Library build

Aim:
Production grade library for pathogen phylodynamics
Ideas:

XMl wrappers for safe model building in BEAST
bacterial phylodynamics module:

species specific configurations / workflows from raw data (TB, MRSA, Kleb...)
clonal expansion coalescent model (CaveDive) [collaboration]
birth-death skyline models (BDSky and MTBD) [based on our papers]

SARS-CoV-2 models for variants and national / subnational configs [collaboration SSI]
Nanopore preprocessing using Random Forests [based on preprint]
integration with Nextflow to run BEAST + BEAGLE on GPU

Features:

pydantic model oriented
dynamic config of models
test suites + docs
user friendly releases
command line interface

Deployment:

FastAPI server + Vue
continuous integration

I'd like to make model classes that can be inherited to define specific sub-models. Models represent configurations of the BEAST XML and are built from XML blocks (beastling.blocks)
from beastling.models import BirthDeathSkylineSerial

class MRSA(BirthDeathSkylineSerial):
    pass

Each model inherits from the base Beastling class.

For the terminal client configuration, it'd be cool if we could use YAML templates that configure the model (and can be default configured by users) and let users modify arguments not provided in the file for on-the-fly command line configuration.
I have a template with the base click library for this, but would rather use Typer so need to check out how to modify the context object (since it depends on click it should be managable)

Something like this in a very basic sense ^^

Very cool 😎 I like this idea. I think having the model specification/XML generation separated from any deployment would be very useful for 3rd parties wanting to use this library. Also would it be possible to cut out the YAML and have users directly specify the models in python (eg dataclass)? This would enable easy dynamic model creation.

Yeah awesome, we should do that! I think the YAML thing still comes from letting users specify their own template for the command line interface, e.g. when users provide a template and configure an empty string for a parameter, the CLI will prompt the user for that specific param (in interactive mode) or it is required to be specified on the command line.
Does that makes sense? That way users can specify their CLI commands for specific models in a template file.
param1: default value
param2: ''
param3: null

In the CLI:
Interactive, prompts user for param2
beastling -i -t template.yaml

Required command line:
beastling --param2 test

Can you explain the dynamic config? I'm not too familiar! Maybe I'm thinking too much on the user end right now.

Yes! I think that’s a great way to do it. I’m just thinking more about it as a library that is consumed by other apps than an application used by users, but both are important. Programmatic control of BEAST config would be very useful and would open up an interface between python and BEAST.


indexpack: ReadUnits passes the digest to the callback with the unit. [phab:D440]

Created by fromberger at 2015-08-01 04:33:48:
The ReadUnits method of an *indexpack.Archive can be used to scan the contents
of the pack, but there is currently no good way for the callback to learn the
digest of the unit it's given.  This change adds an extra argument that passes
the digest string.
Tests and consumers fixed up.

shahms accepted this revision at 2015-08-03 15:07:52

schroederc accepted this revision at 2015-08-03 15:09:03

fromberger closed via commit dc8e23fdf11efa20facf1214292bc029bb675727 at 2015-08-03 15:41:47


[Constraint system] Implement switch support for function builders.

Implement support for switch statements within function builders. Cases can
perform arbitrary pattern matches, e.g.,
tuplify(true) { c in
  "testSwitchCombined"
  switch e {
  case .a:
    "a"
  case .b(let i, _?), .b(let i, nil):
    i + 17
  }
}

subject to the normal rules of switch statements. Cases within function
builders cannot, however, include “fallthrough” statements, because those
(like “break” and “continue”) are control flow.
The translation of performed for switch statements is similar to that of
if statements, using buildEither(first:) and buildEither(second:) on
the function builder type.
This is the bulk of switch support, tracked by rdar://problem/50426203.

@swift-ci please smoke test

@swift-ci please test source compatibility

@swift-ci please smoke test

@swift-ci please smoke test


Windows filesystem does not allow ":" used in timestamp

Running the code on Windows fails. No ":" allowed in filenames.
Timestamp in main.py needs to be changed to timestamp = time.strftime("%Y%m%d-%H-%M-%S") or similar.

Hey thanks for this heads-up. We have never run experiments on Windows so did not realize this. Feel free to change this locally.

Of course I had changed it locally already. Just felt to let you know about the issue.
Closing an easy to fix bug without making the fix is an interesting approach. 🤔
Never mind, who is using windows anyway 😉

I have added a bullet point in README for this issue. One reason I do not want to change this at the moment is that there are a lot of parsing scripts built based on the current format of logging files. At the current moment I find it hard to make sure all parsing functions will still work okay. However, the whole evaluation and result analysis are going to change a lot so that is why I decide to let people to handle this locally if they encounter a similar issue with a pointer to this issue.

@zifanw505
If possible can you add a tutorial on implementing this paper?
It will be really helpful for new interns trying to implement this paper.


Migrate to HerbSpecification.jl

HerbData.jl has been deprecated in favor of HerbSpecification.jl. I've updated the benchmarks to use the new Problem type that includes a problem name field and arrays of IOExamples instead of Examples for the problem specification.
Closes #9 and #16.
The package will not precompile, and tests won't pass until https://github.com/Herb-AI/HerbGrammar.jl/pull/54 is merged (and released, I guess?), thus, the draft PR.
The refactor I needed to do involved more than renaming symbols (I had to copy the variable name for each problem to the name field of the constructor), so I scripted it. In case anyone wants to take a peak, the script is in a branch here.

Hijacking the PR to update to HerbGrammar=0.2.0 and HerbCore=0.2.0 conventions.
Grammar -> AbstractGrammar

Sorry, ironically made a mess of this PR by rebasing/cleaning up commits. It's now rebased on dev to reflect the changes from the SyGuS PR. Should be ready for review/merge @THinnerichs

I will re-add the formatting we had, i.e. new line for each IOExample.


joplin-desktop: 2.12.18 -> 2.13.6

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/project/joplin/versions.
meta.description for joplin-desktop is: An open source note taking and to-do application with synchronisation capabilities
meta.homepage for joplin-desktop is: https://joplinapp.org
Updates performed

Version update

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
found 2.13.1 with grep in /nix/store/2y7qia4smg3fyzz25ggw4lgq049x9q6f-joplin-desktop-2.13.1
found 2.13.1 in filename of file in /nix/store/2y7qia4smg3fyzz25ggw4lgq049x9q6f-joplin-desktop-2.13.1

Rebuild report (if merged into master) (click to expand)

1 total rebuild path(s)

1 package rebuild(s)

First fifty rebuilds by attrpath
joplin-desktop

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/2y7qia4smg3fyzz25ggw4lgq049x9q6f-joplin-desktop-2.13.1 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A joplin-desktop https://github.com/r-ryantm/nixpkgs/archive/07f390490ea2a899383ce1fde76a1bb6f831e9d1.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/07f390490ea2a899383ce1fde76a1bb6f831e9d1#joplin-desktop

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/2y7qia4smg3fyzz25ggw4lgq049x9q6f-joplin-desktop-2.13.1
ls -la /nix/store/2y7qia4smg3fyzz25ggw4lgq049x9q6f-joplin-desktop-2.13.1/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

1 package built:

joplin-desktop

Maintainer pings
cc @HugoReeves @qjoly for testing.

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/project/joplin/versions.
meta.description for joplin-desktop is: An open source note taking and to-do application with synchronisation capabilities
meta.homepage for joplin-desktop is: https://joplinapp.org
Updates performed

Version update

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
found 2.13.2 with grep in /nix/store/c11szdcyhmyfwsxcy0ms30mn2adi4jm7-joplin-desktop-2.13.2
found 2.13.2 in filename of file in /nix/store/c11szdcyhmyfwsxcy0ms30mn2adi4jm7-joplin-desktop-2.13.2

Rebuild report (if merged into master) (click to expand)

1 total rebuild path(s)

1 package rebuild(s)

First fifty rebuilds by attrpath
joplin-desktop

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/c11szdcyhmyfwsxcy0ms30mn2adi4jm7-joplin-desktop-2.13.2 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A joplin-desktop https://github.com/r-ryantm/nixpkgs/archive/05802c4878a402f13ba591a2182f35ca84cbff31.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/05802c4878a402f13ba591a2182f35ca84cbff31#joplin-desktop

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/c11szdcyhmyfwsxcy0ms30mn2adi4jm7-joplin-desktop-2.13.2
ls -la /nix/store/c11szdcyhmyfwsxcy0ms30mn2adi4jm7-joplin-desktop-2.13.2/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

1 package built:

joplin-desktop

Maintainer pings
cc @HugoReeves @qjoly for testing.

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/project/joplin/versions.
meta.description for joplin-desktop is: An open source note taking and to-do application with synchronisation capabilities
meta.homepage for joplin-desktop is: https://joplinapp.org
Updates performed

Version update

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
found 2.13.6 with grep in /nix/store/rqz8ff71vh0as28h6csq8l84nrmb2frx-joplin-desktop-2.13.6
found 2.13.6 in filename of file in /nix/store/rqz8ff71vh0as28h6csq8l84nrmb2frx-joplin-desktop-2.13.6

Rebuild report (if merged into master) (click to expand)

1 total rebuild path(s)

1 package rebuild(s)

First fifty rebuilds by attrpath
joplin-desktop

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/rqz8ff71vh0as28h6csq8l84nrmb2frx-joplin-desktop-2.13.6 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A joplin-desktop https://github.com/r-ryantm/nixpkgs/archive/c3cc25c972c57780ac37ae8b736f09c34f9e1d12.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/c3cc25c972c57780ac37ae8b736f09c34f9e1d12#joplin-desktop

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/rqz8ff71vh0as28h6csq8l84nrmb2frx-joplin-desktop-2.13.6
ls -la /nix/store/rqz8ff71vh0as28h6csq8l84nrmb2frx-joplin-desktop-2.13.6/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

1 package built:

joplin-desktop

Maintainer pings
cc @HugoReeves @qjoly for testing.

Closed by #281166.


KAFKA-2614; No more clients can connect after TooManyConnectionsException threshold (max.connections.per.ip) is reached

Call ConnectionQuotas.decr when calling Selector.close and when disconnections happen.
Expand SocketServerTest to test for this and to close sockets.
Refactor and clean-up SocketServer and Acceptor to make the code easier to understand.

Tests passed locally.

System tests passed: http://jenkins.confluent.io/job/kafka_system_tests_branch_builder/97/

@junrao Fixed the issue you mentioned, tests passing locally. I also moved some comments I had mistakenly left on the commit into the "Files changed" tab so make the review easier.

