silx.gui: support imageaggregate in _plot2d

Checklist:

[ ] The PR title is formatted as: <Module or Topic>: <Action> <Summary> (see contributing guidelines)

This PR enables:

[ ] Using ImageAggregated filters into the Image view of silx view

I'm not sure if the slot _aggregationModeChanged and setAggregatedImage are well placed into into the class Plot2View

how about this approach?

About the _ComplexImageView, I'm not sure how to implement the filter without changing the ImageComplexView class

Do you mean adding the Aggregation items in the class where the self._plot is? (StackView and ArrayImagePlot as you said)
In the case of _Plot2dView the plot is what is called widget, but yes, _Plot2dView is the class creating the plot anyway

Do you mean adding the Aggregation items in the class where the self._plot is? (StackView and ArrayImagePlot as you said)

Yes, StackView and ArrayImagePlot which are the widgets that create and add/remove the ImageAggregatedItem to the plot (there is not necessarily a self._plot in there). Doing so will make those widgets self-consistent.

I made a PR on your branch with a few updates/fixes: https://github.com/EdgarGF93/silx/pull/3
I let you review it and merge if you agree with it, else let's discuss it.
Apart from that, this looks good to me! Thanks for the work and your patience !

Looks good to me, thanks Thomas!


Don't render context menu when it is not visible

Currently, when the ContextMenu's state swaps out to isVisible: false, the class react-contextmenu--visible is added to the <nav> child rendered by ContextMenu.
This means, without css on the page, it is impossible to hide the context menu. It creates a dependency which would be better circumvented if it didn't render that at all. I can create a PR for that change if desired, but I'm not sure this is desired yet.
Why this is frustrating:
We are using aphrodite for all of our styles. This is a pretty strong trend in JS frameworks lately (though it's not the only way), as it allows components to be packaged up with styles without requiring extra css. What aphrodite does is create a <style> tag in the head with css rules declared by JS, these rules map back to the element by a generated css class name. Some of our components have no means of adding css to the page other than like this.
So something using this library would also require external css as an added dependency, or be forced to add a css rule to the page, which is less than ideal.
Solutions:
A solution I'm not crazy about for this problem: allow us to define styles for these different states. <ContextMenu styleWhenNotVisible={{}} ... />.
Better solution: There really isn't much styling in this library. MenuItem has some but children are free to be styled and structured freely. In fact, the only reason I am using MenuItem, is to leverage it's auto-closing from onClick behavior. Including opacity: 0 is really less of a css concern and more of a JS concern (whether or not to show, as opposed to how to show, as reflected by the name of the state variable, isVisible), and as such, should just be managed by the JS by determining whether to render or not render.
Agree?

I've have not use any CSS-in-JS libs yet. So, I will have to think through it.

Here's a great comparison of the different techniques, but there's also some links down below with some motivations behind doing it.
https://github.com/MicheleBertoli/css-in-js
The biggest thing is that you don't create build dependencies on users using your library. That would include enforcing css be pre-existing on the page. But like I mentioned, this library doesn't call for much styling at all, so if you remove the few places styling is required (to get minimum use out of the lib), it will save us trouble.
See also Material-UI's discussion on how they handle styling: http://www.material-ui.com/#/customization/styles

Cool, I'll take a look.

I cannot simply "not render" the context-menu. The reason why context-menu is always rendered is that I need its dimensions to calculate its position before hand.
What I can do is add opacity toggle. That should work for everyone.


Support for Nova 4

Not sure if this package is actively maintained. But would be nice to have Nova 4 support now that it's out. @Tarpsvo

Several forks have implemented support for Nova 4
I had a look at a few of them and this one is the one I went with https://github.com/joostvanhoof/nova-notes-field

Nova 4 support added in version 3.0.0.


Update Registry to 0.4.9.-RC2

As a developer,
I want to update the DT-Registry to 0.4.0,
so that we do not have one Registry instance in Argo unsynched.
Link

relates to https://github.com/eclipse-tractusx/traceability-foss/issues/636
https://github.com/eclipse-tractusx/item-relationship-service/issues/359

Hints / Details

Override the metadata of the new version of the Registry inside our helm values file. This way we should be able to synchronize dev/test at the same time
see issue on registry repo: https://github.com/eclipse-tractusx/sldt-digital-twin-registry/issues/129

Acceptance Criteria

[ ] Update toi latest version of https://github.com/eclipse-tractusx/sldt-digital-twin-registry/releases/tag/digital-twin-registry-0.4.9-RC2
[ ] https://argo.dev.demo.catena-x.net/applications/argocd/tracex-dt-registry-dev and https://argo.dev.demo.catena-x.net/applications/argocd/tracex-dt-registry-test are both green and synched
[ ] Deployment is upt to date with new DT registry version

Out of Scope

...

created #823 to also migrate to the new IRS version

[x] Update toi latest version of https://github.com/eclipse-tractusx/sldt-digital-twin-registry/releases/tag/digital-twin-registry-0.4.9-RC2

migrated to 0.4.9

[x] https://argo.dev.demo.catena-x.net/applications/argocd/tracex-dt-registry-dev and https://argo.dev.demo.catena-x.net/applications/argocd/tracex-dt-registry-test are both green and synched
[x] Deployment is upt to date with new DT registry version

Not possible to test. PR looks good to me. Ready for review @jzbmw


How to use /opt/rocm/llvm/bin/clang with non default GCC compilers on HPC clusters?

A subtitle for this issue would be: "The default HIP clang compiler cannot find GCC compilers on HPC clusters in non-default paths".
It's hard to find a place for this issue since it's related to HIP packaging, but also to clang interaction with GCC compilers. For now I want to start a discussion here and if you think there is a better place for this, then it can be moved.
The main problem I want to talk about is about the default /opt/rocm/llvm/bin/clang compiler installed with the ROCm 3.5 toolsuite used to compile HIP code by using the default system packages. This compiler being standard clang, it relies on a GCC installation for a number of things.
One problem appears on HPC clusters, where the compilers are never in a standard path (they are usually in a shared filesystem). module or other tools are used to switch between different compiler versions and setup all the correct include, library, ..., paths. This issue is even worse in a Red Hat system, where the default system compiler is GCC 4.8.x which cannot even compile C++11 or higher code.
Details
In effect, on a typical Red Hat based cluster, these are the candidate GCC installation found:
[tcojean@methane ~]$ /opt/rocm/llvm/bin/clang -v
clang version 11.0.0 (/data/jenkins_workspace/centos_pipeline_job_3.5/rocm-rel-3.5/rocm-3.5-30-20200528/7.5/external/llvm-project/clang 6c08b900599eee52e12bce1e76b20dc413ce30e7)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /opt/rocm/llvm/bin
Found candidate GCC installation: /usr/lib/gcc/x86_64-redhat-linux/4.8.2
Found candidate GCC installation: /usr/lib/gcc/x86_64-redhat-linux/4.8.5
Selected GCC installation: /usr/lib/gcc/x86_64-redhat-linux/4.8.5
Candidate multilib: .;@m64
Candidate multilib: 32;@m32
Selected multilib: .;@m64

Despite having a GCC 9.2.0 module loaded (item 6):
[tcojean@methane ~]$ module li
Currently Loaded Modulefiles:
  1) git/2.20.1/gcc-7.2.0-7ww6                  3) htop/2.2.0/gcc-7.2.0-gqld                  5) the-silver-searcher/2.1.0/gcc-7.2.0-ot5x
  2) cmake/3.16.2/gcc-7.2.0-aoyx                4) hwloc/2.0.2/gcc-7.2.0-wllc                 6) gcc/9.2.0/gcc-7.2.0-3mdu

This is easily explained by the way that clang finds GCC:

When compiling clang, one can specify a path to a GCC installation with the -DGCC_INSTALL_PREFIX CMake flag (see [1]). This of course only works when manually compiling clang directly for a target system. In addition, AFAIK one can only specify one GCC compiler in this case (HPC clusters often have many compiler version concurrently which they keep updating).
As far as I can see, clang otherwise looks for a GCC installation in the default paths (/usr/lib/gcc/...). For redhat systems, it also explicitly looks for devtoolsets, see [2].

Main question
The main question is then the following: what is the standard/recommended way of installing and managing /opt/rocm/bin/llvm/clang on a HPC cluster?

Should HPC cluster administrators compile a custom clang for every GCC compiler they install by setting the GCC_INSTALL_PREFIX correctly each time? Similarly, is the HIP stack packaged inside https://spack.io or another HPC packaging system which allows to do this automatically?
Is there a way to make clang work with modules or other environment variables to find extra GCC compilers?
Is it expected that symlinks to compiler versions are always set in /usr/xxx ?
Should HPC system administrators limit themselves to Red Hat's devtoolset since clang currently supports this (currently, on the systems where I tried HIP/ROCm 3.5 this is what we have done, but we are missing a lot of compiler versions this way).

clang has a compiler switch called --gcc-toolchain that seems to support this kind of usage, do you mind giving that a try?
--gcc-toolchain=, -gcc-toolchain
Use the gcc toolchain at the given directory

Thanks for the reply!
It does work, but you need to pass in a lot of other flags (to find libraries, headers, related binaries such as crtbegin.o). For a simple example to work, this is what I have to do to compile properly:
/opt/rocm/llvm/bin/clang++ c++11_issue.hip.cpp -std=c++11 \
--gcc-toolchain=/nfs/apps/spack/opt/spack/linux-centos7-x86_64/gcc-7.2.0/gcc-9.2.0-3mdu5gl5jymnhvqnmfaavtex2zguy2gt/lib/gcc/x86_64-pc-linux-gnu/9.2.0/ \
-I/nfs/apps/spack/opt/spack/linux-centos7-x86_64/gcc-7.2.0/gcc-9.2.0-3mdu5gl5jymnhvqnmfaavtex2zguy2gt/include/c++/9.2.0/ \
-I/nfs/apps/spack/opt/spack/linux-centos7-x86_64/gcc-7.2.0/gcc-9.2.0-3mdu5gl5jymnhvqnmfaavtex2zguy2gt/include/c++/9.2.0/x86_64-pc-linux-gnu/ \
-L/nfs/apps/spack/opt/spack/linux-centos7-x86_64/gcc-7.2.0/gcc-9.2.0-3mdu5gl5jymnhvqnmfaavtex2zguy2gt/lib/gcc/x86_64-pc-linux-gnu/9.2.0/ \
-B/nfs/apps/spack/opt/spack/linux-centos7-x86_64/gcc-7.2.0/gcc-9.2.0-3mdu5gl5jymnhvqnmfaavtex2zguy2gt/lib/gcc/x86_64-pc-linux-gnu/9.2.0/ \
-o compiled_with_clang++.exe

My test example is a very simple example compiled with C++11, since the default Red Hat compiler does not support C++11 that is sufficient to show success.
Overall, it's not very practical, but it's technically possible to add support for this as part of our application's CMake, if that's what we need to do.
For reference, here is the simple example:
#include <sstream>
#include <string>

static std::string foo(int bar) {
        std::ostringstream oss{};
        oss << "This is a dummy string with a " << bar;
        return oss.str();
}

int main(){
        auto str = foo(0);
        auto str2 = foo(20);
        return 0;
}

On success, there should be the following nm output. Notice the std::__cxx11 prefix for the specific standard library functions.
[tcojean@methane ~]$ nm compiled_with_clang++.exe | c++filt | grep char_traits
                 U std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::str() const@@GLIBCXX_3.4.21
                 U std::basic_ostream<char, std::char_traits<char> >::operator<<(int)@@GLIBCXX_3.4
                 U std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()@@GLIBCXX_3.4.21
                 U std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream()@@GLIBCXX_3.4.26
                 U std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@@GLIBCXX_3.4.21
                 U std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)@@GLIBCXX_3.4

Just to add a bit of data here: ICC has some tooling support that addresses their version of this issue, with a script that will allow you to generate a config file for a given GCC toolchain and will pass all of the associated flags automatically. If there's some technical reason that the --gcc-toolchain option can't automatically handle everything (as opposed to a bug), a similar solution would be helpful.
In the worst case I can play games with module files (or ask our admins to) but that's not an easy-to-maintain fix.

