Re-apply HarborCluster resource does not affect the minio resource when minio not ready

Steps to reproduce the problem:
Deploy the harbor-operator with custom minio image HARBORCLUSTER_STORAGE_IMAGE=quay.io/goharbor/minio:RELEASE.2020-08-13T02-39-50Z

Apply the full_stack.yaml
The minio pod will not ready due to the pull rate limitation of the dockerhub
Remove the version field in the minIOSpec of full_stack.yaml so that the harbor operator can change to use the minio image provide by the HARBORCLUSTER_STORAGE_IMAGE env.
Re-apply the full_stack.yaml

Expected behavior and actual behavior:
Want the minio pods were removed and use the image from quay.io, but they are still pending in ImagePullBackOff status

re-apply minio does not work.

Remove the version field in the minIOSpec of full_stack.yaml so that the harbor operator can change to use the minio image provide by the HARBORCLUSTER_STORAGE_IMAGE env.

There is no version field in the minIOSpec now.

If old minioCR set some filed but remove in the new minioCR, it will not do reconcile because of
equality.Semantic.DeepEqual(old, new)


feat!: Add MaxCollateralShare, MaxBorrowUtilization, and MinCollateralLiquidity

Description

ADR defining new market health parameters and which message types they restrict
Moves collateral utilization to the same ADR
Adds new params to proto
TODO: Implements the new restrictions

closes: #1093 #1095 #1036 and some other things that weren't made into issues first
Currently backtracks on #1107 due to second thoughts - see discussion

Author Checklist
All items are required. Please add a note to the item if the item is not applicable and
please add links to any relevant follow up issues.
I have...

[x] included the correct type prefix in the PR title
[x] added ! to the type prefix if API or client breaking change
[x] added appropriate labels to the PR
[x] targeted the correct branch (see PR Targeting)
[x] provided a link to the relevant issue or specification
[x] added a changelog entry to CHANGELOG.md
[x] included comments for documenting Go code
[x] updated the relevant documentation or specification
[ ] reviewed "Files changed" and left comments if necessary
[ ] confirmed all CI checks have passed

Reviewers Checklist
All items are required. Please add a note if the item is not applicable and please add
your handle next to the items reviewed if you only reviewed selected items.
I have...

[ ] confirmed the correct type prefix in the PR title
[ ] confirmed all author checklist items have been addressed
[ ] reviewed state machine logic
[ ] reviewed API design and naming
[ ] reviewed documentation is accurate
[ ] reviewed tests and test coverage
[ ] manually tested (if applicable)

Codecov Report

Merging #1141 (105dba8) into main (6c9be69) will increase coverage by 0.06%.
The diff coverage is 100.00%.

:exclamation: Current head 105dba8 differs from pull request most recent head 3240fac. Consider uploading reports for the commit 3240fac to get more accurate results

@@            Coverage Diff             @@
##             main    #1141      +/-   ##
==========================================
+ Coverage   43.82%   43.88%   +0.06%
==========================================
  Files          65       65
  Lines        8393     8402       +9
==========================================
+ Hits         3678     3687       +9
  Misses       4472     4472
  Partials      243      243

Impacted Files
Coverage Δ

x/leverage/client/tests/tests.go
100.00% <100.00%> (ø)

x/leverage/types/token.go
75.00% <100.00%> (+2.41%)
:arrow_up:

This PR as been split up:

Documentation (#1152)
Proto (#1159)
After those merge, I will take the remaining code in this PR (i.e. the implementation of MaxSupplyUtilization and related calculations), turn them into a small PR, and close this.

seams like we can close now to avoid confusions. You can keep your branch locally.


Add tasks

For all the OpenAPI specs I found on https://docs.databricks.com/dev-tools/api/index.html (there were a lot that didn't have openapi json/yaml.
from cookiecutter.main import cookiecutter
from prefect_collection_generator.rest import populate_collection_repo

extra_context = {
    "collection_name": "prefect-databricks",
    "collection_short_description": "Prefect integrations interacting with Databricks",
}
collection_template_url = "https://github.com/PrefectHQ/prefect-collection-template"
service_name = "Databricks"
urls = [
    "https://docs.databricks.com/_static/api-refs/account-2.0-aws.yaml",  # account
    "https://docs.databricks.com/_static/api-refs/queries-dashboards-2.0-aws.json",  # query dashboards
    "https://docs.databricks.com/_static/api-refs/history-2.0-aws.yaml",  # query history
    "https://docs.databricks.com/_static/api-refs/gitcredentials-2.0-aws.yaml",  # git credentials
    "https://docs.databricks.com/_static/api-refs/global-init-scripts-2.0-aws.json",  # global init scripts
    "https://docs.databricks.com/_static/api-refs/ip-access-list-aws.yaml",  # ip access list
    "https://docs.databricks.com/_static/api-refs/jobs-2.1-aws.yaml",  # jobs 2.1
    "https://docs.databricks.com/_static/api-refs/mlflow-2.0-aws.yaml",
    "https://docs.databricks.com/_static/api-refs/permissions-2.0-aws.yaml",
    "https://docs.databricks.com/_static/api-refs/repos-2.0-aws.yaml",
    "https://docs.databricks.com/_static/api-refs/token-management-2.0-aws.json",
]
routes = None
overwrite = True

cookiecutter(
    collection_template_url,
    no_input=True,
    checkout="prefect_defaults",
    extra_context=extra_context,
    overwrite_if_exists=True
)

populate_collection_repo(
    service_name,
    urls,
    routes=routes,
    overwrite=overwrite,
)

Generates all this!

Superseded by https://github.com/PrefectHQ/prefect-databricks/pull/6


go fix hkdf in JXcore or remove it

here's the code in question: https://github.com/jxcore/jxcore/blob/master/src/wrappers/crypto_extension.cc

@yaronyg - will do a quick doc on what needs remediation.. any more tests, etc.

See the email I sent you with a bunch of issues.

@yaronyg  - shouldn't this be an external / addon instead of being core to JxCore (or NodeJS)? We could still get the native speed if we follow an AddOn approach.  I've gone through nodejs add-ons and they're fairly straight-forward, especially with the 'nan' helper. Also, Async support if this is blocking the JS thread really should be there.
Also, what is the use case(s) and where in a codepath / call sequence is this happening? what are the performance targets? I ask as what makes the vNext hkdf method that @mpodwysocki had done not-performant enough to meet "some requirement"?
Is this called 1,000/second or is this something done per session intermittently?  If it's 400/ops or 800/ops in the pure JS version, why isn't that enough?
Also, of the variables (see the benchmark code below) what is static per session, server, etc. And what truly needs to be optimized. I ask as the boringssl sync'd here,
you'll see that the "keys", the "ikm", "secret" are all parameters and potentially CPU consuming as well. So, just doing "derive" may not be enough. Have we a benchmark that says "derive" is 90% of something of the overall time?
suite.add('HKDF test', function() {
  var pubKey = crypto.createECDH('secp256k1').generateKeys();
  var expirationBuffer = crypto.randomBytes(8);
  var sxy = crypto.createECDH('secp256k1');
  sxy.generateKeys();
  sxy = sxy.computeSecret(pubKey);
  HKDF('sha256', sxy, expirationBuffer).derive('', 32);
})

today we determined that the benefit of just doing HKDF.derive based upon the updated boringssl implementation is not enough and the hkdf.js implementation is to be used until a later point. Given the primary load is done in the steps prior (computesecret & generatekeys) we'd have to extend even further the native implementation.
At a later date will revisit, and also revisit potentially native addon vs. jxcore - core implementation.

Given that this code doesn't appear to be working too well, it hasn't been updated since the original commit, and it's no longer used by Thali, we have decided to delete it. We are essentially going to revert https://github.com/thaliproject/jxcore/commit/9cfbe48ec6a0a2cfd992fed9e33d1bcde2ede027

The revert has been committed https://github.com/thaliproject/jxcore/commit/a556067002a643fd695659f49de61980ef20f005


Feature/smhe 134 smart recipe g meter installation

https://ci.opensmartgridplatform.org/view/Nightly/job/OSGP_open-smart-grid-platform_nightly/1658/

https://ci.opensmartgridplatform.org/view/Nightly/job/OSGP_open-smart-grid-platform_nightly/1661/

https://ci.opensmartgridplatform.org/view/Nightly/job/OSGP_open-smart-grid-platform_nightly/1663/


ParcelAnnotationProcessor.process take lot amount of time.

Hi, from asyncprofiler i can see the ParcelAnnotationProcessor.process dominating my android build and cpu process.

it seems spend most of time to FileOutputStream.write.

Do you have any clue what may causing this ? my project contains lot of parcel annotated class, so i am not sure if it expected or not for that process taking that long.
Let me know if you need additional information. Thank you in advance.
I attached the flame chart below
flamechart.zip

This is interesting.  Could you give me a ballpark of how any parcel annotated classes you're working with?

Basically something like this: https://github.com/doniwinata0309/build-perf-test/blob/test/parceler/androidAppModule1/src/main/java/com/tes1.java
But some are more complex and extending from few parents, also contains field from custom object.
I just created 300+ dummy parcel class on this project
https://github.com/doniwinata0309/build-perf-test/tree/test/parceler
That will produce this flamegraph

android_build-6.7-flames.svg.zip
So it seems this process that taking so long
https://github.com/johncarl81/transfuse/blob/master/transfuse-support/src/main/java/org/androidtransfuse/transaction/CodeGenerationScopedTransactionWorker.java#L49

Right, ok... looking at it deeper, it looks like it's taking a long time to flush the FileOutputStream to disk.  Not sure if we'll be able to do anything about this.
A while ago we implemented incremental processing to the annotation processor - does it take this long every time, or only on the first clean build?

