cluster fails to restart when service_catalog = true

When we stop the server and restart it, then we get this k8s service catalog error
Origin version : 3.9.0-alpha3
Command used:
ansible-playbook -i inventory/cloud_host playbook/cluster.yml -e openshift_node=masters -e openshift_release_tag_name=v3.9.0-alpha.3 --tags "down"
ansible-playbook -i inventory/cloud_host playbook/cluster.yml -e openshift_node=masters -e openshift_release_tag_name=v3.9.0-alpha.3 --tags "start"

Error
{
  "changed": true,
  "cmd": [
    "oc",
    "cluster",
    "up",
    "--version=v3.9.0-alpha.3",
    "--host-config-dir=/var/lib/origin/openshift.local.config",
    "--host-data-dir=/var/lib/openshift/data",
    "--host-volumes-dir=/var/lib/openshift/volumes",
    "--host-pv-dir=/var/lib/openshift/pv",
    "--use-existing-config=True",
    "--public-hostname=<IP_ADDRESS>",
    "--routing-suffix=<IP_ADDRESS>.nip.io",
    "--loglevel=1",
    "--service-catalog=True"
  ],
  "delta": "0:00:13.124961",
  "end": "2018-03-28 10:00:57.619554",
  "msg": "non-zero return code",
  "rc": 1,
  "start": "2018-03-28 10:00:44.494593",
  "stderr": "I0328 10:00:46.889982    3674 helper.go:585] Copying OpenShift config to local directory /tmp/openshift-config211463473",
  "stderr_lines": [
    "I0328 10:00:46.889982    3674 helper.go:585] Copying OpenShift config to local directory /tmp/openshift-config211463473"
  ],
  "stdout": "-- Checking OpenShift client ... \n-- Checking Docker client ... \n-- Checking Docker version ... \n-- Checking for existing OpenShift container ... \n-- Checking for openshift/origin:v3.9.0-alpha.3 image ... \n-- Checking Docker daemon configuration ... \n-- Checking for available ports ... \n-- Checking type of volume mount ... \n\n   Using nsenter mounter for OpenShift volumes\n-- Creating host directories ... \n-- Finding server IP ... \n\n   Using public hostname IP <IP_ADDRESS> as the host IP\n   Using <IP_ADDRESS> as the server IP\n-- Checking service catalog version requirements ... \n-- Starting OpenShift container ... \n\n   Starting OpenShift using container 'origin'\n   Waiting for API server to start listening\n   OpenShift server started\n-- Registering template service broker with service catalog ... \nFAIL\n   Error: cannot register the template service broker\n   Caused By:\n     Error: cannot create objects from template openshift-infra/template-service-broker-registration\n     Caused By:\n       Error: unable to recognize servicecatalog.k8s.io/v1beta1, Kind=ClusterServiceBroker: no matches for servicecatalog.k8s.io/, Kind=ClusterServiceBroker",
  "stdout_lines": [
    "-- Checking OpenShift client ... ",
    "-- Checking Docker client ... ",
    "-- Checking Docker version ... ",
    "-- Checking for existing OpenShift container ... ",
    "-- Checking for openshift/origin:v3.9.0-alpha.3 image ... ",
    "-- Checking Docker daemon configuration ... ",
    "-- Checking for available ports ... ",
    "-- Checking type of volume mount ... ",
    "",
    "   Using nsenter mounter for OpenShift volumes",
    "-- Creating host directories ... ",
    "-- Finding server IP ... ",
    "",
    "   Using public hostname IP <IP_ADDRESS> as the host IP",
    "   Using <IP_ADDRESS> as the server IP",
    "-- Checking service catalog version requirements ... ",
    "-- Starting OpenShift container ... ",
    "",
    "   Starting OpenShift using container 'origin'",
    "   Waiting for API server to start listening",
    "   OpenShift server started",
    "-- Registering template service broker with service catalog ... ",
    "FAIL",
    "   Error: cannot register the template service broker",
    "   Caused By:",
    "     Error: cannot create objects from template openshift-infra/template-service-broker-registration",
    "     Caused By:",
    "       Error: unable to recognize servicecatalog.k8s.io/v1beta1, Kind=ClusterServiceBroker: no matches for servicecatalog.k8s.io/, Kind=ClusterServiceBroker"
  ]
}

Same error with Origin version 3.9.0

I don't see any easy way around this for the time being... It's probably some weird race condition during startup

Problem resolved since origin 3.9.0 latest version as service catalog has been released using openshift-playbook or minishift. Can we check again using cluster up and close it if it works ?


added new cloud functions

Added new cloud function
Function that triggers user firestore
and after the user has changed avatar id, the function checks: that such an id is in the user's photo collection or a non-empty id is set, otherwise it changes to the previous identifier

@googlebot I signed it!

@googlebot I signed it!

@googlebot I fixed it.

closing for same reason as #648


The current github-sync.sh doesn't support SSH as described in readme

You have

If source_repo is private or with another provider, either (1) use an authenticated HTTPS repo clone url like<EMAIL_ADDRESS>or (2) set a SSH_PRIVATE_KEY secret environment variable and use the SSH clone url (emphasis added)

https://github.com/repo-sync/github-sync/blob/3832fe8e2be32372e1b3970bbae8e7079edeec88/github-sync.sh#L32
Still sets the remote url to https which prevents the use of SSH key secrets.
Please advise if there is something else which I might be missing in configuring this to work and I've just overlooked?

Closing as I'm not sure I'm correct.

Got it working by adding<EMAIL_ADDRESS>as the full source_repo

Got it working by adding<EMAIL_ADDRESS>as the full source_repo

Hi @R-K-H have you resolved the issue? looks like this is still HTTPS not SSH
Even HTTPS, how to set ${{access_token}}?
Thanks.


Import pulumi code and import sigstore GH data

Summary
This PR import the Pulumi GitHub sync from https://github.com/cpanato/pulumi-github-sync, setup the pulumi account and import the existing GitHub Sigstore data to Pulumi
We have a Pulumi open source project account
TODO:

add the CI automation, in progress here: https://github.com/sigstore/community/pull/59
Add more documentation (will do as follow-up)
and check the integration with Pulumi, need this PR and #59 to test

/assign @dlorenc @lukehinds @bobcallaway

I think the only real thing this is missing is some documentation. At a minimum we should get:

Instructions on how to operate the infrastructure for the infra team
Instructions for community members on how to add themselves to the org
Instructions for community members on how to create and configure a new repo

If this is a pure import, then I think we should leave it as is rather than review the permissions now. IMO, we should get this merged and operational, then do a pass on the actual permissions and see what we can clean up.

community members on how to ad

was planning to do this in a follow-up to reduce the PR size and make it easier to review

was planning to do this in a follow-up to reduce the PR size and make it easier to review

Sgtm


refactor(semantic): check directive by current_scope_id

Current dependencies on/for this PR:

main

PR #2411   👈

This stack of pull requests is managed by Graphite.


adding basic auth details for as2 connectors

The implementation has changed after architecture review. We have another PR for this change now - https://github.com/mulesoft/docs-connectors/pull/573/files


Use standard formula for CDB_ZoomFromScale

This comes from #197
The maximum zoom, previously limited to 23 is now limited to a higher value, and is returned even
when the scale denominator is 0 (for which the actual level would be infinite) to avoid breaking
some cases where a 0 is used as a dummy scale denominator as here:
https://github.com/CartoDB/Windshaft/blob/2cd43d4b2ca2b3487ede8423f698b282c6e53af4/lib/windshaft/backends/attributes.js#L81
This would be a problem for example for the queries used for overview tables, which will yield no result for a null zoom level, causing that example to fail.

@rafatower please review

I'm keeping the CASE to avoid converting the function to PL/PGSQL

:+1:


[Question] about penalty term

I was going through the code of "feature_histogram.hpp" and got a question about the penalty terms in the loss function. Its gain is evaluated in
static double GetLeafSplitGainGivenOutput(double sum_gradients, double sum_hessians, double l1, double l2, double output) {
    const double sg_l1 = ThresholdL1(sum_gradients, l1);
    return -(2.0 * sg_l1 * output + (sum_hessians + l2) * output * output);
  }

The output is the leaf value that incorporates both the penalizing effect of reg_alpha (l1) and reg_lambda (l2).
My question: Where is the l1 penalty being added to the gain? I'd expect a + l1 * abs(output) somewhere. Maybe I am not looking at the right code piece?

@mayer79 it is not linear model or neural networks, the l1 is not added into gain directly.
The L1 and L2 are applied into leaf outputs, then we use "regularized" outputs to calculate split gains.

@guolinke hmm, bhe l2 penalty is added to the gain (`output * output * l2), so I was expecting the same for l1. XGBoost adds it, see the answer to my question https://github.com/dmlc/xgboost/issues/4464

@mayer79 this function is introduced in this PR:
it is another form of:
double abs_sum_gradients = std::fabs(sum_gradients);
double reg_abs_sum_gradients = std::max(0.0, abs_sum_gradients - l1);
return (reg_abs_sum_gradients * reg_abs_sum_gradients) / (sum_hessians + l2);

which is the same as:
https://github.com/dmlc/xgboost/blob/17df5fd296aaff18123c53a777f24111b3dd7336/src/tree/split_evaluator.cc#L145
for another form of xgboost:
weight * (2.0 * stats.sum_grad + stats.sum_hess * weight
        + params_.reg_lambda * weight)
        + 2.0 * params_.reg_alpha * std::abs(weight);

where weight is
-ThresholdL1(stats.sum_grad, params_.reg_alpha) / (stats.sum_hess + params_.reg_lambda);

Combine them, you will find it is the same as the one used in lightgbm.

