Support expr_form in run and startCommand

This adds initial support for expr_form which addresses #82.
Here is a little snippet i used for testing.
        SaltStackClient client = new SaltStackClient(URI.create("http://<IP_ADDRESS>:8000"));
        client.getConfig().put(ClientConfig.SOCKET_TIMEOUT, 0);
        Map<String, Object> result =  client.run("salt", "", AuthModule.AUTO, "local", new NodeGroup("min123"), "test.ping", new ArrayList<>(), new HashMap<>());
        result.forEach((key, value) -> {
            System.out.println(key + " -> " + value);
        });

        Token token = client.login("salt", "", AuthModule.AUTO);

        ScheduledJob job = client.startCommand(new MinionList("minion1", "minion4"), "test.ping", new ArrayList<>(), new HashMap<>());
        System.out.println("Job ID: "+ job.getJid());
        job.getMinions().forEach(System.out::println);
        Map<String, Object> result2 = client.getJobResult(job);
        result2.forEach((key, value) -> {
            System.out.println(key + " -> " + value);
        });

Closing it, will reopen a new PR from a branch in the SUSE repository since I added some fixes there.


Signals and shorthands

Resolves #2
Input signals

[x] explicit function
[x] implicit app-db
[x] one pair of :<- [::sub-name] sugar
[x] multiple pairs of sugar

Computation function

[x] explicit function
[x] :-> sugar (ignores subscription params, only depends on input signals)
(fn [db _] (:foo db)) => :-> :foo
[x] :=> sugar (flattens the params and removes sub name)
(fn [db [_ x y]] (+ x y)) ⇨ :=> (fn [db x y] (+ x y))

Tests
clj -M:cljd:test compile hti.re-dash-test && flutter test

[x] happy path
[ ] reset state between each test case (since the tests are read-only and don't alter the state it doesn't really matter)
[x] actual values from derived subscriptions (can't seem to get the value of a Cell (subscription) in a test case)
[ ] syntax error exceptions

Looking very good so far

I'm happy to merge/release this unless you're still finishing off a few things?

@wkok i was hoping https://github.com/Tensegritics/ClojureDart/pull/243 would get merged so i could use use_fixtures :each here, but it's been getting stale.
i'll add tests for the syntax error cases then let's get this merged <3

@wkok I added tests for the error cases. It's good to go~


KAFKA-4786: Wait for heartbeat thread to terminate in consumer close

@hachikuji @ijuma Can you take a look? Thanks.
At the moment, consumer.close() marks heartbeat thread as closed, but doesn't do a join, so the thread may still be alive when close() returns. I could update the test to waitForCondition and give some time for the thread to terminate, but I changed the implementation to do a join() similar to what the producer does when force closing the I/O thread, since it is nice to have everything cleaned up before close() returns.

LGTM (for real this time). Merging to trunk and 0.10.2.


Video Input

Since there is capability for multi image input, is that possible to get video input as well?
Some VLMs support video like Qwen2-VL and MiniCPM-V 2.6.
Thanks!

Thanks for the suggestions @chigkim!
This feature is already on the backlog as described here #75

Sorry about that! I missed it.

No worries!
It's great that you open this issue, it does bring the importance to light.
Could you comment in this PR #75 as well?


Test fails using yarn@berry and webpack since v27

🐛 Bug Report
Testing webpack build fails using yarn@berry since jest v27
test.js
const webpack = require('webpack');

test('simple', () => {
    expect(() => {
        webpack({
            entry: './main.js'
        })
    }).not.toThrow();
});

output
expect(received).not.toThrow()

    Error name:    "Error"
    Error message: "Cannot find module 'pnpapi' from '/.../.yarn/cache/enhanced-resolve-npm-5.8.2-b25228f39b-1af3f6bcb9.zip/node_modules/enhanced-resolve/lib'·
    Require stack:
      .yarn/cache/enhanced-resolve-npm-5.8.2-b25228f39b-1af3f6bcb9.zip/node_modules/enhanced-resolve/lib/index.js
      .yarn/$$virtual/webpack-virtual-7b5d4f14ba/0/cache/webpack-npm-5.40.0-421f019ffd-1d13fff8f7.zip/node_modules/webpack/lib/FileSystemInfo.js
      .yarn/$$virtual/webpack-virtual-7b5d4f14ba/0/cache/webpack-npm-5.40.0-421f019ffd-1d13fff8f7.zip/node_modules/webpack/lib/Compilation.js
      .yarn/$$virtual/webpack-virtual-7b5d4f14ba/0/cache/webpack-npm-5.40.0-421f019ffd-1d13fff8f7.zip/node_modules/webpack/lib/Compiler.js
      .yarn/$$virtual/webpack-virtual-7b5d4f14ba/0/cache/webpack-npm-5.40.0-421f019ffd-1d13fff8f7.zip/node_modules/webpack/lib/webpack.js
      .yarn/$$virtual/webpack-virtual-7b5d4f14ba/0/cache/webpack-npm-5.40.0-421f019ffd-1d13fff8f7.zip/node_modules/webpack/lib/index.js
      index.test.js
    "

          at resolveSync (.yarn/cache/resolve-patch-55fcdb097c-c4a515b760.zip/node_modules/resolve/lib/sync.js:102:15)

