nixos/plasma: use upstream xsession/wayland files

Motivation for this change
An updated version of https://github.com/NixOS/nixpkgs/pull/56988
Wayland still does not work and ~/.local/share/sddm/wayland-session.log is empty after a failed Wayland login,as journalctl -u display-manager.
I will fix the override after making Wayland work
Things done

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
Built on platform(s)

[ ] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[ ] Ensured that relevant documentation is up to date
[ ] Fits CONTRIBUTING.md.

So the wayland session still quit on startup,but now it does not seem to leave any traces,whether in the journal nor in ~/.local/share/sddm/wayland-session.log `.
@worldofpeace any ideas why?

Maybe the description of #44139 will help?

The wayland entry is present in sddm,but does not work.
Still ,I need to check with QT_DEBUG_PLUGINS=1;QML_IMPORT_TRACE=1;

Also need to check for wrapQtApps

@hameerabbasi Checked with the suggested patch,still not working,got in .local/share/sddm/wayland-session.log ;
dbus-daemon[16640]: [session uid=1001 pid=16640] Activating service name='org.freedesktop.systemd1' requested by ':1.0' (uid=1001 pid=16644 comm="/nix/store/90n7mvl7n0zl98wx0jjx2syfma34xhka-dbus-1" label="kernel")
dbus-daemon[16640]: [session uid=1001 pid=16640] Activated service 'org.freedesktop.systemd1' failed: Process org.freedesktop.systemd1 exited with status 1
dbus-update-activation-environment: warning: error sending to systemd: org.freedesktop.DBus.Error.Spawn.ChildExited: Process org.freedesktop.systemd1 exited with status 1
qt.qpa.plugin: Could not load the Qt platform plugin "wayland-org.kde.kwin.qpa" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: wayland-org.kde.kwin.qpa, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb.

"/nix/store/bkdyka5fa5f707a6hvx8l6v2s37wvwvd-kwin-5.18.5-bin/bin/kwin_wayland" ("--xwayland", "--libinput", "--exit-with-session=/nix/store/2vqimab57z8f8cpbzkax9cwnb1rl997j-plasma-workspace-5.18.5/libexec/startplasma-waylandsession") exited with code 6
startplasmacompositor: Shutting down...
startplasmacompositor: Done.

@pasqui23 see https://github.com/NixOS/nixpkgs/issues/43757#issuecomment-618710712
Specifically, env KWIN_FORCE_OWN_QPA=1 kwin_wayland --version fixes this particular error for me.

@matklad adding said variable to environment.sessionVariables still does not fix it for me

Adding KWIN_FORCE_OWN_QPA=1 and increasing limit (0004-start_kdeinit-environ-hard-limit.patch) to 1<<20 makes startplasma_wayland work for me

For anyone wondering: plasma on wayland is not quite stable on NixOS, screenshots can't be taken because of X-KDE-DBUS-Restricted-Interfaces attribute absence, and plasmashell has some bugs (Task manager shows no apps) because of same reason

And finally the wayland session works!

I can confirm that this works when rebased onto nixos-unstable (see 0835411ea6ee199fb13fa0e68b60323430706459, I had to resolve a merge conflict).

I can confirm that this works when rebased onto nixos-unstable (see 0835411ea6ee199fb13fa0e68b60323430706459, I had to resolve a merge conflict).

Also want to mention that we don't have testing for the plasma5 wayland session... but this isn't a straightforward task so I'd be fine if it's not committed in this pull request. However we will need a release note highlight.

Also want to mention that we don't have testing for the plasma5 wayland session... but this isn't a straightforward task so I'd be fine if it's not committed in this pull request. However we will need a release note highlight.

Also, a weird issue occurs when using the wayland session: sometimes the right click menu appears as a new window,complete with titlebar decoration.

For curiosity, is kwin's src/plugins directory built by nixpkgs?

I've applied this to my nixpkgs and am currently using the wayland session. Very exciting, thank you for working on this!

I'm gonna rebase, write a release note, and then open an issue to get a wayland test.

I've been trying this in a VM but it wasn't working for me... Need to investigate, but I'm wondering if anyone in the thread was testing in a VM. It's relevant because this module handles setup that, if regressed, won't be apparent right away without a clean state.

No,I haven't test it in a VM @worldofpeace .

If I understand the question, it is possible (and indeed likely) that I had not previously run Plasma on this computer, so I wouldn't have had existing state to migrate or anything. I don't normally use Plasma so I wouldn't be able to test much more extensively, personally.

I have tested it on my pc with my personal plasma configuration.
It does not look like it has most problems besides the one I've mentioned.
As I've said the setup is now handled in services.xserver.displayManager.setupCommands, which only xinit and xpra do not respect.

Tested on my PC. It almost works but still have some critical issues for daily use.

Task Manager/Taskbar failed to list windows opened. It shows nothing but pinned buttons. I can only switch between windows by Alt-Tab. Other components/widgets work fine.
Input method doesn't work.
services.xserver.dpi is ignored. Not sure if this is intended. Is there any replacement option for wayland?
Some KDE settings are lost and reset to the default, including mouse speed, animation speed and all shortcuts.
Screenshot (Spectacle) doesn't work. Printed Error: Could not take a screenshot. Here's the console log. Not sure if it's an issue of spectacle or plasma.

Error calling KWin DBus interface: "org.kde.kwin.Screenshot.Error.NoAuthorized" "The process is not authorized to take a screenshot"
QPixmap::scaled: Pixmap is a null pixmap
qt.qpa.wayland: Wayland does not support QWindow::requestActivate()
qt.qpa.wayland: Wayland does not support QWindow::requestActivate()

I have what I think is a working solution for a couple of your issues I'm cleaning up, @oxalica. I'll ping this issue with the PR proposing the changes.

@oxalica try with pipewire enabled for the screenshot issue

Finally I got things to work.

Input method doesn't work.

It can be fixed by manually set QT_IM_MODULE. All environment.variables are not set in wayland session, since /etc/profile is not respected.
Isn't start script running in a login shell? Do we need to manually source it here?

services.xserver.dpi is ignored. Not sure if this is intended. Is there any replacement option for wayland?

Setting forceFontDPIWayland=144 under [General] section in ~/.config/kcmfonts fixes it. startplasma-wayland will read this value and set QT_WAYLAND_FORCE_DPI for all programs (See code).
@pasqui23

try with pipewire enabled for the screenshot issue

It's fixed by #116549 without pipewire.

After #110536, the analog/digital clock widget got broken on (only) ayland. :cry:
Note that time of analog clock is incorrect and fixed. The digital clock is below the analog clock and it shows nothing.

Guys, I'm spamming some of the old KDE wayland issues/PRs to ensure we get some testers. This comment is written from a plasma wayland session spawned from sddm after applying this PR (and the one-liner mentioned in a comment) which basically gets it going: https://github.com/NixOS/nixpkgs/pull/117102

@peterhoeg which one-liner?
And you didn't hit anything not working without #116549?

@peterhoeg which one-liner?

I have updated the PR's first post with all the details, but basically you just need to point sddm at the directory with the wayland sessions:
services.xserver.displayManager.sddm.settings.Wayland.SessionDir =
  "${pkgs.plasma5Packages.plasma-workspace}/share/wayland-sessions";

And you didn't hit anything not working without #116549?

The pager doesn't show icons for the running applications but otherwise no, not
really. It's not possible for me to use as a daily driver though until I sort out the
custom keyboard mappings, but that's not Plasma's fault.

@samueldr , reading your linked PR, I'm guessing this is why the pager/task manager do not show any icons.

@samueldr - with your PR the task manager/pager both work! hidpi support is still horrible  so I can't really try it out until I'm on a desktop again.

@pasqui23, when using systemd to manage the session (necessary patches are in master but haven't hit unstable yet), I can use the upstream sessions for both x11 and wayland without modification:
services.xserver.displayManager.sddm.settings.X11.SessionDir =
  "${pkgs.plasma5Packages.plasma-workspace}/share/xsessions";

services.xserver.displayManager.sddm.settings.Wayland.SessionDir =
  "${pkgs.plasma5Packages.plasma-workspace}/share/wayland-sessions";

This is admittedly only tried out with a user that already has everything set up, so I don't know if things will break without all the setup handled by our currect launcher script. That just needs to be tested.
But this got me thinking. Now that both GNOME and KDE use systemd, we could also start running these various scripts through systemd which of course also allows to share them in a cleaner way.
First we ensure that plasma uses systemd:
systemd.user.services = {
  plasma-run-with-systemd = {
    description = "Run via systemd";
    wantedBy = [ "basic.target" ];
    environment.XDG_CONFIG_HOME = "$HOME/.config";
    serviceConfig.Type = "oneshot";
    script = ''
      set -eEuo pipefail

      # use systemd to manage the session
      echo -e "[General]\nsystemdBoot=true" > $XDG_CONFIG_HOME/startkderc
    '';
  };

Then we run what is currently handled in our session wrapper script:
  plasma-early-setup = {
    description = "Early Plasma setup";
    wantedBy = [ "graphical-session-pre.target" ];
    environment = {
      XDG_CACHE_HOME = "$HOME/.cache";
      XDG_CONFIG_HOME = "$HOME/.config";
    };
    serviceConfig.Type = "oneshot";
    script = ''
      set -eEuo pipefail

      # The KDE icon cache is supposed to update itself automatically, but it uses
      # the timestamp on the icon theme directory as a trigger. This doesn't work
      # on NixOS because the timestamp never changes. As a workaround, delete the
      # icon cache at login and session activation.
      # See also: http://lists-archives.org/kde-devel/26175-what-when-will-icon-cache-refresh.html
      rm -fv $XDG_CACHE_HOME/icon-cache.kcache

      # xdg-desktop-settings generates this empty file but
      # it makes kbuildsyscoca5 fail silently. To fix this
      # remove that menu if it exists.
      rm -fv ''${XDG_CONFIG_HOME}/menus/applications-merged/xdg-desktop-menu-dummy.menu

      # Qt writes a weird ‘libraryPath’ line to
      # ~/.config/Trolltech.conf that causes the KDE plugin
      # paths of previous KDE invocations to be searched.
      # Obviously using mismatching KDE libraries is potentially
      # disastrous, so here we nuke references to the Nix store
      # in Trolltech.conf.  A better solution would be to stop
      # Qt from doing this wackiness in the first place.
      trolltech_conf="''${XDG_CONFIG_HOME}/Trolltech.conf"
      if [ -e "$trolltech_conf" ]; then
        ${pkgs.gnused}/bin/sed -i "$trolltech_conf" -e '/nix\\store\|nix\/store/ d'
      fi

      # Remove the kbuildsyscoca5 cache. It will be regenerated
      # immediately after. This is necessary for kbuildsyscoca5 to
      # recognize that software that has been removed.
      rm -fv $XDG_CACHE_HOME/ksycoca*

    ${pkgs.plasma5Packages.kservice}/bin/kbuildsycoca5
    '';
  };
};

Something like the trolltech.conf patching could also be split into a separate
unit as it applies to all environments in which people could possibly run qt
applications. So one way to deal with this would be to define a
graphical-early-setup.service for generic stuff and
plasma-early-setup.service, gnome-early-setup.service, etc.

