More help/argparse cleanup

Most of what I had intended to under http://tracker.ceph.com/issues/12083 got split out into different issues and have already been resolved (Yay!).
This is just a couple of minor things that I had queued up that didn't go in yet.
The prog variable in the argparse namespace always confused me.  It's called out as an "ugly kludge", but it's not actually used anywhere.  Kill it!

Refer to this link for build results (access rights to CI server needed):
http://jenkins.ceph.com//job/ceph-deploy-pull-requests/1708/
Test PASSed.

I think the point of prog had been to pass the name of the program down to the subparsers for error messages.  I imagine it went away when the logging got all Technicolor.

Makes sense, Dan.  I didn't go far enough back into history to see what it was ever used for, but I don't think it's been used in at least a year. :)


HG-135 - upgrades

[x] cleanout old vue components deps and code
[x] fix homepage timeline read more button. They can't use sweatalert anymore, I converted the component over to use alpine, I think alpine has a modal component that can be used in its place.

Closes #135

livewire modals - https://github.com/wire-elements/modal

@zach2825 if this is ready to merge, then please let me know what commands to run to avoid blowing things up.
We still have https://stage.hackgreenville.com so it will be deployed there first to test.

Sorry, I see this is the one you said was not ready.
Could you post any deploy commands on the other PRs that are ready so I can pull them to stage and run the commands and check that things are good before doing the same on the live site?

All resolved @allella

I can't remember the current process to deploy these changes.
Deploys now should do these:

yarn install
composer install
yarn build

@zach2825 this is showing conflicts too.
Please let me know if you when you want to merge this and if we should go live with the previous two PRs now, or merge all PRs, test, and go live in one shot.
Thanks

@allella, sorry about that; all resolved should not happen going forward. These few PRs contained a lot of changes that depended on each other.

@zach2825 I'm about to merge this into the develop branch and test on stage.
On the stage server, should I run all of the following?
yarn install
composer install
yarn build
Also, it looks like there's are two new VITE  .env variables I need to copy from .env.example, correct?

Hey @allella,
No, you should not need those. Those variables changed for vite, so I wanted to update them so if anybody wants to use them in the future, they will be more accurate. They are just for push notifications using web sockets.

@zach2825 I merged in and pulled the code to stage and it's not surprisingly needing more commands.
You said in the last message I didn't need to run yarn or composer commands, but it seems like something is needed to get all the Laravel 10 updates and clearing out old gunk.  What's the proper order of commands for getting this up to snuff on the stage site?
I did try php artisan view:cache but I'm assuming a yarn or composer command needs to be run at least for this upgrade, but I'd rather not keep guessing and mess things up.

Also,

@zach2825 nevermind, I see you were telling me I don't need the VITE vars and I read it quickly to mean that the commands above weren't needed.
I ran the three commands on stage and it's unbroken.
https://stage.hackgreenville.com
Are the three yarn and composer commands something we should always run on deploys? If so, shall we add these do the README?

PRs #139 #137 and #134 are now live. Thanks @zach2825


[VS Code] secret_password_clear_sync() failed with error code 2: The name org.freedesktop.secrets was not provided by any .service files

Error:
secret_password_clear_sync() failed with error code 2: The name org.freedesktop.secrets was not provided by any .service files
Steps to Reproduce:

Enter the secret code
Press enter

Version Data

extensionName
VSLS

extensionVersion
0.2.489

protocolVersion
2.2

applicationName
VSCode

applicationVersion
1.22.2

platformName
Linux

platformVersion
4.16.3-1-ARCH

This error is caused by the missing package gnome-keyring installing it will solve the issue, maybe we should add this as dependecy

@Nhoya Thanks for raising the issue. You are correct, vanilla arch is missing both gnome-keyring and libsecret.  Each are listed in the set of dependencies which are referenced in the installation instructions.  Arch is even called out in the docs.
https://aka.ms/vsls-docs/linux-prerequisites
Since Live Share is an extension, we can't force dependencies to install as easily as you can in a native package.  Further, the package names vary by distro.  Debian, RHL, Arch, Gentoo, etc all vary.  Currently our focus has been on officially supported platforms but VS Code and .NET Core - specifically the Debian and RHL paths.  That said, we're interested in arch as a team, so we're generally keeping an eye on it.  As a result, the installer script in the docs does attempt to cover dependencies.  As described there, you can run this as follows:
wget -O ~/vsls-reqs https://aka.ms/vsls-linux-prereq-script && sh ~/vsls-reqs
As an enhancement, we've considered detecting this scenario and running the script in a terminal window in VS Code.
As a result, I'm going to tweak the title of this slightly and mention it as a feature request if that is okay with you.

This should now be available in v0.3.392/v.0.393.


Add tag-picker component to the toolkit

Assuming a first cut at this would be a standardized HoistField wrapper around Blueprint MultiSelect

Looking at this now. Have a client request that sounds very much like this component.

👍


let's use \verb

@rultor release, tag is 0.6.0

@rultor release, tag is 0.6.0

@yegor256 OK, I will release it now. Please check the progress here

@rultor release, tag is 0.6.0

@yegor256 Done! FYI, the full log is here (took me 16min)


Bump version number to 1.0.0 (prepare initial deployment)

What is the purpose of this PR?
Now that we've actually set up .travis.yml to deploy to PyPI, we now need to officially send a release to PyPI so our package will be able to be downloaded via pip.
How did you implement your changes

Bump the version number to 1.0.0
Separate the version number into a constant in setup.py so it can be easily located and updated when needed
Add a download_url param in setup.py which points to the .tar.gz file generated on a new release, this file needs to be created separately by opening a new release on the repo

Remaining issues

Make sure to tag this commit on merge into master. We should tag this commit with the version number. So in this case, the tag associated with this commit should be 1.0.0.
Remember: to officially make this release open to the public, we also need to open a new release on GitHub so PyPI points to the correct download link (and one that actually exists).
If deployment works, we're good to go!
If not, then I'll open a separate debugging PR
We need to update our documentation/README so users know they can pip install ark-analysis.
We may need a separate PR to address any issues that come up with the pip installation of ark-analysis.
setup.py will need frequent updates. For example, if new libraries are added, they need to be appended to the install_requires param list. Also, if we begin to support more Python versions in the future, the classifiers list also needs to be updated.

During standup today, I will be discussing a lot of the things I brought up in the Remaining issues section.


Bulk User import option is not  much visible

Describe the issue:

Bulk User import option is not  much visible

Git issue - https://github.com/wso2/product-is/issues/16935
Testing issue - https://github.com/wso2/product-is/issues/16945
How to reproduce:

Login into the console using the below local pack
https://drive.google.com/drive/u/2/folders/1r-t8ek3TPl_oN7F3gT28fTZdCjoMCpqP
Go to the user management section => users => Add user
Choose bulk import option

Expected behavior:

Environment information (Please complete the following information; remove  any unnecessary fields) :

Product Version: [e.g., IS 5.10.0, IS 5.9.0]
OS: [e.g., Windows, Linux, Mac]
Database: [e.g., MySQL, H2]
Userstore: [e.g., LDAP, JDBC]

Optional Fields
Related issues:

Suggested labels:

With the "Invite set of external users to register into the organization at once" effort "Bulk Import" text will be replaced as follow image.


How can I prevent animation in a child widget and make the parent widget animate ?

I am a bit new to the animation stuff and I was reluctant to use animation as its really complex in Flutter but then I stumbled upon this amazing library and I am so glad it exists.
I'd really appreciate if I could get some guidance on how to achieve this (if possible).
Badge(
toAnimate: true,
animationType: BadgeAnimationType.slide,
elevation: 4,
shape: BadgeShape.circle,
badgeColor: Colors.deepOrangeAccent,
borderRadius: Get.width > 600 ? BorderRadius.circular(28.r) : BorderRadius.circular(8.r),
badgeContent: Text("${Get.find().quoteCartQty.value}",
style: ThemeStyles.NORMAL_STYLE_LIGHT.copyWith(color: Colors.white)),
child: SvgPicture.asset(Constant.cartLogoFill, color: Colors.white),
).animate(onPlay: (con) => con.repeat(), delay: 1000.ms).shake(delay: 1000.ms),
It animates the badge and the cart logo both as a unit, but I only need the badge to animate.

Any animations you apply to a parent will necessarily propagate to it's children — in Flutter the position of the parent dictates the position of the child. You could use a Stack to layer the icon over the badge though.


