break down NewStatusVerifier

Signed-off-by: kerthcet<EMAIL_ADDRESS>Please provide a description of this PR:
Break NewStatusVerifier down as this function does too much things. See todo

Hi @kerthcet. Thanks for your PR.
I'm waiting for a istio member to verify that this patch is reasonable to test. If it is, they should reply with /ok-to-test on its own line. Until that is done, I will not automatically test new commits in this PR, but the usual testing commands by org members will still work. Regular contributors should join the org to skip this step.
Once the patch is verified, the new status will be reflected by the ok-to-test label.
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/ok-to-test

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ping @istio/wg-user-experience-maintainers

/cc @hanxiaop as UX maintainer


Fix omission of Sspm and Supm from RVA23/RVB23

Churn in the pointer-masking extensionology led us to inadvertently omit Sspm and Supm from the profiles; these were meant to be added at the same time that Ssnpm was added, with Supm's existence following from Ssnpm's existence and Sspm being an extension option.

Approved out-of-band by @kasanovic


feat: custom locale pattern matcher

Added a module option to modify pattern matching logic to be a regex of choice
Also:

check our defined locale codes to match the provided regex
added documentation
return 404 if the locale provided to the route matches the regex but not our locale codes (mimick vue-router behaviour) in middleware

Resolves #39

Hello, that's awesome! Thank you so much; you did even better than I planned. I adjusted the package names in the tests, and everything else seems great.


Posts should NOT be allowed to be  edited to 'Requesting Help' ,if its originally created for 'Offering Help'

Posts should NOT be allowed to be edited to 'Requesting Help' ,if its originally created for 'Offering Help' and Vice Versa.
.
Steps: 1.Create a post using 'Create a New Post' from Help Board.

Choose 'Offering Help'. ENter details and Save
Now choose Edit and change to "Requesting Help" tab      and save

Expected:Posts should NOT be allowed to be edited to 'Requesting Help' ,if its originally created for 'Offering Help' and Vice Versa.
.

I don't have a way to verify the fix right now but it looks like if you remove this else claus on line 63 in the client/src/componets/createpost/EditForm.js it will prevent the value from being overwritten. Then you would just have to find a way to remove the buttons from that header.

  const handleFormData = (field) => (e) => {
    if (e.target) {
      setFormData({ ...formData, [field]: e.target.value });
    } else { >>>>{* this else claus *} <<<<<
      const helpmap = { 1: "offer", 2: "request" };
      setFormData({ ...formData, [field]: helpmap[e] });
    }

I don't have a way to verify the fix right now but it looks like if you remove this else claus on line 63 in the client/src/componets/createpost/EditForm.js it will prevent the value from being overwritten. Then you would just have to find a way to remove the buttons from that header.

  const handleFormData = (field) => (e) => {
    if (e.target) {
      setFormData({ ...formData, [field]: e.target.value });
    } else { >>>>{* this else claus *} <<<<<
      const helpmap = { 1: "offer", 2: "request" };
      setFormData({ ...formData, [field]: helpmap[e] });
    }


⚠ Bofrost.lu has degraded performance

In b0d0429, Bofrost.lu (https://www.bofrost.lu) experienced degraded performance:

HTTP code: 200
Response time: 2677 ms

Resolved: Bofrost.lu performance has improved in 3ad1840 after 22 minutes.


Screen flashes when using fade-in

First created this issue on the mortie repo without realizing it was the abandoned one.
When I enable --fade-in the screen flashes before showing the indicator and then fading in the screenshot background. With or without other effects enabled.

I’ve reproduced it on Sway 1.8. It’s really annoying, but I don’t know how to fix it. :/

From my brief testing, it seems like using ext-session-lock-v1 causes the screen to go black for a moment until it is drawn to. Perhaps the solution would be to create the window and draw to it before locking the session, but I'm not sure whether that's even possible.
This issue also seems to be present on regular https://github.com/swaywm/swaylock, so maybe this should be reported upstream and use whatever fix they implement (if any).

as of right now, Archlinux's swaylock doesn't have any discernible flashing, but swaylock-effects does

mortie's fork is not affected by this black flash. I've seen it only after swaylock-effects AUR repo switched to jirutka's one.


feature request: apiary blueprint markdown files

This will depend on snowcrash.
$ snowcrash apiary.apib -l

OK.
warning: (10)  headers asset is expected to be a pre-formatted code block, every of its line indented by exactly 12 spaces or 3 tabs :13012:63

Can you please explain for the uninitiated, preferably in full sentences:

what is apiary
what is snowcrash
what am I supposed to see above
what Vim filetype you want to check
what application is supposed to run the checks
what is the typical workflow for the files you want to check
where can I find the relevant applications
where can I find sample files that produce the errors you want to detect.

apiary is the company behind api blueprint. They open source the latter. If you choose to you can pay them to host your files, etc, otherwise you're on your own to build APIs. They extend markdown simple markdown to give meaning to request, response, routes, parameters, body, and headers.

API Blueprint is the specification of markdown for writing API documentation.
Snowcrash is the parser.
apiblueprint is the vim filetype from vim-apiblueprint.
snowcrash is the application you would run against the markdown files for the checks. Typically they end with .apib.
Typical workflow is open, edit, save, run snowcrash -l <input file> to get a list of errors/warnings. Fix errors, warnings, retry.
I'll look into generating some sample files to hit the error conditions.

Thanks!

Good summary, thank you.  I think I can figure out the error format from the sources, but a few sample files would still come in handy.

Ok, done in 5214f00.


Fix link to Auth Guide in readme

Summary
Fix link to Auth Guide in readme
Before:

After:

Requirements (place an x in each [ ])

[x] I've read and understood the Contributing Guidelines and have done my best effort to follow them.
[x] I've read and agree to the Code of Conduct.

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

Thank you @asherf!


Changing mapStateToProps doesn't hot reload?

Not sure if this is expected or not. But when updating mapStateToProps components don't seem to re-execute the mapStateToProps function.

Yeah, with the tooling overhaul it's a bit of grey area right now. Let's keep it open.

Let's track this in https://github.com/gaearon/babel-plugin-react-transform/issues/26 instead. You can also keep using React Hot Loader until it is fixed. With React Hot Loader, mapStateToProps should get reloaded just fine. When the issue in Babel plugin is fixed, it will work with React Transform too.

You might be interested in https://github.com/reactjs/redux/pull/1455.

This is fixed in React Hot Loader 3.
It is built with lessons learned from both React Hot Loader and React Transform.
It’s still in alpha but I encourage you to check it out!

This is fixed in React Hot Loader 3.
It is built with lessons learned from both React Hot Loader and React Transform.
It’s still in alpha but I encourage you to check it out!

@gaearon Great stuff! ran into this today when teaching redux to someone. I'll give it a whirl :)


Yahoo Provider error

Hello,
When i try to login with yahoo i get this error:
A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond <IP_ADDRESS>:443

this was a problem from iis server, i solve this.


Interrupt oplog entry

Resolves #239
Created follow-up task #289

wasi::directories_replay test broken, to be checked


[Question] How to set the value of the form field from another one before applying filters?

For example I have a form with two fields, some filters and validators:
$factory = new \Zend\Form\Factory();
$form = $factory->createForm([
    'elements' => [
        [
            'spec' => [
                'name' => 'fieldOne',
                'type'  => 'Text',
            ],
        ],
        [
            'spec' => [
                'name' => 'fieldTwo',
                'type' => 'Text',
            ],
        ],
    ],
    'input_filter' => [
        'fieldOne' => [
            'filters' => [
                ['name' => 'StringTrim'],
            ],
            'validators' => [
                new \Application\Validator\FieldOneValidator(),
            ],
        ],
        'fieldTwo' => [
            'filters' => [
                ['name' => 'StringToUpper'],
            ],
        ],
    ],
]);

If fieldOne is valid and fieldTwo is empty, then I need to set the filtered value form fieldOne into fieldTwo and filter it.
$form->setData([
    'fieldOne' => '    test    ',
    'fieldTwo' => '',
]);
if ($form->isValid()) {
    $form->getData(); // ['fieldOne' => 'test', 'fieldTwo' => 'TEST']
}

$form->setData([
    'fieldOne' => '    test    ',
    'fieldTwo' => 'not empty',
]);
if ($form->isValid()) {
    $form->getData(); // ['fieldOne' => 'test', 'fieldTwo' => 'NOT EMPTY']
}

How to realize this?

This venue is intended for reporting issues/bugs.  For assistance with how to do specific things with the framework please use our IRC channel (#zftalk on Freenode) or StackOverflow.


RegEx works in file search, but fails in "Find in Project"

Hi,
I don't know if this is really an error or I'm just missing something, but the following behaviour seems odd to me.
I'm using RegEx to find and replace some html patterns.
Text to find:

</div>
<!-- end: main body -->

Text to replace

</main>
<!-- end: main body -->

RegEx I'm using

<\/div>(\s|\n)*<\!--\send:\smain\sbody\s-->

This works fine when I use it in a single file, but fails when I use the Find in Project search feature.
I'm using Atom 1.0.19 on Mac OS X 10.10.5 (14F27).
I created a few files for testing, you can find them at https://www.dropbox.com/s/25wr27ys6mzy2o7/atom-test.zip?dl=0
You can recreate this error by searching in one file for

<\/div>(\s|\n)*<\!--\send:\smain\sbody\s-->

and then use it with the Find in Project search.

From what I understand Find in Project use atom/scandal which seems to do regex search on a line per line basis. Because your regex span multiple line, it'll never match.
Alternatively other operation are done on chunk of text, and while there's some check to ensure the chunk will cut on a newline, there's no grantee the chunk will not cut in between those lines.

