Feature/support strings in setters

Related to https://github.com/shkm/enummer/issues/13
When dealing with forms, values will be received as strings. This pull request adds a simple .to_sym method when serialising the array.
I also added a little hint about how to run tests locally

@luctus looking good! Would you mind removing the coverage folder and squashing down to one commit? Thanks!

@luctus looking good! Would you mind removing the coverage folder and squashing down to one commit? Thanks!

Great to hear! sure thing, I'll add that coverage folder to the .gitignore too.


Abundance classification

This PR implements abundance classification that is introduced in this paper:
Sizhong Yang, Matthias Winkel, Dirk Wagner, Susanne Liebner, Community structure of rare methanogenic archaea: insight from a single functional group, FEMS Microbiology Ecology, Volume 93, Issue 11, November 2017, fix126, https://doi.org/10.1093/femsec/fix126
New functions include:

getAbundant(): taxa above abundance threshold
getLowAbundant(): taxa below abundance threshold (and between conditionally & permanently rare thresholds)
getPermanentlyRare(): taxa below abundance threshold and below permanently rare threshold
getConditionallyRaret(): taxa below abundance threshold and above conditionally rare threshold

TODO:

[ ] Update documentation
[ ] Clean code and check that everything works
[ ] Add unit tests
[ ] Consider names getPermanentlyLowAbundant() and getConditionallyLowAbundant(). They are longer but more distinct from getRare() which is based on prevalence.

Is getLowAbundant needed if it is just a complement of getAbundant?

Abundant taxa: Taxa with an average abundance exceeding abundant.th.

Low abundant / rare taxa: Taxa with an average abundance not exceeding abundant.th. Optionally, if specified, they must also satisfy the condition:
condition.th >= (abundance_max / abundance_min) > permanent.th.

Conditionally rare taxa (CRT): Taxa with an average abundance not exceeding abundant.th and with a maximum-to-minimum abundance ratio (abundance_max / abundance_min) greater than condition.th.

Permanently rare taxa (PRT): Taxa with an average abundance not exceeding abundant.th and with a maximum-to-minimum abundance ratio (abundance_max / abundance_min) less than or equal to permanent.th.

In the simplest case it is complement, but in the article they further classified the rare taxa

Is the Shade et al. manuscript also taken into account?

See: https://github.com/microbiome/miaTime/pull/103


Restore Message from Symfony email

What steps will reproduce the problem?
$originalMessage = Yii::$app->mailer->compose()
<EMAIL_ADDRESS><EMAIL_ADDRESS>    ->setTextBody('Test')
    ->attach('/path/to/attachment.pdf')
    ->setSubject('Test');

 $email = $originalMessage->getSymfonyEmail();

 $restoredMessage = new yii\symfonymailer\Message(['email' => $email]);

What's expected?
A message can be succesfully restored from the source Symfony\Component\Mime\Email object.
What do you get instead?
An yii\base\UnknownPropertyException with the message Setting unknown property: yii\symfonymailer\Message::email.
What is the use-case?
An email queue that stores the message on disk. The Symfony email message can be serialized and stored on disk. However, when it is unserialized there is no way to restore the yii\symfonymailer\Message object and send it.
Additional info

Q
A

Yii version
<IP_ADDRESS>

Yii SymfonyMailer version
2.0.4

SymfonyMailer version
v6.4.4

PHP version
8.1.27

Operating system
Debian

I have come to understand this is a non-issue since the Message object itself can also be serialized.

I have come to understand this is a non-issue since the Message object itself can also be serialized.

Could you please explain a bit further how you solved this?


Collectable Model

An ID field to uniquely identify Collectables may work better than using the name of the Collectable. Depending on if we would like Collectables to be able to have the same name or not.


Hope to add feature: set default shell

Is your feature request related to a problem? Please describe.
When my system's shell is bash, but I want to use fish as my terminal shell, I find that currently I can't do that.
Describe the solution you'd like
I want to add a setting that allows users to set the default shell for the terminal.

I also wanted to change the shell to fish, which is set as my default, as soon as I found out that the shell doesn't behave normally. I was surprised to see that the terminal doesn't respect the system defaults, and furthermore that it's not shell-agnostic.

it should respect the default system shell. i use fish, so this is a deal breaker for me.

Agree with the sentiment, please consider making the product shell-agnostic.
This would even engage windows users who are stuck in WSL trying to deploy Wave or powershell perhaps.

Sadly warp doesn't care about fish users either.. oh well, back to the default terminal then I guess.

bu bye (need fish compat).

Related to #144 ?

Since this is legacy now and all shells are supported. It should be pretty easy to let the user choose, which shell is used by default for a terminal block, in the config.

So fish works now?

Yes. You can find the exact setting on the configuration-page on the website. You will have to edit the config-file and set the default shell path for new terminal blocks to fishs path.

Thanks that does give me fish but none of my opening config files seem to run.

@jubishop does fish load different settings files depending on whether it was launched as a "login shell" or not? I wonder if waveterm does or does not launch shells in this mode?

Yes it does but even basic etc/profile isn’t running which should be fired
further up stack from anything fish is doing
cheers,

Justin Bishop http://jubishop.com/

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Reply to this email directly, view it on GitHub
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Thanks! This let me finally migrate to Wave from Warp.


Time series analysis

This issue is to write down the idea about time series analysis on the data.

Is it possible to capture the increasing/decreasing trend at each location? Downtown / others?
Is there any difference between summer and other seasons since the students will be out?

Time series analysis would be better suited for Bullet 2, whereas k-means clustering would be better suited for Bullet 1, no?


Various fixes for modular code gen

This PR contains various fixes for modular code gen.
How to reproduce the issues I've fixed:

Enable modular code gen
Add views to .drift files (which listens to a table from another file)
Add .drift file with table but NO queries (select/insert/update/delete) and then add it to a join in another file
add query that DOES insert/update/delete

I've removed my attempts to fix the unneeded modular accessor getters

Thanks for the additional fixes. I've added a view to the examples/modular project and I can see that the problems there are fixed.  I've also separated the users.drift file into one table file and a query file in an attempt to reproduce the other issues, but I'm not entirely sure if I got that right.

A workaround is just to create a query in the .drift file

If it's easy to reproduce, can you bring the examples/modular example in this repository into a state where an accessor should be generated but isn't? I'd love to take a look at what's happening in the analyzer for that case, this sounds like something that really should be fixed.

If it's easy to reproduce, can you bring the examples/modular example in this repository into a state where an accessor should be generated but isn't? I'd love to take a look at what's happening in the analyzer for that case, this sounds like something that really should be fixed.

Sure can do. The problem is actually the opposite. An

Drift get
Drift => this.accessor('table') is created when
Drift doesn't exist (because the .drift file didn't have any queries) because a different .drift file referenced the table.

I think I managed to fix the unnecessary accessors being generated. Thanks for all your help!

Its fixed all of my previous issues, however it has introduced a new issue.
I have a .drift file which has:

imports other .drift files (for foreign keys)
creates table

Then i have another .drift file which:

imports the previous .drift file
uses it in a join

Then second is trying to create an accessor to the first, but first doesn't have a ModularAccessor class.

Here is a sample project:
https://github.com/North101/moor/tree/modular_gen_bug/examples/modular2

Thanks! Should be fixed in fb3d832f0f4b145dc197e35cb75629f4fb6f38be.

Thats all of my issues solved. Thanks!


Extensions for subtype of a class marked @Observable generate compile error

Description
I cannot add a subtype (class, enum, struct) to a class marked with @Observable macro. If I add an extension to this subtype, I get compile error:

Circular reference resolving attached macro 'Observable'

Steps to reproduce
@Observable
class MyObservableClass {
    var property1 = ""
    var property2 = MyClass()
}

extension MyObservableClass {
    class MyClass {
        var property = ""
    }
}

extension MyObservableClass.MyClass {
    var test: String { "test \(property)" }
}

Expected behavior
It must be compilable because the following version is compilible:
@Observable
class MyObservableClass {
    var property1 = ""
    var property2 = MyClass()
}

extension MyObservableClass {
    class MyClass {
        var property = ""
        var test: String { "test \(property)" }
    }
}

Environment
Xcode 15.0 beta (15A5160n)
Swift 5.9
Target: iOS 17.0

@Model has the same problem. Do all macros exhibit it?

@JessyCatterwaul Yes. It's always the same pattern.
TypeA with a Macro
extension type B nested in type A
extension for type B → compile error

Are there any workarounds around this issue?

One workaround is to place the extension(s) in a separate file.

Just ran into this as well; here's a perhaps even more minimal example:
@Observable
final class Outer {
	struct Inner {}
}

extension Outer.Inner {}

+1 to this issue being a problem that definitely comes up quite a bit in every day work.
Also, regarding this:

One workaround is to place the extension(s) in a separate file.

This can work most of the time, but sometimes it can be difficult. For example a macro applied to a generic type that needs to conditionally conform to Equatable:
@SomeMacro
struct Wrapper<T> { var value: T }

extension Model: Equatable where T: Equatable {}  // 🛑 Circular reference

If this extension is moved into a separate file then you lose the automatic synthesis of Equatable, and so that is unfortunate.

Add a new case:
enum Namespace {
    @SomeMacro
    struct SomeStruct { }
}

extension Namespace.SomeStruct { }  // 🛑 Circular reference

Hello, any progress here?

We shipped a few macros this week and have had about a dozen folks report this bug to us. Would be nice to have the issue triaged.

It seems that this issue has been fixed in Xcode 15.1 Beta 3.

It seems that this issue has been fixed in Xcode 15.1 Beta 3.

Hi @DevYeom, I am not able to confirm this. Both the example provided in this issue still fails to compile:

As does a simpler repro of the problem:

I am using Xcode 15.1 beta 3 (15C5059c) to test this. Can anyone else confirm that it is fixed?

I'm so sorry for my misleading.
The issue I had was not related to @Observable, but rather with the custom member macro I created.
The message I encountered was as follows, and it was resolved in Xcode 15.1 Beta 3.

Circular reference expanding member attribute macros on 'Something'

With the amount of macros being utilized now by many libraries, including Apple's this problem becomes much more prominent, and also very cryptic to even understand that the harmless extension is causing it. Hope it will get addressed.

It'd be nice to at least have some acknowledgement of the problem from the core team. While we understand that there are plenty of bugs out there that need attention and triage, this one has quite a bit of activity and reach, and was opened pretty promptly the week of WWDC23.