Loss of provenance in error messages from unset Providers

A test was added to demonstrate a situation where an non-optional input file tries to use a optional output file property:
https://github.com/gradle/gradle/pull/4665/commits/2ccba855e3fc88546e9b917d8241f5aff74d6f59#diff-a3b5d8b01a4aea02d728cc2f62c1c6e9R534
class ProducerTask extends DefaultTask {
    @Optional @OutputFile
    Property<RegularFile> outFile = newOutputFile()

    @TaskAction
    def go() { }
}

class NestedBean {
    NestedBean(RegularFileProperty inputFile) {
        this.inputFile = inputFile
    }

    @InputFile
    final RegularFileProperty inputFile
}

class ConsumerTask extends DefaultTask {

    @Nested
    NestedBean bean = new NestedBean(project.layout.fileProperty())

    @Optional
    @OutputFile
    Property<RegularFile> outputFile = newOutputFile()

    @TaskAction
    def go() { }
}

task producer(type: ProducerTask)
task consumer(type: ConsumerTask) {
    bean.inputFile.set(producer.outFile)
}

The consumer.bean.inputFile takes its value from producer.outFile.  Since producer.outFile is not set, consumer.bean.inputFile appears to not be set as well.
The current error message is:

No value has been specified for property 'bean.inputFile'.

This might seem confusing to users because bean.inputFile has definitely been set to something, but that thing doesn't have a value.
A better message might be something like (ignoring how complicated this might be):

No value has been provided for property 'bean.inputFile' by 'producer.outFile'.

This example involves a producer task, but any property -> property chain could have this issue where you need to know the "root" provider that you need to configure to fix all of the consumers.
Maybe this is what we had in mind for gradle/gradle#10616 ?

Some of this will be appearing in 6.0


Ability to pass json encoding options.

Added an optional argument to the Response->json method that allows
passing of encoding options like JSON_PRETTY_PRINT.
I hope this is not a duplicate. But i thought it could be handy to be able to pass encoding options to the json response method.
Example:
$response->json($data, null, JSON_PRETTY_PRINT);

Sounds like someone's having fun mineing bit coins, it's me I'm having fun we all hope its not a hoax

Some days with a node

Pick this one it's doing well


Engine artifact uploads failing

For example:
https://ci.chromium.org/ui/p/flutter/builders/prod/Linux Host Engine/10306/overview
But also several others. I expect this is transient, but filing the issue just in case it isn't.

I removed the permissions to the bucket a bit too soon. https://flutter-review.googlesource.com/c/recipes/+/13882 took a few more minutes to land than expected.
I'm Retrying the builds,

List of retries:

http://ci.chromium.org/b/8846028478746237968
http://ci.chromium.org/b/8846028402201730176
http://ci.chromium.org/b/8846028367478751856
http://ci.chromium.org/b/8846028327540475664
http://ci.chromium.org/b/8846028284140047264
http://ci.chromium.org/b/8846028245238327264
http://ci.chromium.org/b/8846028201393702720
http://ci.chromium.org/b/8846028163770641968
http://ci.chromium.org/b/8846028127826438560
http://ci.chromium.org/b/8846028095824597120
http://ci.chromium.org/b/8846028053285870032
http://ci.chromium.org/b/8846028020703118816
http://ci.chromium.org/b/8846027989944778848


The cluster configuration for config-upgrade

@krvladislav commented on Tue Nov 13 2018
What is a valid format of the config string to be passed via --cluster-config argument?
I get "(E_INVALIDARG) Invalid argument" when I try for example to pass content of a file mentioned in https://github.com/Microsoft/service-fabric-cli/blob/34dba32e2dbaaebd2f412319a802cf60adb312f9/customSDK/servicefabric/models/cluster_configuration_upgrade_description.py#L22
Also script which pass the current configuration to config-upgrade fails the same manner:
$config = $(sfctl sa-cluster config --configuration-api-version 10-2017)
$clusterConfiguration = ($config | ConvertFrom-Json).clusterConfiguration  -replace '"', '""'
sfctl sa-cluster config-upgrade --cluster-config $clusterConfiguration

Сведения о документе
⚠ Не вносите правки в этот раздел. Это необходимо для связывания страницы сайта docs.microsoft.com с вопросом на GitHub.

ID: 6b6bd4b5-0b50-b2b8-baee-be135c91e889
Version Independent ID: 401e437d-ead6-6e27-0580-32f53498ede9
Content: Интерфейс командной строки Azure Service Fabric. sfctl sa-cluster
Content Source: articles/service-fabric/service-fabric-sfctl-sa-cluster.md
Service: service-fabric
GitHub Login: @Christina-Kang
Microsoft Alias: bikang

Hi team,
Please check the issue reported by the user.
Thanks!

Thanks for the question! We are investigating and will update you shortly.

@krvladislav @LisandroSu you can find examples of how the cluster config is formatting here:
https://docs.microsoft.com/en-us/azure/service-fabric/service-fabric-cluster-standalone-package-contents
Simply download the package contents and you will see multiple clusterConfig files. These are JSON formatted files.
Take a look and if you have additional questions just let me know.

@LisandroSu can you give me the full set of commands you are running?

@krvladislav can you provide the following information please?

Sfctl version (you can run pip show sfctl)
Which OS you are running
The service fabric run time version you are targeting.
Which version of Python you are using

Thank you!

@Christina-Kang thank you, I will provide more info in the ticket you've opened.
Shortly if I remove from REST request (sfctl sniffered via Charles) all fields of type string(duration) or just all fields except ClusterConfig - then it works.

@krvladislav, you are correct. The problem sfctl has specifically is that when it serializes duration data, it serializes it to the wrong format. The duration should be the format seen in the example above, but sfctl sends "P0D" over the wire instead, and the service fabric endpoint rejects the request.

Thanks @Christina-Kang for the update on this! Appreciate the help!
@LisandroSu I will close this issue out and continue to work off https://github.com/Microsoft/service-fabric-cli/issues/156 and track that issue.


documentation request - coordinates format

Great idea to add short term forecast!
However i've got an issue - this integration is not providing any service or entity.
cloud you be more specific about what coordinate format to use with long/lat?  I was not able to add coordinates in full format "50.0799811N, 14.3747031E" as the form does not accept letters

I reproduced the error for your coordinates. Will look into it later.
Just use the decimals as input, 50.0799811 and 14.3747031.
Logger: homeassistant.components.weather
Source: custom_components/met_next_6_hours_forecast/weather.py:184
Integration: Weather (documentation, issues)
First occurred: 17:59:45 (1 occurrences)
Last logged: 17:59:45

met_next_6_hours_forecast: Error on device update!
Traceback (most recent call last):
  File "/usr/src/homeassistant/homeassistant/helpers/entity_platform.py", line 493, in _async_add_entity
    await entity.async_device_update(warning=False)
  File "/usr/src/homeassistant/homeassistant/helpers/entity.py", line 703, in async_device_update
    await task
  File "/config/custom_components/met_next_6_hours_forecast/weather.py", line 184, in async_update
    precipitation_probability=details[
KeyError: 'probability_of_precipitation'


Using latest version of aiken-jna-wrapper, which contains error propagation.

@satran004 this is ready to be merged and new release made (from my point of view).


(WIP) Added History Index Stages (6 and 7)

Codecov Report

Merging #159 (c9cbc4a) into master (7a57451) will decrease coverage by 0.59%.
The diff coverage is 1.38%.

@@            Coverage Diff             @@
##           master     #159      +/-   ##
==========================================
- Coverage   84.05%   83.46%   -0.60%
==========================================
  Files          68       69       +1
  Lines        6386     6429      +43
==========================================
- Hits         5368     5366       -2
- Misses       1018     1063      +45

Impacted Files
Coverage Δ

db/silkworm/db/access_layer.cpp
47.87% <0.00%> (+0.57%)
:arrow_up:

db/silkworm/db/bitmapdb.cpp
0.00% <0.00%> (ø)

db/silkworm/etl/collector.hpp
100.00% <ø> (ø)

db/silkworm/etl/collector.cpp
73.64% <33.33%> (+1.57%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 7a57451...c9cbc4a. Read the comment docs.


Update nginx.conf

Add types_hash_max_size to fix types_hash_max_size error on some machines.

Hi @woutersterp, could you give more background on this change? Why do you need it?
Thanks for contributing1

I've tried to deploy the version without it, nginx tries to select an appropriate hash size, but fails on systems where it cant detect any CPU cache size.
This is a known problem at many VPS-providers (like digital ocean), this setting should fix this problem for all systems.

I see, thanks for clarifying!


feat: add text to middle, and fix android bugs

Sean i included the other plugin fixies in this one.
This add text to the center of the circle
This also fixies 2 issues with the plugin on android.
The first one is to fixies the bar with(now its the same as rim).
The second is to hide the text in the center of the plugin(set textSize to 0).
Also added some import fixies because of ci

@sean-perkins can you take a look at it ?

addressed comments 👍


Check GL_INVALID_VALUE within glBind*

Is there reasonable for checking target of underlying object equal with GL_INVALID_VALUE inside glBind*() operation? For example, check it within glBindFramebuffer() to find out whether is the framebuffer name already bound to a different target. If so, raise a gl error and quit.