Thanks for the patch. LGTM


fix: update IAM protos

This PR was generated using Autosynth. :rainbow:
Here's the log from Synthtool:
synthtool > Executing /tmpfs/src/git/autosynth/working_repo/synth.py.
synthtool > Ensuring dependencies.
synthtool > Pulling artman image.
latest: Pulling from googleapis/artman
Digest: sha256:0e6f3a668cd68afc768ecbe08817cf6e56a0e64fcbdb1c58c3b97492d12418a1
Status: Image is up to date for googleapis/artman:latest
synthtool > Cloning googleapis.
synthtool > Running generator for google/pubsub/artman_pubsub.yaml.
synthtool > Generated code into /home/kbuilder/.cache/synthtool/googleapis/artman-genfiles/js/pubsub-v1.
.eslintignore
.eslintrc.yml
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/support_request.md
.jsdoc.js
.kokoro/common.cfg
.kokoro/continuous/node10/common.cfg
.kokoro/continuous/node10/docs.cfg
.kokoro/continuous/node10/lint.cfg
.kokoro/continuous/node10/samples-test.cfg
.kokoro/continuous/node10/system-test.cfg
.kokoro/continuous/node10/test.cfg
.kokoro/continuous/node12/common.cfg
.kokoro/continuous/node12/test.cfg
.kokoro/continuous/node8/common.cfg
.kokoro/continuous/node8/test.cfg
.kokoro/docs.sh
.kokoro/lint.sh
.kokoro/presubmit/node10/common.cfg
.kokoro/presubmit/node10/docs.cfg
.kokoro/presubmit/node10/lint.cfg
.kokoro/presubmit/node10/samples-test.cfg
.kokoro/presubmit/node10/system-test.cfg
.kokoro/presubmit/node10/test.cfg
.kokoro/presubmit/node12/common.cfg
.kokoro/presubmit/node12/test.cfg
.kokoro/presubmit/node8/common.cfg
.kokoro/presubmit/node8/test.cfg
.kokoro/presubmit/windows/common.cfg
.kokoro/presubmit/windows/test.cfg
.kokoro/publish.sh
.kokoro/release/docs.cfg
.kokoro/release/docs.sh
.kokoro/release/publish.cfg
.kokoro/samples-test.sh
.kokoro/system-test.sh
.kokoro/test.bat
.kokoro/test.sh
.kokoro/trampoline.sh
.nycrc
.prettierignore
.prettierrc
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
README.md
codecov.yaml
renovate.json
samples/README.md
synthtool > Replaced '  }\n\\s*/\\*\\*\n\\s+\\* The DNS address for this API service\\.' in src/v1/subscriber_client.js.
synthtool > Replaced '../../package.json' in src/v1/publisher_client.js.
synthtool > Replaced '../../package.json' in src/v1/subscriber_client.js.
synthtool > Replaced 'https:\\/\\/cloud\\.google\\.com[\\s\\*]*http:\\/\\/(.*)[\\s\\*]*\\)' in src/v1/doc/google/protobuf/doc_timestamp.js.
synthtool > No replacements made in src/**/doc/google/protobuf/doc_timestamp.js for pattern toISOString\], maybe replacement is not longer needed?
npm WARN deprecated<EMAIL_ADDRESS>Please note that v5.0.1+ of superagent removes User-Agent header by default, therefore you may need to add it yourself (e.g. GitHub blocks requests without a User-Agent header).  This notice will go away with v5.0.2+ once it is released.

><EMAIL_ADDRESS>postinstall /tmpfs/src/git/autosynth/working_repo/node_modules/core-js
> node scripts/postinstall || echo "ignore"

Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!

The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
> https://opencollective.com/core-js
> https://www.patreon.com/zloirock

Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)

><EMAIL_ADDRESS>postinstall /tmpfs/src/git/autosynth/working_repo/node_modules/protobufjs
> node scripts/postinstall

><EMAIL_ADDRESS>prepare /tmpfs/src/git/autosynth/working_repo
> npm run compile

><EMAIL_ADDRESS>compile /tmpfs/src/git/autosynth/working_repo
> tsc -p . && cp -r src/v1 build/src/ && cp -r protos build/ && cp -r proto build/ && cp smoke-test/*.js build/system-test && cp test/*.js build/test

npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY<EMAIL_ADDRESS>(node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for<EMAIL_ADDRESS>wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

added 960 packages from 1353 contributors and audited 6075 packages in 31.025s
found 0 vulnerabilities

><EMAIL_ADDRESS>fix /tmpfs/src/git/autosynth/working_repo
> eslint --fix '**/*.js' && gts fix

installing<EMAIL_ADDRESS>installing<EMAIL_ADDRESS>synthtool > Cleaned up 2 temporary directories.
synthtool > Wrote metadata to synth.metadata.

@alexander-fenster still trying to wrap my head around some of these changes. It looks like maybe this is adding support for an options object, but there was no change to the gapic or documentation, is that a bug? Or am I just way off on this one?

@callmehiphop IAM protos (the source for JSON compilation) are now taken from ./node_modules/google-gax/protos, and they come there from nodejs-proto-files. The changes actually reflect the current state of IAM protos (from what I see).
I can only explain the changes by my mistake when I made several PRs from my local workspace and seems like I screwed up the generated protos :)
We can merge this now, and I'm pretty sure no new changes will come after that.

@alexander-fenster awesome, thanks for breaking it down for me!


Solve the scalability issue around fix_data.yaml files

The Flutter team has been using data-driven fixes for a while and the data file used to power those fixes is now 4348 lines long. That’s hard to read and hard to maintain. Requiring that all of the data be in a single file, while it makes it easy to find the data, isn’t scalable. We need to work with Michael and Kate to define a new structure for the data that will scale over time.

Duplicate of https://github.com/dart-lang/sdk/issues/47941


"Borșa" is listed in the drop-down menu

Description:
When user writes "Borșa" the location appears in the drop-down menu next to the comune and the county which is a part according to the law
Precondition:
The website is up an running.

Step 1
Write in the search bar "Borșa"
Expected results
The location appears in the drop-down menu as "Comuna Borșa, CLUJ"


pick_final_models.div.py references Robetta

Hello,
Fantastic work and thank you so much for releasing this to the public! I have encountered several issues with running trRosetta2 on Ubuntu:

some dependencies, like scikit learn had to be installed manually
the DB variable is not passed properly to all SStor_pred scripts, I had to change the paths in the main*.py files from /projects/ml/ manually myself
On a single Nvidia Geforce RTX 2080 Ti I quickly run out of memory when the Tensorflow library is loaded during trRefine. I fixed this by setting the conda environment variable "conda env config vars set TF_FORCE_GPU_ALLOW_GROWTH=true" and limiting the CPUs to 4 for this single step (other steps I use 20 CPUs)
during the DeepAccNet-msa step I get the following error:
`/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found/home/robetta/rosetta_server_beta/bin/lddt: not found

/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
/bin/sh: 1: /home/robetta/rosetta_server_beta/bin/lddt: not found
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/patchy/anaconda3/envs/casp14-baker/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home/patchy/anaconda3/envs/casp14-baker/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/patchy/trRosetta2/trRefine/pick_final_models.div.py", line 70, in calc_lddt_dist
lddt_1 = float(os.popen("/home/robetta/rosetta_server_beta/bin/lddt -c %s %s | grep Glob"%(pose_i, pose_j)).readlines()[-1].split()[-1])
IndexError: list index out of range
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/patchy/trRosetta2/trRefine/pick_final_models.div.py", line 113, in
raw_dist = pool.map(calc_lddt_dist, args)
File "/home/patchy/anaconda3/envs/casp14-baker/lib/python3.6/multiprocessing/pool.py", line 266, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/patchy/anaconda3/envs/casp14-baker/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
IndexError: list index out of range`
The problem is that trRosetta2/trRefine/pick_final_models.div.py has the following lines 70-71 referencing to a Robetta function.
lddt_1 = float(os.popen("/home/robetta/rosetta_server_beta/bin/lddt -c %s %s | grep Glob"%(pose_i, pose_j)).readlines()[-1].split()[-1])     lddt_2 = float(os.popen("/home/robetta/rosetta_server_beta/bin/lddt -c %s %s | grep Glob"%(pose_j, pose_i)).readlines()[-1].split()[-1])
Any idea how to circumvent this? Thank you!

Ah nevermind, I just figured out that lddt is already part of the trRosetta2 package! I changed the path to reference trRosetta2/lddt/lddt and now everything works!

Also I just noticed crop="dicont" should be crop="discont" in run_pipeline.sh

@martinpacesa could share the code that you fix? Thanks.

What error are you getting? It really is just a question of adjusting the proper paths, because in some cases the paths are fixed.

I have now changed the paths to relative ones. Some other bugs were fixed too. You may pull the updated code and try once again.

line 68 in run_pipeline.sh still says crop="dicont"

fixed this one too. thanks for catching all these bugs!

Glad to help, thanks for sharing the code!!
I had one question, do you think there is a protein size limit that I can fold on a single 11Gb GPU? I just noticed that a 900AA protein ran fine, but with 1000AA the tensorflow gave a memory error. Just wondering if it's related or I have some other problem there.

GPU memory should not be a problem for trRosetta if crop="discont" is used in step 5 of the pipeline. trRefine (step 7) may fail though on bigger proteins because of insufficient GPU memory. Which step is causing errors in your case?

I had it during trRefine, like I said, anything below 900AA ran fine, I am now running a 1400AA protein to see if I get the same error. This is the error I got during the folding of the 1000AA protein (from trRefine.stderr):
trRefine.txt

From what I found, this error might come from when the tensorflow tries to allocate bigger memory chunks, is it possible to make it allocate smaller chunks?

I have managed to solve the issue by reducing the limit for cropping to 500:
if [ $LEN -gt 500 ] then     crop="discont" else     crop="cont" fi
Is there a downside to reducing it from 700?

crop="discont"  works better for big proteins and is a bit more accurate at recapitulating domain-domain interactions compared to crop="cont". The latter on the other hand gives a bit more accurate predictions for individual domains. We haven't benchmarked this thoroughly but I feel that reducing $LEN down to 500 should be fine.

Thank you for the answer! I will keep the 500 value for now and report back if I see any issues.