A class of these circularity issues were fixed by https://github.com/apple/swift/pull/67689, which is included in Xcode 15.1 Beta 3 where some folks are seeing their specific test cases resolved. However, the circular reference while resolving macro 'X' errors can be manifestations of slightly different circularity paths in the type checker, which is why other people are still seeing the issue.

Would love to see this fixed please!!

Checked the latest snapshot this morning and sadly this is still a problem!

NOOOOOOOOOOO!!!
Posting this has worked in another open-source project, so maybe it will work here! If we all collectively pray to the patron saint of computer programming, Saint Isidore of Seville, perhaps it will be addressed very soon 🙏

Also experiencing this issue

Still seeing in Xcode 15.3 and Swift 5.10, as well.

Please give some love to this issue, Swift core team! ❤🙏

Yup this is a pretty bad one especially since it's a huge challenge for macros which make these extensions in the same file.

This is fixed in https://github.com/apple/swift/pull/71365

@hborla Awesome! Would you know if we planned to patch this on the 5.10 branch?

@hborla , thank you very much for the fix !
Do u happen to know what release this fix is planned to be included in ?
Would be very nice to get this fix out sooner :)

Reading here and here:

confirmed that Swift 6 will be released this year, replacing the previously anticipated Swift 5.11
...
Swift 6 is set to launch in 2024, alongside Xcode 16 in September, marking the first major update since Swift 5's release five years ago. This update builds on the features introduced in the Swift 5.x series, such as async/await, existentials, and macros.

So seems like the fix will be in upcoming Swift 6, in September


checking pid of the process using tpu

@skye Could you please review this?

@sshahrokhi  Can you please check @skye's comments and keep us posted ? Thanks!

I don't know how I missed the email with @skye's comments on this PR, but thanks a lot for all the great reviews!

I added a two more comments. Feel free to resolve, but this is also fine as-is.

Thanks @skye for the comments, I applied them.


Merge develop into master

Pull Request Test Coverage Report for Build 95

0 of 0 (NaN%) changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 55.556%

Totals

Change from base Build 91:
0.0%

Covered Lines:
50

Relevant Lines:
90

💛  - Coveralls


Error Message

Need to complete a proper error message.

The "Error Handling" (f7848a9) commit prints out error messages for 2 errors. Those errors are invalid user input and when the datafile does not exist.


Soft deletes support in BlobStoreRepository and using it for Remote Store

Description
[Describe what this change achieves]
Related Issues
Resolves #[Issue number to be closed when this PR is merged]

Pending

Performance tests
Failing UT fix

Check List

[x] New functionality includes testing.

[x] All tests pass

[x] New functionality has been documented.

[x] New functionality has javadoc added

[x] Commits are signed per the DCO using --signoff
[x] Commit changes are listed out in CHANGELOG.md file (See: Changelog)

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.
For more information on following Developer Certificate of Origin and signing off your commits, please check here.

Please add PR description and resolve conflicts.

Closing it for now. We will revisit it once we are ready to support it comprehensively .


The latest version - v<IP_ADDRESS> is not available on CocoaPods

The previous version is available on CocoaPods and we can ingest it into our iOS project as below:
pod 'OneDsCppSdk.iOS', '<IP_ADDRESS>'

However, the latest version - v<IP_ADDRESS> is not available on CocoaPods.
Please publish the latest build to CocoaPods so we can upgrade.
Thanks.

@guojiubo - The 1DS maintainers doesn't publish CocoaPods version. It is community-driven. And would suggest you to publish one if required.


Exporting node types

is there any way to export node types via some endpoint / similar feature like: https://www.bounteous.com/sites/default/files/export-node-frpm-crx-lite.png
?
sample output file nodetypes.cnd:
<'sling'='http://sling.apache.org/jcr/sling/1.0'>
<'nt'='http://www.jcp.org/jcr/nt/1.0'>
<'oak'='http://jackrabbit.apache.org/oak/ns/1.0'>
<'jcr'='http://www.jcp.org/jcr/1.0'>
<'mix'='http://www.jcp.org/jcr/mix/1.0'>
<'rep'='internal'>
<'slingevent'='http://sling.apache.org/jcr/event/1.0'>

[sling:OrderedFolder] > sling:Folder
  orderable
  + * (nt:base) = sling:OrderedFolder version

[oak:Unstructured]
  - * (undefined) multiple
  - * (undefined)
  + * (nt:base) = oak:Unstructured version

[nt:linkedFile] > nt:hierarchyNode
  primaryitem jcr:content
  - jcr:content (reference) mandatory

seems that https://jackrabbit.apache.org/api/2.12/org/apache/jackrabbit/spi/commons/nodetype/compact/CompactNodeTypeDefWriter.html need to be used and exposed in some servlet:
  final CompactNodeTypeDefWriter cnd = new CompactNodeTypeDefWriter((Writer)res.getWriter(), session, true);
            final NodeTypeIterator iter = session.getWorkspace().getNodeTypeManager().getAllNodeTypes();
            while (iter.hasNext()) {
                cnd.write((NodeTypeDefinition)iter.nextNodeType());
            }
            cnd.close();

I need this to be able to provide nodetypes.cnd file to OakPAL tool which validates packages before installing them on Sling.

What do you actually need here - an export of one or several nodetypes given in the request (e.g. all nodetypes whose name is matching a given pattern), or the export of the nodetype(s) that apply to a given resource, or something else?

@stoerr as you can see on snippet above, it prints all nodetypes registered in oak repository. I need them to perform offline validation of package to be deployed using in-memory oak repository which will be fed by exported node types using this missing endpoint/servlet.

all nodetypes whose name is matching a given pattern

all node types without any filtering.

@pun-ky Since you asked so nicely :-) and even provided the crucial code yourself, I whipped up a quick implementation for that. I hope that's what you need - it's in the new release 1.2.12 of the composum core. It's URL is /bin/cpm/nodes/debug/nodetypes and has an optional nameregex parameter where you could restrict the types if you need to - since you don't it's fine if you skip it and thus get everything. I also provided it in form of a Sling console plugin, since that was the form in which I had wished for it sometimes. Please let us know if there is some trouble.

It's okay. Thank you very much 👌🙂


Enabled stale bot.

Proposing this as discussed on Thanos sync.
Closing Thanos issues after 90 days
Signed-off-by: Bartek Plotka<EMAIL_ADDRESS>

This is quite spammy change, as many issues will be closed (: Waiting for more approvals for this!

This did not work... Plan to move to: https://github.com/actions/stale on GH action where we have more insight as it's just a cron CI job


Use meson for Unix build as well so that .pc files are provided

Checklist

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

As with the Windows build (#16), apparently missing pkg-config files are causing problems on the Unix side as well. It seems that pygobject has been failing to find pycairo and instead succeeding by building pycairo as an in-tree subproject, resulting in bits of pycairo (including a header, the py3cairo.pc file, and a Python egg file) being included in the most recent Linux/OSX builds.
This switches to using meson for the Unix build as well, since it provides the necessary pkg-config files. I also added pytest testing for parity with the pygobject build.

Hi! This is the friendly automated conda-forge-linting service.
I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.
I do have some suggestions for making it better though...
For recipe:

License is not an SPDX identifier (or Other) nor an SPDX license expression.

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

pypy is unhappy, and it looks like a disagreement between meson and conda-forge as to where the pypy python libraries should be installed.
Meson:
$PREFIX/lib/pypy3.6/site-packages/cairo

Pip/existing package:
$PREFIX/lib/python3.6/site-packages/cairo

I don't think there's a way to tell meson to put them somewhere else, so the best option would probably be to move them manually.


Temperature adjustment fixed for temperature sensors

In device edit window you can fill in an adjustment for the temperature.
Filling in any value did not have any effect on the temperature registered.
This change implements this functionality

Thanks!


Events don't bind to labels

onclick, onmouseover, etc. do not bind to the label text box.
This can be pretty confusing for users; they'll expect that the title will also trigger events (e.g., such as displaying a modal with information about phase changes or events in a data set).

Looks like a bug in the event handler code. I'm happy to look at a PR fixing this


Error:

The Plugin is not working, it's showing: Could not load icon 'icons/icon16.png' specified in 'icons'.
Could not load manifest.
What to do?


CAPI: Pagination List All + tag fix

Add pagination + tag fix
Seems like the last PR on this file removed all the quotes around the json keys.
in order to avoid a large PR and risking editing the wrong portion of the doc I just pasted my changes for the GET /list endpoint

🚀 Deployed on https://657ba2d3b7c5af09b6f97064--cozy-fox-0defec.netlify.app


[BUG] Can't paint foliage at all in Godot v3.4.4 stable mono official on Windows 11

v3.4.4 stable mono official (419e713a2)
Gardener 1.0.0
Windows 11
Issue description
Foliage cannot be painted. I setup Gardner according to the documentation, set collision layers, add a mesh and try to drag with the left mouse button in the viewport. Nothing happens, the bubble does not move at all. I can however resize the bubble via right click and drag.
Steps to Reproduce
Create a new Gardener object in the scene
Add a mesh. I add an obj file, as I don't have mesh files - the file filter does not permit it but it seems to be displayed properly in the small preview rectangle.
Select the mesh as foliage and try to paint it by left clicking and dragging - nothing happens, the bubble won't even move. No errors are displayed in the console.

Did you set up collisions for your mesh?

Yes, please make sure you've set up a Physics Body (preferably static) and collision shapes (with proper layers) for you landscape.

I have tested painting using a demo project included in Releases, and had no trouble whatsoever.
Report if you still experience this issue after setting up the landscape body+collision.

Thanks, setting up a static body with a collision shape solved the problem. Sorry for the false positive.


IkigaJSON does not support swift5?

When I used LkigaJSON for ios application in xcode 10.2, I found that swift5 was not supported.

It should work just fine. I'm regularly behind in releasing cocoapod builds compared to SPM builds since my personal primary use cases target SPM. However, my own iOS project running Swift 5 is compiling just fine. Could you post some details about the error you're finding?

You create an ios project, and then pod 'IkigaJSON', '>= 1.1 ', buid it with an error.

I figured out this morning that SwiftNIO 1.x only supports Swift 4.x compilation mode. But Cocoapods seems to configure that just fine on my end. Things only start failing once I explicitly change its compilation mode to 5.0. Is that what you're doing?

I released a 2.x IkigaJSON built on top of SwiftNIO 2.0 made only for Swift 5.