Our Incremental build doing pretty well,  we only got issue for clean/full build.
I see, it seems the huge number of input and disk IO speed that made it slower. Especially when there are several workers working in the same time. Normally 1 module may take 2 minute to complete, but when they are compiled in parallel (we set 5 workers can run in parallel) it will takes 4 minutes for each module to complete.
Do you think we do something with FileOutputStream  under JCodeModel library by modifying tranfuse library ? perhaps i can try some approach mentioned here: https://stackoverflow.com/a/20555164  or https://www.oracle.com/technical-resources/articles/javase/perftuning.html

Would buffering do the trick then? - maybe just wrap the given OutputStream here with BufferedOutputStream ?

possibly, i will try to modify it a little bit later. thank you for pointing that out.
If you also have some alternative please let me know, i will love to try it

I tried to modify it https://github.com/johncarl81/transfuse/blob/master/transfuse-core/src/main/java/org/androidtransfuse/gen/FilerSourceCodeWriter.java#L53
to this code:
int bufferSize = 8 * 1024;
OutputStream os = new BufferedOutputStream(
resource.openOutputStream(),
bufferSize
);
But the issue not fixed.
From this class:
https://github.com/johncarl81/transfuse/blob/master/transfuse-support/src/main/java/org/androidtransfuse/transaction/CodeGenerationScopedTransactionWorker.java#L49
But how FilerSourceCodeWriter used in that file ? It seems use CodeWriter instead FilerSourceCodeWriter right ?

ah sorry, it does use the FilerSourceCodeWriter, just realise it extending that class

Seems to be the same even i use buffer with size 8kb and 32kb.

There may be no way around it.  I'll try to fire it up on my machine to see how slow it is on different hardware.

https://github.com/johncarl81/transfuse/issues/233
There is new issue to adress this, we can try to use JavaFileObject.openWriter as alternative. I will it next week.

hi @johncarl81
https://github.com/johncarl81/transfuse/pull/234
this PR  solve my issue and my build is faster now. do you mind to check it later ? thanks

Can we close @doniwinata0309 ?

yes thank you. is it going to delivered on next release of parceler (1.1.14 i guess) ?

Yes


fix: incorrect env var in otelcol config

Incorrect env var for the honeycomb api key means we weren't exporting traces. Whoops.

bors r+


delete user account

Value Proposition
As a user, I want to delete my user account and all my data, so that the app has no information about me anymore.
Description

Acception Criteria

[ ] A delete button in UserProfile modal
[ ] After click on delete a modal asks "Do you really want to delete your account and all your data?"
[ ] Delete function deletes user information and regarding trips / destinations / todos
[ ] After deletion, user will be signed off an lead to the login screen

Tasks

[ ] Create a DeleteAccountButton component
[ ] Place the delete button inside the UserProfile component
[ ] Write a function that deletes all user data based on the email address
[ ] Write a delete-account-modal component with a button to acknowledge deletion
[ ] Assign the delete function, the modal, signout, and redirect to loginpage to the delete button

Hi Sebastian,
that's a nice feature dealing personal data.
Is there any personal data saved besides the email address and the name of the user?

No - i just save the email address. :)


Mapped Product Clicked to select_item

select_item contains the items event property (docs). select_content does not contain items (docs)
This is significant because the other GA4/Firebase ecommerce events such as:

view_item_list (docs)
view_item (docs)
purchase (docs)
etc

All contain the items property.
A fairly standard ecommerce flow is:

View Product List (view_item_list)
Select Product from List (could be select_item, but is currently select_content)
View Product Detail Page (view_item)
Add to Cart (add_to_cart)
Checkout Steps (begin_checkout)
Purchase (purchase)

All of the above steps are replicated with Firebase/GA4 events. All of those events, except for select_content have items, which map to the products array for the Segment implementation. select_content breaks a pattern and is preventing our products from appearing in Firebase/GA4 when our Segment Product Clicked event is fired.
We are proposing that Product Clicked gets mapped to select_item instead of select_content.
Docs:

Current Segment -> Firebase/GA4 Event Name Mapping

cc: @jordantannenbaum1

Thanks @vlee90 !  I'll make a release shortly.  Nice find, thank you for that!

Done.  See 1.3.3.


fixing --add-resourceMapping semantic convention support

Description
--add-resourceMapping was not generating proper semantic conventions based attributes causing namespace.name to be duplicated
Type of Change

[X] Bug Fix

Codecov Report

Merging #184 (6c55ed5) into main (04b8e96) will not change coverage.
The diff coverage is n/a.

:exclamation: Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more.
@@           Coverage Diff           @@
##             main     #184   +/-   ##
=======================================
  Coverage   29.53%   29.53%
=======================================
  Files          29       29
  Lines        3945     3945
=======================================
  Hits         1165     1165
  Misses       2693     2693
  Partials       87       87


Use a set version of ocamlformat

This is good practice to set the version and profile to use in .ocamlformat

Indeed it is, thank you.


Allow-list quarkus deprecation warning.

Until https://github.com/quarkusio/quarkus/issues/37072 is fixed so as to reduce test noise.
Related: #220

This also allow-lists the for the JFRPerf test since it re-uses the quarkus microprofile allow-listed lines in its setup.

FYI there is approved fix https://github.com/quarkusio/quarkus/pull/37130 (but not merged, so might be worth to wait a day to see how it goes)

Even better, thanks!

Fixed with https://github.com/quarkusio/quarkus/issues/37072 instead.


Improve HTML encode to handle single quotes

This library is great! I found that it doesn't HTML escape single quotes, so here's a small PR...

Thanks! I thought single quotes didn't really need to be escaped. Did you find a case where it's an issue?

Ok, thanks for the explanation. I'll review this in more detail tonight, but I can already say that:

You didn't implement the #else case in HtmlHelper
HtmlTemplate.Write needs the same changes

I'm thinking this should also handle chars outside of the ASCII range, let me take a quick look at that too

I don't think that's really required, everything handles Unicode now.

I released this in v0.4.3 - thanks! 🙂

Amazing, thanks @ltrzesniewski


Remove inactive users

Description
Describe what this change achieves
Issues Resolved
List any existing issues this PR resolves
Check List

[ ] A summary of changes made is included in the CHANGELOG under ## Unreleased
[ ] New functionality includes testing.
[ ] New functionality has been documented in the README if applicable.

Personally I've ignored most repositories except maybe 5-6 where I actually have done some participation or a bit of interest. I try to do a review occasionally when time permits. But I use chef less and less. It's up to you if you want me removed as I are not super active and that is completely understandable, but if you don't mind I can stay for the time being.

@damacus probably best to drop me, while I’d love to keep contributing, it’s just not in the cards for me for the time being.

@xorima and I have been chatting about how we can assign moderators to cookbooks without needing to be team members, something like home-assistant or k8s. Where people will be on a list and be notified via a bot.

Personally I've ignored most repositories except maybe 5-6 where I actually have done some participation or a bit of interest. I try to do a review occasionally when time permits. But I use chef less and less. It's up to you if you want me removed as I are not super active and that is completely understandable, but if you don't mind I can stay for the time being.

I'm in the same boat as @Raboo; there's a handful of repos we use and would be interested in maintaining as needed, but I could also do that on the outside and just watch those repositories and contribute fixes to issues as they arise.
There isn't a lot of movement in our Chef usage and will continue to shrink in the coming years as we continue to push more workloads to containers.

Ace, which repos are they?
We'll start makin a list
On 10 Apr 2023, 19:19 +0100, 'Jared Kauppila' via Board @.***>, wrote:

Personally I've ignored most repositories except maybe 5-6 where I actually have done some participation or a bit of interest. I try to do a review occasionally when time permits. But I use chef less and less. It's up to you if you want me removed as I are not super active and that is completely understandable, but if you don't mind I can stay for the time being.
I'm in the same boat as @Raboo; there's a handful of repos we use and would be interested in maintaining as needed, but I could also do that on the outside and just watch those repositories and contribute fixes to issues as they arise.
There isn't a lot of movement in our Chef usage and will continue to shrink in the coming years as we continue to push more workloads to containers.
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because your review was requested.Message ID: @.***>

@xorima and I have been chatting about how we can assign moderators to cookbooks without needing to be team members, something like home-assistant or k8s. Where people will be on a list and be notified via a bot.

There is a small downside to this, the contributors won't be eligible for Free Github Code Pilot.

So there's the rub, we probably would expect more contributions to be a core member at that point. We could show that as a benefit.
Right now, people are indeed getting Co-Pilot for very little contribution back to the org.

Ace, which repos are they? We'll start makin a list

It's not as big of a list as I would have thought:

aws
iis
java
tomcat
trusted_certificate

Calling all current members!
We're looking at removing current members who are no longer actively participating in code reviews. This mean we can increase our GitHub membership (to increase our runners)
As this is an opensource org, you can of course still contribute. However, right now we're probably just destroying your notifications. If you'd like to stay please let me know in this post by the end of the month (end of April 2023).
@TD-4242, @BackSlasher, @brianhays, @mengesb, @flaccid, @rshade, @RyanJarv, @iennae, @sbotman, @shoekstra, @teknofire, @Raboo, @snkutlu, @ev0ldave, @gsreynolds, @atheiman, @scopenco, @jeffbyrnes, @pschaumburg, @sinfomicien, @majormoses, @Stromweld, @brianbianco, @fernandoaleman, @zmaupin, @ryantiger658, @mohitsethi, @darwin67, @marcosvm, @mbaitelman, @mburns, @zimmerry, @limitusus, @EMH333, @nuclearsandwich, @jakauppila, @frank-m, @detjensrobert, @mvangoor, @stevendanna, @derekgroh

@damacus I'd like to stay on if that's okay 👍

It's ok to pr me out

I'd like to stick around and take responsibility for a few repos.
I am tweaking my role at work to allow for more open-source work as part of my job duties.

I've had a very hard time allocating for sous-chefs time but I have several major projects for https://github.com/sous-chefs/jenkins that are in my queue. If possible I would like to remain a maintainer.

I would like to stay, if that's okay.

Sorry I have not been active for a while, I do from time to time review stuff. As others I am in a similar situation where our chef usage is shrinking. Once my org is entirely off chef I think I will ask to be removed to save my inbox.

That sounds excellent @limitusus however I can see there haven't been any commits to that repository except for standard files for 2.5 years.
This is a cost-saving exercise for us, and whilst we love having a large community. A large community can still be helping out on Slack, and commenting on pull requests without needing to be in the organisation. 👍🏼


Question about metadata

Hi, thanks for this great work! May I ask if it is possible to share how the metadata being created? I read the paper about how the graph being created and wondering if this part of the code can also be released.
Thanks a lot for your help!

Hi @vincentlux  sure, I can do that. Just to confirm, by metadata, do you mean creating the graph based on the grid points?

Hi @ChanganVR thanks a lot! Exactly, I am wondering how to interact with the matterport original data to create grid points and the graph. Thanks for your help!