I'm setting up our new AMD GPU cluster, and running into the same problem.
Very preliminary, but setting:
export HIPCC_COMPILE_FLAGS_APPEND="--gcc-toolchain=$(realpath -m $(which gcc)/../..)"

seems to have gotten things working, at least enough for me to run the ROCm validation suite.
@tcojean I think you might have passed the wrong directory to --gcc-toolchain; probably should have been /nfs/apps/spack/opt/spack/linux-centos7-x86_64/gcc-7.2.0/gcc-9.2.0-3mdu5gl5jymnhvqnmfaavtex2zguy2gt.

Running fedora server 40 [beta] with ROCm 6.0.2, it appears that with default repo installation the issue persists-
C compiler "/opt/rocm/llvm/bin/clang" not found: exec: "/opt/rocm/llvm/bin/clang": stat /opt/rocm/llvm/bin/clang: no such file or directory

What is the command for reproducing the issue?

Sorry about the delay, I will have to double-back on that hopefully soon and get all the details, getting sidetracked with work and some other projects for the time being.
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Subject: Re: [ROCm/HIP] How to use /opt/rocm/llvm/bin/clang with non default GCC compilers on HPC clusters? (#2120)
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@tcojean Please provide the command for reproducing the issue. Thanks!

Hi @tcojean. Closing ticket due to lack of activity. Please feel free to re-open ticket if you still need assistance. Thanks!


ISPN-10656 ClassNotFoundException: io.agroal.pool.DataSource

https://issues.jboss.org/browse/ISPN-10656

Replaced with https://github.com/infinispan/infinispan/pull/7354


examples: fix surface refresh approuch for webgpu

Move surface refresh approuch from engine side to user size to syncronize behavior with gl and sw renderers
Checked on static and animated examples

Checked on static and animated examples

@SergeyLebedkin Could you please explain what should be different?


View::setViewTheme is currently broken from a package point of view

Currently, if a package calls View::getViewTheme at any point it is either useless or broken:
To take effect this must be called at the on_before_render event time, but at that time, the View class already called loadViewThemeObject() which caches locally some objects such as package and themeObject...
so changing the theme at that point will break the page instead of changing the theme.

@aembler can this fix make it for 5.7.4?


[QuickStart] Add mockgen as a dependency to the instructions

Objective
Improve the onboarding experience for devs to Shannon.
Origin Document

Goals

Smoother onboarding experience for new devs

Deliverables

[ ] Add mockgen to the quickstart guide
[ ] Add a Makefile helper to error out if mockgen is not installed when running various commands
[ ] Add links / instructions on how to install mockgen
[ ] Ensure that running make install_ci_deps is in the quickstart docs

Creator: @Olshansk
Co-Owners: @red-0ne

following the steps of the quickstart guide, get an error about missing dependency mockgen,  I figured out the need to run make install_ci_deps, then I ran make go_develop_and_test but failed after 10m with the errors that are on the attached file.

Step 2.2 does not explain that the address could be retrieved from the same way as step 2.1 (it was obvious to me, but not for everyone maybe?)
Why not add the log of the address to the create command?

Step 3.2 has a grammatical issue I think...

We need a blockchain node (i.e. a backend data node) backend data node to configure a supplier. Since LocalNet is already has a running anvil service, we can re-use that as our backend.

Step 3.3 does not explicitly explain that the cat ... command will create a file for those that are not very well versed on bash.

Step 3.5 failed with the following error: {"level":"error","error":"listen tcp :9090: bind: address already in use","message":"failed to listen on address for metrics"}
Checking what is using the port 9090, the result was:
lsof -i :9090
COMMAND    PID          USER   FD   TYPE DEVICE SIZE/OFF NODE NAME
tilt    242516 overlordyorch   93u  IPv4 832033      0t0  TCP localhost:9090 (LISTEN)
tilt    242516 overlordyorch   94u  IPv6 832034      0t0  TCP ip6-localhost:9090 (LISTEN)

Also, so far I have checked on the tilt website there is a RelayMiner already running on the local cluster, so maybe it should not be there until this step is reached.

Step 3.5 explicitly ask to open a new terminal and leave the relay miner running, then on Step 4.3 the command poktrolld query application show-application $SHANNON_APPLICATION --node tcp://<IP_ADDRESS>:36657 use the previously exported env variable $SHANNON_APPLICATION but it will not be available on the new terminal windows because is a new session.
Maybe a better way to handle this is creating an .bashrc_shannon file and load it with source or something like that (dunno so much about bash)

The warning on Step 4.5 probably could be better and use something like:
echo -e "<IP_ADDRESS>\tanvil\n<IP_ADDRESS>\trelayminers" | sudo tee -a /etc/hosts

There is something on Step 5.1 that is weird to me, I can send a relay, and then the next one fail, the next one works, the next one fail and so on... Please check the image:

also checking the Grafana dashboard I just see as expected 3 relays, because it was successful only 3 times on my tries.

Why Step 5.1 send  relay to  http://localhost:42069 that is running inside of the cluster if on steps 4.5 & 3.5 we are required to start AppGateServer and RelayMiner locally (on the bash)

Got some feed from another individual which I capture below.
Going to tackle everything next week but just aggregating it all in one place first.
In addressing tutorial feedback, challenges due to complexity in the pocket universe terminology were highlighted. Clarity on terms like Shannon and relay is suggested for better understanding, aiming to simplify the content for newcomers. Streamlining the onboarding process by emphasizing key concepts early, particularly the significance of relaying, could enhance clarity for beginners.

Transitioning to community engagement strategy, users are encouraged to engage on platforms like the Cosmos Hub forum to gain insights into their needs. This approach can facilitate the identification of relevant issues faced by node operators within the cosmos community, promoting a greater understanding of user perspectives and challenges.

Concerning improving communication, a need for clearer problem statements regarding contributions to the cosmos community was noted. Recommendations include defining challenges tackled and seeking input from active forums, fostering ecosystem exploration for potential solutions. Drawing attention to this lack of clarity could lead to more effective communication and solution development within the community.

Overall, the feedback loop suggests a desire for refinement in content delivery and communication strategies within the cosmos community. Addressing complexities, streamlining content for new participants, engaging users actively, and refining problem statements can collectively enhance user experience, foster community growth, and promote collaborative problem-solving within the cosmos ecosystem.


Title case is currently not title case

The current implementation of title case is not actual title case, in the sense that it simply capitalises each word. Notwithstanding the ability to set $ignore words, I think we could do better.
I have ported John Gruber's title casing script to PHP; would you accept a PR altering the toTitleCase method to use this technique?

Went ahead and opened a PR anyway :) #171


Clear 2FA token field on invalid input

fixed: #5816

Thank you @ppiyakk2!

Thanks, @ppiyakk2! If you'd like a suggestion for a next task to do, reply and say so! :)

thanks! @brainwane @ewdurbin


vLEI Test Issue

@pfeairheller Please find the new vLEI test issue

Test is working fine, closing issue


ignore symlinks in sysfs when iterating directories

Prevents error when attempting to read a symlink as a regular file.
Related to https://github.com/prometheus/node_exporter/issues/1465

Same problem as #206


Chinese font display erro

Describe the bug
I try to generate a report in which data is including Chinese characters. it can't display directly. I try to modify the matplotlib config file, but it doesn't work.

Could you provide the minimal information to reproduce this error? This guide can help crafting a minimal bug report.

the minimal code you are using to generate the report

which environment you are using:

operating system (e.g. Windows, Linux, Mac)
Python version (e.g. 3.7)
jupyter notebook, console or IDE such as PyCharm
Package manager (e.g. pip, conda  conda info)
packages (pip freeze > packages.txt or conda list)

a sample or description of the dataset (df.head(), df.info())


perf: Optimize access permissions of variables

What is the purpose of the change
see #8218
Brief changelog
Verifying this change

Checklist

[x] Make sure there is a GitHub_issue field for the change (usually before you start working on it). Trivial changes like typos do not require a GitHub issue. Your pull request should address just this issue, without pulling in other changes - one PR resolves one issue.
[x] Each commit in the pull request should have a meaningful subject line and body.
[x] Write a pull request description that is detailed enough to understand what the pull request does, how, and why.
[x] Check if is necessary to patch to Dubbo 3 if you are work on Dubbo 2.7
[ ] Write necessary unit-test to verify your logic correction, more mock a little better when cross module dependency exist. If the new feature or significant change is committed, please remember to add sample in dubbo samples project.
[x] Add some description to dubbo-website project if you are requesting to add a feature.
[ ] GitHub Actions works fine on your own branch.
[ ] If this contribution is large, please follow the Software Donation Guide.

Codecov Report

Merging #8219 (8d354ed) into 3.0 (e2d1ec0) will decrease coverage by 0.21%.
The diff coverage is 75.00%.

@@             Coverage Diff              @@
##                3.0    #8219      +/-   ##
============================================
- Coverage     63.58%   63.37%   -0.22%
+ Complexity      313      310       -3
============================================
  Files          1074     1074
  Lines         45211    45165      -46
  Branches       6807     6774      -33
============================================
- Hits          28749    28622     -127
- Misses        13272    13336      +64
- Partials       3190     3207      +17

Impacted Files
Coverage Δ

.../dubbo/rpc/cluster/router/script/ScriptRouter.java
69.38% <50.00%> (ø)

...apache/dubbo/rpc/cluster/router/tag/TagRouter.java
30.43% <60.00%> (+0.32%)
:arrow_up:

.../rpc/cluster/router/condition/ConditionRouter.java
70.65% <66.66%> (+0.42%)
:arrow_up:

...pache/dubbo/rpc/cluster/router/AbstractRouter.java
89.47% <100.00%> (+39.47%)
:arrow_up:

...rpc/cluster/router/condition/config/AppRouter.java
100.00% <100.00%> (ø)

...ster/router/condition/config/ListenableRouter.java
31.70% <100.00%> (-1.63%)
:arrow_down:

...cluster/router/condition/config/ServiceRouter.java
100.00% <100.00%> (ø)

.../rpc/cluster/router/mock/MockInvokersSelector.java
88.88% <100.00%> (ø)

...ng/transport/dispatcher/all/AllChannelHandler.java
68.96% <0.00%> (-27.59%)
:arrow_down:

...ng/transport/dispatcher/WrappedChannelHandler.java
47.82% <0.00%> (-15.22%)
:arrow_down:

... and 46 more

Continue to review full report at Codecov.

