add ability to rewrite the ENTRYPOINT

Sometimes it might be useful to define an ENTRYPOINT in the Docker image, or some Docker images already have it.
For debugging, however, it might be practical to overwrite the entrypoint with e.g. /bin/bash. The standard docker command has this feature as:
docker run --entrypoint=/bin/bash
Unfortunately, there is no similar functionality in udocker. This could be a nice enhancement.
BTW, 'udocker run' has "--nometa" flag which helps, i.e. skips the defined ENTRYPOINT, but it also seem to reset some other metadata, which can be useful.

I have literally just run into exactly the same issue!

Ah... maybe not... sorry for the noise...

I had a quick look at this. There is an --entrypoint option in udocker.py at:
https://github.com/indigo-dc/udocker/blob/775308bfdc10c7d67c221ed62e1f401449a327fd/udocker.py#L7738
The best I could tell from the code is that if "entryp" is set as a string it will completely overwrite the command with that value and discard any other "cmd" values:
https://github.com/indigo-dc/udocker/blob/775308bfdc10c7d67c221ed62e1f401449a327fd/udocker.py#L2734
However, if "entryp" reaches this point as an array it will try to incorporate the rest of the run command "cmd" values as parameters.
In my case, I wanted to do this:
udocker run --rm -v /tmp/scripts:/tmp/scripts randomDockerImageWithEntrypoint:latest /bin/bash /tmp/scripts/my_script.sh
The docker image I want to use is built with an entrypoint that the script itself calls - I need to override this...
If I try to reset the entrypoint as docker suggests (https://docs.docker.com/engine/reference/run/#entrypoint-default-command-to-execute-at-runtime):
udocker run --rm -v /tmp/scripts:/tmp/scripts --entrypoint="" randomDockerImageWithEntrypoint:latest /bin/bash /tmp/scripts/my_script.sh
the builtin entrypoint fires rather than the command I specify on the command line.
If I try:
udocker run --rm -v /tmp/scripts:/tmp/scripts --entrypoint=/bin/bash randomDockerImageWithEntrypoint:latest /tmp/scripts/my_script.sh
the script is not executed - it just runs bash.
However if I try:
udocker run --rm -v /tmp/scripts:/tmp/scripts --entrypoint="/bin/bash /tmp/scripts/my_script.sh" randomDockerImageWithEntrypoint:latest
my_script.sh fires - hurra!
Perhaps Im missing something, but this feels like udocker entrypoint handling does not match that of Docker.
Best,
J

A fix is provided in v1.3.0. https://github.com/indigo-dc/udocker/releases/tag/v1.3.0


Fix encoding of optional TaggedImplicit object

Sorry, not familiar with TaggedParser and OptTaggedParser. Had to drop it from the test.

Hi, after review, I can confirm the problem in the serialization of TaggedValue<Implicit>. Thank you for your bug report, and the PR!
I am looking for the other APIs and will commit this before a new release.

Merged, thanks!


Feature/record disambiguation page

Hi @gtvj and @danbentley
Would you be able to approve this PR if all is OK? The editorial has been approved.
@gtvj would you be able to check that the HTML/CSS I have written is OK? I've checked it in Chrome/Firefox/IE11, with WAVe and Lighthouse, and at 400% zoom. To see the disambiguation page, you may need to add the Kong credentials to your .env file and then restart your docker containers (you can do this using the docker UI). The URL is here: http://localhost:8000/catalogue/MAF/42/8/
A question as well @gtvj - should I include the gtm script as well in this branch, since this is the first branch to include some analytics data?
@danbentley My "Introduce code to include analytics JSONs" commit proposes a technique for including the metrics JSON files. Does this look ok to you? We would then simply use this block to include the metrics JSON on the other applications. The empty JSON values would need to be populated via the backend though.
Thanks :+1:
Screenshot:

Thanks Ash! This looks good.
For a bit of background, when we populate the datalayer with content from the backend, we may create a custom filter to make testing easier, especially if the requirements become more complex (like branching logic, for example)
Additionally, we'll use json_script to output the JSON:

Safely outputs a Python object as JSON, wrapped in a

@gtvj I noticed I haven't added the metrics tags to the cards yet - I was going to do this during the Explorer branch as this is where I would properly add the card tags and loops. Is this OK?
I can add a container name to the template now.

Hi @AshTNA - in answer to your question above, I don't think we need to include the GTM script at this point. Helen and Heather need to set it up from their end and I'd like most of the changes relating to GTM to come in within a single PR when they've confirmed things are working on ds-wagtail-frontend (though I can see there is backend dataLayer work being added here as well as a data-container-name attribute).

Thanks @gtvj - I've made these changes. :+1:


System 5gr1__1__1.A__1.D missing template ligand to holo ligand atom order stacks

It seems that system 5gr1__1__1.A__1.D is missing valid data in ligand_template2resolved_atom_order_stacks (returning an empty atom stack for both the template ligand and holo ligand atom orders.
Is this intended or is this an error? Curious if there is something I should do to work around this (currently, I just skip those systems, but I'm not sure if there's a better or recommended approach).

After looking at the log, it seems this is a problem for more than just this one system (there are a few others with the same or similar issues seemingly resulting from a failure to align the template to the ligand mol)

2024-10-14 22:15:00,174 | plinder.core.structure.atoms:214 | WARNING : get_template_to_mol_matches: could not match template fully - retry with unmatched bonds set as UNSPECIFIED
Too many matching bond pairs (1854) so can't continue.
Too many matching bond pairs (1841) so can't continue.

For now, I'm skipping these systems, but I am curious if there is a filter I can apply when querying the plindex to avoid/prune these systems in advance.

I also ran into this problem when parsing rdkit molecules from the holo structure. Are there any cached molecules somewhere, to skip generation of all conformations every time...
2024-10-15 15:11:50,521 | plinder.core.structure.atoms:140 | WARNING : generate_conformer: default EmbedMolecule - failed, try using useBasicKnowledge=False

@rachitk - thanks for reporting this - the issue was due to RascalMCES algorithm having too low of the default limit for maxBondMatchPairs - increased it in the new PR to 5000 and it fixes the given system. And should make it unlikely to re-occur, but please let me know if you still experience problems with this.
@maciejwisniewski-drugdiscovery  - this is a feature request - it sounded reasonable and quick to add - included in the same PR.
You can now load PlinderSystem with passing an additional flag skip_3d_confgen=True, eg:
system1 = PlinderSystem(system_id="5gr1__1__1.A__1.D", skip_3d_confgen=True)
system1.holo_structure.input_ligand_conformers['1.D']

This then simply returns 2D coordinates for the ligands without attempting to generate a reasonable 3D molecule - this way it is a couple times faster when loading a system, but should be used only for methods when the method is not expecting a 3D molecule as an input.
PR for the above issues: https://github.com/plinder-org/plinder/pull/77
You can wait it for it to be merged or you can already start testing it from the branch.
Closing for now, but feel free to re-open when appropriate. :)


chore: release main

:rock: I've created a release for you
crash-handler: 4.1.4
4.1.4 (2024-07-01)
Dependencies

The following workspace dependencies were updated

dependencies

@dotcom-reliability-kit/log-error bumped from ^4.1.3 to ^4.1.4

fetch-error-handler: 0.2.5
0.2.5 (2024-07-01)
Bug Fixes

add type declarations for fetch-error-handler (36490d1)

log-error: 4.1.4
4.1.4 (2024-07-01)
Dependencies

The following workspace dependencies were updated

dependencies

@dotcom-reliability-kit/logger bumped from ^3.1.2 to ^3.1.3

logger: 3.1.3
3.1.3 (2024-07-01)
Bug Fixes

add type declarations for the logger (b514c2a), closes #946

middleware-log-errors: 4.1.4
4.1.4 (2024-07-01)
Bug Fixes

add type declarations for error-logging (9d65e0a)

Dependencies

The following workspace dependencies were updated

dependencies

@dotcom-reliability-kit/log-error bumped from ^4.1.3 to ^4.1.4

middleware-render-error-info: 5.1.4
5.1.4 (2024-07-01)
Bug Fixes

add type declarations for error-rendering (f6ceed0)
bump entities in /packages/middleware-render-error-info (da0ad99)

Dependencies

The following workspace dependencies were updated

dependencies

@dotcom-reliability-kit/log-error bumped from ^4.1.3 to ^4.1.4

opentelemetry: 2.0.2
2.0.2 (2024-07-01)
Dependencies

The following workspace dependencies were updated

dependencies

@dotcom-reliability-kit/log-error bumped from ^4.1.3 to ^4.1.4
@dotcom-reliability-kit/logger bumped from ^3.1.2 to ^3.1.3

This PR was generated with Release Please. See documentation.

:robot: Release is at https://github.com/Financial-Times/dotcom-reliability-kit/releases/tag/crash-handler-v4.1.4 :sunflower:

:robot: Release is at https://github.com/Financial-Times/dotcom-reliability-kit/releases/tag/fetch-error-handler-v0.2.5 :sunflower:

:robot: Release is at https://github.com/Financial-Times/dotcom-reliability-kit/releases/tag/log-error-v4.1.4 :sunflower:

:robot: Release is at https://github.com/Financial-Times/dotcom-reliability-kit/releases/tag/logger-v3.1.3 :sunflower:

:robot: Release is at https://github.com/Financial-Times/dotcom-reliability-kit/releases/tag/middleware-render-error-info-v5.1.4 :sunflower:

:robot: Release is at https://github.com/Financial-Times/dotcom-reliability-kit/releases/tag/opentelemetry-v2.0.2 :sunflower:


Documented WebDriver with python code examples

get_window_size
set_window_size
get_window_position
set_window_position
maximize_window
fullscreen_window

@diemol thoughts on using the w3c commands instead of legacy? This PR (and the current Java examples) show the OSS way of doing it and do not provide examples using the preferred w3c get_window_rect command. Or maybe we provide both? @hazmeister

Hmm I'm not actually finding a Java command for getting window rect...

