🐛 Bug Report: Cannot start the newly created backstage app

📜 Description
I created a new backstage app with npx @backstage/create-app@latest and when trying to run with yarn dev, I got following error:
Error: The SQLite driver does not support plugin division mode 'schema'
    at Sqlite3Connector.getClient (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-defaults/src/entrypoints/database/connectors/sqlite3.ts:192:13)
    at DatabaseManagerImpl.getDatabase (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-defaults/src/entrypoints/database/DatabaseManager.ts:138:37)
    at Object.getClient (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-defaults/src/entrypoints/database/DatabaseManager.ts:79:34)
    at Function.create (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-defaults/src/entrypoints/auth/plugin/keys/DatabaseKeyStore.ts:58:35)
    at Function.create (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-defaults/src/entrypoints/auth/plugin/keys/DatabasePluginKeySource.ts:50:45)
    at createPluginKeySource (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-defaults/src/entrypoints/auth/plugin/keys/createPluginKeySource.ts:40:36)
    at Object.factory (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-defaults/src/entrypoints/auth/authServiceFactory.ts:53:29)
    at Object.factory (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-plugin-api/src/services/system/types.ts:321:9)
    at <anonymous> (/Users/psychiatrichwj/dev-portal/backstage/node_modules/@backstage/backend-app-api/src/wiring/ServiceRegistry.ts:334:29)

👍 Expected behavior
Newly created app should start without a problem
👎 Actual Behavior with Screenshots
Newly created app failed to start
👟 Reproduction steps
Create a new application, and run yarn dev
📃 Provide the context for the Bug.
No response
🖥 Your Environment
Sqlite version:
SQLite version 3.43.2 2023-10-10 13:08:14
Enter ".help" for usage hints.
Connected to a transient in-memory database.
Use ".open FILENAME" to reopen on a persistent database.

👀 Have you spent some time to check if this bug has been raised before?

[X] I checked and didn't find similar issue

🏢 Have you read the Code of Conduct?

[X] I have read the Code of Conduct

Are you willing to submit PR?
None

Did you make any changes to the app or config?

No. A pluginDivisionMode setting must be somewhere in your config; this is thrown by our code and as far as I can tell it's all defaulted to the value 'database' unless explicitly configured to something else. Could you for example have an app-config.local.yaml that has a partial database config in it? Your config files are merged together in layers, so the setting may not be in the file you expect it to be.


Doc build may fail with docutils 0.13.1

In Travis it works, but I had to run "pip install docutils==0.12" in my machine. Please, let me know if it happens with anybody else.

I'm closing this issue as docutils is at 0.13.1 now.


Scatter plot misaligned?

The scatter plot on the left should not look like this.  The full (grey) and selected (color) should be the same by default on load.

I see this on both the test datasets on lsst-dev

another example.  the colored point are definitely flipped (at least)

Fixed in HoloViews 1.13.0b9.


Turn off generic Instagram locations

It would be good if we have option to turn off Instagram generic locations because sometime they are not accurate.

Fix is now merged to master


Recommendations are not getting generated when we deploy kruize on power architecture

Is your feature request related to a problem? Please describe.
i want to test these 2 scenarios :
try with test pod that apparently requests too much (makes it harder to find a node to run on)
2.   Try with test pod that apparently requests too little (causes repeated eviction)
so when i am trying to deploy pod with larger limits , then pod is not coming up because of failedScheduling error that's why kruize is not generating recommendations . and if pod have lesser limits then also kruize is not showing recommendations.
{
"application_name": "kruize",
"resources": {
"requests": {
"memory": "0.0M",
"cpu": 0.0
},
"limits": {
"memory": "0.0M",
"cpu": 0.0
}
}
}
I also tried with acme-air then also application-pod didn't generate recommendations.
Describe the solution you'd like
I know that If the cpu usage of the app is below a threshold, it wont generate recommendations , as Kruize did not get enough data to generate a recommendation. So I want to know what is the threshold value.

I tried this for both the scenarios:
Scenario -1
If we try with test pod that apparently requests too much (makes it harder to find a node to run on)   ->>>
Then pod will remain in Pending state with the error : FailedScheduling
and kruize will not show anything , output for recommendations will be empty array.
Example:
pod.yaml
apiVersion: v1
kind: Pod
metadata:
  name: my-pod
spec:
  containers:
  - name: my-container
    image: nginx
    resources:
      requests:
        cpu: 2
        example.com/foo: 1
      limits:
        example.com/foo: 1

[root@kruize-aaruni-inf kruize]# oc get pods |grep pod
my-pod                                         0/1     Pending   0          102s
[root@kruize-aaruni-inf kruize]# oc describe pod my-pod
Name:         my-pod
Namespace:    openshift-monitoring
Priority:     0
Node:
Labels:
Annotations:  openshift.io/scc: anyuid
Status:       Pending
IP:
IPs:
Containers:
  my-container:
    Image:      nginx
    Port:
    Host Port:
    Limits:
      example.com/foo:  1
    Requests:
      cpu:              2
      example.com/foo:  1
    Environment:
    Mounts:
      /var/run/secrets/kubernetes.io/serviceaccount from default-token-7w949 (ro)
Conditions:
  Type           Status
  PodScheduled   False
Volumes:
  default-token-7w949:
    Type:        Secret (a volume populated by a Secret)
    SecretName:  default-token-7w949
    Optional:    false
QoS Class:       Burstable
Node-Selectors:
Tolerations:     node.kubernetes.io/memory-pressure:NoSchedule
                 node.kubernetes.io/not-ready:NoExecute for 300s
                 node.kubernetes.io/unreachable:NoExecute for 300s
Events:
  Type     Reason            Age        From               Message
  ----     ------            ----       ----               -------
  Warning  FailedScheduling    default-scheduler  0/6 nodes are available: 6 Insufficient example.com/foo.
  Warning  FailedScheduling    default-scheduler  0/6 nodes are available: 6 Insufficient example.com/foo.
In order to check the recommendations label the pod :
[root@kruize-aaruni-inf kruize]# oc label -n openshift-monitoring pod my-pod app.kubernetes.io/name=my-pod
pod/my-pod labeled
Get the Recommendations :
[root@kruize-aaruni-inf kruize]# curl http://kruize-openshift-monitoring.apps.kruize-aaruni.cp.fyre.ibm.com/recommendations?application_name=my-pod
[]
Scenario-2
Try with test pod that apparently requests too little (causes repeated eviction)
If the cpu usage of the app is below a threshold, it wont generate recommendations , as Kruize did not get enough data to generate a recommendation.
In our case its same ->
pod-min.yaml ::
apiVersion: v1
kind: Pod
metadata:
  name: my-pod-min
spec:
  containers:
  - name: my-container
    image: nginx
    resources:
      requests:
        cpu: "150m"
        memory: "50Mi"
      limits:
        cpu: "500m"
        memory: "128Mi"

[root@kruize-aaruni-inf kruize]# oc get pods |grep pod
my-pod                                         0/1     Pending   0          23m
my-pod-min                                 1/1     Running   0          37s
Label the pod to get recommendations :
[root@kruize-aaruni-inf kruize]# oc label -n openshift-monitoring pod my-pod-min app.kubernetes.io/name=my-pod-min
pod/my-pod-min labeled
Get the recommendations ->
[root@kruize-aaruni-inf kruize]# curl http://kruize-openshift-monitoring.apps.kruize-aaruni.cp.fyre.ibm.com/recommendations?application_name=kruize
[
  {
    "application_name": "kruize",
    "resources": {
      "requests": {
        "memory": "0.0M",
        "cpu": 0.0
      },
      "limits": {
        "memory": "0.0M",
        "cpu": 0.0
      }
    }
  }
]
[root@kruize-aaruni-inf kruize]#
[root@kruize-aaruni-inf kruize]# curl http://kruize-openshift-monitoring.apps.kruize-aaruni.cp.fyre.ibm.com/recommendations?application_name=my-pod-min
[
  {
    "application_name": "my-pod-min",
    "resources": {
      "requests": {
        "memory": "0.0M",
        "cpu": 0.0
      },
      "limits": {
        "memory": "0.0M",
        "cpu": 0.0
      }
    }
  }
]

@AaruniAggarwal Thank you for trying out kruize !
Normally we recommend that you run your pods that are being monitored by kruize with no requests and limits set (or with very high limits set). This helps kruize to understand what is the real usage and hence can recommend the right set of values.
Is there any reason why you are running with the above constraints ?

@AaruniAggarwal Thank you for trying out kruize !
Normally we recommend that you run your pods that are being monitored by kruize with no requests and limits set (or with very high limits set). This helps kruize to understand what is the real usage and hence can recommend the right set of values.
Is there any reason why you are running with the above constraints ?

@dinogun Thanks for responding.
I tried with acme-air application in which no requests and limits were set. I added the customers in acme-air then also no recommendations were generated.
[root@ocs-sridhar-rhceph-8d86-bastion ~]# curl http://kruize-openshift-monitoring.apps.ocs-sridhar-rhceph-8d86.ibm.com/recommendations?application_name=acmeair-customer-db
[
  {
    "application_name": "acmeair-customer-db",
    "resources": {
      "requests": {
        "memory": "0.0M",
        "cpu": 0.0
      },
      "limits": {
        "memory": "0.0M",
        "cpu": 0.0
      }
    }
  }
]
And in scenario1 , which I pasted above I set the very high limits due to which pod didn't come up.
Yes, I was asked to test these 2 scenarios and check whether kruize is generating right recommendations or not on power (ppc64le) architecture.

@dinogun Thanks for responding.
I tried with acme-air application in which no requests and limits were set. I added the customers in acme-air then also no recommendations were generated.
[root@ocs-sridhar-rhceph-8d86-bastion ~]# curl http://kruize-openshift-monitoring.apps.ocs-sridhar-rhceph-8d86.ibm.com/recommendations?application_name=acmeair-customer-db
[
  {
    "application_name": "acmeair-customer-db",
    "resources": {
      "requests": {
        "memory": "0.0M",
        "cpu": 0.0
      },
      "limits": {
        "memory": "0.0M",
        "cpu": 0.0
      }
    }
  }
]
And in scenario1 , which I pasted above I set the very high limits due to which pod didn't come up.
Yes, I was asked to test these 2 scenarios and check whether kruize is generating right recommendations or not on power (ppc64le) architecture.

That's why I wanted to know is there any specific example for these 2 scenarios with which I can test with

That's why I wanted to know is there any specific example for these 2 scenarios with which I can test with

Any update on this issue ?

Any update on this issue ?

The two scenarios that you are trying out are not good test cases. Thus, Kruize can't give you good recommendations because of that.
We would like to know a bit more about why are you testing these 2 specific scenarios. Any particular reasons for this?

The two scenarios that you are trying out are not good test cases. Thus, Kruize can't give you good recommendations because of that.
We would like to know a bit more about why are you testing these 2 specific scenarios. Any particular reasons for this?

Also, you can try applying load when using the acme-air application. If you run into any problems while applying load, @shruacha1234 should be able to help you out.

Also, you can try applying load when using the acme-air application. If you run into any problems while applying load, @shruacha1234 should be able to help you out.

