segmentation fault running "brew doctor"

Hi,
I'm getting a segmentation fault when running the command "brew -v doctor." I also seem to be getting this error on "brew missing." Here's my config:
HOMEBREW_VERSION: 1.7.4-67-gd639559
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: d639559c4de48faad79d3ecb1ec84dc851ea66f2
Last commit: 78 minutes ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 846248c9f7160132e7822b66fc445e4193bac3f1
Core tap last commit: 3 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_GIT: git
HOMEBREW_GITHUB_API_TOKEN: set
CPU: octa-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 9.0 build 900
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 9.0.4, 1.8.0_152, 1.8.0_131, 1.8.0_92, 1.8.0_76, 1.8.0_74, 1.8.0_60, 1.7.0_76
macOS: 10.12.6-x86_64
CLT: <IP_ADDRESS>.1.1510905681
Xcode: 9.2
XQuartz: 2.7.11 => /opt/X11

And here's the error:
/usr/local/Homebrew/Library/Homebrew/cache_store.rb:29: [BUG] Segmentation fault at 0x000000012afffffe
ruby 2.3.7p456 (2018-03-28 revision 63024) [universal.x86_64-darwin9.0]

-- Crash Report log information --------------------------------------------
   See Crash Report log file under the one of following:
     * ~/Library/Logs/CrashReporter
     * /Library/Logs/CrashReporter
     * ~/Library/Logs/DiagnosticReports
     * /Library/Logs/DiagnosticReports
   for more details.
Don't forget to include the above Crash Report log file in bug reports.

Bug reports are welcome.
For details: http://www.ruby-lang.org/bugreport.html

If you have any suggestions, please let me know. I just noticed this behavior starting today.
Thanks

Same here, after upgrade to xcode10.

@PureWhiteWu can we see your brew config output?

@mlevin2 Have you upgraded Homebrew/Ruby/Xcode/macOS recently?

@MikeMcQuaid
HOMEBREW_VERSION: 1.7.5-5-gccb08f1
ORIGIN: https://github.com/Homebrew/brew
HEAD: ccb08f12588dff93858a6e24eefad2d738a16cdc
Last commit: 3 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 4de1a06503cbae3d9c1cd5d06dc4541c2b798c01
Core tap last commit: 3 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_GIT: git
HOMEBREW_GITHUB_API_TOKEN: set
CPU: octa-core 64-bit skylake
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 10.0 build 1000
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.2, 1.8.0_181
macOS: 10.13.6-x86_64
CLT: <IP_ADDRESS>.1.1535735448
CLT headers: N/A
Xcode: 10.0
XQuartz: N/A

@PureWhiteWu Same question to you: did you upgrade to Xcode 10 recently?

@mlevin2 @PureWhiteWu FYI rm "$(brew --cache)/linkage.db" will temporarily resolve your issue. Please stick around and answer questions, though, I'd love to figure this out.

@MikeMcQuaid Yes, I upgraded to Xcode 10 this morning.

@PureWhiteWu Try to rm -rf /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby.

FWIW, my crashlog and config is here.

@resistor4u and @mlevin2 (and anyone else who reads this): please upload your $(brew --cache)/linkage.db somewhere I can download it and then you can remove it with $(brew --cache)/linkage.db which should fix your issue. That'll help me fix it for other people. Thanks!

@MikeMcQuaid hi, this helps, thanks!
If there's anything I can help, feel free to ask me.

@MikeMcQuaid hi, this helps, thanks!
If there's anything I can help, feel free to ask me.

@MikeMcQuaid Thanks! Removing linkage.db corrected the problem. If you'd like to see my broken version of linkage.db, you can grab it from https://www.dropbox.com/s/lglmzm7bs286l32/linkage.db?dl=0

@MikeMcQuaid Attached a zip of linkage.db plus the output of brew config in my case. I'll include the latter inline here as well:
HOMEBREW_VERSION: 1.7.5-9-gc1e26f5
ORIGIN: https://github.com/Homebrew/brew
HEAD: c1e26f5677f054940e80471a0c86032c1bef9267
Last commit: 7 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: a180a510ca41071b2826441d49c1bb314503186e
Core tap last commit: 2 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_GIT: git
CPU: octa-core 64-bit skylake
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 9.1 build 902
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10, 1.8.0_162, 1.8.0_121
macOS: 10.13.6-x86_64
CLT: N/A
Xcode: 9.4.1
XQuartz: 2.7.11 => /opt/X11

Homebrew-4923-EddieRingle-1.zip

@MikeMcQuaid here is a link to my linkage.db, but note that it's the file that was created after I deleted the offending cache. If you get to the bottom of this, please do follow up - I'm interested to know what the cause was.

@MikeMcQuaid Hi, my brew crashed again, and here's my linkage.db
linkage.db.zip

Same here. Here's my linage.db: dl=0https://www.dropbox.com/s/yemv0a9359xeee9/linkage.db.zip?dl=0
HOMEBREW_VERSION: 1.7.5
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: d639559c4de48faad79d3ecb1ec84dc851ea66f2
Last commit: 2 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 338fcc63351c2a5d6ccaed6b52bfe805876d02a3
Core tap last commit: 28 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_GIT: git
CPU: octa-core 64-bit ivybridge
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.17.1 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.2, 1.8.0_161, 1.6.0_65-b14-468
macOS: 10.13.6-x86_64
CLT: N/A
Xcode: 10.0
XQuartz: 2.7.11 => /opt/X11

Here's my linkage.db
Note that I am not using Xcode 10, as I'm still running macOS 10.12:
HOMEBREW_VERSION: 1.7.5-11-g47bebcd
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 47bebcdeca14ba52de3fd0067ab3aefe91fa2ec5
Last commit: 23 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core.git
Core tap HEAD: 12378f017b4e9843e09f76d199dc86e22cda2a22
Core tap last commit: 23 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEVELOPER: true
HOMEBREW_GIT: git
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_NO_ANALYTICS_THIS_RUN: 1
CPU: octa-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 9.0 build 900
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 1.8.0_144
macOS: 10.12.6-x86_64
CLT: <IP_ADDRESS>.1.1510905681
Xcode: 9.2
XQuartz: 2.7.11 => /opt/X11

I think I might be experiencing a related issue, except instead of crashing, ruby is going into an endless loop when running brew doctor or brew upgrade. I left it running overnight, and it's definitely hung, and not just slow. I have to kill -9 the ruby process.
I am going to open a separate issue, but thought I would mention it here in case they're related.
My brew config:
$ brew config --verbose
HOMEBREW_VERSION: 1.7.5-40-g1ff42f9
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 1ff42f90586a5f600aa34b9edf8f8e842f2fc461
Last commit: 4 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 56c500b569c724b049be7ab9e12d9693f85522f9
Core tap last commit: 4 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_GIT: git
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_INSTALL_BADGE: ☕
HOMEBREW_VISUAL: vim
CPU: octa-core 64-bit skylake
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 10.0 build 1000
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.2, 1.8.0_181
macOS: 10.13.6-x86_64
CLT: <IP_ADDRESS>.1.1535735448
CLT headers: N/A
Xcode: 10.0
XQuartz: 2.7.11 => /opt/X11

Ran into the same issue after upgrading to Xcode 10. Verified that I had installed all the components of Xcode 10 and also reinstalled homebrew - nothing worked.
Followed the recommendation on https://github.com/Homebrew/brew/issues/4485
rm -fr ~/Library/Caches/Homebrew/

That resolved my issue.
Here is my homebrew config:
HOMEBREW_VERSION: 1.7.5
ORIGIN: https://github.com/Homebrew/brew
HEAD: d639559c4de48faad79d3ecb1ec84dc851ea66f2
Last commit: 4 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 6211f5ecec518d449ab5460754dfc7ebe5a6c302
Core tap last commit: 76 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_GIT: git
HOMEBREW_GITHUB_API_TOKEN: set
CPU: octa-core 64-bit kabylake
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 10.0 build 1000
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.2, 9.0.4, 1.8.0_181, 1.8.0_171
macOS: 10.13.6-x86_64
CLT: <IP_ADDRESS>.1.1535735448
CLT headers: N/A
Xcode: 10.0
XQuartz: N/A


[Document Intelligence] Duplicate contents in Add-on capabilities page

These two paragraphs are duplicated.
https://github.com/MicrosoftDocs/azure-docs/blob/0247e2e3ce127d3e0b0a238d2d789b6239bd3b03/articles/ai-services/document-intelligence/concept-add-on-capabilities.md?plain=1#L29-L31

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

ID: 13fd769f-df2b-7e83-2c27-4bf326444388
Version Independent ID: 350374f0-df13-0b33-e422-65cfd343aa32
Content: Add-on capabilities - Document Intelligence - Azure AI services
Content Source: [articles/ai-services/document-intelligence/concept-add-on-capabilities.md] (https://github.com/MicrosoftDocs/azure-docs/blob/main/articles/ai-services/document-intelligence/concept-add-on-capabilities.md)
Service: azure-ai-document-intelligence
GitHub Login: @jaep3347
Microsoft Alias: lajanuar

@toothache
Thanks for your feedback! We will investigate and update as appropriate.

@toothache
I've delegated this to @jaep3347, a content author, to review and share their valuable insights.

Hi @toothache, this issue has been resolved. Thanks again for your feedback.
cc: @RamanathanChinnappan-MSFT

#please-close


Accesing a dynamic component

Hi,
Given the following:
@Component({
  selector: 'my-app',
  templateUrl: './app.component.html',
  styleUrls: [ './app.component.css' ]
})
export class AppComponent  {
  name = 'Angular 6';
  component = DynamicComponent;
  onClick($event) {
    alert($event);
  }
}

How do I access the instance of the DynamicComponent to set a property?
Attempting access in a @ViewChild() does not seem to work.
NB. I note that the docs state that there is access to the component? I can't seem to get it though

I want to remind that it is more convenient to use auto binding on the dynamic component. *ngxComponentOutlet makes auto binding and inputs and outputs.
<ng-container *ngxComponentOutlet="component"></ng-container>
// instead of
<app-dynamic [ngxComponentOutlet]="component" [Input]="..."></app-dynamic>

Also, you can use context for binding. Context has a higher priority than the inputs in the component.
<ng-container *ngxComponentOutlet="component; context { item: '' }"></ng-container>

If you still need to access a dynamic component, then use ngxComponentOutletActivated output.
<ng-template
  [ngxComponentOutlet]="component"
  (ngxComponentOutletActivate)="onActivate($event)"
></ng-template>


Fix for SSLError: cacert.pem missing

The file cacert.pem was never included in wheels because the setuptools flag include_package_data=True wasn't set, causing issue #396.
This PR fixes that.
I don't know where you're trying to go with future versions, as your pipenv/vendors directory is almost empty now. So I have based this branch on the v5.1.2 tag.

