Added check for data changes

Moved set_status call further down the build_kubeconfig
method and added a check for differences in kubeconfig.
LP#1822021

Discovered this PR causes a regression on (LP#1833089)[https://bugs.launchpad.net/charm-kubernetes-master/+bug/1833089].

Discovered this PR causes a regression on LP#1833089.

Was unable to repeat the issue. Seems all clear.

I hate to be the :tada: :hankey: but I have some concerns that this might not be the best option. I agree it is 100% going to keep things matching our config. My concern is a couple of things:

In the past, before this bug to write it every hook, a user could ssh into the machine and add some specific content to the config file and it would stay until they did something such as upgrading, adding or removing a relation, or changing config. This may be poor assumptions by the users.
The performance issue. I think it is my games background coming through here where it simply doesn't matter, but it bothers me that we're going to generate disk i/o every hook for this when it seems we should know if things have changed.

I feel like the proper solution is to track down what flag is causing us to hit this every hook. This is a change to behavior in the last 6 months or maybe just a change where it is noticeable now? It just seems like we know if this data has changed enough to write it without reading the file back in from disk.
Maybe I'm just nitpicking too much. @kwmonroe will keep me in line.

In the past, before this bug to write it every hook, a user could ssh into the machine and add some specific content to the config file and it would stay until they did something such as upgrading, adding or removing a relation, or changing config. This may be poor assumptions by the users.

That may have been true, but it's certainly not now.. For the benefit of those that aren't sure, consider this:
## from juju client, see we wrote config at 17:36
$ juju debug-log -i kubernetes-master/1 --tail | grep kubeconfig
...
unit-kubernetes-master-1: 17:36:54 INFO unit.kubernetes-master/1.juju-log status-set: maintenance: Writing kubeconfig file.
...

## on k8s-master/1:
$ date
Thu Jul 18 22:40:11 UTC 2019

$ tail -2 config
    password: NYOKYEVwZuSXQ7mnYErQzBvwtMMjSONU
    username: admin

$ echo "- name: knobby" >> config

$ tail -2 config
    username: admin
- name: knobby

$ date
Thu Jul 18 22:40:19 UTC 2019

## back on the juju client, see we wrote config again at 17:41
...
unit-kubernetes-master-1: 17:41:56 INFO unit.kubernetes-master/1.juju-log status-set: maintenance: Writing kubeconfig file.
...

## back on k8s-master/1:
$ date
Thu Jul 18 22:43:44 UTC 2019

$ tail -2 config
    password: NYOKYEVwZuSXQ7mnYErQzBvwtMMjSONU
    username: admin

Our - name: knobby has been clobbered.

The performance issue. I think it is my games background coming through here where it simply doesn't matter, but it bothers me that we're going to generate disk i/o every hook for this when it seems we should know if things have changed.

Agreed, but at least it's a read every hook and not a write.  That's something, right?

I feel like the proper solution is to track down what flag is causing us to hit this every hook.

There isn't a flapping flag that's causing this.  It's caused by flags being present.  We'll build_kubeconfig every time we have certs and a loadbalancer or certs without an lb.

This is a change to behavior in the last 6 months or maybe just a change where it is noticeable now? It just seems like we know if this data has changed enough to write it without reading the file back in from disk.

The @when decorators guarding the calls to build_kubeconfig have been around for a few years (see blame).  What has changed in the past 6ish months is that we now set a status when we write the kubeconfig:
https://github.com/charmed-kubernetes/charm-kubernetes-master/commit/3555652452aff2ada0635dbad430f8dc69947fc4
So whatcha want to do @hyperbolic2346?  Remove the log or live with a read vs write every hook? ;)
I suppose we could check for changes to server, ca_crt_path, client_pass, and keystone since those are what is passed to create_kubeconfig. That would save the disk read, but feels like an opportunity to miss a change in the future if we add new flags/config that should trigger create_kubeconfig.  Wadda you think?

FWIW I think we should simply change the status_set to a debug log and move on. We should also not write a log line just to say "nothing changed!" - that's just spam.
#1 and #2 above don't bother me. The charm owns the file and is free to clobber user changes. User can make a copy if they need to. We're likely doing disk IO every hook anyway (unitdata.kv()).
The points are valid, but they're not important enough for us to spend a lot of time here, in light of what else we have in the queue. The biggest risk here is not #1 and #2, but that we try to get clever to avoid unnecessary writes, and end up introducing a bug where we fail to write when we should.

Seeing that the change is just notifying the user and not a behavior of calling this function constantly, I am much happier leaving it. I thought calling it each hook was a new thing. I also agree that we should avoid breaking things trying to get fancy.


[nri-metadata-injection] missing podAnnotation for k8s-metadata-injection Job

Describe in detail the feature/behavior/change you'd like to see.
I would like to be able to set podAnnotations for the job on the chart nri-metadata-injection so I can add the annotation "consul.hashicorp.com/connect-inject": "false". The job runs infinitely as the envoy sidecar and consul sidecar processes don't end when the job runs to completion.
If I was able to set pod annotations on the job I would be able to disable the sidecar injection and have the job run to completion.
Is your feature request related to a problem? Please describe.
Users who enable sidecar injection by default won't be able to kill the injection job, as the envoy proxy process doesn't end when the job finishes, and the pod stays running.
Currently podAnnotations are enabled for the deployment. I don't see any reason why they wouldn't also be enabled for the job.

We appreciate you taking the time to bring this to our attention. After reviewing this issue, we are unable to commit on a timeline to resolution. When committing to resolve an issue, we take into account the type of issue, the customer impact, and the development effort required. If the situation changes, we will revisit this decision.
If you need information about how to contribute to fixing this issue, I left an explanation here: https://github.com/newrelic/helm-charts/pull/794#issuecomment-1118795491
We encourage community contributions and are happy to collaborate on design proposals and pull requests. See our PR guidelines in the README. If you have any further questions or comments about this, please let us know by replying to this issue.


[PROPOSAL] Optimize max score calculation in Hybrid Search

What/Why
What are you proposing?
The max score calculation per shard in the Query Phase of hybrid search is done by iterating over the score-docs (results), instead we can just keep a track of max score at the collector level and  update its value when the score is calculated.
Current logic is
private float getMaxScore(final List<TopDocs> topDocs) {
        if (topDocs.isEmpty()) {
            return 0.0f;
        } else {
            return topDocs.stream()
                .map(docs -> docs.scoreDocs.length == 0 ? new ScoreDoc(-1, 0.0f) : docs.scoreDocs[0])
                .map(scoreDoc -> scoreDoc.score)
                .max(Float::compare)
                .get();
        }
    }

where topDocs represent the result found from different subqueries in that particular shard.
Instead we can add a variable
private int maxScore=0.0f;

and later in the collect method where hybrid scores are calculated.
Add a condition in here
if(score>maxScore){
  maxScore=score;
}

By this way we will reduce the latency by
(Number of Shards) x (Number of topDocs found on each shard)
What problems are you trying to solve?
Reducing the latency in Hybrid Search
What is the developer experience going to be?
No changes in the developer experience.
Are there any security considerations?
Nope
Are there any breaking changes to the API
No breaking changes

It's good idea @vibrantvarun, we're calculating maxScore at the coordinator level today, we should be able to skip same computation at the shard level.
In your PR https://github.com/opensearch-project/neural-search/pull/765 you changed the logic at the shard level, not skipped it. Can you clarify why we kept the logic at shard level?

It's good idea @vibrantvarun, we're calculating maxScore at the coordinator level today, we should be able to skip same computation at the shard level. In your PR #765 you changed the logic at the shard level, not skipped it. Can you clarify why we kept the logic at shard level?

Currently, with my change We are now not calculating the max score. We are just tracking it by finding the max score amongst the what has already been computed.
I don't want to keep it 0.0 because if someone just hits hybrid query without normalization then atleast the results should have some sanity. On top of that, I do not have to do any extra computation to calculate the max score. (I consider comparison of scores between each other by current logic is done in constant time computation so we can ignore that)

It's good idea @vibrantvarun, we're calculating maxScore at the coordinator level today, we should be able to skip same computation at the shard level. In your PR #765 you changed the logic at the shard level, not skipped it. Can you clarify why we kept the logic at shard level?

Currently, with my change We are now not calculating the max score. We are just tracking it by finding the max score amongst the what has already been computed.
I don't want to keep it 0.0 because if someone just hits hybrid query without normalization then atleast the results should have some sanity. On top of that, I do not have to do any extra computation to calculate the max score. (I consider comparison of scores between each other by current logic is done in constant time computation so we can ignore that)

that constant time for score comparison is for each hit, for each search request it's num_of_sub_query_hits. If we can save some CPU cycles we need to add it, that falls under umbrella of performance optimization. I would not care about results of hybrid query without normalization processor, that is not the right setup and we should not support it. Unless we're not failing any response is fine.


editor hangs (deletion of dependent project)

Context: I have two github projects, A and B. They are both loaded locally in my arcade editor. A depends on B.
Actions (from home page)

delete B from Project pane;
try to load A and watch the whole thing hang.

Fixed.


[UI] Convert MesheryProgressBar.js and MeshAdapterConfigComponent.js to functional component

Current Behavior
MesheryProgressBar and MeshAdapterConfigComponent are class-based components.
Desired Behavior
MesheryProgressBar and MeshAdapterConfigComponent should be functional components.
Implementation
Convert all the Class-based components to new updated functional components. It is important here to convert a class-based component to a functional component you may need to convert some functions as well. Check if the function is used in other components or not.
Also, make sure to use the hooks while converting them. For example, you need to covert withNotify with useNotification hook. Please check if a hook for functional components is available and use that.
Here is a quick blog that will help you get started with : Link
Contributor Guides and Handbook

🎨 Wireframes and designs for Meshery UI in Figma (open invite)
🖥 Contributing to Meshery UI
🙋🏾🙋🏼 Questions: Discussion Forum and Community Slack

@suzy-g38 comment on this issue to get assigned.

If this issue is not fixed, i would like to contribute to this issue. Please assign @Rajdip019 @saurabh100ni . I previously converted MesheryNotification to functional.

@suzy-g38 do you have any updates about the issue ?