Erase output after stopping spinner

This should prevent any "leftovers" from the spinner which is useful especially when there's further output being written after stopping the spinner and spinner & output would clash otherwise.

Apparently there's an assumption that it's already happening, but it's not... not sure if there's any better way of fixing it.

Sorry for the delay.  Thanks for the work on this!

Eh, delay? Like 6 hrs you mean? :smiley: That's actually quite an amazing reaction time!
Thank you!

I'm honored that people would use or improve my code so the least I can do is be prompt. :D


Check for existence of pygments css file before overwriting it

When there is no pygments.css files in _static (for whatever reason, see below for more context), then furo's build_finished hook fails with the following error:
Handler <function _overwrite_pygments_css at 0x7fdd1d8aeee0> for event 'build-finished' threw an exception (exception: [Errno 2] No such file or directory: '/sage/local/share/doc/sage/inventory/en/reference/_static/pygments.css')

This is fixed by first checking for the existence of this file, before we attempt to overwrite it.
Context: In sage, we use a custom html builder that preprocesses the documentation files and extracts inventory files for intersphinx (see https://github.com/sagemath/sage/blob/develop/src/sage_docbuild/ext/inventory_builder.py). In this preprocessing step, we don't generate any html and also don't have a _static directory.

Hiya! Thanks for this PR.
Just to make sure I understand what this is for, is there a specific reason that Sage uses an HTML builder for being able to process the intersphinx file? Would it be possible for that builder to be a non-html builder (eg: Sphinx's linkcheck is done in a custom builder, if I remember correctly)

Thanks for your suggestion. I've played around a bit and used the DummyBuilder (that linkcheck is also using) and it seems to work well.
So it appears that my original motivation for this PR is gone. I leave it up to you to decide if you want to include the change nonetheless.

In that case, this is not needed. Thanks for the PR and for looking into alternative approaches! :)


bcftools overlapping variants issue

Hey there.
Getting an error on the last step in the medaka workflow
bcftools consensus -f PQPR059970.preconsensus.fasta PQPR059970.pass.vcf.gz -m PQPR059970.coverage_mask.txt -o PQPR059970.consensus.fasta

It gives me the following
Note: the --sample option not given, applying all records regardless of the genotype
The fasta sequence does not match the REF allele at MN908947.3:6312:
   .vcf: [C]
   .vcf: [A] <- (ALT)
   .fa:  [N]AAAACCAGTTGAAACATCAAAT.......rest of the reference........

This seems to relate to these 2 issues from bcftools
https://github.com/samtools/bcftools/issues/961
https://github.com/samtools/bcftools/issues/600
That they fixed using the latest github builds, rather than the 1.9 release.
I'm in the middle of compiling bcftools from source to give this a test to see if it fixes it.
I'll let you know how that goes.
Cheers
James

Yea, using
bcftools 1.10.2-86-ge313e0f
Using htslib 1.10.2-85-g16f62c5

didn't fix it. sigh. Any thoughts?

I can second that. Had multiple instances where this happened. I was not able to generate a consensus sequence here.
Is there any possibility you can check out https://github.com/samtools/bcftools/commit/21fd8dad371f191c2fbdcc1e18ea1ed1268962bf and update bcftools in the pipeline?

I can second that. Had multiple instances where this happened. I was not able to generate a consensus sequence here.
Is there any possibility you can check out https://github.com/samtools/bcftools/commit/21fd8dad371f191c2fbdcc1e18ea1ed1268962bf and update bcftools in the pipeline?

Hi,
We saw this issue too. The root cause is mainly because XXX.pass.vcf and XXX.fail.vcf gave different mutation description for same loci of genome. To be more specific, for example, loci 7065 in XXX.fail.vcf showed “GA -> G”, which means loci 7066 is deletion, but XXX.pass.vcf showed loci 7066 is a “A-G” SNP. Then what ARTIC will do is to follow the fail.vcf to mask loci 7066 as “N” in your preconsensus.fasta via “artic_mask” first. Then try to generate consensus using the SNP described in pass.vcf (it will give the error you described since the pass.vcf showed the 7066 is “A”, but in preconsensus.fasta, it was changed to “N” already).
The in-house fix in our team is to scan each described mutation in both vcf files (for the failed assemblies only), in cases of discordance at the same loci, use the mutation found in XXX.pass.vcf (higher quality ones) when creating consensus assembly, and ignore the XXX.fail.vcf call (low-quality ones). Then you can continue the rest of artic steps using the newly generated vcf files (use artic_mask to generate the preconsensus.fasta, then use the above mentioned command to generate consenus via bcf_tools).
Also there might be source code based fixes already in the live code of artic (https://github.com/artic-network/fieldbioinformatics), the version here is for Artic network SOP which is not that frequently updated.
Hope it can help you.
Regards,
Shaokang

Hi,
We saw this issue too. The root cause is mainly because XXX.pass.vcf and XXX.fail.vcf gave different mutation description for same loci of genome. To be more specific, for example, loci 7065 in XXX.fail.vcf showed “GA -> G”, which means loci 7066 is deletion, but XXX.pass.vcf showed loci 7066 is a “A-G” SNP. Then what ARTIC will do is to follow the fail.vcf to mask loci 7066 as “N” in your preconsensus.fasta via “artic_mask” first. Then try to generate consensus using the SNP described in pass.vcf (it will give the error you described since the pass.vcf showed the 7066 is “A”, but in preconsensus.fasta, it was changed to “N” already).
The in-house fix in our team is to scan each described mutation in both vcf files (for the failed assemblies only), in cases of discordance at the same loci, use the mutation found in XXX.pass.vcf (higher quality ones) when creating consensus assembly, and ignore the XXX.fail.vcf call (low-quality ones). Then you can continue the rest of artic steps using the newly generated vcf files (use artic_mask to generate the preconsensus.fasta, then use the above mentioned command to generate consenus via bcf_tools).
Also there might be source code based fixes already in the live code of artic (https://github.com/artic-network/fieldbioinformatics), the version here is for Artic network SOP which is not that frequently updated.
Hope it can help you.
Regards,
Shaokang

Hi @Psy-Fer,  @mi-koch and @Shaokang123
Firstly - sorry for not replying sooner (in particular to @Psy-Fer...). This sounds like something that needs fixing - I will open an issue over in the artic pipeline repo. Before I do, can @mi-koch and @Psy-Fer confirm if @Shaokang123's suggestion would explain their issue?
The explanation makes sense to me - the pipeline would fall over at the consensus step if we had overlapping vars in the PASS/FAIL. That being said, I'm not sure if we want to rescue these sites - the mask might be the preferred behaviour in the case of uncertainty with respect to the reference.
Either way, this needs a fix. The question is, do we mask in this scenario or do we rescue the pass variant. I think we default on one and then offer a flag to do the other. In the next pipeline release we have a --strict flag which performs some more stringent vcf checks prior to masking, maybe the strict mode could also tackle this. Thoughts @nickloman ?

Hi @Psy-Fer,  @mi-koch and @Shaokang123
Firstly - sorry for not replying sooner (in particular to @Psy-Fer...). This sounds like something that needs fixing - I will open an issue over in the artic pipeline repo. Before I do, can @mi-koch and @Psy-Fer confirm if @Shaokang123's suggestion would explain their issue?
The explanation makes sense to me - the pipeline would fall over at the consensus step if we had overlapping vars in the PASS/FAIL. That being said, I'm not sure if we want to rescue these sites - the mask might be the preferred behaviour in the case of uncertainty with respect to the reference.
Either way, this needs a fix. The question is, do we mask in this scenario or do we rescue the pass variant. I think we default on one and then offer a flag to do the other. In the next pipeline release we have a --strict flag which performs some more stringent vcf checks prior to masking, maybe the strict mode could also tackle this. Thoughts @nickloman ?

I generally agree we'd mask a site that was in conflict pass and fail in the overlap, as the pipeline is intended to be conservative. You could maybe add an option to allow such sites to be rescued.

I generally agree we'd mask a site that was in conflict pass and fail in the overlap, as the pipeline is intended to be conservative. You could maybe add an option to allow such sites to be rescued.

Dear all,
thank you all for the responses. I was also digging around in the vcf files but was not able to tackle the issue. Thanks for the input @Shaokang123!
Since running everything with artic 1.1.3 now, this problem did not occur anymore. I also re-ran the failed samples with 1.1.3, which ended up in consensus sequences being produced. So all good from my side!
Thanks again for all the effort!

Dear all,
thank you all for the responses. I was also digging around in the vcf files but was not able to tackle the issue. Thanks for the input @Shaokang123!
Since running everything with artic 1.1.3 now, this problem did not occur anymore. I also re-ran the failed samples with 1.1.3, which ended up in consensus sequences being produced. So all good from my side!
Thanks again for all the effort!

Hi @will-rowe and @nickloman,
Thanks for your comment.
In our particular in-house test, this error only occurred when there was a conflict between “indel of fail.vcf” and “SNP of pass.vcf”. In one of our tests, we have a few datasets using same single sars-cov-2 sample with high repeat number (n=32), and only 1 or 2 out of the 32 repeats have the conflicted indel description in the fail.vcf, which indicates the one in fail.vcf is a false positive report. In addition, here I also uploaded one pair of the vcf files, in which the loci 7066 in pass.vcf (SNP) and loci 7065 in fail.vcf (indel) have conflicts. The quality descriptions support pass.vcf much more (high DP and high score), indicates the false positive indel in fail.vcf is likely caused by some ONT noises.
So our in-house solutions in our particular cases to support pass.vcf are based on above mentioned test and data. But I also agree with @nickloman to make it conservative. So I would think to add a flag like “--strict” and let the users to tweak and decide by themselves to mask the conflict loci or use the high quality ones may be the best in next artic release.
vcfs.zip
Regards,
Shaokang

Hi @will-rowe and @nickloman,
Thanks for your comment.
In our particular in-house test, this error only occurred when there was a conflict between “indel of fail.vcf” and “SNP of pass.vcf”. In one of our tests, we have a few datasets using same single sars-cov-2 sample with high repeat number (n=32), and only 1 or 2 out of the 32 repeats have the conflicted indel description in the fail.vcf, which indicates the one in fail.vcf is a false positive report. In addition, here I also uploaded one pair of the vcf files, in which the loci 7066 in pass.vcf (SNP) and loci 7065 in fail.vcf (indel) have conflicts. The quality descriptions support pass.vcf much more (high DP and high score), indicates the false positive indel in fail.vcf is likely caused by some ONT noises.
So our in-house solutions in our particular cases to support pass.vcf are based on above mentioned test and data. But I also agree with @nickloman to make it conservative. So I would think to add a flag like “--strict” and let the users to tweak and decide by themselves to mask the conflict loci or use the high quality ones may be the best in next artic release.
vcfs.zip
Regards,
Shaokang

So, just to follow up on 2 options for how we could do this.

prior to generating the consensus, use bcftools norm --check-ref s ... to update the reference sites in *.pass.vcf to reflect any Ns which were introduced as a result of low coverage/fail vars. This will include pass variants from the final consensus at sites where low quality variants are also found / low coverage regions.

run the bcftools consensus command with an exclude statement to ignore any sites which are marked as N in the preconsensus. This will exclude any variants from the final consensus at sites where low quality variants are also found / low coverage regions.