To Reproduce
https://github.com/irudoy/yarn-berry-webpack-jest-repro/tree/new
Expected behavior
The test is successfully passed.
Link to repl or repo (highly encouraged)
https://github.com/irudoy/yarn-berry-webpack-jest-repro/tree/new – v27 (not working)
https://github.com/irudoy/yarn-berry-webpack-jest-repro/tree/new-2 – v26 (working)
envinfo
  System:
    OS: macOS 11.4
    CPU: (16) x64 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
  Binaries:
    Node: 14.17.0 - /usr/local/bin/node
    Yarn: 2.4.2 - /usr/local/bin/yarn
    npm: 6.14.13 - /usr/local/bin/npm

I assume this is due to #10847 - @merceyz any idea?

Yeah most likely, we can change the defaultResolver to handle requests for pnpapi itself
if (path === 'pnpapi') return require.resolve('pnpapi', { paths: [options.basedir] })

Friendly ping. Can I help somehow with it?

Still actual for v27.0.6 @SimenB @merceyz


Underscore should not be escaped

When trying to run the following with the underscore escaped in {Get-ItemProperty $\_.PSPath}:
$TimeZone = Get-ChildItem "HKLM:\Software\Microsoft\Windows NT\CurrentVersion\Time zones" | foreach {Get-ItemProperty $\_.PSPath}; $TimeZone | sort Display | Format-Table -Auto PSChildname,Display

A user gets the following error:
Get-ItemProperty : Cannot find path 'C:\Users\thomas.pike.admin\$\_.PSPath' because it does not exist.
At line:1 char:102
+ ... entVersion\Time zones" | foreach {Get-ItemProperty $\_.PSPath}; $Time ...
+                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : ObjectNotFound: (C:\Users\thomas.pike.admin\$\_.PSPath:String) [Get-ItemProperty], ItemN
   otFoundException
    + FullyQualifiedErrorId : PathNotFound,Microsoft.PowerShell.Commands.GetItemPropertyCommand

The correct code is (without the escaped underscore):
$TimeZone = Get-ChildItem "HKLM:\Software\Microsoft\Windows NT\CurrentVersion\Time zones" | foreach {Get-ItemProperty $_.PSPath}; $TimeZone | sort Display | Format-Table -Auto PSChildname,Display

Docs Build status updates of commit 378b46e:
:clock10: Full build: the average full build time is 12 min(s) 14 sec(s), this is based on the last 1000 build(s) for this repository.

Docs Build status updates of commit 378b46e:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

exchange/exchange-ps/exchange/client-access/Set-MailboxRegionalConfiguration.md
:white_check_mark:Succeeded
View (exchange-ps)

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

Docs Build status updates of commit a13dc82:
:clock10: Full build: the average full build time is 12 min(s) 14 sec(s), this is based on the last 1000 build(s) for this repository.

Docs Build status updates of commit a13dc82:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

exchange/exchange-ps/exchange/client-access/Set-MailboxRegionalConfiguration.md
:white_check_mark:Succeeded
View (exchange-ps)

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


Visualize embeddings in 2 or 3 dimensions

Is your feature request related to a problem? Please describe.
Visualize data to get a better overview of "missed" spots or clusters of instances that a model got wrong.
Describe the solution you’d like
Dimension reduction for easy visualization of datapoints
Describe alternatives you’ve considered
-
Additional context
Requested by GeorgePearse on Discord

@jens @jhoetter I think the core value of visualization of low dimensionality data is to see whether there are any clusters/classes you've completely missed so far, and if so, how large are they. Hard to understand that from the current UI design.

After the embeddings you could just have a "select dimensionality reduction" option with PCA, t-sne, and UMAP as the dimensionality reduction methods (UMAPs worked best for me in the past).

Also helps with Active Learning if you can see a cluster of instances that the model gets wrong.

