No timeout on the "Wating Liveness and Readiness" phase

The is no timeout on the "Liveness and Readiness" phase so that, in case a deployment does not work or a Job fails, Spray is waiting forever in an infinite loop.
Similarly to the "--timeout" parameter of Helm, having a similar parameter on Spray would enable to define a timeout to be applied for both the regular Helm inner commands and for the "Liveness and Readiness" phase.

Solved by https://github.com/gemalto/helm-spray/pull/19


!Rar2017_64bit

Is this build variable still used?

It probably shoud be removed and always use the long codepath.
I guess I removed the setting/testing of it at some point accidently.  It was added alongside Rar5 support it seems.


Missing license?

Hi there,
I'm interested in forking this module and making changes so it can be used outside of a Laravel context. Unfortunately there's no license and I'm not keen on making any changes without a license.
Is there any chance a license can be added?

@ScopeyNZ  sorry for the late delay, somehow I missed the notification and was in vacation, yes offcourse, I will set this package with MIT license.
So you're free to go, regards.


fixed BinnedSpikeTrain.bin_edges property

Fixes https://github.com/NeuralEnsemble/elephant/issues/255.

Coverage increased (+0.02%) to 75.522% when pulling bcfd56b08a14668eec9cec0da0ac9967dd837f63 on INM-6:fix/bin_edges into a833a9678ce17804d9994ebc5b6d640100194e49 on NeuralEnsemble:master.


Add model output type checks for OnnxInferenceModel (#285)

* If model output type not supported exception will be thrown

* Exception message contains recommendation to use predictRaw() method

* Add test demonstrating usage of onnx model with unsupported output type

* Minor changes after apply of auto-format

It's not an actual fix of #285  but temporary solution to facilitate releasing of 0.4. Later we will implement support of ONNX output types such as Sequence and Map


Add .html to redirects

Going to https://www.erlang.org/doc/man/zlib redirects to https://www.erlang.org/doc/apps/erts/zlib however notice "zlib" is not "selected" in the sidebar:

only when we click it in the sidebar it is:

and the difference is:

https://www.erlang.org/doc/apps/erts/zlib
https://www.erlang.org/doc/apps/erts/zlib.html

This makes a big difference in apps with lots of modules like stdlib:

https://www.erlang.org/doc/apps/stdlib/gen_server
https://www.erlang.org/doc/apps/stdlib/gen_server.html

In the latter case, ExDoc highlights the module name and importantly scrolls sidebar down to its position.
If possible, I believe a quick fix is to add .html extension to redirects. Otherwise, we can look into support it in ExDoc somehow.

On netlify all URLs can be given without the .html extension, so even if we fix the redirects, google search and others can crawl to the variant without .html extension. So I think this problem needs to be solved in ex_doc.

Got it, thanks, I'll look into it.

If it would not break anything (and be even possible, no idea) would you be open to „un-prettify” links on Netlify, that is, non-.html urls would redirect to with .html? The benefits would be possible better SEO, instead of having both /gen_server and /gen_server.html links out there we’d standardize on the latter which would match ExDoc generated ones using autolinking feature.

For now, I have fixed ExDoc to handle URLs without .html, there were three spots, but there are probably more. We could also setup a redirect on ExDoc side though.
Regarding better SEO, I recommend Erlang to set the --canonical flag/config. This way, Erlang can keep a history of OTP versions hosted, but Google will only redirect to the main, latest one. This will solve both the .html issue AND any versioning. Here is where we set canonical in Elixir, we set it for everything, except for nightly/main builds: https://github.com/elixir-lang/elixir/blob/f0ebedc627220fef490ea2382432332d2d250466/lib/elixir/scripts/mix_docs.exs#L6
PS: if there are any questions if all versions should point to the latest one as canonical, this seems to have been the consensus in the Elixir community. People were getting frustrating from Elixir v1.12 being the top results while 1.16 was out (and so on).

I've opened #143 to address some issues. I don't think I can make Netlify redirect all URLs without .html to the .html version, but I can look into it.

@garazdawi we could also set the redirect by injecting some JS code in <head> but perhaps canonical is enough.

Closing this for now. Please let me know if you encounter any more issues.


[DOC] scientific reference - Series and Panel types

This PR addresses issue #1781, and is written in preparation of #1739.
This contains one (currently non-linked) page of scientific reference, which defines "series" and "panels".
Reviewers should concentrate on:

well-definedness and coherence of mathematical formalism
agreement with general intuition of time series and panels
formatting of the rst file

FYI @Lovkush-A, would especially appreciate your review (due to your pure math background)

note to self: we want to add sub-sections with three examples (with different properties)

Thinking about your comments, @lmmentel.
This should be useful for users in general, the current structure might restrict it too much to those with formal math background.
Would it be better if we structure it as follows, for each object introduced:

intuition
3 examples
formal definition
notes

instead of starting (and potentially intimidating the reader) with formal definition?

Thinking about your comments, @lmmentel.
This should be useful for users in general, the current structure might restrict it too much to those with formal math background.

Would it be better if we structure it as follows, for each object introduced:

intuition
3 examples
formal definition
notes
instead of starting (and potentially intimidating the reader) with formal definition?

Yeah that seems more accessible, especially if you plan to connect it to the knowledge that users might have about vectors, arrays, series, dataframes matrices etc.

do we need to say anything about how Series can represent other kinds of ordered data, not just time series?

Well, am I not doing that? I'm introducing "indexed series" in general, where the index can be anything, and "time series" is the sub-case where we have an index that is interpreted as time, which means it must be a sub-set of the (one-dimensional) reals.

need to somehow make clear the difference between a dataframe with index 0,...,n representing a time series and one representing 'tabular data' (where the order of the rows does not matter)

The abstract type for tabular data would be different. You would have equivalence up to permutation of rows, which in the case of a time series you do not have. Perhaps adding this as a note?
It might be confusing to most people, since "equivalence up to permutation of rows" is not a conceptual element that they would be aware of, since in the computer, they are looking at actual, distinct rows.

I disagree! The ordering of the variables matters, in my opinion and personal conceptual model.

There are classes/functions in which we automatically rearrange the columns to match what was seen during fit. To me, this means that we consider permutations of variables/columns as symmetries of the scitype.
I do not see why one would want the order of the variables as a part of the conceptual model. (except maybe to make definitions easier to write down...). For me, it is additional structure that one is keeping track of, which has no scientific meaning. Do you know any scientific questions that change if you swap two columns around? Forecasting multivariate series with cols A,B,C is the same question to forecasting B,A,C, as far as I know.

I was wondering whether we want named variables - i.e., should we include column index in the definition, or not?

I think so. Especially since pandas dataframes are the 'foundational' datatype in our codebase (as opposed to numpy arrays, say)

do we need to say anything about how Series can represent other kinds of ordered data, not just time series?

Well, am I not doing that?.

No. To quote: "We use the scitype Series to type univariate and multivariate time series"

I'm introducing "indexed series" in general, where the index can be anything, and "time series" is the sub-case where we have an index that is interpreted as time, which means it must be a sub-set of the (one-dimensional) reals.

I dont know if I am being pedantic, but we do need to say something about how with time series there is assymettry between past and future, but in other kinds of real-indexed series (eg the arrow head data) there might not be the assymetry.

The abstract type for tabular data would be different. You would have equivalence up to permutation of rows, which in the case of a time series you do not have. Perhaps adding this as a note?

I think we should add this as a note. It is precisely this property (i think) that distinguishes between tabular data and time series data. (random thought...is it possible to have sklearn but where fundamental objects are sets of rows, rather than ordered lists of rows. 🤔 )

It might be confusing to most people, since "equivalence up to permutation of rows" is not a conceptual element that they would be aware of

They might not be aware of it in those terms (in the same way most users would be confused by the rest of the document). However, I presume they are used to the fact that in sklearn, if you jumble up the rows, it should not affect one's model.

do we need to say anything about how Series can represent other kinds of ordered data, not just time series?

Well, am I not doing that?.

No. To quote: "We use the scitype Series to type univariate and multivariate time series"

Ok, this is going to get subtle.
In sktime, so far, we assume that all indices are time, or at least time-like, i.e., indexed series with an index supported in the reals. The Series scitype is a type attached to univariate and multivariate time series. Should I instead say, univariate and multivariate indexed series with a time-like index domain? That would be quite confusing, although more precise.

I'm introducing "indexed series" in general, where the index can be anything, and "time series" is the sub-case where we have an index that is interpreted as time, which means it must be a sub-set of the (one-dimensional) reals.

I dont know if I am being pedantic, but we do need to say something about how with time series there is assymettry between past and future, but in other kinds of real-indexed series (eg the arrow head data) there might not be the assymetry.

That there is assymmetry is mirrored by the absence of the assumption that we have symmetry - is that not good enough? Perhaps the examples should point this out?

(random thought...is it possible to have sklearn but where fundamental objects are sets of rows, rather than ordered lists of rows. 🤔 )

The best concrete data type for that would still be the pd.DataFrame, no? With the interface convention that all operations carried out must be invariant under row permutations of individual data containers?

Ok, this is going to get subtle.

Yes it is!  I am confused by what the term "time series" means in your formalisation. Quoting the document:
- "may choose to say that s is a time series if \mathcal{T} is totally ordered and (order)-isomorphic to a sub-set of \mathbb{R}, in a context where elements of \mathcal{T} are interpreted as time stamps"

is the arrowhead dataset a time series, under your conceptualisation? if yes, then I think the definition above is inaccurate, because the index in arrowhead is not interpreted as time. (or is it?? i dont think it should be...)

Should I instead say, univariate and multivariate indexed series with a time-like index domain? That would be quite confusing, although more precise.

Why is this confusing? To me, saying the arrow head dataset is a time series is confusing (given definitions above). 'Time-like' seems understandable.
if we are going to write formal mathematical definitions, presumably the aim is precision. otherwise, I dont see who this benefits. mathematicians (like me) will be confused and most non-mathematicians will skip the formalities and just use the examples and intuition anyway.

That there is (potential) asymmetry in an object satisfying the definition is mirrored by the absence of the assumption that we have symmetry - is that not good enough? Perhaps the examples should point this out?

I think this depends on what you want 'time series' to mean. For me, if time series index really correspond to time stamps, then the assymetry is implicitly a part of the definition and so we should explicitly mention it.


Periodic test failure in ConcurrentKeyExtentCacheTest

I have found that my build with tests wil periodically fall in the ConcurrentKeyExtentCacheTest in the master branch.  If I simply restart the build from that module then it will always succeed and continue on:
[ERROR] Failures:
[ERROR]   ConcurrentKeyExtentCacheTest.testExactEndRows:115 expected:<256> but was:<255>

This could be due to the test now using SecureRandom.

Nevermind.  I don't think SecureRandom is affecting the random number count.


⚠ Mobitopup has degraded performance

In 5633ad7, Mobitopup (https://napcard.voz.tech) experienced degraded performance:

HTTP code: 200
Response time: 3539 ms

Resolved: Mobitopup performance has improved in 01c4e9d.


