Error message - BAM file shares no contigs with GTF - Knight eQTL rnaseq call

From the step of rnaseqc_call, 8 bam files returned with an error message indicating BAM file shares no contigs with GTF
and this error message is preventing moving forward to the next step for these 8 bam files.
Here is one of the error message from one of the bam files
[tb755bc6d14ec7dca]: Executing script in Singularity returns an error (exitcode=11, stderr=/mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/PA00003164.rnaseqc.gene_tpm.gct.stderr). The script has been saved to /home/cl4215/.sos/f09861f58d65b381/singularity_run_20397.sh. To reproduce the error please run: singularity exec  /mnt/vast/hpc/csg/snuc_pseudo_bulk/eight_celltypes_analysis/SuSiE/containers/rna_quantification.sif /bin/bash /home/cl4215/.sos/f09861f58d65b381/singularity_run_20397.sh
Below is submitted command
nohup sos run ~/githubrepo/xqtl-pipeline/code/molecular_phenotypes/calling/RNA_calling.ipynb rnaseqc_call \
    --cwd /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq \
    --samples /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/xqtl_protocol_data.fastqlist    --data-dir /mnt/vast/hpc/csg/cl4215/ROSMAP/knight \
    --gtf /mnt/vast/hpc/csg/cl4215/mrmash/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.gtf \
    --container /mnt/vast/hpc/csg/snuc_pseudo_bulk/eight_celltypes_analysis/SuSiE/containers/rna_quantification.sif  \
    --reference-fasta /mnt/vast/hpc/csg/cl4215/mrmash/reference_data/GRCh38_full_analysis_set_plus_decoy_hla.noALT_noHLA_noDecoy.fasta \
    --bam_list /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/xqtl_protocol_data_bam_list \
    -c /mnt/vast/hpc/csg/molecular_phenotype_calling/csg.yml -j 10 -q csg2

@Chunmingl i see some tips online that might help -- did you try those? One other obvious thing to check is if your BAM files is intact, that is, if the size of the BAM files in question is much smaller than others that work.

The bam files were intact, and the qc files looked ok. however, many more samples returned the same errors after rerunning from rnaseq call. @hsun3163
tail /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.rnaseqc.gene_tpm.gct.stderr
BAM file shares no contigs with GTF
BAM file shares no contigs with GTF
BAM file shares no contigs with GTF
BAM file shares no contigs with GTF

As it occurs, the bam file is empty. Can you point me to the analysis notebook that documenting all your analysis as we discussed?
hs3163@csglogin:/mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test$ ls -lah  /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961*
-rw-r--r-- 1 cl4215 hgrcgrid_statgen    0 May 23 15:12 /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.Aligned.sortedByCoord.out.bam
-rw-r--r-- 1 cl4215 hgrcgrid_statgen 3.6G Jun  3 18:38 /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 cl4215 hgrcgrid_statgen  144 May 28 10:27 /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.rnaseqc.gene_tpm.gct.stderr
-rw-r--r-- 1 cl4215 hgrcgrid_statgen    0 May 24 13:18 /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.rnaseqc.gene_tpm.gct.stdout
-rw-r--r-- 1 cl4215 hgrcgrid_statgen 6.3M Jun  4 02:13 /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.rsem.genes.results
-rw-r--r-- 1 cl4215 hgrcgrid_statgen  15M Jun  4 02:13 /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.rsem.isoforms.results
-rw-r--r-- 1 cl4215 hgrcgrid_statgen   73 Jun  4 01:58 /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.rsem.isoforms.stderr
-rw-r--r-- 1 cl4215 hgrcgrid_statgen 506K Jun  4 02:13 /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.rsem.isoforms.stdout

I submitted in bash scripts. Here are the some of the scripts I have previously run.
/home/cl4215/githubrepo/mrmash_ROSMAP/Knight/knight_rnaseq3.sh
/home/cl4215/githubrepo/mrmash_ROSMAP/Knight/knight_rnaseq4.sh

please do document the analysis in the notebook going forward...it would be hard to keep track of bash scripts.
that being said, how is
/mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/xqtl_protocol_data_bam_list

generated ?

for the star output step:  I ran it multiple times (including test running with a smaller sample size ) - most of the time it ended with no error message but the status of the job did not seem complete.
tail /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/errout/knight_staroutput3.log
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.

for the star output step: I ran it multiple times (including test running with a smaller sample size ) - most of the time it ended with no error message but the status of the job did not seem complete.
tail /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/errout/knight_staroutput3.log
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.
INFO: Waiting for the completion of 2 tasks.

Given the complexity of the issue, again, please prepare a notebook documenting all the command you have ran and the log file associated with each command. Otherwise it is impossible to look into.

Here is the summarized notebook of scripts and log files
/home/cl4215/githubrepo/mrmash_ROSMAP/Knight/knight_contigs_GTF.ipynb

Here is the summarized notebook of scripts and log files /home/cl4215/githubrepo/mrmash_ROSMAP/Knight/knight_contigs_GTF.ipynb

can you fork the fungi-QTL-analysis repo, and send a pr to upload this notebook (preferable along with other notebooks that are relevant to the xQTL project)?  I don't really have access to notebooks that are not in my home dir due to the way jupyterlab works.

Pr is sent

Pr is sent

Apparently the two samples' STAR failed due to walltime. can you rerun the two samples in a new cwd with increased walltime by setting --walltime in the SOS command?
hs3163@csglogin:/mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/test$ qacct -j 5473097
==============================================================
qname        csg.q
hostname     node48
group        cl4215
owner        cl4215
project      NONE
department   defaultdepartment
jobname      job_t3c81fbcdec02417a
jobnumber    5473097
taskid       undefined
account      sge
priority     0
qsub_time    Sat May 27 17:00:29 2023
start_time   Sat May 27 17:26:43 2023
end_time     Sat May 27 22:26:44 2023
granted_pe   orte
slots        8
failed       37  : qmaster enforced h_rt, h_cpu, or h_vmem limit
exit_status  137                  (Killed)
ru_wallclock 18001s
ru_utime     0.175s
ru_stime     0.034s
ru_maxrss    7.410KB
ru_ixrss     0.000B
ru_ismrss    0.000B
ru_idrss     0.000B
ru_isrss     0.000B
ru_minflt    8013
ru_majflt    0
ru_nswap     0
ru_inblock   0
ru_oublock   16
ru_msgsnd    0
ru_msgrcv    0
ru_nsignals  0
ru_nvcsw     5076
ru_nivcsw    6
cpu          141516.840s
mem          4653.239TBs
io           492.403GB
iow          0.000s
maxvmem      35.705GB
arid         undefined
ar_sub_time  undefined
category     -u cl4215 -q csg.q -l h_rt=18000,h_vmem=40G -pe orte 8

I received an error message
/mnt/vast/hpc/csg/cl4215/ROSMAP/knight/errout/knight_staroutput7.log
ERROR: [picard_qc (picard_qc)]: [picard_qc]: Failed to execute process
"bash(fr"""set -e\ntouch {_output[0]:n}.CollectMultipleMetrics...["cord_bam"].zap()\n\n"
name 'job_size' is not defined
[STAR_output]: Exits with 1 pending step (STAR_output)

the submitted script can be accessed in the recent pull request:
fungen-xqtl-analysis/analysis/Wang_Columbia/knight/eQTL/knight_STAR_Output7.sh

I received an error message /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/errout/knight_staroutput7.log
ERROR: [picard_qc (picard_qc)]: [picard_qc]: Failed to execute process
"bash(fr"""set -e\ntouch {_output[0]:n}.CollectMultipleMetrics...["cord_bam"].zap()\n\n"
name 'job_size' is not defined
[STAR_output]: Exits with 1 pending step (STAR_output)

the submitted script can be accessed in the recent pull request: fungen-xqtl-analysis/analysis/Wang_Columbia/knight/eQTL/knight_STAR_Output7.sh

Some one have had this issue before, which was solved after updating their sos, can you try again after updating your sos?


Pinging all running BT services on wake up

Fixes #742
This PR is [ready] for review.
Risk
This PR makes [no] API changes.
Testing Plan
Tested successfully on branch
https://github.com/smartdevicelink/sdl_android/compare/develop...feature/mt_multiplexing
with situation described in issue - Router Service running with USB transport, then BT is toggled from OFF to ON. Can look into unit tests if necessary.
Bug Fixes

Fixes bug described in issue.

CLA

[ X ] I have signed the CLA

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Merging #743 into develop will decrease coverage by <.01%.
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##             develop     #743      +/-   ##
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=============================================
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=============================================
  Hits            6514     6514
- Misses          9026     9029       +3
  Partials         307      307

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Waves doesn't seem to work

I don't see the wave effect when I click buttons in my web app or on http://gwt-material.appspot.com/.  I tested with Chrome 41, Safari 7.1.3, and Internet Explorer 11.  Other effects do work, eg the animation for onmouseover on a button.  Relevant code is:
<m:MaterialButton text="Button" waves="light" color="blue" />
Am I missing something?

<button class="btn blue" data-position="bottom" data-delay="50">
Download
</button>

I don't see the class waves-effect

Waves has been tested on many devices and many browsers, this is a problem with your code


[BUG] Websocket - No option to set Headless mode, always running in headless = true

Context:

Playwright Version: 1.21.0
Operating System: Mac
.NET version:  NA
Browser:  All
Java - JDK 11
Extra: NA

Code Snippet
To launch the playwright server in local machine.
DEBUG=pw: npx playwright run-server --port 8084 //To start Playwright Server*
From java snippet, connect to playwright server and trying to launch browser in headfull mode.
Playwright playwright = PlaywrightImpl.create(null);
ConnectOptions options = new ConnectOptions();
options.setTimeout(20);
Browser browser = playwright.chromium().connect("ws://<IP_ADDRESS>:8084/", options);

As part of ConnectOptions - we dont have any options to set headless mode to true. It is always launching the chrome always in headlessmode.
Help us help you! Put down a short code snippet that illustrates your bug and
that we can run and debug locally. For example:
public class Sample {
	public static void main(String args[]) {
		Playwright playwright = PlaywrightImpl.create(null);
		ConnectOptions options = new ConnectOptions();
		options.setTimeout(20);
		Browser browser = playwright.chromium().connect("ws://<IP_ADDRESS>:8084/", options);
		browser.newPage().navigate("https://www.google.com");

	}
}```

**Describe the bug**

How to launch the browser in headfull mode when we running the cases through Web Socket.

Related java - Posted in wrong repo. Closing!!