@saurabh100ni I was going to create the pr but I am facing some issues regarding the linting error for the pull I took. That's why it is taking time.
Another thing I want to mention somebody else had already convert the MeshAdapterConfigComponent.js from class based to functional which was my work and I was assigned to the task. I found this when I took the pull some days ago. Still I made some changes in that component(very minor) which I found relevant in my logic.

I see,  it's cool if you are making progress with that ^ ^


chore: move snyk to dev dependencies

closes #91

:tada: This PR is included in version 1.1.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


avoid error on missing albumartist and mb_albumartistid

Make sure task.items[0] is set before checking attribs

OK, cool -- I'm glad to help out.  Thanks for beets, and for making a
proper solution to this!
-s.
On Fri, Dec 16, 2011 at 04:47:36PM -0800, Adrian Sampson wrote:

Thanks for catching this oversight. I went with a slightly different fix -- looking for the first non-None item rather than skipping altogether when the first item is None -- but your change pointed me right to the problem.
(There's a test in the above commit as well.)

Reply to this email directly or view it on GitHub:
https://github.com/sampsyo/beets/pull/14#issuecomment-3186701

--
Scott Hepler
System Administration and Web Development
802.281.4392


fix: include checkout step for package laytto injector helm chart

What this PR does:
Which issue(s) this PR fixes:

Fixes #1005
Special notes for your reviewer:
Does this PR introduce a user-facing change?:

/cc @Xunzhuo


New version: NMFk v0.2.1

Registering package: NMFk
Repository: https://github.com/TensorDecompositions/NMFk.jl
Created by: @montyvesselinov
Version: v0.2.1
Commit: 008f4d5a278c9f8fd6f648f6221257e547784740
Git reference: master

[noblock]
fails because of Plotly

Plotly doesn't install on a regular Julia install?

[noblock]
Plotly doesn't install on a regular Julia install. We already discussed it; please manually merge; we had the same issue for 0.2.0.


Default author on 'tensegribuntu'

Can we purge the default authorship of Drew Sabelhaus on Tensegribuntu? This will allow us to more easily track who committed what on their own virtual machines (without all of these commit messages reverting to Drew's name)

If no one gets to this by mid-September, I can take care of it then when I'm generating the cluster image.


Guardian UI: Use find / replace for FM_CONFIG_API env var instead of rebuilding project in docker

https://github.com/fedimint/ui/blob/master/Dockerfile.guardian-ui#L5-L7
This site should be able to run on really lean & weak hardware since it's just a basic web app, but doing the build can blow out memory on some smaller machines. A quick find / replace would be much more efficient than doing a full build. Should also improve start-up times dramatically when not using the default env var.

This was fixed by #72


Update README.md

Change comment on installing libconfuse in Ubuntu to acknowledge libconfuse is available in apt, but is the wrong version, bringing it in line with the CentOS comments regarding libconfuse.

Thanks for making that more clear.


columnlines for augmented matrices

This is a first stab at addressing issue #42.
It works fine for the usual case of a single solid columnline. But it fails for multiple solid columnlines because of interference with how AsciiMath parses the | character.
It might be possible to prevent |, from being interpreted as the start of an absolute value bracket, if that seems reasonable and not too hacky.

Checking for |, seems to work, and I can't think of negative side effects.

This seems to be working as expected, and since there's been no comments, I'm going to merge it.


Sort places by kind then population

Refs mapzen/vector-datasource#168.
Instead of sorting by scalerank, assigns a numeric value to the place kinds that can come from OSM or NE and uses that to order the results. Also, fixes the population comparator to return an int, as previously it was comparing strings.

Generally looks good, but I think we should keep reference to scalerank. Features should first be sorted by the curated minimum zoom (scale rank) – this allows small population places to show up earlier than they might otherwise, and likewise to suppress features that have a large population but should be collided out by another large(r) sized neighbor. This works well with Natural Earth now, and will be extended with Who's On First integration.
To give the OSM place types effective minimum zoom properties (and to feed those into this sort, see related https://github.com/mapzen/vector-datasource/issues/178 for also returning the min zoom in the tile response), reference this bit in the query code: https://github.com/mapzen/vector-datasource/blob/master/queries/places.jinja2#L47
        {% if zoom >= 3 %}, 'sea'{% endif %}
        {% if zoom >= 4 %}, 'state', 'province'{% endif %}
        {% if zoom >= 8 %},  'city', 'town'{% endif %}
        {% if zoom >= 10 %}, 'borough', 'suburb', 'quarter'{% endif %}
        {% if zoom >= 11 %}, 'village'{% endif %}
        {% if zoom >= 12 %}, 'hamlet', 'neighbourhood'{% endif %}
        {% if zoom >= 13 %}, 'locality', 'isolated_dwelling', 'farm'{% endif %}

For OSM places that lack population, we could use the default population numbers per OSM place type listed on the wiki.

This will be a lot simpler shortly. After #41 (and mapzen/vector-datasource#178) are closed then the majority of the logic for defaulting scalerank will be there rather than here, and this will almost go back to its previous implementation.

This has become a trivial one-liner now. @rmarianski could you review, please?

@rmarianski how's it looking now?

:+1:


Inconsistent types in http response

Is your feature request related to existing pfSense functionality that is missing from the API? Please describe.
https://<IP_ADDRESS>/api/documentation/#FIREWALL_2FRULE
Is your feature request related to a problem? Please describe.
Different response type in some fields, for example for
curl  -XDELETE 'https://<IP_ADDRESS>/api/v1/firewall/rule and curl  -XGET 'https://<IP_ADDRESS>/api/v1/firewall/rule
.data.created.time, .data.updated.time and .data.tracker is of type string
curl  -XPOST 'https://<IP_ADDRESS>/api/v1/firewall/rule
.data.created.time, .data.updated.time and .data.tracker is of type int
curl  -XPUT 'https://<IP_ADDRESS>/api/v1/firewall/rule
.data.created.time,  .data.tracker is of type string
.data.updated.time is of type int
This is just an example I am sure it's across the board
Describe the solution you'd like
Standardize http response to any request in
same field to string or int for example
.data.created.time, .data.updated.time and .data.tracker is of type string
OR
.data.created.time, .data.updated.time and .data.tracker is of type int
Additional context

Hey!
This looks to be a duplicate of #41 and #173. In summary, most if not all data typing is lost when data is written to the XML configuration. This is because pfSense only parses it's XML configuration as strings and arrays of strings. A translation piece would need to written for each endpoint that converts the response back to the accepted input format. That is an item that's planned for v2.0.0 but given the complexity this adds it will be some time before such a thing will be integrated. Keep an eye on #41 for any progress being made in the meantime.
Thanks!


On mobile, accounts with v1 progress can’t import

I’m not sure how widespread this is yet, but I was able to reproduce it on my phone and someone else’s phone. To be clear, it seems to be something in the v1 cookies that is causing an unexpected bug (syntax issue maybe?)
If you have a fresh account (no v1 cookies), it seems to work fine.

Looks like this:

Unable to reproduce on desktop on prod (democratized.space). Maybe I can debug it on my phone somehow. Looking into that later this weekend.

Going to create a debug page (accessible to everyone because why not) that shows all cookies and localStorage prettyPrinted on a page. Then we can push this to prod and see if it reveals any useful info about why the upgrader isn't working.

I built the /debug page to debug this issue. It allowed me to see all the cookies on my personal device, where I could root cause the issue with trial and error.
It turns out that when I'm parsing for items, anything with an alphanumeric suffix will fail. It's expecting item-${itemCount} and being too greedy, so item-1-cooldown (an old cookie key convention that was used in very early v1) causes an exception (Presumably. That error is getting suppressed).


Remove unnecessary logging

Remove unnecessary logging

Coverage increased (+0.004%) to 65.477% when pulling 3b6cced77bb59adb30ed712fd038349c44adadcf on DocMerlin:master into 0f2e1d83dabf8caf1e1b2a72e18fde12902b7f89 on chewxy:master.


Incrementally update

We should only re-parse the nodes that are affected.

This is not that important, as the average time of command parsing is less than 1 ms.

Closing as this is quite difficult to implement and we haven't hit any performance issues with the parsers yet.


setAsDefaultProtocolClient not working in appx

Hello,
as the title says, setAsDefaultProtocolClient isn't working when creating an appx file, but it does in my .exe file.
In my Electron main file I have the following line:
app.setAsDefaultProtocolClient('moodlemobile');
I'm using electron-builder to package the app. I added a "protocols" attribute in my package.json and I included the moodlemobile protocol in there too. To package the app, I run:
build --dir
This creates a .exe file. If I run this .exe file, my app starts and it's able to capture links with moodlemobile:// protocol just fine. Everything works perfect.
After that, I run electron-windows-store to create an appx file. If I install this appx file and run the app, it does NOT capture the moodlemobile:// links, it's as if I didn't have the app installed. This is the command I'm using to create the appx:
electron-windows-store --input-directory .\dist\win-unpacked --output-directory .\build --flatten true -a .\resources\desktop -m .\AppXManifest.xml --package-name MoodleDesktop
I tried using the default manifest and it doesn't work either. Any ideas?

I was able to make it work by adding these lines in my manifest and overriding the default manifest created by electron-windows-store:
<Extensions>
    <uap:Extension Category="windows.protocol">
        <uap:Protocol Name="moodlemobile">
            <uap:DisplayName>Moodle Mobile URI Scheme</uap:DisplayName>
        </uap:Protocol>
    </uap:Extension>
</Extensions>

It could be interesting to support this using the command so people doesn't need to create their own manifest.
Anyway, I'm closing the issue :)

Hi @dpalou,
Is it possible to use your manifest extension with electron-builder?
Thank you.

If you have installed electron-builder locally for a particular project, the quickest but not elegant way is to add  section provided above to node_modules/electron-builder/templates/appx/appxmanifest.xml (it should be inserted inside  section).
setAsDefaultProtocolClient call and an appropriate code to process the args are the same.

Hi @abardik,
I don't know if it's possible. We have our own manifest and we override the default one when we package the appx using electron-windows-store.