Cleanup based on Kotlin Conventions

This PR includes the following:

Wrap functions in objects for better structure
Rename the functions to adhere to Kotlin naming conventions
Make function names more meaningful for readability

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@8d87ae0). Click here to learn what that means.
The diff coverage is 97.16%.

@@            Coverage Diff            @@
##             master       #6   +/-   ##
=========================================
  Coverage          ?   91.94%
  Complexity        ?       46
=========================================
  Files             ?       24
  Lines             ?      236
  Branches          ?       15
=========================================
  Hits              ?      217
  Misses            ?        8
  Partials          ?       11

Impacted Files
Coverage Δ
Complexity Δ

src/main/kotlin/verysecuresystems/Main.kt
0% <0%> (ø)
0 <0> (?)

...rc/main/kotlin/verysecuresystems/api/WhoIsThere.kt
100% <100%> (ø)
2 <2> (?)

...n/kotlin/verysecuresystems/SecuritySystemServer.kt
100% <100%> (ø)
2 <2> (?)

...rc/main/kotlin/verysecuresystems/SecuritySystem.kt
100% <100%> (ø)
2 <2> (?)

.../kotlin/verysecuresystems/diagnostic/Diagnostic.kt
100% <100%> (ø)
2 <2> (?)

src/main/kotlin/verysecuresystems/web/Web.kt
100% <100%> (ø)
2 <2> (?)

src/main/kotlin/verysecuresystems/api/ByeBye.kt
100% <100%> (ø)
2 <2> (?)

src/main/kotlin/verysecuresystems/api/Api.kt
100% <100%> (ø)
2 <2> (?)

...rc/main/kotlin/verysecuresystems/api/KnockKnock.kt
90% <90%> (ø)
2 <2> (?)

Continue to review full report at Codecov.

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@daviddenton please review the changes in this PR, eager to get feedback on the cleanup.

Thanks vm for the contribution. We're not going to merge it, but since you went to so much effort, I'd like to take a bit of time to explain why. Consider this the start of a conversation, happy to elaborate further... :)
The http4k-by-example app is very much written in the "House style" of the http4k team, which definitely does divert from the standard Kotlin idioms, but is one that we have settled on after a few years (and several hundred microservices) being written using the lib. This style is also the one we use on the actual http4k APIs, and one that we recommend to others to adopt to maximise codebase cleanliness and developer productivity.
One element of this style that people often find unusual is the usage of named object with invoke() methods or functions with CapitalNames(). Consider the following example:
class MyFilterClass(private val field: String) : Filter {
	...
}

vs
object MyFilterObject {
	operator fun invoke(field: String) : Filter = ...
}
vs

fun MyFilterFunction(field: String) : Filter = ...
}
All 3 versions create the same API, and hence we are able to switch at will betwen them without breaking client code. However, by using `MyFilterObject` or `MyFilterFunction`, we can avoid creating a lot of classes which may not actually have any identity or state - as far as the IDE is concerned there is only one type here `Filter` and thus extracting variables, fields or arguments will result in the extracted type being `Filter`, whereas with the first version, `MyFilterClass` will be used.

Choosing between `MyFilterObject` and `MyFilterFunction` is a style choice - I generally (and probably inconsistently) use the object version when there are helper functions or fields/constants which can also live inside the definition of `MyFilterObject`.

The application of that general approach lies a bit opposed to the style introduced in this PR. For instance - SecuritySystem IS an HttpHandler function which can be swapped out for any other HttpHandler, so the usage of `getHttpHandler()` masks that. Similarly, ByeBye IS a ContractRoute (which is also an HttpHandler usable when testing).

@daviddenton thanks for the detailed explanation. Most of what you said makes sense.
A small question though, I thought the object wrappers will help organize the function within the package structure. If we write functions without any such wrapper, how do we organize them in a big codebase with hundreds of other functions in the same package?

Floating functions are a namespace pollution concern - but since they are floating within a package, they effectively expose the same amount of pollution as using the object version. The only difference between the 2 is that using objects you can collect functions and vals into a neatly "moveable" package. For using functions, you need to be mindful to private/internal them within the files that they are used.

@daviddenton thanks for the detailed review and prompt responses, we can go ahead and close this PR now.


[BEAM-9434] performance improvements reading many Avro files in S3

The implemented solution consists in an extension of the FileSystem classes for S3, that allows filtering of the matched objects. The filter consists in a mod hash function of the filename.
This mechanism is exploited by a parallel partitioned read of the files in the bucket, realised in the AvroIO and FileIO classes by means of the new hint . withHintPartitionInto(int)
The net effect is that a controlled number of tasks is spawn to different executors, each having a different partition number; each executor reads the entire list of files in the bucket, but matches only those files whose modhash matches the partition number.
In this way, all the executors in the cluster read in parallel.

Thank you for your contribution! Follow this checklist to help us incorporate your contribution quickly and easily:

[ ] Choose reviewer(s) and mention them in a comment (R: @username).
[ ] Format the pull request title like [BEAM-XXX] Fixes bug in ApproximateQuantiles, where you replace BEAM-XXX with the appropriate JIRA issue, if applicable. This will automatically link the pull request to the issue.
[ ] Update CHANGES.md with noteworthy changes.
[ ] If this contribution is large, please file an Apache Individual Contributor License Agreement.

See the Contributor Guide for more tips on how to make review process smoother.
Post-Commit Tests Status (on master branch)

Lang
SDK
Apex
Dataflow
Flink
Gearpump
Samza
Spark

Go

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Java

Python

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XLang
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Pre-Commit Tests Status (on master branch)

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Java
Python
Go
Website

Non-portable

Portable
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See .test-infra/jenkins/README for trigger phrase, status and link of all Jenkins jobs.

@iemejia @andeb please review and let me have your comments. I have more evidence of the tests that I've been carried out, and I'm happy with the performance gains. However, I'm keen to understand if the approach is sound. I look forward to hearing from you

Awesome work, it looks good to me

R: @lukecwik do you mind having a look and giving me feedback on this PR? Thanks I look forward to hearing from you

Adding a filesystem API that all filesystems need to implement is going to raise some questions in the Apache Beam community. Asked some follow-ups on BEAM-9434 to see if the issue is localized to Spark.

Adding a filesystem API that all filesystems need to implement is going to raise some questions in the Apache Beam community. Asked some follow-ups on BEAM-9434 to see if the issue is localized to Spark.

@lukecwik Ok I see.
Technically speaking, it is not mandatory to implement in every filesystem, but effectively in order to properly support the hint in every filesystem it is.
I considered a few alternatives:

the current one, throwing an UnsupportedOperationException if a filesystem does not support it
a default implementation that does a wasteful filtering before returning the results (not scalable)
implementing it for all filesystem

The reality is, I haven't got a mean of testing the last option on anything else than S3, otherwise the last option is the best approach imho.
Let me know what are the opinions.
Also, looks like to me that the filesystems classes are internal to the framework, not supposed to be used directly by end users. In which case maybe another option is viable, which is renaming appropriately the new hint, and don't make it mandatory by means of the framework to consider the hint.
In other words, I'm saying that we can hint to use N partitions, but the runtime can just ignore the hint if that's not supported by the underlying filesystem.
I can modify the code in this way if that's viable.
Happy to hear back from you guys, and thanks for the feedback.

The expansion for withHintManyFiles uses a reshuffle between the match and the actual reading of the file. The reshuffle allows for the runner to balance the amount of work across as many nodes as it wants. The only thing being reshuffled is file metadata so after that reshuffle the file reading should be distributed to several nodes.
In your reference run, when you say that "the entire reading taking place in a single task/node", was it that the match all happened on a single node or was it that the "read" happened all on a single node?

The expansion for withHintManyFiles uses a reshuffle between the match and the actual reading of the file. The reshuffle allows for the runner to balance the amount of work across as many nodes as it wants. The only thing being reshuffled is file metadata so after that reshuffle the file reading should be distributed to several nodes.
In your reference run, when you say that "the entire reading taking place in a single task/node", was it that the match all happened on a single node or was it that the "read" happened all on a single node?

Both.
Reading the metadata wouldn't be a problem, it also happens on every node in the proposed PR.
But the actual reading also happens on one node with unacceptably high reading times.
What you say applies to the case of "bulky" files. For those, the shuffling stage chunks the files and shuffle reading of each chunk.
However, my solution particularly applies to the case where there is a high number of tiny files (I think I explained better in the Jira ticket).
In this latter case, the latency of reading each file from S3 dominates, but no chunking / shuffling happens with the standard Beam.

This is the fundamental difference between the base and the current PR. Notice, in the base case there's only 2 tasks (the entire job is a join of two independent readings) whereas when using 10 partitions there are 20 tasks for doing the same work.
This is reflected in the executors being used and in the time to complete (16 minutes with 2 tasks, 2.3 minutes with 20).
See below the comparison of execution data.

I understand what your saying and how your solution resolves the problem.
I'm trying to say that the problem shouldn't occur in the first place because AvroIO.read should expand to MatchAll that contains a Reshuffle followed by ReadMatches
Reshuffle should ensure that there is either a repartition between MatchAll and ReadMatches, is it missing? If it isn't missing, they why is the following stage only executing on a single machine?

Unfortunately the problem happens for me, that is why this work started. Let's see if we can understand the root cause for it.

Reshuffle should ensure that there is a repartition between MatchAll and ReadMatches, is it missing (it is difficult to tell from your screenshots)? If it isn't missing, they why is the following stage only executing on a single machine (since repartition shouldn't be restricting output to only a single machine)

It's clearly not missing as in the base case I'm using withHintMatchesManyFiles().
Still what happens is that the entire reading is on one machine (see second last screenshot "summary metrics for 2 completed tasks"). The impression I have is that when the physical plan is created, there is only one task detected that is bound to do the entire reading on one executor. Consider that, I am doing something really plain, just reading from two buckets, joining the records and writing them back to S3. Did you try this yourself to see if you can reproduce the issue?
I had a look at the code of Reshuffle.expand() and Reshuffle.ViaRandomKey, but I have some doubts on what is the expected behaviour in terms of machines / partitions.
How many different partitions shall Reshuffle create? Will there be 1 task per partition? and how are the tasks ultimately assigned to the executors?
Maybe you can help me understand the above / point me to the relevant documentation. That should hopefully help me troubleshoot this.

Any thoughts on the above @lukecwik @iemejia ? I did not hear back from you in a couple of days.

Sorry about the long delay but Reshuffle should produce as many partitions as the runner thinks is optimal. It is effectively a redistribute operation.
It looks like the spark translation is copying the number of partitions from the upstream transform for the reshuffle translation and in your case this is likely 1.
Translation: https://github.com/apache/beam/blob/f5a4a5afcd9425c0ddb9ec9c70067a5d5c0bc769/runners/spark/src/main/java/org/apache/beam/runners/spark/translation/TransformTranslator.java#L681
Copying partitions:
https://github.com/apache/beam/blob/f5a4a5afcd9425c0ddb9ec9c70067a5d5c0bc769/runners/spark/src/main/java/org/apache/beam/runners/spark/translation/GroupCombineFunctions.java#L191
@iemejia Shouldn't we be using a much larger value for partitions, e.g. the number of nodes?

