[explore] Filter Select not working for int and bool

[x] I have checked the superset logs for python stacktraces and included it here as text if any
[x] I have reproduced the issue with at least the latest released version of superset
[x] I have checked the issue tracker for the same issue and I haven't found one similar

Superset version
0.18.2
Expected results
Integer and boolean column values get fetched for the Filter Select drop-downs in explore view.
Actual results
Selecting a column for filtering which is of type integer or boolean will not populate the select field with the column's distinct values.
2017-05-25 07:18:07,705:ERROR:root:1 is not JSON serializable
Traceback (most recent call last):
  File "/opt/apps/superset/venv_py3_test/lib64/python3.4/site-packages/superset/views/base.py", line 49, in wraps
    return f(self, *args, **kwargs)
  File "/opt/apps/superset/venv_py3_test/lib64/python3.4/site-packages/flask_appbuilder/security/decorators.py", line 52, in wraps
    return f(self, *args, **kwargs)
  File "/opt/apps/superset/venv_py3_test/lib64/python3.4/site-packages/superset/views/core.py", line 1090, in filter
    payload = json.dumps(datasource.values_for_column(column))
  File "/usr/lib64/python3.4/json/__init__.py", line 230, in dumps
    return _default_encoder.encode(obj)
  File "/usr/lib64/python3.4/json/encoder.py", line 192, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib64/python3.4/json/encoder.py", line 250, in iterencode
    return _iterencode(o, 0)
  File "/usr/lib64/python3.4/json/encoder.py", line 173, in default
    raise TypeError(repr(o) + " is not JSON serializable")
TypeError: 1 is not JSON serializable

Steps to reproduce

register the superset maintenance table main.ab_user in superset
Enable Filter Select for it and make some columns of type int or bool filterable
explore the table and select one of the above columns for filtering

Columns of type float seem to work as expected, though, at least with the SQLite backend.
I tested it by registering another column for the above table, which is defined by id * 0.1 and making this column filterable of course.

One more remark: If employed in a filter slice, all of the mentioned dtypes (str, int, bool, float) seem to work nicely. It is just the Filter Select in explore that is affected.

Can you try changing the line in the stacktrace from
payload = json.dumps(datasource.values_for_column(column))
to
payload = json.dumps(datasource.values_for_column(column), default=utils.json_int_dttm_ser))?
At least the error should show the type it's struggling with. Most likely some numpy related type.

@mistercrunch: Your fix seems to work, as tested with the 'active' and 'id' columns of said table.
I forgot to mention — and this might make a difference — the described behavior was invbestigated with a clean installation in a fresh python 3 venv, using just the default SQLite database.
I will also investigate this in our PostgreSQL environment...

@mistercrunch: I now tested your solution in combination with a Postgres backend:
Integer columns now seem to work nicely. However, as I already anticipated somehow, boolean columns are not 100% compatible. While the lookup query apparently works, the distinct values are not displayed properly in the drop-down selector.
The selector correctly features two distinct options, however, they are both just blank.

The two options seem to represent the correct false and true values (in alphabetic order), as can be confirmed by querying with any of these filter values set.
I got the idea that the difference between SQLite's and Postgres' boolean types is that the former uses 0 and 1 as representation, while the later employs false and true. So maybe it's all about casting these values to the strings that get printed in the selector list.

BTW: The very same behavior can be observed, when this boolean column is included into a filter slice. Not quite sure whether I should file a new issue for this — apparently — Postgres-specific problem...

Hello, I experience the same behavior connecting the tool to an Impala table.
The only workaround that I Found is to create a new column with the expression:
CASE my_bool_column WHEN true THEN 'True' ELSE 'False' END

I guess, we need to file a new issue for the bool-specific part, as this one is closed already.
@ZamoraAndres could you do this maybe, and also reference this very issue? I only have my phone at hand right now...
Btw, casting the bool value to string is the easiest workaround in Postgres. Maybe this also works in Impala?

@ZamoraAndres check out #3007 please and whether the Boolean representation in Impala is false/true (and not 0/1 like in SQLite) just like in Postgres. In this case we should just add Impala to the list of affected DBs over there.


bt asset can get corrupted

create a bt asset
select the asset, open the editor, dont save it
-run the scene and make a gameobject use the bt

the asset in result will be corrupted

Exception thrown while invoking [OnOpenAssetAttribute] method 'Bonsai.Designer.BonsaiWindow:OpenCanvasAsset (int,int)' : NullReferenceException: Object reference not set to an instance of an object
Bonsai.Designer.BonsaiCanvas.CreateNode (Bonsai.Core.BehaviourNode behaviour) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiCanvas.cs:49)
Bonsai.Designer.BonsaiCanvas.ReconstructEditorNodes (System.Collections.Generic.IEnumerable`1[T] treeBehaviours) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiCanvas.cs:182)
Bonsai.Designer.BonsaiCanvas..ctor (Bonsai.Core.BehaviourTree tree) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiCanvas.cs:27)
Bonsai.Designer.BonsaiEditor.SetBehaviourTree (Bonsai.Core.BehaviourTree tree) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiEditor.cs:306)
Bonsai.Designer.BonsaiWindow.BuildCanvas () (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:196)
Bonsai.Designer.BonsaiWindow.SetTree (Bonsai.Core.BehaviourTree bt, Bonsai.Designer.BonsaiEditor+Mode mode) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:219)
Bonsai.Designer.BonsaiWindow.OpenCanvasAsset (System.Int32 instanceID, System.Int32 line) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:443)
UnityEngine.GUIUtility:ProcessEvent(Int32, IntPtr) (at /Users/builduser/buildslave/unity/build/Modules/IMGUI/GUIUtility.cs:187)

Unable to duplicate.
Following your steps I get a null exception because the blackboard is null. Which is to be expected when creating BehaviourTrees from the CreateAssetMenu. (Blackboard is not set)
At runtime, the assets are not modified. The game objects use a clone of the BT asset, so corruption of the original assets would be unlikely.
Any BT assets open in an BT Editor window will also be saved before going into Play mode.
Are there other ways you were able to duplicate this issue?

Side note: I pushed a fix so null blackboards are not cloned when a BT Asset is cloned.

i will retry to reproduce today

it is still reproducible:
https://www.youtube.com/watch?v=IBfNhm4JkAg&feature=youtu.be

Pushed a fix.

BT assets are auto saved when the Unity Editor is exiting Edit Mode (before entering play mode) by using EditorApplication.playModeStateChanged
Hopefully this fix makes auto-saving much more stable.

there is an extra bug to fix related to this,
when entering play mode with unsaved bt not saved and selected:
NullReferenceException: Object reference not set to an instance of an object UnityEditor.GameObjectInspector.ClearPreviewCache () (at /Users/builduser/buildslave/unity/build/Editor/Mono/Inspector/GameObjectInspector.cs:210) UnityEditor.GameObjectInspector.OnDisable () (at /Users/builduser/buildslave/unity/build/Editor/Mono/Inspector/GameObjectInspector.cs:198) UnityEditor.AssetDatabase:SaveAssets() Bonsai.Designer.BonsaiSaver:SaveTree(TreeMetaData, BonsaiCanvas) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiSaver.cs:192) Bonsai.Designer.BonsaiSaver:SaveCanvas(BonsaiCanvas, TreeMetaData) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiSaver.cs:80) Bonsai.Designer.BonsaiWindow:QuickSave() (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:358) Bonsai.Designer.BonsaiWindow:OnDisable() (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:89)
in BonsaiSaver line 188 changed the following:
  // Sort the nodes in pre order so it is easier to clone the tree.
  canvas.Tree.SortNodes();

  SaveTreeMetaData(meta, canvas);
  var currentObject = Selection.activeObject;
  Selection.activeObject = null;
  AssetDatabase.SaveAssets();
  Selection.activeObject = currentObject;

Did you reproduce this with the latest changes and with the same steps?

this was reproduced with getting latest

creating a new bt asset
-open it
-add nodes
-keep it open and assign to component to run it
play scene

i remember having this issue before also, it is a known unity bug they never fixed
https://forum.unity.com/threads/clearpreviewcache-error.714896/

I unable to replicate on Unity 2019.3.14f1
Ill try to search for alternatives to OnDisable so BT assets can be saved on window close and when a reload occurs.

I pushed a fix in the branch: fix/btsave
This removes saving from OnDisable.
Saving is done explicitly when the window is destroyed (OnDestroy), before assembly reloads, and before entering play mode.
Could you test the changes in fix/btsave?

i got latest in new project in 2019.3 and i got same error while running a bt & having the window open.
NullReferenceException: Object reference not set to an instance of an object UnityEditor.GameObjectInspector.ClearPreviewCache () (at <6f28216fea9f453abf2e05b770ed3ee4>:0) UnityEditor.GameObjectInspector.OnDisable () (at <6f28216fea9f453abf2e05b770ed3ee4>:0) UnityEditor.AssetDatabase:SaveAssets() Bonsai.Designer.BonsaiSaver:SaveTree(TreeMetaData, BonsaiCanvas) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiSaver.cs:192) Bonsai.Designer.BonsaiSaver:SaveCanvas(BonsaiCanvas, TreeMetaData) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiSaver.cs:80) Bonsai.Designer.BonsaiWindow:QuickSave() (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:360) Bonsai.Designer.BonsaiWindow:OnDisable() (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:81)

i got latest in new project in 2019.3 and i got same error while running a bt & having the window open.
NullReferenceException: Object reference not set to an instance of an object UnityEditor.GameObjectInspector.ClearPreviewCache () (at <6f28216fea9f453abf2e05b770ed3ee4>:0) UnityEditor.GameObjectInspector.OnDisable () (at <6f28216fea9f453abf2e05b770ed3ee4>:0) UnityEditor.AssetDatabase:SaveAssets() Bonsai.Designer.BonsaiSaver:SaveTree(TreeMetaData, BonsaiCanvas) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiSaver.cs:192) Bonsai.Designer.BonsaiSaver:SaveCanvas(BonsaiCanvas, TreeMetaData) (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiSaver.cs:80) Bonsai.Designer.BonsaiWindow:QuickSave() (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:360) Bonsai.Designer.BonsaiWindow:OnDisable() (at Assets/BonsaiBehaviourTree-master/Designer/Editor/BonsaiWindow.cs:81)

This error should be gone in the branch fix/btsave since OnDisable no longer does any saving.

yes it is fixed indeed now, will keep testing more


feature: add PagerDuty to event providers

Fixes #6
Changes proposed in this pull request:

Adding PagerDuty to event providers
Enabling and disabling providers from config

Thanks @amgadramses!


