#18 modify require to blanket files to ensure deep coverage

That's cool @jschilli - just tested this out with an imported utility and it picked it up.  We still won't get coverage on modules that aren't imported, but that's a minor concern.
Sorry that I haven't been active on this project and thanks for the update!


Have config be similar to the new hardhat setup

If you run npx hardhat for a new repo, they have a new option called Create an advanced sample project. We should set this repo up to match their syntax.

Checkout https://github.com/PatrickAlphaC/decentralized-raffle for some context.
That one is also in typescript though

@pappas999 were you able to review the PR?

just went through everything, LGTM. One thing I had to do though (unrelated to your change), was I had to increase the mocha-timeout in hardhat.config.js from 100000 to 300000, because the integration tests on kovan were timing out. Do you get this issue @shivam-agarwal-0 ? Wondering if it's just kovan being slow, my machine, or something else
Either way, that is unrelated to your PR, and if a change to the timeout is required, we can raise a seperate PR for it

@pappas999 I am not facing any timeout issues, all test cases are passing with 100000 value.

thanks @shivam-agarwal-0


Documentation for custom formatting is missing

The doc here says:

The formatter can be configured in a deno.json file. You can specify custom rules, plugins, and settings to tailor the formatting process to your needs.

But it never says how. The documentation for Dprint has lots of options, which address what I wanted to do. But how do we pass those through to the Deno formatter? I tried including them in deno.json, but deno fmt complained about any options outside of the tiny subset that's documented.

Ugh, I thought this was a sub-area of the Deno repo. Closing.


Fixed the search column for same table relations

I have a customers table which is related to customers via parentCustomer.
When I try to search it uses the following expression as the column name:
LOWER(`customers` as `laravel_reserved_0`.`name`)

which clearly doesn't make sense since the table alias should only be added to the FROM table_name section of the query.
My code above checks if our "searchable column name with table prefix" has an as inside and only gets the table_alias.searchable_column from it.
BEFORE:
LOWER(`customers` as `laravel_reserved_0`.`name`)

AFTER
LOWER(`laravel_reserved_0`.`name`)

Released on https://github.com/yajra/laravel-datatables/releases/tag/v10.1.4, thanks 🚀


Update terragrunt.hcl

Ran Plan for dir: ap-southeast-1/ec2/prod/test-ec2 workspace: default
Plan Error
running "terragrunt plan --no-color -out $PLANFILE" in "/atlantis-data/repos/neeltom92/infrastructure-aws/18/default/ap-southeast-1/ec2/prod/test-ec2": exit status 127: running "terragrunt plan --no-color -out $PLANFILE" in "/atlantis-data/repos/neeltom92/infrastructure-aws/18/default/ap-southeast-1/ec2/prod/test-ec2":
sh: terragrunt: not found


Custom Variables

Hello,
I am trying to add custom variables to my front matter in a certain directory. Right now I have the basic options like Title, Description.... That I am linking to in my HTML file with {{ .Title }},
{{ .Description }}.... I would like to have custom options so that i can have more customization with my layout while still using Markdown. If I simply use the {{ .Content }} code it limits everything to one background and one column. But if I have other variable options I can insert them with more flexibility. Any ideas?

Hello there,
this seems more like a support question for the Hugo Forum (https://discuss.gohugo.io/). As for variables you can already assign custom variables (or "Parameters"), e.g. inside your Front-Matter, see http://gohugo.io/templates/variables/ - You can then access the custom variables/params inside your templates with {{ .Params.myparam }}.


 If a test is executed like
.../project/rfbrowser>robot tests\.
and the test contains the function without arguments like
Take Screenshot
a file .../project/rfbrowser.png is created.
Maybe a filename should be required?

Fixed in aab154f6c39a4d68eac0f886997a3d5c10160ddf


Fix the worker count in the generated config file.

The generated config file still has the worker count of 5, not 3. This led to issues in development as connections were quickly used up causing jobs to be stuck.
I think this was missed as part of #137

Ahh, indeed! Good catch. Thank you! 🙏🏻


[5.3] Auth views from config/auth.php, rather than being hardcoded

This will provide an easy way to customize the Auth views for packages. I also submitted the PR to change laravel/laravel to use views from this configuration laravel/laravel#4010

See comment on other PR. I would rather just have a convention here rather than add more configuration values. Thanks.

So a package with custom views should overwrite resources/views/auth scaffolding?


Added close method to callback list.

This enables await feed.close() to block until it's actually closed.

@dpaez @tinchoz49 Is there something I can do to get these tests passing? I'm not sure if they're being caused by my change. 😅

Hey @RangerMauve I will take a look today ;)

I fixed the issue and to speed up a little bit I put the close method. Published in v2.1.0 :+1:

as always thanks for the help @RangerMauve !

Thank you @tinchoz49 ! Always great to see this library flourish. 💜 Honestly makes a huge difference when making stuff with hypercore. 😤


Issue with import 'max_28_days' from 'homeassistant.components.utility_meter'

Hi!
I have a problem with enabling component on my HA instance. After adding powercalc to custom_component, reboot HA, adding below to to configuration.yaml:
powercalc:
power_sensor_naming: "{} Powersensor"
I got below error while checking configuration in HA server control panel:
Component error: powercalc - cannot import name 'max_28_days' from 'homeassistant.components.utility_meter' (/usr/src/homeassistant/homeassistant/components/utility_meter/init.py)
I'm running HA version core-2021.9.4 and HassOS version 6.5.
Regards,
Szymon

I've moved to latest HA and there is no configuration issues.
Thanks!


11/5/2019 Publish

Docs Build status updates of commit e44d66d:
:clock10: Full build: the average full build time is 7 min(s) 3 sec(s), this is based on the last 255 build(s) for this repository.

Docs Build status updates of commit e44d66d:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

latest/docs-ref-autogen/acr/scope-map.yml
:white_check_mark:Succeeded
View (azure-cli-latest)

latest/docs-ref-autogen/acr/token.yml
:white_check_mark:Succeeded
View (azure-cli-latest)

latest/docs-ref-autogen/ams/asset.yml
:white_check_mark:Succeeded
View (azure-cli-latest)

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.


fix: Simplify match statements to if let

👋🏾 Hello again.
This PR fixes the issue of using match statements where you can use if let. Not a performance fix or any other advantages besides readability for now, but given a big enough project, match statements can cause (if I remember correctly) the compile time to grow rapidly.

Not able to run the test script locally, since I do not have Salmon installed(You guys seem to not ship Darwin/OSX binaries for that)

Thanks!  Yea, to get a pre-compiled binary on Darwin/OSX you'd have to use conda right now (or pull from one of the quay images it generates). Our CI setup us such that we don't automatically make OSX builds.


Refactored job store string to locator (resolves #864, resolves #991, resolves #992)

Job store string has now been refactored completely. The syntax for each job store locator has been documented in the job store option help message. Minor corrections to outdated documentation have also been made.

Error tracked in #760

@hannes-ucsc ready

@hannes-ucsc since the property methods were axed the documentation only shows up in the job store help method. Is this enough?

only shows up in the job store help method. Is this enough?

Yes.

@hannes-ucsc ready


Speed improvement reading ese db

Hi, first up thanks for providing the ESE reader to the community! After noticing some very slow reading on large ESE databases, I did some debugging to find this bottleneck.
A call to self.header in record.py that checks for its existence results in several other calls to read the data for no reason if it does exist! This quick fix now correctly just checks for None.
The resulting speed improvement is 2x due to removing the time-consuming and extra reads on each record read on at least some large ese databases I have.
Testing results:
PREVIOUSLY
=====================================
1000 row fetch time = 00:00:51.165512
=====================================
NOW
=====================================
1000 row fetch time = 00:00:23.718492
=====================================

Adding some more context - not obj is in most cases the same as obj is None but here due to the underlying datastructure representing obj,  the behaviour is different.
This is one of those hard to detect issues via just reading code.

Damn, very nice catch! There are probably indeed some places where this applies, we'll need to try and search for those 😄.
For even more context, the exact reason why it's so slow is because of the __len__ implementation for the cstruct Instance class: https://github.com/fox-it/dissect.cstruct/blob/ffbf4f83169d5c6db2448d42c0e2fa5cec5c874a/dissect/cstruct/types/instance.py#L40-L41
It's worth noting that the upcoming "v4" refactor of cstruct now sets a proper __bool__ for those types, which should be a lot faster (approximately 17x with a small benchmark, but it scales with the structure size and is of course still a lot slower when just comparing against None):
https://github.com/fox-it/dissect.cstruct/blob/cb9e881cb79e97dca8f899096ec89c1af78c3d3a/dissect/cstruct/types/structure.py#L676-L685
Comparing against None is indeed the correct method. We generally try to catch this in code review but there are some places where it slips through.

@DissectBot agree

Damn, very nice catch! There are probably indeed some other places in Dissect where this applies, we'll need to try and search for those 😄.
For even more context, the exact reason why it's so slow is because of the __len__ implementation for the cstruct Instance class. Python falls back to this method because the class doesn't have a __bool__ method: https://github.com/fox-it/dissect.cstruct/blob/ffbf4f83169d5c6db2448d42c0e2fa5cec5c874a/dissect/cstruct/types/instance.py#L40-L41
It's worth noting that the upcoming "v4" refactor of cstruct now sets a proper __bool__ for those types, which should be a lot faster (approximately 17x with a small benchmark, but it scales with the structure size and is of course still a lot slower when just comparing against None): https://github.com/fox-it/dissect.cstruct/blob/cb9e881cb79e97dca8f899096ec89c1af78c3d3a/dissect/cstruct/types/structure.py#L676-L685
Comparing against None is indeed the correct method. We generally try to catch this in code review but there are some places where it slips through.

Excellent, looking forward to the new release.


removed deprecated SYCL code to resolve warning messages

Existing Sample Changes
Description
Removed deprecated SYCL features to resolve compiler warnings.
Type of change
Please delete options that are not relevant. Add a 'X' to the one that is applicable.

[x] Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

[x] Command Line

I compiled and ran the sample using the current oneAPI release and the sample's GNUmakefile to confirm that the previous warnings were gone.

This sample works with the Intel oneAPI Base Toolkit 2023.2.1 but I couldn't test against the 2024.0 base kit because I don't have access.

@hagabb Can you resubmit to the development branch? You may need to close this PR and reopen a new one if that is easier.

Closing this PR. Will resubmit to development branch.


