text:
Create initial models for project selection

The project selection portion of the website needs several models.  Initially, the thought is the following set of models:

[x] Dataset

[x] id (unique, integer)
[x] name (string)

[ ] ProjectSelector

[x] id (unique, integer)
[ ] input_dataset (integer, nullable)
[ ] input_selection (integer, nullable)
[ ] filters (list of integers)
[ ] output (integer)

[ ] Filter

[x] id (unique, integer)
[ ] name (string)

[ ] Selection

[x] id (unique, integer)

[ ] ProjectTransformer

[x] id (unique, integer)
[ ] input_selection (integer)
[ ] transforms (list of integers)

[ ] Transform

[x] id (unique, integer)
[ ] name (string)

[ ] Analysis

[x] id (unique, integer)
[ ] input_selection (integer)

As the model is revised (to rename/add/remove models or attributes), the list above is updated.  Completed models (in the associated branch) are checked.

Here is the initial brainstorming session for the models.

repo: bgsu-pal/paclab-www


text:
Agreement

Fixes #38 and fixes #53

Add privacy agreement
Add 13+ confirmation

Maybe I was a bit unclear here, I apologize. The privacy policy should be 1 file.  The service agreement should be 1 file (not 16 files).

Is it possible to get the text up next to the checkboxes? Right now that whole 'row' is clickable, even the white space.  Yet the text is not clickable because it is 'help' text.

Regarding the modal that pops up.  Can we make it much wider?  I think theres a way to make modals 'wide' instead of this skinny thing we get now.  Also the text - can we stick that into something that scrolls?  So ideally the dialog is fully visible (including the button to close it) and the text scrolls within the modal.

source: gharchive/pull-request

authors: psybers rebbrunner

license_type: permissive

license_source: github-api


text:
Fix color comparisons with newlines

It seems like the color comparison breaks if getColorCode returns lowercased none.
Before:

The second line outputs a white segment separator, which shouldn't be there.
Relevant trace is:
λ1 left_prompt_segment:27 cmdand 	foreground='%F{none}'
λ1 left_prompt_segment:29 if 	[[ 012 != NONE ]]
λ1 left_prompt_segment:29 if 	isSameColor none 012
λ1 isSameColor:1 if 	[[ none == NONE || 012 == NONE ]]
λ1 isSameColor:5 cmdsubst 	getColorCode none
λ1 getColorCode:2 if 	[[ none == <-> ]]
λ1 getColorCode:8 	local colorName=none
λ1 getColorCode:10 if 	[[ none == none ]]
λ1 getColorCode:11 then 	echo -n none
λ1 isSameColor:5 	local color1=none
λ1 isSameColor:6 cmdsubst 	getColorCode 012
λ1 getColorCode:2 if 	[[ 012 == <-> ]]
λ1 getColorCode:4 then 	echo -n 012
λ1 getColorCode:5 then 	return
λ1 isSameColor:6 	local color2=012
λ1 isSameColor:8 	return 1
λ1 left_prompt_segment:30 then 	echo -n '%K{none}%F{012}'

Line 29 of left_prompt_segment is:
if [[ $CURRENT_BG != 'NONE' ]] && ! isSameColor "${backgroundColor}" "$CURRENT_BG"; then
So, the check for isSameColor none 012 returns false:
λ1 left_prompt_segment:29 if 	[[ 012 != NONE ]]
λ1 left_prompt_segment:29 if 	isSameColor none 012

After:

(The last segment separator is not of matter here)

Merged into master as part of #944, and will be part of the v0.6.6 release!

authors: bhilburn dritter

license: MIT


text:
The repository is large

Clean git clone takes more than 1GB
→ du -hs RxInfer.jl
1.3G	RxInfer.jl

This is primarily due the gh-pages branch and the Documenter output hosted there. Images, etc. tend to be regenerated for each build and that easily adds up. It looks like currently deploys "per version" sit around 25MB each.
Consider the following output generated when checking out the gh-pages branch (I removed the .git folder).
18M	./v2.6.0
17M	./v2.3.0
23M	./v2.12.0
17M	./v2.2.0
18M	./v2.11.0
22M	./v2.11.3
22M	./v2.14.1
16M	./v2.0.1
23M	./v2.13.0
24M	./v2.14.2
28M	./v2.11.1
18M	./v2.10.3
792K	./v1.1.0
18M	./v2.8.0
22M	./v2.13.2
22M	./v2.14.0
18M	./v2.9.0
18M	./v2.10.1
23M	./v2.15.0
18M	./v2.10.2
18M	./v2.5.0
18M	./v2.7.0
16M	./v2.0.2
18M	./v2.4.0
23M	./dev
18M	./v2.10.4
17M	./v2.3.1
18M	./v2.4.1
22M	./v2.11.2
16M	./v2.0.0
16M	./v2.1.0
780K	./v1.0.0
500M	.

This gets exacerbated by the fact that every commit to main results in a new deployment, i.e. a regenerated dev, which will amount for a large part of the remaining 800MB and stays in Git "forever".
You'll want to set something up using, for instance, git-filter-repo on the gh-pages branch to clean out old deployments to dev, potentially remove older versions of documentation and only keep the last release for a minor, etc.

This task has been added to the milestone for tracking and prioritization.

Thanks @bauglir , I ended up wiping the entire gh-pages and recreating it with the orphan status. It helped for now
→ du -hs .
165M	.

Depending on whether you'd like to maintain some form of history, the easiest solution to prevent this from becoming too bad is set the forcepush option to deploydocs to true so that any deployment overwrites the previous deployment.

source: gharchive/issue

authors: bauglir bvdmitri


text:
"x³" error

Run program
Click on "x³"

Actual result: error
Expected result: nothing

Repeated on "√" "x²" "1/x" "←"

repo: bidolah/Calculator

license: mit

license_source: bigquery


text:
Clarify that a rawdata directory is not a prescription

https://github.com/bids-standard/bids-specification/blob/40f4fbb0649a8dab65f4327df342251ad841bfb8/src/common-principles.md?plain=1#L289-L291
although this sentence might make it seem as if it were. (re: discussion at sprint)

I suppose we could just add

(Note that rawdata here is an arbitrarily-chosen name. BIDS specifies the contents of a dataset, not the names of directories containing datasets.)

authors: effigies sappelhoff

repo: bids-standard/bids-specification


text:
TEMP: just check if RTD is picking up this to build

Ref: #484

Yeay, it works!


text:
Retain functionality works inconsistently

Version: 3.3.3
Deployment Config: Windows 11, OpenJDK 21.0.5, Standalone mode, Default configuration
Tools: Using Mqtt-Stresser for pub/sub
A Steps:

Connect 50 Clients, each client publishes 1 messages on 1 Topic (test\client-1, test\client-2, test-client-3....) with QOS 1, Retain true.

Behavior:
No message being retained.
B Steps:

Delete Data\retain_data folder
Start Stand alone server
Connect 50 Clients, each client publishes 1 messages on 1 Topic (test\client-1, test\client-2, test-client-3....) with QOS 1, Retain true.

Behavior:
Only 10 topics are retained and the rest do not get retained
C Steps:

Connect 50 Clients, each client publishes 1 messages on 1 Topic (test\client-1, test\client-2, test-client-3....) with QOS 0, Retain true.

Behavior:
It seems that only 10 messages every get retained, is this a configuration flag

"It seems that only 10 messages every get retained, is this a configuration flag"
I think there is no such a limit for the retain storage. How do you find that the message is not retained, e.g by subscribing the topic? I think may be BifroMQ can add a listRetainMessage in api server.

@Gujiawei-Edinburgh, in the info log there was the following line: RetainMessageMatchLimit=10, is it possible that this has to do with the reported behavior?  seems that this configuration sets the match limit for a retain message topic subscription match? where can we change this config from?

