Create an exe installer or write an ultra detailed installation guide for unexperienced windows users [Feature request]:

What do you need?
Fabric looks like incredibly powerful tool but i have errors or issues on almost every installation step and it is just to difficult to understand and deal with something what requires experience in coding etc.

@chislerr, you don't actually need coding experience to run and use Fabric. For real! On a Windows machine, you can do it in two ways, and both involve simply pasting and executing commands.
Method 1: Using WSL (Windows Subsystem for Linux)

Enable WSL:
Open PowerShell as an administrator and run:
Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

Update WSL:
After restarting your PC, run:
wsl --update

Install a Linux Distro:
For example, to install Ubuntu, run:
wsl --install -d Ubuntu-24.04

Set Up Ubuntu:
After installation, set up your user and run these commands one by one:
sudo apt-get update -y
sudo apt-get upgrade -y
sudo apt install git -y

Install Python, Pip, and Pipx:
Run the following commands:
sudo apt install python3
sudo apt install python3-pip python3-venv
python3 -m pip install --user pipx

Clone and Install Fabric:
Execute these commands:
git clone https://github.com/danielmiessler/fabric.git
cd fabric
pipx install numpy
python -m pipx install chroma-hnswlib --include-deps
pipx install .
fabric --setup

Now, everything should work fine.
Method 2: Without Using WSL

Ensure Git and Python Are Installed:
Make sure you have both installed on your machine.

Run the Following Commands:
python -m pip install --upgrade pipx
git clone https://github.com/danielmiessler/fabric.git
cd fabric
pipx install numpy
python -m pipx install chroma-hnswlib --include-deps
pipx install .
fabric --setup

After following these steps, everything should work fine and you’ll be ready to go.
I hope this makes it easier for you to understand that you don't need coding experience. You just need to know how to operate Linux and execute commands, and the same goes for Windows.

I'd say go with WSL Get a feel of Linux of not already. It also gives you the flexibility to run other programs that isn't just possible on Windows due to package compatiblity etc.

Additionally, it's worth noting that if you encounter the following error:
PS C:\Users\User\fabric> pipx install .
Fatal error from pip prevented installation. Detailed pip output can be found in:
    C:\Users\User\pipx\logs\cmd_2024-01-02_10.12.30_pip_errors.log

pip encountered an issue while building the package:
    chroma-hnswlib

Below are some potentially relevant errors from the pip install process:
    error: subprocess-exited-with-error
    error: Microsoft Visual C++ 14.0 or later is required. You can acquire it through the "Microsoft C++ Build Tools" at: https://visualstudio.microsoft.com/visual-cpp-build-tools/

The error message likely indicates a missing dependency: the absence of build tools. Simply follow the provided link, C++ Build Tools, to download and install the required tools. Once Fabric operates smoothly, you can choose to uninstall the C++ build tools if they are no longer needed. Fabric will continue to function flawlessly thereafter. This guidance is specifically for Windows machines.
For Linux machines, execute the following commands to address the same issue:

Update pip: python -m pip install --upgrade pip
Update wheel: pip install --upgrade wheel
Update setuptools: pip install --upgrade setuptools
Install build-essential: sudo apt-get install build-essential

After completing these steps, retry the aforementioned process, which should now execute without any hitches.

Thanks for the response guys.
I still believe that exe file to install fabric without any issues is just most convenient option for windows users.
But I tried @epeuu Method 1 because I thought earlier about trying out linux. And it helped a lot to move forward, although still not without issues and errors. I spent time to research and deal with them and almost finished this hole process but at the and of it when everything seems to look ok i got this error:
fabric: command not found
It shows after I type "fabric --setup" like it was in guide. and because it is not something as common as other issues I don't know what to do next.

P.S. found out that it doesn't recognize any of commends related to fabric. Like fabric-webui etc.

okay i just solved all problems i mentioned earlier. Thanks a lot for your help guys, still stay by my point about exe installer tho. It will be too much work and time to put in just to install for the majority of normies. But they still have a lot of potential to help improving this project so Fabric Ai needs exe or very detailed explanation(which is also fine but amount of different potential errors is so huge that i don't really know is it worth it at the end of the day).
Thanks for the help once more.

If the installation completed without any issues, it's likely that Fabric isn't in your system's PATH, which is why it cannot be found. Try restarting your terminal, as this might resolve the issue. However, the main problem is probably that Fabric is not in the PATH, so the system cannot locate the command.
For Windows, the PATH for Fabric is C:\Users\{username}\.local\bin. Add this directory to your environment variables, then restart your terminal, and it should work fine.
On a Linux machine, after running the command pipx install . and ensuring it completes without errors, run pipx ensurepath to automatically add Fabric to the PATH. Alternatively, you can manually add it to the PATH.
Once you've done this, close the terminal, open a new one, and execute fabric --setup again. It should work perfectly now.


bumping image for httpd for CVE

libcap-2.48-5.el8 (RHSA-2023:4524: libcap security update (Moderate)) -->  libcap-2.48-9.el9_2.x86_64

/cc @lance @tommyd450


TLS 1.2 Support?

IBM Cloud only gives Databases for Redis
TLS and self-signed certificate support
All connections to Databases for Redis are TLS 1.2 enabled, so the driver you use to connect need to be able to support TLS encryption.
Any chance of TLS support?

Kitura-Redis makes use of BlueSockets.
You can enable SSL for Sockets using BlueSSLService.
https://github.com/IBM-Swift/BlueSocket See add-ins.
I just implemented it for an SSL Azure Redis Connection: https://github.com/geertberkers/Kitura-redis/commit/cb155b773880d3b9400a091676383f31b6ccfa4f#diff-3dee9532a6dd98c74cf9174823992791R47
You can speficy your own SSLConfiguration, for me none certificates of private keys were needed.


[dv,flash_ctrl] Fix handling program resolution

Description
The flash program sequence generator doesn't have a constraint that avoids program requests crossing program window boundaries (which are aligned at 64 bytes (8 flash words). Rather than detecting this and expect an error and drop the update, prog_flash rewrites the request. Unfortunately this rewrite generates multiple writes to the same locations when multiple consecutive writes are requested.
I think we should have no rewrites, but rather have the constraint solver be configured to avoid crossings, and perhaps enhance the dedicated tests that check that crossing errors are generated.

Thanks for filing this issue @matutem . I agree that this should be looked at. For now, I am putting it into M5 / V3.


Include REFER into allowed methods, fix #304

Looks like a good first bug for me.

As I commented on #304 I think that this should be dynamically added to the Allow header when a .on('refer') handler is created.  If there is no handler for the REFER method and we advertise support, what will the UA do when it receives a REFER?

If there is no handler for the REFER method and we advertise support, what will the UA do when it receives a REFER?

Send NOTIFY with the body of SIP/2.0 603 Declined.

this should be dynamically added to the Allow header when a .on('refer') handler is created

I believe this approach is against the robustness principle. Additionally, it will require re-INVITE.

It will not send a NOTIFY with a body of 603 decline.  It will send a SIP response with 603 Decline - a negative final response which would terminate the transaction for the REFER.
I was unaware that the REFER handler is on the session rather than the UA, this obviously makes it more difficult to create a handler and dynamically build the Allow: header methods that are included in the INVITE request since the session does not exist.
We are discussing the PR further internally and will follow up shortly.

It will not send a NOTIFY with a body of 603 decline.

Why do you think so? It should pretty obvious from the code I've linked, here is the appropriate log:
Tue Mar 29 2016 17:45:34 GMT+0300 (EEST) | sip.transport | received WebSocket text message:

REFER sip:oodsbj2d@<IP_ADDRESS>:37637;transport=ws;ob SIP/2.0
Record-Route: <sip:<IP_ADDRESS>:5061;transport=tls;r2=on;lr;ftag=96946d9d6aee226a>
Record-Route: <sip:<IP_ADDRESS>;r2=on;lr;ftag=96946d9d6aee226a>
To: "username" <sip:anonymous.62dt19@anonymous.invalid>;tag=t0m22dobg2
From: <sip:1@example.com>;tag=96946d9d6aee226a
Contact: <sip:1@<IP_ADDRESS>:5061;transport=tls;did=b88.6d969753>
Call-ID: tj71pmq3qu51e604bhcu
CSeq: 2 REFER
Accept: application/sdp
Accept: application/media_control+xml
Accept: application/csta+xml
Accept: application/presentation_token_control+xml;q=1.0;m=video
Accept: message/sipfrag
Supported: norefersub
User-Agent: *
Via: SIP/2.0/WSS <IP_ADDRESS>:10443;branch=z9hG4bK657a3ab23c8102181337d7748df9c630090414f2;rport
Via: SIP/2.0/TLS <IP_ADDRESS>:5061;branch=z9hG4bKfb8d.021d0d7.0
Authorization: Digest username="1", realm="example.com", nonce="56fa960e000161b429f69386d77bd17a8e4259e8478bcdde", uri="sip:oodsbj2d@<IP_ADDRESS>;transport=tcp;did=b88.5fca2501", response="f5424ddfb5449d07f5515607059ea733", algorithm=MD5
Max-Forwards: 10
Refer-To<EMAIL_ADDRESS>Content-Length: 0

LoggerFactory.js:72 Tue Mar 29 2016 17:45:43 GMT+0300 (EEST) | sip.inviteclientcontext | REFER received
LoggerFactory.js:72 Tue Mar 29 2016 17:45:43 GMT+0300 (EEST) | sip.transport | sending WebSocket message:

SIP/2.0 202 Accepted
Via: SIP/2.0/WSS <IP_ADDRESS>:10443;branch=z9hG4bK657a3ab23c8102181337d7748df9c630090414f2;rport
Via: SIP/2.0/TLS <IP_ADDRESS>:5061;branch=z9hG4bKfb8d.021d0d7.0
To: "username" <sip:anonymous.62dt19@anonymous.invalid>;tag=t0m22dobg2
From: <sip:1@example.com>;tag=96946d9d6aee226a
Call-ID: tj71pmq3qu51e604bhcu
CSeq: 2 REFER
Supported: outbound
User-Agent: SIP.js/0.7.3
Content-Length: 0

LoggerFactory.js:72 Tue Mar 29 2016 17:45:43 GMT+0300 (EEST) | sip.transport | sending WebSocket message:

NOTIFY sip:1@<IP_ADDRESS>:5061;transport=tls;did=b88.6d969753 SIP/2.0
Route: <sip:333c9357db@<IP_ADDRESS>:10443;transport=wss;lr;ovid=1a886ecf>
Route: <sip:<IP_ADDRESS>:5061;transport=tls;lr;ovid=1a886ecf>
Via: SIP/2.0/WSS ws.example.com;branch=z9hG4bK3287965
Max-Forwards: 70
To: <sip:1@example.com>;tag=96946d9d6aee226a
From: "username" <sip:anonymous.62dt19@anonymous.invalid>;tag=t0m22dobg2
Call-ID: tj71pmq3qu51e604bhcu
CSeq: 2272 NOTIFY
Event: refer
Subscription-State: terminated
Content-Type: message/sipfrag
Supported: outbound
User-Agent: SIP.js/0.7.3
Content-Length: 20

SIP/2.0 603 Declined

I believe this is a bug - if there is no handler setup, the UA should respond with a 4XX-6XX response as indicated by https://tools.ietf.org/html/rfc3515#section-2.4.2.
A NOTIFY with a reason code in the body should only be sent if the UA has accepted the REFER and is in a pending state of processing it.

