do not have any potential alternates. Please run MapCaller with "-monomorphic" instead of "-gvcf". In fact, MapCaller outputs the similar results with Freebayes when putting "-gvcf." I compared MapCaller's output (-monomorphic) to Freebayes's output (--report-monomorphic) and they looked similarly, though the QUAL of all monomorphic loci are set to 0. I am not sure how to calculate the QUAL for those loci.

Thanks for the implementation!
I believe I spot some inconsistencies in the outputs, for which I might create separate issues if relevant.
MapCaller -ploidy 1 -i MTB_anc.fasta -f ERR2653232_1.fastq -f2 ERR2653232_1.fastq -monomorphic

Reference coordinates are shifted by 1bp.
Null character "^@"  in position 1.

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
MTB_anc 1       .       ^@      .       0       .       DP=1;NS=1;DUP=0;GT=0|0
MTB_anc 2       .       T       .       0       .       DP=7;NS=7;DUP=4;GT=0|0

Deleted reference bases are not tagged differently.
For example, Pilon uses a 'Del' tag to indicate loci removed by a variation in another line.
Coordinate '79548' appears two times but with distinct nucleotides? It should be "C", right?

grep -w '79548' -B1 -A10 output.vcf

MTB_anc 79547   .       G       .       0       .       DP=343;NS=343;DUP=5;GT=0|0
MTB_anc 79548   .       CCCGGTGGAC      C       14      PASS    DP=385;AD=181;DUP=5;AF=0.470;GT=0|1;TYPE=DELETE
MTB_anc 79548   .       A       .       0       .       DP=348;NS=347;DUP=5;GT=0|0
MTB_anc 79550   .       C       .       0       .       DP=167;NS=167;DUP=1;GT=0|0
MTB_anc 79551   .       C       .       0       .       DP=170;NS=170;DUP=3;GT=0|0
MTB_anc 79552   .       G       .       0       .       DP=172;NS=172;DUP=2;GT=0|0
MTB_anc 79553   .       G       .       0       .       DP=176;NS=176;DUP=2;GT=0|0
MTB_anc 79554   .       T       .       0       .       DP=178;NS=178;DUP=1;GT=0|0
MTB_anc 79555   .       G       .       0       .       DP=186;NS=186;DUP=5;GT=0|0
MTB_anc 79556   .       G       .       0       .       DP=194;NS=194;DUP=4;GT=0|0
MTB_anc 79557   .       A       .       0       .       DP=198;NS=198;DUP=2;GT=0|0
MTB_anc 79558   .       C       .       0       .       DP=383;NS=383;DUP=3;GT=0|0
MTB_anc 79559   .       G       .       0       .       DP=391;NS=391;DUP=5;GT=0|0

Positions with secondary alignments are not reported.
In the following example,<PHONE_NUMBER>17 region is comprised by a high number of reads with multiple optimal alignments.

grep -w '103871' -C1 output.vcf

MTB_anc 103870  .       G       .       0       .       DP=7;NS=7;DUP=0;GT=0|0
MTB_anc 103871  .       T       .       0       .       DP=3;NS=3;DUP=0;GT=0|0
MTB_anc 104617  .       A       .       0       .       DP=2;NS=2;DUP=1;GT=0|0

IGV output

Hello,
Thank you for reporting the errors. I've found those bugs and corrected them. Please update MapCaller to v.0.9.9.d. Now issue#1 and #2 have been fixed. Those errors were due to wrong position calculation. However, issue#3 involves ambiguous alignments. The algorithm of MapCaller ignores all read alignments with multiple mapping coordinates. In such cases, it is difficult to tell which coordinate is correct, therefore, we just ignore all such alignments. In fact, MapCaller will report them as CNV events in the future version. Please let me know if you have any suggestions about how to deal with those regions.
You may specify output name by using "-vcf FileName.vcf". Thank you again.

Thanks for the fixes!

Concerning sites affected by secondary alignments, my suggestion would be for them to be reported as DP=0 but with a new metric that records the number of discarded reads. Please refer to #23 .

Curiously, I noticed that if I use genome ERR502929, the first reference position is not reported. This doesn't happen with the example provided above.

Do you have plans to incorporate a metric such as "mean base quality in pileup" as a complement or alternative to QUAL? In the current release, one has to get this information from bam files...

Hello,
I'd like to explain why some positions are not reported when you applying "-monomorphic". It is because the read depths at those positions are "0". That is no any read alignment mapped to those regions. I also checked Freebayes's result when applying "report-monomorphic", it also produces nothing for those regions. I was wondering if you still want MapCaller to output all positions regardless of read depths.

Hi, I'd like to know how to calculate the mean base quality. Is it the average base quality of all read bases at a specific position or it is the average base quality of the ALT allele?

I was wondering if you still want MapCaller to output all positions regardless of read depths.

yes, i would like to see every site reported in -monomorphic mode, including DP=0 sites.

Is it the average base quality of all read bases at a specific position or it is the average base quality of the ALT allele?

Good question. What specific VCF tag/field are you wanting to put this result into?

Since MapCaller does not output read alignments to a SAM/BAM file, it would consume memory space to store information for statistic output. I was planing to output a simplified read alignment and gather required information from that file after variants are called. The VCF tag for average base quality can be Qual, and it represent the average quality of four bases, such as (30,20,20,28).


Superfluid Indicator on Pool Card view

Would be useful to be able to see at a glance on the grid view which pools have superfluid, especially of you have a lot of pools and want to double-check if you have enabled superfluid.

