sway/workspaces: setting to not warp to window when scrolling

Tl;dr
This adds an option, it defaults to true which is the old behavior, when switching workspaces in the sway plugin using the mouse wheel, it uses sway ipc calls to disable mouse warp, and enable it again.
Why?:
When using the mouse to switch workspaces I don't want my mouse to move programmatically.
Issues:

I haven't found a way to read the in memory currently active setting for mouse warp, to only do this if mouse warp ins enabled currently. I don't know if it is possible via sway ipc. I don't think reading the setting file is the way to go, as you can edit settings in situ using ipc calls. The effect this has is that if this setting is set away from the default in waybar it will enable mouse warp ephemerally if you use the mouse scroll wheel to switch workspaces. I don't know if this is a big issue, since this is not the default behavior.
I haven't done the same for switching workspaces using left click. If upstream is open to merging this, this might be something that should be added before merging. It's the same chain of though, if my hand is on the mouse, the mouse should not be moved other than by me, as that is a jarring experience.

Why did I add Request for comment to the title?:
Because I this is my first time opening a merge request to a C++ project
Background:
Why do I have mouse warping on at all? Well when I was using i3wm I was doing some typing, example passwords, etc. using shell scripts, dmenu and xdotool. I had issues with this, like the text not being typed into the text field, just weird issues where the workaround was to just use xdotool to move the mouse again to make sure the window had focus. This didn't work like exactly the same in sway. So I was looking for a way to just make it work in my workflow. Then I discovered that if I enabled mouse warping I never had this issue. But it is very jarring for the mouse to move to a window when I use the mouse to switch workspaces using the sway module in waybar.
Have I tested this code?:
I've ran with these changes for 3 months,  when 0.9.18 was released in the repos of my distro was reminded to open this merge request since it overwrote the binary I had on my disk. I used git apply to check if the changes worked on 0.9.18, and I have been using that since 4 days.

LGTM!
Can you also update the Github wiki? thx 🙏

@Alexays Of course! done!

This does not actually "default to true" like the PR description, so scrolling to change workspaces will enable mouse wraping with the default config.

@q234rty Sorry about this, after reading your comment I have fixed it locally, compiled it and tested it.
I'll make a new PR momentarily!

@q234rty @Alexays A new PR to fix my mistake has been opened https://github.com/Alexays/Waybar/pull/2293


Helping with Flashcard list

Helping with the Flashcard list and fixing some other bugs as well
Moved stylesheet to _Layout, so all views will have access to it.
Moved all code from _Flashcard partial to Index -- since the _Flashcard partial only holds 1 flashcard, not the list itself.
In Index:
Re-added back the js file reference as the Student View needs it to reach the js methods being called from the view.
Changed the loop end variable from the hard-coded 5 to the NumberOfFlashCards.
Changed the DisplayFor from CardQuestion to AvailableCards[i - 1].CardQuestion.
Removed the buttons' paths since they produce errors, since the paths don't exist.

Since @Chriscruzz17 is waiting on this code, this change is set to merge into his branch only, and he's approved the change, I am going to go ahead and merge it into his branch, since he's waiting on it.


Duplicate keys shown with which-key.nvim

Problem
When I press operator + motion combination, screenkey shows duplicate characters like this:

Actually pressed
Screenkey showing

gg
g..x4

zz
z..x4

vw
v w w

viw
v i w i w

zt
z t z t

Steps to reproduce

Install the plugin folke/which-key.nvim
Activate :ScreenKey
Press keys mentioned above
Observe the content in screenkey window

Screenkey log output
No log shown.
Expected behavior
No response
Neovim version (nvim -v)
NVIM v0.10.1
Terminal name/version
tmux 3.4

Sorry for the late reply! After testing, I believe it's the plugin folke/which-key.nvim causing this issue.

Thanks for the information. I don't use which-key, but I'll try to figure out why this happens when I have time.

Thank you!

Hi, just wanted to add that I'm having the same issue together with which-key.
Pressing the keys mentioned (such as g, z and v) brings up the which-key popup that shows your vim keybinds.
(screenshot, I'm pressing g here):
I haven't read the docs for it but the popup, whilst open, it does seem to duplicate your input regardless of the combination of keys pressed.
i.e; instead of inputting g g to get to the first line of the file, typing a non-existing keybind like g G will also output g G g G on Screenkey.

Seems like it duplicates your inputs (or the last input) the instant you use a key that triggers the which-key popup to appear (which is any operator key that can be combined with a motion key).

@johe96 thank you for the additional info.

Sorry for the very late attempt at fixing this. When using screenkey with which-key, screenkey shows each mapping twice.
After this commit, this issue is partially fixed:

when you execute a mapping that is defined in your config (or set by some plugin you use), screenkey will show it only once, as it should
when you execute a mapping like gg or zA (basically any vim builtin mapping) screenkey will show it twice because of which-key

This issue will be resolved when I manage to fix #52. Until then, can someone give me feedback on the mentioned commit?
It's on the dev branch.


[stable/coredns] prometheus metrics not reachable

Helm version: v2.6.0
Kubernetes version: v1.5.7
Chart: stable/coredns
Prometheus is not able to scrape the coredns even if middelware.prometheus.enabled is set.
A port is missing on the pod and the middleware is only listening on localhost resulting in connection refused errors on the prometheus side.

Fixed by #1748


Add ADADELTA algorithm

Just one more optimization algorithm. I wonder if that will be helpful for others.
Paper: http://www.matthewzeiler.com/pubs/googleTR2012/googleTR2012.pdf
Test plan:
$ luarocks make optim-1.0.5-0.rockspec
$ cd test
$ luarocks make

$ th test_adadelta.lua
Rosenbrock test
x=
 0.9932
 0.9861
[torch.DoubleTensor of dimension 2]

fx=
1	1
1001	0.85674832729526
2001	0.65380034382089
3001	0.45083429533603
4001	0.27774607313817
5001	0.14830309667068
6001	0.06446454527491
7001	0.019846854100354
8001	0.0029878163396553
9001	0.00021361750977478
10001	6.034663542954e-05

$ th test_adagrad.lua
Rosenbrock test
x=
 1.0000
 1.0000
[torch.DoubleTensor of dimension 2]

fx=
1	1
1001	0.0096629336429242
2001	0.0011605963642662
3001	0.00017238390470642
4001	0.00037591610790092
5001	4.4145804955209e-06
6001	7.1646069394023e-07
7001	1.1654181321944e-07
8001	1.8974400763049e-08
9001	3.090397609615e-09
10001	5.0341388774798e-10

@soumith , mind to take a quick look?

:clone() is doing a malloc at every iteration. this can lead to weird memory consumption that you will find hard to debug. can you remove the need for :clone() at all places in this file?

otherwise, this looks good to me.

@soumith , I used typeAs + resizeAs + add, not sure if that's what you meant. But I feel that clone is more straightforward and will potentially costs less operations.

@urikz I think you missed my point completely :), typeAs + resizeAs also do malloc, the idea is to not do malloc at every iteration, but keep temporary buffers in the state itself which are reused constantly.
This other PR that also does ADADELTA is an example of what I mention: https://github.com/torch/optim/pull/55/files

@soumith , LoL, I completely failed the mission =) Alright, so I fixed the memory issue (at least I think so). Feel free to merge either this one or other PRs - I'm fine with both ways.

By the way, there is another pull request from @ketranm (https://github.com/torch/optim/pull/55). Maybe it is best to decide which one to go with, but at this moment, both needs some minor changes.

@koraykv, Thanks for the comments - I updated the code.

I am going to close this request, since I have already merged the other one. Thanks for the implementation. Please keep them coming!

@koraykv , sure! =)


[UIE-32] Add types for Dropzone

Currently, any use of the Dropzone component in TypeScript requires a ts-ignore or ts-expect-error because, without any other type information, our types for react-hyperscript-helpers assume that components' children should be an array of React nodes. Dropzone, however, accepts a function as a child. This converts Dropzone.js to TypeScript and adds types for Dropzone's props.

Rebased in order to run SonarCloud scan.


displayName is not set for the component of "@yamada-ui/toggle"

script: component-display-name
package: @yamada-ui/toggle
Description
The component "@yamada-ui/toggle" uses forwardRef, but displayName is not set, making it difficult to see the display in React Developer Tools.
Additional Information
Set displayName and __ui__ after each component definition.
For example, like this.
const Component = forwardRef((props, ref) => {
  ...
})

Component.displayName = 'Component'
Component.__ui__ = 'Component'

Replace 'component' with the name of the component. For example, for a Select component, it is 'Select'.
__ui__ is an identifier required for internal use by Yamada UI. Be sure to set it together with displayName.

As this is my first time contributing to an open-source project, would it be alright if I took on this challenge?


AtlasTexture texture returns wrong size

Godot version
v3.4.beta.custom_build [a5159f352]
System information
PopOS 21.04
Issue description
Tried to printout generated AtlasTexture with 32x48px (actual) size.

i filled transparent pixels with purple color for readablility.
extends Sprite

func _ready():
	print(texture.get_data().get_size())

# output (30, 43)
# i believe this is are trimmed size of texture.

meanwhile inspector displays correct size...

another weird behiavour is, if you try apply outline shader, resulting image is, white outline must surrounds texture.

