-Runtime dotnet -Version 2.2.5 Could not find/download: ".NET Core Runtime" with version = 2.2.5

throw "Could not find/download: "$assetName" with version = $Sp ... +     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~     + CategoryInfo          : OperationStopped: (Could not find/...ET Core support:String) [], RuntimeException     + FullyQualifiedErrorId : Could not find/download: ".NET Core Runtime" with version = 2.2.5 Refer to: https://aka.ms/dotnet-os-lifecycle for information on .NET Core support

Can you verify if this works when you are connected to the Internet?  See https://github.com/microsoft/vscode-azurearmtools/wiki/Troubleshooting-DotNet-Acquisition#could-not-finddownload-net-core-runtime-with-version--225.  Thanks.

Thanks

Sounds like it's working.  Please re-open if not.

thank you anyway


Support lpt and dev

Changes Unknown when pulling 61465b002d83d14e186eb896e2fba4116fb55878 on nobodyiam:support-lpt into ** on ctripcorp:master**.


Fix typo

Coverage remained the same at 94.94% when pulling 83b59a995e1f489a323866e58ec80f52c4570c6f on fix-typo into 8c172c35f9e833032d23df4d6b9aa0fdb4b399b6 on master.


update jQuery plugin to be compatible with ES/CommonJS modules

After this change, the following should be possible:
import $ from "jquery";
import Headroom from "headroom.js"
import registerJQueryHeadroom from "headroom.js/dist/jQuery.headroom.js";

registerJQueryHeadroom($, Headroom);

$("header").headroom();

Added a tests for jquery, and refactored the test suite so we can run the exact same set of tests for vanilla and jquery solutions.

I'm considering bundling Headroom with the jquery plugin itself, so the above code sample would be reduced to a much less boilerplate-y:
import $ from "jquery";
import registerJQueryHeadroom from "headroom.js/dist/jQuery.headroom.js";

registerJQueryHeadroom($);

$("header").headroom();


python310Packages.rich: 12.5.1 -> 12.6.0

Description of changes
https://github.com/Textualize/rich/blob/master/CHANGELOG.md#1260---2022-10-02
Things done

Built on platform(s)

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

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
22.11 Release Notes (or backporting 22.05 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
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[x] Fits CONTRIBUTING.md.

@ofborg eval
passthru.tests build for me, aarch64-linux & macos 10.15


Pseudo packages: src is included in the compiled beam file

... and it shouldn't be!

Hrm, the debug output during the file processing looks correct:
===> Package files for source dir "/private/tmp/my-lfe-lib/src":
[#{package_file => "/private/tmp/my-lfe-lib/src/my/lfe/lib/util/thing.lfe",
   source_file  => "/private/tmp/my-lfe-lib/src/my.lfe.lib.util.thing.lfe",
   source_path  => "/private/tmp/my-lfe-lib/src"}]

The problem seems to happen once the compiler takes over:
===> Config: [{outdir,"/private/tmp/my-lfe-lib/_build/default/lib/my-lfe-lib/ebin"},
                     debug_info,
                     {i,"include"},
                     return,verbose]
===> Compile results: {ok,[{ok,'src.my.lfe.lib.util.thing',[]}],[]}
===>      Compiled my.lfe.lib.util.thing.lfe

In particular, that bit of debug output shows src.my.lfe.lib.util.thing whereas in the package code, there was no extraneous src prefix :-(

Confirmed that the temporary file created is named correctly:
ls -al src/
Permissions Size User       Date Changed Name
.rw-r--r--   223 dmcgreggor  6 Aug 19:18 my-lfe-lib.app.src
drwxr-xr-x     - dmcgreggor  6 Aug 19:18 my
.rw-r--r--   263 dmcgreggor  6 Aug 19:50 my-lfe-lib.lfe
.rw-r--r--    85 dmcgreggor  6 Aug 20:46 my.lfe.lib.util.thing.lfe

lfe_comp:file is being passed these two arguments:

"/private/tmp/my-lfe-lib/src/my.lfe.lib.util.thing.lfe"

 [{outdir,"/private/tmp/my-lfe-lib/_build/default/lib/my-lfe-lib/ebin"},
                 debug_info,
                 {i,"include"},
                 return,verbose]

But it's returning this:
{ok,[{ok,'src.my.lfe.lib.util.thing',[]}],[]}

And generating this:
ls -al _build/default/lib/my-lfe-lib/ebin

Permissions Size User       Date Changed Name
.rw-r--r--  1.3k dmcgreggor  6 Aug 20:43 my-lfe-lib.beam
.rw-r--r--   223 dmcgreggor  6 Aug 20:52 my-lfe-lib.app
.rw-r--r--  1.2k dmcgreggor  6 Aug 20:52 src.my.lfe.lib.util.thing.beam

Oh, fer fock's sake. Bad copy/paste in the test .lfe file. There's no bug here.
Closing as invalid ...


[FEATURE REQUEST] kraken tool kubeconfig

What keywords did you search in Kraken issues before filing this one? (If you have found any duplicates, you should instead reply there.): kubeconfig

Is this a BUG REPORT or FEATURE REQUEST? (choose one): FEATURE REQUEST
If this is a FEATURE REQUEST, please:

Describe in detail the feature/behavior/change you'd like to see.

Ability to use kraken to merge the config file of your choice to your kube config. This will help in the areas of helm and management in general. sub commands should include
-merge
-remove
-backup (optional flag also when performing the above tasks)

this has a high risk of breaking the users environment, we are going to pass for now.


Type in classOf[T] is not added to occurrences in semanticDB

object Main{
  val a = classOf[Int]
}

In the example Int symbol will not be added to occurrences. @sswistun-vl is taking a look at it.

Should we also add the occurence for classOf ? @olafurpg what do you think?

I think we should add occurrences to classOf

I looked into this a bit, and I found that we have the following trees for classOf[...].
classOf[Int]

Literal(
  value = Constant(
    value = TypeRef(pre = ThisType(sym = package scala), sym = class Int, args = List())
  )
)

classOf[List[Int]]

Literal(
  value = Constant(
    value = TypeRef(
      pre = SingleType(
        pre = SingleType(pre = ThisType(sym = package <root>), sym = package scala),
        sym = package object scala
      ),
      sym = type List,
      args = List(TypeRef(pre = ThisType(sym = package scala), sym = class Int, args = List()))
    )
  )
)

This is because

type-checker generate and replace classOf[...] with Literal(Constatnt(...))

https://github.com/scala/scala/blob/5cc8ebbd712ca5a0e051a1075af55bc64ad7a2da/src/compiler/scala/tools/nsc/typechecker/Typers.scala#L4312-L4314
https://github.com/scala/scala/blob/5cc8ebbd712ca5a0e051a1075af55bc64ad7a2da/src/reflect/scala/reflect/internal/TreeGen.scala#L281-L294

While it is possible to extract symbols from types, unlike type tree (like AppliedTypeTree) we can't get position information from Types.


Cake: Use within Cake

Hi, it would be great if some kind of addin, helper or eg to use with Cake.
Thanks

How would GitInfo integrate with Cake? Should it act as a tool that executes msbuild on GitInfo's target file and returns on object with all the metadata collected by GitInfo?


Add additional labels to function deployments

Currently, when we deploy a function as a knative Service, we add two labels boson.dev/function=true and boson.dev/runtime=[runtime]. It might be also useful to add the builder used to create the image. Since the image name and digest are already captured in the Service definition, I don't think that's necessary to add as a label. But would it make sense to allow for a  labels section in func.yaml which would allow developers to easily apply labels to their functions. E.g.
labels:
  type: telegram.message
  botId: language.filter

What do you all think?

Seems like a good idea to me, if there is the need for it now.  Labels is also a very generic concept so our abstraction remains intact (just like our discussion around Secrets).

Agree, good idea.

It might be also useful to add the builder used to create the image

I tried this, but labels have restrictions on the characters that can be used, and a slash as in quay.io/boson-project/some-builder is not acceptable.


Implement new method: Seq#removeAll(Predicate<? super T>)

fix #1367

[Current coverage][cc-pull] is 95.36%

Merging [#1368][cc-pull] into [master][cc-base-branch] will decrease coverage by <.01%

File ...rent/FutureImpl.java (not in diff) was modified. more

Misses 0
Partials +1
Hits -1

@@             master      #1368   diff @@
==========================================
  Files            86         86
  Lines         10086      10094     +8
  Methods           0          0
  Messages          0          0
  Branches       1823       1823
==========================================
+ Hits           9620       9626     +6
- Misses          337        338     +1
- Partials        129        130     +1

Powered by Codecov. Last updated by [1f3ad8d...990889f][cc-compare]
[cc-base-branch]: https://codecov.io/gh/javaslang/javaslang/branch/master?src=pr
[cc-compare]: https://codecov.io/gh/javaslang/javaslang/compare/1f3ad8d5dfefa29bf1b991f490a84d2199af509f...990889fd5746c9a2753d15d333916f3637058138
[cc-pull]: https://codecov.io/gh/javaslang/javaslang/pull/1368?src=pr

Tests slightly redundant, but OK :smile:

looks good, thank you!
/cc @danieldietrich

@paplorinc I made changes by your comments

Many thanks, LGTM!