Again tried with acme-air and this time i added more customers .
Earlier i was adding 10000 customers by using this command :
curl http://HOSTNAME:PORT_NUMBER/customer/loader/load?numCustomers=10000
And now I increased the customers by 10 times :
curl http://HOSTNAME:PORT_NUMBER/customer/loader/load?numCustomers=100000 .
And this time recommendations got generated.
Before adding load :
[root@kruize-inf acmeair]# curl http://kruize-openshift-monitoring.apps.kruize.cp.fyre.ibm.com/recommendations?application_name=acmeair-customer-db
[
{
    "application_name": "acmeair-customer-db",
    "resources": {
      "requests": {
        "memory": "0.0M",
        "cpu": 0.0
      },
      "limits": {
        "memory": "0.0M",
        "cpu": 0.0
      }
    }
  }
]

After adding load :
curl http://HOSTNAME:PORT_NUMBER/customer/loader/load?numCustomers=100000
[root@kruize-inf acmeair]# curl http://kruize-openshift-monitoring.apps.kruize.cp.fyre.ibm.com/recommendations?application_name=acmeair-customer-db
[
  {
    "application_name": "acmeair-customer-db",
    "resources": {
      "requests": {
        "memory": "194.6M",
        "cpu": 0.5
      },
      "limits": {
        "memory": "233.5M",
        "cpu": 1.0
      }
    }
  }
]

Again tried with acme-air and this time i added more customers .
Earlier i was adding 10000 customers by using this command :
curl http://HOSTNAME:PORT_NUMBER/customer/loader/load?numCustomers=10000
And now I increased the customers by 10 times :
curl http://HOSTNAME:PORT_NUMBER/customer/loader/load?numCustomers=100000 .
And this time recommendations got generated.
Before adding load :
[root@kruize-inf acmeair]# curl http://kruize-openshift-monitoring.apps.kruize.cp.fyre.ibm.com/recommendations?application_name=acmeair-customer-db
[
{
    "application_name": "acmeair-customer-db",
    "resources": {
      "requests": {
        "memory": "0.0M",
        "cpu": 0.0
      },
      "limits": {
        "memory": "0.0M",
        "cpu": 0.0
      }
    }
  }
]

After adding load :
curl http://HOSTNAME:PORT_NUMBER/customer/loader/load?numCustomers=100000
[root@kruize-inf acmeair]# curl http://kruize-openshift-monitoring.apps.kruize.cp.fyre.ibm.com/recommendations?application_name=acmeair-customer-db
[
  {
    "application_name": "acmeair-customer-db",
    "resources": {
      "requests": {
        "memory": "194.6M",
        "cpu": 0.5
      },
      "limits": {
        "memory": "233.5M",
        "cpu": 1.0
      }
    }
  }
]


Add a THEORY.md

Add a THEORY.md document that describes the mechanics behind the primaryuse cases for chef-vault.  Closes issue #109

Merged into release_2.5 branch


[FEAT]: Make the club logo clickable that redirects to home

Current Behaviour
Nothing happens when clicked on the logo
Expected Behaviour
On clicking the logo, it should redirect to the home page.
I would like contributors outside the organization to contribute on this.

Can you assign this issue to me?

Sure, you can start working. Make sure you star the repo as well.


[zh] Sync secrets-good-practices.md

Localize this file for the first time:
content/zh-cn/docs/concepts/security/secrets-good-practices.md

Preview: https://deploy-preview-37052--kubernetes-io-main-staging.netlify.app/zh-cn/docs/concepts/security/secrets-good-practices/

/approve


Make minor changes to setup.*

I made another change to specify the include path in the file headers. That lets Cython have a better understanding of the relationship which is desirable when editing the files by hand


cannot post multi-part with file

Hello,
while using Postman to test an image upload to freeimage.host, it works as supposed to.
But when I use Java code, it fails. Maybe it is a bug, but i am not sure since the same code works for imgbb.com!
POSTMAN
POST: https://freeimage.host/api/1/upload/
PARAMS: key=6d207e02198a847aa98d0a2a901485a5
BODY: source=an image filename from local filesystem
JAVA
File f = new File(an image filename from local filesystem);
HttpRequest httpRequest = HttpRequest.post( "https://freeimage.host/api/1/upload/" )
.part("key", apikey)
.part("source", f.getName(), f)
.send("");
or
File f = new File(an image filename from local filesystem);
HttpRequest httpRequest = HttpRequest.post( "https://freeimage.host/api/1/upload/" )
.part("key", apikey)
.part("source", f.getName(), f);
httpRequest,code();
Java fails with HTTP response status code 403.

In Java code the apikey is "6d207e02198a847aa98d0a2a901485a5".


feat(aws): add automatically detect AWS EC2 AMI costs

Issue #778
Initial support

@alikhajeh1, this is ready for initial review.
There are strange thing with failed test. It expects correct pricing (±67$, the same as aws_instance test) but locally it doesn't fails on that and put 155$

Thanks @ekifel, closing this PR just now since I've not had a chance to dive into this more. We need to do some more investigation into checking the creds, since at the moment this adds significant time for each EC2 resource.  I'll pick this up again at a later date and will reopen the PR then.


Probably bindParameters bug

ORM Version: 1.0.3
Code
$database = $ormFactory->database('example');
$database->execute('SHOW TABLES');

Expected
All OK
Actual

Argument 1 passed to Spiral\Database\Driver\Driver::bindParameters() must be an instance of Spiral\Database\Statement, instance of Doctrine\DBAL\Driver\PDOStatement given, called in .../vendor/spiral/database/src/Driver/Driver.php on line 275

I'm still trying to understand the cause of the problem. Maybe I'm doing something wrong =))))

Yes that's right. I tried to reuse the existing connection with another ORM, but missed this call. LOL.
https://github.com/spiral/database/blob/master/src/Driver/Driver.php#L163
It seems necessary to create new PDO connections specifically for the Cycle ='(

Since PDO is stateful - yes. But I can try to make it happen.

Also, what are you looking can be changed. Statement extends PDO statement so it should be possible to fallback to lower level implementation.

But I can try to make it happen.

Not worth it, what I'm trying to combine difficult compatible - these are not implementation problems

FYI, statement casting is not required anymore, you can share PDO between drivers I believe.


提供一下英文文档

rt

@Wzb3422

@Wzb3422

Working on it now.
cc @FuzzyFade

Closing for #10
Love u babies


Trying to initialize the ACCUSchedule module with an unexpected flag.

When I follow the installation instruction I get this error when I connect to the running application.
Oops! Something went wrong when starting your Elm program.

Trying to initialize the `ACCUSchedule` module with an unexpected flag.
I tried to convert it to an Elm value, but ran into this problem:

Expecting a String at _.apiBaseUrl but instead got: undefined

Ah, now I see this warning from the server:
15:27:39 client.1   |  WARNING in API_BASE_URL environment variable is undefined.
15:27:39 client.1   |  WARNING in ./~/opal-runtime/src/nodejs.js

I guess i need to set this environment variable to ... something.

I think this is because you haven't created a .env file. It's mentioned in the readme, but i could probably emphasise it more.

Right you are. I inadvertently skipped that bit.

I feel it has to be said, I missed it as well.

I've created #48 to deal with this.


Enhance logging info for better diagnostic of connection shutting down

Codecov Report
Base: 43.32% // Head: 43.14% // Decreases project coverage by -0.18% :warning:

Coverage data is based on head (677fcdb) compared to base (ff83aae).
Patch coverage: 0.00% of modified lines in pull request are covered.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #425      +/-   ##
==========================================
- Coverage   43.32%   43.14%   -0.18%
==========================================
  Files         119      119
  Lines       35837    35841       +4
==========================================
- Hits        15526    15464      -62
- Misses      20311    20377      +66

Impacted Files
Coverage Δ

src/sp/transport/mqtt/broker_tcp.c
0.89% <0.00%> (-0.01%)
:arrow_down:

src/sp/transport/mqtts/broker_tls.c
0.58% <ø> (ø)

src/sp/transport/mqttws/nmq_websocket.c
2.46% <ø> (ø)

src/core/tcp.c
72.10% <0.00%> (-6.85%)
:arrow_down:

src/supplemental/http/http_client.c
21.73% <0.00%> (-5.22%)
:arrow_down:

src/core/timer.c
92.20% <0.00%> (-5.20%)
:arrow_down:

src/sp/transport/ws/websocket.c
77.47% <0.00%> (-1.71%)
:arrow_down:

src/sp/transport/ipc/ipc.c
75.69% <0.00%> (-1.49%)
:arrow_down:

src/core/list.c
84.61% <0.00%> (-1.29%)
:arrow_down:

src/core/aio.c
94.37% <0.00%> (-1.19%)
:arrow_down:

... and 5 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

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[FEATURE] Disabled tui-root Scroll Bar

🚀 Feature request
Is your feature request related to a problem?
I already use custom scrolling in my webapp, and when adding the <tui-root> element to my app it causes there to be 2 different scroll bars.
I'm not fully sure if this isn't already a feature, I could not find any documentation on it.
Describe the solution you'd like
I'd ideally like a property on the tui-root component that would allow a user to disable the custom scrolling
E,g
<tui-root [disabledScrolling]="true"></tui-root>

Describe alternatives you've considered
I'm not really sure there could be any other ways to control this other then possible write some css to override the normal behavior to make the scroll bar have a width of 0

Hi @benfl3713. Thank you for bringing this up. You can hide tui-root scrollbar with this global style:
tui-root > tui-scroll-controls {
  display: none;
}

BTW, we use custom global scrollbar so we can hide it when modal dialogs are open. We need to think how best to handle this if we want to make them configurable.

@waterplea Hi Alex, I want to disable the scrollbar when I open the Sidebar in my case.
I didn't find how you did that in the case of modal for inspiration.
Thanks

@khalilou88 it's kind of hardcoded in tui-root. I suppose it's a good idea to get an API in place for that.

@waterplea thanks for your reply.
An api ? like a token (TUI_ROOT_SCROLL_REF) that contains the element "tui-root > tui-scroll-controls"
And hide/show the scroll with code when needed?


🏗 [ADMIN] - @joshuadavidthomas

DSF member

[X] I am a DSF member

Why do you want to join?
As I've gotten more experience, I've realized the value in sharing what I've learned along the way. I try to blog, but I'm not much of a writer and writing well takes a ton of time. Additionally, I try to contribute where I can to public third-party packages.
If I could step into an admin role where I can help out maintainers with some of the drudgery, meta stuff around maintaining a package, so they can focus more of their attention on the package itself, well I think I would be a good fit for that. In my capacity as a member of the Jazzband org, that's generally the type of contributions I have made.
Plus, through this organization, in addition to the typical installable Django apps, I could see where a catalog of public GitHub Actions or Python/Django packages around maintaining packages that is used by Django Commons repos but that anyone could use would be a great contribution to the community.
Please tell us about your packaging experience?
Through my work, I maintain a number of third-party Django packages:

django-email-relay
django-flyio
django-opfield
django-q-registry
django-simple-nav
django-twc-toolbox
wagtail-heroicons

As well as two templates, one for actual Django projects and one for installable packages/apps:

django-twc-package
django-twc-project

None of them are super popular, some I maintain better than others (😂), but they all share the same modern Python packaging approach using only a pyproject.toml file and hatch as a build backend.
I also have experience building and packaging Python projects using other approaches (setup.{cfg,py}, setuptools, build, etc..) but it has been a bit since meaningfully interacting with packages in that way. Similarly, I have used tools like poetry in the past and have dabbled with rye on a couple projects.
Please tell us about your GitHub Actions experience?
I have extensive GitHub Actions experience. As mentioned previously, as a Jazzband member that's generally the types of contributions I have made: tweaking the job matrix when a new Python/Django version is released or and old one goes EOL.
I'm also big into fully leveraging the platform to help making maintaining a project easier. For instance, instead of maintaining a job matrix by hand, I use the ability for nox (my testing tool of choice for distributable packages) to output it's own job matrix in a JSON format and use that to create the test matrix for GitHub Actions:
https://github.com/westerveltco/django-simple-nav/blob/39b54464892910c4c1f140a103776526dd15efac/.github/workflows/test.yml#L32-L34
https://github.com/westerveltco/django-simple-nav/blob/39b54464892910c4c1f140a103776526dd15efac/.github/workflows/test.yml#L42
As well, going beyond the typical push or pull_request workflow triggers, I have fully automated the release process here using the release.released trigger and the PyPI Trusted Publisher authentication: https://github.com/westerveltco/django-simple-nav/blob/39b54464892910c4c1f140a103776526dd15efac/.github/workflows/release.yml
I have also written a few custom actions to be used in other GHA workflows, though nothing anything more involved than the composite actions.
How long do you expect to be involved with Django Commons?
As long as the time requirements were reasonable, I see no reason not to be involved in at least some capacity as long as I'm still using Django. If the time burden became too much for me to handle or I transitioned to a new position where I was not using Django day-to-day, I would reassess then.
Code of Conduct

[X] I agree to follow Django Commons's Code of Conduct

Thanks Josh! I'm going to let this sit for a week to give time to other folks to apply.