[5.8] config will loos PDO::MYSQL_ATTR_SSL_VERIFY_SERVER_CERT value

Laravel Version: 5.8.3
PHP Version: 7.2.16
Database Driver & Version: MySQL 5.7.24

Description:
database config file will filter \PDO::MYSQL_ATTR_SSL_VERIFY_SERVER_CERT => false, in some case that would a important attribute must to pass.
Steps To Reproduce:
just connect a self-sign server.
Maybe
 'options' => extension_loaded('pdo_mysql') ? [
               \PDO::MYSQL_ATTR_SSL_VERIFY_SERVER_CERT => false,
            ] : [],

You can just edit this file in your own project if you like.


SARA-R510M8S: How to use cellular network and GNSS network simultaneously?

Hi! I'm working with the SARA-R510M8S on the ESP-IDF platform. I'm looking to get a constant location from the GNSS module while also maintaining an MQTT connection over the cellular network. I've gotten each part working independently, but once I try to do both at once, I lose the first network (GNSS or Cellular) despite which network I bring up first. I've followed some of the steps mentioned in #155 and merged it with the MQTT example.
Essentially my problem is that I can't seem to keep both networks on at the same time. I've included the main part of my code below. Any thoughts? Thank you!
static const uDeviceCfg_t gDeviceCfg = {
		.deviceType = U_DEVICE_TYPE_CELL,
		.deviceCfg = {
				.cfgCell = {
						.moduleType = U_CFG_TEST_CELL_MODULE_TYPE,
						.pSimPinCode = NULL,
						.pinEnablePower = -1,
						.pinPwrOn = -1,
						.pinVInt = -1,
						.pinDtrPowerSaving = -1},
		},
		.transportType = U_DEVICE_TRANSPORT_TYPE_UART,
		.transportCfg = {
				.cfgUart = {.uart = 2, .baudRate = U_CELL_UART_BAUD_RATE, .pinTxd = 21, .pinRxd = 19, .pinCts = -1, .pinRts = -1, .pPrefix = NULL},
		},
};

// NETWORK configuration for cellular
static const uNetworkCfgCell_t gNetworkCfg = {
		.type = U_NETWORK_TYPE_CELL,
		.pApn = SIM_APN,
		.timeoutSeconds = 6000,
};

// NETWORK configuration for GNSS
static const uNetworkCfgGnss_t gnssNetworkCfg = {
		.type = U_NETWORK_TYPE_GNSS,
		.moduleType = U_GNSS_MODULE_TYPE_M8,
		.devicePinPwr = -1,
		.devicePinDataReady = -1};

void init_modem(void) {
	uPortInit();
	uDeviceInit();

	// Open the device
	returnCode = uDeviceOpen(&gDeviceCfg, &devHandle);
	uPortLog("Opened device with return code %d.\n", returnCode);

	if (returnCode == 0)
	{
		uPortLog("Bringing up GNSS...\n");
		if (uNetworkInterfaceUp(devHandle, U_NETWORK_TYPE_GNSS, &gnssNetworkCfg) == 0)
		{
			uPortLog("Starting continuous location.\n");
			returnCode = uLocationGetContinuousStart(devHandle, U_GNSS_POS_STREAMED_PERIOD_DEFAULT_MS, U_LOCATION_TYPE_GNSS, NULL, NULL, gnssCallback);
			if (returnCode != 0)
			{
				uPortLog("Unable to start continuous location!\n");
			}
		}
		else
		{
			uPortLog("Unable to bring up GNSS!\n");
		}

		// Bring up the network interface
		uPortLog("Bringing up the network...\n");
		if (uNetworkInterfaceUp(devHandle, U_NETWORK_TYPE_CELL,
														&gNetworkCfg) == 0)
		{
			pContext = pUMqttClientOpen(devHandle, NULL);
			if (pContext != NULL)
			{
				uPortLog("Connecting to MQTT broker \"%s\"...\n", MY_BROKER_NAME);
				if (uMqttClientConnect(pContext, &connection) == 0)
				{
					uMqttClientSetMessageCallback(pContext, messageIndicationCallback, (void *)&messagesAvailable);

					uSecurityGetSerialNumber(devHandle, topic);

					xTaskCreate(mqttRead_task, "mqttRead_task", 1024 * 4, NULL, 5, &mqttRead_taskHandle);
					returnCode = 0;

					uPortLog("Subscribing to topic \"%s\"...\n", topic);
					if (uMqttClientSubscribe(pContext, topic, U_MQTT_QOS_AT_MOST_ONCE))
					{
						uPortLog("Publishing \"%s\" to topic \"%s\"...\n",
										 message, topic);
						if (uMqttClientPublish(pContext, topic, message, sizeof(message) - 1, U_MQTT_QOS_AT_MOST_ONCE, false) == 0)
						{
							returnCode = 0;
						}
						else
						{
							uPortLog("Unable to publish our message \"%s\"!\n", message);
						}
					}
					else
					{
						uPortLog("Unable to subscribe to topic \"%s\"!\n", topic);
					}
				}
				else
				{
					uPortLog("Unable to connect to MQTT broker \"%s\"!\n", MY_BROKER_NAME);
				}
			}
			else
			{
				uPortLog("Unable to create MQTT instance!\n");
			}
		}
		else
		{
			uPortLog("Unable to bring up the network!\n");
		}
	}
	else
	{
		uPortLog("Unable to bring up the device!\n");
	}
}

Thanks for posting, and sorry that you're having trouble with this.  At a first glance your code looks fine; I think we would conventionally bring the cellular network up first, then the GNSS network, but it shouldn't make any difference.
Would you be able to post the debug output from ubxlib here, so that I can see the nature of the failure?

Thanks for the quick response @RobMeades. After some additional testing this morning, I've found that I actually am able to use both networks this way. Sorry for the confusion. My test is to be able to receive MQTT messages while also getting a GNSS fix.
What's interesting though, is that if I bring up cellular first and then GNSS, I am not able to receive MQTT messages. I've attached a partial log below.
I can confirm that the code above does work though, so I don't need any further help. The cell connection is more important than GNSS so I would prefer to bring it up first, but what I have will work. Thanks!
log.txt
I'm happy if you're happy, so feel free to close this issue. 🙂

That's excellent news.  And it seems, from your log, that I have made another of those "schoolboy" errors in the MQTT example code, which is that I have:
https://github.com/u-blox/ubxlib/blob/2f39e1b03d8ecf1c0735599bed9aafecb0c98a13/example/mqtt_client/mqtt_main.c#L326-L327
...whereas of course that should be:
if (uMqttClientSubscribe(pContext, topic,
                         U_MQTT_QOS_EXACTLY_ONCE) == 0) {

D'oh!  Is that what you were referring to with the "Unable to subscribe to topic" message in the attached log?  Will fix...

Yes, thank you!

FYI, the MQTT example is fixed in 1c57c42930e69a7e049ab19185e8b9f1f49c2fe1: it happened to work in our case because the function can return 0, 1 or 2 (it returns the QOS of the subscription).


fix: update input adornment color

[x ] I have followed (at least) the PR section of the contributing guide.

close: #25000

I'm uploading #25090 to solve this problem


WeaveDNS integration with Kubernetes

Name resolution in Kubernetes
Kubernetes uses an optional (but installed by default) add-on to assign name records to virtual service IPs.

DNS records are served by SkyDNS, which in turn requires its own instance of etcd.
DNS records are injected into SkyDNS by kube2sky, which connects to Kubernetes' API Server to listen for new/deleted services.

The dns add-on itself is exposed as a normal Kubernetes service (with a fixed IP for obvious reasons) and deployed as a replication controller.
All pods whose dnsPolicy is set to ClusterFirst (default value) will use the the kubernetes dns service.
This is achieved by kubelet by adding nameserver <dnsServiceIP> to the /etc/resolv.conf file of the pod containers. To make this possible, you need to pass the --cluster-dns=<dnsServiceIP> when launching the kubelet instance in all the Kubernetes nodes of the cluster.
Record format
Here is a sample record: kubernetes.default.svc.cluster.local, where each subdomain stands for:

kubernetes: service name
default: Kubernetes namespace where the service lives.
svc: namespacing for services? (AFAIK that's the only possible value so far)
cluster.local: base domain of the cluster.

needs to be passed to all kubelets as --cluster-domain=cluster.local to setup search lists in /etc/resolv.conf
needs to be passed to skydns and kube2sky in order to construct records.

Why replace the DNS add-on by WeaveDNS

Simplification/Less moving parts. There the dns add-on requires 4 extra containers (kube2sky, skdns, etcd, healtz). Having an extra, dedicated etcd instance on top of the etcd instance already used for master coordination is confusing for newcomers (at least I recall I was and I ended up spending a few hours trying to reuse the main etcd instance).

Stronger coupling with WeaveDNS in installations already using Weave, namely Kubernetes Anywhere which doesn't currently use WeaveDNS since it's currently incompatible with the kubernetes DNS model.

Cross-cloud service discovery. Being able to connect multiple clouds seamlessly in a secure manner is one of Weave Net strengths. Not being able to do cross-cloud service from Kubernetes when it's used in one of the clouds reduces this advantage.

Higher fault/partition tolerance. It's a nice side-effect but probably a weak reason in itself. Although the dns-addon only deploys one pod replica by default, this could be increased or even use have a replica per node using a DaemonSet (for a large number of nodes this would hammer the API Server though). Also, there's no point in making service resolution more resilient than services themselves.

Changes required

WeaveDNS would need to support records which are not associated with a particular node (since services are not node-specific) and accept records conforming the servicename.namespace.svc.clusterdomain scheme.

kube2weavedns: We would need to implement the equivalent of kube2sky. This can be done in a separate container/pod, but for higher simplicity it may be worth considering to embed it into WeaveDNS. The embedding variant, may make authentication against the Kubernetes API Server more complicated.

Optionally, make the normal container-based WeaveDNS records consistent with the Kubernetes naming scheme. In fact, container-level records don't make sense in Kubernetes since all the containers of the same pod live in the same networking namespace and share the same IP. Alternatives:

podname.namespace.pod.clusterdomain for pod-level records. However, podname is atomatically-generated guarantee uniqueness when using Replication Controllers/Daemon Sets, so it may not be all that useful.
replicationControllerName.namespace.rc.clusterdomain/daemonSetName.namespace.ds.clusterdomain

Other considerations
SkyDNS supports SRV records and extensions like Wildcards which users may be relying on.