Okay, so after I have pulled the newest version of the code from github, I get the following error right after running hhsearch:
/home/patchy/trRosetta2/run_pipeline.sh: line 53: 14657 Segmentation fault      (core dumped) $HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr -v 0 > $WDIR/log/hhsearch.stdout 2> $WDIR/log/hhsearch.stderr
HHBLITS and PSIPRED seem to run fine but the hhsearch error log is empty

I have 128 Gb of RAM and don't see it running out of memory, I did not have issue with the previous version of the code where hhsuite was called locally

I can confirm the segmentation fault only happens during the hhsearch step and only in the newly built conda environment, in the environment built in the previous version it works fine

Removing the hhsuite from the conda environment fixes the segmentation fault error, I could not figure out why it occurs though.

I am still having trouble folding proteins above 800AA with the RTX 2080 Ti with 11 Gb VRAM. During the trRefine step, the tensorflow module runs out of memory. Obviously ideally I would get more VRAM, but currently it's hard to get your hands on a set of two graphics cards around here (thanks crypto). Is there a way to run trRefine on the CPU?

Yeah, we are also having same issues with long proteins. An easy workaround is to run trRefine on a cpu  by modifying line #131 of the run_pipeline.sh script to:
CUDA_VISIBLE_DEVICES="" python $PIPEDIR/trRefine/run_trRefine_DAN.py -msa_npz $WDIR/t000_.msa.npz \

In my tests it takes around 10 mins to process a 1300aa-long protein using 4 cpu cores and 32gb of RAM.

Thanks a lot for the tip!!! I will give it a go and let you know.

Yeah, we are also having same issues with long proteins. An easy workaround is to run trRefine on a cpu by modifying line #131 of the run_pipeline.sh script to:
CUDA_VISIBLE_DEVICES="" python $PIPEDIR/trRefine/run_trRefine_DAN.py -msa_npz $WDIR/t000_.msa.npz \

In my tests it takes around 10 mins to process a 1300aa-long protein using 4 cpu cores and 32gb of RAM.

This did not seem to work for me, I get the following error. As far as I understand it's due to my CPU architecture?
trRefine.txt


Something cause the skins folder to be backed up and cleared

Before Reporting

[X] I found no existing issues matching my bug
[X] My issue is not caused by the Millennium interface inside Steam (Themes, Plugins & Update Panel). If it is, make a issue report in this repo.
[X] My issue is not caused by a theme

Describe the Bug
What situation can cause the skins folder to be backed up and cleared.
Expected Behavior
How can I avoid this from happening.
Steps To Reproduce
I don’t know
Operating System
Windows
Anything else?
No response

Specific items in the skins folder will be deleted if they in the skin.json they have github information. This tells Millennium the theme is supposed to be a GitHub repository, and if it isn't a github repository, i.e. it doesn't contain a .git folder, Millennium assumes its broken and backs it up and re-clones the live version from GitHub.
If you're looking to fix this on a specific theme, just remove the github section from the skin.json and it will stop. Keep in mind it will also stop the theme from getting updates though too.

Okay, I got it


nerdfont conflicts with audit 2.6.6 which stalls the display manager (lightdm) and prevents login to x

Issue description
nerdfont causes lightdm to halt \ delay for a prolonged time after audit was updated to 2.6.6.
Steps to reproduce
minimal configuration.nix for build-vm: https://gist.github.com/RamKromberg/a12c04bd24ba91e1faf4f7b1dd7b5faf

The configuration.nix linked above is far from minimal ... A minimal config would be something like
{ pkgs, ... }:
{
  services.xserver.enable = true;
  fonts.fonts = [ pkgs.nerdfonts ];
  # Strictly unecessary, lets us test login if we get that far:
  users.mutableUsers = false;
  users.users.foo = { isNormalUser = true; password = "foo"; };
}

To assess interaction audit, build one config with boot.kernelParams = [ "audit=0" ] and one without.

the issue disappeared without a good explanation. disk fragmentation causing a prolonged disk search was proposed... a bit flipping after the build was complete (disk error) was also mentioned.
Regardless, I'm no longer able to reproduce the issue on either metal no vm so I'm closing it down.

the issue reappeared... a workaround and a theory explaining the problem were proposed... I'll keep the issue open until something lands in unstable \ unstable small for me to check since people might need the workaround if they stumble on the same issue.

@RamKromberg did you re-open this issue intentionally?

@the-kenny Yeah. It was gone one minute and back the next. There was some irc discussions regarding how the font cache is built and some package changes... But I didn't follow up on the technical details and I haven't tested the proposed solution (as opposed to the nix.useSandbox = true; workaround) or heard if it ever ended up in master so I can't close this just yet.
Since it happened in the unstable-small channel, very few people would have noticed it when it happened. So, in case this leaks to other channels, I'm keeping this open so if someone runs into this they'll know about the workaround at least.

I'm closing this since I've cut back to using just a handful of font packages and can't be bothered downloading and compiling the 3+ gb of fonts necessary to test the problem.


iOS 9.xxx.xx

First time when an app goes in background, it stops working. After resuming then sending app in background 2nd time and so on works perfectly. Any solution for this.

As for me it's not working on iOS 9.3.2 (iPhone 4S), the sound fades out quickly when I press the home button. I tried going back and forth to the app but the sound always fades out.
I'm using the cordova-plugin-media  plugin to read a webradio stream.
@shahidj Are you also using the cordova-plugin-media  plugin?
On Android I see the notification appear and the I can still hear the sound (but even without this plugin, I can still hear the sound, at least for some time, or if I don't open too many other apps).


$j (...).lobiPanel is not a function

Hi
I'm having an issue regarding the tooltip function. I'm also using 2 jQueries available on my page.
Here is the error message throwing every time i click the tooltip:
$j (...).lobiPanel is not a function
Here is the arrangement of my sources:
link rel='stylesheet' href='css/jquery-ui.min.css'/>
link rel='stylesheet' href='css/bootstrap.min.css'/>
link rel='stylesheet' href='css/lobipanel.min.css'/>
script type='text/javascript' src='js/jquery.1.11.min.js'>
script type='text/javascript' src='js/jquery-ui.min.js'>
script type='text/javascript' src='js/bootstrap.min.js'>
script type='text/javascript'>
var $j = jQuery.noConflict(true);
/script>
script type='text/javascript' src='js/lobipanel.min.js'>
I don't know if there's a conflict between 2 jQueries or what. Thanks in advance for the help :)

This is to close the issue. the script "


caravel/tasks.py ?

Seems it got removed in this commit https://github.com/airbnb/caravel/pull/974, not sure if it was on purpose or not
Let me know if i'm totally missing something.
Thanks
Caravel version
master branch
Expected results
caravel worker
should fire up some async workers
caravel/tasks.py ? seems to have disappeared
Actual results
Starting SQL Celery worker.
Celery broker url:
redis://caravel-redis:6379/0
Traceback (most recent call last):
  File "/usr/local/bin/caravel", line 155, in <module>
    manager.run()
  File "/usr/local/lib/python2.7/dist-packages/flask_script/__init__.py", line 412, in run
    result = self.handle(sys.argv[0], sys.argv[1:])
  File "/usr/local/lib/python2.7/dist-packages/flask_script/__init__.py", line 383, in handle
    res = handle(*args, **config)
  File "/usr/local/lib/python2.7/dist-packages/flask_script/commands.py", line 216, in __call__
    return self.run(*args, **kwargs)
  File "/usr/local/bin/caravel", line 151, in worker
    c_worker.run(**options)
  File "/usr/local/lib/python2.7/dist-packages/celery/bin/worker.py", line 212, in run
    state_db=self.node_format(state_db, hostname), **kwargs
  File "/usr/local/lib/python2.7/dist-packages/celery/worker/__init__.py", line 95, in __init__
    self.app.loader.init_worker()
  File "/usr/local/lib/python2.7/dist-packages/celery/loaders/base.py", line 128, in init_worker
    self.import_default_modules()
  File "/usr/local/lib/python2.7/dist-packages/celery/loaders/base.py", line 121, in import_default_modules
    tuple(maybe_list(self.app.conf.CELERY_INCLUDE))
  File "/usr/local/lib/python2.7/dist-packages/celery/loaders/base.py", line 103, in import_task_module
    return self.import_from_cwd(module)
  File "/usr/local/lib/python2.7/dist-packages/celery/loaders/base.py", line 112, in import_from_cwd
    package=package,
  File "/usr/local/lib/python2.7/dist-packages/celery/utils/imports.py", line 101, in import_from_cwd
    return imp(module, package=package)
  File "/usr/local/lib/python2.7/dist-packages/celery/loaders/base.py", line 106, in import_module
    return importlib.import_module(module, package=package)
  File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
ImportError: No module named tasks

Steps to reproduce
just run caravel worker

@wyndhblb , module is called now sql_lab.
Caravel worker works on master and airbnb_prod branches.
Please change CELERY_IMPORTS = ('caravel.tasks', ) to CELERY_IMPORTS = ('caravel.sql_lab', )

Much thanks  .. figured i was missing something.


tests_l2: Remove workaround for fixed issue #107

Remove GPU workload workaround for https://github.com/intel/intel-technology-enabling-for-openshift/issues/107. Issue fixed in >= OCP 4.14.11 version
Signed-off-by: vbedida79<EMAIL_ADDRESS>

LGTM


Added isJson and isXML functions to Response class

Two new functions have been added to check if the response return is json or xml

This could be really useful; in a lot of my Connectors, I do things like this:
public function hasRequestFailed(Response $response): ?bool
{
    // if psr response is json
    $contentType = $response->getPsrResponse()->getHeader('Content-Type');

    if (in_array('application/json', $contentType)) {
        return ! empty($response->json('errors'));
    }

    return null;
}

This PR would simplify it like this:
public function hasRequestFailed(Response $response): ?bool
{
    if ($response->isJson()) {
        return ! empty($response->json('errors'));
    }

    return null;
}

I would argue, though, that I prefer a more strict comparison than str_contains() proposed in this PR.

@SRWieZ Thank you for your support.


chore(deps): upgrade dependencies

Upgrades project dependencies. See details in workflow run.

Automatically created by projen via the "upgrade-main" workflow

Codecov Report

Merging #52 (330cd0d) into main (c706ca9) will not change coverage.
The diff coverage is n/a.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
@@           Coverage Diff           @@
##             main      #52   +/-   ##
=======================================
  Coverage   77.74%   77.74%
=======================================
  Files          11       11
  Lines         364      364
  Branches       32       32
=======================================
  Hits          283      283
  Misses         81       81

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Performance optimizations for Intel CPUs

In this issue some performance optimizations for multi-core CPUs were offered.
I prepared these as a pull-request. Also, I added SW prefetching, which helps to improve performance additionally.
It was tested for HIGGS data set (1m x 28) in comparison with Intel® DAAL.