After migrating the Gitea application as a whole, the old repository doesn't display commits count and public activity properly

Gitea Version
1.15.7 built with GNU Make 4.1, go1.16.10 : bindata, sqlite,
Git Version
git version 2.34.1
Operating System
Ubuntu 20.04.1
How are you running Gitea?
GitHub Repository Release Page Download.
Using systemd.
Database
SQLite
Can you reproduce the bug on the Gitea demo site?
No
Log Gist
No response
Description
The following content is from deepl translator:
After migrating the Gitea application as a whole, the old repository doesn't display commits count and public activity properly:

The submitted quantity is not displayed properly：

For example, before the migration, there were 53 commits in the gitea repository, and after the migration, the number of commits visible on the gitea page was also 53. However, if I commit a new commit in my local git repository and push it to gitea, no matter how much I refresh the page, the number of commits visible on the gitea page will be 53 and will not show the latest 54.

If I restart gitea and refresh the page again I can see that the commit count is updated to 54, but if I continue to upload new commits from local, it will still repeat the above description unless I restart again.

Public Activity cannot be displayed properly：

In addition to the previous issue, the new commit activity is not displayed in the Public Activity, I submitted 3 commits to test if they are valid, but the latest commit activity is not displayed:

And, both of these issues are only with the old repository before the migration, the new repository created after the migration everything is fine.
Screenshots
No response

As an admin user on the administration dashboard settings page click the resynchronize hooks page

As an admin user on the administration dashboard settings page click the resynchronize hooks page

Solved! Thank you so much!

Since 1.16, this problem won't occur again, 1.16 will auto re-sync the hooks if the Gitea app path changes. So the issue can be closed.


Angular version of dragula

I just want to let you know that I have made angular version of dragula. I will be working on it continuously and slowly diverse more and more from origin. But also I will be keeping track with your changes and optionally implementing them. Thank you very much for great code base! Its most beautiful drag&drop implementation I have seen so far now.
Link to my fork: https://github.com/luckylooke/dragular

Sounds good. I'd be more interested if you managed to use dragula as is in dragular. Do you think that's possible without changing dragula too drastically?

I am planning to add some other features I will use in my own projects. But
maybe I will make some simple plugin system to keep core light.
I had to change dragula code because of dubled implementations. I was using
features of framework to make dragula even lighter. There are more
posibilities to make more parts better angular-way and probably I will make
them. I hope you dont mind.
On Jun 20, 2015 10:07 PM, "Nicolas Bevacqua"<EMAIL_ADDRESS>wrote:

Sounds good. I'd be more interested if you managed to use dragula as is
in dragular. Do you think that's possible without changing dragula too
drastically?
—
Reply to this email directly or view it on GitHub
https://github.com/bevacqua/dragula/issues/89#issuecomment-113815207.

Well that was kind of my point, you could've still used dragula and add your custom features in the directive that wraps it. This feels like reinventing the wheel.
From the "what have I done" section in your readme,

replacing crossvent with angular's thing: saves you `833B
replacing contra.emitter by $scope.$emit: saves you from listening on the event and doing $scope.$emit within the directive. saves you 553B
encapsulation inside an angular service factory: you can still do this if you were to use dragula
directive: you can still do this
service/directive in a module: same

Well.. its just begining. And also sometimes reinventing the wheel can be useful link. You did the same, because there were already drag&drop libraries, it is about point of view.
I dont see any problem with my version of dragula. I think that it can be useful to people. If not, no problem, they just wont use it. I have made it for my purpose and I just share it to others. There always will be link back to original dragula so they can encapsulate it into angular service/directive by themselves. It is not difficult to anybody using angular regularly.
Building my features upon dragula would make code even bigger and less readable.
For example if I want to catch dragula events in parent scopes I have to do this:
in child controller
dragula($('element')).on('drag', function (el) {
  $scope.$emit('drag', el);
})

in parent controller
    $scope.$on('drag', function(e, el) {
       // do stuff
    });

Whether if I use my fork dragular it would be:
in child controller
dragularService($element, {
      scope: $scope
    });

parent controller part is the same.
And some features even cannot be added without changing the dragula code. I am planning to allow custom classes if provided via options.classes. They are now hardcoded inside dragula, so I have to move them into options, which cannot be done from outside. Etc.. etc..
I am not gonna convince you anymore that it make sense to make separated version, it is OK to me that you dont like the idea.
Keep coding like you did and I will be glad. :)

Point was you can still make a dragularService wrapper around dragula that facilitaties its interactions with Angular without forking dragula as a whole. Not trying to convince you of anything, just helping out. Enjoy the cutlery!

@luckylooke ended up writing up an official Angular version of dragula. https://github.com/bevacqua/angular-dragula
Hope it helps and that you consider merging back. Would love you as a contributor to that repo.

I will consider it later, thank you for your offer.


hotfix: Inconsistent test failure

Summary of the PR
Enum.ToString() output is undefined when dealing with aliases, as any
alias can be picked.  Patched TestChainLoadWithError so it will pass
regardless of which alias is returned.
Related issues, Discord discussions, or proposals
#706
Further Comments
This is a 'harmless' issue, as the error messages are intended for debugging
purposes.  The patch makes the test pass consistently.

Can you pull latest main please, the force pushes have made the diff go wonky.

Merged

@HurricanKai area owner signoff


VM: availability-set convert command should expose arg to set FD number

Managed disk based AV set has less FD count than  unmanaged version, w/o this arg, the conversion will fail for invalid FD count.

Suggest to do it with #3511, when we can use the /sku to have the best defaults


Generated icon is smaller than default Adwaita

When running Adwaita on Ubuntu 19.04 using gnome vanilla package.  The icons generated are smaller than the other icons.

I took some screenshots and was comparing the size difference in GIMP.  Here it is:

Are the icons not supposed to be the same size?  Is Canonical not using the proper upstream Adwaita icons or ???

So I noticed that the icon is smaller only at the smallest zoom level in Nautilus.

right! i got that on README todo, but i completely forgot to fix it, because i dont resize them; i will created the smaller sizes in a few days! sorry!


Use of legacy event object causes "SCRIPT438" error in some browsers

Various event handler functions are accessing the legacy event object rather than using an event handler parameter.

https://github.com/adityakahb/amegmen/blob/v1.0.3/src/ts/amegmen.ts#L569
https://github.com/adityakahb/amegmen/blob/v1.0.3/src/ts/amegmen.ts#L639
https://github.com/adityakahb/amegmen/blob/v1.0.3/src/ts/amegmen.ts#L704
https://github.com/adityakahb/amegmen/blob/v1.0.3/src/ts/amegmen.ts#L721
https://github.com/adityakahb/amegmen/blob/v1.0.3/src/ts/amegmen.ts#L740

In some browsers the legacy error object is different to the event handler parameter.
Specifically, in IE 9, the legacy error object is an instance of MSEventObj that does not support the preventDefault method. This leads to the following console error

SCRIPT438: Object doesn't support property or method 'preventDefault'

Reference: https://all-markup-news.com/dom-level-3-events-support-in-ie9/

Registration using the HTML event attributes (and their properties) will simultaneously enable the MSEventObj (legacy event object) through the window.event property as well as the new DOM event via the event handler parameter. We do this because the HTML event attribute registration technique is ambiguous—e.g., did the web developer expect the new DOM Events model or the old IE one?

Reference: https://developer.mozilla.org/en-US/docs/Web/API/Window/event

You should avoid using this property in new code, and should instead use the Event passed into the event handler function. This property is not universally supported and even when supported introduces potential fragility to your code.
Note: This property can be fragile, in that there may be situations in which the returned Event is not the expected value.

Reference: https://dom.spec.whatwg.org/#dom-window-event

Web developers are strongly encouraged to instead rely on the Event object passed to event listeners, as that will result in more portable code.

Suggested fix is to always use an event handler parameter and never use the legacy event object.

Updated EventHandlers with v1.0.5 release to include event parameter.


POSIX: Wshadow warning in signal.h

When building with CONFIG_POSIX_API=y and including signal.h,  given warning can be seen (example for nrf/samples/openthread/coap_client sample in NCS, build: west build -p -b nrf52840dk_nrf52840):
In file included from /home/mab6/ncs/zephyr/include/zephyr/posix/time.h:62,
                 from /home/mab6/ncs/nrf/subsys/nrf_security/include/mbedtls/platform.h:56,
                 from /home/mab6/ncs/modules/lib/openthread/src/core/crypto/mbedtls.cpp:39:
/home/mab6/ncs/zephyr/include/zephyr/posix/signal.h:124:95: warning: 'int sigaction(int, const sigaction*, sigaction*)' hides constructor for 'struct sigaction' [-Wshadow]
  124 | int sigaction(int sig, const struct sigaction *ZRESTRICT act, struct sigaction *ZRESTRICT oact);
      |                                                                                ^

This is because both function int sigaction() and structure struct sigaction are declared with the same name.
As sigaction seems to be a generic function, should the declaration be wrapped with TOOLCHAIN_IGNORE_WSHADOW_BEGIN/TOOLCHAIN_IGNORE_WSHADOW_END to get rid of that warning?

@maciejbaczmanski - please make a PR


[SR-11560] OSS Swift 5.1 does not recognise macCatalyst as a platform.

Previous ID
SR-11560

Radar
rdar://problem/68869888

Original Reporter
@Lukasa

Type
Bug

Environment
Swift version 5.1 (swift-5.1-RELEASE)
Target: x86_64-unknown-linux-gnu

Additional Detail from JIRA

Votes
1

Component/s
Compiler

Labels
Bug

Assignee
@devincoughlin

Priority
Medium

md5: b512a39de2bfe46bfd0ebc6402d51081

Issue Description:
If you have an availability annotation that wants to version guard the Catalyst SDK, this triggers warnings when using the OSS version of Swift. This seems like an unnecessary hardship to bear until the next Swift release:
warning: unrecognized platform name 'macCatalyst'
@available(iOS 13.0, macOS 10.15, watchOS 6.0, tvOS 13.0, macCatalyst 13.0, *)

I believe this was resolved by https://github.com/apple/swift/pull/29017.


UX suggestions

Always display icons together with text, and vice versa.  Right now it seems in the top buttons the text only shows up on hover, IMO it should just show all the time.

Make it so that when you hover over something clickable (e.g. the web view), the mouse pointer coverts to the "pointer" (the little glove with the pointer finger).  I like the color change, but this cursor change on hover is the universal idiom for "I can be clicked and it will do something!"  In CSS this rule is something like

a:hover {
    cursor: pointer;
}

if I recall correctly.
I think I had one more, so I'll post if I remember it.