@lmtierney That’s because Java doesn’t expose the getWindowRect command by itself. It used the command under the covers for getting window size and position, but doesn’t expose the command to return the whole rect.

@jimevans Do you know of a reason why we aren't? Did I miss a discussion? The WebElement has a getRect on it

Given the large sections of missing contents in the docs, I would vote that we merge this PR for now. There’s nothing stopping someone from adding a second code block with an alternate approach, but for Selenium today this code works. When version 4 ships, this snippet can be easily updated.

@hazmeister fair point. Thank you for the PR @liushilive!

Completely agree with @hazmeister! Thanks for merging @lmtierney


problem to install xsar and xsarsea python3.10

Following the installation documentation: https://cyclobs.ifremer.fr/static/sarwing_datarmor/xsarsea/installing.html
An error occur with openCV and numpy:
Collecting opencv-python
  Downloading opencv_python-<IP_ADDRESS>-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (60.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.5/60.5 MB 12.6 MB/s eta 0:00:00
  Downloading opencv_python-<IP_ADDRESS>-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (60.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 MB 10.0 MB/s eta 0:00:00
  Downloading opencv_python-<IP_ADDRESS>-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (60.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.3/60.3 MB 10.0 MB/s eta 0:00:00
  Downloading opencv_python-<IP_ADDRESS>-cp310-cp310-manylinux2014_x86_64.whl (60.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.3/60.3 MB 6.4 MB/s eta 0:00:00
  Downloading opencv-python-<IP_ADDRESS>.tar.gz (89.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.2/89.2 MB 8.4 MB/s eta 0:00:00
  Installing build dependencies ... error
  error: subprocess-exited-with-error

  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [927 lines of output]
      Ignoring numpy: markers 'python_version == "3.6" and platform_machine != "aarch64" and platform_machine != "arm64"' don't match your environment
      Ignoring numpy: markers 'python_version >= "3.6" and sys_platform == "linux" and platform_machine == "aarch64"' don't match your environment
      Ignoring numpy: markers 'python_version >= "3.6" and sys_platform == "darwin" and platform_machine == "arm64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.7" and platform_machine != "aarch64" and platform_machine != "arm64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.8" and platform_machine != "aarch64" and platform_machine != "arm64"' don't match your environment
      Collecting setuptools
        Downloading setuptools-65.5.1-py3-none-any.whl (1.2 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 13.0 MB/s eta 0:00:00
      Collecting wheel
        Downloading wheel-0.38.4-py3-none-any.whl (36 kB)
      Collecting scikit-build
        Downloading scikit_build-0.16.2-py3-none-any.whl (78 kB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.1/78.1 kB 4.8 MB/s eta 0:00:00
      Collecting cmake
        Downloading cmake-3.25.0-py2.py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23.7 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.7/23.7 MB 25.6 MB/s eta 0:00:00
      Collecting pip
        Downloading pip-22.3.1-py3-none-any.whl (2.1 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 30.9 MB/s eta 0:00:00
      Collecting numpy==1.19.3
        Downloading numpy-1.19.3.zip (7.3 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 37.8 MB/s eta 0:00:00
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'done'
      Collecting packaging
        Downloading packaging-21.3-py3-none-any.whl (40 kB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 2.0 MB/s eta 0:00:00
      Collecting distro
        Downloading distro-1.8.0-py3-none-any.whl (20 kB)
      Collecting pyparsing!=3.0.5,>=2.0.2
        Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 7.0 MB/s eta 0:00:00
      Building wheels for collected packages: numpy
        Building wheel for numpy (pyproject.toml): started
        Building wheel for numpy (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error

        × Building wheel for numpy (pyproject.toml) did not run successfully.
        │ exit code: 1
        ╰─> [877 lines of output]
            setup.py:67: RuntimeWarning: NumPy 1.19.3 may not yet support Python 3.10.
              warnings.warn(
            Running from numpy source directory.

possible explanations to investigate are:

[ ] 'jinja2<=3.0.3', in xsar/setup.py
[ ] 'numpy<=1.21',  # numba needs numpy<=1.21 in xsarsea/setup.py

if opencv is installed via conda. The problem is different:
First thtere this pip error:
Successfully built xsarsea
Installing collected packages: typer, numpy, llvmlite, numba, cftime, netCDF4, xrft, xsarsea
  Attempting uninstall: numpy
    Found existing installation: numpy 1.23.4
    Uninstalling numpy-1.23.4:
      Successfully uninstalled numpy-1.23.4
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
xsar 0.9.1 requires jinja2<=3.0.3, but you have jinja2 3.1.2 which is incompatible.
Successfully installed cftime-1.6.2 llvmlite-0.39.1 netCDF4-1.6.2 numba-0.56.4 numpy-1.21.0 typer-0.7.0 xrft-1.0.0 xsarsea-0.3.dev56+g0ccc3e3

then import xsarsea works.
while  import xsar never ends (strace last hints is pointing to cartopy).
tested on a ubuntu 22.04 and python 3.10 conda env.


IPAM controller operator crashes on Openshift

Setup Details
FIC Version : 0.1.5
CIS Version : 2.7.1
FIC Build: f5networks/f5-ipam-controller:latest
CIS Build: f5networks/k8s-bigip-ctlr:latest
BIGIP Version: Big IP x.x.x
AS3 Version: 3.x
Orchestration: K8S/OSCP
Orchestration Version:
Additional Setup details: Operator version from OLM is 0.0.1
Description
IPAM controller operator manager gets OOM Killed when reconciling F5IpamCtlr resources. The memory request/limit should raised on for the operator pod.
Steps To Reproduce

Install F5 IPAM controller operator
Create a F5IpamCtrl resource
The controller gets OOMKilled by Openshift dureing reconciliation.

Expected Result
Operator is not OOMKilled.

@bukovjanmic please try with the latest operator. Suggest to reinstall the operator and try a new CIS instance.


Fix version in makefile

OLD:
jessie at debian in ~/notary on fix-makefile
$ ./bin/notary version
notary
 Version:    '1.0-rc1'
 Git commit: 'ab66379'

WITH PATCH:
jessie at debian in ~/notary on fix-makefile
$ ./bin/notary version
notary
 Version:    1.0-rc1
 Git commit: ab66379

Signed-off-by: Jessica Frazelle<EMAIL_ADDRESS>

LGTM!


Latest version of xcode Command Line tools breaks sparsehash.

What steps will reproduce the problem?
1. Compile on Mac OS X Maverick with XCode Command Line Tools March 2014

What is the expected output? What do you see instead?

I was expected correct compilation

I have attached the log.

What version of the product are you using? On what operating system?

Latest SVN (116).
Mac OS X 10.9.2
Compiler: XCode Command Line Tools March 2014

Please provide any additional information below.

Original issue reported on code.google.com by<EMAIL_ADDRESS>on 24 Mar 2014 at 5:52
Attachments:

error.log

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public entities, optional import of base class module, and various Swift 1.2 fixes

@justin, I merged the current feature/swift12 branch with my fixes so this pull request should have just the changes I made and be "mergeable" into the feature/swift12 branch. let me know if you have any issues with it.

Thanks @dave256


Show error/message if Electrum server is not available for a coin

Can't add coins: ZCL, BTCH in electrum mode. Portfolio coins window refreshes but there is no selected coin.
For example: BTC, ZEC, HUSH works good

This is implemented now, as i saw in the newest version


AIWalkerController makes Pedestrians invisible in Lidar in 0.9.15

CARLA version: 0.9.15
Platform/OS: Linux Ubuntu 20.04
Problem you have experienced: Pedestrians are invisible in Lidar when an AIWalkerController is attached to them since .
What you expected to happen: Pedestrians are always visible in Lidar
Steps to reproduce:

spawn a pedestrian with an AIWalkerController controlling their behavior
Spawn a Semantic Lidar Sensor on the ego vehicle
Check the lidar pointcloud, and see that the pedestrian is not visible.

See also #6911 for a related issue with walkers becoming invisible in recordings.
All of this works fine with no problems in 0.9.14, but is broken since 0.9.15.
This might be related to "Optimizations" alluded to in the changelog regarding the collision mesh not being loaded as, but I can't test that. Either way, the issue was already confirmed by other users in Issue #6911

@Pyrestone you're right. I took a look into the commit where these changes are mentioned and found that they disabled the actor physics and collisions for walkers. I assume that disabled physics causes the lidar rays to move through the walkers. I found two ways how you can solve this issue:

Using Python code
This way you don't have to rebuild the Carla client library. Just insert this piece of code after starting the WalkerAIControllers

for actor in all_actors:
  if "walker.pedestrian." in actor.type_id:
    actor.set_collisions(True)
    actor.set_simulate_physics(True)

Edit WalkerAIController.cpp
Remove these three lines and rebuild the Carla client library. Maybe this undoes the alleged performance improvements, though you can see walkers in the lidar again :)

This has been fixed, update the dev branch, feel free to reopen it if it occurs again


num >= 20 - return "Huge"  instruction are not correct, to pass it should be num < 20 - return "Huge"

Challenge Chaining If Else Statements has an issue.
User Agent is: Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/50.0.2661.87 Safari/537.36.
Please describe how to reproduce this issue, and include links to screenshots if possible.
My code:

function testSize(num) {
  // Only change code below this line
 if(num < 5){
   return "Tiny";
 } else if (num < 10){
   return "Small";
 } else if (num < 15){
   return "Medium";
 } else if (num >= 20){
   return "Large";
 }else{
   return "Huge";
 }

  return "Change Me";
  // Only change code above this line
}

// Change this value to test
testSize(7);

@bobbytanwer the instructions are correct. You'll need to return "Huge" whenever num >= 20. If you get stuck with a challenge, please ask questions to the Help Room. Happy coding!

my test size 20 and test size 25 =huge but they are not passing


HTTP Requests for undefined gitignore types should return status 404

Idiomatic HTTP dictates that a webserver's response to a request for a non-existent resource should set HTTP status code 404 (not found).
This is not the case when requesting a gitignore type which doesn't exist, e.g.:
$ curl -sD - https://www.gitignore.io/api/foo
HTTP/2 200
date: Thu, 02 Aug 2018 14:06:22 GMT
content-type: text/plain; charset=utf-8
content-length: 173

# Created by https://www.gitignore.io/api/foo

#!! ERROR: foo is undefined. Use list command to see defined gitignore types !!#

# End of https://www.gitignore.io/api/foo

Sending an appropriate HTTP response code would help when writing scripts which use gitignore.io to automatically detect when a requested type doesn't exist.