A simple indicator like this would work, but would be nice to also indicate whether you have enabled it or not, maybe a tickbox next to the purple flask icon?
Ricardo | Notional

5/10 meeting - We discussed this as a clearer way to show that a pool is superfluid vs the stroke. In that case, this icon would not show that you have a superfluid position, just that a pool is superfluid.

Let's ship refactor with just #477 card modifications and icebox this for now.

6/7 meeting - We will do this, but @victortokaito we'll need a new design for the new pool cards.

Awesome looking forward to the new card design
Ricardo | Notional

Hi Ricardo, we are putting this on hold as we feel adding icons to each superfluid card could be redundant and visually distracting (especially on mobile). Do you feel that the "Superfluid Pools" title + stroke is contextually sufficient?

.

Hi sorry I missed this comment, the Title is fine but it still doesn't tell me which of My Pools are superfluid and may be requiring my attention to enable it. I would have to go through each one to find out, if I have 20 pools it can be alot.


I can't get "echo $MYENV " in the container

when I into the container, use commend "nsenter --target --mount --uts --ipc --net --pid"
I want get my ENV , example echo $MYENV ,it show none
[root@localhost /]# docker inspect <CONTAINER_ID> --format '{{ .Config.Env}}'
[MYENV=hello]
[root@localhost /]#  nsenter --target $(docker inspect <CONTAINER_ID>  --format '{{ .State.Pid}}') --mount --uts --ipc --net --pid
[root@localhost /]# echo $MYENV

[root@localhost /]#

Curious; is there a reason for you to not use docker exec instead of this project?

Curious; is there a reason for you to not use docker exec instead of this project?

Yeas, when I used docker exec  into my-container ,I can use echo $MYENV got my environment variable. But I uesed nsenter  into my-container , I can't got it.

@sober-wang I would suggest to use docker exec then.
This repository (jpetazzo/nsenter) was created before docker exec existed. But now that we have docker exec it shouldn't be necessary anymore.
Thank you!


fix: re-implement Psbt (de)serialization from/to readers/writers

Backportt #3255 to bitcoin v0.32.
One change is different from the original patch, import DisplayHex and remove imports of String and Vec.

bitcoin on 0cd87931efe87133aabcbb2ea1c8f365d6c6ff96 does not build with --no-default-features. (Unsure if 0.32.x is in our "broken CI" era or what. Thank goodness I fixed my local CI before this!)

cargo test --no-default-features from workspace root gives false positive ... again :)

I think we can merge this without ack from @Kixunil, its just a backport, its been open over 48 hours, and he ack'ed the original PR.


change how we calculate the temp dir

update how we calculate the temp dir in setup_xcodeproj.dart. Before we were getting the temp dir and making sure that it existed (Directory.systemTemp.create()). The intent was to create a new temp subdir though (Directory.systemTemp.createTempSync('...').
also, prefer to use dart:io calls where they exist to shelling out

On the bot, we were seeing this command executed:
/bin/rm -rf /tmp

(https://uberchromegw.corp.google.com/i/client.flutter/builders/Mac/builds/481/steps/drive sample_app/logs/stdio)
@chinmaygarde

Other than the likely async error, lgtm.

why didn't travis catch that?

Filed https://github.com/dart-lang/sdk/issues/26065


add ssh keys to manually created hosts (so rancher cli works)

Rancher versions:
rancher/server: 1.6.10
rancher/agent:  v1.2.6
Docker version: (docker version,docker info preferred)
Operating system and kernel: (cat /etc/os-release, uname -r preferred)
Type/provider of hosts: (VirtualBox/Bare-metal/AWS/GCE/DO)
AWS through spotinst integration.
Setup details: (single node rancher vs. HA rancher, internal DB vs. external DB)
singlenode
Environment Template: (Cattle/Kubernetes/Swarm/Mesos)
Cattle
Spotinst is adding AWS spotinsts through a direct call the rancher/agent:v1.2.6
i.e. sudo docker run --rm --privileged -v /var/run/docker.sock:/var/run/docker.sock -v /var/lib/rancher:/var/lib/rancher rancher/agent:v1.2.6  ...
These nodes come up but with very little information and even though they are on aws with ssh keys that I have provided, rancher does not have access to the keys.   I am wondering if there is a way automatically or from the rancher cli to add the proper host key to rancher DB.

Unfortunately, there is not. The ability to access hosts from the CLI is accomplished by using docker-machine to create the machine and persisting and using the docker-machine configuration.

I'll close this out @kgk as this feature would need to be implemented here first. We can revisit if it gets added to docker-machine.


Allow users to define defaults on a per-DAG basis

Not all DAGs will want to have the same default database, schema, or
conn_id. This feature will allow users to define these features using
the dag_defaults

@dimberman what do you think of moving this to a draft PR, until we get back to this work?


Introduce interface for ToObject/ToObject

We know deserialization speed is an issue but currently all the code to extract data from the response is implemented as extension methods in DictionaryExtensions
Suggest we lift this into an interface and then implement as a class which is set on ODataSettings. This will form the groundwork to introduce other deserialization mechanisms and make it easier to see performance gains etc

We need something like this, however I question whether exposing custom serializer from/to IDictionary is suboptimal. Remember that results are not retrieved as key/value pairs. They are received as either XML or JSON documents, and the best performance would be reached if we offer custom serialization right from there. I believe Newtonsoft.Json can be hooked straight to ReponseReader.
Thank you for bringing it up and let's give this idea some more thoughts.

