willAuthError query executes twice

When a willAuthError is present in auth-exchange it results to queries being executed twice.
I saw that there was a PR that fixed the same issue but even that does not seem to fix the error.
If willAuthError is removed and we rely only on didAuthError then everything is working as expected.
Sorry that i am not provided a reproducible case but i think the issue is present in also a very simple auth-exchange scenarios

The only way this can be caused, as far as I can tell is when a duplicate operation already reached the exchange.
The authExchange prevents willAuthError (and didAuthError) from being run again when they trigger a refresh, i.e. a call to getAuth.
The first failing operation is then queued up for a retry while a subsequent duplicate would simply wait for the promise. However, this would imply that a duplicate has reached the exchange in the first place, which shouldn't be possible as long as you've got a dedupExchange in place, as we'd typically expect.

Here you are
https://codesandbox.io/s/funny-https-rj8jb
I modified the exchange to return willAuthError after 5 seconds from initialisation. This replicates an expiring jwt token
In order to test
login
wait 5 seconds
press toggle
The query will execute 2-3 times


docs(nx): replace out of date library name in the readme

PR Checklist
Please check if your PR fulfills the following requirements:

[x] The commit message follows our
guidelines: https://github.com/goetzrobin/spartan/blob/main/CONTRIBUTING.md#-commit-message-guidelines
[ ] Tests for the changes have been added (for bug fixes / features)
[ ] Docs have been added / updated (for bug fixes / features)

PR Type
What kind of change does this PR introduce?

[ ] Bugfix
[ ] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no api changes)
[ ] Build related changes
[ ] CI related changes
[x] Documentation content changes
[ ] Other... Please describe:

Which package are you modifying?

[ ] accordion
[ ] alert
[ ] alert-dialog
[ ] aspect-ratio
[ ] avatar
[ ] badge
[ ] button
[ ] calendar
[ ] card
[ ] checkbox
[ ] collapsible
[ ] combobox
[ ] command
[ ] context-menu
[ ] data-table
[ ] date-picker
[ ] dialog
[ ] dropdown-menu
[ ] hover-card
[ ] input
[ ] label
[ ] menubar
[ ] navigation-menu
[ ] popover
[ ] progress
[ ] radio-group
[ ] scroll-area
[ ] select
[ ] separator
[ ] sheet
[ ] skeleton
[ ] slider
[ ] switch
[ ] table
[ ] tabs
[ ] textarea
[ ] toast
[ ] toggle
[ ] tooltip
[ ] typography

What is the current behavior?
I think the README.md referenced a wrong library name.
Closes #
What is the new behavior?
Does this PR introduce a breaking change?

[ ] Yes
[x] No

Other information

Accepted your suggestion. Should I squash the commits, or it is fine this way?

Accepted your suggestion. Should I squash the commits, or it is fine this way?

We can squash them as part of the merging :) thank you!


Feedback for: engine/installation/linux/debian.md

File: engine/installation/linux/debian.md
linux-image-extra-* does not exist anymore on Debian (tried on Jessie)
It looks like jessie comes with aufs in the standard kernel, and stretch adds it via DKMS:
http://stackoverflow.com/questions/37110291/how-to-enable-aufs-on-debian

you are correct.
#1391
I havn't checked on Debian Testing yet, but the Packages mentioned don't exist on any Debian branch.
It was most likely copied from engine/installation/linux/ubuntu.md without checking.

Thanks, that was fast. As mentioned - I haven't tested stretch (testing) yet either, but according to above link one needs a DKMS package on stretch. I may test it over the next cpl days, stretch is most likely going to be released in Feb or Mar 2017.

Tested on stretch. It dtrt by pulling in the required aufs packages as a dependency, so nothing to be done here.

This has been fixed.


Add support for ORTModelForObjectDetection

Feature request
Hi, I went through optimum's code base and could not find support for object detection models. Is there plan to add ORTModelForObjectDetection just like ORTModelForImageClassification exists? Would be great to have this feature.
Object detection task is also supported as part of transformers pipeline feature so I guess it should be possible to support this as part of optimum?
Motivation
I want to leverage onnx support for YOLOS model
Your contribution
I would be happy to help in adding support for this feature if someone can guide me.

We are currently working on adding ONNX export features in optimum, and could add support to this architecture as well.

Sounds great, thanks @mht-sharma! Looking forward to have this available!

Hello @shivalikasingh95 , great suggestion! If you want to contribute to adding ORTModelForObjectDetection, I suggest:

Reading https://github.com/huggingface/optimum/blob/main/CONTRIBUTING.md
Most of the work will be extending modeling_ort.py, you can take inspiration from example from https://github.com/huggingface/optimum/blob/6dc2cf23b962a2a57879f0ce71f933f49670dd12/optimum/onnxruntime/modeling_ort.py#L978-L1020 . Here one caveat is that models for object detection may have have different classes, for example we have DetrObjectDetectionOutput, OwlViTObjectDetectionOutput, YolosObjectDetectionOutput, etc. As far as I know, there is no map in transformers of a model to its corresponding output class. So a solution could be to output simply a ModelOutput.
Complete the test_quantization.py, test_modeling.py, test_optimization.py with tests for the new class
Optionally, add the new class in trainer.py and pipelines.py for pipeline support
Ping me once you open a PR

Let us know if you are interested in contributing to this!

@fxmarty, apologies for the delay in my response. Last week was a bit tight. And sure I'd be happy to contribute to this. The points you have mentioned are very helpful and gives me enough to get started.
However, I'm currently working on another PR for transformers library. It's a model contribution so it's taking some time.
I can take up ORTModelForObjectDetection post finishing that. Hope that's not a problem?

Of course no worries! Don't hesitate to open a draft PR once you are on it if you need any help; if a team member wants to implement the class earlier let's follow on in this issue 🤗

Awesome thanks @fxmarty! I'll keep you posted regarding status on this. Will definitely open up a draft PR once I get started to get some guidance.
And sure, in case any team member wants to take up this task, let me know here :)

Any news?


We need the What’s New Page as we use it frequently

What's New page now in the beta version. Need to document the process for updating the Together page and Oxygen page for each version.

Now renamed to Release History and in the September release


Fixed a few of the paths to include 'src', and added the branching option to git clone

The changes I made apply to v2.0 as well, not sure how this is being maintained and if there was a way I should have changed base so that the changes reflect in both v1.0 and v2.0?

@bobbiejc and I have discussed where changes like this should be added.  I'll close this PR and @bobbiejc will reopen a PR against master.  From master, we can update the versioned branches.


Nordic localization

Related to https://github.com/antonpup/Aurora/issues/523.
Added nordic localization (plain keyboard layout & KeyUtil mapping).
This dev->dev PR replaces closed master->master PR https://github.com/antonpup/Aurora/pull/525.

Thank you for the fix & contribution!


[BUG]: Title cannot load model saved to local drive does no

Describe the bug
A clear and concise description of what the bug is.I saved my model to my local driver, but when I tried to load it into my project, nothing happened. The saved file had a zip file containing 3 individual files. However, when I save my model to Google docs and the downloaded it, I got a file with the extension .tw and that file readily loaded in teaching machine
To Reproduce
Steps to reproduce the behavior:

Go to '...'
Click on '....'
Scroll down to '....'
See error

Relevant Links
Link to code to reproduce bug
Expected behavior
A clear and concise description of what you expected to happen. I expected to be able to load a model shed to my local drive
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):

OS: [e.g. iOS]windows 10
Browser Chrome
Version latest

Smartphone (please complete the following information):

Device: [e.g. iPhone6]
OS: [e.g. iOS8.1]
Browser [e.g. stock browser, safari]
Version [e.g. 22]

Additional context
Add any other context about the problem here.

User error.  I was able to save to local drive with .tm extension and then reload the model and retrain.


How to get in contact with you

Hi JT
Is there a way to get in contact with you?
Best regards
Eduard

I'm @jntrnr on twitter or jt#8411 on discord


lambda function code for slack integration

Moving the lambda function code from the devops repo.

I've added apidump to this PR too.


Make it so that dependabot PRs can access secrets

Dependabot branches are failing CI

Take a look at https://hugo.alliau.me/2021/05/04/migration-to-github-native-dependabot-solutions-for-auto-merge-and-action-secrets/#share-your-secrets-with-dependabot.

GitHub are working on this in https://github.com/dependabot/dependabot-core/issues/3253#issuecomment-940182533.
I will track this in another project.


Modal backdrop should be added before the modal object

Modal backdrop should be added before the modal object, not appended to the body. Cause if the modal is placed not as a body child the backdrop gets over the modal.

This seems to have been opened by mistake. Closing as duplicate of #19355.


filter topics by short names

Relates to #5
We've been seeing consistent failures of getTopics() system-tests on CircleCI. After digging in, I believe the issue is that we are are half-initializing several Topic objects and comparing the names of said objects against the names returned from the API.
Why is that an issue? Well unless a project id environment variable is set, we use a placeholder {{projectId}} that could cause the comparison to fail, which would explain the failing tests. This will instead compare the short names which should be unique ids.

Codecov Report

Merging #16 into master will not change coverage.
The diff coverage is n/a.

