Add yolo mode to rustfix

I'm really confused about how travis works...

travis.sh: 2: [: nightly: unexpected operator

Err, you probably need to start that file with #! /bin/sh. But, seriously, add this to the travis yaml instead
script:
- |
  cargo build &&
  if [[ "$TRAVIS_RUST_VERSION" == nightly* ]]; then
    cargo test -- --nocapture
  fi

Feel free to merge, and maybe squash the travis struggle commits if you want


"Click to subscribe" banner

Adds block for sticky banner that links to 'kmg.com.np/subscribe'

Thank you @cyclonejet


KeV energy type

[X]  basis classes
[X] recipeBuilder
[X] KeV handling hatches
[ ] KeV transfer pipes
[x] quantum computer to generate KeV
[x] KeV using MultiblockController

lol it's not ready at all


Fetch all required information from Gerrit for background refresh.

Currently, background refreshes of data from Gerrit silently fail due to the error:
    TypeError: Cannot read property 'undefined' of undefined
        at Changelist.getCurrentRevision (gerrit.js:268)
        at Changelist.getCategory (gerrit.js:191)
        at gerrit.js:411
        at Array.forEach (<anonymous>)
        at SearchResult.getCategoryMap (gerrit.js:410)
        at gerrit.js:452
        at Array.forEach (<anonymous>)
        at SearchResults.getCategoryMap (gerrit.js:451)
        at update (badge.js:94)
        at badge.js:46

This is triggered because getCurrentRevision requires CURRENT_REVISION to be sent in the request to Gerrit, but the background badge refresh requests a non-detailed fetch of information, which doesn't include this.
This CL adds CURRENT_REVISION to the set of non-detailed information, resolving the above error.
I've kept the current detailed/non-detailed split, because requesting DETAILED_ACCOUNTS roughly triples the payload size in my (very brief) experiments.

Should hopefully resolve #23

Sorry for the delay and thank you for the fix.


README updates for ilab 0.18.0

Introduces README updates to represent the current state of how to run the ilab commands

Checklist:

[ ] Commit Message Formatting: Commit titles and messages follow guidelines in the
conventional commits.
[ ] Changelog updated with breaking and/or notable changes for the next minor release.
[ ] Documentation has been updated, if necessary.
[ ] Unit tests have been added, if necessary.
[ ] Integration tests have been added, if necessary.

@Mergifyio backport release-v0.18


[improve][client] Drop jcommander dependency in Pulsar java client

Fixes #18932

Motivation

Pulsar add the jcommander as dependency in pulsar-common module, but it should be an optional dependency because most people don't need it in client side.
Modifications

Make the jcommander in pulsar-common with true.
Verifying this change

[x] Make sure that the change passes the CI checks.

(Please pick either of the following options)
This change is a trivial rework / code cleanup without any test coverage.
(or)
This change is already covered by existing tests, such as (please describe tests).
(or)
This change added tests and can be verified as follows:
(example:)

Added integration tests for end-to-end deployment with large payloads (10MB)
Extended integration test for recovery after broker failure

Does this pull request potentially affect one of the following parts:

If the box was checked, please highlight the changes

[x] Dependencies (add or upgrade a dependency)
[ ] The public API
[ ] The schema
[ ] The default values of configurations
[ ] The threading model
[ ] The binary protocol
[ ] The REST endpoints
[ ] The admin CLI options
[ ] The metrics
[ ] Anything that affects deployment

Documentation

[ ] doc
[ ] doc-required
[x] doc-not-needed
[ ] doc-complete

Matching PR in forked repository
PR in forked repository:

cc @syhily

Generally I don't think that you can pass compilation with this change. And it makes usage depends on this feature like https://github.com/apache/pulsar-site/blob/4e4f394960f0632bbc12cfad1a43dc132462464e/tools/pytools/lib/execute/config_doc_generator.py become vague to use.
Please follow https://pulsar.apache.org/contribute/personal-ci/ and attatch the test report here.

Have you ever verified your changes? How do you verify it? Please provide related description. This change looks in a wrong direction and without further explanation or verification, it won't get merged.

After a second consideration, this change may work since the downstream users can opt-out the jcommand dependency now. And for config docs generator it's possible that classpath.txt already cover the dependencies. I'll try to verify it.

optional means that this dependency is used to compile some classes in this module. If you rely on these classes, you should explicit add the optional dependency in you module.
So we may have to download the jcommander and add to the classpath instead. Or we can create a new module for generating all the docs as Flink has already done.

Compile locally fails with:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.10.1:compile (default-compile) on project pulsar-client-original: Compilation failure: Compilation failure:
[ERROR] /home/tison/Brittani/pulsar/pulsar-client/src/main/java/org/apache/pulsar/client/impl/conf/CmdGenerateDocumentation.java:[21,28] package com.beust.jcommander does not exist
[ERROR] /home/tison/Brittani/pulsar/pulsar-client/src/main/java/org/apache/pulsar/client/impl/conf/CmdGenerateDocumentation.java:[27,2] cannot find symbol
[ERROR]   symbol: class Parameters
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :pulsar-client-original

Compile locally fails with:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.10.1:compile (default-compile) on project pulsar-client-original: Compilation failure: Compilation failure:
[ERROR] /home/tison/Brittani/pulsar/pulsar-client/src/main/java/org/apache/pulsar/client/impl/conf/CmdGenerateDocumentation.java:[21,28] package com.beust.jcommander does not exist
[ERROR] /home/tison/Brittani/pulsar/pulsar-client/src/main/java/org/apache/pulsar/client/impl/conf/CmdGenerateDocumentation.java:[27,2] cannot find symbol
[ERROR]   symbol: class Parameters
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :pulsar-client-original

Compile locally fails with:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.10.1:compile (default-compile) on project pulsar-client-original: Compilation failure: Compilation failure:
[ERROR] /home/tison/Brittani/pulsar/pulsar-client/src/main/java/org/apache/pulsar/client/impl/conf/CmdGenerateDocumentation.java:[21,28] package com.beust.jcommander does not exist
[ERROR] /home/tison/Brittani/pulsar/pulsar-client/src/main/java/org/apache/pulsar/client/impl/conf/CmdGenerateDocumentation.java:[27,2] cannot find symbol
[ERROR]   symbol: class Parameters
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :pulsar-client-original

Compile locally fails with:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.10.1:compile (default-compile) on project pulsar-client-original: Compilation failure: Compilation failure:
[ERROR] /home/tison/Brittani/pulsar/pulsar-client/src/main/java/org/apache/pulsar/client/impl/conf/CmdGenerateDocumentation.java:[21,28] package com.beust.jcommander does not exist
[ERROR] /home/tison/Brittani/pulsar/pulsar-client/src/main/java/org/apache/pulsar/client/impl/conf/CmdGenerateDocumentation.java:[27,2] cannot find symbol
[ERROR]   symbol: class Parameters
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :pulsar-client-original

@nicoloboschi Yes. This's what I proposed in https://github.com/apache/pulsar/issues/18932#issuecomment-1354110598

Closing...
Inactive.


pnpm doesn't work with waku/router

https://github.com/dai-shi/waku/blob/07ac23eb174e439ae73185495924a8a4bde90f75/src/middleware/lib/rsc-handler-worker.ts#L180-L186

Related: https://github.com/vitejs/vite/issues/8991


Remove duplicate Rectangle#packedLength;

Thanks, it looks like there are duplicate pack and unpack functions as well, care to remove them before I merge?

@mramato I saw that, but the type annotations for pack are different. One takes a Rectangle and the other a BoundingSphere.

Yes, but JavaScript does not have function overloading so really the second one just overwrites the first one.  Rectangle is the correct annotation, BoundingSphere is not.  After you remove everything, just make sure the 3 parts (packed/pack/unpack) are grouped together in the file, since they are related.  Thanks.

Should I squash?

No need, we don't really curate our commit history.  Thanks again.


Password grant is not working for users migrated from from non unique id user stores from APIM 2.6.0 to APIM 4.0.0

Description
$subject
Steps to Reproduce

Started the APIM server 2.6.0 created few test users using and migrated the APIM 2.6.0 to APIM 4.0.0 U2 (218)
Generate access token using the previously created users using the Password grant & the Access token generation happens without issues.
Update the APIM 4.0.0 to the Latest(278) or U2-219 & then the token generation for the migrated users will fail with the following response. But the token generation using the password grant will be working for the newly created users after the migration

Affected Component
APIM
Version
4.0.0
Environment Details (with versions)
No response
Relevant Log Output
No response
Related Issues
No response
Suggested Labels
No response

Fix PRs: https://github.com/wso2/carbon-kernel/pull/3974, https://github.com/wso2/carbon-kernel/pull/3973


Release/12.0.0

Codecov Report

Merging #89 (c3aa8fa) into master (19f90d4) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #89   +/-   ##
=======================================
  Coverage   96.92%   96.92%
=======================================
  Files          13       13
  Lines         651      651
  Branches       92       92
=======================================
  Hits          631      631
  Misses         20       20

Impacted Files
Coverage Δ

...ib/services/ya-api-loader/ya-api-loader.service.ts
100.00% <ø> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 19f90d4...c3aa8fa. Read the comment docs.


Problem on process_bindingmoad.py

Hi there, thanks for an interesting implemantion of DiffSBDD. I have encountered the following problem when I try to preprocess the bindingmoad dataset:
#failed: 130: 100%|█████| 130/130 [00:00<00:00, 11105.76it/s]
Traceback (most recent call last):
  File "/home/user/Code/DiffSBDD/process_bindingmoad.py", line 571, in <module>
    lig_coords = np.concatenate(lig_coords, axis=0)
  File "<__array_function__ internals>", line 180, in concatenate
ValueError: need at least one array to concatenate

How should I fix this problem? Thanks

OK, i figure out what happening. basedir should not contain BindingMOAD_2020. 😂

Can you explain how you solved this issue in more detail? Did you have the directory BindingMOAD_2020 in the same directory as your code? Did you modify the script somehow?


checkpoint after Alice funds, or ensure Alice has not funded before funding procedure

Maker Alice was restarted during a swap after funding, but prior to accordant lock finalizing, so before Bob sent her his buysig.
After Alice restarts, Bob sees finalized accordant lock and sends her his buysig, but Alice has not restored the swap yet.
Alice restores the swap and since she hasn't checkpointed that she's funded, she auto-funds agains.
So we should either checkpoint after Alice funds, or Alice must first watch the accordant lock address and ensure it has not been funded before creating the funding request (currently, only checks whether address is watched thereafter, and doesn't check whether it already has txs).