The output resp. leaf weights are definitively similar, fully agree with that. But are the split gains? The additive term params_.reg_alpha * std::abs(weight) is difficult to track in lgb. I will need paper and pen ;-).

@guolinke: going again through the calculations showed that you are completely (and obviously) right. Thx for the explanations.


Godot C# exports crash on launch if solution/project/assembly names don't match

Tested versions

Reproducible in v4.2.2.stable.mono.official [15073afe3]

System information
M2 macOS - Sonoma 14.4.1
Issue description / repro steps
This is very easy to repro on both macOS and Windows.

Make a new Godot project named "GodotRepro"
Make a scene with anything in it (I just added icon.svg as a Sprite2D to be able to tell that the project launched correctly)
Attach a C# script to the root of the scene. Use the Node2D template, although it's just the existence of C# that matters for this repro.
Either rename the .sln file that got created or rename the dotnet/project/assembly_name project setting to "Repro" (not "GodotRepro")

At this point, if you press the ▶ button in the editor, the game will run, but if you export to macOS or Windows, the resulting app will segfault.
It would be good if Godot could detect that you're in a scenario where your assembly name doesn't match your solution or project and tell you about it. These repro steps were a simplified version of what I had done, which is to make a game for many, many hours and then finally try exporting it only to find that the resulting app would crash. 😢
Minimal reproduction project (MRP)
repro.zip
Other notes
If anyone searching for this issue finds themselves in this situation, the solution is very easy: just make sure your assembly name matches everywhere that it's referenced. For me, I just renamed my .sln file and also the project name within it. They're all Game now. 😅

Godot is not building your C# project because it can't find it, so it assumes it's a GDScript-only project. The crash happens because the game tries to load a .cs Resource but .NET is not initialized (since the exported game is not a C# game).
In Godot 4.3, you'll get an error if you try to export a game with .cs Resources but Godot can't find the C# project.

https://github.com/godotengine/godot/pull/87829.

Ahh, thank you for the explanation! 🙏 I'm glad to hear that it's going to be fixed, too. 🙂


[Enhancement] Pre-process Audio

There is an interesting set of Nvidia models for audio processing:
https://docs.nvidia.com/deeplearning/maxine/audio-effects-sdk/index.html
Of particular interest are:

Noise Removal/Denoising
Acoustic Echo Cancellation (AEC)

The first could clean up input audio before it gets passed to ASR. The second takes two streams, the recorded audio and Glados's voice output, and could help remove her voice from what she's listening too. This would improve the 'interruption' feature significantly!
Looking for coders to help out with this!

The docs say it needs CUDA 11.8+
This will need to be upgraded:
https://github.com/dnhkng/GlaDOS/blob/main/Dockerfile#L1

@joecryptotoo Do you want to try working on this?

@joecryptotoo Do you want to try working on this?

I don't think I have the skills for this one, but I'm happy to help research it.

https://github.com/NVIDIA/MAXINE-AFX-SDK/tree/v1.3.0

That repo looks surprisingly old for audio AI!

This microservice might do the job.
https://catalog.ngc.nvidia.com/orgs/nvidia/teams/maxine/helm-charts/ucf-audio-multistream

I tried to download the SDK for this thing so I can run it on my Linux server on my RTX 4090 but it looks like they only support these Nvidia products on Linux: a40/a30/a2/v100/a10/t4/a16/a100
while any RTX GPU can be use on Windows

I found a discussion about this on reddit here: https://www.reddit.com/r/linux/comments/vs9pdd/for_those_who_also_want_nvidia_rtx_voice_on_linux/
Someone suggested this project as an alternative:
https://github.com/Rikorose/DeepFilterNet

See also https://pypi.org/project/audio-denoiser/

this is a really cool feature in my opinion, any luck so far?

would denoising or echo cancellation type approach really solve this issue?

The best option is to use a conference room microphone/speaker combo. They do hardware noice cancellation, and dont waste GPU VRAM on a signal processing model.


Record and prompt auth type and auth files

Record and prompt auth type and auth files

Codecov Report

Merging #971 into develop will increase coverage by 0.06%.
The diff coverage is 51.06%.

@@              Coverage Diff              @@
##             develop     #971      +/-   ##
=============================================
+ Coverage      41.71%   41.77%   +0.06%
- Complexity       773      778       +5
=============================================
  Files            153      155       +2
  Lines           5531     5570      +39
  Branches         780      780
=============================================
+ Hits            2307     2327      +20
- Misses          3055     3074      +19
  Partials         169      169

Impacted Files
Coverage Δ
Complexity Δ

...microsoft/azure/maven/auth/AzureClientFactory.java
0% <0%> (ø)
0 <0> (ø)
:arrow_down:

...java/com/microsoft/azure/auth/AzureAuthHelper.java
79.76% <100%> (+0.49%)
34 <0> (ø)
:arrow_down:

...m/microsoft/azure/auth/configuration/AuthType.java
100% <100%> (ø)
1 <1> (?)

...va/com/microsoft/azure/auth/AzureTokenWrapper.java
36% <36%> (ø)
4 <4> (?)

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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render tests have validation errors

We've removed the render tests, so this issue no longer applies.


Add San Diego

In this PR, we add a page for San Diego with a corresponding link in the towns menu.  All is working on local tests.

LGTM


Adds the Sync Map and Scene Views sample

I noticed that rotation is not always synced between the map view and the scene view. Sometimes it is, sometimes it isn't. Have you looked into that? It may be a bug.

Also, is Scenes the category used by the other SDK for this sample?

@philium This should be good to go. There is still some debate on name/category so I think we can revisit that later.

What about the rotation issue? Did you investigate that?

I wasn't able to de-sync the rotation at all.

Oh, I guess if you rotate the map view the scene view doesn't necessarily rotate. I would think this is a consequence of using the AGSViewpointType.centerAndScale to get the viewpoint, but this is what the implementations used on the other platforms so I'm not too concerned.


SHA256 Fix: InfamousJoeG.cybr-cli version 1.0.1

[x] Have you signed the Contributor License Agreement?
[x] Have you checked that there aren't other open pull requests for the same manifest update/change?
[x] This PR only modifies one (1) manifest
[x] Have you validated your manifest locally with winget validate --manifest <path>?

[x] Does your manifest conform to the 1.5 schema?

Note: <path> is the name of the directory containing the manifest you're submitting.

Microsoft Reviewers: Open in CodeFlow

I don't understand the issue here.  Can someone please explain?

Hello @infamousjoeg,
The package manager bot determined there was an issue with installing the application correctly. Please check the application installs correctly. Once repaired, please push an update to your pull request.
Template: msftbot/validationError/installation/general

I don't understand the issue here. Can someone please explain?

/azp run

Hi @infamousjoeg,
This appears to be an ephemeral error, sorry for any concern caused.

I've ran winget install --manifest ... successfully.  The pipeline is not providing any information.  Is this normal?

Automatic Validation ended with:

Installation failed with exit code -1978335187
2023-08-30 18:44:30.535 [FAIL] Installer failed security check. Url: https://github.com/infamousjoeg/cybr-cli/releases/download/v1.0.1-release/cybr-cli_1.0.1-release_windows_amd64.zip Result: 0x80004005

This is the same error as before, and 0x80004005 is essentially a 404 File Not Found error in some ways, so this usually clears after a retry. Here, however, it recurred. Please check your systems to ensure that they're uninfected. This might be a false positive, and we can retry again tomorrow.

Extremely weird.  I'm able to download directly using the URL it reported using.  Also, able to do the same via winget install --manifest ... using the manifest I've committed here.
I am trying to fix a SHA256 mismatch... could that be an issue here?  I imagine it's just targeting the local manifest like I do in my tests, as well, so probably not relevant.

@StephenGillie,
Is there something I can do here to move this forward?  I'm kind of lost on what I can provide since tests from my end  all check out.

/azp run


[Bug]: Connect to private gitlab failed due to SSLException

Is there an existing issue for this?

[X] I have searched the existing issues

Description
I followed the documentation how to use version control with git, and the git repository is my private gitlab repository with http and ssh protocal.
I deployed the key and grant write permissions to that key. But when connect to my private gitlab, I got the error:
Internal server error while processing request
From the log, I found SSLException happened: appsmith-gitlab-error.txt
And I'am sure the private gitlab is reachable from the appsmith.
How to solve this problem? Does appsmith only support https protocal's gitlab?
Steps To Reproduce

Version Control with Git（private gitlab）
Deploy the key and grant write permissions
The private gitlab is reachable from appsmith
Connect to the private gitlab, I got Internal server error while processing request，the log shows SSLException

How to solve this problem?
Public Sample App
No response
Version
appsmith 1.8.4

Is appsmith you were trying is cloud hosted(app.appsmith.com) or self-hosted?

Is appsmith you were trying is cloud hosted(app.appsmith.com) or self-hosted?

self-hosted

Copy your private gitlab SSL to /appsmith-stacks/ca-certs in crt format and restart/spin the docker container and check.

@zachary-guo Could you please whitelist cs.appsmith.com in your network? From the error it looks like the Appsmith server was unable to fetch the data from this server - cs.appsmith.com

@manikumarnune123 I can't find /appsmith-stacks direcotry. is it directly under / ? or should it under a relative direcotry? should I create that directory manually?

@zachary-guo Could you please whitelist cs.appsmith.com in your network? From the error it looks like the Appsmith server was unable to fetch the data from this server - cs.appsmith.com

I deploy appsmith locally with docker, there is no need to visit outside world. I followed manikumarnune123's step, create gitlab ssl cert, but I don't know where copy the cert to.

@zachary-guo In order for you to use the git sync feature we need to connect to cs.appsmith.com else this feature will not work.