@peterhoeg please add this issue to the wayland project

This could use a rebase

@SuperSandro2000 rebased this branch onto master

Now that https://github.com/NixOS/nixpkgs/issues/118650 is fixed, let's merge this so that we can land Plasma Wayland by 21.11

While #118650 fixed with most bugs resolved, #139459 should also be merged before stabilizing plasma wayland session
This patch changes detected app ids, and in case if someone adds window rules before applying this patch - those rules will be broken after merge

@peterhoeg can we merge this?

Yes please!

Ok I've done it @peterhoeg

This change wasn't converted from markdown to docbook and broke eval on staging-next. This was already visible on the CI changes on this pull request.
https://github.com/NixOS/nixpkgs/runs/3863386514

This change wasn't converted from markdown to docbook and broke eval on staging-next. This was already visible on the CI changes on this pull request.
https://github.com/NixOS/nixpkgs/runs/3863386514

fixed in #141818

I believe this regressed the clock widget of plasma on Xorg. Can somebody verify please? I bisected to this particular PR. Will test a revert of it shortly.

@pasqui23 @peterhoeg @oxalica What do you think?

klauncher does not have __NIXOS_SET_ENVIRONMENT_DONE set for me on wayland.

Well, that is not working for bash.
- The option definition `programs.bash.enable' in `/etc/nixos/configuration.nix' no longer has any effect; please remove it.

@mohe2015
Could you try running kwriteconfig5 --file startkderc --group General --key systemdBoot true and relogin? This enables "run with systemd mode" for plasma. Maybe it can fix environment variables.


which page of Carl Book does the equation of P8 line 2 follow from?

which page of "A Practical Guide to Splines (revised ed., Carl De Boor 1978)" [red box] does the equation [green box] of P8 line 2 in your paper follow from? Frankly, I have difficult to find the similar Equation in Carl's Book.
Could you give me a hand ?

it's a new result from our paper


some function of MonsterHunterRise cant be hooked.

can comfirm: object "snow.player.PlayerQuestBase" 's function "getAdjustActionAttack" cant be hooked.
can confirm the function has been called by cheat engine's break point.

Upload your re2_framework_log.txt please.

re2_framework_log.zip

This is from my end using getAdjustActionAttack hook
[2023-06-15 10:01:59.538] [REFramework] [info] [ScriptRunner] Module path C:\Program Files (x86)\Steam\steamapps\common\MonsterHunterRise\MonsterHunterRise.exe
[2023-06-15 10:01:59.538] [REFramework] [info] [ScriptRunner] Creating directories C:\Program Files (x86)\Steam\steamapps\common\MonsterHunterRise\reframework\autorun
[2023-06-15 10:01:59.538] [REFramework] [info] [ScriptRunner] Loading scripts...
[2023-06-15 10:01:59.538] [REFramework] [info] [ScriptState] Running script C:\Program Files (x86)\Steam\steamapps\common\MonsterHunterRise\reframework\autorun\HBGNormalLv3Cheat.lua...
[2023-06-15 10:01:59.539] [REFramework] [info] About to create a weak table for usertype int __cdecl sol_lua_push<struct sdk::RETypeDefinition>(struct sol::types<struct sdk::RETypeDefinition *>,struct lua_State *,struct sdk::RETypeDefinition *)
[2023-06-15 10:01:59.539] [REFramework] [info] Created a weak table for usertype int __cdecl sol_lua_push<struct sdk::RETypeDefinition>(struct sol::types<struct sdk::RETypeDefinition *>,struct lua_State *,struct sdk::RETypeDefinition *)
[2023-06-15 10:01:59.539] [REFramework] [info] About to create a weak table for usertype int __cdecl sol_lua_push<struct sdk::REMethodDefinition>(struct sol::types<struct sdk::REMethodDefinition *>,struct lua_State *,struct sdk::REMethodDefinition *)
[2023-06-15 10:01:59.539] [REFramework] [info] Created a weak table for usertype int __cdecl sol_lua_push<struct sdk::REMethodDefinition>(struct sol::types<struct sdk::REMethodDefinition *>,struct lua_State *,struct sdk::REMethodDefinition *)
[2023-06-15 10:01:59.569] [REFramework] [info] [HookManager] Using actual function @ 0x140cea310 for wrapper function @ 0x14065ee70
[2023-06-15 10:01:59.569] [REFramework] [info] [HookManager] Adding hook for 'getAdjustActionAttack' @ 0x140cea310...
[2023-06-15 10:01:59.569] [REFramework] [info] [HookManager] Reusing existing hook...
[2023-06-15 10:01:59.569] [REFramework] [info] [HookManager] Hook assigned ID 919
[2023-06-15 10:01:59.569] [REFramework] [info] [HookManager] Hook 919 added for 'getAdjustActionAttack' @ 0x140cea310

the log tells its hooking 0x140cea310 instead of wrapper function 0x14065ee70.
0x14065ee70 is snow.player.PlayerQuestBase.getAdjustActionAttack(snow.hit.userdata.PlHitAttackRSData, snow.CharacterBase) (a virtual function)
However 0x140cea310 is snow.enemy.EnemyGrappleParam.clear()
Which seems not related.

void* get_actual_function(void* possible_fn) {
    if (possible_fn == nullptr) {
        return nullptr;
    }

    auto actual_fn = possible_fn;
    auto ip = (uintptr_t)possible_fn;

    // Disassemble the first few instructions to see if there is a jmp to an actual function.
    for (auto i = 0; i < 10; ++i) {
        hde64s hde{};
        auto len = hde64_disasm((void*)ip, &hde);
        ip += len;

        if (hde.opcode == 0xE9) { // jmp.
            actual_fn = (void*)(ip + hde.imm.imm32);
            break;
        }
    }

    if (possible_fn != actual_fn) {
        spdlog::info("[HookManager] Using actual function @ {:p} for wrapper function @ {:p}", actual_fn, possible_fn);
    }

    return actual_fn;
}

if I return the possible_fn directly, the method hook is worked.
Here is the instruction of this getAdjustActionAttack method

A workaround to this is to set ignore_jmp parameter to true when calling sdk.hook. I'll see if I can modify get_actual_function to check if control flow ends abruptly.

i think this isuue is because the function get_actual_function checking jmp(0xE9) in 10 lines of asm, but after getAdjustActionAttack  9 lines there's a jmp. so in get_actual_function maybe need a check for ret(0xC3).

Should be fixed in 322f513d581911749894153f5d1849eeafb71790


Publish-BcContainerApp fails with "The remote server returned an error: (403) Forbidden.”

Hello,
using the following script to publish App to a sandbox environment we return error 403:
$authContext = New-BcAuthContext -refreshToken XXXXX
$saasEnvironment = "sandbox"

[string[]]$apps = Get-ChildItem 'XXXX' -Recurse -filter "*_SAAS.app" -Exclude "*Test*"
Publish-BcContainerApp -appFile $apps -bcAuthContext $authcontext -environment $saasEnvironment -syncMode ForceSync

That is the output:
Der Remoteserver hat einen Fehler zurückgegeben: (403) Unzulässig.  (ms-correlation-x = 2a3ee4f0-34ba-441f-a72d-f07439d029eb)
In C:\Program Files\WindowsPowerShell\Modules\BcContainerHelper\2.0.5\BcSaaS\Get-BcEnvironments.ps1:29 Zeichen:9
+         throw (GetExtenedErrorMessage $_.Exception)
+         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : OperationStopped: (Der Remoteserve...d-f07439d029eb):String) [], RuntimeException
    + FullyQualifiedErrorId : Der Remoteserver hat einen Fehler zurückgegeben: (403) Unzulässig.  (ms-correlation-x = 2a3ee4f0-34ba-441f-a72d-f07439d029eb)

Sorry for german language, had no time to switch language to english.
Any ideas what is wrong there?
Kind regards

Looks like the authcontext is wrong.
You cannot get environments.
New-BcAuthContext -devicelogin will give you ann authcontext - try with that.

Thanks for fast reply.
Unfortunately that was not the problem, also with a fresh AuthContext the error remains:
PS C:\Windows\system32> $authContext = New-BcAuthContext -includeDeviceLogin
$saasEnvironment = "sandbox"

[string[]]$apps = Get-ChildItem 'XXXX' -Recurse -filter "*_SAAS.app" -Exclude "*Test*"
Publish-BcContainerApp -appFile $apps -bcAuthContext $authcontext -environment $saasEnvironment -syncMode ForceSync
Attempting authentication to https://api.businesscentral.dynamics.com/Common using device login...
To sign in, use a web browser to open the page https://microsoft.com/devicelogin and enter the code DW7N4NC9K to authenticate.
Waiting for authentication...
Authenticated from xx.xx.xxx.xxx as user xxxxxxxxxxxxxxxx
Authenticated to common, using tenant id xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxx
Der Remoteserver hat einen Fehler zurückgegeben: (403) Unzulässig.  (ms-correlation-x = 3d9e6bea-cd75-4f56-ad2d-b37c3ae0d17f)
In C:\Program Files\WindowsPowerShell\Modules\BcContainerHelper\2.0.5\BcSaaS\Get-BcEnvironments.ps1:29 Zeichen:9
+         throw (GetExtenedErrorMessage $_.Exception)
+         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : OperationStopped: (Der Remoteserve...d-b37c3ae0d17f):String) [], RuntimeException
    + FullyQualifiedErrorId : Der Remoteserver hat einen Fehler zurückgegeben: (403) Unzulässig.  (ms-correlation-x = 3d9e6bea-cd75-4f56-ad2d-b37c3ae0d17f)

Could you email me the hidden info here - user etc.

The issue here is that the Publish-BcContainerApp function uses Get-BcEnvironment to test whether the environment passed exists.
Get-BcEnvironment needs delegated admin permissions.
Publishing to dev endpoint doesn't
I will remove the test. If the environment doesn't exist, it will fail on publishing anyway.

Shipped in 2.0.6-preview355

Shipped in BcContainerHelper 2.0.6


Install to prefix/lib; use Release build type

Checklist

[x] Used a fork of the feedstock to propose changes
[x] Bumped the build number (if the version is unchanged)
[ ] Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
[x] Ensured the license file is being packaged.

