Filtered matrices implemented as views of raw matrices

From @nlhepler

It would be cool/efficient if there was an option for filtered matrices to refer to the original sc_group dataframe(s) along with the selection(s) along each axis, so that associated metadata is not duplicated, and relationships are preserved.

Since early on in Scanpy workflows, we expressed filtering as masking instead of actually modifying data. This comes down to storing masks in .var and .obs with canonical names.
For instance, filtering by highly variable genes through sc.pp.highly_variable_genes adds a field highly_variable to .var, which masks all genes of low variance.
Whether tools rather adopt implementing "filtering through masking" vs. "tracing filtering in connecting sc_groups" has probably several pros and cons. One advantage of the former is that it avoids duplication of data.

This is an interesting problem which we tried to tackle in the ExperimentSubset package for the Bioconductor toolchains. The major limitation of just using a masking for cells/features is when a new annotation gets produced that is only the length of the masked object. For example, if the obs data frame is the length of the original raw matrix but certain QC tools only work on the non-empty drops (e.g. doublet detection). You could subset the matrix based on the empty drop masking and run the tool, but then your new vector of doublet calls is only the length of the non-empty droplets and not the length of the original raw matrix. If you wanted to store back in the original obs data frame, you would have to add NAs or something which is very undesirable IMO. Thus, having a separate obs/var data frame for each subset is advantageous from that perspective.
The downside of using sc_groups for different subsets is redundancy of the data as @falexwolf mentioned. We got around this by making a special subset class in which the new subsetted matrix is actually just a pointer to the parent matrix with the indices. Then a new SCE object is used for that subset which has the ability to store additional matrices that are the same dimension as the subset as well as the new obs (colData) and vars (rowData) which match the subset.

Thank you for the interesting reference and expounding on this, @joshua-d-campbell!
I agree with the points made!
I just want to make a connection with the scoping discussion of the present repository, for instance, here.

Should data provenance tooling as in ExperimentSubet (connecting & representing different subsets through pointers) be a part of the fundamental data structure & matrix-api?
Or does one merely want to foresee metadata slots that will enable plugging in different data provenance tools that establish pointers between datasets & groups?

In both cases (1 & 2), it'd make sense to account for ExperimentSubset (either for designing the slot of the metadata schema or for foreseeing some hard-coded pointer structure related to subsetting). One should probably also look at other conventions and tools around data provenance.

It is definitely a good question. I don't think data provenance just for "record keeping" sake needs to be a part of the first iteration of the matrix api, although it may be nice to include in a future version. The only reason we have to use pointers in the ExperimentSubset class is to eliminate data redundancy between the subset and the original matrix (i.e. we don't actually create a new matrix when creating a subset, we just point to the subset of rows/columns in the parent matrix). The provenance that comes with the pointer is just a nice bonus. However, it may a bit easier for you in the first round of the api implementation just to have redundant data in the between the original matrix and the subset. Although I'm still looking over things, my initial vote would be to have each new subset be a new sc_group so that way all sc_groups have the same set of cells/features which would match with the cells/features in the obs/var data frames for that sc_group.
Then ExperimentSubset-like functionality can be added in the future without the user really having to know that there was a change (i.e. they don't need to know whether a copy of the data is being stored in a subset or if it is just a point to data in the original matrix). The major work is really in the accessor functions that retrieve data in the matrix. They need to know whether to grab the data as usual or go grab a subset of the data from the parent matrix.

The way we (TileDB) intend to address this issue generically (i.e., for all applications we model as arrays) is via a feature we are currently working on and call array views. These will be similar to non-materialized table views, quite common in Databases. In addition to facilitating the use cases described in this thread, it will be quite useful for us for implementing fine-grained access policies on arrays (data owners will be able to share any number of different array views, instead of the original array).

Just to further help describe the challenge, here is a visual summary of a real-world use case where subsetting is done for both QC at the initial stages but also at later stages to re-analyze subsets of cells. Note that separate cell annotations (i.e. cluster labels) were produced for each of the later subsets and therefore each subset needed its own obs data frame. Although per @stavrospapadopoulos, it sounds like it could be handled on the backend with non-materialized table views (assuming that there is a way to store annotation matrices like the obs without having a corresponding materialized data matrix), it is not entirely clear to me how the current API description handles this more complex use case.

CC @adamgayoso, who has been looking into approaches for this around scvi-tools

As of today this has not been implemented yet and there are no plans to do so in the near term. However it is worth maintaining it open in case we would to revisit it later


Python 3.11 wheels

Fixes #12

Thanks for merging this @horta! Do you mind tagging to do a release?


Add unit tests for SA1004

This diagnostic is also enabled by default now.
Fixes #229

Should we also report warnings for multiline xml comments?

Should we also report warnings for multiline xml comments?

Probably, but I'm thinking that should be a separate issue. It wouldn't be the first time we implemented support for single-line documentation comments but left out the multi-line version.

Im okay with not supporting multiline documentation for now. I have not seen anyone using them


Build storminess on master

Merging #150 seems to have made the build fail inconsistently and unexpectedly

https://travis-ci.org/redfin/react-server/builds/132744187
npm ERR! node v6.2.0
npm ERR! npm  v3.8.9
npm ERR! code ELIFECYCLE
npm ERR<EMAIL_ADDRESS>prepublish: `npm run clean; gulp build`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the<EMAIL_ADDRESS>prepublish script 'npm run clean; gulp build'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the react-server package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     npm run clean; gulp build
npm ERR! You can get information on how to open an issue for this project with:
npm ERR!     npm bugs react-server
npm ERR! Or if that isn't available, you can get their info via:
npm ERR!     npm owner ls react-server
npm ERR! There is likely additional logging output above.
npm ERR! Please include the following file with any support request:
npm ERR!     /home/travis/build/redfin/react-server/packages/react-server-integration-tests/npm-debug.log
    at ChildProcess.exithandler (child_process.js:202:12)
    at emitTwo (events.js:106:13)
    at ChildProcess.emit (events.js:191:7)
    at maybeClose (internal/child_process.js:850:16)
    at Process.ChildProcess._handle.onexit (internal/child_process.js:215:5)
npm ERR! Linux 3.13.0-40-generic
npm ERR! argv "/home/travis/.nvm/versions/node/v6.2.0/bin/node" "/home/travis/.nvm/versions/node/v6.2.0/bin/npm" "run" "bootstrap"
npm ERR! node v6.2.0
npm ERR! npm  v3.8.9
npm ERR! code ELIFECYCLE
npm ERR! @ bootstrap: `npm i; lerna bootstrap`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the @ bootstrap script 'npm i; lerna bootstrap'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the  package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     npm i; lerna bootstrap
npm ERR! You can get information on how to open an issue for this project with:
npm ERR!     npm bugs
npm ERR! Or if that isn't available, you can get their info via:
npm ERR!     npm owner ls
npm ERR! There is likely additional logging output above.
npm ERR! Please include the following file with any support request:
npm ERR!     /home/travis/build/redfin/react-server/npm-debug.log
The command "npm run bootstrap" failed and exited with 1 during .
Your build has been stopped.

https://travis-ci.org/redfin/react-server/builds/132732945
Errored while running npm script 'test' in 'react-server-cli'
Error: Command failed: npm run test
(node:4128) fs: re-evaluating native module sources is not supported. If you are using the graceful-fs module, please update it to a more recent version.
npm ERR! Linux 3.13.0-40-generic
npm ERR! argv "/home/travis/.nvm/versions/node/v6.2.0/bin/node" "/home/travis/.nvm/versions/node/v6.2.0/bin/npm" "run" "test"
npm ERR! node v6.2.0
npm ERR! npm  v3.8.9
npm ERR! code ELIFECYCLE
npm ERR<EMAIL_ADDRESS>test: `gulp test`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the<EMAIL_ADDRESS>test script 'gulp test'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the react-server-cli package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     gulp test
npm ERR! You can get information on how to open an issue for this project with:
npm ERR!     npm bugs react-server-cli
npm ERR! Or if that isn't available, you can get their info via:
npm ERR!     npm owner ls react-server-cli
npm ERR! There is likely additional logging output above.
npm ERR! Please include the following file with any support request:
npm ERR!     /home/travis/build/redfin/react-server/packages/react-server-cli/npm-debug.log
    at ChildProcess.exithandler (child_process.js:202:12)
    at emitTwo (events.js:106:13)
    at ChildProcess.emit (events.js:191:7)
    at maybeClose (internal/child_process.js:850:16)
    at Process.ChildProcess._handle.onexit (internal/child_process.js:215:5)
Errored while running RunCommand.execute
Error: Command failed: npm run test
(node:4128) fs: re-evaluating native module sources is not supported. If you are using the graceful-fs module, please update it to a more recent version.
npm ERR! Linux 3.13.0-40-generic
npm ERR! argv "/home/travis/.nvm/versions/node/v6.2.0/bin/node" "/home/travis/.nvm/versions/node/v6.2.0/bin/npm" "run" "test"
npm ERR! node v6.2.0
npm ERR! npm  v3.8.9
npm ERR! code ELIFECYCLE
npm ERR<EMAIL_ADDRESS>test: `gulp test`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the<EMAIL_ADDRESS>test script 'gulp test'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the react-server-cli package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     gulp test
npm ERR! You can get information on how to open an issue for this project with:
npm ERR!     npm bugs react-server-cli
npm ERR! Or if that isn't available, you can get their info via:
npm ERR!     npm owner ls react-server-cli
npm ERR! There is likely additional logging output above.
npm ERR! Please include the following file with any support request:
npm ERR!     /home/travis/build/redfin/react-server/packages/react-server-cli/npm-debug.log
    at ChildProcess.exithandler (child_process.js:202:12)
    at emitTwo (events.js:106:13)
    at ChildProcess.emit (events.js:191:7)
    at maybeClose (internal/child_process.js:850:16)
    at Process.ChildProcess._handle.onexit (internal/child_process.js:215:5)
npm ERR! Test failed.  See above for more details.
The command "npm test" exited with 1.
Done. Your build exited with 1.

@doug-wade - lerna bootstrap runs multiple installs concurrently.  Maybe the clean during one is clobbering the build for another?  We might not be able to run clean during prepublish.  Maybe we could add it instead as lerna prepublish script?

@gigabo I can't find anything in the lerna docs or site about a lerna prepublish; do I just add a scripts hash to lerna.json?

@doug-wade - Looks like it requires a scripts/prepublish.js to live in each package.
Short term let's at least just get the clean out of our npm prepublish to get builds passing.  Just having the option to clean before publishing is a good step forward. :)


1292 allow importing voxel models through the asset explorer

Description
Allow Importing .grd & .pal files via new VoxelModel assets.

Still unfinished, só para reviewers verem e apontarem anything I may be doing wrong.


