PropTypes.shape behaviour changed between versions

Hey there, somewhere between 0.38.0 and 0.42.0 it seems this behaviour changes, just question if this is a bug or the change was expected?
In 0.38.0 this works
store-shape.js
export default PropTypes.shape({
  subscribe: PropTypes.func.isRequired,
  dispatch: PropTypes.func.isRequired,
  getState: PropTypes.func.isRequired
});

some-component.js
  // @flow weak

  return React.createClass({
    propTypes: {
      store: StoreShape.isRequired
    }

 ... somewhere else ...
this.props.store.getState(); // Does this line error

But after upgrading to 0.42.0 that line will now error ...

Flow: call of method getState. Method cannot be called on possibly undefined value undefined

I found that if I inline the definition it won't pick that error up ...
  return React.createClass({
    propTypes: {
      store: PropTypes.shape({
        subscribe: PropTypes.func.isRequired,
        dispatch: PropTypes.func.isRequired,
        getState: PropTypes.func.isRequired
      }).isRequired
   }

We are just introducing flow to our codebase, hence old style React.createClass

Hmm, sounds like something could be up. We changed a bunch of stuff with React.createClass in 0.42, but what you're describing definitely doesn't sound right.
I tried to reproduce with the information provided here, but I can't. Can you share a repro case that exhibits the issue so I can debug? Thanks.
This is what I tried:
const React = require("react");
const {PropTypes} = React;

const StoreShape = PropTypes.shape({
  subscribe: PropTypes.func.isRequired,
  dispatch: PropTypes.func.isRequired,
  getState: PropTypes.func.isRequired,
});

React.createClass({
  propTypes: {
      store: StoreShape.isRequired,
  },
  m() {
    this.props.store.getState();
  },
});

Hi @samwgoldman ... sorry for delay ... ok found the thing, and its not a big issue (or even a issue at all)
First your example worked, but in my case StoreShape is defined in another file, then I realised that my store-shape file doesn't have // @flow at the top.
Doh! ... I've been bitten by that lots as we are migrating more and more stuff to use flow.
That said the behaviour for did change between versions, so I feel slightly less silly for making the mistake here. And guessing the current behaviour should be expected.
Apologies for the false alarm


Using maven api to get artifact latest versions

with this change we wont need to update vraptor and plugins versions manually
after each release. It fetch maven versions via http when vraptor site is deployed.
closes https://github.com/caelum/vraptor4/issues/966

:gem:


To test creation:

Run the server and log in as privileged user
Go to create a challenge
Attempt to set expiry date to before current date (It shouldn't let you)

To test display:

Create a challenge with a valid expiry date
Log into admin portal
Edit said challenge to expire before now
Go back home
Ensure that challenge isn't displayed in any way (either marker or list)

To test completion:

Go to the complete challenge screen of the previously edited challenge (/create-response/{challengeid}/)
Attempt to submit response
You should be redirected to home and an error message is displayed

To test multiple submission fix:

Go to the complete challenge screen of a previously completed challenge (Expired or not) (/create-response/{challengeid}/)
You should be redirected to home with an error message

Details:
Added expiry date + time in challenge creation
Added features preventing users from completing challenges twice and completing expired challenges
Made it so only unexpired challenges are displayed
Challenges must finish after creation date
TODO:
Use this code to implement weekly challenges

 Implement expiry for challenges


Full refresh for Singer, Airbyte and Go native sources

Problem
At the moment, full refresh for subj doesn't work well. It first truncates table, and then starts to fill table once again. It means that during the run data is inconsistent.
Solution
We have a mechanism for transactional full refresh which we use in Jitsu SDK backed sources. We should utilize same thing for all other types of sources.
Cleanup deprecated tables.

Is there any workaround?


decoder_attentions in showAttentions does not sum up to 1 for each timestep

When trying to show attention score for each generated token using showAttention function, I find that each row of the decoder_attentions does not sum up to 1, which seems strange for the attention mechanism. Most values are very small. Not sure if it is a bug?

Close the issue since we're developing new models on the task and it's solved in fact.


Multiple target debugging: Should be able to let targets depend on others

VSCode Version: Code 1.7.1 (02611b40b24c9df2726ad8b33f5ef5f67ac30b44, 2016-11-03T13:53:14.822Z)
OS Version: Windows_NT ia32 6.1.7601
Extensions:

Extension
Author
Version

csharp
ms-vscode
1.4.1

debugger-for-chrome
msjsdiag
2.2.0

other extensions not
important for this issue
---

When you configure multi target debugging you should be able to configure which configuration depends on others. When you configure to debug a coreclr web application and you want to debug also the javascript via Debugger for chrome, the chrome configuration should be started after the coreclr has started. Because otherwise the browser starts although there is no running web server.
Steps to Reproduce:

Setup a core and chrome launch configuration similar to this

{
	"version": "0.2.0",
	"configurations": [
		{
			"name": "Launch Core",
			"type": "coreclr",
			"request": "launch",
			"preLaunchTask": "build",
			"program": "${workspaceRoot}\\bin\\Debug\\netcoreapp1.0\\MyWebApp.dll",
			"args": [],
			"cwd": "${workspaceRoot}",
			"stopAtEntry": false,
			"internalConsoleOptions": "openOnSessionStart",
			"env": {
				"ASPNETCORE_ENVIRONMENT": "Development"
			}
		},
		{
			"name": "Launch Chrome",
			"type": "chrome",
			"request": "launch",
			"url": "http://localhost:5000",
			"sourceMaps": true,
			"webRoot": "${workspaceRoot}/wwwroot"
		},
		{
			"name": "dotnet + chrome",
			"type": "composite",
			"request": "launch",
			"configurationNames": [
				"Launch Core",
				"Launch Chrome"
			]
		}
	]
}

Run "dotnet + chrome"
You will see that that browser starts although the core application is still compiling or starting

Expected behavior:
The chrome configuration should start after the dotnet app has compiled and started.
PS: Most of the times the browser doesn't even start. Then I get the message, that I should configure my launch.json see Bug #14964

This is fixed in the vscode insider where you can manually launch one configuration after the other by pressing play multiple times. This will be in the december release ntoes


Improve logging

Logging right now is just some print statements which will be redirected to a log file inside the docker container. This is very bad for debugging and should be improved soon

Implemented logging with loguru


Help needed: App2App Testo Combustion app with Microsoft Field Service

Hello,
For a customer I work for I try to use the App2App interface in order to receive measurement data. However, I am a bit stuck. I hope you can help me.
I use: testot330://start?bundleid=com.microsoft.crm.crmphone.fieldServices in order to open the Testo Combustion app, as described in the section Workflow. I try this with a Field Service app by Microsoft.
Once I execute the code the testo app will open and connect to a Testo 330 device.
However, nothing seems to happen afterwards. Not automatically, nor when I manually save a measurement. In the readme it says select export via JSON/JTF. I do not see an export button or something similar. How does the caller app receives the url?
How does this step work exactly? Do you maybe have an example?
Thanks in advance.

Hello @RobbertvDijk,
when the testo Combustion App is called via the App2App interface the export button (bottom right of the screen) should give you the option to export the JSON back to the caller app, which then in your case will try to call the following URL:
testoapp+com.microsoft.crm.crmphone.fieldServices://data?json=[base64_encoded_json_data].
On Android the caller app needs to register an intent-filter in the AndroidManifest.xml: <data android:scheme="testoapp+androiddatareceiverdemo" />
Full demo AndroidManifest.xml:
<?xml version="1.0" encoding="utf-8"?>
<manifest xmlns:android="http://schemas.android.com/apk/res/android"
    package="de.testo.androiddatareceiverdemo" android:versionName="1.1" android:versionCode="1" >

    <application
        android:allowBackup="true"
        android:icon="@mipmap/ic_launcher"
        android:label="@string/app_name"
        android:supportsRtl="true"
        android:theme="@style/AppTheme">
        <activity android:name=".AndroidDataReceiverDemo" android:launchMode="singleTask">
            <intent-filter>
                <action android:name="android.intent.action.MAIN" />
                <category android:name="android.intent.category.LAUNCHER" />
            </intent-filter>
            <intent-filter>
                <data android:scheme="testoapp+androiddatareceiverdemo" />
	        <action android:name="android.intent.action.VIEW" />
	        <category android:name="android.intent.category.DEFAULT" />
	        <category android:name="android.intent.category.BROWSABLE" />
            </intent-filter>
            <intent-filter>
                <data android:scheme="file"/>
                <data android:host="*"/>
                <data android:mimeType="application/json" />
                <action android:name="android.intent.action.VIEW" />
                <category android:name="android.intent.category.BROWSABLE" />
                <category android:name="android.intent.category.DEFAULT" />
            </intent-filter>
        </activity>
    </application>
    <supports-screens android:largeScreens="true" android:normalScreens="true" android:anyDensity="true" android:smallScreens="true"/>
    <uses-permission android:name="android.permission.READ_EXTERNAL_STORAGE" />
</manifest>

If you have any further questions please let us know.

Hello @gwaldvogel ,
Thank you very much for your answer. For me it is now clear what should be done.
Unfortunately the Android app we are using is developed and managed by Microsoft. We do not have the possibility to change things like the AndroidManifest.xml.
Do we have another option to receive data from the Testo device to our Field Service App?
Some details:

Devices: Testo 330
Testo app: testo Combustion App Android

Thanks again!

Hello @gwaldvogel
Is there also no way to directly connect using JS through an API for  Testo 330 ?
Thanks,
Suyash

Is there also no way to directly connect using JS through an API for Testo 330 ?

You could try accessing the Device2Device API by sending a GET Request to http://localhost:53757/data while the testo Combustion App is running in the background. If you use a different app you will have to adapt the port accordingly. This might work, but can be unreliable on some devices that  are more trigger happy with closing apps that are running in the background.

Hello @gwaldvogel ,
Indeed we get a JSON response back. However, when we try to make the request from our App, we get CORS origin issues. Any suggestions?

The testo Combustion app sends Access-Control-Allow-Origin: *, you shouldn't have any issues with CORS. Are you using the most recent version of the testo Combustion app?

@spandey1988 The testo App should send you the correct CORS header, can you verify that the issue is not due to your http library?

Is there also no way to directly connect using JS through an API for Testo 330 ?

You could try accessing the Device2Device API by sending a GET Request to http://localhost:53757/data while the testo Combustion App is running in the background. If you use a different app you will have to adapt the port accordingly. This might work, but can be unreliable on some devices that are more trigger happy with closing apps that are running in the background.
@robbertvdijk this might also be a possible solution for your problem.

Hello, Is anywhere more documentation about this JS API?  I'm intending to get the data from Dynamics 365 Field Service Mobile app and looks like the only way to personalize it is adding client side scripts
@robbertvdijk Were you able to make it work ?  What was your approach ?