@saraheem If your subscribed topic, i.e. topic filter, has wildcard, e.g. * or #, it will match multiple topics. If so, during matching process, if the number of matched topics exceeds the limit which is 10 by default, you cannot get all the retained messages. You can write your own setting provider to override the default settings.

authors: Gujiawei-Edinburgh saraheem

repo: bifromqio/bifromq


text:
mqtt 集群压测导致内存溢出然后宕机

系统内存溢出导致所有节点都宕机
集群3个节点（32C,64G)(20,54,124 三台)，23w客户端，每隔5S发 40K body 压测，经过1d 15h 后节点 124 报错然后宕机，error.log
2024-06-23 05:55:49.530 ERROR   [basekv-client-executor-3] --- c.b.b.baserpc.AbstractResponsePipeline  [AbstractResponsePipeline.java:93] Request handling with error in pipeline@205972377
java.util.concurrent.CompletionException: java.lang.ArrayIndexOutOfBoundsException: Index -2 out of bounds for length 5
	at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:315)
	at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:320)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:936)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.dist.server.scheduler.DistCallScheduler$DistWorkerCallBatcher$BatchDistCall.lambda$execute$21(DistCallScheduler.java:233)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$RequestTask.finish(ManagedRequestPipeline.java:433)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$ResponseObserver.onNext(ManagedRequestPipeline.java:472)
	at io.grpc.stub.ClientCalls$StreamObserverToCallListenerAdapter.onMessage(ClientCalls.java:474)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInternal(ClientCallImpl.java:675)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInContext(ClientCallImpl.java:660)
	at io.grpc.internal.ContextRunnable.run(ContextRunnable.java:37)
	at io.grpc.internal.SerializingExecutor.run(SerializingExecutor.java:133)
	at io.micrometer.core.instrument.internal.TimedRunnable.run(TimedRunnable.java:49)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:842)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -2 out of bounds for length 5
	at com.baidu.bifromq.dist.server.RunningAverage.log(RunningAverage.java:29)
	at com.baidu.bifromq.dist.server.DistResponsePipeline.lambda$handleRequest$1(DistResponsePipeline.java:98)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	... 19 common frames omitted

随之出现堆内存溢出，gc 日志
[2024-06-23T05:55:45.250+0800][5888][gc] GC(14028) Garbage Collection (Allocation Rate) 12046M(42%)->2672M(9%)
[2024-06-23T05:55:58.390+0800][5888][gc] GC(14029) Garbage Collection (Allocation Rate) 12930M(45%)->1808M(6%)
[2024-06-23T05:56:19.354+0800][5888][gc] GC(14030) Garbage Collection (Proactive) 15498M(54%)->16020M(56%)
[2024-06-23T05:56:25.267+0800][5888][gc] GC(14031) Garbage Collection (Allocation Rate) 19278M(67%)->20070M(70%)
[2024-06-23T05:56:28.742+0800][5888][gc] GC(14032) Garbage Collection (Allocation Rate) 21576M(75%)->22608M(79%)
[2024-06-23T05:56:29.783+0800][5888][gc] GC(14033) Garbage Collection (Allocation Rate) 22670M(79%)->24064M(84%)
[2024-06-23T05:56:30.439+0800][5888][gc] GC(14034) Garbage Collection (Allocation Rate) 24222M(84%)->8768M(31%)
[2024-06-23T05:56:37.055+0800][5888][gc] GC(14035) Garbage Collection (Allocation Rate) 12050M(42%)->6164M(21%)
[2024-06-23T05:56:46.477+0800][5888][gc] GC(14036) Garbage Collection (Allocation Rate) 11210M(39%)->12542M(44%)
[2024-06-23T05:56:51.639+0800][5888][gc] GC(14037) Garbage Collection (Allocation Rate) 14532M(51%)->16076M(56%)
[2024-06-23T05:56:56.412+0800][5888][gc] GC(14038) Garbage Collection (Allocation Rate) 17584M(61%)->19366M(68%)
[2024-06-23T05:56:58.342+0800][5888][gc] GC(14039) Garbage Collection (Allocation Rate) 19404M(68%)->20662M(72%)
[2024-06-23T05:56:59.909+0800][5888][gc] GC(14040) Garbage Collection (Allocation Rate) 20690M(72%)->21826M(76%)
[2024-06-23T05:57:01.286+0800][5888][gc] GC(14041) Garbage Collection (Allocation Rate) 21870M(76%)->22812M(80%)

之后其他两台节点频繁打印 can not connect 24后也宕机。warn.log 如下
2024-06-23 05:57:08.313  WARN   [cluster-tcp-transport] --- c.b.b.b.transport.TCPTransport          [TCPTransport.java:247] Failed to connect to address: /10.89.144.124:8899
java.util.concurrent.ExecutionException: io.netty.channel.AbstractChannel$AnnotatedConnectException: finishConnect(..) failed: Connection refused: /10.89.144.124:8899
	at io.netty.util.concurrent.DefaultPromise.get(DefaultPromise.java:351)
	at com.baidu.bifromq.basecluster.transport.TCPTransport.lambda$getChannel$8(TCPTransport.java:321)
	at io.netty.util.concurrent.DefaultPromise.notifyListener0(DefaultPromise.java:590)
	at io.netty.util.concurrent.DefaultPromise.notifyListeners0(DefaultPromise.java:583)
	at io.netty.util.concurrent.DefaultPromise.notifyListenersNow(DefaultPromise.java:559)
	at io.netty.util.concurrent.DefaultPromise.notifyListeners(DefaultPromise.java:492)

BifroMQ

Version: [3.1.1]
Deployment: [Cluster]

To Reproduce
压测客户端，23w client, 每隔5S 发送 body 40k qos =0 的消息，
*** PUB Client ***:

MQTT Connection:

ClientIdentifier:
etc...

MQTT Pub:

Topic:
QoS: [0]
Retain: [false]

Expected behavior
Logs
124 最先出问题
error.log 如下：全部都是如此
2024-06-23 05:55:49.530 ERROR   [basekv-client-executor-3] --- c.b.b.baserpc.AbstractResponsePipeline  [AbstractResponsePipeline.java:93] Request handling with error in pipeline@205972377
java.util.concurrent.CompletionException: java.lang.ArrayIndexOutOfBoundsException: Index -2 out of bounds for length 5
	at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:315)
	at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:320)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:936)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.dist.server.scheduler.DistCallScheduler$DistWorkerCallBatcher$BatchDistCall.lambda$execute$21(DistCallScheduler.java:233)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$RequestTask.finish(ManagedRequestPipeline.java:433)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$ResponseObserver.onNext(ManagedRequestPipeline.java:472)
	at io.grpc.stub.ClientCalls$StreamObserverToCallListenerAdapter.onMessage(ClientCalls.java:474)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInternal(ClientCallImpl.java:675)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInContext(ClientCallImpl.java:660)
	at io.grpc.internal.ContextRunnable.run(ContextRunnable.java:37)
	at io.grpc.internal.SerializingExecutor.run(SerializingExecutor.java:133)
	at io.micrometer.core.instrument.internal.TimedRunnable.run(TimedRunnable.java:49)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:842)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -2 out of bounds for length 5
	at com.baidu.bifromq.dist.server.RunningAverage.log(RunningAverage.java:29)
	at com.baidu.bifromq.dist.server.DistResponsePipeline.lambda$handleRequest$1(DistResponsePipeline.java:98)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	... 19 common frames omitted
2024-06-23 05:55:49.530 ERROR   [basekv-client-executor-2] --- c.b.b.baserpc.AbstractResponsePipeline  [AbstractResponsePipeline.java:93] Request handling with error in pipeline@663109504
java.util.concurrent.CompletionException: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 5
	at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:315)
	at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:320)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:936)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.dist.server.scheduler.DistCallScheduler$DistWorkerCallBatcher$BatchDistCall.lambda$execute$21(DistCallScheduler.java:233)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$RequestTask.finish(ManagedRequestPipeline.java:433)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$ResponseObserver.onNext(ManagedRequestPipeline.java:472)
	at io.grpc.stub.ClientCalls$StreamObserverToCallListenerAdapter.onMessage(ClientCalls.java:474)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInternal(ClientCallImpl.java:675)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInContext(ClientCallImpl.java:660)
	at io.grpc.internal.ContextRunnable.run(ContextRunnable.java:37)
	at io.grpc.internal.SerializingExecutor.run(SerializingExecutor.java:133)
	at io.micrometer.core.instrument.internal.TimedRunnable.run(TimedRunnable.java:49)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:842)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 5
	at com.baidu.bifromq.dist.server.RunningAverage.log(RunningAverage.java:29)
	at com.baidu.bifromq.dist.server.DistResponsePipeline.lambda$handleRequest$1(DistResponsePipeline.java:98)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	... 19 common frames omitted
2024-06-23 05:55:49.530 ERROR   [basekv-client-executor-1] --- c.b.b.baserpc.AbstractResponsePipeline  [AbstractResponsePipeline.java:93] Request handling with error in pipeline@537959386
java.util.concurrent.CompletionException: java.lang.ArrayIndexOutOfBoundsException: Index -4 out of bounds for length 5
	at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:315)
	at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:320)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:936)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.dist.server.scheduler.DistCallScheduler$DistWorkerCallBatcher$BatchDistCall.lambda$execute$21(DistCallScheduler.java:233)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$RequestTask.finish(ManagedRequestPipeline.java:433)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$ResponseObserver.onNext(ManagedRequestPipeline.java:472)
	at io.grpc.stub.ClientCalls$StreamObserverToCallListenerAdapter.onMessage(ClientCalls.java:474)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInternal(ClientCallImpl.java:675)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInContext(ClientCallImpl.java:660)
	at io.grpc.internal.ContextRunnable.run(ContextRunnable.java:37)
	at io.grpc.internal.SerializingExecutor.run(SerializingExecutor.java:133)
	at io.micrometer.core.instrument.internal.TimedRunnable.run(TimedRunnable.java:49)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:842)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -4 out of bounds for length 5
	at com.baidu.bifromq.dist.server.RunningAverage.log(RunningAverage.java:29)
	at com.baidu.bifromq.dist.server.DistResponsePipeline.lambda$handleRequest$1(DistResponsePipeline.java:98)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	... 19 common frames omitted