Please see https://github.com/orgs/django-commons/discussions/19. I'm not sure if the tag actually pinged you.

Thanks for your interest Josh! Right now the roster is full, but the expectation is that we'll cycle people in and out of roles over time. I'll circle back with you when we get to that point.

@tim-schilling Thanjs for the update. That's very exciting that there was so much interest this early in helping out! 🎉
Happy to help out the mission of the org in anyway I can. 😄

Hi @joshuadavidthomas, do you mind marking your membership as public? This helps show people have confidence in the org. https://github.com/orgs/django-commons/people


troubleshoot: convert to using common makefile and scripts

Issue #, if available:
Description of changes:
Adds checksums and artifacts validation and switches to using the new common makefile and build scripts.
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troubleshoot-tooling-presubmit
403d211903ae7ff5a66fc682a0e45682cf1a4c90
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Avoid copying the data on squeeze and unsqueeze.

This change is likely to break a lot of models as it will result in non-contiguous tensors at various places. On the other end, it avoids some unnecessary copies in transformers that use the qkv layout for the self-attention weights.


plots: Update "smoothtemplate to matchlinear`

The linear template has different sizes and additional features (i.e. on hover labels).

Closed in https://github.com/iterative/dvc-render/pull/40


Questions about features

Hi guys,
I'm mobile developer and I liked flutter so much. I already  did use native platform, xamarin, nativescript and j2objc.
I have same questions about flutter:

How flutter work with sqlite? Can I use a sqlite dart plugin in flutter?

Can I use in real projects or is not recommended? How old is flutter? flutter has a road map with future plans?

Can I access images (ios and android) using native platform resource structure? (res/drawable, icon.png icon@2x.png).

Can I interact with another apps? For example facebook login or google login. Android's onActivityResult can implemented with Custom platform-specific code?

Can I work with android services? For example, alarm app that open specific activity with reminder or finalize action, or so a push notifications that, when pressed, too open specific activity. Can I get activity data bundle to redirect app to widget x or widget y?

All "magic" happen only in one FlutterViewController (ios) and one FlutterActivity (android)? If yes, this is answer to same questions.

These are same questions that passed in my head after read the documentation. I'm not found issues with this questions or if found did not is clear.
Sorry if my english is ugly.
Thanks!

I'm not sure the issue tracker is the best place for questions and answers.  It's more for tracking problems or requesting new features.  These sorts of questions are better asked on the mailing list https://groups.google.com/forum/#!forum/flutter-dev or on Stack Overflow.  I'll answer them briefly here, but if you want to follow up, please do so on the mailing list.

How flutter work with sqlite? Can I use a sqlite dart plugin in flutter?

We don't have any built-in support for sqlite.  You'd need to make a plugin.

Can I use in real projects or is not recommended? How old is flutter? flutter has a road map with future plans?

Flutter is currently a technology preview.  People have written production apps with Flutter, but you should be aware that the project will continue to evolve.  We haven't published a roadmap (see https://en.wikipedia.org/wiki/Forward-looking_statement for some context), but you can see what we're currently working on by looking at the milestones in our issue tracker.

Can I access images (ios and android) using native platform resource structure? (res/drawable, icon.png icon@2x.png).

Not directly.  We have our own resource format.  See https://flutter.io/assets-and-images/.

Can I interact with another apps? For example facebook login or google login. Android's onActivityResult can implemented with Custom platform-specific code?

Yes.  The plugin system is what lets you do that.

Can I work with android services? For example, alarm app that open specific activity with reminder or finalize action, or so a push notifications that, when pressed, too open specific activity. Can I get activity data bundle to redirect app to widget x or widget y?

Yes.  The plugin system is what lets you do that.

All "magic" happen only in one FlutterViewController (ios) and one FlutterActivity (android)? If yes, this is answer to same questions.

You can have multiple FlutterViewController/FlutterActivity visible at once if you like.  The most common case is to have one though.
Thanks!

FWIW here's the docs for how our plugins work and how you can make your own: https://flutter.io/platform-plugins/


Change Fixvalues

At the moment I Change the Fixvalues with a REST command directly send from Home assistant. I only Change "WW Sollwert".
Would be nice to do this with your custom component.
Read all changeable values and generate a Switch for ON/OFF entitys, Input_Select for multiple Status Like ON/OFF/Auto and a Climate entity for Tempratures and so on...
Do you think this is possible?

The CMI API I use for the queries is read only. Which rest command do you use to change the values?

Its not the official API but it works ;)
rest_command:
heizung_warmwasser_34_grad:
url: http://USERNAME:PASSWORD@cmi.fritz.box/INCLUDE/change.cgi?changeadrx2=0400144414D101&changetox2=34.0
headers:
Referer: http://cmi.fritz.box/schema.html
heizung_warmwasser_43_grad:
url: http://USERNAME:PASSWORD@cmi.fritz.box/INCLUDE/change.cgi?changeadrx2=0400144414D101&changetox2=43.0
headers:
Referer: http://cmi.fritz.box/schema.html
I have debugged the web-request and try and error. The Header Referer is not optional! It will not work without this header...
I dont know if a generic solution is possible.
I want to achive the following:
-> like a thermostat in HA:
-> current_temprature = WW_ISTWERT
-> set_temprature = WW_SOLLWERT
this should be a real climate-entity in HA -> nice and usable UI

In the CMI, one can define MODBUS sources as inputs. see https://help.ta.co.at/EN/CMIHELP/modbus_1.htm?ms=CQAQCA%3D%3D&st=MA%3D%3D&sct=MA%3D%3D&mw=MjQw#
The inputs are read in a defined interval.
Would it be possible to provide MODBUS outputs which could be used as inputs as described above?
That is, you don't have to set the value from HA, but the CMI requests it. Therefore, no API to write to the CMI is needed.
I would like to use an information available in HA as an input to control heater circuit 2.

How about this:
use Deers TA-CMI integration for reading values from CMI and acting on these data in HA for comfort only.
then use the HA modbus component (see here: https://www.home-assistant.io/integrations/modbus/) for writing data to the UVR?
at least thats what I will try to setup, as i want a pwm pump and a pmw controlled relay to act on settings collected by HA and then provided by modbus to CMI. and just in case if HA goes down, the uvr will have a backup plan for emergency operations with no comfy, but still hot water and heating available...

I think that the suggested way of mannebk79 is the best solution to change values. So I will close the issue.


Wrap private headers into BlueLib framework

Tested locally, all test can pass. Current Xcode on CircleCI is not up to date, it may fail

thanks for refactoring this! Let me know when it is ready to be reviewed.

ready for review @oliverhu, @ob


[BENS] Add subgraph for mode domain name service

Used the subgraph-writer tool to create the mode-subgraph for indexing the Mode Name Service.

result
total 14188, 14029 domains in sdg1.domain, 159 invalid domains

curl -X POST --data '{"jsonrpc":"2.0","method":"eth_call","params":[{"to":"0xca3a57e014937c29526de98e4a8a334a7d04792b","data":"0x18160ddd"},"latest"],"id":1}' https://sepolia.mode.network | jq .result
"0x000000000000000000000000000000000000000000000000000000000000376c"
/var/lib/docker/containers/f33d936a1dc3f3fba98cb3f5c1e0d8558818605a235f04f57f4e7fe9c4d8d312# wc -l invalid.log
159 invalid.log

LTGM, tested in staging environment


unable to parse schema: type of kind OBJECT can not be used as input

Looks like being able to pass a custom object as an input value is not allowed although it appears to be part of the graphql api:
http://graphql.org/learn/queries/#mutations
Is this something that's planned or would you be willing to accept a pull request for this?

Whoops.  User error.

So I arrived here after a quick googling and wondered what was wrong, and wished OP has posted how he solved :).
So here is how:
I wrote the Input type as:
  ...
}

And it should be:
  ...
}

I am pretty sure this is like the fifth time I come to this bug to realize my mistake as well :crying_cat_face: . It would be nice if the error message contained something like "Maybe you meant to use 'input XXX' instead of 'type XXX' in your schema?"

Hello Folks, I'm getting similar error and tried everything within my knowledge by going through whatever I could find online. Please let me know what I'm missing here.
Error:
panic: field "Pet": type of kind OBJECT can not be used as input
        used by (*resolver.RootResolver).AddPet

I have schema defined in a different package, below is my schema:
const Schema = `schema {
    mutation: Mutation
}

type Pet {
    id: String!
    name: String!
    tag: String!
}

input PetInput {
    id: String!
    name: String!
    tag: String!
}

type Mutation {
    addPet(pet: PetInput!): Pet!
}`

Here is my resolver code:
type RootResolver3 struct {
	p *model.Pet
}

func (r *RootResolver3) AddPet(ctx context.Context, args *PetInput) (*model.Pet, error) {
     // some code
}

func (pet *RootResolver3) Id(ctx context.Context) *string {
	return &pet.p.Id
}
func (pet *RootResolver3) Name(ctx context.Context) *string {
	return &pet.p.Name
}
func (pet *RootResolver3) Tag(ctx context.Context) *string {
	return &pet.p.Tag
}

Not sure how you got from an almost working solution in #381 to this one. :)
I assume your PetInput is defined as this:
type PetInput struct {
  ID string
  Name string
  Tag string
}

If that is not the case please include it.
The error message is because you are defining args as a pointer of type PetInput, when it should actually be defined like
args struct {
  Pet PetInput
}

In GraphQL the input parameters are named and can be provided in any order. That's why you need the additional struct.
I even guess your args can be defined as
args struct {
  Pet model.Pet
}

Based on your schema, there is no difference between Pet and PetInput. So it is most likely that you can use the same struct for both GraphQL types.
Furthermore your AddPet method returns *model.Pet but at the same time your resolver declares methods for receiving the ID, name and tag. You most likely want to return a PetResolver which implements these methods or enable resolving fields directly from your model.Pet in the options when parsing your schema.
There are good examples provided for simple issues like these in the readme.