What would you propose for this?
$ curl -sD - https://www.gitignore.io/api/foo,joe
HTTP/2 200
date: Thu, 02 Aug 2018 14:14:51 GMT
content-type: text/plain; charset=utf-8
content-length: 252
set-cookie: __cfduid=d5179f13602983e49ef984bdcf324e0dd1533219291; expires=Fri, 02-Aug-19 14:14:51 GMT; path=/; domain=.gitignore.io; HttpOnly
via: 1.1 vegur
expect-ct: max-age=604800, report-uri="https://report-uri.cloudflare.com/cdn-cgi/beacon/expect-ct"
server: cloudflare
cf-ray: 4441273e99b8ae02-BOS

# Created by https://www.gitignore.io/api/foo,joe

#!! ERROR: foo is undefined. Use list command to see defined gitignore types !!#

### Joe ###
# File backups
*~
# Gets created when joe crashes
DEADJOE

# End of https://www.gitignore.io/api/foo,joe

In this case there is one template that is valid and a second template that is invalid?

@joeblau That's an excellent point.
Here's a similar discussion: https://github.com/json-api/json-api/issues/230.
My gut feeling is that if any resource requested is not found, the whole response should get a 404 status.

@b0o - Can you test the staging endpoint and verify that it's doing everything you expect?
curl -sD - https://staging.gitignore.io/api/foo
Once you've verified it, I'll push staging to prod.

@joeblau Now I'm getting 404 on every request, even if the resource exists:
$ curl -sD - https://staging.gitignore.io/api/linux
HTTP/2 404
date: Thu, 02 Aug 2018 16:58:06 GMT
content-type: text/plain; charset=utf-8
content-length: 426
set-cookie: __cfduid=da8b39dbeddc3a108750fab75de6b17e81533229086; expires=Fri, 02-Aug-19 16:58:06 GMT; path=/; domain=.gitignore.io; HttpOnly
via: 1.1 vegur
expect-ct: max-age=604800, report-uri="https://report-uri.cloudflare.com/cdn-cgi/beacon/expect-ct"
server: cloudflare
cf-ray: 444216600dd6add0-SMF

# Created by https://www.gitignore.io/api/linux

### Linux ###
*~

# temporary files which can be created if a process still has a handle open of a deleted file
.fuse_hidden*

# KDE directory preferences
.directory

# Linux trash folder which might appear on any partition or disk
.Trash-*

# .nfs files are created when an open file is removed but is still being accessed
.nfs*

# End of https://www.gitignore.io/api/linux

Ah I know what the problem is.

@joeblau Seems to be working as expected now. Thank you so much for making this change so promptly!


Simpliy debian install file

Only the msd/ subdirectory contains temporary build files. It's safe to * for everything else.

@XECDesign


feat: support dark mode

This pull request adds support for automatic dark mode, only on the documentation section.

The home page is unchanged (no dark mode), except for slight code highlighting changes (which are global)
The original documentation light theme is unchanged
I slightly improved the formatting on docs.view.php (indentation, element alignments, added a few comments for readability)

Do you mind if I we widen the main container? It seems very narrow to me... I think Tailwind's default prose is not really thought for larger screens. Making it slightly larger is, well, slightly better for the eyes:

I'll open another PR if you're okay with that.

Very nice!!

Deployed 💪 https://tempestphp.com/docs/framework/01-getting-started


Change message bus unsubscribe event driver

Fixes #53

Tested in IE11 and Chrome.
Tested application canceling beforeunload to ensure unload is still unregistering the window when user confirms closing window.


OriginalCommandElements Usage Order

While using "OriginalCommandElements" the values added to this always occur before any created parameters.
For instance using one of your sample JSON files:  HERE
The usage of this command would output to "docker" as:  docker image rm id "YourValue"
For some executables the order in which you output the parameters must be defied in a proper order.  For instance Android ADB.  You must define your device serial number prior to any other parameters.
Take this ADB command to get a directory listing:  adb.exe -s SERIAL shell ls
If I were to use "shell", "ls" within the "OriginalCommandElements" it would output my command to ADB as:  adb.exe shell ls -s SERIAL
This command would immediately fail.
It would be nice if the output order were to be configurable in some way.  Either adding a new parameter like "OriginalCommandElementsOrder" or perhaps even within the normal parameter section like:
"Parameters": [
    {
        "OriginalName": "-s",
        "Position": 0,
        "Name": "Serial",
        "ParameterType": "string",
        "Mandatory": true,
        "NoGap": false,
        "Description": "Device serial number",
        "ValueFromPipeline": true,
        "ValueFromPipelineByPropertyName": true
    },
    {
        "Position": 1,
        "Name": "OriginalCommandElements"
    }
}

The actual implementation of this would need to be discussed with the internal team to best determine this though.

Would be nice if this can be added. Currently trying to use the sc.exe to create services remotely, but cannot figure a way out how to add the original \servername in front of the OriginalCommandElements.
Example:
"Verb": "New",
"Noun": "ScService",
"OriginalName": "C:\Windows\System32\sc.exe",
"OriginalCommandElements": ["create"],
"SupportsShouldProcess": true,
"ConfirmImpact": "High",
"DefaultParameterSetName": "Default"
In this case, optionally you can also give the \servername in front of sc \servername create, is this possible already to-do?
(Don't ask me why I'm using sc.exe, as there are plenty of alternatives) ;)

Isn't this what the parameter flag ApplyToExecutable is for ?
Basically the build order seems to be
  <parameters flagged "apply to executable">

@jhoneill has it correct, ApplyToExecutable is used for this very purpose. They are also sorted, so you may put those in whatever order is appropriate by including that information.


Accentued caracters

Hi,
How can i have a valid output with accentued caracters ?
For the moment when i convert a such caracter i have a question mark.
intégration -> int�gration
Cheers

Hi,
I did some simple tests and in my case accented characters like àèìòù seem to work fine, when I just input them with the keyboard.
For sure at worst you could encode them as HTML entitites, e.g. à è ì etc.: (see this for more info)... but could you please attach the markdown file you are trying to convert, so I can test it and see?

Hi please find attached the incriminated file :)
Cheers
Le Mardi 10 janvier 2017 11h34, Fabio Cevasco<EMAIL_ADDRESS>a écrit :

Hi,I did some simple tests and in my case accented characters like àèìòù seem to work fine, when I just input them with the keyboard.For sure at worst you could encode them as HTML entitites, e.g. à è ì etc.: (see this for more info)... but could you please attach the markdown file you are trying to convert, so I can test it and see?—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or mute the thread.

Mmmm can't find any file... could you attach it to the github issue or send it by email to<EMAIL_ADDRESS>Thanks!

Cannot reproduce; closing this issue.


Reserach how to scale the pinning-server

Currently we are using an integrated ipfs + orbitdb node for pinning, this doesn't scale that well.
Data is stored in the ipfs node, orbitdb also stores some data in the ./orbitdb folder. There are some paths to investigate:

Use one ipfs node and multiple orbitdb nodes that connect to it. This means that all 3box-js clients would connect to the same ipfs node (same ipfs multiaddr) but their orbitdb metadata would be saved on different nodes.

Use multiple nodes that have both ipfs & orbitdb  This means that each 3box-js node would need to know which node to connect to in order to get their data replicated.

A combination of above with n ipfs nodes & m orbitdb nodes, where n < m  I'm not sure this has any advantage over the first two alternatives.

The result of this research should be to compare the pros/cons of these and any additional setups for pinning, and suggest a way of implementing atleast one of them.

@c-castillo is this part of what you are doing currently?

@oed yes, it's a good summary

@c-castillo ok, should we put this to in progress then?
So once you are done with the research you can outline how it will be implemented so that everyone else is aware of how it works 🙂

@c-castillo I was thinking about this the other day. I liked your idea of sharding based on the modulo on the hash of your odb-address. I think we can extend it like this:
calculate your shard id by: sid = h(odb-addr) % n where n is number of shards.
When you send your address to the pinning server use pubsub room with name: 3box shard <sid>
Now we can have pinning servers that listen to different pubsub rooms (one server might listen to multiple).


