Dask 2023.5.0 python tests break 3.8+ test environment for Airflow

Describe the issue:
Dask 2023.5.0 breakes tests for Airflow for Python 3.8 - most likely because the "distribured tests" and related leave side effects after running tests (/tmp directory in following tests is pointing to dask scratch space)
Minimal Complete Verifiable Example:
After releasing dask our tests started to fail The only real chanve in our test suite is that we attempted to upgrade
to latest dask (previous suite of tests completed few hours ago, so the only upgraded dependency since was dask:
This is visible here:
https://github.com/apache/airflow/actions/runs/4960905632/jobs/8877036912#step:4:17652
147c147
< dask==2023.4.1
---
> dask==2023.5.0
156c156
< distributed==2023.4.1
---
> distributed==2023.5.0

Also you can see that Python 3.7 is still green - because the new dask is Python 3.8+ and the builds has not changed any dependencies:
Summary: Constraints constraints-source-providers:3.7:

Constraints generated in /files/constraints-3.7/constraints-source-providers-3.7.txt

No changes in constraints - exiting

With those dependencies upgraded, an unrelated test started to fail::
https://github.com/apache/airflow/actions/runs/4960905632/jobs/8877333352#step:6:8621
It shows:
        path = sys.path[0] + "/tests/kubernetes/pod.yaml"
>       with open(path) as stream:
E       FileNotFoundError: [Errno 2] No such file or directory: '/tmp/dask-scratch-space/scheduler-8895yk3s/tests/kubernetes/pod.yaml'

It looks like running tests from this sute leave sys.path[0] set to   /tmp/dask-scratch-space/scheduler-8895yk3s as side effect. This does not happen on Python 3.7, it only happens on Python 3.8+. (NOTE: Because new dask is Python 3.8+ only).
This test works fine in isolation, no problem, but our test suite executes dask tests before
  tests/executors/test_dask_executor.py ....ss....                         [ 11%]
  tests/executors/test_debug_executor.py .........                         [ 11%]
  tests/executors/test_executor_loader.py ................ss               [ 12%]
  tests/executors/test_kubernetes_executor.py .F.......................... [ 13%]

And tests from dask import the test suite friom dask:
https://github.com/apache/airflow/blob/main/tests/executors/test_dask_executor.py
try:
    # utility functions imported from the dask testing suite to instantiate a test
    # cluster for tls tests
    from distributed import tests  # noqa
    from distributed.utils_test import cluster as dask_testing_cluster, get_cert, tls_security

    skip_tls_tests = False
except ImportError:
    skip_tls_tests = True
    # In case the tests are skipped because of lacking test harness, get_cert should be
    # overridden to avoid get_cert failing during test discovery as get_cert is used
    # in conf_vars decorator
    get_cert = lambda x: x

Anything else we need to know?:
We are just limiting dask to < 2023.5.0 to handle it , but it would be nice to fix it asap.
Environment:

Dask version: 2023.5.0
Python version: 3.8+
Operating System: Linux
Install method (conda, pip, source): pip

I'm a little confused about what's going on here.  I think the failing tests are in test_kubernetes_executor.py not test_dask_executor.py
What should sys.path[0]  be pointing to ?  Sys.path being monkey patched somewhere ? Perhaps using dask.config.get("temporary-directory") might work instead of hardcoded paths ?

What is in sys.path[0] in our tests is the "airflow's" /opt/airflow  - where the sources of airflow are available when running the tests.
And as I explained above - this is a side effect of dask tests. Those tests should NEVER change global state. They do.
The unit tests of dask executor in the new version modify sys.path[0] and do not clean up after themselves. They override system path with test directory of dask and forget to clean after themselves.  Usually this is done with patching which modify system path and clean up after the tests are done. Leaving behind modified global state is a very bad code-smell and it should not happen. The tests of dask executor are using the imported test suite from dask and apparently it's the suite that leaves things behind.
Unfortunately (for us) dask tests in Python have been implemented and managed by the dask team and we have no capacity or possibility to  manage it so every time such tests fail we have to freeze the version of dependency from dask and let the dask team fix it (happened 2 times in the past).  This is cumbersome and since we have no capacity to make any changes there, basically any time it happens we open an issue or discuss in the discort of dask to fix the problem and until they do we just freeze the version that caused the problem (which we already did in https://github.com/apache/airflow/pull/31259). We are not going to modify our tests to handle side-effects from the new dask provider.
The result of it is that users of dask executor will use old version of the dependency until it is fixed by dask team.
There is an easy way out though.
Better solution would be, that DASK team takes over back the maintenance of their dask executor and releases the executor on their own. We have just implemented https://cwiki.apache.org/confluence/display/AIRFLOW/AIP-51+Removing+Executor+Coupling+from+Core+Airflow and 3rd-party companies that integrate with airflow can release their providers independently https://github.com/apache/airflow/blob/main/PROVIDERS.rst#rd-party-providers so that they can make sure whatever they release as dependency is up-to-date. I think this is the right direction for Dask.
Do you want to go that path? I think we would be super happy to pass the maintenance of dask executor and the related tests to your team back.

Thanks @potiuk. My guess is https://github.com/dask/distributed/pull/7802 is related to the change in behavior that's causing problems for the airflow test suite. I opened https://github.com/dask/distributed/pull/7838 as a possible fix.

Thanks! Looks pretty much like it - once you have a release candidate up in PyPI - I will be able to test it - it will be enough to remove the limit in Airflow and make a "full tests needed" PR with it.

Q: Is there a place (mailing list or smth) where I can subscribe to new releases? Right now we are upper-bound so we won't automatically upgrade. Or maybe this is all but guaranteed that it will be released in next release and I should put != for the broken versions in our deps?

Yeah, https://github.com/dask/distributed/pull/7838 will be included in the next release (we release every two weeks -- next one should be next Friday, May 26)

Thanks for quick fix!
I will exclude just these versions and they should get upgradeded automatically when released then!


Frame.show fails with frozen modules

I think the stacktrace explains it:
    bottom_frame.show(perror)
  File "/home/maartenbreddels/miniconda/envs/dev/lib/python3.7/site-packages/viztracer/prog_snapshot.py", line 41, in show
    with open(node.filename) as f:
FileNotFoundError: [Errno 2] No such file or directory: '<frozen importlib._bootstrap_external>'

Noted, will fix by the end of today.


Update rename-transact-sql.md

"ALTER DATABASE" cannot be used to rename databases in Azure Synapse Analytics.
Currently, Serverless SQL pool does not supported for "ALTER DATABASE MODIFY NAME" and SQL Dedicated Pools cannot be renamed.
Test scenario is attached
Test Scenario - Rename SQL Pools.docx
.

@charithcaldera : Thanks for your contribution! The author(s) have been notified to review your proposed change.

@ronortloff,
Can you review the proposed changes?
IMPORTANT: When the changes are ready for publication, add a #sign-off comment to signal that the PR is ready for the review team to merge. Thanks.
#label:"aq-pr-triaged"

@vvasic-msft,
Can you review the proposed changes?
IMPORTANT: When the changes are ready for publication, add a #sign-off comment to signal that the PR is ready for the review team to merge. Thanks.
#label:"aq-pr-triaged"
#assign:@MicrosoftDocs/public-repo-pr-review-team

The following users don't have valid GitHub IDs, or are not collaborators on this repo: microsoftdocs/public-repo-pr-review-team

Correct, it's not supported in serverless.
#sign-off

@vvasic-msft: I'm sorry - only the author of this article, @ronortloff, can sign off on your changes. But we do have an exception process - if you are on the Microsoft content or product team for this product area, you can ask the PR review team to review and merge it by sending mail to the techdocprs alias.


Fix: Python 3 tests not to use Mbed OS master

This fixes Python 3 tests not to use Mbed OS master, but fixed version (Mbed OS 5.9.0)

Temporary fix to unlock Mbed-CLI master until Mbed OS tools are fixed.
cc @theotherjimmy @cmonr


Whisper example: files must be opened in binary mode

Fixed the whisper example in readme.md. Files must be opened in binary mode, otherwise it will not work.
All Submissions:

[x] Have you followed the guidelines in our Contributing document?
[x] Have you checked to ensure there aren't other open Pull Requests for the same update/change?
[x] Have you added an explanation of what your changes do and why you'd like us to include them?

Hey @Tamnac! Thanks for this. Can you share an example of a file / format that would fail without this change? Currently we use spec/fixtures/files/audio_sample.mp3

OK, makes sense - have updated the specs to match this also and seem to work fine.

Thanks for your contribution!


Clarifying Table

https://github.com/MicrosoftDocs/OfficeDocs-SkypeForBusiness/issues/3568

@JohanFreelancer9 Copy editing is needed for this PR. Thanks.

@tonysmit PR has been copyedited and is ready for final review, could you please check and merge? Thanks!

@TokyoScarab - are you internal? Where did you get this information?


Provide the swagger URL in Publisher REST API for api creation.

In automating the API creation process using Publisher REST APIs, for creating an API we can use the below API:
https://host:port/api/am/publisher/v0.11/apis.
But, in the request JSON we have to pass the swagger definition as a string in "apiDefinition" parameter.
It is much convenient to provide the swagger URL in request JSON instead of the entire swagger as a string.

With APIM 3.0 Publisher REST API (V1.0) you can provide the swagger URL with additional properties and create an API. Please refer the REST API V1.0 documentation here


Correct typo in parser/services.go L52

For the commit msg style can you please follow this guide: https://docs.teamhephy.com/contributing/submitting-a-pull-request/
Just rename the commit msg to something like fix(services): correct typo...

@Cryptophobia It's ok, I'll check the guidelines.


Armitage saying: "java.net.SocketException: Unexpected end of file from server"

Hello,
I am trying to open Armitage. I am running a Kali Virtual Box install Kali-Linux-2020.3-vbox-amd64. But Armitage says: "java.net.SocketException: Unexpected end of file from server". I found one forum saying that I could not use "<IP_ADDRESS>" as my ip address, but the Virtual Box internet is weird, and what hostname -i println's says connection refused. What should I do?

Leaving the hostname blank causes Armitage to flip between "Connected: logging in", and "Remote Host Terminated the Handshake".

After uninstalling Kali's metasploit-framework and reinstalling with Rapid7s installer, re-initializing the db, etc., etc...I ended up with the same error message.  The whole point of the re-installation was to try and get Armitage working again from issue(s) #224 #228 #229
Honestly, it doesn't look like anyone will be working on fixing Armitage at this point...and if you can live without the noisy/lazy "hail mary" feature, you're better off with just metasploit console.  I think hail mary was pretty much the only reason I even dealt with this tool.

After uninstalling Kali's metasploit-framework and reinstalling with Rapid7s installer, re-initializing the db, etc., etc...I ended up with the same error message.  The whole point of the re-installation was to try and get Armitage working again from issue(s) #224 #228 #229
Honestly, it doesn't look like anyone will be working on fixing Armitage at this point...and if you can live without the noisy/lazy "hail mary" feature, you're better off with just metasploit console.  I think hail mary was pretty much the only reason I even dealt with this tool.