Hey @nils-werner, thanks for taking the time to put this together. Unfortunately we'd already added this in 06acad1 but it seems a release was never cut with that fix.
We're currently in a state where we're moving away from vendoring, but have had some CI issues I haven't had time to address yet. For that reason we really can't cut a release with a fix for this but I'll try to get something out asap.
Thanks again for your contribution!

Maybe this could go in a hotfix 5.1.3 release, to fix the issue until the new release without vendoring is released?

We may be able to go back to 06acad1 and cut a release from that point but the vendoring removal commits have already been merged into master.
I'm currently traveling without a laptop so I'm unable to verify that tests are working across platforms at that commit. If @kennethreitz has the time to look into this, that may be an option.
I'm however slightly uncomfortable with doing this. Either placing the cacerts.pem file on the path or installing requests 2.14 or earlier should fix this temporarily. I think we can get this fixed in the next couple days on master which would be preferred.
I'll leave it to Kenneth to make a final call here.


Fixed unexpected heads up notification.

Signed-off-by: Pavel Kirilin<EMAIL_ADDRESS>Description
Unexpected behaviour of heads up notification was fixed.

Fixes #48
Type of change
Just put an x in the [] which are valid.

[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 not work as expected)

Thanks for the fix @s3rius! Merging this to the repo.
By the way, please tell us how did you stumble across this repository.
Thanks once again for your contribution.


Wrong operator values

https://3v4l.org/NMrv2/vld
$i = 1;
echo $i++ + ++$i;

PHP correctly returns 4 because it adds 1 + 3. VLD however says for the operands ~2, ~3 - which is clearly wrong (but the result ~4 is correct).

VLD doesn't show the values, but the (internal) variable number that the PHP engine uses. Change your initial value to something else (say 42) and the VLD output will be the same.


Plugin doesn't work with EAP 2022.1

Good evening,
I looked for this issue but is not registered yet.
I'm working with the WebStorm EAP 2022.1 version and the plugin is not recognised, requires the IDE build 213 as this image below.

Incompatible after upgrade to 2022.2.


Option inheritsAttrs = false is missing in

What problem does this feature solve?
I do not want the inheritsAttr
What does the proposed API look like?
inheritsAttrs(false)

I do not know how to remove the attribute inheritance using

It can be also changed like this

Вы можете добавить дополнительный тег скрипта со следующим:
< скрипт >
    экспорт по  умолчанию  {
        inheritAttrs : false
    }
</ script >

Don't you think it probably looks unwieldy?

Use the chat or the forum for questions, thanks

I hope setup will be added with "inheritAttrs: false"


fixed go.mod

fixes https://github.com/apenella/simple-go-helloworld/issues/1

Hi @gedw99!
Thank you for your contribution. It helps keep this project up to date. However, before merging it into the main branch, I will make some small changes to adapt your modifications to my workspace.


force persisting the tombstone file

Like #573 but for the tombstone file.

ping @krasi-georgiev

LGTM thanks.


CustomApp Example - OnEnter

Looks like the example for CrudRoute in https://marmelab.com/admin-on-rest/CustomApp.html hasn't got updated for the changes for authentication/OnEnter
Uncaught TypeError: onEnter is not a function
at Function.CrudRoute.createRouteFromReactElement (CrudRoute.js:45)
at RouteUtils.js:69
at forEachSingleChild (ReactChildren.js:51)
at traverseAllChildrenImpl (traverseAllChildren.js:77)
at traverseAllChildrenImpl (traverseAllChildren.js:93)
at traverseAllChildren (traverseAllChildren.js:172)
at Object.forEachChildren [as forEach] (ReactChildren.js:71)
at createRoutesFromReactChildren (RouteUtils.js:65)
at Function.createRouteFromReactElement (RouteUtils.js:35)

@djhi @fzaninotto are you guys sure about this? ;/
ncaught TypeError: hook.apply is not a function
at Array. (TransitionUtils.js:22)
at TransitionUtils.js:94
at TransitionUtils.js:71
at next (AsyncUtils.js:39)
at loopAsync (AsyncUtils.js:56)
at runTransitionHooks (TransitionUtils.js:70)
at runEnterHooks (TransitionUtils.js:93)
at createTransitionManager.js:99
at runTransitionHooks (TransitionUtils.js:50)
at runChangeHooks (TransitionUtils.js:110)
And incidently I can't work out what I'm supposed to do here as  any of my attempts seem to end up with a "Converting circular structure to JSON" message

No, you're right, it's still not fixed.

and for reference, the circular json structure error was due to the documented BC break (renaming filter->filters), so figured that out too


how to toggle series?

Now I can only show or hide serie, when i click on name of serie. But i need to toggle series, f.e. i click on the name of 1 serie and all other series will be hidden and only serie 1 will be shown.

can you please tell me how to check the visibilty of each series all of them?


[Blocker] Relation selector are still Required in the AntForm even when the BluePrint is not

Describe the bug
My relations all look slike :
    relation({
      id: "requiredConsumables",
      to: "Consumables",
      isMany: true,
      representedBy: "fullName",
      ui: {
        label: "Required Consumables",
      },
      field: field({
        id: "requiredConsumablesIds",
        ui: {
          list: false,
        },
        type: field.types.OBJECT_ID,
        isArray: true,
        isRequired: false,
        defaultValue: [],
      }),
    }),

However, in the generated form, the selector ALWAYS require some value, even though it shouldn't (I've set the blueprint's field to isRequired: false and defaultValue: []).

Hello @Fen747, try adding isRequired: false  to the relation object, currently you are having it on the field object only, which makes the relation required

Should we display a warning when both relation and field requiredness mismatch?

Sure we should. It's kinda perturbing to know where I need to put some info, etc. For example, I want to keep the auto generated XXXid name, but have it be an empty array by default, should I set the field option in the relation just to have this defaultValue ? Or do I need to add defautlValue in the relation directly ?
IMHO, the field option should not exists, we just set everything in the relation, even default value, and just have an optional fieldName string.


updated download link to official website The-Unarchiver

I changed the download link to the one located on the official website.

Thank you for the contribution. It was merged directly as 30c282693478ed49474f6457e9d9c1cb282794bb to keep commit history cleaner. Your contribution is still credited to you.


Allocation errors on a V100

I consistently get cudaMalloc allocation errors when allocating the generic buffer. I think this is because the V100 is using 32 tree walk blocks per SM, and has 84 SMs. Using the preset values in node_specs.h, it ends up trying to allocate ~5.7 GB. While in theory there should be plenty of memory available on the device, I get consistent failures to allocate this array.
I've temporarily worked around it by reducing to 8 tree walk blocks per SM, but I imagine this will hurt performance.
What would be the preferred way to reduce the size of the generic buffer so that allocation succeeds? Is reducing the number of tree walk blocks preferable, or perhaps I should reduce NTHREAD?
Or maybe I've missed something else entirely? Is there a fixed upper limit on contiguous array allocations for cuda? I wouldn't think so. It's possible that 6GB is just too big to find a contiguous block, but with the device practically empty I figured it should be possible.

Interesting. I'm not aware of there being a limit on the maximum memory allocation size, and 6GB should easily fit in that memory. I don't have access to a V100 so I can't test it out from my side.
The reduction in tree walk blocks per SM will hurt performance, but so will reducing NTHREAD, probably even more so.
Another thing that you can try is to lower: LMEM_STACK_SIZE here.  The 'only'  problem with this is that you risk getting invalid results. This is size indicates how many tree nodes can be cached for further processing when going down the tree. If you have a very small opening angle then you will need a higher buffer size. However, if your angle is such that only a small fraction of the tree has to be traversed then you can safely lower that number.
It would require a bit of trial and error to find which number works for you, also it might depend on the system that you are simulating if it will change over time.
It might be worth to ask NVIDIA if there is a limit on the maximum memory, or try to test the allocation in a standalone program that does nothing else than allocating the large buffer. If it works in a standalone program then you can consider moving the allocation of generalBuffer1 to an earlier part of the program, so from here to, for example, here in the hope that the memory is not fragmented yet and that the allocation succeeds.


load_dataset() method

I’d like to have Pyleoclim ship with a few key datasets that we can easily load for testing and docs, the way it’s done in Seaborn:
tips = sns.load_dataset("tips")
The datasets would be a subset of what is currently in the data directory of this repository.

Considerations:

which datasets to include? SOI, LR04, and ... ?
save in original format (csv, lipd) or as JSON objects?

save in original format (csv, lipd) or as JSON objects?

Since the files are being stored in git, ASCII files are preferred. This is because a sensible git-diff can be done. So a minor change to a csv or JSON file will cause minimal changes in the "eyes" of git, but a minor change to a binary file will always have the effect of completely rewriting the file. It just adds bulk to the git history.
That said, you probably need to test against each of the file types that the package can read from.
One way that I've done this in the past is to add a data folder in the package and put something like this in the package __init__.py:
PACKAGE_DIR = Path(__file__).parent.resolve()
DATA_DIR = PACKAGE_DIR.joinpath("data").resolve()

It looks like you already have include_package_data=True, in your setup.py so those files will be included by default. There are other alternatives as well. You can add the data folder outside of the package, then in setup.py you'd need to add a data_files or package_data to point to them.
You'll also need to add a helper function to link between dataset name and the path to the data. I assume you'll also be loading the data inside this function.
Given that you have a few 10s of KB sample files, I think the above approach is the easiest to build and maintain. You mentioned how seaborn does something similar. They actually keep their sample data in a separate repo and also implement some smart cacheing. Their load_dataset function is here if you want to take a look. Your method may look similar.

Soon the package won't be reading from LiPD directly so I would say let's concentrate on JSON/csv and make it as small as possible

Agreed. For docstring examples that use lipd files, we can leverage the lipdverse via pylipd when that is operational, but for now let's focus on JSON or CSV datasets.  @khider , I was thinking of having:

LR04
SOI
NINO3-AIR (for Coherency, Correlations, etc)
HadCRUT5 (for trends)

Anything else?

@CommonClimate can you confirm the source for those files?

LR04: https://github.com/LinkedEarth/paleoPandas/blob/main/data/LR04.csv
SOI: I'm assuming you want this one (https://github.com/LinkedEarth/paleoPandas/blob/main/data/soi_data.csv) since it had an edit 6 days ago?
NINO3-AIR: unsure, maybe oni.csv?
HadCRUT5: 'https://www.metoffice.gov.uk/hadobs/hadcrut5/data/current/analysis/diagnostics/HadCRUT.<IP_ADDRESS>.analysis.summary_series.global.annual.csv' ?

Yes to all the ones you had, and good find on the HadCRUT5 one.
Re: NINO3-AIR, sorry for being so terse; it is in fact this dataset: https://github.com/LinkedEarth/Pyleoclim_util/blob/master/example_data/wtc_test_data_nino_even.csv
I would all it by the label "NINO3-AIR", though.
Let me know if you hit any roadblocks!