Sorry about this and thanks for the report. Closing in favor of https://github.com/atom/scandal/issues/5


DTFS2-4177 - Maker confirm cover start date

Under this commit the maker can review the UKEF application (condition / unconditional) decision and confirm the cover start dates of the issued facilities. Following changes have been pushed:

GEF UI - Cover date constant for uniformity
Introduction of various date related helper functions for EPOCH calculation, past date check and date in range check.
Introduction of two facilities helper functions responsible for returning all the facilities (cover date not confirmed) as NJK custom table rows and returning facility cover start date.
Errors, Success and / or Facilities are only send as parameters to NJK when not null for concise code
Unit test - Updated mock data
UKEF cover start date controller - Identified whether the cover start date is valid based on conditions specified, if it is then update the facility or throw appropriate error message
UKEF decision accepted value now passed to the gef-ui/templates/partials/review-decision.njk if previously accepted by the maker.
GEF Facility model - Condition check and introduction of new attribute to save facility cover start date confirmation by the maker.
Updated style

I've noticed that gef-ui/public/css/styles.css got removed.
I believe this is used to style the page - this is referenced inside index.njk file


Add Slaughterhouse preset

(closes #4466)

Let's see if we can get the tag changed back to amenity=slaughterhouse
Combining it with landuse=industrial makes problems for us, because it's not a landuse.  People who write the wiki don't know better.


merge release-219 into develop

Should be no diff from develop but I messed up the merge order of 218, 219, and develop

closing because there is merge conflict and if I resolve merge conflict in Github, develop will end up merged into release-219 first


Update README.md

Company Using AWS Data Wrangler Section
Issue #, if available:
Description of changes:
By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

Updates to readme


[BUG] Error when reading an empty blob with BlobClient.DownloadToAsync

Bug description
When an empty (0-byte) blob is being read with BlobClient.DownloadToAsync(Stream..), an exception is thrown:

Azure.RequestFailedException: The range specified is invalid for the current size of the resource
Status: 416 (The range specified is invalid for the current size of the resource.)
ErrorCode: InvalidRange

The issue seems similar with  #https://github.com/Azure/azure-sdk-for-net/issues/10827 which seems to be fixed, however the problem still appears.
Expected behavior
The call should not crash and an empty stream should be returned.
Actual behavior
Azure.RequestFailedException is thrown:
Unhandled Exception: Azure.RequestFailedException: The range specified is invalid for the current size of the resource.
RequestId:3462f82e-001e-004e-2ea5-232c62000000
Time:2020-05-06T12:57:52.6984058Z
Status: 416 (The range specified is invalid for the current size of the resource.)
ErrorCode: InvalidRange

Headers:
x-ms-request-id: ...
x-ms-client-request-id: ...
x-ms-version: 2019-07-07
x-ms-error-code: InvalidRange
Date: Wed, 06 May 2020 12:57:52 GMT
Server: Windows-Azure-Blob/1.0,Microsoft-HTTPAPI/2.0
Content-Length: 249
Content-Range: bytes */0
Content-Type: application/xml
   at Azure.Storage.Blobs.BlobRestClient.Blob.DownloadAsync_CreateResponse(ClientDiagnostics clientDiagnostics, Response response)
   at Azure.Storage.Blobs.BlobRestClient.Blob.<DownloadAsync>d__0.MoveNext()
   at System.Threading.Tasks.ValueTask`1.get_Result()
   at Azure.Storage.Blobs.Specialized.BlobBaseClient.<StartDownloadAsync>d__45.MoveNext()
   at Azure.Storage.Blobs.Specialized.BlobBaseClient.<DownloadInternal>d__44.MoveNext()
   at Azure.Storage.Blobs.Specialized.BlobBaseClient.<DownloadAsync>d__43.MoveNext()
   at Azure.Storage.Blobs.PartitionedDownloader.<DownloadToAsync>d__5.MoveNext()
   at Azure.Storage.Blobs.Specialized.BlobBaseClient.<StagedDownloadAsync>d__58.MoveNext()
   at Azure.Storage.Blobs.Specialized.BlobBaseClient.<DownloadToAsync>d__56.MoveNext()
   at Azure.Storage.Blobs.Specialized.BlobBaseClient.<DownloadToAsync>d__52.MoveNext()
   at Azure.Storage.Blobs.Specialized.BlobBaseClient.<DownloadToAsync>d__48.MoveNext()

To Reproduce
Call
var memoryStream = new MemoryStream();
await blobClient.DownloadToAsync(memoryStream);
on an 0-byte blob:
using System.IO;
using System.Text;
using System.Threading.Tasks;
using Azure.Storage.Blobs;

namespace BlobClientDownloadToAsyncErrorEmptyBlob
{
    internal static class Program
    {
        static async Task Main()
        {
            const string storageAccountConnStr = "DefaultEndpointsProtocol=https;AccountName=....;AccountKey=...;EndpointSuffix=core.windows.net";

            // create the container
            BlobServiceClient blobServiceClient = new BlobServiceClient(storageAccountConnStr);
            BlobContainerClient containerClient = blobServiceClient.GetBlobContainerClient("testcontainer");
            await containerClient.CreateIfNotExistsAsync();

            // write the blob
            const string blobContent = ""; // empty string
            BlobClient blobClient = containerClient.GetBlobClient("testblob");
            await blobClient.UploadAsync(new MemoryStream(Encoding.UTF8.GetBytes(blobContent)), overwrite: true);

            // read the 0-bytes blob
            var memoryStream = new MemoryStream();
            // throws  Azure.RequestFailedException: The range specified is invalid for the current size of the resource.
            // Status: 416 (The range specified is invalid for the current size of the resource.)
            // ErrorCode: InvalidRange
            await blobClient.DownloadToAsync(memoryStream);

            // ...
        }
    }
}

Environment:

Azure.Storage.Blobs 12.4.1 package; Azure.Core 1.2.0; Azure.Storage.Common 12.4.0
Windows 10 .NET Framework 4.7.2 or 4.6.2 (running in a console app or in an Azure App Service)
Visual Studio 2019
Azure StorageV2 account; Access tier: Standard/Hot

Hi,
I was able to reproduce your issue.
Looks like the only way to work around this is to call the regular Download method and use the copyTo Stream
BlobDownloadInfo download = blob.Download();
using (MemoryStream stream = new MemoryStream())
{
     download.Content.CopyTo(stream);
}

--
Looks like we give it a range when attempting to staged download. The service does not seem to like this that much because it throws a 416, when providing a range on trying to download an empty blob. I will update this issue once more investigation has been done.

This bug was resolved with https://github.com/Azure/azure-sdk-for-net/pull/12845


Support modules with bundled prebuilds for electron

All new native modules I've been writing, use a new technique where I bundle all prebuilds inside the npm tarball and the pick the right one at runtime. A huge benefit of this is that using these modules with electron just works, no compilation needed.
However when people use electron-rebuild, it forces the prebuilded modules to rebuild by running node-gyp rebuild instead of running the install script if present in package.json. Ironically this breaks some of my modules that support electron out of the box cause it tries to recompile them without running a preinstall script specificed by the install script.
Anyway to fix this?
As an example try my sodium-native module. It is a native module that works across node/electron without needing any recompilation that breaks when electron-rebuild tries to recompile it, cause it isn't running the install script instead node-gyp like npm does.

Idea: A fix would be to run the install script with electron if present. Thoughts?

can confirm, I have to do:
cd node_modules/sodium-native && npm run preinstall && cd - && electron-rebuild

to stop electron-rebuild erroring out with sodium-native.

Alternatively a quick fix would be a --skip option that I can tell people to use when using my modules that support electron.

FYI, this works perfectly fine, npm rebuild --runtime=electron --target=$(electron --version) --disturl=https://atom.io/download/atom-shell --abi=$(electron --abi)

@mafintosh is the --dist-url argument necessary?

oh I see, because this is just npm rebuild it won't have the headers otherwise 👍

@mafintosh I was talking with someone working on Rust a while back and we were discussing a similar issue to this one.  The potential solution we arrived on was checking if the module exposed a "electron-rebuild" script, and if so we would run that instead of the node-gyp rebuild.
Would this be a valid solution for your issue as well?

@MarshallOfSound My main use case is just skipping any recompile steps as my thing already works on electron so yes. However if you electron-rebuild just ran the script I linked I wouldnt have to make any changes so much prefer that.

@mafintosh That command rebuilds everything in the current npm module including nested and transitive dependencies regardless of type, rebuild state and other factors we care about.  The reason we use the current strategy is to avoid rebuilds when the module has already been built and to avoid rebuilding development dependencies / other dependencies a user wishes to ignore.

@MarshallOfSound couldnt you just only execute that command in the deps you wanna rebuild? Or do the equivalent of what the command does yourself in the repos you wanna rebuild?

@mafintosh Executing npm rebuild doesn't just affect the module in the CWD it affects all that modules dependencies as well which can have wild side effects.  Also it means we can't track if the module is rebuilt for Electron or not.  I'd much prefer to find a solution which doesn't involve a fundamental change in how we rebuild modules.
Is there some kind of script, file or dependency that we can search for to exclude your electron compatible prebuilts from our list?
Without know how your prebuilt scripts work could you simply create a .forge-meta file in the correct place so we don't attempt to rebuild the module?
https://github.com/electron/electron-rebuild/blob/master/src/rebuild.ts#L99

@MarshallOfSound yea you can look for ./prebuilds/{platform}-{arch}/electron-{electron-abi}.node. fx on macOS (darwin) it'll look like this, prebuilds/darwin-x64/electron-50.node. If that file is present you should just skip the recompilation. That'd be super awesome!!