IndexError not raised

Reporting a bug

[x] I have tried using the latest released version of Numba (most recent is
visible in the change log (https://github.com/numba/numba/blob/master/CHANGE_LOG).
[x] I have included below a minimal working reproducer (if you are unsure how
to write one see http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports).

import numba as nb
import numpy as np

def foo():
    return np.zeros(5)[6]

foo()  # raises IndexError
nb.jit(foo)()   # returns something
nb.njit(foo)()  # returns something

I would have expected compiled code to also raise an exception?
If I am missing some subtlety in numba behavior, perhaps needs to be added here ?
Took me a while to figure out an off-by-one error.

Thanks for the report. Numba supports bounds checking but it's opt-in in the jit decorators via the kwarg boundscheck=True, docs: http://numba.pydata.org/numba-doc/latest/reference/jit-compilation.html?highlight=boundscheck#numba.jit
Example
from numba import njit
import numpy as np
@njit(boundscheck=True)
def foo():
  return np.zeros(5)[6]
foo() # raises IndexError

A PR with an addition to note that bounds checking is off by default and how to switch it on in this doc would be welcomed if you have time, thanks!

Ah, it all makes sense now, thanks for clarifying.
Will open a PR.
On Wed, Jul 8, 2020, 5:15 PM stuartarchibald<EMAIL_ADDRESS>wrote:

Thanks for the report. Numba supports bounds checking but it's opt-in in
the jit decorators via the kwarg boundscheck=True, docs:
http://numba.pydata.org/numba-doc/latest/reference/jit-compilation.html?highlight=boundscheck#numba.jit
Example
from numba import njitimport numpy as np@njit(boundscheck=True)def foo():
return np.zeros(5)[6]foo() # raises IndexError
A PR with an addition to note that bounds checking is off by default and
how to switch it on in this doc
https://numba.pydata.org/numba-doc/dev/reference/pysemantics.html would
be welcomed if you have time, thanks!
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AutoGen Framework

Delete

https://github.com/user-attachments/assets/99dca5ee-d7ff-48f7-b01e-f2c8e50388fc

https://github.com/user-attachments/assets/587920ed-9e6f-4b6a-917d-d74e71ef26fc


Add mTLS version as attributes.

Describe the feature request
Today we have connection.mtls boolean property that Indicates whether a request is received over a mutual TLS, It will be nice if we can add the version of the mTLS as attribute.

Closing in favor of #13791 (which should now be the umbrella bug for better telemetry around mTLS).


[Android] GoogleMaps.create() does not respect the Camera.target options

I'm submitting a ...  (check one with "x")

[ ] question
[ X ] any problem or bug report

OS:  (check one with "x")

[ X ] Android
[ ] iOS
[ ] Browser

cordova information:  (run $> cordova plugin list)
cordova-plugin-device 2.0.3 "Device"
cordova-plugin-googlemaps 2.7.1 "cordova-plugin-googlemaps"
cordova-plugin-ionic-keyboard 2.2.0 "cordova-plugin-ionic-keyboard"
cordova-plugin-ionic-webview 4.1.1 "cordova-plugin-ionic-webview"
cordova-plugin-splashscreen 5.0.3 "Splashscreen"
cordova-plugin-statusbar 2.4.3 "StatusBar"
cordova-plugin-whitelist 1.3.4 "Whitelist"

If you use @ionic-native/google-maps, please tell the package.json (only @ionic-native/core and @ionic-native/google-maps are fine mostly)
@ionic-native/core :  4.20.0
@ionic-native/google-maps : 4.21.0

Current behavior:

When you pass an options object with camera.target set.
Calling GoogleMaps.create("divId", options), will show the map.
But retrieving the camera position when the map is ready, shows that the CameraPosition.Target is not exactly the value that is passed via options
Expected behavior:

The getCameraPosition().target should have exactly the same value as options.camera.target
Screen capture or video record:

Related code, data or error log (please format your code or data):
https://github.com/ebhsgit/gmap-test/tree/bug-incorrect_cameraTarget

Running the code will result in the following lines in Console
com.ionicgmapstest I/chromium: [INFO:CONSOLE(110)] "-----Map.TARGET mapOptions [lat: 65.9667] [lng: -18.5333]", source: http://localhost/build/main.js (110)
com.ionicgmapstest I/chromium: [INFO:CONSOLE(115)] "-----Map.TARGET mapReady [lat: 65.96669994339966] [lng: -18.53329986333847]", source: http://localhost/build/main.js (115)

Support this plugin activity
I appreicate if you give me a beer :beer: from here

The maps sdk adjusts the camera position to contain the given bounds. Not fit exactly to the given bounds

I see.
Thanks for the information


Issue 26490 remove replacebr

This PR:

removes the replacebr rule option inside ExpensiMark.rules

Fixed Issues
$ https://github.com/Expensify/App/issues/26490
$ https://github.com/Expensify/App/issues/16982
Tests
Unit testing

Updated existing tests which are affected by this change to pass
Added new unit testing

Testing in the expensify-app

On your local dev environment of expensify-app, open node_modules/expensify-common/lib/ExpensiMark.js file
Remove replacebr rule
Run the app and test with the following recordings

https://github.com/Expensify/expensify-common/assets/30532000/05da9434-565c-41d5-8ddf-a5f5cd9f9727
https://github.com/Expensify/expensify-common/assets/30532000/4fd9da4a-8995-4c49-9282-f6c131a3ad91
https://github.com/Expensify/expensify-common/assets/30532000/671a105d-2af7-4f8d-9f1f-40218b50cd5b
https://github.com/Expensify/expensify-common/assets/30532000/941a2d8c-40ce-42c6-82bb-203c0f15c846
https://github.com/Expensify/expensify-common/assets/30532000/d9b475ee-0f8e-4c3a-abd7-454108805e3e
QA
Same as test

Please add test strings in Tests step for easier test. Example: #573.

Thanks, addressed by https://github.com/Expensify/expensify-common/pull/606/commits/7992a004cd3abaddb74f4444c409e9675956cb79

@0xmiroslav Do I need to add those cases to the unit testing or to the test strings in the PR description?

@0xmiroslav can you please do the review checklist on this one?
Thanks!

@0xmiroslav After this PR is merged, do I need to create another PR in the App to update the expensify-common package version? What will be measured as the days for the PR merged - this PR or another PR for App?
Upwork contract says that if I can get merged within 3 days, I can get 50% bonus, but if merged after 9 days, I will get penalty

@0xmiroslav Yes, we can see the same result in the current staging environment.
I assume if we want to fix it, we will need to create another issue and address it, but as we don't really want the edit mode to be exactly as the original text, it can be decided by the product team.

@danieldoglas Is there anything I need to do to merge this PR?

@danieldoglas Can you please update the version of expensify-common?


Update keywords

Add new, struct, unsafe, and throw
Drop java_new, java_get, java_set

@jaschdoc We got new, but I suppose there is others to look at.

Oh I did not see this


migrate to clap

given the structopt library is in maintenance mode and itself suggests to make the migration

it might also be a good idea to maybe just move the main.rs into a different crate in repository to enable flags on it so that it the library doesn't pull up dependencies required just for binary.

Concept ack on both changes.
I don't plan to work on this in the near future

I can take this up would be glad to contribute

is it fine if we move the main.rs file into examples? That will make these three optional:

structopt -> replace by clap
env_logger

Sure I think I am aligned with both the suggestions:

move main.rs into cli crate
feature gate Config parsing

Just one more confirmation these would be two new crates so would the name be

blocks_iterator (lib)
blocks_iterator_cli (main)

Should the examples still lie in lib crate or they can be moved as well?

Ack for the names, not sure for the examples honestly, whatever you think it's more appropriate.


Added HTTP Range

Fixes: https://github.com/Azure/azure-sdk-for-cpp/issues/1136

Perfectly suits current situation😄

I had a similar thought @Jinming-Hu, but in this case I think we all just want to help @vhvb1989 with this PR because of his impressive turnaround ;)

I had a similar thought @Jinming-Hu, but in this case I think we all just want to help @vhvb1989 with this PR because of his impressive turnaround ;)

Yes, absolutely. I also have a lot of comments in this PR. I just said it for fun.

Should we add a ctor and validate offset/length are not negative? And that length isn't 0?

Should we add a ctor and validate offset/length are not negative? And that length isn't 0?

I think that validation needs to happen on Server side. The SDK usually does not do input validation

But won't the SDK/protocol layer be creating instances of Ranges? What if the client library authors write buggy code and create an invalid range with negative values before passing it to the service?

This isn't MQ related, everything else belongs in January (the next milestone we release v-next), even if we finished them early.


Package request: tmux-weather

Project description
Tmux plugin for showing weather in status bar. Presumably the Nix package name would be tmuxPlugins.weather
Metadata

source URL: https://github.com/xamut/tmux-weather
license: mit
platforms: wherever tmux, bash, curl, and sed are supported

I would like to try this out.


emacs-ycmd in Emacs Ipython Notebook (EIN)?

This may be more of a ycmd thing than emacs-ycmd, but I figured I'd ask here first.
Is there any way to get emacs-ycmd completions working within EIN (If not familiar with EIN, it basically allows you to edit jupyter notebooks within emacs. repository: https://github.com/millejoh/emacs-ipython-notebook/)
I have completions working just fine for standard python files. I'm guessing the issue is that jupyter (ipython) notebooks use a different file extension than typical python files (since, at least as I understand, ycmd identifies which completer to use based on the filetype - although I could very well be wrong about that).

(My "short response" has turned into a bit of a rambling thinking-out-loud...)
It might be possible, but I'm not sure how much work it would take. The first issue I can think of is that ipython notebooks are not pure Python code, so the completion mechanism would need to know how to tell the difference. When we communicate with ycmd, we ship off the full text of the file being completed, so perhaps emacs-ycmd could figure that out at the client end. If EIN has facilities for extracting code blocks, it might be very easy. As part of the request to ycmd we can also specify the file-type, i.e. python in this case, so these seems like good steps along the way. File-type and contents might be enough for ycmd to work with.
We also send the path to the file as part of the request, and I'm not entirely sure what ycmd does with that. If we send the full text of a code block plus a filename which actually contains a superset of that codeblock, I don't know what will happen. Presumably it will actually work since, in general, the contents we send across are from modified buffers which don't match the file contents, i.e. ycmd evidently works fine in this case.
So I guess what I'm saying is that it doesn't seem unreasonable! And it would be super-cool if it worked. Do you have any capacity to try implementing it? I don't know when I'll get a chance.

Also, does EIN work well for you? I've tried it a few times, and I always run into strange hangs and stuff. I'd love to be able to work with notebooks entirely within emacs, but the state of ein has always been a bit lacking for me.

That sounds like a promising avenue to at least look in to. I'm still a bit of an eLisp novice unfortunately, but I'm not adverse to looking in to this more. I have to get up to speed on how emacs-ycmd and ycmd are working, though. The dev who has taken over EIN (@millejoh) may also be able to shed some light on this.
As for your other question, I haven't run into any major hiccups with EIN, although I'm primarily just using it for testing code snippets / exploratory data analysis (I primarily work with scientific python stuff), so I can't speak to a very wide array of use cases. Generally, though, it works quite well ("it just works", as the expression goes).