Initial Biorad Bioplex PR (Structure Only)

Add bioplex structure and tests
Add util to values to parse values out of xml

@nathan-stender Incorporated your suggestions, I ended up just using a generic .find() instead of specifying the layers within the xml like I was doing when using indices. I could alternatively use .find("tag1/childtag2"), let me know if you have thoughts


List of events I'm organizing

From @kyyberi on October 15, 2015 5:59
As a member I want to see list of events I am organizing
Copied from original issue: APIOps/portal#13

This issue was moved to APIOps/apiops-meetup#17


SVC / CNVKIT Parallelization

Hi,
Thanks for the help getting the svc tests to run and work. I got it to successfully complete on samples using cnvkit. However, it takes a very long time. During the detect_sv stage, bcbio fires up an array of engine computing nodes like it usually does, however it seems as though only one of the engines is actually doing anything. The others are just sitting there doing nothing. Is there some way to fix this? Let me know if you need any more information.
Thank you,
Luke

Luke -- thanks for the feedback. We're actively working on moving CNVkit coverage calculation to be more efficient and run as part of the original coverage calculation. You can see #1549 for the discussion and work in progress. Sorry about the issues as we work through ways to improve this.

Thanks for a response! I kind of understand. Does taking 24 hours to do 10 samples seem like what you would expect? I'm still a bit confused why only one engine is doing something at this stage. It seems like for each sample, the cnvkit tool calculation should be independent of the other samples, so it would be able to work on n samples at a time, where n is the number of engines. This is how alignment works: there are ten engines and ten samples can be aligned all at once. Just trying to clarify to make sure I'm not doing anything wrong that is making it take so long. Thank you.

Luke -- do you mean that a single compute node is running and everything else is idle? That's unexpected. Sorry I misunderstood and thought it was about core usage on a node versus distribution over multiple nodes. Is it possible the other samples finished and it's working on one remaining one, or is this the behavior with a fresh run? It might be useful to see what bcbio-nextgen-debug.log looks like near when things are parallelizing poorly to see if we can spot the issue if that's not it. Hope this helps.

Hi Brad. So the cnvkit appears to have a couple of stages. Firs there is a pre alignment and alignment. Both of those parallelize perfect. The second cnvkit starts to fill in the structural directory, the problem starts.  I have tried it many times, and it that happens every time.  This is when it starts making the -dedup-0.targetcoverage.cnn files and continues on after that. There are no 'errors' in any of the logs. After the dedup files are made there is a process that takes a very long time:
[2016-10-03T15:52Z] sh-0-7.local: CNVkit fix
[2016-10-03T15:52Z] sh-0-7.local: Processing target: 03_22-dedup
[2016-10-03T15:53Z] sh-0-7.local: Keeping 1870766 of 2475767 bins
[2016-10-03T15:53Z] sh-0-7.local: Correcting for GC bias...
[2016-10-03T15:53Z] sh-0-7.local: Correcting for density bias...
[2016-10-03T15:53Z] sh-0-7.local: Processing antitarget: 03_22-dedup
[2016-10-03T15:54Z] sh-0-7.local: Wrote /local-scratch/lsturm/10025321/bcbiotx/c95d16ca-afcd-42ed-a999-5098cbe126ae/tmpOLeGe7/03_22-dedu
p.cnr with 1870766 regions
[2016-10-03T15:54Z] sh-0-7.local: CNVkit segment
[2016-10-03T15:54Z] sh-0-7.local: Dropped 3456 outlier bins:
[2016-10-03T15:54Z] sh-0-7.local:    chromosome     start       end           gene     log2  depth    weight
[2016-10-03T15:54Z] sh-0-7.local: 0           1   1039045   1039278       C1orf159 -20.4036    0.0  0.147322
[2016-10-03T15:54Z] sh-0-7.local: 1           1   1312971   1313364    RP5-890O3.3 -19.7061    0.0  0.229711
[2016-10-03T15:54Z] sh-0-7.local: 2           1   1441852   1442121         ATAD3A -20.8506    0.0  0.256985
[2016-10-03T15:54Z] sh-0-7.local: 3           1   1886089   1886310       C1orf222 -21.1129    0.0  0.125634
[2016-10-03T15:54Z] sh-0-7.local: 4           1   1994858   1995100          PRKCZ -21.5981    0.0  0.394638
[2016-10-03T15:54Z] sh-0-7.local: 5           1   2251695   2251716          MORN1 -21.2462    0.0  0.084898
[2016-10-03T15:54Z] sh-0-7.local: 6           1   3399068   3399251       ARHGEF16 -21.3290    0.0  0.187698
[2016-10-03T15:54Z] sh-0-7.local: 7           1   6061590   6061813         KCNAB2 -21.2794    0.0  0.358464
[2016-10-03T15:54Z] sh-0-7.local: 8           1   6368318   6368448          ACOT7 -21.3758    0.0  0.393380
[2016-10-03T15:54Z] sh-0-7.local: 9           1   6492248   6492446           ESPN -21.8917    0.0  0.277944
[2016-10-03T15:54Z] sh-0-7.local: 10          1   6613029   6613296           NOL9 -21.1577    0.0  0.394181
[2016-10-03T15:54Z] sh-0-7.local: 11          1   8271538   8271674  RP11-431K24.3 -21.4266    0.0  0.416070
[2016-10-03T15:54Z] sh-0-7.local: 12          1   8402739   8402889        SLC45A1 -21.0107    0.0  0.176264
[2016-10-03T15:54Z] sh-0-7.local: 13          1   8521673   8521845           RERE -21.2213    0.0  0.331006
[2016-10-03T15:54Z] sh-0-7.local: 14          1   9126583   9126827         SLC2A5 -20.3015    0.0  0.386099
[2016-10-03T15:54Z] sh-0-7.local: 15          1   9866083   9866387         CLSTN1 -20.4954    0.0  0.474021
[2016-10-03T15:54Z] sh-0-7.local: 16          1  10214974  10215255          UBE4B -20.0910    0.0  0.163019
[2016-10-03T15:54Z] sh-0-7.local: 17          1  10391017  10391226          KIF1B -21.3953    0.0  0.449161
[2016-10-03T15:54Z] sh-0-7.local: 18          1  11077621  11077895         TARDBP -22.6548    0.0  0.457547
[2016-10-03T15:54Z] sh-0-7.local: 19          1  11171947  11172174           MTOR -20.6815    0.0  0.560245
[2016-10-03T15:54Z] sh-0-7.local: ...
[2016-10-03T15:57Z] sh-0-7.local: Wrote /local-scratch/lsturm/10025321/bcbiotx/3a30193e-3930-43c1-8cba-2504b172d77e/tmpn_6w0q/03_22-dedu
p.cns with 126 regions
During this stage only one compute node is running too. The tool is still usable, but it takes a very long time to do a few samples. Do you have any idea why most of the compute nodes are idle? Is there something specific I could give you from the debug log.
Cheers,
Luke

Luke;
Thanks for the additional details. Which version of bcbio are you running? If it's not the latest development could you try updating to that bcbio_nextgen.py -u development. We recently added a fix which improves resource usage at this step by better allocating cores:
https://github.com/chapmanb/bcbio-nextgen/commit/c7fb6ead93f7a8b24cb4b85633a8466f66d52184
I hope this will result in more than one parallelization engine spinning up and better use of total cores.
If you're still having issues, it would be useful to see more of the log. You could add as a gist (https://gist.github.com/). It would specifically be useful to see the Resource request and following lines prior to the structural variant calling so we can understand what bcbio is trying to allocate and why. Thanks much for the help debugging.

I think the problem might be the problem:
[2016-10-03T03:35Z] sh-0-7.local: Resource requests: cnvkit; memory: 3.00; cores: 16
[2016-10-03T03:35Z] sh-0-7.local: Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job
[2016-10-03T03:35Z] sh-0-7.local: CNVkit coverage
[2016-10-03T03:35Z] sh-0-7.local: Processing reads in 03_20-dedup.bam
[2016-10-03T03:36Z] sh-0-7.local: Time: 42.087 seconds (40379 reads/sec, 2376 bins/sec)
[2016-10-03T03:36Z] sh-0-7.local: Summary: #bins=100000, #reads=1699421, mean=16.9942, min=0.0, max=748.08
[2016-10-03T03:36Z] sh-0-7.local: Percent reads in regions: 5.056 (of 33610841 mapped)
[2016-10-03T03:36Z] sh-0-7.local: Wrote /local-scratch/lsturm/10025321/bcbiotx/427373ba-e8c2-43d6-87fb-d77523f0bb01/tmpD0a93
x/03_20-dedup-0.targetcoverage.cnn with 100000 regions
Only one job got configured. Does this help?

Luke -- thanks, this is definitely the source of the issue with running on a single core. It's a bit hard to diagnose what is causing it though. A couple of thoughts:

Are you updated to the latest development version with the fix mentioned above?
How many samples are in your input file?

I hope a multisample input file with the latest development version will do the right thing for you.

I updated to the latest development version, and it still is only requesting one job at that stage. In my config file, I am doing 10 samples. I have the 10 different algorithm sections doing svcaller: [cnvkit], each with their one associated data file to their BAM. Should I be doing it differently?

Luke -- I'm at a bit of a loss of what to suggest. You're doing everything right and it seems like it should spin up more nodes here. I've been trying to reproduce this without success. All I can think of is that you could send me your sample YAML either as a gist or via e-mail, and also the command you use to run bcbio. I can try to see if I can spot anything from that. Sorry to not have more of an idea of what is wrong.

Thanks so much for sticking with me to to try to find a solution!
Here is the gist: https://gist.github.com/lsturm1/a90267d91c18fa7855fd02dee851dc84
Hopefully it is something silly.

Luke;
Thanks for posting the configuration, this helps a lot. The issue is that you have all of these samples in a single batch. bcbio then merges all of your samples into that batch so they can get processed together during the CNVkit calling step. At this point bcbio doesn't have the facilities to re-parallelize the processing out to other cores so will run everything on that machine.
We're currently working on an improved parallelization approach using CWL which can handle cases like this in a better way and could pre-parallelize the slow steps of CNVkit and then only do the merge and call in the final batch, but this is not really ready for use right now to help you here.
Practically it might be worth deciding if you need these to be called in a pool with CNVkit or can call them in a different way that helps avoid needing to batch them all together. If they do need to be pooled, you'll unfortunately need to wait for processing on a single machine.
Sorry to not have a better solution but hope this helps explain what is going on here.

