npm-script-test-by-topologies

Moves cluster_setup.sh scripts into package scripts
Adds directories (--dir) to allow for multiple topologies to exist at once
Adds init / start / stop scripts for individual topologies and all
Pre-loads MONGODB_URL env var to run test for a given topology

we discussed maintaining this all in one script


disabled horizontal resizing of textarea

removed horizontal textarea resizing as not to break responsiveness when adjusted.
Before

After

Thanks, looks good to me.

Thanks, looks good to me.


fix/184 active annotation confusion

Fix confusing global_edit_suggestion default
Description
Closes #184.
Also adds missing fields to ULabelSubtask type (state.edit_candidate)
PR Checklist

[X] Merged latest main
[X] Version number in package.json has been bumped since last release
[X] Version numbers match between package package.json and src/version.js
[X] Ran npm install and npm run build AFTER bumping the version number
[X] Updated documentation if necessary (currently just in api_spec.md)
[X] Added changes to changelog.md

Breaking API Changes
I don't think so

Applied review changes and added some clarifying comments in 3a6272d


add codecov to python tests

/azp run

Codecov Report

Merging #621 into master will decrease coverage by 83.24%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #621       +/-   ##
==========================================
- Coverage   84.28%   1.03%   -83.25%
==========================================
  Files         154     154
  Lines        7443    7443
  Branches      452     452
==========================================
- Hits         6273      77     -6196
- Misses       1170    7366     +6196

Impacted Files
Coverage Δ

...rosoft/ml/spark/cognitive/SearchIndexSchemas.scala
0% <0%> (-100%)
:arrow_down:

...spark/core/serialize/params/TransformerParam.scala
0% <0%> (-100%)
:arrow_down:

...icrosoft/ml/spark/lightgbm/LightGBMConstants.scala
0% <0%> (-100%)
:arrow_down:

...la/com/microsoft/ml/spark/opencv/OpenCVUtils.scala
0% <0%> (-100%)
:arrow_down:

...rosoft/ml/spark/core/schema/ImageSchemaUtils.scala
0% <0%> (-100%)
:arrow_down:

...cala/org/apache/spark/ml/NamespaceInjections.scala
0% <0%> (-100%)
:arrow_down:

...ft/ml/spark/cognitive/AnomalyDetectorSchemas.scala
0% <0%> (-100%)
:arrow_down:

...crosoft/ml/spark/core/schema/SchemaConstants.scala
0% <0%> (-100%)
:arrow_down:

...ala/com/microsoft/ml/spark/train/AutoTrainer.scala
0% <0%> (-100%)
:arrow_down:

.../spark/core/serialize/params/ParamSpaceParam.scala
0% <0%> (-100%)
:arrow_down:

... and 142 more

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Added dark mode support

I moved the colors to the assets and made them invert for dark mode so it looks more like what GitHub does when it's in dark mode.

Thanks @kyledold! Really like the idea of moving the colors to the Assets 👍
The only problem I see by inverting the colors is that it could be a bit confusing. In dark mode it actually looks like you made more contributions in the days that you made less, don't you think so?

Hey,
Hmmm...maybe I need to tweak the colors slightly for when its a level 4 color.
What I was trying to do was match what Github was doing in their dark vs light mode (like below).

Also this has recently stopped working for me, are you aware of any changes to that Github have made recently that would break this widget?

Yeah, maybe we can try with darker colors for less contributions and brighter (but not pale) for more contributions.

Also this has recently stopped working for me, are you aware of any changes to that Github have made recently that would break this widget?

Yes, they changed some stuff which made the HTML parsing fail, I've fixed that in 1.0.3 but it's not live yet, still pending approval.

Agreed, I'll try tweaking the colors after 1.0.3 is merged :)

@AnderGoig I've made some changes to the colors (for dark mode only) so hopefully it looks a bit clearer now which days there were more contributions.

Yeah, much better now in my opinion! Thanks for your contribution 🙂


fix: surface vunnel logs with provider log level if possible

Currently there won't be any logging surfaced from vunnel providers when grype-db isn't set to debug because all vunnel logs are being logged from go at the debug level.  Since the vunnel log level is configurable separately, this changes the default go log level output from vunnel to be Info and additionally attempts to parse the actual log level from the vunnel calls and log at the corresponding level from go.

there may be an edge case about multi-line log entries that need to carry the state from the previously processed line, but I didn't try it out with grype-db + vunnel explicitly to see if it could be done / what would happen (if it's an issue it can be a future enhancement).

Yeah, it does kinda happen with exception stacktraces in that the first line gets logged correctly as ERROR but then the trace just gets logged as info, but that is good enough for now I think.


Binary Release for 0.6.1

Hey there,
great to see the nice fix in #80 making it into 0.6.1 however I was hoping to update kubernetes/kops to use the new version, however that relies on downloading the release binary rather than source code ( see here: https://github.com/kubernetes/kops/blob/8df55b8571c1cd6dc5e6f7fba56175bf0945fb74/upup/pkg/fi/cloudup/apply_cluster.go#L1183 )
As such it would be great if you could publish the binary of the 0.6.1 release.
Thanks!

Thanks for the note - my oversight. Will get this fixed up

No worries, and thanks for all your work on this!

Closing this as there's binaries for 0.6.3 and that's good enough for us, thanks!


XMLGregorianCalendar years & seconds precision

Submitted by David Bau, entered initially by Joe Fialli.
Concerning javax.xml.datatypes.XMLGregorianCalendar:
To permit correct behavior on validation tests, it is important that, like
Duration, the calendar type be able to handle large years and more than
three digits of fractional seconds; it would also be optimal if the number
of significant digits of seconds were remembered, so that dates can be
nicely round-tripped to XML. I recommend that this information be able to
be held by the XmlGregorianCalendar implmentation and accessible by its own
API, but truncated when queried by the ordinary Calendar API.
Environment
Operating System: All
Platform: All
Affected Versions
[2.0 draft]

this seems to be already there


Add soil horizon property check to SoilLayer schema.

Won't do ... easier to have layers and horizons.


add: rule for checking includes map

Added checking of anchors by the includes map. The includes map must be located at the place where the check is launched

[x] get includes map path from config
[x] add test
[ ] to make a path to the includes map in the configuration from the foliant-md-linter (https://github.com/holamgadol/foliant-md-linter/pull/13)

bump version in  package.json, please


Spatial Navigation support

Spatial Navigation as described here: https://wicg.github.io/spatial-navigation/

+1

CSS Spatial Navigation Level 1 is now published on W3C
https://www.w3.org/TR/2019/WD-css-nav-1-20190423/

@mihaiav I'd have to presume that WD link won't recieve updates after 2019-04-23, so rather this: https://www.w3.org/TR/css-nav/ for latest publication.


Load data via swr or react-query

User story
Currently we have implemented our own data fetching hooks in https://github.com/vitessce/vitessce/blob/main/packages/vit-s/src/data-hooks.js#L76 but this is not a best practice.
Preferred solution
Investigate

https://github.com/vercel/swr
https://github.com/TanStack/query

It seems like react-query is much more full-featured, so i would go with that one. See experiment at https://github.com/vitessce/vitessce/blob/1563817956e4794de1956bb656509b8c566bc805/packages/vit-s/src/data-hooks.js#L204


Settings - Button Labels Fix

Fix issue causing button labels to overflow onto sibling buttons in the Settings module

Looks like this has sat here for a bit. Any word on the status of this merge?

Doesn't appear to be any activity on this project in almost a year. Someone may have to fork it and take over the project perhaps.


cannot reshape array of size 3 into shape (92,92,3)

Hi there! I'm having trouble to run this
bash shells/create_dataset.sh
The error is this:
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
patch size: 92 24 16
n_all_files: 0
patches:	 0
Traceback (most recent call last):
File "tests/test_dataset.py", line 36, in
o_val, dtype=np.uint8).reshape((92, 92, 3))
ValueError: cannot reshape array of size 0 into shape (92,92,3)
Traceback (most recent call last):
File "tests/test_dataset.py", line 36, in
o_val, dtype=np.uint8).reshape((92, 92, 3))
ValueError: cannot reshape array of size 0 into shape (92,92,3)
Traceback (most recent call last):
File "tests/test_dataset.py", line 36, in
o_val, dtype=np.uint8).reshape((92, 92, 3))
ValueError: cannot reshape array of size 0 into shape (92,92,3)
Traceback (most recent call last):
File "tests/test_dataset.py", line 36, in
o_val, dtype=np.uint8).reshape((92, 92, 3))
ValueError: cannot reshape array of size 0 into shape (92,92,3)
Traceback (most recent call last):
File "tests/test_transform.py", line 55, in
(args.ortho_original_side, args.ortho_original_side, 3))
ValueError: cannot reshape array of size 0 into shape (92,92,3)
Traceback (most recent call last):
File "tests/test_transform.py", line 55, in
(args.ortho_original_side, args.ortho_original_side, 3))
ValueError: cannot reshape array of size 0 into shape (92,92,3)
Traceback (most recent call last):
File "tests/test_transform.py", line 55, in
(args.ortho_original_side, args.ortho_original_side, 3))
ValueError: cannot reshape array of size 0 into shape (92,92,3)
Traceback (most recent call last):
File "tests/test_transform.py", line 55, in
(args.ortho_original_side, args.ortho_original_side, 3))
ValueError: cannot reshape array of size 0 into shape (92,92,3)
Any ideas?
Thank you very much for your time!