I thought about this a bit more, and one complication is how we'll report our position to ycmd. To get completions, we send to ycmd the code itself as well as our position in that code (line, column). Currently we derive that simply from the position in the emacs buffer, but of course that seems like it won't work so well for notebooks.
We'd need to first decide whether we send across all of the code in the notebook for each completion request, or just the current snippet. Since there are almost always dependencies between the snippets, and because the notebook authors often expect them to be treated as continuous (e.g. imports from one snippet are used in another), I think we'll need to send it all.
With that decided, we'd need to figure out how to determine our position in the conglomerate, independent of our position in the emacs buffer. I don't have any brilliant ideas on that right now, but perhaps some sort of narrowing scheme could work.
If you feel like taking a swing at this, I'll be more than happy to help. I'm no expert in elisp, but I learned what I have by jumping into the deep end (this project being part of that deep end!) If you want to see how emacs talks to ycmd, you can look at ycmd--request. This is where we initiate the HTTP message to the ycmd server (all communication is JSON in HTTP). Also look at ycmd--standard-content which is where we gather up the components which are part of almost every message we send to the server: file path, line number, etc. See ycmd-get-completions for a high-level function that puts all of the parts together...this is probably your best guide to getting started. You can see how this function is used if you look at company-ycmd--get-candidates.
If I find the time and inspiration I might take a swing at this as well, but I can't promise. I'm working on a book and that's taking up pretty much all of my spare time :-/

I agree, I think that the most logical thing is to send the entire set of code blocks. As you said, there are almost always dependencies between the different code blocks, and jupyter notebooks (at least, in the most basic sense) treats the whole workspace as one big namespace even though you can separate the snippets of code out into different executable segments.
Part of the question about how to approach it may be dependent on how EIN treats those blocks of code. I'm a bit bogged down with work stuff for the next few days, but I'll talk with the EIN dev and start reading through the docs you recommend this week. I'm sure I'll be back with questions soon ;)


Using dynamic environment

Explain your changes
Suppose there is a related issue with enough detail for a reviewer to understand your changes fully. In that case, you can omit an explanation and instead include either “Fixes #XX” or “Updates #XX” where “XX” is the issue number.
Checklist

[x] I have read the “Pull requests” section in the contributing guidelines.
[x] I agree to the terms within the code of conduct.

🛟 If you need help, consider asking for advice over in the Kinde community.

This PR is fixing a issue where env variables are imported only at builtime.

This LGTM :+1: , I created an issue against this PR linking to the original comment made in slack for more context.


is there away to get today result if i use search  with params in YOUTUBE

Hi @anmancontent, yes this is possible. I wrote an example of filtering a search request here - examples/filter-search.py.
From some quick reverse engineering, it looks like the params needed to only list results for the last day are EgIIAg%3D%3D
Hope that helps

thanks , this help alot i got today results and i got the idea to do some custom filtering


Add a CMake example

Adding a cmake example can help get started for C/C++ users for dora :)

This repo should work.

Thanks @Xxchang for the repo!
Would it be possible to modify one of the existing example or create a new example as a PR so that other people can get inspired if they are facing the same difficulties.
Thanks again!

Closed by #381


<EMAIL_ADDRESS>

Integrate addon 3.8.0 to new release branch.
Also fix test case in ECSqlRead.test.ts that was never backported to 3.7

@ColinKerr @rschili you guys might want to add to NextVersion.md detailing the changes to the ecdb profile

Related?
--[ FAILURE: @itwin/core-backend ]------------------[ 1 minute 33.3 seconds ]--

  379 passing (1m)
  1 failing

  1) bind Id64 enumerable
       ecsql reader simple using query reader:

      AssertionError: expected '0x34' to equal '0x32'
      + expected - actual

      -0x34
      +0x32

Related? Failed on Windows and MacOS. Linux didn't get there yet.
--[ FAILURE: @itwin/core-backend ]------------------[ 1 minute 33.3 seconds ]--

  379 passing (1m)
  1 failing

  1) bind Id64 enumerable
       ecsql reader simple using query reader:

      AssertionError: expected '0x34' to equal '0x32'
      + expected - actual

      -0x34
      +0x32

PR val didn't run properly, so native changes didn't get tested with itwinjs-core. Because of this we missed a test case, and the fix wasn't backported. I included the change, so now it should pass.
Also fixing PR val in imodel-native 3.x since it appears to be outdated


require declarationinfo for api extractor

Superseded by https://github.com/Zemnmez/monorepo/pull/524


Conversion to plugin?

I wanted to know if this is being planned to be converted to a plugin rather than a theme. I get the aspect of making a theme for simplicity, but also it is technically a plugin.

yes it can be one day but for the moment its just a css change !

maybe one day !


Closed Connection on bad quality status

Hi,
in a test setup where one subscribed node is giving back a bad quality status the connection is automatically closed by the Method ThreadTarget in Client.cs even if other nodes are still working as expected. But I would like to keep up the connection up and running. Do you know how to do that? Is it a bug in Client.cs?
Best regards
Thomas

Hello Thomas,
Reading a node with bad quality status should not close the connection. Connections are automatically closed when reading an invalid message (decoding error) but I may be wrong. Otherwise the client only disconnects when you call the method. Please upload a Wireshark capture and I can investigate further.
By the way, if you are using this library for any projects, there is no obligation but I would be very interested in hearing where and how. I would appreciate your permission to use that information in my list of use cases. If you prefer email, my email is my username @gmail.com
Thanks.

Hi,
we are using your library in our Digital Twin Solution for Unity (see https://realvirtual.io). You can reference to our solution if you would like.
I am not a Wireshark expert so I am describing you here how to reproduce the problem.
Our test opcua server is the C++ demo server from Unified automation which you could get here:
https://www.unified-automation.com/de/downloads/opc-ua-servers.html
In the demo server we subscribe to the node
ns=2;s=Demo.Dynamic.Scalar.Quality_DynamicValue
Only when subscribing to this node the conneection is closed by ThreadTarget in Client.cs.
Thanks a lot
Thomas

Great, thanks!
I don't have login for unified-automation, would you be able to upload that in a zip file here?

I have send you a download link to your mail. Thanks a lot.

Hello Thomas,
Looks like an exception in the demo app in the callback NotifyDataChangeNotifications. Please change to:
public override void NotifyDataChangeNotifications(uint subscrId, uint[] clientHandles, DataValue[] notifications)
{
	for (int i = 0; i < clientHandles.Length; i++)
	{
		Console.WriteLine("subscrId {0} handle {1}: {2}", subscrId, clientHandles[i], notifications[i].Value?.ToString());
	}
}

The issue was that node sometimes publishes notifications[i].Value as null.

While not robust in the sample application, you would need to handle exceptions during callbacks so they don't bubble up to the client's connection thread. Let me know if that works.
Thanks,
Nauful

Hi, thanks a lot - your hint solved the issue.

Great, let me know if anything else comes up.


Re-Structure the Project

Restructure the Project Folder like all Backend Stuff move on Server Folder and all Frontend Stuff move on Client Folder.
Please assign me! @tusharzalte

@ZapeeoSheikh have you merge that this issue?


Use require to load support files instead of load

I've run into a situation where I would like to control the load order for files in the features/support folder.
I got the impression, from reading The Cucumber Book, that Cucumber would behave similar to RSpec and only autoload features/support/.  I tried moving the files into features/setup/ and manually requiring the files from env.rb.  I quickly discovered that Cucumber wants to take over and load everything, regardless of the sub folder.  (To be precise, RSpec doesn't autoload files in spec/support unless it's specifically configured to do so.)
Next I tried moving all the files back into the features/support folder, but having File A explicitly require File B t to make sure File B is loaded before File A is executed.  Unfortunately, this doesn't work either because Cucumber uses the load method to load the support files.  Is there any reason Cucumber couldn't use require instead of load in this method?
https://github.com/cucumber/cucumber-ruby/blob/master/lib/cucumber/rb_support/rb_language.rb#L107
That would give us much more flexibility in controlling the order of how support files are loaded.  require would guarantee the file is only loaded once.  It wouldn't matter if Cucumber got to it first or I manually required it somewhere.
As it stands now, my only options are to combine the two dependent files into a single file, OR, move files outside of the feature folders; neither of which are good options.  The use of load blocks any attempt to establish order because it will blindly load the file even if it has already been loaded.

I don't believe there's a good reason for using load, no. Probably just an accident of history. I'll give it some thought.
I'm not near the code but do all the tests pass if you change it?

It looks like there are about 70 failures.

Ah interesting. The test failures seem to mostly be down to this which allows all Cucumber's own tests to be run in the same Ruby process. This is for performance - it's much slower to run the test suite when we work with files and processes for each scenario.
So Cucumber itself might work fine, but our tests are relying on the use of load, I think. We could build a new strategy for the Aruba process that uses fork which would be faster than the spawning strategy, but that might be too much of a yak-shave.
What do you think @roberts1000? Are you keen to dig any deeper?

So you're saying there's a chance.... :)
I wish I could contribute more to the discussion at this point, but this the first time I've looked at the internals of Cucumber.  I'm interested in digging deeper.  I'll need to carve out some time to get up to speed on Cucumber development.

@roberts1000 have you tried using require_relative instead of require?
I have a custom World class in a file under my support folder and then a helpers.rb file inside the same folder.
Custom world depends on helpers, so in my world file I have this:
require_relative 'helpers'

class CustomWorld
  include Helpers
  # other code
end

And it works just fine.
Now, if what you need is to have a file loaded first, then you can simply use require_relative from env.rb itself, for instance, I have a base_page.rb file where I have defined my Page class, that all my other pages inherit from, but I didn't want to have to require it in all the page files, so in my env file I just did this:
require_relative 'pages/base_page'
And now it is loaded before all the other support files, so I can use its contents from anywhere.

We can use require or require_relative to control the load order to an extent.  You're correct that it will ensure your file is loaded before you use it.  The problem is that Cucumber uses the load method internally which is not going to play nice with require or require_relative.  I suspect if you add some put statements in the helpers.rb`, you'll find that it's being loaded twice.  This can cause problems.
require and require_relative are smart enough to not load a file twice.  load however is not, and they don't play nice together.  If require fires first, load will come along and load it again.  If load fires first, require... will load it again.

@alvaroemmanuel it is not the order which is the issue, it is the fact that it will load a file more than once and thus execute any dangling code multiple times.

Thinking about this some more, I wonder if we could have two, configurable strategies, so the user can choose whether to use load or require during their test run. That would allow us to continue to use load in our own tests, but I'd have thought 80% of our regular users would be happy with require.