Sorry about the long delay

My time to apology @lukecwik. I was busy on something else as well as trying to settling in this new life of working from home due to the virus

It looks like the spark translation is copying the number of partitions from the upstream transform for the reshuffle translation and in your case this is likely 1

Gotcha. And yes, I can confirm that the value for the partitions is 1, not only in my case. Fact of the matter, the number of partitions is calculated (in a bizarre way) only for the root RDD (Create), containing only the pattern for the s3 files -- a string like s3://my-bucket-name/*.avro. From that moment onwards it is copied all the way through. So with one pattern is always one.
This confirms my initial impression when I wrote:

The impression I have is that when the physical plan is created, there is only one task detected that is bound to do the entire reading on one executor

I have changed the PR, reverting the original one and now - after your analysis - I am setting the number of the partitions in the reshuffle transform translator.
I am using the value of the default parallelism for Spark, already available in the Spark configuration options for Beam.
So essentially with this PR the Spark configuration:
--conf spark.default.parallelism=10 is the replacement for the hint I wrote initially.
I have tested this PR with the same configuration as the initial one, and the performance is identical. I can now see all the executors and nodes processing a partition of the read, as one expects. I also did a back-to-back run with the vanilla Beam and I can confirm the problem is still there.
I deem this implementation is superior to the first one. Let me have your opinions on it. Also paging in @iemejia
I have seen the previous build failing, I think the failing tests were unrelated to the changes; keen to see a new build with these code changes.

Thanks for the follow-up.

Thanks @ecapoccia nice work!

Thank you guys @iemejia @lukecwik it was good for me to learn a bit about the internals.


Prototype of the cli utility for AOT/Trim applications

Description
Hi, I have prepared a prototype for AOT support. If this concept suits everyone, then I will continue to develop in this direction.
Related issue(s)
Issue: #187

Since this is a prototype, and it will not last in its current form, I did not pay attention to the purity of git. I'm sorry, I won't do this in the future.

@yurvon-screamo how about I take a stab at #136 this weekend as that is a pre-requiste for a cli tool. If you could review #199 that would be helpful and ideally also #200


eas publish : Error: Unable to resolve module fs

Build/Submit details page URL
No response
Summary
I'm trying to run eas publish but I get the error
it works fine when I eas build
Managed or bare?
bare prebuild project
Environment

  expo-env-info 1.0.5 environment info:
    System:
      OS: macOS 13.5
      Shell: 5.9 - /bin/zsh
    Binaries:
      Node: 20.5.0
      Yarn: 1.22.19
      npm: 9.8.0
      Watchman: 2<IP_ADDRESS>
    Managers:
      CocoaPods: 1.11.3
    SDKs:
      iOS SDK:
        Platforms: DriverKit 22.4, iOS 16.4, macOS 13.3, tvOS 16.4, watchOS 9.4
    IDEs:
      Android Studio: 2021.3 AI-213.7172.25.2113.9123335
      Xcode: 14.3.1/14E300c - /usr/bin/xcodebuild
    npmPackages:
      expo: ^49.0.0 => 49.0.6
      react: 18.2.0 => 18.2.0
      react-dom: 18.2.0 => 18.2.0
      react-native: 0.72.3 => 0.72.3
      react-native-web: ~0.19.6 => 0.19.7
    npmGlobalPackages:
      eas-cli: 3.18.3
    Expo Workflow: bare

Error output
[expo-cli] Error: Unable to resolve module fs from<EMAIL_ADDRESS>fs could not be found within the project or in these directories:
[expo-cli]   node_modules/@nozbe/watermelondb/node_modules
[expo-cli]   node_modules
[expo-cli]
[expo-cli]    5 | exports.default = void 0;
[expo-cli]    6 | var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
[expo-cli] >  7 | var fs = require("fs");
...

Reproducible demo or steps to reproduce from a blank project
init expo project
install and configure watermelon db using expo plugin!
guide : https://www.themorrow.digital/blog/how-to-use-watermelondb-with-react-native-expo

Same Issue here.
have you found any solution?

same issue


README.md should contain infos on how to get going once installed

The README.md should contain some infos on how to get going once the install has succeeded.

probably a hint on how to run sshuttle to be able to access the installation
pointer into the testbed docs (-> https://docs.osism.tech/testbed/usage.html#webinterfaces) or where appropiate

yes. thanks for moving.


Azure Devops unit test example doesn't fail build when tests fail

When following the steps listed in the Executing Unit Tests section (using SPFx 1.7), the Azure Pipelines task will succeed regardless of whether there are any failing tests. I was expecting the build to fail if the tests fail.
I think the --ship argument needs to be added to the Gulp task as the gulp test command only seems exit with a non-zero exit code on production builds.

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 6db891d3-c14d-9bae-80fc-cedaf2eb5982
Version Independent ID: aae8a107-ee2a-7b9c-9022-9946b7f65909
Content: Implement Continuous Integration and Continuous deployment using Azure DevOps
Content Source: docs/spfx/toolchain/implement-ci-cd-with-azure-devops.md
Product: sharepoint
GitHub Login: @spdevdocs
Microsoft Alias: spdevdocs

@gregwilton sorry for the late reply. Since then we've updated the documentation to leverage Jest instead of Karma which was removed. Did you get a chance to try again with the new testing configuration?


GPT4 Turbo

Hi,
How should I update your source code to use GPT 4 Turbo?
Also, I would really appreciate it if you could give commands for compilation and web server launch.

Models have been updated here.
https://github.com/fitchmultz/chat-with-gpt


ModelView._url_for_* does not take into account the app's root_path

Checklist

[X] The bug is reproducible against the latest release or master.
[X] There are no similar issues or pull requests to fix it yet.

Describe the bug
In ModelView, there are several methods called from the within the templates, eg. _url_for_delete(), _url_for_details().
These methods don't work/take into account the possibility that the admin panel might be behind a proxy, or otherwise subpathed for any reason.
Any href generated with the {{ url_for(...) }}-style works correctly, since under the hood in Starlette, they are calling request.url_for(), which takes into account the root_path.
However, _url_for_delete() uses app.url_path_for(), which does not.
Steps to reproduce the bug
Create an app like:
from fastapi import FastAPI
from sqladmin import Admin, ModelView

app = FastAPI(root_path="/app")  # relevant change to example code
admin = Admin(app, engine)

class UserAdmin(ModelView, model=User):
    column_list = [User.id, User.name]

admin.add_view(UserAdmin)

Expected behavior
All URLs on the admin panel should be prefixed with the root_path, ie "/app" in the example above.
Actual behavior
All URLs generated in the {{ url_for(...) }} form work, but certain URLs (most obviously the View/Edit/Delete buttons - there may be more but I don't know of them) are broken, or link to the wrong address.
Debugging material
These are the links I refer to above. They are broken links when root_path is set on the Starlette/FastAPI app.

Environment
OS: Ubuntu 22.04
Python: 3.10
sqladmin: 0.6.1
Additional context
As a workaround, one could conceivably override the _url_for_*() methods to prefix the root_path themselves.
I would argue the best way would be to pass the context to _url_for_*(), so that something like:
request = context["request"]
return request.url_for(
            "admin:details",
            identity=slugify_class_name(obj.__class__.__name__),
            pk=pk,
        )

could be used (see https://github.com/encode/starlette/blob/58b82b07b913645fa968a4e23a0707226f56fe97/starlette/templating.py#L70)

Hi,
Yes the approach you mentioned make sense to me. If you are interested please do a PR otherwise I'll do it later.


Integrate review feedback into Exchange baseline

🗣 Description

This update includes the following changes to the M365 Exchange Security Configuration Baseline:

Changes to improve overall consistency of format and language throughout
Grammar and spelling fixes
Language and verbiage updates for increased reader clarity

This update does NOT include any materially significant changes to the number of or content in policy items in the baseline itself that would require a change in settings to align with the baseline recommendations.
💭 Motivation and context

The updates included further refine and improve the overall readability and clarity of the baseline document.  The result should be a baseline that is easier to interpret and use as a reference for M365 tenant administrators.
Closes #534
🧪 Testing

Compare the separately provided Word version with track changes of the Exchange baseline document with the changes in the markdown in this branch.
Accepted/modified suggested changes as appropriate and mirrored in markdown, rejected and additional changes commented in Word and sync'd to markdown as needed.
Manual review of markdown and ensure that the automated markdown test on the PR passes.

✅ Pre-approval checklist

[x] This PR has an informative and human-readable title.
[x] Changes are limited to a single goal - eschew scope creep!
[x] All future TODOs are captured in issues, which are referenced
in code comments.
[x] All relevant type-of-change labels have been added.
[x] All relevant repo and/or project documentation has been updated
to reflect the changes in this PR.
[x] All new and existing tests pass.

✅ Pre-merge checklist

✅ Post-merge checklist

@ahuynhMITRE Please follow all hyperlinks to ensure that they work appropriately including between sections of the document.


isolating a continuation doesn't work

See https://github.com/disruptek/cps/tree/threads

I have a cheat for this, I think.

Doing it differently.


Multiple/different health bar

Hi!
I really appreciate your work, i use this system a lot!
I was wondering if you could add a way to create multiple health bars like the one you already have on yoru sheet, maybe with changing names and changing the number of squares.
Even multiple ones on the sheet with different names and squares each!
I would love to see that!
I am planning on running a campaign that uses both health and "plot armor".

What I have in mind is a segmented health bar with dark/light shades of four colors - dark as they get checked:

scratch - green
hurt - orange
very hurt - red
incapacitated - purple
near death - gray/black
With Near Death checked, the whole bar would pulse.
Whether this will turn out to work in practice is uncertain - I'll have to try it. ;)

I think core foundry allows for another toolbar.
We haven't done anything yet for house-rule custom stats.
We will eventually be doing something to allow for modules extending what's there.
It looks like I'll finally get to using this soon.
One other thing to try in the next round -
In my own sandbox, I've been playing with a "dP" die - --/-/0/+/++. You roll two of them and they give you a dF -4 to +4 spread but the outcomes are much more spread out from the 0/+1/-1 that dominate 4dF. With more hits in the wings and crits approximately as frequent as 1 and 20 on a D20, I think it will make for more exciting roleplaying.

So far so good - this afternoon I have pictures of what I have in mind.

Ready to rock:
A little tattered:
Almost down:

These are SVG approximations of what I want to do.

Is this a useful representation of the character's status?
Are the colors reasonable?
Critique welcomed.

It also now looks like I'll have to put the checkboxes to update status in the Token HUD where all the other user interaction takes place. I figure I can offer them in two rows, with scratches and hurt above, just below the resource bar, and very hurt, incap, and near death just below that, as there are fewer boxes of each type and they'll be clicked less often (one can only pray ;) ). Hopefully I can keep it compact without inconveniencing the finger-pokers.