Hi @vincentlux, the scripts are added. Please check out these two files: https://github.com/facebookresearch/sound-spaces/blob/master/scripts/generate_matterport3d_metadata.py, https://github.com/facebookresearch/sound-spaces/blob/master/scripts/generate_replica_metadata.py

Hi @ChanganVR, got it, thanks a lot for your help!

Hi @ChanganVR, one more question, may I ask how you generated these grid points? Since I can't find it from the original matterport dataset, I am confused about how to get these grid points and the original graph.pkl (both are inputs to the generate_matterport3d_metadata.py). Again, thanks for your help in advance!

@vincentlux sorry about the late reply. The grid points are generated beforehand and need to be fixed. You just need to use the existing grid points to generate new graphs with the scripts I shared with you.

@ChanganVR  Wonderful work!


[Bug] Some query results from information_schema.columns are incorrect

Search before asking

[X] I had searched in the issues and found no similar issues.

Version
dev 1.0.1
What's Wrong?
MySQL [testdb]> show databases;
+--------------------+
| Database           |
+--------------------+
| abc                |
| testdb           |
...
MySQL [testdb]> select table_schema,table_name from information_schema.columns where table_schema='abc';
Empty set (0.05 sec)
What You Expected?
The result of following query is not empty.
select table_schema,table_name from information_schema.columns where table_schema='abc';
How to Reproduce?
Still have not...
Anything Else?
No response
Are you willing to submit PR?

[ ] Yes I am willing to submit a PR!

Code of Conduct

[X] I agree to follow this project's Code of Conduct

I can not reproduce the problem. Could you give more info to reproduce the problem?

This is an issue introduced by vectorization,  it just reproduce when  set enable_vectorized_engine=true;

I have reproduce the problem while set enable_vectorized_engine=true;. Thanks~
I will try to fix it. Please assign this issue to me.

I have reproduce the problem while set enable_vectorized_engine=true;. Thanks~
I will try to fix it. Please assign this issue to me.

done

@lide-reed @nextdreamblue the problem already fixed, please merge the codes and try again.


Make sure ODB driver is connected in extractor

The overflowDB driver allows setting an output filename via driver.dbfilename($filename), however, this is only picked up if connect is called. As for gremlin drivers, the extractor must therefore call driver.connect on the overflowdb driver.

Will merge once tests are green


bug found

Describe the bug
I have a script running instaLoder twice a day.
A few days ago apparently, it stopped working. I just noticed today. Checking the logs, indeed, it says the session file is not present (weird, because it always was).
When trying to launch instaloader (with --stories for example) it asks to type the password. Then is displays Fatal error: Login: Checkpoint required. Point your browser to [URL] - follow the instructions, then retry...
Problem: even if I open URL, click on "it was me", next time I run instaloader, the same thing happens.
To Reproduce
Try to launch an instaloader command requiring a login. An error happens, saying a checkpoint it required.
Open URL is given, and click "It was me"
Relaunch the command: the same thing happen
Expected behavior
After opening the URL and validating the login, it should work.
Instaloader version
4.3.2

@gs2713089 are you a spam bot? If not, in what way do you think copy-pasting #589 as a new issue, with a nondescript title such as "bug found", would be useful?

No, it got paste by mistake.


Emit error message on cerr << error_code

This helps makes sample code with errors a bit easier on the eyes.

cerr << error now emits the error message.
error_message(error_code) now returns a const char * since its primary use is in printf and C functions.
Because error_code lives in the simdjson namespace, you can now omit the simdjson:: prefix when calling error_message() because of C++'s namespace lookup.
Code that uses the json_parse (which returns an int) is unaffected. simdjson::error_message(int) returns const string & as before.
Added missing error message for DEPTH_ERROR
basictests now validates that all error codes are associated with error messages (and that they are paired with the correct message)

The readme didn't match my regex, but once I've made the next few changes I'm going to make a readme / tutorial with all the new happiness.


Relaxed stride checking in numpy 1.12 causes bottleneck unit test failures

Hi, this is what reproduces the problem on my machine (linux mint):
In [1]: import numpy as np

In [2]: import bottleneck as bn

In [3]: print('numpy:', np.__version__)
numpy: 1.12.0

In [4]: print('bottleneck:', bn.__version__)
bottleneck: 1.2.0

In [5]: a = np.ones((3, 2))

In [6]: np.sum(a[:, [1]]), bn.nansum(a[:, [1]])
Out[6]: (3.0, 1.0)

In [7]: np.sum(a[:, [1]].copy()), bn.nansum(a[:, [1]].copy())
Out[7]: (3.0, 3.0)

This has been hitting the xarray test suite on debian.
Thanks!

It works fine with numpy 1.11 which is what bottleneck 1.2 supports. So my guess is that you are using numpy 1.12. My second guess is that the unit test failures with numpy 1.12 is due to the change in numpy's relaxed stride checking. My third guess is that I don't understand what relaxed stride checking is. (That last one is not a guess.)
I've added your example as a unit test.

OK, I made the fix in master.

That was fast! Thanks a lot.

 Thanks for reporting and thanks for a simple example.

Consider issuing a bug fix release including this fix? I don't think it break any NumPy 1.11 users...

A bug in numpy 1.12.0 prevented me from making a bug fix release. But it should be possible now that 1.12.1 is out.
Ugh. The current blocker is here: #166.

See #168


Structure.ansisType vocabularies are not showing in MD docs.

Also Substrate.geneticType.

so ansis:type only (sp:Pedality-type
or sp:Artificial-aggregates-structure)
to type exactly 1 ?

issue 2.
For geneticType is this ansis:genesis? If so, already appears to be bound to enums within the schema eg subst:Rock-genesis-hardened-artificial - enums from table 37 in yellow book


MINOR separate throughput sensors for commit, process, and punctuate ops

commitTimeSensor, processTimeSensor, and punctuateTimeSensor are being used like timeSensor.record(latencyTime / numberOfOps), which measures the average latency for a batch of operations, but rate and total metrics were not being computed correctly. This PR adds a throughput sensor for each of commit, process, and punctuate operations which is used like thoughputSensor.record(numberOfOps).
Unfortunately I don't have time right now to add tests, but because I already had this change started I wanted to submit a PR so it wouldn't get forgotten about.
Committer Checklist (excluded from commit message)

[ ] Verify design and implementation
[ ] Verify test coverage and CI build status
[ ] Verify documentation (including upgrade notes)

@vvcephei


User agent

Hello, I noticed in the settings, there is an option "add a user agent because some streams don't work without a user agent", I don't know how to add and which user agent to choose, user agent of android tv or google tv ? it will be great to make things easier to add presets, a kind of list of different user agents of various and different devices so we can try and see which use agent works, thank you so much !

Hi, since there are many values and the user-agent can be anything, an arbitrary input field is used. To find the right option for the playlist, you need to understand what value the provider expects.

Very Interesting ! Thank you ! I will try to undestand which playlist i use and which user agent choose but for the moment, my playlist works normally and without problem and no needing to choose a uger agent for the moment........thank you again for your awesome efforts to make this wonderful software :) 🥇


Docker and linux host cleanup/teardown

Docker images are built with more friendly (but still unique) names derived from
the name of the image file.
Docker teardown and cleanup now works. When linux host exits, it will kill any
remaining docker processes (aka containers) and remove their images. This
involves obtaining the container-ID from docker, which we do using the -cidfile
option to docker run. Other minor fixes in docker factory.
Docker test script checks to make sure binaries are built as static. This avoids
the cryptic and misleading error messages from docker for non-static binaries.
Since tao run accepts docker args too, we can now name the demo_server image and
more easily link the demo_client image to it.
Renamed build_standalone.sh to build_static.sh. I have no idea what "standalone"
means, but a "static binary" is what we need for docker. That requires no netgo
or any other cgo code.

I agree that build_static is better than build_standalone. I named it that because if you read info online you might be misled into thinking that Go's binaries are already statically built. But that's not exactly true, hence the weird name for the incantation to make them so.

LGTM, other than my minor comments above

I addressed your concerns, rebased, and pushed to master.


Change button text for commenting and closing an issue at the same time

Close  #10468
Without SimpleMDE/EasyMDE, using Simple Textarea, the button text could be changed when content changes.
After introducing SimpleMDE/EasyMDE, there is no code  for updating the button text.

should we backport to v1.18?

I think it's fine to backport to 1.18, since there seems to be still many days before 1.19-release.

:trumpet: :robot:


Read any schematic

from any version
efficiently (no instanciation of pblock at load time)
see https://github.com/1b8/schematic and https://github.com/wtfaremyinitials/minecraft-schematic for inspiration

Could be useful too: https://minecraft.gamepedia.com/Schematic_file_format

It seems like the new standard for schematics is https://github.com/SpongePowered/Schematic-Specification
WorldEdit support it as read and write, while it support the old MCEdit schematic format only for reading:
https://github.com/EngineHub/WorldEdit/tree/master/worldedit-core/src/main/java/com/sk89q/worldedit/extent/clipboard/io
This new format use a palette and encode the version in the file, it is still nbt based.

I think it would be a good idea to have some sort of loader to load not just schematics, but any format and be able to load it into something like prismarine-world. It doesn't have to replace this, it can still be a low level loader but it would be much easier to consistently support different formats like construction, schematic, structure, mcstructure, etc. This is what I'm working toward for mceditor, so conceptually it would be done with a schematic world provider, and also an exporter.

@extremeheat yeah I think having an exporter to pworld (https://github.com/PrismarineJS/prismarine-schematic/issues/3) can be a good way to have a unified interface with other things.
pworld support block stuff of any size, and we can add stuff to it as we go (for example entities can definitely go to pworld)
we could support several formats here

thanks @Karang for implementing both sponge and mcedit formats
one possible next step is trying to parse a bunch of schematics from https://github.com/rom1504/minecraft-schematics-dataset to check if it works well
I expect we'll hit the problem of version detection and conversion between versions.
I'm not sure yet whether we should just group schematics per version or try to unify them all by converting to a single good version (with a bit of loss)

working on that now.
First I'm trying to do the nbt parsing for all schematics.
I found https://static.planetminecraft.com/files/resource_media/schematic/1829/old-fallen-castle-1532283303.schematic that crashes node when trying to parse. Investigating

https://github.com/Podshot/MCEdit-Unified/blob/master/pymclevel/schematic.py
https://github.com/EngineHub/WorldEdit/blob/master/worldedit-core/src/main/java/com/sk89q/worldedit/extent/clipboard/io/MCEditSchematicReader.java
^ references

basically done


Resulting code is not from Babel

The resulting Babel code is somehow transformed after the plugin ran.