gc 日志：
[2024-06-23T05:55:20.815+0800][5888][gc] GC(14025) Garbage Collection (Allocation Rate) 11356M(40%)->3736M(13%)
[2024-06-23T05:55:26.425+0800][5888][gc] GC(14026) Garbage Collection (Allocation Rate) 7222M(25%)->3638M(13%)
[2024-06-23T05:55:36.003+0800][5888][gc] GC(14027) Garbage Collection (Allocation Rate) 11362M(40%)->3690M(13%)
[2024-06-23T05:55:45.250+0800][5888][gc] GC(14028) Garbage Collection (Allocation Rate) 12046M(42%)->2672M(9%)
[2024-06-23T05:55:58.390+0800][5888][gc] GC(14029) Garbage Collection (Allocation Rate) 12930M(45%)->1808M(6%)
[2024-06-23T05:56:19.354+0800][5888][gc] GC(14030) Garbage Collection (Proactive) 15498M(54%)->16020M(56%)
[2024-06-23T05:56:25.267+0800][5888][gc] GC(14031) Garbage Collection (Allocation Rate) 19278M(67%)->20070M(70%)
[2024-06-23T05:56:28.742+0800][5888][gc] GC(14032) Garbage Collection (Allocation Rate) 21576M(75%)->22608M(79%)
[2024-06-23T05:56:29.783+0800][5888][gc] GC(14033) Garbage Collection (Allocation Rate) 22670M(79%)->24064M(84%)
[2024-06-23T05:56:30.439+0800][5888][gc] GC(14034) Garbage Collection (Allocation Rate) 24222M(84%)->8768M(31%)
[2024-06-23T05:56:37.055+0800][5888][gc] GC(14035) Garbage Collection (Allocation Rate) 12050M(42%)->6164M(21%)
[2024-06-23T05:56:46.477+0800][5888][gc] GC(14036) Garbage Collection (Allocation Rate) 11210M(39%)->12542M(44%)
[2024-06-23T05:56:51.639+0800][5888][gc] GC(14037) Garbage Collection (Allocation Rate) 14532M(51%)->16076M(56%)
[2024-06-23T05:56:56.412+0800][5888][gc] GC(14038) Garbage Collection (Allocation Rate) 17584M(61%)->19366M(68%)
[2024-06-23T05:56:58.342+0800][5888][gc] GC(14039) Garbage Collection (Allocation Rate) 19404M(68%)->20662M(72%)
[2024-06-23T05:56:59.909+0800][5888][gc] GC(14040) Garbage Collection (Allocation Rate) 20690M(72%)->21826M(76%)
[2024-06-23T05:57:01.286+0800][5888][gc] GC(14041) Garbage Collection (Allocation Rate) 21870M(76%)->22812M(80%)

54 节点：
error.log
2024-06-23 05:58:10.205 ERROR   [basekv-client-executor-3] --- c.b.b.baserpc.AbstractResponsePipeline  [AbstractResponsePipeline.java:93] Request handling with error in pipeline@261676605
java.util.concurrent.CompletionException: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 5
	at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:315)
	at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:320)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:936)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.dist.server.scheduler.DistCallScheduler$DistWorkerCallBatcher$BatchDistCall.lambda$execute$21(DistCallScheduler.java:233)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$RequestTask.finish(ManagedRequestPipeline.java:433)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$ResponseObserver.onNext(ManagedRequestPipeline.java:472)
	at io.grpc.stub.ClientCalls$StreamObserverToCallListenerAdapter.onMessage(ClientCalls.java:474)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInternal(ClientCallImpl.java:675)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInContext(ClientCallImpl.java:660)
	at io.grpc.internal.ContextRunnable.run(ContextRunnable.java:37)
	at io.grpc.internal.SerializingExecutor.run(SerializingExecutor.java:133)
	at io.micrometer.core.instrument.internal.TimedRunnable.run(TimedRunnable.java:49)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:842)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 5
	at com.baidu.bifromq.dist.server.RunningAverage.log(RunningAverage.java:29)
	at com.baidu.bifromq.dist.server.DistResponsePipeline.lambda$handleRequest$1(DistResponsePipeline.java:98)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	... 19 common frames omitted
2024-06-23 05:58:10.205 ERROR   [basekv-client-executor-1] --- c.b.b.baserpc.AbstractResponsePipeline  [AbstractResponsePipeline.java:93] Request handling with error in pipeline@1633905364
java.util.concurrent.CompletionException: java.lang.ArrayIndexOutOfBoundsException: Index -2 out of bounds for length 5
	at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:315)
	at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:320)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:936)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.dist.server.scheduler.DistCallScheduler$DistWorkerCallBatcher$BatchDistCall.lambda$execute$21(DistCallScheduler.java:233)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	at java.base/java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:911)
	at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
	at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$RequestTask.finish(ManagedRequestPipeline.java:433)
	at com.baidu.bifromq.baserpc.ManagedRequestPipeline$ResponseObserver.onNext(ManagedRequestPipeline.java:472)
	at io.grpc.stub.ClientCalls$StreamObserverToCallListenerAdapter.onMessage(ClientCalls.java:474)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInternal(ClientCallImpl.java:675)
	at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1MessagesAvailable.runInContext(ClientCallImpl.java:660)
	at io.grpc.internal.ContextRunnable.run(ContextRunnable.java:37)
	at io.grpc.internal.SerializingExecutor.run(SerializingExecutor.java:133)
	at io.micrometer.core.instrument.internal.TimedRunnable.run(TimedRunnable.java:49)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:842)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -2 out of bounds for length 5
	at com.baidu.bifromq.dist.server.RunningAverage.log(RunningAverage.java:29)
	at com.baidu.bifromq.dist.server.DistResponsePipeline.lambda$handleRequest$1(DistResponsePipeline.java:98)
	at java.base/java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:934)
	... 19 common frames omitted