Now that this issue is getting into the project, I'm changing the issue name from the requested name to the name of the proposed solution.

I think those colors are good to represent health status.
I don't understand the difference between the 3 options, other than colors, how will the third indicate that i am more wounded than the first?
It's nice to see than you are back at work for this project!

So wounds in Fudge are done with checkboxes on scratches, hurt, very hurt, incapacitated, and near death. The amount of damage you suffer determines which set of boxes gets checked. However, if you have checked all the boxes for one set, your next check overflows into the next. In this way you can suffer "death by papercuts".
So as more of each section of the bar "goes dark", you are running out of boxes at that level and are therefore in greater peril.
As for how many checkboxes you start with, that's a measure of how robust your character is. In any game I've played, nobody has ever had more than 4 slots for scratches, 3 for hurt, 2 for very hurt, and 1 incapacitated. Typically, it's 3/2/2/1.

I've set out a roadmap for this project. It's rough - I did it by seasons, and we shall see whether I can keep to it. I'm looking at 2.1.0 near Samhain, 2.2.0 near Imbolc, and 2.3.0 near Ostara.

This one involves PIXI stuff, so it's a little more involved than some of the others. Add to that the need to supply a mechanism for pluggable wounds systems, since some Fudge-based systems use very different ones, and the complexity ramps up. I think I need to get the pluggable mechanisms in place before we revisit this one, so it will move down the priority stack.


vscode-extensions.usernamehw.errorlens: 3.2.4 -> 3.4.0

Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[x] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
[x] Tested execution of all binary files (usually in ./result/bin/)
21.11 Release Notes (or backporting 21.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 138767 run on x86_64-linux 1

1 package built:

vscode-extensions.usernamehw.errorlens


[TE] rootcause - rich metric selector

Improve visualization of metrics selector on root cause page. Displays metric names similar to metrics table, with dataset subscript and dimension values. Also enables quick-selection of metrics with pre-existing dimensions.

Very nice css


transaction problem

i defined a rule and the actions will call multi java service method. if one method execute failed,however the transaction  not rollbacked

You can throw the corresponding exception in the listener, and the outer layer can handle the transaction rollback based on that exception.For example, here


fix(webapck.config): Fix and set the open page as the "/#/mind" page

Now when running npm start,  it opens the page /#/ which is an empty page and it is confusing to many developers.
This PR is to set the open page to /#/mind which shows the mind graph.
related: https://github.com/gaoli/GGEditor/issues/58

Close this as we will show a nav page for both #mind and #flow.


Use willReturn() methods in tests

Use willReturn(), willReturnSelf() and willReturnCallback() methods in tests

Coverage decreased (-0.1%) to 99.871% when pulling b5550891932411d2f951a7dddc6aade9afd138d7 on peter-gribanov:use_willReturn into ccae99e82025eb371b4375f4c62639151dc87a65 on gpslab:master.

Coverage decreased (-0.1%) to 99.871% when pulling b5550891932411d2f951a7dddc6aade9afd138d7 on peter-gribanov:use_willReturn into ccae99e82025eb371b4375f4c62639151dc87a65 on gpslab:master.

Coverage decreased (-0.1%) to 99.871% when pulling b5550891932411d2f951a7dddc6aade9afd138d7 on peter-gribanov:use_willReturn into ccae99e82025eb371b4375f4c62639151dc87a65 on gpslab:master.

Coverage decreased (-0.1%) to 99.871% when pulling b5550891932411d2f951a7dddc6aade9afd138d7 on peter-gribanov:use_willReturn into ccae99e82025eb371b4375f4c62639151dc87a65 on gpslab:master.

Coverage decreased (-0.1%) to 99.871% when pulling b5550891932411d2f951a7dddc6aade9afd138d7 on peter-gribanov:use_willReturn into ccae99e82025eb371b4375f4c62639151dc87a65 on gpslab:master.

Coverage decreased (-0.1%) to 99.871% when pulling b5550891932411d2f951a7dddc6aade9afd138d7 on peter-gribanov:use_willReturn into ccae99e82025eb371b4375f4c62639151dc87a65 on gpslab:master.


picker组件增加ts校验

Coverage increased (+0.1%) to 65.166% when pulling 9cbbe88c88a5904db2166d06137b8600d056cf87 on edison-hm:dev-ts into f41f93c4f9ba1292e6d0d809ab8ac5b8d31e2e1d on ZhonganTechENG:dev-ts.


Upgrade spirv-reflect

This renames spirv-reflect's String.
The goal of this is avoiding a very annoying side effect of having two String types: on the MSVC debugger (others may be affected), Godot Strings may be interpreted as spirv-reflect Strings, which will show wrong members with wrong values, hindering the ability to inspect their values and making debugging very hard.
At first I tried to hide the visibility of the struct with static, but MSVC was still finding and using it.

Duplicate of https://github.com/godotengine/godot/pull/50025, but this has been solved upstream so the proper fix is to update our version:
https://github.com/KhronosGroup/SPIRV-Reflect/issues/122

Repurposed to upgrade spriv-reflect.

Thanks!


Added Order view controller by Daniel Ozone

Fix issue with the editing mode on the order, when you click the edit button it doesn't show the red dot next to the item.

Modify button on the end of the order page an change for "Checkout" button this should lead to the checkout page.
Add checkout page, where you add number of people in the table and according to that show a total amount at the end of the page. Maybe 25 per people would be ok.


Create a web service that allows storing and receiving images from a file system

File store implementation is available here:

https://github.com/nosqlgeek/aimm-filestore

Can be hosted, or executed locally for development purposes.

Aktuelle Implementation basiert rein auf lokalen Filesystem Zugriff


Failing Tests

Hi,  I forked this repo to add support for CJSX / coffee-react.   I haven't made any changes yet, but tests are failing.   I wonder if maybe I don't have something installed that I need?
tail of results from npm build && mocha:
77 passing (2s)
7 failing

Istanbul tests should find if branch with no else:
first statement

expected - actual

{
"end": {

"column": 29

"column": 30
"line": 2
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:345:66)

Istanbul tests should find switch/case branches:
first statement

expected - actual

{
"end": {

"column": 22

"column": 23
"line": 6
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:468:66)

Istanbul tests should find functions:
first statement

expected - actual

{
"end": {

"column": 22

"column": 23
"line": 2
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:589:66)

Istanbul tests should find multi-line functions:
first statement

expected - actual

{
"end": {

"column": 22

"column": 23
"line": 6
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:683:66)

Istanbul tests should find functions in a class:
class statement

expected - actual

{
"end": {

"column": 10

"column": 11
"line": 4
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:786:66)

Istanbul tests should find name of anonymous class:
class fn

expected - actual
 "column": 4
 "line": 1

}
}

"name": "_Class"

"name": "(anonymousClass)"
}

at Context. (test/istanbul/test.coffee:864:59)

Coverage tests should handle nested recursion correctly:
AssertionError: expected 5 to equal 10

expected - actual

-5
+10
at Context. (test/tests.coffee:107:27)

bwilkerson@IT-SEA14730-MBP:~/projects/zulily/coffee-coverage$ npm -v
4.1.2
bwilkerson@IT-SEA14730-MBP:~/projects/zulily/coffee-coverage$ node -v
v7.5.0
bwilkerson@IT-SEA14730-MBP:~/projects/zulily/coffee-coverage$ mocha -v
error: unknown option `-v'
bwilkerson@IT-SEA14730-MBP:~/projects/zulily/coffee-coverage$ mocha --version
3.2.0

These were definitely passing last I ran them, but that was a while ago -
I'm guessing some package has upgraded to a newer version and is causing
chaos.  I'll look into it on Tuesday (Monday is a holiday here).
On Sat, Feb 18, 2017 at 12:47 PM, Bee<EMAIL_ADDRESS>wrote:

Hi, I forked this repo to add support for CJSX / coffee-react. I haven't
made any changes yet, but tests are failing. I wonder if maybe I don't have
something installed that I need?
tail of results from npm build && mocha:
77 passing (2s)
7 failing

Istanbul tests should find if branch with no else:
first statement

expected - actual

{
"end": {

"column": 29
"column": 30
"line": 2
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:345:66)
2.
Istanbul tests should find switch/case branches:
first statement

expected - actual

{
"end": {

"column": 22
"column": 23
"line": 6
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:468:66)
3.
Istanbul tests should find functions:
first statement

expected - actual

{
"end": {

"column": 22
"column": 23
"line": 2
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:589:66)
4.
Istanbul tests should find multi-line functions:
first statement

expected - actual

{
"end": {

"column": 22
"column": 23
"line": 6
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:683:66)
5.
Istanbul tests should find functions in a class:
class statement

expected - actual

{
"end": {

"column": 10
"column": 11
"line": 4
}
"start": {
"column": 0

at Context. (test/istanbul/test.coffee:786:66)
6.
Istanbul tests should find name of anonymous class:
class fn
  expected - actual

   "column": 4
   "line": 1

  }
  }
  - "name": "_Class"

"name": "(anonymousClass)"
}

at Context. (test/istanbul/test.coffee:864:59)
7.
Coverage tests should handle nested recursion correctly:
AssertionError: expected 5 to equal 10

expected - actual

-5
+10
at Context. (test/tests.coffee:107:27)
bwilkerson@IT-SEA14730-MBP:/projects/zulily/coffee-coverage$ npm -v
4.1.2
bwilkerson@IT-SEA14730-MBP:/projects/zulily/coffee-coverage$ node -v
v7.5.0
bwilkerson@IT-SEA14730-MBP:~/projects/zulily/coffee-coverage$ mocha -v
error: unknown option `-v'
bwilkerson@IT-SEA14730-MBP:~/projects/zulily/coffee-coverage$ mocha
--version
3.2.0
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/benbria/coffee-coverage/issues/84, or mute the thread
https://github.com/notifications/unsubscribe-auth/ABsF-wUoKDHLSTQXQLzmxSB5vyKoRpMQks5rdy6egaJpZM4MFMXV
.

Any status update here?  I'm still seeing failing tests... most with just a column off by one.


OpenSSL hash functions are deprecated in FIPS mode.

OpenSSL is switching to EVP API for MD5/SHA256 digests.
The old SHA256_Init(), SHA256_Update() and etc. are deprecated and not even allowed when FIPS mode is enabled.
Using these old APIs will result in assertion failure.
A patch is submitted, please take a look and merge: #582

merged


Update README.md

请确认以下事项

[x] 提交的项目均是自己的原创工作。如果您正在帮助其他人添加项目，请确认已经取得项目所有者的许可。
[x] 项目链接可访问。如果这是一个 GitHub 项目，它有 README(.md) 文件，并且不含受版权保护的材料。
[x] 项目相关课程的作业提交已截止。

So what's wrong if the greeting program printing "#Error: Resource not accessible by integration"?

Sorry for disruption! It seems that GitHub's official workflow is not working. I'll remove that.

Required checks passed. Maybe something wrong with the greeting scripts? @skyzh

Required test passed. It seems there are something wrong with the greeting script.

removed in #40


set condition flags after "IN" with "ORA A"

Otherwise READ and WRITE always return success with the SD FDC status code in A because of the preceeding "XRA A".