@MarshallOfSound please could you cut a new release with this fix?


Update StatisticsClient integration tests

Add test to fetch bitmap from Statistics service
Add test to fetch timemap from Statistics service
Add test to fetch sizemap from Statistics service

Resolves: OLPEDGE-1232
Signed-off-by: ashevchu<EMAIL_ADDRESS>

Codecov Report

Merging #121 into master will not change coverage.
The diff coverage is n/a.

@@          Coverage Diff           @@
##           master    #121   +/-   ##
======================================
  Coverage    83.5%   83.5%
======================================
  Files          43      43
  Lines         852     852
  Branches      130     130
======================================
  Hits          712     712
  Misses        105     105
  Partials       35      35

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[Request] Possibility to log the QRCode to a logger or intercept

Hi @Auties00 ,
Currently the QR is printed to the console/terminal.
In previous versions it was also possible to print the QRCode to a file.
But I'm using SLF4J as logging, to log everything from the application to a rolling file.
Can you make it possible to provide a logger or receive/intercept the QR code somewhere to be able to log myself.
Now there is logging at 2 places ...
Thanks in advance!
Kind regards,

Hi @Auties00 ,
Currently the QR is printed to the console/terminal. In previous versions it was also possible to print the QRCode to a file.
But I'm using SLF4J as logging, to log everything from the application to a rolling file. Can you make it possible to provide a logger or receive/intercept the QR code somewhere to be able to log myself. Now there is logging at 2 places ...
Thanks in advance! Kind regards,

The option was previously available inside listeners(onQrCode(BitMatrix)), but it has now been moved to the Options class. You can still use the old QrHandlers there


Adds celery.toml for loading custom Celery config [#821]

Purpose
This PR provides a way for a user to override any element of the Celery config. Originally this ticket was only to investigate overriding the event_queue_prefix var, however I would anticipate customising Celery config to be a relatively common use case given the variety of implementations.
Changes

Adds celery.toml to store celery config overrides based on the new lowercase settings.
Attempt to load in config from celery.toml when instantiating the celery_app on the worker.

Checklist

[x] Update CHANGELOG.md file

[x] Merge in main so the most recent CHANGELOG.md file is being appended to
[x] Add description within the Unreleased section in an appropriate category. Add a new category from the list at the top of the file if the needed one isn't already there.
[x] Add a link to this PR at the end of the description with the PR number as the text. example: #1

[ ] Applicable documentation updated (guides, quickstart, postman collections, tutorial, fidesdemo, database diagram.
If docs updated (select one):

[ ] documentation complete, or draft/outline provided (tag docs-team to complete/review on this branch)
[ ] documentation issue created (tag docs-team to complete issue separately)

[ ] Good unit test/integration test coverage
[ ] This PR contains a DB migration. If checked, the reviewer should confirm with the author that the down_revision correctly references the previous migration before merging
[ ] The Run Unsafe PR Checks label has been applied, and checks have passed, if this PR touches any external services

Ticket
Fixes #821

@seanpreston can you lowercase the new values so it matches with #871 ?

@seanpreston can you lowercase the new values so it matches with https://github.com/ethyca/fidesops/pull/871 ?

@ThomasLaPiana if it's OK with you I'll do this in a follow-up, since I'd like to get this merged and into a minor release today, and we won't have the changes from #871 in that release.


[transfer-to-object] TTO support in test scenario

Description
This adds support for transfer-to-object/Receiving tickets in the test scenario.
In order to do this a "proper" object store needed to be added to the test scenario since we cannot count on caching to keep the object for us like we can with dynamic fields in test scenario tests.
This adds such a test by creating a shared InMemoryStorage (wrapped in a mutex since tests can be multi-threaded and we need internal mutability). Two handles are then created for this -- one for the storage read operations, and another is added to the context extension so that we can place "objects-to-be-received" into this store when we create the Receiving ticket.
This might generally be useful for other tests as well/refactoring the test scenario to be more realistic but I will leave any such investigations for another day.
Test Plan
Added tests for the new features to the test scenario tests.

If your changes are not user-facing and not a breaking change, you can skip the following section. Otherwise, please indicate what changed, and then add to the Release Notes section as highlighted during the release process.
Type of Change (Check all that apply)

[ ] protocol change
[ ] user-visible impact
[ ] breaking change for a client SDKs
[ ] breaking change for FNs (FN binary must upgrade)
[ ] breaking change for validators or node operators (must upgrade binaries)
[ ] breaking change for on-chain data layout
[ ] necessitate either a data wipe or data migration

Release notes

Am I losing my mind or did I review this already? Or something similar?

Am I losing my mind or did I review this already? Or something similar?
I don't think so? But maybe I'm losing my mind too...

Am I losing my mind or did I review this already? Or something similar?

Shared object deletion support probably?

@tnowacki and @amnn just bumping this to see if we can get this in soon/if there's anything left outstanding before we can land this. Have been fielding some requests for adding TTO support in test scenario.


The integration is private error

Was adding to test on my server following the README  link and hit an error

Hi @mabry1985, did you get it working on your Discord server?


fix(seed): fixed correct answer typo in explanation of question 2

Pre-Submission Checklist

[x] Your pull request targets the staging branch of freeCodeCamp.
[x] Branch starts with either fix/, feature/, or translate/ (e.g. fix/signin-issue)
[x] You have only one commit (if not, squash them into one commit).
[x] All new and existing tests pass the command npm test. Use git commit --amend to amend any fixes.

Type of Change

[x] Small bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds new functionality)
[ ] Breaking change (fix or feature that would change existing functionality)
[ ] Add new translation (feature adding new translations)

Checklist:

[x] Tested changes locally.
[x] Addressed currently open issue (replace XXXXX with an issue no in next line)

Closes #16245
Description

Fixed the typo in the correct answer in the explanation from [['A', 'B', 'C']] to [['A'], ['B'], ['C']].

@saurishkar, great catch! Thank you for the fix. Everything LGTM!


prototype for preview buffer for git_branches picker

This PR is a prototype for a builtin preview for the git_branches picker in case you would be open to consider it.

The user can specify what type of log_cmd to display, in the demo below you can see different commands in action.
I have modified the original cmd for branches by adding --format='%(refname:short)': it should help with the parsing of the branches names (removing *, spaces and all other symbols)

I might need some guidance for the following:

can one use the treesitter parser to syntax highlight the git logs? I saw in the codebase that there is such option but I could not make it work
if the user specifies a log_cmd that isn't a "git command", then the preview may fail with some obscure errors: how can one ensure that for "bad commands" we catch the exception first and default to the default self.opts.log_cmd? I tried to pcall the vim.system but I do not what type of exception we want to capture.

Examples:
With the default log_cmd we have:

With
git = {
  branches = {
    log_cmd = "git diff --stat main",
..
}

we have

Ty @gennaro-tedesco!

This PR is a prototype for a builtin preview for the git_branches picker in case you would be open to consider it.

That would be welcome, I’m sure some users will like the consistency in UI vs the fzf native previewer.

can one use the treesitter parser to syntax highlight the git logs? I saw in the codebase that there is such option but I could not make it work

You can set the file type to git which is what fugitive uses for basic highlighting, otherwise there are all sorts of treesitter tricks as also now used in blines|git_blame (try it out, really cool) you can set treesitter for any part of the text:
https://github.com/ibhagwan/fzf-lua/blob/6d7c08ed7871696764084350ab1803cb9ee9454e/lua/fzf-lua/win.lua#L901-L951

if the user specifies a log_cmd that isn't a "git command", then the preview may fail with some obscure errors: how can one ensure that for "bad commands" we catch the exception first and default to the default self.opts.log_cmd? I tried to pcall the vim.system but I do not what type of exception we want to capture.

I’d rename it to cmd to be consistent with all other commands / previewer settings, as for thr error I’d rather avoid the exception and display the detailed error message directly in the buffer and set it to plain text, similar to how inaccessible files or binary file preview info msg is displayed in the file/buffer previewer.

Another thing I’d prefer changing is avoid usage if vim.system as its synchronous and the experience will  be bad with a long running commands / big repo, I’d prefer using a terminal buffer and running the command that way which is async, there’s already framework laid out for such cases which is used for previewing images using chafa, etc:
https://github.com/ibhagwan/fzf-lua/blob/6d7c08ed7871696764084350ab1803cb9ee9454e/lua/fzf-lua/previewer/builtin.lua#L630

TBH, although I like this, unless we’re adding more add-value features to this I don’t see a real benefit other than having the same builtin previewer layout, while nice, all the other git previewers are native, git commits, status, blame, log, all of these use a native previewer (shell command inside fzf, which also comes with the benefit of piping into git-delta).
What is the real reasoning you wish to have this one different than all the other git previewers? Also aside from the git hash which can be highlighted there’s no treesitter benefit to the log message itself as it’s not code.

The reasoning was to slowly provide builtin previewers for all providers, given that they are neovim buffers they would offer more configurability than the fzf previewer.
You're right of course that there is no added value besides a little more configurability and aesthetic, we can close the PR if there is no other idea on top.

If there’s no real problem why fix it :)
2+ years nobody complained it’s not a neovim buffer.