Strange behavior when connecting

Hello!
I'm trying to deploy a Laravel application using Capistrano. So far, I created an SSH key in the remote server and added it to my Bitbucket repository, for the server to be able of cloning it. First, I connect to the server with ssh <username>@<server direction>, and I test the git commands, such as clone, ls-remote, and so on. They all work. Then, when Capistrano tries to do so after connecting as <username>, it fails. Why so, if I have proved the connection from server to Github?
I hope you all the best, thanks for your awesome tool

I would suggest reading http://capistranorb.com/documentation/faq/why-does-something-work-in-my-ssh-session-but-not-in-capistrano/

Capistrano uses a concept called SSH agent forwarding. This means that the git commands are authenticated using the SSH key from your local machine, not the SSH that you manually set up on your server.
Therefore you need to ensure that the SSH key that you are using to connect to your server is the same one that Bitbucket uses to authorize access to your repository.
Finally, and this probably goes without saying, but when you configure the :repo_url in Capistrano, make sure you are using the SSH format (i.e. as opposed to HTTPS). For example:
set :repo_url, "git@bitbucket.org:myusername/myrepo.git"

I would suggest reading http://capistranorb.com/documentation/faq/why-does-something-work-in-my-ssh-session-but-not-in-capistrano/

I read the linked document, and it makes sense. But I don't see how loading or not loading those .profile etc files affects the connection to git. My .profile, .bash_profile and .bashrc files only contain lines about loading rvm scripts. But still "git ls-remote" works when I ssh to the server, but does not work when I do "cap production deploy" on my local machine.

https://stackoverflow.com/questions/65095020/capistrano-3-14-cannot-get-connection-to-my-git-during-deployment/65177046#65177046
Capistrano seemed to use forward agent by default, which screws up my deployment.


Fixed an issue with forgotten binary sign. Fixed encode_packet_output…

…_type test to support both python2 and python3

Looks good. Thanks. :+1:


Primitives repository mdlz-prmtz

Hey, I'm using just standalone Radix System, but I'd like to see, how the primitives are implemented without installing the whole radix package. Is there a reason why it's a private repo?

Hey @potty 👋
Thanks for reaching out. I hope Radix System is working well for you. Please keep in mind we're heavily working on all Radix related packages and they're all in alpha at the moment, so semver versioning hasn't even started properly. Although I don't foresee any big breaking changes happening in Radix System since it's so low-level.
Styled System v5.1.0 implemented a new Variant API which is inspired by Radix System's, you can see here: https://styled-system.com/variants/
So I'm now considering whether to keep it or remove it from our library. Just a heads up.
Now back to your questions 😅

I'd like to see, how the primitives are implemented without installing the whole radix package.

Just to clarify, Radix and the Modulz Primitives are separate things. Radix consumes the Primitives and adds its own look and feel onto them. If you just want to see how Radix is customising the Primitives, you don't need to install Radix, you can browse some of the Components on Github, like the Slider

Is there a reason why it's a private repo?

Yes, this is still quite new and not ready to be publicised, we published it to NPM so we could dogfood it. So far it's working really well, but I wouldn't recommend using it yet. Everything will probably change in the next few months :)
Thanks so much for your interest in these libraries, let me know if you have any more questions.
Cheers!

Thanks for your response! I'm asking because I'm building my custom primitives and wanted to get some inspiration from Radix ones. Currently, I'm using primitives that were part of this repo some time ago, but maybe it would be nice if I could use just the Radix primitives directly in my project to build components on it. :)
I like the Variant API and I think the question is similar to whether you are going to reexport css function from styled-system. I don't know how well-typed is variant on styled-system side, but I would keep it consistent and leave it on styled-system side if possible.
Also, I have a question about component props. I have some Box component https://jsfiddle.net/pL6e9k1a/ . Suggestions for props works fine, but not prop values, also prop values are not type-checked. No dealbreaker, but would be really nice. So my question is whether I'm doing something wrong or it's how it works currently.
If there is anything I can help you with, especially with strongly typed styled-system/Radix components, just let me know! Really appreciate your work on this whole thing!

@potty hey!  Sorry for the delay, we were busy preparing and attending Clarity conference.
As of Styled System v5.1.0, the variant API has ben updated to be aligned with the one from Radix.
Right now I'm considering whether to remove it completely from Radix and just rely on SS's one, but I need to run some tests first.
https://github.com/styled-system/styled-system/blob/master/CHANGELOG.md#v510-2019-08-12
Regarding TS, @jxnblk is considering re-writing Styled System in Typescript, if this goes ahead, it'll be much better than what I'm currently doing, which is adding Types later on.

However, if you see anything that could be improved please feel free to contribute!
Cheers


About the results on ogbp-pcba in the process of finetune

Hi, thanks for your exciting Graphormer. I have a question when I use Graphormer v2 to pretrain on PCQM4Mv2 and finetune on ogbp-pcba or hiv. The evaluated metric ap on pcba in finetune is that '2022-03-13 12:44:53 | INFO | main | ap: 0.02584909547397629'. However, the results of leaderboard is about 0.3. The other condition is that the AUC on hiv in finetune is about 0.3(' | INFO | main | auc: 0.32)' while it is 0.8 on OGB. Thus, I want to know the reason. Maybe the hyper-parameter is not matched or the max-epoch is too small? Thank you very much.

Thanks for using Graphormer.
For PCBA, if this feature is urgent for you, please kindly click the thumb up reaction at this https://github.com/microsoft/Graphormer/issues/70, and we will promote the priority.
For Hiv, would you provide your python environment and all instructions to obtained your result? If your instructions are correct, it should be at least 0.8 AUC on Hiv. see #90 .

Thank you, I have tried graphormer to pretrain and finetune in v2.0 last week. This week, I try v1.0 to pretrain and finetune on ogbp-molhiv and pcba, and obtain expected results.

Hi, thanks for your work.
For PCBA, I can only get 'pcqm4mv1_graphormer_base_for_molhiv' for pre-training. However, its num-classes is 1, while the num-classes of PCBA is 128. I would like to ask if the pre-trained model 'pcqm4mv1_graphormer_base_for_molhiv' could train PCBA and how to use it.
Thanks very much.


fix: OpenShift Installation docs

What type of PR is this?

/kind bug

What does this PR do / why we need it:
#539
Have you updated the necessary documentation?

[x] Documentation update is required by this PR.
[x] Documentation has been updated.

Which issue(s) this PR fixes:
Fixes #539
Closes #539
How to test changes / Special notes to the reviewer:
Please follow the doc to verify the installation of the operator on an OpenShift Cluster.

also while undeploy faced this error
Error from server (NotFound): error when deleting "STDIN": configmaps "argocd-operator-manager-config" not found

also while undeploy faced this error Error from server (NotFound): error when deleting "STDIN": configmaps "argocd-operator-manager-config" not found

I dont see this, can you please re-try
configmap "argocd-operator-manager-config" deleted

/lgtm


Re-skeletonize

🗣 Description
This pull request re-skeletonizes this repository.  It also adds support for all the platforms we normally support, although that followed almost automatically from the re-skeletonization.
💭 Motivation and context
This repository needs to be re-skeletonized since it was based on an ancient version of a skeleton that lacked even a Lineage configuration.  It also needs to support Debian Buster, Bullseye, etc. so that it can support the plan to move CyHy off of Debian Stretch.
🧪 Testing
Automated testing passes.
✅ Pre-approval checklist

[x] This PR has an informative and human-readable title.
[x] Changes are limited to a single goal - eschew scope creep!
[x] All relevant type-of-change labels have been added.
[x] I have read the CONTRIBUTING document.
[x] These code changes follow cisagov code standards.
[x] All relevant repo and/or project documentation has been updated to reflect the changes in this PR.
[x] All new and existing tests pass.

I also wanted to bring up that the dependency cisagov/ansible-role-logrotate needs to be updated the same way as this repo.

@mcdonnnj - Please see cisagov/ansible-role-logrotate#8.


Added a program to convert given BGR image to Gray image

With this PR I am adding a program to convert the given BGR_image to Gray

Hey @dilipvijjapu, was this issue assigned to you?


Disconnect when Meteor application reloads

Hi,
I've been using Robomongo for a while but I want to switch to Mongoclient.
I'm using Mongoclient with a Meteor application and everything works fine until I edit some server side code and the app has to reload. Robomongo reconnects but Mongoclient loses connection and when I try to reconnect manually it keeps loading, so I have to restart the whole application to reconnect. It would be nice if it reconnects like Robomongo.
Thanks

Hello,
could you please kindly share which distribution and version are you using ?
Also what exactly do you mean by editing server side code ?

Please re-open this issue with specific details.


Move search button underneath for mobile layouts

Allows the search box to be as big as possible on smaller screens.
This also includes a shift from pixels to ems for the button width to make it relative to the font rendering which was causing an issue on IE8, Windows XP.
Desktop/tablet

Mobile

Can we have the button full-width for mobile please? Considering that the majority of users are right handed, a button all the way over to the left will be a stretch.


introduce an option to disable http/2

What does this PR do?
This PR adds a config option to disable http/2. This is needed in cases like described in #6608 where the backend doesn't work with http/2 but the request isn't automatically switched to http/1.1
Motivation
I wanted a fix for #6608
More

[ ] Added/updated tests --> I didn't find the right place where I could put this. If you could point me in the right direction, I'd be happy to try and add a test as well
[X] Added/updated documentation

Additional Notes
This is my first traefik PR and actually my first PR in Go, so sorry in advance for any stupid mistakes and thanks for feedback where I went wrong

Hello @tfenster,
Thanks for your time and your interest in Traefik !
The issue that you want to solve seems to come from the backend side.
At least, with IIS, the negotiation goes wrong and the fallback to HTTP1.1 is not working, which is not the case for all http servers.
As HTTP2 has become a standard, we are not willing to allow it deactivation as a global behavior.
We believe that it would lead to unwanted side effects.
Thus, an upcoming feature will be to set up the ServersTransport options by service thanks to #7203
We may reconsider your proposal, if you wait for it to be merged and take advantage of this new feature, to limit the scope of the deactivation of HTTP2 for only one service, and not as a global configuration.
WDYT ?

@rtribotte That 100% makes sense for me. I was actually looking for something more limited and only did it globally because I couldn't find a good place for it. But doing it by service of course is a lot better. (And I agree that the actual problem probably is the backend but as the chances are between 0 and non-existent that I can get a fix in IIS, I would love a workaround in Traefik...)
Would you have a rough idea when #7203 will be merged? I understand that you can't make promises, just a noncommittal best guess

Hello @tfenster,
Sorry for the delay, even a noncommittal best guess was something i couldn’t give you at the time of your answer.

Do you think you can still make the changes ?
Thanks again for your time and interest in Traefik !

Hello @rtribotte,
No problem, thanks for letting me know. I'll try to make my changes again and get back

@tfenster I'm looking forward to this change.. It will help me out a lot.

@jcuzzi same here ;) I was stuck with other stuff, hope to get it done this or next weekend

Hello @tfenster,
Maybe you have already seen that a pull request has been opened to disable HTTP/2 by using the ServersTransports feature introduced in #7203.
Will you have the time to update your PR or we can close it in favor of #7203?

I was hoping to get this done over the holidays, but if the other PR covers the issue, then I am happy to close this one and find something else to do :)

@tfenster thanks again for your time and your contribution!
Closed in favor of #7645


First stab at updating for Wave 3.0 (ReSharper 9.2-RC3)

Hi there,
I recently upgraded to the nightlies and noticed ForTea wasn't available as an extension so I decided to take a few minutes to bump it up to Wave 3.  This is the first I've looked over the code so I might have b0rked something but it's working great in 2013 and 2015 with the locally packaged version so I thought I'd share.
It was all straight forward -- I grabbed the pre-release 9.2 SDK and changed the interface implementations that required it.  There was one added property in "T4LanguageSpecificDaemonBehavior.cs" called RunInFindCodeIssues that I wasn't sure if it should be true or false which I set to true.
Thanks for the great tool.  I've used this for several years now and it's been awesome and a huge money saver (minus the ReSharper license which I had anyway).  The only option until recently has been a $99 tool that doesn't do anything more than ForTea.  Well done.
Take care,
Matt

Thank you, looks fine to me! I appreciate the contribution.