Sure, I was just proposing this as an initial change as it would have minimal impact but start the process off.
I'm not sure whether NewtonSoft.Json would work OOB with things like odata annotations or dynamic types, so it might be necessary to do this in stages to keep full functionality.
What I could see from a first-cut analysis it should be possible to speed up the property assignment logic by caching the property accessors or using something like Castle.Windsor's proxy creators handle this, but I want to quantify the improvement etc hence wrapping it all in an interface


[Documentation]: Could we have consistent naming for roctx?

Description of errors
In this page: https://rocm.docs.amd.com/projects/roctracer/en/latest/reference/roctx-spec.html#roctx-spec we see roctx being referred to as ROC-TX and rocTX in the very first line. There is no consistent naming for this library. What should it be? The name that is recommended can then be used in all our documentation pages such as those for our profiling tools.
Attach any links, screenshots, or additional evidence you think will be helpful.
No response

@bgopesh , please follow the conversation here for guidance on what to use in the rocprofv3 documentation.


Glossary page for languages is showing terms from English langauge

This is a Bug Report

Problem:
I have just seen that the glossary page for differet languages is  also showing terms from the English language instead of showing only terms from the language I selected . I expected  to see only terms specific to the chosen language.
Example Italian page has Englsish terms: https://kubernetes.io/it/docs/reference/glossary/?all=true
Proposed Solution:
Update the glossary page to show terms based on the selected language only and not included English
Page to Update:
https://kubernetes.io/docs/reference/glossary

The website is designed to use the English glossary entry if a localized one is missing.
We could add some styling to make it obvious that an entry is a fallback to English.
/area localization


Switch to running an actual Vault server during tests

After updating dependencies, we were having difficulty getting the Vault-related tests passing again using the internal Vault test server tooling. This changes our strategy to instead run an actual Vault server that all tests can share. While this does introduce an external dependency for tests on the vault binary, it requires us to import far fewer vault-related packages for testing.
Now we:

exec a vault server in dev mode before running any tests
scan its stdout for the auto-generated root token and expose it for authentication
use the official vault-client-go package to configure the required secret engines
run tests
stop the vault server

@psi and @shakahl Instead of adding an external dependency to run a vault server for ourselves - There is a thing called testcontainers where basically, during test initialization phase we can tell it to run a vault server and it runs a vault docker container for you. Then you can programatically access root-token, push secrets before tests starts. Once the test are done, it will automatically remove the container for you. The only dependency you need is to have docker installed in your machine. It works in GHA too. It's really is an awesome project and I have used it multiple times when I was a java engineer for running test dependencies
There is a module for vault-server in golang too if you want to try it out. https://golang.testcontainers.org/modules/vault/

This looks great, @jppakalapati. I can give it a shot tomorrow.


Add type hints

Is your feature request related to a problem? Please describe.

Type hints are just a general improvement :)
Describe the solution you'd like

Provide in-line type hints and mark the package as providing types by including a py.typed file in the distribution.
Additional context
You could also provide type stubs as pyright can automatically generate them for you, removing some of the work required for this:
pyright --createstub locust

Oh, are they not visible when doing a package install? (as opposed to a source install)
Or do you mean a type hint for a specific thing?
Either way, PRs welcome!


Update deps

Hi @diegoceccarelli. This PR just upgrades the dependencies of a few libs used in your project. This is a part of some work we did for spotlight and we think it would be best to upstream a few changes. Let me know what you think. I didn't do much testing in this, but maybe @naveenmadhire and @dav009 could double check this.
PS: it doesn't seem that lucene is used here. Should we remove it as a dep ?

Thanks @tgalery, merged and I removed the Lucene dependency, when I wrote json-wikipedia I was indexing also the collection, that's why there was the dependency. Let me know when you're in London ;)


Use sample repo for application name

Fixes
https://issues.redhat.com/browse/RHTAPBUGS-327

Description
Use sample repo name to create application name.

Type of change

[ ] Feature
[x] Bugfix
[ ] Code style update (formatting, renaming)
[ ] Refactoring (no functional changes, no api changes)
[ ] Build related changes
[ ] Documentation content changes
[ ] Other (please describe):

Screen shots / Gifs for design review
https://github.com/openshift/hac-dev/assets/20013884/1b2fa378-e173-468d-93a3-9686bf1b3aa3

How to test or reproduce?
Create a sample in new application.

Browser conformance:

[ ] Chrome
[x] Firefox
[ ] Safari
[ ] Edge

/retest


Fix not working controls

@egdbear Sorry I have not reacted to this (see the notice on the project). Can you describe the need and solution?

Merged it anyway.. known/fixed should not have a problem


[BotoomNavigation] Why is it called this if it has no code to stick it to the bottom of the page.

[x] I have searched the issues of this repository and believe that this is not a duplicate.

Summary 💡
It is surprising to me that no part of this component actually makes it a "Bottom..." anything.
It would be nice if the developer could easily pass a prop or two to specify placement & stickiness of the component.
Something like taking a sticky (bool) & placement ('top' or 'bottom') to control this behavior so it's not required to use custom CSS to achieve this.
I'd be happy to take a crack at it if this is deemed a worth addition to the library.

This component doesn't handle layout. It's up to the users to implement it.

Yes, I understand that which is why I opened the issue. Why call it **Bottom**Navigation if no part of the component places it on the bottom of anything?  The name is misleading.

It's meant to be display at the bottom of the page, on mobile https://material.io/components/bottom-navigation/.


chore: update mimalloc to 2.1.6

update mimalloc to 2.1.6

@romange I will need this in df :)

Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 77.23%. Comparing base (d30de86) to head (3c43d8a).
Report is 63 commits behind head on master.