See https://projector.tensorflow.org/ for reference


[SUGGESTION] Scaffold tweaks

List of Scaffold tweaks:

Scaffolds should work as ladders aswell. Or even better, how they work in 1.14 (Not solid, and you can travel inside, but that's ideal situation)
Left-clicking should extend scaffold UP, and Shift+left-click should place in direction your BODY is facing (second part is implemented already, but work with simple L-click)
Mining level set to 0 (so you can break with open arm)
Breaking speed make similar to "Leaves", so you can break it faster

-=<I like how you get all connected blocks back if Shift-break, keep it>=-

I've tried to get them to act like ladder but sadly it's not in my skillset. When updating this mod to 1.12 it broke the ladder functionality and I can't get it back ever since. The break speed and harvest levels make sense though so I'll look into those.


drivers: eth_enc28j60: moved to dts

Driver for networking device Microchip ENC28J60 is used as SPI slave,
moved to DTS type definition. Samples dns_resolve, echo_client and
echo_server use this device on Arduino 101 board.
Fixes #10894 Ethernet device
Signed-off-by: Andrei Gansari<EMAIL_ADDRESS>

Codecov Report

Merging #11686 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master   #11686   +/-   ##
=======================================
  Coverage   48.23%   48.23%
=======================================
  Files         279      279
  Lines       43291    43291
  Branches    10359    10359
=======================================
  Hits        20881    20881
  Misses      18270    18270
  Partials     4140     4140

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Attempt to fix tiling

Hi Jan @biovoxxel ,
this is not a bugfix yet (please don't merge it).
I'm just trying to set up a minimal-working-example. I wrote a little main() function that uses your pushGridTile function and works. Can you modify that main() function in a way that I can reproduce the issue you had? I'm not sure if I understand the issue yet.
Feel free to push to my repository/branch.
Cheers,
Robert

I adapted the test using your main method and it shows that the plugin actually works as intended. What does not work is the macro functionality of the very same method. In an IJ Macro the pushed image seems to be not recognizable. Test macro see: https://github.com/biovoxxel/clijx-dev/blob/main/clijx-dev/src/test/resources/CLIJx_dev_test.ijm

Ah I see @biovoxxel ,
I presume it's because the image is pushed with an unspecified name. Would you mind trying this right after you called clij2.push()?
CLIJHandler.getInstance().pushInternal(buffer, imp.getTitle());

Source: https://github.com/clij/clij2/blob/master/src/main/java/net/haesleinhuepf/clij2/plugins/PushTile.java#L117
The issue is that the image has to be registered in the list of images that are accessible from Macro. You know, in macro there are not variables that can hold images. The image variables in CLIJ macros are strings that contain an image name. Hence, the image has to be registered in the list of available images.
Let me know if this helps!

That did the job @haesleinhuepf. Thanks!!!
The new version is uploaded for pushing and pulling tiles. it also contains a working test example in the main() method of the PullGridTileToImage class which shows the intended typical application case (fusing tiles with blending options when voronoi border labels are missing)


Parser: give syntax error on comma after newline in argument list

Fixes #6513
Code like this:
foo(x
, y)

currently doesn't give a syntax error, but it should (like in Ruby). We can of course discuss whether it should really be a syntax error or not. My reasoning is that the comma signals that more arguments are coming, and it's confusing that the comma starts the next line. For example, if we remove the parentheses:
foo x
, y

that won't compile. So code with and without parentheses should look more or less the same (maybe this is a weaker argument, but still...).
I believe in many other languages this is a syntax error too.
This of course is a breaking change, but I doubt there are many out there that write code like this.
This syntax option was available for many other things, like method arguments, but not available in some other things, like array literals. Now it's unified to give a syntax error.

Hmmm... actually, Java, C# and Python allow such syntax. But Ruby and Go don't. So I guess it's a matter of preference.
Right now it's behaving in a way or another depending on the case, so it's not unified. Let's use this PR to discuss what should we do with this. Maybe this PR is fine, it hurts my eyes a bit to see that stray comma there :-P

This syntax (leading comma) was used in JS community, but isn't used widely nowadays. I guess everybody realised it's ugly.


feat: optimise ux for slack component

Because

Now, there are several weird parts in Slack component.

This commit

Modify the weird parts to optimise UX.

@chuang8511
Can you describe the weird parts in the commit message?


Use owncloud docker for testing

Can use this :
https://github.com/owncloud/pyocclient/blob/master/.travis.yml#L14

done : https://github.com/noveens/js-owncloud-client/commit/a7b82b8843e792976831e71f69bd85605ed49fe4


Accusations manager

Scope
What is changing with this PR?
This PR introduces the base accusation system to analyse consensus round state data. This PR does not contain any specific accusation detection logic as those will be build based on this system.
Why?
Why are we doing this?
Todos
If any, what are the follow-up tasks required other than merging this PR? Have they been arranged?