Refocusing UI to allow exclusion of background traits

in road map due April

in road map due April

https://docs.google.com/document/d/1agaBcPxuCws0pKnuZh_PJylk5TO84FG9YGgpxIXzZpY/edit?usp=sharing

Testing 2021-06-14:

Separate trait and background trait columns are very clear and fit well with the other columns in both the Association and Study tables, e.g. on a publication page (http://snoopy.ebi.ac.uk:9580/gwas/publications/30267110)
Separate fields at the top of each Study page are also very clear and well formatted (e.g. http://snoopy.ebi.ac.uk:9580/gwas/studies/GCST007192)
The "include background traits data" checkbox on the Trait page (e.g. http://snoopy.ebi.ac.uk:9580/gwas/efotraits/EFO_0004246) is a useful feature. It seems to perform the correct filtering when clicked: e.g. there are 91 associations annotated with EFO_0004246, 26 where it is a background trait, so when "include background traits data" is unticked, 91 - 26 = 65 associations displayed. Same for studies: 19 total - 8 with background trait = 11 after checkbox is unticked. @ljwh2 I think this is a nice way to allow users to see both sets of data, but I think maybe background traits should be "off" by default and users can opt in to adding them (at the moment they are "on" by default) - what do you think?
Tried searching for the same trait in the main search results (http://snoopy.ebi.ac.uk:9580/gwas/search?query=mucocutaneous lymph node syndrome) - weirdly this gives different numbers (46 associations and 15 studies), which doesn't match either the "with background traits" or "with our background traits" numbers above... but maybe this is also complicated by the child traits?
LocusZoom diagram on Trait page: the diagram includes all associations by default and filters out the background trait annotations when you untick the box. As above, I think this is a nice feature but should be the other way around (i.e. background traits off by default, you can add them if you want)
I found one study (http://snoopy.ebi.ac.uk:9580/gwas/studies/GCST90013538) where the background trait was correctly split out for the study but not for each association. I'm not sure how we could systematically check for other examples like this.

Oddly, for the example study above with the incorrectly annotated associations (http://snoopy.ebi.ac.uk:9580/gwas/studies/GCST90013538), when I click on the individual variant links, the resulting Variant pages do not contain any studies or associations (e.g. http://snoopy.ebi.ac.uk:9580/gwas/variants/rs6017006)...
So maybe there is something else going on with this study

@eks-ebi good catch! data in DB and in Solr Search server is correct, it's UI thing, I'm investigating.

@eks-ebi The study that has split studies but not associations was a submission, I wonder if that had some effect? Do you have any other examples of submissions with a background trait?

Overall functionality looks great!
I agree scientifically it would be better to exclude background traits by default if possible (unchecked box) BUT this requires us to define behaviour of traits which are only background (note - an example of this is Trypanosoma cruzi seropositivity). We can discuss, but on balance it may be better to leave as is.
I noticed an issue for traits that have both child terms and background traits. Unchecking background traits seems to exclude child traits as well. Unchecking and rechecking child traits adds them back in.
Example: hypertension EFO:0000537
755 associations, 91 studies.
Uncheck background traits:
394 associations, 33 studies.
Uncheck child traits as well:
394 associations, 33 studies.
Recheck child traits:
515 associations, 58 studies.
Another example is schizophrenia EFO:0000692, behaviour is the same.

Cheers, well spotted! I have deployed a fix.

@eks-ebi Re-tested checking and unchecking child & background boxes, works as expected now.
We discussed and decided it would be better to have the background traits box unticked by default.

'Apply efo traits to associaitons' to associations now takes into account background traits as well, they can be seen later on in the association page

Tested UI again today: I've looked through all the different pages (Trait, Study etc.) and everything looks correct. Ticking/unticking the bg trait box working fine.
Not sure if anything else specific needs testing?

Testing the Curation interface:
The 'Apply efo traits to associations' button works well: I added a bg trait to a study that already had a main trait --> the button left the main trait as it was and added bg trait to all associations.

@ala-ebi let me know if there's anything else that needs testing

We discussed adding a tooltip for the background trait field in the UI.
Proposed text:
"A trait that is not directly analysed in the GWAS, but is shared by all study participants as a common characteristic."
@ljwh2 Does this look ok?

Yes I'm happy with that @eks-ebi

filled background traits in 'All studies v1.0.3' downloads

@ala-ebi
I've checked 'All studies v1.0.3' download and all of the background traits seem to be displayed correctly.

I've also checked the tooltip mentioned above and it looks good on the Study page. But I think it would be good to also display the same tooltip in other places where the term "background trait" appears:

In the column header in the Associations and Studies tables:

On the Trait page next to the background traits checkbox

@ljwh2 Would you agree?

done

FAQs now updated to explain background traits, committed to documentation branch:
https://github.com/EBISPOT/gwas-ui/blob/documentation/goci-interfaces/goci-ui/src/main/docs/faq-content.adoc


[owners] Bring everything together for using the virtual repo

This PR:

uses the bootstrapping module in the info server
migrates the botstrapper to use a virtual repo instead of a local repo
warms up the in-memory cache during bot initialization
adds a missing await before a promisified function
updates app.yaml for GAE deployment

@danielrozenberg Hold off on reviewing this, I'm splitting it into a handful of smaller changes (this grew larger/more chaotic than expected)


shared/net: add GetNetIPAddresses() and improve GetStringIPAddresses()

extend shared/net for better compatibility around net.IP usage and string addresses

@karasz without a _test.go file?

@karasz without a _test.go file?

for now no _test.go.


error in scanning

main: Done!
failed: XML syntax error on line 124: invalid characters between </compilerEndOption and >

Fixed in latest release.


Add the examples link to readme again

Wasn't really sure where to put it. Feel free to make suggestions

@cjpillsbury looks like Wes made the changes and it needs your review to merge.


VP9 support

Hello,
for web delivery compatibility reason i would/should encode in VP9 in WebM container.
As Av1an support libvpx, could be possible for rav1ator-cli  to support VP9 too ?
Thank you !

Thanks for the request! I'll look into it


Add reader for spikes sorted by Phy.

Hi @joshigold, here's some code to read spikes from Phy, in additoin to Plexon.  Since this is a shared repo, I figured it made sense to make a PR.
Here's how I used it locally:
% Pick a .plx file, plus Phy files generated by Kilosort for the same .plx file.

monkeyDir = '/home/ninjaben/Desktop/codin/gold-lab/plexon_data/MrM/';
plxFile = fullfile(monkeyDir, 'Raw', 'MM_2022_11_28C_V-ProRec.plx');
[~, plxBaseName] = fileparts(plxFile);
phyFile = fullfile(monkeyDir,  'Kilosort', 'MM_2022_11_28C_V-ProRec-results', 'phy', 'params.py');
convertedFile = fullfile(monkeyDir, 'Converted', 'Sorted', plxBaseName);

%% Task and behavioral data from .plx file, spikes from phy files.
file_in = {plxFile, phyFile};
file_type = [];
spm = 'spmADPODR5';
spike_list = [zeros([1000, 1]), (0:999)'];
sig_list = 49:51;
keep_matCmds = 0;
keep_dio = 1;
flags = 0;
messageH = [];
rawFlag = false;

fprintf('Building FIRA ...\n');
tic();
bFile(file_in, ...
    file_type, ...
    spm, ...
    convertedFile, ...
    spike_list, ...
    sig_list, ...
    keep_matCmds, ...
    keep_dio, ...
    flags, ...
    messageH, ...
    rawFlag);
toc();

I'll go ahead and merge this.  But the (closed) PR here can still be a nice way to see what the change was.


fix (apps-list.component.html)  set black pixel instead of empty src

empty src caused stream of errors and cpu load

LGTM

Coverage remained the same at 59.693% when pulling 25028d4e5def55f39cc731814c232a7b8b65d2c7 on nikage:app-store@charts-list-fix-memory-leak into e42b5de5d0e8c1a4aa46e4de7ba075b80099ffec on supergiant:master.


fix targetPath regexp

Directory name includes query params while generating route, but it shouldn't.

@egoist I never worked with ream generator, please advise if the PR makes sense?


grpc_json_transcoder: to support escaped json_name in query parameters

Signed-off-by: Wayne Zhang<EMAIL_ADDRESS>For https://github.com/envoyproxy/envoy/issues/21151

Updated grpc-httpjson-transcoding repo to have this change.
Add some unit tests for different json_name case:

a proto message field
  // To test json name is percentage decoded
  string search_decoded = 3 [json_name = "search[decoded]"];

  // To test json name is percentage encoded
  string search_encoded = 4 [json_name = "search%5Bencoded%5D"];

with query parameter names in following
* search[decode]:   work
* search%5Bdecode%5D:  work

* search[encode] :     fail
* search%5Bencode%5D:    work

/lgtm deps

/test envoy-presubmit

I think the test failure is flaky.  The error is
Server terminated abruptly (error code: 14, error message: 'Socket closed', log file: '/build/tmp/_bazel_envoybuild/b570b5ccd0454dc9af9f65ab1833764d/server/jvm.out')

Could someone help to retest it?  Thanks

/retest

/retest
to let the windows artifacts finish compiling

/retest

@lizan / @qiwzhang when will this be released? I see there have been some releases since this was merged, but this change wasn't included in them. Thanks!

Probably will be in next Envoy release from top of three, v1.23.0.  Not sure when it will be.  Recent envoy releases are all security patches.


D406 auto-detect pydocstyle

command: ruff .
version: ruff 0.0.247
pyproject.toml: https://github.com/home-assistant/core/blob/3a34f818e8add8527ec66c85a4066162d2a715d9/pyproject.toml#L267-L274

We currently ignore D406 on the Home Assistant repository, and I would like to remove that code from the ignore list.
We also currently have a mixture of numpy and google styles, so we are not setting the convention at this stage.
What I don't understand right now is why Args: passes but not Returns: in the following docstring:
def get_gas_price(data: EasyEnergyData, hours: int) -> float | None:
    """Get the gas price for a given hour.

    Args:
        data: The data object.
        hours: The number of hours to add to the current time.

    Returns:
        The gas market price value.
    """

I would expect either both Args and Returns to fail, or neither.

Will take a look at this today.

Cc @frenck, for information.

#3325 will improve this quite a bit, in that any docstring that contains (e.g.) Args will be treated as Google-style, any docstring that contains (e.g.) Parameters will be treated as NumPy-style, etc. (assuming you haven't set a convention in your config).