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #283      +/-   ##
==========================================
- Coverage   77.60%   77.23%   -0.38%
==========================================
  Files         103      107       +4
  Lines        7824     8038     +214
==========================================
+ Hits         6072     6208     +136
- Misses       1752     1830      +78

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Update to Swift 3.1

Add 'ExcludeFileReader' framework as Carthage dependency.

Codecov Report

Merging #53 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #53   +/-   ##
=======================================
  Coverage   93.07%   93.07%
=======================================
  Files          61       61
  Lines        1690     1690
=======================================
  Hits         1573     1573
  Misses        117      117

Continue to review full report at Codecov.

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Differentiation of matrix product causes crash when the sizes are identical

When calling the ts::MatProdNode::incrementGradient() method, an if statement is used to figure out the order of the operands :
https://github.com/PurplePachyderm/tensorslow/blob/24607ffd4930b0c8cac577de3706cd7647e24b19/src/autodiff.cpp#L96-L101
However, when the two matrices have the same size, one of the 2 partial derivatives will fall in case 1 while it should fall in case 2. This results in a matrice with an incorrect size, thus creating an error when incrementing the derivative in the ts::Tensor::grad() method.
For instance, this problem may occur when using a multilayer perceptron with two consecutives layers of the same size (thus resulting in a 1x1 matrix).
We have to find a solution to figure out in which case we are regardless of the matrices sizes.

Dear @PurplePachyderm. That is indeed an interesting bug; good catch. I'm not sure to have grasped exactly what is going on. If you want we can organise a call so we can discuss it around the specific perceptron example.
But... my intuition is that maybe you need to store the information about the order of operands during the forward computation; so when you initially build the ts::MatProdNode.
What do you think ?

I also think this would be a way to fix it.
Actually, I think the bug happens when :

A is a nxn matrix
B is a nxm matrix
we compute A*B, which is of size nxm

In that case, the childDerivative for A is the transpose of B^T, so a mxn matrix. Since A^T (childDerivative) has m columns and the derivative of A*B (this->values[j]) also has m rows, it falls in the first case. Because of it, we compute a product of (mxn) x (nxm) = (mxm) instead of (nxm) x (mxn) = (nxn).
In the perceptron example, we have exactly this case, with m=1.
I wonder if this could just be fixed by switching the order of the if statements? I'll try this, as well as storing the size of both operands in the ts::MatProdNode. I'm quite confident this bug can be solved relatively easily.

I agree with your analysis.

The proposed solution solved the issue !


Add support for windows and multiple os

will build on windows,linux and mac.

It looks like Java is not supported on windows in Travis, so another alternative is to try circleci.

circle ci only support java 11 out of the box, so need to explicitly compile to java 8:
https://stackoverflow.com/questions/49509330/kotlin-compile-to-java-1-8

Hey @oshai , have you considered using github actions for releases? You can use linux, macos and windows runners in the same workflow, and Java versions can be configured using actions/setup-java.
I have set up releasing to Maven Central using github actions recently, if you are interested you can check out my config: PublishingConfiguration.kt, release.yml.

implemented in another cl in 2.1.15


[3TR7] Pipeline reproduction (SPM - deriv)

Softwares

fmriprep,
SPM12 (7219),
ipython and associated python packages (Python 3.6.7, matplotlib 3.0.3, pandas 0.24.1, and nilearn 0.5.0, nibabel 2.3.3,  numpy 1.16.2,
mricron for visual quality check

Input data
derivatives (fMRIprep)
Additional context
some subjects were excluded from the analysis based on predifined criteria
List of tasks
Please tick the boxes below once the corresponding task is finished. :+1:

[x] :ok_hand: A maintainer of the project approved the issue, by assigning a :checkered_flag:status: ready for dev label to it.
[x] :deciduous_tree: Create a branch on your fork to start the reproduction.
[x] :sunrise: Create a file team_{team_id}.py inside the narps_open/pipelines/ directory. You can use a file inside narps_open/pipelines/templates as a template if needed.
[x] :inbox_tray: Create a pull request as soon as you completed the previous task.
[ ] :brain: Write the code for the pipeline, using Nipype and the file architecture described in docs/pipelines.md.
[ ] :blue_book: Make sure your code is documented enough.
[ ] :snake: Make sure your code is explicit and conforms with PEP8.
[ ] :microscope: Create tests for your pipeline. You can use files in tests/pipelines/test_team_* as examples.
[ ] :microscope: Make sure your code passes all the tests you created (see docs/testing.md).

@alexpron: I am adding you as assignee on this issue (just for the time of the hackathon) so that we can more easily see which pipelines are open for new contributions in https://github.com/orgs/Inria-Empenn/projects/1/views/1


Community Meeting, September 28, 2021

At noon Eastern, 9am Pacific, 4pm UTC; find your time
Video call link: https://meet.google.com/ohf-kwvd-mrp
Or dial: (US) +1<PHONE_NUMBER> PIN: 936<PHONE_NUMBER>#
More phone numbers: https://tel.meet/ohf-kwvd-mrp?pin=9361820877398
Or join via SIP<EMAIL_ADDRESS>This issue will collect prospective agenda topics. Add topics you'd like to discuss below!

@stevekuznetsov discussing (demoing?) transparent multi-shard list (#175)
@imjasonh progress on namespace-wide scheduling/moving

dynamic type-discovering informer (also useful for syncer?)
GVKs and GVRs, oh my!

Ongoing fixes related to namespace management:

adminssion, controller.
Have to continue with RBAC ...

