Clipping prior to alignment of reads to genome

Hi,
Looking forward to trying this out. I notice you suggest using cutadapt prior to aligning reads. Is not clipping adaptors, then aligning with soft-clipping in STAR a suitable alternative, or is there a particular reason why adaptor clipping is important for downstream aptardi steps?
Many thanks,
Mary-Ellen

Hii Mary-Ellen,
Many thanks for checking out aptardi and reaching out. Not clipping adapters is fine. This is more of a personal preference of how you like to process your reads, and I've done it both ways.
Have a good weekend,
Ryan

From: Mary-Ellen Lynall @.>
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To: luskry/aptardi @.>
Cc: Subscribed @.***>
Subject: [luskry/aptardi] Clipping prior to alignment of reads to genome (#9)
[External Email - Use Caution]
Hi,
Looking forward to trying this out. I notice you suggest using cutadapt prior to aligning reads. Is not clipping adaptors, then aligning with soft-clipping in STAR a suitable alternative, or is there a particular reason why adaptor clipping is important for downstream aptardi steps?
Many thanks,
Mary-Ellen
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Many thanks - very helpful to know.
Best wishes,
Mary-Ellen


Twig Inline css Brackets issue

Mac (10.4):
VS Code Version: 1.33.1
beautify Version: 1.4.10

Hello,
Having an issue when I need to include an inline <style> block in a .twig template so as to pull data into style (such as background images or text alignments.
What I want to write is:
.class-{{nameFromTwig}} {
  prop: val;
}

/* or */

.class {
  prop: {{valFromTwig}}
}

and what i get is:
.class- {
	{
		nameFromTwig
	}
}

{
	prop: val;
}

/* or */

.class {
  prop: {
    {
      valFromTwig
    }
  }
}

Obviously its an unfortunate clash of language grammer but it would be super helpful if there was a way to format correctly!

I can't find a way either. Sorry.

Thanks for response.

I have found adding style to the html.format.contentUnformatted in the settings.json file fixes this for me.
Like this:
"html.format.contentUnformatted": "pre,code,textarea,style"
Hope this helps.


luci-theme-openwrt-2000: Add doctype to header

Without a doctype, the browser is put into quirks mode. In quirks mode, Webkit (Safari on macOS and iOS) ignores display: block; for <td> elements which causes the firewall page (among others) to display improperly.
Without doctype:

With doctype:

Noticed the same, thank you!


azure.core.exceptions.HttpResponseError: Operation returned an invalid status 'Forbidden'

What could be causing this error?

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

ID: 79dc9f6e-d128-4ef9-322e-2f33f570e012
Version Independent ID: d99ed8d4-0977-e6a0-230e-bd3f2738bd2e
Content: azure.identity.CertificateCredential class
Content Source: docs-ref-autogen/azure-identity/azure.identity.CertificateCredential.yml
GitHub Login: @lmazuel
Microsoft Alias: lmazuel

403 Forbidden usually means the service rejected your request because the authenticated principal isn't authorized to perform the requested action. Can you please share more detail about the error you're seeing, like a code snippet and stack trace?


BaseTransportClient - [localhost/<IP_ADDRESS>:9300]

Hi!
I'm having a problem with "org.xbib.elasticsearch.support .client.BaseTransportClient" that insists in connect in localhost:9300, even if I pass the host in settings.
I've changed the "network.host " in elasticsearch.yml to "localhost" and the JDBC worked! But in my network elasticsearch will dont.
Here's my file:
#!/bin/sh

bin=/usr/share/elasticsearch/elasticsearch-2.0.0/elasticsearch-jdbc-<IP_ADDRESS>/bin
lib=/usr/share/elasticsearch/elasticsearch-2.0.0/elasticsearch-jdbc-<IP_ADDRESS>/lib

echo '
{
    "elasticsearch" : {
         "cluster" : "elasticsearch",
         "host" : "srvidx",
         "port" : 9300
    },
    "type": "jdbc",
   "jdbc": {
      "driver": "com.microsoft.sqlserver.jdbc.SQLServerDriver",
      "url": "jdbc:sqlserver://SRVBD01;databaseName=DB",
      "user": "user",
      "password": "pass",
      "sql": " SELECT id as _id, * FROM table ",
      "poll": "10m",
      "strategy": "simple",
      "index": "transparencia",
      "type": "despesas"
   }
}
' | java \
    -cp "${lib}/*" \
    -Dlog4j.configurationFile=${bin}/log4j2.xml \
    org.xbib.tools.Runner \
    org.xbib.tools.JDBCImporter

And thats the line where the connection occurs:
[15:56:03,870][INFO ][org.xbib.elasticsearch.support.client.BaseTransportClient][pool-3-thread-1] trying to connect to [localhost/<IP_ADDRESS>:9300]

UPDATE:
I'm using ElastichSearch 2.0 and JDBC <IP_ADDRESS>.
Thanks!

You need to move everything under the jdbc element, like this
echo '
{
   "jdbc": {
      "url": "jdbc:sqlserver://SRVBD01;databaseName=DB",
      "user": "user",
      "password": "pass",
      "sql": " SELECT id as _id, * FROM table ",
      "index": "transparencia",
      "type": "despesas",
      "elasticsearch" : {
         "cluster" : "elasticsearch",
         "host" : "srvidx",
         "port" : 9300
      }
   }
}
' | java \
    -cp "${lib}/*" \
    -Dlog4j.configurationFile=${bin}/log4j2.xml \
    org.xbib.tools.Runner \
    org.xbib.tools.JDBCImporter

Note, that poll, and driveris not supported any more, and there is also no morestrategy: simple`

Wow man!
It worked like a charm!
I'm migrating to version 2.0, so it did not set the parameters yet.
Thank you so much.

I am facing the same issue.
My Config is this:
{
"type" : "jdbc",
"jdbc" : {
"schedule" : "0 0-59 0-23 ? * ",
"statefile" : "statefile.json",
"url" : "jdbc:mysql://localhost:3306/testseries",
"user" : "",
"password" : "",
"sql" : "**",
"index" : "tests",
"type" : "tests",
"autocommit":"true",
"elasticsearch" : {
"cluster" : "elasticsearch",
"host":"localhost"
"port" : 9200
},
"metrics" : {
"enabled" : true
}
}
}
and I can see a log line as:
[17:43:00,813][INFO ][org.xbib.elasticsearch.helper.client.BaseTransportClient][pool-4-thread-1] trying to connect to [localhost/<IP_ADDRESS>:9200]
Not what I am expecting. ES is running on localhost:9200

Please open separate issue, do not add comments to old closed issues.
JDBC importer <IP_ADDRESS> is for ES 2.3.4 only.
Please use transport port 9300. HTTP on 9200 is not supported. ES 5 is also not supported yet.


Extracts PDFLinkService and PDFHistory APIs

Subset of #5947

/botio-linux preview

Returning to the previous position in the document appears to be broken.
Steps to reproduce:

Open https://mozilla.github.io/pdf.js/web/viewer.html and scroll down.
Refresh the page and see that the viewer is at the same position as where you left.
Now open http://<IP_ADDRESS>:8877/dc48345fcb000e1/web/viewer.html and scroll down.
Refresh the page and see that the viewer is not at the previous position anymore, but just starts at the top again.

@timvandermeij history will work only if the same viewer.html domain is used -- verify with different preview at http://<IP_ADDRESS>:8877/ (instead of mozilla.github.io)

/botio-windows preview

https://github.com/yurydelendik/pdf.js/blob/refact-hist-link/web/viewer.js#L1170 needs to be changed as well, PDFViewerApplication.parseQueryString -> parseQueryString.

/botio-linux preview

Looks good, thank you for re-factoring this!

Nice work!


Remove a remote tag

I'd like to delete the tags sjackman/linuxbrew:core and sjackman/linuxbrew:ubuntu. I don't see how to do that from the web interface or the Docker CLI.

I would also like to be able to delete tags from the hub but can't get it working. This is what I tried:
curl -X DELETE --header Referer:curl -k -s --user tomfotherby:blah https://index.docker.io/v1/repositories/blah1/blah2/tags/2014-07-21_4ba8999_1c79e97

Forbidden (403)

CSRF verification failed. Request aborted.

You could save ALOT of space on your servers if you fix this.

+1

I think this is being worked on; see https://github.com/docker/distribution/issues/422. Given that the "closed source" Docker Hub is based on the open source version, I expect it to arrive there as well after it's been implemented.
so for those interested, subscribe to that issue.

Because the API doesn't provide a delete, I went to do my periodic manual cleanup which involves clicking the little cross next to unused tags on the docker hub page a few hundred times. But today the tags management page in docker hub (https://registry.hub.docker.com/u/user/repo/tags/manage/) isn't showing the usual huge list of pages of tags, I see only 1 page (30 ish rows). Has something changed? Are Docker reaping old tags now? (or is it just that the pagination is no longer shown?)

@tomfotherby could you send that question to<EMAIL_ADDRESS>because that's really a question for the team supporting Docker Hub, and the maintainers of the open source project have no insight in that.
There's also a public beta for upcoming changes in docker hub. Perhaps you can if that brings improvement in this area; https://hub-beta.docker.com

Reading through this issue and the discussion again, I don't think there's anything the open source project can do here; all issues seem to be related to Docker Hub, for which issues are handled via<EMAIL_ADDRESS>(or https://support.docker.com).
For the open source registry, this is being worked on in https://github.com/docker/distribution/issues/422.
For that reason, I'm going to close this issue. Feel free to comment here if you disagree or think I've closed this by mistake.

@tomfotherby could you send that question to<EMAIL_ADDRESS>because that's really a question for the team supporting Docker Hub

I emailed<EMAIL_ADDRESS>
Dear Docker Hub Support Team,
When I view the tags of one of my private repos ( https://registry.hub.docker.com/u/me/myrepo/tags/manage/ ) I see a massive list of 1003 tags. The pagination on this page has gone since dockercon 2015. I would like to delete unused tags via a API call.
I'm trying this:
curl -X DELETE -k -s --user tomfotherby:secret https://index.docker.io/v1/repositories/me/myrepo/tags/mytag

but I get a CSRF error. Is there a way to to remove tags from the hub pragmatically? beacuse I can't remove 1003 old tags by hand using the website.

The response:

Unfortunately, we do not recommend using API calls to delete tags. It has abnormal effects over repository. Those API calls are only for Private Registry. We will release V2 Endpoint later this year, which would be more stable and easy to use.
For now, you can list the tags you want to delete, put them in a file and send it to me and I will delete those for you.

Thanks for adding that information, and taking the time to contact support @tomfotherby :+1: :heart: !