Attached is Alice's log, @h4sh3d can provide Bob taker log if needed (Alice's log should be self-sufficient imo).
alice-double-fund.log

Thank you for the report, I think correct solution is that after a restore, needs funding should only be issued once the address has been checked by the syncers. Adding another checkpoint does not really solve the issue - Alice might terminate after she funded, but before the funding was registered in swapd.


fix: allows customizing the title of the API page

PR Checklist
Please check if your PR fulfills the following requirements:

[ ] Tests for the changes have been added (for bug fixes/features)
[ ] Docs have been added/updated (for bug fixes/features)

PR Type
What kind of change does this PR introduce?

[x] Bugfix
[ ] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no API changes)
[ ] Build related changes
[ ] CI-related changes
[ ] Documentation content changes
[ ] Other... Please describe:

Issue Number

Issue Number: #171
Does this PR introduce a breaking change?

[ ] Yes
[x] No

Other information

:tada: This PR is included in version 17.6.12 :tada:
The release is available on:

v17.6.12
GitHub release

Your semantic-release bot :package::rocket:


QueuedStoreGroup should call #onChange when UseCase#dispatch is called

Currently, QueuedStoreGroup should not call QueuedStoreGroup#emitChange() when UseCase#dispatch is called.
#40 support only didExecutedUseCase events.
It is unexpected behavior for user.
We should support UseCase#dispatch events.
Algorithm
QueuedStoreGroup check changed stores and QueuedStoreGroup#emitChange() on following case:

when emit root didExecutedUseCase events
- when emit every didExecutedUseCase events if { asap : true} option is enabled
when emit UseCase#dispatch events
- every type

This UseCase loading events like this:
class DispatchAndFinishAsyncUseCase extends UseCase {
    execute() {
        // dispatch event
        this.dispatch({
            type: "DispatchAndFinishAsyncUseCase",
            isLoading: true
        });
        return new Promise((resolve) => {
            setTimeout(() => {
                this.dispatch({
                    type: "DispatchAndFinishAsyncUseCase",
                    isLoading: false
                });
            }, 1000);
        });
    }
}

We also should handling throw error events

Added checking onUseCaseError


Update coverage report to codecov

Change coverage upload to codecov - unsure if it supports lcov, but only one way to find out...

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@ea7a6c1). Click here to learn what that means.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master     #606   +/-   ##
=========================================
  Coverage          ?   90.50%
=========================================
  Files             ?      146
  Lines             ?    52389
  Branches          ?        0
=========================================
  Hits              ?    47414
  Misses            ?     4975
  Partials          ?        0

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update ea7a6c1...f211601. Read the comment docs.


&src argument gives bad<EMAIL_ADDRESS>path (vite 5)

the import for the file in question:
import rebrandedImage from "../../../images/example.jpeg?preset=800&src"

the preset:
imagePresets({
     800: widthPreset({
          widths: [800],
          loading: "lazy",
          formats: {
            png: { quality: 70 },
            jpeg: { quality: 70 },
          },
      })
})

what am i missing?
vite: 5.0.8
sharp: 0.33.2

updating the title as seeing this is the exposed virtual id, I am assuming that this is resulting from a breaking api change in vite 5

I think it's related to this change:
https://github.com/vitejs/vite/pull/14818

Apologies, I found I had this image with any vite plugin that touched images, so i think it had something to do with my install or config approach


AttributeError: module 'numpy' has no attribute 'float64'

Hi, I used pip install git+https://github.com/jcrozum/PyStableMotifs to install the package. Installation was successful with all the requirements fulfilled. When I try to import PyStableMotifs in jupyter notebook, I keep getting the following attribute error.
AttributeError                            Traceback (most recent call last)
 in
1 #import PyStableMotifs as sm
2 #import PyBoolNet
----> 3 import PyStableMotifs
C:\Anaconda\lib\site-packages\PyStableMotifs_init_.py in
1
2 try:
----> 3     import PyBoolNet
4 except ImportError as e:
5     print(e)
C:\Anaconda\lib\site-packages\PyBoolNet_init_.py in
4 from future import print_function
5
----> 6 import PyBoolNet.Attractors
7 import PyBoolNet.Basins
8 import PyBoolNet.Commitment
C:\Anaconda\lib\site-packages\PyBoolNet\Attractors.py in
7 import random
8
----> 9 import PyBoolNet.FileExchange
10 import PyBoolNet.PrimeImplicants
11 import PyBoolNet.StateTransitionGraphs
C:\Anaconda\lib\site-packages\PyBoolNet\FileExchange.py in
7 import datetime
8
----> 9 import PyBoolNet.PrimeImplicants
10 import PyBoolNet.InteractionGraphs
11 import PyBoolNet.QuineMcCluskey
C:\Anaconda\lib\site-packages\PyBoolNet\PrimeImplicants.py in
3 import PyBoolNet.FileExchange
4 import PyBoolNet.QuineMcCluskey
----> 5 import PyBoolNet.InteractionGraphs
6 import PyBoolNet.Utility.DiGraphs
7 import PyBoolNet.Utility.Misc
C:\Anaconda\lib\site-packages\PyBoolNet\InteractionGraphs.py in
5 import math
6 import os
----> 7 import networkx
8
9 import PyBoolNet.StateTransitionGraphs
C:\Anaconda\lib\site-packages\networkx_init_.py in
113 from networkx.generators import *
114
--> 115 import networkx.readwrite
116 from networkx.readwrite import *
117
C:\Anaconda\lib\site-packages\networkx\readwrite_init_.py in
13 from networkx.readwrite.nx_yaml import *
14 from networkx.readwrite.gml import *
---> 15 from networkx.readwrite.graphml import *
16 from networkx.readwrite.gexf import *
17 from networkx.readwrite.nx_shp import *
C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py in
312
313
--> 314 class GraphML(object):
315     NS_GRAPHML = "http://graphml.graphdrawing.org/xmlns"
316     NS_XSI = "http://www.w3.org/2001/XMLSchema-instance"
C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py in GraphML()
342     else:
343         # prepend so that python types are created upon read (last entry wins)
--> 344         types = [(np.float64, "float"), (np.float32, "float"),
345                  (np.float16, "float"), (np.float_, "float"),
346                  (np.int, "int"), (np.int8, "int"),
AttributeError: module 'numpy' has no attribute 'float64'
Could you please help me fix this? Thank you!

This looks like a networkx error related to some sort of incompatibility between networkx and numpy. I suggest updating netwokx and numpy:
pip install --upgrade numpy, networkx

Let me know if that fixes the problem for you.

Yes, this did work. I had to upgrade matplotlib similarly. Thanks for the help!

Great, glad it worked!


Init

@charsyam @tzvetkoff The code is pushed and the local tests are passing. I gotta figure out how to get Github Actions working, but other than that this is ready for polishing up and releasing. Do you see anything that we should adjust?

Closing. Inactive.


[NOT FOR MERGE YET] Ciao controller unused code removal

On #1160 I report out some unused/unreachable code sections in our tree. This PR fixes a small subset of those issues focusing on ciao-controller and datastore.

Coverage increased (+0.1%) to 66.125% when pulling eedaefea111d13cb7716f67d373a77874fc1b635 on rbradford:ciao-controller-unused-removal into 8d711902ec2ab2001b4a4cc489f48c6a227f323f on 01org:master.

Coverage increased (+0.1%) to 66.154% when pulling 24a8814e969b283479870c5fdef31a78e1575b88 on rbradford:ciao-controller-unused-removal into f49ce47369e37e47c143d2a82ac545085c800d83 on 01org:master.


4.0.1 sometimes reports an empty error message

Describe the bug
The new version sometimes reports an empty error message
I was not able to narrow down the conditions but was able to compile a simple test
To Reproduce
// SPDX-License-Identifier: UNLICENSED

pragma solidity ^0.8.9;

contract Test {
  uint256 _x;

  constructor() {}

  function testMe1() public view returns (uint256) {
    require(false, "Error");
    return _x;
  }

  function testMe2(uint256 x) public {
    require(false, "Error");
    _x = x;
  }
}

import { expect, use } from "chai";
import { solidity } from "ethereum-waffle";
import { ethers } from "hardhat";

import { Test } from "../typechain-types";

use(solidity);

describe("Test", function () {
  let testInstance: Test;

  beforeEach(async function () {
    [this.owner, this.receiver] = await ethers.getSigners();

    const testFactory = await ethers.getContractFactory("Test");
    testInstance = await testFactory.deploy();
  });

  it("testMe1", async function () {
    const tx = testInstance.testMe1();
    await expect(tx).to.be.revertedWith("Error");
  });

  it("testMe2", async function () {
    const tx = testInstance.testMe2(1);
    await expect(tx).to.be.revertedWith("Error");
  });
});

Software versions

ethereum-waffle 4.0.1
@nomiclabs/hardhat-waffle 2.0.3
Package manager (yarn, npm, or pnpm?) npm
Node version (node --version) 16.14.2
Solidity version 0.8.9

Additional context

Add any other context about the problem here
Include screenshots if applicable

Looks like it does not properly extract the error message for a view function - we might have not covered this - I'll take a look at that.

Hmm no, it seems to be working fine in our tests.
@TrejGun What is your installed version of @nomiclabs/hardhat-ethers?

@rzadp 2.1.0

@TrejGun I was able to reproduce the issue (outside of our repository). I will continue to look into it.

@TrejGun Is your installed version of hardhat higher than 2.9.3? My investigation shows that this problem happens then.
You can try downgrading hardhat to 2.9.3 to make it work, or wait for a fix on our side - looks like it should not be difficult.

@rzadp thanks for the quick response
indeed my hardhat is 2.10.1
I will wait for the fix and run my tests again to report to you

@TrejGun Please give Waffle 4.0.2 a try.