Thanks @stefanberkner for the detailed reply. I was able to get through https://github.com/graph-gophers/graphql-go/issues/381 but ended up here. Hope I'm not running in circles. :)
Initially I was using the single struct as you mentioned to avoid redundancy. I had Pet as type and input in Schema but it was not working so thought of having separate PetInput.
Maybe I should have posted that error.
I reverted back to single struct Pet
type Pet struct {
	Id   string
	Name string
	Tag  string
}

Added Pet as input in Schema:
type Pet {
    id: String!
    name: String!
    tag: String!
}

input Pet {
    id: String!
    name: String!
    tag: String!
}

type Mutation {
    addPet(pet: Pet!): Pet!
}

To add further, as my server is running with UseFieldResolvers(), I removed the extra methods from the resolver. Now my Resolver looks like this:
func (r *RootResolver3) AddPet(ctx context.Context, args struct{ Pet *model.Pet }) (*model.Pet, error)

This throws below error:
panic: invalid type: Pet
If I use args struct{ Pet model.Pet }, still the error persists.

Your code, without the pointers, should be correct. But now you renamed PetInput into Pet in your schema, which causes it to be declared twice, once as type and once as input. Please note, that in order to work, you can still use the same struct in go, but have two different definitions in your schema.

If that still doesn't help, please create a small repo to show the issue.

@stefanberkner Looks like I was making a rookie mistake with the graphql schema definition. Thanks for being patient. It worked after I changed the input name in schema to PetInput.


How do I use sidebar with a fullwidth top header?

I'm trying to use this plugin to create the sidebar, but I need a top header aswell for the entire viewport. As it is now, the sidebar dominates the left (or right) side, leaving the attempts to create a fullwidth header div out.
Is there anyway to achieve this?

The sidebar is positioned absolute. So just wrap it in a container that keeps space for the header will do.

How would you do that? I can't seem to make it work.
 <Router>
      <Router>

          {/* Div wrapped around like this? With 50px space */}

            <Sidebar {...sidebarProps}>
              {menuButton}

            </Sidebar>

      </Router>


Ensure ProgressLoggingFixture build service is fully initialized

Before registering it as a listener as it could start receiving events from a separate thread immediatelly.

@bot-gradle test this

OK, I've already triggered the following builds for you:

PullRequestFeedback build

@bot-gradle test and merge

Your PR is queued. See the queue page for details.

OK, I've already triggered a build for you.


Added OAuth2 token refresher for Gitlab

Fixes the bug (reported here) introduced by recent changes to Gitlab token expiration. Blatant copy-paste of Gitea implementation (please feel free to improve if problematic), but tested and working on our local Drone deployment.

 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.

any update?

Is there any reason why this has not been merged yet ? Any Gitlab >=15.0.0 is pretty much broken without this. Since it's just refreshing the token older Gitlab Versions should not have any Problems as far as i can see.


(notepadplusplus) IconUrl is wrong

https://github.com/chocolatey/chocolatey-coreteampackages/blob/edcff7ffc5e59d7ad2ff170987d5b7b4d0fb4195/automatic/notepadplusplus/notepadplusplus.nuspec#L36
It should point to the result of https://raw.githubusercontent.com/chocolatey/chocolatey-coreteampackages/master/icons/notepadplusplus.png

This should get automatically fixed by the Update-IconUrl.ps1 script. I will leave this to @AdmiringWorm to take a look at.

Cool

I've added a change to the update icon url script in https://github.com/chocolatey/chocolatey-coreteampackages/commit/14cbbb83a8d3c95c04be9434bc400ed5aa87a9d2
this will then update the icon urls the next time the notepad++ packages is updated.
I'll leave this open until then though.


New Release

Hello, would it be possible to create a new release to include #111 in a release version? :)
I'm not a fan of having to pull git versions of packages.
Thank you!

@arokem Can you build a new release please?

Done


chore(package): update devDependencies

Notable Changes

Commit Message Summary (CHANGELOG)
chore(package): update `devDependencies`

Type

[x] Chore

SemVer

[x] Fix (:label: Patch)

Issues

None

Checklist

[x] Lint and unit tests pass with my changes
[x] I have added tests that prove my fix is effective/works
[x] I have added necessary documentation (if appropriate)
[x] Any dependent changes are merged and published in downstream modules

Coverage remained the same at 98.058% when pulling 63537330db4efa822defe8f93726f0187117511d on chore/devDeps into c1306bdb3cba5832b7b859dd455feba3f0bdd0af on master.

Coverage remained the same at 98.058% when pulling 63537330db4efa822defe8f93726f0187117511d on chore/devDeps into c1306bdb3cba5832b7b859dd455feba3f0bdd0af on master.


Victor VosMottor: Blacklist taninsima.com

Victor VosMottor requests the blacklist of the website taninsima\.com. See the MS search here and the Stack Exchange search in text, in URLs, and in code.

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

Single TP, not eligible.


Remove public enabled option is not taking effect

When changing remove public enabled on the theme, configuration is saved but the behavior is not changed

Duplicate of #701. Is assigned to Bianca

Note that this is a SynBioHub1 issue actually, since it does not work with SBH1 either


traffic_ctl: Remove the hardcoded big buffer and use a stream buffer instead.

This is only for traffic_ctl
The approach is to use a simple stream buffer instead of the big allocation. In the past we had to create a super buffer as a workaround to allocate big responses from the JSONRPC server,  this pr is made tackle that issue so on small responses this will just use the fixed buffer(100x smaller than before), if response contains more than the fixed buffer then it will save the data into a stringstream and reuse the already allocated buffer.
Fixes https://github.com/apache/trafficserver/issues/10052

[approve ci autest]


Add Multi-Search template API

Closes #2107
Checklist

[x] By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license and subject to the Developers Certificate of Origin.
For more information on following Developer Certificate of Origin and signing off your commits, please check here.

@msfroh: Any interest in taking a look at this one?

Looks good to me overall!
Let me see if I can get some users with more experience with the _msearch APIs to take a look...

Looks good to me overall!
Let me see if I can get some users with more experience with the _msearch APIs to take a look...

That would be great!


Working Type Alias Example

Hi all,
since Key was recently removed, it is not entirely clear, how to reach the same functionality using type aliases. I would like to create two different instances of the class (with different parameters), and inject them using those aliases.
Does anybody have a working example? Thanks

ok, it seems that I've found what I've been looking for in the tests:
def test_callable_provider_injection():
    Name = NewType("Name", str)
    Message = NewType("Message", str)

    @inject
    def create_message(name: Name):
        return "Hello, " + name

    def configure(binder):
        binder.bind(Name, to="John")
        binder.bind(Message, to=create_message)

    injector = Injector([configure])
    msg = injector.get(Message)
    assert msg == "Hello, John"


Re-center image view after changing imageSize

Fixes https://github.com/kciter/Floaty/issues/135

Thank you!


Fix ExcludeSystemEventsFilter Regex

The value for the Regex in the ExcludeSystemEventsFilter convenience function includes leading and trailing / characters. Using this function will cause all events not also including a leading and trailing / character to be filtered from the subscription, not just system events.
All test have been run and are passing locally following the test guidelines contained in the README.

Hey @amccall-eigt,
Thanks for opening that PR!
Could you consider adding some tests to it, please?
You can have a look at this PR if you need some ideas (it's in Rust though): https://github.com/EventStore/EventStoreDB-Client-Rust/pull/135/files

Hey @YoEight,
I found this issue while evaluating EventStore for an upcoming project. We actually aren't going to move ahead with EventStore, and I don't have any additional time to put into the PR right now.
I might have some time to add tests in the next couple of weeks, if you would like to let this PR sit here until then.

Done here: https://github.com/EventStore/EventStore-Client-Go/pull/116


Unzip doesn't handle embedded folder in zip file

Hisoft Modula 2.zip
Unzipping this seems to make the embedded folder name as the file name after unzip (truncated), but the file type is the type as expected.
I would expect the embedded folder name to be sort of ignored.

Which flavour and version of UNZIP are you using?
Lars Nelson did some work stripping pathnames for the Z-System release - and this hasn't been
backported to the other versions (I think).  I'll have a look at this when I get time this coming weekend.
In the meantime as a work-around, please try re-creating the zip file without pathnames (extract the files then create a new zip by adding files without a directory specification - i.e. do it when the current directory has the files you wish to add).
If you're using Windows, select the group of files (using Ctrl-left mouse click to select each file) right click and choose Send-to compressed folder from the File Explorer.
For Linux/macOS something like -
cd /tmp
unzip ~/Downloads/Hisoft.Modula.2.zip
cd Hisoft\ Modula\2/
mv ./-VERSION.130 ./VERSION.130
zip -j hisoftmod2.zip *


Always report what's getting downloaded and to where

Signed-off-by: Pedro Algarvio<EMAIL_ADDRESS>

My changes make it so relenv fetch and relenv toolchain fetch always display the url and location but relenv build will only display the url and location under CICD (So as not to interfere with the fancy 'ui')


Segmentation Fault on NRP

When attempting to run the orange example on NRP it failed after running for about 80 minutes with the following error:
WARN: Killing pending tasks (2)
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGBUS (0x7) at pc=0x00007f169850cb12, pid=8, tid=0x00007f1681b1eb10
#
# JRE version: OpenJDK Runtime Environment (8.0_212-b04) (build 1.8.0_212-b04)
# Java VM: OpenJDK 64-Bit Server VM (25.212-b04 mixed mode linux-amd64 compressed oops)
# Derivative: IcedTea 3.12.0
# Distribution: Custom build (Sat May  4 17:33:35 UTC 2019)
# Problematic frame:
# C  [ld-musl-x86_64.so.1+0x50b12]  memcpy+0x2c
#
# Core dump written. Default location: /workspace/alucinor/core or core.8
#
# An error report file with more information is saved as:
# /tmp/hs_err_pid8.log
/bin/bash: line 1:     8 Segmentation fault      nextflow run systemsgenetics/AnnoTater -name loving-crick

The output references a report file that I think is saved somewhere on NRP but I have no idea how to look for it let alone get it.

Attempted to run it again last night on NRP. It failed with a completely different error:
Error executing process > 'nr_index'

Caused by:
  Host is unreachable (Host unreachable)

WARN: Killing pending tasks (2)

@4ctrl-alt-del The first error looks like nextflow itself had a segfault, this has happened to me before but I think it's usually something you can ignore and just run again. As for the second error, you can zoom in on the nr_index process to see why this error is happening.

How do I "zoom in"?

@4ctrl-alt-del we can chat on zooming in as that's just debugging with Nextflow.