I suggest is godot trims transparent pixels from texture, need option to generate atlas as is with transparent pixels.
Steps to reproduce

open attachment

Minimal reproduction project
New Game Project.zip

AtlasTexture texture returns wrong size

@boruok It's rather the opposite - it returns the correct size but its get_data() returns data only for its region property (margin isn't taken into account in there). And you're the one who implemented for AtlasTexture.get_data() like that in #53157.

I suggest is godot trims transparent pixels from texture, need option to generate atlas as is with transparent pixels.

I'd say get_data() for AtlasTexture should either create an Image with all relevant data (region + all transparent pixels included) or it should be unsupported. Current implementation (returning data just for the region) isn't consistent with what get_data() is supposed to return (all data for the given Texture). So I'd opt for changing AtlasTexture.get_data() to return all the data. And if someone wants just the data for the region then it still could be retrieved manually the same way the current implementation of AtlasTexture.get_data() works:
# 3.x
var at: AtlasTexture = ...
var region_data: Image = at.atlas.get_data().get_rect(at.region)

@Calinou i think it's good practice to develop games with user device at mind, its can be potato machine or lowend smartphone. Especially for mobile devices, where you user session are limited with battery. As far as rendering is most expensive process it would be good if godot engine provide builtin texture packing tool.

Without these optimizations in place, you might as well use standard textures with the Region property to crop them.

But in that way it's nearly impossible to keep track/manage all of your textures. If you have 320+ items and more on the way. Meanwhile engine can arrange atlas by itself (adding, removing, updating existing items) by now.
Anyway i suggest allow user to decide to trim or not imported textures.

Just got bit by this. We have a ton of regions specified in StyleBoxes throughout our large game. I am going through and putting stuff into spritesheets now and all the Styleboxes have the wrong coordinates now.
If the developer expects a texture of a certain size and with certain contents, then the engine should give the developer what they asked for. Even things like scaling artifacts are changed by having a border of transparent pixels.

I created a PR which has a new option for AtlasTexture imports to disable this behaviour:
https://github.com/godotengine/godot/pull/57163

@jasonwinterpixel thanks!


Problem getting cifti data

Describe the bug
I have ran the singularity of xcp engine 1.0 successfully. I wanted to get CIFTI outputs so have reran using version 1.2.1. However, I do not get any CIFTI outputs, and furthermore the files in my fcon folder all have zero bytes.
I have been using fmriprep version 20.0.5, and the cifti filename is sub-A00008965_task-rest_space-fsLR_den-91k_bold.dtseries.nii. Should I put the cifti path in my cohort file?
Many thanks,
Rob
Cohort file
Paste cohort file between the triple backticks
id0,img
sub-A00000844,sub-A00000844/func/sub-A00000844_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
...,...,...

Design File
Paste your entire design (.dsn) file between the triple backticks
#!/usr/bin/env bash

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
# This design file stores the values of all variables required to
# execute a complete neuroimage processing pipeline. You may
# execute the analysis specified in this design file by calling
# (in any v4 or higher bash terminal):
#
# xcpEngine -d <design> -c <cohort> -o <output> <options>
#
# Variables fall into five general categories:
# * ANALYSIS VARIABLES are used at all stages of this analysis.
# * PIPELINE specifies the modules that comprise the analysis.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the module that
#                  calls them.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are typically array variables with array
#                  indices equal to the value of the primary
#                  subject identifier. They will appear only in
#                  localised design files.
###################################################################

###################################################################
# ANALYSIS VARIABLES
###################################################################

analysis=fc_$(whoami)
design=/home/k1201869/data_bind/src/brain_glu_schi/preprocessing/fc-36p_despike.dsn
sequence=anatomical
standard=MNI%2x2x2

###################################################################
# PIPELINE
###################################################################

pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,norm,qcfc

###################################################################
# 1 PRESTATS
###################################################################

prestats_rerun[1]=1
prestats_cleanup[1]=1
prestats_process[1]=FMP

###################################################################
# 2 CONFOUND2
###################################################################

confound2_rps[2]=1
confound2_rms[2]=0
confound2_wm[2]=1
confound2_csf[2]=1
confound2_gsr[2]=1
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=2
confound2_custom[2]=
confound2_censor[2]=0
confound2_censor_contig[2]=0
confound2_framewise[2]=fds:0.167,dv:2
confound2_rerun[2]=1
confound2_cleanup[2]=1

###################################################################
# 3  REGRESS
###################################################################

regress_tmpf[3]=butterworth
regress_hipass[3]=0.01
regress_lopass[3]=0.08
regress_tmpf_order[3]=1
regress_tmpf_pass[3]=2
regress_tmpf_ripple[3]=0.5
regress_tmpf_ripple2[3]=20
regress_dmdt[3]=2
regress_1ddt[3]=1
regress_smo[3]=6
regress_sptf[3]=susan
regress_usan[3]=default
regress_usan_space[3]=
regress_rerun[3]=0
regress_cleanup[3]=1
regress_process[3]=DMT-DSP-TMP-REG

###################################################################
# 4 FCON
###################################################################

fcon_atlas[4]=all
fcon_metric[4]=corrcoef
fcon_thr[4]=N
fcon_rerun[4]=0
fcon_cleanup[4]=1

###################################################################
# 5 REHO
###################################################################

reho_nhood[5]=vertices
reho_roikw[5]=0 # does nothing at the moment
reho_sptf[5]=susan
reho_smo[5]=6
reho_rerun[5]=0
reho_cleanup[5]=1

###################################################################
# 6 ALFF
###################################################################

alff_hipass[6]=0.01
alff_lopass[6]=0.08
alff_sptf[6]=susan
alff_smo[6]=6
alff_rerun[6]=0
alff_cleanup[6]=1

###################################################################
# 7 ROIQUANT
###################################################################

roiquant_atlas[7]=all
roiquant_globals[7]=1
roiquant_vol[7]=0
roiquant_rerun[7]=0
roiquant_cleanup[7]=1

###################################################################
# 8 NORM
###################################################################
norm_primary[8]=1
norm_rerun[8]=0
norm_cleanup[8]=1

##################################################################
# 9 QCFC
###################################################################
qcfc_atlas[9]=power264
qcfc_sig[9]=fdr
qcfc_rerun[9]=0
qcfc_cleanup[9]=1

Error message
Paste your error message between the backticks

Current processing step:
Localising subject metadata...
····································································
· [Parsing subject identifiers]
· [Creating output directory]
· [/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828]
· [Initialising space mapping]
· [Initialising derivative maps]
· [Initialising atlas system]
· Ingress
· [Native space: sub-A00000828_anatomical]
· [Standard space: MNI]
· [Anatomical space: sub-A00000828_anatomical]
· [Priming analytic audit]
· [Priming quality assessment]

Current processing step:
Localising image
····································································
· [Verifying that images are present]
· [Conforming and localising images]

Current processing step:
Localising design
····································································
· [Writing localised design]
· [Evaluating subject variables]
cp: cannot open '/xcpEngine/space/MNI/MNI-2x2x2.nii.gz' for reading: Permission denied

Current processing step:
Ensure matching orientation
····································································
· Input: /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828~TEMP~.nii.gz
· Template: /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
· Output root:
· checking the orientation of img and template
· img and template orientation are not the same
· make it: LPI -> NO-DSET

Current processing step:
getting data from fmriprep directory
····································································
· checking refvolume and structural orientation
 file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_referenceVolume.nii.gz does not exist .
/xcpEngine/core/functions/exec_ants: line 1: 20696 Segmentation fault      ${ANTSPATH}/"${@}"
 file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_struct.nii.gz does not exist .
 file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_referenceVolume.nii.gz does not exist .
/xcpEngine/core/functions/exec_ants: line 1: 20700 Segmentation fault      ${ANTSPATH}/"${@}"
 file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_referenceVolume.nii.gz does not exist .
/xcpEngine/core/functions/exec_ants: line 1: 20704 Segmentation fault      ${ANTSPATH}/"${@}"
· generate mask and referenceVolumeBrain
 file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_referenceVolume.nii.gz does not exist .
/xcpEngine/core/functions/exec_ants: line 1: 20709 Segmentation fault      ${ANTSPATH}/"${@}"
Image Exception : #22 :: ERROR: Could not open image /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_structmask
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/xcpEngine/core/functions/exec_fsl: line 1: 20713 Aborted                 ${FSLDIR}/bin/"${@}"
 file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_mask.nii.gz does not exist .
 file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_referenceVolume.nii.gz does not exist .
/xcpEngine/core/functions/exec_ants: line 1: 20716 Segmentation fault      ${ANTSPATH}/"${@}"
Cannot open volume /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_mask for reading!
Cannot open volume /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_mask for reading!
· Quality assessment
Error in readNifti(mask1path) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_segmentation.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(mask1path) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/prestats/sub-A00000828_segmentation.nii.gz'
Execution halted

Current processing step:
Generating confound matrix
····································································
· Generating temporal mask
· [Computing framewise displacement]
· [Computing DVARS]
· [Selecting quality criteria]
· [Quality criterion: fd < .334000000]
· [Quality criterion: dvars < 2]
· [Applying framewise threshold to time series]
· [Evaluating data quality]
· relative maximum motion
· relative mean motion
· Including realignment parameters
· Including csf
· Including gsr
· Including wm
· [Including 1 derivative(s)]
· [Including 2 power(s)]

Current processing step:
Validating confound model
····································································

Current processing step:
Demeaning and detrending BOLD timeseries
····································································
· [Applying polynomial detrend]
· [Order: 2]
· [Executing detrend: Confound matrix]
Cannot open volume -mul for reading!