Got it, and agree, I think it would be preferred 99% of time to use require instead of load, at least for the common user, so I will +1 the idea of a setting that defaults to require, but can be changed to use load instead if needed, just as @mattwynne suggested.

run into the similar problem, one workaround is to put the base class file or included rb file in folders to have them in right order with folder name, say

_base folder has screen_base.rb
screen folder has screen1.rb, screen2.rb  (all are sub class of screen_base)

this way, classes in _base folder are loaded first, then other folders.
it works, but... kind of...

It's still pending and should not be closed.

If @mattwynne or @roberts1000 could point me to some active links (Given the original links are 3 years old nearly), I'll have a little dive into this as most of the tidying up I did for rails is now in PR.
Not saying I'll get anywhere with this, but I'll take a stab

Hi @luke-hill.  I haven't followed the project in a while so I'm out the loop.  I did a quick search for load  (with a space at the end) and found this.  It might get you started.

@mattwynne Can I get you to look over a mini-spike I have for this, at some point in the next few days.
I've found it quite easy to switch these through configuration settings (I've got 2 different ways of doing this, so have pushed both into a branch), I'm just writing a couple of unit tests as an initial POC. I'll push something up to this repo tonight/tomorrow.
Obviously I have no idea if that's what you're happy with. I encountered the same issue as @roberts1000 - One unit test fails precisely because it prevents this functionality (Being able to only load once), and then a truckload of tests fail because aruba re-writes to the same temporary file names, which obviously won't be re-loaded in during the same ruby thread being used and as such about 50% of the features fail for undefined step

Ironically I write about this in the blog post coming out @p0deje, so I will be able to cover this use case.
I'll alter the usage accordingly @mattwynne in the PR and fix up the tests / merge with master

This is now in master

@luke-hill Do you know if this will fix things for cucumber-rails as well? Or is it necessary to do a similar change over there?

As cucumber-rails uses cucumber then yes it "should" fix things.
Obviously with a variety of auto-loaders present things may get messy. Once we've released a cut of the gem which is compatible, we will update people accordingly.

@luke-hill Looking forward to the release. Thanks for fixing this!

@stripedpumpkin - I just realised that as we now have an rc cut of this gem, we could do a new version of cucumber-rails for this if you would like?

@luke-hill That would be great. We could try it on a branch and see how that goes.


No 'Toggle Explorer & Manage Accounts & Add account' buttons present

Storage Explorer Version: 1.5.0
Platform/OS Version: Windows 10
Architecture: ia32
Build Number: 20181022.4
Commit: 492b519a
Regression From: Previous release 1.4.4
Steps to Reproduce:

Launch the Storage Explorer -> Check the top left of the Storage Explorer.

Expected Experience:
'Toggle Explorer & Manage Accounts & Add account' buttons present at the top of left in storage explorer.
Actual Experience:
No 'Toggle Explorer & Manage Accounts & Add account' buttons present at the top left of storage explorer.

More Info:
This issue doesn't reproduce on Mac/Linux.

Fixed.


Use . instead of , when numbering.

In english, we use . instead of . to number things. e.g:
1. A
2. B
3. C
4. D

instead of
1, A
2, B
3, C
4, D

Is it possible to configure this? Or how would i modify it to do this? Can you point me to the right place.

在英语中，我们使用 . 而不是 . 进行编号。例如：
1. A
2. B
3. C
4. D

代替
1, A
2, B
3, C
4, D

可以这样配置吗？或者我将如何修改它来做到这一点？你能指出我正确的地方吗？

thanks, just need few changes
https://github.com/teedoc/teedoc/blob/d6fe63a68137f467c4b3d4782c4805e4501a85f1/plugins/teedoc-plugin-theme-default/teedoc_plugin_theme_default/assets/main.js#L210-L224
and
https://github.com/teedoc/teedoc/blob/d6fe63a68137f467c4b3d4782c4805e4501a85f1/plugins/teedoc-plugin-theme-default/teedoc_plugin_theme_default/assets/light.css#L535-L544
I'm also considering whether it's appropriate to use roman numerals in the table of contents, or just use numbers

Thanks, I have done PR #11 to fix this. It should keep the chinese "、" when the locale is set to zh, otherwise it will use the .

I optimized code (https://github.com/teedoc/teedoc/commit/4f378d8c05686d6f9fce125dbd4d879f27253f5b) after you PR, now it looks:
Cinese:

Others:

Before:
Chinese:

Others:

But I remain don't know if roman number should be used like this:

But I remain don't know if roman number should be used like this:

I think its okay, I think it depends on what you prefer


Automated Package Upgrade

:tada: This PR is included in version 5.0.424 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Document hot and cold Observable behavior

Would it make sense to add a column to the "Observable behavior" table in ReadMe to state whether each Observable is hot or cold?
Some (like observeConnectionStateChanges) are obvious, but with others it's perhaps not so clear.

Closed by #332


[21.11] openssl_1_1: 1.1.1n -> 1.1.1o

Fixes command injection in the c_rehash script, which at the same time
is also considered obsolete and should be replaced by openssl rehash.
https://mta.openssl.org/pipermail/openssl-announce/2022-May/000224.html
Fixes: CVE-2022-1292
(cherry picked from commit a7be3b2607fef40cb8a9a04ea4ee7753ad8a58e0)
Description of changes

Things done

Built on platform(s)

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

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

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

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
22.05 Release Notes (or backporting 21.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[x] Fits CONTRIBUTING.md.

Yep, that's why I went with staging for unstable as well.


Configure CI to test for Python 3.9 to 3.11

Right now the Python version in CI is not fixed and this has resulted into inconsistency between local and CI environments. Let's add the configuration to run testing for Python 3.9 to 3.11.

Closed via #231.


Array.reduce method does not get type-checked correctly

Array.reduce method does not get type-checked correctly.
Eample:
/**
 * @type {Array<number>}
 */
const arr = [1,2,3]
const sum = arr.reduce((a, b) => a + b, 0);

Raises these errors:
./src/js/index.js:12:12: ERROR - [JSC_UNKNOWN_EXPR_TYPE] could not determine the type of this expression
  12| const sum = arr.reduce((a, b) => a + b, 0);
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

./src/js/index.js:12:33: ERROR - [JSC_UNKNOWN_EXPR_TYPE] could not determine the type of this expression
  12| const sum = arr.reduce((a, b) => a + b, 0);
                                       ^

Even though the callback parameters are obviously number and the result as well.
Compiler Version: v20221102
Build command:
java -jar ./scripts/closureCompiler.jar \
  --entry_point=./src/js/index.js \
  --js=./src/**.js \
  --dependency_mode=PRUNE \
  --warning_level=VERBOSE \
  --js_output_file=./dist/bundle.js \
  --module_resolution=WEBPACK \
  --compilation_level=ADVANCED \
  --jscomp_error=checkDebuggerStatement \
  --jscomp_error=unusedLocalVariables \
  --jscomp_error=reportUnknownTypes \
  --jscomp_error=strictCheckTypes;

The type-signature of Array.prototype.reduce is defined in the externs, at
https://github.com/google/closure-compiler/blob/master/externs/es3.js#L704
It seems like the correct type for reduce would be for the callback first argument and the initial value to both be of type R rather than ?/*.

I have just noticed - method Array.reduceRight suffers from the same problem


ipfs-force-community-droplet.yaml

The format has been modified, please check

Closing this out. You do not have any commit history with the ipfs-force-community or venus.


Make rustzx-core crate no-alloc friendly

Basically, rustzx-core in the 99% cases only allocates some big Vec chunks with fixed sizes, therefore, if we can eliminate the direct usage of alloc by adding a new abstraction for memory manager to HostContext, rustzx-core can be ported almost to any platform, even without any sophisticated allocators (memory manager simply could return sequential chunks of a single big static buffer to rustzx).
I see the following steps to implement this:

Fix blocking issue #65
Add MemoryManager & DynamicMemory traits to host module

pub trait DynamicMemory {
    type MemoryChunk: DynamicMemory;
    fn allocate(&mut self, size: usize) -> MemoryChunk
}

pub trait  DynamicMemory {
    fn as_slice(&self) -> &[u8];
    fn as_mut_slice(&mut self) -> &mut [u8];
}

Replace all Vec/Box usages with DynamicMemory
Remove alloc dependency
Implement DynamicMemory and DynamicMemory  in rustzx app based on Vec

closing as non-goal for the project


TypeError: require(...) is not a function

Laravel Mix Version: 6.0.39 (npm list --depth=0)
Node Version (node -v): 17.0.1
NPM Version (npm -v): 8.1.0
OS: MacOs 11.6.1

Description:
npm run dev failes with :
TypeError: require(...) is not a function
when building Tailwindcss and one have this:
plugins: [
        require('@tailwindcss/forms')({
            strategy: 'class',
        })

    ],

npm run dev fails
Steps To Reproduce:

laravel new test
cd test
composer require laravel/breeze
php artisan breeze:install
npm install
modify taiwindcss.config.js to include the plugin as described above
npm run dev

observe the error

The error is saying the result	of	require('@tailwindcss/forms') is not a function. It's using an older version that doesn't return a function but an object of type { handler: Function, config: undefined }.
Upgrade your version in package.json to ^0.3.4.


Multi select - cannot delete added item on iPad/iPhone

Items added in multi select cannot be deleted using the x icon on iPad/iPhone.

This works for me, I have a ui multiple search selection dropdown and I can tap the X to delete selections on iPad. Can you provide a fiddle?

Touch events are still not  handled wonderfully in dropdown. You will see click lag on mobile without using fastClick. The use cases are pretty complex. You can't assume someone with touch events will not use a mouse (consider a tablet with a mouse attached).
I will have to delay providing a proper solve for this. I should however prevent multiple from toggling on touch

I am using iPad 2 Safari directly with Semantic UI official website examples.

I'm no longer having issues with this after updates. I

It is ok now.


[Story]: Add TGIS and Caikit OOTB Serving Runtime

Goal
Add manifest files for the OOTB Custom Serving Runtimes for TGIS and CaiKit
Dependency issue

https://github.com/opendatahub-io/odh-dashboard/issues/1912

Itemized goals

Add manifest for TGIS
Add manifest for Caikit
Ensure they are OOTB
Ensure they are only targeted for KServe

Aspects continued elsewhere
No response
Mocks

https://www.sketch.com/s/45df001b-2441-4124-a436-5ae1abb409c9/a/L4ewQGl

We need to get the specs for this @danielezonca @Xaenalt can you help us out here please?


DNS over UDP relay

Perform DNS resolution through Shadowsocks' UDP relay.
Deprecate DNS (SOCKS/TCP) resolver, remove dependencies.

Thank you for the review @jab! You brought up important code health issues, as well as best development practices. Overall, I think we should create issues for these and instead of fixing them in this PR.


ChatScroller: Enable external selector

ChatScroller: Enable external selector

(GIF: Demo of ChatScroller controlling a parent scrollable node)
This update enhances ChatScroller to be able to control scrollable
nodes that may exist as parent nodes (instead of child only).
ChatScroller has also been refactored with the latest HSDS conventions,
including propConnect and Typescript.