Where did you put the dataset?

In data, i didn't change anything on the script of the README file. but I had some trouble downloading the images. Do you think that can be the problem?
Thank you very much!

Hi, friend. I have tired out to compile the environment which can make the codes run, and I changed Ubuntu from 14.04 to 16.04, and OpenCV from 3.0.0 to 3.4.1,, but it failed many times, either OpenCV irregular installation or Boost could not found targets.
Could you please tell me your installation in detail? What versions are your cmake, anaconda, boost, and OpenCV. Thanks so much for your kindly help.

@flor88 hi ,my friend,Have you completed the whole process with the Readme now?I have a lot of problem to ask you,
Thanks so much for your kindly help.

Hi @Kkevin4! Yes, I followed the Readme file, but I made changes, the details are in my previous comment. :)


Are the extensions compatible with Aspire 9?

I don't know much on the breaking changes in Aspire 9.
I know it supports WaitFor natively, but how about the other extensions. I'm especially interested in the YARP extesion.

@davidfowl @DamianEdwards
I'm in the process of upgrading to Aspire 9. I wonder if you had on top of your head the answer to the compatibility of the YARP resource with the new version before I found it out the hard way. :D


[1.19.2] [Client Crash] NPE on Create Track logistic

Describe the Bug
Don't get the error again, don't know how to reproduce. Only one Crash report
Reproduction Steps
Only Playing on Server with Create Modpack
Expected Result
Don't Crash
Screenshots and Videos
No response
Crash Report or Log
https://pastebin.com/qiufudnk
Operating System
Windows 11
Mod Version
0.5.0i
Minecraft Version
1.19.2
Other Mods
No response
Additional Context
No response

Fixed in https://github.com/Creators-of-Create/Create/commit/7f60ae95f6e97d8fbae292ea34b1cc12223ba02d


FeatureProvider fails

FeatureProvider fails if two calls try calling require()  at the same time.

Workaround for the moment, needs a permanent solution (Feature names in main config?)

6d3515a803c8405d54244bd8e2476697b54a4701 solves the issue


Exceptions when allocating memory for native arrays from another thread in Unity

It looks like Unity UnsafeUtility's Malloc doesn't like to be used outside of the main thread. I'm using UniTask's UniTask.SwitchToThreadPool(); to repro it.
Version Used: 0.2.2
ArgumentException: Could not allocate native memory. If this allocation was made from a managed thread outside of a job, you must use Allocator.Persistent or Allocator.TempJob.
Cathei.LinqGen.Hidden.UnsafeUtils.ArrayAlloc[T] (System.Int32 size) (at Library/PackageCache/com.cathei.linqgen@81661744fc/Runtime/Unity/UnsafeUtils.cs:27)
Cathei.LinqGen.Hidden.DynamicArrayNative`1[T]..ctor (System.Int32 capacity) (at Library/PackageCache/com.cathei.linqgen@81661744fc/Runtime/Core/Collections/Native/DynamicArrayNative.cs:17)
Cathei.LinqGen.Hidden.PooledListNative`1[T]..ctor (System.Int32 capacity) (at Library/PackageCache/com.cathei.linqgen@81661744fc/Runtime/Core/Collections/Native/PooledListNative.cs:20)
Cathei.LinqGen.Hidden.ThenByKey_6`3+Enumerator[TSelector_6,TSelector_7,TSelector_8].InitState () (at LinqGen.Generator/Cathei.LinqGen.Generator.LinqGenSourceGenerator/LinqGen.1.cs:758)
Cathei.LinqGen.Hidden.ThenByKey_6`3+Enumerator[TSelector_6,TSelector_7,TSelector_8].MoveNext () (at LinqGen.Generator/Cathei.LinqGen.Generator.LinqGenSourceGenerator/LinqGen.1.cs:779)
TargetPreview.Scripts.Targets.Extensions.TargetCueExtensions.AsTargetCues (System.Collections.Generic.IEnumerable`1[T] cues) (at

Thanks for reporting this, this happened because LinqGen was using Allocator.Temp for temporary native allocation.
The issue is fixed in v0.2.3, and it will use Allocator.Persistent for codes that outside of job system.


Add "ignore sub-packages" option for offline repos

The option existed in the local setting for offline repos but was not working. Neither was it possible to set the option when creating a new offline repo. It's now working properly.
Closes https://github.com/abapGit/abapGit/issues/5924

PS: A bit of SE80 reorder.

after package reorg

Replaced by https://github.com/abapGit/abapGit/pull/5948


Remove irrelevant commands

Legacy commands like add edit delete should not be included in the program. For simplicity, just remove them from AddressBookParser

solved

Refer to PR #137 .


Review Ticket week 4

Quiz App
App Blog
Home Page
Performance task planning

I think that Luka deserves a 2.7 because he met all the requirements on his assignments for this week and I like how he personalized the quiz to what he likes: Soccer. One thing that he could have done and I suggest for him to do is to embed the quiz onto his blog, it would have made the blog more interactive and better


Scaling issue

There a issue on the scaling factor when importing to ssbh. Not sure why it happens but it only happens when its playing the animation. Going to the part of the scaling animation without being played shows that it scales correctly.  Here a drop of the video as Github limit is 10mb. https://drive.google.com/file/d/1LRY0CXtYbUEIjGoTVp4_pslizqrv3vuG/view?usp=share_link

What files and animation files are you working with? I'll need to be able to reproduce this on my end to see if it's a bug.

Its not a bug on ssbh. Seems to be the blender plugin is not exporting the right scale factor


attach msgid to all replayable events

JOIN/PART/KICK/QUIT should get msgids.

TAGMSG too (?)
We should start storing history events for TAGMSG. This is related to #395.

Yeah let's do the same for TAGMSG as well, for sure.

#442 has a struct that pairs the msgid with the message; let's put the server time in there too to simplify the bookkeeping.

Implemented in #477


Load an AWQ model via python API

Hi, I recently wanted to use litserve to deploy a service and use litgpt to load the model. However, due to video memory reasons, I wanted to use an AWQ model. However, I did not see the method of loading the awq model in the python API document. Do you have any methods?

If you want to quantize an original model to lower the VRAM consumption, you can use BitsandBytes quantization that does it on-the-fly: https://github.com/Lightning-AI/litgpt/blob/main/tutorials/quantize.md
But if you have weights in AWQ format and want to load them to LItGPT - it's not supported.
There was an attempt to support AutoGPTQ (that should also support AWQ format) in #924, but it was never merged.
(Making that PR up-to-date might could be a cool contribution 😉).

thanks for your reply :)


pair_id disambiguation

We are starting to look at paired sequencing data and I am starting to wonder how one determines uniqueness of a pair of sequences. This is related to #246 but I thought it worthy of a separate discussion so that we might be able to get a quick resolution on the issue.
From the spec it says the pair_id is a "Valid sequence_id that was determined by experimental or computational means to be associated with the current Rearrangement on the cellular level".
I see that sequence_id is supposed to be unique within a "file". I assume this means the uniqueness comes from the sequence_id assignment provided at the fasta file level when sequencing was done. Is that correct? So I believe it is expected that sequence_id is not unique within a repository???
If this is the case, I am wondering about our definition of pair_id. pair_id is a unique sequence_id to which the given sequence has been determined to be a paired chain. If as above, I assume that the sequence_id is not unique within the repository, then it is possible to have collisions on pair_id. What would be the disambiguation rule for a pair_id? It seems like one would require a sample_processing_id (which is where the fasta level sequence_id would be assigned) and a data_processing_id (as one might have a paired chain from a single SampleProcessing annotated with two different annotation tools).
So the query to find a paired sequence for a given sequence S is:
       "op":"and",
        "content": [
            { "op":"=","content": {"field":"sequence_id","value":S.pair_id}},
            { "op":"=","content": {"field":"data_processing_id","value":S.data_processing_id}},
            { "op":"=","content": {"field":"sample_processing_id","value":S.sample_processing_id}},
	]

This is somewhat complex, and hard to explain in documentation - I have inferred this from my understanding which may or may not be correct.
Given that the relationship between two sequences in a paired chain is similar in scope to single cell relationships, I wonder if we should have a similar definition for pair_id as we do for cell_id, which is defined as follows: "Identifier defining the cell of origin for the query sequence." Basically have a unique identifier for each pair in the paired chain?
I am not sure this solves the problem, in that we still have the uniqueness issue that needs to be sorted out.