Hi @GuzmanHrz ,
I've got a working solution now. Eventually what I did was create a button in our Field Service app which opens the Testo app. Then we have a manual step where the user saves a measurement (the app will copy a JSON with measurement data to the clipboard automatically. This is a feature of the Testo app). Now this JSON message can be pasted in our Field Service system and a Javascript function will read the message and the measurement data is further processed in our system.
This works quite well, but as you can read it is not totally automated.

Hey @gwaldvogel : Any suggestions on how we can get it working ? We are almost there in retrieving the data. Only the CORS issue is blocking us. Apparenlty with browsers it works but with the app it is not allowed.

Hello!  Did you find a way to access the data from the app?

Hi @GuzmanHrz , I've got a working solution now. Eventually what I did was create a button in our Field Service app which opens the Testo app. Then we have a manual step where the user saves a measurement (the app will copy a JSON with measurement data to the clipboard automatically. This is a feature of the Testo app). Now this JSON message can be pasted in our Field Service system and a Javascript function will read the message and the measurement data is further processed in our system.
This works quite well, but as you can read it is not totally automated.

Thanks for your reply @robbertvdijk unfortunately looks like my customer doesn't like that approach and are looking for something fully automated still I'm not sure if is possible.

Hello @gwaldvogel , Is anywhere more documentation about this JS API? I'm intending to get the data from Dynamics 365 Field Service Mobile app and looks like the only way to personalize it is adding client side scripts

We have an OpenAPI description here: https://github.com/testo/tjf/blob/public/api/testoApi.yaml
Most of the endpoints tagged with t300 should work on the testo Combustion App & testo 330 too.


vite:dep-scan transformations can cause syntax errors confusingly reported by esbuild

For example, if you write the code (notice await in a comment):
// something something await
watch(() => result.data.value, data => {
}, { immediate: true })

The code here: https://github.com/vitejs/vite/blob/d3142cf706624c51f92ab28475d6679f3141ff76/packages/vite/src/node/optimizer/scan.ts#L221-L223
will produce the following code to get sent to esbuild:
// something something void       watch(() => result.data.value, data => {
}, { immediate: true })

User will just see this error:
 > /component.vue:53:9: error: Expected identifier but found "{"
    53 │       }, { immediate: true })
       ╵          ^

error during build:
Error: Build failed with 1 error:
html:/component.vue:53:9: error: Expected identifier but found "{"

Does a proper parse need to happen to not secretly cause these issues or would a naive 'in comment' or 'in string' heuristic be good enough? At the very least it would maybe be nice to see what the code esbuild errored on but that seems non-trivial given it is just provided entries and then communicates back progress asynchronously?

It would be ideal to avoid incurring the cost of full AST parses here. It seems this edge case is easy to fix though.

That's a nice fix. Thanks!

It seems like this problem also applies to the use of for await loops to;
    for await (const x of y) {
        console.log(x);
    }

In this case await is still replaced with void and is causing an syntax error
 error: Expected "(" but found "void"
     │     for void (const x of y) {

@rangoy are you experiencing this error in development? you might need to force esbuild to higher version as it seems there have been a for loop code generation fix in this version https://github.com/evanw/esbuild/releases/tag/v0.12.2

@Niputi, I'm experiencing this in development when running yarn  dev.
I haven't traced the to the core but what I see is that it is related to the same replace;
I can use one of the following workarounds to get it working now;

If i remove the space after await it works after the new change.
for await(const x of y) {}  instead of for await (const x of y) {}
I think this works because the new version of the regex only matches when there's a space after await.

Move the for await loops out of

I'm not sure if I get the reason why these replaces has to be done but I guess adding a new replace before the one changed in  cbfc3e9 could solve the issue
Something like (untested)
js = js.replace(/\bfor\s+await(\s)/g, 'for$1')


[dv] Document how to reproduce CI (Private) failure

related to #5786
Signed-off-by: Weicai Yang<EMAIL_ADDRESS>

@sriyerg @imphil @rswarbrick thanks for the comments. I have updated the wording. PTAL.


feat: Push for Amazon Devices

Type: feat
Platform: android 4.x webview
Ionic Push needs to expand to include support for Amazon Device Messaging for Amazon Fire devices.

Greetings @nealvs!
My sensors indicate that you need to update your issue through our custom issue form. We are now requiring all issues to be submitted this way, to ensure that we have all of the information necessary to fix them as quickly as possible.
Click Here To Update Your Issue
I will have no choice but to close this issue if it is not resubmitted through the form. Please fill out the rest of the form, so that I may use my friendly robot powers to assist you.
Thank you!

HI @nealvs, mind posting over at Ionic IO issues page for the platform stuff so the platform team can help? https://github.com/driftyco/ionic-io-issues/issues


Emit logs at the severity specified at the call site.

Description of changes

Emit logs at the severity specified at the call site rather than the logLevel of SwiftLogger.
Make the logging level of SwiftLogger defer to the underlying logger.
Lower the severity of some logs in the CRTClientEngine to align with [1] as these seem to be logging about inner detail.

[1] https://github.com/swift-server/guides/blob/main/docs/libs/log-levels.md
Scope

[X] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

Closing.  Will overhaul logging before SDK general availability.


Add support for pipeline_tag in ModelHubMixin

Would be good to be able to set a custom pipeline_tag. Mentioned by @julien-c in https://github.com/jasonppy/VoiceCraft/pull/90#discussion_r1566439191.

The docs for this PR live here. All of your documentation changes will be reflected on that endpoint. The docs are available until 30 days after the last update.

Thanks for the review!


[FEATURE] Allow overriding target and rel attributes of links

Is this a unique feature?

[X] I have checked "open" AND "closed" issues and this is not a duplicate

Is your feature request related to a problem/unavailable functionality? Please describe.
Hi,
First of all, I want to congratulate on the fantastic work that has been done with this library; it has been incredibly useful for a project i'm working on.
Current Situation
Currently, the library does not offer a way to dynamically update the target and rel attributes of a link within the LinkTool. This limitation affects a use case where we need these attributes to be customizable for different links.
Would you be willing to allow for a change where these link attributes can be dynamic?
Proposed Solution
I propose modifying the existing link updating logic to include target and rel props. This change will allow users to dynamically set these attributes when creating or editing links.
From what I inspected in the code, this seems to be the place where we could offer the possibility to override these attributes:
DefaultToolbarRender.tsx
const linkNode = {
  type: 'link',
  children: [{ text: link.title }],
  props: {
    target: link?.target ?? '_blank', // Suggested change: Add target prop
    rel: link.rel ?? 'noreferrer',    // Suggested change: Add rel prop
    nodeType: 'inline',
    url: link.url,
    title: link.title,
  },
} as SlateElement;

Screenshots
Here is a screenshot of the custom LinkTool component I am using, which demonstrates the need for these dynamic attributes:

Do you want to work on this issue?
Yes
If "yes" to the above, please explain how you would technically implement this (issue will not be assigned if this is skipped)
I plan to implement the proposed changes by updating the onUpdateLink callback to include target and rel attributes in the link properties. This will allow these attributes to be dynamically set when creating or editing links.
Implementation Steps:

Identify the Code Snippet: Locate the code snippet where the link properties are defined.
Modify the Code: Update the code to include target and rel attributes in the link properties. Here is the relevant code snippet with the proposed changes:

Copy code
const linkNode = {
  type: 'link',
  children: [{ text: link.title }],
  props: {
    target: link?.target ?? '_blank', // Suggested change: Add target attribute
    rel: link.rel ?? 'noreferrer',    // Suggested change: Add rel attribute
    nodeType: 'inline',
    url: link.url,
    title: link.title,
  },
} as SlateElement;

@silverlila, thanks for reporting that issue! We are super excited to see your willingness to work on it.
Consider joining our Telegram Dev Community, where we can respond faster and discuss it in detail.
Please check CONTRIBUTING.md to get the steps started.
If you see how we can improve the contributing guide, please let us know 🙏

Added in v4.3.1 thanks to @silverlila


Enable multiple user accounts?

Since Stringer already has a users table, I suppose it wouldn't be hard to add multiple user capabilities?
Google Reader is shutting down really soon, it would be nice if we can set up one Stringer instance and share it with a few friends instead of creating dedicated instances for everyone who wants to use it.
Maybe this is against Stringer's philosophy, but...yeah...I think this is a nice feature to have.

+1
I want to install one instance of stringer for all my family.

This was now implemented by @mockdeep

This is available now. You should see an admin settings link at the bottom of the page. There you can enable user signups.


How to get the currently scanned line as a string?

Hey, this project is awesome!
Since I don't find any mailinglists I just opened a new issue.
I am trying to get the line that is currently analyzed as a string. Is there a 'native' way or do I have to do it myself?
Cheers

Sure, this is certainly possible with a little bit of work as the following example shows.
// showlines.l to show lines on which a match was found
%{
std::string line; // the line that holds the line on which a match was found
%}

%%

\n.*    line = text(); matcher().less(1); // keep only \n in the match, so we can advance over the line with other patterns

\d+     |
\w+     std::cout << text() << " found on: " << line << std::endl; // digits and words are printed with the line found (note that a line starts with \n)

.       // ignore everything else in this demo

%%

Compile with:
reflex --main showlines.l
c++ -o showlines lex.yy.cpp -lreflex
Example:
./showlines < showlinesl
There is only one caveat: this will not work for the first line in a file scanned, since line is not populated until the second line on the input. Perhaps adding \A.* as a pattern works to fix this, by matching the start of input with \A, but the problem could be that less(1) removes its first character and less(0) is dangerous as it could lead to infinite matching attempts.

Thanks mate ;)

A bit late perhaps, but I should add that the RE/flex 1.5.0 has new methods to get the line where the match occurs using two new methods matcher().line() and matcher().wline() (wide string). A third method, matcher().span() extends the match to the entire line.

Hello,
that's certainly useful, I will check it out. Thanks for the improvement.


[Question] vpn-tcp with private kubernetes API server

Hey there, had a question regarding private kubernetes API servers. Right now our kubernetes cluster is totally private on AWS, and we use an OpenVPN connection to proxy into our VPC (this is not hooked up to the kube-dns or kubernetes ip pool).
We're also a Go shop, so it looks like we need to use --method vpn-tcp to do local development with telepresence, but this isn't playing nicely with telepresence (as stated in the docs).
Was wondering if there are any workarounds to get --method vpn-tcp working with a private Kubernetes API server.
Thanks!

Could you be more specific about what issues you have with using vpn-tcp and Go?
Also, have you looked at the container method? https://www.telepresence.io/tutorials/docker.

@willtrking Just checking to see if I understand. You are using Go, so the inject-tcp method is not a good option for you. You are using a VPN to connect to your Kubernetes cluster, so the vpn-tcp method does not work for you.
I think Richard has the right idea. You may be best off using the container method, which does not interact with the host's networking because it performs most of its networking magic inside Docker.
Are you able to get a shell that can talk to your Kubernetes cluster like this?
><> kubectl get service qotm
NAME      TYPE        CLUSTER-IP     EXTERNAL-IP   PORT(S)   AGE
qotm      ClusterIP   <IP_ADDRESS>   <none>        80/TCP    60d
><> telepresence --docker-run --rm -it fedora curl qotm
Volumes are rooted at $TELEPRESENCE_ROOT. See https://telepresence.io/howto/volumes.html for details.