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For Java syntax, it does work well. However, there are two reasons for those changes

All of variables with protected modifier have defined setters and getters in AbstractRouter.

It is best to provide only one way to modify the same variables, however, there are two ways to visite those variables:

use protected modifier to access directly
use setter and getter to access

I think the best way is to use setter and getter to access variables, because the interface of Router already defines some abstract getter methods, like Router#getUrl(), Router#isForce(), Router#getPriority() etc.
public interface Router extends Comparable<Router> {
    ......
    URL getUrl();

    boolean isForce();

    int getPriority();
    ......
    @Override
    default int compareTo(Router o) {
        if (o == null) {
            throw new IllegalArgumentException();
        }
        return Integer.compare(this.getPriority(), o.getPriority());
    }
}


Most of the Edit this page links in docs are broken

e.g. on this page https://juliageo.org/GeometryOps.jl/v0.1.10/source/methods/clipping/intersection "Edit this page" sends you to a missing file. Presumably something is incorrect in
https://github.com/JuliaGeo/GeometryOps.jl/blob/d7781532e8bacd75de03ae13adfdfc92df0cade3/docs/make.jl#L33-L42
(assuming that's what generates the EditURL? I've had similar annoyances with EditURL in the past).

This is a DocumenterVitepress issue, since the Vitepress engine doesn't allow per-page edit links.  Will have to look into it a bit more but we may have to roll and "Edit this page..." button ourselves.


How to disable HAProxy authentication

How can I disable HAProxy authentication (by manully editing haproxy.cfg) because of HAProxy passes its authentication info to the site and the site returns 401

What I did is commented the following in the haproxy.cfg file:
...
# Splash Cluster configuration
frontend http-in
    bind *:8050
#
#    http basic auth
#    acl auth_ok http_auth
#    http-request auth realm Splash if !auth_ok
#    http-request allow if auth_ok
#    http-request deny
#
   # don't apply the same limits for non-render endpoints
    acl staticfiles path_beg /_harviewer/
    acl misc path / /info /_debug /debug

    use_backend splash-cluster # if auth_ok !staticfiles !misc
    use_backend splash-misc # if auth_ok staticfiles
    #  use_backend splash-misc # if auth_ok misc
...

I am getting the following error when trying to disable HAProxy authentication. What is going wrong?
haproxy_1  | <7>haproxy-systemd-wrapper: executing /usr/local/sbin/haproxy -p /run/haproxy.pid -db -f /usr/local/etc/haproxy/haproxy.cfg -Ds  haproxy_1  | [ALERT] 341/045812 (6) : parsing [/usr/local/etc/haproxy/haproxy.cfg:63] : error detected while parsing switching rule : no such ACL : 'auth_ok'. haproxy_1  | [ALERT] 341/045812 (6) : parsing [/usr/local/etc/haproxy/haproxy.cfg:64] : error detected while parsing switching rule : no such ACL : 'auth_ok'. haproxy_1  | [ALERT] 341/045812 (6) : Error(s) found in configuration file : /usr/local/etc/haproxy/haproxy.cfg haproxy_1  | [ALERT] 341/045812 (6) : Fatal errors found in configuration. haproxy_1  | <5>haproxy-systemd-wrapper: exit, haproxy RC=1 aquarium_haproxy_1 exited with code 1

This is incredibly annoying.. These credentials are meant to be private, so one could limit access to Splash instance facing the internet. Instead  these credentials get forwarded to every website you crawl. Unless you additionally use a proxy, you're effectively letting everyone know where your Splash instance is and what its credentials are...

@nirvana-msu setting those got me past the 401 code, THANK YOU. although, it looks like it still does not go through scraper api proxy :(


Fixed problems with HTTP requests

Check if this PR fulfills these requirements:

[x] My changes respect the Kodi add-on development rules
[x] I have read the CONTRIBUTING document.
[x] I made sure there wasn't another Pull Request opened for the same update/change
[x] I have successfully tested my changes locally

Types of changes

[ ] New feature (non-breaking change which adds functionality)
[ ] Feature change (non-breaking change which change behaviour of an existing functionality)
[ ] Improvement (non-breaking change which improve functionality)
[x] Bug fix (non-breaking change which fixes an issue)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Description

The Requests module has persistent connections enabled by default, that send "connection: keep-alive" in the headers, Netflix does not use persistent connections and this prevents connection from being returned to the pool that can causing failures with new requests, as seen on Issue #914 and #1004
In case of Feature change / Breaking change:
Describe the current behavior

Describe the new behavior

Screenshots (if appropriate):

Hi Stefano,
thanks for the update. will you place it on of the repository? I usually do my update from the Kodi on PI from the repository.
If I need to copy as zip on USB to use it with my PI, where do I find it here?

Hi Stefano,
thanks for the update. will you place it on of the repository? I usually do my update from the Kodi on PI from the repository.
If I need to copy as zip on USB to use it with my PI, where do I find it here?

Steffano....the code looks fine...but...I cant find where the Connecton Header is being set....

Steffano....the code looks fine...but...I cant find where the Connecton Header is being set....

last test I made it works great if I switch tittle during playback, but...if I have  a playlist....it failed once the curent title ends

last test I made it works great if I switch tittle during playback, but...if I have  a playlist....it failed once the curent title ends


Adding a feedback section

Issue Description
[Describe the problem or request here.]
Steps to Reproduce (if applicable)

[Step 1]
[Step 2]
[Step 3]

Expected Behavior
[Describe what you expected to happen.]
Current Behavior
[Describe what actually happened.]
Possible Solution (optional)
[Provide suggestions or ideas for how to address this issue.]
Additional Context (optional)
[Add any other relevant information here, such as screenshots, related issues, or notes.]

@khushi1711 please fill the issue descriptions so that we can get much clearer picture of your issue


nodejs environment, mraa/uart functions not able to read data that does not end with '\n'

If incoming data ends with '\n', SerialPort.dataAvailable() returns true.
If incoming data does not end with '\n', SerialPort.dataAvailable() returns false.
 var SerialPort=new mraa.Uart(0);
 var devPath=SerialPort.getDevicePath();
 console.log(SerialPort.dataAvailable(1000));

Are you sure you have baud rate setup correctly? I just tested this and it works as expected:
In [6]: x = m.Uart("/dev/ttyS0")
In [7]: x.setBaudRate(115200)
In [18]: x.read(10)
Out[18]: bytearray(b'ds')
In [19]: x.dataAvailable()
Out[19]: True
In [21]: x.read(10)
Out[21]: bytearray(b'ds\r')

I just plugged a FTDI 6 pin UART to my PC and used minicom to send 'ds' without carriage return and then sent one with carriage return, see the difference. What do you have on the other end of the serial line?

Thank you! After I changed JS code(line 3, a different name), it works now. Moverover, it could not get data length of received. Not sure if you have comment on it?
var SerialPort=new mraa.Uart(0);
var devPath=SerialPort.getDevicePath();
var sp=new mraa.Uart(devPath);

The length of the received data? It's just a normal JS type, grab it's length however you want. It should already have the correct size.


DataGridRow not highlighted when selected and hovered on

Describe the bug
DataGridRow not highlighted when selected and hovered on.
To Reproduce

Build the sample app.
Go to the Data tab, scroll down until you see the "WPF UI DataGrid" sample.

Expected behavior

The rows should be highlighed on hover and on click.

Screenshots
https://user-images.githubusercontent.com/57174311/192426848-f4edae99-8354-4d44-a42d-a625fa8f2720.mp4
OS version
Windows 11 22H2
.NET version
.NET 6.0.401
WPF-UI NuGet version
Built from source, development branch commit 299a90e966c9eba4cb45a9044039d694b4053c41.
Additional context
This is due to the VisualStates for the WPFUI default DataGridRow style are not implemented:
https://github.com/lepoco/wpfui/blob/299a90e966c9eba4cb45a9044039d694b4053c41/src/Wpf.Ui/Styles/Controls/DataGrid.xaml#L226-L371
I have a sample implementation based on the WindowsCommunityToolkit's DataGrid for UWP:
which gives this result:

The Windows Community Toolkit implementation basically:

Sets the opacity to 0.8 on mouse hover, 0.6 on selected, and 0 otherwise.
Sets the color to the system accent color on selected.

Note that unlike other WPFUI controls such as TreeViewItem, the sample DataGridRow implementation does not have a 0:0:0.16 animation duration. Everything happens instantly similar to the WCT DataGrid.
If the code and screenshot above seem appropriate please let me know so I can open a pull request with it.

When i apply this fix the selected color seems too dark when the theme is  on light and if you change it back and forth from dark/theme then its normal.
Dark doesn't seems to have this issue.
The grid text seems to to be aligned on top.
How can this be streched over the whole cell, so that its 'centered'?

When i apply this fix the selected color seems too dark when the theme is on light and if you change it back and forth from dark/theme then its normal.

You can try to change the opacity in the VisualStateGroup and make it lighter.

The grid text seems to be aligned on top.
How can this be streched over the whole cell, so that its 'centered'?

Try editing the style, find any ContentPresenter you can see, and set the HorizontalContentAlignment and VerticalContentAlignment to Stretch.

This should be implemented.

Will this style issue be resolved soon? Without this selected style, the datagrid is incomplete.

@pomianowski is there a chance for this to get some attention please, or are you now fully focused on transferring WPF-UI to WPF?
I (and I guess many other devs) am using DataGrid a lot and having no selection highlight for me is a major obstacle, so I would really appreciate it if this got properly implemented.

A fix has been implemented here, but someone will need to clean it up and open an actual PR.
Feel free to use that code in your own fork long as you put my name as a co-author in the commit.


Fix fallback to English

The previous code would return the 'en' string in case the locale specified as
an argument couldn't be found.

I realize I never replied to this one. I kind of think that instead of silently falling back to English locale, Plurr should better throw an error instead (at least in strict mode). In any case, such functionality (and corresponding tests) will need to be implemented across all implementations. This is why I'm not merging this, but keeping open for future reference.

Note the current code is broken and this PR fixes it. Regardless of which approach you want to take in the future, IMO this should be merged and published. We are also using this patched version internally.

Ok, thanks for clarification. Will do.


Information panel for parameters in Variant Service could be more informative

Working on the new tutorial...we need to put more text in here that describes the aligners and the snp callers.

Including @levinas . Got a piece of information from him the other day concerning bwa-mem-strict but still need info for the other parameters as well.

Updated helper text in https://github.com/dmachi/p3-web/pull/56


feat(C++): Added Fibonacci series with a twist

Fibonacci Series with a twist where in all prime numbers and multiples of 5 are replaced by "0"

can you put the code in /codes


Toggle component groups

This doesn't use cookies yet, so it's only a session based thing for now.

