Avoid boxing in MultiVisitor

Get rid of all the boxing/heap allocations in visit_all_rules, and rely on a stack-allocated heterogenous linked list instead.
In my small GraphQL application (use-case is a high volume of rather simple queries), this brings me from about 17k to 20k rps. Working on getting some more detailed and relevant numbers, in the meantime I thought I'd already put this up for review.
Let me know what you think!

As promised, here are some more detailed numbers.
Without the patch:
Running 30s test @ http://localhost:3000/graphql
  2 threads and 10 connections
  Thread Stats   Avg      Stdev     Max   +/- Stdev
    Latency   585.81us  405.66us  23.94ms   95.20%
    Req/Sec     8.51k     1.61k   12.04k    56.31%
  Latency Distribution
     50%  533.00us
     75%  692.00us
     90%  848.00us
     99%    1.23ms
  510122 requests in 30.10s, 70.54MB read
Requests/sec:  16947.29
Transfer/sec:      2.34MB

With the patch:
Running 30s test @ http://localhost:3000/graphql
  2 threads and 10 connections
  Thread Stats   Avg      Stdev     Max   +/- Stdev
    Latency   537.27us  219.46us   8.27ms   75.96%
    Req/Sec     9.14k     1.89k   12.84k    53.41%
  Latency Distribution
     50%  493.00us
     75%  655.00us
     90%  806.00us
     99%    1.17ms
  546657 requests in 30.10s, 75.59MB read
Requests/sec:  18161.19
Transfer/sec:      2.51MB

Nice, thanks!
As a comment on all these performance PRs; I think adding an LRU cache from Hash(query) to AST(query) for validated queries would be a great improvement for performance - parsing and validating is probably 90% of Juniper's overhead.
I've been thinking of implementing that, but it would require the API to expose some kind of global state object, or use lazy_static!. It might also require exposing some configuration parameters.


<IP_ADDRESS>_Prttyp_Final

HealingItem&Use
Item&Use
All Added and Checked

LGTM! but please "git pull" and resolve conflict before Pull request TT.


Opening Local HTMLS

Hey,
Your package is great. For some reason I cannot view htmls on my computer though. When I copy and paste a local file path of an html, the package overwrites the C:/ to html:// everytime. or rather, it inserts html:// before the c:/, which of course loads a blank page.
Is there someway to get around this? Please advise.
Thanks,
Zac

I'm sorry but the package Web-Browser has been deprecated in favor of the package Browser-Plus.  I should make the notice bigger.

Oh, I see. I will take note of that, thanks for the reply.


scripts: Cleanup shell script formatting

Signed-off-by: Stefan Berger<EMAIL_ADDRESS>

Some consistency for code formatting would be 'adequate'...

LGTM


Java Version

Could you please define the minimal Java version?

I'll be home again this evening and can make the change then

Yes.
Imagine a server where we validate totp is 1 minute behind of real time. so we need to be able to set a window like checking code from -2 mins to now and to +2 mins.

Great, it's because my server is most likely can't go higher than v8 and as far as I see your lib. requires higher version.

Yep, but should be able to Run on 1.8 i think, should Not be a big Problem

17
17
UTF-8

OK, could you please check if it is save to set 8 as a compiler?

As of 3.0.1 java 11 is required. Latest java 8 version is 2.7.0.

OK, it's QRGen that is using Java 11.
I will see if I can use 2.7

'''
[3F90:0163-0630] 05/05/2024 01:27:14 PM  HTTP JVM: java.lang.NoClassDefFoundError: org.apache.commons.codec.binary.Base32
[3F90:0165-0630] 05/05/2024 01:27:14 PM  HTTP JVM:      at de.tomino.AuthSys.generateSecretKey(AuthSys.java:51)
'''
Cant make it work, unfrotunatelly.
Could you please see if we can use Java8?

@dpastov works now on 1.8, tested 1.8 to 22

great! thanks, it is odd but it did not work on my server (but that is an old IBM Domino server with Java 8). I will try to figure out why it did not run.


NEW: Pass func/method in hooks

Codecov Report

Merging #42 into master will increase coverage by 0.08%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master      #42      +/-   ##
==========================================
+ Coverage   95.48%   95.57%   +0.08%
==========================================
  Files           8        8
  Lines         266      271       +5
==========================================
+ Hits          254      259       +5
  Misses         12       12

Impacted Files
Coverage Δ

time_execution/decorator.py
100% <100%> (ø)
:arrow_up:

Continue to review full report at Codecov.