@rzadp thanks, works like a charm

@TrejGun did you make it work with hardhat 2.1.0?  I downgraded to hardhat 2.9.3 and still didn't work :/
here my dependencies:
    "@nomiclabs/hardhat-ethers": "2.1.0",
    "@nomiclabs/hardhat-etherscan": "^3.0.0",
    "@nomiclabs/hardhat-waffle": "^2.0.3",
    "@typechain/ethers-v5": "^10.1.0",
    "@typechain/hardhat": "^6.1.0",
    "@types/chai": "^4.3.0",
    "@types/mocha": "^9.0.0",
    "@types/node": "^16.4.13",
    "@typescript-eslint/eslint-plugin": "^4.29.1",
    "@typescript-eslint/parser": "^4.29.1",
    "chai": "^4.3.4",
    "dotenv": "^10.0.0",
    "eslint": "^7.29.0",
    "eslint-config-prettier": "^8.3.0",
    "eslint-config-standard": "^16.0.3",
    "eslint-plugin-import": "^2.23.4",
    "eslint-plugin-node": "^11.1.0",
    "eslint-plugin-prettier": "^3.4.0",
    "eslint-plugin-promise": "^5.1.0",
    "ethereum-waffle": "^4.0.4",
    "ethers": "5.6.9",
    "hardhat": "^2.9.3",
    "hardhat-contract-sizer": "^2.4.0",
    "hardhat-deploy": "^0.9.29",
    "hardhat-gas-reporter": "^1.0.7",
    "prettier": "^2.7.1",
    "prettier-plugin-solidity": "^1.0.0-dev.23",
    "sol-merger": "^4.0.0",
    "solhint": "^3.3.6",
    "solidity-coverage": "^0.7.17",
    "ts-node": "^10.4.0",
    "typechain": "^8.1.0",
    "typescript": "^4.5.4"

@TrejGun @rzadp
I was looking more deeply into the code and I found the error. When I get the error string, the reason is inside simple quotes but the regex is searchig for double quotes here: https://github.com/TrueFiEng/Waffle/blob/master/waffle-chai/src/matchers/revertedWith.ts#L89 If I change the regex to single quotes, it reads the message and it is not anymore empty. I can imagine it is regarding the operating system, but it is only a quick guess :)

I'm on mac


[feat] charity to help the people the coin represents

Hello Dogecoin Developers,
I am new to this program so I apologize for probably coming off as a newb. I am here because I followed the posts about leaving potential ideas for future use of the coin. Let me start with saying in no way do I come close to understanding anything technical about programming so I am definitely not going to critique anything Dogecoin stands to represent. What I would like to offer is my idea to set up a charity fund that will receive automatic donations by some method of taking any percentage even just the smallest from each coin that is spent, bought, or by staking. I truthfully haven’t thought that part through because I feel it is not my place to decide that over y’all.
The part I have given thought to is the charity. I have 3 kids about 5-7 hrs apart. This allowed me to get an understanding of emotions and feelings that in my opinion represent the majority of their generations. In particular I feel as if the idea of “Love” or simply respecting each individual as a human has been diminishing since generations above mine (I am 35).  I really don’t know what to say might have caused this but it has to be a number of things. I think top influencing factors would have a lot to do with governmental influence using media and technology accompanied with lack of parental guidance.
If this coin is supposed to represent the people than why not potentially using my idea in some way. I would also think that if Elon wants to use it for future space exploration, we will need the people to be here as well.  Either way I guess I just needed to try and get my charity idea out there since I have been thinking about it for quite some time now and don’t know how to get the idea to potential backers. I don’t want any money or dogecoin.  I have put quite a bit of thought to my idea regarding financing and charity uses so if it interests the Doge Team then hit me back. My email is<EMAIL_ADDRESS>Thank y’all very much for your time and sorry if I came off as a weirdo lol.

Hi! Don't give up hope! It won't go to hell, at least never permanently. People are
One of the things that many of the "neo banks" do in their apps is automatically take your change or a percentage of what you spend into a vault, that then accumulates and you can spend it on charity or save some money for your new car... fully flexible. I think we can do the same with any Dogecoin wallet, to implement this.
I don't think this is a good feature for Dogecoin Core. But it could be a great and valuable feature for a mobile wallet. I'm not sure if any of the mobile wallets has this right now.
I made you a post on reddit here: https://www.reddit.com/r/dogecoindev/comments/nlssas/from_github_charity_to_help_the_people_the_coin/ for people to comment. I will close & lock this issue here as it is not related to Dogecoin Core.


Could you also post the evaluation results of the standard models on COCO 2017 val?

Currently it seems the standard models only report results on COCO 2017 test. However, since the evaluation results on COCO 2017 val is easier to obtain, I think it would be better to also post those results.
Otherwise users, who are not aware of the difference of COCO 2017 val and test, might get confused when their own evaluation results are not the same as the results reported.

Please refer to #281. We will add results on the validation set in README in future.


What are the software minimum requirements?

What are the requirements? I'm getting a lot of
PHP Parse error:  syntax error, unexpected '' (T_ENCAPSED_AND_WHITESPACE), expecting identifier (T_STRING) or variable (T_VARIABLE) or number (T_NUM_STRING) errors for lines like https://github.com/Fortyseven/MediaHut/blob/912f04fd33038a7212518762fdc318d5f40c5553/build/index.php#L97 and https://github.com/Fortyseven/MediaHut/blob/912f04fd33038a7212518762fdc318d5f40c5553/build/index.php#L307
I'm trying to use PHP 7.0

I used 8.1.2 for development on this, but it had been a while since I'd worked with PHP from scratch, so I wasn't really focusing on version differences and compatibility.
I'll update the docs to indicate this, but also try and avoid the newer features so it's more compatible. :+1:


Fix cases where return value was neither a task id nor nil

There were 2 issues fixed here.

If the task already existed, it returned true, because that's what $log.warn returns
If report_sync were set to true it would return the group_hash itself.

Fixing 2 cleanly made the code unindent, so this is easier to review with whitespace off.


How can I record the LiDAR values ?

In the sample scene testScene, the Lidar camera is points only in one direction. How can I use the camera, similar to how you did on the video.  I am unable to find that scene.

Its already integrated with the Udacity provided scene.


What Proxy Information?

[The section which describes setting a system proxy is a bit vague as to what the proxy address and port number should be? Is this a proxy that's required only if an organization uses a proxy to access the internet or should there be a default that should be used?]

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

ID: 4096fac2-6f38-0e29-45a7-5eedc9abbd30
Version Independent ID: 49e53671-fc49-3614-f7d7-0071ebbdc73d
Content: Connect Operations Manager to Azure Monitor
Content Source: articles/azure-monitor/platform/om-agents.md
Service: log-analytics
GitHub Login: @MGoedtel
Microsoft Alias: magoedte

Thanks for your comment. The feedback has been shared with the content owner for further review. Thanks for your patience.

@bzabber - Yes, that is what the article states, if there is a proxy in-between the OpsMgr management server and the Azure service, you need to specify the proxy server address/port in order to allow it to communicate through the proxy server.  I hope this answers your question.  #please-close as this isn't a documentation issue.


Extend QuizSession so that sessions can be timed

Add an integer argument duration (in seconds) to the QuizSession component. If this argument is defined, start a timer in QuizSession. Display the timer somewhere on the screen (to begin with, perhaps near the "check" button). After duration seconds, tell the user in QuizFooter that the time has run out, and after the user confirms, call the callback function onResult("timeout") to exit the QuizSession.
To begin with, the duration could be set only in exam mode to 10 minutes.

I think this issue is available (right, @nico-miarka?), but rather low priority. The timer should occur in "exam mode", but exam mode only makes sense once there are many exercises.
I just created issue #9, which might be more interesting. Up to you of course

We won't work on this for the next few months, and possibly never.


Comment in commands?

Maybe I missed something, but how should I comment a line in the commands file?

For now you can't...
Would you like it to be possible?

It would be nice, at least to perform quick tests by enabling/disabling commands easily

I plan to implement it the bash way:
*BONJOUR*|*SALUT*==say "Bonjour $username"
*AU REVOIR*|*BYE*==say "Au revoir $username"; jv_exit
#*TEST*==say "Ca fonctionne!"
*VERSION*==say "Je suis en version $jv_version"
#*REPETE (*) ET (*)==say "(1) (2)"
#*SENS*VIE*==say "43"


linode-cli: 5.17.2 -> 5.17.2

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.
meta.description for linode-cli is: "The Linode Command Line Interface"
meta.homepage for linode-cli is: "https://github.com/linode/linode-cli"
meta.changelog for linode-cli is: ""
Updates performed

Ran passthru.UpdateScript

To inspect upstream changes

Compare changes on GitHub

Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
Warning: no invocation of /nix/store/gwz3g4dz3880nkdh8dvx6v3lcpq6i5l4-linode-cli-5.17.2/bin/linode-cli had a zero exit code or showed the expected version
Warning: no invocation of /nix/store/gwz3g4dz3880nkdh8dvx6v3lcpq6i5l4-linode-cli-5.17.2/bin/.linode-cli-wrapped had a zero exit code or showed the expected version
0 of 2 passed binary check by having a zero exit code.
0 of 2 passed binary check by having the new version present in output.
found 5.17.2 with grep in /nix/store/gwz3g4dz3880nkdh8dvx6v3lcpq6i5l4-linode-cli-5.17.2
found 5.17.2 in filename of file in /nix/store/gwz3g4dz3880nkdh8dvx6v3lcpq6i5l4-linode-cli-5.17.2

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

2 total rebuild path(s)

1 package rebuild(s)

1 x86_64-linux rebuild(s)
1 x86_64-darwin rebuild(s)

First fifty rebuilds by attrpath
linode-cli

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/gwz3g4dz3880nkdh8dvx6v3lcpq6i5l4-linode-cli-5.17.2 \
  --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 linode-cli https://github.com/r-ryantm/nixpkgs/archive/af5b4c1de398c0432ea250fa0f8820ae1355b7c4.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/gwz3g4dz3880nkdh8dvx6v3lcpq6i5l4-linode-cli-5.17.2
ls -la /nix/store/gwz3g4dz3880nkdh8dvx6v3lcpq6i5l4-linode-cli-5.17.2/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

Maintainer pings
cc @ryantm for testing.