Just having those datasets would save us a huge amount of work, and we can always add more when we see how you've done it.

Hi @kcpevey, I was able to load datasets correctly yesterday in an old environment, but I had to build a new one so I can test @MarcoGorelli 's resample() PR.  When I try to load the NINO3 dataset, I get the following error, which seems to imply that Python is not looking for metadata.yml in the right place:
ts = pyleo.utils.load_dataset('nino3')
Traceback (most recent call last):

  Cell In[3], line 1
    ts = pyleo.utils.load_dataset('nino3')

  File ~/opt/miniconda3/envs/pyleopd/lib/python3.10/site-packages/pyleoclim/utils/datasets.py:71 in load_dataset
    metadata = get_metadata(name)

  File ~/opt/miniconda3/envs/pyleopd/lib/python3.10/site-packages/pyleoclim/utils/datasets.py:51 in get_metadata
    all_metadata = load_datasets_metadata()

  File ~/opt/miniconda3/envs/pyleopd/lib/python3.10/site-packages/pyleoclim/utils/datasets.py:25 in load_datasets_metadata
    with open(path, "r") as stream:

FileNotFoundError: [Errno 2] No such file or directory: '/Users/julieneg/opt/miniconda3/envs/pyleopd/lib/python3.10/site-packages/example_data/metadata.yml'

I conda-installed everything from the package's environment.yml (commenting out the offending Linux package thing), so I am not sure what is wrong here. How would we troubleshoot?   I would say the 4 that @CommonClimate listed are a good start

Yes, and Deborah and I are discussing a good example of a MultipleSeries object, which will be required to test/demo that part of the package.

re: "decide on an approach", isn't this resolved now? (metadata.yml)

Yes, just marked it as resolved per the discussion here

Per the meeting today, I'll un-assign myself to this one and let USC take over :)

@khider we need easily loadable examples of

MultipleSeries
EnsembleSeries

I see that the Pyleoclim repo's example_data folder currently contains a file called crystalcave_ens.json. Should this be added to our list of loadable datasets? If so, can you do that?  For MultipleSeries, do we want to wait for pyLipd to be able to load the Euro2k dataset or can there be a json solution to that?

Closing this as the method now exists and works well ; we can always add more datasets later.

This is what we have now:
'SOI',
'NINO3',
'HadCRUT5',
'AIR',
'LR04',
'AACO2',
'nino_json'

Just one question for @kcpevey : how would users know what datasets are available? Is there an easy way for them to pull info from metadata.yml?

Sounds perfect, thank you!
Speaking of documentation: we've decided to make ours more minimal, and pandas-like, so the usual >>> syntax works. Please let us know if you have any questions on this!


fgdc Time Period - Current tag

The time period (timeperd) section has a current (current) element which is has the domain ['ground condition' | 'publication date' | free text].  Any thoughts where this might  transfer to in mdJson?  Do we even need to worry about it?  Other time period fields will all be kept by the reader.

As recommended in our weekly conference call, current will be placed in timePeriod.description.  This also roughly follows NOAA's FGDC to ISO mapping.


[Proposal] Should we provide MacOS style widgets under cupertino.dart?

Currently the Cupertino widgets library only provides an iOS style CupertinoAlertDialog, among other iOS style widgets.
There are no MacOS equivalents available in the widgets catalogue.
Use case
Consider the following code, which shows a dialog for the current platform using existing widgets from the SDK.
If I were to show a MacOS style dialog for TargetPlatform.macOS, I'd have to write my own dialog.
  switch (Theme.of(context).platform) {
    case TargetPlatform.android:
    case TargetPlatform.fuchsia:
    case TargetPlatform.linux:
    case TargetPlatform.windows:
      return showDialog<T>(
        builder: (context) => AlertDialog(/* configuration */),
        context: context,
      );
    case TargetPlatform.iOS:
    case TargetPlatform.macOS:
      return showCupertinoDialog(
        builder: (context) => CupertinoAlertDialog(/* configuration */),
        context: context,
      );
  }

Example of such a dialog from VSCode:

Proposal
I'd propose to re-evaluate what exactly should be in the cupertino widgets library.
Currently it provides some iOS-style widgets (probably not the newer ones defined by Apple).
It does not provide anything that follows the MacOS style (dialogs, buttons, etc.)
Should we even include MacOS style widgets in the SDK itself?
Maybe we can get away with adding a (first-party*) widgets library for MacOS style widgets?
The same happened for windows with fluent_ui, so why not?
*Since cupertino is part of the SDK, I'm not sure if this should be first-party or not.
There is a reason why the plus plugins are a thing.

We have no current plans to expand the widget libraries to include macOS desktop widgets. IF you're interested in these, I would recommend checkking out https://pub.dev/packages/macos_ui


use too much memory at quadview examples

It seems to create three StackHelper object when implement quadview examples, and the memory three times the same also.
Is there a better way to do this?

Yes, the example was never meant to be used as reference but more of quick ways to go. That should be cleaned up to provide reference implementations...
Ideally, you should just use 1 material and share it across slices.

I'm confused,the example create three StackHelper object because it has three view.
And I'm looking for a way,which is three view share one StackHelper object to achieve reduce the use of memory.
If that doesn't work, does that mean that I have to create 'StackHelper' myself? And create three SliceHelper by this 'StackHelper'.

Thank you very much for your answer.
Is it means will use three times dedicated GPU memory?
I'm loading an about 150MB DICOM data to single view(just axial), the memory rise about 500MB, and the dedicated GPU memory rise about 0.2GB.
But I'm loading the 150MB data to three view(axial, sagittal and coronal), the memory rise about 500MB, the dedicated GPU memory rise about 0.8GB.
The 0.8GB is horrible, I want know how reduce the footprint of this part of memory.

i'm having the same problem, loading 5 dicom files, with 4 views. the browser consumes more than 4GB of memory


Fixed -Overflow Issue in bottom bar and "#satellite" division #20

Hi,
Issue #20 Fixed,  I'm looking to your feedback,
Thank You

@rkverma2022 pull to refresh should not synchronise whole data. there is already an option to sync data in settings. instead it should synchronise the satellite coordinates and show a toast or something saying the satellites coordinates are updated.

So, only the coordinates of all satellite should be refreshed at home Page, is it?

@rkverma2022 it should refresh the current location of the satellite.


Check for duplicate permalinks and throw an error (Fixes #1867)

Here's one way issue #1867 could be fixed: by checking for duplicate permalinks after all the pages have been created.

@egonSchiele thanks for this suggestion; this works, but I think it would be simpler and more effective to track this on the rendering sitde of it.


Feat/#257 open browser

Codecov Report

Merging #260 into develop will increase coverage by 0.07%.
The diff coverage is 100%.

@@             Coverage Diff             @@
##           develop     #260      +/-   ##
===========================================
+ Coverage     28.7%   28.77%   +0.07%
===========================================
  Files           50       50
  Lines         5515     5511       -4
  Branches      1172     1169       -3
===========================================
+ Hits          1583     1586       +3
+ Misses        2865     2859       -6
+ Partials      1067     1066       -1

Flag
Coverage Δ

#rnvunittests
28.77% <100%> (+0.07%)
:arrow_up:

Impacted Files
Coverage Δ

packages/rnv/src/platformTools/runner.js
29.13% <100%> (ø)
:arrow_up:

packages/rnv/src/platformTools/web/index.js
22.22% <100%> (+0.2%)
:arrow_up:

packages/rnv/src/systemTools/exec.js
61.76% <0%> (+2.8%)
:arrow_up:

Continue to review full report at Codecov.

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Maven plugin parameter name to Settings.KEYS mapping

From a test-consistency perspective it would be nice to have some sort of mapping that contains the maven plugin parameter name (as listed in the maven plugin's generated plugin.xml or helpmojo.xml) as the key and its equivalent Settings.KEYS as the value.
This is not a problem per se but requires a lot of tedium on my end when I upgrade between versions.
Solution I'd like
A .properties file that maps the maven plugin parameter name to the Settings.KEYS assigned value.
A .properties file would have something like this
...
dataDirectory=data.directory
databaseDriverName=data.driver_name
databaseDriverPath=data.driver_path
databasePassword=data.password
databaseUser=data.user
enableExperimental=analyzer.experimental.enabled
enableRetired=analyzer.retired.enabled
failBuildOnAnyVulnerability=fail.build.on.any.vulnerability
failBuildOnCVSS=fail.build.on.cvss
failOnError=fail.on.error
...

With this, I can then efficiently construct parameters for the plugin that looks at the Settings object's value and determines if the assigned value is equal to the default value defined in the plugin, if it is not then pass that value on to the plugin.
Alternatives I've considered
Currently creating a .properties file by manually looking at the code in BaseDependencyCheckMojo and Settings.KEYS.
Considered a feature request where plugin parameter names are the camelCase equivalent as the  Settings.KEYS
i.e. analyzerArtifactoryEnabled instead of artifactoryAnalyzerEnabled for the plugin maps to analyzer.artifactory.enabled.
The other solution I've considered submitting as a feature request is to use the alias property in the @Parameter annotation on the fields of BaseDependencyCheckMojo that can map to a Settings.KEYS.
Example:
    @Parameter(property = "databasePassword", alias="data.password")
    private String databasePassword;

I just looked at the alias attribute and found that it does not affect the output of the help goal:
mvn org.owasp:dependency-check-maven:5.2.1-SNAPSHOT:help -Ddetail=true -Dgoal=check
I saw no evidence that the alias was displayed.  In addition, some of the parameter to property configurations are complicated - such as suppressionFile and suppressionFiles which may get combined into an array and set to the property suppression.file.
I'm not sure I fully understand your problem statement - why is this mapping needed in your use case?

Thank you for responding Jeremy.
Use Case
The reason for doing this is to make sure scans are being executed in the same fashion (maven pom vs straight file scan) I need to be sure the parameters being passed in are consistent with the properties defined in my scan. I'm using the maven invoker plugin to do this in one fell swoop.
What I'm currently doing
Using the Maven Invoker library I am using the Settings object to add parameters to the maven options by looking at properties file that maps the Settings.KEYS value to the maven parameter name (as demonstrated in the first code block of my proposed feature).  Using this map I create a map that has the maven parameter name to Settings value map. Using another properties file that contains the maven parameter name to default parameter value I filter the maven parameter name to Settings value map to only retain the entries that are not default values. I then do some other processing (such as creating a modified maven settings.xml for certain things) and finally pass the non-default parameters on to the maven invoker.
Does it work?
It works like a charm! But it's a pain to do updates.  As newer versions of dependency check are released more options are being added that allows for much more robust reports and better detection, the flip-side is that I have to map the new properties to their equivalent maven options manually which can be somewhat tedious and error prone due to me being a human.
After typing this all out it would probably be just as much of a pain for you to do this, but since your plugin code generates most of this data I feel the better solution is to use the existing Parameter annotations to achieve this.
Why am I doing this?
I am currently working on converting non-dependency managed projects to dependency managed projects as well as vulnerability mitigation.  From a testing/comparison perspective I want the folks I'm helping do this have able to see that the dependencies detected are close, if not the same to each other.
Why other users may find this useful
While this doesn't cover every single aspect (such as the artifactory bearer token, needing to be in the settings xml, which I have code to handle that) it does significantly help with maintenance as well as give users migrating from the CLI to the maven plugin and vice versa a very clear migration path settings-wise.
Solution using existing the Parameter annotation
The intention of the using the alias field in the @Parameter annotation is so that during runtime I can parse the plugin descriptor, META-INF/plugin.xml, which is generated from annotations and javadoc.  Currently it has all of the metadata needed to do what I want to do with the exception of knowing which Settings.KEYS value that parameter is ultimately used for in the Settings Object. So including the alias field could be used to add that information in the plugin.xml as well as allowing a user to specify the Settings.KEYS value as a configuration element in the pom file itself. This simplifies my originally proposed feature from manually creating a separately maintained .properties file to a modification of an existing maintained java class.