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Better cache handling and construction

Caches should be disabled by default, but easily enabled via a Builder pattern when constructing the Crate. Also add the ability to clear caches for a list of assets, for when I.e. a folders contents are only required in one Activity but we don't want to invalidate all caches just to free up the memory.

https://github.com/oriley-me/crate/commit/207a5bfb635cf838877b8919be50568e631e991a


SafeAreaView not working in Newer Iphones(iPhone Xs Max, iPhone XR, iPhone Xs)

[ ] Review the documentation: https://facebook.github.io/react-native
[ ] Search for existing issues: https://github.com/facebook/react-native/issues
[ ] Use the latest React Native release: https://github.com/facebook/react-native/releases

Environment
OS: macOS High Sierra 10.13.6
Node: 8.11.3
Yarn: 1.9.4
npm: 5.6.0
Watchman: 4.9.0
Xcode: 10
Android Studio: 3.2 AI-181.55<IP_ADDRESS>14246
Description
-Also Bottom Tab navigator is also not Working.(Note: Works with the iPhone X fine)

Can you post the import you are using for SafeAreaView? I remember having issues with the pure JS version of SafeAreaView included in React Navigation. That one was hard coding the height of the iPhone X, which changed for the XS/...
If you are using the RN version one import {SafeAreaView} from 'react-native', you shouldn't have any issues on the latest versions of React Native.

@siddhantjaiswal9098 please post your which RN version you use and if you use React Navigation also post a version of this library. We cannot help you if you're not using the latest React Native version.
@bartolkaruza XS and other new models are now working also fine with JS-based solution

@radko93 i am using RN :- 0.55.4

@bartolkaruza yes i am importing SafeAreaView from react-native but issue still persist


Mac OS github not able to access github for sync due to login issue

Password authentication was removed?

`remote: Support for password authentication was removed on August 13, 2021.
remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
fatal: Authentication failed for 'https://github.com/arty01238/xpipe-sync.git/'
Unable to fetch from remote repository https://github.com/arty01238/xpipe-sync.git
Please make sure that:

You have the correct repository URL
Your repository URL matches the rules regarding a .git suffix (Some remotes require a .git suffix, some require it to be omitted, others do not care)
Your configured git user has the necessary access right via credentials or a token
You have internet connectivity`

Yeah as the link in the error message mentions, GitHub disabled password authentication and replace it with tokens instead. When it asks you for a password on the CLI, you should input a token instead. You can find these at https://github.com/settings/tokens

So when the username and password come up, use the username and a token for password?

Yes. I didn't design this, that is what the GitHub does. I know it's confusing though

It really is confusing. Like, you think they would make this thing easier.
On Tue, Dec 10, 2024 at 7:23 AM Christopher Schnick <
@.***> wrote:

Yes. I didn't design this, that is what GitHub does. I know it's confusing
though
—
Reply to this email directly, view it on GitHub
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I will improve that in the next release vice forcefully overriding the password prompt

This is now fixed in the latest release by replacing the password prompt with one asking for your token


Cannot use Table.X. Please make sure it is bound to this function

While running pnpm sst build, I'm getting the following error:
Error: Cannot use Table.EventStore. Please make sure it is bound to this function.
    at Object.get (file:///xxx/node_modules/.pnpm/@serverless-stack+node@1.18.2/node_modules/@serverless-stack/node/util/index.js:8:27)
    at file:///xxx/.build/lib/index.js:666390:20
    at ModuleJob.run (node:internal/modules/esm/module_job:198:25)
    at async Promise.all (index 0)
    at async ESMLoader.import (node:internal/modules/esm/loader:409:24)
    at async file:///xxx/.build/run.mjs:93:17

Trying to debug the flow has led me to this:

I'm probably missing something, but why is the target {}?
If there's any more information needed, please let me know (there's no issue template).