Change the installation dir from /usr/lib64 to /usr/lib. Also, use Release build type to enhance performance.

Hi! This is the friendly automated conda-forge-linting service.
I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

@conda-forge-admin, please rerender


Per project downloadable expression matrix files

Allow use to select expression matrix data output format (Loom, ??)
Pass input files via Collections interface or ???
Possibly genes tab for parameterizing Matrix service

Metadata (across bundles; potentially provided directly by Query Module). These types of filters will enable users to select cells based on their biological characteristics, for example, all kidney cells, or all cells prepared using the 10x v2 assay.
Numerical filtering (on gene expression values, and also QC metrics). These types of filters will, for example, enable users to query for cells according to their expression of key marker genes, or exclude cells with low quality scores.

┆Issue Number: HCAB-315

To allow browser download of related matrix input files see https://github.com/HumanCellAtlas/metadata-schema/issues/623.

See also:
https://app.zenhub.com/workspaces/dcp-5ac7bcf9465cb172b77760d9/issues/humancellatlas/matrix-service/291
https://app.zenhub.com/workspaces/dcp-5ac7bcf9465cb172b77760d9/issues/humancellatlas/matrix-service/292

Blocked by https://app.zenhub.com/workspaces/dcp-5ac7bcf9465cb172b77760d9/issues/humancellatlas/matrix-service/293


Transition flickering

Check that this is really a bug

[X] I confirm

Reproduction link
https://codesandbox.io/s/loving-star-wni617?file=/index.html
Bug description
Transition flickering chrome
Expected Behavior
No response
Actual Behavior
No response
Swiper version
9.0.0
Platform/Target and Browser Versions
Windows Chrome 110.0.5481.178
Validations

[X] Follow our Code of Conduct
[X] Read the docs.
[X] Check that there isn't already an issue that request the same feature to avoid creating a duplicate.
[X] Make sure this is a Swiper issue and not a framework-specific issue

Would you like to open a PR for this bug?

[X] I'm willing to open a PR

Your issue is closed because it is not filled correctly. Before you open an issue please review the contributing guideline.
Please fill the issue template correctly and:

Clearly describe the issue including steps to reproduce when it is a bug.
Make sure you fill in the earliest version that you know has the issue.
Provide live link or JSFiddle/Codepen or website with isssue

It will save a lot of time for other contributors to check your issue and fix it.


FIX: plot pattern and filter average param

Adding in Average parameter to plot_patterns and plot_filters
cc: @kingjr

thanks @kdoelling1919 !


make -j10 error

Hello,
I tried to install your library on my Ubuntu 22.04 machine with CUDA 11.8. I reached all the way to command make -j10 however, I got the following error and I'm not sure how to resolve it since I didn't find any solutions online:
[ 98%] Linking CXX executable ../../bin/viewer
/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>collect2: error: ld returned 1 exit status
make[2]: *** [src/apps/CMakeFiles/viewer.dir/build.make:141: bin/viewer] Error 1
make[1]: *** [CMakeFiles/Makefile2:2898: src/apps/CMakeFiles/viewer.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[100%] Linking CXX executable ../../bin/train
/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>/usr/bin/ld: /home/hadil/Work/TRIPS/External/libtorch/lib/libtorch_cuda.so: undefined reference to<EMAIL_ADDRESS>collect2: error: ld returned 1 exit status
make[2]: *** [src/apps/CMakeFiles/train.dir/build.make:141: bin/train] Error 1
make[1]: *** [CMakeFiles/Makefile2:2861: src/apps/CMakeFiles/train.dir/all] Error 2
make: *** [Makefile:156: all] Error 2

Can you please advise? I'd be happy to share any additional information you may need.

Hi,
looks like some cuda methods are not linked correctly. Can you retry the build with this block here:
conda activate trips

export CONDA=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
export CC=gcc-9
export CXX=g++-9
export CUDAHOSTCXX=g++-9

unset CUDA_HOME

mkdir build
cd build

cmake -DCMAKE_PREFIX_PATH="./External/libtorch/;${CONDA}" ..

make -j10

and if that doesn't work, can you post the output of the cmake -DCMAKE_PREFIX_PATH="./External/libtorch/;${CONDA}" .. call?

Hi @lfranke thank you for getting back to me! I'm not sure what the issue was for me but I tried the installation from scratch and did the following changes:

Installed cudann manually by downloading the version I needed from the Nvidia Cudnn archives because I have CUDA 11.8 installed on my machine and I couldn't find a compatible cudnn version through conda (before I was installing through conda and that was downloading the cuda 11.1 toolkit which might have been causing conflict).
Noticed that conda install cmake=3.26.4 was giving an error due to dependencies conflicts so I just did conda install cmake and got it to install version 3.22.1.
Noticed the same issue as cmake with protobuf so I installed it by doing conda install protobuf (without specifying version) and got it to install version 3.20.3.
Not sure if this helped but i added the path to my installed cuda (/usr/local/cuda-11.8/bin and lib64) to the $CONDA path.

After making the above changes, I got make -j10 to just produce the error that you mentioned in your repo about @GLIBCXX_3.4.30. Did the fix that you suggested and everything worked perfectly.
I was able to run the viewer to see the train scene!


After a build is done, the new animation context menu of MGear 3.4 is not working and Maya viewport heads up display are gone

After any build the heads up display are gone from the viewport, and is impossible to bring them back. Just closing Maya and re open it will solve it.
The new feature of MGear 3.4 context menu isn't working either after a build has been done. I need to uncheck Mgear viewport menu and check it again to make it work
To Reproduce
Make a build
Screenshots

@nestorcolt which version of Maya are you on?
Thanks

@nestorcolt which version of Maya are you on?
Thanks


Inconsistency in matplotlib

Information

Qiskit Terra version:0.14.2
Python version:3.7.6
Operating system:Windows 10

What is the current behavior?
The current issue which can be seen from the file is that measuring q1 gives a broader arrow of 1 line instead of conventional 2 line narrower arrow.
Steps to reproduce the problem
It can be seen in the file
What is the expected behavior?
Suggested solutions
Checking the qiskit-terra file and looking for some bug in the matplot library section.

If this unintentional can someone assign it to me?

If you have the source, this has been fixed in the current master and the fix should also be in the next release.

ok thanks for informing.


missed a couple of spots in issue#137

Codecov Report

Merging #141 into master will decrease coverage by 1.6%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #141      +/-   ##
==========================================
- Coverage   92.86%   91.26%   -1.61%
==========================================
  Files          15       15
  Lines         561      561
==========================================
- Hits          521      512       -9
- Misses         40       49       +9

Impacted Files
Coverage Δ

dwave/system/samplers/dwave_sampler.py
70.52% <0%> (-4.22%)
:arrow_down:

dwave/system/flux_bias_offsets.py
81.48% <0%> (-3.71%)
:arrow_down:

dwave/system/composites/embedding.py
94.69% <0%> (-2.66%)
:arrow_down:

dwave/system/cache/database_manager.py
96.18% <0%> (-0.77%)
:arrow_down:

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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Fix interface of uncontrolled

This is motivated by the discussion on https://github.com/klarna/ui/pull/121#pullrequestreview-18855061
The new API for the uncontrolled would be:
uncontrolled({
  prop: 'value',
  defaultProp: 'defaultValue',
  handlers: {
    onChange: ({value: currentValue}) => (e) => e.target.value,
    onClear: () => () => '',
    onDoubleClick: ({value: currentValue}) => () => `${currentValue}${currentValue}`
  }
})(Input)

[ ] Documentation

Why put them under handlers Isn't that implied by the on prefix?

All documentations are incomplete and many names are rather incorrect. I will merge this and make another PR fixing that, I want to try out this solution in the consuming project.

Discussion for naming continues in here: https://github.com/klarna/higher-order-components/issues/9#issuecomment-276739545


Can you expand on why certain classes are ignored?

We've discovered the large set of ignored exceptions are swallowing some exceptions that we would very much like to hear about.
Some of these seem like exceptions that most people would want to know about, such as:

AbstractController::ActionNotFound one of my routes leads to an action I didn't find, I'd like to know about this
ActionController::InvalidAuthenticityToken if 90% of my users start seeing this error, I need to know about it
ActionController::ParameterMissing My front-end code and back-end code are out of sync, and my tests miss a code path, I need to know this
ActiveRecord::RecordNotFound if I use a find! to trigger an exception, I expect to be told when that find returns no records, especially if I manually Bugsnag.notify(...) the exception in a rescue

Can you expand in the documentation why these errors are the default set? As it stands I plan to reduce ignore_classes to [] so that all errors start showing up, but it would be useful to know why this set wound up containing all the things it contains.

+1 on this. There was an error that caused a template to blow up from an ActiveRecord::RecordNotFound, and I was hoping to have been notified by bugsnag instead of it being ignored. The ignore list caught me by surprise.

The answer seems to be somewhat lost to the mist. Going forward we shouldn't have these as defaults. It would be a breaking change to rethink this, but moving this kind of configuration into an option or a deliberate choice in a before_notify callback would prevent confusion.

We've moved all of the pre-existing ignore classes into a middleware that now marks them as info severity, meaning the default behaviour should be to report all errors and exceptions.


microsites

Codecov Report

Merging #75 into series/0.6.x will decrease coverage by 7.37%.
The diff coverage is n/a.

@@               Coverage Diff                @@
##           series/0.6.x      #75      +/-   ##
================================================
- Coverage         64.51%   57.14%   -7.38%
================================================
  Files                 9        9
  Lines               248      280      +32
  Branches             21       21
================================================
  Hits                160      160
- Misses               88      120      +32

Continue to review full report at Codecov.

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Add WAF through terraform

Describe the task
Create WAF ACLs using terraform, and add WAF to the cloudfront and api gateway and cognito
Acceptance Criteria

[ ] WAF ACLs has been created through terraform

One for Cloudfont with Global region, with 5 rules:
- Amazon IP reputation list (AWS-AWSManagedRulesAmazonIpReputationList)
- Core rule set (AWS-AWSManagedRulesCommonRuleSet)
- Known bad inputs (AWS-AWSManagedRulesKnownBadInputsRuleSet)
- Linux operating system (AWS-AWSManagedRulesLinuxRuleSet)
- SQL database (AWS-AWSManagedRulesSQLiRuleSet)
One for Api Gateway with Canada region, with the same 5 rules as above
One for Cognito with Canada region, with 3 rules, because the other two rules block the access outside Canada, Nick and Jota can't access to FAM when added those two rules
- Amazon IP reputation list (AWS-AWSManagedRulesAmazonIpReputationList)
- Known bad inputs (AWS-AWSManagedRulesKnownBadInputsRuleSet)
- Linux operating system (AWS-AWSManagedRulesLinuxRuleSet)

[ ] WAF has been added to the cloudfont, api gateway and cognito through terraform

[ ] Added a comment for the ACL for Cognito, explain why we can only have three rules

Aditional info
Test this out in the TOOLS environment - hack-away!