Awesome! :+1:


Setting it up

How do i turn it on? im kinda new with this stuff and i want to use it but i dont know how to, i dont know what "slash_ids" is and i think its not working for me. How do i set up  the discum?

That is what i get when i try to open Setup.py

Ifs it's a discum installation issue please refer to the discum repo link in the readme they can help you install that on their side

Gonna be closing as haven't heard back for a bit

Gonna be closing as haven't heard back for a bit


Set up new Amplitude projects

Set up two new Amplitude projects, preventing old events to be logged incorrectly.
Acceptance criteria:
1 - App sending events to new Amplitude projects App and Development.
2 - Remove old projects
3 - Amplitude dashboard with KPIs for the new projects.

Amplitude dashboard will be updated in #528


A Visually Impaired User's Request for Assistance with ChatGPT Account Access

Hello!
I am a visually impaired user (blind), and my main purpose of using ChatGPT software is to explore the prospects of the software in visual assistance. This software is very important to me, it helps me understand the information I want to know in an unprecedented way. For example, in the process of programming, I often encounter places that I don't understand or make mistakes. Due to my visual impairment, it is relatively inefficient for me to find answers through search engines, and some content is presented in the form of pictures. However, ChatGPT interacts with me in a conversational way and provides me with text descriptions so that I can immediately hear the information and knowledge I need through a screen reader. This conversational interaction makes me feel very excited and satisfied. However, a few months ago I encountered some problems. I found that I could not log in and showed that I had no permission. I was very confused because in my impression, I had never done any inappropriate behavior. I hope you can understand my situation and help me solve this problem.
If you need to provide any additional information or documents, I am willing to cooperate. In addition, in future use, I will continue to use ChatGPT and API in accordance with regulations. I will abide by OpenAI's usage regulations and maintain a good network environment. Thank you for your help and look forward to your reply🍻.

I recommend reaching out to the support team or the administrators of the software you're using to address the login issue. They should be able to assist you and provide the necessary permissions to access the software

I have contacted OpenAI's support mailbox before creating this question,
but I didn't get a response, can you help me🍻
Rudra Pratap @.***> 于2023年5月18日周四 13:04写道：

I recommend reaching out to the support team or the administrators of the
software you're using to address the login issue. They should be able to
assist you and provide the necessary permissions to access the software
—
Reply to this email directly, view it on GitHub
https://github.com/openai/openai-cookbook/issues/428#issuecomment-1552402451,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AJCWG7V2T2L3PBNO4JNWPLLXGWUUFANCNFSM6AAAAAAYF3S5GQ
.
You are receiving this because you authored the thread.Message ID:
@.***>

I'm sorry about your situation but this repo is not the right place. Recommend contacting support.


Cmake embedded flag

Reference issue #321

@pfultz2 @atamazov Please re-review.

@daniellowell  Can we add a stage to Jenkins to exercise this path in the tests?


Backport HSEARCH-3365 to branch 5.10 - Backport Jenkinsfile to older, still maintained branches

https://hibernate.atlassian.net//browse/HSEARCH-3365
Just testing that PRs build correctly before I merge, no need to review.

Pull Request Test Coverage Report for Build 1

0 of 0   changed or added relevant lines in 0 files are covered.
162 unchanged lines in 18 files lost coverage.
Overall coverage decreased (-0.6%) to 83.899%

Files with Coverage Reduction
New Missed Lines
%

engine/src/main/java/org/hibernate/search/store/impl/FSSlaveDirectoryProvider.java
1
80.23%

elasticsearch/src/main/java/org/hibernate/search/elasticsearch/util/impl/gson/ES2NormsTypeJsonAdapter.java
1
0.0%

elasticsearch/src/main/java/org/hibernate/search/elasticsearch/schema/impl/Elasticsearch50SchemaTranslator.java
1
94.44%

elasticsearch/src/main/java/org/hibernate/search/elasticsearch/util/impl/gson/ES2FieldDataTypeJsonAdapter.java
1
0.0%

elasticsearch/src/main/java/org/hibernate/search/elasticsearch/analyzer/impl/Elasticsearch2AnalyzerStrategy.java
2
85.56%

elasticsearch/src/main/java/org/hibernate/search/elasticsearch/dialect/impl/es50/Elasticsearch50Dialect.java
2
80.0%

engine/src/main/java/org/hibernate/search/util/impl/Executors.java
3
46.15%

elasticsearch/src/main/java/org/hibernate/search/elasticsearch/work/impl/factory/Elasticsearch2WorkFactory.java
3
87.5%

elasticsearch/src/main/java/org/hibernate/search/elasticsearch/schema/impl/Elasticsearch2SchemaValidator.java
7
87.8%

elasticsearch/src/main/java/org/hibernate/search/elasticsearch/query/impl/Elasticsearch2QueryFactory.java
9
0.0%

Totals

Change from base Build 7:
-0.6%

Covered Lines:
23741

Relevant Lines:
28297

💛  - Coveralls


Issue with CheckTx propogation using ABCI++ socket interface

Bug Report
Setup
CometBFT version (use cometbft version or git rev-parse --verify HEAD if installed from source):
v0.38.12 (via docker build)
Have you tried the latest version: yes/no
yes
ABCI app (name for built-in, URL for self-written if it's publicly available):
layer-sdk - Rust application, not publically available.
Connects using tendermint-abci sockets
Environment:

OS (e.g. from /etc/os-release): Linux / Ubuntu 22.04
Install tools:
Others:

node command runtime flags:
cometbft start
Config

What happened?
I connect a local Rust ABCI node to CometBFT (both as local docker containers, via docker compose).
On a single node, "everything" works fine. Well, except after a check_tx returns a success, the tx is neither added to mempool (not present in prepare_proposal) nor propogated when I connect to a peer.
Early on, during some 0.38.0-rc.X, I saw this, and cached the approved tx locally and fed it in prepare_proposal. The app runs "fine" like this, but only single node.
Recently, I attempted to connect a second non-signing node via p2p, and it is able to run all blocks. However, when I submit a tx to the rpc of the non-validating full-node, it never appears in the mempool of the validating node.
I return the following struct back to cometbft in response to checktx:
ResponseCheckTx { code: 0, data: b"", log: "[]", info: "", gas_wanted: 2270289, gas_used: 2270289, events: [], codespace: "sdk" }
Note: I just added codespace (was empty before) to try to debug.
What did you expect to happen?
I expected it to enter the mempool properly
How to reproduce it

I cannot (yet) share how to reproduce, but happy to get some info so I can provide a better report.
First, I was wondering if you have seen a similar error before or have any input on the return values. Is there something I am obviously missing and should do differently?
Second, I am happy to turn up specific logging if there is something else I can provide you (let me know what to do and I will attach). There is no mention of check_tx on either node with info level logging on cometbft.
Third, I was wondering if you had any minimal tests using abci socket to external process I could see as a test, and then try to adapt it into a test case for my issue.
Logs

dump_consensus_state output

Anything else we need to know

Hey @melekes i know this is impossible to debug on your side with this info. Could you provide me any logs/debugging info I could look at cometbft side to understand the mempool/checktx interactions better (which log flags to enable, not all as it is too verbose to see anything)
I would like to produce a minimal test case to recreate this. Ideally with Rust over abci socket. Do you have some minimal dummy app in rust I could use as a starting point?

I would like to make a minimal test case with https://github.com/informalsystems/tendermint-rs/blob/main/abci/src/application/kvstore/main.rs
and comet bft as two different processes, so I can see if the bug is on “your side” or “my side”. And if it is in my code, at least have a minimal example that works, which I can start to debug from
I dug through the repo looking for some test running this over abci sockets, but I cannot find it anywhere. Is there any e2e test for the rust abci server implementation?

You should try using the debug level logging on the mempool. But unfortunately, a lot of debug log entries were removed from the mempool for performance purposes (I think), so you'll probably need to manually add some.
You can also try the /unconfirmed_txs RPC endpoint.

After playing around with this for a while, it turns out that the issue was due to block max_gas parameter being set to -1, which was the default in comet init (at least in May). Now, that is treated as non-gas rather than infinite I think, so the tx were all being dropped.
I never did find logs for that, but after trying to debug comparing to sample apps, we set max_gas to 10000000, and it suddenly worked.
Not sure when this behavior changed, but it would be nice to document it better (ideally error on negative values parsing the genesis if they change behavior)

We have it documented here: https://docs.cometbft.com/v0.38/spec/abci/abci++_app_requirements#blockparamsmaxgas

BlockParams.MaxGas
The maximum of the sum of GasWanted that will be allowed in a proposed block. This is not enforced by the consensus algorithm. It is left to the Application to enforce (ie. if transactions are included past the limit, they should return non-zero codes). It is used by CometBFT to limit the transactions included in a proposed block.
Must have MaxGas >= -1. If MaxGas == -1, no limit is enforced.

But you are saying that -1 has changed behavior? If so we definitely have to check and fix.

I know those docs and that behavior (for context, I have used tendermint since 2017 and used to work at AiB).
I also know -1 is only good for local testing / devnets, and anything public needs a limit or you can create fun DoS attacks on the chain.
However, my last test was showing me that a 90000 gas tx was consistently dropped from the mempool when it passed check_tx when mas_gas was -1. And when I changed it to 10000000, it suddenly worked (same binary).
If you could tell me what log flags to enable, I could show you the cometbft logs.
But I bet you could make a testcase for this

I also know -1 is only good for local testing / devnets, and anything public needs a limit or you can create fun DoS attacks on the chain.

Absolutely. The point is how gas is used by different networks, that has never clear to me (I'd say, us).

If you could tell me what log flags to enable, I could show you the cometbft logs.

As I said, unfortunately a lot of refactoring in mempool code has removed most of the debug log entries, because they were costly. We are fixing that in recent issues/PRs. So with upstream code I am afraid that the only way to debug is by relying on the response returned to the RPC client.

But I bet you could make a testcase for this

Would you mind to open an issue describing this situation in more detail. We probably can reproduce the scenario, if it is indeed valid, and find solutions.


ClickCommand("Save & Close")

Question
i want to know about ClickCommand("Save & Close")?
i want to edit my other service right now using nurse recruitment.
i want to edit the Sales Sample.
For example i am having a scenario which i am going to implement another button and button name is Click Me . i just need to pass Click Me.
for eg
xrmApp.CommandBar.ClickCommand("Click Me);
.Is this command will click on button by the text or i have to define X path or id else where.