I think in light of the earlier conversation, we want option 2. So I'll add this to the next release PR.


Deployment guide (and more)

(Update) We've started releasing a few deployment guides:

[x] Heroku ⚡ Bolt for JavaScript (released 2020-10-07)

Guide
Pull request

[x] AWS Lambda ⚡ Bolt for JavaScript (released 2020-12-10)

Guide
Pull request

[ ] Container platform

Please leave comments on what guide you'd like next!

Description
Produce a documentation guide which describes the process of deploying a Bolt app to various hosting platforms. This is a list of possible hosting providers, in roughly priority order:

AWS Lambda (most requests to date)
Heroku (easiest) - Deploy to Heroku button
Docker (most wide reach)
Azure (Functions, Web App, etc)
Google Cloud Platform (Firebase, Functions, Cloud Run, etc)
AWS (other services)
Zeit Now
Cloud Foundry
Codesandbox.io

Currently, we believe providers 1 through 4 are substantial enough for the first iteration of this guide.
We are looking for comments regarding:

Which hosting platforms are important to you, or do you think should be prioritized sooner?

Do you have any experience with the specific hosting providers mentioned, and can you advise on strategies you would recommend for the deployment to those providers?

Related work:
General:

[ ] Do we need a custom receiver for any of these deployment targets?
[ ] In serverless environments, how can we preserve the benefits of deploying small functions (independent scaling, cold boot time, etc)? Can we solve this by integrating Bolt with a message queue or similar technology offered by the serverless platform?
[ ] Where should the templatized apps live? How do we reduce code duplication amongst them? AWS Quickstarts seem to all live in the same Org and have a contributors guide. Azure ARMs also seem to live in the same repo, which contains their contributing guide. Should the external repos just contain scripts which clone the one sample code repo?

AWS:

[ ] How can we continue processing a request after the response is ended in Lambda?
[ ] Cloud Formation templates for coordination between AWS services such as Lambda, API Gateway, data storage, etc.
[ ] AWS Quickstarts
[ ] AWS Serverless Application Repository

Heroku:

[ ] "Deploy to Heroku" button, app.json
[ ] Listing on https://elements.heroku.com/ marketplace

Docker:

[ ] docker-compose.yml and Dockerfile
[ ] Host an image on hub.docker.com

Azure:

[ ] Azure Resource Manager (azuredeploy.json) template(s), "Deploy to Azure" button
[ ] ARM template marketplace: https://azure.microsoft.com/en-us/resources/templates/

Requirements (place an x in each of the [ ])

[x] I've read and understood the Contributing guidelines and have done my best effort to follow them.
[x] I've read and agree to the Code of Conduct.
[x] I've searched for any related issues and avoided creating a duplicate issue.

Hello, I have opened an issue regarding health checks of the application, it's related to cloud deployment https://github.com/slackapi/bolt/issues/283

Quick update for the container service support: We've published a simple example app demonstrating how to build a Docker image for Bolt JS apps. https://github.com/slackapi/bolt-examples-aws-re-invent-2020/tree/main/lightsail-containers/javascript
Although we don't have guide document on the website yet, the steps to build a Docker image is the same for other platform services.

Closing this since we have a Heroku and Lambda guide available. We also have an examples/ directory where we can continue to add more hosting examples as people request them.
We may want to import our AWS guides from https://github.com/slackapi/bolt-examples-aws-re-invent-2020 to showcase AWS Gateway Lambda and Lightsail


The wiki page "Develop in IDEA" has some incorrect steps

Description
Some steps under Title "Configuring dependencies and compiling the application" on the Develop in IDEA wiki page are incorrect. Will cause failure to start using IDEA.
The current steps are as follows:
5.Create new library ECLIPSE (name and case are important)
6.Click the "Add" button. Select the folder eclipse-ide-path/plugins
Should be:
5.Click the "Add" button. Select Java. Select the folder eclipse-ide-path/plugins. Click OK button. Choose all modules exclude dbeaver. Click OK button.
6.Change the library name to ECLIPSE (name and case are important)
DBeaver Version
devel
Operating System
No response
Database and driver
No response
Steps to reproduce
1.Open wiki page Develop in IDEA
2.Scroll to title "Configuring dependencies and compiling the application"
Additional context
No response

Hello @heartdance,
Why do you think it should be that way? For me, it works perfectly fine (adding the entire plugins directory).

I don't mean to choose which dependencies under the plugins directory, but to add these dependencies to which modules. And these two steps do not correspond to the view actually seen in IDEA.

Ah, I see. You're talking about the additional step that actually is not required. IIRC, you can just click "Cancel".


Added a TypeScript generator

Fixes #337.
This PR generalizes the Flow declaration generator to a TypeScript one so that TypeScript users can also benefit. Most of the code was unmodified, but I customized the template file to operate better for TypeScript consumers.

Looks awesome.

Awesome, thanks!

nice! Any way you can push a release in the next couple of days?

Got 3 compile errors when using typescript 2.1.4.
node_modules/github/lib/index.d.ts(1328,18): error TS2314: Generic type 'Array<T>' requires 1 type argument(s).
node_modules/github/lib/index.d.ts(1413,19): error TS2314: Generic type 'Array<T>' requires 1 type argument(s).
node_modules/github/lib/index.d.ts(1420,19): error TS2314: Generic type 'Array<T>' requires 1 type argument(s).

In all cases it was fixed by replacing Array with Array<string>


error with method passwordExpired() from Models\User.php

Laravel Version: 5.7
Adldap2-Laravel Version: 4.0
PHP Version: 7.2.4
LDAP Type: ActiveDirectory

Description:
users()->find('john doe');
            dd($user->passwordExpired());
 ?>
Error: DateTime::setTimestamp() expects parameter 1 to be integer, float given

Hi @ricardo91,
Are you using the 32-bit version of PHP?

I'am using a Wamp server 32-bit version 3.13

Ok, this is an issue currently when using a 32-bit due to the integer being larger than 32-bit can support, and converting it to a float dynamically.
Going to see if I can resolve it. Thanks!


[GHSA-547x-748v-vp6p] Dash apps vulnerable to Cross-site Scripting

Updates

Affected products
Description

Comments
on pip dash-core-components v2 and dash-html-components v2 are just placeholder packages that import the code from the core dash package so are not vulnerable

Hi @graingert, thank you for your contribution. Unfortunately, we are unable to update the description of the CVE record because the ID was issued by Snyk. To get it updated, you need to contact Snyk via<EMAIL_ADDRESS>

@JonathanLEvans can you update just the version range of the affected packages?

Thanks @graingert - I'll write to Snyk about this

Snyk has updated their reports to exclude the PyPI v2.0.0 of dash-html-components and dash-core-components
https://security.snyk.io/vuln/SNYK-PYTHON-DASHHTMLCOMPONENTS-6226336
https://security.snyk.io/vuln/SNYK-PYTHON-DASHCORECOMPONENTS-6226334
(Actually they updated them right away on Monday, I just didn't check back until today)
I still see <=2.0.0 for these on https://github.com/advisories/GHSA-547x-748v-vp6p - anything else we need to do to get this updated?


Not an editor command: SftpSend

Hi! Today I try install your plugin, but after install and setup reqs (install in python pysftp and pynvim) I get this error:
Not an editor command: SftpSend
I use neovim 8 with lua (if more detail I use astronvim last version)
Can you help me, please?

You need to run :UpdateRemotePlugins after you install/update the plugin.
Using vim-plug, the easiest way is to set it up like this:
Plug 'dcampos/nvim-sftp-sync', { 'do': ':UpdateRemotePlugins' }

Using packer:
use { 'dcampos/nvim-sftp-sync', run = ':UpdateRemotePlugins' }

I don't know much about AstroNvim, but from what I've seen it uses packer.

But my neovim base on Lua =(  Sorry, I just choise other lib for this =(

But my neovim base on Lua =(

Mine too. You just have to call :UpdateRemotePlugins, it's a Neovim built-in command, it doesn't matter if your config is Lua or Vimscript based.

Sorry, I just choise other lib for this =(

No problem. Good luck!


Error: Extranonce2 size is 2 (minimum is 4).

Greetings,
I'm getting this error from Nicehash pool testing. Extra nonce subscribe option doesn't change anything (I'm not sure if it should, its the only option I found mentioning extra nonce.) Any solution for this? Thank you.

It seems that I found an answer on bitcointalk:
"Hey guys.
I want to connect Nicehash to my proxy. But it got the error: "Disconnected. Remote pool extranonce2 size too small (min=4)." from Nicehash.
Can I set the extranonce2 to 4 anywhere?
Greetings
You want to connect your proxy to Nicehash, not Nicehash to your proxy. The error is from your proxy, not from Nicehash, and it says that Nicehash, not your proxy, is using too small extranonce2. Your proxy expects the size to be at least 4, Nicehash says 3. There is nowhere you could set 4 as you obviously cannot change how Nicehash servers are configured. The only way would be to make the proxy accept size 3."
Is there any way to make stratum proxy to accept extranonce size to be 2 or 3?


Collaborative editor

Do we have any plan to support Collaborative editor or  Do we have any in build method to get the data in the Object model like ProseMirror.

No, Squire is not designed with this in mind and would need a completely different architecture, to the point it would be a whole new project.

Do you have any plan to start ?

No plans at this time.


Bufferline not hidden after deleting buffer in vertical split

I have g:lightline#bufferline#min_buffer_count set to 2, but the bufferline remains visible if I :bd a buffer in a vertical split. The following gif shows the problem with an example:

@noib3 does this issue still occur if you try the branch bugfix/delay-event-handler?