MINOR: update upgrade notes for Streams API; message format 0.10 requiered

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/kafka-pr-test-coverage/215/

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/kafka-pr-test-coverage/222/

Retest this please.

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/kafka-pr-test-coverage/255/

Retest this please

Retest this please

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/kafka-pr-test-coverage/308/

Retest this please.

Retest this please.

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/kafka-pr-test-coverage/365/

LGTM.
@mjsax since apache jenkins is unstable these days, for doc changes if local unit test passed, feel free to merge it.

Merged to trunk and cherry-picked to 1.1 branch.


Bot stopped playing after long "video not available in" error

Here's the full log: http://prnt.sc/ajmq5e | http://prnt.sc/ajmpxj
Happened again: http://prntscr.com/ak2qvi | http://prntscr.com/ak2r36
Happens a lot... Here's another log: http://prntscr.com/ambglf

If this is an issue with youtube-dl should i just post something on their github or what?

Doesn't look like this happens very often.  If its still happening consider making an issue on the ytdl repo.


Conflict between Fastlane and Firebase App Distribution

*** Steps to file a bug ***

Try updating to the latest version of this plugin, and fastlane
If the issue persists, fill out the sections below
Delete this section and submit

Issue Description
[11:21:08]: 59: end
[11:21:08]: 60: end
[11:21:08]: => 61: xczvxzcvl;kjb `````` ``
[!] Syntax error in your Fastfile on line 61: Fastfile:61: syntax error, unexpected backtick literal, expecting end-of-input
xczvxzcvl;kjb
Configuration
desc "Lane for distribution"
lane :distribute do
gradle(
task: "assemble",
build_type: "Release",
properties: {
"android.injected.signing.store.file" => ENV['SIGNED_STORE_FILE'],
"android.injected.signing.store.password" => ENV['SIGNED_STORE_PASSWORD'],
"android.injected.signing.key.alias" => ENV['SIGNED_KET_ALIAS'],
"android.injected.signing.key.password" => ENV['SIGNED_KEY_PASSWORD']
}
)
      firebase_app_distribution(
          app: ENV['APP_ID'],
          groups: "developer",
          release_notes: "[수정사항]\n -  UserAgent 삭제 (심사 전 테스트)",
          debug: true,
          firebase_cli_token: ENV['FIREBASE_TOKEN']
      )
  end

Complete verbose output

Environment
Window
Fastlane :  2.220.0
Firebase app distribution : 0.9.1
Android Studio Jellyfish | 2023.3.1
-> It works well with Fastlane 2.214.0 and Firebase App Distribution 0.7.1.

Library
Version

fastlane
[2.220.0]

fastlane-plugin-firebase_app_distribution
[0.9.1]

Hi @only2433 !

[11:21:08]: => 61: xczvxzcvl;kjb `````` ``

Any idea where this is coming from? Supposedly it's from line 61 of your Fastfile. Is it possible, that that file was somehow corrupted?
The issue seems unrelated to the update of fastlane itself or the fastlane-plugin-firebase_app_distribution.


Update podspec version to 0.3.2

I would like to update the podspec file so that CocoaPods users can use the latest version of the library. After the merge, tagging with 0.3.2 and then pod repo push is needed.

Thanks @sandordilong - sorry, I've neglected the podspec updates! I'll publish the pod spec as soon as I overcome an error it's throwing.

The podspec is now published as v0.3.4 @sandordilong - thanks for your help!

Hi @johnpatrickmorgan! Thanks for the pod update and your work!


Some libraries from node_modules (or every) do not compiled by babel

Environment
"@haul-bundler/babel-preset-react-native": "^0.16.0",
<EMAIL_ADDRESS>"^0.17.0",
"@haul-bundler/cli": "^0.17.0",
"@haul-bundler/core": "^0.17.0",
"react": "16.9.0",
"react-native": "0.61.5",
Description
Looks like haul babel presset ignores node_modules, but some libraries which need to be compiled,like rn-viewpager.
Bundle crashes on class static property, which works fine if i write that right in my App.tsx.

Maybe it is a not an issue, cause i understand that not every node_module should be compiled,
but what should i do in this case? (except choosing another lib)
To reproduce

react-native init
yarn add haul -> init -> start
--empty project works fine--
yarn add rn-viewpager
add minimal code

import { IndicatorViewPager, PagerDotIndicator } from 'rn-viewpager';

const App = () => (
    <>
        <IndicatorViewPager
            style={{ height: Dimensions.get('window').height }}
            indicator={(
                <PagerDotIndicator
                    pageCount={3}
                />
            )}
        >
            <Text>TEST</Text>
            <Text>TEST</Text>
            <Text>TEST</Text>
        </IndicatorViewPager>
    </>
);

It also solves with custom babel/ts config from recipe.
export default makeConfig({
  bundles: {
    index: {
      entry: withPolyfills('./index.ts'),
      transform({ config }) {
        config.module.rules = [
          {
            test: /\.tsx?$/,
            exclude: '/node_modules/',
            use: [
              {
                loader: 'babel-loader',
              },
              {
                loader: 'ts-loader',
              }
            ]
          },
          ...config.module.rules,
        ];
      },
    },
  },
});

looks like it's happening since issue 220.
if i console.log the passed config in transform function, it does not looks like node_modules were excluded from babel, but behavior suggests otherwise.

@Natteke not every node_module package is excluded, some are transpiled but the great majority is not.


Fix error with names over 32 characters

Fixes(hopefully) a bug where it wouldn't correctly check new tup names against the database if the name was over 32 characters, leading to errors if the command is otherwise successful and it tries to register.

oops thanks


Survey/Observation Cardinality

One report may link to many surveys, observations, entities?
e.g. annual report for a tenure may have multiple bores, seismic, and scientific surveys and samples.

This is taken from SOSA isResultOf https://www.w3.org/TR/vocab-ssn/#SOSAisResultOf
When I look at the reports that are in the reports list, there would only be one report per survey.
Worth going through the reports list and validating that.
The bores are linked by feature of interest.
Samples are linked to the survey (see survey model).
Observations and results are linked to the samples.

@KellyVance please close if you are satisfied with the response.

Nothing specific I can add here sorry. I can say, generically, that its most important to get the shape of the models and the class of objects in them: Report, Sample, Survey etc. Cardinalities can be fiddled with easily enough and, in many cases, it may pay to err on the side of flexibility for all those cases that break convention. We can always query out outliers and deal with them, rather than forcing them in model constraints.

Closing issues as per conversation re: one survey may relate to many datasets


Vite.js v2 occasionally crashes during development in VS Code on Windows 10

⚠ IMPORTANT ⚠ Please check the following list before proceeding. If you ignore this issue template, your issue will be directly closed.

[x] Read the docs.
[x] Use Vite >=2.0. (1.x is no longer supported)
[x] If the issue is related to 1.x -> 2.0 upgrade, read the Migration Guide first.

Describe the bug

A clear and concise description of what the bug is.

My react project is created by yarn create @vitejs/app <repo-name> --template react-ts.
When I start vite command yarn dev and save files it shows this error and stops vite runtime (it crashes sometimes sooner sometimes later):
15:53:57 [vite] hmr update /src/App.tsx
node:events:353
      throw er; // Unhandled 'error' event
      ^

Error: EBUSY: resource busy or locked, lstat 'C:\DumpStack.log.tmp'
Emitted 'error' event on FSWatcher instance at:
    at FSWatcher._handleError (C:\Users\bransky\projects\_playground\vitejs-issue-watcher-reproduction\node_modules\vite\dist\node\chunks\dep-055fc131.js:11574:10)
    at ReaddirpStream.NodeFsHandler._boundHandleError (C:\Users\bransky\projects\_playground\vitejs-issue-watcher-reproduction\node_modules\vite\dist\node\chunks\dep-055fc131.js:10070:43)
    at ReaddirpStream.emit (node:events:376:20)
    at emitErrorNT (node:internal/streams/destroy:188:8)
    at emitErrorCloseNT (node:internal/streams/destroy:153:3)
    at processTicksAndRejections (node:internal/process/task_queues:80:21) {
  errno: -4082,
  code: 'EBUSY',
  syscall: 'lstat',
  path: 'C:\\DumpStack.log.tmp'
}
error Command failed with exit code 1.
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.

Reproduction

Please provide a link to a repo that can reproduce the problem you ran into.
A reproduction is required unless you are absolutely sure that the the problem is obvious and the information you provided is enough for us to understand what the problem is. If a report has only vague description (e.g. just a generic error message) and has no reproduction, it will be closed immediately.

https://github.com/MatejBransky/vitejs-issue-watcher-reproduction
(it's the unchanged project right after the command yarn create @vitejs/app <repo> --template react-ts)
I think it's related to some background services which run during VS Code session because if I try to reproduce it within external terminal and project is not opened in VS Code then it's still working..but when I try to open project with VS Code then it crashes.
VS Code version: 1.52.1
System Info

vite version: 2.0.0-beta.48 (already exists in v 2.0.0-beta.12)
Operating System: Windows 10 Pro (19042.746)
Node version: 15.4.0
Package manager (npm/yarn/pnpm) and version: yarn v1.22.5

Logs (Optional if provided reproduction)

Run vite or vite build with the --debug flag.
Provide the error log here.

