stratospheric water vapor prod/loss option in pchem

Closes #111. This is zero diff with default AGCM options.

the !fli2 comment lines everywhere should do

the !fli2 comment lines everywhere should do

the !fli2 comment lines everywhere should do

Ben, do you mean should be deleted?
Feng put them in CVS tag which made my life easier with merging this tag with git. I can delete them now.

the !fli2 comment lines everywhere should do

Ben, do you mean should be deleted?
Feng put them in CVS tag which made my life easier with merging this tag with git. I can delete them now.

the !fli2 comment lines everywhere should do

Ben, do you mean should be deleted?
Feng put them in CVS tag which made my life easier with merging this tag with git. I can delete them now.

Yes, please delete them, no point in littering the code with comments.

the !fli2 comment lines everywhere should do

Ben, do you mean should be deleted?
Feng put them in CVS tag which made my life easier with merging this tag with git. I can delete them now.

Yes, please delete them, no point in littering the code with comments.

the !fli2 comment lines everywhere should do

Ben, do you mean should be deleted?
Feng put them in CVS tag which made my life easier with merging this tag with git. I can delete them now.

Yes, please delete them, no point in littering the code with comments.

Done. I left only one !fli2 comment left which has a meaningful part attached to it.

the !fli2 comment lines everywhere should do

Ben, do you mean should be deleted?
Feng put them in CVS tag which made my life easier with merging this tag with git. I can delete them now.

Yes, please delete them, no point in littering the code with comments.

Done. I left only one !fli2 comment left which has a meaningful part attached to it.

This PR is certainly zero-diff, if  H2O_ProdLoss: 0  (the default).
If  H2O_ProdLoss: 1,  the model fails, reporting
Error getting varid for variable H2OprRate         -49
NetCDF: Variable not found
Of course this is because the standard species.data file is missing the production rate.
Does it make sense to provide a version of species.data that includes the necessary rate fields,
for general users?  If so, can it be listed as an option in  gcm_run.j ?

This PR is certainly zero-diff, if H2O_ProdLoss: 0 (the default).
If H2O_ProdLoss: 1, the model fails, reporting
Error getting varid for variable H2OprRate -49
NetCDF: Variable not found
Of course this is because the standard species.data file is missing the production rate.
Does it make sense to provide a version of species.data that includes the necessary rate fields,
for general users? If so, can it be listed as an option in gcm_run.j ?

In this case this PR should be contingent on GEOSgcm_App repository? According to @sstrode this update works with S2Sv3 tag. What is different with species.data in S2Sv3 and in current set up?

This PR is certainly zero-diff, if H2O_ProdLoss: 0 (the default).
If H2O_ProdLoss: 1, the model fails, reporting
Error getting varid for variable H2OprRate -49
NetCDF: Variable not found
Of course this is because the standard species.data file is missing the production rate.
Does it make sense to provide a version of species.data that includes the necessary rate fields,
for general users? If so, can it be listed as an option in gcm_run.j ?

In this case this PR should be contingent on GEOSgcm_App repository? According to @sstrode this update works with S2Sv3 tag. What is different with species.data in S2Sv3 and in current set up?

The species.data file used in Sarah's S2Sv3 simulation, where  H2O_ProdLoss: 1, has the variables 'H2OprRate' and 'H2OlsRate'. I bet the model is crashing because it cant find these variables in file. See header information below.
float H2OprRate(time, lev, lat) ;
H2OprRate:short_name = "H2OProdRate" ;
H2OprRate:long_name = "H2O_chemical_prod_rate" ;
H2OprRate:units = "kg kg-1 s-1" ;
float H2OlsRate(time, lev, lat) ;
H2OlsRate:short_name = "H2OLossRate" ;
H2OlsRate:long_name = "H2O_chemical_loss_rate" ;
H2OlsRate:units = "s-1" ;
Perhaps the species.data file that has the H2OprRate and H2OlsRate becomes the default file now?

There's a species.data file that works with this code, but I suspect it should not be the default since it is set up for pre-industrial conditions.

There's a species.data file that works with this code, but I suspect it should not be the default since it is set up for pre-industrial conditions.

I suggest that the version of species.data with H2O prod and loss be copied into GMAO shared space, and that it be listed as an option in gcm_run.j, with appropriate comments.  That means a PR for GEOSgcm_App, as @yvikhlya mentioned.

I will work with @sstrode on this.


Redundant "gpu" in filename copied from target

The naming scheme for uberjars truncates the chip from the os argument only for GPU javacpp.platforms. This results in the following error on GPU builds:
Traceback (most recent call last):
File "C:\Users\Skymind AI Berhad\.konduit\konduit-serving\build_jar.py", line 105, in <module>
os.path.join(args.source, args.target),
File "c:\users\skymind ai berhad\appdata\local\continuum\miniconda3\lib\shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Skymind AI Berhad\\.konduit\\konduit-serving\\konduit-serving-uberjar\\target\\konduit-serving-uberjar-0.1.0-SNAPSHOT-all-windows-x86_64-gpu-gpu.jar'

This fix tested by running python build_jar.py with os arguments windows-x86_64, windows-x86_64-gpu, linux-armhf

That looks like a poor workaround. Why does it do this in the first place? Is it something that needs to be fixed in JavaCPP?

Shouldn't be a JavaCPP issue. To my understanding (sorry if I misunderstood):
The user passes one of the following --os arguments:
https://github.com/KonduitAI/konduit-serving/blob/7ac4cda58e4718641ef32b613c1681f2461ec0f7/build_jar.py#L23-L28
which is truncated if it contains "gpu" into a valid JavaCPP platform:
https://github.com/KonduitAI/konduit-serving/blob/7ac4cda58e4718641ef32b613c1681f2461ec0f7/build_jar.py#L62
The javacpp.platform is passed directly to mvnw here:
https://github.com/KonduitAI/konduit-serving/blob/4953e1a1c43ffdc07fc4a9e4afa620a09f7e2f38/build_jar.py#L63-L70
and the jar is built with filename:
https://github.com/KonduitAI/konduit-serving/blob/f0b829ec13e1fc3f675cfc6dbd85dec26f14defe/konduit-serving-uberjar/pom.xml#L59
I did not notice the platform variable earlier, sorry. I'll use that variable instead, but I'm not sure if that makes this fix any better.

Hum, why does this script forces us to specify an OS to start with? And why doesn't it make use of the Maven profiles made for that instead of redoing it in Python?
https://github.com/bytedeco/javacpp-presets/wiki/Reducing-the-Number-of-Dependencies
Before starting to rewrite everything in Python, please let me know what is missing from JavaCPP! From what I understand, I don't think anything is missing, so I won't be able to help if you keep all that information to yourself. @ShamsUlAzeem @maxpumperla

Fixed in my other PR.


python3Packages.tblite: fix simple-dftd3 dependency passing

Description of changes
Closes #285286
In #284057 I've introduced the simple-dftd3 python bindings in addition to the fortran package. The Tblite python bindings are requiring for the fortran package, while I've now passed the simple-dftd3 python bindings by accident, however.
Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
24.05 Release Notes (or backporting 23.05 and 23.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

@GrahamcOfBorg build python3Packages.tblite


An error occurred while installing flash-attn

Hi, thanks for your brilliant work!
When I installed flash-attn on the 3090，The following error occurs：
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h:2207:11: note: in template argument for type ‘bool’
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h: In instantiation of ‘pybind11::object pybind11::detail::object_api::operator()(Args&& ...) const [with pybind11::return_value_policy policy = (pybind11::return_value_policy)1u; Args = {pybind11::object&, pybind11::str}; Derived = pybind11::detail::accessorpybind11::detail::accessor_policies::str_attr]’:
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/pytypes.h:976:30:   required from ‘pybind11::str pybind11::str::format(Args&& ...) const [with Args = {pybind11::object&, pybind11::str}]’
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/pybind11.h:1643:79:   required from here
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h:2215:29: note: candidate: template<pybind11::return_value_policy policy, class ... Args, class> pybind11::detail::unpacking_collector pybind11::detail::collect_arguments(Args&& ...)
unpacking_collector collect_arguments(Args &&...args) {
^~~~~~~~~~~~~~~~~
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h:2215:29: note:   template argument deduction/substitution failed:
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h: In substitution of ‘template<bool _Cond, class _Tp> using enable_if_t = typename std::enable_if::type [with bool _Cond = (! pybind11::detail::args_are_all_positional<{pybind11::object&, pybind11::str}>()); _Tp = void]’:
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h:2214:11:   required from ‘pybind11::object pybind11::detail::object_api::operator()(Args&& ...) const [with pybind11::return_value_policy policy = (pybind11::return_value_policy)1u; Args = {pybind11::object&, pybind11::str}; Derived = pybind11::detail::accessorpybind11::detail::accessor_policies::str_attr]’
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/pytypes.h:976:30:   required from ‘pybind11::str pybind11::str::format(Args&& ...) const [with Args = {pybind11::object&, pybind11::str}]’
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/pybind11.h:1643:79:   required from here
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h:2214:67:   in constexpr expansion of ‘pybind11::detail::args_are_all_positional<{pybind11::object&, pybind11::str}>()’
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h:2214:11: error: constexpr call flows off the end of the function
typename = enable_if_t<!args_are_all_positional<Args...>()>>
^~~~~~~~
/home/haogao/anaconda3/envs/bevfusion/lib/python3.8/site-packages/torch/include/pybind11/cast.h:2214:11: note: in template argument for type ‘bool’
error: command 'gcc' failed with exit status 1
I can't solve it.
Thanks！

The error seems to be with pybind11 in Pytorch? Are you able to compile the example extension from Pytorch?
https://github.com/pytorch/extension-cpp
(cd cuda && python setup.py install).
The issue could be due to mismatch in Pytorch version, CUDA version, or GCC version.

When I try cd cuda && python setup.py install , The following question arises:
/home/haogao/miniconda3/envs/bevfusion/lib/python3.8/site-packages/torch/utils/cpp_extension.py:788: UserWarning: The detected CUDA version (11.1) has a minor version mismatch with the version that was use
d to compile PyTorch (11.3). Most likely this shouldn't be a problem.

The version mismatch could be the cause of the problem (Pytorch CUDA extensions are generally finicky about CUDA versions).
Can you try with a machine where CUDA version matches Pytorch version (e.g. 11.3)?


/contribute/page-templates returns 404

This is a Bug Report

Problem: "Not found" / 404 returned by https://kubernetes.io/docs/contribute/style/page-templates/
Proposed Solution:

Fix redirect (need to identify correct page)
Seems other pages just redirect to /docs/contribute/ - could that be a solution?