@noib3 does this issue still occur if you try the branch bugfix/delay-event-handler?

@mengelbrecht no, that branch works fine. Should I keep using that or will some fix get merged into master?

@mengelbrecht no, that branch works fine. Should I keep using that or will some fix get merged into master?

@noib3 I merged the fix to master.

@noib3 I merged the fix to master.


super confusing req.param vs req.params

Today I learned that req. param in sailsjs doesn't mean query params. It considers URL path params, body payload, and query string params in that order, and overriding happens in the same order. There is another method called req.params to read path params.
I understood the need to have one more method which considers all 3 params. Maybe the naming is bad?

Hi @lokesh1729!
You can read @mikermcneil's explanation of this here: https://stackoverflow.com/a/9243020/14159178


Swagger link template not filled out

Swagger link in Home page does not point to https://<host>/docs but https://<host>/{url}. Meanwhile using /docs works fine

Im at work, i'll be back to you ASAP, but they looks like easy fixable happy accidents (🥲), i should be able to fix them by this afternoon (timez-eur)

would you please download 0.8.5 and confirm this is gone? :)

Solved. Thanks!


Publish in npmjs

Any reason why you have not published this in npmjs...that way I can ensure the latest version gets used automatically in my nodejs app

Hi,
It actually is on npmjs: https://www.npmjs.com/package/javascript-lp-solver


Maybe use a database instead of JSON files

I am not sure what happens when two persons try to edit the same contributor. In the worst case the file gets corrupted. And when that happens, in the worst case the whole contributor list breaks.

Version 2.x uses Doctrine.


Update documentation for Holographic Remoting 2.0.18 release.

Docs Build status updates of commit 9e122b3:
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Line 17: [Suggestion] Link 'https://docs.microsoft.com/en-us/uwp/api/windows.graphics.holographic.holographicviewconfiguration' contains locale code 'en-us'. For localizability, remove 'en-us' from links to most Microsoft sites. NOTE: This Suggestion will become a Warning on 12/20/2019.

For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.

Docs Build status updates of commit 1d749ad:
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Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.


Change data source for resolver that extends Amplify-generated one

Which Category is your question related to?
api
Amplify CLI Version
7.6.8
Provide additional details e.g. code snippets
Is this possible to change data source for new resolver that extends Amplify-generated one in new version of graphQL transformer (V2)?

Hi @jk171505, you should be able to achieve what you need by using CDK to define custom VTL resolvers as described here: https://docs.amplify.aws/cli/graphql/custom-business-logic/#vtl-resolver.
Please let us know if you still have any issues

@lazpavel where do I define the exact slot for which I want to change the data source?

Can I accomplish the same by defining the data source for specific slot in CustomResources.json?

I see, the link above will allow you to create and configure a custom resolver and not to update a different data source for a slot on an extended resolver.
For that you could use the documented way to extend a resolver (e.g: Mutation.createModelB.postAuth.2.req.vtl) and then use amplify override api and update the datastore for the specific appsyncFunction as below:
import { AmplifyApiGraphQlResourceStackTemplate } from '@aws-amplify/cli-extensibility-helper';

export function override(resources: AmplifyApiGraphQlResourceStackTemplate) {
resources.models["**ModelB**"].appsyncFunctions["Mutationcreate**ModelB**postAuth1FunctionMutationcreate**ModelB**postAuth1Function.AppSyncFunction"].dataSourceName = "**ModelATable**";
}

Thanks! That's exactly what I needed.

@lazpavel  Is there a difference between the replacement of **ModelB** and **ModelATable** in your example? I'm confused by this, so if model A is named "Item" should **ModelATable** be "Item" or "ItemTable"?

@Dennis-Dekker you are basically changing the dataSource for ModelB to ModelA. You should also add the suffix 'Table', so it should be:
resources.models["Item"].appsyncFunctions["MutationcreateItempostAuth1FunctionMutationcreateItempostAuth1Function.AppSyncFunction"].dataSourceName = "SomeOtherItemTable";

@jk171505 Do you know if I can reference a Lambda DataSource in this case? If yes, that would be awesome.

This is my override.ts:
import { AmplifyApiGraphQlResourceStackTemplate, AmplifyProjectInfo } from '@aws-amplify/cli-extensibility-helper';

export function override(resources: AmplifyApiGraphQlResourceStackTemplate, amplifyProjectInfo: AmplifyProjectInfo) {
    const model = resources.models["User"];
    model.appsyncFunctions["MutationcreateUserpreUpdate0Function.AppSyncFunction"].dataSourceName = "UniqueUsernameCheckLambdaDataSource";
}

On amplify push I' m getting this error:
Cannot set properties of undefined (setting 'dataSourceName')
Amplify version is 12.3.0.
Is what explained in this issue still valid?

@ggorge-etiqa Did you ever solve this? I'm facing the same issue.

This is my override.ts:
import { AmplifyApiGraphQlResourceStackTemplate, AmplifyProjectInfo } from '@aws-amplify/cli-extensibility-helper';

export function override(resources: AmplifyApiGraphQlResourceStackTemplate, amplifyProjectInfo: AmplifyProjectInfo) {
    const model = resources.models["User"];
    model.appsyncFunctions["MutationcreateUserpreUpdate0Function.AppSyncFunction"].dataSourceName = "UniqueUsernameCheckLambdaDataSource";
}

On amplify push I' m getting this error:
Cannot set properties of undefined (setting 'dataSourceName')
Amplify version is 12.3.0.
Is what explained in this issue still valid?

Yes, this is still valid solution with amplify cli v 12.11.1
For the function name you can also take a look into your build folder, where you can also find the generated resolvers. Here you can also find the CloudFormation stacks. Find the stack for your origin model. Find your function. The function should have this syntax: FunctionNameAppSyncFunctionRandomString.
You need the FunctionName part und use it in override.ts:
model.appsyncFunctions["FunctionName.AppSyncFunction"].dataSourceName = "SomeOtherItemTable";


Refactor application detail component

What this PR does / why we need it:
Which issue(s) this PR fixes:
Fixes #
Does this PR introduce a user-facing change?:

NONE

/approve


TypeError when using "lambda wildcards:" to call function inside HTTPRemoteProvider.remote()

Snakemake version
7.3.0
Describe the bug
I would like use a function to extract URLs from a dataframe that is subset according to wildcards in the output directive.
However, when definign the input like HTTP.remote(lambda wildcards: my_function(wildcards.sample)) I get the  the TypeError shown below.
I am providing a minimal working example below, that demonstrate that a rule without lambda works (rule download_working), a rule using lambda and not HTTP.remote work theoretically (the local file is obviously not found), and a rule download_not_working that resembles my use case.
My understanding is that the return-value of the lambda function is not evaluated inplace. However, I didn't find a way to force this evaluation. Given that using lambda in input directive works in general, I am suspecting this is related to the implementation of HTTP.remote. Please let me know if his assumption is wrong :)
Logs
snakemake -j1 -p --forceall
TypeError in line 26 of /tmp/snakemake-remote/Snakefile:
Invalid type (<class 'function'>) passed to remote: <function <lambda> at 0x7f091e3b7e60>
  File "/tmp/snakemake-remote/Snakefile", line 26, in <module>

Minimal example
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
import shutil

HTTP = HTTPRemoteProvider()

def get_link(n=1):
    return f"abyssal.uber.space/hash/{n}"

rule all:
    input:
        "downloaded_file.1.txt",
        "downloaded_file.2.txt",
        "downloaded_file.2.txt"

rule download_working:
    input: HTTP.remote(get_link())
    output: "downloaded_file.1.txt"
    run:
        shutil.move(input[0], output[0])
        print(f"downloaded to {output[0]}")

rule download_not_working:
    input: HTTP.remote(lambda wildcards: get_link(wildcards.n))
    output: "downloaded_file.{n}.txt"
    run:
        shutil.move(input[0], output[0])
        print(f"downloaded to {output[0]}")

rule download_not_working_local:
    input: lambda wildcards: get_link(wildcards.n)
    output: "downloaded_file.{n}.txt"
    run:
        shutil.move(input[0], output[0])
        print(f"downloaded to {output[0]}")

OK, I could workaround this by using a wrapper/decorator as shown below. It's still not clear to me if the behavior shown in the issue description is as expected and would be keen to learn if and why :)
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
import shutil

HTTP = HTTPRemoteProvider()

def get_link(n=1):
    return f"abyssal.uber.space/hash/{n}"

rule all:
    input:
        "downloaded_file.1.txt",
        "downloaded_file.2.txt",
        "downloaded_file.2.txt"

def as_http_remote(func):
   """ make function a HTTPRemoteProvider """
    def inner(*args, **kwargs):
        return_value = func(*args, **kwargs)
        return HTTP.remote(return_value)
    return inner

# wrap it!
get_link_as_http_remote = as_http_remote(get_link)

rule download_with_wrapper_working:
    input:
        lambda wildcards: get_link_as_http_remote(wildcards.n)
    output: "downloaded_file.{n}.txt"
    run:
        shutil.move(input[0], output[0])
        print(f"downloaded to {output[0]}")


Suggestion

Hi. I have developed a Gym League Script but am no longer interested in maintaining the script.
Please take a look at my de-obfuscated source code and take whatever you want!
https://github.com/audaxide/roblox/blob/main/scripts/gl.lua

not an issue


appveyor template should not use deploy_script to publish artifacts

Currently template script suggest to use deploy_script: section for artifacts publishing.
Meanwhile, this section is skipt on PRs, so people cannot download artifacts to test bits from PRs.
@KarolKaczmarek thought?

I suggest use on_finish section for artifacts publishing

I think it makes sense to move it (just artifacts publishing, not nuget package) to on_finish to make testing easier. We should update template and eventually appveyor.yml for all repos as well.

@KarolKaczmarek - would it be possible to automate the update of AppVeyor.yml in all repos like you did for another AppVeyor issue a couple of months ago or should they be updated manually?

yup, we could do that

@KarolKaczmarek I also like your idea to version the template

Today on deploy_script: there are a helper function Invoke-AppveyorAfterTestTask that does the following

(Optional) Produce and upload Wiki documentation to AppVeyor.
Set version number in Module Manifest to build version
Zip up the module content and produce a checksum file and upload to AppVeyor.
Pack the module into a Nuget Package.
Upload the Nuget Package to AppVeyor.
Execute custom AppVeyor AfterTask. Used by "Harness model", i.e SharePointDsc.