I think I found the issue, it has to do with when I call it.
I have a module called x.service.ts which has something like:
import { createMicroService } from "@app/shared/core";
import { Table } from "@serverless-stack/node/table";

export const xService = createService({
  name: "xService",
  tables: {
    EventStore: {
      name: Table.EventStore.tableName
    },
  },
});

xService was used to create lambda handlers, but it was used in the stack itself. Meaning, I imported @serverless-stack/node and called it before the stack was built. To facilitate this, I changed it to:
import { createMicroService } from "@app/shared/core";

export const xService = createService({
  name: "xService",
  tables: {
    EventStore: {
      name: ({ Table }) => Table.EventStore.tableName
    },
  },
});


Steps to use APIs

Hi,
Thank you for building this tool! I'm very excited to implement it.
I might have missed this but may I know where can I find the tutorial on steps to use the APIs?
Do I sequentially implement these functions?

I've tried cross comparing the steps in CLI but failed to match the function names.
Would really appreciate your help on this!
Thank you,
Justine

Hello @justinesjw,
Thanks for your interest in Sopa :)
For now, I only provide a documentation of the API. I will add in the next few weeks some tutorials on how to use the sopa.stats functions for instance, but I'm not sure to provide a tutorial for every API function because I thought most users may prefer using the CLI (or directly the Snakemake pipeline).
A few questions to understand what you want to do (this will help me to really answer your question and improve the documentation):

Why do you prefer using the API rather than the CLI or Snakemake pipeline?
What kind of segmentation to you want to perform (Cellpose? Baysor? Custom segmentation?)
In which steps of Sopa (if not all) are you interest in? According to the illustration of the pipeline here: https://gustaveroussy.github.io/sopa/
Are you familiar with the spatialdata library?

Thanks

Hello @quentinblampey,
Thanks for your reply. :) Awesome! Excited for your tutorials. Will try out Snakemake pipeline!
Regarding the questions:
Q1 : As I am more familiar with R and Python I would prefer API over CLI. Also, for documentation purposes, I'm interested in a library which can streamline my scripts. Currently, I am running Baysor on it's own.
Q2/3 : I am interested in cell segmentation and do not have any preference on methods. Similar to most, I noticed that the default Xenium segmentation mis-segment a high portion of cells and would like to see how other methods perform? I am also excited to use your explorer function!
Q4 : My analyses are heavier on R packages though I am starting to use Squidpy which helped me understand spatialdata structures.
Thanks!
Best,
Justine

Hello @justinesjw,
Thanks for your answers, I better understand your usage now! Indeed, if you want to include Sopa into your own scripts, then the API is the best way to go. I just wanted to make sure that this was what you wanted (because the snakemake pipeline or the CLI are usually the first choices).
I finally released version 1.0.2 with the new tutorial on the API usage. I will be happy to improve this tutorial based on your feedback!

Hello @justinesjw, have you had a chance to look at the tutorials?
If you have some questions, I'll be happy to help, and I can update the API tutorial. Else, if everything is clear, let me know if I can close the issue!

Hey @quentinblampey,
Thanks for the tutorials, they were helpful and informative!
I'm still exploring among platforms!
I'll close this issue for now.

Ok great! Don't hesitate to re-open it in the future if you have new questions 🙂


[WIP] Test CI(3)

Build Failed  with Spark 2.1.0, Please check CI http://<IP_ADDRESS>:8080/job/ApacheCarbonPRBuilder/2554/

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/carbondata-pr-spark-1.6/446/


Floating point used as pandas index for error probability

Steps to reproduce

python run_threshold.py uf toric 1000 -l 8 10 12 -p 0.09 0.10 0.11 (directly from README)
python run_threshold.py uf toric 1000 -l 8 9 10 12 -p 0.09 0.10 0.11

Issues

toric_graph_2D_uf_.csv contains seemingly duplicate rows where the p index is the same, i.e.

L,p,N,succes
8,0.09,1000.0,816.0
8,0.09,2000.0,1588.0
8,0.1,1000.0,732.0
8,0.1,2000.0,1470.0
8,0.11,1000.0,627.0
8,0.11,2000.0,1272.0
10,0.09,0.0,0.0
10,0.09,1000.0,795.0
10,0.1,0.0,0.0
10,0.1,1000.0,710.0
10,0.11,0.0,0.0
10,0.11,1000.0,659.0
12,0.09,0.0,0.0
12,0.09,1000.0,819.0
12,0.1,0.0,0.0
12,0.1,1000.0,721.0
12,0.11,0.0,0.0
12,0.11,1000.0,638.0

Exception: cannot handle a non-unique multi-index!

This is because sim.py appends decoder data to a pandas MultiIndex through a floating point, introducing slight variations depending on how this value is read.
Proposed solution
Write the p column as data, not as an index. Replace with labels that can be uniquely defined, e.g. integers.