For web ACL for Cloudfront, AWS says:
Private Zenhub Image
However, I am facing an error:
│ Error: reading WAFv2 WebACLs: WAFInvalidParameterException: Error reason: The scope is not valid., field: SCOPE_VALUE, parameter: CLOUDFRONT
│ {
│   RespMetadata: {
│     StatusCode: 400,
│     RequestID: "4867c2ce-9e12-4931-b752-9c997aefd894"
│   },
│   Field: "SCOPE_VALUE",
│   Message_: "Error reason: The scope is not valid., field: SCOPE_VALUE, parameter: CLOUDFRONT",
│   Parameter: "CLOUDFRONT",
│   Reason: "The scope is not valid."
│ }

This seems to indicate the ACL created for Cloudfront has issue, perhaps something is missing for Cloudfront WAF ACL resource block.

When merging pr to main, terraform deployment fail due to the WAF resource already exists (previously WAS were added from AWS console manually).
Manually deleted WAS and redeploy resolve the issue.
Next release (TEST/PROD) we will need to remove these manually added WAF first before deployment.
@gormless87

When merging pr to main, terraform deployment fail due to the WAF resource already exists (previously WAS were added from AWS console manually).
Manually deleted WAS and redeploy resolve the issue.
Next release (TEST/PROD) we will need to remove these manually added WAF first before deployment.
@gormless87


GROOVY-9821: STC: check "T" from "? extends T" for list/map properties

https://issues.apache.org/jira/browse/GROOVY-9821

Merged, thanks!


Pipenv cannot find Python

I'm using pipenv in the following docker image:
FROM python:3.6.4
RUN mkdir /app
WORKDIR /app
ADD ./ /app/
RUN pip install pipenv
RUN pipenv install --system --deploy

pipenv install command fails.
Describe your environment

Docker
Python version: 3.6.4
Pipenv version: 11.1.1

Expected result
All dependencies installed successfully.
Actual result
pipenv install fails with the following error:
 ---> Running in fb1741a0385e
Installing dependencies from Pipfile.lock (a1fc0a)…
Traceback (most recent call last):
  File "/usr/local/bin/pipenv", line 11, in <module>
    sys.exit(cli())
  File "/usr/local/lib/python3.6/site-packages/pipenv/vendor/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/pipenv/vendor/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.6/site-packages/pipenv/vendor/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.6/site-packages/pipenv/vendor/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.6/site-packages/pipenv/vendor/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/pipenv/cli.py", line 197, in install
    selective_upgrade=selective_upgrade
  File "/usr/local/lib/python3.6/site-packages/pipenv/core.py", line 1835, in do_install
    pre=pre, requirements_dir=requirements_directory
  File "/usr/local/lib/python3.6/site-packages/pipenv/core.py", line 1372, in do_init
    requirements_dir=requirements_dir.name)
  File "/usr/local/lib/python3.6/site-packages/pipenv/core.py", line 856, in do_install_dependencies
    requirements_dir=requirements_dir
  File "/usr/local/lib/python3.6/site-packages/pipenv/core.py", line 1473, in pip_install
    c = delegator.run(pip_command, block=block)
  File "/usr/local/lib/python3.6/site-packages/pipenv/vendor/delegator.py", line 267, in run
    c.run(block=block, binary=binary)
  File "/usr/local/lib/python3.6/site-packages/pipenv/vendor/delegator.py", line 156, in run
    s = PopenSpawn(self._popen_args, **pexpect_kwargs)
  File "/usr/local/lib/python3.6/site-packages/pipenv/vendor/pexpect/popen_spawn.py", line 46, in __init__
    self.proc = subprocess.Popen(cmd, **kwargs)
  File "/usr/local/lib/python3.6/subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "/usr/local/lib/python3.6/subprocess.py", line 1344, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/python -m pip': '/usr/local/bin/python -m pip'
ERROR: Service 'backend_1' failed to build: The command '/bin/sh -c /bin/bash -c "pipenv install --system --deploy"' returned a non-zero code: 1

Additional info
When I use bash for install command like this:
RUN ["/bin/bash", "-c", "pipenv install --system --deploy"]
it works fine.
The issue appeared in version 11.1.1, 10.1.2 worked fine.
Since changing the shell fixes the issue, I'm not really sure it's pipenv problem, but since it broke with the pipenv update, I think we need at least investigate it.

fixed


Use full covariance matrix when taking weighted mean of Measurements

closes #8

It turned out to be easier than I expected to get the covariance matrix from a vector of correlated Measurements and just use the full matrix method for weighted mean and mswd, so that should work for now

If we want to fully deal with systematic uncertainties in the input ratios, the next step is probably  to use Measurements.correlated_values to generate a vector of Measurements for each isotopic ratio that includes the proper covariance structure...

Oh wahou, that's really a clean solution. I can confirm that my example now works. Thx for the reactivity! The changes should also be propagated to the function mswd() I assume.

If we want to fully deal with systematic uncertainties in the input ratios, the next step is probably to use Measurements.correlated_values to generate a vector of Measurements for each isotopic ratio that includes the proper covariance structure...

That would be neat. But is there not a limit to using Measurements.jl? I thought that linear error propagation theory should not be apply to correlated quantities and/or non-linear functions and we have both here. Or did I miss something?

Should be set as of v0.3.5!


mp GO:0019430 removal of superoxide radicals

could
GO:0019430 removal of superoxide radicals
be a descendant of
GO:0061691 detoxification of hydrogen peroxide
?
(so it gets captured by our cellular detoxification slim term)
Reported by: ValWood
Original Ticket: geneontology/ontology-requests/11731

Fixed - see #12124


Update README.md

fix path 4 Linux/mini_ipmi_lmsensors.py

Alright. But it's not the only incorrect path. :)


Add initial Makefile #111

@fjuma I see I forgot to clean the part in the scripts that print the directory
that was just for testing purposes, I'll update

I'll update
done


Upvoting our own answer

I can actually able to upvote my own answer. In stackoverflow, they wont allow upvoting our own answers. Can i fix this?

Hi @maharshi-b Off course you can try and fix it, I would love to have your PR with a quick fix on this feature. Please remember to keep your local code base up to date and push your PR to develop branch.

Hey @maharshi-b are you working on this or should I take it on?

Hi @oma0256 i am beginner to webdev, still learning. i cannot do that now. You can do it. Go..

Closing.


Server production bundle not created

Maybe I'm missing something, but it seems the production bundle is not created when building the project (no folder named .vite-ssg-dist/)
I tried a clean vitesse project and get the same problem : no server production bundle !

.vite-ssg-dist is a temporary folder for SSG and will be removed after the build. Please note SSG is note SSR which does not have a server bundle. You may want to use vite-ssr for it. https://github.com/frandiox/vite-ssr


feat: allow configurable child shutdown timeouts

Thank you  for the work done in https://github.com/theacodes/nox/pull/393! It did fix some odd issues but brought to light one more. We have a few tests that spin up docker containers and then clean them up after the pytest session exits but these take upwards of 10-15 seconds to fully clean up. I think that making the timeout configurable may be acceptable although I'm not sure if this is the best approach. Let me know what you think.
The goal of this change is to allow you to set the timeout on the CLI, in the noxfile.py, or individually on each session.run invocation. If this is acceptable I'll work on updating docs and tests. Thanks!

Thanks for the feedback!

Generally, it's preferred to open an issue first.

I'm sorry, I would if I had known. I don't think there is a PR template on this project is there? I'll maybe open an issue about adding one of those with some guidelines then.

Have you considered using pytest fixtures for your Docker containers?

Yes, actually that is what is going on :) Pytest spins up and down containers, but when it tries to shut them down after receiving SIGINT noxs end up SIGKILLing pytest and we get containers left around on out CI hosts. This has become apparent after I switched the project in question over to a matrix strategy build on github so after the first test failure a SIGTERM gets sent to the other running matrix tests as I'm sure you know.

While you can always argue for more configurability, every little knob we add increases maintainance effort permanently, so I'd like to first consider alternative solutions.

I 100% understand and agree. If there is a workaround I'm willing to implement it, but I think this will probably effect more than a few other users of nox unless I happen to be doing things in a strange way (which I hope I'm not)

Also, have you considered modifying the Docker containers to improve their shutdown time?

I'm not really sure what all I could speed up, I think it's just a problem of combined IO load on the CI hosts at some points. It can be as fast as 1-2 seconds to clean it up sometimes but it's always longer than 0.3 seconds. Docker-compose with databases always seems a little sluggish to me on cleanup for some reason.

The option help says that it's for the delay between SIGTERM and SIGKILL. But the implementation is for the delay between SIGINT and SIGTERM. Possible confusion?

Oh you're totally right, I think in this case the configurable timeout should be moved to the second one? I was reading the code wrong.

There are two timeouts involved in the existing shutdown process, the delay before SIGTERM and the delay before SIGKILL. In tox 3, both are configurable, and have names that make their purpose clear (interrupt_timeout and terminate_timeout). You chose the generic name shutdown_timeout, and wired that to the interrupt timeout. Why did you select this one of the two timeouts, and how should we handle future feature requests for configuring the other timeout?

Good to know about tox, I should have looked there for naming standards to follow. In this case because tox has the functionality already then I would personally want to match tox's naming and probably provide both as options to the user. If you would only want one, this should probably be named terminate_timeout and have control over the timeout before the SIGKILL do you agree?

I should have set this to draft mode to begin with, I didn't mean for you to accept this without a discussion :) Thanks again

I do see you have a CONTRIBUTING file however, I apologize I should have looked for one.

Should I start a related Issue for this?

Thanks for explaining your use case. And no worries about opening an issue now, I think we can take it from here.
What are your thoughts about adding parameters interrupt_timeout and terminate_timeout to session.run, and omitting the CLI options? I feel that the command-line interface isn't achieving much here, in addition to the parameters.
We'll also need docs and a test. For the docs, you can update the docstrings of session.run and session.run_always.

I don't think there is a PR template on this project is there? I'll maybe open an issue about adding one of those with some guidelines then.

I agree, that would be helpful.

What are your thoughts about adding parameters interrupt_timeout and terminate_timeout to session.runpopen, and omitting the CLI options? I feel that the command-line interface isn't achieving much here, in addition to the parameters.

That actually makes a lot more sense, CLi options aren't probably needed for this and having separate variables that match tox naming also makes sense. Should a default also be read from the config options so it could be set in the noxfile as nox.options.<option_name> or should it only be allowed as a kwarg to session.run that then gets passed to popen?