Hmm, in rereading this, I think this is actually more precisely defining and is helping to disambiguate sequence_id rather than pair_id.

I must've missed something along the way... That definition of pair_id seems rather odd to me.
Having pair_id work exactly the same as clone_id and cell_id makes more sense to me (just a grouping variable). In most protocols, I would expect pair_id and cell_id to be identical.
Seems like it'd be a lot easier to find collisions too, because you'd just have to looks for pair_id values that maps to 3+ rows.

Hi Brian, I will take the chance here to add a point to the issue. I was also about to open a ticket concerning pair_id. I'm not sure if this is still valid but In #169 you defined it as:

pair_id: identifier for rearrangements that have a chain pairing, unique ID within the repertoire for each unique pair.
cell_id: identifier for rearrangements that come from a single cell, unique ID within the repertoire for each unique cell.

a "Valid sequence_id that was determined by experimental or computational means [...]" sounds also a bit strange to me, although I'm not yet an expert. Can it be that the definition from #169 was to be updated in the spec? (sorry if this was already discussed, I am still diving a bit adrift in the ocean of tickets)
About my question:
as Jason points, in the single cell context, one cell will normally have two sequences for one rearrangement, thus one cell will have a unique cell_id  and a unique pair_id  shared by two sequences within one cell. However, not so infrequently, we also see the presence of three sequences  (one heavy and one kappa and one lambda) and in some cases, even four meaning two or three different pair_id's for a unique cell_id.
given that each row in our data is a single cell, for creating a unique pair_id corresponding to its belonging cell and avoid repeating each row  "pair_id-x" number of times, we wonder if it would make sense to have an extra ?table? with the sequence in question, the cell_id and the pair_id that maps to the original row?

as Jason points, in the single cell context, one cell will normally have two sequences for one rearrangement, thus one cell will have a unique cell_id and a unique pair_id shared by two sequences within one cell. However, not so infrequently, we also see the presence of three sequences (one heavy and one kappa and one lambda) and in some cases, even four meaning two or three different pair_id's for a unique cell_id.

Ah, yeah, good point.   To cover that with the current pair_id definition you'd need to force a pair of "master" pair_id values for the entire set or do some sort of categorical clustering things to track down all members of a give cell.
I'm a bit fuzzy on why we needed pair_id in addition to cell_id. Something to do with semantics being wrong for PCR ligation protocols? I can't recall off the top of my head... I'll have to look back through the issues.

a "Valid sequence_id that was determined by experimental or computational means [...]" sounds also a bit strange to me, although I'm not yet an expert. Can it be that the definition from #169 was to be updated in the spec? (sorry if this was already discussed, I am still diving a bit adrift in the ocean of tickets)

Actually, that was my mistake. The current spec has "Valid sequence_id that was determined by experimental or computational means [...]" and I made up the other definition because I actually thought it was the same as for cell_id (as @javh suggested). Sorry for the confusion. The current definition is for the sequence_id, but I agree with @javh that it makes sense for that to be changed unless there is a reason not to...

I'm a bit fuzzy on why we needed pair_id in addition to cell_id. Something to do with semantics being wrong for pairing done by PCR ligation protocols? Not sure. I can't recall off the top of my head... I'll have to look back through the issues.

Would this make sense. For a single B cell with six receptor sequences, all would have the same cell_id. In this case, I assume the productive heavy and light are the paired chains, so they would have the same pair_id, but the other four unproductive would not have a pair_id???

In this case, I assume the productive heavy and light are the paired chains, so they would have the same pair_id, but the other four unproductive would not have a pair_id???

Yes, I think so. But then the heavy chain from a cell with an allelic inclusion should actually have two pair_ids: one for the H+K pairing and one for the H+L.
As a historical matter, I think pair_id was introduced for Adaptive's pairing protocol, which does not involve single cells. Still, I think the nuances we are talking about here are worth being able to distinguish anyway.

Would this make sense. For a single B cell with six receptor sequences, all would have the same cell_id. In this case, I assume the productive heavy and light are the paired chains, so they would have the same pair_id, but the other four unproductive would not have a pair_id???

This would make pair_id:null entirely redundant with productive:False. Which is not awful, but I think not a reason to have pair_id.

As a historical matter, I think pair_id was introduced for Adaptive's pairing protocol, which does not involve single cells. Still, I think the nuances we are talking about here are worth being able to distinguish anyway.

They are still inferred a cell association though, correct? If so, cell_id seems appropriate to me.

We have discussed this issue today, and came up with some points. I've tried to illustrate them with these two example tables with our sciReptor data. I think this does not solve the question about the uniquenes of the pair_id but it might help to bring some ideas.
in the single cell context:

apair_id  is not a pointer to one sequence_id but rather it groups different sequence_id's belonging to one cell creating end to end relationships to its originall cell_id (table 2 mapping to table 1).

as a very rare example we see in cell_id = 296, a relation between 2 H to 1 K and 1 L, [less rare are i.e. 115 and 119 with one productive H and two productive L (Kappa and/or Lambda)] all are productive and therefore we would assign pair_ids [5 to 8] grouping those sequnces.

pair_id is a representation of a receptor that has more meaningful biological information (#207), in our case it is the starting point to annotate reactivity.

cell_id
sequence_id
consensus_rank
locus
length
igblast_productive

115
1249
2
K
419
1

115
165
1
K
436
1

115
887
1
H
539
1

119
1460
1
K
420
1

119
846
2
L
442
1

119
679
1
L
443
0

119
1258
1
H
548
1

296
1228
1
K
430
1

296
970
1
L
442
1

296
1044
2
H
543
1

296
845
1
H
545
1

The second table is what we have come up with, and something that i wanted to bring for discussion as a solution to map pair_id's to cell_id's for each single cell database. note that the cell_id column is not necesary (is here for visualization purposes) as each sequence_id from the second table will lead to the cell_id of the first one.

pair_id
sequence_id
cell_id

1
1249
115

1
165
115

2
1249
115

2
887
115

3
1460
119

3
1258
119

4
846
119

4
1258
119

5
845
296

5
1228
296

6
845
296

6
970
296

7
1044
296

7
1228
296

8
1044
296

8
970
296

In our case, both pair_id and cell_id in paralell do not create complete redundancy in some experiments. With this, non productive sequences can still be under a single cell_id but won't have a pair_id as in the case of sequence_id = 679 from the first table.

This would make pair_id:null entirely redundant with productive:False. Which is not awful, but I think not a reason to have pair_id.

No, because you could have a cell with only the heavy chain detected, in which case pair_id:null but productive:True. Or any bulk application, where all of the rearrangements have pair_id:null

They are still inferred a cell association though, correct? If so, cell_id seems appropriate to me.

I dug up the following:

We probably need an pair_id field in Rearrangement to represent chain pairing separate from cell_id. Corresponds with is_paired=True (wherever we put that - at or downstream from SoftProcessing).

Originally posted by @javh in https://github.com/airr-community/airr-standards/issues/169#issuecomment-452063537
Unfortunately, the minutes from that meeting, in their entirety, are:

We exclusively discussed GitHub issue #169. Complications across different types of protocols led us to conclude the following:
The metadata should have a boolean flag for whether the rearrangement data is paired at the SoftwareProcessing level (is_paired), along with the current "single_cell" boolean flag at the CellProcessing level for whether it's single-cell. Each of these flags lets the user know whether "pair_id" (a new rearrangement field) and/or "cell_id" are meaningfully set in the associated data file.

Maybe @laserson remembers more?
I also found this:

With the wisdom of hindsight: See #169 and #206 => Use of cell_id to annotate chain linkage has been deprecated, instead an additional paired_id field was introduced (as single cell and chain pairing are not always associated).

Originally posted by @bussec in https://github.com/airr-community/airr-standards/issues/165#issuecomment-541961406
So it sounds like this is already integrated into the spec...

@franasa I think in your example data, cells 119 and 296 should not have pair IDs, because it is unclear which is the biological pairing. (I'm assuming that such a scenario is a doublet; if you can really prove that they are true single cells with both heavy and light chain inclusions then your assignments are correct.)
Either way, the AIRR Rearrangements format would have:

sequence_id
productive
locus
pair_id
cell_id

1249
T
IGK
1
115

165
T
IGK
2
115

887
T
IGH
1,2
115

etc, where I've left out non-AIRR "custom" fields and converted productive and locus to match the schema. The primary identifier here is sequence_id, from which you can get both pair_id and cell_id.
Going back to @bcorrie's original question, I believe that sequence_id is unique within a RearrangementSet, and a rearrangement_set_id is unique within a Repertoire. Or maybe sequence_id is directly unique within a Repertoire. Either way, it seems to me that pair_id and cell_id should follow that same rule. So if you have just the pair_id and you want to get cell_id, you'd query the Repertoire for all Rearrangements matching the former field and then look at the latter. Does that meet your needs?