Thanks! I'll make sure to resolve this in the next release.

Solved in #26


Update instructions for complex-number exercise

Introducing z in the definition of a complex number
Formatting to have the code as separate blocks instead of inline with the rest of the text that made reading difficult.

Here is the link to the community forum post.

@ignazioc @kotp This exercise originates from https://github.com/exercism/problem-specifications/tree/main so fixes should be done there and then they are synced down.


feat(images): Adding iOS Image Cache Limits

By default React Native would set NSCache.totalCostLimit to 20MB and the single image size limit to 2MB (bitmap size). The default cache size may not be enough for applications that make heavy use of images.
But thanks to this commit now you can configure the image cache size on iOS by adding RCTSetImageCacheLimits in your app App Delegate.
This feature should be available from v0.69.0-rc.0

PR Reference
https://github.com/facebook/react-native/pull/33554

@Simek since this method is already available since v0.69.0-rc.0 should i also edit the versioned docs?

@huntie updated the docs, please kindly check. thank you

Updated @Simek, please kindly check again. Thank you.

Oke thank you @Simek.


Question: integrate CORS in permissions

We have a public API that we use on our own website. It's protected with CORS but we would like to add IP restrictions on certain endpoints in case it's accessed directly, e.g. a direct POST-request. We would like to make it a little harder for people to work around CORS in case they are being smart and write their own proxy or similar.
Is it possible to see if a request has gone through CORS validation and if so, if it passed?
Or am I trying to build something that's nearly impossible here?

Got it. Sorry for my poor understanding of CORS. I guess what I am after isn't possible.
Thanks for your explanation!


Material strings can become unruly.

When you print a material a list of all its elements are included. For depleted fuel this can become ... very unruly. Should implement a numpy style snip that cuts out a lot of the middle bits.

I keep coming back: and really wanting the composition sorting.

In addition the elements should be sorted by composition. It's hard for anyone but a materials scientist to see that: 'magnesium', 'aluminum', 'silicon', 'chromium', 'manganese', 'iron', 'copper', 'zinc', 'tin' is aluminum-6061.

Should again consider https://github.com/idaholab/MontePy/discussions/344#discussioncomment-8337827 for material labeling (not necessarily the sorting)

To clarify this isn't about writing to file this is just for printing when examining a material:
print(material)

I'm a little surprised that MCNP doesn't support named materials - or do they? If, so, could just be on the user to do so. If not, you could still leverage the JSONification for this.

Do you mean by being able to label m1 as water or being able to define a material as being water?

@MicahGale I feel like either would resolve the issue right? But AFAICT, there isn't any native way to do this in MCNP.

Yes you are right, neither of these features is supported by MCNP natively, much to everyone's chagrin.
So next steps on your idea: I think all of these would be a separate issue:

Extend the scope of #76.
Add common composition data (at least elemental) data to simplify generating new materials. I am warry of doing this as we would then be responsible for a rather large data set. Though people can't sue us over getting it wrong, they can still complain loudly.

2. Add common composition data (at least elemental) data to simplify generating new materials. I am warry of doing this as we would then be responsible for a rather large data set. Though people can't sue us over getting it wrong, they can still complain loudly.

Honestly, I don't think it will be long before people request the PNNL Material Compendium anyhow


HDDS-2131. Optimize replication type and creation time calculation in S3 MPU list call.

What changes were proposed in this pull request?
Optimize listMultiPartUpload to not read from openKeyTable.
What is the link to the Apache JIRA
https://issues.apache.org/jira/browse/HDDS-2131
How was this patch tested?
Ran related unit tests.

/retest

And also this is missing S3 end change to use the replication type and replication factor and show them in S3StorageType format.
Need to use this class for conversion. https://github.com/apache/hadoop-ozone/blob/master/hadoop-ozone/s3gateway/src/main/java/org/apache/hadoop/ozone/s3/util/S3StorageType.java

Thanks for pointing this one out, where does this change go?
Do you mean we should add S3StorageType to org.apache.hadoop.ozone.om.response.s3.multipart.S3InitiateMultipartUploadResponse#S3InitiateMultipartUploadResponse

And also this is missing S3 end change to use the replication type and replication factor and show them in S3StorageType format.
Need to use this class for conversion. https://github.com/apache/hadoop-ozone/blob/master/hadoop-ozone/s3gateway/src/main/java/org/apache/hadoop/ozone/s3/util/S3StorageType.java

Thanks for pointing this one out, where does this change go?
Do you mean we should add S3StorageType to org.apache.hadoop.ozone.om.response.s3.multipart.S3InitiateMultipartUploadResponse#S3InitiateMultipartUploadResponse

This was already taken care of. Sorry I thought this is missing.