Testing the kcp-ingress on the DW controller over KCP scenario

creating duplicate of objects (splitter pattern may bring problems according to controller logic)

Recording: https://youtu.be/p7Az2MeeGic
Next: https://github.com/kcp-dev/kcp/issues/177


Add Anagram Checker, Collatz Sequence, and Fibonnacci to ProblemAndSolutions in PYTHON

I'm new to open source contribution but I know this project will put me on track.
Thanks.

Sure @Pymode-Dev! You can contribute in any possible way! All Contributions are welcome till they're meaningful!

Can you please assign this issue?


temperature-pressure MS plotting

Hi @AlexanderKrabbe ,
This PR creates a new Measurement class called ReactorMeasurement which inherits from MSMeasurement and adds to that the essential series Temperature and Pressure. It makes plots like ixdat's EC-MS plots, but with temperature taking the place of potential and pressure taking the place of current.
The ReactorMeasurement class would be a great place to add all kinds of cool methods, like calculating conversion as a function of temperature, etc. Just like for a MSMeasurement, you can get MS sensitivity factors with MSInlet.gas_flux_calibration and then add them to your ReactorMeasurement using my_reactor_meas.calibrate(ms_cal_results=[my_cal_H2_M2, ...])
You will need to specify the technique and aliases for pressure and temperature when reading TPMS data with reader="cinfdata" or "ixdat". An example is given in test_ixdat_reader_TPMS using the example data you sent me. You will need to change data_dir but otherwise should run. Let me know if it works!

Ooh, sorry about that, @AlexanderKrabbe , I should have made the PR to a different branch on your fork. I wanted you to have it on your most up-to-date branch ASAP, but forgot it would go into your open PR to ixdat: main.
Let me know if there's anything I can do to help clean up at this point? And also if you'd like to wait until you've added some flesh to ReactorMeasurement before merging to main?


Get Android sample apps building on JDK 11

Update to AGP 7, so now the full NullAway build runs on JDK 11.  The sample apps no longer build on JDK 8.

Just testing on CI, no need for any review yet.  I'd like to land #529 first

Pull Request Test Coverage Report for Build #646

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 89.651%

Totals

Change from base Build #635:
0.0%

Covered Lines:
4106

Relevant Lines:
4580

💛  - Coveralls

@lazaroclapp this one is ready for review now.  We probably also want to change our CI config to mostly test on JDK 11.  We can do that in a follow-up PR, though happy to do it here if you think that's better


[BEAM-2770] Add @Experimental and ImmutableList.copyOf

Some final API polish, making sure @Experimental annotations are on all the public SQL API classes, and immutable objects always return ImmutableLists for private members instead of the mutable members themselves.

R: @XuMingmin @xumingming

Changes Unknown when pulling 670c2ee3f3ab03df60b89eb7f4d16760d43e0bd5 on takidau:misc-api-cleanups into ** on apache:DSL_SQL**.

Changes Unknown when pulling c2acb54f6756786bcfe12e9faf32950fd6260c5e on takidau:misc-api-cleanups into ** on apache:DSL_SQL**.

@takidau can you merge the PR? Seems I don't have write access now.

trying to merge...

merged, please close it when you've time.

Nice, thank you! Closing.


Generates files with a wrongs paths.

If not set same file_path and group_path, generamba generates files with a wrongs paths.

Blocker 👍


Feature/verified support

Adds verify support to UI
Comments out description for now

[x] Check that you pass the basic compilation and unit tests by running grunt

Coverage decreased (-0.005%) to 8.106% when pulling 4a8f5594b88486162ed50c32169978856b76c2a4 on feature/verified_support into 7ac1e720e546af13a9bdf9c4a392af328cad5501 on develop.

Coverage decreased (-0.005%) to 8.106% when pulling e9909bc4b002690dec116c9501790e6d409d3887 on feature/verified_support into 7ac1e720e546af13a9bdf9c4a392af328cad5501 on develop.


Change value of an attribute

This is not really an issue.
Is this function already implemented to modify DOM?
Thanks.

Wondering the same thing. I definitely love the simplicity of this crate. A mutation API would be even better!
Already plans to work on this? Open to a PR?


Add hotkey to clear localStorage

Addresses #267.  Kind of cheesy, but hopefully it'll be helpful to someone.
For Hacktoberfest :)  (hacktoberfest.digitalocean.com)

@alexose Thanks!
We will definitely review.

Hi @alexose Thanks a lot for the PR ! :)
I am sorry to bother you with this but could you please remove the build files from the PR ?
Build files should not be included in PRs they are automatically generated with each new release: not your fault, we still need to  amend the README to make that more clear.
Thanks in advance !

No trouble at all.  I actually went back and forth on whether I should include the build files or not... guessed wrong!  :P

haha , we were also on the fence for a while , but it is simpler and more reliable this way !
Thanks for the changes and the PR !


[Bug] Inputs update does not work when there is a binding inside it

Description
Repro: JS Snippets app
Steps to reproduce the behaviour:

Update a snippet with bindings
Switch rows
The input does not update anymore

@hetunandu seems similar to #10026, If not please open it again.

Not related. This is because there are bindings that are part of the data

Quoting @Nikhil-Nandagopal
I'm not able to reproduce it now and since it's not too prevalent a case let's close it


option to disable automake on certain cases

i ran into some issues in the past on plugin-generated buffers (i think it was with gita)
disabled mine on &buftype ==# 'nofile'
and on empty(glob(expand('%'))) (this could probably be better written, like empty(bufname('%')), not sure if that's more performant)

A non-empty buftype should get ignored already: https://github.com/neomake/neomake/blob/f2bb4aeeb2a76b76c39d2a99372f64c0278274a8/autoload/neomake/configure.vim#L366-L372

I do not think that an empty bufname should get ignored by default - that is what tempfiles are meant to handle.