Another important reason to do this is being able to do cross-cloud service discovery. Again, this comes from real example in which a user would incrementally like to transition to Kubernetes on a public cloud from on-premise (I edited the issue accordingly).

👍

Note Kubernetes has switched to using SkyDNS as a library rather than a service. https://github.com/kubernetes/kubernetes/pull/23930


feat: add last 4 digits to card list

Details

Fixed Issues

$ https://github.com/Expensify/App/issues/47324
PROPOSAL: https://github.com/Expensify/App/issues/47324#issuecomment-2287721795
Tests

Precondition: User account needs to have a few cards added.

Login into the app.
In the URL bar navigate to /search/filters/card (add this after domain eg. https://staging.new.expensify.com).
Verify that the cards in the list have a subtitle indicating the last four digits the card is ending in.

[x] Verify that no errors appear in the JS console

Offline tests

QA Steps

Precondition: User account needs to have a few cards added.

Login into the app.
In the URL bar navigate to /search/filters/card (add this after domain eg. https://staging.new.expensify.com).
Verify that the cards in the list have a subtitle indicating the last four digits the card is ending in.

[x] Verify that no errors appear in the JS console

PR Author Checklist

[x] I linked the correct issue in the ### Fixed Issues section above
[x] I wrote clear testing steps that cover the changes made in this PR

[x] I added steps for local testing in the Tests section
[x] I added steps for the expected offline behavior in the Offline steps section
[x] I added steps for Staging and/or Production testing in the QA steps section
[x] I added steps to cover failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[x] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)
[x] I tested this PR with a High Traffic account against the staging or production API to ensure there are no regressions (e.g. long loading states that impact usability).

[x] I included screenshots or videos for tests on all platforms
[x] I ran the tests on all platforms & verified they passed on:

[x] Android: Native
[x] Android: mWeb Chrome
[x] iOS: Native
[x] iOS: mWeb Safari
[x] MacOS: Chrome / Safari
[x] MacOS: Desktop

[x] I verified there are no console errors (if there's a console error not related to the PR, report it or open an issue for it to be fixed)
[x] I followed proper code patterns (see Reviewing the code)

[x] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick)
[x] I verified that the left part of a conditional rendering a React component is a boolean and NOT a string, e.g. myBool && <MyComponent />.
[x] I verified that comments were added to code that is not self explanatory
[x] I verified that any new or modified comments were clear, correct English, and explained "why" the code was doing something instead of only explaining "what" the code was doing.
[x] I verified any copy / text shown in the product is localized by adding it to src/languages/* files and using the translation method

[x] If any non-english text was added/modified, I verified the translation was requested/reviewed in #expensify-open-source and it was approved by an internal Expensify engineer. Link to Slack message:

[x] I verified all numbers, amounts, dates and phone numbers shown in the product are using the localization methods
[x] I verified any copy / text that was added to the app is grammatically correct in English. It adheres to proper capitalization guidelines (note: only the first word of header/labels should be capitalized), and is either coming verbatim from figma or has been approved by marketing (in order to get marketing approval, ask the Bug Zero team member to add the Waiting for copy label to the issue)
[x] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named "index.js". All platform-specific files are named for the platform the code supports as outlined in the README.
[x] I verified the JSDocs style guidelines (in STYLE.md) were followed

[x] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[x] I followed the guidelines as stated in the Review Guidelines
[x] I tested other components that can be impacted by my changes (i.e. if the PR modifies a shared library or component like Avatar, I verified the components using Avatar are working as expected)
[x] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[x] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[x] I verified that if a function's arguments changed that all usages have also been updated correctly
[x] If any new file was added I verified that:

[x] The file has a description of what it does and/or why is needed at the top of the file if the code is not self explanatory

[x] If a new CSS style is added I verified that:

[x] A similar style doesn't already exist
[x] The style can't be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(theme.componentBG))

[x] If the PR modifies code that runs when editing or sending messages, I tested and verified there is no unexpected behavior for all supported markdown - URLs, single line code, code blocks, quotes, headings, bold, strikethrough, and italic.
[x] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[x] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.
[x] If the PR modifies a component or page that can be accessed by a direct deeplink, I verified that the code functions as expected when the deeplink is used - from a logged in and logged out account.
[x] If the PR modifies the UI (e.g. new buttons, new UI components, changing the padding/spacing/sizing, moving components, etc) or modifies the form input styles:

[x] I verified that all the inputs inside a form are aligned with each other.
[x] I added Design label and/or tagged @Expensify/design so the design team can review the changes.

[x] If a new page is added, I verified it's using the ScrollView component to make it scrollable when more elements are added to the page.
[x] If the main branch was merged into this PR after a review, I tested again and verified the outcome was still expected according to the Test steps.

Screenshots/Videos

Android: Native
https://github.com/user-attachments/assets/12b23a0b-5942-4b91-bd5b-77a2ddeb0002

Android: mWeb Chrome
https://github.com/user-attachments/assets/19d68cd8-920b-4561-a916-80d837de1e8e

iOS: Native
https://github.com/user-attachments/assets/b11842fc-6748-4c63-84b0-6d22b6625e53

iOS: mWeb Safari
https://github.com/user-attachments/assets/ee4536e0-005f-4216-b333-609a98641b49

MacOS: Chrome / Safari
https://github.com/user-attachments/assets/4a46f5f8-fba5-4601-8d12-bedc959e25b9

MacOS: Desktop
https://github.com/user-attachments/assets/22c9e87a-7fa6-4b21-944a-ae040b7009f1

Reviewer Checklist

[ ] I have verified the author checklist is complete (all boxes are checked off).
[ ] I verified the correct issue is linked in the ### Fixed Issues section above
[ ] I verified testing steps are clear and they cover the changes made in this PR

[ ] I verified the steps for local testing are in the Tests section
[ ] I verified the steps for Staging and/or Production testing are in the QA steps section
[ ] I verified the steps cover any possible failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[ ] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)

[ ] I checked that screenshots or videos are included for tests on all platforms
[ ] I included screenshots or videos for tests on all platforms
[ ] I verified tests pass on all platforms & I tested again on:

[ ] Android: Native
[ ] Android: mWeb Chrome
[ ] iOS: Native
[ ] iOS: mWeb Safari
[ ] MacOS: Chrome / Safari
[ ] MacOS: Desktop

[ ] If there are any errors in the console that are unrelated to this PR, I either fixed them (preferred) or linked to where I reported them in Slack
[ ] I verified proper code patterns were followed (see Reviewing the code)

[ ] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick).
[ ] I verified that the left part of a conditional rendering a React component is a boolean and NOT a string, e.g. myBool && <MyComponent />.
[ ] I verified that comments were added to code that is not self explanatory
[ ] I verified that any new or modified comments were clear, correct English, and explained "why" the code was doing something instead of only explaining "what" the code was doing.
[ ] I verified any copy / text shown in the product is localized by adding it to src/languages/* files and using the translation method
[ ] I verified all numbers, amounts, dates and phone numbers shown in the product are using the localization methods
[ ] I verified any copy / text that was added to the app is grammatically correct in English. It adheres to proper capitalization guidelines (note: only the first word of header/labels should be capitalized), and is either coming verbatim from figma or has been approved by marketing (in order to get marketing approval, ask the Bug Zero team member to add the Waiting for copy label to the issue)
[ ] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named "index.js". All platform-specific files are named for the platform the code supports as outlined in the README.
[ ] I verified the JSDocs style guidelines (in STYLE.md) were followed

[ ] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[ ] I verified that this PR follows the guidelines as stated in the Review Guidelines
[ ] I verified other components that can be impacted by these changes have been tested, and I retested again (i.e. if the PR modifies a shared library or component like Avatar, I verified the components using Avatar have been tested & I retested again)
[ ] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[ ] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[ ] If a new component is created I verified that:

[ ] A similar component doesn't exist in the codebase
[ ] All props are defined accurately and each prop has a /** comment above it */
[ ] The file is named correctly
[ ] The component has a clear name that is non-ambiguous and the purpose of the component can be inferred from the name alone
[ ] The only data being stored in the state is data necessary for rendering and nothing else
[ ] For Class Components, any internal methods passed to components event handlers are bound to this properly so there are no scoping issues (i.e. for onClick={this.submit} the method this.submit should be bound to this in the constructor)
[ ] Any internal methods bound to this are necessary to be bound (i.e. avoid this.submit = this.submit.bind(this); if this.submit is never passed to a component event handler like onClick)
[ ] All JSX used for rendering exists in the render method
[ ] The component has the minimum amount of code necessary for its purpose, and it is broken down into smaller components in order to separate concerns and functions

[ ] If any new file was added I verified that:

[ ] The file has a description of what it does and/or why is needed at the top of the file if the code is not self explanatory

[ ] If a new CSS style is added I verified that:

[ ] A similar style doesn't already exist
[ ] The style can't be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(theme.componentBG)

[ ] If the PR modifies code that runs when editing or sending messages, I tested and verified there is no unexpected behavior for all supported markdown - URLs, single line code, code blocks, quotes, headings, bold, strikethrough, and italic.
[ ] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[ ] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.
[ ] If the PR modifies a component or page that can be accessed by a direct deeplink, I verified that the code functions as expected when the deeplink is used - from a logged in and logged out account.
[ ] If the PR modifies the UI (e.g. new buttons, new UI components, changing the padding/spacing/sizing, moving components, etc) or modifies the form input styles:

[ ] I verified that all the inputs inside a form are aligned with each other.
[ ] I added Design label and/or tagged @Expensify/design so the design team can review the changes.

[ ] If a new page is added, I verified it's using the ScrollView component to make it scrollable when more elements are added to the page.
[ ] If the main branch was merged into this PR after a review, I tested again and verified the outcome was still expected according to the Test steps.
[ ] I have checked off every checkbox in the PR reviewer checklist, including those that don't apply to this PR.

Screenshots/Videos

Android: Native

Android: mWeb Chrome

iOS: Native

iOS: mWeb Safari

MacOS: Chrome / Safari

MacOS: Desktop

⚠ Also you did not add any test steps in the PR description, meaning that I as a reviewer and the QA team (post merge) would not know what to do in order to test this.
You should add this in the Tests area:
**Precondition**: User account needs to have a few cards added.

1. Login into the app.
2. In the URL bar navigate to `/search/filters/card` (add this after domain eg. https://staging.new.expensify.com).
3. Verify that the cards in the list have a subtitle indicating the last four digits the card is ending in.

cc @daledah

We got confirmation from design that we want to use Ending in to which we also got confirmation for spanish translation being Terminada en.