Current processing step:
Despiking BOLD timeseries
····································································
· [Executing despike: Primary analyte]
· [Executing despike: Derivative images]
· [Executing despike: Confound matrix]

Current processing step:
Temporally filtering image and confounds
····································································
· [butterworth filter]
· [High pass frequency: 0.01]
· [Low pass frequency: 0.08]
Cannot open volume -mul for reading!

Current processing step:
Converting BOLD timeseries to confound residuals
····································································
· [Computing confound correlations]
· [Executing detrend]
Cannot open volume -mul for reading!

Current processing step:
Spatially filtering image
····································································
· [Configuring SUSAN]
· No appropriate USAN: reconfiguring pipeline
· to smooth to uniformity instead
/xcpEngine/core/functions/configure: line 2: regress_sptf[3][3]=uniform: command not found
/xcpEngine/core/functions/write_config: line 3: regress_sptf[3][3]: bad substitution
Exception caught during reference file reading

itk::ImageFileReaderException (0x55772cdb8040)
Location: "unknown"
File: /tmp/ants/build/ITKv5-install/include/ITK-5.0/itkImageFileReader.hxx
Line: 139
Description:  Could not create IO object for reading file /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
The file doesn't exist.
Filename = /xcpEngine/space/MNI/MNI-2x2x2.nii.gz

 file /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
/xcpEngine/core/functions/exec_ants: line 1: 26312 Segmentation fault      ${ANTSPATH}/"${@}"
niiRead(): error opening file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/regress/boldtoMNI.nii.gz
niiRead(): error opening file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/regress/lh_surface.nii.gz
niiRead(): error opening file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/regress/boldtoMNI.nii.gz
niiRead(): error opening file /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/regress/rh_surface.nii.gz

While running:
/xcpEngine/thirdparty/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-create-dense-scalar /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/regress/sub-A00000828_residual.dscalar.nii -left-metric /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/regress/sub-A00000828_residual_lh.func.gii -right-metric /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/regress/sub-A00000828_residual_rh.func.gii

ERROR: NAME OF FILE: sub-A00000828_residual_lh.func.gii
PATH TO FILE: /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/regress

File does not exist.

/xcpEngine/core/functions/write_config: line 3: regress_sptf[3][3]: bad substitution

Current processing step:
Functional connectome: HarvardOxford
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_HarvardOxford.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_HarvardOxford.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: aal116
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_aal116.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_aal116.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: desikanKilliany
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_desikanKilliany.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_desikanKilliany.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: glasser360
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_glasser360.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_glasser360.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: gordon333
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_gordon333.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_gordon333.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: power264
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_power264.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_power264.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: schaefer100x17
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer100x17.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer100x17.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: schaefer100x7
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer100x7.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer100x7.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: schaefer200x17
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer200x17.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer200x17.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: schaefer200x7
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer200x7.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer200x7.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: schaefer400x17
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer400x17.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer400x17.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Functional connectome: schaefer400x7
····································································
· Mapping network to image space
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· Computing network timeseries
Error in readNifti(roipath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer400x7.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(roipath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/sub-A00000828_atlas/sub-A00000828_schaefer400x7.nii.gz'
Execution halted
· Computing adjacency matrix
Error in read.table(tsPath, header = F) : no lines available in input
Calls: as.matrix -> unname -> read.table
Execution halted
Error in read.table(amatPath, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted
· Determining node coverage
Error in read.table(opt$input, header = F) : no lines available in input
Calls: as.matrix -> read.table
Execution halted

Current processing step:
Computing voxelwise ReHo
····································································
· Determining voxel neighbourhood
· Vertices
· Computing regional homogeneity (ReHo)
· Standardising ReHo values

Current processing step:
Spatially filtering ReHo map
····································································
· Filter: susan
· Smoothing kernel: 6 mm
· Generating a mask using 3dAutomask
· Standardising ReHo values

Current processing step:
Spatially filtering image
····································································
· [Configuring SUSAN]
· No appropriate USAN: reconfiguring pipeline
· to smooth to uniformity instead
/xcpEngine/core/functions/configure: line 2: alff_sptf[cxt][6]=uniform: command not found
/xcpEngine/core/functions/write_config: line 3: alff_sptf[cxt][6]: bad substitution

Current processing step:
Amplitude of low-frequency fluctuations
····································································
· At smoothness 0 mm
· Ensuring integer periods
· Odd volume count: Excising first volume
· Computing power spectrum
· Computing square root of amplitudes
· Extracting power spectrum at the low frequency band
· 0.01 Hz is approximately position 2
· of the power spectrum. There are about 24 frequency
· positions corresponding to the passband (0.08 - 0.01 Hz)
· in the power spectrum.
· Computing the amplitude of low-frequency fluctuations (ALFF)
· Standardising ALFF values
/xcpEngine/core/functions/write_config: line 3: alff_sptf[cxt][6]: bad substitution
cp: cannot open '/xcpEngine/space/MNI/MNI-2x2x2.nii.gz' for reading: Permission denied

Current processing step:
Normalising using ANTs
····································································
· [Selecting transforms to apply]
· [Normalising primary dataset]
· [Applying composite diffeomorphism to primary dataset]
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [Applying composite diffeomorphism to derivative images:]
· [alff]
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [alffZ]
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [reho]
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [rehoZ]
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [rehoZ_sm6]
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [reho_sm6]
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted

Current processing step:
Preparing depth map
····································································
· Segmentation:
· Output: /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/qcfc/sub-A00000828_depthMap.nii.gz
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
readlink: invalid option -- 'i'
Try 'readlink --help' for more information.

Current processing step:
Aligning depth map
····································································
· Resampling to 6mm isotropic: minimally preprocessed
· Resampling to 6mm isotropic: denoised
· Aligning depth map to sequence space

Current processing step:
Preparing summary graphics
····································································
· Acquiring arguments
· Generating visuals
Warning messages:
1: Use of `ts$value` is discouraged. Use `value` instead.
2: Use of `ts$value` is discouraged. Use `value` instead.
3: Use of `ts$value` is discouraged. Use `value` instead.
4: Use of `ts$value` is discouraged. Use `value` instead.
5: Use of `ts$value` is discouraged. Use `value` instead.
6: Use of `ts$value` is discouraged. Use `value` instead.
Error in readNifti(maskpath) :
  Failed to read image from path /home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/qcfc/sub-A00000828~TEMP~-onion-rs.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(maskpath) :
  nifti_image_read: failed to find header file for '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/qcfc/sub-A00000828~TEMP~-onion-rs.nii.gz'
Execution halted

Current processing step:
Estimating loss of temporal degrees of freedom
····································································
· 7.137621 number of spikes FD
/xcpEngine/modules/qcfc/qcfc.mod: line 253: 0           +     7.137621         : syntax error: invalid arithmetic operator (error token is ".137621         ")
· 0 number of spikes FD
/xcpEngine/modules/qcfc/qcfc.mod: line 262: nSpikesDV: command not found
· Total lost tDOF: 0

Current processing step:
Estimating post-processing DVARS
····································································
· [Computing DVARS]
Error in getopt_options(object, args) :
  Error in getopt(spec = spec, opt = args) : flag "n" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
Traceback (most recent call last):
  File "/xcpEngine/core/report.py", line 405, in <module>
    moving = load_img(outdir+'/norm/'+prefix+'_intensityStd.nii.gz')
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/image.py", line 1063, in load_img
    return check_niimg(img, wildcards=wildcards, dtype=dtype)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/_utils/niimg_conversions.py", line 251, in check_niimg
    raise ValueError("File not found: '%s'" % niimg)
ValueError: File not found: '/home/k1201869/data_bind/data/braingluschi/denoised/36pdespike122/sub-A00000828/norm/sub-A00000828_intensityStd.nii.gz'
Sentry is attempting to send 0 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit

Runtime Information
Singularity
#$ -m n
#$ -N xcp
#$ -o /home/k1201869/glu_rs/src/logs/xcp_o$TASK_ID
#$ -e /home/k1201869/glu_rs/src/logs/xcp_e$TASK_ID
module load singularity
set SIMG='/home/k1201869/singularity_images/xcpEngine122.simg'
set TEMP_COHORT='/home/k1201869/glu_rs/src/brain_glu_schi/preprocessing/temp/tempcohort_$SGE_TASK_ID.csv'
singularity run -B /home/k1201869/glu_rs:${HOME}/data_bind
${HOME}/singularity_images/xcpEngine122.simg
-c ${TEMP_COHORT}
-d ${HOME}/data_bind/src/brain_glu_schi/preprocessing/fc-36p_despike.dsn
-r ${HOME}/data_bind/data/braingluschi/BIDS_data/
-o ${HOME}/data_bind/data/braingluschi/denoised/36pdespike122/ \
Additional context

pls pull for latest docker image

Thank you, that works! Could I also please ask a question about the connectivity matrices generate by FCON - for e.g. Desikan-Killany are these calculated in surface space or is it from a version of the atlas that has been sampled into volumetric space?

all in volume space

Thank you again.
One more freesurfer related question: I now have 'sub-XXX_residual_{r/l}h.func.gii' in the 'regress' folder.