There are 2 other changes I'm about to make as a result of this:

the 603 Decline in the notify should be a 503 Service Unavailable

we should actually be 603 Declining

Thanks for the PR!

Couldn't find followRefer (callback) in the docs.


Run sbt plugin scripted tests in different step than normal tests

Current coverage is 17.43%

Merging #98 into master will not affect coverage as of e1a4249

@@            master     #98   diff @@
======================================
  Files           36      36
  Stmts          522     522
  Branches        52      52
  Methods          0       0
======================================
  Hit             91      91
  Partial          0       0
  Missed         431     431

Review entire Coverage Diff as of e1a4249

Powered by Codecov. Updated on successful CI builds.


Google big query

Here is the PR for Google Big Query.  The code will build and compile.  It needs Google credentials in a file to run queries against Google Big Queries

I wonder if we couldn't simplify this connector by doing two things:

Only ask for the key file, not the project name (as it's in the file) or the database, as once you're authenticated, you can query any database in any project.
Don't show the left-hand sidebar, for the same reasons.

I can test adding only the key file and think that should be pretty straight forward.  For not showing the left hand side navigation would this only be for Big Query or all connectors.  We would have to modify the UI to make this work as well which would expand the PR quite a bit.  Your thoughts?

I thought that for some connectors we already supported disabling the left-hand schema browser, no?

Well, "support" is a strong word :) see https://github.com/plotly/falcon/blob/aca36085383e8da553686134471d96846209d682/app/components/Settings/Preview/Preview.react.js#L378

I could turn it off but it would turn it off for everyone (including users who have databases and schemas build it).  I can give it a try and see what happens

Well, the alternative might be to allow users to specify full-qualified database names (e.g. the-psf.downloads) and use those to populate the schema browser?

@nicolaskruchten I believe that is the preview section.  The part you would want to turn off is TableTree.  This makes the call to get the schema which is where the problem comes from.  The easiest thing to do would be to make database option and only pass keyfile.  If database is defined then it would try to get the database schema information.  If the database is not defined then it would return an empty array.
This solution would allow us to contain the changes within one location (i.e. the bigquery.js file) and would not impact any changes on the UI
Does this make sense?

Yes, that’s roughly what I was imagining. What do you think about
fully-qualified table names?
On Sat, Oct 13, 2018 at 15:57 Shannon Lal<EMAIL_ADDRESS>wrote:

@nicolaskruchten https://github.com/nicolaskruchten I believe that is
the preview section. The part you would want to turn off is TableTree. This
makes the call to get the schema which is where the problem comes from. The
easiest thing to do would be to make database option and only pass keyfile.
If database is defined then it would try to get the database schema
information. If the database is not defined then it would return an empty
array.
This solution would allow us to contain the changes within one location
(i.e. the bigquery.js file) and would not impact any changes on the UI
Does this make sense?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/plotly/falcon/pull/525#issuecomment-429570709, or mute
the thread
https://github.com/notifications/unsubscribe-auth/AAMbAxKnolg8z0tRS7sQUTD6PpsgfOH4ks5ukkWegaJpZM4XXrYr
.

I supposed a fully qualified database name (sorry, that’s what I meant
rather than table) basically works out to project and database like we
currently have, UX wise
On Sat, Oct 13, 2018 at 17:15 Nicolas Kruchten<EMAIL_ADDRESS>wrote:

Yes, that’s roughly what I was imagining. What do you think about
fully-qualified table names?
On Sat, Oct 13, 2018 at 15:57 Shannon Lal<EMAIL_ADDRESS>wrote:

@nicolaskruchten https://github.com/nicolaskruchten I believe that is
the preview section. The part you would want to turn off is TableTree. This
makes the call to get the schema which is where the problem comes from. The
easiest thing to do would be to make database option and only pass keyfile.
If database is defined then it would try to get the database schema
information. If the database is not defined then it would return an empty
array.
This solution would allow us to contain the changes within one location
(i.e. the bigquery.js file) and would not impact any changes on the UI
Does this make sense?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/plotly/falcon/pull/525#issuecomment-429570709, or mute
the thread
https://github.com/notifications/unsubscribe-auth/AAMbAxKnolg8z0tRS7sQUTD6PpsgfOH4ks5ukkWegaJpZM4XXrYr
.

Ok.  Let me look at fully qualified db names again.  It may take a bit to dig into this to see what options we have

These commits were squash-merged into master. Thanks @shannonlal !


HP LaserJet P1102 needs option usb-no-reattach=true when printing from remote client

Hi, I'm running Arch Linux with kernel 4.16.6-1-ARCH and CUPS 2.2.7-2 on all the pcs involved.
My HP LaserJet P1102 always worked just fine with CUPS when printing from the same pc it is attached to (via usb). Instead, when printing from other clients on the LAN it could only print the first document; after that no other document (from local and remote) could be printed until I turned the printer off and then back on. (Strangely, the documents which didn't get printed showed as printed in the jobs history).
Today I managed to overcome this issue by doing...
lpadmin -p [MyPrinterName] -o usb-no-reattach-default=true
It seems strange to me that the problem only presented when printing from a remote client, so I don't know wether it would be ok to add...
# HP LaserJet P1102
0x03F0 0x002A no-reattach
...to /usr/share/cups/usb/org.cups.usb-quirks

Can’t hurt...

[master 050d26570] Add a USB quirks rule for the HP LaserJet P1102 (Issue #5310)
[branch-2.2 ff52b652c] Added a USB quirks rule for the HP LaserJet P1102 (Issue #5310)


Upgrade test env to use Kube 1.22

Signed-off-by: Dan Sun<EMAIL_ADDRESS>
What this PR does / why we need it:
Which issue(s) this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close the issue(s) when PR gets merged):
Fixes #
Special notes for your reviewer:

Updated e2e test env with Istio 1.12 and Knative 1.0.0
Updated local integration test with Kube 1.22 testing env.

Release note:

@Suresh-Nakkeran @andyi2it Can you help review this?

/lgtm


Add page for websocket

closes #536
Guide people on how to use the websocket APIs available

A few things to note:

I removed ## Available websocket APIs because 1) I didn't know how to do links!! and 2) they might all change anyway when we reshuffle the protos/move the subscription endpoints into their own section
The new page doesn't appear in the sidebar anywhere, I wasn't sure where it should live
We have a problem with the enums being ints instread of strings: I don't think there is anywhere in the autogenerate docs that would tell someone what each int means!


update to cardano api 846

Update cardano-api and other related dependencies to match those of cardano-node 8.11
See issue 39 for detail

@MaximilianAlgehed> any chance you can look at this one soon?


No editing options appear after uploading

Using Firefox from a Steam Deck on desktop mode. I upload a save file and no options appear to actually edit the save, only to download the save again.

I've tried this on two machines, both running on Fedora 41, using LibreWolf, with the same extensions. One of them works properly, and the other one replicates the behavior described in this issue.
My guess as to what might be the cause is: a missing dependency, or a configuration difference.


Can the model be applied to the improvement of gray image pixels?

What do you mean by "improvement"? Could you provide an example of what exactly you are hoping to accomplish?


Avoid type name conflicts in generated code.

can happen when we have types with the same name in different namespaces.

Hi rvuistin, I had to revert this pull request due to it breaking parts of the code generation. Specifically it broke code-generation for the static method BuildWrapperDictionary that is part of the LinqToXsdTypeManager class that gets generated for each namespace.
If you go to this diff (go to the W3C XMLSchema v1.xsd file, and then scroll to the very last diff in that file), you will see the issue. Without the BuildWrapperDictionary() method working correctly, then complexType content model validation and untyped XElement conversion fails at runtime.


feat: generate wind profiles during HIFLD grid-building

Pull Request doc
Purpose
Generate wind profiles at the same time as we build the HIFLD grid, so that we can leverage the plant-specific attributes of each wind farm to generate better profiles (partial fulfillment of #227).
What the code is doing

build_wind joins the wind-specific data table with the wind plants in the main plant data frame, then calls the individual calculation introduced in #249.
create_csvs is extended with the additional inputs needed by build_wind.

Testing
Tested manually: profiles are created which match the expected timespan, and columns match the indices of wind generators.
Usage Example/Visuals
def create_csvs(
    DESIRED_OUTPUT_CSV_DIRECTORY,
    wind_directory=YOUR_WIND_CACHE_DIR,
    year=2020,
    YOUR_NREL_EMAIL,
    YOUR_NREL_API_KEY,
    solar_kwargs={"cache_dir": YOUR_SOLAR_CACHE_DIR},
):

Time estimate
30 minutes. This is a draft PR since it depends on #256, but has been tested and performs as expected.

This has been rebased and re-tested, so is ready for a full review.


swDest with relative folder prefix not supported.

Library Affected:
workbox-webpack-plugin
Browser & Platform:
OSX
Issue or Feature Request Description:
As part of upgrading next-offline to v5 Alpha, we noticed that specifying a folder prefixed swDest value such as /static/service-worker.js is ignored and the SW file is output at the default service-worker.js destination.
It appears that this line in workbox-build/src/lib/bundle.js causes this due to its use of path.basename which ignores the provided folder prefix. For example:
path.basename('/foo/bar/baz/asdf/quux.html');
// Returns: 'quux.html'

path.basename('/foo/bar/baz/asdf/quux.html', '.html');
// Returns: 'quux'

Reproduction Steps:
See https://github.com/hanford/next-offline/pull/158#issuecomment-513647451 and use the code from that Pull Request.

Thanks for testing this out! I'll take a look.


CI/CD enhancements

Better build program

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@980cfff). Click here to learn what that means.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master      #42   +/-   ##
=========================================
  Coverage          ?   97.97%
=========================================
  Files             ?       56
  Lines             ?     2075
  Branches          ?        0
=========================================
  Hits              ?     2033
  Misses            ?       42
  Partials          ?        0

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 980cfff...362d953. Read the comment docs.

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@980cfff). Click here to learn what that means.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master      #42   +/-   ##
=========================================
  Coverage          ?   97.97%
=========================================
  Files             ?       56
  Lines             ?     2075
  Branches          ?        0
=========================================
  Hits              ?     2033
  Misses            ?       42
  Partials          ?        0

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 980cfff...362d953. Read the comment docs.


Filtering reagents

About the PR

Adds a filter to the guide on Chemicals, Medicine and Botanicals
Media

[x] I have added screenshots/videos to this PR showcasing its changes ingame, or this PR does not require an ingame showcase

Changelog

:cl:

add: Added filter for reagents

Well, okay

@Hebiman while this is Okay as is, it should probably be a bit smarter than it currently is. Namely:
Instead of textual search, search for elements that implement an ISearchable, and ask that element "do you fit this pattern". Only hide ISearchable elements, and also make guidebook document generation output a special richtext that's ISearchable.

public interface ISearchable
{
    public bool CheckMatchesSearch(string query);
}

the chemical box UI element can then say it's a match if the query is approximately equal (i.e. ignoring capitalization) to the name of the chemical it represents, and in the future could also be made to query properties of the chemical like how much it heals/etc.