@zachary-guo In order for you to use the git sync feature we need to connect to cs.appsmith.com else this feature will not work.

@AnaghHegde But I use private gitlab, in this case, does it necessary to connect to cs.appsmith.com ?

@zachary-guo Yes, it does. In the Community Edition for a workspace, a user can connect up to 3 private repositories to an app.

@zachary-guo Yes, it does. In the Community Edition for a workspace, a user can connect up to 3 private repositories to an app.

@AnaghHegde After whitelist to cs.appsmith.com, this time I got a different tip：
GIT CONFIGURATION ERROR
SSH Key is not configured properly. Did you forget to add SSH key to remote? Can you please try again by reconfiguring the SSH key with write access
Actually, I have done the 【deploy key】action with grant write permissions, what's the problem ?

@zachary-guo Please follow the steps from this doc - https://docs.appsmith.com/advanced-concepts/version-control-with-git/connecting-to-git-repository#for-gitlab and refer to this youtube video for adding the GitLab repository.


Documentation not found

The readme links to http://pythonhosted.org/cssselect2/ for the documentation, but it gives a 404 Not Found error.

Fixed, thanks!

A pleasure, but it still doesn't work for me.  The new link just redirects to the old one...
I find documentation for cssselect but not cssselect2... does it work for you?

Ah, yes. I pushed that "fix" in a hurry and should have checked. The docs link is a 404 because there aren’t any docs. I’ve removed the link.
I wouldn’t recommend using cssselect2 in its current state. It’s really at the "experimenting" stage. I kinda got stuck at https://github.com/SimonSapin/cssselect2/issues/1 and then moved on to other things. If you just want to use a selector matching thing today, practically I’d recommend cssselect (not 2) despite its flaws. If you’d want to develop one, cssselect2 could

You should also remove the link on the pypi page as well (the one linked to from the readme).  and ahh, okay, I will take a look at that issue tomorrow or something.
At the moment I just wanted to do some research of the software out there for css parsing, figuring out which package does what etcetera and if it will suit our needs, and this package had a nice example that covers tinycss2 as well.
I develop for matplotlib, an open-source python graph plotting programme, and a project we have had a project on the back burner for a while about introducing CSS-like style sheets which would greatly improve the usability and flexibility of the software.  If you want to get a feel for what we had in mind you can take a look at https://github.com/matplotlib/matplotlib/blob/master/doc/devel/MEP/MEP26.rst
I shy away from tinycss and cssselect as they do too much, not generic enough for custom element and property names, etcetera.
But yes, right now just play-time, and seeing if we can save ourselves some code by using an external library :).

I’ve rewritten the README to explain that this is not maintained: https://github.com/SimonSapin/cssselect2/blob/13895eed8b/README.rst


Add dev tools to pyproject.toml

Given that these dev tools is used to maintain the project, it makes sense to add them as dev dependencies so that contributors don't have to install them manually.
Tools which have been installed:

black
isort
pre-commit

This looks like the netlify integration is broken because markdown released a new version on March 14th which is incompatible with the latest version of mkdocstrings-python.
I added this "markdown<3.6" as an attempt at a workaround, but not sure if you wanted to handle that a different way.

black
isort

We are using ruff to replace these two. You may need to update the contributing guide as well.

Sure, sounds good. Will do.

Done and updated.


CLOUD-2868 OpenJDK 11 RHEL8 image

https://issues.jboss.org/browse/CLOUD-2868
This depends upon the following changes made to cct_module:
https://github.com/jboss-openshift/cct_module/pull/335

Problems to fix:

[ ] the image contains OpenJDK  8 too
failing tests:

[ ] features/image/java/java_s2i.feature:9  Check incremental builds cache .m2
[ ] features/image/java/java_s2i.feature:309  Check java perf dir owned by jboss (CLOUD-2070)

The perf dir check, at least, is failing because "spring-boot-sample-simple" from  https://github.com/jboss-openshift/openshift-examples is terminating shortly after start-up:
start-up logs
/usr/local/s2i/run: line 15: /opt/jboss/container/maven/default//scl-enable-maven: No such file or directory
Starting the Java application using /opt/jboss/container/java/run/run-java.sh ...
INFO exec  java -javaagent:/opt/jboss/container/jolokia/jolokia.jar=config=/opt/jboss/container/jolokia/etc/jolokia.properties -XX:+UseParallelOldGC -XX:MinHeapFreeRatio=10 -XX:Ma
xHeapFreeRatio=20 -XX:GCTimeRatio=4 -XX:AdaptiveSizePolicyWeight=90 -XX:MaxMetaspaceSize=100m -XX:+ExitOnOutOfMemoryError -cp "." -jar /deployments/spring-boot-sample-simple-1.5.0
.BUILD-SNAPSHOT.jar
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.jolokia.util.ClassUtil (file:/opt/jboss/container/jolokia/jolokia-jvm-1.5.0.redhat-1-agent.jar) to constructor sun.security.x509.X500Name
(java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.String)
WARNING: Please consider reporting this to the maintainers of org.jolokia.util.ClassUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
I> No access restrictor found, access to any MBean is allowed
Jolokia: Agent started with URL https://<IP_ADDRESS>:8778/jolokia/

Is jolokia the problem here?

Is jolokia the problem here?

No, disabling it wtih

The perf thing is (at least) https://github.com/jboss-openshift/openshift-examples/issues/38


Add perl-module-install to Dockerfile so Text::Markdown installs

Thanks for the PR @stigtsp, but I think this might have been fixed in 1e4585bbdc588a25cbf8671f4ee626a772fbc42a?

@jhthorsen Yep, seems like it. But does that make Module::Install a runtime dependency?

It wouldn't be a problem for most cases. But one case would be for nixpkgs where tests will succeed without Module::Install, but fail runtime if the module isn't declared as a dependency for the closure, I've hacked in a test for it in the build https://github.com/NixOS/nixpkgs/pull/88940/files#diff-01e16fbbd11c9a1dddb0abc99d8c59efR40-R41


Still able to scroll

I've tried this on Codepen and a simple page seems to work fine.
When I add it to my website, the script runs and the overflow style is applied to the body, but, I'm still able to scroll up and down the page? (Win 10 Chrome v97.0.4692.99)
Happy to provide a link privately.

yup same here.

@Staples1010 @zackees did you find a solution for this?

@nicoladj77 Sadly no :(

Try to add in your CSS:
 body, html { height: 100%; }
And also it will be better to share the example.

Try it with this package. If it doesn't work, describe the problem in detail and I'll fix it
npm i body-scroll-lock-upgrade


imported .png return plain objects instead of urls.

Steps to reproduce

Create an empty vue 3 project.
do import img from<EMAIL_ADDRESS>(I do it with alias, whatever).
log it or use it.

What is expected?
logs like this /assets/qwe876qwe.png
What is actually happening?
logs this: {} without any props or specific prototype.
System Info
Win10x64 Pro latest, Intel 14600kf, 32Gb ram, almost empty.

Any additional comments?
After this and that templating issue, I've realized, that png still do not work.

what's plugins you use? your plugin may transform images to objects. try import img from '@/assets/img.png?url' to see if it works

?url doesn't seem to do anything.
plugins:
vitePlugins: [
    vueJsx(),
    namedDirectory(),
    vue(),
    // imagemin({}),
    svgLoader({defaultImport: 'component'}),
    rollupCSSCompression(),
    replace({
      preventAssignment: true,
      'process.env.PROJECT': JSON.stringify(__dirname.split(/[\\\/]/g).pop())
    }),
    process.env.NODE_ENV=='bundle-anal' && visualizer()
  ].filter(Boolean).map(({...p}, i) => ({...p, name: p.name || `vite_plugin_${i}`})),
  plugins: [
    {
      name: '[test-transform-html-pre]',
      transformHtml: {
        order: 0, // 0 means call this hook before parse and generate resources
        executor: async ({ htmlResource }) => {
          htmlResource.bytes = [...Buffer.from(Buffer
            .from(htmlResource.bytes as any)
            .toString()
            .replace('{head}', '<meta head />')
            .replace('{styles}', '<meta style />')
            .replace('{ssr}', '<meta ssr />')
          )]
          return htmlResource
        }
      }
    },
    {
      name: '[test-transform-html-post]',
      transformHtml: {
        order: 2, // 2 means call this hook after parse and generate resources
        executor: async ({ htmlResource }) => {
          htmlResource.bytes = [...Buffer.from(Buffer
            .from(htmlResource.bytes as any)
            .toString()
            .replace(/<meta (\w+?) \/>/g, '{$1}')
          )]
          return htmlResource
        }
      }
    }
  ]

Also I've tried
assets: {
      include: ['png']
    },

in compilation.

Seems that commenting out rollupCSSCompression of fela-vue somehow does the trick. In vite or rollup it works perfectly though.

Also, take a look at .map(({...p}, i) => ({...p, name: p.name || vite_plugin_${i}})), line. This hack make it compatible with farm (porting from vite), by adding names to all plugins, even those that have not. Somehow farm throws on nonamed plugins.

I see, it's compatibility issue of vite plugins, I'll try to fix it later

Yep, sure - it's done! Yoo-Hoo! 谢谢你，亲爱的朋友! 😃

不客气！感谢支持和反馈


Update hyperv-guest.nix

for better disk performance in hyper-v, as recommended by Microsoft:
https://docs.microsoft.com/en-us/windows-server/virtualization/hyper-v/best-practices-for-running-linux-on-hyper-v

Motivation for this change
Things done

[ ] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)

[ ] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nix-review --run "nix-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[ ] Ensured that relevant documentation is up to date
[ ] Fits CONTRIBUTING.md.