Are these generated from the fsLR files in the fmriprep folder, or upsampled from the fsaverage5?
Is there a way to specify getting denoised images in fsaverage5/6 or fsnative space?

Thanks
Rob

Dear @a3sha2
Sorry - one more query, I've kept in same issue as it is related to the CIFTI maps
In the regress folder are 'subid-residual_{l/r}h.func.gii' the surface equivalents of 'subid-residualised.nii.gz'?
I ask because I have extracted the time series from the surface files and the connectivity matrixes generated from these look as though they may not have been denoised, as almost no negatively weighted connections (in contract to the matrices in the fcon folder which I believe have been generated from subid-residualised.nii.gz)
Thank you again!

Dear @a3sha2
Sorry, the issues does in fact seem to still be here
In the regress folder are 'subid-residual_{l/r}h.func.gii' the surface equivalents of 'subid-residualised.nii.gz'?
I ask because I have extracted the time series from the surface files and the connectivity matrixes generated from these look as though they may not have been denoised, as almost no negatively weighted connections (in contract to the matrices in the fcon folder which I believe have been generated from subid-residualised.nii.gz)
Thank you again!

how man nodes or vertices do you have?
you might have  flip the matrix of time series

I'm using the gordon atlas so 333 nodes (and I have 165 timepoints), I thought it was that initially but the connectivity matrix I get using the below approach is 333*333 so I don't think it is
def gordon_surface_conn(sub_id, denoised_path):
    ''' Returns a Gordon connectivity matrix from a
    XCP denoised file in surface space '''

    atlas_l_path = f'/home/k1201869/glu_rs/data/atlas_data/gordon/Parcels_L_164.func.gii'
    atlas_r_path = f'/home/k1201869/glu_rs/data/atlas_data/gordon/Parcels_R_164.func.gii'
    surf_image_l_path = f'{denoised_path}/sub-{sub_id}/regress/sub-{sub_id}_residual_lh.func.gii'
    surf_image_r_path = f'{denoised_path}/sub-{sub_id}/regress/sub-{sub_id}_residual_rh.func.gii'

    surf_image_l = surface.load_surf_data(surf_image_l_path)
    atlas_image_l = surface.load_surf_data(atlas_l_path)
    surf_image_r = surface.load_surf_data(surf_image_r_path)
    atlas_image_r = surface.load_surf_data(atlas_r_path)

    l_roi_timecourses = []
    # We don't include the first roi as this is background
    for i in np.unique(atlas_image_l)[1:]:
        roi_idxs = np.where(atlas_image_l==i)
        l_roi_timecourses.append(np.mean(surf_image_l[roi_idxs], axis=0))

    r_roi_timecourses = []
    # We don't include the first roi as this is background
    for i in np.unique(atlas_image_r)[1:]:
        roi_idxs = np.where(atlas_image_r==i)
        r_roi_timecourses.append(np.mean(surf_image_r[roi_idxs], axis=0))

    bilat_timecourses = np.array(l_roi_timecourses + r_roi_timecourses)

    correlation_measure = ConnectivityMeasure(kind='correlation')
    connectivity_matrix = correlation_measure.fit_transform([bilat_timecourses.T])[0]

    return connectivity_matrix

@robmcc10
I expect the connectivity matrix to be the same as volume. what is space of the gordon parcel you are using? remember _residual_rh.func.gii is in fsaverage ( not fsaverage5).

The gordon parcellation is in the same space as _residual_rh.func.gii (163842 vertices)

pls can you share your Parcels_L_164.func.gii and Parcels_R_164.func.gii

They are the parcels available at https://sites.wustl.edu/petersenschlaggarlab/resources/
Thanks for looking into this

sorry for late response. The issue is in your python code, the last line.
remove the transform here   connectivity_matrix = correlation_measure.fit_transform([bilat_timecourses.T])[0] by change it to connectivity_matrix = correlation_measure.fit_transform([bilat_timecourses])[0].
after that you can compare your result with  just simple connectivity_matrix =np.corrcoef(bilat_timecourses)

I'm not sure this is is as the timecourses matrix needs to be transposed otherwise one gets a matrix that is number_time_points * number_timepoints as opposed number_nodes * number_nodes.
np.corrcoef(bilat_timecourses) gives an almost identical result to correlation_measure.fit_transform([bilat_timecourses.T])[0]
Both still have this same issue of having way fewer negative edges (and a  generally very different network structure) to the connectivity matrices calculated from the volumes

The issue was not xcp related but a lack of correspondence between freesurfer and hcp vertices, sorry for any confusion! To map the gordon atlas from hcp to freesurfer space do the following (instructions below for right hemisphere):

Download  R.sphere.32k_fs_LR.surf.gii from

https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/standard_mesh_atlases
and R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii from
https://github.com/Washington-University/HCPpipelines/blob/master/global/templates/standard_mesh_atlases/fs_R
Run:
wb_command -label-resample Parcels_R.func.gii R.sphere.32k_fs_LR.surf.gii fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii BARYCENTRIC right.fsaverage164.label.gii


Is there already an existing .java file for using YOLOv7tiny in OpenBot?

I want to use my custom trained yolov7 tiny model in Openbot.
Can someone help me with the functions/parameters in the java script required for using that model?

Are you able to convert into tflite? What does the input and output look like? Are you using the standard Coco labelmap?

yes, it is already converted to tflite and I am using the standard coco labelmap.
Which information do you need about input/output?

Duplicate of #335


Add Image File Helper functions

The Image File Helper Functions are quite important when working with the already existing graphics API and I believe they are not in NetObsBindings yet, see here for the code.

Aded ObsImage class to <IP_ADDRESS>-alpha


Increase minimum CMake version to allow builds on Focal Fossa (Noetic)

Related to https://github.com/ros-industrial/ros_industrial_issues/issues/67

Thanks :+1:


Add test capabilities and editor features

All the faces can be added and stored as clips immediately regardless of whether or not they are in a sprite sheet. There is also a new character called professor plum who was created for the sake of ensuring everything worked. I also added an editorconfig file because code formatting is kinda nice to have. My editorwindow binds with the m_sprite property of the SpriteRenderer. Though I should have the frames array only contain one frame but it shouldn't affect anything.

I'd be more than happy to close this pull request and merge to a new branch when you're ready. I just wanted to make sure that I could actually make a pull request.

Sounds good 🙂. I created a editor-mods-and-test-capabilities branch in the main repo that you can target this PR towards.
Just to make sure - are these all of the changes you wanted to merge in or were you still working on it? I should have some time this weekend to take a closer look at what was done - but we'll hold off on merging until you've completed what you wanted to merge. Just let me know!


Redundant Dockerfile required in order to push to correct repo

Using 0.58 version :

Create devcontainer.json

{
  "image":"mcr.microsoft.com/devcontainers/base:ubuntu",
  "features": {
    "ghcr.io/devcontainers/features/node:1": {
      "version": "16.18.1"
    },
    "ghcr.io/devcontainers-contrib/features/bash-command:1": {
      "command": "pip3 install jinja2 PyYAML"
    }
  }
}

Build and try push to your repository :

devcontainer --log-level trace --workspace-folder . build --config devcontainer.json --image-name <YourCustomRepo>:<YourCustomTag>  --platform linux/arm64,linux/amd64 --push true

This Results with :

exporting to image:

ERROR: failed to solve: failed to push docker.io/library/vsc-base-image-360ebb83a1aa22c95928798ea8b92eedca9aac8ca2cc4a873ab7b5223cedfebd-features:latest: push access denied, repository does not exist or may require authorization: server message: insufficient_scope: authorization failed

Expected: build is successfull and pushed to custom repo in registry.
Actual: It seems to try push to ibrary/vsc-base-image instead of my repo, and fails
When i replace the image property with build to Dockerfile which has the image inside it, it just works :
{
  "build": {
    "dockerfile": "Dockerfile"
  },
  "features": {
    "ghcr.io/devcontainers/features/node:1": {
      "version": "16.18.1"
    },
    "ghcr.io/devcontainers-contrib/features/bash-command:1": {
      "command": "pip3 install jinja2 PyYAML"
    }
  }
}

Dockerfile :
FROM mcr.microsoft.com/devcontainers/base:ubuntu

it works and pushes to the custom repo as required.

Hi 👋
Thanks for opening this issue, I was able to reproduce this as well.

Actual: It seems to try push to ibrary/vsc-base-image instead of my repo, and fails

When the dev container is built with an image property, it is pushing an incorrect image. This definitely looks like a bug. // cc @chrmarti

@gauravsaini04 Can you help prioritize fixing this issue?