@@          Coverage Diff          @@
##           master    #16   +/-   ##
=====================================
  Coverage     100%   100%
=====================================
  Files           8      8
  Lines         830    830
=====================================
  Hits          830    830

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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Generate Presigned URLs

Overview
It's nice to be able to generate presigned URLs for download/upload so you don't need to worry about passing around auth credentials.
It's often a little non-obvious how to do these with the downstream clients and each client handles the operation pretty differently so this feels like something that could fit nicely into cloudpathlib.
Proposed Interface/ implementation
I'd imagine the code for this looking something like the below implementation. The S3Path implementation works and is tested, the others (GSPath/AzureBlobPath) aren't actually tested but are about what the code would look like.

from datetime import datetime, timedelta

class CloudPath:
    def generate_presigned_url(self, expire_seconds: int = 300):
        raise NotImplementedError

class S3Path(CloudPath):
    def generate_presigned_url(self, expire_seconds: int = 300):
        object_key = "/".join(list(self.parts)[2:]) # Everything after the bucket name
        url = self.client.client.generate_presigned_url(
            "get_object",
            Params={"Bucket": self.bucket, "Key": object_key},
            ExpiresIn=expire_seconds,
        )

class GSPath(CloudPath):
    def generate_presigned_url(self, expire_seconds: int = 300):
        object_key = "/".join(list(self.parts)[2:]) # Everything after the bucket name
        gs_client = path.client.client
        creds = gs_client.credentials
        gs_bucket = path.client.client.get_bucket(path.bucket)
        gs_blob = gs_bucket.blob(object_key)
        url = gs_blob.generate_signed_url(
            version="v4",
            expiration=timedelta(seconds=expire_seconds),
            service_account_email=creds.service_account_email,
            access_token=creds.token,
            method="GET"
        )
        return url

from azure.storage.blob import ResourceTypes, BlobSasPermissions, generate_blob_sas

class AzureBlobPath(CloudPath):
    def generate_presigned_url(self, expire_seconds: int = 300):
        object_key = "/".join(list(self.parts)[2:]) # Everything after the bucket name
        az_client = self.client.client
        sas_token = generate_blob_sas(
            az_client.account_name,
            container_name=self.container,
            blob_name=object_key,
            account_key=az_client.credential.account_key,
            permission=BlobSasPermissions(read=True),
            expiry=datetime.utcnow() + timedelta(seconds=expire_seconds)
        )
        url = f"https://{az_client.account_name}.blob.core.windows.net/{self.container}/{object_key}?{sas_token}"
        return url

The above implementation only handles downloads. Uploading via presigned urls/tokens is a bit weird across the different clouds but still doable. Happy to research that step more if it's of interest.
Happy to contribute the implementation, just want to make sure it's on track with the goals of the project.

Yeah, this is awesome.
Curious for your take on a couple related design decisions:

Does it make sense to have a generic url function that can get a presigned but also can get the vanilla if you're in an auth'd context? (I think #21 was trying to get at that)
Does it make sense to at the same time we're researching these URL formats, implement something like CloudPath.from_url constructors (or just support it in __init__ that can parse out the region/container, etc. and return the cloud path? This came up in #157. Doing that might be sufficient to support the upload scenario where you can do something like CloudPath.from_url(presigned_url).upload_from(my_local_path)

The as_url method described in that issue sounds good to me. I think in order to do either you'll need to be an authed context so just an explicit presign bool parameter would work well.

S3Path("s3://bucket/file.txt").as_url()
# > https://bucket.amazons3.com/file.txt

S3Path("s3://bucket/file.txt").as_url(presign=True, expire_seconds=100)
# > https://bucket.amazons3.com/file.txt?presign=accesstokenwithexpiry

The issue with the from_url is S3 e.g. returns a multi-part request back when you want to presign an upload.
https://boto3.amazonaws.com/v1/documentation/api/latest/guide/s3-presigned-urls.html#generating-a-presigned-url-to-upload-a-file
Also, I think it'd need to be an explicit upload_file not upload_from for S3 as well since you need to pass a Bucket and Key as a part of the signature.

I'm sure there's a way to design a good API for this, but maybe we take this in 2 steps and start with generating presigned urls in the as_url method?

Great, let's start with the as_url (maybe we just call it url?).
On the implementation, we like to isolate all communication with the provider to the *Client classes themselves, so let's implement the core logic on those objects and then just have a thin wrapper on the Path classes themselves.
One other small note is that instead of object_key = "/".join(list(self.parts)[2:]), you can get keys either with self.key which most cloud providers have or generically with self._no_prefix_no_drive (which, IIRC, may contain a leading slash depending on providers).

Nice! That object_key thing I was doing was obviously bad, I just hadn't looked through the source code too much.
Started a Draft PR with the majority of the implementation in the respective Client classes.


OrientGraphFactory.getNoTx keeps warning on IO errors

The application uses OrientDB 2.1.8. I setup the connection pool with:
private OrientGraphFactory graphFactory = new OrientGraphFactory("remote:localhost/mydb", "admin", "admin").setupPool(1, 10)

Sometimes I request TX connections (graphFactory.getTx()) other times I need NOTX connections (graphFactory.getNoTx()).
When the application starts everything works as expected. If I don't use the application for a while (let's say a couple of hours) every time I get a NOTX connection I see the following warnings:
2016-02-02 23:19:06.312  WARN 99988 --- [io-8080-exec-10] c.o.orient.client.remote.OStorageRemote  : Caught I/O errors from Not connected (local socket=?), trying to reconnect (error: java.io.IOException: Channel is closed)
2016-02-02 23:19:06.315  WARN 99988 --- [io-8080-exec-10] c.o.orient.client.remote.OStorageRemote  : Connection re-acquired transparently after 3ms and 1 retries to server '<IP_ADDRESS>:2424/mydb': no errors will be thrown at application level

With TX connection I see the same warning only the first time a stale connection from the pool it's used. It seems that stale TX connections are correctly replaced but the same doesn't work if the connection is NOTX.

Do you have any proxy in the middle that could drop the connection after a while (timeout) ?

There are no proxies or other stuff that could drop the connection.
Is it correct to have TX and NOTX connections in the same pool? Should I create separate pools?

Do you have super long transaction could cause a timeout? Or maybe many threads with a small network pool?

I have changed my code. I now have two connection pools: one for TX connections, the other for NOTX.
The application now works as expected without hogging the logs with IO warnings.
When a stale connection is picked from the pool it is correctly replaced with a 'good one' (I basically see one warning for each stale connection).
It seems that OrientGraphFactory is not able to handle properly a pool with both TX and NOTX connections. I think this is reasonable. It would be good to throw an Exception (or a log warning) when an application requests both connection types from a single pool.
What do you think? If you are OK with this I could have a look at the code and create a PR.

Hi Fabrizio,
makes sense. If you could do a PR would be amazing!

I see very similar warnings in an application I have that uses factory.getTx:
2016-06-29 02:19:08,831 WARN  OStorageRemote - Caught I/O errors from /<IP_ADDRESS>:2424 (local socket=/<IP_ADDRESS>:48306), trying to reconnect (error: java.io.EOFException)
2016-06-29 02:19:08,832 WARN  OStorageRemote - Connection re-acquired transparently after 1ms and 1 retries to server '<IP_ADDRESS>:2424/grid': no errors will be thrown at application level
2016-06-29 02:19:09,264 WARN  OStorageRemote - Caught I/O errors from /<IP_ADDRESS>:2424 (local socket=/<IP_ADDRESS>:48314), trying to reconnect (error: java.io.EOFException)
2016-06-29 02:19:09,265 WARN  OStorageRemote - Connection re-acquired transparently after 1ms and 1 retries to server '<IP_ADDRESS>:2424/grid': no errors will be thrown at application level
2016-06-29 02:19:37,952 WARN  OStorageRemote - Caught I/O errors from Not connected (local socket=?), trying to reconnect (error: java.io.IOException: Channel is closed)
2016-06-29 02:19:37,953 WARN  OStorageRemote - Connection re-acquired transparently after 1ms and 1 retries to server '<IP_ADDRESS>:2424/grid': no errors will be thrown at application level
2016-06-29 02:19:41,339 WARN  OStorageRemote - Caught I/O errors from /<IP_ADDRESS>:2424 (local socket=/<IP_ADDRESS>:48397), trying to reconnect (error: java.io.EOFException)
2016-06-29 02:19:41,341 WARN  OStorageRemote - Connection re-acquired transparently after 2ms and 1 retries to server '<IP_ADDRESS>:2424/grid': no errors will be thrown at application level
2016-06-29 02:20:36,697 WARN  OStorageRemote - Caught I/O errors from Not connected (local socket=?), trying to reconnect (error: java.io.IOException: Channel is closed)
2016-06-29 02:20:36,698 WARN  OStorageRemote - Connection re-acquired transparently after 1ms and 1 retries to server '<IP_ADDRESS>:2424/grid': no errors will be thrown at application level
2016-06-29 02:21:37,939 WARN  OStorageRemote - Caught I/O errors from Not connected (local socket=?), trying to reconnect (error: java.io.IOException: Channel is closed)
2016-06-29 02:21:37,941 WARN  OStorageRemote - Connection re-acquired transparently after 1ms and 1 retries to server '<IP_ADDRESS>:2424/grid': no errors will be thrown at application level
2016-06-29 02:22:37,653 WARN  OStorageRemote - Caught I/O errors from Not connected (local socket=?), trying to reconnect (error: java.io.IOException: Channel is closed)
2016-06-29 02:22:37,655 WARN  OStorageRemote - Connection re-acquired transparently after 2ms and 1 retries to server '<IP_ADDRESS>:2424/grid': no errors will be thrown at application level
``

This flood of warning logs on our client typically happens when we restart the OrientDB server, and then steps when we read/write again to the database once it's back up.

hi @natemurthy,
It's normal that we will se a lot of this logging when a server is restarted, it should fade away after a bit of usage, we did some clean up of the logs in recent versions so as usual keep updated with the last hotfix.

This has been fixed in 2.2.7
Related to #6468


Add example of domain redirects

This addition (and small whitespace trim) will give an example of how whole domains are redirected.

It's preferred to avoid wunder specific domains in examples and configurations, whenever possible. Production redirect examples can be found in repository search. Adding this example to internal faq document could work too.


topic is removed from message?