Hello developer, I need to read and write when I have been unable to complete, can you help me to see why

The image is my code

https://tagui.readthedocs.io/en/latest/reference.html#excel

网址https://tagui.readthedocs.io/en/latest/reference.html#excel

我写的有问题是吗

@XiaoluoMax for datatables, you need to have headers, see this - https://tagui.readthedocs.io/en/latest/advanced.html#datatables-for-batch-automation
But if you are trying to read from Excel, there is no need to specify t.xlsx in your tagui command.


Fix typo

Coverage remained the same at 100.0% when pulling 3c0ccbac69cd2f9be91696eede13e839e89982d3 on shenjiayu:master into 3faf41610980b09842d1621e792b580b19cf550d on mirrorjs:master.

Thanks!


Fix Least Common Multiple method

There is currently a method called lcm that lives in /lib/lcm.js.
It is incomplete and needs to be fixed!

Acceptance Criteria:

Running yarn test lcm results in tests passing.
You have written a skeleton method for someone else to work on.
You have written tests surrounding your skeleton method.
Running yarn lint does not print any errors to the console!
Optional: write one or two more tests surrounding the method you are solving to account for potential edge cases.

Please include the skeleton of a new method + an accompanying test for someone else to work on at the time of creating a pull request! A pull request will most likely be denied if it does not contain a skeleton method for someone else to work on! For more information, please read the Contributing Guide.
Thank you so much for your contribution!

Hi, can I work on this?

@zuzanatoldyova Yes please! I will keep this locked to you for 24 hours. If you need more time please just let us know. We are looking forward to your contribution.

Hi, I just saw that this was already solved by someone else in pr #410

Hey @zuzanatoldyova ! Sorry about that. We try to keep up with issues as best we can. Feel free to improve the existing implementation if you'd like. Or find a new issue :) Thanks!


toggle hidden comment with arrow left or h

I can't count how many times I've pressed the left arrow to un-hide a comment and have been kicked back out the the sub. I figured if I'm having this problem others might as well.
This simple change checks to see if the comment is hidden on KEY_LEFT or h key presses and if it is, it un-hide it instead of exiting to the subreddit
EDIT: You won't hurt my feelings if this doesn't get added, I just thought it might be useful :)

I think core problem here is the RIGHT isn't a very intuitive key for toggling comments. Every other directional key is used to navigate between comments and pages. The reason I did it this way was because it made it easy for me to browse everything with only one hand on the arrow keys.
For a while I was also using SPACE to toggle comments. It actually works really well if you're using hjkl, but is a little awkward combined with the arrow keys. I would say try that out for a while and let me know how it feels.

Sounds good. It agree is still kind awkward to hide comments (that move left) by pressing the right arrow.

Maybe the CTRL key would be a good mapping. Combined with SPACE that would be convenient for both arrow key users and hjkl users.

closing for now


React15 throws warning for unknown prop

description

how to reproduce

render <FlexView column></FlexView>

specs
omit FlexView's prop before passing them to the div wrapper
misc
{optional: other useful info}

We're already doing this! it was an error in another project:


Plugin export/import feature

Hi @romanovskyj ! The tool is really nice and it worked for my simple Kong 1.0.3 setup with services and routes!
I had a quick look into the code and found out that there is PluginsPath and looks like export/import for plugins is planned but I didn't see it was used in https://github.com/romanovskyj/gongfig/blob/master/pkg/actions/export.go
Are you planning to add plugin export/import feature?

Hi, all collections are fully supported and plugins also. https://github.com/romanovskyj/gongfig/blob/master/pkg/actions/export.go#L164 it is obtained here. Anyway, if your plugin is not exported correctlt, let me know.

Git it! thank you very much!


Incorrect index value when scrolling

Okay, I'm now using latest version of scroll.  The issue I'm having is that the datasource.get() function is being called the first time with an index == 1.  Is that what it's supposed to do? I'm not understanding this.
It makes three calls to the API (with count set to 3).
first call -- index == 1 (returns 3 objects)
second call -- index == 4 (returns 3 objects)
third call -- index == -2 (returns 0 objects) (I'm now preventing this one from being called at all)
I expected the first call index value to be 0.  Isn't it zero-relative?
Anyway, I decremented index before making the API call to work around that.
However, after scrolling around a bit, the index value is incremented by 3, until suddenly it goes from 15 down to 5.  Continuing to scroll backwards, it makes the call with index==2 (and then with index=-1 but I prevent that).  So it's impossible to scroll back to see the first object.  I expected that it should only increment/decrement by count (in this case 3).  Is that not the case?
What am I not understanding here, or is this a bug?

The math involved in deciding what items to return is a bit confusing. Unfortunately there is not much to be done to simplify it because it is the direct result of how unpredictable the scrollbars can be.
To make life easier I would suggest to follow the pattern published in the examples i.e. here

And what about added the possibility to start counting at zero? I mean that makes more sense since when you want to get the first element in JS (or any other programming language) you access it with index zero, e.g. [1, 2, 3][0]. Sure people can work around that but this behaviour is very unintuitive (I just notice it by accident) and why not allow an attribute that simple defines the index of the first value?


Add missing commits

Hi Mario, I'd like to get this into the master branch soon but it needs its commits caught up. Thanks.


Add more essential categories and built a load more button for categories.

1: I added the more 9 essential categories with AI generated images as you say.
2: I also add a load more feature for loading one category row one by one. after all the categories are loaded in DOM the load more button will be disappeared.
Please go through the changes and merge it.

Please merge this with main branch, Thank you!


Add unit testing Athena policy

Added unit testing for the Athena template policy. Ref.  #1137
Issue #, if available:
#1137
By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

@nheijmans Can you please add this test case in the same pull request (#1137)
Also, along with updating the unit test case you need to add the output json files in the below locations

https://github.com/awslabs/serverless-application-model/blob/master/tests/translator/output/all_policy_templates.json
https://github.com/awslabs/serverless-application-model/blob/master/tests/translator/output/aws-us-gov/all_policy_templates.json
https://github.com/awslabs/serverless-application-model/blob/master/tests/translator/output/aws-cn/all_policy_templates.json
Please make sure make pr passes


Construct typescript documention is not ready for most of a day

I'm getting this message "Documentation in typescript is still not ready for this package. Come back soon. If this issue persists, please let us know by creating an issue."
Here's a screenshot:

How long is too long for the construct hub to generate this information?
Here are some links:
https://constructs.dev/packages/@rayova/cdk-serverless-nextjs/v/0.0.8?lang=typescript
https://constructs.dev/packages/@rayova/cdk-serverless-nextjs/v/0.0.9?lang=typescript
https://constructs.dev/packages/@rayova/cdk-serverless-nextjs/v/0.0.10?lang=typescript
https://constructs.dev/packages/@rayova/cdk-serverless-nextjs/v/0.0.11?lang=typescript
https://constructs.dev/packages/@rayova/cdk-serverless-nextjs/v/0.0.12?lang=typescript

It appears those packages fail installing with the following error:
'/tmp/A98984/node_modules/.bin/npm' command exited with code 228

Alright it appears this fails to process because it runs out of disk space while trying to install:
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write

2021-09-11T22:09:08.590Z	b59384f1-5747-4487-a0a2-8729f349f7ed	INFO	Installing package<EMAIL_ADDRESS>--
npm WARN old lockfile
npm WARN old lockfile The package-lock.json file was created with an old version of npm,
npm WARN old lockfile so supplemental metadata must be fetched from the registry.
npm WARN old lockfile
npm WARN old lockfile This is a one-time fix-up, please be patient...
npm WARN old lockfile
npm WARN deprecated<EMAIL_ADDRESS>The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
npm WARN deprecated<EMAIL_ADDRESS>The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
npm WARN deprecated<EMAIL_ADDRESS>Please upgrade to @mapbox/node-pre-gyp: the non-scoped node-pre-gyp package is deprecated and only the @mapbox scoped package will recieve updates in the future
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write
npm WARN tar TAR_ENTRY_ERROR ENOENT: no such file or directory, lstat '/tmp/E6d8I1/node_modules/@rayova/cdk-serverless-nextjs/node_modules/next/dist/compiled/find-cache-dir'
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write
npm WARN tar TAR_ENTRY_ERROR ENOSPC: no space left on device, write
npm WARN tar TAR_ENTRY_ERROR ENOENT: no such file or directory, lstat '/tmp/E6d8I1/node_modules/@sls-next/lambda-at-edge/dist/image-handler'
npm ERR! code ENOSPC
npm ERR! syscall write
npm ERR! errno -28
npm ERR! nospc ENOSPC: no space left on device, write
npm ERR! nospc There appears to be insufficient space on your system to finish.
npm ERR! nospc Clear up some disk space and try again.
npm ERR! A complete log of this run can be found in:
npm ERR!     /tmp/fake-homeVap6K9/.npm/_logs/2021-09-11T22_09_57_632Z-debug.log

We are going to (hopefully soon) deploy an ECS-backed version of this process, which will not have the same disk space limitation the current approach has, which should alleviate this problem.

In the meantime, I'm trying to improve our signalling of this particular condition...

We are going to (hopefully soon) deploy an ECS-backed version of this process, which will not have the same disk space limitation the current approach has, which should alleviate this problem.

Sounds good to me! Thank you.


Could not render a timeline block. Please correct the input.

I installed the plugin via pip and copied the .css file to the file system, and
extra_css:
  - stylesheets/index.css
  - stylesheets/blog.css
  - stylesheets/resume.css
  - stylesheets/academics.css
  - stylesheets/neoteroi.css

markdown_extensions:
  - attr_list
  - md_in_html
  - neoteroi.projects
  - neoteroi.timeline

::timeline::

- content: First implementation.
  icon: ':material-rocket-launch-outline:'
  sub_title: 2022-Q1
  title: Launch

::/timeline::

[timeline(./docs/gantt/timeline.yaml)]

but it throws

Hi mate, did you manage to solve the problem?