We got conflicts @daledah

:hand: This PR was not deployed to staging yet because QA is ongoing. It will be automatically deployed to staging after the next production release.

@luacmartins The above-reported performance issue was caused by another PR (https://github.com/Expensify/App/pull/46645) for which I just reviewed the fix PR (https://github.com/Expensify/App/pull/47891) today which is pending performance testing and merge.
The same report was posted on all recently merged PRs which are in sync with main.

Thanks @ikevin127! I removed the blocker label.

🚀 Deployed to staging by https://github.com/luacmartins in version: 9.0.25-0 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
failure ❌

🕸 web 🕸
success ✅

🚀 Deployed to staging by https://github.com/luacmartins in version: 9.0.25-0 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
failure ❌

🕸 web 🕸
success ✅


Upm support

Hi,
I moved the plugins folders,
created package.json,
removed default settings asset
I haven't tried it in a real project yet.

Thanks for your response,
Changing value of Editor\GameJolt\Tools.cs 'ManagerPrefabPath'  probably broke the old .unitypackage file structure. It may be necessary to find a solution to this before merge.

Thanks for your response,
Changing value of Editor\GameJolt\Tools.cs 'ManagerPrefabPath' probably broke the old .unitypackage file structure. It may be necessary to find a solution to this before merge.

right, good point. Probably best to keep both paths, if the old path exists -> move file (+meta file) to new path

I've created a upm-support branch in my repo too, so if you just retarget this PR to that branch, we can merge it and I'll take care of some open issues, like upgrading from older packages and stuff.


Sprites sometimes miss a champion

The champion sprites sometimes miss the last champion (last released).
e.g. : https://lol-item-sets-generator.org/sets/597848171a9c4f250017d0b8 (misses Kayn)

This might be the issue :
[GENERATOR] Generating the ChampionIcon sprites ...
  league-sprites Initializing a new generator ... +0ms
  league-sprites Initializing API +3ms
  league-sprites Initialized API +542ms
  league-sprites Initializing a new generator : done ! +1ms
  league-sprites Generating ... +6ms
  league-sprites Requesting 'ChampionIcon' data ... +6ms
  league-sprites Requesting champions icons ... +2ms
  league-sprites Got 137 requests to execute. Executing ... +834ms
  league-sprites Requests executed.
Shuting down Kue ...
Exiting ...

The sprites generator closes early, maybe because of a non-handled internal error.


add sample for aurora serverless v2 scheduled scaling

Moves samples to samples directory.
Adds new sample for scheduled auto-scaling of Aurora Serverless V2.
By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.

In the README.md > Contents >
The link to Scheduled Autoscaling Aurora Serverless V2
Is broken and Is pointing to : https://github.com/aws-samples/data-for-saas-patterns/blob/feat/scheduled- scaling-apgv2/README.md#scheduling-autoscaling-aurora-serverless-v2
The link should resolve to : https://github.com/aws-samples/data-for-saas-patterns/blob/feat/scheduled- scaling-apgv2/README.md#scheduled-autoscaling-aurora-serverless-v2

[Scheduled Autoscaling Aurora Serverless V2](README.md#scheduled- autoscaling-aurora-serverless-v2)

The samples/multi-tenant-vector-database/amazon-aurora/cdk/ README.md file needs update as well to include the samples sub- directory.
Deployment Instructions
Step 2
cd data-for-saas-patterns/multi-tenant-vector-database/amazon-aurora/ cdk
Confirm validating the NAG rules for Lambda in the CDK project ( aurora serverless v2 scheduled scaling)
It was difficult for me to identify the dbClusterId for the Aurora Serverless cluster needs to be set in the cdk.context.json ( Just a comment and No fix required)
In the “scheduled-aurora-serverless-scaling” sample readme, post deployment instructions there was no mention of how to validate the scheduled scaling has run based on the defined cron parameters. I could not find a CLI command to read the scaling configuration and the current ACU. Looks like cloud watch metrics are the only way to monitor. Do you want to hint how to validate ?

Thanks @nihilg !
I've addressed all your comments in the latest commit: https://github.com/aws-samples/data-for-saas-patterns/pull/3/commits/94c7b90893c8960cd05c649c03b5506895c21db2

Review complete !!


After creating of draft release, main is merged into develop using fast-forward

Conceptually, develop and main are two separate branches. After a release is made from develop, main is merged into develop. Because develop and main have the same tree at that point, this merge is automatically done as a fast-forward merge. At that point, develop and main point to the exact same commit.
I think it would make more sense to make an actual merge commit, such that this action always leads to two separate branch tips. This should already be the case if a release is made from a branch different than develop.
What do you think, @DaniBodor?

I don't really see the issue here, but your suggestion sounds fine as well.

This has now been fixed with the release of v1.2.0.


fix resource name, for FCS

otherwise instead of expected FSStrings.resources will use FSharp.Compiler.Service.netstandard.FSStrings.resources
ref #4150

@enricosada, thanks for this.

Thank you


Resources affording other resource actions (linking)

Given this blueprint (currently valid syntax):
# Author [/author/{id}]
- Parameters
    - id (number) - Id of the author
- Attributes
    - email (string) - Email of the author

## Retrieve Author [GET]
- Relation: self
- Response 200 (application/json)
    - Attributes (Author)

I want to be able express that another resource affords the "Retrieve Author" action without the need to duplicate the "Retrieve Author".
For example like this:
# Blog Post [/blogpost/{id}]
- Parameters
    - id (number) - Id of the Blog Post
- Attributes
    - content (string) - Content of the Blog Post

## Retrieve [GET]
- Relation: self
- Response 200 (application/json)
    - Attributes (Blog Post)

## Action Retrieve Gist Author
- Relation: author (Author[self])

This enables linking of the resources and hence HATEOAS description.

Can you please update the last part of the example? It's not exactly clear.

@pksunkara that is just a sketch of my idea. Yes, it is introducing the Action keyword


Enable support for Fabric Private Chaincode

Is your feature request related to a problem? Please describe.
Fabric Private Chaincode is a new type of Fabric Chaincode which allows to execute smart contracts with the help of trusted execution environments (i.e., Intel SGX) to enhance protection of a smart contract and data.
Fabric Private Chaincode requires the use of external builders / chaincode-as-a-service feature in Fabric. Adding support for this may required to resolve issue #1284 first.

Stale issue, closing it


Apply to CSCW Workshop

https://sites.google.com/umn.edu/critical-public-tech
https://sites.google.com/umn.edu/critical-public-tech/callforparticipation?authuser=0

https://docs.google.com/document/d/1xwn3v-s-IxJlKBrO1CXoKaf8FCBtB5WyEQrLg4z6fG8/edit?usp=sharing


B 17910 hal sc creates or modifies a shipment 2 merging from main story to main

Agility B-17910
Summary
I have verified the items in the H&AL are correctly shown, and have added the downstream action of the closeout office added to the H&AL, as that is part of the flow for editing/creating a move for the SM.
Verification Steps for the Author
These are to be checked by the author.

[ ] Tested in the Experimental environment (for changes to containers, app startup, or connection to data stores)
[ ] Have the Agility acceptance criteria been met for this change?

Verification Steps for Reviewers
(Playwright test for the SM creating a move and the SC getting to the H&AL page not included)
These are to be checked by a reviewer.

[ ] Has the branch been pulled in and checked out?
[ ] Have the BL acceptance criteria been met for this change?
[ ] Was the CircleCI build successful?
[ ] Has the code been reviewed from a standards and best practices point of view?

Setup to Run the Code

Instructions for starting the MilMove application
Instructions for running tests

How to test

Access the
Login as a service member
Create a ppm
Log in as SC
Navigate to the move that was newly created
Edit details of the move
Observe the changes populate properly in the audit history tab
Create a new PPM for the service member
Observe the changes populate in the audit history tab

To make it easier, you can run my automation steps for this:
https://gist.github.com/landan-parker-0/fb8d17ab88b79dabd56d83eb3591bec6
Just dump that into a file named scEditsServiceMemberPPM or something within the test folder: office, where the other playwright flows are.
It will show up as a test
You can run it with command line.
yarn playwright test -g 'services counselor edits ppm'
Status: SUBMITTED

Pro-gear: Yes

Pro-gear weight: 245 lbs

Spouse pro-gear weight: 357 lbs

Estimated weight: 602 lbs

Expected departure date: 17 Feb 2024

Sit expected: Yes

SIT estimated storage start: 17 Feb 2024

SIT estimated storage end: 24 Feb 2024

SIT estimated storage weight: 526 lbs

Pickup postal code: 63653

Destination postal code: 29101

SIT location: DESTINATION

SIT estimated cost: $104.09

PPM estimated incentive: $22,603.25

Frontend

[ ] There are no aXe warnings for UI.
[ ] This works in Supported Browsers and their phone views (Chrome, Firefox, Edge).
[ ] There are no new console errors in the browser devtools.
[ ] There are no new console errors in the test output.
[ ] If this PR adds a new component to Storybook, it ensures the component is fully responsive, OR if it is intentionally not, a wrapping div using the officeApp class or custom min-width styling is used to hide any states the would not be visible to the user.
[ ] This change meets the standards for Section 508 compliance.

Backend

[ ] Code follows the guidelines for Logging.
[ ] The requirements listed in Querying the Database Safely have been satisfied.

Database
The history fetcher sql file has changed
https://github.com/transcom/mymove/blob/2d9d1bbeb70cdb73a8283892c5265953b539e329/pkg/assets/sql_scripts/move_history_fetcher.sql
move_logs AS (
  SELECT
    audit_history.*,
    jsonb_agg(jsonb_strip_nulls(
      jsonb_build_object(
        'closeout_office_name',
        (SELECT transportation_offices.name FROM transportation_offices WHERE transportation_offices.id = uuid(c.closeout_office_id))
      ))
    )::TEXT AS context,
    NULL AS context_id
  FROM
    audit_history
  JOIN move ON audit_history.object_id = move.id
  JOIN jsonb_to_record(audit_history.changed_data) as c(closeout_office_id TEXT) on TRUE
  WHERE audit_history.table_name = 'moves' group by audit_history.id
),

Any new migrations/schema changes:

[ ] Follows our guidelines for Zero-Downtime Deploys.
[ ] Have been communicated to #g-database.
[ ] Secure migrations have been tested following the instructions in our docs.