Bump dependencies

Stuck on location is not defined. Thought it has something to do with $page.query replaced by $page.url.searchParams but doesn't seem to be that.

Okay, reheated and rebased this on master.
Kept SSR off in the end via a src/hooks.js. Probably something to look into later on.
We're at next.286 now so past all the breaking changes, but not latest latest. Didn't want to risk anything I haven't tested. What's here should be fine (including major version bumps).

Now at 1.0.0-next.297 so running latest and greatest.

This is pretty bizarre. For some reason choosing the location call ignores the /area bit leading to errors on the deployed version but it works just fine locally.


Galaga Mode

Summary
Leaving up to @jt-moriarty
TODO

[ ] ???

See https://github.com/jt-moriarty/Super-2021-Swadge-FW-Sandbox

@Dacvak's feedback based on the 12/22 build (which isn't finished, I know)

[ ] Have powerups drift leftward over time
[ ] Add a difficulty option
[ ] Add some incentive to collect powerups later in the game. Maybe have the weapon degrade over time? Maybe require more powerups per weapon upgrade?
[ ] More enemies, more bullet hell!
[ ] Dac offered to do sprite work, but I know you have a person already
[ ] Loved the reflect mechanic

Do a little cleanup from https://github.com/AEFeinstein/Super-2021-Swadge-FW-Sandbox/pull/120, then close this out


Update from development branches

Still writing the paring struct generator. Thinking of an easy algorithm to eliminate all the zeros without affecting performance improvement too much.


Ehancements for Contributors section.

I added default Boostrap classes to the un-ordered list which contains the people that have contributed the project. I also added minimal CSS to space out "The next one can be you. Contribute to this site :)" text from the list itself.

Let me know if you find any issues with this change. Thank you

Looks much better, thank you.
fix #28


[question] Why config file is in ~/Documents?

Summary of the new feature / enhancement
In https://learn.microsoft.com/en-us/powershell/module/microsoft.powershell.core/about/about_profiles?view=powershell-7.3#the-profile-files

Current User, All Hosts
Windows - $HOME\Documents\PowerShell\Profile.ps1
Linux - ~/.config/powershell/profile.ps1
macOS - ~/.config/powershell/profile.ps1

Current user, Current Host
Windows - $HOME\Documents\PowerShell\Microsoft.PowerShell_profile.ps1
Linux - ~/.config/powershell/Microsoft.Powershell_profile.ps1
macOS - ~/.config/powershell/Microsoft.Powershell_profile.ps1

I feel confused: why powershell (in windows) put its config in ~/Documents?
According to standard, it seems to be ~/AppData/Local/ or ~/AppData/Roaming/?
Proposed technical implementation details (optional)
No response

I think it's a historical thing. AppData didn't exist in Windows XP and only appeared with Windows vista. (IIRC)
It should be where  [System.Environment]::GetFolderPath([System.Environment+SpecialFolder]::ApplicationData  points but changing it creates more annoyance than leaving it where it is.

I feel confused: why powershell (in windows) put its config in ~/Documents?

I do not like this too. I think this is due to Microsoft's desire to transfer everyone to the clouds, to OneDrive (where Documents folder is if your account is not local).

Well it's been there long before OneDrive existed, and we're trying to move it out of there partially because of how it interacts poorly with cloud services. So no, that's not why.
I think this is a duplicate of #15552. I'm unsure why it is in documents in the first place (@jhoneill's explanation sounds reasonable) but we're working on moving it.

we're working on moving it

Thanks for your effort!

I think this is a duplicate of #15552.

Looks similar. Close.


Added test for find by display name

According to the docs, it should be possible to find an element based on its display name. I simply added a test to assure that.

I'm not sure why the coverage decreased, since I only added one test to an existing feature.

@marlonbernardes very strange indeed ;P hahaha

The coverage is messed up because of babel... feel free to ignore it.
Also, thanks! This is great. Not sure why i never had this covered :/


new popover impl for model dropdown

Previously the model dropdown (that lets you choose the LLM) used the VSCodeDropdown from @vscode/webview-ui-toolkit. This component (1) does not work nicely with React and React types, (2) is tricky to style owning to how it chose to use slots, and (3) does not support the more complex popover design for this UI component in the Figma.
While this change does not implement that new design yet, it brings in a new popover/select list implementation that will alleviates the problems with VSCodeDropdown and will allow us to implement the more complex popover design.
There are only 2 known changes:

Minor styling differences
When the model dropdown is focused, the up/down arrows do not change the value. You need to press Enter and then use the up/down arrows (or use the mouse).

Related to https://github.com/sourcegraph/cody/issues/3792

Test plan
CI

If we can find a good existing UI component in some library that lets us implement keyboard-accessible lists like in the Figma, we should use it.

Thank you, @philipp-spiess!


HIVE-27317: Temporary (local) session files cleanup improvements

What changes were proposed in this pull request?
When ClearDanglingScratchDir service identifies the dangling sessions to clean HDFS FS, we will be cleaning files/dirs in HiveConf.ConfVars.LOCALSCRATCHDIR (local FS) as well.
Why are the changes needed?
When Hive session is killed, no chance for shutdown hook to clean-up tmp files. This causes accumulation of tmp files/dirs in local FS as below;
> ll /tmp/user/97c4ef50-5e80-480e-a6f0-4f779050852b*
drwx------ 2 user user 4096 Oct 29 10:09 97c4ef50-5e80-480e-a6f0-4f779050852b
-rw------- 1 user user    0 Oct 29 10:09 97c4ef50-5e80-480e-a6f0-4f779050852b10571819313894728966.pipeout
-rw------- 1 user user    0 Oct 29 10:09 97c4ef50-5e80-480e-a6f0-4f779050852b16013956055489853961.pipeout
-rw------- 1 user user    0 Oct 29 10:09 97c4ef50-5e80-480e-a6f0-4f779050852b4383913570068173450.pipeout
-rw------- 1 user user    0 Oct 29 10:09 97c4ef50-5e80-480e-a6f0-4f779050852b889740171428672108.pipeout

Does this PR introduce any user-facing change?
No. The same service will have additional functionality.
How was this patch tested?
Unit test.

@kgyrtkirk there is only one failed test which imho is not related with the patch, please see below;
The test is org.apache.hadoop.hive.cli.TestMiniTezCliDriver#testCliDriver[tez_union_with_udf]
And the reason why it failed;
Caused by: org.apache.hive.com.esotericsoftware.kryo.KryoException: java.lang.OutOfMemoryError: GC overhead limit exceeded

@kgyrtkirk thank you for relaunching. This time all the tests are passed;
All tests are passing
Nice one! This run fixed 45 tests and now all 47675 tests for this pipeline are passing.

But init-metastore for init@oracle failed as below;
[2023-05-05T13:59:42.088Z] waiting for oracle to be available...
[2023-05-05T14:04:48.851Z] timeout reached before the port went into state "inuse"
script returned exit code 1

@sercanCyberVision congrats on your first Apache Hive contribution!

@veghlaci05 please revert !!! builds are taking 6hr now http://ci.hive.apache.org/job/hive-precommit/job/PR-4293/9/

Hi @deniskuzZ
I know I am new at this, and probably missing something, but as I see there is only one build which took 3 hours before this commit.
All other previous and recent builds took around 8.5 hours. Even in once case it is 15 hours;
http://ci.hive.apache.org/job/hive-precommit/job/PR-4383/2/
http://ci.hive.apache.org/job/hive-precommit/job/PR-4381/5/
http://ci.hive.apache.org/job/hive-precommit/job/PR-4376/3/
http://ci.hive.apache.org/job/hive-precommit/job/PR-4366/6/
http://ci.hive.apache.org/job/hive-precommit/job/master/1753/

Hi @deniskuzZ I know I am new at this, and probably missing something, but as I see there is only one build which took 3 hours before this commit.
All other previous and recent builds took around 8.5 hours. Even in one case it is 15 hours;
http://ci.hive.apache.org/job/hive-precommit/job/PR-4383/2/ http://ci.hive.apache.org/job/hive-precommit/job/PR-4381/5/ http://ci.hive.apache.org/job/hive-precommit/job/PR-4376/3/ http://ci.hive.apache.org/job/hive-precommit/job/PR-4366/6/ http://ci.hive.apache.org/job/hive-precommit/job/master/1753/

master is broken and some of the jobs are failing with:
http://ci.hive.apache.org/job/hive-precommit/job/master/1758/testReport/junit/org.apache.hadoop.hive.ql.txn.compactor/TestCrudCompactorOnTez/Testing___split_22___PostProcess___testRebalanceCompactionWithParallelDeleteAsSecondPessimisticLock/

@deniskuzZ can you help fixing this? I think we can just change the permission after creating scratch dir in hdfs in unit test here.
https://github.com/sercanCyberVision/hive/blob/00c63e9645021923dbbef1d868873dbf5a9fc2f2/itests/hive-unit/src/test/java/org/apache/hadoop/hive/ql/session/TestClearDanglingScratchDir.java#L153
Asking your help because I am not able to reproduce the issue. Also checked the other builds, this issue happens in one build out of 6 builds after the commit.