Hi mate, did you manage to solve the problem?

Haven't yet. I have no idea how to solve it. I suppose it may because of the unmatch between mkdocs version and neoteroi version?

Well, it works, thanks!

How can I help to improve the tutorial


integrate react native with js-jose

Hi,
I write an application that receives data in JSON format and I want to validate the data source before the application starts to process the data.
currently the data is stored in Amazon and the application is written in React Native (version 0.45.1).
I wonder:
Is it possible to integrate jose package with react native?
If yes, how?
In the 1st stage I will have static data in Amazon, so I wonder how I can sign the data with jose
Thanks

js-jose requires WebCrypto to be present in your environment, either natively in the browser or with a polyfill. You an use it to sign whatever data you want.


feat(pruner): shared deletion limit

With the addition of headers and transactions pruning for the needs of snapshots, it becomes even harder to manage the batch sizes for pruner, so we both not hit the MDBX freelist issues and still prune the data.
This PR refactors the batch sizes into one shared limit for maximum number of deleted entries per pruner run. Each prune part deletes as much as possible, it decreases the deletion limit, and further parts use new limit. It also means that prune parts now have different priority, because e.g. if receipts, which are pruned first, consume the deletion limit fully, consequent parts won't prune anything.
Tested on Sepolia:
2023-10-03T09:53:13.435908Z  INFO reth::node::events: Pruner finished tip_block_number=4415292 elapsed=730.074493ms parts={SenderRecovery: (true, 0), Receipts: (true, 0), ContractLogs: (true, 202), AccountHistory: (true, 288), StorageHistory: (true, 1232)}

PR itself lgtm. last_pruned_block_number becomes a confusing name if we consider snapshots though (since it will be at a higher height than the first block to prune from the snapshot) , and we might want to change it in the future.


Finish porting Razor.Evolution tests

Fixed legacy tests
Added TagHelperDescriptorJsonConverter and added serialization tests

@rynowak @pranavkm @NTaylorMullen

🆙 📅

🆙 📅

🆙 📅 FYI only. I'll merge these to one big PR.


How to build a patch version

I'd like to figure out how to build a patch version, like php 7.4.32 maybe.
I guess I figured it out, with:
bin/spc download --all -U "php-src:https://www.php.net/distributions/php-7.4.32.tar.gz"
./bin/spc build bcmath,openssl,tokenizer,sqlite3,pdo_sqlite,ftp,curl --build-cli --build-fpm
./buildroot/bin/php --version
PHP 7.4.32 (cli) (built: Sep 15 2023 11:18:05) ( NTS )
Copyright (c) The PHP Group
Zend Engine v3.4.0, Copyright (c) Zend Technologies

But the canonical way to do this would improve the README. It looks like the key is deleting the downloads and source directories first? The first time I did it I got 7.4.33, which I had apparently been built earlier.
Actually supporting the patch version in spc fetch would be a win too.
My goal is to provide a workaround for the occasional DDEV user who wants a particular patch version for testing or comparison. It's certainly not common.

There is a --clean option for download which will delete previously downloaded files & extracted source.

If you just want to compile a different version of PHP immediately after compiling one version of PHP, you can consider deleting the source directory and downloads/php-*.tar .gz file, and then run the bin/spc download command and the bin/spc build command again.

@stloyd it does seem that --clean is incompatible with all the other arguments; if you use it nothing else happens. For example, with bin/spc download --clean --all  -U "php-src:https://www.php.net/distributions/php-${STATIC_PHP_VERSION}.tar.gz"

@rfay Yeah. It's just an alias to rm -rf those dirs. I'm not sure people need a bin/spc clean:download command.

Thanks for the help, all.


Using ports other than 80/443 on the proxy

I am using this compose file with my domain at the VIRTUAL_HOST & LETSENCRYPT_HOST. HTTP is loading correctly but HTTPS results in a 500 or 503 Error. Any info on how to resolve this is much appreciated.
Thanks
Kamran

Here is my docker-compose - I am also using ports 8282 for HTTP and 30443 for HTTPS (currently using OS X server on 80 and 443):
`version: '3'
services:
db:
image: mariadb
command: --transaction-isolation=READ-COMMITTED --binlog-format=ROW
restart: always
volumes:
- db:/var/lib/mysql
environment:
- MYSQL_ROOT_PASSWORD=passowrd
env_file:
- db.env
redis:
image: redis
restart: always
app:
build: ./app
restart: always
volumes:
- nextcloud:/var/www/html
environment:
- VIRTUAL_HOST=nc.example.com
- LETSENCRYPT_HOST=nc.example.com
-<EMAIL_ADDRESS>- MYSQL_HOST=db
env_file:
- db.env
depends_on:
- db
- redis
networks:
- proxy-tier
- default
cron:
build: ./app
restart: always
volumes:
- nextcloud:/var/www/html
entrypoint: /cron.sh
depends_on:
- db
- redis
proxy:
build: ./proxy
restart: always
ports:
- 8282:80
- 30443:443
labels:
com.github.jrcs.letsencrypt_nginx_proxy_companion.nginx_proxy: "true"
volumes:
- certs:/etc/nginx/certs:ro
- vhost.d:/etc/nginx/vhost.d
- html:/usr/share/nginx/html
- /var/run/docker.sock:/tmp/docker.sock:ro
networks:
- proxy-tier
letsencrypt-companion:
image: jrcs/letsencrypt-nginx-proxy-companion
restart: always
volumes:
- certs:/etc/nginx/certs
- vhost.d:/etc/nginx/vhost.d
- html:/usr/share/nginx/html
- /var/run/docker.sock:/var/run/docker.sock:ro
networks:
- proxy-tier
depends_on:
- proxy
volumes:
db:
nextcloud:
certs:
vhost.d:
html:
networks:
proxy-tier:`
Here is what I get when I run the compose.

Hi. Letsencrypt http-01 challenge can only happen over ports 80 and 443, there is no way to obtain a certificate with this container if your proxy container can't use those ports.

Hi, is it possible I can modify something or is there another (docker-compose) setup I can use to get this working. I heard about virtual ports...but not sure how to use them or what they do. I am basically using this config with the ports changed:
https://github.com/nextcloud/docker/tree/master/.examples/docker-compose/with-nginx-proxy/mariadb-cron-redis/apache
Thanks

This is a Letsencrypt hard requirement, there is nothing you can do to change this, your only alternative if you can't clear and use ports 80 and 443 is to get your certificate through another LE client that supports other challenges methods. This container only work with http-01 challenge.

Thanks for the info. Do you know of any clients that will allow me to do this? I am fairly new to docker and nextcloud so I am not sure.
Are they any major issues of not using SSL? I should be fine as long as I only connect on a secured connection right?
Alternatively I am using port 80 and 443 since I am running profile manager on OS X server...it also has a web service (apache) built in and I can have the base URL forward to the ports.

You can take a look at traefik, which supports dns-01 challenges.
Regarding using or not using SSL, well I tend to use it no matter what, with self generated certificate if the service is not public and if I can't get a trusted cert and/or setup automated renewal of a trusted cert for this service. I won't go into the details of why SSL by default, there are a lot of people who already wrote about it way better than I would.
If you want to use a self generated certificate and need help, don't hesitate to ask.
If you can configure OSX Server to use SNI and redirect incoming request to the nginx proxy when needed, that would work too but you'll lose the automation when spinning up new containers with other VIRTUAL_HOST / LETSENCRYPT_HOST, as you'll need to append OSX Server Apache's configuration each time.
If you can configure OSX Server to use ports others than 80 and 443, you could also do the reverse, ie adding a static configuration to nginx proxy and having it forward traffic to OSX Server ports.

Closing due to inactivity.


Client side routing not working on load of a specific route or refresh

Either I'm going nuts or client side routing is not working properly in 1.2.0. In 1.1.9 you could load into mysite.com/#/books and you'd get the correct route displaying. As would refreshing a particular route. In 1.2.0 neither of these things work and you get a 'notfound'. Haven't had a chance to look into it further yet.

+1 很蛋疼


Allow apptainer images to be automatically downloaded

Depending on the target users, auto-download of missing apptainer images could be convenient. However, it trades off the educational aspect of downloading images.
An option suggested during the ENIGMA workshop was to instruct the user with a command to download a missing image; similar to git commands.

Related to #249


remove the unless api in column nullable

What problem does this PR solve?
Remove the unless api in ColumnNullable：`insert_null_elements` replace by `insert_many_defaults`

Problem Summary:
Release note
None
Check List (For Author)

Test

[ ] Regression test
[ ] Unit Test
[ ] Manual test (add detailed scripts or steps below)
[x] No need to test or manual test. Explain why:

[ ] This is a refactor/code format and no logic has been changed.
[ ] Previous test can cover this change.
[ ] No code files have been changed.
[ ] Other reason

Behavior changed:

[x] No.
[ ] Yes.

Does this need documentation?

[x] No.
[ ] Yes.

Check List (For Reviewer who merge this PR)

[ ] Confirm the release note
[ ] Confirm test cases
[ ] Confirm document
[ ] Add branch pick label

Thank you for your contribution to Apache Doris.
Don't know what should be done next? See How to process your PR.
Please clearly describe your PR:

What problem was fixed (it's best to include specific error reporting information). How it was fixed.
Which behaviors were modified. What was the previous behavior, what is it now, why was it modified, and what possible impacts might there be.
What features were added. Why was this function added?
Which code was refactored and why was this part of the code refactored?
Which functions were optimized and what is the difference before and after the optimization?

run buildall

run buildall


Remove extraneous dependency on Grunt.js

Grunt is not relevant to this tutorial. lets remove it!

Fixed.


Avoid sending confirmation email

I have installed devise_invitable. When someone is invited, two email are sent. One confirmation and one invitation. I want to skip the confirmation email. Can anyone help me?
I have version 1.3.2 of devise_invitable and 3.2.2 of devise

I had a similar problem, I was calling save on the user inside the invite! block. Fixed by rearranging some code.


2021 Anual Report: intro tweet

Provide the actual tweet content between the commented colons

In 2021 we had a lot of improvements in Kubernetes: find many of them and much more on our recently published 2021 Annual Report! https://github.com/kubernetes/steering/blob/main/reports/summary-2021.md

https://twitter.com/K8sContributors/status/1532429719777443840?s=20&t=bpSj0UrMSXhvZQOuOsi0Gg, this tweet is already posted.

https://twitter.com/K8sContributors/status/1532429719777443840?s=20&t=bGVZFJ7VvQR2NUhIoopI_Q, sorry but this tweet is already done.