Screenshots

![image](https://github.com/transcom/mymove/assets/148263228/c717cefe-41a7-40a5-9141-08c945dc4ed4)

You're missing playwright/tests/office/txo/tooFlowsNTS.spec.js changes from your int branch. Other than that it looks the same


docs: update README (take over #131)

take over #131

Proposed Changes
I have structured the README. Only the essential information is retained in the README, and I've made changes to store each document in the docs directory. This is based on the structure of the CodeQL repository.
(If there are any rules or standards we must adhere to within the GitHub organization, I would like to make further adjustments to comply with them.)
Readiness Checklist
In addition, I made the following changes:

Removal of the Table of Contents: GitHub's markdown preview has an automatic table of contents generation feature. It's unlikely we need to maintain this ourselves.
Removal of permalinks to each document: Most users should notice that the documents are stored in the docs directory. Managing permalinks can be cumbersome, so I believe it's best to remove them.

Author/Contributor
Note: In this PR, since only documentation updates are being made, I don't anticipate any linting or testing issues to arise.

[x] If documentation is needed for this change, has that been included in this pull request
[x] run make lint and fix any issues that you have introduced
[x] run make test and ensure you have test coverage for the lines you are introducing

Reviewer

[ ] Label as either bug, documentation, enhancement, infrastructure, or breaking

It seems there are still some points that need correction. After making the changes, I will undraft the PR.

it looks like a few of the docs like the json output, measuring time and others in the docs directory aren't all referenced in the  README. I think each doc should at least get a mention in the readme.

Thank you for the wonderful review!!
Regarding "I think each doc should at least get a mention in the readme.", are you suggesting adding a section with links to each item as in the following example?
## links

- []

Yes that would be great.

Thank you for the wonderful review!! I made three changes.

I've reverted the changes to the footnote.
I've reverted the changes to the example use case.
I've added a section with links to each document in the README.

@zkoppert looks like merging this has accidentally done some of the changes that we did in https://github.com/github/issue-metrics/pull/137 prior to this.

@spier Good Catch! I'll get that corrected. https://github.com/github/issue-metrics/pull/140


Segmentation Fault when Calculating Spatial Autocorrelation

Description
Dear Squidpy Team,
Previously I have used Squidpy's 'gr.spatial_autocorr` function to calculate the Moran's I values for genes to great effect. However, recently, I find that using the function, for however many genes, causes my Python to crash. I find that it happens even when I try to reproduce the Visium H&E tutorial, and it also happens when I try and run the code using either Python 3.8 or Python 3.10.
Below is the code I ran:
import scanpy as sc
import anndata as ad
import squidpy as sq

import numpy as np
import pandas as pd

sc.logging.print_header()
print(f"squidpy=={sq.__version__}")

# load the pre-processed dataset
img = sq.datasets.visium_hne_image()
adata = sq.datasets.visium_hne_adata()

sq.gr.spatial_neighbors(adata)

genes = adata[:, adata.var.highly_variable].var_names.values[:1000]
sq.gr.spatial_autocorr(
    adata,
    mode="moran",
    genes=genes,
    n_perms=100,
    n_jobs=1,
)

The versions of all the Python modules I am using are:
scanpy==1.9.1 anndata==0.8.0 umap==0.5.3 numpy==1.23.3 scipy==1.9.1 pandas==1.5.0 scikit-learn==1.1.2 statsmodels==0.13.2 python-igraph==0.10.1 pynndescent==0.5.7
squidpy==1.2.2

And this is the following error I get:
OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
Segmentation fault: 11

The above warning about omp_set_nested has happened in the past but has not been an issue. The segmentation fault is the new occurrence that I do not get. If you have any advice on how to fix this, I would greatly appreciate it. Thank you!
Best wishes,
Axel.

I think it's numba, what's the numba version?

Hi @giovp, this tracks to me, as I think I updated numba recently for a different Python package. My numba version is currently 0.56.2.

Hi @giovp,
I see, thank you for clarifying! Until it gets fixed in a later version of squidpy, I'm personally fine with reinstalling squidpy in a virtual environment where I pin the numba version to 0.55.0.
Thanks again for your help!

you're welcome and apologies, it's on my todo list.

we should really try to get numba (and numpy) up to date for 1.3

hi @axelalmet ,
I think this issue is fixed, in main now there is no pin to numba version,. I also encountered sometime the kernel dying but usually refreshing with a new conda env should work. We tested the function with latest numba.


Request Android record permission when needed

Fixes #26506

Works perfectly on my phones (Xiaomi Pocophone F1 with Android 9 and Samsung Galaxy S3 with Android 7.1.2) with the Mic Record demo.
Starting the app triggers this permission request as expected:

Then the recording feature works. Subsequent runs don't re-require the permission.

Awesome, thanks for the testing!

@BastiaanOlij Should be relevant for your work :)

Thanks!

Beautiful! I'm going to redo the permissions logic for ARCore so it requests the camera permissions through this. I'll probably do a separate PR for just the camera permissions once I get my head around it.

@marcelofg55, I'm trying to duplicate this for the camera, if i understand the changes correctly, you now call request permissions from the audio driver.
If permissions were previously given this returns true and the audio driver initialises.
If no permissions where previously given the dialog opens but since code continues we return false.
When the user accepts the permissions we get a signal from the OS which is handled in onRequestPermissionsResult but what I'm missing is how you now trigger the audio driver to initialize now that it can?

@BastiaanOlij check this: https://github.com/godotengine/godot/blob/master/platform/android/java_glue.cpp#L1586
Basically onRequestPermissionsResult calls that function on java_glue.cpp and capture_start is called to initialize the audio input.


Added Highly Reusable Stepper component

Fixes #58
Commit Summary
Added Highly Reusable Stepper component that can be customizable via props

These components were added in further PRs. Thanks for your contribution @ffalpha :)


serialport issue trying to initiate 2 Tessel 2's - Pre-compiled module is missing: Could not locate the bindings file.

Greetings, thank you in advance for your dedication. This is my first time posting here, bear with me if additional info is needed. Quick backstory. I'm playing around with a Johnny Five Inventors Kit to both learn some coding, and I'm trying to make a diecast drag race system. I have a nice start, it has a "Christmas tree" and 2 controllers, records reaction times, red light fouls, drives servos to open the startgate. times are being sent to a webserver and displaying on a wifi dashboard. I have a webcam attached streaming to the dashboard. Its coming together BUT....I ran out of pins on the Tessel and need a second one for finish line sensors and perhaps some motion detection (not sure how I'm going to detect and snap a photo finish)
Here is what i have been using to initiate a single board and it works well.
const Tessel = require("tessel-io")
const Five = require("johnny-five")
const board = new Five.Board({
io: new Tessel()
})
I plugged in the second board to the first ones USB and adjusted my init as follows: Now I'm getting serialport messages about pre-compiled modules being missing and not locating the bindings file.
const Tessel = require("tessel-io")
const Five = require("johnny-five")
const boards = new Five.Boards(["A","B"])({
io: new Tessel()
})
2nd EDIT: this is the complete output, I realized i left stuff out.
WARN Pre-compiled module is missing<EMAIL_ADDRESS>WARN Please file an issue at https://github.com/tessel/t2-cli/issues/new with this warning.
WARN
WARN This warning might be caused by one of the following:
WARN
WARN 1. A pre-compiled binary has not yet been built for this module.
WARN 2. The binary didn't compile correctly for the platform that you're developing on.
WARN    Binaries that are Linux-only or even OpenWRT-specific may cause this issue.
WARN    Try to npm install --force the affected module, then rerun your deployment command.
WARN 3. The binary may be platform specific and impossible to compile for OpenWRT.
WARN Pre-compiled module is missing<EMAIL_ADDRESS>WARN Please file an issue at https://github.com/tessel/t2-cli/issues/new with this warning.
WARN
WARN This warning might be caused by one of the following:
WARN
WARN 1. A pre-compiled binary has not yet been built for this module.
WARN 2. The binary didn't compile correctly for the platform that you're developing on.
WARN    Binaries that are Linux-only or even OpenWRT-specific may cause this issue.
WARN    Try to npm install --force the affected module, then rerun your deployment command.
WARN 3. The binary may be platform specific and impossible to compile for OpenWRT.
ERR! Error: ENOENT: no such file or directory, stat '/home/curt/.tessel/binaries/usb-1.7.1-Release-node-v57-linux-mipsel/Release/usb_bindings.node'
ERR!     at Object.statSync (node:fs:1156:3)
ERR!     at Object.statSync (/home/curt/.nvm/versions/node/v16.0.0/lib/node_modules/t2-cli/node_modules/graceful-fs/polyfills.js:312:16)
ERR!     at Object.copySync (/home/curt/.nvm/versions/node/v16.0.0/lib/node_modules/t2-cli/node_modules/fs-extra/lib/copy-sync/copy-sync.js:31:86)
ERR!     at /home/curt/.nvm/versions/node/v16.0.0/lib/node_modules/t2-cli/lib/tessel/deployment/javascript.js:408:16
ERR!     at Map.forEach ()
ERR!     at /home/curt/.nvm/versions/node/v16.0.0/lib/node_modules/t2-cli/lib/tessel/deployment/javascript.js:381:23
ERR!     at new Promise ()
ERR!     at Object.exportables.injectBinaryModules (/home/curt/.nvm/versions/node/v16.0.0/lib/node_modules/t2-cli/lib/tessel/deployment/javascript.js:373:10)
ERR!     at /home/curt/.nvm/versions/node/v16.0.0/lib/node_modules/t2-cli/lib/tessel/deployment/javascript.js:643:23
ERR!     at Project.collect (/home/curt/.nvm/versions/node/v16.0.0/lib/node_modules/t2-cli/node_modules/t2-project/lib/index.js:186:7) {
ERR!   errno: -2,
ERR!   syscall: 'stat',
ERR!   code: 'ENOENT',
ERR!   path: '/home/curt/.tessel/binaries/usb-1.7.1-Release-node-v57-linux-mipsel/Release/usb_bindings.node'
ERR! }
WARN Pre-compiled module is missing<EMAIL_ADDRESS>WARN Please file an issue at https://github.com/tessel/t2-cli/issues/new with this warning.
WARN
WARN This warning might be caused by one of the following:
WARN
WARN 1. A pre-compiled binary has not yet been built for this module.
WARN 2. The binary didn't compile correctly for the platform that you're developing on.
WARN    Binaries that are Linux-only or even OpenWRT-specific may cause this issue.
WARN    Try to npm install --force the affected module, then rerun your deployment command.
WARN 3. The binary may be platform specific and impossible to compile for OpenWRT.
INFO Writing project to RAM on lobot (1128.96 kB)...
INFO Deployed.
INFO Running twoboards.js...
/tmp/remote-script/node_modules/bindings/bindings.js:135
throw err;
^
Error: Could not locate the bindings file. Tried:
→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>→<EMAIL_ADDRESS>at bindings (/tmp/remote-script/node_modules/bindings/bindings.js:126:9)
at Object. (/tmp/remote-script/node_modules/serialport/node_modules/@serialport/bindings/lib/linux.js:1:119)
at Module._compile (module.js:652:30)
at Object.Module._extensions..js (module.js:663:10)
at Module.load (module.js:565:32)
at tryModuleLoad (module.js:505:12)
at Function.Module._load (module.js:497:3)
at Module.require (module.js:596:17)
at require (internal/module.js:11:18)
at Object. (/tmp/remote-script/node_modules/serialport/node_modules/@serialport/bindings/lib/index.js:1:346)
T2 version from both Tessels
INFO Tessel Environment Versions:
INFO t2-cli: 0.1.23
INFO t2-firmware: 0.2.0
INFO Node.js: 8.11.3
I'm running all this from an Ubuntu Ubuntu 20.04.2 LTS. I have seen a few posts on this and it seems those resolutions either did not work or did not apply. I've tried switching my Node around to different version to no avail. Interestingly I wanted to try node v6 due to a post I saw but I cannot even get the T2 cli to work with that version. I just returned back to what i was using (v16.0.0.)