@moonheart08 I'll see what I can do with that. I'm rusty on the C# so mainly did what I found easiest.
From what I understand this would need to go on the GuideReagentEmbed. Going to get around that later.
I see that the RemoveLegsFallTest for some reason, so I need to fix that. Maybe I need to merge in the newest master for that one to fix itself since I don't think I touched anything near that.

@moonheart08 I'll see what I can do with that. I'm rusty on the C# so mainly did what I found easiest.
From what I understand this would need to go on the GuideReagentEmbed. Going to get around that later.
I see that the RemoveLegsFallTest for some reason, so I need to fix that. Maybe I need to merge in the newest master for that one to fix itself since I don't think I touched anything near that.

It's a spurious fail. And correct, GuideReagentEmbed would implement it.

@moonheart08 Thanks for the suggestion, looks less jank now with the new interface.
Had to implement a new method for finding the ISearchable interface since the other methods were written to find Control classes and I fell that they should stay that way.
I don't know if the interface is in the right place as I didn't really see a pattern for where you store interfaces in the repo.
Any other suggestions are welcome.

One last thing @Hebiman, please use file scoped namespaces. We do not use namespace blocks.


MDX - fix "reset" and don't allow tabbing

Don't allow "tabbing" for rich-text. Tabs in markdown represent code blocks, so this isn't something we want to support.
Fixes bug where "reset" wasn't working for rich text.

The e2e error is due to timeout which is the "classic" e2e error we've been experiencing.


Is localization a goal for this crate?

Languages might not only use different words for minutes and seconds, but the way the information is displayed might change completely (like in Japanese).

No, only English formatting.


[JuliaCon/proceedings-review] DOI of paper by Besard et al.

The checklist at https://github.com/JuliaCon/proceedings-review/issues/138 tells me that archival references should have a DOI listed. Here is the DOI of the paper by Besard et al.: https://ieeexplore.ieee.org/document/8471188

See also https://github.com/JuliaCon/proceedings-review/issues/138#issuecomment-1796282098

Thanks, we will update it accordingly.


Disable workflow

Coverage increased (+0.05%) to 28.377% when pulling f1d8742a3111ab53afcbb9ca6956a2b59d2ec6ae on calixteman:disable_workflow into 31078dbfb3c725732c5c1d7989eac569b6a4ee1f on mozilla:master.


Can't create a new project

Describe the bug
Can't create a new project
To Reproduce
Steps to reproduce the behavior:

curl -o docker-compose.yml https://raw.githubusercontent.com/Flagsmith/flagsmith/main/docker-compose.yml && docker compose -f docker-compose.yml up
wait until it's up

access the url in this line Please go to the following page and choose a password: http://localhost:8000/password-reset/confirm/MQ/c06wfn-a4188fd4e41d50c19b33d2b499e5ffad

now click on create project

the button is disabled
Expected behavior
I should be able set the project name to continue the project
Screenshots
All been added to the steps in the issuee
How are you running Flagsmith?

[x] Self Hosted with Docker
[ ] Self Hosted with Kubernetes
[ ] SaaS at flagsmith.com
[ ] Some other way

Additional context
I tried it also on multiple browsers (vivaldi and chrome) also my host is ubuntu
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.3 LTS"

Ah ok - this will explain things: https://github.com/Flagsmith/flagsmith/issues/3231


How do you add a variable that can be accessed by the clones+ extention?

When I use a code block that uses a variable, such as "create clone with [] set to 1", it doesn't show any variables, how do I create one?

...by creating a variable in the Variables category. (Clones+ uses normal Scratch variables.)

I have normal scratch variables though, but it doesn't show up.

They show up for me (the variables have to be for this sprite only for them to show up).

Oh yeah that's why, all of mine are global, thanks!

Please close the issue

Oh ok

The comments are live?!

How do you close it?

Oh I found out


libs: add module dataclass_utils

Include function and mixin for dataclass instances "deep comparison".

Codecov Report

Merging #54 into develop will increase coverage by 1.26%.
The diff coverage is 100%.

@@             Coverage Diff             @@
##           develop      #54      +/-   ##
===========================================
+ Coverage    65.23%   66.49%   +1.26%
===========================================
  Files           19       20       +1
  Lines          952      988      +36
  Branches       132      145      +13
===========================================
+ Hits           621      657      +36
  Misses         285      285
  Partials        46       46

Impacted Files
Coverage Δ

cl_sii/libs/dataclass_utils.py
100% <100%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 7aad935...00ca181. Read the comment docs.


Fix completions with newer versions of vscode language server

This fixes #2591

The failure on appveyor isn't due to your change we encounter this issue from time to time due to running out of artefact space on appveyor

Thanks for fixing this @Prior99 , much appreciated! 💯 (And thanks for the review, @Akin909 !)
I'm following up with the build issue, and #2603 should address it - but I'll bring this in now since the build passed prior to uploading the artifacts.


Add chocolatey tools dir

By default, chocolatey installs to C:\tools\php. See https://github.com/composer/composer/issues/5881
Add this to GetCommonLocations in the next release.

Done in d03b811


Tokenstream Factory Contract - 2.0

Requirements:

[x] Ability to create new Organization contracts for each new organization (should only have to pass the address)
[x] The organization should have the proper roles to manage the streams like we do now (set up the owner with the address passed in) ** use Open Zeppelin Access Control
[x] The Organization contract should be able to handle each new stream internally (no new contract)
[x] Owner to be able to assign Factory_Managers to manage streams (creation and updates), this is only in the organization contract.
[x] Ability to update the cap and the time on each stream by the Owner or the Factory_Manager, this is only in the organization contract.

I would like to contribute to this.

I suppose we need to outline v3 of this contract and implement it alongside the new front-end to complete the new app.
Currently, the contract requires separate transactions to fund each stream, when we could fund all streams from the same reservoir (per org).
We should also be able to operate each org as a "pool" where streams are just whitelisted users instead of separate deployed contracts.
I'm starting on a first iteration of this v, but thought I'd say this is the next thing to formalize.


Windows 32 bit support for Service Map in Azure

It appears based upon the Microsoft Azure portal that there are 32 bit Windows Agents available for use with the Service Map in Azure, however this document clearly states that only 64 bit is supported. Also this Microsoft user voice suggests there are 32 bit agents available https://feedback.azure.com/forums/267889-log-analytics/suggestions/6744349-support-for-windows-2003-and-2008-servers-32-bit
Please confirm the support on this?

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

ID: 97f8ee3c-f9c2-91c6-1ea0-48754de93979
Version Independent ID: bca92218-863f-2ec9-82a2-fcf277b75c14
Content: Configure Service Map in Azure
Content Source: articles/azure-monitor/insights/service-map-configure.md
Service: azure-monitor
GitHub Login: @MGoedtel
Microsoft Alias: magoedte

Thanks for the comment, we are investigating and will get back to you shortly.

@femsulu I am closing this comment as found the answer that 32 bit is not supported at this time for Service Map.


configured deployment and service files for eks

Brief summary of the change made
Are there any other side effects of this change that we should be aware of?
Describe how you tested your changes?
Pull Request checklist
Please confirm you have completed any of the necessary steps below.

[ ] Meaningful Pull Request title and description
[ ] Changes tested as described above
[ ] Added appropriate documentation for the change.
[ ] Created GitHub issues for any relevant followup/future enhancements if appropriate.

Closed in favour of: https://github.com/EnAccess/micropowermanager/pull/320


specification energy ranges

Coverage increased (+2.1%) to 86.143% when pulling 211d62311711ed489982dc5c7b9dffd170431ea6 on arcondello:1.0.0_specification_energy_ranges into dc119f4b651e53eb8bd6dd40a0dae7febb201658 on dwavesystems:1.0.0.


Hi

I have a problem opening google image results in encrypted mode..
& your addon couldn't help cause it leads me directly to the site
when i need the link google gives me including suggestions for
each image i open in a new tab.
(Ps: i need to always make searches using encrypted mode)
For exemple, for this search:
https://encrypted.google.com/search?hl=en&tbm=isch&q=Chocolate+truffle&nfpr=1&oq=&gs_l=#imgdii=yehk1XyGdGOk2M:&imgrc=hewqPbVUYaF6JM:
When i put single results to new tabs, i get this ex, this structure of page that i need:
https://www.google.com/imgres?imgurl=http%3A%2F%2Fimg.taste.com.au%2Fb8WVb5nl%2Ftaste%2F2016%2F11%2Fpeanut-butter-truffles-85908-1.jpeg&imgrefurl=http%3A%2F%2Fwww.taste.com.au%2Frecipes%2Fpeanut-butter-truffles%2F43ff7365-32af-47a0-b839-e1594a580f14&docid=0qyAUPxv1fl6aM&tbnid=x8JGyVDUhOBUPM%3A&vet=10ahUKEwj6rbax_fTWAhUFWhoKHR_FCvUQMwiFAigJMAk..i&w=3000&h=2000&hl=en&bih=865&biw=1400&q=Chocolate truffle&ved=0ahUKEwj6rbax_fTWAhUFWhoKHR_FCvUQMwiFAigJMAk&iact=mrc&uact=8
& for this search, i don't know how it happened, but it seems that google
prevents the display of search result in new tabs with its related thumbs
because i use pornographic terms:
https://encrypted.google.com/search?safe=off&hl=en&gl=us&pws=0&complete=0&tbm=isch&sa=1&q=porn&nfpr=1&oq=porn&gs_l=psy-ab.3...518346.518752.0.5189<IP_ADDRESS>.<IP_ADDRESS>.0..0.0....0...1.1.64.psy-ab..0.0.0....0.2w0pLoeWKBU
When i open one image to a tab, i get the famous stupid  "redirect notice"
The previous page is sending you to https://blablah..
If you do not want to visit that page, you can return to the previous page.
https://www.google.com/imgres?imgurl=https%3A%2F%2Fbi.phncdn.com%2Fvideos%2F201706%2F03%2F118925191%2Foriginal%2F(m%3Deaf8Ggaaaa)(mh%3DmGFVKRqc-iLGMgY3)12.jpg&imgrefurl=https%3A%2F%2Fwww.pornhub.com%2Fview_video.php%3Fviewkey%3Dph593256d72c861&docid=HOH0p8sSpfKHpM&tbnid=knuEW42vwalbJM%3A&vet=10ahUKEwi9i92jgvXWAhXCrxoKHZPIBewQMwgpKAQwBA..i&w=320&h=240&hl=en&gl=us&safe=off&bih=865&biw=1670&q=porn&ved=0ahUKEwi9i92jgvXWAhXCrxoKHZPIBewQMwgpKAQwBA&iact=mrc&uact=8
How could i prevent this behavior ? without sending images i popen directly to their
origin site ?
here's my search engine in bookmarks:
https://encrypted.google.com/search?hl=en&gl=us&safe=off&pws=0&complete=0&tbs=ctr:us&tbm=isch&q=%s

I don't think you can, the URL looks the same to me, you can have either or. Always skipping or never skipping.

& do you know away i could force a site like pinterest or others, i'd
individually add to a script to open sites in the foreground & not new
windows ?
i don't want to use the firefox setting that applies to all sites, cause
some sites force users to open ads before opening the target link
On Tue, Oct 17, 2017 at 12:01 AM, Sebastian Blask<EMAIL_ADDRESS>wrote:

Closed #56
https://github.com/sblask/webextension-skip-redirect/issues/56.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/sblask/webextension-skip-redirect/issues/56#event-1295775114,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AZgywpC2t-qLLgwiA-kxJqALMrD8Hj3gks5ss9JEgaJpZM4P6eLq
.