Terms

[X] This request is not a duplicate of an existing issue.
[X] I have provided as much information as I can to help resolve this issue.

Description
It seems the node removes TOPIC from the message.
Is there a way to keep the topic through the node?
steps-to-reproduce
Feed a message with topic and it comes out without
Actual Behavior
Feed a message with topic and it comes out without
Version
1.5.1
JSON of node setup
[
    {
        "id": "5f156cada4cfd3a0",
        "type": "Thing Update",
        "z": "39f9e2f8e099f89d",
        "nodeName": "update light State",
        "name": "",
        "thingType": "Fights",
        "debug": false,
        "updates": [],
        "x": 670,
        "y": 3240,
        "wires": []
    }
]

Sure thing.  I just released v1.6.0 that now passes through the original msg object (excluding msg.payload).  msg.topic and any other msg.SOMETHING should come through on all the outputs.  Please let me know if that works like you wanted it to.

Just tried the new version and works like a charm.
Thank you!


limitColors(1) never returns white or black

$img = Image::make($file);
$img->limitColors(1);
$color = $img->pickColor(0,0);

given black image it returns rgb(4,2,4)
for white image, the result is rgb(252, 254, 252)

The color quantization process is under the control of the respective driver methods. For GD this is imagetruecolortopalette  and for Imagick Imagick::quantizeImage. Unfortunately, I can't say what's going on under the hood.


Node.js support via browser (DOMStorage) emulation

This commit adds Node.js support by means of emulation DOMStorage
(specifically localStorage).
A specific banner for node.js has been added (setting up the emulation).
The grunt 'concat' task has been expanded to generate output files for node.js,
i.e. by prepending this node.js emulation banner to the webpacked output file.
The grunt 'test' task has been expanded to include local node.js tests, these
are implemented via the subtask 'mochaTest' based upon 'grunt-mocha-test'.

This library has been added a development dependency to package.json.

Added a ~450LOC test file to verify the functionality of localForage under node
This commit introduces a dependency on 'dom-storage', which is a tiny ~140LOC
implementation of DOMStorage inside node.
Changed the main field of package.json to point to the node output file.
Added the 'browser' field to package.json with the old main field value.

Hello,
I am aware that this pull request will be rejected, according to the;
'Features localForage will reject' --> node.js support.
Yet I'm proposing this pull request for others to find, when they require node
support in the future. I created this since I needed node support for two
reasons, namely;

Running the same code on both client and server.

This enables rapid prototyping by maxizing code reusability.
It helps out new programmers, as they only need to learn one new library.
As the library has a simple key-value interface, it's easy to eventually
port code to redis or another more optimal backend key-value storage.

Testing browser code locally (outside of the headless browser configuration).

One case where this makes sense, is by the above, i.e. testing local code,
which utilizes this library outside of the browser context.
Another case can be when resources or time is limited, testing directly
in node is usually faster than within a headless browser environment.

Nevertheless; this pull request addresses: #345 and #57.

While writing my unit tests; I found two pieces of unexpected behaviors.
I have not tested the browser behavior yet. As such I cannot tell if the they
are reproducable, or they stem from bugs in the emulation layer.
I just want to (de)confirm my understanding of the API.
The two cases are:

removeItem

it('should not allow removing invalid keys', function(done) {
    localforage.removeItem('key', function(err)
    {
        ...
    });
});

Being run on an empty storage, I would expect an error (we're trying to remove,
a non existing key).

keys

it('should start out empty (value check)', function(done) {
    localforage.keys(function(err, keys)
    {
        ...
    });
});

Being run on an empty storage, I would expect keys to be '[]', but this is not
the case.

That's great and simple! If this doesn't get merged, then we should make a
custom driver for it. I can start experimenting with such implementation if
you are fine with it. We could probably create a github organization like
localforage-extensions if @tofumatt is ok with such naming.

--
Thodoris Greasidis
Computer, Networking &
Communications Engineer

Wow, this is actually quite cool. I agree, we shouldn't reject this on principle if it's not too intrusive to the code. I'll have a review soon.

tofumatt

On 19 Apr 2016, at 01:56, Skeen<EMAIL_ADDRESS>wrote:
Hello,
I am aware that this pull request will be rejected, according to the;
'Features localForage will reject' --> node.js support.
Yet I'm proposing this pull request for others to find, when they require node
support in the future. I created this since I needed node support for two
reasons, namely;
Running the same code on both client and server.
This enables rapid prototyping by maxizing code reusability.
It helps out new programmers, as they only need to learn one new library.
As the library has a simple key-value interface, it's easy to eventually port code to redis or another more optimal backend key-value storage.
Testing browser code locally (outside of the headless browser configuration).
One case where this makes sense, is by the above, i.e. testing local code, which utilizes this library outside of the browser context.
Another case can be when resources or time is limited, testing directly in node is usually faster than within a headless browser environment.
Nevertheless; this pull request addresses: #345 and #57.
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly or view it on GitHub

@thgreasi: A custom driver would be fine with me; all I really wanted was node.js support and hence I went with the easiest and quickest implementation that would fulfill my requirements.

The argument being that utilizing a client-side library for server-side is somewhat 'wrong', and hence you should not expect superb performance or metrics, only correctness.

@tofumatt: When during your review please keep a few things in mind, which may be deal-breakers:
The package.json 'browser field' has been added, and the 'main field' has been changed; package.json:55+56

This affects the ordinary functionality of the library, i.e. it COULD break stuff. Thorough testing would be required; also the 'browser field' is not even in the real package.json standard, but rather posted here.

We specifically need to check, whether the bundlers we want to support actually respect it. According to this webpack may need a work around, while jspm and browserify seem to respect it as is.

The code should be modified to pass the jshinter, such that the actual testing errors mentioned here, actually show up on travis.

I will look into this first thing, when I get into the office in a few hours. We need to discuss these diverging test cases, but before looking further into these; I'll test the correspondence with the browser implementation.

We need unit tests for 'iterate' and the entire promises based Data API.

Travis now builds and fails to two mentioned test cases.
I have tested these two test cases on in the browser environment (via. js-fiddle);

removeItem

The browser does not throw an error when removing a non-existent element, so the node.js implementation seems in sync with the browser implementation.
-- I'm curious however as to why this does not happen?

keys

The browser returns an empty array '[]', when there are no keys stored. This is the behavior I expected, and hence I conclude that the failure is in the node.js implementation. I'll look into this.

keys did in fact return an empty array on node.js as well, my method of checking was improper. As such the node.js implementation seems to be completely in-sync with the browser one, in regards to the provided unit tests.
-- We still miss unit tests for iterate and the entire promise based data api.

Agree this is a nice feature to have, ideally without needing a custom adapter. It'd be good to double check that this is the best possible implementation, though, since in Node we have more options than just a Local Storage shim.

I just took a look at dom-storage, and based on the implementation, I would strongly advise against using it in LocalForage. It advertises itself as mostly designed for unit testing, and that shows in the source.
Notice that it works by relying on fs.readFileSync/fs.writeFileSync/etc., which is slow and synchronously blocking. For LocalForage to have a good reputation as a storage engine that works well in all environments, this would be a poor choice for a default.
As an alternative suggestion, how about:

Writing a custom adapter that uses node-websql via the WebSQL adapter, or that uses level via a custom implementation, then
opening a PR to use that adapter by default in Node and then use the other three adapters in the browser.

Another alternative is to just rewrite the existing WebSQL adapter to use node-websql (which does the appropriate "browser" switching automatically), in which case the only change to localforage core would be to set the list of adapters to [idb, websql, localstorage] in the browser and [websql] in Node.

I guess I have to agree with @nolanlawson, due to the quality of dom-storage, maybe this pull request should be rejected.
I don't mind this; I expected this pull request to be rejected on principle.
I just wanted to publish my proof-of-concept for others to find.
@nolanlawson suggestions for alternative implementations sound excellent to me, but quite frankly my patch fulfills my own requirements (proof-of-concept prototyping), and I'm afraid I wont be implementing he's suggestions.

Sorry, I wasn't trying to make you feel unwelcome. :( I think this PR demonstrates a desire to have localforage run in Node, and we should definitely move in that direction.

Oh, I do not feel unwelcome at all! ^.^
I'm just stating that my desire to have localforage run on Node was purely for proof-of-concept projects, not for production quality projects, which shows by the fact that I decided to utilize a somewhat random localStorage shim rather than implement a better solution.
Hence, I simply agree with you, that while dom-storage might be fine for proof-of-concept kinda deals, it is indeed not a production quality library.
A production quality implementation would be nice to have, but it was simply not worth the effort for my use case :).

I don't know how it works, but there is "A drop-in substitute for the browser native localStorage API that runs on node.js"
https://github.com/lmaccherone/node-localstorage


Removing subject_ids argument in TUHAbnormal example.

Related with the issue #377.
Removing a deprecated parameter in the TUHAbnormal example.

So is this correct @gemeinl ?

No, actually not correct.
The function load_example_data has an argument subject_ids which does not have any effect anymore, due to the changes introduced here. Therefore, the entire dataset will be loaded instead of just 10 recs.
We still need this argument, however, its meaning has changed. It is not subjects we are refering to but recordings. I suggest to rename the argument to n_recordings and give this as input to TUHAbnormal which has the same argument (see https://github.com/braindecode/braindecode/blob/884a78b2fb306047d444352ac4dcd9b503324fca/braindecode/datasets/tuh.py#L207-L208).

Many thanks for the explication @gemeinl. I was wondering, can you review it again to make sure everything is correct?

I suggest to stick as close to the original code as possible.
So change the input argument n_subject to n_recordings in load_example_data and create the recorind_ids for TUHAbnormal inside as before.

Done @gemeinl.