Guessing that Services IP range is <IP_ADDRESS>/20. Services started after this point will be inaccessible if are outside this range; restart telepresence if you can't access a new Service.

{
  "hostname": "qotm-1371672344-c3nv8",
  "ok": true,
  "quote": "A small mercy is nothing at all?",
  "time": "2017-11-21T22:56:31.776806",
  "version": "1.1"
}
><>


Samples for dotnet and python

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

@CharithW

DS_STORE has been commited
Shall we rename the byoc-api to something like weather-api (or something)?


Cache oEmbed endpoint's derived image metadata (image dimensions)

Problem

The embed endpoint retrieves image height and width if they do not exist on the record:
https://github.com//WordPress/openverse/blob/HEAD/api/api/views/image_views.py#L91-L97
There are two problems:

The endpoint does this without caching the result so must remake the request every time it is requested
This is valuable data that should 100% be back-filled to the catalog when available for a given result

Description

Luckily, we can address both of these with one fix: cache the result in Redis. While we'll need further work to backfill the data into the catalog (probably as part of https://github.com/WordPress/openverse/issues/420) if we cache this data in Redis with a stable key, we can prevent unnecessary duplicate requests and set the other project up for success.
Cache these with a key along the following lines:
imgdims:{identifier.replace("-", "")}
Ensure the identifier has hyphens removed to optimise the Redis key size. See #2400 for more details.
Save the image dimensions to this cache as a comma separated string: {width},{height}. We don't need a hashmap here and a string will be slightly smaller long-term.
Before requesting the image in the endpoint, check the cache first and reuse the dimensions from there if they exist.
Additional context

Related to https://github.com/WordPress/openverse/issues/1486 and https://github.com/WordPress/openverse/issues/420
@stacimc Do you know if this would be fundamentally unnecessary if #1486 is implemented? Would the result of that work result in all images having dimensions in the catalog immediately upon ingestion regardless of provider?

@stacimc Do you know if this would be fundamentally unnecessary if https://github.com/WordPress/openverse/issues/1486 is implemented? Would the result of that work result in all images having dimensions in the catalog immediately upon ingestion regardless of provider?

For #1486 we would populate dimensions in the catalog at ingestion for all providers, yes. Once implemented, we'd immediately get image dimensions for newly ingested data and for non-dated DAGs, but we'd need to backfill records for dated providers. Luckily, I think there's only Metropolitan to worry about so that ought to be very quick with the new batched_update DAG :)


feat(): promise optional success/error msg

In some cases there is no success or error msg
eg. redirect after success.

any update on this PR?

Been trying to figure out how to skip error messages in the case of user cancellation, is there anything holding up getting this in?

This would be immensely useful

Sorry for the long wait! Made two small changes:

Use toast.dismiss instead of toast.remove for a smoother exit
Also trigger this behaviour if returned message is empty as suggested by @rcbevans

Merging now 👍

This is now release with 2.5.1! 🥳


Add randomBool function

Hey mate, Thanks a lot for your contribution. :raised_hands:

Hey bro, Thank you for developing this awesome tool. :fire:


myjenkins: Use Docker daemon from host

Instead than running a separate Docker daemon,
run service myjenkins bind mounting host .
See https://jpetazzo.github.io/2015/09/03/do-not-use-docker-in-docker-for-ci/
Fix https://github.com/gmacario/easy-jenkins/issues/31
Signed-off-by: Gianpaolo Macario<EMAIL_ADDRESS>

Testing fails.
Mounting volume-provided directories does not seem to work in nested Docker containers
Submitted upstream https://github.com/docker/docker/issues/21510
DO NOT MERGE until upstream issue solved, or a workaround is identified.