Please verify if Service Administrator will lose access after change directory

@HannahHsiao commented on Fri Apr 19 2019
Please verify if Service Administrator will lose access after change directory. Service Administrator shouldn't lose access after change directory. Thank you.

文件詳細資料
⚠ 請勿編輯此區段。 這是 docs.microsoft.com ➟ GitHub 問題連結的必要項。

ID: da261ee4-3348-b520-a27c-98f9d9ef40cc
Version Independent ID: 13d12189-ee46-8058-dd99-058adc69f1c5
Content: 將現有的 Azure 訂用帳戶新增至您的租用戶 - Azure Active Directory
Content Source: articles/active-directory/fundamentals/active-directory-how-subscriptions-associated-directory.md
Service: active-directory
Sub-service: fundamentals
GitHub Login: @eross-msft
Microsoft Alias: lizross

@CeciAc commented on Fri Apr 19 2019
Hello, @HannahHsiao
Your contribution is much appreciated. Our team can only answer feedback related to the documentation.
Please kindly log your product feedback by using the button "Give Product Feedback" at the bottom of the DOCS page.
If you have any feedback related to the documentation, please feel free to log it through this channel.
We truly appreciate your contribution to our articles.
Kind regards,
Microsoft DOCS International Team

@HannahHsiao commented on Fri May 03 2019
Hello, @CeciAc,
The doc is incorrect. The Service Administrator won't lose access after change directory.

Hi team,
User is reporting incorrect information in the documentation
best regards

@CeciAc Thanks for the feedback! I have assigned the issue to the content author to evaluate and update as appropriate.

@Mike-Ubezzi-MSFT
Please assign this issue to @rolyon as he's looking into this with the product group.

Hi @HannahHsiao
I did a test of this scenario and the best that I can tell the documentation is correct. I changed a subscription to a different directory while signed in with a user that was different than the Service Administrator. After making the change, the Service Administrator was not maintained. The Service Administrator was changed to the user that initiated the change.
thanks

Hi @HannahHsiao
I'll request to close this issue. Let us know if you have any additional feedback about the docs.
thanks

@MicrosoftDocs/azure-cxp-triage
#please-close


When TM crash, transaction not rollback

[ ] I have searched the issues of this repository and believe that this is not a duplicate.

Ⅰ. Issue Description
When TM crash, transaction not rollback
Ⅱ. Describe what happened

public ObjectResponse buy(BusinessDTO businessDTO) {
System.out.println("开始全局事务，XID = " + RootContext.getXID());
ObjectResponse objectResponse = new ObjectResponse<>();
ObjectResponse response = buy(businessDTO);

    System.exit(0);

    objectResponse.setStatus(RspStatusEnum.SUCCESS.getCode());
    objectResponse.setMessage(RspStatusEnum.SUCCESS.getMessage());
    objectResponse.setData(response.getData());
    return objectResponse;
}

I forgot to add @GlobalTransactional.
If TM crash, the transaction will be timeout rollback.


How to choose GPU #1 if you execute commands in conda env?

Ask a question:
If you execute the command in docker to select GPU #1:
NV_GPU=1 docker run ......

How to choose GPU #1 if you execute commands in conda env?
python3 src/main.py --config=......

Hi! Sorry for the late reply!
I think you can try to export the environment variable CUDA_VISIBLE_DEVICES=x if you want to select GPU #x.

@TonghanWang Thank You.


add ec2 required fields

I'm going through some our scripts so I'll PR what I find wrong, mostly required parameters missing
http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-ec2-security-group-egress.html#cfn-ec2-securitygroupegress-groupid
http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-ec2-vpn-gatewayrouteprop.html#cfn-ec2-vpngatewayrouteprop-routetableids

Thanks!


How to get 3D keypoints in order to evaluate in NoW challenge?

Thanks for your greate work! I'm a recruit for 3d reconstruction , and I want to evaluate my model in NoW challenge. I follow the guide from https://github.com/soubhiksanyal/now_evaluation
python check_predictions.py <predicted_mesh_path> <predicted_mesh_landmark_path> <gt_scan_path> <gt_lmk_path>

There is a little doubt about the <predicted_mesh_landmark_path>. It looks like the file containing 3D coordinates of 7 key points. Can you give me some advice or guidance on obtaining the 3D coordinates of key points？ Thanks again!

Hi, we first select 7 vertices on the template mesh (mean shape) as keypoints indicated by NoW, Then we automatically calculate the 3D coordinates of 7 keypoints for each subjects from their reconstructed meshes.

Hi! thank you for releasing the code for your amazing research!  When I evaluate my model (pre_model also be evaluated) in NoW challenge,  I also follow the guide from https://github.com/soubhiksanyal/now_evaluation.
python check_predictions.py <predicted_mesh_path>
this code exports the input mesh to predicted_mesh_export.obj . when I open the mesh in MeshLab, I find it not a face shape. it just like that:

I find the page said: "The used mesh loader is unable to load OBJ files with vertex colors appended to the vertices. I.e. if the OBJ contains lines of the following format v vx vy vz cr cg cb\n, export the meshes without vertex colors."
I wonder if the reason is the obj file outputed by test obtained the vertex colors.
Again, thank you for your attention!

Hi! thank you for releasing the code for your amazing research! When I evaluate my model (pre_model also be evaluated) in NoW challenge, I also follow the guide from https://github.com/soubhiksanyal/now_evaluation.
python check_predictions.py <predicted_mesh_path> this code exports the input mesh to predicted_mesh_export.obj . when I open the mesh in MeshLab, I find it not a face shape. it just like that:

I find the page said: "The used mesh loader is unable to load OBJ files with vertex colors appended to the vertices. I.e. if the OBJ contains lines of the following format v vx vy vz cr cg cb\n, export the meshes without vertex colors."
I wonder if the reason is the obj file outputed by test obtained the vertex colors.
Again, thank you for your attention!

Hi! thank you for releasing the code for your amazing research! When I evaluate my model (pre_model also be evaluated) in NoW challenge, I also follow the guide from https://github.com/soubhiksanyal/now_evaluation.
python check_predictions.py <predicted_mesh_path> this code exports the input mesh to predicted_mesh_export.obj . when I open the mesh in MeshLab, I find it not a face shape. it just like that:

I find the page said: "The used mesh loader is unable to load OBJ files with vertex colors appended to the vertices. I.e. if the OBJ contains lines of the following format v vx vy vz cr cg cb\n, export the meshes without vertex colors."
I wonder if the reason is the obj file outputed by test obtained the vertex colors.
Again, thank you for your attention!

Hi~ I meet the same issue in the first time with default test.py. On the 66 line in test.py , it save the .obj file using save_mesh()function, and you can edit the function in 215 line in facerecon_model.py, just remove the
vertex_colors=np.clip(255. * recon_color, 0, 255).astype(np.uint8)

In this way, I can get the correct .obj file after executing check_predictions.py.
By the way, did you get 3d coordinates  of 7 key points? I'm still a little confused about that.. Thanks for your attention.

Hi! thank you for releasing the code for your amazing research! When I evaluate my model (pre_model also be evaluated) in NoW challenge, I also follow the guide from https://github.com/soubhiksanyal/now_evaluation.
python check_predictions.py <predicted_mesh_path> this code exports the input mesh to predicted_mesh_export.obj . when I open the mesh in MeshLab, I find it not a face shape. it just like that:

I find the page said: "The used mesh loader is unable to load OBJ files with vertex colors appended to the vertices. I.e. if the OBJ contains lines of the following format v vx vy vz cr cg cb\n, export the meshes without vertex colors."
I wonder if the reason is the obj file outputed by test obtained the vertex colors.
Again, thank you for your attention!

Hi~ I meet the same issue in the first time with default test.py. On the 66 line in test.py , it save the .obj file using save_mesh()function, and you can edit the function in 215 line in facerecon_model.py, just remove the
vertex_colors=np.clip(255. * recon_color, 0, 255).astype(np.uint8)

In this way, I can get the correct .obj file after executing check_predictions.py.
By the way, did you get 3d coordinates of 7 key points? I'm still a little confused about that.. Thanks for your attention.

sorry, I just saw your answer. This solved my problem, Thank you!
For the question about getting 3d coordinates of 7 key points, I guess we need to get 3d coordinates of 7 key points in the BFM model(Maybe in the function save_mesh of facerecon_model.py) In 68 landmarks, We could use the landmarks with indices [36,39,42,45,33,48,55] , But I don't know if it works on the problem. Thanks for your attention.

Hi @YuDeng,
For computing, the 7 3D locations for the NoW benchmark is the following procedure correct?

Use the 7 landmark points from the similarity_Lm3D_all.mat and find the index of the nearest vertices for those in the mean shape.
Use the same indices in the final shape to get the 3D landmark points

I found that just selecting 7 key landmarks by the array that you mentioned, the result of distance calculated by now_evaluate  was very large.

Hi @YuDeng,
For computing, the 7 3D locations for the NoW benchmark is the following procedure correct?

Use the 7 landmark points from the similarity_Lm3D_all.mat and find the index of the nearest vertices for those in the mean shape.
Use the same indices in the final shape to get the 3D landmark points

Hi have you found the correct indices of these 7 landmarks?

Hi! thank you for releasing the code for your amazing research! When I evaluate my model (pre_model also be evaluated) in NoW challenge, I also follow the guide from https://github.com/soubhiksanyal/now_evaluation.
python check_predictions.py <predicted_mesh_path> this code exports the input mesh to predicted_mesh_export.obj . when I open the mesh in MeshLab, I find it not a face shape. it just like that:

I find the page said: "The used mesh loader is unable to load OBJ files with vertex colors appended to the vertices. I.e. if the OBJ contains lines of the following format v vx vy vz cr cg cb\n, export the meshes without vertex colors."
I wonder if the reason is the obj file outputed by test obtained the vertex colors.
Again, thank you for your attention!

Hi~ I meet the same issue in the first time with default test.py. On the 66 line in test.py , it save the .obj file using save_mesh()function, and you can edit the function in 215 line in facerecon_model.py, just remove the
vertex_colors=np.clip(255. * recon_color, 0, 255).astype(np.uint8)

In this way, I can get the correct .obj file after executing check_predictions.py.
By the way, did you get 3d coordinates of 7 key points? I'm still a little confused about that.. Thanks for your attention.

thanks a lot for your contribution


Add blog post for 3.4

Release publish in progress: https://buildkite.com/bazel-trusted/bazel-release/builds/162#906252ea-518c-4199-99da-5ce5330a3bf4


Add cmap argument for mne.viz.utils.plot_sensors

What does this implement/fix?
A cmap argument for the mne.viz.utils.plot_sensors().
Additional information
The colormap currently used is mpl's 'jet'. _get_cmap() converts None to rcParams["image.cmap"], therefore, this PR changes the default colormap of the function.

@agramfort, I tried to build the docs and check styling, but other than that I'm quite lost with CIs, sorry.

Will need https://github.com/mne-tools/mne-python/pull/11723 to be green, will merge that into this PR once it lands in main...


Update BS conversion assessment to include OT

Description of feature
As in title, I can do it.

hi I think I have fixed that try pulling the fix_OB_output again.