+1

+1

+1, we cannot remove tags anymore via the web-ui, so we need some way to remove tags (besides deleting the repo).

+1
For private repos with collaborators, deleting and re-creating the repository every time a rogue tag makes its way to the hub is impractical.

+1

+1

USER POLL
The best way to get notified when there are changes in this discussion is by clicking the Subscribe button in the top right.
The people listed below have appreciated your meaningfull discussion with a random +1:
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+1!
Why is this not in the :whale: web UI?
I'd really like to remove deprecated tags to avoid user confusion.

+1 and subscribed

+1

+1
Why is this not in the web UI ?

+1

For those wanting in in the Web UI on Docker Hub; Docker Hub is closed source, and managed by a different team; feedback for Docker Hub can be provided in a separate issue tracker, and there's already an issue open for this; https://github.com/docker/hub-feedback/issues/68

Ah, thank you @thaJeztah for linking the issue!
I'll fallow this as well.

+1


Make query parameter optional in searchUsers

Don't forget to bump the version as well

Bumped to 0.6.0 since the type signature of searchUsers is changed.


Escape ninja output inserted into HTML

Ninja query or error output may contain characters that need to be
escaped when being inserted into HTML.  Replace &, ", <, and > with
their & equivalent.

Haha :-) Not sure what the threat model is, but this gives you an alert on click (which this patch would fix):
$ cat build.ninja
rule test
  command = echo $out = $var
build "$ onclick=javascript$:alert('hi'): test
build test1: test "$ onclick="javascript$:alert('hi')

https://docs.python.org/2/library/cgi.html says "If the value to be quoted might include single- or double-quote characters, or both, consider using the quoteattr() function in the xml.sax.saxutils module instead." – that'd mean using different escapers for attributes and tag contents, which makes things more complicated, and depending on xml.sax seems a bit unfortunate anyways.
Since nothing currently uses single quotes, I think using cgi.escape() should be fine (and in a few decades, we can assume py 3.2 and use html.escape which does escape single quotes).

Replaced with cgi.escape

Thanks!


CouchDB index support for implicit collections

Allow CouchDB index creation on implicit collection of organisations.
Indexes can be created for specific organisation's implicit collections at:
META-INF/statedb/couchdb/collections/_implicit_org_<MSP_ID> directory of the chaincode package.
Common indexes for all the organisations' implicit collection can be created at:
META-INF/statedb/couchdb/collections/_implicit_org_* directory of the chaincode package.
( * acts as wildcard for all organisation MSP ids. )
Type of change

New feature

Description
Updated chaincode deployment handler to check if the indexes are for implicit collection if given collection directory name not explicitly defined in collection config. If the implicit collection indexes belong this handling peer's organisation or passed as global implicit collection indexes (using * notation), then indexes are created on corresponding implicit collection.
Additional details

Please review the way of fetching localMspId directly using viper at NewDB constructor function.
Added few more tar file entries to represent implicit collection indexes in unit tests. (However UT TestHandleChainCodeDeployOnCouchDB was already failing due to some other error)

Related issues

#4780

We'll want an integration test for both the single org use case and all org use case.
It should be feasible to extend the existing CouchDB index integration test here:
https://github.com/hyperledger/fabric/blob/main/integration/ledger/couchdb_indexes_test.go

Not many people use Windows for Fabric, but still, asterisk is now allowed in Windows directory names. Maybe use _implicit_all_orgs?


Authentication fails when not adding database name at the end of uri

Hi,
I have an issue when passing a password with a character '?' needing to be percent encoded (as specified in https://www.mongodb.com/docs/manual/reference/connection-string/)
When using this in cypress.config.ts with escaped '?'
mongodb: {
	uri<EMAIL_ADDRESS>        database: 'mydatabase',
        collection: 'mycollection',
      },

I get error authentication failed when using cy.mindMany

When using this in cypress.config.ts with unescaped '?'
      mongodb: {
        uri<EMAIL_ADDRESS>        database: 'mydatabase',
        collection: 'mycollection',
      },

I get error Password contains unescaped characters when using cy.mindMany

I can connect to the mongodb using Studio 3T with no problem:

Environment:

Cypress: 12.8.1
cypress-mongodb: 5.3.0
TypeScript: 4.9.5
mongoDB: 5.0.6

Is escaping of chars in password supported?
Thx

I finally managed to make it work by adding database name at the end of uri like this
      mongodb: {
        uri<EMAIL_ADDRESS>        database: 'mydatabase',
        collection: 'mycollection',
      },

Is it me that missed something in the documentation?

Hi, I do not think you did anything wrong, I'll have to investigate. Thank you for posting a workaround in the meantime

I don't know (neither understand) why, but it's working without the workaround. Maybe that the mongodb configuration (or version) changed.
So this ticket can be closed.


Use pipelines for SocketOutput

Changed socket output to be based on pipelines
Changed connection filter glue to be based on pipelines
Codegen that used MemoryPoolIterator for output now uses WritableBuffer
Made UvWriteReq async/await friendly with LibuvAwaitable<T>
Deleted MemoryPool and friends

TODO:

Cancellation isn't handled, it needs to be. Will do this in another PR once we get https://github.com/dotnet/corefxlab/pull/1332
Little bit cleanup
Port relevant SocketOutput tests (they are commented out now)
Initial performance test

/cc @pakrym

Will make all of the nit feedback in a subsequent commit.

This is merged

07cbf7faa95034639ff42df2f2057974dcf8a055


Continuous Integration: Added build and deployment of Windows installer to the release workflow

Checklist:

[x] The PR title is formatted as: <Module or Topic>: <Action> <Summary> (see contributing guidelines)

Merge PR #4112 first!
This PR adds the build, test and deployment to github release assets of Windows "fat binaries" to the release workflow.
This is one more step to further automate the release process and allows to completely stop using the previous release CI.
It also removes the update of sphinx-panels which is no longer used.

could you rebase please to avoid having commit of the 'release documentation' into this PR (commit 4a55e0f)

Rebased after merge of PR https://github.com/silx-kit/silx/pull/4112


Colors not displaying with mintty (mingw, git bash for windows)

My coworkers running windows with python 3.x and click 6.7 are having hard time with click's colors. Looks like the problem is with the click.echo function when printing colors with click.style. Note that the colors displays properly with python's own print (no matter if colorama is installed or not).
This all is with the terminal that "git bash for windows" ships with. Everything works normally with powershell.

Since Git for Windows uses mintty, which is not a real Windows console, this is to be expected. Any Windows program will think that it's output is redirected since it essentially sees pipes as it's stdio. click will detect this and disable colors accordingly:
https://github.com/pallets/click/blob/2e856a5281a29eb4293059b37427643c3d52a19a/click/_compat.py#L574-L579
You can use winpty, which is included with GfW, to run your Python scripts. They will than see a real console and should work normally. I think they explain about this in the GfW installer, but not everyone bothers to read all of that and just hit next, next next. (That's also how they often end up with malware).
It might be possible to detect mintty and enable colors, but there are also plenty of other IDE terminals, CI environments, and what not. Which can handle colors, but use pipes. So where do you cross the line... There were many attempts to push hacks of this nature into colorama, none of them were merged though. colorama is kind of abandoned.

Thanks for getting back with this. I did some research on this and came in conclusion that the mintty is the reason behind this, and instructed others (that use windows) to use other terminal emulator.
If you feel so, you can close this issue.


Missing binaries for 1.36.0

The latest release, https://github.com/googleapis/api-linter/releases/tag/v1.36.0, does not have any binaries uploaded to it.

+1

Ack

https://github.com/googleapis/api-linter/releases/tag/v1.36.1 has binaries generated by CI so I've fixed that. I will upload binaries for v1.36.0 manually though, then close this.

I've added binaries to v1.36.0 using that tag & the proper version constant for the api-linter version command.


[BUG] Text and Formatting Not Saving

Module Version: v0.5.1
Describe the bug
Text and formatting is uneditable on a previously created entry.
To Reproduce
Steps to reproduce the behavior:

Go to any notes or text editing section on a previously created entry.
Click to edit the field.
Exit the entry.
Return to the entry.
The text has reverted.

Expected behavior
The formatting and text should keep the formatting of the most recent change. Perhaps a "save" button to force it.
Browser:
Local game
Foundry Version:
0.6.6
Game System:
D&D5e
Additional context
One Journal is installed.

Confirmed, same here.

Confirmed, happening with me too.

Having the same thing. Can confirm there's no use of any raw HTML in the input - just text.
This happens after:

closing and opening the quest
hitting enter after creating an objective
adding a reward

My guess is that the description save functionality is not actually writing to disc.

We're having the same issue. The GM is able to edit the descriptions. If the players try to edit the description, they do not save.

I am also having this same problem, but as a DM.  The text saves if I create a new quest, but doesn't save if I am editing already written text. Doesn't matter if I hit the save button or try to edit through HTML

This might be a dupe of https://github.com/Forien/foundryvtt-forien-quest-log/issues/97
That  fix did it for me.


Project Details Added

The Details about the project have been included in the readme.md file

@jaydip-pawar checkout the PR!

checkout my updated work @jaydip-pawar

@samvid2020 can you add the features and maintained by section?

Sure :)


Does this crate need libc?

I don't see it being used.

Thank you for bringing this up. It is fixed now by #38


remove hub crds

Signed-off-by: Ray Harris<EMAIL_ADDRESS>

/hold

@ray-harris do these same scripts need to be pulled out of the docker and makefiles?

@cameronmwall The only script being removed is gather-crds.sh and it's not referenced in any of the Docker or make files.

/unhold

/lgtm


Log raw IMU measurements from the pi3hat interface

Pull Request Test Coverage Report for Build<PHONE_NUMBER>3
Details

79 of 79 (100.0%)  changed or added relevant lines in 4 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.2%) to 90.044%

Totals

Change from base Build<PHONE_NUMBER>5:
0.2%

Covered Lines:
2632

Relevant Lines:
2923

💛  - Coveralls


Resolving technical conflicts?

How do we resolve technical conflicts? Ideally the governance model should never come into play, but we should write a model that prepares for large differences of opinion in technical direction for the project. How do we resolve these conflicts when developers disagree long enough that action needs to be taken?

BDFL Model?
Leadership team?
Consensus only?
Majority vote?
?

You might be interested in the survey that was done here in preparation for the Python governance vote:
https://www.python.org/dev/peps/pep-8002/
In short, a frequent pattern is for projects to evolve away from a BDFL model to a more distributed model, which scales better and is more resilient. The latter often includes a supervision / overseeing body with varying decisional power depending on the project (often called "steering committee" though I like Astropy's "CoCo" aka coordination committee).