Support filtering variables in the variable explorer based on JMC

Some imports generate a ton of variables (like types defined etc) that we don't filter by default.
We could use the 'file' value we get from Jupyter to filter out types that aren't in the workspace. These would be non user code.
See this bug for a reason why:
microsoft/vscode-python#10301

I'm assuming this is complete since I haven't noticed non-JMC variables. Let me know if that's not the case with an example


The model weights were updated 17 hours ago and now loading them causes the error

Error message when loading new weights from lambdalabs/sd-image-variations-diffusers:
AttributeError: module transformers has no attribute CLIPImageProcessor

updated transformers to 4.25.0.dev0
With this version I get the following error:
TypeError: getattr(): attribute name must be string when loading

Same error:
AttributeError: module transformers has no attribute CLIPImageProcessor
Any solution?

@artyemk this one with CLIPImageProcessor is solved by installing 4.25.0.dev0 transformers version from transformers repo. In the nets configs they mention that they work with this version, but the next error with getattr() i haven't solved yet

Other solution is to checkout previous version of nets configs and weights

@KyriaAnnwyn I tried to solve this issue by running
pip install --upgrade git+https://github.com/huggingface/transformers.git
But now I get another error:
AttributeError: 'CLIPVisionModelWithProjection' object has no attribute 'get_image_features'

@artyemk seems like the version of transformers you got is 4.24. Check this please