Notify maintainers
cc @

I rebased on top of master and cleaned up the commit message a bit :)


How to traverse to nth node using DOM render? I am trying to test equality of select options.

Using render, how can we traverse to nth node, say, 2nd or 3rd select option and match this for equality? Using shallow or mount, I understand we have at, but for render?
Your environment
node 6
API

[x] render

Version

library
version

Enzyme
3.3.0

React
16.2.0

Adapter

[x] enzyme-adapter-react-16

Since render is just a cheerio wrapper, you can use cheerio's API to traverse.

Thanks @ljharb, I figured that out later but I reached nth node by calling next(). If you know, can you tell me to reach to  particular index directly. Like 3rd in the options or 5th select of the page for example.

Cheerio has .eq as well as .slice, those may help.


can not support in razor?

i want to use it in CSHTML
something like:

@Html.ActionLink<HomeController>(c => c.Index(5))

Razor does not like generic, so you have to surround the call in brackets:

@(Html.ActionLink<HomeController>(c => c.Index(5)))

so I got it. thanks a lot. do you have any mvc pager library? do you recommend something?

@JeffreyChan You can use https://github.com/kpi-ua/X.PagedList for paging.

Thanks a lot.


Use environment specific retry queue.

Closes #580
The issue was it was dead-lettering to an exchange with no bound queues, because everything's set up for an environment specific queue.

Hm I just approved but then I thought.. do we want a test here?

Uh. I don't know what we would test or how. I guess I could check to make sure the queue name is right?

Could we test that the queue we push it to is "#{the_queue_we_pulled_it_from}_retry"?

@hackmastera Yeah, that's what I proposed. Added test.

Coverage remained the same at 100.0% when pulling 127133c76da4d13764d7ecffb8bac55b1815cf0e on rabbitmq_retry_queue into 60a2f12ae8e34f540d4b5aea75a9aaffe74b9dec on master.


Swap the positions of grouping & headshape

The headshape dropdown should be at the top, and should not be named attributes.

This is done and further UI improvements in a2edf18


Allow home page to be easily authored in markdown

Presently, it looks like the only way to put content in the home page on a hugo site with a theme is to override the theme, by creating a file /layouts/index.html, where the contents of the home page must be inserted manually using HTML. The {{ partial "foo.html" . }} syntax can only be used to include partials which also must be HTML, not markdown.
The only way I can think of working around this is to have layouts/index.html such that it ierates over all pages, and simply filters them based on the presence of a parameter, like so:
{{ range .Data.Pages }}
	{{ if isset .Params "homeContent" }}
		{{ .Content }}
	{{ end }}
{{ end }}

However, this seems like a rather roundabout, and inefficient, way of going about things. Is there a better way?

:+1:

I tried using markdownify filter (which was added here: https://github.com/spf13/hugo/pull/652) but this doesn't work as the filter takes a string and not template.Html...
{{ partial "home.md" . | markdownify }}

Hi. My site will only have one page, and I'd like to write it in Markdown. Can you help? I still want to use Hugo because of the csv dynamic content feature.
https://stackoverflow.com/questions/30030631/how-to-build-single-page-site-from-markdown

I'm going to try to fix this.

@scottcwilson talk to @spf13 -- he had a solution in place for this, that we had to roll back cause it had some side effects.

So my initial solution was to add in a page handler to the homepage rendering function so it could handle a node (as it does now) or a page whose content was located in index.md. This proved problematic with pagination and overall quite a bit messier than I hoped.
A better approach would be to add support for nodes to have a content field and support nodes having content. We could actually do a lot of really neat things once that feature is in place with some of the automatically created urls (like taxonomy index pages) but before getting too far ahead I'd focus on just the home page (but think about how it would affect other places)..
Some things that need to happen:

We need  a mechanism and pattern to map content files to nodes. I think this is easy for the homepage just call it content/index.md, but the mapping functionality should be generic enough to be able to work for other nodes as well.
Make sure that the nodes don't appear in the Site.Pages slice. (I'm not 100% sure on this)
Check for any other conflicts.
Add documentation and tests.

The tests I already wrote for the code I submitted should still work, we just needed a better implementation.
You can find my imperfect implementation at https://github.com/spf13/hugo/commits/spf13-content-homepage

Also see #1051 -- if a Node has content it should also have frontmatter with proper title and params etc.

A general solution for nodes to contain content would be a really nice improvement!  It might make sense to provide a {{ .Site.Nodes }} variable or similar at the same time, so #1303 can be addressed.

Will be handled in #2297.

i know this thread is old,but i just happened to have the same issue..is it solved yet?

is it solved yet?

yes.


Error: Could not find or load main class org.gradle.wrapper.GradleWrapperMain - Help!

I searched stackoverflow.com, etc., with no luck. The only thing that I know about Android development is that if I see the word "Gradle", it's not going to be a good morning. Any help would be appreciated.
Note that I can create a new project and it runs fine.
Steps to Reproduce

I downloaded a student's flutter project
I cleaned the project
I attempted to run it and got this error:

Error: Could not find or load main class org.gradle.wrapper.GradleWrapperMain
Caused by: java.lang.ClassNotFoundException: org.gradle.wrapper.GradleWrapperMain
Exception: Gradle task assembleDebug failed with exit code 1
Logs

Logs

flutter run
Multiple devices found:
...
[1]: sdk gphone64 arm64 (emulator-5554)
[2]: sdk gphone64 arm64 (emulator-5556)
[3]: iPhone 14 Pro Max
[4]: macOS (macos)
[5]: Chrome (chrome)
Please choose one (To quit, press "q/Q"): 1
Using hardware rendering with device sdk gphone64 arm64. If you notice graphics artifacts, consider enabling software rendering with "--enable-software-rendering".
Launching lib/main.dart on sdk gphone64 arm64 in debug mode...
Building with Flutter multidex support enabled.
Error: Could not find or load main class org.gradle.wrapper.GradleWrapperMain
Caused by: java.lang.ClassNotFoundException: org.gradle.wrapper.GradleWrapperMain
Running Gradle task 'assembleDebug'...                             699ms
Exception: Gradle task assembleDebug failed with exit code 1

[✓] Flutter (Channel stable, 3.3.9, on macOS 13.0.1 22A400 darwin-arm, locale en-US)
    • Flutter version 3.3.9 on channel stable at /Applications/flutter
    • Upstream repository https://github.com/flutter/flutter.git
    • Framework revision b8f7f1f986 (3 days ago), 2022-11-23 06:43:51 +0900
    • Engine revision 8f2221fbef
    • Dart version 2.18.5
    • DevTools version 2.15.0

[✓] Android toolchain - develop for Android devices (Android SDK version 33.0.0)
    • Android SDK at /Users/mprogers/Library/Android/sdk
    • Platform android-33, build-tools 33.0.0
    • Java binary at: /Applications/Android Studio.app/Contents/jre/Contents/Home/bin/java
    • Java version OpenJDK Runtime Environment (build 11.0.12+0-b1504.28-7817840)
    • All Android licenses accepted.

[✓] Xcode - develop for iOS and macOS (Xcode 14.1)
    • Xcode at /Applications/Xcode.app/Contents/Developer
    • Build 14B47b
    • CocoaPods version 1.11.3

[✓] Chrome - develop for the web
    • Chrome at /Applications/Google Chrome.app/Contents/MacOS/Google Chrome

[✓] Android Studio (version 2021.2)
    • Android Studio at /Applications/Android Studio.app/Contents
    • Flutter plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build 11.0.12+0-b1504.28-7817840)

[✓] VS Code (version 1.73.1)
    • VS Code at /Applications/Visual Studio Code.app/Contents
    • Flutter extension version 3.52.0

[✓] Connected device (5 available)
    • sdk gphone64 arm64 (mobile) • emulator-5554                        • android-arm64  • Android 13 (API 33) (emulator)
    • sdk gphone64 arm64 (mobile) • emulator-5556                        • android-arm64  • Android 13 (API 33) (emulator)
    • iPhone 14 Pro Max (mobile)  • FB304F21-DA39-47D4-9B60-B99D485C8B86 • ios            • com.apple.CoreSimulator.SimRuntime.iOS-16-1 (simulator)
    • macOS (desktop)             • macos                                • darwin-arm64   • macOS 13.0.1 22A400 darwin-arm
    • Chrome (web)                • chrome                               • web-javascript • Google Chrome 107.0.5304.121

[✓] HTTP Host Availability
    • All required HTTP hosts are available

• No issues found!

I found that GradleWrapperMain was being called in gradlew, a bash script. I echoed the $CLASSPATH in my working project and my students', and compared them. Part of the assignment name was 1/3 complete, and, needless to say, that slash did  not go down well.


fix: solveByElim would add symm hypotheses to local context and make impossible-to-elaborate terms

Rather than adding symm hypotheses to the local context, it now adds them to the list of hypotheses derived from the local context.
This is not ideal for performance reasons, but it at least closes #3922.
In the future, solveByElim could maintain its own cache of facts that it updates whenever it does intro.

@semorrison I took a stab at this issue. It's likely a performance regression, but it's a big usability improvement, so maybe it's ok in the meantime?

Adding full-ci so I can look at Mathlib.