I have been trying to figure out the problem but haven't found the solution yet. The relevant test ternary statement is const a = false ? false ? 1 : 2 : 3. After esbuild-plugin-babel's onLoad is called and the content is transformed, I log the results in the onLoad callback and get var a = false ? (false ? 1 : 2) : 3; for that line—which is good. I also double checked with babel.transform to make sure the extendscript preset works well.
But when I check the final esbuild output file, the brackets disappeared. I am somewhat aware that the plugins for esbuild aren't the last line of bundling process, so it probably modified the babel output and removed the brackets. I am not too familiar with what goes on in esbuild between calling the plugins and writing to output, but it would be helpful if you might know the answer.

See https://github.com/fusepilot/babel-preset-extendscript/issues/15
Possible solution: https://github.com/evanw/esbuild/issues/1010#issuecomment-803865232

I am able to make Babel's code the resulting output if I first put esbuild's output in a temporary folder, then have Babel watch and transform those files with extendscripts preset. However, if I want to include core.js polyfills (i.e. Array.includes), I will have to pre-Babel with esbuild-plugin-babel since it generates imports that needs to be bundled, then build with esbuild, then post-Babel again with extendscript.
One current problem I am running into right now is that core.js generates regex with unescaped forward slashes (/function\b(?:\s|\/\*[\S\s]*?\*\/|\/\/[^\n\r]*[\n\r]+)*([^\s(/]*)/), which throws Expected: ; when run. The main problematic portion I am testing with is var foo = /[/]/, which throws the same error due to the forward slash. I am not too familiar with esbuild or Babel, so if you know how to make either of them escape forward slashes in regex it would be helpful.

This is exactly why babel-preset-extendscript is used because core-js uses polyfills (which alter the prototype) and generates code that is incompatible with Extendscript.
I'm interested to see your core-js setup though, because it might lead to a better solution than babel-preset-extendscript. Could you make an example repo for it?

I am not too sure what you mean by more core-js setup. I put the following in plugins prop for esbuild:
babel({
  filter: /[^.text].js/,
  config: {
    presets: [
      ['@babel/preset-env', {
        modules: false,
        useBuiltIns: 'usage',
        corejs: '3.26'
      }]
    ]
  }
})

This is the pre-Babel that's supposed to help with polyfill. I am presuming the other incompatibilities between core-js and extendscript should be ironed out by babel-preset-extendscript in the post-Babel process. It could work if babel-preset-extendscript just escapes forward slashes in regex to make it work with core-js.
As I have dug deeper into babel-preset-extendscript, I realized it's an extension that's no longer maintained, and I have been encountering bugs that I personally don't have the know-how to fix (i.e. this most recent issue). When I have more time, I will look for other transpilers that transpile to es3 as potential replacement for babel-preset-extendscript. For now, I am planning to skirt around with my own poly/ponyfill, which means I can't use external npm packages since they sometimes cause issues with extendscript.


Bounding box format

Thank you for making your work public!
I have some remarks or noticed some things regarding the format of the bounding boxes of PubMed dataset.

Given that the bounding boxes following Pascal VOC format, i.e. x_min, y_min, x_max, y_max, why does the calculation of area here take the last two values? I get that it should mean calculating the width times the height but in this case these aren't it I suppose?
If that's the case it thus follows a wrong loss calculation shown here and here as in the train mode the target is in COCO format and in the eval mode it is still in the Pascal VOC format?

Can anyone point the misunderstanding I make above or clarify?
Looking forward for the discussion!

Looks like it gets fixed in the transforms here

I commented the area line out entirely and nothing seemed to break, so I'm assuming nothing accesses that key (coco seems to do its own area calc?)
As for the format in the loss function it seems like the normalize transform converts from xyxy to cxcywh - so the loss fn can convert back properly

It seems to be that way, though I still can't find where that is being handled.
Yes, you are correct, it's not very intuitive doing the conversion inside the normalize transform but I suppose it does the work.
Thanks for the discussion @HenryL27:)
Closing this issue for now.


Add camera to LIO-SAM to texture and color point cloud

Hey guys, would it be possible to add camera images to LIO-SAM to texture and color the point cloud( not just for visual odometry ), and if so what are the possible ways to go about doing it? Maybe there are already some ready packages to add the camera images in or it could be done with some software as post-processing after we've scanned and collected the cloud with a Lidar and IMU

Did you find anything else?

There are two main packages now regarding the question:

R3LIVE
FAST-LIVO


The footer is not aligned: should be present in the middle

Is your feature request related to a problem? Please describe.
The footer is not aligned: should be present in the middle
Describe the solution you'd like
I would like to shift it to the middle
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.

I can align it in the center.
Assign this issue to me I want to work on it.

@ShubhaSwarup your issue is solved by me

fixed issue #260


zero3_init_flag:true does not activate zero.init() for transformers models

System Info
- `Accelerate` version: 0.21.0.dev0
- Platform: Linux-5.15.0-1023-aws-x86_64-with-glibc2.31
- Python version: 3.10.11
- Numpy version: 1.24.3
- PyTorch version (GPU?): 2.0.1+cu118 (True)
- PyTorch XPU available: False
- System RAM: 1121.82 GB
- GPU type: NVIDIA A100-SXM4-80GB
- `Accelerate` default config:
        - compute_environment: LOCAL_MACHINE
        - distributed_type: MULTI_GPU
        - mixed_precision: bf16
        - use_cpu: False
        - num_processes: 8
        - machine_rank: 0
        - num_machines: 1
        - gpu_ids: all
        - rdzv_backend: static
        - same_network: True
        - main_training_function: main
        - downcast_bf16: no
        - tpu_use_cluster: False
        - tpu_use_sudo: False
        - tpu_env: []

Information

[ ] The official example scripts
[X] My own modified scripts

Tasks

[ ] One of the scripts in the examples/ folder of Accelerate or an officially supported no_trainer script in the examples folder of the transformers repo (such as run_no_trainer_glue.py)
[X] My own task or dataset (give details below)

Reproduction
I'm trying to activate DeepSpeed's Zero-3 zero.init() for transformers models with the accelerate launcher. Ordinarily, I would expect to see the following message in the logs when zero3_init_flag: true is set in the accelerate config (full config below):
Detected DeepSpeed ZeRO-3: activating zero.init() for this model

However, I'm finding this is not the case unless I use the default accelerate config and provide a path to a separate DeepSpeed config JSON using the transformers.TrainingArguments.deepspeed argument. Is some additional step required to activate zero.init() for transformers models with accelerate?
Steps to reproduce are provided below.

Create main.py with the following contents:

# main.py
from transformers import AutoModelForCausalLM, HfArgumentParser, TrainingArguments
from dataclasses import dataclass

@dataclass
class ModelArguments:
    model_name_or_path: str

def main():
    parser = HfArgumentParser((ModelArguments, TrainingArguments))
    model_args, training_args = parser.parse_args_into_dataclasses()
    model = AutoModelForCausalLM.from_pretrained(
            model_args.model_name_or_path,
        )

if __name__ == "__main__":
    main()

Create accelerate_ds3.yaml with DeepSpeed ZeRO-3 attributes:

# accelerate_ds.yaml
compute_environment: LOCAL_MACHINE
deepspeed_config:
  gradient_accumulation_steps: 1
  gradient_clipping: 1.0
  offload_optimizer_device: none
  offload_param_device: none
  zero3_init_flag: true
  zero3_save_16bit_model: true
  zero_stage: 3
distributed_type: DEEPSPEED
downcast_bf16: 'no'
machine_rank: 0
main_training_function: main
mixed_precision: bf16
num_machines: 1
num_processes: 8
rdzv_backend: static
same_network: true
tpu_env: []
tpu_use_cluster: false
tpu_use_sudo: false
use_cpu: false

Run the following command with a small model (note, no Detected DeepSpeed ZeRO-3: activating zero.init() for this model  message will appear in the logs):

ACCELERATE_LOG_LEVEL=info TRANSFORMERS_VERBOSITY=info accelerate launch --config_file=accelerate_ds3.yaml main.py --output_dir=scratch --model_name_or_path=EleutherAI/pythia-70m

As a point of comparison, now use the default accelerate config:

accelerate_default.yaml
compute_environment: LOCAL_MACHINE
distributed_type: MULTI_GPU
downcast_bf16: 'no'
gpu_ids: 0,1
machine_rank: 0
main_training_function: main
mixed_precision: bf16
num_machines: 1
num_processes: 2
rdzv_backend: static
same_network: true
tpu_env: []
tpu_use_cluster: false
tpu_use_sudo: false
use_cpu: false

and now run with the --deepspeed argument from transformers.TrainingArguments (now the Detected DeepSpeed ZeRO-3: activating zero.init() for this model message will appear in the logs):
ACCELERATE_LOG_LEVEL=info TRANSFORMERS_VERBOSITY=info accelerate launch --config_file=accelerate_default.yaml main.py --output_dir=scratch --model_name_or_path=EleutherAI/pythia-70m --deepspeed=deepspeed_z3_config.json

where deepspeed_z3_config.json is the following config:
{
  "bf16": {
    "enabled": "auto"
  },
  "optimizer": {
    "type": "AdamW",
    "params": {
      "lr": "auto",
      "betas": "auto",
      "eps": "auto",
      "weight_decay": "auto"
    }
  },
  "scheduler": {
    "type": "WarmupLR",
    "params": {
      "warmup_min_lr": "auto",
      "warmup_max_lr": "auto",
      "warmup_num_steps": "auto"
    }
  },
  "zero_optimization": {
    "stage": 3,
    "overlap_comm": true,
    "contiguous_gradients": true,
    "sub_group_size": 1e9,
    "reduce_bucket_size": "auto",
    "stage3_prefetch_bucket_size": "auto",
    "stage3_param_persistence_threshold": "auto",
    "stage3_max_live_parameters": 1e9,
    "stage3_max_reuse_distance": 1e9,
    "stage3_gather_16bit_weights_on_model_save": true
  },
  "gradient_accumulation_steps": "auto",
  "gradient_clipping": "auto",
  "steps_per_print": 2000,
  "train_batch_size": "auto",
  "train_micro_batch_size_per_gpu": "auto",
  "wall_clock_breakdown": false
}

As far as I can tell, _hf_deepspeed_config_weak_ref isn't being set when zero3_init_flag: true, but apologies if this is simply user error. I also wasn't sure whether to open this issue in accelerate or transformers, so please let me know if you'd like it moved.
Expected behavior
Seeing evidence in the logging that zero.init() is being activated for a model when zero3_init_flag: true. As far as I can tell, this isn't being activated since loading large models like Falcon 40B is making the CPU go OOM (which shouldn't happen with zero.init())

cc @pacman100

Hello @lewtun, the issue arises from the fact that the Accelerator object is created during Trainer object creation. The weakref is set during the Accelerator object creation. Please let me know if the above PR resolves the issue.