Thanks, @scharch. That's immensely helpful.

No, because you could have a cell with only the heavy chain detected, in which case pair_id:null but productive:True. Or any bulk application, where all of the rearrangements have pair_id:null

Ah, that's a good point. So if I'm following the intent correctly here, then pair_id:null is basically meant to serve the same purpose as is_paired:False, but at the individual sequence level? If that's correct, then we should make that explicit in the schema docs.

Either way, it seems to me that pair_id and cell_id should follow that same rule.

I agree, and I believe that rule should be they are a grouping variable with a user-defined value, which should be unique within a DataProcessing for a Repertoire.
In other words, I think the pair_id description should be changed from this:
                Valid sequence_id that was determined by experimental or computational means to
                be associated with the current Rearrangement on the cellular level.

to something more like this similar to the cell_id description
                Identifier defining paired rearrangements that was determined by
                experimental or computational means.

A discussion in Haifa introduced a potential problem. It was mentioned that in a single cell, an IGH may form a pair with an IGL, but that the same IGH could form a pair with an IGK. This implies that a single rearrangement record can be in more than one pair, and thus pair_id is not a single value but potentially a list of values. I guess looking back through the comments, I see mention of this, as @scharch shows 1,2 as a pair_id value. The problem with using a list is that simple queries cannot be used to extract the pairs. Likewise, we've been trying to avoid lists in the AIRR TSV format.

For what it’s worth, this is also observed in alpha beta T cells where they can express two alpha chains, so it would be good to have this worked out for both cell types.
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A discussion in Haifa introduced a potential problem. It was mentioned that in a single cell, an IGH may form a pair with an IGL, but that the same IGH could form a pair with an IGK. This implies that a single rearrangement record can be in more than one pair, and thus pair_id is not a single value but potentially a list of values. I guess looking back through the comments, I see mention of this, as @scharchhttps://github.com/scharch shows 1,2 as a pair_id value. The problem with using a list is that simple queries cannot be used to extract the pairs. Likewise, we've been trying to avoid lists in the AIRR TSV format.
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Maybe in such cases it makes sense to list the heavy/beta chain twice? So my previous example would become:

sequence_id
productive
locus
pair_id
cell_id

1249
T
IGK
1
115

165
T
IGK
2
115

887
T
IGH
1
115

887
T
IGH
2
115

...except that I assume we'd have to give the duplicated heavy/beta chains separate sequence_ids, which may probably raises a different set of issues...

...except that I assume we'd have to give the duplicated heavy/beta chains separate sequence_ids, which may probably raises a different set of issues...

Yeah, unfortunately, duplicating the rearrangement records will raise other issues, especially with calculating quantities and counts...
Maybe we should start allowing arrays to be represented in some select fields, like pair_id, where we have greater ability to specify the content. Having 1,2 as the value in the TSV seems a lot simpler than other ideas.

Following @schristley, do we agree that we could represent some fields as arrays and if yes does the below suggestion for pair_id spec looks reasonable?
pair_id:
            type: array
            description: Valid list of sequence_id that was determined by experimental or computational means to be associated with the current Rearrangement on the cellular level.
            example:
                - ABC314159
                - ABC314160
            x-airr:
                miairr: true
                required: true
                nullable: true
                adc-api-optional: false
                set: 6
                subset: data (processed sequence)
                name: Paired-chain index

Hrm. I don't think we have consensus per se, but I'm strongly opposed to pair_id mapping to sequence_id as that's rather anti-tidy. You can't perform a group-by operation on the column and it would differ from behavior of other *_id fields in the spec. You could certainly enforce the convention in your specific dataset that the pair_id is the same as the sequence_id of the heavy/beta chain in the pair_id set, but I don't think that should be part of the spec.
As far as the list goes, officially supporting lists (nested columns) in the TSV would break the rules. Currently, we say:

Nested delimiters are not supported by the schema explicitly and should be avoided. However, if multiple values must be reported in a single column for an application specific reason, then the use of a comma as the delimiter is recommended.

http://docs.airr-community.org/en/latest/datarep/format.html#formatspecification
We discourage nested delimiters because it's a bit of an anti-pattern. Changing that would be a very large change, in my opinion.
So... I guess the big question for me is, what does a list of pair_id get you in terms of a practical use case?  To use @scharch's example from above, how does this:

sequence_id
productive
locus
pair_id
cell_id

1249
T
IGK
1
115

165
T
IGK
2
115

887
T
IGH
1,2
115

Facilitate analyses in a way that the following does not?

sequence_id
productive
locus
pair_id
cell_id

1249
T
IGK
1
115

165
T
IGK
1
115

887
T
IGH
1
115

Some downstream determination needs to be made about how to analyze the VH:VL pairs. Is it somehow made easier be the former?
(You could set some rule that the first table represents doublets or allelic inclusion and the later a bispecific antibody, but that seems confusing and error prone.)

Hrm. I don't think we have consensus per se, but I'm strongly opposed to pair_id mapping to sequence_id as that's rather anti-tidy. You can't perform a group-by operation on the column and it would differ from behavior of other *_id fields in the spec. You could certainly enforce the convention in your specific dataset that the pair_id is the same as the sequence_id of the heavy/beta chain in the pair_id set, but I don't think that should be part of the spec.

Yes, I think we were leaning towards @javh's approach where the pair_id is "just" an ID that groups things.

We discourage nested delimiters because it's a bit of an anti-pattern. Changing that would be a very large change, in my opinion.

I agree with this, and think we would only want to do that if absolutely necessary... In particular, if as a result of the single cell extension pull request (#211) we define a Cell object (and maybe a Receptor object?) that can capture this relationship much more accurately, I would be very hesitant to make such a fundamental change to the Rearrangement spec without having the other entities sorted out first.
It seems like the wrong approach to force what seem to be increasingly complex relationships into the Rearrangement object.

As far as the list goes, officially supporting lists (nested columns) in the TSV would break the rules.

Actually, I think the proposed usage might fit within the rules. Allelic inclusion is expected to be uncommon, and representing it could perhaps be considered "multiple values [that] must be reported in a single column for an application specific reason"...?

Facilitate analyses in a way that the following does not?

I think the main objection would be that it sacrifices clarity/explicitness. It also makes it closer to redundant with cell_id, since I think the current non-single-cell pairing approaches can't see inclusions.

Actually, I think the proposed usage might fit within the rules. Allelic inclusion is expected to be uncommon, and representing it could perhaps be considered "multiple values [that] must be reported in a single column for an application specific reason"...?

What we meant by "application specific reason" was something along the lines of "if your tools really needs to do this then go ahead, but our API isn't going to parse it and other people's tools are under no obligation to do so either".

Should've put this in the same comment above. Oh well, typing faster than I could think...
We could take the same attitude as the *_call fields with pair_id. If the use case for a list is rare enough, then just have the official spec be a single id value, but maybe the occasional tool would use a list in a non-official manner.

We could take the same attitude as the *_call fields with pair_id

Yeah, that's exactly what I had in mind. Not wedded to it, but seems easier than anything else we've discussed.

TL;DR Let's trash pair_id and use a "virtual" cell object instead.
Given the pains that pair_id is creating, @srlak, @franasa and me had a brainstroming session, the outcome of which I will try to summarize below.
Markup: biological entity and data object
Basic assumptions

The two biological entities that we want to represent for single-cell(-like) data are cell and receptor.
Properties of a cell:
a. A cell is modeled as a bag that contains DNA/RNA molecules encoding Ig/TCR chains.
b. A cell can express one or more receptor species.
c. A cell is represented by a cell object that has a unique cell_id identifier.
d. A cell can have additional observable properties (e.g., flow profile, transcriptome), which should be attributable to the cell object.
Properties of a receptor:
a. A receptor is modeled as the combination of two non-identical types of Ig/TCR polypeptide chains (i.e., ignoring #297)
b. As polypeptides, the chains must be encoded by productively rearranged sequences.
c. A receptor is represented by a receptor object that has a unique receptor_id identifier.
d. A receptor can have additional observable properties (e.g., affinity against an antigen), which should be attributable to the receptor object.
Relationships between cell and receptor objects:
a. A cell MAY be associated with one or more receptor objects.
b. A receptor MAY be associated with one or more cell objects.
c. Associating a cell and a receptor is a valid operation if and only if the cell is associated with all rearrangement objects required to encode the receptor.