Strike the word "success".


teuthology/beanstalk: use pystalkd instead of beanstalkc

For some python3.X version the beanstalkc is not support, and the
pystalkd is compatible for python 3.X.
Signed-off-by: Xiubo Li<EMAIL_ADDRESS>

I am running the teuthology-suite under python3.5 and hit the errors:
2020-04-22 09:12:48,633.633 DEBUG:teuthology.packaging:Querying https://shaman.ceph.com/api/search?status=ready&project=ceph&flavor=default&distros=centos%2F8%2Fx86_64&sha1=4163a4bee565b28e9d84559bb9c33e5364da48fc
Traceback (most recent call last):
  File "/home/xiubli/teuthology/venv/bin/teuthology-schedule", line 5, in <module>
    from scripts.schedule import main
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/scripts/schedule.py", line 4, in <module>
    import teuthology.schedule
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/teuthology/schedule.py", line 4, in <module>
    import teuthology.beanstalk
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/teuthology/beanstalk.py", line 1, in <module>
    import beanstalkc
ImportError: No module named 'beanstalkc'
Traceback (most recent call last):
  File "/home/xiubli/teuthology/venv/bin/teuthology-suite", line 8, in <module>
    sys.exit(main())
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/scripts/suite.py", line 165, in main
    return teuthology.suite.main(args)
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/teuthology/suite/__init__.py", line 144, in main
    run.prepare_and_schedule()
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/teuthology/suite/run.py", line 357, in prepare_and_schedule
    num_jobs = self.schedule_suite()
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/teuthology/suite/run.py", line 586, in schedule_suite
    self.write_rerun_memo()
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/teuthology/suite/run.py", line 322, in write_rerun_memo
    log_prefix="Memo: ")
  File "/home/xiubli/teuthology/venv/lib/python3.5/site-packages/teuthology/suite/util.py", line 449, in teuthology_schedule
    subprocess.check_call(args=args)
  File "/usr/lib/python3.5/subprocess.py", line 581, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/xiubli/teuthology/venv/bin/teuthology-schedule', '--name', 'xiubli-2020-04-22_09:12:46-fs:basic_functional-wip-lxb-volume-client-py3-2020-04-22-1-distro-basic-smithi', '--num', '1', '--worker', 'smithi', '--priority', '120', '-v', '--first-in-suite', '--seed', '5145']' returned non-zero exit status 1

Shouldn't that be added to the requirements file(s) then?

Shouldn't that be added to the requirements file(s) then?

Yeah, right, will update it.

well we do not use beanstalkc, we use beanstalkc3, not following what this patch is about

@lxbsz https://pypi.org/project/beanstalkc3/ it supports any of python 3

@lxbsz https://pypi.org/project/beanstalkc3/ it supports any of python 3

Okay, seems there has something wrong with the virtualenv setup locally. will check it.
Thanks

according to your log:
/home/xiubli/teuthology/venv/bin/teuthology-schedule

there is venv, are you sure you've set your virtualenv correctly?
when you use ./bootstrap it is creating virtualenv directory, thus I think you just set it manually, and missed some step or dependencies.

according to your log:
/home/xiubli/teuthology/venv/bin/teuthology-schedule

there is venv, are you sure you've set your virtualenv correctly?
when you use ./bootstrap it is creating virtualenv directory, thus I think you just set it manually, and missed some step or dependencies.

There is no any error when setting the evn and I am using the steps from https://docs.ceph.com/docs/master/dev/developer_guide/running-tests-locally/.

There is no any error when setting the env and I am using the steps from https://docs.ceph.com/docs/master/dev/developer_guide/running-tests-locally/.

this link does not work for me, seems like service is down

@lxbsz well, seems like this doc is outdated and there is no py3 related information at all, so I supposed you've tried it and made a mistake, according to the logs:
Running your first test
^^^^^^^^^^^^^^^^^^^^^^^^^^
The Python tests in Ceph repository can be executed on your local machine
using `vstart_runner.py`_. To do that, you'd need `teuthology`_ installed::

    $ git clone https://github.com/ceph/teuthology
    $ cd teuthology/
    $ virtualenv -p python2.7 ./venv
    $ source venv/bin/activate
    $ pip install --upgrade pip
    $ pip install -r requirements.txt
    $ python setup.py develop
    $ deactivate

Which is already incorrect.

@lxbsz well, seems like this doc is outdated and there is no py3 related information at all, so I supposed you've tried it and made a mistake, according to the logs:
Running your first test
^^^^^^^^^^^^^^^^^^^^^^^^^^
The Python tests in Ceph repository can be executed on your local machine
using `vstart_runner.py`_. To do that, you'd need `teuthology`_ installed::

    $ git clone https://github.com/ceph/teuthology
    $ cd teuthology/
    $ virtualenv -p python2.7 ./venv
    $ source venv/bin/activate
    $ pip install --upgrade pip
    $ pip install -r requirements.txt
    $ python setup.py develop
    $ deactivate

Which is already incorrect.

The test case are only support the py3 now, the following is the steps:
$ virtualenv --python=python3 venv
$ source venv/bin/activate
$ pip install 'setuptools >= 12'
$ pip install git+https://github.com/ceph/teuthology#egg=teuthology[test]
$ deactivate

The test cases will only support the py3 now, the following are the steps:
$ virtualenv --python=python3 venv
$ source venv/bin/activate
$ pip install 'setuptools >= 12'
$ pip install git+https://github.com/ceph/teuthology#egg=teuthology[test]
$ deactivate

Not sure I understand, which test cases do you mean. And where from you've found this instruction, but this FOR SURE not the correct way of setting up virtual environment for teuthology, like you've tried to use it, i.e. teuthology-suite. The teuthology[test] is not supposed to install all the required dependencies.
Now, when we figured that out, we can close this PR as invalid.

when we figured that out, we can close this PR as invalid.

Yeah, sure.

@lxbsz thanks


Propagate Java install probing failure on configuration attempt

in order to better diagnose CI failures

Feedback build https://builds.gradle.org/viewQueued.html?itemId=13094412


Handle var() globally

Closes #417, we handle this the same way as cascading values.
If we detect the use of var(), it will be unsafe and the value will be rendered as string.

I see your point, I think we can put them exactly the same place as we put  on them Parser grammar.
I also have some thoughts on how we place  on the grammar, will create an abt that.


Data changes can't be saved using Value Panel

Description
When editing values in the Value panel in DBeaver, changes are not saved. This issue affects text fields and JSON fields. Previously, changes made in the Value panel could be saved directly, but now they require editing in the cell itself for changes to be applied. Additionally, after modifying a value in the Value panel, the Save icon remains unavailable, indicating that DBeaver doesn't recognize the change.

DBeaver Version
24.2.4
Operating System
Windows 11 23H2
Database and driver

Database: PostgreSQL 15.8
Driver: postgres-jdbc

Steps to reproduce

Open DBeaver and connect to the relevant database.
Navigate to the table with the fields (e.g., text or JSON) that need to be edited.
Open the Data Editor for this table.
Click on a field, open the Value panel, and make a change (e.g., modify text content or JSON).
Notice that the Save icon is not enabled, even though a modification was made in the Value panel.
Attempt to save the change (if applicable, commit the transaction if auto-commit is disabled).

Additional context
No response

@escnmnegrete Thanks for your report.

I reproduced the issue with json but not with text. Could you make a screen recording with text?


Various fix

Various fix:

update README
remove build.sh cuz it makes docker build starting from the beginning each time I call docker build
add

/usr/local/bin/docker-gen -only-exposed /app/nginx.tmpl /etc/nginx/conf.d/default.conf
nginx -s reload

when $simp_le_return -eq 0 in letsencrypt_service.
I can't test it since ERROR:simp_le: ACME server returned an error: rateLimited :: There were too many requests of a given type :: Error creating new cert :: Too many certificates already issued for: example.com.
But I think it should fix it. If you see a better fix @dmp1ce, tell me.

I think @JrCs may have had everything in build.sh to cut down on the image size. I'm not sure about that though.
I tend to agree that having all the steps in the Dockerfile is nicer for developing.
Everything else looks good. Thank you for adding the docker-gen regeneration. I'll probably merge later today.

Hum I don't think that build.sh will reduce final image size cuz at the end the same files are in the image. But for sure, users building with `build.sh``will have less intermediates images and then more size will be taken on the hard drive.
I don't think it's an issue cuz what is important is the final image size since most of the users don't build the image but will pull it directly from docker hub.
Cool if you can merge but I would prefer you to test it if you can before (as I said I can't for now due to limitation from letsencrypt servers).

Testing now. Do you want your name in the Dockerfile MAINTAINER? I'm going to add mine and remove jwilder.

Sure :-)

Maybe you can also remove the github link showing that it's a fork and add a message to the README that it's a fork from jwilder/nginx-proxy explaining the reason why you created it.

All my tests passed.

I deleted all my certificates and on the first run the certificates were downloaded and URL changed from http to https.
I changed my valid_min time from 30 days to 100 days which causes simp_le to renew everytime it checks which correctly replaced the old certification.
I had multiple domains on one VIRTUAL_HOST www. and non www and multiple VIRTUAL_HOST containers. That also passed.

Nice work!
I'll update the maintainers and add a brief explination in the README.
What is your email you want to use @hadim ?

You can use<EMAIL_ADDRESS>

Don't remove the build.sh.
It's the piece to reduce the image size.
If you don't use a script to build your image size will grow by 200Mo (git, python, gcc, and all the dependencies).
When you add something, add it after the build.sh in the dockerfile (so the build.sh will not be reexecuted every time) and when all is correct move the command from the dockerfile to the build.sh script

I don't understand because python will still be needed (and here) to execute simp_le ?

About the issue your fix it's not correct.
To fix the issue we must recreate the nginx configuration with docker-gen if at least one certs have been create/updated.
The fix is in my todo list.

How do you check the image size ? Because docker images returns only the virtual size and it's different depending on the other image on your system.

@hadim yes for python, but every time you use a RUN command it will create a new layer.
And so your final image wiil have layers with git, compiler (gcc), all tools to compile whith python (python-dev, python-pip), etc..

Sure and that is great when you use docker build but as I said most of the users will do a docker pull and so only download the final layer.

So the size won't change.

With docker image and virtualsize. Virtual size is the sum of all the layer size.
Mine is only 224.1 MB, look at yours

223.7 MB. As I said the size will vary according to your system but if you use docker pull the size will be the same for everyone.

I don't understand why you say the fix it's not correct ? I am updating the nginx config each time a new certificates is created. What is wrong with that ? What alternative do you propose ?

If you really want to reduce the number of layer, you can merge RUN commands on the Dockerfile (using &&). But I don't think using a script like build.sh is necessary. It add unecessary noise in my opinion.