@ajs124 The specVersion evolves independently of the version for this. That said this is very out of date now so lets let it regenerate.


Optimization: calculates wrong number of rides

The number of rides is not calculated correctly in the shift "Frühschicht".
Before Optimization:

After Optimization:

Expectations:

Frühschicht should be optimized first
Frühschicht, 29 Rides are ignored.

This has been fixed:

the early shift is optimized first
the depot-objects(purple) are build for all shifts
the correct number of rides is displayed after optimization

Screenshot:


Support for ??? "Empty Coalesce" operator

My issue is exactly what Kyle says here in the context of prettier's twig formatter: https://github.com/trivago/prettier-plugin-twig-melody/issues/47#issue-611254163
Is a custom syntax many people use in Craft, and while it makes sense to throw an error since it's not official twig syntax, I am wondering whether it is possible to, in preference order:
a) include support anyway
b) personally create a custom rule that makes this ok
c) disable twigcs for these lines
I understand (a) probably doesn't make sense until twig officially supports it. But I thought I'd put it out there since it probably wouldn't hurt anything either. (b) would be great too, but I'm not sure if it's possible. I would rather not do (c) though it's better than nothing, and I'm not sure if it is supported either.
As a side note, if (c) is not possible, I would think it an important feature request!

I got a chance to look into this more.
Looks like all we'd need for option (a) is to modify RulesetBuilder.php:
        $ops = $this->using(self::OP_VARS, [
            ...
            ['$➀\?\?\?➁$', $this->binaryOpSpace('???')], // Add this, must appear before following line
            ['$➀\?\?➁$', $this->binaryOpSpace('??')],
            ...
        ];

For people who don't use that syntax, it wouldn't hurt them, though I understand reluctance to include unofficial syntax in an official ruleset. But I'm curious if I could get a maintainer's thoughts. If you're not opposed, I'll submit a PR.
In the meantime, I was able to extend the RegEngineRule rule using a custom ruleset builder to get what I need, though it's more convoluted than I would have hoped, and am wondering if we might consider making an easier way to add new operators to the list.
class CustomRulesetBuilder extends RulesetBuilder {
    public function build(): array
    {
        $newOps = $this->using(self::OP_VARS, [['$➀\?\?\?➁$', $this->binaryOpSpace('???')]]);

        $build = parent::build();
        $expr = $build['expr'];
        $build['expr'] = array_merge(
            $newOps,
            $expr,
        );
        return $build;
    }
}

class CustomRuleset implements RulesetInterface
{
    private int $twigMajorVersion;

    public function __construct(int $twigMajorVersion)
    {
        $this->twigMajorVersion = $twigMajorVersion;
    }

    public function getRules()
    {
        $configurator = new RulesetConfigurator();
        $configurator->setTwigMajorVersion($this->twigMajorVersion);
        $builder = new CustomRulesetBuilder($configurator);

        return [
            new Rule\RegEngineRule(Violation::SEVERITY_ERROR, $builder->build()),
            new Rule\TrailingSpace(Violation::SEVERITY_ERROR),
            new Rule\UnusedMacro(Violation::SEVERITY_WARNING, $this->resolver),
            new Rule\UnusedVariable(Violation::SEVERITY_WARNING, $this->resolver),
        ];
    }
}


Tutorial: update docker tag

Closes #1558

LGTM! We should revert it after the tutorial (I forget which issue is tracking those changes)


update

add: uglified version of code (smaller footprint)
add: orginization of files
add: regex checks
add: debug option
add: temporary thickness
remove: individual set/temp/revert functions
add: call bus - more info in readme.md
update: readme.md to match additions/edits
update: transitions speed key is now time
fix: wordwrap
update: version 0.7.0 -> 0.7.1
update: readme.md to reflect new additions
add: ability to randomize the progress bar, with parameters
add: trail progress bar
add: mini video link
todo: create demo page w/ new features

decided to close this PR, new PR coming soon with a new system of managing the progress bars


add progress reporting when rebuilding HNSW index

@geirst please review
@havardpe @andreer FYI

example log snippet with this change:
[2024-11-19 13:51:25] EVENT   state/1 name="load.attribute.start" value="{"documentsubdb":"product.0.ready","name":"embedding"}"
[2024-11-19 13:51:27] WARNING Cannot use saved HNSW index for ANN, index parameters have changed
[2024-11-19 13:51:27] EVENT   state/1 name="hnsw.index.rebuild.start" value="{"name":"embedding","execution":"multi-threaded"}"
[2024-11-19 13:52:27] EVENT   state/1 name="hnsw.index.rebuild.progress" value="{"name":"embedding","percent":19.94368005631994}"
[2024-11-19 13:53:27] EVENT   state/1 name="hnsw.index.rebuild.progress" value="{"name":"embedding","percent":35.53376446623553}"
[2024-11-19 13:54:27] EVENT   state/1 name="hnsw.index.rebuild.progress" value="{"name":"embedding","percent":50.36084963915036}"
[2024-11-19 13:55:27] EVENT   state/1 name="hnsw.index.rebuild.progress" value="{"name":"embedding","percent":64.71463528536472}"
[2024-11-19 13:56:27] EVENT   state/1 name="hnsw.index.rebuild.progress" value="{"name":"embedding","percent":78.77072122927878}"
[2024-11-19 13:57:27] EVENT   state/1 name="hnsw.index.rebuild.progress" value="{"name":"embedding","percent":92.42170757829243}"
[2024-11-19 13:58:00] EVENT   state/1 name="hnsw.index.rebuild.complete" value="{"name":"embedding","time.elapsed.ms":393512.0}"
[2024-11-19 13:58:00] EVENT   state/1 name="load.attribute.complete" value="{"documentsubdb":"product.0.ready","name":"embedding","time.elapsed.ms":395209}"


[duckdb][integration] Get branch updated to work w/ main

Background / motivation
There are a handful of tests failing.
Get duckdb pr up-to-date with main.
TODOs / DoD

[ ] Duckdb pr has main integrated

Tests and various cleanups have been implemented such that we could complete this task and merge it into duckdb-integration PR


Unexplained failure (flake?) in TestFetchHistoricalJoinedEventDenied

This synapse CI run failed its complement step:
❌ TestFetchHistoricalJoinedEventDenied (3.12s)
      apidoc_room_history_visibility_test.go:86: Deploy times: 8.596861ms blueprints, 2.906504072s containers
      client.go:490: POST hs1/_matrix/client/r0/createRoom => 401 Unauthorized (6.765927ms)
      apidoc_room_history_visibility_test.go:23: CSAPI.MustDo POST http://localhost:49237/_matrix/client/r0/createRoom returned HTTP 401
  2022/01/25 15:15:13 ============================================

  2022/01/25 15:15:13 47530ed878655a1e50112a0c67b2c672848fc91e76cfe3cd99a811c04996c368 : Server logs:
  Signature ok
  subject=CN = hs1
  Getting CA Private Key
  2022/01/25 15:15:13 ============== 47530ed878655a1e50112a0c67b2c672848fc91e76cfe3cd99a811c04996c368 : END LOGS ==============

rerunning the job, it succeeded.
Unclear if complement is at fault or the test.

I have a suspicion this is synapse reporting readiness before being able to actually receive room creation calls like this, though I might be wrong.
Multiple similar versions of this test exists, and all of these create rooms directly at the start, so if this is a legitimate test flake, i think we'd be seeing a lot more of it.
Regardless, thanks for filing.

It's the first instruction issued to Synapse, and in the failed test Synapse returns a 401 to /createRoom but 200 OK in the passing test. This doesn't feel like a Complement issue. There's nothing here that can race. If, however:

synapse reporting readiness before being able to actually receive room creation calls like this

Then yes, that would be a race and is something which needs to be fixed in the Synapse dockerfile. In practice this means that /versions will 200 OK but /createRoom will 401.
We're now logging the HTTP response body for this call in https://github.com/matrix-org/complement/commit/8b4724be6ba0551d5e43b6ef0dd2de3548ef5414 which should help elucidate things.

Thanks both. that sounds much more plausible. Let's close this for now; I'll keep an eye on on synapse CI runs.


Feature request: don't space out some operators

In particular, ^ and maybe also / and *.
a * x ^ 2 + b * x + c / d

would look better as
a*x^2 + b*x + c/d

Need to come up with a way to present this in options, unless op list is fixed (ie ^ * and /)


Calendar IOB and COB showing Zero

Since Dev 5.1.0, the calendar shows zero COB and IOB, when IOB is positive.

Fixed in dev


Improve makefile run

Summary
Call makefile run on the built binary instead of using go
Add arguments to the executable (so we can pass config and other flags)

Will improve with frontend branch


Feature idea: new pipeline step mode to separate lock taking and releasing

Feature Request
Currently the lock(...) { ... } acts on a closure, selecting a resource according to pipeline developer request and releasing it when the closure is done. This limits resource locking to be a step inside one stage.
For larger scripted pipeline jobs that would use the same locked resource instance (without a chance that someone else queued and waiting would intercept it between lock{} calls in different stages), it would be beneficial to have a new lock step mode that would select the resource, lock it, and return the lock object maybe the name returned into a variable like supported already, but not release the lock. Then the job can use this resource in its many stages, and finally explicitly release the lock when it is no longer needed.
(Maybe also release the lock automatically when the build ends with whatever result and reason... or maybe not, or do so optionally - in one project we did have a practical case for reserving SUT's from broken test cases for developers to investigate).

Reading into history, this was tackled in #185 and earlier PRs and issues, but nothing got merged yet :(

This limits resource locking to be a step inside one stage.

In scripted pipeline you can use how many stages you need inside the lock closure. From my practice shall be resource lock only for necessary time. It means release as soon as possible. Because other jobs waits for it.
In my environment I use the step input (or something like that) and the mail has been send to user who starts the build. It is done in timeOut() step. This is allowed via build parameter.  And everybody in company is fine with this solution. Maybe this idea helps you. But anyway I will look in the mentioned PRs and try to finish it. How important is this issue for you? Just to plain my next steps.