/close


[POC] Make AppHeader themeable without @mui/styles

I've achieved this by looking at https://github.com/mui/material-ui/blob/master/packages/mui-material/src/AppBar/AppBar.js and copying the parts which I deemed as relevant 😅

Nice work, I really like this approach 👍🏼
Making styles dependent on vars/props was sometimes an issue with the previous approach, this seems to work well here, as you can pass custom props into each slot.
I think we should try to refactor some of the more complex components, with this approach.
If that works well we can refactor all other components and remove the legacy @mui/styles package.
Maybe:

CometAdminTooltip
CometAdminFormFieldContainer
CometAdminToolbarBackButton & CometAdminToolbarItem
CometAdminErrorBoundary
CometAdminColorPicker

Maybe it also makes sense to create a factory to create the slots of a component.
Sort of like this:
const { Root, FooBar } = createThemableComponentSlots("CometAdminAppHeader", {
    Root: {
        component: MuiAppBar,
        overridesResolver: ({ position, color }, styles) => [
            styles.root,
            styles[`position${capitalize(position)}`],
            styles[`color${capitalize(color)}`],
        ],
        styles: ({ theme, position, color }) => css`
            // Styles for Root slot.
        `,
    },
    FooBar: {
        component: "div",
        overridesResolver: ({ foo }, styles) => (foo ? [styles.fooBar, styles.fooBarFoo] : [styles.fooBar]),
        styles: <FooBarProps>({ theme, foo }) => css`
            // Styles for FooBar slot.
        `,
    },
});

Instead of this:
const Root = styled(MuiAppBar, {
    name: "CometAdminAppHeader",
    slot: "Root",
    overridesResolver({ position, color }, styles) {
        return [styles.root, styles[`position${capitalize(position)}`], styles[`color${capitalize(color)}`]];
    },
})(
    ({ theme, position, color }) => css`
        // Styles for Root slot.
    `,
);

const FooBar = styled("div", {
    name: "CometAdminAppHeader",
    slot: "FooBar",
    overridesResolver({ foo }, styles) {
        return foo ? [styles.fooBar, styles.fooBarFoo] : [styles.fooBar];
    },
})<FooBarProps>(
    ({ theme, foo }) => css`
        // Styles for FooBar slot.
    `,
);

@johnnyomair @jamesricky Should we merge this? Or are you waiting for Niko's approval?

@thomasdax98 this is just a POC for the first component. I thought that @jamesricky would implement his suggestion and apply it for all components. He could do this in this PR, or we could close it, or merge it and implement the suggestion in a follow-up PR

@thomasdax98 @johnnyomair I'll put this on draft for now until I actually get to implementing this for all components.


win: almost fix race detecting ESRCH in uv_kill

It might happen that only using WaitForSingleObject() with timeout 0 could return WAIT_TIMEOUT as the process might not have been signaled yet. To improve things, first use GetExitCodeProcess() and check that status is not STILL_ACTIVE. Then, to cover for the case that the exit code was actually STILL_ACTIVE use WaitForSingleObject(). This could still be prone to the race condition but only for that case.
Fixes: https://github.com/nodejs/node/issues/51766

I think this is done @vtjnash ptal, thanks


Wma/fix steppers

This allows us to emit a fast stepper loop even when we can't prove that A_lvl_i <= phase_stop, by using the loop guard to ensure the property as well as check when we need to break. Ideally we could consolidate the logic inside the stepper. fixes #308

Although this could be cleaner, it looks good to me as well and I think we need to merge it.


specify http_proxy information as wget::fetch attribute

Currently, HTTP-Proxy information for wget::fetch  can be specified by setting the top scope variables $::http_proxy and/or $::https_proxy. However, I think it is generally bad practice for a Puppet module to rely on the presence of certain global variables (if every module would do it that way, it would be a totally mess).
In my opinion, this piece of information should be specified as parameter for wget::fetch.

see #61


Linking problem on OS X in http / ssl packages

When trying to compile this nop program with ponyc 0.1.7 on OS X:
use "net/http"

actor Main
  new create(env: Env) =>
    Server(recover Listener end, recover Service end)

class Listener
  fun ref listening(server: Server ref) => None
  fun ref not_listening(server: Server ref) => None
  fun ref closed(server: Server ref) => None

class Service
  fun apply(request: Payload val): Any => None

I get a link failure of:
Undefined symbols for architecture x86_64:
  "_GENERAL_NAME_get0_value", referenced from:
      _ssl_X509_all_names in service.o
ld: symbol(s) not found for architecture x86_64
unable to link

Maybe I'm doing something wrong, but it the link failure seems wrong.

The openssl provided by Apple is quite old, unfortunately. You'll need a more recent one. I suggest libressl:
brew install libressl

Wow, fast turn around. That was it, thanks!

Great, glad it worked!

Reopening, because we should list libressl and pcre2 as brew dependencies in the ponyc formula.

Closing. Opening new issues.


[$500] auto submit is not working on the NewDot Test Workspace - Contractors

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Version Number:
Reproducible in staging?: needs reproduction
Reproducible in production?: needs reproduction
If this was caught during regression testing, add the test name, ID and link from TestRail:
Email or phone of affected tester (no customers):
Logs: https://stackoverflow.com/c/expensify/questions/4856
Expensify/Expensify Issue URL:
Issue reported by: @danieldoglas
Slack conversation: https://expensify.slack.com/archives/C049HHMV9SM/p1706287561831329
Action Performed:

Set up auto submit (daily) for the expense reports in the OD
Create an expense report on the workspace chat NewDot Test Workspace - Contractors

Expected Result:
Should get submitted as per the auto schedule option selected
Actual Result:
Not submitted automatically
Workaround:
unknown
Platforms:

Which of our officially supported platforms is this issue occurring on?

[ ] Android: Native
[ ] Android: mWeb Chrome
[ ] iOS: Native
[ ] iOS: mWeb Safari
[X] MacOS: Chrome / Safari
[ ] MacOS: Desktop

Screenshots/Videos
Add any screenshot/video evidence

View all open jobs on GitHub
Upwork Automation - Do Not Edit

Upwork Job URL: https://www.upwork.com/jobs/~0171e9448ec33f398b
Upwork Job ID:<PHONE_NUMBER>754946048
Last Price Increase: 2024-01-31

Starting leave so re-assigning!

@danieldoglas , this needs to be internal... right?

Yep, it does. I think it will fit into #wave5 or #wave6 since it's related to submitting receipts

Thanks @danieldoglas , added to Wave 5 and commented in that room
https://expensify.slack.com/archives/C05DWUDHVK7/p1706921786138959

bumping to weekly since it was applied a status on the Wave5 project

I think this is actually a Critical bug as it means OldDot scheduled submit settings aren't being respected in NewDot. Is this reproducible @mallenexpensify @ntdiary?

All right I'll ask QA to check

Closing based on: https://expensify.slack.com/archives/C02MW39LT9N/p1708453407651559


[Bug] Block syncing can hang

Happened to me once for ~2 minutes, but resumed on its own. It's probably not related to the node itself, but let's keep track of it in case others encounter it.
2022-08-19T08:11:27.410185Z TRACE Requesting block 3772 of 6662
2022-08-19T08:13:32.965693Z  INFO Synced up to block 3673 of 6662 - 55% complete (est. 3 minutes remaining)

I haven't noticed it happen in a long time now, nor seen any reports from other users.


Storybook Story Source is not changed when user clicks different versions of component

Detailed description

Describe in detail the issue you're having.

on http://react.carbondesignsystem.com The Story Source doesn’t change when you click the different versions of the component. For example, DataTables component Story Source (after clicking “show info”) is the same for “with toolbar”, “with sorting”, “with selection”, etc… Should the source update with these different versions of the component?

Is this issue related to a specific component?

At least the DataTable storybook, I haven't looked at other components story books

What did you expect to happen? What happened instead? What would you like to see changed?

I expect the story source to update to reflect the different version of DataTables clicked

What browser are you working in?

Google Chrome Version 69.0.3497.81 (Official Build) (64-bit)

Steps to reproduce the issue

Go to http://react.carbondesignsystem.com
Click DataTable on the left hand menu
Click through the different sub categories of DataTable and notice the Story Source (shown by clicking "show info" in the upper right corner) is the same for all the different versions.

@alohr51 Looks that all stories you brought up have very similar story source, only difference I can see is the render prop. Probably that's why you thought all the same? Did you look at the "with dynamic content" story? Thanks!

I was pointing out more about how for example with toolbar doesn't show the Story Source that has the toolbar or search bar. Shouldn't the Story source for that look like the render from the story here
All i see in the story source is below (when I expect to see whats in the link above). Is this normal?
<DataTable rows={[{
      id: 'a',
      name: 'Load Balancer 3',
      protocol: 'HTTP',
      …
    },{
      id: 'b',
      name: 'Load Balancer 1',
      protocol: 'HTTP',
      …
    },{
      id: 'c',
      name: 'Load Balancer 2',
      protocol: 'HTTP',
      …
    }]} headers={[
    {key: 'name',header: 'Name'},
    {key: 'protocol',header: 'Protocol'},
    {key: 'port',header: 'Port'},
    …
  ]} render={render} />

I see that @alohr51 - I was referring to render={render} thing at the bottom BTW where I guess Storybook cannot show the function implementation as a prop value. Given the only difference is such obfuscated function, every sub-story looked the same?

Yupp! I think @asudoh nailed it. Unfortunately with the DataTable stories, most of the implementation details are in the render method. Storybook isn't able to bring out that method, and instead only prints the name.
You can always search for the stories using this feature of GitHub: https://github.com/IBM/carbon-components-react/find/master specifically searching for DataTable/stories which will show you all the files that contain the story source 👍
Going to close this for now, hope this helps!

@asudoh yes each sub-story looked the same, so it was confusing when I was copying the code from the toolbar story and didn't see the toolbar in my own application.
Is this a limitation of StoryBook? I feel like others might go down the same confusing path as I did and won't know about https://github.com/IBM/carbon-components-react/find/master

Here is an example of what I mean, screen shots usually help
DataTable with sorting

DataTable with toolbar

as you can see they look the exact same even though one has the toolbar and one doesn't

Correct, this is intended. The only difference between the stories is the render method. Unfortunately Storybook doesn't embed the method directly.


Fix source maps not working in Camunda Modeler crash reports

What should we do?

[ ] Investigate why source maps in the client bundle are not working in our crash reports.
[ ] Fix the situation

Why should we do it?
Source maps allow us to reliably reproduce issues recorded.

We should also not upload *Spec.js files, as they are now present within the uploaded artifacts in Sentry.

We should also not set an array of plugins as a tag. It turns out that Sentry does not allow non-primivite values as tags:

We should also consider disabling this feature for nightlies, as we're uploading nightly sourcemaps to Sentry every night.