Oh yes, I remembered the last one.  In any case where you're displaying something that goes host => container e.g. volumes and ports, make sure that you get the order consistent with what Docker displays (it always is host => container).

Thanks for the suggestions @nathanleclaire! :)

:+1:

Made buttons more obvious, and there are tooltips on hover


Replace generic List return type with IList

Fixes https://github.com/aspnet/AspNetCore.Docs/issues/14761
Return IList<T> instead, per https://docs.microsoft.com/visualstudio/code-quality/ca1002?view=vs-2019.

Framework guidelines are for the framework.

@rynowak Is this rule still a good idea for .NET Core?

Rules like this are not relevant for controllers.
This is guidance for creating a maintainable public API surface that will be used by other libraries, so that you can evolve it without binary breaking changes. None of these things are concerns with an MVC action method.


Strange hanging provider verification

I've been running into a strange verification issue, where my build just hangs. Locally, it seems to reliably run just fine (M1 Mac and also via intel emulation in Docker).
The setup:

Pact Go project (https://github.com/pact-foundation/pact-go/blob/wip/test-plugin-only/examples/plugin/provider_plugin_test.go)
An HTTP provider test that uses the MATT plugin.
Example build hang: https://github.com/pact-foundation/pact-go/actions/runs/3756820589/jobs/6383332478
Logs from the Matt Plugin in the same job. Note I've separated some sections with newlines to aid visibility where the plugin has been started up.

2022/12/22 10:07:12 lumberjack logging initialised
2022/12/22 10:07:12 [DEBUG] initialised logging
2022/12/22 10:07:12 [INFO] server on port 43957
2022/12/22 10:07:12 [INFO] InitPlugin request: plugin-driver-rust 0.2.2
2022/12/22 10:07:12 [INFO] UpdateCatalogue request: [type:TRANSPORT  key:"matt" key:"matt"  values:{key:"content-types"  value:"text/matt;application/matt"}]

2022/12/22 10:08:00 lumberjack logging initialised
2022/12/22 10:08:00 [DEBUG] initialised logging
2022/12/22 10:08:00 [INFO] server on port 43251
2022/12/22 10:08:00 [INFO] InitPlugin request: plugin-driver-rust 0.2.2

2022/12/22 10:08:00 lumberjack logging initialised
2022/12/22 10:08:00 [DEBUG] initialised logging
2022/12/22 10:08:00 [INFO] server on port 38435
2022/12/22 10:08:00 [INFO] InitPlugin request: plugin-driver-rust 0.2.2

2022/12/22 10:08:00 lumberjack logging initialised
2022/12/22 10:08:00 [DEBUG] initialised logging
2022/12/22 10:08:00 [INFO] server on port 34817

The test times out after 30s (default Golang test timeout). If you notice, the plugin is actually started 4 times (resulting in 4 separate processes on different ports). 3 of them received an InitPlugin request and the first also received the UpdateCatalogue request.
Running locally, I can see that 3/4 of the matt processes were started and continue to run after the tests complete:
  UID   PID  PPID   C STIME   TTY           TIME CMD
  502 28591     1   0  9:21pm ttys001    0:00.01 /Users/matthew.fellows/.pact/plugins/matt-0.0.7/matt
  502 28653     1   0  9:21pm ttys001    0:00.01 /Users/matthew.fellows/.pact/plugins/matt-0.0.7/matt
  502 28715     1   0  9:21pm ttys001    0:00.02 /Users/matthew.fellows/.pact/plugins/matt-0.0.7/matt

This doesn't seem to happen with the protobuf plugin, so I do have my suspicions of this being a matt plugin specific problem.
Update
So I increased the test timeout by another 100s to get past the Golang timeout (in case that was all it was. It wasn't). The build failed with a verification error code of 2 (https://github.com/pact-foundation/pact-go/actions/runs/3758088926/jobs/6386014379#step:5:2542) which indicates the verification process wasn't able to run.
This leads me further down the "matt plugin" problem, but there are no obvious logs to indicate the process was killed/died or panic'd (I've also wrapped the plugin's main process in a panic recover(), so it would catch and log any of those). What's also confusing, is that this plugin works with the Pact JS builds on linux. But it does seem like the driver is trying to start the plugin and run the verification, but something goes wrong and it has to continually try and start a new plugin process.
The logs from the plugin are interesting, with an extra plugin process starting this time:
2022/12/22 13:02:45 lumberjack logging initialised
2022/12/22 13:02:45 [DEBUG] initialised logging
2022/12/22 13:02:45 [INFO] server on port 35233
2022/12/22 13:02:45 [INFO] InitPlugin request: plugin-driver-rust 0.2.2
2022/12/22 13:02:45 [INFO] UpdateCatalogue request: [key:"matt"  values:{key:"content-types"  value:"text/matt;application/matt"} type:TRANSPORT  key:"matt"]
2022/12/22 13:03:47 lumberjack logging initialised
2022/12/22 13:03:47 [DEBUG] initialised logging
2022/12/22 13:03:47 [INFO] server on port 36493
2022/12/22 13:03:47 [INFO] InitPlugin request: plugin-driver-rust 0.2.2
2022/12/22 13:03:47 lumberjack logging initialised
2022/12/22 13:03:47 [DEBUG] initialised logging
2022/12/22 13:03:47 [INFO] server on port 37547
2022/12/22 13:03:47 [INFO] InitPlugin request: plugin-driver-rust 0.2.2
2022/12/22 13:03:47 [INFO] UpdateCatalogue request: [type:MATCHER  key:"v3-includes" type:MATCHER  key:"v2-max-type" key:"json"  values:{key:"content-types"  value:"application/.*json,application/json-rpc,application/jsonrequest"} type:MATCHER  key:"v2-min-type" type:MATCHER  key:"v3-number-type" type:TRANSPORT  key:"matt" type:MATCHER  key:"v4-not-empty" key:"matt"  values:{key:"content-types"  value:"text/matt;application/matt"} type:CONTENT_GENERATOR  key:"json"  values:{key:"content-types"  value:"application/.*json,application/json-rpc,application/jsonrequest"} type:MATCHER  key:"v3-null" type:MATCHER  key:"v2-minmax-type" type:MATCHER  key:"v3-date" key:"text"  values:{key:"content-types"  value:"text/plain"} key:"xml"  values:{key:"content-types"  value:"application/.*xml,text/xml"} type:MATCHER  key:"v3-integer-type" type:MATCHER  key:"v4-max-equals-ignore-order" key:"multipart-form-data"  values:{key:"content-types"  value:"multipart/form-data,multipart/mixed"} type:MATCHER  key:"v4-array-contains" type:MATCHER  key:"v1-equality" type:MATCHER  key:"v4-minmax-equals-ignore-order" type:CONTENT_GENERATOR  key:"binary"  values:{key:"content-types"  value:"application/octet-stream"} type:MATCHER  key:"v3-decimal-type" type:MATCHER  key:"v4-semver" type:MATCHER  key:"v3-time" type:MATCHER  key:"v2-regex" type:MATCHER  key:"v4-min-equals-ignore-order" type:MATCHER  key:"v2-type" type:MATCHER  key:"v4-equals-ignore-order" type:MATCHER  key:"v3-datetime" type:MATCHER  key:"v3-content-type"]
2022/12/22 13:03:47 lumberjack logging initialised
2022/12/22 13:03:47 [DEBUG] initialised logging
2022/12/22 13:03:47 [INFO] server on port 41019
2022/12/22 13:03:47 [INFO] InitPlugin request: plugin-driver-rust 0.2.2
2022/12/22 13:03:47 lumberjack logging initialised
2022/12/22 13:03:47 [DEBUG] initialised logging
2022/12/22 13:03:47 [INFO] server on port 41107

What I found really interesting, is that the github agent detected the orphaned processes:
2022-12-22T13:18:57.6873264Z Cleaning up orphan processes
2022-12-22T13:18:57.7135586Z Terminate orphan process: pid (6006) (matt)
2022-12-22T13:18:57.7156236Z Terminate orphan process: pid (6014) (matt)
2022-12-22T13:18:57.7173464Z Terminate orphan process: pid (6023) (matt)

These were the first three plugins started by the framework, my assumption is that the last one the driver started (PID 6031) was shutdown by the framework (albeit I can't see any logs to validate this). This indicates the processes didn't die, but somehow the driver lost track of them or deliberately orphaned them?

So after rubber ducking, I noticed that the pact file curiously had the following:
...
  "metadata": {
    "pactRust": {
      "ffi": "0.3.18",
      "mockserver": "0.9.8",
      "models": "1.0.2"
    },
    "pactSpecification": {
      "version": "4.0"
    },
    "plugins": [
      {
        "configuration": {},
        "name": "matt",
        "version": "0.0.1"
      },
      {
        "configuration": {},
        "name": "matt",
        "version": "0.0.2"
      },
      {
        "configuration": {},
        "name": "matt",
        "version": "0.0.4"
      },
      {
        "configuration": {},
        "name": "matt",
        "version": "0.0.5"
      }
    ]
  },
...

Note the version of the plugin in the test itself was 0.0.7. I presumably hadn't run and committed the pact file with the latest version, but that might explain why the plugin was started 5 times.
Interestingly, even though 0.0.7 wasn't in the pact file, it was specified in the test itself, and that was the only version that was started up (as all of the log files were obtained from that version).
The other plugin tests were reliably working because this just so happened to be the only test that didn't write to a shared pact directory which was cleaned out prior to each test run - so that is likely the explanation for how so many plugins were stored in the pact file.
What next
Given the difficultly in tracking this down, is there a change we can make to either make the problem more visible to the user or perhaps preventing having multiple unused plugins written to the pact file?