Can you merge? @robintibor

Could you solve the conflicts @bruAristimunha before I merge?

Done @cedricrommel.


Remove blue border styling

Hello, as you in the pic, there is a light blue border around the select element when I click it and expands. Can you tell me how to remove it? I have tried various css selection but did not do the trick.

Hi, how about this:
.bootstrap-select .dropdown-toggle:focus {
    outline: 0 !important;
}


Expose total bandwidth

Figured I should put the Bandwidth module in rust-libp2p to good use.
Currently untested, will go for lunch first now :-)

Adding 15 nodes to an existing network of ~20 nodes; graph made with rate(kademlia_exporter_meta_libp2p_bandwidth_inbound[1m] ).

Mind sharing a bit more on your use-case?

Sure! It's mostly in my current test case, where I have between 50 and 300 nodes running on Kubernetes to do some tests. That's the same sentence from https://github.com/libp2p/rust-libp2p/issues/2164 :-)
I'm doing research on peer-to-peer social network systems (https://www.rubdos.be/academic/, public source code: https://gitlab.com/etrovub/smartnets/glycos/), and I've replaced my own Kademlia implementation with libp2p ~three weeks ago. Next week I'll start implementing all the new topping layers that I've been working on the past three years...
If you're interested in a chat, feel free to hit me up on Matrix/Signal/mail!


[DOCS-201] Update API Methodologies

Changelog
Followed same pattern as discussed with CSM. Based additional content on internal Confluence article.
Added
n/a
Updated

Page
Deploy Preview
Comment

[API Methodologies]
[Link]
[Comment]

Preview This Change
To see how this change looks in production, scroll down to Deploy Preview. Select the link that looks like https://deploy-preview-<num>--cobalt-docs.netlify.app/
Variables
Help us support a “Write once, publish everywhere” single source of truth. If you see a line that looks like:
{{% asset-categories %}}
You’ve found a shortcode that we include in multiple documents.
You’ll find the content of the shortcode in the following directory:
https://github.com/cobalthq/cobalt-product-public-docs/tree/main/layouts/shortcodes
That shortcode has the same base name as what you see in the PR, such as asset-categories.html.
Checklist for PR Author
[ ] Did you check for broken links and alt text?
Be sure to check for broken links and Alt Text issues. We have a partially automated process,
as described in this section of our repository README:
Test Links and Alt Attributes.

Thanks for your patience with this, @ana-dashuk-cobalt . I've incorporated short codes where it made sense.
Lesson -- besides always checking with vale, don't overdo it with shortcodes on other files. I had rebase/conflict issues.


Added VerifiedColumn annotation

When used, this annotation will verify the authenticity of the data
stored in the corresponding column and will warn and thrown an exception
if the data failed verification.

Great idea! Proceed with the salt!

Hmmmm.... It's weakness will be swapping will still work, and we don't enforce uniqueness across shards.

If this PR is still relevant, then please fix conflicts, rebase and get a green CI build.
If the PR is no longer relevant please close.
This PR will be closed at the end of January 2021 otherwise.

If this PR is still relevant, then please fix conflicts, rebase and get a green CI build.
If the PR is no longer relevant please close.
This PR will be closed at the end of January 2021 otherwise.

Closing request as per previous announcement.

Closing request as per previous announcement.


plz re-add dist folder

Could you please consider re-adding the dist folder? I'm using Bower to fetch always the latest version of jQuery.EAN13. Without the dist folder it get's really difficult.

I think it is some kind of ugly to have the compiled code checked into the version control. Also even some authors of Bower consider deprecating it.
I would recomment to switch to npm as a package manager. By using it, you automatically get the latest builds as you would with bower and the dist folder.
I now switched from Grunt to only use npm and published the code also to npmjs.com so you don't have to build it every time. Simply use npm install jquery-ean13 to get it.
I hope this solution works for you.

Some people doesnt want this s*** of npm and just a simple raw file.

jquery does it. And react. And angular. However, tree.js does not do it.
You may download the compiled files always from the release section without using npm. I would also recommend this as the compability between releases is not guaranteed when you hotlink the library.


[docs] Document how TestCafe works

Describe how TestCafe works, including:

Reverse proxy & script injection
Babel compilation
Isolated test runs: TestCafe starts each test from a clean page state - test page is reloaded, cookies & storages are cleared

Done


Add web proxy mounting at ROOT for testing

For local testing with a ROOT such as /terminology/, the service from localhost:3555 must be mounted at $HOST/terminology/. I use an additional web server to do so, but this could also be integrated into server.js.

For me, it works if I just don't set ROOT. It will then proxy the /terminology/ subpath of uri.gbv.de as well. Maybe not the intended solution, but it seems to be working as expected for me.

Without setting ROOT

the start page (list of concept schemes) is not served at /terminology/ but at /
assets such as client.css are not loaded from /terminology/ but from /

We could change this lines to serve assets from $ROOT and show an error message at / when $ROOT is set. HTTP Proxy is then optional, e.g.
 ProxyPass /terminology/ http://localhost:3555/terminology/
  ProxyPassReverse /terminology/ http://localhost:3555/terminology/

Configuration and mounting has been refactored (see README).


Avoid switch fall-through warnings

Add a few comments and an unreachable break in cxxrtl to silence implicit fallthrough warnings. For some reason, the g++9 configuration on travis doesn't allow comments to silence the warnings, even though this should be enabled by -Wextra. Not that this is too big of a deal, but specifying the warning option explicitly might just fix it.

jfyi, I have pushed a bugfix for this PR in 8ec3b6d to avoid the following compiler warning with clang.
claire@hopper:~/Work/yosys$ make PRETTY=0 frontends/ast/genrtlil.o
[Makefile.conf] INSTALL_SUDO := sudo
[Makefile.conf] ENABLE_VERIFIC:= 1
mkdir -p frontends/ast/
clang -o frontends/ast/genrtlil.o -c   -Wall -Wextra -ggdb -I. -I"./" -MD -D_YOSYS_ -fPIC -I/usr/local/include -std=c++11 -Os -DYOSYS_ENABLE_READLINE  -DYOSYS_ENABLE_PLUGINS -DYOSYS_ENABLE_GLOB -DYOSYS_ENABLE_ZLIB -I/usr/include/tcl8.6 -DYOSYS_ENABLE_TCL -DYOSYS_ENABLE_ABC -I/usr/local/src/verific_lib/verilog -I/usr/local/src/verific_lib/vhdl -I/usr/local/src/verific_lib/database -I/usr/local/src/verific_lib/util -I/usr/local/src/verific_lib/containers -I/usr/local/src/verific_lib/hier_tree -DYOSYS_ENABLE_VERIFIC -DYOSYS_ENABLE_COVER frontends/ast/genrtlil.cc
frontends/ast/genrtlil.cc:933:3: warning: unknown attribute 'fallthrough' ignored [-Wunknown-attributes]
                YS_FALLTHROUGH
                ^
./kernel/yosys.h:161:28: note: expanded from macro 'YS_FALLTHROUGH'
#  define YS_FALLTHROUGH [[gnu::fallthrough]];
                           ^
frontends/ast/genrtlil.cc:1029:3: warning: unknown attribute 'fallthrough' ignored [-Wunknown-attributes]
                YS_FALLTHROUGH
                ^
./kernel/yosys.h:161:28: note: expanded from macro 'YS_FALLTHROUGH'
#  define YS_FALLTHROUGH [[gnu::fallthrough]];
                           ^
frontends/ast/genrtlil.cc:1826:3: warning: unknown attribute 'fallthrough' ignored [-Wunknown-attributes]
                YS_FALLTHROUGH
                ^
./kernel/yosys.h:161:28: note: expanded from macro 'YS_FALLTHROUGH'
#  define YS_FALLTHROUGH [[gnu::fallthrough]];
                           ^
3 warnings generated.

claire@hopper:~/Work/yosys$ clang --version
clang version 6.0.0-1ubuntu2 (tags/RELEASE_600/final)
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

Ah oops, I missed this. Thanks for the fix!


fix(api): Fix libvim norm! command, add test cases

Extracted from #245 - use common code path for executing normal commands

Looks like this fixes https://github.com/onivim/oni2/issues/934


Fix align for bottom arrow

Hi, @romainberger. You have a good project. Would like to contribute few bugfixes. This is the first.
Arrow was a bit off by few px, could you review it please?
Fixes problem with following cases:

<ToolTip position="left" arrow="bottom">
<ToolTip position="right" arrow="bottom">

A parent for test: <div style={{outline: '1px solid red', height: 0, width: 0}}/>
Haven't tested other cases through. And not sure I got this change right :wink:

Thank for catching that!


Tidy up nuspec files

Conform nuspec descriptions to agree exactly with the README file

They've always been there - I've just tidied it up a little. I'm changing as little as possible here.


[Bug] Some Unity built-in components display strangely

Problem
Fields of some built-in Unity components, such as Outline, are no longer displayed.
Suggestion
Exclude AlchemyEditor from being applied to all Unity built-in components.

This issue was caused by fields in the parent class not being rendered. This has been fixed in v1.0.3.


WIP: TST: add tests for Pythran somersd

Reference issue
https://github.com/scipy/scipy/issues/14544
What does this implement/fix?
Take somersd as an example, firstly implement all the tests by hand.
Hi @rgommers, thank you so much for your detailed suggestions! But I'm a little confused about :

A size-1 array, and (if applicable for the function) a size-0 array
see BUG: RBFInterpolator fails when calling it with a slice of a (1, n) array #14420 for a relevant bug report for non-contiguous inputs and views.