@samruddhikhandale btw seems to be same as https://github.com/devcontainers/cli/issues/370

Hi @samruddhikhandale ,
I have created a PR https://github.com/devcontainers/cli/pull/812
if user procide the --image-name then this specific name will be used to push the docker image with the build command.
but if we do not pass the --image-name then it is using cli-generated-image to push to image and it is failing with the below error:
{
  "outcome": "error",
  "message": "Command failed: docker buildx build --platform linux/amd64 --push --build-context dev_containers_feature_content_source=/tmp/devcontainercli-node/container-features/0.59.1-1714115121385 --build-arg _DEV_CONTAINERS_BASE_IMAGE=mcr.microsoft.com/devcontainers/base:ubuntu --build-arg _DEV_CONTAINERS_IMAGE_USER=root --build-arg _DEV_CONTAINERS_FEATURE_CONTENT_SOURCE=dev_container_feature_content_temp --target dev_containers_target_stage -t vsc-example-push-ca34dc0eddd392c65ec666bc1f7466ba3bc4760f9ef20a68674a2f9a7405218f-features -f /tmp/devcontainercli-node/container-features/0.59.1-1714115121385/Dockerfile.extended /tmp/devcontainercli-node/empty-folder",
  "description": "An error occurred building the container."
}

Awesome, thanks @prathameshzarkar9! Reviewing the PR now.

if we do not pass the --image-name then it is using cli-generated-image to push to image and it is failing with the below error:

That's alright, anyone who wants to publish the image would have to make sure they have logged into the appropriate registries.

Hi @samruddhikhandale ,
review comments addressed, kindly confirm and merge if the changes make sense.

Closing as completed with https://github.com/devcontainers/cli/pull/812


istio connection broken: incompleteRead

Describe what happened:
I got a bunch of error from datadog agent
`2021-05-24 00:25:33 UTC | CORE | ERROR | (pkg/collector/runner/runner.go:292 in work) | Error running check istio: [{"message": "('Connection broken: IncompleteRead(9196 bytes read, 1044 more expected)', IncompleteRead(9196 bytes read, 1044 more expected))", "traceback": "Traceback (most recent call last):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py", line 436, in _error_catcher
yield
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py", line 766, in read_chunked
chunk = self._handle_chunk(amt)
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py", line 710, in _handle_chunk
value = self._fp._safe_read(amt)
File "/opt/datadog-agent/embedded/lib/python3.8/http/client.py", line 614, in _safe_read
raise IncompleteRead(data, amt-len(data))
http.client.IncompleteRead: IncompleteRead(9196 bytes read, 1044 more expected)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/requests/models.py", line 750, in generate
for chunk in self.raw.stream(chunk_size, decode_content=True):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py", line 571, in stream
for line in self.read_chunked(amt, decode_content=decode_content):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py", line 792, in read_chunked
self._original_response.close()
File "/opt/datadog-agent/embedded/lib/python3.8/contextlib.py", line 131, in exit
self.gen.throw(type, value, traceback)
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py", line 454, in _error_catcher
raise ProtocolError("Connection broken: %r" % e, e)
urllib3.exceptions.ProtocolError: ('Connection broken: IncompleteRead(9196 bytes read, 1044 more expected)', IncompleteRead(9196 bytes read, 1044 more expected))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/base.py", line 876, in run
self.check(instance)
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/istio/legacy_1_4.py", line 48, in check
self.process(istio_mesh_config)
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/openmetrics/mixins.py", line 521, in process
for metric in self.scrape_metrics(scraper_config):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/openmetrics/mixins.py", line 492, in scrape_metrics
for metric in self.parse_metric_family(response, scraper_config):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/openmetrics/mixins.py", line 416, in parse_metric_family
for metric in text_fd_to_metric_families(input_gen):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/libs/prometheus.py", line 33, in text_fd_to_metric_families
for line in fd:
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/requests/models.py", line 794, in iter_lines
for chunk in self.iter_content(chunk_size=chunk_size, decode_unicode=decode_unicode):
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/requests/utils.py", line 505, in stream_decode_response_unicode
for chunk in iterator:
File "/opt/datadog-agent/embedded/lib/python3.8/site-packages/requests/models.py", line 753, in generate
raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ('Connection broken: IncompleteRead(9196 bytes read, 1044 more expected)', IncompleteRead(9196 bytes read, 1044 more expected))
"}]`
Describe what you expected:
I want more detail of the error
Steps to reproduce the issue:
Additional environment details (Operating System, Cloud provider, etc):
EKS: 1.16.15
datadog agent version: 7.25.1-jmx

Hallo @huy-hoang-mox, we are going to need more details about your environment. Can you please contact support  about this issue?

Hi, we have pretty same issues with Istiod 1.8.3 and dd-agent 7.25.1
2021-06-07 08:11:40 UTC | CORE | ERROR | (pkg/collector/runner/runner.go:292 in work) | Error running check istio: [{"message": "('Connection broken: IncompleteRead(7281 bytes read, 2959 more expected)', IncompleteRead(7281 bytes read, 2959 more expected))", "traceback": "Traceback (most recent call last):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py\", line 436, in _error_catcher\n    yield\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py\", line 766, in read_chunked\n    chunk = self._handle_chunk(amt)\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py\", line 710, in _handle_chunk\n    value = self._fp._safe_read(amt)\n  File \"/opt/datadog-agent/embedded/lib/python3.8/http/client.py\", line 614, in _safe_read\n    raise IncompleteRead(data, amt-len(data))\nhttp.client.IncompleteRead: IncompleteRead(7281 bytes read, 2959 more expected)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/requests/models.py\", line 750, in generate\n    for chunk in self.raw.stream(chunk_size, decode_content=True):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py\", line 571, in stream\n    for line in self.read_chunked(amt, decode_content=decode_content):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py\", line 792, in read_chunked\n    self._original_response.close()\n  File \"/opt/datadog-agent/embedded/lib/python3.8/contextlib.py\", line 131, in __exit__\n    self.gen.throw(type, value, traceback)\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/urllib3/response.py\", line 454, in _error_catcher\n    raise ProtocolError(\"Connection broken: %r\" % e, e)\nurllib3.exceptions.ProtocolError: ('Connection broken: IncompleteRead(7281 bytes read, 2959 more expected)', IncompleteRead(7281 bytes read, 2959 more expected))\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/base.py\", line 876, in run\n    self.check(instance)\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/istio/legacy_1_4.py\", line 48, in check\n    self.process(istio_mesh_config)\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/openmetrics/mixins.py\", line 521, in process\n    for metric in self.scrape_metrics(scraper_config):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/openmetrics/mixins.py\", line 492, in scrape_metrics\n    for metric in self.parse_metric_family(response, scraper_config):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/openmetrics/mixins.py\", line 416, in parse_metric_family\n    for metric in text_fd_to_metric_families(input_gen):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/datadog_checks/base/checks/libs/prometheus.py\", line 33, in text_fd_to_metric_families\n    for line in fd:\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/requests/models.py\", line 794, in iter_lines\n    for chunk in self.iter_content(chunk_size=chunk_size, decode_unicode=decode_unicode):\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/requests/utils.py\", line 505, in stream_decode_response_unicode\n    for chunk in iterator:\n  File \"/opt/datadog-agent/embedded/lib/python3.8/site-packages/requests/models.py\", line 753, in generate\n    raise ChunkedEncodingError(e)\nrequests.exceptions.ChunkedEncodingError: ('Connection broken: IncompleteRead(7281 bytes read, 2959 more expected)', IncompleteRead(7281 bytes read, 2959 more expected))\n"}]

Curl works perfectly to the same target.
=== istio check ===
Configuration source: file:/etc/datadog-agent/conf.d/istio.d/auto_conf.yaml
Instance ID: istio:d7c1632bad93f119
istio_mesh_endpoint: http://<IP_ADDRESS>:15090/stats/prometheus
- image_name:istio/proxyv2
- kube_container_name:istio-init
- docker_image:istio/proxyv2:1.8.3

cat /etc/datadog-agent/conf.d/istio.d/auto_conf.yaml:
ad_identifiers:
  - proxyv2
init_config:
instances:
  - send_histograms_buckets: true
    send_monotonic_counter: true
    istio_mesh_endpoint: http://%%host%%:15090/stats/prometheus
    metrics:
    - sidecar_injection_failure_total: sidecar_injection.failure_total
    - sidecar_injection_skip_total: sidecar_injection.skip_total
    - envoy_server_hot_restart_epoch: envoy.restart.epoch


[Feature][connector-kudu] support Kerberos authentication

Search before asking

[X] I had searched in the feature and found no similar feature requirement.

Description
support Kerberos authentication
Usage Scenario
No response
Related issues
No response
Are you willing to submit a PR?

[x] Yes I am willing to submit a PR!

Code of Conduct

[X] I agree to follow this project's Code of Conduct

link #5278


Bug: systemd-resolve: command not found

Is there an existing issue for this?