Importantly, these assumption do NOT REQUIRE that the cell has to be observed directly (e.g. by flow or microscopy). It is sufficient if the experimental setup creates a trackable single-cell context (e.g., microfluidics with unique barcodes for each droplet) which allows the subsequent association of an observed rearrangement with a cell.
One of the reasons why we introduced the pair_id, was to be able to annotate stochastic pairing data, like PAIRseq. In these experimental setups, rearrangements are inferred to be associated with each other, based on the correlated presence and absence of the rearrangements in multiple sub-samples under limiting dilution conditions. As these setup do not create a single-cell context, we did not want to use the cell_id field to represent chain linkage, as we thought that this should be reserved for "true" single-cell setups. However, as noted above, most of our single-cell data will not come from directly observed single cells, but from workflows that only preferentially create a single-cell context and subsequently attempt to filter out doublets etc. Finally, the technical reason why stochastic pairing works, is because the DNA/RNA molecules are in the same cell, not because they encode components of the same receptor. Therefore, it will also allow pairing of non-productive chains (although some software might filter those out).
Therefore, we would like to pitch the idea that stochastic pairing should not be represented by pair_id but instead via a "virtual" cell. These cell objects would contain a virtual: true key to indicate that they were inferred. As we now can represent all chain paired data via cell (rearrangement would link n:1 to cell), pair_id could be deprecated. In this model, receptor would be reserved for data that is based on direct observation and would not be linked from rearrangement.

Therefore, we would like to pitch the idea that stochastic pairing should not be represented by pair_id but instead via a "virtual" cell. These cell objects would contain a virtual: true key to indicate that they were inferred. As we now can represent all chain paired data via cell (rearrangement would link n:1 to cell), pair_id could be deprecated. In this model, receptor would be reserved for data that is based on direct observation and would not be linked from rearrangement.

If I understand correctly you are suggesting that at the Rearrangement object level we only need cell_id and we no longer need pair_id? That is cell_id is sufficient to capture both uses? I think this is right, but wanted to confirm...

@bussec I think this is suggesting that the decision we made to have both (see https://github.com/airr-community/airr-standards/issues/165#issuecomment-541961406) has been changed, correct?

@bcorrie Yes, we only need cell_id. The information that the cell was not directly observed is moved to the cell object. Therefore pair_id is not necessary anymore. Any yes, our hindsight is getting close to 20/20.

TL;DR Let's trash pair_id and use a "virtual" cell object instead.

@bussec Very good, this looks good to me. It should work well from an API perspective as well with the obvious creation of cell and receptor endpoints.
The only thing I'm unclear about it this, can you describe a use case where this will occur?

b. A receptor MAY be associated with one or more cell objects.

The only thing I'm unclear about it this, can you describe a use case where this will occur?

b. A receptor MAY be associated with one or more cell objects.

Clonally expanded T cells. I just wanted to state that this is a situation that we need to be able to represent, when designing the cell and receptor objects. This should not be in conflict with clone_id as the latter one captures a sequence (not receptor) based grouping of cells.

Clonally expanded T cells.

Ah I see, so you are thinking of receptors abstractly, that is a single receptor object can represent multiple physical receptor entities (assuming the sequence is identical, and actually I guess the additional observable properties as well)?

Correct.

Ok, how far can that extend? Can that single receptor object be used across multiple repertoires, multiple studies?
From an API perspective, the id is globally (or repository) unique, so you can do a directly query to return the information. So technically it is possible to allow a receptor object to be very broad.
/receptor/:receptor_id

The relationship you defined between cell and receptor is n-to-n, so I'm mainly trying to think about how that will be represented and where it will be stored.
If this requirement was changed, that is each receptor object represents a single physical receptor, that means it could only belong to a single cell, the relationship becomes 1-to-n and is easier to store and manage.

I understand that you would like to avoid n-to-n if possible, but in this case we need it, at least for single-cell. Otherwise we are buying the simplicity of an 1-to-n relation with an eventually non-normalized data structure, which I would like to avoid.
Regarding the scope of receptor_id: Yes, theoretically we can make it global. We just need to be aware that once we move beyond the subject, we need support for multiple MHC haplotypes when annotating reactivity.

From the call:

pair_id never seems to have made it into a release, so we can delete it without having to deprecate it.
Push new Cell and Receptor objects to v2.0.

Given the above, do you think we can close this issue. Paired discussion will continue on in the Cell/Receptor discussion and we are removing pair_id from rearrangements... I would like to close this issue unless anyone objects...

I am ok with closing and moving the discussion to #320.

Are we going to remove pair_id?

Yes, at least that we my understanding from the January DataRep call (see @javh's comment above).

Okay, I missed that call so wanted to check.


Suggestion, change order representation to match common GPU expectations

This is a simple suggestion that may clash with other requirements. It's merely in case this is a possible change.
The definition of point in the library is as follows:
pub struct Point (pub(crate) f32x4);

impl Point {
  #[inline] pub fn w(&self)->f32 { self.0[0] }
  #[inline] pub fn e123(&self)->f32 { self.w() }
  #[inline] pub fn x(&self)->f32 { self.0[1] }
  #[inline] pub fn e032(&self)->f32 { self.x() }
  #[inline] pub fn y(&self)->f32 { self.0[2] }
  #[inline] pub fn e013(&self)->f32 { self.y() }
  #[inline] pub fn z(&self)->f32 { self.0[3] }
  #[inline] pub fn e021(&self)->f32 { self.z() }

This makes perfect sense since multivectors are commonly written with the scalar term on the left most position.
However most hardware designed for geometry, primarily GPUs actually fllow the convention xyzw.
So if one serializes the points as is and send them to a shader, the results will be incorrect. w becomes x, x becomes y and so on, thus you have to write this:
#version 450
#extension GL_EXT_scalar_block_layout : enable

layout(location = 0) in vec4 inPosition;

layout(binding = 0) uniform MVPOnlyUbo
{
  mat4 model;
  mat4 view;
  mat4 proj;
};

void main() {
  gl_Position = proj * view * model * vec4(inPosition.yzw, 1.0);
}

Note the strange recasting inPosition.yzw, this is necessary since the layout the GPU expects and the layout in the library are different. In order to support fast and efficient byte compatibility I would like to suggest moving the w term at the end of the array.
Alternatively the compact point suggested in https://github.com/wrnrlr/g3/issues/4 could also solve this if I get around to implementing it.

Yes I agree this is a shortcoming in the design that is a result of  g3 starting off as a port of klein.
This is also the reason for setting the visibility of the Point members to pub(crate) so this can be changed in the future without breaking anything else.
BTW, I think that most often it is better todo this shuffle on the CPU especially if you are using an index buffer.
I've added some new methods to help with this.
It will be a lot of work™ to implement this change just to save one more shuffle.
In the future I hope to be able to implement some of the internals with a macro and avoid having to do all this by hand.
This change might also make it possible to work nicely with rust-gpu.


[ACR] Add Key Vault TSG for Transfer feature

In response to recent CRI, add Key Vault troubleshooting info to our Transfer TSG. This will help customers self-diagnose managed identity access issues.

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[Question]: Why SimpleFileNodeParser only supports .md, .html and .json

Question Validation

[X] I have searched both the documentation and discord for an answer.

Question
As titled. I thought it's a generic parser based on the name and description.
https://github.com/run-llama/llama_index/blob/b06c888d8319752429096d9a33d8a6a84cc2062a/llama-index-core/llama_index/core/node_parser/file/simple_file.py#L12

This is a (tad outdated) object that tbh we haven't really advertised.
Only HTML, JSON, and MD are included because those are the only file-specific node parses we have written

I'm trying to support different types of files, including code files. Does it mean that I have to implement my own logic determining which parsers/splitters to use based on extensions?

It's actually advertised here as a recommended way to automatically use the best node parser for each type of content, which is apparently not the case - https://docs.llamaindex.ai/en/stable/module_guides/loading/node_parsers/modules.html#file-based-node-parsers

@qizzzh best to implement your own logic imo.
I will make a todo to update that page


List hits something while scrolling

#91605
After a few scrolls up and down during scrolling, the list of something rests on top and from the bottom, and then begins to stretch if you continue the scroll in the corresponding direction.
https://user-images.githubusercontent.com/102767277/223092560-c3e25c72-ff11-40af-98bd-d6b81d1c1aa6.mp4

Sample code

import 'package:flutter/material.dart';

void main() {
  runApp(const MyApp());
}

class MyApp extends StatelessWidget {
  const MyApp({super.key});

  @override
  Widget build(BuildContext context) {
    return MaterialApp(
      title: 'Test AppBar',
      debugShowCheckedModeBanner: false,
      theme: ThemeData(useMaterial3: true, brightness: Brightness.light),
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    );
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}

class CardScreen extends StatelessWidget {
  const CardScreen({super.key});