For me, changing the port to 55553 worked. The default was 5432 for some reason.


[Nest] Sort by script using ISearchRequest

Hi,
Is it possible to sort by script using ISearchRequest from Nest namespace?
I want to achive following request but I cannot see such option in Sort property:
"sort": [
{
"_script" : {
"script" : "doc['priceMatrix.prices.X'].value > 0 ? doc['priceMatrix.prices.X'].value : doc['priceAmount'].value",
"type" : "number",
"params" : {
"factor" : 1.1
},
"order" : "asc"
}
}
],
I've noticed that in DSL query there is SortScript descriptor but I cannot use DSL due to restrictions for aggregations (I cannot create a list of aggregations and pass it to AggregationDescriptor).
I would be very greatfull for an answer.
Paweł

Hey @prychel
Here's how this can be achieved using the object initializer syntax:
var request = new SearchRequest
{
	Sort = new List<KeyValuePair<PropertyPathMarker, ISort>>
	{
		new KeyValuePair<PropertyPathMarker, ISort>("_script", new ScriptSort
			{
				Script = "doc['priceMatrix.prices.X'].value > 0 ? doc['priceMatrix.prices.X'].value : doc['priceAmount'].value",
				Type = "number",
				Params = new Dictionary<string, object>
				{
					{ "factor", 1.1 }
				},
				Order = SortOrder.Ascending
			})
	}
};

Note, we're aware of how verbose this syntax is and it has already been improved in the 2.0:  Sort is just a List<ISort> rather than List<KeyValuePair<PropertyPathMarker, ISort>>.
Also, to access ScriptSort you need to include the Nest.DSL.Descriptors namespace.  This is a bug, but unfortunately can only be fixed in the 2.0 branch since it would introduce a breaking change.


FEAT: Structure users controller

General Info

Pivotal Tracker Story
[ ] Breaking?

Changes
Explain your changes here (in such a way that you would understand why you made them a year from now).
Structured the users controller with bugs i had fixed such as not having plural form
Testing
Explain how you tested your changes.  If testing is not necessary, explain why.
Documentation
Does this PR require documentation.  If so, explain where it can be found.
Checklist

[ ] Name of branch corresponds to story

Good job!


extra_globals.uci may cause macro name clashes

Context: https://github.com/X2CommunityCore/X2CommunityPromotionScreen/blob/fb75c474a57d8267491f96c30b7fe76dbebded04/X2WOTCCommunityPromotionScreen/Src/ModConfigMenuAPI/MCM_API_CfgHelpers.uci#L19-L20
Two mods using customized include files with the same macro names will be incompatible and cause compiler errors.
This needs to be documented. X2ModBuildCommon should also perform a check for macro redefinitions in Globals.uci and error out early, allowing an opt-out with something like // X2MBC-Redefine to ignore in case a redefinition is intended.

Ideally we should find a way where both a dependent mod and a dependency can use MCM, as well as allowing the dependent mod to read the dependency's MCM values. This will probably require some sort of namespacing of the macros.


Add driftdetector for CloudRun

What this PR does / why we need it:
Implement driftdetector for CloudRun.
Even if this PR is merged, it'll not affect the release because the call is not executed.
Which issue(s) this PR fixes:
Fixes #
Does this PR introduce a user-facing change?:

NONE

Looks beautiful. Great job!
/lgtm

here you go 🙌
/approve


Add 'collection' MDC to more consumer logs

As-is, much of the producer logging is unhelpful without being able to discern which collections are receiving traffic.

Nice, I was probably just going to hack that in there per site, MDC is a good call I think. The only thing I haven’t checked (I’m looking at my phone on the way to the grocery store) is if request.getCollection is sufficient for all cases or if you should check the params as well. I have a memory suspicion that it could either be passed as an arg and live as a field, or be shoved in the params, and that getCollection only return the former. Wouldn’t swear on it though. Outside making sure that’s not a problem, lgtm.

is [...] request.getCollection [...] sufficient for all cases or if you should check the params as well.

It looks like request.getCollection only looks at the params actually. The impl is just:
  public String getCollection() {
    return getParams() == null ? null : getParams().get("collection");
  }

...which does seem a little suspect to me generally.  But in our case here I think it should actually be right.  I'm not seeing the collection referenced anywhere, going all the way back to KafkaCrossDcConsumer.pollAndProcessRequests where we create these UpdateRequests.  So if it's coming through at all (which it definitely is) it must be in the params.

Ah, found the line on the producer side where we're creating these requests.  A non-null 'collection' param is set on each one: so our consumer-side MDC logic should be good to go 👍
https://github.com/apache/solr-sandbox/blob/main/crossdc-producer/src/main/java/org/apache/solr/update/processor/MirroringUpdateRequestProcessorFactory.java#L229


Validate refs on scene save

Call ValidateAllRefs() whenever a scene is saved. This behaviour can be enabled/disabled via the "Validate Refs on Save" menu item.
It can be quite useful instead of deriving from ValidatedMonoBehaviour or calling "Validate All Refs" manually every time.

Great idea 👍

Oops, sorry, I forgot to include the meta file so this script doesn't load. I'll add it in a moment.


winrar asking for a password

whats the password

Dude, whe you ran the builder first time, it asked you two questions.

Whether you want to keep the update checker on or not.
The password for the archive (if you left it empty, the password is 'blank').

is there a way to check what it is?

nvm thank you i got it have a good day

nvm thank you i got it have a good day

In future, in case you forgot. The password is inside the config.ini file in the same folder as the builder.


Enable Container run with readonly root filesystem

Therefore moved home directory into data volume and fix right of Erlang Cookie in case of reclaiming a volume on kubernetes.
fixes: #243

I have the same issue that @alwinmark wants to resolve here: The root filesystem on my pod in Kubernetes is read-only, and only the persistent volume mounted into the pod under vernemq/data is read-write.
The solution proposed in this pull request by @alwinmark solved the issue for me.
Is there anything where I could do to help to get this pull request merged?

@hsudbrock hm, I see the issue. I just wasn't sure about any possible further consequences in making the defined data mount the home directory.
Does this actually mean that most users run this with a write-enabled Kubernetes root file system; or is your situation the default?
(I ask because the issue hasn't come up much)

I just wasn't sure about any possible further consequences in making the defined data mount the home directory.

I also did not look more deeply into any further consequences.  What I tried was running verneMQ with the change suggested by @alwinmark, and I did not see any problems yet (but I only published and consumed a few simple messages in my test, nothing fancy). We could also think about alternatives, where we use a second mount for the home directory (so we don't mix it with the data mount); maybe one could even use a mount that does not require a PVC (e.g., mounting a pre-filled erlang cookie file from a configMap, or using an emptyDir mount). With the emptyDir I am not sure if this makes problems, because with that approach the erlang cookie would not survive restarts of the verneMQ pods, and I cannot say with my current Erlang knowledge if we need the erlang cookie to survive pod restarts.

Does this actually mean that most users run this with a write-enabled Kubernetes root file system; or is your situation the default?

To be honest, I don't know what the more common situation is. In my case, the cluster has strict security policies in place, including a read-only root file system. From "googling", this seems to be a security best practice, to lower the attack surface of the cluster (see, e.g., https://docs.bridgecrew.io/docs/bc_k8s_21 as an example for such a policy with a short description). I would guess that such security policies are more common in enterprise settings.

@hsudbrock Thanks for the elaborations. I'm researching alternatives and see what other Erlang projects do. I think if the cookie is the only reason, we can do it from a ConfigMap.
https://blog.differentpla.net/blog/2022/01/09/erlang-cookies-and-kubernetes/

Short update:

I attempted to go the way with the ConfigMap; this was not successful, because I did not manage to mount the erlang cookie while giving it access rights for the owner only (which is required by erlang). When mounting from a ConfigMap, the file always had access rights for more than the owner.
For my purposes, I could now work around requiring a root-only root filesystem (so I do not need a solution for my own purposes anymore) - but am of course still open to helping finding a solution for this pull request here.

@hsudbrock Thanks for your valuable testing & update! I also think, we'll need to merge the general solution using a mount.

Hi everyone, I'm encountering a permission denied error when using a ConfigMap to replace the internal vernemq.conf. Could you please advise on how to resolve this issue?
Permissions ok: Our pod vernemq-2 belongs to StatefulSet vernemq with 3 replicas
Will join an existing Kubernetes cluster with discovery node at vernemq-0.vernemq-headless.vernemq.svc.cluster.local
Did I previously leave the cluster? If so, purging old state.
Cluster doesn't know about me, this means I've left previously. Purging old state...
sed: can't move '/vernemq/etc/vernemq.confAlMekk' to '/vernemq/etc/vernemq.conf': Resource busy
/vernemq/bin/vernemq.sh: line 236: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 238: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 257: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 261: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 266: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 270: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 274: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 278: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 283: /vernemq/etc/vernemq.conf: Permission denied
/vernemq/bin/vernemq.sh: line 401: join_cluster: command not found
config is OK
-config /vernemq/data/generated.configs/app.2<IP_ADDRESS>.07.54.config -args_file /vernemq/bin/../etc/vm.args -vm_args /vernemq/bin/../etc/vm.args
Exec:  /vernemq/bin/../erts-<IP_ADDRESS>/bin/erlexec -boot /vernemq/bin/../releases/2.0.0/vernemq               -config /vernemq/data/generated.configs/app.2<IP_ADDRESS>.07.54.config -args_file /vernemq/bin/../etc/vm.args -vm_args /vernemq/bin/../etc/vm.args                             -pa /vernemq/bin/../lib/erlio-patches -- console -noshell -noinput
Root: /vernemq/bin/..

inside pod:
vernemq-2:~$ ls /etc/vernemq
vernemq.conf  vm.args       vm.args.bak   vmq.acl
vernemq-2:~$ ls -l /etc/vernemq
lrwxrwxrwx    1 root     root            12 May 24 10:03 /etc/vernemq -> /vernemq/etc
vernemq-2:~$ ls -l /etc/vernemq/
total 16
-rw-r--r--    1 root     vernemq        400 May 31 02:58 vernemq.conf
-rw-r--r--    1 vernemq  vernemq        358 May 31 03:01 vm.args
-rw-r--r--    1 vernemq  vernemq        220 May 31 03:01 vm.args.bak
-rw-r--r--    1 vernemq  vernemq          8 May 24 10:00 vmq.acl

much needed fix.


straight doesn't seem to handle emacs-sqlite-builtin properly

What's wrong
See this comment: https://github.com/org-roam/org-roam/issues/2146#issuecomment-1649488358

Please fill out the bug report with the information requested in the template:
## What's wrong

## Directions to reproduce

<!--
Please give instructions for how to reproduce the behavior _starting from an empty `~/.emacs.d`_. Unfortunately, I simply don't have enough time to check out your bug report unless it has clear instructions for this.

straight.el provides a macro, `straight-bug-report`, which can be used to easily create a minimal reproduction case in a clean Emacs environment. Please use this if possible. For instructions, see <https://github.com/radian-software/straight.el#debugging> and the `straight-bug-report` docstring.