I think that today our defacto model (non-ideal) is that we chat for a while and usually come to a good compromise, otherwise I generally make unilateral decisions, except when something is particularly important at which point I try to build concensus (such as in developing the membership policy).
I'd like to see us move to a more balanced model.  I also think that this might make things sluggish if we don't require some additional effort from the steering committee.
My experience has been that getting responses from the current set of owners takes about a week or two, even for simple issues like adding new members.  I would be very happy to see operational decision-making diffuse away from myself, but I do think that this will require a greater engagement from others.
Also, I'd like to see whoever is on that steering committee take on a greater role of engaging with the community, generally through handling issues as they arise.  This is, I think, the best way today to get a good sense of priorities for the project's userbase, which I think should be the final constituency.

I think that day-to-day things will continue to operate informally, even in the face of disagreement. I'm mostly looking for a process here in case some decision becomes heated and the community is split. I think a steering committee approach would be good here, preferably with a rotating set of members over time.

Also, I'd like to see whoever is on that steering committee take on a greater role of engaging with the community, generally through handling issues as they arise. This is, I think, the best way today to get a good sense of priorities for the project's userbase, which I think should be the final constituency.

Agreed.

Judging by the contribution dynamics in Dask, it seems starting with a 3- to 5-person steering committee should be doable.
I agree that imposing rotation requirements is risky in such a small community.

👍 on Leadership team for difficult decision or in case of community split.
Rotation should be encouraged (and forced if some member of the leadership team has not enough time to devote to the project), but not mandatory.

I'm against BDFL in principle, but I also want to add the constraint that people who have central authority also participate consistently in central maintenance.  I think that constraint, if adopted, reduces our candidate pool considerably today, and so we should continue to embrace a more anarchic model (like the SciPy/PyData ecosystem).
To be clear, many people do a ton of work on Dask, but they usually focus on a subproject (like dask.array or dask-kuberentes) or their involvement is intermittent and they disappear for months at a time.
Today I think that I review the vast majority of PRs and handle the vast majority of issues to the core dask projects.  I'll estimate this at 75% +- 10% over the last few months.  I think that because of this I tend to make most technical decisions, and act as BDFL today.
I would very much like to move away from this situation, but I think that we need to move away from both concentrated-decision-making and concentrated-maintenance at the same time.  We've been doing this already using a federated/anarchy model.  As people maintain sub-projects they gain full control over those projects and I step back as quickly as I can.  For example...

Guillaume took over maintenance of dask-jobqueue and was quickly given commit rights and makes most (all?) executive decisions on that project today
Same with Yuvi/Jacob and dask-kubernetes
Same with Jim Crist and dask-yarn (and associated yarn projects)
John Kirkham and Stephan Hoyer are happy to handle dask array issues when pinged on them, and so tend to be consulted / leaned on heavily on issues that arise in that subproject.  I get the sense that they feel a sense of ownership over it and we tend to make decisions on that project after conversation.
Tom more or less controls dask-ml today
Ian Rose controls dask-labextension
I mostly work on dask.distributed independently from other devs these days
...

So on the periphery of Dask there are many people who are both dedicated to the project and, I think, have decent control over parts of it.  They make controversial technical decisions already as individuals or as groups, without interference from a central authority.  These decisions include difficult topics like dropping Python 2, code styling, CI, and so on.  Cross-project integration (like cluster deployment) seem to happen peer-to-peer.
So my current stance on moving away from BDFL is a combination of "yes please" and "central authority requires broad maintenance, which is hard to motivate".  In the absence of multiple central maintainers I think that we want either a large diffuse group (majority voting), or a BDFL.  I also think that we probably want to reduce the power of any central authority, and act more as an ecosystem like SciPy/PyData, with many small autonomous groups.
I also think that increasing the number of central maintainers would be useful.  I suspect that the best chance of this short term would be for Anaconda to fill my previous maintenance spot there, probably with someone like Jim, who has touched a broad swath of the project in the past.

Some Dask folks met in Austin earlier this week.  Some summary of the discussion.
I'm treating this issue now as a general conversation around governance, superceding #2.  There is more conversation here, and it's pretty relevant.
For the NumFOCUS signatories, whose job it is mostly to distribute funds that might arise, we really just care about trustworthiness, and somewhat about diversity of domain.  Some subset of the current owners is maybe a good idea.
For general project leadership we might consider three separate groups:

Technical leadership group
A group of special users that represent different domains (for example pangeo, or consulting companies)
A group of industry partners who meaningfully support the project, either by employing developers to work on the project, or by providing funds directly (for example Anaconda, NVIDIA)

In the end, project decisions would come down to the first technical project leadership group, but the user and industry special interest groups would be consulted and their opinions heard before making any large decisions.  The goal here is to encourage participation from a larger group of people, while keeping decision making within a group that is both trusted by the community, and willing to make difficult decisions.
Also, we discussed that this group will likely make many non-technical decisions.  Some examples follow:

A corporation arrives with money and asks for branding.  For example Maybe Azure wants to fund a high-powered binder deployment for us, but wants a "Deployment powered by Azure" on the bottom of the page.  Does Dask accept this or not accept this?
An "official" Dask talk gets accepted to a conference, but a social issue arises with that conference.  Does the Dask organization continue attending that conference or do we pull the talk.
Someone contributes code to Dask after being paid by a company, but they weren't transparent about their employment or the reason for the contribution.
...

For general project leadership we might consider three separate groups

How do we form and manage these groups?

How do we form and manage these groups?

Carefully :)
I might interpret this question in two ways
How do we as a group assume authority to make these decisions?
When we switched to the set of eight owners in https://github.com/dask/dask/issues/3223 we got consensus from all previous owners and most people who had been active in the project.  Currently in this process I think that we should get consensus from that group, others like yourself that maintain the various dask-foo packages, and representatives of corporations that are considering employing maintainers.  Consensus among that group may not be possible, if so I think that I'm inclined to weight community maintainers over others.
So far consensus seems to be reasonable, but we'll see.
Logistically how do we choose these groups
For the leadership group I think that we should probably have another group meeting among maintainers over video to discuss things.
For the corporate partner group I suggest that we require that they employ about 1 full time employee who maintains OSS Dask projects.  My guess is that Anaconda and NVIDIA are both close to this level, but probably not quite there when it comes to maintenance work.  (maybe Anaconda is?  not sure)
For the user group representatives I think that we want people who actively provide support to downstream user groups.  So someone like @rabernat or @jhamman who don't do a ton of work on Dask itself, but end up filtering up Xarray or Pangeo user issues is useful.  I think that the criteria here would be a certain amount of activity in other community discussion forums.
Membership in both of the latter groups would probably be decided by the leadership group.

Thanks for writing this up, Matt.  I think this accurately captures what we talked about.

I'm inclined to write up a governance document to make some of these discussions more concrete.  I plan to start with something loosely inspired by the Pandas model (core team + BDFL for exception handling) and add in the groups above.

I’d be interested in hearing what caused you to shift your view point from the one you articulated earlier in this thread (namely being against a BDFL model), assuming I’ve read that correctly and haven’t missed something. It seemed there were also a few other people in this thread that preferred a core group that votes. This isn’t to say there may not be a good reason to use a BDFL model, but it would be good to articulate it at least.

Good question.  Mostly it's what was expressed here: https://github.com/dask/governance/issues/5#issuecomment-450676767
And in particular in this comment:

I'm against BDFL in principle, but I also want to add the constraint that people who have central authority also participate consistently in central maintenance.

In February when I supported a core team, folks were supportive of taking on more maintenance.  However I'm still handling the vast majority of issues/PRs, and when I go dark for a few days it's very common that issues/PRs go entirely unanswered.
So while everyone is awesome about maintaining various Dask subprojects from time to time, I don't get the sense that any other individual or institution feels full responsibility to make sure that the lights stay on.  Until that happens I'd like for there to be a core team that makes most decisions, but where I have override privileges (which I suspect I will never use).  If maintenance behaviors change I'd be all in favor of changing governance structures.
One of my main goals for this year is to construct a situation where I can step away for periods of time and still keep the lights on.  So I'm actively invested in changing the situation above.

Draft added in #11
I'm totally happy to modify that heavily.   I just wanted to have something concrete to work on.
I based this off of the Jupyter document (which is fairly similar to Pandas)

This was added in the governance document.  Closing.


[FocusTrap] Finish rename from TrapFocus

Steps to reproduce 🕹
Link to live example:
Steps:

https://github.com/search?q=repo%3Amui%2Fmui-x+TrapFocus&type=code
https://github.com/search?q=repo%3Amui%2Fmaterial-ui+TrapFocus&type=code

Current behavior 😯
FocusTrap still has references as TrapFocus in MUI Core and MUI X codebase.
Expected behavior 🤔
We finished the rename we started in #34216.
I labeled this as a regression as it used to be a consistent terminology. It now feels more confusing than before https://github.com/mui/material-ui/pull/32364#issuecomment-1108255257 as both variations exists.

  Output from `npx @mui/envinfo` goes here.

I'll take this on :)

@shroommu are you still working on that? If yes, may it be assigned to you? If not - I can take over 🙌

@shroommu are you still working on this? if not - I can take, Thanks :)

I guess this is a breaking change if we rename the export.


improvements

data retrieved using retrofit+okhttp
bug fixes
database and setting preference added

Ok this compiles. I am merging. Will go through the commits 2moro.


Fix incorrect link markdown

Noticed that the markdown for the links was incorrect and the links were not working. Change just fixes the links.

@eddywashere

Thanks for the pr @briandela!


fix: update readme.md ramda version before publish

This looks like a very good idea.  I'd actually like to entirely remove make from our build dependencies, and just used node/npm scripts.  It certainly makes it easier to build cross-environments.
But I don't have time to test this today.  I'll try to get to it in the next few days.


Fix for java issue

Hi @gronert-m
Please, can you accept this change so we can use it in the qchecks template.
Thanks a lot,
Best,
Alexandra

@alexandraqn Thanks for this! Could please you do the same for --> https://github.com/worldbank/gld/blob/main/Support/Z - Other Tools/ISIC ISCO universe check/int_classif_universe.ado
Thanks


replace the / in VERSION arg

This should fix the issue with the rancher-agent docker image using an invalid tag name when using a release-v* docker image.

lgtm


Use of initializer lists in tests without type leads to ambiguity (e.g., Box and Ray)

The function ArborX::Details::intersects(const ArborX::Box &, const ArborX::Box &) and function ArborX::Details::intersects(const ArborX::Ray &, const ArborX::Box &) are reported to have the same argument type: {{...},{...}}.
Should the ArborX::Details::intersects(const ArborX::Ray &, const ArborX::Box &) be put in the ArborX_DetailsAlgorithms.hpp? or should ArborX_DetailsAlgorithms.hpp #include ArborX_Ray.hpp?