@deniskuzZ can you help fixing this? I think we can clean the scratch dir which is created for the unit test in this PR after test is completed; https://github.com/sercanCyberVision/hive/blob/00c63e9645021923dbbef1d868873dbf5a9fc2f2/itests/hive-unit/src/test/java/org/apache/hadoop/hive/ql/session/TestClearDanglingScratchDir.java#L153
So, the failed tests will create their own scratchdir instead of dealing with the existing one; https://github.com/sercanCyberVision/hive/blob/7c02f733d6251fec3a0fa9537e48817094204dad/ql/src/java/org/apache/hadoop/hive/ql/exec/Utilities.java#L4952-L4957
Asking your help because I am not able to reproduce the issue.

Looks like there was an issue with the agents, so job was running 2x longer. I think we should provide custom scratch dir in the unit tests.

@deniskuzZ
Followed your suggestion and created both session scratch dirs with all the permissions, and checked them;
> ll ql/target/tmp
drwxrwxrwx  3 sercan sercan 4096 Jun 10 13:10 localscratchdir/
drwxrwxrwx  3 sercan sercan 4096 Jun 10 13:10 scratchdir/

The unit test itself is okay anyway, it passed;
[INFO] Results:
[INFO]
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0

But I am not sure how to proceed now :)
Should we revert this solution and create another PR? Or can you add attached patch to your open PR?
scratchDir_permissions.zip


Some small points?!

Hi
Thanks a lot for putting all this together and thanks for your great blog posts on Medium.
Seems there are some small issues with some variables, if I am not wrong. Can you please, check variables such as imagesS and dataS in the section of training the network?
Thanks a lot.
Best
Vahid

Thanks for pointing these out! I had gone through and renamed some of the variables and cleaned up the code, but I missed those. It should all be consistent now.


localization fail at the same spot

Hello. Thanks for the great works!
I am now running hdl_localization using my own data. I made my own PCD using hdl_graph_slam, and have a right format rosbag file.
It has no problem while running on a small pcd map. I found a problem on a bigger map, it fails to localization always on the same spot. See the video in the link (fails around 3:00) :
https://youtu.be/pI-KB9ZZ8tA
Changed parameters are here:
invert_imu -> true
cool_time_duration -> 0.1
When 'invert_imu' is false, it fails to localization a way before that spot when it is true. So I am using 'invert_imu' as true.
Additionally, I have a warning message. I don't know is it related to my problem, but I am posting it :
"[pcl::VoxelGrid::applyFilter] Leaf size is too small for the input dataset. Integer indices would overflow."
Now, I have a question. Do you remember the 'road-flipped' issue of mine? I thought it is related to the IMU data again, so I checked the source code until 'pose_estimator.hpp'  but I couldn't find any error. (I didn't check inside of 'ukf')
Can you tell me how to solve this problem??

I think it is related to the sparse pointcloud map. So it is even get more score to match the road-plane, than to match the others.
Will it be solved when use a dense pcd map ? If it is, Is there any way to make a more dense pcd map in hdl_graph_slam? What parameters should I change?
Best.

Hi @ktk1501 ,
Yes, I think the sparsity of the map may affect the localization. To make the map dense, you can make "min_edge_interval" and "map_cloud_resolution" smaller (increase the density of keyframes and generate the map with smaller downsample resolution).
https://github.com/koide3/hdl_graph_slam/blob/f7a0472bbb0c48be941fbbe5d3d16c8b01b3e3fe/launch/hdl_graph_slam.launch#L87
https://github.com/koide3/hdl_graph_slam/blob/f7a0472bbb0c48be941fbbe5d3d16c8b01b3e3fe/launch/hdl_graph_slam.launch#L126

Hi @koide3 . Thanks for your kind reply.
I had created the dense map after adjusting some parameters. Then, I ran hdl_localization to localize. But I met another problem.
I am using two rosbag file, I just call it first.bag and second.bag. Localization was works really well on fisrt.bag. The problem I met above was on second.bag. But now, after using dense map, I found localization failure on the first.bag.
The localization failure is not look like the one before. It travels to another place, but yes it happens on the same spot.
You can see the video : https://www.youtube.com/watch?v=Oz5kcGG6y3U
What do think the problem is, and it there any known solution??
Best.

I solved this problem by setting "invert_imu" to false. It was my mistake.
Thanks for you reply.
Best.


How to see large datasets in dive similar to the one in overview

In the overview example, it is shown how to render a large dataset using google protocol buffers. There protostr was passed to document.querySelector("#elem").protoInput in cell 4. How can we implement the same thing in dive? In the dive example a record based json string is used with a much smaller dataset. I am trying to test dive using a dataset of larger size.

Whereas overview takes a proto containing the dataset's feature statistics, dive takes records in json format. How large of a dataset are you planning on trying in number of records and features/columns per records? Dive, since it visualizes all data of all records provided to it in the browser, cannot handle huge datasets  - you would need to sample from the dataset and show a subset of data. We often use dive with tens of thousands of records, but not hundreds of thousands. And each record has a handful of features. The more features per record, the smaller number of records that could be handled before browser memory issues.

Closing this issue. Please reopen if necessary.


Allow feeding certificates via buffer (instead of path)

Summary.

I am trying to make a certificate-based request to an external URL using requests.get. I am trying to feed it the output of a call from the crypto library but it only allows paths.

What you expected.

I should be able to feed cert=(certificate, private_key) as part of a request with byte strings instead of file paths (of course in addition to)
This allows one to possibly avoid storing private keys at the path level and instead import a secured container (JKS for example) containing the key

What happened instead.
The request call seems to only take a file path and results in an error unable to find the file:
OSError: Could not find the TLS certificate file, invalid path: b'-----BEGIN CERTIFICATE-----\n...\n-----END CERTIFICATE-----\n
Reproduction Steps
import requests
import crypto

# Omitting argparse, file.read() commands for brevity in this example
p12 = crypto.load_pkcs12(keystoreFile, keystorePassphrase)

# These following commands output the contents of the loaded keystore
# In order to work around the error, they need to be redirected to new files (certificate.file, private_key.file
# These new file paths needs to be provided to the `requests.get` call
cert = crypto.dump_certificate(crypto.FILETYPE_PEM, p12.get_certificate())
caPem = crypto.dump_privatekey(crypto.FILETYPE_PEM, p12.get_privatekey())

resp = requests.get(APIURL, cert=(cert, caPem), verify=False)

System Information
{
  "chardet": {
    "version": "3.0.4"
  },
  "cryptography": {
    "version": "1.9"
  },
  "implementation": {
    "name": "CPython",
    "version": "3.6.1"
  },
  "platform": {
    "release": "16.6.0",
    "system": "Darwin"
  },
  "pyOpenSSL": {
    "openssl_version": "1010006f",
    "version": "17.1.0"
  },
  "requests": {
    "version": "2.18.1"
  },
  "system_ssl": {
    "version": "100020cf"
  },
  "urllib3": {
    "version": "1.21.1"
  },
  "using_pyopenssl": true
}

So this is a sufficiently unusual use-case that we recommend solving this by passing a SSLContext directly. This can be configured with the appropriate client certs loaded from the underlying library as appropriate.
Does that sufficiently address your use case?

Hmm, passing certificates as env variables might also be a good use case here, it is often used in containerized environments.

@deejay1 Given that it's about three lines of product code to write it for your own apps, I'm not sure it's worth adding it to the core library. Again, I think the SSLContext is the best approach.


Demo notebook

Can you provide a demo notebook for how to use PyCodeGPT for code completion and code generation?

There seem to be PyTorch model here (link was provided in the README.md).

Hi, this is the demo code of PyCodeGPT:
import os
import re
import argparse
from tqdm import tqdm

from transformers import pipeline, set_seed
from transformers import AutoTokenizer, AutoModelForCausalLM
from transformers.pipelines.base import Pipeline

def load_generation_pipe(model_name_or_path: str, gpu_device: int=0):
    model = AutoModelForCausalLM.from_pretrained(model_name_or_path)
    tokenizer = AutoTokenizer.from_pretrained(model_name_or_path)

    pipe = pipeline(
        'text-generation',
        model=model,
        tokenizer=tokenizer,
        device=gpu_device
    )

    print("load generation pipeline from {} over, vocab size = {}, eos id = {}, gpu device = {}.".format(
        model_name_or_path, len(tokenizer), tokenizer.eos_token_id, gpu_device)
    )

    return pipe

def extract_function_block(string):
    return re.split("\nclass|\ndef|\n#|\n@|\nprint|\nif", string)[0].rstrip()

def run_code_generation(pipe, prompt, num_completions=1, **gen_kwargs):
    set_seed(123)

    code_gens = pipe(prompt,
        num_return_sequences=num_completions,
        **gen_kwargs
    )

    return [extract_function_block(code_gen["generated_text"][len(prompt):]) for code_gen in code_gens]

pipe = load_generation_pipe("Daoguang/PyCodeGPT", 0)

gen_kwargs = {
    "do_sample": True,
    "temperature": 0.8,
    "max_new_tokens": 150,
    "top_p": 0.9,
    "top_k": 0,
    "pad_token_id": pipe.tokenizer.pad_token_id if pipe.tokenizer.pad_token_id else pipe.tokenizer.eos_token_id,
    "eos_token_id": pipe.tokenizer.eos_token_id
}

prompt = "def say_hello():"

code_gens = run_code_generation(pipe, prompt, num_completions=5, **gen_kwargs)

print(code_gens)

Thanks for following our work.