Page to Update:

https://kubernetes.io/docs/contribute/style/page-templates/

The last version I could find was https://v1-17.docs.kubernetes.io/docs/contribute/style/page-templates/ so it seems this page was deprecated/removed

/triage accepted


Can't download binary: extremely slow DL speed

Downloading from https://github-production-release-asset-2e65be.s3.amazonaws.com/ can't be finished: tried out more than a day

Downloaded from another ISP


Fails to load components

I could be here early but wanted to share my experience with this.
Chromium would not load any components and DRM content couldn't be played. Widevine install went properly from what I could tell.
Interestingly on first attempt with Brave, I was prompted to install Widevine and I could load DRM content properly. On subsequent runs I was unable to.
macOS 13.5 M1

For posterity, my target device is arm64 Arch. I installed widevine-aarch64 (compiles a patched glibc that took a long time) and registered widevine with Chromium and Firefox. Once I validated DRM content was viewable I took found the installation paths for WidevineCdm and copied them to my gluon_data/{browser} dirs. Gluon opens either browser with DRM support.
My end platform isn't supported by this as arm64 widevine has been found in the wild but not available from Google. No action needed, again, steps above for anyone else who needs it.


[4.1] Fix nested relations on select column

I ran into some problems when trying to add nested relations on a select column in my admin interface. My setup is:

Model App/Models/Category
Model App/Models/Subject, which BelongsTo Category
Model App/Models/Skill, which BelongsTo Subject
Model App/Models/Exercise, which BelongsTo Skill
Controller App/Controllers/Admin/ExerciseCrudController, which has a column
['name' => 'category', 'type' => 'select', 'label' => "Categorie", 'entity' => 'skill.subject.category', 'attribute' => 'title']
Backpack version: 4.1.3

When I try to list the Exercises, I get an error Undefined index: App\Models\Skill at line \\vendor\\backpack\\crud\\src\\app\\Library\\CrudPanel\\CrudPanel.php:443.
I found a few problems with the code below I didn't quite understand, but tried to fix by changing it to the way I guess it was originally intended:

The error was caused by the call to $results[$model], which I think makes no sense as results is always empty at that point in the code
The call $this->getRelatedEntries($currentResult, implode('.', $relationArray)) also seems weird, as $currentResult always is forced to be an array looking at the preceding code, while getRelatedEntries needs a Model.
The call get_class($relation->first()) when $relation is an array was not triggered in my code, but I think it will always fail as an array does not have such a method.

A new inspection was created.

The inspection completed: No new issues

@jnoordsij
Thanks for pitching in.
With your solution how we will have the model here:
https://github.com/Laravel-Backpack/CRUD/blob/1246b534ead8c3da76035f85017b849c619ec296/src/app/Library/CrudPanel/CrudPanel.php#L357

Thanks for replying so fast! I just saw that there were actually some changes in 4.1 that broke the nested relations, but my first idea breaks 1-n relations, so that's not so nice either. Let me look for a solution to that.

A new inspection was created.

A new inspection was created.

The inspection completed: No new issues

@pxpm I think I managed to get everything fixed now, the method should now consistently return an array of the form [ 'deepestNestedModelClassName' => [array of related models]]. Then the getRelatedEntriesAttributes should be able to convert that to a nice $attributes array.

I will give this a go ASAP and let you know my findings.
Thank you very, very much for your effort on solving this issue and putting together a PR! We really appreciate the contribution.
Thanks

The inspection completed: No new issues

Thanks a lot for discovering and fixing this @jnoordsij ! And for testing and reviewing @pxpm . Merging into master right now. It'll be available with composer update later today when it's tagged.
Cheers!

FYI @jnoordsij in the process you got the code quality of CrudPanel back to decent:

🥳 🎉 Thanks a lot!

Nice, that's always a good thing! Thanks @pxpm for reviewing and @tabacitu for merging this.


Pulumi vs. CloudFormation content

We have https://www.pulumi.com/cloudformation/, but having a more detailed and technical page on the pulumi.io site with code for code examples would be useful.
Something along the lines of https://www.terraform.io/intro/vs/cloudformation.html
Related: #549

I'll be doing this as part of https://github.com/pulumi/docs/issues/549.

Fixed by #566


Add API to manually mark services as tombstone

This is an early WIP, sharing here to get some feedback exploring options to implement it.
Issue:
Currently, we don't have a way to tell to Sidecar when a container is about to go down before it actually died. This translated into some errors when rolling out services while Sidecar detects the container as unhealthy and spread the new state in the cluster.
Goal:
Have a way for the sidecar-executor to notify Sidecar in advance when a Mesos task is going to be killed.
Design considerations:
To make it easier, I'm reusing the tombstone state but there may be some edge case I didn't consider here.
The other option is to add a new "draining" state, but it'll make the service state more difficult to understand (not very familiar with the finite-state machine here)

Hey @felixgborrego thanks for the PR. I have some concerns about this approach and suggest a different one. Here's some general comments. More on the code as well.
The first is that re-using the Tombstone status will make it invisible what is happening when we're triggering this state. The second is that the normal processing loop in Sidecar will override this change within 1 a second or two, because an Alive supercedes a Tombstone and the source of truth is:
Docker API -> healthy (sidecar/healthy package) -> state
As long as DockerDiscovery is returning the container and it's healthy according to the health checker, it will get re-populated into the state.
What's required here is a new Status, e.g. DRAINING which is not a Tombstone, and which can be handled as a separate case when updating state. This would also need to be treated like a Tombstone for purposes of gossip messages (they are propagated faster and more widely).

Some further notes:

A new state would need to go here: https://github.com/Nitro/sidecar/blob/master/service/service.go#L20
And here: https://github.com/Nitro/sidecar/blob/master/service/service.go#L158

Should DRAINING have a lifespan like Alive and Tombstone? Just so you can't get stuck draining forever? If so, something like https://github.com/Nitro/sidecar/blob/master/catalog/services_state.go#L32

As long as the state is not ALIVE this will prevent it from being exposed to Envoy: https://github.com/Nitro/sidecar/blob/master/sidecarhttp/envoy_api.go#L301

Happy to set up some time to pair on this with you if needed.

@relistan thanks for your feedback, I'll close this PR exploring options and we'll send a PR with your feedback soon


docs: add doc for loki ingester protocol

What's Changed in this PR

add doc for loki ingester

Checklist

[ ] Please confirm that all corresponding versions of the documents have been revised.
[x] Please ensure that the content in sidebars.ts matches the current document structure when you changed the document structure.
[ ] This change requires follow-up update in localized docs.

what happened if developers manually created table via SQL?

It will fail. because of semantic type mismatch.


How can I retrieve the client id of the app for a system-assigned identity

How can I retrieve the client id of the app for a system-assigned identity? In the identity blade, I only see object id

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

ID: f57d3177-ce9e-ebfa-03a7-45beb8ca3212
Version Independent ID: a59df23d-f3ac-9809-61d3-5741e31f020a
Content: Managed identities overview - Azure App Service
Content Source: articles/app-service/overview-managed-identity.md
Service: app-service
GitHub Login: @mattchenderson
Microsoft Alias: mahender

@rohan51 and @beneuto The feedback below is what the product group shared. Please let us know if you have further questions or concerns.

When requesting a token using MSI, clientId is an optional field and is needed only when user-assigned identities are assigned to the resource. For system assigned, you can skip the clientId and it will default to the system-assigned identity.


Tooltip won't show up on Labels

Operating System: Coding on Windows, viewing on Macintosh (macOS Sierra)
Browser: Google Chrome (Latest)
Potential fixes: Unknown
I created a Label and tried to apply a Tooltip to it but it doesn't like to show up, here's my code:
Universal
This is in a table, path: .table > tbody > tr > th.
The Label element will show up but it seems like the Tooltip isn't even getting recognized at all. I made it so when I hover over the "tr" element, it shows the pointer cursor but I wouldn't think this would be a problem. I don't know of any solutions or fixes at the time. Thanks, Jacob.

What version of Bootstrap?

I was unable to verify this as an issue. I suspect you are not properly initializing the JS.
Here is an example use case: https://codepen.io/judetucker/pen/JKmggd
This is based on v4-alpha.3. Not sure what version you are on. Hope this helps.

@cvrebert The lastest

@judetucker I am on the lastest, not 4 but 3.3.7 or something.


Pattern:  Content group - with cards design QA testing

User Story

As a [user role below]:
DDS Designer

I need to:
test the Content group - with cards

so that I can:
be sure the developer's code correctly works as designed

Additional Information

alpha Dev link (#704 )
Design folder with func specs and visual specs is here: Box

Tasks
Ensure the Content group - with cards pattern has been tested and reviewed by design + dev.
Acceptance criteria

[ ] Pattern is reviewed by designer and design defects are identified
[ ] New issues are opened to log individual defects
[ ] Screenshots of as-is and to-be design should be added to the issue when needed
[ ] Developer associated with building the pattern is assigned to the new issues
[ ] Appropriate labels are added to the issue  eg.  bug, dev

@wonilsuhibm @RobertaJHahn
This pattern is ready for review, thanks!

@RaphaelAmadeu do you have a link to the pattern? I want to make sure I'm testing the correct one, I wasn't sure if it was in ibmdotcom-react or ibmdotcom-react-experimental

@oliviaflory, here it is, https://ibmdotcom-react.mybluemix.net/?path=/story/patterns-blocks-contentgroupcards--default
thanks!


gemspec: Drop EOL'd rubyforge_project property

The RubyGems property rubyforge_project is removed without a replacement.

Thanks!


Implement channel based output

Generate package should send each step progress to the channel.

This feature is in progress. Still lot of refactoring is required

Implemented in v0.1.4


Issues with add link URL control

Hi, 2 issues we encountered with the add link control:

It is not possible to copy text from the input of the url  (neither ctrl+c or _right-click).
If URL prefix (https://) is not entered, it automatically adds the domain name before the URL entered in the link . We solved it using the link hook.

Thanks,
Liad

Confirmed, I will fix the first issue soon.

Hi,
Regarding the 1st issue, now when I try to copy the URL (e.g. https://google.com), it copies the text of the URL instead (e.g. visit Google).
Worth mentioning I am not using allowInsertLinkText (by default it's false).

@liadbe I will take a look tomorrow. I just noticed that this problem does not exist in react-draft-wysiwyg, so it should be repairable.

Hi, I just published v2.3.7 and this issue should be fixed :)

Hi, I thought this issue is behind us. But something weird is happenning, these are the steps to reproduce:

Select text inside the editor and click the 'add link' control
Insert url without url prefix (https://), for example - google.com
Select the linked text in the editor
Press right click -> Copy link address
See that the address copied is not just google.com but with added prefix (probably your domain)

Can u  please have a look on that?
Thanks,
Liad

The editor won't apply any protocol by default, so you input google.com, for browser, it's just a relative path, you can have a try on any website, find a link and remove the prefix of it by using the browser development tool, then right click the link and copy the url of it.