The problem seems to be path mismatch: Since we distribute the code to the clients, each error has a different path from uploaded sourcemap paths. We need to normalize the path before we send them to Sentry. I'm investigating the best practises for that.


feat: add LinearRegression.predict_explain() to generate ML.EXPLAIN_PREDICT  columns

Thank you for opening a Pull Request! Before submitting your PR, there are a few things you can do to make sure it goes smoothly:

[ ] Make sure to open an issue as a bug/issue before writing your code!  That way we can discuss the change, evaluate designs, and agree on the general idea
[ ] Ensure the tests and linter pass
[ ] Code coverage does not decrease (if any source code was changed)
[ ] Appropriate docs were updated (if necessary)

Fixes #379743762 🦕

Doctest failed, but doesn't appear to be related:
FAILED third_party/bigframes_vendored/pandas/core/frame.py::frame.DataFrame.update

_______________________ [doctest] frame.DataFrame.update _______________________
[gw1] linux -- Python 3.12.0 /tmpfs/src/github/python-bigquery-dataframes/.nox/doctest/bin/python
4066
4067             >>> import bigframes.pandas as bpd
4068             >>> bpd.options.display.progress_bar = None
4069
4070             >>> df = bpd.DataFrame({'A': [1, 2, 3],
4071             ...                    'B': [400, 500, 600]})
4072             >>> new_df = bpd.DataFrame({'B': [4, 5, 6],
4073             ...                        'C': [7, 8, 9]})
4074             >>> df.update(new_df)
4075             >>> df
UNEXPECTED EXCEPTION: BadRequest('GET [https://bigquery.googleapis.com/bigquery/v2/projects/bigframes-testing/queries/a0e298c3-d88a-43a3-8ee8-06454d818cbe?maxResults=0&location=US&prettyPrint=false](https://www.google.com/url?q=https://bigquery.googleapis.com/bigquery/v2/projects/bigframes-testing/queries/a0e298c3-d88a-43a3-8ee8-06454d818cbe?maxResults%3D0%26location%3DUS%26prettyPrint%3Dfalse&sa=D): The job encountered an internal error during execution and was unable to complete successfully.')


LGTM automated code review does not work, lgtm.yml file is needed

task has been done, issue could be closed


Plugin not running & not shown at Android Studio Arctic Fox | Built on July 27, 2021

Looks like there is a fix now.
https://stackoverflow.com/a/68739316


Slayer task

a slayer task plugin could be usefull

there's already a slayer plugin, if you wan't something specific please explain more about what you want

I mean where you can do !task

Ah. You should probably update the title of the feature request. Also, for future feature requests I highly recommend putting more effort into choosing the proper title and description in the issue to avoid confusion like this.

sorry will update it asap


Consider ways to split polyfills out of main package

We might be able to use webpack's DefinePlugin and IgnorePlugin to create two versions of the package, one which polyfills new React features for old versions, and one which doesn't. This might require some thought to get it right...

Related, pre-16.2 the polyfills will not be react native compatible (https://github.com/benwiley4000/create-react-15-context/issues/2) (#176).

#218 made this issue obsolete.


2251 accessibility issues on the community list page

References

Fixes #2251

Description
Cdk-tree was re-rendering itself completely on each datasource change because no trackBy function had been defined. It could not establish what was new and what was old. So a quick win :)
Instructions for Reviewers
Build the front end and expand communities and collections on the community list page and contrast with https://demo7.dspace.org/community-list
List of changes in this PR:

trackBy method for cdk-tree
minor styling changes

Thanks @J4bbi. I tested this patch. The stylistic changes seem sane and don't affect the UI presentation significantly, but should improve screen reader's ability to parse the tree.
Regarding the cdk-tree trackBy changes, I can't see any difference in testing. How can I tell that the tree is re-rendering every time? Is this something that is perceivable visually like a flicker when expanding communities and collections, or just makes it slow? Thanks!

Thanks for taking the time to review this @alanorth .
When the cd-tree is loaded on first arriving at https://demo.dspace.org/community-list, everything is fine:

If you then click to expand the node, it will set the focus:

The focus will remain momentarily while the API call is made to establish the children nodes. But the focus will then be dropped because to cdk-tree entirely new data is being loaded, not the same data with some more added.

I've had to use a different example for how the patch works because the demo server has been switched to https://sandbox.dspace.org

Hope that makes it clear?
This is trackBy analogous to d3's key function in binding data if you're familiar with D3.

Thanks, @J4bbi. I see what you mean now. Current behavior without the patch, I see aria-expanded="false" and then it flashes aria-expanded="true" briefly when I expand the node, and then the property disappears.
I verified that the  aria-expanded property is persistent with correct state on each cdk-tree node when expanding and collapsing. Looks good to me!


How to handle auth with multiple instances of the same OAuth backend

Currently, creating a new backend instance logs the current user in with whatever token there is in localStorage. If they log out on that instance, and log in again, they have replaced the token in localStorage, though other backends will not be affected.

Should we facilitate having multiple backends side by side logged in with different accounts?
Should we keep track of all instances created so we could keep them in sync wrt logins/logouts?

Note that these are mutually exclusive: if we log in and log out all instances when you log in/out from one instance, then you can't log in on one instance with different accounts.

I’ve added a syncWith() method to Backend instances, and a syncWith option to the constructor, which does one-way auth sync (for two way sync, you'd just call it twice with the arguments swapped).
I think this kind of easy but explicit opt-in is the best way to go — we don't want to just assume that instances should be in sync, as I can easily think of use cases where this is not desirable.
Once Mavo moves towards using Madata for its storage adaptors, we can just keep track of instances on the Mavo side and call syncWith appropriately.


Changes in toolkit and testcases for increasing stability

This PR increases the stability of the load_image_granule() function in the toolkit and addresses the test case for the same.
This PR increases the accuracy of the test case for the function extract_granule() in the toolkit.
This PR also allows the test functions to automatically delete the unnecessary test files generated during testing of the toolkit.

Coverage decreased (-1.3%) to 74.83% when pulling 96c6e3678d7f7e7441126796bf33652359693f17 on Omkar20895:master into 03fe2d81fe3047fa3c4527e269327e360530c288 on lewismc:master.

I am using this PR for testing in travis-ci and will close it as soon as everything is working okay

Coverage decreased (-1.3%) to 74.83% when pulling eec5199c341a26c0faebf48c1002973a8e290a18 on Omkar20895:master into 03fe2d81fe3047fa3c4527e269327e360530c288 on lewismc:master.

Coverage increased (+0.4%) to 76.552% when pulling 220c5cf381562381c0ba105e566330576fbc897c on Omkar20895:master into 03fe2d81fe3047fa3c4527e269327e360530c288 on lewismc:master.

Everything is working fine now 👍  I am closing this pull request I will squash all the commits and send in a new pull request with a single commit. Thanks.

ack thanks


Documentation is failing to build and publish since #93 was merged

See https://github.com/CycloneDX/cyclonedx-python-lib/runs/4595932920?check_suite_focus=true.
This appears to be the case since #93 was merged.
FYI: @jkowalleck

python markdown requires importlib_metadata which is not installed. hm, that  is strange.
will look into it.

I can't get it to fail locally @jkowalleck ? Very weird.

Last successful run (https://github.com/CycloneDX/cyclonedx-python-lib/runs/4584812203?check_suite_focus=true) pulled in a newer version of Installing markdown (3.3.6) than the latest attempt: Installing markdown (3.3.5)

I'll regen poetry.lock @jkowalleck

And when doing so I get this:
<debug>PackageInfo:</debug> Invalid constraint (importlib-metadata (>='4.4') ; python_version < "3.10") found in markdown-3.3.5 dependencies, skipping

So - looks like the root cause is related to bumping flake8 `>=4.0.1':
If we directly had markdown==3.3.6 as a dev-dependency:
poetry update
Updating dependencies
Resolving dependencies... (0.1s)

  SolverProblemError

  Because no versions of markdown match >3.3.6,<4.0.0
   and markdown (3.3.6) depends on importlib-metadata (>=4.4), markdown (>=3.3.6,<4.0.0) requires importlib-metadata (>=4.4).
  And because flake8 (4.0.1) depends on importlib-metadata (<4.3)
   and no versions of flake8 match >4.0.1,<5.0.0, markdown (>=3.3.6,<4.0.0) is incompatible with flake8 (>=4.0.1,<5.0.0).
  So, because cyclonedx-python-lib depends on both flake8 (^4.0.1) and markdown (^3.3.6), version solving failed.

Isolating dependencies for documentation generation has resolved this immediate problem.


Filter not being applied everywhere.

I am able to fetch soft-deleted entities using a $this->entityManager->find() , i.e. the EntityManger Interface in doctrine. Not sure why this happens but, looks like the filter is not being applied through this.

Also, when using a doctrine query to fetch entities, relations are not being filtered out either.
Given that I have 2 soft-deletable entities A and B, and entity B related to A with a Many:One relation, when, I enable the filter and fetch Entity A, I will get entities from A filtered, but then the query also fetches every entity B related to A and does not filter out soft-deleted entities from B.

Is there something I am missing out?

I have directly added the filter the config/doctrine.php
I enable the filters right before using the doctrine queries too.

Here are a few related issues too,
https://github.com/Atlantic18/DoctrineExtensions/issues/1463
https://github.com/doctrine/orm/issues/6343

Are you using a bundle to install extensions in Symfony, or configured manually?

Up @AdtHO any news ?


Change Active Directory Password : LDAPUnwillingToPerformResult - 53 - unwillingToPerform

Hi!
Thank for your code, it's a very interesting tool for change ldap'user password.
But I can't use it to change password from an Windows Active Directory Server. Test with openldap, not problem.
Here is my setting.ini file :
[html]
page_title = Change your password on example.org
[ldap]
host = xx.xxx.x.x
port = 389
search_filter = samaccountname={uid}
base = dc=my-ad,dc=org
type = ad
ad_domain = my-ad.org
[server]
server = auto
host = localhost
port = 8080

When i want to change a password, i have this error log :
Traceback (most recent call last):
  File "/usr/lib/python3.5/site-packages/bottle.py", line 862, in _handle
    return route.call(**args)
  File "/usr/lib/python3.5/site-packages/bottle.py", line 1732, in wrapper
    rv = callback(*a, **ka)
  File "app.py", line 34, in post_index
    change_password(form('username'), form('old-password'), form('new-password'))
  File "app.py", line 63, in change_password
    change_password_ad(*args)
  File "app.py", line 93, in change_password_ad
    c.extend.microsoft.modify_password(user_dn, old_pass, old_pass)
  File "/usr/lib/python3.5/site-packages/ldap3/extend/__init__.py", line 208, in modify_password
    controls)
  File "/usr/lib/python3.5/site-packages/ldap3/extend/microsoft/modifyPassword.py", line 13, in modify_ad_password
    controls)
  File "/usr/lib/python3.5/site-packages/ldap3/core/connection.py", line 893, in modify
    response = self.post_send_single_response(self.send('modifyRequest', request, controls))
  File "/usr/lib/python3.5/site-packages/ldap3/strategy/sync.py", line 124, in post_send_single_response
    responses, result = self.get_response(message_id)
  File "/usr/lib/python3.5/site-packages/ldap3/strategy/base.py", line 369, in get_response
    raise LDAPOperationResult(result=result['result'], description=result['description'], dn=result['dn'], message=result['message'], response_type=result['type'])
ldap3.core.exceptions.LDAPUnwillingToPerformResult: LDAPUnwillingToPerformResult - 53 - unwillingToPerform - None - 00002077: SvcErr: DSID-03190E49, problem 5003 (WILL_NOT_PERFORM), data 0
 - modifyResponse - None

Any idea for what i have this error? It's seem that you cannot change password like this in Active Directory.