Do you mean size-1 array is like (1, n), and size-0 array is like np.empty(shape=(0, 0)) ? Why would that be a potential problem to Pythran? I think https://github.com/scipy/scipy/issues/14420 is more a problem of views, not a problem of size-1 array..?
For your sketch,
# in class TestMyFunc(PythranFunc)
def pythranfunc(self, x, ):
        "This function is called by the test machinery with various inputs for `x`"
        result = module.funcname(x, ...)  # this is the function call to test, e.g. `stats.somersd`
        expected = # exact result
        assert_allclose(result, expected, rtol=self.rtol, atol=self.atol)

How can pythranfunc be called by the test machinery with various inputs for x? I would expect there is a _gen_types() in PythranFunc, and in pythranfunc, I will call _gen_types() to generate different types of x and test them?
Also, how many types do you think we should cover...? Currently, there are:
        self.ALL_INTEGER = [np.int32, np.int64]
        self.ALL_FLOAT = [np.float32, np.float64]
        self.ALL_COMPLEX = [np.complex64, np.complex128]

cc @serge-sans-paille

I made commit https://github.com/scipy/scipy/pull/14559/commits/805777c5e1e2b4bb14362da093db9a54ec96b03f because of error:cannot collect test class TestSomersD because it has a __init__ constructor. Maybe parametrize is a better way if we can't do __init__ for test class?

Do you mean size-1 array is like (1, n), and size-0 array is like np.empty(shape=(0, 0)) ? Why would that be a potential problem to Pythran? I think #14420 is more a problem of views, not a problem of size-1 array..?

Sorry that was incomplete. I think what I had in mind then was a shape (1,) array with a large stride. What is special about a size-1 array is that there is only a single element, so the strides can (and sometimes are) be large, or zero. So something like:
x = np.array([3])
x.strides = (42,)

I made commit 13f41ed because of error:cannot collect test class TestSomersD because it has a __init__ constructor. Maybe parametrize is a better way if we can't do __init__ for test class?

Ah yes, there is no __init__ because pytest does something special. There is a setup method though that is always called first, so that can be used instead.
The problem with doing for dtype in [np.int32, np.int64, np.float32, np.float64]: is that it gets repeated over and over. You can use parametrize instead of a for-loop if you prefer, that's a bit of a judgement call (it will create multiple separate test cases instead of one, not sure that that's better here). But either way you want to refer to a self.dtypes to not repeat yourself.

how many types do you think we should cover

It would maybe be excessive to call all of them, but let's at least do a few that Pythran does not have the signature for, like uint8, int16 in addition to int32, int64.

How can pythranfunc be called by the test machinery with various inputs for x? I would expect there is a _gen_types() in PythranFunc, and in pythranfunc, I will call _gen_types() to generate different types of x and test them?

I was thinking it's a special name, so PythranFunc will already know how to call it and does so with the various inputs under test. So PythranFunc willl have something like:
    def test_all_dtypes(self):
        _x = np.arange(10)
        for dt in self.dtypes:
            x = _x.astype(dt)
            self.pythranfunc(x)

    def test_views(self):
        ... (etc)

I will call _gen_types() to generate different types of x and test them?

You can try this too. The goal is to be to write tests for new functions that don't have unnecessary boilerplate but are still easy enough to understand.

I was thinking it's a special name, so PythranFunc will already know how to call it and does so with the various inputs under test. So PythranFunc willl have something like:
    def test_all_dtypes(self):
        _x = np.arange(10)
        for dt in self.dtypes:
            x = _x.astype(dt)
            self.pythranfunc(x)

    def test_views(self):
        ... (etc)

Thanks for your detailed reply! But I think it will not work well if we define x in PythranFunc(  _x = np.arange(10)), because for different functions, the input shape may vary, e.g. 1d/2d/3d. Moreover, self.pythranfunc(x) was defined in the Child class and it is hard to check whether the result meets the expectation, because the child class can't know the value of x which is defined in the parent class PythranFunc .  Unless we do something like this? (not sure if it works):
class PythranFunc:
    '''
    Inherit from this class to generate a bunch of relevant test cases
    '''
    def __init__(self):
        self.ALL_INTEGER = [np.int8, np.int16, np.int32, np.int64]
        self.ALL_FLOAT = [np.float32, np.float64]
        self.ALL_COMPLEX = [np.complex64, np.complex128]
        self.dtypes = [] # updated in child class
        self.arguments = [] # updated in child class
        self.index = []# updated in child class
        self.expected = None # updated in child class

    def test_all_dtypes(self):
        for dtype in self.dtypes:
            self.arguments[self.index] = self.arguments[self.index].astype(dtype)
        res = self.pythranfunc(self.arguments)
        assert_allclose(res.statistic, self.expected[0], atol=1e-15)
        assert_allclose(res.pvalue, self.expected[1], atol=1e-15)

There are some failures in Mypy but seems it is unrelated.


Library Search screws draw probability

Describe the bug
When you search your library for X card, the tracker sees all the cards revealed, and for the rest of the game will show 0% probability or no cards left
To Reproduce
Steps to reproduce the behavior:

In a game, trigger an ability that allows you to search your library
Allow the ability to come into effect, and have the UI show all remaining cards in your library
At this point you can either submit a card or cancel

Expected behavior
The tracker should see that the cards have been reshuffled and as such never played
Screenshots
To come soon
Additional context
I think scrying has the same effect, albeit with a single card

Hi! We need screenshots to investigate your issue

I'm still working on getting those screenshots! My luck has been abysmal
and it's really late so I'll try to get some tomorrow
On Sun, 28 Jul 2019 at 00:22, Aquaman88<EMAIL_ADDRESS>wrote:

Hi! We need screenshots to investigate your issue
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/Razviar/mtga-pro-tracker/issues/470?email_source=notifications&email_token=ABSAYS45ZE5XCBXKBZXROOTQBTKDRA5CNFSM4IHKDXK2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD26UIGY#issuecomment-515720219,
or mute the thread
https://github.com/notifications/unsubscribe-auth/ABSAYS24MHCJHWTB72PYD2DQBTKDRANCNFSM4IHKDXKQ
.

Issue confirmed, we are working on fix.


Add samples file option to view CLI

Overview
This pull request adds the -S / --samples-file option to the vcztools view CLI.
This pull request addresses #67, but does not implement the empty-selection semantics.
Testing
I added some validation tests to compare the output from vcztools and bcftools. The tests use the --no-update option because vcztools does not recompute the INFO fields when the user specifies a sample selection (see #45).

Thanks @Will-Tyler!

This pull request addresses #67, but does not implement the empty-selection semantics.

I'll merge this now, but would you like to open another issue to track this?


Add a hook to wait for the completion of fit

Greetings.
I think it would be useful to have a way to know when a fit() operation has actually concluded instead of having to rely on timeouts.
D3 transitions natively provides a end() method which returns a Promise: https://observablehq.com/@d3/transition-end.
Similar hooks could be useful in other spots I am not aware of.

Added the following callback support in the dev

Will be merged with this PR


Please provide an example for modifying and serializing a config file back to disk

Thanks for the report! One of the caveats with this library, however, is that this isn't that well supported because formatting is not preserved. Is that a requirement for you though?

Nope, in my use case the config file is intended to be read and written by the code only.
I worked it out in the end, might provide a PR next week.

Ok great!

Maintenance of this crate has moved to the https://github.com/toml-rs/toml repo.  As a heads up, we plan to move toml to be on top of toml_edit, see https://github.com/toml-rs/toml/issues/340.
Closing this out.  If this is still a problem, feel free to recreate this issue in the new repo.


Spread is spread (parameters)

Clear and concise description of the problem
We no longer want to recover a model from spread by default. The current behavior creates a complicated story for spreading, and leads to confusing emitter logic. The following needs to be done in this order

[x] Decorate brownfield services with @bodyRoot
[ ] Update emitter logic
[ ] Add overrideClientMethod decorator
[ ] Move vendored BodyParameter to core

The final step is not required for the story to be complete, I'm only linking it in this issue as a reference.
Down the line, we also want to look into clearing up the logic in responses too. We will wait for a traits redesign first.
Checklist

[X] Follow our Code of Conduct
[X] Check that this issue is about the Azure libraries for typespec. For feature request in the typespec language or core libraries file it in the TypeSpec repo
[X] Read the docs.
[X] Check that there isn't already an issue that request the same feature to avoid creating a duplicate.

typespec-java 0.18.0 released with this logic

Closing because all of the tcgc work has been completed with the introduction of the @override decorator


feat: implement custom context for framework project

This commit implements a custom context for the framework project. The custom context includes the following features:

Timeout control: Allows setting timeouts for requests.
Request/Response data retrieval: Provides functionality to retrieve request and response data.
Individual request timeout: Allows setting a timeout for individual requests.

Merge the feature/context branch into Main.


Chat: Cyrillic letters for Russian(speaking) users.

I would expect this plugin work SIMILAR to chat timestamps. (Overlays, I would guess).
What do I expect from this plugin, and how would this work:
Option 1:
RuneLite client automatically would recognize the russian keyboard is active.
Currently, you can't type cyrillic letters in OSRS.
Step 1: I would expect a "translator" of some kind, that would convert the Russian Keys into their latin-shortcuts (ie. Я into Ja/Ya, Ю, into Ju/Yu, etc). so the game client can understand the inputs, while your OS Russian Keyboard is active.
Step 2: Afterwards, with an overlay, they would be translated again, and this time visualized as Cyrillic letters.
Option 2:
RuneLite gets a key-combination added, so texts that are meant, would be written in Russian regardless the OS Keyboard layout.
In this case, I would expect a key-combination for RuneLite to switch to Russian keyboard (and ability to switch between Mnemonic or Regular).
Everything else would work as described above.
Avoid conflict with other texts:
I guess, it would be possible to add a pre-condition of some kind, not sure though to be very honest.