[ ] ???

this is a duplicate


Properly handle render calls during async rendering

Currently if the render call is made interleaved with an async rendering process, it will throw due to the nested rendering check.
We should be able to safely handle these case and also ensure that the data is consistent once rendering completes.

я не понимаю что происходит


WebView for Android can not load local source

The  WebView for  Android can not load local source such as souce={{uri="web/index.html"}},It would throw a error webpage not available wherever my local html placed

@facebook-github-bot stack-overflow


Support onRefresh & onscroll events

I am unable to understand how to handle onRefresh & onscroll events if we are rendering Flatilists inside ScrollableTabView.
Great work BTW.

Hey ,
There are two props, for scrollabletabview,
refreshControl and loadMore, send this prop according to tabs


Add test site

I believe it should be solved

I believe it should be solved

Almost, if you check the 'Files Changed'-tab here with the PR. You can see there are some additional changes.
I fixed the language in an earlier commit, this PR seems to undo those changes. Could you restore those files listed with the current main. Ideally the PR would show only changes to the two zip files.

Not working on this pr anymore


Need to add inputString for chatbox dialogs

There is no feature for inputStrings()
The only that exist are inputInt().

I added the following code in the QueueTaskExt.kt class.
``/**

Prompts the player with an input dialog where they can enter text.

@return

The text as a String
*/
suspend fun QueueTask.inputString(description: String = "Enter text"): String {
player.runClientScript(110, description)
terminateAction = closeInput
waitReturnValue()
terminateAction!!(this)
return requestReturnValue as? String ?: ""
}``

Addressed in https://github.com/Tomm0017/rsmod/commit/bdcf4bf3d9f3be8332d6f1da85679303f2ba434f


[Bug] User options display for app after app property change

Summary

[ ] When user edits app property from home page and clicks back on to the app to exit the property pane of the app, the app does not switch back to show Edit and Launch options. User has to click outside of the app icon to enable these options though.
[ ] Property pane of app should exit when user presses the Esc key to make it more keyboard friendly for user

Motivation
When property pane exits on clicking outside of the property pane modal, the expectation for the user is to be able to access normal app operations (Edit, Launch) instead of moving outside of the app icon boundary and then have those options appear.

Can be closed. Its works as expected today.


Add automated style checking

Whatever style conventions we finally agree to, e.g. case for IRIs and annotations, we can REGEX for capitalization either through SHACL or through query.  We can address it between onto_tool and the bundle script.

@rjyounes, @sa-bpelakh, @Jamie-SA
I think we do a lot of this now, what is the situation?

Currently we use SHACL to check:

Min 1 definition - should really be exactly one with either no language tag or a specific tag
Exactly one prefLabel - should really be exactly one with either no language tag or a specific tag
Lowercase labels in properties
Title case label in classes

Additions to get full coverage of the style guide:

Add the sentence case check to skos:definition, skos:scopeNote, skos:note, and skos:editorialNote. A sentence case shape is defined but not used; perhaps this wasn't working?
Check that rdfs:label and rdfs:comment are not used anywhere except in the rdfsAnnotations ontology that is created during the release. We have to make sure the check applies before this file is created.

I also see the need for some refactoring:

Cardinality 1 is enforced in the Title Case, Lower Case, and Sentence Case shapes. Rather than mixing concerns, these should be 2 distinct shapes (one for prefLabel, one for definition) that can be shared by classes and properties.

Min 1 definition - should really be exactly one with either no language tag or a specific tag

Min 1 and exactly 1 are not the same meaning. Not sure what you mean here. We generally avoid min 1 in favor of someValuesFrom

I mean: you should have exactly one definition and exactly one prefLabel, unless they have different language tags.

We can definitely augment the current checks to support the extra suggestions you made. I have become a bit disillusioned with SHACL with respect to reporting the context of complex validations - i.e. if you have some simple sh:property for a value constraint, the report entry will indicate the erroneous value and the nature of the violation, but for more complex conditions build with sh:or, you will get something like OR constrain violated with no further info.
We should create a small test-suite covering the sort of issues we want to detect, and perhaps convert some of the SHACL shapes into SPARQL queries that would provide better information about the failures.