Having trouble with backtrack option

I just pulled the latest version, and am trying out training with backtrack on. I am getting an error:
Initialized dense model in 28 epochs, val loss 9.84e-02, regularization 1.39e+01
Traceback (most recent call last):
  File "/home/psmirnov/Code/Github/lassonet_exp/lassonet/examples/ctrpv2_lassonet_path.py", line 103, in <module>
    path = model.path(inner_train_X, inner_train_y.reshape(-1), X_val=valid_X, y_val=valid_y.reshape(-1))
  File "/home/psmirnov/Code/Github/lassonet_exp/lassonet/lassonet/interfaces.py", line 369, in path
    self._train(
  File "/home/psmirnov/Code/Github/lassonet_exp/lassonet/lassonet/interfaces.py", line 270, in _train
    loss = real_loss
UnboundLocalError: local variable 'real_loss' referenced before assignment

I think in your code, it corresponds to line 260 (I added tracking of some metrics other than loss on the validation set).
I suspect this is happening when val_obj < real_best_val_obj condition on line 249 is not met prior to early stopping breaking out of the loop. I think real_loss would be unassigned then.

Note that the reported loss is not very precise because it's a running loss and also because we don't recompute it after the last epoch.


A few Package.json things

Great work! Noticed just a few things with the package.json as I was looking at source:
L5:

Main should probably point to a processed CJS/UMD file. As it is now, this is pointing to the source file and the min'd file is only minified, it's still using ES6 exports.

You can add a module field to the package.json on L6 and then point it at your minified module. The module field identifies the file as as a ES module vs. a Common JS module.

L28: Should this be ISC? Isn't this repo Creative Commons? I'm not a licensing guru but I'm guessing this was just missed.

Hi @soluml. Any browser that supports ResizeObserver and custom elements also supports ES6 imports, so I don't think I will be transpiling the code. But perhaps I should note that in the README more clearly? I should link to the minified file instead, though, I guess.
I don't know anything about licensing either. The ISC license is very permissive, so I don't think it would cause anyone any problems?

@Heydon I guess I was thinking more in terms of a node ecosystem. If they're requiring this module, some bundlers may expect a CJS module vs. an ES module.  Specifying the file in the module field tells the bundler that this is an ES6 import. If this isn't being used within NPM or a bundler, then I guess it doesn't matter :)
For the license, I just saw that the license file in the root was Creative Commons but the Package.json said this package was ISC. I assumed they should both be one or the other? But I didn't know if they should specifically be different. I don't think either will cause anyone any problems 👍

@soluml Okay, I'll have a think. I very much appreciate the help.

Sure, np, really like the component!


Fix saving grayscale WebP images

I just noticed that there was a problem when saving grayscale images in WebP format.
WebP does not support single-channel images, so we need to save them as RGB, which we were doing.
However, the stride was wrong: I was using the stride as if it were a single-channel image, so we need to recompute it before saving.
This PR addresses this issue.
Fun fact: even though we save a lossless RGB image in WebP, it still takes less disk space than the grayscale PNG, at least for the images I tried.

Sweet. Thanks for the fix :)


Genesis block contains a transaction that can't be retrieved

Is there any particular reason why this is not found? The current block explorer is not displaying the genesis block due to this.
1. Find the genesis block
bin/xsn-cli getblockhash 0
00000c822abdbb23e28f79a49d29b41429737c6c7e15df40d1b1f1b35907ae34

2. Get the block details
bin/xsn-cli getblock 00000c822abdbb23e28f79a49d29b41429737c6c7e15df40d1b1f1b35907ae34
{
  ...
  "tx": [
    "922ab2360f766457416dfc59c6594248c5b79e33c8785bce491c0e01930738f6"
  ],
  ...
}

3. Get the transaction details
bin/xsn-cli getrawtransaction 922ab2360f766457416dfc59c6594248c5b79e33c8785bce491c0e01930738f6 1
error code: -5
error message:
No information available about transaction

if it isn't a transaction, why is it showing this txid 922ab2360f766457416dfc59c6594248c5b79e33c8785bce491c0e01930738f6?

RPC has new message of The genesis block coinbase is not considered an ordinary transaction and cannot be retrieved (code -5)


Automator: update proxy@master in istio/istio@master

Generated by Automator - 2022-02-15T20:28:16+00:00

@istio-testing: The following test failed, say /retest to rerun all failed tests or /retest-required to rerun all mandatory failed tests:

Test name
Commit
Details
Required
Rerun command

integ-pilot-multicluster_istio
54cc578574ed1833e69899146aff74b7939cf168
link
true
/test integ-pilot-multicluster_istio

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

/test integ-pilot-multicluster_istio


acs-engine scale fails: Deployment template validation failed, agent is not defined in the template

Is this a request for help?:
YES

Is this an ISSUE or FEATURE REQUEST? (choose one):
ISSUE

What version of acs-engine?:
Current master.
Version: canary
GitCommit: 13973d0d
GitTreeState: clean

Orchestrator and version (e.g. Kubernetes, DC/OS, Swarm)
Kubernetes
What happened:
Scaling the cluster fails:
acs-engine scale --subscription-id xxxxx --resource-group domain-env-kubernetes --location westeurope --deployment-dir /path_to/_output/env/ --new-node-count 2 --debug
INFO[0000] validating...
DEBU[0000] Resolving tenantID for subscriptionID: xxxxx
DEBU[0000] Attempting to load token from cache. path="yyyyy"
DEBU[0001] Saved token to cache. path="yyyyy"
DEBU[0003] Already registered for "Microsoft.Compute"
DEBU[0003] Already registered for "Microsoft.Storage"
DEBU[0003] Already registered for "Microsoft.Network"
INFO[0005] Name suffix: 87921648
INFO[0005] Starting ARM Deployment (domain-env-kubernetes-2039249985). This will take some time...
INFO[0008] Finished ARM Deployment (domain-env-kubernetes-2039249985). Error: resources.DeploymentsClient#CreateOrUpdate: Failure responding to request: StatusCode=400 -- Original Error: autorest/azure: Service returned an error. Status=400 Code="InvalidTemplate" Message="Deployment template validation failed: 'The resource 'Microsoft.Compute/virtualMachines/k8s-agent-87921648-0' is not defined in the template. Please see https://aka.ms/arm-template for usage details.'."
FATA[0008] resources.DeploymentsClient#CreateOrUpdate: Failure responding to request: StatusCode=400 -- Original Error: autorest/azure: Service returned an error. Status=400 Code="InvalidTemplate" Message="Deployment template validation failed: 'The resource 'Microsoft.Compute/virtualMachines/k8s-agent-87921648-0' is not defined in the template. Please see https://aka.ms/arm-template for usage details.'."

Previously, it was setup using the following configuration:
{
  "apiVersion": "vlabs",
  "properties": {
    "orchestratorProfile": {
      "orchestratorType": "Kubernetes",
      "orchestratorVersion": "1.10.1",
      "kubernetesConfig": {
        "enableDataEncryptionAtRest": false,
        "useManagedIdentity": true,
        "enableRbac": true,
        "networkPolicy": "calico",
        "privateCluster": {
            "enabled": true
        },
        "dnsServiceIP": "<IP_ADDRESS>",
        "serviceCidr": "<IP_ADDRESS>/18",
        "clusterSubnet": "<IP_ADDRESS>/17",
        "etcdDiskSizeGB": "256",
        "dockerEngineVersion": "17.05.*"
      }
    },
    "aadProfile": {
      "serverAppID": "******",
      "clientAppID": "******",
      "tenantID": "******",
      "adminGroupID": "******"
    },
    "masterProfile": {
      "count": 1,
      "dnsPrefix": "env",
      "vmSize": "Standard_A4_v2",
      "vnetSubnetId": "/subscriptions/******/resourceGroups/domain-env-kubernetes/providers/Microsoft.Network/virtualNetworks/env-k8s-network/subnets/env-k8s-master-subnet",
      "firstConsecutiveStaticIP": "<IP_ADDRESS>",
      "vnetCidr": "<IP_ADDRESS>/16"
    },
    "agentPoolProfiles": [
      {
        "name": "agent",
        "count": 1,
        "vmSize": "Standard_A4_v2",
        "vnetSubnetId": "/subscriptions/******/resourceGroups/domain-env-kubernetes/providers/Microsoft.Network/virtualNetworks/env-k8s-network/subnets/env-k8s-worker-subnet",
        "availabilityProfile": "AvailabilitySet"
      }
    ],
    "linuxProfile": {
      "adminUsername": "******",
      "ssh": {
        "publicKeys": [
          {
            "keyData": "******"
          }
        ]
      }
    }
  }
}

We used these commands to deploy the cluster:
acs-engine generate template.json
az group deployment validate --resource-group domain-env-kubernetes --template-file /path_to/_output/env/azuredeploy.json --parameters /path_to/_output/env/azuredeploy.parameters.json
az group deployment create --name domain-env-k8s-cluster --resource-group domain-env-kubernetes --template-file /path_to/_output/env/azuredeploy.json --parameters /path_to/_output/env/azuredeploy.parameters.json

The rollout was successful and the cluster fully functional.
What you expected to happen:
Cluster scaled to 2 nodes.
How to reproduce it (as minimally and precisely as possible):
As described in what happend
Anything else we need to know:

Custom VNET
Tested with multiple master and multiple node setup as well, same result.

@jackfrancis this is the scale bug I mentioned earlier that @danigian reported.


Interface member that is a component doesn't get serialized properly

Release Type: Official Release
Version: beta03
Platform(s): Any
Describe the bug
I have a public member on a script that accepts an interface implementation.
If the implementing class inherits from ScriptComponent it is serialized as a reference and not a new instance. Therefore it's not instantiated, because it refers to something that is defined nowhere.
To Reproduce
Steps to reproduce the behavior:

Create an interface
 public interface ITest { }

Create a script implementing it
 public class Test : ScriptComponent, ITest { }

Create a script that uses the interface as a public member
 public class Runner : StartupScript
 {
     public ITest test;
     public override void Start()
     {
         if (test == null) throw new Exception();
     }
 }

In Game Studio create an entity with Runner script. From dropdown of field test choose Test.

Run game, get an exception

Expected behavior
The script Test is serialized as a new object, thus the field is properly deserialized and not null.
Attached example project
IFaceBugRepro.zip

Please try to add [DataContract] on ITest

[DataContract] is only valid for classes, structs, enums and delegates.