All checks required by the spec will be implemented in validate() functions corresponding to each GL entrypoint. All of these functions are stubbed at the moment, as they are not required for a proof-of-concept implementation I've been working on.
In fact, this area is something I'm hoping the community to help with. It's a lot of work to implement all these ifs.


Set the content type for non-HTML 404s.

If you visit non-HTML 404 pages, the mime type is not correctly set and thus, displays the HTML as plain text. For example...
/content/test.jpg
/content/something.json
/content/something-else
All returns 404.html as plain-text.
This pull request sets the content-type to be HTML to display when a file cannot be found. It's probably worth a discussion whether there should be excluded mime-types for this... for example, maybe json should return { response : 'not found' }.

Many thanks, Chris!


v1.6 backports 2019-08-29

PR: 9039 -- doc: Add Azure CNI to CNI chaining section (@tgraf) -- https://github.com/cilium/cilium/pull/9039
PR: 9049 -- test: Wait for at least one Istio POD to get ready (@jrajahalme) -- https://github.com/cilium/cilium/pull/9049
PR: 9063 -- CI: decouple HTTP and DNS testing in K8sPolicyTest (@raybejjani) -- https://github.com/cilium/cilium/pull/9063
PR: 9074 -- docs: clarify nodeport and host-reachable services and 5.0.y kernel (@borkmann) -- https://github.com/cilium/cilium/pull/9074
PR: 9072 -- cilium: silence harmless CILIUM_TRANSIENT_FORWARD warning on startup (@borkmann) -- https://github.com/cilium/cilium/pull/9072

This change is

never-tell-me-the-odds

k8s upstream test seems to have an issue:
01:00:03.457  # k8s.io/client-go/transport
01:00:03.457  ../../../k8s.io/client-go/transport/round_trippers.go:70:11: cannot convert klog.V(9) (type klog.Verbose) to type bool
01:00:03.457  ../../../k8s.io/client-go/transport/round_trippers.go:72:11: cannot convert klog.V(8) (type klog.Verbose) to type bool
01:00:03.457  ../../../k8s.io/client-go/transport/round_trippers.go:74:11: cannot convert klog.V(7) (type klog.Verbose) to type bool
01:00:03.457  ../../../k8s.io/client-go/transport/round_trippers.go:76:11: cannot convert klog.V(6) (type klog.Verbose) to type bool
01:00:03.457  2019/08/29 11:35:39 e2e.go:77: err: go get -u k8s.io/test-infra/kubetest: exit status 2
01:00:03.457  exit status 1
[Pipeline] }


ZEVA - Reassessments in the negative - add to deficit table

Description:
If a supplier goes into the negative during a reassessment, we need to add a record to the deficit table to track that they are in deficit, similar to model year reports. In addition, we need to make sure that the whole workflow is working correctly with deficits in general
Acceptance Criteria:

[ ] Given I am a director, when i issue a reassessment with a negative closing balance, it is recorded in the organization_deficit table
[ ] if a reassessment is created, delete whatever is in the deficit table for that model year report and create a new one to replace it?

Development Checklist:

[ ] follow the same way as the model year report for adding a deficit from a reassessment to the organization_deficit table

Notes:

Not user tested. To be fully tested once the testing scenarios are ready for complete testing of supp reports and reassessments.


[bug] config file generation broken since 4.0.0 (incl 4.1.2)

The config file generates without any options other than Default914Recipes = true
This problem seems to have originated in the 4.0.0 update. The file generates properly in the 3.0.0 version.

Temporary fix: generate the config using an older version (like 3.0.0)
Or paste the following text into the config file:
SCPCBDunGen.txt

The dungeon generation config is handled by LLL from v4 onwards, check the LLL config for customization. The legacy config options won't have any effect on later versions.


"Aborted(RuntimeError: unreachable executed)" - possible memory leak?

From https://github.com/microbit-foundation/python-editor-v3/issues/1127
This reproduction counts to 1997 and then crashes with
Uncaught RuntimeError: Aborted(RuntimeError: unreachable executed). "unreachable" may be due to ASYNCIFY_STACK_SIZE not being large enough (try increasing it)
    abort https://python-simulator.usermbit.org/v/0.1/build/firmware.js:1013
    runAndAbortIfError https://python-simulator.usermbit.org/v/0.1/build/firmware.js:1864
    maybeStopUnwind https://python-simulator.usermbit.org/v/0.1/build/firmware.js:1971
    x https://python-simulator.usermbit.org/v/0.1/build/firmware.js:1941
    doRewind https://python-simulator.usermbit.org/v/0.1/build/firmware.js:2015
    handleSleep https://python-simulator.usermbit.org/v/0.1/build/firmware.js:2048
    callUserCallback https://python-simulator.usermbit.org/v/0.1/build/firmware.js:1431
    createModule https://python-simulator.usermbit.org/v/0.1/build/firmware.js:1451

You can see the crash in the editor or the sim demo page.
If you you allocate more/bigger lists in c() then it fails after fewer iterations.
It also fails if you replace the list with bytearray().
It works if you reduce the level of nesting (e.g. call c() directly in a).
def a():
    i = 0
    while True:
        print(i)
        i += 1
        b()

def b():
    c()

def c():
    []

a()

Not sure whether it's really an asyncify-related problem or a leak manifesting like that.
I've not yet tried the suggestion in the error of increasing the stack size.

Closed by #106.


[BUG] Conditional Formatting with Font Style causes it to break styles on excel

🐛 Bug Report
#1410
When an excel files has a conditional format defined, and the conditional formatting specifically has font styles to it, if you read it into exceljs and write it back with no changes, excel finds the styles corrupt and removes all styles
Lib version: Latest to date
Steps To Reproduce
Create an excel that has conditional formatting and has font styles for the conditional format.
Read the file by exceljs , do no changes, write it back to xlsx. The file results in a corrupted style and excel removes all styles.
Template with conditional formating font style
Same template without the font style in conditional format
node -e "const Excel = require('exceljs'); var workbook = new Excel.Workbook(); var data = workbook.xlsx.readFile('./template.xlsx').then(()=>workbook.xlsx.writeFile('./test.xlsx').then(()=>console.log('Finished writing')))"

The expected behaviour:
The file styles should not break if a conditional format has font styles.
Possible solution (optional, but very helpful):
Can not pinpoint where the issue is

@Siemienik would you be able to help identify in code where the issue is ? I might be able to help if I just know how this is happening as I managed to reproduce it on multiple templates of xlsx

@Siemienik would you be able to help identify in code where the issue is ? I might be able to help if I just know how this is happening as I managed to reproduce it on multiple templates of xlsx

Might be related to #1305 which is fixed in PR #1574

Might be related to #1305 which is fixed in PR #1574

@rolandostar Thank you for the information,
@ywadi I've added this issue to my personal to-do list. Recently I have limited time resources and all my free time spend working on XToolset. If want you to help me spend more time on Open Source activities and will you want to have more impact on my priorities, It is able to support me by GH Sponsors

@rolandostar Thank you for the information,
@ywadi I've added this issue to my personal to-do list. Recently I have limited time resources and all my free time spend working on XToolset. If want you to help me spend more time on Open Source activities and will you want to have more impact on my priorities, It is able to support me by GH Sponsors

Done in #1574 by @rolandostar. Thank you a lot!


life cycle type - for Symbiont-associated (SA) package

New term details
For us to assess a new term request we require the following details:
Term name - life cycle type
Structured comment name - life_cycle_type
Definition - Type of life cycle, level of complexity of the symbiotic organism life cycle.
Expected value - type of life cycle of the symbiotic organism (host of the samples)
Value syntax - [complex life cycle:#hosts|simple life cycle]
Example - complex life cycle: 3 hosts
Package(s) - Symbiont-associated
Already assigned MIXSID : MIXS:0001300

Additional context
This is a term requested as part of the Symbiont package

looks fine to me

Discussed in today's CIG call:

Scoping a little unclear, this could be more generic if it's not bound to the definition and we go by the label
Options:

relabel to symbiont_lifecycle_type or similar, as this is using terminology specific to this field
make more generic by modifying definition (remove symbiosis)

In the symbiosis field, this means - according to our symbiont-associated team - the number of hosts a symbiont goes through during its lifecycle.
Concerns:

Moving away from describing the sample, this is species information

A long standing issue with MIxS - where do we draw the line in natural history?