Fix UpdateSchemaDestination when source format is set to AVRO

This fixes part of #22372
R: @pabloem @MarcoRob

Thank you for your contribution! Follow this checklist to help us incorporate your contribution quickly and easily:

[x] Choose reviewer(s) and mention them in a comment (R: @username).
[x] Mention the appropriate issue in your description (for example: addresses #123), if applicable. This will automatically add a link to the pull request in the issue. If you would like the issue to automatically close on merging the pull request, comment fixes #<ISSUE NUMBER> instead.
[ ] Update CHANGES.md with noteworthy changes.
[x] If this contribution is large, please file an Apache Individual Contributor License Agreement.

See the Contributor Guide for more tips on how to make review process smoother.
To check the build health, please visit https://github.com/apache/beam/blob/master/.test-infra/BUILD_STATUS.md
GitHub Actions Tests Status (on master branch)

See CI.md for more information about GitHub Actions CI.

Run Java PreCommit

sorry I'll be on vacation for a while so I can't review.

Run Java PreCommit

Run Java PreCommit

sorry about the delay. I'd been on vacation. I'll look...

lgtm thanks @steveniemitz !


bug: Extra fields allowed on some properties.

We don't perform length checks when parsing certain values such as Shadow and Border.
shadow: 0 0 8 7 red something somethingelse wow is a valid shadow currently.
A performant way to get around this would be to add an extra next on the split iterator that ensures an error:
if let Some(_) = colors.next() {
    return Err(ParseColorError);
}

#256 will fix this problem for colors.

I had to refactor some parts of the shadow parser in #256, so this is fixed for shadows too there.


Create/Edit Page - Add unavoidable message on Save errors

Two users are reporting saving edits on the Create/Edit page only to return to the website later to find that their edits were not saved.  When I try to reproduce these errors I get error messages on the save.
So either these users are not getting errors (and are unable to reproduce this situation) or the errors messages are being displayed but are escaping the attention of the users.
Can we add a popup or some other mechanism that is impossible to miss when attempts to save do not work due to errors?

Here is a modal that we can display in the event that a save is not successful.

Confirmed working on ci-master using FF24, Chrome, IE9.  (IE9 does not do animation, but does show message).

Tested on STG
Fixed, it now displays a big Red X and a Red bar over the error field.  The Red bar contains the error message.


Request/Suggestion

It would be nice to have a predefined html element such a  where error messages are displayed so that you can place that  or whatever element in front, back, top or down (or wherever) of a <input> element.
It also would be useful to specified the rules in a HTML5 Custom Data Attribute, e.g.,  data-validate or data-rules
Example:

email
<input type="text" data-validate="{required:true,email:true,messages:{'email':'Invalid email address', 'required':'Required'}}" id="author_email" name="author.email" value="">

Last, but not least, this plug-in is awesome!!!

bump
re: using data attribute


racon removes contig ends with no coverage

Hello,
I'm using racon to polish a close-to-complete genome assembly where most contigs have telomeres on the end. Racon is removing many of these telomeres. Is there any way I can avoid racon removing these sequences? I am already using the -u option.
The table below shows the number of telomere sequences at the end of each contig in the raw (canu) assembly and then each racon iteration. The Lost column shows which iteration of Racon lost most or all of the telomere. (The starts of the contigs look similar.)
Contig          Raw     Racon1  Racon2  Racon3  Racon4  Lost
tig00000037     160     159     163     130     144
tig00000055     128     91      55      0       0       3
tig00000058     56      79      18      0       0       3
tig00000060     142     146     147     133     77
tig00000063     158     29      0       0       0       2
tig00000070     3       2       2       2       1
tig00000082     143     160     151     129     17
tig00000084     61      25      1       0       0       2
tig00000104     154     164     165     165     166
tig00000134     136     148     155     145     76
tig00000158     143     138     86      31      0       4
tig00000182     114     98      85      42      41
tig00000197     124     134     142     144     137
tig00000209     143     152     146     151     149
tig00000218     110     109     44      23      0       4
tig00000238     146     86      88      92      92
tig00003593     49      12      0       0       0       2
tig00003595     142     158     152     130     106
tig00003601     142     149     140     139     140
tig00003605     136     146     116     29      4       4
tig00003607     66      21      0       0       0       2
tig00003608     0       0       0       0       0
tig00306617     138     131     51      7       0       3
tig00306621     154     166     166     165     147

The sequence is definitely being removed from the contig, it is not being polished to some other sequence. For example, here is a rough alignment of each version of the end of tig00000084:
Raw    ...CGACTCACAAGAAAGATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTGGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTTTAGGAGTTAGGGTTAGG
Racon1 ...CGACTCACAAGAAAGATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTTTAGGAG
Racon2 ...CGACTCACAAGAAAGATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATTAGGGTT
Racon3 ...CGACTCACAAGAAAGATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATT
Racon4 ...CGACTCACAAGAAAGATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATT

The PAF files show there are no alignments to the telomeres in the racon1 alignments, which presumably causes the truncation, but I would prefer to retain these sequences for now if possible. Is there a way of doing this?
Many thanks
John

Hi John,
you can try with option -f which will enable multiple mappings per read (vs one by default) and hopefully increase the coverage at contig ends. Not sure why it truncates the ends so much. Are you polishing with short or long reads? What coverage do you have?
Best regards,
Robert

Thanks - I'm polishing with 600x coverage of the genome in MinION 9.4.1 reads called with guppy 3.1.5 from a Circulomics library - >50x coverage in >50kb reads.
I'll try -f, but I'm a bit worried about that, as multi-alignments are often inaccurate (the genome has subtelomeres present at all chromosome ends, so a lot of reads pile up at these regions). I think I'd prefer to leave the sequence as unpolished, rather than risk polishing it incorrectly. Maybe leaving unpolished bases as lower case as per https://github.com/isovic/racon/issues/117 would be useful.
But are you saying you wouldn't expect racon to truncate ends without alignments? Would you have expected it to leave the ends intact, even if there were no reads aligning to it?
The trimming seems like defensible behaviour to me - it's quite possible these ends are incorrect - but I'm running Medaka after racon and I can see a few cases where Medaka has reintroduced the telomere. So it would be great to have an option to keep all the end sequences if possible, so I can do further polishing and checking downstream.
Thanks
John

Racon uses a heuristic postprocesing method which truncates the obtained window consensus at its ends depending on the window coverage. Lets say the average coverage of a window is 50, it will trim both ends until a base occurs with at least 25 coverage. This works pretty good, although sometimes the ends of the complete sequences might suffer if they are circular. The heuristic method (and even msa) are not used when a window has too low coverage. So if you whole telomere has low coverage and is almost 500 bp long, it should not be truncated at all. I am not sure why this is happening here though, as you are using long reads and lots of reads should map to both ends. I can write you a hack to not employ the trimming at sequence beginning and end if you want to try.

Ah! That might explain it to some extent. We have noticed that nanopore only sequences telomeres in one direction - reads are present with telomeres at their ends, but no reads have telomeres at their starts. Something prevents the nanopore from starting at the telomere. So the coverage of telomeres is already half of what it is for the rest of the chromosome.
Also, because very similar subtelomeres occur at every chromosome end, the coverage is often quite high at the contig ends - short reads (as in <2-3kb, not Illumina!) can be aligned with fairly high quality to the 'wrong' subtelomere, because there are plenty of common subsequences.
So it's possible that the average coverage of the end windows is higher due to the subtelomere alignments AND the telomere coverage is lower due to reads having only one direction, so the telomeres get trimmed because they are considerably lower than half the average coverage.
I'll try filtering the reads by length to avoid as much incorrect subtelomeric mapping as possible and see if that improves things. Maybe I could also fake some telomeric reads to get the coverage up as well (although they might not align well if they didn't read through the whole subtelomere, which would probably screw up the polishing for the whole subtelomere...)
Is this truncation ONLY done for the windows at the ends of contigs? Or for every window across the genome?
If it's not too much work, and it will only affect the ends of sequences, I think an option to turn off this truncation would be useful - happy to test it out if you write it.
Thanks
John

Are the numbers in the table total telomere size of both ends or just one of them? Can you see if the beginning is more trimmed than the end?
The trimming is done for each window (of 500bp) in each of the sequences you are polishing. I'll try to add an option for this in couple of hours.

The numbers are total telomere count, for a 6bp telomere - so for example the tig00000084 contig has lengths something like this:
Telomere count       61  25   1   0   0
Telomere seq length 366 150   6   0   0

Here are the number for the contig starts. I've added a lost column to the above table and here, showing which iteration most of the telomere was lost. There are 4 telomeres lost from the starts of contigs, but 10 from the ends, so it looks like there is some orientation effect here. Could try reversing the contigs and rerunning racon if that would be useful.
Contig	        Racon1	Racon2	Racon3	Racon4  Lost
tig00000037	163	144	161	159
tig00000055	122	121	37	27
tig00000058	1	1	1	1
tig00000060	141	92	3	0       3
tig00000063	165	164	166	105
tig00000070	137	62	7	6       3
tig00000082	115	84	81	79
tig00000084	79	89	79	78
tig00000104	165	103	84	84
tig00000134	0	0	0	0
tig00000158	85	108	66	11
tig00000182	149	58	37	1       4
tig00000197	164	164	162	163
tig00000209	96	99	97	84
tig00000218	111	96	91	68
tig00000238	142	82	74	78
tig00003593	157	162	164	165
tig00003595	165	155	82	80
tig00003601	157	82	82	82
tig00003605	1	0	0	0
tig00003607	159	163	163	165
tig00003608	129	82	92	56
tig00306617	139	40	43	0       4
tig00306621	120	127	137	70

(Thanks for offering to look into an option, but no rush - I probably won't get to testing until next week now.)

@johnomics, the beginning of the first window and the end of the last window are not trimmed anymore on branch feature_no_trim. Checkout to it, compile and run like default racon (I did not add an option to enable this behaviour yet).

I have also added an option to disable trimming completely (option --no-trim) to the same branch as above.

Thank you very much for this. I've tested the branch with and without the --no-trimming option. I subsampled the sequence, alignments and reads for tig00000084, using the original PAF file to select tig00000084 alignments with awk, and then extracting the reads from the original read set with seqkit. The files I used are here:
https://drive.google.com/open?id=13_yDnPrjy5Qi9KlrD9Gj-h4QW0Nh8zIo
I then ran racon 1.3.3 on these files, then racon from branch feature_no_trim, then branch feature_no_trim with --no-trimming. Here are the results (name, contig length, end sequence):
Raw           587628 ...ATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTGGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTTTAGGAGTTAGGGTTAGG
Racon 1.3.3   592147 ...ATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTGGGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGGGGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGAGTTAGGGTTAGG
Racon branch  592259 ...ATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTGGGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGGGGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGAGTTAGGGTTAGG
--no-trimming 593291 ...ATATCCCGATGCGAATAAAGTGTGTGTGTCTTGAAAACGTGTGACCATACGCTATCTTCCCAGTCTCCGTAGCCCTCCGTCATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTGGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGGTTAGGGTTAGGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAAGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGGGGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGAGTTAGGGTTAGG

The resulting FASTAs are in the Google Drive folder above.
Without --no-trimming, the end sequence is exactly the same as before, still trimmed - although the contig itself is 112bp longer. But with --no-trimming, the telomere is actually longer than the raw sequence!
So neither of these options straightforwardly resolve the problem - but do you think the no-trimming result looks reasonable (~1kb added in total)?
Please don't worry about this too much - I'll probably just use 1.3.3 with 2 iterations, as that preserves most of the telomeres. But if you think there's something worth following up on here, I'm happy to assist with testing.
Thanks
John

The problem with poa consensus is that long insertions from beginning and end of the POA graph are added into the consensus due to the heaviest path algorithm. That is why we are trimming both consensus ends until sufficient coverage is found. Example graph is bellow (golden nodes are part of the found consensus), in which the end is a big insertion of low coverage:

It is quite odd that iterations 3 or 4 decrease the length of the telomere so drastically. Can you maybe check if some of your contigs share significant overlaps with each other? The other explanation would be that the majority of small reads that cover telomeres all have their best alignment to a small portion of your contigs which results in insufficient coverage at ends of the other contigs (might be solvable with -f option).