Hi,
I've made it work with AD with the following settings:
[html]
page_title = Change your password on example.org
[ldap]
host = LDAPS://xx.xxx.x.x
port = 636
search_filter = samaccountname={uid}
base = dc=my-ad,dc=org
type = ad
ad_domain = my-ad.org
[server]
server = auto
host = localhost
port = 8080

From my research, I found out, that you need to have a certificate, because AD won't allow you to change the password on an unencrypted LDAP connection.

I’ve added a warning to the readme in 334d8236b79fd9438518b1b8039be3f706b55224.


Why does "int | None" transforms into openapi non-nullable integer?

First Check

[X] I added a very descriptive title to this issue.
[X] I used the GitHub search to find a similar issue and didn't find it.
[X] I searched the FastAPI documentation, with the integrated search.
[X] I already searched in Google "How to X in FastAPI" and didn't find any information.
[X] I already read and followed all the tutorial in the docs and didn't find an answer.
[X] I already checked if it is not related to FastAPI but to Pydantic.
[X] I already checked if it is not related to FastAPI but to Swagger UI.
[X] I already checked if it is not related to FastAPI but to ReDoc.

Commit to Help

[X] I commit to help with one of those options 👆

Example Code
from fastapi import FastAPI
from pydantic import BaseModel

app = FastAPI()

class Item(BaseModel):
    id: int | None

@app.post("/items/")
async def create_item() -> Item:
    return Item(id=1)

Description

Open the generated openapi.json spec
Found that id field is "required" with type "integer"
Expects to found id field "required" with type "integer" and "optional" parameter

I know that you can add nullable=True to Field definition, but for me int | None looks monosemantic unlike int | None = None which can describe non-required openapi field with default value in python.
Operating System
Other
Operating System Details
No response
FastAPI Version
0.86.0
Python Version
3.11.0
Additional Context
No response

I'm a bit new here but a similar issue has been raised before #2924. Just by a quick observation, I think the openapi spec will detail when a field is "required" and otherwise the field can be left as None. So adapting your logic above
from fastapi import FastAPI
from pydantic import BaseModel, Field
from typing import Optional

app = FastAPI()

class Item(BaseModel):
    id: int | None
    field_req: int

@app.post("/items/")
async def create_item() -> Item:
    return Item(field_req=1)

Will give the following component part of the open api spec
    "components": {
        "schemas": {
            "Item": {
                "title": "Item",
                "required": [
                    "field_req"
                ],
                "type": "object",
                "properties": {
                    "id": {
                        "title": "Id",
                        "type": "integer"
                    },
                    "field_req": {
                        "title": "Field Req",
                        "type": "integer"
                    }
                }
            }
        }
    }

Notice the required field now contains a list of fields that the client must populate correctly. Hope that helps somewhat.

Thank you @Tiri1992, this is a great answer!


LIBCLOUD-901 Correctly wrap requests library Responses with 4xx/5xx status codes

Correctly wrap requests library Responses with 4xx/5xx status codes
Description
This fixes the constructor of RawResponse to explicitly check if response is not None. This is necessary because the requests library overloads the __nonzero__/__bool__ methods on the Response object to return False if a 4xx or 5xx status code is returned. This has been fixed in the 3.0 branch of requests, but that version hasn't been released yet.
Status
done, ready for review
Checklist (tick everything that applies)
I haven't checked any of these because all I did was make a 10 character change.

[ ] Code linting (required, can be done after the PR checks)
[ ] Documentation
[ ] Tests
[ ] ICLA (required for bigger changes)

great spot. thanks @richardxia for the contribution


Boatload of patches required for Sprint 11

Description
This is a boatload of patches/fixes/hacks needed to get Sprint 11 running in production on mskcc1.foldingathome.org.
Summary of changes
Useful things to carry forward

Added support for optional --experimental-data-file <data.json> argument to specify experimental data used to update compound data, along with ExperimentalCompoundData data model
Removed DEBUG code that set stddev of works to 5 kT arbitrarily
Updated overlap matrix code for pymbar 3.0.3, but will need tweaks to make compatible with 3.0.3 and 3.0.5 APIs for MBAR.computeOverlap()
Added tracebacks in some locations to facilitate debugging
Regenerate hybrid_complex.pdb on the fly if needed, since recent versions of perses eliminate these files. This code could be further optimized if needed---see notes in code.

Horrible bodges

Hacked PDB file path in load_fragment

Todos
Things left to fix:

[ ] Mpro is being imaged into different boxes (likely an issue with simulation setup, not fah-xchem)
[ ] Compound pIC50s on front page appear to be so much more potent than expected
[ ] Add experimental 95% CIs to plots and reported statistics
[ ] Add bootstrapped convergence vs number of samples plots to Transformations page
[ ] Sort out stereochemistry nightmares
[ ] Improve handling of racemic compounds

Status

[ ] Ready to go

Codecov Report

Merging #164 (85ee4ad) into master (2050143) will decrease coverage by 0.03%.
The diff coverage is 20.60%.

There's a major flaw in the snapshot extraction system that will require a significant rewrite.
In brief, our current scheme does the following:

construct an MDTraj Trajectory for the hybrid system
aligns it to the appropriate reference frame
slices out the appropriate snapshot frame
slices out atom subsets for {old|new} {complex|protein|ligand}
writes these out in PDB and SDF formats (using a flaky PDB -> SDF conversion heuristic)

The problem is that atoms that change identity during the transformation are left in their initial state in the hybrid topology used to create the Trajectory. We therefore either need to do this a completely different way, or we need some way to construct a "new hybrid topology" to be used before step 4 or to substitute the appropriate new topology.
We also likely need to substitute out the flaky PDB -> SDF conversion heuristic.

The simplest way forward for now is likely to load old_complex.pdb and new_complex.pdb via MDTraj and use these to build old_hybrid_topology and new_hybrid_topology objects which can then be sliced appropriately. This will avoid the need to build hybrid_topology.pdb, which takes time anyway.
The OpenEye old and new molecules are available via the htf.npz file via
import numpy as np
import mdtraj as md
import openmm # openmm 7.6
from openeye import oechem
htf = np.load('htf.npz', allow_pickle=True)['arr_0'].tolist()
old_oemol = htf._topology_proposal.old_topology.residue_oemol
new_oemol = htf._topology_proposal.new_topology.residue_oemol

but it takes several minutes to extract these, so we will probably want to stick to the heuristic for now.

I've figured out what is going wrong with the snapshot extraction, but it will take another day to fix. Apologies for the delay!
The main causes are:

There is a bug in core22's <xtcAtoms v="solute"/> feature where atoms can be returned out of order that I neglected to fix
perses does not provide sufficient information about which atoms are omitted in the {new|old}_{ligand|protein}.pdb and hybrid_atom_mappings.npz files it writes.

It's straightforward for me to implement a workaround within fah-xchem, but tedious because both the behavior of the core and perses need to be reproduced within fah-xchem until we can solve one or both of the above issues for the next sprint.

There's still a lot more left to be fixed, but we at least have one Sprint 11 dashboard running stably now:
https://fah-public-data-covid19-moonshot-sprints.s3.us-east-2.amazonaws.com/dashboards/sprint-11/sprint-11-2021-12-26-P1800_0A-dimer-neutral-restrained/index.html
This can be merged and we can carry on from here if it is appropriate to do so.
Alternatively, I can keep refining things in this branch.

There's still a lot more left to be fixed, but we at least have one Sprint 11 dashboard running stably now:
https://fah-public-data-covid19-moonshot-sprints.s3.us-east-2.amazonaws.com/dashboards/sprint-11/sprint-11-2021-12-26-P1800_0A-dimer-neutral-restrained/index.html
This can be merged and we can carry on from here if it is appropriate to do so.
Alternatively, I can keep refining things in this branch.

@dotsdl : Changes for Sprint 11 are complete! We should get this merged and carry on as appropriate.
Sprint 12 is starting on Monday.

Sounds good! Reviewing today. We'll pull this in before #155.

I'll fix the tests; all due to website changes.

@dotsdl : Apologies that I haven't yet made the final changes needed to the data model for experimental data.
I had not entirely decided how to handle this, but I believe we need to capture whether the measurement reflects one of several possible states:
stereochemistry = { achiral | racemate | absolute enantiomer | relative enantiomer of {compound_id} }

I hope to be able to complete this on Monday!

No worries @jchodera! Happy to discuss tomorrow during our call as well. Just finished improving the tests for checking website elements.


Pages behaviour

It is somehow not specified on the documentation how the builds are split by pages.
I've tested it and it seems that page N gets the builds with array index i mod N == 0, that is for example for 4 pages:
builder.builds[0] - > Page 1
builder.builds[1] - > Page 2
builder.builds[2] - > Page 3
builder.builds[3] - > Page 4
builder.builds[4] - > Page 1
builder.builds[5] - > Page 2
Please confirm and I can pull request a docs clarification.
Also, is there a way to have any control over this? For example, if I have 2 pages, I might want to split the builds in Page 1 for x86 and Page 2 for x86_64 so they take about the same time, as I also might want to keep variations of Debug or Shared in the same page, to reuse builds that just do different packaging.
Would I have to construct my builds array with x86 on even indexes and x86_64 on odd indexes?
Thanks,
Nuno

Hi, it works exactly like that. About controlling the pages and the configurations, currently is not possible.
If you can submit a PR will be great.
Thanks!

My python knowledge probably will not allow me, but I'll give it a look. Thanks.


Safari 3D transform causing SVG to render blurry

Rendered SVG ok from After Effects, works ok as a stand alone HTML.
When added to the website it causes the SVG to become a large blurred out block. When 3D transform is removed it removes the blurriness and restores it completely to normal.
Works fine in Firefox, Chrome etc just Safari doesn't like 3D transform. Any ideas as to why? What is 3D transform doing?
Thanks
Jack

width: 100%; height: 100%; transform: translate3d(0px, 0px, 0px); transform-origin: 0px 0px 0px;

I use translate3d to create a new layer independent from the rest of the page so it can be hardware accelerated and hopefully doesn't trigger relayout of the rest of the page.
I never noticed it caused blurriness in safari.
Do you have a link I can check?

Makes sense just not sure why it's only messing with Safari..
Bare with me on that one, will get back to you about a link.
As always thanks for the speedy reply!