Hi @bharatviswa504 the tests are failing since we do not have RATIS-707 fix, it is unrelated. Do you want me to rebase and push?

Thank You @swagle for the verification and for the contribution and @anuengineer for the review.


Allow checking the entire ProducerMessage in the mock producers

This is done by introducing MessageChecker, a function which validates
an entire ProducerMessage, and reimplementing the existing expectation
interface on top of that. Since producerExpectation was not a public
API, the only visible effect of this to users of the mock producers
should be slightly different error messages when encoding fails.
To better mimic the real producers’ behavior, this also runs
partitioning before passing the message to the checker. By default all
topics have 32 partitions but this can be configured per-topic in either
producer via the embedded TopicConfig. (This does not allow mocking
unavailable partitions; I don’t see a use case for this which can’t be
better handled by unit testing the partitioner.) This may affect
existing tests if someone was passing a configuration with a
Partitioner that would fail on their test messages, but it seems more
likely they want to know if this is the case (we did).
This is useful for (at least) two reasons,

I would often like to test more than just the message value; services
may need to produce to different topics or with specific partitioning
schemes. In some cases valuable data may only be in the message key,
or I want to test that a header and message body agree.

Since the topic usually also corresponds to the data format, exposing
the topic makes it easier to collect messages of different types
across different topics which may appear in known quantities but
non-deterministic orders. Without the topic this is only possible by
trying to content-sniff the format from the value, which leads to
weaker and more fragile tests.

Sorry, I can't see anything actually broken in the CI, nor a way to trigger a retry myself. Given exit code 28 in the 1.16/2.7.1 case it seems like curl might have timed out trying to install golangci-lint. I ran v1.37.1 (and various other versions) locally with 1.16 and saw no errors.


Retry if API-server instance is shut down

If a k8s instance has multiple API-servers, one of which is being scaled down, existing websocket connections will be terminated and kapp will fail with:

kapp: Error: waiting on reconcile destinationrule/istio-policy (networking.istio.io/v1alpha3) namespace: istio-system: errored: Listing schema.GroupVersionResource{Group:"apiextensions.k8s.io", Version:"v1beta1", Resource:"customresourcedefinitions"}, namespaced: false: Get https://api.cf4k8s.istio.shoot.canary.k8s-hana.ondemand.com/apis/apiextensions.k8s.io/v1beta1/customresourcedefinitions?labelSelector=kapp.k14s.io%2Fassociation%3Dv1.4ea2426af853c41012e6a53e19d4a3b1: http2: server sent GOAWAY and closed the connection; LastStreamID=64781, ErrCode=NO_ERROR, debug=""

Feature request
kapp should use retries to cope with API server instances being scaled down.

interesting, i was pretty sure we already do retries, will check what's going on in this case.

http2: server sent GOAWAY and closed the connection

it's interesting that this is how api-server "drains" connection.

it's interesting that this is how api-server "drains" connection.

IMO, the only thing the API-server can do to properly drain connections is to 1) wait for a certain period for the connections to be terminated and, once this period is over 2) send a GOAWAY and terminate connections itself.
Therefore, kapp should be able to handle such connection terminations.

included in https://github.com/k14s/kapp/releases/tag/v0.31.0


[WIP]Add Parallel Cross Entropy

What does this PR do?

[x] add parallel cross-entropy implementation
[x] add parallel axis propagation rules for cross-entropy
[x] add parallel cross-entropy replacement logic in pass

TODO: Tests need to be modified accordingly to include label inputs in order to trigger the critical path.

The docs for this PR live here. All of your documentation changes will be reflected on that endpoint. The docs are available until 30 days after the last update.

LGTM! Is it for the default backend?

Nanotron backend will also use it because there is a label_mask input in Nanotron which is not compatible with transformers current implementation, the current implementation of shared cross entropy is compatible with transformers implementation, and it does not matter because cross entropy layer does not contain any backend-specific stuffs, it does not even contain a single parameter

If everything is good, can we merge this, I don't have write access to the main branch now :(


Should the runtime be linux-x64 in all cases?