We actually have a need for a lock to be passed between jobs. A job locks a testbed and starts tests. But when job detects a problem with a testbed, it kicks off a "restore testbed" job to lock it again while our original job exits (and lets the lock go out of scope). But then the user has to go to the console of the restore job and hit return once the testbed is fixed, again letting the lock go out of scope.
The problem with the above is that there is a window where another job can acquire the bad testbed before Jenkins runs the restore job. So another job fails trying to use the bad testbed. And things get ugly.
What we really want is for the original job to lock the testbed and either exit or try another testbed. Then ideally we would let the user run an unlock job once the testbed is fixed. The resource would remain locked until the user unlocks it.

This shall works in scripted pipeline
lock('testbed') {
  try {
    ... do your things here ...
  } catch (error) {
   timeout(10) {
      // todo send mail or other notification here
      input message: 'Approve when testbed is fixed', ok: 'OK'
    }
  }
}

tip: when you export in shared-library you will spare a lot of code in future.
ps: I shall really start with  #445


Close down permissions for creating new entities

https://github.com/CityOfDetroit/bloom/pull/10 opened up permissions such that any logged-in user can create new properties and listings (through the data access API). This config lives in backend/core/src/auth/authz_policy.csv and the relevant lines are:
p, user, listing, true, create

and
p, user, property, true, create

We definitely must avoid launching with the permissions in their current state.
The right answer here is probably to remove/change those two lines, so that only admins can create new listings and properties. And then create an admin user that can be used for e.g. importing listing data from HRD. It would also likely be useful to talk to the Exygy team about how they run their listings-importer script such that it has sufficient permissions.
Done criteria: only admins can create listings/properties.

Consider as part of this task adding back in the test removed in PR #24.

Exygy is building out some access controls in the near future. Referencing this issue:

...we need to create a distinction between public and partner users. Rather than create a simple flag, we can do this via role assignment. We currently have two roles in the system, admin and user (and technically anonymous). We can assign the admin and user roles to partner users and leave it so public users have no role.

So in the future, only partners will have roles, which will allow us to easily prevent public users from editing the database. I'm hoping to pick up this work from Exygy if it's not coming up soon on their roadmap.


tmate fails to build on Darwin

I tried to install tmate on OS X 10.10 with a master checkout of nixpkgs (947fdd6b7e7f9281bad024331f242e26bdc68916)
It fails with this error:
Makefile:1314: recipe for target 'msgpack/src/.libs/libmsgpackc.a' failed
make: *** [msgpack/src/.libs/libmsgpackc.a] Error 1
builder for ‘/nix/store/krv41sp7yhdb2wicqdsil33dh2h8bhq4-tmate-1.8.10.drv’ failed with exit code 2
error: build of ‘/nix/store/krv41sp7yhdb2wicqdsil33dh2h8bhq4-tmate-1.8.10.drv’ failed

Full output:
$ nix-env -iA nixpkgs.tmate
installing ‘tmate-1.8.10’
these derivations will be built:
  /nix/store/krv41sp7yhdb2wicqdsil33dh2h8bhq4-tmate-1.8.10.drv
building path(s) ‘/nix/store/vxsrqi1a4a1sz4qfxw97gkw2lwwik3mf-tmate-1.8.10’
unpacking sources
unpacking source archive /nix/store/ik95qxk5wwrazsamk2ihmshk56l8lfj2-tmate-1.8.10-src
source root is tmate-1.8.10-src
patching sources
configuring
main::scan_file() called too early to check prototype at /nix/store/ibaxgfdlvc6ml06nfxx5yybfw5hfg6d8-automake-1.10.3/bin/.aclocal-wrapped line 616.
configure.ac:18: installing `etc/compile'
configure.ac:9: installing `etc/config.guess'
configure.ac:9: installing `etc/config.sub'
configure.ac:7: installing `etc/install-sh'
configure.ac:7: installing `etc/missing'
Makefile.am: installing `etc/depcomp'
main::scan_file() called too early to check prototype at /nix/store/ibaxgfdlvc6ml06nfxx5yybfw5hfg6d8-automake-1.10.3/bin/.aclocal-wrapped line 616.
configure flags: --disable-static --disable-dependency-tracking --prefix=/nix/store/vxsrqi1a4a1sz4qfxw97gkw2lwwik3mf-tmate-1.8.10
checking for a BSD-compatible install... /nix/store/xdxv48i6p4rwv3v74r8bwjni9sck110g-coreutils-8.24/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /nix/store/xdxv48i6p4rwv3v74r8bwjni9sck110g-coreutils-8.24/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-apple-darwin14.5.0
checking host system type... x86_64-apple-darwin14.5.0
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for style of include used by make...  -DWITH_SFTP=OFF -DWITH_SERVER=OFF -DWITH_PCAP=OFF -DWITH_STATIC_LIB=ON -DWITH_GSSAPI=OFF)
-- The C compiler identification is Clang 3.6.2
-- Check for working C compiler: /nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/clang
-- Check for working C compiler: /nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/clang -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Performing Test WITH_FPIC
-- Performing Test WITH_FPIC - Success
-- Performing Test WITH_STACK_PROTECTOR
-- Performing Test WITH_STACK_PROTECTOR - Success
-- Found ZLIB: /nix/store/h1r2brlil9gb9fbvfpv7vnq8ssn9hvin-zlib-1.2.8/include
-- Found PkgConfig: /nix/store/c9i7qd85ll5znmfa1ayx25xllpn08wy7-pkg-config-0.28/bin/pkg-config (found version "0.28")
-- checking for module 'openssl'
--   found openssl, version 1.0.1p
-- Found OpenSSL: /nix/store/gq4dgvhy36g08ji918c72cyy8z498527-openssl-1.0.1p/lib/libssl.dylib;/nix/store/gq4dgvhy36g08ji918c72cyy8z498527-openssl-1.0.1p/lib/libcrypto.dylib
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Could NOT find NaCl (missing:  NACL_LIBRARIES NACL_INCLUDE_DIRS)
-- Looking for argp.h
-- Looking for argp.h - not found
-- Looking for pty.h
-- Looking for pty.h - not found
-- Looking for utmp.h
-- Looking for utmp.h - not found
-- Looking for termios.h
-- Looking for termios.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for util.h
-- Looking for util.h - found
-- Looking for libutil.h
-- Looking for libutil.h - not found
-- Looking for openssl/aes.h
-- Looking for openssl/aes.h - found
-- Looking for openssl/blowfish.h
-- Looking for openssl/blowfish.h - found
-- Looking for openssl/des.h
-- Looking for openssl/des.h - found
-- Looking for openssl/ecdh.h
-- Looking for openssl/ecdh.h - found
-- Looking for openssl/ec.h
-- Looking for openssl/ec.h - found
-- Looking for openssl/ecdsa.h
-- Looking for openssl/ecdsa.h - found
-- Looking for isblank
-- Looking for isblank - found
-- Looking for strncpy
-- Looking for strncpy - found
-- Looking for vsnprintf
-- Looking for vsnprintf - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for poll
-- Looking for poll - found
-- Looking for select
-- Looking for select - found
-- Looking for getaddrinfo
-- Looking for getaddrinfo - found
-- Looking for ntohll
-- Looking for ntohll - not found
-- Looking for htonll
-- Looking for htonll - not found
-- Looking for getaddrinfo in socket
-- Looking for getaddrinfo in socket - not found
-- Looking for inet_pton in nsl
-- Looking for inet_pton in nsl - not found
-- Looking for nanosleep in rt
-- Looking for nanosleep in rt - not found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - not found
-- Looking for forkpty in util
-- Looking for forkpty in util - not found
-- Looking for cfmakeraw
-- Looking for cfmakeraw - found
-- Looking for strtoull
-- Looking for strtoull - found
-- Looking for __strtoull
-- Looking for __strtoull - not found
-- Performing Test HAVE_GCC_THREAD_LOCAL_STORAGE
-- Performing Test HAVE_GCC_THREAD_LOCAL_STORAGE - Success
-- Performing Test HAVE_MSC_THREAD_LOCAL_STORAGE
-- Performing Test HAVE_MSC_THREAD_LOCAL_STORAGE - Success
-- Performing Test HAVE_GCC_VOLATILE_MEMORY_PROTECTION
-- Performing Test HAVE_GCC_VOLATILE_MEMORY_PROTECTION - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Could NOT find Doxygen (missing:  DOXYGEN_EXECUTABLE)
CMake Warning (dev) at CMakeLists.txt:100 (set):
  Policy CMP0053 is not set: Simplify variable reference and escape sequence
  evaluation.  Run "cmake --help-policy CMP0053" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  For input:

    '@CMAKE_SHARED_LIBRARY_PREFIX@ssh@CMAKE_SHARED_LIBRARY_SUFFIX@'

  the old evaluation rules produce:

    'libssh.dylib'

  but the new evaluation rules produce:

    '@CMAKE_SHARED_LIBRARY_PREFIX@ssh@CMAKE_SHARED_LIBRARY_SUFFIX@'

  Using the old result for compatibility since the policy is not set.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at CMakeLists.txt:101 (set):
  Policy CMP0053 is not set: Simplify variable reference and escape sequence
  evaluation.  Run "cmake --help-policy CMP0053" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  For input:

    '@CMAKE_SHARED_LIBRARY_PREFIX@ssh@CMAKE_SHARED_LIBRARY_SUFFIX@'

  the old evaluation rules produce:

    'libssh.dylib'

  but the new evaluation rules produce:

    '@CMAKE_SHARED_LIBRARY_PREFIX@ssh@CMAKE_SHARED_LIBRARY_SUFFIX@'

  Using the old result for compatibility since the policy is not set.
This warning is for project developers.  Use -Wno-dev to suppress it.