16:41:27 [vite] hmr update /src/App.css (x2)
  vite:load 1ms   [fs] /src/App.css +2s
  vite:hmr [self-accepts] src\App.css +7ms
  vite:transform 0ms   /src/App.css +2s
  vite:time 3ms   /src/App.css?import& +2s
  vite:load 3ms   [fs] /src/App.css +2ms
  vite:hmr [self-accepts] src\App.css +2ms
  vite:transform 1ms   /src/App.css +2ms
  vite:time 4ms   /src/App.css?import& +2ms
node:events:353
      throw er; // Unhandled 'error' event
      ^

Error: EBUSY: resource busy or locked, lstat 'C:\DumpStack.log.tmp'
Emitted 'error' event on FSWatcher instance at:
    at FSWatcher._handleError (C:\Users\bransky\projects\_playground\vitejs-issue-watcher-reproduction\node_modules\vit
e\dist\node\chunks\dep-382a279c.js:11575:10)
    at ReaddirpStream.NodeFsHandler._boundHandleError (C:\Users\bransky\projects\_playground\vitejs-issue-watcher-repro
duction\node_modules\vite\dist\node\chunks\dep-382a279c.js:10071:43)
    at ReaddirpStream.emit (node:events:376:20)
    at emitErrorNT (node:internal/streams/destroy:188:8)
    at emitErrorCloseNT (node:internal/streams/destroy:153:3)
    at processTicksAndRejections (node:internal/process/task_queues:80:21) {
  errno: -4082,
  code: 'EBUSY',
  syscall: 'lstat',
  path: 'C:\\DumpStack.log.tmp'
}
error Command failed with exit code 1.
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.

(it crashed at 16:42:10 so it's not related to the last change in the source code)

I think this is related issue: https://github.com/vitejs/vite/issues/1553

I think this is related issue: https://github.com/vitejs/vite/issues/1553

It's really unstable to reproduce it I would love to include more info but I just don't know what's happening. Sometimes it last for a really long time and sometimes it crashes almost immediately (like after a few minutes).

It's really unstable to reproduce it I would love to include more info but I just don't know what's happening. Sometimes it last for a really long time and sometimes it crashes almost immediately (like after a few minutes).

It looks like this is caused by chokidar trying to watch your entire volume. Not sure what could lead to that - and since I can't reproduce this on my windows machine, it can only be a guess in the dark...
I tried only passing windows-style paths to all chokidar methods in beta.49, please try that to see if it makes any difference.

It looks like this is caused by chokidar trying to watch your entire volume. Not sure what could lead to that - and since I can't reproduce this on my windows machine, it can only be a guess in the dark...
I tried only passing windows-style paths to all chokidar methods in beta.49, please try that to see if it makes any difference.

It looks like ok... at least it's still working without any crash.. 👍 I'll send more info later after few dev hours.

It looks like ok... at least it's still working without any crash.. 👍 I'll send more info later after few dev hours.

I saw that error a lot while while working on a Vite app last week . But it was really random.
After reading Evan's comment, I found a reproduction.
Simply creating a new folder on C:\ directory fires this error.
I can reproduce in v2.0.0-beta.48.
v2.0.0-beta.49 works fine ✌

I saw that error a lot while while working on a Vite app last week . But it was really random.
After reading Evan's comment, I found a reproduction.
Simply creating a new folder on C:\ directory fires this error.
I can reproduce in v2.0.0-beta.48.
v2.0.0-beta.49 works fine ✌

Great! Thanks for the fix! I'm the happiest developer in the world because now I can transfer all companys frontend projects (libs and apps) into Vite.js environment! Great work @yyx990803 and others! 🥇

Great! Thanks for the fix! I'm the happiest developer in the world because now I can transfer all companys frontend projects (libs and apps) into Vite.js environment! Great work @yyx990803 and others! 🥇

Good to know the blind guess fix worked! 😅

Good to know the blind guess fix worked! 😅


How to change MySQL port

I am trying to change the port used by my docker container (followed installation instructions) but it always throw an error (I am sure I am missing a step somewhere, but I have followed documentation)
docker-compose up -d nginx mysql

Error message
Error starting userland proxy: Bind for <IP_ADDRESS>:3306 failed: port is already allocated

[x] Edited mysql/my.cnf
      [mysqld]       port=3308
[x] Edited docker-compose.yml
      ports:              - "3306:3308"

Hi @philtrep
it seems that you have already a running container with port binding to 3306.
Furthermore if you want to change the port of your container you have to edit the first one like this:
Edited mysql/my.cnf
[mysqld] port=3306

Edited docker-compose.yml
ports: - "3308:3306"

Or better, just use expose instead of ports if you don't plan on needing to connect to your mysql database from the host. If you're only going to be using it from an application within your docker stack, there's no reason to bind the port on the host. If you're going to use it in production, it's even more important that you DON'T use ports and instead use expose for services like mysql. Only your web-facing services (nginx, apache, caddy, etc) should have their ports bound (i.e. 80 and 443 for HTTP and HTTPS respectively). Otherwise, anyone could connect to your mysql container from the outside world (if they have the password, which they could brute-force if they wanted to).

@francislavoie We tried removing port binding for mysql a few months ago but we then reverted the change because of complaints. The default docker compose file MUST NOT be used in production. You can see my old PR about port binding #339.

Why this type of issue is closed ! even if the issue is still same.
I am facing this type of conflict.
Using Laradock.io , facing conflict between 3306 port for mysql container.
Inside laradock --> Having port number 3306 in
(
mysql folder -> my.cnf & Dockerfile
docker-compose.yml file
.env file
)
in those file used 3306 so many times.
I am being confused. How to solve this , no exact solution.

Why this type of issue is closed ! even if the issue is still same.
I am facing this type of conflict.
Using Laradock.io , facing conflict between 3306 port for mysql container.
Inside laradock --> Having port number 3306 in
(
mysql folder -> my.cnf & Dockerfile
docker-compose.yml file
.env file
)
in those file used 3306 so many times.
I am being confused. How to solve this , no exact solution.

I totally agree, what I did is not technical at all but practical and worked. I used sublime text "find in files" tool
(you can use another IDE/editor/programm) to I looked up 3306 and replaced the coincidences in these files:
C:\Users\dcampos\doc.env:
C:\Users\dcampos\doc\config\database.php:
C:\Users\dcampos\doc\docker-compose.yml:
C:\Users\dcampos\doc\laradock.env:
C:\Users\dcampos\doc\laradock\docker-compose.yml:
C:\Users\dcampos\doc\laradock\mariadb\Dockerfile:
C:\Users\dcampos\doc\laradock\mariadb\my.cnf:
C:\Users\dcampos\doc\laradock\mysql\Dockerfile:
C:\Users\dcampos\doc\laradock\mysql\my.cnf:
C:\Users\dcampos\doc\laradock\percona\Dockerfile:
C:\Users\dcampos\doc\vendor\laravel\sail\bin\sail:
C:\Users\dcampos\doc\vendor\laravel\sail\stubs\docker-compose.yml:
I'm super intelligent I know jeje

Why this type of issue is closed ! even if the issue is still same.
I am facing this type of conflict.
Using Laradock.io , facing conflict between 3306 port for mysql container.
Inside laradock --> Having port number 3306 in
(
mysql folder -> my.cnf & Dockerfile
docker-compose.yml file
.env file
)
in those file used 3306 so many times.
I am being confused. How to solve this , no exact solution.

I totally agree, what I did is not technical at all but practical and worked. I used sublime text "find in files" tool
(you can use another IDE/editor/programm) to I looked up 3306 and replaced the coincidences in these files:
C:\Users\dcampos\doc.env:
C:\Users\dcampos\doc\config\database.php:
C:\Users\dcampos\doc\docker-compose.yml:
C:\Users\dcampos\doc\laradock.env:
C:\Users\dcampos\doc\laradock\docker-compose.yml:
C:\Users\dcampos\doc\laradock\mariadb\Dockerfile:
C:\Users\dcampos\doc\laradock\mariadb\my.cnf:
C:\Users\dcampos\doc\laradock\mysql\Dockerfile:
C:\Users\dcampos\doc\laradock\mysql\my.cnf:
C:\Users\dcampos\doc\laradock\percona\Dockerfile:
C:\Users\dcampos\doc\vendor\laravel\sail\bin\sail:
C:\Users\dcampos\doc\vendor\laravel\sail\stubs\docker-compose.yml:
I'm super intelligent I know jeje


Fixed missing calico tutorials file.

To reproduce missing link issue, from www.projectcalico.org, click resources, tutorials and examples, then "Read It" for "How to use calicoctl in Kubernetes"
Description

Todos

[ ] Tests
[ ] Documentation
[ ] Release note

Release Note

None required

Deploy preview for calico ready!
Built with commit 3023c3443c8275b999f7fe659f5bc628be11a17d
https://deploy-preview-2451--calico.netlify.com

@kisanth88 Thanks for the PR!
I think this is just a broken link in the projectcalico.org site - the equivalent content has been moved here: https://docs.projectcalico.org/v3.5/usage/calicoctl/install
I'll get the projectcalico.org resources link updated. Thanks!


sailsjs.org not working in mac firefox

Navigation on documentation not working. When you go to website from google you see only  list with title and nothing more. When you click for some menu you have error.  Long time i thinking you dont have documentation.
mozilla firefox 36.0.4
macos 10.10.2
UPD.
Sorry. Not working with plugin "live http headers" Close issue.

oh


Validation fixes for HTML issues

1st batch of HTML validation fixes for articles listed in this spreadsheet:
https://microsoft.sharepoint.com/:x:/r/teams/APEX_Aquent/_layouts/15/Doc.aspx?sourcedoc={78386563-16EC-468F-B45C-22EA0C8E272D}&file=biztalk-docs_BuildReport_2022-01-18.xlsx&action=default&mobileredirect=true&share=IQFjZTh47BaPRrRcIuoMjictAS6I4ZyPp3yKv-cMO-E4IRc&CID=ACB6670B-5D5E-489B-9BD9-DA7A5F124530

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Hi @MandiOhlinger, this PR is ready for your review.
cc: @dougeby


Make blog posts easier to find

At the moment, you can add blog posts to projects, and you can click through to them. This isn't very obvious at the moment, so could we improve this?
Maybe include a navigation bar?