warn.log
2024-06-23 05:57:08.023  WARN   [bg-task-executor-3] --- c.b.b.b.b.impl.RangeLeaderBalancer      [RangeLeaderBalancer.java:76] Failed to balance rangeLeaders for there is KVRange with more than one leader!
2024-06-23 05:57:08.263  WARN   [cluster-tcp-transport] --- c.b.b.b.transport.TCPTransport          [TCPTransport.java:98] Outbound channel failure: remote=10.89.144.124/10.89.144.124:8899, cause=recvAddress(..) failed: Connection reset by peer
2024-06-23 05:57:08.265  WARN   [cluster-tcp-transport-3] --- c.b.b.b.transport.TCPTransport          [TCPTransport.java:98] Outbound channel failure: remote=10.89.144.124/10.89.144.124:8899, cause=recvAddress(..) failed: Connection reset by peer
2024-06-23 05:57:08.266  WARN   [cluster-tcp-transport-3] --- c.b.b.b.transport.TCPTransport          [TCPTransport.java:98] Outbound channel failure: remote=10.89.144.124/10.89.144.124:8899, cause=recvAddress(..) failed: Connection reset by peer
2024-06-23 05:57:08.266  WARN   [cluster-tcp-transport-1] --- c.b.b.b.transport.TCPTransport          [TCPTransport.java:98] Outbound channel failure: remote=10.89.144.124/10.89.144.124:8899, cause=recvAddress(..) failed: Connection reset by peer
2024-06-23 05:57:08.313  WARN   [cluster-tcp-transport] --- c.b.b.b.transport.TCPTransport          [TCPTransport.java:247] Failed to connect to address: /10.89.144.124:8899
java.util.concurrent.ExecutionException: io.netty.channel.AbstractChannel$AnnotatedConnectException: finishConnect(..) failed: Connection refused: /10.89.144.124:8899
	at io.netty.util.concurrent.DefaultPromise.get(DefaultPromise.java:351)
	at com.baidu.bifromq.basecluster.transport.TCPTransport.lambda$getChannel$8(TCPTransport.java:321)
	at io.netty.util.concurrent.DefaultPromise.notifyListener0(DefaultPromise.java:590)
	at io.netty.util.concurrent.DefaultPromise.notifyListeners0(DefaultPromise.java:583)
	at io.netty.util.concurrent.DefaultPromise.notifyListenersNow(DefaultPromise.java:559)
	at io.netty.util.concurrent.DefaultPromise.notifyListeners(DefaultPromise.java:492)
	at io.netty.util.concurrent.DefaultPromise.setValue0(DefaultPromise.java:636)
	at io.netty.util.concurrent.DefaultPromise.setFailure0(DefaultPromise.java:629)
	at io.netty.util.concurrent.DefaultPromise.tryFailure(DefaultPromise.java:118)
	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.fulfillConnectPromise(AbstractEpollChannel.java:674)
	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.finishConnect(AbstractEpollChannel.java:693)
	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.epollOutReady(AbstractEpollChannel.java:567)
	at io.netty.channel.epoll.EpollEventLoop.processReady(EpollEventLoop.java:489)
	at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:397)
	at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:997)
	at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
	at java.base/java.lang.Thread.run(Thread.java:842)
Caused by: io.netty.channel.AbstractChannel$AnnotatedConnectException: finishConnect(..) failed: Connection refused: /10.89.144.124:8899
Caused by: java.net.ConnectException: finishConnect(..) failed: Connection refused
	at io.netty.channel.unix.Errors.newConnectException0(Errors.java:166)
	at io.netty.channel.unix.Errors.handleConnectErrno(Errors.java:131)
	at io.netty.channel.unix.Socket.finishConnect(Socket.java:359)
	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.doFinishConnect(AbstractEpollChannel.java:710)
	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.finishConnect(AbstractEpollChannel.java:687)
	at io.netty.channel.epoll.AbstractEpollChannel$AbstractEpollUnsafe.epollOutReady(AbstractEpollChannel.java:567)
	at io.netty.channel.epoll.EpollEventLoop.processReady(EpollEventLoop.java:489)
	at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:397)
	at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:997)
	at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
	at java.base/java.lang.Thread.run(Thread.java:842)

gc 日志：
[2024-06-23T05:56:01.433+0800][14135][gc] GC(13847) Garbage Collection (Allocation Rate) 11640M(41%)->3640M(13%)
[2024-06-23T05:56:11.441+0800][14135][gc] GC(13848) Garbage Collection (Allocation Rate) 11744M(41%)->3648M(13%)
[2024-06-23T05:56:21.413+0800][14135][gc] GC(13849) Garbage Collection (Allocation Rate) 11744M(41%)->3616M(13%)
[2024-06-23T05:56:30.547+0800][14135][gc] GC(13850) Garbage Collection (Allocation Rate) 11878M(41%)->2640M(9%)
[2024-06-23T05:56:39.857+0800][14135][gc] GC(13851) Garbage Collection (Allocation Rate) 9912M(35%)->3746M(13%)
[2024-06-23T05:56:46.522+0800][14135][gc] GC(13852) Garbage Collection (Allocation Rate) 8354M(29%)->3616M(13%)
[2024-06-23T05:56:56.419+0800][14135][gc] GC(13853) Garbage Collection (Allocation Rate) 11620M(41%)->3648M(13%)
[2024-06-23T05:57:06.546+0800][14135][gc] GC(13854) Garbage Collection (Allocation Rate) 11862M(41%)->3662M(13%)
[2024-06-23T05:57:16.492+0800][14135][gc] GC(13855) Garbage Collection (Allocation Rate) 12214M(43%)->3692M(13%)
[2024-06-23T05:57:21.770+0800][14135][gc] GC(13856) Garbage Collection (Allocation Rate) 6790M(24%)->4104M(14%)
[2024-06-23T05:57:30.498+0800][14135][gc] GC(13857) Garbage Collection (Allocation Rate) 11850M(41%)->2742M(10%)
[2024-06-23T05:57:39.932+0800][14135][gc] GC(13858) Garbage Collection (Allocation Rate) 10106M(35%)->3722M(13%)
[2024-06-23T05:57:46.601+0800][14135][gc] GC(13859) Garbage Collection (Allocation Rate) 8302M(29%)->3612M(13%)
[2024-06-23T05:57:55.559+0800][14135][gc] GC(13860) Garbage Collection (Allocation Rate) 11642M(41%)->2740M(10%)
[2024-06-23T05:58:05.006+0800][14135][gc] GC(13861) Garbage Collection (Allocation Rate) 10108M(35%)->3702M(13%)
[2024-06-23T05:58:11.637+0800][14135][gc] GC(13862) Garbage Collection (Allocation Rate) 8354M(29%)->2996M(10%)
[2024-06-23T05:58:29.446+0800][14135][gc] GC(13863) Garbage Collection (Proactive) 14854M(52%)->8874M(31%)
[2024-06-23T05:58:36.792+0800][14135][gc] GC(13864) Garbage Collection (Allocation Rate) 12380M(43%)->13808M(48%)
[2024-06-23T05:58:41.729+0800][14135][gc] GC(13865) Garbage Collection (Allocation Rate) 15582M(54%)->17214M(60%)
[2024-06-23T05:58:44.409+0800][14135][gc] GC(13866) Garbage Collection (Allocation Rate) 17242M(60%)->19128M(67%)
[2024-06-23T05:58:46.013+0800][14135][gc] GC(13867) Garbage Collection (Allocation Rate) 19172M(67%)->20230M(71%)
[2024-06-23T05:58:49.387+0800][14135][gc] GC(13868) Garbage Collection (Allocation Rate) 21424M(75%)->22678M(79%)
[2024-06-23T05:58:50.350+0800][14135][gc] GC(13869) Garbage Collection (Allocation Rate) 22858M(80%)->23862M(83%)
[2024-06-23T05:58:51.066+0800][14135][gc] GC(13870) Garbage Collection (Allocation Rate) 23930M(83%)->14566M(51%)
[2024-06-23T05:58:55.727+0800][14135][gc] GC(13871) Garbage Collection (Allocation Rate) 16828M(59%)->4834M(17%)
[2024-06-23T05:59:15.831+0800][14135][gc] GC(13872) Garbage Collection (Allocation Rate) 17578M(61%)->18548M(65%)
[2024-06-23T05:59:20.766+0800][14135][gc] GC(13873) Garbage Collection (Allocation Rate) 20874M(73%)->22000M(77%)
[2024-06-23T05:59:22.187+0800][14135][gc] GC(13874) Garbage Collection (Allocation Rate) 22010M(77%)->22954M(80%)
[2024-06-23T05:59:23.129+0800][14135][gc] GC(13875) Garbage Collection (System.gc()) 22954M(80%)->22960M(80%)

Configurations
OS(please complete the following information):
JVM:

Version: [ 17]

Performance Related

HOST:

Cluster node count: [3]
CPU: [32]
Memory: [64]

Network:

Bandwidth: [5Gbps]
Latency: []

Load:

PUB count: [230000]
SUB count: [0]
PUB QPS per connection: [0.2msg/s]
Payload size: [40KB]

Additional context
Add any other context about the problem here.

内部压力工具，5台压力机一共发起23w客户端，每个客户端clean session=true，pingTimeout=60s，keepAlive=60s，username=test，password=123456，每个客户端还订阅3个topic比如abc/{clientid}/topic1，abc/{clientid}/topic2，abc/{clientid}/topic3，这些客户端随机连接到服务端3个节点，每个连接每隔5s钟publish一个内容为40KB大小的数据随机到三个topic中的某一个比如test_topic1或者test_topic2或者test_topic3。


text:
add conda test

PR checklist

[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!

[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/quantms branch on the nf-core/test-datasets repository.

[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

You will need conda environment files for the openms package from the openms channel. Otherwise it does not know the correct order of channels to look inside (specifically it wont know about the bioconda channel).
In general, those should ALL be bioconda::openms and bioconda::thirdparty by now.

Should we delete this PR @jpfeuffer ? Im working with @daichengxin in #158

authors: daichengxin jpfeuffer ypriverol

repo: bigbio/quantms


text:
[Snyk] Upgrade @bigcommerce/big-design-icons from 0.23.0 to 0.23.1

This PR was automatically created by Snyk using the credentials of a real user.Snyk has created this PR to upgrade @bigcommerce/big-design-icons from 0.23.0 to 0.23.1.
:information_source: Keep your dependencies up-to-date. This makes it easier to fix existing vulnerabilities and to more quickly identify and fix newly disclosed vulnerabilities when they affect your project.