Intel® DAAL
Current XGBoost
Proposed changes

Time, ms
1344
8600
4238

HW: Intel(R) Xeon(R) Gold 5120 CPU @ 2.20GHz (2 sockets, 14 cores per socket).
Parameters:
"objective": "binary:hinge", "max_depth": "6", "eta": "0.3", "min_child_weight": "0" (DAAL's analog: minObservationsInLeafNode=0), "tree_method", "hist", "n_estimators": "50"
Accuracy before and after my changes - the same: 72.306801.
Some additional optimizations can be done: e.g. parallelization by nodes, optimization of "ApplySplit" functions.

Thanks a lot for assembling this pull request. I will review it and make fixes to pass CI tests.
In the longer run, we can also tweak compiler flags to take advantage of latest features of Intel CPUs. Not all of these flags can be merged into the master CMake build due to compatibility reasons, but we can make a special pre-built binary distribution for AWS C5 instances (which has AVX512).

@RAMitchell I recall you mentioning some failure cases that was triggered by using single-precision float for the accumulator variable. Can you share some examples?

Looks like it may be okay after some experimentation with large datasets. I am not sure how I reached the previous conclusion.

('YearPredictionMSD', 'Time(s)')
('YearPredictionMSD', 'Train RMSE')
('YearPredictionMSD', 'Test RMSE')
('Synthetic', 'Time(s)')
('Synthetic', 'Train RMSE')
('Synthetic', 'Test RMSE')
('Higgs', 'Time(s)')
('Higgs', 'Train Accuracy')
('Higgs', 'Test Accuracy')
('Cover Type', 'Time(s)')
('Cover Type', 'Train Accuracy')
('Cover Type', 'Test Accuracy')
('Bosch', 'Time(s)')
('Bosch', 'Train Accuracy')

xgb-gpu-hist (single precision)
18.9042
7.80142
8.88601
23.2389
13.369
13.5223
18.9742
0.750733
0.747206
64.3457
0.909576
0.892335
12.8371
0.995123

xgb-gpu-hist (double precision)
18.8883
7.79193
8.88281
24.439
13.3822
13.5334
23.429
0.750603
0.747163
67.2516
0.908491
0.891793
12.0918
0.995085

@RAMitchell The change happens within    CPU histogram, if one change GradStat to float some tests should fail.

@SmirnovEgorRu I don't think GHistEntry is parameterized, so currently, no. We'll merge it once the tests pass.

@SmirnovEgorRu Let me know if you need help passing the CI.

@hcho3, looks like it is passed now.
Can we commit it?

@hcho3, yes, you can update, of course.
Do I need to do something here from my side?

@SmirnovEgorRu Make sure to check on "Allow Edits from Maintainers"

Looks like it may be okay after some experimentation with large datasets. I am not sure how I reached the previous conclusion.
('YearPredictionMSD', 'Time(s)')	('YearPredictionMSD', 'Train RMSE')	('YearPredictionMSD', 'Test RMSE')	('Synthetic', 'Time(s)')	('Synthetic', 'Train RMSE')	('Synthetic', 'Test RMSE')	('Higgs', 'Time(s)')	('Higgs', 'Train Accuracy')	('Higgs', 'Test Accuracy')	('Cover Type', 'Time(s)')	('Cover Type', 'Train Accuracy')	('Cover Type', 'Test Accuracy')	('Bosch', 'Time(s)')	('Bosch', 'Train Accuracy')
xgb-gpu-hist (single precision)	18.9042	7.80142	8.88601	23.2389	13.369	13.5223	18.9742	0.750733	0.747206	64.3457	0.909576	0.892335	12.8371	0.995123
xgb-gpu-hist (double precision)	18.8883	7.79193	8.88281	24.439	13.3822	13.5334	23.429	0.750603	0.747163	67.2516	0.908491	0.891793	12.0918	0.995085

@RAMitchell May I ask how do you run gpu hist with double precision? Thanks

@hcho3 any news here?
Can I help here? With defines or something else.

@trivialfis FYI, this is another reason why we should prefer CMake over Makefile, since CMake lets us explicitly test the existence of specific compiler intrinsics such as _mm_prefetch and __builtin_prefetch. With Makefile, we'll have to be overly conservative when adopting compiler intrinsics because we can't test their existence.

@trivialfis Can you take a look at this PR to see if it can be made compatible with your PR #3825?

@hcho3 Please ignore  #3825 and go ahead finishing this PR.  I will take care of the remaining rebase.  After all this one is more important I think.

Codecov Report

Merging #3957 into master will increase coverage by 4.36%.
The diff coverage is 65.51%.

@@             Coverage Diff              @@
##             master    #3957      +/-   ##
============================================
+ Coverage     56.35%   60.72%   +4.36%
============================================
  Files           186      130      -56
  Lines         14775    11722    -3053
  Branches        498        0     -498
============================================
- Hits           8327     7118    -1209
+ Misses         6209     4604    -1605
+ Partials        239        0     -239

Impacted Files
Coverage Δ
Complexity Δ

include/xgboost/base.h
100% <ø> (ø)
0 <0> (ø)
:arrow_down:

src/common/hist_util.h
73.91% <100%> (-7.34%)
0 <0> (ø)

src/common/hist_util.cc
42.61% <64.91%> (-0.12%)
0 <0> (ø)

src/linear/updater_shotgun.cc
91.07% <0%> (-2.6%)
0% <0%> (ø)

src/gbm/gblinear.cc
12.34% <0%> (-2.12%)
0% <0%> (ø)

src/gbm/gbtree.cc
17.1% <0%> (-1.57%)
0% <0%> (ø)

src/learner.cc
26.37% <0%> (-0.65%)
0% <0%> (ø)

src/tree/param.h
86.5% <0%> (-0.42%)
0% <0%> (ø)

python-package/xgboost/core.py
77.38% <0%> (-0.06%)
0% <0%> (ø)

... and 88 more

Continue to review full report at Codecov.

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Provide capability to perform DB sync against project/model for the scale unit DB

This applies to OneBox only environments, where DBsync will go against the main (hub) environment's db.

This is for targeting the Scale Unit DB with DbSync when UseSingleOneBox == true (i.e. both Hub and Scale Unit is found on the same machine), where VS makes it easy to sync single models and perform full sync against the default DB, there is nothing such for the Scale Unit DB.
This functionality should be added to a new menu, unrelated to the scale unit setup itself, but rather a toolbox of QoL tools.

closed by PR #67


[FEATURE REQUEST] Auto-update on dropdown

A feature request. Maybe instead of having to click the update button to refresh the table. Maybe have the table refresh everytime either dropdown is triggered, regardless of selection.

This was popular enough to get two issues submitted, so I intend to make this as a change in the future.


DialogConfirm (two buttons) does not show dialog on Android

I'm using the code similar to this
NativeDialog.OpenDialog("Title", "Description", "Yes", "No", () => Debug.Log("Yes"), () => Debug.Log("No");
Using logcat, the following error was thrown
AndroidJavaException: java.lang.NoSuchMethodError: no static method with name='ShowDialogConfirm' signature='(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Z)V' in class Lcom.pingak9.nativepopup.Bridge;
Is there a way to fix this error?

I bypass this error by remove cancelable MobileNative.showDialogConfirm
javaUnityClass.CallStatic("ShowDialogConfirm", title, message, yes, no, cancelable);
-> javaUnityClass.CallStatic("ShowDialogConfirm", title, message, yes, no);


Notice: Trying to access array offset on value of type bool

in file modules/ps_buybuttonlite/controllers/admin/AdminAjaxPs_buybuttonliteController.php (line 129)
        $image_data = Image::getBestImageAttribute($id_shop, $id_lang, $id_product, $id_product_attribute);
        $id_image = $image_data['id_image'];

Module version 1.0.1

Thanks @dobra947 for the report.
Ping @PrestaShop-maintainers : this repo allow issue on it.

Ping @PrestaShop/prestashop-maintainers

Ping @PrestaShop/prestashop-maintainers

I suppose this is because this repository was once on https://github.com/prestashopcorp organization and was transferred to this organization


Remove LESS

This should get us all the way to completing #56. @battletoilet, please have a look at the build process to see if I've missed anything.

Have you checked out the copy/build steps in FabricBuild.js?

Where is FabricBuild.js?

Overall, looks really good. Biggest issue I can see is a lack of SASS linting/error reporting now that LESS is no longer part of the build at all.
Also, this probably doesn't need to be addressed in this PR, we should consider whether we need some of the leftover config bits from supporting 2 preprocessors, e.g. running a task for setting SassMode explicitly (it's the only mode now) and the sassExtension prop in Config.js.

Also, please remove component-manifest-template.less--that's no longer needed either.


Online deployment

Re-did the online deployment code to work with the local whitening, and the event detection all seems to work.

[x] Write strain ~(and whitened strain)~ from around events in addition to network output
[ ] ~Center events in timeseries?~

For sure! We've had two triggers at the 1/day level, the first corresponding to this superevent. The latter, at<PHONE_NUMBER>, doesn't correspond to anything in GraceDB

Additional to-do: Ran in to RuntimeError: Missing FrEndOfFile structure, which ended the run. Need to figure out why that happens, or just add something to ignore it when it does.

@wbenoit26 did this happen during read_channel? If so, sounds like another edge case of weird things that can happen when you try to read a frame (hey there's another entendre) that hasn't fully written yet. Basically all the checks in there are meant to address that exact problem, so could be worth just adding another check for that error message and sleeping for a tick.

Yeah, I think that's probably the right call. I just want to check whether it's something that gets fixed after a second, or if the file will need to be skipped entirely.

@wbenoit26 Another todo thats not necessary for this PR would be to query iDQ log likelihood channel for events. The iDQ channel should be distributed in the same frames as the strain. Taking a maximum +- 1s from the event time or something like that should be good.

@EthanMarx I think it would be good to get this into the repo for the review process


cc-runtime: Fix kernel param handling & update collect script

Update cc-runtime submodule for two main reasons:

config: Allow user-specified kernel params to take priority
https://github.com/clearcontainers/runtime/commit/feed1be89e391110ab54d330815f7a73029e01ac

Update data collection script to work with Kata.