@zdaoguang Thanks! Love it 👍 Works on my machine too now by changing device=gpu_device to device='cpu'. Working example here.

@zdaoguang
Thanks for sharing the code! Are you able to simplify the code like this one(https://huggingface.co/Salesforce/codet5-large-ntp-py#how-to)?


Should I create encryptor by public key or secret key?

May I know this?
https://github.com/tuneinsight/lattigo/blob/master/ckks/ckks_test.go
Why "testEncryptor" have two ways of creating an encryptor by public key and secret key?
Is there any difference between them? And any difference between the calculation result by encryptors created by public key or secret key respectively?
And I see other testcases all use the encryptor created by secret key. So does it mean encryptor created by public key has any problem, like causing result wrong?
thanks

hi @dragonflight2000,
In term of security, there is no difference between an encryptor using the secret-key or the public-key.
In term of noise, encrypting with the secret-key generate ciphertext with less noise than doing so with the public-key.
Encrypting with the public-key is only tested in rlwe because all the other packages use the rlwe.Encryptor to encrypt.

hi @dragonflight2000,
In term of security, there is no difference between an encryptor using the secret-key or the public-key.
In term of noise, encrypting with the secret-key generate ciphertext with less noise than doing so with the public-key.
Encrypting with the public-key is only tested in rlwe because all the other packages use the rlwe.Encryptor to encrypt.

so is it a better option to use a secret key to create an encryptor rather than to use a public key?
BR

Encryption using the public-key is used by entities that do not have access to the secret-key.
It's probably be a typo, but it doesn't the functionalities.

thank you very much


Customise Ghost port behind reverse-proxy

I'd like to be able to specify a different port for Ghost to run on. I'm running behind a reverse-proxy in Docker so I don't want to forward a host port directly to Ghost; I want to change Ghost itself to run on port 80.
I've tried setting the environment variable server__port: 80, as the Ghost docs suggest this should be interpolated into its configuration. However, this results in an EACCES error.
I can see in the Dockerfile that the port is hard-coded to 2368 in a Ghost config command, so I guess this would need changing to allow a different port to be used. The Ghost docs show that the port can be customised and that config can be read from environment variables so it seems it should be possible to make the port customisable, rather than hard-coding it in the Dockerfile.
Does that sound achievable or have I missed something about how Ghost is bootstrapped that makes this impossible?
Why I want this (background)
I'm building an isomorphic web application, based on Next.js, which will display posts from a Ghost API running in the same Docker stack. Since it's isomorphic, my app needs to access the Ghost API on a consistent URL both from the server and from client web browsers. My development machine has no public URL so accessing the Ghost API from the server needs to route internally through the Docker network. The URL and port used to access the API needs to be the same from within Docker as it is from client web browsers.
One solution would be to forward Ghost's default port from the host machine directly to the Ghost container. My problem with that is I'm likely to run additional projects with a similar setup in future so this will cause port conflicts as soon as I run a second Ghost instance. All my other projects run behind a reverse proxy (Caddy Server) which handles SSL termination and forwards to port 80 on each of my services. I like this setup because it eliminates any chance of port conflicts and minimises the attack surface of my server since I know I can always keep it locked down to just two open ports (80 and 443).
In my mind, the simplest solution is to run Ghost on port 80, set a custom host in my Docker service config to handle internal traffic within the Docker network and configure CaddyServer to forward public requests for the same domain to the Ghost container.

If you're configuring CaddyServer to act as a reverse-proxy, would it be easier to just point CaddyServer at the Ghost container port 2368 instead of port 80?
That said, the reason you're getting an EACCES error when setting the port to 80 is that it's a protected port. Any ports below 1024 are considered "privileged" and as such require root access to run things on them. So, ultimately, Ghost is respecting your environment variable and attempting to bind to port 80, but because it's not running as root it gets an access error.

Hi @acburdine. Thanks for the tip about privileged ports,  I'd forgotten that.
My issue with pointing CaddyServer at Ghost container port 2368 is that CaddyServer isn't listening on that port so I would then need to configure different Ghost URLs in my app depending on whether it's running on a client or server. Since it's an isomorphic app, I'd rather keep to a single URL if possible.

You might be interested in https://github.com/moby/moby/issues/8460#issuecomment-312459310, namely:

$ docker run ... --sysctl net.ipv4.ip_unprivileged_port_start=0 ...

(Requires Linux 4.11+, but works well to remove the silly "privileged ports" restriction that doesn't make any sense inside an isolated network namespace.)

(That and a reverse proxy using the port you want are the only real solutions I see, so if you don't have a kernel that's 4.11 or newer, your only option is unfortunately probably going to be using a reverse proxy in all cases.)

@tianon thanks for the input. Since I'm deploying everything in Docker Swarm Mode stacks I can't use sysctl or cap-add options yet but support for this appears to be on the way so that's something for me to keep an eye on.
In the short term, it looks like my best solution might be to add Ghost's default port to my reverse-proxy and have that forward to my Ghost container.

Makes sense -- so I guess you've got all the information on what your options are here.
I'm going to close since there's nothing actionable for us.  Thanks!
(In the future, these sorts of questions/requests would be more appropriately posted to the Docker Community Forums, the Docker Community Slack, or Stack Overflow.)


Feature Request: Enable Subtitles While Playing a Video

Add a hard key that will cycle through all available subtitles while a video is playing. Maybe KEYCODE_U?

With the way the current remotes have gone to fewer keys or keyboards on remotes, I'll probably have to have an option on the UI to allow changing which subtitle is playing.   With the app now using Exoplayer this is an easier option as ExoPlayer handles displaying of any subtitles

will implement this in 3.0, #401


Store status

Status
READY
JIRA Ticket
SPACON-289
Description
Push the download status of GeoPackage and GeoJson packages through the bridge along with other store status states for all stores.
Todos

[ ] Tests
[ ] Documentation
[ ] License

git fetch --all
git checkout <feature_branch>
./gradlew connectedCheck

@boundlessgeo/spatial-connect

👍


SRVLOGIC-202: Schedule apache-main sync from upstream

Jira:
https://issues.redhat.com/browse/SRVLOGIC-202
IMPORTANT:
Please read the jira comments.
Description of the change:
Set up a GitHub Action to sync our midstream main-apache branch with the upstream main branch every day.
This workflow will run every day at midnight to merge upstream/main to origin/main-apache.
The repository used to test this workflow is fantonangeli/kogito-serverless-operator-fantonangeli-test:
https://github.com/fantonangeli/kogito-serverless-operator-fantonangeli-test/actions
Motivation for the change:
Keep our repository in sync with the upstream Apache repository.
Checklist

[ ] Add or Modify a unit test for your change
[ ] Have you verified that tall the tests are passing?

How to backport a pull request to a different branch?

In order to automatically create a backporting pull request please add one or more labels having the following format backport-<branch-name>, where <branch-name> is the name of the branch where the pull request must be backported to (e.g., backport-7.67.x to backport the original PR to the 7.67.x branch).

NOTE: backporting is an action aiming to move a change (usually a commit) from a branch (usually the main one) to another one, which is generally referring to a still maintained release branch. Keeping it simple: it is about to move a specific change or a set of them from one branch to another.

Once the original pull request is successfully merged, the automated action will create one backporting pull request per each label (with the previous format) that has been added.
If something goes wrong, the author will be notified and at this point a manual backporting is needed.

NOTE: this automated backporting is triggered whenever a pull request on main branch is labeled or closed, but both conditions must be satisfied to get the new PR created.

Review request: @ricardozanini @rgdoliveira

@ricardozanini @rgdoliveira
Please note: to let the Sync CI run, we need to change the default branch to main

@fantonangeli I guess you have permissions to change the default branch to main, right?
If so, you can go ahead and change the default branch to main in all repos.

@fantonangeli I guess you have permissions to change the default branch to main, right? If so, you can go ahead and change the default branch to main in all repos.

I confirm I have the permissions, I can do it right now

@fantonangeli I guess you have permissions to change the default branch to main, right? If so, you can go ahead and change the default branch to main in all repos.

I confirm I have the permissions, I can do it right now
@rgdoliveira
Ooops, I thought I had the permissions as per other repositories, but for this specific one, I cannot change the default branch. Can you please help?


AZ-490: Remove parking_lot mutex from non test code

Wait, scratch that, you haven't removed parking_lot from the deps, and that was, like, a big part of this whole exercise!

Unfortunately parking_lot cannot be removed, as it is used in metrics. The use of parking_lot::mutex is fine there.


[DRAFT] feat: Support just having a main command and spread operator in signature

closing. this is essentially #12 now


[YouTube] Create a compact view in order to emphasize the video titles

Extension
https://www.raycast.com/tonka3000/youtube
Description
I'm the author of the YouTube workflow for Alfred:

After switching to Raycast from Alfred, this is one of the few Alfred workflows that I couldn't stop using. The problem is that the YouTube Raycast extension barely shows the video titles:

I acknowledge the visual appeal of thumbnails, but in this situation, they compromised the selection of a video based on its content, which is best represented by the title.
To address this, I suggest providing a compact view that prioritizes the video titles, even if displaying thumbnails is not feasible.
Who will benefit from this feature?
No response
Anything else?
No response

Switch the view layout in the extension preferences to list instead of grid.