We'll also need docs and a test. For the docs, you can update the docstrings of session.run and session.run_always.

For sure! Thank you for keeping the test coverage high, nox has been incredibly stable for me.

Should a default also be read from the config options so it could be set in the noxfile as nox.options.<option_name> or should it only be allowed as a kwarg to session.run that then gets passed to popen?

IMO it should be passed explicitly as a keyword argument. I don't think we need a configurable global default, and nox.options wouldn't be a good place for that as its attributes should mirror command-line options.

Still need to check test coverage and update docs

Sorry for the delay

Nice! Yep, will do. Thanks!

FTR, a small noxfile.py to test both timeouts:
"""
Usage: nox -- [interrupt_timeout] [terminate_timeout]
Examples:

    $ nox -- 1
    $ nox -- 1 2
    $ nox -- None None

"""
import ast
import nox

bash_program = """
trap '' SIGINT SIGTERM
sleep inf
"""

@nox.session
def test(session):
    timeouts = dict(
        zip(
            ["interrupt_timeout", "terminate_timeout"],
            map(ast.literal_eval, session.posargs),
        )
    )
    session.run("bash", "-c", bash_program, external=True, **timeouts)


Bambino discontinued, Alview is the new tool?

I had opened this issue https://github.com/NCIP/cgr-bambino/issues/2 because the setup script fails at Bambino step. Script is alright but Bambino URL times out.
They have a new tool Alview as @finneyr mentions in the comment https://github.com/NCIP/cgr-bambino/issues/2#issuecomment-154283714.
Maybe this repo needs an update? Thanks.

I'm preping a tar ball to put on github to make so that the jar can be accessed until the system hosting
bambino recovers from an outage.
System is indeed not available from outside world; I can access it from inside the firewall, though.

From: Amanjeev Sethi<EMAIL_ADDRESS>Sent: Saturday, November 07, 2015 8:48 PM
To: DCGenomics/hackathon_v001_rnaseq
Cc: Finney, Richard (NIH/NCI) [E]
Subject: [hackathon_v001_rnaseq] Bambino discontinued, Alview is the new tool? (#2)
I had opened this issue NCIP/cgr-bambino#2https://github.com/NCIP/cgr-bambino/issues/2 because the setup script fails at Bambino step. Script is alright but Bambino URL times out.
They have a new tool Alview as @finneyrhttps://github.com/finneyr mentions in the comment NCIP/cgr-bambino#2 (comment)https://github.com/NCIP/cgr-bambino/issues/2#issuecomment-154283714.
Maybe this repo needs an update? Thanks.
—
Reply to this email directly or view it on GitHubhttps://github.com/DCGenomics/hackathon_v001_rnaseq/issues/2.

@finneyr Thanks a lot! I was merely opening an issue here so that folks here are aware. But many thanks for your help.

System is indeed not available from outside world; I can access it from inside the firewall, though.

That makes some sense. This hackathon was at NCBI so within network, it would have worked. thank you!

Check the bambino_jars.tarhttps://github.com/NCIP/cgr-bambino/blob/master/bambino_jars.tar file now on the git hub site.
It contains documentation and jar files in a tar file.
It does not contain the snp information because it makes the file > 100MB which git rejects with a 403 error ( but remembers and it takes 2 hours reading the documentation on git to figure out how to force it to forget the file).
You can contact me at<EMAIL_ADDRESS>if you need any more files.

From: Finney, Richard (NIH/NCI) [E]
Sent: Saturday, November 07, 2015 8:51 PM
To: DCGenomics/hackathon_v001_rnaseq; DCGenomics/hackathon_v001_rnaseq
Subject: RE: [hackathon_v001_rnaseq] Bambino discontinued, Alview is the new tool? (#2)
I'm preping a tar ball to put on github to make so that the jar can be accessed until the system hosting
bambino recovers from an outage.
System is indeed not available from outside world; I can access it from inside the firewall, though.

From: Amanjeev Sethi<EMAIL_ADDRESS>Sent: Saturday, November 07, 2015 8:48 PM
To: DCGenomics/hackathon_v001_rnaseq
Cc: Finney, Richard (NIH/NCI) [E]
Subject: [hackathon_v001_rnaseq] Bambino discontinued, Alview is the new tool? (#2)
I had opened this issue NCIP/cgr-bambino#2https://github.com/NCIP/cgr-bambino/issues/2 because the setup script fails at Bambino step. Script is alright but Bambino URL times out.
They have a new tool Alview as @finneyrhttps://github.com/finneyr mentions in the comment NCIP/cgr-bambino#2 (comment)https://github.com/NCIP/cgr-bambino/issues/2#issuecomment-154283714.
Maybe this repo needs an update? Thanks.
—
Reply to this email directly or view it on GitHubhttps://github.com/DCGenomics/hackathon_v001_rnaseq/issues/2.

@finneyr  thanks!

@finneyr  You can attach release binaries to Github and give the release URL instead of checking in the jars.tar. Please see: https://github.com/blog/1547-release-your-software


Add (more) FlxAnimate support

This PR purges AtlasFrameMaker, and adds FlxAnimate support to Characters and Lua.
FlxAnimate is way faster than AtlasFrameMaker, and has support with 2018+.

omgomgomgomomgfdjgfdslgfdgfd


How to change Save button location

Hi,
I am a newbie to Serenity, Please tell me how to change the Save Button from top of the griddialog to bottom of the griddialog.
thankx

You can use css or jQuery to move items in the dialog. Search for .s-DialogToolbar class to get toolbar

Iam  able to find out the .s-DialogToolbar class, not able to change the save button from top of the form to bottom of the form as every time i have to go to top to save the form as it is having around 25 fields in the form. Please help with a little bit of procedure to get it done.
Thank you

In your xyzDialog.ts constructor, some like this
    constructor() {
        super();

        var tb = this.element.find('.s-DialogToolbar');
        this.element.append(tb);
    }

change the following file
Views\Templates\EntityDialog.Template.html
with the following content.

        <form id="~_Form" action="">

        </form>

Hi  Estrusco,
constructor() {
super();
    var tb = this.element.find('.s-DialogToolbar');
    this.element.append(tb);
}

This Worked form me. But I want this for all the forms. Where should i implement this to get it on all the forms. Thank you

The solution proposed by @dfaruque is useful to you.

Thank you @Estrusco  and @dfaruque  I Got the solution.

Thank you @Estrusco and @dfaruque I Got the solution.

Can you please tell how to keep both in top and bottom of the dialog


New version: FutureScholars.Paperlib version 2.2.5

Pull request has been created with WinGet Releaser v2 :rocket:
Microsoft Reviewers: codeflow:open?pullrequest=https://github.com/microsoft/winget-pkgs/pull/112851&drop=dogfoodAlpha

Close with reason: Merge conflicts;


Added support for embedded headings and changes to media postprocessor

Added a new preprocessor, "EmbedPreprocessor", which replaces heading internal embeds with the corresponding markdown. The effect is that a flashcard such as the following;
id:<PHONE_NUMBER>726
---
What is Bayes theorem?
===
![Theorem](#Theorem)

will now generate a flashcard containing the embedded content as the back - essentially frees you from having to write notes into the code block directly, keeping the body of your notes as the ground truth. Currently only works for markdown links. Also the embedded content doesn't render in preview mode yet - might fix these later.
Also made a minor change to the media processor, which was having trouble identifying and locating internally embedded files.

Hi @tnewing , I love your ideas and it seems like this repo is not activly maintained. So would you mind me to merge your changes to my own fork? I really want to taste these features right now


Approving a newly created record: Call to a member function applyModificationChanges()

When a model with RequiredApproval is freshly created, a Modification is created correctly. When I approve it using:
$user->approve($modification);
and since it has 0 remaining approvers left it tries to apply the changes and I get:
Call to a member function applyModificationChanges() on null
which makes sense as here:
$modification->modifiable->applyModificationChanges($modification, true);
I guess there is no 'modifiable' (as the record does not exist yet / has no idea).
Am I missing something here? Love your work, works perfect for changes but I can't seem to get it to work for creations.

Thanks for the report, I'll unfortunately only be able to look into this later this week.

I currently do this dirty hack in ApprovesChanges trait (mind you, novice developer):
if ($modification->approversRemaining == 0) {                 if($modification->modifiable_id === null) {                     $polymorphicModel = new $modification->modifiable_type();                     $polymorphicModel->applyModificationChanges($modification, true);                 } else {                     $modification->modifiable->applyModificationChanges($modification, true);                 }             }

Will look into this soon, I promise :grinning:


typocorrect a note error

Proposed changes
Issue Number: no
correct some note errors
Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run build all

run buildall

(From new machine)TeamCity pipeline, clickbench performance test result:
the sum of best hot time: 46.42 seconds
stream load tsv:          546 seconds loaded<PHONE_NUMBER>9 Bytes, about 130 MB/s
stream load json:         21 seconds loaded<PHONE_NUMBER> Bytes, about 107 MB/s
stream load orc:          66 seconds loaded<PHONE_NUMBER> Bytes, about 15 MB/s
stream load parquet:          32 seconds loaded 861443392 Bytes, about 25 MB/s
insert into select:          29.5 seconds inserted 10000000 Rows, about 338K ops/s
storage size:<PHONE_NUMBER>7 Bytes


Compat matrix: add links to subsections

We previously added links to the segwit and RBF subsections on the individual details page, but now that the number of rows in the matrix is growing, I think we should have links to the subsections on the main matrix page too:

tACK. Good idea again @harding !

ACK


Saving

Changes the saving UI such that you can choose multiple directory locations
Creates the ReadWriteController, where the rest of my resource-specific methods are going

(for all of these upcoming ones I'm shooting to break them down in bits of ~100 lines or so)
Next PR:

Implementing the data creation in model
Making project directory actually required (you'll note that my code is written with the requirement that it is, but the only thing that currently suggests so is a red *. That's bad)

The one after it:

Implementing writing files for the different resource types on the controller level
(This PR signals the official end of saving)

The ones after that: Reading
Reading 1:

Implement the required ReadWriteController functions, with error handling

Reading 2:

Hook up reading such that it's part of loading the initial app

Reading 3:

Creating a v basic UI for importing (hooked up to the menu)

That about sums up my evening/pre tomorrow demo plans

This change is

Review status: 0 of 5 files reviewed at latest revision, 2 unresolved discussions.

src/controller/read_write_controller.js, line 88 at r1 (raw file):

     * @type {?string}
     */
    this.hasSaved = localStorage.getItem('hasSavedProjectBefore');

Perhaps a better concept could be

src/view/save_project_popup_view.js, line 50 at r1 (raw file):

	<form>
    Project*
      <input type="file" nwdirectory id="projectDirectory"></input>

Hm, how would the user be able to configure where exactly the sub-resources are saved if the project folder hasn't been created yet? I see that it is optional. Does this mean that the optional file locations are when a user wants to save the resources outside of the project folder?