I thought about it a bit more and here are possible ways to handle this:

Disallow assigning Entity Components as interfaces, because components should be tied to Entities and not instantiated as parts of other components
Allow only Components that implement the interface and are already on the Entity
When the Entity doesn't have a component implementing that interface, but it is selected in another component and serialized as a new object, this component will be added to the Entity during deserialization

What is my particular use case?
I have an interface for character input. It can be either using Input from ScriptComponent to get input or use some other logic (AI) to produce input.
Current workaround:
I have a public, serializable field of type InputController (my script) on the class implementing the interface. So in Game Studio I choose the implementation from the dropdown and than have to drag'n'drop the same entity to the field to get that ScriptComponent reference I need.

Sorry, my bad. The correct solution should be more along those lines:

Add [DataContract] on Test class
Add [DataMember] on Runner.test member (not sure that one is necessary)

Does that work better?
That's what we do for things like LightComponent.Light which is a ILight.

Test already inherits [DataContract] from ScriptComponent and every public field on Runner behaves as if it had [DataMember] on it.
The issue is that when setting a value of type deriving from EntityComponent it is always treated as a reference to an existing component on an existing Enity.
Here in EntityHierarchyElementChangePropagator.cs#L22 we can see the different behaviour between a class that is an EntityComponent and one that isn't. But since that component is created without an Entity, on line 30 we get a NullReferenceException. This exception is swallowed without notifying the user. In result the property gets serialized with a reference GUID that isn't pointing to anything and during the deserialization we get an error and set the field to null.

Ha sorry I didn't realize/skipped over the fact Test is an EntityComponent.
You're right, we make some assumptions that they always belong to an actual component.
And exception being swallowed isn't great either...


:stop action has disappeared on machine and machine_image

Using 0.5, with a machine_image I get:
ERROR: Option action must be equal to one of: nothing, create, destroy, archive!  You passed :stop.

and with a machine I get:
ERROR: machine[dbserver-aws1] (@recipe_files::/home/christine/git/topo-provision/gen/aws_stop.rb line 15) had an error: RuntimeError: Chef::Provisioning::AWSDriver::Driver does not implement stop_machine

Both of these used to work.
Note: For machine_image, it used to stop the instance created to create the image. I think there was then a change that meant the instance was terminated once the image was created. However, for me, the run that creates the image always times out waiting for it to be available, and the image instance isnt terminated. So maybe the problem for machine_image is that it isnt terminated in the case when the image took too long to become available (or on the run after).

Seems like this never actually worked, so closing


bug: typstmt project has been archived

Neovim version (nvim -v)
.
Operating system/version
.
Add the debug logs

[X] I have set log_level = vim.log.levels.DEBUG and pasted the log contents below.

Log file
.
Describe the bug
Hi,
I just want to let you know that typstfmt has been archived and you may want to remove it from the supported formatters (or maybe not, in that case feel free to close this immediately).
Recommendation of the author is to use [typstyle](https://github.com/Enter-tainer/typstyle) instead, which is already supported by conform.nvim.
Thanks for the plugin, it is a fantastic tool!
What is the severity of this bug?
minor (annoyance)
Steps To Reproduce
.
Expected Behavior
.
Minimal example file
No response
Minimal init.lua
-- DO NOT change the paths and don't remove the colorscheme
local root = vim.fn.fnamemodify("./.repro", ":p")

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

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

-- install plugins
local plugins = {
  "folke/tokyonight.nvim",
  {
    "stevearc/conform.nvim",
    config = function()
      require("conform").setup({
        log_level = vim.log.levels.DEBUG,
        -- add your config here
      })
    end,
  },
  -- add any other plugins here
}
require("lazy").setup(plugins, {
  root = root .. "/plugins",
})

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

Additional context
No response

Thanks for the notice! I've marked it as deprecated


Request Falied Error

I get Request Falid error when I try to send a variable. I am new to golang so I don't know if this is something that I am doing.

Repl is public<EMAIL_ADDRESS>

fixed


New calendar for LFX Meetings

Please share any additional details on this topic
There is a new calendar available for projects using LFX meetings, see link below.
https://calendar.aswf.io/
We can also do sub-project-specific calendars...
https://zoom-lfx.platform.linuxfoundation.org/meetings/openexr
Detail what actions or feedback you would like from the TAC
Awareness and determine timing of decommissioning calendars at lists.aswf.io
How much time do you need for this topic?
None

Two actions:

@jmertic to setup up calendar.* links for every project
Check on timing of iCal support

Once both are done, we can shutdown the old groups.io calendar.

Calendars are setup for every project using the calendar subdomain
Will provide update on iCal support by next TAC meeting

iCal support is live; we've used the ical subdomain as a forward.
Below is the full list of forwards for projects

Project
Calendar URL(s)
iCal URL(s)

OpenColorIO
calendar.opencolorio.org calendar.opencolorio.com
ical.opencolorio.org ical.opencolorio.com

openexr
docs.openexr.org docs.openexr.net docs.openexr.com
ical.openexr.org ical.openexr.net ical.openexr.com

openfx
calendar.openeffects.org
ical.openeffects.org

OpenImageIO
calendar.openimageio.org calendar.openimageio.com
ical.openimageio.org docs.openimageio.com

Open Shading Language
calendar.openshadinglanguage.org calendar.openshadinglanguage.com
ical.openshadinglanguage.org ical.openshadinglanguage.com

rez
calendar.rez-project.com calendar.rez-project.org calendar.rez-project.io
ical.rez-project.com ical.rez-project.org ical.rez-project.io

OpenTimelineIO
calendar.opentimeline.io
ical.opentimeline.io

OpenCue
calendar.opencue.io
ical.opencue.io

OpenVDB
calendar.openvdb.org calendar.openvdb.io calendar.openvdb.net
ical.openvdb.org ical.openvdb.io ical.openvdb.net

OpenAssetIO
calendar.openassetio.org
ical.openassetio.org

DPEL
calendar.dpel.org
ical.dpel.org

MaterialX
calendar.materialx.org
ical.materialx.org

RAW to ACES Utility
calendar.rawtoaces.com calendar.rawtoaces.org calendar.rawtoaces.io
ical.rawtoaces.com ical.rawtoaces.org ical.rawtoaces.io


[Frontend]: Add awareness of github projects

What problem or use case are you trying to solve?
One common workflow that users may have when they interact with OpenHands is to do fixes on github repos. Because of this, we could add some ability to select github repos, add tokens to access the repos, etc.
I think @amanape is working on this.

Related / Duplicate? https://github.com/All-Hands-AI/OpenHands/issues/3627

Fixed by #3604


Find reason of null

fix #1756

Thanks, but I don't see this as production ready. I don't know that it's a feature we need, and in this state with printlines it's not a meaningful API. Not inclined to merge.

Thanks, but I don't see this as production ready. I don't know that it's a feature we need, and in this state with printlines it's not a meaningful API. Not inclined to merge.

Sorry to bother you, but this is part of our course project. We don't mean to make any change to the code, just to leave the record and get scores. Could you please keep the commit and pull request record?

Thanks for wasting our time on your point scoring, really appreciate it.


Input core + zbus

@fabiobaltieri that is a PR adding zbus support for the input subsys.

See https://github.com/zephyrproject-rtos/zephyr/pull/54908#issuecomment-1443417749


what is the license?

I can't seem to find a license, is there one y'all had in mind?

MIT! Enjoy!


Swipe down when can't find like button

Fix #30 . Now, when liking a post,
if the button is not found, it will try to
scroll dow by swiping up a little
bit so the like button will be in the view.

add method swipe() under device
rename old swipe() to fling() since
it actually invokes fling() method from
uiautomator2
extend enum Direction with RIGHT and LEFT
add left, right, up and down methods
from uiautomator2 to our device facade.

I like it - gonna test real quick. If it works well, we'll merge to develop and test more.

It also needs added to the hashtag function:
[11/17 03:10:03]     INFO | No likes, let's scroll down. (interact_hashtag_likers.py:166)

I'll add to the hashtag tomorrow. Hopefully when we will have refactored everything then most of the fixes will be applied in one place only.

Going to go ahead and merge this into develop. Will continue testing. I think the crash I reported is just my device. Going to try with another device.


Sort by date added

Hey! Is it possible to add possibility to sort songs in a playlist after time added?

Not at this time unfortunately. We don't have access to that type of data and can't manipulate the website in that way.


Marking Page does not refresh when returning from Grading Page

Marking page does not refresh when returning from a grading page; which can cause confusion after fully grading a student's submission.

Fixed with (39ef88034301ca9aa1b49f343f443834bcd85a7c)


Crates which re-export types from other crates should also re-export the entire crate

For example, quickcheck has:
extern crate rand;

pub use rand::Rng;

This has the problem that all users of quickcheck need to depend on the same version of rand as quickcheck if they want to use the rest of rand's API. If quickcheck had:
pub extern crate rand;

pub use rand::Rng;

then users can use quickcheck::rand to get access to the full rand API to interact with quickcheck, while not being constrained about what version of rand they want for their own purposes.

https://users.rust-lang.org/t/rfc-api-guideline-re-export-a-whole-crate-if-exporting-any/17820

I'll close this one in favour of #176 to try keep discussion focused.


Remove redundancy in Item data structure

Codecov Report

Merging #130 into master will increase coverage by 0.34%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #130      +/-   ##
==========================================
+ Coverage   97.21%   97.56%   +0.34%
==========================================
  Files           6        6
  Lines         287      287
  Branches       33       42       +9
==========================================
+ Hits          279      280       +1
+ Misses          8        7       -1

Impacted Files
Coverage Δ

...re/src/main/scala/org/typelevel/paiges/Chunk.scala
98.21% <100%> (+1.78%)
:arrow_up:

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 6f8cf49...3d48f96. Read the comment docs.


Using PostCSS loader

Feature request

Is your feature request related to a problem? Please describe.
Currently, we have to write all the css prefixes and handle cross browser issues due to unsupported features.

Describe the solution you'd like
We can use postcss-loader with plugins to auto-generate a lot of content for cross browser compatibility.

Also test for IE / Edge / Firefox issues.


test tx_circuit_1tx_2max_eip1559 in tx circuit fake pass, need to fix

What command(s) is the bug in?
No response
Describe the bug
cargo test --features scroll  --package zkevm-circuits --lib -- tx_circuit::test::tx_circuit_1tx_2max_eip1559 --exact --nocapture
[2024-04-08T08:33:58Z ERROR zkevm_circuits::tx_circuit] pk address from sign data 0x202bb2fab1e35d940fde99b214ba49dafbcef62a does not match the one from tx address 0x0000000000000000000000000000000000000000
Context "ECDSA context" used 1 advice columns and 922347 total advice cells in phase 0
Special lookup advice cells: optimal columns: 1, total 126552 cells used in phase 0.
Fixed columns: 1, Total fixed cells: 8032
Context "ECDSA context" used 1 advice columns and 9223
Concrete steps to reproduce the bug. If it's able reproduce via testool, please share test_id from jenkins report
No response

test against latest develop, can pass now.  figured out that it is ought to be fixed by in commit() https://github.com/scroll-tech/zkevm-circuits/commit/b84dfdfbb6215933baa8bab4f4204c72f9b13975#diff-19a12cd7e250530b6476c03e72f46a033d05ef162f3202dae2ee103b07b24802

close as fixed.