  @override
  Widget build(BuildContext context) {
    return Scaffold(
      appBar: AppBar(
        title: Text('Cards'),
        shape: Border.all(color: Colors.transparent),
      ),
      body: ListView(
        padding: EdgeInsets.all(20),
        children: [
          Card(
            child: SizedBox(
              width: 300,
              height: 150,
              child: Center(child: Text('Elevated Card')),
            ),
          ),
          Card(
            elevation: 0,
            color: Theme.of(context).colorScheme.surfaceVariant,
            child: SizedBox(
              width: 300,
              height: 150,
              child: Center(child: Text('Filled Card')),
            ),
          ),
          Card(
            elevation: 0,
            shape: RoundedRectangleBorder(
              side: BorderSide(color: Theme.of(context).colorScheme.outline),
              borderRadius: BorderRadius.circular(12),
            ),
            child: SizedBox(
              width: 300,
              height: 150,
              child: Center(child: Text('Outlined Card')),
            ),
          ),
          Card(
            child: InkWell(
              onTap: () {},
              radius: 120,
              splashColor:
                  Theme.of(context).colorScheme.secondary.withOpacity(0.15),
              highlightColor:
                  Theme.of(context).colorScheme.secondary.withOpacity(0.15),
              borderRadius: BorderRadius.circular(12),
              child: SizedBox(
                width: 300,
                height: 150,
                child: Center(child: Text('Elevated Card (clickable)')),
              ),
            ),
          ),
          Card(
            elevation: 0,
            color: Theme.of(context).colorScheme.surfaceVariant,
            child: InkWell(
              onTap: () {},
              radius: 120,
              splashColor:
                  Theme.of(context).colorScheme.secondary.withOpacity(0.15),
              highlightColor:
                  Theme.of(context).colorScheme.secondary.withOpacity(0.15),
              borderRadius: BorderRadius.circular(12),
              child: SizedBox(
                width: 300,
                height: 150,
                child: Center(child: Text('Filled Card (clickable)')),
              ),
            ),
          ),
          Card(
            elevation: 0,
            shape: RoundedRectangleBorder(
              side: BorderSide(color: Theme.of(context).colorScheme.outline),
              borderRadius: BorderRadius.circular(12),
            ),
            child: InkWell(
              onTap: () {},
              radius: 120,
              splashColor:
                  Theme.of(context).colorScheme.secondary.withOpacity(0.15),
              highlightColor:
                  Theme.of(context).colorScheme.secondary.withOpacity(0.15),
              borderRadius: BorderRadius.circular(12),
              child: SizedBox(
                width: 300,
                height: 150,
                child: Center(child: Text('Outlined Card (clickable)')),
              ),
            ),
          ),
        ],
      ),
    );
  }
}

flutter doctor -v

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    • Flutter plugin version 72.0.4
    • Dart plugin version 223.8617.8

[✓] VS Code (version 1.76.0)
    • VS Code at C:\Users\yablo\AppData\Local\Programs\Microsoft VS Code
    • Flutter extension version 3.60.0

[✓] Connected device (3 available)
    • Windows (desktop) • windows • windows-x64    • Microsoft Windows [Version 10.0.22621.1344]
    • Chrome (web)      • chrome  • web-javascript • Google Chrome 110.0.5481.178
    • Edge (web)        • edge    • web-javascript • Microsoft Edge 110.0.1587.63

[✓] Network resources
    • All expected network resources are available.

• No issues found!

Triage report
I can reproduce this issue on Master (3.9.0-1.0.pre.51). This looks like to only occur when you overscroll in one direction, triggering the stretch animation, then in the same swipe motion, overscroll in the opposite direction. It looks like the previous animation is reset before the next one plays causing a jerk to the end of the stretch as the stretch does not follow the user's finger

Code Sample
import 'package:flutter/material.dart';

void main() {
  runApp(const MyApp());
}

class MyApp extends StatelessWidget {
  const MyApp({super.key});

  @override
  Widget build(BuildContext context) {
    return MaterialApp(
      title: 'Test AppBar',
      debugShowCheckedModeBanner: false,
      theme: ThemeData(useMaterial3: true, brightness: Brightness.light),
      darkTheme: ThemeData(useMaterial3: true, brightness: Brightness.dark),
      home: const CardScreen(),
    );
  }
}

class CardScreen extends StatelessWidget {
  const CardScreen({super.key});

  @override
  Widget build(BuildContext context) {
    return Scaffold(
      appBar: AppBar(
        title: const Text('Cards'),
        shape: Border.all(color: Colors.transparent),
      ),
      body: ListView(
        padding: const EdgeInsets.all(20),
        children: List.generate(
          5, // Change this so that it just starts scrolling
          (_) => const Card(
            child: SizedBox(
              width: 300,
              height: 150,
              child: Center(child: Text('Elevated Card')),
            ),
          ),
        ),
      ),
    );
  }
}

flutter doctor -v (Master)
[!] Flutter (Channel master, 3.9.0-1.0.pre.51, on Ubuntu 22.04.2 LTS 5.15.0-67-generic, locale en_US.UTF-8)
    • Flutter version 3.9.0-1.0.pre.51 on channel master at /home/exabyt3/fvm/versions/master
    ! Warning: `dart` on your path resolves to /usr/lib/dart/bin/dart, which is not inside your current Flutter SDK checkout at /home/exabyt3/fvm/versions/master. Consider adding /home/exabyt3/fvm/versions/master/bin to the front of your path.
    • Upstream repository https://github.com/flutter/flutter.git
    • Framework revision b6963bb2d9 (32 minutes ago), 2023-03-06 02:24:32 -0500
    • Engine revision 54b9893782
    • Dart version 3.0.0 (build 3.0.0-290.0.dev)
    • DevTools version 2.22.2
    • If those were intentional, you can disregard the above warnings; however it is recommended to use "git" directly to perform update checks and upgrades.

[!] Android toolchain - develop for Android devices (Android SDK version 33.0.2)
    • Android SDK at /home/exabyt3/Android/Sdk
    • Platform android-33-ext4, build-tools 33.0.2
    • ANDROID_SDK_ROOT = /home/exabyt3/Android/Sdk
    • Java binary at: /home/exabyt3/programs/android-studio/jbr/bin/java
    • Java version OpenJDK Runtime Environment (build 11.0.15+0-b2043.56-8887301)
    ! Some Android licenses not accepted. To resolve this, run: flutter doctor --android-licenses

[✓] Chrome - develop for the web
    • CHROME_EXECUTABLE = /usr/bin/brave-browser

[✓] Linux toolchain - develop for Linux desktop
    • Ubuntu clang version 14.0.0-1ubuntu1
    • cmake version 3.22.1
    • ninja version 1.10.1
    • pkg-config version 0.29.2

[✓] Android Studio (version 2022.1)
    • Android Studio at /home/exabyt3/programs/android-studio
    • Flutter plugin version 72.1.2
    • Dart plugin version 221.6096
    • Java version OpenJDK Runtime Environment (build 11.0.15+0-b2043.56-8887301)

[✓] VS Code (version 1.76.0)
    • VS Code at /usr/share/code
    • Flutter extension version 3.58.0

[✓] Connected device (2 available)
    • Linux (desktop) • linux  • linux-x64      • Ubuntu 22.04.2 LTS 5.15.0-67-generic
    • Chrome (web)    • chrome • web-javascript • Brave Browser <IP_ADDRESS>

[✓] Network resources
    • All expected network resources are available.

! Doctor found issues in 2 categories.

@Piinks

This should have been fixed by https://github.com/flutter/flutter/pull/116548 which closed this issue https://github.com/flutter/flutter/issues/88741
@exaby73 were you reproducing this at tip of tree?
FYI @jankuss

@Piinks in the video of https://github.com/flutter/flutter/issues/122008#issue-1611213047, you can see that it's reproduced by hitting the edges of the scroll view in the same swipe motion. In https://github.com/flutter/flutter/issues/88741, the view isn't scrollable as there isn't enough items to scroll it. This might be an edge case that wasn't considered

Interesting. Thanks for clarifying!

@Piinks
I believe this behaviour comes from this line here:
https://github.com/flutter/flutter/blob/09518ac72584f818bdfd85c5830ebe884c6de624/packages/flutter/lib/src/widgets/overscroll_indicator.dart#L897
We do not accept the scroll update event for the overscroll when the stretch direction would change, while a receding animation is still playing. This was done to fix another visual abnormality, caused by the stretch direction changing while receding: https://github.com/flutter/flutter/pull/116548#issuecomment-1414872567


Initial update to data mapper mediator page

Purpose
$subject

These changes are covered with https://github.com/wso2/docs-mi/pull/713. Hence closing this PR.


Provide mechanism to map folder names to underscored and dotted ones in icons manifest

[x] I'm sure this issue is not a duplicate?

@robertohuertasm @jens1o

I'm terrible at naming. What should we name this new enum?
I'm thinking of making this enum as flag* type like in .NET.

Thoughts?

https://www.typescriptlang.org/docs/handbook/enums.html
https://basarat.gitbooks.io/typescript/docs/enums.html#enums-as-flags

AdditionalFileextensionTypes

@jens1o May I remind you that we are atalking about folders.

I had written to many php files today(around 35 to get something done). Sorry.
AdditionalFolderExtensionTypes
An extension of folders grouped together... somehow?

Forget flags enum they create confusion in the supportFolders API.
Naming still pending...

@jens1o I'm looking something for something descriptive like the languages we have in supportedFiles.

brainfuck got real.