I'm still stumped on this issue but I did find out that could control LED's with the servo module board so that changed the game and can now finish my project with only one board.   I'll leave this open though feel free to close it and leave a comment for my continuing education =)

I kept quiet on this because I don't really know the answer and can only speculate. The T2 is locked into an older version of node but it looks like this is trying to install the latest version of serialport which almost certainly doesn't work on that older version (hence no precompiled binaries). You might try using older version of Serialport (which may require an older version of Johnny-Five and/or firmata.js).
That said, it's kinda weird that you'd use one T2 to control another, and I'm not sure that could ever work. T2's don't have a fimata-like client the listens to a host for instructions. Everything runs onboard using tessel-io. I do know you can control an Arduino or something similar from a T2, but even that I've not seen it done in practice.
I'm glad you discovered the servo module because that is a far more practical solution.
By the way, your project sounds super cool. When you get it running but sure to tweet about it and tag @nodebots. We'd love to see it in action.

Hey no worries thanks for the reply. The biggest thing you answered for me I think is, can I even plug in 2 boards like that. So I was just being a rookie on that.  What do you do though when you do need more pins for stuff? I know you can initiate 2 boards from the examples on the J5 API site. There is a Boards constructor (did I term that right BTW?) example so it is possible for 2 boards to run 1 program correct?  If they are both just usb tethered or wifi connected, which one does your program go to when you T2 run or push? I'm so confused thinking about it right now but luckily I dont really need the answer now but would still like to know. Eventually I will want to expand on this and will want to be a able to use a second board.
I'm not on Twitter or FB but I'll look for nodebots on IG
But yeah I made progress now. I added a timer and IR finish line beam for one of the lanes and it worked! =)
Thanks again.


Create static pages

ILS should come by default with a set of static pages similar to what users can find in a website. The default content can be something fake because it must be customizable.
Pages to create by default in ILS:

About Us (cmpId: static-page-about-us)
Contacts (cmpId: static-page-contacts)
Privacy (maybe?)

Each page should have simply a title and a content. Static pages links should be displayed in the footer.
What should be customizable:

the title
the content
the name of the link (can differ from the title)
the URL, if possible

Example of a possible static page component:
<StaticPage cmpId={} title={} content={} renderCmp={} />

The overlay that overrides ILS should be able to override existing and add a new page with a simple config, e.g.
const myILSConfig = {
    cmps: {
        'static-page-about-us': {
          link: {
              label: 'About',
              urlPath: '/about'
            },
          title: "About"
          content: "
New content
"
        }
    },
    extraStaticPages: [{
        cmpId: '',
        link: {
          label: 'Opening Hours',
          urlPath: '/opening-hours'
        },
        ---
        title: 'Library Opening Hours',
        content: <OpeningHoursContent /> or '
lorem
'
        --- OR ---
        renderCmp: <FullOpeningHoursContentCmp />
        ---
    }]
]}

Tasks

Add to react-router the possibility of defining routes by config (this link.urlPath)
Implement the static page cmp
Create the "override" functionality to override any component in ILS and inject props from a config object as in the example
Implement the extra static pages

These are the slides from indigo on how they override react components might be worth having a look.
https://codimd.web.cern.ch/p/By7Ar3fUN#/


Conda forge version is extremely old.

While there is a conda forge of this useful module it was last updated more than 2 and a hlaf years ago as of raising this issue: https://anaconda.org/conda-forge/pynrrd.   Is anyone maintaining this package considering updating it now that version 1.0.0 is out?

oops wrong  module


HDDS-2389. add toStateMachineLogEntryString provider in Ozone's ContainerStateMachine.

What changes were proposed in this pull request?
This jira adds toStateMachineLogEntryString provider in Ozone to dump state machine information.
This will help in dumping statemachine information to add more debug logging in Ozone.
What is the link to the Apache JIRA
https://issues.apache.org/jira/browse/HDDS-2389
How was this patch tested?
After the changes, the output is of the format
cmd=WriteChunk, container id=1, block id=1:local id=103249826429730816, chunk=103249826429730816_chunk_4:offset=0:length=1048576, container path=/Users/mukul/code/apache/ozone/oz2/hadoop-ozone/tools/target/test-dir/MiniOzoneClusterImpl-a2eee0ed-29d1-453d-939d-0f3d579fa828/datanode-2/data/containers/hdds/12b781f5-bde6-4c3e-8a62-950824ff71d5/current/containerDir0/1

Thanks for the review @lokeshj1703. I have addressed the review comments.

@mukul1987 Thanks for the contribution! I have merged the PR to master branch.


fix: strip HTTP/2 pseudo-headers and symbol keys from headers

closes https://github.com/sveltejs/kit/issues/11365
cc: @Conduitry @benmccann
This PR gets the Vite HTTPS working again by filtering out two types of keys from the incoming request headers object before we pass it to a new Request object. Doing so prevents the two errors we currently encounter as shown below.

When there's a symbol key in the request headers:

TypeError: Request constructor: init.headers is a symbol, which cannot be converted to a DOMString.
    at webidl.errors.exception (node:internal/deps/undici/undici:3384:14)
    at webidl.converters.DOMString (node:internal/deps/undici/undici:3650:29)
    at webidl.converters.ByteString (node:internal/deps/undici/undici:3658:35)
    at Object.record<ByteString, ByteString> (node:internal/deps/undici/undici:3567:30)
    at webidl.converters.HeadersInit (node:internal/deps/undici/undici:8715:67)
    at Object.RequestInit (node:internal/deps/undici/undici:3624:21)
    at new Request (node:internal/deps/undici/undici:9267:34)
    at getRequest (file:///home/chewteeming/my-app/node_modules/.pnpm/@sveltejs+kit@2.7.3_@sveltejs+vite-plugin-svelte@4.0.0_svelte@5.1.4_vite@5.4.10__svelte@5.1.4_vite@5.4.10/node_modules/@sveltejs/kit/src/exports/node/index.js:122:9)
    at file:///home/chewteeming/my-app/node_modules/.pnpm/@sveltejs+kit@2.7.3_@sveltejs+vite-plugin-svelte@4.0.0_svelte@5.1.4_vite@5.4.10__svelte@5.1.4_vite@5.4.10/node_modules/@sveltejs/kit/src/exports/vite/dev/index.js:497:27
    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)

When there's HTTP/2 pseudo-headers in the request headers (partially reimplements https://github.com/sveltejs/kit/pull/3572/files):

TypeError: Headers.append: ":method" is an invalid header name.
    at webidl.errors.exception (node:internal/deps/undici/undici:3384:14)
    at webidl.errors.invalidArgument (node:internal/deps/undici/undici:3395:28)
    at appendHeader (node:internal/deps/undici/undici:8339:29)
    at fill (node:internal/deps/undici/undici:8325:11)
    at new Request (node:internal/deps/undici/undici:9490:13)
    at getRequest (file:///home/chewteeming/my-app/node_modules/.pnpm/@sveltejs+kit@2.7.3_@sveltejs+vite-plugin-svelte@4.0.0_svelte@5.1.4_vite@5.4.10__svelte@5.1.4_vite@5.4.10/node_modules/@sveltejs/kit/src/exports/node/index.js:118:9)
    at file:///home/chewteeming/my-app/node_modules/.pnpm/@sveltejs+kit@2.7.3_@sveltejs+vite-plugin-svelte@4.0.0_svelte@5.1.4_vite@5.4.10__svelte@5.1.4_vite@5.4.10/node_modules/@sveltejs/kit/src/exports/vite/dev/index.js:497:27

Open to suggestions for a better way to do this.

Please don't delete this checklist! Before submitting the PR, please make sure you do the following:

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[ ] Ideally, include a test that fails without this PR but passes with it.

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[x] Please ensure that 'Allow edits from maintainers' is checked. PRs without this option may be closed.

Since Vite is involved, this is a dev-only issue, right?
The issue we ran into before IIRC is that node-fetch didn't like these headers. That became unnecessary when we switched to Undici.
The function you're modifying in this PR is the main function to generate the Request object in production for various adapters for Node-based systems. This won't immediately make more work in production for apps using them (since the released version of the adapters bundle this code), but eventually it will.
Without looking much at what would be involved with this, my sense is that we should focus on the dev-time code, which would mean adjusting how getRequest is called at https://github.com/sveltejs/kit/blob/8ec471c875345b751344e67580ff1b772ef2735b/packages/kit/src/exports/vite/dev/index.js#L497 rather than adjusting the getRequest implementation.
We may then also need to do something for preview-time. But we shouldn't be doing this extra work to normalize requests in prod builds if it's not necessary.

Turns out the better alternative was to set the no-op proxy config (which fixed another issue the previous implementation had). I'm not sure if the overridden config is in the right place but it doesn't seem to work if done too late such as immediately before configuring the dev and preview server.

preview: https://svelte-dev-git-preview-kit-12907-svelte.vercel.app/
this is an automated message

Awesome to close such a frequently encountered issue! Thanks!!


Create documentation and make the filenames less cryptic

The filenames are reasonably sensible now.