All repos has not aligned to the appveyor.yml template yet.
My understanding is that on_finish: runs on both PR and Branch, regardless of successful PR or branch build (passing tests or not), and deploy_script: runs only when the branch finishes a build successfully (only when tests are passing).
What of items in the number list above, if any, would we want to run in the on_finish event? 🤔
If a branch build fails do we want to publish potentially broken artifacts?


Link badges in README to their respective labels

Link the respective labels to their badges.
You can find the labels here
Copy each label link and use it to wrap their corresponding badge in the README.
Fix
This is an example of the bug label wrapped with it's link.

[ ] good first issue
[ ] help wanted
[ ] enhancement
[ ] bug

Fix only one, so others can have a go too.
Badge screenshot

@Evavic44 Can you review

@Evavic44 Can you review

Merged. Perfect work! @RishiKumarRay 👍🏽

well done @RishiKumarRay

@Evavic44 I have linked PR for bug badge. Can you please review and merge?

I have linked PR for good first issue batch.Can you please review and merge it.

I have updated the help wanted badge. can you please merge the pull request. @Evavic44

Hey @Evavic44 , I have updated the PR. Please check again.

Awesome job. @ShubhamSaini1585 @RishiKumarRay merged and fixed all. Thanks for your PR. 🌟


[GUI] Lines array is generated later

this._lines is generated when the  control is in view. If you create a control that is not in view it will fail.
This makes sure it doesn't fail even when out of view.
Test playground - https://www.babylonjs-playground.com/#XCPP9Y#13890

overall It sounds weird we are going in render if we do not have the required infos ???

overall It sounds weird we are going in render if we do not have the required infos ???

That is the GUI render loop. and I agree. Those objects are only initialized on the first actual render, but the function is running on every render call, even if outside of the frustum.
This requires a slight overhaul of the GUI render loop.


macOS 10.13.4 config.h file not found

After restarting a working react-native project i can no longer get it to build in Xcode because of

The build was working before restarting Xcode, so i am unsure what could have changed. Its it is referenced in node_modules/react-native/third-party/glog-0.3.4/src/signalhandler.cc

Ok seems to be related to react not this https://github.com/facebook/react-native/issues/14382


ui: fix tags selection for add disk offering

Description
Multiple entries were showing in tag selection dropdown of Add disk offering form.

Types of changes

[ ] Breaking change (fix or feature that would cause existing functionality to change)
[ ] New feature (non-breaking change which adds functionality)
[x] 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

[ ] Major
[ ] Minor

Bug Severity

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

Screenshots (if appropriate):

How Has This Been Tested?

UI

@blueorangutan ui

@shwstppr a Jenkins job has been kicked to build UI QA env. I'll keep you posted as I make progress.

UI build: :heavy_check_mark:
Live QA URL: http://qa.cloudstack.cloud:8080/client/pr/4665 (JID-3833)


Footer Link to GitHub Proifile Broken

Links to https://github.com/peter-murach/
You may also want to check the homepage link for tty-screen. It links to http://peter-murach.github.io/tty/.

Thanks for spotting these. I've recently changed my 'identity' and it proved be tons of work.

I have redesigned the site and changed all the links.

If you fancy you can check it out @ https://piotrmurach.github.io/tty/. I believe it does a better job at explaining what tty libraries are for and let's you browser stuff more easily. I would be curious to have your thoughts?

Site is nice, works well. So much so the only bit of semi-useful feed back I can offer is this:
On desktop, when clicking on the API menu, I would be nice if clicking anywhere outside the menu would close it. Currently one has to click on API again :neckbeard:.

Oh, found one thing: the rubygems homepage for tty-screen still points to http://peter-murach.github.io/tty/


Create a page to display credits

Create a page in Angular to display the credits. Different assets require mentioning credits. All these will be displayed in this page.
The articles and videos used to build any feature in the site will also be added in the credits section.
Keep the content static for now. But build it in a way that these can be moved over to a backend application in future and fetched dynamically.
Go through all the features that are currently developed and make a list of them along with any credits that must be associated with them.
Deploy the application and make sure that the feature is visible in the website.

Example credit:

ID: 1

Name: A feature developed in the application

Link to Code: Link to the GitHub repository source code that contains the feature.

List of links associated with the credit e.g. youtube video link, blog post link, etc.

Intro notes: A list of optional short descriptions associated with the credit. All the descriptions will be displayed sequentially with a fade in effect to create a sort of animation. These descriptions will be used as intro to any credit.

Footnotes: A list of optional short descriptions associated with the credit. These will be displayed in sequence with kind of an animation after the credits are displayed.

Completed in branch feature/28


Ninja error

Ninja error reported by @suyashbakshi in Timeloop issue https://github.com/NVlabs/timeloop/issues/130.
Original comment: https://github.com/NVlabs/timeloop/issues/130#issuecomment-1100439685

Hello, I just wanted to give a quick update on this issue. I'm still running into issues while installing timeloop-python. But the issue is rather different now. I have upgraded to a Ubuntu 22.04 VM compared to my earlier version 20.04.
I have built timeloop and accelergy by following the instructions on https://timeloop.csail.mit.edu/. Then I cloned timeloop-python repo and set the TIMELOOP_INCLUDE_PATH and TIMELOOP_LIB_PATH to point to the 'include' and 'lib' dirs of timeloop.
Now when I execute sudo pip3 install -e . for timeloop-python, I get the following error complaining about the TIMELOOP_INCLUDE_PATH env variable.
I'm not entirely sure where am I going wrong with the build process. Any help would be greatly appreciated.
suyash@suyash-virtual-machine:~/work/timeloop-dev/timeloop-python$ sudo pip3 install -e .
Obtaining file:///home/suyash/work/timeloop-dev/timeloop-python
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: pyyaml in /usr/lib/python3/dist-packages (from pytimeloop==0.0.1) (5.4.1)
Installing collected packages: pytimeloop
  Running setup.py develop for pytimeloop
    error: subprocess-exited-with-error

    × python setup.py develop did not run successfully.
    │ exit code: 1
    ╰─> [66 lines of output]
        running develop
        /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:158: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        /usr/lib/python3/dist-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: 0.1.43ubuntu1 is an invalid version and will not be supported in a future release
          warnings.warn(
        /usr/lib/python3/dist-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: 1.1build1 is an invalid version and will not be supported in a future release
          warnings.warn(
        running egg_info
        writing manifest file 'pytimeloop.egg-info/SOURCES.txt'
        running build_ext
        -- The C compiler identification is GNU 11.2.0
        -- The CXX compiler identification is GNU 11.2.0
        -- Detecting C compiler ABI info
        -- Detecting C compiler ABI info - done
        -- Check for working C compiler: /usr/bin/cc - skipped
        -- Detecting C compile features
        -- Detecting C compile features - done
        -- Detecting CXX compiler ABI info
        -- Detecting CXX compiler ABI info - done
        -- Check for working CXX compiler: /usr/bin/c++ - skipped
        -- Detecting CXX compile features
        -- Detecting CXX compile features - done
        CMake Error at CMakeLists.txt:8 (message):
          Please point TIMELOOP_INCLUDE_PATH to your Timeloop headers.

        -- Configuring incomplete, errors occurred!
        See also "/home/suyash/work/timeloop-dev/timeloop-python/build/temp.linux-x86_64-3.10/CMakeFiles/CMakeOutput.log".
        Traceback (most recent call last):
          File "<string>", line 2, in <module>
          File "<pip-setuptools-caller>", line 34, in <module>
          File "/home/suyash/work/timeloop-dev/timeloop-python/setup.py", line 106, in <module>
            setup(
          File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 153, in setup
            return distutils.core.setup(**attrs)
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 148, in setup
            return run_commands(dist)
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 163, in run_commands
            dist.run_commands()
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 967, in run_commands
            self.run_command(cmd)
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command
            cmd_obj.run()
          File "/usr/lib/python3/dist-packages/setuptools/command/develop.py", line 34, in run
            self.install_for_development()
          File "/usr/lib/python3/dist-packages/setuptools/command/develop.py", line 114, in install_for_development
            self.run_command('build_ext')
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 313, in run_command
            self.distribution.run_command(command)
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command
            cmd_obj.run()
          File "/usr/lib/python3/dist-packages/setuptools/command/build_ext.py", line 79, in run
            _build_ext.run(self)
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 339, in run
            self.build_extensions()
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 448, in build_extensions
            self._build_extensions_serial()
          File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 473, in _build_extensions_serial
            self.build_extension(ext)
          File "/home/suyash/work/timeloop-dev/timeloop-python/setup.py", line 97, in build_extension
            subprocess.check_call(
          File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
            raise CalledProcessError(retcode, cmd)
        subprocess.CalledProcessError: Command '['cmake', '/home/suyash/work/timeloop-dev/timeloop-python', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/suyash/work/timeloop-dev/timeloop-python/build/lib.linux-x86_64-3.10/', '-DPYTHON_EXECUTABLE=/usr/bin/python3', '-DVERSION_INFO=0.0.1', '-DCMAKE_BUILD_TYPE=Release', '-GNinja']' returned non-zero exit status 1.
        [end of output]

    note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [66 lines of output]
    running develop
    /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:158: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    /usr/lib/python3/dist-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: 0.1.43ubuntu1 is an invalid version and will not be supported in a future release
      warnings.warn(
    /usr/lib/python3/dist-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: 1.1build1 is an invalid version and will not be supported in a future release
      warnings.warn(
    running egg_info
    writing manifest file 'pytimeloop.egg-info/SOURCES.txt'
    running build_ext
    -- The C compiler identification is GNU 11.2.0
    -- The CXX compiler identification is GNU 11.2.0
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Check for working C compiler: /usr/bin/cc - skipped
    -- Detecting C compile features
    -- Detecting C compile features - done
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Check for working CXX compiler: /usr/bin/c++ - skipped
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    CMake Error at CMakeLists.txt:8 (message):
      Please point TIMELOOP_INCLUDE_PATH to your Timeloop headers.