Having spent some time trying and failing to publish and run a Spark job written using .NET for Spark to Azure Synapse and running it as a Spark Job Definition, I could only get it to work by choosing linux_x64 rather than win-x64 as the runtime. I also used WSL (Ubuntu-20.04) to compile the version that ran successfully.

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

ID: 2d2c5fdd-ac1d-701c-16a4-e5e11585fb6d
Version Independent ID: 5b089102-d0a3-47ec-d898-a054aee107b0
Content: Use .NET for Apache Spark - Azure Synapse Analytics
Content Source: articles/synapse-analytics/spark/spark-dotnet.md
Service: synapse-analytics
Sub-service: spark
GitHub Login: @luisquintanilla
Microsoft Alias: luquinta

@supernoodles I have assigned this issue to content author to investigate and update the document as appropriate.

@Niharikadutta does .NET for Spark on Synapse only support Linux x64?

@luisquintanilla Yes Synapse is only Linux based currently, I will update the document accordingly. Thanks!


Question: Would it be possible to have sync from GitHub?

Thank you so much of this marvellous plugin,
I was wondering if you had any plans/interests into allowing sync back from github?

I have 3 themes in my DS and I find maintaining Figma files for the 3 themes is really time consuming
Having a way to sync my tokens back to a single "white label" file would really rock
Sometimes Figma can get out of control with contributors and it's hard to see the differences between live code and FIGMA, Syncing back from code could help starting on strong bases.

Anyway let me know if that something you could consider? or if you have any tips to handle such workflow
THanks

Hey @edwardbattistini,
I do have interest in a sync back to Figma. However currently I have not worked on this.
I would love to allow a sync from a w3c token file to text styles, color styles, elevation styles and grid styles. So anything that can be added as a style.
Would you be interested in contributing?


Add tests for conversion_options

Is this the right repo for this?

I was testing the new interface that you shared, I selected this by mistake, I closed it from there but it seems that it does not propagate back.


don't run "_init_azure" for every CPI method

[x] Please check this box and fill the data as below once you have run the unit tests.
Code coverage should keeps at 100%.
pushd src/bosh_azure_cpi
  ./bin/test-unit
popd

NOTE: Please see how to setup dev environment and run unit tests in docs/development.md.

Changelog

don't run "_init_azure" for every CPI method

any update on merging this PR @h4xnoodle  ?

@ahelal did some tests and this PR further reduces the GET calls towards the Azure API and would further reduce the risk for getting throttled.
Current CPI version without storage account configuration:
60 calls for List resources in resource group calls
59 calls for Get Storage Account Keys
54 calls for List Storage Account
Current CPI version with storage account configuration:
58 calls for Get Storage Account
58 calls for Get Storage Account Keys
CPI with this PR and storage account configuration:
31 calls for Get Storage Account
31 calls for Get Storage Account Keys
This PR reduces the most frequent API calls by almost 50%. @h4xnoodle can you please review, merge and create a new CPI release with this PR?
Thanks

@aashah Who can merge this, have a quick look at the CPI pipelines and cut a release?

@aashah,  @h4xnoodle, any chance to merge this PR soon?

Rebecca and I are no longer working with Pivotal/contributing to CloudFoundry & BOSH.
/cc @dlresende

We think this works, but it's possible some obscure CPI call is now forgetting to run init. Merging with @mrosecrance and seeing how it fairs in CI.

Reverting temporarily. This commit broke a few integration tests that make the assumption that init will always be run to form child objects to make assertions against. CI is also red for unrelated reasons, so planning on fixing those first then reapplying this commit, then fixing the tests.

Also I believe we were merging against develop instead of master.


Slide2 feedback from luke

luke.stephenson  9:28 PM
2. Rather than expressing that we need to write a function which it takes a string and an int, with:
val resolveSkuQuantity: ((String, Int)) => F[SkuQuantity] = ???
I think it would be clearer to use:
def resolveSkuQuantity(code: String, quantity: Int): F[SkuQuantity] = ???
Not sure if there was a motivation for not having any parameter names in the template.

On consideration, I dont think I'll bother to change this one.
Invocation atm is items.parTraverse(resolveSkuQuantity) and that would get more complex if it were switched to a def with 2 named params - would it be items.parTraverse(resolveSkuQuantity(_, _).tupled)?