Mathlib is easy enough to fix (pushed to lean-pr-testing-3962). Agree we need to fix this despite the possible performance problems.


vectorization

Hi, thanks for the amazing work. Do you know how to vectorize the code for computing normal from depth, it is pretty slow using for loop. I tried to vectorize it but didn't work it out.
https://github.com/udaykusupati/Normal-Assisted-Stereo/blob/491c0d3d2efd0e6c9f97cf84b1688266b9c201d6/convert_normal.py#L52-L57

Hi @udaykusupati, I found a way to vectorize the code in Pytorch but without using val_mask which might cause some information loss. It's pretty hard to vectorize the computation with val_mask because each window would have a different number of valid points.
# XY: 1 x 2 x 240 x 320 (B x C x Height x Width)
# Z:  1 x 1 x 240 x 320 (B x C x Height x Width)

XYZ = torch.cat((XY, Z), dim=1)  # 1 x 3 x 240 x 320
XYZ = F.pad(XYZ, (win_sz // 2, win_sz // 2, win_sz // 2, win_sz // 2), mode='reflect')  # keep the Height and Width of the output the same as input
A = F.unfold(XYZ, kernel_size=win_sz).view(batch, 3, win_sz**2, height, width)  # 1 x 3 x win_size**2, 240, 320
A = patches.permute(0, 3, 4, 1, 2)       # 1 x 240 x 320 x 3 x win_sz**2
A_t = patches.permute(0, 1, 2, 4, 3)     # transpose 1 x 240 x 320 x win_sz**2 x 3
A_At = torch.matmul(patches, patches_t)  # 1 x 240 x 320 x 3 x 3
normal = torch.sum(torch.matmul(patches_t, patches.pinverse()), dim=-2)  # 1 x 240 x 320 x 3
normal = normal.permute(0, 3, 1, 2)  # 1 x 3 x 240 x 320

This would significantly speed up the computation, you can refer to view_as_windows for similar implementation in numpy but since it doesn't filter out the invalid points, it's a bit less accurate than your original implementation. Do you have any ideas on how I should change the value of each window according to the value of the center pixel?


Update Issue - 76155895

default description
URL tested: https://www.google.com/?gws_rd=ssl
Open URL on Browserstack

Property
Value

Browser
Chrome 73.0

Operating System
Windows 8

Resolution
1024x612

Screenshot Attached
Screenshot URL

Click here to reproduce the issue on Browserstack

Updated Screenshot Attached


Improve filtering/prioritization via tj/go-archive

Relies on https://github.com/tj/go-archive/pull/3
Also gives lower presence to .upignore after the UX step; see #84
fixes #50

Ahh interesting, I suppose ideally the ordering alone gives the next node_modules precedence, but if this works that's not bad

hmm seems a little strange that this one requires **, I'm not sure that's the same as GIT

ah damn might have to revert, adding .git should ignore .git/foo etc

yeah - I was just doing extensive testing locally, hold up on this and the other PR

Recap: tj/go-archive#3 allows users to specify only the minimum files to run their api:
* # because we use a wildcard to collect _everything_ to use node_modules in your project add /**
!node_modules/**
!index.js
!package.json


Modularize the functionality into sub-packages

Break up the ouster_tools monolithic package into the following package structure:

[ ] ouster_dhcp_wrapper
[ ] ouster_perf
[ ] ouster_ptp
[x] ouster_h5

Currently working on this on the eloquent-devel-modularization branch. May incrementally merge in changes to eloquent-devel as I make progress.

My plan is to merge the modularization of this collection of packages into a new branch called foxy-devel. I will leave eloquent-devel as-is so there will be no broken links. I know of several sources on the web and elsewhere that is currently pointing to the performance analysis work as the package is currently structured. Given that Foxy releases tomorrow, this seems like nice timing to handle things in this way.


Proposed change to project page

Move the reserved tokens into the cycle UI. Change "Withdraw" and "Mint" to "Distribute". Touch up the Tokens section.

done


Add lodash as to not reinvent the wheel

I figured I'd put this change in for a PR, I find it reasonable. Since this tool uses some custom utils, a utils file (or files, ideally) is certainly necessary. However, some of the utils that were made are very common things and have been solved before.
The lodash util library takes some of the maintenance and testing work away from vee-validate and makes life just a tad easier. I've replaced all the utils that don't need to be re-done manually with their lodash equivalents. The result is a smaller util test and sometimes more capable functions.
Advantages:

The lodash library is just really good
More utils are at the disposal of vee-validate at any given time
Using babel-plugin-lodash allows for clean and targeted imports of lodash utils
There is no need to test utils imported from lodash

Disadvantages:

The change required 3 new dependencies and switched one*

* Since we are using babel-plugin-lodash for lodash imports, we require this functionality in builds. For some reason builds were using buble, which seems awfully inconsistent. While buble provides faster builds for huge projects, the time difference on my machine between buble and babel was marginal. Using babel introduces more consistency between development and builds, which is a good thing in my opinion.

Thanks for this PR, I tested using lodash utils a while ago and it bloated the build size considerably, Maybe I incorrectly set it up then. I'm willing to accept this PR though.

808K	dist         <------>         1.4M	dist

It appears Rollup has tree shaking issues with Rollup and can't properly remove code that's unnecessary. That's unfortunate I guess, I don't think there is a fix for it.


feat: handle empty response from lookup api

:tada: This PR is included in version 1.5.0 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


pull request for e2e test at 11/29/2016 15:26:05

:white_check_mark: Validation status: passed
For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.


Get farmers endpoint

Description
Describe change or new feature here.
Checklist
Remove any items which are not applicable.

[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have made corresponding changes to the documentation
[x] I have added tests that prove my fix is effective or that my feature works AND the tests pass

 Create API endpoints to get all farmers and single farmer


Legg til migreringsjob

Migrate old rows from aktorid to fnr identifier. Setting nr. of replicas to 1, instead of having
to implement leader election to ensure that only one pod is running the job. Will be deployed
during off-work-hours to reduce traffic load from nav.no. The job may have to run several times
depending on inital result, but after all rows have been migrated, the code will be reverted.

Vet ikke om du har testet allerede, men sikkert lurt å teste kjøring i dev før den merges ✌
Ser ellers bra ut 👍


Create UI concept for contributor metrics

As discussed, I propose we integrate this into the 3d view.


Not working on Nuxt.js with TypeScript.

I tried the method of #4 which suggests using the plugin system. I followed the step and got no errors, I tried to test it but the animation is still not popping up.
<font-awesome-icon class="bars" v-if="!enabled" v-on:click="menuEnable" :icon="['fas', 'bars']"/>
<nav class="nav" v-if="enabled">
  <NuxtLink class="link" to="/about">About</NuxtLink>
  <NuxtLink class="link" to="/blog">Blog</NuxtLink>
  <NuxtLink class="link" to="/contact">Contact</NuxtLink>
  <NuxtLink class="link" to="/projects">Projects</NuxtLink>
</nav>

<script lang="ts">
import Vue from "vue";

declare module 'vue/types/vue' {
  interface Vue {
    $anime({}) : void
  }
}

export default Vue.extend({
  ...
  data: () => ({
    enabled: false
  }),
  methods: {
    menuEnable() {
      this.enabled = true;

      this.$anime({
        targets: ".nav",
        translateX: 250,
        duration: 800
      })
    },
    ...
  }
})
</script>

If you are using Nuxt plugin system (manually using external sources in separate plugins) then you do not need this module.
For typescript support, I suggest you manually install anime.js (Follow steps from #4).

Install animejs
Install @types/animejs (dev)
Setup this.$anime using the plugin system and extend the Vulcan interface as per the cookbook.

I also can't debug the incomplete code you provided.


Move pilot-hubs cluster to a regional k8s cluster for better availability

The pilot-hubs cluster (Running everything under *.pilot.2i2.clcoud) is using a simple, single apiserver zonal k8s cluster. While this is mostly ok, this can mean some downtime and reduced API reliability. It also means no 0 downtime k8s apiserver upgrades, so any upgrades of the apiserver (which happen automatically!) will cause outages.
A regional cluster is highly available, and has 3 apiservers running in a HA configuration. Gives us more reliability. https://cloud.google.com/kubernetes-engine/docs/concepts/regional-clusters has more info.
https://2i2c.freshdesk.com/a/tickets/102 is probably caused by intermittent slowness in k8s apiserver response.
Implementation

[x] Make sure regional / zonal is toggleable in our GKE terraform code (https://github.com/2i2c-org/infrastructure/pull/1251)
[ ] Create a new k8s regional cluster for pilot-hubs, as zonal clusters can not be upgraded to regional
[ ] Migrate all existing hubs to new cluster

@yuvipanda +1 from me. Even if it costs marginally more, but increases the reliability and stability of the service, or gives us extra flexibility for upgrades, I think that's preferable.