  Run "cmake
  --help-policy CMP0042" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

  MACOSX_RPATH is not specified for the following targets:

   ssh_shared
   ssh_threads_shared

This warning is for project developers.  Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build
make -C libssh/build ssh_static
make[1]: Entering directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
make[2]: Entering directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
make[3]: Entering directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
make[4]: Entering directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
Scanning dependencies of target ssh_static
make[4]: Leaving directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
make[4]: Entering directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
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[ 66%] Building C object src/CMakeFiles/ssh_static.dir/packet_crypt.c.o
[ 69%] Building C object src/CMakeFiles/ssh_static.dir/pcap.c.o
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make[4]: Leaving directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
[100%] Built target ssh_static
make[3]: Leaving directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
make[2]: Leaving directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
make[1]: Leaving directory '/private/var/folders/w4/_b6cpwnj1jb3jphtzkfrzr8w0000gn/T/nix-build-tmate-1.8.10.drv-0/tmate-1.8.10-src/libssh/build'
cd msgpack; ([ -f Makefile ] || (./bootstrap && ./configure))
./bootstrap: line 120: glibtoolize: command not found
main::scan_file() called too early to check prototype at /nix/store/ibaxgfdlvc6ml06nfxx5yybfw5hfg6d8-automake-1.10.3/bin/.aclocal-wrapped line 616.
configure.in:23: installing `ac/compile'
configure.in:28: installing `ac/config.guess'
configure.in:28: installing `ac/config.sub'
configure.in:3: installing `ac/install-sh'
configure.in:28: required file `ac/ltmain.sh' not found
configure.in:3: installing `ac/missing'
src/Makefile.am: installing `ac/depcomp'
Makefile.am: installing `./INSTALL'
checking for a BSD-compatible install... /nix/store/xdxv48i6p4rwv3v74r8bwjni9sck110g-coreutils-8.24/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /nix/store/xdxv48i6p4rwv3v74r8bwjni9sck110g-coreutils-8.24/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of clang... gcc3
checking if C++ API is enabled...
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking dependency style of clang++... gcc3
checking whether clang and cc understand -c and -o together... yes
checking build system type... x86_64-apple-darwin14.5.0
checking host system type... x86_64-apple-darwin14.5.0
checking how to print strings... printf
checking for a sed that does not truncate output... /nix/store/d6iwvpqdxmsz3xy1mrkmfnbp99sn5r35-gnused-4.2.2/bin/sed
checking for grep that handles long lines and -e... /nix/store/0g84myq00rzqfffpgxwzcn4f470yzhyf-gnugrep-2.21/bin/grep
checking for egrep... /nix/store/0g84myq00rzqfffpgxwzcn4f470yzhyf-gnugrep-2.21/bin/grep -E
checking for fgrep... /nix/store/0g84myq00rzqfffpgxwzcn4f470yzhyf-gnugrep-2.21/bin/grep -F
checking for ld used by clang... /nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/ld
checking if the linker (/nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /nix/store/hi6vb7q5s9q06k49b2jvv07d0wangj6v-cctools-binutils-darwin/bin/nm
checking the name lister (/nix/store/hi6vb7q5s9q06k49b2jvv07d0wangj6v-cctools-binutils-darwin/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin14.5.0 file names to x86_64-apple-darwin14.5.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin14.5.0 file names to toolchain format... func_convert_file_noop
checking for /nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /nix/store/hi6vb7q5s9q06k49b2jvv07d0wangj6v-cctools-binutils-darwin/bin/nm output from clang object... ok
checking for sysroot... no
checking for a working dd... /nix/store/xdxv48i6p4rwv3v74r8bwjni9sck110g-coreutils-8.24/bin/dd
checking how to truncate binary pipes... /nix/store/xdxv48i6p4rwv3v74r8bwjni9sck110g-coreutils-8.24/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... no
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... clang -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fno-common -DPIC
checking if clang PIC flag -fno-common -DPIC works... yes
checking if clang static flag -static works... no
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.5.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... clang++ -E
checking for ld used by clang++... /nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/ld
checking if the linker (/nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/ld) is GNU ld... no
checking whether the clang++ linker (/nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/ld) supports shared libraries... yes
checking for clang++ option to produce PIC... -fno-common -DPIC
checking if clang++ PIC flag -fno-common -DPIC works... yes
checking if clang++ static flag -static works... no
checking if clang++ supports -c -o file.o... yes
checking if clang++ supports -c -o file.o... (cached) yes
checking whether the clang++ linker (/nix/store/7ck6l3zps83c2l784rr7man6fmmz8xzl-clang-wrapper-3.6.2/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.5.0 dyld
checking how to hardcode library paths into programs... immediate
checking dependency style of clang... gcc3
checking if debug option is enabled...
checking for __sync_* atomic operations... yes
configure: creating ./config.status
config.status: error: cannot find input file: `Makefile.in'
Makefile:1314: recipe for target 'msgpack/src/.libs/libmsgpackc.a' failed
make: *** [msgpack/src/.libs/libmsgpackc.a] Error 1
builder for ‘/nix/store/krv41sp7yhdb2wicqdsil33dh2h8bhq4-tmate-1.8.10.drv’ failed with exit code 2
error: build of ‘/nix/store/krv41sp7yhdb2wicqdsil33dh2h8bhq4-tmate-1.8.10.drv’ failed

(triage) does this still happen?

Not on nixpkgs 9c5588e99f269a889739434c33421182e867b282

Okay, then close @pSub


Support for a Dask runner

Adding support for a Dask runner is currently under consideration?
Imported from Jira BEAM-5336. Original Jira may contain additional context.
Reported by: georvic.

Related issue in pangeo-forge-recipes: https://github.com/pangeo-forge/pangeo-forge-recipes/issues/256

In order to kickstart the discussion of implementing a Dask Beam runner, I propose we meet during the week of June 13-17. I have created a When2Meet Poll here - https://www.when2meet.com/?15861604-jLnA4 . If you are interested in attending, please give your availability. Hope to see many people there! 🚀

It would be great if we could a Beam expert to attend this meeting in order to provide guidance on the Beam side. @kennknowles, @TheNeuralBit, @richardliaw - any interest? If the times don't work for you, we can revise the options.

@kennknowles could you make that time?
My apache email is bhulette@, if apache.org emails don't work, it's the same username at google.com

Yes I can make it. (our emails are in the dev@ list thread)

@rabernat do I have the wrong time, or did this call already wrap up?

We moved to Google Meet: https://meet.google.com/tno-iquf-paq?authuser=0
On Wed, Jun 15, 2022 at 1:43 PM Tom Augspurger @.***>
wrote:

@rabernat https://github.com/rabernat do I have the wrong time, or did
this call already wrap up?
—
Reply to this email directly, view it on GitHub
https://github.com/apache/beam/issues/18962#issuecomment-1156756964, or
unsubscribe
https://github.com/notifications/unsubscribe-auth/AAJEKJT5Q3Z4CYWEVR63O2TVPII2RANCNFSM5X2GIIVA
.
You are receiving this because you were mentioned.Message ID:
@.***>

Any update? I find the idea very interesting

@alxmrs seems to be leading the charge on this for now. We have some notes here. https://docs.google.com/document/d/1Awj_eNmH-WRSte3bKcCcUlQDiZ5mMKmCO_xV-mHWAak/edit#heading=h.y0pwg4polebc
We are hoping that the folks at Google may spearhead the implementation of the Beam runner. Another option would be to make and RFP and seek an independent contractor to work on it.

Great timing! I have an initial working prototype here: https://github.com/alxmrs/beam/pull/1


Whats does this error mean ? Failed to update webhook: customresourcedefinitions.apiextensions.k8s.io

What does the below error mean? Does it have any impact on the working?
{"level":"error","ts":"2022-06-20T08:34:29.247Z","logger":"clusterimagepolicy.ConversionWebhook","caller":"controller/controller.go:566","msg":"Reconcile error","knative.dev/traceid":"2d5f13fe-d3ec-4ceb-943c-9aab83337bd4","knative.dev/key":"clusterimagepolicies.policy.sigstore.dev","duration":0.049818436,"error":"failed to update webhook: customresourcedefinitions.apiextensions.k8s.io "clusterimagepolicies.policy.sigstore.dev" is forbidden: User "system:serviceaccount:genesys-system:policy-controller-policy-webhook" cannot update resource "customresourcedefinitions" in API group "apiextensions.k8s.io" at the cluster scope","stacktrace":"knative.dev/pkg/controller.(*Impl).handleErr\n\tknative.dev/pkg@v0.0.0-20220325200448-1f7514acd0c2/controller/controller.go:566\nknative.dev/pkg/controller.(*Impl).processNextWorkItem\n\tknative.dev/pkg@v0.0.0-20220325200448-1f7514acd0c2/controller/controller.go:543\nknative.dev/pkg/controller.(*Impl).RunContext.func3\n\tknative.dev/pkg@v0.0.0-20220325200448-1f7514acd0c2/controller/controller.go:491"}

Closing this issue! It has been fixed very recently.


Exception: Data must be 1-dimensional

Hi, when importing a loom file with scanpy I get the following error.
>>> import scanpy.api as sc
>>> adata = sc.read_loom('/path/to/loom_file.loom')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 186, in read_loom
    dtype=dtype)
  File "/opt/conda/lib/python3.7/site-packages/anndata/base.py", line 672, in __init__
    filename=filename, filemode=filemode)
  File "/opt/conda/lib/python3.7/site-packages/anndata/base.py", line 850, in _init_as_actual
    ['obs_names', 'row_names', 'smp_names'])
  File "/opt/conda/lib/python3.7/site-packages/anndata/base.py", line 287, in _gen_dataframe
    columns=[k for k in anno.keys() if k != index_name])
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/frame.py", line 392, in __init__
    mgr = init_dict(data, index, columns, dtype=dtype)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 212, in init_dict
    return arrays_to_mgr(arrays, data_names, index, columns, dtype=dtype)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 56, in arrays_to_mgr
    arrays = _homogenize(arrays, index, dtype)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 277, in _homogenize
    raise_cast_failure=False)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 658, in sanitize_array
    raise Exception('Data must be 1-dimensional')
Exception: Data must be 1-dimensional

However, I can successfully open the .loom file with loompy.
>>> import loompy
>>> loom_file = loompy.connect("/path/to/loom_file.loom")
>>> loom_file[: , :]
array([[1., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       ...,
       [0., 0., 0., ..., 2., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.]])

Does someone know why? Thanks you.

Does this happen with any loom file or just one specifically?
Would you mind posting a minimal reproducible example we can run? I'm not that familiar with the specifics of loom files and an example that I can run will help me get to this much faster.