The contigs definitely share overlaps at the ends, because they are full chromosomes, and they all feature roughly similar subtelomere sequences ~10kb long. This definitely caused small reads to pile up at some locations and artificially increase the coverage, which is probably causing the filtering at the very ends. I've tried filtering to >20kb reads, but there are still pileups of short alignments from those reads, which cause similar telomere truncations (actually it's a bit worse than before). So I'm going to try filtering the alignments themselves and see if that improves things.

Hi @johnomics ,
I have encountered similar issue. Did you use minimap2 to align reads? Would you please share your commands?
I recently noticed that -a and -c argument are crucial in minimap2 alignment, and may produces different alignment results especially at the terminal positions (https://github.com/lh3/minimap2/blob/master/FAQ.md#1-alignment-different-with-option--a-or--c).
And this do affect the behavior of racon. Without minimap2 -c, racon seems to remove most telomeres. I would like to known if this is the problem.
Best,
Joseph

Hi @cgjosephlee - thank you very much for this, I can confirm that using minimap2 -c for racon alignments retains the telomeres!
@rvaser, please could you consider mentioning this in the README? Seems likely the telomere trimming might only be the most visible effect of using approximate mappings.
Thanks
John

After a few trials, I still see racon remove telomeres (or low coverage regions) in some cases with minimap2 -a.

Are they completely removed, or just trimmed? Is it progressive? I saw some of my telomeres altered in length, which I took to be appropriate refinement of the true telomeres, but none of them had the progressive removal that I was seeing in the examples above.
Tedious to check, but is there any difference between using minimap2 -a SAM output and minimap2 -c PAF output?

Hi @cgjosephlee and @johnomics,
using option -c with Minimap2 will put the CIGAR into PAF which will not be taken into account in Racon and Racon will use Edlib instead to align the overlaps. If you are using -a (SAM output), the CIGAR strings will be used as such. So there is a difference between those two parameters (-c is coupled with edit distance from Edlib, -a is tied with ksw2 alignment from Minimap2). Using -c option with Minimap2 probably discards more false overlaps as alignments are calculated as opposed to plain overlaps based on k-mer indexing.
Sorry for the late response!
Best regards,
Robert

@johnomics
Some of them were trimmed progressively, some were refined and being recognized and some were retained in different iterative runs. So it's in a more complicated situation. Most telomeres were identified in first racon round (better than raw and following rounds).
I did try converting SAM to PAF but long cigar sting in PAF is problematic (#115). I would try to remove cigar in PAF since it is not taken as @rvaser said.

@cgjosephlee, Racon version 1.4.5 should be able to handle any CIGAR length in PAF so you do not have to remove them manually.

Thank you for the information!

Hi @rvaser, out of interest, is the --no-trim feature likely to make it onto the master branch and into a conda recipe in the near future?
I've been working on short viral sequences and having the ends trimmed or not was making a big difference to me. Whilst having a local binary works for development, I'm hoping to include it in a pipeline that will be more widely distributed and is managed with a conda environment.
I would really like to include this software as testing has shown great results with the current pipeline setup! (as an aside: I've currently got a cherrypicked version of the master with the no-trim options as I needed more recent master commits to compile on a mac.)
Thanks!
Áine

Hi Aine,
were you using --no-trim parameter on branch feature_no_trim or not? I am asking because I also removed trimming of first/last window regardless of parameter --no-trim.
Best regards,
Robert

I was using --no-trimming on the feature_no_trim branch.
Full command:
racon/build/bin/racon --no-trimming -t 1 {input.reads} {input.paf} {input.fasta} > {output}
Previously using a conda installed version, with each iteration of racon, I was losing the ends (attached, top is original reference, each below is a consensus generated from each round of racon & minimap2 I ran). The data I'm working on is amplicon-based so read depth is pretty consistent right up to the end of the reads.

With the --no-trimming flag, this end loss no longer happens, so seems like a decent fix.

Available in version 1.4.6 at https://github.com/lbcb-sci/racon.

--no-trimming option in 1.4.6 works perfectly! Telomeres were retained in iterative runs.

Excellent! Thanks for this, it's working well!

Hi @cgjosephlee - can you retain telomeres using minimap2 -c (PAF + Edlib alignments), rather than minimap2 -a (SAM + ksw2 alignments) & --no-trimming? It's great that the latter works for the telomeres, but as @rvaser points out above, there are good reasons to trim, and it might be better to keep trimming on.
However, I'm not sure minimap2 -c is a good idea either, having taken a closer look at the alignments - while minimap2 is now finding alignments right to the end of the contig, and so racon has some information to polish with, the alignments are almost all small chunks of reads that are probably coming from other chromosome ends. So even if the telomeres are being retained, they are probably not accurate. But the issue is about telomere presence, not telomere accuracy, so I'm happy to close this issue if everyone else is!

@johnomics & @cgjosephlee, could you also try mapping with option -f 0 so that minimap2 does not filter out repetitive k-mers? I think that should increase coverage at telomeres.

Ok!
All of these trials are started with a ~54mb fungal genome (canu assembly in 21 contigs, 125x nanopore reads).
I used trf to identify if telomere existed in terminal 5kb windows. The number of scaffolds with telomeres in both ends:
a. racon 1.3.2              , minimap2
b. racon 1.3.2              , minimap2 -a
c. racon 1.4.6 --no-trimming, minimap2 -a
d. racon 1.4.6 --no-trimming, minimap2 -c
e. racon 1.4.6              , minimap2 -c
f. racon 1.4.6              , minimap2 -c -f 0

   raw racon_1 racon_2 racon_3 racon_4 racon_5
a    6      10       0       0       0       0
b           11      10       8       8       6
c           11      11      11      11      11
d           11      11      11      11      11
e           11      11       9       9       8
f           11       9       8       6       6

Regardless of minimap2 setting, racon is able to recover telomeres in first round. This is interesting.
Without --no-trimming, racon trimmed telomeres progressively and finally totally moved it.
-f 0 did not help.

Thanks @cgjosephlee for the evaluation! I am not sure why they are completely trimmed after few rounds. Do you perhaps know the size of them through iterations?

Here is parsed trf output of e, ordered by raw to racon_5.
It seems like each end is edited in different pace.
e.g. tig00000001 START is trimmed and tig00000001 END is retained.
# cols: ctg ctg_len START pos_start pos_end length repeat_size repeat_copies repeat_seq
tig00000001     6794464 START   1       146     146     6       24.5    CCTAAC
tig00000001     6794464 END     6794379 6794464 86      6       14.2    GTTAGG
tig00000011     4954065 START   1       155     155     6       25.5    CTAACC
tig00000011     4954065 END     4953914 4954065 152     6       25.5    TAGGGT
tig00000019     4291540 END     4291404 4291540 137     6       22.5    TAGGGT
tig00000037     3863498 END     3863350 3863498 149     6       24.7    AGGGTT
tig00000041     3850925 END     3850746 3850898 153     6       26.2    GGTTAG
tig00000045     3809958 START   1       150     150     6       25.2    TAACCC
tig00000062     3813806 START   1       141     141     6       24.7    CCTAAC
tig00000062     3813806 END     3813652 3813806 155     6       26.3    AGGGTT
tig00000083     2781522 START   1       160     160     6       26.7    CCTAAC
tig00000083     2781522 END     2781377 2781522 146     6       24.7    TAGGGT
tig00000095     2712376 END     2712225 2712375 151     6       26.0    GGGTTA
tig00009906     5227866 END     5227733 5227866 134     6       22.5    AGGGTT
tig00009907     3598546 START   3       144     142     6       25.7    CCTAAC
tig00009907     3598546 END     3598407 3598546 140     6       23.3    AGGGTT
tig00009908     45269   END     45118   45269   152     6       25.3    AGGGTT
tig00009910     3536766 START   1       131     131     6       21.8    CCCTAA
tig00009910     3536766 END     3536612 3536764 153     6       25.5    AGGGTT
tig00009912     2065533 END     2065380 2065532 153     6       25.5    TAGGGT
tig00009914     1155944 MID     142316  142388  73      6       12.2    GGGTTA
tig00009914     1155944 END     1155799 1155944 146     6       24.2    TAGGGT

Found in both ends : 6
Found in single end: 9
Found in interval  : 1
['tig00000001', 'tig00000011', 'tig00000062', 'tig00000083', 'tig00009907', 'tig00009910']
['tig00000019', 'tig00000037', 'tig00000041', 'tig00000045', 'tig00000095', 'tig00009906', 'tig00009908', 'tig00009912', 'tig00009914']
['tig00009914']
###
tig00000001     6807939 START   1       118     118     6       19.7    CCCTAA
tig00000001     6807939 END     6807852 6807939 88      6       14.7    AGGGTT
tig00000011     4963113 START   1       139     139     6       23.2    AACCCT
tig00000011     4963113 END     4962966 4963113 148     6       24.7    TAGGGT
tig00000019     4300092 END     4299960 4300092 133     6       22.0    GGTTAG
tig00000037     3870216 START   1       151     151     6       25.5    CTAACC
tig00000037     3870216 END     3870071 3870216 146     6       24.2    AGGGTT
tig00000041     3858223 START   1       158     158     6       26.3    TAACCC
tig00000041     3858223 END     3858064 3858223 160     6       26.7    TAGGGT
tig00000045     3817180 START   1       140     140     6       23.3    CTAACC
tig00000062     3821160 START   1       132     132     6       22.2    AACCCT
tig00000062     3821160 END     3821008 3821160 153     6       25.5    AGGGTT
tig00000083     2786265 START   1       158     158     6       26.3    TAACCC
tig00000083     2786265 END     2786117 2786265 149     6       24.8    GTTAGG
tig00000095     2717590 START   1       134     134     6       23.3    CTAACC
tig00000095     2717590 END     2717455 2717590 136     6       22.8    GGGTTA
tig00009906     5237806 START   1       122     122     6       20.2    CCTAAC
tig00009906     5237806 END     5237651 5237806 156     6       25.5    AGGGTT
tig00009907     3605257 START   1       105     105     6       17.5    CTAACC
tig00009907     3605257 END     3605118 3605257 140     6       23.3    AGGGTT
tig00009908     45509   END     45359   45509   151     6       24.8    GTTAGG
tig00009909     30600   START   1       145     145     6       25.2    AACCCT
tig00009910     3544915 START   1       130     130     6       21.7    CCTAAC
tig00009910     3544915 END     3544768 3544915 148     6       24.7    AGGGTT
tig00009911     37029   START   19      152     134     6       23.7    CCTAAC
tig00009912     2069026 START   1       128     128     6       21.7    CCTAAC
tig00009912     2069026 END     2068878 2069026 149     6       24.8    TAGGGT
tig00009913     82842   START   1       142     142     6       24.2    CCTAAC
tig00009914     1158941 MID     142618  142690  73      6       12.2    GGGTTA
tig00009914     1158941 END     1158800 1158941 142     6       23.7    TAGGGT