UnicodeDecodeError

Great code.
But I'm having problems testing with custom images. I'm having this issue.
(dreamgaussian) D:\AI\dreamgaussian\dreamgaussian-main>python main.py --config configs/image.yaml input=data/gt25m.png save_path=gt25m
[INFO] load image from data/gt25m.png...
[INFO] load prompt from data/gt25m.png...
Traceback (most recent call last):
  File "D:\AI\dreamgaussian\dreamgaussian-main\main.py", line 877, in <module>
    gui = GUI(opt)
  File "D:\AI\dreamgaussian\dreamgaussian-main\main.py", line 67, in __init__
    self.load_input(self.opt.input)
  File "D:\AI\dreamgaussian\dreamgaussian-main\main.py", line 367, in load_input
    self.prompt = f.read().strip()
  File "C:\Users\carlo\miniconda3\envs\dreamgaussian\lib\encodings\cp1252.py", line 23, in decode
    return codecs.charmap_decode(input,self.errors,decoding_table)[0]
UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 130: character maps to <undefined>

Can you give me some hints of what can I do to solve it?
thanks

I went to debug and found that I must have "_rgba" on the name of the file.
So, renaming my file from "gt25m.png" to "gt25m_rgba.png" solved the issue.


Accessing Transactions

Could you use this to find details of the transaction by going to a url like
/paypal/{transaction_id}/get

Im trying to access transactions on my account via a dashboard.

@xitude it up to you how to customize your routes , but you need to write the code that handle this logic yourself , for more details watch this video https://www.youtube.com/watch?v=q5Xb5r4MUB8

How can I access the transactions details using the transaction id in Laravel 5.2?

@Gameonn use the transaction id and send get request to the paypal api. I think you can find more details about this in there API doc


Add info about interactive rebase for undoing commits

Add information to ./source-control/git-guidance/readme.md#reverting-and-deleting-commits about interactive rebase.

Hi @annazietlow , can i pick this up and raise a PR?

Hi @annazietlow , can i pick this up and raise a PR?

Created a Pull request https://github.com/microsoft/code-with-engineering-playbook/pull/501 which will close this issue. Request for review

Created a Pull request https://github.com/microsoft/code-with-engineering-playbook/pull/501 which will close this issue. Request for review


rtfm/learn2 error

Getting the following error with the rtfm/learn2 skeleton
'break' not in the 'loop' or 'switch' context in user/plugins/snappygrav/snappygrav.php on line 215

Ooops! I forgot to replace break with exit
However when the program finds true this assumption means that the wkhtmltopdf library folder was not found
Thanks for the tip.


FitUptakeKinetics - error messages

I've started looking at some more sizeable datasets now and have come across the following issue. Unfortunately as you can see, the error message isn't particularly informative, so I'm not sure what I'm looking for. The modelling for each peptide using fitUptakeKinetics abruptly terminates with an error message, although I don't have any insight into which peptide R failed at.
From what I have learned, there may be a few different reasons why this happen, on being that #D > 0; when D = 0 for one peptide I was getting this message. It has occurred again since, although this time I'm not quite sure why and still trying to troubleshoot this.

If it's possible to share some data that would be great. It could be what you suggest which means the initialisation of d might be bad. What happens if you remove those peptides from the analysis?

Shared a peptide where I get this error. In Row 20, D = 0 for this experiment. If I change to 0.1, this error goes away. If I change it to something unrealistic like D = 2, I get the error again. So I think this is happening when fitUptakeKinetics still can't find a good fit even with the retries (this is with the latest version installed).

The example you sent worked for me - it simply returned a HdxStatModel which was empty but this doesn't stop the fitting. The "suingular graident matrix at initial parameter estimates" will appear as it tries different values so you shouldn't worry about that error.
The error that's resulting in the failure is Error: $ ...
could try typing traceback() after you see the error it might give me more clues

> traceback() 15: deviance.default(X[[i]], ...) 14: FUN(X[[i]], ...) 13: FUN(X[[i]], ...) 12: lapply(X = X, FUN = FUN, ...) 11: sapply(nonlin_mod, deviance) 10: differentialUptakeKinetics(object = object, feature = x, start = start,          formula = formula, design = design, maxAttempts = maxAttempts) 9: FUN(X[[i]], ...) 8: lapply(feature, function(x) differentialUptakeKinetics(object = object,         feature = x, start = start, formula = formula, design = design,         maxAttempts = maxAttempts)) 7: .local(object, ...) 6: fitUptakeKinetics(object = hdxstats_tableqDF[, c(1:num_states)],         feature = rownames(hdxstats_tableqDF[, c(1:num_states)])[[1]],         start = list(a = NULL, b = NULL, d = NULL, p = 1)) 5: fitUptakeKinetics(object = hdxstats_tableqDF[, c(1:num_states)],         feature = rownames(hdxstats_tableqDF[, c(1:num_states)])[[1]],         start = list(a = NULL, b = NULL, d = NULL, p = 1)) at hdxstats_use_v3_generic_forOli.R#90 4: eval(ei, envir) 3: eval(ei, envir) 2: withVisible(eval(ei, envir)) 1: source("~/ELN43793/Oli_ManhattenPlot_v2/hdxstats_use_v3_generic_forOli.R")

awesome, could you paste the output of:
hdxstats::differentialUptakeKinetics

Same syntax as in the fitting? I get the same outcome.