You don't need to create a new nginx config for each certificate that is created.
Only need to create a new nginx config if at least one certificate is create/update at the end of the letsencrypt_service.
About the image, the goal is to reduce the size of the image not the number of layers. So the goal is to have a smaller image size (the sum of all the layers to download).
To reduce the size/number of layers we can use RUN commands with && but it's harder to read and it's "difficult" to add conditionals in it. With a script it easier to write and read. The goal is not to use a SINGLE script to create the image, but one script that install a "functionality' (in our case: install simp_le program and it's dependances)

I'm fine either way with the build.sh step. A smaller 200MB smaller size probably is worth the change if that is the difference when the layers are added up.
I don't think @harim's solution to regenerating nginx configurations is wrong, it just isn't as efficient as it could be. It isn't being run in parrallel so if each certificate is updated then it will regenerate the configuration and restart nginx each time.

Maybe something like this for the regeneration? I didn't test the code.
diff --git a/letsencrypt_service b/letsencrypt_service
index 762be82..8ab1960 100755
--- a/letsencrypt_service
+++ b/letsencrypt_service
@@ -10,6 +10,7 @@ update_certs() {
     # Load relevant container settings
     source "$DIR"/letsencrypt_service_data

+    regenerate_nginx=false
     for cid in "${LETSENCRYPT_CONTAINERS[@]}"; do
         # Derive host and email variable names
         host_varname="LETSENCRYPT_${cid}_HOST"
@@ -38,11 +39,16 @@ update_certs() {
                 ln -sf ./$domain/key.pem       /etc/nginx/certs/$domain".key"

                 # Update certificates configuration in nginx
-                /usr/local/bin/docker-gen -only-exposed /app/nginx.tmpl /etc/nginx/conf.d/default.conf
-                nginx -s reload
+                regenerate_nginx=true
             fi
         done
     done
+
+    if [[ $regenerate_nginx ]]; then
+        /usr/local/bin/docker-gen -only-exposed /app/nginx.tmpl /etc/nginx/conf.d/default.conf
+        nginx -s reload
+    fi
+
     unset LETSENCRYPT_CONTAINERS
 }

@dmp1ce seems ok. But use notify instead of call nginx -s reload every time because if the certificates didn't change we don't need to reload nginx

I agree that @dmp1ce solution is cleaner and more elegant but mine wasn't wrong.
About the size, I think that the use of RUN, && and \ is more readable than the build.sh solution. Now if you prefer the build.sh way both, go for it !

@JrCs If the certificates change but the configuration does not, do we still need to nginx -s reload?


Frontend_Web_Development_HTML_CSS_JS :  Git and bash

Description
Description
Documentation regarding Git and Bash
Domain
Frontend Dev HTML/CSS/JS
Type of Contribution
Documentation
Code of Conduct

[X] I follow Contributing Guidelines & Code of conduct of this project.

/assign Documentation

@moulikagrawal can you assign me this issue

/assign Batch-5 Documentation

/assign documentation


Added 'The Crypt' to the Lists.cs

The Crypt
Website: https://thecrypt.game/
Twitter: https://twitter.com/TheCryptGame
Discord: https://discord.com/invite/aMwetFaz6F

@ponderingdemocritus I'm ready to add The Crypt to the homepage (under Quests) once this is approved.


showRaw() not working when rows argument is vector containing row names

When I use showRaw() with a rows argument consisting of a vector containing row names, I get the following error:

Error in dimnames(x) <- dn :
    length of 'dimnames' [1] not equal to array extent

Running traceback() results in:

2: rownames<- (*tmp*, value = data_summary$rownames[rows])

It appears to stem from this line:
https://github.com/jromanowska/HaplinMethyl/blob/7fc4afdc0c45f38321896fb55323bf1d54dc9372/R/showRaw.R#L98C50-L98C54
There are no issues when rows is integers, or when columns is integers or a vector with column names.
Perhaps rownames(show_matrix) <- data_summary$rownames[rows] should be replaced by an if-else statement conditional on whether all(is.character(rows)) is TRUE or FALSE. If TRUE, use rownames(show_matrix) <- rows, and if FALSE, then use rownames(show_matrix) <- data_summary$rownames[rows].

It looks like the problem might stem from how Haplin's internal f.get.gen.data.cols() works, which is used on line 86. It returns an ff_matrix that has column names, but no row names.
https://github.com/cran/Haplin/blob/8bb309fc06002300850c4cf0a2237867e39eae69/R/f.get.gen.data.cols.R
It makes sense for Haplin:::f.get.gen.data.cols() to do this, considering that the ff reference manual states that

It is recommended not to assign row.names to a large ffdf object.

and I assume this may apply to ff objects as well.
@jromanowska I'm guessing that it is simpler and faster to make changes to functions in HaplinMethyl rather than make changes to Haplin, so perhaps we should either

tweak showRaw so that it can manage to select rows when the user supplies a vector with row names (if possible - I can't think of a specific solution at present), or
change the documentation/description of showRaw to state that you have to use row numbers when extracting particular rows and not row names.

I have now done some tweaks locally so that I can use showRaw in one of preprocessing stages of the pipeline that I'm developing.
I customised Haplin:::f.get.gen.data.cols() so that it is capable of returning an ff_matrix with row names when desirable instead of just column names. I added an argument called include.rownames.
In showRaw, I commented out line 98,

rownames(show_matrix) <- data_summary$rownames[rows] ,

so that the function does not break when rows is a vector with row names/CpG IDs.
Let me know if you would like this fix implemented in Haplin and HaplinMethyl. Alternatively (if it is all right in terms of copyright), we can fix this bug without requiring changes to be made to the Haplin package by adding my customised version of Haplin:::f.get.gen.data.cols() as an internal function in HaplinMethyl.

We need to wait for the new Haplin release to be able to fix that... :-/


Cannot use any 12.7 release after preview 7.

Is there an existing issue for this?

[X] I have searched the existing issues

Describe the bug
I can't seem to use any release after 12.7.0-preview.7.  I end up getting the error Could not load file or assembly 'HotChocolate.Types, Version=<IP_ADDRESS>, Culture=neutral, PublicKeyToken=null'. The system cannot find the file specified.
Steps to reproduce
Install any release of 12.7 after preview 7 via nuget.
Relevant log output
No response
Additional Context?
No response
Product
Hot Chocolate
Version
12.7.0-preview.15

We are doing at the moment fundamental work on StrawberryShake. Closing this issue for now.


Split publishing

All changed packages have been documented.

You can try these changes at https://cadlplayground.z22.web.core.windows.net/prs/3103/
Check the website changes at https://tspwebsitepr.z22.web.core.windows.net/prs/3103/


feature(dotnet) Added basic workerservice to .net templates

Added iworker a worker service that builds on the basic worker service from microsoft.
Added Azure Configuration and Intility logging to program.cs.

LGTM


sql: implement ALTER TABLE LOCALITY !(REGIONAL BY ROW) -> REGIONAL BY ROW

PR: https://github.com/cockroachdb/cockroach/pull/59824
From release notes:

Implemented the ability to ALTER TABLE SET LOCALITY to REGIONAL BY ROW without specifying AS for GLOBAL and REGIONAL BY TABLE tables. [#59824][#59824] {% comment %}doc{% endcomment %}

@rmloveland
I don't think we need to document this any more than you already have done in https://www.cockroachlabs.com/docs/v21.1/set-locality.html ?


How to use with a beans.xml

Works great, but the docs could be a little more explicit. It took me awhile to workout how to use  a beans.xml for which you need this:
@Rule
public WeldInitiator weld = WeldInitiator.from(createWeld().enableDiscovery()
		.inject(this).build();

And to disable  archive isolation you need this:
@Rule
public WeldInitiator weld = WeldInitiator.from(createWeld().enableDiscovery()
		.property(Weld.ARCHIVE_ISOLATION_SYSTEM_PROPERTY, "false"))
		.inject(this).build();

For most use cases weld-unit is a huge simplification over using Arquillian and all that is required. Thanks.

@sbrewin  First of all, thanks for the report. Why do you actually need the archive isolation disabled? To simulate arquillian-weld-embedded behavior? Well, one of the goals of weld-junit was to skip unnecessary scanning of all test classes so that one can concentrate on the classes under test. And also to avoid possible unwanted effects.
So your use case is to add all classes from src/main/java and src/test/java and treat them as if they were in the same bean archive (found beans.xml merged)? We can possibly add one more static method to WeldInitiator (similar to WeldInitiator.createWeld()) which would return a Weld instance with discovery enabled and isolation disabled. Name suggestions?

@mkouba Thanks for your reply. A flat archive is required to test legacy apps that rely on it.
As the required functionality is already present, adding my examples to the Test class injection section of README.md may be adequate.
To more explicitly support this, either WeldInitiator.createWeld(boolean archiveIsolation) or WeldInitiator.createFlatWeld() could be added, both of which should also enable discovery.

Hm, the thing is that if we enable discovery then all beans/descriptors/etc. from the classpath will be discovered for each test (unlike in arquillian-weld-embedded where shrinkwrap is used to specify the deployment). Is this what you expect?

Yes, this meets my expectation, but may not suit all. So, maybe leave auto discovery disabled and to enable it use
@Rule
public WeldInitiator weld = WeldInitiator.from(createFlatWeld().enableDiscovery()
			.inject(this).build();

What do you think?

FYI I've created https://issues.jboss.org/browse/WELD-2426. I think this could be the best solution for this issue. WDYT?

Like it :)


[Bug]: Manage Users -> Delete modal -> Remove button seems to be red in color

Is there an existing issue for this?

[X] I have searched the existing issues

Description
When I click on share and invoke the Manage Users -> Delete modal -> Remove button seems to be red in color as against the expected Orange.
Steps To Reproduce

Login to appsmith and go to your workspace
Click on the Share button and invoke the Manage Users modal.
Select a user and click Delete
This Delete modal has a Remove button

The color of the button is Red in color as against the expected orange.

Public Sample App
No response
Version
Production

Fixed in ADS 2.0


Include http annotations for grpc-gateway users

https://github.com/googleapis/googleapis/blob/master/google/api/http.proto
https://github.com/gengo/grpc-gateway
The end result should look something like:
  rpc Echo(StringMessage) returns (StringMessage) {
    option (google.api.http) = {
      post: "/v1/example/echo"
      body: "*"
    };
  }

The annotations are now included if the -options flag is included with the command.
https://github.com/NYTimes/openapi2proto/commit/e6d71993bc2aedd635af54401ccefa2001fedaaa adds the new flag, logic and text fixtures for this case.


docs: improve README and file structure

Includes minor formatting changes
Rewrite the customization section to accommodate users who have installed this project as a Hugo module
Move images and demo file into a docs directory

Thanks for the PR! 🙏


Disable upload page buttons after initiated upload

Also temporarily closing this one until Nigel can get back to it to reduce the list of open PRs that need to be checked.