Changes:
a63895e versions: Update kernel version
7bf93e2 release: Clear Containers 3.0.16
1412ff8 cc-env: Remove "CC" from output.
5e7d03c vendor: Update virtcontainers vendoring
f515c21 vendor: Update Gopkg.toml for new prune syntax
ef63d36 vendor: Remove constraints from packages not directly vendored
ab1a9f1 build: Add bug URL to help output
719f523 scripts: Fix collect script bug URL
93c71c9 cc-check: Document "unrestricted_guest" requirement
0f8b25d scripts: Ignore qemu startup message
7310433 scripts: Update collect script for Kata
feed1be config: Allow user-specified kernel params to take priority
e7de45d usage: Show project URL in help output
b45d46c release: Clear Containers 3.0.15
e65682c docs: remove references to Clear Containers proxy service

Fixes #27.
Signed-off-by: James O. D. Hunt<EMAIL_ADDRESS>

#24 is merged, I think you can retrigger CI now.
LGTM if CI is green again

Thanks @WeiZhang555. Branch updated.

need an ack from one of @kata-containers/runtime
Just to check @jodh-intel , whilst here, anything new we can pick up with a rebase ?

LGTM


RFP - starleaf

Checklist

[x] The package I am requesting does not already exist on https://chocolatey.org/packages;
[x] There is no open issue for this package;
[x] The issue title starts with 'RFP - ';
[x] The download URL is public and not locked behind a paywall / login;

Package Details
Software project URL : https://support.starleaf.com/installing/starleaf-app/#Mass-dep
Direct download URL for the software / installer : https://s3.eu-central-1.amazonaws.com/downloads3.starleaf.com/app/StarLeaf-Installer-Windows.msi
Software summary / short description: Videoconferencing tool, similar to Zoom/MS Teams.
Dependencies
.NET Framework 4.6
Comments
The .msi does not have version numbering, so i think you will always get the latest version?

Status: Review
https://chocolatey.org/packages/starleaf

Status: Published
https://chocolatey.org/packages/starleaf


Add support for opening a terminal emulator

@exactly-one-kas
why all of these #include  are needed?

hmm for some reason it does not work with flatpak. I will check out
If you go into the CI summary you can download the flatpak package for testing.

@exactly-one-kas
We in the lineedit you are able to enter every command you would like to enter. So you can enter also rm -r /home/$USER. Can it be a problem?
If you change the config file of Gittyup (adding rm -r /home/$USER to the terminal section) and then open Gittyup and try to open the terminal, it will delete everything. Maybe instead of a lineedit, we should only allow specific consoles? And if one would like to have a different one we have to add it.

I'd say if you can write to the user's home folder, you can also put stuff in autostart / .bashrc, so I wouldn't consider this to be security critical
Also the way to open a specific terminal can change over time:
Currently my terminal commandline on Windows is "C:\Program Files\WezTerm\wezterm-gui.exe" start --cwd .
Before a GUI mode wrapper existed I used a custom script to hide the Windows native console.

I cherry picked commit f8c2f0b437d805939aa87c109c02add077708e9a (Fix missing QPainterPath includes, 12th July 2020) to fix build errors.
I'll try and rebase the branch onto the current master to see if that'll fix the flatpak issue - this is a pretty old branch after all

Yes rebase, then I will put the flatpak fixes on top of it

Should we show a small message box if no terminal was found? I fixed the flatpak issue, but for some reason I am not able to create a merge request to your branch.

I'll merge you changes and add a message box

Thank you! I changed also your C Style string list to QStringlist. Was that ok?

That's fine by me

I don't know how I merged the master branch into this one. @kas-luthor Can you merge the Gittyup/open-terminal into your branch and then merge also master into it?

@exactly-one-kas have you started adding a Message Box? Otherwise I will have a look into it so we can merge this one

@stefanknotzer Can you review it too? Especially the last commit

looks fine for me. @stefanknotzer is it fine for you too, then I will merge.


Also clear notifications when deleting a resource.

/cc @lamont-granquist @jkeiser @thommay
This implements https://github.com/thommay/chef-rewind/commit/b69c9a510f1e7a85132dff0ee26fd883192ea12d for the new fancy API.

dangling references are clearly bad...
👍

I'm trying to think through what kind of weirdness could exist with nested contexts any notifications in a different run_context. Also this could still leave dangling subscribes I think?

Sweet, thanks!

The way i wrote the nested contexts notification stuff, at least for delayed notifies it should only queue up on the run_context that contains the resource.


Capture System.IO.InvalidDataException in PackageArchiveReader

Fixing issue https://github.com/NuGet/NuGetGallery/issues/2917

@maartenba , @xavierdecoster :sunflower:

Looks good! :shipit: from my side but maybe @xavierdecoster also wants to have a look at it

:shipit:


There are some references in metadata files to IRI https://spec.edmco…

…uncil.org/fibo/ontology/FND/Utilities/Values. They are not needed and can be safely removed.
Signed-off-by: Robert Trypuz<EMAIL_ADDRESS>Fixes: #43

Values ontology has been removed from VS.


Update README.md

Fix the broken links.

I think the .md links with relative paths are transformed to .html links with relative paths when published to github.io: https://github.blog/2016-12-05-relative-links-for-github-pages/

The generated mlir docs will never work browsing the repo unless we check them in but the platform docs can probably be reworked to work in both places. Here's the code that deploys them: https://github.com/Xilinx/mlir-air/blob/main/.github/workflows/generateDocs.yml#L93-L99 if anyone wants to play with it.

I see, this seems to be a bigger issue than I thought. According to the explanation in Steve's link, the correct form is to write:
[a relative link](another-page.md)
Which gets translated to the appropriate HTML page automatically when published.
Is there a way to test github.io without checking in this commit?

The generated mlir docs will never work browsing the repo unless we check them in but the platform docs can probably be reworked to work in both places. Here's the code that deploys them: https://github.com/Xilinx/mlir-air/blob/main/.github/workflows/generateDocs.yml#L93-L99 if anyone wants to play with it.

Maybe use this instead? https://github.com/actions/deploy-pages

I see, this seems to be a bigger issue than I thought. According to the explanation in Steve's link, the correct form is to write: [a relative link](another-page.md) Which gets translated to the appropriate HTML page automatically when published. Is there a way to test github.io without merging this commit?

I don't think so, but I'd support experimenting here for a bit. We can always revert the changes.

@jnider You can experiment on your own fork and it'll build an associated github.io for it.

I tested it on my own fork as @jackl-xilinx suggested and it works, according to the formatting in the link posted by @stephenneuendorffer .
You can see the .md files browsing the source tree here: https://github.com/jnider/mlir-air/tree/main/docs
And the .html files deployed on github.io (redirected to my personal domain name) here: http://joel.nider.org/mlir-air/
So at least those links can be updated but it doesn't solve the problem for the generated mlir docs.


Could you bump standard to the latest version (5.3.1) please?

Thanks!
Makes a difference:
// Standard 5.2.1 says this is all clean
// Standard 5.3.1 reports correctly 'Unexpected whitespace before semicolon'
for (var _y = moment().format('YYYY'); _y >= 1924 ; --_y) {
  su.yearOptions.push({year: _y, abbrev: _y})
}

+1

There is a pull-request out for upgrading standard to the latest: https://github.com/ricardofbarros/linter-js-standard/pull/89

Hello guys, @devTristan PR fixed this. From now on it will try to use the local standard (project's node_modules/) instead of the bin inside this package. Many thanks to @devTristan


Fix the missing PROMPT assignment if HL_PRINT_MODE is off

When I set HL_PRINT_MODE to off, I expected to get:

but instead, I get:

These changes apply the default prompt settings in any mode

This behavior is intended. Both the prompt and precmd modes have issues, so the off option is there if someone wants to print it themselves. That's really the only use case I considered for this mode. For example, one might assign the computed output from HL_OUTPUT_SEP and HL_OUTPUT_INFO to PROMPT in their own precmd hook.
If for whatever reason someone wants to use Headline without the separator and information lines (a use case I did not consider), it's easy enough to assign PROMPT directly:
HL_PRINT_MODE=off
PROMPT=$HL_PROMPT

The fix for Ctrl + L when HL_THIN=on looks good. Thank you!

This behavior is intended. Both the prompt and precmd modes have issues, so the off option is there if someone wants to print it themselves. That's really the only use case I considered for this mode. For example, one might assign the computed output from HL_OUTPUT_SEP and HL_OUTPUT_INFO to PROMPT in their own precmd hook.
If for whatever reason someone wants to use Headline without the separator and information lines (a use case I did not consider), it's easy enough to assign PROMPT directly:
HL_PRINT_MODE=off
PROMPT=$HL_PROMPT

Thanks for responding. I made a small update to the PR, but I have three objections:

We have only one place where the 'off' mode is working: in the 'if' condition. In the 'else' branch, we simply set PROMPT=$HL_PROMPT in the own hook. So, if anyone wants to rewrite the prompt, they can do it after sourcing the theme. It’s also possible to save the prompt before sourcing the theme, in case you want to preserve the system prompt.

# source ...

add-zsh-hook precmd my-hook
my-hook() {
  PROMPT="->"
}

Why would I use the theme if the 'off' mode returns me to the default prompt?

The RPROMPT is being modified in 'off' mode anyway. It’s unexpected, considering that 'off' mode should fully disable the theme.

That else branch re-assigns the PROMPT variable every time the prompt is printed, so the only way to override is with another hook. Not difficult, but more involved a single PROMPT=$HL_PROMPT. That said, my hypothetical use case for the off mode requires a hook anyway, so my point is moot.
Good question. I guess I don't understand why you would use the off mode. If you set HL_PRINT_MODE to off and don't manually print the HL_OUTPUT_SEP and HL_OUTPUT_INFO, what are you left with? Just the error and clock features? Would be much simpler (and more performant) to just set PROMPT='%(#.#.%(!.!.$)) ' instead of sourcing this whole theme.
A very good point. I am inconsistent about the meaning of off. It should either assign both PROMPT and RPROMPT or neither. After this discussion I am leaning towards your preference of assigning both in all print modes.

So, we have HL_PRINT_MODE set to "off," which controls whether the separator and info line should be printed. Additionally, we have HL_SEP_MODE, which can prevent the printing of the separator. In my opinion, it would be better to remove the "off" mode from HL_PRINT_MODE since the info part of the theme is its main feature, as you mentioned. Should I commit this change?