res <- differentialUptakeKinetics(object = hdxstats_tableqDF[,c(1:num_states)],

                     feature = rownames(hdxstats_tableqDF[,c(1:num_states)])[[1]],

                     start = list(a = NULL, b = NULL,  d = NULL, p = 1))

Error in nlsModel(formula, mf, start, wts) :
singular gradient matrix at initial parameter estimates
Error: $ operator is invalid for atomic vectors

traceback()
6: deviance.default(X[[i]], ...)
5: FUN(X[[i]], ...)
4: FUN(X[[i]], ...)
3: lapply(X = X, FUN = FUN, ...)
2: sapply(nonlin_mod, deviance)
1: differentialUptakeKinetics(object = hdxstats_tableqDF[, c(1:num_states)],
feature = rownames(hdxstats_tableqDF[, c(1:num_states)])[[1]],
start = list(a = NULL, b = NULL, d = NULL, p = 1))

okay, sorry

hdxstats::differentialUptakeKinetics
function (object, feature = NULL, design = NULL, formula = NULL,
start = list(a = NULL, b = 0.001, d = NULL, p = 1), mycolours = brewer.pal(n = 8,
name = "Set2"), maxAttempts = 5)
{
.out <- NULL
if (!is.null(design)) {
colnames(object)[[1]] <- design
}
ldf <- longFormat(object)
ldf$timepoint <- as.numeric(str_match(ldf$colname, "X\s*(.?)\srep")[,
2])
ldf$replicates <- as.numeric(str_match(ldf$colname, "rep\s*(.)\scond")[,
2])
ldf$chargestate <- as.numeric(str_match(ldf$rowname, "_\s*(.)")[,
2])
ldf$condition <- as.factor(str_match(ldf$colname, "cond\s(.*)")[,
2])
if (length(feature) == 1) {
if (!is.null(feature)) {
if (is.null(formula)) {
formula <- value ~ a * (1 - exp(-b * (timepoint)^p)) +
d
}
data <- data.frame(ldf[ldf$rowname == feature, ])
data <- data[, !colSums(is.na(data)) == nrow(data)]
data <- na.omit(data)
if (nrow(data) < 3) {
print("too few data points to fit model")
return()
}
if (is.null(start$a)) {
start$a <- max(data$value)
}
if (is.null(start$d) & length(start) > 2) {
start$d <- min(data$value)
}
nonlin_mod <- vector(mode = "list", length = maxAttempts)
for (j in seq_len(maxAttempts)) {
if (is.null(start$b)) {
start$b <- 10^(j - maxAttempts)
}
nonlin_mod[[j]] <- try(nlsLM(data = data, formula = formula,
start = start, control = nls.lm.control(maxiter = 500,
ftol = 10^{
-8
}), trace = FALSE, lower = rep(0, length(start)),
algorithm = "LM", na.action = na.exclude))
start$b <- NULL
}
jj <- which.min(sapply(nonlin_mod, deviance))
if (is.null(start$b)) {
start$b <- 10^{
jj - maxAttempts
}
}
nonlin_mod <- nonlin_mod[[jj]]
if (inherits(nonlin_mod, "try-error")) {
print("model fit failed, likely exessive missing values")
return(nonlin_mod)
}
myPredict1 <- expand.grid(timepoint = seq(min(data$timepoint,
0), max(data$timepoint), 0.5))
myPredict1$fit <- predict(nonlin_mod, newdata = myPredict1)
datalist <- group_split(data, condition)
nlmod <- lapply(datalist, function(x) {
nonlin_mod <- try(nlsLM(data = x, formula = formula,
start = start, control = nls.lm.control(maxiter = 500,
ftol = 10^{
-8
}), trace = FALSE, lower = rep(0, length(start)),
algorithm = "LM", na.action = na.exclude))
})
if (any(sapply(nlmod, function(x) inherits(x, "try-error")))) {
print("Could not fit model, likely exessive missing values")
return(nlmod)
}
myPredict <- lapply(1:length(nlmod), function(j) expand.grid(timepoint = seq(min(data$timepoint,
0), max(data$timepoint), 0.5)))
myPredict <- lapply(1:length(nlmod), function(j) {
myPredict[[j]] <- predict(nlmod[[j]], newdata = myPredict[[j]])
return(myPredict[[j]])
})
myPredictjoin <- do.call(cbind, myPredict)
colnames(myPredictjoin) <- sapply(datalist, function(x) x$condition[1])
myPredictjoin <- data.frame(myPredictjoin)
myPredictjoin$timepoint <- unlist(expand.grid(timepoint = seq(min(data$timepoint,
0), max(data$timepoint), 0.5)))
myPredict_long <- myPredictjoin %>% pivot_longer(cols = 1:length(datalist))
colnames(myPredict_long) <- c("timepoint",
"condition", "fit")
df <- data.frame(myPredict_long)
df$condition <- gsub("X", "", df$condition)
gg <- ggplot(data, aes(y = value, x = timepoint,
color = condition)) + geom_point(size = 4) +
theme_classic() + geom_line(data = myPredict1,
aes(x = timepoint, y = fit), inherit.aes = FALSE,
size = 2, col = mycolours[2]) + geom_line(data = df,
aes(x = timepoint, y = fit, color = condition),
inherit.aes = FALSE, size = 2) + labs(x = "Exposure",
y = "Deuterium Incoperation", color = "condition",
title = paste0(data$rowname[1])) + scale_color_viridis(alpha = 0.7,
discrete = TRUE)
.nlmod <- .nlsList(nlsmodels = nlmod)
.out <- .hdxstatmodel(nullmodel = nonlin_mod, alternative = .nlmod,
vis = gg, method = "Functional Model",
formula = formula)
}
}
return(.out)
}
<bytecode: 0x3db3b368>
<environment: namespace:hdxstats>