@abubakarafzal if you look at the code of ClickCommand function in the file WebClient.cs of UCI repository, you will find an answer on how it's handled in the code and what you need to do :)

Found that


Dead URL reference in x:context/@href produces unclear error message

When referencing a non existent or unresponsive url in the href attribute of an x:context element, the error message produced says "XML document structures must start and end within the same entity."
This doesn't really explain to the user what the real problem is, i.e. that the document was not available to be processed.
Can it be clarified?
Example xspec attached.
Note: GitHub does not allow upload of .xspec files so this was renamed by adding .txt on the end
intro.xspec.txt

As for the runtime error, it is true that XML document structures must start and end within the same entity doesn't help. To diagnose, you need to see the log:
If you are using oXygen transformation scenario
The ANT [XSpec for XSLT] pane opens automatically on failure. There you can see what the actual error is:
     [java]   FODC0002: I/O error reported by XML parser processing
     [java]   http://xmldb.portinfo.co.uk/xml/4xv/000001.xml

If you are using oXygen XSpec Help plugin
See xspec/oXygen-XML-editor-xspec-support#24

I've made a change to output messages if URIs referenced in stylesheet or `href`` attributes are not available in XSLT tests. With this change, XSpec will produce a report that contains a message about the URI that is not available, instead of stopping with a cryptic message. For example:
Document referenced by context/@href is not available: does-not-exist.xml
Document referenced by expect/@href is not available: does-not-exist.xml
Document referenced by param/@href is not available: does-not-exist.xml
The stylesheet referenced by x:description/@stylesheet is not available: does-not-exist.xsl

This change is in branch issue/400. @cirulls and @AirQuick please take a look. If this change looks okay I'll try to continue adding these messages for XQuery and Schematron tests.
A possible problem I noticed while working on this is that the messages are not included in the JUnit report. I'm not sure if I missed something or if this is an expected behavior or an existing problem with the JUnit report output.

A few random quick thoughts:

mode="test:generate-variable-declarations" checks doc-available() at compile time, but the URL available at compile time may not always available at runtime, particularly when it involves external web services. The check should be done in the same session as doc().
Injecting a dummy document in mode="test:generate-variable-declarations" could be a bad idea. One may write @href="URL" together with @select="if (//text()[contains(., 'available')]) then 'foo' else 'bar'" for example. Such expression will continue working quietly in an unexpected way even when URL go dead.
As for JUnit report, it might be related to #330 or a number of issues written there.

Also, just hiding doc() error is not always more helpful. It could even complicate the problem.
For example, the current master tells what's wrong with <x:context href="https://httpbin.org/" />:
Scenario for testing broken document
Error on line 29 column 3 of https://httpbin.org/:
  SXXP0003: Error reported by XML parser: The element type "link" must be terminated by the
  matching end-tag "</link>".

Scenario for testing broken document
Error at char 4 in xsl:variable/@select on line 43 column 69 of test.xsl:
  FODC0002: I/O error reported by XML parser processing https://httpbin.org/gzip: Invalid
  byte 1 of 1-byte UTF-8 sequence.

The proposed branch does not show these diagnoses.

Thanks for the quick feedback @AirQuick !

I've made a change to check doc-available at runtime.
I removed the generated text in test:generate-variable-declarations. However, now the report does not show if a fail or a message if the document is not available. I think the HTML report can still show a fail and a message if the URI is not available, but my first attempt did not work.
I'll not worry about the JUnit for now.
This could probably be improved with <xsl:try> but that would require XSLT 3.0

I'm afraid even <document/> could be harmful in test:generate-variable-declarations.
	<x:scenario label="Scenario">
		<x:call function="exactly-one">
			<x:param><slide><bogus>Wake up to WonderWidgets!</bogus></slide></x:param>
		</x:call>
		<x:expect href="https://httpbin.org/xml" label="Correct URL" select="slideshow/slide[1]/title" test="slide/title" />
		<x:expect href="https://httpbin.org/xm1" label="Wrong URL"   select="slideshow/slide[1]/title" test="slide/title" />
	</x:scenario>

This scenario terminates on the current master, but the proposed branch returns Success for the 2nd x:expect, because the dummy document turns the expectation into an empty sequence.

Thanks @AirQuick
It seems better to keep the current behavior in which the test terminates if a referenced URI is not available. As you described, the system generated error messages are sometimes helpful, and producing a report might result in false-positives.
I've made a change in branch issue/400 to restore the original behavior to terminate if a referenced URI is not available. URIs referenced in href and stylesheet attributes are checked at compile time and a clear error message is output to the console if a URI is not available, in addition to any error messages that might be system generated.

I've added a similar check for XQuery tests to output a message to console if the query referenced by the query-at attribute is not available at compile time.
The query referenced by description/@query-at is not available: does-not-exist.xq
For Schematron tests, the Schematron compilation process already outputs a clear message if the Schematron referenced by the schematron attribute is not available.
Source file C:\Users\vincent\Projects\xspec\xspec\test\unavailable\does-not-exist.sch does not exist

@vincentml
Looks good to me in general. Some details could be improved, but that should be done in a pull request.
A few things to note:

You may be already aware of it, but I submitted some pull requests to change the Bats test files for Windows. (#284, #285, #286)
Not sure what you mean by "predictable" in 942d7baec314329764426560d325ba5c46d1e409, but it might possibly be related to #185.

I verified that on Oxygen 21.1 build<PHONE_NUMBER>, the following statement is still true

If you are using oXygen transformation scenario
The ANT [XSpec for XSLT] pane opens automatically on failure. There you can see what the actual error is:
     [java]   FODC0002: I/O error reported by XML parser processing
     [java]   http://xmldb.portinfo.co.uk/xml/4xv/000001.xml

and with XSpec Helper view 1.2.1, the following issue is mitigated (i.e. the ANT [XSpec for XSLT] pane opens automatically on failure and you can see the same error as above)

If you are using oXygen XSpec Helper plugin
See xspec/oXygen-XML-editor-xspec-support#24

So I'm closing this issue. Please feel free to reopen, if you don't see the actual error in the same environment.


Setup for working with Uploader

@RatreeOchn needs to setup to prepare to work with Uploader before Zhenya leaves. It would be good to ask Zhenya to share the knowledge about Uploader and Legacy (eg. manually export data, add species, etc).

@RatreeOchn do you have an access to this repo : https://github.com/rfcx/arbimon-uploader?

please follow these steps:

clone the repo to your PC
nvm use to switch to the node requested
npm install
run the app npm run dev

you should see 1 app window + 3 consoles
@RatreeOchn

I have done to set up the Uploader on my local.

@RatreeOchn If your setup works now, you can close this ticket.


User account creation (individual + bulk)

Users should be able to create accounts. Professors should be able to bulk-invite students.

Basic user account creation from #48

Closing because all issues completed.


Development

updating the repo reference point of QGP_Bayes in the Bandframework development branch.

Will make another request with correct changes


Move release notes to releases and not the README.

Old versions that don't have a release on GitHub can probably still be included but, why not keep the release notes in the releases instead? There's also a change log on the website.
\

Because most projects that I work on require it to be in the README and it has become habit for me to do.

There's also a change log on the website.

Yes, I write it. The public wouldn't visit the GitHub page has I don't promote it heavily.

Because most projects that I work on require it to be in the README

wdym require? do you mean they don't use releases? ()

There's also a change log on the website.
Yes, I write it. The public wouldn't visit the GitHub page has I don't promote it heavily.

I'm not talking about the website being replaced. That can stay.

Correct. Most projects I work on, senior managers require all release notes, history, public documentation and details to be stored within a single description file in the project.

Ah, ok.

Changed the closure type to more accurately reflect the issue state.


MSID: 99790 Version: 1 DOI: 10.1101/2<IP_ADDRESS>6608

MSID: 99790
Version: 1
Preprint DOI: https://doi.org/10.1101/2<IP_ADDRESS>6608
Step 1. Awaiting reviews
Editorial to post reviews via hypothesis
Useful links:

DocMap: https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v2/by-publisher/elife/get-by-manuscript-id?manuscript_id=99790
New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
Reviews on sciety: https://sciety.org/articles/activity/10.1101/2<IP_ADDRESS>6608

For trouble shooting (e.g. no Docmaps available):

DocMap issue addressing: https://miro.com/app/board/uXjVNCwK6EI=/
Explore DataHub DocMaps API: https://lookerstudio.google.com/reporting/4c2f0368-babb-4beb-b5b3-497e7e7b0f08/page/ejphD
Unmatched submissions and preprints: https://lookerstudio.google.com/u/0/reporting/9f86204f-3bf7-477c-9b18-5c5ef141bf69/page/p_gxi57ha93c
Unmatched manuscripts spreadsheet: https://docs.google.com/spreadsheets/d/15QcK8w-ssB7109RQEDtFpJPZ0J5HTGxoHa_2TtpMBbg/edit#gid=1336081641

Step 2. Preview reviewed preprint
Production QC content ahead of publication
Instructions:

QC preview: https://prod--epp.elifesciences.org/previews/99790v1
Update ticket with any problems (add blocked label)
When QC OK, add QC OK label to ticket and add publication date and time to https://docs.google.com/spreadsheets/d/1amAlKvdLcaDp5W8Z8g77NmkwbMF5n_u89ArSqPMO8jg
Move card to next column
(At end of the day post link in #enhanced-preprint and ask for PDF to be generated)

Useful links:

Preprint DOI :  https://doi.org/10.1101/2<IP_ADDRESS>6608
Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/99790/v1/reviews
To update the MECA path in the docmap: https://docs.google.com/spreadsheets/d/1mctCQuNFBjSn97Lihy7_vBO6z7-N-oqyLv4clyi6zHg

Step 3: Awaiting search reindex
This step adds the reviewed preprint to the homepage: https://elifesciences.org
The search reindex is triggered once an hour. We need the reviewed preprint to be indexed as the search application serves the journal homepage.
Useful links:

Jenkins pipeline to reindex search can be triggered sooner or monitored here: https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/

Step 4: Published! PDF requested
Waiting for PDF to be generated
Useful links:

PDF tracking: https://docs.google.com/spreadsheets/d/106_XeDjmuBae7gexOTNzg60lapeqjl2aRn9DzupGyS8/

Step 5: Introduce PDF to data folder and git repo
Upload PDF to relevent folder in git repo https://github.com/elifesciences/enhanced-preprints-data/
Step 6: Done!

[ ] Kettle is on!


slim docker images

What's the purpose of this PR
recreate PR (#3530 ) slim docker images
Which issue(s) this PR fixes:
slim docker images
Brief changelog
slim docker images
Follow this checklist to help us incorporate your contribution quickly and easily:

[x] Read the Contributing Guide before making this pull request.
[x] Write a pull request description that is detailed enough to understand what the pull request does, how, and why.
[x] Write necessary unit tests to verify the code.
[x] Run mvn clean test to make sure this pull request doesn't break anything.

version changed, new conflicts, OMG!