So, we have HL_PRINT_MODE set to "off," which controls whether the separator and info line should be printed. Additionally, we have HL_SEP_MODE, which can prevent the printing of the separator. In my opinion, it would be better to remove the "off" mode from HL_PRINT_MODE since the info part of the theme is its main feature, as you mentioned. Should I commit this change?

I like this. To keep things simple, I will merge your PR as it is now and remove the off option myself (since I need to change documentation too).
Again, thank you for your contributions


Clippy is missing in integrations tests

@mgattozzi Hi, I have added "clippy" feature in integrations tests, please check #15

@mgattozzi PS, I could also update .travis.yml for clippy feature

@mgattozzi should I close this?

@mgattozzi should I close this?

Ah no need to close I'm just not great at following up on my oss projects unless I get directly pinged which gives me a phone notification. I'll take a look now!

Ah no need to close I'm just not great at following up on my oss projects unless I get directly pinged which gives me a phone notification. I'll take a look now!


A text label that is displayed when the user hovers over a blank area

Bug, feature request, or proposal:
Bug
What is the expected behavior?
A text label that is displayed when the user hovers over a mat-icon element.
What is the current behavior?
A text label that is displayed when the user hovers over a blank area on the right of a mat-icon element.
What are the steps to reproduce?
If the icon name is 'information', a text label that is displayed when the user hovers over a blank area on the right of a mat-icon element.
But the icon name is 'home', the behavior is normal.
Please refer to the StackBlitz starter: https://tinyurl.com/y9b25qya
Which versions of Angular, Material, OS, TypeScript, browsers are affected?
Angular 6, 7, 8, 9

Duplicate of https://github.com/angular/components/issues/11826.


FIX-#6594: fix usage of Modin objects inside UDFs for apply

What do these changes do?

The PR also fixes https://github.com/modin-project/modin/issues/4919

[x] first commit message and PR title follow format outlined here

NOTE:  If you edit the PR title to match this format, you need to add another commit (even if it's empty) or amend your last commit for the CI job that checks the PR title to pick up the new PR title.

[x] passes flake8 modin/ asv_bench/benchmarks scripts/doc_checker.py
[x] passes black --check modin/ asv_bench/benchmarks scripts/doc_checker.py
[x] signed commit with git commit -s
[x] Resolves #6594
[x] tests added and passing
[x] module layout described at docs/development/architecture.rst is up-to-date

@Retribution98 could you check why test__reduce__ failed on unidist?
The error: KeyError: <weakref at 0x0000025BB1211220; to 'MasterDataID' at 0x0000025BB0F900A0> (that crashed python).

@dchigarev could you approve again?

could you please also elaborate on how the changes fixes the problem?

@dchigarev ready to merge


Related assets

add related info to asset info
display assets in stats in a list instead of a table
group related assets below the parent asset

What kind of change does this PR introduce?
feature

Did you add tests for your changes?
yes

Does this PR introduce a breaking change?
yes, stats output and format changed

What needs to be documented once your changes are merged?

stats.relatedAssets allow to show related assets (they are hidden by default)

What about emitAsset for loaderContext? Can we implement assetInfo for this too? But I think we should do it in separate PR

https://github.com/webpack/webpack/blob/42aabc735160f248dcdc6442aaeb4b803e257146/lib/NormalModule.js#L458
Already supported

display assets in stats in a list instead of a table

Can I get the old behavior somehow via config? I find the new output a little too hard to read.

@wojtekmaj it is still beta, please put your opinion here https://github.com/webpack/webpack/issues/10534


Documentation update - public/sym folder must be writable by web user

Detailed description of the problem
Documentation about setting the file/folder permissions does not include public/sym. Improper permissions on that folder will cause uploading/importing to fail and will cause the gallery to not function at all. Error in the logs:
[2019-11-19 01:21:04] local.ERROR: unlink(/opt/Lychee-Laravel/public/sym/4f50c4f526b1ab51a8e69ade8ad75a6a6af2af2e950f0b89be28fadbafbc7a59.jpg): No such file or directory {"exception":"[object] (ErrorException(code: 0): unlink(/opt/Lychee-Laravel/public/sym/4f50c4f526b1ab51a8e69ade8ad75a6a6af2af2e950f0b89be28fadbafbc7a59.jpg): No such file or directory at /opt/Lychee-Laravel/app/SymLink.php:99)

Steps to reproduce the issue
Steps to reproduce the behavior:

Install following the documentation
Upload or import a photo

@dgptamayo Thanks! Should be fixed now.

See:

https://github.com/LycheeOrg/Lychee-Laravel/wiki/Install
https://github.com/LycheeOrg/Lychee-Laravel/wiki/Install-Steps-on-Debian-Testing


Add derive path

Add derive path
Upgrade wookong-solo to 0.1.4
Path not send to device due to new firmware needed.

Plan to add new command 'select' for switch multi seed.
fn get_seed_amount() ->u32
fn select(public_key, path) -> Result<<Self::Pair as TraitPair>::Public>;
fn choose(index) -> Result<<Self::Pair as TraitPair>::Public>;

any updates?

@kianenigma We are working on the firmware part https://github.com/wookong-dot/sr25519-embedded-c
As soon as it is finished, we will test it with subkey and may submit fixes.

@burdges the implement of soft derive in schnorrkel calls 'witness_bytes' in 'derive_secret_key' which need rand_hack() to get random number for nonce. Could you please make it the 'attach_rng' to let extern random in to do that?

It's now fixed in master, thanks!  I created that problem when I removed the Clone bound on transcripts.  I fixed it by adding a derive_key_simple_rng method in https://github.com/w3f/schnorrkel/commit/ad2190b1c0bbb204690a9959f7cb9427cb073273

@burdges Thanks a lot. It works well.

Any update?

We finished the derive work in the firmware but realized we need deliver another EVB to you for the test. That will not be a good way since the update will come up constantly. So we decide to find some way to simulate the behavior of firmware on desktop OS. QEMU is the first choice and I found some samples written in RUST, so I  can not hold myself to try to use RUST to write entire firmware.... Not a wise plan and wasted a lot of time. So may be you could close this PR and we will do it again when ready.

Okay :)


Team/franchise Info

Thanks for the extensive docs, much appreciated!
One thing I haven't been able to find is detailed team info (old url: https://statsapi.web.nhl.com/api/v1/teams/{teamID}). An endpoint that returns things like division/conference, venue name, site url, first year of play, etc. Has anyone found an endpoint that has those?

I have not been able to find any such endpoint. I suppose the simplest path forward is to maintain a list locally from now on. This seems okay to me as the info is fairly static.
Dropping the csv I've used should anyone need to borrow: teamInfo2022_23.csv

Here's an updated version for the 24-25 season for those interested with Utah added and Arizona dropped.  Also updated a few arena names as well as added a franchiseId column to correspond with the NHL API.
teamInfo2024_25.csv


How to obtain the number of detected object per image for MAE&RMSE

Describe the feature
Motivation
It is inconvenient when i try to compute Mean Absolute Error (MAE) and Root Mean Square Error(RMSE).
How to obtain the number of detected object and the  number of ground truth per image in order to compute the MAE & RMSE.
If you already have this function, please advise me, I will be very grateful.

Hi @xincyu ,
For now, we do not support this function. To obtain the number of objects and GTs per image, they are usually available in the head and you can obtain them from the head's loss function, e.g., here

Hi @xincyu ,
For now, we do not support this function. To obtain the number of objects and GTs per image, they are usually available in the head and you can obtain them from the head's loss function, e.g., here

Thank you very much. I'll do a try


Add functionality to read gridded domain info and land use from input netcdf file

PURPOSE
This PR modifies the gridded version of the Noah-OM model to read gridded domain info (e.g., n_x, n_y, dx, and dy) and land use (i.e., vegtyp) values from a NetCDF input file. Subsequent PRs will add functionality to read additional gridded model variables (e.g., soils, slope, etc).
ADDITIONS
This PR adds GridInfoType.f90, which defines gridinfo_type. The gridinfo_type has member variables to hold read-in gridded input variables. The gridinfo_type has one public type-bound subroutine (gridinfo_type%ReadGridInfo).
The PR-added public gridinfo_type%ReadGridInfo subroutine is primarily intended to make calls to the gridinfo_type's private type-bound subroutines.
The PR-added subroutine gridinfo_type%ReadSpatialInfo reads spatial information (i.e., n_x, n_y, dx, dy, and latitude and longitude values) from the NetCDF file identified by its arguments. The subroutine (i.e., gridinfo_type%ReadSpatialInfo) is intended to be called for every NetCDF file (with the assumption that every gridded input variable will be provided via a separate NetCDF file) to ensure that all variables are provided over the same grid.
This PR adds the 'private' type-bound subroutine gridinfo_type%ReadVegtyp, which is called within gridinfo_type%ReadGridInfo. The primary purpose of gridinfo_type%ReadVegtyp is to read-in gridded land use data.
This PR adds data/netcdf_dummy.nc to facilitate testing. It is a dummy NetCDF file having gridded land use data in the format expected by this PR's code additions. The latitude, longitude, and vegtyp values for grid cell (1,1) match those for the control model run as listed in the pre-PR namelist.input file such that the output from grid cell (1,1) should match the control run while the output from other grid cells is expected to vary.
This PR adds test/analysis/create_dummy_netcdf.py was added to create data/netcdf_dummy.nc. This script was added to facilitate changes to the organization and contents of the input NetCDF file per PR feedback.
CHANGES
namelist.input was modified to remove the scalar vegtyp entry and add an entry for vegtyp_filename, which is the directory/name of the input NetCDF file passed to gridinfo_type%ReadVegtyp.
Changes were made to several of the initialization subroutines for the gridded derived data type members of noahowpgrid_type. Several of these subroutines were modified to take an instance of the gridinfo_type as an argument, often to provide access to n_x and n_y for allocating allocatable arrays but in some cases. Note that land use values are transferred from gridinfo_type to domaingrid_type when gridinfo_type is given as an argument to domaingrid_type%InitTransfer.
TESTING
The PR-modified Noah-owp model was successfully compiled on MacOS using GNU Fortran (Homebrew GCC 13.1.0) 13.1.0.
The PR-added example input NetCDF file (i.e., data/netcdf_dummy.nc contains gridded land use data in the format expected by this PR's code additions. The latitude, longitude, and vegtyp values for grid cell (1,1) match those for the control model run as listed in the pre-PR namelist.input file. Thus, model output from grid cell (1,1) should match the control run while the output from other grid cells may vary. test/analysis/compare_outputnc.py was executed and I observed that all tests passed for grid cell (1,1) while at least one or more tests failed for all other grid cells -- this was the expected result. The output from test/analysis/compare_outputnc.py is: output.txt
The unit tests (test/noahowp_driver_test.f90) were re-executed and output was normal. The output from test/noahowp_driver_test.f90 is: output.txt
NOTES
At this point in time, I am planning for one gridded model input per NetCDF file. In this case, we can add additional private type-bound subroutines to open and read from specific NetCDF files. Each added type-bound subroutine must make a call to gridinfo_type%ReadSpatialInfo immediately after opening the NetCDF file to ensure that the variable is given on the expected grid.
However, if we elect to assume that all gridded inputs will be provided in a singular NetCDF, this code can be easily modified to facilitate that expectation.
Checklist