I don't think this is a feature which we could reliably maintain. In my opinion you'd be better served finding and using some software for keyboard internationalization or keyboard layout and using that instead.

I don't think this is a feature which we could reliably maintain. In my opinion you'd be better served finding and using some software for keyboard internationalization or keyboard layout and using that instead.

I'm using UK-Based (edited) keyboard for latin, and Mnemonic Russian Keyboard Layouts when I use russian language.
Let me describe you exactly in a different way, what I'm talking about with a certain example.
I will use a text that literally means "I live here." I press down the same keys in the same order.
When you use an UK Keyboard (or possibly US) it would look like this:
Ja xivu zdes'.
But when you switch to a (Mnemonic Russian keyboard) the text will look like this:
Я живу здедь.
My problem is the following:
Although the game CAN recognize the text written with UK keyboard (Ja xivu zdes').
The game will not accept the text written with cyrillian letters (Я живу здесь).
I have no problem at all in terms of keyboard layouts or in managing them.
What I want is, an overlay that would REPLACE the (Ja with Я) , (x with ж), (i with и), etc).
I think, that it should be possible with some kind of text-overlay similar to timestamps.


Unnecessary horizontal scrollbar in Firefox

Description
No matter how large or small my browser window is, I always have a horizontal scrollbar (blue) at the bottom, without any obvious reason. It also does not matter whether I'm logged in or not. It does not occur in Chrome. I do not use an ad-blocker.
Screenshots

Gitea Version
1.19.1
Can you reproduce the bug on the Gitea demo site?
No
Operating System
Windows 10 22H2 x64
Browser Version
Firefox 112.0.1 (x64)

Could you try a nightly build? I guess https://github.com/go-gitea/gitea/pull/24211 has fixed the problem.
https://dl.gitea.com/gitea/1.19/

What package? If you'd like to try , you could safely  download the latest binary and replace it, pretty  simple.

Could also verify on https://try.gitea.io/ which runs 1.20, but also should have the fix and be somewhat close of a test.

And yes, don't be afraid of nightlies, they are well tested and in fact I run them in production as well.

Pretty positive this was fixed, closing.


eml_analyzer --text throws cyrillic characters instead of german umlauts

Hi,
I face a issue when parsing outgoing mails:
Extract from the eml-File (save-as via Thunderbird):
"...
This is a cryptographically signed message in MIME format.
--------------ms090908070501060903060609
Content-Type: text/plain; charset=UTF-8; format=flowed
Content-Transfer-Encoding: 8bit
ä
..."
If the plain text contains i. e. a "ä" the output character becomes cyrillic "д" independend from the chosen output format "--text" or "--text --format json".
In comparison an extract from a eml-File that get's parsed correctly:
"...
--eTqZtiOboXMORarM2jeks2PNUJpOw=_O7X
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: quoted-printable
...
"
Any idea?
I add a test-file.
Regards,
MrChang.
test.zip

Hi,
I can confirm the bug on Linux, on Windows it works fine. Looks like the return value of the method Message.get_payload from the python library is based on the OS.
Input Dies ist ein dämlicher Test.
Output on Windows: b'Dies ist ein d\xc3\xa4mlicher Test.'
Output on Linux: b'Dies ist ein d\xe4mlicher Test.'
I added a unit test to test this behaviour on Ubuntu and Windows: https://github.com/wahlflo/eml_analyzer/pull/18
To find and fix the root cause one needs to analyze the Message.get_payload method from the python library.

So @mrchang0815,
The difference between Windows and Linux was caused since the default encoding when the file is read is different. I set it now explicit to utf-8.
I had a look at email library, it looks like that the value 8bit of the Content-Transfer-Encoding: is not considered.
I will create an issue for the standard library. For the meantime I implemented a fix in the eml-analyzer


Minor edit

Reference Issues/PRs
What does this implement/fix? Explain your changes.

load_config function modified

Any other comments?

Codecov Report

Merging #173 (14fa3d2) into dev (a9e2323) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##               dev      #173   +/-   ##
=========================================
  Coverage   100.00%   100.00%
=========================================
  Files            4         4
  Lines          587       587
  Branches        90        90
=========================================
  Hits           587       587

Impacted Files
Coverage Δ

samila/functions.py
100.00% <100.00%> (ø)

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Introduce static analysis and clean up code to pass

Major refactor to get code up to basic Java standards.
Added static analysis tools checkstyle, findbugs, lint, and pmd.
Fixed code to pass all tools
There is some evidence that I've introduced a bug here:
hbase.lite.tes: JNI ERROR (app bug): attempt to use stale Global 0x25e6 (should be 0x25ea)
hbase.lite.tes: java_vm_ext.cc:542] JNI DETECTED ERROR IN APPLICATION: use of deleted global reference 0x25e6
hbase.lite.tes: java_vm_ext.cc:542]     from void com.couchbase.lite.internal.core.C4Replicator.free(
                                             long, java.lang.Object, java.lang.Object)

It occurs infrequently, and I am having trouble reproducing it.  Since this is such a huge commit I want to get it in and fix this and any other regressions, later.

Coverage increased (+2.0%) to 77.846% when pulling 7d129a0304f91cce04183896ca64911fb6fe510b on feature/static-analysis into 6f5cfdcf925b8befe508103147410ac98b17524f on master.

Merging.  Will fix the broken comments in a subsequent commit, today.

Beside the broken comment, there is one breaking API (Database.LOG). Please also fix it as well.


Update regex test

Coverage: 93.428% (+0.2%) from 93.242% when pulling 12b2282e7d592a5e62787a6e4cb1ab1b6ffe4815 on feature/regex-test into 492dd3509f9fcac7043194a744b199bcb1d5ff49 on main.


Enhanced Sequencing Run Logging

Implemented additional logging functionality in order to provide an enhanced end of sequence run log. This takes the form of an end of sequencing run report, an example is shown below:
INFO: ======= Sequencing Run Report =======
INFO: Sequencing Run Start Timestamp:<PHONE_NUMBER>s
INFO: Sequencing Run End Timestamp:<PHONE_NUMBER>s
INFO: Time Elapsed: 20s
INFO: Executed Command: D:\anaconda3\envs\casanovo_env\Scripts\casanovo sequence sample_data\sample_preprocessed_spectra.mgf -o foo.mztab
INFO: Executed on Host Machine: DESKTOP-P03U1SR
INFO: Sequencing run date: 06/21/24 14:15:39
INFO: Sequenced 128 spectra
INFO: Sequence Score CMF: {0.0: 96, 0.5: 96, 0.9: 66, 0.95: 60, 0.99: 8}
INFO: Max Sequence Length: 17
INFO: Min Sequence Length: 6
INFO: Max GPU Memory Utilization: 400mb

All the data to generate this report is recorded on the fly as inference is conducted (i.e. no file parsing). To facilitate this the functionality of the data submodule was extended to add infastructure for run time logging. This will hopefully make it relatively easy to further extend logging and other io functionality in the future.

Changed base to dev, make sure to reflect that locally.

Added more information to the end of run report, namely the number of skipped spectra. Unfortunately the model never sees the spectra that are skipped due to pre-check errors such as having invalid precursor info, so these aren't reflected in the end of run report. They do however appear at other points in the log. A sample log is available below:
INFO: ======= Sequencing Run Report =======
INFO: Sequencing Run Start Timestamp:<PHONE_NUMBER>s
INFO: Sequencing Run End Timestamp:<PHONE_NUMBER>s
INFO: Time Elapsed: 18s
INFO: Executed Command: D:\anaconda3\envs\casanovo_env\Scripts\casanovo sequence sample_data\sample_preprocessed_spectra.mgf -o data/foo -c casanovo.yaml
INFO: Executed on Host Machine: DESKTOP-P03U1SR
INFO: Sequencing run date: 06/24/24 16:28:34
INFO: Attempted to sequence 128 spectra
INFO: Sequenced 72 spectra
INFO: Skipped 56 spectra
INFO: Sequenced 56.25% of total spectra
INFO: Skipped 43.75% of total spectra
INFO: Score Distribution:
INFO: 54 spectra (75.00%) scored >= 0.0
INFO: 54 spectra (75.00%) scored >= 0.5
INFO: 49 spectra (68.06%) scored >= 0.9
INFO: 46 spectra (63.89%) scored >= 0.95
INFO: 8 spectra (11.11%) scored >= 0.99
INFO: Max Sequence Length: 9
INFO: Min Sequence Length: 6
INFO: Max GPU Memory Utilization: 398mb

Unfortunately I don't have access to any sample data that has spectra that are skipped at the inference stage, so I haven't been able to fully test the skipped spectra logging.

Can you describe a bit what the logging_io and prediction_io are and how they're intended to be used? You mentioned it during the meeting yesterday, but it would be useful to have it briefly written out as well.

Can you describe a bit what the logging_io and prediction_io are and how they're intended to be used? You mentioned it during the meeting yesterday, but it would be useful to have it briefly written out as well.

For sure, prediction_io contains the definition for the PredictionWriter interface as well as the definition for PredictionMultiWriter. For the most part, all of the functions in the PredictionWriter class were already implemented by MztabWriter. The PredictonWriter interface defines three member functions, log_prediction, log_skipped_spectra, and save which are all optional to implement by a class that implements the interface. The PredictionWriter interface is intended to provide a consistent interface for writing Casanovo sequence predictions to external IO (namely files and loggers).
PredictionMultiWriter implements the PredictionWriter interface, and maintains an internal list of PredictionWriters. When one of the PredictionWriter functions is called on a PredictionMultiWriter it'll call that member function on all of the PredictionWriters in it's internal list.
logger_io contains the definition of LogPredictionWriter, a PredictionWriter that is used to generate the end of sequencing run report. It maintains a table of predictions (which contains only the predicted peptide sequence and the search engine score at the time of writing), and writes to this table when log_prediction is called. When save is called it writes the end of run report to a logger object that is provided via the constructor.