Provide support for iOS 12

Hello,
That's just a tiny pull request that fixes Swift files on iOS 12. To be honest, I don't have the sufficient knowledge to determine whether the code is still compatible with previous iOS versions but these fixes were suggested by XCode checking out the pod locally.
Have a nice day !

Yes it works !

Thanks @PaoloCuscela !


Use diagonal batching in TorchDataset

Description
Currently, TorchDataset reads from an npz file that contains arrays of shape (n_conformers, n_atoms, *) for atom features.  The atom feature array is padded to a constant n_atoms. This PR will revise HDF5Dataset to instead store an atom feature array of shape (n_atoms, *) and an array that tracks the number of atoms per conformer in an array of shape (n_conformers, ). TorchDataset.__getitem__ will still return an array of atom features for one conformer of shape (n_atoms, *), but it will do so by computing index ranges into the (n_atoms, *) atom feature array rather than direct indexing. Conformer features will still be stored in arrays of shape (n_conformers, *) as before.
Todos

[x] Implement for new TorchDataset code in #11
[x] Remove all hardcoded references to order of properties in properties_of_interest. Use format instead.

Status

[ ] Ready to go

The failing SchNet tests are because diagonal batching is not implemented within SchNet. test_dataset.py needs a test for a dataset with an arbitrary number of conformers in each record (e.g. SPICE). The existing tests were passing with incorrect implementations due to QM9 having one conformer per record.


[GLUTEN-1754][CH] Support aggregate functions with multiple arguments

What changes were proposed in this pull request?
(Please fill in changes proposed in this fix)
Fixes: #1754
How was this patch tested?
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
unit tests
(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)

please add the ut for this, for example: covar_pop

LGTM


withDefaultColorScheme so you can declare the color once and not pass it as a prop everywhere in the app

Description
So we can apply a default color scheme to all components, instead of setting them each time we use a component
Problem Statement
It will save a lot of time knowing that once you choose lets say "orange" as the color scheme, anywhere in the app you drop a button it will be orange, unless you change props..
Proposed Solution or API
import { extendTheme, withDefaultColorScheme } from 'native-base'

const customTheme = extendTheme(
  withDefaultColorScheme({
    colorScheme: 'red',
    components: ['Button', 'Badge'],
  }),
  withDefaultColorScheme({
    colorScheme: 'blue',
    components: ['Alert', 'Table'],
  }),
)

Alternatives
No response
Additional Information
No response

@haibert Thanks for the suggestion. We've added it to our list.


[Documentation Issue]

Page Name: bigquery-usage
Release: ffe5869
jobs = client.jobs()  # API request

Error:
AttributeError: 'Client' object has no attribute 'jobs'

@evmin Thanks a lot for filing this!

@dhermes - No issues!
Pardon me asking, but checking the bigquery client code from the 0.8.0 version I do not see any method resembling job listing.
How do I get the job list?
What would be the right forum to ask this sort of questions?
Thank you!

@evmin It has not been implemented yet. @tseaver Has handled the BigQuery implementation so he can say more.
This is the right forum to ask this sort of question, since the question is a "bug" issue in our docs.

Thank you.
The reason I have asked about the forum was that I have another question - in regards of the positioning of this SDK vs the older libs (both Java and Python). Should I be aiming at using this SDK going forward?
It is much easier to deal with I admit.

Short answer, yes. For APIs that we support, using this library is the "best" way to use them in Python.
Is google-api-python-client the older lib you are referring to?
From our README, "If you need support for other Google APIs, check out the Google APIs Python Client library."
This project is just the gcloud-python library, not the gcloud SDK.

@dhermes Are you planning to support other APIs in the future?

Yes, though they'll be cloud APIs.
@jgeewax Would it be worth having a roadmap doc?

I think that's tricky... I'd love to share future plans and all that, but I hesitate to share commitments externally when it's very possible that things could change rapidly.
If lots of people are asking for this, I think we should consider it more strongly... Is this a common question? Do we have any ballpark on how many people are hesitating on using gcloud-python due to a lack of a roadmap doc?

cf965c4e8b82818bbc4aa4e8524ed3dee905e64b changed docs/bigquery-usage.rst to show using the implemented Client.list_jobs method.


In flutter, when uploading an iOS program to the app store, an error message appears: Invalid Bundle. The bundle Runner.app/Frameworks/sherpa_onnx.frmework does not support the minimum OS Version specified in the Info.plist

In flutter, when uploading an iOS program to the app store, an error message appears: Invalid Bundle. The bundle Runner.app/Frameworks/sherpa_onnx.frmework does not support the minimum OS Version specified in the Info.plist
My fix: modify Info.plist, add
......
SupportedArchitectures

arm64

SupportedPlatform
ios
MinimumOSVersion
13.0
........
Also modify sherpa_onnx_ios.podspec
s.platform = :ios, "13.0"
Hopefully fixed in the release version

Thanks! Please see https://github.com/k2-fsa/sherpa-onnx/pull/1563
We are releasing v1.10.32.
Could you test the new release after
https://github.com/csukuangfj/sherpa-onnx/actions/runs/12012222667/job/33482941789
finishes?

thanks


[Bug]: Page reordering on selection

Is there an existing issue for this?

[X] I have searched the existing issues

Description
Simple and quick fix for now.
On the selection of a page, the tab moves and it's disorienting for a user especially because the order shuffles.
Let's keep it simple and elegant, on click let's not reorder the list keep the position locked.
Remove the "Tick" and keep it simple, on selection the row is highlighted.
Discussion: https://theappsmith.slack.com/archives/CRVRBGU1K/p1680711511055479
Steps To Reproduce
Video attached.
Public Sample App
No response
Environment
Production
Issue video log
https://theappsmith.slack.com/files/U0335E0PK0C/F051JCGDVV5/kapture_2023-04-05_at_21.39.42.mp4
Version
Appsmith v1.9.17-SNAPSHOT

This has been resolved


Images tint color

Hi, I don't know how to achieve the same style than the first example of the library. I want all my icons dark grey, and the selected tab with another icon color. But the library doesn't keep my drawable original colors, and applies a soft grey tint for all of them. How can I set the images color for selected and unselected tabs?

How many tabs do you have?

4 tabs. I don't want to change background color of the tabs, I only want my original images color, or to be able to set the images color programatically.

I think thats a limitation in the Library itself. @roughike?

It's possible with the newest versions.
mBottomBar.useFixedMode();
mBottomBar.setActiveTabColor("#FF0000");


Flyway parsing bug: unable to decrease block depth below 0 in DB2 V11.5

Which version and edition of Flyway are you using?
Flyway Community Edition 6.4.1 by Redgate
If this is not the latest version, can you reproduce the issue with the latest one as well?
(Many bugs are fixed in newer releases and upgrading will often resolve the issue)
Which client are you using? (Command-line, Java API, Maven plugin, Gradle plugin)
Command-line
Which database are you using (type & version)?
Database: jdbc:db2://localhost:50000/iaalunos (DB2/NT64 11.5)
Which operating system are you using?
Windows
What did you do?
(Please include the content causing the issue, any relevant configuration settings, the SQL statement that failed (if relevant) and the command you ran.)
CREATE OR REPLACE
PROCEDURE KHULA.SP_DROP_SUBSCRIPTION_HISTORY ()
BEGIN
--  DECLARE err_notfound CONDITION FOR SQLSTATE '02000';
DECLARE SQLSTATE CHAR(5);
DECLARE sp_specificname varchar(128);
DECLARE sp_speificname_to_drop VARCHAR(1000);

DECLARE cur CURSOR FOR
SELECT specificname FROM sysibm.sysprocedures where procname = 'SP_GET_SUBSCRIPTION_HISTORY' AND PROCSCHEMA = 'KHULA';
OPEN cur;
CurLoop:
LOOP
FETCH cur
INTO sp_specificname;
IF SQLSTATE = '02000' THEN
LEAVE CurLoop;
END IF;
IF sp_specificname IS NOT NULL THEN
SET sp_speificname_to_drop = 'drop specific PROCEDURE KHULA.' || sp_specificname ;
EXECUTE IMMEDIATE sp_speificname_to_drop;
	END IF;

END LOOP CurLoop;
CLOSE cur;
END;
call KHULA.SP_DROP_SUBSCRIPTION_HISTORY();
What did you expect to see?
Successful migration of script.
What did you see instead?
ERROR: Unable to parse statement in src\main\resources\migrations\V1110__SP_DROP_SUBSCRIPTION_HISTORY.sql at line 37 col 1: Flyway parsing bug: unable to decrease block depth below 0

The statement migrates successfully in Flyway Version 4.2.1

Migration completed successfully in Flyway 4.2.0


Upgrade raven-js to @sentry/browser

raven-js is legacy software, sentry has a new browser integration available as @sentry/browser.
I found the upgrade that gitlab did to its own service here https://gitlab.com/gitlab-org/gitlab/-/merge_requests/17715/diffs
It doesn't look like a very complex task.
Would it break existing configurations? This is something I don't know, I assume it could, if custom sites rely on importing raven-js, which wouldn't exist anymore, so this is maybe something for Volto 7.

Even better, guidelines provided on the sentry forums: https://forum.sentry.io/t/switching-to-sentry-javascript/4732

If the API is different should be a breaking, yes.

@sneridagh Is a 7.alpha branch planned already? If this is breaking we need a target for the PR

@pnicolli you can create a PR for master. We are not afraid of raising version numbers. :)
If we have a breaking change we need an entry and a howto in our upgrade guide, that's all. Then we can do a 7.0.0 final release. We only do alpha releases if the change is so fundamental that we need an additional testing/evaluation period.


Chromium 78 rejects importing key

Tried to import the key into Chromium:
Certification Authority Import Error
The file contained one certificate, which was not imported:
mkcert development certificate: Not a Certification Authority

Chromium Version 78.0.3904.87

Can you provide us the steps you followed to import the key? I am not entirely sure what that means.

Ran mkcert router.lan <IP_ADDRESS> which made a .pem and -key.pem file pair.
Opened up chrome://settings/certificates in Chromium. Selected the Authorities tab.
Clicked Import and selected the [bare] .pem file. Checked "Trust this certificate for identifying websites" and OK.
Then I get the error.

It sounds like Chromium wants the issuer to be imported there, not the leaf certificate ("Not a Certification Authority"). You'll find your mkcert CA with mkcert -CAROOT.
Note that the default way to make your mkcert certificates trusted is to use mkcert -install to get the root automatically into the system trust store.