After several updates annotator still crashes on NRP but now with different symptoms since we met last week @spficklin .
Nextflow Output:
$ nextflow -C nextflow.config kuberun systemsgenetics/AnnoTater -v deepgtex-prp -config k8s
Pod started: sleepy-stonebraker
N E X T F L O W  ~  version 19.07.0
Launching `systemsgenetics/AnnoTater` [sleepy-stonebraker] - revision: 3a6106836d [master]
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [3fc8a01d8b]

General Information:
--------------------
  Profile(s):         standard
  Container Engine:   null

Input Files:
-----------------
  Transcript (mRNA) file:     /workspace/alucinor/examples/Citrus_sinensis-orange1.1g015632m.g.fasta

Data Files:
-----------------
  InterProScan data:          /workspace/alucinor/dbs/interproscan/interproscan-5.36-75.0/data
  Panther data:               /workspace/alucinor/dbs/panther/panther
  NCBI nr data:               /workspace/alucinor/dbs/nr
  Uniprot SwissProt data:     null

Output Parameters:
------------------
  Output directory:           /workspace/alucinor/output

WARN: The channel `create` method is deprecated -- it will be removed in a future release
WARN: The channel `create` method is deprecated -- it will be removed in a future release
WARN: The channel `create` method is deprecated -- it will be removed in a future release
[1d/66d9bf] Submitted process > uniprot_sprot_index
[57/216ad9] Submitted process > interproscan (1)
[57/216ad9] NOTE: Process `interproscan (1)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[c2/4bf64d] Submitted process > interproscan (2)
[c2/4bf64d] NOTE: Process `interproscan (2)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[07/a2081b] Submitted process > interproscan (3)
[07/a2081b] NOTE: Process `interproscan (3)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[cc/46fac4] Submitted process > interproscan (4)
[cc/46fac4] NOTE: Process `interproscan (4)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[37/030adf] Submitted process > interproscan (5)
[1d/66d9bf] NOTE: Process `uniprot_sprot_index` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[ef/8bb7c4] Submitted process > interproscan (6)
[37/030adf] NOTE: Process `interproscan (5)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[5f/7be243] Submitted process > interproscan (8)
[ef/8bb7c4] NOTE: Process `interproscan (6)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[51/2477cc] Submitted process > interproscan (7)
[51/2477cc] NOTE: Process `interproscan (7)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[51/64ec62] Submitted process > interproscan (9)
[51/64ec62] NOTE: Process `interproscan (9)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[87/5b15f3] Re-submitted process > interproscan (1)
[87/5b15f3] NOTE: Process `interproscan (1)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[36/b3eac3] Re-submitted process > interproscan (2)
[36/b3eac3] NOTE: Process `interproscan (2)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[ba/1fc40b] Re-submitted process > interproscan (3)
[ba/1fc40b] NOTE: Process `interproscan (3)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[b0/eab735] Re-submitted process > interproscan (4)
[b0/eab735] NOTE: Process `interproscan (4)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[ac/c9c649] Re-submitted process > uniprot_sprot_index
[ac/c9c649] NOTE: Process `uniprot_sprot_index` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[94/8ae03b] Re-submitted process > interproscan (5)
[94/8ae03b] NOTE: Process `interproscan (5)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[b3/c6bdca] Re-submitted process > interproscan (6)
[b3/c6bdca] NOTE: Process `interproscan (6)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[9c/6752db] Re-submitted process > interproscan (7)
[9c/6752db] NOTE: Process `interproscan (7)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[93/a6465c] Re-submitted process > interproscan (9)
[93/a6465c] NOTE: Process `interproscan (9)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (2)
[cc/7e335a] Re-submitted process > interproscan (1)
[cc/7e335a] NOTE: Process `interproscan (1)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[bf/b77aac] Re-submitted process > interproscan (2)
[bf/b77aac] NOTE: Process `interproscan (2)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[a2/beeb6b] Re-submitted process > interproscan (3)
[a2/beeb6b] NOTE: Process `interproscan (3)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[65/b8a814] Re-submitted process > interproscan (4)
[5f/7be243] NOTE: Process `interproscan (8)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1)
[5b/572060] Re-submitted process > uniprot_sprot_index
[65/b8a814] NOTE: Process `interproscan (4)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[7b/404af2] Re-submitted process > interproscan (5)
[5b/572060] NOTE: Process `uniprot_sprot_index` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[2c/93f504] Re-submitted process > interproscan (6)
[2c/93f504] NOTE: Process `interproscan (6)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[c1/45e520] Re-submitted process > interproscan (7)
[c1/45e520] NOTE: Process `interproscan (7)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[e6/556203] Re-submitted process > interproscan (9)
[e6/556203] NOTE: Process `interproscan (9)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[af/60d69b] Re-submitted process > interproscan (1)
[7b/404af2] NOTE: Process `interproscan (5)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (3)
[4d/04d4bb] Re-submitted process > interproscan (2)
Error executing process > 'interproscan (1)'

Caused by:
  Process `interproscan (1)` terminated for an unknown reason -- Likely it has been terminated by the external system

Command executed:

  # Call InterProScan on a single sequence.
  /usr/local/interproscan/interproscan.sh       -f TSV,XML       --goterms       --input Citrus_sinensis-orange1.1g015632m.g.1.fasta       --iprlookup       --pathways       --seqtype n       --cpu 2       --output-dir .       --mode standalone       --applications TIGRFAM,SFLD,SUPERFAMILY,Gene3D,Hamap,Coils,ProSiteProfiles,SMART,CDD,PRINTS,Pfam,MobiDBLite,PIRSF,PANTHER,ProDom
  # Remove the temp directory created by InterProScan
  rm -rf ./temp

Command exit status:
  -

Command output:
  (empty)

Command wrapper:
  failed to open log file "/var/log/pods/deepgtex-prp_nf-af60d69b8398944dafaa6751f7bfd421_b4dc3618-aae1-42a6-9cbb-1111d4b8b591/nf-af60d69b8398944dafaa6751f7bfd421/0.log": open /var/log/pods/deepgtex-prp_nf-af60d69b8398944dafaa6751f7bfd421_b4dc3618-aae1-42a6-9cbb-1111d4b8b591/nf-af60d69b8398944dafaa6751f7bfd421/0.log: no such file or directory

Work dir:
  /workspace/alucinor/work/af/60d69b8398944dafaa6751f7bfd421

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

WARN: Killing pending tasks (1)
[cd/c3d25f] Re-submitted process > interproscan (3)

The nextflow pods fail like so by listing the pods(edited to only show relevant ones):
nf-0078adb7054e494d4126beb5997be320   0/1     ContainerCannotRun   0
nf-07a2081bb14b91da55ea20cdfb83f7ce   0/1     ContainerCannotRun   0
nf-16cf64fed2f31a71c5b6a10074adb37d   0/1     ContainerCannotRun   0
nf-1d66d9bfa25327a55b199d486f390157   0/1     ContainerCannotRun   0
nf-1e3d82e0a449ce29490dd222d74bba7f   0/1     ContainerCannotRun   0
nf-1e3f38e6389bfab8b5769a4d320d00f8   0/1     ContainerCannotRun   0
nf-2c93f504a81c1d580efeaa1272b57323   0/1     ContainerCannotRun   0
nf-350f991eeb346fa80f424230df61aeba   0/1     ContainerCannotRun   0
nf-36b3eac3752b61ab4a014f431c374b61   0/1     ContainerCannotRun   0
nf-37030adf4bb3cf15eabcb17bc386c867   0/1     ContainerCannotRun   0
nf-37c39c333f5f8a0619af8524be89eef7   0/1     ContainerCannotRun   0
nf-3d3ca5e92338652b4a527072b913cb9b   0/1     ContainerCannotRun   0
nf-40a98fa862a3671be782de37c69ceb38   0/1     ContainerCannotRun   0
nf-4fbf7849e74c02f2db6116cd25e5fac6   0/1     ContainerCannotRun   0
nf-512477cc0a4695d3d5157ad772c9b5ee   0/1     ContainerCannotRun   0
nf-5164ec624049083330ae3472e66171bb   0/1     ContainerCannotRun   0
nf-57216ad99d5a2598c2d46ab686f42ed0   0/1     ContainerCannotRun   0
nf-5b572060f014127d19ce649de3f5fccd   0/1     ContainerCannotRun   0
nf-5d9129748cb8da1cff983f40ca105613   0/1     ContainerCannotRun   0
nf-5f7be243d47a2f3d423d308505f7033b   0/1     ContainerCannotRun   0
nf-60f900d6c4d4041765523e21e1900602   0/1     ContainerCannotRun   0
nf-65b8a814cfd1f45cd23de76df03e44a2   0/1     ContainerCannotRun   0
nf-74de832c08ae08cf5b54080a567d5d97   0/1     ContainerCannotRun   0
nf-7a8b4b7ae0069a01b833502cd214ad50   0/1     ContainerCannotRun   0
nf-7b404af203b317917cf042b697eac010   0/1     ContainerCannotRun   0
nf-7bdb137a1555f4569c38fea6e9ffa7f7   0/1     ContainerCannotRun   0
nf-835cafb1458000c2569223baa00fc988   0/1     ContainerCannotRun   0
nf-875b15f357a68b66c2433786d4a9ca06   0/1     ContainerCannotRun   0
nf-90f95c296a72831d0bf3293e27881192   0/1     ContainerCannotRun   0
nf-93a6465c0a758758cb6ee389939657e7   0/1     ContainerCannotRun   0
nf-948ae03b8896ed77c249625b45731225   0/1     ContainerCannotRun   0
nf-9653ded58c2ef48c0030bce88bd32737   0/1     ContainerCannotRun   0
nf-9c6752db58268bb36619ab9711d8a2a4   0/1     ContainerCannotRun   0
nf-a2beeb6b27374abeb8f8dfa773a29c95   0/1     ContainerCannotRun   0
nf-acc9c649c27e80707007f8a4252c6db5   0/1     ContainerCannotRun   0
nf-af60d69b8398944dafaa6751f7bfd421   0/1     ContainerCannotRun   0
nf-b0eab7351dcc264ba82358b25a0cae48   0/1     ContainerCannotRun   0
nf-b3c6bdca7c95b5462994caf0a1678443   0/1     ContainerCannotRun   0
nf-ba1fc40bee86602fdb360e253c65e813   0/1     ContainerCannotRun   0
nf-bfb77aac557543fcc057c13d03939a35   0/1     ContainerCannotRun   0
nf-c145e5205552aa9d3ffb03e1b65a21b4   0/1     ContainerCannotRun   0
nf-c24bf64d574036b12d465f5e257c3539   0/1     ContainerCannotRun   0
nf-c4936b7d5aa3ca588f991b61eadb01cd   0/1     ContainerCannotRun   0
nf-c55f1a09ca91e605b2cb7225b3fec9d6   0/1     ContainerCannotRun   0
nf-cc46fac44d29439581b7c628159f21e9   0/1     ContainerCannotRun   0
nf-cc7e335ac8ab3e7926ee0c5e9f0d7130   0/1     ContainerCannotRun   0
nf-d83a66947a8b5467aea005933f2175dc   0/1     ContainerCannotRun   0
nf-da702cde232c10e27e66c6cf8db8d296   0/1     ContainerCannotRun   0
nf-dd5a33d85229589098906ef25c6f25bf   0/1     ContainerCannotRun   0
nf-e64b4e480d77a0f670cbf1a06f83d5a2   0/1     ContainerCannotRun   0
nf-e65562036991862d43d5755bc0d2a7f6   0/1     ContainerCannotRun   0
nf-eb503542269fa919938d75a76b479f58   0/1     ContainerCannotRun   0
nf-edc41c1ce3186f9b953e129c35a68c95   0/1     ContainerCannotRun   0
nf-edf90d5b07682ff32dcd1ada9546d959   0/1     ContainerCannotRun   0
nf-ef8bb7c4338ec8c8b07f074b77d8ee2e   0/1     ContainerCannotRun   0
nf-f44fdf4f347459801c6213acc98cef40   0/1     ContainerCannotRun   0
nf-f85d06a143a58008ba732034f05b2d14   0/1     ContainerCannotRun   0
nf-faed0088f3308a96d0660ba3cfd82626   0/1     ContainerCannotRun   0

I attempted to run it twice and it produced the identical crash.