BD or MD first with run.py any

Hi,
We have started running the trypsin-benz tutorial and I've a question regarding the run.py step.
When I ran this on A4000 GPU on a workstation I'm getting the following output, but when I ran on the HPC it is running the nam_simulation (i.e. Browndyne2) first.
Thus I'm curious to know if it is possible to run the separate (BD and MD) calculations simultaneously.
Please comment on this for my better understanding.
Thank you and best regards.
Vaibhav
A4000 output
(base) [xxxx@yyyy seekr2]$ python3.8 run.py any /home/niperg/tryp_ben_hidr_tutorial/model.xml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
anchor 0 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 1 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 2 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 3 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 4 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 5 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 6 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 7 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 8 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 9 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 10 has not run the minimum number of steps 0 of 125000000 in swarm index None
running anchor_index: 0 restart: False total_simulation_length: 125000000 num_transitions: 0 swarm index: None
#"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"
1250000,-250376.41525536962,296.89521240530155,177.84127115140652
2500000,-251816.960299053,300.7401145559686,177.84127115140652
3750000,-249775.08480032883,297.9072758462745,177.84127115140652
5000000,-251141.35327599244,297.6162308596486,177.84127115140652
6250000,-250886.5529175289,294.8508385438355,177.84127115140652
7500000,-251429.59675331693,297.38012520319904,177.84127115140652
8750000,-250864.39621214918,296.1578648834993,177.84127115140652
10000000,-251011.7579468072,295.76070438850223,177.84127115140652
11250000,-250754.05444069766,297.1850567116118,177.84127115140652
12500000,-250880.8638553978,295.8717125853891,177.84127115140652
13750000,-251361.46465320792,302.357790197908,177.84127115140652
15000000,-251751.39429811202,299.9408218258437,177.84127115140652
16250000,-249909.23492376693,297.9641657593563,177.84127115140652
17500000,-250831.85557753057,297.31015841402126,177.84127115140652
18750000,-250872.648794075,299.0403939308773,177.84127115140652
20000000,-251404.7889921791,297.7748683698601,177.84127115140652
21250000,-250549.96409982583,301.07466638268477,177.84127115140652
22500000,-250308.76190222194,299.49519508510076,177.84127115140652
23750000,-249980.19527490553,297.75345978110516,177.84127115140652
25000000,-250624.00605515996,302.3343559508517,177.84127115140652
26250000,-250507.18145670742,301.4777494536038,177.84127115140652
27500000,-250228.3289753215,297.5157977352142,177.84127115140652
28750000,-250618.3579239829,299.9698301611076,177.84127115140652
30000000,-251083.14304677257,298.0573303543426,177.84127115140652
31250000,-251045.4935685862,296.4738785135786,177.84127115140652
32500000,-250732.25450399006,300.618752740865,177.84127115140652
33750000,-250150.650192847,296.68024535972495,177.84127115140652
35000000,-251843.7443778594,300.2775982225485,177.84127115140652
36250000,-250836.95118905604,298.35247101304157,177.84127115140652
37500000,-250730.25663781445,297.32925657065,177.84127115140652
38750000,-250681.76350122364,297.8295673493248,177.84127115140652
40000000,-250602.82712599728,301.8936784618029,177.84127115140652
41250000,-250908.67839316884,291.74930158738516,177.84127115140652
42500000,-250592.08901361236,296.4671783286221,177.84127115140652
43750000,-250205.9630815657,299.62388927715705,177.84127115140652
45000000,-251191.23436955502,299.895703373847,177.84127115140652
46250000,-251312.6290877089,295.9285451245737,177.84127115140652
47500000,-250885.78268891945,296.78113468776826,177.84127115140652
48750000,-251039.89442682546,299.17780628575764,177.84127115140652
50000000,-250586.59940173826,293.56036419906906,177.84127115140652
51250000,-251341.73434409965,297.40858264131396,177.84127115140652
52500000,-250785.1078860676,296.41169807661623,177.84127115140652
53750000,-250548.55212000664,299.82566753647023,177.84127115140652
55000000,-251336.17954663094,297.700648296592,177.84127115140652
56250000,-251493.64182420238,297.4044061539442,177.84127115140652
57500000,-250436.24132813164,297.64335069479813,177.84127115140652
58750000,-250900.1289494743,297.87782575301594,177.84127115140652
60000000,-251365.70957936766,299.9146946657265,177.84127115140652
61250000,-251739.93011926254,298.8694927949889,177.84127115140652
62500000,-251018.5306754359,300.8728575753887,177.84127115140652
63750000,-250989.5727051692,301.2254064441114,177.84127115140652
65000000,-251151.17498785816,300.28418159681985,177.84127115140652
66250000,-250811.2604660911,297.125632003862,177.84127115140652
67500000,-250745.48249687115,301.95650385173224,177.84127115140652
68750000,-250896.07283422747,301.1085610457348,177.84127115140652
70000000,-250620.20485602436,299.3786922707276,177.84127115140652
71250000,-249668.51900003082,299.38797967742096,177.84127115140652
72500000,-250026.44720053556,296.880736328326,177.84127115140652
73750000,-251382.91487488337,293.0451477013571,177.84127115140652
75000000,-250798.74752313131,301.3031975570151,177.84127115140652
76250000,-251841.08711535623,300.24075164395157,177.84127115140652
77500000,-250607.52170097549,299.82053728140306,177.84127115140652
78750000,-251339.97406868823,300.0053381759625,177.84127115140652
80000000,-251620.8250389523,298.3618845607552,177.84127115140652
81250000,-251612.2944833946,298.2132969679813,177.84127115140652
82500000,-250558.90810871706,299.03952799174374,177.84127115140652
83750000,-250634.8499758104,300.8930652191651,177.84127115140652
85000000,-251014.51466802903,294.7870487439599,177.84127115140652
86250000,-250786.990156529,295.9250767611833,177.84127115140652
87500000,-251009.94473820366,299.3163430049137,177.84127115140652
88750000,-250342.0269576956,302.3439476150922,177.84127115140652
90000000,-250707.24345579604,294.5966184916818,177.84127115140652
91250000,-250763.4695239584,297.27304561892134,177.84127115140652
92500000,-251729.84289589804,298.48210669852375,177.84127115140652
93750000,-250918.35286462284,296.7007638691411,177.84127115140652
95000000,-251102.30022457894,296.47653030568483,177.84127115140652
96250000,-251151.94991578627,294.0330664425347,177.84127115140652
97500000,-249825.05061047943,300.7539475266632,177.84127115140652
98750000,-251913.89867717726,295.9855820395087,177.84127115140652
100000000,-250226.26716483058,297.799287179786,177.84127115140652
101250000,-249982.53791840328,298.08416196314124,177.84127115140652
102500000,-251413.05335161253,301.5823982733784,177.84127115140652
103750000,-250439.35385266365,297.79579694683963,177.84127115140652
105000000,-250791.20807962585,299.55582695186314,177.84127115140652
106250000,-250653.68977421243,297.91695645628715,177.84127115140652
107500000,-250195.73558695614,295.0807334628034,177.84127115140652
108750000,-251093.61188615602,296.53038741796996,177.84127115140652
110000000,-251480.1944490187,304.1390419674086,177.84127115140652
111250000,-250769.3652417278,294.8156741931179,177.84127115140652
112500000,-250157.7076921661,296.331567877692,177.84127115140652
113750000,-250983.5466161277,300.3119088244567,177.84127115140652
115000000,-250947.34169258294,299.686376747694,177.84127115140652
116250000,-250522.54435569188,301.2849067322041,177.84127115140652
117500000,-250931.10059117898,294.7009081382181,177.84127115140652
118750000,-250664.06582189025,303.4956653291268,177.84127115140652
120000000,-251064.59574373765,297.32083267079287,177.84127115140652
121250000,-251606.44924361142,296.75987865226944,177.84127115140652
122500000,-250993.6611946551,298.8907556879082,177.84127115140652
123750000,-250197.03636861872,295.25539555555633,177.84127115140652
125000000,-249612.35455580102,295.8961460193411,177.84127115140652
Benchmark (ns/day):<PHONE_NUMBER>385334
running anchor_index: 1 restart: False total_simulation_length: 125000000 num_transitions: 0 swarm index: None
#"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"
1250000,-251259.4426750599,294.6629526592754,177.84127115140652
2500000,-250765.72184476117,299.36995856663737,177.84127115140652
3750000,-250848.54080326902,296.31244688110917,177.84127115140652
5000000,-250384.19994499488,293.4496098255166,177.84127115140652
6250000,-250924.3924683323,300.2378917470994,177.84127115140652
7500000,-250770.1583597092,298.09511762078046,177.84127115140652
8750000,-251455.48746547895,297.8792693442864,177.84127115140652
10000000,-250859.59599494375,295.0429203120194,177.84127115140652
11250000,-250136.3151631034,298.3075320749688,177.84127115140652
12500000,-251009.68614812754,294.2744449183289,177.84127115140652
13750000,-250640.44650838315,296.8044192410573,177.84127115140652
15000000,-250418.59393999376,293.78215103701274,177.84127115140652
16250000,-251351.28738953965,297.4008396898686,177.84127115140652
17500000,-251294.72341999668,299.531905809816,177.84127115140652
18750000,-250463.3308101648,303.73813319121285,177.84127115140652
20000000,-250427.12095736945,297.52910853449305,177.84127115140652
21250000,-250973.74070397043,300.3789704509949,177.84127115140652
22500000,-250579.21751565533,298.7562571851669,177.84127115140652
23750000,-251432.9784859363,301.49303895725274,177.84127115140652
25000000,-251110.66937395255,301.46464267108837,177.84127115140652
26250000,-251251.63167706504,299.49951037430156,177.84127115140652
27500000,-250572.44890967244,296.89380434480745,177.84127115140652
28750000,-250140.19067218387,301.1059178934554,177.84127115140652
30000000,-251199.66560487263,294.17380927028927,177.84127115140652
31250000,-250043.40207134187,300.95852182176037,177.84127115140652
32500000,-250791.76140220044,296.47326886836913,177.84127115140652
33750000,-250442.05083427997,301.998836962379,177.84127115140652
35000000,-250590.44339945703,300.5902666019184,177.84127115140652
36250000,-251071.2009507832,300.9992785430724,177.84127115140652
37500000,-251506.3604732894,297.49571766768435,177.84127115140652
38750000,-250895.8533184596,301.5968664245832,177.84127115140652
40000000,-250883.29082193132,298.26300253227936,177.84127115140652
41250000,-251651.47171014082,307.73439340465194,177.84127115140652
42500000,-250305.12439275743,298.0143337338997,177.84127115140652
43750000,-250613.1140536156,297.4515498466713,177.84127115140652
45000000,-250868.51864006324,298.561895048489,177.84127115140652
46250000,-250564.8245985997,297.99240701222277,177.84127115140652
47500000,-251012.72356958687,300.39938744525585,177.84127115140652
48750000,-250392.43096753443,298.58242407492764,177.84127115140652
50000000,-251035.1473082339,296.14095207941426,177.84127115140652
51250000,-251227.71490027197,302.4036548209542,177.84127115140652
52500000,-250522.53721845592,296.81303077479197,177.84127115140652
53750000,-250826.29571607313,298.405325878737,177.84127115140652
55000000,-250120.66219415353,298.0081225182074,177.84127115140652
56250000,-251105.63211397594,297.82980884685645,177.84127115140652
57500000,-250323.36232781573,297.5810193031567,177.84127115140652
58750000,-250623.39771179738,297.0397373693085,177.84127115140652
60000000,-251313.26762351906,292.3351538455054,177.84127115140652
61250000,-250154.16336838342,297.08175895943714,177.84127115140652
62500000,-252308.72308942117,299.07260160561094,177.84127115140652
63750000,-250594.4323346382,301.9754779054601,177.84127115140652
65000000,-251859.11473322287,299.6608428151863,177.84127115140652
66250000,-251087.2070069802,299.6953884748485,177.84127115140652
67500000,-251802.10227993852,297.0937701070965,177.84127115140652
68750000,-251570.61608901946,299.7394249148812,177.84127115140652
70000000,-251306.4699697583,300.08195487568383,177.84127115140652
71250000,-251280.58563445345,298.52583806825453,177.84127115140652
72500000,-250737.1717557311,301.9037488948244,177.84127115140652
73750000,-251257.2719639868,297.70835995995475,177.84127115140652
75000000,-250454.95606256882,300.76403074623505,177.84127115140652
76250000,-251292.47676609014,303.15305000858115,177.84127115140652
77500000,-251573.22319973866,296.6073573182158,177.84127115140652
78750000,-250386.25605534436,302.42128964907766,177.84127115140652
80000000,-250751.07752651232,302.4641231108624,177.84127115140652
81250000,-251387.76963990787,293.865031217276,177.84127115140652
82500000,-250100.21676361188,300.00358798050877,177.84127115140652
83750000,-250601.57886954676,301.3720101791027,177.84127115140652
85000000,-250235.0574428863,295.74220956424205,177.84127115140652
86250000,-251469.80277535156,300.77650223503815,177.84127115140652
87500000,-249988.65012317477,296.276116870113,177.84127115140652
88750000,-250502.05432189978,296.1010129234983,177.84127115140652
90000000,-251968.39292710647,296.60859281762686,177.84127115140652
91250000,-250791.86354266037,295.8910847277333,177.84127115140652
92500000,-250404.56387520768,298.9048408840197,177.84127115140652
93750000,-251154.475504898,296.99560105670747,177.84127115140652
95000000,-251359.19246092672,299.51372660792583,177.84127115140652
96250000,-250764.11982902559,298.4252684757289,177.84127115140652
97500000,-251484.33265610877,299.40898474185764,177.84127115140652
98750000,-250935.99084728095,300.932682078628,177.84127115140652
100000000,-251445.2858629264,301.49998914194157,177.84127115140652
101250000,-250187.6698401617,297.4103964713417,177.84127115140652
102500000,-251637.72404296696,297.3061071492267,177.84127115140652
103750000,-250904.40802089963,300.4314819328267,177.84127115140652
105000000,-251078.05117556825,296.9107071906265,177.84127115140652
106250000,-250952.78594076866,297.01861025279345,177.84127115140652
107500000,-250802.97160940943,296.9837422883592,177.84127115140652
108750000,-250144.81036504335,295.5391186771401,177.84127115140652
110000000,-250408.76959471265,299.5920144289264,177.84127115140652
111250000,-251265.48837245023,298.6026394090152,177.84127115140652
112500000,-251187.4663939576,299.35775457542996,177.84127115140652
113750000,-251361.33346678014,295.0478388167673,177.84127115140652
115000000,-251394.21021181066,301.3376359074994,177.84127115140652
116250000,-251057.08305738913,296.7607983850883,177.84127115140652
117500000,-250673.4803463628,295.2263131829163,177.84127115140652
118750000,-250833.26661640173,299.1149224913304,177.84127115140652
120000000,-251410.9140135313,300.213790546652,177.84127115140652
121250000,-250332.92606316763,298.6392307175874,177.84127115140652
122500000,-251197.99922959972,298.6720200794495,177.84127115140652
123750000,-251727.90174243366,295.2262481836339,177.84127115140652
125000000,-250838.0265258979,298.9726168252748,177.84127115140652
Benchmark (ns/day):<PHONE_NUMBER>19288
running anchor_index: 10 restart: False total_simulation_length: 125000000 num_transitions: 0 swarm index: None
#"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"
1250000,-250963.61889972934,297.8796832262577,177.84127115140652
2500000,-251100.75729331374,297.7754051036002,177.84127115140652
3750000,-250787.89210539637,297.1841722775951,177.84127115140652
5000000,-250622.71299585304,297.06264123069576,177.84127115140652
6250000,-250821.9841966941,295.32203814155105,177.84127115140652
7500000,-249772.9566296395,297.2846601329349,177.84127115140652
8750000,-251087.09847757034,294.96687104952366,177.84127115140652
10000000,-250296.20332069322,297.50360697497297,177.84127115140652
11250000,-251053.39524247777,297.7810223006985,177.84127115140652
12500000,-250609.3133067037,301.9160241174032,177.84127115140652
13750000,-250654.74175767647,299.9137915559968,177.84127115140652
15000000,-251246.0571761001,297.5900131046811,177.84127115140652
16250000,-249805.84242308652,296.1516417954397,177.84127115140652
17500000,-250385.3948628693,293.95899986085556,177.84127115140652
18750000,-250870.40786798252,300.92852254107123,177.84127115140652
20000000,-250905.67367758462,296.4416548335448,177.84127115140652
21250000,-250707.01590270572,298.4641538897293,177.84127115140652
22500000,-251103.76571191382,298.0251731412272,177.84127115140652
23750000,-250857.61640539858,298.2536600109732,177.84127115140652
25000000,-250574.95729532233,297.43102224900605,177.84127115140652
26250000,-251082.92657866422,298.13251092741314,177.84127115140652
27500000,-251642.8137897672,297.66562113432065,177.84127115140652
28750000,-250673.8559527225,300.2280735890014,177.84127115140652
30000000,-250993.53902922152,299.61717458412096,177.84127115140652
31250000,-251593.71903408505,303.1971113478435,177.84127115140652
32500000,-250612.1940932686,296.17957592455355,177.84127115140652
33750000,-251109.1292685545,297.87972097528217,177.84127115140652
35000000,-251504.09697998967,301.89775846431866,177.84127115140652
36250000,-250624.9054595204,299.6020381533652,177.84127115140652
37500000,-250196.6593948789,297.58610478306593,177.84127115140652
38750000,-250772.68634288735,295.9347013668348,177.84127115140652
40000000,-251121.43306054547,300.965484540292,177.84127115140652
41250000,-251319.9035094534,298.1519555442378,177.84127115140652
42500000,-252062.46652876912,299.81752553831586,177.84127115140652
43750000,-250913.95741329156,297.09971023855746,177.84127115140652
45000000,-251023.71011325298,297.6121898078329,177.84127115140652
46250000,-251156.1582629932,301.21430667652606,177.84127115140652
47500000,-250973.7799685821,301.2418667839347,177.84127115140652
48750000,-250061.98426671792,295.67015589823285,177.84127115140652
50000000,-250858.78900723904,300.39840964216665,177.84127115140652
51250000,-249833.1550544314,300.04648956517707,177.84127115140652
52500000,-250755.61106327875,297.6282421147988,177.84127115140652
53750000,-250633.77985838032,296.68933906938247,177.84127115140652
55000000,-249208.43697069818,297.18976749075216,177.84127115140652
56250000,-251849.91741440422,300.7844392343469,177.84127115140652
57500000,-250662.8009897722,297.99908109997284,177.84127115140652
58750000,-250871.8564283948,295.70531975683423,177.84127115140652
60000000,-251025.46409789985,297.01312224961515,177.84127115140652
61250000,-250437.04213957582,297.8969129060293,177.84127115140652
62500000,-250929.3088880726,301.3655435105789,177.84127115140652
63750000,-251365.3793179521,300.7234767423653,177.84127115140652
65000000,-250499.15234704735,300.0873309512295,177.84127115140652
66250000,-250928.9496843838,295.9500399191102,177.84127115140652
67500000,-251202.30126014398,298.7874974974075,177.84127115140652
68750000,-251216.94150573667,294.6608167870472,177.84127115140652
70000000,-250390.27349948348,297.23256132492077,177.84127115140652
71250000,-251404.40668005217,297.1052465295271,177.84127115140652
72500000,-250735.0252188514,295.83046509164376,177.84127115140652
73750000,-250352.66381779732,296.40474659807165,177.84127115140652
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76250000,-251675.50774102146,296.45510815031645,177.84127115140652
77500000,-251600.76772023272,296.54512463258675,177.84127115140652
78750000,-251342.93648028607,293.5898786595307,177.84127115140652
80000000,-251557.576574611,298.3036344967419,177.84127115140652
81250000,-250827.78162114602,298.6237527864562,177.84127115140652
82500000,-251362.96318814694,294.70286897441025,177.84127115140652
83750000,-250847.04300829396,300.2560358190567,177.84127115140652
85000000,-250414.343118208,299.48662507907414,177.84127115140652
86250000,-251087.53326319717,299.710353431438,177.84127115140652
87500000,-250474.6633588774,302.65096347009177,177.84127115140652
88750000,-250881.799825656,299.5173791444326,177.84127115140652
90000000,-251291.59384958865,300.02986660417866,177.84127115140652
91250000,-251566.37239163462,295.7179376227423,177.84127115140652
92500000,-250634.69581886218,295.28119503196945,177.84127115140652
93750000,-251367.401673167,298.4655400438071,177.84127115140652
95000000,-250645.225053536,299.2935865258229,177.84127115140652
96250000,-250860.34303405532,298.6747387437222,177.84127115140652
HPC output
[vaibhav@node1 seekr2-tutorial]$ cat job.50.out
command surface_spheres -probe_radius 1.5 < tryp_ben_receptor.xml > receptor_surface.xml
command inside_points -spheres tryp_ben_receptor.xml -surface receptor_surface.xml -egrid receptor3.dx > receptor_inside.xml
command hydro_params < receptor_inside.xml > receptor_hydro_params.xml
command test_charges < tryp_ben_receptor.xml > receptor_charges.xml
command lumped_charges -pts receptor_charges.xml > receptor_cheby.xml
command make_surface_sphere_list -surface receptor_surface.xml -spheres tryp_ben_receptor.xml -rxn rxns.xml -group receptor -core receptor > receptor_surface_atoms.xml
command mpole_grid_fit -dx receptor0.dx -solvdi 78 -debye 1.79769e+308 > receptor_mpole.xml
command born_integral -in receptor_inside.xml -oeps 78 -debye 1.79769e+308 -ieps 4.000000 > receptor_born.dx
command compute_charges_squared < receptor_charges.xml > receptor_charges_squared.xml
command lumped_charges -pts receptor_charges_squared.xml > receptor_squared_cheby.xml
command surface_spheres -probe_radius 1.5 < tryp_ben_ligand.xml > ligand_surface.xml
command inside_points -spheres tryp_ben_ligand.xml -surface ligand_surface.xml -egrid ligand2.dx > ligand_inside.xml
command hydro_params < ligand_inside.xml > ligand_hydro_params.xml
command test_charges < tryp_ben_ligand.xml > ligand_charges.xml
command lumped_charges -pts ligand_charges.xml > ligand_cheby.xml
command make_surface_sphere_list -surface ligand_surface.xml -spheres tryp_ben_ligand.xml -rxn rxns.xml -group ligand -core ligand > ligand_surface_atoms.xml
command mpole_grid_fit -dx ligand0.dx -solvdi 78 -debye 1.79769e+308 > ligand_mpole.xml
command born_integral -in ligand_inside.xml -oeps 78 -debye 1.79769e+308 -ieps 4.000000 > ligand_born.dx
command compute_charges_squared < ligand_charges.xml > ligand_charges_squared.xml
command lumped_charges -pts ligand_charges_squared.xml > ligand_squared_cheby.xml