[ ] PR has an informative and human-readable title
[ ] Changes are limited to a single goal (no scope creep)
[ ] Code can be automatically merged (no conflicts)
[ ] Code follows project standards (link if applicable)
[ ] Passes all existing automated tests
[ ] Any change in functionality is tested
[ ] New functions are documented (with a description, list of inputs, and expected output)
[ ] Placeholder code is flagged / future todos are captured in comments
[ ] Visually tested in supported browsers and devices (see checklist below :point_down:)
[ ] Project documentation has been updated (including the "Unreleased" section of the CHANGELOG)
[ ] Reviewers requested with the Reviewers tool

@SnowHydrology, I think we're ready for you to have another look. Note that I revised the PR-description to incorporate your comments. But to address the specific points in your previous comment:

netcdf_dummy.nc now has valid lat/longs in agreement with provided dx and dy values following revisions to the script used in its creation (test/analysis/create_dummy_netcdf.py)
The revised  netcdf_dummy.nc has the lat, long, and land use values from the test case (i.e., run/namelist.input in main branch) while all other grid cells have different lat, long, and land use values.
I changed gridlist_type to gridinfo_type


Cannot call get with 'cache' on an undefined object error in the model unit test

Hello Team,
maybe I missed something out, as there is no any kind user reports for that, but still, here is the case:
any kind of validation inside model cause model's unit test to fail with 2.0.0-alpha.2 and ember-cli 0.1.15.
// model
import DS from 'ember-data';
import EmberValidations from 'ember-validations';

export default DS.Model.extend(EmberValidations.Mixin, {
   validations: {
    name: {
      presence: true
    }
  },

  name: DS.attr('string'),
});

});

// model unit test
import {
  moduleForModel,
  test
} from 'ember-qunit';

moduleForModel('user', 'User', {
  // Specify the other units that are required for this test.
  needs: []
});

test('it exists', function(assert) {
  var model = this.subject();
  // var store = this.store();
  assert.ok(!!model);
});

here is the backtrace from the browser

Died on test #1     at Object.test (http://localhost:4200/assets/test-support.js:1693:11)
    at http://localhost:4200/assets/ktd.js:1466:15
    at requireModule (http://localhost:4200/assets/vendor.js:79:29)
    at Object.TestLoader.require (http://localhost:4200/assets/test-loader.js:29:9)
    at Object.TestLoader.loadModules (http://localhost:4200/assets/test-loader.js:21:18)
    at Function.TestLoader.load (http://localhost:4200/assets/test-loader.js:36:24)
    at http://localhost:4200/assets/test-support.js:5294:16: Assertion Failed: Cannot call get with 'cache' on an undefined object.@ 11 ms
Source:
Error: Assertion Failed: Cannot call get with 'cache' on an undefined object.
    at new Error (native)
    at Error.EmberError (http://localhost:4200/assets/vendor.js:25990:23)
    at Object.Ember.assert (http://localhost:4200/assets/vendor.js:17487:15)
    at get (http://localhost:4200/assets/vendor.js:29852:13)
    at lookupValidator (http://localhost:4200/assets/vendor.js:81344:17)
    at exports.default.Ember.default.Mixin.create.buildRuleValidator (http://localhost:4200/assets/vendor.js:81448:68)
    at exports.default.Ember.default.Mixin.create.buildValidators (http://localhost:4200/assets/vendor.js:81414:16)
    at exports.default.Ember.default.Mixin.create.init (http://localhost:4200/assets/vendor.js:81396:12)
    at superWrapper [as init] (http://localhost:4200/assets/vendor.js:31732:22)
    at new Class (http://localhost:4200/assets/vendor.js:47182:16)

and from the phantomjs
not ok 20 PhantomJS 1.9 - User: it exists
    ---
        actual: >
            null
        message: >
            Died on test #1     at http://localhost:7357/assets/test-support.js:2535
                at test (http://localhost:7357/assets/test-support.js:1693)
                at http://localhost:7357/assets/ktd.js:1470
                at http://localhost:7357/assets/vendor.js:79
                at http://localhost:7357/assets/test-loader.js:29
                at http://localhost:7357/assets/test-loader.js:21
                at http://localhost:7357/assets/test-loader.js:36
                at http://localhost:7357/assets/test-support.js:5294: Assertion Failed: Cannot call get with 'cache' on an undefined object.
        Log: >

if I comment out presence validation in the model than tests pass

Also having this issue.

any news on this issue? I got this too

I encountered this issue as well. You need to add 'service:validations' to the needs for your test.
This appears to have been recently added to the README.

ah, thx!

I am going to close this issue for now, feel free to reopen this issue if you feel like it's still relevant and we should take a look at it.


Improving the Gallery page

Putting space between images to not trigger the hover effect
to resolve any problem causing overflow

hey can you elaborate the bug in more detail

Umm it was my first time raising an issue so it is not actually a bug but at few devices dimension the images start overflowing

@Rohan-Hazari Hi there! I'm assigning it to you!
Make sure to ensure the gallery page layout holds well in all screen sizes and also revamp the Card CSS for maintaining a uniform dimensions! All the best!


fix: Auto focus on widget add search field

Description
This PR fix the auto focus issue of the widget add section. Whenever the add section is being opened, search field should be focused by default.
Fixes #31984
Automation
/ok-to-test<EMAIL_ADDRESS>:mag: Cypress test results

[!TIP]
Tests running at: https://github.com/appsmithorg/appsmith/actions/runs/8373176730
Commit: c9ceed6ceb9d8bef23858acc7f1eab0443496781
Workflow: PR Automation test suite
Tags: @tag.Sanity

Summary by CodeRabbit

New Features

Improved user experience by automatically focusing on the search input field in the UI Entity Sidebar.

Closing this since it was removed intentionally.


React 15.5 upgrade, fixed deprecations

This commit removes deprecations regarding React.PropTypes and react-addons-test-utils, see React v15.5.0.
This is a preparation to be able to upgrade to React 16 without further code changes. It also fixes problems I had with Jest snapshot testing when using reactabular with the current React version 15.5.x.

Looks like there's still something missing. Please fix the CI, rebase, and I'll merge. Thanks. 👍

Codecov Report

Merging #297 into master will decrease coverage by 4.5%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #297      +/-   ##
==========================================
- Coverage   72.34%   67.84%   -4.51%
==========================================
  Files          17       17
  Lines         311      311
  Branches       70       70
==========================================
- Hits          225      211      -14
- Misses         86       88       +2
- Partials        0       12      +12

Impacted Files
Coverage Δ

packages/reactabular-dnd/src/draggable-row.js
35.48% <ø> (-16.13%)
:arrow_down:

packages/reactabular-table/src/provider.js
100% <ø> (ø)
:arrow_up:

packages/reactabular-table/src/types.js
95% <100%> (ø)
:arrow_up:

packages/reactabular-dnd/src/move.js
30% <0%> (-17.5%)
:arrow_down:

packages/reactabular-dnd/src/header.jsx
35.29% <0%> (-11.77%)
:arrow_down:

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Sorry, I had forgotten to fix some imports, should have run the tests locally before pushing.

No probs. That's why the CI exists. 👍

Any idea about those

Warning: Failed prop type: Calling PropTypes validators directly is not supported by the prop-types package. Use PropTypes.checkPropTypes() to call them. Read more at http://fb.me/use-check-prop-types

warnings in reactabular-table?  The warning seems to point at https://github.com/reactjs/prop-types/blob/master/README.md#difference-from-reactproptypes-dont-call-validator-functions .
It would be good to fix this before a release.

These warnings result from Jest itself, I will do a PR for a Jest upgrade, the current version 19.0.2 has it fixed.


Refactor the code

Feel free to let me know if you need any more information or if there's anything else I can do to help get this merge.

These changes are very interesting 😄
Nice job 👍🏻


#1008 add support for system property "chromeoptions.mobileEmulation"

Still, I am not sure it's a good idea.
Making this PR to show the idea how to achieve the goal with just 3 lines of code. :)

I like it.

Billion likes!

why not

the test is really weird

@dstoianov What you mean? Why it's bad to close any previously opened browser?

The feature is ok, but the method close in beforEach looks a bit strange

@fabb Basically your question is the same as https://github.com/selenide/selenide/issues/1372.
Answer: no, it's not implemented yet.
But you can do it if you open webdriver by yourself in your code.


Typo in Machine Learning Studio Module Reference

Link to article:
https://docs.microsoft.com/en-us/azure/machine-learning/studio-module-reference/convert-to-csv
Problem:
The 2nd para in the section "More about the CSV format" must be
"Even if you do most of your work in Azure Machine Learning Studio, there are times when you might find it handy to convert your dataset to CSV to use in external tools."
and not
"Even if you do must of your work in Azure Machine Learning Studio, there are times when you might find it handy to convert your dataset to CSV to use in external tools."

Thanks @samratp. I've opened a PR to fix this: https://github.com/MicrosoftDocs/azure-reference-other/pull/123


README instructs users to do strange things to their repositories.

The example use of create-release in the README contains this line:
          tag_name: ${{ github.ref }}

Should a user leave this in while having actions set to trigger for their master/main branch, this will result in a new tag being created called refs/heads/main... This means:

The tag will be the same every time the action tries to create a release

After this action is triggered, trying to simply push to the repository (e.g. git push or git push origin master) will not work. Users will probably try to delete the tag... Examples for "delete a tag" found across the internet look like git push origin :refs/tags/main. The proper way to delete this tag is git push origin :refs/tags/refs/heads/main, but users will probably mistakenly run other commands such as git push --delete origin :refs/heads/main due to the confusing name of this tag, deleting their remote main branch.