Term change suggestion SDG12.1++ - [eco-tourism]

SDG: 12
Target & phrase:  multiple, sustainable consumption string
Suggested term/change: eco-tourism
Reason: we only have ecotourism as one word

Also bio-econom*

Check "lifestyles" - in the python testing, it only resulted in irrelevant results from health


The project should have a mailing list

I don't know if it's too early or how do you feel about this but it seems to me that, being GitHub issues, the only place people can ask questions regarding how to use the library that we should start thinking about having a mailing list.
What do you think about it? @adelevie @Xavdidtheshadow

Well, we could make a google group if we wanted an ok place to ask question.
But, I like having everything tracked in issues because then if something is a bug, it's easy to track the bug lifecycle throughout.


Add Visual Information Fidelity

What does this PR do?
Adds metric visual information fidelity (vif). See #799

Before submitting

[x] Was this discussed/agreed via a Github issue? (no need for typos and docs improvements)
[x] Did you read the contributor guideline, Pull Request section?
[ ] Did you make sure to update the docs?
[ ] Did you write any new necessary tests?

PR review
Anyone in the community is free to review the PR once the tests have passed.
If we didn't discuss your PR in Github issues there's a high chance it will not be merged.

Did you have fun?
Make sure you had fun coding 🙃

:books: Documentation preview :books:: https://torchmetrics--1830.org.readthedocs.build/en/1830/

@bojobo cool adding, feel free to reach out if you need help with anything :]

Will do that, thanks :)
I'll try to be done by next week. Is that early enough to get this metric into the next release? @SkafteNicki

@SkafteNicki
I'm sure that I'm on the right path, but I can't quite get the same results as the packages I'm using for reference.
My implementation is based on the implementation found in sewar as well as on the implementation found in piq. Furthermore, to make sure that the implementation is same as the paper, I've used the published resources (where this .zip contains the MatLab implementation). I've managed to create the same filter as sewer, but I can't get the same result.
Do you see any differences in the implementation? Or any fatal errors?
Also, I'm not quite sure how to implement the tests, since I've almost never done that (I know, I know, shame on me). I'm grateful for any form of help :)

Hi @bojobo, sorry for not responding sooner.
I tried out the code in PR and cannot see a problem with the implementation. Here is the testing script I used:
import sewar
import torch
import numpy as np

preds = np.random.randint(0, 255, (1, 41, 41, 1), dtype=np.uint8)
target = np.random.randint(0, 255, (1, 41, 41, 1), dtype=np.uint8)

compare = sewar.full_ref.vifp(target.squeeze(), preds.squeeze())

from torchmetrics.functional.image.vif import visual_information_fidelity

tm_res = visual_information_fidelity(
    torch.tensor(preds).permute(0,3,1,2),
    torch.tensor(target).permute(0,3,1,2),
    data_range=255.0
).item()

print(compare)
print(tm_res)
print(abs(compare - tm_res))

I get a difference in result of 1e-7 to 1e-9 which. So the implementation seems to be working to me.

@SkafteNicki Thanks for the reply!
I have some follow-up questions.

I don't understand why mypy is failing. I understand the returned message, but if I'm correct, other metrics are computed similarly and don't fail.
ddp=True leads to failing tests. I don't know what I'm missing to make it work. I would appreciate any help.

@SkafteNicki Thanks for the reply! I have some follow-up questions.
* I don't understand why `mypy` is failing. I understand the returned message, but if I'm correct, other metrics are computed similarly and don't fail.

* `ddp=True` leads to failing tests. I don't know what I'm missing to make it work. I would appreciate any help.

Hi @bojobo, I have fixed the typing issue. These two lines were missing:
https://github.com/Lightning-AI/torchmetrics/blob/45cc59192dc2401e3d591e79a447dcda51ddf188/src/torchmetrics/image/vif.py#L44-L45
which informs mypy about the type of the metric states.
For the ddp, I have to look further into that.

@bojobo the ddp test should also pass now.
The only problem was the default tolerance, which i have inscreased from 1e-8 to 1e-7 which is a completely fine tolerance to still be close to the reference:
https://github.com/Lightning-AI/torchmetrics/blob/b1098012115a1b37475b151fd0a8dd3361a2dd10/tests/unittests/image/test_vif.py#L52-L56


Changed the logic respondToSelector in TyphoonBlockComponentFactory

In my case, its need for the test that factory is correctly injected and its selectors contains in TyphoonBlockComponentFactory.
If  TyphoonBlockComponentFactory doesn't respondToSelector, try to check that one of the TyphoonDefinition could respondToSelector.

Hi, @constZinovyev! Can you please add some tests to verify this behavior?

Well.. that makes sence. Thanks for the contribution. Will be available in next version.


RC 4 Platform Browser - ELEMENT_PROBE_PROVIDERS

Looks like we have deprecated
ELEMENT_PROBE_PROVIDERS coming from
import { ELEMENT_PROBE_PROVIDERS } from '@angular/platform-browser';
My app still working after removing that in my app. Not sure if that is the right thing to do.
Any suggestion?
Thanks!

Yes, I have it on my list of things to kill. Will do. Thanks.

@Foxandxss thank you


Added links to run notebooks in SageMaker Studio Lab

As Amazon kindly provides generous Jupyter notebooks environment on SageMaker Studio Lab I thought it would be nice to be able to run pytudes there.

I suppose it is reasonable to add SageMaker. I don't know much about it. But the change should be in py/pytudes.py which is used to generate README.md .

Apologies, I should have studied the repository better. I will update the pull-request with changes to py/pytudes.py.

I regenerated README.md using the updated code, I hope the change is more meaningful now.

Very nice, thank you!


Progress bar running when Link has preventDefault()

Example:
const [mouseDownTime, setMouseDownTime] = useState(0);

  const handleClick = (e: any) => {
    e.preventDefault();
    e.stopPropagation();
    // check if it was a click or a drag
    if (Date.now() - mouseDownTime < 100) {
      window.location.href = e.currentTarget.href;
    }
  };

  const handleMouseDown = (e: any) => {
    e.preventDefault();
    setMouseDownTime(Date.now());
  }

<Link
  href={"/"}
  draggable={false}
  onMouseDown={handleMouseDown}
  onClick={handleClick}
>
    Link
</Link>

https://github.com/Skyleen77/next-nprogress-bar/assets/23238460/2c36c43d-b618-46ca-ac0f-755cd74550c9
Am I doing something wrong? Or is this an issue?

Closing this as this looks like a duplicate of https://github.com/Skyleen77/next-nprogress-bar/issues/52


feat: scan init/ephemeral containers

Description

Related issues

Close https://github.com/aquasecurity/trivy-operator/issues/98

Remove this section if you don't have related PRs.
Checklist

[X] I've read the guidelines for contributing to this repository.
[X] I've added tests that prove my fix is effective or that my feature works.
[X] I've updated the documentation with the relevant information (if needed).
[x] I've included a "before" and "after" example to the description (if the PR is a user interface change).

Does code coverage actually block CI?


support pack run, pack exec, pack install-app  for node backend.

when i run pack --cg node exec src/Main.idr ,I get  error. sh: build/exec/_tmppack: Permission denied
I think there are two reasons

The generated file does not have executable permissions
There is no #!/usr/bin/env node  in the first line of the generated file

Implemented in #157 .


Frontend npm install problems (lyft repository dependencies)

I was trying to build the static part of the amundsen frontend like outlined in the documentation
cd static
npm install
npm run build

This leads to a E401 errors from npm.
Current Behavior
Some of the dependencies in package-lock.json are resolved to a repository hosted by lyft.
This leads to problems building because it seems this is not open for public.
Example:
react-switch is resolved to https://artifactory-npm.lyft.net/artifactory/api/npm/virtual-npm-lyft/react-switch/-/react-switch-6.0.0.tgz which requires some kind of login to access.
Not sure what the reason for this is, but it seems like all of these dependencies could also be resolved by a public repository.
For Example
react-switch could be resolved from https://registry.npmjs.org/react-switch/-/react-switch-6.0.0.tgz
Possible Solution
It is of course possible to delete package-lock.json and rebuild it however this makes it much more complicated to get a working configuration. Manually changing the file for just a couple of dependencies is also not a great solution.
My proposal would be to change package-lock.json to only resolved dependencies to public available repositories.

I came across this issue once as well and saw some occurrences of people facing this in the amundsen slack channel too ...

This might be a nitpick, but to me, the "stale bot" does not seem to make a lot of sense. It just makes it obvious that replies are taking some time... Which I am totally ok with, by the way. Why shouldn't it be ok if there is no reply to an issue for 2 weeks ? Does not seem like auto closing issues helps with anything.

It is still happening, it is connecting to https://artifactory-npm.lyft.net/artifactory/api/npm/virtual-npm-lyft/tree-changes/-/t
ree-changes-0.7.1.tgz which need lyft credential. please prioritise it

Definitely a bug.
I will prioritize this, thanks for your patience!

Check https://github.com/amundsen-io/amundsen/pull/2174 for a fix

Thank you for the fix


import_string masks nested ImportError

I've added a failing test for this: https://github.com/pallets/werkzeug/pull/1271
Steps to replicate:

Given a file /level_one/level_two.py with the following contents:

import does_not_exist

Run import_string('level_one.level_two')

Expected:
An error is raised that mentions does_not_exist
Actual:
An error is raised that nothing about does_not_exist.
Notes:

This is similar to https://github.com/pallets/werkzeug/pull/570/files. Looks like that PR only fixed the case with AttributeErrors.

I'm trying to fix this myself, but I'm not sure about the purpose of the following lines: https://github.com/pallets/werkzeug/blob/73683a2ee741288c18751a4f739b9758a9e18a55/werkzeug/utils.py#L429-L431
I tried commenting them out and the tests still pass.

I know that we should be checking the caught ImportError at https://github.com/pallets/werkzeug/blob/73683a2ee741288c18751a4f739b9758a9e18a55/werkzeug/utils.py#L428 to see whether it actually matches something we expect, and raise if that isn't the case.


Mass Obsoletion: focus on branch 'immune system disorder' (MONDO:0005046)

branch:  'immune system disorder' (MONDO:0005046)
terms to obsolete:

obsoletion candidate ID
obsoletion candidate label

http://purl.obolibrary.org/obo/MONDO_0015822
acquired neutropenia

http://purl.obolibrary.org/obo/MONDO_0015818
aggressive primary cutaneous B-cell lymphoma

http://purl.obolibrary.org/obo/MONDO_0016599
autosomal dominant secondary polycythemia

http://purl.obolibrary.org/obo/MONDO_0016536
autosomal recessive lymphoproliferative disease

http://purl.obolibrary.org/obo/MONDO_0018720
common cystic lymphatic malformation

http://purl.obolibrary.org/obo/MONDO_0016495
functional variant of Guillain-Barre syndrome

http://purl.obolibrary.org/obo/MONDO_0015975
hyper-IgM syndrome with susceptibility to opportunistic infections

http://purl.obolibrary.org/obo/MONDO_0015976
hyper-IgM syndrome without susceptibility to opportunistic infections

http://purl.obolibrary.org/obo/MONDO_0015132
immunodeficiency predominantly affecting antibody production

http://purl.obolibrary.org/obo/MONDO_0017036
Langerhans cell histiocytosis in childhood and adulthood

http://purl.obolibrary.org/obo/MONDO_0020537
occupational allergic alveolitis

http://purl.obolibrary.org/obo/MONDO_0015823
primary immunodeficiency due to a defect in adaptive immunity

http://purl.obolibrary.org/obo/MONDO_0015135
primary immunodeficiency due to a genetic defect in innate immunity

http://purl.obolibrary.org/obo/MONDO_0015133
quantitative and/or qualitative congenital phagocyte defect

http://purl.obolibrary.org/obo/MONDO_0016494
regional variant of Guillain-Barre syndrome

http://purl.obolibrary.org/obo/MONDO_0018745
superficial pemphigus

http://purl.obolibrary.org/obo/MONDO_0019520
syndromic lymphedema

http://purl.obolibrary.org/obo/MONDO_0016493
variant of Guillain-Barre syndrome

Spreadsheet is here

Hi @LCCarmody - I review the orphaned classes and it looks good. I made one comment.
Do you want to proceed with reviewing the 'leaves the branch' terms?