Essentially, we should not use initializer lists without a type preceding them, if only for clarity.

@dalg24

How do we reproduce? You have no other choice than explicitly say whether you mean Box or Ray

You can simply add #include <ArborX_Ray.hpp> in ArborX_DetailsAlgorithm.hpp.

I don't see a compelling reason to change anything at the moment

I was hitting the same issue in my work when a new geometry was introduced (a plane).
Overall, I don't see any downside for explicitly writing Box{{...}} and Sphere{{...},.} instead of {{...}}. Personally, I also find it easier to understand what's being done rather than trying to remember the constructors/initializers.

I am specifically addressing the question Wenjun asked.  Feel free to disambiguate where necessary.


#152 Added Java 8 implementation of Histogram Equalization

Please tag this issue as Hacktoberfest before you merge the pull request


Closing this issue.


Add ROI to the TP Calculator

This feature request is to add a return on investment (ROI) percentage to the TP calculator.
See http://tpcalc.com/ for an example

Added to the develop branch with 2cce25bfc1cffc566bf7162423e233593062ca7c


[BUG]: ResizeMode render video before applying the style props

Version
v6 (Beta)
What platforms are you having the problem on?
Android
Architecture
Old architecture
What happened?
I am the creator of SoSkills App which is available on Apple and Android (more info on https://soskills.fr)
Since beta 6 version is introduced and ExoPlayer is deprecated, i struggled to get resizeMode working as on Alpha version.
Older behavior was to have resizeMode contain when video.height < video.width and a resizeMode cover when video.height > video.width. Both resizeMode allow to me to either center the video or cover the video in fullscreen.
Since beta version, resizeMode cover / contain / none is doing a pre render on the video and only applying style after which generate a resize when the video is appearing on the screen, especially during the loading of the video.
On Alpha version, video was loading with resizeMode and style in the same time, not with some delay.
My best option is to set resizeMode to stretch in order to control the style myself but i admit that this option is not the best cause cover and contain are really useful for scaling the video.
https://github.com/react-native-video/react-native-video/assets/3983160/3a248256-9904-42b5-8ac2-ba6c8530daf4
Reproduction
repository link
Reproduction
Create a FlatList with some videos and try to swipe through videos with resizeMode contain / none / cover on a Android phone.
When you swipe to the next video, set paused props to false and load video: you will see resizeMode applied and style be setted just after.

Did you find any solution?

I've encountered a similar issue as well.
Do we have any solution to prevent the video from scaling during the initial loading phase? This issue only seems to occur on Android

As i said on my initial message, set resizeMode to stretch allow me to scale the videos according to theirs dimensions but sometime i got something more stretched than expected @kosmokoks @haonguyendirox.
So if a fix can be apply to have the same behavior as IOS, could be great.

@douzal34 This issue shall be fixed on 6.0.0 !


Suggestion: Add comments to the default settings.yml file

What about replacing the current settings.yml file with one that includes all the examples from the readme, but commented out, and also contains some comments explaining which parts are optional, which are required, etc?

Yep! That will be good.

Here the default settings.yml:
# current machine's name, optional; it can be used to filter settings or in the commit message
hostname: ""
# selected profile, required
profile: main
# repository to sync the settings with, required
repository:
  # dummy, no sync
  type: dummy

# # sync on local file system
# repository:
#   type: file
#   # path of the local directory to sync with
#   path: ~/Development/settings

# # sync on local git
# repository:
#   type: git
#   # path of the local git repository to sync with
#   path: ~/Development/settings
#   # branch to sync on (set to `master` by default)
#   branch: master

# # sync on remote git
# repository:
#   type: git
#   # url of the remote git repository to sync with
#   url: git@github.com:username/settings.git
#   # branch to sync on (set to `master` by default)
#   branch: master

# # sync on remote directory with rsync
# repository:
#   type: rsync
#   # url of the remote directory to sync with
#   url: server:~/settings
#   # shell used by rsync (set to `ssh` by default)
#   shell: ssh

# # sync on remote directory with webdav
# repository:
#   type: webdav
#   # url of the remote directory
#   url: http://localhost:9988/webdav/server
#   # the username
#   username: webdav-user
#   # the password
#   password: pa$$w0rd!

Is it good?

@daiyam Wow, I'm impressed with how quickly you followed up on this, nice!
I think the point about marking fields as required is a good one. I'd suggest expanding that to all of the other blocks also. The one that jumped out at me was branch, I'm not sure if it's optional because it defaults to master, I assume yes, but I also assume that type and path are required, but they're not marked required, etc. What do you think?


[fpga] Fix clock constraint

For some reason, Vivado moves one of the clock dividers inside clkmgr to the outside of clkmgr. As a result, the path used to find the relevant cell is wrong and the divided clock cannot be properly constrained. This leads to:

a bunch of critical warnings,
~excessively long implementation times, and~
~higher negative slack.~

This PR contains a single commit to fix this path such that the clock can be constrained.
Edit: this PR does not seem to reliably fix the high negative slack and long implementation times.

After doing a FPGA implementation run on my laptop, it turned out that this commit does not reliably solve the problem with big WNS and the excessively long implementation times.
But we should probably fix the timing constraint anyway. I will now adapt the commit message, create an issue to use proper Xilinx primitives and keep debugging.

thanks for the fix @vogelpi
it is strange to me that the location was moved... maybe there's a way to keep it in place.
I wonder what changed recently that causes the WNS to explode...at least when I was looking last week things were still about ~1ns.


Select: Multiselect Touch Fix

Description
Fixes #4284.
What we did?
MudSelect has MudList inside itself, but select and list both have their own onclick implementations. Something deep of the click we have conflicts and select didn't work on touch. So we did:

Added OnClickHandlerPreventDefault parameter to MudListItem (not onClickPreventDefault, we prevent Mud code). If its true we bypass the list click code and directly continue with OnClick event.
In MudSelect set all ListItems prevent to true (to be sure just work select code)
Removed all touch events on select (they caused to fire events twice)

Tested both BSS and WASM
Types of changes

[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 not work as expected)

https://user-images.githubusercontent.com/78308169/160392996-9d87d8cb-88d2-43f3-957e-018874345451.mp4
Checklist:

[x] The PR is submitted to the correct branch (dev).
[x] My code follows the code style of this project.
[ ] I've added relevant tests.

Thanks!

Could we get a release with this fix?

I have told @Garderoben that there is demand for this fix to be released early.

Could we get a release with this fix?

done


failed to load global model from the pretained model

Hi author and other friends,  If I want to test EDTER-Stage II,  how should I set the argument 'checkpoint' and 'global-checkpoint', all of them should be set same ?

https://github.com/MengyangPu/EDTER#3-testing

https://github.com/MengyangPu/EDTER#33-edter-stage-ii-with-single-scale-testing

thanks for your reply, I have read the content of the link, but I have some confused, how should I download the pretrained model "iter_XXXXX.pth" for checkpoint and globalcheckpoint. I have download the 'EDTER-BSDS-VOC-StageII' model

parser.add_argument('--checkpoint', type=str, default='/your path........../EDTER-BSDS-VOC-StageII.pth',
help='the dir of local model')
parser.add_argument('--global-checkpoint', type=str,
default='/your path........../EDTER-BSDS-VOC-StageI.pth',
help='the dir of global model')

parser.add_argument('--checkpoint', type=str, default='/your path........../EDTER-BSDS-VOC-StageII.pth', help='the dir of local model') parser.add_argument('--global-checkpoint', type=str, default='/your path........../EDTER-BSDS-VOC-StageI.pth', help='the dir of global model')

thanks again, I have load the pretrained model successfully


Issue2443/improve relation depracation msg (#3921)

Pull request opened by the merge tool on behalf of #3921

Merged into branches iso5 in 4e3db3287c3485d6ee2984f9df8579b01219e65e


⚠ Bofrost.lu has degraded performance

In e4a3c36, Bofrost.lu (https://www.bofrost.lu) experienced degraded performance:

HTTP code: 200
Response time: 2502 ms

Resolved: Bofrost.lu performance has improved in 95a7612 after 21 minutes.


Revert 6432dde990f73821610d6b7e8f8e21d210404750: Migrate to new Shipkit plugin

Published artifact signing files are no longer generated as of v1.0.20, and hence Coral repo in Bintray cannot be synced with Maven Central. Version 1.0.20 contains two changes. One of the two changes (https://github.com/linkedin/coral/pull/36) upgrades Shipkit plugin to a new version. At the same time, LinkedIn Bintray account did not seem to have recent changes that would make those files no longer be generated. Current theory is that one of the changes in v1.0.20 caused the regression. This patch reverts one of those changes to check if it is correlated.

Reverting seems to have successfully resulted in the files being generated again https://bintray.com/linkedin/maven/coral/1.0.19#files/com%2Flinkedin%2Fcoral%2Fcoral-hive%2F1.0.19.


Proposed feature: restart services (like openvpn client) from the command prompt of opnsense

Today we cannot restart services (in my case, I needed to restart openvpn client) from the command prompt in opnsense. In PFsense there is the pfSsh.php that can be invoked to do that, but I have not found a similar one in OpnSense.
I think it would be a great feature do add to github.

some additional info from the forum, configd calls might look like:
configctl openvpn client list
configctl openvpn client start
configctl openvpn client stop
configctl openvpn client restart

oh.. have been looking for that.. would be great to have it in the docs somewhere (CLI reference .. )

It's possible to reload from the command line now:
# pluginctl openvpn_reload [interface (wan, lan, opt1, ...)]

Beyond this the utility is not strictly needed.

IT IS NOT WORKING

It's possible to reload from the command line now:
# pluginctl openvpn_reload [interface (wan, lan, opt1, ...)]

Beyond this the utility is not strictly needed.

At least for me this did not work (version: OPNsense 19.7.10). What did however work was:
pluginctl -s openvpn restart

Hi together,
pluginctl -s openvpn restart is working for me, too. But only for server1. Is there a option to restart server2 server3?
Best reguards marc,

See cf1f4e00b9a853

Could someone share the magic command for restarting the only vpn client configured from the command line? Apparently pluginctl openvpn does only sync config settings and nothing else, regardless what arguments you give it:
root@q:~ # pluginctl openvpn client1 restart
Syncing OpenVPN settings...done.