Pull Request Test Coverage Report for Build 1456

25 of 25 (100.0%)  changed or added relevant lines in 3 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 100.0%

Totals

Change from base Build 1455:
0.0%

Covered Lines:
5701

Relevant Lines:
5701

💛  - Coveralls


Update lowrisc_ibex to lowRISC/ibex@42827fc9

Update code from upstream repository
https://github.com/lowRISC/ibex.git to revision
42827fc9cd0b2043d5d179cae46b0238a55d3652

[rtl/icache] Switch ECC granularity to 32bits (Tom Roberts)
Update lowrisc_ip to lowRISC/opentitan@1ae03937f (Tom Roberts)
[rtl] Fix lint issues (Greg Chadwick)
[dv/ibex] filter out tests on a per-config basis (Udi Jonnalagadda)

Signed-off-by: Tom Roberts<EMAIL_ADDRESS>

@msfschaffner note this updates the icache ram widths so will affect synthesis


Algorithmic improvements

Fix the cycle_check procedure.
Use Kahn's algorithm in walk_mut. The previous implementation was likely exponential in the amount of nodes.
Change the schedule output order to match the order of computation. (Dependencies before dependents.) Not sure why it was .rev()'d.
No longer require passing the root node into compile(). Kahn's algorithm has to find all sinks anyways, and so having multiple "roots" is now possible.

To confirm I didn't misunderstand something in the old implementation:
use std::time::Instant;
for dmds in 1..20 {
    let start = Instant::now();
    let mut graph = Graph::default();
    let nodes: Vec<_> = (0..dmds*3+1).map(|i| graph.node(i)).collect();
    for dmd in 0..dmds {
        let ao = graph.port(nodes[dmd*3], DefaultPortType::Audio, "output").unwrap();
        let bi = graph.port(nodes[dmd*3+1], DefaultPortType::Audio, "input").unwrap();
        let bo = graph.port(nodes[dmd*3+1], DefaultPortType::Audio, "ouput").unwrap();
        let ci = graph.port(nodes[dmd*3+2], DefaultPortType::Audio, "input").unwrap();
        let co = graph.port(nodes[dmd*3+2], DefaultPortType::Audio, "output").unwrap();
        let di1 = graph.port(nodes[dmd*3+3], DefaultPortType::Audio, "input1").unwrap();
        let di2 = graph.port(nodes[dmd*3+3], DefaultPortType::Audio, "input2").unwrap();
        graph.connect(ao, bi).unwrap();
        graph.connect(ao, ci).unwrap();
        graph.connect(bo, di1).unwrap();
        graph.connect(co, di2).unwrap();
    }
    graph.compile(*nodes.last().unwrap());
    let duration = start.elapsed();
    println!("{}: {:?}", dmds, duration);
}

1: 1.715639ms
2: 1.008397ms
3: 1.925143ms
4: 5.067029ms
5: 22.4722ms
6: 115.726976ms
7: 635.656596ms
8: 3.67741599s
9: 21.40968849s


Retry failed TCP connection to Riemann indefinitely

Currently if the connection to Riemann fails more than twice within a one second window the associated IO actor is stopped and no further retries are attempted.

Patch provided in https://github.com/benmur/riemann-scala-client/pull/12.

Merged, thanks!


Remove rust-version from cargo files

Description
Currently, all of our cargo.tomls specify a rust-version even though we have  rust-toolchain.toml file. This removes that redundancy.

cc @neysofu @vlopes11, do either of you see any downsides here? I think these are just redundant, but don't remember why they were added

rust-toolchain.toml specifies the intended Rust toolchain to develop the workspace in, whereas rust-version lets downstream users know the minimum required rustc version to be able to use the package.
It's a good thing to have both, but only if checked in CI with a tool like https://github.com/foresterre/cargo-msrv, otherwise rust-version will inevitably get out of sync, just like in our case. I'm in favor of removing it. It would be ideal to reintroduce it once we're confident we can provide correct values: https://github.com/Sovereign-Labs/sovereign-sdk/issues/1081.

rust-toolchain.toml specifies the intended Rust toolchain to develop the workspace in, whereas rust-version lets downstream users know the minimum required rustc version to be able to use the package.
It's a good thing to have both, but only if checked in CI with a tool like https://github.com/foresterre/cargo-msrv, otherwise rust-version will inevitably get out of sync, just like in our case. I'm in favor of removing it. It would be ideal to reintroduce it once we're confident we can provide correct values: #1081.

I agree that checking MSRV is good thing, but I believe that at this moment of rapid changes of the repo it might slow as down. So I am voting to remove rust_version now and re-untroduce it later. Because with MSRV we will also have to respect MSRV of core dependencies.

Ah, I'd forgotten this was used for MSRV checks. Yeah, we definitely need at least 1.70 already and will probably keep bumping that for a while. But agreed, let's add this back as things stabilize.


chore: remove redundant whitespace

Would it be fine to refactor or reformat parts of the repository?
I'd like to contribute more, but I thought it could be nice to clean things up a bit, especially the unit tests.
This PR removes 3,000+ redundant lines, as they were a bit annoying while browsing the repo. ^-^'

Removes trailing white space characters.
Removes redundant line breaks.
Fixes indentation of certain functions that used 2 spaces instead of 4.
Adds spaces around operators.

Examples
Multiple Line Breaks
public void functionA() {

}

public void functionB() {

}

Line Break At Start and End of Method
public void myFunction() {

    doA();
    doB();

}

Trailing Blank Lines in Docs
/**
 * Documentation for the class.
 *
 */
public class MyClass {

}

Next Line Curly Instead of Inline
try {

}
catch (Exception ex) {

}

@SethFalco
Sorry, I'm not going to review 253 files :-(

No worries, I'll close this then.
I'll just clean up the relevant files when doing other PRs.


Enroll via the CLI guide is using obsoleted commands

Existing documentation URL(s)
https://developers.cloudflare.com/cloudflare-one/connections/connect-devices/warp/deployment/manual-deployment/#enroll-via-the-cli
What changes are you suggesting?
Running the 3rd step yields this deprecation warning:
$ warp-cli teams-enroll xxx
NOTICE:

Your organization is using Cloudflare for Teams, a security platform that makes
connections to the Internet and applications faster and safer.

What information is available to administrators of my organization?

The following information may be viewed by administrators from your
organization:

* the websites you visit
* the times you visited them

More information is available at:
- https://www.cloudflare.com/application/terms/
- https://www.cloudflare.com/application/privacypolicy/

Accept Terms of Service and Privacy Policy? [y/N] y

Warning: The "teams-enroll" command will be deprecated in a future release. Please use "registration initialize-token-callback" instead

^ last line
Additional information
No response

using version 2024.9.346.0, the teams-enroll command no longer exists, yet is still referenced by the documentation.
$ warp-cli teams-enroll
error: unrecognized subcommand 'teams-enroll'

Usage: warp-cli [OPTIONS] <COMMAND>

For more information, try '--help'.

using version 2024.9.346.0, the teams-enroll command no longer exists, yet is still referenced by the documentation.
$ warp-cli teams-enroll
error: unrecognized subcommand 'teams-enroll'

Usage: warp-cli [OPTIONS] <COMMAND>

For more information, try '--help'.

same there

Also https://developers.cloudflare.com/cloudflare-one/connections/connect-networks/private-net/warp-connector/ references warp-cli accountwhich is also not recognized. Let me know if I need to open a separate issue for this.

Also https://developers.cloudflare.com/cloudflare-one/connections/connect-networks/private-net/warp-connector/ references warp-cli account and warp-cli delete which is also not recognized. Let me know if I need to open a separate issue for this.
No need to open a separate issue -- we are in the process of removing these commands from the WARP Connector setup procedure (#16486).

Replacement (as far as I can tell for wrap-cli teams-enroll is warp-cli registration new <team name>

user:~$ warp-cli registration
Registration settings
Usage: warp-cli registration [OPTIONS]
Commands:
show          Show information about the current registration
new           Register this client (Must be run before first connection!)
delete        Delete current registration
organization  Get the name of the current Teams organization
devices       Display the list of devices associated with the current registration
license       Attach the current registration to a different account using a license key
help          Print this message or the help of the given subcommand(s)


Linux: Unable to launch Code after upgrade to 1.57

Does this issue occur when all extensions are disabled?: Yes

VS Code Version:
1.57.0
b4c1bd0a9b03c749ea011b06c6d2676c8091a70c
x64

OS Version:
Ubuntu 20.04.2 LTS

Steps to Reproduce:

Upgrade vscode to latest version using apt
Start vscode either by clicking the icon in Gnome, or writing "code" in the terminal

I know this bug report doesn't help much, but I do not know what else to include. I did "apt update" this morning, and vscode stopped working after this. When writing "code" in my terminal, nothing happens. No output, nothing. The same has happened to a colleague with the same OS/machine. If there is anything more I should add (logs, etc), I would be more than happy to include it.
I noticed that there are some bug reports on the settings file being corrupted, but that does not seem to have happened to me.

Does it work when you run code --no-sandbox?

@bpasero Yes, that helps!

@erikfroseth how did you install VSCode? Snap?

I installed it using this guide: https://code.visualstudio.com/docs/setup/linux#_debian-and-ubuntu-based-distributions
Downloaded the .deb and did the following steps:
sudo apt install apt-transport-https
sudo apt update
sudo apt install code # or code-insiders

Any chance you are running code as sudo?

No, I'm not running code as sudo. If I try running it as sudo, I get a warning saying You are trying to start Visual Studio Code as a super user ...

How about running with --disable-setuid-sandbox?

It still does not start. It gives me a warning, though: Warning: 'disable-setuid-sanbox' is not in the list of known options, but still passed to Electron/Chromium.
However, I see that entering "code" in my terminal does start some processes that never dies:
erikfroseth@erik-desktop:~$ ps -A | grep code
erikfroseth@erik-desktop:~$ code
erikfroseth@erik-desktop:~$ ps -A | grep code
  43167 ?        00:00:00 code
  43170 ?        00:00:00 code
  43171 ?        00:00:00 code

I have the same problem

@erikfroseth can you make sure to kill all code processes and then try https://github.com/microsoft/vscode/issues/126019#issuecomment-859413252

@deepak1556 Still the same problem :-(

@deepak1556 Still the same problem :-(

Me too

Killing the processes worked fine, and now no more processes appears, but still no sign of vscode starting

We will push https://github.com/microsoft/vscode/issues/126027 for May recovery which will restore --no-sandbox.