The recommended version is 1 version ahead of your current version.
The recommended version was released 24 days ago, on 2023-06-09.

Release notes

Package name: @bigcommerce/big-design-icons

0.23.1 - 2023-06-09@ bigcommerce/examples@0.23.1

0.23.0 - 2023-04-05

    from @bigcommerce/big-design-icons GitHub release notes

Commit messages

Package name: @bigcommerce/big-design-icons

22db780 chore(release): publish
f967642 chore(component): imp (#1233)
9259575 chore(deps-dev): bump lerna from 6.6.1 to 6.6.2 (#1230)
96cb587 chore(deps-dev): bump rimraf from 5.0.0 to 5.0.1 (#1229)
3dab4d2 chore(deps): bump date-fns from 2.29.3 to 2.30.0 (#1227)
088c582 chore(deps): bump @ babel/standalone from 7.21.2 to 7.21.9 (#1226)
4453678 chore(deps-dev): bump fs-extra from 11.1.0 to 11.1.1 (#1224)
a794018 chore(deps): bump styled-components from 5.3.9 to 5.3.10 (#1220)
cf1e4fd chore(deps-dev): bump lint-staged from 13.2.1 to 13.2.2 (#1223)
ac0e9ce chore(deps): bump yup from 1.0.2 to 1.1.1 (#1221)
72ef587 chore(deps): bump @ typescript-eslint/parser from 5.58.0 to 5.59.6 (#1219)
1511124 fix(component): prevent filling out the disabled cells (#1218)
65920b6 chore(deps-dev): bump @ vitejs/plugin-react from 3.1.0 to 4.0.0 (#1216)
6b07905 chore(deps-dev): bump @ types/react from 18.2.0 to 18.2.6 (#1215)
c3c4b6c chore(deps): bump prettier from 2.8.6 to 2.8.8 (#1214)
e1b7976 chore(deps-dev): bump node-fetch from 2.6.9 to 2.6.11 (#1217)
4a52d0c chore(deps): bump @ babel/preset-typescript from 7.21.4 to 7.21.5 (#1212)
1c7e1b9 chore(deps-dev): bump babel-plugin-styled-components from 2.0.7 to 2.1.1 (#1207)
143744d chore(deps-dev): bump @ babel/preset-env from 7.21.4 to 7.21.5 (#1208)
df77375 chore(deps-dev): bump @ babel/cli from 7.21.0 to 7.21.5 (#1209)
5476791 chore(deps-dev): bump @ types/jest from 29.5.0 to 29.5.1 (#1211)
e3d0dd4 chore(icons): fix icon builds (#1205)
c332244 chore(deps-dev): bump @ types/react from 18.0.37 to 18.2.0 (#1204)
6590623 chore(deps-dev): bump @ babel/plugin-transform-runtime (#1202)

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captured in https://github.com/bigcommerce/sample-app-nodejs/pull/181

authors: bc-chaz bcsnyk

repo: bigcommerce/sample-app-nodejs


text:
[ADAM-1361] Fix misnamed ADAM überjar.

Resolves #1361.

Coverage decreased (-0.1%) to 81.93% when pulling 884ba69204bb94917352ff892ee9c999345f203d on fnothaft:issues/1361-spark2-artifact into 2820e940c0df57a3a9c6439060ae4e53f8a466b8 on bigdatagenomics:master.

Coverage decreased (-0.1%) to 81.93% when pulling 884ba69204bb94917352ff892ee9c999345f203d on fnothaft:issues/1361-spark2-artifact into 2820e940c0df57a3a9c6439060ae4e53f8a466b8 on bigdatagenomics:master.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2050/
Test PASSed.

With this
diff --git a/scripts/move_to_spark_2.sh b/scripts/move_to_spark_2.sh
index ebd9fd89..3e83ebdd 100755
--- a/scripts/move_to_spark_2.sh
+++ b/scripts/move_to_spark_2.sh
@@ -19,5 +19,6 @@ find . -name "pom.xml" -exec sed \
     -e "/adam-/ s/_2\.1/-spark2_2.1/g" \
     -e "/utils-/ $substitution_cmd" \
     -e "/adam-/ $substitution_cmd" \
+    -e "/adam_/ $substitution_cmd" \
     -e "/spark.version/ s/1.6.3/2.1.0/g" \
     -i.spark2.bak '{}' \;

the <finalName> element can stay as is.  This PR adds -assembly to the assembly artifact names.

@heuermh Since the assembly jars are largely handled programmatically from the ./bin/adam-* scripts, I don't really see a benefit to changing the JAR name with <finalName>. I'd rather eliminate <finalName> and have one fewer place where things can go wrong in the move_to scripts.

I don't feel strongly either way.

Thank you, @fnothaft

authors: AmplabJenkins coveralls fnothaft heuermh

repo: bigdatagenomics/adam


text:
Issue while saving variants as vcf.

Hi,
With the Cannoli CLI, while trying to save the variants using freebayes as vcf, I get the error:
java.lang.IllegalStateException: Key CIGAR found in VariantContext field INFO at chr3:75621022 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.
	at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:202)
	at htsjdk.variant.vcf.VCFEncoder.write(VCFEncoder.java:141)
	at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:248)
	at org.seqdoop.hadoop_bam.VCFRecordWriter.writeRecord(VCFRecordWriter.java:148)
	at org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter.write(KeyIgnoringVCFRecordWriter.java:60)
	at org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter.write(KeyIgnoringVCFRecordWriter.java:38)
	at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.write(SparkHadoopWriter.scala:358)
	at org.apache.spark.internal.io.SparkHadoopWriter$.$anonfun$executeTask$1(SparkHadoopWriter.scala:132)
	at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1411)
	at org.apache.spark.internal.io.SparkHadoopWriter$.executeTask(SparkHadoopWriter.scala:129)
	at org.apache.spark.internal.io.SparkHadoopWriter$.$anonfun$write$1(SparkHadoopWriter.scala:83)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:127)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:444)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:447)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

How do I go about this?

I faced the same problem. Based on my investigation the root cause of this issue is replacing default headerLines values of variantContexts  with accumulator 's values which is actually empty. Then it ends up without any stored headerLines . When it comes to saving to vcf, it is expected to have the same output headers as stored in this object, otherwise mentioned error is encountered.
val variantContexts = alignments.pipe[VariantContext, VariantContextProduct, VariantContextDataset, BAMInFormatter](
      cmd = builder.build(),
      files = builder.getFiles()
    )

    val headerLines = accumulator.value.distinct
    variantContexts.replaceHeaderLines(headerLines)

The thing is that accumulator is not updated yet because there was no action performed on given variantContexts.  It seems that should be maintained. @heuermh, could you please have a look at this?

Hello @dmaziec1, your analysis of the issue is correct.  I don't have a good idea for a fix -- accumulators are problematic for several reasons.
As a workaround, it might be possible to read in an empty freebayes VCF file and use its headerLines to replace the empty ones set from the accumulator before writing out VCF.

I posted another workaround in #273, please let me know if that works for you.

Yes, it works fine for me

Thanks @dmaziec1, for bringing this issue back to life. And thanks @heuermh, for the changes done. For some reason, I still get the same error.
I was able to work around this issue with a minor change in Adam as shown here
While this worked, the output vcf obtained was not as rich as when I use vanilla FreeBayes.
@dmaziec1, could you share some more info on the genome sequence being used?

While testing #273 I ran some performance tests, albeit only in local mode on my laptop
https://gist.github.com/heuermh/ba33a061957e99b6719ed9712a7ace67
This line from the pull request appends together freebayes-specific header lines and default header lines, which include the CIGAR VCF INFO header line apparently missing in the stack trace above.

Many thanks @heuermh. It was a mistake from my side. I was using the master branch, instead of freebayes-headers.
The changes work perfectly, on a 16 node cluster as well. Also, thanks for pointing out the performance tests. They further justify and strengthen the need for Adam and Cannoli.

Thank you, @Arun-George-Zachariah and @dmaziec1!

authors: Arun-George-Zachariah dmaziec1 heuermh

repo: bigdatagenomics/cannoli


text:
Fix VT bug "9999999" employees affected

Found this extreme number for a VT data row analysis. This number is too high! Something is wrong with either their data, or our scraping.
I tried to access VT website to check why this might be happening, but the website couldnt be accessed.
Does VT have a new website?