Sorry, I missed this message. And I'm not sure what 'reviewing the 'leaves the branch' terms' means, exactly... Same process just see if it is correct?

Yes - similar process. Your spreadsheet is filtered on terms that leave the branch. This means that when we obsolete their parent(s), they will no longer be a type of immune system disorder. The goal is to review the terms, definitions, etc. and decide if they should be a type of immune system disorder (either a child of that parent class or something more specific in that branch) or if it is okay if they leave the branch. You can look at the other parents the term has in columns F-I or you can look at it in the ontology.
If you think it should have a new parent that is in the immune system disorder branch, please add the new parent like before.
If you think it's okay to leave the branch, just leave columns K-N blank but assign your curator confidence, so we know you looked at it.
Thanks @LCCarmody !

no problem, @LCCarmody! Thanks for doing this!

just finished. Have a few uncertainties.

@LCCarmody  I am done reviewing, do you want to review my comments and let me know if you have any questions?

Sorry, if i wasn't clear I am done reviewing. I agreed with Nicole's review--just had some questions about what is a feature. I added in all the requests. @sabrinatoro @nicolevasilevsky

There are some comments from the community that should be reviewed, but this is future work. This issue can be closed for now.


add original AST to recoverable error tokens

I'm not sure if this is the right way to do this, but the idea is that matching untyped arguments would remove all error tokens from semchecked AST so that it can be semchecked again in another context. For this to be possible and ideally to prevent cascading errors, the last child of error token trees is now either a dot for when it's meant to be completely removed, and any other tree if it's meant to be replaced by that tree. It's not clear if this would work, I haven't implemented untyped arguments with this yet.

We could also give "undeclared identifier" and "undeclared module.foobar" errors their own dedicated NIF tags and then defined can "patch" over these more easily.

Apparently the current error generation is broken regardless, an undeclared identifier generates abc (error "undeclared identifier"), and since the argument cursor is to abc it's a complete tree by itself and the error token is completely ignored and not added to the final call arguments. So defined would already (unintentionally) work for undeclared identifiers, but probably not more complex cases like defined(abc.def) which I'll try with this approach.

Feel free to rebase and reopen if I missed something.


Saving model with tf.keras.layers.RNN and stateful=True with save_format='tf' fails

System information

Have I written custom code (as opposed to using a stock example script provided in TensorFlow): yes
OS Platform and Distribution: Linux Ubuntu 18.04
Mobile device if the issue happens on mobile device: -
TensorFlow installed from: binary
TensorFlow version: 2.2.0-dev20200228
Python version: 3.6.9
Bazel version (if compiling from source): -
GCC/Compiler version (if compiling from source): -
CUDA/cuDNN version: CPU only
GPU model and memory: CPU only

Describe the current behavior
Saving a tf.keras.Sequential model with tf.keras.layers.RNN and stateful=True with save_format=tf fails.
Describe the expected behavior
Saving should succeed.
Code to reproduce the issue
import tensorflow as tf

number_of_cells = 2

model = tf.keras.Sequential()

model.add(tf.keras.layers.Input(batch_input_shape=(1, 1, 1)))

cells = []

for _ in range(number_of_cells):
    cells.append(tf.keras.layers.GRUCell(10))

model.add(tf.keras.layers.RNN(cells, stateful=True))

model.compile()

model.save('rnn.tf', save_format='tf')

model2 = tf.keras.models.load_model('rnn.tf')

Other info / logs
Saving succeeds with save_format='h5'.
Traceback in case of failure:
Traceback (most recent call last):
  File "test.py", line 18, in <module>
    model.save('rnn.tf', save_format='tf')
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/keras/engine/network.py", line 1044, in save
    signatures, options)
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/keras/saving/save.py", line 138, in save_model
    signatures, options)
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/keras/saving/saved_model/save.py", line 78, in save
    save_lib.save(model, filepath, signatures, options)
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/saved_model/save.py", line 951, in save
    obj, export_dir, signatures, options, meta_graph_def)
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/saved_model/save.py", line 1027, in _build_meta_graph
    options.namespace_whitelist)
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/saved_model/save.py", line 629, in _fill_meta_graph_def
    signatures = _generate_signatures(signature_functions, resource_map)
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/saved_model/save.py", line 497, in _generate_signatures
    function, mapped_inputs, resource_map)
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/saved_model/save.py", line 449, in _call_function_with_mapped_captures
    resource_map)
  File "/home/test/.local/lib/python3.6/site-packages/tensorflow/python/saved_model/save.py", line 372, in _map_captures_to_created_tensors
    ).format(interior))
AssertionError: Tried to export a function which references untracked object Tensor("2164:0", shape=(), dtype=resource).TensorFlow objects (e.g. tf.Variable) captured by functions must be tracked by assigning them to an attribute of a tracked object or assigned to an attribute of the main object directly.

I have tried on colab with TF Nightly version and was able to reproduce the issue. Please, find the gist here. Thanks!

@padoremu I was able to reproduce the issue with tf-nightly==2.2.0-dev20200228. However, it looks like this was resolved recently. With the recently tf-nightly (!pip install tf-nightly==2.2.0-dev20200303), I was not able to reproduce the issue. Please check the gist here. Thanks!
I am closing this issue as it was resolved. Please feel free to reopen if there is any related issue. Thanks!


build status badge is broken

https://drone.io/github.com/jmoiron/sqlx/latest gives me:
404 Not Found

Drone.io is out of service for public use, unfortunately.

@jmoiron this can be closed


Add cmdline flag for tcp interface

This, in combination with --acquire-port=false, prevents the obnoxious
warning popup in macOS.
Motivation
Fixes the issue described in https://github.com/spacemeshos/go-spacemesh/issues/289#issuecomment-574906535 where macOS prompts the user to allow incoming connections every time the node is run. While this permission is cached by the OS for a production app, there is no way around it in development since it reappears each time the app is recompiled.
To prevent this popup, with this change, run go-spacemesh with --acquire-port=false --tcp-interface <IP_ADDRESS> (a similar flag was added for the new GRPC server in a10ce1e146367942e275a9225eef1fee6f6e38f3).
Changes

adds a new commandline flag
removes the hardcoded "<IP_ADDRESS>" from P2P listener

Test Plan

Run node with and without the new flag and check if it's listening on the right interface

TODO

[ ] Add test

Regarding --acquire-port=false - this makes total sense in development, when you're not actually connecting to a real network. Ideally it shouldn't be something you do manually, but part of the default development config.
It's important that it's enabled by default in real-world use, as it decreases the number of non-routable nodes (by using UPnP to automatically forward ports on the local network).
Do you get this prompt in tests (I never do)? Or do you actually run a node binary on your machine?

Do you get this prompt in tests (I never do)? Or do you actually run a node binary on your machine?

I get this prompt many many times during tests. Every new test that tries to listen on tcp causes it to popup again. I also get it when running the binary locally.

Are we merging this?

Are we merging this?

Just need to add a test, will do asap

bors merge

bors merge


JVM crash in ONNX tests (CI)

See: https://jenkins.konduit.ai/blue/organizations/jenkins/konduitai%2Fkonduit-serving/detail/PR-291/1/pipeline
The aforementioned PR didn't make any ONNX-related changes.
This may be due to this PR: https://github.com/KonduitAI/konduit-serving/pull/292
Perhaps the issues are intermittent and only appear with maven surefire fork count > 0
Edit: it's definitely intermittent

@EmergentOrder
Something you might wanna look at. Can't access the logs in the link above but if this is similar to the logs here: https://jenkins.konduit.ai/blue/organizations/jenkins/konduitai%2Fkonduit-serving/detail/master/74/pipeline/#step-107-log-1227 then I was able to run the tests successfully when I compiled the onnxruntime with debug info with RelWithDebugInfo on macos.


add Cuda{2D,3D}LaunchConfig that maximizes occupancy

Add Cuda2DLaunchConfig and Cuda3DLaunchConfig that uses cudaOccupancyMaxPotentialBlockSize to calculate the best kernel launch parameters.

Can one of the admins verify this patch?

@tensorflow-jenkins test this please

I make some changes because I think it would also be necessary to check the physical limitation of each dimension:
int dev;
cudaGetDevice(&dev);
cudaDeviceProp deviceProp;
cudaGetDeviceProperties(&deviceProp, dev);
int xthreadlimit = deviceProp.maxThreadsDim[0];
int ythreadlimit = deviceProp.maxThreadsDim[1];
int zthreadlimit = deviceProp.maxThreadsDim[2];
int xgridlimit = deviceProp.maxGridSize[0];
int ygridlimit = deviceProp.maxGridSize[1];
int zgridlimit = deviceProp.maxGridSize[2];

@zasdfgbnm Could you add a test for this?

@rmlarsen I add and pass these tests. I also add some explanation of these Cuda{2D,3D,}LaunchConfig into cuda_kernel_helper.h.
The test is a .cu.cc file. To build it, I have to add something to tensorflow.bzl. I'm not sure if I'm doing the correct thing for this change.

@zasdfgbnm thanks for the thorough test!
@tensorflow-jenkins test this please

@zasdfgbnm can you fix the build file formatting errors reported here:
https://ci.tensorflow.org/job/tensorflow-pull-requests-sanity/4433/consoleFull

@tensorflow-jenkins test this please

Check return value of cudaOccupancyMaxPotentialBlockSize
Plus some style fixes.
Although github mark it as outdated, the issue https://github.com/tensorflow/tensorflow/pull/10032#discussion_r118041775 and my question https://github.com/tensorflow/tensorflow/pull/10032#discussion_r118129926  is still there.

@tensorflow-jenkins test this please

@tensorflow-jenkins test this please

@tensorflow-jenkins test this please

@zasdfgbnm can you please rebase to resolve conflicts?

@rmlarsen done

@tensorflow-jenkins test this please

@zasdfgbnm The test failure looks like it's unrelated to your change, so I'll merge it as is. Thanks for the contribution.