Brad,
what is the recommended configuration to process an entire run of samples (e. g. 96) with CNVkit? All samples are germline (there is no tumor/normal pairing). I remember reading somewhere that putting them in a batch in bcbio corresponds to building a reference from all samples. Is that correct?
Ben

Ben;
That's right, samples in a batch get a shared background so it's useful for those that share a common capture to get batched together. Hope this helps.

Brad,
but then only one core is used. How can I use a shared background and still get parallel processing in bcbio?

Ben -- that is true, it will only use one machine for the batch, although will use multiple cores on that machine. Your best bet if you wanted to split the work across multiple machines right now is to group into batches of 8 or 12 or whatever processes in a reasonable time and then each of those batches would have a shared background but be independently parallelizable. Hope this provides a reasonable approach for now.

Brad,
I am using a single machine on AWS and am experimenting how to size it according to the number of samples at hand. I see Resource requests: cnvkit; memory: 6.00; cores: 4 in the debug log, but only one sample is processed at a time.
I know that you guys are probably more into WGS processing at a large scale and I am still dealing with smaller, medium-depth targeted panels. So our requirements may not exactly match.
A number of commands are used redundantly for every sample. Again, I have a large number of identical panels, so this prolongs processing time significantly.

cnvkit.py access: calculating accessible regions and GC content.
cnvkit.py target and cnvkit.py antitarget are also only needed once, since all samples are sequenced with the same panel.

At this moment the overhead in bcbio is so large that I have to use cnvkit separately.
An unrelated question: Why is --avg-size=50 set for cnvkit.py target? I am not looking at tumor deep-sequencing but rather cost-aware germline sequencing. My results with bcbio standard settings turn out to be rather noisy.
Regards
Ben

Ben;
Thanks for the additional details and sorry about the poor performance right now. CNVkit is definitely not optimized for the single machine case and does do redundant work in the preparation. We want to improve and streamline this and will work on improving the parallelism and reducing the multiple runs. I'll take this on after the next release.
The --avg-size settings are meant for restricted panels (less than 1.0 of the genome) to provide additional resolution. Do you have restricted panels with lower relative depth? If so, it sounds like we need to add in some average depth checking here as well to avoid applying them under the wrong conditions.
Thanks again for the feedback and suggestions.

Brad,
I am just scratching at the surface of CNVkit at this moment and my time box is over for now. Maybe we can contribute some code later on to optimize the integration. I really like your mantra that config settings should be standardized or automated (combined with good validation).
Just some thoughts from my short journey with CNVkit:

My panels tend to have a much lower read content off-target compared to the examples from Eric/CNVkit. I therefore have to make my antitarget bins orders of magnitute larger than bcbio standard settings.
The standard bin size on-target (approx 260bp) works much better for me than the 50bp in bcbio.

It would be great if bcbio could compute the optimum bin sizes at runtime. Ideally, these would be adaptive in CNVkit itself depending on the genomic region. In general, I am fighting with relatively high noise and variability in our ordinary data (germline cancer) so that I would tend to increase bin size.
Ben

Ben -- I pushed some fixes that should improve speed for single machine multicore runs by making full use of cores during coverage and segmentation. We're planning to have a new release soon with these fixes and then will tackle additional speed improvements and improving configuration settings for your capture panel cases.
My thought was to estimate depth and percent on/off-target and then use these as parameters for setting target/anti-target. I'll first calculate these as part of the preparation process and then once it's in place follow up with seeing what these report for your cases so we can define thresholds for setting them. Thanks again for helping with this.

Brad,
sounds great! I will report back how cpu utilization looks for me with these changes.
Also the depth estimate is a good idea. I will be happy to try this out on the various sample qualities that I have.

Here's a script to quickly estimate reasonable average bin sizes from scratch: https://github.com/etal/cnvkit/blob/master/scripts/coverage_bin_size.py
If bcbio already has estimates of average on- and off-target depth for the cohort, then you can just divide 100000 by each of those values to get a sensible --avg-size argument value.

Brad,
just some feedback on your latest changes: parallel processing with cnvkit now works much better. Thanks!
The next greatest improvement speedwise would be to remove redunant steps regarding cnvkit.py access, cnvkit.py target and cnvkit.py antitarget.

Eric -- brilliant, thanks for the great script to generalize this. I added support for that in the latest bcbio development, replacing the previous hard coding of sizes based on analysis type and percent coverage. Ben, I hope this will now do the right thing with your target regions in terms of choosing good bin sizes. I'd be happy to tweak further based on your testing.
Ben, glad the parallelization improves speed. Thanks for following up on that. I'll look at moving access calculation to an upstream process since it's not data specific. target/anti-target binning should be data dependent, especially with the new estimation of avg-size, so this makes the most sense to keep as is. Would eliminating redundancy in cnvkit.py access get you the run times you need? Thanks again for all the testing and feedback.

Thanks, looks like a bunch of these speed improvements made it in. Thanks so much everyone!


In javac objects with builders can not reference their associated builder in type parameters.  Works in Eclipse.

In javac objects with builders can not reference their associated builder in type parameters.
Works in Eclipse.
Likely a javac issue as javac and Eclipse do not agree about inner class/interface visibility order resolution.
I have added the example with a workaround.
package lombok.javac.handlers;

import lombok.Builder;
import lombok.Value;
import lombok.javac.handlers.WithBuilderSimpleTest.WithBuilderImpl.WithBuilderImplBuilder;

public class WithBuilderSimpleTest {

    /**
     * Interface placed on types with associated builders to allow them to be handled generically.
     *
     * @param <T> the type
     * @param <BUILDER> the associated builder type
     */
    public interface WithBuilder<BUILDER> {

        /**
         * To builder.
         *
         * @return the builder
         */
        BUILDER toBuilder();
    }

    /**
     * A simple example of a class with a builder and a toBuilder method.
     * Works in eclipse. Fails in javac (1.8.0_u60) with:
     *
     *

     * [ERROR] last round: true
     * [ERROR] WithBuilderSimpleTest.java:[40,63] error: cannot find symbol
     * [ERROR] symbol:  class WithBuilderImplBuilder
     *

     */
    @Value
    @Builder(toBuilder = true)
    public static class WithBuilderImpl implements WithBuilder<WithBuilderImplBuilder> {

        /** The name. */
        String name;

        /** The field. */
        String field;

        /**
         * The Class WithBuilderImplBuilder.
         */
        static class WithBuilderImplBuilder {

        }
    }
}

*** Workaround ***
package lombok.javac.handlers;

import lombok.Builder;
import lombok.Value;
import lombok.javac.handlers.WithBuilderSimpleTest.WithBuilderImpl.WithBuilderImplBuilder;

public class WithBuilderSimpleTest {

    /**
     * Interface placed on types with associated builders to allow them to be handled generically.
     *
     * @param <T> the type
     * @param <BUILDER> the associated builder type
     */
    public interface WithBuilder<BUILDER> {

        /**
         * To builder.
         *
         * @return the builder
         */
        BUILDER toBuilder();
    }

    /**
     * A simple example of a class with a builder and a toBuilder method.
     * Works in eclipse. Fails in javac (1.8.0_u60) with:
     *
     *

     * [ERROR] last round: true
     * [ERROR] WithBuilderSimpleTest.java:[40,63] error: cannot find symbol
     * [ERROR] symbol:  class WithBuilderImplBuilder
     *

     */
    @Value
    @Builder(toBuilder = true)
    // Qualify WithBuilder parameter with enclosing class
    public static class WithBuilderImpl implements WithBuilder<WithBuilderImpl.WithBuilderImplBuilder> {

        /** The name. */
        String name;

        /** The field. */
        String field;

        /**
         * The Class WithBuilderImplBuilder.
         */
        static class WithBuilderImplBuilder {

        }
    }
}

This is a limitation of Javac and has nothing to do with Lombok. Type declaration is outside of the class body and therefore nothing which is inside of the class body (like static classes) is in scope and must be qualified to be visible.

Closing as javac issue


Tie dungeon icons on overworld map to dungeon category

Will entail turning exits into some entity with more state than just a Tile (maybe? Unless MapTiles can have custom data?), or at least retaining Area data that can be matched up.

Also, the map entrance icon should be determined by the map config that is linked to in the Exit entity, so that this connection is consistent and learnable, and doesn't need to be duplicated for every exit


Added label Workflow

why have u deleted a page

why have u deleted a page

@anushbhatia That file is not related to the workflow of github actions

announcement page.html is not required?

announcement page.html is not required?

I just added an action...It is a commit from the previous PR. So I removed it. It will not affect anything.

announcement page.html is not required?

I just added an action...It is a commit from the previous PR. So I removed it. It will not affect anything.

Don't commit that then na. Your PR removes the Announcements Page completely. I have cross verified in the netlify deploy for the PR

Okay, I am fixing it.

announcement page.html is not required?

I just added an action...It is a commit from the previous PR. So I removed it. It will not affect anything.

Don't commit that then na. Your PR removes the Announcements Page completely. I have cross verified in the netlify deploy for the PR

Done, check it now


Only show Pock on desktop

Describe the feature you'd like to have in Pock
I only want to see pock when I'm on the desktop, with no windows active. Otherwise I want to see app controls.
Describe alternatives you've considered
The alternative is not using pock, as this is normal behaviour, except for loosing the dock which pock provides.

You can achieve this behavior by disabling “Hide Control Strip” option in Pock settings and toggling Pock visibility trough its close button on the most left of your Touch Bar.


Would a best practice guide be helpful?

I thought about it for a while and I wonder if a hand book / guide about best practices for open source projects would be a helpful idea? What it would probably include, would be topics like:

Choice of the name (avoid prefixes like Open / Free / SDL)
Source versioning
License information (where to display, what is popular, include artwork licenses)
Dependencies (which ones are popular, where to find information about them)
Build systems (the choices, where to find information about them)
Distribution of binaries
Continuous integration
Bug reports
…

Or is this already existing? It could be geared toward games development though maybe.

Might be interesting: Free and open source development practices in the game community but unfortunately behind paywall. Search directly on the authors homepage or get the text by other means and then summarize here. Is from 2004, so may also be outdated. However, may be a good start for a literature search.

Also see https://modelviewculture.com/resources#engineering for pitfalls like toxic cultures.