I'm getting the same error. Trying to install 4.25.0.dev0 but i'm not sure how. Any advice?
(lambda-diffusers) PS C:\Users\Landon\stable_diffusion\lambda-diffusers> pip install -Iv transformers==4.25.0.dev0
Using pip 22.3.1 from C:\Users\Landon\anaconda3\envs\lambda-diffusers\lib\site-packages\pip (python 3.7)
ERROR: Could not find a version that satisfies the requirement transformers==4.25.0.dev0 (from versions: 0.1, 2.0.0, 2.1.0, 2.1.1, 2.2.0, 2.2.1, 2.2.2, 2.3.0, 2.4.0, 2.4.1, 2.5.0, 2.5.1, 2.6.0, 2.7.0, 2.8.0, 2.9.0, 2.9.1, 2.10.0, 2.11.0, 3.0.0, 3.0.1, 3.0.2, 3.1.0, 3.2.0, 3.3.0, 3.3.1, 3.4.0, 3.5.0, 3.5.1, 4.0.0rc1, 4.0.0, 4.0.1, 4.1.0, 4.1.1, 4.2.0, 4.2.1, 4.2.2, 4.3.0rc1, 4.3.0, 4.3.1, 4.3.2, 4.3.3, 4.4.0, 4.4.1, 4.4.2, 4.5.0, 4.5.1, 4.6.0, 4.6.1, 4.7.0, 4.8.0, 4.8.1, 4.8.2, 4.9.0, 4.9.1, 4.9.2, 4.10.0, 4.10.1, 4.10.2, 4.10.3, 4.11.0, 4.11.1, 4.11.2, 4.11.3, 4.12.0, 4.12.1, 4.12.2, 4.12.3, 4.12.4, 4.12.5, 4.13.0, 4.14.0, 4.14.1, 4.15.0, 4.16.0, 4.16.1, 4.16.2, 4.17.0, 4.18.0, 4.19.0, 4.19.1, 4.19.2, 4.19.3, 4.19.4, 4.20.0, 4.20.1, 4.21.0, 4.21.1, 4.21.2, 4.21.3, 4.22.0, 4.22.1, 4.22.2, 4.23.0, 4.23.1, 4.24.0)
ERROR: No matching distribution found for transformers==4.25.0.dev0
```l

@artyemk this one with CLIPImageProcessor is solved by installing 4.25.0.dev0 transformers version from transformers repo. In the nets configs they mention that they work with this version, but the next error with getattr() i haven't solved yet

I was able to solve installing transformers with this command
pip install --upgrade<EMAIL_ADDRESS>
However now I am also getting the error.
Traceback (most recent call last):
  File ".\im2im.py", line 11, in <module>
    pipe = StableDiffusionImageEmbedPipeline.from_pretrained("lambdalabs/sd-image-variations-diffusers")
  File "C:\Users\Landon\anaconda3\envs\lambda-diffusers\lib\site-packages\diffusers\pipeline_utils.py", line 373, in from_pretrained
    load_method = getattr(class_obj, load_method_name)
TypeError: getattr(): attribute name must be string

I solved this issue by initializing pipe like this:
pipe = StableDiffusionImageEmbedPipeline.from_pretrained(
 "lambdalabs/sd-image-variations-diffusers",
 revision="273115e88df42350019ef4d628265b8c29ef4af5",
 )

@artyemk @hniksoleimani this makes you use old version of weights, but more interesting to test the new one!

@hniksoleimani @artyemk

I solved this issue by initializing pipe like this:
pipe = StableDiffusionImageEmbedPipeline.from_pretrained(
 "lambdalabs/sd-image-variations-diffusers",
 revision="273115e88df42350019ef4d628265b8c29ef4af5",
 )

Thank you this works, however now i'm curious is there a way to run this with a lower memory GPU? for example I see people use .half(), or fp16 how would I do that using this script?
Thanks again for your feedback. I am running on Nvidia 3070 with 8GB.


Installation difficulties on Fedora 32 beta

Error occurs when attempting to install using gem install nokogiri
gem install output
Building native extensions. This could take a while...
ERROR:  Error installing nokogiri:
	ERROR: Failed to build gem native extension.

    current directory: /home/colin/.gem/ruby/gems/nokogiri-1.10.9/ext/nokogiri
/usr/bin/ruby -I /usr/share/rubygems -r ./siteconf20200401-11102-1tvxe7o.rb extconf.rb
checking if the C compiler accepts ... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
	--with-opt-dir
	--without-opt-dir
	--with-opt-include
	--without-opt-include=${opt-dir}/include
	--with-opt-lib
	--without-opt-lib=${opt-dir}/lib64
	--with-make-prog
	--without-make-prog
	--srcdir=.
	--curdir
	--ruby=/usr/bin/$(RUBY_BASE_NAME)
	--help
	--clean
/usr/share/ruby/mkmf.rb:471:in `try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
	from /usr/share/ruby/mkmf.rb:597:in `block in try_compile'
	from /usr/share/ruby/mkmf.rb:544:in `with_werror'
	from /usr/share/ruby/mkmf.rb:597:in `try_compile'
	from extconf.rb:138:in `nokogiri_try_compile'
	from extconf.rb:162:in `block in add_cflags'
	from /usr/share/ruby/mkmf.rb:655:in `with_cflags'
	from extconf.rb:161:in `add_cflags'
	from extconf.rb:416:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /home/colin/.gem/ruby/extensions/x86_64-linux/2.7.0/nokogiri-1.10.9/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /home/colin/.gem/ruby/gems/nokogiri-1.10.9 for inspection.
Results logged to /home/colin/.gem/ruby/extensions/x86_64-linux/2.7.0/nokogiri-1.10.9/gem_make.out

mkmf.log contents
"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I.    -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC  conftest.c  -L. -L/usr/lib64 -L. -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fstack-protector-strong -rdynamic -Wl,-export-dynamic  -m64   -lruby  -lm   -lc "
annobin: conftest.c: ICE: The location of the "-fstack-clash-protection" flag has changed - please rebuild annobin
annobin: conftest.c: ICE: Please contact the annobin maintainer with details of this problem
annobin: conftest.c: Expeceted name: -fstack-clash-protection.  Actual name: -fstack-check=
cc1: error: failed to initialize plugin /usr/lib/gcc/x86_64-redhat-linux/10/plugin/annobin.so
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5:   return !!argv[argc];
6: }
/* end */

Operating system is Fedora 32 beta.
uname -a output
Linux colindesktop 5.6.0-300.fc32.x86_64 #1 SMP Mon Mar 30 15:45:58 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Thank you

Hi @Colin-Suckow, sorry to hear you're having problems. Unfortunately, I don't think what you're seeing is caused by (or can be fixed by) Nokogiri.
I don't know much about annobin, but this looks like an issue with compiler flags. For context, C extensions (like Nokogiri) use the same flags that your ruby executable was compiled with. You can see these flags to verify this statement:
require "rbconfig"
puts RbConfig::CONFIG["CFLAGS"]

Can I ask that you verify that the flags emitted by this code include -fstack-clash-protection? If so, then this means ruby was compiled with flags that are not valid (perhaps because you upgraded gcc or because something else in your system changed after ruby was compiled/installed?).
You may have similar errors compiling other gems with C extensions, like sqlite3, which may also be worth verifying.

You're spot on about other C extensions not working. I'll continue the search elsewhere. Thank you for the reply, it was very helpful. I'll go ahead and close this for you.


[starlink-ast] Update, fix

Update to 9.2.10. But note https://github.com/Starlink/ast/issues/21.
Fixes vcpkg baseline issue.
Removes supports restrictons.

[x] Changes comply with the maintainer guide
[x] SHA512s are updated for each updated download
[x] The "supports" clause reflects platforms that may be fixed by this new version
[x] Any fixed CI baseline entries are removed from that file.
[x] Any patches that are no longer applied are deleted from the port's directory.
[x] The version database is fixed by rerunning ./vcpkg x-add-version --all and committing the result.
[x] Only one version is added to each modified port's versions file.

Thanks :)


bump to v2.3.1

i'm pretty sure the PR workflow is somewhat different, but someone will notice it...

LGTM


Deformable Convolutions v2 - gluon

Description
Feature request for Deformable convolution v2 in gluon.
An example in symbol has been given my the authors referenced below.
References
https://github.com/msracver/Deformable-ConvNets/tree/master/DCNv2_op

Already being solved here : https://github.com/apache/incubator-mxnet/pull/16341


Code blocks with syntax highlighting nested in a list break list layout.

Somewhere between 0.55.1 and 0.55.6, using syntax highlighting on nested code blocks breaks the layout for the order and unordered lists. It appears as though nested highlighted code blocks prevent the closing </ol> and </ul> tags.
Code blocks without syntax highlight work as expected, so I'm not sure if this is an issue with Blackfriday or Chroma.
Here are some examples:
The following markdown:

1. This is a line item with a nested codeblock with the syntax specified.

    ```sh
    This code block renders correctly but breaks the next li.
    For some reason, the fenced code blocks prevent the closing </ol> and </ul> tags.
    ```

2. This `<li>` is nested under the first `<li>` when it shouldn't be.

    ```
    But this nested code block renders as it should, but nested under the nested `<li>`.
    ```

3. And this next line item is also nested under the first `<li>`.

Renders as:

But if I remove the syntax specification from the code block, it works fine:

1. This is a line item with a nested codeblock **without** the syntax specified.

    ```
    This code block and the following line items render correctly.
    ```

2. This `<li>` is works as it should.

    ```
    But this nested code block renders as it should, but nested under the nested `<li>`.
    ```

3. As does this one.

Renders as:

BUT, if there are two nested syntax highlighted code blocks in a list, the 2nd is rendered outside of what should be its parent list and the rest of the list renders as it should:
1. This is a line item with a nested codeblock with the syntax specified.

    ```sh
    This code block renders correctly but breaks the next li.
    For some reason, the fenced code blocks prevent the closing </ol> and </ul> tags.
    ```

2. This `<li>` gets nested.

    ```sh
    But this code block DOES NOT get nested under the line item or the ordered list.
    It is outside of the above `<ol>`.
    ```

3. This `<li>` renders correctly.

Renders as:

Duplicate of #6040


Injectable Memoization

This enables something like this:
@sim.injectable(autocall=False, memoize=True)
def my_utility_func(x, y, z):
    return x + y + z

@sim.column()
def my_col(another_col, my_utility_func):
    result = my_utility_func(1, 2, 3)
    return another_col * result

And if you call my_utility_func again with the input of 1, 2, 3 you'll get back the cached result instead of re-doing the calculation.
Memoization requires autocall=False and that function inputs always be hashable. The memoization cache follows the same rules as other caching, so you can use cache_scope=, sim.clear_cache, sim.disable_cache, and sim.enable_cache as usual.

Want to merge to master and I'll try it out?  Or should I try out and then merge?

I'll merge it, I think it's okay. One thing I noticed is that you're generally not using these utility functions via the simulation framework, you're calling them directly since they are in the global scope. You won't get the memoization going that route, you need to have the function injected by the simulation framework so that you get the version that's been wrapped up with caching.

That makes sense - I'll take a look.

Hmm - it looks to me like they're already injectables.  Is there a place where they're used directly as functions that I need to change?
https://github.com/synthicity/bayarea_urbansim/blob/master/variables.py#L125
https://github.com/synthicity/bayarea_urbansim/blob/master/variables.py#L145
https://github.com/synthicity/bayarea_urbansim/blob/master/variables.py#L152

See line 147 where you're calling parcel_average_price; you're not having parcel_average_price injected, instead you're using it directly from the global namespace. You have decorated parcel_average_price, but the decorator doesn't change the function in the global namespace, it only wraps it within the simulation framework. (This is because when autocall=True the function is wrapped up in a special class and it doesn't make sense to leave that in the global namespace. With autocall=False and memoization it makes more sense to have the wrapped function in the global namespace, but the precedent is set...)
To get the wrapped function from the simulation framework change line 146 to:
@sim.injectable('parcel_sales_price_sqft_func', autocall=False)
def parcel_sales_price_sqft(use, parcel_average_price):
    s = parcel_average_price(use)
    ...

Then the wrapped version of the parcel_average_price function is injected. Similar wherever you use parcel_is_allowed.

OK, that's right.  The problem is that use isn't an injectable - it's a parameter that gets called in a for loop - e.g. for use in uses: parcel_average_price_sqft(use) - I'm not sure how I could turn a parameterized function into a for loop.  I mean, parcel_average_price is an injectable because there's only one parcel_average_price function, but there are many uses that can get passed so I'm not sure how to do that in the simulation framework.  Should I call add_injectable inside the for loop in order to change the use injectable?

I see. Hmm.
One option is to use the things described in the "Running Sim Components a la Carte" section of the docs:
for use in uses:
    sales_price = sim.eval_variable('parcel_sales_price_sqft_func', use=use)