Switch the view layout in the extension preferences to list instead of grid.

Oh, sorry! I can't believe I didn't notice that setting 🫠

No big deal, glad I could help.


Lean 3 backend (take 2)

This set of commits implements a compiler from Lean's core expression type to C++. This is still very much a prototype and needs more testing and features.
I am closing the previous PR and opening a new one since I changed branches, and this second attempt is more tightly integrated with the Lean 3 redesign.
I think there is still a little bit of work left before this code should be merged, I'm currently streamlining the CLI and code, and trying to enable passes to be written in Lean itself.
Previous PR: https://github.com/leanprover/lean/pull/1055

I will merge it during the weekend. I'm flying back to Seattle tomorrow.

Going to do a code review for myself.

Github closed this pull request after I deleted the lean3 branch :(
The master branch is now the old lean3 branch.
Could you open it again?


Changing CommandBlock successCount needs manual block update on comparator

Example code:
CommandBlock.offer(Keys.SUCCESS_COUNT, 5);

After calling this, you need to update the comparator manually for the redstone level to be outputted.

I would say that the TileEntitySuccessCountValueProcessor needs a container.markDirty() before the return.

That would mark the TileEntity for saving. Just doing one of the 5 world.blockupdate methods should suffice


Take multiple arguments in domains buy

Would be useful to check multiple for availability: now domains buy myco.com myco.co.uk
or a text file / stdin?

Sounds like a very good idea!

Thank you for creating this issue!
Please note that – in order for us to be able to handle each feature request with care – we have to consume all of them through a unified pipeline that makes it easier for us to prioritize, track and progress on the features our user base is interested in.
In turn, the Issues tab on this repository is best only be used for reporting bugs, which we can immediately act on.
For well-explained feature requests (like the one you just posted), please contact us at<EMAIL_ADDRESS>so that we can consider adding it to our roadmap.


subprocess.CalledProcessError: Command 'set -o pipefail; export LC_ALL=en_US.utf8 && export LANG=en_US.utf8

Hi. I'm in trouble to run bcbio_nextgen. The subjects have multiple tumors with one paired normal sample. It seemed that ensemble calling was completed, but there are some problems from gemini? (I'm not sure because there are multiple files in  ../work/gemini/ folders including ensemble vcfs and conf/lua files) or peddy?.   I've tried update gemini and other tools and data, but same error occured. I've searched to find similar error (because I solved some problems before), but I have no idea what is wrong....  Could you help me?   the error was like below. Thank you!!
========================================
[2019-12-27T20:08Z] multiprocessing: combine_calls
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_001_tu1: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_001_tu2: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_002_tu1: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_002_tu2: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_002_tu3: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_002_tu4: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_002_tu5: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_002_tu6: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_003_tu1: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_003_tu2: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_003_tu3: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_003_tu4: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_003_tu5: vardict,strelka2,mutect2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_001_CN_N-germline: freebayes,gatk-haplotype,strelka2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_002_CN_N-germline: freebayes,gatk-haplotype,strelka2
[2019-12-27T20:08Z] Ensemble consensus calls for GCMET_003_CN_N-germline: freebayes,gatk-haplotype,strelka2
[2019-12-27T20:08Z] Timing: validation summary
[2019-12-27T20:08Z] Timing: structural variation
[2019-12-27T20:08Z] multiprocessing: detect_sv
[2019-12-27T20:08Z] multiprocessing: finalize_sv
[2019-12-27T20:08Z] Timing: structural variation
[2019-12-27T20:08Z] multiprocessing: detect_sv
[2019-12-27T20:08Z] multiprocessing: finalize_sv
[2019-12-27T20:08Z] Timing: structural variation ensemble
[2019-12-27T20:08Z] Timing: structural variation validation
[2019-12-27T20:08Z] multiprocessing: validate_sv
[2019-12-27T20:08Z] Timing: heterogeneity
[2019-12-27T20:08Z] Timing: population database
[2019-12-27T20:08Z] multiprocessing: prep_gemini_db
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_001_CN_liver_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_001_CN_liver_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_001_CN_liver_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_001_CN_liver_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_001_CN_T_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_001_CN_T_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_001_CN_T_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_001_CN_T_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CN_LND1_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_LND1_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_LND1_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CN_LND1_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CN_T1_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_T1_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_T1_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CN_T1_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CN_T2_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_T2_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_T2_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CN_T2_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CT1_liver1_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CT1_liver1_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CT1_liver1_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CT1_liver1_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CT1_liver2_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CT1_liver2_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CT1_liver2_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CT1_liver2_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CT1_liver3_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CT1_liver3_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CT1_liver3_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CT1_liver3_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CN_LN4_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_LN4_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_LN4_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CN_LN4_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CN_LN6_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_LN6_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_LN6_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CN_LN6_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CN_T_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_T_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_T_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CN_T_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CT1_liver1_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CT1_liver1_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CT1_liver1_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CT1_liver1_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CT1_liver2_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CT1_liver2_tu
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CT1_liver2_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CT1_liver2_tu
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_001_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_001_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_001_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_001_CN_N
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_002_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_002_CN_N
[2019-12-27T20:08Z] Not running gemini, no samples with variants found: GCMET_003_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_N
[2019-12-27T20:08Z] Not running gemini, not configured in tools_on: GCMET_003_CN_N
[2019-12-27T20:08Z] Timing: peddy check
[2019-12-27T20:08Z] multiprocessing: run_peddy
[2019-12-27T20:08Z] Running peddy on /scratch/laki98/GCMET/work/qc/GCMET_001_tu1/peddy/GCMET_001_tu1-effects-annotated-germline.vcf.gz against /scratch/laki98/GCMET/work/qc/GCMET_001_tu1/peddy/GCMET_001_tu1-effects-annotated-germline.ped.
[2019-12-27T20:08Z] Uncaught exception occurred
Traceback (most recent call last):
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; export LC_ALL=en_US.utf8 && export LANG=en_US.utf8 &&  /home/laki98/nextgen/bin/peddy -p 1  --plot --prefix /scratch/laki98/GCMET/work/bcbiotx/tmpwdha8ail/GCMET_001_tu1 /scratch/laki98/GCMET/work/qc/GCMET_001_tu1/peddy/GCMET_001_tu1-effects-annotated-germline.vcf.gz /scratch/laki98/GCMET/work/qc/GCMET_001_tu1/peddy/GCMET_001_tu1-effects-annotated-germline.ped 2> /scratch/laki98/GCMET/work/bcbiotx/tmpwdha8ail/run-stderr.log
' returned non-zero exit status 1.
[2019-12-27T20:08Z] Traceback (most recent call last):
File "/home/laki98/nextgen/bin/peddy", line 11, in
load_entry_point('peddy==0.4.3', 'console_scripts', 'peddy')()
File "/home/laki98/nextgen/anaconda/envs/python2/lib/python2.7/site-packages/pkg_resources/init.py", line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/home/laki98/nextgen/anaconda/envs/python2/lib/python2.7/site-packages/pkg_resources/init.py", line 2852, in load_entry_point
return ep.load()
File "/home/laki98/nextgen/anaconda/envs/python2/lib/python2.7/site-packages/pkg_resources/init.py", line 2443, in load
return self.resolve()
File "/home/laki98/nextgen/anaconda/envs/python2/lib/python2.7/site-packages/pkg_resources/init.py", line 2449, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/laki98/nextgen/anaconda/envs/python2/lib/python2.7/site-packages/peddy/main.py", line 3, in
from .cli import peddy as cli
File "/home/laki98/nextgen/anaconda/envs/python2/lib/python2.7/site-packages/peddy/cli.py", line 17, in
from cyvcf2 import VCF
File "/home/laki98/nextgen/anaconda/envs/python2/lib/python2.7/site-packages/cyvcf2/init.py", line 1, in
from .cyvcf2 import (VCF, Variant, Writer, r as r_unphased, par_relatedness,
File "cyvcf2/cyvcf2.pyx", line 19, in init cyvcf2.cyvcf2
File "init.pxd", line 1038, in numpy.import_array
ImportError: numpy.core.multiarray failed to import
Traceback (most recent call last):
File "/home/laki98/nextgen/anaconda/bin/bcbio_nextgen.py", line 245, in
main(**kwargs)
File "/home/laki98/nextgen/anaconda/bin/bcbio_nextgen.py", line 46, in main
run_main(**kwargs)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
fc_dir, run_info_yaml)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 190, in variant2pipeline
samples = peddy.run_peddy_parallel(samples, run_parallel)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/variation/peddy.py", line 32, in run_peddy_parallel
samples = parallel_fn("run_peddy", [[x] for x in to_run])
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 1003, in call
if self.dispatch_one_batch(iterator):
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 834, in dispatch_one_batch
self._dispatch(tasks)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 753, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 201, in apply_async
result = ImmediateResult(func)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 582, in init
self.results = batch()
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 256, in call
for func, args, kwargs in self.items]
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 256, in
for func, args, kwargs in self.items]
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/utils.py", line 55, in wrapper
return f(*args, **kwargs)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/distributed/multitasks.py", line 24, in run_peddy
return peddy.run_peddy(*args)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/variation/peddy.py", line 103, in run_peddy
do.run(cmd.format(**locals()), message.format(**locals()))
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/home/laki98/nextgen/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; export LC_ALL=en_US.utf8 && export LANG=en_US.utf8 &&  /home/laki98/nextgen/bin/peddy -p 1  --plot --prefix /scratch/laki98/GCMET/work/bcbiotx/tmpwdha8ail/GCMET_001_tu1 /scratch/laki98/GCMET/work/qc/GCMET_001_tu1/peddy/GCMET_001_tu1-effects-annotated-germline.vcf.gz /scratch/laki98/GCMET/work/qc/GCMET_001_tu1/peddy/GCMET_001_tu1-effects-annotated-germline.ped 2> /scratch/laki98/GCMET/work/bcbiotx/tmpwdha8ail/run-stderr.log
' returned non-zero exit status 1.