hdxstats::manhattanplot appears with the correct spelling, so I think I do have the most recent version

Okay, I can see the correct line for the current version, and was able to process that single peptide data without a stop error. I just mustn't have had the newest version. I'll close the issue then, thanks!

Thanks, @nlgittens


empty coverage for buildType "debug"

Current Behavior
With gradle 8.1.1 running task createDebugUnitTestCoverageReport results in correct coverage

However with gradle 8.2 or 8.3 running the same task results in empty coverage

When running similar tasks for other buildTypes createReleaseUnitTestCoverageReport and createSuperBuildTypeUnitTestCoverageReport coverage is correct with all gradles 8.1.1 - 8.3
Expected Behavior
Correct coverage for debug buildType
Context (optional)
No response
Steps to Reproduce
Full repository is here https://github.com/Smatek/JacocoGradleBugSample
To reproduce this, change gradle version in gradle-wrapper.properties
Gradle version
8.1.1 - 8.3
Build scan URL (optional)
No response
Your Environment (optional)
Android Studio Giraffe | 2022.3.1 Patch 1
Tried on Mac and Windows

Have you checked the Android tracker for this issue already being reported?
Have you checked if the problem persists with different versions of the Android plugin?

Updating AGP to 8.2.0-beta06 worked. Thanks for suggestion!


Vietnamese Translation: Documentation

What would you like us to improve?
I would like you to improve the documentation translation process by providing clearer guidelines and instructions for translators.
How important it is?
It is crucial for users who rely on the translated documentation to have clear and accurate information. Therefore, improving the translation process is of high importance to ensure the quality and accessibility of the documentation for all users.

Great suggestion. We're keeping an eye out on working with the Vietnamese-speaking Scroll community for those who want to take on a translation initiative.

Hi Daniel,
Thank you for your reply.
I'm delighted to hear that the Scroll project is considering collaborating with the Vietnamese-speaking community to foster translation initiatives.
I have completed the translation of the entire documentation and hope that it will contribute to the convenience and proficiency of users as well as developers in the community.
Please let me know if any revisions or additions are needed from my end. Thank you, and looking forward to further collaboration!


Just started to get this error. no parameter named 'ensure'

Error: Could not retrieve catalog from remote server: Error 400 on SERVER: no parameter named 'ensure' at /etc/puppetlabs/code/environments/production/modules/elasticsearch/manifests/package.pp:48 on File[/opt/elasticsearch/swdl] at /etc/puppetlabs/code/environments/production/modules/elasticsearch/manifests/package.pp:48 on node webapp.local.dev
Warning: Not using cache on failed catalog
Error: Could not retrieve catalog; skipping run

elasticsearch.pp file
class sc::logstash (
  $package_url   =  'https://download.elasticsearch.org/elasticsearch/release/org/elasticsearch/distribution/rpm/elasticsearch/2.1.1/elasticsearch-2.1.1.rpm',
  $instance_name =  'logstash'
) {

  class { '::elasticsearch':
    autoupgrade                       =>  true,
    manage_repo                       =>  true,
    repo_version                      =>  '2.x',
    java_install                      =>  true,
  }

  elasticsearch::instance { $instance_name: }
}

Duplicate of https://github.com/elastic/puppet-elasticsearch/issues/573


feat(server): allow disabling serve-static middleware entirely

Types of changes

[x] New feature (a non-breaking change which adds functionality)

Description
Allows explicitly disabling serve-static middleware by setting render.static to false.
closes #9362
Checklist:

[x] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly. (PR: #)
[ ] I have added tests to cover my changes (if not applicable, please state why)
[x] All new and existing tests are passing.