There is an (undocumented) setting to ignore filetypes already (https://github.com/neomake/neomake/blob/f2bb4aeeb2a76b76c39d2a99372f64c0278274a8/autoload/neomake/configure.vim#L6), for which I have to add documentation still.


link, but no backing documentation showing for package heckj/Lindenmayer

Please describe the bug
I added the .spi.yml and pushed, and the documentation link now shows for the package heckj/Lindenmayer, but the backing documentation hasn't appeared, instead there's an error page
Explain the steps needed to reproduce the bug

Added .spi.yml, which has two targets listed (Lindenmayer and LindenmayerViews), pushed code
forgot to add the docc plugin, so added that and re-pushed code
Waited 18+ hours before submitting the bug report ;-)

.spi.yml file included in repo:
version: 1
builder:
  configs:
    - documentation_targets: [Lindenmayer, LindenmayerViews]

When I generated the docs myself, there wasn't much of an option to include both in the Github Pages, so I defaulted to just Lindenmayer (https://heckj.github.io/Lindenmayer/documentation/lindenmayer/) - so I'm sure the doc generation is working

Hi Joe, both docs sets are there.

https://swiftpackageindex.com/heckj/Lindenmayer/main/documentation/lindenmayerviews works
https://swiftpackageindex.com/heckj/Lindenmayer/main/documentation/lindenmayer doesn't but
https://swiftpackageindex.com/heckj/lindenmayer/main/documentation/lindenmayer does (note the lowercase "L")

I wonder if Cloudflare is somehow holding on to our error page? Although that should be long expired, it's only 3h. Unfortunately I can't purge it to reset, so we'll have to check back in a bit to see if it shakes itself loose.

And there it is! We need to check why CF is holding on to the error page. I think unless we exclude that from caching it’ll extend the update delay unnecessarily by 3h.
Thanks again for reporting this, I’ll keep this issue open to track the CF change.

Thanks!

This would also be addressed by #1784 , because we'd only offer a link once we know there's content in the bucket. (There'd be still some ways this could 404 for odd reasons so we'd want to avoid caching those regardless.)


Getting AttributeError: 'NoneType' object has no attribute 'device'

`This share link expires in 72 hours. For free permanent hosting and GPU upgrades (NEW!), check out Spaces: https://huggingface.co/spaces
-------state_chatbots------
([],)
----inside
Below is a history of instructions that describe tasks, paired with an input that provides further context. Write a response that appropriately completes the request by remembering the conversation history.
Instruction:What is AI
Response:
there is only a prompt
Traceback (most recent call last):
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/gradio/routes.py", line 384, in run_predict
output = await app.get_blocks().process_api(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/gradio/blocks.py", line 1020, in process_api
result = await self.call_function(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/gradio/blocks.py", line 844, in call_function
prediction = await anyio.to_thread.run_sync(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/anyio/to_thread.py", line 31, in run_sync
return await get_asynclib().run_sync_in_worker_thread(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/anyio/_backends/_asyncio.py", line 937, in run_sync_in_worker_thread
return await future
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/anyio/_backends/_asyncio.py", line 867, in run
result = context.run(func, *args)
File "/home/jupyter/Llama/Alpaca-LoRA-Serve/app.py", line 88, in chat
bot_responses = get_output(
File "/home/jupyter/Llama/Alpaca-LoRA-Serve/gen.py", line 27, in get_output
generated_id = model.generate(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/peft/peft_model.py", line 581, in generate
outputs = self.base_model.generate(**kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
return func(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/transformers/generation/utils.py", line 1490, in generate
return self.beam_search(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/transformers/generation/utils.py", line 2749, in beam_search
outputs = self(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
return forward_call(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/accelerate/hooks.py", line 165, in new_forward
output = old_forward(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/transformers/models/llama/modeling_llama.py", line 770, in forward
outputs = self.model(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
return forward_call(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/transformers/models/llama/modeling_llama.py", line 619, in forward
layer_outputs = decoder_layer(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
return forward_call(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/accelerate/hooks.py", line 165, in new_forward
output = old_forward(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/transformers/models/llama/modeling_llama.py", line 316, in forward
hidden_states, self_attn_weights, present_key_value = self.self_attn(
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
return forward_call(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/accelerate/hooks.py", line 165, in new_forward
output = old_forward(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/transformers/models/llama/modeling_llama.py", line 216, in forward
query_states = self.q_proj(hidden_states).view(bsz, q_len, self.num_heads, self.head_dim).transpose(1, 2)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
return forward_call(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/accelerate/hooks.py", line 165, in new_forward
output = old_forward(*args, **kwargs)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/peft/tuners/lora.py", line 522, in forward
result = super().forward(x)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/bitsandbytes/nn/modules.py", line 242, in forward
out = bnb.matmul(x, self.weight, bias=self.bias, state=self.state)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/bitsandbytes/autograd/_functions.py", line 488, in matmul
return MatMul8bitLt.apply(A, B, out, bias, state)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/torch/autograd/function.py", line 506, in apply
return super().apply(*args, **kwargs)  # type: ignore[misc]
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/bitsandbytes/autograd/_functions.py", line 317, in forward
state.CxB, state.SB = F.transform(state.CB, to_order=formatB)
File "/opt/conda/envs/alpaca-serve/lib/python3.9/site-packages/bitsandbytes/functional.py", line 1698, in transform
prev_device = pre_call(A.device)
AttributeError: 'NoneType' object has no attribute 'device'`