Hi @biosurgeon!
Sorry about the issues!
Could you please post your yaml config file?
Sergey

Hi, @naumenko-sa
could you check the below my yaml config file?
GCMET_1to3.pdf
Young

Now I skip peddy and the process is on going well. (I just  move the peddy command file into somewhere..)
I think the system used numpy in phython3, not in python2, so it seemed the problem was due to python PATH...
I tried to update numpy but numpy was installed in python3 only and I also moved the updated numpy folder into  python2, but there was another error, (ImportError: cannot import name _distributor_init)
Is there anyone who let me know how  I solve this problem?  Pipeline without peddy will be OK?
Thanks

Hi!
Sorry about the delay in responding!
Peddy is one of the quality control tools:
https://github.com/brentp/peddy
So it is not affecting variant calling. However, peddy works ok in many other projects.
Gemini should not be a problem, as since v1.1.1 we are not creating gemini databases by default.
What version of bcbio are you using? In the last releases many python3/python2 bugs were fixed.  What is your output of: bcbio_nextgen.py -v
Sergey

Hi, Sergey,
Thanks for the reply.
The version of bcbio is 1.2.0a.
I updated bcbio (data and tools) several times, as I hoped it will solve the problem.
There are so many pythons in my system (in server), so I wonder it could be a reason...
Do you have any suggestion?
Thanks
Young
[laki98@master config]$ whereis python
python: /usr/bin/python2.7 /usr/bin/python2.7-config /usr/bin/python /usr/lib/python2.7 /usr/lib64/python2.7 /etc/python /usr/include/python2.7 /home/laki98/nextgen/anaconda/bin/python3.6-config /home/laki98/nextgen/anaconda/bin/python3.6m /home/laki98/nextgen/anaconda/bin/python /home/laki98/nextgen/anaconda/bin/python3.6 /home/laki98/nextgen/anaconda/bin/python3.6m-config / /usr/share/man/man1/python.1.gz
[laki98@master work]$ which python
~/nextgen/anaconda/bin/python

Hi Young!
I think it is typical to have many pythons on a system these days. If you have your bcbio/tools/bin and bcbio/anaconda/bin in the PATH you should be fine. Moreover, for the most tools bcbio unsets PATH and makes sure it calls the tool it has on board.
Looking at your yaml config, I see several potential issues:

batch: [GCMET_001_tu1, GCMET_001_tu2. batch is used to specify a tumor-normal pair. I doubt if a sample could be in two batches at the same time, at least I have not tried it this way. You may try to decouple them and do 2 bcbio runs, or one bcbio run with 4 samples;
min_allele_fraction: 0; it is in %. typically we set it to 5% or 1%. You'd want to filter out false positives. Without UMIs you cannot call these <1% VAF variants.
strelka2 does not support python3, there might be issues: https://github.com/Illumina/strelka/issues/156. We have not used it much last time. You may try to remove strelka from your list.
try to simplify your project; maybe for starters just use vardict for tumor and gatk-haplotype for germline, without ensemble calling. I see, you got this from the documentation, so it is our fault. There we should simplify it, too. Once you get your project finished, you may try a more complex setup.

Sergey

Hi Sergey,
Thanks for the comments and suggestions.
I attach the log file below.
My PATH includes ../nextgen/anaconda/bin and ../nextgen/bin (you mean this? because there is no bcbio/tools/bin to me.. galaxy, genomes, anaconda folders are belong to ../nextgen/ )...

I ran bcbio with multiple samples (maximun 4 tumors with one paired normal, so max 4 tumors in one batch) in other environment and there was no error.. so I thought it works.. but I'll try to decouple them, and compare the outcome. (I'm not sure how long it will take, but I will post the result if possible)
For other three issues (min_allele_fraction, strelka2, simplifying), I'll try.

Thank you so much!!
Young
log_files.txt

HI @biosurgeon !
Closing this issue for now. Please feel free to reopen if you are experiencing any issues!
SN


Outlook (New) not removed

Outlook (New) is not properly removed on Windows 11 23H2 Build 22621.3296
I used -RemoveW11Outlook switch
It seems the script did its job, but the pinned item in the Start Menu is still there so the user can click on it and it will install again.

Heya,
Thanks for taking the time to report this. This has actually been addressed in #35.
In short: pinned apps in the start menu can't easily be removed/edited, but Win11Debloat does have an option to completely clear the start menu of all pinned apps. You'll find this option if you select 'Custom mode' in the script menu.

All other apps are removed except Outlook (New ). It is a newly created profile I was testing on and I didn't run any of those apps or check if they are installed or pinned. I can test a bit more and report. Clearing all pinned items from the Start Menu is not something I want to do, I need the selected app gone :)

All other apps are removed except Outlook (New ). It is a newly created profile I was testing on and I didn't run any of those apps or check if they are installed or pinned. I can test a bit more and report.

That's interesting, could you open powershell and run winget list outlook, this should print out a list of any outlook apps installed on your PC. If you could please post the output or a screenshot of the output here. It's possible that you have a different app variant installed.

Clearing all pinned items from the Start Menu is not something I want to do, I need the selected app gone :)

I definitely understand it's not a good solution if you just want specific apps gone.

I'll test again tomorrow and report. .Thx

On the other Windows 11 installation, Outlook (New) was successfully uninstalled on a brand-new profile. So I don't know what happened on other PCs and will monitor the situation.

Interesting. Was the first installation, where outlook was not correctly uninstalled, connected to the internet during setup?

Thanks for reporting back. I'll close the issue for now, but feel free to open a new issue if this issue persists and/or you are able to reproduce the issue.


Create all for the file cli.py

I add class and non-private functions to all. I'm not sure should I add global variable to the list. Please let me know if it's necessary.

Thanks!


User storage and authentication

Implements user routes and Firebase authentication

No longer being used as branch name changed to feat/backend-user-projects. Requested changes have been made.

Closing as duplicate of #106


[Bug]: Backups for Supabase postgres container

Description
Backups are not enabled for the Supabase postgres container.
I think this can be integrated relatively easy.
I can work on a PR if you can give me a hint where to start.
Minimal Reproduction (if possible, example repository)
In cloud version create Supabase service from template.
Exception or Error
No response
Version
v4.0.0-beta.240

I wrote this script:
backup to S3
and only 14 backups on disk:
#!/bin/bash

DATE=$(date +%Y%m%d%H%M)
BACKUP_DIR="/root/backup_db"
DB_USER="supabase_admin"
DB_NAME="supabase"
S3_BUCKET="backup"
R2_ENDPOINT="https://xxxxxxxxxxxxxx.r2.cloudflarestorage.com/backup"

docker exec supabase-db-n4sww80 pg_dump -U $DB_USER $DB_NAME > $BACKUP_DIR/backup_db-$DATE.sql

aws s3 cp $BACKUP_DIR/backup_db-$DATE.sql s3://$S3_BUCKET/backup_db-$DATE.sql --endpoint-url=$R2_ENDPOINT

find $BACKUP_DIR -type f -name "*.sql" -printf "%T+ %p\n" | sort -r | tail -n +15 | awk '{ print $2 }' | xargs rm -f

Thanks, but it would be great if this could be implemented in coolify - like the backup option for standalone postgres.

This will be in the upcoming version. Supabase uses a different postgresql (fork), that is why it was not available.

There doesn't seem to be a way to restore the backup via the UI. Just a download and delete button

Hey andrasbacsai,
first of all - thank you for your incredible work!
For me it looks like the backup functionality for supabase is indeed implemented but it is not possible to get it running for me.
after you've set up a backup job for the supabase postgres container it queues the job and crashes almost immediately with the following error:
Database: postgres
Status: failed
Started At: 2024-07-08 13:14:35
Message: pg_dump: error: query failed: ERROR: permission denied for schema _analytics pg_dump: detail: Query was: LOCK TABLE _analytics.schema_migrations IN ACCESS SHARE MODE
Size: 0 B / 0 kB / 0 MB
Location: N/A

Hey everyone, same issue here, it returns ‘permission denied for schema _analytics’ and I can’t perform the backup of this database instance.


Launch a modal box instead of doing a redirect

Is there a way to launch a modal with the option for sign-in/sign-up instead tho redirect a whole page?

It would be fabulous if the AWS team could come up with something similar to the Auth0 lock modal !

Hi @udf2457 and @cristianedb, thanks a lot for the feedbacks! I will certainly mark this as feature request and bring it up with my team.