Ensure and verify k3s passes kubernetes conformance tests

@erikwilson please link to the PR you submit to register k3s

PR accepted https://github.com/cncf/k8s-conformance/pull/489


re-org of lookup

There's a lot of lookup-related code. I think I could find things mostly in:

polynomials/lookup.rs -> large file
gate.rs -> circuit-agnostic computations
prover.rs -> lots of logic should be abstracted away from that file

I think we should do the following:

[ ] move the chacha-specific code to the chacha gate. Ideally gates should contain the lookup logic that is related to them
[ ] create lazily evaluated statics for the circuit-agnostic computations
[ ] create a lookup folder in circuits/lookup to host the logic of lookups
[ ] move all the lookup code from gate.rs, prover.rs, and polynomials/lookup.rs in this folder. Ideally split in several files.

cc @mrmr1993

PR that introduces the lookup folder: https://github.com/o1-labs/proof-systems/pull/440


NetCDF: HDF error

To report a non-security related issue, please provide:

the version of the software with which you are encountering an issue
netcdf-c v4.7.3 and also master
using hdf5-1.10.5

environmental information (i.e. Operating System, compiler info, java version, python version, etc.)
Ubuntu 16.04
CXX=clang++-7.0 CC=clang-7.0
For compiling HDF5 I used:
CXX=clang++-7.0 CC=clang-7.0 cmake -DCMAKE_INSTALL_PREFIX=/opt/hdf5 ..
For compiling netcdf-c I used:
CXX=clang++-7.0 CC=clang-7.0 \   cmake \       -DCMAKE_INSTALL_PREFIX=/opt/netcdf-c \       -DENABLE_PARALLEL_TESTS=OFF \       -DENABLE_BYTERANGE=ON \       ..
There was no problem at compilation time. Everything build successfully.

a description of the issue with the steps needed to reproduce it
ncdump 3B.nc4

the test file can be downloaded from here
http://tpch-rmm-fk.s3.eu-central-1.amazonaws.com/3B.nc4
If you have a general question about the software, please view our Suggested Support Process.
The problem is that I cannot read an hdf5 file that was converted into nc4. I always get the following error which I don't know where to start looking from:
 precipitationQualityIndex = NetCDF: HDF error Location: file /tmp/netcdf-c/ncdump/vardata.c; line 478   root@fc569074bc6c:/opt/netcdf-c/bin# vim /tmp/netcdf-c/ncdump/vardata.c
Any pointers or suggestions are highly appreciated.

Can you open the file with a C program? (That is, without ncdump).
Try a program that does something like this:
if (nc_open(FILE, 0, &ncid)) ERR;
if (nc_close(ncid)) ERR;

Make sure you check the return codes. Also, upload a copy of the file.
Did this work with previous versions of netCDF?
Also you say you converted a HDF5 into NC4? How exactly? You should be able to read the original HDF5 file directly with netCDF, with no conversion necessary.

I can read the file 3B.nc4 successfully and completely with ncdump-4.7.3 and HDF5-1.10.5 on Mac OS 10.14.6 (Mojave).  However, I find two strange things about this file.

The file time stamp is October 15.  This pre-dates the netcdf-c-4.7.3 release.  Therefore I assume that your problem is specifically with ncdump-4.7.3, and not the nccopy version that made this file.

Chunk sizes are 1024 x 1024.  This is large enough to exceed the default chunk cache, causing ncdump to run absurdly slowly when displaying data arrays.  This is a known problem, but it is a very different problem than your HDF error.

Do you have any HDF environment variables set?  Please show the result of env | grep -i hdf.  Also, sigh, you might as well show ldd on the full path of your ncdump executable.
I think the main problem is in your 4.7.3 ncdump and library.  I suggest focussing on that, not the test file.

Also please show the last line of ncdump with no file or other arguments.  This shows another clue about your ncdump version.

Thanks for the prompt reply @edwardhartnett !
I found the problem with some debugging. The problem was that on my installation I removed zlib library, and although everything compiled properly, I would just get that error.
I fixed the problem by making hdf5 to enable support for zlib
 CXX=clang++-7.0 CC=clang-7.0 cmake -DCMAKE_INSTALL_PREFIX=/opt/hdf5 -DHDF5_ENABLE_Z_LIB_SUPPORT=ON ..
I think the HDF library should have this option enabled by default as people might use it anywhere and disable it otherwise. Thanks anyway!


Timed/Periodic payments helpers

Contracts want to send periodic or timed payments. E.g: "send x ether to this address every week for 5 weeks". Or "Send x ether to this address in 10 days".
We should write a contract that does that securely

Such a feature would be easily implemented via ConditionalEscrows, where only amounts smaller than the currently vested value can be withdrawn. Regarding having someone else execute the transactions, metatransactions are probably the way forward.
Closing to reduce issue clutter.


Can't install cutorch due to "nvcc fatal: Unsupported gpu architecture" even if I have the most recent CUDA toolkit and driver

Cuda toolkit and driver are properly installed. Listing from terminal is below.
-- Found Torch7 in /home/boris/torch/install
-- Removing -DNDEBUG from compile flags
-- TH_LIBRARIES: TH
-- MAGMA not found. Compiling without MAGMA support
-- Autodetected CUDA architecture(s): 2.1(2.0)
-- got cuda version 9.0
-- Found CUDA with FP16 support, compiling with torch.CudaHalfTensor
-- CUDA_NVCC_FLAGS: -gencode;arch=compute_20,code=sm_21;-DCUDA_HAS_FP16=1
-- THC_SO_VERSION: 0
-- Configuring done
-- Generating done
-- Build files have been written to: /home/boris/torch/extra/cutorch/build
[  3%] Building NVCC (Device) object lib/THC/CMakeFiles/THC.dir/THC_generated_THCHalf.cu.o
[  3%] Building NVCC (Device) object lib/THC/CMakeFiles/THC.dir/THC_generated_THCReduceApplyUtils.cu.o
[  3%] Building NVCC (Device) object lib/THC/CMakeFiles/THC.dir/THC_generated_THCBlas.cu.o
[  5%] Building NVCC (Device) object lib/THC/CMakeFiles/THC.dir/THC_generated_THCTensor.cu.o
[  8%] Building NVCC (Device) object lib/THC/CMakeFiles/THC.dir/THC_generated_THCSleep.cu.o
[  8%] Building NVCC (Device) object lib/THC/CMakeFiles/THC.dir/THC_generated_THCStorageCopy.cu.o
[  5%] Building NVCC (Device) object lib/THC/CMakeFiles/THC.dir/THC_generated_THCStorage.cu.o
[  8%] Building NVCC (Device) object lib/THC/CMakeFiles/THC.dir/THC_generated_THCTensorCopy.cu.o
nvcc fatal   : Unsupported gpu architecture 'compute_20'
CMake Error at THC_generated_THCReduceApplyUtils.cu.o.cmake:207 (message):
Error generating
/home/boris/torch/extra/cutorch/build/lib/THC/CMakeFiles/THC.dir//./THC_generated_THCReduceApplyUtils.cu.o
nvcc fatal   : Unsupported gpu architecture 'compute_20'
nvcc fatal   : Unsupported gpu architecture 'compute_20'
CMake Error at THC_generated_THCBlas.cu.o.cmake:207 (message):
Error generating
/home/boris/torch/extra/cutorch/build/lib/THC/CMakeFiles/THC.dir//./THC_generated_THCBlas.cu.o
CMake Error at THC_generated_THCHalf.cu.o.cmake:207 (message):
Error generating
/home/boris/torch/extra/cutorch/build/lib/THC/CMakeFiles/THC.dir//./THC_generated_THCHalf.cu.o
lib/THC/CMakeFiles/THC.dir/build.make:70: recipe for target 'lib/THC/CMakeFiles/THC.dir/THC_generated_THCBlas.cu.o' failed
make[2]: *** [lib/THC/CMakeFiles/THC.dir/THC_generated_THCBlas.cu.o] Error 1
make[2]: *** Waiting for unfinished jobs....
lib/THC/CMakeFiles/THC.dir/build.make:560: recipe for target 'lib/THC/CMakeFiles/THC.dir/THC_generated_THCHalf.cu.o' failed
make[2]: *** [lib/THC/CMakeFiles/THC.dir/THC_generated_THCHalf.cu.o] Error 1
lib/THC/CMakeFiles/THC.dir/build.make:63: recipe for target 'lib/THC/CMakeFiles/THC.dir/THC_generated_THCReduceApplyUtils.cu.o' failed
make[2]: *** [lib/THC/CMakeFiles/THC.dir/THC_generated_THCReduceApplyUtils.cu.o] Error 1
nvcc fatal   : Unsupported gpu architecture 'compute_20'
CMake Error at THC_generated_THCTensor.cu.o.cmake:207 (message):
Error generating
/home/boris/torch/extra/cutorch/build/lib/THC/CMakeFiles/THC.dir//./THC_generated_THCTensor.cu.o
lib/THC/CMakeFiles/THC.dir/build.make:98: recipe for target 'lib/THC/CMakeFiles/THC.dir/THC_generated_THCTensor.cu.o' failed
make[2]: *** [lib/THC/CMakeFiles/THC.dir/THC_generated_THCTensor.cu.o] Error 1
nvcc fatal   : Unsupported gpu architecture 'compute_20'
CMake Error at THC_generated_THCTensorCopy.cu.o.cmake:207 (message):
Error generating
/home/boris/torch/extra/cutorch/build/lib/THC/CMakeFiles/THC.dir//./THC_generated_THCTensorCopy.cu.o
nvcc fatal   : Unsupported gpu architecture 'compute_20'
lib/THC/CMakeFiles/THC.dir/build.make:105: recipe for target 'lib/THC/CMakeFiles/THC.dir/THC_generated_THCTensorCopy.cu.o' failed
make[2]: *** [lib/THC/CMakeFiles/THC.dir/THC_generated_THCTensorCopy.cu.o] Error 1
CMake Error at THC_generated_THCStorageCopy.cu.o.cmake:207 (message):
Error generating
/home/boris/torch/extra/cutorch/build/lib/THC/CMakeFiles/THC.dir//./THC_generated_THCStorageCopy.cu.o
lib/THC/CMakeFiles/THC.dir/build.make:91: recipe for target 'lib/THC/CMakeFiles/THC.dir/THC_generated_THCStorageCopy.cu.o' failed
make[2]: *** [lib/THC/CMakeFiles/THC.dir/THC_generated_THCStorageCopy.cu.o] Error 1
nvcc fatal   : Unsupported gpu architecture 'compute_20'
CMake Error at THC_generated_THCStorage.cu.o.cmake:207 (message):
Error generating
/home/boris/torch/extra/cutorch/build/lib/THC/CMakeFiles/THC.dir//./THC_generated_THCStorage.cu.o
nvcc fatal   : Unsupported gpu architecture 'compute_20'
CMake Error at THC_generated_THCSleep.cu.o.cmake:207 (message):
Error generating
/home/boris/torch/extra/cutorch/build/lib/THC/CMakeFiles/THC.dir//./THC_generated_THCSleep.cu.o
lib/THC/CMakeFiles/THC.dir/build.make:84: recipe for target 'lib/THC/CMakeFiles/THC.dir/THC_generated_THCStorage.cu.o' failed
make[2]: *** [lib/THC/CMakeFiles/THC.dir/THC_generated_THCStorage.cu.o] Error 1
lib/THC/CMakeFiles/THC.dir/build.make:77: recipe for target 'lib/THC/CMakeFiles/THC.dir/THC_generated_THCSleep.cu.o' failed
make[2]: *** [lib/THC/CMakeFiles/THC.dir/THC_generated_THCSleep.cu.o] Error 1
CMakeFiles/Makefile2:172: recipe for target 'lib/THC/CMakeFiles/THC.dir/all' failed
make[1]: *** [lib/THC/CMakeFiles/THC.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2
Error: Build error: Failed building.
boris:torch$ nvcc -V
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2017 NVIDIA Corporation
Built on Fri_Sep__1_21:08:03_CDT_2017
Cuda compilation tools, release 9.0, V9.0.176

Turned out to be not cutorch problem.
The problem was that CUDA 9 toolkit doesn't support my GPU architecture anymore. I had to install version 8 instead.