If `straight-bug-report` is not available or fails you can still create a reproduction case manually. To do this, start with an empty `~/.emacs.d/init.el`, add the bootstrap snippet, and then add any additional code from your init-file that's needed to set up the buggy behavior. Then include a list of steps to follow (commands to run, files to modify, whatever) after Emacs startup.

Make sure you're using the latest version of straight.el. You can do this by including (setq straight-repository-branch "develop") in your init-file before the bootstrap snippet.

Also, unless you are already quite certain that your problem is specific to straight.el, please verify that it cannot be reproduced using package.el. If you can reproduce your problem with package.el, then it's not a bug in straight.el and I can't do anything about it!

If you try these steps and can't reproduce the problem, it must be something particular to your environment or configuration. In this case, you'll have to bisect in order to figure out what is causing the problem. I won't be able to debug a problem that only happens on your computer!
-->

### Version information

* Emacs version:
* Operating system:

Linking to a comment isn't great because it may be edited or deleted.
Providing the information above will ensure we can help you.
Thanks.

Unable to reproduce with the following test case:

Test Case
(straight-bug-report
  :post-bootstrap
  (straight-use-package 'emacsql)
  (print (straight--process-output "ls" "-lah" (straight--build-dir "emacsql"))))

Test run at: 2023-08-07 22:27:28
system-type: gnu/linux
straight-version: prerelease (HEAD -> test/compile, fork/test/compile) f1bd659 2023-08-07
emacs-version: GNU Emacs 30.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.38, cairo version 1.17.8) of 2023-07-25

Output
Bootstrapping straight.el...
Bootstrapping straight.el...done
Looking for gnu-elpa-mirror recipe → Cloning melpa...
Looking for gnu-elpa-mirror recipe → Cloning melpa...done
Looking for nongnu-elpa recipe → Cloning gnu-elpa-mirror...
Looking for nongnu-elpa recipe → Cloning gnu-elpa-mirror...done
Looking for emacsmirror-mirror recipe → Cloning nongnu-elpa...
Looking for emacsmirror-mirror recipe → Cloning nongnu-elpa...done
Looking for emacsmirror-mirror recipe → Cloning el-get...
Looking for emacsmirror-mirror recipe → Cloning el-get...done
Looking for straight recipe → Cloning emacsmirror-mirror...
Looking for straight recipe → Cloning emacsmirror-mirror...done
Building straight...
Building straight...done

Test run with version: prerelease (HEAD -> develop, origin/develop) 095aee3 2023-08-07
Cloning emacsql...
Cloning emacsql...done
Building emacsql...
Building emacsql...done

"total 108K
drwxr-xr-x 3 n n  440 Aug  7 22:27 .
drwxr-xr-x 4 n n   80 Aug  7 22:27 ..
-rw-r--r-- 1 n n 1.8K Aug  7 22:27 emacsql-autoloads.el
lrwxrwxrwx 1 n n   71 Aug  7 22:27 emacsql-compiler.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql-compiler.el
-rw-r--r-- 1 n n  23K Aug  7 22:27 emacsql-compiler.elc
lrwxrwxrwx 1 n n   62 Aug  7 22:27 emacsql.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql.el
-rw-r--r-- 1 n n  17K Aug  7 22:27 emacsql.elc
lrwxrwxrwx 1 n n   68 Aug  7 22:27 emacsql-mysql.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql-mysql.el
-rw-r--r-- 1 n n 6.9K Aug  7 22:27 emacsql-mysql.elc
lrwxrwxrwx 1 n n   65 Aug  7 22:27 emacsql-pg.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql-pg.el
-rw-r--r-- 1 n n 4.5K Aug  7 22:27 emacsql-pg.elc
lrwxrwxrwx 1 n n   67 Aug  7 22:27 emacsql-psql.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql-psql.el
-rw-r--r-- 1 n n 6.3K Aug  7 22:27 emacsql-psql.elc
lrwxrwxrwx 1 n n   77 Aug  7 22:27 emacsql-sqlite-builtin.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql-sqlite-builtin.el
-rw-r--r-- 1 n n 4.1K Aug  7 22:27 emacsql-sqlite-builtin.elc
lrwxrwxrwx 1 n n   76 Aug  7 22:27 emacsql-sqlite-common.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql-sqlite-common.el
-rw-r--r-- 1 n n 9.8K Aug  7 22:27 emacsql-sqlite-common.elc
lrwxrwxrwx 1 n n   69 Aug  7 22:27 emacsql-sqlite.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql-sqlite.el
-rw-r--r-- 1 n n 7.4K Aug  7 22:27 emacsql-sqlite.elc
lrwxrwxrwx 1 n n   76 Aug  7 22:27 emacsql-sqlite-module.el -> /tmp/straight.el-test-UfspM9/straight/repos/emacsql/emacsql-sqlite-module.el
-rw-r--r-- 1 n n 4.1K Aug  7 22:27 emacsql-sqlite-module.elc
drwxr-xr-x 2 n n  120 Aug  7 22:27 sqlite"

Packages:
"straight"                n/a                  develop 095aee3 2023-08-07
"org-elpa"                n/a                  n/a
"melpa"                   n/a                  master fc5b27dd 2023-08-07
"gnu-elpa-mirror"         n/a                  master be1351c 2023-07-14
"nongnu-elpa"             n/a                  main 65b952d 2023-08-04
"el-get"                  melpa                master f3f1edd4 2023-07-25
"emacsmirror-mirror"      n/a                  master 8e7cbfe 2023-08-07
"emacsql"                 melpa                main 6401226 2023-04-17

The issue is with emacsql-sqlite-builtin. I think it may have had to do with recent changes to the recipe, but now things seem to be working fine for me after I pulled all the recipe sources. The user's claim in the linked comment is wrong though, since those files are part of the core emacssql package.


Invalid background color in terminal

Hi,
Thanks a lot for great themes!
I saw issue #2 that doom thems aren't terminal friendly, but I noted that even embedded themes doesn't work in terminal.
I tried to load adwaita them in shell and got different results with/without doom-emacs configuration.
Thanks you in advance!

seems like issue caused by the fact, that I switched them using customize-them.
If them was saved to config file - everything works fine.

Yes, let's close it! Thanks!


chore: bulk update dependencies versions

This closes #85
This closes #84
This closes #83
This closes #82
This closes #81
This closes #80
This closes #79
This closes #78
This closes #77
This closes #76
This closes #75
This closes #74

Pull Request Test Coverage Report for Build 362

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 99.515%

Totals

Change from base Build 331:
0.0%

Covered Lines:
138

Relevant Lines:
138

💛  - Coveralls

@PoomSmart Mind taking a look and approving? 🙏

:tada: This PR is included in version 1.0.3 :tada:
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Injecting ApplicationDbContext is bad practice

Description
Injecting DbContext into blazor server pages is bad practice as it remains for the life of the user session, becomes stale, and generally leaks memory.
The source code shows
@inject ApplicationDbContext AppDbContext

<QuickGrid<EMAIL_ADDRESS>    ...
</QuickGrid>

Page URL
https://learn.microsoft.com/en-us/aspnet/core/blazor/components/quickgrid?view=aspnetcore-8.0&tabs=visual-studio
Content source URL
https://github.com/dotnet/AspNetCore.Docs/blob/main/aspnetcore/blazor/components/quickgrid.md
Document ID
564e71e3-82ed-ce23-4f9f-a00a58734a62
Article author
@guardrex

Hello @mrpmorris ... This is a known issue and being tracked by another work item.

... and btw ... It will be fixed by EOD.


Fix not showing calculation errors in salary calculator

Description :sparkles:
Fix not showing calculation errors in salary calculator
Issues :bug:
Testing :alembic:
Screenshots :camera_flash:

Additional notes :spiral_notepad:

Codecov Report

Merging #755 (03b5c93) into develop (114adca) will decrease coverage by 27.64%.
The diff coverage is 0.00%.

@@             Coverage Diff              @@
##           develop     #755       +/-   ##
============================================
- Coverage    62.86%   35.22%   -27.65%
============================================
  Files          780       68      -712
  Lines        19716     1360    -18356
  Branches      1923      274     -1649
============================================
- Hits         12395      479    -11916
+ Misses        6952      853     -6099
+ Partials       369       28      -341

Impacted Files
Coverage Δ

...efitCalculatorView/SalaryBenefitCalculatorView.tsx
0.00% <0.00%> (ø)

...cation/form/error-summary/ErrorNotificationRow.tsx

frontend/shared/src/components/header/Header.tsx

.../migrations/0024_phone_number_length_validation.py

...components/suomiFiTestIdentification.components.ts

.../migrations/0005_employee_is_living_in_helsinki.py

...end/benefit/applicant/src/hooks/useCompanyQuery.ts

...src/components/jobPostings/JobPostingsSectio.sc.ts

backend/benefit/messages/tests/factories.py

backend/benefit/helsinkibenefit/tests/conftest.py

... and 703 more

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_get_new_index always returns index in PeriodIndexResampler

[ ] closes #xxxx
[ ] tests added / passed
[ ] passes git diff upstream/master | flake8 --diff
[ ] whatsnew entry

Cleans up a method that returned different types depending on the length of the index

was this meant to be a PR?

Yes! Split this out of the other given it wasn't directly impacting the issue.
Does the point make sense?

can you add some tests for validation, or you can just roll this into the other issue

OK I will roll in. Sometimes I know you prefer things split out where it doesn't directly impact; am v happy to roll it in though

Rolling into #12874


SQL Server managed identity authentication instead of secrets

Description
Made changes to support Managed Identity Authentication for SQL Server DB instead of using Secrets.
Related issues
Addresses [issue 122770].
Testing
Tested by creating FHIR service instance using the updated ARM template.
Validated different settings after deployments.
Executed CRUD operations on FHIR service instance.
Executed Export operation on FHIR service instance.
FHIR Team Checklist

Update the title of the PR to be succinct and less than 65 characters
Add a milestone to the PR for the sprint that it is merged (i.e. add S47)
Tag the PR with the type of update: Bug, Build, Dependencies, Enhancement, New-Feature or Documentation
Tag the PR with Open source, Azure API for FHIR (CosmosDB or common code) or Azure Healthcare APIs (SQL or common code) to specify where this change is intended to be released.
Tag the PR with Schema Version backward compatible or Schema Version backward incompatible or Schema Version unchanged if this adds or updates Sql script which is/is not backward compatible with the code.
[ ] CI is green before merge
Review squash-merge requirements

Semver Change (docs)
Patch|Skip|Feature|Breaking (reason)

Hi @v-ajajvanu, we have a PR below that I think already does this using a user assigned managed identity. Can you see if this is similar?
https://github.com/microsoft/fhir-server/pull/3946

/azp run

@mikaelweave Indeed, the changes in this PR and the ones in PR https://github.com/microsoft/fhir-server/pull/3946 are comparable. The only thing that was different was that we were utilizing a system-assigned identity, designating it as the primary user for SQL Server, and modifying the connection string in Key Vault to switch the authentication property to "Active Directory Managed Identity" and delete the user ID and password.
This PR is no longer required because the modifications indicated in PR 3946 have already been merged into the main branch.
Kindly refrain from merging this PR's changes.