[QUERY] / [BUG] 5.0 Connection String Issue

Library name and version
Microsoft.Azure.WebJobs.Extensions.Storage 5.0.0
Query/Question
I started getting this on application startup on my local machine in an Azure Function app after updating the Microsoft.Azure.WebJobs.Extensions.Storage NuGet package from 4.0.5 to 5.0.0.
[2022-03-12T22:13:26.596Z] A host error has occurred during startup operation '9624398c-810f-4633-8140-c0e3c8764d8f'.
[2022-03-12T22:13:26.597Z] Microsoft.Azure.WebJobs.Script.WebHost: Secret initialization from Blob storage failed due to missing both an Azure Storage connection string and a SAS connection uri. For Blob Storage, please provide at least one of these. If you intend to use files for secrets, add an App Setting key 'AzureWebJobsSecretStorageType' with value 'Files'.
[2022-03-12T2

Rolling back the NuGet package fixes it, so I seem to have found a breaking change.
My connection string is set:
"AzureStorage": "UseDevelopmentStorage=true"
Environment
IDE:
Microsoft Visual Studio Community 2022 (64-bit) - Preview
Version 17.2.0 Preview 1.0
.NET SDK (reflecting any global.json):
Version:   6.0.201
Commit:    ef40e6aa06
Runtime Environment:
OS Name:     Windows
OS Version:  10.0.22000
OS Platform: Windows
RID:         win10-x64
Base Path:   C:\Program Files\dotnet\sdk\6.0.201\
Host (useful for support):
Version: 6.0.3
Commit:  c24d9a9c91
.NET SDKs installed:
6.0.200 [C:\Program Files\dotnet\sdk]
6.0.201 [C:\Program Files\dotnet\sdk]
.NET runtimes installed:
Microsoft.AspNetCore.App 6.0.2 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 6.0.3 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.NETCore.App 3.1.22 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 5.0.14 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 6.0.2 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 6.0.3 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.WindowsDesktop.App 3.1.22 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]
Microsoft.WindowsDesktop.App 5.0.14 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]
Microsoft.WindowsDesktop.App 6.0.2 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]
Microsoft.WindowsDesktop.App 6.0.3 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]

@scottkuhl We are looking into it and get back to you for any additional information.

Hello @scottkuhl Thanks for the feedback.
On Microsoft Visual Studio Enterprise 2022 (64-bit), with Azure Blob Storage triggered Function App and the Nuget Package was upgraded to 5.0.0 and the functionality was working, Could you please try updating the VS 2022 or please try on other versions? Please let us know if you need further help in this matter!

Have you tried changing the connection string to this:
"AzureStorage": "UseDevelopmentStorage=true"
I can only recreate the problem using that connection string used for local development.

Have you tried changing the connection string to this:
"AzureStorage": "UseDevelopmentStorage=true"
I can only recreate the problem using that connection string used for local development.

Yeah,,I tried the "AzureStorage": "UseDevelopmentStorage=true" ans started the code debug,,,

Ok, I will update my machine as you suggested and try again this weekend.  Thanks
Scott Kuhl
O’Fallon, Illinois, USA, Earth

From: SatishBoddu @.>
Sent: Wednesday, March 16, 2022 5:48:40 PM
To: Azure/azure-sdk-for-net @.>
Cc: Scott Kuhl @.>; Mention @.>
Subject: Re: [Azure/azure-sdk-for-net] [QUERY] / [BUG] 5.0 Connection String Issue (Issue #27531)
Have you tried changing the connection string to this:
"AzureStorage": "UseDevelopmentStorage=true"
I can only recreate the problem using that connection string used for local development.
Yeah,,I tried the "AzureStorage": "UseDevelopmentStorage=true" ans started the code debug,,,
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You are receiving this because you were mentioned.Message ID: @.***>

I was able to recreate the issue on my machine and another developer machine even when downgrading to v4.  I don't think this is an issue in v5 specifically, so it is unlikely a bug introduced in the Azure SDK.  I am closing this issue and we will look into it further on our end.  Thanks for the help.


feat: Surface parameters fields for database model

SUMMARY

Update the api to surface parameters in GET database. This will be leveraged for whenever a user wants to edit a database assuming configuration type is dynamic.
BEFORE/AFTER SCREENSHOTS OR ANIMATED GIF

TEST PLAN

ADDITIONAL INFORMATION

[ ] Has associated issue:
[ ] Changes UI
[ ] Includes DB Migration (follow approval process in SIP-59)

[ ] Migration is atomic, supports rollback & is backwards-compatible
[ ] Confirm DB migration upgrade and downgrade tested
[ ] Runtime estimates and downtime expectations provided

[X] Introduces new feature or API
[ ] Removes existing feature or API

closing in favor of #14653


Categories for applications

Is there a way to create categories for apps the same way you can for web link?

Mr developer has been rejecting this most requested feature for months lol
However I don't get why he does not like it.
Seems pretty logical to me to have way to partition apps, and could be
turned on/off in settings.
Why oh why?
On Thu, Nov 4, 2021, 4:22 PM samcro1967 @.***> wrote:

Is there a way to create categories for apps the same way you can for web
link?
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Ah, thanks.  Guess I should have searched the issue before I opened this one then LOL.  I will stick with Plugsy then for now.  Like the docker labels approach and not having to modify a confg file, but app categories is worth it for only having to manage a few settings in a config file.

This is something I'd like too. When I used to use the Homer dashboard, I had a separate section for all of the backend admin interfaces... eg postfixadmin, phpmyadmin, wordpress admin, funkwhale backend admin, etc etc. It does seem a little cluttered having everything together in a big list. The justification for having categorised applications is exactly the same as for having categorised bookmarks. I'm considering working around it for the moment by simply using bookmarks for everything - which probably goes against what you actually designed the site to do.

Actually.... you could probably get away with not having application categories if there was a bit more flexibility in the titles. I'm just looking at the layout here and I'm thinking... if I could rename applications to 'Main Applications' and then rename bookmarks to 'Other', I could just use the bookmark categories for the rest ie My Websites, Backend Admin, External Services, Documentation, etc. Anything more could be easily tweaked in the custom CSS section.

I would agree bookmarks could probably be used by extending the code to accept two more docker labels.
- flame.type=bookmark
- flame.bookmark.category=Media

Was just about to request this. +1

This is something I'd really like as well. I'd like to add my applications under the "applications" type, and actual bookmarks under "bookmarks", but instead I end up disabling applications entirely and putting everything under bookmarks, as I really value the categories.

instead I end up disabling applications entirely and putting everything under bookmarks

That's a great idea.

You might wan to check out Plugsy.  It has categories for apps and works with Docker labels.  It does have one config file to maintain, but it is minimal.


Exponentially backoff processing events

@ibuildthecloud

@sonchang Should we go with this approach in the short term and then look at more scalable approach in the future?  If you feel good with that, then I'll review this in depth, right now I haven't looked at the actual backoff calculation logic.

@ibuildthecloud I feel good with that.  With Will's latest request, the earliest I'll probably look at this again is a week from now


winner-undo breaks perspectives

When I switch from perspective A to perspective B and run winner-undo, window layout of B becomes same with A.

Yes, I know. Definitely worth fixing.
I think it can be done by advising the winner-ring function and changing winner rings to key on frame+perspective pairs, rather than just frames. The current perspective would be the one always used (I hope that's not too much of a limitation). Unfortunately, it looks like winner-ring is defined using defsubst instead of defun, so I'm not sure if Elisp advice will work on it.


File copy animation can be colorized

This utility does it for example https://www.softpedia.com/get/Desktop-Enhancements/Other-Desktop-Enhancements/7-Copy-Delete-Animation-Modder.shtml

It is in DLL, not in theme files - I don't like the idea of hard-patching system files.


chore: upgrade charts

updated chart jxgh/jxboot-helmfile-resources from 1.1.256 to 1.1.257

/retest


Simple progress update

Hope you've been doing good, this simply updates to newer dependency versions. Peace

Looks good! Thanks!


[Feature Request] Un-unify crop borders settings or just completely disable cropping for webtoon mode.

Copy of https://github.com/inorichi/tachiyomi/issues/3487
Why/User Benefit/User Problem
If you prefer to use cropping for manga but also frequently read webtoons you're now stuck in a loop of having to turn cropping on and off for every other thing you read. For webtoons, you rarely want cropping do to the misalignments, text cutting, and sometimes adding weird-looking borders to smaller inline images. As for manga, well I have never really found a pressing "non-OCD" need to disable cropping for manga.
What/Requirements
Add a separate toggle for webtoons or just disable cropping for the webtoon view mode by default, or something something new UX stuff.
Technically reopening #972
Was implemented with. https://github.com/inorichi/tachiyomi/commit/18883f1ba3642dc220dac5355c0b207c4407cefb
Was removed with https://github.com/inorichi/tachiyomi/commit/1920568057eee522a7e77f523a5ebe322ee43249 for some unstated reason.
Merged with SY in https://github.com/jobobby04/TachiyomiSY/commit/439b78c39f71e75e9fc2e981ab5c9e0762410d4f I think?

Looks like it was reverted https://github.com/inorichi/tachiyomi/commit/6a5af438ddead33e938eb43265a6fc50c8785022


Refactor remove unless code in exchange and opt some code

Proposed changes
tpcds q23：
before：36s
after：33s

Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run buildall


Support server fuzzing

This PR makes several changes to allow fuzzing of a Roughtime server in roughenough-fuzz:

Extracts server code from roughenough-server.rs into a new Server struct.
Moves the core server processing into a standalone function, suitable for calling from a fuzz wrapper.
Adds a MemoryConfig struct, to allow a fuzz wrapper to easily create a ServerConfig.
Adds a new method Server::send_to_self, gated behind #[cfg(fuzzing)]. It allows the server to feed messages to itself using a separate client UdpSocket instance.
Add a new  --outputflag to roughenough-client, which causes the client to write all of its requests to a file. This can be used to easily generate fuzzer inputs to the server.

I've left this PR as a series of several commits, but I can squash them once you think this is ready to merge.
Developer Certificate of Origin
Version 1.1

Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
1 Letterman Drive
Suite D4700
San Francisco, CA, 94129

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.

Developer's Certificate of Origin 1.1

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I
    have the right to submit it under the open source license
    indicated in the file; or

(b) The contribution is based upon previous work that, to the best
    of my knowledge, is covered under an appropriate open source
    license and I have the right under that license to submit that
    work with modifications, whether created in whole or in part
    by me, under the same open source license (unless I am
    permitted to submit under a different license), as indicated
    in the file; or

(c) The contribution was provided directly to me by some other
    person who certified (a), (b) or (c) and I have not modified
    it.