Comments from Reviewable

Review status: 0 of 5 files reviewed at latest revision, 2 unresolved discussions.

src/controller/read_write_controller.js, line 88 at r1 (raw file):
Previously, chynu (celine choo) wrote…
Perhaps a better concept could be

er, please ignore this comment he he.

Comments from Reviewable

Reviewed 1 of 5 files at r1.
Review status: 1 of 5 files reviewed at latest revision, 3 unresolved discussions.

src/controller/save_project_popup_controller.js, line 64 at r1 (raw file):

    this.view.on('submit', () => {
      // Save location for each directory, or, if none chosen, set a default.
      for (let directory of Object.getOwnPropertyNames(DIRECTORIES)) {

Is this another place where you should be using Object.create(null)?

Comments from Reviewable

Review status: 1 of 5 files reviewed at latest revision, 2 unresolved discussions.

src/view/save_project_popup_view.js, line 50 at r1 (raw file):
Previously, svouse wrote…
Yup :ok_hand:

Hm, I think it would be useful to have some sort of help text there, then, since it is rather unclear as of now what the other three mean.
In the interest of time this isn't a priority, but it probably would be even better to make this a part of a second popup view that you only see when you click a button along the lines of "save in separate places" or something. 0:
:fried_egg:

Comments from Reviewable

Review status: 1 of 5 files reviewed at latest revision, 2 unresolved discussions.

src/view/save_project_popup_view.js, line 50 at r1 (raw file):
Previously, chynu (celine choo) wrote…
Hm, I think it would be useful to have some sort of help text there, then, since it is rather unclear as of now what the other three mean.
In the interest of time this isn't a priority, but it probably would be even better to make this a part of a second popup view that you only see when you click a button along the lines of "save in separate places" or something. 0:
:fried_egg:

sgtm! Added issue #170 ; feel free to add any comments about things I should add to the comment and whatnot

Comments from Reviewable

Reviewed 4 of 5 files at r1.
Review status: all files reviewed at latest revision, 4 unresolved discussions.

src/controller/read_write_controller.js, line 86 at r1 (raw file):

    /**
     * Whether or not the user has saved before.
     * @type {?string}

Boolean

src/controller/read_write_controller.js, line 103 at r1 (raw file):

   * Creates the properly nested directory in which to save the project.
   * @param {!string} directory The resource directory to check (must be one of
   * the get methods in DIRECTORIES)

indent +4 spaces

Comments from Reviewable

Review status: all files reviewed at latest revision, 4 unresolved discussions.

src/view/save_project_popup_view.js, line 50 at r1 (raw file):
Previously, svouse wrote…
sgtm! Added issue #170 ; feel free to add any comments about things I should add to the comment and whatnot

wait o i meant for the user, so that they don't get confused about it. though documentation in code is also important as well (!!). just a sentence or something along the lines of "optional: saving library/whatever outside of project folder"?

Comments from Reviewable

Review status: all files reviewed at latest revision, 5 unresolved discussions.

src/controller/read_write_controller.js, line 97 at r1 (raw file):

    delete DIRECTORIES.name;
    delete DIRECTORY_LOCAL_STORAGE_KEYS.length;
    delete DIRECTORY_LOCAL_STORAGE_KEYS.name;

Remove these.  They seem sketchy and I'm not sure they will work everywhere.

Comments from Reviewable

src/view/save_project_popup_view.js, line 50 at r1 (raw file):
Previously, chynu (celine choo) wrote…
wait o i meant for the user, so that they don't get confused about it. though documentation in code is also important as well (!!). just a sentence or something along the lines of "optional: saving library/whatever outside of project folder"?

Oh cool I totally agree; that's in post-today plans

Comments from Reviewable

Review status: 3 of 5 files reviewed at latest revision, 5 unresolved discussions.

src/controller/read_write_controller.js, line 86 at r1 (raw file):
Previously, rachel-fenichel (Rachel Fenichel) wrote…
Boolean

Done.

src/controller/read_write_controller.js, line 97 at r1 (raw file):
Previously, AnmAtAnm (Andrew n marshall) wrote…
Remove these.  They seem sketchy and I'm not sure they will work everywhere.

Done. (Also per our discussion I've switched to using maps)

src/controller/read_write_controller.js, line 103 at r1 (raw file):
Previously, rachel-fenichel (Rachel Fenichel) wrote…
indent +4 spaces

Done.

Comments from Reviewable

Review status: 3 of 5 files reviewed at latest revision, 5 unresolved discussions.

src/controller/read_write_controller.js, line 97 at r1 (raw file):
Previously, svouse wrote…
Done. (Also per our discussion I've switched to using maps)

a map

Comments from Reviewable

Review status: 3 of 5 files reviewed at latest revision, 5 unresolved discussions.

src/controller/read_write_controller.js, line 106 at r2 (raw file):

   */
  saveBlock() {
    //TODO: fill in

smol nit: console.warn() for unimplemented void functions?

Comments from Reviewable

Review status: 3 of 5 files reviewed at latest revision, 6 unresolved discussions.

src/controller/save_project_popup_controller.js, line 78 at r2 (raw file):

           * directory of the same name as the local storage tag under the
           * directory specified for the project.
           */

Indent this comment to match the block it is within.
My personal preference is to use multiple // on anything that isn't a documentation comment (multiple if need be, like here), so that the documentation stands out.  Your call.

src/view/save_project_popup_view.js, line 56 at r2 (raw file):

      <input type="file" nwdirectory id="toolboxDirectory"></input>

    Workspace
      <input type="file" nwdirectory id="workspaceDirectory"></input>

These aims for one directory per resource type, but in the Tuesday meeting we talked about one filepath per resource in the metadata file. That leaves a number of possible file-path combos that could not be represented by this UI.
Generate this HTML based upon the actual resources that are too be saved.

Comments from Reviewable

Review status: 3 of 5 files reviewed at latest revision, 7 unresolved discussions.

src/view/save_project_popup_view.js, line 87 at r2 (raw file):

      this.toolbox = $('#toolboxDirectory').val();
      this.general_workspace = $('#workspaceDirectory').val();
    	this.hide();

Correct the indent.

Comments from Reviewable

Review status: 3 of 5 files reviewed at latest revision, 7 unresolved discussions.

src/view/save_project_popup_view.js, line 87 at r2 (raw file):
Previously, AnmAtAnm (Andrew n marshall) wrote…
Correct the indent.

Also, this file has tab characters in it, here and above.

Comments from Reviewable

Reviewed 2 of 2 files at r2.
Review status: all files reviewed at latest revision, 5 unresolved discussions.

Comments from Reviewable

Review status: 2 of 5 files reviewed at latest revision, 2 unresolved discussions.

Comments from Reviewable


Fix local

This should work on an ARM mac with Resetta simulation on Lima.

@iandyh
when i run make command at my local. i encountered the error as follows. it's because netskope thing. you can refer to this link.  can you take this into account for local docker image build.
...
cd shibuya && sh build.sh api
docker build -f shibuya/Dockerfile --build-arg env=local -t api:local shibuya
[+] Building 46.1s (8/10)                                                                                docker:orbstack
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 577B                                                                                0.0s
 => [internal] load metadata for docker.io/library/ubuntu:18.04                                                                                1.6s
 => [auth] library/ubuntu:pull token for registry-1.docker.io                                                                                0.0s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 2B                                                                                0.0s
 => CACHED [1/5] FROM docker.io/library/ubuntu:18.04@sha256:152dc042452c496007f07ca9127571cb9c29697f42acbfad72324b2bb2e43c98                                                                                0.0s
 => [internal] load build context                                                                                0.2s
 => => transferring context: 35.98MB                                                                                0.2s
 => [2/5] RUN apt-get update && apt-get install -y curl                                                                                44.2s
 => ERROR [3/5] RUN curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl     && chmod +x ./kubectl     && mv ./kubectl /usr/local/bin/k  0.3s
------
 > [3/5] RUN curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl     && chmod +x ./kubectl     && mv ./kubectl /usr/local/bin/kubectl:
0.190   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
0.190                                  Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
0.312 curl: (60) SSL certificate problem: self signed certificate in certificate chain
0.312 More details here: https://curl.haxx.se/docs/sslcerts.html
0.312
0.312 curl failed to verify the legitimacy of the server and therefore could not
0.312 establish a secure connection to it. To learn more about this situation and
0.312 how to fix it, please visit the web page mentioned above.
------
Dockerfile:4
--------------------
   3 |     RUN apt-get update && apt-get install -y curl
   4 | >>> RUN curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl \
   5 | >>>     && chmod +x ./kubectl \
   6 | >>>     && mv ./kubectl /usr/local/bin/kubectl
   7 |
--------------------
ERROR: failed to solve: process "/bin/sh -c curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl     && chmod +x ./kubectl     && mv ./kubectl /usr/local/bin/kubectl" did not complete successfully: exit code: 60
make: *** [local_api] Error 1

one more thing, db.yaml has still pretty old mariadb image v10.0.23. we should at least update to v10.0.36 because old ver doesn't support arm64 arch.

@iandyh when i run make command at my local. i encountered the error as follows. it's because netskope thing. you can refer to this link. can you take this into account for local docker image build.
...
cd shibuya && sh build.sh api
docker build -f shibuya/Dockerfile --build-arg env=local -t api:local shibuya
[+] Building 46.1s (8/10)                                                                                docker:orbstack
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 577B                                                                                0.0s
 => [internal] load metadata for docker.io/library/ubuntu:18.04                                                                                1.6s
 => [auth] library/ubuntu:pull token for registry-1.docker.io                                                                                0.0s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 2B                                                                                0.0s
 => CACHED [1/5] FROM docker.io/library/ubuntu:18.04@sha256:152dc042452c496007f07ca9127571cb9c29697f42acbfad72324b2bb2e43c98                                                                                0.0s
 => [internal] load build context                                                                                0.2s
 => => transferring context: 35.98MB                                                                                0.2s
 => [2/5] RUN apt-get update && apt-get install -y curl                                                                                44.2s
 => ERROR [3/5] RUN curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl     && chmod +x ./kubectl     && mv ./kubectl /usr/local/bin/k  0.3s
------
 > [3/5] RUN curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl     && chmod +x ./kubectl     && mv ./kubectl /usr/local/bin/kubectl:
0.190   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
0.190                                  Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
0.312 curl: (60) SSL certificate problem: self signed certificate in certificate chain
0.312 More details here: https://curl.haxx.se/docs/sslcerts.html
0.312
0.312 curl failed to verify the legitimacy of the server and therefore could not
0.312 establish a secure connection to it. To learn more about this situation and
0.312 how to fix it, please visit the web page mentioned above.
------
Dockerfile:4
--------------------
   3 |     RUN apt-get update && apt-get install -y curl
   4 | >>> RUN curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl \
   5 | >>>     && chmod +x ./kubectl \
   6 | >>>     && mv ./kubectl /usr/local/bin/kubectl
   7 |
--------------------
ERROR: failed to solve: process "/bin/sh -c curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl     && chmod +x ./kubectl     && mv ./kubectl /usr/local/bin/kubectl" did not complete successfully: exit code: 60
make: *** [local_api] Error 1

maybe we can add the comment. But I think I'll exclude the logic in the script because this is unique to us.

several things, db.yaml has still pretty old mariadb image v10.0.23. we should at least update to v10.0.36 because old ver doesn't support arm64 arch.
also, kubectl port-forward applies external-port:internal-port mapping to loopback address (<IP_ADDRESS>) as default. but it doesn't listen all incoming request from Host OS. we need to listen 8080 and 3000 port as '<IP_ADDRESS>' INADDR_ANY. so need to add up --address option in the kubectl port-forward command to expose directives at makefile. (this would be required when we run shibuya along with any VMs.)