Sorry @JimiC what would be the idea here? I'm not sure to understand how you want to tackle this.

If I understand correctly. You're planning to create some sort of automation that will allow the folders to support _ and . syntax.  I guess these flags will affect all the extensions in a specific folder definition.If that's the case I think this would not be a desirable scenario.
Let's take this as an example:
{ icon: 'git', extensions: ['.github', '.git', 'submodules', '.submodules'], format: FileFormat.svg },

Let's say I want to support underscores for submodules and only dots for the others. How would a flag support this?
In my opinion, just adding the _  as another extension is the easiest an clearer way to proceed. Unless your idea solves this issue :wink:

@robertohuertasm By introducing a new flags enum.
enum Map {
  none,
  dotted = 1 << 1,
  leadingUnderscore = 1 << 2,
  trailingUnderscore = 1 << 3,

  leadingUnderscoreAndDotted = leadingUnderscore | dotted,
  fullyUnderscored = leadingUnderscore | trailingUnderscore,
  all = dotted | fullyUnderscored,
}

and API like:
    { icon: 'aws', extensions: ['aws'], map: [map.dotted], format: FileFormat.svg },

Still I don't see the point of doing this. I mean, I don't see it solving any issue but adding complexity instead.
In the case I presented before, I would need to split the entry in order to support the scenario while just by adding one string it would be solved. And still, it would be all grouped into one entry.

After discussing this with @robertohuertasm, we decided to drop the implementation of this feature.
@jens1o You can restore #996.


Screenshots me instead if player id i choose

Hey, this is an amzing script, i love it, just one issue, it screenshots the person why types /screenshot (1 or 2 or 3 or 4 or etc..) if anyone does /screenshot -1 it does everyone perfectly fine, any fix let me know thank you

I have the same issue.


distro-base: fix kind image installing containerd

Issue #, if available:
Description of changes:
By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.

/lgtm
/approve


Could not load xacc_iontrap

From the latest qcor/cli docker image...
[2022-02-17 13:56:17.041] [xacc-logger] [error] [XACC Error] Could not load xacc_iontrap, error message: Bundle#14 start failed: Error loading shared library libxacc-circuit-optimizers.so: No such file or directory (needed by /usr/local/aideqc/qcor/plugins/libxacc-iontrap.so)
[2022-02-17 13:56:17.041] [xacc-logger] [error] [XACC Error] Framework Exiting

Of course just deleting xacc_iontrap gets you going, but there are some link problems with the plugin that should be fixed. I think, specifically, it is linking and using functions from another plugin, which is not something we should be doing.

@ausbin I think you should try to get the GateFusion dependency out of this plugin at some point. The best way might be to create an interface at the quantum/gate/utils package level that GateFuser in circuit-optimizers can inherit from and contribute GateFuser as a plugin to the service registry under that new type. Then you can remove the link from xacc-circuit-optimizers on your iontrap plugin, and only rely on xacc-quantum-gate.

Hi @amccaskey, sorry for the slow turnaround on my end. Attempt at a fix here: #521


Confusion in documentation

I'm reading the documentation on mio::Poll and getting a little bit confused about the following sentense:

If operation fails with WouldBlock, then the caller should not treat this as an error and wait until another readiness event is received.

Does this sentence means:

...caller should not treat this as an error, but rather wait until another readiness event is received.

Or:

...caller should not treat this as an error, and should not wait until another readiness event is received.

I'm not a native english speaker. Please ignore this post if I misunderstood the sentense.

Oh no worries and thanks for the report! This sentence is intended to use the "but rather" meaning. The intent being conveyed here is that even if Poll indicates that an object is ready for being read this isn't a guarantee and when you actually read the object you may still get WouldBlock. This phenomenon isn't an erroneous situation, though, it's just how Poll works. The sentence here is intended to say that it's a normal and expected occurrence.
Does that make sense?

Is there a change that needs to happen to the source or is this issue resolved?

The documentation needs to be reworded to avoid the ambiguity.


[FLINK-26331] Make cleanup retry strategy configurable similar to how the task restart is configurable

The goal is to align the user experience for retry functionality. I created a follow-up ticket FLINK-26359 to cover the actual alignment in the code.
What is the purpose of the change
Introduced CleanupOptions
Brief change log
TODO
Verifying this change
TODO
Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): no
The public API, i.e., is any changed class annotated with @Public(Evolving): yes
The serializers: no
The runtime per-record code paths (performance sensitive): no
Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Kubernetes/Yarn, ZooKeeper: yes
The S3 file system connector: no

Documentation

Does this pull request introduce a new feature? no
If yes, how is the feature documented? docs

The compiled docs look like that:

Thanks @autophagy for your review. I applied your comments, squashed the commits and rebased the branch. I will merge it after the final CI run succeeds.

Test failure unrelated to changes: FLINK-26387 I'm going to merge the PR


Wrong values-large/dimens/md_preference_content_inset value

Hello,
There's an issue with the md_preference_content_inset dimensions in values-large.
To make it consistent with normal Android preferences (like SwitchPreference, etc.), it should be (instead of its unique value of 28dp for all large screens):
values-large/dimens.xml: 28dp
values-large-v21/dimens.xml: 16dp
values-large-v22/dimens.xml: 24dp
Thank you,
Stéphane.

Preferences will be going away in version 2 of this library.

Oh that's bad news. Use them a lot. Why will preferences go away?


x/sys: does not build on linux/sparc64, stuck on porting attempt

What version of Go are you using (go version)?

$ go version
go version unknown linux/sparc64
$ gcc --version
gcc 12.2.0

Does this issue reproduce with the latest release?

Running with no changes, I get:
golang.org/x/sys/cpu
golang.org/x/sys/unix
# golang.org/x/sys/cpu
/root/go/pkg/mod/golang.org/x/sys@v0.0.0-20200615200032-f1bc736245b1/cpu/cpu.go:17:30: error: reference to undefined name ‘cacheLineSize’
   17 | type CacheLinePad struct{ _ [cacheLineSize]byte }
      |                              ^
github.com/matrix-org/dendrite/cmd/kafka-producer
# golang.org/x/sys/unix
/root/go/pkg/mod/golang.org/x/sys@v0.0.0-20200615200032-f1bc736245b1/unix/dirent.go:16:12: error: reference to undefined name ‘isBigEndian’
   16 |         if isBigEndian {
      |            ^

After this commit, and trying to write unix/asm_linux_sparc64.s(started with just copying over loong64's), I get this error:
# golang.org/x/sys/unix
unix/asm_linux_sparc64.s:9:10: fatal error: textflag.h: No such file or directory
    9 | #include "textflag.h"
      |          ^~~~~~~~~~~~
compilation terminated.

I assume this is why there was a gc requirement. On sparc64, gccgo is the only option.
So, how would I get an assembly file compileable with gccgo? Is there a way to make it work with textflag.h, or a way to make it work without it?
Thanks for your time, I am really excited about getting x/sys running on my sparcbox, and hopefully soon everyone elses =^D

The various asm files in x/sys are not used by gccgo.  For example, asm_linux_loong64.s has a go:build line that says that the file is only built with the "gc" tag.  That means it is only built when using the gc compiler, not when using gccgo.
You'll need to add a cpu/cpu_sparc64.go file to define cacheLineSize appropriately, and you'll need to figure out why the sparc64 build tag was not used to pick up unix/endian_big.go.