You can debug further by inspecting the output of an individual pod:
kubectl logs <pod-name>

And also by inspecting the work directory of the process that failed (at least the one that nextflow prints when it terminates):
cd  /workspace/alucinor/work/af/60d69b8398944dafaa6751f7bfd421
ls -al

kubectl logs  (This is the same for ALL crashed pods)
failed to open log file "/var/log/pods/deepgtex-prp_nf-f5c1244025c3be17f2b1a93ef8d61276_7bfa933c-1a09-40a5-a4b4-528ac1a0a142/nf-f5c1244025c3be17f2b1a93ef8d61276/0.log": open /var/log/pods/deepgtex-prp_nf-f5c1244025c3be17f2b1a93ef8d61276_7bfa933c-1a09-40a5-a4b4-528ac1a0a142/nf-f5c1244025c3be17f2b1a93ef8d61276/0.log: no such file or directory

Looking at /workspace/alucinor/work/...:
total 10
drwxr-xr-x 1 root root    3 Oct 28 20:07 .
drwxr-xr-x 1 root root    2 Oct 28 20:07 ..
-rw-r--r-- 1 root root  342 Oct 28 20:07 .command.log
-rw-r--r-- 1 root root 8606 Oct 28 20:07 .command.run
-rw-r--r-- 1 root root  130 Oct 28 20:07 .command.sh

cat .command.log:
failed to open log file "/var/log/pods/deepgtex-prp_nf-ca10407be0e24fb80121ed298ecb6d23_216a3a19-406f-4ab9-a847-4fbba65abeb6/nf-ca10407be0e24fb80121ed298ecb6d23/0.log": open /var/log/pods/deepgtex-prp_nf-ca10407be0e24fb80121ed298ecb6d23_216a3a19-406f-4ab9-a847-4fbba65abeb6/nf-ca10407be0e24fb80121ed298ecb6d23/0.log: no such file or directory

cat .command.run
#!/bin/bash
# NEXTFLOW TASK: uniprot_sprot_index
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}

nxf_tree() {
    local pid=$1

    declare -a ALL_CHILDREN
    while read P PP;do
        ALL_CHILDREN[$PP]+=" $P"
    done < <(ps -e -o pid= -o ppid=)

    pstat() {
        local x_pid=$1
        local STATUS=$(2> /dev/null < /proc/$1/status egrep 'Vm|ctxt')

        if [ $? = 0 ]; then
        local  x_vsz=$(echo "$STATUS" | grep VmSize | awk '{print $2}' || echo -n '0')
        local  x_rss=$(echo "$STATUS" | grep VmRSS | awk '{print $2}' || echo -n '0')
        local x_peak=$(echo "$STATUS" | egrep 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
        local x_pmem=$(awk -v rss=$x_rss -v mem_tot=$mem_tot 'BEGIN {printf "%.0f", rss/mem_tot*100*10}' || echo -n '0')
        local vol_ctxt=$(echo "$STATUS" | grep '\bvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
        local inv_ctxt=$(echo "$STATUS" | grep '\bnonvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
        cpu_stat[x_pid]="$x_pid $x_pmem $x_vsz $x_rss $x_peak $vol_ctxt $inv_ctxt"
        fi
    }

    pwalk() {
        pstat $1
        for i in ${ALL_CHILDREN[$1]:=}; do pwalk $i; done
    }

    pwalk $1
}

nxf_stat() {
    cpu_stat=()
    nxf_tree $1

    declare -a sum=(0 0 0 0 0 0 0 0)
    local pid
    local i
    for pid in "${!cpu_stat[@]}"; do
        local row=(${cpu_stat[pid]})
        [ $NXF_DEBUG = 1 ] && echo "++ stat mem=${row[*]}"
        for i in "${!row[@]}"; do
        if [ $i != 0 ]; then
            sum[i]=$((sum[i]+row[i]))
        fi
        done
    done

    [ $NXF_DEBUG = 1 ] && echo -e "++ stat SUM=${sum[*]}"

    for i in {1..7}; do
        if [ ${sum[i]} -lt ${cpu_peak[i]} ]; then
            sum[i]=${cpu_peak[i]}
        else
            cpu_peak[i]=${sum[i]}
        fi
    done

    [ $NXF_DEBUG = 1 ] && echo -e "++ stat PEAK=${sum[*]}\n"
    nxf_stat_ret=(${sum[*]})
}

nxf_sleep() {
  sleep $1 2>/dev/null || sleep 1;
}

nxf_mem_watch() {
    set -o pipefail
    local pid=$1
    local trace_file=.command.trace
    local count=0;
    declare -a cpu_stat=(0 0 0 0 0 0 0 0)
    declare -a cpu_peak=(0 0 0 0 0 0 0 0)
    local mem_tot=$(< /proc/meminfo grep MemTotal | awk '{print $2}')
    local timeout
    local DONE
    local STOP=''

    [ $NXF_DEBUG = 1 ] && nxf_sleep 0.2 && ps fx

    while true; do
        nxf_stat $pid
        if [ $count -lt 10 ]; then timeout=1;
        elif [ $count -lt 120 ]; then timeout=5;
        else timeout=30;
        fi
        read -t $timeout -r DONE || true
        [[ $DONE ]] && break
        if [ ! -e /proc/$pid ]; then
            [ ! $STOP ] && STOP=$(nxf_date)
            [ $(($(nxf_date)-STOP)) -gt 10000 ] && break
        fi
        count=$((count+1))
    done

    echo "%mem=${nxf_stat_ret[1]}"      >> $trace_file
    echo "vmem=${nxf_stat_ret[2]}"      >> $trace_file
    echo "rss=${nxf_stat_ret[3]}"       >> $trace_file
    echo "peak_vmem=${nxf_stat_ret[4]}" >> $trace_file
    echo "peak_rss=${nxf_stat_ret[5]}"  >> $trace_file
    echo "vol_ctxt=${nxf_stat_ret[6]}"  >> $trace_file
    echo "inv_ctxt=${nxf_stat_ret[7]}"  >> $trace_file
}

nxf_write_trace() {
    echo "nextflow.trace/v2"           > $trace_file
    echo "realtime=$wall_time"         >> $trace_file
    echo "%cpu=$ucpu"                  >> $trace_file
    echo "rchar=${io_stat1[0]}"        >> $trace_file
    echo "wchar=${io_stat1[1]}"        >> $trace_file
    echo "syscr=${io_stat1[2]}"        >> $trace_file
    echo "syscw=${io_stat1[3]}"        >> $trace_file
    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
}

nxf_trace_mac() {
    local start_millis=$(nxf_date)

    /bin/bash -ue /workspace/alucinor/work/ca/10407be0e24fb80121ed298ecb6d23/.command.sh

    local end_millis=$(nxf_date)
    local wall_time=$((end_millis-start_millis))
    local ucpu=''
    local io_stat1=('' '' '' '' '' '')
    nxf_write_trace
}

nxf_trace_linux() {
    local pid=$$
    local num_cpus=$(< /proc/cpuinfo grep '^processor' -c)
    local tot_time0=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
    local cpu_time0=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
    local io_stat0=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
    local start_millis=$(nxf_date)

    command -v ps &>/dev/null || { >&2 echo "Command 'ps' required by nextflow to collect task metrics cannot be found"; exit 1; }

    /bin/bash -ue /workspace/alucinor/work/ca/10407be0e24fb80121ed298ecb6d23/.command.sh &
    local task=$!

    exec 10> >(nxf_mem_watch $task)
    local mem_proc=$!

    wait $task

    local end_millis=$(nxf_date)
    local tot_time1=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
    local cpu_time1=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
    local ucpu=$(awk -v p1=$cpu_time1 -v p0=$cpu_time0 -v t1=$tot_time1 -v t0=$tot_time0 -v n=$num_cpus 'BEGIN { pct=(p1-p0)/(t1-t0)*100*n; printf("%.0f", pct>0 ? pct : 0) }' )

    local io_stat1=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
    local i
    for i in {0..5}; do
        io_stat1[i]=$((io_stat1[i]-io_stat0[i]))
    done

    local wall_time=$((end_millis-start_millis))
    [ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}"

    echo "nextflow.trace/v2"           > $trace_file
    echo "realtime=$wall_time"         >> $trace_file
    echo "%cpu=$ucpu"                  >> $trace_file
    echo "rchar=${io_stat1[0]}"        >> $trace_file
    echo "wchar=${io_stat1[1]}"        >> $trace_file
    echo "syscr=${io_stat1[2]}"        >> $trace_file
    echo "syscw=${io_stat1[3]}"        >> $trace_file
    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
    echo "write_bytes=${io_stat1[5]}"  >> $trace_file

    echo 'DONE' >&10
    wait $mem_proc 2>/dev/null || true
    while [ -e /proc/$mem_proc ]; do nxf_sleep 0.1; done
    [ ${NXF_OWNER:=''} ] && chown -fR --from root $NXF_OWNER /workspace/alucinor/work/ca/10407be0e24fb80121ed298ecb6d23/{*,.*} || true
}

nxf_trace() {
    local trace_file=.command.trace
    touch $trace_file
    if [[ $(uname) = Darwin ]]; then
        nxf_trace_mac
    else
        nxf_trace_linux
    fi
}

nxf_date() {
    local ts=$(date +%s%3N); [[ $ts == *3N ]] && date +%s000 || echo $ts
}

nxf_env() {
    echo '============= task environment ============='
    env | sort | sed "s/\(.*\)AWS\(.*\)=\(.\{6\}\).*/\1AWS\2=\3xxxxxxxxxxxxx/"
    echo '============= task output =================='
}

nxf_kill() {
    declare -a children
    while read P PP;do
        children[$PP]+=" $P"
    done < <(ps -e -o pid= -o ppid=)

    kill_all() {
        [[ $1 != $$ ]] && kill $1 2>/dev/null || true
        for i in ${children[$1]:=}; do kill_all $i; done
    }

    kill_all $1
}

nxf_mktemp() {
    local base=${1:-/tmp}
    if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX
    else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX
    fi
}

on_exit() {
    exit_status=${nxf_main_ret:=$?}
    printf $exit_status > /workspace/alucinor/work/ca/10407be0e24fb80121ed298ecb6d23/.exitcode
    set +u
    [[ "$tee1" ]] && kill $tee1 2>/dev/null
    [[ "$tee2" ]] && kill $tee2 2>/dev/null
    [[ "$ctmp" ]] && rm -rf $ctmp || true
    exit $exit_status
}

on_term() {
    set +e
    [[ "$pid" ]] && nxf_kill $pid
}

nxf_launch() {
    /bin/bash /workspace/alucinor/work/ca/10407be0e24fb80121ed298ecb6d23/.command.run nxf_trace
}

nxf_stage() {
    true
}

nxf_unstage() {
    true
    [[ ${nxf_main_ret:=0} != 0 ]] && return
}

nxf_main() {
    trap on_exit EXIT
    trap on_term TERM INT USR1 USR2

    NXF_SCRATCH=''
    [[ $NXF_DEBUG > 0 ]] && nxf_env
    touch /workspace/alucinor/work/ca/10407be0e24fb80121ed298ecb6d23/.command.begin
    set +u
    set -u
    [[ $NXF_SCRATCH ]] && echo "nxf-scratch-dir $HOSTNAME:$NXF_SCRATCH" && cd $NXF_SCRATCH
    nxf_stage

    set +e
    local ctmp=$(set +u; nxf_mktemp /dev/shm 2>/dev/null || nxf_mktemp $TMPDIR)
    local cout=$ctmp/.command.out; mkfifo $cout
    local cerr=$ctmp/.command.err; mkfifo $cerr
    tee .command.out < $cout &
    tee1=$!
    tee .command.err < $cerr >&2 &
    tee2=$!
    ( nxf_launch ) >$cout 2>$cerr &
    pid=$!
    wait $pid || nxf_main_ret=$?
    wait $tee1 $tee2
    nxf_unstage
}

$NXF_ENTRY

cat .command.sh
diamond makedb       --threads 2       --in /annotater/uniprot_sprot/uniprot_sprot.fasta       --db uniprot_sprot

I am at a complete loss, am I typing the basic command wrong? This is what I run:
nextflow -C custom_nextflow.conf kuberun SystemsGenetics/AnnoTater -v deepgtex-prp -profile k8s

The containers now at least run in NRP. They immediately go to an error state because the diamond/interproscan programs fail. But at least now they have meaningful failure logs and get past container creation so I am closing this. A new issue has been made for the new type of annotater failure.