@borismu  how can i know if CUDA 9 toolkit doesn't support my GPU architecture or it does plz ? (commands)


Add export version to consignment endpoint

Would this be a breaking change? The export is expecting updateExportLocation and this is being removed and changed to updateExportData You can't deploy the export or the API first without breaking the export I don't think. Does that sound right?
If it is then we should add in a field for the existing mutation without the export version, either by putting in a static value or by changing the database to make the field nullable then changing it back once the export has switched over to use the new endpoint.
If I've missed something and we can deploy without breaking anything then ignore me.

Yes, you're right; this is a breaking change. Cool, I'll add a temporary default value

I think I've figured out a solution to prevent any breaking. Let me know what you think.


Preparation of the guide for the meeting (issue #53 related)

Guide was moved to Source, here are the links to the pdf and jupiter files:
https://cocalc.com/projects/cdcf3856-3e8b-4d1c-bcb2-5c42ba749d83/files/UCZESTNICY/Guide_Source/Source/[PL] [Guide] [Programming]Wprowadzenie ODESystem.ipynb
https://cocalc.com/projects/cdcf3856-3e8b-4d1c-bcb2-5c42ba749d83/files/UCZESTNICY/Guide_Source/Source/Output/[PL][Guide][Programming][PL][Guide][ODESystem]Obsługa klasy ODESystem.pdf


Route options not found

hello i have a problem route options not found in revel. im using vuejs with axios.

this is my code in file routes in revel
`GET /posts PostController.Index
POST /posts PostController.Create
PUT /posts PostController.Update
GET /posts/:id PostController.Show
DELETE /posts/:id PostController.Delete`

Was there any additional log messages on the server ?
On Mon, Jul 23, 2018 at 8:52 AM, Juancesar123<EMAIL_ADDRESS>wrote:

hello i have a problem route options not found in revel. im using vuejs
with axios.
[image: image]
https://user-images.githubusercontent.com/16625151/43087690-a4fcbf06-8eca-11e8-8035-a648277a0bf7.png
this is my code in file routes in revel
`GET /posts PostController.Index
POST /posts PostController.Create
PUT /posts PostController.Update
GET /posts/:id PostController.Show
DELETE /posts/:id PostController.Delete`
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/revel/revel/issues/1350, or mute the thread
https://github.com/notifications/unsubscribe-auth/ABUsBqqj9t5FCW2RI2GuS1zo0jcjvGi7ks5uJfFDgaJpZM4VbP2l
.

You may just need to add an options handler into your routes config file.  Especially if you're trying to do a CORS request.

If vue.js was posting the information it would not find the route. I am closing this for now, feel free to reopen if still an issue

Hi, I have the same problem could anyone show any example about how to add options method to the router?
I'am getting 404: status=404 duration_seconds=0.0005185 method=OPTIONS start=2019/05/28 15:46:14 section=requestlog   ip=<IP_ADDRESS>
INFO  15:46:14    app server_adapter_go.go:158: Request Stats
I'm new in revel.
Thank you

Here's an example that might help.  I have this running in my BaseController which gets inherited by all controllers that I want to use CORS with.
//in BaseController

//Method for retrieving the request origin from the request referer
func (c BaseController) GetOrigin() string {
  referer := c.Request.Header.Get("Referer")
  re := regexp.MustCompile("^http[s]?\\:\\/\\/[\\w\\:\\.\\d\\-]+")
  return re.FindString(referer)
}

//CORS OPTIONS response for handling CORS preflight
func (c BaseController) Options() revel.Result {
  c.Response.Out.Header().Set("Access-Control-Allow-Origin", c.GetOrigin())
  c.Response.Out.Header().Set("Access-Control-Allow-Credentials", "true")
  c.Response.Out.Header().Set("Access-Control-Allow-Methods", "POST, GET, PUT, OPTIONS, DELETE")
  return nil
}

Next, in your conf/route file add:
OPTIONS    /*                                BaseController.Options

That should allow you to send an OPTIONS request and have it routed to a controller.  The response should automatically allow the origin being pulled from the request.  If you want to limit the origin, feel free to change the line containing c.GetOrigin(). Hope this helps.

Many thanks for your quick answer!
I've tried to reproduce your example in my code.
I' still getting Access to XMLHttpRequest at 'http://localhost:9000/player/AHSHDHSDH' from origin 'http://localhost:3000' has been blocked by CORS policy: Request header field content-type is not allowed by Access-Control-Allow-Headers in preflight response.
do you know why is it happening that?

package controllers
import (
"github.com/revel/revel"
"regexp"
)
type App struct {
*revel.Controller
}
func (c App) Index() revel.Result {
return c.Render()
}
func (c App) GetOrigin() string {
referer := c.Request.Header.Get("Referer")
re := regexp.MustCompile("^http[s]?\:\/\/[\w\:\.\d\-]+")
return re.FindString(referer)
}
//CORS OPTIONS response for handling CORS preflight
func (c App) Options() revel.Result {
c.Response.Out.Header().Set("Access-Control-Allow-Origin", c.GetOrigin())
c.Response.Out.Header().Set("Access-Control-Allow-Credentials", "true")
c.Response.Out.Header().Set("Access-Control-Allow-Methods", "GET,PUT,POST,DELETE,PATCH,OPTIONS")
return nil
}

@jonathanbrenman What does your conf/routes file look like?

Yes! I always kill and restart the process when I change something out of the controllers lol

Hmmm....I wonder.  Try moving the OPTIONS /* statement to be the first line in your routes conf and try that.  If that doesn't work, then let's start adding debug statements to your Options method to see if it's even being called.

I did that and restart the process and this what I'm getting:

ion=App.Options namespace=App\\ start=2019/05/29 13:34:09 status=0 section=requestlog
INFO  13:34:13    app server_adapter_go.go:158: Request Stats                            section=requestlog ip=<IP_ADDRESS> method=OPTIONS action=App.Options namespace=App\\ duration_seconds=0.0000759   path=/player/17VSVW1503594373 start=2019/05/29 13:34:13 status=0
INFO  13:34:13    app server_adapter_go.go:158: Request Stats                            method=OPTIONS action=App.Options namespace=App\\ start=2019/05/29 13:34:13 status=0 duration_seconds=0.0000582  path=/player/17VSVW1503594373 section=requestlog  ip=<IP_ADDRESS>
INFO  13:34:13    app server_adapter_go.go:158: Request Stats                            namespace=App\\ start=2019/05/29 13:34:13 section=requestlog  ip=<IP_ADDRESS> action=App.Options status=0 duration_seconds=0.0000557  path=/player/PVAZPK1542995892 method=OPTIONS

OK, that looks correct.  Can you verify that your routing is correct to the controller itself by adding output statements to the Options method?  Either log them or console out is fine, just to ensure it's making it to the Options method of your App controller.  Also, in your web console under network, what does the request and response look like for a valid action using CORS?  In otherwords, if you send a request to a method that exists in your App controller, say Ping() that writes out "Pong" or something.  What does the request and response look like for CORS preflight OPTIONS request?

I added to Options function: fmt.Println("do i actually called?"), and it is not working, like the options function is blocked out by the cors.

Access to XMLHttpRequest at 'http://localhost:9000/player/17VSVW1503594373?external_playlist=168,166,171' from origin 'http://localhost:3000' has been blocked by CORS policy: Request header field content-type is not allowed by Access-Control-Allow-Headers in preflight response.

Here other pic

Ok, I found the problem now!!! the issue was now on the client side I was doing the request with this xmlhttp.setRequestHeader('Content-Type', 'application/json') and for go i don't need it because it is already responded a json.
But you still helped me with the options cors!
Thank you very much for your help!!

Okay, great. Glad you found the issue. Have a good one.


Replace all print statement by click.echo

All the print statements that display information about the current context in the application should be replaced by the click.echo command.
Or better, declare a module that contains the logic of rendering in the terminal.
So that the click.echo could be encapsulated in a 'echo' function inside this module.

https://github.com/zergov/flashcards/commit/28fe587fd2817e607cf1b4c47dd4a96b4e32842b


Add a reset API to State

What problem does this solve or what need does it fill?
If I want to reset the game's current state (to trigger both the on_exit and on_enter systems, or just reinitialize everything within the state), I must manually exit the state and then re-enter it.
What solution would you like?
A built-in method in the API that would allow me to do state.reset().
I'm not familiar with the project's source code and have no idea how feasible that is.
What alternative(s) have you considered?
It can be done without much overhead by reserving a ResetCurrentState state that's only used for this, doesn't trigger any startup systems/systems, and immediatly state.pushes the last active state on enter, but this is cumbersome to setup and really seems like boilerplate code that could be avoided.

Hmm this is interesting, however what do we plan to have reset set the state to?
Current you construct a state and give it the initial state, however that state can be lost, so having a reset function might be difficult.
One possibilty is providing reset for states that implement Default and resetting them to the default value.

Hmm this is interesting, however, what do we plan to have reset set the state to?

I think he means "reenter" the current state and rerun its on_enter and on_exit systems. For example, suppose you have a Level state. To advance to the next level, you could increment a LevelNum resource and then "reset" the state, which will call the on_enter and on_exit systems regenerating the level, etc., and the difficulty could scale based on the LevelNum resource.
Currently, calling push or set with the current state does nothing.


remove trailing dash from cmd

Dash instructs shellcheck there are no options after the dash. But sometimes SublimeLinter provides args for shellcheck.
For example, I need shellcheck to follow source commands. It can be achieved with -x or --external-sources option:
$ shellcheck
No files specified.