.NET Core 1.0.1

You can read about .NET Core 1.0.1 in the announcement: Announcing September 2016 Updates for .NET Core 1.0.
Please report any issues you find with .NET Core 1.0.1 here, either responding to this issue or creating a new issue.
Please include the following information plus any other info that you think is relevant:

OS version
Repro steps
Repro code (if you can share it / is relevant)
Error messages
Whether this worked before
Method of installing .NET Core

Couldn't use normally
[root /]# dotnet

Microsoft .NET Core Shared Framework Host

  Version  : 1.0.1
  Build    : cee57bf6c981237d80aa1631cfe83cb9ba329f12

Usage: dotnet [common-options] [[options] path-to-application]

Common Options:
  --help                           Display .NET Core Shared Framework Host help.
  --version                        Display .NET Core Shared Framework Host version.

Options:
  --fx-version <version>           Version of the installed Shared Framework to use to run the application.
  --additionalprobingpath <path>   Path containing probing policy and assemblies to probe for.

Path to Application:
  The path to a .NET Core managed application, dll or exe file to execute.

If you are debugging the Shared Framework Host, set 'COREHOST_TRACE' to '1' in your environment.

To get started on developing applications for .NET Core, install .NET SDK from:
  http://go.microsoft.com/fwlink/?LinkID=798306&clcid=0x409

Exit code: 129
[root /]# uname -a
Linux localhost.localdomain 2.6.32-042stab111.11 #1 SMP Tue Sep 1 18:19:12 MSK 2015 x86_64 x86_64 x86_64 GNU/Linux
[root /]# dotnet version
Failed to load /opt/dotnet/shared/Microsoft.NETCore.App/1.0.1/libcoreclr.so, error: libunwind.so.8: cannot open shared object file: No such file or directory
Failed to bind to CoreCLR at '/opt/dotnet/shared/Microsoft.NETCore.App/1.0.1/libcoreclr.so

Thanks @zeusro. I cannot tell which distro you are using from your uname command above. Can you share that?

OS version

Win 10 Enterprise 1511

Repro steps

Opening a solution in Visual Studio 2015 Professional Update 3

Error messages

The following error occurred attempting to run the project model server process (1.0.0-preview2-003131).
No connection could be made because the target machine actively refused it [::ffff:<IP_ADDRESS>]:51753.
The project model server process provides intellisense, build, and reference information to Visual Studio and without it your experience will be very limited. Please try closing and reopening Visual Studio to see if that corrects the problem. Alternatively, check that the .NET core SDK is properly installed.

Whether this worked before

It did.

Method of installing .NET Core

Using the downloader available here.

@richlander
[root /]# cat /proc/version
Linux version 2.6.32-042stab111.11<EMAIL_ADDRESS>(gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Tue Sep 1 18:19:12 MSK 2015

[root /]# getconf LONG_BIT
64

[root /]# cat /etc/redhat-release
CentOS Linux release 7.2.1511 (Core)

Windows 10, install from https://www.microsoft.com/net/core#windows.
During installation I am getting:
[1C24:1920][2016-09-14T11:24:01]e000: Error 0x80072efd: Failed to send request to URL: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe, trying to process HTTP status code anyway. [1C24:1920][2016-09-14T11:24:01]e000: Error 0x80072efd: Unknown HTTP status code 0, returned from URL: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:1920][2016-09-14T11:24:01]e000: Error 0x80072efd: Failed attempt to download URL: 'https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe' to: 'C:\Users\user\AppData\Local\Temp\{972C0DB7-C179-4FA8-93B5-DE2865D7C4EC}\DotNetCLI_x64' [1C24:1920][2016-09-14T11:24:01]w343: Prompt for source of package: DotNetCLI_x64, payload: DotNetCLI_x64, path: C:\Users\user\Downloads\packages\DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:26E4][2016-09-14T11:24:01]i319: Applied execute package: SetupBlocked_Install, result: 0x0, restart: None [18B0:2068][2016-09-14T11:24:01]i301: Applying execute package: Preparation_Uninstall_ASPNET, action: Install, path: C:\ProgramData\Package Cache\fc8ffa76-3957-38e7-be57-a4904a842328\Preparation_rc2_53.exe, arguments: '"C:\ProgramData\Package Cache\fc8ffa76-3957-38e7-be57-a4904a842328\Preparation_rc2_53.exe" /d' [1C24:26E4][2016-09-14T11:24:02]i319: Applied execute package: Preparation_Uninstall_ASPNET, result: 0x0, restart: None [18B0:2068][2016-09-14T11:24:02]i301: Applying execute package: ANCM_IISExpress_x64, action: Repair, path: C:\ProgramData\Package Cache\{C2BB4C41-59DC-487E-9CCF-1E21C3AC9139}v1.0.1967\packages\ancm_iis_express_x64_en_rc2_39.msi, arguments: ' ARPSYSTEMCOMPONENT="1" MSIFASTINSTALL="7"' [1C24:1920][2016-09-14T11:24:04]i338: Acquiring package: DotNetCLI_x64, payload: DotNetCLI_x64, download from: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:1920][2016-09-14T11:24:04]e000: Error 0x80072efd: Failed to send request to URL: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe, trying to process HTTP status code anyway. [1C24:1920][2016-09-14T11:24:04]e000: Error 0x80072efd: Unknown HTTP status code 0, returned from URL: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:1920][2016-09-14T11:24:04]e000: Error 0x80072efd: Failed attempt to download URL: 'https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe' to: 'C:\Users\user\AppData\Local\Temp\{972C0DB7-C179-4FA8-93B5-DE2865D7C4EC}\DotNetCLI_x64' [1C24:1920][2016-09-14T11:24:04]w343: Prompt for source of package: DotNetCLI_x64, payload: DotNetCLI_x64, path: C:\Users\user\Downloads\packages\DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:26E4][2016-09-14T11:24:05]i319: Applied execute package: ANCM_IISExpress_x64, result: 0x0, restart: None [18B0:2068][2016-09-14T11:24:05]i325: Registering dependency: {b837b432-47cc-42bf-88e4-876d726dfb7c} on package provider: IISExpress_AspNetCore_Module,x64, package: ANCM_IISExpress_x64 [1C24:1920][2016-09-14T11:24:08]i338: Acquiring package: DotNetCLI_x64, payload: DotNetCLI_x64, download from: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:1920][2016-09-14T11:24:08]e000: Error 0x80072efd: Failed to send request to URL: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe, trying to process HTTP status code anyway. [1C24:1920][2016-09-14T11:24:08]e000: Error 0x80072efd: Unknown HTTP status code 0, returned from URL: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:1920][2016-09-14T11:24:08]e000: Error 0x80072efd: Failed attempt to download URL: 'https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe' to: 'C:\Users\user\AppData\Local\Temp\{972C0DB7-C179-4FA8-93B5-DE2865D7C4EC}\DotNetCLI_x64' [1C24:1920][2016-09-14T11:24:08]w343: Prompt for source of package: DotNetCLI_x64, payload: DotNetCLI_x64, path: C:\Users\user\Downloads\packages\DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:1920][2016-09-14T11:24:11]i338: Acquiring package: DotNetCLI_x64, payload: DotNetCLI_x64, download from: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:1920][2016-09-14T11:24:11]e000: Error 0x80072efd: Failed to send request to URL: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe, trying to process HTTP status code anyway. [1C24:1920][2016-09-14T11:24:11]e000: Error 0x80072efd: Unknown HTTP status code 0, returned from URL: https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe [1C24:1920][2016-09-14T11:24:11]e000: Error 0x80072efd: Failed attempt to download URL: 'https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe' to: 'C:\Users\user\AppData\Local\Temp\{972C0DB7-C179-4FA8-93B5-DE2865D7C4EC}\DotNetCLI_x64' [1C24:1920][2016-09-14T11:24:11]e000: Error 0x80072efd: Failed to acquire payload from: 'https://download.microsoft.com/download/5/5/7/557D02A5-C3D0-4EF6-A570-4F75CD0DA5BF/packages/DotNetCore.1.0.1-SDK.1.0.0.Preview2-003131-x64.exe' to working path: 'C:\Users\user\AppData\Local\Temp\{972C0DB7-C179-4FA8-93B5-DE2865D7C4EC}\DotNetCLI_x64' [1C24:1920][2016-09-14T11:24:11]e313: Failed to acquire payload: DotNetCLI_x64 to working path: C:\Users\user\AppData\Local\Temp\{972C0DB7-C179-4FA8-93B5-DE2865D7C4EC}\DotNetCLI_x64, error: 0x80072efd. [1C24:26E4][2016-09-14T11:24:11]e000: Error 0x80072efd: Cache thread exited unexpectedly. [18B0:2068][2016-09-14T11:24:11]i372: Session end, registration key: SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\{b837b432-47cc-42bf-88e4-876d726dfb7c}, resume: ARP, restart: None, disable resume: No [18B0:2068][2016-09-14T11:24:11]i371: Updating session, registration key: SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\{b837b432-47cc-42bf-88e4-876d726dfb7c}, resume: ARP, restart initiated: No, disable resume: No [1C24:26E4][2016-09-14T11:24:11]i399: Apply complete, result: 0x80072efd, restart: None, ba requested restart:  No

If I upgrade my project to 1.0.1 via nuget, then rebuild and deploy to production IIS server (with latest DotNetCore 1.0.1 Windows Hosting package installed) I get HTTP Error 502.5 - Process Failure - running the compiled .exe for the app reveals that it can't find Microsoft.AspnetCore.Server.Kestrel, Version 1.0.0 , so something is hanging on to the old reference. Kestrel 1.0.1 is reference in the project.json.

@webprofusion-chrisc How does your project.json look like?

project.json: https://gist.github.com/webprofusion-chrisc/acf9f999be369e7ec94d310e9080a5c4
May be a little unusual as it's basically using dotnet 4.6 due to other dependencies (Soap stuff)

Ok, resolved for me. I hadn't installed the updated VS2015 tooling,  although I'd updated my nuget packages in the solution and hosting bundle on the server. I'd tried reverting to 1.0.0 of the Kestrel and MVC assemblies and that obviously worked. After installing the VS tooling update I updated my nuget packages back to 1.0.1 and it worked in production.

I maybe missing it somewhere, but it maybe useful to add some instructions of what exactly need to be updated as versions get upgraded. I bumped the versions from 1.0 to 1.0.1 and had a litany of build issues (had to make sure VS and CLI were updated, as well as project.json changes)
Just to help streamline the process?

When upgrading another project I found that to get it to build I needed to add a runtimes section to the project.json:
 "runtimes": {     "win10-x64": {}   }
The project was previously building and working in production without that.

Running Asp.Net MVC Core project in Visual Studio 2015 with Update 3 I get:
The program '[9412] dotnet.exe' has exited with code -2147450749
When I changed the setting
"Microsoft.NETCore.App": {
"version": "1.0.1",
"type": "platform"
},
back to version 1.0.0 the web app runs in IIS Express. I followed this blog for updating my project: https://blogs.msdn.microsoft.com/dotnet/2016/09/13/announcing-september-2016-updates-for-net-core-1-0/

I have the same problem as @webprofusion-chrisc. After reading the changelog I didn't see anything indicating this was required. I rolled back to v1.0.0 and I am still forced to provide the runtimes section in project.json

@DamianEdwards @piotrpMSFT @livarcocc , Any of you guys know what may have changed to cause a required runtimes section?

@zeusro did you install all of the required dependencies?