Can you run db.yaml though? Somehow with colima, I can run it....Based on Colima docs, it seems it's possible: https://github.com/abiosoft/colima/discussions/631#discussioncomment-5107608
What docker deskstop solution you are using? I think we can upgrade the new version but one of the concern is I don't want DB to have big version gap with the one running in prod.
About port-forwarding, I don't fully get what you mean. After port-forward, you should be able to to go to localhost:8080 to check the UI?

@iandyh

maybe we can add the comment. But I think I'll exclude the logic in the script because this is unique to us.
right. i forgot that shibuya is oss.

as for  db.yaml stuff, I've run the shibuya over multipass and orbstack (tho its' paid, tho...) both are VM based solution to use docker engine, both has treated guest os as arm64 based. thats the reason. but I will try Colima.
as for port-forwarding, multipass and orbstack has assigned private ip address to vm so I confirm shibuya UI over http://<IP_ADDRESS>:8080/  (multipass has used subnet 192.168.64.*)

@rsw-a yeah, looking at your answer, I guess it's due to the different container runtime we are using locally. If colima works for you, I can update the README to require the developer to use Colima. Otherwise providing support for different runtime could be very challenging...

I am able to run shibuya on local with multipass VM and kind in it, with this change.
Also as mentioned by Kimura-san regarding DB image, the issue is below
Does not have arm64 image: https://hub.docker.com//mariadb/tags?page=&page_size=&ordering=&name=10.0.23
Have arm64 image from this version: https://hub.docker.com//mariadb/tags?page=&page_size=&ordering=&name=10.0.36
So version "image: mariadb:10.0.36" works in arm64 VM in local [file: kubernetes/db.yaml].


Problem with TF runtime optimized deployment

Expected Behavior
Referring to this notebook: https://github.com/GoogleCloudPlatform/vertex-ai-samples/blob/main/notebooks/community/vertex_endpoints/optimized_tensorflow_runtime/bert_optimized_online_prediction.ipynb.
Actual Behavior
Deployment with the TF runtime should pass.
Steps to Reproduce the Problem

Run https://github.com/GoogleCloudPlatform/vertex-ai-samples/blob/main/notebooks/community/vertex_endpoints/optimized_tensorflow_runtime/bert_optimized_online_prediction.ipynb.
It will fail for tf_opt_gpu_deployed_model. Logs attached.
downloaded-logs-20220726-171156.json.zip

Specifications
Colab

@vlasenkoalexey

Same happens with tf_opt_lossy_gpu_deployed_model too:
downloaded-logs-20220726-172037.json.zip

Looks like you modified Colab and trying to deploy your models on NVIDIA K80:
I0726 11:47:56.340117      26 gpu_device.cc:1616] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10882 MB memory:  -> device: 0, name: Tesla K80, pci bus id: 0000:00:04.0, compute capability: 3.7

Optimized TensorFlow Runtime is not supporting old GPUs, see documentation: https://cloud.google.com/vertex-ai/docs/predictions/optimized-tensorflow-runtime

Sorry for flagging this without reading the documentation. Maybe including a note about it in the Colab would be helpful?


Remove OHLC / Change to config.

Move OHLC selection into configuration for primary chart indicators only, see #73

Closing: The OHLC config for all series/indicators has been removed and the configuration of individual indicators is covered by #73


Failing at BBBECSSTACK

Describe the bug
A clear and concise description of what the bug is.
Using installation script, ECS fails with
The following resource(s) failed to create: [BBBECSCapacityProvider].
Invalid request provided: CreateCapacityProvider error: ECS Service Linked Role does not exist. Please create a Service linked role for ECS and try again. (Service: AmazonECS; Status Code: 400; Error Code: ClientException;
To Reproduce
Steps to reproduce the behavior:

Go to cloudformation Stacks
Click on BBBECSSTACK
BBBECSCapacityProvider
create_faileds

Expected behavior
Expecting TURN Server and Autoscaling to install correctly
Screenshots

Desktop (please complete the following information):
EC2 instance running UBUNTU 16.04
MacOS
Additional context
Sorry, a bit inexperienced with AWS im just looking to setup as a Proof Of Concept, but cannot get past this error. Any help is appreciated and thanks for such an excellent resource!

Hi,
it seems the service linked role for ECS is missing in your account. Can you try to create it using the following documentation or basically this command via the CLI (please add the profile to the cli command if you work with profiles):
aws iam create-service-linked-role --aws-service-name ecs.amazonaws.com
https://docs.aws.amazon.com/AmazonECS/latest/developerguide/using-service-linked-roles.html
let me know if this solves your issue.

It's not a bug. But a question
Once we deploy the application if we want to make any changes to the code ( theme, or some other customization), how can we deploy it to this stack?
We are already using a single server model and I know developers  ( I am not a developer) customized a lot that.
Also, it's said that the auto-scaling will not work dynamically and we need to set the desired numbers manually. Is it correct?  Once we change the Maximum number, is there an image to start the new instance automatically?

Hey Serveradmin, please open a new issue and do not hijack one of another user.  ty!

Solved, Added that command and i'd also added an incorrect region in my
config. Thanks.
Now i cannot access conference.gomentor.net (my url) via browser...Ping
times out while NSLookup returns successfully.
On Mon, Sep 21, 2020 at 11:17 PM Dave<EMAIL_ADDRESS>wrote:

Hey Serveradmin, please open a new issue and do not hijack one of another
user. ty!
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/aws-samples/aws-scalable-big-blue-button-example/issues/2#issuecomment-696529812,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AOKBDP2JREJJ7ZG4S7S4N43SHA6RLANCNFSM4RVBTWTA
.

Hi,
i can see that the ALB is listening file and there is a destination using a redirect 301:

Connected to conference.gomentor.net (<IP_ADDRESS>) port 443 (#0)
ALPN, offering h2
ALPN, offering http/1.1
successfully set certificate verify locations:
CAfile: none
CApath: /etc/ssl/certs
TLSv1.3 (OUT), TLS handshake, Client hello (1):
TLSv1.3 (IN), TLS handshake, Server hello (2):
TLSv1.2 (IN), TLS handshake, Certificate (11):
TLSv1.2 (IN), TLS handshake, Server key exchange (12):
TLSv1.2 (IN), TLS handshake, Server finished (14):
TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
TLSv1.2 (OUT), TLS change cipher, Change cipher spec (1):
TLSv1.2 (OUT), TLS handshake, Finished (20):
TLSv1.2 (IN), TLS handshake, Finished (20):
SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
ALPN, server accepted to use h2
Server certificate:
subject: CN=*.gomentor.net
start date: Sep 22 00:00:00 2020 GMT
expire date: Oct 22 12:00:00 2021 GMT
issuer: C=US; O=Amazon; OU=Server CA 1B; CN=Amazon
SSL certificate verify ok.
Using HTTP2, server supports multi-use
Connection state changed (HTTP/2 confirmed)
Copying HTTP/2 data in stream buffer to connection buffer after upgrade: len=0
Using Stream ID: 1 (easy handle 0x55d109d73f50)

GET / HTTP/2
Host: conference.gomentor.net
User-Agent: curl/7.64.0
Accept: /

Connection state changed (MAX_CONCURRENT_STREAMS == 128)!
< HTTP/2 301
< server: awselb/2.0
< date: Tue, 22 Sep 2020 14:19:29 GMT
< content-type: text/html
< content-length: 150
< location: https://conference.gomentor.net:443/b
<

301 Moved Permanently

301 Moved Permanently

* Connection #0 to host conference.gomentor.net left intact
i can access via: https://conference.gomentor.net
be sure to use https!
ping is not working as at least at the default Security Groups build via cloudformation ICMP inbound is not allowed ;)
does this solve it for you?

Hi,
Yes everything works perfectly. Thank you 🙏
Is there a discussion channel, or something like that? I had a few
questions...about this in production
On Tue, Sep 22, 2020 at 7:22 AM Dave<EMAIL_ADDRESS>wrote:

Hi,
i can see that the ALB is listening file and there is a destination using
a redirect 301:

Connected to conference.gomentor.net (<IP_ADDRESS>) port 443 (#0)

ALPN, offering h2

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: none

CApath: /etc/ssl/certs

TLSv1.3 (OUT), TLS handshake, Client hello (1):

TLSv1.3 (IN), TLS handshake, Server hello (2):

TLSv1.2 (IN), TLS handshake, Certificate (11):

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

TLSv1.2 (IN), TLS handshake, Server finished (14):

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

TLSv1.2 (OUT), TLS change cipher, Change cipher spec (1):

TLSv1.2 (OUT), TLS handshake, Finished (20):

TLSv1.2 (IN), TLS handshake, Finished (20):

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server accepted to use h2

Server certificate:

subject: CN=*.gomentor.net

start date: Sep 22 00:00:00 2020 GMT

expire date: Oct 22 12:00:00 2021 GMT

issuer: C=US; O=Amazon; OU=Server CA 1B; CN=Amazon

SSL certificate verify ok.

Using HTTP2, server supports multi-use

Connection state changed (HTTP/2 confirmed)

Copying HTTP/2 data in stream buffer to connection buffer after
upgrade: len=0

Using Stream ID: 1 (easy handle 0x55d109d73f50)

GET / HTTP/2
Host: conference.gomentor.net
User-Agent: curl/7.64.0
Accept: /

Connection state changed (MAX_CONCURRENT_STREAMS == 128)!