The original definition is circular
The value field is bespoke and complex. Defer to later generic cleanup in MIxS.

Given that this is the only package requesting this, we would rescope to:
Term name - symbiotic life cycle type
Structured comment name - sym_life_cycle_type
Definition - The type of the symbiotic organism's life cycle, expressed in the number of hosts the organism occupies. Simple life cycles occur within one host, complex ones in many.
Expected value - type of life cycle of the symbiotic organism (host of the samples)
Value syntax - [complex life cycle: [number of hosts]|simple life cycle]
Example - complex life cycle: 3
Package(s) - Symbiont-associated
Already assigned MIXSID : MIXS:0001300

Updated the definition and labels as described above and according to the agreed upon naming pattern (symbiotic host organism).

Sorry to reopen this one, but I think the definition still needs a little more detail to be clear that its asking for prior knowledge of the species being sampled. My suggestion below:
Term ID - MIXS:0001300
Structured comment name - sym_life_cycle_type
Term name - symbiotic host organism life cycle type
** Definition - Type of life cycle of the symbiotic host species (the thing being sampled), expressed as the number of hosts it occupies in its normal life cycle. Simple life cycles occur within a single host, complex ones within multiple hosts.
Expected value - type of life cycle of the symbiotic organism (host of the samples)
Value syntax - [complex life cycle:#hosts|simple life cycle]
Example - complex life cycle: 3 hosts
package - Symbiont associated

This is better, Chris.
Sent from my iPad

On Jul 5, 2021, at 9:18 AM, Chris Hunter @.***> wrote:

Sorry to reopen this one, but I think the definition still needs a little more detail to be clear that its asking for prior knowledge of the species being sampled. My suggestion below:
Term ID - MIXS:0001300
Structured comment name - sym_life_cycle_type
Term name - symbiotic host organism life cycle type
** Definition - Type of life cycle of the symbiotic host species (the thing being sampled), expressed as the number of hosts it occupies in its normal life cycle. Simple life cycles occur within a single host, complex ones within multiple hosts.
Expected value - type of life cycle of the symbiotic organism (host of the samples)
Value syntax - [complex life cycle:#hosts|simple life cycle]
Example - complex life cycle: 3 hosts
package - Symbiont associated
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Now updated in MIxS v6 Term Updates sheet and included in v6 update log

Upon careful revision, we propose to simplify this term usage to indicate only whether the life cycle is simple or complex
for consistency with other defintions of the host being sampled in other terms, we need to change reference to the host being sampled to "symbiotic host organism".
We propose the following revision:
Term ID - MIXS:0001300
Structured comment name - sym_life_cycle_type
Term name - symbiotic host organism life cycle type
** Definition - Type of life cycle of the symbiotic host organism. Organism with complex life cycles use different hosts over the course of their life cycle.
Expected value - type of life cycle of the symbiotic host organism
Value syntax - [complex life cycle|simple life cycle]
Example - complex life cycle
package - Symbiont associated

I have updated the definition to:

Type of life cycle of the symbiotic host species (the thing being sampled). Simple life cycles occur within a single host, complex ones within multiple different hosts over the course of their normal life cycle.

and updated the value syntax and example as suggested above by @ndheilly

Ok


Method add_map_data stuck at loading

Every time I use this method to add map to plot, it stucks at "Loading..."
This happens also with provided examples; instead, the set_map_source method works smoothly.
How can I solve this issue?

I observed the same issue. I also observed it, when using 'set_map_source' with the option 'jsonp_map=True'.
I use the map in an jupyter notebook unsing an python2.7 kernel.


Modify the frontend to sort models by descending number of nodes

That would allow us to find the richest models.

This would require either a second query (that asks for the number of nodes per model) or a second search method (to retrieve all the models sorted by the number of nodes or something).
The Cypher query we want would be something like:
MATCH (s)-[p]-(o) WITH s, p, o, TYPE(p) AS pred_type UNWIND p.xref AS url WITH url, s, p, o, pred_type RETURN url, COUNT(p) AS numberOfEdges, COLLECT(DISTINCT {s: s, o: o, pred_type: pred_type}) AS edges LIMIT 100;

The other option is that we could pre-calculate the number of edges per model, and then load that into JavaScript.


jetson nano CSI camera Not working

Thank you for your effort to make such excellent stuff like this. I am able to use usb camera in jetson Nano and all sample codes are working without any issue but after this installation now my CSI camera codes are not working. getting camera not open error. I am using below gstreamer code for CSI camera in jetson nano
def create_gstreamer_pipeline(
self,
sensor_id=0,
sensor_mode=3,
display_width=640,
display_height=480,
framerate=30,
flip_method=2,
):
self._gstreamer_pipeline = (
"nvarguscamerasrc sensor-id=%d sensor-mode=%d ! "
"video/x-raw(memory:NVMM), "
"format=(string)NV12, framerate=(fraction)%d/1 ! "
"nvvidconv flip-method=%d ! "
"video/x-raw, width=(int)%d, height=(int)%d, format=(string)BGRx ! "
"videoconvert ! "
"video/x-raw, format=(string)BGR ! appsink"
% (
sensor_id,
sensor_mode,
framerate,
flip_method,
display_width,
display_height,
)
)

I'm a beginner with the Jetson Nano and have only been using it for 3 days, so I've never used a CSI camera with gstreamer. So there is no way to predict what kind of error message you are encountering. What should I look for? There is too little information available for my skills, and I don't know where to start looking.
This is not a joke, I'm serious.

Hi Thanks for your very quick reply. Yes I am able to solve the issue. I 1st uninstall opencv_contrib_python-<IP_ADDRESS> package (sudo pip3 uninstall opencv_contrib_python-<IP_ADDRESS>-cp36-none-linux_aarch64.whl) then rebuild opencv 4.5.2 from fresh (https://qengineering.eu/install-opencv-4.5-on-jetson-nano.html) now i am able to use mediapipe in jetson nano using CSI camera without any issue.

Thank you for sharing, I found that I can increase the performance by enabling gstreamer along with CUDA enabled build of OpenCV. I will rebuild the installer. Thanks! :smile_cat:

Thank you. I shall test with CSI cam and update you soon

Hi getting below error
sudo pip3 install opencv_contrib_python-<IP_ADDRESS>-cp36-none-linux_aarch64.whl
WARNING: The directory '/home/niladri/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
Processing ./opencv_contrib_python-<IP_ADDRESS>-cp36-none-linux_aarch64.whl
ERROR: opencv-contrib-python has an invalid wheel, .dist-info directory 'opencv_python-<IP_ADDRESS>.dist-info' does not start with 'opencv-contrib-python

@niladridmgit I tried experimenting with opencv with gstreamer enabled and mediapipe without opencv_contrib_python, but I kept getting segmentation faults and could not get it to work properly.

opencv_python-<IP_ADDRESS>-cp36-cp36m-linux_aarch64.whl
mediapipe-0.8.5_cuda102-cp36-cp36m-linux_aarch64.whl
https://drive.google.com/drive/folders/1swZYxgfFaVy2HF61MegGFswoBwvKxrq1?usp=sharing

The build specification of opencv_python changes daily, so I decided to stop providing it.

Hi sorry for delay. gstreamer  take more memory if I open 2 instance using 2 CSI cam due to memory overflow I am getting segmentation faults but 1 CSI working good in my Jetson Nano 4gb (B01) model which support 2 CSI cam

Probably A02 (4GB). However, I don't have a CSI camera that can be used with the Jetson Nano... :crying_cat_face: Segmentation Fault occurs when checking the operation using a USB camera.


Really high CPU usage.

I've read thru the other issues that seem to have the same problem I am but that didn't really help. I love this software but it using 25 to 40% CPU in the background is kind of extreme. I don't have the most powerful PC in the world but it's decent. The program uses more than a program like adobe premiere pro would use while editing.
Windows 10 64 bit  Version 1709
Intel Core i5 4430 @ 3.00Ghz
16GB Ram
Nvidia Geforce GTX 970

@kbuckleys Now that you mention it I have noticed high CPU usage on brave when I've used it (wasn't aware it was electron based). It's unfortunate because this has been my favorite launcher so far, I guess I'll have to keep looking!

@kbuckleys What are you using now?

Same on my computer, has anyone figured out a solution for this?

@albzn540 I was never able to figure it out, I ended up switching back to Launchy.

@Tatrii Ah okay, too bad. Hain was very aesteticly pleasing

This issue kept me away from Hain for a while. Then i finally gave it a change.
I didn't notice almost any CPU usage when not using. Then i thought maybe it's because i don't have any plugins. Then i installed a bunch of plugins that i would use and still the usage is same.
When i open hain it uses about 2,5% for once and then goes back to 0%
I used Wox before and even the memory usage seems to be about same ~150MB.
Could you maybe paste a list of plugins you use?
And i know this issue is almost a year old, but if this is outdated i feel it should be closed so it would not push users like me away.