[x] Verify & access current VT website

[x] Figure out if it's our problem or their problem
[ ] Either fix our platform scraper integration, or contact VT about their erroneous data

Looks like you're referring to this record, which indeed contains the incorrect data at source. The ideal solution would be to contact VT and ask them to correct the record.
If they're unable or unwilling, we should treat this as a task for downstream error in the standardization repo. That way we keep high fidelity to the data and avoid opening the door to lots of edge-case handling in the core scraping framework.

Thanks, @zstumgoren! Good thinking, I'll handle it downstream in the standardization repo and will contact VT about getting the record fixed.

This is being fixed here, with the value reset as None.
https://github.com/biglocalnews/warn-transformer/pull/60

authors: palewire ydoc5212 zstumgoren

repo: biglocalnews/warn-scraper


text:
Created wiki "joining mobile devices beta enrollment" program

iOS instructions updated at
https://github.com/bigpanther/shipanther/wiki/Mobile-devices-beta-program-enrollment
@harsimranmaan  please update android instructions as well.
Thanks

Done

authors: harsimranmaan schima

repo: bigpanther/shipanther


text:
🛑 Breeze Medical Invoicing is down

In 2805e45, Breeze Medical Invoicing (https://breezemedicalinvoicing.com) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Breeze Medical Invoicing is back up in 19d42af after 1 hour, 32 minutes.

repo: bigupjeff/my-site-uptime-monitor


text:
Add predictive gene scores as Decipher does

Is your feature request related to a problem? Please describe.
Decipher has a number of useful predictive scores. We don't.
Describe the solution you'd like
Add the predictive scores just like Decipher has.
Describe alternatives you've considered
N/A
Additional context

Skipping sHet for now.

repo: bihealth/annonars


text:
Use "Folder Name" to override expected iRODS collection in assay plugins?

Looks like we have many sample sheets now where the Folder Name for e.g. extracts has been filled out. However, in e.g. the DNA Sequencing assay plugin we still define the expected iRODS collection name by the Library Name or Extract Name even if the Folder Name is present in the same node. This may be confusing to users.
TBD: In the future, should we make it so that Folder Name overrides the node name for the iRODS collection if set?
Comments are very much welcome.

@sellth noted that this is not a standard ISA standard field and implementing such an override would complicate things further. I'm inclined to agree, but keeping this open for possible further comments.

repo: bihealth/sodar-server


text:
Landing zone status updating not working in project details card

This is due to currentUserURL and zoneStatusURL being missing. It seems we define these variables in ZoneListView, but not in the landingzones details card, where we use the same Javascript file.
I will also see about adding UI tests for this, as this failing has gone completely undetected for some time.

Fixed.


text:
Flags cannot be stored for variants

Describe the bug
Flags cannot be saved for variants.
Expected behavior
Saving flags should be possible.
Additional context
N/A

Root Cause Analysis
An earlier patch made the variant flag details view use the global small variant store rather than passing in the stores and variants as props. This must be rolled back.

repo: bihealth/varfish-server


text:
net/rpc/warden: p2c负载均衡，某个节点负载过高

延迟Lag的积分系数应该多一定程度的降权，以及坏打分节点可以多一个O(N)的尝试，N<=3

#130

repo: bilibili/kratos


text:
sniper 跟 kratos 的关系是？

B站前有 kratos 后有 sniper ，如何选型呢？

kratos 功能比较多，朝着大而全方向演进。sniper 是 b 站漫画部门在用的框架，功能很少，代码也很少。与其说 sniper 是一个框架，不如说是一种推荐的开发约定，更多的是为大家提供一种设计参考。当然了，也欢迎大家直接使用。
如何选型这个问题很容易。
你可以试着阅读 sniper 的 README 文件，并将所有文件内链接的文件（其实不多）都看一遍。如果你看完了，你就能够得出是否选用 sniper 的判断。如果你不愿意读，那就选 kratos :smile:

repo: bilibili/sniper


text:
harden against empty arrays in DL responses

I've been told that if an array field exists we don't need to check if it's an array, but we should check that it has elements. In other words:
if (message.attachments)                 HandleAttachment(message.attachments[0])
should become:
if (message.attachments && message.attachments.length > 0)                 HandleAttachment(message.attachments[0])
but we don't need to do:
if (message.attachments && message.attachments.isArray() && message.attachments.length > 0)                 HandleAttachment(message.attachments[0])
One possible approach is to clean this up on intake inside DirectLine().

I fixed as many of these as I could find. We could use more test cases.

repo: billba/botchat


text:
Incompatible with F5 v14+

This project cannot be imported to F5 BIG-IP v14 and higher. Any chance it's going to be updated for compatibility, or any chance a future release of F5 will allow for backwards compatibility for projects that are still tcl based?
Thanks Bill.

@smilam there is work to bring this functionality native to BIG-IP at some point. contact me at bill@f5.com for more info.

authors: billchurch smilam


text:
Remove cfg-if dependency

cfg-if makes the code a bit more readable, but it's only used in two places. It can be easily replaced with #[cfg(...)], removing the only required dependency for the project and even shaving off a few lines.
I realize that this is an opinionated change, and while it would be nice to have zero dependencies, the readability improvement may be worth it, especially considering that cfg-if is a small crate that's likely to be required by other crates anyways.

This is actually something I've been meaning to do for a while. I think it ends up being more readable without cfg-if (although it was certainly easier for me to use cfg-if as a novice Rust developer). And as a plus, rustfmt can format the import blocks now. Thank you!

authors: billyrieger dmarcuse

repo: billyrieger/bimap-rs


text:
AttributeError: 'dict' object has no attribute 'to_dict'

Hi, thank you so much for sharing this tool. I am very interested in using your script to get a masked.bam file to use it for subsequent variant calling analysis.
I already try the two different commands.
I obtained the calmd.bam output file when I run the samtools calmd -b command, but I did not obtain the masked.bam file.
And when I runned : ./revelio.py -f genome.fa input.bam masked.bam
I obtained this error:
Traceback (most recent call last):
File "./revelio.py", line 445, in
main(args.inbam,args.outbam,args.QUALITY,args.THREADS,args.temp,args.fasta)
File "./revelio.py", line 94, in main
header = original.header.to_dict()
AttributeError: 'dict' object has no attribute 'to_dict'
Many thanks in advance for your help

Very sorry for the very late reply @nelia89, I somehow missed this issue! I hope you were able to solve it by yourself? It seems to me that you have not installed software dependencies prior to running Revelio, as to_dict() is a method from the pysam library. The error is stating that it does not recognise the method, which indicates that the library has not been loaded.
Please refer to the instructions on the landing page on Github for installing pysam with conda.


text:
Provenance Domain/modified - not able to type a modified date

Not able to type in the modified date in the modified text box - my impression is that the dataset/workflow has been modified and not the BCO. The date that a BCO is being modified should be automatically generated.

We are a bit averse to automatic date generation unless something in the IEEE spec suggests we should use it for a given field.

@CollectorsCorner,
This is a FEATURE not a BUG. The modified and created fields are auto-populated by the portal.

repo: biocompute-objects/portal


text:
create a Job class

Job objects should be returned from SystemContext.__call__, and should contain (at least) the complete job markdown, and the workflow uuid that gets stored as part of that jobs provenance. That workflow uuid can then be used, for example, in naming the markdown files that q2d3 is creating, which would provide a link from the Artifact objects that get created when the job is run to the actual code that was run, if the interface wants to track that (note that the created artifact's provenance does already have a reference to the workflow template that generated it).

:+1: It could also hold the expected filepaths of the completed artifacts.

+1
Sent from my phone, please excuse typos and brevity.
On Mar 9, 2016 6:59 PM, "Evan Bolyen" notifications@github.com wrote:

[image: :+1:] It could also hold the expected filepaths of the completed
artifacts.
—
Reply to this email directly or view it on GitHub
https://github.com/biocore/qiime2/issues/23#issuecomment-194617546.

Parent or child relationships?
On Mar 9, 2016 7:14 PM, "Greg Caporaso" notifications@github.com wrote:

+1
Sent from my phone, please excuse typos and brevity.
On Mar 9, 2016 6:59 PM, "Evan Bolyen" notifications@github.com wrote:

[image: :+1:] It could also hold the expected filepaths of the completed
artifacts.
—
Reply to this email directly or view it on GitHub
https://github.com/biocore/qiime2/issues/23#issuecomment-194617546.

—
Reply to this email directly or view it on GitHub
https://github.com/biocore/qiime2/issues/23#issuecomment-194640733.