    -- Configuring incomplete, errors occurred!
    See also "/home/suyash/work/timeloop-dev/timeloop-python/build/temp.linux-x86_64-3.10/CMakeFiles/CMakeOutput.log".
    Traceback (most recent call last):
      File "<string>", line 2, in <module>
      File "<pip-setuptools-caller>", line 34, in <module>
      File "/home/suyash/work/timeloop-dev/timeloop-python/setup.py", line 106, in <module>
        setup(
      File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 153, in setup
        return distutils.core.setup(**attrs)
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 148, in setup
        return run_commands(dist)
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 163, in run_commands
        dist.run_commands()
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 967, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command
        cmd_obj.run()
      File "/usr/lib/python3/dist-packages/setuptools/command/develop.py", line 34, in run
        self.install_for_development()
      File "/usr/lib/python3/dist-packages/setuptools/command/develop.py", line 114, in install_for_development
        self.run_command('build_ext')
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command
        cmd_obj.run()
      File "/usr/lib/python3/dist-packages/setuptools/command/build_ext.py", line 79, in run
        _build_ext.run(self)
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 339, in run
        self.build_extensions()
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 448, in build_extensions
        self._build_extensions_serial()
      File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 473, in _build_extensions_serial
        self.build_extension(ext)
      File "/home/suyash/work/timeloop-dev/timeloop-python/setup.py", line 97, in build_extension
        subprocess.check_call(
      File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '/home/suyash/work/timeloop-dev/timeloop-python', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/suyash/work/timeloop-dev/timeloop-python/build/lib.linux-x86_64-3.10/', '-DPYTHON_EXECUTABLE=/usr/bin/python3', '-DVERSION_INFO=0.0.1', '-DCMAKE_BUILD_TYPE=Release', '-GNinja']' returned non-zero exit status 1.
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

Sure.
suyash@suyash-virtual-machine:~/work/timeloop-dev/timeloop-python$ echo $TIMELOOP_INCLUDE_PATH
/home/suyash/work/timeloop-dev/timeloop/include
suyash@suyash-virtual-machine:~/work/timeloop-dev/timeloop-python$ echo $TIMELOOP_LIB_PATH
/home/suyash/work/timeloop-dev/timeloop/lib/

Hello, is there any possible solution to this? I would really like to use Timeloop-python for my research work.
If there are any known "environments" (operating system, dependency versions etc.) where Timeloop-python is working for others, I'd be interested in knowing that too and will try to setup a similar environment.

Reproduced the ninja issue on Ubuntu 20.02. We are working on it. Please bear with us.

On Ubuntu 20.04 export the following env variable:

Then torpedo everything, do a clean git clone and try rebuilding. It should work.

Thank you, I will try this and get back to you.

Hello, thank you! The command you suggested seems to have fixed the issue. The pip installation finished successfully:
~/work/timeloop-dev/timeloop-python$ pip3 install .
Defaulting to user installation because normal site-packages is not writeable
Processing /home/suyash/work/timeloop-dev/timeloop-python
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: pyyaml in /usr/lib/python3/dist-packages (from pytimeloop==0.0.1) (5.4.1)
Building wheels for collected packages: pytimeloop
  Building wheel for pytimeloop (pyproject.toml) ... done
  Created wheel for pytimeloop: filename=pytimeloop-0.0.1-cp310-cp310-linux_x86_64.whl size=365771 sha256=3c4d6137575463985c90c96b2c4c355f60ec01f7f1f94270309dd80d6ad155b2
  Stored in directory: /home/suyash/.cache/pip/wheels/68/f4/1d/31df7c8878faa3da9b844d2c39a8870a604874d379c053f770
Successfully built pytimeloop
Installing collected packages: pytimeloop
Successfully installed pytimeloop-0.0.1

However, now when I run the "timeloop-model.py" tool with the "sample.cfg" from "timeloop-dev/timeloop/configs/model", it gives the following error. Is the config file format different for pyTimeloop? Or am I missing something?
~/work/timeloop-dev/timeloop-python$ timeloop-model.py ~/work/timeloop-dev/timeloop/configs/model/sample.cfg
free(): invalid pointer
Aborted (core dumped)

Hello, so I realized that the timeloop-model.py and timeloop-mapper.py requires 3 config files as input: arch, prob and mapper/model settings (which was causing the segfault in my previous post). However, for a mapper configuration file that works without any issue with the native (C++) timeloop tool, the same config file results in the below mentioned error for me when running with timeloop-python (timeloop-mapper.py). Could you please help me understand the issue with this?
I have attached the arch, map (for mapper) and prob config files (converted them to "txt" format to be able to upload on github but I provide them in yaml format as input param to timeloop-mapper.py).
test_arch.txt
test_map.txt
test_prob.txt
Following is the error that I get:
$ timeloop-mapper.py test_arch.yaml test_prob.yaml test_map.yaml
[INFO] 2022-05-28 14:08:57,745 - pytimeloop.accelergy_interface.invoke_accelergy - execute:/home/suyash/.local/bin/accelergy tmp-accelergy.yaml --oprefix timeloop-mapper. -o ./ > timeloop-mapper.accelergy.log 2>&1

MESSAGE: attempting to read problem shape from file: /home/suyash/work/timeloop-dev/timeloop/problem-shapes/cnn-layer.yaml
[INFO] 2022-05-28 14:08:57,780 - pytimeloop.mapspace.MapSpace - Initializing Index Factorization subspace.
  Factorization options along problem dimension R = 6
  Factorization options along problem dimension S = 6
  Factorization options along problem dimension P = 6
  Factorization options along problem dimension Q = 6
  Factorization options along problem dimension C = 1287
  Factorization options along problem dimension K = 4752
  Factorization options along problem dimension N = 1
Mapspace Dimension [IndexFactorization] Size:<PHONE_NUMBER>
Mapspace Dimension [LoopPermutation] Size:<PHONE_NUMBER>00
Mapspace Dimension [Spatial] Size: 64
Mapspace Dimension [DatatypeBypass] Size: 512

Mapspace split! Per-split Mapping Dimension [IndexFactorization] Size:<PHONE_NUMBER> Residue: 0
['energy']
terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 1) >= this->size() (which is 1)
Aborted (core dumped)

I would greatly appreciate any help!

@suyashbakshi Thanks for reporting the issue. This was actually fixed last week. Could you try doing a git pull and reinstall?
Also, PyTimeloop's focus right now is for programatically using Timeloop's features, not as replacement for the timeloop-model and timeloop-mapper binaries. The output formatting was low in my priority so it isn't implemented. PyTimeloop won't print the results in timeloop-mapper.stats.txt. That will be coming in the future.

Thank you for the update. No problem, I only wish to use the basic functionality of the "model" and "mapper" from my python scripts, which as I understand are being supported.
On another note, it appears that the examples have not been updated in the "examples/" dir. Since naively running the example results in a segfault, it may be tricky for a new user to find the problem. I'm adding my findings from debugging here just for reference. For instance, the example: https://github.com/Accelergy-Project/timeloop-python/blob/f415a2dae9691fa95e827d206af00ac37dce8595/examples/model.py
if executed as it is, resulted in a segfault.
I understand following changes are required to correct them:

Change the following line:
https://github.com/Accelergy-Project/timeloop-python/blob/f415a2dae9691fa95e827d206af00ac37dce8595/examples/model.py#L6
to:
from pytimeloop.app import model

following line:
https://github.com/Accelergy-Project/timeloop-python/blob/f415a2dae9691fa95e827d206af00ac37dce8595/examples/model.py#L35
to:
app = model.ModelApp(config, '.')

Also directly printing eval_stats here:
https://github.com/Accelergy-Project/timeloop-python/blob/f415a2dae9691fa95e827d206af00ac37dce8595/examples/model.py#L37
only returns an object of type "bindings.model.EvaluationResult"
To get the results, one would need to print the stats as follows:

print("Utilization: ",eval_stats.utilization)
print("Energy: ",eval_stats.energy)
print("Algorithmic computes: ",eval_stats.algorithmic_computes)
print("Actual compute: ",eval_stats.actual_computes)
print("Cycles: ",eval_stats.cycles)
print("Last level accesses: ",eval_stats.last_level_accesses)

I hope this would be helpful.

@suyashbakshi Thanks for pointing out the bug. This was written very early in PyTimeloop development. They're quite outdated, as you pointed out. I think I will just delete those and point users to the bin/ folder since that one will always be up to date.


Python couldn't get the same results as those from web UI's preview tab

Describe the bug
Python LlamaParse is not getting the same results as those I got from the web UI preview.
parser = LlamaParse(
    api_key=...
    result_type="markdown",  # "markdown" and "text" are available
    verbose=True,
    language="ch_sim",
    use_vendor_multimodal_model=True,
    vendor_multimodal_model_name="openai-gpt4o",
    vendor_multimodal_api_key=os.environ['OPENAI_API_KEY'],
)

is getting different results from those in the UI's preview tab, which are
more or less satisfactory. The result I got from Python SDK seems not
getting use_vendor_multimodal_model=True, and also not respecting
the language argument I set too.
Job ID
cac11eca-1350-45e9-889b-a844a962d003
Screenshots

Client:
Please remove untested options:

Frontend (cloud.llamaindex.ai)
Python Library

Options
Multimodal

I am running these in a Jupyter-lab notebook. After restarting the kernel and rerunning every step. I am getting the expected results. Closing this issue.


Add MetaCoq to the Coq Platform

Currently there are 1.0-8.15 and 1.0-8.16 versions in the opam released packages that could be included in the platform. We are trying to release 1.1 versions as well (https://github.com/coq/opam-coq-archive/pull/2323/checks?check_run_id=8494250374). What would be the timeline for getting into the next platform for an 1.1 for 8.15 and 8.16 version?
This should be in the extended/experimental section for now, API changes are quite likely in the future.

Smoke tests could be examples/metacoq_tour_prelude.v and examples//metacoq_tour.v, the latter depends on the first one.

@mattam82 : the time window for getting into 2022.09 closes about 2 days after I managed to fix all issues from the switch to Ocamlfind in 8.16.0. It is hopefully Friday or Monday. The next release is planned in March 2023.

Tracker: (https://github.com/coq/platform/issues/274)

MetaCoq 1.1 packages were released for Coq 8.14, 8.15 and 8.16, so if possible we'd like to get those included in the 2022.09 platform.