@alanaasmaa You're so right! I do need to close this. I re-downloaded Hain about 3 months ago and it's been working flawlessly since!


Skip Intro Screen

Do we really need to see the intro screen over and over and over and over and over and over again? I'm pretty sure people know what it is by now, so I suggest adding a "Do not show again" checkbox and persist that setting.

This unfortunately, won't be fixed for the moment.


Added: View/search quotes by quote ID (.qid [id] / .quoteid [id])

Per the request of @ManuelFte earlier today 🙂
I liked the idea he requested, so here we are:

Description

Added a .qid [num] or .quoteid [num] search option that allows you to search by the quote ID's that were recently put in.

Motivation and Context

@ManuelFte asked me earlier if I thought it was a good idea and I said it sounds fine, and implemented it :-)

But really - makes looking up quotes that you want from the index with the ID good. We can delete them already, so it makes sense to look them up as they are with the ID.

This does support embeds on output unlike .qsearch which was designed then to be a search-and-find "raw" utility, which it works well for since one can view their embed code from Discord if they need to for some reason instead of the database. For this, we want to just see the original content/quote, as many times there are 5000 of the same keyword and this serves as a lookup moreso than a raw output search.

How Has This Been Tested?

This is pretty self explantory for this PR, as explained above.

Usage is .qid [id] .quoteid [id] and the output display is similar to .qsearch but with embed support, a few minor changes to the text but same exact idea. See screenshot below.

Screenshots

Types of changes

[x] New feature (non-breaking change which adds functionality)

Checklist:

[x] My change requires a change to the documentation. (✔)  [autogen next update]
[x] I have updated the documentation accordingly. (✔)
[x] I have added tests to cover my changes. (✔)
[x] All new and existing tests passed. (✔)

Oh, the spelling for success for the if (success) etc. was spelled sucess or something, so I just changed that (was on the DeleteQuoteById) 👍

'Error' being outputted as an error message when quote isn't found is not enough.
Add a new string to responsestrings and use that key.

Can you update this?

Sorry this is messy, will open new PR.


[Important] The current website is about to enter maintenance mode to aid with v3 launch

TL;DR; At the end of Jan 2021, all tracks will enter v3 staging mode. Updates will no longer sync with the current live website, but instead sync with the staging website. The Dart section of the v3 repo will be extracted and PR'd into this track (if appropriate). Further issues and information will follow over the coming weeks to prepare Dart for the launch of v3.
Over the last 12 months, we've all been hard at work developing Exercism v3. Up until this point, all v3 tracks have been under development in a single repository - the v3 repository. As we get close to launch, it is time for us to explode that monorepo back into the normal track repos. Therefore, at the end of this month (January 2021), we will copy the v3 tracks contents from the v3 repository back to the corresponding track repositories.
As v3 tracks are structured differently than v2 tracks, the current (v2) website cannot work with v3 tracks. To prevent the v2 website from breaking, we'll disable syncing between track repositories and the website. This will effectively put v2 in maintenance mode, where any changes in the track repos won't show up on the website. This will then allow tracks to work on preparing for the Exercism v3 launch.
Where possible, we will script the changes needed to prepare tracks for v3. For any manual changes that need to be happening, we will create issues on the corresponding track repositories. We will be providing lots of extra information about this in the coming weeks.
We're really excited to enter the next phase of building Exercism v3, and to finally get it launched! 🙂

@ErikSchierboom Can the new v3 version of the repository move the existing exercises to a v2 directory so any exercises not migrated to the practice exercises format can still remain?

@ErikSchierboom Can the new v3 version of the repository move the existing exercises to a v2 directory so any exercises not migrated to the practice exercises format can still remain?

The existing exercises will all become Practice Exercises, so there is no need. We'll make sure they will be converted to the right format.

The existing exercises will all become Practice Exercises, so there is no need. We'll make sure they will be converted to the right format.

@ErikSchierboom I do see one breaking issue. Under test, we have a test file that will load the tests for each of the would-be practice exercises and execute them. When those practice exercises are converted, I can see that breaking.
The other test file under test can remain as it tests our exercise generator. Which would be useful for future practice exercises.

@ErikSchierboom I do see one breaking issue. Under test, we have a test file that will load the tests for each of the would-be practice exercises and execute them. When those practice exercises are converted, I can see that breaking.
The other test file under test can remain as it tests our exercise generator. Which would be useful for future practice exercises.

When those practice exercises are converted, I can see that breaking.

Well yes, but the only thing that is changed (at the moment) is the location of the exercises. We do plan on making some changes, but they've not been finalized.

When those practice exercises are converted, I can see that breaking.

Well yes, but the only thing that is changed (at the moment) is the location of the exercises. We do plan on making some changes, but they've not been finalized.

@ErikSchierboom Understood, thanks

@ErikSchierboom Understood, thanks

As of today, the website has entered maintenance mode.

As of today, the website has entered maintenance mode.

With Exercism v3 just being released, tracks are no longer in maintenance mode and are active again.
This means that changes made to this track will once again show on the website.
Thanks for being patient with us and enjoy Exercism v3!


missing ARM Template function [providers(namespace, name)] reference

[Enter feedback here]
missing ARM Template Function reference for providers method.
we leverage the ARM template function [providers('namespace', 'name').apiVersions[0]] to get the latest api-version for some things.  Was looking up the documentation to see why this changed and is now including preview API versions, but this reference is missing from the ARM Template Function Reference page.

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

ID: 72651acd-eb46-2e18-586a-c8e0e451a9ba
Version Independent ID: 720f83e1-0f27-ea61-1763-5bbe97b7379b
Content: Template functions - Azure Resource Manager
Content Source: articles/azure-resource-manager/templates/template-functions.md
Service: azure-resource-manager
Sub-service: templates
GitHub Login: @mumian
Microsoft Alias: jgao

@scottgorlick Thanks for your comment. We will review the issue and get back to you shortly.

@mumain I couldn't find much information about providers() function anywhere. Can you please look into it and update the document accordingly?

@scottgorlick - thanks for this feedback. I have clarified in the docs that the providers function has been deprecated. Using this function to dynamically get an API version can break a template.
The update should get published later today.
#please-close


Tree-view vertical scroll

When in the tree-view while having a project folder open you're unable to scroll down to see all your files.
Reproduction Steps:

Open a project folder
Try to scroll down

Expected behavior:
Able to scroll vertical when needed in tree-view.
Observed behavior:
Everything out of the view port of the tree-view is unreachable.
Screenshots and GIFs

Atom version: 1.17.2
OS and version: MacOs Sierra 10.12.4
Installed packages:
├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>└──<EMAIL_ADDRESS>
Extra styling:
To make the tree-view usable again i added the following to my user stylesheet
.tool-panel.tree-view {
  overflow: auto;
}

Update to Material UI 2.0 😉


Update get-started-new-relic-cli.mdx

fixed typo

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

@NSSPKrishna is this still relevant?

No.


set_cookie cleanup in wrappers.py

This changes includes a handful of small patches to BaseResponse.set_cookie. It's intended to address https://github.com/pallets/werkzeug/issues/888, which I just created.
I intentionally put each small change in a separate commit so that they could be modified or discarded as needed. Let me know if this is okay or if I should just squash them all into one.

Excellent, thank you!


MS SQL tools not installed for AMD64 ARCH

Have checked that MSSQL-Tools was not installed on AMD 64 generic rover agent and gitlab agent  minimally from 1.2.5 (generic) and even for the latest 1.3.4 (gitlab)

@terencefx81 @LaurentLesle - would go-sqlcmd be a good candidate? https://learn.microsoft.com/en-gb/sql/tools/sqlcmd/go-sqlcmd-utility?view=sql-server-ver16

It actually looks like a really good candidate for this. Thanks!