Thank you! I will appreciate this feature


Expanding ZSH prompt with current Terraform workspace name

Hi, I would like a segment for terraform workspace, here we have the plugin for zsh.
https://github.com/robbyrussell/oh-my-zsh/tree/master/plugins/terraform
to be able to do something like
POWERLEVEL9K_LEFT_PROMPT_ELEMENTS=('os_icon' 'todo' 'dir' 'vcs' 'terraform')

Here's a simple custom one you can drop in your .zshrc:
zsh_terraform() {
  # break if there is no .terraform directory
  if [[ -d .terraform ]]; then
    local tf_workspace=$(/usr/local/bin/terraform workspace show)
    echo -n "$tf_workspace"
  fi
}

# Terraform Segment
POWERLEVEL9K_CUSTOM_TERRAFORM="zsh_terraform"
POWERLEVEL9K_CUSTOM_TERRAFORM_BACKGROUND=057
POWERLEVEL9K_CUSTOM_TERRAFORM_FOREGROUND=015

# Add terraform segment to your prompt
POWERLEVEL9K_LEFT_PROMPT_ELEMENTS=(custom_terraform)


File setup.py still contains code for building Allium extension.

The file setup.py needs to be updated to remove Allium references. Will post PR soon-ish.

Fixed in https://github.com/Aareon/chickenticket/commit/8e04839786ef7e24aaec4c9a36eef23b56c77daa
Closing


Typescript under windows?

Normally you use the tsc.exe file to compile typescript on windows. Is it possible to use the current Typescript implementation to use under windows as it seems to use node.
Setting the bin setting to C:\Program Files (x86)\Microsoft SDKs\TypeScript\tsc.exe does not work as it creates the following error:
Error Output: module.js:340

This is a super old question but in case anyone found it through Google like I did. Set the nodeBin parameter to null and it will use the tscBin parameter as a binary instead of a parameter to node.
If you are using this with Symfony, like me, you can do it like this:
filters:     typescript:         node: ~         bin: /path/to/tsc/bin


[ENH] - Move to JupyterLab 4.x

Feature description
It's been over 6 months since JupyterLab 4.x was released and we're still on 3.x.  Upgrade JupyterLab to 4.x
Value and/or benefit
To be able to use latest features and use extensions that are unsupported on JupyterLab < 4.x
Anything else?
No response

Relevant PR: https://github.com/nebari-dev/nebari-docker-images/pull/101

Somewhat related: https://github.com/conda-incubator/jupyterlab-conda-store/issues/29

closed by https://github.com/nebari-dev/nebari-docker-images/pull/101


Remove dummy package

The package has no obvious use and will fail go test ./... for the last time. 🍻
Note that this also removes a Dockerfile.dummy with no obvious consumer. I'd like to clarify before merge what purpose that package had and that this missing docker image won't have any negative impact.

Coverage remained the same at 25.578% when pulling 332f813c848b3c085fb6dc751ab7d3d625e84bec on remove-dummy into 064611f0c6f8de9c6b9c6b6ac8f0f4024607220b on master.

We used it create test nodes at one point but it's fallen behind and isn't used anymore. Purge it.


Update ome-faq.yml

Updated remove encryption conditions

@KCCross  to review and merge

@JohanFreelancer9 - kindly do the copy editor review for this PR. Thanks

@KCCross Please merge this PR. Thanks


Refactor JSON tag parsing

Following on from #617... turns out this was done in 3 places, so I've yanked it out into its own parsing function and added more tests for blank names in JSON tags.
Looks like there's some more duplication and refactoring that can be done here, but I suppose this is a good start.

:+1:  thanks for doing this :)


OS X support

We would like to add OS X support (even if just from a tracking perspective). Are there on ongoing efforts in this direction?

(duplicates #34)
There is no work yet on OS X support. The ptrace facility we use on Linux is not available on OS X, so the tracing part would have to be adapted.
It can probably be built on dtrace, which is a similar system call tracing facility that is available on OS X. I do not know (yet) how that would work, but either we can do that in real time (following events via some sort of API) or get a log of the process tree (via the dtrace(1) utility?). All that remains is translating the events we care about (those who read or write files) into our trace database format. Then the rest should work with minor adaptation.
Let me know if you want to work on this and what I can do to help!
Also note that there might be legal issues involved when distributing packages (or virtual machines to reproduce packages on), but I don't believe anything in the tracing software is illegal.

@remram44 - our goals are a little different. can we capture sufficient information for someone to play back in a similar environment or a different environment. we don't need to be exact. so for us being able to capture, analyze, and augment the config.yml file is more important than  eidetic playback.
a colleague had created this injectable library: https://github.com/vladistan/ProvTrace/tree/master/Mac
also for our needs we would be ok with sudo privileges for tracing.
so the plan is not to be a general purpose replacement but a partial replacement with caveats rather than not having any option.

@satra OS X support is definitely in our todo list, but not a priority right now, in particular because we focus on "almost exact" reproducibility, and as @remram44 mentioned, there might be legal issues involved, etc.
From what you said, you focus more on provenance capture than actually replay, is that correct? If you would like to add OS X support for capturing the provenance, that would be great -- this would be a great addition! Let us know if you want to further discuss these ideas.

a colleague had created this injectable library: https://github.com/vladistan/ProvTrace/tree/master/Mac

An injectable library might be good enough, but for the kind of provenance we want, dtrace might be easier. It looks like getting system call events is very easy (cf /usr/bin/filebyproc.d: one-line...), filtering it and parsing it into our trace.sqlite3 should be doable.


implement "visible" scope

Some progress! But definitely not working yet.
Very much :confused_dog: here. Would love some help,
ideally live at the next community meeting that I can attend.
No need to look at this in advance.
Things to discuss (notes to self):

seems like containment = null is correct for "visible"
scope, and it seems like that's what the code says,
but...vscode begs to differ. halp?

we yield multiple ranges but only one gets used
if primary cursor is offscreen, we get an error
indicating that the range is not found

definition of visible: i propose we leave it up to
VSCode, which mean does not include folded or partially
visible lines. the value of visible is that it does
exactly what it says on the tin.
testing strategy: use lots of newlines?
did I find all the places that need updating?

Fixes #1607

seems like containment = null is correct for "visible"
scope, and it seems like that's what the code says,
but...vscode begs to differ. halp?

What do you mean by containment = null?

we yield multiple ranges but only one gets used
if primary cursor is offscreen, we get an error
indicating that the range is not found

definition of visible: i propose we leave it up to
VSCode, which mean does not include folded or partially
visible lines. the value of visible is that it does
exactly what it says on the tin.

This would be my second proposal in my inline review comment

testing strategy: use lots of newlines?

That's a tough one. We struggle to test visible range stuff because we don't know how big the window is. Probably the best way to test this would be to leverage the fact that the editor is actually an abstract interface, but we haven't done anything like that yet. We will in the future, but I'd be tempted to punt on that. I'd probably just have a test with and without folds and declare victory

did I find all the places that need updating?

I think so. If the test passes you're probably good. In fact you were more thorough than we usually are 😅

Come to think of it, this probably shouldn't be a scope type at all. I think it probably makes more sense as a mark
@AndreasArvidsson wdyt?

What do you mean by containment = null?

You can ignore. I mistakenly thought that the way to return a disjoint/union range was by yielding each of its pieces. Then I noticed that it behaved wrong, tried to figure out why, in my flailing found docs indicating that the wrong containment scope iterator setting would potentially explain the behavior I saw, and assumed that that was wrong.

You can ignore. I mistakenly thought that the way to return a disjoint/union range was by yielding each of its pieces. Then I noticed that it behaved wrong, tried to figure out why, in my flailing found docs indicating that the wrong containment scope iterator setting would potentially explain the behavior I saw, and assumed that that was wrong.

Sorry, I didn't understand anything you said after "You can ignore". But I'm happy to leave it there 😄

Thanks for all the help. PTAL. Note the new commit message.

If I recall correctly, the decision was to implement this one as a modifier for now? Or just close until we understand it better? I'm fine either way

yep, we're going to try it as a modifier. Still in my queue!

@josharian You want me to take this one? Implementing this as a modifier should be easy.

@AndreasArvidsson great! That’d be lovely.

@josharian Your wish is my command ;)
https://github.com/cursorless-dev/cursorless/pull/2094

Breaking news, ChatGPT has no sense of humor.

Closing this. Thanks again, Andreas.

You're very welcome :)


Cucumber vs Gherkin

Cucumber:
  type: programming
  extensions:
  - .feature
  tm_scope: text.gherkin.feature
  aliases:
  - gherkin
  ace_mode: text
  color: "#5B2063"

Something seems off here.
From https://github.com/cucumber/cucumber/wiki/Gherkin :

Gherkin is the language that Cucumber understands.

This mirrors my understanding. The language is Gherkin. Cucumber is but one framework which uses it. There are others, e.g. SpecFlow.