I suggest changing the tag_name line in the README's example use to something along the lines of tag_name: release-${{ github.sha  }} to ensure the example works out-of-the-box without any unusual issues.

Another tag name that worked for me is tag_name: ${{ github.run_number }}, which I found friendlier than the sha:

run_number: stringA unique number for each run of a particular workflow in a repository. This number begins at 1 for the workflow's first run, and increments with each new run. This number does not change if you re-run the workflow run.

Another tag name that worked for me is tag_name: ${{ github.run_number }}, which I found friendlier than the sha:

run_number: stringA unique number for each run of a particular workflow in a repository. This number begins at 1 for the workflow's first run, and increments with each new run. This number does not change if you re-run the workflow run.

Came here just for this, I messed up my master branch in my repository because I was trying to test the example.
At least some comments stating why you shouldn't do it with a non-tagged branch could have helped me avoid this situation.

There was probably an implicit assumption by whoever wrote the README that people would be using this conditionally with version tags so I think there were assuming the step/job would have if: startsWith(github.ref, 'refs/tags/v') which is probably what anyone using some release action like this should have.

@ash0x0 for best practice use I would agree but in some simple projects (such as the one that prompted me to make this issue) it can be useful to just build any commit and create an artifact for it.


Remove tab link

Questions
Answers

Description?
Removes the usage of pre 1.6 link style, using tab as a parameter.

Type?
refactor

BC breaks?
no

Deprecations?
no

Fixed ticket?

Sponsor company

How to test?

Does not need QA, this style of link is obsolete at least since <IP_ADDRESS> - see https://github.com/PrestaShop/PrestaShop/blob/<IP_ADDRESS>/admin-dev/index.php.


Add role to manage icingaweb2

I have such role for my own project; it's not already published, if you wan i can try to create a merge request based on this role and how you write your collection. Please let me know if you are already working on this issue!

Hi, at the moment we don't have anything concrete for the icingaweb2 role. If you have some code to share, feel free to open a PR and we'd be happy to review it and get it merged

started a new MR to implement this, it's still a draft but do not hesitate to share some feedback there #149


1.13 chat handling spams messages

Type /jobs 2
Typing space after will continue to spam messages.

Try restarting your computer and server, as this may be a Java error because it has already happened to me.


jq has --compact-output, jaq has --compact

Although both use the short -c, they differ on the long version, as I found when dropping jaq in place of jq in a few of my codebases:
error: Found argument '--compact-output' which wasn't expected, or isn't valid in this context

  Did you mean '--compact'?

This looks really easy to bring into alignment, if that's desirable.
https://github.com/search?q=repo%3A01mf02%2Fjaq compact&type=code

Hi @colindean, you're absolutely right. I changed this now. Have a good day!


Save passwords entered on webpages via ddg-browser

It is already possible to auto-fill passwords already stored in a password manager or the ios-vault.
Compared to safari, DDG seems to lack the possbility to save new credentials into the vault entered within DDG. At least whenever I try, there is no prompt to save credentials after I hit "enter" on a login page. Credentials have to be added manually or via SAFARI.
If it is possible to hand over the credentials, it would be valuable to add this to DDG to make it THE standalone browser.
All the best,
Fred

Tested on: iPhone 12 mini, iOS 14.7.1

Hi Fred,
Thanks for your feedback and we definitely agree.  iOS doesn’t support this “out of the box” but we are planning to support it in the future.
I’m going to close this out because it’s already on our development timeline.
Thanks again!


Use correct tiktoken encoding based on LLM model

I find that both embedding and LLM predictor using the global tiktoken as their tokenizer and use "gpt-2" for encoding.
https://github.com/jerryjliu/llama_index/blob/468e8443a9c0ba4f36dcf043b169ca9e3a3125bb/gpt_index/utils.py#L50
However, the default model for embbeding is text-embedding-ada-002 and the LLM predictor is text-davinci-003, which uses cl100k_base and p50k_base encoding respectively. Furthermore, the user may choose their custom LLM model like gpt-3.5-turbo or gpt-4, and the encoding should also be cl100k_base.

Encoding name
OpenAI models

cl100k_base
gpt-4, gpt-3.5-turbo, text-embedding-ada-002

p50k_base
Codex models, text-davinci-002, text-davinci-003

r50k_base (or gpt2)
GPT-3 models like davinci

For these reasons, I suggest BaseEmbedding and LLMPredictor should choose correct encoding based on the model used, not using the global immutable one.
If you need some help, I can work on it and make a pull request against it.
Reference

Tiktoken cookbook

You are absolutely right. This is something we've been wanting to improve on.
Would be amazing if you could open a PR for it!

It would be great to have this fixed! I assume such a fix will improve the accuracy in calculating whether a long chain of text should be split into two nodes (or kept in a single one) before making HTTP request(s) to the LLM?


Gather basic system facts as part of the plan execution.

What are some basic system facts?

http://docs.ansible.com/ansible/playbooks_variables.html#information-discovered-from-systems-facts

We could make a script (similar to modules) that grabs facts.  It could be deployed during plan setup

yep, pre-modules transfer. This should also ideally plug in with facter.


High Scores array

create a high-scores array to display names and initials of high scores
create a display of the scores when view high scores is clicked

Completed


fix(auth): ntlm and negotiate

@Grueslayer this should do it, right?
empty ones result in:
curl -s -X 'GET' --negotiate -u ':' -H 'accept:application/json' -A 'kulala.nvim/3.4.0' --cookie-jar '/home/marco/.local/share/nvim/tmp/kulala/cookies.txt' 'https://httpbin.org/get'

and
curl -s -X 'GET' --ntlm -u ':' -H 'accept:application/json' -A 'kulala.nvim/3.4.0' --cookie-jar '/home/marco/.local/share/nvim/tmp/kulala/cookies.txt' 'https://httpbin.org/get'


I can't get Graphs

HI, I can't get Graphs.
Try by testing script
./zbxtg.py xxxxxxx test "$(echo -e 'zbxtg;graphs: \nzbxtg;graphs_period=3600\nzbxtg;itemid:12345\nzbxtg;title:ololo')"
then I get
Traceback (most recent call last):
File "./zbxtg.py", line 940, in
main()
File "./zbxtg.py", line 885, in main
zbx.login()
File "./zbxtg.py", line 295, in login
auth=requests.auth.HTTPBasicAuth(self.basic_auth_user, self.basic_auth_pass))
File "/usr/local/lib/python2.7/dist-packages/requests/api.py", line 119, in post
return request('post', url, data=data, json=json, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/requests/sessions.py", line 530, in request
resp = self.send(prep, **send_kwargs)
File "/usr/local/lib/python2.7/dist-packages/requests/sessions.py", line 643, in send
r = adapter.send(request, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/requests/adapters.py", line 516, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=80): Max retries exceeded with url: /zabbix// (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fe2f6f6c8d0>: Failed to establish a new connection: [Errno 111] Connection refused',))
But I get message in telegram without Graphs.

Sorry, may be closed


fix: wget linux-install-etcd-client.sh 404 in ci

 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.rongxin seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.You have signed the CLA already but the status is still pending? Let us recheck it.


Fix Disconnect Bug

Disconnect Frame was malformed
Disconnect Frame was send over Data Channel, should send over
Communication Channel

The code looks good, however, indentation of the seems to be wrong (8 rows instead of 4 that the other code is using). Can you please fix this?

copy paste error
double definition of function disconnect!


buildkite: retrieve secrets from aws sm

fixes https://redpandadata.atlassian.net/browse/PESDLC-1527
buildkite currently reads secrets from the s3 secrets bucket into env vars for use by the pipeline. these secrets were copied into aws secretsmanager and this PR updates the pipeline so it uses the seek-oss/aws-sm plugin to read the secrets from aws secretsmanager for the https://buildkite.com/redpanda/helm-charts pipeline. there is no functionality change because the env vars are kept the same name and values.

@RafalKorepta fyi i've posted you a link in jira


[http] API changes to split path header normalization and forwarding

Signed-off-by: Asra Ali<EMAIL_ADDRESS>Commit Message: Configuration for path normalization so that normalization can be configured for internal only use and/or forwarding.
Additional Description: Just API changes. normalize_path and merge_slashes to be deprecated. I will remove the runtime docs changes if that looks good.
The plan:

Make ConnManagerUtility and Router friend classes with HeaderMap
Create private HeaderMap methods: setNormalizedPath that ConnManagerUtility calls prior to filter processing and routing that sets private members original_path_ and normalized_path_. Then restoreOriginalPathIfUnchanged called by Router if we are doing internal-only normalization that restores :path with the original header only filters didn't change the path.
No HTTP filters have access to the original path for forwarding to prevent misuse.

Risk Level: Low, just API
Release notes: TODO on implementation
Runtime Guard: TODO on implementation. Runtime guard to overwrite forwarding http_connection_manager.forward_normalized_path (can revert right now)
Starts: https://github.com/envoyproxy/envoy/issues/6589

/cc @chaoqin-li1123

@mattklein123 could you please take another look? Controls have individual messages, hopefully the internal/full transformation interaction is more clear.


[26.x][WFLY-15572] Upgrade fastinfoset 1.2.18

Fixes https://issues.redhat.com/browse/WFLY-15572
Upstream:
https://github.com/wildfly/wildfly/pull/14839

Thanks, @boris-unckel


VSCode Native Notebooks Survey

Survey after > 100 actions in notebooks (+remind me later)
Survey after > 5 & not used for 5 days (+remind me later)
Survey after < 5 operations in notebooks & closed it (+remind me later)

Validated. Did enough executions to trigger it, and got the banner up which linked correctly to the survey online.


Update FilterMonitor.js

isFiltered isn't always passed a string so fails sometimes. This fixes the issue.

It's up in v1.1.2. Thanks for the contribution and the details!


Adjust results tab splitted view after error

Hi guys,
Each time I run the query and results tab pops up it does so in splitted view (one part is error message itself and the other part is copy of sql query which usually coincides from what can be seen in the editor tab above panel tab).
Currently there is an option to show error message as a dialogue window, but I don't want to mess with closing the annoying windows each time I face the error. There is also an option to fold the part with sql part, but when I rerun the query it unfolds again. It's also annoying to fold this part of results pane each time.
It would be great to have some settings checkbox which allows to show only error message without copy of SQL code. Or at least somehow pin the folding position (so it will not reset after each query run)

Thank you for request.