or
for use in uses:
    with sim.injectables(use=use):
        sales_price = sim.eval_variable('parcel_sales_price_sqft_func')

But another thought is whether these functions need to be registered as injectables at all. I might be able to rewire the memoize decorator a little so it can be used on its own, then you'd drop the sim.injectable bit and instead do sim.memoize(cache_scope='iteration') and you'd use the function from the global scope as you've been doing. The downside there is that the function would not be available via injection or get_injectable.

Hmm, I don't love the idea of calling the function from the global scope.  I like that the sim framework knows about all the code that gets run for the simulation in a fairly direct way.  I think one of the eval_variable solutions should work.  So if I do
for use in uses:
sales_price = sim.eval_variable('parcel_sales_price_sqft_func', use=use)

If the variable parcel_sales_price_sqft_func also takes parcel_average_price as an injectable, that will get injected right?  So when I set use=use I'm adding additional parameters, but not eliminating the use of injectables that are already registered?

Right, you're temporarily supplementing any already registered stuff.

OK I'll try that!

I've been mulling the idea of iterable injectables. Like you'd register a list and it would serve the contents up one at a time. You could imagine that being used with the 'year' during simulation runs. And if you had two iterable injectables you'd end up with the product of those. But I haven't totally puzzled out all the implications and logistics of that idea.

The thought had occurred to me, especially since I mainly use this for creating columns that are parameterized (e.g. a price for each land use) and could be returned as a dataframe.


Airlocks can now be opened only by moving towards them

Fixes https://github.com/space-wizards/space-station-14/issues/1023

This feels like the kind of thing that should be fixed in the physics engine instead so the collision events don't get raised when, well, there's no collision.

I don't think this is a physics engine problem, unless you want to really change the way collisions are raised. In my testing, I was only able to get the issue to work by actually colliding with the door.

I think a collision event is being raised because collision is happening. If we want doors to only open for certain directions of collision, this might be the way to go.

Yeah but the real weird thing is how I could walk into the airlock by just heading straight at it, stop before it triggers a collision, then walk the other way and actually trigger a collision. Something's messed up with that either way.

Fixes #1023
I think you meant 1024 :)

I think you meant #1024 :)

Yeah, sorry for the wrong link, corrected.

I merged this but added a comment that it is merely a workaround.


EF Core: update the documenation on how to write a provider

Hi, I'm trying to get my head around writing a custom EF Core provider. I'm looking at the EF Core codebase and the blog post by Arthur Vickers as suggested. However, I don't see the correlation between the blog post and the codebase.
For example, the first step in the blog indicates to implement IDatabaseProviderServices. However, a search of the solution yields no results for IDatabaseProviderServices.
What am I missing?

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

ID: 1b7a5729-3ab9-2d56-fabb-678256cfc5e1
Version Independent ID: 0c546b6d-05b6-6f6f-3ad7-f31380d4562a
Content: Writing a Database Provider - EF Core
Content Source: entity-framework/core/providers/writing-a-provider.md
Product: entity-framework
GitHub Login: @anmiller
Microsoft Alias: divega

I think Arthur's post is from EFCore 1.X, because I have also found no existence of any DatabaseProviderServices.
Looking at code is probably the way to go now. I'm going to try and follow the step by step creation of the Cosmos DB provider.
Out of curiosity, for what database are you writing a provider? I was looking at doing Azure Table Storage.

Please notice there are big differences between writing a Relational provider and a non-relational provider. I am in the process of writing a Relational provider, and you may find the commit story and currently tiny provider codebase helpful. The provider does not currently implement Migrations or Scaffolding or Model extensions, which helps keeping it small, but it can create databases and tables and run queries against Northwind.

@MisinformedDNA Thanks, Dan. I'll take a look at it.

@ErikEJ Hi Erik. Yes, I'm looking to implement a relational provider. Just the basics such as you've implemented so far will be good enough to get me started. Which project should I be looking at?

This one https://github.com/GibraltarSoftware/VistaDB.EFCore (develop branch)

Excellent! Thank you, @ErikEJ.

Back to the OP, the documentation needs to be updated to either not mention @ajcvickers post, or add a note of caution that it's for an old, incompatible version.

@MisinformedDNA Updating the docs is on my list, but unfortunately not very near the top. I will get to it as soon as I can.

Duplicate of https://github.com/aspnet/EntityFramework.Docs/issues/681.

Hi Team,
I am working on a service fabric project and the data is stored in a reliable collection (in memory).
I am planning to write a custom EF Core provider to do CRUD operations in Reliable collections.
Can you provide me the basic steps to create a custom provider?

@balukantu This is tracked by #681


Cranelift: vconcat is not implemented in the interpreter

👋 Hey!
.clif Test Case
test interpret

function %vconcat_i32x4(i32x2, i32x2) -> i32x4 {
block0(v0: i32x2, v1: i32x2):
    v2 = vconcat.i32x2 v0, v1
    return v2
}
; run: %vconcat_i32x4([1 2], [3 4]) == [1 2 3 4]

function %vconcat_i64x2(i64, i64) -> i64x2 {
block0(v0: i64, v1: i64):
    v2 = vconcat.i64 v0, v1
    return v2
}
; run: %vconcat_i64x2(1, 2) == [1 2]

Steps to Reproduce

Run cargo run -- test ./the-above-file.clif in the cranelift directory of this repository

Expected Results
The test to pass!
Actual Results
    Finished dev [unoptimized + debuginfo] target(s) in 0.15s
     Running `/home/afonso/git/wasmtime/target/debug/clif-util test lmao.clif`
thread 'worker #0' panicked at 'not implemented: Vconcat', cranelift/interpreter/src/step.rs:1073:28
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
 ERROR cranelift_filetests::concurrent > FAIL: panicked in worker #0: not implemented: Vconcat
FAIL lmao.clif: panicked in worker #0: not implemented: Vconcat
1 tests
Error: 1 failure

Versions and Environment
Cranelift version or commit: main
Operating system: Linux
Architecture: x86_64
Extra Info
The above test is failing in this assertion.
Some documentation about the expected behavour of vconcat can be found here.

After discussion offline with @cfallin, I think we should close this in favor of deleting this instruction, which I've written up in #5463. That is also a good first issue for anyone who wants to tackle it.


[Bug]: list_order_items_by_next_token gives 400 Client Error: Bad Request for url

Python Version
3.9
Python Amazon MWS (PAM) Version
1.0dev (GitHub develop branch)
Has your copy of PAM been altered in any way?
No, I HAVE NOT made changes to the MWS code
Describe the issue
When we try to use "list_order_items_by_next_token" we get following error 400 in response.
Expected behavior
We are getting more and more orders from amazon and are over the fetchlimit for "list_orders".
Now we try to use the next_token for fetch remaining orders and expected to get orders back, but we running on response error 400.
We were running on dev11 before installing dev18 but getting always token invalid back.
So we update but run in response error instead.
If i use the token from "order_list" in the scratchpad it is working.
mws_error.txt
MWS Credential check

[X] I have removed my MWS credentials from any tracebacks and code samples

List order items by next token relates to a request for list_order_items() when there are more items returned than fit on one page.
If you received a token from a list_orders() request, you can either provide the token back to the same list_orders(next_token=next_token) call, or use list_orders_by_next_token(). Otherwise MWS seems to be responding correctly, that your token is being used on an incorrect operation.

Sorry for the trouble, didnt recognized i choosed the wrong method for the orders.
Thanks for the quick answer.


Merge Downstream

Recommend this is squash merged

Merging, last change was a docs merge conflict. Previous commit passed gates.


fix: codeowners

Nope:

I should see that actions are blocked until your approval.

FIXED! Please rename master branch to main

Moreover, can you edit labels to match these.
Note: Name & Emoji are very important.


WIP: Update dependencies with MPI build tags

Checklist

[x] Used a fork of the feedstock to propose changes
[x] Bumped the build number (if the version is unchanged)
[ ] Reset the build number to 0 (if the version changed)
[x] Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
[x] Ensured the license file is being packaged.

closes #9

Change the URLs to reflect recent move to gitlab and uam.es from
launchpad
Add zlib as explicit dependency
Add xylar as maintainer

Hi! This is the friendly automated conda-forge-linting service.
I wanted to let you know that I linted all conda-recipes in your PR (recipe) and found some lint.
Here's what I've got...
For recipe:

Failed to even lint the recipe, probably because of a conda-smithy bug :cry:. This likely indicates a problem in your meta.yaml, though. To get a traceback to help figure out what's going on, install conda-smithy and run conda smithy recipe-lint . from the recipe directory.

Hi! This is the friendly automated conda-forge-linting service.
I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

Various problems, obviously.  I'll work on this as I have time.  Suggestions are welcome.

@zerothi, I worked on this PR a bit more and I have to say I wasn't able to make any headway.  The errors I'm seeing just don't make any sense at all to me.  In some cases, it seems to be complaining about errors in files after preprocessing but I can't find the preprocessed files to figure out which line is actually the problem or why.
In the nompi cases, it can't find netcdf.mod even though I've verified that it's in the include path that's being passed via -isystem to the compiler.  Again, I'm baffled.
Given that siesta isn't a software I use, I'm inclined to leave it to those who do.  It just happened to be the only conda-forge package that I saw as potentially benefiting from the new MPI matrix build I did of netcdf-fortran.


add example of fourier interpolation

Codecov Report

Merging #55 (a1ded43) into dev (9e10678) will decrease coverage by 0.45%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev      #55      +/-   ##
==========================================
- Coverage   58.89%   58.44%   -0.46%
==========================================
  Files          13       13
  Lines        1107     1107
==========================================
- Hits          652      647       -5
- Misses        455      460       +5

Impacted Files
Coverage Δ

src/symmetry/SymOp.jl
84.84% <0.00%> (-3.04%)
:arrow_down:

src/symmetry/spglib.jl
71.60% <0.00%> (-2.47%)
:arrow_down:

src/BZMeshes.jl
93.82% <0.00%> (-1.24%)
:arrow_down:

src/Cells.jl
63.44% <0.00%> (-1.08%)
:arrow_down:

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Change to the next workspace (relative on monitor including empty workspaces) from the last workspace adds an empty workspace instead of going back to the first workspace

Hyprland Version
Hyprland, built from branch  at commit 1b48642fd15c433c53876f1b933dcd46265caf8f dirty (). Tag: v0.30.0
Bug or Regression?
Bug
Description
Disclaimer : I don't know if this is a bug or I am just dumb and don't understand how it works
So I use two monitors. I bound workspaces to each of the monitor (1,2,3,4,5 on the first monitor and 6,7,8,9,10 on the last monitor).
I configured a keybind to change to the next workspace (relative on monitor including empty workspaces): bind = $mainMod, N, workspace, r+1.
What I expected is it changes to the next workspace that is bound on the same monitor/exists on that monitor, so when it is on the last workspace, it will go back to the first workspace. I expected this because I have a keybind to move window to the next monitor relatively (with the same '+1' : bind = $mainMod, O, movewindow, mon:+1) and it works (I can move the window from the first monitor to the second monitor and vice versa)