Instead of using the “any” argument for run.py, use the “any_md” argument.

Hi,
Strangely I'm getting the following message with any_md option.
I just copied the input files from workstation to HPC and wanted to run the MD part of the calculation which has taken > 10 days on the workstation (A4000).
Does the model.xlm or any other input file saves any record of how far the calculation has proceeded?
Please suggest if I need to make some changes to the model.xlm or any other file to run all BD and MD from fresh to compare the performance of the A100 vs A4000 cards.  There is only 10-15 % difference between the two card w.r.t. Amber22 pmemd.cuda jobs.
Thanks
[xxxx@xxxx seekr2-tutorial]$ tail job.54.out
Nothing was run because all criteria are satisfied.

Yeah since you copied over the files, it thinks the calculation is finished because of the checkpoint files in each of the anchors. To force rerun, use the -f argument for run.py.

Ok, just did that and it is running the nam_simulation again.
Can I expect it to run the MD part after this?
Is it possible to simultaneously run BD and MD parts since they use CPU and GPU respectively?
thanks for quick response.

Hi,
The calculation seems to have terminated prematurely.
Output related only to BD is printed even after using run.py -f option.
The any_md option also doesn't run any MD simulation.
Do I need to run the prepare.py step also on the HPC?
Please suggest. thank you
[xxxx@xxxx seekr2-tutorial]$ cat job.55.out
BrownDye 2.0: Version of 13 Jun 2022
running BD: b_surface restart: False trajectories to run: 1000000 trajectories so far: 1000000 number of transitions 0
moving to directory: /home/vaibhav/seekr2-tutorial/b_surface
running command: bd_top input.xml
moving to directory: /home/vaibhav/seekr2-tutorial/b_surface
running command: nam_simulation receptor_ligand_simulation.xml

Would you please post the exact run command you are using? I'm not sure why this is happening.

These are the exact commands I'm using in slurm script.
please suggest
source /home/software/miniconda3/bin/activate
conda activate myseekr2
python /home/software/seekr2/seekr2/run.py -f any model.xml
(base) [xxx@node1 seekr2-tutorial]$ conda activate myseekr2
(myseekr2) [xxx@node1 seekr2-tutorial]$ python
Python 3.8.13 (default, Mar 28 2022, 11:38:47)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

Hi, Just a gentle reminder, if you can respond to this and the workstation difficulties I'm facing with seekr2?
Thank you very much for your support. Best regards. Vaibhav

I'm currently on vacation, but I believe the short solution to your problem is to use "any_md" as mentioned previously in this thread:
python /home/software/seekr2/seekr2/run.py any_md model.xml -f

Alternatively, you can run the anchors by integer:
python /home/software/seekr2/seekr2/run.py 0 model.xml -f

One can even use multiple GPUs if available on a node:
python /home/software/seekr2/seekr2/run.py 0 model.xml -f -c 0 &
python /home/software/seekr2/seekr2/run.py 1 model.xml -f -c 1 &
python /home/software/seekr2/seekr2/run.py 2 model.xml -f -c 2 &
python /home/software/seekr2/seekr2/run.py 3 model.xml -f -c 3 &
wait

There should be no need to rerun prepare.py.
All programs display useful instructions for how to run them with the '-h' argument. I also suggest carefully reviewing all documentation, especially if I am not accessible.

Hi,
I tried the first and second options you suggested (since I've only one GPU), but in vain.
The MD part of the calculation won't run and it prints a message saying nothing to do.
Nothing was run because all criteria are satisfied.
Thus I tried to do the tutorial from scratch on the HPC as given here.
In this new trial, I'm getting the following error in the hidr step which looks related to the hidr.py script.
Please have a look and let me know, how can I possibly fix the same?
Thank you
Error is shown below
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
File "/home/software/seekrtools/seekrtools/hidr/hidr.py", line 366, in
hidr(model, destination, pdb_files, dry_run, equilibration_steps,
File "/home/software/seekrtools/seekrtools/hidr/hidr.py", line 190, in hidr
hidr_simulation.run_SMD_simulation(
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekrtools-0+untagged.64.g33c013b-py3.8.egg/seekrtools/hidr/hidr_simulation.py", line 479, in run_SMD_simulation
system, topology, positions, box_vectors = run_window(
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekrtools-0+untagged.64.g33c013b-py3.8.egg/seekrtools/hidr/hidr_simulation.py", line 386, in run_window
add_forces(sim_openmm, model, anchor, restraint_force_constant, cv_list,
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekrtools-0+untagged.64.g33c013b-py3.8.egg/seekrtools/hidr/hidr_simulation.py", line 266, in add_forces
myforce = make_restraining_force(cv, variables_values_list)
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekrtools-0+untagged.64.g33c013b-py3.8.egg/seekrtools/hidr/hidr_simulation.py", line 222, in make_restraining_force
cv.add_groups_and_variables(myforce, variables_values_list)
TypeError: add_groups_and_variables() missing 1 required positional argument: 'alias_id'
~
My batch file is shown below
#!/bin/bash
#SBATCH --job-name=seekr2job1   ##job name
#SBATCH -N 1   ##number of nodes requires
#SBATCH --nodelist=node1
#SBATCH --ntasks-per-node=22  ##number of cpu requires
##SBATCH --time=95:50:20    ##time optional
#SBATCH --error=job.%J.err   ## Job error
#SBATCH --output=job.%J.out  ##job out put if any
#SBATCH --partition=GPU_NODES     ##partition name
#SBATCH --gres=gpu:1       ## number of gpu card requires
source /home/software/miniconda3/bin/activate
conda activate myseekr2
python /home/software/seekrtools/seekrtools/hidr/hidr.py any model.xml -M SMD -p tryp_ben.pdb

I'm now back from vacation.
I've run tests of SEEKR2 to see if there was a problem with the "any_md" or integer arguments of the run.py program and everything seems to work as expected.
Without force overwrite:
$ python ~/seekr2/seekr2/run.py any_md model.xml
Nothing was run because all criteria are satisfied.