Add missing blocks to the dycore Jacobian

Purpose

This PR adds a couple of missing blocks to the dycore Jacobian and modifies the linear solver to handle them. This improves the stability of two longrun simulations that were previously failing (Held-Suarez with topography and aquaplanet with topography).
This comes with a slight performance penalty (e.g., the single-GPU Held-Suarez longrun goes from 1.7 hours to 2.2 hours), but we can probably lower this by further optimizing the linear solver. If we wanted to, we could also specialize the solver for simulations without topography, which would bring the performance of those cases back to what it was before this PR.
Content

Account for the $\dfrac{\partial u^3}{\partial u_h}$ derivative, which scales with $g^{3h}$ and is therefore significant in simulations with topography. This adds the tridiagonal $\dfrac{\partial\mathcal{E}\rho}{\partial u_h}$, $\dfrac{\partial\mathcal{E}\rho e_{tot}}{\partial u_h}$, and $\dfrac{\partial\mathcal{E}\rho\chi}{\partial u_h}$ blocks to the Jacobian.
Account for the $\dfrac{\partial\kappa}{\partial u_h}$ derivative. This scales with $g^{hh}$ and $g^{3h}$, so it is relevant both with and without topography. However, it only adds the bidiagonal $\dfrac{\partial\mathcal{E}u_3}{\partial u_h}$ block to the Jacobian, which, along with the $\dfrac{\partial\mathcal{E}u_3}{\partial u_3}$ block, is smaller than similar blocks by a factor of roughly $(\dfrac{u}{c})^2$. In the future, we might want to drop both of these blocks if they do not significantly improve stability. Since they do not affect the structure of the linear solver, we will keep them in for now.
Account for the $\dfrac{\partial p}{\partial\rho q_{tot}}$ derivative, which is significant in simulations with moisture. This adds the bidiagonal $\dfrac{\partial\mathcal{E}u_3}{\partial\rho q_{tot}}$ block to the Jacobian, along with the tridiagonal $\dfrac{\partial\mathcal{E}\rho e_{tot}}{\partial\rho q_{tot}}$ block in simulations with implicit diffusion.
Account for the $\dfrac{\partial e_{tot}}{\partial\rho}$ and $\dfrac{\partial\chi}{\partial\rho}$ derivatives. These add the tridiagonal $\dfrac{\partial\mathcal{E}\rho e_{tot}}{\partial\rho}$ and $\dfrac{\partial\mathcal{E}\rho\chi}{\partial\rho}$ blocks to the Jacobian in simulations with implicit diffusion.
Increase the memory limits for the single-GPU dry and moist baroclinic wave jobs, the 4-GPU dry baroclinic wave job, the 1-moment microphysics job, and the prognostic EDMFX aquaplanet flame graph job.
Slightly increase the allocation test limits of the diagnostic EDMFX and gravity wave flame graph jobs.

[x] I have read and checked the items on the review checklist.

Is this ready for testing? Maybe @akshaysridhar could try running some topography simulations.

@szy21 There seem to be a couple of performance+GPU issues, but other than that this is ready for testing. I'm trying out the longruns here.

CPU longruns: https://buildkite.com/clima/climaatmos-longruns/builds/1303
GPU longruns: https://buildkite.com/clima/climaatmos-gpulongruns/builds/10
@szy21 Would you mind taking a look at the results before I merge this in?

I looked at some of the dycore simulations that are done and they look good. Feel free to merge this in. Thanks!

The GPU pipeline seems to be 40% slower though. Is this as expected?

Yeah this PR replaces the simple diagonal solver for the diffusion matrix with an iterative solver. This needs to run on every iteration of the higher-level solver for the full Jacobian, so it'll have a significant performance effect. This PR also adds a bunch of additional blocks to the Jacobian, and these currently take a while to compete.

Ok, sounds good to me. Just want to let people who work on performance know (@simonbyrne @sriharshakandala).

From the flame graphs, it looks like the new blocks are the main source of the performance hit. So, we might want to change something in ClimaCore to speed up long chains of matrix-matrix multiplications. I'll look into this when I get back.

I did want to know whether this helps with the topography runs though. I'm ok with merging it in for now as 40% is not too bad, or @akshaysridhar can test with this branch. Either way is fine.

Hmm, looks like more memory increases are required. Before I merge this in, I'll try dropping some of the new Jacobian blocks in simulations without topography, which will probably improve the performance of those simulations.

CPU longruns: https://buildkite.com/clima/climaatmos-longruns/builds/1355
GPU longruns: https://buildkite.com/clima/climaatmos-gpulongruns/builds/24
Performance issues appear to be resolved. I'll merge this in when the longruns are done.

The longrun looks fine. Feel free to merge it.


Fixes #55 Upgrade to Angular 7

Fixes #55
Fixed Unit Tests.
Fixed the prod build failure.

Thanks for the contribution — sorry I didn't get around to this sooner. I've merged https://github.com/third774/ng-bootstrap-form-validation/pull/65 since it was newer and cut a new release.

@third774 , no problem


No variable or method x for y, thrown after a potentially raising method is called

This is as minimal as I could get it:
def foo(a, b)
  bar(a) + (b * 2)
end

def bar(a)
  when a == 1
    return (a.to_s * 5)
  else
    raise "<(a)> must be 1!"
  end
end

STDOUT.puts(foo(1, 3))

This is expected to print "111116\n", but instead it raises the following error:
Uncaught Exception: No variable or method `b` for Kernel
  from `b` at .../example.mt:2:13
  from `+` at .../example.mt:2:3
  from `foo` at .../example.mt:13:13
  from `puts` at .../example.mt:13:8

This is where the error occurs:
def foo(a, b)
  bar(a) + (b * 2) # "No variable or method `b` for Kernel"
end

If you remove the raise ..., the error is not thrown

I misread this issue the first few times and assumed there was a rescue on bar, so I was attributing the bug with how ExceptionHandler deals with popping scopes.
The fact that there isn't a rescue or ensure involved here is more confusing. A raise that doesn't get executed shouldn't have any effect on the surrounding code, and I'm really not sure how it could be leaking like this. Will definitely need to look more into it.

Messed around with it a little bit and it looks like this is actually an issue with return. Here's a minimized example that raises the same error:
def bar(a)
  return a
end

def foo(a, b)
  bar(a)
  b
end

foo(1, 3)

Removing the explicit return from line 2 fixes the error. With that, this issue is probably happening in the Invocation struct, where invoke handles rescuing BreakException, NextException, and ReturnException.

I think explicit returns/breaks might also have issues with restoring the correct value of self. This failed build occurred because an explicit return in IO#gets skipped popping a value from the self_stack: https://travis-ci.org/myst-lang/myst/builds/341175297

Some more testing makes this look like an issue with scope_stack rather than self_stack. Still looking into it.


charts/osm: add namespace to preset-mesh-config resource

Description:
The preset-mesh-config resource was not namespaced.
Resolves #4083

Affected area:

Functional Area

Install
[X]

Please answer the following questions with yes/no.

Does this change contain code from or inspired by another project? no

Did you notify the maintainers and provide attribution?

Is this a breaking change? no

Codecov Report

Merging #4084 (68c990d) into main (9587d45) will increase coverage by 0.04%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #4084      +/-   ##
==========================================
+ Coverage   69.03%   69.08%   +0.04%
==========================================
  Files         205      205
  Lines       11242    11242
==========================================
+ Hits         7761     7766       +5
+ Misses       3429     3424       -5
  Partials       52       52

Flag
Coverage Δ

unittests
69.08% <ø> (+0.04%)
:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files
Coverage Δ

pkg/crdconversion/crdconversion.go
75.00% <0.00%> (+5.43%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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This change was backported to release-v0.10.


Added support for Stateful Managed Instance Groups

Supporting both stateful disks for all instances or for specific instances of the Managed Instance Group as documented here

Hi @stenio123, thank you for your contribution. It looks like the build fail due Terraform linting (fmt) and also the variables.tf should be sorted alphabetically.

Thank you for the quick feedback. Looking into it.
Regarding the tests on tests/examples, does it use the # tftest:modules=2:resources=2 at the bottom of the test?
No idea where that came from in the earlier examples :-D

@ludoo I really like your idea of bundling the stateful config variables, however I am running into all sorts of issues managing this complex object... you can check the ongoing discussion here https://discuss.hashicorp.com/t/loop-with-conditional-using-object-known-only-after-apply-oh-my/32639
Is there somewhere in the repo where you might have seen a similar situation that I can use as an example? I am concerned about overcomplicating things unnecessarily. Thanks!

Hey, thanks for spending time on this! This type of error is nasty, basically the rule is keys used in for_each need to be static (i.e. not computed at runtime), while values can be dynamic. I can try and have a look at it tomorrow, don't go crazy on this!

Thank you! I think I got it after the latest reply on the Hashicorp forum, at least all tests are passing :-)
Let me stress test it a bit and clean up everything and will update today after lunch. The only thing is I believe I might still have the error on tests/examples/test_plan.py since I dont really understand where it gets the values from. Will do some digging before pushing.

Hello I made the requested changes and regular tests passing. Questions -
1- Could you please advise where I can find "check_documentation.py"? I checked the ci folder and have no idea what linting tests are being made, so dont know how to address the error
2- Related to that, not sure what is expected from "tests\examples"
Thanks!

Sorry, I should have explained earlier. :)
The READMEs are checked against the output of tools/tfdoc.py, which creates and injects the vars/outputs tables present at the bottom of each README file. If you're ok with creating a Python virtualenv and installe requirements from the tools folder, just run tfdoc from the root folder and pass the module's directory as its only argument.
As for examples, they are automatically run as tests, the tftest comment in them states the number of resources and modules used in plan.
If you prefer me to do the small fixes above, we can merge this into a branch, and I'll then do them myself before branching to master. No big deal if you prefer this way of course!


Upload photo unimplemented

Due to time and resource constraints; this item has been bumped to the next iteration due to its low priority

Due to iteration 4's focus on bug fixes, this story has been removed from the scope of the project


ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/psutil/_psutil_osx.abi3.so, 0x0002): tried: '/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/psutil/_psutil_osx.abi3.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/psutil/_psutil_osx.abi3.so' (no such file), '/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/psutil/_psutil_osx.abi3.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))

ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/psutil/_psutil_osx.abi3.so, 0x0002): tried: '/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/psutil/_psutil_osx.abi3.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/psutil/_psutil_osx.abi3.so' (no such file), '/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/psutil/_psutil_osx.abi3.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
这个怎么解决啊

这种百度一下应该能自己解决了


Validator matches() check fails on second match check

I'm using this pattern:
/^(\d{5}[,]?)+$/igm
Basically, it accepts a list of 5 digit numbers with a comma-delimiter (ie 73111,85111,98222,08881...).
When I run the following code the first time (after reload):
matches('73111,85111,98222,08881', /^(\d{5}[,]?)+$/igm);
It runs fine and get a true, as expected.  However, if I run the code again (without reloading), I get a false, even though the data has not changed.
Any reason why this would be doing this?

After looking at the source code for matches, it is using the test method on a regex pattern.
Here is the reason this is happening:

When you're using /g, the regex object will save state between calls (since you should be using it to match over multiple calls). It matches once, but subsequent calls start from after the original match.

Yeah this how g works rather than a bug in the library. You'd have the same behavior calling /../.test() multiple times.