You can even miss to give the last two args and will to the same thing.

https://forum.opnsense.org/index.php?PHPSESSID=jbh1saml0mb9nvnsd7cvm5kstd&topic=19240.msg88421#msg88421

https://forum.opnsense.org/index.php?topic=19240.msg88421#msg88421

I am afraid this does not help me because my pfsense is only an openvpn client and not a server. It only has one client configured and no servers. Based on the forum link I suspect that that command works only for restarting servers, not clients.

If you only have one client you should not have a problem prior to the patch. As said earlier "pluginctl -s openvpn restart" restarts the first OpenVPN instance it finds.


Glob cache key disambiguates a prepended project directory

Fixes #3995

@kingerja confirms this fixes the issue.


Advice: development terms related to the plant endodermis

Review of recent QC reports showed that there are some plant genes annotated to %endoderm% biological process terms. The two I was looking at were CACAO annotations to 'endodermal cell fate specification , GO:0001714'. It looks like most (all?) such terms are linked (transitively?) to the CL term for endoderm. Reading the def of the above term doesn't give the clue that it is animal specific.

The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an endoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed. Source: GOC:go_curators)

There are several plant anatomy terms that share this root word and GO BP terms exist that look from the surface like they would apply to plants as well.
https://browser.planteome.org/amigo/search/ontology?q=endoderm
http://amigo.geneontology.org/amigo/search/ontology?q=endoderm
Example paper:
SCARECROW-LIKE23 and SCARECROW jointly specify endodermal cell fate but distinctly control SHORT-ROOT movement
http://doi.org/10.1111/tpj.13038
How would you like to handle this situation?
Should we request terms that are specific to the plant endodermis like 'plant endodermal cell fate specification?' Does it make sense to rename the existing generic sounding terms to something like 'animal endodermal cell fate specification?'

@lreiser Looping you in.

It appears that endoderm (animal embryo) and endodermis (plant ground tissue) were meant to indicate the inner cell layer in different anatomical contexts. Thus it would not make sense to mix them together. As it was pointed out, the existing GO terms are defined by the animal specific term CL:00000223 endodermal cell.
Is the word "endomermis" restricted to plants? If so:
I think it would be best if GO have endodermis-specific terms that are logically defined with a CL or Uberon term (perhaps "cell of endodermis", "endodermis, respectively). The CL and Uberon terms would be defined as plant-specific and the GO terms will inherit the taxon constraints.
In GO, we could have terms that are, e.g. "endodermal cell fate specification, plant ground tissue" and they are 'siblings' (not child) of "endodermal cell fate specification". @pgaudet Are terms like that OK still?

Thanks for looking into this @raymond91125
This does seem reasonable, the animal and plant processes must be very different.
So, we'd need to split  GO:0035987 endodermal cell differentiation - I dont see plant annotations to the other terms when you query http://amigo.geneontology.org/amigo/search/ontology?q=endoderm
Thanks, Pascale

Thanks @pgaudet  and @raymond91125 for your insights.
I think the logical definitions for the plant-specific terms should use PO terms as neither CL nor UBERON contain plant terms.  That may have changed but I don't think so.
https://browser.planteome.org/amigo/term/PO:0000252
The two existing terms with A. thaliana annotations that I see are the following:
endodermal cell fate specification
http://amigo.geneontology.org/amigo/term/GO:0001714
endodermal cell differentiation
http://amigo.geneontology.org/amigo/term/GO:0035987
Having separate terms for the plant processes would be great and we can transfer the annotations from the animal one to the plant one after they are created. There are multiple parents for the current terms, some of which are generic but some are animal specific so the sibling status may be only appropriate under some of those parent terms.
plant endodermal cell fate specification
plant endodermal cell differentiation

Probably want to look at the taxon constraints here too. I am pretty sure  that at some point may have moved some TAIR annotations because of previous taxon constraint. But  I can't remember...

https://browser.planteome.org/amigo/term/PO:0000252 endodermis is a tissue. Is there a PO for endodermal cell?

It was requested a while ago on the PO tracker. I'm trying to see if there's any progress possible.
https://github.com/Planteome/plant-ontology/issues/618

+[Term]
+id: GO:0160057
+name: plant endodermal cell fate specification
+namespace: biological_process
+def: "The process in which a cell becomes capable of differentiating autonomously into a plant endodermal cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed." [PMID:26415082]
+is_a: GO:0001708 ! cell fate specification
+created_by: rynl
+creation_date: 2022-10-25T05:56:54Z
+
+[Term]
+id: GO:0160058
+name: plant endodermal cell differentiation
+namespace: biological_process
+def: "The process in which a relatively unspecialized cell acquires specialized features of a plant endodermal cell." [PMID:21735349]
+is_a: GO:0030154 ! cell differentiation
+created_by: rynl
+creation_date: 2022-10-25T06:12:17Z

Thanks. Please reopen or start a new ticket when plant endodermal cell becomes available and we can add the logical definition.

@raymond91125  Will do. Thank you.


How to make statistics script using summary?

Hi, all
I want parameter distribution analysis script for pretrained models.
I do not want special script for each model, just want single program to do it.
Some person advised me to use the summary graph.
tensorflow/tensorflow/tools/graph_transforms/summarize_graph_main.cc
I check the code and fell that the code does not support extracting parameters from pb file.
I wrote a draft code to analyze;
https://github.com/ElectronNest/dist_nn/blob/master/testloads_nn.py
Any suggestion is welcome, and I am beginner, please explain softly.
Best,
Syouyu

Thank you for your post. We noticed you have not filled out the following field in the issue template. Could you update them if they are relevant in your case, or leave them as N/A? Thanks.
Have I written custom code
OS Platform and Distribution
TensorFlow installed from
TensorFlow version
Bazel version
CUDA/cuDNN version
GPU model and memory
Exact command to reproduce

N/A or how to make statics script


Curve: Prevent forcing 1.0 min value to 0.99

The setters are called when the property is first initialized, and before
that its default min and max are 0.0 and 1.0 respectively.
If you configured min_value to 1.0 and max_value to e.g. 3.0, since the
min_value setter can be called before that of max_value (which thus still
defaults to 1.0), the min will be set to 0.99.
Same conflict could happen with a configured max_value of 0 if its setter
is called before that of a valid, negative min value.

Not sure if it's the cleanest way to do a tri-state "boolean", if anyone has a better proposal, go ahead :)

Although it fixes the issue, it's a long-lasting issue I keep worrying about in Godot's serialization system in general: when a property's value depends on another to be validated, you can no longer automatically serialize the object by randomly iterating over its properties. This is avoided by luck or hips&hoops in the engine so far, but I had the issue several times even when writing plugins.
A few workarounds:

Hack it, like you did. Works but makes the code a bit confusing.
Don't validate on set, but we have to because we have mixed inspection and serialization
Don't validate at all: this might mathematically work in some cases but could be confusing
Have a way to properly know when the object has fully been auto-serialized in order to post-validate. Or, have a way to pre-validate the data, or to customize serialization entirely with a function. But once again I'm not sure if we want that in the engine.


Except list slot type all the slots are converted to a single value

Rasa version: latest
Python version: 3.6
Operating system (windows, osx, ...): windows
Issue:
All the slot types apart from list type slot get converted to a single value
Content of domain file (domain.yml) (if relevant):
entities:
 - cities
slot:
 cities:
  type: unfeaturized

Input: /inform{"cities": ["new york", "paris"]}
Current Output: slot{"cities": "paris"}
Expected Output: slot{"cities": ["new york", "paris"]}

I found the reason which led to this. In domain,py, we update the slot values in function slots_for_entities

Thanks for raising this issue, @tabergma will get back to you about it soon✨
Please also check out the docs and the forum in case your issue was raised there too 🤗

You are right, a slot can just be a list or unfeaturized. Not both. We should change that.
It seems like you are already into the topic, do you want to fix it yourself and create a PR?

👍 Great, thanks! Let me know if I you need feedback/help.

@DivyashaAgrawal are you working on this?


Wrong version number taken in some cases

For example when a plugin like this is in the list:
Product Sales Report for WooCommerce version 1.4.8
https://github.com/moderntribe/tampermonkey-scripts/blob/a1b7b618fc98c98a2d436c905c6faab79d725812/premium-forum-plugin-versions.user.js#L59

Here's a sample:
https://theeventscalendar.com/support/forums/topic/cancelled-deleted-tickets-not-updating-stock/

This was fixed with a recent PR.


Fix directory traversal

RH Infosec contacted us, as someone pointed that one instance was
vulnerable to directory traversal attack, and so environment could be
leaked.
This patch should fix that.

@Humbedooh
Could you request a CVE for this?
The reporter is:
Dzmitry Smaliak
<EMAIL_ADDRESS>Thanks!

HI @Humbedooh bumping this.


Processing, Selector, Selector item widget  are not proper working

Technical
Description
Processing, Selector, Selector item widget  are not proper working
Steps to reproduce

Create a new project in Design Editor
Drag&Drop the "Processing" widget in the Mobile Profile
Drag&Drop the "Processing", "Selector", "Selector item" widgets in the Wearable Profile

Expected behaviour
The widget is good working
Actual behaviour
It is not properly displayed

Ok.  The patch is merged.


Time sync issue with uxr_sync_session()

I'm using an ESP32 with the micro-ROS component using a custom transport (serial port), and in my application I do a periodical rmw_uros_sync_session() call with a rather short time-out. The idea is that I want to make sure the clock doesn't drift during longer recordings, but I also keep the timeout short so it doesn't interfere with all my sensor sampling, basically it's not a big thing if the sync fails every once in a while since the periodic sync is mainly there to correct any drift.
But, every now and then I notice that we suddenly got a jump backwards in time. Looking into this in more detail I found that it happens some times after a successful sync following an unsuccessful one (unsuccessful due to timeout), but far from every time. Another thing I noticed is that the jump backwards in time was always half the time I set between my sync attempts.
After having a quick look at the code I would guess that this is caused by having an unprocessed timestamp_reply due to timing out before it's processed, since the calculations done in process_timestamp_reply() would cause this "sync period / 2" delay. Then on the next sync, the old reply is then processed and the new reply is left for the next sync() causing the time-shift to be persistent even after more syncs.
Not sure how this can be fixed best. Perhaps there's some way to invalidate previous timestamp replies when issue a new sync request, or add a id field to the request so that we can verify that we process the correct reply when calculating the session->time_offset.

Could you provide a quick replicator?