@bpasero Big kudos to you and the team for super fast response! Thank you very much for your help


[Extension types] Failure to recognize constant results of extension type constructors in switches

Example:
enum Bool {
  _true._(true),
  _false._(false);
  final bool isTrue;
  const Bool._(this.isTrue);
  const factory Bool(bool value) = _BoolHelper;
}

extension type const _BoolHelper._(Bool _) implements Bool {
  const _BoolHelper(bool isTrue) : this._(isTrue ? Bool._true : Bool._false);
}

void main() {
  var b = Bool(DateTime.now().millisecondsSinceEpoch > 0); // True.
  var ago = switch (b) {
    const Bool(false) => "Some time ago",
    const Bool(true) => "More recent",
  };
  print(ago); // More recent
}

This code runs in CFE and prints "More recent".
The analyzer reports the following:
  error - switch-const-value-fail.dart:15:13 - The type 'Bool' is not
          exhaustively matched by the switch cases since it doesn't
          match 'Bool._true'. Try adding a wildcard pattern or cases
          that match 'Bool._true'. - non_exhaustive_switch_expression

Since the actual two constant values of the switch cases are indeed Bool._false and Bool._true (it can't be any other value, since it's an enum, and it's not the same value), the switch should be exhaustive.
The front-end recognizes the actual constants from evaluating const Bool(false) and const Bool(true).

@kallentu

Surfacing this to @scheglov
BTW thank you for fixing the other related bugs. I appreciate it a lot!

This issue was fixed by 0ab26a77519b316372a2249af1c853e3645d4296.


changed OP Number to Registration Number

Proposed Changes

Fixes #9513
change 1

@ohcnetwork/care-fe-code-reviewers
Merge Checklist

[ ] Add specs that demonstrate bug / test a new feature.
[ ] Update product documentation.
[ ] Ensure that UI text is kept in I18n files.
[ ] Prep screenshot or demo video for changelog entry, and attach it to issue.
[ ] Request for Peer Reviews
[ ] Completion of QA

Summary by CodeRabbit

New Features

Updated label for the patient_no field from "OP Number" to "Registration Number" when the suggestion is not "A".
Enhanced validation for the patient_no field to ensure it is required when the suggestion is "A".
Adjusted handling of the suggestion field to set specific values in the form state, including setting consultation_notes to "Patient declared dead" for suggestion "DD".

Bug Fixes

Improved error handling logic to display appropriate error messages based on form state.

Closing as changes would need to be made in the new branch (a lot has changed); also don't work on the issues until they are assigned 👍  These issues in particular are blocked.


[FR] Hope annotated highlights could show indicator flags

Describe your request
At the moment, I can't confirm if one of my highlights contains the comments I wrote earlier.
I can only click on them to confirm.

The following is the display of readwise reader

I agree that this would be a hugely beneficial feature.


fix(http1): don't add content-length to head resp

Head responses should not have content-length implicitly set by hyper.
Fixes #2835

thank you for the quick response :)


[Editor] Fix closing then reopening asset when undocked

Description

Remove visibility logic check when closing event is raised so the asset window can actually close, otherwise it's hidden in limbo and the asset can't be reopened.
I have also removed the check in the CurveEditor code, but didn't test that which I'm not sure if it exists anymore.
Motivation and Context

This bug is occurring to due to adding the new forked AvalonDock.
Not sure if this logic check was originally meant as some workaround for some bug in the original AvalonDock, eg. it raised close event when it shouldn't have, or if there's some condition where this is raised and we don't want it to close?
Types of changes

[ ] Docs change / refactoring / dependency upgrade
[X] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist

[ ] My change requires a change to the documentation.
[ ] I have added tests to cover my changes.
[ ] All new and existing tests passed.

Ok, so I wrote that code 4 years ago. There were indeed some issues with the CurveEditor, but of course I don't remember most of it (unfortunately I don't seem to have kept any of my notes).
I'll look at the commit messages on my old fork and try to figure out what was happening at that time. I do remember that at the time the ÌsActive, IsHiddenand other visibility properties on aRadPane` had some strange behaviors.

Thanks for investigating. I think the code I deleted was specifically for when the original AvalonDock was first introduced, so not sure if you know what happened to that.
I think you can ignore the CurveEditor. Looking at the code, it's placed inside a LayoutAnchorable which is the problematic control, not the CurveEditor itself (though, as said before I think it's not used anymore, so probably not too much of a concern)

@Basewq the curve editor is used to animate particles.


[7.186.2] Language bug upon package version creation when installing dependencies with validation skipped

Summary
When trying to create a new package version, if the dependent package was created without validation, then language errors might occur. Might be related to previous issue #1883
Steps To Reproduce:
Repository to reproduce: dreamhouse-lwc

Ensure that you are connected to a DevHub with a default language != English (or language on user is != English, not sure how default language is set in build orgs). In my case this is Norwegian. Also ensure that the language option in project-scratch-def.json is set to en_US:
 "language": "en_US",

Create new folder archive and add a custom object Archive__c with the Vowel parameter in the object file:
    <startsWith>Vowel</startsWith>

Create a new package using sfdx package create -n archive -r archive -t Unlocked -v myhuborg

Successfully create new version of archive package using sfdx package version create -p archive -w 10 -x -v myhuborg -f config/project-scratch-def.json --skip-validation
NB! This is created without validation

Create second folder archive-field. Add Archive field "Test_Field__c"

Create second package using sfdx package create -n archive-field -r archive-field -t Unlocked -v myhuborg

Add archive package as dependency to archive-field package

Create version of archive-field package using sfdx package version create -p archive-field -w 15 -x -v myhuborg -f config/project-scratch-def.json

Expected result
A new package version of archive-field is successfully created
Actual result
Error (1): Multiple errors occurred:
(1) Det oppstod en feil ved forsøk på å installere en pakkeavhengighet. ID 04t090000003oVs: Archive__c: Cannot specify a startsWith attribute for this language
System Information
{
  "cliVersion": "sfdx-cli/7.186.2",
  "architecture": "darwin-x64",
  "nodeVersion": "node-v18.13.0",
  "pluginVersions": [
    "@dxatscale/sfpowerscripts 20.2.11 (user)",
    "@eon-com/eon-sfdx 1.9.4 (user)",
    "@oclif/plugin-autocomplete 1.4.2 (core)",
    "@oclif/plugin-commands 2.2.4 (core)",
    "@oclif/plugin-help 5.2.1 (core)",
    "@oclif/plugin-not-found 2.3.17 (core)",
    "@oclif/plugin-plugins 2.2.4 (core)",
    "@oclif/plugin-search 0.0.11 (core)",
    "@oclif/plugin-update 3.1.0 (core)",
    "@oclif/plugin-version 1.2.1 (core)",
    "@oclif/plugin-warn-if-update-available 2.0.23 (core)",
    "@oclif/plugin-which 2.2.9 (core)",
    "1commerce 0.0.10 (user)",
    "alias 2.1.19 (core)",
    "apex 1.4.3 (core)",
    "auth 2.3.12 (core)",
    "community 2.1.5 (core)",
    "config 1.4.23 (core)",
    "custom-metadata 2.0.16 (core)",
    "data 2.1.22 (core)",
    "generator 2.0.17 (core)",
    "info 2.3.5 (core)",
    "limits 2.2.3 (core)",
    "org 2.2.24 (core)",
    "packaging 1.12.4 (core)",
    "schema 2.2.3 (core)",
    "signups 1.2.12 (core)",
    "source 2.3.16 (core)",
    "telemetry 2.0.7 (core)",
    "templates 55.2.3 (core)",
    "trust 2.3.0 (core)",
    "user 2.2.1 (core)",
    "@salesforce/sfdx-plugin-lwc-test 1.0.1 (core)",
    "salesforce-alm 54.8.5 (core)",
    "sfdmu 4.26.2 (user)",
    "sfpowerkit 6.0.1 (user)"
  ],
  "osVersion": "Darwin 21.6.0",
  "shell": "zsh",
  "rootPath": "/Users/user/.local/share/sfdx/client/7.186.2-b2fe485"
}

Additional information
This error does not occur when downgrading sfdx version to 7.179.0. However, after creating a new package version on 7.179.0 with validation skipped, installing 7.186.2 and creating a new version of archive-fields --> the bug occurs again
If the archive package is created with validation, then the bug does not occur

Hello, does anybody know of any known workaround to address this problem?

@JorisOldeBijvank If I remember correctly I do not get this error when the latest package dependency was created with validation. We have just downgraded our CLI versions to below 7.186 until it is resolved
I have an ongoing case with Salesforce Support regarding this, they have been trying to recreate the bug for some time

@petter-eikeland Thank you for your comment.
Unfortunately, downgrading our CLI version causes problems with the new naming conventions of Global Value Sets.
I have to keep my fingers crossed until it is resolved, and in the meantime, I will try to deploy the source directly to the org without a package and see if that'll work.

@JorisOldeBijvank Seems like the newest RC contains a fix, have not tested it yet

Ah, great. Thanks for letting me know!

Seems like this is fixed with the newest RC!


[BUG] Many mypy errors from python_interpreter.py

Required prerequisites

[X] I have read the documentation https://camel-ai.github.io/camel/camel.html.
[X] I have searched the Issue Tracker and Discussions that this hasn't already been reported. (+1 or comment there if it has.)
[X] Consider asking first in a Discussion.

What version of camel are you using?
master/HEAD
System information

Problem description
@lightaime @dandansamax
Let's fix mypy errors in the newly added code before we make mypy mandatory.
mypy --install-types --non-interactive --namespace-packages -p camel
camel/utils/python_interpreter.py:85: error: Need type annotation for "fuzz_state" (hint: "fuzz_state: Dict[<type>, <type>] = ...")  [var-annotated]
camel/utils/python_interpreter.py:88: error: Incompatible default for argument "state" (default has type "None", argument has type "dict[str, Any]")  [assignment]
camel/utils/python_interpreter.py:88: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
camel/utils/python_interpreter.py:88: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
camel/utils/python_interpreter.py:169: error: Argument 1 to "_execute_ast" of "PythonInterpreter" has incompatible type "expr | None"; expected "AST"  [arg-type]
camel/utils/python_interpreter.py:190: error: Incompatible types in assignment (expression has type "str | None", variable has type "alias")  [assignment]
camel/utils/python_interpreter.py:195: error: "Index" has no attribute "value"  [attr-defined]
camel/utils/python_interpreter.py:224: error: Argument 1 to "_assign" of "PythonInterpreter" has incompatible type "expr"; expected "Name | _ast.Tuple"  [arg-type]
camel/utils/python_interpreter.py:231: error: Argument 1 to "len" has incompatible type "_ast.Tuple"; expected "Sized"  [arg-type]
camel/utils/python_interpreter.py:232: error: Argument 1 to "len" has incompatible type "_ast.Tuple"; expected "Sized"  [arg-type]
camel/utils/python_interpreter.py:234: error: No overload variant of "zip" matches argument types "expr_context", "Any"  [call-overload]
camel/utils/python_interpreter.py:234: note: Possible overload variants:
camel/utils/python_interpreter.py:234: note:     def [_T_co, _T1] zip(cls, Iterable[_T1], /, *, strict: bool = ...) -> zip[tuple[_T1]]
camel/utils/python_interpreter.py:234: note:     def [_T_co, _T1, _T2] zip(cls, Iterable[_T1], Iterable[_T2], /, *, strict: bool = ...) -> zip[tuple[_T1, _T2]]
camel/utils/python_interpreter.py:234: note:     def [_T_co, _T1, _T2, _T3] zip(cls, Iterable[_T1], Iterable[_T2], Iterable[_T3], /, *, strict: bool = ...) -> zip[tuple[_T1, _T2, _T3]]
camel/utils/python_interpreter.py:234: note:     def [_T_co, _T1, _T2, _T3, _T4] zip(cls, Iterable[_T1], Iterable[_T2], Iterable[_T3], Iterable[_T4], /, *, strict: bool = ...) -> zip[tuple[_T1, _T2, _T3, _T4]]
camel/utils/python_interpreter.py:234: note:     def [_T_co, _T1, _T2, _T3, _T4, _T5] zip(cls, Iterable[_T1], Iterable[_T2], Iterable[_T3], Iterable[_T4], Iterable[_T5], /, *, strict: bool = ...) -> zip[tuple[_T1, _T2, _T3, _T4, _T5]]
camel/utils/python_interpreter.py:234: note:     def [_T_co] zip(cls, Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], /, *iterables: Iterable[Any], strict: bool = ...) -> zip[tuple[Any, ...]]
camel/utils/python_interpreter.py:319: error: Argument 1 to "_assign" of "PythonInterpreter" has incompatible type "expr"; expected "Name | _ast.Tuple"  [arg-type]
camel/utils/python_interpreter.py:346: error: Item "str" of "str | alias" has no attribute "asname"  [union-attr]
camel/agents/embodied_agent.py:130: error: Dict entry 0 has incompatible type "str": overloaded function; expected "str": "BaseToolAgent"  [dict-item]
Found 12 errors in 2 files (checked 38 source files)