This hit the neurohackademy hub today, as a transient k8s master failure 'borked' the hub. It failed with:
[I 2022-07-30 02:24:19.658 JupyterHub log:189] 200 POST /hub/api/users/nicobruno92/activity<EMAIL_ADDRESS>86.49ms
ERROR:asyncio:Unclosed client session
client_session: <aiohttp.client.ClientSession object at 0x7f8f3d70d6a0>
[E 2022-07-30 02:24:20.351 JupyterHub reflector:351] Watching resources never recovered, giving up
    Traceback (most recent call last):
      File "/usr/local/lib/python3.9/site-packages/kubespawner/reflector.py", line 285, in _watch_and_update
        resource_version = await self._list_and_update()
      File "/usr/local/lib/python3.9/site-packages/kubespawner/reflector.py", line 228, in _list_and_update
        initial_resources_raw = await list_method(**kwargs)
      File "/usr/local/lib/python3.9/site-packages/kubernetes_asyncio/client/api_client.py", line 185, in __call_api
        response_data = await self.request(
      File "/usr/local/lib/python3.9/site-packages/kubernetes_asyncio/client/rest.py", line 193, in GET
        return (await self.request("GET", url,
      File "/usr/local/lib/python3.9/site-packages/kubernetes_asyncio/client/rest.py", line 177, in request
        r = await self.pool_manager.request(**args)
      File "/usr/local/lib/python3.9/site-packages/aiohttp/client.py", line 535, in _request
        conn = await self._connector.connect(
      File "/usr/local/lib/python3.9/site-packages/aiohttp/connector.py", line 542, in connect
        proto = await self._create_connection(req, traces, timeout)
      File "/usr/local/lib/python3.9/site-packages/aiohttp/connector.py", line 907, in _create_connection
        _, proto = await self._create_direct_connection(req, traces, timeout)
      File "/usr/local/lib/python3.9/site-packages/aiohttp/connector.py", line 1206, in _create_direct_connection
        raise last_exc
      File "/usr/local/lib/python3.9/site-packages/aiohttp/connector.py", line 1175, in _create_direct_connection
        transp, proto = await self._wrap_create_connection(
      File "/usr/local/lib/python3.9/site-packages/aiohttp/connector.py", line 992, in _wrap_create_connection
        raise client_error(req.connection_key, exc) from exc
    aiohttp.client_exceptions.ClientConnectorError: Cannot connect to host <IP_ADDRESS>:443 ssl:default [Connect call failed ('<IP_ADDRESS>', 443)]

[C 2022-07-30 02:24:20.352 JupyterHub spawner:2326] Pods reflector failed, halting Hub.
ERROR:asyncio:Task was destroyed but it is pending!
task: <Task pending name='Task-3' coro=<shared_client.<locals>.close_client_task() running at /usr/local/lib/python3.9/site-packages/kubespawner/clients.py:58> wait_for=<Future pending cb=[<TaskWakeupMethWrapper object at 0x7f8f3e126d60>()]>>
Exception ignored in: <coroutine object shared_client.<locals>.close_client_task at 0x7f8f3f9c09c0>
RuntimeError: coroutine ignored GeneratorExit

And then restarted, but then kinda got 'stuck' leading to new servers not being started https://2i2c.freshdesk.com/a/tickets/163.
I restarted the pod to unbork it, but we should really be moving this to a regional cluster.

We should push forward https://github.com/2i2c-org/team-compass/issues/423 in order to effectively coordinate and schedule the downtime that this migration will inevitably incur

I raised the priority on 423 to reflect this need, @sgibson91.

Another option that is easier is to just start up another cluster (same project) that's regional, and put all new hubs there. And over time, things just move over there.

Another option that is easier is to just start up another cluster (same project) that's regional, and put all new hubs there. And over time, things just move over there.

Even when that is an option, I think we definitely need to make an iteration on https://github.com/2i2c-org/team-compass/issues/423 and maybe this one is the forcing function to make that happen 😉.

just start up another cluster (same project) that's regional

I am +0.5 on this only because it means we could called the new cluster something other than pilot-hubs and finally eradicate pilot from 2i2c! But agree that 423 will be much more broadly impactful to our operations.

I am +0.5 on this only because it means we could call the new cluster something other than pilot-hubs and finally eradicate pilot from 2i2c!

You are tempting me to reprioritize, @sgibson91 😉!
"Joke" aside,

But agree that 423 will be much more broadly impactful to our operations.

Another option that is easier is to just start up another cluster (same project) that's regional, and put all new hubs there. And over time, things just move over there.

Even when that is an option, I think we definitely need to make an iteration on 2i2c-org/team-compass#423 and maybe this one is the forcing function to make that happen 😉.

I actually think we should just do it this way now. We can probably copy over data and change ingress/URL points much more "behind the scenes". We could do what I did with the Pangeo hubs and say "we will be running backups and X and Y datetimes,, data created after Y definitely won't be migrated".
How we communicate that message to every community on the cluster would still need a rudimentary version of 423

I actually think we should just do it this way now.

I can't quite parse which of the two levels of quoting 'this way' refers to :D Can you clarify, @sgibson91?

Sorry @yuvipanda , I'm now agreeing with you!

How we communicate that message to every community on the cluster would still need a rudimentary version of 423

From @yuvipanda in #423:

I think a canonical list of community reps + a process to email them is a better fit than one group with everyone.

I think that would be the rudimentary process we would need to follow.
I would add the emails should be sent from support so we have any thread centralized.
I bet it would not be easy to coordinate a good shared time, but maybe I am wrong with my intuition...

I bet it would not be easy to coordinate a good shared time, but maybe I am wrong with my intuition...

This is why I think spinning up a new cluster, duplicating the hubs on it, and then using rsync to move the home directories will be a better scenario. There doesn't need to be a downtime as we just change the IP address the A records point to. And we can minimise the amount of data lost by running a few rsyncs up to the point of switching the IPs.

Sounds like a reasonable plan to me!

A related update: We caught a bug in Kubespawner that is causing the hub to be unable to restart after a k8s master outage in https://github.com/jupyterhub/kubespawner/issues/627

Huge thanks to @sgibson91 for leading the effort in getting that bug fixed in kubespawner! It has been deployed now, but we should still move at some point soon.


light-client: Replace serde_cbor with serde_json

Fixes #1026.
Fixes #1038.

[x] Referenced an issue explaining the need for the change
[x] Updated all relevant documentation in docs
[x] Updated all code comments where relevant
[x] Wrote tests
[x] Added entry in .changelog/

Codecov Report

Merging #1133 (088f320) into master (cd3e391) will not change coverage.
The diff coverage is 83.3%.

@@          Coverage Diff           @@
##           master   #1133   +/-   ##
======================================
  Coverage    64.7%   64.7%
======================================
  Files         231     231
  Lines       15637   15637
======================================
  Hits        10121   10121
  Misses       5516    5516

Impacted Files
Coverage Δ

light-client/src/store/sled/utils.rs
72.0% <66.6%> (ø)

light-client/src/errors.rs
84.2% <100.0%> (ø)

testgen/src/vote.rs
84.8% <0.0%> (-0.9%)
:arrow_down:

testgen/src/light_block.rs
76.6% <0.0%> (+0.5%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
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@xla This PR was merged but I don't see these changes in main branch.

main is effectively a fork off of tendermint-rs v0.23.x, since Tendermint Core v0.35/v0.36 were abandoned. See https://github.com/informalsystems/tendermint-rs/discussions/1179
This would need to be ported across to main again.


Support for Laravel's Fluent object?

Larastan Version: 0.7.12
--level used: 6

Description
When properties are added to the Illuminate\Support\Fluent class, Larastan says the properties are undefined.
Access to an undefined property Illuminate\Support\Fluent::$myFluentProperty

Hello Michael! Thank you for your report.
Could you share a bit of your code and some context?

An example:
use Illuminate\Support\Fluent;

$fluent = new Fluent(['foo' => 'bar']);

self::assertSame($fluent->foo, 'bar');

Results in
Access to an undefined property Illuminate\Support\Fluent::$foo.

Try adding these lines to your phpstan.neon.
parameters:
    universalObjectCratesClasses:
        - Illuminate\Support\Fluent

From https://github.com/nunomaduro/larastan/pull/924#issuecomment-917716385


Creating an isoseq3 compatible output

Hi guys, just documenting the spec for isoseq3 support
What I did:
As you know, I've posted the data and processing script here
Basically, I processed the reads with longbow and ran the combined extracted data through isoseq3 tag.
When trying to dedup the reads with isoseq3 dedup, it would say terminate called without an active exception. Aborted.
Liz says this is because the read group tag is messed up. We have a script to iterate through our bams and change the RG:Z: tag so that the read group is constant. We also change the zm:i: tag to a unique counter since ZMWs are no longer unique. Unfortunately, this is ridiculously slow and it would be nice to have an isoseq3 compatible output from longbow.
Old tags (after isoseq3 tag --design 16B-10U-T):

ec:f:9.77338
np:i:8
rq:f:0.999347
sn:B:f,13.13,19.2964,4.94478,8.61356
we:i:2756052
ws:i:110592
zm:i:59572499
YS:f:-5961.52
RC:i:0
XQ:Z:44/46,0/0,56/60,48/50,30/32,46/46,0/0,44/60,48/50,30/32,46/46,0/0,58/60,48/50,32/32
YQ:Z:0.9397
YN:Z:mas15
YV:i:1
YG:i:3
YK:Z:N
SG:Z:10x_Adapter:0-22,random:23-698,Poly_A:699-727,3p_Adapter:728-752
RG:Z:9e129d4c
XC:Z:TCAGGTGCAGGTCGGA
XM:Z:TCCTGCGCAT
XA:Z:XC-XM

New tags:

XC:Z:TCAGGTGCAGGTCGGA
XM:Z:TCCTGCGCAT
ic:i:1
im:Z:m64013e_211031_055434/1/ccs
is:i:1
it:Z:TCAGGTGCAGGTCGGATCCTGCGCAT
zm:i:60314
RG:Z:e4927d21