Update with rustfmt, clippy and add to CI

Should finish #12. Makes updates recommended by clippy and rustfmt and also adds them to GitHub Actions checks

Does this fail a test on clippy / rustfmt failures, or just warn with details?

Right now it fails, but I think it would make sense for either of those checks to be a warning instead

Ah. I ask because there's been some tension regarding formatting requirements (but not Clippy, actually) being seen as a cause of friction / contributor barrier to entry on the actual Rust project, so I was curious. One thing that was pointed out was that the formatting run can be automated to occur before a merge commit, which I like a lot, but have no idea how to do. I like the idea of a warning for either / both tools, though, and we should discuss adopting that more widely if people are amenable.

That makes sense! I usually have my editor set up to run rustfmt on save, but I can imagine for clippy in particular that might be more difficult.
For running before a merge commit, I think with GitHub Actions now you can have a separate user make changes and then commit them to a branch. I'd be a little worried about automated commits for the formatter, but that isn't really based on much and if it becomes an issue I think we could set that up.
Changing these to warn instead of failing seems like a good next step for now, and I can update that here, thanks for the comments!

Any other thoughts on this before I merge?


Can we get a new release soon and update js-ipld on js-ipfs?

Is this possible, @vmx? For the js-ipfs 0.28 release?

@diasdavid Feel free to do a release (or if you want, I can also do the release). It would be under the current name js-ipld-resolver. Let's target proper naming and description (https://github.com/ipld/js-ipld/issues/112) for the next release.

@vmx why not deprecate the old name and release with the new name?

@diasdavid: If we can sort out #112 that's fine for me.

@vmx I believe you have everything you need from https://github.com/ipld/js-ipld/issues/112#issuecomment-367770576

@diasdavid So I should just change the package name name and publish a 0.28 under the new name?

@vmx exactly and then deprecate ipld-resolver with the message to use just ipld.

And of course, updating it in js-ipfs-unixfs-engine and js-ipfs too :)

I don't know if there's any guidelines for deprecation messages. What a about using this one:

WARNING: This project has been renamed to "ipld". Install using "ipld" instead.

Sorry, I should've closed #93 and not this one. This one needs more work (and code changes on other packages).

@diasdavid The js-ipfs-unixfs-engine update will take a bit as currently some tests fail: https://github.com/ipfs/js-ipfs-unixfs-engine/issues/203

thanks @vmx, just incorporated your fixes, updated deps and released js-ipfs-unixfs-engine \o/

Almost there https://github.com/ipfs/js-ipfs-unixfs-engine/pull/206

got it. Confused with the refactor on js-ipfs which I also merged :) Thanks for being on top of things!

@diasdavid If you do another js-ipfs-unixfs-engine release, I think we are ready to go from an js-ipld perspective. One there's a new release of js-ipfs I'll deprecate js-ipld-resolver.

All packages that depended on ipld-resolver (https://github.com/ipfs/js-ipfs, https://github.com/ipfs/js-ipfs-unixfs-engine) switched to just "ipld". I will close this issue when I deprecated js-ipld-resolver, which I will do once https://github.com/ipfs/js-ipfs is releases. Else people will get deprecation messages during installation.

I can't deprecate ipld-resolver:
$ npm deprecate ipld-resolver@'<= 0.14.1' 'WARNING: This project has been renamed to "ipld". Install using "ipld" instead.'
npm ERR! code E422
npm ERR! Unprocessable Entity : ipld-resolver

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/vmx/.npm/_logs/2018-03-02T13_06_01_826Z-debug.log

@vmx have you reached out to npm support?

@diasdavid No I haven't, I thought I'm doing something wrong.

@vmx have you tried just with npm deprecate<EMAIL_ADDRESS>

@diasdavid Yes, also without version and putting the quotes around the name and version.


[Android] Kotlin support library dependency no longer required

At the moment, all Flutter Android Kotlin templates contain a dependency on the Kotlin support library. E.g.:
https://github.com/flutter/flutter/blob/0e2f51dfd04eca2935318389a75e8bc112809342/packages/flutter_tools/templates/app_shared/android-kotlin.tmpl/app/build.gradle.tmpl#L67-L69
Starting from Kotlin 1.4, the Kotlin Gradle plugin adds the dependency on the standard library automatically by default: (ref)

You no longer need to declare a dependency on the stdlib library in any Kotlin Gradle project, including a multiplatform one. The dependency is added by default.
The automatically added standard library will be the same version of the Kotlin Gradle plugin, since they have the same versioning.
For platform-specific source sets, the corresponding platform-specific variant of the library is used, while a common standard library is added to the rest. The Kotlin Gradle plugin will select the appropriate JVM standard library depending on the kotlinOptions.jvmTarget compiler option of your Gradle build script.

The current Kotlin version in the templates is 1.6.10:
https://github.com/flutter/flutter/blob/1bfb7400c8ce546fd19ffd93b458ded583d9ada5/packages/flutter_tools/lib/src/android/gradle_utils.dart#L32
So the explicit dependency to the Kotlin support library dependency is no longer required.

Hi @davidmigloz I get crashes with or without the Kotlin references https://github.com/flutter/flutter/issues/98223#issuecomment-1040338050


support for callback configuration and ca injection

Feature Request
CRDs (for version conversion), ValidatingWebhookConfiguration and MutatingWebhookConfiguration (see also #1325) all need to define callbacks.
OLM should help setup the callback and inject the needed ca.
Is your feature request related to a problem? Please describe.
Today OLM does not provide support in setting up callbacks. These are dependent on the cluster in which the operator is being deployed and therefore OLM is the right place in which to put this logic.
Describe the solution you'd like
Assuming the callback is served by the operator pod itself, one way could be to create a service serving a certificate secret.
The service could have a single port and different contexts in case more than one callback is configured. The created secret would be mounted on the pod at a well known location by OLM.
The operator would then be able to use the secret to serve TLS callback connections.

@awgreene Can you take a look?


Real-time segmentation

Hey @GustavZ, as mentioned is the previous threads I am looking into efficient segmentation networks that can be run on the TX2. Would you mind looping me in to the conversation regarding the mask implementation? Me and rest of the team at my university are all very interested in this subject and would like to figure out the best approach for doing real-time segmentation.

I am currently working my way through the following projects / papers to come up with a ssd modification that allows segmentation in parallel to bounding box detection.
Please feel free to add code proposals or other sources if you find some.
I will keep you up to date as i proceed.

https://github.com/soo89/Rainbow-SSD
https://github.com/kmlee-snu/run
https://github.com/hszhao/PSPNet
https://github.com/rykov8/ssd_keras
https://github.com/pierluigiferrari/ssd_keras
https://github.com/mrgloom/awesome-semantic-segmentation

Thanks for the links--I will be looking through them as well!
I'm also wondering if you are open to plain old segmentation models? I've found a model that is meant to achieve 7fps on the TX1: https://github.com/Eromera/erfnet_pytorch
I'll need to test it out after reading up on PyTorch but assuming the GPU RAM usage isn't overwhelming I'm considering running both the detector and the segmentation model at once.

yeah you can do this ofcourse! its a valid workaround, but i want to achieve a network that can do both simultaniously :)

Gotcha--in this case you might want to take at look at the differences between the Box predictors used for the SSD and the Mask-RCNN networks here: https://github.com/tensorflow/models/blob/master/research/object_detection/core/box_predictor.py.
I suspect you can add segmentation for the SSD boxes to use some sort of encoder-decoder network like you mentioned before. The FCN on the Mask-RCNN stuff is way too heavy for real-time. I'll have to try this later as well but unfortunately time constraints dictate I stick with what works for now!

@Kowasaki any news about this topic from your side?

@GustavZ Unfortunately no. The SSDlite-Deeplab model described in the mobilenet v2  paper is the best bet I think, but I haven't had time to look over how to implement that whole thing.
Have you found anything that works well with SSD? The SSD-Lite part described in the paper may be worth a shot.


-mc option not working for code 504/503?

Hello,
I wanted to code this myself but there is ffuf. I wanted to match response code 504 and 503, when the server timeouts for a large period of time. When ffuf reaches the limit of time, it directly skips it. Would be possible to just throw it to code 504? Since if it is taking quite a lot of time to response, probably means it will timeout.
The only fix to this I know would be to put the timeout limit to like 60 seconds, but that would make ffuf really slow. I want to send it directly to code 504 if the max time of timeout is reached.

Hi @marcelo321, this is pretty unusual usage, but looks interesting!
Probably verbose+output-log and parse it at the end would be the best option, at moment, have you checked that?

Hi, that's unfortunately kind of out of scope for ffuf. The functionality of ffuf is to allow users to match and limit based on what the server responds.
This request is kind of opposite, and I feel that having it would be kind of lying to the user as ffuf really isn't getting any HTTP response back, and assigning a non-response to an actual HTTP status code would be artificial.
That said, I see and appreciate the need behind this request, a kind of hacky workaround to accomplish what you are after would be to use -debug-log timeouts.log and parse the log file for paths afterwards. This unfortunately only gives relevant information when fuzzing URLs (instead of say, POST data).
I have been planning to add some timing attack features in the future, so this would probably be acknowledged at that phase.


Go bindgen todos

I would like to initiate a new tracking issue to categorize all the necessary steps in improving the Go bindgen experience. These steps will be divided into three categories: short-term, middle-term, and long-term. The duration of each term is not precisely defined at this point, but short-term goals would be tackled immediately after the merge of PR #471 into the main branch. Long-term goals are expected to be completed beyond 2023, while middle-term goals fall somewhere in between.
Short Term

[ ] Renable variants tests
[ ] Figure out utf16 string conversion from Go to C and vice versa. This will re-enable tests/runtime/string tests
[ ] Improve the ergonomics of Go bindings, including splitting interfaces to different go packages, and the variant, result and option's generated APIs.
[ ]  Use Ns to create local variables to improve readable on the genereated Go code.

Middle Term

[ ] Investigate how go:generate will help to generate the bindings for user programs without using the CLI

Long Term

[ ] change the TinyGo runtime to mainline Go compiler once it supports WASI target.
[ ] change the arhitecture from depending on C bindings to the component model canonical ABI

Performance-wise, I have done some rudimentary benchmark tests on a standard HTTP server that dispatches each HTTP request to a wasm component compiled from Rust and TinyGo. Here is the result:
Rust

TinyGo

You can see that the Rust compiled Wasm component's throughput is three times that of TinyGo. I suspect that the performance difference largely is contributed by the double copy of memory in type conversion between Go and C.