Usage: shellcheck [OPTIONS...] FILES...
  -a                --check-sourced          Include warnings from sourced files
  -C[WHEN]          --color[=WHEN]           Use color (auto, always, never)
  -e CODE1,CODE2..  --exclude=CODE1,CODE2..  Exclude types of warnings
  -f FORMAT         --format=FORMAT          Output format (checkstyle, gcc, json, tty)
  -s SHELLNAME      --shell=SHELLNAME        Specify dialect (sh, bash, dash, ksh)
  -V                --version                Print version information
  -x                --external-sources       Allow 'source' outside of FILES

Next Setting will work only if there is no trailing dash in cmd:
// SublimeLinter Settings - User
{
    "linters": {
        "shellcheck": {
            "args": "-x"
        }
    }
}

I think the right way to do this would be to put ${args} before the dash. @kaste ?

@Wasapl you want to make the change? Otherwise I’ll look into it some time next week.

@braver Here is the update!

w00t


Updates to readme and packages

This PR addresses following tasks:

tidy up README to list runtime images and move long tutorial to a separate file.
update python package versions.
pull common packages to requirements_common.txt and reuse it across runtimes.

@rabbah Can you add yourself / other relevant reviewers? Thank you!

I do not think we can update package versions in existing runtimes because this would break compatibility. Usually you do newer versions of libraries in runtimes for newer versions of languages but leave the verions of packages in older runtimes. If you want newer versions of a package for an action you can always use a virtual env. I personally did an update of versions of runtimes and I was told to revert to older version of packages

Updating the versions of existing packages is OK. Vendors are more cognizant of these updates but we can keep things up to date.
There are some things in the README that should be updated (for example, we remove the "loop" from "actionloop") but since those exist in the current docs, we can fix this subsequent to the refactoring.
Thanks @sciabarracom sciabarra for the review and thanks @code247 for the contribution 🎉
Do you have a CLA on file with Apache, I could not find one.

Not sure what's going on with Travis. @code247 are you rebased to master?

The https://github.com/apache/openwhisk/blob/59b67fe96f44e573f3348afed966a1cdaf80ddf2/tools/actionProxy/invoke.py is here and its use is straightfoward: python3 invoke.py init <file> and python invoke.py run '<json>'. It is equivalent to almost all the curl you wrote but simpler to use.

@dgrove-oss can we disable the travis check on PRs? There's an issue with Travis reporting max users/seats exhausted. I'm going to try to run the Travis job as a GHA.

We can change the required checks by editing .asf.yaml.

fwiw, the last travis run on this PR failed because of a missing license header, not a max user problem

Thanks @dgrove-oss - the travis link wasn't showing me the build. Of course, I should've gone to Travis' dashboard directly.
the previous build: https://app.travis-ci.com/github/apache/openwhisk-runtime-python/builds/238685042
the current build: https://app.travis-ci.com/github/apache/openwhisk-runtime-python/builds/239149380

yeah, its on my back burner list to go through all of the readme.md files and add /github to the travis url piece like I did here: https://github.com/apache/openwhisk-runtime-docker/commit/4f85c3924663ba871af672d3cfe35efcf31f0e20

thanks @code247 🎉


[BUGFIX]Restart controller and restore port allocator when port allocation leak happens

Ⅰ. Describe what this PR does

Restart controller and restore port allocator when port allocation leak happens
Add warning logs to indicate some ports may already be leaked

Ⅱ. Does this pull request fix one issue?

NONE
Ⅲ. List the added test cases (unit test/integration test) if any, please explain if no tests are needed.
no tests are needed
Ⅳ. Describe how to verify it

Set a tight port range with helm install --set runtime.alluxio.portRange=20000-20010 fluid fluid
Create a dataset with AlluxioRuntime.
Delete the corresponding ConfigMap <dataset-name>-alluxio-values. Then delete the dataset, now the allocated port is leaked.
Create a new dataset.
The alluxioruntime-controller should exit with error code and restart to restore port allocator.

Ⅴ. Special notes for reviews

@TrafalgarZZZ
Please fix the CI. Thanks.
W0413 15:41:44.241245   51935 client_config.go:622] error creating inClusterConfig, falling back to default config: unable to load in-cluster configuration, KUBERNETES_SERVICE_HOST and KUBERNETES_SERVICE_PORT must be defined
--- FAIL: TestGooseFSEngineReleasePorts (0.00s)
    --- FAIL: TestGooseFSEngineReleasePorts/spark (0.00s)
panic: runtime error: invalid memory address or nil pointer dereference [recovered]
	panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x18 pc=0x62524a]


retrieve sentence_text by calling evidence.get_sentence_text(sent_id uuid) - to be replaced by the SentenceAPI lateron

unrelevant with CQL


How can I use GoRun to run a simple .go file?

Hi, I'm learning golang and I came across your amazing plugin. I do have a question related to the GoRun command, which is how can I use GoRun to run a simple .go file?
Let's say I only have a main.go file. I can use :!go run main.go, but it's quite boring. Can I use GoRun instead? Is it supported atm? If I use :GoRun main.go, it just say go run main.go succeeed and doesn't print the results. Thank you :pray:
The main.go file is just this:
package main

import "fmt"

func main() {
	a := 2
	b := 2

	if a < b {
		fmt.Println("a is smaller than b")
	}

	if a > b {
		fmt.Println("a is larger than b")
	}

	if a == b {
		fmt.Println("a is equal to b")
	}
}

Do you have any output from quickfix.  Also you can run with floating terminal.

If I run GoRun main.go, quickfix won't open. Just vim.notify go run main.go succeeed. No results output.
If I run GoRun main.go -F, the result will be printed out:
a is equal to b

[Process exited 0]

You should see this in quickfix.

Could you either try init.lua in playground folder or send a minium init.lua for me to reproduce?

Hi man, I check it again and now quickfix will prints out results. Floating window also works fine.
1 small problem is that while quickfix prints out the correct results, there's also a notify go run main.go failed, it's very odd.

Hmm.. I wonder if there's an option to disable the promt?

Not really. You can disable vim.notify to popup by disabling the UI hook (I think it is dressing.nvim) once the go.nvim is loaded.

Yeah I mean having something in the setup function for go.nvim to not use the vim.notify when using GoRun, but this is such a minor issue. The floating window is working very nice already.
I use this to execute the file:
vim.keymap.set(
	"n",
	"<Leader>x",
	function() vim.cmd("GoRun " .. vim.fn.expand("%") .. " -F") end,
	{ noremap = true, silent = true }
)

Thanks for the update.
I update the title, in case anyone also sees the notification incorrect message. Feel free to post your setup here and reopen the issue.


Adds Visualizer Component

Adds a Redux store to electron main to share store info between windows
Resolves #50

[x] Create a Redux Store in the Electron Main process to mirror the application state and allow shared state across windows without needing to pass data through an ipc hack.
[x]  Create Visualizer component conditionally shown only on Visualizer job pages
[x] Add interactivity to Visualizer component
[x] Add server api for "live" updating of Visualizers in action

[x] Create actions and reducers to be able to handle "live" updating of Visualizers

[x] Add a window state to track previously viewed Visualizations
[x] Clean up Visualization items from the server on window close

Also:

[x] Add Visualization view to individual Visualization inspection windows

BONUS: windowState already handles the cleanup of these files with no changes!

Looking good @jakereps! https://github.com/qiime2/qiime2/pull/76 just got merged, so we should be able to use extract and get_index_paths on a Visualization object to create a sandboxed iframe.

Looks like we should use the electron webview tag for this instead of an iframe!

Ready for review whenever you get a chance, @ebolyen!

@jakereps, functionally looks pretty awesome! starting a code review now

Code looks great @jakereps, just need to version bump and figure out a different way to identify a running state (thanks webpack!)

Thanks for the review @ebolyen! Should be good to go! The webpack issue was surprisingly easier to solve than I thought it'd be. React.Component.displayName for the win!

:space_invader: :space_invader: :space_invader:
:sparkler: :black_large_square: :sparkler:
:black_large_square: :sparkler: :black_large_square:
:1234: :black_large_square: :1234:


Private Channel

Are the private channels bound to the experation date of the Team ?

@Mr4green Thank you for submitting feedback.
I think the best way forward is if you open a service ticket in your tenant so this can get resolved ASAP. Based on the outcome let me know if it is something that can be called out in the docs.
Please follow this link to contact support for business products:https://docs.microsoft.com/office365/admin/contact-support-for-business-products
Please keep us posted here on the resolution so we can feed whatever information you discover into the content.


Upgrade to ArcGIS Pro

This is a year old issue. @daren-thomas are we expecting this? I believe it would be a great add on. but i would get the issue out of the list if we do not plan to develop it any time soon.

@JIMENOFONSECA I am currently working on the decoupling of CEA from ArcGIS which would make moving to ArcGIS Pro much easier. But personally I don't think it is important. If you like we can delete this.

Yep i do not see it coming in the next couple of years...
Best, Jimeno
On 20 Mar 2017, at 21:48, Daren Thomas <notifications<EMAIL_ADDRESS>wrote:
@JIMENOFONSECAhttps://github.com/JIMENOFONSECA I am currently working on the decoupling of CEA from ArcGIS which would make moving to ArcGIS Pro much easier. But personally I don't think it is important. If you like we can delete this.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/architecture-building-systems/CEAforArcGIS/issues/91#issuecomment-287763786, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIjrgprbmuEohlLv5N_cpHxFDEyA8DmVks5rnoOtgaJpZM4Hyv2Y.