But, what happened is when I change to the next workspace on the last workspace, it stayed on the last workspace. When there is a workspace that has window in it, it adds an empty workspace with the same label as the last active workspace.
How to reproduce
Bind workspaces to monitor. On the last workspace, change to the next workspace (relative on monitor including empty workspaces).
Crash reports, logs, images, videos
https://github.com/hyprwm/Hyprland/assets/80519948/1c59de79-5ca6-4789-9e66-064648afe269

seems to work fine for me
please show the video with the output of hyprctl activeworkspace or socat -U - UNIX-CONNECT:/tmp/hypr/$HYPRLAND_INSTANCE_SIGNATURE/.socket2.sock
also update hyprland to a newer version
looks like a waybar bug tbh

please show the video with the output of hyprctl activeworkspace or socat -U - UNIX-CONNECT:/tmp/hypr/$HYPRLAND_INSTANCE_SIGNATURE/.socket2.sock

Here's the video:
https://github.com/hyprwm/Hyprland/assets/80519948/9c735987-05bf-4015-a37b-5928b73a108b

also update hyprland to a newer version

It's the latest on arch repo, I guess I'll try the git version then

looks like a waybar bug tbh

I don't think waybar has any influence in adding workspace

Hyprland, built from branch main at commit 7b32b4214d028a173c8192bddaa9e43503326080 dirty (layout: avoid redundant size sets on new fullscreen).
Tag: v0.31.0-63-g7b32b421
I tried using newer version, but it still does the same behaviour

that's how that dispatcher works https://wiki.hyprland.org/Configuring/Dispatchers/#workspaces
it goes to the next workspace on that monitor
by adding a workspace rule you're not saying that only those workspaces can go on that monitor, you're saying those workspaces can only go on that monitor
to achieve the behavior you want you can easily make a simply script to change the workspace to the one you want to
the wrong numbering, like I said seems like a waybar issue


Pull Request:  Dealing with issue #9 and having Setup Teardown work on this addin.

I cherry-picked Brian Ku's tests.
Reviewed the issue and it matched a problem I was having when trying to use the addin.
Setup Methods and Teardown was ignored .  Caused  tests to fail.
Did minor change to make that work done.  Also added in there to ignore tests that should have been ignored due to the attribute.

I have tests that is not retried if it fails in a setup method and Ignore methods that are running when they shouldn't. Looks like this PR solves that issue? Any plans to merge it?


It's possible to merge two tdigest structs?

I don't have the mathematical background to answer this question, but it's possible to merge two tdigest structs and keep the same or similar results as if all the values were computed into a single struct?
I'm working in a distributed application and would be nice to be possible to do the process on multiple nodes, later we could shuffle the results around and merge them.

I think I got the answer: https://github.com/prometheus/prometheus/issues/2682#issuecomment-299492218


[CONTRIBUTING] Specify what's the policy for merging pull requests

What is currently missing?

Currently, the way a PR should be merged is not defined. One maintainer might do "merge commit" another one "sqash and merge" and another one "rebase and merge".
How could this be improved?

By defining in CONTRIBUTING.md the policiy maintainers need to follow in this regard.
Is this a feature you would work on yourself?

[ ] I plan to open a pull request for this feature

If they have enough rights, yes


Containerize IGV as an example of pure-js visualization

See if we can articulate a base image that would demonstrate how pure-js visualization could be done with a containerized static webserver and mounted data.

done


Add meeting 33 blog post

This is the long article, there are a few things that need to be done:

[x] Remove weird notes with question marks.
[x] Add links. -> So that CI works. 🚀
[x] Change quotation marks to : „“
[x] Check that all code is marked as code.
[x] Curious question - how does freezeyt behave with emoticons? I'll try it in my fork, but I need all links functioning, otherwise freeze will end up with an error.
[x] What to do with emoticons in the article?
[x] Check that the sentences that make sense.
[x] Check the the facts are correct.
[ ] Add some reference to meeting 01 blog post - so that someone who would like to join would have these two blog posts together. They are the longest ones but at the same time they are the "most important" - the first one describes why did the project start and the basics, and this one should describe the current status of the project.

Thanks a lot for the review. Are the missing to-do items from the first comment OK?

All except "Add some reference to meeting 01 blog post " should be OK, once the suggestions are applied.
I wonder if the reference should be from the main page rather than from the first blog post?

I wonder if the reference should be from the main page rather than from the first blog post?

I meant it in the way to link to the first blog post from this article.

once the suggestions are applied.

Your suggestions are applied, It's a few commits up.

Ah! Then that's OK – the reference is there :)


buffered async gif processing

need to buffer the gif processing so we don't use so much memory
not running into limits, but would like to keep minimal footprint
this issue is not referring to incorrect usage of ffmpeg, and rather the creation of a massive numpy array just before piping to ffmpeg. this could potentially be chunked up and we can build the gif over a series of calls. maybe unneccessary or a future gif implementation

wontfix for now because not real issue


add TM-align

TM-align is for two protein 3D structure comparision, the  source code of TM-align is  https://zhanggroup.org/TM-align/TMalign.cpp.

@robertaboukhalil this PR is ok?

Hey, I'm traveling but will take a look as soon as I'm back mid next week, thanks!

Hey, I'm traveling but will take a look as soon as I'm back mid next week, thanks!

ok


Small images in Colab and demo

I've tested images with the Colab demo and got weird result.
Am I doing something wrong?

https://images.app.goo.gl/qeYDhHrcNFwvfuVm9
https://images.app.goo.gl/d2K8PAQL5DY97YYJ6
https://images.app.goo.gl/b2smudtZ1dXn5dBX6

Hi, thanks for your attention.
It is strange.. I have tried the first image, and the result looks well. I have no idea about your results.
You may can try this demo.

Now the result is good in both the Colab notebook and the web demo. I didn't change anything so I'm not sure why.
Thanks

This image looks weird in both Colab and the web demo:
https://images.app.goo.gl/xzhDTVhZM6zzFzgJ6

I think it depends on the image resolution. Maybe Google images first let you download a small thumbnail but if you wait you'll download the original image.
Do we need to upscale the image in the notebook and demo if it's too small?
Example:
Small:

Big:

Oh... Yes.. The model will fail if the input image is too small. Please make sure the short side of the input image is larger than 256.

There is a problem in lines:
https://github.com/ZHKKKe/MODNet/blob/master/demo/image_matting/colab/inference.py#L90
https://github.com/ZHKKKe/MODNet/blob/master/demo/image_matting/colab/inference.py#L96
im = F.interpolate(im, size=(im_rh, im_rw), mode='area')

I've tried adding recompute_scale_factor=True but it gives me another warning.
Any idea how to downscale with interpolate?

@benbro
For your questions:
Q1: Any idea how to upscale with interpolate?
You may can use opencv to resize the image, then convert it to a torch Tensor.
Is it possible to have a version of the model for smaller images? Maybe it'll run faster?
The provided pre-trained model is trained by the samples of size 512x512. Therefore, it may fail in small images.
If you use smaller images to train the model, it should be faster and more robust for small images.

Thanks


[CBR-422] Fix acid-state memory leak

Description
Each time the node applies a block (which happens a lot when the node is synching with the block chain) we call an acid-state applyBlock transaction. The argument to this transaction is a map from account IDs (which belong to the wallet) to updates to those accounts. For an empty wallet, this map would be empty, but we would nonetheless still call the transaction. This transaction then gets written to the DB log, making it grow unnecessarily; what's worse, due to (what I think is) a bug in acid-state, this also needs to a memory leak. I've filed this separately at https://github.com/acid-state/acid-state/issues/103 . For now, the most important fix for us (useful independently) is to avoid doing a DB transaction at all when this map is empty. During node synching when there is no wallet this will reduce the number of DB transactions to zero (since there are no accounts in the wallet at all). When there are wallets/accounts, we will still have a small memory leak, but it will grow much slower, and moreover each time we create a DB checkpoint (which we do anyway), the leak is cleaned up (at least, I hope so -- that's what my small-scale test suggests, as reported in that acid-state ticket; I haven't verified whether this also translates to the our use case).
This PR also makes one another important fix: in the zooming code, we are effectively injecting state -> state functions into the strict update monad. We should make sure that these functions cannot leave the state in non-whnf. I initially thought that this was the culprit here, but it turned out not to be. Not totally convinced that this change is really necessary, since we always create these state to state functions using the StrictStateT monad, but may as well leave it in, in case we manually construct a function someplace else.
Finally, this adds some Buildable instances for some types that didn't have them; I used that during debugging and figured may as well leave it in as it may be useful in the future.
Linked issue

Type of change

[x] 🐞 Bug fix (non-breaking change which fixes an issue)
[ ] 🛠 New feature (non-breaking change which adds functionality)
[ ] ⚠ Breaking change (fix or feature that would cause existing functionality to change)
[ ] 🏭 Refactoring that does not change existing functionality but does improve things like code readability, structure etc
[ ] 🔨 New or improved tests for existing code
[ ] ⛑ git-flow chore (backport, hotfix, etc)

Developer checklist

[ ] I have read the style guide document, and my code follows the code style of this project.
[ ] If my code deals with exceptions, it follows the guidelines.
[ ] I have updated any documentation accordingly, if needed. Documentation changes can be reflected in opening a PR on cardanodocs.com, amending the inline Haddock comments, any relevant README file or one of the document listed in the docs directory.
[ ] CHANGELOG entry has been added and is linked to the correct PR on GitHub.

Testing checklist

[ ] I have added tests to cover my changes.
[ ] All new and existing tests passed.

QA Steps

Screenshots (if available)

This is actually not quite right. When we skip applying a block altogether, we skip creating checkpoints -- which is correct only if there are no wallets yet.


do not copy slice cap

Copying slice cap is not necessary and will cause extra memory usages if there are multiple slices derived from the same underlying array.

I agree that your example (adapted now that play.golang.org supports public packages) is not handled by deepcopy.
But I insist that your proposed change is not a light change that just fixes things. It would break the current behavior for users that require the capacity to be preserved. Preserving or not preserving slice capacity are two different copy strategies that deserve two different implementations.


Remove rkhunter

rkhunter has a vulnerability where it fetches it's definition updates from sourceforge over http, which means it's ripe for a MITM attack. Reference: http://www.cvedetails.com/cve/CVE-2017-7480/
Remove rkhunter.
/cc @davbo @stephenharker

Thanks @surminus this looks good to me but I'll leave it to someone who knows govuk-puppet to review the code changes.


IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices

This error is raised when using plot_history_vect_ed.

This was coming from a miswritte in the function. It is now corrected.


LitePullConsumerSubscribe testcase not work [4.6.0]

BUG REPORT

Please describe the issue you observed:

I run the example below, but it doesn't work when the consumer group subscribe the topic the first time(I mean the consumer group have never consumed the topic). The consumer can not consume any message, include old messages and new messages.
testcase file:
https://github.com/apache/rocketmq/blob/rocketmq-all-4.6.0/example/src/main/java/org/apache/rocketmq/example/simple/LitePullConsumerSubscribe.java