Implement SSL

Fixes #167.
The most straightforward way to add SSL support to the driver was to use OpenSSL, so that's what I went with. This has the downside of not working on systems without OpenSSL installed, so in the interest of still allowing people on such systems to compile/use the driver, I added SSL as an optional feature. This adds a bit of complexity to the code in the form of needing [cfg(feature = "ssl")] in a lot of places, but I think this is preferable to users on systems without SSL installed by default (e.g. Windows) to still use the driver. I also elected to have the driver default to not including SSL support, and an informative error message is given if the user tries to connect with SSL without enabling it to ensure that nobody thinks that they're using SSL when they're actually not.

It would be doable, although it would be a bit funky. The tests would need need SSL certificates and private keys, so they would either have to be manually added to the repo or generated with a sort of script that would have to be invoked before the test. Then a separate mongod would have to be run with the correct arguments (something like mongod --sslMode requireSSL --sslPEMKeyFile server.pem --sslCAFile ca.pem) for the client to test against.
If we decide to go this route, our tests would then require 3 separate mongod's, which is starting to get a little unwieldy. It's probably worth looking into using something like this to make setting them up a bit easier.

A set of certs and pkeys confined to an ssl test folder wouldn't be too bad, I think. Perhaps we can do a separate mongod for this PR and follow-up with mongo-orchestration?

Works for me! I'll push another commit to the PR adding the test, certs, and keys once I get a chance

:wave: sorry for the delayed follow-up, was waiting to see if there was any followup to ciphers. more thoughts inlined now that I've looked at some other uses of the OpenSSL crate.

@saghm, seeing a lot of branching cases here with the feature flag and with_ssl methods. What if we generalized the ssl: Option<SslConfig> field + with_ssl methods and required a StreamConnector to be passed around? Something like:
// stream.rs
pub trait StreamConnector {
  fn connect(&self, hostname: &str, port: u16) -> io::Result<Stream>;
}

pub struct TcpStreamConnector;

impl StreamConnector for TcpStreamConnector {
  fn connect(&self, hostname: &str, port: u16) -> io::Result<Stream> {
    TcpStream::connect(host, port);
  }
}

pub struct SslStreamConnector {
  pub ca_file: String,
  pub certificate_file: String,
  pub key_file: String,
  pub verify_peer: bool,
}

impl StreamConnector for SslStreamConnector {
  fn connect(&self, hostname: &str, port: u16) -> io::Result<Stream> {
    // Use ssl file opts
  }
}

// mod.rs
pub struct ClientOptions {
  ...
  pub stream_connector: StreamConnector,
}

impl ClientOptions {
  pub fn new() -> ClientOptions {
    ClientOptions {
      ...
      stream_connector: TcpConnector::new(),
    }
  }

  pub fn with_stream_connector(connector: StreamConnector) -> ClientOptions {
    ...
  }
}

Sounds good to me. I can implement that within the next day or so, unless you'd prefer to do it yourself.

np, whenever you have time. sorry about the back-and-forth — wish it was easier to collaborate :)

No worries! I was mainly asking if you wanted to make the change because you had basically already written all the necessary code, and I wanted to give you the option of not having me steal your work.

So it turns out that using traits for StreamConnector and Stream don't work out that wonderfully. Using StreamConnector efficiently requires that it be clonable, as methods like TopologyDescription::add_missing_hosts would need to pass it multiple times. Unfortunately, any trait that implements a method with itself in the type signature (such as Clone::clone) or even with a generic type parameter (like fn clone<T>(&self) -> T where T: StreamConnector, which is one hacky workaround I tried) aren't able to be used as trait objects. This means that we'd have to pass StreamConnectors around everywhere by generic type parameters with bounds, which in practice turns out to "infect" almost every type in the library (up to and including all the major public-facing ones: Client, Database, Collection, and Cursor). This is pretty suboptimal; requiring users to deal with a generic parameter on Client, Database, Collection, and Cursor for the sake of having cleaner code is questionable, but having users not compiling with SSL doing it for the sake of code that they're not even compiling is just plain rude.
Fortunately, the brilliant idea of passing around a StreamConnector works quite well with the original strategy of using an enum for TCP vs. SSL. The resulting code only requires conditional compilation in two places; lib.rs, for extern crate openssl and ClientOptions::with_ssl and stream.rs, for the actual implementation of the SSL variant of the enum.
On a related note, implementing Stream as a trait doesn't quite work either; returning a Result<Box<TcpStream>> for a Result<Box<Stream>> is not allowed, and casting TcpStream to Stream is only allowed when Stream is Sized...which brings us back to the original problem of having to use generics instead of trait objects. This is also quite easily fixed by making Stream an enum rather than a trait.

ah, awesome! thanks for looking into this — looks like it turned out pretty clean/self-contained overall. I'll do a good pass-through this weekend, if not tonight.

Btw, given how many iterations this PR has gone through, I think it's a prime candidate for me to finally try out the merge and squash option on Github, which I've never actually gotten around to doing. Any objections for me merging it like that (and hopefully not accidentally doing something stupid)?

hah! I've been using squash and merge for a while now and it's fantastic -- keeps the history readable at a high level, but links to the PR for more depth.
Pretty straightforward, just make sure you edit the sub-description before confirming the merge :)

Oh, I did not realize it linked to the PR, that's pretty awesome! And yep, I was definitely planning on explicitly setting a good commit message.

A changelog is definitely a good idea. As for what specifically the new version should be after this change, are you opposed to bumping to 0.2.0? Obviously there isn't much of a behavioral change for users not using SSL, but this seems to be a pretty significant step towards maturity for the driver, so I feel like (pre-1.0) minor version jump might be a good fit for it.
I'm not super worried about tagging for the driver, as Cargo/crates.io will be used almost exclusively instead cloning and manually compiling the driver. I suppose it could be useful for users who want to fork the driver to add custom functionality for it though, so I wouldn't be opposed to making sure we tag every new release.

FYI the Travis build on my fork for this PR failed due to the test timing a command taking too long with SSL. It passed for when the build for this repo ran, so I'm not super worried. I'm guessing this is just the fact that SSL is slightly slower than regular TCP, although it might even just be a coincidence that it happened with SSL and was just a random fluke.
I've restarted the build to see if it happens again, but I'm hoping/expecting that it won't.

yeah I'm cool with 0.2.0 — it kinda breaks away from semantic versioning, but I agree it has some symbolic weight that'll be good for it.

Technically, nothing really "breaks away" from semantic versioning when you're pre-1.0 :)


Conditional Playbooks

Is your feature request related to a problem?
Enable a user to setup a output based execution path of the playbook.
Please describe.
Describe the solution you'd like
The user can do the following on top of the output of a step.
Execute a conditional expression to create a boolean result. For this, rules will be applied on the step output. These rules can be:

For timeseries result: an aggregation function on top of the result to create the LHS of the expression. Supported functions are average, sum, max, min, latest. The function can be applied as a rolling window of configured time slice or on whole as a cumulative
For table result: count of rows or a string based operator allowing equals or substring match on a particular column value of type string. And numerical operators for column values of type numeric.

Based on the expression, user can configure next step in the execution sequence. The next step will be a child to the original step.

Once someone lands on this playbook page, they click on ‘Start Execution’ button and with each step execution they are shown the output and the next step in sequence as per the conditional path.
User can still choose to execute any step they want.
All outputs, expression results and clicks will be recorded in the playbook execution
Once user starts, a timeline view shows currently executed step, its output, its interpretation w.r.t next step and information on the next step.

Describe alternatives you've considered
Additional context
Add any other context or screenshots about the feature request here.
Thank you for your feature request!

Development of this feature can be tracked here- https://github.com/DrDroidLab/PlayBooks/pull/248

Development of this feature is complete and is available in the latest stable release.


Kafka repeatedly failing healthcheck

Every time I launch the kafka package it fails the healthcheck and there is no information as to why in the logs.

I've gone onto the mesos slaves running the process and am unable to curl the port that kafka is running on, and nothing pertaining to the get request shows up in the logs for the task.

It turns out this is specific to instance types. For some reason Kafka launches fine on m3.xlarge DCOS slave instances, but the healthcheck is unreachable and times out on r3.8xlarge DCOS instances.

Hey @john-dodson this was resolved in #58 the problem was related to the number of acceptor thread jetty was setting by default was based on number of processors. The thread pool was also default so the situation becomes only acceptor and no worker threads.

So if the the Mesosphere DCOS guys build a new jar and update their config the issue should be resolved, correct?

@john-dodson that sounds like so, @joestein are you able to publish a new jar on universe yourself or do you need us to?

@dmitrypekar is working on the pr for the universe changes today. I already pushed the jar to s3 or we can use the one from the tag release https://github.com/mesos/kafka/releases/tag/<IP_ADDRESS>

Pushed PR to universe: https://github.com/mesosphere/universe/pull/179
It will update kafka-mesos jar to <IP_ADDRESS> version

@john-dodson Is the problem fixed? Could the issue be closed?

@john-dodson please re-open if you are still having issue but this should be resolved now, thanks.


⚠ Samsung has degraded performance

In 9546fa8, Samsung (https://samsung.com) experienced degraded performance:

HTTP code: 200
Response time: 2321 ms

Resolved: Samsung performance has improved in 3005d29.


Refactor PartitionParquetScroogeSource

Refactor PartoitionParquetScroogeSource to include the changes to made to the partitioned hive parquet source and sink.

We have a proper Source and Sink implementation for Parquet now.