Error trying to render a cookie cutter

The Error displayed is the following:
Syntax error
Line: 10,col: 8
(blob:1E053920-8CA1-4E3A-910C-C6F37A44857D)

The object is this:
//!OpenSCAD
edgeThickness = 0.4;
cutter_sizes = 4;
wallHeight = 17;
wallFlareWidth = 14;
wallFlareThickness = 2;
minWallWidth = .8;
maxWallWidth = .8;
insideWallFlareWidth = 1;
insideWallFlareThickness = 1.5;
minInsideWallWidth = 1;
maxInsideWallWidth = 3;
featureHeight = 14;
minFeatureThickness = 0.8;
maxFeatureThickness = 0.8;
connectorThickness = 2;
size = 25.4*cutter_sizes;

module dummy() {}

scale = size/25.108;

module ribbon(points, thickness=1, closed=false) {
    p = closed ? concat(points, [points[0]]) : points;

    union() {
        for (i=[1:len(p)-1]) {
            hull() {
                translate(p[i-1]) circle(d=thickness, $fn=8);
                translate(p[i]) circle(d=thickness, $fn=8);
            }
        }
    }
}

module cookieCutter() {

path0=scale*[[-2.604,305.284],[-2.961,290.904],[-3.050,283.568],[-3.006,280.906],[-2.961,280.545],[2.805,288.678],[1.814,291.470],[-0.099,297.214],[-0.906,299.960],[-1.349,301.962],[-1.373,302.531],[-1.231,302.729],[-0.898,302.494],[0.269,300.934],[0.810,300.408],[1.276,300.152],[1.672,300.132],[2.005,300.313],[2.280,300.661],[2.678,301.717],[2.911,303.022],[3.057,305.653],[-2.604,305.284]];
render(convexity=10) linear_extrude(height=(wallHeight)) ribbon(path0,thickness=min(maxWallWidth,max(0.001,minWallWidth)));
render(convexity=10) linear_extrude(height=(wallHeight+1)) ribbon(path0,thickness=edgeThickness);
difference() {
 render(convexity=10) linear_extrude(height=wallFlareThickness) ribbon(path0,thickness=wallFlareWidth);
 translate([0,0,-0.01]) linear_extrude(height=wallFlareThickness+0.02) polygon(points=path0);
}
}

translate([0,-280.545*scale,0]) cookieCutter();

It works fine in the desktop version of OpenSCAD: http://imgur.com/a/vEu8S

Hi @Moosieus  I think it is due to the list comprehension : path0=scale*[[-2.604,305.284],[-2.961 ....
So it would be the same as issue #162 : sadly list comprehensions are not supported by OpenJscad (yet)

This issue was moved to jscad/openscad-openjscad-translator#16


Implement an interface with the fortran-language-server

We should implement the interface that FORTRAN Intellisense has into Modern Fortran. The Intellisense extension is not supported anymore, similar to the language server itself and taking control of the interface to the fortls would allow us to interface with it better.

@gnikit - you were helping me with an issue I was having with getting Modern Fortran/Intellisense/Fortran Language Server to work with VS Code in the fortls repository on Friday (https://github.com/hansec/fortran-language-server/issues/212), and I've found my way over here looking for a way to test out the dev version of this extension.
Is there any way to obtain a vsix file for the dev branch? I'm trying to work out whether having all of my fixed format files labeled as "Fortran90" is preventing variable definitions from my include files from showing on hover. We've got a mixture of fixed and free form code in our repository and I'm not yet sure whether this will be an issue with the language server.

Here is the .vsix of the dev build, just change the extension name from .zip to .vsix (github does not allow arbitrary extensions to be uploaded) linter-gfortran-3.0.0.zip
In general, to build this you can check out this branch locally and run npm ci && vsce package. Assuming you have node.js, npm and vsce.
This branch should solve your hover issues. Let me know if you notice anything weird or something does not work.
FYI there is still a fair bit of work be done mainly on the fortran-language-server side of things. As it currently stands we have no way to pass certain options to fortls because fortls has no interface.

Thank you for that - I was able to get it installed and working (we don't have access to node.js, so I couldn't create the package myself). This definitely fixed my issue with being able to use the Fortran language mode with my fixed form files, however for some reason the hover is still not working on variables defined in an include file, whether I'm in a free form or fixed form file.
For example, a basic code snippet within one of my fixed form subroutines looks like this (except with proper fixed form format):
include 'start.prm'

INTEGER COUNT

DO 200 COUNT = 1, MAXCOUNT
      ... stuff
200 CONTINUE

The variable MAXCOUNT is defined in the include file start.prm as follows:
integer, parameter :: MAXCOUNT = 4

I am able to hover over COUNT and see its declaration and show all the places where it's referenced, but nothing comes up when I hover over MAXCOUNT. I'm wondering if I'm setting something up incorrectly.

Try associating the file extension '.prm' with the language, i.e.
 "files.associations": {
   "*.prm": "FortranFixedForm"
 },


Improves FluxBoundarConditions class documenation.

I've two fairly involved PR in the works, so I'm breaking off the parts of those PRs that are self-contained and creating branches directly off master.  This is the first of several to come.


make hyperlinks point to plclub repo version

at the moment of opening this PR I only went through quickstart.rst to update hyperlinks to point to plclub/ github account's version of repo (off from antalsz). I can try updating more files before we merge this in, feel free to leave it open for a while to increase the probability that I do that. Also anyone else can feel free to push to this branch if they see hyperlinks in other files.

@quinn-dougherty Thanks for all these changes. I'll merge this when you feel it's in a state to be merged.

module index is hyperlinked at the bottom of the docs and goes nowhere. Where should it point? or should the hyperlink just be deleted?

I'm not sure about this one, either. Maybe we should just remove this.

@quinn-dougherty Since there are not many updates in the past few days, perhaps I should merge this PR?

roger that, please do! Haven't seen anything else in the docs lately.

Thank you!


stash documentation issue.

The documentation of stash on git-scm.com says "Calling git stash without any arguments is equivalent to git stash push" which is not true and not same as what git documentation says when I use terminal help:

git help stash

Hey @nkrishnawat
thanks for reporting your issue, but it seems weird. The documentation on the git-scm website, it's extracted from the git man pages, so the information on https://git-scm.com/docs/git-stash should be the same that shows when you write $ git stash --help.
On my machine, both have the same content. Which git version are you using?
$ git --version
git version 2.17.0

The manpages found on the site are built directly from the text in the main git repository, which is also what you see from git help stash. Presumably you have an older version of git locally; git stash save was deprecated in favor of git stash push in v2.16.
You can view the documentation for older versions of git by clicking the Version X.Y.Z link at the top of each manpage on git-scm.com. That will show you all the places where this particular page changed, and you can click through to a specific version (e.g., https://git-scm.com/docs/git-stash/2.14.0).


float-right class on img not working with Outlook (2007, 2010, 2013, 2016)

The image float-right class does not seem to work on several Outlook clients.
How can we reproduce this bug?
I'm using a fresh installed foundation project (installed as described in docs)
I'm adding the inky code to add aligned images (as provided in the docs).
<row>
    <columns>

    </columns>
</row>

What did you expect to happen?
I would have expected that the last images would appear right aligned.
What happened instead?
The most clients show the expected result. this is not the case for outlook
What email clients does this happen in?
Outlook 2007, 2010, 2013, 2013 120 DPI, 2016, Windows 10 Mail

Have the same problem, ANYBODY HERE?

Without seeing all your code, I'm not totally sure.
But I had this issue and it was down to the parent td not expanding full width thus not allowing the image to fully align right.

What happened instead of aligning right? Can we have a screenshot?

In my case they just aligned left, I've just post an issue which included the same here:
https://github.com/zurb/foundation-emails/issues/703

Floats only work in Outlook Office 365. You must align the table / tr / td to the right.

@DerekBess how is that going to be possible with Inky?

@Ispoor I had a similar issue with right-aligning button, and was able to use the following:
// enable the button alignment class 'align-right'
table.button.align-right {
  display: inline-block;
  float: right;
}

So you might be able to adapt this for he code you have?

@davehoran floats are not supported in Outlook 2007+ though?
See: https://www.campaignmonitor.com/css/

So what I've done is add a class of 'align-right' to the column the image is in and also added a style of 'display:inline-block' to the image'
<columns small="12" large="6" class="align-right">
Then used the following CSS code:
`
.align-right {
text-align:right;
table,
tr,
th {
	text-align:right;
}

}
`

Nice solution


Randomness in reference scripts with --test-only

While running some experiments related to https://github.com/pytorch/vision/issues/4559, I tried the following:
diff --git a/references/classification/train.py b/references/classification/train.py
index a71d337a..1a429801 100644
--- a/references/classification/train.py
+++ b/references/classification/train.py
@@ -147,7 +147,7 @@ def load_data(traindir, valdir, args):
     print("Creating data loaders")
     if args.distributed:
         train_sampler = torch.utils.data.distributed.DistributedSampler(dataset)
-        test_sampler = torch.utils.data.distributed.DistributedSampler(dataset_test)
+        test_sampler = torch.utils.data.distributed.DistributedSampler(dataset_test, shuffle=False)
     else:
         train_sampler = torch.utils.data.RandomSampler(dataset)
         test_sampler = torch.utils.data.SequentialSampler(dataset_test)

torchrun --nproc_per_node=1 references/classification/train.py --model resnet18 --test-only --pretrained

I was hoping to get reproducible results across executions, i.e. always the same accuracy, but it seems like I still get a bit of variations across a few runs:
Test:  Acc@1 69.766 Acc@5 89.068
Test:  Acc@1 69.764 Acc@5 89.072
Test:  Acc@1 69.764 Acc@5 89.072
Test:  Acc@1 69.766 Acc@5 89.068

Does anyone know where this randomness might come from?

BTW looks like the actual accuracy of resnet18 is a fair bit higher than what we report on the docs: 69.494 | 88.882


docs: fix README and create documentation entry for dvclive

Part of iterative/dvc.org/issues/2026

Any chance you could make a quick draft for the needed API refs in https://dvc.org/doc/api-reference and maybe expand the README in this repo if needed to cover all the features @pared ? No need for details at first, just trying to cover everything even if it's just a brief mention of what you can do/how. Thanks

Related to https://github.com/iterative/dvc.org/pull/2227

What is the state of this issue after https://github.com/iterative/dvclive/pull/71 ? Is this blocked by https://github.com/iterative/dvc.org/issues/2443 ?