If the consumer group have consumed some messages before , (may be consumed by DefaultPushConsumer), then the testcase works.

Please tell us about your environment:
rocketmq 4.6.0

Can you try if the same issue still exists in the latest version ？

4.7.0  still not work


climate.set_preset_mode is broken

Home Assistant release with the issue:
0.96
Last working Home Assistant release (if known):
0.95.4
Operating environment (Hass.io/Docker/Windows/etc.):
hassio
Component/platform:
Component/platform:
Configured via frontend
Description of problem:
I have an automation that should set away mode as soon as I leave home via a device tracker trigger
I'm using generic_thermostat
climate:
  - platform: generic_thermostat
    name: Room Cool
    heater: switch.room_ac
    target_sensor: sensor.average_room_temp
    ac_mode: true
    min_temp: 16
    max_temp: 40
    min_cycle_duration:
      minutes: 1
    initial_hvac_mode: "off"
    target_temp: 27
    away_temp: 40
    cold_tolerance: 0.5
    hot_tolerance: 0.5

this service call does not set the away mode in my climate entity
  - service: climate.set_preset_mode
    data:
      entity_id: climate.room_cool
      preset_mode: "away"

please fix

I believe I have the same issue. Also I may be being stupid but I can't see the alternative options for preset_mode when using the "generic_thermostat".

@pvizeli can you suggest a workaround to this while we are waiting for the fix?
this thing completely break every automations I have on the climate entity.

@sblantipodi Please don't tag random developers, that is not appreciated. We are all working as hard as we can to solve all issues. Thanks 👍

@sblantipodi any workarounds? I'm trying to build a similar thing using generic_thermostat.

away mode is working for me with the new climate, but how do I turn off away mode now?

@carlgarton
in 0.96 the way to turn off away mode was:
{
  "entity_id": "climate.room_heat",
  "preset_mode": ""
}

in 0.96.4 this way does not work anymore and you need to do
{
  "entity_id": "climate.room_heat",
  "preset_mode": "none"
}

obviously there is nothing in the changelog or in the docs.
I think that HA is not "a users product" and no way near to be an "usable product for production use". It's impossible for users to follow those modifications if nothing are written in the docs or in the changelog. Climate is only one of the many entities that suffers from this problems.
Hope that HA will became a good product in the future but for now, with this "way to proceed" it's only a toy and a waste of time for people who try to use it in a production environment.
Probably this is not the kindest feedback devs can receive but those are my two cents after 8 months spent fixing problems with trials and errors.

Sharing in the pain here .. I attempted to upgrade to 0.96.5, and my radiotherm entities disappeared - I have a couple of (undocumented?) config entries (away_temperature_cool and away_temperature_heat), and use the climate.set_away_mode service in an automation. I was able to get the entities back by removing those config options, but I can't find ANY way to effect an "away mode" - climate.set_preset_mode is not (yet?) implemented in the radiotherm component.
Digging through commit history, seems this is due to https://github.com/home-assistant/home-assistant/pull/23899
Sure would be nice if there were stable and development branches. I've reverted to 0.95.4 for now. Hopefully radiotherm will get a proper implementation of "away mode" soon (my CT50s actually have a "holiday" mode, which seems pertinent).

Hi, I have spent what seems days in converting all my automation, scripts and node red flows to get the new climate working - but everything all OK again now. My problem was answered by sblantipodi, so thanks. It is a simple case of {"preset_mode":"away"} and {"preset_mode":"none"} for me. OK, these are node red, but in yaml would translate to, (just checked and worked)
test_away:
alias: TestAway
sequence:
- service: climate.set_preset_mode
entity_id: climate.stat_hallway
data:
preset_mode: 'away'                     #or 'none' to turn off
Unsure of radiotherm and your integration with the CT50 as i use the HA generic thermostats and have a customer built system, but it may help you. Hope it works for you too.

Thanks, but I did try that, and as I noted, climate.set_preset_mode appears to be unimplemented for radiotherm (at this time):
   ...
   File "/store/hass/lib64/python3.7/site-packages/homeassistant/components climate/__init__.py", line 399, in async_set_preset_mode
     self.set_preset_mode, preset_mode)
     result = self.fn(*self.args, **self.kwargs)
   File "/store/hass/lib64/python3.7/site-packages/homeassistant/components/climate/__init__.py", line 394, in set_preset_mode
     raise NotImplementedError()
 NotImplementedError


Minor B-Tree fixes

Added create_btreemap_dump_file()
Use PACKED_HEADER_SIZE instead of size_of::<BTreeHeaderV1>() for now
Other minor changes

The changes LGTM, but I'm a bit unclear as to what these changes fix exactly. Do you mind elaborating in the PR description?

The changes LGTM, but I'm a bit unclear as to what these changes fix exactly. Do you mind elaborating in the PR description?

Added a bit more  details. In general, I'm not sure about this solution is the best one, but it definitely more correct than the previous size_of...
IMO  the approach we took previously with packed structures was in a way a nice solution. Maybe, adding just u8 arrays inside the packed struct is the solution. WDYT?


IOError: Could not prepare index seq for mm10 by any method

I tried to install bcbio on a Linux system using:
python bcbio_nextgen_install.py --cores 6 --tooldir path-to-tools --datatarget rnaseq --genomes mm10 --aligners star  --distribution ubuntu    path-to-bcbiodata
Install ran for a while and looked fine until it got to the genome data:
bcbio_install_log_err.txt
Any hints on what I should try instead?
The bcbiodata dir now contains:
18G     anaconda
4.0K    config
12K     galaxy
16K     genomes
364K    manifest

Thanks for your quick reply and the bug fix.
It didn't work with just re-running the install command, but that might be due to me trying something else in between, so I tried with a fresh full install again.
I got quite a bit further, it did download the genome (ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz) and created the mm10.fa / mm10.fa.fai / mm10.dict
Then STAR "finished successfully"
Preparing genome mm10 with index rtg
Formatting FASTA data
Processing "path-to-bcbiodata/genomes/Mmusculus/mm10/seq/mm10.fa"
This looks like a genome reference, but is not recognized. You should enable sex-aware processing by manually installing an appropriate reference.txt containing chromosome metadata.  See the user manual for more information.
[...]
Running GGD recipe: mm10 transcripts 2018-10-10_92
--2019-02-05 16:10:04--  https://s3.amazonaws.com/biodata/annotation/mm10-rnaseq-2018-10-10_92.tar.xz
[ this is fetched successfully, but then ]

Running GGD recipe: mm10 rmsk 20180319
Traceback (most recent call last):
File "path-to-bcbiodata/anaconda/bin/bcbio_nextgen.py", line 221, in
install.upgrade_bcbio(kwargs["args"])
File "path-to-bcbiodata/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 105, in upgrade_bcbio
upgrade_bcbio_data(args, REMOTES)
File "path-to-bcbiodata/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 366, in upgrade_bcbio_data
cbl_deploy.deploy(s)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/init.py", line 63, in deploy
_setup_vm(options, vm_launcher, actions)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/init.py", line 109, in _setup_vm
configure_instance(options, actions)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/init.py", line 269, in configure_instance
setup_biodata(options)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/init.py", line 251, in setup_biodata
install_proc(options["genomes"], ["ggd", "s3", "raw"])
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 325, in install_data
env.galaxy_home, env.tool_data_table_conf_file, env.cores, approaches)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 349, in install_data_local
_prep_genomes(env, genomes, genome_indexes, ready_approaches, data_filedir)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 495, in _prep_genomes
_index_to_galaxy(env, org_dir, ref_file, gid, genome_indexes, manager.config)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 543, in _index_to_galaxy
galaxy.prep_locs(env, gid, indexes, config)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/galaxy.py", line 123, in prep_locs
update_loc_file(env, ref_index_file, str_parts)
File "path-to-bcbiotools/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/galaxy.py", line 105, in update_loc_file
out_handle.write(line + "\n")
UnboundLocalError: local variable 'line' referenced before assignment
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 287, in
main(parser.parse_args(), sys.argv[1:])
File "bcbio_nextgen_install.py", line 44, in main
subprocess.check_call([bcbio, "upgrade"] + _clean_args(sys_argv, args))
File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['path-to-bcbiodata/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--cores', '6', '--tooldir', 'path-to-bcbiotools/', '--datatarget', 'rnaseq', '--genomes', 'mm10', '--aligners', 'star', '--distribution', 'ubuntu', '--data']' returned non-zero exit status 1

Thanks for continuing to work on this and apologies about the continued issues. This was another bug I introduced during the refactoring which just got fixed by @pprieto: https://github.com/chapmanb/cloudbiolinux/pull/282 If you can manage to remove the existing cloudbiolinux and re-run it should hopefully pick up here and finish successfully for you this time. I appreciate all the patience working through these issues and sorry about the extra problems.

Thanks for the quick reply. I had seen pprieto's PR right after I posted my question and was hoping it would do the fix.
I tried with your previously suggested approach of rm -rf tmpbcbio-install and re-running the install command. However, it then fails on a numpy import. ImportError: No module named numpy
But before that, I get
The following packages will be SUPERSEDED by a higher-priority channel:
[...]
  numpy              conda-forge::numpy-1.15.4-py27_blas_o~ --> pkgs/main::numpy-1.15.4-py27h7e9f1db_0

And it downloads other packages then, but not the numpy one?
I attach the full log:
bcbio_install_log_err2.txt

Unfortunately not, seems I killed my numpy there...
I still get the ImportError: No module named numpy if I try the upgrade command.

Sorry about this issue, I'm not sure what happened here but you hopefully can fix that with:
path-to-bcbiodata/anaconda/bin/conda install -c conda-forge -y 'numpy=1.15*'

and then bcbio should be operational again to run the upgrade command. Hope this fixes it for you.

Thanks for the help, that seems to have done the trick!

bcbio-nextgen data upgrade complete.
Upgrade completed successfully.


Restoring database runs mysql in verbose mode

System information:

OpenSUSE Leap 15.1
DBeaver 6.3.2

Connection specification:

MySQL 8+
mariadb-client package as native client

Describe the problem you're observing:
Importing a database seems to always force a -v (verbose) flag on mysql native client, regardless on verbosity settings, which forces it to print all the queries made to the stdout, which then are viewed in dbeaver.  Dbeaver 6.2.5 (and probably some later ones) doesn't have this issue.
Adding --silent doesn't help. Adding any non-existent flag causes the operation to end in error, which allows you to see the flags with which the mysql is ran.
Steps to reproduce, if exist:
Import any file via tools -> restore database. All the queries are printed out.

I can confirm it happens to me as well:
Sys info:

Ubuntu 19.10 Eoan
DBeaver 6.3.2

Connection specification:

MySQL 8.0.18 (dockered in dev machine)
com.mysql.jdbc.Driver

I attach a screenshot too, as a lot of garbled output is seen on the window. The process, as @brtastic explains, is quite slow.

Thanks for the bug report

verified


make validation upload in pba and pbj manager

Coverage increased (+0.02%) to 5.986% when pulling d2fb648b98d5832b1fe80eacb9f1214f399c805a on JanuitaM:dev into 7d70482dff773a0d732cb33bff03bfea38277323 on danliris:dev.


[AutoRelease] t2-workloadssapvirtualinstance-2024-02-20-43646(can only be merged by SDK owner)

https://github.com/Azure/sdk-release-request/issues/4844
Live test success
https://dev.azure.com/azure-sdk/internal/_build?definitionId=4807
BuildTargetingString
azure-mgmt-workloadssapvirtualinstance
Skip.CreateApiReview
true

issue link:https://github.com/Azure/sdk-release-request/issues/4844

/check-enforcer override