Failed to serialize 'FanoutSearch.Action' to a type object.

my environment:
Ubuntu16.04 x64
.NetCore 2.1.4
GraphEngine.Core 1.0.9083  (I build it myself,The NuGet package outdated.)
GraphEngine.LIKQ 1.0.9083
My main test code:
           Global.LocalStorage.LoadStorage();             TrinityConfig.HttpPort = 80;             FanoutSearchModule.EnableExternalQuery(true);             FanoutSearchModule.SetQueryTimeout(3000);             FanoutSearchModule.RegisterIndexService(Indexer);             FanoutSearchModule.RegisterExpressionSerializerFactory(ExpressionSerializerFactory);             TrinityServer server=new TrinityServer();             server.RegisterCommunicationModule<FanoutSearchModule>();             server.Start();
the exception throws at
`
public class ExpressionSerializer:IExpressionSerializer
{
private static XmlSerializer m_serializer = null;
private static NodeFactory m_factory = null;
    public ExpressionSerializer()
    {
        m_serializer=new XmlSerializer();
        m_serializer.AddKnownType(typeof(FanoutSearch.Action));
        m_factory=new NodeFactory();
    }

    public string Serialize(Expression pred)
    {
        //Exception throws here
        return pred.ToXml(m_factory,m_serializer);
    }

    public Func<ICellAccessor, Action> DeserializeTraverseAction(string pred)
    {
        var func_exp = m_serializer.Deserialize<LambdaExpressionNode>(pred)
            .ToExpression<Func<ICellAccessor, FanoutSearch.Action>>();
        return func_exp.Compile();
    }

    public Func<ICellAccessor, bool> DeserializeOriginPredicate(string pred)
    {
        var fun_exp = m_serializer.Deserialize<LambdaExpressionNode>(pred)
            .ToExpression<Func<ICellAccessor, bool>>();
        return fun_exp.Compile();
    }
}`

Exceptions Trace:
Unhandled Exception: System.Runtime.Serialization.SerializationException: Failed to serialize 'FanoutSearch.Action' to a type object.
at Serialize.Linq.Nodes.TypeNode.ToType(IExpressionContext context)
at Serialize.Linq.Nodes.ConstantExpressionNode.set_Value(Object value)
at Serialize.Linq.Nodes.ConstantExpressionNode.Initialize(ConstantExpression expression)
at Serialize.Linq.Nodes.ExpressionNode1..ctor(INodeFactory factory, TExpression expression)    at Serialize.Linq.Nodes.ConstantExpressionNode..ctor(INodeFactory factory, ConstantExpression expression)    at Serialize.Linq.Factories.NodeFactory.Create(Expression expression)    at Serialize.Linq.Nodes.LambdaExpressionNode.Initialize(LambdaExpression expression)    at Serialize.Linq.Nodes.ExpressionNode1..ctor(INodeFactory factory, TExpression expression)
at Serialize.Linq.Nodes.LambdaExpressionNode..ctor(INodeFactory factory, LambdaExpression expression)
at Serialize.Linq.Factories.NodeFactory.Create(Expression expression)
at Serialize.Linq.Extensions.ExpressionExtensions.ToText(Expression expression, INodeFactory factory, ITextSerializer serializer)
at Serialize.Linq.Extensions.ExpressionExtensions.ToXml(Expression expression, INodeFactory factory, IXmlSerializer serializer)
at People_LIKQ.ExpressionSerializer.Serialize(Expression pred) in /home/coder/Documents/NetCore/LIKQ-Examples/People-LIKQ/ExpressionSerializer.cs:line 30
at FanoutSearch.ExpressionSerializer.Serialize(Expression pred)
at FanoutSearch.FanoutSearchDescriptor.<>c.b__22_0(Expression pred)
at System.Linq.Enumerable.SelectListIterator2.ToList()    at System.Linq.Enumerable.ToList[TSource](IEnumerable1 source)
at FanoutSearch.FanoutSearchDescriptor.Serialize()
at FanoutSearch.FanoutSearchDescriptor._ExecuteQuery()
at FanoutSearch.FanoutSearchDescriptor.GetEnumerator()
at People_LIKQ.Program.LikqQurety() in /home/coder/Documents/NetCore/LIKQ-Examples/People-LIKQ/Program.cs:line 73
at People_LIKQ.Program.Main(String[] args) in /home/coder/Documents/NetCore/LIKQ-Examples/People-LIKQ/Program.cs:line 37

For dotnet core you should add Serializer.Linq  as dependency for both Trinity and Likq project, this is an implement issue of Serializer.Linq.
Also @yatli, i found that my previous commit was merged to one project file, but lost the Serializer.Linq  for dotnet core.

Add code link for reference, in method 'IsCandidateCompilationLibrary'.

@chaosddp thanks for your input! I’m also wondering how to make this work with coreclr. As for Serializer.Linq, I think coreclr references are transitive so you only have to add the reference at the leaf.

Are you sure a reference to Serialize.Linq is mandatory on LIKQ itself? Looks like it’s got some black magic in that library wrt assembly loading

@chaosddp  I  pull the newest source code and added Serializer.Linq as dependency for both Trinity.Core and Likq project, and rebuild GraphEngine.Core GraphEngine.LIKQ, and add refrence Serializer.Linq in both TSL and Program project, But I still get the same error, and some new error output "ghashtable.c:324: assertion 'hash != NULL' failed" as below:
Unhandled Exception: System.Runtime.Serialization.SerializationException: Failed to serialize 'FanoutSearch.Action' to a type object.
at Serialize.Linq.Nodes.TypeNode.ToType(IExpressionContext context)
at Serialize.Linq.Nodes.ConstantExpressionNode.set_Value(Object value)
at Serialize.Linq.Nodes.ConstantExpressionNode.Initialize(ConstantExpression expression)
at Serialize.Linq.Nodes.ExpressionNode1..ctor(INodeFactory factory, TExpression expression)    at Serialize.Linq.Nodes.ConstantExpressionNode..ctor(INodeFactory factory, ConstantExpression expression)    at Serialize.Linq.Factories.NodeFactory.Create(Expression expression)    at Serialize.Linq.Nodes.LambdaExpressionNode.Initialize(LambdaExpression expression)    at Serialize.Linq.Nodes.ExpressionNode1..ctor(INodeFactory factory, TExpression expression)
at Serialize.Linq.Nodes.LambdaExpressionNode..ctor(INodeFactory factory, LambdaExpression expression)
at Serialize.Linq.Factories.NodeFactory.Create(Expression expression)
at Serialize.Linq.Extensions.ExpressionExtensions.ToText(Expression expression, INodeFactory factory, ITextSerializer serializer)
at Serialize.Linq.Extensions.ExpressionExtensions.ToXml(Expression expression, INodeFactory factory, IXmlSerializer serializer)
at People_LIKQ.ExpressionSerializer.Serialize(Expression pred) in /home/coder/Documents/NetCore/LIKQ-Examples/People-LIKQ/ExpressionSerializer.cs:line 30
at FanoutSearch.ExpressionSerializer.Serialize(Expression pred)
at FanoutSearch.FanoutSearchDescriptor.<>c.b__22_0(Expression pred)
at System.Linq.Enumerable.SelectListIterator2.ToList()    at System.Linq.Enumerable.ToList[TSource](IEnumerable1 source)
at FanoutSearch.FanoutSearchDescriptor.Serialize()
at FanoutSearch.FanoutSearchDescriptor._ExecuteQuery()
at FanoutSearch.FanoutSearchDescriptor.GetEnumerator()
at People_LIKQ.Program.LikqQurety() in /home/coder/Documents/NetCore/LIKQ-Examples/People-LIKQ/Program.cs:line 73
at People_LIKQ.Program.Main(String[] args) in /home/coder/Documents/NetCore/LIKQ-Examples/People-LIKQ/Program.cs:line 37
ghashtable.c:324: assertion 'hash != NULL' failed
ghashtable.c:324: assertion 'hash != NULL' failed
ghashtable.c:324: assertion 'hash != NULL' failed
ghashtable.c:324: assertion 'hash != NULL' failed
ghashtable.c:324: assertion 'hash != NULL' failed
ghashtable.c:324: assertion 'hash != NULL' failed
ghashtable.c:324: assertion 'hash != NULL' failed

@yatli, yes that the problem, and i just remembered that we can reference System.Runtime instead as workaround as my previous commit, so that we LIKQ will not dependence on any other 3rd packages.
@BenDerPan i will have a try, since i still keep an old version without updating.

@yatli i found the issue that Serialize.Linq trying to load assembly for 'GraphEngine.LIKQ', but actually it should be "FanoutSearch", at line 32 here, seems like RuntimeLibary using PackageId as name here.

@BenDerPan as a temporary workaround you can change the packageid of FanoutSearch to 'FanoutSearch', then the tests will pass.

@chaosddp you rock! I'm submitting an issue to Serialize.Linq to reference your findings. For now, I'll set the assembly name to GraphEngine.LIKQ to work around this.

hey, what do you want me to change in Serialize.Linq?

hi @esskar! I believe we understand the code and our workaround will address this issue temporarily. We do hope that the assembly loader behaves consistently with netfx and netstandard. I know it's a bit of a trouble for netcore11 because there were no proper support for assembly enumeration, but anyway my suggestion on this is to:

add a new target netstandard2.0 which does support assembly enumeration from AppDomain.
for netcore11, try to figure out the assembly name from the package id returned from using Microsoft.Extensions.DependencyModel.

@yatli
I just hit this exception.  Is this something you'll be able to fix soon, so the unit tests work?

@PhilPJL yup, in a day or two I’ll get to work on this.

i just published Serialize.Linq 1.7.0 with support for .net standard 1.3 and 2.0
does this help with your issue?

ooh @esskar that's great news! trying rightaway, will report back in a few mins. tried to work on this issue two hours ago and it's still 1.6 :D

@esskar just confirmed version 1.7.0 is working for netcoreapp2.0. thank you for your quick update!

i am glad i could help, and thanks for using my library. i was totally unaware of that.


Specify Postgres version requirement in docs

When detailing the prerequisites for deploying an Edgehog instance on the documentation, specify that only Postgres v13+ is supported.
Update development tooling to use Postgres v13, to be in line with the minimum version supported and advertised for production environments. This way tests are run against the oldest supported Postgres version, catching bugs and missing Postgres features early instead of deploying to production and finding out the hard way.

Pull Request Test Coverage Report for Build 1336d1030c31b58420d74337db14431d07c1647f-PR-571
Details

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 80.449%

Totals

Change from base Build c2933ecfc91add058cd978dc53d7ab30afa46191:
0.0%

Covered Lines:
1218

Relevant Lines:
1514

💛  - Coveralls


Fix lines of code badge (or at least try to)

I don't know if the problem is with shields.io, or if some repo setting is blocking it from checking, but at least the badge is showing up now.

Yeah, the tokei service has recently been almost permanently down.
I am even considering removing the badge altogether as it almost never works.

I saw this on the Shields.io website.

If your GitHub badge errors, it might be because you hit GitHub's rate limits. You can increase Shields.io's rate limit by adding the Shields GitHub application using your GitHub account.

I tried to look through a few other repos that use the badge - it all shows unavailable for all of them

It turns out shields.io uses the same api to get the data for that badge, so it's the same problem with extra steps. I think I've found some alternative solutions tough.

ghloc

![Endpoint Badge](https://img.shields.io/endpoint?url=https%3A%2F%2Fghloc.vercel.app%2Fapi%2FDiligentGraphics%2FDiligentTools%2Fbadge)
https://github.com/pajecawav/ghloc-web
sloc

![Lines of code](https://sloc.xyz/github/DiligentGraphics/DiligentTools)
https://sloc.xyz/github/DiligentGraphics/DiligentTools

What is sloc?