(d) I understand and agree that this project and the contribution
    are public and that a record of the contribution (including all
    personal information I submit with it, including my sign-off) is
    maintained indefinitely and may be redistributed consistent with
    this project or the open source license(s) involved.

Hi @Aaron1011! This is really awesome.
I'm very impressed you based this on 1.1 as I'm churning on that a lot, sorry if it caused you extra work.
I'm going to go ahead and merge this to 1.1 so you can keep going. I think a errant hyper reference broke the build. I'm not sure if I introduced it or one of your changes.

@Aaron1011 thanks for your continued contributions to Roughenough.  I've added you as a contributor to roughenough and roughenough-fuzz so you can commit directly. You're the first roughenough contributor other than myself and I honestly never expected to attract much interest!
I don't have any grand "governance" plans. For now, how about we mutually coordinate future releases? Additionally, given your more extensive experience as a contributor if you have suggestions on how we best coordinate a small project like this, I'm open to them.


Local notification on script describe

Issue
A describe sent by a room script may trigger locally generated notifications that will result in texts like:

??? made a description

If a script property exists in the event, no notification should be created.

Resolved in PR #333


The default number of blocks to keep in the cache is 512.
Fixed Issue(s)

#6009


chore: update pydid to ^0.3.3

This should have a pretty minimal impact on things while enabling resolution of Documents with nonconforming @context attributes (spec defines that context must be a list of strings, some docs have embedded contexts). Also solves the bug mentioned in this comment from forever ago: https://github.com/hyperledger/aries-cloudagent-python/pull/1218#issuecomment-890591874

Codecov Report

Merging #1562 (632867e) into main (072437b) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #1562   +/-   ##
=======================================
  Coverage   95.75%   95.75%
=======================================
  Files         527      527
  Lines       32308    32308
=======================================
  Hits        30938    30938
  Misses       1370     1370


Invalid return url from build scan since 2.60.0

Describe the bug
We have noticed that since updating to the latest 2.61.2 release, the xray_data_url value being returned from running jf build-scan is no longer a valid URL as it does not contain the Xray host name.
It would appear to be related to the changes from https://github.com/jfrog/jfrog-cli-security/pull/106 that were added in 2.60.0
I am wondering if it is related to the fact that we supply the --server-id argument to the jf build-scan command?
Current behavior
Receive results similar to the following (note the incomplete URL):
...
[Debug] JFrog Xray version is: 3.69.3
[🔵Info] Waiting for Build Scan to complete...
[Debug] Sending HTTP GET request to: https://artifactory.somecompany.com/xray/api/v2/ci/build/some-build/1.2.3
[Debug] The resulted url from API is https://au.artifactory.somecompany.com/, and the CLI config url is
[🔵Info] The scan data is available at: ui/builds/some-build/1.2.3/1722401114525/xrayData?buildRepo=artifactory-build-info
DEBUG: [
  {
    "xray_data_url": "ui/builds/some-build/1.2.3/1722401114525/xrayData?buildRepo=artifactory-build-info"
  }
]
...

Reproduction steps
For an Artifactory/Xray instance with a different API Base URL compared to the CLI:

Add a server configuration using jf config add 'SERVER-ID' ...
Run a build scan using jf build-scan --server-id 'SERVER-ID' ...

Expected behavior
Given the example in the current behaviour, we'd expect to see the following as the returned URL:
{
    "xray_data_url": "https://artifactory.somecompany.com/ui/builds/some-build/1.2.3/1722401114525/xrayData?buildRepo=artifactory-build-info"
}

JFrog CLI version
2.60.0
Operating system type and version
Linux
JFrog Artifactory version
No response
JFrog Xray version
No response

Hello @santhonisz Thanks for reporting this.
I would like to see the details of your jfrog-cli configuration.
Can you please share the version of your jfrog cli config and details on https://artifactory.somecompany.com/?
these details can be found in ~/.jfrog jfrog-cli.conf file (can be v1,v2,v3,v4,v5,v6) don't share password/access-token only share the following:
"url": ,
"artifactoryUrl":,
"distributionUrl": ,
"xrayUrl": ,
"serverId": ,
 and the version of the config (v6 for example)

Hi @dortam888,
Ok, checking the file I can see that only artifactoryUrl and xrayUrl are defined e.g.
"artifactoryUrl": "https://artifactory.somecompany.com/artifactory/",
"xrayUrl": "https://artifactory.somecompany.com/xray/",

I think I've figured out why this is. We are running the Xray scan in a CI pipeline, where the required JFrog server configuration is added with the following command. Note we don't pass the --url (JFrog Platform URL) parameter as it is optional and not required for the scan to be performed.
jf config add XRAY-CI --overwrite --user [REDACTED] --artifactory-url https://artifactory.somecompany.com/artifactory --xray-url https://artifactory.somecompany.com/xray --access-token [REDACTED]

Interestingly if I run this command locally I get prompted to supply the JFrog Platform URL, but as our CI build agents define CI=true the interactive prompts are disabled in our pipelines and hence the config is added without the JFrog Platform URL.
None of this changes the fact that the code added in https://github.com/jfrog/jfrog-cli-security/pull/106 should probably be smartened up to handle when the JFrog Platform URL is not supplied e.g. is empty, in which case it should fall back to the previous behaviour or possibly use the xrayUrl instead of the url etc.

Thanks @santhonisz
You're correct it's a valid use case and I will add a fix to the next version.
Thanks for reporting that!

@santhonisz the PR for fix is merged and will be released in the next version of the JFrog CLI.


Can't run tests with newest update (1.9.2)

Please provide the environment you discovered this bug in.
We use nx with analog vitest
Which area/package is the issue in?
vitest-angular
Description
Everytime I run the tests I get the error:
ReferenceError: exports is not defined in ES module scope
This file is being treated as an ES module because it has a '.js' file extension and '/Users/reneachtelik/workspace/fhp-bike/node_modules/.pnpm/@analogjs+vitest-angular@1.9.2_@analogjs+vite-plugin-angular@1.9.2_<EMAIL_ADDRESS>contains "type": "module". To treat it as a CommonJS script, rename it to use the '.cjs' file extension.
 ❯ ../../../node_modules/.pnpm/@analogjs+vitest-angular@1.9.2_@analogjs+vite-plugin-angular@1.9.2_@angular-devkit+build-angu_tfhrvuljhjniigrh7pmftb3w5m/node_modules/@analogjs/vitest-angular/setup-zone.js:2:23
      1| "use strict";
      2| Object.defineProperty(exports, "__esModule", { value: true });
       |                       ^
      3| require("zone.js");
      4| require("zone.js/plugins/sync-test");
 ❯ src/test-setup.ts:1:1

project is esm only.
Please provide the exception or error you saw
ReferenceError: exports is not defined in ES module scope
This file is being treated as an ES module because it has a '.js' file extension and '/Users/reneachtelik/workspace/fhp-bike/node_modules/.pnpm/@analogjs+vitest-angular@1.9.2_@analogjs+vite-plugin-angular@1.9.2_<EMAIL_ADDRESS>contains "type": "module". To treat it as a CommonJS script, rename it to use the '.cjs' file extension.
 ❯ ../../../node_modules/.pnpm/@analogjs+vitest-angular@1.9.2_@analogjs+vite-plugin-angular@1.9.2_@angular-devkit+build-angu_tfhrvuljhjniigrh7pmftb3w5m/node_modules/@analogjs/vitest-angular/setup-zone.js:2:23
      1| "use strict";
      2| Object.defineProperty(exports, "__esModule", { value: true });
       |                       ^
      3| require("zone.js");
      4| require("zone.js/plugins/sync-test");
 ❯ src/test-setup.ts:1:1

Other information
Happens only with the newest update
I would be willing to submit a PR to fix this issue

[ ] Yes
[X] No

Is this Nx 20?

Make sure your vite.config.ts is named vite.config.mts if its just for testing which will force ESM.

Can you provide a reproduction? I could see this happening if it's running in ESM-only mode, but Nx doesn't run as ESM. What version of Vitest?

Hi, we encountered a very similar problem (same error message). For us, it is connected to the pool = "threads" option that seems to change how module loading works (or doesn't work).
Here is a complete reproduction guide: https://github.com/fabian-paus/angular-vitest-bug
The error can simple be reproduced by:

Setting up an analogjs project: npm create analog@latest
Then changing the test config to pool = "threads" (or "forks")

The problem can be "solved" by editing @analogjs\vitest-angular\package.json to "type": "commonjs".
I am a novice on this whole CommonJS / ESM debacle. But I tried looking into @analogjs\vitest-angular. It seems to contain CommonJS code (require syntax), but is marked as "type": "module", which indicates ESM syntax (import, export).
It seems that with pool = "vmThreads" vitest somehow ignores this inconsistency.
Changing the config from .ts to .mts did not change anything.
The error is reproducible on any system and version that I tried:

Windows and Linux
Node 22.11 and 20.18
Vitest version 1.6 and 2.1.4

The fix has landed in Analog 1.9.3-beta.1 for testing

I had the same problem and it was caused by https://github.com/analogjs/analog/pull/1434, downgrading to v1.9.2-beta.3 and all was working as before. It's curious that it would be affected by "type": "module".
My Vitest file are already vite.config.mts.

@Yberion interesting, I wouldn't have expected that. So everything is back working with the latest beta?

@jahusa02 ok cool

@Yberion interesting, I wouldn't have expected that. So everything is back working with the latest beta?

Yeah it is now working with the last beta.
But still confused about why adding nx to optimizeDependencies.exclude  would suddently cause this problem. Perhaps esbuild was optimizing the code and translating it somehow to ESM compatible code.

@Yberion interesting, I wouldn't have expected that. So everything is back working with the latest beta?

Yeah it is now working with the last beta.
But still confused about why adding nx to optimizeDependencies.exclude  would suddently cause this problem. Perhaps esbuild was optimizing the code and translating it somehow to ESM compatible code.

Probably so. nx is still CommonJS right now, so it would try to optimize it along with its dependencies, which could lead to a bit of "over optimizing"

Analog 1.9.3 is released with the fix


fix argument name for ipv6 masking

running the code without this rename causes alloy to stop during config loading. Line 327 expects the argument name "mask_ipv6_value".
Tested the fix locally and it worked for me.