Maybe try again?
I added device_map={'': 0} to from_pretrained method

I also get this


Use configuration-properties in clients HiveConf

I'd like to use the configuration-properties that I can set in the waggle-dance-server.yml in HiveConf that is used to create Thrift Clients.
Currently we use the properties only in the Handler (the server), it would be good if we can set properties and override settings used in the clients.
For instance see ThriftMetastoreClient it contains this code:
   retries = HiveConf.getIntVar(conf, HiveConf.ConfVars.METASTORETHRIFTCONNECTIONRETRIES);
But there is currently no way to override this cause we create the HiveConf ourselves in CloseableThriftHiveMetastoreIfaceClientFactory. Thus that values is hardcoded to the Hive default  3.
Acceptance Criteria:

Use theconfiguration-properties(see WaggleDanceConfiguration class) when creating the HiveConf for the clients.
Documents it's use in the README (it seems to be a hidden feature now).

#90 Waggle Dance Glue PR adds this feature

Hey @patduin , would this look something like this? https://github.com/HotelsDotCom/waggle-dance/compare/issue-77?

@patduin is this worth keeping open? Is the above PR from @AnanaMJ something we want to merge?

maybe keep this one as it might have a fix already. We just need to check backward compatiblity/implications. etc...


UI Confusion in Iris Button Configuration on Exercise/Iris Settings Page

Problem:
Currently, on the Exercise / Iris Settings page, the configuration of the iris button appears confusing with "enable/disable." At first glance, I mistakenly perceived that having it positioned on the right indicated it was disabled.
Proposal:
Change the labeling to enabled/disabled -> enabled
Screenshot:

Which version of Artemis are you seeing the problem on?
6.7.3
What browsers are you seeing the problem on?
Chrome, Safari, Microsoft Edge, Firefox

I think we should use a completely different button with different modes and not a simple switch. It could be like the choice of easy, medium, hard for the difficulty of exercises, but just with two states: enabled (green) and disabled (red)
The selected one should then be highlighted

The same issue is also present in "Hestia Settings" and "Code Editor Settings" buttons.  I am going to handle this in the next couple days.


Where does mup install the Meteor application directory?

Where does mup install the Meteor application directory on a Ubuntu EC2 instance?  I need to create a directory under the application folder and can't find it.

see: https://github.com/arunoda/meteor-up#server-setup-details
On Thu Jan 22 2015 at 10:31:47 AM Aaron Adams<EMAIL_ADDRESS>wrote:

Where does mup install the Meteor application directory on a Ubuntu EC2
instance? I need to create a directory under the application folder and
can't find it.
—
Reply to this email directly or view it on GitHub
https://github.com/arunoda/meteor-up/issues/231.

Thanks.


Yatin: Watch meeracfo.com

Yatin requests the watch of the watch_keyword meeracfo\.com. See the MS search here and the Stack Exchange search in text, in URLs, and in code.

meeracfo\.com has been seen in 1 true positive, 0 false positives, and 0 NAAs.

meeracfo\.com has been seen in 1 true positive, 0 false positives, and 0 NAAs.

Approved by tripleee in Charcoal HQ

Approved by tripleee in Charcoal HQ


Create a footer white-14

One need to make this component using HTML and Tailwind CSS. I would suggest to use Tailwind Playgrounds to make things faster and quicker.
Here is a reference to the component.

After building the component please raise a PR with a screenshot of the component and add the component in Footer/footer-white-14.html.
If you need to use any icon please use it from Hero Icons
Good luck.

Hey @rupsha014  Could I work on this?

@Aspireve sure

@Aspireve are u still working on it?

Yes was just trying to learn a bit of tailwind but I guess Ill be able to do it soon

You can build 2 circles using CSS behind the image. @Aspireve

Can I work on this issue?

Sure. @kunal00000

Is there any reference for mobile view? If possible please provide it.

For now there is no reference to mobile view, sorry for that. Just make sure it doesn't break use your own creativity. @kunal00000


Prowjobs: adding a wrapper binary to the prowjobs. Uploads results to GCS.

Results are parsed by testgrid and gubenator.

/gocheck

/gocheck

/retest


docs: add data-content

Fix #1498
Reproduce the change made in Sphinx 7
https://github.com/sphinx-doc/sphinx/commit/8e730ae303ae686705ea12f44ef11da926a87cf5#diff-a5066e933cbf65adc46e0d1ab9a0b44e0a53ca64cc95dca7e6aa902aed6bd468R105
I did it from my phone, can @vkbo or @kay-kim test this branch to confirm the fix?

Tested with Sphinx 7.2.6, and it seems to work. Also still worked on 6.2.1 as before,

Also tested (reran pydata docs).  Looks great!  Thanks much!


Conditionally specify columns does not work

I want conditionally specify which columns table will have.
Usually I use ternary operator to hide something in the React by this does not work with React Bootstrap table. See example below.
export const BetDistributionTable = (props: BetDistributionTableProperties) => {
    const betType = props.showBetType
        ? <TableHeaderColumn width="200" dataField="betType" dataSort={true} isKey={true}>Тип ставки</TableHeaderColumn>
        : null;
    return <BootstrapTable data={props.data} bordered condensed hover trClassName=""
        options={{ defaultSortName: "date", defaultSortOrder: "desc" }}>
        <TableHeaderColumn width="200" dataField="date" dataSort={true} isKey={true}
            dataFormat={dateFormatter}>Date</TableHeaderColumn>
        {betType}
    </BootstrapTable>;
}

Try to use keyField on BootstrapTable so that it can avoid you need to handle key column(isKey) particularly.

generateColumns() {
    return mycolumn.map((column) => {
        return <TableHeaderColumn>....</TableHeaderColumn>
    });
}

<BootstrapTable data={ myData } keyField='id'>
    { this.generateColumns }
</BootstrapTable>

is that helpful for you?

and I saw your PR also, if you follow the solution above, is that still possible have null value in react childrens?