Apperently it stands for "source lines of code".

@MichaelHinrichs Do you know if there is a way to exclude ThirdParty directory?

https://github.com/DiligentGraphics/DiligentTools/blob/master/.tokeignore

The documentation says .ignore file can be used, but it does not seem to work.

Would you prefer to use ghloc instead?

ghloc does not seem to support ignore files. Also, it is very scarcely used as opposed to sloc, so I will stick with sloc for now.

Completed in 59f3c00d18852c77911407e040099b9f5d34d1b7 and 17c77de9ccf6af42827eb9eab61bc2bf75689375


Minor: consolidate parquet custom_reader integration test into parquet_exec

Which issue does this PR close?
re #3463
Rationale for this change
The easier it is to find existing parquet tests the easier it is to evaluate our coverage
What changes are included in this PR?
Move the custom reader test into the parquet_exec suite, and apply some touchups
The first commit moves the file and then the second cleans up the test code a bit
Are these changes tested?
They are all tests
They are run like:
cargo test  --test parquet_exec

And you can see the output like:
...
test parquet::custom_reader::route_data_access_ops_to_parquet_file_reader_factory ... ok

Are there any user-facing changes?
No tests only

cc @crepererum

@Ted-Jiang  or @crepererum  I wonder if you would have time to review this PR?


Code block CSS class missing language prefix

In a previous version when I used a code block with a specific language, the class name would appear as language-php. After updating to the latest version, the class name is now only php.
Is there a configuration setting somewhere to be able to automatically add the language prefix?
Or should the code blocks now be marked up to also include the prefix?

The latest version switched Markdown parsers, so I suspect that's the source of this change, but I'll take a look!

Both php and language-php are fine here. Code highlighting is done by highlight.js or similar package. Markdown parser just inserts the class that you assigned to it. In this case it's php or language-php. Please, show your final html parsed code and check what package you are using to highlight the code.

I understand that both are fine. The issue is that before php alone would result in a final html parsed code with class="language-php" and after the change in Markdown parsers  the output is just class="php".

@jreviews are you using Prism for syntax highlight? Prism requires language-* class to be added to class attribute. That's why Parsedown generates it. But highlight.js, shipped with Jigsaw templates, doesn't require it. If you are not using highlight.js, could you try it as workaround?

I can make changes needed inside my project to get this working. However, the point of this issue is that any previous project that expected to have the language-* prefix as it did before, now needs to be updated to take this into account.

@jreviews Fortunately, the new parser exposes a configuration setting for that class name prefix, and I think we should set the default to match the previous Parsedown behavior so we don't break a bunch of existing Jigsaw sites. I've updated that in #426, and also added a way for those config settings to be more easily accessed in bootstrap.php, should anyone want to remove the language-* prefix (or change any other PHP Markdown setting).

Thank you!


Website freezes on expanding Andaman and Nicobar islands

Describe the bug
Website freezes when expanding to district view of Andaman and Nicobar islands on phone (Chrome/Android).
To Reproduce

Expand table entry of Andaman and Nicobar Islands
Tap on any district

Additional context
Appears to be a problem with the complexity and/or size of the Andaman and Nicobar islands map JSON. A solution might be to simplify the map.

Whoa good catch!

https://www.covid19india.org/maps/andamannicobarislands.json is 135KB(zipped) and 652KB(unzipped). the arcs key has too much data that mobile can handle. tested on One plus 7. It took like 2 - 3 minutes to unfreeze.

Was this fixed? Because it works perfectly fine on my low-end device.

@varungupta3009 Don't think it was. It still freezes on my phone. The weird part is that it works fine on Firefox mobile.

@shuklaayush I would like to work on this. could you assign me?

@varungupta3009 Don't think it was. It still freezes on my phone. The weird part is that it works fine on Firefox mobile.

Yes. Turns out that it hangs on Chrome, but it's perfectly fine on Chrome Canary. I was using Canary on both. So it's an optimization issue that will probably be fixed in the near future.

@varungupta3009 Don't think it was. It still freezes on my phone. The weird part is that it works fine on Firefox mobile.

Yes. Turns out that it hangs on Chrome, but it's perfectly fine on Chrome Canary. I was using Canary on both. So it's an optimization issue that will probably be fixed in the near future.

Thanks! I guess there's nothing to fix then.


Day/Week view bug on 3/12/2017 & 3/11/2018

Hey, been using this component for a while and it's pretty awesome. I just wanted to bring up a really obscure bug I found - on Sunday 3/12/2017 and Sunday 3/11/2018 (maybe more days too, but I only checked about a year's worth of days), the day/week view is missing the last hour block (TimeSlotGroup component, I think) in the calendar, 11:00PM - 12:00AM. In addition, if the calendar is selectable and you click 2:00 AM on one of those days, the event will pass the clicked time as 3:00 AM. The same goes for all times between 2:00AM and 2:59AM inclusive; it'll add on an extra hour to what you actually clicked. You can see the missing hour block & the selectable click issue on the demo site itself - for example in the "Selectable" example in the week view - by looking at one of the days I mentioned.

I also mentioned this #325


double-beep: Watch cricketdugout.com

double-beep requests the watch of the watch_keyword cricketdugout\.com. See the MS search here and the Stack Exchange search here.

cricketdugout\.com has been seen in 1 true positive, 0 false positives, and 0 NAAs.

Approved by Nisse Engström in Charcoal HQ


Make extensions section in extensions pack expandable/collapsible

From @jwarkentin in #89962
Make the section expandable with a button/link at the bottom middle or left of the list of extensions that just says "Show more" or "Show all extensions" or something to that effect?
That way the readme is still visible but the user can choose to expand the extension list as part of the one scrollable content area.

I do not think this will work because this will give only little space for the read me.

The expandable/collapsible section should be part of the same scrollable area as the readme. Then it's not a problem at all. It should effectively be inserted as an expandable section within the readme.

Read Me is rendered as a separate web view (iFrame) as it is Markdown. I think it is not easy to include extension packs in Read Me. Hence they are made separate sections.
@mjbvz Any suggestions?

@sandy081 We control the rendering of the webview so you could add extension pack info inside of it: https://github.com/microsoft/vscode/blob/9f1aa3c9feecd04a79d22fd6752ba14a83b48f1b/src/vs/workbench/contrib/update/browser/releaseNotesEditor.ts#L320
I believe that would be the most simple fix

I see.

I think a simple chevron next to the extension pack details to collapse it should do the trick.


File not found due to unexpected prefix in directory names

Hi folks,
I was running rnaseq but got error message file not found as following:
[2017-07-04T22:57Z] piccolo002-181: Unexpected error
Traceback (most recent call last):
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 50, in _setup_logging
yield config
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 295, in generate_transcript_counts
return ipython.zip_args(apply(rnaseq.generate_transcript_counts, *args))
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 129, in generate_transcript_counts
data["count_file"] = featureCounts.count(data)
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/featureCounts.py", line 22, in count
sorted_bam = bam.sort(in_bam, dd.get_config(data), order="queryname")
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/bam/init.py", line 377, in sort
if bam_already_sorted(in_bam, config, order):
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/bam/init.py", line 447, in bam_already_sorted
return order == _get_sort_order(in_bam, config)
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/bam/init.py", line 451, in _get_sort_order
with open_samfile(in_bam) as bam_handle:
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/bam/init.py", line 231, in open_samfile
return pysam.Samfile(in_file, "rb")
File "pysam/libcalignmentfile.pyx", line 397, in pysam.libcalignmentfile.AlignmentFile.cinit (pysam/libcalignmentfile.c:5831)
File "pysam/libcalignmentfile.pyx", line 558, in pysam.libcalignmentfile.AlignmentFile._open (pysam/libcalignmentfile.c:7556)
IOError: file /groups/springer/han/CDK46_response_201701/MCF7/work/align/6_hours_0_3_Abemaciclib/1_2017-07-04_MCF7_star/6_hours_0_3_Abemaciclib.bam not found
[2017-07-04T22:57Z] piccolo002-192: Unexpected error
However, I found the file under a folder with a similar but different name:
./MCF7/work/align/6_hours_0_3_Abemaciclib/16_2017-07-04_MCF7_star:
total 3219218
-rw-rw-r-- 1 hj84 springer 996431246 Jul  4 18:39 6_hours_0_3_Abemaciclib.transcriptome.bam
-rw-rw-r-- 1 hj84 springer 441385052 Jul  4 18:40 6_hours_0_3_Abemaciclib.bam
-rw-rw-r-- 1 hj84 springer   3911856 Jul  4 18:40 6_hours_0_3_Abemaciclib.bam.bai
-rw-rw-r-- 1 hj84 springer 689346155 Jul  4 19:02 6_hours_0_3_Abemaciclib.nsorted.bam
-rw-rw-r-- 1 hj84 springer 633874059 Jul  4 19:03 6_hours_0_3_Abemaciclib.nsorted.primary.bam
Apparently, the prefix of the directories differed but I have no clue what caused that. Could anyone help me out?
Thanks in advance!
MCF7.zip

We generate a lane number here:
https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/pipeline/run_info.py#L765
and it depends on the ordering of the run details in the YAML file. Did the ordering get swapped in the YAML file that is in the config directory between reruns? That would definitely cause this issue.

The ordering in the generated YAML file did get swapped. Do you have an idea what I should deal with that?

Thanks, sorry about that we weren't really anticipating this happening. Did files get added in between the runs? It kind of looks like that.  I think for future runs adding files to the bottom of the CSV file should work okay, because the rest of the files will maintain their ordering. As it is, now I think the easiest path forward to is nuke the work directory and start over. If that is super painful to do then we could try to fix it but that would involve figuring out the original order, rearranging the CSV file and putting the new samples at the end, deleting all the files related to the new files and then restarting. From the logs it looks like these samples aren't particularly deep so I think its probably easier to start over.