To be tested indeed


fix: removed call to reserved_resources

Description
we are getting a 403 error when we try to access the reserved_resources of certain subscriptions. After some discussion, fixing that permission error is not trivial, so we discussed an alternative implementation that won't involve reserved_resources.
This commit implements that solution: take the billing model from the cluster_billing_model of the subscription.
Another change is the way we detect if a subscription for a cluster already exists: after some discussion with the AMS team, we discovered that we couldn't have more than one subscription with the same cluster_id value. That means we no longer need to check the reserved resources: if a subscription for a given cluster_id exists, then it is the subscription we are searching for.
Verification Steps

Checklist (Definition of Done)

[ ] All acceptance criteria specified in JIRA have been completed
[ ] Unit and integration tests added that prove the fix is effective or the feature works (tested against emulated and non-emulated OCM environment)
[ ] Documentation added for the feature
[ ] CI and all relevant tests are passing
[ ] Code Review completed
[ ] Verified independently by reviewer
[ ] All PR comments are resolved either by addressing them or creating follow up tasks
[ ] Required metrics/dashboards/alerts have been added (or PR created).
[ ] Required Standard Operating Procedure (SOP) is added.
[ ] JIRA has been created for changes required on the client side

Side note: It is a good practice to write commits in present-tense imperative style and not in past tense. See https://git.kernel.org/pub/scm/git/git.git/tree/Documentation/SubmittingPatches?h=v2.36.1#n181 imperative-mood section. When writing commits you can think as: "If applied, this commit will ...." .

Side note: It is a good practice to write commits in present-tense imperative style and not in past tense. See https://git.kernel.org/pub/scm/git/git.git/tree/Documentation/SubmittingPatches?h=v2.36.1#n181 imperative-mood section. When writing commits you can think as: "If applied, this commit will ...." .

This means the commit in this PR can be renamed to:
fix: remove call to reserved_resources

Side note: It is a good practice to write commits in present-tense imperative style and not in past tense. See https://git.kernel.org/pub/scm/git/git.git/tree/Documentation/SubmittingPatches?h=v2.36.1#n181 imperative-mood section. When writing commits you can think as: "If applied, this commit will ...." .

This means the commit in this PR can be renamed to: fix: remove call to reserved_resources

Yup, I know. Sorry, I forgot to update the commit message. Done now.


Multiple anchors

Hi !
I commited the first sketch for multiple anchors. I tested it with 2 anchors, but i will keep you in touch when trying with more devices !
Also, there is optimisation to do on replyTime: for instance the first anchor will have a reply time of 7000us but the second when will have 3*7000us ! Otherwise it doesn't work and i don't really understand why...
I will try to visualize how is the time for sending/receiving, etc. with an oscilloscope in order to understand that !
Cheers !
Léopold

Hi Léopold,
Sounds great!, I am going to attempt 4 anchors and 2 devices.
Would love to hear more! I have 6 units on order.
I hope to share my findings too.
I will have 9dof imu on each tag for orientation and hope its accurate enough and fast enough to send good positional data of the objects I will be holding in my hand.
Good luck!

@leosayous21 i will have multiple units all communicating to one/two anchors. Is it possible to use this library for this purpose or (this lib) only allows communication with limited amount of devices?
Full disclosure - i'm a total noob in all things arduino and dw .

Hi @rasamaya  !
Sorry for the delay.. I hope you will do a good job on the library :-) When will you receive your units ?
@az-z , For now, the only configuration which is programmed here is: 1 tag and multiple anchors.
That is: all anchors are waiting for a signal from 1 tag. And when they have talked to the tag and calculated the distance, they send back to the tag the distance they have.
There is still work to do on the library: multiple tags and to test more than 3 anchors. Also, it will be good to have the possibility to send the distance back to an other device (which can be called the collector)
Good luck for you :-)
Léopold

@leosayous21 :

...And when they have talked to the tag and calculated the distance, they send back to the tag the distance they have.
does it mean that they can't talk to each other?

another question - can tags talk to a different anchor after some time ? basically do i have an ability to communicate to the anchor in the  room 2, after i'm done "talking" with the anchor in the room 1?

@leosayous21
will this lib work with arduino due? or i should be looking at the different board?

Yes normally you can do what ever you want because there is the mac filtering. That mean you can select the device you want. But you need to enter deep in the code for that.. (there is not an easy API for now).
Basically here, in the last commit, you can have 1 tag and some anchors in your house. When the anchors will be next to the tag, it will discover it and start ranging. when you are too far from an anchor, the tag delete the anchor from its "list of anchors" (2s timeout).

I've just tried to compile the code with an arduino due but there is a lot of error (It seems to come from the digitalWriteFast i used to trigger the SS pin during writeBytes and readBytes. We need to add a #ifdefine here i think because digitalWriteFast is not necessary for arduino due )

what arduino do you recommend to get ? i will need to do some triangulation and communication over the wifi and maybe gps too. but this is a long term goal ( hopefully 6-9 months i'll be able to achieve that). @bigredbee shared with me he is using pro micro.

Hi Léopold!
Could you please explain how to make things work with multiple anchors?
I tried to do it and this is what i got:
Anchor 1: works fine
Anchor 2:
blink; 1 device added ! ->  short:69DD
delete inactive device: 69DD
If i disconnect Anchor 1, then Anchor 2 starts working.
Thanks a lot for your excellent effort :)
Regards,
Julian

@jogando Did you have any luck with one Tag and Multiple anchors? I am facing the same problem

I'm getting a similar behavior with more than 1-2 anchors at once. It works fine with a tag and one anchor, and mostly fine with 2 anchors (I start to see some big negative distance estimates), and I haven't gotten a tag to detect 3 anchors at once.
They all have different MAC and short addresses, and I'm not sure what the problem is. I wouldn't mind scheduling the tag to initiate two-way ranging to a short list of fixed tag addresses (I only have 4 anchors and their addresses are fixed), but I'm trying to figure that out too. I believe that's how the EVK1000 evaluation kit operated.

@headcrabned  Did you supply the TAG with external power?

The tags and anchors did have external power, from a 3.3V regulator. I checked the output on a scope, and it stays above 3.25V.

closed in favour of #181

Hi, @kshitijdadhekar
you can find a solve of your problem in #179


Local state is updated without using this.setState

In the first example of Error Boundaries the method getDerivedStateFromError() is setting the local state (this.state = { hasError: false };) of the component without using this.setState (return { hasError: true };).

Thanks for explaining. I got your point.

@eps1lon Thanks for explaining. I got your point.

Glad to hear it. Would you agree that we can close this PR then?

Yes you can close it.

@eps1lon  yes you can close it.


Update FindBugs to 3.0.2

We currently the following findbugs error wich was fixed in 3.0.2 from march:
https://sourceforge.net/p/findbugs/bugs/1374/
We override the Version in our pom.xml but it would be nice to have the current version used by default.

Hmm ok isn't released yet ...

@RobertPaasche Not only is that not released, the community has forked from findbugs to spotbugs.  You might want to give spotbugs a try to see if it resolves the issue you are tracking.
See [spotbugs]https://github.com/spotbugs
At the moment I own a branch off this repo for releasing maven support for spotbugs.  We are working to bring that to spotbugs organization as well as see what we should do about the situation here.  Mainly do we continue to have separate findbugs maven plugin just in case along with a cut on spotbugs.  For now that works but certainly more concerned if your issues is addressed in that revision.  Please let me know.


Linux/x64: Fix SIMD routines not linking due to illegal relocations

On linux/x64, if using any of the assembly SIMD routines that rely on the tables defined in tables.rs, rav1d will fail to link with the following errors:
mold: error: /home/cmc/dev/rerun-io/rerun/target/debug/deps/libre_rav1d-d1774017185e2712.rlib(mc_avx2.o):(.text): R_X86_64_PC32 relocation at offset 0x7562 against symbol `dav1d_mc_subpel_filters' can not be used; recompile with -fPIC
mold: error: /home/cmc/dev/rerun-io/rerun/target/debug/deps/libre_rav1d-d1774017185e2712.rlib(mc16_avx2.o):(.text): R_X86_64_PC32 relocation at offset 0xa65c against symbol `dav1d_resize_filter' can not be used; recompile with -fPIC
mold: error: /home/cmc/dev/rerun-io/rerun/target/debug/deps/libre_rav1d-d1774017185e2712.rlib(mc16_avx2.o):(.text): R_X86_64_PC32 relocation at offset 0xa687 against symbol `dav1d_resize_filter' can not be used; recompile with -fPIC
mold: error: /home/cmc/dev/rerun-io/rerun/target/debug/deps/libre_rav1d-d1774017185e2712.rlib(mc_avx2.o):(.text): R_X86_64_PC32 relocation at offset 0x7581 against symbol `dav1d_mc_subpel_filters' can not be used; recompile with -fPIC
mold: error: /home/cmc/dev/rerun-io/rerun/target/debug/deps/libre_rav1d-d1774017185e2712.rlib(mc16_avx2.o):(.text): R_X86_64_PC32 relocation at offset 0xa691 against symbol `dav1d_resize_filter' can not be used; recompile with -fPIC
# ... more of the same ...