I've done some porting of the python component model MVP to pure go here: https://github.com/patrickhuber/go-wasm/tree/6015b8d07aaa1fc902fee44b01d1ebd6fded3d65/abi
More tests are needed for records, variants etc but strings and basic types are working.

@patrickhuber glad to hear! Let me know if you ran into any issues.

I completed the unit tests suite included in the component model MVP. I'm going to try to replace some of the generated code with the go abi I created and see what challenges I run into.

Awesome!! @patrickhuber


JSON builder does not handle properly GStrings

When post'ing JSON data, looks like the builder only allows String values.
The following fails with a StackOverflowException
def value =  "a"
client.post() {
    json param: value
}

The following works:
def value =  "a"
client.post() {
    json param: value.toString()
}

Thanks for reporting this.  Should be fixed in v0.5.2 which should show up in maven central within the hour.


PUP-8949 use install_options with 'latest' methods

Prior to this commit ...
The 'latest_with_new_pip' and 'latest_with_old_pip methods' (called by the
'latest' method) failed to execute pip install with the resource's
install_options attribute, potentially resulting in a lack of idempotency.
With this commit ...
Any 'install_options' are applied whenever 'install' is executed.

CLA signed by all contributors.

jenkins please test this on debian8-64a,debian8-32a,debian9-64a,debian9-32a,fedora28-64a,fedora29-64a,osx1012-64a,osx1013-64a,osx1014-64a,redhat5-64a,centos6-64a,centos6-32a,redhat7-64a,redhat8-64a,redhatfips7-64a,sles11-64a,sles11-32a,sles12-64a,sles12-POWERa,sles15-64a,solaris10-64a,solaris114-64a,ubuntu1404-64a,ubuntu1404-32a,ubuntu1604-64a,ubuntu1604-32a,ubuntu1804-64a,windows2016-64a,windows2019-64a

looks good, please add rspec/acceptance tests

I've added unit tests, but would need help with acceptance tests as none exist now.

We are generally missing acceptance tests for package managers ...
I had similar issue for yum/rpm and I created some basic tests: https://github.com/puppetlabs/puppet/blob/90fa5152fa5c92e7d499fe0d38c10636c7d7e737/acceptance/tests/provider/package/rpm_ensure_install_multiversion_package.rb
Pls check and let me know if more help is needed.

I added a commit with potential acceptance tests.
I did not run them yet, I need to learn/setup them locally.

I’ve added multiple acceptance tests. If the others need to be broken out
into another PR, or they need to be refactored, please let me know.
Tom Kishel
Senior Support Engineer
<EMAIL_ADDRESS>Puppet. The shortest path to better software.

There is a potential issue or two with PATH in our acceptance test environment ... documented in comments in acceptance/tests/provider/package/gem.rb

I think this is done. I’ll submit a separate PR for gem acceptance tests, and post my findings regarding path issues in beaker.

jenkins please test this on debian8-64a,debian8-32a,debian9-64a,debian9-32a,fedora28-64a,fedora29-64a,osx1012-64a,osx1013-64a,osx1014-64a,redhat5-64a,centos6-64a,centos6-32a,redhat7-64a,redhat8-64a,redhatfips7-64a,sles11-64a,sles11-32a,sles12-64a,sles12-POWERa,sles15-64a,solaris10-64a,solaris114-64a,ubuntu1404-64a,ubuntu1404-32a,ubuntu1604-64a,ubuntu1604-32a,ubuntu1804-64a,windows2016-64a,windows2019-64a


Implement client for artifact show and versions.

Depends on https://github.com/shakenfist/shakenfist/pull/976

CI failure is unrelated.


everyday working map

@imjohnzakkam,  This is the most important part which almost everyone wants i.e. heat map of numbers of question solved per day like present in Codeforces and Leetcode.

I'm sorry replying to you after so long, it is very hard to get the problems solved by each user in the CodeChef API so we think it can't be done, but thanks for your idea! If you want you can fork and request a pull, would be glad ;)


Review Mexico scrapers

@yolile reports that the publisher sends new links via email regularly but we've not been able to ascertain a programmatic way of getting the latest data. It may or may not be the same data as we get via the current API URL - we should compare.

Also - inai and CDMX - may have updates that require changes to the scrapers

Also - found reference to "Ministry of Communications Telecom PPP" in the CRM - but couldn't find any data


THRIFT-3876 haxe js/nodejs client

only http transport is supported
testing of browser js made via phantomjs
tutorial of browser js uses haxe-php web server for files delivery
default implementation of haxe's HttpClient reimplemented/patched:

browser js implemented to support binary encoding (avoid any utf8 conversions)
for nodejs implemented non-async client (via ChildProcess.spawnSync and it's slow)

makefile for tests updated to avoid sleeps (it kills server when client stops)

Good work!

Some of the added files lack the ASF Header. Not sure about package.json, but phantom-js-client.test.js should have one.

It does seem like this could be refactored into a base implementation holding the common code and then an implementation per #ifdef branch that was introduced to clean it up.

@Jens-G

phantom-js-client.test.js should have one.
ASF header has been added

Was this set of changes tested with "make cross" as part of the build?

@Jens-G any thoughts on what needs to happen next?

After I read that the cross tests doesn't need to be made because "it doesn't work anyway" my enthusiasm for this patch was basically send to zero . First, this is a plain lie. Second, when I read such statements it gives great insight into the attitude of the contributor. I'm not willing to even look at it anymore under that premise.

I don't care either , I had the particular issue and shared fix for the issue
I do not have time to create JIRAs for unrelated stuff nor to implement cross-platform things .
of course even asking me todo so I'm seeing for the first time in my life and I have never seen in any other foss projects
though, any maintainer have all the rights todo anything he wants

So I agree that changes like this need representation in the cross test.  It would be nice if folks could patch up any ill will and move this forward.


Allowing magnitude entries above 32k blows up SB binary pack

Magnitude vales above 32k are incorrectly handled by PackBinarySuperblock(std::string sBlock).
struct BinaryResearcher
{
    std::array<unsigned char, 16> cpid;
    int16_t magnitude;
};

Uses a signed 16 bit integer, but htobe16 is unsigned. This means that values above 32767 will actually be represented as negative BinaryResearcher.magnitudes. This corrects itself in the unpack though, but is still not a good idea.

This is not really directly an issue anymore. We will still be limiting the magnitude to 32k or less for security reasons.


Wizard's config to hideFooter

As we have hideHeader, in some wizard we need to hideFooter (the change could be dynamic) allow full size windows for the main content.
In https://github.com/patternfly/patternfly-ng/blob/master/src/app/wizard/examples/wizard-basic-example.component.ts#L107 replace by:
     this.wizardConfig = {
       title: 'Wizard Title',
       sidebarStyleClass: 'example-wizard-sidebar',
       stepStyleClass: 'example-wizard-step',
      hideFooter: true
     } as WizardConfig;

to enable hideFooter option.

This would allow the wizard to be used as a modal, but it would break the PatterfnFly wizard pattern.
Since #115 has been closed, I'll close this issue as well.


Bug in readme-text

readme-text fails if find-readme didn't find a README.
I've made a small fix here: https://github.com/daimrod/manifest/commit/f34c88b7c121c82721e7d1e8cb6991742bceadc5

Ah, I just noticed that same bug and pushed a fix. Thanks for filing the issue.


code suggestion

chore: fix acronyms
chore: use tb variable for testing.TB
fix: potential Slowloris Attack
refactor: restore the context, do not create one
fix: use the expect Content-Type for OpenAPI
chore: remove useless variables
chore: rename method and variable to comply the acronym
chore: use http constant
test: fix inverted got-want
test: make sure to close res.Body
test: make sure to context is cancelled
refactor: simplify panic recovery
refactor: use type assertion and errors.Is to validate the server aborted
refactor: do not use sprintf when sprint can be used
refactor: invert if statement to make it clearer

I applied the requested changes and suggestions

Sorry if it seems like I'm being overly critical during the code review,
this type is not official, i'll fix it and merge this pr


Total time for the Mission should be 1 hour 15 mins

Mission URL: https://developers.sap.com/mission.cp-starter-integration-cpi.html
Here the total time for the Mission should be 1 hour 15 mins
Set Up Integration Suite Trial - 30 mins
Design and Test Your First Integration Flow - 45 mins
Total- 1 hr 15 mins
Labels:
Landscape: trail1, trail2, trail3
Label: SCPTest-2010A
Scenario Label: SCPTest-cloudin
Priority: Low
Best Regards,
Priyanka

Hi @PriyankaShivakumar,
Thanks for the feedback.
Hi @thecodester and  @MichaelCzcz ,
Could you please update the mission time to 1 hr 15 mins?

Appreciate your help.

Hi @PriyankaShivakumar ,
The concern has been addressed and updated in the system.
The issue can be closed now.


Initial solution of Integration tests control.

'sbt test' now does no run Integration tests
To run IT ot DB tests is needed to call extra command defined in .sbtrc

@miroslavpojer Please help me understand why there is testIT and testDB. Wouldn't testIT be enough?

Both commands are solved in different ways. So a different name.
Tests in database 'module' are testing db functions - so testDB looks ok.
testDB is used on request of @benedeki - see comments above.

Both commands represent a generic group of Integration tests so testIT is a generic name, sure. I will use it everywhere, where I do not have any reason to change - see reasons for testDB above.

@miroslavpojer Please help me understand why there is testIT and testDB. Wouldn't testIT be enough?

* Both commands are solved in different ways. So a different name.

* Tests in database 'module' are testing db functions - so `testDB` looks ok.

* `testDB` is used on request of @benedeki - see comments above.

Both commands represent a generic group of Integration tests so testIT is a generic name, sure. I will use it everywhere, where I do not have any reason to change - see reasons for testDB above.

Thanks for explanation. I guess If we intend to follow a convention of having a "database" module in our projects for sql functions and their tests it's reasonable to have a dedicated command.

This item depends on:

AbsaOSS/atum-service#196
By Dependent Issues.

This item depends on:

AbsaOSS/atum-service#196
By Dependent Issues.


Don’t set a log level on import

In 4233e0773d03b12eb52b2205cd007569c836c33f we started calling logging.basicConfig and in 40bdcbb88653162c13b839f886a53967c66c1fd1 we changed the global log level to INFO. This means that everyone’s logging configuration is overridden (not nice) and they start seeing INFO-level noise from all modules!
Python modules should never call any code with global side effects on import. logging.basicConfig goes into __main__.
@falexwolf said that the goal was to have similar output to scanpy’s. The problem is that scanpy uses its own logging infrastructure instead of python’s. My proposal:

get rid of this side effect
get rid of scanpy’s logging infrastructure and use python’s (theislab/scanpy#256)

We can still use our own logging format and set scanpy and anndata to INFO level like this:
logger = logging.getLogger(__name__)
logger.propagate = False  # Don’t pass log messages on to the root logger and its handler
logger.setLevel('INFO')

handler = logging.StreamHandler(sys.stderr)  # Why did we use stdout?
handler.setFormatter(logging.Formatter('%(message)s'))
handler.setLevel('INFO')
logger.addHandler(handler)

See https://github.com/theislab/scanpy/issues/256#issuecomment-418711035.
Regarding use of stdout: stderr makes all your notebooks red on the slightest warning. Looks awful.

hahaha this is a completely unexpected reason for this decision.
well, logs belong into stderr. maybe we can autodetect if we’re in an ipython notebook like this, and use stdout in case we are.