With force overwrite:
$ python ~/seekr2/seekr2/run.py any_md model.xml -f
anchor 0 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 1 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 2 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 3 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 4 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 5 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 6 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 7 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 8 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 9 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 10 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 11 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 12 has not run the minimum number of steps 0 of 10000000 in swarm index None
anchor 13 has not run the minimum number of steps 0 of 10000000 in swarm index None

Same for integer arguments.
The only reason you should be getting the "Nothing was run because all criteria are satisfied." message is if you forgot the "-f" argument to force rerun. Also, are you sure that you're using the latest version of the SEEKR2 software?
As for the problem with hidr.py, that is a recent bug, thank you for finding it. I've just pushed the bugfix to the seekrtools repository.

As you can see from the top command on the node below, I did include the -f argument nonetheless I'm getting the message nothing to run.
Is it a bug in my installation?
Please suggest. thank you.
1522846 vaibhav   20   0 6465084 266084  80684 R 100.0   0.2   0:08.62 python /home/software/seekr2/seekr2/run.py any_md model.xml -f
(base) [vaibhav@node1 seekr2-tutorial]$ more job.97.out
Nothing was run because all criteria are satisfied.
(base) [vaibhav@node1 seekr2-tutorial]$ more job.97.err
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
(base) [vaibhav@node1 seekr2-tutorial]$
(base) [vaibhav@node1 seekr2-tutorial]$ more seekr2job.batch
#!/bin/bash
#SBATCH --job-name=seekr2job1   ##job name
#SBATCH -N 1   ##number of nodes requires
#SBATCH --nodelist=node1
#SBATCH --ntasks-per-node=22  ##number of cpu requires
##SBATCH --time=95:50:20    ##time optional
#SBATCH --error=job.%J.err   ## Job error
#SBATCH --output=job.%J.out  ##job out put if any
#SBATCH --partition=GPU_NODES     ##partition name
#SBATCH --gres=gpu:1       ## number of gpu card requires
source /home/software/miniconda3/bin/activate
conda activate myseekr2
#python /home/software/seekr2/seekr2/prepare.py input_tryp_ben_hidr.xml
#python /home/software/seekr2/seekr2/run.py any model.xml -f
python /home/software/seekr2/seekr2/run.py any_md model.xml -f

OK, I'm running two sets of simulations on the HPC 1) where files are copied from the workstation and 2) started the tutorial from scratch.
The 1st gives the same "Nothing to do " error message.
For the 2nd (from scratch) simulation I got the seekrtools error which was resolved but now I'm getting NaN coordiate error with openmm. Does it indicate that input pqr or pdb file is not in the right format or something else?
Please suggest. thank you
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
File "/home/software/seekrtools/seekrtools/hidr/hidr.py", line 366, in
hidr(model, destination, pdb_files, dry_run, equilibration_steps,
File "/home/software/seekrtools/seekrtools/hidr/hidr.py", line 190, in hidr
hidr_simulation.run_SMD_simulation(
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekrtools-0+untagged.65.g549ac37-py3.8.egg/seekrtools/hidr/hidr_simulation.py", line 480, in run_SMD_simulation
system, topology, positions, box_vectors = run_window(
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekrtools-0+untagged.65.g549ac37-py3.8.egg/seekrtools/hidr/hidr_simulation.py", line 396, in run_window
sim_openmm.simulation.step(total_number_of_steps)
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/openmm/app/simulation.py", line 141, in step
self._simulate(endStep=self.currentStep+steps)
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/openmm/app/simulation.py", line 206, in _simulate
self.integrator.step(10) # Only take 10 steps at a time, to give Python more chances to respond to a control-c.
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/openmm/openmm.py", line 13872, in step
return _openmm.LangevinIntegrator_step(self, steps)
openmm.OpenMMException: Particle coordinate is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan

From inside the seekr2/ directory, type "git log" and paste the first 10 or so lines here.

This is what I see with git log command.
I guess you want to check if the bugfix has been applied or not, right?
commit caa21a87edb93f410b500759aef3035b46f0034b (HEAD -> master, origin/master, origin/dev, origin/HEAD)
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Thu Aug 18 23:22:49 2022 -0600
extraneous print statements removed

commit fbbc8e34cf42e5f80901da35af5b3405e282be90
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Thu Aug 18 18:03:46 2022 -0600
Implemented Voronoi CV and anchors. Also corrected some bugs with RMSD CV and added missing check functions.

commit 277bc19176ebab182403117ec640eb5fb258e76f
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Wed Aug 10 11:20:00 2022 -0600
working on developing Voronoi Tesselation CVs and anchors.

commit b395a164a08724d8378c90a1fdcd685d6fc4c7ce
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Fri Aug 5 09:27:38 2022 -0600
Fixed bug affecting short Elber trajectories

commit 7b895a23b1930667aed16f42fd6193f52cc1f624
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Thu Aug 4 15:39:48 2022 -0600
increasing run.py CONVERGENCE_INTERVAL to a larger number

commit 139587878ba7ac4247c253f4ff8b573a7576ab64
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Tue Aug 2 16:39:45 2022 -0600
Fixed anchor connections of bulk states in Grid combos.

commit f54e48e01ad288b531349df951fb4569655e66df
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Tue Aug 2 14:22:02 2022 -0600
Updated tests for new Toy system state_point.

commit c521d263c752df9a37ceb271fdbaa7e3baf06a48
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Tue Aug 2 11:37:47 2022 -0600
Fixed state_point definitions for toy systems with more than one particle

commit 414d3ac8f4e493497d865a28f00eb8fe610c36c1
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Fri Jul 29 16:55:54 2022 -0600
Added warning to model.xml not to modify by hand.

commit 60605f47bbfd6d648377f0e51b3c389783785614
Author: Lane Votapka<EMAIL_ADDRESS>Date:   Fri Jul 29 14:17:28 2022 -0600

Yes, I was trying to see if you have the latest version, which you seem to.
Alright, let's try this manually...
From the directory where model.xml and the anchor_* folders are located, type the following command:
rm anchor_*/prod/*

From there, you should be able to run without the "Nothing was run" message.
Also, would you be willing to attach your model.xml file to this thread for me to look at?

For the file copied from the workstation.
Oops, I accidentally removed all the anchor folders since the command you suggested didn't work.
Then I had to also remove the b_surface folder for the prepare.py step to work, which finished quickly and correctly.
Then the run.py any model.xml step is running now. Looks like it is running the BD part of the calculation.
The old model.xml1.txt and new model.xml.txt files are attached herewith for your reference if that helps.
Just wondering if the BD and MD simulations are independent, why can't we run both simultaneously?
model.xml.txt
model.xml1.txt

This calculation again stopped after nam_simulation step.
Now I've submitted with run.py any model.xml -f option to check if that runs the MD portion of the calculation.
I'll paste the update soon. thank you

Nothing seems wrong with your model.xml files. If you delete the files in each anchor's prod/ directory, there is no way that SEEKR could think that the MD portion is finished.
Do you want to just leave out the BD entirely? If so, then you can remove the entire <browndye_settings_input> block in the input XML and replace it with a line containing: "<browndye_settings_input/>", which will set that variable to None and no BD will be run.
Are you able to send me your system? If you send me your input XML and all input files in a way that I can easily run prepare.py, then I can try out your system to see if anything is wrong.

Again only the BD portion ran and it did not run the MD part of the calculation.
I'm some what puzzuled.
As suggested I've shared a link to all the input files here.
Please do check at your end and help me understand where I'm making a mistake.
Thank you

Once I can get to it, I'll take a look at your files and see if I can reproduce the problem.

Aha, I see your problem now. You do not have any <pdb_coordinates_filename> tags filled. This is fine if you want to use HIDR with the "-p" argument to assign a starting PDB, but without any PDB files in any of the anchors, run.py doesn't do anything. So you need to use HIDR to assign the starting PDBs in the model and then you can use run.py

Hi,
I ran the HIDR calculation and then it is correctly proceeded to MD part of the calculation.
Now the question is how much speed up I can expect on this A100 card compared to the A4000 (10 days) that I have on the workstation.
I guess not much or is it?
I've attached the output in case it helps you guess the time it is likely to take for this calculation on A100.
Thanks again for your valuable suggestions and insights.
best regards, Vaibhav
job.117.out.txt

All SEEKR calculations will print a benchmark once finished, so if you run short jobs using, say the "-t 10000" argument, then you can see how fast the calculation is running on each card.

Sounds like this issue is resolved, I'll go ahead and close it.


"unknown return code: -2"

I have a write::ZlibEncoder which always panicks with unknown return code: -2 on mem.rs:226. I'm using the zlib backend (zlib v1.2.11, libz-sys 1.0.13) with flate2 v0.2.17.
In zlib's header, error code -2 is Z_STREAM_ERROR which means that the stream state was inconsistent on a call to deflate(). The relevant backtrace is:

7:     0x55ecdd79bdc8 - flate2::mem::Compress::compress::h944fc62bd5cc0d94
at /.cargo/registry/src/github.com-1ecc6299db9ec823/flate2-0.2.17/src/mem.rs:226
8:     0x55ecdd79bf23 - flate2::mem::Compress::compress_vec::h8e04b6895a662a0e
at /.cargo/registry/src/github.com-1ecc6299db9ec823/flate2-0.2.17/src/mem.rs:251
9:     0x55ecdd79b705 - <flate2::mem::Compress as flate2::zio::Ops>::run_vec::h0547d0514c764c38
at /.cargo/registry/src/github.com-1ecc6299db9ec823/flate2-0.2.17/src/zio.rs:31
10:     0x55ecdd516ac0 - <flate2::zio::Writer<W, D> as std::io::Write>::write::h52ff979bdb398a3e
at /.cargo/registry/src/github.com-1ecc6299db9ec823/flate2-0.2.17/src/zio.rs:143
11:     0x55ecdd5162ab - <flate2::zlib::EncoderWriter as std::io::Write>::write::h8e5590d20a34db48
at /.cargo/registry/src/github.com-1ecc6299db9ec823/flate2-0.2.17/src/zlib.rs:102
12:     0x55ecdd47f2ef - std::io::Write::write_all::h95d0008b89f6db59
at /buildslave/rust-buildbot/slave/stable-dist-rustc-linux/build/src/libstd/io/mod.rs:944
13:     0x55ecdd48033e - std::io::impls::<impl std::io::Write for &'a mut W>::write_all::hf6742d17386c5ea7
at /buildslave/rust-buildbot/slave/stable-dist-rustc-linux/build/src/libstd/io/impls.rs:51

The code using ZlibEncoder is:
let mut zlib = ZlibEncoder::new(Vec::new(), Compression::Best);
serde_json::to_writer(&mut zlib, data).unwrap();
zlib.finish().unwrap()

The ZlibEncoder works flawlessly with the minizip backend

Thanks for the report! Do you have some sample data that causes this? (just to add a test case with)

Sorry, but no. Most of the data is transient. I can try finding a minimal test case later today if needed.