I think that #71 covers pretty much all relevant changes required for this to be closed, but we could leave this open and polish it according to iterative/dvc.org#2443. So far README is lacking:

installation methods
links to related technologies
link to Contributing (though call for collaboration is probably enough for now)
licen[c/s]e & citation


Take advantage of d lang scoped imports

Currently we have far too many imports at file and global level (more so in the unit test code). In d it is possible to use scoped imports which can bring many benefits including self dependency management of a block of code. I think it can also help reduce executable size and help with compilation speed.

This is a bit too wide ranging, and it's an "issue" that will crop back as development proceed. We regularly clean up the code, so marking this as WONTFIX.


Ability to sort versions and selection for the main download-button

Is your feature request related to a problem?
The problem is, that you currently can't reorder versions and the main download-button always refers to the latest version, that was uploaded.
I encountered this issue, when I uploaded some older versions of my plugin (for completeness's sake), as I uploaded the oldest version last. While the version number indicated the latest version, it's quite unintuitive, that it's at the very bottom. Additionally, when clicking the download button on the very top of the project's page, it downloads the version, that was uploaded most recently.
This is an issue, for creators, that upload pre-existing projects, due to migrating to Hangar (or just making it available there), as they may upload versions in bulk and in any order.
Describe the solution you'd like.
In my mind, the optimal solution and most intuitive solution for this would be to let people drag and drop the versions along the list.
For the download-button on the top-right of the project-page, there should be a settings option, to select a version.
A possible implementation of which could let one choose a release-channel and version. To not loose the default (and current) behavior, the options could be optional. If no channel is selected, the latest version (at the top of the list) is chosen, and if a channel, but no specific version is chose, the latest version of the specified channel is chosen.
Describe alternatives you've considered.
There are probably many other ways, to improve this. For example, there could be a system, similar to Modrinth, with featured versions. (Also, their system of filtering for a specific version is a good idea.)
Other
No response

I don't know any site that lets you create versions/releases in a non-chronological order, it doesn't seem like something that provides too much benefit vs. just uploading it the right order initially given it adds complexity both on the backend and visually


test-branch/execute-job/quoted-authorization/b4dc6890-0c78-4971-8624-e03aa734aa80

PR for testing 319d72795ee4955d2237b7de0d3e8ff9228c3eea

/canonical/self-hosted-runners/run-workflows 319d72795ee4955d2237b7de0d3e8ff9228c3eea


Fade out background when closing

A small suggestion, when closing overlays, the background pops from black to transparent which looks a bit jarring. Just like how the background fades in when opening, it would be nice if it fades out when closing overlays.
Currently, a hackish way to accomplish this is by adding a small CSS snippet:
.c-offcanvas-bg.is-animating.overlay.is-open {
    background: rgba(0, 0, 0, 0.68);
}

.c-offcanvas-bg.is-animating.overlay {
    background: none;
}

I think the best way would be however to replace is-animating with two classes called is-opening and is-closing

@TheTimeWalker thanks for the feedback


NTR: clathrin pit assembly (and other related clathrin coating edits)

I'm annotating PMID:26589353, where Syt11 inhibits clathrin-mediated endocytosis by limiting membrane invagination and pit formation (Fig 8).
I'd like to add a couple of new terms, and I think some revisions are needed to existing terms:

I don’t think ‘clathrin coat assembly (GO:0048268)’ should be under ‘vesicle coating (GO:0006901). In the CC section, we have ‘clathrin coat of coated pit ; GO:0030132’ and ‘clathrin vesicle coat’. Since both pits and vesicles can be coated with clathrin, the vesicle parent is too specific. GO:0048268.
Based on its existing definition, rename ‘coated pit ; GO:0005905’ to ‘clathrin-coated pit’.
broad synonym: coated pit
Create new term in TG:
clathrin-coated pit assembly ; GO:NEW
exact synonym: coated pit assembly
exact synonym: coated pit formation
HAS_PART: membrane invagination ; GO:0010324
HAS_PART: clathrin coat assembly ; GO:0048268
Add relationship:
clathrin-mediated endocytosis ; GO:0072583
—[part_of]clathrin-coated pit assembly ; GO:NEW
Create regulation terms in TG for the annotation of Synaptotagmin-11, which limits the pit-formation step in clathrin-mediated endocytosis.

Any comments from anyone who knows more about this area than me? ... e.g. what other types of coated pits there are....
Thanks!

@rebeccafoulger , can you make these edits or do you need me to do them for you?  I don't know more about coated pits than what's in this issue but am in charge of GH this week.  Thanks.

I can do the edits @tberardini: was just hoping someone might weigh-in on clathrin coats first!

From a brief survey, it looks like there aren't any other kinds of coated pits but that the history of the term was first 'bristle coated pits', then they figured out that the bristles were made of clathrin.
http://cshperspectives.cshlp.org/content/6/5/a016725.long

Thanks Tanya. Getting back to this, I've started my edits:

Removed ‘clathrin coat assembly (GO:0048268)’ from under ‘vesicle coating (GO:0006901)’
Based on its existing definition, renamed ‘coated pit ; GO:0005905’ to ‘clathrin-coated pit’.

Will create the TG term when my clathrin coat assembly name change filters through.

Next step, a new term in TermGenie: GO:1905224 Label: clathrin-coated pit assembly

I wonder if there should be just one term
clathrin mediated endocytosis clathrin coat assemby
instead of
clathrin coat assembly,
and
clathrin coated pit assembly.
Isn't the pit just the early  membrane invagination  stage of
clathrin mediated endocytosis clathrin coat assembly?
They don't seem to be 2 separate processes?
See
https://github.com/geneontology/go-ontology/issues/12509
and the figures in this recent review
http://www.ncbi.nlm.nih.gov/pubmed/24322426
Also "clathrin coat assembly" will occurs as part of clathrin-mediated  transport  between other compartments. Here you are referring to endocytosis
I don't think you can do:
clathrin-mediated endocytosis ; GO:0072583
—[part_of]clathrin-coated pit assembly ; GO:NEW
without specifying that it is the endocytic one (AP2 adaptor complex containing)
https://en.wikipedia.org/wiki/Clathrin_adaptor_proteins
There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes.[4] AP2 adaptor complex associates with the plasma membrane and is responsible for endocytosis.[5] AP3 is responsible for protein trafficking to lysosomes and other related organelles.[6] AP4 is less well characterised.
This agrees with the reviews and the intro in  the paper I am curating now PMID:26749213.
The membrane invagination part is performed by BAR domain proteins
https://github.com/geneontology/go-ontology/issues/12387
This process occurs in many contexts (different BAR domains proteins)
and this could be the step which is regulated here.....
I put some recommendations
https://github.com/geneontology/go-ontology/issues/12509
before I saw this ticket.

Clathrin coats don't just form on the pits though Val. In the CC node, we have terms for:
clathrin coat of coated pit ; GO:0030132
clathrin vesicle coat ; GO:0030125
Hence why I was planning to add in a HAS_PART relationship.

Yeah sorry I didn't explain.
The pit becomes the vesicle though? So isn't there only one process "clathrin coat assembly"
(it starts on the pit, but  eventually becomes the coat?). Or do clathrin coats form on some pits which never become vesicles?
It sin't really clear to me what clathrin coated pit assembly involves...It sounds like the membrane invagination stage  of vesicle formation (maybe?).

I have been approving a few of our community papers related to membrane trafficking/transport processes. There are quite a few terms where I'm confused based on what these recent  papers say (and I haven't opened all of the tickets yet...)
Maybe I could tag all of these  "vesicle transport" and we  could have a look with @dosumis
when you are in the GO office (maybe with Ruth by Skype as your projects seem to use these terms frequently).

Clathrin coats don't just form on the pits though

The pit becomes the vesicle though? So isn't there only one process "clathrin coat assembly" ...

Clathrin also coats buds that form (and give rise to vesicles) on the trans-Golgi network membrane. The TGN vesicle buds aren't called coated pits. (Brief summary [here] (http://walz.med.harvard.edu/Research/Vesicular_Coat_Proteins/).)

Is the term clathrin-coated pit assembly for the membrane curvature step, or the coat assembly step? The process of coat assembly is the same process on the pit and the vesicle (it doesn't appear to be 2 different processes). Does that make sense?

This is nice, molecular mechanism:

Clathrin also coats buds that form on the trans-Golgi network membrane. The TGN vesicle buds do give rise to vesicles but aren't called coated pits. (Brief summary here.)

Yeah this is for clathrin-mediated endocytosis. This coat  uses AP1 complex. The Golgi ones use different AP complexes. So all terms will need to specify 'endocytosis'.
Becky I see what you are doing now.
I would have said the steps for endocytosis are:
membrane invagination, nucleation
cargo loading,
coat assembly (the coat begins to form on the pit, but continues...where does the pit end and the vesicle begin?...It might be easier not to mention the pit here, or to say it begins as a pit and ends as a vesicle!)
This is also a great example for how annotations are propagated over has_part
What would you annotate to
clathrin-coated pit assembly?
Which terms would you use for a proteins which was involved in the membrane curvature step of endocytosis ....I know everyone is going to say "this would work better in LEGO" but I'm also interested if this was modelled in LEGO what would be exported for display on the gene pages.
I'll flag this as an example, because we can't use LEGO until we are satisfied that we get comprehensive annotations out for the gene pages

I was planning that 'clathrin-coated pit assembly' included both the membrane invagination and the clathrin-coat assembly steps. I considered having 'clathrin-coated pit assembly' is_a: 'membrane invagination'. But the fact that we have the term 'clathrin coat of coated pit ; GO:0030132' suggests that the pit includes the clathrin coat. And therefore I thought assembly of the coat is a step in pit formation/assembly.

Just bumped into the same issue myself.  Parking OE screenshot here for now

.... relationship to endocytosis = ...

Plan of action:
Strategy: split clathrin-mediated endocytosis into parts based on this figure
FIGURE 2 | The clathrin-coated vesicle cycle.
Molecular mechanism and physiological functions of clathrin-mediated endocytosis
Harvey T. McMahon & Emmanuel Boucrot PMID:21779028

Start and end and major steps should be enumerated in the definition.

[ ] nucleation
[ ] cargo selection
[ ] coat assembly

SubClassOf clathrin coat assembly
Question: should this be under vesicle coating - even though it happens prior vesicle formation.  OTOH, it seems reasonable to put it under vesicle coating given that the ultimate output (after scission) is coated vesicle.

[ ] scission
[ ] uncoating

Added outstanding relationships:
GO:1905224 Label: clathrin-coated pit assembly:
HAS_PART: membrane invagination ; GO:0010324
HAS_PART: clathrin coat assembly ; GO:0048268
Rest of ticket will be dealt with in David's transport edits.