The problem not in the isKey or such.
I think very often in React use following pattern
const header = showHeader ?
Header
 : null
return
{header}
;

When I construct <TableHeaderColumn> objects like that React Bootstrap table does not like it.
I have table with 10 columns and couple of them could be shown/hidden as needed. I definitely could create workaround which will produce array of <TableHeaderColumn> components but think that RBT will benefit from having such simple way to dynamically create columns.

ok, got it, but one more question, if you used hidden on TableHeaderColumn is helpful for you?

Let me try. I don't even consider this given how ingrained pattern which I show to you.


Not working with julia version 1.10.1 on linux systems

Affects: JuliaCall
Describe the bug

The new version 1.10.1 release broke the package juliacall on Linux systems.
When importing the package from python a segmentation fault occurs.
How to reproduce:

Have julia version 1.10.1 installed in your system (or no version at all, since juliacall installs julia if not present).
create a clean conda environment with python (3.9 or superior tested).
run pip install juliacall
open python interactive session and run import juliacall

Note: this does not happen with version 1.10.0 and on Mac devices.
Your system
The bug is present both on manjaro linux (Manjaro Linux x86_64, kernel: 6.1.71-1-MANJARO) and on Ubuntu (Ubuntu 20.04.5 LTS x86_64, kernel 5.15.0-1054-azure).
I raised the issue also on the julia github

I experienced this as well, and came here to look if this was reported already, I'm using a Debian (testing-branch) system, using Python 3.11 and Julia 1.10.1.

Also https://github.com/JuliaLang/julia/issues/53363

For people looking for a fix:
import juliapkg
juliapkg.require_julia("=1.10.0")
juliapkg.resolve()
from juliacall import Main as jl
jl.println("hello world!")

I can reproduce this error with default python 3.11.4 from  ubuntu 23.04, but it works with pyenv python versions 3.11.6, 3.11.8 & 3.12.2

https://github.com/conda-forge/python-feedstock/issues/222
Looks like pyjulia already experienced some issues with statically linked Python.

I ran the command and got 0.
I'm running python version 3.10.13 and julia version 1.10.1 and it causes the segfaults.

I ran the command from a new virtualenv and got a 1, but since I didn't personally create the original virtual env (which I had already deleted), I'm not fully sure that I'm reproducing the same configuration

I got a 0. Indeed I switched to PythonCall from PyJulia exactly because PyJulia had problems with statically linked python. This is also an issue over at conda-forge I believe. to further check if python is statically linked, I use echo $(which python) && ldd $(which python):
echo $(which python) && ldd $(which python)
/home/user/micromamba/envs/ahf/bin/python
        linux-vdso.so.1 (0x00007fffe4b75000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x000074ff836c9000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x000074ff836c1000)
        libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x000074ff836b9000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x000074ff835c9000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x000074ff833b9000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x000074ff833b1000)
        /lib64/ld-linux-x86-64.so.2 (0x000074ff83d99000)

And we can see that it is statically linked, because there is no link to libpython.so

I have never been able to reproduce this issue and still cannot.
x@fedora:~$ python -c "import sysconfig; print(sysconfig.get_config_var('PY_ENABLE_SHARED'))"
1

This is consistent with @cjdoris's hypothesis.

Unfortunately, the build flags depend on the maintainer (not just the default build flags from Python).
On my system (Ubuntu), the Debian-provided python3 is OK and the Ubuntu-provided python3.11 is bad.
However, they are both shared:
$ python3 -c "import sysconfig; print(sysconfig.get_config_var('PY_ENABLE_SHARED'))"
1
$ python3.11 -c "import sysconfig; print(sysconfig.get_config_var('PY_ENABLE_SHARED'))"
1

The direct test is to inspect the relocations in the binary:
$ readelf -rW $(which python3.11) | grep environ
0000000000a92620  000006a400000005 R_X86_64_COPY<PHONE_NUMBER>a92620<EMAIL_ADDRESS>+ 0
$ readelf -rW $(which python3) | grep environ
0000000000562cb8<PHONE_NUMBER>000006 R_X86_64_GLOB_DAT<PHONE_NUMBER>000000<EMAIL_ADDRESS>+ 0

The R_X86_64_COPY relocation causes the segfault

Also as a heads up, there's a work-around being landed for 1.10.3: https://github.com/JuliaLang/julia/pull/53643

PySR users also experiencing this issue: https://github.com/MilesCranmer/PySR/issues/561

There's a new version of juliacall out which requires julia <=1.10.0, so if you upgrade juliacall things should work again. I'll allow 1.10.3 and 1.11 again later once those are out and shown to work OK.

I confirmed that JuliaCall works with 1.10.3 so I have made a release (JuliaCall 0.9.20) with the updated julia compat entries.


First batch import to https://topo.transport.data.gouv.fr

We need to import some data in the official instance.
After adding one dataset for test (the one in the tests?), we'll import all dataset found in https://transport.data.gouv.fr/.
For this we also need to create a producer for each transport's dataset
Note: :warning: the official instance will still be in beta, we may yet delete all data without notification :boom:

hop, all the datasets from transport.data.gouv.fr/ were added, we now have 167 producers, 133824 stop points, 47819 stop areas, and 6945 routes