Creating editor feature profiles doesn't work

Godot version:
v4.0.dev.custom_build.8b06d4275
OS/device including version:
Windows 10
Issue description:
Creating editor feature profiles doesn't work. It just puts this in the console whenever tried:
ERROR: Cannot create file 'feature_profiles/newprofile.profile'.
   at: (editor\editor_feature_profile.cpp:200)
ERROR: Cannot open directory 'feature_profiles'.
   at: (editor\editor_feature_profile.cpp:351)

https://user-images.githubusercontent.com/12120644/120512827-ae807980-c399-11eb-94bf-fe036bca180b.mp4
Steps to reproduce:

Create new project
Open Manage Editor Features...
Press Create Profile

Minimal reproduction project:
new project

How did you start Godot? There's an issue where an incorrect CWD can cause Godot to try to write files to an invalid directly.

How did you start Godot? There's an issue on Windows where an incorrect CWD (such as C:\Windows\System32\) can cause Godot to try to write files to an invalid directly.
Also, does this occur if you move the Godot executable to the C: drive and run it there?

I downloaded the windows-editor zip from github actions so I didn't have to compile

@Calinou While I've noticed the same issue while debugging, it still happens if you run the executable directly.

I also experienced the same issue on macOS.

I can confirm this on Linux too:
❯ godot-init /tmp/b
Godot Engine v4.0.dev.custom_build.ff648e250 - https://godotengine.org
Vulkan API 1.2.162
Using Vulkan Device #0: NVIDIA - NVIDIA GeForce GTX 1080
- Vulkan multiview supported:
  max views: 32
  max instances: 134217727
- Vulkan subgroup:
  size: 32
  stages: STAGE_VERTEX, STAGE_TESSELLATION_CONTROL, STAGE_TESSELLATION_EVALUATION, STAGE_GEOMETRY, STAGE_FRAGMENT, STAGE_COMPUTE, STAGE_RAYGEN_KHR, STAGE_ANY_HIT_KHR, STAGE_CLOSEST_HIT_KHR, STAGE_MISS_KHR, STAGE_INTERSECTION_KHR, STAGE_CALLABLE_KHR
  supported ops: FEATURE_BASIC, FEATURE_VOTE, FEATURE_ARITHMETIC, FEATURE_BALLOT, FEATURE_SHUFFLE, FEATURE_SHUFFLE_RELATIVE, FEATURE_CLUSTERED, FEATURE_QUAD, FEATURE_PARTITIONED_NV
  quad operations in all stages

ERROR: Error loading default feature profile: dddsds
   at: _notification (editor/editor_feature_profile.cpp:303)
ERROR: Cannot open directory 'feature_profiles'.
   at: _update_profile_list (editor/editor_feature_profile.cpp:336)

This was accidentally broken by https://github.com/godotengine/godot/pull/49050. There used to be get_settings_dir exposed and used across the editor to retrieve the root of the settings/configuration directory. It is used by feature profiles, as well as script templates for example. In #49050 during refactoring an internal variable config_dir was exposed via get_settings_dir, and settings_dir while kept was never set.
I'll talk with @reduz which one to keep and make a PR fixing this issue.


Longer epitope sequences

Hi Frank,
First of all congrats and thanks to share this great tool!
I've managed to run it on a small subset of our own patients. We usually test the immunogenicity of neoantigens as longer epitopes (in general 25-mers). Is it possible to get a longer peptide sequence than the outputted predicted minimal epitopes? Like 25- or even 40-mer around the junctions. Maybe that's already an option but I couldn't find it.
Thanks again!
Pierre

Hi @p-levy,
Glad you are able to run the tool, correct me if I am wrong, you are hoping to get longer sequence flanking the splicing junction (25mer or 40mer) compared to what is currently reported 9mer or 10mer.
This is not coded in the current program, as when I started this project, we were particularly interested in MHC-I presented peptides which typically ranges from 8-11mer, and 9mer and 10mer covers the majority. But I think I might have the codes (Another project I am working on) that might be able to help you:
Given each SNAF reported Junction chromosome coordinates (chrx:xxxxx-xxxxx(strand))
Step 1: Download hg38 fasta and build a dictionary as below
from Bio.SeqIO.FastaIO import SimpleFastaParser
dict_fa = {}  # {chrom:seq}
with open(path_to_hg38.fa,'r') as in_handle:
    for title,seq in SimpleFastaParser(in_handle):
        dict_fa[title] = seq

Step 2: Given SNAF coordinate, retrieve the flanking sequence as long as you want
from Bio.Seq import Seq
MAX_PEP_LEN=11
MIN_PEP_LEN=8
overhang = 50
# phase definition refer to https://www.biostars.org/p/63864/
item = 'chrx:xxxxx-xxxxx(+)'
chrom,coord = item.split(':')
coord,strand = coord.split('(')
strand = strand.rstrip(')')
start,end = coord.split('-')
start,end = int(start),int(end)
if strand == '+':
    first_section = dict_fa[chrom][start-overhang:start]
    second_section = dict_fa[chrom][end-1:end-1+overhang]
elif strand == '-':
    old_first_section = dict_fa[chrom][start-overhang:start]
    old_second_section = dict_fa[chrom][end-1:end-1+overhang]
    # reverse complement process
    first_section = Seq(old_second_section).reverse_complement()
    second_section = Seq(old_first_section).reverse_complement()
# consider phase = 0
defacto_first = first_section[-(3*(MAX_PEP_LEN-1)):]
defacto_second = second_section[:(3*(MAX_PEP_LEN-1))]
defacto_junction = defacto_first + defacto_second
defacto_peptide = str(Seq(defacto_junction).translate(to_stop=False))
# consider phase = 1
defacto_first = first_section[-(3*(MAX_PEP_LEN-1)+2):]
defacto_second = second_section[:(3*(MAX_PEP_LEN-1)+1)]
defacto_junction = defacto_first + defacto_second
defacto_peptide = str(Seq(defacto_junction).translate(to_stop=False))
# consider phase = 2
defacto_first = first_section[-(3*(MAX_PEP_LEN-1)+1):]
defacto_second = second_section[:(3*(MAX_PEP_LEN-1)+2)]
defacto_junction = defacto_first + defacto_second
defacto_peptide = str(Seq(defacto_junction).translate(to_stop=False))

if '*' not in defecto_peptide:
    print(defecto_peptide)

Step 3: run NetMHCpan4.1
def run_netMHCpan(software_path,peptides,hlas,length,cmd_num=1,tmp_dir=None,tmp_name=None):
    # set the default
    if tmp_dir is None:
        if not os.path.exists(os.path.join(os.path.dirname(os.path.abspath(__file__)),'scratch')):
            os.mkdir(os.path.join(os.path.dirname(os.path.abspath(__file__)),'scratch'))
        tmp_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),'scratch')
    if tmp_name is None:
        tmp_name = 'input_{}.pep'.format(os.getpid())
    # reformat/create to the strings that we need
    peptides_path = os.path.join(tmp_dir,tmp_name)
    with open(peptides_path,'w') as f:
        for pep in peptides:
            f.write('{}\n'.format(pep))
    # netMHCpan has a hard limit for 1024 characters for -a, so to be safe, 90 HLA as max for one goal, each input format 11 character 'HLA-B57:01,'
    if len(hlas) <= 90:
        hla_strings = ','.join(hlas)
        if cmd_num == 1:
            reconstruct = ' || '.join(['$3 == ' + '"{}"'.format(pep) for pep in peptides])
            cmd = '{} -p {} -a {} -BA -l {} | awk \'BEGIN {{OFS = "\\t"}} {{if ({}) {{print $3, length($3),$2,$13,$16,$18}}}}\''.format(software_path,peptides_path,hla_strings,length,reconstruct)
            '''
            ../external/netMHCpan-4.1/netMHCpan -p ./test.pep -a HLA-A01:01,HLA-A02:01 -BA -l 9 | awk 'BEGIN {OFS = "\t"} {if ($3 == "AAAWYLWEV" || $3 == "AAGLQDCTM" || $3 == "AARNIVRRA") {print $3, length($3),$2,$13, $15}}'
            '''
        try:
            df = pd.read_csv(StringIO(subprocess.run(cmd,shell=True,capture_output=True).stdout.decode('utf-8')),sep='\t',header=None)
            df.columns = ['peptide','mer','hla','score','binding_nM','identity']
        except:   # no stdout, just no candidates
            df = pd.DataFrame(columns=['peptide','mer','hla','score','identity'])

def run_netMHCpan_wrapper(peptide,hlas):
    # hlas is a list, each hla allele follow that format[HLA-A02:01]
    netMHCpan_path = '/path/to/netMHCpan-4.1/netMHCpan'
    df = run_netMHCpan(software_path=netMHCpan_path,
                       peptides=[peptide],
                       hlas=hlas,
                       length=len(peptide),
                       cmd_num=1,
                       tmp_dir=None,
                       tmp_name=None)
    return df

Step 4: Immunogenicity Prediction
Currently DeepImmuno only supports 9 and 10mer, but there are other tools I am aware of that have more flexible length requirement such as DeepHLApan.

Hi Frank,
Thanks for your prompt and detailed answer! I played a bit with the code you shared and that's already helpful. However, I realized that what I would really like is to focus on the junctions where at least the first section is within an annotated CDS. Then I'd like to get the AA-seq of custom length (e.g. 25-mer) around the junction but only using the phase of the annotated CDS. Is there an "easy" way to do that? That would be great!
All the best,
Pierre

Hi @p-levy,
I see, for my current project, I actually decided to take all three phases due to now increasing report on non-canonical ORFs (cryptic ORFs) and the well-characterized mechanisms illustrating why it is common in cancer.
Ref1: https://www.nature.com/articles/s41587-021-01021-3
Ref2: https://www.nature.com/articles/s41586-023-06500-y
But I understand your need, I actually implemented this in the SNAF, but it is kind of obsolete and I haven't really rigorous tested this function, but I can share.
In your download database folder, you will find two required input:
[1] df_start_codon.txt
[2] Homo_sapiens.GRCh38.91.gtf
You followed this code block (https://github.com/frankligy/SNAF/blob/main/snaf/snaf.py#L62-L96) to get two variable dict_start_codon and phase_inferer_gtf_dict.
I have a function to get_support_phase here (https://github.com/frankligy/SNAF/blob/main/snaf/snaf.py#L98-L189), but the phase definition here is a bit different (probably only makes sense to me) and don't want to confuse you, so I just want to explain the logic and you can modify the code as you need.

Hoping this could help,
Frank

Thanks! I'll test this asap.

Hi Frank,
It took me a while but I think that thanks to your help I'm almost getting what I want. I still have two questions:

Is there somewhere in the outputs a list of all cancer-specific junction coordinates, irrespective of if some of the resulting peptides are HLA binders. So far I've been using the coord values reported in the T_antigen_candidates.txt files but I feel like junctions with non binders are not included there as the maximum binding affinity seems to be 2.

You're strategy to get the defacto_peptide sequence given above works pretty well in general. However I was wondering what would happen if the size of the peptide I'd want to retrieve would be greater than the size of some whole exons. This strategy would then be translating from intronic sequences, right? Do you think of an alternative to work with cDNA/CDS coordinates?