I still have a slight problem with  "clathrin-coated pit assembly" as I can't see how it differs from "clathrin coat assembly" at the process level (or the membrane invagination, nucleation stage). The processes seem pretty well worked out here (enough to add beginnings and ends?)
in the steps of this process, membrane invagination and cargo selection precede clathrin coat assembly?
Maybe you can explain to me, are you attending Noctua meeting?
Which genes are you annotating to "clathrin-coated pit assembly"?

I am "lurking" here, after Rebecca @rebeccafoulger leaves UCL

I've also just lurked! And it seems that ticket #12583 is also partly related to this topic, as @ValWood mentioned.

Maybe we could discuss this ticket on Thursday afternoon ?

@ValWood : Maybe we could discuss this ticket on Thursday afternoon ?
Do you mean during the weekly GO ontology eds meeting?  If yes, I will put on the agenda.

I meant during @rebeccafoulger Becky's leaving lunch, but yes either /or ;)

Oh!  Discuss away during leaving lunch if you can stand it and please update this ticket with results.

well...after lunch...

Okay- will dig out my original paper that started this thread off! See you tomorrow Val.

This ticket ended up as a launching point for fixing lots of related stuff.  Don't think it should be too hard to finish.  I'll refamliarise myself with it.

Hi @dosumis - still lurking ;) -  any updates?

Was this one finished?

Hm... 'uncoating of endocytic vesicle' is not ticked in the 28 Jul 2016 Plan of Action by @dosumis (And it does not get displayed in QuickGO, so maybe still ongoing?)

Looks like the outstanding issue here is 'uncoating of endocytic vesicle' (the term still doesn't exist), but we have 'clathrin coat disassembly'; is the sufficient ?
If this is not needed - can we close the ticket @ValWood @BarbaraCzub @dosumis

Hi @pgaudet It's been on my to-do list to add this term, but I see your point about 'clathrin coat disassembly'. In fact 'clathrin-coated vesicle uncoating' is an exact synonym of 'clathrin coat disassembly'.
The only reason why I think it may be worth adding a new term 'uncoating of endocytic vesicle' (as a child of 'vesicle uncoating' and a parent of 'clathrin coat disassembly') is to make it possible to annotate other proteins (maybe caveolin... or others?). But the words 'caveolin/caveola' and 'coat' do not seem to occur together in scientific literature, so perhaps indeed this new term is not needed (unless there are other protein coats which should be considered?). @RLovering @paolaroncaglia do you have any suggestions regarding this?

Hi @BarbaraCzub
First, I modify my previous suggestion: the most appropriate term might be 'GO:0072319 vesicle uncoating'. If you find protein mediating the disassembly of endocytic vesicles I would agree creating the term, but caveolin is part of the coat, as far as I understand, so it would not be appropriate.
Also, we don't have 'endocytic vesicle coating', so are you sure the disassembly exists ?
I would hold off creating the term until we understand the process.
Thanks, Pascale

I'll check in Protein2GO reports whether Rebecca had any Tickets Pending that would explain why she needed this term.
Thanks,
Barbara

@BarbaraCzub
Sorry I'm busy with other tasks and can't look into this straight away, but I made a note to keep an eye on this thread. If it's still needed, I'll address your question(s) on Wed.
Thanks,
Paola

Thank you @paolaroncaglia
I reviewed Rebecca's Tickets Pending in Protein2GO and I did not find anything relating to this issue, so I will close it now.
Thanks,
Barbara


Videos with colons results in file name halts

When downloading a video with a ":" in it, the file name halts it's output when that happens, so for example: Emotional OST of the Day(Day51): Steins;Gate - Solitude will result in "Emotional OST of the Day(Day51) being downloaded, which, in turn has some implication for another thing I'm implementing this into.

Works for me without problem. The file is saved as Emotional Ost of the Day(Day 51): Steins;Gate - Solitude.mp3. youtube-mp3-downloader doesn't replace colons.

http://i.imgur.com/kzVKVBF.png - This is a list of files downloaded files using a bot. Explorer shows them as having 0 bytes of data, ie. being empty, though clicking on properties reveals that they downloaded "properly", they also play properly through the bot I've implemented it in, but cause it to crash afterwards, which is a bug with that API. It only happens with files with a colon in them.

So, you're using Windows? Then I guess colons are not allowed in file names... You can add a replace rule for that in https://github.com/tobilg/youtube-mp3-downloader/blob/master/lib/YoutubeMp3Downloader.js#L65
I can release a new version not earlier than next week.

I just pushed a new version (0.4.2) to NPM, which replaces also colons and semicolons.


Feature:  Add .. and possibility to keep menu after having selected new directory

Potential new improvements.
Add:

Being able to go back/up in directory (as done by ..).
After selecting a direcroy, keep menu alive with new directories.
Hitting Return 2x exits in that current one.

The goal of this module is to provide a simple way to generate "menus" in Powershell - directory navigation is just a simple examples, not part of this module.


vendor: Update virtcontainers and runtime-spec vendoring

Rely on latest virtcontainers version introducing the new vendoring of runtime-spec v1.0.0-rc5. Virtcontainers also includes new structures for compatibility with runtime-spec structures changes between versions 1.0.0-rc4 and 1.0.0-rc5.
This patch also updates the current vendoring of the runtime to the version 1.0.0-rc5.

Coverage remained the same at 34.322% when pulling c9cb65c246ccece7cfc53839d6e0a48b2c9228f3 on sboeuf/vendor_virtcontainers into c86d422f3872e440f7d7d77f917532e625c3b0dd on master.

lgtm

lgtm


uv_udp_set_ttl not supported for TizenRT

TTL support is almost working for TizenRT but flag IPV6_UNICAST_HOPS is missing:
https://github.com/Samsung/libtuv/blob/master/src/unix/udp.c#L811
This issue prevents successful configuration of TTL in IoT.js for two tests.
test_dgram_setttl_client.js:
https://github.com/Samsung/iotjs/blob/master/test/run_pass/test_dgram_setttl_client.js#L36
test_dgram_setttl_server.js
https://github.com/Samsung/iotjs/blob/master/test/run_pass/test_dgram_setttl_server.js#L45

@pmarcinkiew I think uv_udp_set_ttl and uv_udp_get_ttl will work for IPv4 on TizenRT, and we need to support it.


help: Refer to group settings for create/manage group at org level.

Right now, we are referring to the roles instead of groups since we have not enabled that UI for these settings.

Screenshots and screen captures:

Self-review checklist

[ ] Self-reviewed the changes for clarity and maintainability
(variable names, code reuse, readability, etc.).

Communicate decisions, questions, and potential concerns.

[ ] Explains differences from previous plans (e.g., issue description).
[ ] Highlights technical choices and bugs encountered.
[ ] Calls out remaining decisions and concerns.
[ ] Automated tests verify logic where appropriate.

Individual commits are ready for review (see commit discipline).

[ ] Each commit is a coherent idea.
[ ] Commit message(s) explain reasoning and motivation for changes.

Completed manual review and testing of the following:

[ ] Visual appearance of the changes.
[ ] Responsiveness and internationalization.
[ ] Strings and tooltips.
[ ] End-to-end functionality of buttons, interactions and flows.
[ ] Corner cases, error conditions, and easily imagined bugs.

I guess we will want to change these labels to something like "Who can manage all user groups", or similar, but only once we've done the upcoming semantics changes that come with the group-level "who can add users to this group" feature.

Merged, though I think we'll need another update pass in the next week or two as we merge more transition changes.

Yeah, let's fix up the intro text when we're a bit further along.


CFE-897,CFE-907: feat: add code to call v2 from v1

Description
CFE-907 is a sub-task of the story CFE-897 which is part of the epic CFE-896
It adds a call from v1 to v2, in order to be able to redirect the flow to v2 .
The --v2 flag when specified builds a new command specific for v2 with its own flag set.
Flag set for v1:
./bin/oc-mirror --help
Flag set for v2:
./bin/oc-mirror --help --v2
Type of change
Please delete options that are not relevant.

[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update

How Has This Been Tested?
ImageSetConfig:
apiVersion: mirror.openshift.io/v1alpha2
kind: ImageSetConfiguration
mirror:
  operators:
    - catalog: registry.redhat.io/redhat/redhat-operator-index:v4.12
      packages:
        - name: aws-load-balancer-operator

MirrorToDisk:
./bin/oc-mirror -c /home/aguidi/go/src/github.com/aguidirh/oc-mirror/alex-isc/isc.yaml file:///home/aguidi/go/src/github.com/aguidirh/oc-mirror/CFE-907 --v2

DiskToMirror:
./bin/oc-mirror -c /home/aguidi/go/src/github.com/aguidirh/oc-mirror/alex-isc/isc.yaml --from /home/aguidi/go/src/github.com/aguidirh/oc-mirror/CFE-907 docker://localhost:7000 --v2

Checklist:

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] My changes generate no new warnings
[ ] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes
[ ] Any dependent changes have been merged and published in downstream modules

/lgtm

/label acknowledge-critical-fixes-only


Update Discord Link

The discord invite link is expired.

seems fixed now it goes to discord.com/invite/celo


[Ethan] Final Commit

All testing is now complete and the Readme up to date. Enjoy!

Good work, Jay!  Thanks for your help


Artifacts_mobile—Hide description until click

hide the description but give an affordance that the user can open the description

transform: translateY(240px);
transition: 1s;


Error: cannot open 'jsbind'

When running nim js fig8_js_interactive.nim  I get the error

nim-plotly/src/plotly/plotly_js.nim(1, 8) Error: cannot open 'jsbind'

Sorry about that. The jsbind module was missing as a dependency. Until the PR is merged, just install that module.
Also when running the javascript example, you will have to either change the output filename to nimcache/fig_javascript.js or change the index_javascript.html to match the example filename.

Cool. Thanks for the quick response
søn. 23. sep. 2018 12.36 skrev Vindaar<EMAIL_ADDRESS>
Sorry about that. The jsbind module was missing as a dependency. Until
the PR is merged, just install that module.
Also when running the javascript example, you will have to either change
the output filename to nimcache/fig_javascript.js or change the
index_javascript.html to match the example filename.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/brentp/nim-plotly/issues/23#issuecomment-423806866,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AG77lgC9smHCi6IJBIzvu_jC-Mkpoot0ks5ud2Q8gaJpZM4W1o1M
.


Fix Duplicate key exception for yieldlab targeting

If the same targeting parameter is set for multiple ad units the prebid server will crash with 500 as the merging fails.
Fix inspired by this SO answer

Thanks @rpanchyk for merging this so fast. I was about to write some tests as well :joy: Will come in another PR ;)

Sure, thanks.


Add the default port documentation and remove incorrect CA note

Adding the default DNS-over-TLS port to the godoc and remove the note about multiple CAs as it's not applicable.