Hi @ivirshup, it seems that is happens to every file. Here's an reduced example straight from Seurat itself, and it gives me the same error. Thank you for your time!
example_seurat.zip

Sorry, I've been traveling for a bit and haven't had a chance to look too deeply at this yet. On my side, I'm able to read loom files from the HCA.
Could you send the code that generated that file? It'd be even more helpful if you could write the smallest example possible which generates a file that scanpy can't read.

Hi there @ivirshup, I have made a minimal computational generated Seurat object in R, then tried to import   it in Python using loompy and it seems fine. However using Anndata it gives the same error. I am going to send the script that I used, and the exported file, if it's useful. Thank you!
### In R

library(Matrix)
library(Seurat)
library(loomR)

# Constructing sparse matrix
x = c(1:10)
matrix = sparseMatrix(i = x, j = x, x = x)
rownames(matrix) = x
colnames(matrix) = x

# Constructing Seurat object and following its documented pipeline
seurat_object = CreateSeuratObject(counts = matrix)
seurat_object = NormalizeData(seurat_object, normalization.method = "LogNormalize", scale.factor = 10000)
seurat_object = FindVariableFeatures(seurat_object, selection.method = "vst", nfeatures = 2000)
all.genes = rownames(seurat_object)
seurat_object = ScaleData(seurat_object, features = all.genes)
seurat_object = RunPCA(seurat_object, features = VariableFeatures(object = seurat_object))

# Exporting object
as.loom(seurat_object, filename = "/path/to/seurat_object.loom")

### In Python

import scvelo as scv
import loompy

loom_file = loompy.connect("/home/AD/praposo/seurat_object.loom")
loom_file[:, :]

array([[ 1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  2.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  3.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  4.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  5.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.,  6.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.,  0.,  7.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  8.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  9.,  0.],
       [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0., 10.]])

# Importing object
adata = scv.read("/path/to/seurat_object.loom", cache=True)

# Resultant error
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/conda/lib/python3.7/site-packages/scanpy/readwrite.py", line 79, in read
    backup_url=backup_url, cache=cache, **kwargs)
  File "/opt/conda/lib/python3.7/site-packages/scanpy/readwrite.py", line 477, in _read
    adata = read_loom(filename=filename, **kwargs)
  File "/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 186, in read_loom
    dtype=dtype)
  File "/opt/conda/lib/python3.7/site-packages/anndata/base.py", line 672, in __init__
    filename=filename, filemode=filemode)
  File "/opt/conda/lib/python3.7/site-packages/anndata/base.py", line 850, in _init_as_actual
    ['obs_names', 'row_names', 'smp_names'])
  File "/opt/conda/lib/python3.7/site-packages/anndata/base.py", line 287, in _gen_dataframe
    columns=[k for k in anno.keys() if k != index_name])
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/frame.py", line 392, in __init__
    mgr = init_dict(data, index, columns, dtype=dtype)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 212, in init_dict
    return arrays_to_mgr(arrays, data_names, index, columns, dtype=dtype)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 56, in arrays_to_mgr
    arrays = _homogenize(arrays, index, dtype)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 277, in _homogenize
    raise_cast_failure=False)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 658, in sanitize_array
    raise Exception('Data must be 1-dimensional')
Exception: Data must be 1-dimensional

Information that might be useful
R Software versions
R - 3.5.1
Matrix library - 1.2.17
Seurat library - 3.0.0
loomR library - <IP_ADDRESS>00
Python Software versions
Python - 3.7.1
conda - 4.6.14
loompy - 2.0.16
anndata - 0.6.19
numpy - 1.16.3
pandas - 0.24.2
scanpy - 1.4.1
scikit-learn - 0.20.0
sklearn-pandas - 1.8.0
velocyto - 0.17.17
seurat_object.zip

Great! That is exactly what I need.
While getting an environment setup was certainly painful (new R install), I can't reproduce this issue. The file that code creates reads in fine for me (I did only check reading with anndata.read_loom).
It looks like some of the python packages you used are a little out of date. Maybe updating those will help? Here's some version info from my end:

 Python versions
scanpy==1.4.3 anndata==0.6.20 umap==0.3.9 numpy==1.16.4 scipy==1.3.0 pandas==0.24.2
scikit-learn==0.21.2 statsmodels==0.9.0 loompy==2.0.17

 R versions
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin18.5.0 (64-bit)
Running under: macOS Mojave 10.14.4

Matrix products: default
BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Seurat_3.0.1     loomR_<IP_ADDRESS>00 hdf5r_1.2.0      R6_2.4.0

loaded via a namespace (and not attached):
 [1] httr_1.4.0          tidyr_0.8.3         viridisLite_0.3.0
 [4] jsonlite_1.6        bit64_0.9-7         splines_3.6.0
 [7] lsei_1.2-0          R.utils_2.8.0       gtools_3.8.1
[10] Rdpack_0.11-0       assertthat_0.2.1    ggrepel_0.8.1
[13] globals_0.12.4      pillar_1.4.1        lattice_0.20-38
[16] reticulate_1.12     glue_1.3.1          digest_0.6.19
[19] RColorBrewer_1.1-2  SDMTools_1.1-221.1  colorspace_1.4-1
[22] htmltools_0.3.6     cowplot_0.9.4       Matrix_1.2-17
[25] R.oo_1.22.0         plyr_1.8.4          pkgconfig_2.0.2
[28] bibtex_0.4.2        tsne_0.1-3          listenv_0.7.0
[31] purrr_0.3.2         scales_1.0.0        RANN_2.6.1
[34] gdata_2.18.0        Rtsne_0.15          tibble_2.1.2
[37] ggplot2_3.1.1       ROCR_1.0-7          pbapply_1.4-0
[40] lazyeval_0.2.2      survival_2.44-1.1   magrittr_1.5
[43] crayon_1.3.4        R.methodsS3_1.7.1   future_1.13.0
[46] nlme_3.1-139        MASS_7.3-51.4       gplots_<IP_ADDRESS>
[49] ica_1.0-2           tools_3.6.0         fitdistrplus_1.0-14
[52] data.table_1.12.2   gbRd_0.4-11         stringr_1.4.0
[55] plotly_4.9.0        munsell_0.5.0       cluster_2.0.8
[58] irlba_2.3.3         compiler_3.6.0      rsvd_1.0.1
[61] caTools_<IP_ADDRESS>    rlang_0.3.4         grid_3.6.0
[64] ggridges_0.5.1      htmlwidgets_1.3     igraph_<IP_ADDRESS>
[67] bitops_1.0-6        npsurv_0.4-0        gtable_0.3.0
[70] codetools_0.2-16    reshape2_1.4.3      gridExtra_2.3
[73] zoo_1.8-6           dplyr_0.8.1         future.apply_1.2.0
[76] bit_1.1-14          KernSmooth_2.23-15  metap_1.1
[79] ape_5.3             stringi_1.4.3       parallel_3.6.0
[82] Rcpp_1.0.1          sctransform_0.2.0   png_0.1-7
[85] tidyselect_0.2.5    lmtest_0.9-37

  File "/opt/conda/lib/python3.7/site-packages/anndata/base.py", line 287, in _gen_dataframe
    columns=[k for k in anno.keys() if k != index_name])

It could be that in a previous version we didn't account for multi-dimensional .col and .row annotations in loom: the error hints to trying to initializing a column in .obs with something higher dimensional from loom (say, the PCs or X_pca). Evidently this is not possible and should instead go into .obsm. I'm not sure whether we do account for this now. But the fact that Isaac managed to run the code hints to it. 🙂

Yes, we're doing it these days: https://github.com/theislab/anndata/blob/a9390d6fca537fafdf9e93f1b85a91c10af7ca58/anndata/readwrite/read.py#L169 😄

@ivirshup, I updated the python modules exactly as you have, and it worked! Thank you very much!
@falexwolf Thank you for letting me know that!

Great! That is exactly what I need.
While getting an environment setup was certainly painful (new R install), I can't reproduce this issue. The file that code creates reads in fine for me (I did only check reading with anndata.read_loom). Additionally, I can read in the file you sent.
It looks like some of the python packages you used are a little out of date. Maybe updating those will help? Here's some version info from my end:
Python versions
R versions

Updating all these packages works! Thanks! @ivirshup

It works for me too!!

FWIW, I also tried updating the packages and still had an issue. Found that a few of my attributes had the shape (11990,1) but they needed to be (11990,). Removing the extra dimension with [:,0] fixed the issue.


Issue Template Updates for Figma link

Current Behavior
The project's current issue templates are missing an open invitation link where new contributors can join the community's Figma team and view user interface designs and other UX projects.
Desired Behavior
Each template that has a reference to Figma in its resources section should an invite link added.
Implementation
In each issue template that refers to Figma, replace the current line referring to Figma with this line:
- 🎨 Wireframes and [designs for Meshery UI](https://www.figma.com/file/SMP3zxOjZztdOLtgN4dS2W/Meshery-UI) in Figma [(open invite)](https://www.figma.com/team_invite/redeem/qJy1c95qirjgWQODApilR9)```

Acceptance Tests

All references to Figma include the "open invite" link.

Contributor Resources
The meshery.io website uses Jekyll and GitHub Pages. Site content is found under the master branch.

See the Contributing to Meshery.io Website section of the readme.md and other contributing instructions, too.
See Meshery site designs in this Figma designfile. Fill-in the Layer5 Community Member Form and join the Layer5 Community Slack for access.

Hi @leecalcote I would like to contribute on this. Can i please get assigned to this?

I would also like to collaborate with @yashchaddha, can I be assigned to this, please.

Closing the issue as completed via #212


Add support minValue and maxValue fields

Is your feature request related to a problem? Please describe.
As a CHWI would like to collect the vital signs of a user but also be able to evaluate/validate the threshold of various observation details collected from a patient
Describe the solution you'd like
Add support minValue and maxValue fields in a questionnaire as currently not working. Allows one to define the   thresholds for checking Vital signs  - https://github.com/opensrp/fhircore/issues/528
Describe alternatives you've considered
N/A
Additional context

Would you like to work on the issue?
Propose @syedowaisali90, for now, to work on this issue

@Tarun-Bhardwaj, @jingtang10 Can you assign @syedowaisali90 this issue?