Thanks a lot for the explanation and quick fix @pacman100 ! I can confirm that using your PR branch resolves the issue


Clarify some threat model assumption when Falco is deployed in a K8s cluster

/area documentation
What would you like to be added:
Quoting the last security audit report of Jan 2023 (section 5.1 A note on threat actors , page 8):

Considering Falco might be installed on Kubernetes clusters nodes, it's safe to assume that most
users will be non-trusted unprivileged users, or diminished root users in containers. Indeed by
default, as root in Kubernetes pods, the default set of Linux capabilities is restricted, which means
root doesn't have all capabilities, like CAP_SYS_ADMIN or the ones allowing to reboot or remove
and add kernel modules. In addition, other security mechanisms limit the access to /proc or
/sys as root.

The plurality of "root status" in containers environment creates some confusion. Linux capabilities,
namespace and the various security modules allow to create more complex combination of rights.
However, considering the most used configuration it should be clarified that regular users on
the system, i.e., unprivileged users or containerized root users in Kubernetes pods are the main
threat. Root users on the host and root users in privileged containers should be out of the scope of
the threat actors. As a matter of fact, privileged containers with root users are almost equivalent
to root processes on the host: all except the process Linux namespace are disabled, all capabilities
are granted, virtual file systems are unmasked and LSMs are disabled. It's trivial to pivot from a
privilege container process to "complete root" on the host.

Update the Falco documentation to make the assumption "that most users will be non-trusted unprivileged users, or diminished root users in containers" explicit when Falco is deployed in a K8s cluster. In case that assumption wasn't valid for the adopter use case, the documentation should clearly state that, without additional strategies, a malicious actor may disable Falco, thus voiding its security value.
Why is this needed:
The current documentation might confuse our users and expose them to potential security issues. Making them fully aware of the intended threat model would mitigate such risk.

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cc @LucaGuerra @incertum

"that most users will be non-trusted unprivileged users, or diminished root users in containers"

I agree that improving the documentation on "users" and privileges in the cloud ecosystem is crucial. It is important to provide a clear distinction between Linux and audit users, including elaborating on the concept of sometimes users representing individuals with interactive access. Furthermore, yes it would be beneficial to clarify the meaning of "root" in the context of effective Linux capabilities and privileges, emphasizing the potential damage that could occur if such a user were compromised.
Lastly, while the quoted statement may hold true statistically, it does not necessarily encompass a generic threat model or reflect what each organization truly values. Ultimately, the focus should be on identifying and protecting the specific "crown jewels" of your organization, which can vary greatly from one organization to another.

... without additional strategies, a malicious actor may disable Falco ...

Kindly asking to clarify this?
Disabling Falco may not be as simple as one might think, depending on the deployment configuration. In fact, I believe it is easier for logging to be circumvented through obfuscation techniques or resource exhaustion tricks. Consequently, the community would greatly appreciate documentation that dives into this topic, providing insights into the challenges associated with disabling Falco and more importantly offering guidance on effective measures to mitigate the risks of logging evasion.

intended threat model

Linux security monitoring is unique in every organization because of factors such as the organization's environment, system architecture, risk profile, security objectives, compliance requirements, the evolving threat landscape, and available resources. These factors influence the specific security monitoring needs and approaches of each organization.
Therefore, an alternative approach is to educate the adopter on effectively using Falco and customizing it to align with their organization's requirements and threat model. This approach aims to set realistic expectations and provide additional educational resources beyond Falco's scope. It recognizes that Linux security monitoring encompasses various technologies that span multiple domains, and empowering the adopter with knowledge in these areas can lead to better utilization of Falco and overall security monitoring practices.
Technologies and domains Falco touches: Linux kernel and eBPF, Offensive security, Cyber defense, Incident response, Production deployment and operationalization, Performance optimization and stability, Data pipelines and scale, Big Data and Data Science.

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/help
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@leogr:
This request has been marked as needing help from a contributor.
Please ensure the request meets the requirements listed here.
If this request no longer meets these requirements, the label can be removed
by commenting with the /remove-help command.

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

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/close

@poiana: Closing this issue.

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Allow import VMs from site other than github.com

I would like to import VMs from OneDrive via utm://downloadVM?url= When I do this, UTM says, failed to parse download URL

That’s not an UTM issue. OneDrive probably doesn’t allow for direct downloading. You’re probably downloading a webpage preview.

It is a raw file. I have checked.

 The URL just doesn't show it.


Fix error in template - too long custom details key

Fixes #
Proposed Changes

@Amitbergman : I fixed it in parallel in another PR. You can delete this one. Thanks for helping out!


MFA Multi-factor authentication description is not updatable

When MFA for the user is enabled, dialog box to ask for code looks like below:

How do I update the Multi-factor authentication description? I searched for it in casdoor admin panel as well as in documentation but could not find any way to update it.

according to

it is a fixed text and cannot be change

according to

it is a fixed text and cannot be changed

@dacongda This is going to be big problem for any production system then. Right? Just setting the description to empty would make more sense than current one.

you are right, we will try to remove it or make it editable in the future

Thanks for the super fast turn around on this issue @hsluoyz @dacongda .

@hsluoyz @dacongda Thank you for making the change so quickly!  We're really impressed.  The current prompt, however, is a little confusing for our users as the next step in the MFA process is to click "Send Code" - users don't yet have an authentication code.  We are wondering if you could please change the prompt to this instead:
"You have enabled Multi-factor Authentication. Please click Send Code and follow the prompts to finish your login process"
Thanks

I can raise the PR for the same if that helps.

@maknahar it can be other ways than "Send Code"

But in TOTP mode, there's no send button for user to click, maybe you can check the MFA mode and show relevant description, anyway, you're welcome to contribute.

@dacongda @hsluoyz I have raised this PR https://github.com/casdoor/casdoor/pull/3280 to handle this. For TOTP based MFA description remain as is. For SMS/Email based MFA, message is updated to inform user that an action is required before they could enter the code.


fix(tpc): use mlly to resolve third-party-capital

🔗 Linked issue
fix #135

❓ Type of change
hey this PR fix an issue with third-party-capital. Since tpc composables are generated in .nuxt, we need to resolve the path of third-party-capital from @nuxt/script within the users node_modules as users won't install it.

[ ] 📖 Documentation (updates to the documentation or readme)
[x] 🐞 Bug fix (a non-breaking change that fixes an issue)
[ ] 👌 Enhancement (improving an existing functionality)
[ ] ✨ New feature (a non-breaking change that adds functionality)
[ ] 🧹 Chore (updates to the build process or auxiliary tools and libraries)
[ ] ⚠ Breaking change (fix or feature that would cause existing functionality to change)

📚 Description

Thanks!


Faint triangular (and other) markers show on flatmap.

Release v2.2.10 of the viewer shows faint triangular markers, as seen here -- all is well with release v2.2.9.

This is in fact due to mapmaker creating a geometric element for the SVG group that has the nodes.


Move file processing logic from cli into core

Current file processing logic and config make no sense to exist in the cli.
We should have an abstraction for the output format - currently, this is an only string and support different file layouts inside graphback source code.
For example:
Default file layout - can contain current folder structure
GraphQL Modules file layout can contain graphql modules implementation
Runtime layout - do not persist files - allows using solution at runtime.

@MStokluska doing some spike about this.

Outdated


KAN overrides nn.Module train()

Hi,
KAN overrides the base function train (link), and uses it for a different purpose. Someone using KAN, assuming that it acts the same as any nn.Module, will encounter an error when calling model.train() as they usually would.
This will lead to issues when combining KAN in a larger module with batchnorms and dropouts which need the model.train() call.
For example:
import torch.nn as nn
from kan import KAN

device = "cuda"

model = nn.Sequential(
    nn.Conv1d(3, 8, 3),
    nn.BatchNorm1d(8),
    nn.Dropout1d(),
    # ...
    KAN(width=[8, 8, 3], grid=5, k=3, device=device)
)
model.to(device)

print(model)

for epoch in range(10):
    model.train()
    # train loop
    # ...

    model.eval()
    # eval loop
    # ...

This throws an error:
File "C:\Users\todos\PycharmProjects\kan-examples\train_error.py", line 18, in <module>
    model.train()
  File "C:\Users\todos\anaconda3\envs\torch_opf_clone\lib\site-packages\torch\nn\modules\module.py", line 2394, in train
    module.train(mode)
  File "C:\Users\todos\anaconda3\envs\torch_opf_clone\lib\site-packages\kan\KAN.py", line 881, in train
    batch_size = dataset['train_input'].shape[0]
TypeError: 'bool' object is not subscriptable

Thanks, that's a very good point! I think it's important to make KAN easily combined with other modules. In that case, it might be reasonable to change  the train method to a different API? Any suggestion? Maybe trainKAN?

Also, the grid update technique is essential in KAN training. In this case, I guess it's more advisable to define a model as a class and write one's own train() method to make sure KAN grids are updated properly.

You're gonna be more familiar with the use, but here's my take:
A quick fix would be to just rename the class method, whatever seems reasonable (not training though, because it's a property of nn.Module  (link)).
However, I think it's better to have it as a standalone function, more as an example, because, as it is now, it's highly specific to your use case (e.g., progress bar, saving plots (I see it can be disabled, but still)). Anyone else is going to want to implement their own training loop.
As for update_grid_from_samples, I think a good training example script and docs can emphasize it's importance, and then the user can call it himself as in model.update_grid_from_samples(...). What do you think?
Here's an example script from a different library which has a model with a function similar to update_grid_from_samples (see this line). As long as the example clearly shows the usage, the user can do it himself.