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

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


adb.exe has stopped working - Windows

I used command prompt but it said that adb stopped working. How can I fix this?
Error .txt

This is a bug in adb (either on your device or the client).
Which adb do you use? The one bundled with the scrcpy release?
What is your Android version/device?
What is the result of adb devices?


Support controls in more k8s topologies

Adds the ability for more k8s topologies to have controls displayed in the frontend by plugins. Namely Service, DaemonSet, StatefulSet, Cronjob.
Fixes #3107

@rade PTAL


Change grow factor according to the memory in rh hash

Changelog entry
RobinHood hash will grow less on low memory.
...
Changelog category

New feature

Additional information
...

I think RH code assumes capacity is power-of-2


message1 is initially missing from broadcast message picker dropdown

The default "message1" broadcast message is shown on the broadcast picker field, but if you click the field to show the menu it's not listed as an option there until a block with that broadcast message is dragged onto the main workspace.

The "message1" is displayed along with "New message"


HTTP Source doesn't return all the responses

Code to reproduce the issue:
https://esnextb.in/?gist=83ba64f55956c469399eba0a4cd4658a
import xs from 'xstream'
import {run} from '@cycle/run'
import {makeDOMDriver, h, div, button} from '@cycle/dom'
import {makeHTTPDriver} from '@cycle/http'
import R from 'ramda'

import delay from 'xstream/extra/delay';

function main (sources) {
  const posts$ = sources.HTTP.select('posts').flatten()
    .map(R.prop('body'))
  const comments$ = sources.HTTP.select('comments')
    .debug('comments before flatten')
    .flatten()
    .map(R.prop('body'))

  const commentRequest$ = posts$
    .map(R.map(R.prop('id')))
    .map(R.take(5))
    .map(ids => xs.fromArray( ids
      .map( id => ({
        url: `https://jsonplaceholder.typicode.com/comments?postId=${id}`,
        type: 'JSON',
        category: 'comments'
      })))
    ).flatten()

  const state$ = comments$.fold((total, comments) => total.concat(comments), [])
    .debug('state$')
  const DOM = state$
    .map(comments => h('div', {}, comments.map(c => h('p', {}, c.postId))))

  const HTTP = commentRequest$.startWith({ url: 'https://jsonplaceholder.typicode.com/posts', type: 'JSON', category: 'posts' })
  return {
    DOM,
    HTTP
  }
}
run(main, {
  DOM: makeDOMDriver('#app'),
  HTTP: makeHTTPDriver()
})

is this a known issue?

make HTTP request to get a response of array of posts
use posts ids to create an array of comments requests
xs.fromArray( the new comments requests )
read the HTTP response, accumulate all the comments
display on DOM

network calls happens.. but only the last post's comments gets rendered
my assumption is that the fast burst of request from the array of ids is the problem
the http driver couldn't process all the responses in time?
Expected behavior:
All comments gets rendered
Actual behavior:
Only the last request made gets through
Versions of packages used:
{
    "xstream": "10.2.0",
    "@cycle/run": "1.0.0-rc.9",
    "@cycle/dom": "15.0.0",
    "@cycle/http": "12.0.0",
    "ramda": "0.23.0"
}

it's because of the synchronous fromArray, flatten gets the last one.. I think this is intended behavior
to fix this:-
if you care about sequence, use flattenSequentially
import flattenSequentially from 'xstream/extra/flattenSequentially'

//...
const comments$ = sources.HTTP.select('comments')
  .compose( flattenSequentially )
  .map(R.prop('body'))

if you don't care about the sequence, use flattenConcurrently
import flattenConcurrently from 'xstream/extra/flattenConcurrently'

//...
const comments$ = sources.HTTP.select('comments')
  .compose( flattenConcurrently )
  .map(R.prop('body'))


Benchmarking and some performance improvements

Some benchmarking results are here: https://docs.google.com/spreadsheets/d/1I7QycnED7qC8MK8qoiSu8SkrTkAj1xqBPcSXziozo7M/edit#gid=0
They show the absolute and relative performance of python and different SHAs to do various things to a URL (parse, escape, abspath, etc.) 1M times. They are grouped by example URL (base and relative), and highlighted cells show what metrics were specifically targeted for optimization by a particular commit.
There are more opportunities for improvement, but I think I'll table this for now.
@b4hand @neilmb @martin-seomoz @tammybailey @tanglyh

LGTM


fix: bump go-w3up, check content headers

Summary
Bumps go-w3up and also makes the change it implements here.
Details

Note: even though we use go 1.21 and the error described by the w3s team happens with go 1.22, this seems to fix things.
The content-length check is all we need, and things work without updating to go-w3up v0.0.3...but we might as well bump it since it doesn't affect the behavior. If needed, we can remove the dep update and use go-w3up v0.0.2, and things will work.

How it was tested

Tried bumping to go-w3up v0.0.3, and I still received an empty server response, with the server logging this error: failed archiving CAR: status code: 403

Made the recommend check in rcpt.Out().Ok().Headers.Values for the content-length, and then uploading random / new files worked:{
   "root": "bafybeihx5mvoz7vdnjevt4724mpwm5eh6mhqrle22axx2yx4haast4dlli",
   "shard": "bagbaiera64rrqwenr7gmw6g2q6r4uchk36nobfnhg2362e6ujsfqoryzntcq"
}

Hero!


Add New API endpoint: UpdateVlanIpRange

Description
A new endpoint that will allow the shrinking and extending of public IP range
This PR extends #3997
(1) ipv4 startip and endip can be changed, gateway and netmask can NOT be changed
(2) ipv6 startip and endip can be changed, gateway and cidr can NOT be changed
(3) if an ip is allocated but not in new ip range, operation will fail
(4) if an ip is allocated,  operation will fail if try to change "forsystemvms".

Types of changes

[ ] Breaking change (fix or feature that would cause existing functionality to change)
[x] New feature (non-breaking change which adds functionality)
[ ] Bug fix (non-breaking change which fixes an issue)
[ ] Enhancement (improves an existing feature and functionality)
[ ] Cleanup (Code refactoring and cleanup, that may add test cases)

Feature/Enhancement Scale or Bug Severity
Feature/Enhancement Scale

[x] Major
[ ] Minor

Bug Severity

[ ] BLOCKER
[ ] Critical
[ ] Major
[ ] Minor
[ ] Trivial

Screenshots (if appropriate):
How Has This Been Tested?

@blu@blueorangutan package

@blueorangutan package

@nvazquez a Jenkins job has been kicked to build packages. I'll keep you posted as I make progress.

Packaging result: :heavy_check_mark: el7 :heavy_check_mark: el8 :heavy_check_mark: debian :heavy_check_mark: suse15. SL-JID 1185

@blueorangutan test

@nvazquez a Trillian-Jenkins test job (centos7 mgmt + kvm-centos7) has been kicked to run smoke tests

Trillian test result (tid-1994)
Environment: kvm-centos7 (x2), Advanced Networking with Mgmt server 7
Total time taken: 33500 seconds
Marvin logs: https://github.com/blueorangutan/acs-prs/releases/download/trillian/pr5411-t1994-kvm-centos7.zip
Smoke tests completed. 89 look OK, 0 have errors
Only failed tests results shown below:

Test
Result
Time (s)
Test File

@DaanHoogland @davidjumani thanks for review.
updated pr as per your comments.

@blueorangutan package

@weizhouapache a Jenkins job has been kicked to build packages. I'll keep you posted as I make progress.

Packaging result: :heavy_check_mark: el7 :heavy_check_mark: el8 :heavy_check_mark: debian :heavy_check_mark: suse15. SL-JID 1298

@blueorangutan test

@sureshanaparti a Trillian-Jenkins test job (centos7 mgmt + kvm-centos7) has been kicked to run smoke tests

@blueorangutan package

@weizhouapache a Jenkins job has been kicked to build packages. I'll keep you posted as I make progress.

Packaging result: :heavy_check_mark: el7 :heavy_check_mark: el8 :heavy_check_mark: debian :heavy_check_mark: suse15. SL-JID 1302

@blueorangutan test

@weizhouapache a Trillian-Jenkins test job (centos7 mgmt + kvm-centos7) has been kicked to run smoke tests

Trillian test result (tid-2110)
Environment: kvm-centos7 (x2), Advanced Networking with Mgmt server 7
Total time taken: 36051 seconds
Marvin logs: https://github.com/blueorangutan/acs-prs/releases/download/trillian/pr5411-t2110-kvm-centos7.zip
Smoke tests completed. 89 look OK, 0 have errors
Only failed tests results shown below:

Test
Result
Time (s)
Test File

Trillian test result (tid-2111)
Environment: kvm-centos7 (x2), Advanced Networking with Mgmt server 7
Total time taken: 34901 seconds
Marvin logs: https://github.com/blueorangutan/acs-prs/releases/download/trillian/pr5411-t2111-kvm-centos7.zip
Smoke tests completed. 89 look OK, 0 have errors
Only failed tests results shown below:

Test
Result
Time (s)
Test File

Merging based on approvals, manual and smoke test results.


[2.0.0 REVIEW] JSON Schema definition is missing additionalItems and patternProperties in the schema object

The schema object is missing additionalItems and patternProperties: https://github.com/asyncapi/asyncapi/blob/master/versions/next/schema.json#L325

Closing as it's correct. OpenAPI schemas don't have these properties.


test: add e2e test for CAS instances.

DO NOT MERGE.
This PR is created only to run the e2e test for PR #850.

Closing this PR since the #855 has been merged.


Why no show_accuracy=True for Graph model?

For a Sequential model, I can do
model.fit(..., show_accuracy=True)
which will show the accuracy on the train set (and also validation set, if given). I tend to visualize these over the epochs.
For a Graph model, this option is missing. Why? Can it be easily added? After all they are both derived from the Model class...

I think that the multiple output capability makes it difficult to add a show_accuracy parameter that will work for every situation. You could write a custom callback to calculate it, it's a little bit of work but hopefully it won't be very hard.