Lmk if you need more info

Hi Roger,
This is now fixed in branch jts_fixed_length_random_model. That branch still needs some testing before it is merged into main, but in testing, it does seem to do the trick.
A few important points: we've updated the statistical model to also perform the CBC/UMI annotation, which should make it easier to get fully-annotated reads without needing to run our external CBC/UMI annotation tool or isoseq3. We're not correcting/deduping the reads within Longbow yet, so you'll still need to run isoseq3 dedup.
Some quality of life improvements: the filter command now takes two arguments for output files: -o (for reads passing filters), and -x (for reads failing filters), which means the filter command can now accept piped input and emit piped output. By default, failing reads are just sent to /dev/null. Also, you no longer need to specify the annotation model to every command; this will be autodetected from the program group written into the BAM header. I've also fixed a minor bug with the internal sharder, which was occasionally running into boundary issues towards the end of files.
Finally, Longbow doesn't alter read group names. However, IsoSeq3 seems to do so. I'm not certain what the correct behavior here should be:
$ samtools view -H /data/m64013e_211031_055434.hifireads.bam | grep '^@RG' | awk '{ print $2 }'
ID:9e129d4c
samtools view -H /data/annotated.chunk1.bam | grep '^@RG' | awk '{ print $2 }'
ID:9e129d4c
$ samtools view -H /data/filtered.chunk1.bam | grep '^@RG' | awk '{ print $2 }'
ID:9e129d4c
$ samtools view -H /data/segmented.chunk1.bam | grep '^@RG' | awk '{ print $2 }'
ID:9e129d4c
$ samtools view -H /data/extracted.chunk1.bam | grep '^@RG' | awk '{ print $2 }'
ID:9e129d4c
$ samtools view -H /data/dedup.chunk1.bam | grep '^@RG' | awk '{ print $2 }'
ID:e4927d21
The following commands will now perform all the processing steps:
longbow annotate -f -c 1/300 -t 30 -o annotated.chunk1.bam m64013e_211031_055434.hifireads.bam
longbow filter -f -o filtered.chunk1.bam annotated.chunk1.bam
longbow segment -f -o /data/segmented.chunk1.bam /data/filtered.chunk1.bam
longbow extract -f -o /data/extracted.chunk1.bam /data/segmented.chunk1.bam

# Dedup should really be run on all the merged data, but I've included it here for demonstration purposes
isoseq3 dedup /data/segmented.chunk1.bam /data/dedup.chunk1.bam

Or equivalently:
longbow annotate -c 1/300 -t 30 m64013e_211031_055434.hifireads.bam | longbow filter | logbow segment | longbow extract -o /data/extracted.chunk1.bam
isoseq3 dedup /data/segmented.chunk1.bam /data/dedup.chunk1.bam

You can build this branch from source, or if you prefer, I've made a Docker image that already has this branch installed: us.gcr.io/broad-dsp-lrma/lr-longbow:0.4.7-kvg2 .
Let me know how this works for you.  Jonn and I will finish up the testing for this branch and let you know when its merged into main.

Sorry it took me a bit to figure out that the CBC/UMI annotation was part of a different model. I can confirm that the QOL improvements work well, at least in my testing. However, I did run into some problems. I thought it would be cleaner to just do a fresh clone and build from there. Below are the exact steps I took:
git clone https://github.com/broadinstitute/longbow.git

cd longbow

git checkout jts_fixed_length_random_model

python3 -mvenv venv
. venv/bin/activate
pip3 install -r dev-requirements.txt
pip3 install -e .

I can confirm that this installed correctly because I can see the mas15v2 model in src/longbow/utils/model.py. The annotation seems to run fine without complaining:
[INFO 2021-11-29 14:18:28 annotate] Invoked via: longbow annotate -m mas15v2 -c 1/300 -t 16 -o mas_aml_1.ann.bam ../data/m64013e_211031_055434.hifireads.bam
[INFO 2021-11-29 14:18:28 annotate] Running with 16 worker subprocess(es)
[INFO 2021-11-29 14:18:30 annotate] Using mas15v2: The standard MAS-seq 15 array element model.
[INFO 2021-11-29 14:19:04 annotate] Annotating 9643 reads from chunk 1/300 (reads 1-9643)
Progress: 100%|███████████████████████████████████████████████████████| 9643/9643 [10:28<00:00, 15.34 read/s]
[INFO 2021-11-29 14:29:33 annotate] Annotated 9643 reads with 36534 total sections.
[INFO 2021-11-29 14:29:33 annotate] Done. Elapsed time: 665.43s. Overall processing rate: 14.49 reads/s.

What's weird is that when I try to filter, the vast majority of reads fail filtering:
[INFO 2021-11-29 14:40:05   filter] Invoked via: longbow filter -o mas_aml_1.filt.bam mas_aml_1.ann.bam
[INFO 2021-11-29 14:40:05   filter] Writing reads that conform to the model to: mas_aml_1.filt.bam
[INFO 2021-11-29 14:40:05   filter] Writing reads that do not conform to the model to: /dev/null
Progress: 0 read [00:00, ? read/s][INFO 2021-11-29 14:40:06   filter] Using mas15v2: The standard MAS-seq 15 array element model.
[INFO 2021-11-29 14:40:06   filter] Filtering according to mas15v2 model ordered key adapters: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Progress: 9643 read [00:09, 1000.88 read/s]
[INFO 2021-11-29 14:40:15   filter] Done. Elapsed time: 9.70s.
[INFO 2021-11-29 14:40:15   filter] Total Reads Processed: 9643
[INFO 2021-11-29 14:40:15   filter] # Reads Passing Model Filter: 771 (8.00%)
[INFO 2021-11-29 14:40:15   filter] # Reads Failing Model Filter: 8872 (92.00%)
[INFO 2021-11-29 14:40:15   filter] Total # correctly ordered key adapters in passing reads: 771
[INFO 2021-11-29 14:40:15   filter] Total # correctly ordered key adapters in failing reads: 4881
[INFO 2021-11-29 14:40:15   filter] Avg # correctly ordered key adapters per passing read: 1.0000 [16]
[INFO 2021-11-29 14:40:15   filter] Avg # correctly ordered key adapters per failing read: 0.5502 [16]

Curiously, when I run on the normal mas15 model, I only get a 65% pass rate as opposed to the >99% pass rate with the current main branch. I haven't dug more into the failed reads, but will soon.

After a fresh pull/build this morning and testing on a chunk of 5' data, this seems to be working (~98% pass rate) and isoseq3 dedup doesn't complain. Thanks guys!

hello  can you share me you code from ccs to downstream steps ?


Bump Bouncy Castle libs to 1.72

BC 1.72 has been released and contains a bunch of fixes and PRs we were able to upstream :)
The release is not yet available on Maven Central, but will be soon.

Unfortunately, simply bumping BC to 172 reveals some breaking tests.
Most of those are related to ModificationDetectionCodes.
My suspicion is that some streams are not fully read using the BC172 code, which results in wrong checksum calculations and invalid packet tags.
Not sure, how to fix this yet.

Fixed by wrapping InputStreams into BufferedInputStreams before wrapping into BCPGInputStreams.
See https://github.com/bcgit/bc-java/issues/1257


Left Keys in Ignition.

From: https://github.com/fedecia/gmail-sender-oauth/blob/master/test/client_secret.json
{"installed":{"client_id":"1081826302113-deknk5sgd6n2vutgv3l4ub4530qqc8kh.apps.googleusercontent.com","project_id":"protean-willow-165021","auth_uri":"https://accounts.google.com/o/oauth2/auth","token_uri":"https://accounts.google.com/o/oauth2/token","auth_provider_x509_cert_url":"https://www.googleapis.com/oauth2/v1/certs","client_secret":"yWDet9Tz2Ck02mONqSeVuoHo","redirect_uris":["urn:ietf:wg:oauth:2.0:oob","http://localhost"]}}

Not sure if you want your Google App APIs open for public use or if they have been secured. Overall good clean code! 👍

thanks but i created this dummy app for testing of the module


Implement an EMF im- and export facility

Does this make sense to re-implement in TS? If someone uses EMF, they are most likely in a Java environment, and then could use the Java LW-ECore bridge.

Good point! But then I'd also like to be able to use the Java implementation more easily, e.g. as a CLI. I'll make an issue {i|o}n the Java repo.


How to compose expression to compare property with enum value?

I didn't find a way how to bind visibility with enum compare condition:
<WrapPanel Margin="5" Visibility="{c:Binding 'MyProperty==Value1'}">
Instead of Value1 I tried also MyEnumType.Value1, local:MyEnumType.Value1, nothing helps, everything result is 'Visible' with error:
System.Windows.Data Warning: 40 : BindingExpression path error: 'Value1' property not found on 'object' ''TabModel' (HashCode=42904806)'. BindingExpression:Path=local; DataItem='TabModel' (HashCode=42904806); target element is 'WrapPanel' (Name=''); target property is 'Visibility' (type 'Visibility')

Good morning, Alexey! Thank you for your issue.
The problem is that by default, any word other than numbers , string constants, or class math is considered as property of a view model. In the future it would be nice to make support for enum and other classes. As long as, you can give each enum value number and use it instead it name in xaml

When I use number associated to enum, it is also doesn't work, Error returned:
Binding error: calc converter can't convert expression{0}==0: Двоичный оператор Equal не определен для типов "bfsys.Status" и "System.Int32".

Try to
(int)yourProperty == 0

Again error:
Binding error: one of source fields is Unset, return null
System.Windows.Data Error: 5 : Value produced by BindingExpression is not valid for target property.; Value='' MultiBindingExpression:target element is 'WrapPanel' (Name=''); target property is 'IsEnabled' (type 'Boolean')
The code was:
<WrapPanel Margin="5" IsEnabled="{c:Binding '(int)Status == 0'}">
Anyway, workaround is not urgent for me already (so, you can close this ticket). If you can implement in future comparing with direct enum value - it will be great.

Sorry, yes, I have taken note your issue, it is really very interested, and I will try to come up with it in near feature

Enums are supported in version <IP_ADDRESS>, nuget package will be available in nuget after indexing


Idris 2 0.3.0 support

0.3.0 has just been released, so this issue is a reminder to check what's changed and make sure nothing is broken.

I'm not currently able to run Idris2 0.3.0 with idris2 --ide-mode. I'm getting Uncaught error: (implicit):1:1--1:1:Prelude not found. There was one failed make test during compilation, so I might try rebuilding it. In the meantime, is anyone else able to run it?

I'm not currently able to run Idris2 0.3.0 with idris2 --ide-mode. I'm getting Uncaught error: (implicit):1:1--1:1:Prelude not found. There was one failed make test during compilation, so I might try rebuilding it. In the meantime, is anyone else able to run it?