Thanks! Yeah my concern is that people just call the train() method for the combined model, finding it's not working well. I agree with you that it'd be great to have an example to show how users can define their own new class (instead of using nn.Sequential) and define their own train method. If you are working on that example (like the one you showed above), feel free to PR to upload it to tutorials, but no pressure! :) Also no need to worry about styles (which I can take care of later).

I would suggest renaming the train method to something like fit as the logic of the train clashes with the nn.Module's train

I have encountered some difficulties when trying to train KAN as a module of the combined model. Looking forward to the example you've mentioned!

@KindXiaoming  and @GentleFiona I believe your issues are not related to the problem raised in this issue, kindly open another issue as to not confound this problem with something else

Can you please tell me if this issue is resolved? I introduced KAN into my model to replace MLP which produced this error.

Sorry too many demos used model.train() as the API, so it is good amount of work to change it to some other API (plus, some users are already familiar with using train() instead of say fit()). It is advised to write your own training loop for the whole model. Or if you don't care about interpretability that much, you may use other repos which may not need grid update, e.g., ChebyShev KAN.

Sorry too many demos used model.train() as the API, so it is good amount of work to change it to some other API (plus, some users might be already familiar with using train() instead of say fit()). It is advised to write your own training loop for the whole model. Or if you don't care about interpretability that much, you may use other repos which may not need grid update, e.g., ChebyShev KAN.

Thanks

Yes,of course ,i'm struggling in this problem too!!and i use this https://github.com/Blealtan/efficient-kan/tree/master to success my workflow(resnet3d+kan),but i'm not sure that this is a perfect modification or not.May be i need to learn more theoretical stuff.

The same problem affects model.eval(), too. I wonder how it is possible to change a model that contains KAN layers into eval mode to avoid dropouts. Will that be solved as part of the fix in #205?

The update today (version 0.2.0) changed model.train() to model.fit()

@KindXiaoming  please close this issue


Extract Sulu configuration

Move the sulu configuration into an own file, so that we can avoid merge conficts. Should be handled at composer install like parameters.yml.dist

i think i have done this! @danrot reopen if you think its not enough!


Specify shade plugin version

Some training attendees had problems with running the project in Idea IDE because of "missing" shade-plugin.

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

Covered already in master, closing.


google drive tool: new endpoint for google drive tool auth deletion

Description
This PR adds a new endpoint which handles deleting google drive tool auth.
HTTP Request Method: DELETE
Path: /v1/tool/auth
Request Body:
{
    "tool_id": "<tool_id_to_be_deleted>"
}

Note that currently, the only supported tool_id is google_drive.
Expected Response:
{
    "status": "success"
}

Issue
fix TLK-875
Dependencies
None
TODO

[ ] Add tests and docs: Please include testing and documentation for your changes

AI Description

This PR introduces a new endpoint for deleting tool authentication and updates the GoogleDriveAuth class to include a delete_tool_auth method.
Summary
The changes in this PR allow for the deletion of tool authentication, specifically for Google Drive. The new endpoint, /tool/auth, is added to the router in src/backend/routers/auth.py. It defines the logic for removing the corresponding ToolAuth from the database for the requesting user. Additionally, the GoogleDriveAuth class in src/backend/tools/google_drive/auth.py is updated to include a delete_tool_auth method, which handles the deletion process.
Changes

Introduce a new endpoint, /tool/auth, for deleting tool authentication.
Implement the delete_tool_auth method in the GoogleDriveAuth class.

The new endpoint currently returns {"status": "success"} on successful tool auth deletion. Should it return anything else?
CC @tomtobac / @knajjars / @BeatrixCohere

Codecov Report
Attention: Patch coverage is 13.15789% with 33 lines in your changes missing coverage. Please review.

Project coverage is 76.86%. Comparing base (b05ce43) to head (ea3e8e2).

Files
Patch %
Lines

src/backend/routers/auth.py
12.90%
27 Missing :warning:

src/backend/tools/google_drive/auth.py
14.28%
6 Missing :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #654      +/-   ##
==========================================
- Coverage   77.10%   76.86%   -0.24%
==========================================
  Files         238      238
  Lines       10455    10491      +36
==========================================
+ Hits         8061     8064       +3
- Misses       2394     2427      +33

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:loudspeaker: Have feedback on the report? Share it here.


Update auth library and release

gax: 1.2.1
gax-grpc: 0.18.1
auth: 0.7.0

Codecov Report

Merging #320 into master will not change coverage.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master     #320   +/-   ##
=========================================
  Coverage     69.81%   69.81%
  Complexity      355      355
=========================================
  Files            73       73
  Lines          1925     1925
  Branches        157      157
=========================================
  Hits           1344     1344
  Misses          513      513
  Partials         68       68

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LGTM


help for environment:merge is vague

Following on from #421, the merge command also has vague help.

"merge" sounds similar to "sync" - are these operations related at all? If so, what's the difference?
"merge" is a git term, sync isn't. Is environment:merge about merging code? The help doesn't mention code, branches, tags or other git refs.
The example talks about a "parent" but doesn't elaborate. What does parent refer to?
Does this move anything to/from my development laptop?
Do databases change as a result of this command?

I haven't dared to run environment:merge or environment:sync yet!

This commit is in version 2.13.1, by the way:
https://github.com/platformsh/platformsh-cli/commit/d3118dc3e2c509378d1c6bd6bb037b7d9a929ef9


Avoid importing from solid-bootstrap-core top-level?

Currently the largest shippest-to-client NPM module in my app is solid-bootstrap-core.  Notably, the entire 48kB NPM module is being included, partly because I'm using Meteor as my bundler, which (still) doesn't have tree shaking.  I'm importing the specific files I need from solid-bootstrap, but a bunch of that code has `import ... from "solid-bootstrap-core".  (I see about 40 instances of this.)
Would you be amenable with replacing this imports with the specific file needed, e.g. "solid-bootstrap-core/esm/Overlay"? This should only help tree-shakers, and would be great for use in Meteor.

Hey Erik.  For sure open to a PR for this  ...I appreciate it.  TBH if you want to take the lead on this project you are most welcome to.

Cool, thanks! I'll take a stab at this. And happy to help maintain, though "lead" may be a bit strong. :-)


Update pyqt to enable dark mode (macOS)

Dark mode on macOS mojave should be enabled in [pyqt 5.12][https://www.qt.io/blog/2018/11/08/qt-macos-10-14-mojave].

Actually the version seems right, but need to activate some flags to enable dark mode.


test: Cypress - Bug Fix 21191

Description

Automated bug - https://github.com/appsmithorg/appsmith/issues/21191

Type of change

Regression bug automation

How Has This Been Tested?

Cypress test runs

Checklist:
QA activity:

[ ] Test plan has been approved by relevant developers
[ ] Test plan has been peer reviewed by QA
[ ] Cypress test cases have been added and approved by either SDET or manual QA
[ ] Organized project review call with relevant stakeholders after Round 1/2 of QA
[ ] Added Test Plan Approved label after reveiwing all Cypress test

/ok-to-test sha=3c6d970

/ok-to-test sha=1895cdf

/ok-to-test sha=8ed064f

/ok-to-test sha=7e4c1de

/ok-to-test sha=4bf4b80

/ok-to-test sha=71c1a63


Updated metric_type schema to support custom metrics

metric_type can be alphanumeric characters and it can also have
underscores

LGTM


Pin Conda and Python versions when setting up Conda environment

This prevents Conda from automatically trying to update itself or Python when installing new packages. These updates can break the Conda installation.
For an example which is currently broken, try telling conda to install Jupyterhub and then interacting with conda on the command line.
gcloud dataproc clusters create conda-jupyterhub --initialization-actions=gs://dataproc-initialization-actions/conda/bootstrap-conda.sh,gs://dataproc-initialization-actions/conda/install-conda-env.sh --metadata 'CONDA_PACKAGES="jupyterhub"'
gcloud compute ssh conda-jupyterhub-m
conda
Traceback (most recent call last):
File "/opt/conda/bin/conda", line 7, in
from conda.cli import main
ModuleNotFoundError: No module named 'conda'

/gcbrun


add allow_pickle for reuters

Starting with numpy 1.16.3 the default of allow_picke in np.load has changed from True to False.
This means that all occurrences of
with np.load(path) as f:

in Keras datasets need to be changed to
with np.load(path, allow_pickle=True) as f:

otherwise we get
ValueError: Object arrays cannot be loaded when allow_pickle=False

See also https://github.com/tensorflow/tensorflow/commit /79a8d5cdad942b9853aa70b59441983b42a8aeb3 which did this for imdb.
This PR does this for reuters.

Hi, any news on this? Thanks!

@skeydan thank you for your contribution , can you please add some description to the PR why this change was submitted ?

Sorry - description updated :-)

you're welcome :-)


fix: update link to the create-openapi-repo

Changes the link (and its text)to the create-openapi-repo as the repository was transferred to the Redocly organization and renamed.

Thanks!


Improve Slack output

Right now it's quite basic, let's aim for something like this:

It will require some app rearchitecting, and some features in quoad, like https://github.com/outillage/quoad/issues/3

Working on it right now


CheckBox has some unneeded member variables (that should be private)

CheckBox has some unneeded member variables (that should be private)

Fixed in #84


[ci] Run analyze with minimum resolved packages

Since our CI always runs on clean projects, they always get the latest resolved versions of dependencies, so won't catch the easy-to-make mistake of introducing use of a new dependency API without updating the minimum version of that dependency to the version that introduced that API.
This adds a new --downgrade flag to analyze to run flutter pub downgrade before analyzing, and adds a new CI step to run in that mode. (This won't catch runtime mistakes, but as with the "legacy analyze" runs this catches the most common type of mistake at a fraction of the CI cost of running all tests again.)
Also fixes all the existing violations flagged by the new step.
Fixes https://github.com/flutter/flutter/issues/108992
Pre-launch Checklist

[x] I read the Contributor Guide and followed the process outlined there for submitting PRs.
[x] I read the Tree Hygiene wiki page, which explains my responsibilities.
[x] I read and followed the relevant style guides and ran the auto-formatter. (Unlike the flutter/flutter repo, the flutter/plugins repo does use dart format.)
[x] I signed the CLA.
[x] The title of the PR starts with the name of the plugin surrounded by square brackets, e.g. [shared_preferences]
[x] I listed at least one issue that this PR fixes in the description above.
[x] I updated pubspec.yaml with an appropriate new version according to the pub versioning philosophy, or this PR is exempt from version changes.
[x] I updated CHANGELOG.md to add a description of the change, following repository CHANGELOG style.
[x] I updated/added relevant documentation (doc comments with ///).
[x] I added new tests to check the change I am making, or this PR is test-exempt.
[x] All existing and new tests are passing.