Not able to install in Windows

C:\Python27\Scripts>python get-pip.py
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting pip
c:\users\pc\appdata\local\temp\tmpse7zyx\pip.zip\pip_vendor\urllib3\util\ssl_.py:354: SNIMissingWarning: An HTTPS request has been made, but the SNI (Server Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
c:\users\pc\appdata\local\temp\tmpse7zyx\pip.zip\pip_vendor\urllib3\util\ssl_.py:150: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, 'ssl.c:499: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version'),)': /simple/pip/
c:\users\pc\appdata\local\temp\tmpse7zyx\pip.zip\pip_vendor\urllib3\util\ssl.py:150: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, 'ssl.c:499: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version'),)': /simple/pip/
c:\users\pc\appdata\local\temp\tmpse7zyx\pip.zip\pip_vendor\urllib3\util\ssl.py:150: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, 'ssl.c:499: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version'),)': /simple/pip/
c:\users\pc\appdata\local\temp\tmpse7zyx\pip.zip\pip_vendor\urllib3\util\ssl.py:150: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, 'ssl.c:499: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version'),)': /simple/pip/
c:\users\pc\appdata\local\temp\tmpse7zyx\pip.zip\pip_vendor\urllib3\util\ssl.py:150: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='pypi.org', port=443): Read timed out. (read timeout=15)",)': /simple/pip/
c:\users\pc\appdata\local\temp\tmpse7zyx\pip.zip\pip_vendor\urllib3\util\ssl_.py:150: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
ERROR: Could not find a version that satisfies the requirement pip (from versions: none)
ERROR: No matching distribution found for pip

Python : 2.7

What version of Python 2.7 did you install? 99% chance that it's a very old release. Upgrading the latest version will probably resolve this for you.

Please see the readme.


Add Docker development environment

Summary
This PR adds a docker-compose.yml file to help spin up a Splunk server for development. The Splunk server can be spun up with the command make splunk, from the root of the repository.
Ticket Link
Fixes https://github.com/mattermost/mattermost-plugin-splunk/issues/50

Codecov Report

Merging #51 (ef1608b) into master (00df927) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #51   +/-   ##
=======================================
  Coverage   13.24%   13.24%
=======================================
  Files           7        7
  Lines         385      385
=======================================
  Hits           51       51
  Misses        326      326
  Partials        8        8

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 00df927...ef1608b. Read the comment docs.

The plugin always uses https (https://github.com/mattermost/mattermost-plugin-splunk/blob/0d6e455c4c90156bbda2b0278f569b10f499a8cd/server/command/util.go#L17) This seems like a bug to me and should be fixed.
If one comments out that line, the error message is a bit more clear: http://localhost:8000/services/authentication/current-context returns a 404.

Let's merge this. I've tested the PR myself and it works like a charm. @mickmister Are you fine what that?


sharpen-simple-navigation needs to support a button (not link) for login

To get to the Auth0 login page, we need to make a POST request and not a GET request.
Fore reference, here is a snippet of code that successfully gets us to the Auth0 login page and what we need to be able to support.
<%= button_to t('buttons.log_in'),
                  '/auth/auth0',
                  id: 'login-button',
                  data: { turbo: "false" },
                  class: 'link',
                  method: :post %>

Maybe instead of making the link data a parameter to the component, can we pass it something instead in case we need to change how this works?

I am creating a general purpose slot for custom navigation in this component. I will also create a new class for styling buttons as simple links. Example:
<sharpen-simple-navigation background="sunrise" brand-href="https://sharpen.com">
  <div slot="custom-nav">
    <button class="sharpen-link">Log In</button>
  </div>
</sharpen-simple-navigation>

Released in 0.11.0


Windows CI regression Late July 2022

Until this morning, CI was happy:
https://github.com/ami-iit/idynfor/runs/7501627916?check_suite_focus=true
Now it is red:
https://github.com/ami-iit/idynfor/actions/runs/2735194992
The diff between working and not working is:
--- <unnamed>
+++ <unnamed>
@@ -1,4 +1,3 @@
-
   + assimp                                      5.2.4  hc2aa0de_0          conda-forge/win-64        2MB
   + asttokens                                   2.0.5  pyhd8ed1ab_0        conda-forge/noarch       22kB
   + backcall                                    0.2.0  pyh9f0ad1d_0        conda-forge/noarch       14kB
@@ -18,8 +17,8 @@
   + cxx-compiler                                1.4.2  h2d74725_0          conda-forge/win-64        5kB
   + decorator                                   5.1.1  pyhd8ed1ab_0        conda-forge/noarch       12kB
   + eigen                                       3.4.0  h2d74725_0          conda-forge/win-64        1MB
-  + eigenpy                                     2.7.7  py39h3ce40e6_0      conda-forge/win-64      981kB
-  + executing                                   0.8.3  pyhd8ed1ab_0        conda-forge/noarch       19kB
+  + eigenpy                                     2.7.8  py39h3ce40e6_0      conda-forge/win-64      972kB
+  + executing                                   0.9.0  pyhd8ed1ab_0        conda-forge/noarch       19kB
   + flang                                       5.0.0  he025d50_20180525   conda-forge/win-64        3MB
   + flang_win-64                                5.0.0  h13ae965_20180526   conda-forge/win-64        5kB
   + fortran-compiler                            1.4.2  h9655429_0          conda-forge/win-64        5kB

So probably it is an eigenpy 2.7.8 regression.

The problem could be that on Linux and macOS for some reason Python 3.10 is installed, while on Windows Python 3.9 is installed.


Probability cutoff?

Hello,
First of all again, many thanks for developing this great tool. I open this issue because I wanted to know which probability cutoff is recomended, in your opinion,  as a minimum to trust a 3Diaa prediction.
I haven't found such a rule of thumb in the documentation, and neither a clear definition of what is this probability cutoff (which, as far as I understand, is related to the NNs prediction -is this correct?-).
Many thanks in advance and sorry to bother with this.
Cheers,
Mauricio

Hi,
thanks again for your interest in our tools! :)
I asssume you are referring to the coverage/precision plot that we added to the most recent version of the paper (Fig. SOM S5 - also attached here).
You are right: the probability that this plot is referring to is the output probability of the CNN put on top of ProstT5 embeddings to predict 3Di directly from AA-input. So it just takes the raw output (logits) of this network and uses them as a proxy for reliability.
I am always a bit hesitant to give precise thresholds for those because depending on your specific use case this threshold might differ. So in case you have a use case where you rather want to have more hits at the cost of accepting some more false-positives, you might accept a bit lower cutoff than if your setup is vice versa (rather less FPs but then also less coverage).
As a general starting point, you might want to start filtering out sequences that have on average a probability of <=0.4.
That being said: I think @gbouras13 looked into this in more detail for phages using a cutoff of 0.5. Maybe he can give some more input?

Hi @mheinzinger, In the output_probabilities.csv file there are fasta headers and numbers ranging from 0 to 100. How is this calculated is it the same as the one you described above.
How does the model handle non-standard characters such as 'X' present in sequence files and how does it effect the probability values. Also how does the size of the proteins affect the probability.
I have also noticed on some fasta files I cannot generate output_probabilities.csv files as it runs into this error.
/opt/conda/lib/python3.10/site-packages/numpy/_core/fromnumeric.py:3596: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/opt/conda/lib/python3.10/site-packages/numpy/_core/_methods.py:136: RuntimeWarning: invalid value encountered in divide
  ret = arr.dtype.type(ret / rcount)
Traceback (most recent call last):
  File "/app/ProstT5/scripts/predict_3Di_encoderOnly.py", line 389, in <module>
    main()
  File "/app/ProstT5/scripts/predict_3Di_encoderOnly.py", line 377, in main
    get_embeddings(
  File "/app/ProstT5/scripts/predict_3Di_encoderOnly.py", line 287, in get_embeddings
    prob = int( 100* np.mean(probabilities[batch_idx, :, 0:s_len]))
ValueError: cannot convert float NaN to integer

Good point - sorry for the confusion.
Numbers in the CSV are simply multiplied by 100 but it refers to the same probabilities (always taking the softmax of the logits output by the CNN which predicts 3Di as defined here: https://github.com/mheinzinger/ProstT5/blob/main/scripts/predict_3Di_encoderOnly.py#L274 ).
X is handled as wildcard for unknown/non-standard amino acids.
How their presence exactly affects the probability is not sth that I investigated in detail because those cases are rather rare.
That being said: given that the probability is an average over the full sequence and it is rather rare that sequences have >5% missing/non-standard AAs, I doubt  that having a small number of "X" in your input changes the predicted probability much.
As long as your protein is below 400 residues (close to our upper length during training), I do not think that the predictions are affected much. If you go beyond 400, performance will decrease but I did not quantify by how much. Looking at some isolated examples indicated that the approach "Predict 3Di via ProstT5 and search with Foldseek against some DB" still works fine. If you intend to use the predicted 3Di for sth different, the situation might change.
The interesting bit about the special use-case outlined above (using ProstT5 3Di prediction for foldseek input) is that even if 3Di predictions might not be perfect, mistakes usually happen between tokens that are coding for similar structural conformations (just imagine 3 tokens coding for alpha-helices and our predictor fails at distinguishing them). As a consequence, Foldseek still gives good hits even if the predicted 3Di is not perfectly aligning with the groundtruth.

Can you also comment on this error? I get this when I use it on my fasta file. I cannot make predictions for many files and get the output probabilities. If I switch off writing the probabilities I can output 3Di fasta files for these fasta files. Is it because the model is not able to predict the probabilities for some sequences?
/opt/conda/lib/python3.10/site-packages/numpy/_core/fromnumeric.py:3596: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/opt/conda/lib/python3.10/site-packages/numpy/_core/_methods.py:136: RuntimeWarning: invalid value encountered in divide
  ret = arr.dtype.type(ret / rcount)
Traceback (most recent call last):
  File "/app/ProstT5/scripts/predict_3Di_encoderOnly.py", line 389, in <module>
    main()
  File "/app/ProstT5/scripts/predict_3Di_encoderOnly.py", line 377, in main
    get_embeddings(
  File "/app/ProstT5/scripts/predict_3Di_encoderOnly.py", line 287, in get_embeddings
    prob = int( 100* np.mean(probabilities[batch_idx, :, 0:s_len]))
ValueError: cannot convert float NaN to integer

We have  'X' s in many of our sequences due to sequencing errors and it will be greater than 5% too, so I will need to see how this could be handled. The other question is what are the other wild-card entries that the model can handle. For ex: In our sequences we tend to add * to the last aa. Does the * need to be removed before giving it to the model?

Yes, always remove * from any sequence. - The model does not know how to handle those. This might also be responsible for the error you see above.
Other wildcards are ambigious AAs. But given that those cases appear so rarely, its not likely that the model learnt a good representation for those. I would recommend sticking to the 20 standard AAs/3Dis and replace anything else by "X" (and remove anything artificial, s.a., the asterisk which just indicates end-of-sequence).