It's working for me, on Windows 10, compiled in MSYS2.
When I do idris2 --ide-mode I get 000018(:protocol-version 2 0)

It's working for me, on Windows 10, compiled in MSYS2.
When I do idris2 --ide-mode I get 000018(:protocol-version 2 0)

My Prelude bug was unrelated to the new version, it's something to do with the linker paths, which I solved by just compiling it with Nix. The latest is version is out on the unstable channel.
It doesn't look like much has changed in the new release related to the IDE protocol. The only difference my units tests turned up is in the :metavariables response. Premise names previously had 3 empty spaces in front of them for some reason, now they have 2 empty spaces. That doesn't even affect anything, because I apparently still haven't gotten around to adding the premises to the List Metavariables command.

My Prelude bug was unrelated to the new version, it's something to do with the linker paths, which I solved by just compiling it with Nix. The latest is version is out on the unstable channel.
It doesn't look like much has changed in the new release related to the IDE protocol. The only difference my units tests turned up is in the :metavariables response. Premise names previously had 3 empty spaces in front of them for some reason, now they have 2 empty spaces. That doesn't even affect anything, because I apparently still haven't gotten around to adding the premises to the List Metavariables command.


Update Version to <IP_ADDRESS>.0.0

Adapter version '<IP_ADDRESS>.0.0', partner version '~> <IP_ADDRESS>'

Not to be merged. The <IP_ADDRESS>.0 version already supports this new partner SDK version.
We are keeping this branch alive until the automated process is updated to ignore these edge cases, to prevent it from recreating the branch again on the next update.


Javascript code formatting of post-increment operator (i++) is wrong on solutions page

The code formatting of the solution below is incorrect.  It executes without error and is colored correctly by GitHub so this appears to be a bug.
The post-increment operator in the following code (i++) seems to be incorrectly parsed as the binary addition operator(+) with a missing argument as opposed to the unary post-increment(++) operator with only one argument.

function Xbonacci(s, n){
  var len = s.length, i = len - 1;
  while (i++ < n) {
    s[i] = s.slice(i - len).reduce(sum, 0);
  }
  return s.slice(0, n);
}

Source: www.codewars.com/kata/556e0fccc392c527f20000c5/solutions/javascript

Thanks for reporting. Updating our version of CodeMirror would probably help but unfortunately we are stuck on an older version until we can get the time to do an upgrade, which involves basically redoing our integration due to breaking changes on their end.

I don't think updating CodeMirror would help, since the solutions page appears to be using highlight.js (https://highlightjs.org/).  I can reproduce this bug in the current version of highlight.js using one of Codewars CSS sheets:

<link rel="stylesheet" href="http://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.2.0/styles/default.min.css">
<link href="http://d3l8wp33uu8nxs.cloudfront.net/assets/application-f1025241cadf54fd707645a4935c0b1a.css" media="screen" rel="stylesheet" type="text/css">

function Xbonacci(s, n){
  var len = s.length, i = len - 1;
  while (i++ < n) {
    s[i] = s.slice(i - len).reduce(sum, 0);
  }
  return s.slice(0, n);
}

This could probably be reported upstream as well, since I didn't see an issue for this at https://github.com/isagalaev/highlight.js/issues, and it's reproducible on the latest version.
After looking at this more closely, I finally have an explanation as to why the highlighting is so inconsistent between the editor and the solutions page: there are two different highlighting solutions at play here: CodeMirror and highlight.js.
Perhaps the inconsistency should be a separate bug?  I have wondered why code that looks good colored in the editor suddenly looks awful when I get to the solutions page.
Additionally, I saw another variation of this problem today.

This one also has a less than comparison after the ++.  I wonder if that's what triggers the problem?
Source: http://www.codewars.com/kata/55e1990978c60e5052000011/solutions/javascript

Closing this because this is third party issue and regular expression based syntax highlighting can never be perfect.
We may consider switching to use CodeMirror to do the highlighting in the future.


feat: ds input validation

Changes

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Fix issue downloading files as blob on some sites (#2599)

Task/Issue URL: https://github.com/duckduckgo/Android/issues/2599
Description
Fix issue downloading files as blob on some sites which need to show several pages during the download process.
Steps to test this PR
Feature 1

Connect to a Web site such as the CAF's site: https://www.caf.fr/ or the website: https://attestation-vaccin.ameli.fr/
Try to download an attestion document
The PDF file is well downloaded and can be retrieved from the Downloads screen

Changes

Before
After

The file was not downloaded wihout even a error message shown to the user
The file is well downloaded and can be viewed from the Downloads screen

@anikiki  assigning this to you? feel free to close if it’s not valid anymore.

Hi, I don't understand if there is an issue with this pull request

Hi, I don't understand if there is an issue with this pull request

Hi @bonninf ! Thanks for opening the Pull Request. We noticed this makes changes to the app/src/main/res/raw/blob_converter.js file and we need to be sure no regression will be introduced.

@anikiki anything to do here?

It’s been a month and no response, closing this PR. Feel free to open it up again once the conflicts are solved and progress has been made.


BWA Fails with Output directory already exists for more than 1 executor

When bwa runs on more than 1 executor, it seems the output directory is attempted to be created multiple times. Fails with error:
User class threw exception: org.apache.hadoop.mapred.FileAlreadyExistsException: Output directory chr17.7500000-7515000.aligned.sam already exists

org.apache.hadoop.mapred.FileAlreadyExistsException seems to be the issue that bubbles to the top. The real issue was that psshing in and memory mapping the bwa index did not work for a subset of the workers, so those workers were failing with an index not found error. However, I am not sure why this resulted in a org.apache.hadoop.mapred.FileAlreadyExistsException from the Hadoop application page.

Could it be that when the failed nodes retried they were allocated the same region of the genome as already running on another node?  Is this an issue for Cannoli?

I'm closing this as not an issue with Cannoli -- please reopen if you would like.


Fix data101 image, update readme/contributing

this builds locally, but was failing here.  why!?!?

building locally, i successfully install environment.yml:
Step 40/55 : RUN TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '
 ---> Running in b38f50e7f211
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.3.0
    latest version: 24.7.1

Please update conda by running

    $ conda update -n base -c conda-forge conda

Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working...
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working...

done

here, however, it's failing w/a massive dep hell:
  Could not solve for environment specs
  The following packages are incompatible
  ├─ coverage 7.2.2  is installable with the potential options
  │  ├─ coverage 7.2.2 would require
  │  │  └─ python >=3.10,<3.11.0a0  with the potential options
  │  │     ├─ python [3.10.14|3.11.8|...|3.9.19] would require
  │  │     │  └─ openssl >=3.2.1,<4.0a0 , which can be installed;
  │  │     ├─ python [3.10.7|3.10.8|3.11.0|3.9.14|3.9.15] would require
  │  │     │  └─ openssl >=1.1.1s,<1.1.2a , which conflicts with any installable versions previously reported;
  │  │     ├─ python [3.10.10|3.10.11|3.11.1|3.11.2|3.11.3] would require
  │  │     │  └─ openssl >=3.1.0,<4.0a0  with the potential options
  │  │     │     ├─ openssl [3.3.1|3.3.2], which can be installed;

...and another 1k+ lines

ok, it looks like it's passing now...  i did have to unpin the following packages to get it to build, however:
- pillow # ==9.2.0
- pytest # ==7.1.2
- sympy # ==1.10.1

i'll see what's installed, deploy on staging and confirm w/data101 staff that these are 'ok'.


Add bam-readcount

bam-readcount runs as part of the fp_filter.  We either need to
A) modify the false-positive filter to keep the bam-readcount output
B) run bam-readcount separately on the final VCF
I'm not sure if B would be preferable because we would also get readcounts for DoCM variants.  See #126 for potential changes to the workflow involving the fp_filter.

@susannasiebert I'll be working on #126 with the intention of still producing a single "final" merged, annotated VCF. This would be the input to bam-readcount. We would (optionally) run bam-readcount one more time to get the read counts for pVAC-Seq.

When rewriting bam-readcount.cwl, you should compare to https://github.com/genome/fpfilter-tool.
There were some recent changes to avoid the die on MNPs. MNPs or complex variants with the same length as the REF allele are skipped.  #128 should help but I'm not confident GATK will resolve all complex variants. For example biallelic block substitutions like this tool specifically handles:
http://genome.sph.umich.edu/wiki/Vt#Decompose_biallelic_block_substitutions


Convert excel dates and fix string indexing

I've added logic to convert Excel dates stored as number of days from 01.01.1900 into ABAP dates. Cells values are treated as dates when cell style references standart number 14 for dates. Some resources:

https://social.msdn.microsoft.com/Forums/office/en-US/e27aaf16-b900-4654-8210-83c5774a179c/xlsx-numfmtid-predefined-id-14-doesnt-match?forum=oxmlsdk
https://stackoverflow.com/questions/33276651/when-uploading-excel-file-with-a-date-it-looks-like-41851-not-7-31-2014

Thanks for your support @dehero


0.2.0/1.19/biome ducktape

Thickets are no longer hugeomoungousinourus, and biomes are laid out a bit nicer to blend similar biomes together, and create transitions like
thicket -> forest -> highlands
wisteria woods are small and sort of rare to feel special
please test this and make sure the biomes "feel" good

Superceded by #729 ?

Superceded by #729 ?

shouldn't be, I just merged it in because it was hard to test biomes when it's almost all thicket, and at least 1 biome doesn't generate at all.

Superceded by #729 ?

It probably should be.


Fix auto merge conflict 5812 [skip ci]

fix auto-merge conflict at #5812. Keep the jni version in branch-22.08
NOTE: this must be merged as a merge commit

build