I've added an example script. I'd like somewhere that clearly spells out how to input the arguments to the sampling function (in particular that for the square we don''t input the dimension).

The paper-diagrams-script.py and EXAMPLES.py are probably good enough documentation


Prevent the back button from being pressed

What a great, simple to use Package.
I need a function to prevent the back button from being pressed, because I use this dialog while synchronizing data and to prevent
Unhandled Exception: Failed assertion: boolean expression must not be null

kind of error, because progress_dialog no longer exist in widget tree
For this reason I add the following line to my code.
I hope you can add this function, because maybe many people need it.
Thanks.
  Widget build(BuildContext context) {
    final DialogTheme dialogTheme = DialogTheme.of(context);
    //start from this line
    return WillPopScope(
        onWillPop: () => Future.value(false),
        child: AnimatedPadding(
  //to this line

sure thank you for pointing out

thank you its fixed now


Session timeouts in a couple hours.

Integration stops working entirely after about 4 hours spamming the following error:
Retrying API call: 'user/login'

Restarting full: '3144' - 'login failed, loginId is empty, please login again.'

It seems there was some work done about it before:
https://github.com/NeoAcheron/midea-ac-py/compare/master...Michael0yodi:master
Not sure If the fix is supposed to be in the library or on the homeassistant side.

Those should be incorporated here I think, plus I added some changes in b9c64be520b8eafb8ddc0320e0406bd19947ef91 which helped before.
I don't experience this issue, but then I do have to disable polling with the fan_only_workaround option, so maybe that could be why.

Ok, sorry for the delay. Further testing with fan_only_workaround doesn't affect it. In a couple hours after the first connect if you press any button it just begins to spam
Restarting full: '3144' - 'login failed, loginId is empty, please login again.'
Retrying API call: 'user/login'

And this continues until hass restart.  Is there a chance that restart full doesn't get triggered in client.py?

Found it! The issue was on my side. For some reason it was pulling the wring midea lib. Works as expected in both modes now.


Update styles.css

Removes this small padding created by empty headers that occur when "show relationship type" is disabled. See video.
https://user-images.githubusercontent.com/73286100/148697214-c03e4338-2b3d-46f0-9d4d-6a79c08a5be9.mov

Nice! Thanks alot :)


VMs not reboot persistent - kubelet not starting because of swap

Hi,
thanks for sharing this!
After setting up a working cluster the individual VMs are not reboot safe. After a reboot the kubelet was not start because of swap being enabled. The playbooks does a 'swapoff -a' which is not persistent.
One way of diabling swap in a persistent way would be to create a SystemD service to turn it off before starting Kubelet. Like this:
# /etc/systemd/system/swapoff.service

[Unit]
Description=Swapoff, kubelet requirement
After=network.target
Before=kubelet.service

[Service]
Type=oneshot
ExecStart=/sbin/swapoff -a
RemainAfterExit=true

[Install]
WantedBy=multi-user.target

Where would be the best place in the code to implement this? I would be happy to give a pull request a shot.
Cheers,
Thomas

Hi @twillert, thank you for your report, I think you can implement this in k8s-setup role.

fixed #147 .


smp_ros: 1.0.1-0 in 'kinetic/distribution.yaml' [bloom]

Increasing version of package(s) in repository smp_ros to 1.0.1-0:

upstream repository: https://github.com/ksatyaki/smp_ros.git
release repository: https://github.com/ksatyaki/smp_ros-release.git
distro file: kinetic/distribution.yaml
bloom version: 0.6.4
previous version for package: 1.0.0-0

smp_ros
* Add mrpt as a dependency in package.xml
* Contributors: Chittaranjan Swaminathan

Sorry for back-to-back pull requests.
Build failed previously due to the absence of  tag for MRPT. Now it compiles on Jenkins.


[Performance]: 1P1D Disaggregation performance

Proposal to improve performance
I try to reproduce the P&D 1P1D benchmark to compare performance with chunked prefill  https://github.com/vllm-project/vllm/blob/main/benchmarks/disagg_benchmarks/disagg_performance_benchmark.sh. TTFL is higher than what I expected. Because the overhead benchmark only shows ~20-30ms level. What's more, seems ITL is also much higher than chunked prefill.

GPU device: 2* L40S.
Model: Qwen/Qwen2.5-7B-Instruct
Parameters: gpu-memory-utilization 0.6 + kv_buffer_size 10e9
dataset input 1024 output 50.

/cc @KuntaiDu
Report of performance regression

Misc discussion on performance
No response
Your current environment (if you think it is necessary)
The output of `python collect_env.py`

Before submitting a new issue...

[X] Make sure you already searched for relevant issues, and asked the chatbot living at the bottom right corner of the documentation page, which can answer lots of frequently asked questions.

50-token output is too long for 1P1D setup. For disaggregated prefill to have similar performance as chunked prefill, the prefill workload v.s. decode workload should be roughly 1:1 (in terms of runtime). I would suggest trying just 8 tokens and rerun the benchmark.

Also, disaggregated prefill does not improve throughput compared to chunked prefill (chunked prefill typically has higher batch size as it can batch prefill request, so its throughput is typically higher). The main goal of disaggregated prefill is to decouple the prefill and the decode instance so that people can tune TTFT without affecting ITL, or tune ITL without affecting TTFT.

GPU device: 2* L40S.
dataset input size 1024 output size 6 (default value)
model: Qwen/Qwen2.5-7B-Instruct

chunk-size 512

chunk-size 2048

I notice the default chunk size has been recently to 2048 so I change back to 512 and add another test result. Seems the 1P1D ITL is still higher. Actually, what makes me confused is ITL itself should not be affected by anything, TTFT may start to queuing but decode machine only handles 100 request * 6 tokens decoding, why does it become slow..
I did remember I tested the PR branch last month, it works as expected but not sure what has been changed or any tricks on the configuration

Same experimental results. Don't know why.

Copy-pasted from my response in slack:
The ITL is higher, because in the current version sometimes the KV cache transfer may fail, and when failure happens, the decode instance needs to redo the prefill, which inflates ITL.
About the matching, I empirically measured the prefill time, and the ITL, and found that 6 is roughly the number that makes T_prefill = 5 x ITL
The ITL is higher, because in the current version sometimes the KV cache transfer may fail, and when failure happens, the decode instance needs to redo the prefill, which inflates ITL.
This happens rarely (but happens in high QPS), and we had a fix in an old version of PR (but we removed that fix as it complicates the code and make it harder for code review --- we will contribute that part of code back).

The current issue is likely that the asynchronous transmission operations are conflicting with the computation operations (for reasons unknown), leading to various illegal memory accesses, data corruption in send/recv tensors, and performance degradation (as mention in this post).
To my best knowledge, NCCL operations running on another stream should have no impact on normal compute stream in vLLM. However, illegal memory access errors frequently appear when QPS is large (like 128 query/second with 1024 token length input), which appears (to me) that somehow the NCCL operations are conflicting the other CUDA operations. According to error log, I try to set CUDA_LAUNCH_BLOCKING=1 to envs and all errors disappear, so I suspect that maybe the "asynchronous" NCCL operations are not fully async.
Not sure if my observation is correct. Any ideas?

I observed that the GPU utilization of the decode instances is very low.


Fix version file URL property

The current URL is a 404.
Now it's fixed.
Tagging @Orthethac because not everyone has GitHub notifications enabled for pull requests.

Hey sorry, I've been away from KSP. Hoping to get back into it. Thanks for the fix!


[PF-2783] Add read only file permission bits

Currently, when a user mounts a bucket as read only and runs ls -l inside the mounted bucket, the files will have incorrect permission bits set. The default 644 (rx-r--r--) set by gscfuse. @mbookman proposed using the --file-mode and --dir-mode flags in gcsfuse to set the correct read only file permissions on files and directories. This PR does just that!

Test failures are related to the rbs workspace creation issue. Merging as it is unrelated to the changes of this PR.


Arm version can not be exec on phytium d2000 (arm64 v8)

Arm version can not be exec on phytium d2000 (arm64 v8)
but recompile on this hardware platform,it runs normally
Good project

Hello @xiaohelong, correct, I dont provide any Linux ARM64 builds. Only ARMv6. Certainly something that could be included.

arm64 is now available with the latest release


List of used plugins

https://github.com/quackduck/devzat-wolframbot
https://github.com/Arkaeriit/devzat_forth
https://github.com/Arkaeriit/Devzat_Time_Teller
https://github.com/Arkaeriit/devzat-censor (still in trial phase)

There is also the Hackclub emoji one and the card one but I don't know where their code are.

https://github.com/Merlin04/devzat-hc-emoji and https://github.com/Merlin04/devzat-plugin-duckpoll


Any plans for supporting TLS 1.3?

Hi,
Are there any plans to support TLS 1.3?
Thanks!

Hi,
as soon as .NET will support TLS 1.3 this lib will do it as well.
Best regards
Christian


Preserving full-strength validation & error reporting

One of many issues around GitHub-based content management for bio.tools.

###UPDATE###


Any License ?

Hi, nice work. I would like to know what license this is distributed by as there is none specified.
Thank you.

license added.

Thank you. 👍
I will close this issue.


Upgrade to Selenium 2.45.0

This pull requests updates current atoms to latest stable release of Selenium.
All atoms were updated by your guidelines.
Except for the deps file (tools/atoms_build_dir/build.desc)
It was updated to make sure that we can build it by using the latest go util inside the Selenium repo
Also, fragment is_online was removed because it doesn't exist in the current Selenium repo.

Hey.
Thanks for this PR.
If memory serves me well though, updating atoms will most certainly require code changes: between Selenium 2.39 and 2.45 I bet the internal differ a lot.
Did you run the tests?
Did everything still hold?


max number of tasks per dask worker

I am using SGECluster to submit thousands of tasks to dask workers. I want to request a feature to specify max number of tasks per worker to improve cluster usage. For example, if it takes 4 hours to process a task, and the wall time limit for a worker is set to 5 hours (to make sure a single task can run through; and if the compute node goes abnormal, it will time out in 5 hours), then with the current dask configuration, each worker will waste 1 hour to run through the second task, and this second task will eventually get killed and resubmit to another worker. This is a waste of the compute cluster resource. So is it possible to specify max number of tasks X handled by each dask worker? Once a dask worker finishes handle X tasks (with whatever final status), then the dask worker (SGE job) will automatically get killed so we won't waste computing resource in the cluster.
Wish for similar feature for SLURMCluster as well. And appreciate for alternative workarounds.

moved to distributed board.