@wasade, not sure I understand your question. This would likely just be a simple struct-like object. If you are talking about workflows calling other workflows (and tracking it), the execution model isn't that sophisticated. We leave those decisions to super-systems (like Qiita).

Ah, okay. Just wondering if a job knew it's relationships. For instance, I
imagine a workflow might trigger a series of serial jobs, or a map/reduce
pattern.
On Mar 9, 2016 7:31 PM, "Evan Bolyen" notifications@github.com wrote:

@wasade https://github.com/wasade, not sure I understand your question.
This would likely just be a simple struct-like object. If you are talking
about workflows calling other workflows (and tracking it), the execution
model isn't that sophisticated. We leave those decisions to super-systems
(like Qiita).
—
Reply to this email directly or view it on GitHub
https://github.com/biocore/qiime2/issues/23#issuecomment-194643729.

authors: ebolyen gregcaporaso wasade


text:
Rake task is not "grepable"

bundle exec rake -T | grep maintenance
# nothing
bundle exec rake -W maintenance:start
# nothing
bundle exec rake maintenance:start
# works just fine

Took me some time to find out what is going on.

Yeah, that's unfortunate. It's because turnout uses rake rules rather rather than rake tasks. I went into some detail on it in an earlier issue.

authors: adamcrown stereobooster

repo: biola/turnout


text:
Restore viz column in simulations table | make API return enough information for table to know whether there is data that can be visualized

The viz column disappeared completely and clicking on any of the actual runs has the viz part grayed out, even for the runs that do have CSV results.

This is already discussed in #1797. The Viz column was intentionally removed because the API doesn't provide enough information to know whether there are results are not. The API only says whether there was an output (report OR plot).
The visualization is still working. You may need to refresh your browser. If you still the error, please post a specific description of how to reproduce the error.

Hard refresh of the browser worked, design chart tab is no longer grayed out on the runs that do have results.
However, it seems that the simulations detail page is able to distinguish on a successful run whether it has CSV output (tab available) vs PDF output (tab greyed out) - shouldn't it be possible then to use the same logic to populate the viz links column?

Yes, the simulations table component needs to subscribe to another endpoint which has this information, as the view simulation component is doing. I haven't had time to do this yet. I've been working to make sure 5 simulation tools are working with examples for each.

can this be closed?

can this be closed?

Ideally, the column of "Viz" buttons should be restored to the simulations tables. Unless @bilalshaikh42 just took care of this, I think the column is still commented out.

Ideally, the column of "Viz" buttons should be restored to the simulations tables. Unless @bilalshaikh42 just took care of this, I think the column is still commented out.

I added back the viz button in #2267. The summary table still isn't using the results endpoint to detect if data is available to visualize. Instead, the "Design viz" tab is now always enabled; when no report is available, it displays a message that says no data is available rather than displaying the visualization design form.

authors: bilalshaikh42 jonrkarr moraru

repo: biosimulations/Biosimulations


text:
Submit GINsim 3.0.0b

id: ginsim
version: 3.0.0b
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GINsim/57bf66ab5316bf678a53ce617d503b70c1d70567/biosimulators.json
specificationsPatch:
version: 3.0.0b
image:
url: ghcr.io/biosimulators/biosimulators_ginsim/ginsim:3.0.0b
validateImage: true
commitSimulator: true

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (4.6 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.6 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.HasBioContainersLabels (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (5.4 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Warnings:
Unexpected reports were produced:
  simulation.sedml/Figure_4a

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Model `model` may be invalid.

    - The model file `BIOMD0000000562_url.xml` may be invalid.

      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object.

         The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.

        Reference: L3V1 Section 4.5

         The <compartment> 'main' has no discernable units.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `./simulation.sedml` may be invalid.

    - Model `model` may be invalid.

      - The model file `BIOMD0000000562_url.xml` may be invalid.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object.

           The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.

          Reference: L3V1 Section 4.5

           The <compartment> 'main' has no discernable units.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

    Plots (1):

      Figure_4a: 4 curves

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (2):

    Succeeded: 2

    Skipped: 0

    Failed: 0

Summary of tests

Executed 73 test cases

Passed 43 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 30 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log:

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:
Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000086

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000027

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log:

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log:

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log:

sedml.SimulatorProducesLinear3DPlots (0.1 s)
Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)
Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.1 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsAlgorithmParameters (0.1 s)
Test that a simulator supports setting the values of parameters of algorithms
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsModelAttributeChanges (0.1 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The SED document is invalid.
  - Model `model` is invalid.
    - The changes of the model are invalid.
      - Change 3 is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/@qual:required` are not defined. Only the following namespaces are defined for the target: `sbml`.

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.4 s)
Test that a simulator supports multiple time courses with non-zero initial times
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_ginsim/ginsim:3.0.0b' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Model `model` may be invalid.

    - The model file `BIOMD0000000562_url.xml` may be invalid.

      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object.

         The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.

        Reference: L3V1 Section 4.5

         The <compartment> 'main' has no discernable units.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `./simulation.sedml` may be invalid.

    - Model `model` may be invalid.

      - The model file `BIOMD0000000562_url.xml` may be invalid.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object.

           The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.

          Reference: L3V1 Section 4.5

           The <compartment> 'main' has no discernable units.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 1: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Simulation `simulation` is invalid.

      - Initial time must be 0, not `5.0`.

The image for your simulator is valid!

Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of ginsim to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.

repo: biosimulators/Biosimulators


text:
Add bfloat16_t::operator+=(a) overload for float argument type

Will perform significantly faster than when doing bf16 += bfloat16_t{f}, for a bfloat16 bf16, and a 32-bit float argument f.
Might yield slightly more precise results. For example, for bf16 += d, when d is a denormal 32-bit float (as tested).

Thanks for your approval, @jeggermont

maybe also add a += operator for integer types ?

Nice suggestion, but I'm not sure if it's necessary. Because when bfloat16_t::operator+=(float) is added, an expression like bf16 += 42 will just work fine, calling the float overload. Right?

FYI, Very encouraging feedback from Evarist @emfomenk on my corresponding pull request at Intel's OneDNN library:  "bfloat16: add operator+=(a) overload for float as argument type", https://github.com/oneapi-src/oneDNN/pull/780


text:
Getting Trends from different countries

How can we get trends from different countries?
It does not support proxy.

I have tried but it is required that login in twitter for getting trends from a different location. To login is not easy using html-request. I tried however twitter perceived as a bot a few minutes later.

authors: erenbesli ozanbayram

repo: bisguzar/twitter-scraper


text:
PHP 8.0 Support

Please add support php 8.0 in composer.json

Pode utilizar esse fork https://github.com/rlzdesenv/validador-cpf-cnpj

repo: bissolli/validador-cpf-cnpj


text:
Fix screen scraper compatibility with lolminer 1.45

The text output for lolminer is slightly different from 1.46+ (e.g. difficulty line is parsed differently).  The application should be able to handle these types of variations.
See #191 for architectural support.

Screen scraper support is being eliminated.

repo: bitcobblers/multiminer


text:
Settings

Design goals:
To give the user a means to see and modify their settings. I'm particularly unhappy with this part of the wallet, maybe this entire settings can be hidden away somewhere else, or behind a modal.
Currently it doesn't make good use of space, because there just isn't that much in the settings for the user to modify.

Settings (you can also click on the buttons to see the flow.
LINK

@natiwa Perfect!

Settings design preview

test

authors: Cobra-Bitcoin natiwa

repo: bitcoin-dot-org/Bitcoin-Wallet


text:
Alphabetize Websites Section

Moved WORDS to the bottom of Websites section of Bitcoin-only.

Cheers!

repo: bitcoin-only/bitcoin-only


text:
Move to Material Design and Reactive Forms

This moves the Angular forms to Material Design and Reactive Forms.
Lots of small updates, DLCs can be built from Offer or Accepted (via Tor or files). Extended DLC file operations are hidden in this release.
This currently over-validates the New Offer forms when editing collateral and payout amounts. It would ideally not validate when some fields haven't been touched yet.

I think it would be better to bump the refund date by 1 week by default so if the oracle doesn't attest right away the refund tx doesn't become valid

It would be nice to have a pre-filled value for the possible range of collateral in the Your Collateral field. The contract I am using for this code review is https://oracle.suredbits.com/contract/enum/bf36b3825011b2d1eedf7f7649fa98c20889b5c187e373f7b103c3c7950edbb5 which has a maximum value of 100k sats

I like how you have the the information icon next to other fields, i think we should add it to the Create Offer result too saying something like

You need to send this hex encoded offer to your counterparty along with your tor address [fill in tor address here]. Your counterparty will accept the offer if they find the terms of the offer agreeable. If they accept your offer, your wallets will build a bitcoin transaction representing the [eventId] bet.