[X] I have searched the existing issues

Orb version
1.0.0
Current behavior
The orb tries to use the systemd-resolve command which is not present/not installed on the machine image. I'm using the ubuntu-2404:current image.
Minimum reproduction config
This is the output of the "VPN setup" step:
<IP_ADDRESS>
<IP_ADDRESS>
<IP_ADDRESS>
<IP_ADDRESS>
<IP_ADDRESS>
<IP_ADDRESS>
/bin/bash: line 39: systemd-resolve: command not found
^@^@<14>Aug 20 08:57:05 update-systemd-resolved: Link 'tun0' coming up
<14>Aug 20 08:57:05 update-systemd-resolved: Adding DNS Routed Domain .
<14>Aug 20 08:57:05 update-systemd-resolved: Adding IPv4 DNS Server <IP_ADDRESS>
<14>Aug 20 08:57:05 update-systemd-resolved: Adding IPv4 DNS Server <IP_ADDRESS>
<14>Aug 20 08:57:05 update-systemd-resolved: SetLinkDNS(4 2 2 4 8 8 8 8 2 4 8 8 4 4)
<14>Aug 20 08:57:05 update-systemd-resolved: SetLinkDomains(4 1 . true)
<14>Aug 20 09:03:10 update-systemd-resolved: Link 'tun0' going down

Other
No response

I think a viable solution would be to replace this command with resolvectl status


How to build locust on local machine

Hi,
I am very new to this.
Just want to understand how to build locust on local ( MAC machine ) after making some changes to code base for locust ?

$ python setup.py develop
or
$ pip install -e .


new c6a and c6i missing from some regions

Some regions have the new type 6 instances for c and r hosts. I don't see them in ec2.shop.

Thank you!


Cloud firestore data retrieving doesn't work anymore after packaging my java application (MacOS)

Environment :
MacOS, Java JDK :  jdk-14.0.1.jdk (Maven project)
Firebase Admin SDK : com.google.firebase:firebase-admin:jar:7.0.1
Problem :
When I try to retrieve data with firestore, it works great as long as the application is not packaged.
But when I package the application (on MacOS only, to .app or to .dmg), the application doesn't reach to retrieve the data. The firebase connection work and I get the firestore database which isn't null, but when I use the 'get()' method to retrieve the data, it loops and causes a timeout.
Step to reproduce :
I create a project to reproduce :
[https://github.com/thboulay/JavaFirestorePackage]
Difference between before and after package :
When I run the project AFTER packaging, I get the following error (if I run it before packaging, with Intellij for example, no error and no problem to retrieve the data) :
Dec 02, 2020 10:09:37 AM io.grpc.netty.shaded.io.netty.channel.DefaultChannelId defaultProcessId WARNING: Failed to find the current process ID from ''; using a random value: -1254263216 Error when trying to start firebase java.util.concurrent.ExecutionException: com.google.api.gax.rpc.DeadlineExceededException: io.grpc.StatusRuntimeException: DEADLINE_EXCEEDED: deadline exceeded after 49.985915988s. [buffered_nanos=295866600, buffered_nanos=49697872776, waiting_for_connection] at com.google.common.util.concurrent.AbstractFuture.getDoneValue(AbstractFuture.java:564) at com.google.common.util.concurrent.AbstractFuture.get(AbstractFuture.java:545) at com.google.common.util.concurrent.FluentFuture$TrustedFuture.get(FluentFuture.java:86) at com.google.common.util.concurrent.ForwardingFuture.get(ForwardingFuture.java:62) at com.thboulay.FirebaseTest.start(FirebaseTest.java:45) at com.thboulay.JavaFirestorePackage.main(JavaFirestorePackage.java:8) Caused by: com.google.api.gax.rpc.DeadlineExceededException: io.grpc.StatusRuntimeException: DEADLINE_EXCEEDED: deadline exceeded after 49.985915988s. [buffered_nanos=295866600, buffered_nanos=49697872776, waiting_for_connection] at com.google.api.gax.rpc.ApiExceptionFactory.createException(ApiExceptionFactory.java:51) at com.google.api.gax.grpc.GrpcApiExceptionFactory.create(GrpcApiExceptionFactory.java:72) at com.google.api.gax.grpc.GrpcApiExceptionFactory.create(GrpcApiExceptionFactory.java:60) at com.google.api.gax.grpc.GrpcExceptionCallable$ExceptionTransformingFuture.onFailure(GrpcExceptionCallable.java:97) at com.google.api.core.ApiFutures$1.onFailure(ApiFutures.java:68) at com.google.common.util.concurrent.Futures$CallbackListener.run(Futures.java:1050) at com.google.common.util.concurrent.DirectExecutor.execute(DirectExecutor.java:30) at com.google.common.util.concurrent.AbstractFuture.executeListener(AbstractFuture.java:1176) at com.google.common.util.concurrent.AbstractFuture.complete(AbstractFuture.java:969) at com.google.common.util.concurrent.AbstractFuture.setException(AbstractFuture.java:760) at io.grpc.stub.ClientCalls$GrpcFuture.setException(ClientCalls.java:545) at io.grpc.stub.ClientCalls$UnaryStreamToFuture.onClose(ClientCalls.java:515) at io.grpc.internal.ClientCallImpl.closeObserver(ClientCallImpl.java:426) at io.grpc.internal.ClientCallImpl.access$500(ClientCallImpl.java:66) at io.grpc.internal.ClientCallImpl$1CloseInContext.runInContext(ClientCallImpl.java:416) at io.grpc.internal.ContextRunnable.run(ContextRunnable.java:37) at io.grpc.internal.SerializingExecutor.run(SerializingExecutor.java:123) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: io.grpc.StatusRuntimeException: DEADLINE_EXCEEDED: deadline exceeded after 49.985915988s. [buffered_nanos=295866600, buffered_nanos=49697872776, waiting_for_connection] at io.grpc.Status.asRuntimeException(Status.java:533)
Dependencies :
com.google.firebase:firebase-admin:jar:7.0.1 already exists in destination.
com.google.api-client:google-api-client:jar:1.30.10 already exists in destination.
com.google.oauth-client:google-oauth-client:jar:1.31.0 already exists in destination.
com.google.http-client:google-http-client-jackson2:jar:1.36.0 already exists in destination.
com.google.api-client:google-api-client-gson:jar:1.30.10 already exists in destination.
com.google.http-client:google-http-client-gson:jar:1.36.0 already exists in destination.
com.google.http-client:google-http-client:jar:1.35.0 already exists in destination.
org.apache.httpcomponents:httpclient:jar:4.5.12 already exists in destination.
org.apache.httpcomponents:httpcore:jar:4.4.13 already exists in destination.
com.google.code.findbugs:jsr305:jar:3.0.2 already exists in destination.
com.google.j2objc:j2objc-annotations:jar:1.3 already exists in destination.
io.opencensus:opencensus-api:jar:0.24.0 already exists in destination.
io.opencensus:opencensus-contrib-http-util:jar:0.24.0 already exists in destination.
com.google.api:api-common:jar:1.9.2 already exists in destination.
javax.annotation:javax.annotation-api:jar:1.3.2 already exists in destination.
com.google.auto.value:auto-value-annotations:jar:1.7.2 already exists in destination.
com.google.auth:google-auth-library-oauth2-http:jar:0.20.0 already exists in destination.
com.google.auth:google-auth-library-credentials:jar:0.20.0 already exists in destination.
com.google.cloud:google-cloud-storage:jar:1.110.0 already exists in destination.
com.google.guava:failureaccess:jar:1.0.1 already exists in destination.
com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava already exists in destination.
org.checkerframework:checker-compat-qual:jar:2.5.5 already exists in destination.
com.google.errorprone:error_prone_annotations:jar:2.3.4 already exists in destination.
com.fasterxml.jackson.core:jackson-core:jar:2.11.0 already exists in destination.
com.google.apis:google-api-services-storage:jar:v1-rev20200430-1.30.9 already exists in destination.
com.google.code.gson:gson:jar:2.8.6 already exists in destination.
com.google.cloud:google-cloud-core:jar:1.93.6 already exists in destination.
com.google.api.grpc:proto-google-common-protos:jar:1.18.0 already exists in destination.
com.google.cloud:google-cloud-core-http:jar:1.93.6 already exists in destination.
com.google.http-client:google-http-client-appengine:jar:1.35.0 already exists in destination.
com.google.api:gax-httpjson:jar:0.74.0 already exists in destination.
com.google.api:gax:jar:1.57.0 already exists in destination.
io.grpc:grpc-context:jar:1.30.0 already exists in destination.
com.google.api.grpc:proto-google-iam-v1:jar:0.13.0 already exists in destination.
com.google.protobuf:protobuf-java:jar:3.12.2 already exists in destination.
com.google.protobuf:protobuf-java-util:jar:3.12.2 already exists in destination.
org.threeten:threetenbp:jar:1.4.4 already exists in destination.
com.google.cloud:google-cloud-firestore:jar:1.35.0 already exists in destination.
com.google.cloud:google-cloud-core-grpc:jar:1.93.6 already exists in destination.
io.grpc:grpc-core:jar:1.30.0 already exists in destination.
com.google.android:annotations:jar:<IP_ADDRESS> already exists in destination.
io.perfmark:perfmark-api:jar:0.19.0 already exists in destination.
commons-logging:commons-logging:jar:1.2 already exists in destination.
commons-codec:commons-codec:jar:1.11 already exists in destination.
com.google.api.grpc:proto-google-cloud-firestore-admin-v1:jar:1.35.0 already exists in destination.
com.google.api.grpc:proto-google-cloud-firestore-v1:jar:1.35.0 already exists in destination.
com.google.api.grpc:proto-google-cloud-firestore-v1beta1:jar:0.88.0 already exists in destination.
io.opencensus:opencensus-contrib-grpc-util:jar:0.24.0 already exists in destination.
io.grpc:grpc-protobuf:jar:1.30.0 already exists in destination.
io.grpc:grpc-protobuf-lite:jar:1.30.0 already exists in destination.
org.codehaus.mojo:animal-sniffer-annotations:jar:1.18 already exists in destination.
io.grpc:grpc-api:jar:1.30.0 already exists in destination.
com.google.api:gax-grpc:jar:1.57.0 already exists in destination.
io.grpc:grpc-auth:jar:1.30.0 already exists in destination.
io.grpc:grpc-netty-shaded:jar:1.30.0 already exists in destination.
io.grpc:grpc-alts:jar:1.30.0 already exists in destination.
io.grpc:grpc-grpclb:jar:1.30.0 already exists in destination.
org.apache.commons:commons-lang3:jar:3.5 already exists in destination.
org.conscrypt:conscrypt-openjdk-uber:jar:2.2.1 already exists in destination.
io.grpc:grpc-stub:jar:1.30.0 already exists in destination.
com.google.guava:guava:jar:29.0-android already exists in destination.
org.slf4j:slf4j-api:jar:1.7.25 already exists in destination.
io.netty:netty-codec-http:jar:4.1.50.Final already exists in destination.
io.netty:netty-common:jar:4.1.50.Final already exists in destination.
io.netty:netty-buffer:jar:4.1.50.Final already exists in destination.
io.netty:netty-codec:jar:4.1.50.Final already exists in destination.
io.netty:netty-handler:jar:4.1.50.Final already exists in destination.
io.netty:netty-resolver:jar:4.1.50.Final already exists in destination.
io.netty:netty-transport:jar:4.1.50.Final already exists in destination.