Reproducible example code
Command lines:
mypy --install-types --non-interactive --namespace-packages -p camel
mypy --install-types --non-interactive --namespace-packages -p test

Traceback
No response
Expected behavior
No response
Additional context
No response

@dandansamax thanks for the swift fix


Support @RequestPart annotation

TLDR: @RequestPart parameters should have paramType of form and models should be generated for @RequestPart annotated parameters.

When using the @RequestPart annotation, the paramType attribute for that parameter is incorrect (unless the parameter is a MultipartFile). When making an api operation that uses a file upload, we can no longer use @RequestBody, instead it must be @RequestPart, which means the overall request Content-Type becomes mulitpart/form-data.
While this all works fine if the if the file upload is the only parameter, once you try to add additional parameters (i.e. pieces that will be included in its own boundary), it no longer works (at least not with swagger-ui, because the spec is incorrect).
The other issue is the parameters annotated as @RequestPart do not have their models added to the generated spec files.
So given the following example, swagger-ui should create a form that takes a text input and file input (which it does), however the request parameter is using paramType 'body', and when the form is submitted, only the file gets submitted in the request.
@ApiOperation(value = "")
@RequestMapping(value = "/issue", method = RequestMethod.POST)
@ResponseBody
public MyResponse issueRequest(
        @ApiParam(required = true) @RequestPart MyRequest request,
        @ApiParam(required = true) @RequestPart MultipartFile document)

Using the custom annotation readers, I am able to work around the paramType issue, but not adding the model to the spec issue.

It seems Swagger does NOT display Model | Example value section for @RequestPart in 2.7.0 version. It just displays undefined as data Type next to the text field. It works if you change @RequestPart into @RequestBody.

@zerkowsm this is fixed via #1965 in the next release

Thanks for the information @dilipkrish . When do you plan to release that?

Hopefully in a week. trying to round out some bugs before that.

:+1:

Hello, i see again this issue in springfox-boot-starter:3.0.0
I have an endpoint with both Pojo and Multipart file.
I can successfully call the endpoint with Postman tool if I set it:
 @PostMapping(value = "/sito", consumes = {MediaType.MULTIPART_FORM_DATA_VALUE})     public void insertSito(@RequestPart(name = "edifici", required = false) MultipartFile file,                            @RequestPart(name="sito") CreateSitoDTO creationRequest) {
But swagger shows ONLY the file part (that is the only optional one btw...).
If i switch the json part to @RequestBody, swagger shows both the elements, but fails to call the endpoint,
what i get is:
org.springframework.web.servlet.handler.AbstractHandlerExceptionResolver: Resolved [org.springframework.web.HttpMediaTypeNotSupportedException: Content type 'multipart/form-data;boundary=----WebKitFormBoundaryr6riTHMZjZyrkhQI;charset=UTF-8' not supported]
I'm currently using spring-boot 2.5.7 and springfox-boot-starter 3.0.0 (NOT snapshot)

Someone solved the problem described by @ndorigatti? i have the same scenario and I don't know how to fix it


Error running nanopolish on MAP006 dataset

Hi,
I've been trying to run the nanopore paper pipeline on several other datasets (besides the one used in the paper).
Namely, I'd like to run the latest nanopolish on MAP006 dataset.After I managed to get the fasta headers right, I've gotten a long series of following errors:
Computing consensus for scf7180000000013:3200000-3210200
nanopolish: nanopolish_squiggle_read.cpp:84: void SquiggleRead::load_from_fast5(const string&):
Assertion `model.size() == 1024' failed.

To be more specific, these are 2d reads from MAP006_1-downloads/pass folder.
I've successfully manged to run older version of nanopolish on nanopore paper dataset (and a subset of it). Can you tell what I'm doing wrong this time, or maybe point me in the direction where to look further?

Please use the latest code.

Thank you for a quick reply. I really appreciate it.
I thought I was using the latest version, but it seems I did something wrong while upgrading from an earlier one. After performing a clean install, it worked. Sorry for not doing my homework before posting here.
However, (there always seems to be a "however") during the polishing, I got two "Assertion failed messages". The process finished, bit I couldn't merge the segments, because some of them were missing. Do you have any advice how I could get it to work?
Running the nanopolish:
python nanopolish/scripts/nanopolish_makerange.py draft_genome.fasta | parallel --results nanopolish.results -P 8 nanopolish/nanopolish consensus -o nanopolish.{1}.fa -w {1} --r raw.reads.pp.fa -b raw.reads.pp.sorted.bam -g draft_genome.fasta -t 4

Assertion failed messages:
nanopolish: src/nanopolish_consensus.cpp:599: void run_splice_segment(HMMRealignmentInput&, uint32_t): Assertion `!data.empty()' failed.
nanopolish: src/nanopolish_consensus.cpp:599: void run_splice_segment(HMMRealignmentInput&, uint32_t): Assertion `!data.empty()' failed.

Merging segments:
python nanopolish/scripts/nanopolish_merge.py draft_genome.fasta nanopolish.*.fa > polished_genome.fasta
ERROR_MISSING scf7180000000010 0
ERROR_MISSING scf7180000000010 1
ERROR_MISSING scf7180000000010 2
ERROR_MISSING scf7180000000014 1

Can you check whether the first 10,000 bases of scf7180000000010 has any
reads mapped to it?
Jared
On Wed, Oct 28, 2015 at 4:22 AM, Krešimir Križanović <
<EMAIL_ADDRESS>wrote:

Thank you for a quick reply. I really appreciate it.
I thought I was using the latest version, but it seems I did something
wrong while upgrading from an earlier one. After performing a clean
install, it worked. Sorry for not doing my homework before posting here.
However, (there always seems to be a "however") during the polishing, I
got two "Assertion failed messages". The process finished, bit I couldn't
merge the segments, because some of them were missing. Do you have any
advice how I could get it to work?
Running the nanopolish:
python nanopolish/scripts/nanopolish_makerange.py draft_genome.fasta | parallel --results nanopolish.results -P 8 nanopolish/nanopolish consensus -o nanopolish.{1}.fa -w {1} --r raw.reads.pp.fa -b raw.reads.pp.sorted.bam -g draft_genome.fasta -t 4
Assertion failed messages:
nanopolish: src/nanopolish_consensus.cpp:599: void run_splice_segment(HMMRealignmentInput&, uint32_t): Assertion !data.empty()' failed. nanopolish: src/nanopolish_consensus.cpp:599: void run_splice_segment(HMMRealignmentInput&, uint32_t): Assertion !data.empty()' failed.
Merging segments:
python nanopolish/scripts/nanopolish_merge.py draft_genome.fasta nanopolish.*.fa > polished_genome.fasta
ERROR_MISSING scf7180000000010 0
ERROR_MISSING scf7180000000010 1
ERROR_MISSING scf7180000000010 2
ERROR_MISSING scf7180000000014 1
—
Reply to this email directly or view it on GitHub
https://github.com/jts/nanopolish/issues/24#issuecomment-151760778.

I looked at the bam file generated by nanopolish, and there are reads mapped to scf7180000000010, with position less then 10000.

This should be fixed in 3bb2c69306, like issue #23. Please reopen if it still occurs


General Discussion

Hey guys, this is just a general discussion thread to figure out what works, what doesn't work, and suggestions for changes. This is a completely open forum, so feel free to bring up anything!
And feel free to fork this project! Pull requests are always welcome. :)

@lindseydiloreto This is IMHO the best resource to get started with plugin dev for Craft. Now it would be great if it was ported to craft 3...

I finally finished porting the Business Logic plugin template over to Craft 3, and actually converted it to a Business Logic module template instead. In Craft 3, it makes far more sense that someone would need this architecture as a module instead of a plugin.
Business Logic is dead. Long live Business Logic!  👑
This time, I did an even deeper dive into the included components (Variables, Controllers, Services), writing up the purpose of each piece, and how they all tie together in the big picture.
https://doublesecretagency.github.io/craft-businesslogic/
And now, almost five years later, I feel comfortable closing this thread. 🙂


Option to keep Authorization headers in cross-domain redirects

Q
A

Bug?
perhaps?

New Feature?
no

Version
6.3.2

Actual Behavior
When a redirect happens between a different domain, the Authorization header is stripped. See https://github.com/guzzle/guzzle/blob/73bf0937061461ca45292a93aa3b7e9010f2e753/src/RedirectMiddleware.php#L197
This is by design (see https://github.com/guzzle/guzzle/pull/1207), so probably for good reason.
But in some cases, this leads to 401 errors as the Authorization is stripped.
Expected Behavior
It should be possible to keep the Authorization headers, even when redirecting to other domains.
Steps to Reproduce
The Google Nest API is affected by this: https://developers.nest.com/documentation/cloud/how-to-read-data
The curl example is working
curl -v -L \
  -H "Content-Type: application/json" \
  -H "Authorization: Bearer c.<my token>" \
  -X GET "https://developer-api.nest.com/"

The same example in Guzzle is failing with a 401. When viewing in curl, the first result is:
< HTTP/1.1 307 Temporary Redirect
< Location: https://firebase-apiserver25-tah01-iad01.dapi.production.nest.com:9553/

curl then includes the same header to the redirect, and 200 OK is returned. Guzzle will strip the header and fail with a 401.
Possible Solutions
Add a new option to allow_redirects, eg. strip_authorization with a default to true, but can be overridden.
 The Python example do extra checks themselves, so I guess it is not super common.
Workaround in this case would be to just create 2 requests without allowing redirects. (Like the Python examples)

Has anyone found a workaround?