It might be nice to link the oracle on the oracle explorer, I think this could be done with this API endpoint on the explorer https://gist.github.com/Christewart/a9e55d9ba582ac9a5ceffa96db9d7e1f#getting-an-oracles-username
If the oracle does not exist on the oracle explorer, i think it is ok to display the public key hex like you do now

nit: It would be nice to have commas separating numbers especially with sats as they tend to be larger numbers

The MAX button isn't working for me on this page, nothing gets filled in

So i'm running into an issue with accepting an offer via Tor. It doesn't seem like the tor negotiation is working for me on d88a8f556fa648facfdbc26f7c288aa432379e2e
When i paste in my offer, and then my peers tor address, i get a dialog popping up to save the file rather than just doing the negotiation behind the scenes

Tor Accept Offer should be working again with the latest commit.

So things worked for me on 129afd62c4983bebe65ed71df34a250d0ac96b6d
One thing that didn't quite work is updating the DLC table view from status=Accepted -> status=Broadcasted. IIRC you said there isn't any polling implemented on the UI currently. Is that still the case? If so (and its a known limitation), i'm cool with merging this

There is no state polling on the UI yet.

repo: bitcoin-s/bitcoin-s-ts


text:
Mockito is in multibit-hd.jar - required ?

There are 3.2 MB of mockito classes in the multibit-hd.jar.
These probably don't need to be in the released jar.

Agreed. We should clear out any test scope JARs.

I tweaked the pom to make the mockito jar test scope. I think it was the only one that was missed.
The multibit-hd.jar has decreased from 23,833,494 to 22,405,150 bytes. (A 6% decrease).
Awaiting review and closing

Verified build of multibit-hd.jar is now about 19Mb. Shade plugin reports no unnecessary JARs being included so it's all good.
Closing.

authors: bitcoin-solutions gary-rowe

repo: bitcoin-solutions/multibit-hd


text:
Use Plotly.NET

Generates:

coverage: 99.177% (+0.08%) from 99.097%
when pulling 5d0ae065279e7230f126efc1e35513e200276d57 on users/alexpeck/plotlynet
into ccafac024cdf1dcf058b51a7a5b247ddd9b0006c on main.

Benchmark results:

authors: bitfaster coveralls


text:
Large videohub 288

Hi.
I'm trying to control the largest 288x288 videohub, but it makes Companion very slow to respond to anything.  I've not wiresharked the data yet, but I think it's pulling lots of data from the videohub.  As soon as i disable the interface it returns to normal CPU levels.
Thanks

Hmm, 288x288 shouldn't really be a problem for companion, but i've never tested it. Could you do a wireshark and upload it here? :)

I expect this is a case of the module flooding companion with data.
For a 40x40 videohub, it is generating 3282 presets, totalling 1.3MB of json. I expect this to scale roughly linearly based on the number of inputs, so for a 288 input model, thats somewhere in the region of 165888 presets, totalling 65MB.
The module doesn't look conservative at emitting updates to those (it uses the input names when generating them, so whenever one changes they will need invalidating), which could cause a bit of a flood of data if they change often

I think this is resolved now. see #31

authors: Julusian globaluk willosof

repo: bitfocus/companion-module-bmd-videohub


text:
Cloud Backup healthcheck doesn't work on iOS

The Cloud Backup healthcheck doesn't work on iOS, it just shows success message without checking access to the files

Verified this issue on keeper app v 1.2.19(417)

authors: ben-kaufman cakesoft-swati

repo: bithyve/bitcoin-keeper


text:
Implement options templates/data records

As noted in #29, options templates and options data records are missing a correct implementation. The current workaround is a for flowsets with ID 1, which is always the Options Template Flowset. The mixing might lead to errors, therefore correct handling is needed
cc @j-licht

@j-licht could you please try e43980f in your setup?

@bitkeks works for me

Thanks for testing! I'll include this fix in the next version/release.

@j-licht could you please try again with commit 5adde00 ?

I've get this, maybe only python 3.8 related error:
Traceback (most recent call last):
  File "./main.py", line 20, in <module>
    export = netflow.parse_packet(binascii.unhexlify(pkt.packet.payload.payload.payload), templates[pkt.packet.payload.src])
  File "/home/nas/.local/lib/python3.8/site-packages/netflow/utils.py", line 57, in parse_packet
    return V9ExportPacket(data, templates["netflow"])
  File "/home/nas/.local/lib/python3.8/site-packages/netflow/v9.py", line 503, in __init__
    otfs = V9OptionsTemplateFlowSet(data[offset:])
  File "/home/nas/.local/lib/python3.8/site-packages/netflow/v9.py", line 326, in __init__
    for scope_counter in range(option_scope_length / 4):  # example: option_scope_length = 4 means one scope
TypeError: 'float' object cannot be interpreted as an integer

Could you solve this? It's because it uses / (giving a float) instead of //

authors: bitkeks j-licht


text:
Update logback-classic to 1.5.10

About this PR
📦 Updates ch.qos.logback:logback-classic from 1.5.4 to 1.5.10
Usage
✅ Please merge!
I'll automatically update this PR to resolve conflicts as long as you don't change it yourself.
If you'd like to skip this version, you can just close this PR. If you have any feedback, just mention me in the comments below.
Configure Scala Steward for your repository with a .scala-steward.conf file.
Have a fantastic day writing Scala!

⚙ Adjust future updates
Add this to your .scala-steward.conf file to ignore future updates of this dependency:
updates.ignore = [ { groupId = "ch.qos.logback", artifactId = "logback-classic" } ]

Or, add this to slow down future updates of this dependency:
dependencyOverrides = [{
  pullRequests = { frequency = "30 days" },
  dependency = { groupId = "ch.qos.logback", artifactId = "logback-classic" }
}]

labels: test-library-update, early-semver-patch, semver-spec-patch, commit-count:1

Superseded by #138.


text:
🛑 Luogu CDN is down

In 2de98e6, Luogu CDN (https://cdn.luogu.com.cn/fe/loader.js?ver=20230228-2) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Luogu CDN is back up in b26102b after 9 minutes.

repo: bitsstdcheee/luogu-status


text:
🛑 Luogu Ti is down

In acdd4a2, Luogu Ti (https://ti.luogu.com.cn/problemset) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Luogu Ti is back up in bbea285 after 11 minutes.


text:
🛑 CSP 报名系统 is down

In e245ddb, CSP 报名系统 (https://cspsjtest.noi.cn/) was down:

HTTP code: 0
Response time: 0 ms

Resolved: CSP 报名系统 is back up in d2bc6ce after 11 minutes.


text:
可以加一个删除本地记录的按钮么

我看了自己的记录，然后帮朋友看了，现在我打开记录里面有我和他两个人的记录光看UID的话还不好区分，我尝试删掉文件再解压，记录还是在的。希望可以加一个可以删除记录的功能

v0.1.0 加了

authors: NgaiHoChan biuuu

repo: biuuu/star-rail-warp-export


text:
"\n" not parsed correctly

"\\n" is parsed as "\\\n"
This is also true of any string where "\n" appears but the \ before the n is escaped itself.
You can test this also by inputting: (display "\\n") into the REPL.

I have also written a fix here though I recommend at some point the parser should be rewritten entirely.

@yhara if you want to look into a nice tokenizer that is easy to modify. You can look at my LIPS Scheme project. The tokenizer can be extracted, look into a Lexer class and Lexer._rules. It's a simple state machine (unfortunately the whole library is in one file, I was not able to split it into modules, because of cyclic dependencies).

Upon further analysis of the parser code I have realized that the jsScheme, which the parser uses code from, is licensed under the GNU GPL. I believe that this license requires the entirety of biwascheme to be licensed under the GNU GPL if it uses it. Thus, I believe that in order for biwascheme to not violate the GNU GPL, either the parser as a whole needs to be replaced (perhaps with the one from jcubic's LIPS), or the project needs to be re-licensed under the GNU GPL.
I have closed my pull request as I don't wish to make major changes to the licensing of the project by myself, but if biwascheme chooses to go down that route my version of biwascheme with this issue patched is located here: https://github.com/GeethanPfeifer/biwascheme . Note that I have changed the license of this repository to comply with the GNU GPL.
All the best,
Geethan

authors: GeethanPfeifer jcubic

repo: biwascheme/biwascheme