Note that this ticket's creation arose from the following discussion: https://groups.google.com/g/google-cloud-firestore-discuss/c/u2XYqr6U1H0/m/AQlzI65aAwAJ

Should probably be reported directly at https://github.com/googleapis/java-firestore

Update: I was able to reproduce the timeout. Thanks for the excellent reproduction app! I have no idea yet what the root cause is but I will investigate and reply back here when I have something to report.

Update: I've opened a ticket with another GitHub repository: https://github.com/googleapis/gax-java/issues/1259. Let's see what happens with the discussion there.

Do you have any news on this subject? A workaround?

Unfortunately, there is no update yet to give. I'm still waiting for a response on the issue opened in the gax-java repository and I wouldn't expect a response until mid-January due to the holidays. I should warn you, though, that although your use case is valid, the reality is that it's a corner case that could be challenging to find a timely resolution to. Since all of the code involved is open source, if you have a chance to dig down into it that would be incredibly helpful in speeding up the official resolution. Sorry I don't have better news.


SWARM-1324: @Configurable zipkin fraction properties

[x] Have you followed the guidelines in our Contributing document?
[x] Have you created a JIRA and used it in the commit message?
[x] Have you checked to ensure there aren't other open Pull Requests for the same issue?
[x] Have you built the project locally prior to submission with mvn clean install?

Motivation:
Zipkin could not be configured through project-default.yml
Changes:
Added @Configurable attributes
Result:
Zipkin doesn't require a custom main() anymore

@bobmcwhirter mind a review? I've touched the configurables


Offline install/upgrade links for UCP 3.0.2 on Windows only point to Windows Server 1709 image

Problem description
The offline install and upgrade links for UCP 3.0.2 on Windows - here and here - point to the Windows Server 1709 specific image https://packages.docker.com/caas/ucp_images_win_1709_3.0.2.tar.gz. For Windows Server 2016 there is a separate image https://packages.docker.com/caas/ucp_images_win_2016_3.0.2.tar.gz, which needs to be called out in the documentation.
Problem location

https://docs.docker.com/ee/ucp/admin/install/install-offline/
https://docs.docker.com/ee/ucp/admin/install/upgrade-offline/

Project version(s) affected
UCP 3.0.2
Suggestions for a fix
Include version specific links for Windows Server 2016 and Windows Server 1709

Fixed in https://github.com/docker/docker.github.io/pull/6988


FIX-#3442: Add support for dt.hour in omnisci

Signed-off-by: izamyati<EMAIL_ADDRESS>
What do these changes do?

[x] commit message follows format outlined here
[x] passes flake8 modin/ asv_bench/benchmarks scripts/doc_checker.py
[x] passes black --check modin/ asv_bench/benchmarks scripts/doc_checker.py
[x] signed commit with git commit -s
[x] Resolves #3442
[x] tests added and passing
[x] module layout described at docs/development/architecture.rst is up-to-date
[ ] added (Issue Number: PR title (PR Number)) and github username to release notes for next major release

@Garra1980, please add a release note as part of a new PR.


Docs?

I'm looking around at different php GraphQL packages, and noticed an issue on Lighthouse stating that this package might be a better fit than Webonyx's. Is there documentation for this package?

Not yet, although now that we are nearing v1 we will put up something soon. Thanks for the reminder.


Ensure shifted keys are released

When presssing a SHIFT + any_key combination and releasing the SHIFT key before any_key, the any_key code is not sent.
This change will ensure any_key code is relesed before the SHIFT to ensure target system receives the right keyup event

Wouldn't this be incorrect behavior? If the following key events occur locally:

Press SHIFT
Press A
Release SHIFT
Release A

Then the events sent to the remote desktop should be exactly that. It would be incorrect to reorder the events to:

Press SHIFT
Press A
Release A
Release SHIFT

@mike-jumper the problem we are trying to solve are different key codes with and without SHIFT modifier.
Lets say we have 1 key that sends code x when no modifier is pressed and y when SHIFT is pressed. Under normal circumstances it would be like:

Press SHIFT
Press 1 -> sends keydown x.
Release 1 -> sends keyup x.
Release SHIFT

But when we do it in a different order, there is a race condition. There are two posibilities:

Press SHIFT
Press 1 -> sends keydown x.
Release SHIFT
Release 1 -> sends keyup x.

This is expected behavior, however when doing this relatively slowly we can end up with following state:

Press SHIFT
Press 1 -> sends keydown x.
Release SHIFT
Release 1 -> sends keydown + keyup y.

This means, that there is no sent keyup for x.

What do you see when you press the key sequence in question on the key event tester:
https://guacamole.apache.org/pub/tests/guac/keyboard-test.html

First press is fast, second is the same but a little bit slower:

And what keyboard layout are you using locally?

@mike-jumper US keyboard. Also tried it with Slovak keyboard (different key), same results:

Is there an associated JIRA issue to join the discussion?
I observed that reset() does not seem to work in all situations, usual case is a user using ctrl-tab or alt-tab, switching local browser tabs or windows, when refocusing the guacamole session the alt key is often stuck, even when reset() is called. We use a custom web client using guacamole-client, german keyboard layout de-de-qwertz.

@m1k1o - The issue you're seeing appears due to key repeat behavior. I don't think we should solve that behavior by reordering key events, but instead investigate and correct whatever is causing the shifted version of the key to not be released as its unshifted counterpart repeats. It may be a browser quirk that the keyboard support needs to work around, or it may be a bug in the client-side tracking of key state.
@everflux - What you describe sounds like something different and may not be a bug in Guacamole. If you encounter the same behavior in the latest release of the standard, unmodified Guacamole stack (1.4.0), then yes please open a JIRA. If you only encounter the issue with your modified webapp, then the issue lies with your webapp and you should request assistance in troubleshooting your app on the mailing list.

@everflux we also created our own web client and ran into similar issues. We connect to a Linux server using XRDP and needed support for shortcuts such as Ctrl + Alt + T which open a terminal on a Linux Desktop. The keyboard implementation from Guacamole doesn't forward the t key correctly. Here is a simplified version of our keyboard implementation which handles the shift key correctly (keyup events match the keydown event) and supports the before mentioned key combinations: https://41t3yq.csb.app/

@monken:

we also created our own web client and ...

Please be sure to test against the mainline Apache Guacamole webapp before reporting an issue as a bug in Guacamole. See: https://guacamole.apache.org/faq/#test-against-latest-version

If what you describe is reproducible against mainline Apache Guacamole, the issue ("t" not being sent correctly if Ctrl+Alt are held) does not sound related to this at all (a key repeat issue specifically tied to Shift) except for the fact that the keyboard is involved. If you think you've found a bug in the keyboard handling, please open an issue in our JIRA. If you also think you have a solution, please open a PR.

I do not see the behavior you describe testing against https://guacamole.apache.org/pub/tests/guac/keyboard-test.html:

@mike-jumper thanks for chiming in. I'm not seeing the same output. I'm testing this on Chrome on MacOS


Added missed esp policy

esp is added with esp_lifetime instead of esp_policy, corrected it.

@wilderrodrigues  Can you please review this PR

Thanks, @jayapalu
In order to give a LGTM, I checked the way it was used with the ipsectunnel.sh script. Indeed, it should be esp_policy instead of esp_lifetime.
LGTM :+1:

Removed convert_sec_to_h() on esp_policy.
@wilderrodrigues Please review this commit also

@jayapalu
LGTM


Mac Address issue in IOS

Hi,
I am using Plugin.BLE, I am facing one issue, I am unable to get Mac Id of the discovered devices by advertisements. Amazing fact is i am able to get Mac address of discovered devices in Android. I am using same plugin for both. can you help me in this issue or suggest me how can i get Mac address of discovered devices in IOS xamarin forms. In Android version, it is available in "e.Device.NativeDevice" which I get from advertisements but in IOS plugin i am unable to get Mac address of discovered devices.
Please help me in it, if there is any solution for it.