@wrussell1999 Do you mean a navigation bar at the top, with all the options, like Home,blogs, CV, etc. And on clicking on blogs option, the list of blogs will be displayed.

Something like that yes! I'll leave it up to you folks to decide how you want to design it!

Heyo, my team and I will work on this issue; could you assign it to us?

Closing this issue. Feel free to reopen it if needed.


The EDID being read should notify the softcore

On the Atlys we don't have access to the hotplug line, so we don't know when a new device is plugged in. Most devices will however read the EDID information right after being connected. Hence if we have yet to see a valid signal, the EDID being read is a good sign we should try looking for one.
Hence the softcore needs to be notified when the EDID is read.

This is possible a duplicate of https://github.com/timvideos/HDMI2USB-misoc-firmware/issues/39

It is straight forward to set hdmi_in0_connected (https://github.com/timvideos/HDMI2USB-misoc-firmware/blob/master/firmware/lm32/hdmi_in0.c#L95) to 1 when the EDID is being read.
But on which condition set it back to 0? How can we detect the source has been unplugged?
Do we keep hdmi_in0_connected set to 1 regardless?

I think we want a hdmi_in0_edid_started and a hdmi_in0_edid_finished notifications (maybe with timestamps?). Like normal interrupts, they should be triggered by the gateware and then clearable by the lm32 firmware.

Can someone test this on Atlys board / hdmi2usb target?
https://github.com/fallen/HDMI2USB-misoc-firmware/commit/5d771720b6553665b87058ae7fbe1d077dd0a5f6


Housekeeping

[X] I'm sure this issue is not a duplicate

Icon Type

[X] File Icon
[ ] Folder Icon

Icon Type

[ ] Extension
[X] Filename
[ ] Language ID

Original Icon
The same icon we use for .gitignore
Icon Information
https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
More Information:
https://github.com/vscode-icons/vscode-icons/issues/3198 looks like it was working before. This is a file that defines what revisions to ignore in lists/histories.

The icon is associated via a filename
https://github.com/vscode-icons/vscode-icons/blob/75f297812e6a7f21c97e80cb950f71c47d0346a5/src/iconsManifest/supportedExtensions.ts#L1971
Additionally, it’s associated via the ignore language ID.
Does this issue still exist? Is the file name lower case? What’s the language ID when you open the file?

It's working in the latest version. The language id was gitignore.


Does supercede parameter exist?

Hi All,
Could you please clarify does "supercede" option exist or not? https://ui-router.github.io/ng1/docs/latest/interfaces/transition.transitionoptions.html#supercede
I'm using the following uirouter versions:
"@uirouter/angular": "6.0.1",
"@uirouter/angular-hybrid": "10.0.1",
"@uirouter/angularjs": "1.0.25",
"@uirouter/core": "6.0.4",

There is type, right? It should be super[s]ede.

supercede has been added in "@uirouter/angular": "6.0.3",


Hiding team management UI when user is not authorized to manage the team

Fixes #1992

Added property on detail view model which will be used to hide/show the team management UI elements
Set the property from the AuthorizableItinerary.CanManageTeamMembers value
Update UI with conditional blocks to hide the team management UI elements when TeamManagementEnabled is false
Added test to validate value is being set as expected.

Thanks @stevejgordon, good side fixes, too, as always!


wolfictl vex sbom subcommand

This PR introduces the wolfictl vex sbom subcommand. This enables wolfictl to generate vex documents from SBOMs containing wolfi packages.
Follow-up to #11 , needing a rebase after merging that one.
/cc @luhring
wolfi ctrl vex sbom --help
wolfictl vex sbom: Generate a VEX document from wolfi packages listed in an SBOM

The vex sbom subcommand generates VEX documents describing how vulnerabilies
impact Wolfi packages listed in an SBOM. This subcommand reads SPDX SBOMs and
will recognize and capture all packages identified as Wolfi OS components
by its purl. For example, if an SBOM contains a package with the following
purl:

<EMAIL_ADDRESS>
wolfictl will read the melange configuration file that created the package and
create a VEX document containing impact assessments in its advisories and
secfixes.

wolfictl will read the melange config files from an existing wolfi-dev/os clone
or, if not specified, it will clone the repo for you.

Usage:
  wolfictl vex sbom [flags] sbom.spdx.json

Examples:
wolfictl vex sbom<EMAIL_ADDRESS>sbom.spdx.json

Flags:
      --author string   author of the VEX document
  -h, --help            help for sbom
      --repo string     path to a local clone of the wolfi-dev/os repo
      --role string     role of the author of the VEX document

/hold as the SBOM algorithm needs some improvements

OK, the initial implementation of this is done!
Here is an example of a run using the SBOM attached to this PR. I'm attaching the produced VEX document too. @luhring as you'll see, the installed packages (according to the SBOM) are included in the subcomponents list as we discussed. We can eliminate them but I think it makes sense to keep them there.
Invocation
wolfi vex sbom  pkg/vex/testdata/git.spdx.json

Output:
{
  "id": "merged-vex-e45086b18fbc879c482f6c2a304f3909a6e3a827fcebaefafc9a937df7600b9a",
  "format": "text/vex",
  "author": "",
  "role": "",
  "timestamp": "2022-12-28T22:07:05.495089156-06:00",
  "statements": [
    {
      "vulnerability": "CVE-2018-25032",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/zlib@1.2.13-r1?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2020-8927",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/libbrotlicommon1@1.0.9-r0?distro=wolfi",
        "pkg:apk/wolfi/libbrotlidec1@1.0.9-r0?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2020-8927",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/libbrotlicommon1@1.0.9-r0?distro=wolfi",
        "pkg:apk/wolfi/libbrotlidec1@1.0.9-r0?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2022-29458",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/ncurses@6.3-r2?distro=wolfi",
        "pkg:apk/wolfi/ncurses-terminfo-base@6.3-r2?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2022-29458",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/ncurses@6.3-r2?distro=wolfi",
        "pkg:apk/wolfi/ncurses-terminfo-base@6.3-r2?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2022-37434",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/zlib@1.2.13-r1?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2022-39046",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/glibc@2.36-r3?distro=wolfi",
        "pkg:apk/wolfi/glibc-locale-posix@2.36-r3?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2022-39046",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/glibc@2.36-r3?distro=wolfi",
        "pkg:apk/wolfi/glibc-locale-posix@2.36-r3?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2022-40674",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/expat@2.5.0-r0?distro=wolfi"
      ],
      "status": "fixed"
    },
    {
      "vulnerability": "CVE-2022-43680",
      "products": [
        "pkg:oci/git@sha256:54a88f29b889d82e57712206973db99089caf4074232bb16df8c72605aaaa410?arch=amd64&mediaType=application%2Fvnd.oci.image.manifest.v1%2Bjson&os=linux"
      ],
      "subcomponents": [
        "pkg:apk/wolfi/expat@2.5.0-r0?distro=wolfi"
      ],
      "status": "fixed"
    }
  ]
}

Example generated VEX document attached here: image.vex.json.gz


feat(doc): Add index & filename guides

According to the outcome of the last TSC meeting (https://www.notion.so/sentry/93d1ddb057af4a4db67c9b741c5ab495?v=e97ab611c4b54951a6ca3e10e13be16e&p=99c691667f724ad080cb958103a36d54),  I am updating this handbook by adding a section on using the index file in a component folder.
This PR also adds best practices when naming a file.

I just noticed which repository this is in. Should we also have these changes in getsentry/develop as well? I thought that repository was the 'new place' for internal/external development docs.

Sure I will move the new guidelines to the new repository :)


ReferenceError: process is not defined in some cases

Hey there,
First of all, I really love the work you have done here! :)
I have used the plugin before, but I am now experiencing an issue when trying to import some modules (and transforming to an iife file).
I am getting a ReferenceError: process is not defined error when run in the browser.
my rollup.config.js looks like:
// import babel from 'rollup-plugin-babel';
import commonjs from 'rollup-plugin-commonjs';
import nodeResolve from 'rollup-plugin-node-resolve';

export default {
  format: 'iife',
  plugins: [
    nodeResolve({
      jsnext: true,
      main: true
    }),
    commonjs({
        // non-CommonJS modules will be ignored, but you can also
        // specifically include/exclude files
        include: 'node_modules/**',  // Default: undefined

        // if true then uses of `global` won't be dealt with by this plugin
        ignoreGlobal: false,  // Default: false

        // if false then skip sourceMap generation for CommonJS modules
        sourceMap: false  // Default: true
      })
    ]
};

and in my index.js i am only doing:
import PromiseWorker from 'promise-worker';

I tried importing other npm modules but others (like three) failed as well.
Have I messed someting up in my config?
The code is in this repo if you want to try it out yourself.

Okay I fixed it myself. Apparently I had to include the rollup-plugin-node-globals.
My config now looks like:
// import babel from 'rollup-plugin-babel';
import commonjs from 'rollup-plugin-commonjs';
import nodeResolve from 'rollup-plugin-node-resolve';
import globals from 'rollup-plugin-node-globals';
import builtins from 'rollup-plugin-node-builtins';

export default {
  format: 'iife',
  plugins: [
    nodeResolve({
      jsnext: true,
      main: true,
      module: true
    }),
    commonjs({
        // non-CommonJS modules will be ignored, but you can also
        // specifically include/exclude files
        include: 'node_modules/**',  // Default: undefined
        browser: true,
        preferBuiltins: false,
        // if true then uses of `global` won't be dealt with by this plugin
        ignoreGlobal: false,  // Default: false

        // if false then skip sourceMap generation for CommonJS modules
        sourceMap: false  // Default: true

        // explicitly specify unresolvable named exports
        // (see below for more details)
        // namedExports: { './module.js': ['foo', 'bar' ] }  // Default: undefined
      }),
      globals(),
      builtins()
    ]
};


Inline style are applied differently to https://mjml.io/try-it-live

When I run my mjml template in the mjml.io try-it-live my inline styles are applied as I was expecting.
https://mjml.io/try-it-live/QMEUiLOGHD
But when running through mjml.net using the anglesharp PostProcessors I see inline styles added to every tag and not the inlines styles I've specified.
In the try it live mso-hide is added, in mjml.net it is not.
In try it live, only styles in the inline are applied, in mjmj.net a bunch of styles are added in. Not sure where they are coming from.
Attached template, and mjml.net output.
mjmj_template.txt
renderedhtml.txt
Thanks.