I wonder if this was maybe fixed by https://github.com/alexcrichton/flate2-rs/pull/69? Could you try testing out the master branch?

Sorry for the delay. Yes, the master branch seems to be working now.


Nightshade requires a special nginx proxy exporters config

Nightshade's omero-web.conf proxies another server, so the omero web django prometheus exporter doesn't exist on nightshade.
The alternative to using prod-omero-web and prod-omero:!prod-omero-web would be a new group (prod-)omero-server
Updated: As discussed in Slack:

prod-omero has been renamed omero-server
all prod- prefixes have been removed

Last commit changes reload to restart to avoid silently config errors.

Could it bail the playbook on an nginx configtest? Clearly it didn't fail badly enough for NGINX to stop working. Usually a bad config will do that.

You can't use ansible's validate: because it attempts to validate a temporary copy of the proposed file which is in a temporary location. configtest could only be used after the templated file has been put in place, in which case restarted should also bail if the config is incorrect.

Management tools PR coming too I guess?

Seems reasonable.
(ansible)2018-06-28 16:44 LS27172:ansible kenny$ ansible-playbook --check -i ~/forks/management_tools/ansible/inventory/prod-hosts -l ome-dundeeomero.openmicroscopy.org ~/forks/prod-playbooks/omero/omero-monitoring-agents.yml  --ask-become-pass --become  | grep -B 1 changed
SUDO password:
TASK [openmicroscopy.omero-prometheus-exporter : omero prometheus exporter | install omero-prometheus-tools] **************************************************************************************
changed: [ome-dundeeomero.openmicroscopy.org]
--
RUNNING HANDLER [openmicroscopy.omero-prometheus-exporter : restart prometheus-omero-exporter] ****************************************************************************************************
changed: [ome-dundeeomero.openmicroscopy.org]
--
TASK [Create nginx proxy for prometheus exporters] ************************************************************************************************************************************************
changed: [ome-dundeeomero.openmicroscopy.org]
--
RUNNING HANDLER [restart nginx] *******************************************************************************************************************************************************************
changed: [ome-dundeeomero.openmicroscopy.org]
--
PLAY RECAP ****************************************************************************************************************************************************************************************
ome-dundeeomero.openmicroscopy.org : ok=32   changed=4    unreachable=0    failed=0

I'll try it in live mode once the users log out of OMERO.web.

Deployed to ome-dundeeomero.
(ansible)2018-06-28 17:05 LS27172:ansible kenny$ ansible-playbook --check -i ~/forks/management_tools/ansible/inventory/prod-hosts -l ome-dundeeomero.openmicroscopy.org ~/forks/prod-playbooks/omero/omero-monitoring-agents.yml  --ask-become-pass --become  | grep -B 1 changed
SUDO password:
TASK [openmicroscopy.omero-prometheus-exporter : omero prometheus exporter | install omero-prometheus-tools] **************************************************************************************
changed: [ome-dundeeomero.openmicroscopy.org]
--
RUNNING HANDLER [openmicroscopy.omero-prometheus-exporter : restart prometheus-omero-exporter] ****************************************************************************************************
changed: [ome-dundeeomero.openmicroscopy.org]
--
PLAY RECAP ****************************************************************************************************************************************************************************************
ome-dundeeomero.openmicroscopy.org : ok=31   changed=2    unreachable=0    failed=0

@manics - want to check it's done something?

Looks good to me

PLAY RECAP ****************************************************************************************************************************************************************************************
ns-web-pub.openmicroscopy.org : ok=24   changed=12   unreachable=0    failed=0
ns-web.openmicroscopy.org  : ok=24   changed=12   unreachable=0    failed=0

Good to merge. Needs https://github.com/openmicroscopy/management_tools/pull/802 for matching inventory groups.


feat: support for python 3.12

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

Comparison is base (b0c422b) 89.53% compared to head (a981fe6) 89.53%.

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Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #1521   +/-   ##
========================================
  Coverage    89.53%   89.53%
========================================
  Files          194      194
  Lines         6357     6357
========================================
  Hits          5692     5692
  Misses         665      665

Flag
Coverage Δ

py3.8-ubuntu-22.04-pandas
89.53% <ø> (ø)

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As a property agent who has not much free time, I can obtain my queries and search results quickly even when my database of contacts is very large.

Match and filter commands achieve this


Supporting experimental language features

I'm wondering what the best way to support a feature such as property initialisers, where it's a syntax error without using the specific babel plugin. I've tried specifying the babel-eslint parser, but you also need to be able to explicitly enable the babel-plugin-transform-class-properties plugin. I believe it's now at stage 2, so I don't think it's too far out of line to want to use.

Just enable that plugin in your .babelrc and the babel-eslint parser will pick it up.

That moment when you realise the solution was right under your nose :p
Thank you and sorry for wasting your time!

No problem 😀


Default Jest test is failing

This is default test for view which is generated by react-native init ProjectName command:
import 'react-native';
import React from 'react';
import Index from '../index.ios.js';

// Note: test renderer must be required after react-native.
import renderer from 'react-test-renderer';

it('renders correctly', () => {
  const tree = renderer.create(
    <Index />
  );
});

In my index file I started to use <Button> component and it works awesomely fine in simulator. However when I ran test command I had a failed test with exception:
 dmitri@MacBook-Pro-Dmitri  ~/github/fanburst/FanburstApp   master  npm test

><EMAIL_ADDRESS>test /Users/dmitri/github/fanburst/FanburstApp
> jest

 PASS  __tests__/index.android.js (6.547s)
 FAIL  __tests__/index.ios.js
  ● Test suite failed to run

    /Users/dmitri/github/fanburst/FanburstApp/node_modules/apsl-react-native-button/Button.js:53
              <Text
              ^
    SyntaxError: Unexpected token <

      at transformAndBuildScript (node_modules/jest-runtime/build/transform.js:284:10)
      at Object.<anonymous> (index.ios.js:17:28)
      at Object.<anonymous> (__tests__/index.ios.js:3:15)

Test Suites: 1 failed, 1 passed, 2 total
Tests:       1 passed, 1 total
Snapshots:   0 total
Time:        9.343s
Ran all test suites.
npm ERR! Test failed.  See above for more details.

Any ideas?

Hi @voronianski!
I have no idea, Jest test are working fine in the component, please double check your Jest configuration. Closing by now, seems more a Jest/test environment issue. Please let me know if you find the solution.


Does not make a sound on real OPL3 hardware

Just found out about this interesting project!
However, the provided vgz files in the output directory does not make a sound on a real OPL3 chip. I tested on the RetroWave OPL3: https://github.com/SudoMaker/RetroWave
While VGM play can output sound, but IMO it might be too prefect and ignores real world limitations like bandwidth limitation for commands. Some hand crafted PCM emulation(actually converted from SN76489) can play just fine on real hardware. Here are the VGM files:
aaah get ready.zip

I look into it in the morning, but I have been playing output from the
utility on a real YMF-262m chip as part of my PugPuter 6309 project. I've
tested all of the provided examples, I believe. I wrote the playback
software in this case though, so maybe the output from the utility doesn't
adhere to the VGM spec in some way. It seems to play alright in Winamp, but
it may be more tolerant of malformed input.
On Sat, Dec 28, 2024, 6:40 AM Yukino Song @.***> wrote:

Just found out about this interesting project!
However, the provided vgz files does not make a sound on a real OPL3 chip.
I tested on the RetroWave OPL3: https://github.com/SudoMaker/RetroWave
While VGM play can output sound, but IMO it might be too prefect and
ignores real world limitations like bandwidth limitation for commands. Some
hand crafted PCM emulation(actually converted from SN76489) can play just
fine on real hardware. Here are the VGM files:
aaah get ready.zip
https://github.com/user-attachments/files/18266029/aaah.get.ready.zip
—
Reply to this email directly, view it on GitHub
https://github.com/caiannello/WAV2VGM/issues/1, or unsubscribe
https://github.com/notifications/unsubscribe-auth/ACOFYRJ37H4YJJ6QQ6YIVOT2H2E4LAVCNFSM6AAAAABUJXLIPGVHI2DSMVQWIX3LMV43ASLTON2WKOZSG43DCNRYGYZDCNQ
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You are receiving this because you are subscribed to this thread.Message
ID: @.***>


Consider linking to ajv-inspector

I had to create a project to inspect schemas and I based it on ajv. Maybe you want to link to that project on the README.md for ajv.
https://github.com/e0ipso/ajv-inspector

cool, thank you, I will have a look

Hi, sorry it takes some time to comment...
At the moment the package seems to have quite a few undocumented limitations. Please see the issues I've submitted.
Happy to reference it here once the limitations are removed or documented. Also ci build / test coverage would be good.
Closing the issue for now, please re-open when the issues are addressed.


Import error: Could not find declaration file for module 'graphiql'

I'm having an issue adding this module to my Node.js Koa application.  The application is built with Webpack.
Visual Studio Code is showing the following error on the import statment:
Could not find a declaration file for module 'graphiql'. '/Users/coreyquillen/Workspace/universal-javascript/node_modules/graphiql/dist/index.js' implicitly has an 'any' type.
I'm getting the following error at runtime:
instanceOf.mjs:34 Uncaught ReferenceError: require is not defined     at eval (instanceOf.mjs:34)     at Module../node_modules/graphql/jsutils/instanceOf.mjs (desktop.js:5527)     at __webpack_require__ (desktop.js:20)     at eval (definition.mjs:46)     at Module../node_modules/graphql/type/definition.mjs (desktop.js:5851)     at __webpack_require__ (desktop.js:20)     at eval (validate.mjs:4)     at Module../node_modules/graphql/type/validate.mjs (desktop.js:5923)     at __webpack_require__ (desktop.js:20)     at eval (graphql.mjs:4)

Hi...I have the same problem in my React/Typescript project....any developments on this ?

@andrectw this all should be ameliorated by 0.17.0. we have a webpack example merged now as well. when we upgraded our underlying LSP version for codemirror-graphql (and thus graphiql) we had added a dynamic require() without specifying extensions which broke webpack module resolution. i'm getting reports that it works fine with the example webpack configs. feel free to re-open if you still have an issue with 0.17.0


Linting: Aggressive ruff pass (ruff v0.3.4)

ruff check --select ALL . --fix --unsafe-fixes --preview --show-fixes; ruff format .

Fixed 3 errors:

docs/conf.py: 1 × RET505 (superfluous-else-return)
src/g/init.py: 1 × RUF022 (unsorted-dunder-all)
tests/test_cli.py: 1 × PT006 (pytest-parametrize-names-wrong-type)

Codecov Report
Attention: Patch coverage is 50.00000% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 72.15%. Comparing base (77c30a8) to head (3be17e6).