< HTTP/2 301
< server: awselb/2.0
< date: Tue, 22 Sep 2020 14:19:29 GMT
< content-type: text/html
< content-length: 150
< location: https://conference.gomentor.net:443/b
<
301 Moved Permanently
301 Moved Permanently

Connection #0 to host conference.gomentor.net left intact

i can access via: https://conference.gomentor.net
be sure to use https!
ping is not working as at least at the default Security Groups build via
cloudformation ICMP inbound is not allowed ;)
does this solve it for you?
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Hey,
good to read about your success. we do not have any channel or chat yet. feel free to write the questions into a fitting (new) issue and we can have a discussion here ;)
Cheers!

Hi,
it seems the service linked role for ECS is missing in your account. Can you try to create it using the following documentation or basically this command via the CLI (please add the profile to the cli command if you work with profiles):
aws iam create-service-linked-role --aws-service-name ecs.amazonaws.com
https://docs.aws.amazon.com/AmazonECS/latest/developerguide/using-service-linked-roles.html
let me know if this solves your issue.

I faced similar issue and your solution helped me in solving it.


add theme to seciton heading

plugs in a theme system for section heading and adds a dark theme

But do change "default" to "light"


Handle editable projects with pyproject.toml

Fixes #199.

@woodruffw Oops, meant to give you the chance to review this. Feel free to review after-the-fact or just ignore!

LGTM! I was in the middle of reviewing but had no feedback, so nothing of value was missed from me 😅


Ren’Py apps crash after splash screen

Describe the issue
In live container, any app made with the Ren’Py engine crashes immediately after the splash screen is displayed.
If sideloaded directly in SideStore, it runs normally.
Instructions to reproduce
https://github.com/user-attachments/assets/955479f0-1fd6-4a85-8f77-f701930a333c
What version of LiveContainer are you using?
Version 3.1.0-release (main/c586e79)
Other
https://renpy.org/doc/html/ios.html

Well, after some investigation, I found that this is an issue with dlsym. DDLC linked against both OpenGLES and MetalENGLE , which both contain OpenGL api. If directly sideloaded, dlsym correctly returns OpenGL functions in MetalENGLE, while in LiveContainer, OpenGLES functions are returned, and since no OpenGL context is setup, glGetString returned 0 and DDLC crashed.
If I force dlsym to return functions in MetalENGLE, DDLC can launch without issue. I'm looking for a way to make dlsym behave "correctly" like when being sideloaded.

Well, after some investigation, I found that this is an issue with dlsym. DDLC linked against both OpenGLES and MetalENGLE , which both contain OpenGL api. If directly sideloaded, dlsym correctly returns OpenGL functions in MetalENGLE, while in LiveContainer, OpenGLES functions are returned, and since no OpenGL context is setup, glGetString returned 0 and DDLC crashed.
If I force dlsym to return functions in MetalENGLE, DDLC can launch without issue. I'm looking for a way to make dlsym behave "correctly" like when being sideloaded.

Before this issue is resolved, could you add a debug option to select which library (MetalENGLE or OpenGLES) OpenGL functions are returned from for testing? :)

It's fixed, please try https://github.com/hugeBlack/LiveContainer/actions

It's fixed, please try https://github.com/hugeBlack/LiveContainer/actions

Thanks : )
感谢，确实解决了，话说hugeBlack/LiveContainer的commit未来会被推到khanhduytran0/LiveContainer吗

会的，等内容足够了就会合并到这个仓库里面


fix gpx file parsing

to_polygon always closes the list of parsed
GPX points inside the GPXFile object.
Since it is used while parsing the GPX file it always
resulted in a closed list of GPX points even if that
was not the case.

Coverage increased (+0.01%) to 87.97% when pulling 9e2e81e55a519b424440c249d9031cbec7233c35 on leoroos:master into f9e39ca1b451709b829a6f2621de03fa0c25a43b on nofxx:master.

Coverage increased (+0.01%) to 87.97% when pulling 9e2e81e55a519b424440c249d9031cbec7233c35 on leoroos:master into f9e39ca1b451709b829a6f2621de03fa0c25a43b on nofxx:master.

fixing commit information


[FEATURE]: Amethyst official relay & server

Is your feature request related to a problem? Please describe.
One of the issues with using public relays right now is they limit you. They usually have limits on how much and how frequently you pull info. This could be be an issue when we are trying to do more advanced stuff on the client side like fancy metrics or even something as simple as showing reliable followers count or maybe even push notifications.
Describe the solution you'd like
These are just my initial thoughts, apart from decentralized relays that do their job as usual, we could have an official amethyst relay and also run a server/database along with it that pulls info from Amethyst relay (and maybe some more big relays) and our server processes that info for the client to display more interesting info without public relays ever being a bottleneck.
This could also be additional paid services for people use amethyst.
Just drinking beer and brainstorming. Happy to convert this from an issue to discussion if y'all want it.
I would love to know the thoughts of everyone on what you think of it.
Bounty (in Bitcoin sats) offered for the implementation
Could potentially consider hosting it and cover some costs.

I don't like this idea. Amethyst is currently the best nostr client for Android (and possibly just the best nostr client all around). I think it should stay as neutral as possible, client-only. Users can get any relay specific features they need (more space, lower latency, faster, better uptime, etc.) by using or paying for different relays as they need.
I would look for another client if Amethyst started depending on its own relay to function properly.

I would look for another client if Amethyst started depending on its own relay to function properly.

I think depending is the wrong word to use here. Nothing in the feed of the user would show up from Amethyst relay. In fact using the relay can be opt-in.
The relay along with the server could simply be used to offer cooler stuff. Doing everything client side isn't possible, clients have limitations and always rely on servers.

@niteshbalusu11 have you looked at the Relay Implementations section of nostr.net? There are lots of projects to work on for doing cool stuff with relays.

@niteshbalusu11 have you looked at the Relay Implementations section of nostr.net? There are lots of projects to work on for doing cool stuff with relays.

Right, but you're still depending on a relay to pull from, which is a server?
Maybe I am missing you point.

In the context of nostr, what is the difference between a relay and a server? Either our identities & data are portable, or they aren't. If a nostr client additionally saves separate data on proprietary / centralized servers, and that centralized server is required for the app to be fully functional (to do the "cool stuff" as you say), then it defeats the purpose of this nostr experiment.
I want all the "cool stuff" to be something any relay can do, and that any client can use. If you have ideas for any way to improve relays, that would be great -- you should make some suggestions to the relay projects like nostream or strfry. There are many relay projects to look into. For now, this particular project is only about a client. Sure, Amethyst could also build a relay implementation, but why? Sure, Vitor could run an "Amethyst relay" (like relay.damus.io) and use that as a default connection for new users, but this would just again be a standard relay, not specific to Amethyst.

Let's try to avoid a relay setup... Clients building up servers/relay services is a centralizing incentive. We should strike to build in-app tools to educate users on the relays they choose and help them choose better ones.

Don't want to upset more people. Closing this.


remove caching

caching was keeping hold of documents that are never cleared within normal usage within the production system, resulting in overrunning memory and crashed tiled instances

Description
Remove @lru_cache decorators from functions in DatasetFromDocuments() that led to tiled crashes.
Motivation and Context
#740
How Has This Been Tested?
Tested locally with the same server environment described in the issue. After changes, memory usage never went above 1.0% with the same dataset that was causing the server process to increase at 10GB per client run.

Some notes:

The caches in question were bounded on number of items rather than byte size, and that is an important lesson learned. The byte size could grow very large because the items could include "filled" events with image data.
We could refine the caches, with lower bounds, bounds that account for byte size. But this kind of caching, designed to expedite repeated requests, is better handled generically closer to the outer edge of the application, in a response cache.


Minor Ninja generator fixes for Windows

@bradking Would you mind also having a look at this?

Thanks.  However, the & change breaks some tests, such as RunCMake.CMP0060.  Please try running the full test suite.  Build CMake itself using the Ninja generator and then run ctest -j 4 at the top of the build tree.
Are you sure about & v. &&?  Can you link to documentation about it?

Looking at the official documentation again I see why there would be test failures: While it's true that & is used to separate multiple commands, it executes the next command no matter whether the previous was successful or not. I.e. it corresponds to Unix' ;. To execute the next command only on success of the previous one still && needs to be used. Sorry for the confusion.
As the other commit in my PR is not important enough on its own, I'll simply close this. Thanks again for the thorough review.


Escaping

Oni Version: 0.3.6
Operating System: Mac High Sierra
Issue: When in :terminal mode, in ranger, ESC doesn't register in ranger (or other terminal programs, like running vim in :terminal mode), and goes to vim editing mode
Expected behavior: ESC should register in ranger (Testing in terminal version of neovim)
Actual behavior: ESC causes you to go to vim mode, making it impossible to esc out
Steps to reproduce: Just try and run vim in :terminal mode, and you'll see how the ESC is registered very confusingly.
I'd love to help work on this issue as well, but I have no idea where to start.

This is most likely due to the Oni default config having this in it: https://github.com/onivim/oni/blob/b2ef17fde057d55eeb6ac78e1e3c0a73bd279c18/vim/default/bundle/oni-vim-defaults/plugin/init.vim#L21
You can disable the default config if you want (with "oni.useDefaultConfig": false,), which would stop this. Though, if you do that you may want to move some of the settings from the default config into any custom vim config you have. There is some more details on that at the bottom of: https://github.com/onivim/oni/wiki/How-To:-Minimal-Oni-Configuration
Ideally, we'd remove that entirely, and move the config into an Oni option, so its more easily changed.

Thank you!!!


Doesn't work on Wayland

It seems wayland is not supported in SFML.
Failed to open X11 display; make sure the DISPLAY environment variable is set correctly

As of https://github.com/adamsoutar/velocity/commit/2d01a24a0c5c33fa5e55ea2c6767b813ae69f595 , velocity should work on Wayland machines without X back-compat.
Just cargo run from /velocity-sdl. The port is less complete than SFML (arrow keys, Ctrl modifiers etc. don't work yet), but it should be enough to check if porting to SDL can provide Wayland support.


Fixed dependencies

After removing the c prefix from the resources in CitrixXenDesktop7,
these composite resource stopped working

Looks good - that's what you get for renaming resources at the last minute!

Forgot to actually merge!


Data explorer UI does not work well with dark theme

Hi I'm experiencing that the stripes tabel for data explorer pane is not working well with dark syntax theme (below). The text too light compared to background in the white colored row,  I'm using the atom dark syntax theme.

I think the dark striped rows follow the syntax theme but the light striped rows not changing according to the theme.
Thanks
Andi Buwono

Hi, I think, I know the problem. The css styling of the stripes is conflicting with "data-explorer" package. So I think this is not a bug related to hydrogen-python. Sorry for the inconvenience.
Thank You