Hi @mauriciolangleib ,
Very interesting question! I have been playing around with some thresholds as part of my work on using ProstT5 with Phold (https://github.com/gbouras13/phold).
In my experience, the ProstT5 confidence metric is not highly correlated with the structure's pLDDT (r=0.2 or so), so you can't treat it as such, which was somewhat unexpected for me.
Another thing I considered was whether it was better to using embeddings-based annotation approaches that Michael has developed earlier (https://github.com/gbouras13/phold) for such low ProstT5 confidence proteins.
I thought that if EAT outperformed for these low confidence proteins, then it suggested the ProstT5 predictions for low confidence proteins were not to be trusted very much. But it turns out ProstT5 + Foldseek outperformed EAT even for low confidence proteins.
I took a bunch of ProstT5 confidence thresholds 0.3,0.4,0.5,0.6 etc and ran EAT for proteins below comparing to ProstT5 + Foldseek.
From 0.4 and above, the results indicated that ProstT5+ foldseek clearly did a better job than EAT at the remote homology detection task with phage proteins. For 0.3, the effect was also present (but not as strong, confounded by the fact that there aren't that many low confidence proteins in the dataset), and seemed to be doing no worse.
So in practice I decided to do no confidence filtering in Phold, but need to do a deeper dive on these really low confidence proteins.
As Michael said above in this thread, the 'wrong' tokens are probably coding for similar structural conformations (just quoting what he wrote) so the softmax confidence metric isn't a fantastic way of accounting for confidence, given such tokens are favourably scored in Foldseek's scoring matrix.
I think most importantly for all your considerations above is: if your use case is the one outlined above (using ProstT5 3Di prediction for foldseek input), the approach still works remarkably well even if 3Di predictions might not be perfect. The point is that mistakes usually happen between tokens that are coding for similar structural conformations (just imagine 3 tokens coding for alpha-helices and our predictor fails at distinguishing them). As a consequence, Foldseek still gives the same/very similar hits even if the predicted 3Di is not perfectly aligning with the groundtruth.

Another thing to think about is whether for long proteins or other low confidence proteins, the mean might be low, but ProstT5 might locally have high confidence (e.g. within specific domains). Therefore, on the remote homology task, it still may have much useful information if you can detect such homology domains. A beautiful thing about ProstT5 + Foldseek is that you get alignment information at a sub-protein level like this. I'm going to try and test this idea soon too.
Also, in Phold you can get per protein and per residue confidence information output in a JSON file in the parameters if that makes it easier for you to do your own experiments. :)
George


update dead links

Proposed changes:
These are minor changes to documentation that fix a few dead links following the release of Rasa Enterprise 1.0

@carlad I don't think that this PR fixes the error you had here 🤔

@carlad I don't think that this PR fixes the error you had here 🤔

That error doesn't appear on main as the docs/how-to-deploy.mdx page no longer exists.


Unhandled error when database connection is not available

Sentry link

(Redacted for security reasons, contact staff if you're interested)
Private link: https://sentry.io/organizations/openverse/issues/3599736424/?project=6107216
Description

Presently if the database connection disappears, the /healthcheck/ endpoint (and others) will raise an OperationalError.
We could catch this particular exception and return a 500. This might signal to AWS that the service needs to be replaced though, which wouldn't necessarily correct the underlying issue. We could alternatively catch the exception only during the API database's known maintenance window. That was what instigated these Sentry events, but again that'd still raise an unhandled exception. Interested to hear what folks think the best approach here might be @WordPress/openverse-api.

Reproduction

just up
docker stop openverse-api-db-1
Visit http://localhost:50280/v1/images/

We could alternatively catch the exception only during the API database's known maintenance window. That was what instigated these Sentry events, but again that'd still raise an unhandled exception

Why would this still raise an unhandled exception?
I'm kind of curious what the suggested approach is for handling these maintenance windows. Have we asked around about how other folks deal with these? There must be some way to reasonable degrade during these times but a DB that isn't available seems like it would thwart a lot of applications' critical paths.

Sorry I should have clarified, this would still raise an unhandled exception if the database were unavailable outside the window, which would leave us with the same Sentry alert being raised in the end.
I imagine that folks who have a mission-critical RDS setup might have database replication/redundancy set up, and they might also have the maintenance windows set up such that they don't overlap. That'd mean that at least one database is active at any given time even if maintenance is occurring on one of them.

I see! We'd only use the try/except during the window? :thinking:
I guess to me it seems like this is something that means the service will not work. The healthcheck is right to fail (500 seems reasonable event). Which leads me to think that we should solve this more holistically rather than trying to do a patch over the window of time.
My hunch is also that they have database replicas that have different maintenance windows, but maybe we could ask around and figure out how to actually fix this? In my view even doing this patch to just handle the error in the healthcheck endpoint wouldn't actually make anything better, it'd just silence the error. Though maybe I am not understanding a critical part of the issue's proposal.

That sounds reasonable! It's also worth noting that AWS documentation says:

Enabling the Multi-AZ configuration on your RDS instance might help in minimizing the downtime required during some maintenance operations.

Perhaps that's something we could pursue. As for this issue, do you think we should serve a 500 and also reraise the exception? I agree that silencing alerts during the maintenance window isn't that useful because the reality is that our service is still down.

I think we'd want to raise a 429 and then log an error? 500 in my understanding is more for when we're like totally out of options, but 429 at least communicates the precise issue (an upstream dependency, the database, was not reachable).


docs: Add documentation for the use_forwarded_values field

Description
Ran into this issue today. added some documentation to help with this gotcha.
Motivation and Context
My cloudfront wouldn't deploy because of this issue
Fixes #120
Breaking Changes
Non-breaking
How Has This Been Tested?
This is a doc change only. markdown preview below

This PR is included in version 3.2.2 :tada:


GH2297 - Extended NUnit3Settings to support alternative app.config

Modified NUnit3Settings class to support new ConfigurationFile property that maps to --configfile=app.config for the nunit-console runner
In the 3.8.0 release of the nunit-console runner, a new command line argument was added that supports loading the app.config file from an alternative path or file.
Here is the new 3.8.0 feature: https://github.com/nunit/nunit-console/issues/246

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

@devlead Is there anything you would like me to add to this PR or anything I can add to #2297 to clear anything up?

Relates to #2297


User Stories - Driver experience

Description
As a driver I want my car not to stop suddently but smoothly so that I would have a better driving experience
Acceptance Criteria
The car slows down before reaching the 30cm from the obstacle

Car slows down before completely halting its movement after detecting a collision approaching


Adding ColorMatcher Game

ColorMatcher #2113
Close #2113

Checklist:

[x] I have mentioned the issue number in my Pull Request.
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have created a helpful and easy to understand README.md

@MohitGupta121 Could you check it out

@MohitGupta121 @pranjay-poddar  Could you add the gssoc and level labels


Improve memory issues

There are instances where a Godot Object could be deleted by adding it to an array / dictionary wihtout having any other References or calling call_deferred with it as an argument. This should be fixed. Maybe by introducing a proxy method for call_deferred and changing list handling for Array and Dictionary

I think, this is unnecessary. Doing something with proxy methods is not 100% save. I don't see there any fix which could be done in reasonable time and in GDScript, you also have to call free or queue_free to free the node and memory. So I think, I should just delete the destructor


请问支持动态插值扫描吗？

比如我中文是“我想要1个苹果”，
{
    "key": "我想要{{count}}苹果"
}

i18next.t('key', { count: 10 });

这个暂不支持。目前没有想到好的方案。如果让代码自己扫描识别，很难知道用户希望哪些单词要作为插值。人为干预需要插值的地方话，能实现，不过我没想好通用点的设置规则

This issue has been automatically locked since there has not been any recent activity after it was closed. Please open a new issue for related bugs.
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Breadcrumbs/selectbox dropdown does not relayout after resizing panel

VSCode Version: stable and insiders

Steps to Reproduce:

Click on a breadcrumb/selectbox so the dropdown shows up
Resize panel
:bug: Observe the dropdown does not relayout

Created a PR #113723 that blocks mouse interaction with the rest of the UI (same as the context menu) in case that's a good fix

Created a PR #113723 that blocks mouse interaction with the rest of the UI (same as the context menu) in case that's a good fix


How to use 2 GPUs for inference

Hello，I want to use 2 GPUs to inference, But I don't know how to run it in 2 GPUs, thanks.

Hello, demo does not support 2GPUs. But you can use multiple GPUs by using dist_test.py with the corresponding config. In particular, you can modify the data paths here and use dist_test.py.


When run the gateway_artifact_migrator.sh, it doesn't work as expected in MacOS env

Description:
When executing the gateway_artifact_migrator.sh in mac os, it prints unwanted characters in the synapse files and those files are duplicating.
Steps to reproduce:
Follow the Step2 in [1]
[1] https://apim.docs.wso2.com/en/3.0.0/install-and-setup/upgrading-wso2-api-manager/upgrading-from-200-to-300/#step-2-upgrade-api-manager-to-300
Affected Product Version:
migration from 200,210,250 -> 3.x version
Environment details (with versions):

OS: MacOS
Env (Docker/K8s):local environment

Cause of the issue:
When analyzing the existing script, it is trying to replace the content using sed command.
Eg:-
"sed -i -e 's/org.wso2.carbon.apimgt.usage.publisher.APIMgtThrottleUsageHandler/org.wso2.carbon.apimgt.gateway.handlers.analytics.APIMgtThrottleUsageHandler/'"
Mac OS X is based on BSD UNIX env and sed command is not working as it behaves in Linux env.
Therefore,  \n and \t  do not work as newline characters and tab characters. Moreover, as it contains sed -i -e, it always backup the existing files renaming "filename-e" and replace the strings.

Fixed in the latest version


Python subprocess breaks out of venv

Example:
https://git.libcamera.org/libcamera/libcamera.git/tree/utils/tracepoints/meson.build
Running find_program('./gen-tp-header.py')
It winds up running
/usr/bin/python3 /blah/blah/blah/libcamera/utils/tracepoints/./gen-tp-header.py ...

gen-tp-header.py has a helpful #!/usr/bin/env python3 line, but that gets lost and we go to system Python which doesn't have some things installed that I have installed in the currently active venv and I was counting on using the venv. I assume ninja is doing work to break out of the supplied python3 that's first on PATH because of the venv, so, it shouldn't do that!

Could you inspect the ninja files that meson generated? Most likely, it is meson that refers to globally-installed python by absolute path. Ninja knows nothing about python etc. it just executes commands as specified in build.ninja.

This seems to be unrelated to Ninja. -> Meson