/label docs-approved

/label px-approved

/label qe-approved


Profiles: Strange quick input margins

When creating a new profile, the input has no margins:

Compare that with the rename one:

I am using the quick pick in the same way for both and I do not know how they are rendered differently. So moving to @TylerLeonhardt for his insights.

Ah so the difference seems to be that the first one isn't the first quickpick that is shown... first we see:

Then we see the first input box you've shared.
So I'm thinking theres some CSS class bleeding through


Building with shared dynamic zlib : undefined symbol: BIO_f_zlib

Hello I'm trying to make stunnel's compression work, it gave me an error that it needs openssl to use zlib, so I downloaded the same version as  my Ubuntu 22 original openssl 3.0.2 then rebuilt it both dynamically and statically, I get this error
undefined symbol: BIO_f_zlib
There aren't exactly any working tutorials out there either, I didn't think doing this would be this hard.

You need to use zlib (or enable-zlib which is completely equivalent) during the Configure step of the build as written in INSTALL.md.

Closing since this is marked as resolved.


Fix documentation link in README.md

About this change - What it does
Fix documentation link in README.md
Why this way
The repository migrated to new organization, so the documentation migrated to new URL as well.

Duplicate of #469, please merge one of these and close another one.

Closing as duplicate of https://github.com/Aiven-Open/guardian-for-apache-kafka/pull/469
Thanks for pointing it out @rominf!


Automated cherry pick of #3953: Fix egress e2e test

Cherry pick of #3953 on release-1.7.
#3953: Fix egress e2e test
For details on the cherry pick process, see the cherry pick requests page.

/test-e2e
/test-ipv6-e2e
/test-ipv6-only-e2e
/skip-conformance
/skip-networkpolicy

Codecov Report

Merging #3969 (fcea037) into release-1.7 (ac0c298) will decrease coverage by 8.39%.
The diff coverage is 40.00%.

@@               Coverage Diff               @@
##           release-1.7    #3969      +/-   ##
===============================================
- Coverage        63.68%   55.28%   -8.40%
===============================================
  Files              293      415     +122
  Lines            43224    60355   +17131
===============================================
+ Hits             27528    33369    +5841
- Misses           13472    24291   +10819
- Partials          2224     2695     +471

Flag
Coverage Δ

integration-tests
35.14% <ø> (?)

kind-e2e-tests
49.20% <40.00%> (-0.46%)
:arrow_down:

unit-tests
44.54% <ø> (-0.04%)
:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files
Coverage Δ

pkg/agent/route/route_linux.go
49.38% <40.00%> (+1.42%)
:arrow_up:

...g/agent/apiserver/handlers/featuregates/handler.go
4.54% <0.00%> (-77.28%)
:arrow_down:

...kg/apiserver/registry/system/supportbundle/rest.go
22.17% <0.00%> (-50.44%)
:arrow_down:

pkg/support/dump.go
7.90% <0.00%> (-49.16%)
:arrow_down:

pkg/support/dump_others.go
0.00% <0.00%> (-44.74%)
:arrow_down:

...g/agent/apiserver/handlers/addressgroup/handler.go
5.00% <0.00%> (-35.00%)
:arrow_down:

...agent/apiserver/handlers/appliedtogroup/handler.go
5.00% <0.00%> (-35.00%)
:arrow_down:

pkg/ovs/ovsctl/ofctl.go
24.65% <0.00%> (-16.44%)
:arrow_down:

pkg/agent/nodeportlocal/k8s/annotations.go
84.44% <0.00%> (-15.56%)
:arrow_down:

...nt/apiserver/handlers/serviceexternalip/handler.go
37.03% <0.00%> (-14.82%)
:arrow_down:

... and 152 more

/test-e2e


Fields creation when vertically regridding broken

The creation of fields when performing vertical regridding is broken in the release 2.0 branch. The issue is that the vector component names were being used in all circumstances when they were not defined.

Fixed by #183


bug: trouble quickfix takes ghostly control of cursor

Did you check docs and existing issues?

[X] I have read all the trouble.nvim docs
[X] I have searched the existing issues of trouble.nvim
[X] I have searched the existing issues of plugins related to this issue

Neovim version (nvim -v)
0.9.2
Operating system/version
win10 22h2
Describe the bug
executing trouble.open("quickfix") and putting the cursor under the trouble group results in the cursor moving by itself. It moves one column at a time to the right until it reaches the end of the line, then it goes to the next line, starting at the first column. This repeats until it reaches the last column of the last line.
Additionally the theme is broken and the main buffer is replaced with a second trouble buffer.
From this,

To this,

Steps To Reproduce

install cmake and put on PATH
install clang/clangd and put on PATH
clone the c++ test repo (gist)
In the test repo run nvim -u repo.lua
:CMakeSelectConfigurePreset - choose default
:CMakeGenerate
:CMakeBuild (choose ALL_BUILD if necessary)

There should be build errors - check with :cope, then close them :ccl
8. :lua require'trouble'.open'quickfix'
9. <CR> to ignore the missing web-devicons warning
10. Watch the cursor take control of itself.
Expected Behavior
The trouble quickfix buffer should open, the cursor should not go crazy, and the already-open buffer should not have its content replaced.
Repro
-- DO NOT change the paths and don't remove the colorscheme
local root = vim.fn.fnamemodify("./.repro", ":p")

-- set stdpaths to use .repro
for _, name in ipairs({ "config", "data", "state", "cache" }) do
  vim.env[("XDG_%s_HOME"):format(name:upper())] = root .. "/" .. name
end

-- bootstrap lazy
local lazypath = root .. "/plugins/lazy.nvim"
if not vim.loop.fs_stat(lazypath) then
  vim.fn.system({ "git", "clone", "--filter=blob:none", "https://github.com/folke/lazy.nvim.git", lazypath, })
end
vim.opt.runtimepath:prepend(lazypath)

-- install plugins
local plugins = {
  "folke/tokyonight.nvim",
  "folke/trouble.nvim",
  -- add any other plugins here
  {
    "Civitasv/cmake-tools.nvim",
    dependencies ={"nvim-lua/plenary.nvim"},
  }
}
require("lazy").setup(plugins, {
  root = root .. "/plugins",
})

vim.cmd.colorscheme("tokyonight")
-- add anything else here

https://github.com/folke/trouble.nvim/assets/2996796/2f6e8c52-6e8e-43ea-be52-a30a7a93c4c1
screen recording of the phenomenon

See also:

https://github.com/folke/trouble.nvim/issues/87

Thanks @YodaEmbedding for highlighting previous reports, and thanks @folke for the plug-in and the fix


[FLINK-4997] Extending Window Function Metadata

This PR aims to introduce what discussed in FLIP-2.
WindowedStream apply methods have been overloaded in order to support ProcessWindowFunction (and its rich counterpart).
Streaming runtime internals have been modified in order to support the new function, however fully backward compatibility to WindowFunction (and its rich counterpart) is guaranteed by silently wrapping it with a ProcessWindowFunction.
This PR implementation strictly follow what decided in the FLIP, nothing has been changed for AllWindowedStream.
Windows documentation has been overhauled in order to illustrate ProcessWindowFunction API.

R: @aljoscha could you take a look ?

The changes look very good! 👍
I'll rebase on top of the recent changes that introduced new fold()/reduce() and will also reshuffle/squash the commits a bit to make the history clearer. I hope that's alright.
I'll also change the name of the process() method in InternalWindowFunction back to apply() so that we have less changes and the core of the changes is more obvious. You could change that name in a future PR if you'd like but it's purely internal. I hope this is also alright.
A word on commit titles: we normally use imperative mood, i.e. "Extend WindowFunction Metadata" instead of "Extending ..." or "Extends ...". Initially, this might seem strange but you can think of a commit as being the command to do something.  And I hope you'll keep up the good work in the code. 😃
Btw, do you also want to do the same changes for AllWindowedStream?

Hi,
Thank you for both your review and your suggestions! It is good to learn something new everyday!
Regarding InternalWindowFunction, that's alright, although we may need to change it in the future in order to support more metadata.
About AllWindowedStream, of course I would like to, should I open a new issue and make a new PR?

@VenturaDelMonte sorry, it was my suggestion to change InternalWindowFunction#apply to process. Anyway, great work 👍

@VenturaDelMonte  Yes to AllWindowedStream (Issue, PR).
And yes, we need to extend the interface of InternalWindowFunction in the future and we can also change the name to process in a separate commit. I just wanted to reduce the amount of unrelated changes.

@manuzhang thank you for your feedback and no problem!
@aljoscha 👍

@VenturaDelMonte Any updates here ?

@manuzhang I finished reviewing and the code is good to go but I'm currently adding more tests before merging this because I realised that we are lacking there a bit.
See https://issues.apache.org/jira/browse/FLINK-5237

@manuzhang the other PR is ready since few days, you can find it here: #2946 .
@aljoscha do you plan to add more tests also for AllWindowedStream?

@VenturaDelMonte, that could require yet more tests, yes. We'll see once I'm done with those for the regular windows.

@aljoscha ok, then let me know, please, if I can help somehow.

@aljoscha @VenturaDelMonte This seems to be taking a long time. What is the progress now ?

I finally merged it! Thanks for staying with this for so long and working on this, @VenturaDelMonte 😃
Hopefully, we can now make faster progress.
Could you please close this PR?


Request - example using web sockets.

Perhaps community would benefit from a small example using web sockets in addition to classic ajax requests. I'm clear on how to send messages to the server but not sure how to deal with messages arriving from the server.

I would be interested in such an example as well.
I have a project that will require this feature, but I won't be working on that for a month or more, so an example would be good place to start.

Great idea! I will add one.

Here is an example using redux-logic with websockets https://jsfiddle.net/jeffbski/baqz3rkj/
It basically sends whatever msg you type to the websocket service at echo.websocket.org and then it adds all the responses (which are the same since it is an echo service) to a list and displays them.

Hi, I am trying to use/modify this code. I want the client to send back a message when it receives a specific message from the server. I am dispatching the response message sending with store.dispatch in msgRec before returning { type: MSG_REC }. But this seems to lead to msgRec being called again with the same message.
Note that I have also merged SEND_MSG_CHANGED and MSG_SEND together, as my message is not send through a form field.
I am thinking that sending the message triggers MSG_LISTEN and somehow calls msgRec again with the same message. Any advice would be appreciated. Thank you.

Nevermind, I forgot that getState.wsConnected would not work for me, as I am using a selector, so selector.wsConnected(getState()) fixed things up.

Excellent! Thanks for updating us @therealgilles

FYI. I have a more recent example using redux-logic@2 and rxjs@6
https://codesandbox.io/s/m38l7n745y

@jeffbski: The example is missing error handling through failType. How should I add it back in?