Imo this is a bit over-engineered. Instead, we can just log directly where specific information is available using the Python loggers, rather than having to pass it all upstream to these new interfaces. Your implementation is precisely with the Python logger does after all: having a universal interface that multiple writers can hook into and write to different outputs. So we don't need to reinvent that.
So I'd just log the PSM statistics in the MzTabWriter, which is where you have the PSMs. Skipped spectra are logged in the reader, which is where the skipping actually happens (or will happen after the DepthCharge upgrade). (The current spectrum skipping logging is also incorrect and adds non-negligible overhead, which should be avoid for only logging.) Other stuff can similarly be logged in other relevant locations, etc.

Oh ok sounds good - so just to be clear should all of the PSM processing (e.g. the score distribution calculation) and logging happen in the MzTabWriter? Also, should skipped spectra logging just be delayed until the depth charge upgrade is implemented?

Yes, I think that's the logical place, considering that all PSMs are aggregated there.
Of course the over-engineering is my personal feeling. We could ask @wfondrie to weigh in as well.
Logging the number of skipped spectra can indeed be delayed for now.

I agree that this solution is overengineered for addressing just the post run logging. My reasoning for implementing it this way is having a PSM io interface would make it relatively easy to extend the PSM io in general. For example if we want to support other output formats like parquet or csv in the future and add a command line option to specify multiple output formats (say you want to write the PSMs to csv and mzTab) it would be relatively easy to do this, or if an end user wants to write PSMs to an external component like a database they could write their own PredictionWriter module to handle this.

Fair enough, I'll get everything moved to the mzTab writer.


[bug] Unable to Access xui.one via Browser in Ubuntu 20.04  Docker Container

I am trying to install and run xui.one on a container of Ubuntu 20.04. The installation appears to complete successfully, and the logs show the following message:
Installation completed!
Continue Setup: http://<IP_ADDRESS>/v8BmrcW

Here, <IP_ADDRESS> is the container's IP address. However, when I try to access the given link in my browser, I get the following error:
"<IP_ADDRESS> took too long to respond."
I also tried accessing http://localhost/v8BmrcW, but it didn't work either.

Are there any additional steps or configurations I need to perform for accessing xui.one in a browser? Or is there any logic error in my docker files?
Any help or suggestions would be highly appreciated!

any way to make the container use http://<IP_ADDRESS>/v8BmrcW instead? would that even work?

@aniel300 I have tried this by changing the getip function in https://github.com/Itz-Agasta/xui.one-installer/blob/main/install.python3.py but it does not seem to work.  when accessing the link by replacing the <IP_ADDRESS> with my IP or localhost I'm getting the same error but this time at port 80 NGINX is running.  Do you have any other suggestions?

what about using a base from linuxserver or similar?

i will ahare aome images of xc (not xui) later on that might be helpful as well.

on my dont work  i cant access the portal


Fixed some typos

Little changes in the readme.md , contributing.md and code_of_conduct.md

thanks for your contribution. We'll merge it once we got Travis CI build passing.

All commits squashed into one .

any updates here @NinjaCoderDev? Please revert your changes in code_of_conduct.md, we'll merge afterwards.

closed due to inactivity


Added popov.link

This PR is:

[X] Adding a new domain
[ ] Updating existing domain size
[ ] Changing domain name
[ ] Removing existing domain from list
[ ] Website code changes (512kb.club site)
[ ] Other not listed

[X] I used the uncompressed size of the site
[X] I have included a link to the GTMetrix report
[X] The domain is in the correct alphabetical order
[X] This site is not an ultra lightweight site
[X] The following information is filled identical to the data file

I confirm that I have read the FAQ section, particularly the two red items around minimal pages and inappropriate content and I attest that this site is neither of these things.

[X] Check to confirm

- domain: popov.link
  url: https://popov.link/
  size: 11.5
  last_checked: 2023-08-30

GTMetrix Report: https://gtmetrix.com/reports/popov.link/5g3yinpE/

Thanks!


Config sample videocap

Fixing the following issues -

https://github.com/Dronecode/camera-streaming-daemon/issues/162
https://github.com/Dronecode/camera-streaming-daemon/issues/164
https://github.com/Dronecode/csd_docs/issues/22

@hamishwillee Kindly review.


Docs: Update Getting Started tutorial

Update tutorial
Update Screenshots

@udanna, Gal updated the doc with all the recent changes in the product.
Please review and edit as needed.
Thanks

Gal, The "Pending Changes" image is very big and should be reduced to the actual size on the screen. If the size is automatic on the entire screen, try to add a transparent layer on both side.

Done

@GalCegla @udanna who is next? who is waiting for who?

@GalCegla @udanna who is next? who is waiting for who?

I'm not aware of any pending tasks in my end🙂

@yuval-hazaz @GalCegla @iddan since almost everything was indicated as changed due to the auto-formatting in VisualStudio, even though it seems that the changes focused on screen captures, which I couldn't see in Edit mode, wanted to look at https://app.amplication.com/ to understand what was changed. But I see you've committed all so I'll just go on to the next task in line... Also, I'd like to remind everybody that you shouldn't expect immediate responses. Take into account that it can take a few days until I get to it.


Classify template braces as special braces

Hi @marijnh ! 👋
Not sure if I did this correctly (and also not sure whether you want to accept this change), but I thought I'd give it a try to classify template braces (including the starting dollar brace) as a "special brace".
I did this by looking at the Lezer parser grammar for JavaScript and finding that there was this templateDollarBrace and templateClosingBrace.
https://github.com/lezer-parser/javascript/blob/afdc2da19789486e8f42c966a2daddd54907614c/src/javascript.grammar#L442
However, I'm not sure if those are accessible how I have it in this PR.
If you are amenable to this change, but it is not working, feel free to let me know and I can fix it (I may need a bit of a hint how).

This is to improve the communication to developers that the dollar and braces are not a string literal part of the template string (and also improve the color contrast):
Prism.js / VS Code:

CodeMirror:

That node, because it doesn't start with an upper-case letter, wasn't included in the tree, and thus can't be styled. Attached patches should add this properly.

Ah great, thanks! Would this be included in a new version soon (I'm assuming either<EMAIL_ADDRESS>or @codemirror/lang-javascript@0.20.0)?
I looked in the current version 0.19.6, but I couldn't see it: https://unpkg.com/browse/<EMAIL_ADDRESS>

I've tagged @codemirror/lang-javascript 0.19.7 and @lezer/javascript 0.15.3

Thanks for publishing! Just tried it out in https://github.com/upleveled/theme-vs-code-dark-plus/commit/b3fdce61066a6bb81396aa9fccaea64ef1f20f78 , works! 🙌


Typo in BasicEncoder.h in initialization of m_previous_state

Typo?
m_previous_state - pin_state();

should be
m_previous_state = pin_state();

So it should!
Thank you for taking the time to notice and notify me.
I will change the file immediately. Feel free to close the issue at your leisure.

Looks good!


Update how-to-configure-the-backup-biztalk-server-job.md

Change the important note that says the <destination path> should be set to a different computer ... I add it or hard drive. And also add another reason why you should that, not only for avoid potential data loss but also performance improvement

:white_check_mark: Validation status: passed

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Details

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


feature: Update Where Resolver to combine locations and synctargets from KubeStellar namespace

Feature Description
Now that the locations and synctargets are in the KubeStellar namespace, it is necessary for the Where Resolver to be updated to combine locations and synctargets from the KubeStellar namespace, not the IS, with edgePlacements in order to create singlePlacementSlice objects.
Proposed Solution
Update the Where Resolver to use location and synctarget objects from the KubeStellar namespace and not the IS workspace/space
Want to contribute?

[ ] I would like to work on this issue.

Additional Context
No response

not relevant for ks-0.20 (no more Where Resolver).
closing as not relevant.


offline search for mirror drives

What are the relevant tickets?
Closes https://github.com/mitodl/ocw-hugo-themes/issues/1174
Description (What does it do?)
This PR adds the Fuse.js library to the project and utilizes it to provide offline search functionality in the www-offline theme, used as the home page of mirror drives. The search icon is now displayed in the header on pages that aren't the search page, linking to a new search.html page at the root. In https://github.com/mitodl/ocw-studio/pull/1705, we set up ocw-studio to publish a file under content/websites for each website that has been published live at least once inside the root website, ocw-www. This content is currently being used to generate a paginated list of sites at the root when using the www-offline theme in index.html. In search.html, we put that same list into an array in Javascript and feed it into Fuse.js as a data source, indexing on primary_course_number and title. The search page mostly replicates a basic version of the online search without any facets or resource search, providing links to sites relative to the root of the mirror drive in the same way the paginated index does. Everything is done in raw Javascript right in a script tag on the page to avoid any issues with CORS when viewing the page without a web server offline.
Screenshots (if appropriate):

How can this be tested?

Clone ocw-hugo-themes on this branch as well as https://github.mit.edu/ocw-content-rc/ocw-www and ocw-hugo-projects on the cg/www-offline-enable-section branch
In ocw-hugo-themes, run yarn install to make sure you install the latest dependencies
In ocw-hugo-themes, run yarn build /path/to/ocw-content-rc/ocw-www/ /path/to/ocw-hugo-projects/ocw-www/config-offline.yaml
Browse to your ocw-content-rc/ocw-www/dist folder and double click on index.html
Click the search icon in the header
Type any query you want here and search for courses
Click on any of the courses and verify that the path in your browser looks something like file://path/to/ocw-content-rc/ocw-www/dist/courses/course-name
These courses will not be present because this isn't a full mirror drive build, but if you want to test browsing to an offline site this way you can download the course ZIP from the live site, create a courses folder under dist and extract it there to a folder matching the courses name` property

Release process
https://github.com/mitodl/ocw-hugo-projects/pull/255 should be merged and released before this PR

@ChristopherChudzicki all set for another look


Logging current client connections?