Thanks for the info!! Glad to know I don't need to learn sparc64 asm :D.
I added the cpu_sparc64.go file, and it builds successfully! The bigendian error disappeared after that. Black magic o.o
I am a bit confused for what to set cacheLineSize to. Different sparc64 CPUs have different values, looking at cpu_arm64.go it seems like I should use the highest of the bunch?
Sadly, it looks like it fails a good deal of tests:
root@sparcy /var/tmp/tmp/sys-sparc64 # go test ./...
ok      golang.org/x/sys/cpu    0.174s
ok      golang.org/x/sys/execabs        0.170s
ok      golang.org/x/sys/internal/unsafeheader  0.179s
--- FAIL: TestPktInfo (0.01s)
    --- FAIL: TestPktInfo/udp4 (0.00s)
        ???:1: Got packet from <IP_ADDRESS>, want <IP_ADDRESS>
    --- FAIL: TestPktInfo/udp6 (0.00s)
        ???:1: Got packet from ::, want 2001:db8::1
--- FAIL: TestDevices (0.00s)
    --- FAIL: TestDevices//dev/null_1:3 (0.00s)
        ???:1: for /dev/null Major(0x0) == 0, want 1
        ???:1: for /dev/null Minor(0x0) == 0, want 3
        ???:1: for /dev/null Mkdev(1, 3) == 0x103, want 0x0
    --- FAIL: TestDevices//dev/zero_1:5 (0.00s)
        ???:1: for /dev/zero Major(0x0) == 0, want 1
        ???:1: for /dev/zero Minor(0x0) == 0, want 5
        ???:1: for /dev/zero Mkdev(1, 5) == 0x105, want 0x0
    --- FAIL: TestDevices//dev/random_1:8 (0.00s)
        ???:1: for /dev/random Major(0x0) == 0, want 1
        ???:1: for /dev/random Minor(0x0) == 0, want 8
        ???:1: for /dev/random Mkdev(1, 8) == 0x108, want 0x0
    --- FAIL: TestDevices//dev/full_1:7 (0.00s)
        ???:1: for /dev/full Major(0x0) == 0, want 1
        ???:1: for /dev/full Minor(0x0) == 0, want 7
        ???:1: for /dev/full Mkdev(1, 7) == 0x107, want 0x0
    --- FAIL: TestDevices//dev/urandom_1:9 (0.00s)
        ???:1: for /dev/urandom Major(0x0) == 0, want 1
        ???:1: for /dev/urandom Minor(0x0) == 0, want 9
        ???:1: for /dev/urandom Mkdev(1, 9) == 0x109, want 0x0
    --- FAIL: TestDevices//dev/tty_5:0 (0.00s)
        ???:1: for /dev/tty Major(0x0) == 0, want 5
        ???:1: for /dev/tty Mkdev(5, 0) == 0x500, want 0x0
--- FAIL: TestStatx (0.00s)
    ???:1: Statx: returned stat mode does not match Stat
    ???:1: Statx: returned stat ctime does not match Stat
    ???:1: Statx: returned stat mtime does not match Stat
    ???:1: Statx: returned stat mode does not match Lstat
    ???:1: Statx: returned stat ctime does not match Lstat
    ???:1: Statx: returned stat mtime does not match Lstat
--- FAIL: TestFstatat (0.00s)
    ???:1: Stat/Fstatat: got dev 30, expected<PHONE_NUMBER>80
    ???:1: Stat/Fstatat: got ino 1, expected<PHONE_NUMBER>85184
    ???:1: Stat/Fstatat: got mode 33188, expected 0
    ???:1: Stat/Fstatat: got size 8192, expected<PHONE_NUMBER>
    ???:1: Lstat/Fstatat: got dev 30, expected<PHONE_NUMBER>80
    ???:1: Lstat/Fstatat: got ino 1, expected<PHONE_NUMBER>97952
    ???:1: Lstat/Fstatat: got mode 41471, expected 0
    ???:1: Lstat/Fstatat: got size 8192, expected<PHONE_NUMBER>
--- FAIL: TestFchmodat (0.00s)
    ???:1: Fchmodat: failed to change symlink mode: expected -rwxrwxrwx, got ----------
--- FAIL: TestUtimesNanoAt (0.00s)
    ???:1: UtimesNanoAt: wrong mtime: got {0 0}, expected {3333 0}
FAIL
FAIL    golang.org/x/sys/unix   0.988s
ok      golang.org/x/sys/unix/internal/mkmerge  0.290s
?       golang.org/x/sys/windows/mkwinsyscall   [no test files]
FAIL

You can take a look at the cpu_sparc64.go I wrote here.
Any tips on where to go from here? Am a bit lost on where these tests might be failing..
I appreciate your time :)

Yes, cacheLineSize should be the largest cache size used on the processor architecture.
The tests suggest that Stat isn't working, which suggests that the Stat_t type in the file ztypes_linux_sparc64.go is somehow incorrect.  That is just a guess, though.

aaaaahrg I'm getting stuck on this.
I'm not using the docker method, as I want the information from my running system to be used, to see if there's any differences. Plus, Docker('s deps) requires go 1.18 to build. As far as I'm aware, gcc12 only supports up to go 1.16.
I took a look at Stat_t, and I have 0 idea how to fix this by hand. Looking at mkpost.go, I of course commented out the docker check, but it seems to hang endlessly. Using print messages I narrowed down the freezing to this line:
b, err := ioutil.ReadAll(os.Stdin)
I'm running it directly like this, not sure if this is how I'm supposed to do it:
GOOS="linux" GOARCH="sparc64" go run mkpost.go
I keep looking at the test results, then the tests, and I'm just.... baffled. Like TestPktInfo. The test is so so simple, and it fails miserably. Same thing with the /dev/random test....
I'll keep assuming it's something wrong in ztypes_linux_sparc64.go (or one of the other unix/*linux_sparc64.go files).
I'll keep working on it, but in the meantime, if I can get some hints with this mkpost.go (or any possible alternative ways to get the info I need) I would SUPER greatly appreciate it :D

Update: Writing a script to try every possible value combination in Stat_t. Will leave overnight, maybe, just maybe, by morning I'll have something that passes tests :D

So I finally understood what to do to generate these the right way. I don't really know go, so they were hard for me to follow, and I misunderstood.
Although when I run go tool cgo -godefs linux/types.go, I get an error about not being able to find abi/abi.h. Which, is generated with mkall.go. However when I go run mkall.go, I get an error about needing to be on amd64. An interesting chicken and the egg scenario :D
Anyways, I'm again back to getting the values by hand. The whole script thing I mentioned above didn't work too well :/.
I'm trying to adapt /usr/include/asm/stat.h, and comparing it to ztypes_linux_sparc64.go, but in the ztypes I see this Timespec field for the time values. At the moment I'm leaving that as is, as I don't understand what it is, but is there a chance this could be incorrect?


React.js tutorial (Dec. 2015) uses deprecated component UserComponent

The tutorial is [Tutorial: Build a React.js Application With User Authentication] (https://stormpath.com/blog/build-a-react-app-with-user-authentication/), posted in Dec. 2015.
The Profile Page section uses UserComponent, which has been deprecated.
I wonder what we should be using now instead of UserComponent?
Thanks,
Bing

Oh... I found out about the answer in the error message :) We should use Contexts (link) instead.
However, I still have concerns: according to the [official Facebook React guide] (https://facebook.github.io/react/docs/context.html), the user is Contexts should discouraged. I wonder if Stormpath would implement the API without Contexts in the future?

Thank you! The blog post has been fixed since some time so I'm going to go ahead and close this issue. Also, regarding the use of contexts. There's definitely thoughts in place to make the library more generic and get rid of too much dependency on contexts:)


Cut new release for Contour 1.9

Contour 1.9 brought the first alpha of the new ExtensionService CRD. It'd be really nice to have a new release with this included!
Thanks!

0.19 should have 1.9, and HEAD has 1.10


[BUG] already existed cert-manager related resources block vela install

Existed cert-manager related resources like role/rolebinding/ValidatingWebhookConfiguration which might be deployed by Istio, will block vela install.
➜  /Users/zhouzhengxi/Downloads/kubevela git:(master) bin/vela install
- Installing Vela Core Chart:
Error: rendered manifests contain a resource that already exists. Unable to continue with install: Role "cert-manager-cainjector:leaderelection" in namespace "kube-system" exists and cannot be imported into the current release: invalid ownership metadata; annotation validation error: missing key "meta.helm.sh/release-name": must be set to "vela-core"; annotation validation error: missing key "meta.helm.sh/release-namespace": must be set to "oam-system"

similar with #340

ref to #701

Fixed in #711.

Fixed in #711.


bat command is currently outdated

First and foremost, amazing app and great idea. But as I tried to install this app it seemed that bat command changed to batcat on ubuntu due to name clash with another package. So after I changed pager_cmd = "bat -n" to pager_cmd = "batcat -n" everything started to work.
Maybe there is a need to change command bat to batcat

Hi! Thanks for the headsup! This change only affects bat on Debian and Ubuntu, on other distributions such as Arch, the binary is still called bat. The issue is explained on the official github page of bat.
Right now this project is a very minimal solution for displaying lyrics, so I personally wouldn't implement checking for the the distribution to use the correct command. I think changeing the variable is an easy fix for any user.
I will update the README of the project to let users know about this issue.


Use mock placeid2dcid config in TEST env

Nice change, but what's the context for it?

Hao is trying to run this and found he need to access the actual gcs, so fixing that


setup when update

when component did update,the nextProps.children.length > prevProps.children.length. reSetup it

when the react-swipe componentDidUpdate
nextPorps.children.length > prevProps.children.length
there's style error;
so maybe we can reSetup It let be ok!


Not compatible with Aether II

Mod Version:
1.7.10-<IP_ADDRESS>
Forge Version:
<IP_ADDRESS>4 (1.7.10)
Link to crash log (if applicable):
https://gist.github.com/amed12345/8b5067a4cd35b52f35506838834f3860
Description:
Happens when I try to enter Aether II trough the portal.
Im not sure but I think it has a problem with the step sound. Without Dynamic Surroundings the problem doesn't occur.
It also doesnt work with twilight forest

oh yeah, twilight forest also doesn't work

whateveeeeeer its working on the newest mod version, sorryyyyyyyyy xdd

Heh.  Sometimes you just can't explain it.  I presume that things are still working for you?

Going to close the issue out as addressed.  Let me know if you have any further issues. :)