We only talk about inline "mj-style" attributes as described here: https://documentation.mjml.io/#mj-style
This feature converts css declarations to inline styles and is not stable yet. Everything else is well covered, we run comparison tests over all sample email templates: https://github.com/SebastianStehle/mjml-net/tree/main/Tests/Templates


implement pointrcnn on Windows?

Hi! I want to implement pointrcnn on Windows? how to do this please I follow the instruction but this error appear "error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe' failed with exit code 2" when run execute build_and_install.sh on WIN10?

@gehadza This error is because of the cpp interprater on windows (MSVC), you should use gcc like on linux, mac

The error log, you haven't posted it, how can we know where the compiling error lies?

Hi! I want to implement pointrcnn on Windows? how to do this please I follow the instruction but this error appear "error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe' failed with exit code 2" when run execute build_and_install.sh on WIN10?

Could you tell me how you fixed the problem


Flux functions that depend explicitly on space

This came up in #356: It would be nice to allow flux functions that depend explicitly on space x, e.g. for linear advection with variable coefficients. There are at least two possible approaches:

Just provide the space coordinate explicitly as argument to all flux functions (calcflux and all numerical fluxes)
Create a trait for this property, e.g. has_variable_coefficients(equations) = Val(false) as default value and use that for dispatch. This would be similar to our approach for nonconservative terms used in the MHD equations.

If we choose the first approach, we should benchmark carefully whether there are any performance issues with this.

I think this is a good suggestion in general. However, there are two questions that we might also want to consider when addressing this issue:
i) Should we also pass t in that case to be consistent with other methods, which IIRC always accept both x and t and never just one of them?
ii) How to handle variable coefficients that are not a (simple) function of space or time, but that should be prescribed as part of the initialization? I am thinking about linearized Euler equations or acoustic perturbation equations, where you need to specify, e.g., mean density or speed of sound etc. in often a non-trivial manner. Thus re-calculation of the coefficients is typically either not feasible (for performance reasons) or not possible (if they are from an input file) - in that case, you need permanent storage for these additional coefficient variables.
Especially ii) is a lot tougher to answer than the original issue, I think, but we should have at least the scenario in mind before deciding which way to go.
P.S.: @ranocha I took the liberty of adding numbers to your suggestions to reduce ambiguity.

i) Should we also pass t in that case to be consistent with other methods, which IIRC always accept both x and t and never just one of them?

Good point, we should definitely allow time-dependent coefficients.

ii) How to handle variable coefficients that are not a (simple) function of space or time, but that should be prescribed as part of the initialization? I am thinking about linearized Euler equations or acoustic perturbation equations, where you need to specify, e.g., mean density or speed of sound etc. in often a non-trivial manner. Thus re-calculation of the coefficients is typically either not feasible (for performance reasons) or not possible (if they are from an input file) - in that case, you need permanent storage for these additional coefficient variables.

That's also a good point. A solution might be to introduce a possible storage for auxiliary variables, which could also be used to store the primitive variables (see #54). Then, we can decide whether we want to pass the auxiliary variables as additional argument (might be cleaner) or whether we want to augment the vector of conserved variables when calling get_node_vars. In that case, we could use functions like update_coefficients!(semi, t) that will update the auxiliary variables if necessary and we won't need to pass the time explicitly to flux functions etc. These kind of auxiliary variables will also provide the necessary cache for parabolic problems when we want to store the gradients separately. The default choice would be to use nothing as auxiliary variables and functions like get_node_vars (or similarly named variants, get_node_aux_vars???) would need to be specialized to return nothing accordingly. We would also need a mechanism to decide how AMR should handle auxiliary variables

do nothing (when storing things that need to be re-evaluated anyway, e.g. gradients, primitive variables)
use AMR transfer operators as usual (for variable coefficients given as initial data)
use something like update_coefficients!(semi, t) for coefficients given as functions

On the other hand, it's probably just okay to use a number of auxiliary variables which can also be zero.
julia> Array{Float64, 3}(undef, 0, 4, 5)
0×4×5 Array{Float64,3}

julia> Array{Float64, 3}(undef, 0, 4, 5)[:, 1, 1]
Float64[]

julia> ntuple(n -> Array{Float64, 3}(undef, 0, 4, 5)[n, 1, 1], 0)
()

julia> using StaticArrays

julia> SVector{0,Float64}(ntuple(n -> Array{Float64, 3}(undef, 0, 4, 5)[n, 1, 1], 0))
0-element SArray{Tuple{0},Float64,1,0} with indices SOneTo(0)

This kind of auxiliary variables could live for example in semi.cache.elements.

Having such auxiliary variables together with semi.cache.elements would make sense to me as well, since this is exactly where I put such variables when I implemented this features in my previous code ZFS :-) However, one challenge to consider is what to do when you have several orthogonal features that all require theses auxiliary variables. E.g., you want to store primitive variables because you need them in the source terms where they would be expensive to calculate (for whatever reason), while at the same time you need mean values for your linearized system. In that case:

Do you use a single data structure? But how to properly access the different categories of data then, e.g., in get_node_aux_vars?
Do you use one data structure per category? But how to pass them to different functions then, given that we want to be able to keep using node-based functions?

Regarding the AMR mechanism: I think these are exactly the three types of update mechanisms we need to support.

What kind of applications of these auxiliary variables will we have in the (near) future? Right now, I don't think we will have, say, hundreds of auxiliary variables. In that case, it shouldn't be a performance issue to store them in one place as a single vector. The order and kind of auxiliary variables will depend on the equations, so they will be specified and used correctly using multiple dispatch.
On the other hand, we could also distinguish the three different kinds of auxiliary variables determined by their AMR behavior and store them in three different vectors with a convenience function returning all of them together.

Hm, you are right. Let's KISS: one storage location for all auxiliary nodal variables, and everything else is trait-based. This looks to me like the least intrusive approach for a full set of features, and if we need something more complex in the future, we'll re-evaluate. This way, each system of equations can support these variables, and it just depends on the way the equation is created. As long as the total number of auxiliary variables will become part of the equation type, we can dispatch/trait anywhere it's required.

We had a discussion at this week's Trixi meeting about how to implement such variable coefficients for the acoustic perturbation equations (see related PR #450). In this case, the coefficients represent time-averaged quantities of the mean flow field, such as mean density, mean velocity, or mean speed of sound. Several possible approaches were considered:

Treat variable coefficients as if they were state variables and store them in u, after the actual conservative state. Then set their fluxes to zero such that they are never updated. This is probably the least intrusive approach, but it is not very clean and has a performance overhead. Also, it does not allow to easily treat the coefficients specially where it might be required, e.g., for AMR.
A modification of the first approach, where we still store variable coefficients in u but modify the volume integral, surface integral, and other relevant routines to just ignore the additional coefficients to reduce computational overhead.
Modify the existing solver such that it treats all problems as variable coefficient problems. That is, variable coefficient data is passed to each function that potentially might need it. For equations that don't need it, the passed data is just an empty tuple/SVector. The downside here is that we add code to many routines that every user has to take into account but only a subset actually uses.
Create a new solver for such variable coefficient problems that allows to store the coefficients separately and pass them explicitly into every function that may require them. This has the advantage that we have a lot of flexibility regarding special treatment of such variable coefficient problems, with the downside that it creates another implementation variant.

There was no final conclusion on what the best approach would be for us in Trixi. Instead, we decided to approach this iteratively by starting out with a simple and easy-to-implement approach, and upgrade it in case we face serious issues or once variable coefficient problems start playing a more important role. In case of #450, we specifically decided to use the first approach for now (store and treat the coefficients as additional conservative quantities with zero-valued fluxes).

Has anything changed in the past 1,5 years regarding this issue? For instance, what about equation dependent function signatures, i.e., for flux? Then one would only read and pass $t$ and $\boldsymbol x$ if actually needed.
Reason I am bringing this up again is that for instance the advection equation in form $$u_t + a(x) u_x = 0$$ with $$a(x) = \begin{cases} 1 & x \leq x_\max/2 \ 1000 & x_\max/2 < x \leq x_\max \end{cases} $$

I believe that the approach @andrewwinters5000 took for the shallow water equations with variable bathymetry could be adapted here. If a(x) doesn't depend on time, it can be represented in the same basis as the solution, stored as a "dummy" field in the ODE, and extracted within the flux function to compute a(x) * u(x).
A similar approach would be to simply store a vector of values for a(x) within the equations struct and extract it each time to compute the flux. The downside to this is that it forces equations to depend on the discretization, which isn't as clean.
Your suggestion about creating equations which explicitly depend on space/time should also work - if you'd like, we can help you add something like this.

The workaround @jlchan mentioned is described in one of our tutorials: https://trixi-framework.github.io/Trixi.jl/stable/tutorials/adding_nonconservative_equation
Sadly, we did not have the time to design a proper solution to this issue.


[Rollout] Production rollout, 2024-07-17

Main build: https://dnceng.visualstudio.com/internal/_build/results?buildId=2492328&view=results
Rollout issue: https://github.com/dotnet/dnceng/issues/3429

Closing PR as it has been decided no rollout this week.