Sure, you can use this repo https://github.com/erikboto/microros-sync-bug-trigger.
The example uses a really low timeout (3ms) since it triggers the bug on the first run, so it's easy to reproduce. In our actual application it's 5 ms, where it works most of the times but just fails sometimes. Using 5 ms here will always work so the bug is never triggered, since there's not a lot of interrupts or other threads running.
I'm using a https://www.olimex.com/Products/IoT/ESP32/ESP32-DevKit-LiPo/open-source-hardware board, but I guess any HW will result in the same thing. On this board I'm using the "USB-uart" for microROS, and then I set up the log output to a UART on one of the GPIO pins.
The microROS agent I run using the docker images: docker run -it --rm -v /dev:/dev -v /dev/shm:/dev/shm --privileged --net=host microros/micro-ros-agent:humble serial --dev /dev/ttyUSB1 -b 921600 -v3

Why do you need to sync time so quickly? This approach was designed to calculate drift between clocks and then assume a certain stability for the drift variance.
Which is your use case?

Well this minimal replicator isn't really representative of how we are using it, here it is taken to an extreme just to replicate the issue. The reason I want to use a short timeout is that the system also samples sensors at high sample rates so I want to make sure the sync affects this as little as possible. So the real use-case is just to be able to call sync() with a short timeout, but with a long time between sync() calls, without risking that future sync() calls trigger this bug where an old reply is parsed causing the round-trip time calculations to be way off.
My understanding was that the sync() call measures the round-trip time, which it uses to set the offset from the received timestamp. But is there some periodical timestamp message coming from the microROS agent even if I don't call sync() again, that it can use to avoid long term drift? Or how does it calculate the drift? (I'm by no means a time-sync expert so I might be missing something that is obvious to you).

This approach uses an NTP-like algorithm for calculating the time offset between the MCU and the Agent's clocks. This is not a high-precision approach that targets to provide a valid (POSIX-like) time reference to an MCU that probably boots with a POSIX timestamp set to zero.
Ideally, the sync procedure shall be run once a startup and it will be used internally in Micro XRCE-DDS Client to offset the timestamp as you can see here: https://github.com/eProsima/Micro-XRCE-DDS-Client/blob/0c6743ffa358f26ca9433e951c534ec2f96be37a/src/c/core/session/session.c#L1194.
One approach that you can use is configuring the on_time callback in the session using this uxr_set_time_callback and control when you want to use or reject the  wire protocol timing info. You have an example here: https://github.com/eProsima/Micro-XRCE-DDS-Client/blob/master/examples/TimeSyncWithCb/main.c
In any case, as you are right and time sync responses shall not be processed out of sync call, I have prepared this PR: https://github.com/eProsima/Micro-XRCE-DDS-Client/pull/382 Could you take a look and validate that it fixes your use case?
Finally you have some documentation about this feature here: https://micro-xrce-dds.docs.eprosima.com/en/latest/time_sync.html

I had a quick look at the commit and I don't think it will solve the issue I see, which is that the old reply is read the next time I call sync(). So in my case session->waiting_for_time_sync will be true but it will read the old timestamp reply instead of the new one. But I will test it anyway to confirm.
Yeah using a custom on_time() callback could definitely work to make sure I don't set the time wrong, but it would still leave me in state where I always parse the reply from the previous sync() call which means that the new reply gets left for the next time. So I can't ever "catch up" and process the extra timestamp reply that is left in some buffer (at least that's what I think is happening).

You are right, replies from different requests still can cause problems.
It seems that the wire protocol is not designed to handle this because the definition of the sync request and reply does not provide any kind of request_id so we cannot differentiate between responses to different requests.


URL Cleanup

This commit updates URLs to prefer the https protocol. Redirects are not followed to avoid accidentally expanding intentionally shortened URLs (i.e. if using a URL shortener).
Fixed URLs
Fixed Success
These URLs were switched to an https URL with a 2xx status. While the status was successful, your review is still recommended.

http://www.apache.org/licenses/LICENSE-2.0 migrated to:
https://www.apache.org/licenses/LICENSE-2.0 (https result 200).

Ignored
These URLs were intentionally ignored.

http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd
http://www.w3.org/2001/XMLSchema-instance

Closing in favour of https://github.com/spring-cloud-incubator/spring-cloud-square/pull/19.


Implement valuable-serde crate

It should be possible to implement Serde's Serialize trait for valuable::Value. This should enable using Serde's existing serializer ecosystem with valuable.

@taiki-e is this something you would be interested in taking on? If it is, you can assign the issue to yourself.

I've tried it before: https://github.com/tokio-rs/valuable/blob/84c6992b55981181d7b75bb79fcf26428994a019/valuable/examples/serde.rs
If I remember correctly:

As for implementing Seriarize on Value: I changed some fields such as StructDef::name from &'a str to &'static str, but there were no other major problems.
As for implementing Valuable on impl Seriarize: It was very difficult and I could not get it to work well.

I will try to update it to the current valuable trait and see if it works.

Draft implementation is here: https://github.com/tokio-rs/valuable/pull/23


wcag color cog

The WCAG formula/algorithm for determining the contrast between two colors uses the luminance of these colors. That is: sRGB is converted into linear RGB, then the different channels are multiplied with three weights (R 0.2126, G 0.7152, B 0.0722) and then added up to get the luminance.

return the number and 2 swatches, one c1 > c2 and the other c2 > c1, that say Tsubaki

https://www.neilbickford.com/blog/2020/10/18/computing-wcag-contrast-ratios/


Documentation: update Kafka-ui/readme.md doc with a latest feature list and go through the rest

Describe the bug
Current readme.md doesn't have the KSQL DB, while even videos have it included.
Maybe along with the 0.5 release, with addition of an RBAC info and data masking references.
Set up

Steps to Reproduce

Steps to reproduce the behavior:

Expected behavior

Screenshots

Additional context

Hello, I would like to give this a try. Can you point me to the video? What info should I include in teh read me?

Hello, @uyentdang . Thanks for the initiative! But I'm afraid the only person able to provide an up to date feature list for KafkaUI is no longer with the team. Once we have sufficient resources, we'll pick up this task.
As for the video, it is right on the readme.md page in the root of kafka-ui repository, the very first one, and it was meant just as an example.


Upgrade centos image and revert tdp mmu workaround/mohammed

/test-integration-metal3-dev-tools-centos

/hold
unhold after centos e2e ci is green


Extra error details

Tack on extra information from .errors property, if present.

This will make problems much easier to diagnose, thanks a lot @ralphtheninja!

Patch is probably fine because it doesn't break common patterns like if (/github error/i.test(err)). But I'm not familiar with this family of modules, your call ;)
If you wanna stay safe you could instead do Object.defineProperty(err, 'errors', { value: errors }).


Fix Responsive Issue #3929

Fix Responsive Issue #3929

@deepaksinghgusain227
when we come back to website view from responsive view, header section need to reload again https://prnt.sc/ui8491

@deepaksinghgusain227
please resolve conflicts

make new pr that's i want to close the pr


Support Non-Interactive Mode for agenta-cli commands

In order to implement this we aim to enhance the agenta init command to support a non-interactive mode, which would allow automation and integration into various workflows without the need for user intervention. This would be particularly useful in CI/CD pipelines and scripting use cases.
Currently, the interactive setup requires user input, restricting our ability to fully automate the initialization process.
At present, executing agenta init does not provide a way to specify the organization or how to initialize the app (either as a "Blank App" or "Start from template").
We plan to add two click options and their associated logic to the agenta init command:
@click.option("--organization")
@click.option("--start-from")

Same thing for
agenta variant serve
agenta variant serve (overwrite)

fixed in
https://github.com/Agenta-AI/agenta/pull/1621


VirtualGraphComposite: Improve error message for out-of-range qubit

If an embedding specifies a qubit that is outside the range of the child sampler, it would be nice to see a more specific error -- users might not always be aware of the ranges of different solvers.
embedding = {'x': {1}, 'y': {5}, 'z': {0,4}, 'a': {4000}}
sampler = VirtualGraphComposite(DWaveSampler(), embedding, flux_biases=False)
KeyError                                  Traceback (most recent call last)
 in ()
----> 1 sampler = VirtualGraphComposite(DWaveSampler(), embedding, flux_biases=False)
/usr/local/lib/python2.7/dist-packages/dwave/system/composites/virtual_graph.pyc in init(self, sampler, embedding, chain_strength, flux_biases, flux_bias_num_reads, flux_bias_max_age)
128         # Derive the structure of our composed from the target graph and the embedding
129         #
--> 130         source_adjacency = embutil.target_to_source(target_adjacency, embedding)
131         try:
132             nodelist = sorted(source_adjacency)
/usr/local/lib/python2.7/dist-packages/dwave_embedding_utilities.pyc in target_to_source(target_adjacency, embedding)
140     # v is node in target, n node in source
141     for v, n in iteritems(reverse_embedding):
--> 142         neighbors = target_adjacency[v]
143
144         # u is node in target
KeyError: 4000

Closed in #532.


Add composer --no-cache for release:create

Sometimes composer seems to be missing some fresh updates commits in upstream because of cache. We should explicitly ignore cache to always pull the latest code.

Unless someone tells me this is a problem we are still having, I don't think it's worth spending time on this.


docs: update relationship field with example variations

Description
Add to relationship field documentation. Related to: https://github.com/payloadcms/payload/discussions/204 also https://github.com/payloadcms/payload/discussions/187

[x] I have read and understand the CONTRIBUTING.md document in this repository

Checklist:

[x] I have made corresponding changes to the documentation

@DanRibbens commit b5d272f seems to cover all scenarios and is clearly written. Thumbs up from me :+1:


Repo organisation

Hello @dubadub  @Seth-Harlaar
There are several points I would like to address with you, because right now I'm not feeling super easy regarding this repo organization.

It seems that right now, this repo is going through big changes, with creation of other git sub-repo for specific language (python in this case). Although on paper it makes a lot of sense, I hope the drawbacks of this decision are also very clear for you . Multi-repo organization can quickly become a pain to manage, and it is also way more difficult for external contributor to work on this project. For instance, in my case, right now I need to fork also the second repository, update my fork of the main repo to link it to the fork of the subrepo, and be careful to never push this commit when contributing to the original repo.
Also I'm a bit sad to see that these important changes were pushed on master without discussion with the community (well, we are not a lot right now but still ^^) I think the main maintainers of a repo should respect the same coding convention than community members, by opening PR and waiting a few days for feedback before merging on master.
This last point is especially true given the fact that the current split between both repo doesn't seem to be well defined. Currently the python repo is a big copy-pasting of this repo, and this repo still contains python code for testing and packaging... I think it would have been way cleaner to work on this multi-repo setup in a branch and wait for it to be ready before merging on master. (well, more specifically work on 2 branches, one in both repo, been careful that both branch stay in sync, and merge both at the same time)

Also, now that I think about it, I'm not sure to understand why the python repo is a dependence of the C repo. Shouldn't it be the other way around, with the C repo autonomous and the python repo having the C version as dependency ?