@bparrishMines Follow-up from discussion today. It did require minor tool changes because we have to run downgrade in every package individually.


[xcodeproj] Header search paths for standalone and workspace build.

I have actually not been able to build the product of the xcode project in this repo, but it was quite evident that the relative paths weren’t updated to reflect the project restructuring you recently made. Can you verify that it builds and explain to me how it is supposed to be build in a standalone fashion?

Fixes the build when the project is included in a Xcode workspace that also includes React. This applies to CocoaPods installations of React as well.

Bump.

Closing, very old, not sure it still applies.


Introduce new scheduling protocol

The new scheduling protocol includes a bunch changes:

activations are scheduled without trigger, there is only a simple activation with the current tick
completions only include the ActorRef of the actor that is completed (no more trigger id) and possibly a new tick

Some minor side whish that may could be added here: In all_tbw we actually have some fixed timeOut for SimScheduler which is hard coded to ten minutes which could/should be supported by config to make this adaptable.

@danielfeismann I believe that timeout was for debugging purposes anyways, since after that time passed, scheduler state was dumped

@sebastian-peter True, this one only logs. I miss interpreted this. There is another timeout with the same duration...


Removing score threshold parameter of faiss _similarity_search_with_r…

Removing score threshold parameter of faiss _similarity_search_with_relevance_scores as the thresholding part is implemented in similarity_search_with_relevance_scores method which calls this method.
As this method is supposed to be a private method of faiss.py this will never receive the score threshold parameter as it is popped  in the super method similarity_search_with_relevance_scores.
@baskaryan @hwchase17

in fact, do we even need to implement _similarity_search_with_relevance_scores on FAISS at all, since it's now also implemented on base class

in fact, do we even need to implement _similarity_search_with_relevance_scores on FAISS at all, since it's now also implemented on base class

Agreed @baskaryan , I also feel the same that we do not need it. But I thought for the future, we can keep it if some additional functionality needs to be developed or added.

@baskaryan @hwchase17 Tagging for higher visibility.


Is VIRTUAL CONTEXT a good description of MEMGPT ?

Just to be sure: so MEMGPT uses the principle of PAGING, that is used in Operating Systems to circumvent the limitation of RAM size, when a much larger memory size is needed? Which is called VIRTUAL MEMORY. In the case of LLMs we could call it VIRTUAL CONTEXT ?

Yep that's correct!


docs(firebase_auth): Removed duplicates; fixed typos; removed "unnecessary use of a null check"

Description
Docs:
Fixing typos, removing duplicates
Code:
Removed the "unnecessary use of a null check". Actually, it wasn't me but a compiler forced me to do it!
Checklist
Before you create this PR confirm that it meets all requirements listed below by checking the relevant checkboxes ([x]).
This will ensure a smooth and quick review process. Updating the pubspec.yaml and changelogs is not required.

[X] I read the Contributor Guide and followed the process outlined there for submitting PRs.
[X] My PR includes unit or integration tests for all changed/updated/fixed behaviors (See Contributor Guide).
[X] All existing and new tests are passing.
[X] I updated/added relevant documentation (doc comments with ///).
[X] The analyzer (melos run analyze) does not report any problems on my PR.
[X] I read and followed the Flutter Style Guide.
[X] I signed the CLA.
[X] I am willing to follow-up on review comments in a timely manner.

Breaking Change
Does your PR require plugin users to manually update their apps to accommodate your change?

[ ] Yes, this is a breaking change.
[X] No, this is not a breaking change.

I am not sure why some tests failed to be honest. I would like a help from somebody, I just changed the text in the docs mostly


Higher resolution videos

This includes two different things

[ ] Being able to export current videos at a higher resolution. Albeit the sprites are low-res, the letters could be better seen
[ ] Use sprites from HD version and generate HD-like videos

Upstream: https://github.com/micah5/ace-attorney-reddit-bot/issues/24

I can help on the HD Sprites and UI, I have some assets from the Steam version ripped from the game.

Hi!
Thanks for your offer!
Could you upload them/provide a link to them in any hosting service?
Thanks

Sure! It may take some time to find them in the files (I don't remember the file names, but I do have tools to extract the files), do you have Discord so I can send them there once I find the files?

Sure, contact me on Luigi003#9689


Move to content type

cc @wvanbergen

Not sure if I like this, it feels a bit over-engineered to me.

The Accept header is always the same, so I don't see the point of making that dynamic. A constant is perfect for this.
For the Content-Type header, serialization format and version are always the same. The only thing that differs is the embedded format, which can only have to values. When the value differs, the handling implementation** of it needs to be different as well, so you can just as well use a static constant there as well.

(** e.g. produce_avro and produce_binary need to be implemented separately anyway.)

Yeah I'm going back on this, I wanted to allow changing version etc but overkill


Propose adding Plane.isometric to built-in planes

Currently there are a number of built-in planes like Plane.XY, YZ, front, top, etc. I propose adding a Plane.isometric built-in plane that will (1) allow aligning objects to the viewers isometric view direction (tested against OCP CAD Viewer and CQ-editor) (2) Provide access to a less trivial plane definition that could help improve robustness of unit tests (none of the Plane.isometric axes align with the global XYZ axes). There may also be some benefits to the 2D exporters, since providing an easier-to-access isometric view direction could be helpful for e.g. "more intelligible" 2D representations of 3D objects.

Looks good to me.  Thanks!


Transparent header for appBar

Describe the feature in detail (code, mocks, or screenshots encouraged)
I would like to know if there is any possibility to make the appBar transparent or translucent so that you can see the page content through it. I'm using 'background="bg-transparent"' as prop, but this only makes the background colour change to the same colour as the background, however the page content is hidden behind the menu once you scroll. I would like to know if it is possible to reduce or eliminate this opacity.
What type of pull request would this be?
Enhancement
Provide relevant links or additional information.
No response

In theory, that should already work.
Are you using the AppBar together with the AppShell and if so, in which slot did you put your AppBar?

Yes, something like this code in my root +layout.svelte
</svelte:head>
<Modal components={modalRegistry} />
<Toast position="t" />
<Drawers />
<AppShell>
<svelte:fragment slot="header">
    <Header />
</svelte:fragment>
  <div class="grid place-content-center h-full sm:py-6">
    <slot />
  </div>
</AppShell>

And then in my component 'Header' using app bar
<AppBar background="bg-transparent" slotTrail="!space-x-2">
Is there any way to get a transparent background?

What you're doing should make the AppBar transparent, as desired. But what you may be seeking is a sticky header that also overlaps the page contents. See the docs here for details on this. It requires moving the AppBar to the AppShell pageHeader slot and setting some additional CSS styling:
https://www.skeleton.dev/components/app-shell#using-an-app-bar

Not exactly, my intention is not a sticky header, it's to make the page visible through the appBar, as a transparent header, actually it takes on the colours of the background, but the content is covered by the header.
Thank you in any case for your answers :)

@gzuuus then again, what you provided should work. Here's a quick example with/without the transparent background prop set:

@gzuuus then again, what you provided should work. Here's a quick example with/without the transparent background prop set:

Yes, but I have this behaviour, you can see how the content is cut from the header.

@gzuuus this is because it's in the header slot which is fixed ABOVE the page content. It'll never overlap the content - which is why you see that harsh looking line. This is why we suggested migrating to the sticky header approach. By default the sticky header will be above the content, but as you scroll it'll overlap while remaining affixed to the top.
Once again, I'd highly encourage you follow the directions for this linked above:
https://www.skeleton.dev/components/app-shell#using-an-app-bar
We use this setup for the Skeleton Labs website, though with a semi-transparent AppBar rather than one that's fully transparent:
https://www.skeletonlabs.co/


Python3 Output

Is anyone still maintaining this project? Got it working great on python 3 for INPUT, very little latency. Broadband running at 70mbps dl, 18mbps ul, almost full speed. However, on OUTPUT, there is a long delay before anything happens, and then the best I can get is 4mbps dl, 3mbps ul. This is running example code. Anyone have any ideas? Anyone still reading these? Appears to be the same for me with python 2 as well.

May be my laptop (although no idea why). No problem on server.


[BUG] Submit-PnPSearchQuery fails when using the "-All" parameter

All of a sudden when making a Submit-PnPSearchQuery with the "-All" parameter it throws the following error:
We didn't understand your search terms. Make sure they're using proper syntax.
Here is my module information, and the operating system is Windows
ModuleType Version    Name                                ExportedCommands

Manifest   1.12.0     PnP.PowerShell                      {Add-PnPAdaptiveScopeProperty, Add-PnPPropertyBagValue, Add-PnPSiteClassification, Copy-PnPFolder...}
Manifest   1.10.0     PnP.PowerShell                      {Add-PnPAdaptiveScopeProperty, Add-PnPPropertyBagValue, Copy-PnPFolder, Export-PnPClientSidePage...}

We are seeing similar issue, we are using SP API's direct though. Don't think it's a PNP issue, looks like it's SP API. Have lodged a MS support request
Case Details Search API Failing (#2406040030001324)
This is the API endpoint we are hitting (just in case we have a MS engineer lurking here)
POST
https://xxx.sharepoint.com/sites/xxx/_api/search/postquery
Request
<hidden, has sensitive info>
Response
{
"odata.error": {
"code": "-1, Microsoft.Office.Server.Search.REST.SearchServiceException",
"message": {
"lang": "en-US",
"value": "We didn't understand your search terms. Make sure they're using proper syntax."
}
}
}


Huggingface Demo I implemented

Guys , I implemented your  awesome work to HuggingFace as a demo . People can try your work . You can reach me for any edit
https://huggingface.co/spaces/SerdarHelli/diffusion-point-cloud

That's cool!!!
Thank you for your contribution! I have added a link to it on the README and my homepage.
Thanks again!