My hunch is perhaps they're hitting the issue where the NuGet VS tooling drops the "type": "platform" from the reference, which effectively changes the project to stand-alone and thus would force the requirement of a runtimes section.

Yeah, that would do it. @yishaigalatzer do you know why the nuget tooling is doing that?

I don't know the root cause @emgarten should be able to take a look. My guess is that we require a rid restore where before there was an implicit rid running in restore based on the machine you run on

Updating through the NuGet UI calls into the project system to update project.json, "type": "platform" is dropped during that edit.  NuGet 3.5.0 RTM (not released yet) will have a workaround for this issue.

@richlander , do we have a known issues list for the release?

on macOS Sierra, (fresh install) the latest installer didn't set the correct path - dotnet in terminal returned command not found
OS version
macOS Sierra
Repro steps
Fresh install of macOS without prior dotnet core
Repro code (if you can share it / is relevant)
Error messages
command not found
Whether this worked before
Method of installing .NET Core
package installer
Ran
ln -s /usr/local/share/dotnet/dotnet /usr/local/bin
and started working

@Petermarcu Known issues would appear here: https://github.com/dotnet/core/blob/master/release-notes/1.0/1.0.1-release-notes.md. There are not any listed yet.
/cc @leecow

@h3smith which shell are you using? Also, can you please check if the /etc/paths.d/dotnet file is in its place?

OS Version:
Windows 8.1 Enterprise
Repro Steps:
Updating .NetCore.App in existing project via Nuget.
Similar issue occurs as @jamesabolton reported and have to edit the project.json file as described.  However, IIS Express would not launch when trying to debug. in 1.0.1  When I rolled back to 1.0.0, IIS Express would launch.

@chrisgreen42 I started having the same issue. I brought up a command prompt, navigated to my project's folder and tried to run the web app:
E:\Programming\GitHub\HuskyRescueCore\src\HuskyRescueCore>dotnet run
Project HuskyRescueCore (.NETCoreApp,Version=v1.0) was previously compiled. Skipping compilation.
The specified framework 'Microsoft.NETCore.App', version '1.0.1' was not found.
  - Check application dependencies and target a framework version installed at:
      C:\Program Files\dotnet\shared\Microsoft.NETCore.App
  - The following versions are installed:
      1.0.0
  - Alternatively, install the framework version '1.0.1'.

At that point I realized I didn't actually install 1.0.1 which you can get here. Now I can debug via VS again.

@blackdwarf  Do you mean libunwind,libicu?YES,I followed the steps as https://www.microsoft.com/net/core#centos says.
sudo yum install libunwind libicu
curl -sSL -o dotnet.tar.gz https://go.microsoft.com/fwlink/?LinkID=827529
sudo mkdir -p /opt/dotnet && sudo tar zxf dotnet.tar.gz -C /opt/dotnet
sudo ln -s /opt/dotnet/dotnet /usr/local/bin

Solution of @chrisgreen42  worked for me. Installed .NET Core Installer x86 and debugging works in Visual Studio.

Since installed .NET 1.0.1 I am having problems working on a project still targeting 1.0.0.
I am using 1.0.1 successfully in some solutions but an open source project https://github.com/HTBox/allReady still targets the prior release in our master branch.
OS is Windows 7
When trying to debug the application from VS 2015 I get the following error:
System.IO.FileLoadException was unhandled
Message: An unhandled exception of type 'System.IO.FileLoadException' occurred in Unknown Module.
Additional information: Could not load file or assembly 'Microsoft.AspNetCore.Server.Kestrel, Version=<IP_ADDRESS>, Culture=neutral, PublicKeyToken=adb9793829ddae60' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
The application is targeting Kestrel 1.0.0 in the project.json
I don't believe there are any other changes except for the install of .NET core. I've tried deleting the packages folder and local nuget cache with no improvement.

Further to my recent comment after upgrading the project to use 1.0.1 it runs. This is not ideal though since until the project formally moves to this version I can only work on it by adjusting my dependencies and avoiding checking them in.

@ellismg did we up the libunwind version number by any chance for 1.0.1, do you know?

@blackdwarf No.  I don't believe there were any changes in native dependencies or their versions for 1.0.1

This is surely a case of RTFM & PEBKAC. That said, when it comes to "dotnet run", if NuGet cannot and will not magically update 'Microsoft.NETCore.App' and gives you the message "Alternatively, install the framework version '1.0.1'", this is to suggest that the command reminds the user that they need to download the necessary installer. I got stuck in a headspin wondering why NuGet has failed me on my Mac.

i had the same problem as @webprofusion-chrisc. The solution was to add a binding redirect for Microsoft.AspNetCore.Server.Kestrel. My project is an empty asp.net core app (no mvc dependencies at all)

@Sierra
$ ln -s /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib /usr/local/lib/
no error
$ ln -s /usr/local/opt/openssl/lib/libssl.1.0.0.dylib /usr/local/lib/
no error
$ dotnet
-bash: dotnet: command not found
$ brew link --force openssl
Warning: Refusing to link: openssl
Linking keg-only openssl means you may end up linking against the insecure,
deprecated system OpenSSL while using the headers from Homebrew's openssl.
Instead, pass the full include/library paths to your compiler e.g.:
-I/usr/local/opt/openssl/include -L/usr/local/opt/openssl/lib
$ sudo port upgrade openssl
--->  Scanning binaries for linking errors
--->  No broken files found.

OS: Linux version 4.7.0-kali1-amd64<EMAIL_ADDRESS>(gcc version 5.4.1 20160803 (Debian 5.4.1-1) ) #1 SMP Debian 4.7.5-1kali3 (2016-09-29)

dotnet:
Product Information:
 Version:            1.0.0-preview2-003131
 Commit SHA-1 hash:  635cf40e58

dotnet restore => Segmentation fault

(gdb) run
Starting program: /usr/local/bin/dotnet restore
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

Thread 14 "dotnet" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fff5cfab700 (LWP 5552)]
0x00007fffe24a2ddd in ?? () from /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0

cat project.json
{
  "version": "1.0.0-*",
  "buildOptions": {
    "debugType": "portable",
    "emitEntryPoint": true
  },
  "dependencies": {},
  "frameworks": {
    "netcoreapp1.0": {
      "dependencies": {
        "Microsoft.NETCore.App": {
          "type": "platform",
          "version": "1.0.1"
        }
      },
      "imports": "dnxcore50"
    }
  }
}

Problem also exists on 4.3 kernel.
dotnet installed via:

    sudo apt-get install curl libunwind8 gettext
    curl -sSL -o dotnet.tar.gz https://go.microsoft.com/fwlink/?LinkID=827530
    sudo mkdir -p /opt/dotnet && sudo tar zxf dotnet.tar.gz -C /opt/dotnet
    sudo ln -s /opt/dotnet/dotnet /usr/local/bin

I'm seeing the following error on VS 2015. I've uninstalled all the SDKs and tooling packages and reinstalled just the latest and I'm still seeing this.

I figured it out. It looks like JustMock gets in the way. I had to disable it and then this error went away.

I had similar issue with an existing project after installing VS 2017 RC.
For me the solution was adding˛"sdk": {"version": "1.0.0-preview2-003131"} to global.json
(Maybe this helps some googler in the future)

Closing this and pointing to 1.0.2. https://github.com/dotnet/core/issues/294


Show category question answers for none multi select fields.

Fixes #2216

@Parbhat This seems to work but is it the correct way to solve this issue?


Issue with Ollama Function – Only Agent Response, No Tool Calls

Checked other resources

[X] I added a very descriptive title to this issue.
[X] I searched the LangGraph/LangChain documentation with the integrated search.
[X] I used the GitHub search to find a similar question and didn't find it.
[X] I am sure that this is a bug in LangGraph/LangChain rather than my code.
[X] I am sure this is better as an issue rather than a GitHub discussion, since this is a LangGraph bug and not a design question.

Example Code
from langchain_core.messages import AIMessage
from langgraph.graph import END, StateGraph
from typing import TypedDict
from langchain_core.tools import tool
from langchain_experimental.llms.ollama_functions import OllamaFunctions
from langchain_core.pydantic_v1 import BaseModel, Field
from langchain.prompts import PromptTemplate
from termcolor import colored
import json
# Import tools from tools.py
from tools import get_current_weather, get_system_time

# using OllamaFunctions from experimental because it supports function binding with llms
model = OllamaFunctions(
    base_url="http://localhost:11436",
    model="llama3.1",
    format="json"
    )

model_with_tools = model.bind_tools(
    tools=[get_current_weather, get_system_time],
)

tool_mapping = {
    'get_current_weather': get_current_weather,
    'get_system_time': get_system_time,
}

# Define Agent Prompt template for llama3
agent_request_generator_prompt = PromptTemplate(
    template=
    """
    <|begin_of_text|>
    <|start_header_id|>system<|end_header_id|>
        You are a Smart Agent.

        You evaluate every request and utilize available tools if you have to.
    <|eot_id|>
    <|start_header_id|>user<|end_header_id|>
    Conduct a comprehensive analysis of the request provided\

    USER REQUEST:\n\n {initial_request} \n\n

    <|eot_id|>
    <|start_header_id|>assistant<|end_header_id|>
    """,
    input_variables=["initial_request"],
)

agent_request_generator = agent_request_generator_prompt | model_with_tools
# result = agent_request_generator.invoke({"initial_request": "What is the weather in woodbury in MN?"})
# print(result)
# input("...")

# Pydantic Schema for structured response
class Evaluation(BaseModel):
    result: bool = Field(description="True or False", required=True)

# Prompt template llama3
category_generator_prompt = PromptTemplate(
    template=
    """
    <|begin_of_text|>
    <|start_header_id|>system<|end_header_id|>
        You are a Smart Router Agent. You are a master at reviewing whether the original question that customer asked was answered in the tool response.
        You understand the context and question below and return your answer in JSON.
    <|eot_id|>
    <|start_header_id|>user<|end_header_id|>
    CONTEXT: Conduct a comprehensive analysis of the Initial Request from user and Tool Response and route the request into boolean true or false:
        True - used when INITIAL REQUEST appears to be answered by TOOL RESPONSE. \
        False - used when INITIAL REQUEST is not answered by TOOL RESPONSE or when TOOL RESPONSE is empty \

            Output either True or False \
            eg:
            'True' \n\n
    INITIAL REQUEST:\n\n {research_question} \n\n
    TOOL RESPONSE:\n\n {tool_response} \n\n

    JSON:
    <|eot_id|>
    <|start_header_id|>assistant<|end_header_id|>
    """,
 input_variables=["research_question", "tool_response"],
)

structured_llm = model.with_structured_output(Evaluation)
category_generator = category_generator_prompt | structured_llm

# result = category_generator.invoke({"research_question": "What is the weather in woodbury in MN?", "tool_response":"65C, Sunny"})
# print(result)
# input("...")