Get the number of clients in a room in a cluster environment

public Iterable<SocketIOClient> getRoomClients(String room) {
        //This value is the total number of clients in the current room in the cluster
        Set<UUID> sessionIds = roomClients.get(room);

        if (sessionIds == null) {
            return Collections.emptyList();
        }
        //At this time, it is filtered out. Clients that are not in the current server in the current room
        List<SocketIOClient> result = new ArrayList<SocketIOClient>();
        for (UUID sessionId : sessionIds) {
            SocketIOClient client = allClients.get(sessionId);
            if(client != null) {
                result.add(client);
            }
        }
        //So the number of clients in the current room I get is only for the current server, not for the entire cluster
        return result;
    }

retry commit


[Feature Request] Flag to change ECMAScript version target

Specifically, it'd be nice to have an easy way to serve ES2017 locally without having to manually automate changing and reverting tsconfig files (async/await is a bit messy to debug as-is).

I think what I was asking for was a way to override the tsconfig.app.json setting, either in a CLI flag or angular.json, specifically so that I could have ng serve use ES2017 while ng build does ES5.
As noted, the reason for this is that stepping through async/await code in the debugger would be way easier than the ES5 equivalent that TypeScript generates.

FYI https://github.com/angular/angular-cli/issues/13216


When backend commits on a branch, test the front-end with it

We should do this with the dispatcher project. When there is a commit on a branch of the backend, the dispatcher project should be triggered. The dispatcher should trigger the frontend test. The branch name of the backend commit should be passed as a parameter. The parameter value determines what branch to check out for the backend during the front-end test.

On Tuesday May 31 we discussed changes that involve both the front-end and the back-end. The conclusion was that ibis-ladybug, the backend, is the artifact that we release. It has as dependency the front-end: a web jar. The backend should trigger a test of the front-end that checks out the code corresponding to the webjar. This is the test of issue #173. The test described with this issue may not be needed. I propose we discuss that later. For now, I move this issue out of the sprint.

I suggest we close this issue. @MatthijsSmets you asked me to update the ladybug and ladybug-frontend GitHub actions. The ladybug backend GitHub action still triggers the ladybug-frontend test. The ladybug-frontend test should always start the frontend with ng serve and it should test that instance of the frontend.
This is implemented in the following PRs:

https://github.com/wearefrank/ladybug-frontend/pull/479.
https://github.com/wearefrank/ladybug/pull/262


Procedure for running the graphql indexer in kubernetes

Before creating a helmchart, let's just make the stack runnable in k8s with custom yaml's and manual steps

let's see if we can use https://kubernetes.io/docs/tasks/configure-pod-container/translate-compose-kubernetes/

Done


Updating Languages to Ruby

Updating the primary language to Ruby.
Closes #14

Approving. Documentation changes only.


OpenWhisk Knative Runtime - NodeJS

This PR introduces the OpenWhisk NodeJS runtime which can be build/serve on Knative and/or OpenWhisk platforms.
@mrutkows and I have been working off of a private repo at https://github.com/mrutkows/openwhisk-knative-build. It's now at a point where we can share our work with the community and continue working off of dev tools.
I have copied the entire private repo into sub directory knative-build under dev tools.
There are lots of documentation, how tos, and test cases for your reference.

Merging so that we can make it more accessible as an experimental feature proposal for comm. members to try to use (or even open issues against).

Merging so that we can make it more accessible as an experimental feature proposal for comm. members to try to use (or even open issues against).


Value Prediction Scenario Gives Index Out Of Bounds Of Array Error/Exception

System Information (please complete the following information):

Model Builder Version (available in Manage Extensions dialog): <IP_ADDRESS>6603
Visual Studio Version: 16.11.0

Describe the bug

I ran into the issue while I was training some data with the Value Prediction Scenario and the Model Builder was going through each Regression Type after it got through the 3rd type
Clear description of the problem: The Model Builder fails and gives an error stating an index was out of bounds of an array, it is able to get through the first 2 or 3 regression types just fine, but then gives the previous error.

To Reproduce
Steps to reproduce the behavior:

When Creating a new .mbconfig file select the Value Prediction Scenario and select the Local CPU as the environment
Create a .csv file with the data provided in the "Additional context" section and load that
Select "Output" and the Label and leave all other values the same
Start Training for 10 seconds
See error

Expected behavior
I would expect the Model Builder to successfully complete the training, therefore allowing me to move on from there and add more data if needed.
Screenshots
Model Builder Output
Additional context
The data I was using is:
Operation,Input,Output
sqrt,4,2
sqrt,9,3
sqrt,16,4
sqrt,25,5
sqrt,36,6
sqrt,49,7
sqrt,64,8
sqrt,81,9
sqrt,100,10

@LittleLittleCloud  I can repro this issue with the provided data on latest main model builder: <IP_ADDRESS>6502, could you help to check again?

@LittleLittleCloud I can repro this issue with the provided data on latest main model builder: <IP_ADDRESS>6502, could you help to take a look again?

Yes, this issue is the same one I'm getting, if that's you're asking.

Can complete the training without error on ML.Net Model Builder: <IP_ADDRESS>5501 (Main)


bad argument #1 to 'size'

I'm trying to run the hierMIL model. I first did ./prep_milnet.sh bags_and_cases which is creating four files "BAGS_AND_CASES_MILNET_TEST.hdf5", "BAGS_AND_CASES_MILNET_TEST.info", "BAGS_AND_CASES_MILNET_word_mapping.txt", "BAGS_AND_CASES_MILNET.hdf5".
In milnet/main.lua providing -data as BAGS_AND_CASES_MILNET.hdf5 and -seg_data as BAGS_AND_CASES_MILNET_TEST.hdf5 and I'm facing error while the " th main.lua" which I couldn't resolve. I'm attaching a screenshot for it.

Thanks :)

@Bayesian4042 Did you find the solution for the issue you mention. I am facing the same issue.

@Bayesian4042 Did you find the solution for the issue you mention. I am facing the same issue.

@imcurren  I did solve but I don't remember exactly. I think I tried to uninstall Lua and Cuda for Torch. Try this once :

cutorch: https://github.com/torch/cutorch
export CUDNN_PATH="/usr/local/cuda/lib64/libcudnn.so.7"
./home/amohania/torch/install/bin/torch-activate

Let me know if this works 👍


GIFs import, do not play, washed out color

As you can see, in UE 4.26 the plugin does indeed enable GIF import:

However, after importing, GIFs don't play, they appear washed out, and they aren't recognized as 2D texture objects usable with things like UI elements.
Any idea what the issue here is?

Here's a look at the original GIF file I am working with.

Fixed by set bIgnoreGammaConversions = true;
Please checkout 0.4.6: https://github.com/neil3d/UnrealAnimatedTexturePlugin/releases/tag/v0.4.6


Improved Camera SE 5 Pre-release not work properly with Quick Light SE!

Improved Camera SE 1.0 Prerelease 5 does not work properly with Quick Light SE https://www.nexusmods.com/skyrimspecialedition/mods/12633?tab=description

bQuickLightLighting=0
Change above to 1 or enable it via the menu under fixes.


[handle actor function raise panic]

https://github.com/vsdmars/actor/blob/23d200bbc085e45b4ed2088ccd59e76c680aafce/localActor.go#L98
Actor should handle callback function if it panics.

done.


chore: Add LICENSE

MIT.

Codecov Report
Base: 99.13% // Head: 99.13% // No change to project coverage :thumbsup:

Coverage data is based on head (4aca819) compared to base (1463e41).
Patch has no changes to coverable lines.

Additional details and impacted files
@@           Coverage Diff           @@
##           master       #2   +/-   ##
=======================================
  Coverage   99.13%   99.13%
=======================================
  Files           1        1
  Lines         116      116
=======================================
  Hits          115      115
  Misses          1        1

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

:umbrella: View full report at Codecov.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.


Passing Integer Params

Hi,
Great package, just one thing that bother me is the option for integer input optimization. For my function i've got about 4 integers and 1 float, currently i'm doing param1=int(param1) in my function to overcome this, but, i'm wasting steps since it tries various times with 4.2, 4.1, 4.24 which are all actually 4 in my code.
Is there a way around it?
Thank you

This issue has been brought up a few times and to my knowledge there is no simple, standard way to do it.
Your solution is a simple one that works for many cases. However, if you're finding that it is not serving  your needs, I'm afraid you will have to come up with something else, or perhaps look in the literature for what other may have done.
ps: I do find that adding a bit of noise to the GP (alpha parameter in sklearn 1.18) helps when dealing with discrete variables, the added flexibility compensates for the ill-defined continuous variable.


Ability to override gw templates folder location

https://www.reddit.com/r/GuildWars/comments/v1mgtq/game_reads_the_wrong_template_folder/?utm_source=share&utm_medium=ios_app&utm_name=iossmf

57 85 f6 75 14 68 f9 01 00 00


onefuzz agent does not build from github release bundle

Information

Onefuzz version: 8.5.0
OS: Mariner

Provide detailed reproduction steps (if any)

wget https://github.com/microsoft/onefuzz/archive/refs/tags/8.5.0.tar.gz
tar -xzf 8.5.0.tar.gz
cd onefuzz-8.5.0/src/agent
cargo build

Expected result
Packages build successfully
Actual result
Package build fails while trying to build build.rs in onefuzz-agent and onefuzz-task due to the following code:
fn main() -> Result<(), Box<dyn Error>> {
    let sha = run_cmd(&["git", "rev-parse", "HEAD"])?;

Where the code is assuming that this is running in a git repo, which it won't be if the tarball is downloaded. This means that a patch needs to be applied in order to get the package building when building from source for into an RPM for example.
AB#162819

@cswindle can you DM me on teams please.

Spoke with cswindle offline.


How can i use presentViewController?

I wanna use mordal. But doesn't work navigation Items.
ViewController *vc = [[ViewController alloc] init];
vc.modalTransitionStyle = UIModalTransitionStyleFlipHorizontal;
[self presentViewController:vc animated:YES completion:nil];

[self dismissViewControllerAnimated:YES completion:nil];

This has worked for me
[self.frostedViewController presentViewController:vc animated:YES completion:nil];