Versioned DataObject canView() not behaving as expected

DataObject's with the Versioned extension applied aren't behaving as expected.
Looking at the 3.3 changelog  it mentions that "versioned by default will now deny canView permissions on objects that are not published" so expecting that canView() on published/Live DataObject's should return true but it returns false (unless logged in as an ADMIN).
Versioned DataObject
<?php
class PagePhoto extends DataObject {
   private static $extensions = [
      'Versioned'
   ];
}

after creating a record and publishing in the CMS
Adding to my controller
function init()
{
  parent::init();

  // Make sure we're not logged in
  if ($member = Member::currentUser()) {
    $member->logOut();
  }

  // Get one Published PagePhoto record
  $versionedObject_Live = Versioned::get_by_stage('PagePhoto', 'Live')->first();

  echo "Can view new versionedObject_Live? = " . var_export($versionedObject_Live->canView(), true);
  exit;
}

This always returns false. This looks to be due to Versioned::canView() only returning false|null
DataObject::canView() ignores null and falls back on a ADMIN permission check.
Tried to put together a test case for this but failed - sorry!

Returning null means "no opinion" so it'd fall back to whatever your canView is on the object in question.
What does the PagePhoto canView return?

DataObject::canView() ignores null and falls back on a ADMIN permission check.

You need to override your canView() for models that should be readable by non-admins. In the absence of Versioned, you'd still have the same problem.
Do:

class MyModel extends DataObject {

	/**
	 * @param Member $member
	 * @return boolean
	 */
	public function canView($member = null) {
		$extended = $this->extendedCan(__FUNCTION__, $member);
		if($extended !== null) {
			return $extended;
		}
		return true;
	}
}


Allow JS asset to register with type=module

This pull request allows to register js asset with type="module" attribute for script tag.

As it is specified here: https://developer.mozilla.org/en-US/docs/Web/HTML/Element/script/type
If you pass to type attribute some other value than module or JavaScript MIME type, then script content is required. Now it's not possible to set content to script tag so other values are not possible anyway.
If I rename module method to type, then I should add content method as well for clarity. What do you think about that?

Fair enough, thanks!


Add support for loading terraform data sources

Looking into the possiblity of PoC'ing this terraform operator I noticed that there's no way to load additional terraform context beyond the module.
I have a situation where there are modules available for use but these require references to existing AWS shared resources loaded via terraform datasources.
Example:
data "aws_sns_topic" "alerts" {
  name = "slack-feed-product_alerts"
}

data "aws_security_group" "rds_default" {
  tags = {
    Name = "rds-shared-security-group"
  }
}

module "db" {
  source         =<EMAIL_ADDRESS>
  vpc_security_group_ids              = [data.aws_security_group.rds_default.id]
  alerts_sns_topic_arn                = data.aws_sns_topic.alerts.arn
}

Describe the solution you'd like
Provide an alterative field to inject custom terraform hcl code to be able to able to overcome such situations. Not sure if there's a better way to handle this as these data sources are specific to the resources, but an hcl field of sorts would allow us to cater to it.
Describe alternatives you've considered
Looking at the source code for the operator, we can probably use the providersConfig field, as a workaround, to inject any terraform configuration and it would likely work (as it parses directly into the template), but it is not intuitive and can be a bit confusing given the name.
Additional context
Add any other context or screenshots about the feature request here.

@saviogl thanks for opening the issue here
Data resources are specific to the module you are trying to run. The terraform operator will basically create a root module on top.
The providersConfig and the backend fields are there because these are set on the root module.
Why can't these data resources be part of the module that you're trying to reference?

Hi @IbraheemAlSaady thanks for the quick reply.
I'm familiar with the implementation. In my case these modules are not necessarily under my control, and so although I agree we could embed these resources into the module, not sure will always be possible.
In this case, I'll manage to work around it and patch the module, but not sure if there are any other use cases that could benefit from it.
For now I'll close the issue to keep things clean


Send markdown instead of HTML

I fixed a bug where the HTML sent was including link to a non working URL in every line of the medium article. I found that by simply sending the markdown, medium was handling it perfectly. I kept the mechanism of adding a title first if there wasn't.
I also added a sentence that says : "Original article : https://urltoarticle.com" below the title
Known issue to fix :
When sending code blocks inside numbered list medium is reseting the number, I will be trying to replace the numbered list to a bulleted list in an attempt to make it look good in the coming days.

But there's no guarantee that posts in Nikola are markdown.

You make a point, indeed 😆
I will try to find another way then

Closing due to no activity.


docs(ApplicationFlags): add descriptions to each flag

Please describe the changes this PR makes and why it should be merged:
If applicable, please reference Discord API Docs PRs or commits that influenced this PR:

Reverted the Active flag changes since the upstream pr was closed


ESPHome 2023.4.0 validation failure

With the version of Home Assistant 2023.4 I get the capture error, how do I have to fix it so that everything continues to work as before?

Please update your YAML: Search for uart0 and replace all occurrences with uart_0.

perfect, thank you very much


Use protected properties and methods

This allows classes to extend the Parser class and overwrite certain methods.

Thanks for the PR @jenssegers ! I've merged this in now with a plan to release tomorrow


Fix examine text for stackable untradables to not show a GE value

Fixes issue #5841

You should maybe do the same thing with alch price as well

Are there items with 0 gp alch values? I do agree the code should be formatted that way though because logically it makes more sense.

Bones


ReferenceError: totalHeight is not defined

When button is drawn in function draw(), the button's text cannot be seen and other elements in the draw function are disabled.

Can you please provide a Minimal, Reproducible Example?


Codestyle: unify codestyle across all files

unifying codestyle across files

we have to ignore one line for pylint -- irrespective of the rest of the changes -- see inline comment in pymovments.utils.downloads


Images do not load until mouseover of slide

I added the carousel to my angular 8 app, and it works great, except I noticed that the images do not appear until I mouse over a slide. Instead it loads the carousel in the correct proportions with a blank slide, like this:

The rendered html looks like this:

Once I mouseover the the slide, the image and other content load and display properly. The code for the carousel I am using is as follows
<mat-carousel
timings="500ms ease-in"
[autoplay]="false"
color="primary"
maxWidth="auto"
[maintainAspectRatio]="false"
[slideHeight]="'500px'"
proportion="25"
slides="5"
[loop]="false"
[hideArrows]="false"
[hideIndicators]="false"
[useKeyboard]="true"
[useMouseWheel]="false"
orientation="ltr"

  <mat-carousel-slide [image]="'assets/images/screenshots/goals.png'" [hideOverlay]="true">

              Goals

              Set a long term vision for your organization and track your progress.

  </mat-carousel-slide>
  <mat-carousel-slide [image]="'assets/images/screenshots/rocks.png'" [hideOverlay]="true">

              Rocks

              Bridge the gap between where you are and where you need to be. Rocks are targeted,
              90 day initiatives that focus departments towards improving in a specific,
              measureable manner.

  </mat-carousel-slide>

Note: I do have a workaround for this. I discovered that forcing change detection in ngAfterViewInit caused the slides to display correctly. Ideally though, this should not be required.

I had a similar issue. Triggering change detection fixed it for me:
Inject a ChangeDetectorRef in your constructor like so
constructor(
    private cd: ChangeDetectorRef
}

and then detect changes after view is initialized
ngAfterViewInit(): void {
    this.cd.detectChanges();
}


Moves creation of LOI to LoiRepository

Moves logic for creation of LOI to LoiRepository. Also, removes the creation of intermediate state LocationOfInterest and directly generates the mutation.
This is similar to https://github.com/google/ground-android/pull/2495 where the goal is to simplify the save LOI flow by reducing the number of steps involved.

@gino-m @sufyanAbbasi  PTAL?

Thank you @shobhitagarwal1612 for the update!


Metrics existence and metrics paramters divergence between platform and API(v5 and v4)

Hi,
Me and my team are having some difficulties using your API. My fellow analysts want to use metrics that exist in your platform, but those same metrics are not available through the API, which makes the process more manual. The metrics are: conversion page visit, conversion add to card, paid pin clicks, and paid saves (as named in the platform).
Also, there are parameters in some metrics that are available in the API, but are different from the platform. We are especially concerned with the total order value (checkout) metric, which for the click/engagement/view parameter assignment we can access the 7/0/0 in the platform, but with the API we can only access highers than 7/1/1.
Could you help us with these? Thanks
Victor Martins,

Hello @victorfmartins,
Thank you for taking your time to use our API and offer feedback! Our team did notice some inconsistencies with the metrics available in our docs vs what our API provides and are working on fixing those issues. We should have an update in within the next couple weeks.
Thank you

Hi, @jquittograham
I appreciate your return, thank you.
I will be waiting for the update then, good job for you.
Cheers

Hello,
I am pleased to inform you that we have just released version v5.3.0 of our API today which includes a new ads reporting endpoint https://developers.pinterest.com/docs/api/v5/. The specific metrics you asked about, as well as many more, are available through this new endpoint. Please let me know if you have anymore questions or updates.
Thanks again!


Protospacer location

This branch adds an option -l to crispr_sites that outputs the chromosomal location of each located protospacer and writes it to output.
This output will be used by offtarget to return both offtargets and their locations.
The indexing arithmatic to do this was delicate and has been tested manually on hg38. Suggestions for ways to clean up the indexing arithmetic/parallel arrays greatly appreciated.

This PR is now feature complete - it contains changes to crispr_sites to output locations of protospacers (use -l flag) and changes to offtarget to serve up locations in response to a new HTTP request.


Generate PodIdentityAssociation resource.

https://github.com/aws-controllers-k8s/community/issues/1944
This patch regenerates the controller with new instructions that brings
the PodIdentityAssociation resource. New generation instructions:
  PodIdentityAssociation:
    fields:
      ClusterName:
        references:
          resource: Cluster
          path: Spec.Name

The patch also adds e2e tests and utility functions to manage service
accounts. TODO(@a-hilaly) move this utility to acktest library.
Signed-off-by: Amine Hilaly<EMAIL_ADDRESS>By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

/retest

/lgtm


Converted the namespace bundle unload into async operation

Motivation
Reworked the namespace bundle unload REST handler to be asynchronous. This avoid getting stuck in the Jetty threads calling into themselves when we try to unload the entire namespace.

Move this change to 2.6.2, because the #7773 depends on this pr.


Refactor remove old typeloader Part 2

Finally Remove the TypeLoader class + some cleanup

This is ready for review when https://github.com/mRaPGmbH/GraphCool/pull/14 is merged.


Updated the broadcast address

Coverage remained the same at 95.44% when pulling<PHONE_NUMBER>279fcf5b90d2e11c50e7d77dbdcbb3 on tk120404:patch-1 into d60fc24be094777b7df2afbf381ac986deba0114 on dashersw:master.