class AgentState(TypedDict):
    research_question: str
    tool_response: str
    agent_response: AIMessage
    agent_call_count: int = 0
    tool_call_count: int = 0

def agent(state: AgentState):
    print(colored("STATE at agent start:", "magenta"), colored(state, "cyan"))
    input("Paused ... Hit Enter to Execute Agent Logic...")
    last_ai_message = agent_request_generator.invoke({"initial_request": state["research_question"]})
    state["agent_call_count"] += 1
    #append the response to the agent_response list in the state
    if last_ai_message is not None:
        state["agent_response"] = last_ai_message
        if last_ai_message.content is not None and last_ai_message.content != "" :
            state["tool_response"]=last_ai_message.content
    print(colored("STATE at agent end:", "magenta"), colored(state, "cyan"))
    input("Paused Hit Enter to go to Should Continue Logic...")
    return state

def should_continue(state: AgentState):
    print(colored("STATE at should_continue start:", "magenta"), colored(state, "cyan"))
    input("Paused at Should Continue Start")
    print(colored("Evaluating whether the Question is Answered by the tool response or not... Please wait...", "red"))
    result = category_generator.invoke({"research_question": state["research_question"],
                                         "tool_response":state["tool_response"]
                                        })
    if isinstance(result, Evaluation):
        # Access the 'result' attribute from Evaluation
        print(colored("Is tool response good and should the flow go to END node? ", "cyan"), colored(result.result, "yellow"))
        input("Paused at Should Continue Mid")

        if result.result:  # If result is True
            print(colored("Return end", "red"))
            return "end"
        else:  # If result is False
            print(colored("Return continue", "green"))
            return "continue"
    else:
        print("Result is not an Evaluation instance, returning 'end' as default.")
        return "end"

def call_tool(state: AgentState):
    print(colored("STATE at call_tool start:", "magenta"), colored(state, "cyan"))
    input("Paused at call_tool Start")
    agent_response = state["agent_response"]

    if hasattr(agent_response, 'tool_calls') and len(agent_response.tool_calls) > 0:
        tool_call = agent_response.tool_calls[0]
        tool = tool_mapping[tool_call["name"].lower()]
        try:
            tool_output = tool.invoke(tool_call["args"])
            state["tool_call_count"] += 1
            print(colored("Tool output:", "magenta"), colored(tool_output, "green"))
            if tool_output is not None:
                state["tool_response"] = tool_output
        except Exception as e:
            print(f"Error invoking tool: {e}")
            # Handle the error or log it as needed
    else:
        print("No tool calls found in agent response.")
    print(colored("STATE at call_tool end:", "magenta"), colored(state, "cyan"))
    input("Paused at call_tool End")
    return state

workflow = StateGraph(AgentState)

workflow.add_node("agent", agent)
workflow.add_node("action", call_tool)

workflow.set_entry_point("agent")

workflow.add_conditional_edges(
    "agent",
    should_continue,
    {
        "continue": "action",
        "end": END,
    },
)
workflow.add_edge("action", "agent")

app = workflow.compile()

#helper method to visualize graph
def save_graph_to_file(runnable_graph, output_file_path):
    png_bytes = runnable_graph.get_graph().draw_mermaid_png()
    with open(output_file_path, 'wb') as file:
        file.write(png_bytes)

save_graph_to_file(app, "output-05.png")

# research_question = "What's the current system time?"
research_question = "Tell me a joke?"
# research_question = "How is the weather in Woodbury MN today?"
# research_question = "What is the cause of earthquakes?"

state : AgentState = {"research_question": research_question,
                      "tool_response": [] ,
                      "agent_response": [],
                      "agent_call_count": 0,
                      "tool_call_count": 0
                      }
result = app.invoke(state)
print("\n")
print(colored("FINAL STATE at end:", "magenta"), colored(result, "cyan"))

print(colored("FINAL RESPONSE at end:", "magenta"), colored(result["tool_response"], "cyan"))

Error Message and Stack Trace (if applicable)
STATE at agent start: {'research_question': 'Tell me a joke?', 'tool_response': [], 'agent_response': [], 'agent_call_count': 0, 'tool_call_count': 0}
Paused ... Hit Enter to Execute Agent Logic...
STATE at agent end: {'research_question': 'Tell me a joke?', 'tool_response': "Here's one: Why couldn't the bicycle stand up by itself? Because it was two-tired!", 'agent_response': AIMessage(content="Here's one: Why couldn't the bicycle stand up by itself? Because it was two-tired!", additional_kwargs={}, response_metadata={}, id='run-409504c1-afb2-49f7-8ace-bc08c89fdd33-0'), 'agent_call_count': 1, 'tool_call_count': 0}
Paused Hit Enter to go to Should Continue Logic...
STATE at should_continue start: {'research_question': 'Tell me a joke?', 'tool_response': "Here's one: Why couldn't the bicycle stand up by itself? Because it was two-tired!", 'agent_response': AIMessage(content="Here's one: Why couldn't the bicycle stand up by itself? Because it was two-tired!", additional_kwargs={}, response_metadata={}, id='run-409504c1-afb2-49f7-8ace-bc08c89fdd33-0'), 'agent_call_count': 1, 'tool_call_count': 0}
Paused at Should Continue Start
Evaluating whether the Question is Answered by the tool response or not... Please wait...
Traceback (most recent call last):
  File "/home/poc/agentic-workflow/langgraph-learning/tutorials/example_1.py", line 203, in <module>
    result = app.invoke(state)
             ^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langgraph/pregel/__init__.py", line 1749, in invoke
    for chunk in self.stream(
  File "/home/miniconda3/lib/python3.11/site-packages/langgraph/pregel/__init__.py", line 1477, in stream
    for _ in runner.tick(
  File "/home/miniconda3/lib/python3.11/site-packages/langgraph/pregel/runner.py", line 58, in tick
    run_with_retry(t, retry_policy)
  File "/home/miniconda3/lib/python3.11/site-packages/langgraph/pregel/retry.py", line 29, in run_with_retry
    task.proc.invoke(task.input, config)
  File "/home/miniconda3/lib/python3.11/site-packages/langgraph/utils/runnable.py", line 412, in invoke
    input = context.run(step.invoke, input, config)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langgraph/utils/runnable.py", line 184, in invoke
    ret = context.run(self.func, input, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langgraph/graph/graph.py", line 95, in _route
    result = self.path.invoke(value, config)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langgraph/utils/runnable.py", line 176, in invoke
    ret = context.run(self.func, input, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/poc/agentic-workflow/langgraph-learning/tutorials/example_1.py", line 121, in should_continue
    result = category_generator.invoke({"research_question": state["research_question"],
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_core/runnables/base.py", line 3024, in invoke
    input = context.run(step.invoke, input, config)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_core/runnables/base.py", line 5354, in invoke
    return self.bound.invoke(
           ^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_core/language_models/chat_models.py", line 286, in invoke
    self.generate_prompt(
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_core/language_models/chat_models.py", line 786, in generate_prompt
    return self.generate(prompt_messages, stop=stop, callbacks=callbacks, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_core/language_models/chat_models.py", line 643, in generate
    raise e
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_core/language_models/chat_models.py", line 633, in generate
    self._generate_with_cache(
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_core/language_models/chat_models.py", line 851, in _generate_with_cache
    result = self._generate(
             ^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_experimental/llms/ollama_functions.py", line 305, in _generate
    functions = [convert_to_ollama_tool(fn) for fn in functions]
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_experimental/llms/ollama_functions.py", line 305, in <listcomp>
    functions = [convert_to_ollama_tool(fn) for fn in functions]
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/miniconda3/lib/python3.11/site-packages/langchain_experimental/llms/ollama_functions.py", line 86, in convert_to_ollama_tool
    schema = tool.model_construct().model_json_schema()
             ^^^^^^^^^^^^^^^^^^^^
AttributeError: type object 'Evaluation' has no attribute 'model_construct'

Description
I have encountered an issue where the ollama function returns only the agent's response but does not invoke any associated tools, as expected. I have ensured that all required libraries and dependencies are properly installed, but this behavior persists.
System Info
"pip install langgraph httpx ipython graphviz langchain langchain_openai langchain_experimental langchain-ollama termcolor rich ollama openai docker"
platform (linux)
python version 3.11
langgraph==0.2.46
langchain==0.2.17
langchain-experimental==0.0.65
langchain-core==0.2.43

I am also facing the same issue, Any update on it?


linter: no-empty-file does not respect disable directive comments

When oxlint -D no-empty-file is run on a file like this:
/* eslint-disable no-empty-file */

no-empty-file's reported error is not filtered out by DisableDirectives.

closed via #4010


Add support for web scraping

This change adds the basics required to support scraping:

A web.py package that wraps selenium/chromium and can extract screenshots
Javascript code (find_leaf_nodes.js) that finds all leaf nodes with words in an HTML document. This is in JS specifically so that we can reuse it for other use cases (e.g. a Chrome plugin) where the text gets extracted client-side
A new WebDocument class (+ a bit of supportive refactoring) that wraps the web driver
Tests + documentation

You're legendary, Impira team, was just trying to implement this functionality myself. FWIW the web scraping part LGTM

Nice to hear! Have you taken it for a spin yet?

No, haven't got the chance yet @ankrgyl

Okay no worries @jagilley let me know when you do! Merging this in now

Works great, thank you @ankrgyl!


Passport auth

The main goal here is to replace everyauth, because it is using a soon to be unsupported auth mechanism for github. It's also been several years since everyauth has had a commit. Passport is getting ongoing support and feels like a good option for replacement.
I've also gone ahead and replaced jade with pug, which was very easy. I did this because npm auditing said that a dependency of the version of jade we use had an RCE advisory open.
I put all of the authentication logic in the ProxyDomain class that I created to rewrite the Domain class, this was mainly for ease of testing having everything in one file. I don't have an issue with moving it, but I think the separation would really only matter if we intended to add more auth schemes.
I did manual testing with all three auth schemes, including checking required email, domain, and github org, and handling for public paths.
Looking forward to getting some feedback on the changes.

This looks great and came together amazingly fast. It'll take me a little bit to work through the full set of changes.

I just noticed that this is branched from deploy-production.  While deploy-production theoretically represents the right code to branch from, this should be a PR to merge into the multi-domain branch (which should probably be merged to master already)

@mchesler I've updated the base branch.

Ok, removed everyauth. I believe that's the last thing to do.


Export required machines, power, etc to a .csv file

Is your feature request related to a problem? Please describe.
Printouts aren't very useful (bug has been filed). An even better way to take the information for off-line processing would be to export the required machines and power to a spreadsheet.
Describe the solution you'd like
.csv file containing text (no icons) of each item to be build and power required.
Describe alternatives you've considered
Considered using a printout and doing a pen/paper mark-up. Didn't work due to printing bug.
Additional context
Add any other context or screenshots about the feature request here.

LOL, it is already there. Nice!


Plot data with API call

I have this annoying problem that i cant plot the data when i make an API call. Maybe this is trivial but i have no clue what is going on here
//global variable
let output;

async function getStockData() {

    // make the POST request to the endpoint
    const response = await fetch('http://<IP_ADDRESS>:8000/stock-data', {
      method: 'POST',
      headers: {
        'Content-Type': 'application/json'
      },
    });

    const output = await response.json();

  };

<Chart width={600} height={150}>
  <CandlestickSeries data={output}/>
</Chart>

Any idea how to plot the data from the function getStockData() that makes the api call?

https://svelte.dev/repl/e360e79b07ed436d8d79c6697f4962c6?version=3.55.0