Fixed path precedence for _run command

Is there anything that have fixed by this change?

I updated ubuntu version for some gem_bundler tests and they failed.

I updated ubuntu version for some gem_bundler tests and they failed.

There are two bundlers in ubuntu?

The problem binary is rake. Think one is installed as dependency with ruby-dev package inside /usr/bin and another inside /usr/local/bin when updating gem.

Hopefully this will not break many things.


feat: [FileCollection] add function to reatain multiple patterns

Description
Supersedes #8953
Add a method to FileCollection that accepts an array of strings to retain multiple patterns in the file collection.
Checklist:

[X] Securely signed commits
[X] Component(s) with PHPDoc blocks, only if necessary or adds value
[X] Unit testing, with >80% coverage
[X] User guide updated
[X] Conforms to style guide

LGTM! Thank you.

Thanks. I assume adding a similar function for removePattern()  would just be for convenience sake since removePattern() can be called consecutively to remove multiple patterns, opposed to calling retainPattern consecutively.


HMR is not working when base option in vite.config.ts is not '/'

  export default defineConfig({
-   base: '/',
+   base: '/elsewhere/',
    ...

HMR is not working when base option in vite.config.ts is not '/'.

Duplicate of #18, fixed in main, will be available in next patch (probably in a few days)!


handling-exceptions python tutorial

Populate exceptions/handling-exceptions.py with a tutorial and challenge.

Hello! Can you assign this to me?

sure @jbolanosc


Greedy LSA (a new idea for contribution)

Hi, Thank you for your interesting work!
I want to integrate your work with Greedy Layer-Wise Training of Deep Networks. Do you have any comments and ideas for its integration?

Dear @Obile19
Thank you for comment!
That's great. All you need to do is change the layer module lines
You can contact me If you need assistance during with the integration process.


WIP FIX Dispatcher synchronization

Aims to address https://github.com/paris-saclay-cds/ramp-board/issues/154
Fix by @glemaitre
Not sure how to unit-test this.
With this fix applied once a submission is sent there is a delay of 10-15 s for the server to respond. I'm not sure if it is related.
@glemaitre feel free to take over this PR..

Hello @rth! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file ramp-frontend/ramp_frontend/views/ramp.py:

Line 431:80: E501 line too long (84 > 79 characters)

Yep I think it was a quick hotfix but we should have something better.
I did not have time to commit it yet but basically we should copy the file within the function add_submission. Like this the copy will happen before the commit to the database and it will be safe.
Setting the state is a bit brittle. If you are not aware that you set the state of the submission, it could be tricky to know about it.

I did not have time to commit it yet but basically we should copy the file within the function add_submission. Like this the copy will happen before the commit to the database and it will be safe

Can we not let the dispatcher create that file instead? That would remove the need for syncronization between the DB and the file system. Related to the discussion in https://github.com/paris-saclay-cds/ramp-board/issues/188

Yep but we need to store the file into the database. This is a better long term solution I think.

Addressed your comment.
Though there is an issue with this approach still. Turns out that the submissions that were marked with "check" permanently, were due to the fact that gunicorn worker timed-out (after 30 sec), particularly when the server had some load. Meaning that sending a submission can take more than 30 s which is a lot.
Now I increased the gunicorn timeout to 1 hour, and this works, but understanding why it takes so long to make a submission with the frontend would be useful.

FWIW, it's a regular (physical) hard drive, there is no reason why interactions with the file system or writing into the DB would teake that long.
Maybe disabling wrting to the DB for user_interactions would help somewhat.


adding initial tests for plotting

and fixed an error with plotting functions that I think I caused when I merged with master.
I will set this PR as work in progress as I will be adding more tests.

@falexwolf regaring #204  the image that didn't work for you is this?

Yes, the correct plot. I re-enabled the feature with https://github.com/theislab/scanpy/commit/2a869d6060ba0de12feaf08a809bdf745d39ef10, but I figure you'll have a more elegant solution. 🙂

Yes, this is the correct plot. I re-enabled the feature with https://github.com/theislab/scanpy/commit/2a869d6060ba0de12feaf08a809bdf745d39ef10. 🙂
You're tests look very good! Seems like a great solution. :smile:
How about, instead of commiting extra image files to the test repo, using the image files that we use for the docs? See here https://github.com/theislab/scanpy/tree/master/docs/api. It would be great to test whether what one sees in the docs is actually still the same as the current version produces.
The conflicts are solely due to the fact that I renamed kwargs to kwds as this fits better with the  "parameters" (instead of "args") convention.

I will take a look later to see how we can integrate better the visualizations, the tests and the documentation. I will put back kwds also.
Have you consider adding another dataset to the repository? This will be good for showing examples.

I don't feel well adding a large dataset to the repository. Adding something subsampled and rather low-dimensional would be fine.
Alternatively, you could also just add a dataset that is automatically downloaded: as here or here. As both travis and readthedocs will cache this, it should be a viable solution that avoids bloating the repository with several MB of data.

@falexwolf I like the idea of downloading the data on the fly!
For an idea of a small dataset that is already filtered and normalized, do you know if  the pbmc data from 10x Genomics has some restrictions? ... nevermind, they have a Creative Commons licence.

I think we can merge this for now. I will add other tests I think next week.
There is something I don't understand: For the docs, I see that an image is presented together with the API documentation. E.g. api.pl.dotplot But I don't see how is this image is referred in the function description. How does this work?

@flying-sheep could you explain it?

Sorry, but I think there still is a range-related bug in the tests:
E           matplotlib.testing.exceptions.ImageComparisonFailure: Image sizes do not match expected size: (376, 439, 3) actual size (376, 440, 3)

my local tests pass. Which means that I will need to check the version of matplotlib. As soon as I can I will take a closer look.

Test are passing now!
@flying-sheep can you tell me more about the images that appear in the automatic API documentation?

Sure! I made it as easy as possible, by adding it directly to the autosummary template. api_image is defined in scanpy/docs/conf.py here.
Just add your (.png) image to scanpy/docs/api using the qualified name of the function, e.g. scanpy/docs/api/scanpy.api.pl.dotplot.png

OK, merged this into master on the command line after fixing plotting/anndata.py, where some changes would have otherwise been reversed...
Thank you very much, Fidel! Really cool!

I hope that soon I can add some figures into the documentation and add further test.

Am 23.07.2018 um 23:12 schrieb Alex Wolf<EMAIL_ADDRESS>OK, merged this into master on the command line after fixing plotting/anndata.py, where some changes would have otherwise been reversed...
Thank you very much, Fidel! Really cool!
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React components functions in static routes definition

Regarding static.config.js, the docs says:
...
component: 'src/containers/Home', // specify the react component that will render this route
...

well, I expected this to accept a "react component"... but got it wrong :stuck_out_tongue_winking_eye:
I tried to supply a react class component there, then I got an error:
TypeError: template.replace is not a function
I went to see the portion of the code throwing this error  (in node_modules/react-static/lib/static.js line 407) and in fact I see react-static doesn't expect a component in component:, rather it expects a string representing the path of a component.
Is it the desired behavior ?
Would it be possible to test if supplied component: value is a function?
if (typeof template === 'function') {
   // ignore subsequent imports and use provided function instead
}

I tried to do it myself in hope to submit a PR but stopped after other side effects. So I ask: what are the consequences of using a function instead of a path ?

This should be better documented. There is in fact a very strict data serialization layer between the config/static code and browser-side code for several reasons. To satisfy that separation, react components for routes cannot be directly passed in the config. The only place in the config that is safe to use react is actually the Document class.

Hmmm...
Is this immutable ? or is there any hope to see components: accept react components ?
In fact it is a bit confusing because the docs also tends to make analogy with react-router which accepts react components as routes.

What you're referring to is Auto routing. By passing the source to a
component, react static can Auto build the react router navigation routes
for you. You can of course use manual routing though, where you don't
reference a component, and simply handle your routes using react router as
normal. There is a large section on this in the docs.
On Wed, Dec 6, 2017 at 2:35 PM Jonarod<EMAIL_ADDRESS>wrote:

Hmmm...
Is this immutable ? or is there any hope to see components: accept react
components ?
In fact it is a bit confusing because the docs also tends to make analogy
with react-router which accepts react components as routes.
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Nope, I got that.
I am referring to static.config.js and the components: key we have to ship with each routes.
[{
    path: '/',
    component: 'src/containers/Home', // specify the react component that will render this route
  },
...

It was just to my impression that I could throw a function to it instead of a path.
Now yes, if that is intentional and will NOT change, I suggest to update the docs to mention something like:
...
component: 'src/containers/Home', // specify the PATH of a react component that will render this route
...

Agreed. If you would like to PR that change, that would be great
On Wed, Dec 6, 2017 at 3:36 PM Jonarod<EMAIL_ADDRESS>wrote:

Nope, I got that.
I am referring to static.config.js and the components: key we have to
ship with each routes.
[{
path: '/',
component: 'src/containers/Home', // specify the react component that will render this route
},...
It was just to my impression that I could throw a function to it instead
of a path.
Now yes, if that is intentional and will NOT change, I suggest to update
the docs to mention something like:
...
component: 'src/containers/Home', // specify the PATH of a react component that will render this route
...
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Fix #1156, make HelpCommand respect subcommands case-sensitivity and abbreviation

This pull request will fix #1156.

Codecov Report

Merging #1172 into master will increase coverage by 0.02%.
The diff coverage is 100.00%.

@@             Coverage Diff              @@
##             master    #1172      +/-   ##
============================================
+ Coverage     94.29%   94.31%   +0.02%
  Complexity      455      455
============================================
  Files             2        2
  Lines          6661     6651      -10
  Branches       1792     1790       -2
============================================
- Hits           6281     6273       -8
+ Misses          102      101       -1
+ Partials        278      277       -1

Impacted Files
Coverage Δ
Complexity Δ

src/main/java/picocli/CommandLine.java
94.15% <100.00%> (+0.02%)
314.00 <1.00> (ø)

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Merged.
@NewbieOrange Thank you very much for the PR and for your patience during the reviews!
Your contributions are much appreciated!