Hi @LiftTrack,
I'm the friendly issue checker.
It seems like (100.00 %) you haven't used our issue template :cry: I think it is very frustrating for the repository owners, if you ignore them.
If you think it's fine to make an exception, just ignore this message.
But if you think it was a mistake to delete the template, please close the issue and create a new one.
Thanks!

AFAIK you can't get the MAC Addresses in iOS.
https://developer.apple.com/forums/thread/8442
If you really need the Mac Address, you need to put it in the Advertisement as payload (obv. only works if you develop the device itself, too).

AFAIK you can't get the MAC Addresses in iOS. https://developer.apple.com/forums/thread/8442

Yes, this is simply not possible on iOS (platform limitation). Unfortunately raising three issues at once does not help either ;)
In any case, this is pretty much an FAQ, so maybe we should actually set up an FAQ page to clarify such questions ...?


bug: Visual Issues with GH data

Description
When working on Grasshopper to Power BI workflow for a tutorial, i faced a bug. I created a Speckle object inside Grasshopper. I connected the GH geometry as the displayValue key for the object. And I added two custom parameters too, Area and Department.

I received this data in Power BI and filtered out only Speckle objects from the flat list of elements. I visualized the GH data in 3D using 3D Viewer Visual. But there are 3 issues when using Visual with Speckle data:

Selection doesn't work when i connect "Filtered" data

When i receive Grasshopper data in Power BI and filter only the Speckle objects i created (and remove meshes and breps from the Source data),  selection items in the Visual stops working.

Shadows are way too dark

Inconsistent behavior: Visual Zooms in when tooltip info connected

When i connect "Department" key that i extracted from the received data as the "Tooltip Info", Visual zooms in for whatever reason. Zoom Extent on change option is turned on.

Sometimes i couldn't reproduce this.
Streams Used
https://speckle.xyz/streams/4f6eeaa421/branches/intro-gh-powerbi

#47


Ubuntu 20.04 terminal blank, no prompt, can't type any commands

Version
Microsoft Windows [Version 10.0.22000.1219]
WSL Version

[X] WSL 2
[ ] WSL 1

Kernel Version
No response
Distro Version
Ubuntu 20.04
Other Software
no other software, just opening the Ubuntu 20.04 terminal
Repro Steps
Click on Ubuntu 20.04 icon to open a terminal, or issue wsle.exe command in Windows Search bar.
Expected Behavior
I except the terminal window to open with a prompt that allows me to type code.
Actual Behavior
When I open a terminal I get a blank terminal with no cmd prompt and I cannot type anything.  No wsl.exe commands get executed and no error gets produced.  wsl.exe --version just never returns anything.
Diagnostic Logs
Also submitted via Feedback Hub.
WslLogs-2022-11-11_12-26-11.zip

Having exact same problem, but with Debian <IP_ADDRESS>.

@lpm-nova how long has your problem persisted?  My Ubuntu 20.04 app was working fine yesterday through at least 18:00 EST.  I noticed the problem this morning just after 10:00 EST but I'm not sure when between those times it first began.

Can you provide the output of wsl.exe -l -v ?

@jessicarowell everything was working fine yesterday.
@Biswa96 wsl.exe is completely unresponsive.

@Biswa96 I went into system32 dir and checked my wsl.exe file's properties. It's 10.0.22621.1. 192 KB, modified 5/7/2022

hrm, just did wsl.exe -l -v and nothing.
but I did wsl-exe --version and it's returning:
WSL version: <IP_ADDRESS>
Kernel version: <IP_ADDRESS>
WSLg version: 1.0.45
MSRDC version: 1.2.3575
Direct3D version: 1.606.4
DXCore version: 10.0.25131.1002-220531-1700.rs-onecore-base2-hyp
Windows version: 10.0.22621.819

@Biswa96 same for me - it's completely unresponsive.
@lpm-nova - where on your computer are you entering wsl.exe --version and getting output (e.g., are you entering in the search bar, or in cmd prompt, or somewhere else)?  I can't get any output at all.

@jessicarowell  I was running the command in the cmd prompt. Though earlier I DID click on the windows\system32\wslconfig.exe executable.
I have absolutely no clue if that did anything, but just in case it did, I'm letting you know.

@lpm-nova Hmm...interesting.  I tried both those things - first clicking on windows\system32\wslconfig.exe and then entering wsl.exe --version in Windows cmd prompt and got nothing.  It just never returns anything.

It's magically working now...

@lpm-nova That's great!  Mine is still broken...hope someone posts some suggestion soon. It's frustrating that I can't even provide @Biswa96 with the result of wsl.exe -l -v because the WSL console is unresponsive.

Same problem here. For me, it happens when I have wsl running and I put pc to sleep or hibernate, after waking up, I work as usual but after that, it does not shut down on its own and even wsl --shutdown stops working. -l -v is not working, and I have to manually kill the wsl preview process (with the little blue penguin icon) in task manager and then try again to start working.

@Biswa96 My Docker Desktop also hung (t was "starting" all day).  I force-shutdown Docker Desktop using Task Manager, and confirmed that it shut down, but that didn't fix the problem.  I can see in Task Manager the VmmemWSL process is at 98% CPU usage and 1.6GB RAM usage, but I am unable to force-shutdown ("The operation could not be completed.  Access is Denied").  Following what @muhammadsalmanafzal said, I tried wsl --shutdown and it hangs, just like any wsl command I issue.

This morning it works.  I don't see that any updates were applied last night.    This morning, Docker Desktop is running fine.  The vmmemWSL process that was running in the background at 98% CPU and 1.6GB RAM is gone from Task Manager.  wsl.exe -l -v opens at this address: /mnt/c/Windows/system32 and no output.

how about this problem now is what condition. my WSL just don't respond anything.

I have also same problem from 2 days

I am having the same issue. I open an Ubuntu cmd and it does not show anything. It also does not let me close it


Added to_delete to inferred connections and ensure output sockets can drive inferred and manual connections simultaneously

This PR moves around the check for deletes so we can pass the flag appropriately on inferred connections. I also added a test to make sure output sockets can pass values to children and manually connected components
via T. Kyle on GIPHY

bors try

bors merge


Object reference not set to an instance of an object

Honestly not sure if this is even really a thing to worry about, but it is something i see on a server restart each time.
[Error  :jtv_biomes.jtv_biomes] Object reference not set to an instance of an object  at Jotunn.Managers.ZoneManager.CreateClonedLocation (System.String name, System.String baseName) [0x00008] in <09aadbf6260840f5b368fc453d15b9fc>:0

I am getting the same error report every time I cross into a new area of the map.  The keeps repeating until the game becomes unplayable due to lag.  Any help would be greatly appreciated.


Editor window - two buttons same thing

I'm unsure why above the tree there are two buttons that appear to do the same thing - the pin and the arrows?
By Julian

Sorted in new design


Update http4s-blaze-client, ... to 0.21.20

Updates

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

from 0.21.14 to 0.21.20.
I'll automatically update this PR to resolve conflicts as long as you don't change it yourself.
If you'd like to skip this version, you can just close this PR. If you have any feedback, just mention me in the comments below.
Configure Scala Steward for your repository with a .scala-steward.conf file.
Have a fantastic day writing Scala!

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

labels: library-update, semver-patch

Superseded by #471.


libstdc++.so.6: version `GLIBCXX_3.4.26' not found

Hello,
I am facing some issue when i try to launch the AppImage version of the app (it do the same with the .deb)
I'm using Debian 10 and this is the error :

All my packages are up to date, i hope you can do something about that,
Thanks !

Hello,
Did you build the app yourself from the dev branch by any chance?

Hi, yeah but it do the same.

Alright,
At the moment, only the master branch is safe to build and ship for all platforms.
The others branches are not safe to build and ship. You should only be able to npm run dev on most platform.

Ok so i managed to build the app from the main repo with the following :
git clone --single-branch --branch master https://github.com/Kylart/KawAnime.git && cd KawAnime
npm i
npm run dist:linux
cd dist
./KawAnime 0.4.2.AppImage

It show the message to add the shortcut like on the dev version then there is a segfault (see screen).

I also tested by installing the .deb but it end with a segfault too. (i have installed all the dependencies of course)
Tell me if you need samples or something else.

Do this AppImage work?

No, It do the same error message that at the beginning.
I'm going to create a Debian VM to see if it's me or not, doens't want to take your time for nothing if it's the case.
I will reply here when i get the result.

So nothing change when i try to launch it from the VM, there is exactly the same error.
Using Debian 10, everything up to date.

Alright, I tried on a fresh Debian 10 as well.
Try install g++ package, it kinda worked for me

Hmmm still don't work for me since i already have it. I close the issue cause it seems that i'm the only one that have this problem, perhaps i do something bad...


Devtooling-182: Refactoring Responsemanagement ResponseAsset

I think you forgot to update the reference in tf_export. Also Johns PR has caused a lot of merge conflicts. Once you resolve them it should be good to merge