After 3 years, replaced an old Ubuntu 18 server running OpenVPN with a new VM running Ubuntu <IP_ADDRESS>.
As promised, Nyr's wonderful script delivered a fully configured VPN server in less than 2 minutes, and using his bulk-client-add script, created over 50 user profiles as well in a few minutes to send out to clients.
The only thing missing is that the following command run under ~/.bashrc  used to return all currently connected clients
cat /etc/openvpn/server/openvpn-status.log
In the current version (2.5.5) installed by the script, there doesn't appear to be any connection logs created under /var/log/openvpn or in /etc/openvpn/server.
Is there an easy fix to get that working again?
Thanks!

This changed with commit cb8730b6213c579bf015ceadd2a1b18b887fc9a5.
The new location is:
/run/openvpn-server/status-server.log


Added the vesting with fee and oracle check example

If anyone is looking for this, it has gotten its complete own repository and is featured in https://github.com/OpShin/awesome-opshin
https://github.com/cardano-apexpool/opshin-smart-contract-examples/tree/main/vesting_oracle_fee


Icons problem

After installing this extension, every icon on github has "cross pointer" cursor instead of normal

just uninstall it ;)


Add java formatter using eclipse file format

See Maven2 Java Formatter Plugin

I didn't find good (acceptable) solution. I don't want a auto formatting.


Issues with Loading Database for Training OpenFold Multimer

Hi,
I am learning to train OpenFold-Multimer using just the alignments and mmcifs provided by AlphaFold/OpenFold. I used the following command to run the training, which I found to run fine when I train the monomer version of OpenFold:
python train_openfold.py pdb_data/mmcif_files alignment_data/alignments/ pdb_data/mmcif_files/ multimer/ 2021-10-10 --train_chain_data_cache_path pdb_data/data_caches/chain_data_cache.json --template_release_dates_cache_path pdb_data/data_caches/mmcif_cache.json --config_preset "model_1_multimer_v3" --obsolete_pdbs_file_path pdb_data/obsolete.dat --num_nodes 4 --seed 121924 --gpus 16 --max_epochs 15 --precision bf16-mixed
However, I keep running into the following error:
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 725, in looped_samples
mmcif_data_cache = dataset.mmcif_data_cache
AttributeError: 'OpenFoldSingleMultimerDataset' object has no attribute 'mmcif_data_cache'. Did you mean: 'mmcif_data_cache_path'?
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 725, in looped_samples
mmcif_data_cache = dataset.mmcif_data_cache
AttributeError: 'OpenFoldSingleMultimerDataset' object has no attribute 'mmcif_data_cache'. Did you mean: 'mmcif_data_cache_path'?
srun: error: nid001388: task 5: Exited with exit code 1
srun: Terminating StepId=21060918.0
I changed dataset.mmcif_data_cache to dataset.mmcif_data_cache_path in the file openfold/data/data_modules.py but then I ran into another error:
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
srun: error: nid001385: tasks 2-3: Exited with exit code 1
srun: Terminating StepId=21060799.0
Do you have any suggestions on how to fix these issues? Thank you in advance.

Perhaps try reverting your code change and using the input --train_mmcif_data_cache_path instead of --train_chain_data_cache_path for multimer training. There are a few known bugs with training in this issues log but you should be able to get the command to run without modifying the code. - community member


Error when pulling images from Quay.io

Output of docker version:
$ docker version
Client:
 Version:         1.12.3
 API version:     1.24
 Package version: docker-common-1.12.3-9.git47e22f2.fc25.x86_64
 Go version:      go1.7.3
 Git commit:      47e22f2/1.12.3
 Built:
 OS/Arch:         linux/amd64

Server:
 Version:         1.12.3
 API version:     1.24
 Package version: docker-common-1.12.3-9.git47e22f2.fc25.x86_64
 Go version:      go1.7.3
 Git commit:      47e22f2/1.12.3
 Built:
 OS/Arch:         linux/amd64

Output of docker info:
$ docker info
Containers: 6
 Running: 0
 Paused: 0
 Stopped: 6
Images: 55
Server Version: 1.12.3
Storage Driver: btrfs
 Build Version: Btrfs v4.6.1
 Library Version: 101
Logging Driver: journald
Cgroup Driver: systemd
Plugins:
 Volume: local
 Network: overlay host bridge null
Swarm: inactive
Runtimes: oci runc
Default Runtime: oci
Security Options: seccomp
Kernel Version: 4.8.8-300.fc25.x86_64
Operating System: Fedora 25 (Workstation Edition)
OSType: linux
Architecture: x86_64
Number of Docker Hooks: 2
CPUs: 4
Total Memory: 15.38 GiB
Name: drax
ID: I42H:Y2Z6:LECC:L7YW:ORMV:3OZE:7ZCA:QIYH:UPLE:R76L:AXGI:QX6O
Docker Root Dir: /var/lib/docker
Debug Mode (client): false
Debug Mode (server): false
Registry: https://index.docker.io/v1/
Insecure Registries:
 <IP_ADDRESS>/8
Registries: docker.io (secure)

Additional environment details (AWS, VirtualBox, physical, etc.):
$ dnf info docker
Last metadata expiration check: 6 days, 19:01:02 ago on Wed Nov 23 22:14:37 2016.
Installed Packages
Name        : docker
Arch        : x86_64
Epoch       : 2
Version     : 1.12.3
Release     : 9.git47e22f2.fc25
Size        : 60 M
Repo        : @System
From repo   : updates
Summary     : Automates deployment of containerized applications
URL         : https://github.com/projectatomic/docker
License     : ASL 2.0
Description : Docker is an open-source engine that automates the deployment of any
            : application as a lightweight, portable, self-sufficient container that will
            : run virtually anywhere.
            :
            : Docker containers can encapsulate any payload, and will run consistently on
            : and between virtually any server. The same container that a developer builds
            : and tests on a laptop will run at scale, in production*, on VMs, bare-metal
            : servers, OpenStack clusters, public instances, or combinations of the above.

$ cat /etc/os-release
NAME=Fedora
VERSION="25 (Workstation Edition)"
ID=fedora
VERSION_ID=25
PRETTY_NAME="Fedora 25 (Workstation Edition)"
ANSI_COLOR="0;34"
CPE_NAME="cpe:/o:fedoraproject:fedora:25"
HOME_URL="https://fedoraproject.org/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=25
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=25
PRIVACY_POLICY_URL=https://fedoraproject.org/wiki/Legal:PrivacyPolicy
VARIANT="Workstation Edition"
VARIANT_ID=workstation

Steps to reproduce the issue:

docker pull quay.io/pypa/manylinux1_x86_64

$ docker pull quay.io/pypa/manylinux1_x86_64
Using default tag: latest
Trying to pull repository quay.io/pypa/manylinux1_x86_64 ...
json: cannot unmarshal bool into Go value of type docker.APIErrors

The ubuntu:1604 image from DockerHub works fine

$ docker pull ubuntu:16.04
Trying to pull repository docker.io/library/ubuntu ...
sha256:3b64c309deae7ab0f7dbdd42b6b326261ccd6261da5d88396439353162703fb5: Pulling from docker.io/library/ubuntu
af49a5ceb2a5: Pull complete
8f9757b472e7: Pull complete
e931b117db38: Pull complete
47b5e16c0811: Pull complete
9332eaf1a55b: Pull complete
Digest: sha256:3b64c309deae7ab0f7dbdd42b6b326261ccd6261da5d88396439353162703fb5
Status: Downloaded newer image for docker.io/ubuntu:16.04

Describe the results you received:
Describe the results you expected:
Additional information you deem important (e.g. issue happens only occasionally):

@wallrj quay.io is serving docker registry V1 API. This docker has a feature enabled by default: signatures verification. Signatures verification does not work against V1 registries. There is a knob you can add to your /etc/sysconfig/docker in order to disable this feature and pull again from quay.io. The option to set is --signature-verification=false.

@runcom Thanks for the fast reply. --signature-verification=false worked.
It's a shame Docker doesn't give a more meaningful error message ☹

It's a shame Docker doesn't give a more meaningful error message

good point, let me take a look at the code to see if I can show a proper error message.

@runcom: Actually, we serve both V2 and V1, converting between them automatically if pushed by one version and pulled by another. I'm not sure why your Docker binary is using the V1 protocol, as the majority of our requests served are done via V2 at this point. Are there any custom protocol checks outside of the vanilla Docker version?

@runcom: Actually, we serve both V2 and V1, converting between them automatically if pushed by one version and pulled by another. I'm not sure why your Docker binary is using the V1 protocol, as the majority of our requests served are done via V2 at this point. Are there any custom protocol checks outside of the vanilla Docker version?

@josephschorr we saw that docker pull quay.io/pypa/manylinux1_x86_64 isn't found on the V2 registry, and you can download it with docker because if an image isn't found in V2 - it falls back to V1 and you can pull it successfully from V1. The difference here is that our docker uses a custom library to do image signature verification and it does only support V2 at this point (erroring out with the above error).

I'll investigate further though.

@runcom: Except we don't fallback. If you pull via V2, you get V2. We convert to V2 in real-time if the image was only pushed via V1. Looking at the logs, I just pulled the image via V2 on my local machine.

@josephschorr right, still looking, we may probably have a bug somewhere

@josephschorr thanks a lot for chiming in - found the root cause https://github.com/containers/image/pull/176 (tested our docker and it's indeed now pulling from V2 as you said) - thanks again.

Excellent.  Thanks @josephschorr

Glad we were able to find the cause!