Found in both ends : 11
Found in single end: 7
Found in interval  : 1
['tig00000001', 'tig00000011', 'tig00000037', 'tig00000041', 'tig00000062', 'tig00000083', 'tig00000095', 'tig00009906', 'tig00009907', 'tig00009910', 'tig00009912']
['tig00000019', 'tig00000045', 'tig00009908', 'tig00009909', 'tig00009911', 'tig00009913', 'tig00009914']
['tig00009914']
###
tig00000001     6808656 START   1       32      32      6       5.3     CTAACC
tig00000001     6808656 END     6808569 6808656 88      6       14.7    AGGGTT
tig00000011     4963611 START   1       136     136     6       22.7    CCTAAC
tig00000011     4963611 END     4963466 4963611 146     6       24.3    TAGGGT
tig00000019     4300687 END     4300553 4300687 135     6       22.5    TAGGGT
tig00000037     3870489 START   1       88      88      6       14.7    CCTAAC
tig00000037     3870489 END     3870340 3870489 150     6       25.0    AGGGTT
tig00000041     3858484 START   1       141     141     6       23.5    CTAACC
tig00000041     3858484 END     3858331 3858484 154     6       25.3    TAGGGT
tig00000045     3817561 START   1       146     146     6       24.3    CTAACC
tig00000062     3821571 START   1       132     132     6       22.2    AACCCT
tig00000062     3821571 END     3821422 3821571 150     6       25.0    AGGGTT
tig00000083     2786471 START   1       148     148     6       24.7    CCTAAC
tig00000083     2786471 END     2786332 2786471 140     6       23.3    TAGGGT
tig00000095     2717876 START   1       134     134     6       22.8    ACCCTA
tig00000095     2717876 END     2717738 2717876 139     6       22.8    TAGGGT
tig00009906     5238475 START   1       126     126     6       20.7    CCTAAC
tig00009906     5238475 END     5238322 5238475 154     6       25.0    AGGGTT
tig00009907     3605545 START   1       103     103     6       17.2    AACCCT
tig00009907     3605545 END     3604378 3604438 61      6       10.2    CCTAAC
tig00009907     3605545 END     3605406 3605545 140     6       23.3    AGGGTT
tig00009908     45524   END     45373   45524   152     6       25.3    AGGGTT
tig00009909     30582   START   1       137     137     6       22.7    CCTAAC
tig00009910     3545172 START   1       128     128     6       21.3    TAACCC
tig00009910     3545172 END     3545025 3545172 148     6       24.7    AGGGTT
tig00009912     2069268 START   1       131     131     6       21.7    CCTAAC
tig00009912     2069268 END     2069123 2069268 146     6       24.5    TAGGGT
tig00009913     82786   START   1       88      88      6       14.7    CCTAAC
tig00009914     1158999 MID     142609  142681  73      6       12.2    GGGTTA
tig00009914     1158999 END     1158863 1158999 137     6       22.8    GGTTAG

Found in both ends : 11
Found in single end: 6
Found in interval  : 1
['tig00000001', 'tig00000011', 'tig00000037', 'tig00000041', 'tig00000062', 'tig00000083', 'tig00000095', 'tig00009906', 'tig00009907', 'tig00009910', 'tig00009912']
['tig00000019', 'tig00000045', 'tig00009908', 'tig00009909', 'tig00009913', 'tig00009914']
['tig00009914']
###
tig00000001     6809062 END     6808976 6809062 87      6       14.5    AGGGTT
tig00000011     4963763 START   1       136     136     6       22.7    CCTAAC
tig00000011     4963763 END     4963619 4963763 145     6       24.2    TAGGGT
tig00000019     4300570 END     4300437 4300570 134     6       22.3    TAGGGT
tig00000037     3870547 END     3870396 3870547 152     6       25.3    AGGGTT
tig00000041     3858545 START   1       139     139     6       23.2    AACCCT
tig00000041     3858545 END     3858392 3858545 154     6       25.3    TAGGGT
tig00000045     3817646 START   1       141     141     6       23.5    CCTAAC
tig00000062     3821602 START   1       129     129     6       21.7    CCTAAC
tig00000062     3821602 END     3821453 3821602 150     6       25.0    AGGGTT
tig00000083     2786584 START   1       145     145     6       24.3    TAACCC
tig00000083     2786584 END     2786449 2786584 136     6       22.7    TAGGGT
tig00000095     2717798 START   1       110     110     6       18.3    CTAACC
tig00000095     2717798 END     2717655 2717798 144     6       23.3    TAGGGT
tig00009906     5238611 START   1       122     122     6       20.2    CCTAAC
tig00009906     5238611 END     5238465 5238611 147     6       24.0    AGGGTT
tig00009907     3605733 START   1       79      79      6       13.2    AACCCT
tig00009907     3605733 END     3604566 3604626 61      6       10.2    CCTAAC
tig00009907     3605733 END     3605594 3605733 140     6       23.3    AGGGTT
tig00009908     45505   END     45355   45505   151     6       25.3    AGGGTT
tig00009909     30578   START   1       134     134     6       22.3    TAACCC
tig00009910     3545099 START   1       128     128     6       21.3    TAACCC
tig00009910     3545099 END     3544953 3545099 147     6       24.5    AGGGTT
tig00009911     37025   START   1       136     136     6       23.7    CCTAAC
tig00009912     2069247 START   1       130     130     6       21.7    CCTAAC
tig00009912     2069247 END     2069103 2069247 145     6       24.3    TAGGGT
tig00009913     82779   START   1       87      87      6       14.5    CTAACC
tig00009914     1158854 MID     142437  142509  73      6       12.2    GGGTTA
tig00009914     1158854 END     1158727 1158854 128     6       21.3    TAGGGT

Found in both ends : 9
Found in single end: 9
Found in interval  : 1
['tig00000011', 'tig00000041', 'tig00000062', 'tig00000083', 'tig00000095', 'tig00009906', 'tig00009907', 'tig00009910', 'tig00009912']
['tig00000001', 'tig00000019', 'tig00000037', 'tig00000045', 'tig00009908', 'tig00009909', 'tig00009911', 'tig00009913', 'tig00009914']
['tig00009914']
###
tig00000001     6809107 END     6809021 6809107 87      6       14.5    AGGGTT
tig00000011     4963915 START   1       141     141     6       23.7    CCTAAC
tig00000011     4963915 END     4963775 4963915 141     6       23.5    TAGGGT
tig00000019     4300923 END     4300790 4300923 134     6       22.3    TAGGGT
tig00000037     3870575 END     3870424 3870575 152     6       25.0    AGGGTT
tig00000041     3858663 START   1       129     129     6       21.5    CTAACC
tig00000041     3858663 END     3858511 3858663 153     6       25.3    TAGGGT
tig00000045     3817740 START   1       146     146     6       24.3    CTAACC
tig00000062     3821657 START   1       122     122     6       20.7    CCTAAC
tig00000062     3821657 END     3821513 3821657 145     6       24.2    AGGGTT
tig00000083     2786586 START   1       145     145     6       24.3    TAACCC
tig00000083     2786586 END     2786451 2786586 136     6       22.7    TAGGGT
tig00000095     2717907 START   1       53      53      6       8.8     ACCCTA
tig00000095     2717907 END     2717798 2717907 110     6       18.3    GGGTTA
tig00009906     5238813 START   1       129     129     6       21.3    TAACCC
tig00009906     5238813 END     5238667 5238813 147     6       24.0    AGGGTT
tig00009907     3605814 START   1       79      79      6       13.2    AACCCT
tig00009907     3605814 END     3604655 3604715 61      6       10.2    CCTAAC
tig00009907     3605814 END     3605683 3605814 132     6       22.0    AGGGTT
tig00009908     45279   END     45122   45279   158     6       26.3    AGGGTT
tig00009909     30552   START   1       127     127     6       21.2    AACCCT
tig00009910     3545373 START   1       128     128     6       21.3    TAACCC
tig00009910     3545373 END     3545228 3545373 146     6       24.3    AGGGTT
tig00009911     37049   START   1       137     137     6       23.2    AACCCT
tig00009912     2069247 START   1       131     131     6       21.7    CCTAAC
tig00009912     2069247 END     2069106 2069247 142     6       23.7    TAGGGT
tig00009913     82776   START   1       87      87      6       14.5    CTAACC
tig00009914     1159092 MID     142619  142691  73      6       12.2    GGGTTA
tig00009914     1159092 END     1158992 1159092 101     6       16.8    GGTTAG

Found in both ends : 9
Found in single end: 9
Found in interval  : 1
['tig00000011', 'tig00000041', 'tig00000062', 'tig00000083', 'tig00000095', 'tig00009906', 'tig00009907', 'tig00009910', 'tig00009912']
['tig00000001', 'tig00000019', 'tig00000037', 'tig00000045', 'tig00009908', 'tig00009909', 'tig00009911', 'tig00009913', 'tig00009914']
['tig00009914']
###
tig00000001     6809188 END     6809102 6809188 87      6       14.5    AGGGTT
tig00000011     4963882 START   1       153     153     6       25.5    CTAACC
tig00000011     4963882 END     4963742 4963882 141     6       23.5    TAGGGT
tig00000019     4300852 END     4300725 4300852 128     6       21.3    TAGGGT
tig00000037     3870685 END     3870533 3870685 153     6       25.5    AGGGTT
tig00000041     3858715 START   1       122     122     6       20.3    TAACCC
tig00000041     3858715 END     3858559 3858715 157     6       26.3    TAGGGT
tig00000045     3817878 START   1       141     141     6       23.5    CCTAAC
tig00000062     3821796 START   1       116     116     6       19.5    CTAACC
tig00000062     3821796 END     3821647 3821796 150     6       25.0    AGGGTT
tig00000083     2786661 START   1       145     145     6       24.3    TAACCC
tig00000083     2786661 END     2786526 2786661 136     6       22.7    TAGGGT
tig00000095     2717630 START   1       51      51      6       8.5     CCTAAC
tig00009905     29614   START   1       93      93      6       16.0    CTAACC
tig00009906     5238688 START   1       129     129     6       21.3    TAACCC
tig00009906     5238688 END     5238545 5238688 144     6       23.5    AGGGTT
tig00009907     3605773 START   1       76      76      6       12.7    CCTAAC
tig00009907     3605773 END     3604632 3604692 61      6       10.2    CCTAAC
tig00009907     3605773 END     3605661 3605773 113     6       18.5    AGGGTT
tig00009908     44941   END     44784   44941   158     6       26.3    AGGGTT
tig00009909     30384   START   1       79      79      6       13.7    CCTAAC
tig00009910     3545216 START   1       128     128     6       21.3    TAACCC
tig00009910     3545216 END     3545078 3545216 139     6       23.2    AGGGTT
tig00009911     37038   START   1       135     135     6       22.7    CCTAAC
tig00009912     2069300 START   1       127     127     6       21.2    CCTAAC
tig00009912     2069300 END     2069162 2069300 139     6       23.2    TAGGGT
tig00009913     82753   START   1       87      87      6       14.5    CTAACC
tig00009914     1159066 MID     142651  142723  73      6       12.2    GGGTTA
tig00009914     1159066 END     1158966 1159066 101     6       16.8    GGTTAG

Found in both ends : 8
Found in single end: 11
Found in interval  : 1
['tig00000011', 'tig00000041', 'tig00000062', 'tig00000083', 'tig00009906', 'tig00009907', 'tig00009910', 'tig00009912']
['tig00000001', 'tig00000019', 'tig00000037', 'tig00000045', 'tig00000095', 'tig00009905', 'tig00009908', 'tig00009909', 'tig00009911', 'tig00009913', 'tig00009914']
['tig00009914']

-f 0 doesn't make much difference for me either; with -c, it extends some telomeres, but shortens others.