From what I can see, the example is not tracking the connection status, it's tracking the state of the connect/disconnect button, which is not the same thing.
I am not sure how to implement error handling. If you could point me to an example or documentation, it would be great.
The older version of the example also had a retry mechanism in case of disconnection, which is missing here. In my app, it means I have to manually hit refresh to reconnect the socket, whereas it was automatic before.
I am trying to see if I can adapt the older version to rxjs@6 but I am not yet well versed on it. Any help/advice will be appreciated.


Custom IDs RFC (draft)

This list should also include functions, right? https://github.com/appwrite/rfc/pull/26/files#diff-f081b69425c96526b8f8e5d6a842fd7e6fcb328c90f0ec2c483d631cb5199543R54
Is customID case-sensitive?
Is there any way to achieve auto-completition on front-end since we have this? For example if I create collection "unfinishedOrders", can my IDE auto-complete me so I dont end-up typing "unfiinshedOrders" by mistake?
36 is long enough, but since clients can create it, maaabye some day someone will use dynamic data in document/collection ID, such as "chatBetweenUser8491568495AndUser879489465". Could this limit be editable in ENV? https://github.com/appwrite/rfc/pull/26/files#diff-f081b69425c96526b8f8e5d6a842fd7e6fcb328c90f0ec2c483d631cb5199543R71
What happens if I try to create function that already exists, or maybe even tag? It will throw error or update it? Update seems to be more friendly solution but may break a lot of current setups.

This list should also include functions, right? https://github.com/appwrite/rfc/pull/26/files#diff-f081b69425c96526b8f8e5d6a842fd7e6fcb328c90f0ec2c483d631cb5199543R54
Is customID case-sensitive?
Is there any way to achieve auto-completition on front-end since we have this? For example if I create collection "unfinishedOrders", can my IDE auto-complete me so I dont end-up typing "unfiinshedOrders" by mistake?
36 is long enough, but since clients can create it, maaabye some day someone will use dynamic data in document/collection ID, such as "chatBetweenUser8491568495AndUser879489465". Could this limit be editable in ENV? https://github.com/appwrite/rfc/pull/26/files#diff-f081b69425c96526b8f8e5d6a842fd7e6fcb328c90f0ec2c483d631cb5199543R71
What happens if I try to create function that already exists, or maybe even tag? It will throw error or update it? Update seems to be more friendly solution but may break a lot of current setups.

@Meldiron nice insight.

I should include Functions
I believe IDs will be case sensitive
I don't think auto completion will be possible at the moment, can't figure out in my head how it would work
I think we want to limit the id so that we can validate, keep it secure
If id already exists it should throw and error, don't like the idea of updating it, might be friendly but error prone

This list should also include functions, right? https://github.com/appwrite/rfc/pull/26/files#diff-f081b69425c96526b8f8e5d6a842fd7e6fcb328c90f0ec2c483d631cb5199543R54
Is customID case-sensitive?
Is there any way to achieve auto-completition on front-end since we have this? For example if I create collection "unfinishedOrders", can my IDE auto-complete me so I dont end-up typing "unfiinshedOrders" by mistake?
36 is long enough, but since clients can create it, maaabye some day someone will use dynamic data in document/collection ID, such as "chatBetweenUser8491568495AndUser879489465". Could this limit be editable in ENV? https://github.com/appwrite/rfc/pull/26/files#diff-f081b69425c96526b8f8e5d6a842fd7e6fcb328c90f0ec2c483d631cb5199543R71
What happens if I try to create function that already exists, or maybe even tag? It will throw error or update it? Update seems to be more friendly solution but may break a lot of current setups.

@Meldiron nice insight.

I should include Functions
I believe IDs will be case sensitive
I don't think auto completion will be possible at the moment, can't figure out in my head how it would work
I think we want to limit the id so that we can validate, keep it secure
If id already exists it should throw and error, don't like the idea of updating it, might be friendly but error prone

Agree about updating the ID, it might create lots of confusion, especially around permissions. We might be able to create an internal auto-completion service for the console, that might also be consumed by the VS Code extension, but this requires more research around ID search and the relevant index performance.

I got a bit confused with these custom IDs, as with this feature, my function (or collection, or document) will ALWAYS have the same ID and name. Is there a use-case when I would use a different custom ID and name?

I got a bit confused with these custom IDs, as with this feature, my function (or collection, or document) will ALWAYS have the same ID and name. Is there a use-case when I would use a different custom ID and name?

Not sure I understand what you mean. You can choose a custom ID, you can't update it. You can choose a name and you CAN update it. If you need to update the custom ID, you can just create a new resource.

I got a bit confused with these custom IDs, as with this feature, my function (or collection, or document) will ALWAYS have the same ID and name. Is there a use-case when I would use a different custom ID and name?

Not sure I understand what you mean. You can choose a custom ID, you can't update it. You can choose a name and you CAN update it. If you need to update the custom ID, you can just create a new resource.

I see, makes sense.


Handle the DataCount section

This is a relatively recent addition to the bulk-memory-ops proposal

The intention was to change the order to have DataCount as section 12, but not the ids. I've run this through wasm-bindgen's test suite and it doesn't break tests, which exercises wasm implementations of Node/Firefox/Chrome, so I'm relatively confident at least that this is not a breaking change


Transfer learning

Hi, first, thanks for making this great OSS library, much appreciated.
Im interested in taking the pretrained ZINC based model and further train it with sentences from my data set. The reason for this approach is that my dataset is small, only a few thousand SMILES. So Im trying to take a page from the CNN book where you can take a pretrained image recognition model and further specialized for your use case.
Is there any way to achieve that within your library?

Thanks!
mol2vec uses word2vec implementation from Gensim and it doesn't seem to support this: https://radimrehurek.com/gensim/models/word2vec.html

As it turns out you actually can. Here is what Ive done: after preparing the corpus with cli tool provided here.
from gensim.models import word2vec corpus=[] with open('corpus.cp', 'r') as f:     for i, line in enumerate(f):         corpus.append(line) model = word2vec.Word2Vec.load('model_300dim.pkl') model.train(corpus, total_examples=len(corpus), epochs=10) model.save('updatedmodel.pkl')

That's useful. Thanks for sharing!


conmon/pause: Simplify default CFLAGS

-std, -O, and -W are all options that the caller should be able to set for themselves.  This commit moves those defaults into .travis.yml.  Package managers and other folks building the binaries can set these up as they see fit.

This means anyone compiling this conmon project will have to set these flags.  Why not just move these up in the makefile and make then easily over-ridable.

This means anyone compiling this conmon project will have to set these flags.

Don't folks compiling C already set their intended CFLAGS already?  For example, I have CFLAGS set in /etc/portage/make.conf on my Gentoo hosts.

Why not just move these up in the makefile and make then easily over-ridable.

Like:
CFLAGS = -std=c99 -Os -Wall -Wextra
override CFLAGS += $(shell pkg-config --cflags glib-2.0)

I'd be ok with that, but it's not obvious that folks who leave CFLAGS unset want us mucking with the compiler's default optimization, etc.  I don't think we want to require folks to use make CFLAGS= … to get their compiler's defaults.

No they don't.
Every Package I have used had its hard coded CFLAGS, and I would have to override the defaults.

On Thu, Feb 22, 2018 at 11:39:26PM +0000, Daniel J Walsh wrote:

No they don't.

If they don't have preferences, I'd rather leave “chosing sane
defaults” to their compiler.  conmon and pause don't care if they've
been compiled as C90, C99, C11, or another C.  My local cc wraps GCC
6.4, where -std defaults to gnu11 for C code.  There's no reason to
push that back to C99.
Similarly, I prefer my compiler's default -O0 in development and -O2
in production, which is what I get with this patch.
I don't expect package managers care one way or the other about the -W
settings I'm moving here.

Every Package I have used had its hard coded CFLAGS, and I would
have to override the defaults.

You'd have to override the defaults because you disagree with your
compiler's defaults?  I think that's a good reason for you to set
CFLAGS and use projects that respect external CFLAGS settings.  It
doesn't seem like a good reason to start baking your preferences into
all of the projects you use.

-std=c99 -Os  are specific to the project, what standard is used and the preferred optimization (size in this case).  They should be configured by default and overridable if needed.

On Fri, Feb 23, 2018 at 08:09:21AM +0000, Giuseppe Scrivano wrote:

-std=c99 -Os  are specific to the project, what standard is used
and the preferred optimization (size in this case).  They should be
configured by default and overridable if needed.

Do we have grounds for an optimization preference?  I don't see a
reason to assume the compiler has a bad optimization default in
general, and I don't see why this project has particular optimization
needs.  I'd rather leave that decision between the compiler
maintainers and the packager/builder.
The -std option is less clearcut.  Neither conmon nor glib are c90
compatible.  If I merge this PR with the in-flight pedantic cleanups
in #1368 and #1371, the only remaining c99 and c11 warnings are for
function / void * conversion.  But c90 generates lots of warnings
about unsupported functionality.  I've pushed be09ce7fb → 86f222dec to
turn those “you're trying to compile with c90” warnings into a
preprocessor error.  So I agree that this project does not support
c90.  That's still not a reason to have a preference between c99 and
c11.  I'd be ok flipping a coin and picking one, but there's no way
for a caller to override:
override CFLAGS += -std=c99 $(shell pkg-config --cflags glib-2.0) …
and while a caller can override:
CFLAGS = -std=c99
override CFLAGS += $(shell pkg-config --cflags glib-2.0) …
they could also accidentally clobber the -std setting by expressing a
preference for some other option (e.g. CFLAGS=-Wpedantic) and not
setting -std.  Is there a standard solution to this problem?  I'm
comfortable with the 86f222dec guards and:
override CFLAGS += $(shell pkg-config --cflags glib-2.0) …
which will work if the caller prefers c99 or later and error cleanly
if the caller prefers c90.  But if there is a way to gently nudge
compiler c90 preferences up to c99 or later, I'm happy to add that.

Since we had no consensus on this one I am going to close this PR.

Since we had no consensus on this one I am going to close this PR.

master currently provides no way for a caller to override these defaults.  If the approach I took here is not acceptable (for reasons that still aren't clear to me), would you accept a PR with this alternative?

Yes I have no problem modifying the Makefile to take CFLAGS := ...


/api/projects shows 401 (Unauthorized)

api's are not working

I met the same error and couldn't find any solution from Google. Please help me.
Thanks in advance.

could you please be more specific - the sample is running live and I just deployed it on heroku with no issue.

After I traced the codes with Chrome DevTools for a long time, I found that it should be a reCAPTCHA
Certification problem.
The 401 Unauthorized error disappeared when I filled my own site key and secret key respectively in /www/index.html#L257 and /server/config.js#L41.

Thx @CharlesCLLu , I added a readme setup instructions


Update user view page to use a dropdown instead of text area for role

References user story #278
Currently the user view page uses a textfield instead of a drop down to show user roles. Change it to a drop down that shows either user or admin. Also update backend endpoint to verify that the sent up role is "user" or "admin".

We should do this for the building field for the devices page as well