Automated cherry pick of #80: Add missing files Cherry pick of #80 on v0.7-branch. #80: Add missing files

This change is

/lgtm
/approve


unpin Pangolin data

What do you think if we unpin the underlying data for Pango lineages? So we can have the newest lineage assignments as new lineages become available... which also means we need to reinstate auto deployment, but that is a separate conversation.
I can only test the changes don't break things once they're on staging fyi.

I think we'll get best results by pinning to specific versions for a couple reasons:

We won't have or deploys fail unexpectedly due to changes unrelated to our code
Somewhat more importantly: the result each of those "RUN" commands gets cached in our CI pipeline. So even if the underlying version of pangolin / pangolin-data change, our CI builds won't actually re-run those commands and install the latest version unless something breaks the cache. Changing a version number will break the cache.

Good points!! Is there an easy way to keep our Pango lineages up to date then? Lineage definitions evolve as new lineages become available. For example SPHERE call today mentioned XBB.1.16 that's of interest but we don't have the definition for that lineage in our system, so Chicago will not know even if an XBB.1.16 show up in their samples


Stack sticky notes when clicked

If two notes are stacked, and you click the bottom one, it should be brought to the top.

working on this bby

Finished this, but needs to be updated with using the z position attribute of position I believe. I currently did it where it changes the position of the note in the array and adds it to the end which makes it appear on top.


Nimbus beaconcha.in stats don't show validator

Needs to be resolved upstream
https://github.com/gobitfly/eth2-client-metrics-exporter/issues/17

Requested that Nimbus implement this natively: https://github.com/status-im/nimbus-eth2/issues/6804


feat: shadcn library implementation

Complete refactor of UI components
Chakra UI removed since it doesn't work with Server Components.
Shadcn/ui components implemented instead in whole website.

This is great, thank you!


Interface for editing a treasury

Overview

Allow treasury managers to be able to configure the token to be transferable and stakeable, if desired.
Acceptance criteria

The treasury manager should be able to edit the treasury:

[ ] Set the tokens as transferable
[ ] Set the treasury as stakeable

Technical considerations

Tasks

@poplexity Viter has investigated the smart contract and has identified that it is possible to edit a treasury later. We're wondering if a treasury that doesn't have the token as transferable has any value. If it doesn't, we should set the token as transferable when creating the treasury.

This is addressed in the issue #207

This is being addressed in issue #207
so I close this one


Generate new x509 certificates for TLS testing

#349
Generated new x509 certificates for TLS testing.
Check List

[x] New functionality includes testing.

[x] All tests pass

[ ] New functionality has been documented.

[ ] New functionality has javadoc added

[x] Commits are signed per the DCO using --signoff

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

Codecov Report

Merging #350 (93e4986) into main (d6bdd7b) will increase coverage by 0.04%.
The diff coverage is n/a.

:exclamation: Current head 93e4986 differs from pull request most recent head ea4a592. Consider uploading reports for the commit ea4a592 to get more accurate results

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
@@             Coverage Diff              @@
##               main     #350      +/-   ##
============================================
+ Coverage     72.77%   72.81%   +0.04%
- Complexity     3045     3046       +1
============================================
  Files           381      381
  Lines         19013    19013
  Branches       1472     1472
============================================
+ Hits          13836    13844       +8
+ Misses         4581     4574       -7
+ Partials        596      595       -1

see 4 files with indirect coverage changes
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Withdraw announcement w/o healthy endpoints for TrafficPolicy Cluster

What this PR does / why we need it:
This PR ensures that BGP announcements are withdrawn for extrernalTrafficPolicy Cluster when no healthy endpoint is available. This is essential for geo redundancy setups with multiple datacenters, where traffic should be automatically shifted via BGP to the fail over datacenter when a service gets unhealthy.
Which issue(s) this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close the issue(s) when the PR gets merged):
Fixes #312
Special notes for your reviewer:
The largest addition is healthyEndpointExists, which mostly is a copy of nodeHasHealthyEndpoint, but without the filtering on a specific node. The logic is the same.
The real change is the else if branch in ShouldAnounce.

Corporate CLA might take a bit, I'm on it :-/

Any news on a CLA? Unfortunately I can't take patches without one, that's part of the deal where Google allowed me to open-source this :(

Hi @danderson, no progress unfortunately, but I'm still on it.
Is the PR otherwise acceptable for you? Anything to adapt?

The change looks fine (and addresses something I didn't think of at all, since I don't run anycast services), I think it's ready to merge as soon as the cla/google robot is happy.

rebased to current master


How do i use a already active/made tournament?

I already have a tournament ready, and I want to display some information or do whatevere in my application. How can I achive this?

wiki dosen't have a lot of explaining.

This library ist a wrapper of the Challonge REST API, meaning that it only makes each endpoint accessible through Java. I would recommend checking out the Challonge API docs for a full reference of available functions. All the endpoints are accessible via the Challonge class.


darwin: generate apple packages preparing for update macos sdk

Motivation for this change
macos sdk is outdated for a long time (#101229), this PR provides scaffolds and candidates for future updating.
Except for normalizing package name as ${pname}-${version}-${sdkName}, in essence this PR doesn't update any packages. We may want a smooth update process divided into small tasks instead of a large package commit.
Things done
Generate package sources and rewrite some function names.
Will cause mass rebuild due to some derivation names normalized, but it should not cause any actual change in compiling.
cc @matthewbauer

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

[ ] NixOS
[x] 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 nixpkgs-review --run "nixpkgs-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.

Success building all apple packages and the depending bootstrap packages, except #108651.
add cc @siraben @SuperSandro2000

Success building all apple packages and the depending bootstrap packages, except #108651.
add cc @siraben @SuperSandro2000

I saw this already earlier. If I understand it correctly this should make the update process easier but does not actually change any packages?
Also please change the commit message and PR title to something starting with darwin: or darwin.appke_sdk.

I saw this already earlier. If I understand it correctly this should make the update process easier but does not actually change any packages?
Also please change the commit message and PR title to something starting with darwin: or darwin.appke_sdk.

If I understand it correctly this should make the update process easier but does not actually change any packages?

Yes.
We hesitate to update apple_sdk is mainly because we make up a header-only Libsystem, which is required for bootstrap. But for many other apple packages in apple-source-releases, there are few packages depending on them individual, and could be updated without a mass impact. For example, network_cmds is marked as insecure because of openssl-1.0.2u since 2019, we could keep it up-to-date instead of sticking to osx-10.11.6.
My plan is to take down those light-depended packages one by one, the PR could make it easier.

If I understand it correctly this should make the update process easier but does not actually change any packages?

Yes.
We hesitate to update apple_sdk is mainly because we make up a header-only Libsystem, which is required for bootstrap. But for many other apple packages in apple-source-releases, there are few packages depending on them individual, and could be updated without a mass impact. For example, network_cmds is marked as insecure because of openssl-1.0.2u since 2019, we could keep it up-to-date instead of sticking to osx-10.11.6.
My plan is to take down those light-depended packages one by one, the PR could make it easier.

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:
https://discourse.nixos.org/t/prs-ready-for-review/3032/445

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:
https://discourse.nixos.org/t/prs-ready-for-review/3032/445

@veprbl could you review this?

@veprbl could you review this?

@veprbl I have rewrite some function name back and add new function with suffix _ , hope this would make it easier to review.

@veprbl I have rewrite some function name back and add new function with suffix _ , hope this would make it easier to review.

gentle ping @matthewbauer

gentle ping @matthewbauer


Create ASDF validator to compare nested datastructures

This could be used for instance to ensure we have given coordinate systems in a CSM. That is useful for programmatic evaluation of weldx files according to a schema.

maybe we can first create a validator for the CSM and derive a more general solution based on that


cluster size always zero using cuda-cluster

Using cuda-cluster for some down-sampled robosense pointcloud,  the cudaExtractCluster always return zero cluster, while normal pcl::EuclideanClusterExtraction works fine.
env:
jetson xavier nx
jetpack 4.6
ubuntu18.04
cuda10.2
sample pcd file:  sample_pcd.zip
run the cuda-cluster demo with modified 'extractClusterParam' in testCUDA
  ecp.minClusterSize = 5;
  ecp.maxClusterSize = 2500000;
  ecp.voxelX = 0.2;
  ecp.voxelY = 0.2;
  ecp.voxelZ = 0.2;
  ecp.countThreshold = 20;

tried different ClusterParams several times, none succeed(:

anyone knows the meaning of ecp.countThreshold here?  please help.
when i set the countThreshold to zero, the func may return one or two cluster sometimes.


[Extensibility] Codeunit 7302 "WMS Management" - Error in params: OnBeforeBinContentLookUp

The event publisher, OnBeforeBinContentLookUp passes in the BinCode without the var-flag. This means that it will exit with an incorrect value if you're using the IsHandled-flag.
Publisher:
    [IntegrationEvent(false, false)]
    local procedure OnBeforeBinContentLookUp(LocationCode: Code[10]; ItemNo: Code[20]; VariantCode: Code[10]; ZoneCode: Code[10]; WhseItemTrackingSetup: Record "Item Tracking Setup"; CurrBinCode: Code[20]; BinCode: Code[20]; var IsHandled: Boolean)
    begin
    end;

Function where it's invoked:
    procedure BinContentLookUp(LocationCode: Code[10]; ItemNo: Code[20]; VariantCode: Code[10]; ZoneCode: Code[10]; WhseItemTrackingSetup: Record "Item Tracking Setup"; CurrBinCode: Code[20]) BinCode: Code[20]
    var
        BinContent: Record "Bin Content";
        IsHandled: Boolean;
    begin
        IsHandled := false;
        OnBeforeBinContentLookUp(LocationCode, ItemNo, VariantCode, ZoneCode, WhseItemTrackingSetup, CurrBinCode, BinCode, IsHandled);
        if IsHandled then
            exit(BinCode);

The correct publisher should be:
    [IntegrationEvent(false, false)]
    local procedure OnBeforeBinContentLookUp(LocationCode: Code[10]; ItemNo: Code[20]; VariantCode: Code[10]; ZoneCode: Code[10]; WhseItemTrackingSetup: Record "Item Tracking Setup"; CurrBinCode: Code[20]; var BinCode: Code[20]; var IsHandled: Boolean)
    begin
    end;

Thanks for reporting this. We agree, and we’ll publish a fix asap, either in an update for the current version or in the next major release. Please do not reply to this, as we do not monitor closed issues. If you have follow-up questions or requests, please create a new issue where you reference this one.