Update http4s-client, http4s-dsl, ... to 0.21.24

Updates

org.http4s:http4s-client
org.http4s:http4s-dsl
org.http4s:http4s-server

from 0.21.6 to 0.21.24.
GitHub Release Notes - Version Diff
I'll automatically update this PR to resolve conflicts as long as you don't change it yourself.
If you'd like to skip this version, you can just close this PR. If you have any feedback, just mention me in the comments below.
Configure Scala Steward for your repository with a .scala-steward.conf file.
Have a fantastic day writing Scala!

Ignore future updates
Add this to your .scala-steward.conf file to ignore future updates of this dependency:
updates.ignore = [ { groupId = "org.http4s" } ]

labels: library-update, semver-patch

Superseded by #147.


NIMBUS-394 :: Application Support (Merge M6 changes to M7)

Description
Merge M6 to M7

You did it @jayantchaudhuri!
Thank you for signing the Anthem Opensource Software CLA.


Add GeoJSON serialization to Area object

I noticed the Area object has wkb and wkt methods, but lacks the geojson method.
I guess this is because the geojson methods in Node and Way are implemented on the node-osmium side rather than relying on libosmium's GeoJSON serialization; with the current API, the same thing is not possible to do for areas.
I've hacked up a fix that uses libosmium's GeoJSONFactory to serialize an Area, and then parses the resulting string using JSON.parse. It feels a bit iffy, but seems to do the job.
Since this is my first dive into node-osmium/libosmium, I totally expect there to be better ways to do this. Any pointers on alternatives or improvements would be great!

You are right, your solution is a bit "iffy". I found a better one and just committed it. There is now a geojson() function on the Area object, too.

Thanks, your fix does indeed look much cleaner!


Remove feature flagged mouse/touch/keyboard event data

procaptcha-react - collector component
procaptcha - collector helper funcs
provider - service for adding to mongo

TODO: what is this ticket?

https://github.com/prosopo/captcha/pull/1078


C#: add generic version of Node.FindNode()

Right now, there is only:
Node FindNode(string mask, bool recursive = true, bool owned = true);
Ideally, there would also be a generic version like there is for GetChild() and GetNode().
T FindNode<T>(string mask, bool recursive = true, bool owned = true) where T : class;
Godot version:
3.2

Closing, as feature proposals should be discussed on the Godot proposals repository. This repository is now used for bug reports only.

Closing, as feature proposals should be discussed on the Godot proposals repository. This repository is now used for bug reports only.


Helm chart publish

Add publishing/packaging of chart to GitHub pages to allow easy consumption of chart and updates

Done

Done


Import bundle

To avoid confusion...
Currently the only API to ingest the set of resources in real time is to POST Bundle. This API has performance and stability issues, which prompted this new work.
My goal was to extend efficient $import logic to real time calls. We should not, at least now, add any extra logic beyond $import, which might have performance impact.
$import uses ndjson as input format. Very efficient. Hence new endpoint should use this format. There is a demand, for customer convenience, support bundle format, so it was enabled too. By no means, this endpoint is a replacement of current generic bundles processing logic.
We should avoid inheriting any complexity allowed by generic bundle format. For example, $import logic (so new endpoint logic) requires resource id. We should avoid attempts to extend functionality by enabling identity search to identify resource. Maybe in future, but not now.
To avoid confusion (added because of bundle format) about what functionality is supported, I suggest refraining from using bundle in endpoint name. I suggest clarifying intent in the documentation.
This endpoint will process batch in a single database call, hence it inherently equivalent to the transaction bundle. It also either PUTs all input resources or none. This makes output response trivial (no need to have complex output logic generic bundles have).
When using bundle format, it would be nice to ignore all bundle components except Resource. We should be clear about it in the documentation. BTW I am not sure that we need to make documentation change now, we can wait till first customer provides feedback.

/azp run

I believe that before merging this new endpoint, we should discuss the boundaries of this new ingestion.
Customers relying on Bundles today are already expecting the same bundle response structure, operation outcomes, errors handling, conditional operations, POST, Deletes, etc.

I intentionally created separate endpoint to make sure that customers are making cautious decision when they start using it. This endpoint is not a generic bundle processing endpoint, so there should not be expectations that input and output are the same.

/azp run

/azp run

/azp run


Horizontal/Vertical stretching for AKNodeOutputPlot/WaveformPlot

This is not a bug, but a feature request.
It would be nice to have an option for horizontal/vertical stretching. Currently if you use the MicrophoneAnalysis project in buffer mode and play a sine wave at 10 kHz, you cannot see the sine wave.
If you implement a pinch to zoom gesture and zoom in or adjust the scale in the AKNodeOutputPlot, the waveform is no longer smooth.

Understandable, thank you for the clarification.


Abstract out magic precision number usages across transaction components

this 18 should probably be feeAsset.precision and abstracted out
Originally posted by @0xdef1cafe in https://github.com/shapeshift/web/pull/1076#discussion_r816344975

grep entire codebase for 18 and replace.

This needs an estimate of work hours before it can be bountied

2 hours

Hi, can I start working on this ?
I've applied to this task on gitcoin too more than a day ago.

Hey @Eunoia1729, you've been approved - you may now start work 🔥


fix(deps): replace deepmerge with defu

Currently unnecessary since deepmerge can be used by vue-meta.


Fix Convenience mixin for React example

I only started using refluxjs so maybe I am missing something, but I thought that it's the update that we should listenTo rather than the store.

I was missing something indeed :) I'll close this, it all makes sense.


Updates with Unity 2021 changes

Overview

Updates the namespace (no longer experimental) for PrefabStageUtility
Fixes Assets\MRTK\Tools\MSBuild\Scripts\Utilities.cs(132,17): error CS0269: Use of unassigned out parameter 'guid'
Fixes multiple instances of error CS0618: 'EditorUserBuildSettings.wsaSubtarget' is obsolete: 'EditorUserBuildSettings.wsaSubtarget is obsolete and has no effect. It will be removed in a subsequent Unity release.'
Fixes multiple instances of error CS0618: 'WSASubtarget' is obsolete: 'WSASubtarget is obsolete and has no effect. It will be removed in a subsequent Unity release.'
Fixes multiple instances of error CS0165: Use of unassigned local variable 'colliderByTransform'
Fixes multiple instances of error CS0165: Use of unassigned local variable 'rendererBoundsByTransform'

Changes

Fixes: #9937

/azp run


No reference to what ServiceBus library is currently deployed & used by LogicApps

Neither this page nor the reference page that's supposed to have technical details of the ServiceBus Connector provide any guidance as to what version of ServiceBus library is being used/deployed to Azure LogicApps right now.
There are documented wire compatibility issues between the new version (Microsoft.Azure.) and old one (Windows.Azure.), so I'd suggest this page to at least acknowledge them and preferably provide mitigation strategies.

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

ID: c2aeacc5-5b74-c4be-335e-c7e768854e4a
Version Independent ID: d8693b52-fdd6-cc68-bc12-26807454a80b
Content: Exchange messages with Azure Service Bus - Azure Logic Apps
Content Source: articles/connectors/connectors-create-api-servicebus.md
Service: logic-apps
GitHub Login: @ecfan
Microsoft Alias: estfan

@kevinlam1, did you have more comments after @radumg provided more details?

@radumg, could you please answer Kevin's question so that we can make progress on this thread? Thanks!
"I'm trying to get clarity on why that information is needed. This will help us make sure we are communicate the right information in the right and in the correct place."

@radumg, could you please answer Kevin's question so that we can make progress on this thread? Thanks!
"I'm trying to get clarity on why that information is needed. This will help us make sure we are communicate the right information in the right and in the correct place."

Sure, the info is needed because

the current & up-to-date version of ServiceBus NuGet does not work out of the box with the current LogicApps ServiceBus connector
there is not enough publicly-available information that helps developers troubleshoot or indeed fix the incompatibility issue
since LogicApps ServiceBus connector version cannot be changed when authoring a workflow afaik, as devs we can only control the ServiceBus NuGet version we use in our code, but we need to know which one to use

Hi @radumg, thanks for providing the additional information.
@kevinlam1, please review and make suggestions for handling this need? Thanks!

@jonfancey, can you help answer questions about this customer's scenario?

@jonfancey, ping on helping to answer which version of Service Bus library is used by Logic Apps? They want to know because:

The current & up-to-date version of Service Bus NuGet does not work out of the box with the current LogicApps Service Bus connector.

There is not enough publicly-available information that helps developers troubleshoot or indeed fix the incompatibility issue.

Since LogicApps Service Bus connector version cannot be changed when authoring a workflow afaik, as devs we can only control the Service Bus NuGet version we use in our code, but we need to know which one to use.

Need to respond about compatibility issues:
#assign @kevinlam1
#assign @jonfancey

@KetanChawda-MSFT: Please un-assign kevinlam1, please? Thanks!

@ShyamSunder90: I know this question is quite stale, but just to close the loop, can you help answer this question? Thanks!

#assign @ShyamSunder90

@ketan-chawda-msft: Please unassign @jonfancey? Thanks!

@ShyamSunder90: Can you help answer? If not, because this thread has been open so long without a resolution, I'll close the issue this week.

@ecfan this connector is owned by LA team. Please check with Rama.

@ShyamSunder90: Can you help answer? If not, because this thread has been open so long without a resolution, I'll close the issue this week.

Thanks for following this up @ecfan and trying to get an answer for us, appreciate it!
As direct feedback for the product team of where we are now as customers :

it's been 9 months since we've asked a seemingly simple question (what library & version are used)
we've already wasted too much time trying to cater to Logic App's temperamental handling and prodding a black box due to insufficient documentation and lack of solutions
we've already migrated our original workload that required this off Logic Apps
we're abandoning further use of the Logic Apps product for any production or workloads other than quick throw-aways

Hi @radmug,
The Logic Apps team responded that the current version is .NET Framework WindowsAzure.ServiceBus 5.0.2, but can be updated in the future. I've forwarded your explanation about the problem, so hopefully they can determine a solution that we can doc for other customers. I'm very sorry to hear your feedback, so I'm including a couple others for awareness. I'll be happy to close this issue for you.
CC: @jonfancey, @divyaswarnkar
Thanks for following this up @ecfan and trying to get an answer for us, appreciate it!

As direct feedback for the product team of where we are now as customers :

it's been 9 months since we've asked a seemingly simple question (what library & version are used)
we've already wasted too much time trying to cater to Logic App's temperamental handling and prodding a black box due to insufficient documentation and lack of solutions
we've already migrated our original workload that required this off Logic Apps
we're abandoning further use of the Logic Apps product for any production or workloads other than quick throw-aways

@ketan-chawda-msft: #please-close

Thank you @ecfan 🙌 !