'Image Export Name' cleared when I'm wrinting

Bug Description
The text i'v write in Image Export Name is removed.
To Reproduce
Select the image and click on plugin tab to set name, when I write some thing in filed It's cleared.
Versions:

OS: Win 10
XD: 42.022.11
plugin: 2.0.0
Flutter: 2.2.3

This seems to be working to me:

Could you provide more information and reopen this issue? Are other text fields in the plugin working? Is this intermittent or consistent? Is it clearing as you type, or when you exit the field?


removing service bus bindings and templates

fixes #104

@alrod can you review

@soninaren, looks good


Adding CSS to the dropdown box of every option on the home page

Is there an existing issue for this?

[x] I have searched the existing issues

Describe the bug
The dropdown menu is lacking some design and doesn't look much attractive.I can make it look more eye-catchy and user experience will be improved.
What happened?
No response
Expected behavior
No response
Screenshots
No response
Record

[X] I agree to follow this project's Code of Conduct
[X] I'm a GSSOC'24 contributor
[X] I want to work on this issue

@arghadipmanna101 Please assign me this issue. I want to work on it


gopkgs: unstable-2017-12-29 -> 2.0.1

Motivation for this change
Bump gopkgs to latest release (and thus remove unstable)
Things done

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)

[x] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[x] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
[x] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[x] Fits CONTRIBUTING.md.

@GrahamcOfBorg build gopkgs

Success on x86_64-darwin (full log)
Attempted: gopkgs
Partial log (click to expand)
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
find: '/nix/store/c6gglkxlkgvp1qjysdvjiv29911ga3wv-gopkgs-2.0.1': No such file or directory
/nix/store/9c2h55lp3a793gibgk20jijsk1dll7yb-gopkgs-2.0.1-bin

Success on x86_64-linux (full log)
Attempted: gopkgs
Partial log (click to expand)
shrinking RPATHs of ELF executables and libraries in /nix/store/4nwfkffhd8pnkz4zl37l0pskkwbrrkxi-gopkgs-2.0.1-bin
shrinking /nix/store/4nwfkffhd8pnkz4zl37l0pskkwbrrkxi-gopkgs-2.0.1-bin/bin/gopkgs
cannot find section .dynamic
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/4nwfkffhd8pnkz4zl37l0pskkwbrrkxi-gopkgs-2.0.1-bin/bin
patching script interpreter paths in /nix/store/4nwfkffhd8pnkz4zl37l0pskkwbrrkxi-gopkgs-2.0.1-bin
checking for references to /build in /nix/store/4nwfkffhd8pnkz4zl37l0pskkwbrrkxi-gopkgs-2.0.1-bin...
cannot find section .dynamic
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
/nix/store/4nwfkffhd8pnkz4zl37l0pskkwbrrkxi-gopkgs-2.0.1-bin

Success on aarch64-linux (full log)
Attempted: gopkgs
Partial log (click to expand)
shrinking RPATHs of ELF executables and libraries in /nix/store/2ips2l5mq1i29h3lfyr5bh8ksr767r6y-gopkgs-2.0.1-bin
shrinking /nix/store/2ips2l5mq1i29h3lfyr5bh8ksr767r6y-gopkgs-2.0.1-bin/bin/gopkgs
cannot find section .dynamic
strip is /nix/store/y4ymnvgxygpq05h03kyzbj572zmh6zla-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/2ips2l5mq1i29h3lfyr5bh8ksr767r6y-gopkgs-2.0.1-bin/bin
patching script interpreter paths in /nix/store/2ips2l5mq1i29h3lfyr5bh8ksr767r6y-gopkgs-2.0.1-bin
checking for references to /build in /nix/store/2ips2l5mq1i29h3lfyr5bh8ksr767r6y-gopkgs-2.0.1-bin...
cannot find section .dynamic
strip is /nix/store/y4ymnvgxygpq05h03kyzbj572zmh6zla-binutils-2.30/bin/strip
/nix/store/2ips2l5mq1i29h3lfyr5bh8ksr767r6y-gopkgs-2.0.1-bin


[Question] : Is it faster than Dictionary in C#

A key value database is basically a dictionary so wouldn't .NET Dictionary be already enough

UltraLiteDB is in fact slower than a dictionary. This is a database library, which allows you to keep a large key-value stores out of RAM and on disk in a permanent way. Use this is you have a large dictionary that you want to look up values from without having to have the whole thing loaded at all times, or when you want your changes to be saved after your application restarts.


4.0.0 roadmap

[x] deps update
[x] use es6
[x] cleanup assets, move to npm
[x] understand short repo links nodeca/ndoc, generate homepage from it
[x] drop fstools (glob + mkdirp)

Short repo link do not require any changes - replace {package.homepage} with https://github.com/{package.repository} and everything will work.


Distinguish schema node namespace/prefix from namespace/prefix yang statements. E.g. for belongs-to { prefix }

Separate the prefix/namespace attributes of each schema-node inherited through origin module from  prefix/namespace yang sub-statement attributes, e.g. import { prefix } and belongs-to { prefix }.

I have been pondering this for a long time. Like the initial stuff didn't feel right and we got a collision, clearly we want to have proper cardinality / non-optional for Module.namespace and Module.prefix, whereas I think node_namespace must be optional.

I'd prefer a shorter name, how about s/node_namespace/ns/g?
Do you reckon we need a node_prefix at all? I added prefix early on but I think that was a mistake, like maybe I was thinking of how extensions have a prefix or type names have a prefix part, but do we really need a prefix attribute at all? If we do, how about pfx?

I'm renaming node_namespace -> ns. Also I think it's a good idea to remove the inherited prefix field. Especially when doing module bundle compilation having the local prefixes resolved into proper global namespaces as soon a possible will simplify things.

LGTM. I can't help but wonder if this breaks extensions, which is sort of lacking test cases. I'll fix that separately, if that's the case. Merging.


[Bug]: Outdated pyautogen package gets installed under Python 3.12

Describe the bug
Outdated pyautogen package gets installed under Python 3.12
Steps to reproduce

conda create -n testversion
conda install python=3.12
pip install pyautogen

Outputs:
Successfully installed NumPy-1.26.3 aiohttp-3.9.1 aiosignal-1.3.1 attrs-23.2.0 certifi-2023.11.17 charset-normalizer-3.3.2 diskcache-5.6.3 flaml-2.1.1 frozenlist-1.4.1 idna-3.6 multidict-6.0.4 openai-0.28.1 pyautogen-0.1.14 python-dotenv-1.0.0 requests-2.31.0 termcolor-2.4.0 tqdm-4.66.1 urllib3-2.1.0 yarl-1.9.4
Expected Behavior
Should be an error saying no package found.
Screenshots and logs
No response
Additional Information
No response

@sonichi


Feature/improve components

SUMMARY
What type of PR is this? (check all applicable)

[ ] - ♻ Refactor
[ ] - ✨ Feature
[ ] - 🐛 Bug Fix
[ ] - 👷 Optimization
[ ] - 📝 Documentation
[ ] - 🔖 Release
[ ] - 🚩 Other

DETAILS

Closed as this was already merged to main branch


fix several bugs

Codecov Report

Merging #329 into release-rc4 will increase coverage by 0.14%.
The diff coverage is 19.31%.


Errors in Winton and Semtner thermodynamics

There are errors in the neXtSIM Lagrangian implementation of the Winton (2000) and Semtner (1976) thermodynamics models.

In the Winton model, I use "I = I_0*Qsw" without taking into account that I_0 is 0 with (thick enough) snow cover
In the Semtner model, I don't apply the gamma fudge factor, and only the beta fudge factor through the albedo scheme - but not the one we usually use.

Both errors stem from improper treatment of the penetration of short-wave radiation into the ice, so a fix to both fits together.
These are being addressed in neXtSIM Lagrangian by adding I (the penetrating short-wave radiation) as an output to IABulkFluxes and using this in the Winton and Semtner models. A similar approach should be taken in neXtSIM_DG.

Fixes implemented and merged.


Dont change color if Cancel pressed, and open with initial color.

I take it this is the fix for the bug with the colorpicker returning None's? I'll take a look at it and will most likely add it in.

Yes, and it also makes the colorpicker default to whatever is the current color.
Only tested on Linux btw.


refactor(@vtmn/css): badge, text-input, button

…dicated class
Pull Request checklist
🚨 Please review the guidelines for contributing to this repository.

[x] Make sure you are requesting to pull a topic/feature/bugfix branch. Don't request your main!
[x] Check the commit's or even all commits' message styles matches our requested structure.
[x] Check your code additions will fail neither code linting checks nor unit test.
[x] Check PR name, it must follow the https://www.conventionalcommits.org pattern
[x] If it's a new component in CSS, ask for design review

Description

Button is now aligned with the the flex property, it removes some useless variables and remove some display bug of height sometimes
Badge no longer requires the class vtmn-badge--without-icon as it is now managed by a pseudo selector
Some useless classes have been removed for the text-input, no impact
In storybook, the block class is now flex and display things in row with tailwind classes. Some components' showcases have been updated but it changes nothing visually
Links and Badges now have a default font-weight.
The Button inside Popover is now a primary-reversed instead of a tertiary variant. It has changed due to accessibility reasons.

Does this introduce a breaking change?

Yes : The class vtmn-badge--without-icon can be removed safely as it is now managed with a css pseudo-selector :empty

Other information

❤ Thank you!

Thanks @GaspardMathon, amazing work :tada:


Update to new MahApps version; Bugifx in "Must.NotBeEmpty"; Window CenterOnOwner

Must.NotBeEmpty rule was not working if field was initialized with an empty string.
Version of MahApps was obsolate.

Thank you for your PR! I appreciate that you found and fixed the validator bug.
I suggest we slim changes down to the minimum:

Add the validator bug fix.
Update Mahapps and required resource keys.

The other package stuff I'd leave unchanged (at least for now) because they could cause unexpected breaks for consumers.
I could help out with this during the weekend.

Thanks for reviewing. Sorry, it seems that my visual studio has some configuration that does not fit to your needs. But it seems that you have picked the right stuff, thats good! It would be good if you also take the CenterOwner configuration as well as setting the owner of the dialog window to the current app, so it will be displayed in the center of the screen.
Thank you very much for the project anyway. i will contrubute on this as good as i can!

Thanks! Yes, we'll take only the relevant parts.

if you also take the CenterOwner configuration as well as setting the owner of the dialog window to the current app, so it will be displayed in the center of the screen.

I agree. It should have been the default behavior.