Files
Patch %
Lines

docs/conf.py
0.00%
1 Missing :warning:

Additional details and impacted files
@@           Coverage Diff           @@
##           master      #23   +/-   ##
=======================================
  Coverage   72.15%   72.15%
=======================================
  Files           5        5
  Lines         158      158
=======================================
  Hits          114      114
  Misses         44       44

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


Unable to Debug Jest tests with Typescript

VSCode Version: Code 1.13.1 (379d2efb5539b09112c793d3d9a413017d736f89, 2017-06-14T18:13:05.928Z)
OS Version: Darwin x64 16.6.0
Extensions:

Extension
Author
Version

EditorConfig
EditorConfig
0.9.3

npm-intellisense
christian-kohler
1.3.0

tslint
eg2
0.16.0

path-autocomplete
ionutvmi
1.5.1

graphql-for-vscode
kumar-harsh
1.4.2

debugger-for-chrome
msjsdiag
3.1.6

vim
vscodevim
0.9.0

Steps to Reproduce:

Clone the reproduction case here: https://github.com/blargity/vscode-ts-jest-debugger
Run yarn
Try to run the Tests configuration in VSCode

Note: this is not the only configuration we've tried. Even setting inline source maps doesn't seem to do anything:
$ node --version
v8.1.2
$ npm --version
5.0.3
$ yarn --version
0.27.5
$ tsc --version
Version 2.4.1

I'd really appreciate any help I can get debugging this and figuring out how we can run our tests using the debugger. Once you get used to using the VSCode debugger you want to use it for everything!

Here's the trace from running that debugger task.
vscode-node-debug2.txt

Just wanted to verify that the issue is a bit different in 1.14.1. It now runs, then stops, but my breakpoints aren't hit, and I see no output from Jest anywhere, so it doesn't look to me like it's running successfully. Here's an updated trace: vscode-node-debug2.txt

This is a known issue with Node. Using a version <8 might help: https://github.com/Microsoft/vscode/issues/28007#issuecomment-306383975

I downgraded to 7.10.1 and still see no output from my tests in the terminal. I should see Jest output somewhere regardless of the debugger's ability to attach, right?

No, if the debugger can't attach, then it can't receive output from the program to display it in the console, but if you set"console": "integratedTerminal", then it will run jest in the integrated terminal and you'll see output there at least.


Have a useful and meaningful README.md at top repo level

Description:
Need to have a proper README.md
Right now, it is empty.

Added some content with https://github.com/ballerina-platform/ballerina-examples/pull/791

This is added now.


add home/end shortcuts to memory viewer

You can now press Home/End to jump to the top/end of the memory addresses. Please give it a test :)
If this project is still active I can also contribute: "add search class shortcut to class nodes. opens a memory viewer with its start / end address pre-configured". Let me know if it sounds like a reasonable feature.
Thanks!

this PR is defective


Cannot create ListArray of element type float32

To reproduce (in pyarrow v0.8.0):
import pyarrow as pa
l = [[1.2, 3.4], [9.0, 42.0]]
pa.array(l, type=pa.list_(pa.float32()))

Results in "ArrowNotImplementedError: value type not implemented".
float64 works without problem.

I think this is https://issues.apache.org/jira/browse/ARROW-1345, same as #1430, but we should make sure


CSP Level 3 changes - "Child-src" Deprecated, Replaced by "frame-src" that is undeprecated, and "worker-src" is added

The CSP level 3 Editors draft specifies that child-src is now deprecated. Generally these "editor drafts" are what browsers use to implement from. The following changes are important:
"frame-src"

Was previously deprecated, is now undeprecated
Defers to "child-src" if not present, which in turn defers to "default-src" if not present

"worker-src"

Added to spec
Defers to "script-src" if not present, which in turn defers to "default-src" if not present

"child-src"

deprecated

I will research what changes are necessary and create a pull request shortly

Hi @PrinsFrank,
I have release a new version that support CSP level 3, however, this is a breaking change upgrade. If you have encountered any problem in upgrade progress,  open a new issue or reply in this issue and I will do my best to help you solve the problem.

Closing due to inactivity. If you have any question, feel free to open a new issue with a reference to this one.


Allow size as a percent for torusd. Fixes #175

This is correct; though the Config struct should change slightly after this because there's a subtlety between storage-size presented to the cluster and storage size used (backends might need a little space for its own bookkeeping). Right now the flag is the former, and this refers to the latter.
It's an easy calculation, and this can go in first, but it spawns a tiny followup issue.

One thing I noticed while testing this is that it's really easy to get a percent of the drive that isn't an event multiple of the torus blocksize.
It's easy enough to make the blocksize line up, but it seems like it's currently not easy to get the torus blocksize, as it seems to be set in two different places depending on which MDS is being used. I can hard code the values in, but that feels like a sub-optimal solution. Another idea would be to adjust the size in storage/mmap_file.go after the blocksize has been determined.
Any thoughts on which way would be the better approach?

Better approach is to always follow the blocksize from the MDS; if it's over, just shrink it a bit smaller to align to the blocksize. You have to initialize the MDS anyway before torusd can come up, so that's nto a problem.

[~barakmich] I added resizing to bring the volume down to the closet even multiple. That should complete this, assuming everything checks out okay.

Merged! Sorry about the delay.


'Confirm Task' button is not disabled after system throws 'error assigning task' error message

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Action Performed:

Open an existing chat/ start a new chat
Click on 'Actions' icon
Click on 'Assign task' button
Enter title > click on 'Next' button
Click on 'Confirm task' button

Expected Result:
Confirm task button shouldn't be clickable once the system throws an error saying 'error assigning task'
Actual Result:
Confirm task button is clickable once system throws an error
Workaround:
Can the user still use Expensify without this being fixed? Have you informed them of the workaround?
Platforms:

Which of our officially supported platforms is this issue occurring on?

[ ] Android / native
[ ] Android / Chrome
[ ] iOS / native
[ ] iOS / Safari
[x] MacOS / Chrome / Safari
[ ] MacOS / Desktop

Version Number: 1.3.34-1
Reproducible in staging?: y
Reproducible in production?: y
If this was caught during regression testing, add the test name, ID and link from TestRail:
Email or phone of affected tester (no customers):
Logs: https://stackoverflow.com/c/expensify/questions/4856
Notes/Photos/Videos: Any additional supporting documentation
https://github.com/Expensify/App/assets/43996225/3640439f-6eab-4cc9-aa57-8ed47a75595f
https://github.com/Expensify/App/assets/43996225/0c201d16-ca5b-481b-8d8f-3c1befd596e4
Expensify/Expensify Issue URL:
Issue reported by: @Natnael-guchima
Slack conversation: https://expensify.slack.com/archives/C049HHMV9SM/p1687797690671519
View all open jobs on GitHub

Proposal
Please re-state the problem that we are trying to solve in this issue.
'Confirm Task' button is not disabled after system throws 'error assigning task' error message.
What is the root cause of that problem?
We does not check there is a error or not before click Confirm task in NewTaskPage.js.
What changes do you think we should make in order to solve the problem?
We should disable if there is a error.
	<FormAlertWithSubmitButton
		isAlertVisible={!_.isEmpty(errorMessage)}
+   	isDisabled={!_.isEmpty(errorMessage)}
		message={errorMessage}
		onSubmit={() => onSubmit()}
		enabledWhenOffline
		buttonText={props.translate('newTaskPage.confirmTask')}
		containerStyles={[styles.mh0, styles.mt5, styles.flex1, styles.ph5]}
	/>

What alternative solutions did you explore? (Optional)
None.

Unable to reproduce the error flow. Asking in slack.

Going to close for now since it's no longer reproducible. I asked @Natnael-Guchima to ping me in the slack thread if he's able to reproduce again and I'll reopen if so.


Allow any var that sourced from a require in disallowMultipleVarDecl

Hi,
In disallowMultipleVarDecl, when using allExcept require, what do you think about allowing all vars that sourced from a require call?
For example, this is currently failing on the Emitter var
var fs = require('fs'),
    Emitter = require('events').EventEmitter;

How about allowing such cases?
I played a little bit with the rule and came up with this:
https://github.com/ValYouW/node-jscs/commit/999c71457ec30571223ebc1dae28014686fccb5b
Not sure it's 100% ok as I am not so familiar with esprima...

---
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I think that would be a good idea, i think current behaviour could be considered as bug

@ValYouW maybe paste some code and play around with http://astexplorer.net/ if you want to make a PR for it later

Ahh, sorry for all the commits mess...
Created a PR #1849 (with tests) lets discuss it there...


Elements lose hover after some time

After adding some elements the previous ones lose the hover border and actions:
https://github.com/measuredco/puck/assets/8821661/999eb753-7545-4411-9425-12e95d68c1f8

Thanks for this report @localhosted. Suspect it might be resolved by https://github.com/measuredco/puck/pull/37, which reimplements a lot of the hover functionality. Let's re-test once #37 is merged.

Hi @localhosted  - can you confirm if this is still occurring in the 0.8.0 canary?

Closing as can't reproduce


[Idea] Patching for pollyfills loaded after Zone.js

Hi,
Is there any reason not to patch polyfills if they're loaded after Zone.js? If a library you're using pulls in a MutationObserverpolyfill, shouldn't that polyfill have the same behaviour as if it was loaded prior to Zone.js?
I think this could be done by adding a setter on global[x] so that whenever that property is set after zone.js applies its patches (such as by a polyfill), it will be patched accordingly (e.g. if x is "MutationObserver").
@btford, @vicb

A polyfill will need to use an API that's already patched.
For example, a polyfill for MutationObserver might use setTimeout to preserve the semantics of MutationObserver. Because Zone.js has already patched setTimeout, the MutationObserver polyfill will also be patched.

Is that really guaranteed? For example, webcomponentsjs's MutationObserver polyfill uses setImmediate if it's available, which I don't believe zone.js polyfills…?
Seems to open the door to inconsistent behaviour between code running on platforms requiring polyfills and those not. I suppose some variance is somewhat inevitable, but it can at least be mitigated by patching the polyfill.

Is that really guaranteed?

Yes.
Zone.js does patch setImmediate: https://github.com/angular/zone.js/blob/master/lib/patch/browser.js#L14-L18
If there was a native browser API Zone.js didn't patch that a polyfill used, the fix should be to patch the native browser API.
Patching both the polyfills and the underlying API would result in an API being patched twice, which is also incorrect behavior.

Ahh, okay. Thanks Brian.
From:  Brian Ford
Reply-To:  "angular/zone.js"
Date:  Monday, 20 July 2015 16:35
To:  "angular/zone.js"
Cc:  Matt
Subject:  Re: [zone.js] [Idea] Patching for pollyfills loaded after Zone.js (#148)
Is that really guaranteed?
Yes.
Zone.js does patch setImmediate: https://github.com/angular/zone.js/blob/master/lib/patch/browser.js#L14-L18
If there was a native browser API Zone.js didn't patch that a polyfill used, the fix should be to patch the native browser API.
Patching both the polyfills and the underlying API would result in an API being patched twice, which is also incorrect behavior.
—
Reply to this email directly or view it on GitHub.


Android 11 and issue in API 30 Permission issue and fetch pdf file path from storage not convert into file

    How library manage this permission in android 11? please give us suggestion.