Hey @Net-Mist.
Thanks for sharing your concerns. I absolutely agree with all your three points. Right now we don't have any process in place as there's only one contributor in this repo (@Seth-Harlaar) and its in early-ish stage. This makes it hard for other people to step in and help. If you don't mind joining our forces, I'll add you as a maintainer and then three of us agree on process (goals, roadmap, reviews, etc). How does this sound?
Also linking @Accacio as I've seen his interest in project too.

Hey @dubadub
Thanks a lot for the proposition, I would be happy to become a maintainer of this repo.
I think it's important to have our discussion somewhere public, so anyone could join and add his own opinion.
Maybe we could open one issue which will be a To Do list of all the tasks that need to be done. Then, for every tasks, we can open another issue to discuss it and clearly define the spec of the implementation.
Another solution, maybe a bit too much for now but that can be interesting if the project become bigger is to use the "project" feature of Github. We could create a Kanban board  (using the project tab on github https://github.com/cooklang/cooklang-c/projects) with 5 columns:

Backlog: list of all the tasks that need to be done at some point, but not yet clearly defined
To Do: list of all the tasks clearly defined that are not started yet
Doing: list of tasks with open Pull Request in draft mode
Code Review: list of tasks with corresponding Pull Request done and waiting for review
Done: tasks with corresponding PR merged

What do you think ?

Fantastic! Thank you very much. I sent you an invite. The plan forward sound good to me. Tomorrow I'll describe in an issue what we have in mind. I'm totally for trying projects if you like.

@Net-Mist @Seth-Harlaar I outlined my thinking here https://github.com/cooklang/cooklang-c/issues/23. Feel free to offer your ideas and add your comments.

Going to close the issue since the issues outlined here are being discussed and addressed in #23 .


[env select] - validate env name exists

When running azd env select foo , azd is not validating that foo is an existing environment.  Azd is setting the env name to foo without creating the environment. This causes that running azd provision next would ask if you want to create the foo environment.
Example:

Expected:
Should azd fail if azd env select receives one environment name which does not exists?

Should azd fail if azd env select receives one environment name which does not exists?

Yeah, this feels like a reasonable thing for us to be doing here.


Pipeline editor prevents multiple input links on first node added after open

For whatever reason, I can no longer associate multiple nodes as inputs to a single node like the following:

Instead, I see this...

I'm using master with a last commit of Friday evening: a52f2704bd8d7d95968834553cc9bbd8af8a84a6
Although this is also happening on @marthacryan's prevent-circular branch while looking at #744.
@lresende also confirmed.

@vabarbosa found that there appears to be a relationship between the cardinality of the inputs specified in the pipeline file and this issue.  I found that most all inputs have a cardinality of min: 0, max: 1 - so this would prevent a second input.  If I manually update my pipeline file to specific min: 0, max: -1, I can successfully add two inputs to that node.
It also appears as though the FIRST notebook added to the pipeline gets the limitation on inputs while other nodes have NO cardinality specified for either inputs or outputs.  However, there must be some way to have other nodes with the input restriction, but I can't reproduce that at the moment.

I did some research into this and tracked down the twofold issue here:

As @kevin-bates described above we set the cardinality for input as min: 0, max: 1 where it should be min: 0, max: -1 to allow multiple inputs (This of course assumes I'm correctly understanding the meaning of an input cardinality in canvas). This is an "easy fix" that will address the immediate problem.

Canvas is only setting the input and output cardinality on the first node added after opening a pipeline editor. This seems to be coming from the function convertNodeTemplate here: https://github.com/elyra-ai/canvas/blob/release-6.1.23/canvas_modules/common-canvas/src/object-model/object-model.js#L1129 which we call to create our nodeTemplate (Note that this function has not changed even in master, though it has moved within the file). That function includes a line that "clones" the app_data using JSON.parse(JSON.stringify()) and has a comment explaining that it's important since app_data.ui_data is later deleted and it doesn't want to affect the template, just this instance. Yet later in the function it passes the input and output JSON to the function convertPort right below. This function has much of the same behavior for inout and output as convertNodeTemplate did for app_data but it's missing the "clone" step. This means that the input and output ui_data is deleted from our template after the first node (the template being recreated each time the editor is opened). Given that nodes with a cardinality set seem to behave as we want them to in Elyra, fixing this is not an immediate issue for use, but we should raise this on the canvas repo.

Updated title to reflect what's going on.

Note: canvas has fixed the bug on their end now so our update to latest canvas will address point 2 above

This issue has been fixed in the Elyra/canvas code.


Add CodeXGLUE-text-to-text benchmark for documentation translation

Add  this benchmark for documentation translation to the evaluation harness: https://huggingface.co/datasets/code_x_glue_tt_text_to_text

few-shot setting (see CoNaLa and Spider tasks for examples)
fine-tning

Hi, I am interested in taking this up !

Great, let us know if you need any help!


Connection to database failed Error

I keep getting this error: Connection to database failed
I have MariaDB 10 installed on Ubuntu 14.04
I followed this guide to install PowerDNS:
https://www.digitalocean.com/community/tutorials/how-to-install-and-configure-powerdns-with-a-mariadb-backend-on-ubuntu-14-04
So I am not sure what I can possibly be doing wrong. I have created another database as well but still same error.

PDNS Manager will create its own database structure, so it is better if you create a empty one for it.
Can you provide the PHP error log of the installation? Have you checked you have all dependencies installed notably php5-mysqlnd.

Googling it seems that the log would be stored in: /var/log/httpd/php_error_log but that file is blank. I have created an empty database and still same error message.

I think I found it: http://hastebin.com/biqajobijo.coffee

According to the log you tried it using the mysql user root with no password. Are you able to login on the shel with mysql -uroot ? It seems to be a problem with your credentials.

I have tried mysql with no root password but i don't really like that idea for security reasons. I am able to login in via shell.

I should mention I tested the credentials idea by punching a bunch of gibberish and I got another error that access was denied.

According to your log you did not supply a password to the installer, so it tries to connect as root with no password to the database. Of a security perspective this would be fatal. If the above command works with only mysql -uroot then your mysql server is configured without root password. So please make shure that your credentials are valid. The information you give is inconsistent.

I will make a screencast then of this, I mean I am not insane.

I tested the installation with the current version using ubuntu 14.04 half a hour ago. Also your provided log says that the installer is trying to use no password and the user root: Access denied for user 'root'@'localhost' (using password: NO)
As a general recommendation you should not use root as the user for PDNS Manager. Instead create a new one with access to its own database. Also assign strong passwords to all users (root and the one for pdns manager). You can test your configuration on the shell using mysql -uusername -ppassword

Well now I got a completely different problem not even sure:
https://www.youtube.com/watch?v=T_dPyCgF2vI&feature=youtu.be&hd=1

Okay well that seems to be a different problem. Either this is a bug in the installer of PDNS Manager, or a problem in your client. Which browser and version are you using? Do you use Addons like NoScript? If you have a second browser installed you can try with that one. I would then be also intressted which browser in which version you tried.

I have tried both Chrome and Firefox I have no plugins at all.

Please open the Installer in Firefox and open the network tab of the developer console. (F12)
Fill out the form and klick on the "Install" button. There should be requests popping up now. Right click any of them and use the "Save as HAR" button to save all requests and the responses.
Please note that all passwords are available in clear text in this log.
Paste this log on pastebin or somewhere else and provide us with the link, thank you.


Java helloworld with local dev and oci functions

the license part should be like this at the end of the readme.md
License Copyright (c) 2024 Oracle and/or its affiliates.
Licensed under the Universal Permissive License (UPL), Version 1.0.
See LICENSE for more details.

done


go_router_builder persist dialogs and bottom sheets on routing to different routes

Steps to reproduce
Using go_router_builder for generating routes introduces the behavior that Dialogs and BottomSheets stay opened on screen, while navigating to different routes
Expected results
I expect that the Dialogs are closed, if another route is called.
Actual results
Dialogs persist on Screen
Code sample
Code sample
Repo

Screenshots or Video

Screenshots / Video demonstration
With Bug (go_router_builder routes)
https://github.com/user-attachments/assets/d902acd9-c2e4-41d1-b606-0e0d60a86e2c
Without Bug (handcrafted routes)
https://github.com/user-attachments/assets/bffe07c3-4f51-4c5c-a86d-ca8ac071a1c7

Logs
No response
Flutter Doctor output
Doctor output
 flutter doctor -v
[✓] Flutter (Channel stable, 3.24.5, on macOS 15.0.1 24A348 darwin-arm64, locale de-DE)
    • Flutter version 3.24.5 on channel stable at /Users/user/Library/flutter
    • Upstream repository https://github.com/flutter/flutter.git
    • Framework revision dec2ee5c1f (6 days ago), 2024-11-13 11:13:06 -0800
    • Engine revision a18df97ca5
    • Dart version 3.5.4
    • DevTools version 2.37.3

[✓] Android toolchain - develop for Android devices (Android SDK version 35.0.0)
    • Android SDK at /Users/user/Library/Android/sdk
    • Platform android-35, build-tools 35.0.0
    • Java binary at: /Applications/Android Studio.app/Contents/jbr/Contents/Home/bin/java
    • Java version OpenJDK Runtime Environment (build 21.0.3+-79915917-b509.11)
    • All Android licenses accepted.

[✓] Xcode - develop for iOS and macOS (Xcode 16.0)
    • Xcode at /Applications/Xcode.app/Contents/Developer
    • Build 16A242d
    • CocoaPods version 1.15.2

[✓] Chrome - develop for the web
    • Chrome at /Applications/Google Chrome.app/Contents/MacOS/Google Chrome

[✓] Android Studio (version 2024.2)
    • Android Studio at /Applications/Android Studio.app/Contents
    • Flutter plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build 21.0.3+-79915917-b509.11)

[✓] Connected device (4 available)
    • iPhone von user (mobile) • 00008110-001229C43413A01E • ios            • iOS 17.6.1 21G93
    • macOS (desktop)                       • macos                     • darwin-arm64   • macOS 15.0.1 24A348 darwin-arm64
    • Mac Designed for iPad (desktop)       • mac-designed-for-ipad     • darwin         • macOS 15.0.1 24A348 darwin-arm64
    • Chrome (web)                          • chrome                    • web-javascript • Google Chrome 130.0.6723.119
    ! Error: Browsing on the local area network for iPhone Small King. Ensure the device is unlocked and attached with a cable or associated with the same local area network
      as this Mac.
      The device must be opted into Developer Mode to connect wirelessly. (code -27)

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

• No issues found!