Closing in favor of #3278.


mchem katex plugin

https://mhchem.github.io/MathJax-mhchem/
https://github.com/KaTeX/KaTeX/blob/master/contrib/mhchem/README.md

Probably will not make it built-in, but will expose the setup to make it configurable on user-side

See https://sli.dev/custom/config-katex.html

Old topic, but it took me a while to figure this out, so other people might have the same issue.
It worked for me by creating a dummy ./setup/katex.ts that loads katex/contrib/mhchem:
import "katex/contrib/mhchem";
import { defineKatexSetup } from "@slidev/types";

export default defineKatexSetup(() => {});


Roll forward "Strip Python wheel binary" again

Fix the hash checking mechanism
Upgrade pip before using wheel

Related PR #18276

The prod:grpc/core/experimental/grpc_build_artifacts_multiplatform is passed for this new pull request. I think it is confident that the procedure will work.
https://source.cloud.google.com/results/invocations/00ce2559-8a14-4b51-ada0-401b207640c2/targets
Downsized binary wheels: https://pantheon.corp.google.com/storage/browser/grpc-testing-kokoro-prod/test_result_public/prod/grpc/core/master/macos/grpc_build_artifacts/5300/20190308-121015/github/grpc/artifacts/python_macos_x64_python3.7/

Unfortunately, this turns out to break the linux distrib tests :-(
They started failing here: https://source.cloud.google.com/results/invocations/98c11d21-a520-493c-a566-1b8ebebafee4/log
+ for file in '"$@"'
+ /tmp/tmp.Xt9O7UWrLp/bin/python -m wheel unpack /var/local/jenkins/grpc/input_artifacts/grpcio-1.20.0.dev0-cp27-cp27m-macosx_10_9_x86_64.whl --dest-dir /tmp
usage: __main__.py [-h] {unpack,pack,convert,version,help} ...
__main__.py: error: unrecognized arguments: --dest-dir /tmp
+ return 1
+ FAILED=true
+ '[' '' '!=' '' ']'
+ docker rm -f build_and_run_docker_a638f3ea-3f91-43ba-a553-405b94d1f195
build_and_run_docker_a638f3ea-3f91-43ba-a553-405b94d1f195
+ '[' true '!=' '' ']'
+ exit 1


Split highlight annotation div into multiple divs

This patch aims to fix issue #12504.
Instead of using Annotation::Rect for the div dimensions, we use several divs where dimensions are in QuadPoints and then set mouse handlers on each of them.

/botio-linux test

Unfortunately the reference tests above show a regression for firefox-annotation-highlight-without-appearance-page1. I'll open a new issue for this.

Aside from the things mentioned in follow-up issue #12576, this patch does look exactly like what I would expect code-wise and works fine for the original issue and most other files, so thank you for that!


Issue with permissions when showing journals to players.

This is a minor thing: when a GM shows a player a journal that the player has Owner-level permission to, the journal will display as intended.
However, if the permission is anything less than Owner, the journal will always show up with the default background:

The other features from Stylish Journal seem to still work ok, though.

Well that's interesting. I'll have to investigate why that is. Not sure I can do anything about it, but we'll see.

Fixed in v1.6.1 rolling out soon.

Fixed in v1.6.1 rolling out soon.

Thank you (both for the fix and the great work with this module ;) )


Features implementation

In this pull request I am delivering the features requested by the task assignment as follow:

Rails  App creation as API.
Create a table using PostgreSQL Database to store different greeting messages.
Provide API endpoints that selects a random greeting from the DB table.
Using a controller with an action to deliver the greeting messages.
Added rail routes to the API endpoints.
Testing connections to Frontend.

Hi @mwanawabangona, ( and also @codecaiine )
Please, enlight me... as I have this in my Backend's README.md file:

And in the frontend I have this APIś link (as mentioned in the assignments):

I could not understand your comment (neither the from the previous code reviewer), could you provide me more details on how exactly I should proceed? Thanks in advance.


core: partially address race with native retain on stream state

Description: Our memory model requires a native retain on stream state that must be available for the duration of the lifecycle of the native stream. This partially addresses a race where the retain might not be in place before the stream is reset - resulting in a leak. In order to fully address this, the retain must be completed such that it prevents re-ordering and is visible to other threads.
Signed-off-by: Mike Schore<EMAIL_ADDRESS>

rebased


Fixes some stuffs

Hi,
did you test your changed while the game was not installed?
I think, the vars,php change maybe break it.

I have the game running. I didn't noticed any breaks by moving the includes of vars.php.

I will check this and merge this.

all what he did is working fine :)

Thanks!

Just for notice, this pr break the game, if its not installed.

Yes i have reconized it by installing on a test machine. I will do a pull request again if i have changed it.


Updated Get/Remove and Add-SPOGeoAdministrator

Get-SPOGeoAdministrator
Remove-SPOGeoAdministrator
Add-SPOGeoAdministrator

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.:x: j0rt3g4 sign nowYou have signed the CLA already but the status is still pending? Let us recheck it.

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@j0rt3g4 - please remove the visual studio files.. Only the cmdlet references should be checked in.

You can make sure they are in your  .gitignore  file so they don't get checked in.

I will do it . No problem

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@j0rt3g4  - it looks like the PR is still trying to add some files that aren't cmdlet reference files. Can you check above?

Will do

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update tar up to version 6 but uses old version 2.2

What / Why

I installed the latest version of tar(npm I tar). when I am trying to install react.js in global(npm I -g create-react-app --save) it shows an error(npm WARN deprecated<EMAIL_ADDRESS>This version of tar is no longer supported, and will not receive security updates. Please upgrade asap.)

n/a

Where
npm windows 10

n/a

Who

n/a

References

n/a

This is not a but with node-tar.  npm will only show that warning if something inside your tree is using an older version of tar.  In this case it appears to be tar-pack inside create-react-app
$ npm ls tar
cra@ /Users/wraithgar/Development/npm/scratch/cra
└─┬<EMAIL_ADDRESS>  └─┬<EMAIL_ADDRESS>    └──<EMAIL_ADDRESS>


Example links cut off

On a small display, the example links
advanced search * GO process overview * Genome browser
are cut off to the point where you cant see the genome browser link

It might be nice to knock off a few of the Smart phone tickets soon too, since so many people now seem to use PomBAse on smart phones.
This will be a nice thing to announce when the glitches are fixed.... news item  front page  feature, twitter, pombelist)
...but we don't need to announce individual fixes. We'll just tell people improvements have been made once you are happy

I've improved the display on small screens.

It might be nice to knock off a few of the Smart phone tickets soon too,

I've been slowly chipping away at them.  There are still quite a lot though.
If there are any that are higher priority, let me know.

@Antonialock  could you look through these and flag the ones that should be done before we announce.
If they are only cosmetic we can make them lower priority

It seems you have done them all. The 2 remaining are low priority.

Now down to one (which I can't fix).  It was easier to do them at the same time because they're related.

yeah we aren't so worried about videos....

I've had a quick look around the website on my phone (I have a very large screen) and it looks fine.


Enable null key and value for metadata kafka xlang

Enable nullable keys and values for byte array kafka records when using kafka xlang with metadata.
Imported from Jira BEAM-14297. Original Jira may contain additional context.
Reported by: johnjcasey.

Unable to assign user @johnjcasey. If able, self-assign, otherwise tag @damccorm so that he can assign you. Because of GitHub's spam prevention system, your activity is required to enable assignment in this repo.

this can be closed @damccorm


improve documentation, add doctests, fix bugs found on the way

I realized that after #8 some docstrings I didn't want to include (e.g. _findmin, which hopefully will be gone soon, ref #9) were there, and others didn't exist (e.g. match and explain). So here I've tried to fix that.

preview is at https://beacon-biosignals.github.io/KeywordSearch.jl/previews/PR11/, which you can get from clicking the "details" button in the "documenter deploy" check

Marking as draft since I want to do some more doc changes

Ok, I made a bunch of changes, which I tried to group into clear commits. I found two bugs when improving the docs:

fix_punct wasn't removing \n's, which meant the test in the docstring for word_boundary wasn't passing-- but since it was just a docstring instead of a doctest, I didn't know. I changed fix_punct to catch this, and made the test into a doctest
match_all wasn't defined for NamedQuerys, so I added that and added tests

I decided to embrace doctests, in particular for testing printing, because it's easy to update them if the printing changes (see docs/fix_doctests.jl. I've added a bunch, and added them to runtests.jl so that they get tested as part of CI.
I think the codecov drop is spurious; the lines it says that are not covered are line 31-34 in printing.jl (https://app.codecov.io/gh/beacon-biosignals/KeywordSearch.jl/compare/11/changes#D1L31), but those are covered by the doctests for the show method for Or etc. I think maybe that print_tree_rstrip function is getting inlined and then codecov doesn't see coverage for it?

I rebased after merging the others and fixed an issue with the printing. Not totally sure what happened, but I think doctests are very sensitive to whitespace, i.e. you need to start with the julia> line right after the ```jldoctest line.
I also learned from https://discourse.julialang.org/t/show-and-showcompact-on-custom-types/8493/4 that 3-argument show is preferred over checking compact as I was doing-- that's good to know, because compact wasn't triggering for arrays, only things like Sets An array of Corpuss will use the 2-argument show to print the entries, but a corpus alone will use the 3-argument one, so I use a 1-liner in the 2-argument version and add more details in the 3-argument one.


[DOC] An example demonstrating how to leverage different kernels. We can ideally show how different kernels are useful too on a small simulated data.

          We should have an example demonstrating how to leverage different kernels. We can ideally show how different kernels are useful too on a small simulated data.

Originally posted by @adam2392 in https://github.com/py-why/pywhy-stats/issues/15#issuecomment-1609708052

A related issue is including a few very short-examples of the API in the README.
cc: @bloebp in case you have time to add w/e you were thinking in