Provide latest node js support for image

Provide latest node js support for image

If we have for node-10 that will be helpful

as this is not maintained anymore, I'm maintaining my fork over here: https://github.com/schliflo/docker-puppeteer


Outline View for CSS doesn't list media queries

Hello,
This is a feature request for CSS/SCSS/SASS views; would it be possible to show specific media queries in the outline tree instead of, or in addition to, the class names?
Thanks!
Best,
Giordan

hi bot, it's not listed; I definitely searched already


Adapt v3 tests to v3/v4 conversion

[ ] Review existing tests related to v3 configuration and see if we can adapt them to v3/v4 conversion
[ ] Create test (if it does not exist) for obfuscated secrets
[ ] Create test (if it does not exist) for discovery + databind

Planned as NEWRELIC-3689


Display official strain nomenclature

Description
As a PDXfinder user, I want to easily find information about the strain used to generate PDX model.
The current view is of the non-official name which is not harmonized.

Acceptance criteria

[ ] official strain nomenclature is visible

Query of dev db shows specimen number by Host Strain Nomenclature:
sourcehttps://app.zenhub.com/files/78657127/7d285104-766d-4b28-b927-39a19a99931e/download
source2https://app.zenhub.com/files/78657127/d424e7ee-c13d-4446-a2dc-c13d0df1a56f/download
It is clear that the database needs cleaning

I think another document should be prepared with some guide lines to names and host strain nomenclatures with accept names for common host strains and formatting for their nomenclatures.
Here is a query of common name by symbol https://app.zenhub.com/files/78657127/4510a6a4-e09b-4637-a30e-8e69cf6481c6/download

@zperova, @CsabaHalmagyi, @Afollet : I'm adding a tooltip when you hover over Host Strain Name. Any thoughts?

I think that is a good approach.
There are these "Not Specified" Host Strain Names. For Example: http://dev.pdxfinder.org/data/pdx/crl/CRL-2835
I wonder if there is a way to gracefully handle this "Not Specified". Maybe in this exception the Host Strain Nomenclature can just be displayed in the cell? "Not Specified" is just distracting from useful information being displayed.

@mauroz77 This looks very nice! I think this is a much cleaner solution than having an additional column. Can it handle the formatting? in the provided example "Foxn1" should be Italics and "nu" superscript.
I agree with @Afollet about the Not specified cases. It's really sad to look at the models that have "Not specified" in almost every single field... Makes me think there is another data clean-up to be done - that can be aligned with the assignment of the "FAIR score" for the models.

@Afollet I could set the in the dto the value for the nomenclature if the host strain name is Not Specified. But, would the nomenclature be different to Not Specified as well? I was looking at my local data and one node with host strain name Not Specified has the nomenclature (symbol) with that value as well. I'm copying the prod database to my local machine to see if I can find other values.
@zperova we can put format to the tooltip but I think the value should be stored in the database with the corresponding html: Foxn11nu. Otherwise the frontend would not have enough information to know how to format it

@mauroz77 Host Strain Nomenclature is a hard requirement. The Host Strain Nomenclature should be more consistent than the Host Strain Name and is a hard requirement for the DB. If we have neither have values then it might as well say "Not Specified".  This should be a small minority of cases that we can only fix by contacting the data providers.
@zperova
I agree with Mauricio. We would have to store the HTML tags or use some kind of vocabulary to resolve how to format this strings. Some of the Host Strain Nomenclatures have HTML tags in them currently, but this is something I've been trying to clean from the database.


"method not found" error in release version

If I publish my web service, and therefore also build in release mode I get the following error.
Each method call returns "Method not found" error.
{"jsonrpc":"2.0","error":{"code":-32601,"message":"Method not found","data":"The method does not exist / is not available."},"id":1}
Why is this so?

This is urgent !

What does the code look like where you are creating your service?

I also have this issue. The code for registering the service looks like this:
private static object[] _services = new object[] { new ProductsService() };
The service methods ok are found when in Debug mode, but not when running in Release mode. It is a Windows Service application that I am developing.
Please can you advise?

Is there a service Init function that you can override that is part of the windows service life cycle?

Thanks for the reply Austin.
I figured out that it was due to Release mode optimisations. The services weren't being initialised since they technically weren't being used at that point in the code.
I added a static constructor to the class containing the code in my previous comment to force the services to initialise.


Compile of App fails when using customized Application App

Describe the issue
We try to compile an app which has a reference to "application": "<IP_ADDRESS>" in app.json.
The application.app was modified by us (own publisher and id).
Our customized application (and all of there dependencies to propagate) is located in the Symbols folder ("Any Publisher_Application_<IP_ADDRESS>.app") but not published in the container.
There is no Application App published  in container cause its created with -useNewDatabase.
Scripts used to compile and cause the issue
Compile-AppInNavContainer -appProjectFolder C:\ProgramData\NavContainerHelper\Extensions\anycontainer\App -containerName anycontainer -credential $Credential -appSymbolsFolder "C:\ProgramData\NavContainerHelper\Extensions\anycontainer\Symbols"

Full output of scripts
Using Symbols Folder: C:\ProgramData\NavContainerHelper\Extensions\anycontainer\Symbols
Downloading symbols: Microsoft_Application_15.3.40074.41933.app
Url : http://<IP_ADDRESS>:7049/BC/dev/packages?publisher=Microsoft&appName=Application&versionText=<IP_ADDRESS>&tenant=default
Compile-AppInNavContainer : Ausnahme beim Aufrufen von "DownloadFile" mit 2 Argument(en):  "Der Remoteserver hat einen Fehler zurückgegeben: (404)
Nicht gefunden."
In Zeile:1 Zeichen:1
+ Compile-AppInNavContainer -appProjectFolder C:\ProgramData\NavContain ...
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : NotSpecified: (:) [Compile-AppInNavContainer], MethodInvocationException
    + FullyQualifiedErrorId : WebException,Compile-AppInNavContainer

Additional context
I think the Problem is maybe around here: https://github.com/microsoft/navcontainerhelper/blob/5441d2b2e31307d99ec097b813f7321d361026e3/AppHandling/Compile-AppInNavContainer.ps1#L289
Currently publisher and name of the app will always be compared. The problem could be solved by not checking the publisher when the app is called "Application", right?

I think you are right.
Have you tried to set Publisher to Microsoft (of the Application.app)? - then I would assume it works and the propagated dependencies should be loaded.

You're right. If I change Publisher of Application App to "Microsoft" everything works fine.
But it should also work with a custom Publisher, isn't it?

It should. but in the meeting yesterday, I heard for the first time that the recommendation was to change the publisher of the Application App as well:-(
I will fix the containerhelper, but in the meantime, you can keep the publisher as Microsoft for the Application App only.

that's what I'm going to do. I'm just asked again to make sure we got it right. :)
THX

We will keep this issue open so you can see when this is fixed in NavContainerHelper

Shipped in <IP_ADDRESS>


Add links to genes in the phylogenic tree

Hello,
I'd like to add links to existing genes in the phylogenic tree view.
As far as I know, on the GNB side, we have a list of existing genes associated with a specific tree, so it should be fairly simple:

When reaching an end node, check if the name is in the set of genes
If yes, replace the name in the graph by an link pointing to the gene (or an onclick -> Redirect...)

It would be done by passing two optional props to the tree : a set of genes, and a base url to build the url.

Might be better to pass a Dict with the gene_id as key and the url as value, and manage the url construction on the GNB side

Another issue is that we store the gene_id, but in the tree it might have a prefix, so it will not match directly

My idea for this would be that the Tree component takes an optional LeafNode component argument, so that any customization (like having linkouts) can be implemented on the user side.

Agreed, a custom callable would be more flexible. (and would avoid having to update this lib every time we need to add something in GNB)
I also agree on the 'user need to validate the data'. (Plus it's acceptable to just render the name if the gene is not in the DB I think)

Indeed, one of the reasons I moved this out of the genenotebook code base is that I use it in other projects as well.

Implemented in https://github.com/genenotebook/react-bio-viz/commit/f720386c46cf6fe0d6bcf4998f41a45046ed9bdd

Alright, closing the issue here since it's now a GNB-side issue


[MEDIUM] Axios Cross-Site Request Forgery Vulnerability

Github reported a new dependabot security alert at: https://github.com/cdk8s-team/cdk8s-redis/security/dependabot/13

Stale


do not allow to edit an app if it's not running latest Platformatic

We should also explain why the "edit" is blocked.  in some form.

Sounds good to me. Besides disabling the button, the only addition we should make to the design is to state clearly that the Platformatic Version needs to be updated to edit an application. We should go for the following solution:

CC: @marcopiraccini @mcollina

@mcollina just one point. Currently we don't know which version is running Platformatic until...it's running.  In other words, if an application has never started we don't know the version (which is actually the "last known version" really), which will be any version semver compatible with the dependency in package.json.  This is because we currently get the info of the version from the runtime APIs (which is OK becasue this will work also remotely).
I see three options here:

We disable the button in the case we don't know the version
When we click on "edit" we check the current ACTUAL installed version (with npm ls ) given that fact that if we edit the app it MUST be local.

We disable the button in the case we don't know the version

If the last known version was old, I would show the button. If we don't know it, we don't show the warning at all.

When we click on "edit" we check the current ACTUAL installed version (with npm ls ) given that fact that if we edit the app it MUST be local.

The button must be for local-only apps.
Note a npm ls might not be enough because yarn or pnpm would require different commands.

Hi @mcollina
I'm closing this one because the described behavior (my last comment) it's already on meraki 1.0.1.
Reopen the issue if the solution doesn't match requirements.


[Event Request] OnAfterNoOnAfterValidate on Pages 46, 47, 54, 55, 95-98, 508,510 , 6651, 6661

Please enter a new Event trigger OnAfterNoOnAfterValidate in the corrsponding subpages, so that we can react on the Event before other Code execution is done later:
LOCAL NoOnAfterValidate()
InsertExtendedText(FALSE);
IF (Type = Type::"Charge (Item)") AND ("No." <> xRec."No.") AND
(xRec."No." <> '')
THEN
CurrPage.SAVERECORD;
SaveAndAutoAsmToOrder;
IF Reserve = Reserve::Always THEN BEGIN
CurrPage.SAVERECORD;
IF ("Outstanding Qty. (Base)" <> 0) AND ("No." <> xRec."No.") THEN BEGIN
AutoReserve;
CurrPage.UPDATE(FALSE);
END;
END;
//++++++++++++++++++++++++++++++++++++++
OnAfterNoOnAfterValidate(VAR rec);
//--------------------------------------

Thanks for reporting this. We agree, and we’ll publish a fix asap, either in an update for the current version or in the next major release. We will update this issue with information about availability.

Thanks for reporting this. We agree, and we’ll publish a fix asap, either in an update for the current version or in the next major release. We will update this issue with information about availability.