Thanks again!
Pierre


Assisted alignment case C deficiencies

Case C of assisted alignment has the following problems:

Removal of backlash deadband does not seem to be working properly. In some cases it looks like the slew is too far and in other cases it looks like not far enough.
If object rate of motion is slow, the algorithm may drop the object off at a location where it will take several minutes before the object crosses center of frame. Need to find a way to drop the object at a location where it will only take 30 seconds or less for it to cross frame center.
The last step to align the object's motion vector with center of frame by slewing in one axis takes too long

Made some refinements that hopefully address the last two deficiencies called out in the description but the code is untested. I don't see any bugs in the code that would lead to the first defect; more likely the backlash deadband estimates were bad or the backlash behavior of the mount is not consistent.

This issue is obsolete due to a change in alignment strategy--see #43.


$off not working Vue.js 2

Hey There,
Thanks for the plugin, I'm having an issue unsubscribing from events tho.
In one component route I have in the mounted function:
this.$events.$on('integrations-xpm-connected', (data) => {
       console.log('test');
      });

Then in the beforeDestroy function:
this.$events.$off('integrations-xpm-connected');

However, if I navigate to a new route, then come back, the event gets fired twice when called.
if I call this.$events.$off() with no particular event specified, it unsubscribes.
Any ideas?

sorry about the delay, for some reason I never got a notification for this issue.. that or I overlooked it terribly.
I'm not sure off the top of my head, but I'll try and get around to writing some tests for this soon. In the mean time, if you figure it out then I'd really appreciate a PR. :)

@sn0rcha @cklmercer I'm having this issue too, but I don't think it has to do with $off, but rather the lifetime of Vue components. If you have two of the same component alive at the same time, and you're listening to an event on both of them, your event handler will effectively be called twice.

Tried to resolve this issue using https://www.npmjs.com/package/vue-event-handler
Appreciate any success.

Thanks for the idea, worked well  for me.


Modrinth Version vs. Maven Version mismatch

The Modrinth version numbers and Maven version numbers do not match, which can cause confusion.

this seems like the same version to me?

It's only 1.1.1 in the version number and version title.

wasnt aware anyone cared about that, changed
also made sure FLK as embedded was added to all versions

The original issue, as reported, is still not fixed...

yall have too many fields /lh

done, gonna link this to #56 rq as a note


Add tags to community CSVs, add new script to generate tags, and update existing scripts to reflect tag support

This PR:

Adds a new "tags" column to all point location CSVs. These tags are used in conjunction with this Data-API PR https://github.com/ua-snap/data-api/pull/497 to allow us to decide which communities should show up as selectable places in which webapps. Our initial reason for doing this was to add additional Alaska military locations to Arctic-EDS without them also appearing in Northern Climate Reports or ARDAC Explorer. This will also make it easy to add circumpolar locations to ARDAC Explorer without them also appearing in Northern Climate Reports or Arctic-EDS (to be tackled soon as a separate PR).
Adds a new tag_point_locations.py script that reads in existing point location CSV files from vector_data/point and determines how they should be tagged. It writes the freshly-tagged CSVs out to a .gitignore'ed subdirectory, utilities/tagged_csvs.
Adds tag support to the add_point_location.py script.
Moves the IEM polygon check out of create_updated_ncr_shapefiles.py and into the new tag_point_locations.py script. Now, only communities within Alaska, British Columbia, and Yukon that fall within the IEM polygon are tagged with the ncr tag, and only communities tagged with ncr will be selectable from NCR. So, this solves the same problem in a different but more flexible way. I've also renamed create_updated_ncr_shapefiles.py to create_shapefiles.py since the shapefiles created by this script are used for all of our webapps.

These changes affect only point locations currently, but in the future we may want to consider tagging polygons also. Something to consider another time / in another PR.
To test, run the tag_point_locations.py script and confirm that the CSV outputs in the utilities/tagged_csvs subdirectory match the ones in vector_data/point, and spot check the rows of each CSV file to make sure the chosen tags make sense. Also, try running the modified create_shapefiles.py script and spot check the shapefile outputs for sanity.

I ran the new tag_point_locations.py script and have verified the tags are present both in the (untracked) tagged_csv directories and in the tracked points directory. I also ran the create_shapefiles.py script and loaded all the outputs in the all_places directory in QGIS and clicked around to spot check various polygons and points - everything looks good and I see the new tags for the communities as well! I also verified that the add_point_location.py tool still works as expected by trying the test in the example usage in the script like this: python add_point_location.py 'Vanta' 'AK' 'US' 99.9999 -99.9999 --optional_name='Bubba' --tags 'ncr,eds'
I'm making two minor commits (one typo, and a note about where to launch the scripts from) and then merging.


GitHub actions update

Use the new output file.
https://docs.github.com/en/actions/using-jobs/defining-outputs-for-jobs

Codecov Report
Base: 86.70% // Head: 86.70% // No change to project coverage :thumbsup:

Coverage data is based on head (f6c6dd8) compared to base (d2ba584).
Patch has no changes to coverable lines.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #328   +/-   ##
=======================================
  Coverage   86.70%   86.70%
=======================================
  Files          18       18
  Lines        2143     2143
=======================================
  Hits         1858     1858
  Misses        285      285

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

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thanks!
superseded by #330


Issue launching docker image

Disclaimer: I'm somewhat of a docker n00b, but your help is greatly appreciated!!
Launching the docker image and mounted the package and config files and getting errors/crashing.

Here's the error log I'm getting:

Try /etlegacy/etmain as your mount path☺


Number assignment in .tfvars file reported as incorrect type

vaiables.tf:
variable test {}

variables.tfvars:
test = 42

42 highlighted with warning inspection as Incorrect type, expected 'string'

cc @maxmanuylov


click.discord.com - false positive

The subdomain click.discord.com has reappeared on the list, and it is a false positive. It is responsible for the ability to verify login from a new IP address on the Discord service.
Found 3 lists exactly matching 'click.discord.com':

  - [https://raw.githubusercontent.com/StevenBlack/hosts/master/hosts](https://<IP_ADDRESS>/admin/groups-lists.lp?listid=1)
    block list
    added:         2023-10-26 22:36:56
    last modified: 2023-10-26 22:36:56
    last updated:  2023-11-14 08:23:01 (154,803 domains)
    enabled, used in 1 group
    comment: "Migrated from /etc/pihole/adlists.list"
    matching entries:
    - click.discord.com

  - [https://blocklist.sefinek.net/generated/<IP_ADDRESS>/forks/StevenBlack.fakenews-gambling-porn.txt](https://<IP_ADDRESS>/admin/groups-lists.lp?listid=73)
    block list
    added:         2023-10-28 05:41:48
    last modified: 2023-10-28 05:41:48
    last updated:  2023-11-14 08:24:13 (217,945 domains)
    enabled, used in 1 group
    no comment
    matching entries:
    - click.discord.com

  - [https://blocklist.sefinek.net/generated/<IP_ADDRESS>/forks/StevenBlack.hosts.txt](https://<IP_ADDRESS>/admin/groups-lists.lp?listid=79)
    block list
    added:         2023-10-28 05:41:48
    last modified: 2023-10-28 05:41:48
    last updated:  2023-11-14 08:24:18 (154,803 domains)
    enabled, used in 1 group
    no comment
    matching entries:
    - click.discord.com

@StevenBlack Thanks for doing all the hard work for me. :)

@StevenBlack even when this gets updated, and I just sent an email to pgl about this, too, yoyo.org is still on paused as per 0f8ad83645bcecedf980bd682fb77d5c18410ce1.

Seriously, this subdomain is still on the blocklist? People, have mercy ;-;


Fixed Broken Links (Issue #618)

As suggested by @SauravMaheshkar, I have fixed the 3 links and redirected them to examples/old/ directory.

@bopardikarsoham Looks like there are two PRs for the same issue. Which one should we work off of?

Closing since this is a duplicate.


Taking advantage of new c#6 features

c#6 allow String interpolation wich is way more readable and nameof() so why not using it ?
for example mount and unmount were a little wrong ...

Hi @TrabacchinLuigi ,
Thank you for your contribution !
There is not reason to not use it :smiley:

this very rapid merge incourages me to do more ... :+1:


Pub 654 - Retrieve existing subscription criteria

JIRA link
https://tools.hmcts.net/jira/browse/PUB-654
Change description
added subscription management api call

Currently build fails as refactoring is not finished, pushed only changes for visibility


[fuzz result] thread 'main' panicked: slice index starts at 8 but ends at 5

use pulldown_cmark::Options;

fn main() {
    let string = "- [x]\t\t\n\\\n-";

    let mut opts = pulldown_cmark::Options::empty();

    opts.insert(Options::ENABLE_TASKLISTS);
    opts.insert(Options::ENABLE_HEADING_ATTRIBUTES);

    for _ in pulldown_cmark::Parser::new_ext(string, opts) {}
}

thread 'main' panicked at pulldown-cmark-0.11.0/src/firstpass.rs:1965:49:
slice index starts at 8 but ends at 5

https://github.com/pulldown-cmark/pulldown-cmark/blob/d7632acbe066b81a7f4b23c72fdb18c85f9cb1ea/pulldown-cmark/src/firstpass.rs#L1964-L1965
Btw, this is a label:fuzzer_finding, but cannot add this myself :)

Thanks for reporting!


link to app in operation detail

Hey Bnj,
This is my poc for displaying a link to another app in the operation details.
Do you think it's the good way to do it ?
Bye

Looks good at first glance! Please make sure to base your branch onto incoming, to prevent complex merge (ideally, I'd like to have fast-forward merges only, so rebasing FTW).


Deprecated method

This method to connect to Dynamics has been deprecated. The code still advises users to follow this approach. It should be highlighted that the code is deprecated.

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 6114d6c3-688b-765a-9a96-fb656fe748a4
Version Independent ID: 687f9106-e35a-5295-670d-0b4061dbda3e
Content: Sample: Authenticate users with Dynamics 365 Customer Engagement web services (Developer Guide for Dynamics 365 Customer Engagement (on-premises))
Content Source: ce/customerengagement/on-premises/developer/sample-authenticate-users-web-services.md
Service: crm-online
GitHub Login: @JimDaly
Microsoft Alias: jdaly

@phecke  This sample is using OrganizationServiceProxy, it should show using CrmServiceClient.
Can you fix it?


Remove ufo_sources profile from the list of imported checks into the Universal profile

This is somewhat related to #3715
Currently, the ufo_sources checks are imported into the Universal profile, essentially making them "universal" as well.
The UFO checks are not necessary for workflows that only care about running Font Bakery on font binaries.
I'd like to propose taking them out of the universal imports.

The scope of the universal profile is: "quality checks for universally accepted good practices."
Not everybody uses an UFO workflow, but for those who do, the things the checks validate are universally accepted.
If you are working exclusively with font binaries, those UFO checks will be automatically skipped because Font Bakery is smart enough to detect that. The same is also valid for other file types such as designspaces, that you mentioned at #3725
An alternative could be to define profiles by file type, but that was not the way the project was structured. Profiles are instead defined by vendor-specific needs versus universally agreed upon checks.

OK. Thanks for the explanation.