DOC: Add description of default bounds to linprog

closes #6139
By default linear programming bounds variables to be non-negative causing some confusion for users not familiar with LP. This PR explicitly states the default bounds (lb = 0, ub = np.inf) and that they may be set by using the bounds parameter.
@mdhaber @ilayn

@ilayn All fixed. I've changed  0 < x < oo to  x >= 0 this aligns the documentation with how it is normally written.

There are still some issues; you can see what the documentation looks like here:
https://8824-1460385-gh.circle-artifacts.com/0/html-scipyorg/optimize.html
For instance, there is a missing line break in the linprog documentation constraints. There are several differences between the interior point and simplex problem statement definitions, including  remaining ASCII art and formatting as code. There are extra ’ characters that I don't think are intended in the simplex documentation.

@mdhaber could you tell me how you got the link? The failing test isn't related to the changes, but I'd like to have a look over the built docs to see if it's formatted properly.

Link is availabile inside Circle CI under the artifacts tab (I think you also need to login). This is the latest one https://8837-1460385-gh.circle-artifacts.com/0/html-scipyorg/optimize.html

Link is availabile inside Circle CI under the artifacts tab (I think you also need to login).

I think that that's only visible if you have commit rights on scipy Github repo (not 100% sure). The alternative is to build locally; if you already have an in-place build that you've been working up a PR in then it's basically cd doc && make html - html docs are then accessible from doc/build/html/index.html).
About the rendered version of this PR: that didn't look perfect before, and the extra lines added aren't rendered correctly. I think you want to use ``::` so the problem is rendered as code. Will comment inline.

@rgommers yes, i think you have to have commit rights. Or at least be logged into CI. I know I couldn't see artifacts before I got commit rights (and looked CI and GitHub account).
There used to be a trick for generating the link yourself based on a base URL and the four digit number in CircleCI, but it didn't work last time I tried.
@kai-striega if you have trouble building docs locally, just push and ping me; I'll send the link.

@mdhaber could you take a look? I've tried building them locally and now seem O.K.

I'll try to restrict my attention to whether this issue is resolved and clear mistakes.
On the linprog documentation, yes, issue is resolved. Although we also switched to @ from *, which I think makes ^T unnecessary.
It says upper bound is np.inf at the top and None elsewhere, but isn't explicit that they're equivalent so it seems inconsistent.
In any case, "By default bounds are (0, None) (non-negative)" needs a period.
In simplex documentation.
Minimize: c^T @ x

Subject to: A @ x == b
                0 >= x

the words are in teletype. They're weren't in simplex.
And it's x >= 0
In the callback description:
"The phase of the optimization being executed. In phase 1 a basic feasible solution is sought and the T has an additional row representing an alternate objective function."
From the reader's perspective, what is T? And it's not even part of the OptimizeResult anymore, so probably don't need to mention it at all.
Reference links (like [3]) should be linked by including underscores... I think before? See examples in the docstrings with underscores and how they link.
For status messages, all of them are the short versions except:
Serious numerical difficulties which could not resolved using     a more robust, albeit less efficient, solver encountered
which looks weird because not turns green. How about just Numerical difficulties encountered.
https://8890-1460385-gh.circle-artifacts.com/0/html-scipyorg/generated/scipy.optimize.OptimizeResult.html#scipy.optimize.OptimizeResult
renders strangely at the bottom.
Also some of these are not applicable for linprog.
But I am getting carried away. Yes, the issue about default bounds not being obvious is addressed, but the things above might be changed while we're at it. Of course there are lots of other things I might change, so they can also wait.

@mdhaber I've changed the docstring for simplex (again) and reformatted the docstring example to match, set the upper bound as None and set [3] to be hyperrefs. I think the other changes can wait until you are finished with the revised simplex method.