@YukiAttano Thanks for the report and repo. I observed that when we tap on Go to Home, it does pop the route but doesn't close the dialog. When we close it, we see that we are on first screen. This behavior reminds me of this open issue that you can check to see if it resembles your case or not.

@YukiAttano Thanks for the report and repo. ...

yes you are right, it seems to be related. I guess my example will help to pin down to root cause.

@YukiAttano
I suggest you to follow-up in that issue for better tracking. You may share your findings, code and example so that it will help to be at one place, as, this could be the root-cause per mentioned comment.
I will close this as a duplicate. If you disagree, write in comments and I'll reopen it.


pytest errors

While attempting to add tests for #23, I hit a couple of pytest errors:
1: test_inspector is hardcoded to look for D:\pycharm_projects in the exception object. As I am running in a different directory, this test fails.
2: Many different tests use cwd when they should use e.g. os.path.realpath(__file__) instead.
3: Even though the main code works with either pyyaml or ruamel.yaml, test_multiprocessing is hardcoded to use ruamel.yaml - and Murphy's law meant that of course I had only pyyaml installed.
All easily fixed - I'll throw up a PR in a bit. Don't know where this project falls on the sliding scale between 'a billion tiny PRs' and 'one huge PR'.

Thanks for your finding.

1: test_inspector is hardcoded to look for D:\pycharm_projects in the exception object. As I am running in a different directory, this test fails.

Sorry, I was in a hurry at that time so I left it as is. Should have used regex instead.

2: Many different tests use cwd when they should use e.g. os.path.realpath(file) instead.

Pytest is invoked inside that tests directory, so Path.cwd() is fine.
The longer version if needed, will be Path(__file__).parent.
The reason for cwd is the tests directory is that some tests need to call the external py files, which are in the same directory.
So using the tests directory as cwd made writing tests easier.
If there is a reason for using os.path.realpath(__file__), please let me know.

3: Even though the main code works with either pyyaml or ruamel.yaml, test_multiprocessing is hardcoded to use ruamel.yaml - and Murphy's law meant that of course I had only pyyaml installed.

Yeah, I should have rewritten that better. But since the ruamel.yaml was supported later, I used it over pyyaml.


JS Deployment needs configuration

We need to be able to configure some URLs and other variables different for localhost and production. See discussion here.
@HelgeKrueger would you mind to create the initial architecture e.g. with just the GraphHopper API URL to be configurable? I'll do the rest :) !

Implemented this via envify. Will provide a PR soon

Implemented this, please enhance if necessary like for nominatim URL etc (put them in the options_dev.js)

The PR #590 was therefor easily deployable to GraphHopper Maps. Let me know if there are issues!

Reopening due to error reports

Should be fixed via a new approach.

Something that should be configured here as well is the CORS handling. If setup my production environment I get the following exception when accessing the geocoding API:
Cross-Origin Request Blocked: The Same Origin Policy disallows reading the remote resource at http://graphhopper.com/api/1/geocode?limit=6&type=json&key=myKey&q=wer. (Reason: CORS header 'Access-Control-Allow-Origin' missing).

Maybe http vs. https?

I was using http to serve my site.
I guess it is related to the datatype. I found information on the internet that for cross-origin request one should use jsonp.
http://stackoverflow.com/questions/25310450/cross-domain-javascript-cors-concept
http://stackoverflow.com/questions/3506208/jquery-ajax-cross-domain
This is also mentioned in the GHRequest.js at the datatype definition. // use jsonp here if host allows CORS.

jsonp is something old and should be replaced with CORS. We support CORS on the server side (for geocoding&routing) and so the JS should have no problem with it. Maybe you need to enable it in JS via $.support.cors = true;?

I was using http to serve my site.

but for geocoding you seem to use http://graphhopper.com?

Thanks. Using https for the graphopper API fixed my issue.


[Tool]ci test

Fixes #issue
What type of PR is this:

[ ] BugFix
[ ] Feature
[ ] Enhancement
[ ] Refactor
[ ] UT
[ ] Doc
[ ] Tool

Checklist:

[ ] I have added test cases for my bug fix or my new feature
[ ] This pr will affect users' behaviors
[ ] This pr needs user documentation (for new or modified features or behaviors)

[ ] I have added documentation for my new feature or new function

Bugfix cherry-pick branch check:

[ ] I have checked the version labels which the pr will be auto-backported to the target branch

[ ] 3.1
[ ] 3.0
[ ] 2.5
[ ] 2.4

[FE PR Coverage Check]
coverage check fail. please retry. :fearful:
Please let me know when error again.
com.naver.nid.cover.parser.coverage.exception.ParseException: java.nio.file.NoSuchFileException: /home/runner/_work/starrocks/starrocks/fe/fe-core/target/result

[FE PR Coverage Check]
:heart_eyes: pass : 0 / 0 (0%)

[FE PR Coverage Check]
coverage check fail. please retry. :fearful:
Please let me know when error again.
com.naver.nid.cover.parser.coverage.exception.ParseException: java.nio.file.NoSuchFileException: /var/local/env/230627/starrocks/fe/fe-core/target/result

[FE PR Coverage Check]
coverage check fail. please retry. :fearful:
Please let me know when error again.
com.naver.nid.cover.parser.coverage.exception.ParseException: java.nio.file.NoSuchFileException: /home/runner/_work/starrocks/starrocks/fe/fe-core/target/result

[FE PR Coverage Check]
:heart_eyes: pass : 0 / 0 (0%)


Scan import through API returns a 'not valid JSON' error

Issue Type

[X] Bug

Description
I am having the python script which uploads the scan results to the Dojo server using API. From the documentation example I formed my request. The request looks like this:
print 'Importing the scan'
import_scan_url = 'https://defectdojo.company.net:443/api/v1/importscan/'

import_data_json = """
{
  "minimum_severity": "Info",
  "scan_date": """ + todays_date + """,
  "verified": false,
  "file": """ + file_for_importing + """",
  "lead": "",
  "tags": "",
  "active": false,
  "engagement": "/api/v1/engagements/5/",
  "resource_uri": "",
  "scan_type": ""
}
"""

post = requests.post(import_scan_url, headers=headers, data=import_data_json )

Unfortunately, the server returns this error:
{"error": "Request is not valid JSON."}
I'm not entirely sure what am I missing.

Take a look at the slack channel or use the defectdojo api.


Update position of registered custom generate_reply functions for contrib/ agents per PR #794

Why are these changes needed?
PR #794 added registration of async human input handler.  This bumped the position of the other default registered generate reply functions by 1. Two contrib/ agents were updated per this change (their generate_reply function was bumped by 1 to account for change), but three contrib/ agents were missed.  This completes the bump by 1 for those three agents.
Related issue number
PR #794
Checks

[ ] I've included any doc changes needed for https://microsoft.github.io/autogen/. See https://microsoft.github.io/autogen/docs/Contribute#documentation to build and test documentation locally.
[ ] I've added tests (if relevant) corresponding to the changes introduced in this PR.
[ ] I've made sure all auto checks have passed.

Codecov Report
Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (a107233) 26.63% compared to head (f8e97b8) 30.73%.

Files
Patch %
Lines

autogen/agentchat/contrib/teachable_agent.py
0.00%
1 Missing :warning:

autogen/agentchat/contrib/text_analyzer_agent.py
0.00%
1 Missing :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #871      +/-   ##
==========================================
+ Coverage   26.63%   30.73%   +4.10%
==========================================
  Files          28       28
  Lines        3725     3725
  Branches      847      847
==========================================
+ Hits          992     1145     +153
+ Misses       2660     2495     -165
- Partials       73       85      +12

Flag
Coverage Δ

unittests
30.73% <33.33%> (+4.16%)
:arrow_up:

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Support lists in the Launch UI

This task is to support entering list/collection values in the Launch UI.
For the initial implementation, collections can be entered as JSON-parseable array strings. Collections, by convention, are homogenous. So assuming that we can correctly parse the array string, the values in the array can all be run through the same sub-validator.

This is implemented by lyft/flyteconsole#33


Add basic functionality to write labels subgroups

Remaining tasks:

[x] Add test for labels/<subgroup_name>
[ ] Assert that written labels have same dims and resolution levels as parent group images
[ ] Update example notebook

Codecov Report

Merging #14 (d8ef45d) into main (e586114) will increase coverage by 0.22%.
The diff coverage is 100.00%.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
@@            Coverage Diff             @@
##             main      #14      +/-   ##
==========================================
+ Coverage   91.43%   91.66%   +0.22%
==========================================
  Files          11       11
  Lines         946      972      +26
==========================================
+ Hits          865      891      +26
  Misses         81       81

Impacted Files
Coverage Δ

src/faim_hcs/Zarr.py
97.79% <100.00%> (+0.27%)
:arrow_up:

tests/test_Zarr.py
98.94% <100.00%> (+0.13%)
:arrow_up:

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Add PRESENTATIONS-merge to documentation jobs page.

Addresses https://trello.com/c/noND43JK/618-document-presentations-merge and staged at https://ci.openmicroscopy.org/job/CONTRIBUTING-merge-docs/ws/src/contributing/_build/html/ci-docs.html.

Tries to follow the style of entries for similar jobs.


Bug: Empty tab name in fugitive status buffer

Self Checks

[x] I'm using the latest lualine.
[x] I didn't find the issue in exsisting issues or prs.

How to reproduce the problem

Use :cd to change directory to a git repo.
Open fugitive status buffer with :Git.

Expected behaviour
Tab has something that represent the "fugitve status buffer".
Actual behaviour
Empty tab name.
Minimal config to reproduce the issue

call plug#begin("/root/lualine_fugitive/.local/share/nvim/plugged")
" Your plugins go here like
Plug 'nvim-lualine/lualine.nvim'
Plug 'tpope/vim-fugitive'

call plug#end()

" Your Viml part of config goes here
" colorscheme onedark

lua << END
-- Your lua part of config goes here
require'lualine'.setup {
  tabline = {
    lualine_a = {
      {
        "tabs",
        max_length = vim.o.columns / 3,
        mode = 2,
      },
    },
    lualine_b = {},
    lualine_c = {},
    lualine_x = {},
    lualine_y = {},
    lualine_z = {},
  },
}

END

" Instructions:
" -------------------------------------------------------------
" Load this config with nvim_isolated_conf.sh -l /root/lualine_fugitive
" Remember to run :PlugInstall after changing plugin section
" Also delete the comments before putting this file on issue
" That will reduce noise
" You can delete /root/lualine_fugitive once you're done

Aditional information
Tab:label() here use fnamemodify() with :t to get the last path component. But the fugitive status buffer name is the .git folder with path separator appended. So the returned tab label is empty string.

Thank you!