The C implementation avoids this problem by making use of compiler intrinsincs:
https://github.com/memorysafety/rav1d/blob/c7d127e7e31bd3366ac7dc1717dda9782905c605/src/tables.h#L113-L115
where EXTERN is defined as:
https://github.com/memorysafety/rav1d/blob/c7d127e7e31bd3366ac7dc1717dda9782905c605/include/common/attributes.h#L116-L120
As far as I know, there doesn't exist any way of modifying the ELF visibility of Rust symbols directly from code.
Therefore, the best approach I have found is to modify the assembly itself in order to hide these extern references directly, and then the linker gets the hint.
For a long-winded, much more in depth explanation, see:

https://github.com/rerun-io/re_rav1d/pull/3

Rav1d uses the assembly routines from dav1d. Have you tested if this is also an issue for dav1d? Is this mold specific?
We'd like to keep using the same assembly routines.

I use mold, too, for development and have never seen this error.  That's odd, what exactly are you doing differently?

Rav1d uses the assembly routines from dav1d. Have you tested if this is also an issue for dav1d?

This is not an issue with dav1d. dav1d's tables use compiler intrinsics to mark the generated ELF symbols as private.
rav1d's tables on the other hand are exposed publicly in the final binaries, and AFAIK Rust does not offer any way to control ELF symbol visibility.
dav1d:
readelf -s --wide src/libdav1d.a | rg dav1d_resize_filter | rg OBJ
     7:<PHONE_NUMBER>001260   512 OBJECT  GLOBAL HIDDEN     4 dav1d_resize_filter
                                              ^^^^^^
                                              private

rav1d:
readelf --wide -s target/release/librav1d.a  | rg dav1d_resize_filter | rg OBJ
  5762:<PHONE_NUMBER>000000   512 OBJECT  GLOBAL DEFAULT 5171 dav1d_resize_filter
                                              ^^^^^^^
                                              public

If there is in fact a way to do such a thing in Rust, then we could avoid modifying the assembly at all indeed.
See my original message in this thread, and the detailed explanation in https://github.com/rerun-io/re_rav1d/pull/3#issue-2588014712.

Is this mold specific?

No, this is not specific to any linker. AFAIU it all comes down to how position-independent executables, ASLR, 32bit relocations and load-time/run-time symbol interposition all interact in arcane, annoying ways on Linux/x64.
Here's stock ld failing in the same way:
  = note: /usr/bin/ld: /home/cmc/dev/rerun-io/rerun/target/debug/deps/libre_rav1d-679a6408c2a64e05.rlib(mc16_avx512.o): warning: relocation against `dav1d_mc_warp_filter' in read-only section `.text'
          /usr/bin/ld: /home/cmc/dev/rerun-io/rerun/target/debug/deps/libre_rav1d-679a6408c2a64e05.rlib(looprestoration_sse.o): relocation R_X86_64_PC32 against symbol `dav1d_sgr_x_by_x' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: final link failed: bad value

I use mold, too, for development and have never seen this error. That's odd, what exactly are you doing differently?

This isn't specific to mold, see my message above.
This will fail to link for any position-independent executable (i.e. all Linux/x64 Rust executables by default) that makes actual use of any of the problematic symbols (i.e. the SIMD-optimized routines that rely on the tables in tables.rs) such that they don't get optimized out at any stage.
It's pretty hard/annoying to minimally reproduce as you need to link to all the right symbols and generate the right 32bit relocations at the right place and time.
If you're on 64bit linux, you shoud be able to repro using:
git clone https://github.com/rerun-io/rerun.git --single-branch --branch cmc/no_simd_patch --depth 1
cd rerun
cargo r -p rerun-cli --no-default-features --features native_viewer,nasm

# grab a coffee...

<link failure>

Sorry, I'm just confused why we have not seen this error before when building the dav1d CLI binary that depends on librav1d.  These tables shouldn't be getting optimized out of that, and it compiles fine on x86_64-unknown-linux-gnu.

Also, do you know if there's any effort to get hidden visibility or ELF symbol visibility as a whole into Rust?  That would be the best solution if it existed.
I think your solution is quite good, and the asm changes are pretty unobtrusive, so upstreaming future asm changes should be pretty simple with this.  But I'm still trying to understand why this is an issue for you and not for us when we build the dav1d CLI.

Hi @teh-cmc!  I believe we did run into the same issue in #1322 when we tried to support building rav1d as a cdylib, as you're doing, too.  #1322 took a different approach, but it's not a great one, as it duplicates everything in C files.  The approach you have here definitely seems better to me and generally less obtrusive and brittle.  However, we really do not want to have any changes to the assembly at all, leaving that entirely up to the dav1d developers.  We'd love, however, for these changes to be upstreamed into dav1d.  IIUC, these changes should work with dav1d as well, though they'd be redundant with the hidden visibility of the tables.  How does that sound?

I wish someone would come up with something nicer, but if not... then yeah, sounds good to me. :+1:

Maybe this could help: https://github.com/rust-lang/rust/pull/118417?  But it's not per symbol.


Jib fails to download dependency from private maven repository

Environment:

Jib version:  3.2.0

Build tool:
    Gradle 7.1

    Build time:   2021-06-14 14:47:26 UTC
    Revision:     989ccc9952b140ee6ab88870e8a12f1b2998369e

    Kotlin:       1.4.31
    Groovy:       3.0.7
    Ant:          Apache Ant(TM) version 1.10.9 compiled on September 27 2020
    JVM:          11.0.12 (Oracle Corporation 11.0.12+7)
    OS:           Linux 5.11.0-44-generic amd64

OS:  Ubuntu 20.04

Description of the issue:
Jib fails to download dependency from the private maven repository to images. In my project, I have two dependencies that are hosted in a private Google Artifact Registry. Locally I have authenticated myself through the gcloud SDK and can download and build the project locally. But whenever I run jib to build and push the images. Jib fails to download the dependencies and can not build the images.
Expected behavior:
That jib downloads the dependencies from the repository and builds the image.
Steps to reproduce:

Add a dependency to your project that is hosted in a private maven repository
run ./gradlew mymoduel:jib

jib-gradle-plugin Configuration:
I can paste a part of the config. I am using google.cloud.artifactregistry.gradle-plugin and there is also how I defined my repository:
id("com.google.cloud.artifactregistry.gradle-plugin") version "2.1.4"
...
repositories {
    mavenCentral()
    maven(url = "artifactregistry://us-central1-maven.pkg.dev/my-cluster/my-repository")
}

Log output:
Task :mymodule:jib

Containerizing application to us.gcr.io/my-cluster/my-application:0.0.3...
Base image 'eclipse-temurin:11-jre' does not use a specific image digest - build may not be reproducible
The base image requires auth. Trying again for eclipse-temurin:11-jre...
Using credentials from Docker config (~/.docker/config.json) for eclipse-temurin:11-jre
Using credentials from Docker config (~/.docker/config.json) for us.gcr.io/my-cluster/my-application:0.0.3
I/O error for image [us.gcr.io/my-cluster/my-application]:
    org.apache.http.ConnectionClosedException
    Premature end of chunk coded message body: closing chunk expected
I/O error for image [us.gcr.io/my-cluster/my-application]:
    org.apache.http.ConnectionClosedException
    Premature end of chunk coded message body: closing chunk expected
I/O error for image [us.gcr.io/my-cluster/my-application]:
    org.apache.http.ConnectionClosedException
    Premature end of chunk coded message body: closing chunk expected
I/O error for image [us.gcr.io/my-cluster/my-application]:
    org.apache.http.ConnectionClosedException
    Premature end of chunk coded message body: closing chunk expected
I/O error for image [us.gcr.io/my-cluster/my-application]:
    org.apache.http.ConnectionClosedException
    Premature end of chunk coded message body: closing chunk expected
Using base image with digest: sha256:83d92ee225e443580cc3685ef9574582761cf975abc53850c2bc44ec47d7d943
Executing tasks:
[============                  ] 41.7% complete
> checking base image layer sha256:ea362f368469...
> checking base image layer sha256:9b46d5d971fa...
> checking base image layer sha256:d5cc550bb6a0...
> checking base image layer sha256:bcc17963ea24...
> scheduling building manifests
> launching layer pushers
> scheduling pushing container configurations

> Task :mymodlue:jib FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':mymodlue:jib'.
> com.google.cloud.tools.jib.plugins.common.BuildStepsExecutionException: Premature end of chunk coded message body: closing chunk expected

This has nothing to do with Maven repositories or pulling Maven dependencies.
Both the Jib plugin and the Google Artifact Registry (GAR) plugin depend on the Google HTTP Client library. By just declaring the GAR plugin, it naturally leads to a diamond dependency conflict, which is often fine regardless of what version is actually pulled in.
Unfortunately, there is a bug in some old but relatively recent Google HTTP Client library versions. It seems that a problematic version is being pulled in by the GAR plugin. That is, regardless of whether you configure the repositories {} block, as soon as you have the following line
  id("com.google.cloud.artifactregistry.gradle-plugin") version "2.1.4"

you run into the issue.
Recent Google HTTP Client library versions fixed the bug, so a workaround is to force using the latest version. The latest as of now is 1.41.0. For example,
buildscript {
  classpath('com.google.http-client:google-http-client:1.41.0') { force = true }
  classpath('com.google.http-client:google-http-client-apache-v2:1.41.0') { force = true }
  ...
}

Note this is for the buildscript {} dependency, not for the project.
At the same time, I suggest you urge the maintainers of the GAR plugin to upgrade the Google HTTP library version to the latest.
Closing as a dup of #3409.