Map Point and Select Point Tools broken after Pro build 2.4.19824

The CC Map Point and Select Point Tools seem to be broken on Pro builds after 2.4.19843
Repro steps:

Install Pro  2.4.19824 or later
Install CC Addin
Attempt to use either the Map Point or Select Point Tools
Click on the map, the cursor changes to the cursor below (instead of the correct Tool crosshair cursor) and the map just flashes white when clicked on

Cursor:

@ljuru and @dfoll noticed this testing. Tested on ArcGISPro.2.4.19843 -  ArcGISPro2.4.19854
Research so far:

I traced the problem down to the Tool's OverlayControl no longer working.
I tested the SDK Tool Overlay sample and this is working fine:
https://github.com/Esri/arcgis-pro-sdk-community-samples/tree/master/Map-Exploration/MapToolWithOverlayControl (but this sample is much simpler than what we have going on with the CC Tool's Flash Animation)
At this point, I'm still not sure what recent Pro change may have broken this so we may need some support from Core on this

Update: after some investigation, it appears that the cursor shown
is a spurious resize cursor for the the Tool's Overlay - but OverlayControlCanResize = false so not sure why this cursor is now showing up and intercepting map clicks, seems like a new SDK bug.

Emailed Core with OverlayControl issue:
After Pro Build 2.4.19843 (5/21), the MapTool OverlayControl now always shows a resize cursor and intercepts our mouse clicks (so no map clicks make it to the tool).

OverlayControlCanResize = false so not sure why this resize behavior and cursor is now showing up in Pro 2.4 and intercepting map clicks, seems like possibly a new bug.

We've had some back-and-forth with the SDK team to try to explain the issue and determine the cause.  @ljuru determined that the coordinate map tool stopped working between builds 19823 (worked) and 19824 (stopped working) so the SDK team is going to see what may have changed between these builds to affect this.

The SDK Team was extremely helpful in helping us to identify what was happening with the Map Tool Embedded Control Overlay.
Just to summarize the discussions:

The Map Tool Embedded Control Overlay was never really intended to be used the way we are using it, as a Canvas that covers the map and allows mouse clicks to be passed through,
a. The reason ours worked was just a coincidence of timing that set the overlay size to 0,0 at startup (because the View was not yet visible), a bug fix at 2.4 changed this sequence so the view was visible and the full size of the canvas was correctly being set
At Pro 2.1 another more general purpose control was added the MapView Overlay Control, but we found that this too intercepts mouse clicks - so a change is being added to 2.5 to allow mouse clicks through to the map if the control is not hit test visible - to support this case of a full map overlay that also has map interaction.

So for now, the least risky approach was for us to just make a minor tweak to restore the control/canvas to its pre 2.4 behavior (return a size of 0,0, until we want to play the animation)
This change/fix was added in PR #613 (tested on 2.2 and 2.4 Beta 2) and ready for QC

tested the map point tool and flashing on Pro 2.2, 2.3 and 2.4 build number: 19921


Returning a custom response code

Question about GraphQL Shield
I've looked in the docs as well as googling to my best ablities about this, but forgive me if I missed it.
I'm looking at returning a custom error response from my graphql api. I'm aware that I can return a custom error message inside my rules, however despite the error message, the response from my API will always be 200. How do I return my error so that is contains a 401 response code?

I think that depends on your client. As far as I know, Apollo only returns 400 if there was a connection problem or something similar. GraphQL's error reponse still counts as 200, but I might be wrong.

Hey so, I was messing around with something completely unrelated, and figured out how to achieve this with Qraphql Yoga.
The trick is to just make sure you have access to the response object in context:
new GraphQLServer({
  schema,
  context: ({request, response}) => {
    return {
      req: request,
      res: response,
    }
  }),
  middlewares: [permissions],
}).start(() =>
  console.log(
    `🚀 Server ready at: http://localhost:4000\n⭐ See sample queries: http://pris.ly/e/ts/graphql-auth#using-the-graphql-api`,
  ),
)

Then you should just be able to access the context from your rules:
  isAuthenticatedUser: rule()(async (parent, args, context) => {
    const userId = getUserId(context)
    if (!userId)
        context.res.status(401)
    return Boolean(userId)
  }),

This should break any of the existing rules, but should change the response status as well.

Oh wow! This is really cool! Thank you for sharing it.


Links in Readme.md are broken

Hi there, I am new to ydn-db.
I noticed the links in the Read.me are broken.
https://yathit.github.io/ydn-db/getting-started.html - for example.

Thank you. I have fixed it now.


One Piece Pirate Warriors 3 fails to start

Please describe your issue as accurately as possible. If you run into a problem with a binary release, make sure to test with latest master as well.
Important: When reporting an issue with a specific game or application, such as crashes or rendering issues, please include log files and a D3D11 Apitrace (see https://github.com/apitrace/apitrace) so that the issue can be reproduced. In order to create a trace, run wine apitrace.exe trace -a dxgi YOURGAME.exe. DO NOT use DXVK together with apitrace!
Software information
One Piece Pirate Warriors 3 (Steam)
System information

GPU: GeForce GTX 960
Driver: Nvidia 430.14.0
Wine version: Wine TKG 4.8
DXVK version: https://github.com/Joshua-Ashton/d9vk/commit/58669173dd95f00e800ce28f3caf03dd18512426

Apitrace file(s)
https://drive.google.com/file/d/1vs87TTatDP9mpyo9eDxMmMpQQMZi91U_/view?usp=sharing
Log files

d3d9.log:
oppw3_d3d9.log

Game crashes with a gray screen almost instantly after loading. I pasted the errors from the terminal into the d3d9 log. Please let me know if I can improve this bug report.
EDIT: Replaced the trace file with a native Windows one.

err:   D3D9: GetBackBuffer: iBackBuffer > 0 not supported

Yeah this'd cause it. I'll see what I can do to work around this

Can you try on the getbackbuffer-hack branch and see what affect this has?

Alright, I'll try when I get a chance.

So it doesn't crash immediately now, but it only displays a black screen. Audio plays and controller input is accepted. The console is spammed by apitrace's "warning: caught exception 0xc0000005", "flushing trace", and "D3D9: GetBackBuffer: iBackBuffer > 0 queried. Returning index 0."
Here is the updated trace and log, if you're curious.
oppw3_d3d9_getbackbuffer_hack.log
Trace:
https://drive.google.com/file/d/1v8bY7ZKWsfXwr6xZeL6ut2xH2rC43bzW/view?usp=sharing

I changed the trace file in the description to one obtained from Windows, if that's helpful.

The apitrace plays back well with the latest master, but I don't know if you want me to delay closing the bug until the backbuffer stuff gets merged in.

So, I tried running the actual game, and it still seems to crash almost instantly. The apitrace still works well (albeit with the backbuffer warnings), so I'm not sure what's going on. I'm using a 32-bit prefix, just in case, but the same thing happened with the 64-bit prefix. Also, I haven't tried it with Proton recently, if that makes a difference.
d3d9.log:
oppw3_d3d9.log
trace:
https://drive.google.com/file/d/18oywHbJhIeCwhLwa7M1MXYRyKliC83z2/view?usp=sharing

Also, I haven't tried it with Proton recently, if that makes a difference.

There is a bug with Proton 4.11: https://www.protondb.com/app/331600
If you want to try, use 4.2.
On my side, tested with #793 and the issue is still the same.

@NerosTie Good to know. I usually compile proton-tkg, but sometimes something goes wrong and I have to use an official version, so it's helpful knowing which ones work and which don't.


Bugfix : add missing link to libscopmath

libscopmath.a was linked to libcorenrnmech with shared library
but was missing in case of static library
ar doesnt provide way to link two static libraries together.
Hence extrat objects and then combined those together.

fixes #303 #306

Interesting that travis CI is showing:
 Simulation Statistics
1861 Number of cells: 20
1862 Number of compartments: 804
1863 Number of presyns: 21
1864 Number of input presyns: 20
1865 Number of synapses: 21
1866 Number of point processes: 41
1867 Number of transfer (gap) targets: 0
1868 Number of spikes: 37
1869 Number of spikes with non negative gid-s: 37
1870
1871
1872[Traviss-Mac:63157] *** Process received signal ***
1873[Traviss-Mac:63157] Signal: Segmentation fault: 11 (11)
1874[Traviss-Mac:63157] Signal code: Address not mapped (1)
1875[Traviss-Mac:63157] Failing at address: 0x0
1876[Traviss-Mac:63157] [ 0] 0   libsystem_platform.dylib            0x00007fff7afb5b5d _sigtramp + 29
1877[Traviss-Mac:63157] [ 1] 0   ???                                 0x000070000043a6f0 0x0 +<PHONE_NUMBER>44560
1878[Traviss-Mac:63157] [ 2] 0   mca_rml_oob.so                      0x000000010ca55db0 orte_rml_oob_send_buffer_nb + 942
1879[Traviss-Mac:63157] [ 3] 0   libopen-rte.40.dylib                0x000000010be419c7 pmix_server_log_fn + 308
1880[Traviss-Mac:63157] [ 4] 0   mca_pmix_pmix3x.so                  0x000000010c8dd563 server_log + 850
1881[Traviss-Mac:63157] [ 5] 0   mca_plog_default.so                 0x000000010ca13846 mylog + 503
1882[Traviss-Mac:63157] [ 6] 0   mca_pmix_pmix3x.so                  0x000000010c95a08f pmix_plog_base_log + 1015
1883[Traviss-Mac:63157] [ 7] 0   mca_pmix_pmix3x.so                  0x000000010c924ff2 pmix_server_log + 2059
1884[Traviss-Mac:63157] [ 8] 0   mca_pmix_pmix3x.so                  0x000000010c90bcbb pmix_server_message_handler + 5279
1885[Traviss-Mac:63157] [ 9] 0   mca_pmix_pmix3x.so                  0x000000010c9626e3 OPAL_MCA_PMIX3X_pmix_ptl_base_process_msg + 735
1886[Traviss-Mac:63157] [10] 0   libevent-2.1.7.dylib                0x000000010bf8b2e6 event_process_active_single_queue + 633
1887[Traviss-Mac:63157] [11] 0   libevent-2.1.7.dylib                0x000000010bf886ba event_base_loop + 1062
1888[Traviss-Mac:63157] [12] 0   mca_pmix_pmix3x.so                  0x000000010c930338 progress_engine + 26
1889[Traviss-Mac:63157] [13] 0   libsystem_pthread.dylib             0x00007fff7afbe2eb _pthread_body + 126
1890[Traviss-Mac:63157] [14] 0   libsystem_pthread.dylib             0x00007fff7afc1249 _pthread_start + 66
1891[Traviss-Mac:63157] [15] 0   libsystem_pthread.dylib             0x00007fff7afbd40d thread_start + 13
1892[Traviss-Mac:63157] *** End of error message ***
1893/Users/travis/build/BlueBrain/CoreNeuron/build/tests/integration/ring_permute2/integration_test.sh: line 13: 63157 Segmentation fault: 11  /usr/local/bin/mpiexec -n 2 $SRUN_EXTRA /Users/travis/build/BlueBrain/CoreNeuron/build/bin/x86_64/special-core --datpath /Users/travis/build/BlueBrain/CoreNeuron/tests/integration/ring --tstop 100. --celsius 6.3 --mpi --outpath /Users/travis/build/BlueBrain/CoreNeuron/build/tests/integration/ring_permute2 --cell-permute 2
1894Error status value: 139

I will take a look!

Couldn't reproduce the issue again on travis or locally with valgrind. As we are not changing any MPI logic in this PR, I will go ahead with the merge.