Not sure what the problem is then. :/


colab error

ValueError                                Traceback (most recent call last)
 in <cell line: 1>()
----> 1 automatic_coloring_pipeline = StableDiffusionReferenceOnlyPipeline.from_pretrained(
2     "AisingioroHao0/stable-diffusion-reference-only-automatic-coloring-0.1.2"
3 ).to(device)
4 automatic_coloring_pipeline.scheduler = UniPCMultistepScheduler.from_config(
5     automatic_coloring_pipeline.scheduler.config
1 frames
/usr/local/lib/python3.10/dist-packages/diffusers/pipelines/pipeline_utils.py in download(cls, pretrained_model_name, **kwargs)
1683                     custom_components[component] = module_candidate
1684                 elif module_candidate not in LOADABLE_CLASSES and not hasattr(pipelines, module_candidate):
-> 1685                     raise ValueError(
1686                         f"{candidate_file} as defined in model_index.json does not exist in {pretrained_model_name} and is not a module in 'diffusers/pipelines'."
1687                     )
ValueError: unet/stable_diffusion_reference_only.models.unet_2d_dobule_condition.py as defined in model_index.json does not exist in AisingioroHao0/stable-diffusion-reference-only-automatic-coloring-0.1.2 and is not a module in 'diffusers/pipelines'.

@loboere The temporary fix was fixed by fixing the diffusers version to 0.21.0. It seems that some new type checks have been added and custom modules are not supported. I will take a closer look.


[stable/rabbitmq] "helm del --purge release" does not remove "release-rabbitmq" Stateful Sets

Is this a request for help?:

Is this a BUG REPORT or FEATURE REQUEST? (choose one):
A bug or wrong behaviour

Version of Helm and Kubernetes:
helm version

Client: &version.Version{SemVer:"v2.7.0", GitCommit:"08c1144f5eb3e3b636d9775617287cc26e53dba4", GitTreeState:"clean"}
Server: &version.Version{SemVer:"v2.7.0", GitCommit:"08c1144f5eb3e3b636d9775617287cc26e53dba4", GitTreeState:"clean"}

kubectl version

Client Version: version.Info{Major:"1", Minor:"8", GitVersion:"v1.8.0", GitCommit:"6e937839ac04a38cac63e6a7a306c5d035fe7b0a", GitTreeState:"clean", BuildDate:"2017-09-28T22:57:57Z", GoVersion:"go1.8.3", Compiler:"gc", Platform:"darwin/amd64"}
Server Version: version.Info{Major:"", Minor:"", GitVersion:"v1.9.0", GitCommit:"925c127ec6b946659ad0fd596fa959be43f0cc05", GitTreeState:"clean", BuildDate:"2018-01-26T19:04:38Z", GoVersion:"go1.9.1", Compiler:"gc", Platform:"linux/amd64"}

Which chart:
rabbitmq: 0.7.5
What happened:
Command:
helm del --purge release

release "release" deleted

Dependency:
- name: rabbitmq
    version: 0.7.5
    repository: https://kubernetes-charts.storage.googleapis.com/

Values:
rabbitmq:
  rbacEnabled: false
  rabbitmq:
    username: my-user
    password: my-password
  persistence:
    enabled: false
  resources:
    requests:
      memory: 256Mi
      cpu: 300m
  replicas: 1

Problem:
running the helm delete command helm del --purge release does not remove the statful set.
Everything gets removed but the release-rabbitmq Stateful Sets and the pod related to it release-rabbitmq-0
What you expected to happen:
I expect that rabbitmq to be removed also when the deployment is removed, that was the behaviour when deployment was used instead of stateful sets
How to reproduce it (as minimally and precisely as possible):
Deploy chart that depends on rabbitmq version 0.7.5
Anything else we need to know:

Anyone looking at this? I am not sure if other people had this issue before.

I second that. The StatefulSet does not seem to be deleted when deleting the RabbitMQ release. Observed with rabbitmq-1.1.2. Tiller logs below:
[kube] 2018/05/25 15:07:29 Starting delete for "exasperated-alligator-rabbitmq" Service
[kube] 2018/05/25 15:07:29 Starting delete for "exasperated-alligator-rabbitmq" StatefulSet
[kube] 2018/05/25 15:07:29 Using reaper for deleting "exasperated-alligator-rabbitmq"
[kube] 2018/05/25 15:07:29 the server could not find the requested resource
[kube] 2018/05/25 15:07:29 Starting delete for "exasperated-alligator-rabbitmq-endpoint-reader" RoleBinding
[kube] 2018/05/25 15:07:29 Starting delete for "exasperated-alligator-rabbitmq-endpoint-reader" Role
[kube] 2018/05/25 15:07:29 Starting delete for "exasperated-alligator-rabbitmq" ServiceAccount
[kube] 2018/05/25 15:07:29 Starting delete for "exasperated-alligator-rabbitmq-config" ConfigMap
[kube] 2018/05/25 15:07:29 Starting delete for "exasperated-alligator-rabbitmq" Secret
[tiller] 2018/05/25 15:07:29 executing 0 post-delete hooks for exasperated-alligator
[tiller] 2018/05/25 15:07:29 hooks complete for post-delete exasperated-alligator
[storage] 2018/05/25 15:07:29 updating release "exasperated-alligator.v1"


CompletionTests unhandled exceptions on background thread cause agent to terminate

Test run shows about 90 tests not executed, and it's due to our friend:
System.InvalidCastException: 'Unable to cast object of type 'TestUtilities.Mocks.MockTextVersion' to type 'Microsoft.VisualStudio.Text.ITextVersion2'.'

Ex: CompletionTests.SignatureHelp
ReportUnhandledException tries to take care of the InvalidCastException, but it tries to show a dialog, and TaskDialog.ForException calls into MockVsUIShell methods that are not implemented, and the end result is that the NotImplementedException takes down the test agent.
ReportUnhandledException should find a way of failing the test without taking down the test agent, and without trying to show UI.

ReportUnhandledException should be asserting first, which should bring the test down before it tries to display UI.

Here the test ouput:
Test Name:	SignatureHelp
Test FullName:	PythonToolsMockTests.CompletionTests.SignatureHelp
Test Source:	C:\Projects\huguesv\PTVS\Python\Tests\PythonToolsMockTests\CompletionTests.cs : line 349
Test Outcome:	Failed
Test Duration:	0:00:00

Result Message:	The agent process was stopped while the test was running.

And the 'Tests' view in VS output window:
------ Run test started ------
Warning: Test Run deployment issue: The assembly or module 'Microsoft.VisualStudio.Shell.15.0' directly or indirectly referenced by the test container 'c:\projects\huguesv\ptvs\buildoutput\debug15.0\raw\binaries\pythontoolsmocktests.dll' was not found.
Warning: Test Run deployment issue: The assembly or module 'Microsoft.VisualStudio.Shell.Framework' directly or indirectly referenced by the test container 'c:\projects\huguesv\ptvs\buildoutput\debug15.0\raw\binaries\pythontoolsmocktests.dll' was not found.
Warning: Test Run deployment issue: The assembly or module 'StreamJsonRpc' directly or indirectly referenced by the test container 'c:\projects\huguesv\ptvs\buildoutput\debug15.0\raw\binaries\pythontoolsmocktests.dll' was not found.
Warning: Test Run deployment issue: The assembly or module 'Microsoft.ServiceHub.Client' directly or indirectly referenced by the test container 'c:\projects\huguesv\ptvs\buildoutput\debug15.0\raw\binaries\pythontoolsmocktests.dll' was not found.
Warning: Test Run deployment issue: The assembly or module 'Microsoft.VisualStudioTools.VSTestHost.15.0' directly or indirectly referenced by the test container 'c:\projects\huguesv\ptvs\buildoutput\debug15.0\raw\binaries\pythontoolsmocktests.dll' was not found.
One of the background threads threw exception:
System.NotImplementedException: The method or operation is not implemented.
   at Microsoft.VisualStudioTools.MockVsTests.MockVsUIShell.GetDialogOwnerHwnd(IntPtr& phwnd) in C:\Projects\huguesv\PTVS\Common\Tests\MockVsTests\MockVsUIShell.cs:line 81
   at Microsoft.PythonTools.Infrastructure.TaskDialog.ShowModal() in C:\Projects\huguesv\PTVS\Python\Product\VSCommon\Infrastructure\TaskDialog.cs:line 167
   at Microsoft.PythonTools.Infrastructure.VSTaskExtensions.ReportUnhandledException(Exception ex, IServiceProvider site, Type callerType, String callerFile, Int32 callerLineNumber, String callerName, Boolean allowUI) in C:\Projects\huguesv\PTVS\Python\Product\VSCommon\Infrastructure\VSTaskExtensions.cs:line 91
   at Microsoft.PythonTools.Intellisense.TaskProvider.Worker(Object param) in C:\Projects\huguesv\PTVS\Python\Product\PythonTools\PythonTools\Intellisense\TaskProvider.cs:line 537
   at System.Threading.ThreadHelper.ThreadStart_Context(Object state)
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)
   at System.Threading.ThreadHelper.ThreadStart(Object obj)
========== Run test finished: 1 run (0:00:44.3308614) ==========


Fix for unable to update nodejs version (see #1599)

…ridge/homebridge-config-ui-x)
:recycle: Current situation
Line 420 executes:
curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | sudo gpg --dearmor --yes -o /etc/apt/keyrings/nodes
so the key is stored in /etc/apt/keyrings/nodes
In line 426 the old file "rm -f /usr/share/keyrings/nodesource.gpg" is deleted
However line 432 hasn't been updated, as it still refers to this old file, which is now deleted:
echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_${majorVersion}.x nodistro main" | sudo tee /etc/apt/sources.list.d/nodesource.list
:bulb: Proposed solution
Line 432 should be changed to refer to /etc/apt/keyrings/nodes:
echo "deb [signed-by=/etc/apt/keyrings/nodes] https://deb.nodesource.com/node_${majorVersion}.x nodistro main" | sudo tee /etc/apt/sources.list.d/nodesource.list
:gear: Release Notes
This pull request makes a simple change to update the reference to the key file in the /etc/apt/sources.list.d/nodesource.list
Without this nodejs cannot be updated properly.

Am going to bundle in into beta-4.51.1