I started over, didn't get the '[file] not found' message. However, I got another one, as follows:
[2017-07-06T00:19Z] piccolo002-182: Converting Sailfish to Sleuth format.
[2017-07-06T00:19Z] piccolo002-182: Loading required package: methods
[2017-07-06T00:19Z] piccolo002-188: ^[[00m^[[1m[2017-07-05 20:19:15.284] [jointLog] [info] wrote 24 bootstraps
[2017-07-06T00:19Z] piccolo002-182: Error in setnames(quant, c("target_id", "length", "tpm", "est_counts")) :
[2017-07-06T00:19Z] piccolo002-182:   Can't assign 4 names to a 5 column data.table
[2017-07-06T00:19Z] piccolo002-182: Calls: prepare_fish_for_sleuth -> sapply -> lapply -> FUN -> setnames
[2017-07-06T00:19Z] piccolo002-182: Execution halted
[2017-07-06T00:19Z] piccolo002-178: ^[[00m^[[1m[2017-07-05 20:19:15.450] [jointLog] [info] wrote 29 bootstraps
[2017-07-06T00:19Z] piccolo002-182: Uncaught exception occurred
Traceback (most recent call last):
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/groups/bcbio/bcbio_dev/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /groups/bcbio/bcbio_dev/anaconda/bin/Rscript -e 'library("wasabi"); prepare_fish_f$
Loading required package: methods
Error in setnames(quant, c("target_id", "length", "tpm", "est_counts")) :
Can't assign 4 names to a 5 column data.table
Calls: prepare_fish_for_sleuth -> sapply -> lapply -> FUN -> setnames
Execution halted
' returned non-zero exit status 1
It seems like the numbers of columns didn't match, but I have no idea where were the columns from and how to solve it. Could you please help me again? Thanks!

Great, glad that helped. This error is due to having an outdated version of wasabi, I'm not sure why this old version is persisting. I disabled this conversion so if you update to the development version with:
bcbio_nesxtgen.py upgrade -u development

this should be disabled. Alternatively, updating wasabi should work, you can do that by opening up the R that comes with bcbio with:
/groups/bcbio/bcbio_dev/anaconda/bin/R

and updating to the current version of wasabi:
devtools::install_github("COMBINE-lab/wasabi")

Hope one of those gets you going.

Unfortunately, I don't have the permission to execute either of them (orchestra.med.harvard.edu). Are there other ways I can do?

Hi,
I am updating the code in orchestra. you can try in a one of hour again.
Let us know if you find further issues there.
cheers

On Jul 6, 2017, at 11:10 AM, Han-Ying<EMAIL_ADDRESS>wrote:
Unfortunately, I don't have the permission to execute either of them (orchestra.med.harvard.edu). Are there other ways I can do?
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub https://github.com/chapmanb/bcbio-nextgen/issues/1996#issuecomment-313425551, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HE8lybsS4sjc1OfhESXihSlbs0_Lks5sLPkCgaJpZM4OObnG.

Han-Ying, Lorena and Rory;
I pushed fixes to the bcbio install process which will force an upgrade to the latest R which should include the up to date wasabi. A standard upgrade should now do it but let me know if you run into any issues at all.

The work has been properly done. That really helps! Thanks a lot!

Thanks Brad!


[FR] Support starting/stopping Azure MySQL server

Is your feature request related to a problem? Please describe.
We would like to be able to use the broker to start and stop Azure MySQL server instances in order to reduce costs.
https://docs.microsoft.com/en-us/azure/mysql/how-to-stop-start-server
Describe the solution you'd like
Open to any suggestions.
Describe alternatives you've considered
N/A
Additional Context
There does not seem to be a way to do this natively with Terraform, the only option I can see would be using local-exec provisioner with the az CLI embedded into the broker.
Priority
Low
Platform
Azure
Applicable Services
csb-azure-mysql

Any ideas how to express this through the cf cli? How might it fit in the 'create-service', 'bind', 'unbind', 'delete-service' flow?

Probably something similar to performing failover for Azure SQL FOG. E.g. something like:
cf create-service csb-azure-mysql stop stop-my-db. # stops the server
cf delete-service stop-my-db # starts the server

@claassen The team has flagged this as a "contribution wanted" sort of feature. Unfortunately, cannot allocate ENG resources to make this happen anytime soon.


fix #5995

There were several issues in the resize logic of the panel addon which would only allow it to work with static sizes:

the panel setSize function assumed that when newHeight parameter is null, only width had changed. However on window resize event the function will be called without parameters at all.

the panel setSize function would overwrite the height of the wrapper. If it has a percent value it would be converted to pixels on the first run.

Panels might change their height upon window resize, leading to miscalculation of the remaining height for the main editor, thus panels need to listen to resize events, too.

in the version we are still using in our project CodeMirror would also cache the height of the container and would not trigger the setSize function, since the container is replaced by panel plugin and thus the wrong height is compared to the cache. However this cache seems to be removed already in the current version. (onResize in global_Events.js)

So, frankly, this module is a terrible hack. But since existing users might be relying on it, I rather leave it as it is than making the hacks even more convoluted and possibly breaking them in new ways. I don't remember what I was thinking when I first wrote some of this code, but the very concept seems deeply flawed, so I don't think it can be saved.
I recommend you either fork the addon locally or try to replace it with a simpler, less broken approach that serves your use case. Would that work for you?

Well, after digging through this for two days, I think I understand it well enough to say that actually nothing should break.
If you used absolute sizes before this change, it will still work after the change.
If you used percentage values before, it didn't work and now will, and if somebody got it to work, than it was most certainly some kind of event handler that calculates the new sizes manually and calls setSize(). This approach would be unnecessary now but would also still work...
After all, it is your decision and since we don't import CodeMirror via npm, I already fixed it for our product.
My intention was to improve CodeMirror/the panel addon for everyone... (and also we wouldn't have to maintain this change when we update someday 😄 )

Hm, all right, let's iterate a bit more. If the built-in window resize handler already calls the setSize method, why do you need to explicitly hook it up through an additional handler? It seems the current PR will always end up calling setSize twice for resize events—once through the built-in resize handler, and once via your handler and changed.

Yes that's right (at least sometimes). The panels themselves might change their size when the window resize is triggered, either because they have relative sizes themselves or due to line wrapping in their content.
However this is ignored by the current implementation. When cm.state.panels.heightLeft is recalculated inside setSize, the height of the panel(s) is ignored, assuming they didn't change.
Hence I added the handler inside the panel, which checks if the height has changed and only if it has (the check in line 74 if (newHeight == this.height) return; ) _setSize will be called again to correct the wrong height from the first call.
This means that with N panels, _setSize will be called at least once and up to N+1 times, since the call is triggered by the panel itself.
A better approach would be of course to recalculate the height based on all panels each time in setSize.
This would make cm.state.panels.heightLeft completely obsolete, resulting in basically a rewrite of the whole module, which I tried to avoid...

This does sound like the overwriting setSize method should just always do the measuring, so that the resize handler can be dropped.

This does sound like the overwriting setSize method should just always do the measuring, so that the resize handler can be dropped.

Done.

Thanks, looks a lot more coherent now.


Send end status after 03:30

Strange bug, but in network playing, with audioplayer version, when I set the position after 03:30 of a track, even this track is 5 minutes or more, it will send a end status and stop.

Unfortunately this is a issue with audioplayer
I tried to find a solution for it but a part of C++ code is behaving strangely SeekTo(uint64_t position)
after 210 second when position passed to SeekTo(uint64_t position) the number be something different (exactly a very big integer)

@poka-IT
currently you can use this
thanks to maintel
dependency_overrides:
  audioplayers_windows:
    git:
      url: https://github.com/kflutter/audioplayers
      path: packages/audioplayers_windows
      ref: 263b4cc648d39a79455c221897a2c699f9d1c4c0

audioplayers know in the main package.


Re-render View on Schema Config Change

Update WidgetChooser to redraw views on schema change
Fix issue(https://github.com/makinacorpus/angular2-schema-form/issues/85)

@ZheyangSong Nice catch! I was sure it was that kind of small thing you can read thousands of time in the code without realizing it was actually the problem :)
Thanks for the fix. I will make a release.

1.0.0-beta.6 is released

@ebrehault Glad to be able to contribute. I'm happy to know that you guys respond, merge PR and release a new NPM package in a timely manner. Thanks.
As I use this component, I see sort of heavy form markup generated. I'd like to know if there is plan on improving this. Amongst the markup problems, some small relevant things include the rendered action buttons don't have type attribute, the generated form mark up is not wrapped by a form element and etc. I understand that this project started as an intermediate solution before the angular-schema-form community braces Angular. But I still wonder if there is any plan on resolving these problems and making it production-ready. Are the users of this component expected to extend/override the lib to fix such problems?
If you can share the design decisions behind this implementation, I probably can help with resolving some of them at spare time.

As I use this component, I see sort of heavy form markup generated. I'd like to know if there is plan on improving this.

That's definitely in our plans.

the generated form mark up is not wrapped by a form element

I am not sure I get what you mean, to me it looks like it is wrapped in a form tag.

I understand that this project started as an intermediate solution before the angular-schema-form community braces Angular.

Well, not exactly, we started it because ASF was not migrating to Angular, but our intent is not to create an intermediary solution (even if we might consider merging our effort with ASF if they decide to move).
Our objective is totally to get a production-ready version as soon as possible.

Are the users of this component expected to extend/override the lib to fix such problems?

Certainly not, it should be fix in the core.

If you can share the design decisions behind this implementation, I probably can help with resolving some of them at spare time.

We are considering changing the implementation (see #78), and the discussion is totally open.
Any help is greatly appreciated :)

@ebrehault Thanks for the detailed answers. I'm exited to know that there is on-going work to make this component better. And I'd certainly be willing to help.
As of the form tag, for my case, the outmost tag is sf-form. Please refer to the screenshot below). Not sure if I haven't used the component properly.

Oh right! That's actually a regression I hadn't noticed. That's very bad on the semantic point of view.
I made a fix: https://github.com/makinacorpus/angular2-schema-form/commit/364737b4519f6fd103005ac32a5b2fc04fa382ea


Make it easy in flutter.yaml to bundle specifically Roboto and Noto

MD uses both of these.
https://www.google.com/design/spec/style/typography.html#typography-typeface
We'll want to make it easy to bundle these "by default" with one line changes, something like:
flutter.yaml

- fonts:
  - roboto
  - nato

maybe? @jason-simmons
At which point probably the flutter create template wants to include them? (since the framework always wants these fonts)?

Rather than using the fonts key for this feature, we should probably use something like uses-material-design: true that's a signal to include these fonts (and whatever other resources the material.dart library needs).  This is similar to how material-design-icons is a more opinionated version of assets.

As an example, if your app uses-material-design we should include the menu and back-arrow icons because those are used by the built-in Scaffold widget.

I like the uses-material-design: true proposal. sgtm.

I'm going to introduce uses-material-design: true with #994

Here's a source for Roboto with a clear license:
https://github.com/google/fonts/tree/master/apache/roboto
Noto looks a bit more involved:
https://www.google.com/fonts/specimen/Noto+Sans

https://github.com/flutter/flutter/pull/2315 creates a bunch of mechanism that will be useful for resolving this issue.

@collinjackson will want to use this in the firechat example once it works.

this should probably be included by default when you run "flutter create" since that generates a Material app for you

Yeah, we should be able to extend the pattern that we're using for the icon font to include roboto.  The one wrinkle is that we don't need to include roboto on android.

@jason-simmons did this.