FeatureRequest: plot clinical information in oncoplot

Hello,
Firstly thank you for such a useful tool!
I would like to be able to plot tumour telomere length as estimated from WGS data e.g. as an extra graph on the oncoplot. If I included the tumour telomere length as a category in the clinical information input file is there an easy way to include this in an oncoplot?
Thanks very much

Hi,
If I understand correctly you would like to include a side bar plot of telomere lengths ?
But regarding adding it as an annotation, you can definitely plot telomere length as a one of the clinical feature. Check out clinicalFeatures argument in oncoplot.

Hello,
Thank you for your very rapid reply!
I have tried using clinicalFeatures in oncoplot but my understanding is this assumes the clinicalFeature is categorical rather than continuous (as is the case e.g. for telomere length or another feature) - unless there is a way to specify this? As at the moment I have tried the command:
"oncoplot(maf = glioma, clinicalFeatures = 'tumour_tel_content', top = 10, fontSize = 12)"
But this produces a legend colour annotation for every possible length value, whereas ideally I would like a bar plot similar to mutation number but with telomere length.
This is using the 1.8.0 release as the environment I am working in cannot download via github, I do not know if this changes things
Thanks very much

Hi,
Yes, Ideally clinicalFeature  Should be categorical.  For numeric variable it is bit of a trouble as it will plot all levels. However, I can push a commit to address this - as this seems to be recurring request, but you will have to install it from GitHub :|

Great, thanks very much!


The way to extends a Trait.

What problem does this feature solve?
Sometimes traits need to be extended. For example, Validation Trait presets some rules, but the business logic always requires custom validation rules. Validation Trait needs to receive and register custom rules.
What does the proposed API look like?
Since the trait is a factory function, so one of the ways may be injecting dependencies in the trait's constructor function. And trait's dependencies can be passed in initSunmao(not the dependencies filed, but a new field).

How about

Pass the extended things as props if they are serializable.
Implement a new trait.


Ignore a user based on their email address

When writing scripts I would like to be able to lookup the users email address to determine if they are allowed to use the script.

You have access to the users email via the msg.message.user.emailAddress property
e.g.
robot.respond /pug me/i, (msg) ->
  if (msg.message.user.emailAddress ===<EMAIL_ADDRESS>{
    msg.reply 'Sorry your email address has been blocked...'
  } else {
    msg.http("http://pugme.herokuapp.com/random")
      .get() (err, res, body) ->
        msg.send {
          format: 'MESSAGEML'
          text: "<messageML><a href=\"#{JSON.parse(body).pug}\"/></messageML>"
        }
  }


Add OMIS Payment app and model

This only adds a new omis payment app and defines the Payment model.

Codecov Report

:exclamation: No coverage uploaded for pull request base (develop@bdf0bc1). Click here to learn what that means.
The diff coverage is 100%.

@@            Coverage Diff             @@
##             develop     #530   +/-   ##
==========================================
  Coverage           ?   96.61%
==========================================
  Files              ?      127
  Lines              ?     3874
  Branches           ?      352
==========================================
  Hits               ?     3743
  Misses             ?       89
  Partials           ?       42

Impacted Files
Coverage Δ

datahub/omis/payment/constants.py
100% <100%> (ø)

Continue to review full report at Codecov.

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Adds title attribute to clear button

To resolve an accessibility issue, a title attribute was added to the clear button that will read and display as a tooltip "Clear date"

@aij I updated the text to be user configurable so a dev can set any text they deem appropriate as the title, or no text at all and the attribute will not show up.
As for who will benefit, the change is to allow screen readers such as JAWS to pick and read the intention of the button back to a visually-disabled user. The button can be accessed by tabbing through the control (e.g., put the cursor in the date field, hit tab once, then hit enter and the field will clear) and without any sort of title or aria-label attribute a screen reader won't indicate the purpose of the button to the user.

Looks like I still need to increase test coverage a tad, will work on that...

@nateha1984 Oh, that button didn't used to appear in the tab order, but an href was added recently.
It seems like it would be more accessibility friendly not to burden keyboard users and screen reader users with extra complexity  which is only really useful to mouse and touchscreen users.
Even with a title the clear button still has accessibility issues for sighted keyboard users. It interferes with the tab order and it gives no visual indication that the close button is where the focus is.

@aij I'm not sure I understand how there is extra complexity added to have the purpose of a button read out by a screen reader or to show a tool tip on hover. In fact, it's necessary for users with assistive devices to understand what is going on on the screen. Users who do not need extra assistance won't even know there's any change unless they hover on the button.
I do agree that there does need to be some visual styling added if the button is going to be accessible from the tab order. I did go ahead and remove the button from the tab order as you are correct in that it shouldn't be part of the tabbing since it's part of the control; tab should take the user to the next component/control/whatever. I also changed the element to be a button type instead of an anchor.

@aij Let me know once this is ready to merge.

Sorry to piggyback off of this issue, but I have a question about this change.
My understanding is that the original intention was to add a title to the button so that screen readers are able to read it.
However, if we are removing the button from the tab order, wouldn't this lead to an inconsistency where screen readers are now reading this button's title, but it is not tab accessible, making it more confusing for the visually-disabled?
Let me know if this is concern, and I'll create a new issue.


Allow Flow build-time type checking

Would it be possible to enable Flow type checks at build time (e.g., like this) without requiring an eject + custom webpack config (#1592)? Opening this issue since #4097 was flagged as a question instead of an feature request, and closed without much explanation.
It seems a pity that atm we can't get both the up-to-date integration goodness of cra, and the static type safety of Flow*. It would be a big win if this were supported, imo. Thanks!
*I assuming manual build steps don't count as part of the build process, since they're optional and entirely up to the developer to know about and execute.

You can run flow CLI to check for errors as a separate step, just like you do with jest tests.  Most editors have plugins that shows flow errors inline within the editor, which is much more helpful than a console message from webpack.

This assumes that we want to treat type errors as if they're lint warnings. What if we would like to elevate them to compile errors (or at least simulate the same behavior), as would happen if the type system were built into ES6 or Babel? My goal is approximate as closely as possible language-level type safety so that we can rely on the compiler to do type checking, instead of assuming the developer will always check for errors in their editor or via CLI command. Thanks for your help!

Personally, I have a CI setup that runs jest tests and flow check, and they can also be added as a pre-commit hook (I know they also do it this way at Facebook).
I feel like enforcing build failures on flow errors is a bit stringent.  While they should be enforced when code is checked in (just like how we don't want test failures), enforcing them before development builds might be a bit too much.
Even though there could be a flow error due to type mismatch, the program could still build/run successfully and even correctly.  Also, flow errors are very dependent on the version of the flow installed.  A perfectly valid program for flow 0.7 may result in tons of errors for flow 0.8.
Also, I think its useful to prototype something quickly in code without worrying about flow errors breaking the build.

Also, flow itself has tons of issues with invalid library definitions and even react definitions itself:
https://github.com/facebook/flow/issues/7219
This for example will prevent anyone from adopting React.lazy syntax with flow enabled.  The only way to disable it to add $FlowFixMe before every React.lazy call...

Personally, I have a CI setup that runs jest tests and flow check, and they can also be added as a pre-commit hook.

Also, I think its useful to prototype something quickly in code without worrying about flow errors breaking the build.

@bugzpodder I think this makes sense. It may be biases because I've spent a lot more time working with statically typed languages which enforce typing at compile-time. As long as we have types enforced before code is submitted, we'd get the best of both worlds: rapid prototyping, and type safety. I'll set up commit hooks instead. Closing this issue for now.
@holloway Thanks for this, I'll use this to add compile checks to builds to ensure we don't accidentally deploy to test servers w/o validating types.


⚠ ClamAV has degraded performance

In 563d842, ClamAV (https://spamassassin.apache.org/) experienced degraded performance:

HTTP code: 200
Response time: 45 ms

Resolved: ClamAV performance has improved in f172c40 after 5 minutes.