The documentation says the objective function is cT @ x; shouldn't this just be c @ x because that is the code used to perform the dot product between c and x? That was my point before, that ^T wasn't necessary since @ suggests that we are writing code, not math notation, and in code we write c @ x.
"By default bounds are (0, None) (non-negative) If a sequence containing a single tuple is provided..." needs a period between "(non-negative)" and "If"
I haven't checked whether it's present in the  scipy.optimize.OptimizeResult, but I remember that _postprocess should output the residuals of the equality constraints (just like it outputs the slack for the inequality constraints). If that is included in the OptimizeResult it should be documented in all four files (linprog, interior-point, simplex, and verbose callback).
Interior point documentation says:
"Minimize a linear objective function subject to linear equality constraints, linear inequality constraints, and simple bounds using the interior point method of [4]."
but that is no longer reflected in the mathematical problem description.
I should have brought this up before, but I'm conflicted in which should be changed. On one hand., the mathematical problem description in Interior point documentation is accurate for _linprog_ip. However, the reader might be confused that the problem description for the main linprog routine does not match this mathematical problem description, only the text description.
[scipy.optimize.linprog_verbose_callback](https://8901-1460385-gh.circle-artifacts.com/0/html-scipyorg/generated/scipy.optimize.linprog_verbose_callback.html#scipy.optimize.linprog_verbose_callback) still shows:
Serious numerical difficulties which could not resolved using a more robust, albeit less efficient, solver encountered

@mdhaber I've made changes to you mentioned above, plus some in the remaining function docs (hopefully for the last time)
I've also changed the documentation of the interior-point method, to match the mathematical formulation (i.e. s.t. equality and non-negativity constraints) then modified the notes section in linprog saying the problem is converted to standard form.

@Kai-Striega That approach sounds OK, but:
"Before applying either method a presolve procedure based on [8]_ and converted attempts to standard form."
doesn't make sense. Note that
"After presolve, the problem is transformed to standard form by converting the (tightened) simple bounds to upper bound constraints, introducing non-negative slack variables for inequality constraints, and expressing unbounded variables as the difference between two non-negative variables."
already appeared at the end of the notes. I think that is a more logical place to put that bit about standard form.
But neither are in a very prominent place; still I think that only users familiar with linear programming standard form will understand why the problem form changes. Perhaps there could be a note in each of the methods documentations calling attention to the difference and explaining that it is the result of the problem provided to linprog being converted to standard form.
Also con is still missing from the OptimizeResult returned by linprog.
"Solve the following linear programming problem via a two-phase simplex algorithm of the form:"
doesn't strictly make sense.
Sorry to point out more things : / I know you want this "simple" thing to be done : )

I'll take a look this weekend and hopefully merge!


Add work path CLI option

As mentioned in #6855 the use of environment variables to configure gitea - although common practice - is confusing and frustrating for non-docker users. Environment variables are somewhat opaque to most users and can't easily be inferred from the command.
This PR adds a new option to the main command-line allowing you to set the work-path, overriding the GITEA_WORK_DIR variable and build defined AppWorkDir as necessary.

contrib/pr/checkout.go:46 needs to be updated, but otherwise this looks good.

Sorry this is turning into a game of whack-a-mole...

Codecov Report

Merging #6922 into master will decrease coverage by 0.04%.
The diff coverage is 25%.

@@            Coverage Diff             @@
##           master    #6922      +/-   ##
==========================================
- Coverage   41.42%   41.37%   -0.05%
==========================================
  Files         440      440
  Lines       59744    59706      -38
==========================================
- Hits        24746    24703      -43
- Misses      31761    31765       +4
- Partials     3237     3238       +1

Impacted Files
Coverage Δ

modules/setting/setting.go
47.32% <25%> (-0.26%)
:arrow_down:

models/pull.go
49.71% <0%> (-1.89%)
:arrow_down:

routers/repo/view.go
42.02% <0%> (-1.02%)
:arrow_down:

models/repo_list.go
67.89% <0%> (+1.05%)
:arrow_up:

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Add axioms to each setting datum which quality they are about

According to the updated design pattern docs, we can add axioms on all the setting datums we defined which will link these to the qualities that they set (are about).
EDIT: previously referenced this relation as being RO:causally influences, but after discussion with Lars Vogt, this is wrong, as my understanding of causality in this context was too broad. Hence, I changed it to "is about", which is already changed in the docs. But the axioms cna/should still be asserted.

overarching issue (epic) of: https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/102


Unable to Upload xlsx

Unable to upload model_data.xlsx on Chrome:

model_data.csv appears to work fine.

Memory is full. May be we should remove other applications we don't use and clean uploaded data.

I had this issue last week as well. I used certain commands to remove stopped docker containers and dangling images which freed up 40% of the space. I had also removed a number of unwanted applications maybe there might be more? But removing images was the most effective.

May be we should not be creating 5 images. May be 3 is enough. Lets hope that helps. As far I know dockers works by layer of snapshots. So this could be least effective if creating extras images has no overhead.