Should we also disable the second serve-static middleware instance defined a bit later in the code (https://github.com/nuxt/nuxt.js/pull/9365/files#diff-b8c2d26ed3fd075596a838c69b36c537536ae6973cafffdbf481fec464c9b6cfR104-R110)?

@antoinerey Ideally users shouldn't hit /_nuxt/ requests and reverse proxy should cache/handle them.

TODO:

Docs
Types for false value: https://github.com/nuxt/nuxt.js/blob/9a32fa18afeda72244c50e6a916fa2bc3e9c7ca1/packages/types/config/render.d.ts#L75

👋 By any chance, any update about when this will be released?

Hi @antoinerey there is no specific time but you can use nuxt-edge or for types, in package.json installing @nuxt/types-edge

Thanks for the prompt answer!
I'm not sure we want to move from the stable channel to the edge one, so we'll probably work on our patience skill. 😁


THRIFT-3622: remove auto_ptr use in the codebase because it is deprecated

The build failure is about node.js version dependencies which curiously is in an unrelated but active pull request for THRIFT-4074.  There were no errors in Travis CI to worry about here; waiting for Appveyor before merging.

Build job #7 failed because it failed to download something from a site I can get to just fine (github, holding "phantomjs").  Not related to the PR.


[vpj] Remove hadoop-hdfs dependency

Remove hadoop-hdfs dependency

This dependency pulls in jackson versions that have vulnerabilities. Turns out, this might not be needed. If tests pass, we can merge this instead of trying to fix the gradle stuff.
How was this PR tested?

GH CI
Does this PR introduce any user-facing changes?

[X] No. You can skip the rest of this section.
[ ] Yes. Make sure to explain your proposed changes and call out the behavior change.

When running tests locally, I found that there is a NSME error thrown:
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hdfs.DistributedFileSystem


Fix URL in About dialog

PR to follow...

See https://github.com/kapilratnani/JSON-Viewer/pull/23

Merged


Changed ajax dependency to vue-resource instead of jQuery

Only lightly tested

Hi @garhbod - Thanks for this! Since Evan You retired vue-resource and suggested to use axios instead I think vue-model should follow this and replace $.ajax with axios instead of vue-resource. I already started to use axios for some tests which were based on your changes. Cheers for that. I will provide an axios implementation if @aarondfrancis has nothing against it and will close this PR for now.

@thorsteneckel Any chance to get a hold of your axios implementation?

Sure! I'll create a branch and let you know. Should be done next week.

Thanks!


chore(update) fix security vulnerability found in marked <0.6.1

WS-2019-0024
moderate severity
Vulnerable versions: >= 0.5.0, < 0.6.1
Patched version: 0.6.1
A flaw was found in nodejs-marked versions from 0.5.0 to before 0.6.1. Affected versions of this package are vulnerable to Regular Expression Denial of Service (ReDoS). Input to the host variable is vulnerable when input contains parenthesis in link URIs, coupled with a high number of link tokens in a single line.

@EugeneHlushko Preview deploy failed because...?

Hmm looks like : Command did not finish within the time limit


Combat achievements for OSB

🚀 Feature Proposal
Just an idea that I think could be kinda cool and fun.
(I'm unsure how feasible this is due to the bot having a limited amount of slash commands available)
Combat achievements on OSB

--How it would work--
You could send your minion to kill a specific boss and try and complete x combat achievement task.
Combat achievements could be for all bosses and all raids, for example;
completing the perfect tob task could require high kc and max boost score and have a very low success rate? you could include minion learning so that your minion gets good at certain tasks allowing you to help out other people in the community complete the group tasks.
There could also be tasks that are just having a certain kc on a boss, e.g;
Grotesque Guardians | Grotesque Guardians Veteran | Kill the Grotesque Guardians 1000 times.
--Rewards--
rewards would include the slayer helms to flex as cosmetics

other rewards could include;
kill per hour/speed boosts at certain bosses/raids/inferno/jad
reduced food/supply usage at bosses/raids/inferno/jad
potentially more rewards if anyone has any other ideas.

Could be for bso too, I don't play that so unsure.

I love the idea of combat achievements, a first step if we want it to be similar to OSRS would be to change our current combat system tho. That way proper RNG and kill times for monsters can be achieved along with any specific item tasks. Like killing a monster with just fists etc.
Without it, a lot of assumptions would have to be coded.